title: shRNA_LRP2_5

city: paris

first: kimberley

last: Delaunay

address: 15 rue de l'école de médecine

country: France

institute: Inserm

data_processing:
Quality of raw data was evaluated with FastQC.
Poor quality sequences were trimmed or removed with fastp tool, with default parameters, to retain only good quality paired reads.
Illumina DRAGEN bio-IT Plateform (v3.10.4) was used for mapping on hg38 reference genome and quantification with gencode v42 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Assembly: hg38
Supplementary files format and content: Matrix table with estimated number of reads and tpm counts for every gene and every sample.

source_name: Human induced pluritpotent stem cells

growth_protocol: Protocol for differentiating human-induced pluripotent stem cells (hiPSCs) into retinal pigment epithelial (iRPE) cells. HiPSCs are first cultured on Matrigel, detached and transferred to form three-dimensional embryoid body (EB) aggregates. These EBs are then cultured in neuronal induction medium for 10 days, then in retinal differentiation medium (RDM) for a further 3 days. From day 13 onwards, EBs are continuously cultured in RDM until the appearance of pigmented foci, generally between days 30 and 40. These pigmented iRPE cells are manually microdissected, reseeded on Matrigel and cultured until mature. Mature iRPE cells are then expanded and cultured in Transwells to acquire their oriented character. One week before the experiment, the medium is replaced by phenol red-free DMEM with 10% FBS.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
1 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: for each transfection 6µl siRNA triplex, a pool of 3 target-specific 19-25 nt siRNAs (Santa Cruz, sc-40103) or siRNA scrumble (Santa Cruz, sc- 37007) or Fluorescein Conjugated Control siRNA (Santa Cruz, sc-36869) were diluted into 100µl siRNA transfection medium (Santa Cruz, sc-36868,). This solution was mixed v/v with a diluted siRNA transfection reagent (Santa Cruz, sc-29528) solution. The siRNA mixture was added to the apical surface of iRPEs coated onto Transwell during 6 hours.  Without removing the siRNA mixture, serum concentrated medium (2X) was added for 18 hours incubation. After incubation, cells were placed in fresh medium during 24 hours. Then, cells were collected for RNA extraction.

value: Human induced pluritpotent stem cells

value: shRNA LRP2


title: shRNA_LRP2_4

status: Public on Jun 06 2025

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: treatment


title: Control_3

value: Scrumble


title: Control_4


title: shRNA_LRP2_2


title: Control_2


title: shRNA_LRP2_1


title: shRNA_LRP2_3


title: PDX441, CUT&Tag, H3K27me3

city: Dallas

first: Ram

last: Mani

state: Texas

address: 5323 Harry Hines Blvd NB6.444

department: Pathology

country: USA

institute: UT Southwestern Medical Center

library_source: genomic

data_processing:
CUT&Tag sequencing reads were mapped to the hg19 genome using Bowtie 2 (v2.1.0).
Duplicate reads were filtered out with Picard (v2.20.3) and reads with low mapping quality (MAPQ < 30) were excluded using Samtools (v1.9).
Peak calling was performed using SEACR (1.3) with IgG as the control.
Deeptools (v2.4.2) was also used to produce average coverage figures.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: Endometrial cancer Patient-Derived Xenograft(DPX)

extract_protocol:
CUT&Tag was performed using the CUTANA CUT&TAG kit (EpiCypher, 14-1102) according to the manufacturer’s instructions.
Libraries were prepared using the CUTANA CUT&TAG kit (EpiCypher, 14-1102), and library quality was assessed using an Agilent TapeStation 4200.

tag: tissue

value: Endometrial cancer PDX

tag: antibody


title: Control_1


title: PDX441, CUT&Tag, IgG

value: Endometrial cancer Patient-Derived Xenograft(DPX)

value: IgG


title: PDX333, CUT&Tag, IgG


title: PDX441, CUT&Tag, H3K27ac


title: PDX333, CUT&Tag, H3K27ac


title: PDX333, CUT&Tag, H3K4me3


title: PDX333, CUT&Tag, H3K27me3


title: PDX164, CUT&Tag, H3K27me3


title: PDX164, CUT&Tag, H3K4me3


title: PDX164, CUT&Tag, H3K27ac


title: Ishikawa, CUT&Tag, IgG

source_name: Ishikawa cells

tag: cell line

value: Ishikawa cells

value: Endometrial cancer cell lines


title: Ishikawa, CUT&Tag, H3K4me3


title: Ishikawa, CUT&Tag, H3K27me3


title: Ishikawa, CUT&Tag, H3K27ac


title: AN3CA, CUT&Tag, IgG

source_name: AN3CA cells

value: AN3CA cells


title: AN3CA, CUT&Tag, H3K27me3


title: AN3CA, CUT&Tag, H3K27ac


title: AN3CA, CUT&Tag, H3K4me3


title: PDX441, CUT&Tag, H3K4me3


title: PDX441, H3K27ac, ChIP

data_processing:
The raw reads were aligned to the hg19 reference genome using BWA (v0.7.17-r1188)
Picard (v2.20.3) was used to remove duplicate reads
Peak detection was performed with MACS2 (v2.1.0), utilizing default settings and input DNA as a control.
Deeptools (v2.4.2) facilitated the generation of bigWig files.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Chromatin Immunoprecipitation was performed by crosslinking cells and tissues in 1% formaldehyde for 8 minutes, following by quenching in 1.25M Glycine. Lysis and enrichment were carried out using the HighCell ChIP kit Protein G following manufacturer's instructions (Diagenode).
Next Generation Sequencing library preparation was carried out using KAPA Hyper Prep kit (KAPA Biosystems) and TruSeq adapters (Integrated DNA Technologies). A quality check of the purified libraries was carried out using the 4200 TapeStation(Agilent).

tag: chip antibody

value: H3K27ac, (Active Motif, Cat No.  39133)


title: PDX441, Input


title: PDX333, H3K27ac, ChIP


title: PDX333, Input


title: Ishikawa, H3K27ac, ChIP, PAX2 over expression

value: PAX2 over expression


title: Ishikawa, Input, empty vector

value: empty vector


title: PDX164, Input


title: AN3CA, Input, shRNA PAX2

value: shRNA PAX2


title: AN3CA, H3K27ac, ChIP, shRNA PAX2


title: AN3CA, Input, shRNA non-target

value: shRNA non-target


title: Ishikawa, Input, PAX2 over expression


title: PDX164, CUT&Tag, IgG


title: Ishikawa, H3K27ac, ChIP, empty vector


title: AN3CA, H3K27ac, ChIP, shRNA non-target


title: PDX164, ATAC-Seq

data_processing:
ATAC-Seq reads were aligned to the hg19 genome using Bowtie 2 (v2.1.0).
To ensure data quality, duplicate reads were removed with Picard (v2.20.3) and reads with low mapping quality (MAPQ < 10) were excluded using Samtools (v1.9).
Peaks were identified using MACS2 (v2.1.0).
Average coverage plots were generated with Deeptools (v2.4.2).
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Tumors were finely chopped and lysed in ATAC-seq lysis buffer. Following this, nuclei were washed and incubated in Tn5 transposase mixture.
Libraries were constructed using Nextera adapters (Illumina) and the KAPA HiFi Hotstart Ready mix.


title: PDX441, ATAC-Seq


title: sgOGDHL_2_Enza 3

city: Los Angeles

first: Andrew

middle: Scott

last: Goldstein

state: CA

address: 610 Charles E Young Dr East

department: Urology

institute: University of California, Los Angeles

description: Library name: sample18

data_processing:
The alignment was performed using STAR [2] with human reference genome GRCh38. The Ensembl Transcripts release GRCh38.107 GTF was used for gene feature annotation. For normalization of transcripts counts, TPM normalized counts were generated.
Assembly: GRch38
Supplementary files format and content: TXT files contain normalized TPM Values and Gene counts

source_name: prostate cancer

growth_protocol: Cells were cultured in RPMI 1640 containing 10% FBS and 1% Pen-Strep.

extract_protocol:
RNA was extracted using the Quigen Rneasy Kit
Libraries for RNA-Seq were prepared with KAPA mRNA HyperPrep Kit. The workflow consists of mRNA enrichment and fragmentation, first strand cDNA synthesis using random priming followed by second strand synthesis converting cDNA:RNA hybrid to double-stranded cDNA (dscDNA), and incorporates dUTP into the second cDNA strand to maintain strand origin information. cDNA generation is followed by end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in a half lane. Sequencing was performed on Illumina NovaSeq X Plus for PE 2x50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.

treatment_protocol: Cells were maintained in vehicle (DMSO) or 10uM Enzalutamide for 6 Weeks

value: prostate cancer

value: 16D CRPC

tag: genotype

value: OGDHL gRNA 2

value: 10uM Enza 6 weeks


title: PDX333, ATAC-Seq


title: sgOGDHL_2_Enza 1

description: Library name: sample16


title: sgOGDHL_1_Enza 2

description: Library name: sample14

value: OGDHL gRNA 1


title: sgAAVS Enza 3

description: Library name: sample12

value: Control gRNA


title: sgOGDHL_2_Enza 2

description: Library name: sample17


title: sgAAVS Enza 2

description: Library name: sample11


title: sgOGDHL_1_Enza 3

description: Library name: sample15


title: sgAAVS Enza 1

description: Library name: sample10


title: sgOGDHL_2_DMSO 1

description: Library name: sample7

value: Vehicle


title: sgOGDHL_2_DMSO 3

description: Library name: sample9


title: sgOGDHL_2_DMSO 2

description: Library name: sample8


title: PDX164, H3K27ac, ChIP

value: Endometrial cancer Patient-Derived Xenograft(DPX)

value: Endometrial cancer PDX


title: sgOGDHL_1_Enza 1

description: Library name: sample13


title: sgOGDHL_1_DMSO 1

description: Library name: sample4


title: sgAAVS DMSO 3

description: Library name: sample3


title: sgAAVS DMSO 2

description: Library name: sample2


title: 5-10KAAVSBW-2

description: Library name: sample5

data_processing:
The alignment was performed using STAR with human reference genome GRCh38. The Ensembl Transcripts release GRCh38.107 GTF was used for gene feature annotation. For normalization of transcripts counts, TPM normalized counts were generated.
Assembly: GRch38
Supplementary files format and content: TXT files contain normalized TPM Values and raw counts

source_name: Xenograft Tumor

growth_protocol: Cells were cultured in RPMI 1640 containing 10% FBS and 1% Pen-Strep prior to implantation in vivo

extract_protocol:
RNA was extracted using the Qiagen RNeasy Kit
Libraries for RNA-Seq were prepared with KAPA mRNA HyperPrep Kit. The workflow consists of mRNA enrichment and fragmentation, first strand cDNA synthesis using random priming followed by second strand synthesis converting cDNA:RNA hybrid to double-stranded cDNA (dscDNA), and incorporates dUTP into the second cDNA strand to maintain strand origin information. cDNA generation is followed by end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in a half lane. Sequencing was performed on Illumina NovaSeq X Plus for PE 2x50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.

treatment_protocol: Mice were not treated

value: Xenograft Tumor


title: 4-10KAAVSBW-L

description: Library name: sample4


title: 3-100KAAVSVB-R

description: Library name: sample3


title: 8-100KOGDHL2-R

description: Library name: sample8

value: OGDHL gRNA


title: 7-100KOGDHL2930-2

description: Library name: sample7


title: 9-100KOGDHL2-2

description: Library name: sample9


title: 2-1MAAVSBW-2

description: Library name: sample2


title: 6-100KOGDHL2930-R

description: Library name: sample6


title: 1-1MAAVSBW-L

description: Library name: sample1


title: LuCaP167CR, Hi-C

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

institute: Emory University

data_processing:
Reads were processed using runHiC pipeline with chromap as the aligner
Assembly: hg38
Supplementary files format and content: .mcool maps of chromatin contact

source_name: Prostate

growth_protocol: 1.Prostate cancer cell lines LNCaP cells were maintained in RPMI1640 with 10% fetal bovine serum (FBS), 1% penicillin and streptomycin and NCI-H660 cells were maintained in ATCC-formulated RPMI-1640 Medium (Catalog No.30-2001) with 0.005 mg/ml Insulin, 0.01 mg/ml Transferrin, 30nM Sodium selenite, 10 nM Hydrocortisone, 10 nM beta-estradiol, 5% fetal bovine serum. 2. LuCaP PDX were maintained in NOD SCID male mice which were purchased from Charles River Laboratories.

extract_protocol:
FOXA2-D14, D21 and D28 LNCaP cells, NCI-H660 cells and the cells from LuCaP PDXs were fixed with 2% formaldehyde (final concentration) at room temperature for 10 min, followed by adding 2.5 M glycine to a final concentration of 0.2 M to quench the reaction.
Hi-C libraries were generated using the Arima-HiC+ kit (Arima Genomics, A510008) for cell line and PDXs, Arima-HiC+ FFPE Kit (Arima Genomics, A101060) for CRPC and NEPC FFPE samples. The Hi-C libraries were sequenced with paired-end 2 × 150 bp using Illumina NovaSeq6000.

treatment_protocol: LNCaP cells were infected with FOXA2 overexpression virus and fallowed up by 28 days, cells were collected at D14, D21 and D28 for Hi-C analysis.

value: Prostate

value: LuCaP167CR PDX

value: Prostate cancer cell

value: WT


title: sgAAVS DMSO 1

description: Library name: sample1


title: LuCaP147CR, Hi-C

value: LuCaP147CR PDX


title: LuCaP105CR, Hi-C

value: LuCaP105CR PDX


title: LuCaP173.1, Hi-C

value: LuCaP173.1 PDX


title: LuCaP86.2CR, Hi-C

value: LuCaP86.2CR PDX


title: LuCaP93, H3K4me1 ChIP

data_processing:
Reads were aligned to the hg19 reference human genome using bowtie2
Assembly: hg19
Supplementary files format and content: bigwig generated from bam

growth_protocol: Prostate cancer cell lines LNCaP, 22Rv1 and LuNE cells were maintained in RPMI1640 with 10% fetal bovine serum (FBS), 1% penicillin and streptomycin and  NCI-H660 cells were maintained in ATCC-formulated RPMI-1640 Medium (Catalog No.30-2001) with 0.005 mg/ml Insulin, 0.01 mg/ml Transferrin, 30nM Sodium selenite, 10 nM Hydrocortisone, 10 nM beta-estradiol, 5% fetal bovine serum. 2. LuCaP PDX were maintained in NOD SCID male mice which were purchased from Charles River

extract_protocol:
PCa cells were crosslinked with 1% formaldehyde (Thermo fisher, Cat#28908)) for 10 min at room temperature with gentle rotation and then quenched for 5 min with 0.125 M glycine. Chromatin was sonicated to an average length of 200–600 bp using an E220 focused-ultrasonicator (Covaris).
ChIP–seq libraries were prepared from 3–5 ng of ChIPed DNA using NEBNext Ultra II DNA Library Prep Kit (NEB, E7645S), according to the manufacturer’s instructions.

treatment_protocol: 1.LNCaP cells were co-infected with FOXA2 virus along with either sgNC or sgNKX2-1 virus and infected cells were collected at D7, D14, D21 and D28 for ChIP analysis  2. LuNE cells were infected gRNAs targeting control (sgNC), NKX2-1 (sgNKX2-1), FOXA2 (sgFOXA2) or shRNAs targeting control (shCtrl), P300 (shP300), CBP (shCBP), the cells were collected for ChIP analysis 5 days after infection. 3. LuNE cells were treated with DMSO or CCS1477 (500nM) for 24h and collected for ChIP analysis.

value: LuCaP PDX

value: H3K4me1, Abcam, Cat#ab8895


title: sgOGDHL_1_DMSO 2

description: Library name: sample5

value: prostate cancer

value: 16D CRPC

value: OGDHL gRNA 1


title: sgOGDHL_1_DMSO 3

description: Library name: sample6

value: Vehicle


title: HL60-coculture-shNKX2-1_1

city: Taipei

first: Pinghsing

last: Tsai

state: Taiwan

address: Rm. 825, 7F., No.322, Sec. 2, Shipai Rd., Beitou D

country: Taiwan

institute: Taipei Veterans General Hospital

data_processing:
RNA seq
sequence reads were trimmed for adaptor sequence / low-quality sequence using basespace defult process
read count extraction and normalization were performed using R and EdgeR
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each sample
ATAC-Seq
The ATAC-seq pipeline was employed for processing and analyzing sequencing data, utilizing default parameters. The raw ATAC-seq fastq reads were aligned to the hg19 reference genome using the BWA Aligner (v1.1.4) on the basespace platform. The signal intensity present in the bedgraph files was determined as the fold enrichment of the signal per million reads within a sample compared to a modeled local background, utilizing the bdgcmp function in MACS2. Differential accessible peaks were detected using the MACS2 package and annotated with the ChIPseeker package.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files contain information on the distribution and enrichment of intersected peaks for both the control and shNKX2-1 samples.
Spatial Transcriptomics
The raw sequencing reads undergo processing using Space Ranger pipeline version 2.0.1. Sequences were aligned to mm10 genome.
Assembly: mm10
Supplementary files format and content: Spaceranger count pipline output files (Tab-separated values files and matrix files) Aligned tissue images: Spatial_lung_parental.tif; Spatial_lung_shNkx2-1.tif Cytassist image: Spatial_lung_parental_cytassist.tif; Spatial_lung_shNkx2-1_cytassist.tif Scalefactors in json format: Spatial_lung_parental_alignment.json; Spatial_lung_shNkx2-1_alignment.json
scRNA-seq
The raw sequencing reads undergo processing using Cell Ranger pipeline version 6.1.2. Sequences were aligned to mm10 genome.
Assembly: mm10
Supplementary files format and content: Cellranger count pipline output files (Tab-separated values files and matrix files)

growth_protocol: HCC827 and HL-60 cells were cultured in RPMI-1640 media supplemented with 10% Fetal Bovine Serum (FBS), 100 mg/mL streptomycin, and 100 U/mL penicillin in a humidified atmosphere at 37°C.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (QIAGEN, Hilden, Germany) and quantified by NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) following the manufacturer's protocol.  TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer's instructions.

treatment_protocol: Puromycin dihydrochloride stock was prepared by dissolving it in water to achieve a concentration of 50 mg/mL. The solution was then filtered through a 0.22 µm filter and stored in aliquots at –20 °C. To establish stable cell lines, 2 µg/mL of the dissolved puromycin was added to fresh culture media, while the control group received fresh culture media with only water. All mixtures were thoroughly mixed

value: NKX2-1 Knockdown


title: HCC827-shNKX2-1


title: HL60-coculture-shNKX2-1_2


title: HCC827-shCtrl


title: R. subcapitata, 24 h exposure, PFTeDA, sample16

city: Duluth

first: Peter

last: Schumann

state: MN

address: 6201 Congdon Blvd

institute: United States Environmental Protection Agency

data_processing:
Sequencing was performed in a 1x100bp single read format using Illumina NovaSeq SP flow cells (Illumina, Inc., San Diego, CA, USA).
The R. subcapitata reference genome (GCA_003203535.1) was indexed using STAR v2.7.10a (Dobin et al., 2012) using the following parameters: genomeSAindexNbases = 11, sjdbOverhang = 99, and sjdbGTFfeatureExon = gene.
The raw, 1x100bp single end FASTQ sequence files were trimmed, quality filtered (Phred score <15), and had UMIs and adapter sequences removed after deduplication using fastp v0.23.2 (Chen 2023, Chen et al., 2018).
Quality reads were aligned and mapped to the indexed reference genome using STAR. The resulting alignment files were sorted by coordinates and indexed by sample using Samtools v1.15.1 (Danecek et al., 2021).
Aligned reads were quantified with respect to gene features using the “featureCounts” program (v2.0.6) of the subread package (Liao et al., 2014). A 1,400 bp extension was added to each read at the 5’ end as most reads aligned at unannotated 3’ untranslated regions (UTR) of the genome and gene features with the largest overlap were counted. The quantified reads were organized into separate (tab-delimited) count matrix files for each chemical treatment group where columns represented samples and rows represented genes.
Assembly: GCA_003203535.1
Supplementary files format and content: count matrices with rows as gene features and columns as samples

molecule: polyA RNA

organism: Raphidocelis subcapitata

source_name: whole body

growth_protocol: reared in Woods Hole MBL media at 24°C with constant light (~250 µmol/m2/s)

extract_protocol:
RNA was extracted from pooled homogenates (Plant/Fungi Total RNA Purification kits, #31900, Norgen Biotek, Ontario, Canada) with a protocol slightly modified from the manufacturer’s instructions.  First, the algae were centrifuged, and the supernatant was aspirated.  Glass beads (0.5 mm) were added to each well and the plate went through five cycles of freezing with liquid nitrogen and bead milling for 2 minutes.  Next, 400 µl of kit Buffer C was added to each well and then the manufacturer’s procedure was followed.
Libraries were prepared using the Lexogen QuantSeq 3’ mRNA-Seq V2 Library Prep Kit with UDI (Unique Dual Index) and QuantSeq UMI (Unique Molecular Identifier) module with PhiX spike-in making up ~5% of the total reads in each lane. The UMI module (https://faqs.lexogen.com/faq/quantseq-umi-module) added a random, 6nt sequence to the start of each read 1 (R1), followed by a constant, 4nt (TATA) spacer. Preparation followed manufacturer’s recommendations. Completed libraries were quality checked and quantified using Qubit dsDNA HS and Agilent 4200 TapeStation HS DNA1000 assays. Libraries were pooled in equimolar amounts and quantified using the Invitrogen Collibri Quantification qPCR kit.

treatment_protocol: Using 96-well plates, two PFAS per exposure were serially diluted in algae media (Woods Hole MBL media) with a Biomek i5 liquid handler to final nominal exposure concentrations of 100, 32, 10, 3.2, 1, 0.3, 0.1, and 0.03 uM with five replicates per concentration of each PFAS.  There were also 8 control replicates (no PFAS) and two concentrations of CuSO4 (0.75 and 1.5 mM) with three replicates each as positive controls.  All PFAS and control replicates were arranged on a 96-well plate in a predetermined systematic layout such that each concentration was distributed to equal numbers of edge and interior wells.  All wells contained 0.33% solvent.  Prior to exposure, the cells per ml of a R. subcapitata culture in exponential growth was adjusted to approximately 5 x 10^6 cells/ml.  Each well of exposure plates was loaded with 800 µl of algal suspension.  All assays were conducted in four replicate, 96-well plates using deep-well plates sealed with optically clear adhesive covers.  Three of the replicate plates were randomly designated for transcriptomic analysis while the fourth plate was used for phenotypic measurements.  Algae were kept in suspension during incubation by shaking using a temperature controlled orbital shaker.

value: whole body

tag: developmental stage

value: Exponential Growth Stage

value: PFTeDA (DTXSID3059921)


title: R. subcapitata, 24 h exposure, PFTeDA, sample18


title: R. subcapitata, 24 h exposure, PFTeDA, sample19


title: R. subcapitata, 24 h exposure, PFTeDA, sample21


title: R. subcapitata, 24 h exposure, PFTeDA, sample20


title: R. subcapitata, 24 h exposure, PFTeDA, sample15


title: R. subcapitata, 24 h exposure, PFTeDA, sample14


title: R. subcapitata, 24 h exposure, PFTeDA, sample11


title: R. subcapitata, 24 h exposure, PFTeDA, sample13


title: R. subcapitata, 24 h exposure, PFTeDA, sample7


title: R. subcapitata, 24 h exposure, PFTeDA, sample8


title: R. subcapitata, 24 h exposure, PFTeDA, sample10


title: R. subcapitata, 24 h exposure, PFTeDA, sample12


title: R. subcapitata, 24 h exposure, PFTeDA, sample6


title: R. subcapitata, 24 h exposure, PFTeDA, sample9


title: R. subcapitata, 24 h exposure, PFTeDA, sample2


title: R. subcapitata, 24 h exposure, PFTeDA, sample1


title: R. subcapitata, 24 h exposure, PFTeDA, sample3


title: R. subcapitata, 24 h exposure, DMSO, sample32

value: DMSO (DTXSID2021735)


title: HL60-coculture-shCtrl


title: R. subcapitata, 24 h exposure, PFTeDA, sample4


title: R. subcapitata, 24 h exposure, 8:2FTS, sample21


title: R. subcapitata, 24 h exposure, DMSO, sample31


title: R. subcapitata, 24 h exposure, 8:2FTS, sample18


title: R. subcapitata, 24 h exposure, 8:2FTS, sample17


title: R. subcapitata, 24 h exposure, PFTeDA, sample17


title: R. subcapitata, 24 h exposure, 8:2FTS, sample19


title: R. subcapitata, 24 h exposure, 8:2FTS, sample16


title: R. subcapitata, 24 h exposure, 8:2FTS, sample15


title: R. subcapitata, 24 h exposure, 8:2FTS, sample13


title: R. subcapitata, 24 h exposure, 8:2FTS, sample14


title: R. subcapitata, 24 h exposure, 8:2FTS, sample11


title: R. subcapitata, 24 h exposure, 8:2FTS, sample10


title: R. subcapitata, 24 h exposure, PFTeDA, sample5


title: R. subcapitata, 24 h exposure, 8:2FTS, sample8


title: R. subcapitata, 24 h exposure, 8:2FTS, sample6


title: R. subcapitata, 24 h exposure, 8:2FTS, sample12


title: R. subcapitata, 24 h exposure, 8:2FTS, sample9


title: R. subcapitata, 24 h exposure, 8:2FTS, sample7


title: R. subcapitata, 24 h exposure, DMSO, sample33


title: R. subcapitata, 24 h exposure, 8:2FTS, sample5


title: R. subcapitata, 24 h exposure, 8:2FTS, sample4


title: R. subcapitata, 24 h exposure, 8:2FTS, sample3


title: R. subcapitata, 24 h exposure, 8:2FTS, sample20


title: R. subcapitata, 24 h exposure, DMSO, sample30


title: R. subcapitata, 24 h exposure, DMSO, sample29


title: R. subcapitata, 24 h exposure, DMSO, sample28


title: R. subcapitata, 24 h exposure, 6:1 FTOH, sample19


title: R. subcapitata, 24 h exposure, 6:1 FTOH, sample17


title: R. subcapitata, 24 h exposure, 6:1 FTOH, sample18


title: R. subcapitata, 24 h exposure, 6:1 FTOH, sample16


title: R. subcapitata, 24 h exposure, 6:1 FTOH, sample14


title: R. subcapitata, 24 h exposure, 6:1 FTOH, sample15


title: R. subcapitata, 24 h exposure, 8:2FTS, sample2


title: R. subcapitata, 24 h exposure, 8:2FTS, sample1


title: R. subcapitata, 24 h exposure, 6:1 FTOH, sample12


title: R. subcapitata, 24 h exposure, 6:1 FTOH, sample20


title: R. subcapitata, 24 h exposure, 6:1 FTOH, sample11


title: R. subcapitata, 24 h exposure, 6:1 FTOH, sample10


title: R. subcapitata, 24 h exposure, 6:1 FTOH, sample9


title: 778C_001_GEX_CZI-IA13003106

city: Palo Alto

first: Lattice

last: Data Coordination

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

description:
Library name: 778C_001_GEX_CZI-IA13003106_lib
scRNA-seq of mononuclear cells from pooled:skin of body,mesenteric lymph node

library_source: transcriptomic single cell

data_processing:
raw_matrix_normalized:False; raw_matrix_value_scale:linear; raw_matrix_background_barcodes_included:False
Assembly: GRCh38, GENCODE32
Supplementary files format and content: h5ad, count matrix

extract_protocol:
Tissue was obtained from deceased organ donors at the time of organ acquisition for clinical transplantation through an approved protocol and material transfer agreement via LiveOnNY, the organ procurement organization for the New York metropolitan area and through the Cambridge Biorepository for Translational Medicine. Each tissue was subjected to a tissue-specific protocol to maximize mononuclear cell (MNC) recovery and viability across a diversity of sites. A series of detailed protocols are available on protocols.io (https://dx.doi.org/10.17504/protocols.io.bwrjpd4n, https://dx.doi.org/10.17504/protocols.io.bwr9pd96, https://dx.doi.org/10.17504/protocols.io.bwsapeae, https://dx.doi.org/10.17504/protocols.io.bwq4pdyw, https://dx.doi.org/10.17504/protocols.io.bwq7pdzn, https://dx.doi.org/10.17504/protocols.io.bwr6pd9e, https://dx.doi.org/10.17504/protocols.io.bz4qp8vw). Each individual tissue single cell suspension (500,000 or 1,000,000 cells) was hash tagged to allow pooling of tissue samples. CITE-seq labeling used either a TotalSeq-C cocktail containing 137 protein targets (10x 5’ libraries) or TotalSeq-A cocktail containing 277 protein targets (10x 3’ libraries).
For scRNA-seq experiments, single cells were loaded onto the channels of a Chromium chip (10x Genomics). cDNA synthesis, amplification, and sequencing libraries were generated using either the Single Cell 5′ Reagent (v1 and v2) or 3′ Reagent (v3) Kits. TCRαβ and BCR paired VDJ libraries were prepared from samples made with the 5′ Reagent kit. All libraries were sequenced on either an Illumina NextSeq 500/550 or NovaSeq 6000 instrument.

tag: donor id

tag: age

value: 50-54 years

tag: dev stage

value: adult stage

tag: Sex

value: female

tag: ethnicity

value: Unknown

tag: source

tag: suspension cell_depletion_factors

tag: suspension treatment_summary

value: 1.34 nM of phorbol 13-acetate 12-myristate and ionomycin and 8.1 nM of ionomycin for 2 hours

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

value: FALSE

tag: sample preservation_method

value: fresh

tag: death type

value: circulatory death

tag: library protocol

tag: raw matrix_genome_annotation

tag: raw matrix_value_units

value: UMI

tag: raw matrix_feature_keys

value: gene symbol, antibody target

tag: raw matrix_assays

value: snRNA-seq, CITE-seq

tag: enriched cell_type

value: mononuclear cell

tag: assay type

value: scRNA-seq


title: R. subcapitata, 24 h exposure, 6:1 FTOH, sample13

tag: tissue

value: whole body

tag: developmental stage

tag: treatment


title: R. subcapitata, 24 h exposure, 6:1 FTOH, sample8

value: Exponential Growth Stage


title: 778C_001_GEX_CZI-IA13003105

description:
Library name: 778C_001_GEX_CZI-IA13003105_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

tag: donor id

tag: age

tag: dev stage

tag: Sex

tag: ethnicity

tag: source

value: Cambridge Biorepository for Translational Medicine


title: R. subcapitata, 24 h exposure, 6:1 FTOH, sample7


title: 778C_001_GEX_CZI-IA13003103

description:
Library name: 778C_001_GEX_CZI-IA13003103_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

tag: suspension cell_depletion_factors

tag: suspension treatment_summary

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

tag: sample preservation_method

tag: death type


title: R. subcapitata, 24 h exposure, 6:1 FTOH, sample6


title: 778C_001_GEX_CZI-IA13003101

description:
Library name: 778C_001_GEX_CZI-IA13003101_lib
scRNA-seq of mononuclear cells from pooled:skin of body,mesenteric lymph node,jejunum lamina propria

tag: library protocol

tag: raw matrix_genome_annotation

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: raw matrix_assays

tag: enriched cell_type


title: 778C_001_GEX_CZI-IA13003104

description:
Library name: 778C_001_GEX_CZI-IA13003104_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

tag: donor id

tag: age

tag: tissue

tag: assay type


title: 778C_001_GEX_CZI-IA13003102

description:
Library name: 778C_001_GEX_CZI-IA13003102_lib
scRNA-seq of mononuclear cells from pooled:skin of body,mesenteric lymph node,jejunum lamina propria

tag: dev stage

tag: Sex

tag: ethnicity

tag: source


title: R. subcapitata, 24 h exposure, 6:1 FTOH, sample3

tag: developmental stage

tag: treatment


title: R. subcapitata, 24 h exposure, 6:1 FTOH, sample2


title: R. subcapitata, 24 h exposure, 6:1 FTOH, sample4


title: 778C_001_GEX_CZI-IA13003100

description:
Library name: 778C_001_GEX_CZI-IA13003100_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

tag: sample preservation_method

tag: death type


title: R. subcapitata, 24 h exposure, 6:1 FTOH, sample1


title: R. subcapitata, 24 h exposure, PFPB, sample21

value: PFPB (DTXSID60663110)


title: 778C_001_GEX_CZI-IA13003097

description:
Library name: 778C_001_GEX_CZI-IA13003097_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

value: 50-54 years

tag: library protocol

tag: raw matrix_genome_annotation

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: raw matrix_assays


title: 778C_001_GEX_CZI-IA13003098

description:
Library name: 778C_001_GEX_CZI-IA13003098_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

tag: donor id

tag: age

value: adult stage

tag: tissue

tag: enriched cell_type

tag: assay type


title: 778C_001_GEX_CZI-IA13003099

description:
Library name: 778C_001_GEX_CZI-IA13003099_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

tag: dev stage

tag: Sex

value: female

tag: ethnicity

tag: source


title: R. subcapitata, 24 h exposure, PFPB, sample20

tag: developmental stage

tag: treatment


title: R. subcapitata, 24 h exposure, PFPB, sample19


title: 778C_001_GEX_CZI-IA13003095

description:
Library name: 778C_001_GEX_CZI-IA13003095_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

value: Unknown

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

tag: sample preservation_method

tag: death type


title: R. subcapitata, 24 h exposure, PFPB, sample18


title: 778C_001_GEX_CZI-IA13003093

description:
Library name: 778C_001_GEX_CZI-IA13003093_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

tag: library protocol

tag: raw matrix_genome_annotation

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: raw matrix_assays


title: 778C_001_GEX_CZI-IA13003094

description:
Library name: 778C_001_GEX_CZI-IA13003094_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

tag: donor id

tag: age

tag: tissue

tag: enriched cell_type

tag: assay type


title: R. subcapitata, 24 h exposure, PFPB, sample16

tag: developmental stage


title: R. subcapitata, 24 h exposure, PFPB, sample17

tag: treatment


title: R. subcapitata, 24 h exposure, PFPB, sample15


title: 778C_001_GEX_CZI-IA13003092

description:
Library name: 778C_001_GEX_CZI-IA13003092_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

tag: dev stage

tag: Sex

tag: ethnicity

tag: source

tag: suspension cell_depletion_factors


title: 778C_001_GEX_CZI-IA13003091

description:
Library name: 778C_001_GEX_CZI-IA13003091_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

tag: sample preservation_method

tag: death type

tag: library protocol


title: R. subcapitata, 24 h exposure, 6:1 FTOH, sample5


title: R. subcapitata, 24 h exposure, PFPB, sample14


title: 778C_001_GEX_CZI-IA13003096

description:
Library name: 778C_001_GEX_CZI-IA13003096_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

tag: donor id

tag: raw matrix_genome_annotation

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: raw matrix_assays


title: DNA from CNS tumor tissue patient 32

type: genomic

city: Cairo

first: Shahenda

last: El-Naggar

address: 1 Sekket El Emam, El Madbah El Kadeem Yard, Sayeda Zeinab

department: Research Department

country: Egypt

institute: Children’s Cancer Hospital Egypt 57357

hyb_protocol: Illumina, Infinium MethylationEPIC

scan_protocol: Illumina iScan System

data_processing:
Raw signal intensities were extracted from IDAT files using the minfi Bioconductor package. Quality control steps for the samples included checking for sample swaps and assessing detection p-values. Functional normalization (FunNorm) was applied for normalization, after which beta values was extracted.
Minfi bioconductor package was apllied on R softeware. P-value was detected and FunNorm for normalization was applied

label: biotin

source_name: pediatric pineal parenchymal tumors

label_protocol: Illumina, Infinium MethylationEPIC

extract_protocol: Genomic DNA was extracted from FFPE tissue samples using QIAamp DNA FFPE tissue kit (Qiagen) and quantified using the DENOVIX Fluorometer (ds DNA High Sensitivity). DNA quality was determined using the Illumina FFPE QC kit (Illumina Inc.)

value: Male

tag: tissue type

value: FFPE

tag: tissue

value: pediatric pineal parenchymal tumors


title: R. subcapitata, 24 h exposure, PFPB, sample13

tag: developmental stage

tag: treatment


title: 778C_001_ADT_CZI-IA13011830

description:
Library name: 778C_001_ADT_CZI-IA13011830_lib
CITE-seq of mononuclear cells from pooled:skin of body,mesenteric lymph node

library_source: other

molecule: other

tag: age

tag: dev stage

tag: Sex

tag: ethnicity

tag: suspension treatment_summary

value: 1.34 nM of phorbol 13-acetate 12-myristate and ionomycin and 8.1 nM of ionomycin for 2 hours

value: FALSE

value: fresh

value: circulatory death

value: CITE 10x 5' v2

tag: enriched cell_type

tag: assay type

value: CITE-seq

tag: antibodies/tags

value: TotalSeq-C Human Universal Cocktail


title: 778C_001_ADT_CZI-IA13011829

description:
Library name: 778C_001_ADT_CZI-IA13011829_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

tag: donor id

tag: source

tag: suspension cell_depletion_factors

tag: living at_sample_collection

tag: sample preservation_method

tag: death type

tag: library protocol

value: UMI

value: gene symbol, antibody target

value: snRNA-seq, CITE-seq

value: mononuclear cell


title: 778C_001_ADT_CZI-IA13011828

description:
Library name: 778C_001_ADT_CZI-IA13011828_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

value: 50-54 years

value: adult stage

tag: tissue

value: Cambridge Biorepository for Translational Medicine

tag: raw matrix_genome_annotation

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: raw matrix_assays


title: R. subcapitata, 24 h exposure, PFPB, sample12

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment

value: PFPB (DTXSID60663110)


title: 778C_001_ADT_CZI-IA13011827

description:
Library name: 778C_001_ADT_CZI-IA13011827_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

tag: age

tag: dev stage

tag: Sex

value: female

tag: ethnicity

value: Unknown

tag: suspension treatment_summary

value: 1.34 nM of phorbol 13-acetate 12-myristate and ionomycin and 8.1 nM of ionomycin for 2 hours

tag: enriched cell_type


title: 778C_001_ADT_CZI-IA13011826

description:
Library name: 778C_001_ADT_CZI-IA13011826_lib
CITE-seq of mononuclear cells from pooled:skin of body,mesenteric lymph node,jejunum lamina propria

tag: donor id

tag: source

tag: suspension cell_depletion_factors

tag: living at_sample_collection

value: FALSE

value: fresh

value: circulatory death

tag: assay type

tag: antibodies/tags


title: R. subcapitata, 24 h exposure, PFPB, sample10

tag: tissue


title: R. subcapitata, 24 h exposure, PFPB, sample11


title: 778C_001_ADT_CZI-IA13011825

description:
Library name: 778C_001_ADT_CZI-IA13011825_lib
CITE-seq of mononuclear cells from pooled:skin of body,mesenteric lymph node,jejunum lamina propria

tag: sample preservation_method

tag: death type

tag: library protocol

value: CITE 10x 5' v2

tag: raw matrix_genome_annotation

tag: raw matrix_value_units

tag: raw matrix_feature_keys

value: CITE-seq

value: TotalSeq-C Human Universal Cocktail


title: DNA from CNS tumor tissue patient 31

tag: Sex

value: Male

tag: tissue type

value: FFPE

value: pediatric pineal parenchymal tumors


title: 778C_001_ADT_CZI-IA13011824

description:
Library name: 778C_001_ADT_CZI-IA13011824_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

tag: age

value: 50-54 years

tag: dev stage

value: adult stage

tag: ethnicity

value: UMI

value: gene symbol, antibody target

tag: raw matrix_assays

value: snRNA-seq, CITE-seq

value: mononuclear cell


title: R. subcapitata, 24 h exposure, PFPB, sample8

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment

value: PFPB (DTXSID60663110)


title: 778C_001_ADT_CZI-IA13011823

description:
Library name: 778C_001_ADT_CZI-IA13011823_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

tag: donor id

value: female

value: Unknown

tag: source

value: Cambridge Biorepository for Translational Medicine

tag: suspension cell_depletion_factors

tag: living at_sample_collection

value: FALSE

value: fresh

tag: enriched cell_type

tag: assay type


title: R. subcapitata, 24 h exposure, PFPB, sample7

tag: tissue


title: 778C_001_ADT_CZI-IA13011822

description:
Library name: 778C_001_ADT_CZI-IA13011822_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

tag: sample preservation_method

tag: death type

value: circulatory death

tag: library protocol

value: CITE 10x 5' v2

tag: raw matrix_genome_annotation

tag: raw matrix_value_units

value: CITE-seq

tag: antibodies/tags

value: TotalSeq-C Human Universal Cocktail


title: DNA from CNS tumor tissue patient 04

tag: Sex

value: Male

tag: tissue type

value: FFPE

value: pediatric pineal parenchymal tumors


title: R. subcapitata, 24 h exposure, PFPB, sample6

tag: developmental stage


title: R. subcapitata, 24 h exposure, PFPB, sample5

tag: treatment


title: DNA from CNS tumor tissue patient 11


title: R. subcapitata, 24 h exposure, PFPB, sample9


title: DNA from CNS tumor tissue patient 08

value: Female


title: 778C_001_ADT_CZI-IA13011821

description:
Library name: 778C_001_ADT_CZI-IA13011821_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

tag: donor id

tag: age

value: 50-54 years

tag: dev stage

value: adult stage

tag: ethnicity

value: UMI

tag: raw matrix_feature_keys

value: gene symbol, antibody target

tag: raw matrix_assays

value: snRNA-seq, CITE-seq

value: mononuclear cell


title: DNA from CNS tumor tissue patient 02

tag: tissue


title: DNA from CNS tumor tissue patient 22


title: 778C_001_ADT_CZI-IA13011820

description:
Library name: 778C_001_ADT_CZI-IA13011820_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

value: female

value: Unknown

tag: source

value: Cambridge Biorepository for Translational Medicine

tag: suspension cell_depletion_factors

tag: living at_sample_collection

tag: sample preservation_method

tag: enriched cell_type

tag: assay type


title: DNA from CNS tumor tissue patient 34

tag: Sex


title: DNA from CNS tumor tissue patient 14

tag: tissue type


title: 778C_001_ADT_CZI-IA13011819

description:
Library name: 778C_001_ADT_CZI-IA13011819_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

value: FALSE

value: fresh

tag: death type

value: circulatory death

tag: library protocol

tag: raw matrix_genome_annotation

tag: raw matrix_value_units

tag: antibodies/tags


title: DNA from CNS tumor tissue patient 24


title: R. subcapitata, 24 h exposure, PFPB, sample4

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment

value: PFPB (DTXSID60663110)


title: R. subcapitata, 24 h exposure, PFPB, sample3


title: R. subcapitata, 24 h exposure, PFPB, sample1


title: DNA from CNS tumor tissue patient 20

value: Male

value: FFPE

value: pediatric pineal parenchymal tumors


title: 778C_001_ADT_CZI-IA13011818

description:
Library name: 778C_001_ADT_CZI-IA13011818_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

tag: donor id

tag: age

value: 50-54 years

tag: dev stage

value: adult stage

tag: ethnicity

value: CITE 10x 5' v2

tag: raw matrix_feature_keys

tag: raw matrix_assays

value: CITE-seq

value: TotalSeq-C Human Universal Cocktail


title: DNA from CNS tumor tissue patient 09

tag: tissue


title: R. subcapitata, 24 h exposure, DMSO, sample27

value: DMSO (DTXSID2021735)


title: 778C_001_ADT_CZI-IA13011817

description:
Library name: 778C_001_ADT_CZI-IA13011817_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

value: female

value: Unknown

tag: source

tag: suspension cell_depletion_factors

tag: living at_sample_collection

tag: sample preservation_method

value: UMI

value: gene symbol, antibody target

value: snRNA-seq, CITE-seq

tag: enriched cell_type

value: mononuclear cell

tag: assay type


title: DNA from CNS tumor tissue patient 12

tag: Sex

tag: tissue type


title: 778C_001_ADT_CZI-IA13011816

description:
Library name: 778C_001_ADT_CZI-IA13011816_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

value: Cambridge Biorepository for Translational Medicine

value: FALSE

value: fresh

tag: death type

value: circulatory death

tag: library protocol

tag: raw matrix_genome_annotation

tag: raw matrix_value_units

tag: antibodies/tags


title: DNA from CNS tumor tissue patient 33

value: Female

value: FFPE

value: pediatric pineal parenchymal tumors


title: R. subcapitata, 24 h exposure, PFPB, sample2

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment

value: PFPB (DTXSID60663110)


title: R. subcapitata, 24 h exposure, DMSO, sample26

value: DMSO (DTXSID2021735)


title: R. subcapitata, 24 h exposure, DMSO, sample25


title: R. subcapitata, 24 h exposure, PFUdA, sample21

value: PFUdA (DTXSID8047553)


title: 768B_001_GEX_CZI-IA13073105

description:
Library name: 768B_001_GEX_CZI-IA13073105_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

value: 20-24 years

tag: dev stage

value: adult stage

value: male

tag: ethnicity

value: Unknown

tag: raw matrix_cellranger_assay_chemistry

value: brain stem death

tag: raw matrix_feature_keys

tag: raw matrix_assays

value: scRNA-seq


title: R. subcapitata, 24 h exposure, PFUdA, sample20

tag: tissue


title: DNA from CNS tumor tissue patient 05

tag: Sex

value: Male


title: 768B_001_GEX_CZI-IA13073104

description:
Library name: 768B_001_GEX_CZI-IA13073104_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

tag: source

value: Cambridge Biorepository for Translational Medicine

tag: suspension cell_depletion_factors

tag: living at_sample_collection

value: FALSE

tag: sample preservation_method

value: fresh

value: UMI

value: gene symbol, antibody target

value: snRNA-seq, CITE-seq

tag: enriched cell_type

value: mononuclear cell

tag: assay type


title: DNA from CNS tumor tissue patient 07

tag: tissue type

value: FFPE

value: pediatric pineal parenchymal tumors


title: 768B_001_GEX_CZI-IA13073103

description:
Library name: 768B_001_GEX_CZI-IA13073103_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

tag: death type

tag: library protocol

tag: raw matrix_genome_annotation

tag: raw matrix_value_units


title: 778C_001_ADT_CZI-IA13011815

description:
Library name: 778C_001_ADT_CZI-IA13011815_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node

tag: donor id

tag: age

value: 50-54 years

tag: dev stage

value: female

tag: ethnicity

value: circulatory death

value: CITE 10x 5' v2

value: CITE-seq

tag: antibodies/tags

value: TotalSeq-C Human Universal Cocktail


title: 768B_001_GEX_CZI-IA13073106

description:
Library name: 768B_001_GEX_CZI-IA13073106_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

value: 20-24 years

value: adult stage

tag: Sex

value: male

value: Unknown

tag: tissue

tag: raw matrix_cellranger_assay_chemistry

value: brain stem death

tag: raw matrix_feature_keys

tag: raw matrix_assays

value: scRNA-seq


title: R. subcapitata, 24 h exposure, PFUdA, sample19

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment

value: PFUdA (DTXSID8047553)


title: R. subcapitata, 24 h exposure, PFUdA, sample15


title: 768B_001_GEX_CZI-IA13073099

description:
Library name: 768B_001_GEX_CZI-IA13073099_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

tag: source

value: Cambridge Biorepository for Translational Medicine

tag: suspension cell_depletion_factors

tag: living at_sample_collection

value: FALSE

tag: sample preservation_method

value: fresh

value: UMI

value: gene symbol, antibody target

value: snRNA-seq, CITE-seq

tag: enriched cell_type

value: mononuclear cell

tag: assay type


title: 768B_001_GEX_CZI-IA13073102

description:
Library name: 768B_001_GEX_CZI-IA13073102_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

tag: death type

tag: library protocol

tag: raw matrix_genome_annotation

tag: raw matrix_value_units


title: R. subcapitata, 24 h exposure, PFUdA, sample17

tag: tissue


title: DNA from CNS tumor tissue patient 17

tag: Sex

value: Male

tag: tissue type

value: FFPE

value: pediatric pineal parenchymal tumors


title: R. subcapitata, 24 h exposure, PFUdA, sample14

tag: developmental stage


title: R. subcapitata, 24 h exposure, PFUdA, sample16

tag: treatment


title: R. subcapitata, 24 h exposure, PFUdA, sample18


title: DNA from CNS tumor tissue patient 15

value: Female


title: R. subcapitata, 24 h exposure, PFUdA, sample13


title: 768B_001_GEX_CZI-IA13073007

description:
Library name: 768B_001_GEX_CZI-IA13073007_lib
scRNA-seq of mononuclear cells from pooled:skin of body,thymus

source_name: pooled:skin of body,thymus

value: 20-24 years

tag: dev stage

value: adult stage

value: male

tag: ethnicity

value: Unknown

value: pooled:skin of body,thymus

tag: source

tag: raw matrix_cellranger_assay_chemistry

tag: raw matrix_feature_keys

tag: raw matrix_assays


title: 768B_001_GEX_CZI-IA13073006

description:
Library name: 768B_001_GEX_CZI-IA13073006_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: suspension cell_depletion_factors

tag: suspension treatment_summary

value: 1.34 nM of phorbol 13-acetate 12-myristate and ionomycin and 8.1 nM of ionomycin for 2 hours

tag: living at_sample_collection

tag: sample preservation_method

value: brain stem death

tag: enriched cell_type

tag: assay type

value: scRNA-seq


title: DNA from CNS tumor tissue patient 21

tag: Sex

tag: tissue


title: 768B_001_GEX_CZI-IA13073008

description:
Library name: 768B_001_GEX_CZI-IA13073008_lib
scRNA-seq of mononuclear cells from pooled:skin of body,thymus

tag: age

value: Cambridge Biorepository for Translational Medicine

value: FALSE

value: fresh

tag: death type

tag: library protocol

tag: raw matrix_genome_annotation

tag: raw matrix_value_units


title: 768B_001_GEX_CZI-IA13073005

description:
Library name: 768B_001_GEX_CZI-IA13073005_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

tag: dev stage

tag: ethnicity

tag: source

tag: raw matrix_cellranger_assay_chemistry

value: UMI

value: gene symbol, antibody target

value: snRNA-seq, CITE-seq


title: R. subcapitata, 24 h exposure, PFUdA, sample10

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment

value: PFUdA (DTXSID8047553)


title: R. subcapitata, 24 h exposure, PFUdA, sample9


title: R. subcapitata, 24 h exposure, PFUdA, sample11


title: 768B_001_GEX_CZI-IA13073003

description:
Library name: 768B_001_GEX_CZI-IA13073003_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

tag: donor id

value: 20-24 years

tag: suspension cell_depletion_factors

tag: suspension treatment_summary

tag: living at_sample_collection

tag: raw matrix_feature_keys

tag: raw matrix_assays

value: mononuclear cell


title: 768B_001_GEX_CZI-IA13073101

description:
Library name: 768B_001_GEX_CZI-IA13073101_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

tag: age

value: adult stage

tag: Sex

value: male

tag: tissue

tag: sample preservation_method

tag: enriched cell_type

tag: assay type


title: 768B_001_ADT_CZI-IA12964793

description:
Library name: 768B_001_ADT_CZI-IA12964793_lib
CITE-seq of mononuclear cells from pooled:skin of body,thymus

tag: dev stage

tag: ethnicity

value: Unknown

value: pooled:skin of body,thymus

tag: death type

tag: library protocol

value: CITE 10x 5' v2

tag: raw matrix_genome_annotation

tag: raw matrix_value_units

value: CITE-seq

tag: antibodies/tags

value: TotalSeq-C Human Universal Cocktail


title: 768B_001_GEX_CZI-IA13073004

description:
Library name: 768B_001_GEX_CZI-IA13073004_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: source

value: Cambridge Biorepository for Translational Medicine

tag: suspension cell_depletion_factors

tag: suspension treatment_summary

value: 1.34 nM of phorbol 13-acetate 12-myristate and ionomycin and 8.1 nM of ionomycin for 2 hours

tag: raw matrix_cellranger_assay_chemistry

value: FALSE

value: brain stem death

value: scRNA-seq


title: 768B_001_ADT_CZI-IA12964792

description:
Library name: 768B_001_ADT_CZI-IA12964792_lib
CITE-seq of mononuclear cells from pooled:skin of body,thymus

tag: age

tag: Sex

tag: living at_sample_collection

value: fresh

value: UMI

tag: raw matrix_feature_keys

value: gene symbol, antibody target

tag: raw matrix_assays

value: snRNA-seq, CITE-seq


title: R. subcapitata, 24 h exposure, PFUdA, sample7

tag: tissue

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment

value: PFUdA (DTXSID8047553)


title: R. subcapitata, 24 h exposure, PFUdA, sample5


title: 768B_001_GEX_CZI-IA13073100

description:
Library name: 768B_001_GEX_CZI-IA13073100_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

value: 20-24 years

tag: dev stage

value: adult stage

value: male

tag: ethnicity

value: Unknown

tag: sample preservation_method

tag: death type

tag: library protocol

tag: enriched cell_type

value: mononuclear cell

tag: assay type


title: DNA from CNS tumor tissue patient 10

value: Male

tag: tissue type

value: FFPE

value: pediatric pineal parenchymal tumors


title: R. subcapitata, 24 h exposure, PFUdA, sample4


title: R. subcapitata, 24 h exposure, PFUdA, sample6


title: 768B_001_ADT_CZI-IA12964790

description:
Library name: 768B_001_ADT_CZI-IA12964790_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: source

value: Cambridge Biorepository for Translational Medicine

tag: suspension cell_depletion_factors

value: FALSE

value: brain stem death

value: CITE 10x 5' v2

tag: raw matrix_genome_annotation

tag: raw matrix_value_units

value: CITE-seq

tag: antibodies/tags

value: TotalSeq-C Human Universal Cocktail


title: R. subcapitata, 24 h exposure, PFUdA, sample3

tag: tissue

value: whole body


title: 768B_001_ADT_CZI-IA12964788

description:
Library name: 768B_001_ADT_CZI-IA12964788_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

tag: age

tag: Sex

tag: living at_sample_collection

value: fresh

value: UMI

tag: raw matrix_feature_keys

value: gene symbol, antibody target

tag: raw matrix_assays

value: snRNA-seq, CITE-seq


title: R. subcapitata, 24 h exposure, PFUdA, sample2

tag: developmental stage

value: Exponential Growth Stage

tag: treatment

value: PFUdA (DTXSID8047553)


title: 768B_001_ADT_CZI-IA12960342

description:
Library name: 768B_001_ADT_CZI-IA12960342_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

value: 20-24 years

tag: dev stage

value: adult stage

value: male

tag: ethnicity

value: Unknown

tag: sample preservation_method

tag: death type

tag: library protocol

tag: enriched cell_type

value: mononuclear cell


title: R. subcapitata, 24 h exposure, PFUdA, sample1


title: 768B_001_ADT_CZI-IA12960341

description:
Library name: 768B_001_ADT_CZI-IA12960341_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: source

value: Cambridge Biorepository for Translational Medicine

tag: suspension cell_depletion_factors

value: FALSE

tag: raw matrix_genome_annotation

tag: assay type


title: R. subcapitata, 24 h exposure, PFNA, sample21

tag: tissue

value: PFNA (DTXSID8031863)


title: 768B_001_ADT_CZI-IA12960339

description:
Library name: 768B_001_ADT_CZI-IA12960339_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

tag: age

tag: Sex

tag: living at_sample_collection

value: brain stem death

value: CITE 10x 5' v2

tag: raw matrix_value_units

value: CITE-seq

tag: antibodies/tags


title: R. subcapitata, 24 h exposure, PFUdA, sample8

value: whole body

tag: developmental stage

tag: treatment


title: R. subcapitata, 24 h exposure, PFNA, sample18


title: R. subcapitata, 24 h exposure, PFNA, sample17


title: R. subcapitata, 24 h exposure, PFNA, sample19


title: 768B_001_ADT_CZI-IA12964791

description:
Library name: 768B_001_ADT_CZI-IA12964791_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

tag: dev stage

tag: ethnicity

tag: sample preservation_method

value: fresh

value: UMI

tag: raw matrix_feature_keys

tag: raw matrix_assays

value: TotalSeq-C Human Universal Cocktail


title: 768B_001_ADT_CZI-IA12960336

description:
Library name: 768B_001_ADT_CZI-IA12960336_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: source

tag: suspension treatment_summary

value: 1.34 nM of phorbol 13-acetate 12-myristate and ionomycin and 8.1 nM of ionomycin for 2 hours

tag: death type

tag: library protocol

value: gene symbol, antibody target

value: snRNA-seq, CITE-seq

tag: enriched cell_type


title: R. subcapitata, 24 h exposure, PFNA, sample16

tag: tissue

value: Exponential Growth Stage


title: R. subcapitata, 24 h exposure, PFNA, sample15


title: 759B_001_GEX_CZI-IA12953913

description:
Library name: 759B_001_GEX_CZI-IA12953913_lib
scRNA-seq of mononuclear cells from skin of body

source_name: skin of body

tag: age

value: 20-24 years

value: adult stage

tag: Sex

value: female

value: skin of body

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

tag: raw matrix_genome_annotation

tag: assay type

value: scRNA-seq


title: R. subcapitata, 24 h exposure, PFNA, sample12

tag: developmental stage

tag: treatment

value: PFNA (DTXSID8031863)


title: 759B_001_GEX_CZI-IA12953912

description:
Library name: 759B_001_GEX_CZI-IA12953912_lib
scRNA-seq of mononuclear cells from pooled:jejunal epithelium,jejunum lamina propria

tag: dev stage

tag: ethnicity

value: Unknown

value: Cambridge Biorepository for Translational Medicine

value: FALSE

tag: sample preservation_method

value: brain stem death

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: raw matrix_assays

value: mononuclear cell


title: R. subcapitata, 24 h exposure, PFNA, sample13

value: whole body


title: 759B_001_GEX_CZI-IA12953910

description:
Library name: 759B_001_GEX_CZI-IA12953910_lib
scRNA-seq of mononuclear cells from pooled:blood,spleen,bone marrow,mesenteric lymph node,thoracic lymph node

tag: donor id

tag: source

tag: suspension treatment_summary

value: fresh

tag: death type

tag: library protocol

value: UMI

tag: enriched cell_type


title: R. subcapitata, 24 h exposure, PFNA, sample11

tag: tissue


title: 759B_001_GEX_CZI-IA12953909

description:
Library name: 759B_001_GEX_CZI-IA12953909_lib
scRNA-seq of mononuclear cells from pooled:blood,spleen,bone marrow,mesenteric lymph node,thoracic lymph node

tag: age

tag: Sex

tag: suspension cell_depletion_factors

value: 1.34 nM of phorbol 13-acetate 12-myristate and ionomycin and 8.1 nM of ionomycin for 2 hours

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

tag: raw matrix_genome_annotation

value: gene symbol, antibody target


title: 759B_001_GEX_CZI-IA12953908

description:
Library name: 759B_001_GEX_CZI-IA12953908_lib
scRNA-seq of mononuclear cells from pooled:blood,spleen,bone marrow,mesenteric lymph node,thoracic lymph node

tag: dev stage

tag: ethnicity

tag: sample preservation_method

value: snRNA-seq, CITE-seq

tag: assay type


title: R. subcapitata, 24 h exposure, PFNA, sample10

tag: developmental stage

value: Exponential Growth Stage

tag: treatment


title: 768B_001_ADT_CZI-IA12964789

description:
Library name: 768B_001_ADT_CZI-IA12964789_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

tag: donor id

value: 20-24 years

value: adult stage

value: male

tag: source

value: CITE 10x 5' v2

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: raw matrix_assays

value: CITE-seq

tag: antibodies/tags

value: TotalSeq-C Human Universal Cocktail


title: 768B_001_ADT_CZI-IA12960340

description:
Library name: 768B_001_ADT_CZI-IA12960340_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

tag: age

tag: Sex

value: Unknown

tag: tissue

value: Cambridge Biorepository for Translational Medicine

tag: death type

tag: library protocol

tag: enriched cell_type


title: R. subcapitata, 24 h exposure, PFNA, sample8

value: PFNA (DTXSID8031863)


title: R. subcapitata, 24 h exposure, PFNA, sample20


title: 768B_001_ADT_CZI-IA12960338

description:
Library name: 768B_001_ADT_CZI-IA12960338_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

tag: dev stage

tag: ethnicity

tag: suspension cell_depletion_factors

tag: suspension treatment_summary

tag: living at_sample_collection

value: FALSE

value: brain stem death

tag: raw matrix_genome_annotation

value: mononuclear cell


title: 759B_001_GEX_CZI-IA12953906

description:
Library name: 759B_001_GEX_CZI-IA12953906_lib
scRNA-seq of mononuclear cells from pooled:blood,spleen,thymus,bone marrow,mesenteric lymph node,thoracic lymph node

tag: donor id

value: female

tag: source

tag: raw matrix_cellranger_assay_chemistry

tag: sample preservation_method

value: fresh

value: UMI

tag: assay type

value: scRNA-seq


title: 759B_001_GEX_CZI-IA12953907

description:
Library name: 759B_001_GEX_CZI-IA12953907_lib
scRNA-seq of mononuclear cells from pooled:jejunal epithelium,jejunum lamina propria

tag: age

tag: raw matrix_value_units

tag: raw matrix_feature_keys

value: gene symbol, antibody target

tag: raw matrix_assays

value: snRNA-seq, CITE-seq


title: R. subcapitata, 24 h exposure, PFNA, sample4

tag: tissue

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment


title: 768B_001_ADT_CZI-IA12960337

description:
Library name: 768B_001_ADT_CZI-IA12960337_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,mesenteric lymph node,thoracic lymph node,jejunum lamina propria

value: 20-24 years

tag: dev stage

value: adult stage

tag: Sex

value: male

tag: ethnicity

value: 1.34 nM of phorbol 13-acetate 12-myristate and ionomycin and 8.1 nM of ionomycin for 2 hours

tag: death type

tag: library protocol

value: CITE 10x 5' v2

tag: enriched cell_type

tag: antibodies/tags


title: R. subcapitata, 24 h exposure, PFNA, sample5

value: PFNA (DTXSID8031863)


title: R. subcapitata, 24 h exposure, PFNA, sample3


title: 759B_001_GEX_CZI-IA12953816

description:
Library name: 759B_001_GEX_CZI-IA12953816_lib
scRNA-seq of mononuclear cells from pooled:blood,spleen,thymus,bone marrow,mesenteric lymph node,thoracic lymph node

tag: donor id

value: Unknown

tag: source

value: Cambridge Biorepository for Translational Medicine

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

value: FALSE

tag: raw matrix_genome_annotation


title: 759B_001_GEX_CZI-IA12953905

description:
Library name: 759B_001_GEX_CZI-IA12953905_lib
scRNA-seq of mononuclear cells from pooled:blood,spleen,thymus,bone marrow,mesenteric lymph node,thoracic lymph node

tag: age

value: female

tag: sample preservation_method

value: brain stem death

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: raw matrix_assays

value: mononuclear cell

tag: assay type


title: 759B_001_GEX_CZI-IA12953914

description:
Library name: 759B_001_GEX_CZI-IA12953914_lib
scRNA-seq of mononuclear cells from skin of body

tag: dev stage

tag: Sex

tag: ethnicity

tag: tissue

value: skin of body

tag: suspension treatment_summary

value: fresh

value: UMI

value: scRNA-seq


title: R. subcapitata, 24 h exposure, PFNA, sample2

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment


title: R. subcapitata, 24 h exposure, PFNA, sample1


title: 759B_001_GEX_CZI-IA12953812

description:
Library name: 759B_001_GEX_CZI-IA12953812_lib
scRNA-seq of mononuclear cells from pooled:blood,spleen,thymus,bone marrow,mesenteric lymph node,thoracic lymph node

tag: donor id

value: 20-24 years

value: adult stage

tag: source

tag: suspension cell_depletion_factors

tag: death type

tag: library protocol

value: gene symbol, antibody target

value: snRNA-seq, CITE-seq

tag: enriched cell_type


title: R. subcapitata, 24 h exposure, PFPeA, sample21

value: PFPeA (DTXSID6062599)


title: R. subcapitata, 24 h exposure, PFNA, sample9

value: PFNA (DTXSID8031863)


title: R. subcapitata, 24 h exposure, PFNA, sample6


title: R. subcapitata, 24 h exposure, PFUdA, sample12

value: PFUdA (DTXSID8047553)


title: 759B_001_GEX_CZI-IA12953810

description:
Library name: 759B_001_GEX_CZI-IA12953810_lib
scRNA-seq of mononuclear cells from pooled:blood,spleen,thymus,bone marrow,mesenteric lymph node,thoracic lymph node

tag: age

value: Unknown

value: Cambridge Biorepository for Translational Medicine

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

value: FALSE

tag: sample preservation_method

tag: raw matrix_genome_annotation

tag: raw matrix_value_units


title: 759B_001_GEX_CZI-IA12953911

description:
Library name: 759B_001_GEX_CZI-IA12953911_lib
scRNA-seq of mononuclear cells from pooled:blood,spleen,bone marrow,mesenteric lymph node,thoracic lymph node

tag: dev stage

tag: Sex

value: female

tag: ethnicity

value: 1.34 nM of phorbol 13-acetate 12-myristate and ionomycin and 8.1 nM of ionomycin for 2 hours

value: brain stem death

tag: raw matrix_feature_keys

tag: raw matrix_assays

value: mononuclear cell

tag: assay type


title: 759B_001_GEX_CZI-IA12953811

description:
Library name: 759B_001_GEX_CZI-IA12953811_lib
scRNA-seq of mononuclear cells from pooled:blood,spleen,thymus,bone marrow,mesenteric lymph node,thoracic lymph node

tag: donor id

tag: tissue

tag: source

value: fresh

value: UMI

value: scRNA-seq


title: R. subcapitata, 24 h exposure, PFPeA, sample20

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment


title: R. subcapitata, 24 h exposure, PFPeA, sample19


title: 759B_001_GEX_CZI-IA12953809

description:
Library name: 759B_001_GEX_CZI-IA12953809_lib
scRNA-seq of mononuclear cells from pooled:blood,spleen,thymus,bone marrow,mesenteric lymph node,thoracic lymph node

tag: age

value: 20-24 years

value: adult stage

tag: suspension cell_depletion_factors

tag: death type

tag: library protocol

value: gene symbol, antibody target

tag: enriched cell_type


title: R. subcapitata, 24 h exposure, PFPeA, sample18

value: PFPeA (DTXSID6062599)


title: 759B_001_ADT_CZI-IA12957766

description:
Library name: 759B_001_ADT_CZI-IA12957766_lib
CITE-seq of mononuclear cells from skin of body

value: skin of body

tag: suspension treatment_summary

tag: living at_sample_collection

tag: sample preservation_method

value: CITE 10x 5' v2

tag: raw matrix_genome_annotation

tag: raw matrix_value_units

value: snRNA-seq, CITE-seq

value: CITE-seq

tag: antibodies/tags

value: TotalSeq-C Human Universal Cocktail


title: R. subcapitata, 24 h exposure, PFPeA, sample17


title: 759B_001_GEX_CZI-IA12953815

description:
Library name: 759B_001_GEX_CZI-IA12953815_lib
scRNA-seq of mononuclear cells from pooled:blood,spleen,thymus,bone marrow,mesenteric lymph node,thoracic lymph node

tag: dev stage

tag: Sex

value: female

tag: ethnicity

value: Unknown

value: Cambridge Biorepository for Translational Medicine

tag: raw matrix_cellranger_assay_chemistry

value: FALSE

tag: raw matrix_feature_keys

tag: raw matrix_assays

tag: assay type


title: 759B_001_ADT_CZI-IA12957764

description:
Library name: 759B_001_ADT_CZI-IA12957764_lib
CITE-seq of mononuclear cells from pooled:jejunal epithelium,jejunum lamina propria

tag: donor id

tag: age

tag: tissue

tag: source

tag: suspension cell_depletion_factors

value: 1.34 nM of phorbol 13-acetate 12-myristate and ionomycin and 8.1 nM of ionomycin for 2 hours

value: fresh

value: brain stem death

value: UMI

value: mononuclear cell


title: R. subcapitata, 24 h exposure, PFPeA, sample16

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment


title: R. subcapitata, 24 h exposure, PFPeA, sample15

value: PFPeA (DTXSID6062599)


title: 759B_001_GEX_CZI-IA12953813

description:
Library name: 759B_001_GEX_CZI-IA12953813_lib
scRNA-seq of mononuclear cells from pooled:blood,spleen,thymus,bone marrow,mesenteric lymph node,thoracic lymph node

value: 20-24 years

value: adult stage

tag: living at_sample_collection

tag: sample preservation_method

tag: death type

tag: library protocol

tag: raw matrix_genome_annotation

value: gene symbol, antibody target

tag: enriched cell_type

value: scRNA-seq


title: R. subcapitata, 24 h exposure, PFPeA, sample14


title: 759B_001_ADT_CZI-IA12957763

description:
Library name: 759B_001_ADT_CZI-IA12957763_lib
CITE-seq of mononuclear cells from pooled:blood,spleen,bone marrow,mesenteric lymph node,thoracic lymph node

tag: dev stage

tag: Sex

tag: ethnicity

tag: suspension treatment_summary

value: CITE 10x 5' v2

tag: raw matrix_value_units

value: snRNA-seq, CITE-seq

value: CITE-seq

tag: antibodies/tags

value: TotalSeq-C Human Universal Cocktail


title: 759B_001_ADT_CZI-IA12957762

description:
Library name: 759B_001_ADT_CZI-IA12957762_lib
CITE-seq of mononuclear cells from pooled:blood,spleen,bone marrow,mesenteric lymph node,thoracic lymph node

tag: donor id

tag: age

value: female

value: Unknown

tag: tissue

value: Cambridge Biorepository for Translational Medicine

value: FALSE

tag: raw matrix_feature_keys

tag: raw matrix_assays

tag: assay type


title: 759B_001_ADT_CZI-IA12957761

description:
Library name: 759B_001_ADT_CZI-IA12957761_lib
CITE-seq of mononuclear cells from pooled:blood,spleen,bone marrow,mesenteric lymph node,thoracic lymph node

tag: source

tag: suspension cell_depletion_factors

value: 1.34 nM of phorbol 13-acetate 12-myristate and ionomycin and 8.1 nM of ionomycin for 2 hours

tag: living at_sample_collection

tag: sample preservation_method

value: fresh

value: brain stem death

value: UMI


title: 759B_001_ADT_CZI-IA12957759

description:
Library name: 759B_001_ADT_CZI-IA12957759_lib
CITE-seq of mononuclear cells from pooled:jejunal epithelium,jejunum lamina propria

tag: death type

tag: library protocol

tag: raw matrix_genome_annotation

tag: enriched cell_type

value: mononuclear cell


title: R. subcapitata, 24 h exposure, PFPeA, sample12

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment

value: PFPeA (DTXSID6062599)


title: R. subcapitata, 24 h exposure, PFPeA, sample10


title: R. subcapitata, 24 h exposure, PFPeA, sample13


title: 759B_001_ADT_CZI-IA12957758

description:
Library name: 759B_001_ADT_CZI-IA12957758_lib
CITE-seq of mononuclear cells from pooled:blood,spleen,thymus,bone marrow,mesenteric lymph node,thoracic lymph node

value: 20-24 years

tag: dev stage

value: adult stage

tag: Sex

tag: ethnicity

tag: raw matrix_value_units

value: gene symbol, antibody target

tag: antibodies/tags


title: R. subcapitata, 24 h exposure, PFPeA, sample8

tag: tissue


title: R. subcapitata, 24 h exposure, PFPeA, sample9


title: 759B_001_ADT_CZI-IA12957755

description:
Library name: 759B_001_ADT_CZI-IA12957755_lib
CITE-seq of mononuclear cells from pooled:blood,spleen,thymus,bone marrow,mesenteric lymph node,thoracic lymph node

tag: donor id

tag: age

value: CITE 10x 5' v2

tag: raw matrix_feature_keys

tag: raw matrix_assays

value: snRNA-seq, CITE-seq

tag: assay type

value: CITE-seq


title: 759B_001_ADT_CZI-IA12957756

description:
Library name: 759B_001_ADT_CZI-IA12957756_lib
CITE-seq of mononuclear cells from pooled:blood,spleen,thymus,bone marrow,mesenteric lymph node,thoracic lymph node

value: female

value: Unknown

tag: source

tag: suspension cell_depletion_factors

tag: living at_sample_collection

tag: sample preservation_method

tag: death type

value: TotalSeq-C Human Universal Cocktail


title: R. subcapitata, 24 h exposure, PFPeA, sample7

tag: developmental stage

tag: treatment


title: 759B_001_ADT_CZI-IA12957757

description:
Library name: 759B_001_ADT_CZI-IA12957757_lib
CITE-seq of mononuclear cells from pooled:blood,spleen,thymus,bone marrow,mesenteric lymph node,thoracic lymph node

tag: dev stage

tag: Sex

value: Cambridge Biorepository for Translational Medicine

value: FALSE

tag: library protocol

tag: raw matrix_genome_annotation

tag: enriched cell_type


title: 759B_001_ADT_CZI-IA12957765

description:
Library name: 759B_001_ADT_CZI-IA12957765_lib
CITE-seq of mononuclear cells from skin of body

tag: donor id

tag: ethnicity

tag: tissue

value: skin of body

value: fresh

value: brain stem death

tag: raw matrix_value_units

tag: antibodies/tags


title: R. subcapitata, 24 h exposure, PFPeA, sample5

value: whole body


title: R. subcapitata, 24 h exposure, PFPeA, sample6

value: Exponential Growth Stage


title: 759B_001_ADT_CZI-IA12957754

description:
Library name: 759B_001_ADT_CZI-IA12957754_lib
CITE-seq of mononuclear cells from pooled:blood,spleen,thymus,bone marrow,mesenteric lymph node,thoracic lymph node

tag: age

tag: source

value: UMI

tag: raw matrix_feature_keys

tag: raw matrix_assays

value: mononuclear cell

tag: assay type


title: 759B_001_ADT_CZI-IA12957753

description:
Library name: 759B_001_ADT_CZI-IA12957753_lib
CITE-seq of mononuclear cells from pooled:blood,spleen,thymus,bone marrow,mesenteric lymph node,thoracic lymph node

value: 20-24 years

value: adult stage

tag: suspension cell_depletion_factors

tag: living at_sample_collection

tag: sample preservation_method

tag: death type


title: 759B_001_ADT_CZI-IA12957760

description:
Library name: 759B_001_ADT_CZI-IA12957760_lib
CITE-seq of mononuclear cells from pooled:blood,spleen,bone marrow,mesenteric lymph node,thoracic lymph node

tag: dev stage

tag: Sex

tag: suspension treatment_summary

value: 1.34 nM of phorbol 13-acetate 12-myristate and ionomycin and 8.1 nM of ionomycin for 2 hours

tag: library protocol

value: CITE 10x 5' v2

value: gene symbol, antibody target


title: 759B_001_ADT_CZI-IA12957751

description:
Library name: 759B_001_ADT_CZI-IA12957751_lib
CITE-seq of mononuclear cells from pooled:blood,spleen,thymus,bone marrow,mesenteric lymph node,thoracic lymph node

tag: donor id

value: female

tag: ethnicity

tag: raw matrix_genome_annotation

value: snRNA-seq, CITE-seq

tag: enriched cell_type

value: CITE-seq


title: R. subcapitata, 24 h exposure, PFPeA, sample11

tag: tissue

tag: developmental stage

tag: treatment

value: PFPeA (DTXSID6062599)


title: 759B_001_ADT_CZI-IA12957750

description:
Library name: 759B_001_ADT_CZI-IA12957750_lib
CITE-seq of mononuclear cells from pooled:blood,spleen,thymus,bone marrow,mesenteric lymph node,thoracic lymph node

tag: age

value: Unknown

tag: source

value: Cambridge Biorepository for Translational Medicine

value: FALSE

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: raw matrix_assays

tag: antibodies/tags

value: TotalSeq-C Human Universal Cocktail


title: R. subcapitata, 24 h exposure, PFPeA, sample3

value: whole body


title: 759B_001_ADT_CZI-IA12957752

description:
Library name: 759B_001_ADT_CZI-IA12957752_lib
CITE-seq of mononuclear cells from pooled:blood,spleen,thymus,bone marrow,mesenteric lymph node,thoracic lymph node

tag: dev stage

tag: suspension cell_depletion_factors

tag: living at_sample_collection

tag: sample preservation_method

value: fresh

tag: death type

value: brain stem death

tag: assay type


title: R. subcapitata, 24 h exposure, PFPeA, sample2

value: Exponential Growth Stage


title: R. subcapitata, 24 h exposure, PFPeA, sample1


title: 759B_001_ADT_CZI-IA12957749

description:
Library name: 759B_001_ADT_CZI-IA12957749_lib
CITE-seq of mononuclear cells from pooled:blood,spleen,thymus,bone marrow,mesenteric lymph node,thoracic lymph node

tag: donor id

value: 20-24 years

tag: Sex

tag: ethnicity

tag: library protocol

tag: raw matrix_genome_annotation

value: UMI

value: mononuclear cell


title: R. subcapitata, 24 h exposure, N-EtFOSA-M, sample21

tag: tissue

tag: developmental stage

tag: treatment

value: N-EtFOSA-M (DTXSID1032646)


title: 694B_001_GEX_CZI-IA11512689

description:
Library name: 694B_001_GEX_CZI-IA11512689_lib
scRNA-seq of mononuclear cells from pooled:mesenteric lymph node

source_name: pooled:mesenteric lymph node

tag: age

value: adult stage

value: male

value: pooled:mesenteric lymph node

tag: source

tag: raw matrix_cellranger_assay_chemistry

tag: raw matrix_value_units

tag: raw matrix_feature_keys

value: gene symbol, antibody target

tag: enriched cell_type

value: scRNA-seq


title: R. subcapitata, 24 h exposure, N-EtFOSA-M, sample20


title: R. subcapitata, 24 h exposure, N-EtFOSA-M, sample18


title: R. subcapitata, 24 h exposure, N-EtFOSA-M, sample19


title: 694B_001_GEX_CZI-IA11512688

description:
Library name: 694B_001_GEX_CZI-IA11512688_lib
scRNA-seq of mononuclear cells from pooled:spleen,bone marrow

source_name: pooled:spleen,bone marrow

tag: dev stage

value: Unknown

value: pooled:spleen,bone marrow

tag: suspension cell_depletion_factors

tag: living at_sample_collection

tag: sample preservation_method

tag: raw matrix_assays

value: snRNA-seq, CITE-seq


title: 694B_001_GEX_CZI-IA11512686

description:
Library name: 694B_001_GEX_CZI-IA11512686_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,jejunum lamina propria

tag: donor id

tag: Sex

tag: ethnicity

value: Cambridge Biorepository for Translational Medicine

value: FALSE

tag: death type

tag: assay type


title: R. subcapitata, 24 h exposure, N-EtFOSA-M, sample17

tag: tissue

value: whole body

tag: developmental stage

tag: treatment


title: 694B_001_GEX_CZI-IA11512685

description:
Library name: 694B_001_GEX_CZI-IA11512685_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,jejunum lamina propria

tag: age

tag: source

tag: raw matrix_cellranger_assay_chemistry

value: fresh

value: brain stem death

tag: library protocol

tag: raw matrix_genome_annotation


title: 694B_001_GEX_CZI-IA11485882

description:
Library name: 694B_001_GEX_CZI-IA11485882_lib
scRNA-seq of mononuclear cells from skin of body

value: 20-24 years

tag: dev stage

value: skin of body

tag: suspension cell_depletion_factors

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: enriched cell_type


title: R. subcapitata, 24 h exposure, N-EtFOSA-M, sample14

value: Exponential Growth Stage


title: R. subcapitata, 24 h exposure, N-EtFOSA-M, sample15

value: N-EtFOSA-M (DTXSID1032646)


title: R. subcapitata, 24 h exposure, N-EtFOSA-M, sample16


title: R. subcapitata, 24 h exposure, PFPeA, sample4

value: PFPeA (DTXSID6062599)


title: R. subcapitata, 24 h exposure, N-EtFOSA-M, sample13


title: 694B_001_GEX_CZI-IA11485880

description:
Library name: 694B_001_GEX_CZI-IA11485880_lib
scRNA-seq of mononuclear cells from skin of body

tag: donor id

value: adult stage

tag: Sex

value: male

tag: living at_sample_collection

tag: sample preservation_method

value: UMI

tag: raw matrix_assays

value: mononuclear cell


title: 694B_001_GEX_CZI-IA11485879

description:
Library name: 694B_001_GEX_CZI-IA11485879_lib
scRNA-seq of mononuclear cells from pooled:spleen,bone marrow

tag: ethnicity

value: Unknown

tag: tissue

tag: suspension treatment_summary

value: 1.34 nM of phorbol 13-acetate 12-myristate and ionomycin and 8.1 nM of ionomycin for 2 hours

tag: death type

value: gene symbol, antibody target

tag: assay type

value: scRNA-seq


title: 694B_001_GEX_CZI-IA11512690

description:
Library name: 694B_001_GEX_CZI-IA11512690_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,jejunum lamina propria

tag: age

tag: source

value: Cambridge Biorepository for Translational Medicine

tag: raw matrix_cellranger_assay_chemistry

value: FALSE

tag: library protocol

value: snRNA-seq, CITE-seq


title: 694B_001_GEX_CZI-IA11485881

description:
Library name: 694B_001_GEX_CZI-IA11485881_lib
scRNA-seq of mononuclear cells from skin of body

tag: dev stage

tag: suspension cell_depletion_factors

value: fresh

value: brain stem death

tag: raw matrix_genome_annotation

tag: raw matrix_value_units


title: R. subcapitata, 24 h exposure, N-EtFOSA-M, sample10

value: whole body

tag: developmental stage

tag: treatment


title: R. subcapitata, 24 h exposure, N-EtFOSA-M, sample11

value: Exponential Growth Stage


title: R. subcapitata, 24 h exposure, N-EtFOSA-M, sample12

value: N-EtFOSA-M (DTXSID1032646)


title: 694B_001_GEX_CZI-IA11512687

description:
Library name: 694B_001_GEX_CZI-IA11512687_lib
scRNA-seq of mononuclear cells from pooled:spleen,bone marrow

tag: donor id

value: 20-24 years

tag: Sex

value: pooled:spleen,bone marrow

tag: living at_sample_collection

tag: sample preservation_method

tag: raw matrix_feature_keys

tag: enriched cell_type


title: 694B_001_GEX_CZI-IA11485876

description:
Library name: 694B_001_GEX_CZI-IA11485876_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,jejunum lamina propria

value: adult stage

value: male

tag: ethnicity

tag: tissue

tag: suspension treatment_summary

tag: death type

tag: raw matrix_assays

tag: assay type


title: 694B_001_GEX_CZI-IA11485878

description:
Library name: 694B_001_GEX_CZI-IA11485878_lib
scRNA-seq of mononuclear cells from pooled:spleen,bone marrow

tag: age

tag: dev stage

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: library protocol

value: UMI

value: mononuclear cell


title: R. subcapitata, 24 h exposure, N-EtFOSA-M, sample7

tag: developmental stage

tag: treatment


title: 694B_001_GEX_CZI-IA11485874

description:
Library name: 694B_001_GEX_CZI-IA11485874_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,jejunum lamina propria

tag: donor id

tag: Sex

value: Unknown

value: 1.34 nM of phorbol 13-acetate 12-myristate and ionomycin and 8.1 nM of ionomycin for 2 hours

tag: living at_sample_collection

tag: sample preservation_method

tag: raw matrix_genome_annotation

tag: raw matrix_value_units


title: 694B_001_GEX_CZI-IA11485873

description:
Library name: 694B_001_GEX_CZI-IA11485873_lib
scRNA-seq of mononuclear cells from pooled:spleen,bone marrow

tag: ethnicity

tag: tissue

tag: death type

tag: raw matrix_feature_keys

value: gene symbol, antibody target

tag: enriched cell_type

value: scRNA-seq


title: R. subcapitata, 24 h exposure, N-EtFOSA-M, sample8


title: R. subcapitata, 24 h exposure, N-EtFOSA-M, sample9


title: R. subcapitata, 24 h exposure, N-EtFOSA-M, sample6


title: 694B_001_ADT_CZI-IA11512614

description:
Library name: 694B_001_ADT_CZI-IA11512614_lib
CITE-seq of mononuclear cells from skin of body

tag: age

tag: dev stage

value: skin of body

tag: source

value: Cambridge Biorepository for Translational Medicine

value: FALSE

value: CITE 10x 5' v2

tag: raw matrix_assays

tag: assay type

value: CITE-seq

tag: antibodies/tags

value: TotalSeq-C Human Universal Cocktail


title: R. subcapitata, 24 h exposure, PFNA, sample14

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment

value: PFNA (DTXSID8031863)


title: R. subcapitata, 24 h exposure, N-EtFOSA-M, sample3

value: N-EtFOSA-M (DTXSID1032646)


title: 694B_001_ADT_CZI-IA11512615

description:
Library name: 694B_001_ADT_CZI-IA11512615_lib
CITE-seq of mononuclear cells from skin of body

tag: donor id

value: 20-24 years

value: adult stage

tag: Sex

value: male

tag: suspension cell_depletion_factors

tag: living at_sample_collection

value: fresh

value: brain stem death

tag: library protocol

value: snRNA-seq, CITE-seq


title: R. subcapitata, 24 h exposure, N-EtFOSA-M, sample2

tag: tissue


title: 694B_001_GEX_CZI-IA11485875

description:
Library name: 694B_001_GEX_CZI-IA11485875_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,jejunum lamina propria

tag: ethnicity

value: Unknown

tag: suspension treatment_summary

value: 1.34 nM of phorbol 13-acetate 12-myristate and ionomycin and 8.1 nM of ionomycin for 2 hours

tag: raw matrix_cellranger_assay_chemistry

tag: sample preservation_method

tag: death type

tag: raw matrix_genome_annotation

tag: raw matrix_value_units

value: UMI

value: gene symbol, antibody target

value: mononuclear cell

value: scRNA-seq


title: R. subcapitata, 24 h exposure, PFOA, sample19

value: PFOA (DTXSID8031865)


title: R. subcapitata, 24 h exposure, N-EtFOSA-M, sample1

value: whole body


title: 694B_001_ADT_CZI-IA11512613

description:
Library name: 694B_001_ADT_CZI-IA11512613_lib
CITE-seq of mononuclear cells from skin of body

tag: age

tag: dev stage

value: skin of body

tag: source

value: Cambridge Biorepository for Translational Medicine

value: FALSE

value: CITE 10x 5' v2

tag: raw matrix_feature_keys

tag: raw matrix_assays

tag: enriched cell_type

tag: assay type

value: CITE-seq

value: TotalSeq-C Human Universal Cocktail


title: R. subcapitata, 24 h exposure, N-EtFOSA-M, sample5

tag: developmental stage

value: Exponential Growth Stage

tag: treatment

value: N-EtFOSA-M (DTXSID1032646)


title: 759B_001_GEX_CZI-IA12953814

description:
Library name: 759B_001_GEX_CZI-IA12953814_lib
scRNA-seq of mononuclear cells from pooled:blood,spleen,thymus,bone marrow,mesenteric lymph node,thoracic lymph node

tag: donor id

value: 20-24 years

value: adult stage

tag: Sex

value: female

tag: tissue

tag: suspension cell_depletion_factors

tag: living at_sample_collection

value: fresh

value: brain stem death

tag: library protocol

value: snRNA-seq, CITE-seq


title: R. subcapitata, 24 h exposure, N-EtFOSA-M, sample4


title: R. subcapitata, 24 h exposure, PFOA, sample20


title: 694B_001_ADT_CZI-IA11512607

description:
Library name: 694B_001_ADT_CZI-IA11512607_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,jejunum lamina propria

value: male

tag: ethnicity

value: Unknown

tag: sample preservation_method

tag: death type

tag: raw matrix_genome_annotation

value: UMI

value: gene symbol, antibody target

value: mononuclear cell

tag: antibodies/tags


title: 694B_001_ADT_CZI-IA11512610

description:
Library name: 694B_001_ADT_CZI-IA11512610_lib
CITE-seq of mononuclear cells from pooled:spleen,bone marrow

tag: age

tag: dev stage

value: pooled:spleen,bone marrow

tag: source

value: Cambridge Biorepository for Translational Medicine

value: FALSE

tag: raw matrix_value_units

tag: raw matrix_feature_keys


title: R. subcapitata, 24 h exposure, PFOA, sample21

value: whole body

tag: developmental stage

tag: treatment

value: PFOA (DTXSID8031865)


title: R. subcapitata, 24 h exposure, PFOA, sample15

value: Exponential Growth Stage


title: R. subcapitata, 24 h exposure, PFOA, sample17


title: 694B_001_ADT_CZI-IA11512608

description:
Library name: 694B_001_ADT_CZI-IA11512608_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,jejunum lamina propria

tag: donor id

value: 20-24 years

tag: Sex

value: CITE 10x 5' v2

tag: raw matrix_assays

tag: enriched cell_type

tag: assay type

value: CITE-seq

value: TotalSeq-C Human Universal Cocktail


title: 694B_001_ADT_CZI-IA11512611

description:
Library name: 694B_001_ADT_CZI-IA11512611_lib
CITE-seq of mononuclear cells from pooled:spleen,bone marrow

value: adult stage

tag: ethnicity

tag: tissue

tag: suspension cell_depletion_factors

tag: living at_sample_collection

value: fresh

value: brain stem death

tag: library protocol


title: 694B_001_ADT_CZI-IA11512612

description:
Library name: 694B_001_ADT_CZI-IA11512612_lib
CITE-seq of mononuclear cells from pooled:spleen,bone marrow

tag: age

value: male

value: Unknown

tag: sample preservation_method

tag: death type

tag: raw matrix_genome_annotation

value: snRNA-seq, CITE-seq

tag: antibodies/tags


title: 694B_001_GEX_CZI-IA11485877

description:
Library name: 694B_001_GEX_CZI-IA11485877_lib
scRNA-seq of mononuclear cells from pooled:spleen,bone marrow

tag: dev stage

tag: source

tag: suspension treatment_summary

value: 1.34 nM of phorbol 13-acetate 12-myristate and ionomycin and 8.1 nM of ionomycin for 2 hours

tag: raw matrix_cellranger_assay_chemistry

tag: raw matrix_value_units

value: UMI

tag: raw matrix_feature_keys

value: gene symbol, antibody target

value: mononuclear cell

value: scRNA-seq


title: 694B_001_ADT_CZI-IA11512605

description:
Library name: 694B_001_ADT_CZI-IA11512605_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,jejunum lamina propria

tag: donor id

tag: Sex

value: Cambridge Biorepository for Translational Medicine

value: FALSE

tag: raw matrix_assays

tag: enriched cell_type

tag: assay type


title: 694B_001_ADT_CZI-IA11512604

description:
Library name: 694B_001_ADT_CZI-IA11512604_lib
CITE-seq of mononuclear cells from pooled:mesenteric lymph node

value: 20-24 years

tag: ethnicity

tag: tissue

value: pooled:mesenteric lymph node

tag: suspension cell_depletion_factors

tag: living at_sample_collection

tag: library protocol


title: R. subcapitata, 24 h exposure, PFOA, sample18

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment

value: PFOA (DTXSID8031865)


title: 694B_001_ADT_CZI-IA11512609

description:
Library name: 694B_001_ADT_CZI-IA11512609_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,jejunum lamina propria

tag: age

tag: dev stage

value: adult stage

tag: source

tag: sample preservation_method

value: fresh

tag: death type

value: CITE 10x 5' v2

tag: raw matrix_genome_annotation

value: CITE-seq

tag: antibodies/tags

value: TotalSeq-C Human Universal Cocktail


title: R. subcapitata, 24 h exposure, PFOA, sample16


title: R. subcapitata, 24 h exposure, PFOA, sample14


title: 694B_001_ADT_CZI-IA11512606

description:
Library name: 694B_001_ADT_CZI-IA11512606_lib
CITE-seq of mononuclear cells from pooled:spleen,bone marrow

tag: donor id

tag: Sex

value: male

value: Unknown

value: pooled:spleen,bone marrow

tag: suspension treatment_summary

value: 1.34 nM of phorbol 13-acetate 12-myristate and ionomycin and 8.1 nM of ionomycin for 2 hours

value: brain stem death

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: raw matrix_assays

value: snRNA-seq, CITE-seq


title: 694B_001_ADT_CZI-IA11512602

description:
Library name: 694B_001_ADT_CZI-IA11512602_lib
CITE-seq of mononuclear cells from pooled:spleen,bone marrow

tag: ethnicity

tag: tissue

value: Cambridge Biorepository for Translational Medicine

tag: suspension cell_depletion_factors

tag: living at_sample_collection

value: FALSE

value: UMI

value: gene symbol, antibody target

tag: enriched cell_type

value: mononuclear cell

tag: assay type


title: 694B_001_ADT_CZI-IA11512603

description:
Library name: 694B_001_ADT_CZI-IA11512603_lib
CITE-seq of mononuclear cells from pooled:spleen,bone marrow

tag: age

value: 20-24 years

tag: dev stage

tag: source

tag: library protocol


title: R. subcapitata, 24 h exposure, PFOA, sample11

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment

value: PFOA (DTXSID8031865)


title: R. subcapitata, 24 h exposure, PFOA, sample12


title: 689C_001_GEX_CZI-IA11512684

description:
Library name: 689C_001_GEX_CZI-IA11512684_lib
scRNA-seq of mononuclear cells from skin of body

tag: donor id

value: 40-44 years

value: adult stage

tag: Sex

value: skin of body

tag: raw matrix_cellranger_assay_chemistry

tag: sample preservation_method

value: fresh

tag: death type

value: circulatory death

tag: raw matrix_genome_annotation

value: scRNA-seq


title: 694B_001_ADT_CZI-IA11512600

description:
Library name: 694B_001_ADT_CZI-IA11512600_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,jejunum lamina propria

value: male

tag: ethnicity

value: Unknown

tag: tissue

value: brain stem death

value: CITE 10x 5' v2

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: raw matrix_assays

value: CITE-seq

tag: antibodies/tags

value: TotalSeq-C Human Universal Cocktail


title: 694B_001_ADT_CZI-IA11512601

description:
Library name: 694B_001_ADT_CZI-IA11512601_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,jejunum lamina propria

tag: age

tag: dev stage

value: Cambridge Biorepository for Translational Medicine

tag: suspension cell_depletion_factors

tag: suspension treatment_summary

value: 1.34 nM of phorbol 13-acetate 12-myristate and ionomycin and 8.1 nM of ionomycin for 2 hours

tag: living at_sample_collection

value: FALSE

value: UMI

value: gene symbol, antibody target

value: snRNA-seq, CITE-seq

tag: enriched cell_type

value: mononuclear cell

tag: assay type


title: 689C_001_GEX_CZI-IA11512683

description:
Library name: 689C_001_GEX_CZI-IA11512683_lib
scRNA-seq of mononuclear cells from pooled:lung,liver

tag: donor id

value: 40-44 years

value: adult stage

tag: Sex

tag: source

tag: raw matrix_cellranger_assay_chemistry

tag: library protocol


title: R. subcapitata, 24 h exposure, PFOA, sample8

tag: tissue

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment

value: PFOA (DTXSID8031865)


title: R. subcapitata, 24 h exposure, PFOA, sample10


title: R. subcapitata, 24 h exposure, PFOA, sample7


title: R. subcapitata, 24 h exposure, PFOA, sample6


title: R. subcapitata, 24 h exposure, PFOA, sample9


title: 689C_001_GEX_CZI-IA11485691

description:
Library name: 689C_001_GEX_CZI-IA11485691_lib
scRNA-seq of mononuclear cells from pooled:bone marrow,mesenteric lymph node

value: male

tag: ethnicity

value: Unknown

tag: sample preservation_method

value: fresh

tag: death type

value: circulatory death

tag: raw matrix_genome_annotation

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: raw matrix_assays

value: scRNA-seq


title: 689C_001_GEX_CZI-IA11512682

description:
Library name: 689C_001_GEX_CZI-IA11512682_lib
scRNA-seq of mononuclear cells from pooled:lung,liver

tag: age

tag: dev stage

value: Cambridge Biorepository for Translational Medicine

tag: suspension cell_depletion_factors

tag: suspension treatment_summary

tag: living at_sample_collection

tag: enriched cell_type


title: 689C_001_GEX_CZI-IA11512681

description:
Library name: 689C_001_GEX_CZI-IA11512681_lib
scRNA-seq of mononuclear cells from pooled:bone marrow,mesenteric lymph node

tag: donor id

tag: Sex

tag: source

value: 1.34 nM of phorbol 13-acetate 12-myristate and ionomycin and 8.1 nM of ionomycin for 2 hours

tag: raw matrix_cellranger_assay_chemistry

tag: library protocol

tag: assay type


title: R. subcapitata, 24 h exposure, PFOA, sample3

tag: tissue

tag: developmental stage

tag: treatment


title: R. subcapitata, 24 h exposure, PFOA, sample5


title: R. subcapitata, 24 h exposure, PFOA, sample4


title: 689C_001_GEX_CZI-IA11485688

description:
Library name: 689C_001_GEX_CZI-IA11485688_lib
scRNA-seq of mononuclear cells from skin of body

tag: ethnicity

value: skin of body

value: FALSE

tag: sample preservation_method

tag: death type

tag: raw matrix_genome_annotation

tag: raw matrix_value_units

tag: raw matrix_feature_keys