title: patterned induced neurons, H2C2a_G6-2, Homo sapiens, 4N, minusKCl, piN_Rep1

description:
Library name: H2C2a_G6-2_minusKCl
The raw data are being made available for controlled access on dbGaP.
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw

data_processing:
ATAC-seq data from the human and chimpanzee diploids, autotetraploids, and allotetraploids was aligned to a composite human-chimpanzee genome (hg38 and panTro6) using bwa mem v0.7.17 (Li and Durbin, 2009). Reads with poor alignment or quality were removed (samtools view -F 3844 -q 10) and de-duplicated with samtools v1.3.1 (Li et al., 2009). Bam files were converted to bed files using bedtools v2.26.0 (Quinlan and Hall, 2010), and peaks were called with macs2 v2.1.1.20160309 with the parameters --nomodel --extsize 200 (Zhang et al., 2008). We used reads from diploids and autotetraploids that mapped to the incorrect species as the background for peak calling.
Aligned reads and peaks were then filtered by mapping reads and peaks called in panTro6 to hg38 and vice versa using pslMap from UCSC v363 (Zhu et al., 2007). To generate the chain file used in pslMap, we downloaded panTro6.hg38.all.chain.gz from the UCSC Genome Browser (Navarro Gonzalez et al., 2021) and filtered for orthologous chains as previously described (Turakhia et al., 2020). Reads and peaks were then filtered for those that map uniquely and where the orthologous regions have <5-fold change and <5kb difference in size. Peaks in hg38 coordinates that overlapped ENCODE blacklist regions (Amemiya et al., 2019) or alternate chromosomes were also filtered out. This resulted in reads and peaks in hg38 and panTro6 coordinates for each sample. For allotetraploids, reads and peaks that initially mapped to hg38 were represented separately from those that initially mapped to panTro6.
Reads from diploids and autotetraploids that mapped to the incorrect species were similarly filtered to generate a background mis-mapping file for chimpanzee samples in both hg38 and panTro6 coordinates and for human samples in both hg38 and panTro6 coordinates. We called peaks using macs2 for the background mis-mapping files in hg38 coordinates to identify genomic regions where there were high levels of mis-mapping.
Assembly: hg38
Assembly: panTro6
Supplementary files format and content: bigwig files where reads were first mapped to a composite hg38-panTro6 genome, the appropriate reads were extracted (ex. reads that mapped to panTro6 from a chimpanzee sample), and then those reads were filtered and mapped to hg38
Supplementary files format and content: background_mismapping bigwigs are reads from human samples that incorrectly mapped to panTro6 and reads from chimpanzee samples that incorrectly mapped to hg38 (see data processing steps)
Supplementary files format and content: peak bed files

extract_protocol:
NPCs at D14 of differentiation or piNs at D28 were lyzed in lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween-20) and collected into conical tubes at a final volume of 500µl lysis buffer. The cell suspension was incubated at 4°C for 10min to release nuclei and then pelleted at 830rcf for 10min. Nuclei were resuspended in 1ml lysis buffer and counted. 50,000 nuclei were then pelleted at 830rcf for 10min and resuspended in 50µl of transposition mix (1X TD buffer [10mM Tris-HCl pH7.6, 5mM MgCl2, 10% dimethyl formamide], 0.33X PBS, 0.001% Digitonin, 0.1% Tween-20, 100nM Tn5 transposase [made in house]). The resuspended nuclei were incubated at 37°C for 30min. DNA was then purified and eluted in 21µl H2O using the DNA Clean and Concentrator-5 Kit (Zymo Research, cat #D4014).
20µl of the eluent was PCR amplified with 1X NEBNext High Fidelity PCR Master Mix (New England Biolabs, cat #M0541L) and primer sequences containing Illumina adapters for 72°C for 5min, 98°C for 30s, and then 5 cycles of 98°C for 10s, 63°C for 30s, and 72°C for 1min.  Libraries were purified using the DNA Clean and Concentrator-5 Kit and quantified with the KAPA Library Quantification Kit (Roche, cat #07960140001).

value: patterned induced neurons

tag: kcl treatment

value: minusKCl


title: NGS4532 BP043209 ES-2 DMSO, Replicate 3

status: Public on Aug 12 2025

type: SRA

city: Mississauga

first: James

middle: R

last: Hawley

state: Ontario

address: 7070 Mississauga Road

department: Computational Sciences

country: Canada

institute: Roche Canada

description: Library name: NGS4532_R8338_LIB5457662_SAM24417735

library_source: transcriptomic

data_processing:
RNA-seq reads were first aligned to ribosomal RNA sequences to remove ribosomal reads. The remaining reads were aligned to the human reference genome (GRCh38) using GSNAP version 2013-10-10, allowing a maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 — pairmax-rna = 200000—clip-overlap) (PMID: 27008021). Transcript annotation was based on the Ensembl genes database (release 77). To quantify gene expression levels, the number of reads mapped to the exons of each RefSeq gene was calculated. Differential gene expression was performed with DESeq2. A pre-filter was applied so that only genes with at least a median RPKM value of 10 in one were analyzed. P-values for other genes were simply set to 1 and log fold changes were set to 0 for visualization purposes, but such genes were not included in the multiple testing correction. Q-values were obtained by correcting P-values for multiple hypotheses using the Benjamini-Hochberg procedure. Genes were considered if they had a Q-value of less than 0.05 and were protein-coding. Counts were transformed to log2 counts per million, quantile-normalized, and precision-weighted with the “voom” function of the limma package.
Assembly: GRCh38
Supplementary files format and content: gzipped tab-separated value file

molecule: total RNA

organism: Homo sapiens

source_name: Ovary

growth_protocol: All cell lines used in this study were obtained from American Type Culture Collection (ATCC). They were maintained in RPMI 1640 supplemented with 10% FBS (Sigma-Aldrich Corporation) and 2 mM L-glutamine (Gibco Life Sciences) in a humidified incubator maintained at 37 °C with 5% CO2. Cell line authentication was conducted for Short Tandem Repeat (STR) Profiling using the Promega PowerPlex 16 System (Promega Corporation). This was performed once when receiving new cell lines and compared to external STR profiles of cell lines (when available) to determine cell line ancestry. Cell line authentication was routinely conducted by SNP-based genotyping using Fluidigm multiplexed assays at the Genentech cell line core facility. Cells were assessed with a Vi-CELL Cell Viability Analyzer (Beckman Coulter); viability of at least 90% was required for experiments and screening.

extract_protocol:
For treatment, cells were seeded at 1-2 × 10^5 cells/well on tissue culture treated 6-well plates, and were treated after 12-24 h with experimental compounds. Cell lines were lysed on-plate for RNA isolation using the Qiagen RNeasy Plus Mini Kit (catalog number 74034), and RNA concentration was determined using a NanoDrop 8000 (Thermo Fisher Scientific). For analysis by RNA Fluidigm, 100 ng RNA was subjected to a complementary DNA (cDNA) synthesis reaction using the Applied Biosystems High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific, Cat. No. 4368814), as per the manufacturer’s protocol. A preamplification reaction was then performed with Taqman PreAmp Master Mix (Thermo Fisher Scientific). After amplification, samples were diluted 1:4 with Tris-EDTA, and qPCR was conducted on Fluidigm 96.
RNA integrity was confirmed using a Bioanalyzer 2100 (Agilent Technologies). About 500 ng of RNA was used for library synthesis using the TrueSeq RNA Sample Preparation kit v2 (Illumina). Size of the libraries was confirmed using 2200 TapeStation and High Sensitivity D1K screen tape (Agilent Technologies), and the concentration was determined by a qPCR-based method using the Library Quantification Kit (KAPA). The libraries were multiplexed and then sequenced on Illumina HiSeq2500 (Illumina) to generate 30M single-end 50-base pair reads.

treatment_protocol: For single agent treatments with pan-TEAD experimental compounds or in combination with KRAS G12C, KRAS G12D or EGFR experimental compounds, cells were seeded at 1000 cells/well on tissue culture treated flat bottom 96-well plates. 12-24 h post plating, cells were treated with multipoint titration ranges as indicated of the desired chemical compounds using the HP D300 drug dispenser. Cell growth was assessed using CellTiter-Glo Luminescent Cell Viability Assays (Promega Corporation), and luminescence was read by a 2104 EnVision Multilabel Plate Reader (PerkinElmer). All cell viability data was collected and calculated for at least 5 replicates per time point, per condition. IC50 values for the inhibitors were determined by fitting the nonlinear regression curves generated by GraphPad Prism. To assess colony formation, cells were seeded at 1.5 × 103 cells/well in 40 mL 0.29% soft agar on a base layer of 40 mL 0.6% soft agar and treated with 40 mL 3× concentrated experimental compound. On day 7, 40 mL 4× concentrated experimental compound/well was added. Colonies were imaged and counted on days 7, 10, and 14 using a GelCount colony counter (Oxford Optronix) per the manufacturer’s instructions.

tag: tissue

value: Ovary

tag: cell line

tag: cell type

value: Fibroblast

tag: treatment

value: DMSO

tag: batch


title: NGS4532 BP043209 ES-2 DMSO, Replicate 2

description: Library name: NGS4532_R8338_LIB5457661_SAM24417734


title: BC_16_scRNA

city: Houston

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

country: USA

institute: The University of Texas MD Anderson Cancer Center

library_source: transcriptomic single cell

data_processing:
Cell ranger version 5.0.0
Assembly: GRCh38-2020-A
Supplementary files format and content: Seurat object saved as .rds with full metadata matching manuscript. One file for cancer samples and one file for normal ureter samples.

source_name: bladder

extract_protocol:
10x genomics V3.1 kit
10x genomics V3.1 kit gene expression

value: bladder


title: NGS4532 BP043209 ES-2 G03502181, Replicate 1

description: Library name: NGS4532_R8338_LIB5457654_SAM24417727


title: BC_15_scRNA


title: BC_17_scRNA


title: C2C12 cells, siCCNF, biol rep 2

city: Berkeley

first: Andrew

last: Ingersoll

state: CA

address: 1951 Oxford St

department: MCB

institute: University of California, Berkeley

data_processing:
Reads were mapped to the mouse reference genome using HISAT2, counted, and FPKM were calculated
Assembly: GRCm39
Supplementary files format and content: CSV file containing raw counts and FPKM values for each sample

organism: Mus musculus

growth_protocol: Cells were grown in DMEM supplemented with 5% FBS at 37 degrees Celsius with 5% CO2.

extract_protocol:
Total RNA was extracted from cells using the NucleoSpin RNA kit (Macherey-Nagel)
mRNA was purified from total RNA by polyA enrichment. mRNA was fragmented and cDNA was synthesized. This was followed by end repair, A-tailling, adapter ligation, size selection, amplification and purification.

treatment_protocol: Cells were treated with 30 nM siRNA for 48 hours before harvesting.

value: Myoblast

value: siCCNF


title: BC_14_scRNA


title: NGS4967 LIB5465583 SNU-2292 G03498025 1 uM, G02925614 1 uM, 48 hrs, Replicate 3

description: Library name: NGS4967_R9034_LIB5465583_SAM24427417

source_name: Lung

value: Lung

value: Epithelial


title: patterned induced neurons, H2C2a_G6-2, Homo sapiens, 4N, 30minKCl, piN_Rep1

city: Boston

first: Janet

last: Song

state: Massachusetts

address: 3 Blackfan St

institute: Boston Children's Hospital

description:
Library name: H2C2a_G6-2_30minKCl
The raw data are being made available for controlled access on dbGaP.
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw

library_source: genomic

molecule: genomic DNA

organism:
Pan troglodytes
Homo sapiens

growth_protocol:
Stem cell lines were routinely propagated feeder-free in mTeSR Plus (STEMCELL Technologies, cat #100-0276), and differentiated into neural progenitor cells (NPCs) using the StemDiff SMADi Neural Induction Kit (STEMCELL Technologies, cat #08582) as per the manufacturer’s instructions. Cells were split on D7 using Accutase (Millipore, cat #SCR005) and then harvested at D14 for sequencing.
Stem cell lines were routinely propagated feeder-free in mTeSR Plus (STEMCELL Technologies, cat #100-0276), and differentiated into patterned induced neurons (piNs) via induction of doxycycline-inducible NGN2 and as described in Nehme et al., 2018. Cells were harvested on D28

tag: ploidy

value: N


title: NGS4532 BP043209 ES-2 DMSO, Replicate 1

description: Library name: NGS4532_R8338_LIB5457660_SAM24417733


title: NGS4967 LIB5465582 SNU-2292 G03498025 1 uM, G02925614 1 uM, 48 hrs, Replicate 2

description: Library name: NGS4967_R9034_LIB5465582_SAM24427416


title: patterned induced neurons, H2C2a_G6-2, Homo sapiens, 4N, 2hrKCl, piN_Rep1

description:
Library name: H2C2a_G6-2_2hrKCl
The raw data are being made available for controlled access on dbGaP.
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: C2C12 cells, siCCNF, biol rep 1


title: BC_13_scRNA


title: neural progenitor cells, H2C2a, Homo sapiens, 4N, NPC_Rep1 (RNA-seq)

description:
Library name: H2C2a_1_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt
NPC_allotetraploid_gene_counts_by_allele.txt

data_processing:
RNA-seq data from the human and chimpanzee diploids, autotetraploids, and allotetraploids was analyzed as previously described (Song et al., 2021). Briefly, sequencing reads were trimmed for adapter sequences and assessed for sequencing quality using trimgalore v0.6.6 with cutadapt v2.5 (Martin, 2011) and fastqc v0.11.5 (Andrews et al., 2010). Reads were aligned using STAR v2.7.9a with two-pass mapping (Dobin et al., 2013) to a composite human-chimpanzee genome (hg38 and panTro6). The number of uniquely-mapped reads (MAPQ=255) that overlap each gene was counted using featureCounts from the subread v2.0.0 package (Liao et al., 2014).
For CRISPR inhibition experiments, UMIs were extracted using umi_tools v1.1.2 (Smith et al., 2017) and adapter sequences were trimmed using cutadapt v2.5 (Martin, 2011). Sequencing quality was assessed with fastqc v0.11.5 (Andrews et al., 2010). Reads that map to rDNA (https://www.ncbi.nlm.nih.gov/nuccore/U13369.1) were removed, and remaining reads were aligned using STAR v2.7.9a with two-pass mapping (Dobin et al., 2013) to either the hg38 or panTro6 genome, as appropriate. Reads were then de-duplicated based on UMIs using umi_tools, and the number of reads that overlap each gene was counted using featureCounts from the subread v2.0.0 package with default parameters (Liao et al., 2014).
Assembly: hg38
Assembly: panTro6
Supplementary files format and content: gene count files

growth_protocol:
Stem cell lines were routinely propagated feeder-free in mTeSR Plus (STEMCELL Technologies, cat #100-0276), and differentiated into neural progenitor cells (NPCs) using the StemDiff SMADi Neural Induction Kit (STEMCELL Technologies, cat #08582) as per the manufacturer’s instructions. On D7, cells were split using Accutase (Millipore, cat #SCR005) and infected with lentivirus (if applicable). Cells were harvested at D14 for sequencing.
Stem cell lines were routinely propagated feeder-free in mTeSR Plus (STEMCELL Technologies, cat #100-0276), and differentiated into patterned induced neurons (piNs) via induction of doxycycline-inducible NGN2 and as described in Nehme et al., 2018. Cells were harvested on D28

extract_protocol:
NPCs at D14 or piNs at D28 were collected in Trizol and RNA was extracted with the Direct-Zol Miniprep Kit (Zymo Research, cat #R2052) or the Direct-Zol Microprep Kit (Zymo Research, cat #R2062). Cells infected with lentivirus were collected by FACS prior to RNA extraction.
RNA sequencing libraries were made with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit (Takara Bio) or with the WatchMaker RNA Library Prep Kit with Polaris Depletion (WatchMaker Genomics) and the Twist UMI Adapter System - TruSeq Comp, 96 Samples Plate A (Twist Biosciences, cat #105041).

treatment_protocol: If applicable, cells were infected with lentivirus.

value: neural progenitor cells


title: C2C12 cells, siKEAP1, biol rep 3


title: patterned induced neurons, H2C2a_G11-1, Homo sapiens, 4N, minusKCl, piN_Rep1

description:
Library name: H2C2a_G11-1_minusKCl
The raw data are being made available for controlled access on dbGaP.
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: NGS4967 LIB5465581 SNU-2292 G03498025 1 uM, G02925614 1 uM, 48 hrs, Replicate 1

description: Library name: NGS4967_R9034_LIB5465581_SAM24427415


title: BC_12_scRNA


title: NGS4967 LIB5465580 SNU-2292 G02925614 1 uM, DMSO 0.01%, 48 hrs, Replicate 3

description: Library name: NGS4967_R9034_LIB5465580_SAM24427414


title: BC_11_scRNA


title: C2C12 cells, siKEAP1, biol rep 1


title: patterned induced neurons, H2C2a_G11-1, Homo sapiens, 4N, 2hrKCl, piN_Rep1

description:
Library name: H2C2a_G11-1_2hrKCl
The raw data are being made available for controlled access on dbGaP.
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: NGS4967 LIB5465579 SNU-2292 G02925614 1 uM, DMSO 0.01%, 48 hrs, Replicate 2

description: Library name: NGS4967_R9034_LIB5465579_SAM24427413


title: BC_10_scRNA


title: C2C12 cells, siCONTROL, biol rep 3

value: siCONTROL


title: C2C12 cells, siCONTROL, biol rep 2


title: BC_1_scRNA


title: patterned induced neurons, H2C2a_G1-1, Homo sapiens, 4N, 2hrKCl, piN_Rep1

description:
Library name: H2C2a_G1-1_2hrKCl
The raw data are being made available for controlled access on dbGaP.
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: NGS4967 LIB5465577 SNU-2292 G03498025 1 uM, DMSO 0.01%, 48 hrs, Replicate 3

description: Library name: NGS4967_R9034_LIB5465577_SAM24427411


title: C2C12 cells, siCONTROL, biol rep 1


title: NGS4967 LIB5465578 SNU-2292 G02925614 1 uM, DMSO 0.01%, 48 hrs, Replicate 1

description: Library name: NGS4967_R9034_LIB5465578_SAM24427412


title: NGS4967 LIB5465576 SNU-2292 G03498025 1 uM, DMSO 0.01%, 48 hrs, Replicate 2

description: Library name: NGS4967_R9034_LIB5465576_SAM24427410


title: NDM-T, replicate 4, scRNAseq

city: Tianjin

first: xueying

last: Li

address: 94 Weijin Road, Nankai District

country: China

institute: Nankai University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger sofware v6.1.2
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pancreas

extract_protocol:
Pancreatic tissues were obtained from DM-KPC and NDM-KPC mice. Place a sterile RNase-free culture dish containing an appropriate amount of calcium-free and magnesium-free 1 × PBS on ice, the tissue was transferred into the culture dish and cut it into 0.5 mm2 pieces, the tissues were washed with 1 × PBS, and remove as many non-purpose tissues as possible such as blood stains and fatty layers.
Tissues were dissociated into single cells in dissociation solution (0.35% collagenase IV5,2 mg/ml papain, 120 Units/ml DNase I) in 37 ℃ water bath with shaking for 20 min at 100 rpm. Digestion was terminated with 1× PBS containing 10% fetal bovine serum (FBS, V/V), then pipetting 5-10 times with a Pasteur pipette. The resulting cell suspension was filtered by passing through 70-30um stacked cell strainer and centrifuged at 300g for 5 min at 4 °C. The cell pellet was resuspended in 100ul 1× PBS (0.04% BSA) and added with 1 ml 1× red blood cell lysis buffer（MACS 130-094-183, 10×）and incubated at room temperature or on ice for 2-10 min to lyse remaining red blood cells. After incubation, the suspension was centrifuged at 300g for 5 min at room temperature. The suspension was resuspended in 100 μl Dead Cell Removal MicroBeads(MACS 130-090-101) and remove dead cells  using Miltenyi ® Dead Cell Removal Kit (MACS 130-090-101). Then the suspension was resuspended in 1× PBS(0.04% BSA) and centrifuged at 300 g for 3 min at 4 °C (repeat twice). The cell pellet was resuspended in 50 μl of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion , which needed to be above 85%, single cell suspensions were counted using a haemocytometer/ Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.

value: Pancreas

tag: age

tag: genotype

value: NDM-KP


title: patterned induced neurons, H2C2a_G1-1, Homo sapiens, 4N, 30minKCl, piN_Rep1

description:
Library name: H2C2a_G1-1_30minKCl
The raw data are being made available for controlled access on dbGaP.
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: patterned induced neurons, H1C1b_F10-1, Homo sapiens, 4N, minusKCl, piN_Rep1

description:
Library name: H1C1b_F10-1_minusKCl
The raw data are being made available for controlled access on dbGaP.
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: GCI2

city: fuzhou

first: Huihong

state: fujian

address: shangjie

institute: College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine

description: Library name: Sample5

data_processing:
The sequencing data generated by Illumina NextSeq 500 is raw sequencing data. The raw sequencing data undergoes sequencing Quality Control (Quality Control) to assess whether the sequencing data can be used for subsequent data analysis :QC Then, the trimmed data generated through the preprocessing filtering step (removing the joint sequences and overly short fragments in the Read) is aligned to the reference genome: statistical analysis of the results through comparison is conducted to determine whether the alignment results can be used for subsequent data analysis: If the alignment results are good, Then, quantitative analysis of miRNA expression, nomenclature analysis based on iRNA expression levels, differential expression screening, miRNA target gene analysis, GO functional significance enrichment analysis of target genes, and target gene Pathway were conducted A series of analyses such as significance enrichment analysis: Finally, rich visual views such as scatter plots, volcano plots, and cluster plots will be drawn to facilitate data browsing.
After quality control, the reads were 3’5'-adaptor trimmed and filtered 15 bp reads with cutadapt software.
The trimmed reads were aligned to reference genome with bowtie software.
For each sample, known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) ).
Raw reads were normalized by calculated CPM value.
Assembly: miRBase Release 22
Supplementary files format and content: The xlsx format file contains the CPM value of gene in every sample.

source_name: brain

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).Small RNA libraries were constructed using New England Biolabs (NEB) NEBNext Multiplex Small RNA Library Prep Set for Illumina sequencers and the NEB standard protocol. Individual libraries were constructed using 1µg of total RNA isolated from each sample.
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of 135   155 bp PCR amplified fragments (corresponding to 15   35 nt small RNAs).

value: brain

tag: strain

value: Bilateral carotid artery ligation for 20 minutes


title: GCI3

description: Library name: Sample6


title: GCI1

description: Library name: Sample4


title: NDM-T, replicate 3, scRNAseq


title: patterned induced neurons, H1C1b_F10-1, Homo sapiens, 4N, 30minKCl, piN_Rep1

description:
Library name: H1C1b_F10-1_30minKCl
The raw data are being made available for controlled access on dbGaP.
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw

value: patterned induced neurons


title: C2C12 cells, siKEAP1, biol rep 2


title: NGS4967 LIB5465574 SNU-2292 DMSO 0.02%, 48 hrs, Replicate 3

description: Library name: NGS4967_R9034_LIB5465574_SAM24427408

value: 0.02% DMSO 48 hrs


title: patterned induced neurons, H2C2a_G11-1, Homo sapiens, 4N, 30minKCl, piN_Rep1

description:
Library name: H2C2a_G11-1_30minKCl
The raw data are being made available for controlled access on dbGaP.
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: Sham7

description: Library name: Sample3


title: NDM-T, replicate 2, scRNAseq


title: patterned induced neurons, H2C2a_G1-1, Homo sapiens, 4N, minusKCl, piN_Rep1

description:
Library name: H2C2a_G1-1_minusKCl
The raw data are being made available for controlled access on dbGaP.
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw

value: minusKCl


title: patterned induced neurons, H1C1b_E4-1, Homo sapiens, 4N, minusKCl, piN_Rep1

description:
Library name: H1C1b_E4-1_minusKCl
The raw data are being made available for controlled access on dbGaP.
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: Sham6

description: Library name: Sample2


title: NGS4967 LIB5465573 SNU-2292 DMSO 0.02%, 48 hrs, Replicate 2

description: Library name: NGS4967_R9034_LIB5465573_SAM24427407


title: NDM-T, replicate 1, scRNAseq


title: NGS4967 LIB5465570 SNU-2292 G03498025 1 uM, G02925614 1 uM, 48 hrs, Replicate 2

description: Library name: NGS4967_R9034_LIB5465570_SAM24427404


title: NGS4967 LIB5465575 SNU-2292 G03498025 1 uM, DMSO 0.01%, 48 hrs, Replicate 1

description: Library name: NGS4967_R9034_LIB5465575_SAM24427409


title: patterned induced neurons, H1C1b_E4-1, Homo sapiens, 4N, 30minKCl, piN_Rep1

description:
Library name: H1C1b_E4-1_30minKCl
The raw data are being made available for controlled access on dbGaP.
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: DM-T, replicate 2, scRNAseq

value: DM-KP


title: DM-T, replicate 3, scRNAseq


title: NGS4967 LIB5465569 SNU-2292 G03498025 1 uM, G02925614 1 uM, 48 hrs, Replicate 1

description: Library name: NGS4967_R9034_LIB5465569_SAM24427403


title: patterned induced neurons, H1C1b_A6-2, Homo sapiens, 4N, minusKCl, piN_Rep1

description:
Library name: H1C1b_A6-2_minusKCl
The raw data are being made available for controlled access on dbGaP.
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: patterned induced neurons, H1C1b_E4-1, Homo sapiens, 4N, 2hrKCl, piN_Rep1

description:
Library name: H1C1b_E4-1_2hrKCl
The raw data are being made available for controlled access on dbGaP.
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: Ova-FPM-1

city: Kingston

first: Sebastien

last: Talbot

state: ON

address: 18 Stuart st

department: DBMS

institute: Queen's University

description: Library name: Sample_10

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing as much as 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the mouse reference genome using STAR version 2.5.1b.
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode version M23
Expression values were also computed using RSEM version 1.2.28 based on Gencode version M23 transcript annotations
Assembly: GRCm38
Supplementary files format and content: Tab Separated Values (.tsv) files including raw counts of every sample
Supplementary files format and content: Tab Separated Values (.tsv) files including TPM of  transcripts of gene transcripts every sample

source_name: jugular-nodose complex

extract_protocol:
ThermoFisher PureLink™ RNA Micro Scale Kit
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing

value: jugular-nodose complex

value: TRPV1+ vagal sensory neurons


title: patterned induced neurons, H1C1b_A6-2, Homo sapiens, 4N, 30minKCl, piN_Rep1

description:
Library name: H1C1b_A6-2_30minKCl
The raw data are being made available for controlled access on dbGaP.
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: Ova-FPM-3

description: Library name: Sample_12


title: NGS4967 LIB5465568 SNU-2292 G02925614 1 uM, DMSO 0.01%, 48 hrs, Replicate 3

description: Library name: NGS4967_R9034_LIB5465568_SAM24427402


title: patterned induced neurons, H1C1b_A6-2, Homo sapiens, 4N, 2hrKCl, piN_Rep1

description:
Library name: H1C1b_A6-2_2hrKCl
The raw data are being made available for controlled access on dbGaP.
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: Ova-3

description: Library name: Sample_9


title: patterned induced neurons, H1C1b_F10-1, Homo sapiens, 4N, 2hrKCl, piN_Rep1

description:
Library name: H1C1b_F10-1_2hrKCl
The raw data are being made available for controlled access on dbGaP.
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: NGS4967 LIB5465567 SNU-2292 G02925614 1 uM, DMSO 0.01%, 48 hrs, Replicate 2

description: Library name: NGS4967_R9034_LIB5465567_SAM24427401


title: Naïve, LNP, mRNA, mRNA+Ev., biol rep2, scRNA-seq

city: Cincinnati

first: Yrina

last: Rochman

state: OH

address: 3333 Burnet Avenue

department: Allergy and Immunology

institute: Cincinnati Children's Hospital Medical Center

description: BD Rhapsody™ Platform Naïve - sample tag: SampleTag09_mm, barcode suffix: 5 LNP - sample tag: SampleTag10_mm, barcode suffix: 6 mRNA - sample tag: SampleTag11_mm, barcode suffix: 7 mRNA+Ev. - sample tag: SampleTag12_mm, barcode suffix: 8

data_processing:
Raw single-cell sequencing data from four experimental conditions (Naïve, LNP, mRNA, mRNA+Ev.) were analyzed with v1.12.1 BD Rhapsody WTA Analysis Pipeline (https://scomix.bd.com/hc/en-us/articles/360047408451-BD-Rhapsody-Analysis-Pipeline-Updates) on Seven Bridges Platform (https://www.sevenbridges.com/platform). Sequencing reads in FASTQ files were aligned to GRCm38.p6 reference genome (https://www.gencodegenes.org/mouse/release_M19.html). Cell calling was performed with the disabled “Refined Putative Cell Calling” parameter. Instead, the “Exact Cell Count” input was set to 28,000 cells. Generated feature-barcode matrices from two batches (sample 1 and sample 2) were merged, preserving the experimental condition and the batch information of each cell within its barcode. Merged feature-barcode matrix was then uploaded to SciDAP (https://scidap.com) for all subsequent data analysis steps.
Low-quality cells were removed with Single-cell RNA-Seq Filtering Analysis pipeline (https://github.com/Barski-lab/workflows-datirium/blob/master/workflows/sc-rna-filter.cwl). The workflow was run with the following QC (quality control) thresholds: minimum 500 transcripts per cell, at least 500 but not more than 5,000 genes per cell, maximum 5 percent of transcripts mapped to mitochondrial genes. Doublets were identified and removed by scDblFinder R package (https://f1000research.com/articles/10-979/v2) as part of the above-mentioned pipeline.
The remaining high-quality cells were processed by Single-cell RNA-Seq Dimensionality Reduction Analysis pipeline (https://github.com/Barski-lab/workflows-datirium/blob/master/workflows/sc-rna-reduce.cwl). During the analysis molecular count data were first corrected for technical variability, then integrated by using the pairs of cells sharing a matched biological state as integration anchors. Heterogeneity associated with the cell cycle stage was completely removed. Other configuration parameters included: 1) setting normalization method to “sctglm” which resulted in using glmGamPoi R package within the SCTransform function (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02584-9); 2) limiting the number of the most variable genes for both normalization and integration procedures to 3,000; 3) selecting the first 40 PCs (principal components) for PCA (principal component analysis) and UMAP (Uniform Manifold Approximation and Projection) dimensionality reduction algorithms.
Then, dimensionally reduced single-cell data were clustered with Single-cell RNA-Seq Cluster Analysis pipeline (https://github.com/Barski-lab/workflows-datirium/blob/master/workflows/sc-rna-cluster.cwl). The workflow was run with 40 PCs and 0.5 clustering resolution. For each of the 24 obtained clusters the gene markers were identified by calling FindAllMarkers function (https://satijalab.org/seurat/reference/findallmarkers) with the default parameters. Cluster with damaged cells (low transcripts per cell counts and not specific gene markers) was removed, and both Single-cell RNA-Seq Dimensionality Reduction Analysis and Single-cell RNA-Seq Cluster Analysis pipelines were rerun with 20 PCs and increased to 1.0 clustering resolution. The resulted clusters resembled cell types which were used in the following steps of the analyses.
Assembly: GRCm38.p6
Supplementary files format and content: Gzip-compressed TAB-delimited file with the cell barcodes represented in the mtx file.
Supplementary files format and content: Gzip-compressed TAB-delimited file with the gene names represented in the mtx file.
Supplementary files format and content: Gzip-compressed sparse matrix file with the UMI counts per gene and cell barcode combination.
Supplementary files format and content: Analysis results saved in RDS (R Data Serialization) format. The origin of cells can be tracked through the "new.ident" metadata column as follows: Sample 1 Naïve - A control_1; Sample 1 LNP - B asthma_1; Sample 1 mRNA - C mrna_1; Sample 2 Naïve - E control_2; Sample 2 LNP - F asthma_2; Sample 2 mRNA - G mrna_2.
Supplementary files format and content: Analysis results saved in AnnData (H5AD) format. The origin of cells can be tracked through the "new.ident" metadata at the observation (obs) level as follows: Sample 1 Naïve - A control_1; Sample 1 LNP - B asthma_1; Sample 1 mRNA - C mrna_1; Sample 2 Naïve - E control_2; Sample 2 LNP - F asthma_2; Sample 2 mRNA - G mrna_2.
Supplementary files format and content: Gzip-compressed TAB-delimited file with the identified gene markers for each cell type.

growth_protocol: not relevant

extract_protocol:
One lobe of the lungs was minced and subjected to Liberase TL digestion (0.25 mg/mL) in the presence of DNaseI (0.5 mg/mL) at 37°C for 1 hour. Cells from 2 mice per group were pooled, treated with ACK lysing buffer for 1 minute, washed, passed through a 70-µm cell strainer, and counted using the TC20 Automated Cell Counter (BioRad). Subsequently, cells were processed on the Rhapsody platform following the manufacturer's protocol.
Cells from each treatment group were labeled with individual sample tags (BD® Mouse Single-Cell Multiplexing Kit (Cat. No. 633793)). Before loading into the cartridges, cells were quantified on the Rhapsody scanner following staining with Vybrant® DyeCycle™ Green (Invitrogen, V35004) for 5 minutes at room temperature. Barcoded samples were pooled in equal amounts for each of the four treatment groups (Naïve, LNP, mRNA, mRNA + Ev.), and sixty thousand cells were loaded into each cartridge, with two cartridges used for sequencing. Single cells were isolated with the BD Rhapsody Express Single-Cell Analysis System according to the manufacturer’s recommendations; after the final bead wash step, forty thousand cells were detected as singlets. Libraries were prepared following the BD Rhapsody System mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol (BD Biosciences; 633801) and sequenced at the CCHMC Genomics Sequencing Facility on NovaSeq 6000 using PE (paired end) 100 sequencing format. Following sequencing and preprocessing by the Rhapsody WTA analysis pipeline using exact cell count, 28,000 cells per cartridge were used for the downstream analysis.

treatment_protocol: Naïve- no treatment, LNP - 2 doses LNP i.m. on days 0 and 7, mRNA - 2 doses OVA-mRNA i.m. on days 0 and 7, mRNA+Ev. - 2 doses mRNA i.m. on days 0 and 7 with daily administration of everolimus i.p. for 14 days. LNP, mRNA, and mRNA+Ev. mice were sensitized with OVA+ALUM twice i.p. on days 24 and 36, and then challenged twice intratracheal (days 48 and 49) and twice intranasally (days 50 and 51) with OVA. Lungs were collected two days after last challenge (day 53).

value: all lung cells

value: wild type


title: Ova-2

description: Library name: Sample_8


title: NGS4967 LIB5465572 SNU-2292 DMSO 0.02%, 48 hrs, Replicate 1

description: Library name: NGS4967_R9034_LIB5465572_SAM24427406

value: Lung


title: neural progenitor cells, H2C2f, Homo sapiens, 4N, NPC_Rep2

description:
Library name: H2C2f_2_ATAC
The raw data are being made available for controlled access on dbGaP.
NPC_consensus_ATACseq_peaks.hg38.bed
NPC_background_mismapping.hg38.bw


title: Naïve, LNP, mRNA, mRNA+Ev., biol rep1, scRNA-seq

description: BD Rhapsody™ Platform Naïve - sample tag: SampleTag09_mm, barcode suffix: 1 LNP - sample tag: SampleTag10_mm, barcode suffix: 2 mRNA - sample tag: SampleTag11_mm, barcode suffix: 3 mRNA+Ev. - sample tag: SampleTag12_mm, barcode suffix: 4


title: neural progenitor cells, H2C2f, Homo sapiens, 4N, NPC_Rep1

description:
Library name: H2C2f_1_ATAC
The raw data are being made available for controlled access on dbGaP.
NPC_consensus_ATACseq_peaks.hg38.bed
NPC_background_mismapping.hg38.bw


title: DM-T, replicate 4, scRNAseq


title: Wildtype mouse lung, bleoomycin exposed, vehicle treated (n=3)

city: San Francisco

first: Vincent

last: Auyeung

department: Medicine

institute: University of California, San Francisco

description: 10x Genomics

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were made using the 10x Genomics Cloud Analysis with Cell Ranger software (https://www.10xgenomics.com/products/cloud-analysis)
genome build: mm10
Supplementary files format and content: filtered_feature_bc_matrix

growth_protocol: Mice were maintained under standard housing conditions

extract_protocol:
Lungs were dissociated by dispase inflation as described (doi.org/10.1038/protex.2015.017). Single cell suspensions were sorted for live, CD45-, CD31-, Epcam+ epithelial cells.
Sorted cells counted and loaded onto separate lanes of a Chromium Next GEM Chip (10x Genomics). Chromium Single Cell 3’ v3.1 (10x Genomics) reagents were used for library preparation according to the manufacturer’s protocol. The libraries were sequenced on an Illumina NovaSeq 6000 S4 flow cell.

treatment_protocol: Mice were anesthetized with isoflurane and exposed to a single dose of intranasal bleomycin (3 units/kg). Mice were treated with KIRA8 dissolved in a vehicle consisting of 3% ethanol, 7% Tween-80, and 90% normal saline injected intraperitoneally at 50 mg/kg/day starting on the day of bleomycin exposure. Mice were euthanized by perfusion under anesthesia and removal of the thoracic block on day 10 after bleomycin exposure.

value: Epithelium

tag: agent

value: Bleomycin

value: Vehicle

tag: number of_animals


title: Sham3

description: Library name: Sample1


title: NGS4967 LIB5465571 SNU-2292 G03498025 1 uM, G02925614 1 uM, 48 hrs, Replicate 3

description: Library name: NGS4967_R9034_LIB5465571_SAM24427405

value: Epithelial


title: Ova-1

description: Library name: Sample_7


title: Ova-FPM-2

description: Library name: Sample_11


title: NGS4967 LIB5465565 SNU-2292 G03498025 1 uM, DMSO 0.01%, 48 hrs, Replicate 3

description: Library name: NGS4967_R9034_LIB5465565_SAM24427399


title: neural progenitor cells, H2C2a, Homo sapiens, 4N, NPC_Rep2

description:
Library name: H2C2a_2_ATAC
The raw data are being made available for controlled access on dbGaP.
NPC_consensus_ATACseq_peaks.hg38.bed
NPC_background_mismapping.hg38.bw

value: neural progenitor cells

value: N


title: Wildtype mouse lung, bleomycin exposed, KIRA8 treated (n=3)

description: 10x Genomics


title: DM-T, replicate 1, scRNAseq

value: Pancreas


title: Naive-2

description: Library name: Sample_5


title: NGS4967 LIB5465563 SNU-2292 G03498025 1 uM, DMSO 0.01%, 48 hrs, Replicate 1

description: Library name: NGS4967_R9034_LIB5465563_SAM24427397


title: IRE1a epithelial kockout mouse lung, bleomycin exposed, vehicle treated (n=2)

description: 10x Genomics


title: neural progenitor cells, H2C2a, Homo sapiens, 4N, NPC_Rep1

description:
Library name: H2C2a_1_ATAC
The raw data are being made available for controlled access on dbGaP.
NPC_consensus_ATACseq_peaks.hg38.bed
NPC_background_mismapping.hg38.bw


title: neural progenitor cells, H1C1f, Homo sapiens, 4N, NPC_Rep2

description:
Library name: H1C1f-14_2_ATAC
The raw data are being made available for controlled access on dbGaP.
NPC_consensus_ATACseq_peaks.hg38.bed
NPC_background_mismapping.hg38.bw


title: MeCP2, non-target guide, input, rep2

city: Lausanne

first: Johannes

last: Gräff

address: Station 19

department: SV BMI

country: Switzerland

institute: EPFL

data_processing:
Reads were trimmed for NEBNext Ultra II DNA (TruSeq) adaptors
FastQ files were demultiplexed using bclconvert (v3.9.3, Illumina)
Reads were aligned to the mm10 genome using bowtie2 (v2.4.5) in paired end mode and using default parameters
csaw (v.1.30.1)  was used to call peaks
edgeR (v3.38.4) was used for differential enrichment analysis
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: N2A cells were obtained from ATCC, banked at EPFL and cultured in Dulbecco’s Modified Eagle Medium GlutaMAX™ (Gibco) supplemented with a 1% Penicillin-Streptomycin solution (Gibco) and 10% Fetal Bovine Serum (Gibco).

extract_protocol:
20 million cells were crosslinked using 1% formaldehyde for 10 minutes at RT, followed by lysis in 5 mM HEPES (pH 8), 85 mM KCl, 0.5% NP-40. After centrifugation, nuclei were washed in 5 mM HEPES (pH 8), 85 mM KCl and then sonicated to 100–400 bp using 15 cycles 30” on-off in 1ml of 50 mM Tris-HCl (pH 8), 10 mM EDTA, 1% SDS using a Covaris LE220 sonicator.
NEBNext Ultra II DNA Library Preparation Kit (NEB)

treatment_protocol: Cells were transfected with the appropriate plasmids using Lipofectamine 2000 (Invitrogen) according to manufacturer’s instructions for 48 h before being processed for downstream analyses.

value: neural crest-derived cell line

tag: chip antibody


title: NGS4967 LIB5465562 SNU-2292 DMSO 0.02%, 48 hrs, Replicate 3

description: Library name: NGS4967_R9034_LIB5465562_SAM24427396


title: RRBS_Spz_Uhrf2L1/L1_rep3

city: Illkirch

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

country: France

institute: CNRS

data_processing:
Reads were trimmed to remove low quality bases with Trim Galore v0.4.2 (parameters --rrbs --paired -r1 30 -r2 30 -q 20 --length 20 --stringency 5 --retain_unpaired) and aligned to the mm10 genome with BSMAP v2.74 (parameters -v 2 -w 100 -r 1 -x 400 -m 30 -D C-CGG -n 1).
Methylation scores were calculated using methratio.py in BSMAP v2.74 (parameters -z -u -g) and CpGs were filtered at a minimum of 8 X sequencing depth.
Assembly: mm10
Supplementary files format and content: We provide IGV files containing methylation scores for all CGs with at least 8X sequencing depth.

source_name: Spermatozoa

extract_protocol:
Genomic DNA samples were prepared by proteinase K digestion, phenol/chloroform/Isoamyl alcohol (25:24:1) extraction and precipitation with ethanol.
RRBS libraries were prepared as described in Bender et al. (2021), Methods Mol Biol 2214:207-220. Briefly, between 5 and 100 ng genomic DNA were digested with MspI (Thermo Fisher Scientific) for 5 h at 37°C, end-repaired and A-tailed with 5 U Klenow fragment exo- (Thermo Fisher Scientific) for 40 min at 37°C and ligated to methylated adapters overnight at 16°C with 30 U T4 DNA ligase (Thermo Fisher Scientific) in Tango 1X buffer. Fragments between 150 and 400 bp were excised from a 3% agarose 0.5X TBE gel, purified with the MinElute gel extraction kit (Qiagen) and bisulfite converted with the EpiTect bisulfite kit (Qiagen) with two consecutive rounds of conversion. Final libraries were amplified with PfU Turbo Cx hotstart DNA polymerase (Agilent) with 14-18 PCR cycles and purified with AMPure XP beads (Beckman Coulter).

value: Spermatozoa

value: Uhrf2 L1/L1

tag: developmental stage

value: Adult

tag: Sex

value: Male


title: neural progenitor cells, H1C1f, Homo sapiens, 4N, NPC_Rep1

description:
Library name: H1C1f-6_2_ATAC
The raw data are being made available for controlled access on dbGaP.
NPC_consensus_ATACseq_peaks.hg38.bed
NPC_background_mismapping.hg38.bw


title: Wildtype mouse lung, saline exposed, vehicle treated (n=2)

description: 10x Genomics

value: Saline

value: Wildtype


title: MeCP2, non-target guide, input, rep1


title: NGS4967 LIB5465566 SNU-2292 G02925614 1 uM, DMSO 0.01%, 48 hrs, Replicate 1

description: Library name: NGS4967_R9034_LIB5465566_SAM24427400


title: MeCP2, non-target guide, IP, rep2

value: Flag, Sigma F1804


title: NGS4967 LIB5465560 SNU-2292 DMSO 0.02%, 48 hrs, Replicate 1

description: Library name: NGS4967_R9034_LIB5465560_SAM24427394

value: 0.02% DMSO 48 hrs


title: NGS4967 LIB5465561 SNU-2292 DMSO 0.02%, 48 hrs, Replicate 2

description: Library name: NGS4967_R9034_LIB5465561_SAM24427395

value: Lung


title: RRBS_Spz_Uhrf2L1/L1_rep1


title: MeCP2, non-target guide, IP, rep1


title: neural progenitor cells, H1C1b, Homo sapiens, 4N, NPC_Rep2

description:
Library name: H1C1b_2_ATAC
The raw data are being made available for controlled access on dbGaP.
NPC_consensus_ATACseq_peaks.hg38.bed
NPC_background_mismapping.hg38.bw


title: RRBS_Spz_Uhrf2L1_WT_rep2

value: WT


title: neural progenitor cells, H1C1a, Homo sapiens, 4N, NPC_Rep2

description:
Library name: H1C1a_2_ATAC
The raw data are being made available for controlled access on dbGaP.
NPC_consensus_ATACseq_peaks.hg38.bed
NPC_background_mismapping.hg38.bw


title: NGS4967 LIB5465559 SNU-2292 G03498025 1 uM, G02925614 1 uM, 48 hrs, Replicate 3

description: Library name: NGS4967_R9034_LIB5465559_SAM24427393


title: MeCP2, Arc guide, input, rep1


title: NGS4967 LIB5465564 SNU-2292 G03498025 1 uM, DMSO 0.01%, 48 hrs, Replicate 2

description: Library name: NGS4967_R9034_LIB5465564_SAM24427398


title: RRBS_Spz_Uhrf2L1_WT_rep1


title: neural progenitor cells, H1C1a, Homo sapiens, 4N, NPC_Rep1

description:
Library name: H1C1a_1_ATAC
The raw data are being made available for controlled access on dbGaP.
NPC_consensus_ATACseq_peaks.hg38.bed
NPC_background_mismapping.hg38.bw


title: Naive-1

description: Library name: Sample_4

value: jugular-nodose complex

value: TRPV1+ vagal sensory neurons


title: NGS4967 LIB5465557 SNU-2292 G03498025 1 uM, G02925614 1 uM, 48 hrs, Replicate 1

description: Library name: NGS4967_R9034_LIB5465557_SAM24427391

value: Epithelial


title: RRBS_Spz_Uhrf2_KO_rep2


title: Patient 7 blood neutrophils_scRNA-seq

city: Philadelphia

first: Satish

last: Sati

state: Pennsylvania

address: 421 Curie Blvd, BRB 1039

department: Dermatology

institute: University of Pennsylvania

description:
Library name: SSNeut7
10x Genomics

data_processing:
The scRNA sequencing data was mapped to the GRCh38 reference genome to generate gene count and cell barcode matrices using the “cellranger count” function from cellranger pipeline (version 5.0.1, 10X Genomics).
Assembly: GRCh38
Supplementary files format and content: Raw files are fastq files and Zip files contain three files which correspond to tab separated value file and matrix file.

molecule: polyA RNA

source_name: Blood

extract_protocol:
The skin punch biopsies were incubated in 200 μl of Dispase solution (2mg/mL) for 30 minutes at  37 C. Following the incubation, the epidermis was peeled from dermis with curved forceps, washed in PBS and successively minced into < 1 mm3 pieces, using scalpel in a serum free RPMI 1640 media with DNase I (0.2 mg/mL), 20 mM HEPES and 0.25 mg/ml Liberase TM, Roche. The suspension was incubated for 90 minutes at 37 C. The digestion was stopped by adding 100 μl FBS and 3 μl of 0.5 M EDTA and filtered through a 70-mm cell strainer. The cells were pelleted and washed twice with PBS containing 1% BSA. Finally the cells were resuspended in PBS containing 0.04% BSA and an aliquot was taken for counting.
Library was performed according to the manufacturer's instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion. The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Blood

value: blood neutrophils


title: MeCP2, Arc guide, IP, rep2


title: RRBS_Spz_Uhrf2_KO_rep1


title: NGS4967 LIB5465555 SNU-2292 G02925614 1uM, DMSO 0.01%, 48 hrs, Replicate 2

description: Library name: NGS4967_R9034_LIB5465555_SAM24427389


title: RRBS_Spz_Uhrf2L1/L1_rep2


title: Patient 6 blood neutrophils_scRNA-seq

description:
Library name: SSNeut6
10x Genomics


title: RRBS_Spz_Uhrf2_WT_rep2


title: Patient 5 blood neutrophils_scRNA-seq

description:
Library name: SSNeut5
10x Genomics


title: MeCP2, Arc guide, IP, rep1


title: NGS4967 LIB5465554 SNU-2292 G02925614 1uM, DMSO 0.01%, 48 hrs, Replicate 1

description: Library name: NGS4967_R9034_LIB5465554_SAM24427388


title: RRBS_Spz_Uhrf2_WT_rep1


title: patterned induced neurons, NCRM5, Homo sapiens, 2N, minusKCl, piN_Rep1 (RNA-seq)

description:
Library name: NCRM5_minusKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt

value: patterned induced neurons

value: Y

value: minusKCl


title: patterned induced neurons, NCRM5, Homo sapiens, 2N, 6hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: NCRM5_6hrKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: MeCP2, Arc guide, input, rep2

value: neural crest-derived cell line


title: neural progenitor cells, H1C1b, Homo sapiens, 4N, NPC_Rep1

description:
Library name: H1C1b_1_ATAC
The raw data are being made available for controlled access on dbGaP.
NPC_consensus_ATACseq_peaks.hg38.bed
NPC_background_mismapping.hg38.bw

value: neural progenitor cells

value: N


title: Patient 3 blood neutrophils_scRNA-seq

description:
Library name: SSNeut3
10x Genomics


title: NGS4967 LIB5465553 SNU-2292 G03498025 1 uM, DMSO 0.01%, 48 hrs, Replicate 3

description: Library name: NGS4967_R9034_LIB5465553_SAM24427387


title: patterned induced neurons, NCRM5, Homo sapiens, 2N, 2hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: NCRM5_2hrKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: RRBS_Soma_GFPneg_E13.5f_Uhrf2_KO

source_name: Somatic cells from gonad

value: Somatic cells from gonad

value: Female


title: NGS4967 LIB5465558 SNU-2292 G03498025 1 uM, G02925614 1 uM, 48 hrs, Replicate 2

description: Library name: NGS4967_R9034_LIB5465558_SAM24427392


title: NGS4967 LIB5465552 SNU-2292 G03498025 1 uM, DMSO 0.01%, 48 hrs, Replicate 2

description: Library name: NGS4967_R9034_LIB5465552_SAM24427386


title: Patient 2 blood neutrophils_scRNA-seq

description:
Library name: SSNeut2
10x Genomics


title: RRBS_Soma_GFPneg_E13.5f_Uhrf2_WT


title: patterned induced neurons, H2_B7-2, Homo sapiens, 2N, minusKCl, piN_Rep1 (RNA-seq)

description:
Library name: H2_B7-2_minusKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, H2_B7-2, Homo sapiens, 2N, 6hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: H2_B7-2_6hrKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: Patient 6 unaffected skin_scRNA-seq

description:
Library name: SSC6
10x Genomics

source_name: Skin

value: Skin

tag: tissue type

value: unaffected skin


title: RRBS_PGCs_E13.5f_Uhrf2_KO_rep2

source_name: Primordial germ cells

value: Primordial germ cells


title: NGS4967 LIB5465556 SNU-2292 G02925614 1uM, DMSO 0.01%, 48 hrs, Replicate 3

description: Library name: NGS4967_R9034_LIB5465556_SAM24427390

value: Lung


title: Patient 1 blood neutrophils_scRNA-seq

description:
Library name: SSNeut1
10x Genomics


title: RRBS_PGCs_E13.5f_Uhrf2_WT_rep2

value: WT


title: patterned induced neurons, H2_B7-2, Homo sapiens, 2N, 2hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: H2_B7-2_2hrKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: Patient 5 unaffected skin_scRNA-seq

description:
Library name: SSC5
10x Genomics


title: NGS4967 LIB5465551 SNU-2292 G03498025 1 uM, DMSO 0.01%, 48 hrs, Replicate 1

description: Library name: NGS4967_R9034_LIB5465551_SAM24427385


title: Patient 4 unaffected skin_scRNA-seq

description:
Library name: SSC4
10x Genomics


title: patterned induced neurons, H1H1a_D6-3, Homo sapiens, 4N, 6hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: H1H1a_D6-3_6hrKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, H1H1a_D6-3, Homo sapiens, 4N, minusKCl, piN_Rep1 (RNA-seq)

description:
Library name: H1H1a_D6-3_minusKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, H2_B2-2, Homo sapiens, 2N, 6hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: H2_B2-2_6hrKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: NGS4967 LIB5465549 SNU-2292 DMSO 0.02%, 48 hrs, Replicate 2

description: Library name: NGS4967_R9034_LIB5465549_SAM24427383

value: 0.02% DMSO 48 hrs


title: NGS4967 LIB5465550 SNU-2292 DMSO 0.02%, 48 hrs, Replicate 3

description: Library name: NGS4967_R9034_LIB5465550_SAM24427384

value: Epithelial


title: RRBS_PGCs_E13.5m_Uhrf2_KO_rep2

value: Male


title: RRBS_PGCs_E13.5f_Uhrf2_WT_rep1


title: RRBS_PGCs_E13.5m_Uhrf2_WT_rep1


title: NGS4463 LIB5456712 NCI-H2228 1uM G03498025 + 1uM G02925614, 48 hrs, Replicate 2

description: Library name: NGS4463_R8235_LIB5456712_SAM24416682


title: Patient 1 unaffected skin_scRNA-seq

description:
Library name: SSC1
10x Genomics


title: RRBS_PGCs_E13.5m_Uhrf2_KO_rep1


title: Patient 3 unaffected skin_scRNA-seq

description:
Library name: SSC3
10x Genomics


title: NGS4463 LIB5456713 NCI-H2228 1uM G03498025 + 1uM G02925614, 48 hrs, Replicate 3

description: Library name: NGS4463_R8235_LIB5456713_SAM24416683


title: Patient 6 affected skin_scRNA-seq

description:
Library name: SSP6
10x Genomics

value: affected skin


title: patterned induced neurons, H1H1a_D6-3, Homo sapiens, 4N, 2hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: H1H1a_D6-3_2hrKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt

value: patterned induced neurons


title: NGS4463 LIB5456711 NCI-H2228 1uM G03498025 + 1uM G02925614, 48 hrs, Replicate 1

description: Library name: NGS4463_R8235_LIB5456711_SAM24416681


title: RRBS_Heart_Uhrf2_KO_rep3

source_name: Heart

value: Heart

value: Postnatal day 21


title: patterned induced neurons, H1H1a_D3-2, Homo sapiens, 4N, minusKCl, piN_Rep1 (RNA-seq)

description:
Library name: H1H1a_D3-2_minusKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt

value: minusKCl


title: Patient 5 affected skin_scRNA-seq

description:
Library name: SSP5
10x Genomics


title: patterned induced neurons, H1H1a_D3-2, Homo sapiens, 4N, 6hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: H1H1a_D3-2_6hrKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: Patient 4 affected skin_scRNA-seq

description:
Library name: SSP4
10x Genomics


title: patterned induced neurons, H1_G1, Homo sapiens, 2N, 6hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: H1_G1_6hrKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: NGS4967 LIB5465548 SNU-2292 DMSO 0.02%, 48 hrs, Replicate 1

description: Library name: NGS4967_R9034_LIB5465548_SAM24427382


title: NGS4463 LIB5456707 NCI-H2228 1uM G03498025 + 0.01% DMSO, 48 hrs, Replicate 3

description: Library name: NGS4463_R8235_LIB5456707_SAM24416677


title: Patient 2 affected skin_scRNA-seq

description:
Library name: SSP2
10x Genomics


title: NGS4463 LIB5456708 NCI-H2228 1uM G02925614 + 0.01% DMSO, 48 hrs, Replicate 1

description: Library name: NGS4463_R8235_LIB5456708_SAM24416678


title: Patient 3 affected skin_scRNA-seq

description:
Library name: SSP3
10x Genomics


title: RRBS_Heart_Uhrf2_WT_rep3


title: NGS4463 LIB5456709 NCI-H2228 1uM G02925614 + 0.01% DMSO, 48 hrs, Replicate 2

description: Library name: NGS4463_R8235_LIB5456709_SAM24416679


title: RRBS_Heart_Uhrf2_KO_rep1


title: patterned induced neurons, H1_G1, Homo sapiens, 2N, minusKCl, piN_Rep1 (RNA-seq)

description:
Library name: H1_G1_minusKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, H1_A9-1, Homo sapiens, 2N, minusKCl, piN_Rep1 (RNA-seq)

description:
Library name: H1_A9-1_minusKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: RRBS_Heart_Uhrf2_WT_rep2


title: Patient 1 affected skin_scRNA-seq

description:
Library name: SSP1
10x Genomics


title: NGS4463 LIB5456705 NCI-H2228 1uM G03498025 + 0.01% DMSO, 48 hrs, Replicate 1

description: Library name: NGS4463_R8235_LIB5456705_SAM24416675


title: NGS4463 LIB5456704 NCI-H2228 0.02% DMSO, 48 hrs, Replicate 3

description: Library name: NGS4463_R8235_LIB5456704_SAM24416674


title: RRBS_Liver_Uhrf2_KO_rep2

source_name: Liver

value: Liver


title: RRBS_Heart_Uhrf2_WT_rep1


title: RRBS_Liver_Uhrf2_KO_rep3


title: patterned induced neurons, H1_G1, Homo sapiens, 2N, 2hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: H1_G1_2hrKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt

value: N


title: LOTUS21_1yr

city: Huddinge

first: Dan

last: Sun

address: Alfred Nobels allé 8

department: MedH

country: Sweden

institute: Karolinska Institutet

description: LOTUS sample 4 (1yr)

data_processing:
FASTQ files were demultiplexed using deML v1.1.355. Following demultiplexing, reads from each of the eight samples were quality-filtered, aligned to the hg38 reference genome, and quantified based on GENCODE v35 gene annotations using the zUMIs pipeline v2.9.4f56. CellBender 0.1.057 was employed to remove empty droplets and background noise, and Solo 1.058 was used to eliminate doublets.
Individual cell identities were assigned by first summarizing read counts on reference or alternative alleles using cellsnp-lite 1.2.059, based on ~7.4 million common variants with allele frequency > 5% in the 1000 genomes project phase 3 release. Subsequently, based on the genotyping results, cells were assigned to eight genetic identities (--nDonor 8) using Vireo 0.4.230. A final 27,063 cells with more than 200 detected genes and less than 20% mitochondrial content and successful donor/recipient assignment were retained for further analysis.
Expression matrices from the eight samples were merged, log-normalized, and the normalized expression data of the top 2000 most variable features (selection.method = ‘vst’) were scaled in Seurat 4.1.061. PCA dimensionality reduction was subsequently performed on the scaled data (npcs = 20). Expression was from different samples were integrated by Harmony 0.162. UMAP and clustering were then performed on the integrated harmony reduction.
Assembly: hg38
Supplementary files format and content: *_soloed.h5ad: zUMI, CellBender and solo processed expression data per sample
Supplementary files format and content: metadata.csv: sample info, cell type, and inferred cell origin (donor/recipient) per cell
Supplementary files format and content: barcodes.tsv.gz: list of barcodes
Supplementary files format and content: features.tsv.gz: list of genes
Supplementary files format and content: matrix.mtx.gz: gene expression counts in Matrix Market Exchange format
Supplementary files format and content: umap.csv: umap coordinates

source_name: liver

extract_protocol:
Frozen liver cell suspensions were thawed, filtered through 40um mesh and sorted for alive (DCM acqua, Thermofisher) CD45+ cells (CD45-BV711, Biolegend). Maximum of 12500 cells/sample were loaded for scRNAseq.
Libraries of extracted cells were prepared with Chromium Next GEM Single Cell 3' kit (10x Genomics). Libraries were converted to circular ssDNA using the MGIEasy Universal Library Conversion Kit (MGI Tech) for sequencing on the DNBSEQ platform.

value: liver


title: LOTUS21_6h

description: LOTUS sample 4 (6h)


title: RRBS_Heart_Uhrf2_KO_rep2

value: Female


title: patterned induced neurons, H1_A9-1, Homo sapiens, 2N, 6hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: H1_A9-1_6hrKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: LOTUS16_1yr

description: LOTUS sample 3 (1yr)


title: RRBS_Liver_Uhrf2_KO_rep1


title: NGS4463 LIB5456703 NCI-H2228 0.02% DMSO, 48 hrs, Replicate 2

description: Library name: NGS4463_R8235_LIB5456703_SAM24416673


title: patterned induced neurons, H1H1a_D3-2, Homo sapiens, 4N, 2hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: H1H1a_D3-2_2hrKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, H1_A9-1, Homo sapiens, 2N, 2hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: H1_A9-1_2hrKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: RRBS_Liver_Uhrf2_WT_rep3


title: iALL9 KMT2A-N

city: Oxford

first: Alastair

last: Smith

state: England

address: The MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description: Library name: iALL9_KMT2A-N

data_processing:
FASTQ fils were quality checked using FastQC version v0.12.1. Adapter sequences were removed and low quality reads were trimmed using trim_galore version 0.6.10 using the following parameters: --2colour 20. Reads were aligned to the reference genome hg38 using bowtie2 version 2.5.1 with with default parameters. and blacklisted regions (https://github.com/Boyle-Lab/Blacklist) were removed using bedtools. BigWig files were generated using deepTools bamCoverage 3.5.5 with the following parameters: --extendReads -bs 1 --normalizeUsing RPKM  --minMappingQuality 10 --maxFragmentLength 2000 --minFragmentLength 1 --samFlagInclude 3 --samFlagExclude 4. Peak calling was performed using lanceotron v1.2.6 with the following parameters: -c 0.5
Assembly: hg38
Supplementary files format and content: Bigwigs and Peaks

source_name: KMT2A::AFF1 ALL patient

extract_protocol:
TOPMentation
Briefly, protein A-coupled magnetic beads (10 µl) were incubated with 1 µl of the appropriate antibody for 4 h with rotation at 4 °C in PBS with 0.5% BSA and 1× protease inhibitor cocktail. The antibodies used are detailed in Supplementary Table 1. Cells were single-fixed (1% formaldehyde for 10 min) for histone modifications or double-fixed (2 mM disuccinimidyl glutarate for 30 min, then 1% formaldehyde for 30 min) for transcription/chromatin factors. Fixed samples were lysed in 120 µl of lysis buffer (50 mM Tris-HCl pH 8.0, 0.5% SDS, and 10 mM EDTA, 1× protease inhibitor cocktail) and sonicated using a Covaris ME220 (Woburn, MA) to generate 200–300 bp fragments. The sonicated chromatin was then incubated with Triton-X100 at a final concentration of 1% for 10 min at room temperature to neutralize the SDS in the lysis buffer. The chromatin was pre-cleared for 30 min at 4 °C with rotation using 5 µl protein A-coupled beads to reduce non-specific binding. The antibody-incubated beads were washed in 150 µl Binding Wash Buffer (PBS with 0.5% FCS), and the pre-cleared chromatin was then added to the antibody-coated beads before incubation overnight at 4 °C with rotation. Immunoprecipitated chromatin was washed three times with RIPA buffer (50 mM HEPES-KOH pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, and 0.7% Na deoxycholate). Beads were transferred to a second tube between the first and second wash to remove non-immunoprecipitated fragments that adhered to the tube. The beads were then washed once with Tris-EDTA and once with 10 mM Tris-HCl pH 8.0. The chromatin was then tagmented by resuspending beads in 29 µl Tagmentation Buffer (10 mM Tris-HCl pH 8.0, 5 mM MgCl2, 10% dimethylformamide) and adding 1 µl of transposase (Illumina). Samples were incubated at either 37 °C or 50oC for 5 min 5 mins (dependent on the activity of the transposase lot), and the reaction was terminated by adding 150 µl RIPA buffer. Beads were washed with 10 mM Tris-HCl pH 8.0 to remove any detergent and resuspended in 22.5 µl ddH2O. In order to amplify the tagmented chromatin, 25 µl NEBNext Ultra II Q5 Master Mix (NEB) and indexed amplification primers (125 nM final concentration) were added, and libraries were prepared using the following thermal profile: 72 °C 5 min, 95 °C 5 min, (98 °C 10 s, 63 °C 30 s, 72 °C 3 min) × 12 cycles, 72 °C 5 min. Library clean-up was performed using Agencourt AMPure XP beads at a 1:1 ratio. Samples were sequenced by paired-end sequencing on a NextSeq 500 or on a NovaSeq6000 S4 flow cell.

tag: disease state

value: acute lymphoblastic leukemia (ALL)

value: KMT2A::AFF1 ALL patient


title: NGS4463 LIB5456702 NCI-H2228 0.02% DMSO, 48 hrs, Replicate 1

description: Library name: NGS4463_R8235_LIB5456702_SAM24416672


title: LOTUS14_1yr

description: LOTUS sample 2 (1yr)


title: NGS4463 LIB5456710 NCI-H2228 1uM G02925614 + 0.01% DMSO, 48 hrs, Replicate 3

description: Library name: NGS4463_R8235_LIB5456710_SAM24416680


title: NGS4463 LIB5456701 NCI-H2228 1uM G03498025 + 1uM G02925614, 48 hrs, Replicate 3

description: Library name: NGS4463_R8235_LIB5456701_SAM24416671


title: iALL9 H3K27ac

description: Library name: iALL9_H3K27ac


title: RRBS_Liver_Uhrf2_WT_rep2


title: NGS4463 LIB5456706 NCI-H2228 1uM G03498025 + 0.01% DMSO, 48 hrs, Replicate 2

description: Library name: NGS4463_R8235_LIB5456706_SAM24416676


title: RRBS_Liver_Uhrf2_WT_rep1


title: iALL5 SSRP1

description: Library name: iALL5_SSRP1


title: NGS4463 LIB5456700 NCI-H2228 1uM G03498025 + 1uM G02925614, 48 hrs, Replicate 2

description: Library name: NGS4463_R8235_LIB5456700_SAM24416670


title: LOTUS8_6h

description: LOTUS sample 1 (6h)


title: iALL5 RAD21

description: Library name: iALL5_RAD21


title: NGS4463 LIB5456698 NCI-H2228 1uM G02925614 + 0.01% DMSO, 48 hrs, Replicate 3

description: Library name: NGS4463_R8235_LIB5456698_SAM24416668


title: LOTUS14_6h

description: LOTUS sample 2 (6h)


title: NGS4463 LIB5456699 NCI-H2228 1uM G03498025 + 1uM G02925614, 48 hrs, Replicate 1

description: Library name: NGS4463_R8235_LIB5456699_SAM24416669


title: LOTUS8_1yr

description: LOTUS sample 1 (1yr)


title: iALL5 H3K27me3

description: Library name: iALL5_H3K27me3


title: RRBS_Brain_Uhrf2_KO_rep2

source_name: Brain

value: Brain


title: NGS4463 LIB5456697 NCI-H2228 1uM G02925614 + 0.01% DMSO, 48 hrs, Replicate 2

description: Library name: NGS4463_R8235_LIB5456697_SAM24416667

value: Lung


title: RRBS_Brain_Uhrf2_WT_rep2

value: WT


title: iALL5 AFF1-C

description: Library name: iALL5_AFF1-C


title: EX00014762_30umol/L_24h-Insulin_10nmol/L_24h_6

city: Warthausen

first: Rakesh

last: Santhanam

address: Goetheweg 10

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & Co. KG

description: Library name: LIB2024_066_090_001

data_processing:
Sequencing reads were processed with a pipeline built upon the implementation of the ENCODE’ “Long RNA-seq” pipeline: Filtered reads were mapped against the Homo sapiens (humans) genome hg38/GRCh38 (primary assembly, excluding alternate contigs) using the STAR aligner software (STAR version 2.5.2b) allowing for soft clipping of adapter sequences. For quantification of transcript levels, the annotation files from Ensembl version 86 were used, which corresponds to GENCODE 25
Assembly: hg38/GRCh38
Supplementary files format and content: tab delimited text file include raw counts for each sample

source_name: Adipose

growth_protocol: hMADS cells were cultured in DMEM low glucose (1 g/L) with L- GlutaMAX (Gibco, 11885084) supplemented with 10% fetal bovine serum (FBS) (Gibco, 11500064), 1% Pen/Strep (Gibco, 15070063), 15 mM HEPES (Gibco, 15630056) and 2.5 ng/ml bFGF-2 (Peprotech, 100-18B-50UG). Tissue culture-treated surfaces were used for seeding the hMADS cells. The cells were induced to differentiate at day 2 post confluence (designated as day 0) in Omental Adipocyte Differentiation Medium (Zenbio, OM-DM°500mL)

extract_protocol:
RNA was extracted utilizing RNeasy kit (Qiagen, 74104) following the manufacturer’s protocol. RNA concentration was measured was quantitatively  assessed using the fluorescence Broad Range Quant-iT RNA Assay Kit (Thermo Fisher Scientific) and the Standard Sensitivity RNA Analysis DNF-471 Kit on a 96-channel Fragment Analyzer (Agilent), respectively. Total RNA input of 250 ng was employed for library preparation with the NEBNext. UltraExpress RNA Library Prep Kit for Illumina
RNA- seq libraries were eluted in 30 µL EB Buffer (Qiagen) and were quantified by the High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) on a Synergy HTX (BioTek). Libraries were assessed for size distribution and adapter dimer presence (<0.5%) by the High Sensitivity Small Fragment DNF-477 Kit on a 96-channel Fragment Analyzer (Agilent). Libraries were normalized on the MicroLab STAR (Hamilton)

treatment_protocol: The 9-day old differentiated hMADS cells were starved overnight with starvation medium consisting of DMEM without glucose supplementation with 0.5% BSA (37 °C, 5% CO2). On the following day, for western blot assays, cells were incubated with compounds for 15 min (37 °C, 5% CO2). Insulin was added into corresponding samples and incubated for another 15 min (37 °C, 5% CO2). When the incubation time was finished, cells were washed with PBS and lysed as previously described. For mRNA expression determination, cells were pre- incubated with compounds for 30 min. Insulin was added to the corresponding samples and incubated for another 24 h (37 °C, 5% CO2). When the incubation was finished, the cells were washed with PBS and lysed with RLT buffer supplemented with 1% 2-mercaptoethanol for mRNA isolation and RT-qPCR.

value: Adipose

value: Human multipotent adipose-derived stem cells (hMADS)

value: adipocyte stem cell


title: LOTUS16_6h

description: LOTUS sample 3 (6h)


title: RRBS_Brain_Uhrf2_KO_rep1

value: Male


title: NGS4463 LIB5456696 NCI-H2228 1uM G02925614 + 0.01% DMSO, 48 hrs, Replicate 1

description: Library name: NGS4463_R8235_LIB5456696_SAM24416666

value: Epithelial


title: EX00014762_30umol/L_24h-Insulin_10nmol/L_24h_5

description: Library name: LIB2024_066_089_001


title: iALL5 CTCF

description: Library name: iALL5_CTCF

value: CTCF


title: RRBS_Brain_Uhrf2_WT_rep1

value: Postnatal day 21


title: EX00014762_30umol/L_24h-Insulin_10nmol/L_24h_4

description: Library name: LIB2024_066_088_001


title: EX00014762_30umol/L_24h-Insulin_10nmol/L_24h_3

description: Library name: LIB2024_066_087_001


title: KO5

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

institute: INSERM

data_processing:
Quality of RNA-seq data was assessed using FastQC.
Trimming was performed using Atropos.
Reads were aligned to the transcriptome using STAR
Assembly: mm10
Supplementary files format and content: Table count matrix (raw counts), comma-separated file.

source_name: monocytes

extract_protocol:
Cells were lyzed and mRNA extracted using Qiagen RNEasy Mini kit including on-column DNAse digestion.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA Library Prep Kit (Illumina). 500 ng of RNA was used for each sample. Sequencing was performed in 1 sequencing unit of NovaSeq 6000 (Illumina) (100-nt-length reads, paired end).

value: monocytes


title: iALL5 H2A119ub

description: Library name: iALL5_H2A119ub


title: NGS4463 LIB5456695 NCI-H2228 1uM G03498025 + 0.01% DMSO, 48 hrs, Replicate 3

description: Library name: NGS4463_R8235_LIB5456695_SAM24416665


title: iALL5 H3K27ac-1

description: Library name: iALL5_H3K27ac-1


title: EX00014762_30umol/L_24h-Insulin_10nmol/L_24h_2

description: Library name: LIB2024_066_086_001


title: KO4


title: KO3


title: iALL5 H3K27ac-2

description: Library name: iALL5_H3K27ac-2


title: BI02997598_30umol/L_24h-Insulin_10nmol/L_24h_6

description: Library name: LIB2024_066_084_001


title: EX00014762_30umol/L_24h-Insulin_10nmol/L_24h_1

description: Library name: LIB2024_066_085_001


title: KO2


title: BI02997598_30umol/L_24h-Insulin_10nmol/L_24h_5

description: Library name: LIB2024_066_083_001


title: NGS4463 LIB5456694 NCI-H2228 1uM G03498025 + 0.01% DMSO, 48 hrs, Replicate 2

description: Library name: NGS4463_R8235_LIB5456694_SAM24416664


title: WT4


title: NGS4463 LIB5456691 NCI-H2228 0.02% DMSO, 48 hrs, Replicate 2

description: Library name: NGS4463_R8235_LIB5456691_SAM24416661


title: iALL5 H3K4me1

description: Library name: iALL5_H3K4me1


title: NGS4463 LIB5456688 NCI-H2228 1uM G03498025 + 1uM G02925614, 48 hrs, Replicate 2

description: Library name: NGS4463_R8235_LIB5456688_SAM24416658


title: WT3


title: NGS4463 LIB5456689 NCI-H2228 1uM G03498025 + 1uM G02925614, 48 hrs, Replicate 3

description: Library name: NGS4463_R8235_LIB5456689_SAM24416659


title: iALL5 MENIN

description: Library name: iALL5_MENIN

value: MENIN


title: BI02997598_30umol/L_24h-Insulin_10nmol/L_24h_4

description: Library name: LIB2024_066_082_001


title: NGS4463 LIB5456690 NCI-H2228 0.02% DMSO, 48 hrs, Replicate 1

description: Library name: NGS4463_R8235_LIB5456690_SAM24416660


title: iALL5 KMT2A-N

description: Library name: iALL5_KMT2A-N


title: NGS4463 LIB5456692 NCI-H2228 0.02% DMSO, 48 hrs, Replicate 3

description: Library name: NGS4463_R8235_LIB5456692_SAM24416662


title: BI02997598_30umol/L_24h-Insulin_10nmol/L_24h_3

description: Library name: LIB2024_066_081_001


title: BI02997598_30umol/L_24h-Insulin_10nmol/L_24h_2

description: Library name: LIB2024_066_080_001


title: NGS4463 LIB5456687 NCI-H2228 1uM G03498025 + 1uM G02925614, 48 hrs, Replicate 1

description: Library name: NGS4463_R8235_LIB5456687_SAM24416657


title: WT1


title: iALL5 H3K27ac-3

description: Library name: iALL5_H3K27ac-3


title: iALL5 PAF1

description: Library name: iALL5_PAF1


title: WT2


title: iALL5 PolII-1

description: Library name: iALL5_PolII-1


title: KO1


title: BI02997598_30umol/L_24h-Insulin_10nmol/L_24h_1

description: Library name: LIB2024_066_079_001


title: hTM 3420, DEX

city: Hung Hom

first: Samantha SW

last: Shan

address: 1 Yuk Choi Road

department: School of Optometry

country: Hong Kong

institute: The Hong Kong Polytechnic University

data_processing:
Raw data were analysed by BGI programs and filtered to remove adaptor sequences, contamination, and low-quality reads.
Clean data obtained were mapped to the reference genome using BSMAP software, followed by removal of duplication reads and merging of mapped results of each library.
Assembly: hg38
Supplementary files format and content: text file containing mean methylation levels of control and treatment group

source_name: HTMC

growth_protocol: The hTM cells were plated and incubated at 37°C with lDMEM, low glucose, containing 10% fetal bovine serum (FBS) until confluent and subsequently maintained in low glucose DMEM medium containing 1% FBS for at least a week prior to treatment.

extract_protocol:
Genomic DNA was extracted from hTM cells using a DNeasy Blood and Tissue kit (Qiagen) following the manufacturer's manual, quantified by UV spectroscopy, and then submitted to BGI (China) for WGBS analysis.
According to BGI, the DNA library was first constructed by fragmenting DNA into a mean size of approximately 250 bp by sonication with a Bioruptor (Diagenode), followed by blunt ends formation, which involved 3'-end dA addition, and methylated adaptor ligation, which prevented bisulfite conversion. The ligation products were bisulfite converted with EZ DNA Methylation-Gold kit (Zymo Research) and the different-sized fragments were separated on a 2% TAE agarose gel. Fragments were excised from the agarose gels and purified using a QIAquick Gel Extraction kit (Qiagen), followed by PCR amplification and cyclization.

treatment_protocol: Confluent monolayers of hTM cells were treated with 300 nM DEX or PBS for 7 days.

value: HTMC

value: Primary hTM cells

tag: subject source_id

value: male

value: DEX-treated

value: 300 nM DEX, 7 days


title: NGS4463 LIB5456693 NCI-H2228 1uM G03498025 + 0.01% DMSO, 48 hrs, Replicate 1

city: Mississauga

first: James

institute: Roche Canada

description: Library name: NGS4463_R8235_LIB5456693_SAM24416663

data_processing:
RNA-seq reads were first aligned to ribosomal RNA sequences to remove ribosomal reads. The remaining reads were aligned to the human reference genome (GRCh38) using GSNAP version 2013-10-10, allowing a maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 — pairmax-rna = 200000—clip-overlap) (PMID: 27008021). Transcript annotation was based on the Ensembl genes database (release 77). To quantify gene expression levels, the number of reads mapped to the exons of each RefSeq gene was calculated. Differential gene expression was performed with DESeq2. A pre-filter was applied so that only genes with at least a median RPKM value of 10 in one were analyzed. P-values for other genes were simply set to 1 and log fold changes were set to 0 for visualization purposes, but such genes were not included in the multiple testing correction. Q-values were obtained by correcting P-values for multiple hypotheses using the Benjamini-Hochberg procedure. Genes were considered if they had a Q-value of less than 0.05 and were protein-coding. Counts were transformed to log2 counts per million, quantile-normalized, and precision-weighted with the “voom” function of the limma package.
Assembly: GRCh38
Supplementary files format and content: gzipped tab-separated value file

source_name: Lung

extract_protocol:
For treatment, cells were seeded at 1-2 × 10^5 cells/well on tissue culture treated 6-well plates, and were treated after 12-24 h with experimental compounds. Cell lines were lysed on-plate for RNA isolation using the Qiagen RNeasy Plus Mini Kit (catalog number 74034), and RNA concentration was determined using a NanoDrop 8000 (Thermo Fisher Scientific). For analysis by RNA Fluidigm, 100 ng RNA was subjected to a complementary DNA (cDNA) synthesis reaction using the Applied Biosystems High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific, Cat. No. 4368814), as per the manufacturer’s protocol. A preamplification reaction was then performed with Taqman PreAmp Master Mix (Thermo Fisher Scientific). After amplification, samples were diluted 1:4 with Tris-EDTA, and qPCR was conducted on Fluidigm 96.
RNA integrity was confirmed using a Bioanalyzer 2100 (Agilent Technologies). About 500 ng of RNA was used for library synthesis using the TrueSeq RNA Sample Preparation kit v2 (Illumina). Size of the libraries was confirmed using 2200 TapeStation and High Sensitivity D1K screen tape (Agilent Technologies), and the concentration was determined by a qPCR-based method using the Library Quantification Kit (KAPA). The libraries were multiplexed and then sequenced on Illumina HiSeq2500 (Illumina) to generate 30M single-end 50-base pair reads.

tag: tissue


title: PPP_10umol/L_24h-Insulin_10nmol/L_24h_6

description: Library name: LIB2024_066_078_001

tag: cell line


title: NGS4463 LIB5456685 NCI-H2228 1uM G02925614 + 0.01% DMSO, 48 hrs, Replicate 2

description: Library name: NGS4463_R8235_LIB5456685_SAM24416655

tag: cell type


title: hTM 3420, control

value: vehicle-control

tag: treatment

value: PBS, 7 days


title: iALL5 H3K4me3

description: Library name: iALL5_H3K4me3

value: acute lymphoblastic leukemia (ALL)

value: KMT2A::AFF1 ALL patient


title: PPP_10umol/L_24h-Insulin_10nmol/L_24h_5

description: Library name: LIB2024_066_077_001

value: Adipose

value: Human multipotent adipose-derived stem cells (hMADS)


title: iALL5 H3K79me3

description: Library name: iALL5_H3K79me3


title: hTM 2290, control


title: PPP_10umol/L_24h-Insulin_10nmol/L_24h_4

description: Library name: LIB2024_066_076_001

value: adipocyte stem cell


title: NGS4463 LIB5456683 NCI-H2228 1uM G03498025 + 0.01% DMSO, 48 hrs, Replicate 3

description: Library name: NGS4463_R8235_LIB5456683_SAM24416653

value: Lung

value: Epithelial

tag: batch


title: NGS4463 LIB5456684 NCI-H2228 1uM G02925614 + 0.01% DMSO, 48 hrs, Replicate 1

description: Library name: NGS4463_R8235_LIB5456684_SAM24416654


title: iALL4 KMT2A-N

description: Library name: iALL4_KMT2A-N


title: PPP_10umol/L_24h-Insulin_10nmol/L_24h_3

description: Library name: LIB2024_066_075_001


title: NGS4463 LIB5456682 NCI-H2228 1uM G03498025 + 0.01% DMSO, 48 hrs, Replicate 2

description: Library name: NGS4463_R8235_LIB5456682_SAM24416652


title: hTM 210, DEX

value: female


title: iALL4 H3K27ac

description: Library name: iALL4_H3K27ac


title: NGS4463 LIB5456681 NCI-H2228 1uM G03498025 + 0.01% DMSO, 48 hrs, Replicate 1

description: Library name: NGS4463_R8235_LIB5456681_SAM24416651


title: NGS4463 LIB5456686 NCI-H2228 1uM G02925614 + 0.01% DMSO, 48 hrs, Replicate 3

description: Library name: NGS4463_R8235_LIB5456686_SAM24416656


title: NGS4463 LIB5456680 NCI-H2228 0.02% DMSO, 48 hrs, Replicate 3

description: Library name: NGS4463_R8235_LIB5456680_SAM24416650


title: PPP_10umol/L_24h-Insulin_10nmol/L_24h_2

description: Library name: LIB2024_066_074_001


title: iALL3 SSRP1

description: Library name: iALL3_SSRP1


title: PPP_10umol/L_24h-Insulin_10nmol/L_24h_1

description: Library name: LIB2024_066_073_001


title: hTM 210, control


title: EX00013861_10nmol/L_24h-Insulin_10nmol/L_24h_6

description: Library name: LIB2024_066_072_001


title: iALL5 PolII-2

description: Library name: iALL5_PolII-2


title: NGS4463 LIB5456679 NCI-H2228 0.02% DMSO, 48 hrs, Replicate 2

description: Library name: NGS4463_R8235_LIB5456679_SAM24416649


title: patterned induced neurons, H2C2a_G6-2, Homo sapiens, 4N, 6hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: H2C2a_G6-2_6hrKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt

value: patterned induced neurons

value: N

tag: ploidy

tag: kcl treatment


title: EX00013861_10nmol/L_24h-Insulin_10nmol/L_24h_5

description: Library name: LIB2024_066_071_001


title: NGS4463 LIB5456678 NCI-H2228 0.02% DMSO, 48 hrs, Replicate 1

description: Library name: NGS4463_R8235_LIB5456678_SAM24416648


title: patterned induced neurons, H2C2a_G1-1, Homo sapiens, 4N, 6hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: H2C2a_G1-1_6hrKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: iALL3 CTCF

description: Library name: iALL3_CTCF

value: CTCF


title: patterned induced neurons, H1C1b_F10-1, Homo sapiens, 4N, minusKCl, piN_Rep1 (RNA-seq)

description:
Library name: H1C1b_F10-1_minusKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt

value: minusKCl


title: iALL3 H2A119ub

description: Library name: iALL3_H2A119ub


title: NGS4406 LIB5455029 NCI-H2030 X1.1 1 uM G03498025 + 1 uM G03427947, 48 hrs, Replicate 3

description: Library name: NGS4406_R8074_LIB5455029_SAM24414254


title: EX00013861_10nmol/L_24h-Insulin_10nmol/L_24h_3

description: Library name: LIB2024_066_069_001


title: patterned induced neurons, H1C1b_F10-1, Homo sapiens, 4N, 6hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: H1C1b_F10-1_6hrKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: NGS4406 LIB5455028 NCI-H2030 X1.1 1 uM G03498025 + 1 uM G03427947, 48 hrs, Replicate 2

description: Library name: NGS4406_R8074_LIB5455028_SAM24414253


title: patterned induced neurons, H1C1b_F10-1, Homo sapiens, 4N, 2hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: H1C1b_F10-1_2hrKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: NGS4406 LIB5455027 NCI-H2030 X1.1 1 uM G03498025 + 1 uM G03427947, 48 hrs, Replicate 1

description: Library name: NGS4406_R8074_LIB5455027_SAM24414252


title: iALL4 AFF1-C

description: Library name: iALL4_AFF1-C


title: patterned induced neurons, H2C2a_G6-2, Homo sapiens, 4N, minusKCl, piN_Rep1 (RNA-seq)

description:
Library name: H2C2a_G6-2_minusKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: EX00013861_10nmol/L_24h-Insulin_10nmol/L_24h_2

description: Library name: LIB2024_066_068_001


title: patterned induced neurons, H1C1b_E4-1, Homo sapiens, 4N, minusKCl, piN_Rep1 (RNA-seq)

description:
Library name: H1C1b_E4-1_minusKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: iALL3 H3K27ac-2

description: Library name: iALL3_H3K27ac-2


title: NGS4406 LIB5455023 NCI-H2030 X1.1 1 uM G03427947 + 0.01% DMSO, 48 hrs, Replicate 3

description: Library name: NGS4406_R8074_LIB5455023_SAM24414248


title: EX00013861_10nmol/L_24h-Insulin_10nmol/L_24h_1

description: Library name: LIB2024_066_067_001


title: iALL3 H3K27me3

description: Library name: iALL3_H3K27me3


title: DMSO_0.1%_24h-Insulin_10nmol/L_24h_6

description: Library name: LIB2024_066_066_001


title: NGS4406 LIB5455022 NCI-H2030 X1.1 1 uM G03427947 + 0.01% DMSO, 48 hrs, Replicate 2

description: Library name: NGS4406_R8074_LIB5455022_SAM24414247


title: iALL3 H3K79me3

description: Library name: iALL3_H3K79me3


title: patterned induced neurons, H1C1b_E4-1, Homo sapiens, 4N, 6hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: H1C1b_E4-1_6hrKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: DMSO_0.1%_24h-Insulin_10nmol/L_24h_5

description: Library name: LIB2024_066_065_001


title: patterned induced neurons, H1C1b_A6-2, Homo sapiens, 4N, minusKCl, piN_Rep1 (RNA-seq)

description:
Library name: H1C1b_A6-2_minusKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: NGS4406 LIB5455021 NCI-H2030 X1.1 1 uM G03427947 + 0.01% DMSO, 48 hrs, Replicate 1

description: Library name: NGS4406_R8074_LIB5455021_SAM24414246


title: NGS4406 LIB5455020 NCI-H2030 X1.1 1 uM G03498025 + 0.01% DMSO, 48 hrs, Replicate 3

description: Library name: NGS4406_R8074_LIB5455020_SAM24414245


title: iALL3 H3K4me3

description: Library name: iALL3_H3K4me3


title: DMSO_0.1%_24h-Insulin_10nmol/L_24h_4

description: Library name: LIB2024_066_064_001


title: iALL3 H3K27ac-1

description: Library name: iALL3_H3K27ac-1


title: patterned induced neurons, H1C1b_A6-2, Homo sapiens, 4N, 6hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: H1C1b_A6-2_6hrKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: DMSO_0.1%_24h-Insulin_10nmol/L_24h_3

description: Library name: LIB2024_066_063_001


title: iALL3 H3K4me1

description: Library name: iALL3_H3K4me1


title: patterned induced neurons, H1C1b_A6-2, Homo sapiens, 4N, 2hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: H1C1b_A6-2_2hrKCl_1
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt
piN_allotetraploid_gene_counts_by_allele.txt


title: NGS4406 LIB5455019 NCI-H2030 X1.1 1 uM G03498025 + 0.01% DMSO, 48 hrs, Replicate 2

description: Library name: NGS4406_R8074_LIB5455019_SAM24414244


title: DMSO_0.1%_24h-Insulin_10nmol/L_24h_2

description: Library name: LIB2024_066_062_001


title: NGS4406 LIB5455018 NCI-H2030 X1.1 1 uM G03498025 + 0.01% DMSO, 48 hrs, Replicate 1

description: Library name: NGS4406_R8074_LIB5455018_SAM24414243


title: hTM 2290, DEX

value: HTMC

value: Primary hTM cells

tag: age

value: male

tag: genotype


title: iALL3 H3K27ac-3

description: Library name: iALL3_H3K27ac-3


title: DMSO_0.1%_24h-Insulin_10nmol/L_24h_1

description: Library name: LIB2024_066_061_001


title: iALL3 MENIN

description: Library name: iALL3_MENIN

value: MENIN


title: dCas9_plus_Arc_sgRNA

description: Library name: dCas9_plus_Arc_sgRNA

library_source: genomic single cell

data_processing:
Raw files were aligned and features were counted using default parameters for Cellranger-atac count (Zheng et al. 2017). Signac (Stuart et al. 2021) and Seurat (Hao et al. 2021) with default parameters for downstream processing.
Assembly: mm10 with annotations for EGFP and Cas9
Supplementary files format and content: meta data text file, h5 files for counts matrices and fragment data

source_name: hippocampus, DG

extract_protocol:
8 minutes after the last behavioural testing, DGs from experimental mice were micro-dissected and snap-frozen.
For each condition, the DG from 3 mice were pooled, then processed for nuclei isolation  (Batiuk et al., 2022) and FACS sorting. Library were prepared using the Chromium Next   GEM sc-ATAC sequencing.

value: hippocampus, DG

value: Cas9, EGFP

value: sgRNA Arc


title: iALL3 KMT2A-N

description: Library name: iALL3_KMT2A-N

value: acute lymphoblastic leukemia (ALL)

value: KMT2A::AFF1 ALL patient


title: dCas9_plus_NT_sgRNA

description: Library name: dCas9_plus_NT_sgRNA

value: sgRNA lacZ (non-target)


title: sublibrary_8

description: Library name: sublibrary_8

data_processing:
Sublibraries were aligned with Parse Biosciences "TrailmakerTM (v1.4.1) to a modified version of the mouse genome (mm10) that includes EGFP and Cas9m4 sequences. Sublibraries were then merged using the split-pipe --mode comb command.
Assembly: mm10 with annotations for EGFP and Cas9
Supplementary files format and content: Sample loading table in xlsx format (directly from Parse Bioscience for a;ignments)
Supplementary files format and content: all_genes.csv, cell_metadata.csv, and count_matrix.mtx for all samples - needed for downstream Seurat analysis

molecule: nuclear RNA

extract_protocol:
8 minutes after the last behavioural testing, DGs from experimental mice were micro-dissected and snap-frozen.
Following nuclei isolation (Batiuk et al., 2022) and FACS sorting, nuclei were fixed using the Evercode low- input fixation kit from Parse  and library prepared using the Evercode WT V3 kit from Parse.


title: iALL3 PAF1

description: Library name: iALL3_PAF1


title: iALL3 PolII-1

description: Library name: iALL3_PolII-1


title: NGS4406 LIB5455017 NCI-H2030 X1.1 0.02% DMSO, 48 hrs, Replicate 3

description: Library name: NGS4406_R8074_LIB5455017_SAM24414242

value: Lung


title: EX00014762_30umol/L_24h_5

description: Library name: LIB2024_066_059_001

value: Adipose

value: Human multipotent adipose-derived stem cells (hMADS)

value: adipocyte stem cell


title: NGS4406 LIB5455016 NCI-H2030 X1.1 0.02% DMSO, 48 hrs, Replicate 2

description: Library name: NGS4406_R8074_LIB5455016_SAM24414241

value: Epithelial


title: EX00014762_30umol/L_24h_6

description: Library name: LIB2024_066_060_001


title: NGS4406 LIB5455015 NCI-H2030 X1.1 0.02% DMSO, 48 hrs, Replicate 1

description: Library name: NGS4406_R8074_LIB5455015_SAM24414240


title: sublibrary_7

description: Library name: sublibrary_7


title: iALL3 PolII-2

description: Library name: iALL3_PolII-2


title: iALL3 RAD21

description: Library name: iALL3_RAD21


title: EX00014762_30umol/L_24h_4

description: Library name: LIB2024_066_058_001


title: sublibrary_6

description: Library name: sublibrary_6


title: EX00014762_30umol/L_24h_3

description: Library name: LIB2024_066_057_001


title: NGS4406 LIB5455010 NCI-H2122 1 uM G03498025 + 1 uM G03427947, 48 hrs, Replicate 2

description: Library name: NGS4406_R8074_LIB5455010_SAM24414235

value: Epithelial, Rounded


title: iALL3 AFF1-C

description: Library name: iALL3_AFF1-C


title: NGS4406 LIB5455009 NCI-H2122 1 uM G03498025 + 1 uM G03427947, 48 hrs, Replicate 1

description: Library name: NGS4406_R8074_LIB5455009_SAM24414234


title: EX00014762_30umol/L_24h_2

description: Library name: LIB2024_066_056_001


title: sublibrary_4

description: Library name: sublibrary_4


title: sublibrary_3

description: Library name: sublibrary_3


title: iALL2 KMT2A-N

description: Library name: iALL2_KMT2A-N


title: NGS4406 LIB5455005 NCI-H2122 1 uM G03427947 + 0.01% DMSO, 48 hrs, Replicate 3

description: Library name: NGS4406_R8074_LIB5455005_SAM24414230


title: EX00014762_30umol/L_24h_1

description: Library name: LIB2024_066_055_001


title: NGS4406 LIB5455004 NCI-H2122 1 uM G03427947 + 0.01% DMSO, 48 hrs, Replicate 2

description: Library name: NGS4406_R8074_LIB5455004_SAM24414229


title: BI02997598_30umol/L_24h_6

description: Library name: LIB2024_066_054_001


title: sublibrary_2

description: Library name: sublibrary_2


title: iALL2 H3K4me1

description: Library name: iALL2_H3K4me1


title: NGS4406 LIB5455003 NCI-H2122 1 uM G03427947 + 0.01% DMSO, 48 hrs, Replicate 1

description: Library name: NGS4406_R8074_LIB5455003_SAM24414228


title: BI02997598_30umol/L_24h_5

description: Library name: LIB2024_066_053_001


title: NGS4406 LIB5455002 NCI-H2122 1 uM G03498025 + 0.01% DMSO, 48 hrs, Replicate 3

description: Library name: NGS4406_R8074_LIB5455002_SAM24414227


title: BI02997598_30umol/L_24h_4

description: Library name: LIB2024_066_052_001


title: iALL2 H3K79me2

description: Library name: iALL2_H3K79me2


title: sublibrary_1

description: Library name: sublibrary_1


title: E18_rat_cortex, scRNAseq

first: Alex

last: Pollen

institute: University of California San Francisco

description: Library name: E18_rat_cortex

data_processing:
Genes were quantified using CellRanger v7.0.1, ambient RNA was removed using Cellbender v0.2.1, inhibitory neurons were isolated used conserved markers (DLX1/2/5/6, GAD1/2)
Assembly: GRCr8 (rat), mOrycun1.1 (rabbit), mMonDom1.pri (opossum), SugarGlider_lib1_testN_pseudohap (Sugar glider), ASM1176430v1.1 (ferret), SusScrofa11.1 (pig)
Supplementary files format and content: barcodes.csv contains cell metadata
Supplementary files format and content: genes.csv contains gene metadata
Supplementary files format and content: matrix.mtx contains raw cells by genes CellRanger and Cellbender matrix

organism: Rattus norvegicus

source_name: cortex

extract_protocol:
Regions of interest were dissected and tissue was dissociated in papain. Whole cells from pig, ferret, opossum, rat, and rabbit were resuspended in PBS supplemented with 0.04% BSA for Chromium 10X processing, mouse cells were resuspended in PBS supplemented with 0.1% BSA and sorted for Nkx2.1-cre;Ai14 expression using BD FACSAria Fusion for Chromium 10X processing.
Library was constructed according to manufacturer's protocol

value: cortex

value: WT, E18

value: developing brain


title: NGS4406 LIB5455011 NCI-H2122 1 uM G03498025 + 1 uM G03427947, 48 hrs, Replicate 3

last: Hawley

description: Library name: NGS4406_R8074_LIB5455011_SAM24414236


title: BI02997598_30umol/L_24h_3

description: Library name: LIB2024_066_051_001


title: sublibrary_5

description: Library name: sublibrary_5


title: P20_opossum_striatum, scRNAseq

description: Library name: P20_opossum_striatum

organism: Monodelphis domestica

source_name: striatum

value: striatum

value: WT, P20


title: iALL2 RUNX1

description: Library name: iALL2_RUNX1


title: E18_rat_striatum, scRNAseq

description: Library name: E18_rat_striatum

source_name: striatum, LGE, MGE

value: striatum, LGE, MGE


title: EX00013861_10nmol/L_24h-Insulin_10nmol/L_24h_4

description: Library name: LIB2024_066_070_001


title: BI02997598_30umol/L_24h_2

description: Library name: LIB2024_066_050_001


title: NGS4406 LIB5454998 NCI-H2122 0.02% DMSO, 48 hrs, Replicate 2

description: Library name: NGS4406_R8074_LIB5454998_SAM24414223


title: E23_rabbit_cortex, scRNAseq

description: Library name: E23_rabbit_cortex

organism: Oryctolagus cuniculus

value: WT, E23


title: chALL7 H3K4me3

description: Library name: chALL7_H3K4me3


title: PPP_10umol/L_24h_5

description: Library name: LIB2024_066_047_001


title: BI02997598_30umol/L_24h_1

description: Library name: LIB2024_066_049_001


title: chALL7 H3K79me3

description: Library name: chALL7_H3K79me3


title: iALL2 H3K27me3

description: Library name: iALL2_H3K27me3


title: PPP_10umol/L_24h_6

description: Library name: LIB2024_066_048_001


title: iALL2 H3K4me3

description: Library name: iALL2_H3K4me3


title: NGS4406 LIB5454997 NCI-H2122 0.02% DMSO, 48 hrs, Replicate 1

description: Library name: NGS4406_R8074_LIB5454997_SAM24414222


title: iALL2 H3K27ac

description: Library name: iALL2_H3K27ac


title: P20_opossum_cortex, scRNAseq

description: Library name: P20_opossum_cortex


title: PPP_10umol/L_24h_2

description: Library name: LIB2024_066_044_001


title: chALL7 H3K4me1

description: Library name: chALL7_H3K4me1


title: NGS4406 LIB5455001 NCI-H2122 1 uM G03498025 + 0.01% DMSO, 48 hrs, Replicate 2

description: Library name: NGS4406_R8074_LIB5455001_SAM24414226


title: NGS4406 LIB5454999 NCI-H2122 0.02% DMSO, 48 hrs, Replicate 3

description: Library name: NGS4406_R8074_LIB5454999_SAM24414224


title: chALL4 AFF1-C

description: Library name: chALL4_AFF1-C


title: PPP_10umol/L_24h_4

description: Library name: LIB2024_066_046_001