title: tbk1_updown_1

description:
Library name: TBK1-24
Amplicon-seq of cDNA amplified from primers TBK1_2_2F and TBK1_2_4R

data_processing:
Amplicon-sequencing: Resulting sequences were then mapped to the hg38 reference genome with ENSEMBL GRCH38.95 reference annotations using STAR (Dobin et al. 2013) with default parameters and cryptic exon usage was confirmed using visualization of read coverage and junction reads across the region.
RNA-seq following ASO treatment: Samples were analyzed as described in (Khokhar et al. 2025). Briefly, samples were PEAR-procssed (Zhang et al. 2014), subsampled to 10.7M single reads with seqtk (Li 2018), and mapped using STAR with parameters specified in (Khokhar et al. 2025). Cryptic splice sites were identified CRYPTID-SS as described in (Khokhar et al. 2025) and cryptic exons were identified with CRYPTID-exon
Targeted-RNA sequencing: Samples were analyzed as described in (Khokhar et al. 2025). Briefly, samples were PEAR-procssed (Zhang et al. 2014), subsampled to 112M single reads with seqtk (Li 2018), mapped using STAR with parameters specified in (Khokhar et al. 2025). Kallisto (Bray et al. 2016) was used to estimate gene expression levels in the target-enriched samples and confirm enrichment relative to whole nuclear RNA. Samples were analyzed with CRYPTID-ss to obtain high-confidence cryptic splice sites and processed with CRYPTID-exon to predict exons associated with the detected cryptic splice sites. Exons from the sites with the highest usage were chosen for downstream experimentation following visual inspection of the region and validation by amplicon sequencing.
Assembly: Grch38
Supplementary files format and content: SJ.out.tab files containing splice junctions detected from STAR

growth_protocol: K562 cells were grown in IMDM supplemented with 10% FBS. KNS60 cells were grown in DMEM supplemented with 5% FBS. All cell lines were maintained at 37°C and 5% CO2 until 70% confluent.

extract_protocol:
Amplicon sequencing: Total RNA was extracted from whole cells; For RNA-seq following ASO treatment and Targeted-RNA sequencing: Nuclear RNA was extracted from KNS60 cells as described in (Khokhar etal., 2025)
Amplicon sequencing: PCR amplification was performed using Phire Hot Start II PCR Master Mix (Thermofisher, F126) with a 55°C annealing temperature, 15 second extension time, and 40 cycles. Completed reactions were run on 1% agarose gel. Selected amplicons were sent to Genewiz from Azenta Life Sciences for Amplicon-EZ Next-Generation Sequencing and sequenced on a MiSeq platform in 500-cycle paired-end format.
For RNA-seq following ASO treatment and Targeted-RNA sequencing:
Reverse transcription of nuclear RNA from KNS60 cells isolated as described in (Khokhar et al. 2025) was performed using the High-Capacity cDNA Reverse Transcription Kit (Thermofisher, 4368814) according to manufacturer specifications. Single-stranded cDNA was treated with alkaline hydrolysis buffer (150mM NaOH, 1mM EDTA) to degrade any remaining RNA template. 10X TE buffer, pH 7.4 treatment for 10 minute incubation at 50°C was used to neutralize the hydrolysis reaction. cDNA was purified and buffer-exchanged into 1X TE buffer using 3K MWCO Amicon cartridges. The purified cDNA was added to 1 Unit of SUPERase IN RNase Inhibitor per 100ng cDNA (Invitrogen, AM2696), 1pmol biotinylated probe mix per 16ng cDNA, and 200uL per 400ng cDNA of hybridization/wash buffer (40mM Tris-HCl, 300mM NaCl, 0.2% Tween 20 (w/v), 1% SDS) and the sample was incubated at 60°C for 20 minutes with regular agitation. 500ug of magnetic streptavidin beads (Pierce, 88816) per 400ng of cDNA were added to the reaction and the reaction was again incubated at 60°C for 20 minutes with regular agitation. Following incubation, the beads were immobilized and washed 3x with hybridization/wash buffer. Alkaline hydrolysis buffer was added to destroy the RNA probes and release the enriched cDNA transcripts. 10X TE buffer was used to neutralize the hydrolysis reaction and samples were buffer exchanged into 1X TE using 3K MWCO Amicon cartridges. Samples were purified using ethanol precipitation (2.67X volumes of 100% EtOH and 0.1X volumes 3M sodium acetate).
Second-strand synthesis and library preparation. DNA Polymerase I (E. coli) was used to generate second-strand cDNA from the enriched, single-stranded cDNA. The following reagents were combined: 10X NEBuffer 2, 25mM dNTPs, 10X random primers, DNA polymerase I (NEB, M0209), and water for a total reaction volume of 50uL. The reaction was incubated at 95°C for 60 seconds, 16°C for 4 hours, and 37°C for 1 hour. Second-strand cDNA was ethanol precipitated (2.67X volumes of 100% EtOH and 0.1X volumes 3M sodium acetate).
For RNA-seq following ASO treatment Libraries were prepared using the NEBNext Ultra II FS DNA Library Prep Kit for Illumina,  inputs <100ng (NEB, E7805) according to manufacturer’s instructions. Libraries were sequenced as 2x100 reads on a NextSeq 2000 using NextSeq 1000/2000 P2 Reagents (200 cycles) v3 (Illumina, 20046812).
For Targeted-RNA sequencing: Library preparation was performed using NEBNext Ultra II FS Library Prep Kit. Libraries were sequenced on a NextSeq2000 using 2x100 reads.

treatment_protocol: Cells for targeted-RNA sequencing and amplicon sequencing were untreated.  RNA-seq following ASO treatment: Single ASO transfections in KNS60 cells were performed with Lipofectamine RNAiMAX (Invitrogen, 13778150) with ASOs against their respective targets at a final concentration of 80nM (from an ASO stock concentration of 20uM). The stock ASO concentration:lipid ratio was 4:3. Reagents were combined in Opti-MEM and introduced to cells 24 hours after plating and incubated at 37°C and 5% CO2 for 24 hours.

value: glioblastoma

value: untreated


title: m4-Sham2

status: Public on Feb 26 2026

type: SRA

city: Chongqing

first: Dabin

last: Wu

address: No.1 Medical College Road, Yuzhong District, Chongqing

country: China

institute: Chongqing medical university

description:
Library name: Sample17
m4_Sham2:fpkm

library_source: transcriptomic

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp(0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis.
Assembly: mm10
Supplementary files format and content: csv files include FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific).
Three micrograms of RNA were used as input material for the RNA sample preparations. Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA).

tag: tissue

value: Lung

tag: genotype

value: WT

tag: treatment

value: Irradiation

tag: batch


title: ATAC-seq 20230825_nih3t3_cas9_atmi_ZSWIM3_MIRIN200MM_rep1

city: Haidian District

first: Jiawei

last: Yu

state: Beijing

address: Tsinghua  University

department: School of Pharmaceutical Sciences

institute: Tsinghua University

description:
Library name: 20230825_nih3t3_cas9_atmi_ZSWIM3_MIRIN200MM_rep1
ATAC-seq sample ZSWIM3_MIRIN200MM_rep1

library_source: genomic

data_processing:
ATAC-seq read adaptors were trimmed using cutadapt (version 3.4).
Trimmed reads were aligned to hg38 (human) or mm10 (mouse) using bowtie2 (version 2.4.4) with parameters -X2000 --mm -t -q -N1 -L 25 --no-mixed --no-discordant.
Aligned reads were filtered using samtools (version 1.13) to exclude unmapped reads, unmapped mates, non-primary alignments, vendor/quality-fail reads, and duplicates (SAM flag 1804).
Standard samtools sort and fixmate operations were applied. PCR duplicates were removed using picard MarkDuplicates (version 2.20.4), followed by samtools view filtering (-F1804 -f2). ENCODE blacklist regions were removed in the final alignment set.
For uploaded processed bigWig files, bamCoverage was used with -p 8 --normalizeUsing RPKM --binSize 100.
Assembly: mm10/hg38
Supplementary files format and content: ATAC-seq coverage bigWig

molecule: genomic DNA

extract_protocol:
Cells were collected and washed with ice-cold PBS. Cell pellets were resuspended in ATAC-seq RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% IGEPAL-630, 0.1% Tween-20, and 0.01% digitonin, and incubated on ice for 10 minutes. ATAC-seq RSB containing 0.1% Tween-20 (without IGEPAL-630 or digitonin) was then added for washing. Nuclei were pelleted in a pre-chilled centrifuge. Nuclei were incubated with Tn5 transposase and tagmentation buffer at 37°C for 30 minutes. Stop buffer and Proteinase K were added, and samples were incubated at 55°C for 30 minutes to terminate tagmentation and remove proteins.
PCR was performed to amplify the ATAC library for 5 cycles using KAPA HiFi PCR kit. To determine additional amplification cycles for each sample, qPCR was performed, and the additional cycle number was determined as the cycle reaching one-third of maximal abundance in the qPCR amplification curve. All samples were then amplified for another N+3 cycles, followed by final extension. Libraries were purified with DNA clean beads and sequenced as paired-end libraries on Illumina platforms.

tag: cell line


title: ATAC-seq 20230825_nih3t3_cas9_atmi_ZSWIM3_MIRIN25MM_rep1

description:
Library name: 20230825_nih3t3_cas9_atmi_ZSWIM3_MIRIN25MM_rep1
ATAC-seq sample ZSWIM3_MIRIN25MM_rep1


title: chip_h4k16ac_wt_rep2

city: Planegg-Martinsried

first: Fotios

last: Gkountromichos

address: Großhaderner Strasse 9

department: Molecular Biology

country: Germany

institute: Biomedical Center, Ludwig-Maximilians-Universität München

description: Library name: chip_h4k16ac_wt_rep2

data_processing:
Paired-end CUT&RUN and ChIP-MNase sequencing reads were aligned to the Drosophila melanogaster dm6 reference genome (UCSC) using Bowtie2 (v2.2.9, --local --very-sensitive-local --no-unal --no-mixed --no-discordant)( Maximum fragment sizes were set to 700 bp for CUT&RUN and 1000 bp for ChIP-MNase to accommodate the distinct fragment size distributions of each method. SAM files were converted to BAM format retaining high-quality alignments (samtools v1.22.1, samtools view -q 2), name-sorted, and converted to BED format using BEDtools (v2.31.1) bamToBed to extract fragment coordinates. CUT&RUN data were normalized to total read counts. Scaling factors were calculated as 106 divided by the total number of filtered reads per sample (excluding secondary, supplementary, and unmapped reads, and reads with mapping quality < 30). Normalized coverage tracks were generated using deepTools2 (v3.5.0) bamCoverage at 10 bp resolution with target-specific smoothing (20 bp for MSL2/PPI; 80 bp for H4K16ac/IgG). Pairwise target-to-control comparisons were computed using bamCompare to generate ratio tracks with a pseudocount of 1. Pre-immune serum (PPI) and rabbit IgG were used as negative controls for the targets MSL2 and H4K16ac respectively. For ChIP-MNase data, spike-in normalization was performed using reads aligned to the Drosophila virilis droVir3 genome. Scaling factors were calculated as 106 divided by the spike-in read count for each sample. Normalized to Input coverage tracks were generated using BEDtools (v2.31.1) genomecov and converted to bigWig format using bedGraphToBigWig (UCSC utilities, 3.4.1).
Assembly: Drosophila melanogaster dm6
Supplementary files format and content: Normalized coverage tracks in bigwig format.

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: Drosophila melanogaster S2 cells  were cultured at 26 °C in Schneider’s medium supplemented with 10% FBS and 1% Penicillin-Streptomycin.

extract_protocol:
ChIP-seq on MNase-digested chromatin and sonicated chromatin was performed as previously described in (Albig et al., 2019) and (Jayakrishnan et al., 2025).
Libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645). Strand-specific RNA-seq libraries were prepared from 100 ng of DNase-treated total RNA using the QIAseq FastSelect RNA Library Kit (Qiagen, Cat. No. 334302).

treatment_protocol: Stable transgenic lines expressing roX variants were generated by transfection of roX2 knock out S2 cells (KO-B) using Effectene transfection reagent (Qiagen, Cat. No. 301425) according to the manufacturer. Cells were maintained under blasticidin selection and monitored for transgene expression for 3–4 weeks, then taken out of selection and passaged several times before use in experiments.

value: S2 cells

value: wild-type


title: ATAC-seq 20230825_nih3t3_cas9_atmi_ZSWIM3_DMSO_rep1

description:
Library name: 20230825_nih3t3_cas9_atmi_ZSWIM3_DMSO_rep1
ATAC-seq sample ZSWIM3_DMSO_rep1


title: m2-Sham3

description:
Library name: Sample12
m2_Sham3:fpkm


title: ATAC-seq 20230825_nih3t3_cas9_atmi_TYR_MIRIN25MM_rep3

description:
Library name: 20230825_nih3t3_cas9_atmi_TYR_MIRIN25MM_rep3
ATAC-seq sample TYR_MIRIN25MM_rep3


title: ATAC-seq 20230825_nih3t3_cas9_atmi_ZSWIM3_DMSO_rep2

description:
Library name: 20230825_nih3t3_cas9_atmi_ZSWIM3_DMSO_rep2
ATAC-seq sample ZSWIM3_DMSO_rep2


title: ATAC-seq 20230825_nih3t3_cas9_atmi_TYR_MIRIN25MM_rep1

description:
Library name: 20230825_nih3t3_cas9_atmi_TYR_MIRIN25MM_rep1
ATAC-seq sample TYR_MIRIN25MM_rep1


title: tbk1_exondown_2

city: Worcester

first: Athma

middle: A

last: pai

state: MA

address: 55 Lake Avenue North

department: RNA Therapeutics Institute

country: USA

institute: UMass Chan Medical School

description:
Library name: TBK1-2-4
Amplicon-seq of cDNA amplified from primers TBK1_2_4F and TBK1_2_4R

organism: Homo sapiens

tag: cell type


title: tbk1_exondown_1

description:
Library name: TBK1-2-3
Amplicon-seq of cDNA amplified from primers TBK1_2_3F and TBK1_2_3R


title: ATAC-seq 20230825_nih3t3_cas9_atmi_ZSWIM3_DMSO_rep3

description:
Library name: 20230825_nih3t3_cas9_atmi_ZSWIM3_DMSO_rep3
ATAC-seq sample ZSWIM3_DMSO_rep3


title: ATAC-seq 20230825_nih3t3_cas9_atmi_TYR_MIRIN200MM_rep2

description:
Library name: 20230825_nih3t3_cas9_atmi_TYR_MIRIN200MM_rep2
ATAC-seq sample TYR_MIRIN200MM_rep2


title: m2-Sham1

description:
Library name: Sample10
m2_Sham1:fpkm


title: ATAC-seq 20230825_nih3t3_cas9_atmi_TYR_MIRIN200MM_rep3

description:
Library name: 20230825_nih3t3_cas9_atmi_TYR_MIRIN200MM_rep3
ATAC-seq sample TYR_MIRIN200MM_rep3


title: m2-Sham2

description:
Library name: Sample11
m2_Sham2:fpkm


title: pum1_updown_2

description:
Library name: PUM1-23
Amplicon-seq of cDNA amplified from primers PUM1_2_2F and PUM1_2_3R


title: ATAC-seq 20230825_nih3t3_cas9_atmi_TYR_MIRIN200MM_rep1

description:
Library name: 20230825_nih3t3_cas9_atmi_TYR_MIRIN200MM_rep1
ATAC-seq sample TYR_MIRIN200MM_rep1


title: ATAC-seq 20230825_nih3t3_cas9_atmi_TYR_DMSO_rep2

description:
Library name: 20230825_nih3t3_cas9_atmi_TYR_DMSO_rep2
ATAC-seq sample TYR_DMSO_rep2


title: ATAC-seq 20230825_nih3t3_cas9_atmi_TYR_MIRIN25MM_rep2

description:
Library name: 20230825_nih3t3_cas9_atmi_TYR_MIRIN25MM_rep2
ATAC-seq sample TYR_MIRIN25MM_rep2


title: m2-RT3

description:
Library name: Sample9
m2_RT3:fpkm


title: pum1_upexon_1

description:
Library name: PUM1-2-1
Amplicon-seq of cDNA amplified from primers PUM1_2_1F and PUM1_2_1R


title: ATAC-seq 20230825_nih3t3_cas9_atmi_EMX1_MIRIN25MM_rep3

description:
Library name: 20230825_nih3t3_cas9_atmi_EMX1_MIRIN25MM_rep3
ATAC-seq sample EMX1_MIRIN25MM_rep3


title: m2-RT1

description:
Library name: Sample7
m2_RT1:fpkm


title: ATAC-seq 20230825_nih3t3_cas9_atmi_TYR_DMSO_rep3

description:
Library name: 20230825_nih3t3_cas9_atmi_TYR_DMSO_rep3
ATAC-seq sample TYR_DMSO_rep3


title: m2-RT2

description:
Library name: Sample8
m2_RT2:fpkm


title: ATAC-seq 20230825_nih3t3_cas9_atmi_EMX1_MIRIN25MM_rep1

description:
Library name: 20230825_nih3t3_cas9_atmi_EMX1_MIRIN25MM_rep1
ATAC-seq sample EMX1_MIRIN25MM_rep1


title: m1-Sham3

description:
Library name: Sample6
m1_Sham3:fpkm


title: pik3c3_upexon_1

description:
Library name: PIK3C3-1
Amplicon-seq of cDNA amplified from primers PIK3C3_1F and PIK3C3_1R

value: chronic myeloid leukemia


title: ATAC-seq 20230825_nih3t3_cas9_atmi_EMX1_MIRIN200MM_rep1

description:
Library name: 20230825_nih3t3_cas9_atmi_EMX1_MIRIN200MM_rep1
ATAC-seq sample EMX1_MIRIN200MM_rep1


title: ATAC-seq 20230825_nih3t3_cas9_atmi_EMX1_MIRIN25MM_rep2

description:
Library name: 20230825_nih3t3_cas9_atmi_EMX1_MIRIN25MM_rep2
ATAC-seq sample EMX1_MIRIN25MM_rep2


title: pik3c3_upexon_2

description:
Library name: PIK3C3-2
Amplicon-seq of cDNA amplified from primers PIK3C3_2F and PIK3C3_2R


title: pum1_exondown_1

description:
Library name: PUM1-2-4
Amplicon-seq of cDNA amplified from primers PUM1_2_4F and PUM1_2_4R


title: ATAC-seq 20230825_nih3t3_cas9_atmi_EMX1_MIRIN200MM_rep2

description:
Library name: 20230825_nih3t3_cas9_atmi_EMX1_MIRIN200MM_rep2
ATAC-seq sample EMX1_MIRIN200MM_rep2


title: ATAC-seq 20230825_nih3t3_cas9_atmi_TYR_DMSO_rep1

description:
Library name: 20230825_nih3t3_cas9_atmi_TYR_DMSO_rep1
ATAC-seq sample TYR_DMSO_rep1


title: nf1_exondown_1

description:
Library name: NF1-3-4
Amplicon-seq of cDNA amplified from primers NF1_1_3F and NF1_3_4R


title: m1-Sham1

description:
Library name: Sample4
m1_Sham1:fpkm


title: ATAC-seq 20230825_nih3t3_cas9_atmi_EMX1_DMSO_rep3

description:
Library name: 20230825_nih3t3_cas9_atmi_EMX1_DMSO_rep3
ATAC-seq sample EMX1_DMSO_rep3


title: ATAC-seq 20230825_nih3t3_cas9_atmi_EMX1_DMSO_rep1

description:
Library name: 20230825_nih3t3_cas9_atmi_EMX1_DMSO_rep1
ATAC-seq sample EMX1_DMSO_rep1


title: ATAC-seq 20230825_nih3t3_cas9_atmi_EMX1_DMSO_rep2

description:
Library name: 20230825_nih3t3_cas9_atmi_EMX1_DMSO_rep2
ATAC-seq sample EMX1_DMSO_rep2


title: nf1_upexon_1

description:
Library name: NF1-3-2
Amplicon-seq of cDNA amplified from primers NF1_3_2F and NF1_3_2R


title: m1-Sham2

description:
Library name: Sample5
m1_Sham2:fpkm


title: ATAC-seq 20230315_nih3t3_be_ZSWIM3_rep2

description:
Library name: 20230315_nih3t3_be_ZSWIM3_rep2
ATAC-seq sample ZSWIM3_rep2


title: pum1_updown_1

description:
Library name: PUM1-14
Amplicon-seq of cDNA amplified from primers PUM1_2_1F and PUM1_2_4R


title: ATAC-seq 20230315_nih3t3_be_ZSWIM3_rep3

description:
Library name: 20230315_nih3t3_be_ZSWIM3_rep3
ATAC-seq sample ZSWIM3_rep3


title: ATAC-seq 20230825_nih3t3_cas9_atmi_EMX1_MIRIN200MM_rep3

description:
Library name: 20230825_nih3t3_cas9_atmi_EMX1_MIRIN200MM_rep3
ATAC-seq sample EMX1_MIRIN200MM_rep3


title: ATAC-seq 20230315_nih3t3_be_EMX1_rep3

description:
Library name: 20230315_nih3t3_be_EMX1_rep3
ATAC-seq sample EMX1_rep3


title: ATAC-seq 20230315_nih3t3_be_ZSWIM3_rep1

description:
Library name: 20230315_nih3t3_be_ZSWIM3_rep1
ATAC-seq sample ZSWIM3_rep1


title: golga8a_exondown_1

description:
Library name: GOLGA8A-4
Amplicon-seq of cDNA amplified from primers GOLGA8A_4F and GOLGA8A_4R


title: nf1_updown_1

description:
Library name: NF1-23
Amplicon-seq of cDNA amplified from primers NF1_2_2F and NF1_3_3R


title: ATAC-seq 20230315_nih3t3_be_EMX1_rep2

description:
Library name: 20230315_nih3t3_be_EMX1_rep2
ATAC-seq sample EMX1_rep2


title: m1-RT2

description:
Library name: Sample2
m1_RT2:fpkm


title: m1-RT3

description:
Library name: Sample3
m1_RT3:fpkm


title: ATAC-seq 20210727_mesc_se_SALL4_rep1

description:
Library name: 20210727_mesc_se_SALL4_rep1
ATAC-seq sample SALL4_rep1

source_name: mESC

value: mESC


title: ATAC-seq 20210727_mesc_se_ZFP42_rep2

description:
Library name: 20210727_mesc_se_ZFP42_rep2
ATAC-seq sample ZFP42_rep2


title: Muscle stem cells, WT, rep2

city: Los Angeles

first: Jengmin

last: Kang

state: CA

address: 615 Charles E Young Dr S

institute: University of California, Los Angeles

data_processing:
Raw reads were pre-processed with Trim Galore (v0.4.2) to remove adapters and improve the quality of the reads.
Trimmed reads were then aligned to the mouse GRCm39 genome using STAR aligner, and Subread package (v1.5.1) with featurecounts module was used to generate raw count reads mapped on exonic regions.
Raw counts analysis was done using RStudio software (v4.0.4).
Assembly: mm9
Supplementary files format and content: Count data

source_name: Muscle

extract_protocol:
RNA was extracted from MuSCs using a miRNeasy kit (Qiagen; # 217084) according to the manufacturer’s protocol.
The Smarter Ultra Low Input V4 RNAseq kit (Takara Bio; # 634848) was used to generate cDNA from 2 ng of total RNA. Amplified cDNA was purified using SPRI Ampure Beads (Beckman Coulter; # A63880). The quality and quantity of cDNA were assessed using a High Sensitivity DNA chip on an Agilent 2100 Bioanalyzer. Illumina Nextra-XT kit (# FC-131-1024) was used to generate libraries from 150 pg of amplified cDNA.

treatment_protocol: The inducible CreER recombinase system was activated by injecting Tamoxifen (Sigma-Aldrich; # T5648) at a dose of 20 mg/mL in corn oil. Mice received 2 mg Tamoxifen intraperitoneally daily for five consecutive days.

value: Muscle

value: Primary cell


title: Muscle stem cells, NDRG1 cKO, rep1

value: NDRG1 cKO


title: Muscle stem cells, NDRG1 cKO, rep2


title: hiPSCshBRD2L7

city: Fort Worth

first: Kejin

last: Hu

state: TX

address: 3400 Camp Bowie Boulevard

department: Microbiology, Immunology and Genetics

institute: UNT Health Science Center

description:
Library name: hiPSCL7
allSamples_NormalizedCounts.xlsx
ESC_BJ_iPSC_normalizedCounts.xlsx

data_processing:
Original image data file from high-throughput sequencing (Illumina) is transformed into sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
The human reference genome (assembly GRCH38, release 114) was indexed  using STAR (STAR version 2.7.11b) (runMode  genomeGenerate) on Cheaha supercomputer, and the read fragments of each FASTQ file was aligned to human reference genome using the STAR aligner (version 2.7.11b).
The BAM files were sorted and indexed using SAMtools (version 1.12), and the counting was achieved using FeatureCounts in bioocontainer on Texas Advanced Computing Center (TACC).
The statistics and normalization of the RNA-seq were conducted using the DESeq2 software (version 1.48.1) on a Dell PC.
Assembly: GRCH38, release 113
Supplementary files format and content: normalized read counts in Excel xlsx
Supplementary files format and content: allSamples_NormalizedCounts.xlsx

molecule: polyA RNA

source_name: male

growth_protocol: Human iPS cells were cultured in standard feeder-free and serum-free chemically defined E8 media. Human fibroblast BJ cells were cultured in fibroblast media: DMEM/F12 media supplemented with 10% FBS and 5 ng/mL human bFGF

extract_protocol:
BJ fibroblast cells (ATCC, CRL-2522, foreskin fibroblasts) were cultured in six well plates at a density of 2 00000 cells per well. At 24 hrs post seeding, the medium was removed and 2 mL fresh medium containing polybrene (final concentration = 5 µg/mL) was added to the wells. The viruse preparations were then added into respective wells (day 0). At 18 hrs after virus addition, the virus-containing spent media were removed, and fresh fibroblast medium was added. At 72 hrs (or indicated times) after virus removal (on Day 4), the spent medium was removed and 1 mL of TRIzol (Invitrogen; Cat no. 15596018) was added directly to each well. RNA was extracted following manufacturer’s protocol. After extraction, the RNA was further purified using Quick RNA Miniprep kit (Zymo Research; Cat. no. R1055) using manufacturer’s protocol.   RNA for the nontreated BJ was extracted the same way but without virus transduction. RNA from humna iPSCs or ESCs was prepared using the same kits. Human PSCs were grown in E8 medium
Briefly, mRNA from BJ or human PSCs is purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA is first fragmented randomly by the addition of fragmentation buffer. The Novogene ENB library protocol was used as briefed below (from Novogene). ENB library: Then first strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization (1). In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads.

treatment_protocol: Human fibroblasts BJ were transduced with lentiviral preparation of the indicated genes, shRNA, CRISPR KO constructs or BRD2 mutants (MOI, OCT4, 8; SOX2, 5, KLF4, 5; and all others are 3). At 18 hours post transduction, virus-containing spent media were removed and RNAs were extracted 72 hours (or as indicated) after virus removal using extraction protocols described.

value: male

value: iPSCs

value: NO


title: ATAC-seq 20210727_mesc_se_ZFP42_rep1

description:
Library name: 20210727_mesc_se_ZFP42_rep1
ATAC-seq sample ZFP42_rep1


title: hESH1

description:
Library name: hESH1
allSamples_NormalizedCounts.xlsx
ESC_BJ_iPSC_normalizedCounts.xlsx

value: embyronic stem cells


title: ATAC-seq 20210727_mesc_se_SALL4_rep2

description:
Library name: 20210727_mesc_se_SALL4_rep2
ATAC-seq sample SALL4_rep2


title: ATAC-seq 20230315_nih3t3_be_EMX1_rep1

description:
Library name: 20230315_nih3t3_be_EMX1_rep1
ATAC-seq sample EMX1_rep1


title: golga8a_upexon_1

description:
Library name: GOLGA8A-1
Amplicon-seq of cDNA amplified from primers GOLGA8A_1F and GOLGA8A_1R


title: golga8a_updown_1

description:
Library name: GOLGA8A-23
Amplicon-seq of cDNA amplified from primers GOLGA8A_2F and GOLGA8A_3R


title: ATAC-seq 20210727_mesc_se_ZFP42_rep3

description:
Library name: 20210727_mesc_se_ZFP42_rep3
ATAC-seq sample ZFP42_rep3


title: hiPSCshBRD2L6

description:
Library name: hiPSCshBRD2L6
allSamples_NormalizedCounts.xlsx
ESC_BJ_iPSC_normalizedCounts.xlsx


title: hESH9

description:
Library name: hESH9
allSamples_NormalizedCounts.xlsx
ESC_BJ_iPSC_normalizedCounts.xlsx

source_name: female

value: female


title: ATAC-seq 20210727_mesc_se_SOX2_rep2

description:
Library name: 20210727_mesc_se_SOX2_rep2
ATAC-seq sample SOX2_rep2


title: ATAC-seq 20210727_mesc_se_POU5F1SE_rep2

description:
Library name: 20210727_mesc_se_POU5F1SE_rep2
ATAC-seq sample POU5F1SE_rep2


title: ATAC-seq 20210727_mesc_se_POU5F1SE_rep3

description:
Library name: 20210727_mesc_se_POU5F1SE_rep3
ATAC-seq sample POU5F1SE_rep3


title: ATAC-seq 20210727_mesc_se_SALL4_rep3

description:
Library name: 20210727_mesc_se_SALL4_rep3
ATAC-seq sample SALL4_rep3


title: m1-RT1

description:
Library name: Sample1
m1_RT1:fpkm


title: Muscle stem cells, WT, rep1


title: ATAC-seq 20210727_mesc_se_SOX2_rep3

description:
Library name: 20210727_mesc_se_SOX2_rep3
ATAC-seq sample SOX2_rep3


title: ATAC-seq 20210727_mesc_se_SOX2_rep1

description:
Library name: 20210727_mesc_se_SOX2_rep1
ATAC-seq sample SOX2_rep1


title: Sample 5_VDJ

city: Goteborg

first: Davide

last: Angeletti

address: Medicinaregatan 7a

country: Sweden

institute: University of Gothenburg

description: 10x genomics 5´ v2

library_source: transcriptomic single cell

data_processing:
Raw fastq files were processed through the 10x cellranger pipeline  with reference genome mm10.
Assembly: mm10
Supplementary files format and content: tab separated value files, matrix files and filtered contig files

source_name: infected lung-total CD4 TRM + infected nasal tissue-NP CD4 TRM VDJ

extract_protocol:
The sorted cells were pooled and washed in the Laminar Wash Mini system (Curiox Biosystems) before loading to Chromium Controller and using the Chromium Next GEM Single Cell 5´ Kit v2 (10x Genomics).
Libraries were created using the Library Construction Kit, 5´Feature Barcode Kit, Chromium Single Cell Mouse TCR Amplification Kit, Dual Index Kit TT Set A (PN-1000215) and Dual Index Kit TN Set A (PN-1000250) (10x Genomics) ).Their quality and quantity was assessed using the Agilent Tapestation system and the Qubit Fluorometer (Invitrogen), before being sent for sequencing to the SNP&SEQ Technology Platform, Science for Life Laboratory (Uppsala Biomedical Centre, Uppsala University, Sweden).

treatment_protocol: Mice were infected with Pr8 i.n. 50TCID50. at 30dpi,mice were injected with CD4 FITC (RM4-4) antibody intravenously to label the circulating CD4 T cells (referred as CD4 iv). The mice were completely anesthetized and the lung was perfused with 1X PBS. Nasal tissue and lungs were isolated, digested and processed.

value: lungs + nasal tissue

value: CD4+ TRM

tag: immunophenotype

value: CD4+CD44+CD62L-CD69+ total/HA+/NP+

tag: age

value: 8-12 weeks

tag: number of_mice

value: 5 naive + 25 infected pool

value: influenza A virus PR8 30dpi + naive

tag: hashtags

value: infected lung-total CD4 TRM (TotalSeq™-C0303 anti-mouse Hashtag 3); infected nasal tissue-NP+ CD4 TRM (TotalSeq™-C0305 anti-mouse Hashtag 5)


title: Sample 6_VDJ

description: 10x genomics 5´ v2

source_name: naive nasal tissue-CD4 neg + infected nasal tissue-CD4 neg + infected nasal tissue- NP CD4 TRM + infected nasal tissue- HA CD4 TRM  VDJ

value: nasal tissue

value: 2 naive + 19 infected pool

value: naive nasal tissue-CD4 neg (TotalSeq™-C0308 anti-mouse Hashtag 8); infected nasal tissue-CD4 neg (TotalSeq™-C0306 anti-mouse Hashtag 6 ); infected nasal tissue- NP+ CD4 TRM (TotalSeq™-C0303 anti-mouse Hashtag 3 + TotalSeq™-C0987 anti-APC); infected nasal tissue- HA+ CD4 TRM (TotalSeq™-C0303 anti-mouse Hashtag 3 )


title: Sample 4_VDJ

description: 10x genomics 5´ v2

source_name: infected lung-NP CD4 TRM + infected nasal tissue-total CD4 TRM VDJ

value: infected lung-NP+ CD4 TRM (TotalSeq™-C0303 anti-mouse Hashtag 3); infected nasal tissue-total CD4 TRM (TotalSeq™-C0305 anti-mouse Hashtag 5)


title: H9P69

description:
Library name: H9P69S2
allSamples_NormalizedCounts.xlsx
ESC_BJ_iPSC_normalizedCounts.xlsx

value: WT


title: ATAC-seq 20210727_mesc_se_POU5F1SE_rep1

description:
Library name: 20210727_mesc_se_POU5F1SE_rep1
ATAC-seq sample POU5F1SE_rep1

value: mESC


title: ATAC-seq 20210727_mesc_se_NANOGSE_rep2

description:
Library name: 20210727_mesc_se_NANOGSE_rep2
ATAC-seq sample NANOGSE_rep2


title: ATAC-seq 20210727_mesc_se_NANOGSE_rep1

description:
Library name: 20210727_mesc_se_NANOGSE_rep1
ATAC-seq sample NANOGSE_rep1


title: ATAC-seq 20210727_mesc_se_NANOGSE_rep3

description:
Library name: 20210727_mesc_se_NANOGSE_rep3
ATAC-seq sample NANOGSE_rep3


title: ATAC-seq 20210727_mesc_se_MYC_rep3

description:
Library name: 20210727_mesc_se_MYC_rep3
ATAC-seq sample MYC_rep3


title: BJ72hS3

description:
Library name: BJ72HS3
allSamples_NormalizedCounts.xlsx
ESC_BJ_iPSC_normalizedCounts.xlsx

value: male

value: BJ

value: foreskin fibroblast


title: Sample 3_VDJ

description: 10x genomics 5´ v2

source_name: infected lung HA CD4TRM+infected nasal tissue HA CD4 TRM+naive lung CD4 TRM+naive nasal tissue CD4 TRM VDJ

value: infected lung-HA+ CD4 TRM (TotalSeq™-C0303 anti-mouse Hashtag 3 ); infected nasal tissue-HA+ CD4 TRM (TotalSeq™-C0305 anti-mouse Hashtag 5); naive lung- total CD4 TRM (TotalSeq™-C0308 anti-mouse Hashtag 8); naive nasal tissue- total CD4 TRM ( TotalSeq™-C0309 anti-mouse Hashtag 9 )


title: ATAC-seq 20210727_mesc_se_MYC_rep2

description:
Library name: 20210727_mesc_se_MYC_rep2
ATAC-seq sample MYC_rep2


title: BJ48hS2

description:
Library name: BJ48hS2
allSamples_NormalizedCounts.xlsx
ESC_BJ_iPSC_normalizedCounts.xlsx

value: NO


title: Sample 1_VDJ

description: 10x genomics 5´ v2

source_name: infected lung HA CD4TRM+infected nasal tissue CD4 TRM+naive lung CD4 TRM+naive nasal tissue CD4 TRM VDJ

value: lungs + nasal tissue

value: CD4+ TRM

value: infected lung-HA+ CD4 TRM (TotalSeq™-C0306 anti-mouse Hashtag 6).  ; infected nasal tissue-HA+ CD4 TRM (TotalSeq™-C0307 anti-mouse Hashtag 7 );  naive lung- total CD4 TRM (TotalSeq™-C0308 anti-mouse Hashtag 8);  naive nasal tissue- total CD4 TRM ( TotalSeq™-C0309 anti-mouse Hashtag 9 )


title: BJ48hS3

description:
Library name: BJ48HS3
allSamples_NormalizedCounts.xlsx
ESC_BJ_iPSC_normalizedCounts.xlsx


title: ATAC-seq 20210727_mesc_se_MYC_rep1

description:
Library name: 20210727_mesc_se_MYC_rep1
ATAC-seq sample MYC_rep1


title: Sample 6_GEX

description: 10x genomics 5´ v2

source_name: naive nasal tissue-CD4 neg + infected nasal tissue-CD4 neg + infected nasal tissue- NP CD4 TRM + infected nasal tissue- HA CD4 TRM

value: CD4+CD44+CD62L-CD69+ total/HA+/NP+

value: 8-12 weeks


title: BJ48hS1

description:
Library name: BJ48hS1
allSamples_NormalizedCounts.xlsx
ESC_BJ_iPSC_normalizedCounts.xlsx


title: ATAC-seq 20210727_mesc_se_KLF4_rep3

description:
Library name: 20210727_mesc_se_KLF4_rep3
ATAC-seq sample KLF4_rep3


title: ATAC-seq 20210727_mesc_se_KLF4_rep2

description:
Library name: 20210727_mesc_se_KLF4_rep2
ATAC-seq sample KLF4_rep2


title: ATAC-seq 20210727_mesc_se_FGFR1_rep2

description:
Library name: 20210727_mesc_se_FGFR1_rep2
ATAC-seq sample FGFR1_rep2


title: ATAC-seq 20210727_mesc_se_FGFR1_rep3

description:
Library name: 20210727_mesc_se_FGFR1_rep3
ATAC-seq sample FGFR1_rep3


title: ATAC-seq 20210727_mesc_se_KLF4_rep1

description:
Library name: 20210727_mesc_se_KLF4_rep1
ATAC-seq sample KLF4_rep1


title: Sample 5_GEX

description: 10x genomics 5´ v2

source_name: infected lung-total CD4 TRM + infected nasal tissue-NP CD4 TRM

value: 5 naive + 25 infected pool

value: influenza A virus PR8 30dpi + naive

value: infected lung-total CD4 TRM (TotalSeq™-C0303 anti-mouse Hashtag 3); infected nasal tissue-NP+ CD4 TRM (TotalSeq™-C0305 anti-mouse Hashtag 5)


title: Sample 4_GEX

description: 10x genomics 5´ v2

source_name: infected lung-NP CD4 TRM + infected nasal tissue-total CD4 TRM


title: ATAC-seq 20210218_mesc_cas9_ZSWIM3_rep3

description:
Library name: 20210218_mesc_cas9_ZSWIM3_rep3
ATAC-seq sample ZSWIM3_rep3


title: H1P43

description:
Library name: H1P43
allSamples_NormalizedCounts.xlsx
ESC_BJ_iPSC_normalizedCounts.xlsx

value: embyronic stem cells


title: Sample 2_VDJ

description: 10x genomics 5´ v2

source_name: infected lung total Cd4 TRM+infected lung NP+ CD4 TRM+infected nasal tissue total CD4 TRM+ infected nasal tissue NP CD4 TRM VDJ

value: infected lung-total CD4 TRM (TotalSeq™-C0306 anti-mouse Hashtag 6); infected lung-NP+ CD4 TRM (TotalSeq™-C0306 anti-mouse Hashtag 6 + TotalSeq™-C0987 anti-APC); infected nasal tissue-total CD4 TRM ( TotalSeq™-C0307 anti-mouse Hashtag 7 ); infected nasal tissue-NP+ CD4 TRM (TotalSeq™-C0307 anti-mouse Hashtag 7+  TotalSeq™-C0987 anti-APC)


title: ATAC-seq 20210218_mesc_cas9_ZSWIM3_rep1

description:
Library name: 20210218_mesc_cas9_ZSWIM3_rep1
ATAC-seq sample ZSWIM3_rep1


title: Sample 3_GEX

description: 10x genomics 5´ v2

source_name: infected lung HA CD4TRM+infected nasal tissue HA CD4 TRM+naive lung CD4 TRM+naive nasal tissue CD4 TRM


title: ATAC-seq 20210727_mesc_se_FGFR1_rep1

description:
Library name: 20210727_mesc_se_FGFR1_rep1
ATAC-seq sample FGFR1_rep1


title: ATAC-seq 20210218_mesc_cas9_ZSWIM3_rep2

description:
Library name: 20210218_mesc_cas9_ZSWIM3_rep2
ATAC-seq sample ZSWIM3_rep2


title: SUV 1727 day 6

type: RNA

city: Toronto

first: Veronique

last: Voisin

state: ON

address: 101 College St, room 8-353

country: Canada

institute: University Health Network

hyb_protocol: Total RNA (typically 50–150 ng per reaction) was hybridized with reporter and capture probes from the NanoString Human Immunology v2 panel (NS_Immunology_v2_C2328) according to the manufacturer's instructions (NanoString Technologies). Hybridization reactions were carried out in a thermal cycler at 65 °C for 16–20 hours. After hybridization, samples were processed using the nCounter SPRINT Profiler automated system. Hybridized complexes were immobilized on a cartridge for scanning

scan_protocol: Cartridges were scanned using the NanoString nCounter SPRINT Profiler (Scanner ID: 1711C0513) following the manufacturer's protocol. Scanning was performed at 280 fields of view (FOV), with a binding density of 0.45.

data_processing: Data acquisition was conducted using nCounter Digital Analyzer software version 4.0.0.3. . NanoString data were read using the R nanostringr_0.4.1 package and normalized using RUVSeq_1.36.0 using the combined positive and negative controls as reference. Raw data files (RCC format) were generated automatically by the system.

label: not provided

source_name: OCI AML2

label_protocol: No enzymatic labeling was performed. Each target RNA was hybridized to a specific reporter probe carrying a fluorescent barcode and a capture probe, both provided in the NanoString Human Immunology v2 panel (NS_Immunology_v2_C2328). The reporter probes serve as unique labels for direct digital detection by the nCounter system

growth_protocol: OCI-AML2  cells were grown in Iscove’s modified Dulbecco’s medium (IMDM) containing penicillin (100 U/ml) and streptomycin (100 µg/ml; Wisent) and supplemented with 10% FBS.

extract_protocol: Total RNA was isolated from AML cells using the RNeasy Plus Mini Kit (QIAGEN), and cDNA was prepared using SuperScript IV Reverse Transcriptase (ThermoFisher, MA, USA).

treatment_protocol: OCI AML 2 cells were transduced with SUV3 and PNPase shRNA constructs

value: OCI AML2

value: human AML cell line

value: SUV3 knockdown

tag: timep point


title: SUV 1727 day5


title: ATAC-seq 20210218_mesc_cas9_TYR_rep3

description:
Library name: 20210218_mesc_cas9_TYR_rep3
ATAC-seq sample TYR_rep3

value: mESC


title: ATAC-seq 20210218_mesc_cas9_TYR_rep2

description:
Library name: 20210218_mesc_cas9_TYR_rep2
ATAC-seq sample TYR_rep2


title: ATAC-seq 20210218_mesc_cas9_EMX1_rep3

description:
Library name: 20210218_mesc_cas9_EMX1_rep3
ATAC-seq sample EMX1_rep3


title: ATAC-seq 20210218_mesc_cas9_EMX1_rep2

description:
Library name: 20210218_mesc_cas9_EMX1_rep2
ATAC-seq sample EMX1_rep2


title: ATAC-seq 20210218_mesc_cas9_EMX1_rep1

description:
Library name: 20210218_mesc_cas9_EMX1_rep1
ATAC-seq sample EMX1_rep1


title: SUV 1727 day4


title: ATAC-seq 20201230_nih3t3_cas9_ZSWIM3-L_rep3

description:
Library name: 20201230_nih3t3_cas9_ZSWIM3-L_rep3
ATAC-seq sample ZSWIM3-L_rep3


title: ATAC-seq 20201230_nih3t3_cas9_ZSWIM3-L_rep1

description:
Library name: 20201230_nih3t3_cas9_ZSWIM3-L_rep1
ATAC-seq sample ZSWIM3-L_rep1


title: Sample 1_GEX

description: 10x genomics 5´ v2

source_name: infected lung HA CD4TRM+infected nasal tissue CD4 TRM+naive lung CD4 TRM+naive nasal tissue CD4 TRM


title: SUV 1595 day 6


title: Sample 2_GEX

description: 10x genomics 5´ v2

source_name: infected lung total Cd4 TRM+infected lung NP+ CD4 TRM+infected nasal tissue total CD4 TRM+ infected nasal tissue NP CD4 TRM


title: SP-Cysltr1 KO

city: Chicago

first: Bin

last: Zhang

state: IL

address: 300 E Superior St, Tarry Building, 4-726

department: Medicine

institute: Northwestern University

data_processing:
Data was demultiplexed and counted using Cell Ranger version 6.0.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spleen

extract_protocol:
Total RNA was extracted from freshly prepared cells with chromium single cell 5' reagent kits (PN-1000263) according to the manufacturer's instruction.
10X Genomics Kit 3' v3, 10X genomics Library Construction kit

treatment_protocol: Bone marrow cells were enriched with hematopoietic progenitor cell isolation kit (Stemcell #19856), spleen and tumor samples were enriched with CD45 positive selection kit (Stemcell #18945).

value: Spleen

value: CD45 enriched cells

value: Cysltr1 KO


title: SUV 1595_day5


title: SUV 1595 day4


title: TM-WT

source_name: Tumor

value: Tumor

value: WT


title: ATAC-seq 20201230_nih3t3_cas9_ZIM-L_rep1

description:
Library name: 20201230_nih3t3_cas9_ZIM-L_rep1
ATAC-seq sample ZIM-L_rep1


title: ATAC-seq 20210218_mesc_cas9_TYR_rep1

description:
Library name: 20210218_mesc_cas9_TYR_rep1
ATAC-seq sample TYR_rep1

source_name: mESC


title: ATAC-seq 20201230_nih3t3_cas9_ZIM-L_rep2

description:
Library name: 20201230_nih3t3_cas9_ZIM-L_rep2
ATAC-seq sample ZIM-L_rep2


title: SP-WT


title: ATAC-seq 20201230_nih3t3_cas9_SMPDL3B-L_rep3

description:
Library name: 20201230_nih3t3_cas9_SMPDL3B-L_rep3
ATAC-seq sample SMPDL3B-L_rep3


title: PNPT 1717 day6

value: PNPase knockdown


title: SUV 1727 day 3


title: SUV 1595 day 3


title: BM-Cysltr1 KO

source_name: Bone marrow

value: Bone marrow

value: progenitor enriched cells


title: ATAC-seq 20201230_nih3t3_cas9_ZSWIM3-L_rep2

description:
Library name: 20201230_nih3t3_cas9_ZSWIM3-L_rep2
ATAC-seq sample ZSWIM3-L_rep2


title: ATAC-seq 20201230_nih3t3_cas9_SMPDL3B-L_rep2

description:
Library name: 20201230_nih3t3_cas9_SMPDL3B-L_rep2
ATAC-seq sample SMPDL3B-L_rep2


title: ATAC-seq 20201230_nih3t3_cas9_RPA2-H_rep3

description:
Library name: 20201230_nih3t3_cas9_RPA2-H_rep3
ATAC-seq sample RPA2-H_rep3


title: ATAC-seq 20201230_nih3t3_cas9_ZIM-L_rep3

description:
Library name: 20201230_nih3t3_cas9_ZIM-L_rep3
ATAC-seq sample ZIM-L_rep3


title: TM-Cysltr1 KO


title: PNPT 1717 day5


title: BM-WT


title: ATAC-seq 20201230_nih3t3_cas9_SMPDL3B-L_rep1

description:
Library name: 20201230_nih3t3_cas9_SMPDL3B-L_rep1
ATAC-seq sample SMPDL3B-L_rep1


title: Cysltr1-/-_GM-CSF+EMT6-CM_rep3

description: Sample 18

data_processing:
Reads were aligned to the mouse genome mm10 using HISAT2, version 2.1.0.
Quantification was performed using HTSeq-count, version 0.13.5.
The counts for a gene in each sample was normalized by DESeq2, version 1.34.0.
Assembly: mm10
Supplementary files format and content: HTSeq-count files include raw counts for each gene of each sample generated from HTSeq-count.
Supplementary files format and content: Normalized_counts files include the normalized counts for each gene in all samples generated from DESeq2.

growth_protocol: Bone marrow cells were cultured in complete RPMI 1640 media. (RPMI1640 with 10% FCS, 1% Pen/Strep, 1% Sodium Pyruvate, 1% MEM, 1% Hepes and 1% L-Glutamin)

extract_protocol:
Total RNA was extracted using Direct-zol RNA Miniprep Plus Kit from Zymo Research according to the manufacturer's instruction. 1ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module, Ultra II RNA Library Prep Kit, and Multiplex Oligos (NEB, Cat #E7490, E7775, E6609) according to the manufacturer's instruction.

treatment_protocol: Cells were treated with 40ng/mL GM-CSF or 40ng/mL GM-CSF + 40ng/mL IL-6 or 40ng/mL GM-CSF + 50% v/v 24h EMT6 conditional media as indicated.

tag: agent

value: BM derived cells

value: In vitro myelopoiesis


title: ATAC-seq 20201230_nih3t3_cas9_PI4K2A-L_rep3

description:
Library name: 20201230_nih3t3_cas9_PI4K2A-L_rep3
ATAC-seq sample PI4K2A-L_rep3


title: ATAC-seq 20201230_nih3t3_cas9_RPA2-H_rep1

description:
Library name: 20201230_nih3t3_cas9_RPA2-H_rep1
ATAC-seq sample RPA2-H_rep1


title: PNPT 1717 day4


title: PNPT 1717 day3


title: ATAC-seq 20201230_nih3t3_cas9_PI4K2A-L_rep1

description:
Library name: 20201230_nih3t3_cas9_PI4K2A-L_rep1
ATAC-seq sample PI4K2A-L_rep1


title: ATAC-seq 20201230_nih3t3_cas9_RPA2-H_rep2

description:
Library name: 20201230_nih3t3_cas9_RPA2-H_rep2
ATAC-seq sample RPA2-H_rep2


title: ATAC-seq 20201230_nih3t3_cas9_PI4K2A-H_rep2

description:
Library name: 20201230_nih3t3_cas9_PI4K2A-H_rep2
ATAC-seq sample PI4K2A-H_rep2


title: ATAC-seq 20201230_nih3t3_cas9_PI4K2A-H_rep1

description:
Library name: 20201230_nih3t3_cas9_PI4K2A-H_rep1
ATAC-seq sample PI4K2A-H_rep1


title: ATAC-seq 20201230_nih3t3_cas9_PI4K2A-L_rep2

description:
Library name: 20201230_nih3t3_cas9_PI4K2A-L_rep2
ATAC-seq sample PI4K2A-L_rep2


title: Cysltr1-/-_GM-CSF+EMT6-CM_rep2

description: Sample 17


title: ATAC-seq 20201230_nih3t3_cas9_NDUFS3-L_rep3

description:
Library name: 20201230_nih3t3_cas9_NDUFS3-L_rep3
ATAC-seq sample NDUFS3-L_rep3


title: Cysltr1-/-_GM-CSF+IL-6_rep3

description: Sample 15


title: Cysltr1-/-_GM-CSF+EMT6-CM_rep1

description: Sample 16


title: Cysltr1-/-_GM-CSF+IL-6_rep1

description: Sample 13


title: PNPT 545 day6


title: PNPT 545 day5


title: ATAC-seq 20230725_hek293t_pe_SMPDL3B_PE2_rep2

description:
Library name: 20230725_hek293t_pe_SMPDL3B_PE2_rep2
ATAC-seq sample SMPDL3B_PE2_rep2


title: ATAC-seq 20201230_nih3t3_cas9_NDUFS3-L_rep2

description:
Library name: 20201230_nih3t3_cas9_NDUFS3-L_rep2
ATAC-seq sample NDUFS3-L_rep2


title: Cysltr1-/-_GM-CSF_rep2

description: Sample 11

value: GM-CSF


title: Cysltr1-/-_GM-CSF+IL-6_rep2

description: Sample 14


title: ATAC-seq 20201230_nih3t3_cas9_NDUFS3-H_rep2

description:
Library name: 20201230_nih3t3_cas9_NDUFS3-H_rep2
ATAC-seq sample NDUFS3-H_rep2


title: ATAC-seq 20201230_nih3t3_cas9_PI4K2A-H_rep3

description:
Library name: 20201230_nih3t3_cas9_PI4K2A-H_rep3
ATAC-seq sample PI4K2A-H_rep3


title: ATAC-seq 20201230_nih3t3_cas9_MPP4-L_rep1

description:
Library name: 20201230_nih3t3_cas9_MPP4-L_rep1
ATAC-seq sample MPP4-L_rep1


title: ATAC-seq 20201230_nih3t3_cas9_NDUFS3-H_rep3

description:
Library name: 20201230_nih3t3_cas9_NDUFS3-H_rep3
ATAC-seq sample NDUFS3-H_rep3


title: ATAC-seq 20230725_hek293t_pe_SMPDL3B-sgpair3_PE3_rep3

description:
Library name: 20230725_hek293t_pe_SMPDL3B-sgpair3_PE3_rep3
ATAC-seq sample SMPDL3B-sgpair3_PE3_rep3


title: ATAC-seq 20201230_nih3t3_cas9_NDUFS3-H_rep1

description:
Library name: 20201230_nih3t3_cas9_NDUFS3-H_rep1
ATAC-seq sample NDUFS3-H_rep1


title: ATAC-seq 20230725_hek293t_pe_SMPDL3B_PE2_rep3

description:
Library name: 20230725_hek293t_pe_SMPDL3B_PE2_rep3
ATAC-seq sample SMPDL3B_PE2_rep3


title: ATAC-seq 20201230_nih3t3_cas9_MPP4-L_rep3

description:
Library name: 20201230_nih3t3_cas9_MPP4-L_rep3
ATAC-seq sample MPP4-L_rep3


title: SH-SY5Y

city: Cologne

first: Matthias

last: Fischer

address: Kerpener Str. 62

department: Department of Experimental Pediatric Oncology

institute: University Children’s Hospital of Cologne

description: Library name: SY5Y

data_processing:
Software used for basecalling are HCS1.4.8+RTA1.12.4.2, HCS1.4.8+RTA1.12.4.2 and HCS1.5+RTA1.13.48.
The raw sequencing data was quantified using Kallisto (version 0.44.0) with parameters –bootstrap-samples 100 --bias and the GRCh38 reference genome. The Kallisto transcript level read counts were transformed to gene level counts using the R package tximport (version 1.36.1). To obtain gene expression values, the counts were normalized with DESeq2 (version 1.48.2) and variance stabilizing transformation has been applied. Only genes with at least 10 reads in 10% of the samples were used for further analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes DESeq2 read count values for each cell line
Supplementary files format and content: tab-delimited text file includes DESeq2 VST expression  values for each cell line

source_name: neuroblastoma

growth_protocol: Cell lines were grown in RPMI1640 or DMEM with 10% FBS. All cell lines were cultured without antibiotics and routinely tested negative for mycoplasma.

extract_protocol:
Total RNA was isolated following the TRIzol protocol (Invitrogen).
Library construction was performed according to the standard TruSeqTM protocol.

value: neuroblastoma


title: ATAC-seq 20201230_nih3t3_cas9_MPP4-H_rep3

description:
Library name: 20201230_nih3t3_cas9_MPP4-H_rep3
ATAC-seq sample MPP4-H_rep3


title: Cysltr1-/-_GM-CSF_rep3

description: Sample 12


title: SK-N-SH

description: Library name: SKNSH

value: SK-N-SH


title: ATAC-seq 20201230_nih3t3_cas9_NDUFS3-L_rep1

description:
Library name: 20201230_nih3t3_cas9_NDUFS3-L_rep1
ATAC-seq sample NDUFS3-L_rep1


title: ATAC-seq 20230725_hek293t_pe_SMPDL3B_PE2_rep1

description:
Library name: 20230725_hek293t_pe_SMPDL3B_PE2_rep1
ATAC-seq sample SMPDL3B_PE2_rep1


title: PNPT 545 day4

value: OCI AML2


title: WT_GM-CSF+EMT6-CM_rep1

description: Sample 7


title: SK-N-AS

description: Library name: SKNAS

value: SK-N-AS


title: ATAC-seq 20230725_hek293t_pe_SMPDL3B-sgpair3_PE3_rep1

description:
Library name: 20230725_hek293t_pe_SMPDL3B-sgpair3_PE3_rep1
ATAC-seq sample SMPDL3B-sgpair3_PE3_rep1


title: SK-N-FI

description: Library name: SKNFI

value: SK-N-FI


title: Cysltr1-/-_GM-CSF_rep1

description: Sample 10


title: ATAC-seq 20230725_hek293t_pe_SMPDL3B-sgpair3_PE3_rep2

description:
Library name: 20230725_hek293t_pe_SMPDL3B-sgpair3_PE3_rep2
ATAC-seq sample SMPDL3B-sgpair3_PE3_rep2


title: SK-N-DZ

description: Library name: SKNDZ

value: SK-N-DZ


title: ATAC-seq 20201230_nih3t3_cas9_HMGC-L_rep3

description:
Library name: 20201230_nih3t3_cas9_HMGC-L_rep3
ATAC-seq sample HMGC-L_rep3


title: ATAC-seq 20201230_nih3t3_cas9_MPP4-H_rep2

description:
Library name: 20201230_nih3t3_cas9_MPP4-H_rep2
ATAC-seq sample MPP4-H_rep2


title: WT_GM-CSF+EMT6-CM_rep2

description: Sample 8


title: NBL-S

description: Library name: NBLS

value: NBL-S


title: WT_GM-CSF+EMT6-CM_rep3

description: Sample 9


title: ATAC-seq 20230725_hek293t_pe_SMPDL3B-sgpair2_PE3_rep1

description:
Library name: 20230725_hek293t_pe_SMPDL3B-sgpair2_PE3_rep1
ATAC-seq sample SMPDL3B-sgpair2_PE3_rep1


title: WT_GM-CSF+IL-6_rep2

description: Sample 5


title: ATAC-seq 20201230_nih3t3_cas9_MPP4-H_rep1

description:
Library name: 20201230_nih3t3_cas9_MPP4-H_rep1
ATAC-seq sample MPP4-H_rep1


title: ATAC-seq 20201230_nih3t3_cas9_FKBP2-L_rep3

description:
Library name: 20201230_nih3t3_cas9_FKBP2-L_rep3
ATAC-seq sample FKBP2-L_rep3


title: IMR5-75

description: Library name: IMR575


title: NGP

description: Library name: NGP

value: NGP


title: ATAC-seq 20230725_hek293t_pe_SMPDL3B-sgpair2_PE3_rep3

description:
Library name: 20230725_hek293t_pe_SMPDL3B-sgpair2_PE3_rep3
ATAC-seq sample SMPDL3B-sgpair2_PE3_rep3


title: WT_GM-CSF_rep3

description: Sample 3


title: PNPT 545 day3

value: human AML cell line


title: WT_GM-CSF+IL-6_rep3

description: Sample 6


title: ATAC-seq 20201230_nih3t3_cas9_HMGC-L_rep1

description:
Library name: 20201230_nih3t3_cas9_HMGC-L_rep1
ATAC-seq sample HMGC-L_rep1


title: ATAC-seq 20201230_nih3t3_cas9_HMGC-L_rep2

description:
Library name: 20201230_nih3t3_cas9_HMGC-L_rep2
ATAC-seq sample HMGC-L_rep2


title: ATAC-seq 20230725_hek293t_pe_SMPDL3B-sgpair1_PE3_rep1

description:
Library name: 20230725_hek293t_pe_SMPDL3B-sgpair1_PE3_rep1
ATAC-seq sample SMPDL3B-sgpair1_PE3_rep1


title: ATAC-seq 20230725_hek293t_pe_SMPDL3B-sgpair1_PE3_rep2

description:
Library name: 20230725_hek293t_pe_SMPDL3B-sgpair1_PE3_rep2
ATAC-seq sample SMPDL3B-sgpair1_PE3_rep2


title: Lan-6

description: Library name: LAN6


title: WT_GM-CSF+IL-6_rep1

description: Sample 4


title: ATAC-seq 20201230_nih3t3_cas9_FKBP2-L_rep1

description:
Library name: 20201230_nih3t3_cas9_FKBP2-L_rep1
ATAC-seq sample FKBP2-L_rep1


title: GI-ME-N

description: Library name: GIMEN

value: GI-ME-N


title: IMR32

description: Library name: IMR32


title: jurkat_rpf_72h_his25_rep3

city: Zürich

first: Puneet

last: Sharma

state: Zürich

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

country: Switzerland

institute: ETH

description: Library name: jurkat_rpf_72h_his25_rep3

data_processing:
The reference human genome (GRCh38; annotation version 113) and transcriptome were obtained from ENSEMBL. For ribosome profiling, coding sequences (CDS) were curated in BioMart with the filters (a) Source (transcript): ensembl_havana (b) Transcript type: lncRNA , protein_coding (c) Ensembl Canonical: Only; and attributes (a) Transcript stable ID (b) Coding sequence (c) Upstream flank [18] (d) Downstream flank [18]. Sequences for rRNA and tRNA were obtained from NCBI (Nucleotide) and Genomic tRNA database, respectively. Human proteome (reviewed and canonical) was obtained from UniProt. Gene sets (c2.cp.reactome.v2025.1.Hs.symbols.gmt) for GSEA were obtained from MSigDB.
Bulk RNA-seq: Decoy (full genome) aware indexing of transcriptome was done using Salmon with the parameter “--kmerLen 31”. The paired-end reads from bulk RNA-seq datasets were processed to remove the Illumina universal adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) using Cutadapt (v4.4) with the parameters “--poly-a -q 25 -m 25 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT”. The resulting filtered reads were quantified against the index using Salmon with the parameters “--libType A --gcBias --seqBias –useVBOpt --validateMappings”. Subsequent data analysis was performed with custom scripts in R. Data wrangling and visualization was performed using tidyverse package (v2.0.0). Transcript quantifications were imported using Tximeta and differential expression analysis was conducted using DESeq2 (v1.44). Cluster of genes changing expression with histidine concentrations were identified by likelihood ratio test using the function DESeq(test = "LRT", reduced = ~ 1), where full model was ~ condition (i.e. samples belonging to different histidine concentration). Differentially expressed genes (DEGs) were defined as having adjusted p-value < 1e-06. Genes in upregulated and downregulated clusters were further analyzed for functional enrichment using gProfiler2 (v0.2.3).
Ribosome profiling: Single-end reads were processed to remove adapter (--quality-cutoff 30 --minimum-length 25 --cut 3 --no-indels --discard-untrimmed --adapter CTGTAGGCACCATCAAT) and randomized nucleotides (--cut -6 --quality-cutoff 30 --minimum-length 25) using Cutadapt (v4.4). Resulting filtered reads were mapped to rRNA and tRNA using bowtie (v1.3.1) with the parameters “--best --sam --un”. Reads that failed to align rRNA and tRNA were mapped to coding sequence using bowtie (v1.3.1) with the parameters “--best --sam -m 1 -v 1 --norc --strata”. Coordinate-sorted alignment files were indexed using SAMtools (v1.17). Differential expression analysis was conducted using DESeq2 (v1.44). Differentially expressed genes (DEGs) were defined as having absolute log fold change > 1 and adjusted p-value < 0.05 (Wald test). Codon occupancy was calculated using ribomala package (v0.5.4). Briefly, read length of interest (generally 28-31 nt) were determined based on 3-nt periodicity on the CDS. For each read length, E-, P- and A- site were determined based on the highest ribosome footprint signal upstream of the start site. For each coding sequence, 20 codons from the start and end were excluded, and read counts (e.g. A-site) for each codon were divided by mean across the coding sequence to get relative enrichment. Coding sequences with mean read count of < 0.1 reads/codon were also excluded from the analysis.
Assembly: GRCh38; ENSEMBL annotation version 113
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample
Library strategy: Ribo-Seq

molecule: cytoplasmic RNA

source_name: Peripheral blood

growth_protocol: Jurkat cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) without antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted from cell lysates (in "human lysis buffer" (Kim, Leidel, 2021) using the TRIzol method according to the manufacturer's instructions.
RNA libraries for RNA-seq were prepared using Illumina TruSeq mRNA-Seq library preparation kit following manufacturer's protocol

treatment_protocol: Self-made histidine-free RPMI was supplemented with 25% or 100% histidine and Jurkat cells were culture at initial seeding density 300 000/mL in the respective media for 72 hours

value: Peripheral blood

value: Jurkat

value: T lymphoblast

value: 25 % histidine


title: WT_GM-CSF_rep2

description: Sample 2

value: Bone marrow

value: BM derived cells

value: WT


title: WT_GM-CSF_rep1

description: Sample 1

value: GM-CSF

value: In vitro myelopoiesis


title: ATAC-seq 20201230_nih3t3_cas9_MPP4-L_rep2

description:
Library name: 20201230_nih3t3_cas9_MPP4-L_rep2
ATAC-seq sample MPP4-L_rep2


title: jurkat_rpf_72h_his25_rep2

description: Library name: jurkat_rpf_72h_his25_rep2


title: SK-N-BE(2)C

description: Library name: BE2C

value: neuroblastoma


title: LS

description: Library name: LS

value: LS


title: ATAC-seq 20230725_hek293t_pe_MPP4_PE2_rep2

description:
Library name: 20230725_hek293t_pe_MPP4_PE2_rep2
ATAC-seq sample MPP4_PE2_rep2


title: ATAC-seq 20230725_hek293t_pe_SMPDL3B-sgpair1_PE3_rep3

description:
Library name: 20230725_hek293t_pe_SMPDL3B-sgpair1_PE3_rep3
ATAC-seq sample SMPDL3B-sgpair1_PE3_rep3


title: ATAC-seq 20230725_hek293t_pe_MPP4_PE2_rep1

description:
Library name: 20230725_hek293t_pe_MPP4_PE2_rep1
ATAC-seq sample MPP4_PE2_rep1


title: ATAC-seq 20201230_nih3t3_cas9_FKBP2-L_rep2

description:
Library name: 20201230_nih3t3_cas9_FKBP2-L_rep2
ATAC-seq sample FKBP2-L_rep2


title: jurkat_rpf_72h_his25_rep4

description: Library name: jurkat_rpf_72h_his25_rep4


title: ATAC-seq 20230725_hek293t_pe_MPP4-sgpair3_PE3_rep1

description:
Library name: 20230725_hek293t_pe_MPP4-sgpair3_PE3_rep1
ATAC-seq sample MPP4-sgpair3_PE3_rep1


title: ATAC-seq 20230725_hek293t_pe_SMPDL3B-sgpair2_PE3_rep2

description:
Library name: 20230725_hek293t_pe_SMPDL3B-sgpair2_PE3_rep2
ATAC-seq sample SMPDL3B-sgpair2_PE3_rep2


title: IP_ed_SUV3_566

description: Library name: IP_ed_SUV3_566

library_source: other

data_processing:
The raw sequence data, in the form of FASTQ files, was aligned to the human genome (GRCh38, Homo_sapiens.GRCh38.84.gtf definition file) using the HISAT2 v2.2.1 (Kim et al., 2019) software tool
Accessory programs for the alignment stage include SAMTOOLS v1.14 (Heng et al., 2009). StringTie v2.1.4 (Pertea et al., 2015) were utilized for transcript assembly.
Libraries were sequenced on an Illumina HiSeq-2000 with 100-bp paired-end reads, v3 chemistry.
Assembly: GRCh38
Supplementary files format and content: Gene counts were extracted using HT-seq
Supplementary files format and content: Gene abundance was also expressed as the logarithm of FPKM (fragments per kilobase of exon per million fragments mapped)

molecule: other

extract_protocol:
Cells were lysed in NP-40 lysis buffer (catalog #: J60766) for 30 min on ice. Protein A/G beads (catalog #: 88803) were incubated with J2 antibody in NP-40 lysis buffer for 1hr at room temperature. Cell lysates were then incubated with antibody-conjugated beads for 2hr at 4°C. Beads were then washed with a high-salt PBS buffer (1x PBS, 0.1% Tween, 1 M NaCl) followed by two washes with a low-salt PBS buffer (1x PBS, 0.1% Tween, 0.5 M NaCl). dsRNA was eluted from the immunoprecipitation beads by treating with 1 mg/ml Proteinase K (catalog #: P8044-1G) in NP-40 lysis buffer. The immunoprecipitated RNA was extracted with phenol–chloroform and then precipitated using ethanol
Sequencing libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina, v1.0 (cat. no. E7420) according to the manufacturer’s guidelines

value: human AML cell l ine

value: SUPV3L1 knockdown


title: ATAC-seq 20201230_nih3t3_cas9_FKBP2-H_rep3

description:
Library name: 20201230_nih3t3_cas9_FKBP2-H_rep3
ATAC-seq sample FKBP2-H_rep3


title: CLB-GA

description: Library name: CLBGA

value: CLB-GA


title: ATAC-seq 20201230_nih3t3_cas9_FKBP2-H_rep2

description:
Library name: 20201230_nih3t3_cas9_FKBP2-H_rep2
ATAC-seq sample FKBP2-H_rep2


title: IP_ed_SUV3_1595

description: Library name: IP_ed_SUV3_1595


title: IP_ed_PNPT1_1979

description: Library name: IP_ed_PNPT1_1979

value: PNPT1 knockdown


title: ATAC-seq 20230725_hek293t_pe_MPP4-sgpair2_PE3_rep3

description:
Library name: 20230725_hek293t_pe_MPP4-sgpair2_PE3_rep3
ATAC-seq sample MPP4-sgpair2_PE3_rep3


title: ATAC-seq 20230725_hek293t_pe_MPP4_PE2_rep3

description:
Library name: 20230725_hek293t_pe_MPP4_PE2_rep3
ATAC-seq sample MPP4_PE2_rep3


title: ATAC-seq 20201013_nih3t3_cas9_wt_rep6

description:
Library name: 20201013_nih3t3_cas9_wt_rep6
ATAC-seq sample wt_rep6


title: ATAC-seq 20201230_nih3t3_cas9_FKBP2-H_rep1

description:
Library name: 20201230_nih3t3_cas9_FKBP2-H_rep1
ATAC-seq sample FKBP2-H_rep1


title: ATAC-seq 20230725_hek293t_pe_MPP4-sgpair3_PE3_rep3

description:
Library name: 20230725_hek293t_pe_MPP4-sgpair3_PE3_rep3
ATAC-seq sample MPP4-sgpair3_PE3_rep3


title: ATAC-seq 20230725_hek293t_pe_MPP4-sgpair2_PE3_rep2

description:
Library name: 20230725_hek293t_pe_MPP4-sgpair2_PE3_rep2
ATAC-seq sample MPP4-sgpair2_PE3_rep2


title: ATAC-seq 20230725_hek293t_pe_MPP4-sgpair2_PE3_rep1

description:
Library name: 20230725_hek293t_pe_MPP4-sgpair2_PE3_rep1
ATAC-seq sample MPP4-sgpair2_PE3_rep1


title: ATAC-seq 20201013_nih3t3_cas9_wt_rep5

description:
Library name: 20201013_nih3t3_cas9_wt_rep5
ATAC-seq sample wt_rep5


title: IP_ed_SUV3_1727

description: Library name: IP_ed_SUV3_1727


title: ATAC-seq 20230725_hek293t_pe_MPP4-sgpair3_PE3_rep2

description:
Library name: 20230725_hek293t_pe_MPP4-sgpair3_PE3_rep2
ATAC-seq sample MPP4-sgpair3_PE3_rep2


title: jurkat_rpf_72h_his25_rep1

description: Library name: jurkat_rpf_72h_his25_rep1


title: jurkat_rpf_matched_rna_72h_his25_rep3

description: Library name: jurkat_rpf_matched_rna_72h_his25_rep3

data_processing:
The reference human genome (GRCh38; annotation version 113) and transcriptome were obtained from ENSEMBL. For ribosome profiling, coding sequences (CDS) were curated in BioMart with the filters (a) Source (transcript): ensembl_havana (b) Transcript type: lncRNA , protein_coding (c) Ensembl Canonical: Only; and attributes (a) Transcript stable ID (b) Coding sequence (c) Upstream flank [18] (d) Downstream flank [18]. Sequences for rRNA and tRNA were obtained from NCBI (Nucleotide) and Genomic tRNA database, respectively. Human proteome (reviewed and canonical) was obtained from UniProt. Gene sets (c2.cp.reactome.v2025.1.Hs.symbols.gmt) for GSEA were obtained from MSigDB.
Bulk RNA-seq: Decoy (full genome) aware indexing of transcriptome was done using Salmon with the parameter “--kmerLen 31”. The paired-end reads from bulk RNA-seq datasets were processed to remove the Illumina universal adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) using Cutadapt (v4.4) with the parameters “--poly-a -q 25 -m 25 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT”. The resulting filtered reads were quantified against the index using Salmon with the parameters “--libType A --gcBias --seqBias –useVBOpt --validateMappings”. Subsequent data analysis was performed with custom scripts in R. Data wrangling and visualization was performed using tidyverse package (v2.0.0). Transcript quantifications were imported using Tximeta and differential expression analysis was conducted using DESeq2 (v1.44). Cluster of genes changing expression with histidine concentrations were identified by likelihood ratio test using the function DESeq(test = "LRT", reduced = ~ 1), where full model was ~ condition (i.e. samples belonging to different histidine concentration). Differentially expressed genes (DEGs) were defined as having adjusted p-value < 1e-06. Genes in upregulated and downregulated clusters were further analyzed for functional enrichment using gProfiler2 (v0.2.3).
Ribosome profiling: Single-end reads were processed to remove adapter (--quality-cutoff 30 --minimum-length 25 --cut 3 --no-indels --discard-untrimmed --adapter CTGTAGGCACCATCAAT) and randomized nucleotides (--cut -6 --quality-cutoff 30 --minimum-length 25) using Cutadapt (v4.4). Resulting filtered reads were mapped to rRNA and tRNA using bowtie (v1.3.1) with the parameters “--best --sam --un”. Reads that failed to align rRNA and tRNA were mapped to coding sequence using bowtie (v1.3.1) with the parameters “--best --sam -m 1 -v 1 --norc --strata”. Coordinate-sorted alignment files were indexed using SAMtools (v1.17). Differential expression analysis was conducted using DESeq2 (v1.44). Differentially expressed genes (DEGs) were defined as having absolute log fold change > 1 and adjusted p-value < 0.05 (Wald test). Codon occupancy was calculated using ribomala package (v0.5.4). Briefly, read length of interest (generally 28-31 nt) were determined based on 3-nt periodicity on the CDS. For each read length, E-, P- and A- site were determined based on the highest ribosome footprint signal upstream of the start site. For each coding sequence, 20 codons from the start and end were excluded, and read counts (e.g. A-site) for each codon were divided by mean across the coding sequence to get relative enrichment. Coding sequences with mean read count of < 0.1 reads/codon were also excluded from the analysis.
Assembly: GRCh38; ENSEMBL annotation version 113
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample


title: jurkat_rpf_72h_his100_rep3

description: Library name: jurkat_rpf_72h_his100_rep3

value: 100% histidine


title: BRD2 Input

description: Library name: BRD2_Input_hs_i33

data_processing:
Fastq files were mapped to the human genome GRCh38 with Bowtie2 using single end setting with local alignment. BAM files were filtered to retain reads with a mapping quality >= 20. Peak calling was performed using MACS2 package setting for a fragment size estimate of 200 bp (fragment size selected during library preparation) with default parameters to handle duplicates.
For BAM coverage calculations, BAM files were first sorted and indexed using SAMtools. Indexed BAM files were processed with bamCoverage and BigWig files were used for peak density analysis.
Assembly: GRCH38 (canonical)
Supplementary files format and content: BigWig; peak coverage

source_name: BJ

extract_protocol:
Samples were sent to Active Motif (Carlsbad, CA) for BRD2 ChIP-Seq. Active Motif prepared chromatin, performed ChIP reactions, generated libraries, sequenced the libraries and performed basic data analysis. In brief, human fibroblast cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp with Active Motif’s EpiShear probe sonicator (cat# 53051). Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by SPRI beads clean up (Beckman Coulter) and quantitation by Qubit. Extrapolation to the original chromatin volume allowed determination of the total chromatin yield.  An aliquot of chromatin (30 ug) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 ug of antibody against BRD2 (Bethyl Laboratories, cat number A302-582A). For H3K12ac, 3 µg of antibody was used (MA5-23516, Invitrogen). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NovaSeq (75 nt reads, single end).

treatment_protocol: Human fibroblasts BJ were transduced with lentiviral preparation of BRD2 shRNA or Scramble control. For BRD2 ChIP we used BJ cells carrying an inducible Cas9 construct.

tag: Sex

value: male

value: BJ

value: foreskin fibroblast

value: with random lentivirus integration of reprogramming factors overexpressing OCT4, SOX2, KLF4 and BRD2 with its ET tail deleted

value: NO


title: jurkat_rpf_72h_his100_rep2

description: Library name: jurkat_rpf_72h_his100_rep2

value: Peripheral blood

value: Jurkat

value: T lymphoblast


title: ATAC-seq 20201230_nih3t3_cas9_CIB4-L_rep2

description:
Library name: 20201230_nih3t3_cas9_CIB4-L_rep2
ATAC-seq sample CIB4-L_rep2


title: ATAC-seq 20230725_hek293t_pe_MPP4-sgpair1_PE3_rep3

description:
Library name: 20230725_hek293t_pe_MPP4-sgpair1_PE3_rep3
ATAC-seq sample MPP4-sgpair1_PE3_rep3


title: ATAC-seq 20201230_nih3t3_cas9_CIB4-L_rep3

description:
Library name: 20201230_nih3t3_cas9_CIB4-L_rep3
ATAC-seq sample CIB4-L_rep3


title: jurkat_rpf_matched_rna_72h_his25_rep2

description: Library name: jurkat_rpf_matched_rna_72h_his25_rep2

value: 25 % histidine


title: ATAC-seq 20201013_nih3t3_cas9_wt_rep3

description:
Library name: 20201013_nih3t3_cas9_wt_rep3
ATAC-seq sample wt_rep3


title: ATAC-seq 20201013_nih3t3_cas9_wt_rep4

description:
Library name: 20201013_nih3t3_cas9_wt_rep4
ATAC-seq sample wt_rep4


title: ATAC-seq 20230725_hek293t_pe_MPP4-sgpair1_PE3_rep2

description:
Library name: 20230725_hek293t_pe_MPP4-sgpair1_PE3_rep2
ATAC-seq sample MPP4-sgpair1_PE3_rep2


title: ATAC-seq 20201230_nih3t3_cas9_CIB4-L_rep1

description:
Library name: 20201230_nih3t3_cas9_CIB4-L_rep1
ATAC-seq sample CIB4-L_rep1


title: jurkat_rpf_matched_rna_72h_his25_rep5

description: Library name: jurkat_rpf_matched_rna_72h_his25_rep5


title: IP_ed_PNPT1_1717

description: Library name: IP_ed_PNPT1_1717


title: jurkat_rpf_72h_his100_rep1

description: Library name: jurkat_rpf_72h_his100_rep1


title: KO-1 BRD2 ChIP

description: Library name: KO-1_BRD2_hs_i59

value: sgRNA+Dox


title: BJ-2 BRD2 ChIP

description: Library name: BJ-2_BRD2_hs_i57


title: ATAC-seq 20230725_hek293t_pe_EMX1_PE2_rep3

description:
Library name: 20230725_hek293t_pe_EMX1_PE2_rep3
ATAC-seq sample EMX1_PE2_rep3


title: jurkat_rpf_matched_rna_72h_his25_rep1

description: Library name: jurkat_rpf_matched_rna_72h_his25_rep1


title: KO-2 BRD2 ChIP

description: Library name: KO-2_BRD2_hs_i64


title: jurkat_rpf_matched_rna_72h_his100_rep5

description: Library name: jurkat_rpf_matched_rna_72h_his100_rep5


title: ATAC-seq 20230725_hek293t_pe_MPP4-sgpair1_PE3_rep1

description:
Library name: 20230725_hek293t_pe_MPP4-sgpair1_PE3_rep1
ATAC-seq sample MPP4-sgpair1_PE3_rep1


title: ATAC-seq 20201013_nih3t3_cas9_empty_vector_rep2

description:
Library name: 20201013_nih3t3_cas9_empty_vector_rep2
ATAC-seq sample empty_vector_rep2


title: BJ-1 BRD2 ChIP

description: Library name: BJ-1_BRD2_hs_i56


title: jurkat_rpf_matched_rna_72h_his100_rep2

description: Library name: jurkat_rpf_matched_rna_72h_his100_rep2


title: ATAC-seq 20201013_nih3t3_cas9_wt_rep1

description:
Library name: 20201013_nih3t3_cas9_wt_rep1
ATAC-seq sample wt_rep1


title: ATAC-seq 20230725_hek293t_pe_EMX1-sgpair3_PE3_rep2

description:
Library name: 20230725_hek293t_pe_EMX1-sgpair3_PE3_rep2
ATAC-seq sample EMX1-sgpair3_PE3_rep2


title: jurkat_rpf_matched_rna_72h_his100_rep4

description: Library name: jurkat_rpf_matched_rna_72h_his100_rep4


title: ATAC-seq 20201013_nih3t3_cas9_empty_vector_rep1

description:
Library name: 20201013_nih3t3_cas9_empty_vector_rep1
ATAC-seq sample empty_vector_rep1


title: ATAC-seq 20230725_hek293t_pe_EMX1_PE2_rep2

description:
Library name: 20230725_hek293t_pe_EMX1_PE2_rep2
ATAC-seq sample EMX1_PE2_rep2


title: ATAC-seq 20201013_nih3t3_cas9_empty_vector_rep3

description:
Library name: 20201013_nih3t3_cas9_empty_vector_rep3
ATAC-seq sample empty_vector_rep3


title: ATAC-seq 20230725_hek293t_pe_EMX1_PE2_rep1

description:
Library name: 20230725_hek293t_pe_EMX1_PE2_rep1
ATAC-seq sample EMX1_PE2_rep1


title: IP_ed_PNPT1_545

description: Library name: IP_ed_PNPT1_545


title: jurkat_rpf_matched_rna_72h_his100_rep3

description: Library name: jurkat_rpf_matched_rna_72h_his100_rep3


title: CUT&Tag hek293t_zswim3_h3k9me3_rep1

description:
Library name: hek293t_zswim3_h3k9me3_rep1
CUT&Tag sample hek293t_zswim3_h3k9me3_rep1

data_processing:
Read adaptors were trimmed using cutadapt (version 3.4). Trimmed reads were aligned to hg38 (human) or mm10 (mouse) using bowtie2 (version 2.4.4) with parameters -X2000 --mm -t -q -N1 -L 25 --no-mixed --no-discordant.
Aligned reads were filtered using samtools (version 1.13) to exclude unmapped reads, unmapped mates, non-primary alignments, vendor/quality-fail reads, and duplicates (SAM flag 1804).
Standard samtools sort and fixmate operations were applied. PCR duplicates were removed using picard MarkDuplicates (version 2.20.4), followed by samtools view filtering (-F1804 -f2). ENCODE blacklist regions were removed in the final alignment set.
For coverage bigwig, deepTools bamCoverage was used on aligned BAM files with parameter "--normalizeUsing RPKM --binSize 1" to generate genome coverage bigWig files. For peak calling used in normalization and visualization, MACS2 callpeak used "--nolambda -f BAMPE -g [hs/mm per cell line] --bdg -q 0.05" for H3K27ac.
For peak calling used in normalization and visualization, MACS2 callpeak used "--nolambda -f BAMPE -g [hs/mm per cell line] --bdg -q 0.05" for H3K27ac and CTCF. For H3K27me3 peak calling, "--broad --broad-cutoff 0.1" was added after the H3K27ac parameters. For H3K9me3 peak calling, "--broad --broad-cutoff 0.05" was added after the H3K27ac parameters.
Assembly: hg38/mm10
Supplementary files format and content: coverage bigWig
Supplementary files format and content: MACS2 peaks
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag libraries were generated using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903) following the manufacturer's instructions with minor adjustments. Harvested cells were washed once with 500 μL Wash Buffer and resuspended in 100 μL Wash Buffer. Ten microliters of Concanavalin A beads were added and incubated at room temperature for 10 minutes with intermittent gentle inversion. Bead-bound cells were resuspended in 50 μL pre-chilled Antibody Buffer containing primary antibody against CTCF (Active Motif, 61932), H3K27ac (Abcam, ab4729), H3K9me3 (Active Motif, 39161), or H3K27me3 (Cell Signaling, C36B11), and incubated overnight at 2-8°C.
On day 2, beads were washed and resuspended in 50 μL Dig-wash Buffer supplemented with 0.01 mg/mL secondary antibody (Novoprotein, N269), incubated at room temperature for 30-60 minutes on a tube rotator, and washed three times with 200 μL Dig-wash Buffer. Beads were resuspended in 100 μL Dig-300 Buffer containing 2 μL pA/G-Tnp transposome and incubated for 1 hour at room temperature with gentle rotation. After three washes with 200 μL Dig-300 Buffer, beads were resuspended in 50 μL tagmentation buffer (5× TTBL diluted in Dig-300 Buffer). Tagmentation was performed at 37°C for 60 minutes in a thermocycler with heated lid disabled. To stop reaction and extract DNA, 5 μL Proteinase K, 100 μL Buffer L/B, and 20 μL DNA Extract Beads were added, and DNA was eluted in 20 μL nuclease-free water. Purified DNA was amplified using CUT&Tag Amplification Mix (CAM) and indexed primers (12-14 cycles for ~10,000 cells), then final PCR products were purified using VAHTS DNA Clean Beads (Vazyme, N411). Sequencing libraries were generated on the Illumina NovaSeq 6000 platform.


title: experiment:poolsize2_920 condition:4_4 sample[6]

city: Martinsried

first: Wolfgang

last: Enard

state: Bavaria

address: Grossshaderner Str.2, Anthropology Human Genomics, AG Enard

department: Anthropology and human genomics

institute: LMU Munich

description: Library name: poolsize2_920_4_4_sample6

data_processing:
Quality assessment of the fastq data files was conducted using fastqc (v 0.11.5) [2], followed by polyA trimming using cutadapt (v 4.1) [3]. Subsequent read filtering, mapping, and counting were performed using the zUMIs pipeline (v 2.9.7) [4], with reads mapped to the mouse genome (mm10). Fastq files were sample-demultiplexed using deML [5].
2 Andrews, S. (2010). FastQC: A quality control tool for high throughput sequence data. Available at: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
3 Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal, 17(1), 10-12.
4 Parekh, S., Ziegenhain, C., Vieth, B., Enard, W., & Hellmann, I. (2018). zUMIs- A fast and flexible pipeline to process RNA sequencing data with UMIs. GigaScience, 7(6), giy059.
5 Gabriel Renaud, Udo Stenzel, Tomislav Maricic, Victor Wiebe, Janet Kelso (2015) deML: robust demultiplexing of Illumina sequences using a likelihood-based approach, Bioinformatics, Volume 31, Issue 5, March 2015, Pages 770–772, https://doi.org/10.1093/bioinformatics/btu719
Assembly: GRCm39
Supplementary files format and content: processed data files contain the Barcode (BC) of each sample with the associated counts (N) per feature (type), e.g. Intergenic, Intron, Exon, Ambiguity and Unmapped.

source_name: brain

extract_protocol:
prime-seq - tissue lysis and homogenization in RLT+ buffer + 1 % B-Mercaptoethanol
prime-seq, the prime-seq original protocol  [1] , the original protocol with adaptions and the new, improved protocol  version (Pförtner et al, this study)
1 Janjic, A., Wange, L.E., Bagnoli, J.W. et al. Prime-seq, efficient and powerful bulk RNA sequencing. Genome Biol 23, 88 (2022). https://doi.org/10.1186/s13059-022-02660-8

value: brain


title: ATAC-seq 20201013_nih3t3_cas9_wt_rep2

description:
Library name: 20201013_nih3t3_cas9_wt_rep2
ATAC-seq sample wt_rep2


title: jurkat_rpf_matched_rna_72h_his100_rep1

description: Library name: jurkat_rpf_matched_rna_72h_his100_rep1


title: ATAC-seq 20230725_hek293t_pe_EMX1-sgpair2_PE3_rep3

description:
Library name: 20230725_hek293t_pe_EMX1-sgpair2_PE3_rep3
ATAC-seq sample EMX1-sgpair2_PE3_rep3


title: experiment:poolsize2_920 condition:4_4 sample[8]

description: Library name: poolsize2_920_4_4_sample8


title: CUT&Tag hek293t_zswim3_h3k9me3_rep2

description:
Library name: hek293t_zswim3_h3k9me3_rep2
CUT&Tag sample hek293t_zswim3_h3k9me3_rep2


title: experiment:poolsize2_920 condition:4_4 sample[7]

description: Library name: poolsize2_920_4_4_sample7


title: CUT&Tag hek293t_zswim3_h3k27me3_rep2

description:
Library name: hek293t_zswim3_h3k27me3_rep2
CUT&Tag sample hek293t_zswim3_h3k27me3_rep2


title: ATAC-seq 20230725_hek293t_pe_EMX1-sgpair3_PE3_rep3

description:
Library name: 20230725_hek293t_pe_EMX1-sgpair3_PE3_rep3
ATAC-seq sample EMX1-sgpair3_PE3_rep3


title: ATAC-seq 20201013_nih3t3_cas9_cas9_only_vector_rep3

description:
Library name: 20201013_nih3t3_cas9_cas9_only_vector_rep3
ATAC-seq sample cas9_only_vector_rep3


title: ATAC-seq 20201013_nih3t3_cas9_ZSWIM3_rep2

description:
Library name: 20201013_nih3t3_cas9_ZSWIM3_rep2
ATAC-seq sample ZSWIM3_rep2


title: ATAC-seq 20201013_nih3t3_cas9_cas9_only_vector_rep1

description:
Library name: 20201013_nih3t3_cas9_cas9_only_vector_rep1
ATAC-seq sample cas9_only_vector_rep1


title: CUT&Tag hek293t_zswim3_h3k27ac_rep2

description:
Library name: hek293t_zswim3_h3k27ac_rep2
CUT&Tag sample hek293t_zswim3_h3k27ac_rep2


title: ATAC-seq 20201013_nih3t3_cas9_ZSWIM3_rep1

description:
Library name: 20201013_nih3t3_cas9_ZSWIM3_rep1
ATAC-seq sample ZSWIM3_rep1


title: ATAC-seq 20201013_nih3t3_cas9_cas9_only_vector_rep2

description:
Library name: 20201013_nih3t3_cas9_cas9_only_vector_rep2
ATAC-seq sample cas9_only_vector_rep2


title: ATAC-seq 20230725_hek293t_pe_EMX1-sgpair2_PE3_rep2

description:
Library name: 20230725_hek293t_pe_EMX1-sgpair2_PE3_rep2
ATAC-seq sample EMX1-sgpair2_PE3_rep2


title: CUT&Tag hek293t_zswim3_h3k27ac_rep1

description:
Library name: hek293t_zswim3_h3k27ac_rep1
CUT&Tag sample hek293t_zswim3_h3k27ac_rep1


title: CUT&Tag hek293t_zswim3_h3k27me3_rep1

description:
Library name: hek293t_zswim3_h3k27me3_rep1
CUT&Tag sample hek293t_zswim3_h3k27me3_rep1


title: experiment:poolsize2_920 condition:4_4 sample[5]

description: Library name: poolsize2_920_4_4_sample5


title: experiment:poolsize2_920 condition:4_4 sample[2]

description: Library name: poolsize2_920_4_4_sample2


title: ATAC-seq 20230725_hek293t_pe_EMX1-sgpair1_PE3_rep3

description:
Library name: 20230725_hek293t_pe_EMX1-sgpair1_PE3_rep3
ATAC-seq sample EMX1-sgpair1_PE3_rep3


title: experiment:poolsize2_920 condition:4_4 sample[4]

description: Library name: poolsize2_920_4_4_sample4


title: ATAC-seq 20201013_nih3t3_cas9_ZSWIM3_rep3

description:
Library name: 20201013_nih3t3_cas9_ZSWIM3_rep3
ATAC-seq sample ZSWIM3_rep3


title: ATAC-seq 20230725_hek293t_pe_EMX1-sgpair2_PE3_rep1

description:
Library name: 20230725_hek293t_pe_EMX1-sgpair2_PE3_rep1
ATAC-seq sample EMX1-sgpair2_PE3_rep1


title: experiment:poolsize2_920 condition:4_4 sample[3]

description: Library name: poolsize2_920_4_4_sample3


title: experiment:poolsize2_920 condition:4_4 sample[15]

description: Library name: poolsize2_920_4_4_sample15


title: ATAC-seq 20201013_nih3t3_cas9_ZSWIM3_dead_sgrna_rep3

description:
Library name: 20201013_nih3t3_cas9_ZSWIM3_dead_sgrna_rep3
ATAC-seq sample ZSWIM3_dead_sgrna_rep3


title: experiment:poolsize2_920 condition:4_4 sample[9]

description: Library name: poolsize2_920_4_4_sample9


title: ATAC-seq 20230123_u2os_cas9_ZSWIM3_rep3

description:
Library name: 20230123_u2os_cas9_ZSWIM3_rep3
ATAC-seq sample ZSWIM3_rep3


title: experiment:poolsize2_920 condition:4_4 sample[16]

description: Library name: poolsize2_920_4_4_sample16


title: CUT&Tag hek293t_wt_h3k9me3_rep1

description:
Library name: hek293t_wt_h3k9me3_rep1
CUT&Tag sample hek293t_wt_h3k9me3_rep1


title: ATAC-seq 20201013_nih3t3_cas9_ZSWIM3_dead_sgrna_rep1

description:
Library name: 20201013_nih3t3_cas9_ZSWIM3_dead_sgrna_rep1
ATAC-seq sample ZSWIM3_dead_sgrna_rep1


title: ATAC-seq 20201013_nih3t3_cas9_TYR_rep3

description:
Library name: 20201013_nih3t3_cas9_TYR_rep3
ATAC-seq sample TYR_rep3


title: experiment:poolsize2_920 condition:4_4 sample[14]

description: Library name: poolsize2_920_4_4_sample14


title: experiment:poolsize2_920 condition:4_4 sample[12]

description: Library name: poolsize2_920_4_4_sample12


title: experiment:poolsize2_920 condition:4_4 sample[13]

description: Library name: poolsize2_920_4_4_sample13


title: ATAC-seq 20230123_u2os_cas9_ZSWIM3_rep2

description:
Library name: 20230123_u2os_cas9_ZSWIM3_rep2
ATAC-seq sample ZSWIM3_rep2


title: ATAC-seq 20201013_nih3t3_cas9_TYR_rep1

description:
Library name: 20201013_nih3t3_cas9_TYR_rep1
ATAC-seq sample TYR_rep1


title: CUT&Tag hek293t_wt_h3k27me3_rep2

description:
Library name: hek293t_wt_h3k27me3_rep2
CUT&Tag sample hek293t_wt_h3k27me3_rep2


title: ATAC-seq 20201013_nih3t3_cas9_TYR_dead_sgrna_rep3

description:
Library name: 20201013_nih3t3_cas9_TYR_dead_sgrna_rep3
ATAC-seq sample TYR_dead_sgrna_rep3


title: CUT&Tag hek293t_wt_h3k27me3_rep1

description:
Library name: hek293t_wt_h3k27me3_rep1
CUT&Tag sample hek293t_wt_h3k27me3_rep1


title: ATAC-seq 20201013_nih3t3_cas9_TYR_rep2

description:
Library name: 20201013_nih3t3_cas9_TYR_rep2
ATAC-seq sample TYR_rep2


title: ATAC-seq 20230123_u2os_cas9_ZSWIM3_rep1

description:
Library name: 20230123_u2os_cas9_ZSWIM3_rep1
ATAC-seq sample ZSWIM3_rep1


title: ATAC-seq 20230725_hek293t_pe_EMX1-sgpair3_PE3_rep1

description:
Library name: 20230725_hek293t_pe_EMX1-sgpair3_PE3_rep1
ATAC-seq sample EMX1-sgpair3_PE3_rep1


title: CUT&Tag hek293t_wt_h3k27ac_rep2

description:
Library name: hek293t_wt_h3k27ac_rep2
CUT&Tag sample hek293t_wt_h3k27ac_rep2


title: ATAC-seq 20230725_hek293t_pe_EMX1-sgpair1_PE3_rep1

description:
Library name: 20230725_hek293t_pe_EMX1-sgpair1_PE3_rep1
ATAC-seq sample EMX1-sgpair1_PE3_rep1


title: CUT&Tag hek293t_emx1_h3k9me3_rep2

description:
Library name: hek293t_emx1_h3k9me3_rep2
CUT&Tag sample hek293t_emx1_h3k9me3_rep2


title: ATAC-seq 20201013_nih3t3_cas9_ZSWIM3_dead_sgrna_rep2

description:
Library name: 20201013_nih3t3_cas9_ZSWIM3_dead_sgrna_rep2
ATAC-seq sample ZSWIM3_dead_sgrna_rep2


title: ATAC-seq 20230123_u2os_cas9_TYR_rep1

description:
Library name: 20230123_u2os_cas9_TYR_rep1
ATAC-seq sample TYR_rep1


title: ATAC-seq 20230123_u2os_cas9_TYR_rep3

description:
Library name: 20230123_u2os_cas9_TYR_rep3
ATAC-seq sample TYR_rep3


title: ATAC-seq 20230123_u2os_cas9_TYR_rep2

description:
Library name: 20230123_u2os_cas9_TYR_rep2
ATAC-seq sample TYR_rep2


title: CUT&Tag hek293t_wt_h3k27ac_rep1

description:
Library name: hek293t_wt_h3k27ac_rep1
CUT&Tag sample hek293t_wt_h3k27ac_rep1


title: experiment:poolsize2_920 condition:4_4 sample[11]

description: Library name: poolsize2_920_4_4_sample11


title: CUT&Tag hek293t_emx1_h3k9me3_rep1

description:
Library name: hek293t_emx1_h3k9me3_rep1
CUT&Tag sample hek293t_emx1_h3k9me3_rep1


title: experiment:poolsize2_920 condition:1_4 sample[9]

description: Library name: poolsize2_920_1_4_sample9


title: experiment:poolsize2_920 condition:4_4 sample[10]

description: Library name: poolsize2_920_4_4_sample10


title: CUT&Tag hek293t_emx1_h3k27ac_rep2

description:
Library name: hek293t_emx1_h3k27ac_rep2
CUT&Tag sample hek293t_emx1_h3k27ac_rep2


title: experiment:poolsize2_920 condition:4_4 sample[1]

description: Library name: poolsize2_920_4_4_sample1


title: ATAC-seq 20230123_u2os_cas9_EMX1_rep1

description:
Library name: 20230123_u2os_cas9_EMX1_rep1
ATAC-seq sample EMX1_rep1


title: ATAC-seq 20201013_nih3t3_cas9_EMX1_rep2

description:
Library name: 20201013_nih3t3_cas9_EMX1_rep2
ATAC-seq sample EMX1_rep2


title: experiment:poolsize2_920 condition:1_4 sample[8]

description: Library name: poolsize2_920_1_4_sample8


title: CUT&Tag hek293t_emx1_h3k27me3_rep1

description:
Library name: hek293t_emx1_h3k27me3_rep1
CUT&Tag sample hek293t_emx1_h3k27me3_rep1


title: ATAC-seq 20201013_nih3t3_cas9_EMX1_rep1

description:
Library name: 20201013_nih3t3_cas9_EMX1_rep1
ATAC-seq sample EMX1_rep1


title: experiment:poolsize2_920 condition:1_4 sample[6]

description: Library name: poolsize2_920_1_4_sample6


title: ATAC-seq 20201013_nih3t3_cas9_EMX1_rep3

description:
Library name: 20201013_nih3t3_cas9_EMX1_rep3
ATAC-seq sample EMX1_rep3


title: experiment:poolsize2_920 condition:1_4 sample[7]

description: Library name: poolsize2_920_1_4_sample7


title: ATAC-seq 20201013_nih3t3_cas9_TYR_dead_sgrna_rep2

description:
Library name: 20201013_nih3t3_cas9_TYR_dead_sgrna_rep2
ATAC-seq sample TYR_dead_sgrna_rep2


title: ATAC-seq 20210930_k562_cas9_ZSWIM3_rep3

description:
Library name: 20210930_k562_cas9_ZSWIM3_rep3
ATAC-seq sample ZSWIM3_rep3


title: ATAC-seq 20230123_u2os_cas9_EMX1_rep3

description:
Library name: 20230123_u2os_cas9_EMX1_rep3
ATAC-seq sample EMX1_rep3


title: ATAC-seq 20201013_nih3t3_cas9_TYR_dead_sgrna_rep1

description:
Library name: 20201013_nih3t3_cas9_TYR_dead_sgrna_rep1
ATAC-seq sample TYR_dead_sgrna_rep1


title: ATAC-seq 20201013_nih3t3_cas9_EMX1_dead_sgrna_rep3

description:
Library name: 20201013_nih3t3_cas9_EMX1_dead_sgrna_rep3
ATAC-seq sample EMX1_dead_sgrna_rep3


title: ATAC-seq 20251117_hek293t_rnp_ZSWIM3_6h_rep2

description:
Library name: 20251117_hek293t_rnp_ZSWIM3_6h_rep2
ATAC-seq sample ZSWIM3_6h_rep2


title: CUT&Tag hek293t_wt_h3k9me3_rep2

description:
Library name: hek293t_wt_h3k9me3_rep2
CUT&Tag sample hek293t_wt_h3k9me3_rep2


title: ATAC-seq 20230123_u2os_cas9_EMX1_rep2

description:
Library name: 20230123_u2os_cas9_EMX1_rep2
ATAC-seq sample EMX1_rep2


title: CUT&Tag hek293t_emx1_h3k27me3_rep2

description:
Library name: hek293t_emx1_h3k27me3_rep2
CUT&Tag sample hek293t_emx1_h3k27me3_rep2


title: ATAC-seq 20251117_hek293t_rnp_ZSWIM3_6h_rep1

description:
Library name: 20251117_hek293t_rnp_ZSWIM3_6h_rep1
ATAC-seq sample ZSWIM3_6h_rep1


title: experiment:poolsize2_920 condition:1_4 sample[5]

description: Library name: poolsize2_920_1_4_sample5


title: CUT&Tag hek293t_emx1_h3k27ac_rep1

description:
Library name: hek293t_emx1_h3k27ac_rep1
CUT&Tag sample hek293t_emx1_h3k27ac_rep1


title: ATAC-seq 20210930_k562_cas9_ZSWIM3-L_rep3

description:
Library name: 20210930_k562_cas9_ZSWIM3-L_rep3
ATAC-seq sample ZSWIM3-L_rep3


title: ATAC-seq 20210930_k562_cas9_ZSWIM3_rep1

description:
Library name: 20210930_k562_cas9_ZSWIM3_rep1
ATAC-seq sample ZSWIM3_rep1


title: RNA-seq 20230315_nih3t3_be_ZSWIM3_rep3

description:
Library name: 20230315_nih3t3_be_ZSWIM3_rep3
RNA-seq sample ZSWIM3_rep3

data_processing:
RNA-seq read adaptors were trimmed using cutadapt (version 3.4).
Trimmed reads were aligned to the reference genome using STAR (version 2.5.3a) with parameters "--twopassMode Basic --outSAMstrandField introMotif --quantMode TranscriptomeSAM".
The STAR index was constructed using the Gencode annotation gtf file (version 32 for human or version m23 for mouse) and its corresponding genome reference (hg38 for human and mm10 for mouse).
Post alignment, RSEM (version 1.3.0) was used to extract the final read count from the aligned bam file, with parameters "--no-bam-output --paired-end".
Assembly: mm10/hg38
Supplementary files format and content: raw count matrix (RSEM)
Supplementary files format and content: tpm matrix (RSEM)

extract_protocol:
Dynabeads M-280 sheep anti-Rabbit IgG (Invitrogen, 11201D) were diluted 1:10 in 1× PBS (Invitrogen, AM9624), magnetically washed, and incubated with Nesprin1 antibody (abcam, ab192234) at room temperature for 30 minutes. Antibody-coupled beads were washed and resuspended in cell lysis buffer containing 10 mM HEPES (Gibco, 15630106), 2.5 mM MgCl2 (Invitrogen, AM9530G), 10 mM KCl (Sigma, P9333), 1 mM DTT (ThermoFisher, 707265ML), 0.5% Triton X-100 (Sigma, 93443), and 2 U recombinant RNase inhibitor (Takara, 2313A). A population of 500 GFP-positive cells per sample was sorted into 10 µL lysis buffer in 96-well plates, centrifuged at 700 g for 1 minute, and incubated at 4°C with shaking (300 rpm) for 30 minutes. After magnetic separation, the supernatant was transferred to a new plate for RNA-seq workflow, while nuclei were retained for ATAC-side tagmentation workflow in AR-seq. RNA in the supernatant was purified using 2.2× VAHTS RNA Clean Beads (Vazyme, N412-03) and reverse-transcribed using SMART-seq2.
RNA-seq library construction was performed using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501), following the manufacturer's manual. Libraries were generated from SMART-seq2-derived cDNA and sequenced in paired-end mode on short-read sequencing platforms.


title: ATAC-seq 20201013_nih3t3_cas9_EMX1_dead_sgrna_rep2

description:
Library name: 20201013_nih3t3_cas9_EMX1_dead_sgrna_rep2
ATAC-seq sample EMX1_dead_sgrna_rep2


title: ATAC-seq 20210930_k562_cas9_ZSWIM3_rep2

description:
Library name: 20210930_k562_cas9_ZSWIM3_rep2
ATAC-seq sample ZSWIM3_rep2


title: experiment:poolsize2_920 condition:1_4 sample[4]

description: Library name: poolsize2_920_1_4_sample4


title: ATAC-seq 20230725_hek293t_pe_EMX1-sgpair1_PE3_rep2

description:
Library name: 20230725_hek293t_pe_EMX1-sgpair1_PE3_rep2
ATAC-seq sample EMX1-sgpair1_PE3_rep2


title: ATAC-seq 20251117_hek293t_rnp_ZSWIM3_12h_rep1

description:
Library name: 20251117_hek293t_rnp_ZSWIM3_12h_rep1
ATAC-seq sample ZSWIM3_12h_rep1


title: ATAC-seq 20201013_nih3t3_cas9_EMX1_dead_sgrna_rep1

description:
Library name: 20201013_nih3t3_cas9_EMX1_dead_sgrna_rep1
ATAC-seq sample EMX1_dead_sgrna_rep1


title: RNA-seq 20230315_nih3t3_be_ZSWIM3_rep2

description:
Library name: 20230315_nih3t3_be_ZSWIM3_rep2
RNA-seq sample ZSWIM3_rep2


title: ATAC-seq 20251117_hek293t_rnp_ZSWIM3_12h_rep2

description:
Library name: 20251117_hek293t_rnp_ZSWIM3_12h_rep2
ATAC-seq sample ZSWIM3_12h_rep2


title: experiment:poolsize2_920 condition:1_4 sample[3]

description: Library name: poolsize2_920_1_4_sample3


title: experiment:poolsize2_920 condition:1_4 sample[16]

description: Library name: poolsize2_920_1_4_sample16


title: experiment:poolsize2_920 condition:1_4 sample[15]

description: Library name: poolsize2_920_1_4_sample15


title: ATAC-seq 20210930_k562_cas9_TYR_rep3

description:
Library name: 20210930_k562_cas9_TYR_rep3
ATAC-seq sample TYR_rep3


title: ATAC-seq 20251117_hek293t_rnp_EMX1_6h_rep2

description:
Library name: 20251117_hek293t_rnp_EMX1_6h_rep2
ATAC-seq sample EMX1_6h_rep2


title: experiment:poolsize2_920 condition:1_4 sample[2]

description: Library name: poolsize2_920_1_4_sample2


title: ATAC-seq 20210930_k562_cas9_TYR_rep2

description:
Library name: 20210930_k562_cas9_TYR_rep2
ATAC-seq sample TYR_rep2


title: RNA-seq 20230315_nih3t3_be_EMX1_rep3

description:
Library name: 20230315_nih3t3_be_EMX1_rep3
RNA-seq sample EMX1_rep3


title: ATAC-seq 20210930_k562_cas9_ZSWIM3-L_rep2

description:
Library name: 20210930_k562_cas9_ZSWIM3-L_rep2
ATAC-seq sample ZSWIM3-L_rep2


title: RNA-seq 20230315_nih3t3_be_ZSWIM3_rep1

description:
Library name: 20230315_nih3t3_be_ZSWIM3_rep1
RNA-seq sample ZSWIM3_rep1


title: ATAC-seq 20251117_hek293t_rnp_EMX1_6h_rep1

description:
Library name: 20251117_hek293t_rnp_EMX1_6h_rep1
ATAC-seq sample EMX1_6h_rep1


title: ATAC-seq 20210930_k562_cas9_ZSWIM3-L_rep1

description:
Library name: 20210930_k562_cas9_ZSWIM3-L_rep1
ATAC-seq sample ZSWIM3-L_rep1


title: RNA-seq 20230315_nih3t3_be_EMX1_rep2

description:
Library name: 20230315_nih3t3_be_EMX1_rep2
RNA-seq sample EMX1_rep2


title: experiment:poolsize2_920 condition:1_4 sample[14]

description: Library name: poolsize2_920_1_4_sample14


title: experiment:poolsize2_920 condition:1_4 sample[13]

description: Library name: poolsize2_920_1_4_sample13


title: ATAC-seq 20251117_hek293t_rnp_EMX1_12h_rep1

description:
Library name: 20251117_hek293t_rnp_EMX1_12h_rep1
ATAC-seq sample EMX1_12h_rep1


title: RNA-seq 20230315_nih3t3_be_EMX1_rep1

description:
Library name: 20230315_nih3t3_be_EMX1_rep1
RNA-seq sample EMX1_rep1


title: ATAC-seq 20210930_k562_cas9_TYR_rep1

description:
Library name: 20210930_k562_cas9_TYR_rep1
ATAC-seq sample TYR_rep1


title: ATAC-seq 20210930_k562_cas9_MPP4-L_rep3

description:
Library name: 20210930_k562_cas9_MPP4-L_rep3
ATAC-seq sample MPP4-L_rep3


title: experiment:poolsize2_920 condition:1_4 sample[12]

description: Library name: poolsize2_920_1_4_sample12


title: ATAC-seq 20210930_k562_cas9_MPP4-L_rep2

description:
Library name: 20210930_k562_cas9_MPP4-L_rep2
ATAC-seq sample MPP4-L_rep2


title: ATAC-seq 20250831_hek293t_cas12a_ZSWIM3-2_rep2

description:
Library name: 20250831_hek293t_cas12a_ZSWIM3-2_rep2
ATAC-seq sample ZSWIM3-2_rep2


title: experiment:poolsize2_920 condition:1_4 sample[11]

description: Library name: poolsize2_920_1_4_sample11


title: RNA-seq 20220730_mesc_ssea1_NANOG_be_ssea1_pos_rep3

description:
Library name: 20220730_mesc_ssea1_NANOG_be_ssea1_pos_rep3
RNA-seq sample NANOG_be_ssea1_pos_rep3

value: mESC


title: ATAC-seq 20250831_hek293t_cas12a_ZSWIM3-2_rep1

description:
Library name: 20250831_hek293t_cas12a_ZSWIM3-2_rep1
ATAC-seq sample ZSWIM3-2_rep1


title: RNA-seq 20220730_mesc_ssea1_NANOG_be_ssea1_pos_rep2

description:
Library name: 20220730_mesc_ssea1_NANOG_be_ssea1_pos_rep2
RNA-seq sample NANOG_be_ssea1_pos_rep2


title: ATAC-seq 20251117_hek293t_rnp_EMX1_12h_rep2

description:
Library name: 20251117_hek293t_rnp_EMX1_12h_rep2
ATAC-seq sample EMX1_12h_rep2


title: ATAC-seq 20250831_hek293t_cas12a_ZSWIM3-1_rep2

description:
Library name: 20250831_hek293t_cas12a_ZSWIM3-1_rep2
ATAC-seq sample ZSWIM3-1_rep2


title: experiment:poolsize2_920 condition:1_4 sample[1]

description: Library name: poolsize2_920_1_4_sample1


title: RNA-seq 20220730_mesc_ssea1_NANOG_be_ssea1_pos_rep1

description:
Library name: 20220730_mesc_ssea1_NANOG_be_ssea1_pos_rep1
RNA-seq sample NANOG_be_ssea1_pos_rep1


title: RNA-seq 20220730_mesc_ssea1_NANOG_be_ssea1_neg_rep3

description:
Library name: 20220730_mesc_ssea1_NANOG_be_ssea1_neg_rep3
RNA-seq sample NANOG_be_ssea1_neg_rep3


title: ATAC-seq 20210930_k562_cas9_EMX1_rep3

description:
Library name: 20210930_k562_cas9_EMX1_rep3
ATAC-seq sample EMX1_rep3


title: ATAC-seq 20210930_k562_cas9_MPP4-L_rep1

description:
Library name: 20210930_k562_cas9_MPP4-L_rep1
ATAC-seq sample MPP4-L_rep1


title: ATAC-seq 20250831_hek293t_cas12a_ZSWIM3-1_rep1

description:
Library name: 20250831_hek293t_cas12a_ZSWIM3-1_rep1
ATAC-seq sample ZSWIM3-1_rep1


title: ATAC-seq 20250831_hek293t_cas12a_EMX1-2_rep2

description:
Library name: 20250831_hek293t_cas12a_EMX1-2_rep2
ATAC-seq sample EMX1-2_rep2


title: ATAC-seq 20210930_k562_cas9_EMX1_rep2

description:
Library name: 20210930_k562_cas9_EMX1_rep2
ATAC-seq sample EMX1_rep2


title: experiment:poolsize2_920 condition:1_1 sample[9]

description: Library name: poolsize2_920_1_1_sample9


title: RNA-seq 20220730_mesc_ssea1_NANOG_be_ssea1_neg_rep2

description:
Library name: 20220730_mesc_ssea1_NANOG_be_ssea1_neg_rep2
RNA-seq sample NANOG_be_ssea1_neg_rep2


title: ATAC-seq 20210930_k562_cas9_EMX1_rep1

description:
Library name: 20210930_k562_cas9_EMX1_rep1
ATAC-seq sample EMX1_rep1


title: experiment:poolsize2_920 condition:1_1 sample[8]

description: Library name: poolsize2_920_1_1_sample8


title: ATAC-seq 20250831_hek293t_cas12a_EMX1-2_rep1

description:
Library name: 20250831_hek293t_cas12a_EMX1-2_rep1
ATAC-seq sample EMX1-2_rep1


title: ATAC-seq 20250831_hek293t_cas12a_EMX1-1_rep2

description:
Library name: 20250831_hek293t_cas12a_EMX1-1_rep2
ATAC-seq sample EMX1-1_rep2


title: experiment:poolsize2_920 condition:1_1 sample[7]

description: Library name: poolsize2_920_1_1_sample7


title: experiment:poolsize2_920 condition:1_4 sample[10]

description: Library name: poolsize2_920_1_4_sample10


title: ATAC-seq 20210930_k562_cas9_EMX1-H_rep3

description:
Library name: 20210930_k562_cas9_EMX1-H_rep3
ATAC-seq sample EMX1-H_rep3


title: RNA-seq 20220730_mesc_ssea1_NANOGSE_be_ssea1_pos_rep2

description:
Library name: 20220730_mesc_ssea1_NANOGSE_be_ssea1_pos_rep2
RNA-seq sample NANOGSE_be_ssea1_pos_rep2


title: ATAC-seq 20210930_k562_cas9_EMX1-H_rep2

description:
Library name: 20210930_k562_cas9_EMX1-H_rep2
ATAC-seq sample EMX1-H_rep2


title: experiment:poolsize2_920 condition:1_1 sample[5]

description: Library name: poolsize2_920_1_1_sample5


title: ATAC-seq 20210930_k562_cas9_EMX1-H_rep1

description:
Library name: 20210930_k562_cas9_EMX1-H_rep1
ATAC-seq sample EMX1-H_rep1


title: RNA-seq 20220730_mesc_ssea1_NANOGSE_be_ssea1_pos_rep1

description:
Library name: 20220730_mesc_ssea1_NANOGSE_be_ssea1_pos_rep1
RNA-seq sample NANOGSE_be_ssea1_pos_rep1


title: RNA-seq 20250731_hek293t_rnp_ZSWIM3_rep2

description:
Library name: 20250731_hek293t_rnp_ZSWIM3_rep2
RNA-seq sample ZSWIM3_rep2