title: Human bone marrow trephine of control sample - Rep 2

description: 10x Genomics

value: Bone marrow cells

value: Female


title: Blastoids_PIPseq_nontarg_c2_R1

status: Public on Jul 13 2025

type: SRA

city: Stanford

first: Raquel

last: Fueyo

state: CA

address: 265 Campus Drive

country: USA

institute: Stanford University

library_source: transcriptomic single cell

data_processing:
For each sample and replicate, reads obtained from the Novaseq X were analyzed with Fluent Bio’s proprietary software Pipseeker with default parameters and aligning against the GRCh38 transcriptome index. A background removal step was performed in all samples using CellBender with parameters --fpr 0.01 and --epochs 150. Full count matrices with background RNA removed were further analyzed using Seurat. Cells with more than 10% of mitochondrial counts were eliminated and the number of genes detected was also used for filtering the data. Each object was normalized using Seurat’s LogNormalize method and transformed using ScaleData function removing the unwanted variation originated from mitochondrial contamination or the cell cycle stage. Upon examining Elbow plots, 20 Principal Components were considered significant for unsupervised clustering with the FindNeighbors and FindClusters Seurat functions. Cluster identities were assigned based on the genes specifically marking each cluster according to Seurat’s FindMarkers function and comparing them to lineage markers uncovered in human preimplantation datasets. Seurat objects belonging to the nontarg-CARGO or the LTR5Hs-CARGO blastoids were merged.
Assembly: hg38
Supplementary files format and content: Count matrix (dgCMatrix) of all samples and metadata (txt)

molecule: polyA RNA

organism: Homo sapiens

source_name: clone 2

growth_protocol: Blastoids were generated following protocol in Kagawa et al. 2022

extract_protocol:
Single cells were obtained by resuspending blastoids in Collagenase IV (StemCell Technologies, 07909) and incubating at 37 degrees with mild agitation for 40 minutes. Blastoids were centrifuged again in N2B27 media and the pellet was resuspended in 0.5% Trypsin-EDTA (Fisher Scientific, 15-400-054) and incubated for 10 minutes at 37 degrees. Two further washes were performed with N2B27 and the dissociated cells were passed through a 40 um Flowmi cell strainer.
Libraries were constructed using the PIP-seq T20 3’ Single Cell RNA Kit

tag: cell line

value: clone 2

tag: genotype


title: genomic DNA from NorHep 5azaCdR#2

type: genomic

city: Montreal

first: David

last: Cheishvili

state: Quebec

address: 3655 Sir William Osler

country: Canada

institute: McGill

description:
rep2
NorHep_5aza#2

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to illumina Infinium Human Methylation450 Beadchip using standard Illumina protocolIllumina Infinium protocol

scan_protocol: Illumina Infinium protocol scanned using Illumina HiScan System.

data_processing:
GenomeStudio V2011.1 was used to determine the methylation level at each CpG site as beta value. Normalization to internal controls and background subtraction were applied to determine normalized average beta values.
the non_normalized.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

source_name: NorHep 5azaCdR

label_protocol: Illumina Infinium protocol

growth_protocol: HepG2, SKHep1 cells were maintained in MEM medium (Gibco, Invitrogen, Life Technologies), supplemented with 2 mmol/L glutamine (Sigma-Aldrich), 10% FBS (Gibco), 1 U/mL penicillin and 1 mg/mL streptomycin (Gibco). NorHep were maintained in human hepatocyte cell culture complete medium (Celprogen)

extract_protocol: Phenol-chloroform DNA extraction

tag: source gender

value: male

tag: cell type

value: primary liver cells (NorHep)

tag: sample group

value: inhibition of DNA methyltransferase (DNMT1) with 5-aza-2'-deoxycytidine (5-azaCdR)


title: Blastoids_PIPseq_LTR5Hs_c1_R1

source_name: clone 1

value: clone 1


title: 3-rTNR_rectal_ad_TNR_BALB/c mice

status: Public on Jul 12 2025

city: Suita

first: Tomoaki

last: Hara

address: Yamadaoka 2-2

country: Japan

institute: The University of Osaka

description: Library name: Sample 3-8

library_source: genomic

data_processing:
Sequencing was performed on the Illumina MiSeq platform using the MiSeq Reagent Kit v2 (500 cycles) in 251 bp paired-end mode.
The resulting FASTQ files were processed using QIIME2 version 2020.2.
Sequence denoising was conducted with the DADA2 plugin, and taxonomic assignments were made using the Greengenes 13_8 database.
Assembly: GRCm38
Supplementary files format and content: Excel sheet listing counts across taxonomic ranks
Library strategy: 16S rRNA-seq

organism: mouse gut metagenome

source_name: feaces

extract_protocol:
Genomic DNA was extracted using the GENE PREP STAR PI-1200 system (Kurabo).
The V1–V2 hypervariable regions of the 16S rRNA gene were amplified using the 27Fmod primer (5′-AGRGTTTGATCMTGGCTCAG-3′) and the 338R primer (5′-TGCTGCCTCCCGTAGGAGT-3′).

tag: tissue

value: feaces

tag: treatment

value: Fecal samples collected 2 days after rectal transplantation of rTNR-derived feces into mice that had been fed the MR diet for 13 days.


title: Human bone marrow trephine of MGUS sample - Rep 1

type: RNA

city: Parkville

first: Yunshun

last: Chen

state: VIC

address: 1G Royal Parade

department: ACRF Cancer Biology and Stem Cells

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: 10x Genomics

data_processing: The Xenium Onboard Analysis pipeline (v1.7.1.0 for Human Multi-Tissue and Cancer gene panel, or v.3.0.0.015 for 5k Human Pan Tissue & Pathways gene panel) was run directly on the instrument for imaging processing, cell segmentation, image registration, decoding, deduplication, and secondary analysis to generate the processed data files. Information about the output files can be found in https://www.10xgenomics.com/support/software/xenium-onboard-analysis/latest.

molecule: total RNA

source_name: Trephine

label_protocol: Two pre-designed gene panels (10x Genomics) were used: (i) Human Multi-Tissue and Cancer (377 genes) and (ii) Xenium Prime 5k Human Pan Tissue & Pathways Panel (5,001 genes). Panel content can be found in https://www.10xgenomics.com/products/xenium-panels.

growth_protocol: Bone marrow trephine biopsies from the posterior superior iliac spine were collected from patients undergoing routine investigation of suspected plasma cell disorders. Upon collection, trephines were immediately fixed in 10% neutral buffered formalin for at least 24 hours. Samples were then either embedded directly in paraffin (non-decal) or decalcified with 10% EDTA pH 7.2 solution (Milestone) before paraffin embedding.

extract_protocol: Sectioning was performed at 5 µm on a Leica RM2255 with a water float temperature of 47 °C. Sections were placed on Xenium slides (10X Genomics) and left to dry overnight. Slides were then stored in a sealed dessicator at room temperature for up to a maximum of 14 days.

treatment_protocol: All workstations and equipments were cleaned using RNaseZap™ (ThermoFisher, AM9780) followed by 70% ethanol. All reagents were molecular grade nuclease-free.

tag: condition

value: MGUS

tag: Sex


title: 3-rMR_oral_ad_MR_BALB/c mice

description: Library name: Sample 3-4

value: Fecal samples collected 2 days after oral transplantation of rMR-derived feces into mice that had been fed the MR diet for 13 days.


title: EBV-CD4rejTs, scRNA-seq

city: Bunkyo

first: Miki

last: Ando

state: Tokyo

address: Hongo 2-1-1

department: Hematology

institute: Juntendo University

description: Library name: EBV-CD4rejTs

data_processing:
Raw data were demultiplexed and quantified using Cell Ranger (v7.0.0, 10X Genomics). Downstream analyses used the Seurat R package (version 4.1.1).
Assembly: GRCh38
Supplementary files format and content: Barcode, features, matrix, fastq

source_name: Peripheral blood

extract_protocol:
Approximately 0.12 x 106 cells, viability >80%, were used.Sample was suspended in 50 μl of ice - chilled phosphate-buffered saline + 0.04% bovine serum albumin (Thermo Fisher Scientific) and processed to yield scRNA-seq libraries using 10X Chromium Next Gem Single Cell 3’ Reagent Kits v 3.1 (Dual Index) (10x Genomics, Pleasanton, CA) following standard manufacturer protocols. A Bio-Rad T100 thermal cycler (Bio-Rad, Hercules, CA) was used for PCR. After library quality was assessed using Bioanalyzer 2100 (Agilent, Tokyo, Japan), samples were sequenced (Macrogen, Seoul, South Korea) on the HiseqX (Illumina, San Diego, CA) platform at a depth of 2,000,000 pair reads/sample.
Library was prepared using Chromium Single Cell 3ʹ v3.1 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ v3.1 protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ v3.1 protocol (10x Genomics).

value: Peripheral blood

value: C3H10T1/2 cells

value: mRNA


title: genomic DNA from NorHep ShDNMT1#3

description:
rep3
NorHep_Sh1#3

source_name: NorHep ShDNMT1

value: DNA methyltransferase (DNMT1) knockdown with shRNA


title: 3-rMR_rectal_ad_MR_BALB/c mice

description: Library name: Sample 3-7

value: Fecal samples collected 2 days after rectal transplantation of rMR-derived feces into mice that had been fed the MR diet for 13 days.


title: genomic DNA from NorHep ShDNMT1#2

description:
rep2
NorHep_Sh1#2


title: Blastoids_PIPseq_LTR5Hs_c2_R2


title: 3-rTNR_BALB/c mice

description: Library name: Sample 3-2

value: fed TNR diet for 7 days followed by normal diet for 5 days


title: Human bone marrow trephine of control sample - Rep 1

description: 10x Genomics

value: Bone marrow cells

value: Ctrl

value: Male


title: Human bone marrow trephine of control sample - Rep 3

description: 10x Genomics

value: Female


title: Blastoids_PIPseq_LTR5Hs_c2_R1

value: clone 2


title: S-rMTNR_BALB/c mice

description: Library name: Sample 2-22

value: following the S-MTNR condition, mice were fed a normal diet for 5 days


title: genomic DNA from NorHep 5azaCdR#1

description:
rep1
NorHep_5aza#1

value: male

value: primary liver cells (NorHep)

value: inhibition of DNA methyltransferase (DNMT1) with 5-aza-2'-deoxycytidine (5-azaCdR)


title: ATL-CD4rejTs, scRNA-seq

description: Library name: ATL-CD4rejTs


title: Blastoids_PIPseq_LTR5Hs_c1_R2

value: clone 1


title: ATL-CD4, scRNA-seq

description: Library name: ATL-CD4


title: genomic DNA from NorHep ShDNMT1#1

description:
rep1
NorHep_Sh1#1


title: 3-rMTNR_rectal_ad_MTNR_BALB/c mice

description: Library name: Sample 3-9

value: feaces

value: Fecal samples collected 2 days after rectal transplantation of rMTNR-derived feces into mice that had been fed the MR diet for 13 days.


title: L-rTNR_BALB/c mice

description: Library name: Sample 2-15

value: following the L-TNR condition, mice were fed a normal diet for 5 days


title: M-rMR_BALB/c mice

description: Library name: Sample 2-17

value: following the M-MR condition, mice were fed a normal diet for 5 days


title: 3-rTNR_oral_ad_TNR_BALB/c mice

description: Library name: Sample 3-5

value: Fecal samples collected 2 days after oral transplantation of rTNR-derived feces into mice that had been fed the MR diet for 13 days.


title: S-MTNR_BALB/c mice

description: Library name: Sample 2-12

value: fed normal diet for 12 days followed by MTNR diet for 2 days


title: 3-rMTNR_BALB/c mice

description: Library name: Sample 3-3

value: fed MTNR diet for 7 days followed by normal diet for 5 days


title: L-rMR_BALB/c mice

description: Library name: Sample 2-14

value: following the L-MR condition, mice were fed a normal diet for 5 days


title: M-MTNR_BALB/c mice

description: Library name: Sample 2-9

value: fed normal diet for 5 days followed by MTNR diet for 9 days


title: 3-rMR_BALB/c mice

description: Library name: Sample 3-1

value: fed MR diet for 7 days followed by normal diet for 5 days


title: M-MR_BALB/c mice

description: Library name: Sample 2-7

value: fed normal diet for 5 days followed by MR diet for 9 days


title: S-rTNR_BALB/c mice

description: Library name: Sample 2-21

value: following the S-TNR condition, mice were fed a normal diet for 5 days


title: 3-rMTNR_oral_ad_MTNR_BALB/c mice

description: Library name: Sample 3-6

value: Fecal samples collected 2 days after oral transplantation of rMTNR-derived feces into mice that had been fed the MR diet for 13 days.


title: M-rMTNR_BALB/c mice

description: Library name: Sample 2-19

value: following the M-MTNR condition, mice were fed a normal diet for 5 days


title: genomic DNA from NorHep#2

description:
rep2
NorHep#2

source_name: NorHep

value: male

value: primary liver cells (NorHep)


title: L-C3_BALB/c mice

description: Library name: Sample 2-3

value: fed normal diet until day 14


title: S-rMR_BALB/c mice

description: Library name: Sample 2-20

value: feaces

value: following the S-MR condition, mice were fed a normal diet for 5 days


title: M-rTNR_BALB/c mice

description: Library name: Sample 2-18

value: following the M-TNR condition, mice were fed a normal diet for 5 days


title: S-MR_BALB/c mice

description: Library name: Sample 2-10

value: fed normal diet for 12 days followed by MR diet for 2 days


title: L-rC_BALB/c mice

description: Library name: Sample 2-13

value: fed normal diet until day 19


title: genomic DNA from NorHep#3

description:
rep3
NorHep#3


title: M-TNR_BALB/c mice

description: Library name: Sample 2-8

value: fed normal diet for 5 days followed by TNR diet for 9 days


title: rMTNR-FMT_BALB/c mice

description: Library name: Sample 1-20

value: fed MTNR diet for 15 days and then received fecal transplants once daily for two consecutive days from rMTNR mice donors, and were analyzed one day after the second transplantation.


title: rTNR-FMT_BALB/c mice

description: Library name: Sample 1-19

value: fed MTNR diet for 15 days and then received fecal transplants once daily for two consecutive days from rTNR mice donors, and were analyzed one day after the second transplantation.


title: C-FMT_BALB/c mice

description: Library name: Sample 1-17

value: fed MTNR diet for 15 days and then received fecal transplants once daily for two consecutive days from donors fed normal diet for 15 days, and were analyzed one day after the second transplantation.


title: L-rMTNR_BALB/c mice

description: Library name: Sample 2-16

value: following the L-MTNR condition, mice were fed a normal diet for 5 days


title: L-MTNR_BALB/c mice

description: Library name: Sample 2-6

value: fed MTNR diet until day 14


title: genomic DNA from NorHep#1

description:
rep1
NorHep#1


title: S-TNR_BALB/c mice

description: Library name: Sample 2-11

value: fed normal diet for 12 days followed by TNR diet for 2 days


title: L-MR_BALB/c mice

description: Library name: Sample 2-4

value: fed MR diet until day 14


title: rC_C57BL/6J mice

description: Library name: Sample 1-13

value: fed normal diet until day 15


title: rMTNR-FMT_C57BL/6J mice

description: Library name: Sample 1-24


title: rTNR_BALB/c mice

description: Library name: Sample 1-11

value: fed TNR diet until day 13, followed by a normal diet for 2 days (rTNR)


title: L-TNR_BALB/c mice

description: Library name: Sample 2-5

value: fed TNR diet until day 14


title: L-C2_BALB/c mice

description: Library name: Sample 2-2

value: fed normal diet until day 14


title: L-C1_BALB/c mice

description: Library name: Sample 2-1

value: feaces


title: rMR-FMT_BALB/c mice

description: Library name: Sample 1-18

value: fed MTNR diet for 15 days and then received fecal transplants once daily for two consecutive days from rMR mice donors, and were analyzed one day after the second transplantation.


title: rMTNR_BALB/c mice

description: Library name: Sample 1-12

value: fed MTNR diet until day 13, followed by a normal diet for 2 days (rMTNR)


title: rTNR-FMT_C57BL/6J mice

description: Library name: Sample 1-23


title: C-FMT_C57BL/6J mice

description: Library name: Sample 1-21


title: rMR-FMT_C57BL/6J mice

description: Library name: Sample 1-22


title: MTNR_BALB/c mice

description: Library name: Sample 1-4

value: fed MTNR diet until day 13


title: rMTNR_C57BL/6J mice

description: Library name: Sample 1-16


title: TNR_BALB/c mice

description: Library name: Sample 1-3

value: fed TNR diet until day 13


title: rTNR_C57BL/6J mice

description: Library name: Sample 1-15


title: rMR_C57BL/6J mice

description: Library name: Sample 1-14

value: fed MR diet until day 13, followed by a normal diet for 2 days (rMR)


title: C_BALB/c mice

description: Library name: Sample 1-1

value: fed normal diet until day 13


title: rMR_BALB/c mice

description: Library name: Sample 1-10


title: Wt1

city: Xiamen

first: Huanhuan

last: Ma

address: Xiang'an South Road 4221-120

country: China

institute: Xiamen University

library_source: transcriptomic

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: NCBI:GCA_000001635.8

organism: Mus

source_name: liver

extract_protocol:
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.
In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.

value: liver

value: primary hepatocytes


title: Wt3


title: rC_BALB/c mice

description: Library name: Sample 1-9


title: MTNR_C57BL/6J mice

description: Library name: Sample 1-8


title: Tg1


title: MR_C57BL/6J mice

description: Library name: Sample 1-6

value: fed MR diet until day 13


title: TNR_C57BL/6J mice

description: Library name: Sample 1-7


title: H2AK119Ub ChIP-seq in PCGF2 tamoxifen-treated 24h recovery from TSA treatment rep1

city: Montpellier

first: Marco

last: Di Stefano

address: 141 rue de la Cardonille

country: France

institute: Institut de Génétique Humaine - CNRS

description:
Library name: H2AK119Ub_PCGF2_OHT_REC_rep1
TSA followed by 24 hours of recovery +96h OHT
PCGF2_H2AK119Ub_mOHT_REC_scaled.bw
K119ub_OHT_REC_intersect.broadPeak

data_processing:
Data were mapped using bowtie2 against mm10 and hg19 and duplicates reads were discarded. Unique mouse and human reads were discarded and a donwsampling factor for spike-in normalisation was calulated as in Fursova et al. (2019) and bigwigs were produced directly from deduplicated bam files. For detailed protocol see the Method section of the adjoining paper.
Assembly: mm10
Supplementary files format and content: Processed files are given as a spike-in normalised mouse bigwig file of the two merged replicates except for YY1 where replicates have not been merged. Peak files correspond to high-confidence peaks present in both replicates exceept for YY1 where replicates are presented separately.

organism: Mus musculus

source_name: cell line

growth_protocol: ESC were grown in FBS+LIF media with standard conditions.

extract_protocol:
Chromatin was fixed with 1% formaldehyde for 10 min at RT. To each 12 million mouse cells 1 million HEK cells were added for spike-in calibration. Nuclei were isolated with three different lysis buffers as in Lee et al., 2006 and sonicated in the lysis buffer 3 until the chromatin was disrupted to the size between 200 and 500bp.  For detailed protocol see adjoning paper.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina according to manufacturer's instructions.

treatment_protocol: DMSO: 0.01% DMSO for 4 hours; TSA: 100 ng/ml TSA for 4 hours; REC: 4 hours TSA (100 ng/ml) followed by 24 hours of recovery; reTSA: 4 hours TSA (100 ng/ml) re-treatment; following 24 hours of recovery; reREC: 24 hours of recovery following the second round of TSA treatment. PCGF2 UT DMSO: PCGF4-/- PCGF2fl/fl +0.01% DMSO; PCGF2 OHT DMSO: PCGF4-/- PCGF2fl/fl 72h 800 nM OHT +0.01% DMSO; PCGF2 OHT TSA: PCGF4-/- PCGF2fl/fl 72h 800 nM OHT +4h 100 ng/ml TSA; PCGF2 OHT REC: PCGF4-/- PCGF2fl/fl 96h 800 nM OHT and 24h recovery from TSA treatment

value: cell line

value: mESC

value: PCGF4-/- PCGF2fl/fl

value: 800 nM OHT, 24h recovery from TSA


title: C_C57BL/6J mice

description: Library name: Sample 1-5


title: H2AK119Ub ChIP-seq in PCGF2 tamoxifen-treated TSA-treated rep2

description:
Library name: H2AK119Ub_PCGF2_OHT_TSA_rep2
TSA +72h OHT
PCGF2_H2AK119Ub_mOHT_TSA_scaled.bw
K119ub_OHT_TSA_intersect.broadPeak

value: 100 ng/ml TSA, 800 nM OHT


title: NHA, vial 1

city: Sydney

first: Javier

last: Perez Burillo

state: NSW

address: Chancellery Walk

institute: University of NSW

description: Genomic DNA extracted from breast tumors was genotyped using Infinium HumanHap550-v3 Genotyping BeadChips (Illumina).

hyb_protocol: Illumina Infinium HTS Assay

scan_protocol: iScan

data_processing:
Genomic DNA extracted from Normal Human Astrocytes (NHA) was genotyped using Infinium Global Screening Array (Illumina).
Genotype: AA,AB,BB,or NC (no call)

label: cy3, cy5

source_name: Normal human astrocytes, sourced from Lonza

label_protocol: Illumina Infinium HTS Assay

growth_protocol: NHA were grown in DMEM media supplemented with 10% foetal bovine serum and 1% streptomycin/penicillin at 37°C, 5% CO2

extract_protocol: Genomic DNA was extracted from cells using the PureLink Genomic DNA Mini Kit (Invitrogen, K182001), according to manufacturer's instructions

value: Normal human astrocytes


title: MR_BALB/c mice

description: Library name: Sample 1-2


title: H2AK119Ub ChIP-seq in PCGF2 tamoxifen-treated TSA-treated rep1

description:
Library name: H2AK119Ub_PCGF2_OHT_TSA_rep1
TSA +72h OHT
PCGF2_H2AK119Ub_mOHT_TSA_scaled.bw
K119ub_OHT_TSA_intersect.broadPeak


title: Wt2


title: Tg3


title: H2AK119Ub ChIP-seq in PCGF2 tamoxifen-treated 24h recovery from TSA treatment rep2

description:
Library name: H2AK119Ub_PCGF2_OHT_REC_rep2
TSA followed by 24 hours of recovery +96h OHT
PCGF2_H2AK119Ub_mOHT_REC_scaled.bw
K119ub_OHT_REC_intersect.broadPeak


title: H3K27me3 ChIP-seq in PCGF2 tamoxifen-treated 24h recovery from TSA treatment rep1

description:
Library name: H3K27me3_PCGF2_OHT_REC_rep1
TSA followed by 24 hours of recovery +96h OHT
PCGF2_H3K27me3_mOHT_REC_scaled.bw
K27me3_OHT_REC_intersect.broadPeak


title: ChIP input for PCGF2 tamoxifen-treated 24h recovery from TSA treatment

description:
Library name: input_PCGF2_OHT_REC_rep1
TSA followed by 24 hours of recovery +96h OHT


title: Tg2


title: Cap_PPM55 [SMxDPxSMxSSM]: Sample4072 rep 2

city: Houston

first: Olga

last: Dudchenko

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description:
Library name: HIC12994
Cap_PPM55 [SMxDPxSMxSSM]: Sample4072 Pacific pocket mouse (Perognathus longimembris pacificus) tissue F2 (OR5947/Cap_PPM55/20234) rep 2

data_processing:
Juicer version 1.6; BWA 0.7.17-r1188; 8 threads; openjdk version "1.8.0_412"; Juicer Tools Version 1.9.9
Construction of the chromosome-length Hi-C contact map (BWA, Juicer)
Assembly: PPM_HiRise_rh_HiC (GCA_023159225.1)
Supplementary files format and content: hic: contact maps generated by aligning Hi-C data to reference sequences.

organism: Perognathus longimembris pacificus

source_name: unknown tissue

extract_protocol:
The in situ Hi-C protocol is described in detail in Rao, Huntley et al., 2014.
Illumina PCR-amplified libraries

value: unknown tissue

value: tissue

value: SMxDPxSMxSSM


title: ChIP input for PCGF2 tamoxifen-treated TSA-treated

description:
Library name: input_PCGF2_OHT_TSA_rep1
TSA +72h OHT


title: ChIP input for PCGF2 tamoxifen-treated DMSO control

description:
Library name: input_PCGF2_OHT_DMSO_rep1
DMSO +72h OHT

value: 0.01% DMSO, 800 nM OHT


title: Library_2_liver_all_samples

city: Penicuik

first: Carl

middle: Iain James

last: MILTON

state: Midlothian

address: Flat 8D high street

country: United Kingdom

institute: University of Edinburgh

description: Library name: Library 2

data_processing:
Alignment of reads and generation of gene cell expression matrices used the splitpipe pipeline with the following parameters: - mode all, -chemistry V2. The sub-libraries were combined to form a single dataset using split-pipe --mode comb.
Assembly: Ssal_v3.1, unmasked
Supplementary files format and content: Filtered starsolo matrix output

organism: Salmo salar

source_name: Liver

extract_protocol:
Samples were placed in a six well plate containing tween-salt-tris buffer (TST) and RNase inhibitor (Merck) and the nuclei dissociated by mincing the tissue for 10 minutes with spring scissors (Noyes) alongside intermittent pipetting. The solution was filtered through a 40µm Falcon Cell Strainer before nuclei centrifugation at 4°C for 5 min at 500g and resuspension in salt-tris solution. Nuclei were quality checked and fixed as per the manufacturer's instructions (Parse fixation kit 2.0) then counted using a haemocytometer (Neubauer DHC-N01).
snRNA-seq libraries were generated from the fixed nuclei using a Parse Biosciences Evercode WT v2 Mini kit following the manufacturer’s protocol. The final snRNA-seq libraries were equimolar pooled and sequenced on a NextSeq P3 (200 cycle) Illumina flow cell using the Parse Biosciences Illumina Run Configuration (Read 1: 74 cycles, i7 Index: (Index 1) 6 cycles, Read 2 (barcode): 86 cycles, i5 Index (index 2): 0 cycles) by the University of Edinburgh’s Genetics Core Facility (Edinburgh Clinical Research Facility).

value: Liver


title: H2AK119Ub ChIP-seq in PCGF2 tamoxifen-treated DMSO control rep2

description:
Library name: H2AK119Ub_PCGF2_OHT_DMSO_rep2
DMSO +72h OHT
PCGF2_H2AK119Ub_mOHT_DMSO_scaled.bw
K119ub_OHT_DMSO_intersect.broadPeak


title: H3K27me3 ChIP-seq in PCGF2 tamoxifen-treated 24h recovery from TSA treatment rep2

description:
Library name: H3K27me3_PCGF2_OHT_REC_rep2
TSA followed by 24 hours of recovery +96h OHT
PCGF2_H3K27me3_mOHT_REC_scaled.bw
K27me3_OHT_REC_intersect.broadPeak


title: Library_1_liver_all_samples

description: Library name: Library 1


title: Cap_PPM15 [SM]: Sample4069

description:
Library name: HIC12992
Cap_PPM15 [SM]: Sample4069 Pacific pocket mouse (Perognathus longimembris pacificus) fibroblasts (KB22019/Cap_PPM15/22019)

source_name: fibroblasts

value: fibroblasts

value: fibroblast

value: SM


title: Cap_PPM23 [SSM]: Sample4068 part1

description:
Library name: HIC12947_1
Cap_PPM23 [SSM]: Sample4068 Pacific pocket mouse (Perognathus longimembris pacificus) muscle (OR6837/Cap_PPM23/20954)

source_name: muscle

value: muscle

value: SSM


title: H2AK119Ub ChIP-seq in PCGF2 untreated DMSO control rep2

description:
Library name: H2AK119Ub_PCGF2_UT_DMSO_rep2
DMSO
PCGF2_H2AK119Ub_mUT_DMSO_scaled.bw
K119ub_UT_DMSO_intersect.broadPeak


title: H3K27me3 ChIP-seq in PCGF2 tamoxifen-treated TSA-treated rep2

description:
Library name: H3K27me3_PCGF2_OHT_TSA_rep2
TSA +72h OHT
PCGF2_H3K27me3_mOHT_TSA_scaled.bw
K27me3_OHT_TSA_intersect.broadPeak


title: H3K27me3 ChIP-seq in PCGF2 tamoxifen-treated TSA-treated rep1

description:
Library name: H3K27me3_PCGF2_OHT_TSA_rep1
TSA +72h OHT
PCGF2_H3K27me3_mOHT_TSA_scaled.bw
K27me3_OHT_TSA_intersect.broadPeak


title: 3-C_BALB/c mice

description: Library name: Sample 3-10

value: feaces

value: fed normal diet until day 15


title: Cap_PPM8 [DP]: Sample4066

description:
Library name: HIC12945
Cap_PPM8 [DP]: Sample4066 Pacific pocket mouse (Perognathus longimembris pacificus) muscle (OR8082/Cap_PPM8/--)

value: DP


title: Cap_PPM57 [SMxDPxSMxSSM]: Sample4073

description:
Library name: HIC12951
Cap_PPM57 [SMxDPxSMxSSM]: Sample4073 Pacific pocket mouse (Perognathus longimembris pacificus) tissue F2 (OR5950/Cap_PPM57/20236)


title: Cap_PPM55 [SMxDPxSMxSSM]: Sample4072 rep 1

description:
Library name: HIC12950
Cap_PPM55 [SMxDPxSMxSSM]: Sample4072 Pacific pocket mouse (Perognathus longimembris pacificus) tissue F2 (OR5947/Cap_PPM55/20234) rep 1


title: H3K27me3 ChIP-seq in PCGF2 tamoxifen-treated DMSO control rep2

description:
Library name: H3K27me3_PCGF2_OHT_DMSO_rep2
DMSO +72h OHT
PCGF2_H3K27me3_mOHT_DMSO_scaled.bw
K27me3_OHT_DMSO_intersect.broadPeak

value: cell line

value: mESC

value: PCGF4-/- PCGF2fl/fl


title: Cap_PPM9 [DP]: Sample3938

description:
Library name: HIC12993
Cap_PPM9 [DP]: Sample3938 Pacific pocket mouse (Perognathus longimembris pacificus) muscle (OR8028)


title: Cap_PPM42 [SMxDP]: Sample4071 part1

description:
Library name: HIC12949_1
Cap_PPM42 [SMxDP]: Sample4071 Pacific pocket mouse (Perognathus longimembris pacificus) muscle F1 (OR8209/Cap_PPM42/--)

value: SMxDP


title: Cap_PPM3 [DP]: Sample3937 part 1

description:
Library name: HIC12837_1
Cap_PPM3 [DP]: Sample3937 Pacific pocket mouse (Perognathus longimembris pacificus) heart (OR6628)

source_name: heart

value: heart


title: H3K27me3 ChIP-seq in PCGF2 untreated DMSO control  rep1

description:
Library name: H3K27me3_PCGF2_UT_DMSO_rep1
DMSO
PCGF2_H3K27me3_mUT_DMSO_scaled.bw
K27me3_UT_DMSO_intersect.broadPeak


title: H3K27me3 ChIP-seq in PCGF2 tamoxifen-treated DMSO control rep1

description:
Library name: H3K27me3_PCGF2_OHT_DMSO_rep1
DMSO +72h OHT
PCGF2_H3K27me3_mOHT_DMSO_scaled.bw
K27me3_OHT_DMSO_intersect.broadPeak


title: H2AK119Ub ChIP-seq in PCGF2 untreated DMSO control rep1

description:
Library name: H2AK119Ub_PCGF2_UT_DMSO_rep1
DMSO
PCGF2_H2AK119Ub_mUT_DMSO_scaled.bw
K119ub_UT_DMSO_intersect.broadPeak


title: Cap_PPM45 [SMxDP]: Sample4070

description:
Library name: HIC12948
Cap_PPM45 [SMxDP]: Sample4070 Pacific pocket mouse (Perognathus longimembris pacificus) muscle F1 (OR5682/Cap_PPM45/19973)

value: tissue


title: ChIP input for PCGF2 untreated DMSO control

description:
Library name: input_PCGF2_UT_DMSO_rep1
DMSO


title: H2AK119Ub ChIP-seq in PCGF2 tamoxifen-treated DMSO control rep1

description:
Library name: H2AK119Ub_PCGF2_OHT_DMSO_rep1
DMSO +72h OHT
PCGF2_H2AK119Ub_mOHT_DMSO_scaled.bw
K119ub_OHT_DMSO_intersect.broadPeak


title: Cap_PPM1 [DP]: Sample4067 part1

description:
Library name: HIC12946_1
Cap_PPM1 [DP]: Sample4067 Pacific pocket mouse (Perognathus longimembris pacificus) muscle (OR6929/Cap_PPM1/21055)


title: Cap_PPM14 [SM]: Sample4064 part1

description:
Library name: HIC12915_1
Cap_PPM14 [SM]: Sample4064 Pacific pocket mouse (Perognathus longimembris pacificus) muscle (OR7697/Cap_PPM14/21684)


title: ChIP input for 24h recovery replicate 4

description:
Library name: input_REC_rep4
TSA followed by 24 hours of recovery

value: mESC wt

value: Wild type

value: 24h recovery from TSA treatment


title: Cap_PPM10 [DP]: Sample4065 part1

description:
Library name: HIC12944_1
Cap_PPM10 [DP]: Sample4065 Pacific pocket mouse (Perognathus longimembris pacificus) heart (OR5310/Cap_PPM10/19444)


title: H3K27me3 ChIP-seq in PCGF2 untreated DMSO control rep2

description:
Library name: H3K27me3_PCGF2_UT_DMSO_rep2
DMSO
PCGF2_H3K27me3_mUT_DMSO_scaled.bw
K27me3_UT_DMSO_intersect.broadPeak


title: ChIP input for YY1 in mESC TSA-replicate 1

description:
Library name: input_YY1_TSA_rep1
TSA

value: 100 ng/ml TSA


title: Cap_PPM207 [SSM]: Sample3935 part 1

description:
Library name: HIC12835_1
Cap_PPM207 [SSM]: Sample3935 Pacific pocket mouse (Perognathus longimembris pacificus) muscle (OR7967)


title: SSM_1 [SSM]: Sample3933 part 1

description:
Library name: HIC12833_1
SSM_1 [SSM]: Sample3933 Pacific pocket mouse (Perognathus longimembris pacificus) cryopreserved fibroblasts CP (KB22560)

source_name: cryopreserved fibroblasts

value: cryopreserved fibroblasts

value: fibroblasts

value: fibroblast


title: H3K27ac ChIP-seq mESC 24h recovery after TSA washout rep3

description:
Library name: H3K27ac_REC_rep3
TSA followed by 24 hours of recovery


title: SSM_2 [SSM]: Sample3936 part 1

description:
Library name: HIC12836_1
SSM_2 [SSM]: Sample3936 Pacific pocket mouse (Perognathus longimembris pacificus) heart (OR8321)

value: SSM


title: Ring1B ChIP-seq mESC 24h recovery after TSA washout rep3

description:
Library name: Ring1B_REC_rep3
TSA followed by 24 hours of recovery
Ring1B_mREC_scaled.bw
Ring1B_REC_intersect.broadPeak


title: Cap_PPM1 [DP]: Sample4067 part2

description:
Library name: HIC12946_2
Cap_PPM1 [DP]: Sample4067 Pacific pocket mouse (Perognathus longimembris pacificus) muscle (OR6929/Cap_PPM1/21055)

value: muscle


title: YY1 ChIP-seq of mESC TSA-treated rep1

description:
Library name: YY1_TSA_rep1
TSA


title: Cap_PPM17 [SM]: Sample3932 part2

description:
Library name: HIC12832_1
Cap_PPM17 [SM]: Sample3932 Pacific pocket mouse (Perognathus longimembris pacificus) cryopreserved fibroblasts CP (KB21356)

value: SM


title: ChIP input for mESC TSA replicate 4

description:
Library name: input_TSA_rep4
TSA


title: Ring1B ChIP-seq mESC 24h recovery after TSA washout rep4

description:
Library name: Ring1B_REC_rep4
TSA followed by 24 hours of recovery
Ring1B_mREC_scaled.bw
Ring1B_REC_intersect.broadPeak


title: ChIP input for mESC TSA replicate 3

description:
Library name: input_TSA_rep3
TSA


title: Cap_PPM42 [SMxDP]: Sample4071 part2

description:
Library name: HIC12949_2
Cap_PPM42 [SMxDP]: Sample4071 Pacific pocket mouse (Perognathus longimembris pacificus) muscle F1 (OR8209/Cap_PPM42/--)


title: Cap_PPM7 [DP]: Sample3934 part 1

description:
Library name: HIC12834_1
Cap_PPM7 [DP]: Sample3934 Pacific pocket mouse (Perognathus longimembris pacificus) muscle CP (OR7871)

value: DP


title: ChIP input for 24h recovery replicate 3

description:
Library name: input_REC_rep3
TSA followed by 24 hours of recovery

value: cell line


title: SSM_2 [SSM]: Sample3936 part 2

description:
Library name: HIC12836_2
SSM_2 [SSM]: Sample3936 Pacific pocket mouse (Perognathus longimembris pacificus) heart (OR8321)


title: Ring1B ChIP-seq of mESC TSA-treated rep3

description:
Library name: Ring1B_TSA_rep3
TSA
Ring1B_mTSA_scaled.bw
Ring1B_TSA_intersect.broadPeak


title: H3K9ac ChIP-seq mESC 24h recovery after TSA washout rep4

description:
Library name: H3K9ac_REC_rep4
TSA followed by 24 hours of recovery
K9ac_mREC_scaled.bw
K9ac_REC_intersect.broadPeak


title: SSM_1 [SSM]: Sample3933 part 2

description:
Library name: HIC12833_2
SSM_1 [SSM]: Sample3933 Pacific pocket mouse (Perognathus longimembris pacificus) cryopreserved fibroblasts CP (KB22560)


title: H3K9ac ChIP-seq mESC 24h recovery after TSA washout  rep3

description:
Library name: H3K9ac_REC_rep3
TSA followed by 24 hours of recovery
K9ac_mREC_scaled.bw
K9ac_REC_intersect.broadPeak


title: YY1 ChIP-seq of mESC TSA-treated rep2

description:
Library name: YY1_TSA_rep2
TSA


title: H3K9ac ChIP-seq of mESC TSA-treated rep3

description:
Library name: H3K9ac_TSA_rep3
TSA
K9ac_mTSA_scaled.bw
K9ac_TSA_intersect.broadPeak


title: Cap_PPM10 [DP]: Sample4065 part2

description:
Library name: HIC12944_2
Cap_PPM10 [DP]: Sample4065 Pacific pocket mouse (Perognathus longimembris pacificus) heart (OR5310/Cap_PPM10/19444)


title: Cap_PPM14 [SM]: Sample4064 part2

description:
Library name: HIC12915_2
Cap_PPM14 [SM]: Sample4064 Pacific pocket mouse (Perognathus longimembris pacificus) muscle (OR7697/Cap_PPM14/21684)


title: H3K27ac ChIP-seq of mESC TSA-treated rep3

description:
Library name: H3K27ac_TSA_rep3
TSA


title: Cap_PPM3 [DP]: Sample3937 part 2

description:
Library name: HIC12837_2
Cap_PPM3 [DP]: Sample3937 Pacific pocket mouse (Perognathus longimembris pacificus) heart (OR6628)


title: ChIP input for mESC DMSO replicate 3

description:
Library name: input_DMSO_rep3
DMSO


title: Ring1B ChIP-seq of mESC TSA-treated rep4

description:
Library name: Ring1B_TSA_rep4
TSA
Ring1B_mTSA_scaled.bw
Ring1B_TSA_intersect.broadPeak


title: 79.4, snRNA-seq

city: Belmont

first: Joy

last: Otten

state: Massachusetts

address: 115 Mill Street

institute: McLean Hospital

description: 10x Genomics Visium

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Sspace Ranger (v1.0.0) software
Assembly: mm10

source_name: left hemisphere mice brain

extract_protocol:
Fresh frozen tissue is embedded with OCT and 10um frozen sections were sliced on the cyrostat.  The left hemisphere of the mouse brain is placed on tissue slide at bregma -1.8.
Library was performed according to manufacturers instructions 10x Genomics at the Biomedical Research Center core sequencing facility at the University of British Columbia, Vancouver, Canada. Tissue was permeabilised for 18 minutes according to Visium Spatial Tissue Optimization slide & reagent kit.

value: left hemisphere mice brain

value: Control


title: H3K27ac ChIP-seq mESC in DMSO control rep3

description:
Library name: H3K27ac_DMSO_rep3
DMSO


title: Ring1B ChIP-seq in mESC DMSO control rep4

description:
Library name: Ring1B_DMSO_rep4
DMSO
Ring1B_mDMSO_scaled.bw
Ring1B_DMSO_intersect.broadPeak


title: Ring1B ChIP-seq in mESC DMSO control rep3

description:
Library name: Ring1B_DMSO_rep3
DMSO
Ring1B_mDMSO_scaled.bw
Ring1B_DMSO_intersect.broadPeak


title: ChIP input for mESC DMSO replicate 4

description:
Library name: input_DMSO_rep4
DMSO


title: H3K9ac ChIP-seq of mESC TSA-treated rep4

description:
Library name: H3K9ac_TSA_rep4
TSA
K9ac_mTSA_scaled.bw
K9ac_TSA_intersect.broadPeak


title: Cap_PPM7 [DP]: Sample3934 part 2

description:
Library name: HIC12834_2
Cap_PPM7 [DP]: Sample3934 Pacific pocket mouse (Perognathus longimembris pacificus) muscle CP (OR7871)


title: 79.1, snRNA-seq

description: 10x Genomics Visium

value: Fear conditioned


title: Cap_PPM17 [SM]: Sample3932 part1

description:
Library name: HIC12832
Cap_PPM17 [SM]: Sample3932 Pacific pocket mouse (Perognathus longimembris pacificus) cryopreserved fibroblasts CP (KB21356)


title: H3K9ac ChIP-seq in mESC DMSO control rep4

description:
Library name: H3K9ac_DMSO_rep4
DMSO
K9ac_mDMSO_scaled.bw
K9ac_DMSO_intersect.broadPeak


title: H3K4me1 ChIP-seq mESC in DMSO control rep4

description:
Library name: H3K4me1_DMSO_rep4
DMSO


title: ChIP input for reREC replicate 2

description:
Library name: input_reREC_rep2
TSA + 24h recovery followed by a second TSA treatment and 24 hours of recovery


title: 79.3, snRNA-seq

description: 10x Genomics Visium


title: 79.2, snRNA-seq

description: 10x Genomics Visium


title: 69.4, snRNA-seq

description: 10x Genomics Visium


title: 69.2, snRNA-seq

description: 10x Genomics Visium


title: ChIP input for reREC replicate 1

description:
Library name: input_reREC_rep1
TSA + 24h recovery followed by a second TSA treatment and 24 hours of recovery

value: 24h recovery from a second round of TSA treatment


title: Cap_PPM23 [SSM]: Sample4068 part2

description:
Library name: HIC12947_2
Cap_PPM23 [SSM]: Sample4068 Pacific pocket mouse (Perognathus longimembris pacificus) muscle (OR6837/Cap_PPM23/20954)

value: tissue


title: 69.1, snRNA-seq

description: 10x Genomics Visium


title: skin_Vehicle group rep2:smart-seq

city: Shanghai

first: Zihan

last: Wang

address: No. 555 Zu Chongzhi Road, Zhangjiang, Pudong, Shanghai

department: Shanghai Institute of Materia Medica

institute: University of Chinese Academy of Sciences

description:
Library name: skin_Vehicle_4
smart-seq

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM was used to quantify gene abundances.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: dorsal skin

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RQN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions. The RNA-seq transcriptome librariy was prepared following Illumina Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers. Then the synthesized cDNA was subjected to end-repair, phosphorylation and adapter addition according to library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, the sequencing library was performed on NovaSeq X Plus platform(PE150) using NovaSeq Reagent Kit.

value: dorsal skin


title: skin_Vehicle group rep1:smart-seq

description:
Library name: skin_Vehicle_1
smart-seq


title: skin_CCl4 group rep3:smart-seq

description:
Library name: skin_CCl4_4
smart-seq


title: 61.3, snRNA-seq

description: 10x Genomics Visium


title: skin_CCl4 group rep1:smart-seq

description:
Library name: skin_CCl4_1
smart-seq


title: H2AK119Ub ChIP-seq mESC after second 24h recovery rep2

description:
Library name: H2AK119Ub_reREC_rep2
TSA + 24h recovery followed by a second TSA treatment and 24 hours of recovery
K119Ub_mreREC_scaled.bw
K119Ub_reREC_intersect.broadPeak

value: mESC wt

value: Wild type


title: 69.3, snRNA-seq

description: 10x Genomics Visium


title: Cap_PPM207 [SSM]: Sample3935 part 2

description:
Library name: HIC12835_2
Cap_PPM207 [SSM]: Sample3935 Pacific pocket mouse (Perognathus longimembris pacificus) muscle (OR7967)


title: liver_vehicle group rep3:RNA-seq

description:
Library name: liver_vehicle_3
RNA-seq

value: liver


title: H3K9ac ChIP-seq in mESC DMSO control rep3

description:
Library name: H3K9ac_DMSO_rep3
DMSO
K9ac_mDMSO_scaled.bw
K9ac_DMSO_intersect.broadPeak


title: liver_vehicle group rep2:RNA-seq

description:
Library name: liver_vehicle_2
RNA-seq


title: 61.1, snRNA-seq

description: 10x Genomics Visium


title: skin_CCl4 group rep2:smart-seq

description:
Library name: skin_CCl4_2
smart-seq


title: 61.2, snRNA-seq

description: 10x Genomics Visium


title: 35.4, snRNA-seq

description: 10x Genomics Visium


title: liver_vehicle group rep1:RNA-seq

description:
Library name: liver_vehicle_1
RNA-seq


title: liver_CCl4 group rep2:RNA-seq

description:
Library name: liver_CCl4_2
RNA-seq


title: 35.3, snRNA-seq

description: 10x Genomics Visium


title: liver_CCl4 group rep1:RNA-seq

description:
Library name: liver_CCl4_1
RNA-seq


title: skin_Vehicle group rep3:smart-seq

description:
Library name: skin_Vehicle_5
smart-seq


title: H2AK119Ub ChIP-seq mESC after second 24h recovery rep1

description:
Library name: H2AK119Ub_reREC_rep1
TSA + 24h recovery followed by a second TSA treatment and 24 hours of recovery
K119Ub_mreREC_scaled.bw
K119Ub_reREC_intersect.broadPeak


title: H3K27me3 ChIP-seq mESC after second 24h recovery rep2

description:
Library name: H3K27me3_reREC_rep2
TSA + 24h recovery followed by a second TSA treatment and 24 hours of recovery
K27me3_mreREC_scaled.bw
K27me3_reREC_intersect.broadPeak


title: Mr BMT-treated CSF1RWT/I792T, replicate1, scRNA-seq

first: Bo

last: Peng

address: 138 Yixueyuan Road

department: Institute for Translational Brain Research

institute: Fudan University

description: 10x Genomics

data_processing:
Sample demultiplexing, barcode processing and single-cell 3’ gene counting were carried out with Cell Ranger 7.0.1 (10x Genomics). The 10-bp transcripts/UMI tags were extracted from the reads. Command mkfastq with bcl2fastq 2.0.1 in CellRanger was applied to demultiplex raw base call files from the sequencer into sample-specific FASTQ files. In addition, cellranger-compatible references were produced based on both genome sequences and transcriptome GTF files by using Cell Ranger mkref. These FASTQ files were aligned to the reference genome mm10 with cellranger count by using STAR 2.7.2, Egfp (Gfp) gene was mapped to label Mr BMT cells. Aligned reads were then filtered for valid cell barcodes and UMI to generate filtered gene-barcode matrices.
Assembly: mm10
Supplementary files format and content: tab-seperated  values files and matrix files

source_name: brain

extract_protocol:
The cell suspension was primarily obtained according to our previous protocol29. In brief, the mice were perfused with 0.9% saline and an inhibitor cocktail solution (actinomycin D 5 μg/mL, triptolide 10 μM, anisomycin 27.1 μg/mL), after which the brains of the mice were quickly sliced into 200 μm sections. Next, the sections were incubated in choline chloride solution supplemented with 10 μM NBQX (Tocris, Cat#: 0373), 50 μM APV (Tocris, Cat#: 3693), an inhibitor cocktail, and an influx of oxygen (95% O2 and CO2) for 30 min at 37 °C. Afterward, the sections were digested in 20 U/mL papain (Worthington, LK003178) and 100 U/mL DNase I (Sangon, B100649-0040) for 20 min at 37 °C, and then the sections were incubated in 1 mg/mL protease (Sigma–Aldrich, P5147) and 1 mg/mL dispase (Worthington, LS02106) for 20 min at 25 °C. Next, the sections were gently and repeatedly blown through a pipette into single-cell suspensions and then filtered through 40 μm cell strainers. The cell debris was removed by 30% Percoll (Millipore, P1644) in DPBS supplemented with 0.5% BSA. Finally, the cells were resuspended in DPBS supplemented with 0.5% BSA. Approximately 24,000 cells for each group (N = 3 mice) were loaded for 10x Genomics library preparation. A cocktail of transcriptional and translational inhibitors was included in the cell preparation to prevent ex vivo microglial reactivation28,29.
Single-cell libraries were constructed using a Chromium controller and Chromium single-cell 3 reagent version 2 kit (10x Genomics). Then, the libraries were subjected to a 150 bp paired-end sequencing by HiSeq X Ten (Illumina).

value: brain

value: CSF1R WT/I792T

value: Mr BMT


title: liver_CCl4 group rep3:RNA-seq

description:
Library name: liver_CCl4_4
RNA-seq


title: H3K27me3 ChIP-seq mESC after second 24h recovery rep1

description:
Library name: H3K27me3_reREC_rep1
TSA + 24h recovery followed by a second TSA treatment and 24 hours of recovery
K27me3_mreREC_scaled.bw
K27me3_reREC_intersect.broadPeak


title: naïve CSF1R WT/I792T, replicate1, scRNA-seq

description: 10x Genomics


title: H3K4me3 ChIP-seq mESC after second 24h recovery rep2

description:
Library name: H3K4me3_reREC_rep2
TSA + 24h recovery followed by a second TSA treatment and 24 hours of recovery
K4me3_mreREC_scaled.bw
K4me3_reREC_intersect.broadPeak


title: H3K4me3 ChIP-seq mESC after second 24h recovery rep1

description:
Library name: H3K4me3_reREC_rep1
TSA + 24h recovery followed by a second TSA treatment and 24 hours of recovery
K4me3_mreREC_scaled.bw
K4me3_reREC_intersect.broadPeak


title: 61.4, snRNA-seq

description: 10x Genomics Visium


title: 35.2, snRNA-seq

description: 10x Genomics Visium


title: H3K4me1 ChIP-seq mESC after second 24h recovery rep2

description:
Library name: H3K4me1_reREC_rep2
TSA + 24h recovery followed by a second TSA treatment and 24 hours of recovery
K4me1_mreREC_scaled.bw
K4me1_reREC_intersect.broadPeak


title: CSF1R WT/WT, replicate1, scRNA-seq

description: 10x Genomics

value: CSF1R WT/WT


title: H3K4me1 ChIP-seq mESC after second 24h recovery rep1

description:
Library name: H3K4me1_reREC_rep1
TSA + 24h recovery followed by a second TSA treatment and 24 hours of recovery
K4me1_mreREC_scaled.bw
K4me1_reREC_intersect.broadPeak


title: 35.1, snRNA-seq

description: 10x Genomics Visium


title: Input_double_mutation_rep2

city: San Antonio

first: Peng

last: Zhang

address: 8403 Floyd Curl Drive

institute: UT Health San Antonio

data_processing:
Raw data of each sample was quality controlled by fastqc and trimmed by TrimGalore
clean reads were aligned to mouse reference genome using bowtie2
The raw sam files generated by bowtie2 were sorted and reads on mitochondrion or with low Mapping quality (<30) were filtered using samtools
Sambamba was used to remove PCR duplications
Peak calling was performed with MACS2 with options: -g mm  -B -q 0.05
Assembly: mm10
Supplementary files format and content: BigWig files were generated using deeptools(bamCoverage --normalizeUsing CPM)
Supplementary files format and content: NarrowPeak files were generated using MACS2

source_name: Bone marrow

growth_protocol: The BM cells were harvested from the mice directly

extract_protocol:
The cells were fixed with 1% formaldehyde, lysates were sonicated and the DNA was sheared to an average length of 100 to 300 bp. Histone-DNA complexes were isolated with H3K27me3 antibodies using the True MicroChIP-seq Kit (Diagenode), and then the ChIP DNA was purified using Qiangen kit.
The ChIP libraries were prepared using the MicroPlex Library Preparation Kit (Diagenode) and sequenced with single-end 75 bp on Illumina NextSeq 500 system

treatment_protocol: The Lineage-cKit+ cells were purified from mouse bone marrow cells using beads sorting

value: Lin-cKit+ bone marrow cells

tag: strain

value: Double mutation

tag: chip antibody


title: MTNR

description:
Library name: Sample 2
10x Genomics

data_processing:
Raw sequencing data were processed using Cell Ranger v6.0.0 (10x Genomics) to generate gene expression matrices. Downstream analysis was performed in R using the Seurat package. Cells with fewer than 20% of unique molecular identifiers (UMIs) mapped to mitochondrial genes were retained for further analysis. Gene expression matrices from the control, MTNR, and rMTNR groups were imported and integrated using the SCTransform (SCT) normalization method. Integration features were selected using SelectIntegrationFeatures with nfeatures = 3000, and dimensionality reduction was performed using uniform manifold approximation and projection (UMAP). Cell type annotation was carried out by identifying cluster-specific marker genes using the FindAllMarkers function in Seurat. Cell identities were assigned by comparing identified markers with published cell type-specific gene signatures.
Assembly: GRCm38
Supplementary files format and content: integrated rds file

source_name: intestinal tract

extract_protocol:
Tissues were minced in  mL of DMEM with 10% FBS, ulinastatin (2 μg/mL), and sivelestat (2 μg/mL) at 4 °C. Enzymatic digestion was performed with 25 mL of DMEM containing Collagenase D and DNase at 37 °C for 1 hour. After digestion, 25 mL of DMEM with 10% FBS was added, and the suspension was filtered through 70 μm strainers and then passed through 10 μm strainers. The cell suspension was centrifuged, and the pellet resuspended in ACK buffer at 37 °C to lyse red blood cells. After lysis, cells were washed with PBS and resuspended in DMEM with 10% FBS. Cells were resuspended in PBS at 1000 cells/μL in 100 μL.
Single-cell suspensions were processed using the Chromium Next GEM Single Cell 3′ v3.1 kit (10x Genomics) following the manufacturer's protocol. Libraries were sequenced on the Illumina NovaSeq 6000 platform in paired-end mode (read1: 50 bp; read2: 91 bp).

value: intestinal tract

value: fed MTNR diet until day 13


title: Adipose tissue, Research participant 10 after treatment

city: Lexington

first: Brian

middle: S

last: Finlin

state: KY

address: 900 S. Limestone CTW 575

department: Internal Medicine

institute: University of Kentucky

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome:  Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 2 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.  We then converted this data provied by the company (gene_counts.xlx) to transcripts per million (TPM.XLsx)  and performed a paired T-Test.  Data were filtered to eliminate genes with expression less than 1 TPM (greater than 10 of the 20 samples had to have an expression >1 TPM to be considered for analysis).  P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: TPM file contains transcripts per million (TPM) for each sample, P-values and FDR adjusted P-values for each sample.
Supplementary files format and content: Gene count file contains the raw counts determined by Novogene.

source_name: Subcutaneous Adipose (thigh)

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (#74106, Qiagen) according to the manufacturer’s instructions.  RNA integrity was assessed using an Agilent bioanalyzer.
Total RNA was sequenced by Novogene UC Davis.  Library construction, strategy, and data processing were performed by Novogene.  The details provided below are copied from the project methods document provided by Novogene.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  For the directional library, it was ready after end repair, A tailing, adapter ligation, size selection, USER enzyme digestion , amplification, and purification.

value: Subcutaneous Adipose (thigh)

tag: individual

value: Research participant 10

value: 50 mg mirabegron daily


title: mESCs,adriamycin 8h,Dppa2,CHIP

city: Guangzhou city

first: Mangmang

last: Li

state: Guangdong province

address: 1838 N Guangzhou Ave

department: Department of Cell Biology School of Basic Medical Sciences

institute: Southern Medical University

description: Library name: CHIP136

data_processing:
Basecalls were performed using FastQC v0.12.1 for Novaseq output.
ChlP-seq reads were aligned to the mm10 genome using Bowtie2 version 2.5.1. Use Samtools to extract uniquely aligned reads from the mapping results.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per milion, rpm) and reformatted in the bigWig file format
Peaks were called uing MACS3 v3.0.0b1 with the significance cut-off q-value <=0.05
bigWig files were generated using the Deeptools v3.5.1. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS3 v3.0.0b1 with default settings
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

source_name: mouse embryonic tissue

growth_protocol: R1/E cells were seeded on 0.1% gelatin-coated culture dishes and maintained in mESC culture medium containing DMEM, 15% fetal bovine serum, 0.1 mM β-mercaptoethanol (Sigma, 516732), 100 mM MEM non-essential amino acids, 1 × penicillin/streptomycin, and 1000 U/mL leukemia inhibitory factor (LIF) ). Medium was changed every day, and cells were split every other day.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at room temperature. Chromatin fraction was prepared step by step using Lysis buffer 1 (50 mM Hepes-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), Lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and Lysis buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholdate, 0.5% N-lauroylsarcosine). All the buffers were freshly supplemented with protease inhibitor cocktails (Roche, 4693116001) and 1 mM fresh PMSF.
Chromatin fraction was sonicated with a Bioruptor® Plus (Diagenode) to shear DNA to a size of 300-500 bp. 5 μg of antibody and 50 ul Protein G beads (Genscript，L00664-25) were used to immunoprecipitate DNA-protein complex. After washing 5 times with Wash buffer (50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40 and 0.7% Na-Deoxycholdate), the DNA-protein complex was eluted in TES (10 mM Tris-HCl+1% SDS). After reverse-cross linking and DNA purification, the DNA was quantified using QubitTM 3.0 (Thermo Fisher Scientific, Q33216). 30 ng ChIPed DNA was sent to Novogen for DNA library construction followed by sequencing. Libraries were sequenced on HiSeq PE150.

value: mouse embryonic tissue

value: mouse embryonic stem cells

value: adriamycin 8h

value: apoptosis induction

tag: batch

value: Day 0


title: H3K27ac ChIP-seq mESC after second 24h recovery rep2

description:
Library name: H3K27ac_reREC_rep2
TSA + 24h recovery followed by a second TSA treatment and 24 hours of recovery
K27ac_mreREC_scaled.bw
K27ac_reREC_intersect.broadPeak

value: cell line

value: mESC wt

value: Wild type

value: 24h recovery from a second round of TSA treatment


title: Th17 cells, stimulated and unstimulated, VivoSeq, ADT

city: Birmingham

first: Rob

last: Welner

state: AL

address: 1824 6th Ave S

department: Medicine - Hem/Onc

institute: University of Alabama at Birmingham

description:
Library name: sampleFB
Antibody-Derived Oligonucleotide (ADT) library

library_source: other

data_processing:
Data was processed using CellRanger Count.
Assembly: mm10
Supplementary files format and content: Scanpy processed file: Vivo-seq_processed_Scanpy.h5ad
Supplementary files format and content: CellRanger Output: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger ADT Input: feature_reference.csv
Library strategy: CITE-seq

molecule: protein

source_name: Spleen

growth_protocol: Naive CD4 T cell differentiation to Th17 cells: Briefly, mice were sacrificed, and spleens were dissected and mashed over a 70μm filter in complete IMDM media (IMDM media containing 10% FBS, 100 IU/ml penicillin, 100 μg/ml streptomycin, 1mM sodium pyruvate, 1x non-essential amino acids, 50μM β-mercaptoethanol, 1mM HEPES buffer, and 2mM glutamine). Red blood cells were removed using ACK lysis buffer, and naive CD4 T cells were purified using the MACS Miltenyi negative CD4 T cell selection kit (Militenyi; 130-104-454). To generate Th17 cells, naive CD4 T cells were cultured for 72h at 37C in complete IMDM media (ThermoFisher; 12440046) containing plate-bound anti-CD3 (10μg/ml; clone 145-2C11), anti-CD28 (1μg/ml; clone 37.51), IL-6 (R&D Systems; 406-ML-025/CF; 20ng/ml), recombinant human TGF-β (R&D Systems; 240-B-010/CF; 2.5ng/ml), neutralizing anti-IFN-γ (10μg/ml; clone XMG1.2), and neutralizing anti-IL-4 (10μg/ml; clone 11B11).

extract_protocol:
Extraction per 10X Genomics 3' V3 protocol.
Separate GEX and ADT libraries were prepared per 10X Genomics 3' V3 protocol.

treatment_protocol: After 72h, Th17 cultures were split and half were restimulated with phorbol myristate acetate (PMA; Millipore Sigma; P8139-1MG; 50ng/ml), ionomycin (Millipore Sigma; I3909-1ML; 750ng/ml) and BD GolgiStop (BD Biosciences; 554715) for 3 hours at 37C.  The following hashing scheme was used: All unstimulated culture samples were stained with TotalSeq-B0301 anti-mouse Hashtag1 antibody (designated: Hashtag1) and all stimulated culture samples were stained with Hashtag2. In addition to these hashes, one of six different hashes was used to distinguish each culture and panel combination: cultures A, B, and C for panel1 were stained with Hashtags 3, 4, and 5, respectively while cultures A, B, and C for panel2 were stained with Hashtags 6, 7, and 8, respectively.  Panel1 for inCITE-seq was stained with p-STAT3 Y705 (oYo1), p-p65 S536 (oYo2), and rabbit isotype (oYo3). Panel2 was stained with p-ERK1/2 T202/Y204 (oYo1) and p-FOS S32 (oYo3).  Each of the 12 samples were FACS-sorted to equal representation into a single tube and 10X Genomics 3' scRNA-seq was performed in a single well.

value: Spleen

value: Th17 T cells

value: mixed sample (stimulated, unstimulated)


title: control

description:
Library name: Sample 1
10x Genomics

value: intestinal tract

value: fed normal diet until day 13


title: rMTNR

description:
Library name: Sample 3
10x Genomics

value: fed MTNR diet until day 13, followed by a normal diet for 2 days (rMTNR)


title: mESCs,Dppa2,CHIP

description: Library name: CHIP135

value: WT

value: control


title: Input_double_mutation_rep1

value: Lin-cKit+ bone marrow cells

value: Double mutation


title: Adipose tissue, Research participant 9 after treatment

value: Subcutaneous Adipose (thigh)

value: Research participant 9

value: 50 mg mirabegron daily


title: Adipose tissue, Research participant 8 after treatment

value: Research participant 8


title: Input_Asxl1_mutation_rep2


title: ChIP input for reTSA replicate 2

description:
Library name: input_reTSA_rep2
TSA + 24h recovery followed by a second TSA treatment

value: cell line

value: mESC wt

value: 100 ng/ml TSA re-treatment following 24h recovery from TSA treatment


title: Th17 cells, stimulated and unstimulated, VivoSeq, GEX

description:
Library name: sample
GEX (3' mRNA) library

data_processing:
Data was processed using CellRanger Count.
Assembly: mm10
Supplementary files format and content: Scanpy processed file: Vivo-seq_processed_Scanpy.h5ad
Supplementary files format and content: CellRanger Output: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger ADT Input: feature_reference.csv

value: Spleen


title: Input_Asxl1_mutation_rep1


title: ChIP input for reTSA replicate 1

description:
Library name: input_reTSA_rep1
TSA + 24h recovery followed by a second TSA treatment

value: Wild type


title: Adipose tissue, Research participant 7 after treatment

value: Research participant 7


title: ATAC PMIS-miR-200ac e14.5 rep1

city: Iowa City

first: Brad

last: Amendt

state: IA

address: 51 Newton Road

department: Anatomy and Cell Biology

institute: University of Iowa

description: PMISmiR200ac ATAC

library_source: genomic single cell

data_processing:
CellRanger-ARC version 2.0.2, CellBender version 0.1.0
Raw sequencing reads were aligned to the mm10 genome build using the 10X Genomics toolkit CellRanger-ARC version 2.0.2 (cellranger-arc count), with default settings
Raw RNA UMI count matrices underwent further processing using CellBender. Parameters ("--total-droplets-included = 25000", "--low-count-threshold = 10", and "--epochs = 200", "--expected-cells = 1.5 times the number of nuclei output by CellRanger")
UMI count per nucleus > 200, gene count per nucleus > 150, and mitochondria gene-derived UMI < 25%
ATAC Parameters (nucleosome signal < 1.2, transcription start site (TSS) enrichment > 2 and percent reads in blacklisted regions < 5%)
Assembly: mm10
Supplementary files format and content: tab-delimited .csv file includes raw counts for each barcode in each sample

source_name: Embryonic Heart

extract_protocol:
Nueli were harvested using adapted protcol from 10x Genomics.  10,000 nueli were submitted per sample for GEX and ATAC
Libraries were constructing using the 10x Genomics Chromium Next GEM Signle Cell Multiome + ATAC Reagent Kit.

value: Embryonic Heart


title: Input_Kdm6b_het_rep2


title: Input_Kdm6b_het_rep1


title: H2AK119Ub ChIP-seq mESC after second TSA pulse rep2

description:
Library name: H2AK119Ub_reTSA_rep2
TSA + 24h recovery followed by a second TSA treatment
K119Ub_mreTSA_scaled.bw
K119Ub_reTSA_intersect.broadPeak

source_name: cell line


title: RNA PMIS-miR-200ac e14.5 rep1

description: PMISmiR200ac GEX


title: Adipose tissue, Research participant 6 after treatment

value: Research participant 6


title: Input_WT_rep2

value: wild type


title: ATAC PMIS-miR-200c e14.5 rep1

description: PMISmiR200c ATAC


title: H2AK119Ub ChIP-seq mESC after second TSA pulse rep1

description:
Library name: H2AK119Ub_reTSA_rep1
TSA + 24h recovery followed by a second TSA treatment
K119Ub_mreTSA_scaled.bw
K119Ub_reTSA_intersect.broadPeak


title: Adipose tissue, Research participant 5 after treatment

value: Research participant 5


title: Input_WT_rep1


title: RNA PMIS-miR-200c e14.5 rep1

description: PMISmiR200c GEX


title: H3K27ac ChIP-seq mESC after second 24h recovery  rep1

description:
Library name: H3K27ac_reREC_rep1
TSA + 24h recovery followed by a second TSA treatment and 24 hours of recovery
K27ac_mreREC_scaled.bw
K27ac_reREC_intersect.broadPeak

value: 24h recovery from a second round of TSA treatment


title: H3K27me3 ChIP-seq mESC after second TSA pulse rep2

description:
Library name: H3K27me3_reTSA_rep2
TSA + 24h recovery followed by a second TSA treatment
K27me3_mreTSA_scaled.bw
K27me3_reTSA_intersect.broadPeak


title: ChIP_H3K27me3_double_mutation_rep2

value: Lin-cKit+ bone marrow cells

value: H3K27me3 (Millipore 07-449)


title: Adipose tissue, Research participant 4 after treatment

value: Subcutaneous Adipose (thigh)

value: Research participant 4


title: Adipose tissue, Research participant 3 after treatment

value: Research participant 3

value: 50 mg mirabegron daily


title: ChIP_H3K27me3_double_mutation_rep1

value: Double mutation


title: H3K27me3 ChIP-seq mESC after second TSA pulse rep1

description:
Library name: H3K27me3_reTSA_rep1
TSA + 24h recovery followed by a second TSA treatment
K27me3_mreTSA_scaled.bw
K27me3_reTSA_intersect.broadPeak

value: cell line

value: mESC wt


title: H3K4me3 ChIP-seq mESC after second TSA pulse rep2

description:
Library name: H3K4me3_reTSA_rep2
TSA + 24h recovery followed by a second TSA treatment
K4me3_mreTSA_scaled.bw
K4me3_reTSA_intersect.broadPeak

value: 100 ng/ml TSA re-treatment following 24h recovery from TSA treatment


title: ATAC PMIS-miR-200a e14.5 rep1

description: PMISmiR200a ATAC


title: RNA PMIS-miR-200a e14.5 rep1

description: PMISmiR200a GEX


title: H3K4me3 ChIP-seq mESC after second TSA pulse rep1

description:
Library name: H3K4me3_reTSA_rep1
TSA + 24h recovery followed by a second TSA treatment
K4me3_mreTSA_scaled.bw
K4me3_reTSA_intersect.broadPeak

value: Wild type


title: ChIP_H3K27me3_Asxl1_mutation_rep2


title: ATAC Wild Type e14.5 rep1

description: Wildtpye ATAC

value: Wild-Type


title: Adipose tissue, Research participant 1 after treatment

value: Research participant 1


title: ChIP_H3K27me3_Asxl1_mutation_rep1


title: RNA Wild Type e14.5 rep1

description: Wildtype GEX

value: Embryonic Heart


title: ChIP_H3K27me3_Kdm6b_het_rep2


title: Adipose tissue, Research participant 10 baseline

value: Research participant 10


title: H3K4me1 ChIP-seq mESC after second TSA pulse rep1

description:
Library name: H3K4me1_reTSA_rep1
TSA + 24h recovery followed by a second TSA treatment
K4me1_mreTSA_scaled.bw
K4me1_reTSA_intersect.broadPeak


title: Lung, Dua

first: Zhong

last: Yiye

address: No.800 Dongchuan Road

institute: Shanghai Jiao Tong University

description: 10x Genomics

data_processing:
The final library pool was sequenced on the Illumina NovaSeq 6000 platform and the sequencing data were processed using the Cell Ranger software (10X Genomics).
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 3.1.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, genes.tsv, matrix.mtx)

source_name: lung

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 5’ V3.1 Reagent Kits (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 5’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

value: BALB/C

tag: disease state

value: 4T1 breast cancer model

value: lung

value: female

tag: age

value: 6-8 weeks

value: oncolytic virus therapy


title: Adipose tissue, Research participant 9 baseline

value: Subcutaneous Adipose (thigh)

value: Research participant 9


title: ChIP_H3K27me3_Kdm6b_het_rep1

value: Lin-cKit+ bone marrow cells

value: H3K27me3 (Millipore 07-449)


title: H3K27ac ChIP-seq mESC after second TSA pulse rep2

description:
Library name: H3K27ac_reTSA_rep2
TSA + 24h recovery followed by a second TSA treatment
K27ac_mreTSA_scaled.bw
K27ac_reTSA_intersect.broadPeak

value: cell line

value: mESC wt


title: Adipose tissue, Research participant 8 baseline

value: Research participant 8


title: ChIP_H3K27me3_WT_rep2

value: wild type


title: h3

city: Chongqing

first: hu

last: kaiyao

address: shapingba District of Chongqing

institute: the third military medical university

data_processing:
Removing reads containing sequencing adapter
Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format
Assembly: HISAT2 (v2.0.4)
Supplementary files format and content: Excel files include FPKM values for each Sample.

organism: Rattus norvegicus

source_name: abdominal aortas

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
RNA libraries were prepared for sequencing using standard protocols

value: Sprague-Dawley rats

value: aneurysm treated with NP


title: H3K27ac ChIP-seq mESC after second TSA pulse rep1

description:
Library name: H3K27ac_reTSA_rep1
TSA + 24h recovery followed by a second TSA treatment
K27ac_mreTSA_scaled.bw
K27ac_reTSA_intersect.broadPeak

value: Wild type

value: 100 ng/ml TSA re-treatment following 24h recovery from TSA treatment


title: Adipose tissue, Research participant 2 after treatment

value: Research participant 2

value: 50 mg mirabegron daily


title: h2


title: Adipose tissue, Research participant 7 baseline

value: Research participant 7


title: RNA-seq_DM_rep3

data_processing:
The fastq files were quality controlled by fastqc and trimmed by Trimmomatic
Clean reads were aligned to the reference genome using STAR
The raw read counts of each gene were calculated using HTSeq
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA from individual mice was isolated with RNeasy Plus Mini Kit (QIAGEN)
The RNA libraries were prepared with the NEB Ultra RNA kit and followed by sequencing with a read length of 50 bp using the Illumina NextSeq 500

value: Double mutation


title: ChIP_H3K27me3_WT_rep1


title: Adipose tissue, Research participant 6 baseline

value: Research participant 6


title: h1


title: RNA-seq_DM_rep2


title: rMTNR-FMT_C57BL/6J mice

first: Tomoaki

last: Hara

address: Yamadaoka 2-2

institute: The University of Osaka

description: Library name: Sample 22

data_processing:
Sequencing was performed on an MGI DNBSEQ-G400 platform in a 100-base paired-end mode.
The DNBSEQ control software operated base calling analysis software and delivered raw sequencing data.
Sequence quality of the FASTQ files was assessed using FastQC, and reads were trimmed based on quality scores using Trimmomatic. Trimmed reads were aligned to the mouse reference genome sequences (GRCm38) using Hisat2.
SAM files were converted to BAM format with Samtools, and gene-level read counts were generated using featureCounts.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes count values for each Sample

extract_protocol:
A moderate amount of intestinal tract was placed in ISOGEN (NIPPON GENE), crushed with a mixer, and RNA was extracted according to ISOGEN protocol.
Ribosomal RNA was depleted using Ribo-Zero Plus rRNA Depletion Kit (Illumina) and the library was prepared using a TruSeq Stranded mRNA sample preparation kit (Illumina) without RPB (mRNA Purification Beads) process.

value: intestinal tract

value: fed MTNR diet for 15 days and then received fecal transplants once daily for two consecutive days from rMTNR mice donors, and were analyzed one day after the second transplantation.


title: Adipose tissue, Research participant 4 baseline

value: Subcutaneous Adipose (thigh)

value: Research participant 4


title: rMR-FMT_C57BL/6J mice

description: Library name: Sample 20

value: fed MTNR diet for 15 days and then received fecal transplants once daily for two consecutive days from rMR mice donors, and were analyzed one day after the second transplantation.


title: Adipose tissue, Research participant 5 baseline

value: Research participant 5


title: rTNR-FMT_C57BL/6J mice

description: Library name: Sample 21

value: fed MTNR diet for 15 days and then received fecal transplants once daily for two consecutive days from rTNR mice donors, and were analyzed one day after the second transplantation.


title: m3

value: aneurysm without treatment


title: H3K4me1 ChIP-seq mESC after second TSA pulse rep2

description:
Library name: H3K4me1_reTSA_rep2
TSA + 24h recovery followed by a second TSA treatment
K4me1_mreTSA_scaled.bw
K4me1_reTSA_intersect.broadPeak

data_processing:
Data were mapped using bowtie2 against mm10 and hg19 and duplicates reads were discarded. Unique mouse and human reads were discarded and a donwsampling factor for spike-in normalisation was calulated as in Fursova et al. (2019) and bigwigs were produced directly from deduplicated bam files. For detailed protocol see the Method section of the adjoining paper.
Assembly: mm10
Supplementary files format and content: Processed files are given as a spike-in normalised mouse bigwig file of the two merged replicates except for YY1 where replicates have not been merged. Peak files correspond to high-confidence peaks present in both replicates exceept for YY1 where replicates are presented separately.

extract_protocol:
Chromatin was fixed with 1% formaldehyde for 10 min at RT. To each 12 million mouse cells 1 million HEK cells were added for spike-in calibration. Nuclei were isolated with three different lysis buffers as in Lee et al., 2006 and sonicated in the lysis buffer 3 until the chromatin was disrupted to the size between 200 and 500bp.  For detailed protocol see adjoning paper.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina according to manufacturer's instructions.

value: cell line

value: mESC wt


title: RNA-seq_DM_rep1

value: Lin-cKit+ bone marrow cells


title: m2

value: Sprague-Dawley rats


title: C-FMT_C57BL/6J mice

description: Library name: Sample 19

value: fed MTNR diet for 15 days and then received fecal transplants once daily for two consecutive days from donors fed normal diet for 15 days, and were analyzed one day after the second transplantation.


title: Adipose tissue, Research participant 3 baseline

value: Research participant 3


title: m1


title: RNA-seq_Asxl1_mutation_rep3


title: Lung, Con

description: 10x Genomics

value: BALB/C

value: 4T1 breast cancer model

value: lung

value: female

value: 6-8 weeks

value: control


title: RNA-seq_Asxl1_mutation_rep2


title: rMTNR-FMT_BALB/c mice

description: Library name: Sample 18

value: intestinal tract

value: fed MTNR diet for 15 days and then received fecal transplants once daily for two consecutive days from rMTNR mice donors, and were analyzed one day after the second transplantation.


title: Adipose tissue, Research participant 2 baseline

value: Subcutaneous Adipose (thigh)

value: Research participant 2


title: rTNR-FMT_BALB/c mice

description: Library name: Sample 17

value: fed MTNR diet for 15 days and then received fecal transplants once daily for two consecutive days from rTNR mice donors, and were analyzed one day after the second transplantation.


title: HEK293_Input

city: Austin

first: Svetlana

last: Panina

address: 101 East 21st St.

department: Molecular Biosciences

institute: The University of Texas at Austin

description: Library name: HEK293_Input

data_processing:
After initial assessment of read quality, pThr4 single-end ChIP-Seq reads were mapped onto human reference genome, hg38, using BWA v.0.7.17. with default parameters.
Coverage tracks in .bigwig format were generated from filtered .bam files (mapq > 20). Normalization was performed using log2-ratio of read counts over Input.
TSS/TES profiling was done using plotProfile on matrices generated with 50-bp bins using the computeMatrix function from the deeptools v.2.2.3
Assembly: hg38
Supplementary files format and content: bw, bed

source_name: embryonic kidney

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Crosslinking was performed using 1% formaldehyde for 10 min. Crosslinking was quenched with 0.125 M glycine for 5 min. Cells were successively lysed in lysis buffer LB1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1× PI), LB2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1× PI) and LB3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1× PI). Chromatin was sonicated to an average size of ~200–500 bp using UCD-200 Biorupter (30s on and 30 s off for 30 min). A total of 5 μg of pThr4 antibody (Active Motif, cat: 61361) was pre-mixed in a 50μl volume of Dynabeads protein A or protein G (Invitrogen) and was added to each sonicated chromatin sample and incubated overnight at 4°C. The chromatin-bound beads were washed two times with low salt buffer (0.1% Na Deoxycholate, 1% Triton X-100, 1mM EDTA, 50mM HEPES pH 7.5, 150mM NaCl), once with high salt wash buffer (0.1% Na Deoxycholate, 1% Triton X-100, 1mM EDTA, 50mM HEPES pH 7.5, 500mM NaCl), once with LiCl wash buffer (250mM LiCl, 0.5% NP-40, 0.5% Na-Deoxycholate, 1mM EDTA, 10mM Tris-Cl pH 8.0) and twice in TE buffer. The chromatin was reverse crosslinked overnight at 65°C with shaking at 750rpm. After DNA extraction using phenol-chloroform, the DNA was resuspended in 10mM Tris-HCl pH 8.0.
The extracted DNA was used to construct the ChIP-seq library using the NEBNext Ultra II DNA Library Prep Kit followed by sequencing with an Illumina HiSeq 3000.

treatment_protocol: To prepare pThr4_Mut samples for pThr4 ChIP, we treated HEK293 cell lysate with catalytically dead Ssu72 (Mutant) at 4°C for 30 minutes before binding to the 6D7 antibody. Every Mut sample corresponds to its paired Ssu72-treated sample (rep1, rep2).

value: embryonic kidney

value: normal

value: WT


title: rMR-FMT_BALB/c mice

city: Suita

description: Library name: Sample 16

value: fed MTNR diet for 15 days and then received fecal transplants once daily for two consecutive days from rMR mice donors, and were analyzed one day after the second transplantation.


title: RNA-seq_Asxl1_mutation_rep1

value: Lin-cKit+ bone marrow cells


title: MHCC97L cells

city: Guangzhou

first: Yun

middle: yun

last: Xiao

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

description: Sample 2

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.11.2 was subsequently employed to convert aligned short reads into read counts for each gene model.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes counts for each Sample

growth_protocol: MHCC97H and MHCC97L cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS; HyClone, Logan, UT, USA) at 37 °C in a 5% CO2 incubator.

extract_protocol:
Total RNA from cultured cells was extracted by using the Trizol reagent as the manufacturer instructed.
RNA libraries were prepared for sequencing using NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra RNA Library Prep Kit for Illumina.

value: Hepatocellular carcinoma cells

tag: phenotype

value: low spontaneous metastatic potential


title: Adipose tissue, Research participant 1 baseline

value: Research participant 1


title: RNA-seq_Kdm6b_het_rep3


title: rMTNR_C57BL/6J mice

description: Library name: Sample 14

value: fed MTNR diet until day 13, followed by a normal diet for 2 days (rMTNR)


title: RNA-seq_Kdm6b_het_rep2


title: C-FMT_BALB/c mice

description: Library name: Sample 15

value: fed MTNR diet for 15 days and then received fecal transplants once daily for two consecutive days from donors fed normal diet for 15 days, and were analyzed one day after the second transplantation.


title: HEK293_Ssu72_rep2

description: Library name: HEK293_Ssu72_rep2_ChIP


title: MHCC97H cells

description: Sample 1

value: high spontaneous metastatic potential


title: RNA-seq_WT_rep3

value: wild type


title: HEK293_Ssu72_rep1

description: Library name: HEK293_Ssu72_rep1_ChIP


title: RNA sequencing from transfected k562 cells, replicate 3

city: VANCOUVER

first: Nicole

last: Knoetze

state: British Columbia

address: 675 west 10th avenue

institute: Canada's Michael Smith Genome Sciences Centre

description: Library name: K562_RNA3

data_processing:
The 10bp UMIs were extracted from the sequencing reads using umi-tools (version 1.1.4, bc-pattern=.*AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC(?P<umi_1>.{{10}}).*). Illumina P7 and P5 adapters  were removed using cutadapt (version 4.7, quality_cutoff=10, min_length=80). Reads were mapped to our oligo library using bowtie2 (version 2.5.3). Only the primary alignments were retained, as well as properly paired reads where both reads had a mismatch of 0 with the aligned sequence (samtools version 1.19 -F 780, -f 2, bamtools 2.5.2, NM:0). The number of unique UMIs observed for each oligo was calculated to obtain a DNA and RNA count. Analysis of the STARR-seq data was performed for K562 and Jurkat cells separately. Only oligos with a DNA count >= 10 across all eight replicates were retained. Oligos with an RNA count of 0 in all replicates were also removed. RNA and DNA counts were adjusted for library size using counts per million (CPM). Finally, the DNA replicates were collapsed into a single value by averaging the DNA CPM values. For oligos with an RNA and DNA count greater than zero, an activity score representing the log2(RNA/DNA) was calculated for each replicate (n=3). The activity score for the synthetic background oligo without any motifs was subtracted from the activity score for each oligo to obtain the final, adjusted activity score
Assembly: GRCh37
Supplementary files format and content: Deduplicated counts, CPM normalised counts, and log2fc scores for all oligos and samples

molecule: other

growth_protocol: Jurkat (gifted from the Weng lab) and K562 (ATCC CCL-243) cells were cultured in cRPMI media (RPMI media with 10% FBS, 1% Penicillin/streptomycin, 1mM HEPES, 1mM sodium pyruvate).

extract_protocol:
1ug of DNA of the plasmid library was digested with AgeI-HF (NEB) overnight and then purified by QIAquick PCR purification kit following the manufacturer’s instructions, but eluted in 35μL EB.
18μL of the linearized library DNA was used for the UMI PCR: 7.5μL SS_UMI_r primer (10μM), 50μL KAPA 2x HIFI Hotstart ready mix in a total of 100μL reaction. One cycle of 98 °C for 60s, 65 °C for 30s, and 72 °C for 90s to integrate UMI into the STARR-seq library and then purified using QIAQuick PCR purification kit as per the manufacturer’s instructions, except that the columns were eluted twice with 10 μL EB.  Two sequencing-ready PCR reactions were carried out using 100ng of UMI-tailed template DNA, 2.5μL SS_i5_XX_f primer (10uM), 2.5μL SS_P7seq_r primer (10uM), 25μL KAPA 2x HiFi HotStart Ready Mix in 50μL total reaction. PCR conditions were: 1 cycle at  98oC for 45s, 9 cycles at 98oC for 15s, 60oC for 30s, 72oC for 45s, 1 cycle at 72oC for 120s. PCR reactions are purified using the QIAQuick PCR purification kit as per the manufacturer’s instructions, using only one column and eluting twice with 10μL EB and pooling.. For the RNA libraries, we performed junction PCR (jPCR) as described in Neumayr et al. (2019). Briefly, a 50 µL PCR reaction was prepared containing 20 µL of cDNA, 25 µL of LongAmp 2x Master mix (NEB), and 2.5 µL of each of the SS_intspan_f and SS_P7seq_r 10 µM primers. PCR was performed with initial denaturation at 98 °C for 60 seconds (s), and 16 cycles of denaturation at 98 °C for 15 s, annealing at 65 °C for 30 s, and extension at 72 °C for 70 s, and a final extension at 72 °C for 300 s. The products of jPCR were purified and SPRI beads and quantified using Qubit 1x dsDNA HS reagent (Thermo Fischer Scientific). A final sequencing-ready PCR was performed to add Illumina sequencing adapters to the fragments. Briefly, a 50 µL PCR reaction was prepared containing 20 µL of jPCR products, 25 µL of LongAmp 2x Master mix, and 2.5 µL of each of SS_i5_f and SS_P7seq_r primers at 10 µM. PCR was performed with initial denaturation at 98°C for 45s, 5 cycles of denaturation at 98°C for 15s, annealing at 65°C for 30s, extension at 72°C for 45s, and a final extension at 72°C for 120s. The final sequencing PCR products were purified using SPRI beads


title: HEK293_Mut_rep1

description: Library name: HEK293_Mut_rep1_ChIP

value: Mutant-phosphatase


title: rMR_C57BL/6J mice

description: Library name: Sample 12

value: intestinal tract

value: fed MR diet until day 13, followed by a normal diet for 2 days (rMR)


title: RNA sequencing from transfected k562 cells, replicate 2

description: Library name: K562_RNA2


title: RNA sequencing from transfected k562 cells, replicate 1

description: Library name: K562_RNA1


title: control group_3

city: Yangling

first: xiaoxuan

state: ShaanXi

address: 3 Taicheng Street

institute: Northwest A & F University

description: Library name: sample12

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLc genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: UCSC assembly ID: galGal6 / NCBI Assembly: GCF_000002315.6 (GrCM38)
Supplementary files format and content: 12 text files separated by tabs (in CSV format), each file representing the counts of all genes measured for 4 groups (with each sample undergoing biological replication 3 times).

organism: Gallus gallus

source_name: liver

growth_protocol: LMH  cells were maintained in DMEM/F-12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
At 12 hpi, total RNA was extracted via TRIzol (TaKaRa, Tokyo, Japan).  1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols.

treatment_protocol: The cells were inoculated with CH/SX/201805-1 (MOI = 1), CH/SX/201805-4 (MOI = 1), or a mixture of both (MOI = 0.5 each)

value: liver

value: Leghorn Male Hepatoma cell line

value: NON


title: rMTNR_BALB/c mice

description: Library name: Sample 11


title: RNA sequencing from transfected jurkat cells, replicate 3

description: Library name: Jurkat_RNA3

source_name: Jurkat

value: Jurkat


title: RNA-seq_WT_rep2


title: RNA-seq_WT_rep1


title: rTNR_C57BL/6J mice

description: Library name: Sample 13

value: fed TNR diet until day 13, followed by a normal diet for 2 days (rTNR)


title: control group_1

description: Library name: sample10

value: WT


title: HEK293_Mut_rep2

description: Library name: HEK293_Mut_rep2_ChIP

value: embryonic kidney

value: normal


title: RNA sequencing from transfected jurkat cells, replicate 2

description: Library name: Jurkat_RNA2


title: CH_SX_201805_1+4_3

description: Library name: sample9

value: cells were inoculated with CH/SX/201805-1 (MOI = 0.5) and CH/SX/201805-1 (MOI = 0.5)


title: MTNR_C57BL/6J mice

description: Library name: Sample 8

value: fed MTNR diet until day 13


title: RNA-seq_Kdm6b_het_rep1

value: Lin-cKit+ bone marrow cells


title: DNA sequencing of the plasmid library, replicate 8

description: Library name: plasmid_8

source_name: plasmid

value: plasmid


title: CH_SX_201805_1+4_2

description: Library name: sample8


title: rMR_BALB/c mice

description: Library name: Sample 9


title: TNR_C57BL/6J mice

description: Library name: Sample 7

value: fed TNR diet until day 13


title: DNA sequencing of the plasmid library, replicate 7

description: Library name: plasmid_7


title: CH_SX_201805_1+4_1

description: Library name: sample7


title: CH_SX_201805_4_3

description: Library name: sample6

value: cells were inoculated with CH/SX/201805-4 (MOI = 1)


title: control group_2

description: Library name: sample11


title: DNA sequencing of the plasmid library, replicate 6

description: Library name: plasmid_6


title: MR_C57BL/6J mice

description: Library name: Sample 6

value: fed MR diet until day 13


title: CH_SX_201805_4_2

description: Library name: sample5


title: L. fermentum derived EV treated HEK297T cells

city: Pyeongchag

first: seoah

last: Park

address: 1447-1, Pyeongchang-daero, Daehwa-myeon, Pyeongchang-gun, Gangwon-do, Republic of Korea

country: South Korea

institute: Seoul National University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HEK293T cell line (ATCC, Manassas, VA) was maintained in DMEM (Gibco) with 10% Fetal Bovine Serum (FBS) (Gibco) under 5% CO2 condition at 37°C

extract_protocol: After washing and lysing the cells with Buffer RLT, the complete RNA was extracted using the RNeasy Mini Kit (QIAGEN, Basel, Switzerland) as instructed by the manufacturer, including the on-column DNA digestion stage (RNase-Free DNase Set; QIAGEN).

treatment_protocol: HEK293T cell line (ATCC, Manassas, VA) was treated in DMEM with 10% FBS (Gibco) and Pk2 (10 nM) or not after reaching 80%fluence.


title: DNA sequencing of the plasmid library, replicate 5

description: Library name: plasmid_5


title: L. paracasei derived EV treated HEK297T cells


title: CH_SX_201805_4_1

description: Library name: sample4


title: MTNR_BALB/c mice

description: Library name: Sample 4

value: intestinal tract


title: DNA sequencing of the plasmid library, replicate 4

description: Library name: plasmid_4


title: CH_SX_201805_1_3

description: Library name: sample3

value: cells were inoculated with CH/SX/201805-1 (MOI = 1)


title: RNA sequencing from transfected jurkat cells, replicate 1

description: Library name: Jurkat_RNA1


title: Lc. lactics derived EV treated HEK297T cells


title: S. thermophilus derived EV treated HEK297T cells


title: rTNR_BALB/c mice

description: Library name: Sample 10


title: DNA sequencing of the plasmid library, replicate 3

description: Library name: plasmid_3


title: DNA sequencing of the plasmid library, replicate 2

description: Library name: plasmid_2


title: HEK293T control 2

source_name: HEK293T cells


title: CH_SX_201805_1_2

description: Library name: sample2

value: liver


title: L. salivarius derived EV treated HEK296T cells


title: C_BALB/c mice

description: Library name: Sample 1

value: fed normal diet until day 13


title: CH_SX_201805_1_1

description: Library name: sample1

value: Leghorn Male Hepatoma cell line


title: DNA sequencing of the plasmid library, replicate 1

description: Library name: plasmid_1