title: 2,4-BPS_50_647

tag: index

tag: i5 index_id

value: CGTAACTTA


title: 2,4-BPF_50_645

status: Public on Aug 18 2022

type: SRA

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

library_source: transcriptomic

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.20.0
Alignment was performed using STAR v2.7.8a
Gene counts were performed with qCount in the QuasR R package v1.30.0
Normalization was performed with DESeq2 v1.30.1
Assembly: Biospyder Human Whole Transcriptome Gene Set
Supplementary files format and content: count_table.csv is a genes by samples count matrix of raw counts from the TempO-Seq data alignments.

molecule: total RNA

organism: Homo sapiens

source_name: breast cancer

growth_protocol: MCF-7 cells (ATCC, Manassas, VA) were cultured in Dulbecco's modified Eagle's medium (DMEM; Gibco, Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS; Wisent Bioproducts), and 1% penicillin and streptomycin, at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Cell lysates were used directly for TempO-Seq library building
TempO-Seq gene expression analysis was conducted on exposed and control MCF-7 cell lysates. Libraries were prepared in a 96-well plate format using the TempO-Seq® Human Whole Transcriptome Panel reagent kit (BioSpyder Technologies, Carlsbad, CA, USA), following the manufacturer?s protocol. Human Brain Total RNA and qPCR Human Reference Total RNA (Takara Bio, CA, USA) were included as positive assay controls and a no-lysate control (1X TempO-Seq® R Lysis Buffer only) was included as a negative assay control (two replicates per control). In brief, 2 µl cell lysates were hybridized with the targeted detector oligo (DO) probe mix in 1X TempO-Seq® R Lysis Buffer for 10 min at 70oC followed by a temperature gradient with a ramp rate of 0.5oC/min to 45oC over a 50 min period, followed by a nuclease digestion at 37oC for 90 min to remove excess, unbound, or incorrectly bound DOs enzymatically. Ligation of the DO pairs bound to adjacent target sequences was then completed with a 60 min incubation at 37oC, immediately followed with a 15 min enzyme denaturation at 80oC to generate a pool of amplification templates. All amplification templates (i.e., 10 µl of ligated DOs) were transferred to its corresponding well of the 96-well PCR Pre-Mix and Primers plate. Amplification proceeded with a CFX96 Real-Time PCR Detection System (Bio-Rad, Mississauga, ON, Canada) to attach a unique sequence tag and the sequencing adaptors to each sample using the following PCR program settings: 37oC for 10 min, 95oC for 2 min; 6 cycles of 95oC for 30 sec, 54oC for 30 sec, 72oC for 120 sec; 16 cycles of 95oC for 30 sec; 72oC for 2 min; 72oC for 1 min. The TempO-Seq® libraries were pooled (5 µl of all 96 samples) and purified using the Macherey-Nagel NucleoSpin® Gel and PCR Clean-Up kit (Clontech Laboratories Inc., Bethlehem, PA, USA), according to the manufacturer?s instructions for PCR cleanup with three modifications outlined in the TempO-Seq® Assay User Guide. The pooled, purified TempO-Seq® libraries were sequenced using a NextSeq® 500/550 High Output flow cell (v2 kit, 75 cycles) on an Illumina NextSeq® 500 Sequencing platform (Illumina, San Diego, CA, USA).

treatment_protocol: Cells were maintained for 24 hours in phenol red-free DMEM supplemented with 5% charcoal-dextran stripped FBS (CD-FBS) and seeded  into 96-well plates at a density of 2.5 × 104 cells per well in phenol red-free DMEM supplemented with 5% CD-FBS to eliminate estrogenic components. The next day the medium was removed and replaced with DMEM with 5% CD-FBS containing the chemicals of interest. Cells were exposed in quadruplicate in separate 96-well plates to BPA and 15 alternative chemicals at 10 different concentrations (0.0005, 0.001, 0.01,0.1, 0.5, 1, 5, 10, 50, 100 µM), the positive control 17?-estradiol (E2; 0.0001, 0.001, 0.01, 0.1, 1, 10 nM), dexamethasone (Dex ? a non ER-interacting control; 0.0001, 0.001, 0.01, 0.1, 1 µM) alongside solvent controls (0.1% DMSO; four solvent controls per plate) for 48 hours.

tag: tissue

value: breast cancer

tag: cell line

tag: cell type

value: adenocarcinoma cell line

tag: chemical

tag: chemical long_name

value: 2,4-BPF (BPF Analog)

tag: dose

tag: treatment

tag: batch

value: Plate 1D index H

tag: sequencing pool

tag: technical control

value: F

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

value: TAGCGACAA

value: GATTGTGTT

tag: cas-rn

tag: iupac name


title: D4_Fam122a_KO_3_H3K4me3_ChIP

city: Shanghai

first: Yunsheng

last: Yang

address: Chong-Qing South Road

country: China

institute: Shanghai Jiao Tong University

library_source: genomic

data_processing:
Reads were removed with poor quality calls and mapped to the mouse mm10 reference genome using Bowtie2 (v.2.4.2)
Multiple mapped reads and PCR duplicates were further removed using Sambamba (v.0.6.8) with the parameter: -F “[XS] == null and not unmapped and not duplicate”
Genome coverage bigwig files were generated by deepTools (v.3.5.0) (35) bamCoverage with the parameters ‘--normalizeUsing RPKM --binSize 20’
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Mus musculus

growth_protocol: R1/E cells were maintained in DMEM (Basal Media) supplemented with 15% FBS (Gibco), 1×nonessential amino acids (NEAA) (Gibco), 1×GlutaMAX (Gibco), 1× sodium pyruvate (Gibco), 0.1 mMβ-mercaptoethanol (Sigma), 1,000 U ml−1 leukemia inhibitory factor (LIF) (Millipore), 100 U ml−1 penicillin, and 100 μg ml−1 streptomycin on mitomycin C (Selleck) inactivated mouse embryonic fibroblast (MEF) feeder cells under 5% CO2 at 37°C.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a sonicator (Qsonica Q700).
Libraries for ChIP-seq were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: mESCs were dissociated and 300 cells in 30 μL culture medium without LIF were aggregated to form EB by hanging drop for 2 d or 2.5 × 105 cells cultured with 5 mL medium in 60-mm bacterial culture dish in suspension for mass culture. EBs were harvested and transferred to 60-mm bacterial culture dish with 5 mL medium for 2 to 4 d.

value: mouse embryonic stem cells

tag: genotype

value: Fam122a knockout

value: EB formation

tag: time

value: Day 4

tag: chip antibody

value: H3K4me3 (Abcam, ab8580)


title: D4_Ctrl_H3K4me3_ChIP

tag: cell line

tag: cell type

value: WT


title: D4_Fam122a_KO_1_H3K4me3_ChIP


title: D4_Fam122a_KO_3_H3K27me3_ChIP

value: H3K27me3 (Millipore, 07-449)


title: D0_Fam122a_KO_3_H3K27ac_ChIP

value: Day 0

value: H3K27ac (Abcam, ab4729)


title: D4_Fam122a_KO_1_H3K27ac_ChIP


title: D4_Fam122a_KO_1_H3K27me3_ChIP


title: D4_Fam122a_KO_3_Input


title: D0_Fam122a_KO_3_H3K27me3_ChIP


title: BADGE_50_644

tag: tissue

tag: chemical

value: BADGE

tag: chemical long_name

tag: index

tag: i5 index_id

value: GCACCTATT


title: D4_Fam122a_KO_1_Input

tag: treatment


title: D4_Fam122a_KO_3_H3K27ac_ChIP


title: D0_Fam122a_KO_3_H3K4me3_ChIP


title: D4_Ctrl_H3K27me3_ChIP


title: D4_Ctrl_H3K27ac_ChIP


title: HD 2, PBMC, eTreg, bulk RNA-seq

city: Kashiwa

first: Hiroyoshi

last: Nishikawa

state: Chiba

address: Kahiwanoha 6-5-1

department: Exploratory Oncology Research & Clinical Trial Center

country: Japan

institute: National Cancer Center

data_processing:
Bowtie 2 was used to remove reads mapped to ribosomal RNA, and the remaining reads were mapped to the hg38 reference genome using STAR. After mapping, the raw read counts of the mapped reads were counted with featureCounts.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts

source_name: eTreg cells

extract_protocol: To construct RNA-seq libraries, starting with 100 pg of total RNA, the cDNA was synthesized using a SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA, Mountain View, CA) according to the manufacturer’s instructions. One nanogram of amplified cDNA was used to prepare the RNA-seq libraries for Illumina sequencing. The libraries were constructed with a Nextera XT DNA Sample Preparation kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: Peripheral blood and tumor tissues for bulk RNA-seq were obtained from healthy individuals and NSCLC patients who underwent a surgery for curative resection at the National Cancer Center Hospital East. The PBMCs were isolated by the density gradient centrifugation with Ficoll-Paque (GE Healthcare, Chicago, IL, USA). Tumor tissues were cut into small pieces, and single-cell suspensions were prepared with a gentle MACS Dissociator (Miltenyi Biotec, Bergisch Gladbach, Germany) as previously described (PMID: 31028147). Briefly, after filtrating the lung homogenates with a cell strainer (30 μm), the cells were subjected to a density gradient centrifugation with Ficoll-Paque to separate the tumor cells from TILs. Each T cell subset [naive Treg cells (CD45RA+CD25lowFoxP3lowCD4+), eTreg cells (CD45RA–CD25highFoxP3highCD4+), naive Tconv cells (CD45RA+CD25-CD4+), effector Tconv cells (CD45RA-CD25-CD4+), naive CD8+ T cells (CD45RA+CCR7+CD8+) and effector memory CD8+ T cells (CD45RA-CCR7-CD8+) from healthy individuals’ PBMCs; and eTreg cells, eTconv cells and effector memory CD8+ T cells from cancer patients’ PMBCs and TILs] was sorted with a BD FACSAria Fusion Cell Sorter (BD Biosciences, San Jose, CA) for subsequent bulk RNA-seq and Omni-ATAC-seq analyses. Anti-CD3 (clone: UCTH1), anti-CD4 (clone: RPA-T4) and anti-CD45RA (clone: HI100) mAbs were purchased from BD Biosciences. Anti-CCR7 (clone: G043H7) and anti-CD25 (clone: BC96) mAbs were obtained from BioLegend (San Diego, CA). Fixable Viability Dye eFluor 780 was purchased from Thermo Fisher Scientific (Waltham, MA).

value: eTreg cells


title: 2,4-BPF_10_637

value: breast cancer

value: adenocarcinoma cell line

value: 2,4-BPF (BPF Analog)

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

tag: reference rna

value: GCTATCGAT


title: BPS_10_635

value: BPS

value: Bisphenol S

value: Plate 1D index H

value: F

tag: solvent control

tag: well

tag: i7 index_id

value: GCCGTTACA

tag: cas-rn

tag: iupac name


title: Pergafast201_10_638

tag: cell line

tag: cell type

value: Pergafast 201

value: ATACCGGCA


title: D-8_10_634

tag: tissue

tag: chemical

value: ATACGCAGC


title: 4,4-BPF_50_641

tag: chemical long_name

value: 4,4-BPF (Bisphenol F)

tag: index

value: TAGCGACAA

value: TCTAACCAT


title: 2,4-BPS_10_639

tag: treatment

tag: i5 index_id

value: CGTAACTTA


title: BADGE_10_636

value: BADGE

tag: dose

tag: batch

value: GCACCTATT


title: BPS-MAE_10_640

value: breast cancer

value: adenocarcinoma cell line

value: BPS-MAE

tag: sequencing pool

tag: technical control

value: GGTCTAGCT


title: D4_Ctrl_Input

value: mouse embryonic stem cells

tag: genotype

value: WT

value: EB formation

tag: time

value: Day 4

tag: chip antibody


title: D0_Fam122a_KO_1_H3K27ac_ChIP

value: Fam122a knockout

value: Day 0

value: H3K27ac (Abcam, ab4729)


title: 4,4-BPF_10_633

value: 4,4-BPF (Bisphenol F)

value: Plate 1D index H

value: F

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

value: GCTATCGAT

tag: cas-rn


title: BPS-MAE_5_632

tag: tissue

tag: cell line

tag: cell type

tag: chemical

value: ATTGGTTGC

tag: iupac name


title: D0_Fam122a_KO_1_H3K27me3_ChIP

tag: treatment

value: H3K27me3 (Millipore, 07-449)


title: D0_Fam122a_KO_1_H3K4me3_ChIP

value: H3K4me3 (Abcam, ab8580)


title: D0_Ctrl_H3K27ac_ChIP


title: D0_Ctrl_H3K4me3_ChIP


title: D0_Ctrl_Input


title: D0_Ctrl_H3K27me3_ChIP


title: D0_Fam122a_KO_1_Input


title: D-8_5_626

value: breast cancer

value: adenocarcinoma cell line

tag: chemical long_name

tag: dose

tag: batch

tag: index

tag: i5 index_id

value: ATACGCAGC


title: Pergafast201_5_630

value: Pergafast 201

tag: sequencing pool

tag: technical control

value: ATACCGGCA


title: D0_Fam122a_KO_3_Input

value: mouse embryonic stem cells

tag: genotype

value: EB formation

tag: time

tag: chip antibody


title: D10_Fam122a_KO_3_rep1

data_processing:
Sequencing reads were mapped to mm10 reference genome using STAR (v.2.5.2b)
The transcription levels of annotated genes (FPKM, fragments per kilobase of transcript per million mapped reads) were quantified using HTSeq-count (v.0.6.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: bigWig

extract_protocol:
Total RNA was isolated from mESCs at the indicated days using Trizol reagent (Thermo).
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: mESCs were dissociated and 300 cells in 30 μL culture medium without LIF were aggregated to form EB by hanging drop for 2 d or 2.5 × 105 cells cultured with 5 mL medium in 60-mm bacterial culture dish in suspension for mass culture. EBs were harvested and transferred to 60-mm bacterial culture dish with 5 mL medium for 2 to 5 d. Then a single EB was plated into each well of 0.1% gelatin (Sigma)-coated 24-well microwell and medium was changed every other day.

value: Fam122a knockout

value: cardiac differentiation

value: Day 10


title: D10_Fam122a_KO_3_rep2


title: BADGE_5_628

value: BADGE

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

value: GCACCTATT

tag: cas-rn


title: D10_Fam122a_KO_1_rep2

tag: cell line

tag: cell type


title: BPS_5_627

tag: tissue

tag: chemical

value: BPS

tag: chemical long_name

value: Bisphenol S

tag: treatment

value: Plate 1D index H

value: F

value: GCCGTTACA

tag: iupac name


title: 2,4-BPS_1_623

value: breast cancer

tag: dose

tag: batch

tag: sequencing pool

tag: index

value: TGATTAAGC

tag: i5 index_id

value: CGTAACTTA


title: BPS-MAE_1_624

value: adenocarcinoma cell line

value: BPS-MAE

tag: technical control

tag: reference rna

value: GGTCTAGCT


title: Pergafast201_1_622

value: Pergafast 201

tag: solvent control

tag: well

value: ATACCGGCA


title: D10_Ctrl_rep2

value: mouse embryonic stem cells

tag: genotype

value: WT

value: cardiac differentiation

tag: time


title: D10_Fam122a_KO_1_rep1

tag: cell line

tag: cell type

value: Fam122a knockout

value: Day 10


title: D10_Ctrl_rep1


title: D7_Fam122a_KO_3_rep2

value: Day 7


title: BPS_1_619

tag: tissue

tag: chemical

value: BPS

value: Bisphenol S

value: Plate 1D index H

tag: i7 index_id

tag: cas-rn


title: 2,4-BPS_5_631

value: breast cancer

tag: chemical long_name

tag: dose

tag: treatment

value: F

value: ATTGGTTGC

tag: iupac name


title: D7_Fam122a_KO_3_rep1


title: BADGE_1_620

value: adenocarcinoma cell line

value: BADGE

tag: batch

tag: sequencing pool

tag: index

value: TGATTAAGC

tag: i5 index_id

value: GCACCTATT


title: D-8_1_618

tag: technical control

tag: reference rna

tag: solvent control

tag: well

value: ATACGCAGC


title: 4,4-BPF_5_625

tag: cell line

tag: cell type

value: 4,4-BPF (Bisphenol F)

value: TCTAACCAT


title: 2,4-BPF_5_629

tag: tissue

tag: chemical

value: 2,4-BPF (BPF Analog)

value: GATTGTGTT


title: 4,4-BPF_1_617

tag: i7 index_id

tag: cas-rn


title: D7_Fam122a_KO_1_rep1

value: mouse embryonic stem cells

tag: genotype

value: Fam122a knockout

value: cardiac differentiation

tag: time


title: 2,4-BPF_1_621

tag: chemical long_name

tag: dose

tag: treatment

tag: iupac name


title: D7_Ctrl_rep2

value: WT

value: Day 7


title: D7_Fam122a_KO_1_rep2


title: Pergafast201_0.5_614

value: breast cancer

value: Pergafast 201

tag: batch

value: Plate 1D index H

tag: sequencing pool

tag: index

value: TCAGCTAAT

tag: i5 index_id

value: ATACCGGCA


title: 2,4-BPS_0.5_615

value: adenocarcinoma cell line

tag: technical control

value: F

tag: reference rna

tag: solvent control

tag: well

value: CGTAACTTA


title: D7_Ctrl_rep1

tag: cell line

tag: cell type


title: D4_Fam122a_KO_3_rep1

value: Day 4


title: D4_Fam122a_KO_1_rep2


title: 2,4-BPF_0.5_613

tag: tissue

tag: chemical

tag: i7 index_id

tag: cas-rn


title: BPS_0.5_611

value: BPS

tag: chemical long_name

value: Bisphenol S

tag: dose

value: GCCGTTACA


title: BADGE_0.5_612

value: BADGE

tag: treatment

value: GCACCTATT

tag: iupac name


title: BPS-MAE_0.1_608

value: BPS-MAE

tag: batch

tag: sequencing pool

value: TGCTTATTC

value: GGTCTAGCT


title: D4_Fam122a_KO_3_rep2

value: mouse embryonic stem cells

tag: genotype

value: Fam122a knockout

value: cardiac differentiation

tag: time


title: D4_Fam122a_KO_1_rep1


title: D-8_0.5_610

value: breast cancer

value: Plate 1D index H

tag: technical control

tag: reference rna

tag: index

value: TCAGCTAAT

tag: i5 index_id

value: ATACGCAGC


title: D4_Ctrl_rep1

tag: cell line

tag: cell type

value: WT


title: 4,4-BPF_0.5_609

tag: tissue

value: adenocarcinoma cell line

tag: chemical

value: 4,4-BPF (Bisphenol F)

value: F

tag: solvent control

tag: well

value: TCTAACCAT


title: D0_Fam122a_KO_3

value: Day 0


title: D4_Ctrl_rep2

value: Day 4


title: BPS-MAE_0.5_616

value: BPS-MAE

tag: chemical long_name

tag: dose

tag: i7 index_id

tag: cas-rn


title: Pergafast201_0.1_606

value: Pergafast 201

tag: treatment

tag: batch

tag: sequencing pool

value: TGCTTATTC

value: ATACCGGCA

tag: iupac name


title: BADGE_0.1_604

value: BADGE

tag: technical control

tag: reference rna

value: GCACCTATT


title: 2,4-BPS_0.1_607

value: breast cancer

tag: index

tag: i5 index_id

value: CGTAACTTA


title: D0_Ctrl

tag: cell line

tag: cell type

value: mouse embryonic stem cells

tag: genotype

value: cardiac differentiation

tag: time


title: D0_Fam122a_KO_1

value: Fam122a knockout


title: 4,4-BPF_0.1_601

tag: tissue

value: adenocarcinoma cell line

tag: chemical

value: Plate 1D index H

tag: solvent control

tag: well


title: D-8_0.1_602

tag: chemical long_name

tag: dose

value: F

tag: i7 index_id

value: ATACGCAGC

tag: cas-rn


title: BPS_0.1_603

value: BPS

value: Bisphenol S

tag: treatment

tag: batch

tag: sequencing pool

value: GCCGTTACA

tag: iupac name


title: 2,4-BPF_0.01_597

value: 2,4-BPF (BPF Analog)

tag: technical control

tag: reference rna

tag: index

value: ATTCGAATC

tag: i5 index_id

value: GATTGTGTT


title: 2,4-BPS_0.01_599

tag: cell line

tag: cell type


title: BPS-MAE_0.01_600

tag: tissue

tag: chemical

value: BPS-MAE

value: GGTCTAGCT


title: BADGE_0.01_596

value: breast cancer

value: BADGE

tag: solvent control

tag: well

value: GCACCTATT


title: 2,4-BPF_0.1_605

tag: chemical long_name

tag: dose

value: TGCTTATTC


title: Pergafast201_0.001_590

value: Pergafast 201

tag: i7 index_id

value: ATCGCGACT

value: ATACCGGCA

tag: cas-rn


title: D-8_0.01_594

value: adenocarcinoma cell line

tag: treatment

tag: batch

value: Plate 1D index H

value: F


title: wt macropahes 3

city: Bonn

first: Rayk

last: Behrendt

state: North Rhine-Westphalia

address: Venusberg-Campus 1, 53127 Bonn

department: Institute of Clinical Chemistry and Clinical Pharmacology

country: Germany

institute: Universitätsklinikum Bonn

data_processing:
reads mapping with STAR
reads counting using FeatureCounts from the Subread package.
The raw counts (absolute number of reads) were normalized with the DESeq R package (v.1.6.1) and sample to sample correlation (Pearson's correlation coefficient) was computed based on the normalized counts.
Assembly: mm10 (UCSC)
Supplementary files format and content: tab delimited file with sample size normalized counts per gene (rows) and sample (columns)

source_name: mouse peritoneal macrophages

extract_protocol:
NEBNext Ultra II Directional RNA Lib Prep (Biomek i7) following manufacturer's protocols.
Strand specific RNA-Seq

tag: strain

tag: age

value: 9 weeks

tag: Sex

value: Female

tag: genotype

value: wt


title: wt macropahes 2

value: 13 weeks


title: Samhd1 ko and cGAS-GFP macrophages 2

value: 8 weeks

value: Samhd1 del/del, cGAS-GFP ki/ki


title: 2,4-BPF_0.001_589

value: 2,4-BPF (BPF Analog)

tag: sequencing pool

tag: technical control

tag: reference rna

tag: index

tag: i5 index_id

value: GATTGTGTT

tag: iupac name


title: BADGE_0.001_588

tag: tissue

value: breast cancer

tag: cell line

tag: cell type

tag: chemical

value: BADGE

tag: solvent control

tag: well


title: wt macropahes 1

value: Male


title: BPS-MAE_0.001_592

value: BPS-MAE

tag: chemical long_name

tag: dose

tag: treatment

tag: batch

tag: i7 index_id

value: GGTCTAGCT

tag: cas-rn


title: 2,4-BPS_0.001_591

tag: sequencing pool

tag: technical control

value: ATCGCGACT

value: CGTAACTTA


title: mouse, TIL, CD8+ T cells

data_processing:
Raw Omni-ATAC-seq reads were aligned to the mm10 reference genome using Bowtie 2 with default parameters, and uniquely mapping reads were used for further analysis. ATAC-seq peaks were identified for each sample using MACS2 (with parameters, −q value 0.05 --nomodel --shift 100 --extsise 200). Overlapping peaks in all samples were merged by HOMER mergePeaks.pl, and the merged peak list was produced. The number of raw reads mapped to each merged peak region in the list was counted with featureCounts, and the read counts in all the merged ATAC-seq peaks were quantile-normalized.
Assembly: mm10
Supplementary files format and content: bigWig files

source_name: tumor

extract_protocol:
For the Omni-ATAC-sequencing, samples were isolated as follows: (i) Treg cells (Thy1.1+ CD4+), T conv cells (Thy1.1- CD4+) and CD8+ T cells were prepared from tumors in Foxp3Thy1.1 mice; and (ii) Thy1.1+ CD4+ Treg cells were prepared from the tumors of either Foxp3Thy1.1 or Batf-/- Foxp3Thy1.1mice.
The Omni-ATAC-seq protocol was performed as described previously with minor modifications ((PMID: 28846090). In brief, 5000 to 10000 sorted T cells (for clinical samples), 1000 to 10000 sorted T cells (for murine samples), and 50000 cells (for cell lines) were washed with PBS and then lysed. The cell lysates were resuspended in 50 μl once with TD Buffer containing 2.5 μl of Nextera enzyme (Illumina). The transposition reaction was performed at 37°C for 30 min. The products were then purified with a MinElute polymerase chain reaction (PCR) purification kit (Qiagen, Hilden, Germany), and the fragments for the Omni-ATAC-seq library were amplified for five cycles of PCR. The additional number of PCR cycles was determined for each sample after quantification by real-time PCR. The PCR-amplified products were purified with a MinElute PCR purification kit again.

value: tumor

value: CD8+ T cells

tag: genotype

value: WT


title: BPS_0.001_587

value: adenocarcinoma cell line

value: BPS

value: Bisphenol S

value: Plate 1D index H

value: F

tag: reference rna

tag: index

tag: i5 index_id

value: GCCGTTACA


title: mouse, WT Treg cells, rep3

tag: tissue

value: Treg cells


title: Pergafast201_0.01_598

value: breast cancer

tag: cell line

tag: cell type

value: Pergafast 201

value: ATTCGAATC

value: ATACCGGCA

tag: iupac name


title: mouse, WT Treg cells, rep1


title: mouse, TIL, Treg cells


title: BPS_0.01_595

tag: chemical

tag: solvent control

tag: well


title: 4,4-BPF_0.001_585

tag: chemical long_name

value: 4,4-BPF (Bisphenol F)

tag: dose

tag: treatment

value: TCTAACCAT


title: mouse, WT Treg cells, rep2


title: BPS-MAE_0.0005_584

value: BPS-MAE

tag: batch

tag: i7 index_id

value: TGGAACGCT

value: GGTCTAGCT

tag: cas-rn


title: D-8_0.001_586

tag: sequencing pool

tag: technical control

value: ATCGCGACT

value: ATACGCAGC


title: mouse, Batf ko Treg cells, rep2

value: tumor

tag: genotype

value: Batf knockdown


title: mouse, Batf ko Treg cells, rep1


title: 2,4-BPS_0.0005_583

value: adenocarcinoma cell line

value: Plate 1D index H

tag: reference rna

tag: index

tag: i5 index_id

value: CGTAACTTA


title: Pergafast201_0.0005_582

tag: tissue

tag: cell line

tag: cell type

value: F


title: 4,4-BPF_0.01_593

value: breast cancer

tag: chemical

tag: solvent control

tag: iupac name


title: Samhd1 ko and cGAS-GFP macrophages 1

tag: strain

tag: age

value: 8 weeks

tag: Sex

value: Female

value: Samhd1 del/del, cGAS-GFP ki/ki


title: mouse, TIL, Tconv cells

value: Tconv cells

value: WT


title: RGC015

city: Guangzhou

first: Sheng

last: Liu

address: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

description: Retinal ganglion cells, scRNA-seq

library_source: transcriptomic single cell

data_processing:
Previously published pipeline STAR version 2.7.0
Assembly: mm10
Supplementary files format and content: Comma-Separated Values files and matrix files

source_name: Retina

extract_protocol:
The retina is isolated and flat-mounted under dim red light (created with BioRender.com). A retinal ganglion cell is patched and its responses to blue and green spotlight stimuli are recorded. The cell content is aspirated. RNA is processed using Smart-seq2 protocol to get transcriptomic data.
the cDNA library was sequenced on the NovaSeq 6000 instrument and 150-bp paired-end reads were set up. Each sample was sequenced to approximately 10 million reads

value: Retinal ganglion cells

value: Retina

value: 7-9 weeks old


title: 2,4-BPF_0.0005_581

tag: chemical long_name

value: 2,4-BPF (BPF Analog)

tag: dose

tag: treatment

tag: batch

tag: well

tag: i7 index_id

value: TGGAACGCT

value: GATTGTGTT


title: BADGE_0.0005_580

value: BADGE

tag: sequencing pool

tag: technical control

tag: reference rna

tag: index

value: GCACCTATT

tag: cas-rn


title: BPS_0.0005_579

tag: tissue

tag: cell line

tag: cell type

value: adenocarcinoma cell line

tag: chemical

value: BPS

value: Bisphenol S

value: Plate 1D index H

tag: i5 index_id

value: GCCGTTACA


title: D-8_0.0005_578

value: breast cancer

value: F

tag: solvent control

value: ATACGCAGC

tag: iupac name


title: RGC009

description: Retinal ganglion cells, scRNA-seq

tag: strain

tag: age


title: 4,4-BPF_0.0005_577

tag: chemical long_name

value: 4,4-BPF (Bisphenol F)

tag: dose

tag: treatment

tag: batch

value: TCTAACCAT


title: RGC016

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina


title: RGC010

description: Retinal ganglion cells, scRNA-seq

value: 7-9 weeks old


title: RGC018

description: Retinal ganglion cells, scRNA-seq


title: No cells; media only_0_576

value: No cells; media only

value: No cells; media only_0

value: Plate 2C index E

tag: sequencing pool

tag: technical control

value: T

tag: well

tag: i7 index_id

value: TAGCTCTTC

value: AAGTAGGCT


title: RGC026

description: Retinal ganglion cells, scRNA-seq

tag: tissue


title: RGC008

description: Retinal ganglion cells, scRNA-seq


title: No cells; 1X Lysis buffer_0_575

tag: cell line

value: adenocarcinoma cell line

value: No cells; 1X Lysis buffer

value: No cells; 1X Lysis buffer_0

tag: reference rna

tag: index

value: TAACGCGTC

tag: cas-rn


title: RGC017

description: Retinal ganglion cells, scRNA-seq

tag: cell type


title: No cells; Brain +ve control_0_574

value: breast cancer

tag: chemical

value: No cells; Brain +ve control

value: No cells; Brain +ve control_0

tag: solvent control

value: F

tag: i5 index_id

value: GCAGATGCA

tag: iupac name


title: RGC027

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age


title: No cells; Universal human +ve control_0_573

value: No cells; Universal human +ve control

tag: chemical long_name

tag: dose

tag: treatment

value: No cells; Universal human +ve control_0

tag: batch

value: AGCAAGGTC


title: RGC029

description: Retinal ganglion cells, scRNA-seq

value: 7-9 weeks old


title: RGC028

description: Retinal ganglion cells, scRNA-seq


title: RGC021

description: Retinal ganglion cells, scRNA-seq


title: RGC020

description: Retinal ganglion cells, scRNA-seq


title: RGC019

description: Retinal ganglion cells, scRNA-seq


title: Cells, no treatment_0_568

value: Cells, no treatment

value: cells, no treatment

value: Cells, no treatment_0

value: Plate 2C index E

tag: sequencing pool

tag: technical control

value: T

tag: well

tag: i7 index_id

value: GACTTCATT


title: DMSO_571

tag: tissue

value: breast cancer

tag: cell line

value: adenocarcinoma cell line

value: DMSO Pool 2

value: DMSO 0.1%

value: DMSO

tag: reference rna

tag: index

value: TAGCTCTTC

value: AAACACCTT


title: DMSO_572

tag: cell type

tag: chemical

value: F

tag: solvent control

value: TTCCGAATT

tag: cas-rn


title: RGC022

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age


title: DMSO_570

tag: chemical long_name

tag: dose

tag: i5 index_id

value: ACAACCATC

tag: iupac name


title: RGC023

description: Retinal ganglion cells, scRNA-seq

value: 7-9 weeks old


title: Cells, no treatment_0_566

value: Cells, no treatment

value: cells, no treatment

tag: treatment

value: Cells, no treatment_0

tag: batch

tag: sequencing pool

tag: technical control

value: GCAGATGCA


title: RGC030

description: Retinal ganglion cells, scRNA-seq

tag: tissue


title: Dex_100_564

value: breast cancer

tag: cell line

value: Dex

value: Plate 2C index E

tag: reference rna

tag: well

tag: i7 index_id

value: GACTTCATT


title: DMSO_569

tag: cell type

value: adenocarcinoma cell line

tag: chemical

value: DMSO Pool 2

value: DMSO 0.1%

value: DMSO

tag: solvent control

value: T

tag: index

value: GTGCATTAG


title: Dex_1000_565

tag: chemical long_name

value: F

value: AGCAAGGTC

tag: cas-rn


title: RGC024

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: RGC032

description: Retinal ganglion cells, scRNA-seq


title: Cells, no treatment_0_567

value: Cells, no treatment

value: cells, no treatment

tag: dose

tag: treatment

value: Cells, no treatment_0

tag: i5 index_id

value: TAACGCGTC

tag: iupac name


title: RGC025

description: Retinal ganglion cells, scRNA-seq

tag: tissue


title: Dex_10_563

value: breast cancer

tag: cell line

value: Dex

tag: batch

value: Plate 2C index E

tag: sequencing pool

tag: technical control

value: AAACACCTT


title: BPA_100_560

tag: cell type

value: adenocarcinoma cell line

value: BPA

tag: reference rna

tag: well

tag: i7 index_id

value: TGCATGACA

value: AAGTAGGCT


title: Dex_1_562

tag: chemical

tag: chemical long_name

value: F

tag: solvent control

tag: index

value: GACTTCATT

value: ACAACCATC


title: RGC050

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age


title: BPS-MPE_100_559

value: BPS-MPE

tag: dose

tag: treatment

tag: i5 index_id

tag: cas-rn


title: RGC034

description: Retinal ganglion cells, scRNA-seq

tag: tissue

value: 7-9 weeks old


title: TGSA_100_558

tag: cell line

value: TGSA

tag: batch

tag: sequencing pool

value: GCAGATGCA

tag: iupac name


title: RGC035

description: Retinal ganglion cells, scRNA-seq

tag: cell type


title: RGC033

description: Retinal ganglion cells, scRNA-seq


title: BTUM_100_557

value: breast cancer

value: BTUM

tag: technical control

tag: reference rna

tag: well

tag: i7 index_id

value: AGCAAGGTC


title: BPC_100_554

tag: chemical

value: BPC

tag: chemical long_name

value: BPC (Bisphenol C)

value: Plate 2C index E

tag: solvent control

tag: index


title: RGC043

description: Retinal ganglion cells, scRNA-seq

tag: strain

tag: age


title: BPAF_100_556

value: adenocarcinoma cell line

value: BPAF

value: BPAF (Bisphenol AF)

tag: dose

tag: treatment

value: TGCATGACA

tag: i5 index_id

value: TTCCGAATT

tag: cas-rn


title: RGC036

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

tag: tissue


title: RGC031

description: Retinal ganglion cells, scRNA-seq

value: Retina


title: RGC051

description: Retinal ganglion cells, scRNA-seq


title: DCDPS_100_555

tag: cell line

value: DCDPS

value: Bis (4-chorophenyl) Sulfone

tag: batch

tag: sequencing pool

value: F

value: AAACACCTT

tag: iupac name


title: BPAP_100_553

value: breast cancer

tag: cell type

value: BPAP

value: BPAP (Bisphenol AP)

tag: technical control

tag: reference rna

tag: well

value: GTGCATTAG


title: RGC037

description: Retinal ganglion cells, scRNA-seq

value: 7-9 weeks old


title: TGSA_50_550

tag: chemical

value: TGSA

tag: chemical long_name

value: Plate 2C index E

tag: solvent control

tag: i7 index_id

value: TAAGGTAGC

value: GCAGATGCA


title: RGC039

description: Retinal ganglion cells, scRNA-seq

tag: strain

tag: age


title: Dex_0.1_561

value: adenocarcinoma cell line

value: Dex

tag: dose

tag: treatment

tag: index

value: GACTTCATT

tag: i5 index_id


title: BPA_50_552

tag: tissue

tag: cell line

value: BPA

tag: batch

value: AAGTAGGCT

tag: cas-rn


title: RGC044

description: Retinal ganglion cells, scRNA-seq

tag: cell type

value: Retinal ganglion cells

value: Retina


title: RGC045

description: Retinal ganglion cells, scRNA-seq


title: BTUM_50_549

value: BTUM

tag: sequencing pool

tag: technical control

value: F

tag: reference rna

value: AGCAAGGTC

tag: iupac name


title: BPAP_50_545

value: breast cancer

tag: chemical

value: BPAP

tag: chemical long_name

value: BPAP (Bisphenol AP)

tag: solvent control

tag: well


title: RGC047

description: Retinal ganglion cells, scRNA-seq

tag: strain

tag: age

value: 7-9 weeks old


title: RGC040

description: Retinal ganglion cells, scRNA-seq


title: DCDPS_50_547

value: DCDPS

value: Bis (4-chorophenyl) Sulfone

tag: dose

tag: treatment

value: Plate 2C index E

tag: i7 index_id

tag: index

value: AAACACCTT


title: BPAF_50_548

tag: tissue

tag: cell line

value: adenocarcinoma cell line

value: BPAF

value: BPAF (Bisphenol AF)

tag: batch

value: TAAGGTAGC

tag: i5 index_id

value: TTCCGAATT


title: RGC048

description: Retinal ganglion cells, scRNA-seq

tag: cell type

value: Retinal ganglion cells

value: Retina


title: RGC046

description: Retinal ganglion cells, scRNA-seq


title: BPC_50_546

value: BPC

value: BPC (Bisphenol C)

tag: sequencing pool

tag: technical control

value: F

tag: reference rna

value: ACAACCATC

tag: cas-rn


title: BPS-MPE_10_543

value: breast cancer

tag: chemical

value: BPS-MPE

tag: chemical long_name

tag: solvent control

value: TCAGTACAT

value: TAACGCGTC

tag: iupac name


title: RGC042

description: Retinal ganglion cells, scRNA-seq

tag: strain

tag: age

value: 7-9 weeks old


title: RGC041

description: Retinal ganglion cells, scRNA-seq


title: RGC049

description: Retinal ganglion cells, scRNA-seq


title: TGSA_10_542

value: TGSA

tag: dose

tag: treatment

value: Plate 2C index E

tag: well

tag: i7 index_id

value: GCAGATGCA


title: BPA_10_544

tag: tissue

tag: cell line

value: adenocarcinoma cell line

value: BPA

tag: batch

tag: index

value: AAGTAGGCT


title: BPS-MPE_50_551

tag: cell type

tag: sequencing pool

tag: technical control

value: TAAGGTAGC

tag: i5 index_id


title: RGC052

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina


title: RGC038

description: Retinal ganglion cells, scRNA-seq


title: RGC053

description: Retinal ganglion cells, scRNA-seq


title: BTUM_10_541

tag: chemical

value: BTUM

tag: chemical long_name

tag: reference rna

value: AGCAAGGTC

tag: cas-rn


title: DCDPS_10_539

value: DCDPS

value: Bis (4-chorophenyl) Sulfone

value: F

tag: solvent control

value: AAACACCTT

tag: iupac name


title: BPAF_10_540

value: breast cancer

value: BPAF

value: BPAF (Bisphenol AF)

tag: dose

tag: treatment

value: TCAGTACAT

value: TTCCGAATT


title: BPC_10_538

value: adenocarcinoma cell line

value: BPC

value: BPC (Bisphenol C)

value: Plate 2C index E

tag: well

tag: i7 index_id

value: ACAACCATC


title: RGC054

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

tag: tissue

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: RGC060

description: Retinal ganglion cells, scRNA-seq

tag: cell type


title: RGC055

description: Retinal ganglion cells, scRNA-seq


title: RGC061

description: Retinal ganglion cells, scRNA-seq


title: BPS-MPE_5_535

tag: cell line

value: BPS-MPE

tag: batch

tag: sequencing pool

tag: index

value: ATTCGCTCT

value: TAACGCGTC


title: RGC057

description: Retinal ganglion cells, scRNA-seq


title: RGC056

description: Retinal ganglion cells, scRNA-seq


title: RGC058

description: Retinal ganglion cells, scRNA-seq


title: BTUM_5_533

tag: chemical

value: BTUM

tag: chemical long_name

tag: technical control

value: F

tag: i5 index_id

value: AGCAAGGTC


title: DCDPS_5_531

value: breast cancer

value: DCDPS

value: Bis (4-chorophenyl) Sulfone

tag: reference rna

tag: solvent control

value: AAACACCTT

tag: cas-rn

tag: iupac name


title: RGC059

description: Retinal ganglion cells, scRNA-seq


title: RGC062

description: Retinal ganglion cells, scRNA-seq


title: BPAF_5_532

value: adenocarcinoma cell line

value: BPAF

value: BPAF (Bisphenol AF)

tag: dose

tag: treatment

tag: well

tag: i7 index_id

value: TTCCGAATT


title: BPA_5_536

tag: tissue

tag: cell type

value: BPA

value: Plate 2C index E

value: AAGTAGGCT


title: RGC069

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: BPC_5_530

tag: cell line

value: BPC

value: BPC (Bisphenol C)

tag: batch

tag: sequencing pool

tag: index

value: ATTCGCTCT

value: ACAACCATC


title: RGC063

description: Retinal ganglion cells, scRNA-seq


title: RGC065

description: Retinal ganglion cells, scRNA-seq


title: RGC070

description: Retinal ganglion cells, scRNA-seq


title: BPAP_5_529

value: breast cancer

tag: chemical

value: BPAP

tag: chemical long_name

value: BPAP (Bisphenol AP)

tag: technical control

value: F

tag: i5 index_id

value: GTGCATTAG


title: RGC064

description: Retinal ganglion cells, scRNA-seq


title: BPA_1_528

value: adenocarcinoma cell line

tag: reference rna

tag: solvent control

value: ACTCATGTA

tag: cas-rn

tag: iupac name


title: RGC066

description: Retinal ganglion cells, scRNA-seq


title: BPS-MPE_1_527

value: BPS-MPE

tag: dose

tag: treatment

tag: well

tag: i7 index_id

value: TAACGCGTC


title: BPAP_10_537

tag: tissue

tag: cell type

value: Plate 2C index E

value: TCAGTACAT


title: TGSA_1_526

tag: cell line

value: TGSA

tag: batch

value: GCAGATGCA


title: BTUM_1_525

value: BTUM

tag: sequencing pool

tag: index

value: AGCAAGGTC


title: TGSA_5_534

tag: chemical

tag: chemical long_name

value: ATTCGCTCT


title: RGC071

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: RGC067

description: Retinal ganglion cells, scRNA-seq


title: RGC068

description: Retinal ganglion cells, scRNA-seq


title: BPAF_1_524

value: breast cancer

value: BPAF

value: BPAF (Bisphenol AF)

tag: technical control

tag: reference rna

tag: solvent control

tag: i5 index_id

value: TTCCGAATT


title: DCDPS_1_523

value: adenocarcinoma cell line

value: DCDPS

value: Bis (4-chorophenyl) Sulfone

tag: dose

tag: treatment

value: F

value: ACTCATGTA

value: AAACACCTT

tag: cas-rn

tag: iupac name


title: RGC080

description: Retinal ganglion cells, scRNA-seq

tag: cell type

tag: tissue


title: BPAP_1_521

tag: cell line

value: BPAP

value: BPAP (Bisphenol AP)

tag: batch

value: Plate 2C index E

tag: well

tag: i7 index_id

value: GTGCATTAG


title: RGC079

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells


title: BPC_1_522

tag: chemical

value: BPC

tag: chemical long_name

value: BPC (Bisphenol C)

tag: sequencing pool

tag: index

value: ACAACCATC


title: TGSA_0.5_518

value: breast cancer

value: TGSA

tag: technical control

tag: reference rna

value: GTTTATACT

value: GCAGATGCA


title: BPA_0.5_520

value: adenocarcinoma cell line

value: BPA

tag: solvent control

tag: i5 index_id

value: AAGTAGGCT


title: RGC081

description: Retinal ganglion cells, scRNA-seq

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: RGC072

description: Retinal ganglion cells, scRNA-seq


title: RGC082

description: Retinal ganglion cells, scRNA-seq


title: BTUM_0.5_517

value: BTUM

tag: dose

tag: treatment

value: F

value: AGCAAGGTC

tag: cas-rn

tag: iupac name


title: RGC073

description: Retinal ganglion cells, scRNA-seq

tag: cell type

tag: tissue


title: RGC074

description: Retinal ganglion cells, scRNA-seq


title: RGC076

description: Retinal ganglion cells, scRNA-seq


title: RGC083

description: Retinal ganglion cells, scRNA-seq


title: BPAF_0.5_516

tag: cell line

value: BPAF

value: BPAF (Bisphenol AF)

tag: batch

value: Plate 2C index E

tag: well

tag: i7 index_id

value: TTCCGAATT


title: RGC075

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells


title: RGC078

description: Retinal ganglion cells, scRNA-seq


title: BPAP_0.5_513

value: breast cancer

tag: chemical

value: BPAP

tag: chemical long_name

value: BPAP (Bisphenol AP)

tag: sequencing pool

tag: index

value: GTGCATTAG


title: RGC088

description: Retinal ganglion cells, scRNA-seq


title: BPC_0.5_514

value: adenocarcinoma cell line

value: BPC

value: BPC (Bisphenol C)

tag: technical control

tag: reference rna

tag: solvent control

value: GTTTATACT

tag: i5 index_id

value: ACAACCATC


title: DCDPS_0.5_515

value: DCDPS

value: Bis (4-chorophenyl) Sulfone

tag: dose

tag: treatment

value: AAACACCTT


title: BPS-MPE_0.1_511

value: BPS-MPE

value: F

value: GAACTGTAT

value: TAACGCGTC

tag: cas-rn

tag: iupac name


title: BPA_0.1_512

tag: tissue

tag: cell type

value: BPA

value: Plate 2C index E

value: AAGTAGGCT


title: RGC084

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: RGC090

description: Retinal ganglion cells, scRNA-seq


title: BPAF_0.1_508

value: breast cancer

tag: cell line

value: adenocarcinoma cell line

value: BPAF

value: BPAF (Bisphenol AF)

tag: batch

tag: well

tag: i7 index_id

value: TTCCGAATT


title: BPS-MPE_0.5_519

tag: chemical

tag: chemical long_name

tag: sequencing pool

tag: index

value: GTTTATACT


title: RGC085

description: Retinal ganglion cells, scRNA-seq


title: TGSA_0.1_510

value: TGSA

tag: technical control

tag: reference rna

tag: solvent control

tag: i5 index_id

value: GCAGATGCA


title: BTUM_0.1_509

value: BTUM

tag: dose

tag: treatment

value: F

value: AGCAAGGTC

tag: cas-rn

tag: iupac name


title: RGC077

description: Retinal ganglion cells, scRNA-seq

tag: cell type

tag: tissue

tag: strain

tag: age


title: RGC089

description: Retinal ganglion cells, scRNA-seq


title: TGSA_0.01_502

tag: cell line

tag: batch

tag: well

tag: i7 index_id

value: GGGTTGTTA


title: BPC_0.1_506

tag: chemical

value: BPC

tag: chemical long_name

value: BPC (Bisphenol C)

value: Plate 2C index E

tag: sequencing pool

tag: index

value: GAACTGTAT

value: ACAACCATC


title: BPA_0.01_504

value: breast cancer

value: BPA

tag: technical control

tag: reference rna

tag: solvent control

tag: i5 index_id

value: AAGTAGGCT


title: BPAP_0.1_505

value: adenocarcinoma cell line

value: BPAP

value: BPAP (Bisphenol AP)

tag: dose

tag: treatment

value: GTGCATTAG

tag: cas-rn

tag: iupac name


title: BPAF_0.01_500

tag: tissue

tag: cell type

value: BPAF

value: BPAF (Bisphenol AF)

value: TTCCGAATT


title: RGC091

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: BPS-MPE_0.01_503

tag: cell line

value: BPS-MPE

tag: batch

value: F

tag: well

tag: i7 index_id

value: GGGTTGTTA

value: TAACGCGTC


title: HFD #2 [ANg1.5]

city: Boston

first: Aneesh

last: Bapat

state: Massachusetts

address: 55 Fruit Street

department: CVRC

country: USA

institute: Massachusetts General Hospital

data_processing:
Fastqc used to determine: the per base sequence quality, the per base sequence content, per base N content, sequence length distribution, adapter and k-mer content and sequence duplication levels.
Fastqs alined to mouse genome using STAR aligner.
Alignment bam files indexed to view on Integrative Genome Viewer.
Reads annotated with ENSEML 79 gene transfer file using Salmon.
R package DESeq2 used for differential gene expression analysis.
Assembly: ENSEMBL
Supplementary files format and content: Tab delimited txt file

source_name: Atria

growth_protocol: WT (C57/Bl6) mice were fed either high fat diet (HFD) or control chow starting at 6 weeks of age.

extract_protocol:
RNA was extracted using the Qiagen Rneasy Mini Kit.
NEBNext Ultra RNA Directional Library Prep kit for Illumina

treatment_protocol: Feeding was continued for 10 weeks total, and then right and left atrial tissue were extracted for RNA.

value: Atria

tag: genotype

value: Control chow

tag: time

value: 10 weeks


title: BTUM_0.01_501

value: breast cancer

value: adenocarcinoma cell line

tag: chemical

value: BTUM

tag: chemical long_name

value: Plate 2C index E

tag: sequencing pool

tag: technical control

tag: reference rna

tag: index

value: AGCAAGGTC


title: HFD #3 [ANg1.6]

tag: treatment


title: DCDPS_0.1_507

tag: tissue

value: DCDPS

value: Bis (4-chorophenyl) Sulfone

tag: dose

tag: solvent control

value: GAACTGTAT

tag: i5 index_id

value: AAACACCTT

tag: cas-rn

tag: iupac name


title: HFD #1 [ANg1.4]


title: RGC092

description: Retinal ganglion cells, scRNA-seq

tag: cell type

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: RGC087

description: Retinal ganglion cells, scRNA-seq


title: BPC_0.01_498

tag: cell line

value: BPC

value: BPC (Bisphenol C)

tag: batch

value: F

tag: well

tag: i7 index_id

value: GGGTTGTTA

value: ACAACCATC


title: DCDPS_0.01_499

value: breast cancer

tag: chemical

tag: chemical long_name

tag: sequencing pool

tag: technical control


title: BPAP_0.01_497

tag: tissue

value: adenocarcinoma cell line

value: BPAP

value: BPAP (Bisphenol AP)

tag: treatment

tag: reference rna

tag: index

value: GTGCATTAG


title: BPA_0.001_496

value: BPA

tag: dose

value: Plate 2C index E

tag: solvent control

value: AAGACTCTT

tag: i5 index_id

value: AAGTAGGCT

tag: cas-rn


title: Control diet #3 [ANg1.3]

value: Atria

tag: genotype

value: High fat diet

tag: time

value: 10 weeks


title: RGC012

description: Retinal ganglion cells, scRNA-seq

tag: cell type

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: BTUM_0.001_493

tag: cell line

tag: chemical

value: BTUM

tag: batch

value: F

tag: well

tag: i7 index_id

value: AGCAAGGTC

tag: iupac name


title: TGSA_0.001_494

tag: tissue

value: breast cancer

value: adenocarcinoma cell line

value: TGSA

tag: chemical long_name

tag: treatment

tag: sequencing pool

tag: technical control

tag: reference rna

value: GCAGATGCA


title: RGC011

description: Retinal ganglion cells, scRNA-seq


title: BPS-MPE_0.001_495

value: BPS-MPE

tag: dose

tag: solvent control

tag: index

tag: i5 index_id

value: TAACGCGTC

tag: cas-rn


title: Control diet #2 [ANg1.2]

tag: genotype

tag: time


title: RGC093

description: Retinal ganglion cells, scRNA-seq

tag: cell type

tag: strain

tag: age


title: RGC004

description: Retinal ganglion cells, scRNA-seq


title: DCDPS_0.001_491

tag: cell line

tag: chemical

value: DCDPS

value: Bis (4-chorophenyl) Sulfone

tag: batch

value: Plate 2C index E

tag: well

tag: i7 index_id

value: AAGACTCTT

value: AAACACCTT

tag: iupac name


title: RGC013

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

tag: tissue


title: BPAP_0.001_489

value: BPAP

tag: chemical long_name

value: BPAP (Bisphenol AP)

tag: dose

tag: treatment

tag: sequencing pool

tag: technical control

tag: reference rna

value: GTGCATTAG


title: BPC_0.001_490

value: BPC

value: BPC (Bisphenol C)

value: F

tag: solvent control

tag: index

tag: i5 index_id

value: ACAACCATC

tag: cas-rn


title: RGC005

description: Retinal ganglion cells, scRNA-seq

tag: cell type

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: BPA_0.0005_488

value: breast cancer

tag: cell line

value: adenocarcinoma cell line

tag: chemical

value: BPA

tag: batch

tag: well

value: TCCTCAGCC

value: AAGTAGGCT


title: SAMHD1 Sting dKO macrophages 2

data_processing:
pBWA version 0.5.9-r32-MPI-patch2 against mm9
Reads per exon were computed using bedtools version 2.16.2, summarized per gene based on Ensembl Gene 61 annotation.
The raw counts (absolute number of reads) were normalized with the DESeq R package (v.1.6.1) and sample to sample correlation (Pearson's correlation coefficient) was computed based on the normalized counts.
Assembly: mm9 (UCSC)
Supplementary files format and content: tab delimited file with sample size normalized counts per gene (rows) and sample (columns)

extract_protocol:
Poly-dT-enrichment, DNAse treatment, chemical fragmentation, ss-Synthesis, strand specific library prep according to: Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 2009 Jul 20. doi:10.1093/nar/gkp596
Strand specific RNA-Seq

tag: Sex

value: Female

tag: genotype


title: TGSA_0.0005_486

tag: tissue

value: TGSA

tag: chemical long_name

tag: dose

tag: treatment

value: Plate 2C index E

tag: i7 index_id

value: GCAGATGCA

tag: iupac name


title: BPAF_0.001_492

value: BPAF

value: BPAF (Bisphenol AF)

tag: sequencing pool

tag: technical control

tag: reference rna

tag: solvent control

tag: index

value: AAGACTCTT

tag: i5 index_id

value: TTCCGAATT


title: RGC086

description: Retinal ganglion cells, scRNA-seq

tag: cell type

value: Retinal ganglion cells

tag: strain

tag: age


title: SAMHD1 Cardif dKO macrophages 2

tag: Sex


title: RGC014

description: Retinal ganglion cells, scRNA-seq


title: SAMHD1 Cardif dKO macrophages 1

value: Male

tag: genotype


title: No cells; media only_0_480

tag: tissue

tag: cell line

tag: chemical

value: No cells; media only

value: No cells; media only_0

tag: batch

value: Plate 1C index F

value: T

value: F

tag: well

value: GATAGCGGA

tag: cas-rn


title: SAMHD1 Cardif dKO macrophages 3


title: Control diet #1 [ANg1.1]

value: Atria

tag: treatment

value: High fat diet

tag: time

value: 10 weeks


title: BPC_0.0005_482

value: breast cancer

value: adenocarcinoma cell line

value: BPC

tag: chemical long_name

value: BPC (Bisphenol C)

tag: dose

value: Plate 2C index E

tag: sequencing pool

tag: technical control

tag: reference rna

tag: i7 index_id

value: TCCTCAGCC

value: ACAACCATC

tag: iupac name


title: RGC007

description: Retinal ganglion cells, scRNA-seq

tag: cell type

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: BPS-MPE_0.0005_487

tag: tissue

tag: cell line

value: BPS-MPE

tag: solvent control

tag: index

tag: i5 index_id

value: TAACGCGTC


title: SAMHD1 Sting dKO macrophages 1

tag: Sex

value: Female

tag: genotype


title: BPAP_0.0005_481

tag: chemical

value: BPAP

tag: chemical long_name

value: BPAP (Bisphenol AP)

tag: treatment

tag: batch

value: F

tag: well

value: GTGCATTAG

tag: cas-rn


title: BPAF_0.0005_484

value: breast cancer

value: BPAF

value: BPAF (Bisphenol AF)

tag: dose

tag: sequencing pool

tag: technical control

tag: reference rna

tag: i7 index_id

value: TTCCGAATT

tag: iupac name


title: SAMHD1 macrophages 2

tag: strain

tag: age


title: DCDPS_0.0005_483

tag: tissue

tag: cell line

tag: cell type

value: adenocarcinoma cell line

value: DCDPS

value: Bis (4-chorophenyl) Sulfone

value: Plate 2C index E

tag: solvent control

tag: index

tag: i5 index_id

value: AAACACCTT


title: RGC167

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

value: 7-9 weeks old


title: SAMHD1 Sting dKO macrophages 3

tag: Sex

value: Female

tag: genotype


title: No cells; Universal human +ve control_0_477

tag: chemical

value: No cells; Universal human +ve control

tag: chemical long_name

tag: treatment

value: No cells; Universal human +ve control_0

tag: batch

value: Plate 1C index F

value: T

tag: well

value: GATAGCGGA

value: AGCAAGGTC

tag: cas-rn


title: SAMHD1 macrophages 1


title: RGC168

description: Retinal ganglion cells, scRNA-seq


title: BTUM_0.0005_485

value: breast cancer

value: BTUM

tag: dose

tag: sequencing pool

tag: technical control

value: F

tag: reference rna

tag: i7 index_id

value: TCCTCAGCC

tag: iupac name


title: RGC176

description: Retinal ganglion cells, scRNA-seq

tag: cell type

tag: tissue

tag: strain

tag: age


title: DMSO_473

tag: cell line

value: adenocarcinoma cell line

value: DMSO Pool 2

value: DMSO 0.1%

value: DMSO

tag: solvent control

tag: index

tag: i5 index_id

value: GTGCATTAG


title: wt macrophages 3

tag: Sex

tag: genotype

value: WT


title: Cells, no treatment_0_472

tag: chemical

value: Cells, no treatment

tag: chemical long_name

value: cells, no treatment

tag: treatment

value: Cells, no treatment_0

tag: batch

tag: well

value: AGCCGATTA

value: AAGTAGGCT

tag: cas-rn


title: RGC169

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

value: 7-9 weeks old


title: RGC006

description: Retinal ganglion cells, scRNA-seq


title: 17B-estradiol_10000_470

value: breast cancer

tag: dose

value: Plate 1C index F

tag: sequencing pool

tag: technical control

tag: reference rna

tag: i7 index_id

value: GCAGATGCA

tag: iupac name


title: No cells; Brain +ve control_0_478

tag: tissue

tag: cell line

tag: cell type

value: adenocarcinoma cell line

value: No cells; Brain +ve control

value: No cells; Brain +ve control_0

value: T

tag: solvent control

value: F

value: GATAGCGGA


title: SAMHD1 macrophages 3

tag: strain

tag: age

tag: Sex

value: Female

tag: genotype


title: 17B-estradiol_1000_469

tag: chemical

tag: chemical long_name

tag: treatment

tag: batch

tag: index

tag: i5 index_id

value: AGCAAGGTC


title: DMSO_475

value: DMSO Pool 2

value: DMSO 0.1%

tag: dose

value: DMSO

tag: sequencing pool

tag: technical control

tag: reference rna

tag: well

value: AAACACCTT

tag: cas-rn


title: wt macrophages 1

value: WT


title: Cells, no treatment_0_471

tag: tissue

tag: cell line

tag: cell type

value: Cells, no treatment

value: cells, no treatment

value: Cells, no treatment_0

tag: solvent control

tag: i7 index_id

value: AGCCGATTA

value: TAACGCGTC

tag: iupac name


title: RGC175

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: No cells; 1X Lysis buffer_0_479

value: breast cancer

value: adenocarcinoma cell line

tag: chemical

value: No cells; 1X Lysis buffer

tag: chemical long_name

tag: treatment

value: No cells; 1X Lysis buffer_0

tag: batch

value: Plate 1C index F

value: T

value: F


title: RGC170

description: Retinal ganglion cells, scRNA-seq


title: RGC171

description: Retinal ganglion cells, scRNA-seq


title: wt macrophages 2

tag: Sex

value: Female

tag: genotype


title: DMSO_474

value: DMSO Pool 2

value: DMSO 0.1%

tag: dose

value: DMSO

tag: sequencing pool

tag: technical control

tag: reference rna

tag: index

value: GATAGCGGA

tag: i5 index_id

value: ACAACCATC


title: 17B-estradiol_1_466

tag: tissue

tag: cell line

tag: cell type

tag: solvent control

tag: well

value: AGCCGATTA

tag: cas-rn


title: BPS-MAE_100_464

tag: chemical

value: BPS-MAE

tag: chemical long_name

tag: i7 index_id

value: ACCTGAGGC

value: AAGTAGGCT

tag: iupac name


title: 17B-estradiol_0.1_465

value: breast cancer

tag: treatment

tag: batch

value: GTGCATTAG


title: 2,4-BPS_100_463

value: adenocarcinoma cell line

tag: dose

tag: sequencing pool

value: TAACGCGTC


title: 17B-estradiol_10_467

value: Plate 1C index F

tag: technical control

tag: reference rna

value: AAACACCTT


title: RGC172

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: CT7_8

city: Nedlands

first: Caitlin

middle: M

last: Tilsed

state: WA

address: 6 Verdun St

country: Australia

institute: NCARD,UWA

data_processing:
read alignment with Kallisto
count quantification with tximport
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: count matrix with counts generated from txi import on kallisto aligned samples

source_name: AB1-HA tumor

growth_protocol: subcutaneous tumor growth

extract_protocol:
Frozen tumour dissociation with Trizol followed by chloroform extraction and purification using RNeasy MinElute
Illumina 50bp single-end sequencing

treatment_protocol: 200 mg/kg cyclophosphamide on day 10. Surgery was performed to excise analysed tumor on day 9, day 13 or day 17.

tag: tissue

value: tumor

value: BALB/c

value: 8-10 weeks

tag: gender

value: m

tag: response

value: CR

tag: timepoint


title: RGC173

description: Retinal ganglion cells, scRNA-seq

tag: cell type


title: BADGE_100_460

tag: cell line

tag: chemical

value: BADGE

value: F

tag: solvent control

tag: well

tag: index

tag: i5 index_id

value: TTCCGAATT

tag: cas-rn


title: DMSO_476

value: breast cancer

value: DMSO Pool 2

tag: chemical long_name

value: DMSO 0.1%

tag: dose

tag: treatment

value: DMSO

tag: batch

tag: sequencing pool

value: T

tag: i7 index_id

value: GATAGCGGA

tag: iupac name


title: CT7_7

tag: tissue

tag: strain

tag: age

tag: gender

tag: response

value: PR


title: Pergafast201_100_462

tag: cell line

tag: cell type

value: adenocarcinoma cell line

tag: chemical

value: Pergafast 201

value: Plate 1C index F

tag: technical control

tag: reference rna

tag: solvent control

value: ACCTGAGGC

value: GCAGATGCA


title: RGC164

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

value: 7-9 weeks old


title: 17B-estradiol_100_468

tag: chemical long_name

tag: dose

value: F

tag: well

tag: index

value: AGCCGATTA

tag: i5 index_id

tag: cas-rn


title: CT7_6

tag: tissue

value: tumor

value: BALB/c

value: 8-10 weeks

value: m

value: CR

tag: timepoint


title: RGC165

description: Retinal ganglion cells, scRNA-seq

tag: strain

tag: age


title: CT7_9

tag: gender

tag: response


title: BPS_100_459

value: breast cancer

tag: cell line

tag: cell type

value: BPS

value: Bisphenol S

tag: treatment

tag: batch

tag: sequencing pool

tag: i7 index_id

value: AAACACCTT

tag: iupac name


title: RGC166

description: Retinal ganglion cells, scRNA-seq


title: D-8_100_458

value: adenocarcinoma cell line

tag: chemical

tag: chemical long_name

tag: dose

value: Plate 1C index F

tag: technical control

tag: reference rna

tag: solvent control

tag: well

value: ACAACCATC


title: CT7_10

tag: tissue

tag: strain

tag: age

value: PR

tag: timepoint


title: 2,4-BPS_50_455

tag: cell line

tag: cell type

tag: index

value: TAGCGACAA

tag: i5 index_id

value: TAACGCGTC

tag: cas-rn


title: BPS-MAE_50_456

value: BPS-MAE

tag: treatment

tag: batch

tag: sequencing pool

value: F

tag: i7 index_id

value: AAGTAGGCT

tag: iupac name


title: RGC174

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

value: 7-9 weeks old


title: 4,4-BPF_100_457

tag: chemical

tag: chemical long_name

value: 4,4-BPF (Bisphenol F)

tag: dose

tag: technical control

tag: reference rna

value: ACCTGAGGC

value: GTGCATTAG


title: BADGE_50_452

tag: tissue

value: breast cancer

value: BADGE

tag: solvent control

tag: well

value: TTCCGAATT


title: CT7_4

value: tumor

tag: strain

value: BALB/c

tag: age

value: 8-10 weeks

tag: gender

value: m

tag: response

value: CR

tag: timepoint


title: CT7_2


title: BPS_50_451

tag: cell line

tag: cell type

value: adenocarcinoma cell line

value: BPS

value: Bisphenol S

tag: treatment

tag: batch

value: Plate 1C index F

tag: index

value: TAGCGACAA

tag: i5 index_id

value: AAACACCTT

tag: cas-rn


title: RGC177

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

value: 7-9 weeks old


title: RGC178

description: Retinal ganglion cells, scRNA-seq


title: 2,4-BPF_50_453

value: breast cancer

tag: chemical

tag: chemical long_name

value: 2,4-BPF (BPF Analog)

tag: dose

tag: sequencing pool

tag: technical control

value: F

tag: i7 index_id

value: AGCAAGGTC

tag: iupac name


title: CT7_3

tag: tissue

value: tumor

tag: strain

value: BALB/c

tag: age

tag: gender


title: 2,4-BPF_100_461

tag: cell line

tag: cell type

tag: reference rna

tag: solvent control

tag: well

value: ACCTGAGGC


title: RGC179

description: Retinal ganglion cells, scRNA-seq


title: BPS-MAE_10_448

value: BPS-MAE

tag: treatment

tag: batch

tag: index

value: GCTATCGAT

tag: i5 index_id

value: AAGTAGGCT

tag: cas-rn


title: D-8_50_450

value: adenocarcinoma cell line

tag: chemical

tag: chemical long_name

tag: dose

tag: sequencing pool

tag: technical control

value: ACAACCATC


title: CT7_1

tag: tissue

tag: strain

tag: age

value: 8-10 weeks

value: m

tag: response

value: PR

tag: timepoint


title: RGC180

description: Retinal ganglion cells, scRNA-seq

tag: cell type

value: Retinal ganglion cells

value: Retina


title: CT3_10

tag: gender

value: CR


title: CT7_5


title: 2,4-BPS_10_447

value: breast cancer

tag: cell line

tag: treatment

value: Plate 1C index F

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

value: TAACGCGTC

tag: iupac name


title: RGC181

description: Retinal ganglion cells, scRNA-seq

value: 7-9 weeks old


title: Pergafast201_50_454

tag: chemical

tag: chemical long_name

value: Pergafast 201

tag: dose

tag: batch

value: F

tag: index

value: TAGCGACAA

tag: i5 index_id

value: GCAGATGCA

tag: cas-rn


title: Pergafast201_10_446

tag: tissue

tag: sequencing pool

tag: technical control

value: GCTATCGAT


title: 2,4-BPF_10_445

tag: cell line

tag: cell type

value: adenocarcinoma cell line

value: 2,4-BPF (BPF Analog)

value: AGCAAGGTC


title: BADGE_10_444

value: BADGE

tag: treatment

tag: reference rna

value: TTCCGAATT


title: CT3_8

value: tumor

tag: strain

value: BALB/c

tag: age

value: 8-10 weeks

tag: gender

value: m

tag: response

tag: timepoint


title: BPS_10_443

value: breast cancer

tag: chemical

value: BPS

tag: chemical long_name

value: Bisphenol S

tag: dose

value: Plate 1C index F

tag: solvent control

tag: well

tag: i7 index_id

value: AAACACCTT

tag: iupac name


title: RGC462

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

tag: tissue

value: Retina

value: 7-9 weeks old


title: D-8_10_442

tag: cell line

value: adenocarcinoma cell line

tag: batch

tag: sequencing pool

tag: technical control

value: F

tag: index

value: GCTATCGAT

tag: i5 index_id

value: ACAACCATC

tag: cas-rn


title: 4,4-BPF_10_441

tag: cell type

value: 4,4-BPF (Bisphenol F)

tag: treatment

tag: reference rna

value: GTGCATTAG


title: 4,4-BPF_50_449

tag: chemical

tag: chemical long_name

value: TAGCGACAA


title: BPS-MAE_5_440

value: BPS-MAE

tag: dose

tag: solvent control

value: ATTGGTTGC

value: AAGTAGGCT


title: RGC464

description: Retinal ganglion cells, scRNA-seq

tag: strain

tag: age


title: 2,4-BPF_5_437

tag: tissue

value: breast cancer

value: 2,4-BPF (BPF Analog)

tag: well

tag: i7 index_id

value: AGCAAGGTC

tag: iupac name


title: CT3_6

value: tumor

value: BALB/c

value: 8-10 weeks

tag: gender

value: m

tag: response

value: PR

tag: timepoint


title: Pergafast201_5_438

tag: cell line

value: adenocarcinoma cell line

value: Pergafast 201

tag: batch

value: Plate 1C index F

tag: sequencing pool

tag: technical control

value: F

tag: index

tag: i5 index_id

value: GCAGATGCA

tag: cas-rn


title: 2,4-BPS_5_439

tag: cell type

tag: chemical

tag: chemical long_name

tag: dose

tag: treatment

tag: reference rna

tag: solvent control

value: TAACGCGTC


title: CT3_7

tag: tissue

tag: strain

tag: age

tag: gender


title: BADGE_5_436

tag: cell line

value: BADGE

tag: batch

tag: well

tag: i7 index_id

value: TTCCGAATT

tag: iupac name


title: D-8_5_434

tag: sequencing pool

tag: technical control

tag: index

value: ATTGGTTGC

tag: i5 index_id

value: ACAACCATC

tag: cas-rn


title: CT3_4

tag: response

value: CR

tag: timepoint


title: BPS_5_435

value: breast cancer

tag: cell type

tag: chemical

value: BPS

tag: chemical long_name

value: Bisphenol S

tag: dose

tag: treatment

tag: reference rna

tag: solvent control

value: AAACACCTT


title: RGC463

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

tag: tissue

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: CT3_9

value: tumor

value: BALB/c

value: 8-10 weeks

tag: gender

value: m

value: PR


title: CT3_5


title: RGC182

description: Retinal ganglion cells, scRNA-seq


title: RGC460

description: Retinal ganglion cells, scRNA-seq


title: RGC466

description: Retinal ganglion cells, scRNA-seq


title: 4,4-BPF_5_433

tag: cell line

value: adenocarcinoma cell line

value: 4,4-BPF (Bisphenol F)

tag: batch

value: Plate 1C index F

tag: sequencing pool

tag: technical control

value: F

tag: well

tag: i7 index_id

value: GTGCATTAG

tag: iupac name


title: 2,4-BPS_1_431

value: breast cancer

tag: cell type

tag: chemical

tag: index

value: TGATTAAGC

tag: i5 index_id

value: TAACGCGTC

tag: cas-rn


title: CT3_2

tag: response

tag: timepoint


title: BPS-MAE_1_432

tag: tissue

value: BPS-MAE

tag: chemical long_name

tag: dose

tag: treatment

tag: reference rna

tag: solvent control

value: AAGTAGGCT


title: RGC465

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age


title: Pergafast201_1_430

tag: cell line

value: Pergafast 201

tag: batch

tag: sequencing pool

tag: technical control

tag: well

tag: i7 index_id

value: GCAGATGCA


title: 2,4-BPF_1_429

tag: cell type

tag: chemical

value: 2,4-BPF (BPF Analog)

tag: index

tag: i5 index_id

value: AGCAAGGTC

tag: cas-rn

tag: iupac name


title: BADGE_1_428

tag: tissue

value: BADGE

tag: chemical long_name

tag: dose

tag: treatment

value: TTCCGAATT


title: CT26

value: tumor

tag: strain

value: BALB/c

tag: age

value: 8-10 weeks

tag: gender

value: m

tag: response

value: PR

tag: timepoint


title: D-8_1_426

value: breast cancer

tag: cell line

value: adenocarcinoma cell line

tag: batch

value: Plate 1C index F

tag: sequencing pool

tag: technical control

value: F

tag: reference rna

tag: solvent control

tag: well

value: TGATTAAGC

value: ACAACCATC


title: BPS_1_427

tag: cell type

tag: chemical

value: BPS

value: Bisphenol S

tag: i7 index_id

tag: index

tag: i5 index_id

value: AAACACCTT

tag: cas-rn

tag: iupac name


title: 4,4-BPF_1_425

tag: tissue

tag: chemical long_name

value: 4,4-BPF (Bisphenol F)

tag: dose

tag: treatment

value: GTGCATTAG


title: RGC468

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: RGC469

description: Retinal ganglion cells, scRNA-seq


title: RGC461

description: Retinal ganglion cells, scRNA-seq


title: BPS-MAE_0.5_424

tag: cell line

value: BPS-MAE

tag: batch

tag: sequencing pool

tag: technical control

value: TCAGCTAAT

value: AAGTAGGCT


title: 2,4-BPS_0.5_423

value: breast cancer

tag: cell type

tag: reference rna

tag: solvent control

tag: well

value: TAACGCGTC


title: CT25

value: tumor

value: BALB/c

value: 8-10 weeks

tag: gender

value: m

tag: response

value: PR

tag: timepoint


title: CT3_3

tag: tissue

value: CR


title: Pergafast201_0.5_422

value: adenocarcinoma cell line

tag: chemical

tag: chemical long_name

value: Pergafast 201

value: Plate 1C index F

value: F

tag: i7 index_id

tag: index

tag: i5 index_id

value: GCAGATGCA

tag: cas-rn

tag: iupac name


title: CT24

tag: strain

tag: age


title: RGC195

description: Retinal ganglion cells, scRNA-seq

tag: cell type

value: Retinal ganglion cells

value: Retina

value: 7-9 weeks old


title: CT23


title: CT3_1


title: RGC467

description: Retinal ganglion cells, scRNA-seq


title: RGC197

description: Retinal ganglion cells, scRNA-seq


title: RGC196

description: Retinal ganglion cells, scRNA-seq


title: 2,4-BPF_0.5_421

tag: cell line

value: 2,4-BPF (BPF Analog)

tag: dose

tag: treatment

tag: batch

tag: sequencing pool

tag: technical control

tag: reference rna

value: TCAGCTAAT

value: AGCAAGGTC


title: BPS_0.5_419

tag: tissue

value: breast cancer

tag: chemical

value: BPS

value: Bisphenol S

tag: solvent control

tag: well

value: AAACACCTT


title: CT22

value: tumor

value: BALB/c

value: 8-10 weeks

tag: gender

value: m

tag: response

tag: timepoint


title: BADGE_0.5_420

value: adenocarcinoma cell line

value: BADGE

tag: chemical long_name

value: Plate 1C index F

tag: i7 index_id

tag: index

tag: i5 index_id

value: TTCCGAATT

tag: cas-rn

tag: iupac name


title: D-8_0.5_418

tag: cell line

tag: cell type

tag: dose

tag: treatment

tag: batch

value: F

value: ACAACCATC


title: 4,4-BPF_0.5_417

tag: tissue

tag: chemical

value: 4,4-BPF (Bisphenol F)

tag: sequencing pool

tag: technical control

tag: reference rna

value: GTGCATTAG


title: BPS-MAE_0.1_416

value: BPS-MAE

tag: solvent control

tag: well

value: TGCTTATTC

value: AAGTAGGCT


title: CT21

tag: strain

tag: age

tag: gender

tag: response

value: CR

tag: timepoint


title: RGC198

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

value: 7-9 weeks old


title: 2,4-BPS_0.1_415

value: breast cancer

tag: cell line

tag: chemical long_name

tag: i7 index_id

tag: index

tag: i5 index_id

value: TAACGCGTC

tag: cas-rn

tag: iupac name


title: Pergafast201_0.1_414

tag: tissue

tag: cell type

value: adenocarcinoma cell line

tag: chemical

value: Pergafast 201

tag: dose

tag: treatment

tag: batch

tag: sequencing pool

value: GCAGATGCA


title: RGC199

description: Retinal ganglion cells, scRNA-seq

tag: strain

tag: age


title: 2,4-BPF_0.1_413

value: 2,4-BPF (BPF Analog)

value: Plate 1C index F

tag: technical control

tag: reference rna

tag: solvent control

tag: well

value: AGCAAGGTC


title: CT19

value: tumor

value: BALB/c

value: 8-10 weeks

tag: gender

value: m

tag: response

tag: timepoint


title: CT18


title: BPS_0.1_411

tag: cell line

value: BPS

tag: chemical long_name

value: Bisphenol S

value: F

tag: i7 index_id

tag: index

value: TGCTTATTC

tag: i5 index_id

value: AAACACCTT

tag: cas-rn

tag: iupac name


title: BADGE_0.1_412

tag: tissue

value: breast cancer

tag: cell type

tag: chemical

value: BADGE

tag: dose

tag: treatment

tag: batch

tag: sequencing pool

value: TTCCGAATT


title: RGC200

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: RGC201

description: Retinal ganglion cells, scRNA-seq


title: CT17

tag: gender

tag: response

value: PR

tag: timepoint


title: BPS-MAE_0.01_408

tag: cell line

value: adenocarcinoma cell line

value: BPS-MAE

tag: chemical long_name

value: Plate 1C index F

tag: technical control

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

value: ATTCGAATC

value: AAGTAGGCT


title: CT16

tag: tissue

value: tumor

value: BALB/c

value: 8-10 weeks

value: m


title: 4,4-BPF_0.1_409

tag: cell type

tag: chemical

value: 4,4-BPF (Bisphenol F)

tag: dose

value: F

tag: index

value: TGCTTATTC

tag: i5 index_id

value: GTGCATTAG

tag: cas-rn

tag: iupac name


title: RGC187

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

tag: strain

tag: age


title: RGC188

description: Retinal ganglion cells, scRNA-seq

value: Retina


title: CT20

tag: gender

tag: response

value: CR

tag: timepoint


title: 2,4-BPF_0.01_405

value: breast cancer

tag: cell line

tag: chemical long_name

value: 2,4-BPF (BPF Analog)

tag: treatment

tag: batch

tag: sequencing pool

tag: technical control

tag: reference rna

value: AGCAAGGTC


title: BADGE_0.01_404

tag: tissue

tag: cell type

value: adenocarcinoma cell line

tag: chemical

value: BADGE

tag: dose

value: Plate 1C index F

tag: solvent control

tag: well

tag: i7 index_id

value: TTCCGAATT


title: BPS_0.01_403

value: BPS

value: Bisphenol S

tag: index

value: ATTCGAATC

tag: i5 index_id

value: AAACACCTT

tag: cas-rn

tag: iupac name


title: CT15

value: tumor

tag: strain

value: BALB/c

tag: age

value: 8-10 weeks

tag: gender

value: m

tag: response

value: PR

tag: timepoint


title: 2,4-BPS_0.01_407

tag: cell line

tag: chemical long_name

tag: treatment

tag: batch

tag: sequencing pool

tag: technical control

value: F

tag: reference rna

value: TAACGCGTC


title: D-8_0.01_402

tag: tissue

value: breast cancer

tag: cell type

tag: chemical

tag: dose

tag: solvent control

tag: well

tag: i7 index_id

value: ACAACCATC


title: CT14

tag: strain

tag: age

tag: gender

value: CR


title: 4,4-BPF_0.01_401

tag: cell line

value: adenocarcinoma cell line

value: 4,4-BPF (Bisphenol F)

tag: index

tag: i5 index_id

value: GTGCATTAG

tag: cas-rn

tag: iupac name


title: CT13

tag: response

tag: timepoint


title: BPS-MAE_0.001_400

tag: tissue

value: BPS-MAE

tag: chemical long_name

tag: treatment

tag: batch

value: Plate 1C index F

tag: sequencing pool

tag: technical control

tag: reference rna

value: ATCGCGACT

value: AAGTAGGCT


title: D-8_0.1_410

tag: cell type

tag: chemical

tag: dose

tag: solvent control

tag: well

tag: i7 index_id

value: TGCTTATTC


title: Pergafast201_0.01_406

tag: cell line

value: Pergafast 201

tag: index

value: ATTCGAATC

tag: i5 index_id

value: GCAGATGCA

tag: cas-rn


title: RGC190

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

tag: tissue

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: RGC183

description: Retinal ganglion cells, scRNA-seq


title: RGC189

description: Retinal ganglion cells, scRNA-seq


title: Pergafast201_0.001_398

value: breast cancer

tag: chemical long_name

tag: treatment

tag: batch

value: F

tag: iupac name


title: CT12

value: tumor

value: BALB/c

value: 8-10 weeks

tag: gender

value: m

tag: response

value: PR

tag: timepoint


title: RGC184

description: Retinal ganglion cells, scRNA-seq

tag: cell type


title: 2,4-BPS_0.001_399

value: adenocarcinoma cell line

tag: chemical

tag: dose

value: Plate 1C index F

tag: sequencing pool

tag: technical control

tag: reference rna

tag: solvent control

tag: well

value: TAACGCGTC


title: CT11

tag: tissue

tag: strain

value: CR


title: RGC191

description: Retinal ganglion cells, scRNA-seq

tag: age


title: BPS_0.001_395

tag: cell line

value: BPS

tag: chemical long_name

value: Bisphenol S

tag: treatment

tag: i7 index_id

tag: index

value: ATCGCGACT

tag: i5 index_id

value: AAACACCTT

tag: cas-rn


title: 2,4-BPF_0.001_397

tag: cell type

tag: chemical

value: 2,4-BPF (BPF Analog)

tag: batch

value: AGCAAGGTC

tag: iupac name


title: BADGE_0.001_396

value: breast cancer

value: BADGE

tag: dose

tag: sequencing pool

tag: technical control

tag: reference rna

value: TTCCGAATT


title: D-8_0.001_394

tag: tissue

value: F

tag: solvent control

tag: well

value: ACAACCATC


title: CT10

value: tumor

tag: strain

value: BALB/c

tag: age

value: 8-10 weeks

tag: gender

value: m

tag: response

tag: timepoint


title: RGC185

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

value: 7-9 weeks old


title: CT9

value: PR


title: 4,4-BPF_0.001_393

tag: cell line

value: adenocarcinoma cell line

tag: chemical long_name

value: 4,4-BPF (Bisphenol F)

tag: treatment

value: Plate 1C index F

tag: i7 index_id

tag: index

value: ATCGCGACT

tag: i5 index_id

value: GTGCATTAG

tag: cas-rn


title: Pergafast201_0.0005_390

value: breast cancer

tag: cell type

tag: chemical

value: Pergafast 201

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

value: TGGAACGCT

value: GCAGATGCA

tag: iupac name


title: CT8

tag: tissue

value: tumor

tag: strain

tag: age

tag: gender

value: CR


title: RGC470

description: Retinal ganglion cells, scRNA-seq


title: BPS-MAE_0.0005_392

tag: cell line

value: BPS-MAE

tag: chemical long_name

value: F

tag: reference rna

tag: solvent control

tag: well

value: AAGTAGGCT


title: RGC186

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina


title: CT5

value: BALB/c

value: 8-10 weeks

value: m

tag: response

value: PR

tag: timepoint


title: D-8_0.0005_386

tag: cell type

value: adenocarcinoma cell line

tag: chemical

tag: treatment

value: Plate 1C index F

tag: i7 index_id

tag: index

tag: i5 index_id

value: ACAACCATC

tag: cas-rn


title: 2,4-BPS_0.0005_391

tag: tissue

value: breast cancer

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

value: TAACGCGTC

tag: iupac name


title: RGC192

description: Retinal ganglion cells, scRNA-seq

tag: strain

tag: age

value: 7-9 weeks old


title: 4,4-BPF_0.0005_385

tag: cell line

tag: chemical long_name

value: 4,4-BPF (Bisphenol F)

tag: reference rna

tag: solvent control

tag: well

value: TGGAACGCT

value: GTGCATTAG


title: CT7

value: tumor

tag: gender

tag: response

value: CR

tag: timepoint


title: BADGE_0.0005_388

tag: cell type

tag: chemical

value: BADGE

tag: treatment

value: F

tag: i7 index_id

tag: index

tag: i5 index_id

value: TTCCGAATT

tag: cas-rn


title: 2,4-BPF_0.0005_389

tag: tissue

value: 2,4-BPF (BPF Analog)

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

value: AGCAAGGTC

tag: iupac name


title: CT6

tag: strain

value: BALB/c

tag: age

value: 8-10 weeks

value: m

value: PR


title: RGC193

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina


title: RGC194

description: Retinal ganglion cells, scRNA-seq

value: 7-9 weeks old


title: No cells; 1X Lysis buffer_0_383

value: breast cancer

tag: cell line

value: adenocarcinoma cell line

value: No cells; 1X Lysis buffer

tag: chemical long_name

value: No cells; 1X Lysis buffer_0

value: Plate 2B index H

value: T

tag: reference rna

tag: solvent control

tag: well

value: GATAGCGGA

value: CGTAACTTA


title: No cells; media only_0_384

tag: cell type

tag: chemical

value: No cells; media only

tag: treatment

value: No cells; media only_0

value: F

tag: i7 index_id

value: GGTCTAGCT


title: No cells; Brain +ve control_0_382

tag: tissue

value: No cells; Brain +ve control

value: No cells; Brain +ve control_0

tag: index

tag: i5 index_id

value: ATACCGGCA

tag: cas-rn


title: DMSO_379

value: DMSO Pool 1

value: DMSO 0.1%

tag: dose

value: DMSO

tag: batch

tag: sequencing pool

tag: technical control

value: GCCGTTACA


title: RGC203

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: CT3

value: tumor

value: BALB/c

value: 8-10 weeks

tag: gender

value: m

tag: response

value: CR

tag: timepoint


title: CT2

value: PR


title: DMSO_378

value: breast cancer

tag: cell line

tag: cell type

value: adenocarcinoma cell line

tag: chemical long_name

value: Plate 2B index H

value: F

tag: reference rna

tag: solvent control

value: T

tag: well

value: GATAGCGGA

value: ATACGCAGC

tag: iupac name


title: BPS_0.0005_387

tag: tissue

tag: chemical

value: BPS

value: Bisphenol S

tag: treatment

value: Plate 1C index F

tag: i7 index_id

tag: index

value: TGGAACGCT

tag: i5 index_id

value: AAACACCTT

tag: cas-rn


title: DMSO_377

value: DMSO Pool 1

value: DMSO 0.1%

tag: dose

value: DMSO

tag: batch

tag: sequencing pool

tag: technical control

value: TCTAACCAT


title: CT1

value: tumor

tag: strain

value: BALB/c

tag: age

value: 8-10 weeks

tag: gender

value: m

tag: response

value: PR

tag: timepoint


title: CT4


title: RGC215

description: Retinal ganglion cells, scRNA-seq

tag: cell type

value: Retinal ganglion cells

value: Retina

value: 7-9 weeks old


title: 4287_11C_S18

city: Fukuoka

first: Yasuhiro

last: Nakashima

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Medicine and Bioregulatory Science

institute: Kyushu University

description: processed data file: S7.txt

data_processing:
Raw sequence reads were trimmed for adapters using Trim Galore (v.0.6.7).
Sequences were mapped to the GRCh38 reference genome sequence using HISAT2 (v2.2.1) with default parameters.
Read counts per gene were calculated using featureCounts with -M --fraction parameters.
UMI counts per gene were calculated using UMI-Tools (v1.1.1) with count --method=directional --log2stderr --per-gene --per-cell --gene-tag=XT parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file includes mRNA molecule count value for each sample.

molecule: polyA RNA

source_name: Bone marrow aspiration

extract_protocol:
Mononuclear cells were isolated from bone marrow aspirates using density centrifugation media, and stored at -80℃. After staining with CD38, CD45, CD19, and CD138, Single cell sort of MM cells was performed in 384 well plates using FACS.
Libraries were prepared according to the CEL-Seq2 protocol. Briefly, mRNA from cells sorted into 384-well plates was reverse-transcribed into complementary DNA, with which 12-well samples were pooled. The pooled samples were then amplified by T7 in vitro transcription, and the amplified RNA was fragmented and used to construct final libraries by reverse transcription and PCR amplification. Every PCR product is uniquely labeled by random attachment of barcode sequences to both ends. The libraries were sequenced on Illumina HiSeq 1500 sequencers and the reads were mapped to the GRCh38 human reference genome assembly using HISAT2 (v. 2.2.1).

tag: organ

value: Bone marrow

value: Myeloma cells

tag: selection marker

tag: time point

tag: disease stage

value: Relapse


title: Dex_100_372

tag: tissue

value: breast cancer

tag: cell line

value: adenocarcinoma cell line

tag: chemical

value: Dex

tag: chemical long_name

tag: treatment

value: Plate 2B index H

value: F

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

tag: index

value: AGCCGATTA

value: GCACCTATT

tag: iupac name


title: RGC216

description: Retinal ganglion cells, scRNA-seq

tag: strain

tag: age


title: Cells, no treatment_0_374

tag: cell type

value: Cells, no treatment

value: cells, no treatment

tag: dose

value: Cells, no treatment_0

tag: batch

tag: sequencing pool

tag: technical control

value: T

tag: i5 index_id

value: ATACCGGCA

tag: cas-rn


title: 4287_11A_S17

description: processed data file: S7.txt

tag: organ

tag: selection marker

tag: time point

tag: disease stage


title: RGC217

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

tag: tissue

value: Retina


title: Dex_1_370

tag: cell line

tag: chemical

tag: chemical long_name

tag: treatment

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

value: ATACGCAGC


title: 4287_5O_plus_6O_S16

description: processed data file: S7.txt

value: Bone marrow

tag: cell type

value: Myeloma cells


title: RGC218

description: Retinal ganglion cells, scRNA-seq

tag: strain

tag: age

value: 7-9 weeks old


title: DMSO_380

value: breast cancer

value: adenocarcinoma cell line

value: DMSO Pool 1

value: DMSO 0.1%

tag: dose

value: DMSO

tag: batch

tag: sequencing pool

tag: technical control

tag: index

value: GATAGCGGA

tag: i5 index_id

tag: cas-rn

tag: iupac name


title: RGC202

description: Retinal ganglion cells, scRNA-seq

tag: tissue


title: Dex_0.1_369

tag: cell line

tag: chemical

value: Dex

tag: chemical long_name

tag: treatment

value: Plate 2B index H

value: F

value: AGCCGATTA

value: TCTAACCAT


title: 4287_5M_plus_6M_S15

description: processed data file: S7.txt

tag: organ

tag: selection marker

tag: time point

tag: disease stage

value: Relapse


title: Dex_10_371

tag: cell type

tag: dose

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

value: GCCGTTACA


title: BPA_100_368

value: BPA

tag: batch

tag: sequencing pool

tag: technical control

tag: index

value: ACCTGAGGC

tag: i5 index_id

value: GGTCTAGCT

tag: cas-rn


title: Dex_1000_373

tag: tissue

tag: cell line

tag: chemical

tag: chemical long_name

tag: treatment

value: GATTGTGTT

tag: iupac name


title: 4287_5K_plus_6K_S14

description: processed data file: S7.txt

tag: organ

value: Bone marrow

tag: cell type

value: Myeloma cells

tag: selection marker

tag: time point

tag: disease stage


title: RGC219

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: BPS-MPE_100_367

value: breast cancer

value: adenocarcinoma cell line

value: BPS-MPE

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

value: CGTAACTTA


title: TGSA_100_366

tag: tissue

tag: cell line

tag: chemical

value: TGSA

tag: chemical long_name

tag: treatment

value: Plate 2B index H

value: F

tag: index

tag: i5 index_id

value: ATACCGGCA

tag: cas-rn


title: RGC471

description: Retinal ganglion cells, scRNA-seq

tag: cell type

tag: strain

tag: age


title: RGC220

description: Retinal ganglion cells, scRNA-seq


title: Cells, no treatment_0_376

value: Cells, no treatment

value: cells, no treatment

tag: dose

value: Cells, no treatment_0

tag: batch

tag: sequencing pool

value: T

value: AGCCGATTA

tag: iupac name


title: Cells, no treatment_0_375

tag: technical control

tag: reference rna

tag: solvent control

tag: well


title: RGC207

description: Retinal ganglion cells, scRNA-seq

tag: tissue


title: BTUM_100_365

tag: cell line

tag: chemical

value: BTUM

tag: chemical long_name

tag: i7 index_id

value: ACCTGAGGC

value: GATTGTGTT


title: DCDPS_100_363

value: DCDPS

value: Bis (4-chorophenyl) Sulfone

tag: treatment

tag: index

tag: i5 index_id

value: GCCGTTACA

tag: cas-rn


title: BPAF_100_364

value: breast cancer

tag: cell type

value: adenocarcinoma cell line

value: BPAF

value: BPAF (Bisphenol AF)

tag: dose

value: GCACCTATT


title: RGC208

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: 4287_5G_plus_6G_S12

description: processed data file: S7.txt

tag: organ

value: Bone marrow

value: Myeloma cells

tag: selection marker

tag: time point

tag: disease stage

value: Relapse


title: BPC_100_362

tag: tissue

value: BPC

value: BPC (Bisphenol C)

tag: batch

value: Plate 2B index H

tag: sequencing pool

tag: technical control

value: F

tag: reference rna

tag: solvent control

tag: well

value: ATACGCAGC

tag: iupac name


title: 4287_5E_plus_6E_S11

description: processed data file: S7.txt


title: BPAP_100_361

tag: cell line

tag: chemical

value: BPAP

tag: chemical long_name

value: BPAP (Bisphenol AP)

tag: treatment

tag: i7 index_id

tag: index

value: ACCTGAGGC

tag: i5 index_id

value: TCTAACCAT

tag: cas-rn


title: BPA_50_360

value: breast cancer

tag: cell type

value: adenocarcinoma cell line

value: BPA

tag: dose

value: TAGCGACAA

value: GGTCTAGCT


title: 4287_5C_plus_6C_S10

description: processed data file: S7.txt

tag: organ

value: Bone marrow

tag: selection marker

tag: time point

tag: disease stage


title: BTUM_50_357

tag: tissue

value: BTUM

tag: batch

tag: sequencing pool

tag: technical control

tag: reference rna

tag: solvent control

value: GATTGTGTT


title: RGC472

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: RGC209

description: Retinal ganglion cells, scRNA-seq


title: TGSA_50_358

tag: cell line

tag: chemical

value: TGSA

tag: chemical long_name

tag: treatment

value: Plate 2B index H

value: F

tag: well

tag: i7 index_id

tag: index

value: ATACCGGCA

tag: iupac name


title: DCDPS_50_355

tag: cell type

value: DCDPS

value: Bis (4-chorophenyl) Sulfone

tag: dose

tag: i5 index_id

value: GCCGTTACA

tag: cas-rn


title: BPS-MPE_50_359

tag: tissue

value: breast cancer

value: adenocarcinoma cell line

value: BPS-MPE

tag: batch

tag: sequencing pool

tag: technical control

value: CGTAACTTA


title: RGC210

description: Retinal ganglion cells, scRNA-seq

tag: strain

tag: age


title: BPAF_50_356

tag: cell line

tag: chemical

value: BPAF

value: BPAF (Bisphenol AF)

tag: reference rna

tag: solvent control

value: TAGCGACAA

value: GCACCTATT


title: BPC_50_354

value: BPC

tag: chemical long_name

value: BPC (Bisphenol C)

tag: treatment

tag: well

tag: i7 index_id

value: ATACGCAGC


title: RGC211

description: Retinal ganglion cells, scRNA-seq

tag: cell type

value: Retinal ganglion cells

value: Retina

value: 7-9 weeks old


title: 4287_3O_plus_4O_S8

description: processed data file: S7.txt

tag: organ

value: Bone marrow

value: Myeloma cells

tag: selection marker

tag: time point

tag: disease stage

value: Relapse


title: 4287_5A_plus_6A_S9

description: processed data file: S7.txt


title: RGC204

description: Retinal ganglion cells, scRNA-seq

tag: tissue


title: BPAP_50_353

value: breast cancer

value: BPAP

value: BPAP (Bisphenol AP)

tag: dose

tag: batch

value: Plate 2B index H

tag: sequencing pool

tag: technical control

value: F

tag: index

tag: i5 index_id

value: TCTAACCAT

tag: cas-rn

tag: iupac name


title: 4287_5I_plus_6I_S13

description: processed data file: S7.txt


title: 4287_3M_plus_4M_S7

description: processed data file: S7.txt


title: BPA_10_352

tag: cell line

value: adenocarcinoma cell line

tag: chemical

value: BPA

tag: chemical long_name

tag: treatment

tag: reference rna

tag: solvent control

value: GCTATCGAT

value: GGTCTAGCT


title: BPS-MPE_10_351

tag: cell type

value: BPS-MPE

tag: well

tag: i7 index_id

value: CGTAACTTA


title: 4287_3K_plus_4K_S6

description: processed data file: S7.txt

tag: organ

tag: selection marker

tag: time point

tag: disease stage


title: TGSA_10_350

tag: tissue

value: TGSA

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

tag: index

value: ATACCGGCA


title: RGC212

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: 4287_3I_plus_4I_S5

description: processed data file: S7.txt

value: Bone marrow

value: Myeloma cells

value: Relapse


title: BTUM_10_349

value: breast cancer

tag: cell line

tag: chemical

value: BTUM

tag: chemical long_name

tag: treatment

value: Plate 2B index H

tag: reference rna

tag: i5 index_id

value: GATTGTGTT

tag: cas-rn

tag: iupac name


title: 4287_3G_plus_4G_S4

description: processed data file: S7.txt

tag: organ

tag: cell type

tag: selection marker

tag: time point

tag: disease stage


title: BPAF_10_348

tag: tissue

value: adenocarcinoma cell line

value: BPAF

value: BPAF (Bisphenol AF)

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

value: F

tag: solvent control

tag: well

tag: i7 index_id

value: GCACCTATT


title: BPC_10_346

tag: cell line

tag: chemical

value: BPC

tag: chemical long_name

value: BPC (Bisphenol C)

tag: treatment

tag: reference rna

tag: index

value: GCTATCGAT

value: ATACGCAGC


title: BPAP_10_345

tag: cell type

value: BPAP

value: BPAP (Bisphenol AP)

tag: i5 index_id

value: TCTAACCAT

tag: cas-rn

tag: iupac name


title: RGC213

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

tag: tissue

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: BPS-MPE_5_343

value: breast cancer

value: BPS-MPE

tag: dose

tag: batch

value: Plate 2B index H

tag: sequencing pool

tag: technical control

value: ATTGGTTGC

value: CGTAACTTA


title: DCDPS_10_347

tag: cell line

value: adenocarcinoma cell line

value: DCDPS

value: Bis (4-chorophenyl) Sulfone

value: F

tag: solvent control

tag: well

tag: i7 index_id

value: GCCGTTACA


title: RGC205

description: Retinal ganglion cells, scRNA-seq


title: 4287_3C_plus_4C_S2

description: processed data file: S7.txt

tag: organ

value: Bone marrow

value: Myeloma cells

tag: selection marker

tag: time point

tag: disease stage

value: Relapse


title: DCDPS_5_339

tag: cell type

tag: chemical

tag: chemical long_name

tag: treatment

tag: reference rna

tag: index

tag: i5 index_id

tag: cas-rn


title: 4287-9O-plus-10O_S24

description: processed data file: S6.txt


title: BPA_5_344

tag: tissue

value: BPA

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

value: GGTCTAGCT

tag: iupac name


title: BPAF_5_340

tag: cell line

value: BPAF

value: BPAF (Bisphenol AF)

tag: solvent control

tag: well

tag: i7 index_id

value: GCACCTATT


title: 4287_3A_plus_4A_S1

description: processed data file: S7.txt

tag: organ

tag: cell type

tag: selection marker

tag: time point

tag: disease stage


title: RGC206

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: 4287_3E_plus_4E_S3

description: processed data file: S7.txt


title: TGSA_5_342

tag: tissue

value: breast cancer

tag: chemical

value: TGSA

tag: chemical long_name

tag: treatment

value: Plate 2B index H

tag: reference rna

tag: index

value: ATTGGTTGC

tag: i5 index_id

value: ATACCGGCA

tag: cas-rn


title: BPC_5_338

tag: cell line

value: adenocarcinoma cell line

value: BPC

value: BPC (Bisphenol C)

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

value: F

tag: solvent control

tag: well

value: ATACGCAGC

tag: iupac name


title: 4287-9M-plus-10M_S23

description: processed data file: S6.txt

tag: organ

value: Bone marrow

tag: cell type

value: Myeloma cells

tag: selection marker

tag: time point

tag: disease stage

value: Relapse


title: BPA_1_336

tag: tissue

tag: chemical

value: BPA

tag: chemical long_name

tag: treatment

tag: reference rna

tag: i7 index_id

value: TGATTAAGC

value: GGTCTAGCT


title: RGC224

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: RGC214

description: Retinal ganglion cells, scRNA-seq


title: TGSA_1_334

value: breast cancer

tag: cell line

value: TGSA

tag: dose

tag: batch

value: Plate 2B index H

tag: sequencing pool

tag: technical control

tag: index

tag: i5 index_id

tag: cas-rn


title: 4287-9K-plus-10K_S22

description: processed data file: S6.txt

tag: organ

tag: cell type

tag: selection marker

tag: time point

tag: disease stage


title: RGC222

description: Retinal ganglion cells, scRNA-seq

tag: tissue


title: RGC223

description: Retinal ganglion cells, scRNA-seq


title: RGC221

description: Retinal ganglion cells, scRNA-seq


title: BPS-MPE_1_335

value: adenocarcinoma cell line

tag: chemical

value: BPS-MPE

tag: chemical long_name

tag: treatment

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

value: CGTAACTTA

tag: iupac name


title: RGC225

description: Retinal ganglion cells, scRNA-seq

tag: strain

tag: age


title: BTUM_5_341

tag: cell line

value: BTUM

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

value: F

tag: index

value: ATTGGTTGC

tag: i5 index_id

value: GATTGTGTT

tag: cas-rn


title: 4287-9G-plus-10G_S20

description: processed data file: S6.txt

tag: organ

value: Bone marrow

tag: cell type

value: Myeloma cells

tag: selection marker

tag: time point

tag: disease stage

value: Relapse


title: DCDPS_1_331

tag: tissue

tag: chemical

value: DCDPS

tag: chemical long_name

value: Bis (4-chorophenyl) Sulfone

tag: treatment

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

value: TGATTAAGC

value: GCCGTTACA


title: BTUM_1_333

value: breast cancer

tag: cell line

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

tag: iupac name


title: BPAP_5_337

tag: cell type

value: BPAP

value: BPAP (Bisphenol AP)

tag: index

tag: i5 index_id

value: TCTAACCAT

tag: cas-rn


title: RGC227

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

tag: tissue

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: BPA_0.5_328

value: adenocarcinoma cell line

tag: chemical

value: BPA

tag: chemical long_name

tag: treatment

value: Plate 2B index H

value: F

tag: reference rna

value: TCAGCTAAT

value: GGTCTAGCT


title: BPAP_1_329

tag: cell line

tag: solvent control

tag: well

tag: i7 index_id


title: 4287-9E-plus-10E_S19

description: processed data file: S6.txt

tag: organ

value: Bone marrow

value: Myeloma cells

tag: selection marker

tag: time point

tag: disease stage

value: Relapse


title: 4287-9C-plus-10C_S18

description: processed data file: S6.txt

tag: cell type


title: TGSA_0.5_326

value: TGSA

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

tag: index

tag: i5 index_id

value: ATACCGGCA

tag: cas-rn

tag: iupac name


title: BPS-MPE_0.5_327

tag: tissue

value: breast cancer

tag: cell line

tag: chemical

value: BPS-MPE

tag: chemical long_name

tag: treatment

tag: reference rna

value: CGTAACTTA


title: BPAF_0.5_324

value: BPAF

value: BPAF (Bisphenol AF)

tag: solvent control

tag: well

tag: i7 index_id

value: GCACCTATT


title: BPC_1_330

tag: cell type

value: adenocarcinoma cell line

value: BPC

value: BPC (Bisphenol C)

tag: dose

value: TGATTAAGC

value: ATACGCAGC


title: BTUM_0.5_325

value: BTUM

tag: batch

value: Plate 2B index H

tag: sequencing pool

value: F

value: TCAGCTAAT

value: GATTGTGTT


title: 4287-9A-plus-10A_S17

description: processed data file: S6.txt

tag: organ

value: Bone marrow

value: Myeloma cells

tag: selection marker

tag: time point

tag: disease stage

value: Relapse


title: BPAF_1_332

tag: tissue

value: breast cancer

tag: technical control

tag: index

tag: i5 index_id

tag: cas-rn

tag: iupac name


title: RGC230

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old