title: GroupC_2

description: Library name: 9_S9


title: HepG2.batch1.control.rep1.D04

status: Public on Jul 01 2026

type: SRA

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

description: Library name: HepG2_Batch1_control_1_D04

library_source: other

data_processing:
Reads were aligned using STAR alignment on QIAGEN's CLC workbench software (v25.0.1) and Kallisto alignment on ExpressAnalyst
Raw counts were logCPM normalized and filtered for low abundance (5) and variance (15) using ExpressAnalyst
Normalized counts were analyzed for differential expression using DESeq2
Assembly: CLC workbench used hg38.p14 Ensembl v113 GCA_000001405.29; ExpressAnalyst used hg38.p14 GCA_000001405
Supplementary files format and content: raw files and count files are provided as fastq.gz files and .txt files, respectively.

molecule: other

organism: Homo sapiens

source_name: cell lysate

growth_protocol: from ms

extract_protocol:
cells were lysed in Qiagen's proprietary lysis buffer and used directly for library preparation
ultraplex 3' transcriptome library preparation following Qiagen's UPXome protocol

treatment_protocol: cells were exposed to various concentrations of 6ppd-quinone for 24 hours after seeding at 35,000 cells per well

tag: tissue

value: liver

tag: cell line

tag: cell type

value: hepatocyte

tag: genotype

value: cell line

tag: treatment


title: BPK_0-5_R2_P2

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

description: Library name: s116

library_source: transcriptomic

data_processing:
Reads were demultiplexed from the BCL files and processed into FASTQ files using  DRAGEN analysis v1.3.0 on the Illumina BaseSpace Sequence Hub (Illumina, Inc., San Diego, CA, USA). Processing and quality control of the FASTQ files, differential expression analysis, and exploratory statistical analyses were performed using the R-ODAF_Health_Canada pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada; accessed March 2025), which manages workflows using Snakemake v8.0 (Mölder et al. 2021) and relies on scripts in R (v.4.3.2). The preprocessing steps use fastp v0.23.2 for trimming (Chen et al. 2018), STAR v2.7.8a (Dobin et al. 2013) to perform alignment of raw reads to the reference sequence and the qCount function of the QuasR R package (v1.30.0; (Gaidatzis et al. 2015) to extract the feature counts from the aligned reads (BAM files) using features specified in a GTF file. A samples-by-probes count matrix was produced.
Assembly: Probe sequence set provided by biospyder based on Human Whole Transcriptome kit v2.1
Supplementary files format and content: Tab-delimited table containing read counts per TempO-Seq probe

molecule: total RNA

source_name: Mammary

growth_protocol: MCF-7 cells (ATCC, Manassas, Virginia) were cultured in 10 cm dishes (Corning Falcon No. 353003, Corning, New York) with Dulbecco’s modified Eagle’s medium (DMEM; Gibco, Thermo Fisher Scientific, Waltham, Massachusetts) containing 10% fetal bovine serum (FBS; Wisent Bioproducts, Saint-Jean Baptiste, QC, Canada), and 1% penicillin and streptomycin (P/S; Wisent), at 37°C in a humidified atmosphere (5% CO2).

extract_protocol:
Cells were washed with phosphate-buffered saline and lysed in situ using 2x TempO-Seq lysis buffer diluted with an equal amount of PBS for TempO-Seq library building.
Gene expression was measured using the TempO-Seq Human Whole Transcriptome v2.1 kit (BioSpyder Technologies Inc, Carlsbad, California) as per the manufacturer’s instructions

treatment_protocol: For the experiment, cells were washed with phosphate-buffered saline (PBS) and the media were replaced with phenol red-free DMEM supplemented with 5% charcoal-dextran stripped FBS (CD-FBS) to eliminate estrogens present in commercial media and serum (Atlas et al. 2003) for 24 h. Cells were then seeded into clear 96-well plates (Corning Falcon No. 353075) at a density of 2.0 x 104 cells per well in phenol red-free DMEM supplemented with 5% CD-FBS and 1% P/S. After 24 h, the medium was removed and replaced with phenol red-free DMEM containing 5% CD-FBS and 1% P/S and chemicals of interest. Cells were exposed for 48 h, in quadruplicates, to BPA, the 12 chemicals of interest at eight different concentrations (0.001, 0.01, 0.1, 0.5, 1, 5, 10, 50 µM), 17β-estradiol (E2; 0.1, 1 nM) as a positive control, and at least four plate-matched solvent controls (0.1% DMSO).

value: Mammary

value: Epithelial

value: WT

value: chemical exposure

tag: chemical

value: bisphenol K

tag: dose

tag: batch


title: M1 from animal_22

city: Tempe

first: Noah

last: Snyder-Mackler

state: Arizona

address: 214 Life Sciences C

department: School of Life Sciences

country: USA

institute: Arizona State University

description:
Library name: NSM1613-b2
3 lvl sciRNAseq

library_source: transcriptomic single cell

data_processing:
Converts base calls to fastq files with bcl2fastq/ v.2.20 (RRID:SCR_015058) (Illumina), merge read 1 which contains the barcode to read 2 files.
Removes polyA tails using Trim Galore/v.0.6.7 (RRID:SCR_011847)
Aligns trimmed reads to a reference genome with STAR/v.2.7.6 (RRID:SCR_004463)
Extracts mapped reads and removes duplicates.
Generates UMI counts for exonic and intronic regions of each gene, tabulated according to the unique three-level barcode design in sci-RNA-seq3.
Assembly: rhesus macaque reference genome (Mmul_10)
Supplementary files format and content: all_regions_cell_annotate.csv
Supplementary files format and content: all_regions_count.npz
Supplementary files format and content: all_regions_gene_annotate.csv

molecule: nuclear RNA

organism: Macaca mulatta

source_name: primary motor cortex

growth_protocol: free-ranging population

extract_protocol:
Briefly, tissue was manually pulverized on dry ice, transferred to pre-chilled tubes, and stored at −80°C. For lysis, pulverized tissue was suspended in hypotonic lysis buffer A (0.3 M sucrose, 0.1% Triton X-100, 3 mM MgCl₂, 0.025% IGEPAL CA-630, 1% DEPC in PBS) for 10 min, filtered (40-μm), pelleted, and resuspended in SPBSTM buffer (0.3 M sucrose, 1X PBS, 0.1% TritonX-100, 3 mM MgCl₂, and 1% DEPC). Nuclei were fixed for 10 min in 1.5 mM dithiobis(succinimidyl propionate) (DSP), diluted from a 123 mM stock in DMSO into methanol. After washing in 0.3 M SPBSTM, nuclei were layered onto a 10:1 volume of 1.4 M SPBSTM, centrifuged (3,000 x g, 20 min, 4°C), and resuspended. Nuclei were filtered (20-μm), counted, aliquoted, and cryopreserved in 90% 0.3 M SPBSTM with 10% anhydrous DMSO at -80°C. One library per region was generated using the optimized sci-RNA-seq3 protocol with the following modifications: nuclei were counted using the ImageExpress Pico System (Molecular Devices), and 15,000-20,000 nuclei were loaded per reverse transcription well. Tagmentation used N7 adaptor-loaded Tn5 transposase (Diagenode, C01070010-20), with 6-9 μL of Tn5 per 550 μL of 2X TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl₂, 20% dimethylformamide), distributed at 5uL per well.
sci-RNA-seq3

treatment_protocol: Following veterinary euthanasia, a necropsy was immediately performed during which the brain was perfused by transcardial perfusion with sterile saline. The brain was then removed from the cranium and sagittally sectioned into left and right hemispheres. The left hemisphere was fixed in 10% formalin and not used for this study. The right hemisphere was further sectioned prior to cryopreservation. First, the cerebellum was separated from the cerebrum. The cerebrum was then placed on a custom mold and sectioned coronally into 11 ~0.5 cm-thick slices. All 12 slices (including the cerebellar hemisphere) were individually stored in Whirl-pak bags and flash frozen in a dry-ice/ethanol bath immediately before storage in ultralow (-80°C) freezers. Regions of interest were dissected in sterile, RNase-free conditions on dry ice to minimize RNA degradation. Six 1-mm tissue biopsies were then collected by biopsy punch.

value: primary motor cortex


title: HepG2.batch1.control.rep1.C04

description: Library name: HepG2_Batch1_control_1_C04


title: GroupD_3

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

description: Library name: 7_S7

data_processing:
The bioinformatic workflow began with Illumina bcl2fastq (v2.20) demultiplexing. Read trimming and quality filtering of paired-end data were carried out with fastp (v0.23.2), and adapter sequences were additionally removed using Skewer (v0.2.2). Trimming included automatic adapter detection, removal of low-quality bases, sliding-window filtering (Q ≥ 20), and discarding reads shorter than 36 bp or containing >10 ambiguous nucleotides. PolyG and polyX tails were also clipped to minimize artefacts. Read quality was evaluated with FastQC (v0.11.5) and summarized across samples using MultiQC (v1.14).  Filtered reads were aligned to the Equus caballus reference genome EquCab3.0 (NCBI assembly GCF_002863925.1) using STAR (v2.7.10a) in two-pass mode to enable detection of novel splice junctions. The alignment settings allowed up to 20 multimapped reads and mismatches not exceeding 4% of the read length. Gene-level counts were obtained with HTSeq-count (v0.13.5) from name-sorted BAM files using the Equus caballus gene annotation (GTF file matching EquCab3.0). Reads with mapping quality below 10, as well as secondary or supplementary alignments, were excluded. Mapping quality metrics and coverage statistics were generated with RNA-SeQC (v2.4.2). Differential gene expression analysis was performed in R (v4.2.2) using DESeq2 (v1.38.0). Genes were considered differentially expressed when they exhibited an adjusted p-value < 0.05 (Benjamini–Hochberg correction) and an absolute fold change ≥ 1.2.
Assembly: EquCab3.0 (NCBI assembly GCF_002863925.1)
Supplementary files format and content: counts.tsv

organism: Equus caballus

source_name: skeletal muscle derived cells

growth_protocol: Equine skeletal muscle cells were isolated from post-mortem tissue, which was selected as the most ethically appropriate source for this study. Muscle samples were obtained immediately after the death of a 10-month-old preterm foal that did not survive despite veterinary care, and only after explicit informed consent was provided by the owner.  Prior to extract preparation, skeletal muscle fragments were handled under aseptic conditions, kept at 4 °C during transport, and processed within 4 hours to ensure preservation of cellular integrity for subsequent culture and analysis.

extract_protocol:
Total RNA was isolated using the PureLink RNA Mini Kit with on-column DNase treatment (Ambion, Life Technologies). For each group, three technical replicates were prepared. RNA quantity and purity were measured with a NanoDrop 2000 spectrophotometer (Thermo Scientific, Waltham, MA, USA), and RNA integrity was verified using a TapeStation 2200 system (RNA ScreenTapes, Agilent Technologies, Santa Clara, CA, USA). RNA concentrations ranged from 32 ng/μL to 412 ng/μL, and all samples exhibited RIN values greater than 7.5.
The samples with RIN (RNA integrity number) sufficient RIN ranging from 9.6 – 10.0 (Schroeder et al. 2006), were sent to Library preparation and sequencing by a commercial company (CeGat gGmbH) on NovaSeq 6000 (Ilumina), and finally 100 bp (±50 bp) paired-end reads were generated.

treatment_protocol: Approximately 2 × 10⁵ cells were seeded into T25 flasks pre-coated with 2% gelatin and allowed to attach overnight under standard culture conditions (37 °C, 5% CO₂, atmospheric O₂). The following day, cultures were assigned to experimental groups differing in oxygen tension and exposure duration. Hypoxic cultures were transferred to a HypoxyLab incubator (Oxford Optronix) set to either 3% or 1% O₂, using custom gas mixtures based on N₂ with 5% CO₂ and controlled O₂ levels, delivered at a constant flow rate. Normoxic cultures remained in standard humidified incubators at 37 °C with 5% CO₂ (≈21% O₂). All cultures were maintained in parallel under otherwise identical conditions.

value: skeletal muscle derived cells


title: M1 from animal_21

description:
Library name: NSM1612-b2
3 lvl sciRNAseq


title: HepG2.batch1.control.rep1.B04

description: Library name: HepG2_Batch1_control_1_B04


title: GroupC_1

description: Library name: 6_S6


title: Primary mouse hepatocytes, Mock replicate #3

city: New York

first: Jennifer

last: Gamarra

state: New York

address: 1150 St Nicholas Ave, Russ Berrie Building, Floor 6-613

institute: Columbia University

description: Library name: RJ021

data_processing:
We use bases2fastq version 1.1.0.593880262  for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Ensembl v96, Mouse:GRCm38.p6) using kallisto (0.44.0). We test for differentially expressed genes under various conditions using DESeq2, R packages designed to test differential expression between two experimental groups from RNA-seq counts data.
Assembly: GRCm38.p6
Supplementary files format and content: Tab-delimited text files containing number of raw counts for each gene.

organism: Mus musculus

source_name: primary hepatocytes

extract_protocol:
RNA was extracted from primary hepatocyte samples using RNeasy Mini Kit (Qiagen #73404). RNA concentration and quality was determined by Qubit Bioanalyzer. Standard RNA-seq pipeline at Columbia Genome Center: poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1µg per sample, RIN>8).
STRPOLYA libraries were constructed using Illumina TruSeq RNA Preparation Kit according to the manufacturer’s instructions.

treatment_protocol: Primary hepatocytes were extracted from a WT C57/Bl6J mouse using a two-step collagenase protocol. Primary hepatocytes were plated in Corning M199 +10%FBS + 1%PenStrep for at least 2 hours, that evening cells were switched to serum-free medium (M199 + 1% PenStrep) for 16 hours overnight with or without 6 𝜇M MnCl2. Hepatocytes were pre-treated with 1 or 100 nM of insulin (Gibco #12585014) for 1 hour prior to 10 𝜇M forskolin/1 𝜇M dexamethasone treatment in serum-free medium for 5 hours before cell lysis.

value: primary hepatocytes

value: Mock


title: BPK_0-01_R2_P2

description: Library name: s114


title: HepG2.batch1.control.rep1.A04

description: Library name: HepG2_Batch1_control_1_A04


title: GroupE_2

description: Library name: 5_S5


title: M1 from animal_19

description:
Library name: NSM1610-b2
3 lvl sciRNAseq


title: M1 from animal_20

description:
Library name: NSM1611-b2
3 lvl sciRNAseq


title: BPK_0-1_R2_P2

description: Library name: s115


title: GroupD_2

description: Library name: 4_S4


title: BPK_0-001_R2_P2

description: Library name: s113


title: HepG2.batch1.COL.rep3.H10

description: Library name: HepG2_Batch1_COL_3_H10


title: BPM_10_R2_P2

description: Library name: s112

value: bisphenol M


title: M1 from animal_18

description:
Library name: NSM1609-b2
3 lvl sciRNAseq


title: GroupE_1

description: Library name: 2_S2


title: BPM_5_R2_P2

description: Library name: s111


title: M1 from animal_17

description:
Library name: NSM1608-b2
3 lvl sciRNAseq


title: HepG2.batch1.COL.rep3.G10

description: Library name: HepG2_Batch1_COL_3_G10


title: GroupD_1

description: Library name: 1_S1


title: BPM_0-5_R2_P2

description: Library name: s109


title: HepG2.batch1.COL.rep3.E10

description: Library name: HepG2_Batch1_COL_3_E10


title: M1 from animal_16

description:
Library name: NSM1607-b2
3 lvl sciRNAseq


title: HepG2.batch1.COL.rep3.F10

description: Library name: HepG2_Batch1_COL_3_F10


title: BPM_1_R2_P2

description: Library name: s110


title: HepG2.batch1.COL.rep3.D10

description: Library name: HepG2_Batch1_COL_3_D10


title: S25_0402_vhd_d

city: Chicago

first: Jalees

last: Rehman

state: IL

address: 900 S. Ashland Ave. MBRB 2072, Mailcode 669

department: Biochemistry and Molecular Genetics

institute: UIC

description:
Library name: S25_0402_vhd_d
FFPE Spatial Transcriptome Sequencing

data_processing:
Tissue sections were processed according to the Visium HD Gene Expression User Guide (CG000685) to generate sequencing libraries. Mouse v2 probe set was used for hybridization. Minimum sequencing depth was estimated based on the percentage of tissue-covered capture area using the recommended minimum of 275 million read pairs. Libraries were quantified, pooled and sequenced on Illumina NovaSeq X, generating over 380 million cDNA reads per sample. Data preprocessing was performed using Space Ranger v3.1.2. The 8 µm binning resolution was selected for downstream analysis to balance spatial granularity with sufficient transcript capture per bin. Quality control filtering was performed using Scanpy (v1.10.3). Spots were retained if they contained at least 10 total counts. Additionally, spots with high mitochondrial transcript content were removed by excluding those with >15% mitochondrial counts. Filtered data were used for all downstream analyses.
Assembly: mm10-2020-A
Supplementary files format and content: 10x Genomics Visium HD Space Ranger output: Raw and filtered feature-barcode matrices and spatial coordinates for 2 µm, 8 µm, and 16 µm bin sizes, including tissue_positions.parquet and scalefactors_json.json for each bin level.
Library strategy: Spatial transcriptomics

source_name: Mouse Lung

growth_protocol: LSL-Kras-G12D strain mice (LSL-K-ras G12D/B6.129S4-Krastm4Tyj/J strain; The Jackson Laboratory Strain #:008179) were maintained in a pathogen-free environment at the University of Illinois Animal Care Facility with 12 hours dark and 12 hours light cycle, temperature at approximately 23 °C, and humidity at 40-60%.

extract_protocol:
At experimental end point, Lung lobes are collected and fixed in 4% PFA, and were transferred to 70% ethanol after 24 hours of fixation. The samples were then processed and embedded in paraffin. 5 µm thick consecutive sections were collected from the paraffin blocks of lung samples, using a microtome (Reichert-Jung 2030 Biocut Manual Microtome). Selected sections were stained with Hematoxylin and Eosin (H&E). All steps for tissue preparation and staining were carried out following 10X visium HD guidelines.
Spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium HD Spatial gene expression Slides & Reagent Kit according to manufacturer's protocol. Mouse v2 probe set was used for hybridization.

treatment_protocol: The mice were implanted with Low-power blue light µ-ILED devices to illuminate locally on the left lung. 7-10 days post implantation, the mice received endotracheal delivery of Adenoviral CMV-E-LightR-Cre-miRFP670 for whole lung-wide expression.To induce local optogenetic E-LightR-Cre activity in mouse lungs in vivo, we used wireless activation of blue µ-ILED device, with 10 W transmitting antenna power, 10 Hz frequency and 50 % duty cycle for 24 Hours. Mice were maintained until the experimental endpoint at 8 weeks following light-induced E-LightR-Cre activation, after which lungs were collected for downstream analyses.

value: Mouse Lung

value: E-LightR-Cre + local optoelectronic illumination


title: S26_0106_vhd_d

description:
Library name: S26_0106_vhd_d
FFPE Spatial Transcriptome Sequencing


title: BPM_0-1_R2_P2

description: Library name: s108


title: M1 from animal_15

description:
Library name: NSM1606-b2
3 lvl sciRNAseq


title: M1 from animal_14

description:
Library name: NSM1605-b2
3 lvl sciRNAseq


title: YAP-TG, 2 weeks, repeat 2

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description:
Library name: Sample 4
YAP-TG, 2 weeks, repeat 2

data_processing:
Cell Ranger was applied to align the raw FASTQ files to the mouse reference genome, and to quantify the gene by cell count
Assembly: GRCm39
Supplementary files format and content: tab separated files and mtrix files

molecule: polyA RNA

source_name: liver

extract_protocol:
Liver tissue samples were cryopreserved at the indicated time points as previously performed. Briefly, minced livers were added to freezing media (10% DMSO in FBS), gradually cooled to -80°C and placed in liquid nitrogen for long-term storage. Cryopreserved liver samples were rapidly thawed in a 37°C water bath, freezing media was removed, liver samples were washed in DMEM and then transferred into Miltenyi C-tubes containing Liver Digest Medium (Thermo-Scientific) and processed using the OctoMACS Dissociator (Miltenyi Biotec) with the program “37C_m_LIDK” to yield a single cell suspension. This suspension was filtered through 70 μm cell strainers, washed, resuspended in a 37.5% Percoll density gradient (Sigma-Aldrich) containing 1x Hanks’ Buffered Saline Solution and heparin (1 unit/mL). Cell pellets from the Percoll gradient were briefly incubated in Red Blood Cell lysis buffer, and then washed PBS with 2% FBS (FACS buffer). Cell suspensions were incubated with TruStain FcX™ PLUS (Biolegend, 1:200) prior to staining with CD45 (Biolegend, 1:200). Stained cells were washed in FACS buffer incubated in 7-AAD (Biolegend, 1:2000) and then sorted on the BD FACSAria II (Thermo-Fisher).
Single-cell RNA sequencing libraries were prepared using the 10x Genomics Chromium GEM-X Single Cell 3' Reagent Kits v4 according to the manufacturer’s directions. Libraries were sequenced at the Yale Center for Genomic Analysis on an Illumina NovaSeqX.

value: YAP-TG

tag: age

value: 2 weeks

value: repeat 2


title: BPM_0-05_R2_P2

description: Library name: s107


title: HepG2.batch1.COL.rep3.C10

description: Library name: HepG2_Batch1_COL_3_C10

value: liver

value: hepatocyte


title: M1 from animal_13

description:
Library name: NSM1604-b2
3 lvl sciRNAseq


title: YAP-TG, 2 weeks, repeat 1

description:
Library name: Sample 3
YAP-TG, 2 weeks, repeat 1

value: repeat 1


title: BPM_0-001_R2_P2

description: Library name: s105

value: Mammary

value: Epithelial


title: HepG2.batch1.COL.rep3.B10

description: Library name: HepG2_Batch1_COL_3_B10

value: cell line


title: BPM_0-01_R2_P2

description: Library name: s106

value: WT

value: chemical exposure


title: HepG2.batch1.COL.rep3.A10

description: Library name: HepG2_Batch1_COL_3_A10


title: LATS KO, 2 weeks, repeat 2

description:
Library name: Sample 2
LATS KO, 2 weeks, repeat 2

value: LATS KO


title: M1 from animal_12

description:
Library name: NSM1603-b2
3 lvl sciRNAseq

value: primary motor cortex


title: M1 from animal_11

description:
Library name: NSM1602-b2
3 lvl sciRNAseq


title: LATS KO, 2 weeks, repeat 1

description:
Library name: Sample 1
LATS KO, 2 weeks, repeat 1


title: HepG2.batch1.COL.rep2.H10

description: Library name: HepG2_Batch1_COL_2_H10


title: BPE_50_R2_P2

description: Library name: s104

value: bisphenol E


title: M1 from animal_10

description:
Library name: NSM1601-b2
3 lvl sciRNAseq


title: Red Clover Diet + H polygyrus 9

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

description: Library name: D9

data_processing:
Adaptor sequences and low quality reads removed
Mapped to mouse genome
DEG determined using DESeq2
Assembly: GRCm39
Supplementary files format and content: excel file with count data and gene symbol for each sample

source_name: Small Inestine

extract_protocol:
RNA was extracted using RNeasy kit (Qiagen) following instructions provided by the manufacturer
standard Illumina

value: Small Inestine

tag: strain

value: C57BL/6 JOlaHsd

tag: Sex

value: female


title: HepG2.batch1.COL.rep2.G10

description: Library name: HepG2_Batch1_COL_2_G10


title: BPE_10_R2_P2

description: Library name: s103


title: Red Clover Diet + H polygyrus 8

description: Library name: D8


title: HepG2.batch1.COL.rep2.F10

description: Library name: HepG2_Batch1_COL_2_F10


title: M1 from animal_9

description:
Library name: NSM1600-b2
3 lvl sciRNAseq


title: M1 from animal_7

description:
Library name: NSM1598-b2
3 lvl sciRNAseq


title: M1 from animal_8

description:
Library name: NSM1599-b2
3 lvl sciRNAseq


title: Red Clover Diet + H polygyrus 7

description: Library name: D7


title: HepG2.batch1.COL.rep2.E10

description: Library name: HepG2_Batch1_COL_2_E10


title: BPE_5_R2_P2

description: Library name: s102


title: BPE_1_R2_P2

description: Library name: s101


title: Red Clover Diet + H polygyrus 6

description: Library name: D6


title: HepG2.batch1.COL.rep2.D10

description: Library name: HepG2_Batch1_COL_2_D10


title: BPE_0-5_R2_P2

description: Library name: s100


title: M1 from animal_6

description:
Library name: NSM1597-b2
3 lvl sciRNAseq


title: Red Clover Diet + H polygyrus 5

description: Library name: D5


title: HepG2.batch1.COL.rep2.C10

description: Library name: HepG2_Batch1_COL_2_C10


title: M1 from animal_5

description:
Library name: NSM1596-b2
3 lvl sciRNAseq


title: HepG2.batch1.COL.rep2.B10

description: Library name: HepG2_Batch1_COL_2_B10


title: Red Clover Diet + H polygyrus 4

description: Library name: D4


title: BPE_0-01_R2_P2

description: Library name: s98


title: M1 from animal_4

description:
Library name: NSM1595-b2
3 lvl sciRNAseq


title: BPE_0-001_R2_P2

description: Library name: s97


title: M1 from animal_3

description:
Library name: NSM1594-b2
3 lvl sciRNAseq


title: HepG2.batch1.COL.rep2.A10

description: Library name: HepG2_Batch1_COL_2_A10


title: Red Clover Diet + H polygyrus 3

description: Library name: D3


title: Red Clover Diet + H polygyrus 2

description: Library name: D2


title: HepG2.batch1.COL.rep1.H10

description: Library name: HepG2_Batch1_COL_1_H10


title: PC_UH_R1_P1

description: Library name: s96

value: technical control

value: universal human RNA


title: M1 from animal_2

description:
Library name: NSM1593-b2
3 lvl sciRNAseq


title: Red Clover Diet + H polygyrus 1

description: Library name: D1


title: HepG2.batch1.COL.rep1.G10

description: Library name: HepG2_Batch1_COL_1_G10


title: PC_B_R1_P1

description: Library name: s95

value: brain RNA


title: M1 from animal_1

description:
Library name: NSM1592-b2
3 lvl sciRNAseq


title: Control Diet + H polygyrus 9

description: Library name: C9


title: DMSO_0-1_R10_P1

description: Library name: s94

value: vehicle control

value: dimethyl sulfoxide


title: HepG2.batch1.COL.rep1.F10

description: Library name: HepG2_Batch1_COL_1_F10

value: liver

value: hepatocyte


title: Control Diet + H polygyrus 8

description: Library name: C8


title: EC from animal_55, rep2

description:
Library name: NSM1591-b2
3 lvl sciRNAseq

source_name: entorhinal cortex

value: entorhinal cortex


title: HepG2.batch1.COL.rep1.E10

description: Library name: HepG2_Batch1_COL_1_E10

value: cell line


title: EC from animal_55

description:
Library name: NSM1591
3 lvl sciRNAseq


title: Control Diet + H polygyrus 7

description: Library name: C7


title: DMSO_0-1_R9_P1

description: Library name: s93

value: Mammary

value: Epithelial

value: WT


title: DMSO_0-1_R8_P1

description: Library name: s92


title: Control Diet + H polygyrus 6

description: Library name: C6


title: EC from animal_54, rep2

description:
Library name: NSM1590-b2
3 lvl sciRNAseq


title: HepG2.batch1.COL.rep1.D10

description: Library name: HepG2_Batch1_COL_1_D10


title: HepG2.batch1.COL.rep1.C10

description: Library name: HepG2_Batch1_COL_1_C10


title: EC from animal_54

description:
Library name: NSM1590
3 lvl sciRNAseq


title: Control Diet + H polygyrus 5

description: Library name: C5


title: DMSO_0-1_R7_P1

description: Library name: s91


title: DMSO_0-1_R6_P1

description: Library name: s90


title: Control Diet + H polygyrus 4

description: Library name: C4


title: EC from animal_53, rep2

description:
Library name: NSM1589-b2
3 lvl sciRNAseq


title: HepG2.batch1.COL.rep1.A10

description: Library name: HepG2_Batch1_COL_1_A10


title: HepG2.batch1.COL.rep1.B10

description: Library name: HepG2_Batch1_COL_1_B10


title: EC from animal_53

description:
Library name: NSM1589
3 lvl sciRNAseq


title: DMSO_0-1_R5_P1

description: Library name: s89


title: Control Diet + H polygyrus 3

description: Library name: C3


title: NC_R2_P1

description: Library name: s88

value: lysis buffer


title: HepG2.batch1.CLP.rep3.H12

description: Library name: HepG2_Batch1_CLP_3_H12


title: EC from animal_52, rep2

description:
Library name: NSM1588-b2
3 lvl sciRNAseq


title: Control Diet + H polygyrus 2

description: Library name: C2


title: HepG2.batch1.CLP.rep3.G12

description: Library name: HepG2_Batch1_CLP_3_G12


title: EC from animal_52

description:
Library name: NSM1588
3 lvl sciRNAseq


title: Control Diet + H polygyrus 1

description: Library name: C1


title: HepG2.batch1.CLP.rep3.F12

description: Library name: HepG2_Batch1_CLP_3_F12


title: NC_R1_P1

description: Library name: s87


title: DMSO_0-1_R4_P1

description: Library name: s86


title: EC from animal_51, rep2

description:
Library name: NSM1587-b2
3 lvl sciRNAseq


title: Red Clover Diet 9

description: Library name: B9


title: EC from animal_51

description:
Library name: NSM1587
3 lvl sciRNAseq


title: HepG2.batch1.CLP.rep3.E12

description: Library name: HepG2_Batch1_CLP_3_E12


title: DMSO_0-1_R3_P1

description: Library name: s85


title: EC from animal_50, rep2

description:
Library name: NSM1586-b2
3 lvl sciRNAseq


title: HepG2.batch1.CLP.rep3.D12

description: Library name: HepG2_Batch1_CLP_3_D12


title: Red Clover Diet 7

description: Library name: B7


title: DMSO_0-1_R2_P1

description: Library name: s84


title: Red Clover Diet 8

description: Library name: B8


title: HepG2.batch1.CLP.rep3.C12

description: Library name: HepG2_Batch1_CLP_3_C12


title: Red Clover Diet 6

description: Library name: B6


title: DMSO_0-1_R1_P1

description: Library name: s83


title: HepG2.batch1.CLP.rep3.B12

description: Library name: HepG2_Batch1_CLP_3_B12


title: EC from animal_50

description:
Library name: NSM1586
3 lvl sciRNAseq


title: E2_1_R1_P1

description: Library name: s82

value: chemical exposure


title: Red Clover Diet 5

description: Library name: B5

value: Small Inestine


title: HepG2.batch1.CLP.rep3.A12

description: Library name: HepG2_Batch1_CLP_3_A12


title: E2_0-1_R1_P1

description: Library name: s81


title: EC from animal_49

description:
Library name: NSM1585
3 lvl sciRNAseq


title: EC from animal_49, rep2

description:
Library name: NSM1585-b2
3 lvl sciRNAseq


title: Red Clover Diet 4

description: Library name: B4

value: C57BL/6 JOlaHsd


title: HepG2.batch1.CLP.rep2.H12

description: Library name: HepG2_Batch1_CLP_2_H12


title: BPA_50_R1_P1

description: Library name: s80

value: bisphenol A


title: EC from animal_48, rep2

description:
Library name: NSM1584-b2
3 lvl sciRNAseq


title: BPE_0-1_R2_P2

description: Library name: s99

value: bisphenol E


title: Red Clover Diet 3

description: Library name: B3

value: female


title: HepG2.batch1.CLP.rep2.G12

description: Library name: HepG2_Batch1_CLP_2_G12


title: BPA_10_R1_P1

description: Library name: s79


title: Red Clover Diet 2

description: Library name: B2


title: EC from animal_48

description:
Library name: NSM1584
3 lvl sciRNAseq


title: HepG2.batch1.CLP.rep2.F12

description: Library name: HepG2_Batch1_CLP_2_F12


title: BPA_5_R1_P1

description: Library name: s78


title: EC from animal_47, rep2

description:
Library name: NSM1583-b2
3 lvl sciRNAseq


title: BPA_1_R1_P1

description: Library name: s77


title: HepG2.batch1.CLP.rep2.E12

description: Library name: HepG2_Batch1_CLP_2_E12


title: Red Clover Diet 1

description: Library name: B1


title: EC from animal_47

description:
Library name: NSM1583
3 lvl sciRNAseq


title: BPA_0-5_R1_P1

description: Library name: s76


title: Control Diet 8

description: Library name: A8


title: EC from animal_46, rep2

description:
Library name: NSM1582-b2
3 lvl sciRNAseq


title: HepG2.batch1.CLP.rep2.D12

description: Library name: HepG2_Batch1_CLP_2_D12


title: Control Diet 9

description: Library name: A9


title: BPA_0-1_R1_P1

description: Library name: s75


title: Control Diet 7

description: Library name: A7


title: HepG2.batch1.CLP.rep2.B12

description: Library name: HepG2_Batch1_CLP_2_B12


title: BPA_0-001_R1_P1

description: Library name: s74


title: HepG2.batch1.CLP.rep2.C12

description: Library name: HepG2_Batch1_CLP_2_C12


title: EC from animal_46

description:
Library name: NSM1582
3 lvl sciRNAseq


title: HepG2.batch1.CLP.rep2.A12

description: Library name: HepG2_Batch1_CLP_2_A12


title: BPA_0-01_R1_P1

description: Library name: s73


title: Control Diet 6

description: Library name: A6


title: EC from animal_45, rep2

description:
Library name: NSM1581-b2
3 lvl sciRNAseq


title: Control Diet 5

description: Library name: A5


title: EC from animal_44, rep2

description:
Library name: NSM1580-b2
3 lvl sciRNAseq


title: HepG2.batch1.CLP.rep1.H12

description: Library name: HepG2_Batch1_CLP_1_H12


title: TBPB_10_R1_P1

description: Library name: s71

value: tetrabromophenol blue


title: TBPB_50_R1_P1

description: Library name: s72


title: HepG2.batch1.CLP.rep1.G12

description: Library name: HepG2_Batch1_CLP_1_G12


title: EC from animal_44

description:
Library name: NSM1580
3 lvl sciRNAseq


title: Control Diet 4

description: Library name: A4


title: HepG2.batch1.CLP.rep1.F12

description: Library name: HepG2_Batch1_CLP_1_F12


title: TBPB_5_R1_P1

description: Library name: s70


title: EC from animal_43, rep2

description:
Library name: NSM1579-b2
3 lvl sciRNAseq


title: Control Diet 3

description: Library name: A3


title: TBPB_1_R1_P1

description: Library name: s69


title: HepG2.batch1.CLP.rep1.E12

description: Library name: HepG2_Batch1_CLP_1_E12


title: Control Diet 2

description: Library name: A2


title: EC from animal_43

description:
Library name: NSM1579
3 lvl sciRNAseq


title: GroupA_4

description: Library name: 23_S23

value: skeletal muscle derived cells


title: Control Diet 1

description: Library name: A1


title: HepG2.batch1.CLP.rep1.D12

description: Library name: HepG2_Batch1_CLP_1_D12


title: EC from animal_42, rep2

description:
Library name: NSM1578-b2
3 lvl sciRNAseq


title: TBPB_0-5_R1_P1

description: Library name: s68


title: snRNA-seq LATS 2 wks

description:
Library name: Sample 8
LATS 2 wks

data_processing:
The sequencing data was pre-processed using the beenet software, with 5000 cells. The TCM (transcript count per million) file was used for downstream Seurat single-cell analysis.
Assembly: mm10
Supplementary files format and content: TSV.gz zipped TSV file for transcript by cell TCM count.

extract_protocol:
Single lobes were isolated from mouse liver and snap frozen in liquid nitrogen. On the day of nuclei isolation, snap frozen samples were gently split with a razor blade to yield small chunks of approximately 8-10mm in diameter. Homogenization buffer (HB) was prepared as described95. The sample was placed in a 1.5mL tube with 750uL homogenization buffer (0.1% Triton-X, 1 M dithiothreitol, 242.25 mM sucrose, 24.23 mM KCl, 4.85 mM MgCl2, 9.69 mM Tris-pH 8.0) then dounced 5 times with a loose pestle and 10 times with a tight pestle. The sample was then transferred to a fresh tube and 250 L of HB was added before incubation on ice for 5 minutes. The homogenized sample was then filtered through a 100uM cell strainer (Corning, 08-771-19). Filtrate was then passed through the 35 M strainer cap of a polystyrene test tube (Corning, 08-771-23). The sample was spun down at 500 x g for 5 minutes at 4C. Density gradient purification was performed with Optiprep Density Gradient Medium (Sigma-Aldrich, 92339-11-2) as described in Narayanan et al. 2020. Isolated nuclei were stained in a 1:1 ratio with 0.4% Trypan Blue solution and observed in a hemocytometer under the Echo Rebel Microscope.
Samples were fixed and permeabilized using the Parse Biosciences Evercode™ Fixation kit v2 (ECF2103) according to manufacturer instructions. Samples were then stored at –80C until needed for library preparation. Libraries were prepared using Parse Biosciences Evercode™ Whole Transcriptome v2 barcoding kit according to manufacturer instructions as described in Evercode™ user manual v2.2.2. Libraries were sequenced at the Yale Center for Genome Analysis on the NovaSeqX, 100bp paired-end sequencing.

value: LATS 2 wks


title: TBPB_0-1_R1_P1

description: Library name: s67


title: HepG2.batch1.CLP.rep1.C12

description: Library name: HepG2_Batch1_CLP_1_C12

value: liver


title: EC from animal_42

description:
Library name: NSM1578
3 lvl sciRNAseq


title: snRNA-seq LATS 1 wk

description:
Library name: Sample 7
LATS 1 wk

value: LATS 1 wk


title: TBPB_0-01_R1_P1

description: Library name: s66


title: HepG2.batch1.CLP.rep1.B12

description: Library name: HepG2_Batch1_CLP_1_B12

value: hepatocyte


title: EC from animal_41, rep2

description:
Library name: NSM1577-b2
3 lvl sciRNAseq

value: entorhinal cortex


title: snRNA-seq LATS 4 days

description:
Library name: Sample 6
LATS 4 days

value: LATS 4 days


title: EC from animal_41

description:
Library name: NSM1577
3 lvl sciRNAseq


title: snRNA-seq YAP 2 wks

description:
Library name: Sample 5
YAP 2 wks

value: YAP 2 wks


title: TBPB_0-001_R1_P1

description: Library name: s65

value: Mammary

value: Epithelial

value: WT


title: HepG2.batch1.CLP.rep1.A12

description: Library name: HepG2_Batch1_CLP_1_A12

value: cell line


title: PRed_50_R1_P1

description: Library name: s64

value: chemical exposure

value: phenol red


title: EC from animal_40, rep2

description:
Library name: NSM1576-b2
3 lvl sciRNAseq


title: HepG2.batch1.CLN.rep3.G02

description: Library name: HepG2_Batch1_CLN_3_G02


title: snRNA-seq YAP 1 wk

description:
Library name: Sample 4
YAP 1 wk

value: YAP 1 wk


title: PRed_10_R1_P1

description: Library name: s63


title: HepG2.batch1.CLN.rep3.F02

description: Library name: HepG2_Batch1_CLN_3_F02


title: snRNA-seq YAP 4 days

description:
Library name: Sample 3
YAP 4 days

value: YAP 4 days


title: PRed_5_R1_P1

description: Library name: s62


title: snRNA-seq YAP no doxCTRL

description:
Library name: Sample 2
YAP no doxCTRL

value: YAP no doxCTRL


title: HepG2.batch1.CLN.rep3.E02

description: Library name: HepG2_Batch1_CLN_3_E02


title: EC from animal_39

description:
Library name: NSM1575
3 lvl sciRNAseq


title: PRed_1_R1_P1

description: Library name: s61


title: HepG2.batch1.CLN.rep3.D02

description: Library name: HepG2_Batch1_CLN_3_D02


title: PRed_0-5_R1_P1

description: Library name: s60


title: EC from animal_37, rep2

description:
Library name: NSM1574-b2
3 lvl sciRNAseq


title: HepG2.batch1.CLN.rep3.C02

description: Library name: HepG2_Batch1_CLN_3_C02


title: PRed_0-1_R1_P1

description: Library name: s59


title: EC from animal_37

description:
Library name: NSM1574
3 lvl sciRNAseq


title: Cortical nuclei, Wild Type, Male, Rep M2, Gene Expression

city: San Francisco

first: Kristof

last: Torkenczy

state: CA

address: 1437 S Van Ness Ave, apt 1

institute: Altos Labs

description:
Library name: Sample14_GEX
Sample 14 GEX (WT Male M2)

data_processing:
Raw reads were aligned to the GRCm38 mouse reference genome using the Cell Ranger ARC pipeline (v2.0.2). RNA count matrix and ATAC fragment data were processed using Seurat (v5.2.0) and Signac (v1.14.9), respectively. ATAC reads were re-quantified based on the union of consensus accessible chromatin regions (ACRs). Quality filtering retained cells with 500-100,000 ATAC counts, nucleosome signal < 3, and TSS enrichment > 1. For RNA, filtering thresholds were set to >500 genes detected and <10% mitochondrial reads.
RNA quality filtering was performed using PopsicleR and Seurat, retaining cells with >500 genes detected and <10% mitochondrial reads.
ATAC quality filtering was performed using Signac, retaining cells with 500-100,000 ATAC counts, nucleosome signal < 3, and TSS enrichment > 1.
RNA data was log-normalized and scaled. Dimensionality reduction was performed using PCA (top 2000 variable features) for RNA and LSI (dimensions 2-30) for ATAC.
Accessible Chromatin Regions (ACRs) were identified using MACS3, filtered to standard chromosomes, and merged across samples. ATAC reads were re-quantified based on this union of consensus ACRs.
Assembly: GRCm38
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 format file containing the filtered feature-barcode sparse matrix (including both Gene Expression UMI counts and ATAC peak counts) generated by Cell Ranger ARC.
Supplementary files format and content: atac_fragments.tsv.gz: Gzipped tab-separated file containing ATAC-seq fragment start/end coordinates and cell barcodes.

source_name: Cerebral Cortex

growth_protocol: Mice were housed under a 12 hr / 12 hr light/dark cycle (lights on at 7:00 am) with access to food and water ad libitum. Behavioral experiments and tissue collection were conducted on both male and female mice aged 10-16 weeks old.

extract_protocol:
Nuclei were isolated from frozen cortical tissue (5-10 mg). Tissue was homogenized in 500 μL of nuclei extraction buffer (0.32 M sucrose, 10mM Tris pH 7.4, 5mM CaCl2, 3mM Mg acetate, 1mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/ml Protector RNAse inhibitor) using a dounce homogenizer. The homogenate was filtered through a 70 μm filter and centrifuged through a sucrose cushion (1.8 M sucrose) at 16,000 x g for 30 minutes at 4°C. Nuclei permeabilization was performed following the 10x Genomics protocol (CG000375 Rev B), incubating for exactly 2 min on ice in lysis buffer containing 0.01% NP-40 and 0.001% digitonin.
Transposition, nuclei isolation, barcoding, and library preparation were performed following the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (CG000338 Rev F). Each sample was loaded onto a Chromium Next GEM Chip J to recover approximately 10,000 nuclei per lane. Sequencing libraries were sequenced on an Illumina NovaSeq X.

treatment_protocol: Ppp1r15b-R658C mice harbor a human patient-derived genetic variant in the phosphatase cofactor PPP1R15B, leading to persistent ISR activation.

value: Cerebral Cortex

value: Cortical Nuclei

value: Wild Type

value: Male


title: EC from animal_39, rep2

description:
Library name: NSM1575-b2
3 lvl sciRNAseq


title: PRed_0-01_R1_P1

description: Library name: s58


title: HepG2.batch1.CLN.rep3.B02

description: Library name: HepG2_Batch1_CLN_3_B02

value: liver

value: hepatocyte


title: Cortical nuclei, Wild Type, Male, Rep M1, ATAC-seq

description:
Library name: Sample13_ATAC
Sample 13 ATAC (WT Male M1)

library_source: genomic single cell

molecule: genomic DNA


title: HepG2.batch1.CLN.rep3.A02

description: Library name: HepG2_Batch1_CLN_3_A02


title: PRed_0-001_R1_P1

description: Library name: s57


title: EC from animal_36, rep2

description:
Library name: NSM1573-b2
3 lvl sciRNAseq

value: entorhinal cortex


title: EC from animal_36

description:
Library name: NSM1573
3 lvl sciRNAseq


title: HepG2.batch1.CLN.rep2.H02

description: Library name: HepG2_Batch1_CLN_2_H02


title: EC from animal_45

description:
Library name: NSM1581
3 lvl sciRNAseq


title: THPE_50_R1_P1

description: Library name: s56


title: Cortical nuclei, Wild Type, Female, Rep F2, ATAC-seq

description:
Library name: Sample12_ATAC
Sample 12 ATAC (WT Female F2)

value: Female


title: HepG2.batch1.CLN.rep2.G02

description: Library name: HepG2_Batch1_CLN_2_G02


title: THPE_10_R1_P1

description: Library name: s55

value: Mammary


title: EC from animal_35

description:
Library name: NSM1572
3 lvl sciRNAseq


title: THPE_5_R1_P1

description: Library name: s54

value: Epithelial


title: EC from animal_34, rep2

description:
Library name: NSM1571-b2
3 lvl sciRNAseq


title: HepG2.batch1.CLN.rep2.E02

description: Library name: HepG2_Batch1_CLN_2_E02


title: Cortical nuclei, Wild Type, Female, Rep B20, ATAC-seq

description:
Library name: Sample11_ATAC
Sample 11 ATAC (WT Female B20)


title: THPE_1_R1_P1

description: Library name: s53

value: WT


title: EC from animal_34

description:
Library name: NSM1571
3 lvl sciRNAseq


title: Cortical nuclei, Wild Type, Female, Rep B20, Gene Expression

description:
Library name: Sample11_GEX
Sample 11 GEX (WT Female B20)


title: HepG2.batch1.CLN.rep2.D02

description: Library name: HepG2_Batch1_CLN_2_D02

value: cell line


title: THPE_0-5_R1_P1

description: Library name: s52

value: chemical exposure


title: EC from animal_33, rep2

description:
Library name: NSM1570-b2
3 lvl sciRNAseq


title: Cortical nuclei, Ppp1r15b-R658C, Female, Rep B10, ATAC-seq

description:
Library name: Sample10_ATAC
Sample 10 ATAC (Mutant Female B10)


title: HepG2.batch1.CLN.rep2.B02

description: Library name: HepG2_Batch1_CLN_2_B02


title: Cortical nuclei, Ppp1r15b-R658C, Female, Rep B10, Gene Expression

description:
Library name: Sample10_GEX
Sample 10 GEX (Mutant Female B10)


title: THPE_0-1_R1_P1

description: Library name: s51


title: EC from animal_32, rep2

description:
Library name: NSM1569-b2
3 lvl sciRNAseq


title: EC from animal_33

description:
Library name: NSM1570
3 lvl sciRNAseq


title: HepG2.batch1.CLN.rep2.A02

description: Library name: HepG2_Batch1_CLN_2_A02


title: Cortical nuclei, Ppp1r15b-R658C, Male, Rep B0, ATAC-seq

description:
Library name: Sample9_ATAC
Sample 9 ATAC (Mutant Male B0)


title: THPE_0-001_R1_P1

description: Library name: s49


title: EC from animal_32

description:
Library name: NSM1569
3 lvl sciRNAseq


title: Cortical nuclei, Ppp1r15b-R658C, Male, Rep B0, Gene Expression

description:
Library name: Sample9_GEX
Sample 9 GEX (Mutant Male B0)


title: HepG2.batch1.CLN.rep1.G02

description: Library name: HepG2_Batch1_CLN_1_G02


title: PA08_10_R1_P1

description: Library name: s48

value: plastic additive 08


title: HepG2.batch1.CLN.rep1.H02

description: Library name: HepG2_Batch1_CLN_1_H02


title: HepG2.batch1.CLN.rep3.H02

description: Library name: HepG2_Batch1_CLN_3_H02


title: Cortical nuclei, Ppp1r15b-R658C, Female, Rep A10, ATAC-seq

description:
Library name: Sample8_ATAC
Sample 8 ATAC (Mutant Female A10)


title: EC from animal_40

description:
Library name: NSM1576
3 lvl sciRNAseq


title: EC from animal_31, rep2

description:
Library name: NSM1568-b2
3 lvl sciRNAseq


title: PA08_5_R1_P1

description: Library name: s47


title: EC from animal_31

description:
Library name: NSM1568
3 lvl sciRNAseq


title: HepG2.batch1.CLN.rep1.F02

description: Library name: HepG2_Batch1_CLN_1_F02


title: Cortical nuclei, Ppp1r15b-R658C, Female, Rep A10, Gene Expression

description:
Library name: Sample8_GEX
Sample 8 GEX (Mutant Female A10)


title: Cortical nuclei, Wild Type, Male, Rep M2, ATAC-seq

description:
Library name: Sample14_ATAC
Sample 14 ATAC (WT Male M2)


title: PA08_1_R1_P1

description: Library name: s46


title: Cortical nuclei, Ppp1r15b-R658C, Male, Rep A0, ATAC-seq

description:
Library name: Sample7_ATAC
Sample 7 ATAC (Mutant Male A0)


title: HepG2.batch1.CLN.rep1.E02

description: Library name: HepG2_Batch1_CLN_1_E02


title: EC from animal_30, rep2

description:
Library name: NSM1567-b2
3 lvl sciRNAseq


title: Cortical nuclei, Ppp1r15b-R658C, Male, Rep A0, Gene Expression

description:
Library name: Sample7_GEX
Sample 7 GEX (Mutant Male A0)


title: EC from animal_30

description:
Library name: NSM1567
3 lvl sciRNAseq


title: PA08_0-5_R1_P1

description: Library name: s45


title: Cortical nuclei, Wild Type, Male, Rep M1, Gene Expression

description:
Library name: Sample13_GEX
Sample 13 GEX (WT Male M1)


title: HepG2.batch1.CLN.rep1.D02

description: Library name: HepG2_Batch1_CLN_1_D02


title: PA08_0-1_R1_P1

description: Library name: s44


title: Cortical nuclei, Wild Type, Male, Rep M3, ATAC-seq

description:
Library name: Sample6_ATAC
Sample 6 ATAC (WT Male M3)


title: EC from animal_29, rep2

description:
Library name: NSM1560-b2
3 lvl sciRNAseq


title: EC from animal_35, rep2

description:
Library name: NSM1572-b2
3 lvl sciRNAseq


title: HepG2.batch1.CLN.rep1.C02

description: Library name: HepG2_Batch1_CLN_1_C02


title: PA08_0-05_R1_P1

description: Library name: s43


title: EC from animal_29

description:
Library name: NSM1560
3 lvl sciRNAseq


title: PA08_0-01_R1_P1

description: Library name: s42


title: Cortical nuclei, Wild Type, Female, Rep F2, Gene Expression

description:
Library name: Sample12_GEX
Sample 12 GEX (WT Female F2)


title: EC from animal_28, rep2

description:
Library name: NSM1559-b2
3 lvl sciRNAseq


title: HepG2.batch1.CLN.rep1.B02

description: Library name: HepG2_Batch1_CLN_1_B02


title: Cortical nuclei, Wild Type, Male, Rep M3, Gene Expression

description:
Library name: Sample6_GEX
Sample 6 GEX (WT Male M3)


title: Cortical nuclei, Wild Type, Female, Rep F1, ATAC-seq

description:
Library name: Sample5_ATAC
Sample 5 ATAC (WT Female F1)


title: HepG2.batch1.CLN.rep2.F02

description: Library name: HepG2_Batch1_CLN_2_F02


title: PA08_0-001_R1_P1

description: Library name: s41


title: HepG2.batch1.CLN.rep1.A02

description: Library name: HepG2_Batch1_CLN_1_A02


title: EC from animal_28

description:
Library name: NSM1559
3 lvl sciRNAseq


title: Cortical nuclei, Wild Type, Female, Rep F1, Gene Expression

description:
Library name: Sample5_GEX
Sample 5 GEX (WT Female F1)


title: HepG2.batch1.CAT.rep3.H09

description: Library name: HepG2_Batch1_CAT_3_H09


title: TBBPS_50_R1_P1

description: Library name: s40

value: tetrabromo bisphenol S


title: EC from animal_27, rep2

description:
Library name: NSM1558-b2
3 lvl sciRNAseq


title: Cortical nuclei, Wild Type, Female, Rep B11, ATAC-seq

description:
Library name: Sample4_ATAC
Sample 4 ATAC (WT Female B11)


title: HepG2.batch1.CAT.rep3.G09

description: Library name: HepG2_Batch1_CAT_3_G09


title: EC from animal_27

description:
Library name: NSM1558
3 lvl sciRNAseq


title: TBBPS_5_R1_P1

description: Library name: s38


title: HepG2.batch1.CAT.rep3.F09

description: Library name: HepG2_Batch1_CAT_3_F09


title: TBBPS_10_R1_P1

description: Library name: s39


title: HepG2.batch1.CLN.rep2.C02

description: Library name: HepG2_Batch1_CLN_2_C02


title: EC from animal_26

description:
Library name: NSM1557
3 lvl sciRNAseq


title: Cortical nuclei, Ppp1r15b-R658C, Male, Rep A10, ATAC-seq

description:
Library name: Sample3_ATAC
Sample 3 ATAC (Mutant Male A10)


title: EC from animal_25

description:
Library name: NSM1556
3 lvl sciRNAseq


title: THPE_0-01_R1_P1

description: Library name: s50


title: TBBPS_1_R1_P1

description: Library name: s37


title: Cortical nuclei, Ppp1r15b-R658C, Male, Rep A10, Gene Expression

description:
Library name: Sample3_GEX
Sample 3 GEX (Mutant Male A10)


title: HepG2.batch1.CAT.rep3.D09

description: Library name: HepG2_Batch1_CAT_3_D09


title: TBBPS_0-5_R1_P1

description: Library name: s36


title: Cortical nuclei, Ppp1r15b-R658C, Male, Rep A3, ATAC-seq

description:
Library name: Sample2_ATAC
Sample 2 ATAC (Mutant Male A3)


title: EC from animal_24

description:
Library name: NSM1555
3 lvl sciRNAseq


title: HepG2.batch1.CAT.rep3.C09

description: Library name: HepG2_Batch1_CAT_3_C09


title: TBBPS_0-1_R1_P1

description: Library name: s35


title: Cortical nuclei, Ppp1r15b-R658C, Male, Rep A3, Gene Expression

description:
Library name: Sample2_GEX
Sample 2 GEX (Mutant Male A3)


title: TBBPS_0-01_R1_P1

description: Library name: s34


title: EC from animal_23

description:
Library name: NSM1554
3 lvl sciRNAseq


title: HepG2.batch1.CAT.rep3.B09

description: Library name: HepG2_Batch1_CAT_3_B09


title: Cortical nuclei, Ppp1r15b-R658C, Female, Rep A2, ATAC-seq

description:
Library name: Sample1_ATAC
Sample 1 ATAC (Mutant Female A2)


title: EC from animal_22

description:
Library name: NSM1553
3 lvl sciRNAseq


title: HepG2.batch1.CAT.rep3.A09

description: Library name: HepG2_Batch1_CAT_3_A09


title: TBBPS_0-001_R1_P1

description: Library name: s33


title: EC from animal_21

description:
Library name: NSM1552
3 lvl sciRNAseq


title: Cortical nuclei, Ppp1r15b-R658C, Female, Rep A2, Gene Expression

description:
Library name: Sample1_GEX
Sample 1 GEX (Mutant Female A2)


title: HepG2.batch1.CAT.rep2.H09

description: Library name: HepG2_Batch1_CAT_2_H09


title: Mouse bone marrow cells from Nrf2-/- knockout, BMX-001 and 5-FU, rep 2

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

description: Library name: NBF2

data_processing:
RNA-Seq reads were first trimmed with Trim Galore version 0.6.4, which includes filtering reads shorter than 30 bp and low-quality ends from reads (Phred score: <20) and the option of removing reads with Ns. The quality of reads before and after trimming was checked with FastQC version 0.12.1.
The filtered reads were then used to quantify transcripts in Salmon version 1.4.0 mapping-based mode using a decoy-aware transcriptome built from the GENCODE Mus musculus genome and transcriptome release M30 (GRCm39). Transcript expression values were used to run the differential gene expression analysis in DESeq2 1.38.3 in R version 4.3.0
Genes with a Benjamini-Hochberg adjusted P value lesser than 0.05 and a log2 fold change greater than 1 were considered as differentially expressed. The differential expression result table generated by DESeq2 was annotated with gene information obtained from Ensembl BioMart for Mus musculus (release 104). GO terms enrichment analysis was performed via GOseq version 1.50.0, where terms with Benjamini-Hochberg adjusted P-values < 0.05 were deemed significant. Pathway analysis was performed using Ingenuity Pathway Analysis (QIAGEN Inc., https://digitalinsights.qiagen.com/IPA)
Assembly: GENCODE M30 (GRCm39)
Supplementary files format and content: A featureCounts tab-delimited data matrix which has 5 columns: an ENSEMBL ID in the first column and raw counts in the subsequent columns for each sample. The header has as columns (empty)\t followed by sample names.

source_name: bone marrow

growth_protocol: 8–10 week old male C57BL/6 and athymic NU/J mice were obtained from Jackson Laboratories (Bar Harbor, ME). Male and female Nrf2+/- mice were also obtained from Jackson Laboratories. Nrf2+/- mice were bred and Nrf2-/- knockout status was verified by routine genotyping, as Nrf2-/- mice express a mutant, inactive form at 400 base pairs compared to wild type Nrf2, which is 262 base pairs.

extract_protocol:
Mice were sacrificed and mouse bone marrow was isolated in duplicate.
RNA was extracted from 2x10^6 cells using the RNeasy Mini Kit (Qiagen, 74104). RNA quantity and quality was measured using a Tecan Infinite M200 PRO plate reader using an Infinite 200 Nanoquant plate. RNA sequencing was performed by the City of Hope’s Integrative Genomics and Bioinformatics core in Duarte, California. Sequencing run (151+11+24+151) was performed on the NovaSeq X Series platform with 10B reagent kit (300 Cycle). NovaSeq Control Software 1.2.0.28691 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files

treatment_protocol: Mice were given food and water ad libitum and were exposed to a 12-hour light/dark cycle. Mice were treated with BMX-001 at 0.5 mg/kg 24 hours before and every three days following 5-FU given at 20 mg/kg. Seven days after the first 5-FU dose, mice were given a second dose of 5-FU. Ten days following the first 5-FU dose, mice were sacrificed and mouse bone marrow was isolated.

value: bone marrow

value: Mouse bone marrow cells

value: CB57BL/6 with Nrf2-/- knockout

value: BMX-001 and 5-FU


title: EC from animal_20

description:
Library name: NSM1551
3 lvl sciRNAseq


title: Mouse bone marrow cells from Nrf2-/- knockout, BMX-001 and 5-FU, rep 1

description: Library name: NBF1


title: DABPA_10_R1_P1

description: Library name: s32

value: diallyl bisphenol A


title: DABPA_5_R1_P1

description: Library name: s31


title: EC from animal_19

description:
Library name: NSM1550
3 lvl sciRNAseq


title: HepG2.batch1.CAT.rep2.F09

description: Library name: HepG2_Batch1_CAT_2_F09


title: DABPA_1_R1_P1

description: Library name: s30


title: Mouse bone marrow cells from Nrf2-/- knockout, 5-FU, rep 2

description: Library name: NF2


title: EC from animal_18

description:
Library name: NSM1549
3 lvl sciRNAseq


title: DABPA_0-5_R1_P1

description: Library name: s29


title: HepG2.batch1.CAT.rep2.E09

description: Library name: HepG2_Batch1_CAT_2_E09


title: EC from animal_17

description:
Library name: NSM1548
3 lvl sciRNAseq


title: Mouse bone marrow cells from Nrf2-/- knockout, 5-FU, rep 1

description: Library name: NF1


title: EC from animal_16

description:
Library name: NSM1547
3 lvl sciRNAseq


title: HepG2.batch1.CAT.rep2.D09

description: Library name: HepG2_Batch1_CAT_2_D09


title: DABPA_0-1_R1_P1

description: Library name: s28


title: Mouse bone marrow cells from Nrf2-/- knockout, BMX-001, rep 2

description: Library name: NB2


title: HepG2.batch1.CAT.rep2.C09

description: Library name: HepG2_Batch1_CAT_2_C09


title: EC from animal_15

description:
Library name: NSM1546
3 lvl sciRNAseq


title: DABPA_0-05_R1_P1

description: Library name: s27


title: HepG2.batch1.CAT.rep2.B09

description: Library name: HepG2_Batch1_CAT_2_B09


title: DABPA_0-01_R1_P1

description: Library name: s26


title: Mouse bone marrow cells from Nrf2-/- knockout, BMX-001, rep 1

description: Library name: NB1


title: HepG2.batch1.CAT.rep2.A09

description: Library name: HepG2_Batch1_CAT_2_A09


title: Mouse bone marrow cells from Nrf2-/- knockout, PBS, rep 2

description: Library name: NP2

value: Control


title: EC from animal_14

description:
Library name: NSM1545
3 lvl sciRNAseq


title: DABPA_0-001_R1_P1

description: Library name: s25


title: EC from animal_13

description:
Library name: NSM1544
3 lvl sciRNAseq


title: Mouse bone marrow cells from Nrf2-/- knockout, PBS, rep 1

description: Library name: NP1


title: HepG2.batch1.CAT.rep1.H09

description: Library name: HepG2_Batch1_CAT_1_H09

value: liver


title: Mouse bone marrow cells from wildtype, BMX-001 and 5-FU, rep 2

description: Library name: WTBF2


title: BPK_50_R1_P1

description: Library name: s24

value: bisphenol K


title: HepG2.batch1.CAT.rep1.G09

description: Library name: HepG2_Batch1_CAT_1_G09

value: hepatocyte


title: EC from animal_12

description:
Library name: NSM1543
3 lvl sciRNAseq

value: entorhinal cortex


title: Mouse bone marrow cells from wildtype, BMX-001 and 5-FU, rep 1

description: Library name: WTBF1


title: EC from animal_11

description:
Library name: NSM1542
3 lvl sciRNAseq


title: BPK_5_R1_P1

description: Library name: s22

value: Mammary


title: EC from animal_10

description:
Library name: NSM1541
3 lvl sciRNAseq


title: BPK_10_R1_P1

description: Library name: s23

value: Epithelial


title: Mouse bone marrow cells from wildtype, 5-FU, rep 2

description: Library name: WTF2


title: HepG2.batch1.CAT.rep1.E09

description: Library name: HepG2_Batch1_CAT_1_E09


title: HepG2.batch1.CAT.rep1.F09

description: Library name: HepG2_Batch1_CAT_1_F09


title: BPK_1_R1_P1

description: Library name: s21

value: WT


title: Mouse bone marrow cells from wildtype, 5-FU, rep 1

description: Library name: WTF1


title: EC from animal_9

description:
Library name: NSM1540
3 lvl sciRNAseq


title: HepG2.batch1.CAT.rep1.D09

description: Library name: HepG2_Batch1_CAT_1_D09

value: cell line


title: BPK_0-5_R1_P1

description: Library name: s20

value: chemical exposure


title: HepG2.batch1.CAT.rep1.C09

description: Library name: HepG2_Batch1_CAT_1_C09


title: EC from animal_8

description:
Library name: NSM1539
3 lvl sciRNAseq


title: EC from animal_7

description:
Library name: NSM1538
3 lvl sciRNAseq


title: Mouse bone marrow cells from wildtype, BMX-001, rep 1

description: Library name: WTB1


title: BPK_0-1_R1_P1

description: Library name: s19


title: HepG2.batch1.CAT.rep1.B09

description: Library name: HepG2_Batch1_CAT_1_B09


title: Mouse bone marrow cells from wildtype, BMX-001, rep 2

description: Library name: WTB2


title: BPK_0-01_R1_P1

description: Library name: s18


title: Mouse bone marrow cells from wildtype, PBS, rep 2

description: Library name: WTP2


title: EC from animal_6

description:
Library name: NSM1537
3 lvl sciRNAseq


title: HepG2.batch1.CAT.rep1.A09

description: Library name: HepG2_Batch1_CAT_1_A09


title: EC from animal_5

description:
Library name: NSM1536
3 lvl sciRNAseq


title: Mouse bone marrow cells from wildtype, PBS, rep 1

description: Library name: WTP1


title: BPK_0-001_R1_P1

description: Library name: s17


title: HepG2.batch1.ATA.rep3.H01

description: Library name: HepG2_Batch1_ATA_3_H01


title: EC from animal_4

description:
Library name: NSM1535
3 lvl sciRNAseq


title: BPM_10_R1_P1

description: Library name: s16

value: bisphenol M


title: MEL Mtg16 Mtg16-2XHA 2hWO C

city: Nashville

first: Scott

middle: W

last: Hiebert

state: TN

address: 2220 Pierce Ave.

institute: Vanderbilt University

description: Library name: CUTRUN_Mtg16-2XHA 2hWO C

library_source: genomic

data_processing:
Adaptor trimming was performed using TrimmomaticPE, and trimmed reads were aligned to concatenated mm39+ec (CUT&RUN) or mm39+dm3 (ChIP-Seq) genomes. Resulting alignments were then processed with samtools (v. 1.16.1) to remove low quality reads, count reads aligned to mm39, ec, and dm3 genomes, and remove spike-in reads. Peak calling was performed using MACS2 (v. 2.2.9.1), q 0.01. Read quantification was performed with DiffBind (v. 3.16.0). Differential analysis was performed using DESeq2 (v. 1.46.0) with built-in normalization.
Assembly: mm39
Supplementary files format and content: bigwig
Library strategy: CUT&Run

source_name: MEL Mtg16-FKBP-2XHA

growth_protocol: MEL cells were grown in RPMI 1640 supplemented with 10% heat-inactivated FBS, 1% penicillin/streptomycin, and 1% L-glutamine.

extract_protocol:
CUT&RUN experiments were performed in biological triplicate. Samples were harvested by centrifugation, washed (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine, 1X Roche Complete Protease Inhibitor tablet), and adsorbed to activated Concavalin A beads for 10min at room temperature. Samples were then incubated with primary antibody diluted in digitonin buffer + 2mM EDTA (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine, 0.2% digitonin, 1X Roche Complete Protease Inhibitor tablet) overnight at 4C. The next day, samples were washed and incubated with secondary antibody diluted in digitonin buffer + 2mM EDTA for 1hr at 4C. After secondary antibody incubation, pAG-MNase was added to the samples, then activated with CaCl2 and incubated at 4C for 2hrs. After MNase incubation, the reaction stop buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 50ug/mL RNase A, 50ug/mL glycogen, supplemented with 0.5ng E. coli gDNA per sample) was added and samples incubated for 10min at 37C. Samples were then cleaned using NEB Monarch DNA Cleanup Kit according to manufacturer instructions prior to library preparation. ChIP-Seq experiments were performed in biological triplicate. All buffers were filter sterilized and supplemented with protease inhibitors immediately prior to use (2uL aprotinin and 20uL 0.1M PMSF per 1mL buffer). 10 million cells per immunoprecipitation sample were harvested by centrifugation, washed in PBS, and fixed for 10min at room temperature in 1% methanol-free formaldehyde, then quenched with 0.125M glycine. All subsequent steps were performed on ice or at 4C. Fixed cells were lysed in cell lysis buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton-X-100) that was supplemented with 0.5 million crosslinked S2 cells per sample. After lysis, cells were washed in wash buffer (10mM Tris pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) and then sonicated for 20 cycles with a Bioruptor water bath sonicator (30s on/30s off) in sonication buffer (10mM Tris pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% SDS, 0.5% sarkosyl). Successful sonication (DNA fragments between 100-500bp) were verified via agarose gel electrophoresis for every sample prior to IP. After sonication, samples were quantified using Qubit HS, supplemented with 1% Triton-X-100, and antibody was added, followed by overnight incubation at 4C with rotation. After overnight antibody incubation, samples were incubated with equilibrated Protein A/G Dynabeads (50:50 mix) for 1hr at 4C, followed by 5 successive washes: low salt (20mM Tris pH 8.0, 150mM NaCl, 2mM EDTA, 1% Triton-X-100), high salt (20mM Tris pH 8.0, 500mM NaCl, 2mM EDTA, 1% Triton-X-100), LiCl (10mM Tris pH 8.0, 25mM LiCl, 2mM EDTA, 1% Triton X-100), TE (10mM Tris pH 8.0, 1mM EDTA), and TE. After the final wash, elution buffer (1X TE pH 8.0. 0.1% SDS, 200mM NaCl, 0.8ug/uL proteinase K) was added directly to the beads and samples were de-crosslinked overnight at 65C prior to PCR clean up.
ChIP-Seq and CUT&RUN libraries were prepared using NEBNext Ultra II DNA Library Prep Kit according to manufacturer instructions with minor modifications. The end prep reaction for both library types was performed under the following conditions: 20C 30min, 50C 1hr. ChIP-Seq libraries were prepared with size selection. CUT&RUN libraries were prepared without size selection.

treatment_protocol: 250nM dTAGV1

value: MEL Mtg16-FKBP-2XHA

value: murine erythroleukemia


title: HepG2.batch1.ATA.rep3.G01

description: Library name: HepG2_Batch1_ATA_3_G01


title: EC from animal_3, rep2

description:
Library name: NSM1534-b2
3 lvl sciRNAseq


title: MEL Mtg16 Mtg16-2XHA 2hWO B

description: Library name: CUTRUN_Mtg16-2XHA 2hWO B


title: BPM_5_R1_P1

description: Library name: s15


title: BPM_1_R1_P1

description: Library name: s14


title: EC from animal_3

description:
Library name: NSM1534
3 lvl sciRNAseq


title: HepG2.batch1.ATA.rep3.E01

description: Library name: HepG2_Batch1_ATA_3_E01


title: MEL Mtg16 Mtg16-2XHA 1hWO C

description: Library name: CUTRUN_Mtg16-2XHA 1hWO C


title: EC from animal_2, rep2

description:
Library name: NSM1533-b2
3 lvl sciRNAseq


title: HepG2.batch1.ATA.rep3.D01

description: Library name: HepG2_Batch1_ATA_3_D01


title: MEL Mtg16 Mtg16-2XHA 1hWO B

description: Library name: CUTRUN_Mtg16-2XHA 1hWO B


title: HepG2.batch1.ATA.rep3.C01

description: Library name: HepG2_Batch1_ATA_3_C01


title: MEL Mtg16 Mtg16-2XHA 30mWO C

description: Library name: CUTRUN_Mtg16-2XHA 30mWO C


title: EC from animal_1, rep2

description:
Library name: NSM1532-b2
3 lvl sciRNAseq


title: HepG2.batch1.ATA.rep3.B01

description: Library name: HepG2_Batch1_ATA_3_B01


title: EC from animal_2

description:
Library name: NSM1533
3 lvl sciRNAseq


title: BPM_0-01_R1_P1

description: Library name: s10


title: EC from animal_1

description:
Library name: NSM1532
3 lvl sciRNAseq


title: MEL Mtg16 Mtg16-2XHA 30mWO B

description: Library name: CUTRUN_Mtg16-2XHA 30mWO B


title: NAc from animal_55

description:
Library name: NSM1531
3 lvl sciRNAseq

source_name: nucleus accumbens

value: nucleus accumbens


title: MEL Mtg16 Mtg16-2XHA 30mWO A

description: Library name: CUTRUN_Mtg16-2XHA 30mWO A


title: BPM_0-001_R1_P1

description: Library name: s9


title: HepG2.batch1.ATA.rep2.H01

description: Library name: HepG2_Batch1_ATA_2_H01


title: NAc from animal_54

description:
Library name: NSM1530
3 lvl sciRNAseq


title: MEL Mtg16 Mtg16-2XHA dTAGV1 2h C

description: Library name: CUTRUN_Mtg16-2XHA dTAGV1 2h C


title: NAc from animal_53

description:
Library name: NSM1529
3 lvl sciRNAseq


title: HepG2.batch1.ATA.rep2.F01

description: Library name: HepG2_Batch1_ATA_2_F01


title: BPE_5_R1_P1

description: Library name: s6

value: bisphenol E


title: MEL Mtg16 Mtg16-2XHA dTAGV1 2h A

description: Library name: CUTRUN_Mtg16-2XHA dTAGV1 2h A


title: NAc from animal_52

description:
Library name: NSM1528
3 lvl sciRNAseq


title: MEL Mtg16 Mtg16-2XHA dTAGV1 1h C

description: Library name: CUTRUN_Mtg16-2XHA dTAGV1 1h C


title: HepG2.batch1.ATA.rep2.E01

description: Library name: HepG2_Batch1_ATA_2_E01


title: BPE_1_R1_P1

description: Library name: s5


title: NAc from animal_51

description:
Library name: NSM1527
3 lvl sciRNAseq


title: Cortical nuclei, Wild Type, Female, Rep B11, Gene Expression

description:
Library name: Sample4_GEX
Sample 4 GEX (WT Female B11)

value: Cerebral Cortex

value: Cortical Nuclei

value: Wild Type

value: Female


title: MEL Mtg16 Mtg16-2XHA dTAGV1 1h B

description: Library name: CUTRUN_Mtg16-2XHA dTAGV1 1h B


title: BPE_0-5_R1_P1

description: Library name: s4


title: HepG2.batch1.ATA.rep3.F01

description: Library name: HepG2_Batch1_ATA_3_F01

value: liver


title: NAc from animal_50

description:
Library name: NSM1526
3 lvl sciRNAseq


title: HepG2.batch1.ATA.rep2.C01

description: Library name: HepG2_Batch1_ATA_2_C01

value: hepatocyte


title: MEL Mtg16 Mtg16-2XHA dTAGV1 1h A

description: Library name: CUTRUN_Mtg16-2XHA dTAGV1 1h A


title: BPE_0-1_R1_P1

description: Library name: s3


title: NAc from animal_49

description:
Library name: NSM1525
3 lvl sciRNAseq


title: MEL Mtg16 Mtg16-2XHA 2hWO A

description: Library name: CUTRUN_Mtg16-2XHA 2hWO A


title: MEL Mtg16 Mtg16-2XHA dTAGV1 30m C

description: Library name: CUTRUN_Mtg16-2XHA dTAGV1 30m C


title: HepG2.batch1.CAT.rep3.E09

description: Library name: HepG2_Batch1_CAT_3_E09


title: BPM_0-5_R1_P1

description: Library name: s13


title: BPM_0-05_R1_P1

description: Library name: s11


title: HepG2.batch1.ATA.rep2.B01

description: Library name: HepG2_Batch1_ATA_2_B01


title: BPM_0-1_R1_P1

description: Library name: s12


title: NAc from animal_48

description:
Library name: NSM1524
3 lvl sciRNAseq


title: BPE_0-01_R1_P1

description: Library name: s2


title: MEL Mtg16Mtg16-2XHA dTAGV1 30m B

description: Library name: CUTRUN_Mtg16-2XHA dTAGV1 30m B


title: HepG2.batch1.ATA.rep2.A01

description: Library name: HepG2_Batch1_ATA_2_A01


title: BPE_0-001_R1_P1

description: Library name: s1


title: NAc from animal_47

description:
Library name: NSM1523
3 lvl sciRNAseq


title: MEL Mtg16 Mtg16-2XHA dTAGV1 15m C

description: Library name: CUTRUN_Mtg16-2XHA dTAGV1 15m C


title: HepG2.batch1.ATA.rep1.H01

description: Library name: HepG2_Batch1_ATA_1_H01


title: miRFP670nano-IL-1b_5

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

description: Library name: Sample 20

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 109) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.0.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: hg38
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.

source_name: human endothelial cells

growth_protocol: Human endothelial cells were transduced with adenoviruses to express FLAG-miRFP670nano or FLAG-miP-FERMT3 (=miP-100). The culture medium was then replaced with endothelial cell growth medium 2 (ECGM2, PromoCell) containing 2% FBS every day for 3 days. Four days after infection, cells were lysed for total RNA isolation.

extract_protocol:
Four days after infection, cells were lysed in a lysis buffer containing Tris-HCl pH7.5 (50mM, Applichem, Germany), NaCl (150mM, Merck, Darmstadt, Germany), MgCl2,(10mM, Invitrogen, Schwerte, Germany), NP-40 (1%, Merck) dissolved in UltraPure DNase/RNase-free DW (Invitrogen) and supplemented with NaPPi (10mM, Merck), NaF (20mM, Applichem, Germany), okadaic acid (10nM, LC laboratory, USA), Na3VO4 (2mM, Sigma-Aldrich), PIM, (12µl/ml, Sigma-Aldrich), PMSF (4µl/ml, Carl Roth, Germany), SUPERaseIn RNase Inhibitor (200U/ml, Invitrogen), TURBO DNaseI (25U/ml, Invitrogen). Total RNA was purified using the miRNeasy Micro kit (QIAGEN, Hilden, Germany), according to the manufacturer’s instructions. RNA and library preparation integrity were verified with LabChip Gx Touch (Perkin Elmer).
RNA amounts were normalized and 500ng-1µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit HI Mammalian (Takara Bio). Sequencing was performed on the NextSeq2000 platform (Illumina) using P3 flowcell with 72bp single-end setup.

treatment_protocol: Cells were treated with solvent or interleukin-1β (IL-1β, 20 ng/mL) for 16 h before total RNA isolation.

value: human endothelial cells


title: HepG2.batch1.ATA.rep3.A01

description: Library name: HepG2_Batch1_ATA_3_A01


title: HepG2.batch1.ATA.rep1.G01

description: Library name: HepG2_Batch1_ATA_1_G01


title: MEL Mtg16 Mtg16-2XHA dTAGV1 15m B

description: Library name: CUTRUN_Mtg16-2XHA dTAGV1 15m B


title: NAc from animal_45

description:
Library name: NSM1521
3 lvl sciRNAseq


title: BPE_50_R1_P1

description: Library name: s8

value: Mammary


title: miRFP670nano-IL-1b_4

description: Library name: Sample 19


title: MEL Mtg16 Mtg16-2XHA dTAGV1 15m A

description: Library name: CUTRUN_Mtg16-2XHA dTAGV1 15m A


title: HepG2.batch1.ATA.rep1.F01

description: Library name: HepG2_Batch1_ATA_1_F01


title: NAc from animal_44

description:
Library name: NSM1520
3 lvl sciRNAseq


title: miRFP670nano-IL-1b_3

description: Library name: Sample 18


title: MEL Mtg16 Mtg16-2XHA DMSO C

description: Library name: CUTRUN_Mtg16-2XHA DMSO C


title: HepG2.batch1.ATA.rep1.E01

description: Library name: HepG2_Batch1_ATA_1_E01


title: miRFP670nano-IL-1b_2

description: Library name: Sample 17


title: BPE_10_R1_P1

description: Library name: s7

value: Epithelial


title: NAc from animal_43

description:
Library name: NSM1519
3 lvl sciRNAseq


title: HepG2.batch1.GLY.rep3.H03

description: Library name: HepG2_Batch1_GLY_3_H03


title: HepG2.batch1.ATA.rep1.D01

description: Library name: HepG2_Batch1_ATA_1_D01


title: MutuDC cells, vehicle control

city: Guangzhou

first: Kun

last: Wang

address: 232 Waihuandong Road, Panyu district

country: China

institute: Guangzhou University of Chinese Medicine

data_processing:
Raw sequencing reads were first processed to remove adapters and low-quality bases using trim-galore software. The cleaned reads were subsequently aligned to the mouse reference genome (GRCm38) using HISAT2, a fast and sensitive alignment program designed for high-throughput RNA-Seq data.
Assembly: The genome assembly used for mapping and analysis was the GRCm38 mouse reference genome, obtained from the NCBI database. This assembly provides a comprehensive representation of the mouse genome, facilitating accurate mapping and annotation of RNA-Seq reads.
Supplementary files format and content: The processed data files are provided in CSV format and include raw counts of gene expression across different time points.

source_name: MutuDC

extract_protocol:
Total RNA was isolated from MutuDC cells using the TRIzol Reagent (Invitrogen) following the manufacturer's protocol. Briefly, cells were lysed directly in the culture dish using TRIzol reagent, and the lysates were transferred to tubes. Chloroform was added, and the mixture was centrifuged to separate phases. The aqueous phase was transferred to a new tube, and RNA was precipitated with isopropanol, washed with ethanol, and solubilized in RNase-free water. The quality and quantity of RNA were assessed using the Agilent 2100 Bioanalyzer.
Libraries for RNA sequencing were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2. The protocol involved purifying poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second-strand cDNA synthesis using DNA Polymerase I and RNase H. After end repair, A-tailing, and adapter ligation, the products were purified and enriched with PCR to create the final cDNA library.
The library strategy used was RNA-Seq, which involves direct sequencing of cDNA derived from RNA. This approach is particularly effective for identifying transcript isoforms, studying gene expression levels, and discovering new transcripts. RNA-Seq provides a comprehensive view of the transcriptome and allows for the precise measurement of transcript levels and their isoforms across different biological conditions.

value: MutuDC

value: dendritic cells

value: Vehicle control


title: MutuDC cells, Fanchinoline treatment, 2 hours

value: Fanchinoline treatment


title: BPA_1_R2_P2

description: Library name: s173

value: WT

value: chemical exposure

value: bisphenol A


title: BPA_0-5_R2_P2

description: Library name: s172


title: MEL Mtg16 Mtg16-2XHA DMSO B

description: Library name: CUTRUN_Mtg16-2XHA DMSO B

value: MEL Mtg16-FKBP-2XHA

value: murine erythroleukemia


title: BPA_0-1_R2_P2

description: Library name: s171


title: NAc from animal_42

description:
Library name: NSM1518
3 lvl sciRNAseq

value: nucleus accumbens


title: miRFP670nano-IL-1b_1

description: Library name: Sample 16


title: MEL Mtg16 Mtg16-2XHA DMSO A

description: Library name: CUTRUN_Mtg16-2XHA DMSO A


title: NAc from animal_46

description:
Library name: NSM1522
3 lvl sciRNAseq


title: HepG2.batch1.ATA.rep1.C01

description: Library name: HepG2_Batch1_ATA_1_C01

value: cell line


title: miRFP670nano-solvent_5

description: Library name: Sample 15

value: solvent


title: NAc from animal_41

description:
Library name: NSM1517
3 lvl sciRNAseq


title: HepG2.batch1.ATA.rep1.B01

description: Library name: HepG2_Batch1_ATA_1_B01

value: liver


title: miRFP670nano-solvent_4

description: Library name: Sample 14


title: NAc from animal_40

description:
Library name: NSM1516
3 lvl sciRNAseq


title: HepG2.batch1.CAT.rep2.G09

description: Library name: HepG2_Batch1_CAT_2_G09

value: hepatocyte


title: HepG2.batch1.ATA.rep1.A01

description: Library name: HepG2_Batch1_ATA_1_A01


title: miRFP670nano-solvent_3

description: Library name: Sample 13

value: human endothelial cells


title: MEL Mtg16 H3K4me3 1hWO C

description: Library name: CUTRUN_H3K4me3 1hWO C


title: Caco-2.batch2.SMET.rep3.G03

description: Library name: Caco2_Batch2_SMET_3_G03

value: colon

value: epithelial


title: MEL Mtg16 H3K4me3 2hWO A

description: Library name: CUTRUN_H3K4me3 2hWO A


title: miRFP670nano-solvent_2

description: Library name: Sample 12


title: MEL Mtg16 H3K4me3 1hWO B

description: Library name: CUTRUN_H3K4me3 1hWO B


title: miP100-IL-1b_5

description: Library name: Sample 10


title: Caco-2.batch2.SMET.rep3.H03

description: Library name: Caco2_Batch2_SMET_3_H03


title: NAc from animal_35

description:
Library name: NSM1512
3 lvl sciRNAseq


title: Caco-2.batch2.SMET.rep3.E03

description: Library name: Caco2_Batch2_SMET_3_E03


title: MEL Mtg16 H3K4me3 1hWO A

description: Library name: CUTRUN_H3K4me3 1hWO A


title: miP100-IL-1b_4

description: Library name: Sample 9


title: NAc from animal_34

description:
Library name: NSM1511
3 lvl sciRNAseq


title: Caco-2.batch2.SMET.rep3.D03

description: Library name: Caco2_Batch2_SMET_3_D03


title: MEL Mtg16 H3K4me3 30mWO C

description: Library name: CUTRUN_H3K4me3 30mWO C


title: miP100-IL-1b_3

description: Library name: Sample 8


title: NAc from animal_33

description:
Library name: NSM1510
3 lvl sciRNAseq


title: miP100-IL-1b_2

description: Library name: Sample 7


title: NAc from animal_32

description:
Library name: NSM1509
3 lvl sciRNAseq


title: Caco-2.batch2.SMET.rep3.C03

description: Library name: Caco2_Batch2_SMET_3_C03


title: Caco-2.batch2.SMET.rep3.B03

description: Library name: Caco2_Batch2_SMET_3_B03


title: MEL Mtg16 H3K4me3 30mWO B

description: Library name: CUTRUN_H3K4me3 30mWO B


title: miP100-IL-1b_1

description: Library name: Sample 6


title: Caco-2.batch2.SMET.rep3.A03

description: Library name: Caco2_Batch2_SMET_3_A03


title: miP100-solvent_5

description: Library name: Sample 5


title: NAc from animal_30

description:
Library name: NSM1507
3 lvl sciRNAseq


title: MEL Mtg16 H3K4me3 dTAGV1 2h B

description: Library name: CUTRUN_H3K4me3 dTAGV1 2h B


title: MEL Mtg16 H3K4me3 dTAGV1 2h A

description: Library name: CUTRUN_H3K4me3 dTAGV1 2h A


title: miP100-solvent_3

description: Library name: Sample 3


title: Caco-2.batch2.SMET.rep2.G03

description: Library name: Caco2_Batch2_SMET_2_G03


title: NAc from animal_28

description:
Library name: NSM1505
3 lvl sciRNAseq


title: MEL Mtg16 H3K4me3 dTAGV1 1h C

description: Library name: CUTRUN_H3K4me3 dTAGV1 1h C


title: Caco-2.batch2.SMET.rep2.F03

description: Library name: Caco2_Batch2_SMET_2_F03


title: NAc from animal_27

description:
Library name: NSM1504
3 lvl sciRNAseq


title: MEL Mtg16 H3K4me3 dTAGV1 1h B

description: Library name: CUTRUN_H3K4me3 dTAGV1 1h B


title: AO425_0-05_R2_P5

description: Library name: s427

value: Mammary

value: Epithelial

value: antioxidant 425


title: NAc from animal_25

description:
Library name: NSM1502
3 lvl sciRNAseq


title: Caco-2.batch2.SMET.rep2.C03

description: Library name: Caco2_Batch2_SMET_2_C03


title: HeLa GL cells, STAT5Inh+IFNb, rep2

city: Ulm

first: Konstantin

middle: MJ

last: Sparrer

address: Meyerhofstr. 1

department: Institute of Molecular Virology

institute: Ulm University Medical Center

description:
Library name: Sample11
Column name in processed data file Sample11

data_processing:
Analysis of sequencing results was performed using a custom pipeline consisting of FastQC (56) (version 0.11.9), BEDtools (57)(version 2.30.0) and RSeQC (58) (version 5.0.1) on R (version 4.2.2) for quality control, Trim Galore! (version 0.6.7) for adapter trimming, a custom tool for paired-end matching (Alexander Graf, LAFUGA), STAR  (59) (version 2.7.10b) for mapping to the reference genome (GRCH38.p13) with default settings, featureCounts (60) (subread version 2.0.3) for gene expression counting and DESeq2 (61)(version 1.34.0) on R (version 4.1.3) for differential gene expression on a Galaxy platform (version 24.1, hosted by the Laboratory for Functional Genome Analysis (LAFUGA)).
Further analysis was done in R (version 4.4.1) on RStudio (Posit, version 2024.09.1) with the following packages attached: EnhancedVolcano (version 1.22.0), BiocManager (version 1.30.25), cluster (version 2.1.6), missMDA (version 1.19), factoextra (version 1.0.7), FactoMineR (version 2.11), pheatmap (version 1.0.12), tidyverse (version 2.0.0) and biomaRt (version 2.60.1).
Assembly: GRCh38.p13
Supplementary files format and content: tabular file includes normalized reads for each samples

source_name: HeLa GL

growth_protocol: HeLa GL autophagy reporter cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using QuickRNA Miniprep kit (Zymo). 1000 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using sparQ RNA-Seq HMR Kit (QuantaBio) with sparQ PureMag Beads (QuantaBio) and sparQ UDI Adapters (QuantaBio) following manufacturer's protocols.

treatment_protocol: Cells were treated with 100 uM of STAT5 Inhibitor or left untreated for 1 hour. Cells were then treated with 100 pM Interferon beta or left untreated for 16h.

value: HeLa GL

value: cervical epithelial cells, adenocarcinoma

tag: genetic modification

value: Expression of GFP-LC3B

value: STAT5 Inhibitor+Interferon beta

tag: time


title: NAc from animal_24

description:
Library name: NSM1501
3 lvl sciRNAseq


title: PRed_10_R2_P2

description: Library name: s159

value: WT

value: chemical exposure

value: phenol red


title: NAc from animal_31

description:
Library name: NSM1508
3 lvl sciRNAseq

value: nucleus accumbens


title: Caco-2.batch2.SMET.rep2.B03

description: Library name: Caco2_Batch2_SMET_2_B03

value: cell line


title: HepG2.batch1.ATA.rep2.G01

description: Library name: HepG2_Batch1_ATA_2_G01

value: liver


title: NAc from animal_29

description:
Library name: NSM1506
3 lvl sciRNAseq


title: Caco-2.batch2.SMET.rep2.H03

description: Library name: Caco2_Batch2_SMET_2_H03


title: HeLa GL cells, STAT5Inh+IFNb, rep1

description:
Library name: Sample10
Column name in processed data file Sample10


title: NAc from animal_23

description:
Library name: NSM1500
3 lvl sciRNAseq


title: MEL Mtg16 H3K4me3 dTAGV1 30m A

description: Library name: CUTRUN_H3K4me3 dTAGV1 30m A

value: MEL Mtg16-FKBP-2XHA

value: murine erythroleukemia


title: Caco-2.batch2.SMET.rep2.A03

description: Library name: Caco2_Batch2_SMET_2_A03

value: colon


title: HeLa GL cells, IFNb, rep3

description:
Library name: Sample9
Column name in processed data file Sample9

value: Interferon beta


title: NAc from animal_22

description:
Library name: NSM1499
3 lvl sciRNAseq


title: Caco-2.batch2.SMET.rep2.E03

description: Library name: Caco2_Batch2_SMET_2_E03

value: epithelial


title: MEL Mtg16 H3K4me3 dTAGV1 15m B

description: Library name: CUTRUN_H3K4me3 dTAGV1 15m B


title: HeLa GL cells, STAT5Inh+IFNb, rep3

description:
Library name: Sample12
Column name in processed data file Sample12


title: Caco-2.batch2.SMET.rep1.H03

description: Library name: Caco2_Batch2_SMET_1_H03


title: HeLa GL cells, IFNb, rep2

description:
Library name: Sample8
Column name in processed data file Sample8


title: NAc from animal_21

description:
Library name: NSM1498
3 lvl sciRNAseq


title: MEL Mtg16 H3K4me3 dTAGV1 15m A

description: Library name: CUTRUN_H3K4me3 dTAGV1 15m A


title: Caco-2.batch2.SMET.rep1.G03

description: Library name: Caco2_Batch2_SMET_1_G03


title: NAc from animal_20

description:
Library name: NSM1497
3 lvl sciRNAseq


title: MEL Mtg16 H3K4me3 DMSO C

description: Library name: CUTRUN_H3K4me3 DMSO C


title: Caco-2.batch2.SMET.rep1.F03

description: Library name: Caco2_Batch2_SMET_1_F03


title: HeLa GL cells, STAT5Inh, rep3

description:
Library name: Sample6
Column name in processed data file Sample6

value: STAT5 Inhibitor


title: NAc from animal_19

description:
Library name: NSM1496
3 lvl sciRNAseq


title: MEL Mtg16 H3K4me3 DMSO B

description: Library name: CUTRUN_H3K4me3 DMSO B


title: Caco-2.batch2.SMET.rep1.E03

description: Library name: Caco2_Batch2_SMET_1_E03


title: HeLa GL cells, STAT5Inh, rep2

description:
Library name: Sample5
Column name in processed data file Sample5


title: NAc from animal_18

description:
Library name: NSM1495
3 lvl sciRNAseq


title: MEL Mtg16 H3K4me3 DMSO A

description: Library name: CUTRUN_H3K4me3 DMSO A


title: Caco-2.batch2.SMET.rep1.D03

description: Library name: Caco2_Batch2_SMET_1_D03


title: HeLa GL cells, STAT5Inh, rep1

description:
Library name: Sample4
Column name in processed data file Sample4


title: MEL Mtg16 H3K4me1 2hWO C

description: Library name: CUTRUN_H3K4me1 2hWO C


title: Caco-2.batch2.SMET.rep1.C03

description: Library name: Caco2_Batch2_SMET_1_C03


title: NAc from animal_16

description:
Library name: NSM1493
3 lvl sciRNAseq


title: MEL Mtg16 H3K4me1 2hWO B

description: Library name: CUTRUN_H3K4me1 2hWO B


title: HeLa GL cells, control, rep3

description:
Library name: Sample3
Column name in processed data file Sample3

value: control


title: Caco-2.batch2.SMET.rep1.B03

description: Library name: Caco2_Batch2_SMET_1_B03


title: HeLa GL cells, control, rep2

description:
Library name: Sample2
Column name in processed data file Sample2

value: HeLa GL


title: NAc from animal_15

description:
Library name: NSM1492
3 lvl sciRNAseq


title: Caco-2.batch2.SMET.rep1.A03

description: Library name: Caco2_Batch2_SMET_1_A03


title: HeLa GL cells, control, rep1

description:
Library name: Sample1
Column name in processed data file Sample1

value: cervical epithelial cells, adenocarcinoma


title: MEL Mtg16 H3K4me1 2hWO A

description: Library name: CUTRUN_H3K4me1 2hWO A


title: NAc from animal_14

description:
Library name: NSM1491
3 lvl sciRNAseq


title: MEL Mtg16 H3K4me1 1hWO C

description: Library name: CUTRUN_H3K4me1 1hWO C


title: Caco-2.batch2.PER.rep3.H02

description: Library name: Caco2_Batch2_PER_3_H02


title: NAc from animal_13

description:
Library name: NSM1490
3 lvl sciRNAseq


title: MEL Mtg16 H3K4me1 1hWO B

description: Library name: CUTRUN_H3K4me1 1hWO B


title: Tdiff.1_Riboseq_RP_PKRi_Replicate2

city: Tucson

first: Kevin

last: Rhine

state: AZ

address: 1703 E Mabel St

department: Pharmacology & Toxicology

institute: University of Arizona

description: Library name: Riboseq_Tdiff.1_RP_PKRi-2

data_processing:
For RNA-seq and dsRNA-seq experiments, the fastq files were analyzed using NF-Core. For eCLIP-seq experiments, Skipper was used to analyze the sequencing files. For Riboseq, the xtail package was used to determine footprinting reads and calculate translation efficiency.
Assembly: hg38
Supplementary files format and content: For RNA-seq and dsRNA-seq experiments, the .tsv or .csv file contains the gene counts for each sample as analyzed by NF-Core. For eCLIP-seq, the .tsv file contains the reproducible enriched windows identified by Skipper.
Library strategy: Ribo-Seq

source_name: Transdifferentiated Neurons

extract_protocol:
For RNA-seq and dsRNA-seq experiments, RNA was extracted using Trizol and purified using Rneasy or ethanol precipitation. For eCLIP-seq and Riboseq experiments, RNA was purified using lysis buffer and gel-extracted.
For RNA-seq experiments, librarires were prepared using the Illumina Stranded mRNA Prep (Ligation). For eCLIP-seq experiments, libraries were prepared using an in-house amplification procedure that closely follows the Illumina Stranded protocol.

value: Transdifferentiated Neurons

value: Apparently Healthy

value: Ribosome footprinting, 1 uM PKR inhibitor for 24 h


title: Caco-2.batch2.PER.rep3.G02

description: Library name: Caco2_Batch2_PER_3_G02

source_name: cell lysate


title: HeLa GL cells, IFNb, rep1

description:
Library name: Sample7
Column name in processed data file Sample7

value: Expression of GFP-LC3B


title: Tdiff.1_Riboseq_RP_PKRi_Replicate1

description: Library name: Riboseq_Tdiff.1_RP_PKRi-1


title: MEL Mtg16 H3K4me3 2hWO C

description: Library name: CUTRUN_H3K4me3 2hWO C


title: MEL Mtg16 H3K4me3 2hWO B

description: Library name: CUTRUN_H3K4me3 2hWO B


title: NAc from animal_12

description:
Library name: NSM1489
3 lvl sciRNAseq


title: NAc from animal_39

description:
Library name: NSM1515
3 lvl sciRNAseq


title: MEL Mtg16 H3K4me1 1hWO A

description: Library name: CUTRUN_H3K4me1 1hWO A


title: Caco-2.batch2.PER.rep3.F02

description: Library name: Caco2_Batch2_PER_3_F02


title: Tdiff.1_Riboseq_RP_Ctrl_Replicate2

description: Library name: Riboseq_Tdiff.1_RP_Ctrl-2

value: Ribosome footprinting, 1% DMSO for 24 h


title: NAc from animal_11

description:
Library name: NSM1488
3 lvl sciRNAseq

value: nucleus accumbens


title: miRFP670nano-solvent_1

description: Library name: Sample 11

value: human endothelial cells

value: solvent


title: NAc from animal_36

description:
Library name: NSM1513
3 lvl sciRNAseq


title: Caco-2.batch2.SMET.rep3.F03

description: Library name: Caco2_Batch2_SMET_3_F03

value: cell line


title: MEL Mtg16 H3K4me1 30mWO C

description: Library name: CUTRUN_H3K4me1 30mWO C

value: MEL Mtg16-FKBP-2XHA

value: murine erythroleukemia


title: NAc from animal_37

description:
Library name: NSM1514
3 lvl sciRNAseq


title: Tdiff.1_Riboseq_RP_Ctrl_Replicate1

description: Library name: Riboseq_Tdiff.1_RP_Ctrl-1


title: NAc from animal_10

description:
Library name: NSM1487
3 lvl sciRNAseq


title: Caco-2.batch2.PER.rep3.E02

description: Library name: Caco2_Batch2_PER_3_E02

value: colon


title: MEL Mtg16 H3K4me1 30mWO B

description: Library name: CUTRUN_H3K4me1 30mWO B


title: Caco-2.batch2.PER.rep3.D02

description: Library name: Caco2_Batch2_PER_3_D02

value: epithelial


title: Tdiff.1_Riboseq_Bulk_PKRi_Replicate2

description: Library name: Riboseq_Tdiff.1_Bulk_PKRi-2

value: 1 uM PKR inhibitor for 24 h


title: NAc from animal_9

description:
Library name: NSM1486
3 lvl sciRNAseq


title: NAc from animal_17

description:
Library name: NSM1494
3 lvl sciRNAseq


title: MEL Mtg16 H3K4me3 30mWO A

description: Library name: CUTRUN_H3K4me3 30mWO A


title: Caco-2.batch2.PER.rep3.C02

description: Library name: Caco2_Batch2_PER_3_C02


title: MEL Mtg16 H3K4me1 30mWO A

description: Library name: CUTRUN_H3K4me1 30mWO A


title: Tdiff.1_Riboseq_Bulk_PKRi_Replicate1

description: Library name: Riboseq_Tdiff.1_Bulk_PKRi-1


title: MEL Mtg16 H3K4me1 dTAGV1 2h C

description: Library name: CUTRUN_H3K4me1 dTAGV1 2h C


title: Tdiff.1_Riboseq_Bulk_Ctrl_Replicate2

description: Library name: Riboseq_Tdiff.1_Bulk_Ctrl-2

value: 1% DMSO for 24 h


title: MEL Mtg16 H3K4me3 dTAGV1 2h C

description: Library name: CUTRUN_H3K4me3 dTAGV1 2h C


title: NAc from animal_7

description:
Library name: NSM1484
3 lvl sciRNAseq


title: Caco-2.batch2.PER.rep3.A02

description: Library name: Caco2_Batch2_PER_3_A02


title: MEL Mtg16 H3K4me1 dTAGV1 2h B

description: Library name: CUTRUN_H3K4me1 dTAGV1 2h B


title: NAc from animal_8

description:
Library name: NSM1485
3 lvl sciRNAseq


title: Caco-2.batch2.PER.rep3.B02

description: Library name: Caco2_Batch2_PER_3_B02


title: Tdiff.1_Riboseq_Bulk_Ctrl_Replicate1

description: Library name: Riboseq_Tdiff.1_Bulk_Ctrl-1


title: NAc from animal_6

description:
Library name: NSM1483
3 lvl sciRNAseq


title: MEL Mtg16 H3K4me1 dTAGV1 2h A

description: Library name: CUTRUN_H3K4me1 dTAGV1 2h A


title: iPSC-diff.1_PKR-eCLIP-seq_10uMAA_IP_Replicate2

description: Library name: eCLIP_iPSC-diff.1_10uMAA_PKR_IP-2

data_processing:
For RNA-seq and dsRNA-seq experiments, the fastq files were analyzed using NF-Core. For eCLIP-seq experiments, Skipper was used to analyze the sequencing files. For Riboseq, the xtail package was used to determine footprinting reads and calculate translation efficiency.
Assembly: hg38
Supplementary files format and content: For RNA-seq and dsRNA-seq experiments, the .tsv or .csv file contains the gene counts for each sample as analyzed by NF-Core. For eCLIP-seq, the .tsv file contains the reproducible enriched windows identified by Skipper.

source_name: iPSC-derived Neurons

value: iPSC-derived Neurons

value: eCLIP-seq with PKR immunoprecipitation, 10 uM antimycin A for 30 min


title: Caco-2.batch2.PER.rep2.G02

description: Library name: Caco2_Batch2_PER_2_G02

data_processing:
Reads were aligned using STAR alignment on QIAGEN's CLC workbench software (v25.0.1) and Kallisto alignment on ExpressAnalyst
Raw counts were logCPM normalized and filtered for low abundance (5) and variance (15) using ExpressAnalyst
Normalized counts were analyzed for differential expression using DESeq2
Assembly: CLC workbench used hg38.p14 Ensembl v113 GCA_000001405.29; ExpressAnalyst used hg38.p14 GCA_000001405
Supplementary files format and content: raw files and count files are provided as fastq.gz files and .txt files, respectively.


title: MEL Mtg16 H3K4me1 dTAGV1 1h C

description: Library name: CUTRUN_H3K4me1 dTAGV1 1h C


title: miP100-solvent_4

description: Library name: Sample 4


title: NAc from animal_4

description:
Library name: NSM1481
3 lvl sciRNAseq


title: NAc from animal_5

description:
Library name: NSM1482
3 lvl sciRNAseq


title: iPSC-diff.1_PKR-eCLIP-seq_10uMAA_IP_Replicate1

description: Library name: eCLIP_iPSC-diff.1_10uMAA_PKR_IP-1


title: Caco-2.batch2.PER.rep2.F02

description: Library name: Caco2_Batch2_PER_2_F02


title: iPSC-diff.1_PKR-eCLIP-seq_10uMAA_IN_Replicate2

description: Library name: eCLIP_iPSC-diff.1_10uMAA_PKR_IN-2

value: eCLIP-seq without PKR immunoprecipitation, 10 uM antimycin A for 30 min


title: MEL Mtg16 H3K4me1 dTAGV1 1h B

description: Library name: CUTRUN_H3K4me1 dTAGV1 1h B


title: Caco-2.batch2.PER.rep2.E02

description: Library name: Caco2_Batch2_PER_2_E02


title: NAc from animal_3

description:
Library name: NSM1480
3 lvl sciRNAseq


title: iPSC-diff.1_PKR-eCLIP-seq_10uMAA_IN_Replicate1

description: Library name: eCLIP_iPSC-diff.1_10uMAA_PKR_IN-1

value: Apparently Healthy


title: MEL Mtg16 H3K4me1 dTAGV1 1h A

description: Library name: CUTRUN_H3K4me1 dTAGV1 1h A


title: miP100-solvent_2

description: Library name: Sample 2


title: NAc from animal_2

description:
Library name: NSM1479
3 lvl sciRNAseq


title: MEL Mtg16 H3K4me1 dTAGV1 30m C

description: Library name: CUTRUN_H3K4me1 dTAGV1 30m C


title: Caco-2.batch2.PER.rep2.D02

description: Library name: Caco2_Batch2_PER_2_D02


title: MEL Mtg16H3K4me1 dTAGV1 30m B

description: Library name: CUTRUN_H3K4me1 dTAGV1 30m B


title: NAc from animal_1

description:
Library name: NSM1478
3 lvl sciRNAseq


title: iPSC-diff.1_PKR-eCLIP-seq_5nMAA_IP_Replicate2

description: Library name: eCLIP_iPSC-diff.1_5nMAA_PKR_IP-2

value: eCLIP-seq with PKR immunoprecipitation, 5 nM antimycin A for 6 h


title: miP100-solvent_1

description: Library name: Sample 1


title: NAc from animal_26

description:
Library name: NSM1503
3 lvl sciRNAseq


title: MEL Mtg16 H3K4me3 dTAGV1 1h A

description: Library name: CUTRUN_H3K4me3 dTAGV1 1h A


title: iPSC-diff.1_PKR-eCLIP-seq_5nMAA_IP_Replicate1

description: Library name: eCLIP_iPSC-diff.1_5nMAA_PKR_IP-1


title: CN from animal_55, rep2

description:
Library name: NSM1477-b2
3 lvl sciRNAseq

source_name: caudate nucleus

value: caudate nucleus


title: Caco-2.batch2.PER.rep2.H02

description: Library name: Caco2_Batch2_PER_2_H02


title: Caco-2.batch2.PER.rep2.B02

description: Library name: Caco2_Batch2_PER_2_B02


title: iPSC-diff.1_PKR-eCLIP-seq_5nMAA_IN_Replicate2

description: Library name: eCLIP_iPSC-diff.1_5nMAA_PKR_IN-2

value: eCLIP-seq without PKR immunoprecipitation, 5 nM antimycin A for 6 h


title: Caco-2.batch2.PER.rep2.C02

description: Library name: Caco2_Batch2_PER_2_C02


title: MEL Mtg16 H3K4me1 dTAGV1 30m A

description: Library name: CUTRUN_H3K4me1 dTAGV1 30m A


title: CN from animal_55

description:
Library name: NSM1477
3 lvl sciRNAseq


title: Caco-2.batch2.PER.rep2.A02

description: Library name: Caco2_Batch2_PER_2_A02


title: CN from animal_54, rep2

description:
Library name: NSM1476-b2
3 lvl sciRNAseq


title: MEL Mtg16 H3K4me1 dTAGV1 15m C

description: Library name: CUTRUN_H3K4me1 dTAGV1 15m C


title: MEL Mtg16 H3K4me1 dTAGV1 15m B

description: Library name: CUTRUN_H3K4me1 dTAGV1 15m B