title: DLD-1 cells, AID, +Auxin, 72h, rep1


title: TIL_Bcl6-/-_UT_rep2

status: Public on Dec 19 2024

type: SRA

city: London

first: Maria

last: Vila de Mucha

address: 72 Huntley Street

country: United Kingdom

institute: UCL Cancer Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (v 3.0.2 or v7.0.0) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: Tumour-infiltrating

extract_protocol:
Following dissection, tumors were mechanically disrupted using scissors, followed by digestion with 0.33 mg/ml Liberase TL (Roche) and 0.2 mg/ml DNase (Roche) in serum-free RPMI at 37°C for 30 min. Tumors were dispersed through a 70 μm filter using PBS + 2 mM EDTA and cells resuspended in cRPMI. Lymphocytes were enriched from tumor samples by centrifugation using a Histopaque 1119 density gradient.  (Sigma-Aldrich). Cells were stained using directly conjugated antibodies against extracellular antigens and Live, CD3+ cells sorted.
Single cell RNA sequencing was carried out using the using the Chromium Single Cell 5’ V(D)J Reagent kit, v1 and v2 (10X Genomics). Purified single cell suspensions were loaded onto the 10X Chromium Controller and libraries prepared as per the manufacturer’s instructions, using AMPure beads for size selection and purification and the Bioanalyzer High sensitivity DNA assay (Agilent) to assess cDNA concentration and size of final libraries. Library concentrations were quantified by qPCR using the Illumina Library Quantification kit (KAPA). Libraries were pooled for sequencing at a final concentration of 10 nM. Pooled libraries were sequenced using a NextSeq High output run or on the NovaSeq platform using 26 x 91 paired end reads.

treatment_protocol: C57BL/6J wild-type or transgenic mice were injected subcutaneously with 0.5x10^6 MCA205 cells. Mice received 100 μg αCTLA-4 (clone 4F10-IgG2a, Evitria) on days 6 and 9, and were sacrificed on day 10.

tag: tissue

value: Tumour-infiltrating

tag: cell type

value: Tumor-infiltrating CD3+ T cells

tag: genotype

value: Cd4Cre Bcl6fl/fl

tag: treatment

value: Untreated


title: Smartseq2_73

city: New York

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

data_processing:
SmartSeq2 Analysis: Fastq files from SmartSeq2 libraries were aligned to the mouse genome (mm39) with Gencode M29 annotations using STAR (v2.7.10a). Genome-mapped BAM files were quantified with RSEM (v1.3.1), and the resulting gene/UMI count matrix was processed in Seurat (v4.1.2). Data were normalized using the LogNormalize method, with mitochondrial gene expression and library size bias regressed out via the ScaleData function. Cells with >5% mitochondrial reads were excluded. Clustering, differential expression, and gene signature scoring were performed in Seurat. Differentially expressed genes were identified using the Wilcoxon Rank Sum test, with Bonferroni-adjusted P-values < 0.05 and log2 fold changes > 0.5 considered significant.
Bulk RNA-Seq raw Fastq files were aligned to the mouse genome (mm39) with Gencode M29 annotations using STAR (v2.7.10a). The count matrix was processed in R with the DESeq2 package (v1.34). Genes with fewer than ten reads were filtered out, and sample normalization was applied using a negative binomial distribution model. Differential gene expression between conditions was assessed with the Wald test. Genes with adjusted P-values (FDR) < 0.1 were retained, and log2 fold changes were shrunk using the apeglm algorithm.
10x Genomics Analysis: Fastq files from cDNA and hashtag libraries generated on the Chromium platform (10x Genomics) were processed using Cell Ranger (v7.0.1). The resulting quantification matrix was processed in Seurat (v5.0) with normalization using the SCTransform function. Non-myeloid cell contaminants were removed based on the PanglaoDB_Augmented_2021 database and EnrichR package for R. Cells were classified by biological condition using the HTODemux function. Differentially expressed genes were identified with the Wilcoxon rank test, with Bonferroni-adjusted P-values < 0.05 and log2 fold changes > 0.3 considered significant. Signature scores were calculated using Seurat’s AddModuleScore function.
Assembly: mm10
Supplementary files format and content: Tab files from bulk RNA-Seq tab files containing the STAR gene quantification.
Supplementary files format and content: gene.results from RSEM quantification of Smartseq2 data
Supplementary files format and content: mtx, cellranger output from 10x genomics libraries.
Supplementary files format and content: rds, images of Seurat objects used in the analysis

molecule: polyA RNA

source_name: D-LN

extract_protocol:
Lymph nodes and gut tissue were dissected, finely chopped, and digested in RPMI medium with Collagenase D to obtain single-cell suspensions. For gut-associated lymph nodes, duodenal lymph nodes were identified using anatomical markers. Dendritic cells were isolated from the duodenal lamina propria by separating intestines, removing mucus with PBS and DTT, and stripping epithelium with EDTA. The tissue was further digested with DNaseI and collagenase, followed by Percoll gradient centrifugation to isolate DCs. Single-cell sorting of DCs was conducted into 96-well plates with TCL buffer and stored at –80°C.
Library Preparation for Single-cell RNA-seq (SmartSeq2). Single cells were sorted onto plates, covering all conditions in each replicate. RNA was extracted using RNAClean XP SPRI beads, then reverse-transcribed into cDNA with RT and TSO primers. The cDNA was amplified, cleaned with SPRI beads, and tagmented using the Nextera XT DNA Library Preparation Kit (Illumina). Barcoded libraries were pooled and sequenced on the Illumina Nextseq 550 platform. Library Preparation for Single-cell RNA-Seq (10x Genomics). Cells were labeled with hashtag oligonucleotide (HTO)-tagged antibodies, sorted, and counted for viability. scRNA-seq libraries were generated using the 10x Genomics Chromium system, following the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq SP flowcell at a minimum depth of 30,000 reads per cell. Library Preparation for Bulk RNA-seq. RNA was isolated using RNAClean XP beads. Reverse transcription was performed with specific primers, followed by cDNA amplification with KAPA HiFi HS Ready Mix. The amplified product was cleaned with RNAClean XP beads and tagmented using the Nextera XT DNA Library Preparation Kit (Illumina). Libraries were pooled and sequenced as 75-base single-end reads on an Illumina NextSeq platform.

treatment_protocol: Mice were treated with dietary ovalbumin (OVA) to induce tolerance. For infection conditions, mice were infected with Heligmosomoides polygyrus (H.p.) or Strongyloides venezuelensis (S.v.) to model chronic and acute type 2 immune responses, respectively.

value: D-LN

tag: number of_cells_sorted

value: OV


title: P2_t24 rep3

city: Girona

middle: Pla

last: de Solà-Morales

state: Catalonia

address: Campus Montilivi (EPS-1)

department: Institute for Agricultural and Food Technology

country: Spain

institute: Universitat de Girona

library_source: transcriptomic

data_processing:
Small RNA-Seq reads were trimmed using Trim Galore version 0.6.6 (Krueger, 2021).
Sequences were mapped against Prunus persica reference genome (Prunus_persica_NCBIv2) using STAR software version 2.5.3a (Dobin et al., 2013) with ENCODE parameters for small reads.
Annotated genes were quantified using release 48 of EnsemblPlants annotation with RSEM version 1.3.0 (Li and Dewey, 2011), changing only the default parameter of seed length to 16.
Annotated pre_miRNA gene biotypes were analyzed for differential expression between time points using the DESeq2 v1.26.0 R package (Love et al., 2014). Adjusted p-values below 0.05 were considered to indicate differential expression.
Assembly: Prunus_persica_NCBIv2
Supplementary files format and content: Matrix table with raw gene counts for every Pre miRNA gene and every sample

organism: Prunus persica

source_name: leaf

growth_protocol: Prunus persica var. Big Top (peach) juvenile plants were produced using in vitro technology and grown in individual small pots by a professional grower (Agromillora Iberia S.A., Barcelona, Spain). Prior to experiments they were acclimatized for two weeks in a glasshouse (21ºC, 16/8 h light/dark photoperiod).

extract_protocol:
RNA was extracted from a 200 mg aliquot of ground leaf sample through a TRIzol-based procedure (Invitrogen Life Technologies, Carlsbad, CA, USA) followed by DNAse I (Ambion, Grand Island, NY, USA) digestion and purification with RNeasy MinElute Cleanup Kit (Qiagen, Sollentuna, Sweden). Estimation of RNA concentration was using a NanoDrop ND1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
miRNA-Seq was carried out at the National Centre for Genomics Analysis (Barcelona, Spain). Libraries were prepared using the NEBNext® Small RNA Library Prep Set for Illumina® kit (ref. E7330) according to the manufacturer's protocol. Briefly, RNA was subjected to adaptor 3´and 5´ ligation and first strand cDNA synthesis. Then, DNA fragments having adapter molecules on both ends were selectively enriched by PCR. Library amplification was performed by using NEBNext® Multiplex Oligos for Illumina (Index Primers Set 1, ref. E7335, Index Primers Set 2, ref. E7500, Index Primers Set 3, ref. E7710 and Index Primers Set 4, ref. E7730). Purification steps were then performed using AgenCourt AMPure XP beads (ref. A63882, Beckman Coulter) and final libraries were analyzed using Agilent Bioanalyzer (ref. 5067-4626) to estimate the quantity and check size distribution. A pool was done to perform size selection using 6% Novex TBE PAGE Gels (ref. EC6265BOX) and then the final pool was quantified by qPCR using the KAPA Library Quantification Kit (ref. KK4835, KapaBiosystems) prior to amplification with Illumina's cBot. Libraries were sequenced 1 * 50+8 bp on Illumina HiSeq2500 device

treatment_protocol: For treatment with PpPep2, the five youngest fully expanded leaves of each plant were selected and labelled; PpPep2 1 µM was sprayed onto both abaxial and adaxial leaf surfaces. Plants were incubated under standard conditions in the glasshouse. Treated leaves were detached 1 and 24 h after PpPep2 treatment, the central vein was cut out and the leaf blades were immediately frozen in liquid nitrogen for subsequent RNA extraction.

value: leaf

tag: time


title: TIL_CD4Cre_UT_rep1

description: 10x Genomics


title: HCT116, SY5609, pSer2, ChIP

city: Boulder

first: Olivia

last: Luyties

state: CO

address: 3415 Colorado Ave, JSC Biotech Building

department: Biochemistry

institute: University of Colorado Boulder

library_source: genomic

data_processing:
All samples were sequenced on a NovaSeq 6000 by the Gates Institute Genomics Core at CU Anschutz. Sequencing was done in two runs to achieve greater depth, and resulting fastq files from each run were concatenated and repaired with the bbmap repair function.
Initial sample processing and quality control was performed using the Dowell Lab ChIP-Flow pipeline (https://github.com/Dowell-Lab/ChIP-Flow).
Adapters were trimmed and reads were mapped to the GRCh38 reference genome (UCSC Assembly, December 2013) using hisat2 and bbmap.
Duplicate, multimapping, and non-mapping reads were removed via sambamba. Indices for bams containing only uniquely mapped reads were generated using samtools 1.18.0. Data was then normalized to 1x read coverage via the DeepTools bamCoverage package.
Assembly: hg38
Supplementary files format and content: bigWigs

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HCT116 cells (ATCC# CCL-247) were grown to 70-90% confluency in McCoy’s 5A medium and supplemented with 10% Fetal Bovine Serum and 1% Penicillin/Streptomycin antibiotic at 37°C and 5% CO2.

extract_protocol:
Cells were crosslinked with a final concentration of 1% methanol-free formaldehyde for ten minutes while shaking at 145 RPM on an orbital shaker. Cells were quenched with 2.5 M Glycine to a final concentration of 125 mM for 8-10 minutes. Cells were harvested, washed with ice cold PBS (no calcium, no magnesium), and incubated in NRO buffer at a concentration of 80 μL/1 million cells for five minutes twice. Nuclei were pelleted, frozen in liquid nitrogen, and stored at -76°C for future use. Nuclei were thawed on ice for 1.5-3 hours. Once pellets thawed, nuclei were resuspended in 1 mL Covaris Lysis Buffer B + 1x Protease Inhibitors and incubated for 10 minutes at 4°C with nutation. Nuclei were then washed with 1 mL Covaris Wash Buffer C + 1x Protease Inhibitors and incubated for 10 minutes at 4°C with nutation. Nuclei were washed with 500 μL Shearing Buffer D3 + 1x Protease Inhibitors and resuspended in 1 mL of the same solution per ~20 million cells. Nuclei were then aliquoted into AFA millitubes (1 mL/tube) and sheared on the Covaris M220 Focused Ultrasonicator for 12 minutes at 6°C, duty factor 10%, peak power 75, 200 cycles/burst. Sheared chromatin was divided into 750-780 μL aliquots (~15 million cells/aliquot) into pre-chilled Eppendorf tubes, frozen in liquid nitrogen, and stored at -76°C for future use if not immediately proceeding to the IP step. If needed, sheared chromatin was thawed on ice for 2-3 hours.
Libraries were prepared using the KAPA Hyperprep Kit. 1 ng of total DNA from each sample was diluted in 50 μL 0.1x TE buffer and subjected to end repair and A-tailing. Following ligation, a 0.8x bead cleanup was performed, and the libraries were amplified 14 cycles.

treatment_protocol: Cells treated with SY-5609 received a final concentration of 50 nM. Working concentrations of all inhibitors were created to ensure an equal volume of drug was applied to all conditions except those treated with both inhibitors. Control cells received an equivalent volume of DMSO. Cells were incubated with either inhibitor or DMSO for 30 minutes at 37°C and 5% CO2, at which point IFNγ was added to the same media to a final concentration of 10 ng/mL. Cells were incubated with interferon for 45 minutes at 37°C and 5% CO2.

tag: cell line

value: human colorectal cancer

tag: chip antibody

value: Millipore-Sigma (#04-1571-I)

value: 10ng/mL IFN, 50nM SY-5609


title: DLD-1 cells, AID, Wash, 24h, rep3

city: Chicago

first: Feng

last: Yue

state: IL

address: 303 E Superior St

department: Biochemistry and Molecular Genetics

institute: Northwestern university

data_processing:
Illunuma BaseSpace CLItools v.1.0.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore v.0.6.10
Trimmed sequence reads were mapped to hg38 using STAR.
The TPM value of gene expression was caculated using RSEM.
Assembly: Hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: DLD-1 cells(ATCC ) was gifted by Dr. Ali Shilatifard Lab.DLD-1 cells were cultured in RPMI1640 Medium (Gibco, 11875093) supplemented with 10% fetal bovine serum (ThermoFisher, 12440053) and 1% penicillin–streptomycin.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II directional with Poly-A Selection Kit.

treatment_protocol:
GATA6 protein degradation was induced by treating positive GATA6-IAA7 clones with DLD-1 complete medium supplemented with 500uM IAA (sigma, I5148) for various timepoints.
For IAA washout, we removed IAA 12 hours after IAA treatment. Cells were first washed with 1x DPBS three times and then maintained in DLD-1 complete medium for 24 or 48 hours.
For mouse xenograft, ten 5-6 weeks old athymic nude mice were used for each condition. 1M DLD-1 control or GATA6-KO cells were injected into the right flank of nude mice. Daily measurement of tumor size started 4 days after inoculation. All procedures were performed in accordance with the Institutional Animal Care and Use Committee (IACUC) at Northwestern university

value: colorectal adenocarcinoma

value: -Auxin


title: KPCt.SIY replicate 3

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
Illumina NextSeq 500 using v3 chemistry. NextSeq Software: Control v4.0.0.19, RTA 2.11.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Sequence reads were processed using nf-core/rnaseq workflow revision 3.14.0 and tximport version 1.28.0
Assembly: mm10 with ensembl version 110 annotation
Supplementary files format and content: 210602GerA_intCt.txt.gz is a tab delimited text of integer count data
Supplementary files format and content: 210602GerA_l2tpm.txt.gz is a tab delimited text of log2 TPM data with a +1 offset

source_name: KPCt.SIY cell line (KrasG12D and Trp53-/-) expressing SIY-GFP

growth_protocol: KPCt.SIY and KPS2.SIY cells were seeded in 15 cm dishes and cultured in DMEM supplemented with 10%FBS, 1X HEPES, and 1% Penicillin/streptomycin and collected after 72 hours, when cells were 90% confluent.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Cat#15596026) following the manufacturer’s instruction. The aqueous phase containing the RNA was then purified using the RNeasy MinElute Cleanup Kit (Qiagen, Cat# 74204) according to the manufacturer’s instruction.
NEB polyA prep using 250 ng input and 1 to 5 adaptor dilution with 14 cycles of amplification

value: Lung adenocarcinoma cell line

value: KrasG12D and Trp53-/-; expressing SIY-GFP


title: P2_t24 rep1


title: DLD-1 cells, AID, Wash, 24h, rep2


title: Smartseq2_72


title: KPS2.SIY replicate 1

source_name: KPS2.SIY cell line (KrasG12D, Trp53-/-, Sox2) expressing SIY-GFP and overexpressing SOX2

value: KrasG12D and Trp53-/-; expressing SIY-GFP and with overexpression of Sox2


title: Smartseq2_71

value: Filtered


title: P2_t24 rep2


title: P2_t1 rep3

value: 1 h


title: KPCt.SIY replicate 2

value: KPCt.SIY cell line (KrasG12D and Trp53-/-) expressing SIY-GFP


title: P2_t1 rep2


title: DLD-1 cells, AID, +Auxin, 12h, rep3

value: +Auxin


title: DLD-1 cells, AID, +Auxin, 12h, rep2


title: Smartseq2_70


title: P2_t1 rep1


title: Smartseq2_69


title: Smartseq2_68


title: t0 rep3

value: mock

value: 0 h


title: DLD-1 cells, AID, +Auxin, 12h, rep1


title: DLD-1 cells, AID, ctrl, rep3


title: Smartseq2_66

value: D-LN


title: C57Bl/6J ZEB2 Tg heart 14d IR rep1 [1z-IR]

city: Utrecht

first: Cornelis

middle: J.

last: Boogerd

address: Uppsalalaan 8

department: Developmental Biology and Stem Cell Research

country: Netherlands

institute: Hubrecht Institute

description:
1z-IR
readCounts_raw_cIR_zIR.txt

data_processing:
STAR_2.4.2a mapping to reference genome
read count analysis HTSeq 0.6.1
Assembly: mm10
Supplementary files format and content: raw readcounts in matrix table

source_name: left ventricle

extract_protocol:
TRIzol totalRNA extraction
Illumina TruSeq stranded mRNA

value: left ventricle

value: C57B/6J Zeb2 Tg

value: Ischemia-Reperfusion injury


title: DLD-1 cells, AID, Wash, 24h, rep1


title: C57Bl/6J WT control heart 14d IR rep3 [3c-IR]

description:
3c-IR
readCounts_raw_cIR_zIR.txt

value: C57B/6J Wildtype


title: t0 rep1

value: leaf


title: DLD-1 cells, AID, ctrl, rep1

value: colorectal adenocarcinoma


title: Patient sample, C004, HiC

data_processing:
Illunuma BaseSpace CLItools v.1.0.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore v.0.6.10
The trimmed reads were aligned to the human genome reference hg38 human reference genome using BWA-MEM(v.0.7.17)
Subsequent steps involved the removal of low-quality reads and PCR duplicates. Aligned read pairs were then assembled, and redundant PCR artifacts, as well as read pairs mapped to identical restriction fragments, were eliminated. The binning process involved sorting the reads into various resolutions: 5-kb, 10-kb, 50-kb, 1-Mb, 10-Mb, and 50-Mb. This stage also concurrently implemented ICE normalization. The completion of the binning stage resulted in the creation of ICE normalized matrices in .mcool and .hic file formats.
HiChIP analysis was performed using MAPS (v.2.0.0). The detection of loop interactions was conducted at a 5-kb resolution and was limited to a maximum distance of 1 Mb. A positive Poisson model was employed to pinpoint significant interactions, adhering to a false discovery rate (FDR) of 2%. For the calling of H3K27ac peaks, MACS2 was utilized, with the parameter setting “-p narrow”.
The ChIA-PETwas processed using ChIA-PIPE(v.1.0).
Assembly: hg38
Supplementary files format and content: .hic

source_name: Patient sample

extract_protocol:
In situ Hi-C experiments were performed following the previously described protocol (Rao et al., 2014) with modifications. Briefly, chromatin extracted from crosslinked cells was digested with restriction enzymes, followed by biotin labeling, ligation, and biotin pull down.
HiChIP experiments were performed using Arima HiC+ kit following manufacture’s protocol with modifications. Briefly, 10 million cells were crosslinked with 2% formaldehyde (Millipore Sigma, 252549), followed by cell lysis, restriction enzyme digestion, end repair and biotin labeling, ligation, and shearing following Arima Hi-C procedure. Chromatin was then subjected to immunoprecipitation with H3K27ac antibody (active motif, 39133)
ChIA-PET data was generated following the previously described ChIA-PET protocol 3, 4. Antibody against GATA6 (CST, 5851) was used. The final library was sequenced as 150 PE reads on Illumina Novaseq 6000 platform.
The final library was prepared using the KAPA HyperPrep kit (KAPA, 7962363001). The final library was sequenced as 150 PE reads on Illumina Novaseq 6000 platform.

treatment_protocol: GATA6 protein degradation was induced by treating positive GATA6-IAA7 clones with DLD-1 complete medium supplemented with 500uM IAA (sigma, I5148) for various timepoints.

value: Patient sample

value: sporadic adenocarcinoma

value: BRAF muutant


title: root, organic fertilizer 100, rep 3

city: XiNing

first: JiaHui

last: Yan

state: QingHai

address: Twenty miles of Pu Town, Chengbei District

department: Institute of Plant Protection

country: China

institute: College of Agriculture and Forestry Sciences, Qinghai University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp 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 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.
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.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

organism: Hordeum vulgare

source_name: root

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: root

tag: period

value: flowering period

value: 100% organic fertilizer


title: C57Bl/6J WT control heart 14d IR rep2 [2c-IR]

description:
2c-IR
readCounts_raw_cIR_zIR.txt


title: KPCt.SIY replicate 1

value: KPCt.SIY cell line (KrasG12D and Trp53-/-) expressing SIY-GFP

value: Lung adenocarcinoma cell line

value: KrasG12D and Trp53-/-; expressing SIY-GFP


title: C57Bl/6J WT control heart 14d IR rep1 [1c-IR]

description:
1c-IR
readCounts_raw_cIR_zIR.txt


title: C57Bl/6J ZEB2 Tg heart 14d IR rep3 [3z-IR]

description:
3z-IR
readCounts_raw_cIR_zIR.txt


title: C57Bl/6J ZEB2 Tg heart 14d IR rep2 [2z-IR]

description:
2z-IR
readCounts_raw_cIR_zIR.txt


title: Smartseq2_63

value: OV


title: Patient sample, C003, HiC


title: Smartseq2_67

value: D-LN


title: C57Bl/6J WT heart 14d IR rep3 [914dIR]

description:
914dIR
raw_read_counts_sham_14dIR.txt

value: left ventricle


title: Patient sample, B004, HiC

value: TP53 mutant


title: t0 rep2

value: mock

value: 0 h


title: root, organic fertilizer 100, rep 1


title: root, organic fertilizer 100, rep 2


title: Patient sample, B002, HiC


title: DLD-1 cells, AID, ctrl, rep2

value: +Auxin


title: leaf, organic fertilizer 100, rep 2

value: leaf


title: Smartseq2_65


title: C57Bl/6J WT heart 14d IR rep1 [714dIR]

description:
714dIR
raw_read_counts_sham_14dIR.txt

value: C57B/6J Wildtype

value: Ischemia-Reperfusion injury


title: Smartseq2_64


title: Smartseq2_60


title: Patient sample, B001, HiC

value: Patient sample

value: sporadic adenocarcinoma


title: C75Bl/6J WT heart Sham_rep3 [3sham]

description:
3sham
raw_read_counts_sham_14dIR.txt

value: Sham surgery


title: leaf, organic fertilizer 100, rep 1

value: flowering period

value: 100% organic fertilizer


title: Smartseq2_59


title: Patient sample, A004, HiC


title: C75Bl/6J WT heart Sham_rep2 [2sham]

description:
2sham
raw_read_counts_sham_14dIR.txt


title: root, organic fertilizer 40, rep 3

value: root

value: 40% organic fertilizer


title: Patient sample, A003, HiC


title: Smartseq2_58

value: OV


title: C57Bl/6J WT heart 14d IR rep2 [814dIR]

description:
814dIR
raw_read_counts_sham_14dIR.txt


title: root, organic fertilizer 40, rep 2


title: C75Bl/6J WT heart Sham_rep1 [1sham]

description:
1sham
raw_read_counts_sham_14dIR.txt


title: Smartseq2_62

value: D-LN

value: Filtered


title: Smartseq2_61


title: leaf, organic fertilizer 100, rep 3


title: Patient sample, A002, HiC

value: colitis associated adenocarcinoma

value: TP53 mutant


title: Smartseq2_56


title: TIL_Prdm1-/-_aCTLA-4_rep1

description: 10x Genomics

value: Tumour-infiltrating

value: Tumor-infiltrating CD3+ T cells

value: Cd4Cre Prdm1fl/fl


title: root, organic fertilizer 40, rep 1


title: leaf, organic fertilizer 40, rep 3

value: leaf


title: Patient sample, A001, HiC


title: Smartseq2_55


title: TIL_Prdm1-/-_UT_rep1

description: 10x Genomics

value: Untreated


title: leaf, organic fertilizer 40, rep 2


title: Smartseq2_54


title: DLD-1 cells, WT, HiChIP

value: colorectal adenocarcinoma

value: WT


title: leaf, organic fertilizer 40, rep 1


title: TIL_WT_aCTLA4_rep2

description: 10x Genomics

value: WT (C57BL6/J)


title: Smartseq2_53


title: DLD-1 cells, sgGATA6, HiChIP


title: DLD-1 cells, sgGATA6, HiC


title: TIL_WT_aCTLA4_rep1

description: 10x Genomics


title: DLD-1 cells, WT, HiC


title: TIL_WT_UT_rep1

description: 10x Genomics


title: root, organic fertilizer 0, rep 3

value: flowering period

value: 0% organic fertilizer


title: Smartseq2_57


title: root, organic fertilizer 0, rep 2

value: root


title: Tra2beta iCLIP 3

city: Newcastle upon Tyne

first: Graham

last: Smith

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

data_processing:
Samples were analysed using the 'Demultiplex and Analyse' workflow of the iMAPS server at https://imaps.goodwright.com/:
demultiplexed fastq was produced with ultraplex version 1.2.5
Reads were adapter-trimmmed with Trim Galore version 0.6.7
Reads mapping to rRNA and tRNA were removed with Bowtie version 1.3.1
Remaining reads were mapped to the mouse genome with STAR version: 2.7.9a
The output bam files were indexed, and deduplicatd with UMI-tools version: 1.1.2
GET_CROSSLINKS: cross-link sites were extracted from the bam files in BED format
Assembly: mm39
Supplementary files format and content: bed flles: tab-delimited text containing location of cross-llinks
Library strategy: iCLIP-Seq

source_name: adult mouse testis

extract_protocol:
total testes from adult mouse were homogenised by mincing, and then used for iCLIP according to published procedures (PMID: 21559008)
according to published procedures (PMID: 21559008)

value: adult mouse testis

value: mixed

value: wild type

value: polyclonal anti-Tra2b antibody (Abcam, ab31353)


title: root, organic fertilizer 0, rep 1


title: Smartseq2_52

value: D-LN

value: OV


title: CACO2 cells, AID, aux, CTCF, rep2

data_processing:
Illunuma BaseSpace CLItools v.1.0.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore v.0.6.10
The trimmed reads were aligned to the human genome reference hg38 human reference genome using Bowtie2 (v.2.4.2).
PCR duplicated reads were filtered out using Picard MarkDuplicates (v.2.6.0).
Peak calling for histone marks and transcription factors was performed with MACS2 (v.2.1.1).Peaks located in the ENCODE hg38 blacklist regions were excluded and only peaks with a MACS2-reported q-value <10^-5 and Poisson p-value <0.01 were kept for further analysis.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

growth_protocol: DLD-1 cells(ATCC ) was gifted by Dr. Ali Shilatifard Lab.DLD-1 cells were cultured in RPMI1640 Medium (Gibco, 11875093) supplemented with 10% fetal bovine serum (ThermoFisher, 12440053) and 1% penicillin–streptomycin. Caco-2 cells were cultured in Eagle’s Minimal Essential Medium (ATCC, 30-2003) with 20% fetal bovine serum (ThermoFisher, 12440053) and 1% penicillin–streptomycin. All cells were cultured in a 37°C incubator with 5% CO2.

extract_protocol:
CUT&Tag libraries were prepared per a previously established protocol 5 (https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v2?version_warning=no). Briefly, 0.25M cells were used for each reaction. Two replicates were performed for each experiment. Primary antibodies used were: GATA6(CST, 5851), CTCF (ABclonal, A18627), H3K27ac (active motif, 39133), RAD21 (ABclonal, A18850).
CUT&Tag library was contrucedd following a previously pulished protocol (Kaya-Okur et al. Nature Communication 2019)

value: CTCF(ABclonal, #A18627)


title: CACO2 cells, AID, aux, CTCF, rep1


title: Smartseq2_50


title: Smartseq2_51


title: Tra2beta iCLIP 2


title: Tra2beta iCLIP 1


title: Smartseq2_49


title: CACO2 cells, AID, aux, GATA6, rep2


title: leaf, organic fertilizer 0, rep 3


title: leaf, organic fertilizer 0, rep 2


title: TIL_WT_UT_rep2

description: 10x Genomics

value: Tumour-infiltrating

value: Tumor-infiltrating CD3+ T cells


title: leaf, organic fertilizer 0, rep 1

value: leaf


title: Smartseq2_48


title: Smartseq2_47

value: Filtered


title: CACO2 cells, AID, ctrl, CTCF, rep2

value: colorectal adenocarcinoma


title: EV_ManifestHD_10

city: Barcelona

first: Ana

middle: Gámez

last: Valero

state: Barcelona

address: Universitat de Barcelona, Casanova 143, 4th Floor-Nord

institute: University of Barcelona (Neuroscience Institute)

data_processing:
The quality of the sequenced fastq files was checked using the FastQC software.
Adapter trimming was performed with Cutadapt61 and the trimmed reads were aligned to the human genome (version Ensemble hg19) using STAR aligner (version 2.7.9a)
The obtained sequences were annotated and quantified using SeqCluster and ExceRpt (NIH ExRNA Communication Consortium –ERCC-) bioinformatic tools.
Only sRNAs identified with a minimum of ten counts in at least half of the samples of the tested conditions were considered. Differential expression analyses were performed through negative binomial generalized models implemented in the Bioconductor package DESeq2 from R statistical software.
Assembly: hg19
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: Plasma

extract_protocol:
Extracellular vesicles (EVs) from plasma samples were purified using Size EXclusion Chromatography SEC) followed by ultrafiltration (UF). RNA from these EVs was extracted using miRNeasy Serum/Plasma Advanced Kit from Qiagen.
Small RNA libraries were generated using the NEBNext Small RNA Library Preparation Set for Illumina (New England Biolabs) following the manufacturer’s instructions. Indexed libraries were equimolarly pooled, and the selected band of interest (145-160 bp) was purified.
Single-end sequencing of libraries was then carried out on the Illumina HiSeq 2000 with read lengths of 50 nt, generating at least 8 million reads per sample.

value: Plasma

value: Extracellular vesicles

tag: disease

value: Huntington's disease

value: > 40 CAG


title: CACO2 cells, AID, aux, GATA6, rep1


title: EV_ManifestHD_8


title: Smartseq2_45


title: CACO2 cells, AID, ctrl, GATA6, rep2


title: EV_ManifestHD_7


title: Smartseq2_44


title: CACO2 cells, AID, ctrl, GATA6, rep1


title: EV_ManifestHD_6


title: Smartseq2_43


title: EV_ManifestHD_5


title: DLD-1 cells, AID, ctrl, RAD21, rep1

value: RAD21(ABclonal, #A18850)


title: Krasp16-Met2

city: Riyadh

first: yufei

last: shi

address: PO Box 3354

country: Saudi Arabia

institute: King Faisal Specialist Hospital and Research Centre

description: Library name: Sample 12

data_processing:
The significant DEGs were selected based on the following criteria: Log2 fold change>2, false discovery rate (FDR) <0.001, and p-value from difference test<0.01.
Assembly: Genome assembly GRCm38
Supplementary files format and content: excel data foramt

source_name: cell line

extract_protocol:
Thyroid tumors were collected aseptically from transgenic mice (harbouring BrafV600E (BVE), BVE and Trp53, KrasG12D, and KrasG12D and Cdkn2a, respectivelu) using blunt dissection, mechanically dissociated by mincing and passing through a 40-μM mesh sterile screen, and suspended in DMEM/F12 growth medium (10% fetal bovine serum, 100 units/ml penicillin, 100 ug/ml streptomycin). Cells were cultured in DMEM/F12 growth medium containing 4 mU/mL bovine TSH (Sigma-Aldrich). For establishment of immortalized cell lines, cells were cultured continually for more than 6 months and passaged weekly or bi-weekly at 1:3 ratio with 0.25% trypsin. To establish pulmonary metastatic thyroid cancer cell lines, 1 x 106 cells were injected to tail vain of 5 nude mice for each group. Six weeks after injection, pulmonary metastatic tumors were collected aseptically from the mice using blunt dissection, then mechanically dissociated by mincing and passing through a 40-μM mesh sterile screen, and suspended in DMEM/F12 growth medium for 3 month with a total of 6 passages to eliminate contaminated stromal fibroblasts, lymphocytes, and microphages present in the tumor cell culture. The primary cells were considered as permanent cell lines after six passages. The established metastatic cell lines were named as BVE-Met1, BVEp53-Met1 Kras-Met1, and Krasp16-Met1, respectively. They were re-injected (1 x 106 cells) to a new group of nude mice (n=5 for each group) via tail vain for enrichment of cells with high metastatic potential. Three weeks following injection, lung metastatic tumors were harvested and propagated in DMEM/Ham’s F12 growth medium for 3 month with at least 6 passages. The metastatic cell lines were named as BVE-Met2, BVEp53-Met2, Kras-Met2, and Krasp16-Met2, respectively. The thyroid origin of these cell lines were confirmed by genotyping.
Libraries were constructed using an Illumina (San Diego, Ca, USA) TruSeq RNA Library Prep kit according to the manufacturer’s procedure. RNA-Seq on BGISEQ-500 platform

value: thyroid epithelial cells

value: KrasG12D and Cdkn2a deletion


title: Krasp16-Met1

description: Library name: Sample 8


title: BVE-Met2

description: Library name: Sample 9

value: BRAFV600E mutation


title: Kras-Met2

description: Library name: Sample 11


title: BVEp53-Met2

description: Library name: Sample 10

value: BRAFV600E and Trp53 deletion


title: Kras-Met1

description: Library name: Sample 7

value: KrasG12D mutation


title: Smartseq2_42

value: D-LN

value: OV


title: EV_ManifestHD_9


title: Smartseq2_40


title: EV_ManifestHD_3


title: Smartseq2_46


title: DLD-1 cells, AID, +aux, GATA6, rep2


title: DLD-1 cells, AID, +aux, GATA6, rep1


title: CACO2 cells, AID, ctrl, CTCF, rep1

value: CTCF(ABclonal, #A18627)


title: EV_ManifestHD_2


title: BVE-Met1

description: Library name: Sample 5


title: Smartseq2_39


title: EV_ManifestHD_1


title: DLD-1 cells, AID, +aux, CTCF, rep3


title: Smartseq2_38


title: EV_ManifestHD_4


title: DLD-1 cells, AID, ctrl, CTCF, rep3


title: EV_PremanifestHD_10


title: Kras

description: Library name: Sample 3


title: EV_PremanifestHD_9


title: BVEp53-Met1

description: Library name: Sample 6


title: EV_PremanifestHD_8


title: BVEp53

description: Library name: Sample 2


title: DLD-1 cells, AID, aux, H3K27ac, rep2

value: H3K27ac(Active Motif, #39133)


title: DLD-1 cells, AID, aux, H3K27ac, rep1


title: Smartseq2_37


title: Smartseq2_35


title: EV_PremanifestHD_6


title: Smartseq2_34


title: BVE

description: Library name: Sample 1


title: Smartseq2_41


title: DLD-1 cells, AID, ctrl, H3K27ac, rep1


title: BE_13

city: Shanghai

first: Wei

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

institute: University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SOAP nuke.
Trimmed sequence reads were mapped to the reference genome (hGRC38) using HISAT 4 (v2.1.0).
Read count extraction and normalization were performed using RSEM (v1.2.8).
Assembly: hGRC38

source_name: Lung

growth_protocol: The progenitor cells were isolated from a small amount of airway epithelium obtained through bronchoscopic brushing and were expanded to more than 100 million cells within 3-5 weeks.

extract_protocol:
Total RNA was harvested using TRIzol Reagent (Invitrogen, Life Technologies, USA) followed the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using the BGI-NSG platform following manufacturer's protocols.

value: Lung

value: P63+ lung progenitor cells

value: lung progenitor cells

tag: disease state

value: BE


title: EV_PremanifestHD_7

value: Plasma

value: Extracellular vesicles


title: DLD-1 cells, AID, ctrl, H3K27ac, rep2

value: colorectal adenocarcinoma


title: BE_12


title: Smartseq2_33


title: BE_11


title: EV_PremanifestHD_5

value: Huntington's disease

value: > 40 CAG


title: Smartseq2_32


title: EV_PremanifestHD_4


title: BE_10


title: DLD-1 cells, AID, aux, CTCF, rep1


title: Smartseq2_36


title: BE_9


title: DLD-1 cells, AID, ctrl, CTCF, rep1


title: Smartseq2_30


title: EV_PremanifestHD_2


title: BE_8


title: Smartseq2_31


title: EV_PremanifestHD_1


title: DLD-1 cells, AID, ctrl, GATA6, rep2


title: DLD-1 cells, AID, ctrl, GATA6, rep1


title: Smartseq2_29


title: EV_NonMutationCarrier_10

value: Non

value: < 40 CAG


title: BE_6


title: Smartseq2_28


title: Smartseq2_27


title: DLD-1 cells, AID, aux, CTCF, rep2


title: EV_NonMutationCarrier_9


title: Smartseq2_26


title: BE_5


title: DLD-1 cells, KO, atac, rep1

data_processing:
Illunuma BaseSpace CLItools v.1.0.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore v.0.6.10
The trimmed reads were aligned to the human genome reference hg38 human reference genome using Bowtie2 (v.2.4.2).
PCR duplicated reads were filtered out using Picard MarkDuplicates (v.2.6.0).
Peak calling was carried out using MACS2 (v.2.1.1), and peaks located in the ENCODE hg38 blacklist regions were excluded. Peaks that met specific criteria — a MACS2-reported q-value less than 10^-5 and a Poisson p-value below 0.01 — were retained.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
ATAC-seq was performed following the exact Omni-ATAC protocol. 50,000 viable cells were used, and the lysis condition was optimized for DLD-1. The final library was sequenced as 150 PE reads on Illumina Novaseq 6000 platform.
ATAC-seq library was contructed following the exact Omni-ATAC protocol (Corces et al. Nature Methods 2017) .


title: DLD-1 cells, AID, ctrl, CTCF, rep2


title: EV_PremanifestHD_3


title: EV_NonMutationCarrier_8


title: BE_4


title: BE_7


title: Smartseq2_25


title: EV_NonMutationCarrier_7


title: Smartseq2_24


title: DLD-1 cells, WT, atac, rep2

value: WT


title: BE_3


title: EV_NonMutationCarrier_6


title: Smartseq2_23

value: Filtered


title: DLD-1 cells, AID, wash, atac, rep2

value: Wash


title: EV_NonMutationCarrier_5


title: BE_2


title: DLD-1 cells, KO, atac, rep2


title: DLD-1 cells, WT, atac, rep1


title: Smartseq2_21

value: D-LN

value: OV


title: DLD-1 cells, AID, aux, atac, rep2

value: +Auxin


title: DLD-1 cells, AID, wash, atac, rep1


title: Smartseq2_22


title: BE_1

value: Lung


title: EV_NonMutationCarrier_4


title: EV_NonMutationCarrier_3


title: Smartseq2_20


title: COPD_12

value: P63+ lung progenitor cells

value: COPD


title: DLD-1 cells, AID, aux, atac, rep1


title: COPD_11

value: lung progenitor cells


title: COPD_13


title: EV_NonMutationCarrier_2

value: Plasma


title: Smartseq2_19


title: COPD_10


title: Smartseq2_18


title: DLD-1 cells, AID, ctrl, atac, rep1


title: EV_NonMutationCarrier_1

value: Extracellular vesicles


title: DLD-1 cells, AID, ctrl, atac, rep2

value: colorectal adenocarcinoma


title: Smartseq2_17


title: 35dpt_P63+ progenitors

data_processing:
The resulting sequencing libraries were loaded onto an Illumina NovaSeq with 2 × 150 paired-end kits at Novogene China. The raw sequencing reads were processed using the Cell Ranger v.3.1.0 pipeline from 10× Genomics. This involved demultiplexing the reads, aligning them to the human GRCh38 genome, and quantifying UMI counts per gene per cell to generate a gene-barcode matrix. The data from different samples were aggregated and normalized to the same sequencing depth, resulting in a combined gene-barcode matrix.
Assembly: GRCh38-1.2.0
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz

extract_protocol:
The cell suspension was loaded into Chromium microfluidic chips with 3’ v3 chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed.
Sequencing libraries were constructed with reagents from a Chromium Single Cell 3’ v3 reagent kit (10X Genomics) according to the manufacturer’s instructions.


title: Plasma_Subfraction_NonEVsHigh_C4


title: Smartseq2_16


title: Plasma_Subfraction_NonEVsHigh_C3


title: COPD_8


title: 8dpt_P63+ progenitors


title: COPD_7


title: Plasma_Subfraction_NonEVsHigh_C2


title: SH-SY5Y_siPSF_rep3

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

data_processing:
We used Trimmomatic-038 to trim and crop of Illumina (fastq) data by removing the sequences of adapters.
Mapping to human genome (GRCh38) was performed using HISAT2 2.1.0.
Generate alignments in the SAM format from BAM given single-end reads. The reads were mapped to the human RefSeq by using StringTie ver 2.1.3b.
The expression levels of mapped transcripts were normalized into Fragments Per Kilobase of exon per Million mapped reads (FPKM) to facilitate comparison among different samples.
Assembly: GRCh38
Supplementary files format and content: Summary of FPKM for RefSeq genes

source_name: SH-SY5Y cells

growth_protocol: SH-SY5Y cells were cultured in advanced DMEM/F-12 (ThermoFisher) medium supplemented with 5 mM L-glutamine, 10% fetal bovine serum (FBS), 50 U/mL penicillin, and 50 μg/mL streptomycin.

extract_protocol:
Total RNA was extracted by ISOGEN (Nippon gene, Tokyo, Japan)
TrueSeq stranded mRNA LT sample prep kit (illumina) was used for library construction according to the manufacturer's protocol (Trueseq stranded mRNA reference guide document).

treatment_protocol: To reduce the expression of PSF, we treated cells with 10 nM siRNA targeting PSF (siPSF) or siControl for 72 h.

value: SH-SY5Y cells

value: Human nueronal cells

value: siPSF


title: Smartseq2_14


title: Plasma_Subfraction_NonEVsHigh_C1

value: Non

value: < 40 CAG


title: SH-SY5Y_siPSF_rep2


title: COPD_6


title: COPD_5


title: Plasma_Subfraction_NonEVsHigh_C5


title: SH-SY5Y_siPSF_rep1


title: COPD_9


title: Smartseq2_13


title: Plasma_Subfraction_NonEVsLow_C5


title: Smartseq2_12

value: Filtered


title: COPD_4


title: SH-SY5Y_siCt_rep3

value: siControl


title: COPD_3


title: Plasma_Subfraction_NonEVsLow_C4


title: Smartseq2_11

value: D-LN


title: Plasma_Subfraction_NonEVsLow_C3


title: SH-SY5Y_siCt_rep2


title: SH-SY5Y_siCt_rep1


title: COPD_2


title: COPD_1


title: Smartseq2_15

value: OV


title: Smartseq2_9


title: Smartseq2_10


title: Plasma_Subfraction_NonEVsLow_C2


title: Plasma_Subfraction_NonEVsLow_C1


title: CleanCap, Unmod, minitralize, total RNA input

city: New Haven

first: Carson

last: Thoreen

state: Connecticut

address: 333 Cedar Street

department: Cellular and Molecular Physiology

institute: Yale University

description:
CleanCap DART minitralize IVT
CPM.tsv
Minitralization.CPM.tsv

library_source: other

data_processing:
*library strategy: DART-seq
adapter trimming using bbduk.shk trim=r k=23 mink=11 hdist=1 tpe tbo
PCR duplicate/UMI collapsing using dedupe.sh
UMI trimming using bbduk.sh ftl=10
alignment using STAR soloStrand = Forward alignSJoverhangMin = 999 alignIntronMax = 1  alignIntronMin = 999
Reads quantification by pileup.sh
Assembly: artifitial genome
Supplementary files format and content: tsv, CPM
Supplementary files format and content: tsv, pairing parobability

molecule: other

extract_protocol:
RNA is extracted with hot phenol.
RNA is reverse transcribed with common primer binding to the 3′ end. 5′ Adaptosr with random UMI were ligated to the reverse transcript products. The library was then amplified with primers containing Illumina indice sequences.

value: WT


title: Smartseq2_8

data_processing:
SmartSeq2 Analysis: Fastq files from SmartSeq2 libraries were aligned to the mouse genome (mm39) with Gencode M29 annotations using STAR (v2.7.10a). Genome-mapped BAM files were quantified with RSEM (v1.3.1), and the resulting gene/UMI count matrix was processed in Seurat (v4.1.2). Data were normalized using the LogNormalize method, with mitochondrial gene expression and library size bias regressed out via the ScaleData function. Cells with >5% mitochondrial reads were excluded. Clustering, differential expression, and gene signature scoring were performed in Seurat. Differentially expressed genes were identified using the Wilcoxon Rank Sum test, with Bonferroni-adjusted P-values < 0.05 and log2 fold changes > 0.5 considered significant.
Bulk RNA-Seq raw Fastq files were aligned to the mouse genome (mm39) with Gencode M29 annotations using STAR (v2.7.10a). The count matrix was processed in R with the DESeq2 package (v1.34). Genes with fewer than ten reads were filtered out, and sample normalization was applied using a negative binomial distribution model. Differential gene expression between conditions was assessed with the Wald test. Genes with adjusted P-values (FDR) < 0.1 were retained, and log2 fold changes were shrunk using the apeglm algorithm.
10x Genomics Analysis: Fastq files from cDNA and hashtag libraries generated on the Chromium platform (10x Genomics) were processed using Cell Ranger (v7.0.1). The resulting quantification matrix was processed in Seurat (v5.0) with normalization using the SCTransform function. Non-myeloid cell contaminants were removed based on the PanglaoDB_Augmented_2021 database and EnrichR package for R. Cells were classified by biological condition using the HTODemux function. Differentially expressed genes were identified with the Wilcoxon rank test, with Bonferroni-adjusted P-values < 0.05 and log2 fold changes > 0.3 considered significant. Signature scores were calculated using Seurat’s AddModuleScore function.
Assembly: mm10
Supplementary files format and content: Tab files from bulk RNA-Seq tab files containing the STAR gene quantification.
Supplementary files format and content: gene.results from RSEM quantification of Smartseq2 data
Supplementary files format and content: mtx, cellranger output from 10x genomics libraries.
Supplementary files format and content: rds, images of Seurat objects used in the analysis

extract_protocol:
Lymph nodes and gut tissue were dissected, finely chopped, and digested in RPMI medium with Collagenase D to obtain single-cell suspensions. For gut-associated lymph nodes, duodenal lymph nodes were identified using anatomical markers. Dendritic cells were isolated from the duodenal lamina propria by separating intestines, removing mucus with PBS and DTT, and stripping epithelium with EDTA. The tissue was further digested with DNaseI and collagenase, followed by Percoll gradient centrifugation to isolate DCs. Single-cell sorting of DCs was conducted into 96-well plates with TCL buffer and stored at –80°C.
Library Preparation for Single-cell RNA-seq (SmartSeq2). Single cells were sorted onto plates, covering all conditions in each replicate. RNA was extracted using RNAClean XP SPRI beads, then reverse-transcribed into cDNA with RT and TSO primers. The cDNA was amplified, cleaned with SPRI beads, and tagmented using the Nextera XT DNA Library Preparation Kit (Illumina). Barcoded libraries were pooled and sequenced on the Illumina Nextseq 550 platform. Library Preparation for Single-cell RNA-Seq (10x Genomics). Cells were labeled with hashtag oligonucleotide (HTO)-tagged antibodies, sorted, and counted for viability. scRNA-seq libraries were generated using the 10x Genomics Chromium system, following the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq SP flowcell at a minimum depth of 30,000 reads per cell. Library Preparation for Bulk RNA-seq. RNA was isolated using RNAClean XP beads. Reverse transcription was performed with specific primers, followed by cDNA amplification with KAPA HiFi HS Ready Mix. The amplified product was cleaned with RNAClean XP beads and tagmented using the Nextera XT DNA Library Preparation Kit (Illumina). Libraries were pooled and sequenced as 75-base single-end reads on an Illumina NextSeq platform.


title: IPF_11

value: Lung

value: IPF


title: Plasma_Subfraction_Filtrate_C5


title: IPF_12

value: P63+ lung progenitor cells


title: CleanCap, Unmod, monosme fraction, minitralize rep2

description:
CleanCap DART minitralize rep2
CPM.tsv
Minitralization.CPM.tsv


title: Smartseq2_7


title: CleanCap, Unmod, monosme fraction, minitralize rep1

description:
CleanCap DART minitralize rep1
CPM.tsv
Minitralization.CPM.tsv


title: IPF_10

value: lung progenitor cells


title: Plasma_Subfraction_Filtrate_C4

value: Plasma


title: IPF_9


title: Smartseq2_5


title: IPF_8


title: Plasma_Subfraction_Filtrate_C1

value: Extracellular vesicles


title: IPF_7


title: Smartseq2_3


title: foxm1KD

first: Hanling

last: Wang

address: Shanghai

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Science

data_processing:
Paired-end fastq files were trimmed and uniquely aligned to the hg19 human genome assembly using BWA.
After alignment, reads mapped to the same genomic positions were filtered by PICARD-MarkDuplicates (Galaxy Version 2.18.2.2)
Bam coverage was used to transform the BAM alignment files to their representative BigWig files.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
Assembly: hg19
Supplementary files format and content: bigWig

source_name: LNCap cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Purified DNA was prepared for sequencing as per the manufacturer’s instructions (Illumina). Libraries were quantified and sequenced on the Illumina NovaSeq 6000 Sequencer.

value: LNCap cell line

value: epithelial


title: Plasma_Subfraction_EVs_C3


title: Z8KD

value: ZMYND8 (Bethyl, #A302-090A)


title: IPF_4


title: DC2KO_SV_CD103N_24

value: DC2KO (delta 1+2+3)

value: SV


title: Plasma_Subfraction_EVs_C2

value: Non

value: < 40 CAG


title: CleanCap, Unmod, monosme fraction

description:
CleanCap DART Unmod monosome
CPM.tsv
CPMandRRS_CleanCap.tsv

source_name: HeLa

value: HeLa


title: DC2KO_SV_CD103N_23

value: D-LN


title: IPF_3


title: Plasma_Subfraction_EVs_C4


title: IPF_5


title: K4me1


title: CleanCap, m1Y, total RNA input

description:
CleanCap DART m1Y IVT
CPM.tsv
CPMandRRS_CleanCap.tsv


title: Smartseq2_6

value: OV


title: IPF_2


title: Plasma_Subfraction_Filtrate_C3


title: IPF_1


title: CD1_CupRap_0wksRecov_scRNAseq_1

city: Vancouver

first: Freda

middle: D.

last: Miller

state: BC

department: Michael Smith Laboratories, Department of Medical Genetics

country: Canada

institute: University of British Columbia

description:
Library name: CD1_CupRap_0wksRecov_1
10X Genomics

data_processing:
FASTQ reads were processed and aligned to the wild-type mouse genome (mm10) using Cell Ranger v3 software (cellranger count function) with settings as recommended by the manufacturer (10X Genomics).
The data packages contain the filtered digital gene expression for each sample obtained from the Cell Ranger Single Cell Pipeline.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
For single cell isolation the entire dorsal and lateral V-SVZ were microdissected out. Tissues were finely chopped and incubated in Hibernate A minus calcium medium (Brain Bits) supplemented with 2% B27, 20 units/mL papain, and 0.005% DNaseI for 30 minutes at 37°C in the dark. This enzymatic incubation solution also contained DRAQ5, a membrane permeable dye to stain for live cells (at 5 μM or 3000- fold dilution, Thermo Fisher). After enzymatic treatment, the tissue suspension was centrifuged at 300 x g for 5 minutes and resuspended in HBSS/0.025% BSA. A cell suspension was produced via manual trituration using blunt needles of sequentially decreasing diameter. The resultant cell suspension was filtered through a 40 μm strainer and labeled with 1 μg/mL propidium iodide (PI, Abcam). Viable cells were collected using flow cytometry sorting for propidium iodide-negative and DRAQ5-positive cells.
Libraries were prepared according to the manufacturer's instructions (10X Genomics) using the Chromium Single Cell 3' Library and Gel Bead Kit.

value: Brain

value: Primary Cells

value: V-SVZ

value: Vehicle I.P injection 5 times per week (5% PEG400; 5% Tween 80; and 5% ethanol, reconstituted in PBS), normal powdered chow - for 6 weeks. No recovery prior to collection


title: WT_SV_CD103N_20

value: WT


title: Phf2 KO, replicate 2

city: Vienna

first: Roman

middle: R

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

data_processing:
Basecalling software: Illumina RTA
Quality and adapter trimming was performed using Trim Galore.
Abundant sequence fractions (rRNA) have been removed using bowtie2.
Cleaned raw reads were mapped against the reference genome MGSCv37 (i.e. mm9) using STAR (reverse_stranded).
Mapped reads are assigned to corresponding genes using featureCounts.
Analysis of differentially expressed genes is performed using DESeq2
Assembly: mm9
Supplementary files format and content: Tab-separated text file containing a list of genes which show significantly changed expression or not, sorted by adjusted p-values.

source_name: mouse embryonic fibroblasts

growth_protocol: Primary MEFs (pMEFs) were generated from E13.5 embryos and cultured in full medium (DMEM supplemented with 10% FBS, 0.2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, and non-essential amino acids). Immortalized MEFs (iMEFs) were cultured in the same medium as pMEFs. Phoenix cells were cultured in DMEM supplemented with 10% FBS, 0.2 mM L-glutamine, 100 U/ml penicillin, and 100 µg/ml streptomycin.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen), and its purity was assessed with an Agilent RNA 6000 Nano kit (Agilent). mRNA was purified in two rounds using a Dynabeads mRNA purification kit (Invitrogen). The purified mRNA was fragmented in fragmentation buffer (8 mM Tris, pH 8.2, 50 mM Kac, and 4.5 mM MgAc) and further purified using an RNeasy column. The quality of mRNA isolation and fragmentation was analyzed with an Agilent RNA 6000 Pico kit (Agilent). The fragmented mRNA was used as a template for first-strand cDNA synthesis using random hexamers and the Superscript III First-Strand Synthesis kit (Invitrogen), followed by purification on a Mini Quick Spin column (Roche). Second-strand cDNA synthesis was performed using random hexamers and 200 μM dATP, dCTP, dGTP, and dUTP in the presence of RNase H, Escherichia coli DNA polymerase I, and DNA ligase (Invitrogen). The cDNA samples were purified with a MinElute Reaction Cleanup kit (Qiagen), and >5 ng of cDNA was submitted for library preparation and Illumina deep sequencing.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer's instructions. Briefly, DNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. The libraries were then amplified by PCR for 12 cycles, purified using AMPure XP beads (Beckman Coulter), and quantified by Qubit (Thermo Fisher). Library quality was assessed using an Agilent Bioanalyzer.

treatment_protocol: All experiments with MEFs were performed in quiescence. To achieve this, MEFs were grown to confluence, and then the full medium was replaced with resting medium. For the conditional deletion of floxed Phf2, we used the inducible CreERT2 recombinase expressed from the Rosa26 locus (CreER). Cells were arrested in Opti-MEM (Invitrogen) supplemented with 2% charcoal-treated FBS, 100 U/ml penicillin, 100 µg/ml streptomycin, and 0.5 µM 4-hydroxytamoxifen (4-OHT, Sigma) for 7 days.

value: mouse embryonic fibroblasts

value: Phf2 flox/flox, ERCre/+

value: Tamoxifen


title: K14ac

value: LNCap cell line

value: epithelial

value: H3K14ac (milllipore, #07-353)


title: WT_SV_CD103N_19

value: SV


title: DLD-1 cells, AID, +aux, RAD21, rep1

value: colorectal adenocarcinoma

value: RAD21(ABclonal, #A18850)


title: wild-type, replicate 2


title: Plasma_Subfraction_EVs_C1

value: Plasma

value: Extracellular vesicles

value: Non

value: < 40 CAG


title: Krasp16

description: Library name: Sample 4

value: thyroid epithelial cells

value: KrasG12D and Cdkn2a deletion


title: HC_3

value: Lung

value: P63+ lung progenitor cells

value: lung progenitor cells

value: HC


title: DC2KO_SV_CD103N_22

value: D-LN

value: DC2KO (delta 1+2+3)


title: HC_2


title: Z8K27

value: LNCap cell line

value: epithelial

value: H3K27ac (Abcam, #ab4729)


title: WT_SV_CD103N_21

value: WT

value: SV


title: EVK27

value: EV


title: HC_5


title: Z8brg1


title: HC_4


title: CleanCap, Unmod, total RNA input

description:
CleanCap DART Unmod IVT
CPM.tsv
CPMandRRS_CleanCap.tsv

value: HeLa


title: DC2KO_nSV_CD103N_18

value: nSV


title: CD1_CupRap_0wksRecov_scRNAseq_2

description:
Library name: CD1_CupRap_0wksRecov_2
10X Genomics

value: Brain

value: Primary Cells

value: V-SVZ

value: Vehicle I.P injection 5 times per week (5% PEG400; 5% Tween 80; and 5% ethanol, reconstituted in PBS), normal powdered chow - for 6 weeks. No recovery prior to collection


title: Plasma_Subfraction_Filtrate_C2

value: Plasma

value: Extracellular vesicles

value: Non

value: < 40 CAG


title: HC_6

value: Lung

value: P63+ lung progenitor cells

value: lung progenitor cells

value: HC


title: CleanCap, m1Y, monosme fraction

description:
CleanCap DART m1Y monosome
CPM.tsv
CPMandRRS_CleanCap.tsv

value: WT


title: Plasma_Subfraction_EVs_C5


title: IPF_6

value: IPF


title: EVbrg1

value: LNCap cell line

value: epithelial

value: EV


title: Smartseq2_4

value: D-LN

value: OV


title: scRNA-seq corneal epithelium of healthy monkey

city: Stockholm

first: Jiawei

last: Zhong

address: Blickagången 16, Flemingsberg

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing data from scRNA-seq was processed using CellRanger (Version 3.1.0).
Gene-barcode matrixes were further analyzed using Seurat (version 3.1.0) following the tutorial at https://satijalab.org/seurat/v3.1/integration.html.
We kept cells that expressed >500 genes for subsequent analysis.
Assembly: Macaca_fascicularis_5.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Macaca fascicularis

source_name: Corneal epithelium

growth_protocol: All animal procedures were performed following the Principles for the Ethical Treatment of Non-Human Primates, and were approved of the Institutional Animal Care and Use Committee (IACUC) of the Zhongshan Ophthalmic Center of Sun Yat-sen University (2019-150). The animals were maintained at 25 °C on a 12 hour light, 12 hour dark schedule at Huazhen Laboratory Animal Breeding Centre. Animals were given commercial diet twice a day, and were supplied with fruits once daily and sufficient water.

extract_protocol:
We divided the cornea from anesthetized monkeys and the whole corneal was digested in the solution with Dispase II (10 mg/mL) at 37℃ for 2 hours. Next, the corneal epithelium was carefully dissected using forceps, and was transferred to 1.5 ml EP tube which contained the solution with Dispase II (2.5 mg/mL) at 37℃ for 15 minutes to dissociate the cell aggregates into single cells. EP tube was shaken gently every 5 minutes. Single cell suspensions were diluted at a concentration of about 1000 cells/μL in 0.04% BSA/Ames.
Following the manufacturer’s protocol, Single-cell 3’ Library and Gel Bead Kit V2 (10x Genomics) and Gel Bead Kit (10x Genomics) were used for single-cell RNA-seq libraries preparation. Single cells were lysed and the released RNA was performed barcoded reverse transcription in GEMs. Sequencing libraries were sequenced on Illumina HiSeq X Ten.

treatment_protocol: Macaca fascicularis, including one nineteen-year-old monkey which was diagnosed as diabetes with the parameters of fasting glucose and HbA1c levels and one age-matched healthy monkey, were provided by Huazhen Laboratory Animal Breeding Centre (Guangzhou, China), an accredited primate research center in Guangzhou.

value: control


title: Z8foxm1


title: DC2KO_nSV_CD103N_17

last: Castro

institute: The Rockefeller University

source_name: D-LN

value: DC2KO (delta 1+2+3)

value: nSV


title: dna_ko_hu_1

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

data_processing:
Raw reads were trimmed to remove adapters and low-quality sequences using Trim Galore (version 0.6.6) with the parameters ‘-q 20 --paired’.
Then trimmed reads were uniquely mapped to the human (hg19) using bwa (version 0.7.17). The output SAM files were converted to sorted BAM files using SAMtools (version 1.11).
Read1 was split into forward and reverse strand according to the SAM flag, using SAMtools view ‘-f 64 –F 16’ and ‘-f 80’, respectively.
Genome coverage bigwig files were generated by BEDtools (version 3.5.0) genomecov and bedGraphToBigWig (version 4) with the parameter ‘-scale 10,000,000/read1_number’.
Assembly: hg19
Supplementary files format and content: RFD BigWig files for each sample

extract_protocol:
DNA was labeled with EDU during replication, and clicked with Biotin-Azide. DNA as well as the combined RNA were caught by streptavidin beads.
Strand-specific DNA sequencing library was prepared by TABLE-seq. Strand-specific RNA sequencing library was prepared by the RNA-seq library prep kit (VAHTS, Cat. #NR604) following the manufacturer’s instructions.

treatment_protocol: Cells were crosslinked by 1% PFA at room temperature for 10 min, quenched with 1.25 mM glycine for 10 min with rotation. After washing with PBS, cells were permeabilized in PBS with 0.25% TritonX-100 at room temperature for 30 min, and Click reaction was performed at room temperature for 80 min. Then chromatin was fragmented by sonicating with Bioruptor under the condition of 30 s on and 30 s off for 5 cycles. The supernatants with fragmented chromatin were added to streptavidin beads and incubated at room temperature for 1 h with rotation. After beads washed, the nucleic acids were eluted with elution buffer (100 μl PBS with 1% SDS and 2 mg/mL proteinase K) by incubating at 55 °C for 2 h, followed by 70 °C for 20 min. The eluents were split for DNA and RNA purification, respectively. DNA was purified with Phenol/chloroform/isoamyl alcohol. RNA was extracted with Trizol.

value: HeLa

value: cervical carcinoma cell line

value: DDX39A KO

value: hydroxyurea


title: Phf2 KO, replicate 1

value: mouse embryonic fibroblasts

value: Phf2 flox/flox, ERCre/+

value: Tamoxifen


title: Smartseq2_2

city: New York

first: Tiago


title: DC2KO_nSV_CD103N_16


title: Hi-C of w.t. cells, merged replicates

data_processing:
Basecalling software: Illumina RTA
Hi-C preprocessing of PE fastq files using hicup version 0.7.4
bowtie2 version 2.2.5 mapping against mm9 reference assembly
truncating, mapping, filtering and deduplicating of Hi-C raw data through hicup process, conversion to input files for HOMER software and juicer tools.
Analyzing Hi-C data with Homer for TAD detection and insulation scores.
juicer tools pre version 1.22.01 to derive .hic files (Aiden Lab) containing Hi-C matrices for usage with Juicebox and juicer tools for further Hi-C processing like loop a.k. corner peak calling using hiccups subroutine.
Assembly: mm9
Supplementary files format and content: hic files: contain Hi-C matrices for usage with Juicebox, made with  juicer tools pre command.

extract_protocol:
30 × 10^6 cells were cross-linked in 2% formaldehyde for 10 min and quenched with ice-cold glycine (0.125 M final concentration). Cells were snap-frozen and stored at −80 °C before cell lysis. Cells were lysed for 30 min in ice-cold lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, and 0.2% NP-40) in the presence of protease inhibitors. Chromatin was solubilized in 0.6% SDS at 37 °C for 2h and quenched by 3.3% Triton X-100. Chromatin was digested with 400 units of HindIII overnight at 37 °C. Fill-in of digested overhangs by DNA polymerase I, large Klenow fragment in the presence of 250 nM biotin-14-dATP for 90 min was performed prior to 1% SDS-based enzyme inactivation and dilute ligation with T4DNA ligase for 4 hours at 16 °C. Cross-links of ligated chromatin were reversed overnight by 1% proteinase K incubation at 65 °C. DNA was isolated with 1:1 phenol:chloroform, followed by 30 min of RNase A incubation. Biotin was removed from unligated ends by incubation with 15 units of T4 DNA polymerase. DNA was sheared using an E220 evolution sonicator (Covaris, E220) and size selected to 150 to 350 bp by using AMPure XP beads. After end repair in a mixture of T4 polynucleotide kinase, T4 DNA polymerase, and DNA polymerase I, large (Klenow) fragment at room temperature for 30 min, dATP was added to blunted ends polymerase I, large fragment (Klenow 3′ → 5′ exo-) at 37 °C for 30 min. Biotinylated DNA was collected by incubation in the presence of 10 µL of streptavidin-coated MyOne C1 beads, and Illumina paired-end adapters were added by ligation with T4 DNA ligase for 2 h at room temperature. A PCR titration (primers PE1.0 and PE2.0) was performed prior to a production PCR to determine the minimal number of PCR cycles needed to generate a Hi-C library. Primers were separated from the library using AMPure XP size selection prior 150 bp paired-end reads sequencing using illumina. Hi-C libraries were generated as described in Wutz et al. (2017), with modifications as described below. 3 × 107 MEFs were fixed in 2% formaldehyde for 10 min, after which the reaction was quenched with ice-cold glycine (0.125 M final concentration). Cells were collected by centrifugation (400 g for 10 min at 4°C) and washed once with 50 ml PBS, pH 7.4. After another centrifugation step (400 g for 10 min at 4°C), the supernatant was completely removed and the cell pellets were immediately frozen in liquid nitrogen and stored at −80°C. After thawing, the cell pellets were incubated in 50 ml ice-cold lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, and 0.2% NP-40) for 1 h on ice. After centrifugation to pellet the cell nuclei (400 g for 5 min at 4°C), nuclei were washed twice with 1.2× NEBuffer 2 (New England BioLabs) and transferred to 1.5 ml Eppendorf tubes. The nuclei were then collected by centrifugation step (400 g for 5 min at 4°C) and a resuspended in 450 µl 1.2× NEBuffer 2 (New England BioLabs) with 13.5 µl of 20% SDS (0.6% final concentration), and the nuclei were incubated at 37°C for 2 h with agitation (900 rpm). Triton X-100 was added to a final concentration of 3.3%, and the nuclei were incubated at 37°C for 2 h with agitation (900 rpm). HindIII (New England BioLabs; 1,500 units per 7 million cells) restriction digestion was performed overnight at 37°C with agitation (900 rpm). Using biotin-14-dATP (Life Technologies), dCTP, dGTP, and dTTP (Life Technologies; all at a final concentration of 30 μM), the HindIII restriction sites were then filled in with Klenow (New England BioLabs) for 1 h at 37°C with shaking (700 rpm) for 10 s every 30 s. The nuclei were washed twice with ligation buffer and the ligation was performed for 12 h at 16°C (2,000 units T4 DNA ligase, Thermo Scientific) in a total volume of 100 µl ligation buffer (50 mM Tris-HCl, 10 mM MgCl2, 1 mM ATP, 10 mM DTT, 100 μg/ml BSA, and 0.9% Triton X-100). After ligation, crosslinking was reversed by incubation with proteinase K (40 μl of 10 mg/ml in 300 μl Tris-EDTA buffer [TE]) at 65°C overnight. An additional proteinase K incubation (65 μl of 10 mg/ml per 7 million cells starting material) at 65°C for 2 h was followed by RNase A (Roche; 15 μl of 10 mg/ml per 7 million cells starting material) treatment and two sequential phenol/chloroform (Sigma) extractions. DNA precipitation was performed overnight at −20°C (3 M sodium acetate, pH 5.2 [1/10 volume] and ethanol [2.5 volumes]), and the DNA was then spun down (3,200 g for 30 min at 4°C). The pellets were resuspended in 400 μl TE (10 mM Tris-HCl, pH 8.0 and 0.1 mM EDTA) and transferred to 1.5-ml Eppendorf tubes. After another phenol/chloroform (Sigma) extraction and DNA precipitation overnight at −20°C, the pellets were washed three times with 70% ethanol, and the DNA concentration was determined using Quant-iT Pico Green (Life Technologies). To remove biotin from non-ligated fragment ends, 30–40 μg of Hi-C library DNA was incubated with T4 DNA polymerase (New England BioLabs) for 4 h at 20°C, followed by phenol/chloroform purification and DNA precipitation overnight at −20°C. After a wash with 70% ethanol, sonication was carried out to generate DNA fragments with a size peak around 400 bp (Covaris E220 settings: duty factor, 10%; peak incident power, 140 W; cycles per burst, 200; time, 55 s).
After end repair (T4 DNA polymerase, T4 DNA polynucleotide kinase, Klenow [all New England BioLabs] in the presence of dNTPs in ligation buffer [New England BioLabs]) for 30 min at RT, the DNA was purified (Qiagen PCR purification kit). dATP was added with Klenow exo- (New England BioLabs) for 30 min at 37°C, after which the enzyme was heat inactivated (20 min at 65°C). A double-size selection using AMPure XP beads (Beckman Coulter) was performed: First, the ratio of AMPure XP beads solution volume to DNA sample volume was adjusted to 0.6:1. After incubation for 15 min at RT, the sample was transferred to a magnetic separator (DynaMag-2 magnet; Life Technologies), and the supernatant was transferred to a new Eppendorf tube, while the beads were discarded. The ratio of AMPure XP beads solution volume to DNA sample volume was then adjusted to 0.9:1 final. After incubation for 15 min at RT, the sample was transferred to a magnet (DynaMag-2 magnet; Life Technologies). Following two washes with 70% ethanol, the DNA was eluted in 100 μl of TLE (10 mM Tris-HCl, pH 8.0 and 0.1 mM EDTA). Biotinylated ligation products were isolated using MyOne Streptavidin C1 Dynabeads (Life Technologies) on a DynaMag-2 magnet (Life Technologies) in binding buffer (5 mM Tris, pH 8, 0.5 mM EDTA, and 1 M NaCl) for 30 min at RT. After two washes in binding buffer and one wash in ligation buffer (New England BioLabs), PE adapters (Illumina) were ligated onto Hi-C ligation products bound to streptavidin beads for 2 h at RT (T4 DNA ligase NEB, in ligation buffer, and slowly rotating). After washing twice with wash buffer (5 mM Tris, 0.5 mM EDTA, 1 M NaCl, and 0.05% Tween-20) and then once with binding buffer, the DNA-bound beads were resuspended in a final volume of 90 μl NEBuffer 2. Bead-bound Hi-C DNA was amplified with seven PCR amplification cycles (36–40 individual PCRs) using PE PCR 1.0 and PE PCR 2.0 primers (Illumina). After PCR amplification, the Hi-C libraries were purified with AMPure XP beads (Beckman Coulter). The concentration of the Hi-C libraries was determined by Bioanalyzer profiles (Agilent Technologies) and qPCR (Kapa Biosystems), and the Hi-C libraries were paired-end sequenced (HiSeqv4, Illumina) at VBCF NGS.

treatment_protocol: All experiments with MEFs were performed in quiescence. To achieve this, MEFs were grown to confluence, and then the full medium was replaced with resting medium. For the conditional deletion of floxed Phf2, Wapl, and Smc3 alleles, we used the inducible CreERT2 recombinase expressed from the Rosa26 locus (CreER). Cells were arrested in Opti-MEM (Invitrogen) supplemented with 2% charcoal-treated FBS, 100 U/ml penicillin, 100 µg/ml streptomycin, and 0.5 µM 4-hydroxytamoxifen (4-OHT, Sigma) for 7 days. For the conditional deletion of the floxed CTCF allele, MEFs were cultured for 4 hours in resting medium (DMEM supplemented with 2% FBS), 4 µg/ml polybrene, and Adeno-Cre virus (Penn Vector Core, 1 µl per 1 million cells). The medium was then replaced with resting medium for 7 days.

value: wt


title: wild-type, replicate 1


title: dna_ko_hu_2


title: HC_1

value: Lung

value: P63+ lung progenitor cells

value: lung progenitor cells

value: HC


title: dna_ctrl_hu_2

value: WT


title: dna_ctrl_hu_1


title: WT_nSV_CD103N_13

value: D-LN


title: dna_ctrl_2


title: HA i.m. + Tamox. Liver Mouse7

city: Nantes

first: Amedee

last: Renand

address: 30 Bd Jean Monnet

country: France

institute: CR2TI UMR1064

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina); quality- trimming step was applied to remove low-confidence base calls from the ends of reads using Trimmomatic 0.38; Read alignment: STAR v.2.4.2a; Gene counts were generated with htseq-count 0.11.1
We did trimmed-mean of M values (TMM) normalization on the raw gene counts (normalization). Additionally, because there are many genes which are not expressed in any of the samples (and are therefore uninformative), we require that genes are expressed with at least1counts per million total reads in at least10% of the total number of libraries (filtering).
Assembly: GRCm38.91
Supplementary files format and content: Tab-delimited text file includes the filtered, normalized counts

source_name: Tetramer+HA-specific CD44+CD4+T cells

extract_protocol:
SMART-Seq® v4 Ultra® Low Input RNA Kit protocol (Takara Bio, USA)
NexteraXT_half_vol

treatment_protocol: 200 HA-specific memory CD4+ T cells were FACS sorted. RNA extraction, reverse transcription and PCR steps were directly performed after sorting according to the SMART-Seq® v4 Ultra® Low Input RNA Kit protocol (Takara Bio, USA)

value: Tetramer+HA-specific CD44+CD4+T cells

value: CD4 T cells

value: Balb/c Rosa26 HA floxed TTR-inducible Cre (HA/iCre)

value: Plamsid_HA i.m. + Tamox.


title: DC2KO_SV_CD103P_12

address: 1230 York Avenue

value: DC2KO (delta 1+2+3)

value: SV


title: neural progenitor cell, PRMT7overexpression, rep2

city: Changsha

first: Ting

last: Shen

address: Tongzhipo Road 172

institute: Central South University

description: Library name: H2-P

data_processing:
FastQC v0.12.1 was firstly used to evaluate the quality of the sequencing data.
Quality trimming and adapter clipping were then performed by fastp v0.23.1. Meanwhile, Ribosomal RNA (rRNA) was removed with SortMeRNA v2.1b.
Next, the trimmed and rRNA-cleaned reads are mapped to the human reference genome GRCh38 with HISAT2 v2.1.0.
The mapped reads were quantified by using featureCounts v2.0.1 to generate the original counts expression matrix.
Assembly: hg38
Supplementary files format and content: The csv file lincudes the original counts expression matrix of all samples.

source_name: neural progenitor cell

growth_protocol: The NPCs we used in this study were derived from the differentiation of human embryonic stem cell line H9 using Neural Induction Medium supplied by STEMCELL Technologies. The formed NPCs were cultured in Neural Progenitor Medium also supplied by STEMCELL Technologies.

extract_protocol:
The total RNA were extracted using the Trizol agent according to the manufacturer’s protocol.
The RNA library for RNA-seq  was constructed according to the instruction of VAHTS Universal V8 RNA-seq Library kit (Vazyme, cat no. NR605) .

value: neural progenitor cell

value: PRMT7 overexpression


title: WT_nSV_CD103N_15

value: nSV


title: dna_ctrl_1

value: HeLa

value: cervical carcinoma cell line


title: Hi-C of Wapl-KO, merged replicates

value: mouse embryonic fibroblasts


title: WT_nSV_CD103N_14


title: neural progenitor cell, PRMT7overexpression, rep1

description: Library name: H1-P


title: HA i.m. + Tamox. Liver Mouse6


title: Smartseq2_1

value: OV


title: WT_SV_CD103P_9


title: DC2KO_SV_CD103P_11


title: scRNA-seq corneal epithelium of diabetic monkey

value: diabetes


title: neural progenitor cell, control, rep2

description: Library name: H2-N


title: neural progenitor cell, control, rep1

description: Library name: H1-N


title: 105 N2 mCherry NEG

city: Toronto

first: yacine

last: touahri

address: 2075 Bayview Ave

institute: Sunnybrook Research Institute

data_processing:
Ion Torrent sequencing was performed for 500 flows on an Ion S5XL Sequencer with Ion 540 Chips.
Ion Torrent platform-specific pipeline software (Torrent Suite version 5.8.0; ThermoFisher Scientific) was used to remove polyclonal, low quality and adapter dimer reads and then separate barcoded reads for each sample.
Ion Torrent platform-specific ampliSeqRNA plug-in (v5.8.0.3) was used to analyze the sequencing reads.
Reads were aligned to the human transcriptome reference and target regions flle (hg19_AmpliSeq_Transcriptome_V1.2) With TMAP mapper in Torrent Suite version 5.8.0.
Assembly: hg19 Human genome reference
Supplementary files format and content: text files.  Raw read count and normalized reads count (RPM, reads per million).

source_name: Human cerebral organoids

growth_protocol: We employed a modified Lancaster protocol  that uses dual Smad inhibitors to generate hESC-derived COs that are enriched in cortical gene expression. Aggregated hESCs were cultured with A83-01, an inhibitor of TGF type I receptors (ALK4, ALK5, ALK7), and dorsomorphin, an inhibitor of BMP type I receptors (ALK2, ALK3, ALK6), for 5 days in vitro to induce embryoid body (EB) formation. EBs that reached ~ 400- 600 um diameter were selected for neural induction by culturing between day 5 and day 9 with SB-431542, an ALK4, ALK5, ALK7 inhibitor, along with CHIR-99021, a GSK3β inhibitor that activates Wnt signaling and limits apoptosis . On day 9, EBs of ~500-800 um diameter that had translucent edges, a sign of neuroepithelial induction, were embedded in Matrigel, an undefined ECM preparation that contains collagens, laminins, other ECM molecules and growth factors. Between day 9 and day 13, embedded EBs were grown in Expansion Media. Finally, EBs with clear neuroepithelial cell buds were transferred to a Spin-Omega spinning mini-bioreactor.

extract_protocol:
Total RNA was extracted from FACS-isolated cells using MagMAX-96 total RNA isolation kit (ThermoFisher, AM1830)
Complementary DNA (cDNA) libraries were constructed from the total RNA using the The cDNA libraries were constructed by Ion Ampliseq Library Kit Plus (ThermoFisher Scientific) in accordance with the manufacturer’s manuals.
Targeted RNA sequencing

treatment_protocol: Cerebral organoids were generated from two NEUROG2-mCherry KI hESC lines (#105 and #117) in two independent experiments (N=2 per line). Cerebral organoids were harvested after 45-47 days in vitro. mCherry-high and mCherry-low cells were isolated by FACS and total RNA was extracted.

value: Human cerebral organoids

value: hESCs

value: mCherry negative


title: HA i.m. + Tamox. Liver Mouse3

value: Tetramer+HA-specific CD44+CD4+T cells

value: AdCre i.m. + Tamox.


title: WT_SV_CD103P_8

value: D-LN

value: WT


title: rna_ko_hu_1

data_processing:
Raw reads were trimmed to remove adapters and low-quality sequences using Trim Galore (version 0.6.6) with the parameters ‘-q 20 --paired’.
Then trimmed reads were uniquely mapped to the human (hg19) using bwa (version 0.7.17). The output SAM files were converted to sorted BAM files using SAMtools (version 1.11).
Read1 was split into forward and reverse strand according to the SAM flag, using SAMtools view ‘-f 64 –F 16’ and ‘-f 80’, respectively.
Genome coverage bigwig files were generated by BEDtools (version 3.5.0) genomecov and bedGraphToBigWig (version 4) with the parameter ‘-scale 10,000,000/read1_number’.
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample of RNA-seq

molecule: nuclear RNA

growth_protocol: Dynamic Control of RNA-DNA Hybrid Formation Orchestrates DNA2 Activation at Stalled Forks by RNAPII and DDX39A

value: DDX39A KO

value: hydroxyurea


title: HA i.m. + Tamox. Liver Mouse5

value: CD4 T cells

value: Balb/c Rosa26 HA floxed TTR-inducible Cre (HA/iCre)

value: Plamsid_HA i.m. + Tamox.


title: HA i.m. + Tamox. Liver Mouse4


title: Hi-C of Phf2-KO, merged replicates


title: HA i.m. + Tamox. Liver Mouse2


title: rna_ctrl_hu_1

value: HeLa


title: HA i.m. + Tamox. Liver Mouse1


title: 105 N2 mCherry POS

value: mCherry positive


title: 117 N2 mCherry POS


title: rna_ctrl_hu_2

value: cervical carcinoma cell line


title: rna_ctrl_2


title: Css_Z8__inhibitor-2_1

data_processing:
The mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA). And then fragmented to approximately 200bp. Subsequently, the RNA fragmentswere subjected to first strand and second strand cDNA synthesis following by adaptor ligaion and enrichment with a low-cycleaccording to instructions ofNEBNext® Ultra™ RNA Library Prep Kit for Illumina.
The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit(Thermo Fisher  Scientific, USA). The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp at Ribobio Co. Ltd (Ribobio, China).
HISAT2 was used to align the clean reads to the human reference genome hg19  with default parameters.
HTSeq was subsequently employed to convert aligned short reads into read counts for each gene
Differential expression was assessed by DESeq2 using read counts as input.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include COUNTs number, RPKM or TPM values for each Sample

growth_protocol: LNCap were cultured in RPM1640 media supplemented with 10% FBS or CSS at 37°C under 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. Total RNA was subjected to Hiseq RNA-Seq, performed by RiboBio Co., Ltd.
RNA libraries for RNA-seq were prepared according to instructions of NEBNext® Ultra™ RNA LibraryPrep Kit for Illumina (NEB, USA)

treatment_protocol:
LNCaP EV and LNCaP ZMYND8-OE cells were cultured with CSS in different time point. Each group was performed in two biological replicates.
LNCaP EV and LNCaP ZMYND8-OE cells were treated with or without FOXM1 KD. Each group was performed in two biological replicates.
LNCaP EV and LNCaP ZMYND8-OE cells were treated with or without iZMYND8-34. Each group was performed in two biological replicates.

value: LNCap cell line

value: epithelial

value: CSS; iZMYND8-34

value: Day 3


title: HA i.m. + Tamox. Spleen Mouse4


title: HA i.m. + Tamox. Spleen Mouse3


title: 117 N2 mCherry NEG

value: Human cerebral organoids

value: hESCs

value: mCherry negative


title: DC2KO_nSV_CD103P_6

value: D-LN

value: DC2KO (delta 1+2+3)

value: nSV


title: rna_ctrl_1

value: WT


title: WT_SV_CD103P_7

value: SV


title: 117 N1 mCherry NEG


title: rna_ko_hu_2

value: DDX39A KO

value: hydroxyurea


title: DC2KO_SV_CD103P_10


title: HA i.m. + Tamox. Spleen Mouse5

value: Tetramer+HA-specific CD44+CD4+T cells

value: CD4 T cells

value: Balb/c Rosa26 HA floxed TTR-inducible Cre (HA/iCre)

value: AdCre i.m. + Tamox.


title: 117 N1 mCherry POS

value: mCherry positive


title: Css_Z8_DMSO_1

value: LNCap cell line

value: epithelial

value: CSS; DMSO


title: WT_nSV_CD103P_1


title: Css_inhibitor_2

value: EV

value: CSS; iZMYND8-34

value: Day 3


title: Ab134 ∆pppE, 24h, rep3

city: CHICAGO

first: Yitao

last: Dai

address: 900 S Ashland ave Room 3106, MBRB Building 919 M/C 870

institute: University of Illinois at Chicago

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v3.9.3)
Processed raw reads were mapped to the reference genome assembly (GCA_018282095.1_ASM1828209v1) using Geneious assembler (medium-low sensitivity / fast; advanced settings were unchanged).
Expression levels (RPKM, FPKM, and TPM) were calculated using Geneious (ambiguously mapped reads were count as partial matches).
Assembly: GCA_018282095.1 of Genome assembly ASM1828209v1
Supplementary files format and content: comma-separated values (csv) files include locus tag, protein id, raw read count, TPM, FPKM, and RPKM values of each gene for each sample.

organism: Pseudovibrio brasiliensis

growth_protocol: P. brasiliensis Ab134 wild type and mutants were cultivated at 30˚C in BD Difco™ Marine Broth 2216 (50 ml broth in 250-ml Erlenmeyer flasks) shaking at 200 rpm for 24 hours.

extract_protocol:
RNA was isolated from 24-h triplicate cultures using the RiboPure™-Bacteria kit (Thermo Fisher Scientific) following the manufacturer’s instructions.
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices.

tag: strain

value: deleted pppE


title: Css_inhibitor_1


title: Css_Z8__inhibitor-1_1


title: Ex3abERKO rep 4

type: RNA

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from ovary of mouse lacking both ERa and Erb

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: ovary form mouse lacking both ERa and Erb

label_protocol: Starting with 250-350 ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Ovaries were hymogenized in TRIzol and RNA was extracted following manufactorers protocol.

tag: age

value: 1 year

tag: organ

value: whole ovary


title: 105 N1 mCherry POS

value: Human cerebral organoids

value: hESCs


title: 105 N1 mCherry NEG

value: mCherry negative


title: Ab134 ∆pppE, 24h, rep2


title: DC2KO_nSV_CD103P_4

value: D-LN

value: DC2KO (delta 1+2+3)

value: nSV


title: Css_DMSO_2

value: WT


title: Ab134 ∆pppE, 24h, rep1


title: Css_DMSO_1


title: Ab134 ∆pppD, 24h, rep2

value: deleted pppD


title: HA i.m. + Tamox. Spleen Mouse1

value: Tetramer+HA-specific CD44+CD4+T cells

value: CD4 T cells

value: Balb/c Rosa26 HA floxed TTR-inducible Cre (HA/iCre)

value: AdCre i.m. + Tamox.


title: WT_nSV_CD103P_3


title: DC2KO_nSV_CD103P_5


title: HA i.m. Spleen Mouse4

value: AdCre i.m.


title: HA i.m. Spleen Mouse3


title: Css_siFM1_2

value: LNCap cell line

value: epithelial

value: CSS

value: Day 3


title: Css_Z8_DMSO_2

value: CSS; DMSO


title: Ex3bERKO rep 4

description: Gene expression from ovary of ERb knockout mouse

source_name: ovary from ERb knockout mouse

value: 1 year

value: whole ovary


title: Ex3abERKO rep 3


title: Ex3bERKO rep 3


title: HA i.m. Spleen Mouse2


title: Ex3bERKO rep 2


title: CD1_CupRap_3wksRecov_Rep2_scRNAseq

description: 10X Genomics

value: Brain

value: Primary Cells

value: V-SVZ

value: Rapamycin I.P injection 5 times per week (10 mg/kg rapamycin, R-5000, LC Laboratories; dissolved in 5% ethanol, 5% polyethylene glycol 400 (PEG400), Sigma; 5% Tween 80, Sigma; in PBS), ad libitum 0.3% cuprizone in powdered chow for 6 weeks. 3 weeks recovery prior to collection


title: Ex3abERKO rep 2


title: Css_Z8_siFM1_2

value: WT

value: ZMYND8-OE; siFOXM1


title: Css_Z8_siFM1_1


title: HA i.m. Spleen Mouse1

value: Tetramer+HA-specific CD44+CD4+T cells

value: CD4 T cells


title: NesCre_CupRap_3wksRecov_Rep2_scRNAseq

description: 10X Genomics

value: C57BL/6-Tg(Nes-cre/ERT2) x B6.129X1-Gt(ROSA)26Sortm1(EYFP)Cos/J (NesCreERT2;EYFP)


title: HA i.m. + Tamox. Spleen Mouse2

value: Balb/c Rosa26 HA floxed TTR-inducible Cre (HA/iCre)

value: AdCre i.m. + Tamox.


title: WT_nSV_CD103P_2

value: D-LN

value: nSV


title: Ab134 ∆pppD, 24h, rep1

value: deleted pppD


title: NesCre_Control_3wksRecov_Rep2_scRNAseq

description: 10X Genomics

value: Vehicle I.P injection 5 times per week (5% PEG400; 5% Tween 80; and 5% ethanol, reconstituted in PBS), normal powdered chow - for 6 weeks. 3 weeks recovery prior to collection


title: Css_siFM1_1

value: LNCap cell line

value: epithelial

value: CSS

value: Day 3


title: CD1_CupRap_3wksRecov_Rep1_scRNAseq

description: 10X Genomics

value: Brain

value: Primary Cells

value: V-SVZ


title: day30_oe2

value: WT

value: Day 30


title: NesCre_Control_3wksRecov_Rep1_scRNAseq

description: 10X Genomics


title: Ab134 ∆pppA, 24h, rep2

value: deleted pppA


title: CD1_Control_0wksRecov_scRNAseq

description: 10X Genomics


title: Adult_CTX_MECP2_0.5_Native2hr_CNR

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

data_processing:
Raw reads were trimmed using cutadapt (v2.5) and aligned to mouse reference genome mm10 using bowtie2 (v2.4.2). The duplicate reads were removed using samtools (v1.6) 55. The CUT&RUN final bigwig file was generated using makeUCSC program of HOMER and CUT&TAG bigwig files (CPM and RPKM) files were genearted using bamCoverage tool of deeptools (v.3.5.0)
SICER was used  to identify H3K9me3-enriched regions compared to H3 using parameters of W=500; G=1,500; FDR<0.001.
Assembly: mm10
Supplementary files format and content: bigWig (normalized coverage)
Supplementary files format and content: BED (peaks)

source_name: Brain Cortex

extract_protocol:
For CUT&TAG, cortices were collected from 10-week-old wild type mice, and dounced 15 times in HB buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH pH7.8, 1mM DTT, 0.15 mM spermine, 0.5 mM spermidine, Roche protease inhibitor tablets, 10mM Sodium Butyrate).  IGEPAL CA-630 (Sigma) was added to a final concentration of 0.3% and the lysates were dounced 5 more times.  The lysates were filtered through 40µm cell strainers and spun down at 500g for 5 minutes at 4C.  The pellet was resuspended in cold wash buffer 1 (WB1) (20mM HEPES pH 7.5, 150mM NaCl, 0.2% Tween-20, 0.5 mM spermidine, EDTA-free complete protease inhibitor tablet (Roche), 1mg/mL BSA).  20µl of concanavalin A beads pre-washed with binding buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2) were added to each sample and incubated for 10 minutes at room temperature to bind nuclei to beads.  The supernatant was discarded and 50µl antibody buffer (WB1 with 2mM EDTA, 0.1% Triton) (along with respective antibodies) was added to the beads and incubated overnight at 4C.  Next, the supernatant was discarded, and beads were incubated for 1 hour at room temperature with secondary antibodies diluted 100X in antibody buffer (either pig anti-rabbit antibodies (Novus Biologicals NBP172763) or rabbit anti-mouse antibodies (Abcam ab46540)). After the incubation, beads were washed 3 times with WB1.  The beads were then incubated for 1 hour at room temperature with 0.025µM pA-Tn5 adapter complex diluted in 100 µl wash buffer 2 (WB2) (20mM HEPES pH 7.5, 300mM NaCl, 0.2% Tween-20, 0.5 mM spermidine, EDTA-free complete protease inhibitor tablet (Roche), 1mg/mL BSA). The beads were next washed three times with WB2 and then were incubated for 1 hour at 37C with 300µl tagmentation buffer (WB2 with 10mM MgCl2).  After the incubation, 10ul of 0.5M EDTA, 3µl of 10% SDS, and 2.5µl of 20mg/mL proteinase K were added and incubated for 1 hour at 50°C followed by 70°C for 10 minutes.  The DNA was extracted by phenol-chloroform extractions.  The samples were PCR amplified with KAPA HiFi polymerase along with 1X KAPA HiFi Buffer, 0.3 mM dNTPs, 10µM universal primer (AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTG) and 10µM index primer (CAAGCAGAAGACGGCATACGAGAT[index]GTCTCGTGGGCTCGGAGATGT) with the following cycles: (1) 72C for 5 minutes (2) 98C for 30 seconds (3) 98C for 10 seconds (4) 63°C for 30 seconds (5) 72°C for 1 minute (6) 72°C for 5 minutes, (7) go to step 3 thirteen times (8) 12°C hold.  After the PCR, 25µl of Ampure XP beads (0.5x volume) were added and incubated for 10 minutes at room temperature. The supernatant was transferred to a new tube, and an additional 65µl of AMPure beads were added and incubated for 10 minutes at room temperature. The beads were washed twice with 80% ethanol and libraries were eluted with Qiagen EB buffer.
ChIP Libraries were constructed by using the Ovation Ultralow Library System (Nugen).  All libraries were sequenced using an Illumina NextSeq 500
CUT&RUN and CUT&TAG

treatment_protocol: CUT&RUN experiments were performed exactly as previously described by Stroud et. al, 2020 using freshly harvested cortices from adult mice (7-10 weeks). The exceptions were for control experiments. where we altered the experiments in the following ways: (1) Increased anti-MECP2 antibodies by 20-fold. (2) Increased the pA-MNase incubation time after adding CaCl2 from 30 minutes to 2 hours, (3) instead of collecting fragmented chromatin by passive diffusion out from the nuclei, we performed total DNA extraction as previously described by Skene et. al 2017). ChIP-seq experiments were performed exactly as previously described by Stroud et. al 2017

value: Brain Cortex

value: Wild type

tag: antibody

value: anti-MECP2 (C-terminus) (Chen et al., 2003),


title: Ab134 ∆pppA, 24h, rep1


title: day30_ctrl2

value: EV


title: Ab134 ∆pppA, 24h, rep3


title: siVCPIP1_3

city: Shenyang

first: Zhihao

last: Liu

address: No.36 in sanhao street

institute: China Medical University

description: Library name: Sample6

data_processing:
Using MGISEQ-2000RS sequencing platform
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Transcrips per million (TPM) were calculated.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tpms for each Sample

source_name: pancreatic cancer

extract_protocol:
Lysis of cells with Trizol regent and harvesting of RNA.
RNA libraries for RNA-seq were prepared using MGISEQ-2000RS protocols.

value: pancreatic cancer


title: day3_oe1


title: Adult_CTX_H3_ChIPseq

value: anti-H3 antibodies (Abcam ab1791).


title: Ab134 ∆pppD, 24h, rep3

value: deleted pppD


title: Ex3bERKO rep 1

value: 1 year

value: whole ovary


title: day3_ctrl2

value: LNCap cell line

value: epithelial

value: CSS


title: Ab134 wild type, 24h, rep3

value: wild type


title: CD1_Control_3wksRecov_scRNAseq

description: 10X Genomics

value: Brain

value: Primary Cells

value: V-SVZ

value: Vehicle I.P injection 5 times per week (5% PEG400; 5% Tween 80; and 5% ethanol, reconstituted in PBS), normal powdered chow - for 6 weeks. 3 weeks recovery prior to collection


title: siVCPIP1_1

description: Library name: Sample4


title: NesCre_CupRap_3wksRecov_Rep1_scRNAseq

description: 10X Genomics

value: C57BL/6-Tg(Nes-cre/ERT2) x B6.129X1-Gt(ROSA)26Sortm1(EYFP)Cos/J (NesCreERT2;EYFP)

value: Rapamycin I.P injection 5 times per week (10 mg/kg rapamycin, R-5000, LC Laboratories; dissolved in 5% ethanol, 5% polyethylene glycol 400 (PEG400), Sigma; 5% Tween 80, Sigma; in PBS), ad libitum 0.3% cuprizone in powdered chow for 6 weeks. 3 weeks recovery prior to collection


title: Ex3aERKO rep 4

description: Gene expression from ovary of ERa knockout mouse

source_name: ovary from ERa knockout mouse