title: PA_9

description:
ACTH-secreting pituitary adenoma 9
ACTH_18_S5


title: PA_8

status: Public on Feb 17 2025

type: SRA

city: Moscow

first: Rustam

last: Heydarov

address: 8-2 Trubetskaya str.

country: Russia

institute: I.M. Sechenov First Moscow State Medical University

description:
ACTH-secreting pituitary adenoma 8
ACTH_17_S2

library_source: transcriptomic

data_processing:
Quality of the sequencing reads was assessed using FastQC
Reads were then pre-processed with Trimmomatic to remove adapters and low-quality sections
The trimmed reads were aligned to the reference genome using STAR aligner
Gene-level read counts were obtained using featureCounts from the Subread package
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: pituitary adenoma

extract_protocol:
RNA was extracted using HiPure FFPE RNA Kit (Magen)
Ribosomal RNA depletion and library construction was performed with KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche). KAPA unique dual-indexed primers (Roche) were used for multiplexing samples in a single sequencing run.

tag: tissue

value: pituitary adenoma

tag: Sex

value: Male


title: troglitazone_0.1_24h_2pool1_S188

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S188

library_source: other

data_processing:
Reads were demultiplexed from the BCL files and processed into FASTQ files using bcl2fastq v2.20.0.422.
FASTQ files were aligned to the Human Surrogate+ Tox Panel (S1500+) v2.0 probes reference sequences (provided by BioSpyder) using STAR 2.7.8a.
The qCount function from QuasR was used to extract feature counts specified in a GTF file (provided by BioSpyder) from the aligned reads.
Assembly: Human Surrogate+ Tox Panel (S1500+) v2.0 probes reference sequences (provided by BioSpyder)
Supplementary files format and content: Comma-delimited table containing read counts per TempO-Seq probe

molecule: other

source_name: liver spheroids

growth_protocol: 3D InSight™ Human Liver Microtissues were purchased from InSphero (Wagistrasse, Schlieren, Switzerland) in a 96-well plate format, with a single spheroid per well. The liver spheroids are a co-culture from ten human liver donors and include primarily hepatocytes and Kupffer cells. Upon receipt of spheroids, media were removed and replaced with fresh media (InSphero Human Liver Maintenance Medium–Tox). The Human Liver Maintenance Medium–Tox is optimized for maintenance of phase I metabolism and does not contain additives or serum. Spheroids were acclimated for 24h prior to chemical exposures.

extract_protocol:
At the 24h and 10d time points media were removed, and spheroids were washed with Dulbecco's phosphate-buffered saline (DPBS; Thermo Fisher Scientific Waltham, MA). Spheroids were lysed by adding 10 µl of 1X TempO-Seq lysis buffer (BioSpyder Technologies Inc Carlsbad, CA) to each well. To ensure complete lysis, spheroids were incubated for approximately 10 minutes at 37°C, pipetted up and down several times, and then frozen at -80 °C until library building.
Lysates and technical RNA were hybridized to the detector oligo mix following the manufacturer's instructions provided in the TEMPO-SEQ Human Tox + Surrogate with Standard Attenuation Transcriptome Kit (96 samples). This was followed by nuclease digestion to eliminate excess oligos, detector oligo ligation, and subsequent amplification of correctly ligated oligos, all performed in accordance with the manufacturer's guidelines.
During the amplification stage, each sample was linked to a sample-specific barcode, enabling the pooling of samples for sequencing purposes. Pooled samples were purified using NucleoSpin Gel and PCR clean-up kits from Takara Bio USA, Inc. (Mountain View, CA). The libraries were sequenced in-house using a NextSeq 500 High-Throughput Sequencing System (Illumina, San Diego, California), employing a 50-cycle protocol from a 75-cycle high-throughput flow cell.

treatment_protocol: Spheroids were cultured under sterile conditions with incubation at 37°C, 5% CO2 as per the manufacturer’s instructions. Liver spheroids were exposed for 24h or 10d to compounds and solvent control (0.1% DMSO or water). Culture media (containing the compounds) were replenished every 3 days. Compound exposure concentrations are in Table 1. Each concentration range was run on four parallel plates (for N = 4).

tag: cell line

value: liver spheroids

tag: chemical

value: troglitazone

tag: dose

tag: timepoint

tag: replicate


title: troglitazone_0.1_10d_1pool1_S284

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S284


title: troglitazone_0.1_10d_2pool1_S380

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S380


title: female C57BL/6J mice, DSS R89, Day89

city: Hong Kong

first: Yimeng

last: Li

address: 21 Sassoon Road, Pokfulam Hong Kong

country: China

institute: The university of Hong Kong

description:
Library name: DSS R89
Column name in  processed data.txt: DSS_R89-FPKM

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using hisat2 v2.0.5
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCm38
Supplementary files format and content: Matrix tables with normalized gene counts for every gene and every sample

organism: Mus musculus

source_name: ovary

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovary

tag: genotype

value: WT


title: PA_7

description:
ACTH-secreting pituitary adenoma 7
ACTH_15_S10

value: Female


title: PA_6

description:
ACTH-secreting pituitary adenoma 6
ACTH_13_S4


title: rosiglitazone_0.1_10d_1pool1_S276

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S276

value: rosiglitazone


title: female C57BL/6J mice, DSS R78, Day89

description:
Library name: DSS R78
Column name in  processed data.txt: DSS_R78-FPKM


title: rosiglitazone_0.1_24h_2pool1_S180

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S180


title: aflatoxin B1_1_10d_2pool1_S364

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S364

value: aflatoxin B1


title: female C57BL/6J mice, DSS R38, Day89

description:
Library name: DSS R38
Column name in  processed data.txt: DSS_R38-FPKM


title: female C57BL/6J mice, DSS R29, Day89

description:
Library name: DSS R29
Column name in  processed data.txt: DSS_R29-FPKM


title: PA_4

description:
ACTH-secreting pituitary adenoma 4
ACTH_11_S12


title: PA_5

description:
ACTH-secreting pituitary adenoma 5
ACTH_12_S7


title: aflatoxin B1_1_24h_2pool1_S172

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S172


title: rosiglitazone_0.1_24h_1pool1_S84

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S84


title: female C57BL/6J mice,  Control R126, Day89

description:
Library name: Control R126
Column name in  processed data.txt: control_R126-FPKM


title: benzo[a]pyrene_0.03_24h_1pool1_S12

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S12

value: benzo[a]pyrene


title: aflatoxin B1_1_24h_1pool1_S76

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S76


title: female C57BL/6J mice,  Control R124, Day89

description:
Library name: Control R124
Column name in  processed data.txt: control_R124-FPKM


title: acetaminophen_50_10d_1pool1_S196

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S196

value: acetaminophen


title: acetaminophen_50_24h_2pool1_S100

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S100


title: PA_2

description:
ACTH-secreting pituitary adenoma 2
ACTH_9_S9


title: female C57BL/6J mice,  Control R123, Day89

description:
Library name: Control R123
Column name in  processed data.txt: control_R123-FPKM


title: troglitazone_0.1_24h_1pool1_S92

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S92


title: acetaminophen_50_24h_1pool1_S4

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S4


title: PA_1

description:
ACTH-secreting pituitary adenoma 1
ACTH_8_S6


title: WY-14643_10_10d_2pool1_S355

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S355


title: rosiglitazone_0.1_10d_2pool1_S372

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S372


title: female C57BL/6J mice, DSS82, Day7

description:
Library name: DSS82
Column name in  processed data.txt: DSS82-FPKM


title: WY-14643_10_10d_1pool1_S259

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S259


title: female C57BL/6J mice, DSS81, Day7

description:
Library name: DSS81
Column name in  processed data.txt: DSS81-FPKM


title: RC17 cells, FGF8/FGF17, day 16, rep 2, HTO, B2

city: Copenhagen

first: Erno

last: Hänninen

address: Blegdamsvej 3B

department: reNEW, Novo Nordisk Foundation Center for Stem Cell Medicine

country: Denmark

institute: University of Copenhagen

description: HTO_index: D704, VM_d16_5 FGF8: A0451, VM_d16_6 FGF8: A0452,VM_d16_7 FGF17: A0453,VM_d16_8 FGF17: A0454

data_processing:
The raw sequence data has been preprocessed with the Alevin-fry pipeline
Assembly: hg38
Supplementary files format and content: FGFprocessed.RDS contains quality filtered, normalized and dimensionality reduced single-cell object with cluster annotations.

molecule: protein

source_name: directed to ventral midbrain

growth_protocol: RC17 were cultured in StemMACS iPS Brew XF (Miltenyi Biotec) and passaging was performed using 0.5mM EDTA dissociation at 37°C. For the first 24h after passaging 10µM ROCK inhibitor (Miltenyi Biotec) was included in the media. Specification of hESC towards VM fates was performed in accordance with the Nolbrant et al., 2017 protocol

extract_protocol:
Four batches of paired FGF8- and FGF17-treated day 16 VM progenitors (8 samples total) were thawed in wash media containing DMEM/F12 + 5%KOSR. Cells per sample were stained with 0.5µg of unique cell surface hashing antibody(Biolegend) and incubated for 30 min at 4 degrees. After antibody tagging, cells were washed three times in PBS(wo Ca and Mg) with 0.5%BSA and resuspended at 1000 cells/ul in PBS(wo Ca and Mg) +0.5%BSA
The eight samples were prepared to be run across two 10X sequencing lanes by pooling two batches of paired FGF8 and FGF17 samples at 1:1:1:1 ratio for both sequencing lanes. 10X scRNAseq was combined with CITE-Seq for sample multiplexing to sequence eight different replicates across two protocols.

value: directed to ventral midbrain

tag: cell type

value: hESC

tag: treatment


title: aflatoxin B1_1_10d_1pool1_S268

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S268


title: WY-14643_10_24h_1pool1_S67

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S67


title: estradiol_0.001_10d_2pool1_S347

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S347

value: estradiol


title: RC17 cells, FGF8/FGF17, day 16, rep 1, HTO, B1

description: HTO_index: D702, VM_d16_5 FGF8: A0451, VM_d16_6 FGF8: A0452,VM_d16_7 FGF17: A0453,VM_d16_8 FGF17: A0454


title: estradiol_0.001_10d_1pool1_S251

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S251


title: female C57BL/6J mice, DSS80, Day7

description:
Library name: DSS80
Column name in  processed data.txt: DSS80-FPKM


title: acetaminophen_50_10d_2pool1_S292

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S292


title: female C57BL/6J mice, DSS75 , Day7

description:
Library name: DSS75
Column name in  processed data.txt: DSS75-FPKM


title: PA_3

description:
ACTH-secreting pituitary adenoma 3
ACTH_10_S11


title: estradiol_0.001_24h_2pool1_S155

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S155


title: valproic acid_10_10d_2pool1_S339

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S339

value: valproic acid


title: RC17 cells, FGF8/FGF17, day 16, rep 2, HTO, A2

description: HTO_index: D703, VM_d16_1 FGF8: A0451, VM_d16_2 FGF8: A0452,VM_d16_3 FGF17: A0453,VM_d16_4 FGF17: A0454


title: female C57BL/6J mice,  Control53, Day7

description:
Library name: Control53
Column name in  processed data.txt: control53-FPKM


title: RC17 cells, FGF8/FGF17, day 16, rep 1, HTO, A1

description: HTO_index: D701, VM_d16_1 FGF8: A0451, VM_d16_2 FGF8: A0452,VM_d16_3 FGF17: A0453,VM_d16_4 FGF17: A0454


title: valproic acid_10_10d_1pool1_S243

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S243


title: estradiol_0.001_24h_1pool1_S59

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S59


title: RC17 cells, FGF8/FGF17, day 16, rep 1, RNA, B1

description: HTO_index: D702,VM_d16_5 FGF8: A0451, VM_d16_6 FGF8: A0452,VM_d16_7 FGF17: A0453,VM_d16_8 FGF17: A0454

library_source: transcriptomic single cell


title: female C57BL/6J mice,  Control51, Day7

description:
Library name: Control51
Column name in  processed data.txt: control51-FPKM


title: valproic acid_10_24h_2pool1_S147

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S147


title: valproic acid_10_24h_1pool1_S51

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S51


title: WY-14643_10_24h_2pool1_S163

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S163


title: RC17 cells, FGF8/FGF17, day 16, rep 1, RNA, A1


title: female C57BL/6J mice,  Control10, Day7

description:
Library name: Control10
Column name in  processed data.txt: control10-FPKM


title: RC17 cells, FGF8/FGF17, day 16, rep 2, RNA, A2


title: potassium chloride_30_24h_2pool1_S139

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S139

value: potassium chloride


title: potassium chloride_30_10d_1pool1_S235

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S235


title: potassium chloride_30_24h_1pool1_S43

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S43


title: HET3-C57BL/6J_IAT, Ebf2 p.E165X/+, male 4-week-old

city: ANN ARBOR

first: Tae-Hwa

last: Chun

state: MI

address: 2800 PLYMOUTH RD, NCRC B10-A186, NCRC B10-A186

department: Internal Medicine

country: USA

institute: University of Michigan

description: Library name: 11535-TC-6

data_processing:
The reads were trimmed using Cutadapt v4.8 (Martin, 2011). The reads were evaluated with FastQC (Andrews, 2010) (v0.11.8) to determine quality of the data. Reads were mapped to the reference genome GRCm38 (ENSEMBL 102), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq (Dobin). QC metrics from several different steps in the pipeline were aggregated by multiQC v1.20 (Ewels et al., 2016).
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file that includes raw count data from each sample

source_name: Inguinal Adipose Tissue

extract_protocol:
RNA extraction was performed using QIAshredder (Qiagen) and RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.
RNA-Seq libraries were prepared using NEB Kit following the manufacturer's instructions

value: Inguinal Adipose Tissue

value: HET


title: sucrose_30_24h_1pool1_S35

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S35

value: sucrose


title: HET2-C57BL/6J_IAT, Ebf2 p.E165X/+, male 4-week-old

description: Library name: 11535-TC-5

value: Male


title: PGC, Illumina, rep 3

city: Ann Arbor

first: Kin Fai

last: Au

address: 100 Washtenaw Avenue

department: Department of Computational Medicine and Bioinformatics

data_processing:
For ONT long-read RNA-seq, only the long reads with a quality score (qscore ≥7, passed reads) are used for our study, and these passed reads are uploaded to NCBI GEO.  For Illumina short-read RNA-seq, sequencing adapters are trimmed by Cutadapt (v1.8.1)  with the parameter “-q 20,20 -m 20 --max-n 0.01 --trim-n”.
For identification of gene isoforms, based on the hg38 reference genome and GENCODE annotation (v39), IsoQuant (v3.3.0) is run with the parameter “-d nanopore” for cDNA-ONT data merged from ESC, PE and PGC; and with the parameter “-d nanopore --stranded forward” for dRNA-ONT data merged from ESC, PE and PGC. For each of three samples (ESC, PE and PGC), two sets of gene annotations are derived from IsoQuant using cDNA-ONT and dRNA-ONT data.
To estimate the abundance of these gene isoforms, for each of three samples (ESC, PE, PGC), miniQuant (v1.0.0) is run separately with the two sets of gene annotations (constructed by IsoQuant) and the two dataset combinations: (1) cDNA-ONT derived annotation and cDNA-ONT plus Illumina data, with the parameter "--pretrained_model_path cDNA-ONT --EM_choice hybrid"; (2) dRNA-ONT derived annotation and dRNA-ONT plus Illumina data, with the parameter "--pretrained_model_path dRNA-ONT --EM_choice hybrid". Of note, for each sample, the Illumina data are combined from three replicates when running miniQuant.
For Illumina RNA-seq data alone, for each of three replicates from ESC, ES, PE and PGC sample, we estimate the expression abundance using Kallisto (v0.46.1) with the default parameter, based on GENECODE annotation (v39).
Assembly: hg38
Supplementary files format and content: GTF format files included the gene isoforms identified by IsoQuant from ESC, PE and PGC samples, using cDNA-ONT and dRNA-ONT data, respectively.
Supplementary files format and content: Tab-delimited text files included the expression value (Transcripts per million, TPM) of gene isoforms quantified by Kallisto for each replicate of ESC, DE, PE and PGC samples, using Illumina data.
Supplementary files format and content: Tab-delimited text files included the expression value (Transcripts per million, TPM) of gene isoforms quantified by miniQuant for ESC, PE and PGC samples, using cDNA-ONT plus Illumina data and dRNA-ONT plus Illumina data, respectively.

molecule: polyA RNA

source_name: H1-hESC derived primordial germ cell-like cells

growth_protocol: Definitive endoderm (DE) and pharyngeal endoderm (PE), and primordial germ cell-like cells (PGC) (reference: PMID: 37709760) are differentiated from human ESC (H1-hESC cell line), respectively. See the details in the manuscripts: (1)  DOI: https://doi.org/10.1101/2022.06.26.497457 (from ESC to DE and PE); and (2) PMID: 37709760 (from ESC to PGC).

extract_protocol:
Total RNA is extracted by TRIzol Reagent (Thermo Fisher Scientific), followed by polyA+ RNA enrichment using the Dynabeads mRNA Purification Kit (Thermo Fisher Scientific).
For ESC, PE and PGC, ONT sequencing libraries are prepared using the SQK-PCS109 Kit for PCR-cDNA sequencing (cDNA-ONT), and the SQK-DCS109 Kit for direct RNA sequencing (dRNA-ONT). ONT sequencing is conducted using MiniON/GridION flow cells with R9.4.1 chemistry, with real-time base calling performed by the Guppy software. For ESC, DE, PE and PGC, the library preparation and sequencing of Illumina RNA-seq data are conducted by Novogene company.


title: sucrose_30_10d_2pool1_S323

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S323

value: liver spheroids


title: sucrose_30_24h_2pool1_S131

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S131


title: sucrose_30_10d_1pool1_S227

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S227


title: RC17 cells, FGF8/FGF17, day 16, rep 2, RNA, B2

description: HTO_index: D704, VM_d16_5 FGF8: A0451, VM_d16_6 FGF8: A0452,VM_d16_7 FGF17: A0453,VM_d16_8 FGF17: A0454


title: caffeine_10_10d_2pool1_S315

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S315

value: caffeine


title: caffeine_10_24h_2pool1_S123

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S123


title: WT2-C57BL/6J_IAT, Ebf2+/+, male 4-week-old

description: Library name: 11535-TC-2

value: WT


title: caffeine_10_24h_1pool1_S27

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S27


title: caffeine_10_10d_1pool1_S219

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S219


title: HET1-C57BL/6J_IAT, Ebf2 p.E165X/+, male 4-week-old

description: Library name: 11535-TC-4


title: PE, Illumina, rep 3

source_name: H1-hESC derived pharyngeal endoderm

value: H1-hESC derived pharyngeal endoderm


title: PGC, Illumina, rep 2

value: H1-hESC derived primordial germ cell-like cells


title: WT3-C57BL/6J_IAT, Ebf2+/+, male 4-week-old

description: Library name: 11535-TC-3


title: potassium chloride_30_10d_2pool1_S331

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S331


title: cyclosporin A_1_10d_2pool1_S307

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S307

value: cyclosporin A


title: PGC, Illumina, rep 1


title: WT1-C57BL/6J_IAT, Ebf2+/+, male 4-week-old

description: Library name: 11535-TC-1


title: cyclosporin A_1_10d_1pool1_S211

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S211


title: Mouse Vwf– LT-HSCs WT biol rep 2

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

description: Library name: WT female Vwf- LT-HSC

library_source: genomic

data_processing:
Raw sequencing reads were initially trimmed using cutadapt to remove potential adaptor contamination and low-quality reads based on the default threshold for each EM-Seq profile
The remaining reads were then aligned to the reference mouse genome (mm10) using Bismark (v2.5.1), enabling us to identify methylation states at single- base resolution.
The aligned reads were further filtered using Picard (biotools:picard_tools, RRID:SCR_006525, http://broadinstitute.github.io/picard/) to remove PCR duplicates.
The CpG methylation information was extracted with Bismark’s bismark_methylation_extractor module.
Under-methylated regions (UMRs) were detected using a Hidden Markov Model within iBSTools [https://github.com/methylation/iBSTools]
Differentially methylated regions (DMRs) were identified using Metilene (v.0.2-8), with criteria including a minimum mean DNA methylation difference of 0.2, at least 10 CpG sites, a p-value less than 0.01, and a length greater than 500bp. DMR-associated genes were further annotated using the R package ChIPseeker
Assembly: mm10
Supplementary files format and content: Bigwig (.bw) files containing methylation data for each sample
Library strategy: Enzymatic methyl-seq

molecule: genomic DNA

source_name: Vwf Neg LT-HSCs

extract_protocol:
DNA was isolated using the Qiagen Allprep DNA/RNA micro kit (80284).
DNA from 5000-30000 HSCs was used as input for the NEBNext Enzymatic Methyl-Seq kit (NEB E7120S), and libraries were prepared according to the manufacturer’s instructions. Library quality was assessed using a D5000 screentape (Agilent 5067-5588).

value: Vwf Neg LT-HSCs

tag: age

value: 10-12 months

value: Female


title: PE, Illumina, rep 2


title: cyclosporin A_1_24h_1pool1_S19

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S19


title: benzo[a]pyrene_0.3_10d_2pool1_S299

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S299

value: benzo[a]pyrene


title: PE, Illumina, rep 1


title: Mouse Vwf– LT-HSCs WT biol rep 1

description: Library name: WT male Vwf- LT-HSC


title: cyclosporin A_1_24h_2pool1_S115

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S115


title: benzo[a]pyrene_0.3_10d_1pool1_S203

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S203


title: benzo[a]pyrene_0.3_24h_1pool1_S11

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S11


title: troglitazone_1_10d_2pool1_S379

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S379

value: troglitazone


title: benzo[a]pyrene_0.3_24h_2pool1_S107

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S107


title: Mouse Vwf– LT-HSCs Dnmt3a+/– biol rep 1

description: Library name: HET male Vwf- LT-HSC

value: Dnmt3a HET


title: DE, Illumina, rep 1

source_name: H1-hESC derived definitive endoderm

value: H1-hESC derived definitive endoderm


title: DE, Illumina, rep 2


title: troglitazone_1_24h_2pool1_S187

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S187


title: ESC, Illumina, rep 3

value: human embryonic stem cells


title: DE, Illumina, rep 3


title: Mouse Vwf– LT-HSCs Dnmt3a+/– biol rep 2

description: Library name: HET female Vwf- LT-HSC


title: troglitazone_1_10d_1pool1_S283

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S283


title: troglitazone_1_24h_1pool1_S91

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S91


title: rosiglitazone_1_10d_1pool1_S275

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S275

value: rosiglitazone


title: Mouse Vwf+ LT-HSCs WT biol rep 1

description: Library name: WT male Vwf+ LT-HSC

source_name: Vwf Pos LT-HSCs

value: Vwf Pos LT-HSCs


title: rosiglitazone_1_24h_2pool1_S179

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S179


title: Mouse Vwf+ LT-HSCs Dnmt3a+/– biol rep 2

description: Library name: HET female Vwf+ LT-HSC


title: ESC, Illumina, rep 2


title: ESC, Illumina, rep 1


title: rosiglitazone_1_24h_1pool1_S83

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S83


title: aflatoxin B1_10_10d_2pool1_S363

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S363

value: aflatoxin B1


title: Mouse Vwf+ LT-HSCs Dnmt3a+/– biol rep 1

description: Library name: HET male Vwf+ LT-HSC

value: Male


title: aflatoxin B1_10_24h_1pool1_S75

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S75

value: liver spheroids


title: mCM WT Rep2

city: Paris

first: Marie

last: Kervella

address: 105 boulevard de l'Hôpital

country: France

institute: Inserm

description: Library name: sample 10

data_processing:
Reads were pre-processed using fastp module v0.20.0 and aligned on GRCh38 human or GRCm39 mouse reference genome using star v2.7.5a. Pairs of reads aligned were annotated using gtf annotation files provided by ENSEMBL. Genome-aligned reads were indexed with samtools v1.13 and quantified with qualimap v2.2.2b. The number of reads uniquely mapping coding RNA was compiled in a counting matrix using featureCounts v2.0.1. All steps were submitted to quality control using mutliqc v1.13. Differential analysis was performed using the DESeq2 package on R.
Assembly: GRCh38 human or GRCm39 mouse reference genome
Supplementary files format and content: csv files including differential expression analysis data

source_name: heart sections

extract_protocol:
Cell pellet were collected and RNA were extracted using following Qiagen Rneasy Mini Kit protocol. RNA were collected from heart sections using trizol/chloroform solution and purified on column.
Library were constructed by iGenSeq Plateform of the Brain Insitute (Paris, France) using the TruSeq stranded total RNA library preparation kit, including depletion of RNA (Illumina Inc.)

value: heart sections

value: cardiac cells

value: WT


title: GM00637, Wildtype, none, ATACseq control, gDNA sequencing

city: Tübingen

first: Yingguang Frank

last: Chan

address: Max Planck Ring 9

department: Chan group

country: Germany

institute: Friedrich Miescher Laboratory of the Max Planck Society

data_processing:
Raw FASTQ reads  were extracted with bcl2fastq (version 2.20). Tn5 and Truseq adapter sequences, G repeats due to sequencing artefacts, and reads shorter than 20 bp were trimmed and removed using cutadapt (version 4.0).  Reads were then aligned to human reference genome version hg38 using bwa mem (Version: 0.7.17-r1188). Duplicates were marked and removed using Picard (version 2.18.25). Prior to calling peaks, mitochondrial reads, reads with a mapping quality lower than 20 and reads in hg38 blacklisted regions (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38human/hg38.blacklist.bed.gz) were discarded.  ATAC-seq peak calling was performed using MACS2 (version 2.1.1.20160309) with callpeak –format BAMPE --nomodel –min-length 100 narrowPeak parameters. The number of fragments in each ATACseq peak was quantified with htseq-count (HTSeq version 0.9.1). Subsequently, the count matrix was normalized and differential analysis was carried out in DESeq2 (version 1.30.1) to identify significantly differentially accessible chromatin regions (adjusted p-value <0.05).
Assembly: hg38
Supplementary files format and content: bedgraph files generated from the filtered bamfile for each sample
Supplementary files format and content: narrowPeak, global ATACseq peaks called via macs2 for WT and BLM-/-  samples
Supplementary files format and content: narrowPeak, ATACseq peaks called via macs2 for WT samples ort BLM-/- deficicent samples

growth_protocol: Cell lines derived from Bloom Syndrome and healthy donors were obtained from Coriell Institute (fibroblast cell lines: GM08505, GM00637). LCLs were cultured in RPMI 1640 medium (Gibco, Cat. #21875) supplemented with 15% fetal bovine serum (FBS, Gibco, UK, Cat. #10500), 1% penicillin-streptomycin (P/S, Gibco, US, Cat #15140) and 1% GlutaMAX-I (Gibco, UK, Cat. #35050).  Fibroblast lines were cultured in 1X DMEM (Gibco, UK, Cat. #11960) supplemented with, 1% minimum essential medium non-essential amino acids (MEM NEAA, Gibco, UK, Cat. #11140) and 10% (GM00637) or 15% ( GM08505) fetal bovine serum (FBS, Gibco, UK, Cat. #10500), 1% penicillin-streptomycin (P/S, Gibco, US, Cat #15140) respectively. Cell passaging was performed according to recommendations by Coriell Institute. All cells were cultured at 37°C under 5% CO2.

extract_protocol:
Fibroblasts were first trypsinised (Sigma-Aldrich, Cat. #SLCH3385), pelleted at 300 g for 5 min and washed once with cold 1x Dulbecco's phosphate buffered saline (PBS, Gibco, Cat. #14190).
50, 000 cells were subjected to ATACseq preparation essentially as described in Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396

value: fibroblast

value: Wildtype


title: aflatoxin B1_10_24h_2pool1_S171

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S171


title: Mouse Vwf+ LT-HSCs WT biol rep 2

description: Library name: WT female Vwf+ LT-HSC

value: 10-12 months


title: GM08505, BLM-/-, none, ATACseq control, gDNA sequencing

value: BLM-/-


title: rosiglitazone_1_10d_2pool1_S371

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S371


title: acetaminophen_500_10d_2pool1_S291

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S291

value: acetaminophen


title: acetaminophen_500_24h_2pool1_S99

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S99


title: acetaminophen_500_24h_1pool1_S3

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S3


title: GM00637, Wildtype, none, ATACseq rep2


title: GM00637, Wildtype, none, ATACseq rep3


title: WY-14643_100_10d_1pool1_S258

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S258


title: mCM Lmna Rep2

description: Library name: sample 7

value: Lmna p.H222P/H222P


title: GM00637, Wildtype, none, ATACseq rep1


title: WY-14643_100_10d_2pool1_S354

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S354


title: WY-14643_100_24h_1pool1_S66

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S66


title: GM08505, BLM-/-, none, ATACseq rep3


title: mCM Lmna Rep1

description: Library name: sample 6


title: WY-14643_100_24h_2pool1_S162

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S162


title: estradiol_0.01_10d_1pool1_S250

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S250

value: estradiol


title: estradiol_0.01_10d_2pool1_S346

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S346


title: NOX1 KO Distal Colon

city: Boston

first: Jay

middle: R

last: Thiagarajah

state: MA

address: 300 Longwood Avenue

department: Division of Gastroenterology, Hepatology and Nutrition

institute: Boston Childrens Hospital

description: Library name: Sample 4

data_processing:
Sequencing files were processed using CellRanger (v7.2.0). Analysis was conducted using Seurat (v5.1.0)74 keeping cells containing at least 100 unique genes and features expressed in at least 3 cells. A coarse quality filter was applied to remove cells with greater than 8000 unique genes and 50% of reads mapping to mitochondrial genes.
Assembly: GRCm38.p6
Supplementary files format and content: fastq

source_name: Distal Colon

extract_protocol:
Colonic epithelial cells isolated from WT and NOX1KO littermates by BD Melody sorter from proximal colon or distal colon regions were pooled separately across 2 mice at equal ratios and were resuspended in 1% BSA in PBS and counted with trypan blue staining for cell viability and number. Approximately 30,000 cells per sample were loaded onto separate lanes of the Chromium X Controller.
Gene expression libraries were prepared according to manufacturer instructions using the 10X Genomics Single Cell 3’ Reagent Kit (v3.1 Chemistry Dual Index).

value: Distal Colon

value: Colonic epithelial cells

value: NOX1 KO


title: aflatoxin B1_10_10d_1pool1_S267

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S267


title: estradiol_0.01_24h_2pool1_S154

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S154


title: estradiol_0.01_24h_1pool1_S58

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S58


title: GM08505, BLM-/-, none, ATACseq rep2


title: valproic acid_100_10d_2pool1_S338

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S338

value: valproic acid


title: NOX1 KO Proximal Colon

description: Library name: Sample 3

source_name: Proximal Colon

value: Proximal Colon


title: GM08505, BLM-/-, none, ATACseq rep1


title: acetaminophen_500_10d_1pool1_S195

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S195


title: valproic acid_100_10d_1pool1_S242

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S242


title: mCM WT Rep1

description: Library name: sample 9


title: s92_PFC_ATAC

city: Munich

first: Elisabeth

last: Binder

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

description: Single-cell ATAC sequencing  (10xGenomics)

data_processing:
Alignment of reads to reference (GRCh38, ensembl 98), cell caliing and count matrix generation with cellranger-atac v2.0.0.
Processing with ArchR v1.0.2: per-cell quality control with default parameters and removal of doublets with filter ratio of 2.5. Removal of one donor due to overall low data quality.
Dimensionality reduction with iterative LSI and UMAP embedding. Louvain clustering with resolution 1.0. Filtering of one donor and six clusters with low data quality regarding doublet scores and number of fragments, resulting in 399,439 nuclei from 90 donors.
Calculation of gene scores with ArchR and generation of pseudobulk gene scores.
Peak calling with MACS2.
Assembly: GRCh38
Supplementary files format and content: PeakMatrix.mtx is the peak count matrix in mtx format, PeakSet.csv contains peak metadata in csv format and Peak_CellMetadata.csv contains metadata for each nuclei (including cell type annotation).
Supplementary files format and content: GeneScoreMatrix_Pseudobulk_Normalized.csv contains a matrix with gene scores on the pseudobulk level. Each column contains gene score for a pseudosample (donor/cell type combination). Rows represent genes.

source_name: brain

extract_protocol:
Nuclei were isolated from frozen, dissected brain samples (OFC, BA11; 50 - 60 mg) by dounce-homogenisation in nuclei extraction buffer. Homogenate was layered onto a sucrose cushion and ultra-centrifuged. Nuclei pellet was resuspended in resuspension buffer, filtered through a cell strainer cap, stained with DAPI and counted using a hemocytometer.
Single nuclei ATAC-seq libraries were prepared following the user guide of 10X Genomics (Chromium Single Cell ATAC reagents kits v1.1) with a target recovery of 10,000 nuclei per sample.
Libraries were assessed using a High Sensitivity DNA Analysis Kit for the 2100 Bioanalyzer (Agilent), were then pooled equimolarily and treated with Illumina Free Adapter Blocking Reagent before sequencing on the NovaSeq 6000 System (Illumina).

value: brain

tag: disease status

value: Cases

tag: classification

value: Schizophrenia

value: Female

tag: ethnicity

value: European

tag: ph

tag: pmi

tag: rin

tag: lib batch


title: Wild Type Distal Colon

description: Library name: Sample 2

tag: tissue

value: WT


title: valproic acid_100_24h_2pool1_S146

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S146

tag: cell line

value: liver spheroids


title: mCM Lmna Rep3

description: Library name: sample 8

value: heart sections

value: cardiac cells


title: Wild Type Proximal Colon

description: Library name: Sample 1


title: valproic acid_100_24h_1pool1_S50

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S50

tag: chemical


title: s91_PFC_ATAC

value: Controls

value: Control

tag: Sex

value: Male


title: potassium chloride_300_10d_2pool1_S330

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S330

value: potassium chloride

tag: dose

tag: timepoint


title: potassium chloride_300_10d_1pool1_S234

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S234

tag: replicate


title: s90_PFC_ATAC


title: ATAC-seq Otx2-/- PGCLC aggregates, plus cytokines, day 2 rep2

city: Edinburgh

first: Elisa

last: Barbieri

address: 5 Little France Drive

country: United Kingdom

institute: University of Edinburgh

description: Library name: ATAC Otx2-/- PGCLC d2 cytokines rep2

data_processing:
Quality of reads was assessed by FastQC (v. 0.11.9), index and adaptor sequences were trimmed using TrimGalore (v. 0.6.6) and Cutadapt (v. 1.9.1) followed by a second quality check with FastQC.
Sequences were aligned to the mm10 mouse reference genome using Burrows-Wheeler Alignment (BWA, v. 0.7.16) tool with the maximal exact matches (MEM) option.
Fragments were quality filtered (>10) with Samtools (v. 1.6) and PCR duplicates were marked with Picard (v. 2.23.3) and removed with Samtools. Mitochondrial fragments were eliminated with Samtools.
Mapped reads were shifted by +4 bp for the forward strand and -5 bp for the reverse strand. Shifted bam files were transformed into BED files for peak calling using MACS2.
Bigwig tracks were generated with the bamCoverage option in the python-based DeepTools  (v. 3.5.1).
Assembly: mm10
Supplementary files format and content: bigwig

growth_protocol: Cells were routinely cultured in Serum/LIF media on gelatin plates. PGCLC differentiation was perfomed as previosly descrbied (Hayashi et al, 2011). Cells were first kept in 2i/LIF (N2B27 supplemented with CHIR99021 and PD0325901 ) for at least three passages prior to EpiLC and PGCLC differentiation. EpiLCs were derived for 44 hours in EpiLC medium (N2B27 supplemented with human Activin A and Fgf) and then cultured in suspension in GK15 (GMEM 15% KOSR) for 6 days. Cultures with cytokines were also supplemented with BMP4, BMP8a, SCF, LIF and EGF.

extract_protocol:
Nuclei were resuspended in Tagmentation Master Mix containing Assembled Trasposomes (Active Motif, cat. 53150). Tagmentation was performed in a thermocycler at 37°C for 20 minutes. Tagmented DNA was recovered using the DNA Clean and Concentration-5 kit (Zymo Research, cat. D4013).
Library was prepared using NEBNext High Fidelity 2x PCR Master Mix and indexed primers reported in Buenrostro et al, 2013, using the following protocol: 72°C for 5 minutes, and 98°C for 30 seconds followed by 9 cycles of : 98°C for 10 seconds, 63°C for 30 seconds, 72°C for 1 minute.

treatment_protocol: Otx2-/- Otx2-ERT2 cells were treated with 1 µM of 4-hydroxytamoxifen for the indicated times. To change tamoxifen containing media, aggregates were collected at day 2, washed, resuspended in GK15 and incubated in 5 mm dishes in rotation until day 4 before collection and analysis.

tag: genotype

tag: cell type

value: PGCLC aggregates

tag: time point

value: day 2

value: plus cytokines


title: potassium chloride_300_24h_2pool1_S138

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S138


title: potassium chloride_300_24h_1pool1_S42

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S42


title: ATAC-seq Otx2-/- EpiLCs rep2

description: Library name: ATAC Otx2-/- EpiLC rep2

value: EpiLC

tag: treatment

value: Activin A + bFGF


title: sucrose_300_10d_1pool1_S226

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S226

value: sucrose


title: sucrose_300_10d_2pool1_S322

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S322


title: s88_PFC_ATAC

value: brain

tag: disease status

value: Cases

tag: classification

value: MajorDepression

tag: age


title: cyclosporin A_0.1_24h_2pool1_S116

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S116

value: cyclosporin A


title: sucrose_300_24h_2pool1_S130

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S130

value: liver spheroids


title: s89_PFC_ATAC

tag: ethnicity

value: European

tag: ph

tag: pmi


title: caffeine_100_10d_2pool1_S314

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S314

value: caffeine


title: ATAC-seq Otx2-/- EpiLCs rep1

description: Library name: ATAC Otx2-/- EpiLC rep1


title: caffeine_100_10d_1pool1_S218

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S218


title: ATAC-seq Otx2-/- 2i/LIF ESCs rep2

description: Library name: ATAC Otx2-/- ESC rep2

value: ESC (2i/LIF)


title: s86_PFC_ATAC

tag: tissue

value: Schizophrenia

tag: rin

tag: lib batch


title: caffeine_100_24h_2pool1_S122

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S122

tag: cell line

tag: chemical


title: sucrose_300_24h_1pool1_S34

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S34

tag: dose

tag: timepoint


title: s87_PFC_ATAC

tag: Sex

value: Female


title: ATAC-seq WT PGCLC aggregates, no cytokines, day 2, rep2

description: Library name: ATAC WT PGCLC d2 no cytokines rep2

tag: genotype

value: wild-type

tag: cell type

value: no cytokines


title: cyclosporin A_10_10d_2pool1_S306

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S306

tag: replicate


title: cyclosporin A_10_10d_1pool1_S210

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S210


title: s84_PFC_ATAC

description: Single-cell ATAC sequencing  (10xGenomics)

tag: disease status

value: Male


title: ATAC-seq Otx2-/- 2i/LIF ESCs rep1

description: Library name: ATAC Otx2-/- ESC rep1

tag: time point

tag: treatment


title: caffeine_100_24h_1pool1_S26

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S26


title: s85_PFC_ATAC

tag: classification

tag: age

tag: ethnicity


title: ATAC-seq Otx2-/- PGCLC aggregates, plus cytokines, day 2 rep1

description: Library name: ATAC Otx2-/- PGCLC d2 cytokines rep1

value: PGCLC aggregates

value: day 2

value: plus cytokines


title: ATAC-seq WT PGCLC aggregates, no cytokines, day 2, rep1

description: Library name: ATAC WT PGCLC d2 no cytokines rep1


title: s83_PFC_ATAC

tag: tissue

value: Controls

value: Control

tag: ph

tag: pmi


title: cyclosporin A_10_24h_1pool1_S18

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S18

tag: cell line


title: cyclosporin A_10_24h_2pool1_S114

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S114

tag: chemical


title: Engrafted #9

type: RNA

city: Seoul

first: DONG-MYUNG

last: SHIN

address: Pungnap-2 dong, Songpa-gu

department: Department of Biomedical Sciences

country: South Korea

institute: University of Ulsan College of Medicine

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 Gene Expression Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing:
Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC).
The processed data files are in text format and consist of the TPM values for each sample.

label: biotin

source_name: Engrafted #9

label_protocol: The amplified PCR products representing each single cell transcriptome were biotin-labeled using the GeneChip 3’ in vitro transcription (IVT) kit (Affymetrix, Santa Clara, CA, USA), starting from ‘‘In vitro Transcription to Synthesize Labeled aRNA”.

growth_protocol: Human umbilical cord-derived mesenchymal stem cells (UC-MSCs) used in the present study were grown in low-glucose Dulbecco’s modified Eagle’s medium (DMEM) containing 10% heat-inactivated fetal bovine serum (FBS), human epidermal growth factor (5 ng/ml; Sigma-Aldrich), basic FGF (10 ng/ml), and long-R3 insulin-like growth factor-1 (50 ng/ml; ProSpec, Rehovot, Israel) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol: Total RNA from single cell of the MACS-FACS sorted cells were directly extracted from a 96 well-plate and amlified as described in our previous report (Stem Cells Dev. 2012, PMID:22023227)

treatment_protocol: GFP+ M-MSCs were labeled in the Resovist (a clinically approved superparamagnetic iron oxide) for 1 day before transplantion into STZ induced type I diabetes rat model. At 7 days after transplantation, the engrafted cells were highly purifed using MACS followed by FACS sorting. The MACS-FACS sorted cells were distributed as single cell per well into a 96 well plate containing the cell lysis buffer, including treatment with NP40, Rnase Inhibitors, and V1(dT)24 primer(5ng/ul).

value: Mesenchymal stem cell


title: Engrafted #10

source_name: Engrafted #10


title: s82_PFC_ATAC

value: brain

value: Cases

tag: rin

tag: lib batch


title: benzo[a]pyrene_3_10d_2pool1_S298

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S298

value: liver spheroids

value: benzo[a]pyrene

tag: dose

tag: timepoint


title: Engrafted #8

source_name: Engrafted #8

tag: cell type


title: ATAC-seq WT EpiLCs rep1

description: Library name: ATAC WT EpiLC rep1

tag: genotype

value: EpiLC

value: Activin A + bFGF


title: s81_PFC_ATAC

tag: disease status

value: Schizophrenia

tag: Sex

value: European


title: ATAC-seq WT ESCs rep2

description: Library name: ATAC WT ESC rep2

value: wild-type

value: ESC (2i/LIF)

tag: time point

tag: treatment


title: benzo[a]pyrene_3_10d_1pool1_S202

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S202

tag: replicate


title: Engrafted #7

source_name: Engrafted #7


title: s80_PFC_ATAC

tag: classification

tag: age

value: Female

tag: ethnicity


title: benzo[a]pyrene_3_24h_2pool1_S106

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S106

source_name: liver spheroids


title: Engrafted #6

source_name: Engrafted #6


title: s79_PFC_ATAC

tag: tissue

value: SchizoaffectiveDisorder

tag: ph

tag: pmi


title: ATAC-seq WT ESCs rep1

description: Library name: ATAC WT ESC rep1

tag: cell line


title: benzo[a]pyrene_3_24h_1pool1_S10

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S10

tag: chemical


title: Nox1 WT Repeat 3

description: Library name: Sample 6

data_processing:
preprocessed data
Assembly: version 25 of the mouse GENCODE
Supplementary files format and content: 614_diffExp_q005_Genes_RPKM_table

extract_protocol:
Lyse colonoids recovered from Matrigel in TRIzol™ Reagent. Then isolate RNA according to manufacturer’s instructions. The quality of RNA samples was determined using an Agilent 5400 Bioanalyzer, and all samples for sequencing had RNA integrity (RIN) numbers >8.
cDNA library construction using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® was performed by the Novogene Corporation Inc. (Sacramento, CA), and cDNA libraries were sequenced on an Illumina HiSeq 2000 or Illumina Novaseq 6000 instruments.

value: Distal Colon

value: Organoid

value: WT

tag: batch


title: Engrafted #5

source_name: Engrafted #5


title: Engrafted #4

source_name: Engrafted #4


title: s78_PFC_ATAC

value: Controls

value: Control

tag: rin

tag: lib batch


title: troglitazone_10_10d_2pool1_S378

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S378

value: troglitazone

tag: dose

tag: timepoint


title: Engrafted #3

source_name: Engrafted #3

tag: cell type

value: Mesenchymal stem cell


title: s77_PFC_ATAC

value: brain

tag: disease status

value: Cases

value: BipolarDisorder

tag: Sex

value: Male


title: troglitazone_10_10d_1pool1_S282

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S282

value: liver spheroids

tag: replicate


title: Nox1 WT Repeat 1

description: Library name: Sample 4

tag: genotype


title: ATAC-seq WT EpiLCs rep2

description: Library name: ATAC WT EpiLC rep2

value: EpiLC

tag: time point

value: day 2

tag: treatment

value: Activin A + bFGF


title: troglitazone_10_24h_2pool1_S186

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S186


title: Nox1 KO Repeat 3

description: Library name: Sample 3

tag: tissue

value: Nox1 KO


title: s76_PFC_ATAC

tag: classification

value: Schizophrenia

tag: age

value: Female

tag: ethnicity

value: European

tag: ph


title: Nox1 KO Repeat 2

description: Library name: Sample 2

value: Distal Colon

value: Organoid

tag: batch


title: s74_PFC_ATAC

tag: pmi

tag: rin


title: rosiglitazone_10_10d_2pool1_S370

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S370

tag: cell line

tag: chemical

value: rosiglitazone

tag: dose


title: s75_PFC_ATAC

tag: disease status

tag: lib batch


title: UC #5

source_name: Cultured #5

tag: cell type


title: Engrafted #1

source_name: Engrafted #1


title: Mouse Vwf– LT-HSCs WT biol rep 2

description: Library name: WT female Vwf- LT-HSC

data_processing:
Genialis Expressions software was used for analysis.
Trim Galore (paired-end) was used to remove the first 14 nucleotides from the 5’ end of Read 2 per instructions of the Takara Pico Input Total RNA v3 kit with a quality cutoff of 20 and a Phred score encoding of ASCII+33, other settings default.
Remaining reads were aligned to the reference mouse genome (mm10) using the STAR aligner with default settings
FeatureCounts was used to obtain TPM values.
DESeq2 was used to obtain differentially expressed genes, and genes with a Log2FC >1 and FDR <0.05 were considered significant.
Assembly: mm10
Supplementary files format and content: Tab-delimited txt file contains raw counts for each sample.
Supplementary files format and content: Tab-delimited txt file contains TPM values for each sample.

source_name: Vwf Neg LT-HSCs

extract_protocol:
RNA was isolated using the Qiagen Allprep DNA/RNA micro kit (80284).
Libraries were prepared using the Takara Pico Input Total RNA v3 kit (634485) according to manufacturer instructions.

value: Vwf Neg LT-HSCs

tag: genotype

value: WT

value: 10-12 months

tag: Sex


title: rosiglitazone_10_10d_1pool1_S274

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S274

tag: timepoint

tag: replicate


title: UC #4

source_name: Cultured #4

value: Mesenchymal stem cell


title: Nox1 KO Repeat 1

description: Library name: Sample 1

tag: tissue


title: s72_PFC_ATAC

value: brain

value: Cases

tag: classification

tag: age


title: rosiglitazone_10_24h_2pool1_S178

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S178

value: liver spheroids


title: s71_PFC_ATAC

value: Male

tag: ethnicity

tag: ph


title: Nox1 WT Repeat 2

description: Library name: Sample 5

tag: batch


title: Mouse Vwf– LT-HSCs Dnmt3a+/– biol rep 2

description: Library name: HET female Vwf- LT-HSC

value: Dnmt3a HET


title: rosiglitazone_10_24h_1pool1_S82

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S82


title: UC #2

source_name: Cultured #2


title: UC #1

source_name: Cultured #1


title: Engrafted #2

source_name: Engrafted #2


title: aflatoxin B1_100_10d_2pool1_S362

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S362

value: aflatoxin B1


title: s69_PFC_ATAC

description: Single-cell ATAC sequencing  (10xGenomics)

source_name: brain

tag: pmi

tag: rin


title: s70_PFC_ATAC

value: Controls

value: Control


title: troglitazone_10_24h_1pool1_S90

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S90

tag: cell line

tag: chemical

value: troglitazone


title: Mouse Vwf– LT-HSCs Dnmt3a+/– biol rep 1

description: Library name: HET male Vwf- LT-HSC


title: CornOil_WT3

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

institute: Francis Crick Institute

description:
Lexogen QuantSeq protocol
47

data_processing:
FASTQC version 11.7 was used to assess FASTQ file quality. Trimmomatic version 36 was used to trim adapter sequences from fastq files
Alignment to Ensembl Mus_musculus.GRCm38.89 using STAR 2.5.2 and RSEM version 1.3
Raw counts were normlaised using DESeq2 verion 1.32 using R version 4.10
Differential analysis was done using DESEQ2 Wald’s test
Assembly: GRCm38.89
Supplementary files format and content: tab delimted text files, where columns are samples and rows are ensembl geneIDs

source_name: Liver

extract_protocol:
Trizol
Lexogen QuantSeq™ 3’ mRNA-Seq Library Prep Kit for Ion Torrent (#012)

treatment_protocol: Mice were treated with corn oil (CO), CITCO (10mg/kg)  intraperitoneal (IP), daily, 4d and sacrificed on day 5 for blood and tissue collection.

value: Liver

value: wt

tag: treatment

value: Corn Oil


title: CITCO_CarKO3

description:
Lexogen QuantSeq protocol
46

value: CarKO/hPXR

value: CITCO


title: s73_PFC_ATAC

tag: disease status

value: Female

value: European

tag: lib batch


title: aflatoxin B1_100_24h_2pool1_S170

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S170

tag: dose


title: s67_PFC_ATAC

value: BipolarDisorder

tag: Sex


title: Mouse Vwf– LT-HSCs WT biol rep 1

description: Library name: WT male Vwf- LT-HSC

tag: cell type

value: Vwf Neg LT-HSCs

tag: genotype

value: WT

value: 10-12 months


title: UC #3

source_name: Cultured #3

value: Mesenchymal stem cell


title: Mouse Vwf+ LT-HSCs Dnmt3a+/– biol rep 2

description: Library name: HET female Vwf+ LT-HSC

source_name: Vwf Pos LT-HSCs

value: Vwf Pos LT-HSCs

value: Dnmt3a HET


title: aflatoxin B1_100_24h_1pool1_S74

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S74

value: liver spheroids

value: aflatoxin B1

tag: timepoint

tag: replicate


title: Mouse Vwf+ LT-HSCs WT biol rep 1

description: Library name: WT male Vwf+ LT-HSC

tag: age

value: Male


title: s66_PFC_ATAC

tag: tissue

value: brain

value: Cases

tag: classification

value: Schizophrenia

tag: ethnicity


title: CITCO_hCAR3

description:
Lexogen QuantSeq protocol
45

value: Liver

value: hCAR/hPXR


title: acetaminophen_5000_10d_2pool1_S290

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S290

value: acetaminophen


title: Mouse Vwf+ LT-HSCs WT biol rep 2

description: Library name: WT female Vwf+ LT-HSC

value: Female


title: s68_PFC_ATAC

value: European

tag: ph

tag: pmi


title: Mouse Vwf+ LT-HSCs Dnmt3a+/– biol rep 1

description: Library name: HET male Vwf+ LT-HSC


title: s65_PFC_ATAC

value: Controls

value: Control

tag: rin


title: CITTO_WT3

description:
Lexogen QuantSeq protocol
44

value: wt

value: CITCO


title: CornOil_WT2

description:
Lexogen QuantSeq protocol
43

value: Corn Oil


title: acetaminophen_5000_10d_1pool1_S194

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S194

tag: cell line

tag: chemical


title: s64_PFC_ATAC

tag: disease status


title: aflatoxin B1_100_10d_1pool1_S266

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S266


title: acetaminophen_5000_24h_2pool1_S98

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S98


title: acetaminophen_5000_24h_1pool1_S2

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S2


title: CITCO_CarKO2

description:
Lexogen QuantSeq protocol
42

value: CarKO/hPXR

tag: treatment


title: s63_PFC_ATAC

tag: lib batch


title: CITCO_hCAR2

description:
Lexogen QuantSeq protocol
41


title: s62_PFC_ATAC

value: MajorDepression

tag: Sex


title: JAMLMKO,LPS+ATP,3

city: Jinan

first: huiliang

last: cui

address: 07 Wenhua xi road, Jinan, Shandong

institute: Qilu hospital Shandong University

description: Library name: samples8

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the mm10 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Assembly: GRCm39.111
Supplementary files format and content: Raw_gene_counts_matrix.txt

source_name: macrophage

growth_protocol: The cells were resuspended in fresh DMEM supplemented with 10% fetal bovine serum and 1% Penicillin-Streptomycin.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Macrophages were treated with lipopolysaccharide (LPS) for 8 h at a concentration of 100 ng/ml followed by treatment with adenosine 5'-triphosphate (ATP) for 30 min at a concentration of 5 mM.

tag: cell type

value: macrophage

value: JAML Knockdown

value: LPS+ATP


title: JAMLMKO,LPS+ATP,4

description: Library name: samples9

tag: genotype


title: media only_0_10d_2pool1_S353

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S353

source_name: liver spheroids

value: liver spheroids

value: media only

tag: dose

tag: timepoint


title: JAMLMKO,LPS+ATP,2

description: Library name: samples7


title: s61_PFC_ATAC

value: brain

tag: age

value: Male


title: media only_0_10d_1pool1_S257

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S257

tag: replicate


title: CornOil_WT1

description:
Lexogen QuantSeq protocol
39

tag: tissue

value: Liver


title: JAMLMKO,LPS+ATP,1

description: Library name: samples6


title: media only_0_24h_2pool1_S161

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S161


title: JAMLWT,LPS+ATP,5

description: Library name: samples5

value: WT


title: s59_PFC_ATAC

value: Cases

tag: classification

value: Schizophrenia

value: Female

tag: ethnicity

value: European


title: s60_PFC_ATAC

tag: ph

tag: pmi


title: CITCO_CarKO1

description:
Lexogen QuantSeq protocol
38

value: CITCO


title: media only_0_24h_1pool1_S65

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S65

tag: cell line


title: JAMLMKO,LPS+ATP,5

description: Library name: samples10


title: JAMLWT,LPS+ATP,4

description: Library name: samples4


title: s58_PFC_ATAC

value: Controls

value: Control

tag: rin


title: media only_0_10d_2pool1_S345

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S345

tag: chemical


title: JAMLWT,LPS+ATP,3

description: Library name: samples3

tag: treatment


title: JAMLWT,LPS+ATP,2

description: Library name: samples2


title: media only_0_10d_1pool1_S249

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S249


title: CITTO_WT1

description:
Lexogen QuantSeq protocol
36

value: wt


title: s57_PFC_ATAC

tag: disease status

tag: lib batch


title: s56_PFC_ATAC

tag: Sex


title: gwscreen_plasmid_pool

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

data_processing:
Raw Bam files underwent processing using the crispr-process-nf Nextflow pipeline, available at https://github.com/ZuberLab/crispr-process-nf, which included barcode trimming, filtering, and alignment using Bowtie2. The crispr-mageck-nf Nextflow pipeline, available at https://github.com/ZuberLab/crispr-mageck-nf incorporating MAGeCK, was employed for comprehensive analysis of the CRISPR screen data.
Assembly: Genome wide CRISPR screen: mm10
Supplementary files format and content: Genome wide CRISPR screen: tab delimited file with guides, genes and normalized counts for plasmid pool and sample

source_name: sgRNA library plasmid pool

growth_protocol: All NUP98::KDM5A cell lines were cultured in RPMI 1640 supplemented with 10% FBS, 100 U/ml penicillin and 100 µg/ml streptomycin, 4 mM L-Glutamine, 1 mM Sodium pyruvate, 50 µM 2-Mercaptoethanol and 20 mM HEPES at 37 °C, 5% CO2, and 95% humidity. Primary NUP98::KDM5A PDX AML cells were cultured in IMDM containing 15% BIT 9500 Serum Substitute, 100 ng/ml SCF, 50 ng/ml Flt3-Ligand, 20 ng/ml IL-3, 20 ng/ml G-CSF, 100 µM ß-mercaptoethanol, 50 µg/ml gentamicin, 10 µg/ml ciprofloxacin, 500 nM SR1 and 1 µm UM729 at 37 °C, 5% CO2, and 95% humidity.

extract_protocol:
Genome-wide CRISPR screen: Genomic DNA was isolated by cell lysis (10 mM Tris-HCl, 150 mM NaCl, 10 mM EDTA, 0.1% SDS), proteinase K treatment and DNAse-free RNAse digest, followed by two rounds of phenol extraction and 2-propanol precipitation.
Genome-wide CRISPR screen: Sequencing libraries were generated using a two-step PCR protocol. The first PCR was performed using 0.2 μl of AmpliTaq Gold in 50-μl reactions containing 1 μg of genomic DNA. For each sample, the resulting PCR products were pooled and purified using MBSpure magnetic PCR purification beads and used as input for a second PCR introducing the standard Illumina adapters using 10 ng of DNA template.

treatment_protocol: Genome-wide CRISPR screen: Cells were infected with a lentivirally-packaged sgRNA library at a low multiplicity of infection (MOI) (≤10%). Infected cells were selected using G418 (1 mg/ml), which was kept in the medium until the end of the screen. Screen endpoint samples were harvested after 14 cell doublings.

value: sgRNA library plasmid pool


title: media only_0_24h_2pool1_S153

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S153

data_processing:
Reads were demultiplexed from the BCL files and processed into FASTQ files using bcl2fastq v2.20.0.422.
FASTQ files were aligned to the Human Surrogate+ Tox Panel (S1500+) v2.0 probes reference sequences (provided by BioSpyder) using STAR 2.7.8a.
The qCount function from QuasR was used to extract feature counts specified in a GTF file (provided by BioSpyder) from the aligned reads.
Assembly: Human Surrogate+ Tox Panel (S1500+) v2.0 probes reference sequences (provided by BioSpyder)
Supplementary files format and content: Comma-delimited table containing read counts per TempO-Seq probe

extract_protocol:
At the 24h and 10d time points media were removed, and spheroids were washed with Dulbecco's phosphate-buffered saline (DPBS; Thermo Fisher Scientific Waltham, MA). Spheroids were lysed by adding 10 µl of 1X TempO-Seq lysis buffer (BioSpyder Technologies Inc Carlsbad, CA) to each well. To ensure complete lysis, spheroids were incubated for approximately 10 minutes at 37°C, pipetted up and down several times, and then frozen at -80 °C until library building.
Lysates and technical RNA were hybridized to the detector oligo mix following the manufacturer's instructions provided in the TEMPO-SEQ Human Tox + Surrogate with Standard Attenuation Transcriptome Kit (96 samples). This was followed by nuclease digestion to eliminate excess oligos, detector oligo ligation, and subsequent amplification of correctly ligated oligos, all performed in accordance with the manufacturer's guidelines.
During the amplification stage, each sample was linked to a sample-specific barcode, enabling the pooling of samples for sequencing purposes. Pooled samples were purified using NucleoSpin Gel and PCR clean-up kits from Takara Bio USA, Inc. (Mountain View, CA). The libraries were sequenced in-house using a NextSeq 500 High-Throughput Sequencing System (Illumina, San Diego, California), employing a 50-cycle protocol from a 75-cycle high-throughput flow cell.


title: CITTO_WT2

description:
Lexogen QuantSeq protocol
40

tag: genotype


title: JAMLWT,LPS+ATP,1

description: Library name: samples1

tag: cell type

value: macrophage


title: s55_PFC_ATAC


title: media only_0_24h_1pool1_S57

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S57

tag: dose

tag: timepoint


title: s54_PFC_ATAC

description: Single-cell ATAC sequencing  (10xGenomics)

tag: age


title: 6PVPC1000K

data_processing:
A quality control of raw sequencing data was performed using FastQC (Simon, 2010). Adapter and low quality reads (<Q20) were removed using FASTX_Trimmer (Hannon Lab, 2014) and BBMap (Bushnell, 2014).
Then the trimmed reads were mapped to the reference genome using TopHat (Cole Trapnell et al., 2009). Gene expression levels were estimated using FPKM (Fragments Per kb per Million reads) values by Cufflinks (Roberts et al., 2011).
The FPKM values were normalized based on Quantile normalization method using EdgeR within R (R development Core Team, 2016).
Assembly: rn6
Supplementary files format and content: The processed data files are in text format and consist of the FPKM values for each sample.

organism: Rattus norvegicus

source_name: Rat bladder tissue

growth_protocol: Human embryonic stem-cell (hESC)-derived multipotent stem-cells (M-MSCs) were were cultured with EGM2-MV medium (Lonza, San Diego, CA) on plates coated with rat tail collagen type I (Sigma-Aldrich, St. Louis, MO) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA from the indicated bladder tissues was isolated using the RNeasy Mini Kit (QIAGEN, Valencia, CA), including treatment with DNase I (QIAGEN)
Libraries were prepared from total RNA using the NEBNext Ultra II Directional RNA-Seq Kit

treatment_protocol: Streptozotocin (STZ) was used to induce type I diabetes. After fasting overnight, rats were injected intraperitoneally with STZ (50 mg/kg) dissolved in 0.1 M citrate acid buffer (pH 4.5) solution. For the non-diabetic control group, rats were injected with an equivalent volume of citrate buffer solution. Three weeks after induction of diabetes, stem cells were transplanted into diabetic mice. After 1 weeks, all rats were sacrificed and whole bladder tissues were prepared to isolate total RNA.

tag: tissue

value: Rat bladder tissue


title: media only_0_10d_2pool1_S337

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S337

value: liver spheroids

tag: replicate


title: CITCO_hCAR1

description:
Lexogen QuantSeq protocol
37

value: hCAR/hPXR


title: 4PVPC1000K


title: Piezo1 CKO_NEC2

city: Changchun

first: Zhenyu

address: No.1 Xinmin Street

institute: The First Hospital of Jilin University

description: Library name: Sample11

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: xlsx file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Small intestine

extract_protocol:
Trizol was used to isolate the RNA of intestinal tissues. 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770) following manufacturer's protocols.

value: Small intestine

value: Piezo1 knockout (CKO)


title: s53_PFC_ATAC

value: brain

tag: classification

value: Male

tag: ethnicity


title: Piezo1 CKO_NEC1

description: Library name: Sample10


title: 1PVPC1000K


title: s52_PFC_ATAC

tag: ph

tag: pmi


title: media only_0_24h_2pool1_S145

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S145

tag: cell line

value: media only


title: 4STZ


title: Piezo1 CKO_control3

description: Library name: Sample9


title: s51_PFC_ATAC

value: Cases

value: Schizophrenia

tag: rin


title: media only_0_24h_1pool1_S49

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S49

tag: chemical


title: s49_PFC_ATAC

tag: disease status

value: Female

value: European


title: s50_PFC_ATAC

tag: lib batch


title: 3STZ


title: Piezo1 CKO_control2

description: Library name: Sample8


title: gwscreen_JS056_NUP98_KDM5A

source_name: NUP98::KDM5A (Cas9 clone)

value: NUP98::KDM5A (Cas9 clone)

value: acute myeloid leukemia cells


title: DMSO_0_10d_2pool1_S329

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S329

value: DMSO


title: DMSO_0_10d_1pool1_S233

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S233


title: 2STZ


title: 3sham


title: s48_PFC_ATAC

value: Controls

value: Control

tag: Sex


title: Piezo1 CKO_NEC3

description: Library name: Sample12

tag: genotype


title: Piezo1 flox_NEC3

description: Library name: Sample6

value: floxed control


title: media only_0_10d_1pool1_S241

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S241

value: liver spheroids


title: DMSO_0_24h_2pool1_S137

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S137


title: Piezo1 flox_NEC2

description: Library name: Sample5


title: 2sham

value: Rat bladder tissue


title: DMSO_0_24h_1pool1_S41

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S41


title: Piezo1 flox_NEC1

description: Library name: Sample4

value: Small intestine


title: s46_PFC_ATAC


title: DMSO_0_10d_2pool1_S321

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S321


title: s47_PFC_ATAC


title: SW1736-sh.Ctrl, Replicate2, RBM10-WT

city: New York

first: Gnana

middle: P

last: Krishnamoorthy

state: New York

address: 1275 York Avenue

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering cancer center

description: Library name: SW1736_Sh_scrm_Rep2_IGO_07389_30_S16

data_processing:
Transcript counts were obtained using Partek Flow version 6.0.17.0614 (www.partek.com). Briefly, raw reads were aligned to human assembly hg19 using STAR aligner (STAR-2.5.3a) with default parameters. The aligned reads were quantified to Partek E/M annotation model using hg19 assembly generating gene and transcript counts.
Assembly: hg19
Supplementary files format and content: Matrix table with transcript counts for every gene and every sample

growth_protocol: The biological replicates of RBM10 overexpressing or KD isogenic thyroid cancer cell lines were cultured in vitro, where applicable treated with doxycyclin to induce RBM10 expression for 72 hours prior to RNA-sequencing.

extract_protocol:
RNA was extracted from the 5 isogenic RBM10 overexpressing or KD thyroid cancer cell lines using the Qiagen RNeasy extraction kit
500 ng of total RNA with RQN values of 9.1-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR.  Samples were barcoded and run on a HiSeq in a PE125 run, using the HiSeq 3000/4000 SBS Kit (Illumina).  An average of 100 million paired reads was generated per sample.

tag: cell type

value: Thyroid cancer cell line


title: Piezo1 flox_control2

description: Library name: Sample2


title: Piezo1 CKO_control1

description: Library name: Sample7

value: Piezo1 knockout (CKO)


title: s45_PFC_ATAC

value: brain


title: SW1736-sh.Ctrl, Replicate1, RBM10-WT

description: Library name: SW1736_Sh_scrm_Rep1_IGO_07389_29_S26


title: DMSO_0_10d_1pool1_S225

city: Ottawa

first: Matthew

address: 251 Sir Frederick Banting Driveway

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S225

tag: dose


title: s43_PFC_ATAC

value: Male


title: Piezo1 flox_control1

description: Library name: Sample1


title: DMSO_0_24h_2pool1_S129

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S129

tag: timepoint


title: SW1736-sh.RBM10-B, Replicate2 RBM10-KD

description: Library name: SW1736_Sh_B_Rep2_IGO_07389_28_S12


title: DMSO_0_24h_1pool1_S33

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S33


title: SW1736-sh.RBM10-B, Replicate1 RBM10-KD

description: Library name: SW1736_Sh_B_Rep1_IGO_07389_27_S2


title: s42_PFC_ATAC

description: Single-cell ATAC sequencing  (10xGenomics)

tag: age


title: DMSO_0_10d_2pool1_S313

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S313


title: granulosa cells, hCG, 3h, rep1

city: Lexington

first: Jacqueline

middle: Nichole

last: Southall

state: KY

address: 800 Rose Street

department: OB/GYN

institute: University of Kentucky

data_processing:
Raw sequencing were processed with nf-core/chipseq (-r 2.0.0) pipeline
ChIP-seq reads were trimmed with TRIMGALORE
ChIP-seq reads were aligned to the mouse genome (mm10) using BWA
Peaks were called with MACS2 v2.2.7.1 with the significance cut-off q-value of <0.05
bigWig files were generated from the aligned BAM files to visualize read coverage across the genome. Coverage was calculated using deeptools bamCoverage (v3.5.1) with a bin size of 10 bp and CPM (Counts Per Million) normalization.
Assembly: mm10
Supplementary files format and content: txt

source_name: Ovary

extract_protocol:
Cells were fixed in fresh 11% formaldehyde for 15 minutes, then were quenched with 2.5 M glycine solution. Cells were then sent to ActiveMotif (Carlsbad, CA), were treated with cell lysis buffer, then sonicated with the EpiShear probe sonicator (Active Motif, 53051)
ChIP-Seq libraries were prepared on an automated system (Apollo 342, Wafergen Biosystems/Takara)

treatment_protocol: Ovaries were extracted from PMSG-primed, 25-day-old female mice 3 h after hCG stimulation. Granulosa cells were isolated from the ovaries by follicule pucture.

tag: tissue

value: Ovary

value: Granulosa cells

value: Wildtype

tag: treatment

value: 3h hCG


title: SW1736-sh.RBM10-A, Replicate2 RBM10-KD

description: Library name: SW1736_Sh_A_Rep2_IGO_07389_26_S1


title: SW1736-sh.RBM10-A, Replicate1 RBM10-KD

description: Library name: SW1736_Sh_A_Rep1_IGO_07389_25_S27


title: s41_PFC_ATAC

value: Cases

tag: classification

value: BipolarDisorder

value: Female

value: European


title: s40_PFC_ATAC

value: Schizophrenia

tag: ethnicity


title: DMSO_3

data_processing:
Raw files were preprocessed with prinseq-lite, aligned against the mouse (mm10) reference genome with BWA (version 0.7.17-r1188), post-processed and sorted with samtools (version 1.13). The function bamCoverage from Deeptools (version 3.5.1) was then used to create BigWig files with a binSize of 10 and using CPM for normalization. Also tornado -and profile-plots were created with Deeptools (computeMatrix and then plotHeatmap or plotProfile). Peaks were called with macs2 (version 2.1.0) and the --broad option.
Assembly: ATAC-seq: mm10
Supplementary files format and content: ATAC-seq: BigWig files and peak files for all samples

growth_protocol: All NUP98::KDM5A cell lines were cultured in RPMI 1640 supplemented with 10% FBS, 100 U/ml penicillin and 100 µg/ml streptomycin, 4 mM L-Glutamine, 1 mM Sodium pyruvate, 50 µM 2-Mercaptoethanol and 20 mM HEPES at 37 °C, 5% CO2, and 95% humidity.

extract_protocol:
ATAC-seq: cells were harvested by centrifugation, washed with PBS, counted and subsequent DNA-isolation and library preparation was performed on 50.000 cells using Tagment DNA TDE1 Enzyme and Buffer Kits (Illumina, CA, USA).
ATAC-seq: library preparation was performed on 50.000 cells using Tagment DNA TDE1 Enzyme and Buffer Kits (Illumina, CA, USA).

treatment_protocol: ATAC-seq: cells were treated with DMSO (1:1000 diluted) for 8 hours.

value: acute myeloid leukemia cells

value: DMSO


title: 1sham

value: Rat bladder tissue


title: DMSO_0_10d_1pool1_S217

last: Meier

institute: Government of Canada

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S217

value: liver spheroids

tag: replicate


title: DMSO_0_24h_1pool1_S25

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S25


title: DMSO_0_24h_2pool1_S121

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S121


title: DMSO_2


title: granulosa cells, hCG, 3h, FOS_ChIPseq, rep1


title: HTH83-sh.Ctrl, Replicate1, RBM10-WT

description: Library name: Hth83_Sh_scrm_Rep1_IGO_07389_23_S3

value: Thyroid cancer cell line


title: HTH83-sh.RBM10-B, Replicate2 RBM10-KD

description: Library name: Hth83_Sh_B_Rep2_IGO_07389_22_S13


title: s44_PFC_ATAC

value: MajorDepression

tag: ph

tag: pmi


title: s38_PFC_ATAC

value: brain

tag: rin


title: Mouse megakaryocyte Dnmt3a+/– biol rep 2

description:
Illumina NovaSeq 6000 and NextSeq 2000
FASTQ files combined from runs on both instruments

data_processing:
Raw sequencing reads were initially trimmed using cutadapt to remove potential adaptor contamination and low-quality reads based on the default threshold for each EM-Seq profile
The remaining reads were then aligned to the reference mouse genome (mm10) using Bismark (v2.5.1), enabling us to identify methylation states at single- base resolution.
The aligned reads were further filtered using Picard (biotools:picard_tools, RRID:SCR_006525, http://broadinstitute.github.io/picard/) to remove PCR duplicates.
The CpG methylation information was extracted with Bismark’s bismark_methylation_extractor module.
Under-methylated regions (UMRs) were detected using a Hidden Markov Model within iBSTools [https://github.com/methylation/iBSTools]
Differentially methylated regions (DMRs) were identified using Metilene (v.0.2-8), with criteria including a minimum mean DNA methylation difference of 0.2, at least 10 CpG sites, a p-value less than 0.01, and a length greater than 500bp. DMR-associated genes were further annotated using the R package ChIPseeker
Assembly: mm10
Supplementary files format and content: Bigwig (.bw) files containing methylation data for each sample
Library strategy: Enzymatic methyl-seq

source_name: Megakaryocytes

growth_protocol: Megakaryocyte culture: Bone marrow cells were resuspended in DMEM/ 10% FCS/ 1% p/s / 2 mM L-glutamine with 50 ng/mL TPO and 100 U/mL rHirudin (megakaryocyte medium). The cells were cultured in a 6-well plate (1 well per mouse) in 3 mL media at 37 °C in 5% CO2 for three days. Megakaryocytes were purified using a BSA gradient made with low endotoxin BSA. 2 mL of warm 1.5% BSA in PBS was layered on top of 2 mL of warm 3% BSA in PBS. The cells were resuspended in 1 mL of warm PBS and layered on top of the gradient. The cells were allowed to settle through the gradient at RT for 30 min, and then all volume above 500 μL was removed.

extract_protocol:
DNA was isolated using the Qiagen Allprep DNA/RNA micro kit (80284).
>10 ng of DNA was used as input for the NEBNext Enzymatic Methyl-Seq kit (NEB E7120S), and libraries were prepared according to the manufacturer’s instructions. Library quality was assessed using a D5000 screentape (Agilent 5067-5588).

value: Megakaryocytes

value: 6 months


title: DMSO_0_10d_1pool1_S209

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S209

tag: cell line

tag: chemical


title: s37_PFC_ATAC

tag: disease status

value: Male

tag: lib batch


title: HTH83-sh.Ctrl, Replicate2, RBM10-WT

description: Library name: Hth83_Sh_scrm_Rep2_IGO_07389_24_S14

tag: genotype


title: s36_PFC_ATAC

value: Controls

value: Control

tag: Sex


title: DMSO_0_24h_2pool1_S113

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S113

tag: dose


title: Mouse megakaryocyte WT biol rep 2

tag: cell type

value: WT


title: HTH83-sh.RBM10-A, Replicate2 RBM10-KD

description: Library name: Hth83_Sh_A_Rep2_IGO_07389_20_S15


title: s35_PFC_ATAC

tag: age


title: DMSO_0_24h_1pool1_S17

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S17

tag: timepoint


title: s39_PFC_ATAC

tag: tissue

value: Cases

value: BipolarDisorder


title: DMSO_0_10d_2pool1_S297

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S297


title: Mouse megakaryocyte WT biol rep 1

value: Female


title: Mouse megakaryocyte-erythroid progenitors Dnmt3a+/– biol rep 2

source_name: Megakaryocyte-erythroid progenitors

value: Megakaryocyte-erythroid progenitors


title: s34_PFC_ATAC

tag: classification

value: Schizophrenia

value: European


title: 8305C-sh.Ctrl, Replicate2, RBM10-WT

description: Library name: 8305C_Sh_scrm_Rep2_IGO_07389_18_S7


title: s33_PFC_ATAC

description: Single-cell ATAC sequencing  (10xGenomics)

tag: ethnicity


title: HTH83-sh.RBM10-A, Replicate1 RBM10-KD

description: Library name: Hth83_Sh_A_Rep1_IGO_07389_19_S5


title: DMSO_0_10d_2pool1_S305

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S305

value: DMSO

tag: replicate


title: DMSO_1

value: acute myeloid leukemia cells

tag: treatment


title: DMSO_0_10d_1pool1_S201

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S201

value: liver spheroids


title: Mouse megakaryocyte-erythroid progenitors Dnmt3a+/– biol rep 1


title: s32_PFC_ATAC

tag: ph

tag: pmi


title: 8305C-sh.Ctrl, Replicate1, RBM10-WT

description: Library name: 8305C_Sh_scrm_Rep1_IGO_07389_17_S31

tag: cell line

value: Thyroid cancer cell line


title: HTH83-sh.RBM10-B, Replicate1 RBM10-KD

description: Library name: Hth83_Sh_B_Rep1_IGO_07389_21_S29


title: Mouse megakaryocyte Dnmt3a+/– biol rep 1


title: 8305C-sh.RBM10-B, Replicate2 RBM10-KD

description: Library name: 8305C_Sh_B_Rep2_IGO_07389_16_S24


title: s31_PFC_ATAC

value: brain

value: MajorDepression

tag: rin


title: DMSO_0_24h_1pool1_S9

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S9

tag: chemical


title: 8305C-sh.RBM10-B, Replicate1 RBM10-KD

description: Library name: 8305C_Sh_B_Rep1_IGO_07389_15_S6


title: Mouse megakaryocyte-erythroid progenitors WT biol rep 1

description:
Illumina NovaSeq 6000 and NextSeq 2000
FASTQ files combined from runs on both instruments

value: 6 months


title: s30_PFC_ATAC

tag: disease status

value: SchizoaffectiveDisorder

tag: lib batch


title: negative control_0_10d_2pool1_S377

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S377

value: negative control


title: 8305C-sh.RBM10-A, Replicate2 RBM10-KD

description: Library name: 8305C_Sh_A_Rep2_IGO_07389_14_S8

tag: genotype


title: CX3KO Hypoxic #6

city: San Antonio

first: Astrid

last: Cardona

state: Texas

address: One UTSA Circle

department: Molecular Microbiology and Immunology

institute: University of Texas at San Antonio

data_processing:
CLC Genomics Workbench v21.0.5 by the Universityof Texas at San Antonio Genomics Core (San Antonio, TX)
Aligned to reference mouse genome GRCm39
Assembly: mm10
Supplementary files format and content: Comma-deliniated files contain verbose output from CLC genomics workbench alignment, uncluding TMP, RPKM and unique counts

source_name: Retina

extract_protocol:
Mechanical homogenization followed by Trizol™ extraction
Libraries were constructed by the University of Texas Health Science Center Genome Sequencing Facility (Greehy Children's Cancer Research Institute, San Antonio Texas) utilizing NEB Directional mRNA-seq sample preparation guide (New England Biolabs, Ipswich, MA)

treatment_protocol: Normoxic: animals maintained at ambient oxygen (~22%). Hypoxic: animals maintained at 7.5% oxygen for 7-days

value: Retina

value: Hypoxic


title: negative control_0_10d_1pool1_S281

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S281

tag: dose


title: s28_PFC_ATAC

value: Controls

value: Control

tag: Sex

value: Male


title: s27_PFC_ATAC

tag: age


title: PE121410-RBM10 cells, cloneB, Replicate2, RBM10 re-expression

description: Library name: PE_Cl_B_Rep2_IGO_07389_12_S25

tag: cell type


title: Mouse megakaryocyte-erythroid progenitors WT biol rep 2

value: Megakaryocyte-erythroid progenitors

value: WT

value: Female


title: negative control_0_24h_2pool1_S185

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S185

tag: timepoint


title: 8305C-sh.RBM10-A, Replicate1 RBM10-KD

description: Library name: 8305C_Sh_A_Rep1_IGO_07389_13_S18


title: CX3KO Hypoxic #4

tag: tissue


title: s29_PFC_ATAC

tag: classification

tag: ethnicity

value: European


title: CX3KO Hypoxic #5

tag: treatment


title: negative control_0_24h_1pool1_S89

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S89

tag: replicate


title: CX3KO Hypoxic #3

value: Normoxic


title: s26_PFC_ATAC

description: Single-cell ATAC sequencing  (10xGenomics)

tag: ph

tag: pmi


title: PE121410-RBM10 cells, cloneA, Replicate2, RBM10 re-expression

description: Library name: PE_Cl_A_Rep2_IGO_07389_10_S19

tag: cell line


title: PE121410-RBM10 cells, cloneB, Replicate1, RBM10 re-expression

description: Library name: PE_Cl_B_Rep1_IGO_07389_11_S11


title: DMSO_0_24h_2pool1_S105

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S105

value: liver spheroids

tag: chemical

value: DMSO


title: universal human reference RNA_0_10d_2pool1_S369

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S369

value: universal human reference RNA


title: WT Hypoxic #6

value: Wild Type


title: WT Hypoxic #4


title: universal human reference RNA_0_10d_1pool1_S273

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S273


title: s25_PFC_ATAC

value: brain

tag: disease status

tag: rin


title: WT Hypoxic #5

tag: genotype


title: s24_PFC_ATAC

value: Cases

value: Schizophrenia

tag: lib batch


title: PE121410-RBM10 cells, cloneA, Replicate1, RBM10 re-expression

description: Library name: PE_Cl_A_Rep1_IGO_07389_9_S20

value: Thyroid cancer cell line


title: PE121410 cells, Replicate2, RBM10-mut

description: Library name: PE_Parental_Rep2_IGO_07389_8_S28


title: s23_PFC_ATAC

tag: Sex


title: PE121410 cells, Replicate1, RBM10-mut

description: Library name: PE_Parental_Rep1_IGO_07389_7_S4


title: CX3KO Normoxic #3

value: Retina

value: Hypoxic


title: human brain RNA_0_24h_1pool1_S73

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S73

value: human brain RNA

tag: dose


title: s19_PFC_ATAC

value: SchizoaffectiveDisorder

tag: age

value: Male


title: human brain RNA_0_10d_2pool1_S361

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S361

tag: timepoint


title: universal human reference RNA_0_24h_1pool1_S81

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S81


title: s20_PFC_ATAC

tag: tissue


title: KTC1-RBM10 cells, cloneB, Replicate2, RBM10 re-expression

description: Library name: KTC_Cl_B_Rep2_IGO_07389_6_S22

tag: cell type


title: s21_PFC_ATAC

tag: classification

tag: ethnicity


title: CX3KO Normoxic #2

tag: treatment


title: CX3KO Hypoxic #2


title: KTC1-RBM10 cells, cloneB, Replicate1, RBM10 re-expression

description: Library name: KTC_Cl_B_Rep1_IGO_07389_5_S23


title: universal human reference RNA_0_24h_2pool1_S177

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S177

tag: replicate


title: human brain RNA_0_10d_1pool1_S265

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S265


title: KTC1-RBM10 cells, cloneA, Replicate1, RBM10 re-expression

description: Library name: KTC_Cl_A_Rep1_IGO_07389_3_S10


title: human brain RNA_0_24h_2pool1_S169

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S169


title: CX3KO Normoxic #1


title: CX3KO Hypoxic #1


title: KTC1 cells, Replicate2, RBM10-mut

description: Library name: KTC_Parental_Rep2_IGO_07389_2_S17


title: KTC1-RBM10 cells, cloneA, Replicate2, RBM10 re-expression

description: Library name: KTC_Cl_A_Rep2_IGO_07389_4_S30


title: DMSO_0_10d_1pool1_S193

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S193


title: WT Hypoxic #3


title: s22_PFC_ATAC

description: Single-cell ATAC sequencing  (10xGenomics)

value: BipolarDisorder

tag: ph

tag: pmi


title: s18_PFC_ATAC

value: Controls

value: Control


title: Piezo1 flox_control3

last: Li

description: Library name: Sample3

value: Small intestine

value: floxed control


title: s17_PFC_ATAC

value: Female

value: European


title: KTC1 cells, Replicate1, RBM10-mut

description: Library name: KTC_Parental_Rep1_IGO_07389_1_S21

tag: cell line


title: s16_PFC_ATAC

tag: disease status


title: DMSO_0_10d_2pool1_S289

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S289

value: liver spheroids

tag: chemical

value: DMSO


title: DMSO_0_24h_2pool1_S97

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S97