example_1-1

This is a short description of the atlas.  It should be limited to a couple sentences.

example_2

example_6

Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Assay, etc.); provide the same one for all items/rows.

Component

Filename

Format of a file (e.g. txt, csv, fastq, bam, etc.)

File Format

HTAN Biospecimen Identifier from which these files were derived [https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing]

HTAN Parent Biospecimen ID

HTAN ID

Nucleic Acid Source

Indicate if library preparation was based on revived frozen cells.

Cryopreserved Cells in Sample

The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)

Single Cell Isolation Method

The tissue dissociation method used for scRNASeq assays

Dissociation Method

Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711]

Library Construction Method

Library Layout

The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript

End Bias

An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA

Reverse Transcription Primer

A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix

Spike In

A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]

Sequencing Platform

Total Number of Input Cells

Number of cells and number of nuclei input; entry format: number, number

Input Cells and Nuclei

The date that the libraries were prepared for sequencing (in number of days since sample received in lab)

Library Preparation Date

The date when the sample was dissociated and cells were isolated (date format)

Single Cell Dissociation Date

Date of sequencing library construction part of library construction (in number of days since sample received in lab)

Sequencing Library Construction Date

Date of nucleic acid capture part of library construction (in number of days since sample received in lab)

Nucleic Acid Capture Date

Protocol Link

A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch)

Technical Replicate Group

Length of cell barcode read (in bp): number

Cell Barcode Length

Offset in sequence for cell barcode read (in bp): number

Cell Barcode Offset

Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.

Empty Well Barcode

Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]

Feature Reference Id

Median UMIs per Cell Number

Read1

Read2

The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910]

Spike In Concentration

Length of UMI barcode read (in bp): number

UMI Barcode Length

Start position of UMI barcode in the sequence. Values: number, 0 for start of read

UMI Barcode Offset

Valid Barcodes Cell Number

Indicate if protein expression (EPCAM/CD45) positive/negative data  is available for each cell in CEL-seq2 assays

Well Index

cDNA Length

Offset in sequence for cDNA read (in bp): number

cDNA Offset

entityId

downloadLink

HTAN ID associated with a patient based on HTAN ID SOP

HTAN Patient ID

An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories
defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.

Ethnicity

Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification
of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]

Gender

An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. 
                                                                                                                     

Race

The survival state of the person registered on the protocol.

Vital Status

Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days.

Days to Birth

The patient's age (in years) on the reference or anchor date used during date obfuscation.

Age at Index

The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.

Age Is Obfuscated

Numeric value to represent the calendar year in which an individual was born.

Year Of Birth

The number of years a patient worked in a specific occupation.

Occupation Duration Years

The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.

Premature At Birth

Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.

Weeks Gestation at Birth

Cause of Death

The text term used to describe the source used to determine the patient's cause of death.

Cause of Death Source

Number of days between the date used for index and the date from a person's date of death represented as a calculated number of days.

Days to Death

Numeric value to represent the year of the death of an individual.

Year of Death

Indicate if individual has smoking exposure

Smoking Exposure

The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.

Asbestos Exposure

The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.

Coal Dust Exposure

The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.

Environmental Tobacco Smoke Exposure

The yes/no/unknown indicator used to describe whether the patient was exposed to radon.

Radon Exposure

The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.

Respirable Crystalline Silica Exposure

The average number of cigarettes smoked per day.

Cigarettes per Day

Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.

Pack Years Smoked

The text term used to generally decribe how often the patient smokes.

Smoking Frequency

Time between Waking and First Smoke

The year in which the participant began smoking.

Tobacco Smoking Onset Year

The year in which the participant quit smoking.

Tobacco Smoking Quit Year

Category describing current smoking status and smoking history as self-reported by a patient

Tobacco Smoking Status

The text term used to describe the specific type of tobacco used by the patient.

Type of Tobacco Used

HTAN Biospecimen Identifier from which these files were derived

UCSC Single Cell Browser

A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received.

Treatment or Therapy

Text term that describes the kind of treatment administered.

Treatment Type

The text term used to describe the pathologic effect a treatment(s) had on the tumor.

Treatment Effect

Text term that describes the patient's final outcome after the treatment was administered.

Treatment Outcome

Number of days between the date used for index and the date the treatment ended.

Days to Treatment End

The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment

Treatment Anatomic Site

Number of days between the date used for index and the date the treatment started.

Days to Treatment Start

The text term used to describe the status of the patient's malignancy when the treatment began.

Initial Disease Status

The text term used to describe the regimen or line of therapy.

Regimen or Line of Therapy

Text identification of the individual agent(s) used as part of a treatment regimen.

Therapeutic Agents

Text term to identify the reason for the administration of a treatment regimen. [Manually-curated]

Publication 1

Publication 2

Publication 3