title: MNase-TGFb

data_processing:
sequencing reads were trimmed and filtered for quality and adapter content using version 0.4.5 of TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore), with a quality setting of 15 and running cutadapt (v1.15) and FastQC (v0.11.5). Reads were aligned to mouse assembly mm10 with version 2.3.4.1 of bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and were deduplicated using MarkDuplicates in version 2.16.0 of Picard Tools. To ascertain regions of chromatin accessibility, MACS2 (https://github.com/taoliu/MACS) was used with a p-value setting of 0.001. ChIP and CUT&RUN target enrichment also used MACS2 with the same parameters and scored against matched input or IgG as the control, respectively. The BEDTools suite v2.29.2 (http://bedtools.readthedocs.io) was used to create normalized read density profiles. A global peak atlas was created by first removing blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/ mm10-mouse/mm10.blacklist.bed.gz) then merging all peaks within 500 bp for ChIP and CUT&RUN or taking 500 bp windows around peak summits for ATAC and counting reads with featureCounts (v1.6.1). DESeq2 was used to normalize read density (median ratio method) and to calculate differential enrichment for all pairwise contrasts. Peak-gene associations were created by assigning all intragenic peaks to that gene, and otherwise using linear genomic distance to transcription start site. Peak intersections were calculated using bedtools and intersectBed with 1 bp overlap. Gene set enrichment analysis (GSEA, http://software.broadinstitute.org/gsea) was performed with the pre-ranked option and default parameters, where each gene was assigned the single peak with the largest (in magnitude) log2 fold change associated with it. Motif signatures were obtained using Homer v4.5 (http://homer.ucsd.edu).
Assembly: mm10
Supplementary files format and content: bw

extract_protocol:
Samples containing 1x107 cells were were washed twice with cold PBS and cell pellets were resuspended with cold MNase-RSB (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 1 mM MgCl2). After incubation on ice for 10 min, 10% Nonidet P-40 was added to make a final 0.5% Nonidet P-40 and cells were homogenously mixed by inverting. Nuclei were pelleted at 1300xg for 5 min and resuspended with MNase-digestion buffer (10 mM Tris-HCl pH 8.0, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2, 250 mM sucrose, 0.5 mM dithiothreitol, DTT). Nuclei were incubated with varying concentrations of MNase to optimize the fragmentation (~60% mononucleosome, ~20% dinucleosome, and ~10% trinucleosome). We treated nuclei with 100 U of MNase (Thermo Fisher Scientific, Cat #: 88216). After incubation for 5 min at 37ºC with mixing, stop solution (1% SDS, 100 mM NaHCO3, 20 mM EDTA) was added and incubated at 65ºC for 90 min. DNA fragments were incubated with Tris-HCl pH 7.5, Proteinase K and Glycoblue (Thermo Fisher Scientific, Cat #: AM9515) for 16 h at 65ºC. Mononucleosomal DNA (~147 bp) was extracted using QIAquick Gel Extraction Kit (Qiagen).
Immunoprecipitated DNA was quantified by PicoGreen and the size was evaluated by Agilent BioAnalyzer. Illumina sequencing libraries were prepared using the KAPA HTP Library Preparation Kit according to the manufacturer’s instructions with 0.02-5 ng input DNA and 8-14 cycles of PCR.


title: LNCaP_0m_rep1_STARTseq

status: Public on Sep 26 2024

type: SRA

city: Vancouver

first: Nathan

middle: A

last: Lack

state: BC

address: 2660 Oak S

country: Canada

institute: Vancouver Prostate Centre

description: nascent RNA

library_source: other

data_processing:
Adaptor sequences and low-quality 3′ ends were removed from paired-end reads of all samples using cutadapt (v1.2.1).
Reads shorter than 20 nucleotides were discarded (-m 20 -q 10), and a single nucleotide was trimmed from the 3′ end of all remaining reads to enable successful alignment with bowtie (v1.1.1).
The first in pair flagged reads were filtered to generate signal (bigwig) files for each strand using bedtools genomecov (-bg -5 -strand +/-,respectively).
Assembly: hg19
Supplementary files format and content: BigWig
Library strategy: Start-seq

molecule: other

organism: Homo sapiens

source_name: LNCaP

growth_protocol: LNCaP cells were grown in RPMI with 10% FBS and antiboitics.

extract_protocol:
RNA was extracted using TRIzol.
Libraries were prepared using the TruSeq Small RNA Kit (Illumina)

treatment_protocol: LNCaP cells were grown in phenol red free RPMI (#11835030, GIBCO) with 10% charcoal stripped FBS (#100-119, GemBio) for 3 days and then were stimulated with 10 nM dihydrotestosterone (DHT) (5α-Androstan-17β-ol-3-one, A8380, Sigma) for 30 min, 4 hr, 16 hr or 72 hr.

tag: cell line

value: LNCaP

tag: treatment

value: EtOH


title: 11033_MN_Diff3

city: Minneapolis

first: Ying

last: Zhang

state: MN

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

country: USA

institute: University of Minnesota

library_source: transcriptomic

data_processing:
Raw, paried reads were processed via CHURP pipelien (https://github.com/msi-ris/CHURP) using default setting.
The cleaned gene count table per sample was analyzed with R (v4.1.0) package edgeR to identify differentially expressed genes.
R package clusterProfiler was used for pathway enrichment. Various R packages, including pheatmap and ggplto2, were used to generate visualization plots.
Assembly: GRCh38
Supplementary files format and content: Txt file of Tab separated values

molecule: total RNA

source_name: human MN derived from iPSCs

extract_protocol:
RNA was extracted using TRIZOL extraction protocol, 3nl of total RNA used fr construction of libraries
Library construction and sequencing were done by University of Minnesota Genomic Center according to the manufacter’s instructions (Illumina TruSeq Stranded).

value: human MN derived from iPSCs

tag: genotype

value: WT


title: antiNrf1_control_1

city: Farmington

first: Jinhong

last: Dong

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

description: antiNrf1-control_merged_normalized.bigWig

library_source: genomic

data_processing:
Adapter trimming: cutadapt
Alignment: bowtie2
File manipulation: samtools v1.16.1
File manipulation: https://github.com/guertinlab/seqOutBias v1.4.0
Peak calling: macs3
File manipulation: bedtools
Assembly: hg38
Supplementary files format and content: bigWig counts files
Supplementary files format and content: peak summit counts files

molecule: genomic DNA

growth_protocol: HEK293T-ZNF143-dTAG cells were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (R&D Systems), 1% L-glutamine (Gibco), 1% sodium pyruvate (Gibco), and 1% penicillin-streptomycin (Gibco).

extract_protocol:
After treatment, cells were fixed with 1% formaldehyde for 10 minutes at 37°C and quenched with 125mM Glycine (Fisher) for 10 minutes at 37°C. Plates were moved to ice, and cells were washed and scraped into ice cold PBS containing Complete EDTA-free Protease Inhibitor Cocktail (Roche). Cells were pelleted in aliquots of 2*10^7 cells, snap frozen in liquid nitrogen, and stored at -80°C. Pellets were thawed, and cells were lysed in 1mL ChIP Lysis Buffer (0.5% SDS, 10mM EDTA, 50mM Tris-HCL pH 8.0), with protease inhibitor cocktail added fresh, for 10 minutes with rotation at 4°C. Lysates were sonicated at 70% amplitude for 15 seconds on and 45 seconds off for 4 sets of 20-minute cycles. Sonicated lysates were moved to 1.5ml tubes and clarified by centrifugation at 14,000rpm for 10 min in 4°C. 50μL of the supernatant was diluted into 760μL ChIP Dilution Buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 167mM NaCl, 16.6mM Tris-HCl pH 8.0), with protease inhibitor cocktail added fresh (1*10^6 cells in 200μL). 1ml (4*106 cells) was aliquoted into each of 3 tubes with antibody (7.32μg anti-NRF1 Invitrogen MA5-35366 or 3μg anti-YY1 Invitrogen 703054), and incubated with end-over-end rotation at 4°C overnight. 80μL Protein A/G Magnetic Beads (New England Biolabs) per sample were washed with bead washing buffer (PBS with 0.1% BSA and 2mM EDTA) and then incubated with samples for 90 minutes with rotation at 4°C. The samples were washed once each with low salt immune complex buffer (0.1% SDS, 1% Triton x-100, 2mM EDTA, 150mM NaCl, 20mM Tris HCl pH8.0), high salt immune complex buffer (0.1% SDS, 1% Triton x-100, 2mM EDTA, 500mM NaCl, 20mM Tris Hcl pH 8.0), LiCl immune complex buffer (0.25M LiCl, 1% NP-40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl pH8.0), and 1xTE (10mM Tris-HCl, 1mM EDTA pH8.0). Immune complexes were eluted in elution solution, (1% SDS, 0.1M sodium bicarbonate). 1μl RNase A was added to each sample for 10 min at 37°C. Proteins were digested with the addition of 5μl Proteinase K and incubated in a 65°C water bath overnight.
DNA was purified with a MinElute PCR purification kit (Qiagen), and libraries were prepared with a NEBNext Ultra II Library Prep Kit (New England Biolabs).

treatment_protocol: HEK-293T cells were harvested after either no treatment or after 30 minutes of 50nm dTAGV-1 treatment


title: MNase-SB

city: New York

first: Jun Ho

last: Lee

address: 417 E 68th St

institute: MSKCC

organism: Mus musculus

tag: cell type

value: Lung adenocarcinoma cells


title: 11033_MN_Diff1


title: DRIPc-RNasH

data_processing:
samtools (v1.8) and awk were used to separate positive and negative strand data into bedGraph files using the BEDTools script bedtoolsgenomecov and scaled to the number of mapped reads in each sample.
Assembly: mm10
Supplementary files format and content: bw

extract_protocol:
DNA was extracted by treating cell samples with SDS and Proteinase K at 37ºC overnight, followed by phenol-chloroform isoamyl alcohol extraction using phase lock gel tubes (VWR, Cat #: 10847-800) followed by ethanol precipitation. Extracted DNA was digested with restriction enzyme cocktail (BsrGI (NEB, Cat #: R3575S), EcoRI (NEB, Cat #: R3101S), HindIII (NEB, Cat #: R3104S), SspI (NEB, Cat #: R3132S), XbaI (NEB, Cat #: R0145S)) in NEB buffer 2 with 1 mM spermidine (Sigma Aldrich, Cat #: 05292-1ML-F) and bovine serum albumin (BSA) (NEB, Cat #: B9001) at 37ºC overnight. Digested DNAs were purified by phenol-chloroform isoamyl alcohol (Thermo Fisher Scientific, Cat #: 15593031) extraction using phase lock gel tube followed by ethanol precipitation. 10 μg of digested DNA were incubated with RNase H (NEB, Cat #: M0297S) for 6 h at 37ºC in RNase H buffer. 8 μg of DNA/RNA hybrids treated with RNase H and 8 μg of DNA/RNA hybrids from five separate tubes without RNase H were immunoprecipitated with S9.6 antibodies (Millipore Sigma, Cat #: MABE1095) at 4ºC overnight on rotator. Dynabeads™ Protein G beads were blocked with 2.5 mg/mL UltraPure™ BSA (Thermo Scientific) at 4ºC overnight. The beads were then washed twice with binding buffer (10 mM NaPO4 pH 7.0, 140 mM NaCl and 0.05% Triton X-100, 10 mM Tris-HCl pH 8 and 1 mM EDTA) and incubated with the DNA/RNA-antibody samples at 4ºC for 2 h. The beads were washed three times with binding buffer, followed by incubation with 300 μL of elution buffer and 7 μL of proteinase K at 55ºC for 45 min with mixing. After incubation, DNA/RNA hybrids were separated by magnetic rack and subjected to Phenol-Chloroform Isoamyl alcohol extraction using phase lock gel tubes followed by ethanol precipitation.
Recovered DNA/RNA hybrids were incubated with DNase I (NEB, Cat #: M0303S) at 37ºC for 45 min and DNase I was then inactivated by addition of 1 μL of 0.5 M EDTA, pH 8.0 and incubation at 75ºC for 15 min. Ethanol-precipitated RNA strands were subjected to reverse transcription with IScript reverse transcription supermix (BioRad, Cat #: 1708840) per manufacturer’s instructions. cDNA samples were cleaned by AMPure XP beads to recover DNA fragments 200-500 bp. Eluted fragments were subjected to second strand synthesis with dUTP followed by AMPure XP bead purification. Samples were subjected to sonication using a Diagenode Bioruptor with 15 cycles, end repair (NEB, Cat #: E6050), dATP-tailing (NEB, Cat #: M0212S), and adaptor ligation with TruSeq Single indexes (Illumina, Cat #: 20015960). Libraries then cleared of uracil-containing DNA strands using uracil N-glycosylase (Thermo Fisher Scientific, Cat #: N8080096), amplified, and purified with AMPure XP beads.


title: rS-C

city: seoul

first: Eun Joo

address: 81, Irwon-ro

country: South Korea

institute: encellinc

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Wharton's Jelly

growth_protocol: mesenchymal  stem cells were maintained in MEM alpha supplemented with 10% fetal bovine serum (FBS) and 0.5% gentamycin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using the AccuPrep® Universal RNA Extraction Kit (Bioneer). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

treatment_protocol: WJ-MSCs were grown in culture medium with DMSO or 10uM BPTES(Sigma) for 24 h.

tag: tissue

value: Wharton's Jelly

value: mesenchymal stem cells


title: HCT116 DPF2 R350H, doxorubicin, rep2

city: Daejeon

first: Kim

last: Hyoungmin

address: 291, Daehak-ro, Yuseong-gu, Daejeon, 34141, Rep. of KOREA

department: Department of Biological Sciences

institute: Korea Advanced Institute of Science and Technology

data_processing:
RNA-seq reads were filtered with FastQC (v0.11.4) and trimmed with TrimGalore (v0.6.10).
Reads were alinged to hg38 using STAR (v2.7.5a) with default parameter.
Bam files quantification was performed with featureCount (v1.5.0-p1) with parameter -Q 10.
DEG analysis was perfomed with DESeq2 (v1.36.0).
Assembly: hg38
Supplementary files format and content: Tab-delimited tsv file includes TPM values for each sample.
Supplementary files format and content: Tab-delimited text files include featureCount count values. Input counts file for DESeq2.

growth_protocol: HCT116 cells were maintained in McCoy's 5A (modified) medium supplemented with 10% FBS in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Total RNA was prepared using TRIzol (Invitrogen).
RNA libraries were generated using a TruSeq stranded mRNA library kit (Illumina).

treatment_protocol: HCT116 cells were treated with 0.5 μM doxorubicin for 24 hours.

value: Colon cancer cell line

value: DPF2 R350H

value: Doxorubicin


title: U-C


title: LNCaP_72h_rep1_RNAseq

data_processing:
Reads were aligned to the hg19 human genome built with STAR44 with quant mode (--quantMode TranscriptomeSAM).
Next, “toTranscriptome” bam files were fed into Salmon (v0.14.1)55 to quantify TPM values for (Gencode v19)54 transcripts.
FPKM values were calculated with Cufflinks45 for (Gencode v19) genes.
STAR as the default aligner and converts BAM files into BigWig files using Bedtools47.
Assembly: hg19
Supplementary files format and content: quant.sf (salmon output)
Supplementary files format and content: BigWig

extract_protocol:
Total RNA was collected from the cells using RNeasy kit (Qiagen, #74104,) with DNase I treatment (Qiagen, #79254).
RNAseq library was prepped by Novogene company. In brief, mRNA was enriched by capturing poy A followed by the fragmentaion of Covaris. Library was prepped after cDNA reverse transcription.

value: 72h 10nM DHT


title: LNCaP_16h_rep1_RNAseq

value: 16h 10nM DHT


title: DRIPc-SB


title: LNCaP_16h_rep2_RNAseq


title: HCT116 DPF2 R350H, doxorubicin, rep1


title: LNCaP_4h_rep2_RNAseq

value: 4h 10nM DHT


title: CnR-RNAPII_Dhx9KO_SB

data_processing:
Sequencing reads were trimmed and filtered for quality and adapter content using version 0.4.5 of TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore), with a quality setting of 15 and running cutadapt (v1.15) and FastQC (v0.11.5). Reads were aligned to mouse assembly mm10 with version 2.3.4.1 of bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and were deduplicated using MarkDuplicates in version 2.16.0 of Picard Tools. To ascertain regions of chromatin accessibility, MACS2 (https://github.com/taoliu/MACS) was used with a p-value setting of 0.001. ChIP and CUT&RUN target enrichment also used MACS2 with the same parameters and scored against matched input or IgG as the control, respectively. The BEDTools suite v2.29.2 (http://bedtools.readthedocs.io) was used to create normalized read density profiles. A global peak atlas was created by first removing blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/ mm10-mouse/mm10.blacklist.bed.gz) then merging all peaks within 500 bp for ChIP and CUT&RUN or taking 500 bp windows around peak summits for ATAC and counting reads with featureCounts (v1.6.1). DESeq2 was used to normalize read density (median ratio method) and to calculate differential enrichment for all pairwise contrasts. Peak-gene associations were created by assigning all intragenic peaks to that gene, and otherwise using linear genomic distance to transcription start site. Peak intersections were calculated using bedtools and intersectBed with 1 bp overlap. Gene set enrichment analysis (GSEA, http://software.broadinstitute.org/gsea) was performed with the pre-ranked option and default parameters, where each gene was assigned the single peak with the largest (in magnitude) log2 fold change associated with it. Motif signatures were obtained using Homer v4.5 (http://homer.ucsd.edu). Profile and tornado plots were created using deepTools v3.3.0 by running computeMatrix and plotHeatmap on normalized bigwigs with average signal sampled in 25 bp windows and flanking region defined by the surrounding 3 kb.
Assembly: mm10
Supplementary files format and content: bw

extract_protocol:
For ChIP, 1x107 cells were crosslinked at room temperature for 10 min by swirling with 1% formaldehyde (Sigma Aldrich) followed by addition of 125 mM glycine to quench the reaction. After washing the cells three times with PBS, cells were resuspended with ChIP lysis buffer (50 mM HEPES/KOH pH 7.5, 150 mM NaCl, 0.1% Na-deoxycholate, 1% Triton X-100, 1 mM EDTA, 0.1% SDS) supplemented with protease inhibitors (Roche, cOmplete, mini, EDTA-free protease inhibitor tablets, Cat #: 11836170001) and phosphatase inhibitors (Thermo Scientific, Halt Phosphatase Inhibitor Cocktail, Cat #: 78427, 1:1000). Cell lysates in 1 mL of ChIP lysis buffer were sonicated for sheared chromatin to be 200-500 bp. Supernatants cleared by centrifugation were incubated with the designated antibody at 4ºC overnight on a rotator. Dynabeads™ Protein G were blocked with 2.5 mg/mL UltraPure™ BSA (Thermo Scientific, Cat #: AM2616) at 4ºC overnight. The beads were then washed three times with ChIP buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100) and incubated with the chromatin-antibody samples at 4ºC for 1-2 h. These samples were washed 6 times with high salt ChIP buffer (20 mM Tris, pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% of Triton X-100, 0.1% of SDS) followed by two washings with Tris-EDTA (TE) buffer. Chromatin complexes were eluted twice in TE with 1% ultrapure SDS (Thermo Fisher Scientific) at 65ºC for 15 min, and reverse-crosslinked with RNAse A (Thermo Fisher Scientific, Cat #: EN0531) for 4 h or overnight, followed by incubation with Proteinase K solution (Thermo Fisher Scientific, Cat #: EO0491) for 1 h at 45ºC. DNA was purified using QIAquick PCR Purification Kit (Qiagen). For CUT&RUN, samples were prepared with CUTANA™ ChIC/CUT&RUN Kit (Epicypher, Cat #: 14-1048). For each CUT&RUN reaction, cell pellets (5x105 cells) were washed twice with wash buffer (20 mM HEPES–KOH, pH 8.0; 150 mM NaCl; 0.5mM spermidine; and protease inhibitor (Roche), followed by resuspension with wash buffer. Cells in wash buffer were incubated with activated Concanavalin-A beads for 10 min at room temperature. Beads were resuspended with immunoprecipitation buffer (Wash buffer; 0.01% digitonin; 2 mM EDTA) and incubated with 0.5 µg of designated antibody at 4ºC overnight on a nutator. The following day, beads were washed twice with digitonin buffer (wash buffer including 0.01% digitonin) and incubated with CUTANA pAG-MNase for 10 min at room temperature, followed by wash twice with digitonin buffer. pAG-MNase was activated by incubation with 1 µL of 100 mM CaCl2 for 2 h at 4ºC on nutator. The reaction was terminated by incubation with stop buffer for 10 min at 37 ºC in thermocycler. CUT&RUN enriched DNA was purified using CUTANA DNA purification kit (Epicypher, Cat #: 14-0050).
Immunoprecipitated DNA was quantified by PicoGreen and the size was evaluated by Agilent BioAnalyzer. Illumina sequencing libraries were prepared using the KAPA HTP Library Preparation Kit (Kapa Biosystems, Cat #: KK8234) according to the manufacturer’s instructions with 0.02-5 ng input DNA and 8-14 cycles of PCR.
Barcoded libraries were run on the NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S2 or S4 Reagent Kit (200 or 300 Cycles) (Illumina).


title: HCT116 DPF2 R350H, nontreated, rep1


title: DRIPc-TGFb


title: 11033_pMN_S199

source_name: human pre-MN derived from iPSCs

value: human pre-MN derived from iPSCs


title: CnR-RNAPII_Dhx9KO_TGFb

value: TGF-Beta for 1.5 h


title: HCT116 DPF2 R350H, nontreated, rep2


title: rS-A


title: LNCaP_4h_rep1_RNAseq


title: U-A


title: U-B


title: LNCaP_30m_rep2_RNAseq

value: 30m 10nM  DHT


title: HCT116 WT, doxorubicin, rep1


title: CnR-RNAPII_Ino80KO_TGFb


title: rS-MSC+BPTES

value: BPTES treatment


title: CnR-RNAPII_Ino80KO_SB


title: HCT116 WT, doxorubicin, rep2


title: rS-B


title: rS-MSC


title: CnR-RNAPII_Rreb1KO_TGFb


title: HCT116 WT, nontreated, rep1


title: A549 cells, sh4Control, biol_rep_2

city: Cambridge

first: Tony

last: Kouzarides

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Adapter sequences were trimmed from paired-end reads using Trimmomatic (v0.40-rc1)
Reads were aligned to the human reference genome (GRCh38.p14) using STAR (v2.7.10a), with –quantMode GeneCounts to quantify gene counts with the annotation source NCBI RefSeq reference transcriptome GTF file
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: A549 cells were grown in DMEM supplemented with 1 x penicillin-streptomycin (pen-strep) antibiotics and 10% [v/v] foetal bovine serum (FBS).

extract_protocol:
RNeasy Mini Kit (QIAGEN, 74104) was used for RNA extraction. An additional step of DNase digestion was incorporated after the first wash following the RNase-Free DNase Set protocol (QIAGEN, 79254). 13 µl of rRNA depleted RNA sample were used for the preparation of the RNA-seq library.
The NEXTFLEX® Rapid Directional RNA- Seq Kit 2.0 protocol was followed to perform all the remaining steps for library construction steps.

value: lung carcinoma epithelial cells


title: HCT116 WT, nontreated, rep2


title: U-MSC


title: CnR-RNAPII_Rreb1KO_SB


title: A549 cells, deep_sequencing, shD3#1, biol_rep_3

value: THUMPD3 knockdown


title: A549 cells, deep_sequencing, shD3#1, biol_rep_2


title: MDA PCa 2b cells, enzalutamide resistant, replicate 3

city: Innsbruck

first: Florian

last: Handle

address: Müllerstrasse 44

department: Institute of Pathology, Neuropathology and Molecular Pathology

country: Austria

institute: Medical University of Innsbruck

data_processing:
Read alignment and feature counting was performed with the Rsubread package using the GENCODE release 43 (GRCh38.p13) genome assembly.
Assembly: GRCh38
Supplementary files format and content: counts.txt: Tab-delimited text file with ensemble gene ID, HUGO gene name and gene counts for each sample
Supplementary files format and content: log2CPM.txt: Tab-delimited text file with ensemble gene ID, HUGO gene name and log2 gene counts per million (CPM) for each sample

source_name: MDA PCa 2b

growth_protocol: MDA PCa 2b were cultivated according to the recommendations by ATCC.

extract_protocol:
RNA isolation was performed with the Blirt EXTRACTME TOTAL RNA KIT
Enrichment of mRNA using oligo(dT) beads  followed by strand specific library preparation.

treatment_protocol: Enzalutamide resistance was acquired by firstly exposing the cell line to an initial shock of 10 µM enzalutamide. Subsequently, cells were graduallly exposed to enzalutamide from 0 to 10 µM (increments of 0,5 µM) until cells grew again at a constant rate.

value: MDA PCa 2b

value: 10 uM enzalutamide


title: LNCaP_0m_rep1_RNAseq

value: LNCaP

value: EtOH


title: MDA PCa 2b cells, enzalutamide resistant, replicate 2


title: CnR-RNAPII_WT_TGFb

value: Lung adenocarcinoma cells


title: LNCaP_H3K4me3_16h_rep1_HiChIP

data_processing:
Trim Galore (v.0.5.0) was used to trim adaptors.
HiC-Pro (v3.1.0) was used to process the data. (<MIN_MAPQ = 20, BOWTIE2_GLOBAL_OPTIONS = –very-sensitive–end-to-end–reorder, BOWTIE2_LOCAL_OPTIONS = –very-sensitive–end-to-end–reorder, GENOME_FRAGMENT = MboI_resfrag_hg19.bed, LIGATION_SITE = GATCGATC, LIGATION_SITE = “GATCGATC,” BIN_SIZE = “5000.”> )
FitHiChIP (v10.0) was used to call loops using union of any time points of H3K27ac or H3K4me3 broad and narrow peaks.
The reads were merged from every time point for H3K27ac and H3K4me3 separately, and the reference loop sets were called with the same parameters above.
The contact frequency at the reference loop sets were collected from cool files  at every time point and TMM normalization is applied.
Assembly: hg19
Supplementary files format and content: cool (https://github.com/open2c/cooler)
Supplementary files format and content: BEDPE (custom designed; chr1, start1, end1, chr2, start2, end2, name, TMM along 5 time points)
Library strategy: HiChIP

extract_protocol:
DNA was purified using MinElute column (Qiagen) after reverse crosslinking.
Reverse-crossed IP sample was pulled down with streptavidin C1 beads (Life Technologies) treated with Transposase (Illumina) and was amplified with reasonable cycle numbers based on the qPCR with 5-cycle pre-amplified library.

tag: chip antibody

value: H3K4me3:Diagenode 3C15410003


title: A549 cells, deep_sequencing, shD3#1, biol_rep_1


title: MDA PCa 2b cells, enzalutamide resistant, replicate 1


title: CnR-RNAPII_WT_SB


title: CnR-H3K27me3_TGFb


title: LNCaP_72h_rep2_RNAseq


title: CnR-H3K27me3_SB


title: MDA PCa 2b cells, enzalutamide sensitive (vehicle treated), replicate 3

value: DMSO vehicle


title: A549 cells, deep_sequencing, sh1Control, biol_rep_3

value: WT


title: LNCaP_H3K4me3_30m_rep1_HiChIP


title: LNCaP_30m_rep1_RNAseq


title: LNCaP_0m_rep2_RNAseq


title: MDA PCa 2b cells, enzalutamide sensitive (vehicle treated), replicate 2


title: A549 cells, deep_sequencing, sh1Control, biol_rep_2


title: CnR-H3K27ac_TGFb


title: LNCaP_H3K4me3_0m_rep1_HiChIP


title: MDA PCa 2b cells, enzalutamide sensitive (vehicle treated), replicate 1


title: LNCaP_H3K4me3_72h_rep1_HiChIP

value: 72h 10nM DHT


title: A549 cells, deep_sequencing, sh1Control, biol_rep_1


title: LNCaP_H3K27ac_72h_rep2_HiChIP

value: H3K27ac:Diagenode, 3C15410196


title: CnR-H3K27ac_SB


title: PC3 spheroids, siMED12, rep3

data_processing:
The multiplexed fastq file was split into individual per sample fastq files with STARsolo using the cellular barcodes and PCR duplicates were removed using the UMIs. Read alignment and counting of the individual fastq files were performed in R using the Rsubread package and the Gencode Release 43 (GRCh38.p13)
Assembly: GRCh38
Supplementary files format and content: count_file.txt: Tab-delimited text file with ensemble gene ID, gene symbol and gene counts for each sample
Supplementary files format and content: log2CPM_expression.txt: Tab-delimited text file with ensemble gene ID, gene symbol and log2 transformed CPM gene expression values for each sample

source_name: spheroids

growth_protocol: All cells were acquired from the American Type Culture Collection (ATCC) and cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, and 1% GlutaMAX.

extract_protocol:
Total RNA from spheroids was extracted using the Quick-RNA MagBead kit from Zymo Research.
Library prep was performed with the high throughput 3’ tag BRB-seq kit from Alithea genomics using early barcoding RT primers.

treatment_protocol: Cells were seeded in 6-well plates and incubated for 24 h. Cells were transfected with 25pmol ON-TARGETplus SMARTpools (siCtrl: non-targeting pool, #D-001810-10-05; siMED12: human MED12 siRNA, #L-009092-00-0005) using Lipofectamine RNAiMAX. The medium was changed after 6 h and the cells were cultivated in 2D for 3 days after transfection. Subsequently, the cells were trypsinized and re-seeded in ultra low attachment plates to induce spheroid formation. The spheroids were harvested 4 days after reseeding.

value: spheroids


title: CnR-H3K4me3_TGFb


title: LNCaP_H3K27ac_16h_rep2_HiChIP

value: 16h 10nM DHT


title: PC3 spheroids, siMED12, rep1


title: 22Rv1 cells, Lorecivivint treated, replicate 5

growth_protocol: 22Rv1 were cultivated in standard conditions, as recommended by the ATCC.

treatment_protocol: 22Rv1 were treated with DMSO or 50 nM Lorecivivint (IC50) and harvested after 72h post-treatment

value: 50 nM lorecivivint


title: LNCaP_H3K4me3_4h_rep1_HiChIP

value: 4h 10nM DHT


title: LNCaP_H3K27ac_72h_rep1_HiChIP


title: 22Rv1 cells, Lorecivivint treated, replicate 6


title: LNCaP_H3K27ac_16h_rep1_HiChIP


title: PC3 spheroids, siCtrl, rep2

value: siCtrl


title: PC3 spheroids, siCtrl, rep3


title: CnR-H3K4me3_SB


title: LNCaP_H3K27ac_4h_rep2_HiChIP


title: 22Rv1 cells, Lorecivivint treated, replicate 4


title: CnR-H3K4me1_SB


title: 22Rv1 cells, vehicle treated, replicate 2


title: CnR-H3K4me1_TGFb

value: TGF-Beta for 1.5 h


title: PC3 spheroids, siCtrl, rep1


title: LNCaP_H3K27ac_4h_rep1_HiChIP


title: 22Rv1 spheroids, siMED12, rep3


title: ChIP-DHX9_Rreb1KO_SB


title: ChIP-DHX9_Rreb1KO_TGFb


title: LNCaP_H3K27ac_30m_rep2_HiChIP

value: 30m 10nM  DHT


title: 22Rv1 spheroids, siMED12, rep1


title: CAST-seq on activated T cells treated with Cas9 targeting CD4 and PD1 + PFT-α donor3

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

description:
CAST-seq derived amplicons from gDNA
D649-CD4-PD1-act-30
CD4-PD1_activated_30_FINAL.xlsx

data_processing:
Mate paired reads were merged using BBmerge from BBmap (v38.76) software. BBmap  was also used for filtering and trimming as follow: merged reads containing the designer nuclease target site were filtered-in, whereas PCR mispriming products reads were filtered-out. Linker sequences, Illumina adapter sequences, targeted elongation sequence and bad quality reads were trimmed.
Selected reads were aligned to the human genome GRCh38 (hg38) using Bowtie2 (v2.3.4.2) and the very-sensitive preset parameters. Aligned reads with good mapping quality (MAPQ >15) were selected. The aligned BAM file was converted into bed file using bedtools (v2.27.1).
Translocated sites were identified using the CAST-Seq and D-CAST-Seq pipelines with default parameters, as described on https://github.com/AG-Boerries/CAST-Seq
Assembly: hg38
Supplementary files format and content: Matrix table of translocation sites detected with the D-CAST pipeline. It includes the genomic coordinates of translocated sites, read coverage, alignment score against gRNA, translocation event classification and nearest genes annotation.

source_name: PBMCs

growth_protocol: PBMCs were isolated from buffy coats and enriched for CD4 or CD8 T cells using MojoSort™ Human CD4 T Cell Isolation Kit (Biolegend) or MojoSort™ Human CD8 T Cell Isolation Kit (Biolegend), respectively. The freshly obtained T cells were cultured in complete Roswell Park Memorial Institute (cRPMI) medium, consisting  of  RPMI  1640  (ThermoFisher)  supplemented  with  5  mmol/l  HEPES (ThermoFisher), 2 mmol/l glutamine (ThermoFisher), 50 μg/ml penicillin/streptomycin (ThermoFisher), 5 mmol/l nonessential amino acids (ThermoFisher), 5 mmol/l sodium pyruvate  (ThermoFisher)  and  10%  FBS  (Sigma-Aldrich)  at  a  concentration  of 1x106 cells/ml  for 48h  at  37°C.

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen, Cat. No./ID:  69504) according to the manufacturer’s protocol.
CAST-Seq was performed as previously described (Turchiano et al, 2021) with minor modifications. Briefly, genomic DNA was fragmented by enzymatic digestion (NEBNext® Ultra™ II FS DNA Library Prep Cat.# E7805S) to obtain average fragment lengths of 700 bp. After linker ligation (NEBNext®Ultra™ II FS DNA Library Prep Cat.# E7805S) and DNA purification, two rounds of PCR utilizing Q5 polymerase (NEB, Cat.# M0493S) were performed with the following conditions: 20 cycles at 95°C for 15 s, 63°C (first reaction) or 68°C (second reaction) for 20 seconds, 72°C for 20 seconds.
A third PCR introduced the barcoded Illumina adapter for sequencing (NEB, NEBNext Multiplex Oligos for Illumina, Cat.# E7335, E7500, E7710, E7730). Libraries were sequenced by Azenta Life Sciences using the Illumina NovaSeq platform with a 2 x 150 bp configuration.

treatment_protocol: CD4/PDCD1-double CRISPR editing for CAST-seq: Cas9 RNP nucleofection was performed in a 4D electoporation cuvette with 20 µl of 20 µM CD4 RNP in combination with 20 µl  of 20 µM PD-1 RNP and 5 µl electroporation enhancer.

value: CD4 T cells

tag: activation

value: activated T cells

value: SpCas9+CD4gRNA/PD1gRNA + PFT-α


title: LNCaP_H3K27ac_30m_rep1_HiChIP

value: LNCaP


title: CAST-seq on activated T cells treated with Cas9 targeting CD4 and PD1 + PFT-α donor2

description:
CAST-seq derived amplicons from gDNA
D648-CD4-PD1-act-30
CD4-PD1_activated_30_FINAL.xlsx


title: ChIP-DHX9_WT_TGFb

value: Lung adenocarcinoma cells


title: 22Rv1 cells, vehicle treated, replicate 3


title: 22Rv1 spheroids, siCtrl, rep2


title: ChIP-DHX9_WT_SB


title: CAST-seq on activated T cells treated with Cas9 targeting CD4 and PD1 + PFT-α donor1

description:
CAST-seq derived amplicons from gDNA
CD4-26-2
CD4-PD1_activated_30_FINAL.xlsx


title: LNCaP_H3K27ac_0m_rep1_HIChIP

value: EtOH


title: ChIP-INO80_Rreb1KO_TGFb


title: LNCaP_INPUT_72h_ChIPseq

data_processing:
ChIP-seq data were processed through the ChiLin pipeline.
Reads are aligned to hg19 genome with BWA (v0.7.10).
MACS2 (v2.1.0) is used to call peaks, FDR threshold 0.01.
Bigwig files were generated using bedGraphToBigWig.
Assembly: hg19
Supplementary files format and content: narrowPeak
Supplementary files format and content: broadPeak
Supplementary files format and content: BigWig

extract_protocol:
DNA was purified using MinElute column followed by incubation in the de-crosslinking buffer (1% SDS, 0.1 M NaHCO3 with Proteinase K and RNase A) at 65 oC .
Eluted sample DNA was prepared as the sequencing libraries with the ThruPLEX-FD Prep Kit (Takara bio, # R400675).


title: CAST-seq on activated T cells treated with Cas9 targeting CD4 and PD1 donor3

description:
CAST-seq derived amplicons from gDNA
D649-CD4-PD1-act-0
CD4-PD1_activated_0_FINAL.xlsx


title: 22Rv1 cells, vehicle treated, replicate 1

value: DMSO vehicle


title: 22Rv1 spheroids, siCtrl, rep1


title: LNCaP spheroids, siMED12, rep3


title: ChIP-INO80_Rreb1KO_SB


title: CAST-seq on activated T cells treated with Cas9 targeting CD4 and PD1 donor1

description:
CAST-seq derived amplicons from gDNA
CD4-24-2
CD4-PD1_activated_0_FINAL.xlsx


title: ChIP-INO80_WT_SB


title: LNCaP_INPUT_4h_ChIPseq


title: LNCaP_INPUT_16h_ChIPseq


title: LNCaP spheroids, siMED12, rep2


title: CAST-seq on non-activated T cells treated with Cas9 targeting CD4 and PD1 + PFT-α donor3

description:
CAST-seq derived amplicons from gDNA
D649-CD4-PD1-naive-30
CD4-PD1_naive_30_FINAL.xlsx

value: non-activated T cells


title: ChIP-INO80_WT_TGFb


title: LNCaP spheroids, siMED12, rep1


title: ChIP-SMAD4_Rreb1KO_TGFb


title: CAST-seq on non-activated T cells treated with Cas9 targeting CD4 and PD1 + PFT-α donor2

description:
CAST-seq derived amplicons from gDNA
D648-CD4-PD1-naive-30
CD4-PD1_naive_30_FINAL.xlsx


title: LNCaP spheroids, siCtrl, rep3


title: 22Rv1 spheroids, siCtrl, rep3


title: LNCaP_INPUT_30m_ChIPseq


title: LNCaP_H3K27ac_0m_rep2_HiChIP


title: CAST-seq on non-activated T cells treated with Cas9 targeting CD4 and PD1 + PFT-α donor1

description:
CAST-seq derived amplicons from gDNA
CD4-25-2
CD4-PD1_naive_30_FINAL.xlsx


title: ChIP-SMAD4_Rreb1KO_SB


title: LNCaP spheroids, siCtrl, rep2


title: LNCaP_INPUT_0m_ChIPseq


title: ChIP-SMAD4_WT_TGFb


title: LNCaP spheroids, siCtrl, rep1


title: ChIP-SMAD4_WT_SB


title: LNCaP_H3K4me3_72h_ChIPseq

value: H3K4me3:Diagenode 3C15410003

value: 72h 10nM DHT


title: LNCaP_H3K4me3_16h_ChIPseq


title: CAST-seq on non-activated T cells treated with Cas9 targeting CD4 and PD1 donor2

description:
CAST-seq derived amplicons from gDNA
D648-CD4-PD1-naive-0
CD4-PD1_naive_0_FINAL.xlsx


title: PC3, CDKinh, rep1

data_processing:
The multiplexed fastq file was split into individual per sample fastq files with STARsolo using the cellular barcodes and PCR duplicates were removed using the UMIs. Read alignment and counting of the individual fastq files were performed in R using the Rsubread package and the Gencode Release 43 (GRCh38.p13) genome assembly.
Assembly: GRCh38
Supplementary files format and content: count_file.txt: Tab-delimited text file with ensemble gene ID, gene symbol and gene counts for each sample
Supplementary files format and content: log2CPM_expression.txt: Tab-delimited text file with ensemble gene ID, gene symbol and log2 transformed CPM gene expression values for each sample

growth_protocol: 22Rv1 cells were acquired from the American Type Culture Collection (ATCC) and cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, and 1% GlutaMAX.

extract_protocol:
RNA isolation was performed with the Blirt EXTRACTME TOTAL RNA KIT
Library prep was performed with the high throughput 3’ tag BRB-seq kit from Alithea genomics using early barcoding RT primers.

treatment_protocol: The cells were seeded in 6 well plates and left to attach for 24 hours. Subsequently, they were treated with 1.5 µM of the CDK8/CDK19 inhibitor SEL120-34A or DMSO vehicle for 3 days.


title: CAST-seq on activated T cells treated with Cas9 targeting CD4 and PD1 donor2

description:
CAST-seq derived amplicons from gDNA
D648-CD4-PD1-act-0
CD4-PD1_activated_0_FINAL.xlsx


title: CAST-seq on non-activated T cells treated with Cas9 targeting CD4 and PD1 donor1

description:
CAST-seq derived amplicons from gDNA
CD4-23-2
CD4-PD1_naive_0_FINAL.xlsx


title: ChIP-H4K16ac_SB


title: PC3, DMSO, rep1

value: DMSO


title: CAST-seq on non-activated T cells treated with Cas9 targeting CD4 and PD1 donor3

description:
CAST-seq derived amplicons from gDNA
D649-CD4-PD1-naive-0
CD4-PD1_naive_0_FINAL.xlsx


title: ChIP-IgG_SB


title: ChIP-H2AZ_TGFb


title: 22Rv1, CDKinh, rep3


title: LNCaP_H3K4me3_4h_ChIPseq


title: Untreated sample used as control donor3

description:
CAST-seq derived amplicons from gDNA
use as un-treated control for donor3
UT-D649-A4

value: control

value: no treatment


title: LNCaP_H3K4me3_30m_ChIPseq


title: LNCaP_H3K4me3_0m_ChIPseq


title: 22Rv1, CDKinh, rep2


title: Untreated sample used as control donor2

description:
CAST-seq derived amplicons from gDNA
use as un-treated control for donor2
UT-D648-A4


title: ChIP-H2AZ_SB


title: LNCaP_H3K27ac_72h_rep2_ChIPseq

value: H3K27ac:Diagenode 3C15410196


title: Untreated sample used as control donor1

description:
CAST-seq derived amplicons from gDNA
use as un-treated control for donor1
CD4-27-1


title: ChIP-SMAD2/3_TGFb


title: 22Rv1, CDKinh, rep1


title: H322.Input

city: Houston

first: Carl

last: Gay

state: TX

address: 1515 Holcombe Blvd

department: Thoracic-Head & Neck Med Onc

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Base calling using bcl2fastq v2.17 for Novaseq output
ChIPseq reads were aligned to reference genome using BWA 0.7.9a-r786
Peak calling using MACS2 with q-value cutoff 0.01
Assembly: hg38
Supplementary files format and content: wig file (except for input samples)

growth_protocol: All cell lines were cultured in RPMI (Roswell Park Memorial Institute 1640 Medium, Hyclone, Cat# SH30027.01; no pyruvate) with 10% heat inactivated fetal bovine serum (Gibco, Cat# 1614007), 1% penicillin/streptomycin.  Cell lines were cultured till 90% confluency and kept at low passage numbers and maintained at 37 °C in a humidified 5% CO2-containing incubator.

extract_protocol:
ChiP DNA was prepared according to "Blecher-Gonen, R. et al. High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states. Nat Protoc 8, 539-554, doi:10.1038/nprot.2013.023 (2013)."
Libraries were prepared using the NEBNext Ultra II DNA library prep kit (Cat# E7645S, NEB) according to manufacturer's instructions.

treatment_protocol: No treatment

value: lung adenocarcinoma


title: LNCaP_H3K27ac_72h_rep1_ChIPseq


title: 22Rv1, DMSO, rep3


title: ChIP-SMAD2/3_SB


title: LNCaP_H3K27ac_16h_rep2_ChIPseq

value: 16h 10nM DHT


title: H322.H3K4me1


title: 22Rv1, DMSO, rep2


title: ChIP-RREB1_TGFb

value: TGF-Beta for 1.5 h


title: LNCaP_H3K27ac_16h_rep1_ChIPseq


title: 22Rv1, DMSO, rep1


title: ChIP-RREB1_SB


title: LNCaP_H3K27ac_4h_rep2_ChIPseq

value: 4h 10nM DHT


title: HCC44.Input


title: LNCaP, CDKinh, rep3


title: LNCaP_H3K27ac_4h_rep1_ChIPseq


title: HCC44.H3K4me1


title: Input_Rreb1KO_TGFb


title: LNCaP, CDKinh, rep2


title: Input_Rreb1KO_SB


title: LNCaP_H3K27ac_30m_rep2_ChIPseq

value: 30m 10nM  DHT


title: LNCaP_H3K27ac_30m_rep1_ChIPseq


title: HCC44.H3K27ac


title: Input-WT_TGFb


title: LNCaP, CDKinh, rep1


title: LNCaP, DMSO, rep3


title: H1975.Input


title: LNCaP, DMSO, rep2


title: Input-TGFb


title: H1975.H3K4me1


title: LNCaP_H3K27ac_0m_rep2_ChIPseq


title: Input-WT_SB


title: LNCaP, DMSO, rep1


title: H1975.H3K27ac


title: LNCaP_H3K27ac_0m_rep1_ChIPseq


title: Input-SB


title: LNCaP_FOXA1_72h_ChIPseq

value: FOXA1:Abcam ab23738


title: LNCaP_FOXA1_16h_ChIPseq

value: LNCaP


title: H1693.Input


title: H322.H3K27ac


title: NPC iNSC+SAHA treatment

city: Seoul

first: SeungEun

address: 1 Gwanak-Ro, Gwanak-gu

department: Veterinary

institute: Seoul National University

description: NPC-iNSC-Compound S_1

data_processing:
QuantSeq 3’ mRNA-Seq reads were aligned using Bowtie2 (Langmead and Salzberg, 2012). Bowtie2 indices were either generated from genome assembly sequence or the representative transcript sequences for aligning to the genome and transcriptome.
The alignment file was used for assembling transcripts, estimating their abundances and detecting differential expression of genes. Differentially expressed gene were determined based on counts from unique and multiple alignments using coverage in Bedtools (Quinlan AR, 2010).
The RC (Read Count) data were processed based on quantile normalization method using EdgeR within R (R development Core Team, 2016) using Bioconductor (Gentleman et al.,2004). Gene classification was based on searches done by DAVID (http://david.abcc.ncifcrf.gov/) and Medline databases (http://www.ncbi.nlm.nih.gov/).
Genome_build: hg19 (UCSC)
Supplementary_files_format_and_content: Processed data.xlsx (counts, FPKMs)

source_name: Niemann pick disease type C1 iNSCs+SAHA treatment

growth_protocol: induced neual stem cells was cultured in neural stem cell maintenance media

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen). RNA quality was assessed by Agilent 2100  bioanalyzer using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands),  and RNA quantification was performed using ND-2000 Spectrophotometer (Thermo Inc., DE, USA).
The library was amplified to add the complete  adapter sequences required for cluster generation. The finished library is purified from PCR  components. High-throughput sequencing was performed as single-end 75 sequencing using  NextSeq 500 (Illumina, Inc., USA).
QuantSeq 3` mRNA-Seq

treatment_protocol: SAHA and HNHA treatment to the NPC iNSCs.

value: induced neural stem cells

value: NPC1 mutant

value: SAHA


title: H1693.H3K4me1


title: NPC iNSC+HNHA treatment

description: NPC-iNSC-Compound H_1

source_name: Niemann pick disease type C1 iNSCs+HNHA treatment

value: HNHA


title: DM1_Liver_3 [HL_4]

city: Urbana

first: Zachary

last: Dewald

state: IL

address: 506 South Mathews Ave

institute: University of Illinois Urbana Champaign

data_processing:
Sequnce reads were trimmed for adapter sequence and low quality reads down to 120 bp using Trimmomatic V 0.39
Trimmed reads were alligned to GrCM38/mm10 using STAR aligner V 2.5.2
Gene expression levels and comparison between samples was performed by HtSeq V 0.6.1 and Cuffdiff 2 V 2.2.1. Events were considered significant if expression > 1 FPKM, P-Value<0.01 and FDR < 0.05.
Differential splicing analsysis was performed using rMATS V 3.2.5. Events were considered significant if expression > 1 FPKM, P-Value<0.05, and FDR < 0.1.
Assembly: mm10
Supplementary files format and content: TSV of raw counts, grouped, from CuffDiff, for each comparison (Mbnl1KO vs WT and DM1Liver vs Control)
Supplementary files format and content: xlsx of alternative splicing events, grouped by event type, from rMATS, for each comparison (Mbnl1KO vs WT and DM1Liver vs Control)

molecule: polyA RNA

source_name: Liver Specific DM1

extract_protocol:
RNA was harvested using the Rneasy miniplus kit from Qiagen.
Poly-A RNA enriched library preperation was performed by the High Throughput Sequencing and Genotyping Unit at the Roy J. Carver Biotechnology Center, UIUC

value: Liver

value: hepatocye


title: LNCaP_FOXA1_4h_ChIPseq


title: DM1_Liver_2 [HL_3]


title: DM1_Liver_1 [HL_1]


title: LNCaP_FOXA1_30m_ChIPseq


title: [ATAC-Seq] HCC44, YD23, replicate 2

data_processing:
Base calling using bcl2fastq v2.17 for Novaseq output
ChIPseq reads were aligned to reference genome using BWA 0.7.9a-r786
Peak calling using MACS2 with p-value cutoff 0.05
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
ATAC-seq protocol was perfromed as described in: "Buenrostro, J. D., Wu, B., Chang, H. Y. & Greenleaf, W. J. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol 109, 21 29 21-21 29 29, doi:10.1002/0471142727.mb2129s109 (2015).
Libraries were prepared  using the Nextera DNA Library Preparation Kit according to manufactuerer's instructions.

treatment_protocol: Each cell line was treated at sub-conclufency with DMSO, ACBI1, or YD23 (1µM each) for 96 hours.


title: ApoE-rtTA_3 [2MC_4]

source_name: Control for DM1 Liver comparison

value: ApoE-rtTA


title: WT iNSC

source_name: Wild type iNSC

value: Wild-type

value: untreated


title: LNCaP_FOXA1_0m_ChIPseq

value: EtOH


title: [ATAC-Seq] HCC44, DMSO, replicate 2

value: lung adenocarcinoma

value: DMSO


title: [ATAC-Seq] HCC44, ACBi1, replicate 2


title: ApoE-rtTA_2 [2MC_2]


title: LNCaP_AR_72h_ChIPseq

value: AR:Abcam ab133273

value: 72h 10nM DHT


title: ApoE-rtTA_1 [2MC_1]


title: Bos taurus,pre_4_input RNA

city: Changchun

first: Xiaorui

last: Yang

address: Xincheng Street

country: China

institute: Jilin Agricultural University

data_processing:
Base calling software: BCL convert
Data filter: fastp(0.19.4)，remove adapters, repeat sequences and low quality sequences
reads alignment : HISAT2(2.0.4)
Peak calling diffpeak : R package: exomePeak (1.5.0)
Peak annotation : ANNOVAR
Transcript assembly and quantification : StringTie (2.1.2)
Differential Expression Analysis :R package: edgeR(4.1)
Motif: HOMER(4.10)
Assembly: BOVINE(ensemble V107)
Supplementary files format and content: bigWig

organism: Bos taurus

source_name: hypothalamic

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA). Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification.
the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol
m6A-seq

value: hypothalamic


title: LNCaP_AR_16h_ChIPseq

value: 16h 10nM DHT


title: [ATAC-Seq] H322, YD23, replicate 2


title: [ATAC-Seq] H322, DMSO, replicate 2


title: Fvb_1 [R847]

source_name: Wild Type control for Mbnl1 KO

value: WT


title: LNCaP_AR_4h_ChIPseq

value: LNCaP

value: 4h 10nM DHT


title: Bos taurus,pre_2_input RNA


title: Mbnl1 KO_2 [R897]

source_name: Whole Body DM1 Model_Mbnl1 KO

value: Mbnl1 {delta}E3/{delta}E3


title: LNCaP_AR_30m_ChIPseq

value: 30m 10nM  DHT


title: [ATAC-Seq] H322, ACBi1, replicate 2


title: Bos taurus,pre_1_IP RNA


title: Mbnl1 KO_1 [R890]

value: Liver


title: NPC iNSC

source_name: Niemann pick disease type C1 iNSCs

value: induced neural stem cells

value: NPC1 mutant


title: H1693.H3K27ac


title: LNCaP_AR_0m_ChIPseq


title: [ATAC-Seq] H1975, DMSO, replicate 2


title: LNCaP_72h_rep2_ATACseq

data_processing:
ATAC-seq data were processed through the ChiLin pipeline.
Reads are aligned to hg19 genome with BWA (v0.7.10).
MACS2 (v2.1.0) is used to call peaks, FDR threshold 0.01.
Bigwig files were generated using bedGraphToBigWig.
Assembly: hg19
Supplementary files format and content: narrowPeak
Supplementary files format and content: broadPeak
Supplementary files format and content: BigWig

extract_protocol:
DNA was purified using Qiagen MinElute (#28004),
The nuclei pellets were resuspended in 50 μl of transposition buffer (25 μl of 2× TD buffer, 22.5 μl of distilled water, 2.5 μl of Illumina Tn5 transposase) and incubated at 37 °C for 30 min with shaking at 1000 r.p.m for fragmentation. Transposed DNA was purified using Qiagen MinElute (#28004), and the library was amplified up to the cycle number determined by 1/3rd maximal qPCR fluorescence.


title: Bos taurus,post_4_IP RNA


title: LNCaP_72h_rep1_ATACseq


title: Liver - PTPRK KO high fat - n2

city: Anderlecht

first: Valerie

last: Vandenbempt

state: Vlaams-Brabant

address: Lenniksebaan 808

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Mapping to genome
LogFoldchange and statistical analysis
Assembly: mm9

source_name: Liver

extract_protocol:
Hepatocytes with high-fat and low-fat content were isolated from steatotic livers38. Viable hepatocytes with different lipid contents were separated from dead hepatocytes and non-parenchymal cell types in the cell suspension using Percoll gradient and differential centrifugation.
total RNA quality analysis, library preparation

value: PTPRK knockout

value: High fat


title: [ATAC-Seq] H1975, ACBi1, replicate 2


title: Bos taurus,pre_2_IP RNA


title: Liver - PTPRK KO high fat - n1


title: [ATAC-Seq] H1693, YD23, replicate 2


title: LNCaP_16h_rep2_ATACseq

source_name: LNCaP


title: Bos taurus,post_4_input RNA


title: Liver - PTPRK KO low fat - n3

value: Low fat


title: LNCaP_16h_rep1_ATACseq


title: [ATAC-Seq] H1693, DMSO, replicate 2

value: lung adenocarcinoma


title: Liver - PTPRK KO low fat - n2


title: Bos taurus,post_3_input RNA


title: LNCaP_4h_rep2_ATACseq


title: Bos taurus,post_2_IP RNA


title: Bos taurus,pre_1_input RNA


title: Liver - PTPRK KO low fat - n1


title: [ATAC-Seq] HCC44, YD23, replicate 1


title: LNCaP_4h_rep1_ATACseq


title: [ATAC-Seq] H1975, YD23, replicate 2


title: Bos taurus,post_2_input RNA


title: Liver - WT high fat - n3

value: Wild Type


title: Liver -PTPRK KO high fat - n3


title: [ATAC-Seq] HCC44, DMSO, replicate 1

value: DMSO


title: Liver - WT high fat - n2


title: LNCaP_30m_rep1_ATACseq


title: Liver - WT high fat - n1


title: Bos taurus,post_3_IP RNA


title: LNCaP_30m_rep2_ATACseq


title: Liver - WT low fat - n3


title: [ATAC-Seq] H322, YD23, replicate 1


title: [ATAC-Seq] H1693, ACBi1, replicate 2


title: LNCaP_0m_rep2_ATACseq

value: EtOH


title: Pcos-coc4

city: Rancagua

first: Nicolas

last: Santander

address: Libertador Bernardo O'Higgins 611

country: Chile

institute: Universidad de O´Higgins

data_processing:
Align to hg38  with Rsubread
Quantification with FeatureCounts
Normalization and diffierential expression with DESeq2
Assembly: hg38
Supplementary files format and content: tab delimited file with raw counts for each sample

source_name: PBMC

extract_protocol:
Rneasy Plus micro kit Qiagen
NEBNext Ultra II RNA Library Prep Kit
Unstranded

value: PBMC

value: Monocyte

tag: disease state

value: Pcos

tag: group

value: COC


title: Liver - WT low fat - n2


title: [ATAC-Seq] HCC44, ACBi1, replicate 1


title: Liver - WT low fat - n1


title: [ATAC-Seq] H1975, YD23, replicate 1


title: [ATAC-Seq] H322, ACBi1, replicate 1


title: Pcos-coc3


title: [ATAC-Seq] H1975, DMSO, replicate 1


title: Pcos-coc2


title: LNCaP_0m_rep1_ATACseq

value: LNCaP


title: Liver tissue from Bmp9/10-HSC-KO mice replicate 3

city: Beijing

first: Huan

last: Wang

address: 38 Life Science Park Road

institute: National Center for Protein Sciences, Beijing

description:
KO-25
Liver_tissue_counts.txt

data_processing:
All samples passed quality control based on the results of FastQC.
Reads were aligned to the mouse genome assembly mm10.GRCm38 using HISAT2.
The aligned reads were counted using FeatureCounts.
Differentially expressed genes were determined with DESeq2 program
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
For liver macrophages and endothelial cells, total RNA was isolated with RNeasy plus Mini Kit (Qiagen) according the manufacturer's protocol. For liver tissues, total RNA was isolated with TRIzol (Invitrogen) according the manufacturer's protocol
Library preparation was performed with Hieff NGS™ Ultima Dual-mode RNA Library Prep Kit according the manufacturer's protocol.

tag: strain

value: Liver tissue


title: Bos taurus,pre_4_IP RNA

value: hypothalamic


title: Pcos-coc1


title: [ATAC-Seq] H1975, ACBi1, replicate 1


title: placenta_young_c57_embryo [p_y_c_2__2_4]

type: RNA

city: Magdalenka

first: Adrian

middle: Mateusz

last: Stankiewicz

state: Mazovia

address: Jastrzebiec, ul. Postepu 36A

department: Animal Behaviour

country: Poland

institute: Institute of Genetics and Animal Breeding of the Polish Academy of Sciences

hyb_protocol: According to the manufacturer’s protocol.

scan_protocol: The acquisition and analysis of hybridization intensities were performed using an Agilent DNA Microarray Scanner G2505C. Data were extracted and the background subtracted using the standard procedures included in the Agilent Feature Extraction Software version 10.7.3.1.

data_processing: Statistical analysis of raw data was carried out using the default protocol of the Partek Genomics Suite. For each probe data were logged, normalized using quantile normalization, and annotated using the “GPL21163_noParents.an.txt” annotation file from the Gemma database (Lim et al., 2021). Results were adjusted for multiple comparisons using the FDR step-up method. Genes were considered to be differentially expressed if their absolute values of logged fold changes (base 2 logarithms) reached 1.5 and the adjusted p-value was lower than 0.05.

label_protocol: Genome-wide transcriptomic analysis was performed using SurePrint G3 Mouse GE v2 8x60K microarrays (GPL21163, Agilent Technologies, USA) and Agilent Technologies Reagent Set according to the manufacturer’s instructions. 100 ng of RNA of each sample (n=4 fetuses and placentas per maternal age group per tissue, only male offspring were selected for microarrays purposes) was labeled using Low Input QuickAmp Labeling Kit One-Color (Agilent Technologies, USA) and hybridized on the microarrays according to the manufacturer’s protocol.

extract_protocol: RNA for transcriptomic analyses was extracted from placentas and fetal heads following the manufacturers’ instructions. Total RNA extraction was conducted using the Universal RNA Purification Kit (Eurx, Poland), and included a DNase treatment (Eurx, Poland). The quantity and purity of isolated nucleic acids were validated using a Nanodrop 1000 spectrophotometer (Thermo Fisher Scientific, USA). RNA integrity of selected samples was additionally validated using a Bioanalyzer 2100 microcapillary electrophoresis device (Agilent, USA).

treatment_protocol: Fetuses with their placentas were collected from pregnant BTBR and B6 old (42-65 weeks old, AMA) and young (10-23 weeks old, YMA) females. Mice were ethically euthanized by cervical dislocation 12 days after plug detection. The uterus was isolated from the abdominal cavity followed by dissection of the conceptuses by separating the fetus from the placenta. Then, placentas and fetuses were gently dried with a paper towel and weighed, and the fetal head was separated from the rest of the body. All tissues were then immediately snap-frozen in liquid nitrogen and stored at -80°C until further analyses.

value: placenta

tag: age

value: young


title: Liver tissue from Bmp9/10-HSC-KO mice replicate 1

description:
KO-7
Liver_tissue_counts.txt

value: Liver


title: Pcos-sin5

value: sin


title: placenta_young_c57_embryo [p_y_c_2__2_1]


title: placenta_young_c57_embryo [p_y_c_2__2_3]


title: [ATAC-Seq] H322, DMSO, replicate 1


title: Liver tissue from control mice replicate 3

description:
WT-20
Liver_tissue_counts.txt

value: control


title: placenta_old_c57_embryo [p_a_c__1_2]

value: old


title: placenta_old_c57_embryo [p_a_c__1_4]


title: Pcos-sin4


title: [ATAC-Seq] H1693, DMSO, replicate 1

value: lung adenocarcinoma


title: placenta_young_c57_embryo [p_y_c_2__2_2]


title: Pcos-sin3


title: placenta_old_c57_embryo [p_a_c__1_1]


title: Liver tissue from control mice replicate 2

description:
WT-19
Liver_tissue_counts.txt


title: placenta_young_btbr_embryo [p_y_b__2_4]

value: btbr


title: Liver tissue from Bmp9/10-HSC-KO mice replicate 2

description:
KO-21
Liver_tissue_counts.txt


title: placenta_old_c57_embryo [p_a_c__1_3]


title: ECs from Bmp9/10-HSC-KO mice replicate 3

description:
B27-KO-EC
BMP9/10_EC_count.txt

value: Endothelial cells


title: Pcos-sin2


title: H1792, Y23, replicate 2

data_processing:
Base calling using bcl2fastq v2.17 for Novaseq output
Seqeunces were mapped to hg38 reference genome and transcriptome usingTOPHAT v2.1.1
Mapped reads were counted for each gene using HTseq v0.11.1
Assembly: hg38
Supplementary files format and content: tab delimited text file for raw counts for all samples

extract_protocol:
RNA-isolation protocol was performed using RNAeasy kit (Qiagen) according to manufacturer's instructions
Libraries were constructed from the PolyA selected mRNA using the TruSeq stranded RNA sample preparation kit (Illumina)


title: [ATAC-Seq] H1693, YD23, replicate 1


title: placenta_young_btbr_embryo [p_y_b__2_3]


title: Control-coc5


title: ECs from Bmp9/10-HSC-KO mice replicate 1

description:
B5-KO-EC
BMP9/10_EC_count.txt


title: H1792, ACBi1, replicate 2


title: H1792, DMSO, replicate 2

value: DMSO


title: placenta_young_btbr_embryo [p_y_b__2_1]


title: H1299, Y23, replicate 1


title: Control-coc4

value: PBMC


title: placenta_young_btbr_embryo [p_y_b__2_2]


title: [ATAC-Seq] H1693, ACBi1, replicate 1


title: Liver tissue from control mice replicate 1

description:
WT-2
Liver_tissue_counts.txt


title: H1299, ACBi1, replicate 1


title: placenta_young_c57_embryo [p_y_c_1__1_4]


title: ECs from control mice replicate 3

description:
B26-WT-EC
BMP9/10_EC_count.txt


title: Control-coc3

value: Monocyte


title: Control-coc2


title: Pcos-sin1

value: Pcos


title: H1299, DMSO, replicate 1


title: ECs from control mice replicate 1

description:
B3-WT-EC
BMP9/10_EC_count.txt


title: ECs from control mice replicate 2

description:
B21-WT-EC
BMP9/10_EC_count.txt


title: Control-coc1

value: COC


title: Liver macrophages from Smad4FF cKO replicate 3

description:
B29
SMAD_KC_count.txt

value: Liver macrophages

value: Smad4FF cKO


title: ECs from Bmp9/10-HSC-KO mice replicate 2

description:
B25-KO-EC
BMP9/10_EC_count.txt


title: placenta_young_c57_embryo [p_y_c_1__1_2]


title: Control-sin4


title: placenta_young_c57_embryo [p_y_c_1__1_3]


title: H322, Y23, replicate 2


title: placenta_young_c57_embryo [p_y_c_1__1_1]


title: Control-sin3


title: HCC44, Y23, replicate 2


title: head_young_c57_embryo [h_y_c_2__2_4]

value: head


title: Liver macrophages from Smad4FF cKO replicate 1

description:
B27
SMAD_KC_count.txt


title: Control-sin2


title: H322, DMSO, replicate 2


title: Liver macrophages from Smad4FF replicate 3

description:
B24
SMAD_KC_count.txt


title: HCC44, ACBi1, replicate 2


title: head_young_c57_embryo [h_y_c_2__2_3]


title: Control-sin1


title: Liver macrophages from Smad4FF replicate 2

description:
B3
SMAD_KC_count.txt


title: head_young_c57_embryo [h_y_c_2__2_2]


title: H1792, Y23, replicate 1


title: 02_CRP_6h

city: Kumamoto

first: Yoshihiro

last: Komohara

address: Honjo 1‐1‐1, Chuouku

department: Department of Cell Pathology

country: Japan

institute: Graduate School of Medical Sciences, Kumamoto University

data_processing:
illumina Local Run Manager v2.4.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim galore! v0.6.6
Trimmed sequence reads were mapped to UCSC hg19 using STAR v2.7.3a
Read count extraction and normalization were performed using RSEM v1.3.3
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: blood

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using illumina TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

value: blood

value: macrophage

value: male

value: Cocultured with anti-CD74 antibody (clone LN2)


title: H322, ACBi1, replicate 2


title: 03_CRP_24h

value: Cocultured with anti-CD74 antibody (clone CDLA74-1)


title: head_young_c57_embryo [h_y_c_2__2_1]

value: young


title: Liver macrophages from Smad4FF cKO replicate 2

description:
B28
SMAD_KC_count.txt

value: Liver


title: Liver macrophages from Bmp9/10-HSC-KO mice replicate 3

description:
B5-KO-KC
BMP9/10_KC_count.txt


title: head_old_c57_embryo [h_a_c__1_4]

value: old


title: Liver macrophages from Bmp9/10-HSC-KO mice replicate 2

description:
B27-KO-KC
BMP9/10_KC_count.txt


title: HCC44, DMSO, replicate 2

value: lung adenocarcinoma


title: H322, Y23, replicate 1


title: head_old_c57_embryo [h_a_c__1_3]


title: Liver macrophages from Smad4FF replicate 1

description:
B1
SMAD_KC_count.txt


title: Tail-Fuz:Gpr161 DKO-2

city: Austin

first: Sung Eun

last: Kim

address: 1400 Barbara Jordan Blvd

institute: The University of Texas at Austin

data_processing:
FastQC (version v0.11.8) was applied to check the quality of raw reads.
Trimmomatic (version v0.38) was applied to cut adaptors and trim low-quality bases with default setting.
STAR Aligner version 2.7.1a was used to align the reads.
Picard tools (version 2.20.4) was applied to mark duplicates of mapping.
The StringTie version 2.0.4 was used to assemble the RNA-Seq alignments into potential transcripts. The featureCounts (version 1.6.0)/HTSeq was used to count mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.
Assembly: GRCm39/m39
Supplementary files format and content: Read count matrix as a txt file

source_name: embryos

extract_protocol:
We isolated RNA from the part of embryos with Trizol based Zymo RNA extraction kit with DNAase treatment.
The library was prepared with NEBNext Ultra RNA with Poly-A selection

value: embryos

tag: tissue part

value: Tail

value: embryonic cells

value: Fuz;Gpr161 DKO


title: 01_Control

value: Cocultured with isotype matched antibody


title: Tail-Fuz:Gpr161 DKO-1


title: H322, DMSO, replicate 1

value: DMSO


title: Liver macrophages from Bmp9/10-HSC-KO mice replicate 1

description:
B24-KO-KC
BMP9/10_KC_count.txt

value: Liver macrophages


title: head_young_btbr_embryo [h_y_b__2_4]

value: head

value: btbr


title: Liver macrophages from BMP9/10 control mice replicate 3

description:
B35-WT-KC
BMP9/10_KC_count.txt

value: BMP9/10 control


title: head_old_c57_embryo [h_a_c__1_1]


title: HCC44, Y23, replicate 1


title: Tail-Gpr161 KO-1

value: Gpr161 KO


title: head_old_c57_embryo [h_a_c__1_2]


title: Tail-Fuz KO-2

description: we could not recover this raw data.

value: Fuz KO


title: HCC44, ACBi1, replicate 1


title: HCC44, DMSO, replicate 1


title: head_young_btbr_embryo [h_y_b__2_3]


title: H322, ACBi1, replicate 1


title: Liver macrophages from BMP9/10 control mice replicate 1

description:
B23-WT-KC
BMP9/10_KC_count.txt


title: OT-I T cells expanded with IL2 and stimulated with OVA peptide, tazemetostat treated, H3K27me3 pulldown, replicate1

city: La Jolla

first: Jaroslav

last: Zak

state: CA

address: 10550 North Torrey Pines Rd

department: Immunology and Microbiology

institute: The Scripps Research Institute

description: pulldown

data_processing:
Raw reads were aligned to the mm10 genome using STAR v2.7.6a.
Peak counting and differential abundance analysis were performed using csaw v1.32.0. The input control was used to establish background peak abundance.
Peak annotation was performed using the ChipSeeker package v1.34.1
Assembly: mm10
Supplementary files format and content: List of annotated peaks with differential abundance between tazemetostat and vehicle treated cells. Input sample was used to filter out peaks.

source_name: CD8 T cells

extract_protocol:
In brief, cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp with Active Motif’s EpiShear probe sonicator (cat# 53051). Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by SPRI beads clean up (Beckman Coulter) and quantitation by Clariostar (BMG Labtech). Extrapolation to the original chromatin volume allowed determination of the total chromatin yield.    An aliquot of chromatin (40 ug) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 ug of antibody against H3K27me3 (Active Motif, 39155, Lot 11822023). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries (a custom type, using the same paired read adapter oligonucleotides described by Bentley et al., (2008)) were prepared from the ChIP and Input DNAs on an automated system (Apollo 342, Wafergen Biosystems/Takara).

treatment_protocol: OT-I splenocytes were activated with 500 nM OVA257-264 for three days and then expanded in the presence of Taz (1 µM) or vehicle with IL-2 (60 IU/mL) for 36h. Dead cells were removed by Ficoll gradient and live cells were collected and snap-frozen.

value: CD8 T cells

value: OT-I transgenic

value: tazemetostat H3K27me3 pulldown


title: OT-I T cells expanded with IL2 and stimulated with OVA peptide, tazemetostat treated, H3K27me3 pulldown, replicate2

description: pulldown


title: H1692, Y23, replicate 2


title: Tail-WT-2

value: WT


title: Tail-Fuz KO-1


title: H1692, ACBi1, replicate 2

value: lung adenocarcinoma


title: Tail-Gpr161 KO-2

value: embryos


title: Tail-WT-1

value: Tail


title: Treg TRaGS biol rep 4 [36-535574-Treg_S36]

city: Essen

first: Christina

last: Wenzek

address: Hufelandstr. 55

department: Department of Endocrinology

institute: University Hospital Essen, University Duisburg-Essen

data_processing:
Lexogen BlueBee QuantSeq DE-Pipeline
Assembly: Mus musculus GRCm38
Supplementary files format and content: csv files include normalized counts for each sample

source_name: spleen

extract_protocol:
RNA was havested using Rneasy Kit (Qiagen). RNA concentration was measured with Qubit (Invitrogen) and RNA quality was assessed using Agilent Bioanalyzer pico or nano chips.
Library preparation was performed using Lexogens QuantSeq 3′ mRNA-Seq Library Prep Kit FWD (Lexogen)

treatment_protocol: CD4+ T cells were enriched from total splenocytes by MACS. Subsequently, cells were labelled with fluorochrome linked antibodies and CD25- CD4+ naive T cells and CD25+ CD4+ Treg were isolated by FACS using BD Aria III.

value: spleen

value: CD25+ CD4+ Treg

value: TRaGS


title: H1692, DMSO, replicate 2

value: DMSO


title: Treg TRaGS biol rep 3 [33-534845-Treg_S33]


title: OT-I T cells expanded with IL2 and stimulated with OVA peptide, vehicle treated control, H3K27me3 pulldown, replicate2

description: pulldown

value: vehicle H3K27me3 pulldown


title: Liver macrophages from BMP9/10 control mice replicate 2

description:
B26-WT-KC
BMP9/10_KC_count.txt

value: Liver

value: Liver macrophages


title: OT-I T cells expanded with IL2 and stimulated with OVA peptide, vehicle treated control, H3K27me3 pulldown, replicate1

description: pulldown


title: H1792, ACBi1, replicate 1


title: Head-Fuz:Gpr161 DKO-2

value: Head

value: embryonic cells

value: Fuz;Gpr161 DKO


title: head_young_c57_embryo [h_y_c_1__1_1]

value: head

value: young


title: Treg TRaGS biol rep 2 [18-530201-Treg_S18]


title: head_young_c57_embryo [h_y_c_1__1_3]


title: head_young_c57_embryo [h_y_c_1__1_4]


title: OT-I T cells expanded with IL2 and stimulated with OVA peptide, pooled input control

description: input

value: CD8 T cells

value: OT-I transgenic

value: input


title: Head-Fuz:Gpr161 DKO-1

value: embryos


title: OT-I T cells, tazemetostat treated, 24h, replicate3

data_processing:
Quality control with fasqtQC
Reads were aligned to the GRCm38-mm10 genome and gene counts calculated using STAR v2.7.6a
Raw counts were normalized for library size by DESeq2 v1.38.1
Assembly: mm10
Supplementary files format and content: Gene counts normalized for library size

growth_protocol: OT-I splenocytes were activated with OVA257-264 (SIINFEKL, 500 nM) with 60 IU/mL of IL-2 for three days to obtain CD8+ T cells.

extract_protocol:
RNA extraction was performed usdingh the Arcturus™ PicoPure™ RNA Isolation Kit (KIT0204, ThermoFisher Scientific). Traces of genomic DNA were removed using RNase-Free DNase Set (79254, QIAGEN) following the on-column digesting protocol of the RNA isolation kit.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and  index codes were added to attribute sequences to each sample. Briefly, mRNA was purified  from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out  using divalent cations under elevated temperature in NEBNext First Strand Synthesis  Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer  and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was  subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’  ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to  prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp  in length, the library fragments were purified with AMPure XP system (Beckman Coulter,  Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptorligated  cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was  performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index  (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality  was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Cells were treated with 1uM tazemetostat or vehicle for 24 or 48h in the presence of OVA peptide.

value: tazemetostat

tag: time point


title: Treg TRaGS biol rep 1 [9-529492-Treg_S9]

value: spleen


title: H1975, Y23, replicate 2

value: lung adenocarcinoma


title: Treg TRaWT biol rep 4 [24-529518-Treg_S24]

value: CD25+ CD4+ Treg

value: TRaWT


title: Head-Gpr161 KO-1

value: Gpr161 KO


title: OT-I T cells, tazemetostat treated, 24h, replicate2


title: H1975, ACBi1, replicate 2


title: Treg TRaWT biol rep 3 [21-529517-Treg_S21]


title: Head-Gpr161 KO-2


title: Head-Fuz KO-2

value: Fuz KO


title: OT-I T cells, tazemetostat treated, 24h, replicate1


title: H1692, Y23, replicate 1


title: H1975, DMSO, replicate 2

value: DMSO


title: Head-Fuz KO-1

value: Head


title: Treg TRaWT biol rep 2 [6-529491-Treg_S6]


title: OT-I T cells, vehicle treated, 24h, replicate3

value: vehicle


title: Treg TRaWT biol rep 1 [3-529490-Treg_S3]


title: H1692, ACBi1, replicate 1


title: H1692, DMSO, replicate 1


title: OT-I T cells, vehicle treated, 24h, replicate2


title: CD4 TRaGS biol rep 4 [34-535574-CD4_S34]

value: CD25- CD4+ T cell

value: TRaGS


title: OT-I T cells, vehicle treated, 24h, replicate1


title: Head-WT-1

value: embryonic cells

value: WT


title: CD4 TRaGS biol rep 3 [31-534845-CD4_S31]


title: H1975, Y23, replicate 1


title: 22Rv1 cells, Lorecivivint treated, replicate 6

data_processing:
Processing was performed using the EPI2Me wf-transcriptomes pipeline using the GENCODE release 43 (GRCh38.p13) transcriptome assembly.
Assembly: GRCh38
Supplementary files format and content: all_gene_counts.tsv: Tab-delimited text file with ensemble gene ID and gene counts for each sample
Supplementary files format and content: all_counts_filtered.tsv: Tab-delimited text file with ensemble gene ID, ensemble transcript ID and transcript counts for each sample

extract_protocol:
RNA isolation was performed with the Blirt EXTRACTME TOTAL RNA KIT
Library preparation for Oxford Nanopore long read sequencing was performed with the PCR-cDNA sequencing kit SQK-PCS109 together with the the PCR barcoding kit SQK- PBK004.

value: 50 nM lorecivivint


title: OT-I T cells, tazemetostat treated, 48h, replicate3

value: CD8 T cells

value: OT-I transgenic


title: H1975, ACBi1, replicate 1


title: CD4 TRaGS biol rep 2 [16-530201-CD4_S16]


title: CD4 TRaGS biol rep 1 [7-529492-CD4_S7]


title: 22Rv1 cells, Lorecivivint treated, replicate 5


title: OT-I T cells, tazemetostat treated, 48h, replicate2

value: tazemetostat


title: OT-I T cells, tazemetostat treated, 48h, replicate1


title: 22Rv1 cells, Lorecivivint treated, replicate 4


title: H1299, Y23, replicate 2


title: CD4 TRaWT biol rep 4 [22-529518-CD4_S22]

value: spleen


title: 22Rv1 cells, vehicle treated, replicate 3

value: DMSO vehicle


title: H1792, DMSO, replicate 1

value: lung adenocarcinoma


title: Head-WT-2

value: embryos


title: OT-I T cells, vehicle treated, 48h, replicate3


title: CD4 TRaWT biol rep 3 [19-529517-CD4_S19]

value: TRaWT


title: OT-I T cells, vehicle treated, 48h, replicate2


title: H1975, DMSO, replicate 1


title: 22Rv1 cells, vehicle treated, replicate 2


title: H1299, ACBi1, replicate 2


title: OT-I T cells, vehicle treated, 48h, replicate1


title: 22Rv1 cells, vehicle treated, replicate 1


title: H1299, DMSO, replicate 2


title: CD4 TRaWT biol rep 1 [1-529490-CD4_S1]


title: PBMCs from EL16

status: Public on Sep 25 2024

type: genomic

city: Boston

first: George

middle: J

last: Murphy

state: MA

address: 670 Albany Street

department: Department of Medicine

institute: Boston University / Boston Medical Center

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC v2 beadchip (Illumina) using standard Illumina protocol

scan_protocol: Illumina protocol

data_processing:
SeSAMe package v1.20.0 in R environment
Average Beta in processed data file.

label: Cy3 and Cy5

label_protocol: Illumina protocol

extract_protocol: Qiagen DNA extraction kit CAT#69506

value: PBMC

tag: Sex

value: Male


title: PBMCs from EL55

value: Female


title: PBMCs from EL30


title: PBMCs from EL36


title: PBMCs from EL17


title: PBMCs from EL11


title: PBMCs from EL22


title: PBMCs from EL41


title: PBMCs from EL29


title: PBMCs from EL27


title: PBMCs from EL28


title: PBMCs from EL35


title: CD4 TRaWT biol rep 2 [4-529491-CD4_S4]


title: PBMCs from EL14


title: PBMCs from EL31


title: PBMCs from EL12


title: PBMCs from EL33


title: PBMCs from EL34


title: PBMCs from EL8


title: PBMCs from EL18


title: PBMCs from EL32


title: PBMCs from EL6


title: PBMCs from EL7


title: PBMCs from EL4


title: PBMCs from EL26


title: Aspergillus terreus strain 211, AmB treated after 4h triplicate 2

first: David

last: Eisele

address: Schöpfstraße 41

data_processing:
Raw reads were filtered with SOAPnuke to remove adaptors, unknown bases and low quality reads. Ribosomal RNA was removed as well, generating in the clean reads files
The clean reads were analyzed with Salmon. Salmon was run in quasi-mapping read mode, with the whole genome as a decoy and with the validateMappings option enabled
Assembly: ASM1680841v1
Supplementary files format and content: fastq files containing clean/raw RNA-seq reads

organism: Aspergillus terreus

growth_protocol: WT and ATSec strains were grown in AMM broth for 30 h at 30 °C. Triplicates of each combination of these factors were made, resulting in a total of 24 samples.

extract_protocol:
RNA was extracted with a Promega GmbH kit (Madison, Wisconsin, USA) following the manufacturer’s instructions.
Library construction according to BGI, the company performing the RNA-sequencing: The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the DNBseq platform for the following data analysis study. For this step, the DNBseq platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.

treatment_protocol: Afterwards, the cultures were subjected to either DMSO (control) or 1 µg/ml AmB treatment for 1 h/4 h. Triplicates of each combination of these factors were made, resulting in a total of 24 samples.

value: AmB


title: PBMCs from EL25


title: Aspergillus terreus strain 211, AmB treated after 4h triplicate 3


title: Aspergillus terreus strain 211, AmB treated after 4h triplicate 1


title: Aspergillus terreus strain 211, AmB treated after 1h triplicate 1


title: Aspergillus terreus strain 211, control after 4h triplicate 2

value: control


title: Aspergillus terreus strain 211, control after 1h triplicate 3


title: Aspergillus terreus strain 211, control after 4h triplicate 1


title: Aspergillus terreus strain 211 sectorized derivative, AmB treated after 4h triplicate 3


title: Aspergillus terreus strain 211, AmB treated after 1h triplicate 3


title: Aspergillus terreus strain 211, control after 4h triplicate 3


title: Aspergillus terreus strain 211, AmB treated after 1h triplicate 2


title: Aspergillus terreus strain 211, control after 1h triplicate 1


title: Aspergillus terreus strain 211 sectorized derivative, AmB treated after 4h triplicate 2


title: Aspergillus terreus strain 211, control after 1h triplicate 2


title: Aspergillus terreus strain 211 sectorized derivative, AmB treated after 1h triplicate 1


title: Aspergillus terreus strain 211 sectorized derivative, AmB treated after 4h triplicate 1


title: Aspergillus terreus strain 211 sectorized derivative, AmB treated after 1h triplicate 2


title: Aspergillus terreus strain 211 sectorized derivative, control after 4h triplicate 2


title: Aspergillus terreus strain 211 sectorized derivative, control after 1h triplicate 3


title: Aspergillus terreus strain 211 sectorized derivative, control after 1h triplicate 1


title: Aspergillus terreus strain 211 sectorized derivative, control after 4h triplicate 1


title: Aspergillus terreus strain 211 sectorized derivative, control after 1h triplicate 2


title: Aspergillus terreus strain 211 sectorized derivative, AmB treated after 1h triplicate 3


title: Aspergillus terreus strain 211 sectorized derivative, control after 4h triplicate 3


title: E3

city: Lanzhou

first: Yongxiang

last: Dang

state: Gansu province

address: Peili street

institute: Northwest Normal University

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads  containing ploy-N and the low quality reads were removed to obtain the clean reads. After  removing adaptor and low quality sequences, the clean reads were assembled into expressed  sequence tag clusters (contigs) and de novo assembled into transcript by using Trinity (vesion:  and length of a sequence for subsequent analysis.  2.4) in paired-end method. The longest transcript was choose as a unigene based the similarity  and length of a sequence for subsequent analysis.
The function of the unigenes was annotated by alignment of the unigenes with the NCBI non redundant (NR), SwissProt, and Clusters of orthologous groups for eukaryotic complete  genomes (KOG) databases using Blastx with a threshold E-value of 10−5. The proteins with  the highest hits to the unigenes were used to assign functional annotations thereto. Base onthe  SwissProt annotation，Gene ontology (GO) classification was performed by the mapping  relation between SwissProt and GO term. The unigenes were mapped to the Kyoto  Encyclopedia of Genes and Genomes (KEGG) database to annotate their potential metabolic  pathways.
FPKM and read counts value of each unigene was calculated using bowtie2 and eXpress.  DEGs wereidentified using the DESeq(2012) functions estimateSizeFactors and nbinomTest.  P value < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for  significantly differential expression. Hierarchical cluster analysis of DEGs was performed to  explore transcripts expression pattern. GO enrichment and KEGGpathway enrichment analysis  of DEGs were respectively performed using R based onthe hypergeometric distribution
Assembly: mm10

organism: Morchella sextelata

source_name: mycelium

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s protocol
Then libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit  for Illumina according to the manufacturer’s instructions.

value: mycelium

value: mycelium cells

value: No herbicides were applied


title: E2

value: WT


title: E1


title: D2

value: Acetochlor


title: D1


title: D3


title: C3

value: S-metolachlor


title: B3

value: Pendimethalin


title: C2


title: B2


title: B1


title: C1


title: A1

value: Trifluralin


title: A2


title: A3


title: Mitfmi-vga9/mi-vga9, Mitf mutant3, OB, female, 22 months old

city: Reykjavik

first: Thorarinn

last: Gudjonsson

address: Vatnsmyrarvegur 16

department: Faculty of Medicine

country: Iceland

institute: University of Iceland

data_processing:
Basecalling was performed in real-time using RTA v3.4.4. The process of demultiplexing BCL files and generating FASTQ files was done using bcl2fastq2 v.2.20.
Kallisto pseudocounts with reference transcriptome Mus_musculus.GRCm39
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: Kallisto count files  h5 and tsv files

source_name: Olfactory bulb

extract_protocol:
RNA was isolated using a commercially available kit Monarch Total RNA Miniprep Kit; New England Biolabs Inc., cat# T2010S.
To create RNA libraries Illumina's TruSeq RNA v2 Sample Prep Kit (Illumina, RS-122-2001) was used.

value: Olfactory bulb

value: Female, 22 months old

value: Mitfmi-vga9/mi-vga9 (Mitf mutant)

value: No treatment


title: Mitfmi-vga9/mi-vga9, Mitf mutant2, OB, female, 25 months old

value: Female, 25 months old


title: Mitfmi-vga9/mi-vga9, Mitf mutant1, OB, male, 25 months old

value: Male, 25 months old


title: C57BL/6J (WT), control3, OB, male, 26 months old

value: Male, 26 months old

value: C57BL/6J (WT)


title: C57BL/6J, control1, OB, female, 25 months old


title: C57BL/6J, control2, OB, female, 25 months old


title: RNAseq_oocyte_Cy_1

city: Zhanjiang

first: Yiting

last: Guan

address: 236 Yuanzhu Road

department: Zhanjiang Institute of Clinical Medicine

institute: Guangdong Medical University

data_processing:
The sequencing adapters were removed from the raw RNA-seq reads, and the obtained clean data were aligned to the human reference genome (mm9) using HISAT2 software (version 2.1.0.).
For gene expression quantification, the sequencing reads within each gene were counted, and the counts were normalized using edgeR.
Differentially expressed genes (DEGs) were identified normalized according to DESeq2, |log2FC| > 1 and p < 0.05.
Assembly: mm9
Supplementary files format and content: wig or bedGraph index binary

source_name: oocyte

extract_protocol:
For single oocyte analysis and data processing, 3 oocytes was extracted using a TRIzol reagent following a standard protocol. The RNA integrity was checked on Agilent 2100 BioAnalyzer to conduct quality control (Agilent Technologies).
For RNA-seq data processing, the high-throughput RNA-Seq were performed with the NovaSeq 6000 platform to a depth of 1.5×107 reads.

value: oocyte

value: cyclophosphamide-treated


title: RNAseq_oocyte_Cy_3


title: RNAseq_oocyte_Ctrl_3


title: RNAseq_oocyte_DQ_1

value: cyclophosphamide, dasatinib and quercetin-treated


title: RNAseq_oocyte_Ctrl_2


title: RNAseq_oocyte_Cy_2


title: RNAseq_oocyte_DQ_2


title: Tcells_NTT

city: Vienna

first: Anais

last: Elewaut

address: Vienna Biocenter 1

institute: IMP

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
scRNAseq data was aligned and quantified using cellranger multi v7.1.0 and the build in Probe Set v1.0.1 mm10-2020-A. Barcodes are provided as a separate (barcodes.tsv) file.
Assembly: mm10
Supplementary files format and content: cellranger Hierarchical Data Format h5

source_name: Melanoma tumor

extract_protocol:
Chromium Next GEM Single Cell Fixed RNA Sample preparation kit was used according to the manufacturer's protocol. In brief, 1 x 106 cells were fixed for 22 hours at 4°C, quenched, and long-term stored at -80°C according to 10X genomic Fixation of Cells & Nuclei for Chromium Fixed RNA profiling (CG000478) using Chromium Next GEM Single Cell Fixed RNA Sample preparation kit (PN-1000414, 10X Genomics). 250,000 cells per sample were used for probe hybridization using the Chromium Fixed RNA Kit, Mouse Transcriptome, 4rxn x 4BC (PN-1000496, 10X Genomics), pooled equally and washed following the Pooled Wash Workflow as described in the Chromium Fixed RNA Profiling Reagent kit protocol (CG000527, 10X Genomics).
Library was constructed according to manufacturer’s protocol using the 10x Genomics 3' CellPlex multiplex kit.

treatment_protocol: Tumors were isolated, cut into pieces, and digested for approximately 1.5 h at 37°C with collagenase A (1 mg/ml, Roche) and DNAse (20mg/ml, Worthington) in RPMI-1640 media. Digested tumors were strained through a 70um filter and resuspended in FACS buffer (0.5% BSA, 2mM EDTA). FC-block with anti-CD16/32 (clone 93, BioLegend) was performed for 10 min at 4°C to avoid unspecific antibody binding and staining was performed for 30 min at 4°C degrees. Samples were stained for CD45+ CD3+ CD8+ and live dead exclusion was performed by staining with the fixable viability dye eF780 (1:1000, eBioscience).

value: Melanoma tumor

value: CD8+ T cell


title: Tcells_RTT

description: 10x Genomics


title: RNAseq_oocyte_DQ_3


title: Control-Gfap-mCherry_RNA

city: Ann arbor

first: Thanh

last: Hoang

state: Michigan

address: 1000 wall street

institute: University of Michigan ann arbor

data_processing:
scRNA-Seq: Sequencing results were processed through the Cell Ranger pipeline (10x Genomics) with default parameters.
Assembly: mm10, and custom mm10 with mCherry and Sun1GFP sequences
Supplementary files format and content: Control_mCherry_NMDA_atac_fragments.tsv.gz, Control_mCherry_NMDA_filtered_feature_bc_matrix.h5
Supplementary files format and content: Control_Oct4_NMDA_atac_fragments.tsv.gz, Control_Oct4_NMDA_filtered_feature_bc_matrix.h5
Supplementary files format and content: Rbpj_Oct4_NMDA_atac_fragments.tsv.gz, Rbpj_mCherry_NMDA_filtered_feature_bc_matrix.h5
Supplementary files format and content: Rbpj_mCherry_NMDA_atac_fragments.tsv.gz, Rbpj_Oct4_NMDA_filtered_feature_bc_matrix.h5

source_name: Retina

extract_protocol: scRNA-Seq following 10x V3.1 guideline, scMultiome using 10xGenomics Multiome

value: Retina

value: GFP+ cells

value: Control

tag: library type

value: RNA, 10xMultiome


title: RbpjKO-Gfap-mCherry_RNA

value: RbpjKO


title: RbpjKO-GFAP-Oct4_RNA


title: Control-GFAP-Oct4_ATAC

library_source: genomic single cell

value: ATAC, 10xMultiome


title: RbpjKO-Gfap-mCherry_ATAC


title: Control-Gfap-mCherry_ATAC


title: RNAseq_oocyte_Ctrl_1

value: WT


title: RbpjKO-Gfap-mCherry_scRNA

value: 10xscRNA V3.1


title: Control-GFAP-Oct4_RNA


title: RbpjKO-Gfap-Oct4_scRNA


title: head_young_btbr_embryo [h_y_b__2_2]

value: head

value: young

value: btbr


title: Y1.7_NTT_3A6

description: 10x Genomics

data_processing:
scRNAseq data was aligned and quantified using cellranger multi v7.1.0 and the build in Probe Set v1.0.1 mm10-2020-A. Sample barcodes and estimated cell counts are provided in the supplementary barcodes.csv file.
Assembly: mm10
Supplementary files format and content: cellranger Hierarchical Data Format h5

treatment_protocol: Tumors were isolated, cut into pieces, and digested for approximately 1.5 h at 37°C with collagenase A (1 mg/ml, Roche) and DNAse (20mg/ml, Worthington) in RPMI-1640 media. Digested tumors were strained through a 70um filter and resuspended in FACS buffer (0.5% BSA, 2mM EDTA). FC-block with anti-CD16/32 (clone 93, BioLegend) was performed for 10 min at 4°C to avoid unspecific antibody binding and staining was performed for 30 min at 4°C degrees. Samples were stained for CD45+ cells and live dead exclusion was performed by staining with the fixable viability dye eF780 (1:1000, eBioscience).

value: CD45+ Immune cell


title: Y1.7_RTT_2B12_ACT

description: 10x Genomics


title: Y1.7_RTT_2B12

description: 10x Genomics


title: Y1.7_NTT_3A6_ACT

description: 10x Genomics


title: GH1397_P8

city: New York

first: ZHUXUAN

last: LI

state: NY

address: 417 E 68th St

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Bulk RNA-sequencing data from ex vivo transformation experiments of young and aged cells was compiled object and normalized using the size factor normalization function of DESeq2. Highly variable features were identified using a variance stabilizing transformation. Diffusion maps were generated in scanpy using the top principal components from normalized, log2-transformed count data. The pseudotime position of each sample was then calculated in scanpy in diffusion space using untransformed AT2 cells as root. To identify genes differentially expressed between young and aged ex vivo transformed cells independent of differentiation stage, gene expression models controlling for either passage or pseudotime were fitted in DESeq2 (version 1.26.0).
Assembly: GRCm38/mm10
Supplementary files format and content: txt file includes raw counts for each sample.

source_name: 3D culture

growth_protocol: Cells were seeded the density of 3000 cell/matrigel plug with media change every three days. Recipe of the media: Advanved DMEM/F12, 2% heat-inactivated fetal bovine serum and pen/strep.

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (Qiagen, #217004) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 2 ng total RNA with RNA integrity numbers ranging from 9.0 to 9.7 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech,  #63488), with 12 cycles of amplification. Subsequently, 10 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems, #KK8504) using 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S2 Reagent Kit (200 Cycles) (Illumina).

value: 3D culture

value: 3D fulture from primary mouse cells

value: Tumor


title: AF1337_P7


title: AF1165_P8


title: AF1181_P8


title: AF1183_P8


title: GH2108_P8


title: AF1165_P7


title: RbpjKO-GFAP-Oct4_ATAC


title: AF1183_P7


title: GH2108_P7


title: GH1394_P7


title: AF1181_P7


title: AF1337_P0

value: Normal


title: AF1337_P8


title: AF1337_P6


title: KW1401_P7


title: KW1401_P0


title: AF1165_P0


title: GH1397_P7


title: Input2_rep3

first: Giulio

last: Superti-Furga

address: Lazarettgasse 14

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
read trimming (Galaxy Version 4.8+galaxy1): options: g- GTGGAAAGGACGTGTCACCG…GTTTAAGAGCTA --overlap 10 --discard_untrimmed
gRNA mapping: MAGeCK count (Galaxy Version 0.5.9.2.4).
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited raw gRNA count table
Library strategy: Amplicon-Seq

organism: blank sample

source_name: blank sample

growth_protocol: HCT116 (RRID:CVCL_0291) cells and HCT116 KO clones were cultivated in RPMI 1640 (R8758 Sigma) supplemented with 10% Fetal Bovine Serum (10270-106, Lot 42F8381K, Gibco) and Penicillin-Streptomycin (15140-122, Gibco).

extract_protocol:
Genomic DNA was purified using QIAamp DNA Mini columns (Qiagen)
gDNA was digested overnight with 20U PacI (NEB) and double size-selected to enrich the sgRNA containing fragments (380 bp). Briefly, 0.7 x vol AmpliClean magnetic beads (Nimagen) were added to the sample to bind large gDNA fragments; the cleared supernatant was added to fresh beads (0.6 x volume of the original gDNA sample) to bind the smaller fragments. After size selection, sgRNA sequences were amplified in  with Q5 Polymerase (NEB) using the program recommended by the manufacturer (28 cycles, 65°C annealing temperature). PCR products were further double size-selected to remove residual large gDNA fragments as described above. Purified PCR products were used in barcoding PCRs to add Illumina adapters and indices for pooled sequencing. A detailed protocol can be found on Addgene (https://www.addgene.org/pooled-library/human-transporters/).

treatment_protocol: Cells were transduced with lentiviral particles containing KO library in triplicates and selected with blasticidin to remove non-transduced cells. After 13 days of selection, each replicatewas independently was passaged in standard growth media for a total of five weeks. Samples were harvested for NGS analysis 3 to 7 weeks after transduction.

tag: screening library

value: Human Transporter KO (Addgene  #213695)


title: Input2_rep1


title: Input2_rep2


title: AF1337_P5


title: WT_Input1_rep1


title: KW1401_P8


title: WT_Input1_rep2


title: GH1394_P8


title: AF1337_P3