title: VEKO Female 2

description:
Library name: JP165_pos
10x Genomics


title: H1975-siDYN-1-48h

status: Public on Aug 15 2025

type: SRA

city: Guangzhou

first: 雷名

last: 吴

address: sun-yat san university

country: China

institute: 中山大学药学院

description:
Library name: Sample 8
fpkm_H1975_DYN1
siRNA treatment processed data.xls

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Genome Reference Consortium Human Build 38 patch release 12 (GRCh38.p12)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: lung

extract_protocol:
Cells were harvested, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 mg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: lung

tag: cell line

tag: cell type

value: Non-small cell lung cancer cell

tag: treatment


title: VHEKO Male 2

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

description:
Library name: OP404_pos
10x Genomics

library_source: transcriptomic single cell

data_processing:
Preliminary sequencing results (bcl files) and FASTQ files were generated with the DRAGEN FASTQ Generation, or the DRAGEN BCL Convert workflow optimized for Single Cell RNA Library Kit 1 library prep kit, and the Single Cell RNA Index Adaptors 1-B index adaptor kit, with 28 and 152 Read 1 and 2 cycles respectively.
Assembly: The mm10 reference genome was downloaded from https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz. The transcript sequence and annotation for Vhlpjr.KO, that included the tdTomato transgene, was added manually to the FASTA reference genome file and GTF file respectively using the CellRanger (v6.1.1) mkref function.
Supplementary files format and content: FASTQ files generated for each sample were aligned to the custom reference genome by CellRanger using default parameters. After aligning, for each read pair, cell barcodes and unique molecular identifiers (UMIs) were obtained from Read 1 and read counts per feature were obtained from Read 2. Only those UMIs that could be linked to a valid cell barcode and a gene exon region were included to create the cell by gene count matrix. Reads from Vhl exon 1 were excluded from analysis to prevent ambiguous alignment to Vhlwt or Vhlpjr.KO alleles. Cells were subjected to the following filters: detected genes > 200, fraction of mitochondrially-encoded reads < 0.5, and detected genes < 3*median for each sample. The threshold for mitochondrially encoded reads was set to this value in line with published kidney scRNA-seq studies to account for the high mitochondrial content in the renal tubular epithelium (RTE) cells{Park, 2018 #492}. Cells from different samples and sequencing runs were then aggregated, which sometimes required manual renaming of duplicate cell ‘names’. Downstream analysis was conducted using the R package Seurat v4.0.3 and v5.1.0.
Supplementary files format and content: Processed data made available as Seurat R objects. Two obejcts are provided. 1) Vhl_HIF_genotypes_merged_noumap.rds; contains data from filtered, high-quality VHKO, VEKO, and VHEKO cells as well as data from ConKO and VKO cells downloaded from GSE253168 . 2)  HIF_genotypes_all_umap.rds; contains data from downsampled VHKO, VEKO, and VHEKO cells so that each genotype is represented by equal numbers of cells from male and female mice. This dataset was used for batch correction and dimension reduction.

molecule: polyA RNA

organism: Mus musculus

source_name: kidney

growth_protocol: Mice were housed in individually ventilated cages on a 13 h light/ 11 h dark cycle with food and water provided ad libitum. B6.Vhltm1.1b(tdTomato)Pjr (Vhlpjr.fl) mice were commissioned from Ozgene, Australia and generated using goGermline technology. Vhltm1jae mice (Vhljae.fl) (RRID:IMSR_JAX:012933) were crossed with Tg(Pgk1-cre)1Lni (Pgk1-Cre) (RRID:IMSR_JAX:020811) to generate a constitutively inactivated Vhltm1jae allele (Vhljae.KO). Tg(Pax8-cre/ERT2)CAmat (Pax8-CreERT2) (RRID:IMSR_HAR:9175) mice were obtained via EMMA. Mice carrying conditional alleles for Hif1a (Hif1atm3Rsjo; RRID: MGI:6863863; termed Hifafl) and Epas1 (Epas1tm1.1Mcs; RRID:MGI:3710345; termed Epas1fl) were a gift from Randall Johnson and Simon Celeste respectively. These lines were generated on a B6.129 mixed background but were inter-crossed with C57B6/J animals for at least five generations prior to starting experiments.

extract_protocol:
Kidneys were bisected, the renal capsule removed, and bisected kidneys were macerated for up to 7 min on a bed of ice. Macerated kidneys were then subjected to single-cell dissociation using the Multi-Tissue Dissociation Kit 2 (Miltenyi 130-110-203). Briefly, macerated tissues were suspended in 1.45 ml Buffer X, 30 µl of Enzyme D, 15 µl of Enzyme P, 15 μl of Buffer Y, and 6 µl of Enzyme A, all prepared according to the manufacturer’s instructions. The suspension was then incubated under water at 37°C for 30 min in a shaking incubator set to 150 rpm. Dissociation was stopped by the addition of 150 µl Fetal Bovine Serum (FBS; Sigma F7524) and resuspension in 9 ml of RPMI-1460 medium (Merck R0883). The digest was filtered through a 40 µm cell strainer to remove undigested tissue and the filtrate was centrifuged (300g for 10 min at 4°C). Erythrocytes were eliminated by resuspending dissociated cells in 3 ml of 1x RBC Lysis Buffer (Miltenyi 130-094-183) prepared in deionized water, and incubating for 2 min at RT. Cells were centrifuged (300g for 5 min at 4°C) and resuspended in ice-cold D-PBS before being counted on a Thermo Scientific Countess II machine for total yield and viability.
Sorted cells were prepared into single-cell droplets using the Chromium Next GEM Single-cell kit. 20,000 live cells were loaded per sample on separate Chromium Next GEM Chip G (10X Genomics PN-1000127) channels. cDNA clean-up, amplification and adaptor ligation were performed with the Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10X Genomics PN-1000268). cDNA yield was quantified using the High Sensitivity D1000 ScreenTape Assay (Agilent 5067-5584 and 5067-5585) to optimize the number of reaction cycles for library preparation. Single cell sequencing libraries were prepared using the Library Construction Kit (10X PN-1000190) and Dual Index Kit TT Set A (10X Genomics PN-1000215) sequence indices. Single-cell libraries were sequenced on Illumina NextSeq 2000 sequencing system with P3 200 cycle (Illumina 20040560) reagents. Libraries from up to six samples were pooled in an equimolar ratio, diluted to 650 pM in RSB buffer and mixed with 1% PhiX Control v3 DNA (Illumina FC-110-3001) for sequencing.
Libraries from up to six samples were pooled in an equimolar ratio, diluted to 650 pM in RSB buffer and mixed with 1% PhiX Control v3 DNA (Illumina FC-110-3001) for sequencing.

treatment_protocol: Vhlwt/pjr.fl;Pax8-CreERT2 (“ConKO”), Vhljae.KO/pjr.fl;Pax8-CreERT2 (“VKO”), Vhlwt/pjr.fl;Hif1afl/fl;Pax8-CreERT2 (“ConHKO”), Vhljae.KO/pjr.fl;Hif1afl/fl;Pax8-CreERT2 (“VHKO”), Vhlwt/pjr.fl;Epas1fl/fl;Pax8-CreERT2 (“ConEKO”), Vhljae.KO/pjr.fl;Epas1fl/fl;Pax8-CreERT2 (“VEKO”), Vhlwt/pjr.fl;Hif1afl/fl;Epas1fl/fl;Pax8-CreERT2 (“ConHEKO”), and  Vhljae.KO/pjr.fl;Hif1afl/fl;Epas1fl/fl;Pax8-CreERT2 (“VHEKO”) mice of both sexes were administered tamoxifen (2 mg dose daily for five consecutive days) when they were >20 g in body weight. Mice were harvested either 1-3 weeks (early) or 4-12 months (late) after recombination was induced.

value: kidney

tag: cell origin

value: FAC-sorted PAX8-restricted renal epithelial cells

tag: genotype

tag: cellular vhl_hif1a_and_epas1_status

value: Vhl(KO/KO); Hif1a(KO/KO); Epas1(KO/KO)


title: IWR-1 Biol Replicate 2

city: Salt Lake City

first: Samuel

last: Alper

state: UT

department: Neurobiology

country: USA

institute: University of Utah

description: Dissected trunk tissue surrounding spinal cord injury site

data_processing:
Cutadapt, FASTQC, STAR, featureCounts
Assembly: Danio_rerio.GRCz11.94
Supplementary files format and content: fastq.gz

organism: Danio rerio

source_name: 1mm of trunk tissue including the injury site

growth_protocol: Zebrafish larvae were obtained from an incross of wild type (AB) adult fish and staged according to standardized protocols (Kimmel et al., 1995). Embryonic fish were raised in E3 media supplemented with methylene blue until 24 hours post fertilization. Embryos were raised in E3 without methylene blue after 24 hours post fertilization.

extract_protocol:
Invitrogen Recover All Total Nucleic Acid Isolation Kit for FFPE was used to extract the RNA from the tissue samples
NEBNext Ultra II Directional RNA library preparation with ribo RNA depletion.

treatment_protocol: 5 day old larvae were anesthetized in 0.016% Tricaine (Sigma), and injured by complete transection of the spinal cord at the level of the anal pore using a sharpened and sterilized FST injury tool. Larvae were allowed to recover for 6 hours in E3 before being transferred into media containing E3 with 35μM IWR-1 (Sigma) in 0.25% DMSO or 0.25% DMSO as a vehicle control. Larvae were fed rotifers starting at 1 dpi until fixation at 3 dpi (8 dpf).

value: AB


title: VHKO Male 2

description:
Library name: JH187_pos
10x Genomics

value: Vhl(KO/KO); Hif1a(KO/KO)


title: BCG-310_ERRBS

city: Miami

first: Aristeidis

middle: G

last: Telonis

state: FL

address: 1550 NW 10th Ave

institute: University of Miami

description: Library name: BCG-310_ERRBS

library_source: genomic

data_processing:
Adapters were trimmed from the acquired fastq files with cutadapt (v. 1.18)
Reads were mapped on GRCh37 with bismark and bismark_methylation_extractor (v. 0.22.1)
Assembly: GRCh37
Supplementary files format and content: Table with methylation calls per cytosine in CpG context

molecule: genomic DNA

source_name: Breast tumor

extract_protocol:
DNA was extracted on a Thermo Kingfisher Apex using MagMAX™ DNA Multi-Sample Ultra 2.0
Libraries for ERRBS were made following the protocol of Garrett-Bakeman et al (PMID: 25742437)

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

value: No

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score


title: VEKO Male 1

description:
Library name: JP120_pos
10x Genomics

tag: tissue

value: Vhl(KO/KO); Epas1(KO/KO)


title: HCC827-H(5μM)-24h

description:
Library name: Sample 6
fpkm_HCC827_H
18E treatment processed data.xls

tag: cell line

tag: cell type

tag: treatment


title: BCG-228_ERRBS

description: Library name: BCG-228_ERRBS

value: IA


title: BCG-379_ERRBS

description: Library name: BCG-379_ERRBS

value: IIIB


title: HCC827-L(2.5μM)-24h

description:
Library name: Sample 5
fpkm_HCC827_L
18E treatment processed data.xls

value: lung


title: liver cell, BDF1-6

city: Kyoto

first: Mito

last: Shinohara

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Medical department

country: Japan

institute: Kyoto University

data_processing:
Illumina RTA version 4.12.2 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
The sequenced reads were mapped to the mm10 mouse reference genome using HISAT2 (version 2.2.1), with the GENCODE M23 annotation gtf file after trimming adaptor sequences and low-quality bases by cutadapt-4.6.
The raw count matrix was created using HTSeq (version 2.0.2) with GENCODE M23 annotation gtf file.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RawCounts values for each Sample

source_name: liver

extract_protocol:
Adult livers were homogenized and total RNA was extracted by using TRIzol solution (Invitrogen) and purified by the RNeasy cleanup system (QIAGEN, Valencia, CA). Offspring derived from GS cells cryopreserved on the ISS or on Earth, and from control BDF1 wild-type mice were analyzed. 18 Total samples were analyzed.
The RNAseq libraries were generated using the  Illumina Stranded mRNA Prep Kit (Illumina, San Diego, CA), according to the manufacturer’s instructions.

treatment_protocol: GS cells were established from testes of 2-3 day old mice of the DBA/2 strain as previously described (Kanatsu-Shinohara et al., 2003, Biol. Reprod. 69, 216-616). Cells were cryopreserved for 6 months in ISS or on Earch for 6 months. Upon return to Earth, GS cells were thawed and transplanted into the seminiferous tubules of W mice. Recipents were housed with C57BL/6 female mice.  F1 offspring were sacrificed at 10 wks of age,  and livers were homogenised and total RNA was extracted by using TRIzol solution (Invitrogen) and purified by the RNeasy cleanup system (QIAGEN, Valencia, CA).

value: liver

value: liver cell

tag: genotype

value: wild-type

tag: strain

value: control


title: liver cell, BDF1-4


title: liver cell, BDF1-5


title: BCG-164_ERRBS

description: Library name: BCG-164_ERRBS

tag: age

tag: race


title: BCG-209_ERRBS

description: Library name: BCG-209_ERRBS

tag: ethnicity

tag: er

value: IIB


title: BCG-390_ERRBS

description: Library name: BCG-390_ERRBS

tag: gender

tag: clinical stage


title: BSSR1918_ERRBS

description: Library name: BSSR1918_ERRBS

tag: adi (state_decile)

tag: nseas composite_score


title: HCC827-CON

description:
Library name: Sample 4
fpkm_HCC827_CON
18E treatment processed data.xls

value: Non-small cell lung cancer cell

value: DMSO


title: BSSR1944_ERRBS

description: Library name: BSSR1944_ERRBS

value: Breast tumor

value: White

tag: nseas safety_score

tag: nseas social_cohesion_score


title: H1975-NC

description:
Library name: Sample 7
fpkm_H1975_NC
siRNA treatment processed data.xls

value: siCON


title: VHKO Male 1

description:
Library name: JH186_pos
10x Genomics

value: kidney

tag: cell origin

value: FAC-sorted PAX8-restricted renal epithelial cells

tag: cellular vhl_hif1a_and_epas1_status

value: Vhl(KO/KO); Hif1a(KO/KO)


title: HCC827-NC

description:
Library name: Sample 10
fpkm_HCC827_NC
siRNA treatment processed data.xls

tag: tissue

tag: cell line


title: BSSR3009_ERRBS

description: Library name: BSSR3009_ERRBS

value: Hispanic or Latino

value: ER-positive

value: Female

tag: treatment

value: No

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score


title: BCG-254_ERRBS

description: Library name: BCG-254_ERRBS

tag: age


title: VHKO Female 1

description:
Library name: JH444_pos
10x Genomics

tag: genotype


title: VHEKO Male 1

description:
Library name: OP437_pos
10x Genomics

value: Vhl(KO/KO); Hif1a(KO/KO); Epas1(KO/KO)


title: liver cell, BDF1-3

value: liver

tag: cell type

value: liver cell

tag: strain


title: BCG-155_ERRBS

description: Library name: BCG-155_ERRBS

tag: race

tag: ethnicity

tag: er

tag: gender


title: BCG-148_ERRBS

description: Library name: BCG-148_ERRBS

tag: clinical stage

value: IA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score


title: H1975-L(2.5μM)-24h

description:
Library name: Sample 2
fpkm_NICH1975_L
18E treatment processed data.xls

tag: tissue

value: lung


title: liver cell, Ground-3

value: wild-type

value: Ground


title: H1975-CON

description:
Library name: Sample 1
fpkm_NICH1975_CON
18E treatment processed data.xls

tag: cell line

value: Non-small cell lung cancer cell

value: DMSO


title: BCG-047_ERRBS

description: Library name: BCG-047_ERRBS

value: Breast tumor

value: White

tag: treatment

value: IIA

tag: nseas social_cohesion_score


title: liver cell, Ground-4


title: liver cell, Ground-5


title: liver cell, Ground-6


title: liver cell, Ground-2


title: BCG-023_ERRBS

description: Library name: BCG-023_ERRBS

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score


title: liver cell, Space-5

tag: genotype

value: Space


title: liver cell, Space-4

tag: cell type


title: liver cell, Space-6

tag: strain


title: liver cell, Ground-1


city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description: Library name: I46H9_skinback_VV_D80_AntigenExperienced_GEX

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.0.0.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v7.0.0. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: cells.tsv, matrix_rna.mtx, genes.tsv, matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO.
Supplementary files format and content: Cellranger output files: summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT36

source_name: skin of back, left flank

extract_protocol:
Lymphocytes were prepared by either digestion with liberase (submandibular gland) or mechanical dissociation (spleen) , followed by staining with fluorescent antibodies, hashing with Totalseq-C antibodies against MHCI and CD45,  and flow sorting CD3+ T cells into DMEM+ 2%FCS. Cells were stained using a custom Totalseq-C antibody panel then sorted again into DMEM + 2% FCS
Libraries were prepared according to the 10x Genomics 5'v2 protocol for GEX, VDJ, and FBC

value: skin of back, left flank

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: FALSE

tag: exp name

value: Antigen-experienced and bystander skin resident memory T cells in vaccinia virus infection

tag: lab

value: Kaplan

tag: organism name

tag: genetics

value: wt

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

value: TRUE

tag: infection agent

value: Vaccinia virus (Western Reserve)

tag: infection dose

value: 3x10E6 PFU

tag: treat dose

value: skin scarification of the left flank at D0; DNFB 0.15%, topical, at day 5 on the opposite, right, flank (DNFB pull)

tag: treat mode

value: topical

tag: prep description

value: collagenase XI, hyaluronidase, DNAse I

tag: organ

tag: organ uberon_id

tag: target cells

value: CD8+ T

tag: gating strategy

tag: sample comments

value: CITESeq failed

value: T cells


title: BCG-026_ERRBS

description: Library name: BCG-026_ERRBS

tag: tissue

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

tag: treatment

value: No

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score


description: Library name: I46H9_skinback_VV_D80_AntigenExperienced_FBC

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.0.0.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v7.0.0. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: cells.tsv, matrix_rna.mtx, genes.tsv, matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO.
Supplementary files format and content: Cellranger output files: summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT36
Library strategy: CITE-seq

value: skin of back, left flank

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: FALSE

tag: exp name

value: Antigen-experienced and bystander skin resident memory T cells in vaccinia virus infection

tag: lab

value: Kaplan

tag: organism name

tag: strain

tag: genetics

value: wt

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

tag: infection agent

tag: infection dose

tag: treat dose

tag: treat mode

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: cell type


title: liver cell, Space-3

tag: tissue

value: liver

value: liver cell

tag: genotype

value: wild-type

tag: treatment

value: Space


title: liver cell, Space-2

tag: strain


title: BCG-006_ERRBS

description: Library name: BCG-006_ERRBS

value: Breast tumor

tag: age

tag: race

tag: ethnicity

tag: er

tag: gender

tag: clinical stage

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score


title: liver cell, Space-1

tag: cell type


title: I46H8_LN_VV_D80_TCR

description: Library name: I46H8_LN_VV_D80_TCR

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.0.0.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v7.0.0. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: cells.tsv, matrix_rna.mtx, genes.tsv, matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO.
Supplementary files format and content: Cellranger output files: summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT36
Library strategy: TCR-seq

source_name: inguinal lymph node;axillary lymph node;brachial lymph node

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: infection agent

value: Vaccinia virus (Western Reserve)

tag: infection dose

value: 3x10E6 PFU

tag: treat dose

value: skin scarification of the left flank at D0; DNFB 0.15%, topical, at day 5 on the opposite, right, flank (DNFB pull)

tag: treat mode

value: topical

tag: prep description

value: mechanical dissociation alone

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: sample comments

value: CITESeq failed

value: T cells


title: liver cell, BDF1-2

tag: tissue

tag: cell type

tag: genotype

tag: strain

tag: treatment

value: control


title: H1975-H(5μM)-24h

description:
Library name: Sample 3
fpkm_NICH1975_H
18E treatment processed data.xls

value: lung

tag: cell line

value: Non-small cell lung cancer cell


title: liver cell, BDF1-1


title: BSSR3054_smallRNAseq

description: Library name: BSSR3054_smallRNAseq

data_processing:
Adapters were trimmed from the acquired fastq files with cutadapt (v. 1.18) with parameter -m 15 -e 0.12 filtering out reads without adapters
Reads were processed with isomiRmap (v. 1.0.0) and MINTmap (v.1 .0)
Assembly: GRCh37
Supplementary files format and content: Table with counts per small RNA molecule

extract_protocol:
RNA was extracted with Thermo MagMAX mirVana Total RNA Isolation kit (A27828) on a Thermo Kingfisher Apex
NEBNext® Small RNA Library Prep Set following manufacturer’s instructions for synthesis without size selection (New England Biolabs, E7330L)

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

value: No

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: GS cells, Ground-3

data_processing:
Illumina RTA version 3.10.30 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
The sequenced reads were mapped to the mm10 mouse reference genome using HISAT2 (version 2.2.1), with the GENCODE M23 annotation gtf file after trimming adaptor sequences and low-quality bases by cutadapt-4.1.
The raw count matrix was created using HTSeq (version 2.0.2) with GENCODE M23 annotation gtf file.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RawCounts values for each Sample

source_name: testis

growth_protocol: GS cells cryopreserved for a 6 months in ISS or on Earth.

extract_protocol:
GS cells were established from testes of 2-3 day old mice of the DBA/2 strain as previously described (Kanatsu-Shinohara et al., 2003, Biol. Reprod. 69, 216-616). Cells were cryopreserved for 6 months on the ISS or on Earch. Upon return to Earth, GS cells were thawed and total RNA samples were extracted by using TRIzol solution (Invitrogen) and purified by the RNeasy cleanup system (QIAGEN, Valencia, CA).
The RNAseq libraries were generated using the  Illumina Stranded mRNA Prep Kit (Illumina, San Diego, CA), according to the manufacturer’s instructions.

tag: tissue

value: testis

tag: cell type

value: spermatogonia

tag: genotype

value: space


title: BCG-036_ERRBS

description: Library name: BCG-036_ERRBS

value: Breast tumor

tag: treatment

value: IA


title: GS cells, Ground-2

tag: strain


title: BSSR2060_smallRNAseq

description: Library name: BSSR2060_smallRNAseq

tag: age

tag: race


title: I46H8_LN_VV_D80_FBC

description: Library name: I46H8_LN_VV_D80_FBC

value: inguinal lymph node;axillary lymph node;brachial lymph node

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: FALSE

tag: exp name

value: Antigen-experienced and bystander skin resident memory T cells in vaccinia virus infection

tag: lab

value: Kaplan

tag: organism name

tag: genetics

value: wt

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

tag: infection agent

value: Vaccinia virus (Western Reserve)

tag: infection dose

value: 3x10E6 PFU

tag: treat dose

value: skin scarification of the left flank at D0; DNFB 0.15%, topical, at day 5 on the opposite, right, flank (DNFB pull)

tag: treat mode

value: topical

tag: prep description

value: mechanical dissociation alone

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: sample comments


description: Library name: I46H9_skinback_VV_D80_AntigenExperienced_TCR

tag: tissue

value: skin of back, left flank

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: strain

value: TRUE

value: collagenase XI, hyaluronidase, DNAse I

value: CD8+ T

value: CITESeq failed

tag: cell type

value: T cells


title: GS cells, Ground-1

value: testis

value: spermatogonia

tag: genotype

tag: treatment

value: space


title: BSSR1957_smallRNAseq

description: Library name: BSSR1957_smallRNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

value: No

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: I46H8_LN_VV_D80_GEX

description: Library name: I46H8_LN_VV_D80_GEX

tag: tissue

value: inguinal lymph node;axillary lymph node;brachial lymph node

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: FALSE

tag: exp name

value: Antigen-experienced and bystander skin resident memory T cells in vaccinia virus infection

tag: lab

value: Kaplan

tag: organism name

tag: strain

tag: genetics

value: wt

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

tag: infection agent

value: Vaccinia virus (Western Reserve)

tag: infection dose

value: 3x10E6 PFU

tag: treat dose

value: skin scarification of the left flank at D0; DNFB 0.15%, topical, at day 5 on the opposite, right, flank (DNFB pull)

tag: treat mode

value: topical

tag: prep description

value: mechanical dissociation alone

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: sample comments


title: I46H7_LN_VV_D80_TCR

description: Library name: I46H7_LN_VV_D80_TCR

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

value: CITESeq failed

tag: cell type

value: T cells


title: GS cells, Space-2

value: testis

value: spermatogonia

tag: genotype

tag: strain

tag: treatment

value: ground


title: GS cells, Space-1


title: GS cells, Space-3


title: BCG-389_smallRNAseq

description: Library name: BCG-389_smallRNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

value: No

tag: clinical stage

value: IIB

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: I46H7_LN_VV_D80_GEX

description: Library name: I46H7_LN_VV_D80_GEX

tag: tissue

value: inguinal lymph node;axillary lymph node;brachial lymph node

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: FALSE

tag: exp name

value: Antigen-experienced and bystander skin resident memory T cells in vaccinia virus infection

tag: lab

value: Kaplan

tag: organism name

tag: genetics

value: wt

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

tag: infection agent

value: Vaccinia virus (Western Reserve)

tag: infection dose

tag: treat dose

tag: treat mode

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: sample comments

tag: cell type


title: BCG-385_smallRNAseq

description: Library name: BCG-385_smallRNAseq

tag: tissue

tag: age

tag: race

tag: ethnicity

tag: er

tag: gender

tag: treatment

tag: clinical stage

value: IA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: I46H7_LN_VV_D80_FBC

description: Library name: I46H7_LN_VV_D80_FBC

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: infection agent

tag: infection dose

value: 3x10E6 PFU

tag: treat dose

value: skin scarification of the left flank at D0; DNFB 0.15%, topical, at day 5 on the opposite, right, flank (DNFB pull)

tag: treat mode

value: topical

tag: prep description

value: mechanical dissociation alone

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: sample comments

value: CITESeq failed

value: T cells


title: BCG-344_smallRNAseq

description: Library name: BCG-344_smallRNAseq

tag: tissue

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

tag: treatment

tag: clinical stage

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: I46H6_skinback_VV_D80_bystander_TCR

description: Library name: I46H6_skinback_VV_D80_bystander_TCR

source_name: skin of back, right flank

value: skin of back, right flank

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: FALSE

tag: exp name

value: Antigen-experienced and bystander skin resident memory T cells in vaccinia virus infection

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: infection agent

tag: infection dose

tag: treat dose

tag: treat mode

tag: prep description

value: collagenase XI, hyaluronidase, DNAse I

tag: organ

tag: organ uberon_id

tag: target cells

value: CD8+ T

tag: gating strategy

tag: cell type


title: BCG-343_smallRNAseq

description: Library name: BCG-343_smallRNAseq

tag: tissue

tag: age

tag: race

tag: ethnicity

tag: er

tag: gender

tag: treatment

value: No

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: P2-Post_3, PanCK+

city: Minneapolis

first: Justin

last: Hwang

state: MN

address: 420 Delaware Street SE

department: Department of Medicine

institute: University of Minnesota

description: Library name: P2-Post_3_PanCK+

data_processing:
The Illumina FASTQ sequence files were mapped to each sample and processed to raw counts using the GeoMx NGS pipeline with default settings.
The limit of quantification (LOQ) was set to be the geometric mean of the negative control probes multiplied by the squared standard deviation of the negative control probes. Low probe count AOIs, AOIs with less than 5% of genes above the LOQ, and genes with less than 5% of AOIs above the LOQ were removed.
The counts were then normalized using variance stabilizing normalization (VSN) for subsequent analyses.
Assembly: Human NGS Whole Transcriptome Atlas RNA
Supplementary files format and content: CD45_5_percent_target_segment_filtered.csv: CD45+ AOI counts after gene and AOI filtering (samples with low quality were filtered out)
Supplementary files format and content: PanCK_5_percent_target_segment_filtered.csv: PanCK+ AOI counts after gene and AOI filtering
Supplementary files format and content: CD45_5_vsn_matrix.csv: VSN normalized counts for CD45+ AOIs (samples with low quality were filtered out)
Supplementary files format and content: PanCK_5_vsn_matrix.csv: VSN normalized counts for PanCK+ AOIs

source_name: FFPE tumor

extract_protocol:
Blocks of formalin-fixed paraffin-embedded (FFPE) tumors were prepared for spatial transcriptomic analysis. One 5 µm section from each tumor specimen was placed on a glass slide for Nanostring GeoMx analysis (Seattle, WA). The slide was incubated with Ki-67 antibodies and the Regions of interest (ROIs) were chosen. ROIs were selected after histopathological review of tissue quality. ROIs were further selected for based on the presence of significant quantities of epithelial and immune cells, which was a pre-requisite to acquire significant RNA material from each cell type for subsequent spatial transcriptomic analysis.
GeoMx Digital Spatial Profiling is a probe-based sequencing method to detect RNA spatially in tissue. We used the GeoMx Human Whole Transcriptome Atlas (18,816 genes) to sequence our tissue samples for the three patients.

value: FFPE tumor

value: PanCK+

tag: pre vs_post_covid

value: Post

tag: high covid


title: P2-Post_5, PanCK+

description: Library name: P2-Post_5_PanCK+

tag: tissue

tag: cell type

value: TRUE


title: P2-Post_4, CD45+

description: Library name: P2-Post_4_CD45+


title: P2-Post_6, PanCK+

description: Library name: P2-Post_6_PanCK+


title: P2-Post_4, PanCK+

description: Library name: P2-Post_4_PanCK+


title: P2-Post_3, CD45+

description: Library name: P2-Post_3_CD45+


title: BCG-335_smallRNAseq

description: Library name: BCG-335_smallRNAseq

tag: age

tag: race


title: P2-Post_1, PanCK+

description: Library name: P2-Post_1_PanCK+


title: P2-Post_1, CD45+

description: Library name: P2-Post_1_CD45+


title: I46H6_skinback_VV_D80_bystander_GEX

description: Library name: I46H6_skinback_VV_D80_bystander_GEX

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

value: Kaplan

tag: organism name

tag: strain

tag: genetics

value: wt

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

tag: infection agent

value: Vaccinia virus (Western Reserve)

tag: infection dose

value: 3x10E6 PFU

tag: treat dose

value: skin scarification of the left flank at D0; DNFB 0.15%, topical, at day 5 on the opposite, right, flank (DNFB pull)

tag: treat mode

value: topical

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: sample comments

value: CITESeq failed

value: T cells


title: P2-Pre_5, CD45+

description: Library name: P2-Pre_5_CD45+

tag: tissue

tag: cell type

tag: pre vs_post_covid

value: Pre

tag: high covid

value: FALSE


title: I46H4_LN_VV_D80_GEX

description: Library name: I46H4_LN_VV_D80_GEX

value: inguinal lymph node;axillary lymph node;brachial lymph node

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

value: Antigen-experienced and bystander skin resident memory T cells in vaccinia virus infection

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

value: mechanical dissociation alone


title: I46H4_LN_VV_D80_TCR

description: Library name: I46H4_LN_VV_D80_TCR

tag: age weeks

tag: pool of_mice

tag: infection agent

tag: infection dose

tag: treat dose

tag: treat mode

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells


title: BCG-314_smallRNAseq

description: Library name: BCG-314_smallRNAseq

tag: tissue

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

tag: treatment

value: No

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: BCG-270_smallRNAseq

description: Library name: BCG-270_smallRNAseq


title: P2-Pre_4, PanCK+

description: Library name: P2-Pre_4_PanCK+

value: FFPE tumor

tag: cell type

value: PanCK+

tag: pre vs_post_covid

tag: high covid


title: P2-Pre_4, CD45+

description: Library name: P2-Pre_4_CD45+

tag: tissue


title: I46H2_skinback_VV_D80_bystander_TCR

description: Library name: I46H2_skinback_VV_D80_bystander_TCR

value: skin of back, right flank

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

value: Kaplan

tag: organism name

tag: strain

tag: genetics

value: wt

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

tag: infection agent

value: Vaccinia virus (Western Reserve)

tag: infection dose

value: 3x10E6 PFU

tag: treat dose

value: skin scarification of the left flank at D0; DNFB 0.15%, topical, at day 5 on the opposite, right, flank (DNFB pull)

tag: treat mode

value: topical

tag: prep description

value: collagenase XI, hyaluronidase, DNAse I

tag: organ

tag: organ uberon_id

tag: target cells

value: CD8+ T

tag: gating strategy

tag: sample comments


title: P2-Pre_3, CD45+

description: Library name: P2-Pre_3_CD45+

tag: tissue

tag: cell type

tag: pre vs_post_covid

value: Pre

tag: high covid

value: FALSE


title: BCG-253_smallRNAseq

description: Library name: BCG-253_smallRNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

tag: treatment

tag: clinical stage

value: IA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: P2-Pre_2, PanCK+

description: Library name: P2-Pre_2_PanCK+

tag: tissue

value: FFPE tumor

tag: cell type

value: PanCK+


title: I46H2_skinback_VV_D80_bystander_FBC

description: Library name: I46H2_skinback_VV_D80_bystander_FBC

value: skin of back, right flank

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

value: Antigen-experienced and bystander skin resident memory T cells in vaccinia virus infection

tag: lab

value: Kaplan

tag: organism name

tag: strain

tag: genetics

value: wt

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

tag: infection agent

tag: infection dose

tag: treat dose

tag: treat mode

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: sample comments

value: CITESeq failed

value: T cells


title: P2-Pre_1, PanCK+

description: Library name: P2-Pre_1_PanCK+

tag: tissue

tag: cell type

tag: pre vs_post_covid

value: Pre

tag: high covid


title: I46H2_skinback_VV_D80_bystander_GEX

description: Library name: I46H2_skinback_VV_D80_bystander_GEX

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: FALSE

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

value: Vaccinia virus (Western Reserve)

value: 3x10E6 PFU

value: skin scarification of the left flank at D0; DNFB 0.15%, topical, at day 5 on the opposite, right, flank (DNFB pull)

value: topical

value: collagenase XI, hyaluronidase, DNAse I

value: CD8+ T


title: P2-Pre_1, CD45+

description: Library name: P2-Pre_1_CD45+

value: FFPE tumor


title: P2-Post_2, CD45+

description: Library name: P2-Post_2_CD45+

value: Post

value: TRUE


title: BCG-222_smallRNAseq

description: Library name: BCG-222_smallRNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

tag: treatment

value: No

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: P2-Pre_5, PanCK+

description: Library name: P2-Pre_5_PanCK+

tag: tissue

tag: cell type

value: PanCK+

tag: pre vs_post_covid

value: Pre

tag: high covid

value: FALSE


title: P2-Post_6, CD45+

description: Library name: P2-Post_6_CD45+


title: BCG-187_smallRNAseq

description: Library name: BCG-187_smallRNAseq

tag: age

tag: race


title: P1-Post_6, CD45+

description: Library name: P1-Post_6_CD45+


title: I46H6_skinback_VV_D80_bystander_FBC

description: Library name: I46H6_skinback_VV_D80_bystander_FBC

value: skin of back, right flank

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

value: Antigen-experienced and bystander skin resident memory T cells in vaccinia virus infection

tag: lab

value: Kaplan

tag: organism name

tag: strain

tag: genetics

value: wt

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

tag: infection agent

value: Vaccinia virus (Western Reserve)

tag: infection dose

value: 3x10E6 PFU

tag: treat dose

value: skin scarification of the left flank at D0; DNFB 0.15%, topical, at day 5 on the opposite, right, flank (DNFB pull)

tag: treat mode

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: sample comments

value: CITESeq failed

value: T cells


title: BCG-174_smallRNAseq

description: Library name: BCG-174_smallRNAseq

tag: tissue

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

tag: treatment

tag: clinical stage

value: IA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: I46H4_LN_VV_D80_FBC

description: Library name: I46H4_LN_VV_D80_FBC

value: inguinal lymph node;axillary lymph node;brachial lymph node

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: infection agent

tag: infection dose

tag: treat dose

tag: treat mode

value: topical

tag: prep description

value: mechanical dissociation alone

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: cell type


title: BCG-265_smallRNAseq

description: Library name: BCG-265_smallRNAseq

tag: tissue

tag: age

tag: race

tag: ethnicity

tag: er

tag: gender

value: Female

tag: treatment

value: No

tag: clinical stage

value: IIB

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: P1-Post_5, PanCK+

description: Library name: P1-Post_5_PanCK+

value: FFPE tumor

value: PanCK+

tag: pre vs_post_covid

value: Post

tag: high covid

value: FALSE


title: I46H15_spleen_GEX

description: Library name: I46H15_spleen_GEX

source_name: spleen

tag: tissue

value: spleen

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

value: Antigen-experienced and bystander skin resident memory T cells in vaccinia virus infection

tag: lab

value: Kaplan

tag: organism name

tag: strain

tag: genetics

value: wt

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

value: splenocytes

tag: gating strategy

tag: sample comments

value: CITESeq failed

tag: cell type


title: P2-Pre_3, PanCK+

description: Library name: P2-Pre_3_PanCK+

tag: tissue

tag: pre vs_post_covid

value: Pre

tag: high covid


title: P1-Post_6, PanCK+

description: Library name: P1-Post_6_PanCK+

value: TRUE


title: BCG-118_smallRNAseq

description: Library name: BCG-118_smallRNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

tag: treatment

tag: clinical stage

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: P1-Post_4, PanCK+

description: Library name: P1-Post_4_PanCK+

tag: tissue

value: FFPE tumor

tag: cell type


title: P1-Post_5, CD45+

description: Library name: P1-Post_5_CD45+

tag: pre vs_post_covid

tag: high covid


title: I46H15_spleen_TCR

description: Library name: I46H15_spleen_TCR

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: prep description

value: mechanical dissociation alone

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: sample comments

value: T cells


title: I46H15_spleen_FBC

description: Library name: I46H15_spleen_FBC

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

value: FALSE

tag: cell type


title: BCG-110_smallRNAseq

description: Library name: BCG-110_smallRNAseq

tag: age

tag: race

tag: ethnicity

tag: er

tag: gender

value: Female

tag: treatment

value: No

tag: clinical stage

value: IA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: P1-Post_4, CD45+

description: Library name: P1-Post_4_CD45+

tag: tissue

tag: pre vs_post_covid

value: Post

tag: high covid


title: I46H14_spleen_VV_D80_TCR

description: Library name: I46H14_spleen_VV_D80_TCR

value: spleen

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

value: Antigen-experienced and bystander skin resident memory T cells in vaccinia virus infection

tag: lab

value: Kaplan

tag: organism name

tag: strain

tag: genetics

value: wt

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

tag: infection agent

value: Vaccinia virus (Western Reserve)

tag: infection dose

value: 3x10E6 PFU

tag: treat dose

value: skin scarification of the left flank at D0; DNFB 0.15%, topical, at day 5 on the opposite, right, flank (DNFB pull)

tag: treat mode

value: topical

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: sample comments

tag: cell type


title: P1-Post_3, PanCK+

description: Library name: P1-Post_3_PanCK+

tag: tissue

value: FFPE tumor

value: PanCK+

tag: pre vs_post_covid

tag: high covid

value: TRUE


title: P1-Post_3, CD45+

description: Library name: P1-Post_3_CD45+


title: BCG-057_smallRNAseq

description: Library name: BCG-057_smallRNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

tag: treatment

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: P1-Post_2, PanCK+

description: Library name: P1-Post_2_PanCK+

tag: tissue

tag: cell type

value: Post

value: FALSE


title: I46H14_spleen_VV_D80_GEX

description: Library name: I46H14_spleen_VV_D80_GEX

value: spleen

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

value: Antigen-experienced and bystander skin resident memory T cells in vaccinia virus infection

tag: lab

value: Kaplan

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: infection agent

tag: infection dose

tag: treat dose

tag: treat mode

tag: prep description

value: mechanical dissociation alone

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: sample comments

value: CITESeq failed

value: T cells


title: P2-Post_2, PanCK+

description: Library name: P2-Post_2_PanCK+

tag: tissue

tag: cell type

tag: pre vs_post_covid

tag: high covid


title: BCG-052_smallRNAseq

description: Library name: BCG-052_smallRNAseq

tag: age

tag: race

tag: ethnicity

tag: er

tag: gender

value: Female

tag: treatment

value: No

tag: clinical stage

value: IA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: P1-Post_2, CD45+

description: Library name: P1-Post_2_CD45+

tag: tissue

value: FFPE tumor

tag: cell type


title: I46H14_spleen_VV_D80_FBC

description: Library name: I46H14_spleen_VV_D80_FBC

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

value: wt

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

value: TRUE

tag: infection agent

value: Vaccinia virus (Western Reserve)

tag: infection dose

value: 3x10E6 PFU

tag: treat dose

value: skin scarification of the left flank at D0; DNFB 0.15%, topical, at day 5 on the opposite, right, flank (DNFB pull)

tag: treat mode

value: topical

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: sample comments


title: P1-Pre_4, PanCK+

description: Library name: P1-Pre_4_PanCK+

tag: tissue

tag: cell type

value: PanCK+

tag: pre vs_post_covid

value: Pre

tag: high covid

value: FALSE


title: I46H13_spleen_VV_D80_TCR

description: Library name: I46H13_spleen_VV_D80_TCR

value: spleen

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

value: Antigen-experienced and bystander skin resident memory T cells in vaccinia virus infection

tag: lab

value: Kaplan

tag: organism name

tag: strain

tag: genetics

tag: Sex

value: mechanical dissociation alone


title: BCG-045_smallRNAseq

description: Library name: BCG-045_smallRNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

tag: treatment

value: No

tag: clinical stage

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: P1-Post_1, CD45+

description: Library name: P1-Post_1_CD45+

tag: tissue

value: FFPE tumor

tag: cell type

tag: pre vs_post_covid

value: Post

tag: high covid


title: P1-Pre_3, PanCK+

description: Library name: P1-Pre_3_PanCK+


title: P1-Pre_4, CD45+

description: Library name: P1-Pre_4_CD45+


title: P1-Pre_2, PanCK+

description: Library name: P1-Pre_2_PanCK+


title: I46H13_spleen_VV_D80_GEX

description: Library name: I46H13_spleen_VV_D80_GEX

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

value: wt

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

value: TRUE

tag: infection agent

value: Vaccinia virus (Western Reserve)

tag: infection dose

value: 3x10E6 PFU

tag: treat dose

value: skin scarification of the left flank at D0; DNFB 0.15%, topical, at day 5 on the opposite, right, flank (DNFB pull)

tag: treat mode

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: sample comments

value: CITESeq failed

value: T cells


title: TBCF5326_smallRNAseq

description: Library name: TBCF5326_smallRNAseq

tag: tissue

tag: age

tag: race

tag: ethnicity

tag: er

tag: gender

tag: treatment

tag: clinical stage

value: IIB

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: I46H13_spleen_VV_D80_FBC

description: Library name: I46H13_spleen_VV_D80_FBC

value: spleen

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: FALSE

tag: exp name

value: Antigen-experienced and bystander skin resident memory T cells in vaccinia virus infection

tag: lab

value: Kaplan

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: infection agent

tag: infection dose

tag: treat dose

tag: treat mode

value: topical

tag: prep description

value: mechanical dissociation alone

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: cell type


title: P1-Pre_3, CD45+

description: Library name: P1-Pre_3_CD45+

tag: tissue

value: FFPE tumor

tag: pre vs_post_covid

value: Pre

tag: high covid


title: P1-Pre_2, CD45+

description: Library name: P1-Pre_2_CD45+


title: BSSR3009_smallRNAseq

description: Library name: BSSR3009_smallRNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

tag: treatment

value: No

tag: clinical stage

value: IA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: BSSR2083_smallRNAseq

description: Library name: BSSR2083_smallRNAseq

tag: tissue

value: IIA


title: P1-Pre_1, CD45+

description: Library name: P1-Pre_1_CD45+

tag: cell type

tag: pre vs_post_covid


title: I46H12_LN_VV_D80_TCR

description: Library name: I46H12_LN_VV_D80_TCR

value: inguinal lymph node;axillary lymph node;brachial lymph node

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

value: wt

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

value: TRUE

tag: infection agent

value: Vaccinia virus (Western Reserve)

tag: infection dose

value: 3x10E6 PFU

tag: treat dose

value: skin scarification of the left flank at D0; DNFB 0.15%, topical, at day 5 on the opposite, right, flank (DNFB pull)

tag: treat mode

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: sample comments

value: CITESeq failed

value: T cells


title: BSSR1944_smallRNAseq

description: Library name: BSSR1944_smallRNAseq

tag: tissue

value: Breast tumor

tag: age

tag: race

tag: ethnicity

tag: er

tag: gender

tag: treatment

tag: clinical stage

value: IIB

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: P3-Post_5, PanCK+

description: Library name: P3-Post_5_PanCK+

value: FFPE tumor

tag: cell type

value: PanCK+

tag: pre vs_post_covid

value: Post

tag: high covid

value: FALSE


title: P1-Pre_1, PanCK+

description: Library name: P1-Pre_1_PanCK+

tag: tissue

value: Pre


title: I46H12_LN_VV_D80_GEX

description: Library name: I46H12_LN_VV_D80_GEX

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

value: Antigen-experienced and bystander skin resident memory T cells in vaccinia virus infection

tag: lab

value: Kaplan

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: infection agent

tag: infection dose

tag: treat dose

tag: treat mode

value: topical

tag: prep description

value: mechanical dissociation alone

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: sample comments


title: P3-Post_5, CD45+

description: Library name: P3-Post_5_CD45+

tag: tissue

tag: cell type

tag: pre vs_post_covid

tag: high covid


title: P1-Post_1, PanCK+

description: Library name: P1-Post_1_PanCK+


title: I46H12_LN_VV_D80_FBC

description: Library name: I46H12_LN_VV_D80_FBC

value: inguinal lymph node;axillary lymph node;brachial lymph node

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

value: wt

tag: Sex

value: female

value: TRUE


title: BSSR1918_smallRNAseq

description: Library name: BSSR1918_smallRNAseq

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

tag: treatment

value: No

tag: clinical stage

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: P3-Post_4, PanCK+

description: Library name: P3-Post_4_PanCK+

tag: tissue

value: FFPE tumor

tag: cell type

value: PanCK+

tag: pre vs_post_covid

tag: high covid


title: P3-Post_4, CD45+

description: Library name: P3-Post_4_CD45+

value: Post

value: FALSE


title: P3-Post_3, PanCK+

description: Library name: P3-Post_3_PanCK+


title: P3-Post_2, PanCK+

description: Library name: P3-Post_2_PanCK+


title: P3-Post_3, CD45+

description: Library name: P3-Post_3_CD45+


title: I46H10_skinback_VV_D80_bystander_GEX

description: Library name: I46H10_skinback_VV_D80_bystander_GEX

value: skin of back, right flank

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

value: Antigen-experienced and bystander skin resident memory T cells in vaccinia virus infection

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: infection agent

value: Vaccinia virus (Western Reserve)

tag: infection dose

value: 3x10E6 PFU

tag: treat dose

value: skin scarification of the left flank at D0; DNFB 0.15%, topical, at day 5 on the opposite, right, flank (DNFB pull)

tag: treat mode

tag: prep description

value: collagenase XI, hyaluronidase, DNAse I

tag: organ

tag: organ uberon_id

tag: target cells

value: CD8+ T

tag: gating strategy

tag: sample comments

value: CITESeq failed

value: T cells


title: P3-Post_2, CD45+

description: Library name: P3-Post_2_CD45+

tag: tissue

tag: cell type

tag: pre vs_post_covid

tag: high covid


title: I46H10_skinback_VV_D80_bystander_FBC

description: Library name: I46H10_skinback_VV_D80_bystander_FBC

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

value: Kaplan

tag: organism name

tag: strain

tag: genetics

value: wt

tag: Sex

value: female

value: TRUE

value: topical


title: I46H10_skinback_VV_D80_bystander_TCR

description: Library name: I46H10_skinback_VV_D80_bystander_TCR

tag: age weeks

tag: pool of_mice

tag: infection agent

tag: infection dose

tag: treat dose

tag: treat mode

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells


title: BCG-310_smallRNAseq

description: Library name: BCG-310_smallRNAseq

tag: tissue

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

tag: treatment

value: No

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: BCG-379_smallRNAseq

description: Library name: BCG-379_smallRNAseq

value: IIIB


title: P3-Post_1, PanCK+

description: Library name: P3-Post_1_PanCK+

value: FFPE tumor

tag: cell type

value: PanCK+

tag: pre vs_post_covid

value: Post

tag: high covid

value: FALSE


title: P3-Post_1, CD45+

description: Library name: P3-Post_1_CD45+

tag: tissue


title: BCG-390_smallRNAseq

description: Library name: BCG-390_smallRNAseq

tag: age

tag: race

value: IA


title: P3-Pre_5, PanCK+

description: Library name: P3-Pre_5_PanCK+

value: Pre


description: Library name: I46H1_skinback_VV_D80_AntigenExperienced_TCR

value: skin of back, left flank

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

value: Antigen-experienced and bystander skin resident memory T cells in vaccinia virus infection

tag: lab

value: Kaplan

tag: organism name

tag: strain

tag: genetics

value: wt

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

tag: infection agent

value: Vaccinia virus (Western Reserve)

tag: infection dose

value: 3x10E6 PFU

tag: treat dose

value: skin scarification of the left flank at D0; DNFB 0.15%, topical, at day 5 on the opposite, right, flank (DNFB pull)

tag: treat mode

tag: prep description

value: collagenase XI, hyaluronidase, DNAse I

tag: organ

tag: organ uberon_id

tag: target cells

value: CD8+ T

tag: gating strategy

tag: sample comments

value: CITESeq failed

value: T cells


title: P3-Pre_5, CD45+

description: Library name: P3-Pre_5_CD45+

tag: tissue

value: FFPE tumor

tag: cell type

tag: pre vs_post_covid

tag: high covid


title: BCG-254_smallRNAseq

description: Library name: BCG-254_smallRNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

tag: treatment

value: No

tag: clinical stage

value: IIB

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


description: Library name: I46H1_skinback_VV_D80_AntigenExperienced_GEX

tag: tissue

value: skin of back, left flank

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: FALSE

tag: exp name

value: Antigen-experienced and bystander skin resident memory T cells in vaccinia virus infection

tag: lab

value: Kaplan

tag: organism name

tag: strain

tag: genetics

value: wt

tag: Sex

tag: age weeks

tag: pool of_mice

tag: infection agent

tag: infection dose

tag: treat dose

tag: treat mode

value: topical

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: sample comments

tag: cell type


title: P3-Pre_4, PanCK+

description: Library name: P3-Pre_4_PanCK+

tag: tissue

value: PanCK+

tag: pre vs_post_covid

value: Pre

tag: high covid


title: P3-Pre_4, CD45+

description: Library name: P3-Pre_4_CD45+


title: P3-Pre_3, PanCK+

description: Library name: P3-Pre_3_PanCK+


title: BCG-400_smallRNAseq

description: Library name: BCG-400_smallRNAseq

tag: age

tag: race

tag: ethnicity

tag: er

tag: gender

tag: treatment

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


description: Library name: I46H1_skinback_VV_D80_AntigenExperienced_FBC

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

tag: infection agent

value: Vaccinia virus (Western Reserve)

tag: infection dose

value: 3x10E6 PFU

tag: treat dose

value: skin scarification of the left flank at D0; DNFB 0.15%, topical, at day 5 on the opposite, right, flank (DNFB pull)

tag: treat mode

tag: prep description

value: collagenase XI, hyaluronidase, DNAse I

tag: organ

tag: organ uberon_id

tag: target cells

value: CD8+ T

tag: gating strategy

tag: sample comments

value: CITESeq failed

tag: cell type

value: T cells


title: BCG-228_smallRNAseq

description: Library name: BCG-228_smallRNAseq

tag: tissue

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

tag: treatment

value: No

tag: clinical stage

value: IA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: P3-Pre_3, CD45+

description: Library name: P3-Pre_3_CD45+

value: FFPE tumor

tag: pre vs_post_covid

value: Pre

tag: high covid

value: FALSE


title: P3-Pre_2, CD45+

description: Library name: P3-Pre_2_CD45+

tag: tissue

tag: cell type


title: I16H9_salivarygland_PD1KO_TCR

description: Library name: I16H9_salivarygland_PD1KO_TCR

source_name: submandibular gland

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

value: Brossay

tag: organism name

tag: strain

tag: genetics

value: PD1 KO (CRISPR in B6NJ backcrossed with B6J)

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: prep description

value: liberase, DNAse I

tag: organ

tag: organ uberon_id

tag: target cells

value: all T

tag: gating strategy

value: CD45+ CD3e+

tag: mouse comments


title: BCG-164_smallRNAseq

description: Library name: BCG-164_smallRNAseq

tag: tissue

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

tag: gender

tag: treatment

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: P3-Pre_1, PanCK+

description: Library name: P3-Pre_1_PanCK+

tag: cell type

value: PanCK+

tag: pre vs_post_covid

tag: high covid


title: I16H9_salivarygland_PD1KO_GEX

description: Library name: I16H9_salivarygland_PD1KO_GEX

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: mouse comments

value: T cells


title: BCG-209_smallRNAseq

description: Library name: BCG-209_smallRNAseq

tag: tissue

tag: age

tag: race

tag: ethnicity

tag: er

value: ER-positive

tag: gender

value: Female

tag: treatment

value: No

tag: clinical stage

value: IIB

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: I16H9_salivarygland_PD1KO_FBC

description: Library name: I16H9_salivarygland_PD1KO_FBC

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

value: FALSE

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: cell type


title: P3-Pre_1, CD45+

description: Library name: P3-Pre_1_CD45+

tag: tissue

value: FFPE tumor

tag: pre vs_post_covid

value: Pre

tag: high covid


title: BU3 NGPT 2μM #3

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

data_processing:
Reads were mapped to GRCh38
Counts per gene were summarized using the featureCounts function from the subread package
edgeR package was used to import and filter the counts
Differential expression using MAST models
The limma package with its voom method, namely, linear modelling and empirical Bayes moderation was used to test differential expression (moderate t-test). P-values were adjusted for multiple testing using Benjamini-Hochberg correction (false discovery rate-adjusted p-value; FDR). Differentially expressed genes for each comparison were visualized using Glimma package, and FDR<0.05 was set as the threshold for determining significant differential gene expression. Enrichment analyses were carried out using Fgsea package.
Assembly: GRCh38
Supplementary files format and content: Tab separated file having raw read count for each sample in singular file

source_name: BU3 NGPT

extract_protocol:
RNA was extracted by lysing cells in QIAzol (Qiagen) and subsequently samples were processed using the RNeasy Mini kit (Qiagen), with DNA digestion.
Libraries were generated using the NEBNext Ultra II RNA kit.

tag: cell line

value: BU3 NGPT

value: iPSC derived foregut

tag: time

value: Day 6

tag: treatment

value: DSM 2μM


title: BU3 NGPT 2μM #2


title: BCG-148_smallRNAseq

description: Library name: BCG-148_smallRNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

tag: gender

tag: clinical stage

value: IA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: I16H8_salivarygland_PD1KO_TCR

description: Library name: I16H8_salivarygland_PD1KO_TCR

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

value: Brossay

tag: organism name

tag: strain

tag: genetics

value: PD1 KO (CRISPR in B6NJ backcrossed with B6J)

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: prep description

value: liberase, DNAse I

tag: organ

tag: organ uberon_id

tag: target cells

value: all T

tag: gating strategy

value: CD45+ CD3e+

tag: mouse comments

tag: cell type

value: T cells


title: BU3 NGPT 1μM #3

tag: cell line

tag: time

tag: treatment

value: DSM 1μM


title: BU3 NGPT 1μM #2


title: BCG-047_smallRNAseq

description: Library name: BCG-047_smallRNAseq

tag: tissue

tag: age

tag: race

tag: ethnicity

tag: er

value: ER-positive

tag: gender

value: Female

value: No

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: I16H8_salivarygland_PD1KO_GEX

description: Library name: I16H8_salivarygland_PD1KO_GEX

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

value: FALSE

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: mouse comments

tag: cell type


title: BU3 NGPT 1μM #1

tag: cell line

value: BU3 NGPT

value: iPSC derived foregut

tag: time

value: Day 6

tag: treatment


title: BCG-036_smallRNAseq

description: Library name: BCG-036_smallRNAseq

tag: tissue

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

tag: gender

tag: clinical stage

value: IA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: BU3 NGPT 0μM #3

tag: cell line

tag: cell type


title: P3-Pre_2, PanCK+

description: Library name: P3-Pre_2_PanCK+

value: FFPE tumor

value: PanCK+

tag: pre vs_post_covid

value: Pre

tag: high covid


title: I16H8_salivarygland_PD1KO_FBC

description: Library name: I16H8_salivarygland_PD1KO_FBC

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

value: Brossay

tag: organism name

tag: strain

tag: genetics

value: PD1 KO (CRISPR in B6NJ backcrossed with B6J)

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: prep description

value: liberase, DNAse I

tag: organ

tag: organ uberon_id

tag: target cells

value: all T

tag: gating strategy

value: CD45+ CD3e+

tag: mouse comments

value: T cells


title: BCG-026_smallRNAseq

description: Library name: BCG-026_smallRNAseq

tag: tissue

tag: age

tag: race

tag: ethnicity

tag: er

value: ER-positive

tag: gender

value: Female

tag: treatment

value: No

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: BU3 NGPT 0μM #1

tag: cell line

value: BU3 NGPT

tag: cell type

value: iPSC derived foregut

tag: time

value: Day 6


title: BU3 NGPT 0μM #2


title: I16H7_salivarygland_PD1KO_TCR

description: Library name: I16H7_salivarygland_PD1KO_TCR

tag: tissue

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

value: FALSE

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: mouse comments


title: I16H7_salivarygland_PD1KO_GEX

description: Library name: I16H7_salivarygland_PD1KO_GEX

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

value: Brossay

value: PD1 KO (CRISPR in B6NJ backcrossed with B6J)

tag: cell type


title: BCG-023_smallRNAseq

description: Library name: BCG-023_smallRNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

tag: gender

tag: treatment

tag: clinical stage

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: BCG-155_smallRNAseq

description: Library name: BCG-155_smallRNAseq

tag: tissue

value: ER-positive

value: IIB


title: d25_Hyp3_S12

city: Clayton

first: Laura

last: Perlaza-Jimenez

state: Victoria

address: 15 Innovation Walk

country: Australia

institute: Monash University

data_processing:
CRCh38 primary assembly human reference genome and and human GTF annotation file were downloaded from Ensembl respository and genome was indexed using “STAR” alignment tool.
fastq files were aligned to the reference genome to generate BAM files.
BAM files were sorted and indexed using “samtools” software.
“umi_tools” software was employed to remove duplicated reads based on UMI duplication.
“featureCounts” tool was applied on sorted deduplicated BAM files using the GTF file to obtain the count data for each sample.
All samples count data were imported into R programming language to assemble the gene expression matrix. “biomaRt” R package version 2.46.3 was used to map Ensembl gene Ids to gene symbols.
Assembly: CRCh38
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: Derived from GM04522 fibroblasts (Coriell Inst)

growth_protocol: To generate kidney organoids, we followed the protocol published by Takasato et al, Nature, 2015, with minor modifications. 60,000 human iPS were seeded in Matrigel coated plates and treated with Essential 6 medium supplemented with 4uM CHIR99021 until day 4. Afterwards, the cells are supplemented with Essential 6 medium, 200ng/ml FGF9 and 1ug/ml Heparin. On day 7, 150,000 cells were used to form 3D aggregates that were cultured for 1h with 4uM of CHIR99021 in Essential 6 medium. Afterwards, the medium was changed to 200ng/ml FGF9, 1ug/ml Heparin in Essential E6 until day 13, when cells are cultured with Essential 6 medium only.

extract_protocol:
RNA Extraction (ISOLATE II RNA Mini Kit 50): BIO-52072. Following manufacturer's instruction. All samples were processed starting with 50ng of total RNA
RNA libraries for RNA-seq were prepared at Monash Health Translational Precinct (MHTP), Medical Genomics Facility using Novel RNA-Seq pipeline (Version 01/09/2021). Briefly index is added during initial pA priming and pooled samples amplified using template switching oligo.

treatment_protocol: Eighteen-day old kidney organoids are exposed to hypoxic conditions (1% O2) for 48h. To assess the development of maladaptive repair following acute injuryy, kidney organooids are afterwards placed back into normoxic conditions (21% O2) for an extra 5 days. Samples for analysis are collected on day 20 and day 25 of development for both injury and control groups.

value: Kidney organoids

tag: cell line

value: 522.3 iPSCs - female (16 year old)

value: Kidney cells derived from ips (passage 19)

value: 48h hyp+5d norm cond (d25)


title: BCG-006_smallRNAseq

description: Library name: BCG-006_smallRNAseq

value: Female

value: No

value: IIA


title: d25_Hyp1_S10

tag: cell type


title: BU3 NGPT 2μM #1

value: BU3 NGPT

value: iPSC derived foregut

tag: time

value: Day 6

value: DSM 2μM


title: I16H7_salivarygland_PD1KO_FBC

description: Library name: I16H7_salivarygland_PD1KO_FBC

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

value: Brossay

tag: organism name

tag: strain

tag: genetics

value: PD1 KO (CRISPR in B6NJ backcrossed with B6J)

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

value: FALSE

tag: prep description

value: liberase, DNAse I

tag: organ

tag: organ uberon_id

tag: target cells

value: all T

tag: gating strategy

value: CD45+ CD3e+

tag: mouse comments

value: T cells


title: d25_Norm3_S9

tag: tissue

value: Kidney organoids

tag: cell line

value: 522.3 iPSCs - female (16 year old)

tag: cell type

value: Kidney cells derived from ips (passage 19)

tag: treatment

value: 48h norm+5d norm cond (d25)


title: d25_Norm2_S8


title: BSSR1378_smallRNAseq

description: Library name: BSSR1378_smallRNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

value: No

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: d25_Norm1_S7

tag: tissue


title: BSSR1297_smallRNAseq

description: Library name: BSSR1297_smallRNAseq


title: d20_Hyp1_S4

tag: cell line

value: 48h hypoxic conditions (d20)


title: BSSR1186_smallRNAseq

description: Library name: BSSR1186_smallRNAseq

value: IA


title: I16H6_salivarygland_PD1KO_TCR

description: Library name: I16H6_salivarygland_PD1KO_TCR

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

value: Brossay

tag: organism name

tag: strain

tag: genetics

value: PD1 KO (CRISPR in B6NJ backcrossed with B6J)

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

value: FALSE

tag: prep description

value: liberase, DNAse I

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: mouse comments

tag: cell type


title: I16H6_salivarygland_PD1KO_FBC

description: Library name: I16H6_salivarygland_PD1KO_FBC

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

value: all T

value: CD45+ CD3e+

value: T cells


title: d20_Norm2_S2

value: Kidney organoids

tag: cell line

value: 522.3 iPSCs - female (16 year old)

value: Kidney cells derived from ips (passage 19)

tag: treatment

value: 48h normoxic conditions (d20)


title: d20_Norm3_S3


title: BSSR1153_smallRNAseq

description: Library name: BSSR1153_smallRNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

value: No

tag: clinical stage

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: d20_Norm1_S1

tag: tissue

tag: cell type


title: I16H5_salivarygland_PD1KO_TCR

description: Library name: I16H5_salivarygland_PD1KO_TCR

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

value: Brossay

tag: organism name

tag: strain

tag: genetics

value: PD1 KO (CRISPR in B6NJ backcrossed with B6J)

tag: Sex

tag: age weeks

tag: pool of_mice

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: mouse comments


title: d25_Hyp2_S11

tag: tissue

tag: cell line

tag: cell type

tag: treatment

value: 48h hyp+5d norm cond (d25)


title: I16H6_salivarygland_PD1KO_GEX

description: Library name: I16H6_salivarygland_PD1KO_GEX

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

value: female

value: FALSE

value: liberase, DNAse I

value: all T

value: CD45+ CD3e+

value: T cells


title: Pilot DC-TAP-seq for 203 genes in WTC11 infected with 98 guides in sgOpti-CS vector at MOI10. gRNA

city: Stanford

first: Jesse

last: Engreitz

state: CA

address: 450 Serra Mall

department: Genetics

institute: Stanford University

description:
Library name: WTC11_sgOpti-CS_DC-TAP_MOI10_pilot_gRNA
10x Genomics
wtc11_10_MOI_filtered_feature_bc_matrix.tar.gz

library_source: other

data_processing:
We aligned reads to transcripts and identified cells using the 10x Genomics cloud analysis web browser version with Cell Ranger Count v7.0.0 or v7.0.1 or v7.1.0 or v7.2.0, using the GRCh38-2020-A transcriptome. For DC-TAP-seq and TAP-seq analysis, we input our transcriptome FASTQ files as Targeted Next GEM 3’ Gene Expression libraries with a custom reference file containing bait sequences for the targeted genes. We generated this reference file by subsetting the bait sequences found in 10x Genomics’ human_pulldown_probes.csv file (built on GRCh38-2020-A). For guide RNA (gRNA) analysis, we processed guide FASTQ files as CRISPR Guide Capture libraries using a feature_reference.csv file containing the guide sequences.
Assembly: human hg38
Supplementary files format and content: filtered feature bc matrix file (.tar.gz format) that is output directly from cellranger. Contains matrix, barcodes and features files. The all_guide_info.txt file contains guide UMI information for the pilot TAP-seq sample.

molecule: other

growth_protocol: We grew K562 cells harboring dCas9-KRAB  in RPMI-1640 (Thermo Fisher Scientific, Waltham, MA) with 10% heat-inactivated FBS (HIFBS (Thermo Fisher Scientific), 2 mM L-glutamine, and 100 units/ml streptomycin and 100 mg/ml penicillin. We maintained K562 cells at a density between 100K and 1M per mL. We seeded human iPS cells (WTC11) harboring dCas9-KRAB (Metzl-Raz et al., Stem Cell Res., 2022) in 6-well plates coated with 1:100 LDEV-Free Reduced Growth Factor Basement Membrane Matrix (Thermo Fisher Scientific). The culture medium used was StemFlex Medium supplemented with 10% StemFlex supplement (SF complete media, Thermo Fisher Scientific), 2 µl of Normacin per ml of media (1:500 final, Invivogen), and 0.4 µl of 10 mM Rock Inhibitor (Y-27632 Dihydrochloride, STEMCELL Technologies). After 24 hours of seeding, we continued to maintain the cells with SF complete media without Rock Inhibitor and passaged them with 1 ml of accutase (STEMCELL Technologies) as necessary, aiming to maintain at 80-90% confluence to prevent stacked cell growth.

extract_protocol:
Cells were collected using centrifugation, washed with PBS+BSA and subjected to droplet formation for DC-TAP-seq or TAP-seq or scRNA-seq using the 10x Genomics v3.1 kit.
DC-TAP-seq libraries were constructed according to the protocol detailed in Ray et al 2025 (dx.doi.org/10.17504/protocols.io.3byl4z7drvo5/v1). TAP-seq libraries were prepared according to Schraivogel et al., Nat Methods, 2020 and scRNA-seq libraries with guide capture were generated according to the 10x Genomics protocol.


title: BSSR1131_smallRNAseq

description: Library name: BSSR1131_smallRNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

tag: er

tag: gender

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: Pilot DC-TAP-seq for 203 genes in WTC11 infected with 98 guides in sgOpti-CS vector at MOI6. gRNA

description:
Library name: WTC11_sgOpti-CS_DC-TAP_MOI6_pilot_gRNA
10x Genomics
wtc11_6_MOI_filtered_feature_bc_matrix.tar.gz

tag: cell line


title: Pilot DC-TAP-seq for 203 genes in WTC11 infected with 98 guides in sgOpti-CS vector at MOI2. gRNA

description:
Library name: WTC11_sgOpti-CS_DC-TAP_MOI2_pilot_gRNA
10x Genomics
wtc11_2_MOI_filtered_feature_bc_matrix.tar.gz


title: I16H5_salivarygland_PD1KO_GEX

description: Library name: I16H5_salivarygland_PD1KO_GEX

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: mouse comments

tag: cell type


title: BSSR1123_smallRNAseq

description: Library name: BSSR1123_smallRNAseq

tag: tissue

tag: age

tag: race

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

tag: treatment

tag: clinical stage

value: IA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: BSSR1118_smallRNAseq

description: Library name: BSSR1118_smallRNAseq

value: No


title: I16H5_salivarygland_PD1KO_FBC

description: Library name: I16H5_salivarygland_PD1KO_FBC

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

value: Brossay

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: mouse comments


title: Pilot DC-TAP-seq for 203 genes in WTC11 infected with 98 guides in sgOpti-CS vector at MOI3. gRNA

description:
Library name: WTC11_sgOpti-CS_DC-TAP_MOI3_pilot_gRNA
10x Genomics
wtc11_3_MOI_filtered_feature_bc_matrix.tar.gz

tag: cell line


title: Pilot DC-TAP-seq for 203 genes in WTC11 infected with 98 guides in sgOpti-CS vector at MOI1. gRNA

description:
Library name: WTC11_sgOpti-CS_DC-TAP_MOI1_pilot_gRNA
10x Genomics
wtc11_1_MOI_filtered_feature_bc_matrix.tar.gz


title: I16H4_salivarygland_TCR

description: Library name: I16H4_salivarygland_TCR

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

value: salivarygland

value: wt

value: male

value: pool of 9 males DOB 5/10/22

tag: cell type


title: d20_Hyp2_S5

value: Kidney organoids

value: 522.3 iPSCs - female (16 year old)

value: Kidney cells derived from ips (passage 19)

tag: treatment

value: 48h hypoxic conditions (d20)


title: Pilot DC-TAP-seq for 97 genes in K562 infected with 97 guides in sgOpti-CS vector at MOI14. gRNA

description:
Library name: K562_sgOpti-CS_DC-TAP_MOI14_pilot_gRNA
10x Genomics
k562_14-MOI_filtered_feature_bc_matrix.tar.gz


title: Pilot DC-TAP-seq for 97 genes in K562 infected with 97 guides in sgOpti-CS vector at MOI9. gRNA

description:
Library name: K562_sgOpti-CS_DC-TAP_MOI9_pilot_gRNA
10x Genomics
k562_9-MOI_filtered_feature_bc_matrix.tar.gz


title: BSSR1030_smallRNAseq

description: Library name: BSSR1030_smallRNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

tag: gender

tag: clinical stage

value: IIB

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: d20_Hyp3_S6

tag: tissue

tag: cell line


title: I16H4_salivarygland_GEX

description: Library name: I16H4_salivarygland_GEX

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: prep description

value: liberase, DNAse I

tag: organ

tag: organ uberon_id

tag: target cells

value: all T

tag: gating strategy

value: CD45+ CD3e+

tag: mouse comments

tag: cell type

value: T cells


title: Pilot DC-TAP-seq for 97 genes in K562 infected with 97 guides in sgOpti-CS vector at MOI6. gRNA

description:
Library name: K562_sgOpti-CS_DC-TAP_MOI6_pilot_gRNA
10x Genomics
k562_6-MOI_filtered_feature_bc_matrix.tar.gz

tag: cell line


title: Pilot DC-TAP-seq for 97 genes in K562 infected with 97 guides in sgOpti-CS vector at MOI1 (replicate 2). gRNA

description:
Library name: K562_sgOpti-CS_DC-TAP_MOI1_pilot_rep2_gRNA
10x Genomics
k562_1-MOI_filtered_feature_bc_matrix.tar.gz


title: BSSR1017_smallRNAseq

description: Library name: BSSR1017_smallRNAseq

tag: tissue

tag: age

tag: race

tag: ethnicity

tag: er

value: ER-positive

tag: gender

value: Female

tag: treatment

value: No

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: I16H4_salivarygland_FBC

description: Library name: I16H4_salivarygland_FBC

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

value: salivarygland

tag: cite seq

value: TRUE

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

value: Brossay

tag: organism name

tag: strain

tag: genetics

value: wt

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: mouse comments

value: pool of 9 males DOB 5/10/22

tag: cell type


title: Pilot DC-TAP-seq for 97 genes in K562 infected with 97 guides in sgOpti-CS vector at MOI1 (replicate 1). gRNA

description:
Library name: K562_sgOpti-CS_DC-TAP_MOI1_pilot_rep1_gRNA
10x Genomics
L-SG-TAP_filtered_feature_bc_matrix.tar.gz

tag: cell line


title: I16H3_salivarygland_TCR

description: Library name: I16H3_salivarygland_TCR

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: female

value: pool of 9 females DOB 5/10/22


title: BSSR0997_smallRNAseq

description: Library name: BSSR0997_smallRNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

tag: gender

tag: treatment

tag: clinical stage

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: Pilot DC-TAP-seq for 97 genes in K562 infected with 97 guides in sgOpti-CS vector at MOI 20. gRNA

description:
Library name: K562_sgOpti-CS_DC-TAP_pilot_moi20_gRNA
10x Genomics
H-SG-TAP_filtered_feature_bc_matrix.tar.gz

tag: cell line


title: Pilot DC-TAP-seq for 97 genes in K562 infected with 99 guides in pBA904 vector. gRNA

description:
Library name: K562_pBA904_DC-TAP_pilot_gRNA
10x Genomics
H-DC-TAP_filtered_feature_bc_matrix.tar.gz


title: BSSR0779_smallRNAseq

description: Library name: BSSR0779_smallRNAseq

tag: tissue

value: ER-positive

value: IA


title: Pilot whole transcriptome scRNA-seq with guide capture in K562 infected with 16 guides in pBA904 vector. gRNA

description:
Library name: K562_pBA904_scRNA_pilot_gRNA
10x Genomics
P16-scRNAseq_filtered_feature_bc_matrix.tar.gz


title: I16H3_salivarygland_GEX

description: Library name: I16H3_salivarygland_GEX

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: prep description

value: liberase, DNAse I

tag: organ

tag: organ uberon_id

tag: target cells

value: all T

tag: gating strategy

value: CD45+ CD3e+

tag: mouse comments

tag: cell type

value: T cells


title: BSSR0738_smallRNAseq

description: Library name: BSSR0738_smallRNAseq

tag: tissue

tag: age

tag: race

tag: ethnicity

tag: er

tag: gender

value: Female

tag: treatment

value: No

tag: clinical stage

value: IIB

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: I16H3_salivarygland_FBC

description: Library name: I16H3_salivarygland_FBC

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

value: salivarygland

tag: cite seq

value: TRUE

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

value: Brossay

tag: organism name

tag: strain

tag: genetics

value: wt

tag: Sex

tag: age weeks

tag: pool of_mice

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: mouse comments


title: Pilot DC-TAP-seq for 203 genes in WTC11 infected with 98 guides in sgOpti-CS vector at MOI3. mRNA

description:
Library name: WTC11_sgOpti-CS_DC-TAP_MOI3_pilot_mRNA
10x Genomics
wtc11_3_MOI_filtered_feature_bc_matrix.tar.gz

tag: cell line


title: Pilot DC-TAP-seq for 203 genes in WTC11 infected with 98 guides in sgOpti-CS vector at MOI6. mRNA

description:
Library name: WTC11_sgOpti-CS_DC-TAP_MOI6_pilot_mRNA
10x Genomics
wtc11_6_MOI_filtered_feature_bc_matrix.tar.gz


title: BSSR0680_smallRNAseq

description: Library name: BSSR0680_smallRNAseq

tag: tissue

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

tag: er

tag: gender

tag: treatment

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: Pilot DC-TAP-seq for 203 genes in WTC11 infected with 98 guides in sgOpti-CS vector at MOI10. mRNA

description:
Library name: WTC11_sgOpti-CS_DC-TAP_MOI10_pilot_mRNA
10x Genomics
wtc11_10_MOI_filtered_feature_bc_matrix.tar.gz


title: I16H2_spleen_TCR

description: Library name: I16H2_spleen_TCR

value: spleen

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

value: splenocytes

tag: gating strategy

tag: mouse comments

value: pool of 9 females DOB 5/10/22

tag: cell type


title: Pilot DC-TAP-seq for 203 genes in WTC11 infected with 98 guides in sgOpti-CS vector at MOI2. mRNA

description:
Library name: WTC11_sgOpti-CS_DC-TAP_MOI2_pilot_mRNA
10x Genomics
wtc11_2_MOI_filtered_feature_bc_matrix.tar.gz

tag: cell line