title: neural progenitor cells, H3, Homo sapiens, IgG, NPC_Rep2

description:
Library name: NPC_H3_IgG_R2
The raw data are being made available for controlled access in dbGaP.

data_processing:
Adapters were trimmed with cutadapt v2.5 (Martin, 2011) and sequencing quality was determined with fastqc v0.11.5 (Andrews et al., 2010). Reads 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).. Peak calling with macs2 was performed with matched IgG samples as the background set and the following parameters: --nomodel --shift -100 --extsize 200. Peak calling was also performed for all mapped reads for each TF of interest using macs2 to get the set of consensus peaks.
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: peak bed files
Library strategy: CUT&Tag

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 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 and piNs at D28 were scraped off of tissue culture plates into NE1 lysis buffer (20mM HEPES pH 7.9, 10mM KCl, 0.1% Triton X-100, 3mM MgCl2, 0.5mM Spermidine, 1 tablet Complete Protease Inhibitor EDTA-free per 50ml) and nutated at 4°C for 10min to isolate nuclei. Nuclei were pelleted at 4°C at 200rpm for 10min and then resuspended in 1ml WB150 (20mM HEPES pH 7.5, 150mM NaCl, 0.2% Tween-20, 1g/L BSA, 0.5mM spermidine, 10mM sodium butyrate, 1 tablet Complete Protease Inhibitor EDTA-free per 50ml) for counting. For each library, 500,000 nuclei were aliquoted into a total volume of 1ml WB150. 20µl Concanavalin A bead (Bangs Laboratories, cat # BP531) slurry was prepared per library by washing beads twice in binding buffer (20µM HEPES-KOH pH7.9, 10µM KCl, 1µM CaCl2, 1µM MnCl2) and resuspending in 10µl binding buffer. Beads were added to the nuclei suspension and incubated for 10min at room temperature. Using a magnet, the supernatant was removed, and beads were resuspended in 50µl antibody buffer (WB150 supplemented with 0.1% Triton X-100 and 2mM EDTA) with 1µl primary antibody (rabbit anti-FOSL2: Cell Signaling Technology, cat #19967; rabbit anti-MAZ: Abcam, cat #ab85725; rabbit IgG: Cell Signaling Technology, cat #2729S; rabbit anti-H3K27Ac: abcam, cat #ab4729; rabbit anti-FOS: Cedarlane, cat# 226003) for overnight incubation at 4°C.
The next day, the primary antibody solution was removed and beads were resuspended in 100µl of antibody buffer with 1.2µl of secondary antibody (goat anti-rabbit: Fisher Scientific, cat #NBP172763; goat anti-mouse: Abcam, cat #ab46540). Beads were incubated at room temperature for 1h and then washed 3X with 1ml WB150. Beads were resuspended in 100µl WB300 (20mM HEPES pH 7.5, 300mM NaCl, 0.2% Tween-20, 1g/L BSA, 0.5mM spermidine, 10mM sodium butyrate, 1 tablet Complete Protease Inhibitor EDTA-free per 50mL) containing 2.5µl proteinAG-Tn5 (Epicypher Inc, cat #15-1017) and incubated at room temperature for 1h. Then, beads were washed 3X with 1ml WB300 and incubated in tagmentation buffer (WB300 supplemented with 10mM MgCl2) at 50°C for 1h at 500rpm. DNA was extracted with Phenol/Chloroform, ethanol precipitated with 0.02mg/ml GlycoBlue (Life Technologies, cat #AM9515), and resuspended in 22µl H2O.
For library preparation, 20µl of DNA was PCR amplified with 5X KAPA Hifi Buffer (Roche, cat #KK2101), 0.3mM dNTP (Roche, cat #KK2101), 1µl KAPA HiFi Polymerase (Roche, cat #KK2101), and primers with Illumina adapters in a 50µl reaction at 72°C for 5min, 98°C for 30s, 14 cycles of 98°C for 10s, 63°C for 30s, 72°C for 1min, and 72°C for 5min. DNA was purified using double-sided size selection (0.5X, then 1.2X) with Ampure XP beads (Thermo Fisher, cat #NC0110018). Briefly, 25µl of SPRI beads were added to the PCR reaction, incubated at room temperature for 8 min, and allowed to adhere to the magnet for 8 min. The supernatant was moved to a new tube and 65µl of SPRI beads were added. After 8 min incubation at room temperature, beads were allowed to adhere to the magnet for 8 min, the supernatant was discarded, and beads were washed twice with 200µl 80% EtOH for 30s each. Beads were resuspended in 53µl 10mM Tris-HCl, pH 7.5 and placed on the magnet, and the supernatant was moved to a new tube. The supernatant was then further cleaned by adding 55µl beads, incubated at room temperature for 8 min, washed twice with 200µl 80% EtOH for 30s each, and then eluted in 20µl 10mM Tris-HCl, pH 7.5. Libraries were quantified with the KAPA Library Quantification Kit (Roche, cat #07960140001).

tag: target

value: IgG


title: neural progenitor cells, H3, Homo sapiens, IgG, NPC_Rep3

status: Public on Aug 12 2025

type: SRA

city: Boston

first: Janet

last: Song

state: Massachusetts

address: 3 Blackfan St

country: USA

institute: Boston Children's Hospital

description:
Library name: NPC_H3_IgG_R3
The raw data are being made available for controlled access in dbGaP.

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

value: neural progenitor cells

tag: batch


title: no priming 3

city: seoul

first: hyunju

last: seo

address: CMI, 71 Daehak-ro, Jongno-gu, Seoul, Republic of Korea

country: South Korea

institute: seoul national niversity

description:
Library name: N6
column name im raw_counts_All_Samples.txt: N6

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to GRCh38(NCBI) whole genome using Tophat
FPKM calculation using Cufflink
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

source_name: PBSC

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

value: PBSC

tag: genotype

value: WT

tag: treatment

tag: time


title: neural progenitor cells, H2, Homo sapiens, IgG, NPC_Rep3

description:
Library name: NPC_H2_IgG_R3
The raw data are being made available for controlled access in dbGaP.


title: CRTF_E1_H2C_GN2 (RNA-seq)

description:
Library name: CRTF_E1_H2C_GN2
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.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: Y

tag: ploidy

tag: grna

tag: grna target

value: NTC


title: 083983_GPCR-Library-R1_S3_R1_filtered

city: Lafayette

first: Austin

last: Tedman

state: IN

address: 716 Brown St Apt 4

department: Chemistry

institute: Purdue University

description: Library name: GPCR Library R1

data_processing:
Used STAR Alignment v 2.7.11b
Sequence reads were filtered for low quality and trimmed based on adaptor sequences
Trimmed sequences were mapped to GRCH39.p14 using STAR Alignment benchwork
Assembly: GRCH39.p14
Supplementary files format and content: csv files with RPKM values for each sample

source_name: HEK 293T

growth_protocol: HEK 293T cells were maintained in DMEM supplemented with 10% Fetabl Bovine Serum and 90 units/mL of Penicillin-Streptomycin incubated at 37 C with 5% CO2

extract_protocol:
Total RNA was extracted using Aurum Total RNA Mini Kit (Centrifugation Protocol) with about 3.2 ug of RNA used for sequncing libraries
Library Construction RNA polyA+

value: HEK 293T

value: Embryonic Kidney Cells

value: GPCR


title: U87-D3, biol rep 2

city: Santa Monica

first: Santosh

last: Kesari

state: California

address: 2200 Santa Monica Blvd

department: Translational Neuro-oncology

institute: Saint John Cancer Institute

description:
Library name: U87_R5
Treated with IFN-γ 1µL/mL for Day 3
TPM_U87.csv

data_processing:
Quality control was performed using FastQC, and adapter trimming was conducted with Trim Galore.
Reads were aligned to the GRCh38 human genome using STAR aligner.
Gene counts were generated using featureCounts.
Differential expression analysis was conducted using edgeR. Genes with FDR < 0.05 were considered significant.
Pathway and Gene Ontology enrichment analyses were performed using PANTHER.
Assembly: GRCh38 (Ensembl release 108)
Supplementary files format and content: TPM_*.csv

growth_protocol: U87-MG and U251-MG glioblastoma cell lines were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin at 37°C with 5% CO₂.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. RNA integrity was verified using an Agilent Bioanalyzer 2100 (RIN > 8).
RNA libraries were prepared using the TruSeq RNA Library Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 to generate 150 bp paired-end reads.

treatment_protocol: Cells were treated with 1 μg/mL human IFN-γ (Life Technologies) for up to 28 days. Treatment was either continued or withdrawn after Day 14.

value: Human Glioblastoma Cells

value: IFN-γ 1µL/mL

value: Day 3


title: no priming 2

description:
Library name: N1
column name im raw_counts_All_Samples.txt: N1


title: CRTF_E1_NCRM5_MT1 (RNA-seq)

description:
Library name: CRTF_E1_NCRM5_MT1
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt

value: MAZ


title: FVA3-Ang1 24hour priming_sample 3

description:
Library name: 6_24
column name im raw_counts_All_Samples.txt: 6_24


title: neural progenitor cells, H1, Homo sapiens, IgG, NPC_Rep2

description:
Library name: NPC_H1_IgG_R2
The raw data are being made available for controlled access in dbGaP.


title: neural progenitor cells, H2, Homo sapiens, IgG, NPC_Rep2

description:
Library name: NPC_H2_IgG_R2
The raw data are being made available for controlled access in dbGaP.


title: no priming 1

description:
Library name: N0
column name im raw_counts_All_Samples.txt: N0


title: FVA3-Ang1 1hour priming_sample 3

description:
Library name: 6_1
column name im raw_counts_All_Samples.txt: 6_1


title: neural progenitor cells, H3, Homo sapiens, MAZ, NPC_Rep3

description:
Library name: NPC_H3_MAZ_R3
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.MAZ.hg38.bed


title: neural progenitor cells, H2, Homo sapiens, MAZ, NPC_Rep3

description:
Library name: NPC_H2_MAZ_R3
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.MAZ.hg38.bed


title: neural progenitor cells, H1, Homo sapiens, MAZ, NPC_Rep3

description:
Library name: NPC_H1_MAZ_R3
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.MAZ.hg38.bed


title: FVA3-Ang1 24hour priming_sample 1

description:
Library name: 0_24
column name im raw_counts_All_Samples.txt: 0_24


title: FVA3-Ang1 1hour priming_sample 2

description:
Library name: 1_1
column name im raw_counts_All_Samples.txt: 1_1


title: FVA3-Ang1 24hour priming_sample 2

description:
Library name: 1_24
column name im raw_counts_All_Samples.txt: 1_24


title: FVA3-Ang1 1hour priming_sample 1

description:
Library name: 0_1
column name im raw_counts_All_Samples.txt: 0_1


title: neural progenitor cells, H2, Homo sapiens, MAZ, NPC_Rep2

description:
Library name: NPC_H2_MAZ_R2
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.MAZ.hg38.bed


title: neural progenitor cells, H1, Homo sapiens, MAZ, NPC_Rep2

description:
Library name: NPC_H1_MAZ_R2
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.MAZ.hg38.bed


title: neural progenitor cells, H3, Homo sapiens, FOSL2, NPC_Rep3

description:
Library name: NPC_H3_FOSL2_R3
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOSL2.hg38.bed


title: SC shNC-2, replicate 1, RNA-seq

city: Tianjin

first: xueying

last: Li

address: 94 Weijin Road, Nankai District

country: China

institute: Nankai University

description: Library name: Sample34

data_processing:
For MeRIP-seq, raw sequencing reads underwent quality control using FastQC v0.11.9. Trim Galore v0.6.10 was utilized for adaptor and low-quality base trimming, employing the parameters "--paired --length 20 -q 20 --stringency 3". The resulting reads were mapped to the human genome (hg38) using HISAT2 v2.2.1. m6A peaks were identified using exomePeak v2.16.0. Enriched motifs within the m6A peaks were analyzed using HOMER v4.11. Each peak was annotated using HOMER v4.11. Differentially methylated genes were defined as genes possessing at least one differential m6A peak with a false discovery rate (FDR) < 0.05. For ChIP-seq, quality control on raw sequencing reads was performed by FastQC v0.11.9. Adaptor sequences and low-quality bases were trimmed using Trim Galore v0.6.10 with the following parameters: "-q 20 --phred33 --stringency 3 --length 20 -e 0.1 --paired". The reads were aligned to the hg38 human genome using Bowtie v2.5.1. SAM files were converted to BAM format, sorted, and indexed using samtools v1.16.1. Duplicate reads were marked and removed using MarkDuplicates from the picard v2.27.5 software. Peak calling was performed using MACS2 v2.2.7.1 with the parameters "-f BAM -g hs -B -q 0.05". Differential peak analysis was conducted using DiffBind v3.10.1. For RNA-seq, raw sequencing reads were subjected to quality control analysis using FastQC v0.11.9. Trim Galore v0.6.10 was employed to remove adaptor sequences and low-quality bases, utilizing the following parameters: "-q 20 --phred33 --stringency 3 --length 20 -e 0.1". The sequencing reads were then aligned to the human genome (hg38) using HISAT2 v2.2.1. Gene expression quantification was performed on the transcriptome using the featureCounts function of Rsubread v2.0.3. Differentially expressed genes (DEGs) were identified using the edgeR package v3.42.4 in R. Genes with a log2 (fold change) > 0.75 or log2 (fold change) < -0.75 and a false discovery rate (FDR) < 0.01 were considered as DEGs.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Schwann cell

extract_protocol:
The experiments were performed following the method described in a previous study (Liu, Y., Shi, M., He, X., Cao, Y., Liu, P., Li, F., Zou, S., Wen, C., Zhan, Q., Xu, Z. et al. (2022). LncRNA-PACERR induces pro-tumour macrophages via interacting with miR-671-3p and m6A-reader IGF2BP2 in pancreatic ductal adenocarcinoma. J Hematol Oncol 15, 52. 10.1186/s13045-022-01272-w.).
For MeRIP-seq, Total RNA (30 μg) was purified using DynabeadsTM Oligo(dT)25 (Thermo Fisher, USA) in two rounds to isolate poly(A) RNA. Subsequently, the purified poly(A) RNA was fragmented using the Magnesium RNA Fragmentation Module (NEB, USA, catalog number E6150S) at 86°C for 7 minutes. The fragmented RNA was then incubated with an m6A-specific antibody (Synaptic Systems, Germany, catalog number 202003) in IP buffer (50 mM Tris-HCl, 750 mM NaCl, and 0.5% Igepal CA-630) at 4°C for 2 hours. Next, the IP RNA was reverse transcribed into cDNA using SuperScript™ II Reverse Transcriptase (Invitrogen, USA, catalog number 1896649). PCR amplification was performed with the following conditions: initial denaturation at 95°C for 3 minutes, followed by 8 cycles of denaturation at 98°C for 15 seconds, annealing at 60°C for 15 seconds, extension at 72°C for 30 seconds, and a final extension at 72°C for 5 minutes. The average insert size of the final cDNA library was 300 ± 50 bp. The cDNA library was subjected to paired-end sequencing (PE150) using the Illumina HiSeq X Ten platform (LC-Bio Technology Co., Ltd., Hangzhou, China). For ChIP-seq, the ChIP-seq library was prepared using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme Biotech Co., Ltd, ND607) according to the manufacturer's instructions. The generated DNA library was sequenced using the Illumina HiSeq X Ten sequencing system in paired-end mode. For RNA-seq, Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's instructions. The RNA content and purity of each sample were measured using the NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, DE, USA). The integrity of the RNA was evaluated using the Bioanalyzer 2100 (Agilent, CA, USA) to ensure the RNA Integrity Number (RIN) value greater than 7.0, and further validated by denaturing agarose gel electrophoresis. Two rounds of purification were performed using Dynabeads Oligo(dT)25-61005 (Thermo Fisher, CA, USA) to purify poly(A) RNA from 1 μg of total RNA. Subsequently, the poly(A) RNA was fragmented using the Magnesium RNA Fragmentation Module (NEB, USA, catalog number e6150) at 94°C for 5-7 minutes. The fragmented RNA was then reverse transcribed into cDNA using SuperScript™ II Reverse Transcriptase (Invitrogen, USA, catalog number 1896649). The fragmented RNA was used as a template for cDNA synthesis, which was subsequently converted into U-labeled second-strand DNA using E. coli DNA polymerase I (NEB, USA, catalog number m0209), RNase H (NEB, USA, catalog number m0297), and dUTP Solution (Thermo Fisher, USA, catalog number R0133). A base A was added to the end of each strand to prepare for ligation to the index adapters. Each adapter contained a T-overhang, which allowed the adapter to be ligated to the A-tailed fragment DNA. Single or dual index adapters were ligated to the fragments, followed by size selection using AMPureXP beads. After treatment with thermosensitive UDG enzyme (NEB, USA, catalog number m0280) to remove the U-labeled second-strand DNA, PCR amplification was performed. The amplification conditions included an initial denaturation step at 95°C for 3 minutes, followed by 8 cycles of denaturation at 98°C for 15 seconds, annealing at 60°C for 15 seconds, extension at 72°C for 30 seconds, and a final extension at 72°C for 5 minutes. The average insert size of the final cDNA library was 300 ± 50 bp. Finally, according to the supplier's recommended protocol, paired-end sequencing (PE150) was performed on an Illumina Novaseq™ 6000 platform.

value: Schwann cell

tag: sample group

value: SC shNC


title: SC shCTCF-1, replicate 1, RNA-seq

description: Library name: Sample35

value: SC shCTCF


title: SC shCTCF-2, replicate 1, RNA-seq

description: Library name: Sample36


title: neural progenitor cells, H2, Homo sapiens, FOSL2, NPC_Rep3

description:
Library name: NPC_H2_FOSL2_R3
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOSL2.hg38.bed


title: neural progenitor cells, H1, Homo sapiens, FOSL2, NPC_Rep3

description:
Library name: NPC_H1_FOSL2_R3
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOSL2.hg38.bed


title: SC shNC-1, replicate 1, RNA-seq

description: Library name: Sample33


title: neural progenitor cells, H1, Homo sapiens, IgG, NPC_Rep3

description:
Library name: NPC_H1_IgG_R3
The raw data are being made available for controlled access in dbGaP.


title: neural progenitor cells, H2, Homo sapiens, FOSL2, NPC_Rep2

description:
Library name: NPC_H2_FOSL2_R2
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOSL2.hg38.bed


title: neural progenitor cells, H1, Homo sapiens, FOSL2, NPC_Rep2

description:
Library name: NPC_H1_FOSL2_R2
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOSL2.hg38.bed


title: sgNC-1, replicate 1, RNA-seq

description: Library name: Sample23

value: sgNC


title: sgNC-2, replicate 2, RNA-seq

description: Library name: Sample24


title: sgM16-1, replicate 1, RNA-seq

description: Library name: Sample21


title: sgM16-2, replicate 2, RNA-seq

description: Library name: Sample22


title: NDPC SC-2, replicate 2, RNA-seq

description: Library name: Sample18

value: NDPC SC


title: patterned induced neurons, C3-C, Pan troglodytes, 2N, 2hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: C3-C_2hrKCl_2
piN_human-chimp_gene_counts.txt

organism: Pan troglodytes

value: patterned induced neurons

tag: kcl treatment


title: patterned induced neurons, C3-C, Pan troglodytes, 2N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: C3-C_6hrKCl_2
piN_human-chimp_gene_counts.txt


title: DPC SC-2, replicate 2, RNA-seq

description: Library name: Sample20

value: DPC SC


title: DPC SC-1, replicate 1, RNA-seq

description: Library name: Sample19


title: NDPC SC-1, replicate 1, RNA-seq

description: Library name: Sample17


title: patterned induced neurons, C2-C, Pan troglodytes, 2N, minusKCl, piN_Rep2 (RNA-seq)

description:
Library name: C2-C_minusKCl_2
piN_human-chimp_gene_counts.txt

value: minusKCl


title: patterned induced neurons, C2-C, Pan troglodytes, 2N, 2hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: C2-C_2hrKCl_2
piN_human-chimp_gene_counts.txt

value: Y


title: snATAC-seq in iALL5 and iALL4 KMT2A::AFF1 blasts

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: iALL5_and_iALL4
10x Genomics

library_source: genomic single cell

data_processing:
Single Cell multiome data was aligned using Cell Ranger ARC (v2.0). Using the RNA modality, samples were deconvoluted using souporcell (v2.5) and sample identity was assigned by determination of biological sex using the ratio of XIST expression compared to counts for all genes on chrY.
Assembly: hg38
Supplementary files format and content: fragment files

source_name: Bone Marrow

extract_protocol:
Cryopreserved bone marrow cells were thawed, and 16,000 live CD19+ blasts of KMT2A-AFF1+ ALL patient samples were FACS-sorted and nuclei were extracted using the recommended protocol (Chromium). Male/female sample pairs were loaded together on one Chromium 10x lane for processing with the Single Cell Multiome ATAC + Gene Expression protocol. Sequencing was performed on a NovaSeq 6000, with gene expression libraries sequenced on a PE150 S4 flow cell and ATAC-seq libraries on an SP PE50 flow cell.
10x scMultiome

tag: tissue

value: Bone Marrow

value: Blast


title: neural progenitor cells, H3, Homo sapiens, FOSL2, NPC_Rep2

description:
Library name: NPC_H3_FOSL2_R2
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.FOSL2.hg38.bed

value: neural progenitor cells


title: patterned induced neurons, C2_A6-2, Pan troglodytes, 2N, minusKCl, piN_Rep2 (RNA-seq)

description:
Library name: C2_A6-2_minusKCl_2
piN_human-chimp_gene_counts.txt

value: N


title: patterned induced neurons, C2_A6-2, Pan troglodytes, 2N, 2hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: C2_A6-2_2hrKCl_2
piN_human-chimp_gene_counts.txt


title: snATAC-seq in chALL1 and iALL3 KMT2A::AFF1 blasts

description:
Library name: chALL1_and_iALL3
10x Genomics


title: ipf04fep

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

description: Library name: ipf04fep

library_source: transcriptomic single cell

data_processing:
Cellranger 7.0 was used for demultiplex and alignment.
Assembly: GRCh38-2020-A provided by 10X Genomics
Supplementary files format and content: .h5 files

molecule: polyA RNA

source_name: Lung

extract_protocol:
explant tissue was enzymatic digested and further sorted for CD31- CD45- CD326+ epithelial cells, then further sorted for HTII-280+ or HTII-280- populations.  Each population was independently labeled with TotalSeq anti-human Hashtag antibodies, then pooled at a 1:1 ratio for scRNA-seq.
library construction followed 10x Genomics Chromium Single Cell 3' Reagent Kit User Guide

value: Lung

value: IPF fibrotic


title: ipf04nep

description: Library name: ipf04nep

value: IPF non-fibrotic


title: patterned induced neurons, C1C1a_B7-1, Pan troglodytes, 4N, minusKCl, piN_Rep2 (RNA-seq)

description:
Library name: C1C1a_B7-1_minusKCl_2
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, NCRM5, Homo sapiens, 2N, minusKCl, piN_Rep2 (RNA-seq)

description:
Library name: NCRM5_minusKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, C1C1a_B7-1, Pan troglodytes, 4N, 2hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: C1C1a_B7-1_2hrKCl_2
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, C3-C, Pan troglodytes, 2N, minusKCl, piN_Rep2 (RNA-seq)

description:
Library name: C3-C_minusKCl_2
piN_human-chimp_gene_counts.txt


title: cc05dep

description: Library name: cc05dep

value: Donor


title: neural progenitor cells, H3, Homo sapiens, MAZ, NPC_Rep2

description:
Library name: NPC_H3_MAZ_R2
The raw data are being made available for controlled access in dbGaP.
consensus_peaks.MAZ.hg38.bed

value: MAZ


title: patterned induced neurons, NCRM5, Homo sapiens, 2N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: NCRM5_6hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, C1C1a_B11-1, Pan troglodytes, 4N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: C1C1a_B11-1_6hrKCl_2
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, H2-C, Homo sapiens, 2N, minusKCl, piN_Rep2 (RNA-seq)

description:
Library name: H2-C_minusKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, C1C1a_B11-1, Pan troglodytes, 4N, 2hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: C1C1a_B11-1_2hrKCl_2
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, C1C1a_B7-1, Pan troglodytes, 4N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: C1C1a_B7-1_6hrKCl_2
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, C1C1a_B11-1, Pan troglodytes, 4N, minusKCl, piN_Rep2 (RNA-seq)

description:
Library name: C1C1a_B11-1_minusKCl_2
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, NCRM5, Homo sapiens, 2N, 2hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: NCRM5_2hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, H2-C, Homo sapiens, 2N, 2hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H2-C_2hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, C2-C, Pan troglodytes, 2N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: C2-C_6hrKCl_2
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, C2_A6-2, Pan troglodytes, 2N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: C2_A6-2_6hrKCl_2
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, C1C1a_A11, Pan troglodytes, 4N, 2hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: C1C1a_A11_2hrKCl_2
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, C1C1a_A11, Pan troglodytes, 4N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: C1C1a_A11_6hrKCl_2
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, H2_B7-2, Homo sapiens, 2N, minusKCl, piN_Rep2 (RNA-seq)

description:
Library name: H2_B7-2_minusKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, C1_B2, Pan troglodytes, 2N, minusKCl, piN_Rep2 (RNA-seq)

description:
Library name: C1_B2_minusKCl_2
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, H2_B7-2, Homo sapiens, 2N, 2hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H2_B7-2_2hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, C1_B2, Pan troglodytes, 2N, 2hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: C1_B2_2hrKCl_2
piN_human-chimp_gene_counts.txt


title: ipfn7fep

description: Library name: ipfn7fep


title: cc06dep

description: Library name: cc06dep


title: patterned induced neurons, H1H1a_H6-1, Homo sapiens, 4N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1H1a_H6-1_6hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, H2-C, Homo sapiens, 2N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H2-C_6hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, C1_B12, Pan troglodytes, 2N, 2hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: C1_B12_2hrKCl_2
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, C1_B12, Pan troglodytes, 2N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: C1_B12_6hrKCl_2
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, C1C1a_A11, Pan troglodytes, 4N, minusKCl, piN_Rep2 (RNA-seq)

description:
Library name: C1C1a_A11_minusKCl_2
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, H1H1a_D6-3, Homo sapiens, 4N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1H1a_D6-3_6hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: neural progenitor cells, C2-C, Pan troglodytes, 72060-4, RE-TNIK, RE-TNIK_Rep4 (RNA-seq)

description:
Library name: E7_C2-C_TNIK-72060-4
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt

value: RE-TNIK


title: patterned induced neurons, H2_B7-2, Homo sapiens, 2N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H2_B7-2_6hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, H1H1a_C3-1, Homo sapiens, 4N, minusKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1H1a_C3-1_minusKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: neural progenitor cells, C2-C, Pan troglodytes, 72060-3, RE-TNIK, RE-TNIK_Rep4 (RNA-seq)

description:
Library name: E7_C2-C_TNIK-72060-3
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: patterned induced neurons, H1H1a_C3-1, Homo sapiens, 4N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1H1a_C3-1_6hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: NGS4790 BP043202 NCI-H2804 G03498025-0.1uM

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: NGS4790_R9111_LIB5467520_SAM24428495

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

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.

value: Epithelial


title: NGS4790 BP043202 SK-N-F1 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467521_SAM24428496

source_name: Adrenal

value: Adrenal

value: Neuroblast


title: patterned induced neurons, C1_B12, Pan troglodytes, 2N, minusKCl, piN_Rep2 (RNA-seq)

description:
Library name: C1_B12_minusKCl_2
piN_human-chimp_gene_counts.txt

value: patterned induced neurons


title: patterned induced neurons, H1H1a_H6-1, Homo sapiens, 4N, minusKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1H1a_H6-1_minusKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, H1_G1, Homo sapiens, 2N, minusKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1_G1_minusKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, C1_B2, Pan troglodytes, 2N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: C1_B2_6hrKCl_2
piN_human-chimp_gene_counts.txt


title: NGS4790 BP043202 JL-1 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467518_SAM24428493

source_name: Pleura

value: Pleura


title: patterned induced neurons, H1H1a_D6-3, Homo sapiens, 4N, minusKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1H1a_D6-3_minusKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt

value: minusKCl


title: patterned induced neurons, H1_G1, Homo sapiens, 2N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1_G1_6hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: neural progenitor cells, C2-C, Pan troglodytes, NTC5, NTC, RE-TNIK_Rep4 (RNA-seq)

description:
Library name: E7_C2-C_NTC5
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt

value: Y

value: NTC


title: NGS4790 BP043202 NCI-H2591 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467517_SAM24428492


title: patterned induced neurons, H1H1a_C3-1, Homo sapiens, 4N, 2hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1H1a_C3-1_2hrKCl_2
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_Rep2 (RNA-seq)

description:
Library name: H1_A9-1_minusKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: neural progenitor cells, C2-C, Pan troglodytes, NTC3, NTC, RE-TNIK_Rep4 (RNA-seq)

description:
Library name: E7_C2-C_NTC3
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: NGS4790 BP043202 SK-N-F1 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467513_SAM24428488


title: patterned induced neurons, H1_A9-1, Homo sapiens, 2N, 6hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1_A9-1_6hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: patterned induced neurons, H1H1a_H6-1, Homo sapiens, 4N, 2hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1H1a_H6-1_2hrKCl_2
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_Rep2 (RNA-seq)

description:
Library name: H1_A9-1_2hrKCl_2
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, 2hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1H1a_D6-3_2hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: neural progenitor cells, C2-C, Pan troglodytes, NTC2, NTC, RE-TNIK_Rep4 (RNA-seq)

description:
Library name: E7_C2-C_NTC2
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: H2__GN2__3 (RNA-seq)

description:
Library name: H2__GN2__3
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: NCRM5__T7_2__3 (RNA-seq)

description:
Library name: NCRM5__T7_2__3
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: neural progenitor cells, C2-C, Pan troglodytes, 72060-2, RE-TNIK, RE-TNIK_Rep4 (RNA-seq)

description:
Library name: E7_C2-C_TNIK-72060-2
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: NGS4790 BP043202 JL-1 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467510_SAM24428485


title: H2__T7_2__3 (RNA-seq)

description:
Library name: H2__T7_2__3
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: NCRM5__GN2__3 (RNA-seq)

description:
Library name: NCRM5__GN2__3
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: neural progenitor cells, C3-C, Pan troglodytes, 72060-3, RE-TNIK, RE-TNIK_Rep3 (RNA-seq)

description:
Library name: E5_C3-C_TNIK-72060-3
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: H2__GN2__2 (RNA-seq)

description:
Library name: H2__GN2__2
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: H2__T7_2__2 (RNA-seq)

description:
Library name: H2__T7_2__2
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: NCRM5__T7_2__2 (RNA-seq)

description:
Library name: NCRM5__T7_2__2
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: neural progenitor cells, C3-C, Pan troglodytes, 72060-2, RE-TNIK, RE-TNIK_Rep3 (RNA-seq)

description:
Library name: E5_C3-C_TNIK-72060-2
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: NCRM5__GN2__2 (RNA-seq)

description:
Library name: NCRM5__GN2__2
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: NGS4790 BP043202 HCC845 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467499_SAM24428474

value: Epithelial, Fibroblast


title: patterned induced neurons, H1_G1, Homo sapiens, 2N, 2hrKCl, piN_Rep2 (RNA-seq)

description:
Library name: H1_G1_2hrKCl_2
The raw data are being made available for controlled access in dbGaP.
piN_human-chimp_gene_counts.txt


title: H2__GN3__1 (RNA-seq)

description:
Library name: H2__GN3__1
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt

value: neural progenitor cells


title: neural progenitor cells, C3-C, Pan troglodytes, NTC3, NTC, RE-TNIK_Rep3 (RNA-seq)

description:
Library name: E5_C3-C_NTC3
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: NGS4790 BP043202 NCI-H2052 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467500_SAM24428475


title: NGS4790 BP043202 NCI-H2691 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467498_SAM24428473


title: NCRM5__T7_3__E1 (RNA-seq)

description:
Library name: NCRM5__T7_3__E1
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: NGS4790 BP043202 MSTO-211H G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467496_SAM24428471

value: Fibroblast


title: neural progenitor cells, C2-C, Pan troglodytes, 72060-4, RE-TNIK, RE-TNIK_Rep2 (RNA-seq)

description:
Library name: E4_C2-C_TNIK-72060-4
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: NCRM5__T7_4__E1 (RNA-seq)

description:
Library name: NCRM5__T7_4__E1
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: neural progenitor cells, C3-C, Pan troglodytes, 72060-4, RE-TNIK, RE-TNIK_Rep3 (RNA-seq)

description:
Library name: E5_C3-C_TNIK-72060-4
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: NGS4790 BP043202 NCI-H2804 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467512_SAM24428487

value: Lung


title: neural progenitor cells, C3-C, Pan troglodytes, NTC2, NTC, RE-TNIK_Rep3 (RNA-seq)

description:
Library name: E5_C3-C_NTC2
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: NCRM5__T7_2__E1 (RNA-seq)

description:
Library name: NCRM5__T7_2__E1
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: E5_NCRM5_TNIK-72060-4 (RNA-seq)

description:
Library name: E5_NCRM5_TNIK-72060-4
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: NCRM5__GN3__E1 (RNA-seq)

description:
Library name: NCRM5__GN3__E1
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: NGS4790 BP043202 NCI-H2722 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467493_SAM24428468


title: NCRM5__GN2__E1 (RNA-seq)

description:
Library name: NCRM5__GN2__E1
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: neural progenitor cells, C2-C, Pan troglodytes, 72060-2, RE-TNIK, RE-TNIK_Rep2 (RNA-seq)

description:
Library name: E4_C2-C_TNIK-72060-2
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: NGS4790 BP043202 NCI-H2731 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467494_SAM24428469


title: neural progenitor cells, C3-C, Pan troglodytes, NTC5, NTC, RE-TNIK_Rep3 (RNA-seq)

description:
Library name: E5_C3-C_NTC5
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: H2__T7_2__1 (RNA-seq)

description:
Library name: H2__T7_2__1
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: NGS4790 BP043202 NCI-H2052 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467492_SAM24428467


title: NGS4790 BP043202 NCI-H2591 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467509_SAM24428484


title: E5_NCRM5_NTC5 (RNA-seq)

description:
Library name: E5_NCRM5_NTC5
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: E5_NCRM5_TNIK-72060-2 (RNA-seq)

description:
Library name: E5_NCRM5_TNIK-72060-2
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: neural progenitor cells, C2-C, Pan troglodytes, NTC5, NTC, RE-TNIK_Rep2 (RNA-seq)

description:
Library name: E4_C2-C_NTC5
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: E5_NCRM5_NTC3 (RNA-seq)

description:
Library name: E5_NCRM5_NTC3
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: neural progenitor cells, C2-C, Pan troglodytes, NTC3, NTC, RE-TNIK_Rep2 (RNA-seq)

description:
Library name: E4_C2-C_NTC3
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: E5_NCRM5_NTC2 (RNA-seq)

description:
Library name: E5_NCRM5_NTC2
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: E4_H2-C_TNIK-72060-4 (RNA-seq)

description:
Library name: E4_H2-C_TNIK-72060-4
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: NCRM5__T7_2__1 (RNA-seq)

description:
Library name: NCRM5__T7_2__1
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: NGS4790 BP043202 NCI-H2691 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467490_SAM24428465


title: E4_H2-C_TNIK-72060-3 (RNA-seq)

description:
Library name: E4_H2-C_TNIK-72060-3
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: E5_NCRM5_TNIK-72060-3 (RNA-seq)

description:
Library name: E5_NCRM5_TNIK-72060-3
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: neural progenitor cells, C2-C, Pan troglodytes, 72060-3, RE-TNIK, RE-TNIK_Rep2 (RNA-seq)

description:
Library name: E4_C2-C_TNIK-72060-3
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: NGS4790 BP043202 MSTO-211H G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467488_SAM24428463


title: E4_H2-C_NTC5 (RNA-seq)

description:
Library name: E4_H2-C_NTC5
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: E4_H2-C_NTC3 (RNA-seq)

description:
Library name: E4_H2-C_NTC3
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: NGS4790 BP043202 NCI-H2731 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467486_SAM24428461


title: NGS4790 BP043202 HCC845 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467491_SAM24428466


title: neural progenitor cells, C3-C, Pan troglodytes, 72060-4, RE-TNIK, RE-TNIK_Rep1 (RNA-seq)

description:
Library name: E3_C3-C_TNIK-72060-4
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: E3_H2-C_TNIK-72060-4 (RNA-seq)

description:
Library name: E3_H2-C_TNIK-72060-4
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: NGS4790 BP043202 NCI-H2722 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467485_SAM24428460


title: E3_H2-C_TNIK-72060-3 (RNA-seq)

description:
Library name: E3_H2-C_TNIK-72060-3
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: E4_H2-C_NTC2 (RNA-seq)

description:
Library name: E4_H2-C_NTC2
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: neural progenitor cells, C3-C, Pan troglodytes, 72060-3, RE-TNIK, RE-TNIK_Rep1 (RNA-seq)

description:
Library name: E3_C3-C_TNIK-72060-3
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: E3_H2-C_NTC5 (RNA-seq)

description:
Library name: E3_H2-C_NTC5
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: NGS4790 BP043202 NCI-H226 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467471_SAM24428446


title: neural progenitor cells, C3-C, Pan troglodytes, 72060-2, RE-TNIK, RE-TNIK_Rep1 (RNA-seq)

description:
Library name: E3_C3-C_TNIK-72060-2
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: E3_H2-C_NTC3 (RNA-seq)

description:
Library name: E3_H2-C_NTC3
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: neural progenitor cells, C3-C, Pan troglodytes, NTC5, NTC, RE-TNIK_Rep1 (RNA-seq)

description:
Library name: E3_C3-C_NTC5
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: E3_H2-C_TNIK-72060-2 (RNA-seq)

description:
Library name: E3_H2-C_TNIK-72060-2
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: NGS4790 BP043202 NCI-H2369 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467470_SAM24428445


title: E3_H2-C_NTC2 (RNA-seq)

description:
Library name: E3_H2-C_NTC2
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: NGS4790 BP043202 NCI-H226 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467463_SAM24428438


title: neural progenitor cells, C3-C, Pan troglodytes, NTC3, NTC, RE-TNIK_Rep1 (RNA-seq)

description:
Library name: E3_C3-C_NTC3
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: E2_NCRM5_TNIK-72060-4 (RNA-seq)

description:
Library name: E2_NCRM5_TNIK-72060-4
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: E4_H2-C_TNIK-72060-2 (RNA-seq)

description:
Library name: E4_H2-C_TNIK-72060-2
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: neural progenitor cells, C3-C, Pan troglodytes, NTC2, NTC, RE-TNIK_Rep1 (RNA-seq)

description:
Library name: E3_C3-C_NTC2
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: E2_NCRM5_TNIK-72060-3 (RNA-seq)

description:
Library name: E2_NCRM5_TNIK-72060-3
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: E2_NCRM5_TNIK-72060-2 (RNA-seq)

description:
Library name: E2_NCRM5_TNIK-72060-2
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: E2_NCRM5_NTC5 (RNA-seq)

description:
Library name: E2_NCRM5_NTC5
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: NGS4790 BP043202 VMRC-LCD G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467451_SAM24428426

value: VMRC-LCD


title: neural progenitor cells, C1C1c, Pan troglodytes, 4N, NPC_Rep2 (RNA-seq)

description:
Library name: C1C1c_2_RNA
NPC_human-chimp_gene_counts.txt

value: N


title: E2_NCRM5_NTC3 (RNA-seq)

description:
Library name: E2_NCRM5_NTC3
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: neural progenitor cells, C1C1a, Pan troglodytes, 4N, NPC_Rep2 (RNA-seq)

description:
Library name: C1C1a_2_RNA
NPC_human-chimp_gene_counts.txt


title: E2_NCRM5_NTC2 (RNA-seq)

description:
Library name: E2_NCRM5_NTC2
The raw data are being made available for controlled access in dbGaP.
RE-TNIK_CRISPRi_human-NPC_gene_counts.txt


title: neural progenitor cells, H1H1b, Homo sapiens, 4N, NPC_Rep2 (RNA-seq)

description:
Library name: H1H1b_2_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt


title: neural progenitor cells, H1H1a, Homo sapiens, 4N, NPC_Rep2 (RNA-seq)

description:
Library name: H1H1a_2_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt


title: neural progenitor cells, H3, Homo sapiens, 2N, NPC_Rep2 (RNA-seq)

description:
Library name: H3_2_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt


title: neural progenitor cells, C3, Pan troglodytes, 2N, NPC_Rep2 (RNA-seq)

description:
Library name: C3_2_RNA
NPC_human-chimp_gene_counts.txt


title: NGS4790 BP043202 NCI-H2461 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467447_SAM24428422


title: NGS4790 BP043202 NCI-H2803 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467448_SAM24428423


title: neural progenitor cells, C2, Pan troglodytes, 2N, NPC_Rep2 (RNA-seq)

description:
Library name: C2_2_RNA
NPC_human-chimp_gene_counts.txt


title: neural progenitor cells, H2, Homo sapiens, 2N, NPC_Rep2 (RNA-seq)

description:
Library name: H2_2_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt


title: neural progenitor cells, H1H1b, Homo sapiens, 4N, NPC_Rep1 (RNA-seq)

description:
Library name: H1H1b_1_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt


title: neural progenitor cells, C1, Pan troglodytes, 2N, NPC_Rep2 (RNA-seq)

description:
Library name: C1_2_RNA
NPC_human-chimp_gene_counts.txt


title: neural progenitor cells, H1, Homo sapiens, 2N, NPC_Rep2 (RNA-seq)

description:
Library name: H1_2_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt


title: NGS4790 BP043202 NCI-H290 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467445_SAM24428420


title: NGS4790 BP043202 NCI-H2373 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467446_SAM24428421


title: neural progenitor cells, C2-C, Pan troglodytes, NTC2, NTC, RE-TNIK_Rep2 (RNA-seq)

description:
Library name: E4_C2-C_NTC2
RE-TNIK_CRISPRi_chimp-NPC_gene_counts.txt


title: neural progenitor cells, H1H1a, Homo sapiens, 4N, NPC_Rep1 (RNA-seq)

description:
Library name: H1H1a_1_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt


title: neural progenitor cells, H3, Homo sapiens, 2N, NPC_Rep1 (RNA-seq)

description:
Library name: H3_1_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt


title: NGS4790 BP043202 NCI-H2369 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467462_SAM24428437


title: NGS4790 BP043202 VMRC-LCD G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467443_SAM24428418


title: neural progenitor cells, C1C1c, Pan troglodytes, 4N, NPC_Rep1 (RNA-seq)

description:
Library name: C1C1c_1_RNA
NPC_human-chimp_gene_counts.txt


title: neural progenitor cells, H2, Homo sapiens, 2N, NPC_Rep1 (RNA-seq)

description:
Library name: H2_1_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt


title: NGS4790 BP043202 NCI-H2803 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467440_SAM24428415


title: human NPC, 10X gene expression library, reaction 4

description:
Library name: NCRM5_GE_5
The raw data are being made available for controlled access in dbGaP.

data_processing:
Using cellranger v7.0.0 (10X Genomics), sequencing reads from gene expression libraries were mapped to hg38 or panTro5 and gRNAs expressed in each cell were assigned.
Assembly: hg38
Assembly: panTro5
Supplementary files format and content: tab-separated or comma-separated values or matrix files
Supplementary files format and content: bed file of targeted open chromatin regions

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 infected with a lentiviral pool targeting 106 cis-regulated open chromatin regions. Cells were harvested at D14 for sequencing.

extract_protocol:
At D14, infected cells (BFP+) were sorted by FACS and 4 scRNA-seq reactions were prepared for each cell line using the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (Dual Index) with Feature Barcoding technology for CRISPR Screening (10X Genomics, cat #PN-1000268, #PN-1000269, #PN-1000262, #PN-1000120, #PN-1000127, #PN-1000215, #PN-1000242).
CRISPR gRNA libraries and gene expression libraries were prepared from each reaction using the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (Dual Index) with Feature Barcoding technology for CRISPR Screening (10X Genomics, cat #PN-1000268, #PN-1000269, #PN-1000262, #PN-1000120, #PN-1000127, #PN-1000215, #PN-1000242).

treatment_protocol: Neural progenitor cells were infected with a lentiviral pool targeting 106 cis-regulated open chromatin regions on D7 of differentiation immediately after plating.

value: NPC

value: infected with gRNA library targeting 106 cis-regulated open chromatin regions and control regions


title: neural progenitor cells, C1C1a, Pan troglodytes, 4N, NPC_Rep1 (RNA-seq)

description:
Library name: C1C1a_1_RNA
NPC_human-chimp_gene_counts.txt


title: human NPC, 10X gene expression library, reaction 3

description:
Library name: NCRM5_GE_4
The raw data are being made available for controlled access in dbGaP.


title: neural progenitor cells, C3, Pan troglodytes, 2N, NPC_Rep1 (RNA-seq)

description:
Library name: C3_1_RNA
NPC_human-chimp_gene_counts.txt


title: human NPC, 10X gene expression library, reaction 2

description:
Library name: NCRM5_GE_3
The raw data are being made available for controlled access in dbGaP.


title: NGS4790 BP043202 NCI-H2373 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467438_SAM24428413


title: NGS4790 BP043202 NCI-H290 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467437_SAM24428412


title: human NPC, 10X gene expression library, reaction 1

description:
Library name: NCRM5_GE_2
The raw data are being made available for controlled access in dbGaP.


title: human NPC, 10X CRISPR gRNA library, reaction 3

description:
Library name: NCRM5_CR_4
The raw data are being made available for controlled access in dbGaP.
NPC_4N_CRISPRi_screen_gRNA_feature_ref.csv

library_source: other

molecule: other


title: human NPC, 10X CRISPR gRNA library, reaction 2

description:
Library name: NCRM5_CR_3
The raw data are being made available for controlled access in dbGaP.
NPC_4N_CRISPRi_screen_gRNA_feature_ref.csv


title: human NPC, 10X CRISPR gRNA library, reaction 1

description:
Library name: NCRM5_CR_2
The raw data are being made available for controlled access in dbGaP.
NPC_4N_CRISPRi_screen_gRNA_feature_ref.csv


title: neural progenitor cells, C1, Pan troglodytes, 2N, NPC_Rep1 (RNA-seq)

description:
Library name: C1_1_RNA
NPC_human-chimp_gene_counts.txt


title: neural progenitor cells, C2, Pan troglodytes, 2N, NPC_Rep1 (RNA-seq)

description:
Library name: C2_1_RNA
NPC_human-chimp_gene_counts.txt


title: human NPC, 10X CRISPR gRNA library, reaction 4

description:
Library name: NCRM5_CR_5
The raw data are being made available for controlled access in dbGaP.
NPC_4N_CRISPRi_screen_gRNA_feature_ref.csv


title: NGS4790 BP043202 NCI-H2461 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467439_SAM24428414


title: chimpanzee NPC, 10X gene expression library, reaction 4

description: Library name: C3-C_GE_5


title: NGS4790 BP043201 SK-N-F1 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467425_SAM24428400


title: patterned induced neurons, NCRM5, Homo sapiens, 2N, 2hrKCl, piN_Rep1

description:
Library name: NCRM5_2hrKCl
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

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

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).


title: patterned induced neurons, NCRM5, Homo sapiens, 2N, minusKCl, piN_Rep1

description:
Library name: NCRM5_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: NGS4790 BP043201 NCI-H2804 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467424_SAM24428399


title: patterned induced neurons, NCRM5, Homo sapiens, 2N, 30minKCl, piN_Rep1

description:
Library name: NCRM5_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: neural progenitor cells, H1, Homo sapiens, 2N, NPC_Rep1 (RNA-seq)

description:
Library name: H1_1_RNA
The raw data are being made available for controlled access in dbGaP.
NPC_human-chimp_gene_counts.txt


title: chimpanzee NPC, 10X gene expression library, reaction 2

description: Library name: C3-C_GE_2


title: patterned induced neurons, H2_B7-2, Homo sapiens, 2N, 30minKCl, piN_Rep1

description:
Library name: H2_B7-2_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: patterned induced neurons, H2_B7-2, Homo sapiens, 2N, minusKCl, piN_Rep1

description:
Library name: H2_B7-2_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: NGS4790 BP043201 NCI-H2591 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467421_SAM24428396


title: chimpanzee NPC, 10X gene expression library, reaction 1

description: Library name: C3-C_GE_1


title: patterned induced neurons, H1H1a_H6-1, Homo sapiens, 4N, minusKCl, piN_Rep1

description:
Library name: H1H1a_H6-1_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: NGS4790 BP043201 JL-1 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467422_SAM24428397


title: patterned induced neurons, H1H1a_H6-1, Homo sapiens, 4N, 30minKCl, piN_Rep1

description:
Library name: H1H1a_H6-1_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, H1H1a_H6-1, Homo sapiens, 4N, 2hrKCl, piN_Rep1

description:
Library name: H1H1a_H6-1_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: chimpanzee NPC, 10X CRISPR gRNA library, reaction 4

description:
Library name: C3-C_CR_5
NPC_4N_CRISPRi_screen_gRNA_feature_ref.csv


title: NGS4790 BP043201 SK-N-F1 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467417_SAM24428392


title: chimpanzee NPC, 10X CRISPR gRNA library, reaction 3

description:
Library name: C3-C_CR_3
NPC_4N_CRISPRi_screen_gRNA_feature_ref.csv


title: patterned induced neurons, H1H1a_C3-1, Homo sapiens, 4N, 30minKCl, piN_Rep1

description:
Library name: H1H1a_C3-1_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, H1H1a_D6-3, Homo sapiens, 4N, 2hrKCl, piN_Rep1

description:
Library name: H1H1a_D6-3_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: chimpanzee NPC, 10X CRISPR gRNA library, reaction 2

description:
Library name: C3-C_CR_2
NPC_4N_CRISPRi_screen_gRNA_feature_ref.csv


title: chimpanzee NPC, 10X gene expression library, reaction 3

description: Library name: C3-C_GE_3


title: NGS4790 BP043201 NCI-H2804 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467416_SAM24428391


title: patterned induced neurons, H1H1a_C3-1, Homo sapiens, 4N, minusKCl, piN_Rep1

description:
Library name: H1H1a_C3-1_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: patterned induced neurons, H1H1a_D6-3, Homo sapiens, 4N, minusKCl, piN_Rep1

description:
Library name: H1H1a_D6-3_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, H1H1a_D6-3, Homo sapiens, 4N, 30minKCl, piN_Rep1

description:
Library name: H1H1a_D6-3_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: chimpanzee NPC, 10X CRISPR gRNA library, reaction 1

description:
Library name: C3-C_CR_1
NPC_4N_CRISPRi_screen_gRNA_feature_ref.csv


title: NGS4790 BP043201 NCI-H2591 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467413_SAM24428388


title: patterned induced neurons, H1H1a_C3-1, Homo sapiens, 4N, 2hrKCl, piN_Rep1

description:
Library name: H1H1a_C3-1_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: NGS4790 BP043201 NCI-H2052 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467404_SAM24428379


title: patterned induced neurons, H1_G1, Homo sapiens, 2N, minusKCl, piN_Rep1

description:
Library name: H1_G1_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, H1_G1, Homo sapiens, 2N, 30minKCl, piN_Rep1

description:
Library name: H1_G1_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, C3-C, Pan troglodytes, 2N, minusKCl, piN_Rep1

description:
Library name: C3-C_minusKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: patterned induced neurons, H2_B7-2, Homo sapiens, 2N, 2hrKCl, piN_Rep1

description:
Library name: H2_B7-2_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: patterned induced neurons, H1_G1, Homo sapiens, 2N, 2hrKCl, piN_Rep1

description:
Library name: H1_G1_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: patterned induced neurons, H1_A9-1, Homo sapiens, 2N, minusKCl, piN_Rep1

description:
Library name: H1_A9-1_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: patterned induced neurons, C3-C, Pan troglodytes, 2N, 30minKCl, piN_Rep1

description:
Library name: C3-C_30minKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: patterned induced neurons, H1_A9-1, Homo sapiens, 2N, 30minKCl, piN_Rep1

description:
Library name: H1_A9-1_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, C3-C, Pan troglodytes, 2N, 2hrKCl, piN_Rep1

description:
Library name: C3-C_2hrKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: NGS4790 BP043201 NCI-H2691 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467402_SAM24428377


title: patterned induced neurons, H1_A9-1, Homo sapiens, 2N, 2hrKCl, piN_Rep1

description:
Library name: H1_A9-1_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: patterned induced neurons, C2-C, Pan troglodytes, 2N, minusKCl, piN_Rep1

description:
Library name: C2-C_minusKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: NGS4790 BP043201 JL-1 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467414_SAM24428389


title: NGS4790 BP043201 NCI-H2731 G03498025-0

description: Library name: NGS4790_R9111_LIB5467398_SAM24428373


title: patterned induced neurons, C2-C, Pan troglodytes, 2N, 30minKCl, piN_Rep1

description:
Library name: C2-C_30minKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: neural progenitor cells, H1H1a, Homo sapiens, 4N, NPC_Rep1

description:
Library name: H1H1a_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: NGS4790 BP043201 NCI-H2722 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467397_SAM24428372


title: patterned induced neurons, C2_A6-2, Pan troglodytes, 2N, minusKCl, piN_Rep1

description:
Library name: C2_A6-2_minusKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: neural progenitor cells, H1H1b, Homo sapiens, 4N, NPC_Rep2

description:
Library name: H1H1b_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: neural progenitor cells, H3, Homo sapiens, 2N, NPC_Rep2

description:
Library name: H3_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: neural progenitor cells, H1H1b, Homo sapiens, 4N, NPC_Rep1

description:
Library name: H1H1b_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, H1H1a, Homo sapiens, 4N, NPC_Rep2

description:
Library name: H1H1a_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: neural progenitor cells, H3, Homo sapiens, 2N, NPC_Rep1

description:
Library name: H3_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: NGS4790 BP043201 MSTO-211H G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467400_SAM24428375


title: neural progenitor cells, H2, Homo sapiens, 2N, NPC_Rep2

description:
Library name: H2_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: NGS4790 BP043201 HCC845 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467395_SAM24428370


title: neural progenitor cells, H1, Homo sapiens, 2N, NPC_Rep1

description:
Library name: H1_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: patterned induced neurons, C2_A6-2, Pan troglodytes, 2N, 30minKCl, piN_Rep1

description:
Library name: C2_A6-2_30minKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: NGS4790 BP043201 NCI-H2052 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467396_SAM24428371


title: neural progenitor cells, H2, Homo sapiens, 2N, NPC_Rep1

description:
Library name: H2_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: patterned induced neurons, C2-C, Pan troglodytes, 2N, 2hrKCl, piN_Rep1

description:
Library name: C2-C_2hrKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: MIA PaCa-2, 24H ERK1/2 Inhibitor, Replicate 3

city: Chapel Hill

first: Albert

last: Baldwin

state: NC

address: 450 West Drive

institute: Lineberger Comprehensive Cancer Center

description:
Library name: SCH772984 R3
Column name in gene_count.txt: ERKi_R3

data_processing:
Data processing and analysis was performed in-house by Novogene. Briefly, raw reads were processed by in-house perl scripts removing poly N reads and low quality reads from raw data. Q20, Q30, and GC content was calculated.
Alignments were performed using HISAT v2.0.5 using clean paired-end reads by Novogene.
Counts were determined by Novogene using featureCounts v1.5.0-p3.
Assembly: hg38
Supplementary files format and content: gene_counts is an .xls file and contains raw counts for each gene and sample.

source_name: MIA PaCa-2

growth_protocol: MIA PaCa-2 cells were maintained in DMEM supplemented with 10% fetal bovine serum, 2.5% horse serum, and 1X penicillin/streptomycin. Cells were grown in an incubator at 5% CO2 and 37 degrees C.

extract_protocol:
RNA was extracted using the Zymogen Quick-RNA Mini-Prep kit using the manufacturer's suggested protocol. RNA was quantified using a NanoDrop.
Libraries were constructed by Novogene after receiving samples and performing quality control analysis. Library was checked with Qubit and real-time PCR for quantification.

treatment_protocol: Cells were treated with 1uM SCH772984, 1uM Compound 1, or 0.1% DMSO for 24H before harvesting.

value: MIA PaCa-2

value: Pancreatic Cancer

value: WT


title: patterned induced neurons, C2_A6-2, Pan troglodytes, 2N, 2hrKCl, piN_Rep1

description:
Library name: C2_A6-2_2hrKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: MIA PaCa-2, 24H ERK1/2 Inhibitor, Replicate 1

description:
Library name: SCH772984 R1
Column name in gene_count.txt: ERKi_R1


title: patterned induced neurons, C1C1a_B7-1, Pan troglodytes, 4N, minusKCl, piN_Rep1

description:
Library name: C1C1a_B7-1_minusKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: MIA PaCa-2, 24H TBK1/IKKepsilon Inhibitor, Replicate 3

description:
Library name: CMPD 1 R3
Column name in gene_count.txt: TBK1i_R3

value: 1uM Compound 1


title: NGS4790 BP043201 NCI-H2691 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467394_SAM24428369

value: Epithelial


title: MIA PaCa-2, 24H ERK1/2 Inhibitor, Replicate 2

description:
Library name: SCH772984 R2
Column name in gene_count.txt: ERKi_R2


title: NGS4790 BP043201 HCC845 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467403_SAM24428378


title: NGS4790 BP043201 MSTO-211H G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467392_SAM24428367


title: patterned induced neurons, C1C1a_B7-1, Pan troglodytes, 4N, 30minKCl, piN_Rep1

description:
Library name: C1C1a_B7-1_30minKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw

value: patterned induced neurons


title: MIA PaCa-2, 24H TBK1/IKKepsilon Inhibitor, Replicate 2

description:
Library name: CMPD 1 R2
Column name in gene_count.txt: TBK1i_R2


title: MIA PaCa-2, 24H TBK1/IKKepsilon Inhibitor, Replicate 1

description:
Library name: CMPD 1 R1
Column name in gene_count.txt: TBK1i_R1


title: MIA PaCa-2, 24H DMSO Control, Replicate 3

description:
Library name: DMSO R3
Column name in gene_count.txt: DMSO_R3

value: 0.1% DMSO


title: NGS4790 BP043201 NCI-H2731 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467390_SAM24428365


title: MIA PaCa-2, 24H DMSO Control, Replicate 2

description:
Library name: DMSO R2
Column name in gene_count.txt: DMSO_R2


title: NGS4790 BP043201 NCI-H2722 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467389_SAM24428364


title: MIA PaCa-2, 24H DMSO Control, Replicate 1

description:
Library name: DMSO R1
Column name in gene_count.txt: DMSO_R1


title: patterned induced neurons, C1C1a_B11-1, Pan troglodytes, 4N, minusKCl, piN_Rep1

description:
Library name: C1C1a_B11-1_minusKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw

value: minusKCl


title: HeLa, nb-enDR3-FLAG IP, replicate 1

city: Warsaw

first: Damian

last: Graczyk

address: ul. Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

description:
Library name: HeLa_nb-enDR3_DRIPc_rep1
DRIPc-seq

data_processing:
enDR3-DRIPc, S9.6 DRIPc, enDR3-ChIP, raw sequencing reads were mapped to human genome reference assembly GRh38/hg38 using bowtie2 (version 2.3.5.1) in the paired-end and local mode. The maximal distance between reads of 700 bp was allowed. Only reads with mapping quality equal to or greater than 30 were retained. Duplicate reads were removed. Reads filtering was performed using samtools (version 1.12). bigWig signal files (counts per million normalised) were generated using deeptools (version 3.5.1).
Peaks were called using MACS2 (PMID: 18798982). For stranded data, peaks were called on each strand separately and then merged into one file preserving the strand information. The visual inspection of our and previous data in the genome browser indicated that R-loop peaks are broad. The peaks were, therefore, called in the broad mode. In contrast, enDR3-ChIP-seq data visualisation showed that the peaks are narrow, thus, the peak calling was performed in the narrow mode. Where possible, replicate samples were used, and, as a background reference, an Input sample.
Assembly: hg38
Supplementary files format and content: bigWig, broadPeak (DRIPc-seq)
Library strategy: DRIPc-seq

source_name: Cervical cancer

growth_protocol: Cells were cultured in HyClone DMEM with high glucose, 4 mM L-glutamine, and sodium pyruvate (Cytiva) supplemented with 10% FBS (Gibco) at 37°C in an atmosphere of 5% CO2

extract_protocol:
DRIPc-seq procedure was based on previously published protocols (PMID: 32544226, PMID: 31053798) with some modifications. 1.25 x 106 HeLa cells were seeded onto 60 mm plates. After 24 hours, the culture medium was removed, and cells were washed once with cold PBS and twice with TE buffer (10 mM Tris pH 8.0, 1 mM EDTA). Cell lysis was performed directly on the plate by adding 0.5 mL of lysis buffer (TE supplemented with 0.625 % SDS and 0.0625 mg/mL Proteinase K), and the suspension was immediately transferred to a fresh 2 mL tube and incubated for 4.5 hours at 37°C with gentle mixing every 15 minutes. Afterward, genomic DNA was purified by phenol: chloroform: isoamyl alcohol (25:24:1) extraction and ethanol precipitation. Precipitated DNA was washed with 70% ethanol, air-dried, and resuspended in 30 uL of TE buffer. Next, pure gDNA was sheared by sonication using Bioruptor Plus with a water cooling system (Diagenode) as follows: 3 µg of gDNA diluted to 200 µL in TE was placed in 1.5 mL DNA LoBind Tubes (Eppendorf) and subjected to 30 cycles of sonication 30 s ON, 90 s OFF at a "Low" mode. The length of fragments after sonication was evaluated by running DNA samples before and after shearing on a 1.5 % agarose gel in 1X TAE (40mM Tris pH 8.0, 20 mM acetic acid, 2 mM EDTA) at 70-80 V. Afterward, 4 µg of fragmented gDNA was mixed with 10 µg of  enDR3-3xFLAG or S9.6 antibody, diluted to 1 mL final volume with binding buffer (20 mM Hepes pH 7.4, 150 mM NaCl, 0.05 % Triton X-100), and incubated overnight with gentle rotation in a refrigeration cabinet. The next day, input fractions containing  enDR3-3xFLAG or S9.6 were added to 50 µL of M2 anti FLAG Magnetic Beads (Sigma) or Protein G Dynabeads (Thermo), respectively, and incubated for 2 hours. Additionally, negative controls were prepared by incubating 4 µg of sonicated gDNA with beads without the bait. Following the incubation, the unbound fraction was removed, and beads were washed three times with 500 µL of binding buffer for 5 min with gentle rotation in a refrigeration cabinet. Elution was performed by adding 125 µL of the elution buffer (50 mM Tris pH 8, 1mM EDTA, 0.5% SDS, 0.64 mg/mL Proteinase K) for 45 min at 55°C. Two replicates of each sample were pooled and purified using a DNA clean and concentrator kit (Zymo Research) according to the manufacturer's protocol. After elution with 30 µL of the elution buffer (Zymo Research), half of the eluate was treated with 2 µL of DNAse I (1 U/µL) in 1X DNase I digestion buffer (Thermo Fisher Scientific) for one hour at 37°C. For DNaseI inactivation, 1 µl of 0.5 M EDTA was added for 10 min at 65°C. RNA was purified using the RNA clean and concentrator kit (Zymo Research). ChIP-seq: HeLa Flp-In and derivative cell lines stably expressing enDR3-mEGFP and nb-enDR3-mEGFP were seeded on 100 mm dishes and treated with tetracycline at 25 ng/mL or 38 ng/mL, respectively. After 24 hours, cells were detached with trypsin and counted using hemocytometer. Then, 1.2 x 107 cells were pelleted by centrifugation for 4 min at 300 x g. The culture medium was removed, and cells were washed twice with 5 mL of PBS. Following 4 min centrifugation at 300 x g, cell pellets were suspended in 0.8 mL of cell lysis buffer (10 mM Tris pH 8.0, 10 mM NaCl, 0.1% IGEPAL CA-630) supplemented with protease inhibitors cocktail, 1 mM PMSF, and 40 U/mL RiboLock (RL) RNase Inhibitor (Thermo Fisher Scientific), and incubated on ice for 15 min with gentle inverting every 3 min. Then samples were centrifuged at 700 x g for 5min at 4°C. Supernatants were removed and cell nuclei were lysed with 1.1 mL of nuclei lysis solution (20 mM Hepes pH 7.4, 1 mM EDTA, 100 mM NaCl, 5 % glycerol, 0.5 % Triton X-100, 0.1% SDS) supplemented with protease inhibitors cocktail, 1 mM PMSF, and 40 U/mL RL. Nuclei lysates were transferred into milliTUBE AFA Fiber (Covaris) and sonicated using S220 Focused-ultrasonicator (Covaris) for 8 min at a Peak Power of 150 Watt, 10% Duty Factor and 200 cycles per burst. Chromatin shearing efficiency was examined by running 800 ng of DNA per well on 1.5 % agarose gel in 1X TAE at 70-80 V. Sonicated samples were transferred from milliTubes to 1.5 mL DNA LoBind tubes (Eppendorf) and centrifuged for 10 min at 20 000 x g at 4°C. Supernatants (hereafter inputs) were transferred to fresh LoBind tubes, and protein concentration was estimated by the Bradford method. For NGS and qPCR analyses, 65 µL (7.5 %) of the input fraction was collected, and 40 µL (4.5%) for the western blot analysis. For immunoprecipitation, 1 mg of input was added to 60 µL GFP-trap magnetic beads (homemade) and incubated with gentle rotation overnight at 4°C. The beads were captured using a magnetic stand, washed three times with 500 µL of low salt washing buffer I (20 mM Tris pH 8, 2 mM EDTA, 150 mM NaCl, 0.5% Triton X-100, 0.1% SDS) supplemented with 1X protease inhibitors cocktail. Next, beads were washed three times with 500uL of high salt washing buffer II (20 mM Tris pH 8, 2 mM EDTA, 500 mM NaCl, 0.5% Triton X-100, 0.1% SDS) with 1X protease inhibitors cocktail, and once with 500uL of washing buffer III (10 mM Tris pH 8, 1 mM EDTA, 250 mM LiCl, 1% IGEPAL CA-630, 1% Sodium deoxycholate) without inhibitors. Afterward, beads were washed twice with 500 µL of TE buffer (10 mM Tris pH 8, 1 mM EDTA), and 85 µl of the elution buffer (50 mM Tris pH 8, 50 mM NaHCO3, 1% SDS) was added and incubated for 15 min at 65°C with shaking (the 30s ON, 700 rpm/ 2 min OFF). Eluate (E1) was collected and transferred into a fresh 1.5 mL DNA LoBind tube. The elution step was repeated by adding 85 µl of fresh elution buffer, and the second eluate (E2) was pooled with E1. 20 µL of IPed fraction was collected for western blot analysis. Simultaneously, 85 µL elution buffer was added to the 65 µL of the input fractions and incubated for 15 min at 65°C with shaking (30s ON, 700rpm/2 min OFF). Next, 300 mM sodium chloride and 1 µl of RNase A (10 mg/mL) were added to each input and IPed sample and incubated for 45 min at 37°C in ThermoMixer (the 30s ON, 700 rpm/2 min OFF). Then the Proteinase K at a final concentration of 0.4 mg/ml was added, and the reaction was incubated at 55°C for one hour in ThermoMixer (the 30s ON, 1200 rpm/2 min OFF). DNA was purified using Zymo ChIP DNA clean & concentrator (Zymo Research) according to the manufacturer's protocol. The quality of the ChIP procedure was verified by qPCR.
For DRIPc-seq, purified RNA was used for stranded NGS library preparation using KAPA RNA HyperPrep Kit (Kapa Biosystems) according to the manufacturer's protocol. For ChIP-seq, purified DNA was used directly for NGS library preparation using KAPA RNA HyperPrep Kit (Kapa Biosystems) according to the manufacturer's protocol starting with the second DNA strand synthesis.

treatment_protocol: No treatment

value: Cervical cancer

value: HeLa Flp-In T-Rex

value: Epithelial cells

tag: antibody

value: FLAG


title: patterned induced neurons, C1C1a_B11-1, Pan troglodytes, 4N, 30minKCl, piN_Rep1

description:
Library name: C1C1a_B11-1_30minKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: HeLa, enDR3-FLAG IP, replicate 4

description:
Library name: HeLa_enDR3_DRIPc_rep4
DRIPc-seq


title: HeLa, nb-enDR3-FLAG IP, replicate 2

description:
Library name: HeLa_nb-enDR3_DRIPc_rep2
DRIPc-seq


title: NGS4790 BP043201 NCI-H2369 G03498025-1uM

description: Library name: NGS4790_R9111_LIB5467366_SAM24428341

value: Lung


title: HeLa, enDR3-FLAG IP, replicate 3

description:
Library name: HeLa_enDR3_DRIPc_rep3
DRIPc-seq


title: HeLa enDR3, RNA-seq, replicate 2

description:
Library name: HeLa_enDR3_Rep_2
RNA-seq

data_processing:
Raw sequencing reads were mapped to human genome reference assembly GRCh38/hg38 using STAR (version 2.7.10a) in the paired-end mode and counted using featureCounts from the Subread package (v1.6.4). Duplicate reads were removed. DESeq2 (v1.24.0) R package was used to obtain differentially expressed genes. bigWig signal files (counts per million normalized) were generated using deeptools (version 3.5.1). Duplicate reads were removed.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Total cellular RNA was isolated using TRI Reagent (Sigma). DNA contamination was removed by digestion with TURBO DNase (Thermo Scientific). The RNA was then purified by phenol:chloroform extraction, precipitated with ethanol, suspended in water, and measured in a NanoDrop ND2000 spectrophotometer (Thermo Scientific). A total of 2 mg of purified total RNA was ribodepleted in cytoplasmic rRNA using the Ribo-Zero rRNA Removal Kit (Illumina) according to the manufacturer’s instructions.
The KAPA RNA HyperPrep Kit (Kapa Biosciences) was used to prepare the strand-specific libraries according to the manufacturer’s instructions. To estimate the number of cycles for library amplification, the KAPA Library Quantification Kit (Kapa Biosciences) was used according to the manufacturer’s instructions. The final amplification products (cDNA libraries), in addition to purification with the KAPA RNA HyperPrep Kit, were purified from short fragments on AMPure XP (Beckman Coulter) and then analyzed on the 2100 Bioanalyzer using the High Sensitivity DNA Kit (Agilent). cDNA libraries were prepared in three biological replicates.

value: enDR3-mEGFP-expressing cells


title: patterned induced neurons, C1C1a_A11, Pan troglodytes, 4N, minusKCl, piN_Rep1

description:
Library name: C1C1a_A11_minusKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw

value: N


title: patterned induced neurons, C1C1a_A11, Pan troglodytes, 4N, 30minKCl, piN_Rep1

description:
Library name: C1C1a_A11_30minKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: HeLa, RNA-seq, replicate 3

description:
Library name: HeLa_Rep_3
RNA-seq


title: HeLa enDR3, RNA-seq, replicate 1

description:
Library name: HeLa_enDR3_Rep_1
RNA-seq


title: patterned induced neurons, C1C1a_B11-1, Pan troglodytes, 4N, 2hrKCl, piN_Rep1

description:
Library name: C1C1a_B11-1_2hrKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: NGS4790 BP043201 NCI-H2369 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467374_SAM24428349


title: NGS4790 BP043201 VMRC-LCD G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467355_SAM24428330

value: VMRC-LCD


title: HeLa, RNA-seq, replicate 1

description:
Library name: HeLa_Rep_1
RNA-seq


title: patterned induced neurons, C1C1a_A11, Pan troglodytes, 4N, 2hrKCl, piN_Rep1

description:
Library name: C1C1a_A11_2hrKCl
piN_consensus_ATACseq_peaks.hg38.bed
piN_background_mismapping.hg38.bw


title: HeLa, RNA-seq, replicate 2

description:
Library name: HeLa_Rep_2
RNA-seq


title: NGS4790 BP043201 NCI-H2803 G03498025-0.1uM

description: Library name: NGS4790_R9111_LIB5467352_SAM24428327