title: Day70,reproductive,male,rep1

city: Greeenwood

first: Maryam

last: Nasiri Aghdam

state: SC

address: 114 Gregor Mendel Cir

institute: Clemson University

description: Library name: W10_T_M_1

data_processing:
We demultiplexed the raw barcoded sequence data using bcl2fastq (v2.20.0.422). We performed the initial steps of raw read processing, using the AfterQC pipeline to trim adapters, detect unusual polynucleotide sequences, filter out low-quality reads (Q < 20), and discard short reads (<35 nucleotides). We also generated essential sequence quality metrics. We employed the bbduk command from the BBTools package  to check for ribosomal RNA (rRNA) sequences remaining following ribosomal depletion. We aligned the high-quality sequence reads to the D. melanogaster reference genome release 6 (version 6.13) using the GSNAP aligner  and assigned reads to genes using the Subread package.
Assembly: D. melanogaster reference genome release 6 (version 6.13)
Supplementary files format and content: featureCounts tab-delimited output

organism: Drosophila melanogaster

source_name: Reproductive

extract_protocol:
We strictly randomized all steps of RNA extraction, library preparation and sequencing. We extracted total RNA using the RNeasy Mini Kit (Qiagen, Inc., catalog number 74104). We depleted ribosomal RNA (rRNA) using the Ribo-Zero Gold Kit (Epicentre, Inc.).
We barcoded cDNA from each RNA sample was using NEXTflex DNA Barcodes (Bioo Scientific, Inc.) with an Illumina TruSeq compatible protocol. The pooled library samples were clustered on an Illumina cBot and sequenced on the Illumina Hiseq2500 platform, using 125 bp single-read v4 chemistry.

value: Reproductive

value: Male


title: Eltanexor, H3K27me3, rep2

status: Public on Dec 11 2025

type: SRA

city: HOUSTON

first: Margaret

last: Goodell

state: TX

address: 1 Baylor Plz, Rm N1030

country: USA

institute: Baylor College of Medicine

library_source: genomic

data_processing:
Fastq files quality were controlled using fastqc/multizc
Cut-and-run paired-end reads were trimmed from 3' end using Trimmomatic and unique reads were mapped to the mouse genome (mm10) using Bowtie2
BigWig file for each biological replicates were generated using deepTools (bamCoverage) with counts-per-miillion (CPM) normalization and blacklist subtraction
Cut-and-run reads from biological replicates were then merged for peak calling using MACS3
Quantification of peaks for Cut-and-run sequencing was performed using Subread package (featureCounts)
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
100,000 counted cells were permeabalized with 0.01% Digtonin to perform antibody binding and Mnase digestion. The antibody-enriched DNA fragments were released and used for library construction
Cut-and-run sequencing library preparation was performed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645) according to the manufacturer’s protocol.

tag: cell line

tag: cell type

value: OCI-AML3 (NPM1c degron)

tag: cut-and-run antibody

tag: treatment

value: Eltanexor


title: Day70,reproductive,male,rep2

description: Library name: W10_T_M_3

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: noguide-0-rep2

city: Boston

first: Jaryd

last: Sullivan

address: 185 Cambridge St

institute: Massachusetts General Hospital

description:
Library name: Sample 110
Experiment1

data_processing:
Reads were demultiplexed based on their associated barcode. Up to 1 mismatch in the barcode was allowed. Barcode sequences and terminal G's that were added during template switching were trimmed.
Assembly: Pseudomonas aeruginosa UCBPP-PA14 GCF_000014625.1
Supplementary files format and content: tsv file includes raw counts for each sample

organism: Pseudomonas aeruginosa

growth_protocol: Cells were grown in 96-well plates in LB until mid-log phase

extract_protocol:
50ul of treated cells were mixed with 25ul 3X RNAgem Blue Buffer, incubated at 75C for 10mins and flashfrozen. RNA was extracted using the Direct-zol RNA Miniprep Plus Kit.
cDNA libraries were generated using a modified version of the RNAtag-seq protocol. 500ng of RNA was fragmented, depleted of genomic DNA, dephosphorylated, and ligated to DNA adapters. Barcoded RNAs were pooled and depleted of rRNA. Pools were converted to cDNA using reverse transcriptase template switching with PCR amplification of the Illumina P5 and P7 sequences. cDNA libraries were sequenced on Illumina Nextseq 500 platorm for paired end reads

treatment_protocol: 30ul of mid-log phase cells were mixed with 30ul of 2X rhamnose to a final OD of 0.1. Cells were grown for 6, or 10 hours.

tag: batch


title: noguide-0.0125-rep3

description:
Library name: Sample 114
Experiment1


title: noguide-0-rep1

description:
Library name: Sample 109
Experiment1


title: Eltanexor, MLL, rep1

value: MLL / HRX (Active Motif, #61295)


title: Rat lung CD31+ cells, sham surgery 3 weeks post-surgery, rep3

city: Milwaukee

first: Andrew

middle: D

last: Spearman

state: Wisconsin

address: 8701 Watertown Plank Rd

institute: Medical College of Wisconsin

description:
Library name: R2023-1438
10X Genomics

library_source: transcriptomic single cell

data_processing:
Default parameters using CellRanger (10X Genomics cloud analysis)
Assembly: Norway rat genome; Rnor_6.0.98
Supplementary files format and content: Raw counts matrix

organism: Rattus norvegicus

source_name: Lung

extract_protocol:
Rat lung samples were dissociated using a gentleMACS OctoDissociator (Miltenyi) and multi-tissue dissociation kit 2 (Miltenyi). Cells were washed and resuspended in 0.04% BSA in sterile PBS.
Library preparation was performed using Chromium Next GEM single cell 3' reagent kits (10X Genomics).

value: Lung

tag: genotype

value: Wild-type

value: Sham surgery


title: Rat lung CD31+ cells, Glenn surgery 3 weeks post-surgery, rep1

description:
Library name: R2023-1433
10X Genomics

value: Glenn surgery


title: murA-0.05-rep3

description:
Library name: Sample 108
Experiment1


title: VTP, Menin, rep1

value: Menin (CST, #6891)

value: VTP


title: Eltanexor, H3K27me3, rep1


title: Eltanexor, Menin, rep2


title: noguide-0.0125-rep1

description:
Library name: Sample 112
Experiment1


title: murA-0.05-rep2

description:
Library name: Sample 107
Experiment1


title: Day70,head,male,rep1

description: Library name: W10_H_M_1

source_name: Head

value: Head


title: Eltanexor, MLL, rep2


title: Eltanexor, IgG, rep2

value: mIgG (Abcam, #ab46540)


title: Day70,reproductive,female,rep1

description: Library name: W10_O_F_1

value: Female


title: Eltanexor, XPO1, rep1


title: DTAG, NUP98, rep2

value: DTAG


title: DTAG, MLL, rep2


title: Day70,head,male,rep2

description: Library name: W10_H_M_3


title: Day70,head,female,rep1

description: Library name: W10_H_F_1


title: Eltanexor, IgG, rep1


title: murA-0.0125-rep3

description:
Library name: Sample 105
Experiment1


title: VTP, NUP98, rep1


title: Eltanexor, Menin, rep1


title: Day70,head,female,rep2

description: Library name: W10_H_F_3


title: noguide-0.0125-rep2

description:
Library name: Sample 113
Experiment1


title: DTAG, Menin, rep2


title: murA-0.05-rep1

description:
Library name: Sample 106
Experiment1


title: Eltanexor, NUP98, rep1


title: DTAG, IgG, rep2


title: DTAG, IgG, rep1


title: murA-0.0125-rep1

description:
Library name: Sample 103
Experiment1


title: DTAG, H3K27me3, rep2


title: DTAG, XPO1, rep2


title: DTAG, Menin, rep1


title: Day70,body,male,rep1

description: Library name: W10_B_M_1

source_name: Body

value: Body


title: Day70,reproductive,female,rep2

description: Library name: W10_O_F_3


title: murA-0.0125-rep2

description:
Library name: Sample 104
Experiment1


title: DTAG, H3K27me3, rep1


title: DTAG, XPO1, rep1


title: Day70,body,female,rep2-2

description: Library name: W10_B_F_3_2


title: Day70,body,male,rep2

description: Library name: W10_B_M_3


title: murA-0-rep3

description:
Library name: Sample 102
Experiment1


title: DTAG, MLL, rep1


title: DMSO, XPO1, rep2

value: DMSO


title: murA-0-rep2

description:
Library name: Sample 101
Experiment1


title: DTAG, NUP98, rep1


title: murA-0-rep1

description:
Library name: Sample 100
Experiment1


title: Day70,body,female,rep2-3

description: Library name: W10_B_F_3_3


title: DMSO, IgG, rep2


title: DMSO, MLL, rep2


title: Day70,body,female,rep1

description: Library name: W10_B_F_1


title: Day70,body,female,rep2-1

description: Library name: W10_B_F_3


title: mreB-0.05-rep3

description:
Library name: Sample 99
Experiment1


title: DMSO, XPO1, rep1


title: DMSO, H3K27me3, rep2


title: DMSO, NUP98, rep2


title: DMSO, NUP98, rep1


title: DMSO, Menin, rep1


title: DMSO, Menin, rep2


title: Day63,reproductive,female,rep1

description: Library name: W9_O_F_1

value: Reproductive


title: mreB-0.05-rep2

description:
Library name: Sample 98
Experiment1


title: DMSO, MLL, rep1


title: Day63,reproductive,male,rep2

description: Library name: W9_T_M_3

value: Male


title: Day63,reproductive,female,rep2

description: Library name: W9_O_F_3


title: DMSO, H3K27me3, rep1

value: OCI-AML3 (NPM1c degron)


title: ctrl-RXR-1

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto St

department: Environmental and Occupational Health

institute: University of Pittsburgh

description: Library name: 10319

data_processing:
Bowtie2 v2.5.4
Samtools v1.21
Assembly: mm10
Supplementary files format and content: peak calling

organism: Mus musculus

source_name: brain

extract_protocol:
Brain lysates of mice treated with Bexarotene or Vehicle were sonicated with 3 pulses of 15 sec at amplitude 30, a 120 sec pause and 3 pulses of 15 sec at amplitude 40 using a Model 705 Sonic Dismembrator (Fisher Scientific, Pittsburgh, PA), to obtain fragments of 200–600 bp.
ChIP libraries were generated using TruSeq ChIP Sample Prep Kit (Illumina, San Diego, CA) following manufacturer’s protocols. For each of the steps, samples were purified by AMPure XP beads (Beckman Coulter, Brea, CA). Adapter-ligated samples were separated on a 2% agarose gel to obtain 250–300 bp size-range of DNA fragment to remove unligated adapters. The libraries were validated by Agilent Technologies 2100 Bioanalyzer to check the size, purity, and concentration of the sample before the sequencing

treatment_protocol: The treatment group got 10-day oral administration of Bexarotene (100mg/kg/day), and the control group were treated with vehicle solution (corn oil with 1% DMSO).

value: brain

value: APP/PS+

value: Vehicle


title: ctrl-RXR-2

description: Library name: 20321


title: mreB-0.0125-rep1

description:
Library name: Sample 94
Experiment1


title: Day63,head,male,rep1

description: Library name: W9_H_M_1


title: embryoid body day 14

city: Kagoshima

first: Sumito

last: Matsuya

address: 1-21-24 Korimoto

department: Joint Faculty of Veterinary Medicine

country: Japan

institute: Kagoshima university

description: Library name: ASEBd14

data_processing:
CLC Genomics Workbench 23.0.2
Sequence reads were trimmed using CLC Genomics Workbench 23.0.2 (Quality limit = 0.05).
Trimmed sequence reads were mapped to Apodemus sylvaticus (GCF_947179515.1_mApoSyl1.1) using CLC Genomics Workbench 23.0.2.
Read count extacrion and normalization were performed using CLC Genomics Workbench 23.0.2.
Assembly: GCF_947179515.1_mApoSyl1.1
Supplementary files format and content: xlsx files includesTPM, FPKM and raw counts for each sample

organism: Apodemus speciosus

extract_protocol:
RNA was extracted using the Maxwell RSC simply RNA Cell Kit (Promega).
Library preparation for RNA-seq was performed using the NEBNext Ultra Ⅱ RNA Library Prep Kit for Illumina (NEB) following manifacturer's protocols.

value: embryoid body

value: differentiation


title: mreB-0.0125-rep2

description:
Library name: Sample 95
Experiment1


title: mreB-0-rep1

description:
Library name: Sample 91
Experiment1


title: mreB-0.0125-rep3

description:
Library name: Sample 96
Experiment1


title: Day63,head,female,rep2-2

description: Library name: W9_H_F_3_2


title: mreB-0-rep2

description:
Library name: Sample 92
Experiment1


title: iPS cell

description: Library name: AS_i

value: iPS cell

value: reprograming


title: Day63,head,female,rep1

description: Library name: W9_H_F_1


title: embryoid body day 7

description: Library name: ASEBd7


title: DMSO, IgG, rep1


title: mreB-0.05-rep1

description:
Library name: Sample 97
Experiment1


title: fibroblast

description: Library name: AS_F

value: fibroblast

value: no reprograming


title: Day63,head,male,rep2

description: Library name: W9_H_M_3

value: Head


title: bexa-RXR-2

description: Library name: 10317

value: Bexarotene


title: Donor 1 Colon Tissue

city: South San Francisco

first: Michelle

last: Chen

state: CA

address: 1 DNA Way

department: Cell & Tissue Genomics

institute: Genentech, Inc.

description: Library name: LIB5462722

data_processing:
Libraries were sequenced on a NextSeq2000 or NovaSeq6000 (for HT libraries) targeting 30,000 reads/cell for GEX libraries and 2,000 reads/cell for HTO libraries. Sequenced reads were aligned using the human reference genome GRCh38-2020-A using the CellRanger pipeline (10x Genomics). scRNA-seq data was processed using CellRanger and resulting count matrices were analyzed using Seurat in R. For experiments involving hashing, cells were demultiplexed using the HTODemux function in R. For experiments involving genetic demultiplexing as in the perturbation dataset, the souporcell algorithm was used to distinguish between organoids from unique donors. Doublets were removed from data using the DoubletFinder algorithm. When combining experiments from multiple donors or timepoints, data was batch-corrected using the Harmony algorithm.
Assembly: GRCh38-2020-A
Supplementary files format and content: Processed Seurat objects (.Robj)

molecule: polyA RNA

source_name: Colon

extract_protocol:
Organoids were dissociated using the Neural Dissociation-P kit (Miltenyi). Organoids were pipetted out of their microwell plates and into a deep-well 96 well plate (ThermoFisher) for dissociation. Enzyme mix 1 was prepared according to manufacturer protocols with the addition of Y-27632 for a final volume of 1.5mL per well. Organoids in mix 1 were then placed at 10C for 10 minutes, after which enzyme mix 2 was added. Organoids were kept at 10C throughout dissociation for up to 60 minutes, and were removed every 10 minutes to be pipette mixed with a P1000 pipette to aid in dissociation. Once dissociation was complete, organoids were centrifuged for 3 minutes, 500g, 4C and washed twice with PBS. For pooled experiments involving hashing (perturbation experiment, pooled injury experiments), organoids were resuspended in 100µL cell staining buffer (2% BSA, 0.01% Tween in PBS) and then blocked with 5uL human TruStain FCX blocking buffer (BioLegend) for 10 minutes on ice. 1µL of a unique cell hashing antibody (TotalSeqA: BioLegend) was added per condition for 20 minutes on ice, and cells were pipette mixed after 10 minutes. Organoids were then washed three times with cell staining buffer on ice. After the final wash, organoids were resuspended in 0.04% BSA in PBS, filtered through a 70µm Flowmi cell strainer (Sigma Aldrich) and loaded onto a 10X Chromium X according to manufacturer instructions. For organoid and tissue characterization and pooled injury experiments, the standard 10x 3’ v3.1 kit was used. For some injury experiments, the 10x 3’ low throughput kit was used to compare multiple injuries from the same experiment. For the perturbation dataset, the 10x 3’ high throughput kit was used.
Library preparation was prepared according to published 10x Genomics protocols.

value: Colon


title: Day63,body,male,rep1-2

description: Library name: W9_B_M_1_2

value: Body


title: bexa-RXR-1

description: Library name: 10315


title: Day63,reproductive,male,rep1

description: Library name: W9_T_M_1


title: mreB-0-rep3

description:
Library name: Sample 93
Experiment1


title: Day63,body,male,rep1-1

description: Library name: W9_B_M_1


title: teratoma (CAM)

description: Library name: ASCAM

value: teratoma


title: Day63,head,female,rep2-1

description: Library name: W9_H_F_3

value: Female


title: teratoma

description: Library name: AStera


title: Day63,body,male,rep2

description: Library name: W9_B_M_3

value: Male


title: Ind1_VEH_2.5_3_3

city: Galveston

middle: C.

last: Ward

address: 301 University blvd.

institute: UTMB

description: Library name: iPSC-CM_Ind1_VEH_2.5_3_3

data_processing:
Raw sequencing reads were assessed for quality using MultiQC (v1.26) (Ewels et al., 2016) on Linux-based systems. Reads were aligned to the human reference genome (GRCh38/hg38) using the Rsubread package (v2.16.1) (Liao et al., 2019). Gene-level quantification was performed using the featureCounts() function with the default exon-based annotations provided by Rsubread. Resulting count matrices were imported into R for downstream analysis. Expression values were transformed into log2 counts per million using the cpm() function from the edgeR package (v4.0.16) (Chen et al., 2016).
Assembly: hg38
Supplementary files format and content: Paul_CX_counts_new.txt

growth_protocol: Human iPSC-derived cardiomyocytes were cultured on Matrigel-coated plates at 37°C with 5% CO₂ under atmospheric oxygen conditions using Cardiomyocyte Maintenance Medium composed of 500 mL glucose-free DMEM (A14430-01, ThermoFisher Scientific), 50 mL fetal bovine serum (MT35015CV, Corning), 990 mg galactose (G5388, Sigma-Aldrich), 5 mL 100 mM sodium pyruvate (11360-070, ThermoFisher Scientific), 2.5 mL 1 M HEPES (H3375, Sigma-Aldrich), 5 mL 100X GlutaMAX (35050-061, ThermoFisher Scientific), and 5 mL penicillin-streptomycin.

extract_protocol:
Frozen iPSC-derived cardiomyocyte pellets were thawed on ice and lysed in Buffer RLT supplemented with 1% β-mercaptoethanol, prepared fresh under a fume hood. Lysates were homogenized using QIAshredder columns (Qiagen; 79656) and mixed with 70% ethanol prior to binding to RNeasy Mini spin columns (Qiagen; 74106). On-column DNase I digestion (Qiagen; 79256) was performed using freshly prepared DNase/RDD buffer mix and incubated for 15 minutes at room temperature. Columns were washed sequentially with RW1 and RPE buffers, and RNA was eluted in 30 µL RNase-free water. All centrifugation steps were carried out at >10,000 rpm as recommended. Eluted RNA was immediately placed on ice and stored at –80 °C. RNA integrity and concentration were assessed prior to library preparation.
Polyadenylated mRNA was isolated from 150 ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490L; New England Biolabs). Strand-specific RNA-seq libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7765S; NEB), with dual indexing performed using NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, E6440S). Libraries were prepared in two balanced batches, each containing all treatment conditions and timepoints for three individuals (Batch 1: Individuals 3; Batch 2: Individuals 1). Final library quality and size distribution were evaluated using the Agilent 2100 Bioanalyzer prior to sequencing.

treatment_protocol: 1.5 million iPSC-derived cardiomyocytes were seeded per well in 6-well plates. On day 30 of differentiation, cells were treated with 2.5 µM CX-5461, or vehicle control in fresh cardiomyocyte maintenance media. Cells were harvested at 3, 24 and 48 hours post-treatment. All steps were performed on ice unless otherwise specified. Culture media was aspirated, and cells were washed twice with 1 mL cold PBS. Cells were then scraped in 1 mL PBS into 1.5 mL Eppendorf tubes, followed by a second scrape using 500 µL PBS to collect any remaining cells. Cell suspensions were centrifuged at 7,000 rpm for 8 minutes at 4 °C. The supernatant was carefully removed, and the resulting cell pellets were flash-frozen in ethanol/dry ice and stored at –80 °C until RNA extraction.

tag: Sex

value: female

value: induced pluripotent stem cell-derived cardiomyocytes

tag: time


title: Day63,body,female,rep1

description: Library name: W9_B_F_1


title: Day56,reproductive,male,rep2

description: Library name: W8_T_M_3

value: Reproductive


title: Ind1_CX_2.5_48_2

description: Library name: iPSC-CM_Ind1_CX_2.5_48_2


title: lpxC-0.05-rep1

description:
Library name: Sample 88
Experiment1


title: Donor 3 Colon Tissue

description: Library name: LIB6221778


title: Ind1_VEH_2.5_3_2

description: Library name: iPSC-CM_Ind1_VEH_2.5_3_2


title: lpxC-0.05-rep2

description:
Library name: Sample 89
Experiment1


title: lpxC-0-rep3

description:
Library name: Sample 84
Experiment1


title: lpxC-0.05-rep3

description:
Library name: Sample 90
Experiment1


title: Donor 2 Colon Tissue

description: Library name: LIB5462725


title: Ind1_VEH_2.5_48_3

description: Library name: iPSC-CM_Ind1_VEH_2.5_48_3


title: Ind1_CX_2.5_24_3

description: Library name: iPSC-CM_Ind1_CX_2.5_24_3


title: Ind1_CX_2.5_48_3

description: Library name: iPSC-CM_Ind1_CX_2.5_48_3


title: Ind1_CX_2.5_3_2

description: Library name: iPSC-CM_Ind1_CX_2.5_3_2


title: lpxC-0.0125-rep3

description:
Library name: Sample 87
Experiment1


title: Ind1_VEH_2.5_24_3

description: Library name: iPSC-CM_Ind1_VEH_2.5_24_3


title: Ind1_VEH_2.5_48_1

description: Library name: iPSC-CM_Ind1_VEH_2.5_48_1


title: Day63,body,female,rep2

description: Library name: W9_B_F_3


title: Day56,reproductive,female,rep1

description: Library name: W8_O_F_1


title: lptE-0.05-rep2

description:
Library name: Sample 80
Experiment1


title: Ind1_VEH_2.5_3_1

description: Library name: iPSC-CM_Ind1_VEH_2.5_3_1


title: Day56,reproductive,male,rep1

description: Library name: W8_T_M_1


title: lpxC-0.0125-rep1

description:
Library name: Sample 85
Experiment1


title: Day56,head,male,rep2

description: Library name: W8_H_M_3


title: lpxC-0.0125-rep2

description:
Library name: Sample 86
Experiment1


title: Ind3_VEH_2.5_24_3

description: Library name: iPSC-CM_Ind3_VEH_2.5_24_3


title: Ind1_CX_2.5_3_3

description: Library name: iPSC-CM_Ind1_CX_2.5_3_3


title: Ind1_CX_2.5_3_1

description: Library name: iPSC-CM_Ind1_CX_2.5_3_1


title: Ind1_CX_2.5_24_2

description: Library name: iPSC-CM_Ind1_CX_2.5_24_2


title: Day56,reproductive,female,rep2

description: Library name: W8_O_F_3


title: Ind1_VEH_2.5_24_2

description: Library name: iPSC-CM_Ind1_VEH_2.5_24_2


title: lptE-0.05-rep3

description:
Library name: Sample 81
Experiment1


title: Ind3_VEH_2.5_3_3

description: Library name: iPSC-CM_Ind3_VEH_2.5_3_3


title: lptE-0.0125-rep2

description:
Library name: Sample 77
Experiment1


title: Day56,head,female,rep2

description: Library name: W8_H_F_3


title: lpxC-0-rep1

description:
Library name: Sample 82
Experiment1


title: Ind1_CX_2.5_48_1

description: Library name: iPSC-CM_Ind1_CX_2.5_48_1


title: Ind3_CX_2.5_3_3

description: Library name: iPSC-CM_Ind3_CX_2.5_3_3


title: Day56,head,female,rep1-2

description: Library name: W8_H_F_1_2


title: lptE-0.0125-rep1

description:
Library name: Sample 76
Experiment1


title: Ind3_VEH_2.5_48_2

description: Library name: iPSC-CM_Ind3_VEH_2.5_48_2


title: Ind3_VEH_2.5_48_3

description: Library name: iPSC-CM_Ind3_VEH_2.5_48_3


title: Ind3_CX_2.5_24_2

description: Library name: iPSC-CM_Ind3_CX_2.5_24_2


title: Ind1_CX_2.5_24_1

description: Library name: iPSC-CM_Ind1_CX_2.5_24_1


title: Ind1_VEH_2.5_48_2

description: Library name: iPSC-CM_Ind1_VEH_2.5_48_2


title: lptE-0-rep2

description:
Library name: Sample 74
Experiment1


title: lptE-0.05-rep1

description:
Library name: Sample 79
Experiment1


title: Day56,head,male,rep1-2

description: Library name: W8_H_M_1_2


title: Ind1_VEH_2.5_24_1

description: Library name: iPSC-CM_Ind1_VEH_2.5_24_1


title: Ind3_CX_2.5_48_3

description: Library name: iPSC-CM_Ind3_CX_2.5_48_3


title: Ind3_CX_2.5_24_3

description: Library name: iPSC-CM_Ind3_CX_2.5_24_3


title: Ind3_VEH_2.5_48_1

description: Library name: iPSC-CM_Ind3_VEH_2.5_48_1


title: Ind3_CX_2.5_48_1

description: Library name: iPSC-CM_Ind3_CX_2.5_48_1


title: lptE-0.0125-rep3

description:
Library name: Sample 78
Experiment1


title: Ind3_VEH_2.5_24_2

description: Library name: iPSC-CM_Ind3_VEH_2.5_24_2


title: Ind3_CX_2.5_48_2

description: Library name: iPSC-CM_Ind3_CX_2.5_48_2


title: PGBE 1W 20D

city: Lausanne

first: Marie-Gabrielle

last: Zurich

address: Rue de Bugnon, 7

department: Department of Biomedical Sciences (DBS)

country: Switzerland

institute: University of Lausanne

description: Library name: Sample 64

data_processing:
The NEXTFLOW pipeline was used for the pre-processing of BRB-seq data. Read Alignment and Demultiplexing was done using STAR solo 2.7.9a, using the homo_sapiens hg38 (GRCh38) (Ensembl release 104) genome. BAM Indexing and Raw Sequencing Read QC was done using samtools v1.12 and FastQC v0.11.9
Assembly: homo_sapiens hg38 (GRCh38) (Ensembl release 104)
Supplementary files format and content: .txt processed files contains raw counts per sample

source_name: Human induced pluripotent stem cells (hiPSCs)-derived 3D BrainSpheres

growth_protocol: Neuroprogenitor cells (NPCs) were  grown and amplified in cell culture flasks coated with Geltrex® (Thermo Fisher Scientific) in Neural Expansion Medium (NEM: 45% Neurobasal® Medium, 45% Advanced™ DMEM/F-12 Medium and 10% Neural Induction Supplement, Thermo Fisher Scientific). NPCs were kept at 37°C with 5% CO2. Medium was replaced every two or three days. Cell passages were performed at 90% confluency. BSs were then prepared from the NPCs as previously described (Pamies et al., 2017). At 95 % of NPCs confluency, cells were washed with Dulbecco's Phosphate Buffered Saline (DPBS) and detached from the flasks using StemPro Accutase Cell Dissociation Reagent (GIBCO) for 2-3 min. 2x106 cells per well were plated in 2 mL of NEM in non-treated six-well plates. The plates were placed in an incubator at 37°C and 5% CO2 under constant gyratory shaking (Kuhner orbital plate shaker, 88 rpm) allowing cell aggregation. After two days, cell medium was changed to differentiation medium consisting of Neurobasal Electro Medium, 1% Glutamax (Gibco), 2% B27/Neurobasal Electro, 0.01 μg/mL BDNF (PeproTech), 0.01 μg/mL GDNF (PeproTech) and 1% Penicillin-Streptomycin (10,000 U/mL). Medium changes with NDM were effectuated three times a week and cultures were kept until 8 weeks.

extract_protocol:
Extraction of total RNA was carried out using the Quiagen RNeasy Mini Kit. RNA concentration and integrity was measured using a fragment analyzer.
Samples were sent to Alithea Genomics SA (Lausanne, Switzerland) for library preparation and sequencing using multiplexed 3’-end bulk RNA barcoding and sequencing (MERCURIUS™ BRB-seq service). The generation of bulk RNA Barcoding and sequencing (BRB-seq) libraries was performed using the MERCURIUS™ BRB-seq library preparation kit and following the manufacturer’s manual

treatment_protocol: BSs were exposed to PGBE (CAS 5131-66-8, Merck, purity 99%) and to its metabolite 2BPA (CAS 14620-87-2, Merck, purity 95%). Solutions from the manufacturer were diluted in the differentiation cell culture medium to reach the final concentrations. The pH of the 2BPA solution from the manufacturer was very acidic and therefore was adjusted to 7.0 ± 0.5 before dilution in the medium. Seven-week-old BSs were exposed either one time and collected after 24 h  (acute exposure) or exposed repeatedly at each medium change, i.e., three times, during one week (1W) and collected at the end of the week, to 5, 10 or 20 mM of PGBE and 2BPA. Untreated BSs were used as controls.

value: Human CCD-1079Sk fibroblasts (ATCC CRL-2097)

value: Brain Cells

value: PGBE 20uM 1W exposure


title: Ind3_VEH_2.5_3_2

description: Library name: iPSC-CM_Ind3_VEH_2.5_3_2


title: lptD-0.05-rep1

description:
Library name: Sample 70
Experiment1


title: Day49,reproductive,male,rep1

description: Library name: W7_T_M_1


title: Ind3_CX_2.5_24_1

description: Library name: iPSC-CM_Ind3_CX_2.5_24_1


title: Day56,body,male,rep2

description: Library name: W8_B_M_3


title: lpxC-0-rep2

description:
Library name: Sample 83
Experiment1


title: Day56,body,female,rep2

description: Library name: W8_B_F_3


title: Ind3_VEH_2.5_24_1

description: Library name: iPSC-CM_Ind3_VEH_2.5_24_1


title: Day56,body,male,rep1

description: Library name: W8_B_M_1


title: Day56,head,male,rep1-1

description: Library name: W8_H_M_1


title: lptD-0.05-rep3

description:
Library name: Sample 72
Experiment1


title: PGBE 24h 20D

description: Library name: Sample 62

value: Human induced pluripotent stem cells (hiPSCs)-derived 3D BrainSpheres

value: PGBE 20uM 24h exposure


title: lptD-0.0125-rep3

description:
Library name: Sample 69
Experiment1


title: PGBE 1W 20C

description: Library name: Sample 60


title: Day49,reproductive,female,rep2

description: Library name: W7_O_F_3


title: lptE-0-rep3

description:
Library name: Sample 75
Experiment1


title: PGBE 1W 5D

description: Library name: Sample 63

value: PGBE 5uM 1W exposure


title: Ind3_VEH_2.5_3_1

description: Library name: iPSC-CM_Ind3_VEH_2.5_3_1


title: Day49,reproductive,female,rep1

description: Library name: W7_O_F_1


title: lptE-0-rep1

description:
Library name: Sample 73
Experiment1


title: Day56,head,female,rep1-1

description: Library name: W8_H_F_1


title: lptD-0.0125-rep1

description:
Library name: Sample 67
Experiment1


title: Day56,body,female,rep1

description: Library name: W8_B_F_1


title: Ind3_CX_2.5_3_2

description: Library name: iPSC-CM_Ind3_CX_2.5_3_2


title: PGBE 1W 20B

description: Library name: Sample 56


title: PGBE 24h 20B

description: Library name: Sample 54


title: lptD-0-rep2

description:
Library name: Sample 65
Experiment1


title: Day49,reproductive,male,rep2

description: Library name: W7_T_M_3


title: lptA-0.05-rep3

description:
Library name: Sample 63
Experiment1


title: lptD-0.0125-rep2

description:
Library name: Sample 68
Experiment1


title: lptD-0.05-rep2

description:
Library name: Sample 71
Experiment1


title: lptD-0-rep3

description:
Library name: Sample 66
Experiment1


title: PGBE 24h 5D

description: Library name: Sample 61

value: PGBE 5uM 24h exposure


title: Day49,head,male,rep1-2

description: Library name: W7_H_M_1_2

value: Head


title: PGBE 24h 5B

description: Library name: Sample 53


title: PGBE 1W 5C

description: Library name: Sample 59


title: PGBE 24h 5C

description: Library name: Sample 57


title: Day49,head,female,rep1-1

description: Library name: W7_H_F_1


title: PGBE 24h 0D

description: Library name: Sample 45

value: PGBE 0uM 24h exposure


title: Ind3_CX_2.5_3_1

description: Library name: iPSC-CM_Ind3_CX_2.5_3_1


title: PGBE 1W 5A

description: Library name: Sample 51


title: Day49,head,female,rep2

description: Library name: W7_H_F_3


title: Day49,head,male,rep2

description: Library name: W7_H_M_3


title: PGBE 1W 0C

description: Library name: Sample 43

value: PGBE 0uM 1W exposure


title: PGBE 24h 10D

description: Library name: Sample 46

value: PGBE10uM 24h exposure


title: PGBE 1W 20A

description: Library name: Sample 52


title: PGBE 24h 20C

description: Library name: Sample 58


title: PGBE 1W 5B

description: Library name: Sample 55


title: Day49,body,female,rep2

description: Library name: W7_B_F_3

value: Body


title: lptA-0.0125-rep1

description:
Library name: Sample 58
Experiment1


title: PGBE 24h 20A

description: Library name: Sample 50


title: lptD-0-rep1

description:
Library name: Sample 64
Experiment1


title: lptA-0.05-rep1

description:
Library name: Sample 61
Experiment1


title: Day49,body,male,rep1-2

description: Library name: W7_B_M_1_2


title: Day49,head,female,rep1-2

description: Library name: W7_H_F_1_2

value: Female


title: PGBE 1W 10D

description: Library name: Sample 48

value: PGBE10uM 1W exposure


title: PGBE 1W 10C

description: Library name: Sample 44


title: Day42,reproductive,male,rep2

description: Library name: W6_T_M_3

value: Male


title: PGBE 24h 10A

description: Library name: Sample 34


title: lptA-0.05-rep2

description:
Library name: Sample 62
Experiment1


title: Day42,reproductive,male,rep1

description: Library name: W6_T_M_1


title: PGBE 24h 5A

description: Library name: Sample 49


title: 2BPA_1w_20D

description: Library name: Sample 32

value: 2BPA 20uM 1W exposure


title: 2BPA_1w_5D

description: Library name: Sample 31

value: 2BPA 5uM 1W exposure


title: Day49,body,female,rep1

description: Library name: W7_B_F_1


title: leuS-0.05-rep3

description:
Library name: Sample 54
Experiment1


title: PGBE 24h 10C

description: Library name: Sample 42

value: Human CCD-1079Sk fibroblasts (ATCC CRL-2097)


title: lptA-0.0125-rep3

description:
Library name: Sample 60
Experiment1


title: lptA-0.0125-rep2

description:
Library name: Sample 59
Experiment1


title: Day49,body,male,rep1-1

description: Library name: W7_B_M_1


title: PGBE 1W 10B

description: Library name: Sample 40

value: Brain Cells


title: leuS-0.05-rep2

description:
Library name: Sample 53
Experiment1


title: Day42,reproductive,female,rep1

description: Library name: W6_O_F_1

value: Reproductive


title: PGBE 1W 0B

description: Library name: Sample 39

value: Human induced pluripotent stem cells (hiPSCs)-derived 3D BrainSpheres


title: Day49,body,male,rep2

description: Library name: W7_B_M_3


title: Pp6B_MethylC-Seq

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

data_processing:
For data analysis, adapters were trimmed using Cutadapt with parameter “--minimum-length 50”, and trimmed reads were mapped to the reference genome using BSMAP. The reference genome is "Prunus_persica_NCBIv2" (downloaded from ftp://ftp.ensemblgenomes.org/pub/plants/release-46/fasta/prunus_persica/dna/).
Genome_build: Prunus_persica_NCBIv2
Supplementary_files_format_and_content: The bigWig files give methylation level for all Cs(three contexts) with depth >= 4 in all the samples. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position ( unconverted_C / ( converted_C+ unconverted_C ) ).

organism: Prunus persica

source_name: fruit

extract_protocol: Genomic DNA was extracted from fruits using a DNeasy Plant Maxi Kit (Qiagen) and then was used for library construction using Illumina’s standard DNA methylation analysis protocol and the NEB Ultra II DNA Library Prep Kit. The samples were sequenced at the Genomics Core Facility of the Shanghai Centre for Plant Stress Biology, Chinese Academy of Sciences using Illumina HiSeq2500.

tag: Stage


title: Pp6A_MethylC-Seq


title: lptA-0-rep3

description:
Library name: Sample 57
Experiment1


title: PGBE 1W 0D

description: Library name: Sample 47


title: Day49,head,male,rep1-1

description: Library name: W7_H_M_1


title: leuS-0.0125-rep2

description:
Library name: Sample 50
Experiment1


title: 2BPA_1w_5C

description: Library name: Sample 27


title: PGBE 24h 10B

description: Library name: Sample 38


title: Pp5B_MethylC-Seq


title: PGBE 24h 0C

description: Library name: Sample 41


title: PGBE 1W 0A

description: Library name: Sample 35


title: leuS-0-rep3

description:
Library name: Sample 48
Experiment1


title: PGBE 24h 0A

description: Library name: Sample 33


title: Day42,body,male,rep2

description: Library name: W6_B_M_3


title: 2BPA_24h_20D

description: Library name: Sample 30

value: 2BPA 20uM 24h exposure


title: lptA-0-rep2

description:
Library name: Sample 56
Experiment1


title: lptA-0-rep1

description:
Library name: Sample 55
Experiment1


title: leuS-0-rep2

description:
Library name: Sample 47
Experiment1


title: 2BPA_1w_20B

description: Library name: Sample 24


title: Pp3B_MethylC-Seq


title: Day42,body,male,rep1-2

description: Library name: W6_B_M_1_2


title: PGBE 1W 10A

description: Library name: Sample 36


title: leuS-0-rep1

description:
Library name: Sample 46
Experiment1


title: PGBE 24h 0B

description: Library name: Sample 37


title: leuS-0.05-rep1

description:
Library name: Sample 52
Experiment1


title: Day42,reproductive,female,rep2

description: Library name: W6_O_F_3


title: leuS-0.0125-rep3

description:
Library name: Sample 51
Experiment1


title: 2BPA_24h_5D

description: Library name: Sample 29

value: 2BPA 5uM 24h exposure


title: 2BPA_1w_20C

description: Library name: Sample 28


title: Day42,head,male,rep2

description: Library name: W6_H_M_3


title: Day42,head,male,rep1

description: Library name: W6_H_M_1


title: Day42,head,female,rep2

description: Library name: W6_H_F_3


title: leuS-0.0125-rep1

description:
Library name: Sample 49
Experiment1


title: Pp2B_MethylC-Seq


title: gyrB-0.05-rep1

description:
Library name: Sample 43
Experiment1


title: 2BPA_1w_20A

description: Library name: Sample 20


title: Day35,reproductive,male,rep2

description: Library name: W5_T_M_3


title: 2BPA_24h_5C

description: Library name: Sample 25


title: gyrB-0.05-rep3

description:
Library name: Sample 45
Experiment1


title: 2BPA_24h_20C

description: Library name: Sample 26


title: Pp4B_MethylC-Seq


title: 2BPA_1w_5A

description: Library name: Sample 19


title: Day42,head,female,rep1

description: Library name: W6_H_F_1


title: gyrB-0.0125-rep2

description:
Library name: Sample 41
Experiment1


title: 2BPA_24h_20A

description: Library name: Sample 18


title: WT_3

city: Hefei

first: Yilong

last: Fang

address: Meishan Road

country: China

institute: Anhui medical university

description: Library name: WT_3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0).The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N);3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Assembly: GRCm39
Supplementary files format and content: excel sheets containing count and FPKM for all samples

source_name: RELMa+ peritoneal macrophages

extract_protocol:
Peritoneal macrophages were harvested from CAIA mice via peritoneal lavage with cold PBS. The collected cells were centrifuged, and red blood cells were lysed. RELM-α+ macrophages were subsequently isolated from the total peritoneal cell population using fluorescence-activated cell sorting (FACS) based on surface RELM-α expression. The sorted RELM-α+ macrophages were then plated in complete macrophage culture medium. Total RNA was extracted from the PU.1-deleted and control RELM-α+ macrophages using TRIzol reagent, followed by purification with a column-based RNA cleanup kit. RNA integrity was assessed via Bioanalyzer.
The extracted mRNA is enriched using mRNA Capture Beads. After purification with beads, the mRNA is fragmented using high temperatures. The fragmented mRNA is then used as a template to synthesize the first strand of cDNA in a reverse transcription enzyme mixture system. While synthesizing the second strand of cDNA, end repair and A-tailing are completed. Next, adapters are ligated, and Hieff NGS DNA Selection Beads are used for purification to select target fragments. PCR library amplification is then performed, and finally, detection is carried out using the Illumina Novaseq 6000.

value: RELMa+ peritoneal macrophages


title: 2BPA_24h_5A

description: Library name: Sample 17


title: gyrB-0.05-rep2

description:
Library name: Sample 44
Experiment1


title: 2BPA_24h_5B

description: Library name: Sample 21


title: Day42,body,female,rep1

description: Library name: W6_B_F_1


title: Pp5A_MethylC-Seq


title: gyrB-0-rep3

description:
Library name: Sample 39
Experiment1


title: 2BPA_24h_20B

description: Library name: Sample 22


title: Day35,head,male,rep2

description: Library name: W5_H_M_3

value: Head


title: 2BPA_1w_5B

description: Library name: Sample 23


title: Day42,body,male,rep1-1

description: Library name: W6_B_M_1


title: 2BPA_1w_0D

description: Library name: Sample 15

value: 2BPA 0uM 1W exposure


title: Day42,body,female,rep2

description: Library name: W6_B_F_3


title: Pp4A_MethylC-Seq


title: gyrB-0.0125-rep3

description:
Library name: Sample 42
Experiment1


title: 2BPA_24h_0D

description: Library name: Sample 13

value: 2BPA 0uM 24h exposure


title: Pp3A_MethylC-Seq


title: KO_1

description: Library name: KO_1


title: Day35,head,female,rep1

description: Library name: W5_H_F_1


title: WT_1

description: Library name: WT_1


title: Day35,reproductive,female,rep1

description: Library name: W5_O_F_1


title: Pp2A_MethylC-Seq


title: Day35,reproductive,female,rep2

description: Library name: W5_O_F_3


title: 2BPA_24h_10C

description: Library name: Sample 10

value: 2BPA10uM 24h exposure


title: GNAS organoid treated with doxycyline (Organoid ID: 6582)

city: Nashville

first: Kathleen

middle: E

last: DelGiorno

state: TN

address: 465 21st Ave S

department: Cell and Developmental Biology

institute: Vanderbilt University

description:
Library name: 12509-KA-018
KrasGNAS_combined_raw_counts.csv

data_processing:
Raw sequencing data (FASTQ files) generated on the NovaSeq 6000 were processed through standard quality control pipelines. Base calling was performed using Illumina Real Time Analysis software and NovaSeq Control Software (version 1.8.0). Overall sequencing quality was assessed with MultiQC (version 1.7). Paired-end RNA-sequencing reads (150 bp) were trimmed and quality-filtered using TrimGalore (version 0.6.7). Trimmed reads were aligned to the mm39 mouse reference genome with STAR (version 2.7.9a) using the quantMode GeneCounts option, and gene-level counts were generated using GENCODE comprehensive gene annotations (Release M31).
Assembly: mm39
Supplementary files format and content: Comma separated values file includes raw counts for each sample

source_name: Pancreatic organoids

extract_protocol:
RNA was extracted using the Quick-RNA Miniprep Kit (Zymo)
Library prep was performed using the NEBNext Ultra II RNA Library Prep Kit (E776L) per manufacturer's instructions

treatment_protocol: Cells or organoids were treated with 1-2 ug/mL of doxycyline for 48-72 hours

value: Pancreatic organoids

value: Doxycyline


title: Day35,body,male,rep1

description: Library name: W5_B_M_1

value: Body


title: Day35,reproductive,male,rep1

description: Library name: W5_T_M_1

value: Male


title: 2BPA_24h_10D

description: Library name: Sample 14


title: gyrA-0.0125-rep2

description:
Library name: Sample 32
Experiment1


title: KO_3

description: Library name: KO_3


title: Pp1B_MethylC-Seq


title: WT_2

description: Library name: WT_2


title: gyrA-0.05-rep2

description:
Library name: Sample 35
Experiment1


title: Day35,head,male,rep1-2

description: Library name: W5_H_M_1_2


title: 2BPA_1w_10D

description: Library name: Sample 16

value: 2BPA10uM 1W exposure


title: KO_2

description: Library name: KO_2


title: Day35,head,female,rep2

description: Library name: W5_H_F_3

value: Female


title: gyrB-0-rep1

description:
Library name: Sample 37
Experiment1


title: Pp1A_MethylC-Seq


title: gyrB-0.0125-rep1

description:
Library name: Sample 40
Experiment1


title: gyrA-0.0125-rep1

description:
Library name: Sample 31
Experiment1


title: Day35,head,male,rep1-1

description: Library name: W5_H_M_1


title: gyrA-0.05-rep3

description:
Library name: Sample 36
Experiment1


title: Day35,body,female,rep1

description: Library name: W5_B_F_1


title: gyrA-0.05-rep1

description:
Library name: Sample 34
Experiment1


title: gyrB-0-rep2

description:
Library name: Sample 38
Experiment1


title: Day35,body,male,rep2

description: Library name: W5_B_M_3


title: 2BPA_1w_0B

description: Library name: Sample 7

value: Human CCD-1079Sk fibroblasts (ATCC CRL-2097)


title: GNAS organoid control (Organoid ID: 6582)

description:
Library name: 12509-KA-017
KrasGNAS_combined_raw_counts.csv

value: Control


title: 2BPA_1w_10C

description: Library name: Sample 12

value: Brain Cells


title: Kras; GNAS organoids control  (Organoid ID: 6581)

description:
Library name: 12509-KA-007
KrasGNAS_combined_raw_counts.csv


title: 2BPA_24h_10B

description: Library name: Sample 6

value: Human induced pluripotent stem cells (hiPSCs)-derived 3D BrainSpheres


title: gyrA-0-rep2

description:
Library name: Sample 29
Experiment1


title: 2BPA_1w_0C

description: Library name: Sample 11


title: 2BPA_1w_10A

description: Library name: Sample 4


title: gyrA-0.0125-rep3

description:
Library name: Sample 33
Experiment1


title: 2BPA_1w_0A

description: Library name: Sample 3


title: folA-0.05-rep2

description:
Library name: Sample 26
Experiment1


title: Day28,head,male,rep2

description: Library name: W4_H_M_3


title: folA-0.05-rep1

description:
Library name: Sample 25
Experiment1


title: GNAS organoid control (Organoid ID: 6579)

description:
Library name: 12509-KA-015
KrasGNAS_combined_raw_counts.csv


title: GNAS organoid treated with doxycyline (Organoid ID: 6579)

description:
Library name: 12509-KA-016
KrasGNAS_combined_raw_counts.csv


title: Day28,reproductive,male,rep2

description: Library name: W4_T_M_3

value: Reproductive


title: Kras; GNAS organoids treated with doxycyline  (Organoid ID: 6576)

description:
Library name: 12509-KA-004
KrasGNAS_combined_raw_counts.csv


title: Day28,reproductive,female,rep2

description: Library name: W4_O_F_3


title: Day28,reproductive,female,rep1

description: Library name: W4_O_F_1


title: ATF4 knockdown_Cisp3

city: Ningbo

first: Xiaoyan

last: Sun

address: 247 Renmin Road, Jiangbei District, Ningbo City, Zhejiang Province, China

institute: Fudan University,The First Affiliated Hospital of Ningbo University,

description: Library name: Sample 9

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2software. The mapped reads of each sample were assembled by StringTie in a reference- based approach.
Differentially expressed genes were identified using DESeq2. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was conducted using the Python SciPy library.
Assembly: GRCm39
Supplementary files format and content: csv files includes raw counts for each sample

source_name: kidney

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent at Shanghai Majorbio Biopharm Technology Co.,Ltd(Shanghai, China) according the manufacturer’ s instructions.
RNA purification, reverse transcription, library construction and sequencing were performed according to the manufacturer’s instructions (Illumina, San Diego, CA). The RNAseq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequenced with the NovaSeq X plus sequencer (2 × 150bp read length).

value: kidney

value: Cisplatin


title: folA-0.0125-rep2

description:
Library name: Sample 23
Experiment1


title: Ind6_VEH_0.5_48

description: Library name: iPSC-CM_Ind6_VEH_0.5_48

data_processing:
Raw sequencing reads were assessed for quality using MultiQC (v1.26) (Ewels et al., 2016) on Linux-based systems. Reads were aligned to the human reference genome (GRCh38/hg38) using the Rsubread package (v2.16.1) (Liao et al., 2019). Gene-level quantification was performed using the featureCounts() function with the default exon-based annotations provided by Rsubread. Resulting count matrices were imported into R for downstream analysis. Expression values were transformed into log2 counts per million using the cpm() function from the edgeR package (v4.0.16) (Chen et al., 2016).
Assembly: hg38
Supplementary files format and content: Paul_CX_counts.txt

extract_protocol:
Frozen iPSC-derived cardiomyocyte pellets were thawed on ice and lysed in Buffer RLT supplemented with 1% β-mercaptoethanol, prepared fresh under a fume hood. Lysates were homogenized using QIAshredder columns (Qiagen; 79656) and mixed with 70% ethanol prior to binding to RNeasy Mini spin columns (Qiagen; 74106). On-column DNase I digestion (Qiagen; 79256) was performed using freshly prepared DNase/RDD buffer mix and incubated for 15 minutes at room temperature. Columns were washed sequentially with RW1 and RPE buffers, and RNA was eluted in 30 µL RNase-free water. All centrifugation steps were carried out at >10,000 rpm as recommended. Eluted RNA was immediately placed on ice and stored at –80 °C. RNA integrity and concentration were assessed prior to library preparation.
Polyadenylated mRNA was isolated from 150 ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490L; New England Biolabs). Strand-specific RNA-seq libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7765S; NEB), with dual indexing performed using NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, E6440S). Libraries were prepared in two balanced batches, each containing all treatment conditions and timepoints for three individuals (Batch 1: Individuals 1–3; Batch 2: Individuals 4–6). Final library quality and size distribution were evaluated using the Agilent 2100 Bioanalyzer prior to sequencing.

treatment_protocol: 1.5 million iPSC-derived cardiomyocytes were seeded per well in 6-well plates. On day 30 of differentiation, cells were treated with 0.1 µM or 0.5 µM CX-5461, Doxorubicin (DOX), or vehicle control in fresh cardiomyocyte maintenance media. Cells were harvested at 3 and 24 hours post-treatment. All steps were performed on ice unless otherwise specified. Culture media was aspirated, and cells were washed twice with 1 mL cold PBS. Cells were then scraped in 1 mL PBS into 1.5 mL Eppendorf tubes, followed by a second scrape using 500 µL PBS to collect any remaining cells. Cell suspensions were centrifuged at 7,000 rpm for 8 minutes at 4 °C. The supernatant was carefully removed, and the resulting cell pellets were flash-frozen in ethanol/dry ice and stored at –80 °C until RNA extraction.

value: male

value: induced pluripotent stem cell-derived cardiomyocytes


title: 2BPA_1w_10B

description: Library name: Sample 8


title: Kras; GNAS organoids treated with doxycyline  (Organoid ID: 6580)

description:
Library name: 12509-KA-014
KrasGNAS_combined_raw_counts.csv


title: ATF4 knockdown_Cisp2

description: Library name: Sample 8


title: 2BPA_24h_0C

description: Library name: Sample 9

value: 2BPA 0uM 24h exposure


title: Ind6_VEH_0.5_3

description: Library name: iPSC-CM_Ind6_VEH_0.5_3


title: Day28,head,female,rep1

description: Library name: W4_H_F_1

value: Head


title: ATF4 knockdown_Cisp1

description: Library name: Sample 7


title: folA-0-rep3

description:
Library name: Sample 21
Experiment1


title: Kras; GNAS organoids treated with doxycyline  (Organoid ID: 6581)

description:
Library name: 12509-KA-008
KrasGNAS_combined_raw_counts.csv

value: Pancreatic organoids


title: 2BPA_24h_0A

description: Library name: Sample 1


title: folA-0.05-rep3

description:
Library name: Sample 27
Experiment1


title: gyrA-0-rep1

description:
Library name: Sample 28
Experiment1


title: Day28,reproductive,male,rep1

description: Library name: W4_T_M_1


title: gyrA-0-rep3

description:
Library name: Sample 30
Experiment1


title: Day28,body,male,rep2

description: Library name: W4_B_M_3


title: folA-0-rep2

description:
Library name: Sample 20
Experiment1


title: Kras; GNAS organoids treated with doxycyline  (Organoid ID: 6552)

description:
Library name: 12509-KA-002
KrasGNAS_combined_raw_counts.csv

value: Doxycyline


title: Kras; GNAS organoids control  (Organoid ID: 6580)

description:
Library name: 12509-KA-013
KrasGNAS_combined_raw_counts.csv


title: CISP2

description: Library name: Sample 5


title: Day28,body,male,rep1-2

description: Library name: W4_B_M_1_2

value: Body


title: Ind6_VEH_0.1_3

description: Library name: iPSC-CM_Ind6_VEH_0.1_3


title: Kras; GNAS organoids control  (Organoid ID: 6576)

description:
Library name: 12509-KA-003
KrasGNAS_combined_raw_counts.csv


title: Ind6_VEH_0.1_24

description: Library name: iPSC-CM_Ind6_VEH_0.1_24


title: Day28,body,male,rep1-1

description: Library name: W4_B_M_1

value: Male


title: Day28,body,female,rep2

description: Library name: W4_B_F_3


title: Day35,body,female,rep2

description: Library name: W5_B_F_3


title: 2BPA_24h_10A

description: Library name: Sample 2

value: 2BPA10uM 24h exposure


title: dxr-0.05-rep3

description:
Library name: Sample 18
Experiment1


title: CTR7

description: Library name: Sample 3

value: saline


title: 2BPA_24h_0B

description: Library name: Sample 5

value: Human CCD-1079Sk fibroblasts (ATCC CRL-2097)


title: Ind6_DOX_0.5_48

description: Library name: iPSC-CM_Ind6_DOX_0.5_48


title: Day28,head,male,rep1-2

description: Library name: W4_H_M_1_2


title: Day28,head,female,rep2

description: Library name: W4_H_F_3

value: Female


title: folA-0.0125-rep3

description:
Library name: Sample 24
Experiment1


title: folA-0-rep1

description:
Library name: Sample 19
Experiment1


title: Day21,reproductive,male,rep2

description: Library name: W3_T_M_3


title: Kras; GNAS organoids control (Organoid ID: 6552)

description:
Library name: 12509-KA-001
KrasGNAS_combined_raw_counts.csv

value: Control


title: dxr-0.0125-rep3

description:
Library name: Sample 15
Experiment1


title: Day28,head,male,rep1-1

description: Library name: W4_H_M_1


title: dxr-0.0125-rep2

description:
Library name: Sample 14
Experiment1


title: folA-0.0125-rep1

description:
Library name: Sample 22
Experiment1


title: dxr-0.0125-rep1

description:
Library name: Sample 13
Experiment1


title: Ind6_DOX_0.1_3

description: Library name: iPSC-CM_Ind6_DOX_0.1_3


title: dxr-0-rep3

description:
Library name: Sample 12
Experiment1


title: Ind6_VEH_0.5_24

description: Library name: iPSC-CM_Ind6_VEH_0.5_24


title: Day21,head,male,rep2

description: Library name: W3_H_M_3


title: CISP6

description: Library name: Sample 6


title: Day21,head,male,rep1

description: Library name: W3_H_M_1


title: Day28,body,female,rep1

description: Library name: W4_B_F_1


title: Ind6_VEH_0.1_48

description: Library name: iPSC-CM_Ind6_VEH_0.1_48


title: cAPK_neg_NIH

first: Zvi

middle: I

last: Cramer

state: MA

address: 30 Caldwell St

institute: University of Pennsylvania

description: Library name: cAPK_neg_NIH

data_processing:
fastp
Bowtie2
Samtool sort
BamCoverage
MACS2 callpeak
Assembly: GRCm38
Supplementary files format and content: BED
Library strategy: CUT&Run

source_name: Colorectal Apc, Trp53, Kras Mutant

extract_protocol:
Nuclei were isolated from cultured APK organoid using the kit-supplied Nuclei Extraction Buffer (EpiCypher, Cat. #14-1048-24).
Library preparation was performed with the CUTANA™ DNA Library Prep Kit (EpiCypher, Cat. #14-1001) following the manufacturer’s protocol.

value: colorectal cancer organoids

value: Colorectal adenocarcinoma

value: Apc f/f,Trp f/f,Kras +/G12D


title: CTR1

description: Library name: Sample 1

value: kidney


title: Ind6_DOX_0.5_3

description: Library name: iPSC-CM_Ind6_DOX_0.5_3

value: male


title: CISP1

description: Library name: Sample 4

value: Cisplatin


title: ctrlg-0.05-rep3

description:
Library name: Sample 9
Experiment1


title: dxr-0.05-rep2

description:
Library name: Sample 17
Experiment1


title: Ind6_CX_0.5_24

description: Library name: iPSC-CM_Ind6_CX_0.5_24

value: induced pluripotent stem cell-derived cardiomyocytes


title: Ind6_DOX_0.1_48

description: Library name: iPSC-CM_Ind6_DOX_0.1_48


title: Day21,reproductive,female,rep1

description: Library name: W3_O_F_1

value: Reproductive


title: Ind6_CX_0.5_48

description: Library name: iPSC-CM_Ind6_CX_0.5_48


title: CTR2

description: Library name: Sample 2


title: Ind6_DOX_0.5_24

description: Library name: iPSC-CM_Ind6_DOX_0.5_24


title: Ind6_CX_0.1_48

description: Library name: iPSC-CM_Ind6_CX_0.1_48


title: cAPK_ pos_NIH

description: Library name: cAPK_ pos_NIH


title: dxr-0.05-rep1

description:
Library name: Sample 16
Experiment1


title: DuralMeninges_03

first: Beth

last: Stevens

state: Massachusetts

address: 3 Blackfan Circle, 12220 Center for Life Sciences

institute: Boston Children's Hospital

description:
Library name: pEXP46sMMrMENtP14iSAMPLE03d20200821
10X Genomics 5'

data_processing:
fastq demultiplexing was performed using Cell Ranger 5.0.0 `mkfastq` w/bcl2fastq 2.20.0.422.  Samples were then processed with CellRanger 5.0.0 `multi` to create sample count matrices.  After CellRanger count matrix generation the raw count matrix (all droplets including those not called cells) were used as input for CellBender 0.2.0 `remove-background` to remove ambient RNA.
Assembly: mm10. Ensembl v93 filtered (10X Genomics default: refdata-gex-mm10-2020-A)
Supplementary files format and content: Raw ( for all droplets) & Filtered (droplets called as cells) counts from CellRanger as hdf5 files.
Supplementary files format and content: Ambient RNA removed counts matrix (cells only) from CellBender as hdf5 files.

source_name: Dura Mater

extract_protocol:
Anesthetized mice were injected intravenously (i.v.) with anti-CD45 to label and exclude blood-borne immune cells, transcardially perfused, and then each tissue extracted and enzymatically dissociated into a single cell suspension in the presence of transcriptional/translational inhibitors to prevent ex vivo changes in gene expression. Single cell suspensions were labeled with antibodies and purified by fluorescence activated cell sorting. For the dura and bone marrow, CD45 i.v. negative immune cells and non-immune cells were sorted at a ratio of approximately 1:1 immune to non-immune cells. For the brain-leptomeninges, CD45 i.v. negative microglia and non-microglial immune cells were sorted at a ratio of approximately 1:4 microglia to non-microglial immune cells. Sorted cells were captured and processed on the 10x Genomics 5’ v1.1 platform.
Libraries were constructed as per manufacturers protocol for 10x Genomics 5’ v1.1.

value: Dura Mater

tag: strain

value: WT

tag: age


title: dxr-0-rep1

description:
Library name: Sample 10
Experiment1


title: Ind6_DOX_0.1_24

description: Library name: iPSC-CM_Ind6_DOX_0.1_24


title: Ind6_CX_0.1_3

description: Library name: iPSC-CM_Ind6_CX_0.1_3


title: Day21,body,male,rep1

description: Library name: W3_B_M_1

value: Body


title: dxr-0-rep2

description:
Library name: Sample 11
Experiment1


title: TibiaBoneMarrow_03

description:
Library name: pEXP46sMMrBMtP14iSAMPLE03d20200821
10X Genomics 5'

source_name: Tibial Bone Marrow

value: Tibial Bone Marrow

value: Male


title: DuralMeninges_02

description:
Library name: pEXP46sMMrMENtP14iSAMPLE02d20200821
10X Genomics 5'


title: cAPK_YAP_NIH

description: Library name: cAPK_YAP_NIH

tag: antibody

value: anti-YAP1 antibody (Cell Signaling Technology, Cat. #14074S)


title: cAPK_TEAD_NIH

description: Library name: cAPK_TEAD_NIH

value: anti-TEAD1 antibody (BD Transduction Laboratories, 610923)


title: SkullBoneMarrow_03

description:
Library name: pEXP46sMMrSKBMtP14iSAMPLE03d20200821
10X Genomics 5'

source_name: Calvarial Bone Marrow

value: Calvarial Bone Marrow


title: Ind5_VEH_0.5_3

description: Library name: iPSC-CM_Ind5_VEH_0.5_3


title: Day21,reproductive,male,rep1

description: Library name: W3_T_M_1


title: Ind6_CX_0.5_3

description: Library name: iPSC-CM_Ind6_CX_0.5_3


title: Day14,reproductive,male,rep1

description: Library name: W2_T_M_1


title: SkullBoneMarrow_01

description:
Library name: pEXP38sMMrSKBMtP14iSAMPLE04d20191217
10X Genomics 5'


title: Ind6_CX_0.1_24

description: Library name: iPSC-CM_Ind6_CX_0.1_24


title: TibiaBoneMarrow_01

description:
Library name: pEXP38sMMrBMtP14iSAMPLE05d20191217
10X Genomics 5'


title: Ind5_VEH_0.1_48

description: Library name: iPSC-CM_Ind5_VEH_0.1_48


title: Day21,head,female,rep2

description: Library name: W3_H_F_3

value: Head

value: Female


title: ctrlg-0-rep1

description:
Library name: Sample 1
Experiment1


title: Day21,head,female,rep1

description: Library name: W3_H_F_1


title: ctrlg-0.0125-rep2

description:
Library name: Sample 5
Experiment1


title: Day14,reproductive,male,rep2

description: Library name: W2_T_M_3


title: ctrlg-0.05-rep2

description:
Library name: Sample 8
Experiment1


title: Day21,body,male,rep2

description: Library name: W3_B_M_3


title: Murine Spleen Unstable Treg from EAE Recovery BioRep4

city: Munich

first: Thomas

last: Korn

email: thomas.korn@tum.de, c.sie@tum.de

address: Ismaninger Str. 22

department: Experimental Neuroimmunology

country: Germany

institute: Technical University of Munich

description: Library name: UnstableTreg_SPL_R4

data_processing:
The sequencing data were processed using the Drop-seq pipeline (PMID: 26000488) to generate UMI tables organized by sample and gene.
Assembly: The GRCm38 reference genome was aligned with transcript and gene annotations derived from ENSEMBL.
Supplementary files format and content: TXT files with gene counts (one gene per row, one sample per column)

source_name: Spleen

extract_protocol:
250-2000 Treg or Tconv cells (viability > 90%) were sorted directly into TCL buffer (QIAGEN) plus 1% 2-Mercaptoethanol (Merk) and stored at -80°C until all samples were ready for RNA extraction. The RNA was extracted and purified using the RNAeasy Plus Micro Kit (QIAGEN). The RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies).
Barcode-specific cDNA was synthesized via reverse transcription with Maxima RT polymerase (Thermo Fisher), utilizing an oligo-dT primer containing barcodes, unique molecular identifiers (UMIs), and adaptor sequences. The 5′ end of the cDNA was then extended using primers complementary to the template switch oligo (TSO) site, followed by amplification of full-length cDNA. The cDNA was fragmented using the Nextera XT kit (Illumina), and the 3′-end fragments were amplified with primers incorporating Illumina P5 and P7 overhangs. The P5 and P7 sites were modified to optimize cluster recognition during sequencing, enabling sequencing of the cDNA in read1 and the barcodes/UMIs in read2.

value: Spleen

value: Treg

value: 1000 cells

tag: eae stage

value: Recovery

value: Bio rep 4


title: Day21,reproductive,female,rep2

description: Library name: W3_O_F_3

data_processing:
We demultiplexed the raw barcoded sequence data using bcl2fastq (v2.20.0.422). We performed the initial steps of raw read processing, using the AfterQC pipeline to trim adapters, detect unusual polynucleotide sequences, filter out low-quality reads (Q < 20), and discard short reads (<35 nucleotides). We also generated essential sequence quality metrics. We employed the bbduk command from the BBTools package  to check for ribosomal RNA (rRNA) sequences remaining following ribosomal depletion. We aligned the high-quality sequence reads to the D. melanogaster reference genome release 6 (version 6.13) using the GSNAP aligner  and assigned reads to genes using the Subread package.
Assembly: D. melanogaster reference genome release 6 (version 6.13)
Supplementary files format and content: featureCounts tab-delimited output

extract_protocol:
We strictly randomized all steps of RNA extraction, library preparation and sequencing. We extracted total RNA using the RNeasy Mini Kit (Qiagen, Inc., catalog number 74104). We depleted ribosomal RNA (rRNA) using the Ribo-Zero Gold Kit (Epicentre, Inc.).
We barcoded cDNA from each RNA sample was using NEXTflex DNA Barcodes (Bioo Scientific, Inc.) with an Illumina TruSeq compatible protocol. The pooled library samples were clustered on an Illumina cBot and sequenced on the Illumina Hiseq2500 platform, using 125 bp single-read v4 chemistry.


title: TibiaBoneMarrow_02

description:
Library name: pEXP46sMMrBMtP14iSAMPLE02d20200821
10X Genomics 5'


title: DuralMeninges_01

description:
Library name: pEXP38sMMrMENtP14iSAMPLE01d20191217
10X Genomics 5'


title: Brain_01

description:
Library name: pEXP38sMMrBRAINtP14iSAMPLE02d20191217
10X Genomics 5'

source_name: Brain-Leptomeninges-Choroid Plexus

value: Brain-Leptomeninges-Choroid Plexus


title: ctrlg-0-rep2

description:
Library name: Sample 2
Experiment1


title: Day21,body,female,rep1

description: Library name: W3_B_F_1


title: Day14,reproductive,female,rep2

description: Library name: W2_O_F_3

source_name: Reproductive

value: Reproductive


title: Ind5_DOX_0.5_48

description: Library name: iPSC-CM_Ind5_DOX_0.5_48

value: male

value: induced pluripotent stem cell-derived cardiomyocytes


title: SkullBoneMarrow_02

description:
Library name: pEXP46sMMrSKBMtP14iSAMPLE02d20200821
10X Genomics 5'

value: WT


title: Cochlea, CBA/CaJ, 16W, 100 dB SPL, 2h, 8h post, 3

city: Chicago

first: Jeffrey

last: Savas

state: Illinois

address: 303 E. Chicago Avenue, Ward 12-013

department: Neurology

institute: Northwestern University

description:
Library name: Sample 12
Column name in raw counts: PN8h_3

data_processing:
Raw FASTQ reads were processed with fastp to remove adaptor sequences, poly-N reads, and low-quality reads. Clean data quality metrics (Q20, Q30, and GC content) were assessed. Reference genome and annotation files were obtained from NCBI/UCSC/Ensembl. Genome indexing and alignment were performed with STAR (v2.5) using the Maximal Mappable Prefix (MMP) algorithm, achieving >95.3% total mapping efficiency and >75 million mapped reads per sample across four biological replicates per group. Gene-level counts were obtained with HTSeq (v0.6.1).
Differential gene expression analysis was conducted using iGEAK (R/Shiny-based pipeline). Low-abundance transcripts (read count < 8 in fewer than 3 samples) were filtered out. Data were normalized using edgeR’s TMM (Trimmed Mean of M-values) method. Statistical testing for differential expression was performed with edgeR, and p-values were adjusted for multiple testing with the Benjamini–Hochberg method to control the false discovery rate (FDR). Genes with adjusted p-value < 0.05 and fold-change > 1.5 were considered significantly differentially expressed.
Assembly: mm10 (GRCm38, 2011)
Supplementary files format and content: A tab-delimited text file containing the raw counts for each sample.

source_name: cochlea

growth_protocol: CBA/CaJ mice, male at 16 weeks of age were used in these experiments.

extract_protocol:
For Bulk RNA-sequencing,total RNA was extracted from cochlear tissue using TRIzol reagent (Thermo Fisher) according to the manufacturer’s protocol, and further purified with the RNeasy Plus Mini Kit (Qiagen). Purified RNA was sent to Novogene (Sacramento, CA, USA) for quality control (QC), library preparation, sequencing, and quantitation according to their standard gene expression workflow. RNA degradation and contamination were initially assessed on 1% agarose gels. RNA purity was evaluated using a NanoPhotometer spectrophotometer (IMPLEN, CA, USA), while RNA integrity and concentration were determined using the RNA Nano 6000 Assay Kit with the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Only RNA samples that passed QC were used for library preparation and sequencing.
For library construction, 1 µg of total RNA per sample was used as input. Libraries were prepared with the NEBNext Ultra™ RNA Library Prep Kit for Illumina (NEB, USA) according to the manufacturer’s instructions, with unique index codes added to each sample.

treatment_protocol: Noise exposures were delivered to unanesthetized animals placed in small wire cages within a custom-built sound-attenuated chamber designed by Charles Liberman (Mass. Eye and Ear).

value: cochlea

value: CBA/CaJ

value: 100 dB SPL, 2 hr + 8hr


title: Ind5_VEH_0.5_48

description: Library name: iPSC-CM_Ind5_VEH_0.5_48


title: Murine Spleen Unstable Treg from EAE Recovery BioRep2

description: Library name: UnstableTreg_SPL_R2

value: Bio rep 2


title: ctrlg-0.05-rep1

description:
Library name: Sample 7
Experiment1

data_processing:
Reads were demultiplexed based on their associated barcode. Up to 1 mismatch in the barcode was allowed. Barcode sequences and terminal G's that were added during template switching were trimmed.
Assembly: Pseudomonas aeruginosa UCBPP-PA14 GCF_000014625.1
Supplementary files format and content: tsv file includes raw counts for each sample

extract_protocol:
50ul of treated cells were mixed with 25ul 3X RNAgem Blue Buffer, incubated at 75C for 10mins and flashfrozen. RNA was extracted using the Direct-zol RNA Miniprep Plus Kit.
cDNA libraries were generated using a modified version of the RNAtag-seq protocol. 500ng of RNA was fragmented, depleted of genomic DNA, dephosphorylated, and ligated to DNA adapters. Barcoded RNAs were pooled and depleted of rRNA. Pools were converted to cDNA using reverse transcriptase template switching with PCR amplification of the Illumina P5 and P7 sequences. cDNA libraries were sequenced on Illumina Nextseq 500 platorm for paired end reads


title: Day14,reproductive,female,rep1

last: Nasiri Aghdam

address: 114 Gregor Mendel Cir

institute: Clemson University

description: Library name: W2_O_F_1


title: Ind5_DOX_0.5_3

description: Library name: iPSC-CM_Ind5_DOX_0.5_3


title: ctrlg-0-rep3

description:
Library name: Sample 3
Experiment1


title: Murine Spleen Unstable Treg from EAE Recovery BioRep3

description: Library name: UnstableTreg_SPL_R3

value: Bio rep 3


title: Ind5_VEH_0.1_24

description: Library name: iPSC-CM_Ind5_VEH_0.1_24


title: Murine Spleen Unstable Treg from EAE Recovery BioRep1

description: Library name: UnstableTreg_SPL_R1

value: Bio rep 1


title: ctrlg-0.0125-rep1

description:
Library name: Sample 4
Experiment1


title: Day14,head,male,rep2

description: Library name: W2_H_M_3

source_name: Head

value: Head

value: Male


title: Day21,body,female,rep2

description: Library name: W3_B_F_3

source_name: Body

value: Body

value: Female


title: Ind5_DOX_0.5_24

description: Library name: iPSC-CM_Ind5_DOX_0.5_24


title: Day14,head,female,rep1

description: Library name: W2_H_F_1


title: Ind5_DOX_0.1_48

description: Library name: iPSC-CM_Ind5_DOX_0.1_48


title: Ind5_VEH_0.5_24

description: Library name: iPSC-CM_Ind5_VEH_0.5_24


title: Ind5_DOX_0.1_3

description: Library name: iPSC-CM_Ind5_DOX_0.1_3


title: Cochlea, CBA/CaJ, 16W, 100 dB SPL, 2h, 4h post, 3

description:
Library name: Sample 9
Column name in raw counts: PN4h_3

value: 100 dB SPL, 2 hr + 4hr


title: Day14,body,male,rep2

description: Library name: W2_B_M_3


title: Murine CNS Unstable Treg from EAE Recovery BioRep4

description: Library name: UnstableTreg_CNS_R4

source_name: CNS

value: CNS

value: Treg

value: 1000 cells

value: Recovery

value: Bio rep 4


title: Brain_02

description:
Library name: pEXP46sMMrBRAINtP14iSAMPLE02d20200821
10X Genomics 5'

value: Brain-Leptomeninges-Choroid Plexus

value: WT


title: Day14,body,female,rep2

description: Library name: W2_B_F_3


title: Ind5_DOX_0.1_24

description: Library name: iPSC-CM_Ind5_DOX_0.1_24

value: male

value: induced pluripotent stem cell-derived cardiomyocytes


title: Ind5_VEH_0.1_3

description: Library name: iPSC-CM_Ind5_VEH_0.1_3


title: Ind5_CX_0.5_48

description: Library name: iPSC-CM_Ind5_CX_0.5_48


title: ctrlg-0.0125-rep3

description:
Library name: Sample 6
Experiment1


title: Cochlea, CBA/CaJ, 16W, 100 dB SPL, 2h, 3

description:
Library name: Sample 6
Column name in raw counts: PN0h_3

value: cochlea

value: CBA/CaJ

value: 100 dB SPL, 2 hr


title: Ind5_CX_0.5_3

description: Library name: iPSC-CM_Ind5_CX_0.5_3


title: Murine CNS Unstable Treg from EAE Recovery BioRep5

description: Library name: UnstableTreg_CNS_R5

value: Bio rep 5


title: Cochlea, CBA/CaJ, 16W, 100 dB SPL, 2h, 1

description:
Library name: Sample 4
Column name in raw counts: PN0h_1


title: Cochlea, CBA/CaJ, 16W, 100 dB SPL, 2h, 8h post, 2

description:
Library name: Sample 11
Column name in raw counts: PN8h_2

value: 100 dB SPL, 2 hr + 8hr


title: Day7,reproductive, female, rep2

description: Library name: W1_O_F_3

value: Reproductive


title: Brain_03

description:
Library name: pEXP46sMMrBRAINtP14iSAMPLE03d20200821
10X Genomics 5'

value: Male


title: Cochlea, CBA/CaJ, 16W, mock 3

description:
Library name: Sample 3
Column name in raw counts: Cntr3

value: mock


title: Day14,head,female,rep2

description: Library name: W2_H_F_3

value: Head

value: Female


title: Cochlea, CBA/CaJ, 16W, mock 2

description:
Library name: Sample 2
Column name in raw counts: Cntr2


title: Murine Spleen Stable Treg from EAE Recovery BioRep1

description: Library name: StableTreg_SPL_R1

value: Spleen

value: Treg

value: 1000 cells

value: Bio rep 1


title: Day14,body,male,rep1

description: Library name: W2_B_M_1

value: Body


title: Day7, head, male, rep2

description: Library name: W1_H_M_3


title: Day14,head,male,rep1

description: Library name: W2_H_M_1


title: Cochlea, CBA/CaJ, 16W, 100 dB SPL, 2h, 4h post, 1

description:
Library name: Sample 7
Column name in raw counts: PN4h_1

value: male

value: 100 dB SPL, 2 hr + 4hr


title: Murine CNS Stable Treg from EAE Recovery BioRep5

description: Library name: StableTreg_CNS_R5

value: CNS

value: Recovery


title: Cochlea, CBA/CaJ, 16W, 100 dB SPL, 2h, 4h post, 2

description:
Library name: Sample 8
Column name in raw counts: PN4h_2

value: cochlea

value: CBA/CaJ


title: Cochlea, CBA/CaJ, 16W, 100 dB SPL, 2h, 8h post, 1

description:
Library name: Sample 10
Column name in raw counts: PN8h_1

value: 100 dB SPL, 2 hr + 8hr


title: Day14,body,female,rep1

description: Library name: W2_B_F_1


title: Day7, head, male, rep1

description: Library name: W1_H_M_1


title: Day7,reproductive, male, rep2

description: Library name: W1_T_M_3

value: Reproductive


title: Murine CNS Unstable Treg from EAE Recovery BioRep2

description: Library name: UnstableTreg_CNS_R2

value: Bio rep 2


title: Ind4_VEH_0.5_3

description: Library name: iPSC-CM_Ind4_VEH_0.5_3

value: induced pluripotent stem cell-derived cardiomyocytes


title: Day7, head, female, rep2

description: Library name: W1_H_F_3

value: Head


title: Murine Spleen Stable Treg from EAE Recovery BioRep2

description: Library name: StableTreg_SPL_R2


title: Ind5_CX_0.1_3

description: Library name: iPSC-CM_Ind5_CX_0.1_3


title: Murine CNS Unstable Treg from EAE Recovery BioRep1

description: Library name: UnstableTreg_CNS_R1


title: Ind5_CX_0.5_24

description: Library name: iPSC-CM_Ind5_CX_0.5_24


title: Murine CNS Unstable Treg from EAE Recovery BioRep3

description: Library name: UnstableTreg_CNS_R3

value: Bio rep 3


title: Murine CNS Stable Treg from EAE Recovery BioRep3

description: Library name: StableTreg_CNS_R3


title: Day7, head, female, rep1

description: Library name: W1_H_F_1

value: Female


title: Day7,reproductive, male, rep1

description: Library name: W1_T_M_1

value: Male


title: Ind5_CX_0.1_24

description: Library name: iPSC-CM_Ind5_CX_0.1_24


title: Cochlea, CBA/CaJ, 16W, 100 dB SPL, 2h, 2

description:
Library name: Sample 5
Column name in raw counts: PN0h_2

value: 100 dB SPL, 2 hr


title: Murine Spleen Stable Treg from EAE Recovery BioRep3

description: Library name: StableTreg_SPL_R3

value: Spleen

value: Treg

value: 1000 cells


title: Ind5_CX_0.1_48

description: Library name: iPSC-CM_Ind5_CX_0.1_48

value: male


title: Murine Spleen Stable Treg from EAE Recovery BioRep4

description: Library name: StableTreg_SPL_R4

value: Bio rep 4


title: Ind4_VEH_0.1_48

description: Library name: iPSC-CM_Ind4_VEH_0.1_48


title: Murine CNS Stable Treg from EAE Recovery BioRep1

description: Library name: StableTreg_CNS_R1

value: CNS

value: Recovery

value: Bio rep 1


title: Day7, body, male, rep2

description: Library name: W1_B_M_3

value: Body


title: Ind4_VEH_0.5_48

description: Library name: iPSC-CM_Ind4_VEH_0.5_48


title: Cochlea, CBA/CaJ, 16W, mock 1

description:
Library name: Sample 1
Column name in raw counts: Cntr1

value: cochlea

value: CBA/CaJ

value: mock


title: Day7, body, female, rep2

description: Library name: W1_B_F_3


title: Ind4_DOX_0.5_48

description: Library name: iPSC-CM_Ind4_DOX_0.5_48

value: induced pluripotent stem cell-derived cardiomyocytes


title: Day7,reproductive, female, rep1

description: Library name: W1_O_F_1

value: Reproductive


title: Murine VAT Treg from Naive Stage (250 cells) BioRep2

description: Library name: VAT_Naive_R2

source_name: Visceral adipose tissue

value: Visceral adipose tissue

value: 250 cells

value: Foxp3-GFP mice (C57BL/6)

value: Naïve

value: Bio rep 2


title: Day5,reproductive, male, rep2

description: Library name: 5D_T_M_3

value: Male


title: WT-mT-3

city: Chengdu

first: Weibo

last: Liang

address: Renmin South Road

institute: Sichuan University

description: Library name: Sample 6

data_processing:
The raw FASTQ files underwent initial quality control using FastQC, followed by trimming of adapter sequences and low-quality bases using Trim Galore. The trimmed reads were then decompressed, aligned to the reference genome with HISAT2, and sorted with Samtools. Feature counts were generated using featureCounts to produce a count matrix, which was subsequently used for further analysis. Quality control of the alignment was performed using MultiQC, and the processed data was organized into appropriate directories for downstream analysis.
Assembly: Mouse mm10
Supplementary files format and content: tab-delimited file includes raw read counts for each sample

source_name: Hippocampus

growth_protocol: All mice were housed in cages with ad libitum access to food and water and acclimated to standard conditions (12 h light/dark cycle, temperature: 22–25 °C, relative humidity: 40-60%) for at least one week before the experiment.

extract_protocol:
Hippocampal tissue was isolated from transgenic mice expressing tdTomato fluorescent protein in neurons. Following cardiac perfusion with saline, the brain was rapidly extracted, and the hippocampus was dissected. The hippocampal tissue was washed with ice-cold Hanks' Balanced Salt Solution (HBSS) to remove debris. The cleaned tissue was then transferred into a trypsin-containing solution, finely minced, and incubated at 37°C with gentle shaking for 15 minutes to dissociate single cells. To terminate digestion, DMEM supplemented with 10% FBS was immediately added. The cell suspension was then filtered through a 40-µm cell strainer and centrifuged at 300 g for 5 minutes to collect cells. The pelleted cells were resuspended in PBS containing 1% BSA and subjected to FACS using a BD Melody cell sorter. The cell suspension was loaded into the sample chamber, and tdTomato fluorescence was detected using the PE (Phycoerythrin) channel. Before sorting, forward scatter (FSC) and side scatter (SSC) thresholds were optimized in the flow cytometry software to distinguish live cells from dead cells and debris. A fluorescence threshold was set in the PE channel to differentiate tdTomato-expressing cells from non-expressing cells. Live tdTomato-positive cells were automatically sorted and collected into a collection tube containing culture medium for further analysis.
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.

treatment_protocol: Each mTBI mouse received a single mild controlled cortical impact (CCI).Sham-operated control mice underwent the same procedures except for the impact.

value: Hippocampus

value: WT

value: mTBI


title: Murine CNS Stable Treg from EAE Recovery BioRep4

description: Library name: StableTreg_CNS_R4

value: CNS

value: Treg

value: 1000 cells

value: Recovery

value: Bio rep 4


title: OncoD

city: Augusta

first: Balveen

last: Kaur

state: GA

address: CN-3205, 1410 Laney-Walker Blvd

department: Pathology

institute: Augusta University

description: Library name: UTBK

data_processing:
Raw base call files were processed using Cell Ranger to generate FASTQ files and count matrices
Gene-barcode matrices were filtered and normalized using the Seurat R package
Assembly: mm10 (GRCm38)
Supplementary files format and content: Filtered gene-barcode matrix in HDF5 (.h5) format generated by Cell Ranger

source_name: brain

growth_protocol: Primary GBM12 cells were maintained in 150 mm TC-treated Culture Dishes with 2%FBS DMEM until they were ready to harvest and implant. 200,000 GBM12 cells per mouse were prepared in 2uL of sterile saline.

extract_protocol:
Tumor-bearing brain hemispheres of OncoD- or OncoD-0J1-treated mice were dissociated into single-cell suspension using the Tumor Dissociation Kit and gentleMACS Octo Dissociator from Miltenyi Biotec. Mouse anti-F4/80 MicroBeads UltraPure from Miltenyi Biotec were used to isolate F4/80+ cells which were submitted to single-cell RNA sequencing.
Cells were loaded onto the Chromium X instrument (10X Genomics) and processed using the Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 Dual Index (10X Genomics, cat# 1000268) according to the manufacturer’s protocol. scRNA-seq libraries were generated following standard procedures. Quality control (QC) was performed before sequencing using the Agilent 2100 Bioanalyzer and 2200 TapeStation (Agilent, Santa Clara, CA, USA). Library concentration was measured with a Qubit Fluorometer (Thermo Fisher). Sequencing was carried out on the NovaSeq 6000 system (Illumina Inc., San Diego, CA) following 10X Genomics guidelines.

value: brain

value: F4/80+ cells


title: WT-mT-2

description: Library name: Sample 5


title: c-HIP

description:
Library name: Sample 2
10× Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0.
Assembly: Mouse mm10
Supplementary files format and content: Tab-seperated values files and matrix files

extract_protocol:
Mice were sacrificed 48 hours post injury, and the hippocampus was micro-dissected (n=3 per group) and washed in precooled PBS to remove residual blood. Then, the tissue was flash-frozen in liquid nitrogen and transferred to -80 ℃ until further use.NLB buffer (X-100 (Sigma-Aldrich, St Louis, MO, USA), 0.2 U/μL RNase Inhibitor (Takara, Kyoto, Japan), 250 mM Sucrose, 10 mM Tris-HCl, 3 mM MgAc2, 0.1% Triton 0.1 mM EDTA) was used to homogenize the frozen tissue. Different concentrations of sucrose were applied to purify the nuclei using sucrose density gradient centrifugation. A final concentration of around 1000 nuclei/μL was used for scRNA-Seq.
The scRNA-Seq libraries were built using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3.1 Reagent Kits (10X Genomics, Pleasanton, CA, USA). Briefly, the acquired cell nuclei were loaded into several channels to obtain single-cell Gel Bead-In-Emulsions (GEMs). After reverse transcription, barcoded cDNA was released from the GEM and then purified. After amplification, the barcoded cDNA went through fragmentation, ligation with adaptors, and amplified with index PCR. The Qubit High Sensitivity DNA assay (Thermo Fisher Scientific, Waltham, MA, USA) was applied to quantify the final libraries, and the size distribution was determined by the High Sensitivity DNA chip using Bioanalyzer 2200 (Agilent Technologies, Santa Clara, CA, USA). Novaseq6000 (Illumina, San Diego, CA, USA) was used for sequencing on a 150 bp paired-end run.

value: 8~10-week old

value: Sham


title: Ind4_DOX_0.1_48

description: Library name: iPSC-CM_Ind4_DOX_0.1_48

value: male

value: induced pluripotent stem cell-derived cardiomyocytes


title: t-HIP

description:
Library name: Sample 1
10× Genomics


title: WT-mT-1

description: Library name: Sample 4


title: Murine VAT Treg from Naive Stage (250 cells) BioRep1

description: Library name: VAT_Naive_R1

value: Visceral adipose tissue

value: 250 cells

value: Foxp3-GFP mice (C57BL/6)

value: Naïve

value: Bio rep 1


title: CKO-mT-3

description: Library name: Sample 3

value: Hippocampus

value: Tmsb4x Conditional Knockout

value: mTBI


title: Ind4_VEH_0.5_24

description: Library name: iPSC-CM_Ind4_VEH_0.5_24


title: Ind4_VEH_0.1_24

description: Library name: iPSC-CM_Ind4_VEH_0.1_24


title: Ind4_VEH_0.1_3

description: Library name: iPSC-CM_Ind4_VEH_0.1_3


title: OncoD-0J1

description: Library name: OVJ


title: Murine CNS Treg from EAE Peak (250 cells) BioRep3

description: Library name: CNS_Peak_R3

value: CNS

value: Treg

value: EAE Peak

value: Bio rep 3


title: Day7, body, male, rep1

city: Greeenwood

first: Maryam

description: Library name: W1_B_M_1

value: Body

value: Male


title: WT-sham-2

description: Library name: Sample 8

value: WT

value: Sham


title: Murine CNS Treg from EAE Recovery (250 cells) BioRep4

description: Library name: CNS_Rec_R4

value: EAE Recovery

value: Bio rep 4


title: Ind4_DOX_0.5_3

description: Library name: iPSC-CM_Ind4_DOX_0.5_3

value: male

value: induced pluripotent stem cell-derived cardiomyocytes


title: WT-sham-1

description: Library name: Sample 7


title: Day5,reproductive, female, rep2-1

description: Library name: 5D_O_F_3

value: Reproductive

value: Female


title: Day7, body, female, rep1

description: Library name: W1_B_F_1


title: Murine CNS Stable Treg from EAE Recovery BioRep2

description: Library name: StableTreg_CNS_R2

value: 1000 cells

value: Recovery

value: Bio rep 2


title: Ind4_DOX_0.5_24

description: Library name: iPSC-CM_Ind4_DOX_0.5_24


title: Day5,head, male, rep1

description: Library name: 5D_H_M_1

value: Head


title: Ind4_DOX_0.1_24

description: Library name: iPSC-CM_Ind4_DOX_0.1_24


title: Murine CNS Treg from EAE Peak (250 cells) BioRep1

description: Library name: CNS_Peak_R1

value: CNS

value: Treg

value: 250 cells

value: Foxp3-GFP mice (C57BL/6)

value: Bio rep 1


title: Day5,reproductive, male, rep1

description: Library name: 5D_T_M_1

value: Male


title: Murine CNS Treg from EAE Recovery (250 cells) BioRep3

description: Library name: CNS_Rec_R3

value: Bio rep 3


title: Murine CNS Treg from Naive Stage (250 cells) BioRep4

description: Library name: CNS_Naive_R4

value: Naïve


title: WT-sham-3

description: Library name: Sample 9

value: Hippocampus

value: WT

value: Sham


title: Ind4_CX_0.1_48

description: Library name: iPSC-CM_Ind4_CX_0.1_48

value: male

value: induced pluripotent stem cell-derived cardiomyocytes


title: Day5,reproductive, female, rep2-2

description: Library name: 5D_O_F_3_2

value: Reproductive

value: Female


title: s-1

description: Library name: Sample 4

data_processing:
The paired-end reads from ATAC-seq were processed to remove Illumina adapter sequences using the following parameters: -q 25 –phred33 –length 35 -e 0.1 –stringency 4 –paired. Subsequently, these trimmed sequences were aligned to the reference genomes using bowtie2 (version 2.3.5.1, RRID:SCR_016368), with the mm10 reference genome utilized for mouse samples and hg19 reference genome for human samples. The resulting alignments were sorted using samtools (version 1.5, RRID:SCR_002105). To eliminate duplicate reads, sambamba (version 1.0.0, RRID:SCR_024328) was employed with the markdup -r option. Mitochondrial DNA reads were filtered out using the grep -v chrM command. Bed files were generated using bedtools (version 2.31.0, RRID:SCR_006646) bamtobed command. Peak calling was performed using macs2(version 2.1.0.20150731, RRID:SCR_013291) with the callpeak command and parameters set at -g mm/hs –nomodel -shift -100 -extsize 200. For further analysis, read counts were normalized by calculating reads per kilobase of bin per million reads (RPKM) using deeptools(version 3.3.2, RRID:SCR_016366) bamCoverage with the –normalizeUsing RPKM option.
Assembly: Mouse mm10
Supplementary files format and content: bw files for each sample

extract_protocol:
In brief, the sample was transferred from DMEM+10% FBS to a pre-chilled 2 ml Dounce (Sigma-Aldrich, USA) containing 1 ml of cold 1×homogenization buffer (HB) and thawed for 5 min. The sample was homogenized using an "A" loose pestle until resistance subsided (approximately 10 strokes), followed by further homogenization with a "B" tight pestle for an additional 20 strokes. The homogenate was filtered using a 70 µm Flowmi (Biosharp, China) strainer during transfer to a pre-chilled 2 ml LoBind tube (Eppendorf, USA). Nuclei were pelleted by centrifugation for 5 min at 4 °C and 350 RCF in a fixed-angle centrifuge (Eppendorf, USA). Aspirate the supernatant and discard until a volume of 50ul of liquid remains in the tube. The nuclei were gently resuspended in a total volume of 400 µl of 1×HB. An equal volume (400 µl) of 50% Iodixanol Solution (Sigma-Aldrich, USA) was added and thoroughly mixed by pipetting. A layer of 600 µl of 30% Iodixanol solution was carefully added underneath the 25% mixture, followed by a layer of 600 µl of 40% Iodixanol solution under the 30% mixture. The layered mixtures were then centrifuged for 20 min at 4 °C and 3,000 RCF in a pre-chilled swinging bucket centrifuge with the brake switched off. Care was taken to handle the tubes gently to avoid disturbing the gradient. The nuclei band was collected using a 200 µl volume and transferred to a fresh tube. The nuclei were then diluted by adding 500 µl of ATAC-RSB-Tween Buffer.
The nuclei were enumerated using acridine orange/propidium iodide (AO/PI) (Sigma-Aldrich, USA) staining at a 1:1 ratio of AO/PI to the sample, and an automated cell counter hemocytometer (Countstar, China). Subsequently, 50,000 nuclei were transferred into a 1.5 ml LoBind tube containing 1000 μl of ATAC-RSB-Tween Buffer. The nuclei were centrifuged for 10 min at 500 RCF at 4 °C in a fixed-angle centrifuge. After discarding the supernatant, the nuclei were resuspended in 35 μl of ddH2O and transferred into an EP tube. ATAC-seq library preparation was conducted using the TruePrep DNA Library Prep Kit V2 for Illumina TD501(Vazyme, China). A volume of 15 μl of Tn5 reaction mix (10 μl of 5×TTBL and 5 μl of TTE Mix V50) was added following the kit instructions and thoroughly mixed. The mixture was incubated at 37 °C for 30 min. The resulting product was purified using a MinElute column (MinElute PCR Purification Kit, Qiagen, Germany). The PCR reaction setup included the purified fragmented DNA (24 μl), 5×TAB (10 μl), PPM (5 μl), N5** (5 μl), N7** (5 μl), and TAE (1 μl). PCR amplification was carried out according to the recommended protocol in the manual. The number of cycles was determined based on pre-experiment qPCR, set at 12 cycles, calculated as the cycle number at which the curve reaches the plateau phase in qPCR plus 5. Subsequently, the DNA product was purified again using a MinElute column (MinElute PCR Purification Kit, Qiagen, Germany). DNA sorting was performed using VAHTS DNA Clean Beads (N411 Vazyme) according to the 0.55×/1.0×scheme. Fragmentation analysis of the DNA was conducted using a Cartridge Kit (BiOptic, Taiwan). Finally, the libraries were sequenced using Illumina NovaSeq 6000 sequencing.


title: Murine CNS Treg from EAE Recovery (250 cells) BioRep1

description: Library name: CNS_Rec_R1

value: EAE Recovery


title: Murine VAT Treg from Naive Stage (250 cells) BioRep3

description: Library name: VAT_Naive_R3

value: Visceral adipose tissue


title: Ind4_CX_0.1_3

description: Library name: iPSC-CM_Ind4_CX_0.1_3


title: Day5, body,male, rep1

description: Library name: 5D_B_M_1

value: Body


title: CKO-mT-1

description: Library name: Sample 1

value: Tmsb4x Conditional Knockout

value: mTBI


title: Ind4_CX_0.1_24

description: Library name: iPSC-CM_Ind4_CX_0.1_24


title: Ind4_DOX_0.1_3

description: Library name: iPSC-CM_Ind4_DOX_0.1_3


title: Murine CNS Treg from EAE Recovery (250 cells) BioRep2

description: Library name: CNS_Rec_R2

value: CNS

value: Treg

value: 250 cells

value: Foxp3-GFP mice (C57BL/6)

value: Bio rep 2


title: Murine CNS Treg from Naive Stage (250 cells) BioRep1

description: Library name: CNS_Naive_R1

value: Naïve

value: Bio rep 1


title: Day5, body, female, rep2

description: Library name: 5D_B_F_3


title: Ind4_CX_0.5_48

description: Library name: iPSC-CM_Ind4_CX_0.5_48


title: Day5,head, female, rep2

description: Library name: 5D_H_F_3

value: Head


title: Day5,head, male, rep2

description: Library name: 5D_H_M_3

value: Male


title: Murine Spleen Treg from EAE Recovery BioRep5

description: Library name: SPL_Treg_Rec_R5

value: Spleen

value: 2000 cells

value: Bio rep 5


title: Day5, body, female, rep1

description: Library name: 5D_B_F_1

value: Female


title: mT-1

description: Library name: Sample 1

value: Hippocampus


title: Murine CNS Treg from EAE Peak (250 cells) BioRep2

description: Library name: CNS_Peak_R2

value: EAE Peak


title: Ind4_CX_0.5_24

description: Library name: iPSC-CM_Ind4_CX_0.5_24

value: male

value: induced pluripotent stem cell-derived cardiomyocytes


title: s-2

description: Library name: Sample 5

value: Sham


title: Day5,reproductive, female, rep1

description: Library name: 5D_O_F_1

value: Reproductive


title: Murine Spleen Treg from EAE Recovery BioRep4

description: Library name: SPL_Treg_Rec_R4

value: Treg

value: EAE Recovery

value: Bio rep 4


title: Ind4_CX_0.5_3

description: Library name: iPSC-CM_Ind4_CX_0.5_3


title: BAV_217

city: nanjing

first: yuanyuan

last: wang

address: 818 Tianyuan E Rd, Nanjing, JIANGSU

institute: nanjing medical university

description: Library name: Sample 21

data_processing:
The RNA sequencing data was aligned to the reference genome (hg19) using STAR.
Assembly: hg19
Supplementary files format and content: Tab-separated values files

source_name: aortic valve leaflets

growth_protocol: collect aortic valve leaflets of the bicuspid aortic valve(BAV), tricuspid aortic valve(TAV) and control samples.

extract_protocol:
Total RNAs was extracted from aortic valve leaflets using RNAiso Plus (Takara, 9109). Magnetic beads with oligo-dT were using to isolate mRNA from total RNA.
Library was performed according to the manufacter’s instructions.

value: aortic valve leaflets

tag: group

value: BAV


title: Ind3_VEH_0.1_48

description: Library name: iPSC-CM_Ind3_VEH_0.1_48

value: female


title: BAV_162

description: Library name: Sample 20


title: BMDM, HDL, Control_4

first: Kasey

last: Vickers

address: 2220 Pierce Ave, PRB 312

institute: VUMC

description: Library name: Control_4

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt (v4.8)
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC (v0.12.1)(www.bioinformatics.babraham.ac.uk/projects/fastqc)
Reads were aligned to the Gencode GRCm38.p6 genome using STAR (v2.7.11a). Gencode vM25 gene annotations were provided to STAR to improve the accuracy of mapping. featureCounts (v2.0.6) was used to count the number of mapped reads to each gene.
ComplexHeatmap was used for cluster analysis and visualization. Significantly differential expressed genes with absolute fold change >= 1.5 and FDR adjusted p value <= 0.05 were detected by DESeq2 (v1.42.1)
Genome Ontology and KEGG pathway over-representation analysis was performed on differentially expressed genes using the WebGestaltR package (v1.0.0). Gene set enrichment analysis was performed using GSEA package (v4.3.2) on database (v2022.1.Hs)
Assembly: mouse GRCm38.p6
Supplementary files format and content: tsv file includes fpkm for each sample

source_name: Mouse bone marrow

growth_protocol: Murine bone marrow cells were isolated from the femurs and tibiae of mice and cultured for seven days in treated cell culture plates. Cells were maintained in DMEM supplemented with 10% heat-inactivated fetal bovine serum (Thermo Fisher), 1% penicillin/streptomycin (Gibco), L-glutamine (300 mg/L, Thermo Fisher), sodium pyruvate (110 mg/L), and mGM-CSF (40 ng/ml, PeproTech) for bone marrow-derived macrophage differentiation.

extract_protocol:
Total cellular RNA was isolated using Total RNA Purification kits (Norgen)
Libraries were generated using the NEBNext Ultra II Directional RNA library prep kit for Illumina with multiplex oligos set 1 (NEB).

treatment_protocol: Cells were treated with healthy control or CAC native HDL (1mg/mL) for 6h

value: Mouse bone marrow

value: Bone marrow derived macrophages

value: HDL, Control


title: BMDM, HDL, CAC_8

description: Library name: CAC_8

value: HDL, CAC>21


title: CKO-mT-2

description: Library name: Sample 2

value: Tmsb4x Conditional Knockout

value: mTBI


title: Day5,head, female, rep1

description: Library name: 5D_H_F_1

value: Head

value: Female


title: BMDM, HDL, CAC_7

description: Library name: CAC_7


title: s-3

description: Library name: Sample 6

value: Hippocampus


title: Ind3_VEH_0.5_48

description: Library name: iPSC-CM_Ind3_VEH_0.5_48

value: induced pluripotent stem cell-derived cardiomyocytes


title: Murine CNS Treg from Naive Stage (250 cells) BioRep2

description: Library name: CNS_Naive_R2

value: CNS

value: 250 cells

value: Foxp3-GFP mice (C57BL/6)

value: Naïve

value: Bio rep 2


title: Day5, body,male, rep2

description: Library name: 5D_B_M_3

value: Body

value: Male


title: Murine Spleen Treg from EAE Peak BioRep3

description: Library name: SPL_Treg_Peak_R3

value: Spleen

value: Treg

value: 2000 cells

value: EAE Peak

value: Bio rep 3


title: BAV_27

description: Library name: Sample 17

value: aortic valve leaflets

value: BAV


title: Ind3_VEH_0.5_3

description: Library name: iPSC-CM_Ind3_VEH_0.5_3

value: female


title: Ind3_DOX_0.5_48

description: Library name: iPSC-CM_Ind3_DOX_0.5_48


title: Murine Spleen Treg from EAE Peak BioRep2

description: Library name: SPL_Treg_Peak_R2


title: mT-3

description: Library name: Sample 3

value: Hippocampus

value: mTBI


title: BMDM, HDL, CAC_5

description: Library name: CAC_5

value: Mouse bone marrow

value: Bone marrow derived macrophages

value: HDL, CAC>21


title: Murine Spleen Treg from EAE Recovery BioRep3

description: Library name: SPL_Treg_Rec_R3

value: Foxp3-GFP mice (C57BL/6)

value: EAE Recovery


title: BAV_297

description: Library name: Sample 15

value: Female


title: Ind3_VEH_0.1_3

description: Library name: iPSC-CM_Ind3_VEH_0.1_3

value: induced pluripotent stem cell-derived cardiomyocytes


title: BAV_313

description: Library name: Sample 22


title: BAV_265

description: Library name: Sample 14

value: Male