title: Control hTSC_2

description: Library name: SC_2

value: Trophoblast stem cells


title: ESC-CTCF/WAPL-AID, E14, IAA treated 12 hours

status: Public on Mar 27 2026

type: SRA

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

country: USA

institute: NIH/NCI

description: Library name: Sample 5

library_source: genomic

data_processing:
ATACseq data were processed using the Center for Cancer Research Collaborative Bioinformatics Resource’s ASPEN (ATACseq PipEliNe) version 0.5.2 (https://doi.org /10.5281/zenodo.13755867 and https://github.com/CCBR/ASPEN) to generate signal tracks (bigwigs).
Assembly: mm10
Supplementary files format and content: bigwig files containing reads per genomic content (RGPC) normalized read density.

molecule: genomic DNA

organism: Mus musculus

growth_protocol: ESC were grown on 0.1% gelatin-coated plates in high-glucose DMEM (Gibco) supplemented with 15% FBS, 1:500 LIF (made in house), 0.1 mM non-essential amino acids, 1% glutamax, 1mM Sodium Pyruvate, 55 mM β-mercaptoethanol, and 1% penicillin/streptomycin (all from ThermoFisher Scientific) at 37°C and 5% CO2. Cells were routinely passaged with Trypsin 0.05% (Gibco). Media was changed every other day and passaged every 2-3 days.

extract_protocol:
Briefly, 50,000 cells were first washed with 50ul cold 1X PBS and nuclei were isolated by resuspending the cells in 50ul Lysis Buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630, 0.1% Tween-20, and 0.01% Digitonin) on ice for three minutes. Nuclei were washed once with 1ml Wash Buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, and 0.1% Tween-20) and further resuspended in 50ul Transposition Reaction Mix (Tn5 Transposase, 1X TD Buffer, 0.1% Tween-20, 0.01% Digitonin) for exactly 30 minutes at 37 °C. Following transposition, DNA was purified using the Zymo DNA Clean and Concentrator kit (Zymo, D4033).
Libraries were prepared using the entire purified DNA, Q5 Polymerase, and unique barcoded primers. An initial PCR amplification was performed at 72 °C for 5 minutes followed by 5 cycles of 98 °C, 10 seconds, 63 °C, 30 seconds, and 72 °C 1 minute. Then, tubes were held on ice while a quantitative PCR was run on 5 ul of the pre-amplified library to determine the additional number of cycles needed. PCR reactions were cleaned up with AMPure XP beads (Beckman Coulter) and concentration was determined with KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems). Sequencing was performed on the Illumina NextSeq550 (75 bp pair-end reads).

treatment_protocol: ESC were untreated or treated for the indicated times with indole-3-acetic acid (IAA) at a final concentration of 500nM.

tag: cell line

tag: cell type

value: Embryonic stem cell

tag: genotype

value: CTCF/WAPL-AID

tag: treatment

value: IAA

tag: time

value: 12 hours


title: Frontal cortex, CORT+DFP+LPS, 6 h, A493

city: Toronto

first: Patrick

last: McGowan

state: Ontario

address: 1265 Military Trail

department: Biological Sciences

country: Canada

institute: University of Toronto Scarborough

description:
Library name: CTX_A493
FC-6hr-4
csaw_CTX_6h_vs_CTRL.bed

data_processing:
Raw sequencing reads were processed using Trim Galore (v0.6.7) and FASTQC (v0.11.9) for adapter removal and quality control.
Trimmed reads were aligned to the mouse reference genome GRCm38 (mm10) using Bowtie2 (v2.4.4) with default settings.
ATAC-seq peaks were identified using MACS2 (v2.2.7.1).
Differential accessibility analysis was performed using the Bioconductor package csaw.
Processed BED files correspond to differentially accessible regions in frontal cortex and hippocampus at 6 h, 12 h, and 24 h relative to CORT+DFP+Saline, 6 h baseline controls.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Sample-level MACS2 narrowPeak files containing called accessible chromatin regions for each ATAC-seq library; study-level supplementary BED files contain differentially accessible regions identified by csaw.
Supplementary files format and content: Per-sample processed files are named using sample shorthand (FC or HIP, condition/timepoint, replicate) with the suffix _peaks.narrowPeak. Supplementary csaw BED files are named by tissue (CTX or HPC) and comparison (6 h, 12 h, or 24 h relative to baseline controls).

source_name: Frontal cortex

growth_protocol: Adult male C57BL/6J mice were housed under standard conditions with ad libitum access to food and water.

extract_protocol:
Frozen hippocampus and frontal cortex tissue samples (20–30 mg) were used for ATAC-seq library preparation.
ATAC-seq libraries for hippocampus and frontal cortex were generated from frozen tissue samples (20–30 mg) using the OMNI-ATAC-seq protocol. Sequencing was performed on an Illumina NovaSeq 6000 at the Princess Margaret Genomics Centre (Toronto, ON, Canada) using paired-end 50 bp reads.

treatment_protocol: To model Gulf War Illness-related stress and toxicant exposure, mice received corticosterone (CORT) in the drinking water for 7 days, followed on day 8 by a single intraperitoneal injection of diisopropyl fluorophosphate (DFP), with repeated intermittent CORT administration over 5 weeks. On the final day, mice received either saline or lipopolysaccharide (LPS), and hippocampus and frontal cortex were collected 6 h, 12 h, or 24 h after challenge.

tag: tissue

value: Frontal cortex

value: wild type

value: CORT+DFP+LPS, 6 h


title: ESC-CTCF/WAPL-AID, E14, IAA treated 24 hours

description: Library name: Sample 6

value: 24 hours


title: CD34, BCL11B-dTAG, DMSO, rep3, RNA

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

description:
Library name: RNAseq_CD34_BCL11BdTAG_DMSO_0249
TPM_CD34_017.txt

library_source: transcriptomic

data_processing:
Raw paired-end reads were quality trimmed and adapter trimmed using TrimGalore (v0.4.4) with a quality score cutoff of Q20. Quality trimmed reads were mapped to the GRCh38 reference genome with BWA (v0.7.12-r1039) and converted to bam format using samtools64 (v1.2). Duplicate reads were marked using biobambam2 (v2.0.87). Properly paired and uniquely mapped reads were extracted by samtools (-F 1804 -b -q 1) and converted to paired-end fragment intervals (BEDPE). For coverage calculation, fragments with inferred insert size < 2000 bp were counted and used to compute a library-size scaling factor to normalize signal to a fixed library size. The center 80 bp of these fragments were used to generate genome-wide coverage tracks using bedtools genomecov in bedGraph format (-bg), applying the scaling factor for depth normalization (-scale). BedGraph files were converted to BigWig format using UCSC tools (bedGraphToBigWig) for visualization in IGV and for creating heatmaps. To increase detection of BCL11BdTAG and RUNX1 binding events in CD34+ HSPCs without DMSO or dTAGV-1 treatment, the mapped bam files from both replicates were merged prior to downstream processing.
Raw paired-end reads were quality trimmed and adapter trimmed using TrimGalore (v0.4.4) with a quality score cutoff of Q20. The first 15 bp of each read were clipped to reduce the GC bias introduced by the Tn5 enzyme. Quality trimmed reads were mapped to the GRCh38 reference genome with BWA (v0.7.12-r1039) and converted to bam format using samtools64 (v1.2). Duplicate reads were marked using biobambam2 (v2.0.87). Properly paired and uniquely mapped reads were extracted by samtools (-F 1804 -b -q 1). The center 80 bp of nucleosome-free fragments (fragment size < 109 bp) were extracted using bedtools and converted to scaled genome coverage tracks for visualization on IGV and in heatmaps. The scaling factor was computed from the total number of nucleosome-free fragments to normalize signal to a fixed library size. Peaks were called with MACS2 (v2.1.1.20160309) using nucleosome-free fragments with parameters -f BEDPE --keep-dup all -q 0.01
For CD34+ HSPCs: Paired-end RNA-seq reads were adapter and quality trimmed using Trim Galore (v0.4.4), and read quality was assessed with FastQC. Reads were aligned to the GRCh38 reference genome with STAR (v2.7) in two-pass mode. Coordinate-sorted BAM files, transcriptome alignments, gene counts, and strand-specific RPM-normalized coverage tracks were generated during alignment, and wiggle files were converted to BigWig format using wigToBigWig. Duplicate reads were marked with GATK MarkDuplicates, alignments were indexed with SAMtools, and RNA-seq quality metrics were collected using Picard CollectRnaSeqMetrics. Gene- and isoform-level expression was quantified with RSEM. Differential expression analysis was performed using the edgeR/limma-voom workflow. Genes with counts per million (CPM) ≥ 1 in at least 3 samples were retained using edgeR, and normalized expression values were generated by voom as log2-counts per million. Differentially expressed genes between treatment groups and transduction conditions were identified using linear models with empirical Bayes moderation implemented in limma.
For Jurkat BRU-seq: Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2. Unaligned reads were subsequently mapped strand-specifically to human genome build hg38/GRCh38 using STAR and GENCODE annotation version 27. Gene expression was quantified as previously described (Magnuson et al., 2022) and differential gene expression was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: .bw files contain coverage files in bigwig format
Supplementary files format and content: .narrowPeak files contain MACS2 called peaks
Supplementary files format and content: .txt file contains transcripts per million (TPM) values

molecule: total RNA

organism: Homo sapiens

source_name: Cord Blood

growth_protocol: CD34+ HSPCs were expanded in Stemspan media supplemented with 1X penicillin-streptomycin-glutamine, 100ng/mL SCF, TPO, IL-6 and FLT3-L, and 1 µM stemregenin-1. Jurkat cells were cultured in RPMI-1640 supplemented with 1X penicillin-streptomycin-glutamine and 10% FBS.

extract_protocol:
CUT&RUN was performed on 0.1 – 0.5 million CD34+ HSPCs using the CUTANA ChIC/CUT&RUN kit from EpiCypher (#14-1048-24) following manufacturer’s instructions.
ATAC-seq was performed with 50,000 cells using the Omni-ATAC protocol as described (Corces et al., 2017). Cells were washed once with 1X PBS and then lysed in 50µl cold Cell Lysis Buffer containing 0.01% digitonin for 3 minutes on ice. After cell lysis, 1mL cold Resuspension Buffer was added and cells were immediately spun at 600xg for 10 minutes at 4°C. After removing the supernatant, the nuclei were transposed in 50µl Transposition reaction using the Tn5 enzyme from Illumina for 30 minutes at 37°C. Transposed DNA was purified using a Qiagen MinElute PCR clean-up kit and DNA was eluted in 10µl Elution Buffer.
CD34+ HSPCs were harvested following DMSO or dTAGV-1 treatment and resuspended in TRI Reagent (Sigma). RNA was isolated using the Direct-zol RNA miniprep kit (Zymo Research #R2050). For BRU-seq, cells were lysed directly in Trizol followed by isolation of total RNA and treatment with DNAse (TURBO DNA-free Kit; Invitrogen). The Bru-labeled RNA was immunocaptured using anti-BrdU antibodies (BD Biosciences).
Libraries were constructed using library prep kits from EpiCypher (#14-1001) following manufacturer’s instructions.
Libraries were constructed by amplifying eluted DNA with barcoded primers described in Corces et al., 2017 for 10-12 cycles. The optimal number of cycles was determined by performing a quantitative PCR analysis after the initial 5 PCR cycles. Amplified libraries were purified using AMPure beads to remove fragments less than 200bp and larger than 700 bp. Final barcoded libraries were pooled and sequenced in paired-end mode.
CD34+ HSPCs: RNA was quantified using the Quant-iT RiboGreen RNA assay (ThermoFisher) and quality checked by the 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent) prior to library generation. Libraries were prepared from total RNA with the Illumina Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20040529). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent), 4200 TapeStation D1000 ScreenTape assay (Agilent), or 5300 Fragment Analyzer NGS fragment kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher) or by low pass sequencing with a MiSeq nano kit (Illumina). Paired end 100 cycle sequencing was performed on a NovaSeq X Plus (Illumina).
Jurkat (BRU-seq): Strand-specific libraries were prepared from a modified protocol using the TruSeq Kit (Illumina) as previously described (Paulsen et al., 2013)

treatment_protocol: Cells were treated with 500nM dTAGV-1 or an equivalent volume of DMSO(1ul/mL media) for 6 hours and then immediately harvested for downstream processing.

value: Cord Blood

value: CD34+ HSPC

tag: genetic modifiction

value: DMSO


title: Hippocampus, CORT+DFP+LPS, 6 h, A493

description:
Library name: HPC_A493
HIP-6hr-4
csaw_HPC_6h_vs_CTRL.bed

source_name: Hippocampus

value: Hippocampus


title: Frontal cortex, CORT+DFP+LPS, 12 h, A503

description:
Library name: CTX_A503
FC-12hr-4
csaw_CTX_12h_vs_CTRL.bed

value: CORT+DFP+LPS, 12 h


title: Control hTSC_1

city: Madrid

first: Vicente

middle: Pérez

last: García

state: Madrid

address: C/ Nicolás Cabrera 1

department: Tissue and organ homeostasis

country: Spain

institute: Centro de Biologia Molecular Severo Ochoa

description: Library name: SC_1

data_processing:
Reads were mapped to Homo sapiens GRCh38 genome  assembly using HISAT2 v2.1.0.
Read counts and normalization were performed with SeqMonk software.
Assembly: GRCh38
Supplementary files format and content: Matrix with raw counts for each sample per column

extract_protocol:
Total RNA was extracted using RNeasy mini-Kit and RNase-free DNase (QIAGEN 74106)
RNA-seq libraries were generated from 500ng using TruSeq Stranded mRNA library prop (Illumina, 20020594).

tag: sample group

value: Control hTSC


title: CD34, BCL11B-dTAG, DMSO, rep1, RNA

description:
Library name: RNAseq_CD34_BCL11BdTAG_DMSO_0615
TPM_CD34_017.txt


title: MCF7 hypoxia rep2 input

city: Urbana

first: Prasanth

last: Kannanganattu

state: IL

address: 601 S Goodwin Ave

department: Cell and Developmental Biology

institute: University of Illinois at Urbana-Champaign

description: Library name: Sample_8

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina)
RAP-DNA-seq reads were trimmed of the adaptor sequences then mapped to the human genome using Bowtie2.
Assembly: GRCh38
Supplementary files format and content: Aligned reads in bigwig format

source_name: Breast

growth_protocol: Cells were cultured at 37 degrees Celsius with 5% carbon dioxide.

extract_protocol:
DNA was purified from nuclear lysate.
Libraries were constructed using sparQ DNA Library Preparation kit from Quantabio.

treatment_protocol: Hypoxia treatment was done by incubating the cells in 0.2% oxygen, 5% carbon dioxide chamber for 24 hours. Transient knockdown of MALAT1 was done using ASO.

value: Breast

value: Breast epithelial cell

value: wildtype

value: Hypoxia


title: ESC-CTCF/WAPL-AID, E14, IAA treated 6 hours

description: Library name: Sample 4

value: Embryonic stem cell

value: CTCF/WAPL-AID

value: 6 hours


title: Frontal cortex, CORT+DFP+LPS, 6 h, A492

description:
Library name: CTX_A492
FC-6hr-3
csaw_CTX_6h_vs_CTRL.bed

value: Frontal cortex


title: CD34, empty vector, dTAGV-1, rep3, RNA

description:
Library name: RNAseq_CD34_Empty_dTAG_0249
TPM_CD34_017.txt

value: Empty vector


title: RS-04372479_5-18-2

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

description: Library name: RS-04372479_5-18-2

data_processing:
CDR3 clonotypes were assembled using MiXCR preset workflows for mouse Takara Smart-Seq.
Assembly: mm10
Supplementary files format and content: csv file countaining TCRB-CDR3 clonotype calls for each sample
Library strategy: TCR-Seq

source_name: T cells

growth_protocol: The syngeneic metastatic SCLC model was induced by intravenous tail vein injection of 1×10⁶ N2N1G-GFP/Luc cells into C57BL/6J mice

extract_protocol:
500ng of total RNA was used as input for cDNA synthesis.
T-cell receptor (TCR) repertoire profiling was performed using the SMART-Seq Mouse TCR (with UMIs) kit (Takara Bio, USA) according to the manufacturer’s protocol. First-strand cDNA was generated using SMART (Switching Mechanism at the 5′ end of RNA template) technology, which incorporates unique molecular identifiers (UMIs) during reverse transcription. A 5′-RACE strategy was applied to capture the full-length variable regions of the TRA and TRB chains. Amplified cDNA underwent two rounds of PCR: the first to enrich TCR α/β libraries, and the second to incorporate unique dual indexes (UDIs) for sample multiplexing on patterned flow cells. Libraries were purified using AMPure XP beads (Beckman Coulter) and quantified with Qubit fluorometry (Thermo Fisher Scientific). Library size distribution and quality were assessed on an Agilent 4200 TapeStation using High Sensitivity D1000 ScreenTape. Indexed libraries were pooled equimolarly and sequenced on an Illumina NextSeq platform with 150-bp paired-end read length optimized for CDR3 assembly using a MiXCR preset workflow.

treatment_protocol: 24 days after tumor inoculation, 3×10⁶ untransduced T cells or CAR T cells were administered via tail vein injection.

value: T cells

value: Wild type


title: Hippocampus, CORT+DFP+LPS, 6 h, A492

description:
Library name: HPC_A492
HIP-6hr-3
csaw_HPC_6h_vs_CTRL.bed

value: wild type

value: CORT+DFP+LPS, 6 h


title: CD34, empty vector, dTAGV-1, rep2, RNA

description:
Library name: RNAseq_CD34_Empty_dTAG_0205
TPM_CD34_017.txt

value: Cord Blood

value: CD34+ HSPC


title: Frontal cortex, CORT+DFP+Saline, 6 h, A482

description:
Library name: CTX_A482
FC-CTRL-3
csaw_CTX_6h_vs_CTRL.bed

value: CORT+DFP+Saline, 6 h


title: Hepg2, Torin1, 6h, mRNA-seq, rep3

city: weifang

first: yongqi

last: liu

state: shandong

address: 699 Binhu Road, Xiashan District

country: China

institute: Peking University Institute of Advanced Agricultural Sciences

description: Library name: Hepg2-Torin1-6-3

data_processing:
Raw sequencing data quality was assessed using FastQC to evaluate read quality.
Cleaned reads were aligned to the human reference genome (GRCh38) using HISAT2 with default parameters.
Aligned reads were processed with StringTie for quantification. Expression levels were estimated as transcripts per million (FPKM) for downstream analysis.
Count matrices generated by StringTie were imported into DESeq2 in R to identify differentially expressed genes.
Assembly: GRCh38 (human reference genome)
Supplementary files format and content: Submitted files include raw expression matrix (FPKM) and differential gene analysis (DESeq2 output) for all samples.
Supplementary files format and content: csv files include FPKM values for each Sample

molecule: polyA RNA

growth_protocol: HepG2 and HCT116 cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin at 37°C with 5% CO₂. Cells were seeded at a density of 2 × 10⁵ cells per well in 6-well plates and allowed to adhere overnight.

extract_protocol:
Total RNA extracted using Trizol reagent (Invitrogen). RNA purity verified by Nanodrop (A260/A280 >1.8), integrity by Agilent 2100 Bioanalyzer (RIN >8.0).
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V8 RNA - seq Library Prep Kit for MGI.
Bulk RNA-seq libraries prepared with VAHTS Universal V8 RNA-seq Library Prep Kit for MGI (Vazyme): 2 μg RNA underwent polyA selection, fragmentation, cDNA synthesis, end repair, adapter ligation, and PCR amplification. Libraries sequenced on MGISEQ-2000RS (paired-end).

treatment_protocol: Treatments included IL-6 (50 ng/mL, MedChemExpress, HY-P7044, China), TNF-α (100 ng/mL, MedChemExpress, HY-P7058, China), and Torin1 (1 μM, MedChemExpress, HY-13003, China), with incubation times of 3 and 6 hours. Control groups (MOCK) were treated with an equal volume of complete medium. Followed by one PBS rinse prior to sample collection. Each condition was performed in triplicate.

value: liver cancer stem cell


title: MCF7 hypoxia rep1 input

description: Library name: Sample_7

value: Breast


title: ESC, IAA treated 48 hours

description: Library name: Sample 2

value: WT

value: IAA

value: 48 hours


title: CD34, empty vector, DMSO, rep3, RNA

description:
Library name: RNAseq_CD34_Empty_DMSO_0249
TPM_CD34_017.txt

value: DMSO


title: CD34, empty vector, dTAGV-1, rep1, RNA

description:
Library name: RNAseq_CD34_Empty_dTAG_0615
TPM_CD34_017.txt


title: Frontal cortex, CORT+DFP+Saline, 6 h, A481

description:
Library name: CTX_A481
FC-CTRL-2
csaw_CTX_6h_vs_CTRL.bed


title: MCF7 normoxia rep2 input

description: Library name: Sample_6

value: Breast epithelial cell

value: wildtype

value: Normoxia


title: Hippocampus, CORT+DFP+Saline, 6 h, A481

description:
Library name: HPC_A481
HIP-CTRL-2
csaw_HPC_6h_vs_CTRL.bed

value: Hippocampus


title: MCF7 hypoxia rep2

description: Library name: Sample_4

value: Hypoxia


title: Hippocampus, CORT+DFP+Saline, 6 h, A482

description:
Library name: HPC_A482
HIP-CTRL-3
csaw_HPC_6h_vs_CTRL.bed


title: Frontal cortex, CORT+DFP+LPS, 24 h, A280

description:
Library name: CTX_A280
FC-24hr-1
csaw_CTX_24h_vs_CTRL.bed

value: Frontal cortex

value: CORT+DFP+LPS, 24 h


title: CD34, empty vector, DMSO, rep2, RNA

description:
Library name: RNAseq_CD34_Empty_DMSO_0205
TPM_CD34_017.txt

value: Empty vector


title: Hepg2, Torin1, 6h, mRNA-seq, rep1

description: Library name: Hepg2-Torin1-6-1


title: MCF7 normoxia rep2

description: Library name: Sample_2


title: Hepg2, Torin1, 6h, mRNA-seq, rep2

description: Library name: Hepg2-Torin1-6-2


title: ESC-CTCF/WAPL-AID, E14, IAA untreated

description: Library name: Sample 3

value: Embryonic stem cell

value: CTCF/WAPL-AID

value: Untreated


title: CD34, empty vector, DMSO, rep1, RNA

description:
Library name: RNAseq_CD34_Empty_DMSO_0615
TPM_CD34_017.txt

value: Cord Blood

value: CD34+ HSPC


title: MCF7 hypoxia rep1

description: Library name: Sample_3

value: Breast


title: MCF7 normoxia rep1 input

description: Library name: Sample_5


title: Hepg2, Torin1, 3h, mRNA-seq, rep3

description: Library name: Hepg2-Torin1-3-3

value: liver cancer stem cell


title: Hippocampus, CORT+DFP+LPS, 24 h, A280

description:
Library name: HPC_A280
HIP-24hr-1
csaw_HPC_24h_vs_CTRL.bed

value: wild type


title: ESC, untreated

description: Library name: Sample 1

value: WT


title: Jurkat, BCL11B-dTAG, HA

description: Library name: CUTRUN_Jurkat_BCL11BdTAG_HA

data_processing:
Raw paired-end reads were quality trimmed and adapter trimmed using TrimGalore (v0.4.4) with a quality score cutoff of Q20. Quality trimmed reads were mapped to the GRCh38 reference genome with BWA (v0.7.12-r1039) and converted to bam format using samtools64 (v1.2). Duplicate reads were marked using biobambam2 (v2.0.87). Properly paired and uniquely mapped reads were extracted by samtools (-F 1804 -b -q 1) and converted to paired-end fragment intervals (BEDPE). For coverage calculation, fragments with inferred insert size < 2000 bp were counted and used to compute a library-size scaling factor to normalize signal to a fixed library size. The center 80 bp of these fragments were used to generate genome-wide coverage tracks using bedtools genomecov in bedGraph format (-bg), applying the scaling factor for depth normalization (-scale). BedGraph files were converted to BigWig format using UCSC tools (bedGraphToBigWig) for visualization in IGV and for creating heatmaps. To increase detection of BCL11BdTAG and RUNX1 binding events in CD34+ HSPCs without DMSO or dTAGV-1 treatment, the mapped bam files from both replicates were merged prior to downstream processing.
Raw paired-end reads were quality trimmed and adapter trimmed using TrimGalore (v0.4.4) with a quality score cutoff of Q20. The first 15 bp of each read were clipped to reduce the GC bias introduced by the Tn5 enzyme. Quality trimmed reads were mapped to the GRCh38 reference genome with BWA (v0.7.12-r1039) and converted to bam format using samtools64 (v1.2). Duplicate reads were marked using biobambam2 (v2.0.87). Properly paired and uniquely mapped reads were extracted by samtools (-F 1804 -b -q 1). The center 80 bp of nucleosome-free fragments (fragment size < 109 bp) were extracted using bedtools and converted to scaled genome coverage tracks for visualization on IGV and in heatmaps. The scaling factor was computed from the total number of nucleosome-free fragments to normalize signal to a fixed library size. Peaks were called with MACS2 (v2.1.1.20160309) using nucleosome-free fragments with parameters -f BEDPE --keep-dup all -q 0.01
For CD34+ HSPCs: Paired-end RNA-seq reads were adapter and quality trimmed using Trim Galore (v0.4.4), and read quality was assessed with FastQC. Reads were aligned to the GRCh38 reference genome with STAR (v2.7) in two-pass mode. Coordinate-sorted BAM files, transcriptome alignments, gene counts, and strand-specific RPM-normalized coverage tracks were generated during alignment, and wiggle files were converted to BigWig format using wigToBigWig. Duplicate reads were marked with GATK MarkDuplicates, alignments were indexed with SAMtools, and RNA-seq quality metrics were collected using Picard CollectRnaSeqMetrics. Gene- and isoform-level expression was quantified with RSEM. Differential expression analysis was performed using the edgeR/limma-voom workflow. Genes with counts per million (CPM) ≥ 1 in at least 3 samples were retained using edgeR, and normalized expression values were generated by voom as log2-counts per million. Differentially expressed genes between treatment groups and transduction conditions were identified using linear models with empirical Bayes moderation implemented in limma.
For Jurkat BRU-seq: Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2. Unaligned reads were subsequently mapped strand-specifically to human genome build hg38/GRCh38 using STAR and GENCODE annotation version 27. Gene expression was quantified as previously described (Magnuson et al., 2022) and differential gene expression was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: .bw files contain coverage files in bigwig format
Supplementary files format and content: .narrowPeak files contain MACS2 called peaks
Supplementary files format and content: .txt file contains transcripts per million (TPM) values
Library strategy: CUT&Run

source_name: Jurkat

value: Jurkat

value: T cell acute lymphoblastic leukemia

value: BCL11B-dTAG (CRISPR knockin)

tag: antibody

value: HA (CST3724S)


title: Frontal cortex, CORT+DFP+LPS, 12 h, A262

description:
Library name: CTX_A262
FC-12hr-1
csaw_CTX_12h_vs_CTRL.bed

value: CORT+DFP+LPS, 12 h


title: Jurkat, BCL11B-dTAG, IgG

description: Library name: CUTRUN_Jurkat_BCL11BdTAG_IgG

value: IgG (Epicypher)


title: Hepg2, Torin1, 3h, mRNA-seq, rep1

description: Library name: Hepg2-Torin1-3-1


title: Hepg2, TNF-a, 6h, mRNA-seq, rep3

description: Library name: Hepg2-TNF-a-6-3


title: MCF7 MALAT1KO hypoxia rep2

description: Library name: Sample_35

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina)
RNA-seq reads were aligned to human reference genome GRCh38 assembly using STAR
Raw gene counts were first analyzed by HTSEQ-Count
Assembly: GRCh38
Supplementary files format and content: HTSeq gene count in TSV format

extract_protocol:
RNA was extracted using Trizol and cleaned up using Qiagen RNeasy column.
The polyA RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina), polyadenylated mRNAs were captured with oligodT beads. The total RNAseq were prepared with the Watchmaker Stranded mRNA library kit after Ribosomal RNAs were removed with the Fastselect HRM kit (Qiagen).

treatment_protocol: Hypoxia treatment was done by incubating the cells in 0.2% oxygen, 5% carbon dioxide chamber for 24 hours. Transient knockdown of MALAT1 was done using ASO. Stable knockdown of SRSF1 was done using shRNA.

value: Breast epithelial cell

value: MALAT1 KO

value: Hypoxia


title: Hippocampus, CORT+DFP+LPS, 12 h, A262

description:
Library name: HPC_A262
HIP-12hr-1
csaw_HPC_12h_vs_CTRL.bed

value: Hippocampus


title: MCF7 MALAT1KO hypoxia rep3

description: Library name: Sample_36


title: CD34-016, BCL11B-dTAG, BRG1, dTAGV-1, rep1

description: Library name: CUTRUN_CD34_016_BCL11BdTAG_dTAG_BRG1_rep1

value: BRG1 (CSTD1Q7F)


title: MCF7 MALAT1KO hypoxia rep1

description: Library name: Sample_34


title: MCF7 normoxia rep1

description: Library name: Sample_1

value: wildtype

value: Normoxia


title: MCF7 MALAT1KO normoxia rep3

description: Library name: Sample_33

value: Breast


title: Frontal cortex, CORT+DFP+LPS, 6 h, A244

description:
Library name: CTX_A244
FC-6hr-1
csaw_CTX_6h_vs_CTRL.bed

value: Frontal cortex

value: CORT+DFP+LPS, 6 h


title: CD34-016, BCL11B-dTAG, BRG1, DMSO, rep1

description: Library name: CUTRUN_CD34_016_BCL11BdTAG_DMSO_BRG1_rep1

value: Cord Blood

value: CD34+ HSPC

value: DMSO


title: fibrosis livers, thioacetamide treated, regression 2 weeks-1

city: Osaka

first: Thuy

middle: Thi Thanh

last: Le

state: Osaka

address: 1-4-3 Asahimachi, Abeno-ku

department: Department of Global Education and Medical Sciences

country: Japan

institute: Osaka Metropolitan University Graduate School of Medicine

description:
Library name: regressed_2w_livers_wt1815
10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing and gene expression quantification were performed using Cell Ranger v7.1.0 (10x Genomics)
Assembly: Mouse Mm10
Supplementary files format and content: Tab-separared values files and matrix files

source_name: livers

extract_protocol:
Frozen mouse liver tissues from control, TAA-induced cirrhosis, and regression groups (n = 3 per group) were used for single-cell fixed RNA sequencing. Tissue dissociation and fixation were performed using the Chromium Next GEM RNA Profiling Sample Fixation Kit (10x Genomics, PN-1000414, CA, USA) following the manufacturer’s instructions. Briefly, tissues were weighed to determine the required volume of Fixation Buffer (1 mL per 25 mg of tissue), placed on a pre-chilled glass dish on dry ice, finely minced, and incubated in Fixation Buffer at 4°C for 16–24 hours. After centrifugation at 850g for 5 minutes at room temperature (RT), the supernatant was carefully removed. The pellet was washed twice with chilled PBS and resuspended in Resuspension Buffer on ice. Dissociation Solution (10x Genomics) was pre-warmed to 37°C for 10 minutes, and 2 mL was added to each sample. Samples were transferred into Miltenyi C tubes (Miltenyi Biotec, Cat#130-093-237) and processed using a GentleMACS Octo Dissociator with Heater (Cat#130-096-427) according to the recommended protocol. The resulting cell suspensions were filtered through MACS SmartStrainers (30 μm, Cat#130-098-458), and viable cells were counted using trypan blue or propidium iodide staining (Sigma, Cat#P4170). Finally, single-cell suspensions were stored at –80°C in Quenching Buffer supplemented with Enhancer and Glycerol.
Gene expression profiling was conducted using the Chromium Fixed RNA Profiling Reagent Kit for Singleplexed Samples (10x Genomics, CG000477 Rev C), employing the Mouse Transcriptome Probe Set. Approximately 2,000,000–3,000,000 fixed cells were hybridized for 18 hours at 42 °C with whole-transcriptome probe pairs. After post-hybridization washes, cells were encapsulated in gel beads-in-emulsion (GEMs) using the Chromium X system and Chip Q. Within each GEM, ligated probe pairs were barcoded with 10x GEM Barcodes and Unique Molecular Identifiers (UMIs), followed by heat denaturation and recovery. The barcoded products underwent pre-amplification and purification using SPRIselect beads. Final libraries were generated via sample index PCR using the Dual Index Kit TS Set A and were further purified by size selection. Library quality was assessed using an Agilent Bioanalyzer, and concentrations were determined using the KAPA Library Quantification Kit (Roche). Libraries were sequenced on the DNBSEQ-G400RS platform (MGI Tech) in paired-end mode, using 28 bp for Read 1 (containing the 16 bp GEM barcode and 12 bp UMI) and 100 bp for Read 2 (capturing the probe insert).

treatment_protocol: Thioacetamide-induced liver fibrosis progression and regression after 2 weeks

value: livers

value: all liver cell types

tag: age

value: 8 weeks old

tag: Sex

value: Male


title: CD34-016, BCL11B-dTAG, BRG1, DMSO, rep2

description: Library name: CUTRUN_CD34_016_BCL11BdTAG_DMSO_BRG1_rep2


title: fibrosis livers, thioacetamide treated, regression 2 weeks-3

description:
Library name: regressed_2w_livers_wt1817
10x Genomics


title: lungSPF_3

city: Hangzhou city

first: Liang

last: Huang

address: 866 Yuhangtang Road Xihu District, Hangzhou Zhejiang Province, China

institute: Zhejiang university

description:
Library name: sample54
removed adaptor

data_processing:
STAR v2.7.10a; FastQC v0.12.1
Assembly: GRCm39
Supplementary files format and content: featureCounts

source_name: lung

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: lung


title: fibrosis livers, thioacetamide treated, regression 2 weeks-2

description:
Library name: regressed_2w_livers_wt1816
10x Genomics


title: MCF7 MALAT1KO normoxia rep2

description: Library name: Sample_32

value: Breast epithelial cell

value: MALAT1 KO


title: lungSPF_2

description:
Library name: sample53
removed adaptor


title: MCF7 MALAT1KO normoxia rep1

description: Library name: Sample_31


title: CD34-016, empty vector, BRG1, dTAGV-1, rep2

description: Library name: CUTRUN_CD34_016_Empty_dTAG_BRG1_rep2

value: Empty vector


title: Hepg2, Torin1, 3h, mRNA-seq, rep2

description: Library name: Hepg2-Torin1-3-2

value: liver cancer stem cell


title: CD34-016, BCL11B-dTAG, IgG

description: Library name: CUTRUN_CD34_016_BCL11BdTAG_IgG

value: IgG (Epicypher)


title: fibrosis livers, thioacetamide treated-2

description:
Library name: fibrosis_livers_wt13
10x Genomics

value: thioacetamide treated


title: CD34-016, BCL11B-dTAG, BRG1, dTAGV-1, rep2

description: Library name: CUTRUN_CD34_016_BCL11BdTAG_dTAG_BRG1_rep2

value: BRG1 (CSTD1Q7F)


title: fibrosis livers, thioacetamide treated-3

description:
Library name: fibrosis_livers_wt14
10x Genomics


title: lungSPF_1

description:
Library name: sample52
removed adaptor


title: lungFMT_3

description:
Library name: sample51
removed adaptor


title: MCF7 Wildtype hypoxia rep3

description: Library name: Sample_30

value: Breast

value: WT

value: Hypoxia


title: fibrosis livers, thioacetamide treated-1

description:
Library name: fibrosis_livers_wt11
10x Genomics


title: CD34-016, empty vector, BRG1, dTAGV-1, rep1

description: Library name: CUTRUN_CD34_016_Empty_dTAG_BRG1_rep1

value: Cord Blood

value: CD34+ HSPC


title: MCF7 Wildtype hypoxia rep1

description: Library name: Sample_28


title: CD34-016, empty vector, BRG1, DMSO, rep2

description: Library name: CUTRUN_CD34_016_Empty_DMSO_BRG1_rep2

value: DMSO


title: lungFMT_2

description:
Library name: sample50
removed adaptor


title: Hippocampus, CORT+DFP+LPS, 6 h, A244

description:
Library name: HPC_A244
HIP-6hr-1
csaw_HPC_6h_vs_CTRL.bed

value: Hippocampus

value: wild type

value: CORT+DFP+LPS, 6 h


title: MCF7 Wildtype hypoxia rep2

description: Library name: Sample_29


title: control livers, nontreated-2

description:
Library name: control_livers_wt1199
10x Genomics

value: livers

value: all liver cell types

value: 8 weeks old

value: Male

value: nontreated


title: control livers, nontreated-3

description:
Library name: control_livers_wt1200
10x Genomics


title: lungGF_3

description:
Library name: sample48
removed adaptor

value: lung


title: MCF7 Wildtype normoxia rep3

description: Library name: Sample_27

value: Breast epithelial cell

value: Normoxia


title: CD34-016, empty vector, BRG1, DMSO, rep1

description: Library name: CUTRUN_CD34_016_Empty_DMSO_BRG1_rep1

value: Empty vector

value: BRG1 (CSTD1Q7F)


title: lungGF_2

description:
Library name: sample47
removed adaptor


title: lungFMT_1

description:
Library name: sample49
removed adaptor


title: CD34-016, empty vector, IgG

description: Library name: CUTRUN_CD34_016_Empty_IgG

value: IgG (Epicypher)


title: MCF7 Wildtype normoxia rep2

description: Library name: Sample_26

value: Breast

value: WT


title: control livers, nontreated-1

description:
Library name: control_livers_wt1198
10x Genomics


title: CD34-018, BCL11B-dTAG, RUNX1

description:
Library name: CUTRUN_CD34_018_BCL11BdTAG_RUNX1.bw
Experiment to test if untagged BCL11B induces similar decrease in RUNX1 chromatin occupancy as BCL11B-dTAG

value: Cord Blood

value: CD34+ HSPC


title: CD34-018, BCL11B-dTAG, IgG

description:
Library name: CUTRUN_CD34_018_BCL11BdTAG_IgG.bw
Experiment to test if untagged BCL11B induces similar decrease in RUNX1 chromatin occupancy as BCL11B-dTAG


title: MCF7 Wildtype normoxia rep1

description: Library name: Sample_25


title: lungGF_1

description:
Library name: sample46
removed adaptor


title: HCT116 MALAT1 ASO hypoxia rep2

description: Library name: Sample_24

source_name: Colon

value: Colon

value: Colon epithelial cell

value: MALAT1 ASO

value: Hypoxia


title: 25L008068 | mouse neuron lysate control S4 R2

city: Munich

first: Gil

middle: Gregor

last: Westmeyer

address: Arcisstrasse 21

country: Germany

institute: Technical University Munich

description: Library name: 25L008068

data_processing:
Deduplication via czid-dedup (paired-end mode)
Quant files (*.sf.gz): Quantification via salmon (salmon quant -i {COMBINED_INDEX_SALMON} -l A -1 {R1} -2 {R2} --validateMappings -p 8 -o {OUT_PATH}")
Assembly: hg38, mm39, ARS-UCDI1.2
Supplementary files format and content: Quant files (*.sf.gz): comma seperated plaintext file containing the TPMs and estimated number of reads for a specific sample, including metadata

source_name: brain

growth_protocol: HEK293T cells were cultured in advanced DMEM supplemented wih 10% FCS and passaged by using Accutase at confluency

extract_protocol:
RNA from cell lysate was harvested using the NEB Monarch® Total RNA Miniprep Kit (T2010S). NTVE derived RNA was extracted from the supernatant using the Zymo Research Quick-RNA Viral Kit (R1040).
Libraries were constructed according to the protocols using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus for total RNA runs and Illumina Stranded mRNA Prep for polyA enriched runs

treatment_protocol: 500 ng/ml doycycline for NTVE induction; 50 ng/ml interferon-gamma or ASCL1 transactivation for pertubation.

value: brain

value: murine primary neurons

value: primary neuron

value: primary mouse cortical neurons

tag: rna origin

value: Lysate

value: lysate control

tag: batch


title: CD34-018, BCL11B, IgG

description:
Library name: CUTRUN_CD34_018_BCL11B_IgG.bw
Experiment to test if untagged BCL11B induces similar decrease in RUNX1 chromatin occupancy as BCL11B-dTAG


title: 25L008069 | mouse neuron lysate control S4 R3

description: Library name: 25L008069


title: HCT116 MALAT1 ASO hypoxia rep1

description: Library name: Sample_23


title: liverSPF_3

description:
Library name: sample45
removed adaptor

source_name: liver

value: liver


title: CD34-018, BCL11B, RUNX1

description:
Library name: CUTRUN_CD34_018_BCL11B_RUNX1.bw
Experiment to test if untagged BCL11B induces similar decrease in RUNX1 chromatin occupancy as BCL11B-dTAG


title: HCT116 MALAT1 ASO normoxia rep2

description: Library name: Sample_22

value: Normoxia


title: 25L008066 | mouse neuron lysate control S3 R3

description: Library name: 25L008066


title: 25L008067 | mouse neuron lysate control S4 R1

description: Library name: 25L008067


title: CD34-018, empty vector, IgG

description:
Library name: CUTRUN_CD34_018_Empty_IgG.bw
Experiment to test if untagged BCL11B induces similar decrease in RUNX1 chromatin occupancy as BCL11B-dTAG

value: Empty vector

value: IgG (Epicypher)


title: liverSPF_1

description:
Library name: sample43
removed adaptor


title: liverFMT_3

description:
Library name: sample42
removed adaptor


title: HCT116 MALAT1 ASO normoxia rep1

description: Library name: Sample_21


title: HU16

city: Rochester,

first: Khursheed Ul Islam

last: Ganaie

state: New York

address: 601 Elmwood Ave,

department: Environmental Medicine

institute: University of Rochester

description: Library name: HU16

data_processing:
The raw matrices were processed using the standard Seurat workflow with filtering based on the nfeature_RNA > 200, percent.mt < 30 and nCount_RNA <1e+05. The merged Seurat object underwent Harmony Integration at a resolution of 0.5 and Human Lung dataset from Azimuth application was used for cluster annotation following the dimensionality reduction. Thereafter the standard Seurat, DESeq2 and EnrichR pipelines were used to identify variable features, differentially expressed genes and gene enrichment pathways.
Assembly: GRCh38-2020-A
Supplementary files format and content: market exchange format, This includes background and cell-associated barcodes
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Lung

extract_protocol:
Flash-frozen lung tissues were first chemically fixed to preserve cellular integrity and RNA content. The tissues were minced into small pieces using a sterile blade on a glass surface and transferred to the fixation buffer at a ratio of 1 mL per 25 mg of tissue. The samples were incubated at 4°C for 24 hours without agitation. Following fixation, tissues were washed with PBS and subsequently quenched with the quenching buffer provided in the kit to neutralize the fixative. For dissociation, the fixed tissues were enzymatically digested using a pre-warmed dissociation solution containing the Liberase enzyme. The reaction was performed using a gentleMACS Octo Dissociator (Miltenyi Biotec, Germany) to ensure single-cell suspensions were obtained. The resulting cell suspension was filtered through a 30 μm strainer to remove debris and washed with PBS before proceeding to downstream applications.
The dissociated fixed cells were processed using the 10x Genomics Chromium Fixed RNA Profiling Reagent Kit (10x Genomics, Pleasanton, CA). The processed samples were then loaded onto the 10x Genomics Chromium X instrument, where individual cells were encapsulated into nanoliter-scale Gel Beads-in-emulsion (GEMs) along with reagents necessary for downstream processing. Inside each GEM, probes were ligated, and unique molecular identifiers (UMIs) and barcodes were incorporated into the transcripts. After breaking the emulsions, the barcoded probes were amplified via polymerase PCR, and sequencing-ready libraries were generated using the Chromium Fixed RNA Gene Expression Library Kit, followed by size selection and quality control assessments. The libraries were sequenced with ~200 million PE150 reads per sample on NovaSeq X Plus (Illumina, San Diego, CA). The sequencing reads were analyzed using Cell Ranger 7 (10x Genomics, Pleasanton, CA) and the human reference genome Chromium Human Transcriptome Probe Set v1.0.1 GRCh38-2020-A. The aggregation of the samples was performed using the cellranger aggr function, normalizing for the total number of confidently mapped reads across the libraries.

value: Lung

tag: disease state

value: HIV+

value: female

tag: smoking status

value: Current Smoker


title: 25L008064 | mouse neuron lysate control S3 R1

description: Library name: 25L008064


title: 25L008065 | mouse neuron lysate control S3 R2

description: Library name: 25L008065


title: liverFMT_2

description:
Library name: sample41
removed adaptor


title: HU15

description: Library name: HU15

value: male


title: liverSPF_2

description:
Library name: sample44
removed adaptor


title: HCT116 Scramble ASO hypoxia rep1

description: Library name: Sample_19

value: Colon

value: Colon epithelial cell

value: Scramble ASO


title: 25L008063 | mouse neuron lysate control S2 R3

description: Library name: 25L008063

value: brain

value: murine primary neurons


title: HCT116 Scramble ASO hypoxia rep2

description: Library name: Sample_20

value: Hypoxia


title: Hu14

description: Library name: Hu14

value: Unknown


title: liverGF_3

description:
Library name: sample39
removed adaptor


title: 25L008061 | mouse neuron lysate control S2 R1

description: Library name: 25L008061

value: primary neuron

value: primary mouse cortical neurons

value: Lysate

value: lysate control


title: HCT116 Scramble ASO normoxia rep2

description: Library name: Sample_18

value: Normoxia


title: liverGF_2

description:
Library name: sample38
removed adaptor

value: liver


title: HCT116 Scramble ASO normoxia rep1

description: Library name: Sample_17


title: HU12

description: Library name: HU12

value: Lung

value: HIV+

value: Non Smoker


title: HU3

description: Library name: HU3

value: male

value: Current Smoker


title: 25L008060 | mouse neuron lysate control S1 R3

description: Library name: 25L008060


title: Hu13

description: Library name: Hu13

value: female


title: MB231 MALAT1KO hypoxia rep2

description: Library name: Sample_16

value: Breast

value: Breast epithelial cell

value: MALAT1 KO


title: kidneySPF_3

description:
Library name: sample36
removed adaptor

source_name: kidney

value: kidney


title: MB231 MALAT1KO hypoxia rep1

description: Library name: Sample_15

value: Hypoxia


title: 25L008059 | mouse neuron lysate control S1 R2

description: Library name: 25L008059

value: brain

value: murine primary neurons

value: primary neuron


title: liverGF_1

description:
Library name: sample37
removed adaptor


title: MB231 MALAT1KO normoxia rep2

description: Library name: Sample_14


title: 25L008058 | mouse neuron lysate control S1 R1

description: Library name: 25L008058

value: primary mouse cortical neurons

value: Lysate

value: lysate control


title: kidneySPF_2

description:
Library name: sample35
removed adaptor


title: HU2

description: Library name: HU2

value: Lung


title: liverFMT_1

description:
Library name: sample40
removed adaptor

value: liver


title: HU11

description: Library name: HU11

value: Normal


title: HU10

description: Library name: HU10


title: 25L008057 | mouse neuron supernatant S4 R3 TP7; no forskolin; dox-induced

description: Library name: 25L008057

value: Supernatant

value: timepoint=TP7; no forskolin; dox-induced 48h prior


title: kidneySPF_1

description:
Library name: sample34
removed adaptor


title: 25L008056 | mouse neuron supernatant S4 R2 TP7; no forskolin; dox-induced

description: Library name: 25L008056


title: MB231 Wildtype hypoxia rep 2

description: Library name: Sample_12

value: WT


title: MB231 MALAT1KO normoxia rep1

description: Library name: Sample_13

value: Breast

value: Normoxia


title: MB231 Wildtype hypoxia rep 1

description: Library name: Sample_11

value: Breast epithelial cell


title: 25L008055 | mouse neuron supernatant S4 R1 TP7; no forskolin; dox-induced

description: Library name: 25L008055


title: 25L008062 | mouse neuron lysate control S2 R2

description: Library name: 25L008062


title: kidneyFMT_3

description:
Library name: sample33
removed adaptor

value: kidney


title: kidneyFMT_2

description:
Library name: sample32
removed adaptor


title: kidneyFMT_1

description:
Library name: sample31
removed adaptor


title: 25L008051 | mouse neuron supernatant S1 R3 TP7; forskolin (10uM); dox-induced

description: Library name: 25L008051

value: timepoint=TP7; forskolin 10uM; dox-induced 48h prior


title: HU9

description: Library name: HU9

value: male

value: Current Smoker


title: 25L008052 | mouse neuron supernatant S2 R2 TP7; no forskolin; dox-induced

description: Library name: 25L008052

value: brain

value: murine primary neurons

value: primary neuron


title: HU7

description: Library name: HU7

value: female

value: Non Smoker


title: MB231 Wildtype normoxia rep 2

description: Library name: Sample_10


title: HU6

description: Library name: HU6

value: Lung


title: HU8

description: Library name: HU8

value: Normal


title: 25L008050 | mouse neuron supernatant S1 R2 TP7; forskolin (10uM); dox-induced

description: Library name: 25L008050

value: primary mouse cortical neurons

value: Supernatant


title: kidneyGF_3

description:
Library name: sample30
removed adaptor


title: MB231 Wildtype normoxia rep 1

description: Library name: Sample_9

value: WT


title: kidneyGF_1

description:
Library name: sample28
removed adaptor


title: MCF7 MALAT1 ASO CoCl2 rep1

description: Library name: Sample_7

value: Breast

value: MALAT1 ASO


title: 25L008048 | mouse neuron supernatant S4 R3 TP6; no forskolin; dox-induced

description: Library name: 25L008048

value: timepoint=TP6; no forskolin; dox-induced 48h prior


title: MCF7 MALAT1 ASO CoCl2 rep2

description: Library name: Sample_8

value: Breast epithelial cell


title: MCF7 MALAT1 ASO noCoCl2 rep2

description: Library name: Sample_6

value: DMSO


title: 25L008047 | mouse neuron supernatant S4 R2 TP6; no forskolin; dox-induced

description: Library name: 25L008047


title: HU1

description: Library name: HU1

value: male


title: iSGPCs-P9-2

city: Beijing

first: Wenpeng

last: Song

state: Beijing

address: Department of Stomatology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China

department: Department of Stomatology

institute: Capital Medical University

description: Library name: Sample 13

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: PSCs-derived salivary gland progenitor cells

extract_protocol:
Total RNA was extracted from cells using the TRIzolTM reagent according to the manufacturer’s instructions. The RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). To construct RNA-seq libraries, mRNA was enriched using Oligo dT-attached magnetic beads, fragmented, and reverse-transcribed into cDNA.
The cDNA was then ligated to sequencing adapters, and PCR amplification was performed to enrich the libraries. After the library construction was completed, the library was initially quantified using the Qubit 2.0 Fluorometer (ThermoFisher Scientific, Massachusetts, USA) and then diluted to 1.5 ng/µL. The insert size of the library was subsequently analyzed using the Agilent 2100 Bioanalyzer. Once the insert size met the expected criteria, the effective concentration of the library was accurately determined using qRT-PCR (with the effective concentration being higher than 1.5 nM) to ensure the quality of the library. After the library passed quality control, different libraries were pooled according to their effective concentration and the required target data output for sequencing. The pooled libraries were then subjected to Illumina sequencing.


title: MCF7 MALAT1 ASO noCoCl2 rep1

description: Library name: Sample_5


title: iSGPCs-P6-2

description: Library name: Sample 11

value: PSCs-derived salivary gland progenitor cells


title: iSGPCs-P9-1

description: Library name: Sample 12


title: jejunumSPF_1

description:
Library name: sample25
removed adaptor

source_name: jejunum

value: jejunum


title: 25L008049 | mouse neuron supernatant S1 R1 TP7; forskolin (10uM); dox-induced

description: Library name: 25L008049

value: brain

value: murine primary neurons

value: timepoint=TP7; forskolin 10uM; dox-induced 48h prior


title: kidneyGF_2

description:
Library name: sample29
removed adaptor

value: kidney


title: jejunumSPF_2

description:
Library name: sample26
removed adaptor


title: jejunumFMT_3

description:
Library name: sample24
removed adaptor


title: iSGPCs-P3-2

description: Library name: Sample 9


title: MCF7 Scramble ASO CoCl2 rep2

description: Library name: Sample_4

value: Scramble ASO


title: 25L008040 | mouse neuron supernatant S1 R3 TP6; forskolin (10uM); dox-induced

description: Library name: 25L008040

value: primary neuron

value: timepoint=TP6; forskolin 10uM; dox-induced 48h prior


title: iSGPCs-P6-1

description: Library name: Sample 10


title: MCF7 Scramble ASO noCoCl2 rep2

description: Library name: Sample_2


title: HU5

description: Library name: HU5

value: Lung

value: Normal

value: female

value: Non Smoker


title: jejunumGF_3

description:
Library name: sample21
removed adaptor


title: jejunumFMT_1

description:
Library name: sample22
removed adaptor


title: jejunumFMT_2

description:
Library name: sample23
removed adaptor


title: MCF7 Scramble ASO noCoCl2 rep1

description: Library name: Sample_1

value: Breast


title: HEK293T hypoxia rep2 input

description: Library name: Sample_8

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina)
Assembly: hg38
Supplementary files format and content: BigWig format of SON TSA-DNA-seq data in 20 kb bins

source_name: Kidney

extract_protocol:
DNA was extracted using phenol-chloroform-isoamyl alcohol.
Libraries were constructed using Illumina TruSeq ChIP Sample Prep Kit

value: Kidney

value: Epithelial-like cell derived from human fetal kidney

value: wildtype

value: Hypoxia


title: 25L008038 | mouse neuron supernatant S1 R1 TP6; forskolin (10uM); dox-induced

description: Library name: 25L008038

value: primary mouse cortical neurons

value: Supernatant


title: SGPC_4

description: Library name: Sample 7

value: PSCs-derived salivary gland progenitor cells


title: jejunumSPF_3

description:
Library name: sample27
removed adaptor

value: jejunum


title: 25L008046 | mouse neuron supernatant S4 R1 TP6; no forskolin; dox-induced

description: Library name: 25L008046

value: brain

value: murine primary neurons

value: timepoint=TP6; no forskolin; dox-induced 48h prior


title: 25L008037 | mouse neuron supernatant S4 R3 TP5; no forskolin; dox-induced

description: Library name: 25L008037

value: primary neuron

value: timepoint=TP5; no forskolin; dox-induced 48h prior


title: iSGPCs-P3-1

description: Library name: Sample 8


title: HEK293T hypoxia rep1 input

description: Library name: Sample_7


title: 25L008041 | mouse neuron supernatant S2 R2 TP6; no forskolin; dox-induced

description: Library name: 25L008041


title: jejunumGF_2

description:
Library name: sample20
removed adaptor


title: 25L008039 | mouse neuron supernatant S1 R2 TP6; forskolin (10uM); dox-induced

description: Library name: 25L008039

value: timepoint=TP6; forskolin 10uM; dox-induced 48h prior


title: HEK293T normoxia rep2 input

description: Library name: Sample_6

value: Normoxia


title: SGPC_3

description: Library name: Sample 6


title: jejunumGF_1

description:
Library name: sample19
removed adaptor


title: SGPC_2

description: Library name: Sample 5


title: MCF7 Scramble ASO CoCl2 rep1

description: Library name: Sample_3

value: Breast epithelial cell

value: Scramble ASO


title: 25L008035 | mouse neuron supernatant S4 R1 TP5; no forskolin; dox-induced

description: Library name: 25L008035


title: 25L008036 | mouse neuron supernatant S4 R2 TP5; no forskolin; dox-induced

description: Library name: 25L008036


title: SGPC_1

description: Library name: Sample 4


title: 25L008030 | mouse neuron supernatant S2 R2 TP5; no forskolin; dox-induced

description: Library name: 25L008030


title: HEK293T hypoxia rep2

description: Library name: Sample_4

value: Kidney


title: heartSPF_3

description:
Library name: sample18
removed adaptor

source_name: heart

value: heart


title: heartSPF_2

description:
Library name: sample17
removed adaptor


title: HEK293T hypoxia rep1

description: Library name: Sample_3

value: Epithelial-like cell derived from human fetal kidney

value: wildtype


title: 25L008028 | primary neuron S1_R3_TP5

description:
Library name: 25L008028
Primary mouse cortical neuron

value: primary mouse cortical neurons

value: NTVE expression via AAV


title: iPSCs_3

description: Library name: Sample 3

value: PSCs-derived salivary gland progenitor cells


title: 25L008027 | mouse neuron supernatant S1 R2 TP5; forskolin (10uM); dox-induced

description: Library name: 25L008027

value: Supernatant

value: timepoint=TP5; forskolin 10uM; dox-induced 48h prior


title: heartSPF_1

description:
Library name: sample16
removed adaptor


title: iPSCs_1

description: Library name: Sample 1


title: iPSCs_2

description: Library name: Sample 2


title: HEK293T normoxia rep2

description: Library name: Sample_2


title: heartFMT_3

description:
Library name: sample15
removed adaptor


title: HEK293T normoxia rep1 input

description: Library name: Sample_5


title: heartFMT_2

description:
Library name: sample14
removed adaptor


title: HEK293T normoxia rep1

description: Library name: Sample_1


title: Frontal cortex, CORT+DFP+Saline, 6 h, CT_Con3

description:
Library name: CT_Con3
Reduced representation bisulfite sequencing of mouse frontal cortex DNA
CTX_Con_6h_percent_methylation.tsv

data_processing:
Raw RRBS FASTQ files were processed as single-end reads. Adapters and low-quality bases were trimmed with Trim Galore! using RRBS mode (--rrbs), Phred quality cutoff 30, and FastQC was run on trimmed libraries.
After initial trimming, RRBS diversity adapters were removed using trimRRBSdiversityAdaptCustomers.py.
Trimmed single-end reads were aligned to the mouse reference genome GRCm38 (mm10) using Bismark with Bowtie2, and aligned BAM files were sorted with SAMtools.
Methylation levels for each CpG site were estimated in methylKit from the ratio of methylated to total reads at each locus; processed files are tissue-specific CpG-level percent methylation matrices for CORT+DFP+Saline, 6 h baseline controls versus CORT+DFP+LPS comparisons at 6 h, 12 h, and 24 h.
Differential methylation in the study was assessed using methylKit logistic regression with minimum 10x coverage in every sample, at least 5% methylation difference, and FDR-adjusted p < 0.05.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Processed data files are unfiltered TSV tables containing genomic coordinates (chr, start, end, strand) followed by sample-specific percent methylation values. These files are not restricted to statistically significant differentially methylated CpGs.
Supplementary files format and content: Nine processed files are included: Blood_Con_6h_percent_methylation.tsv, Blood_Con_12h_percent_methylation.tsv, Blood_Con_24h_percent_methylation.tsv, HPC_Con_6h_percent_methylation.tsv, HPC_Con_12h_percent_methylation.tsv, HPC_Con_24h_percent_methylation.tsv, CTX_Con_6h_percent_methylation.tsv, CTX_Con_12h_percent_methylation.tsv, and CTX_Con_24h_percent_methylation.tsv.

source_name: Frontal cortex

growth_protocol: Adult male C57BL/6J mice (8-12 weeks old, approximately 30 g) were obtained from Jackson Laboratory and housed individually under controlled temperature and humidity on a 12 h light/12 h dark cycle with ad libitum access to food and water.

extract_protocol:
Genomic DNA was extracted from whole blood and dissected brain tissues using standard column-based purification methods; only high-quality DNA was used for RRBS library preparation.
RRBS libraries were prepared from 100 ng high-quality genomic DNA using the Ovation RRBS Methyl-Seq System (Tecan Genomics/NuGEN) according to the manufacturer's protocol, followed by bisulfite conversion and library amplification.

treatment_protocol: To model Gulf War Illness-related stress and toxicant exposure, mice received corticosterone (CORT; 200 mg/L in 0.6% ethanol) in the drinking water for 7 days, followed on day 8 by a single intraperitoneal injection of diisopropyl fluorophosphate (DFP; 4 mg/kg). Mice then received periodic CORT administration for 7 days every other week to a total of 5 weeks. On the final day, mice received either saline or lipopolysaccharide (LPS; 0.5 mg/kg, subcutaneous). Whole blood, hippocampus, and frontal cortex were collected 6 h, 12 h, or 24 h after challenge, depending on group.

value: Frontal cortex

value: wild type

value: CORT+DFP+Saline, 6 h


title: MDA-MB-231_ShACO2-NLS-MTS_R3

description:
Library name: MDA-MB-231_ShACO2-NLS-MTS_R3
MDA-MB-231_ShACO2-NLS-MTS_R3

data_processing:
ATAC-seq reads were aligned to the human genome (version GRCh38) with bowtie2. Picard was used to mark and remove the duplicated reads. Accessible peak regions for each replicate were called using MACS2, with a q-value cutoff of 0.05 in paired-end mode. All the peaks in replicates were merged to identify consensus genomic region peaks. UCSC toolkit bigWigAverageOverBed was used to extract the counts of fragments for each replicate and to make a count-table for the differential analysis.
Assembly: GRCh38
Supplementary files format and content: bigwig file for each sample

source_name: breast cancer cell line

growth_protocol: breast cancer cell lines MDA-MB-231 were cultured in DMEM (Gibco, Catalog# 11965092) supplemented with 10% fetal bovine serum (HI-FBS, Gibco, Catalog# 16140071), and 1% Antibiotic-Antimycotic (Gibco, Catalog# 15240062).

extract_protocol:
Approximately, 1 X 106 cells were lysed with QIAzol lysis reagent, followed by the addition of chloroform. Aqueous and organic phases were later separated by centrifugation. Aqueous phases were transferred to a new tube, followed by the addition of 100% ethanol to it, and mixed by pipetting. The sample was later transferred into an RNeasy Mini spin column for collecting total RNA. On-column DNAse digestion was performed to remove residual genomic DNA.
Nuclei were isolated from 50,000 cells. The samples were tagmented by resuspending nuclei in 2.5μL TDE1 transposase (Illumina; FC-121-1030), 25μL TD 2x buffer (Illumina; FC-121-1030), 22.5μL nuclease-free water, followed by incubation at 37°C for 30 minutes. The tagmented DNA fragments were purified by using a Qiagen MinElute PCR Purification kit. The purified DNA fragments were amplified by PCR (10 cycles) using KAPA Hi Fi 2X ready-mix (Roche). The amplified products were purified with AmpureXP beads (Beckman Coulter), followed by verification of the final library profiles by HSD1000 screentape on a Tapestation 4200 (Agilent). The libraries were quantitated using the KAPA Biosystems qPCR kit (Roche) and were pooled together in an equimolar fashion, following experimental design criteria. The resulting pool was then loaded into the appropriate NovaSeq Reagent cartridge and sequenced on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.).

treatment_protocol: MDA-MB-231 cells with shACO2 or shACO2-MTS-NLS were generated.

value: breast cancer cell line


title: 25L008026 | mouse neuron supernatant S1 R1 TP5; forskolin (10uM); dox-induced

description: Library name: 25L008026

value: brain

value: murine primary neurons

value: primary neuron


title: 25L008024 | mouse neuron supernatant S4 R2 TP4; no forskolin; dox-induced

description: Library name: 25L008024

value: timepoint=TP4; no forskolin; dox-induced 48h prior


title: MDA-MB-231_ShACO2-NLS-MTS_R2

description:
Library name: MDA-MB-231_ShACO2-NLS-MTS_R2
MDA-MB-231_ShACO2-NLS-MTS_R2


title: Frontal cortex, CORT+DFP+Saline, 6 h, CT_Con2

description:
Library name: CT_Con2
Reduced representation bisulfite sequencing of mouse frontal cortex DNA
CTX_Con_6h_percent_methylation.tsv


title: 25L008025 | mouse neuron supernatant S4 R3 TP4; no forskolin; dox-induced

description: Library name: 25L008025


title: heartFMT_1

description:
Library name: sample13
removed adaptor


title: Frontal cortex, CORT+DFP+Saline, 6 h, CT_Con1

description:
Library name: CT_Con1
Reduced representation bisulfite sequencing of mouse frontal cortex DNA
CTX_Con_6h_percent_methylation.tsv


title: heartGF_2

description:
Library name: sample11
removed adaptor


title: MDA-MB-231_ShACO2-NLS-MTS_R1

description:
Library name: MDA-MB-231_ShACO2-NLS-MTS_R1
MDA-MB-231_ShACO2-NLS-MTS_R1


title: 25L008023 | mouse neuron supernatant S4 R1 TP4; no forskolin; dox-induced

description: Library name: 25L008023


title: Hippocampus, CORT+DFP+LPS, 24 h, HC_24h4

description:
Library name: HC_24h4
Reduced representation bisulfite sequencing of mouse hippocampus DNA
HPC_Con_24h_percent_methylation.tsv

source_name: Hippocampus

value: Hippocampus

value: CORT+DFP+LPS, 24 h


title: MDA-MB-231_ShACO2_R3

description:
Library name: MDA-MB-231_ShACO2_R3
MDA-MB-231_ShACO2_R3


title: 25L008022 | mouse neuron supernatant S3 R3 TP4; no forskolin; dox-induced

description: Library name: 25L008022


title: heartGF_1

description:
Library name: sample10
removed adaptor

value: heart


title: heartGF_3

description:
Library name: sample12
removed adaptor


title: Hippocampus, CORT+DFP+LPS, 24 h, HC_24h1

description:
Library name: HC_24h1
Reduced representation bisulfite sequencing of mouse hippocampus DNA
HPC_Con_24h_percent_methylation.tsv


title: MDA-MB-231_ShACO2_R1

description:
Library name: MDA-MB-231_ShACO2_R1
MDA-MB-231_ShACO2_R1


title: MDA-MB-231_ShACO2_R2

description:
Library name: MDA-MB-231_ShACO2_R2
MDA-MB-231_ShACO2_R2


title: 25L008020 | mouse neuron supernatant S3 R1 TP4; no forskolin; dox-induced

description: Library name: 25L008020


title: colonSPF_2

description:
Library name: sample8
removed adaptor

source_name: colon

value: colon


title: Hippocampus, CORT+DFP+LPS, 24 h, HC_24h2

description:
Library name: HC_24h2
Reduced representation bisulfite sequencing of mouse hippocampus DNA
HPC_Con_24h_percent_methylation.tsv


title: MDA-MB-231_ShNT_R2

description:
Library name: MDA-MB-231_ShNT_R2
MDA-MB-231_ShNT_R2

value: ShNT


title: 25L008018 | mouse neuron supernatant S2 R2 TP4; no forskolin; dox-induced

description: Library name: 25L008018

value: primary mouse cortical neurons


title: MDA-MB-231_ShNT_R3

description:
Library name: MDA-MB-231_ShNT_R3
MDA-MB-231_ShNT_R3


title: 25L008019 | mouse neuron supernatant S2 R3 TP4; no forskolin; dox-induced

description: Library name: 25L008019


title: Hippocampus, CORT+DFP+LPS, 24 h, HC_24h3

description:
Library name: HC_24h3
Reduced representation bisulfite sequencing of mouse hippocampus DNA
HPC_Con_24h_percent_methylation.tsv


title: colonSPF_1

description:
Library name: sample7
removed adaptor


title: Hippocampus, CORT+DFP+LPS, 12 h, HC_12h2

description:
Library name: HC_12h2
Reduced representation bisulfite sequencing of mouse hippocampus DNA
HPC_Con_12h_percent_methylation.tsv

value: CORT+DFP+LPS, 12 h


title: colonFMT_2

description:
Library name: sample5
removed adaptor


title: Hippocampus, CORT+DFP+LPS, 12 h, HC_12h3

description:
Library name: HC_12h3
Reduced representation bisulfite sequencing of mouse hippocampus DNA
HPC_Con_12h_percent_methylation.tsv


title: MDA-MB-231_ShNT_R1

description:
Library name: MDA-MB-231_ShNT_R1
MDA-MB-231_ShNT_R1


title: 25L008021 | mouse neuron supernatant S3 R2 TP4; no forskolin; dox-induced

description: Library name: 25L008021

value: Supernatant


title: 25L008017 | mouse neuron supernatant S2 R1 TP4; no forskolin; dox-induced

description: Library name: 25L008017


title: C42 ACO2.KO R3

description:
Library name: C42_ACO2.KO_R3
C42_ACO2.KO_R3

source_name: prostate cancer cell line

growth_protocol: Prostate cancer cell line C4-2 were cultured in RPMI-1640 supplemented with 10% fetal bovine serum and 1% Antibiotic-Antimycotic.

treatment_protocol: C4-2 cells with ACO2 knockout were generated.

value: prostate cancer cell line


title: Hippocampus, CORT+DFP+LPS, 12 h, HC_12h1

description:
Library name: HC_12h1
Reduced representation bisulfite sequencing of mouse hippocampus DNA
HPC_Con_12h_percent_methylation.tsv


title: 25L008015 | mouse neuron supernatant S1 R2 TP4; no forskolin; dox-induced

description: Library name: 25L008015


title: 25L008016 | mouse neuron supernatant S1 R3 TP4; no forskolin; dox-induced

description: Library name: 25L008016


title: colonFMT_1

description:
Library name: sample4
removed adaptor


title: Hippocampus, CORT+DFP+LPS, 6 h, HC_6h4

description:
Library name: HC_6h4
Reduced representation bisulfite sequencing of mouse hippocampus DNA
HPC_Con_6h_percent_methylation.tsv

value: CORT+DFP+LPS, 6 h


title: C42 ACO2.KO R2

description:
Library name: C42_ACO2.KO_R2
C42_ACO2.KO_R2


title: Hippocampus, CORT+DFP+LPS, 6 h, HC_6h3

description:
Library name: HC_6h3
Reduced representation bisulfite sequencing of mouse hippocampus DNA
HPC_Con_6h_percent_methylation.tsv

value: wild type


title: colonSPF_3

description:
Library name: sample9
removed adaptor


title: colonGF_3

description:
Library name: sample3
removed adaptor


title: colonGF_2

description:
Library name: sample2
removed adaptor


title: C42 WT R3

description:
Library name: C42_WT_R3
C42_WT_R3

value: WT


title: colonFMT_3

description:
Library name: sample6
removed adaptor


title: 25L008014 | mouse neuron supernatant S1 R1 TP4; no forskolin; dox-induced

description: Library name: 25L008014


title: C42 ACO2.KO R1

description:
Library name: C42_ACO2.KO_R1
C42_ACO2.KO_R1


title: Hippocampus, CORT+DFP+LPS, 6 h, HC_6h1

description:
Library name: HC_6h1
Reduced representation bisulfite sequencing of mouse hippocampus DNA
HPC_Con_6h_percent_methylation.tsv


title: colonGF_1

description:
Library name: sample1
removed adaptor


title: Hippocampus, CORT+DFP+Saline, 6 h, HC_Con3

description:
Library name: HC_Con3
Reduced representation bisulfite sequencing of mouse hippocampus DNA
HPC_Con_6h_percent_methylation.tsv

value: CORT+DFP+Saline, 6 h


title: C42 WT R2

description:
Library name: C42_WT_R2
C42_WT_R2


title: 25L008012 | neuron Target TP3

description: Library name: 25L008012

value: brain


title: 25L008013 | neuron Target TP3

description: Library name: 25L008013

value: murine primary neurons


title: 25L008010 | neuron Target TP3

description: Library name: 25L008010

value: primary neuron


title: 25L008011 | primary neuron S4_R1_TP3

description:
Library name: 25L008011
Primary mouse cortical neuron

value: NTVE expression via AAV


title: C42 WT R1

description:
Library name: C42_WT_R1
C42_WT_R1


title: Pcp2-Cre;NfascFx/Fx;AnkGFx/Fx cerebellar hemisphere (Pcp2-DKO), biol rep 2

city: San Antonio

first: Manzoor

last: Bhat

state: Texas

address: 7703 Floyd Curl

institute: UT Health San Antonio

description:
Library name: DualKO_2
P30 C57BL/6J mouse cerebellar hemisphere; bulk polyA RNA-seq; mixed sex; single-end 100 bp; two lanes (L001, L002).

data_processing:
Raw reads were inspected with FastQC v0.12.1.
Reads were trimmed with Trimmomatic v0.39 (ILLUMINACLIP:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36).
Trimmed reads were aligned to the Mus musculus reference genome GRCm39 (Ensembl release 111) using STAR v2.7.11a with twopassMode Basic and outSAMtype BAM SortedByCoordinate.
Gene-level counts were generated with STAR --quantMode GeneCounts and imported into R 4.3.2. Genes with fewer than 10 total counts across all libraries were excluded, leaving 17,621 features. Differential expression analysis was performed with DESeq2 v1.40.2 (design = ~ condition); adjusted p < 0.05 and |log2FC| >= 0.6 were considered significant. Variance-stabilized data were used for PCA and heatmaps; GO enrichment was performed with clusterProfiler v4.10.1.
Raw FASTQ files are no longer available; this submission includes complete processed gene-level count and normalized expression matrices used for downstream analyses.
Assembly: GRCm39 (Ensembl release 111)
Supplementary files format and content: Tab-delimited text file containing gene-level raw read counts for all samples (rows = genes, columns = samples).
Supplementary files format and content: Tab-delimited text file containing normalized gene expression values for all samples (rows = genes, columns = samples).

source_name: cerebellar hemisphere

growth_protocol: Mice were maintained on a mixed C57BL/6J;129 background in a temperature-controlled facility (23 ± 1°C) on a 12 h light/12 h dark cycle with ad libitum access to food and water. Cerebellar hemispheres were dissected from P32 littermate mice.

extract_protocol:
Cerebellar hemispheres were flash-frozen in liquid N2. Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) with on-column DNase digestion according to the manufacturer’s instructions. RNA integrity was assessed on an Agilent 4200 TapeStation; all samples had RIN >= 8.2.
Poly(A)+ RNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module. Strand-specific libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit with unique dual indices, pooled equimolarly, and sequenced on an Illumina NovaSeq 6000 S4 flow cell.

treatment_protocol: No treatment. Samples were collected from untreated littermate mice of the indicated genotypes.

value: cerebellar hemisphere

value: cerebellar tissue

value: untreated

value: batch 1


title: Pcp2-Cre;AnkGFx/Fx cerebellar hemisphere (AnkG-KO), biol rep 2

description:
Library name: Ank3KO_2
P30 C57BL/6J mouse cerebellar hemisphere; bulk polyA RNA-seq; mixed sex; single-end 100 bp; two lanes (L001, L002).

value: Pcp2-Cre;AnkGFx/Fx (AnkG-KO)


title: Hippocampus, CORT+DFP+Saline, 6 h, HC_Con1

description:
Library name: HC_Con1
Reduced representation bisulfite sequencing of mouse hippocampus DNA
HPC_Con_6h_percent_methylation.tsv

value: Hippocampus


title: Pcp2-Cre;NfascFx/Fx;AnkGFx/Fx cerebellar hemisphere (Pcp2-DKO), biol rep 1

description:
Library name: DualKO_1
P30 C57BL/6J mouse cerebellar hemisphere; bulk polyA RNA-seq; mixed sex; single-end 100 bp; two lanes (L001, L002).


title: C42_ACO2.KO_R3

data_processing:
Pre-alignment quality control was performed using FASTQC v0.11.5.
Sequenced reads (fastq files) were alinged to the human genome GRCh38.p13 (Gencode) using STAR v2.7.9a.
Post-alignment quality control was performed using RSeQC v4.0.0.
Estimated counts at the gene level were quantified using featureCounts v2.0.1.
Assembly: GRCh38
Supplementary files format and content: csv file countaining raw counts at the gene level for all samples

extract_protocol:
Approximately, 1 X 106 cells were lysed with QIAzol lysis reagent, followed by the addition of chloroform. Aqueous and organic phases were later separated by centrifugation. Aqueous phases were transferred to a new tube, followed by the addition of 100% ethanol to it, and mixed by pipetting. The sample was later transferred into an RNeasy Mini spin column for collecting total RNA. On-column DNAse digestion was performed to remove residual genomic DNA.
About 500ng of total RNA was used to make sequencing libraries with the mRNA HyperPrep kit (Roche) as per the manufacturer's instructions. First, Poly(A) RNA was captured using mRNA Capture Beads (KAPA BIOSYSTEMS). RNA was eluted, fragmented, and primed for cDNA synthesis. 1st strand of cDNA is later synthesized with random primers. Later, the RNA template gets removed and a replacement strand is synthesized by incorporating dUTP in place of dTTP to generate ds cDNA. Pure Beads (Roche) were used to separate the ds cDNA from the second strand reaction mix resulting in blunt-ended cDNA. A single ‘A’ nucleotide was then added to the 3’ ends of the blunt fragments. Multiple indexing adapters, containing a single ‘T’ nucleotide on the 3’ end of the adapter, were ligated to the ends of the ds cDNA, preparing them for hybridization onto a flow cell. Adapter ligated libraries were amplified by PCR, purified using Pure Beads, and validated for appropriate size on a 4200 TapeStation D1000 Screentape (Agilent Technologies, Inc.). The DNA libraries were quantitated using KAPA Biosystems qPCR kit and were pooled together in an equimolar fashion, following experimental design criteria. Each pool was denatured and diluted to 350pM with 1% PhiX control library added. The resulting pool was then loaded into the appropriate NovaSeq Reagent cartridge, as determined by the number of sequencing cycles desired, and sequenced on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.).


title: C42_ACO2.KO_R1


title: Hippocampus, CORT+DFP+LPS, 6 h, HC_6h2

description:
Library name: HC_6h2
Reduced representation bisulfite sequencing of mouse hippocampus DNA
HPC_Con_6h_percent_methylation.tsv


title: Whole blood, CORT+DFP+LPS, 24 h, BL_24h3

description:
Library name: BL_24h3
Reduced representation bisulfite sequencing of mouse whole blood DNA
Blood_Con_24h_percent_methylation.tsv

source_name: Whole blood

value: Whole blood

value: CORT+DFP+LPS, 24 h


title: Hippocampus, CORT+DFP+Saline, 6 h, HC_Con2

description:
Library name: HC_Con2
Reduced representation bisulfite sequencing of mouse hippocampus DNA
HPC_Con_6h_percent_methylation.tsv


title: Pcp2-Cre;NfascFx/Fx;AnkGFx/Fx cerebellar hemisphere (Pcp2-DKO), biol rep 3

description:
Library name: DualKO_3
P30 C57BL/6J mouse cerebellar hemisphere; bulk polyA RNA-seq; mixed sex; single-end 100 bp; two lanes (L001, L002).


title: Whole blood, CORT+DFP+LPS, 24 h, BL_24h2

description:
Library name: BL_24h2
Reduced representation bisulfite sequencing of mouse whole blood DNA
Blood_Con_24h_percent_methylation.tsv


title: 25L008008 | neuron Target TP3

description: Library name: 25L008008

value: primary mouse cortical neurons

value: Supernatant


title: 25L008009 | neuron Target TP3

description: Library name: 25L008009


title: Whole blood, CORT+DFP+LPS, 24 h, BL_24h1

description:
Library name: BL_24h1
Reduced representation bisulfite sequencing of mouse whole blood DNA
Blood_Con_24h_percent_methylation.tsv

value: wild type


title: 25L008007 | neuron Target TP3

description: Library name: 25L008007


title: Pcp2-Cre;NfascFx/Fx cerebellar hemisphere (NF-KO), biol rep 3

description:
Library name: NfKO_3
P30 C57BL/6J mouse cerebellar hemisphere; bulk polyA RNA-seq; mixed sex; single-end 100 bp; two lanes (L001, L002).

value: Pcp2-Cre;NfascFx/Fx (NF-KO)


title: C42_WT_R1

description:
Library name: C42_WT_R1
C42_WT_R1

value: prostate cancer cell line

value: WT


title: Pcp2-Cre;AnkGFx/Fx cerebellar hemisphere (AnkG-KO), biol rep 1

description:
Library name: Ank3KO_1
P30 C57BL/6J mouse cerebellar hemisphere; bulk polyA RNA-seq; mixed sex; single-end 100 bp; two lanes (L001, L002).


title: 25L008006 | neuron Target TP3

description: Library name: 25L008006

value: brain

value: murine primary neurons


title: C42_WT_R2

description:
Library name: C42_WT_R2
C42_WT_R2


title: Pcp2-Cre;NfascFx/Fx cerebellar hemisphere (NF-KO), biol rep 2

description:
Library name: NfKO_2
P30 C57BL/6J mouse cerebellar hemisphere; bulk polyA RNA-seq; mixed sex; single-end 100 bp; two lanes (L001, L002).


title: Whole blood, CORT+DFP+LPS, 12 h, BL_12h2

description:
Library name: BL_12h2
Reduced representation bisulfite sequencing of mouse whole blood DNA
Blood_Con_12h_percent_methylation.tsv

value: CORT+DFP+LPS, 12 h


title: 25L008004 | neuron Target TP3

description: Library name: 25L008004

value: primary neuron


title: 25L008005 | neuron Target TP3

description: Library name: 25L008005


title: C42_ACO2.KO_R2

description:
Library name: C42_ACO2.KO_R2
C42_ACO2.KO_R2


title: Human, Putamen, rep 6

city: Dallas

first: Jane

middle: E

last: Johnson

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

description: Library name: Human_put_6

data_processing:
Raw base call (BCL) files were analyzed using CellRanger (v6.0.0)
Gene annotation files of non-human primates were generated using Liftoff tool (v1) using the human gene annotation file as reference. Then the genome files were generated using "CellRanger mkref" using the genome fasta files given below with the newly generated gene anniotation files for these species.
The “mkfastq” command was used to generate FASTQ files and the "CellRanger count" command was used to generate raw gene-cell expression matrices.
Ambient RNA contamination was inferred and removed using CellBender (v0.2.0) with standard parameters
Data were filtered, normalized, integrated, clustered, annotated, and visualized using a Seurat v3 pipeline
Assembly: Human: GRCh38, Chimpanzee: panTro5 (Pan_tro 3.0), Rhesus Macaque: rheMac10 (Mmul_10), Marmoset: calJac3, Bat:GCF_004126475.2_mPhyDis1.pri.v3, Mouse: mm10, Ferret: GCF_011764305.1_ASM1176430v1.1
Supplementary files format and content: barcodes.tsv.gz' contains cell barcodes, 'features.tsv.gz' containts gene symbols, 'matrix.mtx.gz' contains raw counts. 'meta.tsv.gz' contains the meta data.
Supplementary files format and content: In addition to raw data generated in-house, publicly available raw data for mouse and ferrets from publications were used to process the data for this project. Processed data is also included with this dataset.

molecule: nuclear RNA

source_name: Putamen

extract_protocol:
Nuclei for snRNA-seq were isolated from bat putamen and caudate brain tissue. Briefly, the tissue was homogenized in 500 µL of ice-cold Nuclei EZ lysis buffer (EZ PREP NUC-101, Sigma) using a pre-chilled glass Dounce homogenizer. Debris was removed via density gradient centrifugation using Nuclei PURE 2 M sucrose cushion solution and Nuclei PURE sucrose cushion buffer (Nuclei PURE prep isolation kit, no. NUC201-1KT, Sigma Aldrich). These two solutions were mixed in a 9:1 ratio, and 500 µL of the sucrose solution was added to a 2-ml Eppendorf tube. The homogenized nuclei suspension was mixed with 900 µL of sucrose cushion solution by pipetting 10 times, resulting in a 1,400 µL volume, which was carefully layered over the sucrose buffer without mixing. The samples were centrifuged at 13,000 x g for 45 min at 4 °C, and all but 100 µL of supernatant was discarded. Nuclei were resuspended in 300 µL of nucleus suspension buffer (NSB), consisting of 1× PBS, 2% BSA (no. AM2618, Thermo Fisher Scientific), and 0.4 U µL −1 RNAse inhibitor (no. AM2694, Thermo Fisher Scientific). Samples were then centrifuged at 550 x g for 5 min at 4 °C, and all but 50 µL of supernatant was discarded. The nuclear pellet was resuspended in NSB and filtered through a 40-μm Flowmi cell strainer (Bel-Art Products, #H13680-0040) into a new tube. The nuclei concentration was measured using Hoechst and decreased to 1,000 nuclei per µL with NSB if necessary. Cellular nuclei for snRNA-seq were isolated from the putamen and caudate nuclei of human, chimpanzee, and rhesus macaque tissues. Briefly, the tissue was homogenized in 750 µL of ice-cold NP40 lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% Nonidet P40 Substitute, 1 mM DTT, 0.2 U/µL RNAse inhibitor) using a pre-chilled glass Dounce homogenizer. An additional 750 µL of ice-cold NP40 lysis buffer was added, and the mixture was pipette-mixed during a 5-minute incubation on ice. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, resuspended in 1 mL of ice-cold lysis buffer, and incubated on ice for 5 minutes with gentle pipette mixing throughout. The nuclei were then centrifuged again at 500 x g for 5 minutes at 4°C, and all but 50 µL of supernatant was discarded. Next, 500 µL of nucleus suspension buffer (NSB) containing 1× PBS, 1% Ultrapure BSA (no. AM2618, Thermo Fisher Scientific), and 0.2 U/µL RNAse inhibitor (no. AM2694, Thermo Fisher Scientific) was added, and the sample was incubated for 5 minutes on ice without mixing. The pellet was resuspended, centrifuged again at 500 x g for 5 minutes at 4°C, and all but 50 µL of supernatant was discarded. The nuclei were then resuspended in 500 µL of NSB and filtered through a 70-μm Flowmi cell strainer (no. H13680-0070, Bel-Art) into a 1.5 mL tube.
Droplet-based snRNA-seq libraries were prepared using the Chromium Single Cell 3′ v3.1 (10x Genomics) kit, following the manufacturer's protocol. Libraries were sequenced on an Illumina NovaSeq 6000.

tag: sample id

value: male

value: Putamen


title: Human, Putamen, rep 7

description: Library name: Human_put_7

value: female


title: Pcp2-Cre;NfascFx/Fx cerebellar hemisphere (NF-KO), biol rep 1

description:
Library name: NfKO_1
P30 C57BL/6J mouse cerebellar hemisphere; bulk polyA RNA-seq; mixed sex; single-end 100 bp; two lanes (L001, L002).

value: cerebellar hemisphere

value: cerebellar tissue

value: untreated

value: batch 1


title: Whole blood, CORT+DFP+LPS, 12 h, BL_12h1

description:
Library name: BL_12h1
Reduced representation bisulfite sequencing of mouse whole blood DNA
Blood_Con_12h_percent_methylation.tsv

value: Whole blood


title: 25L008003 | primary neuron S1_R2_TP3

description:
Library name: 25L008003
Primary mouse cortical neuron

value: primary mouse cortical neurons

value: Supernatant

value: NTVE expression via AAV


title: Control cerebellar hemisphere, biol rep 3

description:
Library name: SH_FloxControl_3
P30 C57BL/6J mouse cerebellar hemisphere; bulk polyA RNA-seq; mixed sex; single-end 100 bp; two lanes (L001, L002).

value: Control


title: 25L008002 | neuron Target TP3

description: Library name: 25L008002


title: Control cerebellar hemisphere, biol rep 1

description:
Library name: SH_FloxControl_1
P30 C57BL/6J mouse cerebellar hemisphere; bulk polyA RNA-seq; mixed sex; single-end 100 bp; two lanes (L001, L002).


title: 25L008001 | neuron Reference TP2

description: Library name: 25L008001


title: Human, Putamen, rep 4

description: Library name: Human_put_4


title: 25L008000 | neuron Reference TP2

description: Library name: 25L008000


title: Control cerebellar hemisphere, biol rep 2

description:
Library name: SH_FloxControl_2
P30 C57BL/6J mouse cerebellar hemisphere; bulk polyA RNA-seq; mixed sex; single-end 100 bp; two lanes (L001, L002).


title: Whole blood, CORT+DFP+LPS, 6 h, BL_6h4

description:
Library name: BL_6h4
Reduced representation bisulfite sequencing of mouse whole blood DNA
Blood_Con_6h_percent_methylation.tsv

value: wild type

value: CORT+DFP+LPS, 6 h


title: Whole blood, CORT+DFP+LPS, 12 h, BL_12h3

description:
Library name: BL_12h3
Reduced representation bisulfite sequencing of mouse whole blood DNA
Blood_Con_12h_percent_methylation.tsv


title: Human, Putamen, rep 2

description: Library name: Human_put_2


title: P14 CA1 RNA-seq Sal rep1

city: GuangZhou

first: Hao

last: Liu

state: Guangdong

address: No. 1023-1063 Shatai South Road, Baiyun District

institute: Southern Medical University

description:
Library name: Sal_1_RNAseq
CA1 tissue, P14; NEBNext Ultra II Directional RNA + RiboZero Plus

data_processing:
Adapters and low-quality bases were trimmed with fastp v0.23.2. Reads were aligned to mm10 using STAR v2.7.11 (two-pass). Gene-level counts were generated with featureCounts and differential expression was analyzed in DESeq2.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Tab-delimited matrix of raw gene counts (rows=genes, columns=samples): CA1_P14_RNAseq_counts_raw.tsv.

source_name: hippocampus CA1

extract_protocol:
CA1 tissue (~25 mg) was homogenized in TRIzol and total RNA was extracted. RNA integrity was assessed and samples with RIN >= 8.0 were used for library preparation.
NEBNext Ultra II Directional RNA Library Prep Kit with RiboZero Plus (fragmentation 94C 8 min; 13-cycle PCR; dual index).

value: hippocampus CA1

value: Sal


title: P14 CA1 RNA-seq Sal rep2

description:
Library name: Sal_2_RNAseq
CA1 tissue, P14; NEBNext Ultra II Directional RNA + RiboZero Plus


title: Whole blood, CORT+DFP+LPS, 6 h, BL_6h3

description:
Library name: BL_6h3
Reduced representation bisulfite sequencing of mouse whole blood DNA
Blood_Con_6h_percent_methylation.tsv


title: Whole blood, CORT+DFP+LPS, 6 h, BL_6h2

description:
Library name: BL_6h2
Reduced representation bisulfite sequencing of mouse whole blood DNA
Blood_Con_6h_percent_methylation.tsv


title: Whole blood, CORT+DFP+Saline, 6 h, BL_Con4

description:
Library name: BL_Con4
Reduced representation bisulfite sequencing of mouse whole blood DNA
Blood_Con_6h_percent_methylation.tsv

value: CORT+DFP+Saline, 6 h


title: Human, Putamen, rep 5

description: Library name: Human_put_5

value: male


title: Whole blood, CORT+DFP+LPS, 6 h, BL_6h1

description:
Library name: BL_6h1
Reduced representation bisulfite sequencing of mouse whole blood DNA
Blood_Con_6h_percent_methylation.tsv


title: Human, Putamen, rep 3

description: Library name: Human_put_3

value: Putamen


title: 25L007998 | neuron Reference TP2

description: Library name: 25L007998

source_name: brain

value: brain

value: murine primary neurons

value: primary neuron


title: 25L007999 | neuron Reference TP2

description: Library name: 25L007999


title: Human, Caudate Nucleus, rep 5

description: Library name: Human_caud_5

source_name: Caudate Nucleus

value: female

value: Caudate Nucleus


title: Human, Putamen, rep 1

description: Library name: Human_put_1


title: Human, Caudate Nucleus, rep 6

description: Library name: Human_caud_6


title: P14 CA1 RNA-seq Sal rep3

description:
Library name: Sal_3_RNAseq
CA1 tissue, P14; NEBNext Ultra II Directional RNA + RiboZero Plus


title: 25L007997 | neuron Reference TP2

description: Library name: 25L007997


title: P14 CA1 RNA-seq N-bc2S1P rep2

description:
Library name: N-bc2S1P_2_RNAseq
CA1 tissue, P14; NEBNext Ultra II Directional RNA + RiboZero Plus


title: P14 CA1 RNA-seq N-bc2S1P rep3

description:
Library name: N-bc2S1P_3_RNAseq
CA1 tissue, P14; NEBNext Ultra II Directional RNA + RiboZero Plus


title: P14 CA1 RNA-seq N-bc2S1P rep1

description:
Library name: N-bc2S1P_1_RNAseq
CA1 tissue, P14; NEBNext Ultra II Directional RNA + RiboZero Plus


title: 25L007996 | neuron Reference TP2

description: Library name: 25L007996


title: Whole blood, CORT+DFP+Saline, 6 h, BL_Con1

description:
Library name: BL_Con1
Reduced representation bisulfite sequencing of mouse whole blood DNA
Blood_Con_6h_percent_methylation.tsv

value: Whole blood


title: Human, Caudate Nucleus, rep 4

description: Library name: Human_caud_4


title: Whole blood, CORT+DFP+Saline, 6 h, BL_Con3

description:
Library name: BL_Con3
Reduced representation bisulfite sequencing of mouse whole blood DNA
Blood_Con_6h_percent_methylation.tsv


title: Human, Caudate Nucleus, rep 3

description: Library name: Human_caud_3


title: 25L007995 | neuron Reference TP2

description: Library name: 25L007995

value: primary mouse cortical neurons


title: P14 hippocampus H3K27ac ChIP-seq Sal rep2

description:
Library name: Sal_2
H3K27ac ChIP DNA; NEBNext Ultra II DNA kit

data_processing:
Reads were trimmed with Trim Galore and aligned to mm10 with Bowtie2. Alignments were filtered (MAPQ >= 30) and PCR duplicates were removed. Broad peaks were called with MACS2 in broad mode without a matched input control. A consensus peak set and peak-by-sample count matrix were generated, and differential occupancy was analyzed using DiffBind/DESeq2 with Benjamini-Hochberg FDR control. Replicate concordance was assessed by IDR.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Tab-delimited consensus peak count matrix with genomic coordinates and read counts per sample: CA1_P14_H3K27ac_consensus_peak_counts.tsv.

source_name: hippocampus

extract_protocol:
Hippocampal tissue (~60 mg) was fixed in 1% formaldehyde at 4C for 10 min, quenched with 125 mM glycine, lysed and sonicated on a Bioruptor Pico for 30 cycles (30 s ON/30 s OFF) to 200-500 bp. Chromatin (50 ug) was immunoprecipitated overnight with 5 ug anti-H3K27ac (Cell Signaling) and Dynabeads Protein A. After washes, crosslinks were reversed at 65C for 4 h and DNA was purified.
Libraries were built with the NEBNext Ultra II DNA Kit (10 PCR cycles) and sequenced as single-end reads on a NovaSeq 6000.

value: hippocampus


title: Human, Caudate Nucleus, rep 1

description: Library name: Human_caud_1


title: CD4 T cell, REV-Erbβ-DBDoverexpression, 48hr, Replicate 2

city: Jupiter

first: Jonathan

last: Chuck

state: FL

address: 130 Scripps Way, C275

department: Immunology

institute: UF Scripps

description:
Library name: 48hr_β_DBD_OE_Rep2
normalized_counts_DEseq2.csv

data_processing:
Raw counts were transformed into "Relative Log Expression” normalization (RLE) implemented in the DESeq2 package that was used to assess differential expression and perform gene set testing.
Assembly: M.musculus UCSC mm10 build
Supplementary files format and content: Normalized counts

source_name: T Cells

extract_protocol:
Total RNA was extracted using Qiagen RNeasy kits (WT vs KO) of in vitro differentiated Th17 cells.  rRNA-depleted RNA was processed using the TruSeq Stranded Total RNA sample prep kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: T Cells

value: Primary

value: Th17 cell differentiation with retroviral transduction


title: CD4 T cell, REV-Erbβ-ΔDBD overexpression, 48hr, Replicate 2

description:
Library name: 48hr_β_ΔDBD_OE_Rep2
normalized_counts_DEseq2.csv


title: P14 hippocampus H3K27ac ChIP-seq Sal rep3

description:
Library name: Sal_3
H3K27ac ChIP DNA; NEBNext Ultra II DNA kit


title: Human, Caudate Nucleus, rep 2

description: Library name: Human_caud_2


title: Whole blood, CORT+DFP+Saline, 6 h, BL_Con2

description:
Library name: BL_Con2
Reduced representation bisulfite sequencing of mouse whole blood DNA
Blood_Con_6h_percent_methylation.tsv

value: wild type


title: CD4 T cell, REV-Erbβ-H565F overexpression, 48hr, Replicate 2

description:
Library name: 48hr_β_H565F_OE_Rep2
normalized_counts_DEseq2.csv


title: CD4 T cell, REV-Erbβ-DBDoverexpression, 48hr, Replicate 1

description:
Library name: 48hr_β_DBD_OE_Rep1
normalized_counts_DEseq2.csv


title: HEK293T, OMM-Lantern, omitting-Light control, rep2

first: Yuxin

last: Fang

address: Yiheyuan Road No.5

institute: Peking University

description:
Library name: OMM-Lantern_NoLight_rep2
Column name in OMM_all_counts.xlsx: NoLight_rep2
OMM_all_counts.xlsx

data_processing:
Sequencing reads were firstly processed with Cutadapt (v.1.18) to remove adaptors (For subcellular transcriptome data, adaptor1=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, adaptor2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; for cancer cell migration study, adaptor1=CTGTCTCTTATACACATCTCCGAGCCCACGAGAC, adaptor2=CTGTCTCTTATACACATCTGACGCTGCCGACGA; other parameters: -q 20 -O 3 -m 20).
Trimmed reads were mapped against the corresponding genome assemblies using hisat2 (v.2.1.0).
Number of reads mapped to each gene was counted with HTSeq (v0.7.2) (-s no)
Differential expression analysis was carried out by DESeq2 (v.1.16.1)
Assembly: GRCh38 (hg38), Rnor_6.0, GRCm39
Supplementary files format and content: Excel tables include raw counts for each sample.

growth_protocol: HEK293T and MC38 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% (v/v) fetal bovine serum (FBS) and maintained at 37°C with 5% CO2. Cortical neurons were dissected from neonatal Sprague Dawley rats (within 24 hours post-birth), plated onto 10-cm dishes, and cultured with GPM for 3-6 h before switching to neural cell culture medium (Neurobasal medium with 2% (v/v) B-27 supplement, 1% (v/v) GlutaMAX supplement, penicillin and streptomycin). Petri dishes were pre-incubated overnight with 50-100 μg/mL PDL at 37°C. The day of rat dissection was designated as DIV 0 (0 days in vitro), and thereafter, half of the spent culture medium was replaced with fresh neural cell culture medium every 3 days.

extract_protocol:
For the profiling of subcellular transcriptomes, cells were lyzed with TRIzol. Total RNAs were extracted, clicked with biotin handles, enriched with streptavidin-coated beads, and purified again with TRIzol. For the study of cancer cell migration, cells with strong biotin signals were sorted by flow cytometry and lyzed with 0.5% (v/v) Triton X-100 and 0.1 U DNase I.
For the profiling of subcellular transcriptomes, 100 ng Input RNA samples or 5 μL Enrich RNA samples were utilized for NGS library construction. For identifying G3BP1-proximal and OMM-proximal RNAs in the HEK293T cells, rRNAs were removed with Ribo-off rRNA Depletion Kit (Vazyme) following the manufacturer’s protocol. The purified RNAs were dissolved in 5 μL nuclease-free water. NEBNext Ultra II RNA Library Prep Kit for Illumina was used for NGS library construction. RNAs were fragmentated to ~300 nt before first strand synthesis. For the study of cancer cell migration, the sorted cells were used for pseudo-bulk RNA-sequencing library construction following the previously published Sherry2 protocol. Libraries constructed from polyA RNAs (OMM-proximal and G3BP1-proximal RNAs of HEK293T cells, and mRNAs of MC38 cells) were sequenced to a depth of 3 G raw base. And libraries constructed from total RNAs (ERM-proximal RNAs of HEK293T cells and G3BP1-proximal RNAs of rat cortical neurons) were sequenced to a depth of 15 G raw base.

treatment_protocol: For general CAP-seq labeling experiments, HEK293T cells were cultured until the confluence reached 90%, incubated with 10 mM propargylamine (PA) in HBSS for 5 min, and irradiated with blue light for 1-120 seconds. For the induction of stress granules, HEK293T cells were incubated with 0.5 mM sodium arsenite for 5-60 minutes. Primary cultures of rat cortical neurons were transduced with a lentivirus expressing G3BP1-Lantern or Lantern-NES at 3 days in vitro (DIV3). At DIV8, neurons were stimulated with 0.25 mM sodium arsenite for 3 hours, and conducted with the CAP-seq labeling procedure. For the cancer cell migration assay, MC38 cells were seeded on coverslips with a culture-insert to create a 500-μm cell-free gap. 24 hours after removing the culture-insert, migrating cells near the gap and remaining cells far from the gap were selectively labeled with DMD-controlled 450-nm laser and 2 mM Bio-NH2 probe.

value: embryonic kidney cells

value: Lantern-MAVS