title: WT_Con_H3K27ac_HiChIP_SET2_rep2

description: Library name: WT_Con_H3K27ac_HiChIP_SET2_rep2


title: Caco-2.batch1.IMZ.rep3.A05

status: Public on Jul 01 2026

type: SRA

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

description: Library name: Caco2_Batch1_IMZ_3_A05

library_source: other

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

molecule: other

organism: Homo sapiens

source_name: cell lysate

growth_protocol: from ms

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

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

tag: tissue

value: colon

tag: cell line

tag: cell type

value: epithelial

tag: genotype

value: cell line

tag: treatment


title: VV(2e6)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E6 pfu it, rep3, day7

city: Ibaraki

first: Kentaro

last: Ikegami

address: 21 Miyukigaoka, Tsukuba

country: Japan

institute: Astellas Pharma Inc.

description: Library name: A0024

library_source: transcriptomic

data_processing:
The sequencing reads were aligned onto the mm10 genome sequence using open-source software (Spliced Transcripts Alignment to a Reference, ver. 2.7.10b). Reads were counted for each gene for each sample using Rotational Scanning Electron Micrographs.
Assembly: mm10
Supplementary files format and content: The TSV file is an output file from RSEM and contains values such as raw read counts and TPM for each gene.

molecule: total RNA

organism: Mus musculus

source_name: LLC1 tumor

extract_protocol:
Tumor tissues were harvested and quickly suspended in an RNA extraction solution (ISOGEN). Total RNA was isolated according to the manufacturer’s instructions. Total RNA (>1 ug) was used as input for mRNA enrichment using a sequencing kit (SMART-Seq v4 Ultra Low Input RNA Kit).
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA Library Prep Kit following manufacturer's protocols.

value: LLC1 tumor

tag: time


title: WT_Con_H3K27ac_HiChIP_SET2_rep1

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

country: South Korea

institute: Yonsei University College of Medicine

description: Library name: WT_Con_H3K27ac_HiChIP_SET2_rep1

library_source: genomic

data_processing:
Paired-end Hi-C sequencing reads were processed using HiC-Pro (v2.11.4).
Chromatin loops from HiChIP data were identified using FitHiChIP (v8.0). Loop calling was performed in peak-to-all mode (IntType=3) using paired ChIP-seq peaks as input. The bin size was set to 5kb (default), with interaction distance range defined as 10kb to 2Mb. Bias correction was enabled using coverage normalization, and peak-to-all background was used for contact probability estimation (UseP2PBackgrnd = 0). Loops were identified at a threshold of Q-value < 0.00001 for H3K27Ac HiChIP data, Q-value < 0.01 for ATF4 HiChIP data.
Assembly: hg19
Supplementary files format and content: hic contaning validpairs
Library strategy: HiChIP

molecule: genomic DNA

growth_protocol: The human colorectal cancer cell line HCT116 was cultured in RPMI-1640 medium (Welgene) supplemented with 10% fetal bovine serum (FBS; HyClone) and 1% penicillin–streptomycin (Welgene) at 37 ℃ in a humidified incubator containing 5% CO2. Cells were subcultured every 48–72 h.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at room temperature and quenched using 0.125 M glycine for 5 min, followed by washing with cold PBS. After cell lysis, cross-linked chromatin was digested with the DpnII restriction enzyme, with enzyme amounts adjusted in proportion to the number of cells, followed by fill-in with biotin-14-dATP (Jena Bioscience) and proximity ligation. The resulting ligation products were sheared by sonication using a Qsonica sonicator (30 s ON/30 s OFF, 10 cycles) and incubated overnight at 4 ℃ with either an H3K27ac antibody (Abcam, ab4729) or an ATF4 antibody (Cell Signaling Technology, 11815). After sequential washes with standard ChIP wash buffers, chromatin–antibody complexes were reverse cross-linked overnight. De-cross-linked DNA was purified and quantified using Qubit dsDNA HS Assay Kit (Invitrogen, Q32854) and 5 ng of DNA was subjected to biotin pull-down using a streptavidin C-1 magnetic beads.
Tagmentation was directly performed on bead-bound DNA with Tn5 transposase with enzyme amounts adjusted according to the DNA input, followed by washing with appropriate buffers. Tagmented DNA was released from the beads by a simplified PCR procedure and further amplified using Nextera PCR primers. Amplified libraries were size-selected and purified using AMPure XP beads (0.5x–0.75x).

treatment_protocol: Cells were treated with tunicamycin (Sigma-Aldrich) at a final concentration of 0.5 µg ml-1 for 6 h. Cells treated with 0.1% DMSO for the same duration served as vehicle controls.

tag: chip antibody

value: H3K27ac (Abcam #Ab4729)

value: Human colorectal cancer

value: WT

value: 0.1% DMSO


title: VV(2e6)+OXP: oxaliplatin ip, hIL-7/mIL-12-VV 2E6 pfu it, rep1, day7

description: Library name: A0025


title: Caco-2.batch1.IMZ.rep2.H05

description: Library name: Caco2_Batch1_IMZ_2_H05


title: WT_Tm_H3K27ac_HiChIP_SET1_rep2

description: Library name: WT_Tm_H3K27ac_HiChIP_SET1_rep2

value: 0.5 μg/ml tunicamycin


title: WT_Tm_H3K27ac_HiChIP_SET1_rep1

description: Library name: WT_Tm_H3K27ac_HiChIP_SET1_rep1


title: VV(2e6)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E6 pfu it, rep2, day7

description: Library name: A0023


title: Caco-2.batch1.IMZ.rep2.G05

description: Library name: Caco2_Batch1_IMZ_2_G05


title: WT_Con_H3K27ac_HiChIP_SET1_rep2

description: Library name: WT_Con_H3K27ac_HiChIP_SET1_rep2


title: WT_Con_H3K27ac_HiChIP_SET1_rep1

description: Library name: WT_Con_H3K27ac_HiChIP_SET1_rep1


title: VV(2e6)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E6 pfu it, rep1, day7

description: Library name: A0022


title: NFIL3_KO_Tm_RNA_SET5_rep3

description: Library name: NFIL3_KO_Tm_RNA_SET5_rep3

data_processing:
Paired-end sequencing reads were trimmed using TrimGalore (v0.6.4)
The trimmed reads were aligned to the human reference genome hg19 using STAR (v2.6.0c)61 with the parameters --chimSegmentMin 20 --twopassMode Basic --quantMode TranscriptomeSAM.
Reads counts at gene-levels are quantified using RSEM (v1.3.1)62 and normalized to transcripts per million (TPM).
Strand specific reads were selected using SAMtools (v1.3.1), and genome-wide coverage tracks were generated using deepTools (v3.4.3).
hg19
Assembly: RSEM output files including raw counts, TPM values
Supplementary files format and content: normalized bigwig

extract_protocol:
Total RNA was extracted from wild-type HCT116 and transcription factor knockout cells using RiboEx (GeneAll Biotechnology)
Sequencing libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, E7760) following the manufacturer’s protocol.

value: 0.5 μg ml tunicamycin


title: NFIL3_KO_Tm_RNA_SET5_rep2

description: Library name: NFIL3_KO_Tm_RNA_SET5_rep2


title: Caco-2.batch1.IMZ.rep2.F05

description: Library name: Caco2_Batch1_IMZ_2_F05


title: Caco-2.batch1.IMZ.rep2.E05

description: Library name: Caco2_Batch1_IMZ_2_E05


title: OXP: oxaliplatin ip, PBS it. rep3, day7

description: Library name: A0021


title: NFIL3_KO_Tm_RNA_SET5_rep1

description: Library name: NFIL3_KO_Tm_RNA_SET5_rep1


title: NFIL3_KO_Con_RNA_SET5_rep3

description: Library name: NFIL3_KO_Con_RNA_SET5_rep3


title: OXP: oxaliplatin ip, PBS it. rep2, day7

description: Library name: A0020


title: Caco-2.batch1.IMZ.rep2.D05

description: Library name: Caco2_Batch1_IMZ_2_D05


title: NFIL3_KO_Con_RNA_SET5_rep1

description: Library name: NFIL3_KO_Con_RNA_SET5_rep1


title: OXP: oxaliplatin ip, PBS it. rep1, day7

description: Library name: A0019


title: NFIL3_KO_Con_RNA_SET5_rep2

description: Library name: NFIL3_KO_Con_RNA_SET5_rep2


title: WT_Tm_RNA_SET5_rep3

description: Library name: WT_Tm_RNA_SET5_rep3


title: Caco-2.batch1.IMZ.rep2.C05

description: Library name: Caco2_Batch1_IMZ_2_C05


title: WT_Tm_RNA_SET5_rep2

description: Library name: WT_Tm_RNA_SET5_rep2


title: WT_Tm_RNA_SET5_rep1

description: Library name: WT_Tm_RNA_SET5_rep1


title: vehicle: 5%glucose ip, PBS it, rep3, day7

description: Library name: A0018


title: Caco-2.batch1.IMZ.rep2.B05

description: Library name: Caco2_Batch1_IMZ_2_B05


title: Caco-2.batch1.IMZ.rep2.A05

description: Library name: Caco2_Batch1_IMZ_2_A05


title: WT_Con_RNA_SET5_rep3

description: Library name: WT_Con_RNA_SET5_rep3


title: vehicle: 5%glucose ip, PBS it, rep2, day7

description: Library name: A0017


title: WT_Con_RNA_SET5_rep2

description: Library name: WT_Con_RNA_SET5_rep2


title: WT_Con_RNA_SET5_rep1

description: Library name: WT_Con_RNA_SET5_rep1


title: XBP1_KO_Tm_RNA_SET2_rep3

description: Library name: XBP1_KO_Tm_RNA_SET2_rep3


title: vehicle: 5%glucose ip, PBS it, rep1, day7

description: Library name: A0016


title: Caco-2.batch1.IMZ.rep1.H05

description: Library name: Caco2_Batch1_IMZ_1_H05


title: VV(2e7)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E7 pfu it, rep3, day3

description: Library name: A0015


title: XBP1_KO_Tm_RNA_SET2_rep1

description: Library name: XBP1_KO_Tm_RNA_SET2_rep1


title: XBP1_KO_Tm_RNA_SET2_rep2

description: Library name: XBP1_KO_Tm_RNA_SET2_rep2


title: Caco-2.batch1.IMZ.rep1.G05

description: Library name: Caco2_Batch1_IMZ_1_G05


title: XBP1_KO_Con_RNA_SET2_rep3

description: Library name: XBP1_KO_Con_RNA_SET2_rep3


title: XBP1_KO_Con_RNA_SET2_rep2

description: Library name: XBP1_KO_Con_RNA_SET2_rep2


title: VV(2e7)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E7 pfu it, rep2, day3

description: Library name: A0014


title: XBP1_KO_Con_RNA_SET2_rep1

description: Library name: XBP1_KO_Con_RNA_SET2_rep1


title: Caco-2.batch1.IMZ.rep1.F05

description: Library name: Caco2_Batch1_IMZ_1_F05


title: Caco-2.batch1.IMZ.rep1.E05

description: Library name: Caco2_Batch1_IMZ_1_E05


title: VV(2e7)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E7 pfu it, rep1, day3

description: Library name: A0013


title: ATF6_KO_Tm_RNA_SET2_rep2

description: Library name: ATF6_KO_Tm_RNA_SET2_rep2


title: ATF6_KO_Tm_RNA_SET2_rep3

description: Library name: ATF6_KO_Tm_RNA_SET2_rep3


title: VV(2e6)+OXP: oxaliplatin ip, hIL-7/mIL-12-VV 2E6 pfu it, rep3, day3

description: Library name: A0012


title: ATF6_KO_Tm_RNA_SET2_rep1

description: Library name: ATF6_KO_Tm_RNA_SET2_rep1


title: Caco-2.batch1.IMZ.rep1.D05

description: Library name: Caco2_Batch1_IMZ_1_D05


title: VV(2e6)+OXP: oxaliplatin ip, hIL-7/mIL-12-VV 2E6 pfu it, rep2, day3

description: Library name: A0011


title: ATF6_KO_Con_RNA_SET2_rep3

description: Library name: ATF6_KO_Con_RNA_SET2_rep3


title: Caco-2.batch1.IMZ.rep1.C05

description: Library name: Caco2_Batch1_IMZ_1_C05


title: ATF6_KO_Con_RNA_SET2_rep2

description: Library name: ATF6_KO_Con_RNA_SET2_rep2


title: ATF6_KO_Con_RNA_SET2_rep1

description: Library name: ATF6_KO_Con_RNA_SET2_rep1


title: ATF4_KO_Tm_RNA_SET2_rep3

description: Library name: ATF4_KO_Tm_RNA_SET2_rep3


title: VV(2e6)+OXP: oxaliplatin ip, hIL-7/mIL-12-VV 2E6 pfu it, rep1, day3

description: Library name: A0010


title: ATF4_KO_Tm_RNA_SET2_rep2

description: Library name: ATF4_KO_Tm_RNA_SET2_rep2


title: ATF4_KO_Tm_RNA_SET2_rep1

description: Library name: ATF4_KO_Tm_RNA_SET2_rep1


title: Caco-2.batch1.IMZ.rep1.B05

description: Library name: Caco2_Batch1_IMZ_1_B05


title: Caco-2.batch1.IMZ.rep1.A05

description: Library name: Caco2_Batch1_IMZ_1_A05


title: ATF4_KO_Con_RNA_SET2_rep3

description: Library name: ATF4_KO_Con_RNA_SET2_rep3


title: VV(2e6)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E6 pfu it, rep2, day3

description: Library name: A0008


title: VV(2e6)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E6 pfu it, rep3, day3

description: Library name: A0009


title: ATF4_KO_Con_RNA_SET2_rep2

description: Library name: ATF4_KO_Con_RNA_SET2_rep2


title: Caco-2.batch1.IMI.rep3.H06

description: Library name: Caco2_Batch1_IMI_3_H06


title: ATF4_KO_Con_RNA_SET2_rep1

description: Library name: ATF4_KO_Con_RNA_SET2_rep1


title: Caco-2.batch1.IMI.rep3.G06

description: Library name: Caco2_Batch1_IMI_3_G06


title: WT_Tm_RNA_SET2_rep3

description: Library name: WT_Tm_RNA_SET2_rep3


title: WT_Tm_RNA_SET2_rep2

description: Library name: WT_Tm_RNA_SET2_rep2


title: VV(2e6)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E6 pfu it, rep1, day3

description: Library name: A0007


title: OXP: oxaliplatin ip, PBS it. rep3, day3

description: Library name: A0006


title: Caco-2.batch1.IMI.rep3.F06

description: Library name: Caco2_Batch1_IMI_3_F06


title: WT_Tm_RNA_SET2_rep1

description: Library name: WT_Tm_RNA_SET2_rep1


title: WT_Con_RNA_SET2_rep2

description: Library name: WT_Con_RNA_SET2_rep2


title: OXP: oxaliplatin ip, PBS it. rep2, day3

description: Library name: A0005


title: Caco-2.batch1.IMI.rep3.E06

description: Library name: Caco2_Batch1_IMI_3_E06


title: WT_Con_RNA_SET2_rep1

description: Library name: WT_Con_RNA_SET2_rep1


title: WT_Con_RNA_SET2_rep3

description: Library name: WT_Con_RNA_SET2_rep3


title: OXP: oxaliplatin ip, PBS it. rep1, day3

description: Library name: A0004


title: Caco-2.batch1.IMI.rep3.D06

description: Library name: Caco2_Batch1_IMI_3_D06


title: vehicle: 5%glucose ip, PBS it, rep3, day3

description: Library name: A0003


title: WT_Tm_RNA_SET1_rep2

description: Library name: WT_Tm_RNA_SET1_rep2


title: WT_Tm_RNA_SET1_rep1

description: Library name: WT_Tm_RNA_SET1_rep1


title: WT_Tm_RNA_SET1_rep3

description: Library name: WT_Tm_RNA_SET1_rep3


title: Caco-2.batch2.CAR.rep1.F04

description: Library name: Caco2_Batch2_CAR_1_F04


title: WT_Con_RNA_SET1_rep3

description: Library name: WT_Con_RNA_SET1_rep3


title: Caco-2.batch1.IMI.rep3.B06

description: Library name: Caco2_Batch1_IMI_3_B06


title: Caco-2.batch1.IMI.rep3.C06

description: Library name: Caco2_Batch1_IMI_3_C06


title: WT_Con_RNA_SET1_rep1

description: Library name: WT_Con_RNA_SET1_rep1


title: vehicle: 5%glucose ip, PBS it, rep2, day3

description: Library name: A0002


title: WT_Con_RNA_SET1_rep2

description: Library name: WT_Con_RNA_SET1_rep2


title: vehicle: 5%glucose ip, PBS it, rep1, day3

description: Library name: A0001


title: WT_Tm_HiC_rep2

description: Library name: WT_Tm_HiC_rep2

data_processing:
Paired-end Hi-C sequencing reads were processed using HiC-Pro (v2.11.4).
Assembly: hg19
Supplementary files format and content: hic contaning validpairs

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at room temperature and quenched using 0.125 M glycine for 5 min, followed by washing with cold PBS. After cell lysis, cross-linked chromatin was digested with the DpnII restriction enzyme, followed by fill-in with biotin-14-dATP (Jena Bioscience) and proximity ligation. The resulting ligation products were sheared by sonication using a Qsonica sonicator (30 s ON/30 s OFF, 10 cycles) and reverse cross-linked overnight. De-cross-linked DNA was purified and quantified using Qubit dsDNA HS Assay Kit (Invitrogen, Q32854) and 150 ng of DNA was subjected to biotin pull-down using a streptavidin C1 magnetic beads.
Tagmentation was directly performed on bead-bound DNA with Tn5 transposase with enzyme amounts adjusted according to the DNA input, followed by washing with appropriate buffers. Tagmented DNA was released from the beads by a simplified PCR procedure and further amplified using Nextera PCR primers. Amplified libraries were size-selected and purified using AMPure XP beads (0.5x–0.75x).


title: Caco-2.batch1.IMI.rep3.A06

description: Library name: Caco2_Batch1_IMI_3_A06


title: WT_Tm_HiC_rep1

description: Library name: WT_Tm_HiC_rep1


title: VV(2e7)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E7 pfu it, rep3

description: Library name: G-3


title: WT_Con_HiC_rep2

description: Library name: WT_Con_HiC_rep2


title: Caco-2.batch1.IMI.rep2.H06

description: Library name: Caco2_Batch1_IMI_2_H06


title: VV(2e7)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E7 pfu it, rep2

description: Library name: G-2


title: WT_Con_HiC_rep1

description: Library name: WT_Con_HiC_rep1


title: WT_Tm_XBP1_rep2

description: Library name: WT_Tm_XBP1_rep2

data_processing:
Paired-end ChIP-seq reads were trimmed using TrimGalore.
Trimmed reads were aligned to the human hg19 reference genome using BWA (v0.7.17) with default parameters.
Low-quality alingments were filtered using SAMtools with the parameters q 30 –F 1804 –f 2, and duplicate reads were marked using Picard (v2.18.23) with MarkDuplicates function. Uniquely mapped reads were normalized to counts per million (CPM) DNA and duplicate reads were then removed using SAMtools.
Uniquely mapped reads were normalize to generate bigwig file.
Peaks were called for each biological replicate using MACS2 (v2.2.7.1) with the parameters callpeak -f BAMPE --nomodel -g hg19 -q 0.001 --narrow.
Assembly: hg19
Supplementary files format and content: narrowPeak, CPM normalized bigwig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at room temperature and quenched using 0.125 M glycine for 5 min, followed by washing with cold PBS. After cell lysis, chromatin was sheared by sonication using a Qsonica sonicator(30 s ON/30 s OFF, 10 cycles, repeated three times). Lysates were pre-cleared by incubation with protein A/G magnetic beads (Invitrogen) prior to immunoprecipitation. Pre-cleared chromatin was incubated overnight at 4 ℃ with the indicated antibodies.
Tagmentation was then performed directly on bead-bound chromatin using the Nextera DNA Library Prep kit (Illumina) followed by two washes to remove excess transposase. Bead-bound chromatin was incubated overnight  for reverse cross-linking, and the recovered DNA was PCR-amplified using Nextera PCR primers. Amplified libraries were size-selected and purified using AMPure XP beads (0.65x–0.9x)

value: XBP1 (Biolegend, #647502)


title: VV(2e7)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E7 pfu it, rep1

description: Library name: G-1


title: Caco-2.batch1.IMI.rep2.G06

description: Library name: Caco2_Batch1_IMI_2_G06


title: WT_Tm_XBP1_rep1

description: Library name: WT_Tm_XBP1_rep1


title: WT_Con_XBP1_rep2

description: Library name: WT_Con_XBP1_rep2


title: WT_Con_XBP1_rep1

description: Library name: WT_Con_XBP1_rep1


title: VV(2e6)+OXP: oxaliplatin ip, hIL-7/mIL-12-VV 2E6 pfu it, rep3

description: Library name: E-3


title: Caco-2.batch1.IMI.rep2.F06

description: Library name: Caco2_Batch1_IMI_2_F06


title: WT_Tm_ATF6_rep2

description: Library name: WT_Tm_ATF6_rep2

value: ATF6 (Abcam #Ab227830)


title: Caco-2.batch1.IMI.rep2.E06

description: Library name: Caco2_Batch1_IMI_2_E06


title: Caco-2.batch1.IMI.rep2.D06

description: Library name: Caco2_Batch1_IMI_2_D06


title: WT_Tm_ATF6_rep1

description: Library name: WT_Tm_ATF6_rep1


title: VV(2e6)+OXP: oxaliplatin ip, hIL-7/mIL-12-VV 2E6 pfu it, rep2

description: Library name: E-2


title: WT_Con_ATF6_rep1

description: Library name: WT_Con_ATF6_rep1


title: WT_Con_ATF6_rep2

description: Library name: WT_Con_ATF6_rep2


title: VV(2e6)+OXP: oxaliplatin ip, hIL-7/mIL-12-VV 2E6 pfu it, rep1

description: Library name: E-1


title: Caco-2.batch1.IMI.rep2.C06

description: Library name: Caco2_Batch1_IMI_2_C06


title: CHOP_KO_Tm_H3K27ac_SET3_rep2

description: Library name: CHOP_KO_Tm_H3K27ac_SET3_rep2


title: VV(2e6)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E6 pfu it, rep3

description: Library name: D-3


title: WT_Tm_H3K27ac_SET3_rep2

description: Library name: WT_Tm_H3K27ac_SET3_rep2


title: WT_Tm_H3K27ac_SET3_rep1

description: Library name: WT_Tm_H3K27ac_SET3_rep1


title: Caco-2.batch1.IMI.rep2.B06

description: Library name: Caco2_Batch1_IMI_2_B06


title: VV(2e6)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E6 pfu it, rep2

description: Library name: D-2


title: CHOP_KO_Tm_H3K27ac_SET3_rep1

description: Library name: CHOP_KO_Tm_H3K27ac_SET3_rep1


title: Caco-2.batch1.IMI.rep2.A06

description: Library name: Caco2_Batch1_IMI_2_A06


title: XBP1_KO_Tm_H3K27ac_SET2_rep1

description: Library name: XBP1_KO_Tm_H3K27ac_SET2_rep1


title: VV(2e6)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E6 pfu it, rep1

description: Library name: D-1


title: ATF6_KO_Tm_H3K27ac_SET2_rep2

description: Library name: ATF6_KO_Tm_H3K27ac_SET2_rep2


title: XBP1_KO_Tm_H3K27ac_SET2_rep2

description: Library name: XBP1_KO_Tm_H3K27ac_SET2_rep2


title: Caco-2.batch1.IMI.rep1.H06

description: Library name: Caco2_Batch1_IMI_1_H06


title: OXP: oxaliplatin ip, PBS it, rep3

description: Library name: B-3


title: ATF4_KO_Tm_H3K27ac_SET2_rep2

description: Library name: ATF4_KO_Tm_H3K27ac_SET2_rep2


title: WT_Tm_H3K27ac_SET2_rep2

description: Library name: WT_Tm_H3K27ac_SET2_rep2


title: OXP: oxaliplatin ip, PBS it, rep2

description: Library name: B-2


title: ATF4_KO_Tm_H3K27ac_SET2_rep1

description: Library name: ATF4_KO_Tm_H3K27ac_SET2_rep1


title: Caco-2.batch1.IMI.rep1.G06

description: Library name: Caco2_Batch1_IMI_1_G06


title: Caco-2.batch1.IMI.rep1.F06

description: Library name: Caco2_Batch1_IMI_1_F06


title: ATF6_KO_Tm_H3K27ac_SET2_rep1

description: Library name: ATF6_KO_Tm_H3K27ac_SET2_rep1


title: WT_Tm_H3K27ac_SET2_rep1

description: Library name: WT_Tm_H3K27ac_SET2_rep1


title: Caco-2.batch1.IMI.rep1.E06

description: Library name: Caco2_Batch1_IMI_1_E06


title: WT_Tm_H3K27ac_SET1_rep2

description: Library name: WT_Tm_H3K27ac_SET1_rep2


title: OXP: oxaliplatin ip, PBS it, rep1

description: Library name: B-1


title: WT_Tm_H3K27ac_SET1_rep1

description: Library name: WT_Tm_H3K27ac_SET1_rep1


title: vehicle: 5%glucose ip, PBS it, rep3

description: Library name: A-3


title: CHOP_KO_Con_H3K27ac_SET3_rep2

description: Library name: CHOP_KO_Con_H3K27ac_SET3_rep2


title: T cells, PRMT7 KO, replicate 2

city: Montréal

first: Stéphane

last: Richard

state: Québec

address: 3755 Côte Ste-Catherine Road

department: Departments of Oncology and Medicine

institute: Lady Davis Institute - JGH, McGill University

description: Library name: PRMT7KO2

data_processing:
Sequenced reads were first trimmed with Trimmomatic-0.39 to remove the adapter sequence and then mapped to the mouse genome (mm10) through STAR v2.7.11b
Read counts were quantified and normalized through Cufflinks v2.2.1
Assembly: mm10
Supplementary files format and content: xlsx: normalized gene read counts for each sample

molecule: polyA RNA

source_name: Splenocytes from mice

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Mini kit (Ref:74104) according to the manufacturer’s instructions.
Library preparation: polyA- enriched RNA (stranded). Sequencing Type: Illumina NovaSeq PE100 25M. Sequencing fraction: 2 per sample. Primary analysis: Dragen RNA.

value: Splenocytes from mice

value: PRMT7 KO


title: T cells, WT PROTAC, replicate 2

description: Library name: WTPROTAC2

value: WT PROTAC


title: CHOP_KO_Con_H3K27ac_SET3_rep1

description: Library name: CHOP_KO_Con_H3K27ac_SET3_rep1


title: Caco-2.batch1.IMI.rep1.D06

description: Library name: Caco2_Batch1_IMI_1_D06


title: Multiome, central amygdala, RT00287N, CON, human, GEX

city: New Haven

first: Matthew

last: Girgenti

state: CT

address: 34 Park St

department: Psychiatry

country: USA

institute: Yale University

description: Library name: RT00287N_GEX

library_source: transcriptomic single cell

data_processing:
Multiome files were demultiplexed using Cellranger-arc mkfastq
Assembly: hg38
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5,  atac_fragments.tsv.gz

source_name: Central Amygdala

extract_protocol:
Nuclei were isolated from fresh-frozen human central amygdala tissue and purified to generate single-nucleus suspensions for simultaneous chromatin accessibility and gene-expression profiling.
Single-nucleus multiome libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression workflow, which constructs matched ATAC-seq (genomic DNA accessibility) and gene-expression (polyA nuclear RNA) libraries from the same nucleus.

value: Central Amygdala

value: control

tag: batch


title: vehicle: 5%glucose ip, PBS it, rep2

description: Library name: A-2


title: WT_Con_H3K27ac_SET3_rep2

description: Library name: WT_Con_H3K27ac_SET3_rep2


title: WT_Con_H3K27ac_SET3_rep1

description: Library name: WT_Con_H3K27ac_SET3_rep1


title: vehicle: 5%glucose ip, PBS it, rep1

description: Library name: A-1


title: Caco-2.batch1.IMI.rep1.C06

description: Library name: Caco2_Batch1_IMI_1_C06

value: colon


title: XBP1_KO_Con_H3K27ac_SET2_rep2

description: Library name: XBP1_KO_Con_H3K27ac_SET2_rep2


title: mHp_Skin_5

city: Princeton

first: Krist

last: Antunes Fernandes

state: NJ

address: 215 Ewig St

department: MOLBIO

institute: Princeton University

description: Library name: H40

data_processing:
Novogene’s RNA-seq pipeline.
Assembly: GRCm38/mm10
Supplementary files format and content: csv files include count and FPKM values for each samples.

source_name: Epithelial

extract_protocol:
Total RNA was extracted using the RNeasy Micro Kit according to the manufacturer’s instructions.
Library construction was performed using the NEBNext® Ultra™ II RNA Library Prep Kit

treatment_protocol: Epithelial cells were isolated from the lung, small intestine, and skin and sorted directly into lysis buffer for RNA extraction.

value: Skin

value: Keratinocytes


title: XBP1_KO_Con_H3K27ac_SET2_rep1

description: Library name: XBP1_KO_Con_H3K27ac_SET2_rep1


title: Caco-2.batch1.IMI.rep1.A06

description: Library name: Caco2_Batch1_IMI_1_A06

value: epithelial

value: cell line


title: ATF6_KO_Con_H3K27ac_SET2_rep1

description: Library name: ATF6_KO_Con_H3K27ac_SET2_rep1

value: H3K27ac (Abcam #Ab4729)

value: Human colorectal cancer


title: Caco-2.batch1.IMI.rep1.B06

description: Library name: Caco2_Batch1_IMI_1_B06


title: Caco-2.batch1.GLY.rep3.H04

description: Library name: Caco2_Batch1_GLY_3_H04


title: ATF4_KO_Con_H3K27ac_SET2_rep2

description: Library name: ATF4_KO_Con_H3K27ac_SET2_rep2

value: 0.1% DMSO


title: mHp_Skin_4

description: Library name: H39


title: ATF4_KO_Con_H3K27ac_SET2_rep1

description: Library name: ATF4_KO_Con_H3K27ac_SET2_rep1


title: mHp_Skin_3

description: Library name: H38


title: Caco-2.batch1.GLY.rep3.G04

description: Library name: Caco2_Batch1_GLY_3_G04


title: mHp_Skin_2

description: Library name: H37


title: WT_Con_H3K27ac_SET1_rep2

description: Library name: WT_Con_H3K27ac_SET1_rep2

value: WT


title: WT_Con_H3K27ac_SET2_rep1

description: Library name: WT_Con_H3K27ac_SET2_rep1


title: Caco-2.batch1.GLY.rep3.F04

description: Library name: Caco2_Batch1_GLY_3_F04


title: WT_Con_H3K27ac_SET2_rep2

description: Library name: WT_Con_H3K27ac_SET2_rep2


title: mHp_Skin_1

description: Library name: H36


title: Caco-2.batch1.GLY.rep3.E04

description: Library name: Caco2_Batch1_GLY_3_E04


title: WT_Con_H3K27ac_SET1_rep1

description: Library name: WT_Con_H3K27ac_SET1_rep1


title: Input_rep1

description: Library name: Input_rep1

value: Not applied


title: mHp_SI_5

description: Library name: H35

value: Gut

value: Epithelial cells


title: WT_Tm_ATAC_rep2

description: Library name: WT_Tm_ATAC_rep2

data_processing:
Paired-end ChIP-seq reads were trimmed using TrimGalore.
Trimmed reads were aligned to the human hg19 reference genome using Bowtie2 (v2.3.5.1)70 with parameters --end-to-end --very-sensitive --maxins 2000
Low-quality alingments were filtered using SAMtools with the parameters q 30 –F 1804 –f 2, and duplicate reads were marked using Picard (v2.18.23) with MarkDuplicates function. Uniquely mapped reads were normalized to counts per million (CPM) DNA and duplicate reads were then removed using SAMtools. To correct Tn5 transposase-induced offset and to enrich nucleosome-free regions (NFRs), aligned reads were processed using the alignmentSieve function from deepTools with the parameters --maxFragmentLength 140 --ATACshift.
Uniquely mapped reads were normalize to generate bigwig file.
Peaks were called for each biological replicate using MACS2 (v2.2.7.1) with the parameters callpeak -f BAMPE --nomodel -g hg19 -q 0.001 --narrow.
Assembly: hg19
Supplementary files format and content: narrowPeak, CPM normalized bigwig

extract_protocol:
50,000 HCT116 cells were lysed on ice for 10min in lysis buffer containing 10mM Tris (pH 7.4), 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 1% Tween-20, and 0.01% digitonin. Nuclei were subsequently washed with the same buffer lacking NP-40 and digitonin.
Tagmentation was performed using the Nextera DNA Library Prep kit [Illumina, FC-121-1030] according to the manufacturer's instructions. The transposed DNA was purified using the MinElute PCR Purification Kit (QIAGEN, 28006). Purified tagmented DNA was PCR-amplified using Nextera PCR primers, followed by size selection and cleanup with AMPure XP beads (0.5x-1.8x).

value: 0.5 μg/ml tunicamycin


title: Caco-2.batch1.GLY.rep3.D04

description: Library name: Caco2_Batch1_GLY_3_D04


title: Input_rep2

description: Library name: Input_rep2


title: WT_Tm_ATAC_rep1

description: Library name: WT_Tm_ATAC_rep1


title: WT_Con_ATAC_rep2

description: Library name: WT_Con_ATAC_rep2


title: Caco-2.batch1.GLY.rep3.C04

description: Library name: Caco2_Batch1_GLY_3_C04


title: WT_Con_ATAC_rep1

description: Library name: WT_Con_ATAC_rep1


title: mHp_SI_4

description: Library name: H34


title: RNA-Seq_HK1_panobinostat_rep3

city: Fuzhou

first: Guosheng

last: Hu

state: Fujian

address: Fujian Normal University, Cangshan Campus, No.8 Shangsan Road, Cangshan District, Fuzhou, Fujian, China

department: College of Life Sciences

country: China

institute: Fujian normal university

description:
Library name: Sample 6
panobinostat

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg38 genome assembly using STAR version 2.7.10.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: HK1 cells were cultured in 1640 medium supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated using the Eastep Super Total RNA Extraction Kit following the manufacturer’s protocol. DNase I was included in the column digestion to ensure RNA quality.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed using an Illumina HiSeq 3000 system.

treatment_protocol: HK1 cells were treated with control or Panobinostat in 1640 medium supplemented with 10% FBS for three days.

value: panobinostat


title: Caco-2.batch1.GLY.rep3.B04

description: Library name: Caco2_Batch1_GLY_3_B04


title: Multiome, central amygdala, RT00282N, AUD, human, ATAC

description: Library name: RT00282N_ATAC

library_source: genomic single cell

value: alcohol use disorder


title: mHp_SI_2

description: Library name: H32


title: Caco-2.batch1.GLY.rep3.A04

description: Library name: Caco2_Batch1_GLY_3_A04


title: RNA-Seq_HK1_panobinostat_rep1

description:
Library name: Sample 4
panobinostat


title: RNA-Seq_HK1_panobinostat_rep2

description:
Library name: Sample 5
panobinostat


title: RNA-Seq_HK1_DMSO_rep3

description:
Library name: Sample 3
DMSO

value: DMSO


title: mHp_SI_1

description: Library name: H31


title: RNA-Seq_HK1_DMSO_rep2

description:
Library name: Sample 2
DMSO


title: mHp_Lung_5

description: Library name: H25

value: Lung


title: RNA-Seq_HK1_DMSO_rep1

description:
Library name: Sample 1
DMSO


title: GAS muscle, Ino, biol rep 3

city: Suwon

first: Ju-Hyeon

last: Bae

state: Gyeonggi-do

address: Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 2066

department: school of medicine

institute: Sungkyunkwan University

description: Library name: AI015

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Gastrocnemius muscle

extract_protocol:
Total RNA was harvested from GAS muscle using Easyblue reagent (Intron). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Aged male mice (20 months old) received daily oral administration of Ino (0.35 mg/kg) for 10 weeks. Control mice received Veh consisting of 40% polyethylene glycol (PEG), 5% Tween 80, and 0.9% normal saline.

value: Gastrocnemius muscle

value: Muscle

value: Inotodiol

tag: strain


title: mHp_Lung_4

description: Library name: H24


title: Caco-2.batch1.GLY.rep2.F04

description: Library name: Caco2_Batch1_GLY_2_F04

value: colon

value: epithelial


title: GAS muscle, Ino, biol rep 1

description: Library name: AI013


title: Caco-2.batch1.GLY.rep2.G04

description: Library name: Caco2_Batch1_GLY_2_G04

value: cell line


title: GAS muscle, Ino, biol rep 2

description: Library name: AI014


title: GAS muscle, Veh, biol rep 3

description: Library name: AV5

value: Vehicle


title: mHp_Lung_3

description: Library name: H23


title: GAS muscle, Veh, biol rep 2

description: Library name: AV4


title: GAS muscle, Veh, biol rep 1

description: Library name: AV3


title: mHp_Lung_2

description: Library name: H22


title: Caco-2.batch1.GLY.rep2.D04

description: Library name: Caco2_Batch1_GLY_2_D04


title: mHp_Lung_1

description: Library name: H21


title: MYCN+P53/PTEN KD,H3K27ac (ChIP)

city: Memphis

first: Stephen

middle: C

last: Mack

state: Tennessee

address: 262 Danny Thomas Place

institute: St. Jude Children’s Research Hospital

description: Library name: MYCN+P53/PTEN KD, H3K27ac ChIP

data_processing:
Raw paired-end sequencing reads were adapter and quality trimmed using Trimgalore. The trimmed reads were aligned to mouse genome (mm10) using Bowtie2 (v2.5.3),25 and duplicated reads were marked and removed using picard MarkDuplicates (v3.1.1) and Samtools (v1.19.2),respectively, with default parameters. Peaks were called on the resulting bam file using MACS2 (v2.2.9.1), with a q-value threshold of 0.05. Bigwig files were generated for visualization using deeptools (3.5.4).
Assembly: mm10
Supplementary files format and content: bigWig and narrowPeak

source_name: NPCs

extract_protocol:
Cell were collected and fixed using formaldehyde to cross-link and preserve protein/DNA interactions. DNA was then sheared by sonication followed by immunoprecipitation using N-Myc antibody (Active Motif, Cat.#61185) and H3K27ac antibody (ab4729). Cross-linking was then reversed, and ChIP DNA was purified.
ChIP-Seq libraries were generated from the ChIP-DNA using a custom Illumina library type on an automated system (Apollo 342, Wafergen Biosystems/Takara). ChIP-Seq libraries were sequenced on Illumina NextSeq 500 as 75-nt single end reads. Adapter sequences were not trimmed during demultiplexing.

value: NPCs

value: MYCN+P53/PTEN KD


title: P53/PTEN KD,H3K27ac (ChIP)

description: Library name: P53/PTEN KD, H3K27ac ChIP

value: P53/PTEN KD


title: Caco-2.batch1.GLY.rep2.C04

description: Library name: Caco2_Batch1_GLY_2_C04


title: P53/PTEN KD (Input)

description: Library name: P53/PTEN KD, Input


title: mCtr_Skin_5

description: Library name: C20

value: Skin

value: Keratinocytes


title: MYCN+P53/PTEN KD,N-Myc (ChIP), rep1

description: Library name: MYCN+P53/PTEN KD, rep1, N-Myc ChIP

value: N-Myc (Active Motif, Cat.#61185)


title: Caco-2.batch1.GLY.rep2.A04

description: Library name: Caco2_Batch1_GLY_2_A04


title: mESC-derived cortical neurons, day in vitro 12, PCDH19-ICD-OE, rep 2

city: Leioa

first: Sylvia Adriana

last: Newbold

state: Bizkaia

address: Science Park of EHU, Sede building

country: Spain

institute: Achucarro Basque Center for Neuroscience

description: Library name: DIV12_19ICD_2

data_processing:
Paired end reads from Illumina sequencing were trimmed of adaptor sequences with Trim Galore and assessed for quality using FastQC, using default parameters. Reads were mapped to the mouse GRCm38 reference genome using STAR (Dobin et al., 2012) and counts were assigned to transcripts using featureCounts (Liao et al., 2013) with the GRCm38 Ensembl gene build GTF.
Assembly: GRCm38
Supplementary files format and content: raw counts for each sample

source_name: Cell line

growth_protocol: Differentiation into cortical-like neurons was done following the protocol by (Bibel et al., 2004, 2007).

extract_protocol:
RNA extraction was done with RNeasy Kit (Qiagen) in RNase-free conditions following the user’s manual with DNase treatment (Qiagen).
Libraries were prepared following Illumina’s TruSeq Stranded mRNA sample preparation guide.

value: Cell line

value: E14 male mouse embryonic stem cells

value: mESC-derived cortical neuron


title: P53/PTEN KD,N-Myc (ChIP), rep1

description: Library name: P53/PTEN KD, rep1, N-Myc ChIP


title: Caco-2.batch1.GLY.rep1.H04

description: Library name: Caco2_Batch1_GLY_1_H04


title: mCtr_Skin_1

description: Library name: C16


title: Caco-2.batch1.GLY.rep1.G04

description: Library name: Caco2_Batch1_GLY_1_G04


title: ATF6_KO_Con_H3K27ac_SET2_rep2

description: Library name: ATF6_KO_Con_H3K27ac_SET2_rep2

value: H3K27ac (Abcam #Ab4729)

value: Human colorectal cancer

value: 0.1% DMSO


title: mCtr_SI_4

description: Library name: C14

value: Gut

value: Epithelial cells


title: mESC-derived cortical neurons, day in vitro 12, WT, rep 3

description: Library name: DIV12_WT_3

value: WT


title: mESC-derived cortical neurons, day in vitro 12, WT, rep 1

description: Library name: DIV12_WT_1


title: mCtr_SI_3

description: Library name: C13


title: Caco-2.batch1.GLY.rep1.F04

description: Library name: Caco2_Batch1_GLY_1_F04

value: colon

value: epithelial

value: cell line


title: mESC-derived cortical neurons, day in vitro 8, PCDH19-ICD-OE, rep 3

description: Library name: DIV8_19ICD_3


title: Caco-2.batch1.GLY.rep1.E04

description: Library name: Caco2_Batch1_GLY_1_E04


title: mCtr_SI_2

description: Library name: C12


title: mESC-derived cortical neurons, day in vitro 8, PCDH19-ICD-OE, rep 2

description: Library name: DIV8_19ICD_2


title: Caco-2.batch1.GLY.rep1.D04

description: Library name: Caco2_Batch1_GLY_1_D04


title: mESC-derived cortical neurons, day in vitro 8, WT, rep 3

description: Library name: DIV8_WT_3


title: mCtr_SI_1

description: Library name: C11


title: mHp_SI_3

description: Library name: H33


title: mESC-derived cortical neurons, day in vitro 8, WT, rep 2

description: Library name: DIV8_WT_2


title: Caco-2.batch1.GLY.rep2.H04

description: Library name: Caco2_Batch1_GLY_2_H04


title: Caco-2.batch1.GLY.rep1.C04

description: Library name: Caco2_Batch1_GLY_1_C04


title: mESC-derived cortical neurons, day in vitro 8, WT, rep 1

description: Library name: DIV8_WT_1


title: Caco-2.batch1.GLY.rep2.B04

description: Library name: Caco2_Batch1_GLY_2_B04


title: mCtr_Lung_5

description: Library name: C5

value: Lung


title: Lung, 6h post Sham (control), replicate 3

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

description: Library name: lung_SHAM-3

data_processing:
Reads were quality checked with fastQC and no further processing was required
Reads were mapped to the mm39 reference genome with STAR (2.7.10a) and the gencode M30. Read counts were directly obtained using the the featurecounts package
Differential expression analysis was done using the DESeq2 package, with the FDR set at 5%
Assembly: mm39
Supplementary files format and content: tab delimited count matrix with the raw counts per sample

source_name: lung

growth_protocol: All mice were housed in individually ventilated cages at conventional housing conditions (22°C, 14/10h light/dark cycle, dark phase starting at 9 p.m.) in a specific pathogen-free facility. Food (chow diet consisting of 18% proteins, 4.5% fibers, 4.5% fat and 6.3% ashes, Provimi Kliba SA) and water were given at libitum

extract_protocol:
Total RNA was isolated with Aurum Total RNA mini Kit (Bio-Rad) following the manufacturer’s instructions
Library preparation was done using the illumina truseq stranded library kit for sequencing with a for sequencing on the NextSeq500 sequencing device according the the manufacturer's instructions

treatment_protocol: Mice were subject to CLP or sham surgery and 6 hours later livers and lungs were isolated and stored in RNAlater.

value: lung

value: Sham


title: MYCN+P53/PTEN KD,N-Myc (ChIP), rep2

description: Library name: MYCN+P53/PTEN KD, rep2, N-Myc ChIP

value: NPCs

value: MYCN+P53/PTEN KD


title: Caco-2.batch1.GLY.rep1.B04

description: Library name: Caco2_Batch1_GLY_1_B04


title: Lung, 6h post Sham (control), replicate 2

description: Library name: lung_SHAM-2


title: mESC-derived cortical neurons, day in vitro 12, PCDH19-ICD-OE, rep 1

description: Library name: DIV12_19ICD_1

value: Cell line


title: Caco-2.batch1.GLY.rep2.E04

description: Library name: Caco2_Batch1_GLY_2_E04


title: mCtr_Lung_4

description: Library name: C4


title: Caco-2.batch1.GLY.rep1.A04

description: Library name: Caco2_Batch1_GLY_1_A04


title: Lung, 6h post CLP, replicate 3

description: Library name: lung_CLP-3

value: CLP


title: Lung, 6h post CLP, replicate 1

description: Library name: lung_CLP-1


title: mCtr_Lung_3

description: Library name: C3


title: MYCN+P53/PTEN KD (Input)

description: Library name: MYCN+P53/PTEN KD, Input


title: Caco-2.batch1.DIZ.rep3.H11

description: Library name: Caco2_Batch1_DIZ_3_H11


title: mCtr_Skin_2

description: Library name: C17

value: Skin

value: Keratinocytes


title: Liver, 6h post Sham (control), replicate 3

description: Library name: liver_SHAM-3

source_name: liver

value: liver


title: mCtr_Lung_2

description: Library name: C2


title: Caco-2.batch1.DIZ.rep3.G11

description: Library name: Caco2_Batch1_DIZ_3_G11


title: mESC-derived cortical neurons, day in vitro 12, PCDH19-ICD-OE, rep 3

description: Library name: DIV12_19ICD_3

value: E14 male mouse embryonic stem cells

value: mESC-derived cortical neuron


title: Caco-2.batch1.DIZ.rep3.F11

description: Library name: Caco2_Batch1_DIZ_3_F11


title: Liver, 6h post CLP, replicate 3

description: Library name: liver_CLP-3


title: Lung, 6h post Sham (control), replicate 1

description: Library name: lung_SHAM-1


title: Liver, 6h post Sham (control), replicate 2

description: Library name: liver_SHAM-2


title: MC38 tumor, WT mouse

city: Shanghai

first: Mengkai

middle: MK

last: Li

address: Dongchuan street 800

department: School of pharmacy

institute: Shanghai Jiaotong University

description:
Library name: Samples1_WT
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
MC38 tumors from wild-type and LMO7 knockout mice were isolated, prepared into single-cell suspensions using the Miltenyi Biotec gentleMACS Octo Dissociator with Heaters, following the 37C-m-TDK-1 program (Miltenyi Biotec), and passing through 70 µm cell strainers. After red blood cell (RBC) lysis, approximately 10,000 FACS-sorted live cells (1,000 cells/µl suspension) were resuspended in 1x PBS (calcium- and magnesium-free) containing 0.04% BSA (A2153, SIGMA).
The cell suspension was used as input in 10x Chromium Controller System (10x Genomics Inc., product code 120223), and cell barcoding was performed using gel beads in emulsion (GEMs) in assembly chip. GEM reverse transcription (RT) reactions were conducted in a thermocycler at 53°C for 45 minutes, followed by 85°C for 5 minutes, and held at 4°C overnight. SPRIselect dynabeads (B23318, Beckman Coulter) were utilized for GEM recovery after RT. DNA quantities ranging from 2 to 50 ng were used for target enrichment. cDNA amplification, fragmentation, end repair, and A-tailing preparation were performed according to the manufacturer's protocol. Quality control and quantification of the gene expression library were conducted at various stages using high-sensitivity DNA chips and an Agilent 2100 Bioanalyzer (Agilent Technologies). Quality control was performed twice prior to sequencing. Two barcoded scRNA samples were pooled together before sequencing, which was performed on the NovaSeq 6000 S1 platform with a sequencing depth of approximately 300 million reads.

value: tumor


title: C2_2R_EP

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

description:
Library name: C2_2R_EP
EP_RESISTANT

data_processing:
RNA-Seq reads were quality trimed and mapped to themouse genome (mm10)  using hisat2.
Number of reads aligned to the exonic region of each gene were counted using htseq-count.
Assembly: mm10
Supplementary files format and content: tab-delimited text file of raw gene counts  for each sample

source_name: non-endothelial cells

extract_protocol:
Tumours were removed and cut to small pieces with a scissor. Then they were digested using 0.1% collagenase type I diluted in DMEM (Gibco), supplemented with 10% of EGM2 media (Promocell), 1% of BSA (Sigma), DNAse I, 100 mM HEPES and 2 mM EDTA. First the mix of tumour pieces was mixed with the digestion media, and tumours were processed in gentleMACS™ Dissociator (Miltenyi), then incubated at 37 degrees for 30 min, and then processed again in the Dissociator. Homogenized tumours were filtered with a 70 um filter and then the cell pellet was subjected to different procedures. ECs were enriched using a mix of antibodies against CD31, CD144 and ICAM2 (BD) and 30 ul of Dynabeads™ Sheep anti-Rat IgG (ThermoFisher). For bulk RNAseq, cell preparation was directly lysed to isolate mRNA. RNA extraction was performed using the RNeasy Plus Mini Kit.
Extracted RNA samples were sent to the QMUL Genome Centre for processing. Library preps were made with Ribo depletion.

value: non-endothelial cells


title: C2_2R_ECS

description:
Library name: C2_2R_ECS
ECS_RESISTANT

source_name: endothelial cells

value: endothelial cells


title: Co-incubation of OCY-EV and antagomir483-5p (3) followed by ultrafiltration, then hepatocytes under FFA conditions

city: changsha

first: yi

middle: yi

last: wang

address: xiangya road

institute: central south university

description: Library name: OCY-EV+ANTA3

data_processing:
We use HTSeq statistics to compare the Read Count value of each gene as the raw expression amount of the gene, and the Reads count is positively correlated with the real expression level of the gene, as well as the length of the gene and the sequencing depth.
In order to make the gene expression levels comparable between different genes and samples, we used FPKM (Fragments Per Kilo bases per Million fragments) to normalize the expression amount.
Differentially expressed genes (DEGs) were identified using thresholds of a fold change ≥ 2.0 and P-value < 0.05.
Assembly: Mouse mm10
Supplementary files format and content: The processed RNA-seq data is provided in Excel format, containing gene expression values for each sample. The data has been normalized using the [Normalization Method] (FPKM) to account for differences in sequencing depth and gene length. The file includes the following columns: Gene Identifier: The unique identifier for each gene (e.g., Ensembl ID or Gene Symbol). Sample Information: The columns correspond to individual samples, with expression values for each gene in each sample. Expression Values: The processed expression values, which are normalized for downstream analysis. Additional Metadata (if applicable): Information about sample conditions, experimental factors, or other relevant variables.

extract_protocol:
1. Cell Lysis: Disrupt cells using a lysis buffer containing chaotropic salts and β-mercaptoethanol to denature proteins and inhibit RNases. 2. Homogenization: Homogenize the sample to ensure complete cell disruption and RNA release. 3. Phase Separation: Add chloroform and centrifuge to separate RNA into the aqueous phase, while DNA and proteins remain in the organic phase or interphase. 4. RNA Precipitation: Mix the aqueous phase with isopropanol to precipitate RNA, then centrifuge to pellet the RNA. 5. Wash: Wash the RNA pellet with 75% ethanol to remove impurities, followed by centrifugation. 6. Resuspension: Air-dry the pellet and dissolve RNA in RNase-free water or buffer.
Vehicle Group: Cells treated with PBS; OCY-EV+ANTA-NC Group: Aged osteocyte extracellular vesicles were incubated with antagomir-NC for 30 minutes followed by ultracentrifugation, with a final extracellular vesicles intervention concentration of 2 μg/ml; OCY-EV+ANTA Group: Aged osteocyte extracellular vesicles were incubated with antagomir-483-5p for 30 minutes followed by ultracentrifugation, with a final extracellular vesicles intervention concentration of 2 μg/ml.

value: hepatocyte

value: OCY-EV+ANTA


title: Caco-2.batch1.DIZ.rep3.E11

description: Library name: Caco2_Batch1_DIZ_3_E11

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

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

value: colon

value: epithelial

value: cell line


title: Caco-2.batch1.DIZ.rep3.C11

description: Library name: Caco2_Batch1_DIZ_3_C11


title: C1_2R_EP

description:
Library name: C1_2R_EP
EP_RESISTANT


title: C1_BE_EP

description:
Library name: C1_BE_EP
EP_PLACEBO


title: mCtr_SI_5

description: Library name: C15

value: Gut

value: Epithelial cells


title: C2_1R2L_EP

description:
Library name: C2_1R2L_EP
EP_SENSITIVE


title: Caco-2.batch1.DIZ.rep3.B11

description: Library name: Caco2_Batch1_DIZ_3_B11


title: Liver, 6h post Sham (control), replicate 1

description: Library name: liver_SHAM-1

value: WT

value: Sham


title: C2_1R2L_ECS

description:
Library name: C2_1R2L_ECS
ECS_SENSITIVE


title: Caco-2.batch1.DIZ.rep3.D11

description: Library name: Caco2_Batch1_DIZ_3_D11


title: mESC-derived cortical neurons, day in vitro 8, PCDH19-ICD-OE, rep 1

description: Library name: DIV8_19ICD_1

value: Cell line


title: Liver, 6h post CLP, replicate 2

description: Library name: liver_CLP-2

value: CLP


title: Lung, 6h post CLP, replicate 2

description: Library name: lung_CLP-2

value: lung


title: Co-incubation of OCY-EV and antagomir-483-5p (2) followed by ultrafiltration, then hepatocytes under FFA conditions

description: Library name: OCY-EV+ANTA2

value: liver


title: Liver, 6h post CLP, replicate 1

description: Library name: liver_CLP-1


title: mCtr_Lung_1

description: Library name: C1

value: Lung


title: mESC-derived cortical neurons, day in vitro 12, WT, rep 2

description: Library name: DIV12_WT_2

value: E14 male mouse embryonic stem cells

value: mESC-derived cortical neuron


title: MC38 tumor, KO mouse

description:
Library name: Samples2_LMO7_KO
10x Genomics

value: tumor


title: P53/PTEN KD,N-Myc (ChIP), rep2

description: Library name: P53/PTEN KD, rep2, N-Myc ChIP

value: NPCs

value: P53/PTEN KD

value: N-Myc (Active Motif, Cat.#61185)


title: Co-incubation of OCY-EV and antagomir-483-5p (1) followed by ultrafiltration, then hepatocytes under FFA conditions

description: Library name: OCY-EV+ANTA1

value: hepatocyte

value: OCY-EV+ANTA


title: B2_2L_EP

description:
Library name: B2_2L_EP
EP_PLACEBO

value: non-endothelial cells


title: C1_2R1L_EP

description:
Library name: C1_2R1L_EP
EP_SENSITIVE


title: B2_2L_ECS

description:
Library name: B2_2L_ECS
ECS_PLACEBO

value: endothelial cells


title: C1_2R_ECS

description:
Library name: C1_2R_ECS
ECS_RESISTANT


title: Co-incubation of OCY-EV and antagomir-NC 2 followed by ultrafiltration,  then hepatocytes under FFA conditions

description: Library name: OCY-EV+ANTA-NC2

value: OCY-EV+ANTA-NC


title: Caco-2.batch1.DIZ.rep2.F11

description: Library name: Caco2_Batch1_DIZ_2_F11

value: colon

value: epithelial

value: cell line


title: B2_1R_ECS

description:
Library name: B2_1R_ECS
ECS_RESISTANT


title: Caco-2.batch1.DIZ.rep3.A11

description: Library name: Caco2_Batch1_DIZ_3_A11


title: Caco-2.batch1.DIZ.rep2.E11

description: Library name: Caco2_Batch1_DIZ_2_E11


title: A2_BE_ECS

description:
Library name: A2_BE_ECS
ECS_PLACEBO


title: Caco-2.batch1.DIZ.rep2.H11

description: Library name: Caco2_Batch1_DIZ_2_H11


title: A2_1R_EP

description:
Library name: A2_1R_EP
EP_STOP


title: A2_2R_EP

description:
Library name: A2_2R_EP
EP_STOP


title: Co-incubation of OCY-EV and antagomir-NC 3 followed by ultrafiltration,  then hepatocytes under FFA conditions

description: Library name: OCY-EV+ANTA-NC3


title: Caco-2.batch1.DIZ.rep2.G11

description: Library name: Caco2_Batch1_DIZ_2_G11


title: Vehicle 3 treatment under FFA conditions

description: Library name: Veh3

value: Veh


title: B2_1L_EP

description:
Library name: B2_1L_EP
EP_RESISTANT


title: A1_BE_EP

description:
Library name: A1_BE_EP
EP_SENSITIVE


title: A1_2L_ECS

description:
Library name: A1_2L_ECS
ECS_SENSITIVE


title: Caco-2.batch1.DIZ.rep2.D11

description: Library name: Caco2_Batch1_DIZ_2_D11


title: A1_2L_EP

description:
Library name: A1_2L_EP
EP_SENSITIVE


title: A1_1R_EP

description:
Library name: A1_1R_EP
EP_STOP


title: Caco-2.batch1.DIZ.rep2.C11

description: Library name: Caco2_Batch1_DIZ_2_C11


title: A1_1L_EP

description:
Library name: A1_1L_EP
EP_SENSITIVE


title: A1_1R_ECS

description:
Library name: A1_1R_ECS
ECS_STOP


title: Caco-2.batch1.DIZ.rep2.B11

description: Library name: Caco2_Batch1_DIZ_2_B11


title: Vehicle 2 treatment under FFA conditions

description: Library name: Veh2

value: liver


title: Vehicle 1 treatment under FFA conditions

description: Library name: Veh1


title: scRNA_young_old_skin

city: Zurich-Schlieren

first: Ataman

last: Sendoel

address: Wagistrasse 12

country: Switzerland

institute: University of Zurich

description: P60 (young skin), P722 (old skin)

data_processing:
The raw sequencing data consisting BCL files were demultiplexed using the Illumina bcl2fastq software (v2.20.0.422) with default options allowing one mismatch of the sample barcode. The resulting FASTQ files were processed using the BD Rhapsody™ Whole Transcriptome Analysis (WTA) Pipeline (v1.11) hosted at the Seven Bridges Genomics cloud platform (https://www.sevenbridges.com). We created STAR (v2.5.4) reference genome with gencode mouse vM25 (GRCm38.p6) annotations to use in the BD Pipeline. The young and old skin samples were multiplexed using BD Single-Cell Multiplex Kit for Mouse with barcode 5 and 6 respectively. So Single-Cell Multiplex Kit - Mouse was used as an option for Multiplexing_Settings in the pipeline to demultiplex the samples. The UMI counts adjusted by the Recursive Substitution Error Correction (RSEC) method from BD were used for further analysis.
Assembly: Gencode Mouse vM25 (GRCm38.p6)
Supplementary files format and content: *_counts.csv.gz files contain Cell Barcode, Gene Symbol and RSEC adjusted counts.

source_name: epidermis

growth_protocol: All mice were housed at the Laboratory Animal Services Center (LASC) of the University of Zurich in individually-ventilated cages in a humidity- and light-controlled environment (22 °C, 45–50%, 12 h light/dark cycle), and had access to food and water ad libitum.

extract_protocol:
Epidermal cells were isolated from one young (2 month old) and one aged (24 month old) animals as earlier described and processed for single-cell capture with a BD Rhapsody Single-Cell Analysis System with the BD Rhapsody Cartridge Kit (633733). The cell suspension was barcoded using BD Single-Cell Multiplexing Set (Rat anti-mouse MHC-H2 Class I, BD Biosciences, 626545).
Reverse transcription from beads and sequencing library production was carried out according to the manufacturer’s instructions (BD Biosciences, doc ID: 210967 rev. 1.0). Whole Transcriptome Amplification Analysis (WTAs) from BD Rhapsody Cartridges were sequenced in full SP flowcells.

value: epidermis

value: primary skin cells

value: epidermal cells

value: back skin was isolated enzymatically and mechanically, single cells were captured with the BD Rhapsody system


title: Co-incubation of OCY-EV and antagomir-NC 1 followed by ultrafiltration, then hepatocytes under FFA conditions

description: Library name: OCY-EV+ANTA-NC1


title: Sca-1-negative cells

description:
Total RNA footprint
P57, P679

data_processing:
*library strategy: sc-Ribo-seq
We utilized fastp for trimming adapters and moving 10nt UMI sequence to the fastq header with final read length between 26-34 using the options: --umi --umi_loc=read1 --umi_len=10 -a TGGAATTCTCGG --trim_poly_g --trim_poly_x -l 26 --length_limit 34. Next the rRNA and tRNA sequences were removed with the bowtie2 with options -D 20 -R 3 -N 1 -L 15. The remaining  rRNA and tRNA sequencing were removed by ribodetector with the options -t 12 --chunk_size 6000 -l 29. A custom python script was used to generate a fastq file containing 10nt cell barcode and 10nt UMI sequence. The resulting fastq files were aligned to the mouse genome using STAR with options: --soloType CB_UMI_Simple  --soloFeatures Gene Velocyto  --soloUMIlen 10 --soloUMIstart 11 --soloCBlen 10 --soloCBstart 1 --outSAMattributes UR CR AS NH HI nM MD CB --outFilterMultimapNmax 20 --quantMode TranscriptomeSAM --alignEndsType EndToEnd  --outFilterMismatchNmax 1 --soloUMIdedup 1MM_Directional_UMItools --soloCBmatchWLtype 1MM. We created a custom STAR reference genome with sjdb overhang of 33 to match the max(read length)-1. The STAR alignment to the mouse genome was performed in end to end mode with maximum one mismatch allowed for accurate mapping of ribosome footprints. The resulting bam file was cleared up for empty cell barcodes with sambamba followed by UMi deduplication by umi_tools with options --extract-umi-method tag --umi-tag=UR --cell-tag=CB --per-cell. The deduplicated bam files were split into 384 cells by a custom python script based on the pysam library. Then the reads mapping to the CDS regions of the genome in forward strand were counted by featureCounts with options: -M -O --fraction -s 1 -t CDS -g gene_name
Assembly: Gencode version M25 (GRCm38.p6)
Supplementary files format and content: *counts.csv.gz files contain CDS UMI footprint counts per cell for read length 26-34.

extract_protocol:
Cycloheximide (CHX) was injected into the tail vein of female young (2 month) and old (22-26 month) mice two minutes before euthanasia. The back skin was surgically removed and submerged in 1x PBS supplemented with CHX (10 mg/ml) for 5 minutes. The fat was scraped from the back skin and washed once in cold PBS-CHX and then placed in 15 ml 0.25% trypsin for 37 minutes at 37 °C on an orbital shaker, dermis-side facing down. Next, the epidermis was separated from dermis by scraping with a scalpel and torn into smaller pieces. Trypsin was neutralized by adding 1x PBS buffer containing 2% chelexed FBS (FBS-) and CHX, followed by vigorous pipetting to create a single-cell suspension. The cell suspension was filtered sequentially through a 70 μm and a 40 μm strainer, centrifuged for 10 minutes at 400 g and then resuspended in FACS buffer (1x PBS, 2% FBS-, 0.1 mg/ml CHX, 0.05 ng/ml DAPI). Live single cells were sorted on a BD Aria II with a 70 µm nozzle and a flow rate of <300 events per second into 384-well hard-shell plates, pre-filled with 5 μl of light mineral and 50 nl of lysis buffer. Single-cell sequencing libraries were performed as described in Methods.
After ribosome footprint digestion, libraries were generated using the Mosquito® liquid handler (SPT Labtech). As previously described14, a one-pot small-RNA library preparation protocol included the end repair, two RNA ligations, cDNA synthesis, and an indexing PCR. End repair: First, 50 nl of end-repair mix (4.1× T4 RNA Ligase Buffer (New England Biolabs), 16.4 mM MgCl2, 4.1 mM uridine triphosphate (New England Biolabs), 1.37 U/μl T4 Polynucleotide Kinase (New England Biolabs) and 0.77 U/μl SUPERase·In™ RNase Inhibitor was added to each well, and plates were incubated at 37 °C for 1 hour, then held at 4 °C. 3ʹ Ligation: Next, 264 nl of 3ʹ ligation brew (1× T4 RNA Ligase Buffer (New England Biolabs), 1 μM pre-adenylated 3ʹ adapter (OMV630_miRNA4_3App, Integrated DNA Technologies), 35.5% PEG-8000 (New England Biolabs), 0.1% Tween-20 (Sigma-Aldrich), 0.98 U/μl SUPERase In RNase Inhibitor (Invitrogen), and 21.3 U/μl T4 RNA Ligase 2 Truncated KQ (New England Biolabs)) was added to each well and plates were incubated at 4 °C for 18 hours. The cDNA synthesis primer was then pre-annealed to the 3ʹ ligation products by adding 50 nl of the reverse transcription primer mix (5.2 μM reverse transcription primer (OMV572_miRNA4_RT, Integrated DNA Technologies), 13.5 μM adenosine triphosphate (ATP, New England Biolabs), and 1% Tween-20) to each well. The plates were heated to 65 °C for 1 minute, then incubated sequentially at 37 °C for 2 minutes, 25 °C for 2 minutes and finally held at 4 °C.  5ʹ Ligation: 5ʹ adapters were then ligated by adding 156 nl of 5ʹ ligation brew (1× T4 RNA Ligase Buffer, 30.75% PEG-8000, 0.1% Tween-20, 0.5 μM 5ʹ adapter (OMV632_miRNA5_5A_10U, Integrated DNA Technologies), 1.25 U/μl T4 RNA Ligase (Thermo Scientific) and incubated at 37 °C for 2 h and then held at 4 °C. cDNA synthesis: Complementary DNA synthesis was performed by adding 770 nl of reverse transcription reaction with 2.66x of the standard concentration of the RT Buffer (5x RT Buffer, Thermo Fisher Scientific, EP0752), 1.25 mM dNTPs (Promega), 0.1875% Tween-20, 1.875 U/μl SUPERase In RNase Inhibitor, and 9.375 U/μl Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific) to each well. The plate was incubated at 50 °C for 1 hour, followed by 85 °C for 5 minutes, then held at 4 °C. Indexing PCR: For library indexing, 150 nl of 20 μM unique forward index primers (miRv6-PCR_F-cbc; Integrated DNA Technologies) and 3.2 μl of PCR mix (1.5× Q5 Hot Start High-Fidelity 2× Master Mix (New England Biolabs), 0.15% Tween-20, and 0.94 μM reverse index primer (RPI-; Integrated DNA Technologies)) were added to each well. Plates were then incubated at 98 °C for 30 seconds followed by 10 cycles of 98 °C for 15 seconds, 65 °C for 30 sesonds, 72 °C for 30 seconds, and then a final incubation at 72 °C for 5 minutes. Plates were then held at 4 °C before freezing at −20 °C until pooling.

value: epidermal cells excluding Sca-1 positive cells, young and old skin mixed

tag: age

value: young and old mixed

tag: Sex

value: female

value: back skin treated with cycloheximide (Methods), young and old skin cells were sorted into this plate


title: C1_BE_ECS

description:
Library name: C1_BE_ECS
ECS_PLACEBO


title: C1_2R1L_ECS

description:
Library name: C1_2R1L_ECS
ECS_SENSITIVE


title: A1_1L_ECS

description:
Library name: A1_1L_ECS
ECS_SENSITIVE


title: Caco-2.batch1.DIZ.rep2.A11

description: Library name: Caco2_Batch1_DIZ_2_A11


title: Young9

description:
Total RNA footprint
P60

value: young (56-60 days old)

value: back skin treated with cycloheximide (Methods)


title: B2_1L_ECS

description:
Library name: B2_1L_ECS
ECS_RESISTANT

value: endothelial cells


title: Young8

description:
Total RNA footprint
P59


title: A2_1R_ECS

description:
Library name: A2_1R_ECS
ECS_STOP


title: Caco-2.batch1.DIZ.rep1.G11

description: Library name: Caco2_Batch1_DIZ_1_G11


title: Caco-2.batch1.DIZ.rep1.F11

description: Library name: Caco2_Batch1_DIZ_1_F11


title: A2_2R_ECS

description:
Library name: A2_2R_ECS
ECS_STOP


title: A1_BE_ECS

description:
Library name: A1_BE_ECS
ECS_SENSITIVE


title: Atrx+_CTCF

city: HOUSTON

first: Ajay

middle: Kumar

last: Saw

state: TX

address: 7900 Cambdrige St

department: Department of Genomic Medicine

institute: University Of Texas MD Anderson Cancer Center, Houston, Texas, USA.

description: Library name: Atrx+_CTCF

data_processing:
Generated CUT&Tag data underwent quality-control measures using the FASTQC tool and was aligned to the mm9 reference genome with Bowtie2 (version 2.4.5).
BAM files were filtered and Gene annotations were performed using BED files subjected to GREAT (version 4) analysis with Basal plus extension parameters (Proximal: 5kb upstream, 1kb downstream, plus distal up to 1000kb), followed by pathway prediction analysis using Enrichr.
Assembly: mm9
Supplementary files format and content: Bigwig
Library strategy: CUT&Tag

source_name: Primary cell line

growth_protocol: Neuroprogenitor Cells were grown in NeuroCult Basal Medium containing NeuroCult Proliferation Supplement, 20 ng/ml EGF, 10 ng/ml basic FGF, 2 μg/ml heparin (Stemcell Technologies), 50 units/ml penicillin, and 50 μg/ml streptomycin (Thermo Fisher Scientific) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
500,000 cells were washed with 1X Wash Buffer and incubated with Concanavalin A Beads for 30 minutes. Cells were incubated overnight at 4°C using 1ug of anti-CTCF antibody (Diagenode, Cat # C15410206) or IgG (Diagenode, Cat # C15410206) with orbital mixing. The following day, the cells were washed using 1X Wash Buffer containing Protease Inhibitory Cocktail and Digitonin and incubated with Guinea Pig Anti-Rabbit secondary antibody, followed by Tn5 transposomes and Tagmentation procedures.
DNA was eluted using column filters and libraries constructed using i7 and i5 indexing primers, following PCR conditions. Eluted libraries were assessed for quality using a Bioanalyzer and subjected to Nextseq500 MID-300 using 150 bp pair-end read format at the MDACC-ATGC facility.

value: brain

value: Neuroepithelial progenitor cell

value: Control


title: Caco-2.batch1.DIZ.rep1.H11

description: Library name: Caco2_Batch1_DIZ_1_H11

value: colon

value: epithelial

value: cell line


title: p53knockout and ATRXknockout_mNPC input ChIP-seq

description: Library name: JSHS-53KO_G

data_processing:
Raw fastq reads from all ChIP-seq experiments were processed using a Snakemake-based pipeline (PMID: 34059508, https://zenodo.org/record/819971). Initial processing of raw reads was performed with FastQC. Uniquely mapped reads were aligned to the mm9 reference genome using Bowtie version 1.1.2, and duplicate reads were removed with SAMBLASTER before compressing to bam files. For direct comparison of ChIP-seq samples, uniquely mapped reads for each mark were downsampled to 15 million per condition, then sorted and indexed using samtools version 1.5. To visualize ChIP-seq libraries on the IGV genome browser, bigWig files were generated by deepTools version 2.4.0, scaling bam files to reads per kilobase per million (RPKM). Super ChIP-seq tracks were created by merging bam files from each phenotype, sorting and indexing with samtools, and scaling to RPKM with deepTools. Peak identification was performed using the Model-based Analysis of ChIP-seq (MACS) version 1.4.2 and MACS version 2.1.0 peak calling algorithms, with peak enrichment calculated against a whole genome "input" background at a p-value of < 1e-5. Super-enhancers were identified using the Ranking of Super-Enhancers (ROSE) algorithm based on H3K27ac ChIP-seq data.
Assembly: mm9
Supplementary files format and content: bigwig

source_name: brain

extract_protocol:
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) was conducted as previously described (PMID: 34059508). The chromatin shearing conditions were optimized for primary murine neuroepithelial progenitor cells and tissues. The antibodies used in this procedure included H3K9me3 (ab8898), H3K4me1 (ab8895), H3K27ac (ab4729), H3K4me3 (ab8580), H3K79me2 (ab3594), and H3K27me3 (ab6002).
Chromatin immunoprecipitation DNA was used to make library with NEBNext Ultra II DNA Library Prep Kit using kit manual.

value: mNPC

value: Neuroprogenitor


title: Caco-2.batch2.DIP.rep3.E07

description: Library name: Caco2_Batch2_DIP_3_E07


title: Young10

description:
Total RNA footprint
P57

value: epidermis

value: primary skin cells

value: epidermal cells


title: 24L012737_FO_Vehicle_iset1

city: Leipzig

first: Bilal

last: Sheikh

state: Sachsen

address: Philipp-Rosenthal-Str. 27

department: HI-MAG

country: Germany

institute: Helmholtz Zentrum München

description:
Library name: Sample_24L012737_FO_14_15_iset1
>27.5 × 103 reads per cell

data_processing:
Reads were demultiplexing and mapped to the mm10 mouse genome build (GENCODE vM23/Ensembl98) using CellRanger v8.0.1 (10x Genomics) with default parameters.
Assembly: mm10 mouse genome build (GENCODE vM23/Ensembl98)
Supplementary files format and content: Filtered features, barcodes and matrix

molecule: nuclear RNA

source_name: Abdomnal aorta

growth_protocol: The experiment was performed in accordance with the animal ethics laws of Saxony, Baden Württemberg and Hessen, Germany, and were approved by the state animal ethics committee. Female C57BL/6N mice at 8 weeks old were injected intravenously with 1 x 1011 vector genome copies of rAAV8-PCSK9D377Y. After 7 days, the mice were kept on a high fat diet (Ssniff Spezialdiäten, V1534) and treated with fluoxetine or vehicle for 10 weeks. Fluoxetine (Sigma, 56296-78-7) was offered in the drinking water ad libitum at 160 mg/ml with 0.1% saccharine (109185, Sigma). After 10 weeks, mice were sacrificed and perfused with PBS. The abdominal aorta and surrounding perivascular adipose tissue  was dissected and snap frozen.

extract_protocol:
Frozen abdominal aortas were dissociated in 2 ml ice-cold lysis buffer. Lysis buffer was prepared with 5 mM CaCl, 3 mM MgAc, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM Tris (pH 8), 10 mM sodium butyrate, 1 mM Dithiothreitol, cOmplete™ Protease Inhibitor Cocktail (11836145001, Roche) and 1.2U/ml RNAseOUT (10777019, Invitrogen). Aortas were dissociated in the gentleMACS Octo Dissociator system with heaters (MACS Technology, Miltenyi Biotec) using the program “Protein_01.01”. After dissociation, an additional 2 ml lysis buffer (supplemented with 0.4% Triton-X) was added to the gentleMACS tube and the solution was mixed by inversion. Samples were briefly centrifuged and strained through a 70 µm BD-cell strainer. The gentleMACS tube was rinsed with 2 ml lysis buffer (0.2% Triton-X) and the wash was also strained. After centrifugation (4 °C, 1000 xg, 5 min), the supernatant was discarded, and the dissociated tissue was washed with 1 ml PBS. Samples were stained with DAPI (A3672, AppliChem PanReac) and strained into a FACS tube (CLS352235, Corning). Nuclei were sorted on a FACS Aria (BD Biosciences).
snRNA-seq was performed with the 10x Next GEM Single-Cell 3′ GEM kit v3.1 (10x Genomics) according to the instructions from the manufacturer. The nuclei were FACS sorted two samples at a time and ~12,000 nuclei from each aorta were pooled. After centrifugation (4 °C, 300 xg, 5 min), nuclei were resuspended at ~1,000 cells/µl and loaded into the 10x Chromium controller. Fluoxetine and vehicle samples were processed in separate 10x Genomics reactions. Libraries were sequenced on an Illumina NovaSeq with >27.5 × 103 reads per cell.

value: Abdomnal aorta

value: Vehicle


title: Atrx-_CTCF

description: Library name: Atrx-_CTCF


title: Caco-2.batch1.DIZ.rep1.E11

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

address: 21,1111 Lakeshore Blvd, Apt #2

institute: McGill University

description: Library name: Caco2_Batch1_DIZ_1_E11

source_name: cell lysate


title: Caco-2.batch1.DIZ.rep1.D11

description: Library name: Caco2_Batch1_DIZ_1_D11


title: Young3

description:
Total RNA footprint
P60

value: female


title: p53knockout and ATRXknockout_mNPC H3K4me3 ChIP-seq

description: Library name: JSHS-53KO_E


title: Young1

description:
Total RNA footprint
P60

value: young (56-60 days old)


title: Caco-2.batch2.DIP.rep3.D07

description: Library name: Caco2_Batch2_DIP_3_D07


title: p53knockout and ATRXknockout_mNPC H3K79me2 ChIP-seq

description: Library name: JSHS-53KO_D


title: p53knockout and ATRXknockout_mNPC H3K27me3 ChIP-seq

description: Library name: JSHS-53KO_F


title: Caco-2.batch1.DIZ.rep1.C11

description: Library name: Caco2_Batch1_DIZ_1_C11


title: Old12

description:
Total RNA footprint
P722

value: old (22-26 months old)

value: back skin treated with cycloheximide (Methods)


title: p53knockout and ATRXknockout_mNPC H3K27ac ChIP-seq

description: Library name: JSHS-53KO_C

value: brain


title: p53knockout and ATRXknockout_mNPC H3K9me3 ChIP-seq

description: Library name: JSHS-53KO_B


title: p53knockout and ATRXwildtype_mNPC H3K27me3 ChIP-seq

description: Library name: JSHS-53AT_F


title: p53knockout and ATRXknockout_mNPC H3K4me1 ChIP-seq

description: Library name: JSHS-53KO_A


title: p53knockout and ATRXwildtype_mNPC input ChIP-seq

description: Library name: JSHS-53AT_G


title: Caco-2.batch1.DIZ.rep1.A11

description: Library name: Caco2_Batch1_DIZ_1_A11


title: Old4

description:
Total RNA footprint
P758


title: RFPpos-GFPpos-9

first: Qing

state: Shanghai

address: Xuhui Yueyang road 320, ShangHai, China

institute: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

data_processing:
Raw RNA-seq reads were cleaned using fastp (v0.20.0) program, aligned to mm10 using STAR (v2.7.3a)
Only unique mapped reads were kept and counted by featureCounts (v2.0.0)
FPKM and TPM were calculated by stringtie (v2.0)
Genome coverage was counted by bamCoverage (v3.3.1). Differential gene expression was carried out using DESeq2 (v1.30.0), and clusterProfiler (v3.18.1) was used for GO and KEGG analysis in R
Assembly: mm10
Supplementary files format and content: For deep-seq, tale-delimited text file includes number of different reads for each sample. For RNA-seq, tab-delimited text file includes RPKM values for each sample. For WGBS, bed file includes the average methylation sites per 200bp in the genome. For scRNA-seq of E7.5 embryos, cellfocus file includes the representation matrix of different cells.

source_name: Blastocyst

extract_protocol:
For deep-seq, The genomic DNA of various tissues (brain, heart, liver, testis, and tail) from wild-type mice and Gjb235delG/35delG mice derived from diploid compensation, was isolated using the TIANamp Genomic DNA Kit (TIANGEN). This was followed by PCR amplification for Sanger sequencing. Target sites were amplified from the extracted genomic DNA using Phanta® Max Super-Fidelity DNA Polymerase (Vazyme)For RNA-seq, single cells were picked using a Piezo-drill micromanipulator and transferred into a 200 µl tube containing 1.2 µl of lysis buffer. The lysate underwent cDNA amplification with the Single Cell Full Length mRNA Amplification Kit (Vazyme, Cat#N712)
For deep-seq,  the PCR products were then ligated with different barcodes and pooled together. Libraries were generated from adapter-modified PCR products. For RNA-seq, the RNA-seq library was prepared using the TruePrep DNA Library Prep Kit V2 (Vazyme, Cat#TD503) for Illumina sequencing
Libraries of deep-seq and RNA-seq subjected to deep sequencing on Illumina NovaSeq6000 platform following the manufacturer’s instructions (Illumina) to produce 150bp paired-end reads by Genergy Biotechnology Co. Ltd. (Shanghai, China).

value: Blastocyst

tag: genetic modification

value: Actin-RFP transgene


title: Caco-2.batch1.Control.rep3.D03

description: Library name: Caco2_Batch1_Control_3_D03

value: colon


title: Caco-2.batch1.DIZ.rep1.B11

description: Library name: Caco2_Batch1_DIZ_1_B11

value: epithelial


title: p53knockout and ATRXwildtype_mNPC H3K27ac ChIP-seq

description: Library name: JSHS-53AT_C


title: p53knockout and ATRXwildtype_mNPC H3K4me3 ChIP-seq

description: Library name: JSHS-53AT_E


title: Old2

description:
Total RNA footprint
P758


title: nuclease_test

description:
Total RNA footprint
P758

value: back skin treated with cycloheximide (Methods), cells were digested with different ribonucleases and concentrations


title: RFPpos-GFPpos-8


title: p53knockout and ATRXwildtype_mNPC H3K79me2 ChIP-seq

description: Library name: JSHS-53AT_D

value: mNPC


title: p53knockout and ATRXwildtype_mNPC H3K9me3 ChIP-seq

description: Library name: JSHS-53AT_B

value: Neuroprogenitor


title: Caco-2.batch1.Control.rep3.B03

description: Library name: Caco2_Batch1_Control_3_B03

value: cell line


title: RFPpos-GFPpos-7


title: pmCECs, Hemodialysate extract treated, Day 2 2

city: Aachen

first: Dickson

last: Wong

address: Pauwelsstr. 30

institute: University Hospital Aachen

description: Library name: pmCEC_Hemodialysate 2

data_processing:
processed with the publicly available nf-core/RNA-seq pipeline version 3.517 implemented in Nextflow 21.10.6 using Docker 20.10.12
Lane-level reads were trimmed using Trim Galore 0.6.7
Aligned to the mouse genome (GRCm39) using STAR 2.7.9a
Assembly: Gene-level and transcript-level quantification was done by Salmon v1.5.2
Supplementary files format and content: tab-delmited text file with raw count of each sample

source_name: Cardiac endothelial cell

growth_protocol: pmCECs were maintained in the growth medium stated in the Methods of the manuscript.

extract_protocol:
Total RNA was isolated using NucleoSpin TriPrep kit (740966.250, Macherey-Nagel, Germany).
cDNA library prep was performed with Collibri 3' mRNA Library Prep Kit (Thermo Fisher Scientific)

treatment_protocol: pmCECs were treated with hemodialysate for 2 days.

value: Cardiac endothelial cell

value: WT

value: Growth medium+ Hemodialysate extract


title: pmCECs, Hemodialysate extract treated, Day 2 3

description: Library name: pmCEC_Hemodialysate 3


title: p53knockout and ATRXwildtype_mNPC H3K4me1 ChIP-seq

description: Library name: JSHS-53AT_A


title: Caco-2.batch1.Control.rep3.C03

description: Library name: Caco2_Batch1_Control_3_C03


title: pmCECs, Hemodialysate extract treated, Day 2 1

description: Library name: pmCEC_Hemodialysate 1


title: Caco-2.batch1.Control.rep3.A03

description: Library name: Caco2_Batch1_Control_3_A03


title: pmCECs, control, Day 2 3

description: Library name: pmCEC_control 3

value: Growth medium


title: pmCECs, control, Day 2 2

description: Library name: pmCEC_control 2


title: RFPpos-GFPpos-6


title: pmCECs, control, Day 2 1

description: Library name: pmCEC_control 1


title: RFPpos-GFPpos-5


title: 24L012729_FO_Fluoxetine_iset3

description:
Library name: Sample_24L012729_FO_7_9_iset3
>27.5 × 103 reads per cell

value: Abdomnal aorta

value: Fluoxetine

value: 7 and 9


title: 7 Gy Irradiated, organoids, 11 days, mouse 3

city: Groningen

first: Rufina

last: Maturi

address: Antonius Deusinglaan 1

department: Radiotherapy

country: Netherlands

institute: University Medical Center Groningen

description:
Library name: 7 Gy Irradiated, 11 days 3
Smart3SEQ

data_processing:
For the alignment of the fastq files the mouse genome GRCm39 was used. STAR aligner software was used to align the results of the sequencing. Rstudion v4.1.3 was used for downstream analysis and for the generation of CPM files. The R package edgeR was used for normalization and identification of differentially expressed genes.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file including the raw counts from all replicates and conditions is provided.

source_name: Thyroid gland

growth_protocol: Organoids from all animals and conditions were cultured in Matrigel in DMEM/F12, Pen/Strep antibiotics, glutamax 2 mM, EGF 20 ng/ml, FGF2 20 ng/mL, Y27632 10 µM, B27 0.5%. All conditions were kept in culture at 37°C and 5% CO2 until the day of the experiment.

extract_protocol:
For the cDNA library preparation, total RNA was extracted from organoids using Rneasy Mini Kit according to the manufacturer`s instructions and its quality was determined using High Sensitivity RNA ScreenTapes on an Agilent 2100 Bioanalyzer. 100 ng of RNA was used as an input for all samples.
80 ng of highly intact RNA (RIN values > 9) was processed for the cDNA library preparation using the Smart3SEQ protocol, adhering to the manufacturer`s instructions.

treatment_protocol: E

value: Thyroid gland

value: Thyroid gland cells derived from organoids

value: 8-12 weeks old

value: Irradiated, 7 Gy


title: Caco-2.batch1.Control.rep2.D02

description: Library name: Caco2_Batch1_Control_2_D02

value: colon


title: Caco-2.batch1.Control.rep2.C02

description: Library name: Caco2_Batch1_Control_2_C02

value: epithelial


title: 7 Gy Irradiated, organoids, 11 days, mouse 2

description:
Library name: 7 Gy Irradiated, 11 days 2
Smart3SEQ


title: Caco-2.batch1.Control.rep2.B02

description: Library name: Caco2_Batch1_Control_2_B02


title: RFPpos-GFPpos-4

value: Blastocyst

value: Actin-RFP transgene


title: 4 Gy Irradiated, organoids, 11 days, mouse 3

description:
Library name: 4 Gy Irradiated, 11 days 3
Smart3SEQ

value: Irradiated, 4 Gy


title: RFPpos-GFPpos-3


title: 7 Gy Irradiated, organoids, 11 days, mouse 1

description:
Library name: 7 Gy Irradiated, 11 days 1
Smart3SEQ


title: 4 Gy Irradiated, organoids, 11 days, mouse 2

description:
Library name: 4 Gy Irradiated, 11 days 2
Smart3SEQ


title: Caco-2.batch1.Control.rep2.A02

description: Library name: Caco2_Batch1_Control_2_A02

value: cell line


title: Caco-2.batch1.Control.rep1.D01

description: Library name: Caco2_Batch1_Control_1_D01


title: RFPpos-GFPpos-2


title: High Phosphate Exercised Sample 1

city: Columbus

first: Kedryn

last: Baskin

state: OH

address: 460 W 12th Ave

department: Physiology and Cell Biology

institute: The Ohio State University

description:
Library name: XJD947_6_HP18_16_HPE
HPE_1

data_processing:
Fastq files were trimmed using TrimGalore, and aligned using the STAR aligner. Count matrices were analyzed in pairwise comparisons using DESeq2.
Assembly: GRCm39
Supplementary files format and content: excel file containing CPM values and pairwise comparison output from DESeq2

source_name: GP

extract_protocol:
RNA was extracted using the TRI-zol kit and manufacterer instructions. At minumum, 500ng of RNA, quality determined by RIN, was used to generate libraries for each sample.
Libraries were generated by Plasmidsaurus sequencing service. Poly-A mRNA capture, second strand synthesis and tagmentation, and Illumina library amplification.

value: GP

tag: sample group

value: High Phosphate Exercised


title: RFPpos-GFPpos-1


title: 4 Gy Irradiated, organoids, 11 days, mouse 1

description:
Library name: 4 Gy Irradiated, 11 days 1
Smart3SEQ


title: 2 Gy Irradiated, organoids, 11 days, mouse 1

description:
Library name: 2 Gy Irradiated, 11 days 1
Smart3SEQ

value: Irradiated, 2 Gy


title: Caco-2.batch1.Control.rep1.C01

description: Library name: Caco2_Batch1_Control_1_C01


title: Control, organoids, 11 days, mouse 3

description:
Library name: Control 11 days 3
Smart3SEQ

value: Non-irradiated


title: GFPpos-8

value: Actin-GFP transgene


title: Control, organoids, 11 days, mouse 1

description:
Library name: Control 11 days 1
Smart3SEQ


title: Caco-2.batch1.Control.rep1.B01

description: Library name: Caco2_Batch1_Control_1_B01


title: GFPpos-7


title: 7 Gy Irradiated, organoids, 7 days, mouse 3

description:
Library name: 7 Gy Irradiated, 7 days 3
Smart3SEQ


title: Caco-2.batch1.Control.rep1.A01

description: Library name: Caco2_Batch1_Control_1_A01


title: GFPpos-6


title: 7 Gy Irradiated, organoids, 7 days, mouse 1

description:
Library name: 7 Gy Irradiated, 7 days 1
Smart3SEQ


title: 4 Gy Irradiated, organoids, 7 days, mouse 3

description:
Library name: 4 Gy Irradiated, 7 days 3
Smart3SEQ


title: Caco-2.batch1.COL.rep3.H10

description: Library name: Caco2_Batch1_COL_3_H10


title: 7 Gy Irradiated, organoids, 7 days, mouse 2

description:
Library name: 7 Gy Irradiated, 7 days 2
Smart3SEQ


title: Caco-2.batch1.COL.rep3.G10

description: Library name: Caco2_Batch1_COL_3_G10


title: 4 Gy Irradiated, organoids, 7 days, mouse 1

description:
Library name: 4 Gy Irradiated, 7 days 1
Smart3SEQ


title: GFPpos-3


title: Caco-2.batch1.COL.rep3.F10

description: Library name: Caco2_Batch1_COL_3_F10


title: GFPpos-5


title: 2 Gy Irradiated, organoids, 7 days, mouse 1

description:
Library name: 2 Gy Irradiated, 7 days 1
Smart3SEQ


title: Control, organoids, 7 days, mouse 3

description:
Library name: Control 7 days 3
Smart3SEQ


title: Caco-2.batch1.COL.rep3.E10

description: Library name: Caco2_Batch1_COL_3_E10


title: Control, organoids, 7 days, mouse 2

description:
Library name: Control 7 days 2
Smart3SEQ


title: GFPpos-2


title: Control, organoids, 7 days, mouse 1

description:
Library name: Control 7 days 1
Smart3SEQ


title: Caco-2.batch1.COL.rep3.D10

description: Library name: Caco2_Batch1_COL_3_D10


title: GFPpos-1


title: Control, organoids, 5 days, mouse 3

description:
Library name: Control 5 days 3
Smart3SEQ


title: Control, organoids, 5 days, mouse 2

description:
Library name: Control 5 days 2
Smart3SEQ


title: RFPpos-9


title: 42C_VH_6NJ_HomeCage

city: Boston

first: Lisa

last: Goldberg

state: Massachusetts

address: 72 E Concord St, R604

institute: Boston University School of Medicine

description: Library name: 42C_VH

data_processing:
FastQC reports were generated and inspected to check the quality of the dataset
Samples were mapped to the mouse reference genome using Hisat2
Gene-level raw read counts were obtained with featureCounts
Transcript-level read counts were obtained with Kallisto
Normalization and differential expression were done using DESeq2.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file with gene-level raw read counts for each sample
Supplementary files format and content: Tab delimited text file with transcript-level read counts for each sample

source_name: Ventral Hippocampus

extract_protocol:
RNA was extracted using Trizol (Qiagen, Valencia, CA, USA) and RNAeasy extraction kit (Qiagen, Valencia, CA, USA), as previously described(Yazdani, Shen et al. 2016, Goldberg, Zeid et al. 2021). RNA concentration and quality were evaluated using NanoDrop2000 (NanoDrop, Wilmington, DE, USA) and Agilent Bioanalyzer (Agilent, Santa Clara, CA, USA)
Libraries were prepared by the Huck Institutes of the Life Sciences Genomics Core Facility (Penn State University) for 75 bp single-end reads using the Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA).

treatment_protocol: To investigate baseline and learning-induced changes in hippocampal transcriptome that may underlie the observed behavioral differences between B6J and B6NJ, dorsal (DH) and ventral hippocampi (VH) were dissected for RNAsequencing (n=6 per group). To determine the impact of learning on hippocampal transcriptome, three groups were utilized: home cage, fear conditioned, and cue alone.

value: Ventral Hippocampus

value: HomeCage

value: Male


title: RFPpos-8


title: 42C_DH_6NJ_HomeCage

description: Library name: 42C_DH

source_name: Dorsal Hippocapus

value: Dorsal Hippocapus


title: 42B_VH_6NJ_HomeCage

description: Library name: 42B_VH


title: Caco-2.batch1.COL.rep2.H10

description: Library name: Caco2_Batch1_COL_2_H10


title: RFPpos-6


title: 42A_DH_6NJ_HomeCage

description: Library name: 42A_DH


title: 41C_VH_6NJ_HomeCage

description: Library name: 41C_VH


title: Caco-2.batch1.COL.rep2.G10

description: Library name: Caco2_Batch1_COL_2_G10


title: RFPpos-5


title: Caco-2.batch1.COL.rep2.F10

description: Library name: Caco2_Batch1_COL_2_F10


title: 41B_VH_6NJ_HomeCage

description: Library name: 41B_VH


title: 41A_VH_6NJ_HomeCage

description: Library name: 41A_VH


title: 41B_DH_6NJ_HomeCage

description: Library name: 41B_DH


title: Caco-2.batch1.COL.rep2.D10

description: Library name: Caco2_Batch1_COL_2_D10


title: RFPpos-2


title: 40C_DH_6NJ_Cue

description: Library name: 40C_DH

value: Cue


title: Caco-2.batch1.COL.rep2.C10

description: Library name: Caco2_Batch1_COL_2_C10


title: RFPpos-1


title: Caco-2.batch1.COL.rep2.B10

description: Library name: Caco2_Batch1_COL_2_B10


title: 40A_VH_6NJ_Cue

description: Library name: 40A_VH


title: Caco-2.batch1.COL.rep3.C10

description: Library name: Caco2_Batch1_COL_3_C10


title: WT_HCFC and Chil1-/-_HFHC(Tag)

city: Kunming

first: Bo

last: Chen

address: East Outer Ring South Road

institute: YunnanUniversity

data_processing:
FASTQ files obtained from sequencing were processed using BD Rhapsody WTA analysis pipeline(v1.0.1), and aligned to GRCm38 and GencodeM19 for transcript annotation and quantitation.
Further processing was done with Seurat  (cell and gene filtering, clustering, differential gene expression analysis).
Assembly: GRCm38
Supplementary files format and content: BD Rhapsody WTA analysis output

extract_protocol:
Primary parenchymal cells were isolated from mouse liver tissue, and the cells were captured by BD Rhapsody system according to the manufacturer's instructions.
Using the library preparation scheme provided by BD Biosciences, the cDNA was amplified and the transcriptome library was constructed.

value: liver


title: Control, organoids, 5 days, mouse 1

description:
Library name: Control 5 days 1
Smart3SEQ

value: Thyroid gland

value: Thyroid gland cells derived from organoids

value: 8-12 weeks old


title: Caco-2.batch1.COL.rep3.B10

description: Library name: Caco2_Batch1_COL_3_B10

value: colon

value: epithelial


title: 42B_DH_6NJ_HomeCage

description: Library name: 42B_DH


title: 42A_VH_6NJ_HomeCage

description: Library name: 42A_VH


title: Bulk RNAseq of iAstros exposed to Interferon-Beta or PBS_IFN2

city: Dublin

first: Michael John

last: Dolan

state: Dublin 2

address: Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin

country: Ireland

institute: Trinity College Dublin

description: Library name: IFN_2

data_processing:
iAstrocyte: FastQC (v.0.12.1) and MultiQC (v.1.23) were to generate initial quality control (QC) reports. STAR (v.2.7.10b) was used to build the reference index (based on GRCh38) and align reads, then the quality of the generated BAM files was assessed with Samtools (v.1.6) quickcheck (all samples had greater than 94% alignment). The count matrix was generated using featureCounts (v.2.0.6). R (v.4.3.1) was used for subsequent analyses.  iMGL scRNAseq: Cellranger (version 6, 10X Genomics) was used for demultiplexing, barcode preprocessing, generation of fastq files, alignment and the counting of unique molecular identifiers (UMI). We applied Cellranger’s aggr function to all samples to merge and normalize by sequencing depth. We then applied CellBender to remove ambient RNA and technical artifacts due to barcode swapping (Fleming et al. 2023).
Assembly: GRCh38
Supplementary files format and content: Seurat object of iMGL scRNAseq data

source_name: cell line

growth_protocol: iMGL Differentiation: Human H1 embryonic stem cells were cultured in Essential 8 media on Matrigel, dissociated with Accutase, and aggregated in low-adherence plates with ROCK inhibitor. Cells were differentiated through sequential exposure to hematopoietic cytokines (FGF2, BMP4, VEGF, TPO, SCF, IL6, IL3) in HPC medium under hypoxic and then normoxic conditions. By day 10, cells were cryopreserved and later thawed for microglia maturation in iMG media containing M-CSF, IL-34, and TGF-β1. Final maturation occurred between days 30–45 with additional supplementation of CD200 and CX3CL1.  iAstro Differentiation: H1 hESCs were genetically engineered to express doxycycline-inducible NFIB and SOX9 from the AAVS1 locus. After transfection, cells were selected with geneticin and expanded. iAstrocyte induction was initiated with doxycycline in E8 medium, followed by sequential exposure to expansion, FGF, and maturation media containing BMP4, CNTF, and dbcAMP. Cells were dissociated on day 7, replated, and matured in MM medium until day 20 before use.

extract_protocol:
RNA was extracted either with Qiagen RNeasy Mini extraction kit (iAstrocytes) or subjected to single-cell RNA sequencing (iMGLs)
iAstrocye RNA underwent library preparation based on PolyA sequencing. iMGL underwent single-cell library preparation according to 10X Genomics protocol

treatment_protocol: Cells were treated with PBS or 25ng/ml Interferon Beta

value: stemcell astrocyte


title: 39C_VH_6NJ_Shock_Cue

description: Library name: 39C_VH


title: Caco-2.batch1.COL.rep3.A10

description: Library name: Caco2_Batch1_COL_3_A10

value: cell line


title: Caco-2.batch1.COL.rep1.H10

description: Library name: Caco2_Batch1_COL_1_H10


title: RFPpos-4

value: Blastocyst


title: 39B_VH_6NJ_Shock_Cue

description: Library name: 39B_VH


title: MCD


title: 39B_DH_6NJ_Shock_Cue

description: Library name: 39B_DH


title: 40C_VH_6NJ_Cue

description: Library name: 40C_VH


title: Caco-2.batch1.COL.rep1.G10

description: Library name: Caco2_Batch1_COL_1_G10


title: 39A_DH_6NJ_Shock_Cue

description: Library name: 39A_DH


title: T cell KO1, KO2, KO3 pool, scRNAseq

city: Yokohama City

first: Masato

last: Kubo

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Research Center for Integrative Medical Science (IMS)

institute: RIKEN Yokohama Institute

data_processing:
Gene expression obtained in scRNAseq experiments was counted using the featurecounts (version 2.0.1) and an mRNA database based on the mouse RefSeq reference (mm 10).
Assembly: mm10
Supplementary files format and content: read counts

source_name: Spleen

extract_protocol:
PI- Vb5.1-5.2+ CD4+ splenic OTII T cells were sorted into 96 well plates using a FACS Melody(18) and then lysed in a buffer containing dNTPs and oligo(dT)-tailed oligonucleotides with a universal 5'-anchor sequence.
A reverse transcription reaction, which adds 2–5 untemplated nucleotides to the cDNA 3' end, was then performed. A template-switching oligo carrying 2 riboguanosines and a modified guanosine was added to produce an LNA as the last base at the 3' end. After the first-strand reaction, the cDNA was amplified using 25 cycles. Next, Tn5 tagmentation was used to construct sequencing libraries from the amplified cDNA (Nextera XT DNA Library Preparation Kit, Illumina). The sequencing was carried out using NovaSeq6000 equipment (150PE, Illumina).

value: Spleen

value: IL13Ra1f/f, CD11cCre/+


title: 38C_VH_6NJ_Cue

description: Library name: 38C_VH


title: T cell WT3, WT4 pool, scRNAseq


title: 38B_VH_6NJ_Cue

description: Library name: 38B_VH


title: Caco-2.batch1.COL.rep1.E10

description: Library name: Caco2_Batch1_COL_1_E10


title: 40B_DH_6NJ_Cue

description: Library name: 40B_DH