title: THP1,Compound49,24h,ChIPseq,SMARCA4

first: Salih

last: Topal

address: 500 Technology Square Suite 700

institute: Foghorn Therapeutics

description: Library name: THP1_ChIPseq_Compound49_SMARCA4

data_processing:
Reads were aligned using BWA mem with the default parameters
Alignments with a quality lower than 10 were discarded using samtools and duplicated alignments were removed with picard MarkDuplicates tool
Peaks were called with Macs2 callpeak function and fold enrichment coverage tracks were created using the bdgcmp function of the same package
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
cells were fixed with 1% formaldehyde for 15 minutes and quenched with 0.125-M glycine. Chromatin was isolated by adding lysis buffer, then disrupted with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300 to 500 bp with the Active Motif EpiShear probe sonicator (#53051) and cooled sonication platform (53080). Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K, and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 µg) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 20 µL of antibody against PU-1 (Santa Cruz, sc-352), or 4 µL of antibody against H3K27Ac (Active Motif, 39133).
Illumina libraries were prepared by Active Motif using standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation according to the standard Illumina ChIP-seq library.

tag: cell line

tag: cell type

value: AML

value: WT

value: Compound 49


title: lib28620

status: Public on Aug 07 2025

type: SRA

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

country: USA

institute: Benaroya Research Institute

description: Library name: lib28620

library_source: transcriptomic

data_processing:
Fastq files were aligned to the Ensembl version of the human genome (GRCh38) (GenBank assembly accession id GCA_000001405.15), using TopHat (version 1.4.1). The single-paired flag was set to “single,” while all other TopHat parameters were set to defaults
HTSeq-count was used to generate gene counts with mode as “Intersection (nonempty)” and minimum alignment quality set to 0 and otherwise set to default parameters
For quality control, samples were kept that had human aligned counts >250,000 and median CV coverage < 1.1. Genes were filtered to include those that had a trimmed mean of M values (TMM) normalization count of at least 1 in at least 10% of libraries and were classified as protein coding using BioMart. Normalized counts were transformed to log2 counts per million along with observations level weights using voomWithQualityWeights from the “limma” R package version 3.46
Assembly: GRCh38
Supplementary files format and content: counts_raw.tsv
Supplementary files format and content: hgnc_ensembl_id_mapping.tsv
Supplementary files format and content: modules_normalized_expr.tsv
Supplementary files format and content: voom_normalized_gene_expr.tsv

molecule: total RNA

organism: Homo sapiens

source_name: Nasal lavage

extract_protocol:
Cells were sorted into lysis buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara)
Sequencing libraries were constructed from total RNA using TruSeq RNA Sample Preparation Kits v2 (Illumina) and clustered onto a flowcell using a cBOT amplification system with a HiSeq SR v4 Cluster Kit (Illumina). Single-read sequencing was carried out on a HiSeq2500 sequencer (Illumina), using a HiSeq SBS v4 Kit to generate 58-base reads, with a target of approximately 10 million reads per sample

tag: tissue

value: Nasal lavage

tag: Sex

value: female

tag: donorid

tag: treatment

value: Placebo

tag: age months

tag: visit

tag: illness

tag: virus _yn

value: N

tag: eos total

tag: lym total

tag: mac total

tag: squ total

tag: epi total

tag: neut total

tag: enitrox


title: Xmlc2-Cre drove CM-specific Rbpms and Rbpms2 double KO mice rep4

city: San Diego

first: Zeyu

last: Chen

state: CA

address: 9500 Gilman Drive, BFRII 1217

department: School of Medicine

institute: UCSD

data_processing:
Raw RNA-seq reads were quality-controlled using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and trimmed with Trim Galore (v0.6.7) to remove low-quality bases and adapter sequences, obtaining high-quality clean reads
Trimmed reads were aligned to the mouse genome (GRCm38, Mus musculus) using HISAT2 (v2.2.1, PMID: 31375807).
Gene expression quantification was performed using StringTie (v2.2.1, https://doi.org/10.1038/nbt.3122).
Gene counts were obtained with featureCounts (https://doi.org/10.1093/bioinformatics/btt656) and used for differential expression analysis with DESeq2 (https://doi.org/10.1186/s13059-014-0550-8)
Alternative splicing events from RNA-seq data were identified using rMATS (v4.3.0)
Assembly: mm10
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

organism: Mus musculus

source_name: heart

growth_protocol: Rbpms and Rbpms2 floxed mice were generated with CRISPR-Cas9. Cardiomyocyte (CM)-specific Rbpms or Rbpms2 knockout mice were created by crossing Rbpms or Rbpms2 floxed mice with Xmlc2-Cre mice. CM-specific Rbpms and Rbpms2 double knockout mice were created by crossing Rbpms floxed mice with Rbpms2 floxed mice, and then with Xmlc2-Cre mice.

extract_protocol:
Embryonic or neonatal mouse hearts were homogenized in TRIzol (Invitrogen) for RNA extraction according to the manufacturer’s instructions.
The concentration and quality of purified RNA was assessed by Agilent Bioanalyzer 2100. cDNA libraries were constructed using an Illumina TruSeq stranded mRNA kit according to manufacturer’s instructions. Libraries were sequenced with an Illumina NovaSeq 6000 sequencer to a sequencing depth of 80-100 million reads per sample.

value: heart

tag: strain

tag: genotype

value: CM-specific Rbpms and Rbpms2 double KO

tag: time


title: lib28613

description: Library name: lib28613

tag: tissue

tag: Sex

value: Mepolizumab


title: control littermate rep3

value: Wild type


title: Xmlc2-Cre drove CM-specific Rbpms and Rbpms2 double KO mice rep3


title: control littermate rep1


title: THP1,Compound49,24h,ChIP-seq,H3K27ac

city: Cambridge

description: Library name: THP1_ChIPseq_Compound49_H3K27ac

library_source: genomic

molecule: genomic DNA

tag: cell line

tag: cell type

tag: treatment


title: lib28612

description: Library name: lib28612

tag: donorid

tag: age months

tag: visit

tag: illness


title: lib28611

description: Library name: lib28611

tag: virus _yn

tag: eos total

tag: lym total

tag: mac total


title: lib28606

description: Library name: lib28606

tag: squ total

tag: epi total

tag: neut total

tag: enitrox


title: Xmlc2-Cre drove CM-specific Rbpms and Rbpms2 double KO mice rep1

tag: tissue

tag: strain

tag: genotype

tag: time


title: THP1,DMSO,24h,ChIPseq,SMARCA4

description: Library name: THP1_ChIPseq_DMSO_SMARCA4

tag: cell line

tag: cell type

tag: treatment

value: negative control


title: Xmlc2-Cre drove CM-specific Rbpms and Rbpms2 double KO mice rep2


title: THP1,DMSO,24h,ChIP-seq,H3K27ac

description: Library name: THP1_ChIPseq_DMSO_H3K27ac


title: THP1,Compound49,24h,ChIP-seq,PU1

description: Library name: THP1_ChIPseq_Compound49_PU1


title: lib28604

description: Library name: lib28604

tag: Sex

tag: donorid

tag: age months

tag: visit

value: Y


title: Xmlc2-Cre drove CM-specific Rbpms KO mice rep3

value: CM-specific Rbpms KO


title: Xmlc2-Cre drove CM-specific Rbpms KO mice rep4


title: Xmlc2-Cre drove CM-specific Rbpms KO mice rep2


title: lib28603

description: Library name: lib28603

tag: illness

tag: virus _yn

tag: eos total

tag: lym total


title: THP1,DMSO,24h,ChIP-seq,PU1

description: Library name: THP1_ChIPseq_DMSO_PU1


title: lib28605

description: Library name: lib28605

tag: mac total

tag: squ total

tag: epi total

tag: neut total


title: THP1,ChIP-seq,Pooled,Input

description: Library name: THP1_ChIPseq_Pooled_Unput

tag: genotype

value: input


title: lib28601

description: Library name: lib28601

tag: tissue

tag: enitrox


title: iCas9 KPL-1 cells, sgKMT2pool, day14

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

description:
Library name: iCas9_KPL-1_sgKMT2pool_Dox_day14
sgKMT2pool_count_Hayashi.txt

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Reads were aligned and gene expression levels were estimated using RSEM v1.3.1 (RNA-Seq by Expectation-Maximization), with STAR v2.6.0c employed as the aligner to ensure accurate mapping of reads.
Assembly: hg19
Supplementary files format and content: TPM table
Supplementary files format and content: CRISPR screen counts
Library strategy: CRISPR tiling screen

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

extract_protocol:
RNA was extracted using the RNeasy Mini Kit with DNase set (Qiagen) following the manufacturers’ protocols.
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

tag: cell line

tag: cell type

value: breast cancer cell line

value: Functional domains knockout


title: iCas9 KPL-1 cells, sgSETD1A, rep3

description:
Library name: iCas9_KPL-1_sgSETD1A_Dox_day7_rep3
RNA-seq_TPM.txt

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Reads were aligned and gene expression levels were estimated using RSEM v1.3.1 (RNA-Seq by Expectation-Maximization), with STAR v2.6.0c employed as the aligner to ensure accurate mapping of reads.
Assembly: hg19
Supplementary files format and content: TPM table
Supplementary files format and content: CRISPR screen counts

value: SETD1A knockout

tag: treatment


title: lib28595

description: Library name: lib28595

tag: Sex

tag: donorid


title: Liver RNA sample 3

city: Leiden

first: Monica

last: Aguila

address: Zernikedreef 9

country: Netherlands

institute: ProQR Therapeutics

description: Library name: 105466-010-019

data_processing:
Sequencing data were processed using an in-house RNA-Seq bioinformatics pipeline. The pipeline includes adapter trimming with BBDuk, followed by alignment to the GRCh38 primary assembly (Ensembl release 110) using HISAT2. Post-alignment processing, including duplicate marking and additional SAM/BAM file manipulations, was performed using SAMtools
Assembly: GRCh38.110
Supplementary files format and content: csv files for read counts include the FPKM values per sample

source_name: liver

extract_protocol:
RNA was extracted using RLT buffer (QIAGEN) and isolated using the RNeasy Mini Kit (QIAGEN). 1ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-Seq were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S/L) following the manufactures protocol

value: liver

value: WT


title: Liver RNA sample 2

description: Library name: 105466-010-018


title: HepG2 sample 4

description: Library name: 105466-010-004


title: iCas9 KPL-1 cells, sgKMT2pool, day0

description:
Library name: iCas9_KPL-1_sgKMT2pool_Dox_day0
sgKMT2pool_count_Hayashi.txt


title: Liver RNA sample 1

description: Library name: 105466-010-017


title: Xmlc2-Cre drove CM-specific Rbpms2 KO mice rep4

tag: strain

value: CM-specific Rbpms2 KO

tag: time


title: Xmlc2-Cre drove CM-specific Rbpms2 KO mice rep2


title: lib28594

description: Library name: lib28594

value: Nasal lavage

value: female

tag: age months

tag: visit

tag: illness

tag: virus _yn


title: Xmlc2-Cre drove CM-specific Rbpms KO mice rep1


title: iCas9 KPL-1 cells, sgSETD1A, rep2

description:
Library name: iCas9_KPL-1_sgSETD1A_Dox_day7_rep2
RNA-seq_TPM.txt


title: Xmlc2-Cre drove CM-specific Rbpms2 KO mice rep1


title: HepG2 sample 2

description: Library name: 105466-010-002


title: HepG2 sample 3

description: Library name: 105466-010-003


title: lib28592

description: Library name: lib28592

value: N

tag: eos total

tag: lym total

tag: mac total

tag: squ total


title: HepG2 sample 1

description: Library name: 105466-010-001

tag: genotype


title: iCas9 KPL-1 cells, sgSETD1A, rep1

description:
Library name: iCas9_KPL-1_sgSETD1A_Dox_day7_rep1
RNA-seq_TPM.txt


title: lib28584

description: Library name: lib28584

tag: tissue

tag: epi total

tag: neut total

tag: enitrox


title: IHH sample 5

description: Library name: 105466-006-033

source_name: Immortalized human hepatocytes

tag: cell line

value: Immortalized human hepatocytes


title: DAP_dapseq-input_3037

city: Basel

first: Sevi

last: Durdu

address: Fabrikstrasse 24

department: Genome Regulation

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for single-read experiments. Illumina RTA 2.4.11 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for paired-read experiments. ChIP-seq samples were aligned to the mm10 assembly of the mouse genome using QuasR (Gaidatzis et al, Bioinformatics 2015), which internally uses Bowtie 2 (Langmead, Genome Biology 2009). Bowtie was run with QuasR default parameters.
Assembly: mm10
Supplementary files format and content: ExportWig function from the QuasR package was employed to generate the wig files with default parameters except scaling=1e6 and only for single-end experiments setting shift to 120.
Library strategy: DAP-seq

source_name: embryonic stem cells

growth_protocol: Rosetta(DE3)pLysS Competent Cells (Millipore) were induced to express GST-tagged protein encoded in pGEX-6P-1 plasmids for DAPseq (NGN2, MyoD1, bHLH domains of TCF3-E12,TCF3-E47,TCF4,TCF12). 2ml fresh culture were added into 50ml LB and grow to an OD600 of 0.5 and induced with IPTG for 3 hours at 37DEgC for NGN2 and MyoD1 and 16DegC for TCFs. Cells were lysed and soluble fractions were mixed in combinations. GST tagged proteins were isolated using Promega MagneGST beads.

extract_protocol:
DNA was purified by AMPure beads with a ratio of 2:1 beads to sample volume.
Isolated DNA was subjected to library preparation (NEBNext Ultra II DNA Library Prep Kit, Illumina). In the library preparation protocol, samples were amplified using 12 PCR cycles.

treatment_protocol: Protocol was performed for Small-scale DAP-seq using E. coli-expressed recombinant protein as previously described (Bartlett et al, Nature Protocols, 2017) with modifications. Brielfy, freshly isolated GST-bHLH proteins bound to magnetic beads were incubated with 10ug of gemonic DNA sonicated to an average size range of 150-200bp for 1 hour in PBS. Beads were washed 4x with 200ul of PBS + 0.05%NP40, then washed 2x with 200ul PBS. Finally, beads were resuspended in 30ul 10 mM Tris-Cl, pH 8.5 + 2ul 10mg/ml Proteinase K and incubated at 50DegC for 3 hours.

value: embryonic stem cells

tag: cell type

value: mESC

value: DNMT1-/-; DNMT3a-/-; DNMT3b-/-

tag: treatment (proteins)

tag: mouse strain

tag: experiment id


title: lib28583

description: Library name: lib28583

tag: Sex

tag: donorid

tag: treatment

value: Mepolizumab

tag: age months

tag: visit


title: iCas9 KPL-1 cells, sgEmpty, rep1

description:
Library name: iCas9_KPL-1_sgEmpty_Dox_day7_rep1
RNA-seq_TPM.txt


title: iCas9 KPL-1 cells, sgEmpty, rep2

description:
Library name: iCas9_KPL-1_sgEmpty_Dox_day7_rep2
RNA-seq_TPM.txt


title: lib28582

description: Library name: lib28582

value: Placebo

tag: illness

tag: virus _yn

tag: eos total

tag: lym total

tag: mac total


title: IHH sample 4

description: Library name: 105466-006-032

tag: genotype


title: iCas9 KPL-1 cells, sgSETD1A, RNAP2_rep1

description: Library name: iCas9_KPL-1_sgSETD1A_Dox_day7_RNAP2_rep1

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.3.3.1.
Duplication reads were removed from aligned file by using picard-tools-1.56.0
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER v4.7 makeUCSCfile command and comberted to bigwig by bedGraphToBigWig. BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
Cells were fixed with 2 mM DSG for 30 min, followed by 1% formaldehyde for 10 min, and treated with 0.125 M glycine for 5 min. The fixed cells were washed twice with cold PBS. Washed cells were resuspended in ChIP lysis buffer and centrifuged at 3200 rpm for 5 min at 4ºC to collect the nuclei pellet. The pellet was washed with ChIP wash buffer and resuspended in ChIP Shearing Buffer, and then frozen at -80ºC. Nuclear samples were shredded using a Picoruptor (Diagenode) and pre-cleared using Dynabeads protein G (Thermo Fisher Scientific) for 60 min at 4ºC with gentle rotation. Appropriate amounts of antibodies were added to chromatin and incubated overnight at 4ºC.
ChIP-seq libraries were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems).


title: lib28578

description: Library name: lib28578

tag: tissue

tag: squ total

tag: epi total

tag: neut total

tag: enitrox


title: IHH sample 3

description: Library name: 105466-006-031

tag: cell line


title: Xmlc2-Cre drove CM-specific Rbpms2 KO mice rep3

value: heart

tag: strain

tag: time


title: iCas9 KPL-1 cells, sgEmpty, RNAP2_rep1

description: Library name: iCas9_KPL-1_sgEmpty_Dox_day7_RNAP2_rep1

tag: cell type

tag: treatment


title: DAP_tcf4-tcf4_d1_rep1_3037

tag: treatment (proteins)

tag: mouse strain

tag: experiment id


title: DAP_tcf4-tcf4_d2_rep1_3037


title: DAP_tcf4-tcf4_d1_rep2_3037


title: IHH sample 2

description: Library name: 105466-006-030


title: lib28575

description: Library name: lib28575

tag: Sex

tag: donorid

tag: age months

tag: visit

tag: illness

tag: virus _yn

tag: eos total


title: IHH sample 1

description: Library name: 105466-006-029

tag: genotype


title: iCas9 KPL-1 cells, sgEmpty, serine2

description: Library name: iCas9_KPL-1_sgEmpty_Dox_day7_serine2


title: DAP_tcf3e47-tcf4_d2_rep1_3037

tag: tissue


title: lib28567

description: Library name: lib28567

value: cold

tag: lym total

tag: mac total

tag: squ total

tag: epi total

tag: neut total

tag: enitrox


title: HeLa sample 4

description: Library name: 105466-006-027

source_name: HeLa

tag: cell line

value: HeLa


title: iCas9 KPL-1 cells, sgSETD1A, serine2

description: Library name: iCas9_KPL-1_sgSETD1A_Dox_day7_serine2

tag: cell type

value: breast cancer cell line

tag: treatment


title: iCas9 KPL-1 cells, sgSETD1A, H3K4me3

description: Library name: iCas9_KPL-1_sgSETD1A_Dox_day7_H3K4me3

value: SETD1A knockout


title: iCas9 KPL-1 cells, sgEmpty, rep3

description:
Library name: iCas9_KPL-1_sgEmpty_Dox_day7_rep3
RNA-seq_TPM.txt


title: DAP_tcf3e47-tcf4_d2_rep2_3037

tag: treatment (proteins)

tag: mouse strain

tag: experiment id


title: lib28565

description: Library name: lib28565

tag: Sex

tag: donorid

tag: age months

tag: visit

tag: illness


title: HeLa sample 5

description: Library name: 105466-006-028

tag: genotype


title: lib28568

description: Library name: lib28568

tag: tissue

tag: virus _yn

tag: eos total

tag: lym total

tag: mac total


title: iCas9 KPL-1 cells, sgEmpty, H3K4me3

description: Library name: iCas9_KPL-1_sgEmpty_Dox_day7_H3K4me3

tag: cell line


title: lib28564

description: Library name: lib28564

tag: squ total

tag: epi total

tag: neut total

tag: enitrox


title: DAP_tcf4-tcf4_d2_rep2_3037

tag: cell type

tag: treatment (proteins)

tag: mouse strain

tag: experiment id


title: lib28551

description: Library name: lib28551

tag: Sex

tag: donorid

tag: treatment

tag: age months

tag: visit


title: HeLa sample 2

description: Library name: 105466-006-025

tag: genotype


title: DAP_tcf3e47-tcf4_d1_rep1_3037

tag: tissue


title: iCas9 KPL-1 cells, sgSETD1A, rescued WT

description: Library name: iCas9_KPL-1_rescued_WT_Dox_day21_H3K4me3

value: rescued WT


title: lib28579

description: Library name: lib28579

tag: illness

tag: virus _yn

tag: eos total

tag: lym total

tag: mac total


title: HEP3B sample 5

description: Library name: 105466-006-023

tag: cell line

value: WT


title: HeLa sample 1

description: Library name: 105466-006-024


title: MCF7, DRB Treatment, Rep1, ERalpha, ChIP

city: Bengaluru

first: Rajat

last: Mann

state: Karnataka

address: Rajiv Gandhi Nagar, Kodigehalli

country: India

institute: National Center for Biological Sciences

data_processing:
Raw fastq reads were aligned to the hg19 genome for human and dm3 reference genome for drosophila. Reads with quality score less than 30 were filtered out. The reads were first down sampled according to the sample with the lowest sequencing depth. Then, reads were further down sampled according to spike-in factor calculated as shown in (Egan et al., 2016).
Assembly: hg19 (for Human), dm3 (for Drosophila Spike-in)
Supplementary files format and content: bigwig files

source_name: Breast, mammary gland

growth_protocol: MCF-7 cells were maintained in DMEM with 10% FBS and 5% Penstrep. For experiments MCF-7 cells were grown in stripping media with 5% characol stripped FBS and 5% Penstrep for 72 hours.

extract_protocol:
Cells were fixed using 1% formaldehyde for 10 mins at room temperature on an orbital shaker. After 10mins, formaldehyde was quenched using 0.125M glycine for 5mins at room temperature on the orbital shaker. The cells were washed with cold 1XPBS and scraped. The cells were pelleted down at 3000rpm for 5mins at 4°C. The pellets were stored at -80°C. 10 million cells were resuspended in 1 ml of nuclear lysis buffer (NLB) (50mM Tris-HCl pH 7.4, 1% SDS, 10mM EDTA pH 8.0, and 1X PIC) and incubated in ice for 10mins. After nuclear lysis, cells were sonicated using Bioruptor pico for 28cycles with 30secs ON and 30secs OFF settings. The lysate was then spun at 12000rpm for 12mins at 4°C to clear off the cell debris. 100μg of chromatin was used for IP, further 3μg of sonicated S2 chromatin was added as spike-in for only H3K27ac ChIP. The IP was diluted 2.5 times with dilution buffer (20mM Tris-HCl pH 7.4, 100mM NaCl, 2mM EDTA pH 8.0, 0.5% Triton X-10, and 1X PIC). IP was set in a volume of 500μl. Additionally, 50μl was taken out and labelled as 10% input. For IP, main as well spike-in antibody was added in their respective amounts (ERα (sc-8002, Santa Cruz Biotech) 1μg, anti-PolII (Diagenode C15200004) 2μg, H3K27ac (ab4729, Abcam) 1μg and spike-in H2av 0.3ug (61686, Active Motif)). IP was incubated with antibodies overnight at 4°C at constant rotation of 12rpm. After incubation, 15μl of Protein G beads pre-blocked in BSA were added to the mix. It was incubated for 4 hours at 4°C on the rotor. After incubation, the beads were washed with wash buffers I, II, III and 1XTE sequentially (Li et al., 2013). The DNA-protein complexes were eluted from the beads by resuspending the beads in (100mM NaHCO3, 1%SDS, 2μg of RNaseA) at 37°C in a thermomixer with 1400rpm for 30mins. The crosslinked DNA-protein complexes were reverse-crosslinked over night at 65°C by the addition of NaCl. After that 2μl of Proteinase K (20mg/ml) was added to the mix and incubated for 2hours at 45°C. The ChIP DNA was then purified using PCI (Phenol:Chloroform:Isoamylalcohol) and ethanol precipitation. The pellet was resuspended in 10μl of NFW.
library preparation was done using NEBNext Ultra II DNA library Prep kit with Sample Purification Beads (E7103L).

treatment_protocol: After 72 hours cells were treated with β-estradiol (E2758, Sigma-Aldrich) at a concentration of 10nM for 1hour. In case of experiments involving transcription inhibitor treatment, cells were treated with DRB (D1916, Sigma) at 10uM and TRP (T3652, Sigma) at 1uM or DMSO for 1hour. After 1hour of inhibitor treatment, 10nM of E2 was added in the media and processed for ChIP-seq. For experiments involving knockdown, two rounds of transfection were done with the siRNAs. First transfection was done 24hours after cell seeding. Second round of transfection was done after 48 hours of keeping cells in stripping media. For FLAG-RRGG-ERα overexpression plasmids were transfected on the second day (48 hours in stripping media).

value: Breast, mammary gland

tag: cell type

value: epithelial cell

tag: chip antibody

value: Estrogen Receptor alpha Antibody (F-10), sc-8002, scbt

value: DRB (2hr), 17beta-estradiol (1hr)


title: DAP_tcf3e47-tcf3e47_d2_rep1_3037

tag: treatment (proteins)

tag: mouse strain


title: DAP_tcf3e47-tcf3e47_d1_rep2_3037

tag: experiment id


title: MCF7, DMSO Control for DRB, Rep1, ERalpha, ChIP

value: DMSO (2hr), 17beta-estradiol (1hr)


title: DAP_tcf3e47-tcf3e47_d2_rep2_3037

value: embryonic stem cells


title: DAP_tcf3e47-tcf3e47_d1_rep1_3037

value: mESC


title: HeLa sample 3

description: Library name: 105466-006-026


title: DAP_tcf3e47-tcf4_d1_rep2_3037

value: DNMT1-/-; DNMT3a-/-; DNMT3b-/-


title: H9, H3K27me3_H3K27ac, MTR, Post, DNA

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

description:
Tn5 taggmented DNA
read1 file contains genomic fragment; read2 files contains Ab id, UMI and genomic fragments

data_processing:
After sequencing, cell barcodes and UMI information were extracted with modified Reachtools (https://doi.org/10.1038/s41592-021-01060-3). Sequences from fixed positions of Read2 were extracted: 1st-8th for BC3, 39th-46th for BC2, 77th-84th for BC1, 115th-119th for RT-ID in RNA data or for antibody-ID in DNA data, 120th-127th for UMI. Barcode combinations (BC1:BC2:BC3:RT-ID/antibody-ID) were mapped to all possible barcode combinations with Bowtie (version: 1.3.1, doi:10.1186/gb-2009-10-3-r25, version, --norc -m 1 -v 0). Mapped cell IDs and UMI were stored in read names of genome sequences. Trim-galore (version:0.6.10) was used to trim adapter sequences with default settings. Trimmed reads were mapped mapped to GRCh38 using Bowtie2 (version: 2.5.3, DOI: 10.1038/nmeth.1923) for DNA data and STAR (version: 2.7.11b, DOI: 10.1093/bioinformatics/bts635) for RNA data with default settings. Only unique mapped reads were kept by samtools filtering (version: 1.19.2, MAPQ>50 for RNA data and MAPQ>10 for DNA data). For the paired-end mapping data, only proper mapped reads with correct orientation were kept. Duplicated reads were identified by the mapping positions and UMIs for each cellid of RNA data. Duplicated reads were identified by mapping positions only for each cellid of DNA data. RNA deduplicated data were feature counted by custom script with splitpoolquantitation (https://github.com/laurabiggins/nf_yang_wang/tree/main/splitpoolquantitation) and converted to sparse matrix. DNA deduplicated data were converted to fragment files for downstream analyses.
Assembly: GRCh38 for human sample
Supplementary files format and content: Tab-separated fragment files
Library strategy: scMTR-seq

growth_protocol: H9 cells were grown in 5% CO2, 5% O2 at 37°C and maintained in Essential8 medium (ThermoFisher Scientific) on 0.5% Geltrex (ThermoFisher Scientific).

extract_protocol:
H9 cells were dissociated into single cells with TrypLE Express (ThermoFisher Scientific).
Nuclei were prepared with Nuclei Extraction buffer and fixed with 0.2% formaldehyde at room temperature for 5 min. Concanavalin A beads were added to the samples to bind nuclei. Preincubated antibody and proteinA-Tn5-MEBdU were added to the nuclei and incubated at RT for 1 hour or overnight at 4°C. Nuclei were washed three times and tagmented at 37°C for 1 hour in the presence of MgCl2. Reaction was stopped with EDTA. Tagmentation was repeated for sequential tagmentation. Followed, reverse transcription was crried out to capture polyA-mRNA transcripts. Three rounds of split-pool barcoding was performed to add combinatory barcodes for each single cells. Nuclei was counted and aliquoted into sublibraries. Reverse crosslinking was performed at 55°C for 1 hour in reverse crosslinking buffer with proteinase K and RNase inhibtors. PMSF was used to inactivate proteinase K. DNA and cDNA were separated by C1 Streptavidin beads. For DNA library, tagmented genomic DNA fragments were purified with Ampure XP beads. Eluted DNA was performed adapter switching and amplified. For RNA library, templated switch was performed and preammplified. MEA adapters were added to the RNA library by Tn5-MEA mediated tagmentation. The concentration of libraries was measured with a Qubit. Samples were run on a Bioanalyzer to check the size distribution of library fragments before submited for seuqencing.

value: Human primed stem cells

tag: antibody

tag: library type

value: gDNA


title: Animal cap of X.laevis injected with mRNA encoding mrtf-deltaNSAP

city: New York

first: Mark

middle: E.

last: Corkins

state: NY

address: 1468 Madison Ave, Annenburg 25-86

department: CDRB

institute: Mount Sinai

data_processing:
Processed by Novagen
Assembly: Xenopus laevis genomve version 9.2
Supplementary files format and content: Processed readcount files are in comma deliminatee values (CSV-UTF-8) format.
Supplementary files format and content: Columns include: gene_id (Unique transcript number mapped to Xenopus Genome), Sample_Raw (Raw counts); Sample_fpkm (Fragments per kilobase of transcript per million fragments mapped), gene_name (gene symbol), gene_start (Starting location on Xenopus genome), gene_end  (Last/end location on Xenopus genome), gene_strand (Direction of transcript in forward or reverse orientation), gene_length (Size of transcript in base pairs), gene_biotype (Type of transcript, dataset only includes protein-coding genes), gene_description (Longer description of gene), tf_family (Descriptor describing related family of proteins)
Supplementary files format and content: readcount_All.csv files contain raw counts and fpkm counts for all samples in this dataset, readcount_Samplename.csv only contains raw counts and fpkm counts for indicated sample.

organism: Xenopus laevis

source_name: Animal Cap

growth_protocol: X. leavis grown in 0.1xMMR

extract_protocol:
RNA was extracted and purified using RNeasy kit (Qiagen)
cDNA library was prepared by Novogene and processed via paired-end 150 bp sequencing using via Illumina HiSeq2000 analyzers

treatment_protocol: Flag-DN-Mrtf, DNDSAP-Mrtf or DN-MrtfSRFm (0.5 ng) RNA was injected twice into animal pole region of two cell embryos. Ectoderm explants were prepared from injected and control uninjected embryos and cultured until stage 11 for RNA sequencing

value: Wild Type

value: Animal Cap

tag: treatment

value: deltaNSAP-MRTF

tag: developmental stage


title: DAP_tcf3e47-tcf3e12_d2_rep2_3037

tag: genotype


title: HEP3B sample 4

description: Library name: 105466-006-022


title: iCas9 KPL-1 cells, sgSETD1A, rescued deltaSET

description: Library name: iCas9_KPL-1_rescued_deltaSET_Dox_day21_H3K4me3

value: breast cancer cell line

value: rescued deltaSET


title: Animal cap of X.laevis injected with mRNA encoding mrtf-deltaNSRF

tag: tissue

value: deltaNSRF-MRTF


title: HEP3B sample 3

description: Library name: 105466-006-021

value: WT


title: H9, H3K27me3_H3K27ac, MT, IgG5x


title: H9, H3K27me3_H3K27ac, MT, IgG10x


title: DAP_tcf3e47-tcf3e12_d2_rep1_3037


title: H9, H3K27me3_H3K27ac, MT, IgG2x


title: HUH7 sample 5

description: Library name: 105466-006-018


title: Animal cap of X.laevis injected with mRNA encoding mrtf-deltaN

value: deltaN-MRTF


title: DAP_tcf3e47-tcf3e12_d1_rep1_3037


title: HUH7 sample 4

description: Library name: 105466-006-017


title: H9, H3K27me3_H3K27ac, MT, 4h


title: H9, H3K27me3_H3K27ac, MTR, Pre, DNA


title: DAP_tcf3e47-tcf12_d2_rep2_3037


title: hippocampus-1, PXN KO,PXN-S119A KI, P21

city: Taipei

first: Pei-Lin

last: Cheng

address: No. 128 Acdemia Rd., Section 2, Nankang

country: Taiwan

institute: Institue of Molecular Biology, Academia Sinica

description:
Library name: sample11
column names in isoquant.transcript_grouped_counts.tsv: P21_PXN_KI_Hippo1

data_processing:
Nanopore raw data were basecalled and demutiplexed using Dorado (v.0.8.2) followed by read trimming with Porechop (0.2.4).
The reads were then aligned to the mouse reference genome (mm10) using minimap2 with the parameters (-ax splice -t 36 -MD --secondary=yes -Y). The reads were filtered for primary alignments with MAPQ > 50, then sorted and indexed using SAMtools.
The read count of all transcripts were estimated using IsoQuant (v3.6.3) with the reference genome mm10 and  parameters (--data_type nanopore --report_novel_unspliced true --report_canonical all --count_exons ).
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes estimated read counts for each sample

source_name: hippocampus

extract_protocol:
Total RNA was extracted utilizing the RNeasy Mini Kit (Qiagen; Cat# 74104) and its concentration was determined using a Nanodrop 2000 spectrophotometer and a Qubit fluorometer (both from ThermoFisher Scientific). The quality of the extracted RNA was evaluated using a 2100 Bioanalyzer (Agilent).
120 ng total RNA per sample was subjected to cDNA synthesis using SMART-Seq  mRNA with UMI (Takara,Cat. 634763) following manufacturer’s instruction. Samples were amplified for 8 PCR cycles and using  0.5 x AMPure select above 500bp cDNA. The full-length cDNAs weres prepared for long-reads  sequencing using the Oxford Nanopore Ligation Native barcoding Kit 24 V14 ( SQK-NBD114.24) .barcoded cDNA library was loaded onto a PromethION flow cell (pore version 10.4.1, flow cell version FLO-PRO114M) and run on a PromethION P2 solo sequencing device for 72 hours.

value: hippocampus

value: bulk

value: paxillin KO, paxillin-S119A-KI


title: H9, H3K27me3_H3K27ac, MT, IgG1x


title: HUH7 sample 3

description: Library name: 105466-006-016


title: HEP3B sample 2

description: Library name: 105466-006-020


title: hippocampus-2, WT, P21

description:
Library name: sample10
column names in isoquant.transcript_grouped_counts.tsv: P21_Con_Hippo2


title: H9, H3K27me3_H3K27ac, MT, 1h


title: HUH7 sample 2

description: Library name: 105466-006-015


title: DAP_tcf3e47-tcf12_d1_rep2_3037


title: hippocampus-1, WT, P21

description:
Library name: sample9
column names in isoquant.transcript_grouped_counts.tsv: P21_Con_Hippo1


title: HUH7 sample 1

description: Library name: 105466-006-014


title: DAP_tcf3e47-tcf12_d2_rep1_3037


title: hippocampus-1, PXN KO,PXN-S119A KI, P15

description:
Library name: sample7
column names in isoquant.transcript_grouped_counts.tsv: P15_PXN_KI_Hippo1


title: DAP_tcf3e12-tcf4_d2_rep2_3037


title: H9, IgG, ST, -AS

description:
Tn5 taggmented DNA
read1 file contains genomic fragment; read2 files contains genomic fragment

value: Normal rabbit IgG (R&D, #AB-105-C)


title: DAP_tcf3e47-tcf12_d1_rep1_3037

value: embryonic stem cells


title: H9, H3K27me3_H3K27ac, MT, 0.5h


title: HEP3B sample 1

description: Library name: 105466-006-019


title: hippocampus-2, PXN KO,PXN-S119A KI, P15

description:
Library name: sample8
column names in isoquant.transcript_grouped_counts.tsv: P15_PXN_KI_Hippo2


title: Single donor PHH  sample 3

description: Library name: 105466-006-007

source_name: PHH (primary cells)

value: PHH (primary cells)


title: hippocampus-2, PXN KO,PXN-S119A KI, P21

description:
Library name: sample12
column names in isoquant.transcript_grouped_counts.tsv: P21_PXN_KI_Hippo2


title: Animal cap of X.laevis control sample for MRTF

value: control


title: DAP_tcf3e47-tcf3e12_d1_rep2_3037

value: mESC

value: DNMT1-/-; DNMT3a-/-; DNMT3b-/-


title: Single donor PHH  sample 4

description: Library name: 105466-006-008


title: H9, H3K36me3, ST, -AS

value: Human primed stem cells

value: gDNA


title: Single donor PHH  sample 2

description: Library name: 105466-006-006


title: DAP_tcf3e12-tcf4_d2_rep1_3037


title: DAP_tcf3e12-tcf4_d1_rep2_3037


title: H9, H3K27ac, ST, +AS

value: H3K27ac (Abcam, #ab4729)


title: hippocampus-2, WT, P15

description:
Library name: sample6
column names in isoquant.transcript_grouped_counts.tsv: P15_Con_Hippo2


title: hippocampus-1, WT, P15

description:
Library name: sample5
column names in isoquant.transcript_grouped_counts.tsv: P15_Con_Hippo1


title: H9, H3K27me3_H3K27ac, MT, 2h


title: Single donor PHH  sample 1

description: Library name: 105466-006-005


title: Multiple donor PHH sample 4

description: Library name: 105466-006-004


title: DAP_tcf3e12-tcf4_d1_rep1_3037


title: hippocampus-2, PXN KO,PXN-S119A KI, P10

description:
Library name: sample4
column names in isoquant.transcript_grouped_counts.tsv: P10_PXN_KI_Hippo2


title: H9, H3K27ac, ST, -AS


title: DAP_tcf3e12-tcf3e12_d2_rep2_3037


title: H9, H3K27me3, ST, -AS


title: DAP_tcf3e12-tcf3e12_d2_rep1_3037


title: hippocampus-2, WT, P10

description:
Library name: sample2
column names in isoquant.transcript_grouped_counts.tsv: P10_Con_Hippo2


title: H9, H3K27me3_H3K27ac, MTR, Post, RNA

description:
polyA RNA
read1 file contains transcript; read2 files contains RT id and UMI

data_processing:
After sequencing, cell barcodes and UMI information were extracted with modified Reachtools (https://doi.org/10.1038/s41592-021-01060-3). Sequences from fixed positions of Read2 were extracted: 1st-8th for BC3, 39th-46th for BC2, 77th-84th for BC1, 115th-119th for RT-ID in RNA data or for antibody-ID in DNA data, 120th-127th for UMI. Barcode combinations (BC1:BC2:BC3:RT-ID/antibody-ID) were mapped to all possible barcode combinations with Bowtie (version: 1.3.1, doi:10.1186/gb-2009-10-3-r25, version, --norc -m 1 -v 0). Mapped cell IDs and UMI were stored in read names of genome sequences. Trim-galore (version:0.6.10) was used to trim adapter sequences with default settings. Trimmed reads were mapped mapped to GRCh38 using Bowtie2 (version: 2.5.3, DOI: 10.1038/nmeth.1923) for DNA data and STAR (version: 2.7.11b, DOI: 10.1093/bioinformatics/bts635) for RNA data with default settings. Only unique mapped reads were kept by samtools filtering (version: 1.19.2, MAPQ>50 for RNA data and MAPQ>10 for DNA data). For the paired-end mapping data, only proper mapped reads with correct orientation were kept. Duplicated reads were identified by the mapping positions and UMIs for each cellid of RNA data. Duplicated reads were identified by mapping positions only for each cellid of DNA data. RNA deduplicated data were feature counted by custom script with splitpoolquantitation (https://github.com/laurabiggins/nf_yang_wang/tree/main/splitpoolquantitation) and converted to sparse matrix. DNA deduplicated data were converted to fragment files for downstream analyses.
Assembly: GRCh38 for human sample
Supplementary files format and content: Tab-separated matrix files
Library strategy: scMTR-seq

molecule: polyA RNA

value: mRNA


title: hippocampus-1, WT, P10

description:
Library name: sample1
column names in isoquant.transcript_grouped_counts.tsv: P10_Con_Hippo1


title: DAP_tcf3e12-tcf3e12_d1_rep2_3037


title: hippocampus-1, PXN KO,PXN-S119A KI, P10

description:
Library name: sample3
column names in isoquant.transcript_grouped_counts.tsv: P10_PXN_KI_Hippo1


title: H9, RNA_only, MTR, Post, RNA


title: MCF7, exosc3 knockdown, Rep2, ERalpha, ChIP

description: Library name: si_exo_ERalpha_Rep2

extract_protocol:
Cells were fixed using 1% formaldehyde for 10 mins at room temperature on an orbital shaker. After 10mins, formaldehyde was quenched using 0.125M glycine for 5mins at room temperature on the orbital shaker. The cells were washed with cold 1XPBS and scraped. The cells were pelleted down at 3000rpm for 5mins at 4°C. The pellets were stored at -80°C. 10 million cells were resuspended in 1 ml of nuclear lysis buffer (NLB) (50mM Tris-HCl pH 7.4, 1% SDS, 10mM EDTA pH 8.0, and 1X PIC) and incubated in ice for 10mins. After nuclear lysis, cells were sonicated using Bioruptor pico for 28cycles with 30secs ON and 30secs OFF settings. The lysate was then spun at 12000rpm for 12mins at 4°C to clear off the cell debris. 100μg of chromatin was used for IP, further 3μg of sonicated S2 chromatin was added as spike-in for only H3K27ac ChIP. The IP was diluted 2.5 times with dilution buffer (20mM Tris-HCl pH 7.4, 100mM NaCl, 2mM EDTA pH 8.0, 0.5% Triton X-10, and 1X PIC). IP was set in a volume of 500μl. Additionally, 50μl was taken out and labelled as 10% input. For IP, main as well spike-in antibody was added in their respective amounts (ERα (sc-8002, Santa Cruz Biotech) 1μg, anti-PolII (Diagenode C15200004) 2μg, H3K27ac (ab4729, Abcam) 1μg and spike-in H2av 0.3ug (61686, Active Motif)). IP was incubated with antibodies overnight at 4°C at constant rotation of 12rpm. After incubation, 15μl of Protein G beads pre-blocked in BSA were added to the mix. It was incubated for 4 hours at 4°C on the rotor. After incubation, the beads were washed with wash buffers I, II, III and 1XTE sequentially (Li et al., 2013). The DNA-protein complexes were eluted from the beads by resuspending the beads in (100mM NaHCO3, 1%SDS, 2μg of RNaseA) at 37°C in a thermomixer with 1400rpm for 30mins. The crosslinked DNA-protein complexes were reverse-crosslinked over night at 65°C by the addition of NaCl. After that 2μl of Proteinase K (20mg/ml) was added to the mix and incubated for 2hours at 45°C. The ChIP DNA was then purified using PCI (Phenol:Chloroform:Isoamylalcohol) and ethanol precipitation. The pellet was resuspended in 10μl of NFW.
ChIP-seq

value: Breast, mammary gland

value: epithelial cell

value: scr knockdown, 17beta-estradiol (1hr)

value: Estrogen Receptor alpha Antibody (F-10), sc-8002, scbt


title: DAP_tcf3e12-tcf3e12_d1_rep1_3037


title: H9, H3K27me3_H3K27ac, MTR, Pre, RNA


title: DAP_tcf3e12-tcf12_d2_rep1_3037


title: Ishikawa cells, Six1 transfected, progesterone-estrodiol-cyclic AMP treated, rep4 [L002]

city: Calgary

first: Myriam

last: Hemberger

address: 3330 Hospital Dr NW

country: Canada

institute: University of Calgary

description: Library name: SIX1-4_PEC [L002]

data_processing:
Reads aligned using STAR aligner
Assembly: Homo sapiens GRch38_v108
Supplementary files format and content: tab-dilimited text files containing raw counts for each sample

source_name: Ishikawa cells

extract_protocol:
Total RNA was isolated from Ishikawa Cells using Qiagen RNeasy Mini kit (Qiagen, 74104) according to manufacturer's protocol. An average of 3 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq

value: Ishikawa cells

value: Six1 transfected, progesterone, estrodiol, cyclic AMP


title: MCF7, scramble RNA, Rep2, ERalpha, ChIP

description: Library name: si_scr_ERalpha_Rep2

value: exosc3 knockdown, 17beta-estradiol (1hr)


title: H9, RNA_only, MTR, Pre, RNA


title: Ishikawa cells,Six1 transfected, rep4 [L002]

description: Library name: SIX1-4 [L002]

value: Six1 transfected


title: DAP_tcf3e12-tcf12_d1_rep2_3037

value: embryonic stem cells


title: DAP_tcf3e12-tcf12_d1_rep1_3037


title: Tau2

city: Nanjing

first: Zhaokang

last: Cui

address: No. 50, Zhongling Street,

country: China

institute: Jiangsu Academy of Agricultural Sciences

description: Library name: Sample 8

data_processing:
Isolation and purify mRNA from total RNA.
Synthesis the first strand cDNA and synthesis the second strand cDNA.
Purify the double-stranded cDNA with 1.8X AMPure XP beads.
cDNA were end repaired and added A base to the 3’ end and cDNA were ligated adaptors.
Purify and the adaptor purificated library with AMPure XP beads.
Assembly: Btau_5.0.1
Supplementary files format and content: csv file includes count, FPKM, and TPM values for each Sample.

organism: Bos taurus

source_name: M II oocyte

extract_protocol:
Total RNA was extracted from tissues using TRIzol (Invitrogen, Carlsbad, California, USA) according to manual instruction.
For oocyte samples, the TRIzol was directly added to the oocyte sample with the amount 200 μL, followed by vortex mixing and standing for 5-minute. The mixture was centrifuged at 4°C at 12,000xg for 5 minutes, and the supernatant was transferred to a new EP tube for extraction. 300μl of chloroform/isoamyl alcohol (24:1) was added into the transferred supernatant and the mixture was vigorously vortexed to ensure thorough mixing. Then the mixture was centrifuged at 4°C and 12,000xg for 8 minutes. Take the clear upper aqueous layer and repeat the above process one time. After centrifugation, the final upper aqueous layer was carefully transferred to a new 1.5ml EP tube with a 2/3 supernatant volume of isopropanol (for low amount of tissues/ cell, 2µL 5mg/mL glycogen can be added for precipitation), gently inverted to mix well, placed in a -20°C refrigerator for 2 hours. Next, the precipitation mixture was centrifuged with 17500xg at 4°C for 25 minutes. The supernatant was discarded, and the precipitation was washed with 0.9ml of 75% ethanol. The precipitation was suspended by inverting the tube up and down several times. Then the precipitation was collected by centrifuging at 17500g for 3 minutes at 4°C and discarding the supernatant. Repeat the centrifugation to remove supernatant completely and the precipitation was dried in the biosafety cabinet for 3-5 minutes. Finally, 20µL~200µL of DEPC-treated or RNase-free water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Agilent 2100 Bioanalyzer (Agilent, CA, USA).
RNA libraries were prepared for sequencing using standard BGI protocols.

value: M II oocyte

value: germ cell

tag: Sex

value: female

value: microplastics + taurine


title: Ishikawa cells, Six1 transfected, progesterone-estrodiol-cyclic AMP treated, rep3 [L002]

description: Library name: SIX1-3_PEC [L002]


title: Tau1

description: Library name: Sample 7


title: DAP_tcf12-tcf4_d2_rep2_3037

value: mESC

value: DNMT1-/-; DNMT3a-/-; DNMT3b-/-


title: Multiple donor PHH sample 3

description: Library name: 105466-006-003

value: PHH (primary cells)

value: WT


title: Tau3

description: Library name: Sample 9


title: Vsx2 (Re2)

city: Helsinki

first: Sami

last: Kilpinen

address: Viikinkaari 9

department: Faculty of Biological and Environmental Sciences

country: Finland

institute: University of Helsinki

description:
Library name: E12R1_Vsx2_2
E12R1_Vsx2_R2

data_processing:
Reads were demultiplexed using the dual barcode sequences. Demultiplexed reads were aligned against the Mus musculus genome mm10 and the peak calling was performed, using the nf-core (Ewels et al., 2020) pipeline nf-core/cutandrun.
Following software was used in the nf-core/cutandrun pipeline: adapter trimming with TrimGalore!, aligner bowtie2, duplicate filtering with Picard, peakcaller SEACR.
Assembly: mm10
Supplementary files format and content: bigwig files contain the filtered CUT&Tag reads aligned to the mouse (Mus Musculus) genome version mm10.
Library strategy: CUT&Tag

source_name: rhombomere 1

growth_protocol: Embryonic brains were isolated from E12.5 wildtype (ICR) mouse embryos. Embryos were obtained from timed matings, where embryonic day 0.5 (E0.5) was defined as noon of the day of the vaginal plug. All animal experiments were approved by the Laboratory Animal Center, University of Helsinki, and the National Animal Experiment Board in Finland.

extract_protocol:
The samples were processed following the CUT&Tag-It Assay Kit protocol (Active Motif, cat # 53170). Shortly, the cells from freshly dissociated r1 tissues were bound to concanavalin A coated magnetic beads followed by the antibody incubations and washing steps on beads. The following primary antibodies were used: rabbit anti-Gata2 (Abcam, ab109241), rabbit anti-Gata3 (Boster, M00593), rabbit anti-Tal1 (Abcam, ab75739), rabbit anti-Vsx2 (Proteintech, 25825-1-AP-20), rabbit anti-Ebf1 (Boller et al., 2016) rabbit anti-Insm1 (Nordic BioSite, ASJ-IO4DE3-50), rabbit anti-Tead2 (Biorbyt, orb382464), rabbit anti-IgG (Cell Signalling, 66362) and rabbit anti-H3K4me3 (Cell Signalling, 9751).
The library  preparation was done as part of the CUT&Tag-It Assay Kit protocol (Active Motif, cat # 53170) that uses protein A-Tn5 transposomes (pA-Tn5) for tagmentation followed by DNA amplification with Q5 high-fidelity DNA polymerase and dual-barcoding primers. The number of PCR cycles was 14.
The DNA libraries were multiplexed at 10 nM equimolar ratios and sequenced on NextSeq 500 or Aviti. 75 bp paired-end sequences were obtained.

treatment_protocol: r1 tissues were dissected using the constriction at midbrain-hindbrain boundary anteriorly and the extent of cerebellar tissue dorsally as visual landmarks. The ventral part of the r1 was separated and used for the CUT&Tag. r1 tissues from the embryos of one mouse litter were pooled and dissociated together. Cells were then divided between samples, using 200 000 - 250 000 cells per sample. Embryos from different E12.5 mouse litters were used as biological replicates.

value: rhombomere 1

value: E12.5 embryo

value: anterior hindbrain cells

value: wild-type (ICR)

tag: batch


title: Multiple donor PHH sample 1

description: Library name: 105466-006-001


title: Multiple donor PHH sample 2

description: Library name: 105466-006-002


title: H9, H3K27me3, ST, +AS

value: Human primed stem cells

value: gDNA


title: MPs3

description: Library name: Sample 6

value: microplastics


title: Ishikawa cells, Six1 transfected, progesterone-estrodiol-cyclic AMP treated, rep2 [L002]

description: Library name: SIX1-2_PEC [L002]

value: Ishikawa cells

value: Six1 transfected, progesterone, estrodiol, cyclic AMP


title: DAP_tcf12-tcf4_d2_rep1_3037

value: embryonic stem cells


title: MPs2

description: Library name: Sample 5

value: M II oocyte

value: germ cell


title: DAP_tcf12-tcf4_d1_rep2_3037


title: DAP_tcf3e12-tcf12_d2_rep2_3037


title: MPs1

description: Library name: Sample 4

value: female


title: Vsx2 (Re1)

description:
Library name: E12R1_Vsx2_1
E12R1_Vsx2_R1

value: rabbit anti-Vsx2 (Proteintech, 25825-1-AP-20)


title: DAP_tcf12-tcf4_d1_rep1_3037

value: mESC

value: DNMT1-/-; DNMT3a-/-; DNMT3b-/-


title: Ishikawa cells, Six1 transfected, rep2 [L002]

description: Library name: SIX1-2 [L002]

value: Six1 transfected


title: Con3

description: Library name: Sample 3

value: control


title: Gata3 (Re2)

description:
Library name: E12R1_Gata3_2
E12R1_Gata3_R2

value: rhombomere 1

value: E12.5 embryo

value: rabbit anti-Gata3 (Boster, M00593)


title: Ishikawa cells, Six1 transfected, rep1 [L002]

description: Library name: SIX1-1 [L002]


title: DAP_tcf12-tcf12_d2_rep2_3037


title: Con2

description: Library name: Sample 2


title: Gata3 (Re3)

description:
Library name: E12R1_Gata3_3
E12R1_Gata3_R3

value: anterior hindbrain cells

value: wild-type (ICR)


title: Tal1 (Re3)

description:
Library name: E12R1_Tal1_757_3
E12R1_Tal1_R3

value: rabbit anti-Tal1 (Abcam, ab75739)


title: IgG (Re2)

description:
Library name: E12R1_IgG_2
E12R1_IgG_R2

value: rabbit anti-IgG (Cell Signalling, 66362)


title: DAP_tcf12-tcf12_d2_rep1_3037


title: Con1

description: Library name: Sample 1


title: Ishikawa cells, Foxc1 transfected, progesterone-estrodiol-cyclic AMP treated, rep4 [L002]

description: Library name: FOXC1-4-PEC [L002]

value: Ishikawa cells

value: Foxc1 transfected, progesterone, estrodiol, cyclic AMP


title: Ishikawa cells, Foxc1 transfected, rep4 [L002]

description: Library name: FOXC1-4 [L002]

value: Foxc1 transfected


title: DAP_tcf12-tcf12_d1_rep2_3037

value: embryonic stem cells


title: Tal1 (Re2)

description:
Library name: E12R1_Tal1_757_2
E12R1_Tal1_R2


title: Ishikawa cells, Six1 transfected, rep3 [L002]

description: Library name: SIX1-3 [L002]


title: DAP_tcf12-tcf12_d1_rep1_3037


title: Gata2 (Re2)

description:
Library name: E12R1_Gata2_ab_2
E12R1_Gata2_R2

value: rabbit anti-Gata2 (Abcam, ab109241)


title: Gata2 (Re3)

description:
Library name: E12R1_Gata2_ab_3
E12R1_Gata2_R3


title: Ishikawa cells, Foxc1 transfected, progesterone-estrodiol-cyclic AMP treated, rep3 [L002]

description: Library name: FOXC1-3-PEC [L002]


title: DAP_ngn2-tcf4_d2_rep2_3037


title: IgG (Re3)

description:
Library name: E12R1_IgG_3
E12R1_IgG_R3


title: Ishikawa cells, Foxc1 transfected, rep3 [L002]

description: Library name: FOXC1-3 [L002]


title: 2nd mem SG1

city: Sapporo

first: Kensuke

last: Takada

address: N21W11 Kita-ku

institute: Hokkaido University

description: Library name: Sample 3

data_processing:
The obtained raw reads were trimmed and quality-filtered using the Trim Galore (version 0.4.4), Trimmomatic (version 0.36), and cutadapt (version 1.16) software.
The trimmed reads were then mapped to the murine GRCm38 genome using STAR (version 2.7.2b).
Unique-mapped reads on annotated genes were counted using featureCounts (version 1.6.1).
FPKM values were calculated from the mapped reads by normalizing to total counts.
Assembly: GRCm38.p6 (mm10)
Supplementary files format and content: gene-FPKM_name.txt

source_name: Spleen

extract_protocol:
RNA was extracted using Rneasy Plus Micro Kit (Qiagen)
Libraries were prepared using SMART-Seq Stranded Kit (Clontech)

value: Spleen

value: T cells

value: Rora sg/sg


title: Ishikawa cells, Six1 transfected, progesterone-estrodiol-cyclic AMP treated, rep1 [L002]

description: Library name: SIX1-1_PEC [L002]

value: Six1 transfected, progesterone, estrodiol, cyclic AMP


title: 2nd mem WT2

description: Library name: Sample 2

value: WT


title: 2nd mem SG2

description: Library name: Sample 4


title: DAP_ngn2-tcf4_d2_rep1_3037

value: mESC

value: DNMT1-/-; DNMT3a-/-; DNMT3b-/-


title: Ishikawa cells, Foxc1 transfected, progesterone-estrodiol-cyclic AMP treated, rep2 [L002]

description: Library name: FOXC1-2-PEC [L002]


title: 2nd mem WT1

description: Library name: Sample 1


title: Tal1 (Re1)

description:
Library name: E12R1_Tal1_757_1
E12R1_Tal1_R1

value: rhombomere 1

value: E12.5 embryo


title: Gata3 (Re1)

description:
Library name: E12R1_Gata3_1
E12R1_Gata3_R1

value: anterior hindbrain cells

value: wild-type (ICR)

value: rabbit anti-Gata3 (Boster, M00593)


title: Neuron mEERL CD8 T cells rep3

city: Kingston

first: Sebastien

last: Talbot

state: ON

address: 18 Stuart st

department: DBMS

institute: Queen's University

description: Library name: 3_Neuron_mEERL_CM_CD8_T_cells

data_processing:
Adapter trimming and low quality base removal were carried out with Trimmomatic v0.35, and reads were aligned to the mouse reference genome GRCm38 (Gencode M25, Ensembl 100) with STAR v2.7.1. Gene level counts were generated with STAR and RSEM, normalized to fragments per kilobase per million mapped reads, and differential expression was assessed with DESeq2. Genes with a false discovery rate–adjusted P value below 0.20 were considered differentially expressed. Downstream analyses and visualization were performed in RStudio.
Assembly: mm10 (GRCm38, Gencode M25, Ensembl 100)
Supplementary files format and content: tsv files containing raw readcounts from each sample
Supplementary files format and content: tsv files containing TPM normalized values from each sample

source_name: dorsal root ganglia (DRG)

extract_protocol:
Naïve TRPV1cre::tdTomatofl/WT mice were euthanized, and their dorsal root ganglia (DRG) were immediately transferred into DMEM (Corning, 10 013 CV) supplemented with 50 U ml−1 penicillin, 50 μg ml−1 streptomycin (Corning, MT 3001 Cl) and 10 % fetal bovine serum (Seradigm, 3100). The tissue was dissociated for 80 min at 37 °C in HEPES buffered saline (Sigma, 51558) containing 1 mg ml−1 collagenase IV (Sigma, C0130) and 2.4 U ml−1 dispase II (Sigma, 04942078001). After digestion, ganglia were gently triturated through glass Pasteur pipettes of decreasing diameter, centrifuged through a 10 % BSA cushion and plated onto laminin coated (Sigma, L2020) culture dishes. Approximately 4 × 10^4 neurons per dish were maintained for 48 h in Neurobasal A medium (Gibco, 21103 049) supplemented with 0.05 ng μl−1  nerve growth factor (Life Technologies, 13257 019), 0.002 ng μl−1 glial cell line derived neurotrophic factor (PeproTech, 450 51 10), 0.01 mM cytosine β D arabinoside (Sigma, C6645), 200 mM L glutamine (VWR, 02 0131) and B 27 (Gibco, 17504044). Neurons were then co-cultured at a 1:10 ratio with mEERL derived small extracellular vesicles, cytotoxic CD8+ T-cells or both, each condition prepared in T cell medium supplemented with the same concentrations of NGF and GDNF to support neuronal viability. After 48 h, cells were detached with a scraper, washed in flow cytometry buffer (PBS containing 2 % FBS and 1 mM EDTA), passed through a 70 μm filter, and TRPV1+ neurons (FSChigh SSChigh tdTomatohigh) were isolated by fluorescence activated cell sorting directly into TRIzol.
RNA extraction, library construction and sequencing were performed at the IRIC Genomics Platform (Université de Montréal). RNA integrity was confirmed with an Agilent Bioanalyzer (RIN > 7.5). Poly adenylated transcripts were captured and libraries prepared with the KAPA mRNA HyperPrep Kit (Kapa Biosystems, KR1352). Bar coded libraries were sequenced on an Illumina NextSeq 500 using 75 cycle single end reads.

value: dorsal root ganglia (DRG)

value: CD8 Tcell


title: Gata2 (Re1)

description:
Library name: E12R1_Gata2_ab_1
E12R1_Gata2_R1


title: Ishikawa cells, Foxc1 transfected, rep2 [L002]

description: Library name: FOXC1-2 [L002]

value: Ishikawa cells

value: Foxc1 transfected


title: DAP_ngn2-tcf4_d1_rep1_3037

value: embryonic stem cells


title: Ishikawa cells, Foxc1 transfected, progesterone-estrodiol-cyclic AMP treated, rep1 [L002]

description: Library name: FOXC1-1-PEC [L002]

value: Foxc1 transfected, progesterone, estrodiol, cyclic AMP


title: H3K4me3 (Re1)

description:
Library name: E12R1_H3K4me3_1
H3K4me3_R1

value: rabbit anti-H3K4me3 (Cell Signalling, 9751)


title: DAP_ngn2-tcf3e47_d2_rep2_3037


title: Neuron mEERL CD8 T cells rep2

description: Library name: 2_Neuron_mEERL_CM_CD8_T_cells


title: DAP_ngn2-tcf3e47_d2_rep1_3037


title: Ishikawa cells, Foxc1 transfected, rep1 [L002]

description: Library name: FOXC1-1 [L002]


title: DAP_ngn2-tcf3e47_d1_rep2_3037


title: DAP_ngn2-tcf3e47_d1_rep1_3037


title: IgG (Re1)

description:
Library name: E12R1_IgG_1
E12R1_IgG_R1

value: rabbit anti-IgG (Cell Signalling, 66362)


title: Neuron mEERL CD8 T cells rep1

description: Library name: 1_Neuron_mEERL_CM_CD8_T_cells


title: Neuron mEERL rep3

description: Library name: 3_Neuron_mEERL


title: Neuron mEERL rep2

description: Library name: 2_Neuron_mEERL


title: Ishikawa cells, Foxc1 and Six1 transfected, rep4 [L002]

description: Library name: FOXC1+SIX1-4 [L002]

value: Foxc1 and Six1 transfected


title: Ishikawa cells, Foxc1 and Six1 transfected, progesterone-estrodiol-cyclic AMP treated, rep3 [L002]

description: Library name: FOXC1+SIX1-3-PEC [L002]

value: Foxc1 and Six1 transfected, Progesterone, estrodiol, cyclic AMP


title: DAP_ngn2-tcf4_d1_rep2_3037

value: mESC


title: Ishikawa cells, Foxc1 and Six1 transfected, progesterone-estrodiol-cyclic AMP treated, rep4 [L002]

description: Library name: FOXC1+SIX1-4-PEC [L002]


title: Neuron mEERL rep1

description: Library name: 1_Neuron_mEERL


title: Short day samples at Zeitgeber time 20 h replicate B

city: New Haven

first: Chun Chung

last: Leung

state: CT

address: YSB 424, 260 Whitney Avenue

department: MCDB

institute: Yale University

description: Library name: ShortDay_ZT20_Rep_B

data_processing:
Sequencing adapters, poly-A sequences and low quality reads were removed from the raw read file using cutadapt (v3.4) with the following parameters: -q 10,10. Sequences of known mature miRNAs (428 in total, but only 350 unique sequences) and tRFs (1,544,607 in total) were downloaded from miRBase (release 22.1) and the tREX database (2021 release). Bowtie2 (v2.5.1) was used to align reads with the following parameters: -a --end-to-end --score-min L,0,-0.6 --np 0 --rdg 9999,9999 --rfg 9999,9999. SAMTools were used to retrieve alignments where the reads covered the entirety of the sRNA annotations.
Assembly: miRBase (release 22.1) and the tREX database (2021 release)
Supplementary files format and content: Bowtie2-quantified read counts in comma-separated values

organism: Arabidopsis thaliana

source_name: Whole seedlings

growth_protocol: Seeds were sterilized before being sown onto 1/2 Murashige and Skoog medium plates lined with autoclaved filter papers. For germination, seeds were stratified in the dark for 48 hours before being transferred to a growth chamber under a 12L:12D photoperiod . After germination, seedlings were kept in the same condition for 10 days. On day 11, the seedlings were transferred to 16L:8D, 12L:12D, or 8L:16D photoperiod. On day 13, whole seedlings including shoots and roots were harvested and snap-frozen in liquid nitrogen.

extract_protocol:
Total RNA was extracted from approximately 200 mg of pulverized whole Arabidopsis seedlings (shoot, hypocotyl, and root) using TRIzol reagent (ThermoFisher) according to manufacturer’s protocol. RNA samples were treated with RNase-free DNase (QIAGEN, 79254) to remove DNA contaminants. Protein contaminants were removed by extraction with phenol-chloroform mixture (phenol:chloroform:isoamyl-alchohol 25:24:1; Thermo Fisher, AM9730) followed by precipitation using 3 M sodium acetate solution.
All sequencing libraries were prepared at Yale Center for Genome Analysis (YCGA). All samples passed a quality check with ≥7.0 in RNA integration number (Agilent Bio-analyzer). For sRNA-sequencing, small RNAs (expected size ≤40 nucleotides) were size-selected from total RNA samples through gel electrophoresis at YCGA. The NEBNext Small RNA Library Prep Set for Illumina kit was used.

value: Whole seedlings

value: Columbia 0

value: Short day

tag: time


title: Short day samples at Zeitgeber time 20 h replicate A

description: Library name: ShortDay_ZT20_Rep_A


title: Ishikawa cells, Foxc1 and Six1 transfected, rep3 [L002]

description: Library name: FOXC1+SIX1-3 [L002]


title: DAP_ngn2-tcf3e12_d2_rep2_3037

value: DNMT1-/-; DNMT3a-/-; DNMT3b-/-


title: Neuron CD8 Tcell rep3

description: Library name: 3_Neuron_CD8_Tcell


title: Short day samples at Zeitgeber time 16 h replicate C

description: Library name: ShortDay_ZT16_Rep_C


title: DAP_ngn2-tcf3e12_d2_rep1_3037


title: Ishikawa cells, Foxc1 and Six1 transfected, progesterone-estrodiol-cyclic AMP treated, rep2 [L002]

description: Library name: FOXC1+SIX1-2-PEC [L002]


title: Short day samples at Zeitgeber time 16 h replicate B

description: Library name: ShortDay_ZT16_Rep_B


title: DAP_ngn2-tcf3e12_d1_rep2_3037


title: Short day samples at Zeitgeber time 16 h replicate A

description: Library name: ShortDay_ZT16_Rep_A


title: Neuron CD8 Tcell rep1

description: Library name: 1_Neuron_CD8_Tcell


title: Neuron rep3

description: Library name: 3_Neuron


title: Ishikawa cells, Foxc1 and Six1 transfected, progesterone-estrodiol-cyclic AMP treated, rep1 [L002]

description: Library name: FOXC1+SIX1-1-PEC [L002]


title: DAP_ngn2-tcf3e12_d1_rep1_3037


title: Ishikawa cells, Foxc1 and Six1 transfected, rep2 [L002]

description: Library name: FOXC1+SIX1-2 [L002]


title: Short day samples at Zeitgeber time 12 h replicate C

description: Library name: ShortDay_ZT12_Rep_C


title: Ishikawa cells, Foxc1 and Six1 transfected, rep1 [L002]

description: Library name: FOXC1+SIX1-1 [L002]


title: Short day samples at Zeitgeber time 20 h replicate C

description: Library name: ShortDay_ZT20_Rep_C


title: Short day samples at Zeitgeber time 12 h replicate B

description: Library name: ShortDay_ZT12_Rep_B


title: DAP_ngn2-tcf12_d2_rep1_3037


title: DAP_ngn2-tcf12_d2_rep2_3037


title: Short day samples at Zeitgeber time 12 h replicate A

description: Library name: ShortDay_ZT12_Rep_A


title: Ishikawa cells, empty vector control, progesterone-estrodiol-cyclic AMP treated, rep4 [L002]

description: Library name: EV-4_PEC [L002]

value: empty vector control, Progesterone, estrodiol, cyclic AMP


title: 5xFAD;PU.1-high Cortex microglia rep 2

first: Pinar

last: Ayata

state: New York

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mt Sinai

description:
Library name: Sample 37
FADTV6-FADTV-115_S21_L003

data_processing:
Sequencing reads were quality checked and trimmed using Trim Galore (v0.6.4; a wrapper program implementing Cutadapt v2.9 and FastQC v0.11.9)
Reads were then mapped to the GRCm38 (mm10) mouse genome using the HISAT2 package (v2.2.0).
Quantification of reads was then performed using featureCounts (v2.0.0) against the Ensembl v99 annotation.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw count for each sample

source_name: Cortical microglia

extract_protocol:
Cortices were dissected from animals and frozen. Frozen cortices were lysed and microglial mRNAs were isolated using the TRAP protocol
cDNA was generated using Nugen Ovation V2 kit. Libraries were produced using TruSeq DNA Sample kit.  Multiplexed libraries were directly loaded on NextSeq 500 (Ilumina) with High Output single read sequencing for 75 cycles for RNA seq.

treatment_protocol: Mice were ravaged with Tamoxifen at 4-6 weeks of age

value: Cortical microglia

tag: strain

value: Black 6

value: Female

tag: age

value: 6 month old


title: 5xFAD;PU.1-high Cortex microglia rep 3

description:
Library name: Sample 38
FADTV6-FADTV-84_S22_L003

value: Male


title: Neuron rep2

description: Library name: 2_Neuron

value: dorsal root ganglia (DRG)


title: Neuron CD8 Tcell rep2

description: Library name: 2_Neuron_CD8_Tcell

value: CD8 Tcell


title: DAP_ngn2-ngn2_d1_rep2_3037

value: embryonic stem cells

tag: cell line


title: Ishikawa cells, empty vector control, rep3 [L002]

description: Library name: EV-3 [L002]

value: Ishikawa cells

value: empty vector control


title: Ishikawa cells, empty vector control, rep4 [L002]

description: Library name: EV-4 [L002]


title: DAP_ngn2-tcf12_d1_rep1_3037

tag: cell type


title: Short day samples at Zeitgeber time 08 h replicate B

description: Library name: ShortDay_ZT08_Rep_B


title: DAP_ngn2-tcf12_d1_rep2_3037


title: Ishikawa cells, empty vector control, progesterone-estrodiol-cyclic AMP treated, rep3 [L002]

description: Library name: EV-3_PEC [L002]


title: Neuron rep1

description: Library name: 1_Neuron


title: DAP_ngn2-ngn2_d1_rep1_3037


title: Short day samples at Zeitgeber time 08 h replicate A

description: Library name: ShortDay_ZT08_Rep_A


title: Short day samples at Zeitgeber time 08 h replicate C

description: Library name: ShortDay_ZT08_Rep_C


title: Ishikawa cells, empty vector control, progesterone-estrodiol-cyclic AMP treated, rep2 [L002]

description: Library name: EV-2_PEC [L002]


title: 5xFAD;PU.1-low Cortex microglia rep 4

description:
Library name: Sample 35
FADPu6-FADPu-55_S18_L003


title: Short day samples at Zeitgeber time 04 h replicate B

description: Library name: ShortDay_ZT04_Rep_B


title: DAP_myod-tcf4_d2_rep1_3037


title: Ishikawa cells, empty vector control, progesterone-estrodiol-cyclic AMP treated, rep1 [L002]

description: Library name: EV-1_PEC [L002]


title: DAP_myod-tcf4_d2_rep2_3037


title: 5xFAD;PU.1-low Cortex microglia rep 3

description:
Library name: Sample 34
FADPu6-FADPu-262_S17_L003


title: 5xFAD;PU.1-low Cortex microglia rep 2

description:
Library name: Sample 33
FADPu_80_S10


title: Short day samples at Zeitgeber time 04 h replicate A

description: Library name: ShortDay_ZT04_Rep_A


title: Ishikawa cells, empty vector control, rep2 [L002]

description: Library name: EV-2_L001 [L002]


title: Short day samples at Zeitgeber time 24 h replicate C

description: Library name: ShortDay_ZT24_Rep_C


title: Ishikawa cells, Six1 transfected, progesterone-estrodiol-cyclic AMP treated, rep4 [L001]

description: Library name: SIX1-4_PEC [L001]

value: Six1 transfected, progesterone, estrodiol, cyclic AMP


title: 5xFAD;PU.1-high Cortex microglia rep 1

description:
Library name: Sample 36
FADTV6-FADTV-107_S19_L003


title: DAP_myod-tcf3-e47_d2_rep2_3037

value: mESC


title: DAP_myod-tcf4_d1_rep1_3037


title: Ishikawa cells, empty vector control, rep1 [L002]

description: Library name: EV-1 [L002]


title: Ishikawa cells,Six1 transfected, rep4 [L001]

description: Library name: SIX1-4 [L001]

value: Six1 transfected


title: LP, WT, rep11

city: Seoul

first: Jaechul

last: Lim

address: 1 Gwanak-ro, 1 Gwanak-gu

country: South Korea

institute: Seoul National University

description: Library name: LP11

data_processing:
Sequencing reads were aligned to the mouse transcriptome (GRCm38 ensembl v101; cDNA and ncRNA) and quantified by Kallisto (v0.45.0) with a k-mer index 25 and 60 bootstrapping. The expression of transcript was calculated in TPM (transcripts per million). The expression of the gene was calculated by aggregating the TPM of all matched transcripts. Statistical analyses for differentially expressed genes were performed by tximport and DESeq2.
Assembly: mm10 (GRCm38)
Supplementary files format and content: a tab-delimited file including transcript identifiers, length, expected count, and TPM

source_name: Small Intestine, lamina propria fraction

growth_protocol: BALB/cJ female mice were sensitized subcutaenously on d0 and d7 with 5ug endograde OVA + 1mg aluminum hydroxide in 200ul PBS, following anesthetization with ketamine/xylazine IP.  Mice were challenged intragastrically with 20mg of OVA (Sigma grade III) in 200ul water on d14.  MCs were sorted 24 hr later on the FACS Aria.

extract_protocol:
RNA was extracted from sorted mast cells using RNeasy Plus Micro Kit (Qiagen).
Library construction was performed using SMART-seq2 protocol.

treatment_protocol: Single-cell suspensions of small intestinal epithelium and lamina propria were prepared as described . Briefly, the small intestine was isolated and opened longitudinally. Its contents were then rinsed in PBS following removal of Peyer’s patches. The tissue was then cut into 2-3 cm segments and incubated in RPMI media (ThermoFisher) containing 5 mM EDTA, 0.145 mg/mL DTT, and 3% FBS at 37°C with 5% CO2 for 20 min with agitation. Pieces of intestine were washed in RPMI containing 2 mM EDTA to separate the epithelial fraction. Lamina propria digestion was performed using 0.1 mg/mL Liberase TL (Roche #540102001) and 0.5 mg/mL DNAse (DN25, Sigma-Aldrich) in RPMI for 30 min at 37°C with 5% CO2. Digested tissue was sequentially strained through 70 mM and 40 mM strainers and washed in RPMI containing 3% FBS. The epithelial fraction was also subjected to a 30% Percoll density gradient by centrifugation (GE17-0891-01, Sigma Aldrich) in preparation for sorting.  Cells were then stained for flow cytometric analysis. Mast cells from each fraction were then sorted into RLT buffer with 1%BME.  Stain:  Fc block, EMA (live/dead), FceRI-PE, CD11b-APC, CD19-APC/efluor780, CD45-efluor450, CD3-Alexa700, CD117-PE/Cy7.  MCs were gated as live, CD45+ CD19- CD11b- CD3- CD117+ FceRI+

value: female

value: Primary cells

value: Sorted Mast Cells

value: WT

value: BALB/cJ

value: OVA


title: Short day samples at Zeitgeber time 24 h replicate A

description: Library name: ShortDay_ZT24_Rep_A

value: Whole seedlings

value: Columbia 0

value: Short day


title: Short day samples at Zeitgeber time 04 h replicate C

description: Library name: ShortDay_ZT04_Rep_C


title: Equinox day samples at Zeitgeber time 20 h replicate C

description: Library name: EquinoxDay_ZT20_Rep_C

value: Equinox day


title: Short day samples at Zeitgeber time 24 h replicate B

description: Library name: ShortDay_ZT24_Rep_B


title: LP, WT, rep9

description: Library name: LP9

value: Small Intestine, lamina propria fraction

value: PBS


title: DAP_myod-tcf3-e47_d2_rep1_3037

value: embryonic stem cells

value: DNMT1-/-; DNMT3a-/-; DNMT3b-/-


title: LP, WT, rep10

description: Library name: LP10


title: LP, WT, rep8

description: Library name: LP8


title: Equinox day samples at Zeitgeber time 20 h replicate B

description: Library name: EquinoxDay_ZT20_Rep_B


title: DAP_myod-tcf3-e47_d1_rep2_3037


title: Ishikawa cells, Six1 transfected, rep3 [L001]

description: Library name: SIX1-3 [L001]

value: Ishikawa cells


title: DAP_myod-tcf3-e47_d1_rep1_3037

value: mESC


title: 5xFAD;PU.1-low Cortex microglia rep 1

description:
Library name: Sample 32
FADPu_55_S6

value: Cortical microglia

value: Black 6

value: Male

value: 6 month old


title: LP, WT, rep7

description: Library name: LP7

value: female

value: Primary cells

value: Sorted Mast Cells

value: WT


title: DAP_myod-tcf4_d1_rep2_3037


title: DAP_myod-tcf3-e12_d2_rep1_3037


title: LP, Het, rep6

description: Library name: LP6

value: IgE Het

value: BALB/cJ

value: OVA


title: Ishikawa cells, Six1 transfected, progesterone-estrodiol-cyclic AMP treated, rep2 [L001]

description: Library name: SIX1-2_PEC [L001]

value: Six1 transfected, progesterone, estrodiol, cyclic AMP


title: DAP_myod-tcf3-e12_d2_rep2_3037


title: Equinox day samples at Zeitgeber time 16 h replicate C

description: Library name: EquinoxDay_ZT16_Rep_C

value: Whole seedlings

value: Columbia 0

value: Equinox day


title: Ishikawa cells, Six1 transfected, rep2 [L001]

description: Library name: SIX1-2 [L001]

value: Ishikawa cells

value: Six1 transfected


title: LP, Het, rep5

description: Library name: LP5

value: Small Intestine, lamina propria fraction

value: PBS


title: Ishikawa cells, Six1 transfected, rep1 [L001]

description: Library name: SIX1-1 [L001]


title: Ishikawa cells, Six1 transfected, progesterone-estrodiol-cyclic AMP treated, rep1 [L001]

description: Library name: SIX1-1_PEC [L001]


title: LP, WT, rep4

description: Library name: LP4


title: DAP_myod-tcf3-e12_d1_rep2_3037

value: embryonic stem cells

value: mESC

value: DNMT1-/-; DNMT3a-/-; DNMT3b-/-


title: Ishikawa cells, Six1 transfected, progesterone-estrodiol-cyclic AMP treated, rep3 [L001]

description: Library name: SIX1-3_PEC [L001]


title: LP, WT, rep3

description: Library name: LP3

value: female

value: Primary cells


title: Equinox day samples at Zeitgeber time 16 h replicate A

description: Library name: EquinoxDay_ZT16_Rep_A


title: DAP_myod-tcf3-e12_d1_rep1_3037


title: Ishikawa cells, Foxc1 transfected, rep4 [L001]

description: Library name: FOXC1-4 [L001]

value: Foxc1 transfected


title: Equinox day samples at Zeitgeber time 12 h replicate C

description: Library name: EquinoxDay_ZT12_Rep_C


title: DAP_myod-tcf12_d2_rep1_3037


title: Ishikawa cells, Foxc1 transfected, progesterone-estrodiol-cyclic AMP treated, rep4 [L001]

description: Library name: FOXC1-4-PEC [L001]

value: Foxc1 transfected, progesterone, estrodiol, cyclic AMP


title: Equinox day samples at Zeitgeber time 12 h replicate B

description: Library name: EquinoxDay_ZT12_Rep_B


title: Equinox day samples at Zeitgeber time 20 h replicate A

description: Library name: EquinoxDay_ZT20_Rep_A


title: LP, WT, rep1

description: Library name: LP1

value: Sorted Mast Cells

value: WT

value: BALB/cJ


title: LP, WT, rep2

description: Library name: LP2

value: OVA


title: Equinox day samples at Zeitgeber time 12 h replicate A

description: Library name: EquinoxDay_ZT12_Rep_A

value: Whole seedlings

value: Columbia 0


title: DAP_myod-tcf12_d1_rep2_3037


title: Ishikawa cells, Foxc1 transfected, progesterone-estrodiol-cyclic AMP treated, rep3 [L001]

description: Library name: FOXC1-3-PEC [L001]

value: Ishikawa cells


title: DAP_myod-tcf12_d1_rep1_3037


title: IEL, WT, rep10

description: Library name: IEL10

source_name: Small Intestine, intraepithelial fraction


title: Ishikawa cells, Foxc1 transfected, rep3 [L001]

description: Library name: FOXC1-3 [L001]


title: Ishikawa cells, Foxc1 transfected, progesterone-estrodiol-cyclic AMP treated, rep2 [L001]

description: Library name: FOXC1-2-PEC [L001]


title: Equinox day samples at Zeitgeber time 08 h replicate C

description: Library name: EquinoxDay_ZT08_Rep_C

value: Equinox day


title: DAP_myod-myod_d2_rep2_3037


title: IEL, WT, rep11

description: Library name: IEL11

value: Small Intestine, intraepithelial fraction


title: Ishikawa cells, Foxc1 transfected, rep2 [L001]

description: Library name: FOXC1-2 [L001]


title: IEL, WT, rep9

description: Library name: IEL9

value: PBS


title: DAP_myod-myod_d2_rep1_3037

value: embryonic stem cells


title: Equinox day samples at Zeitgeber time 08 h replicate A

description: Library name: EquinoxDay_ZT08_Rep_A


title: Ishikawa cells, Foxc1 transfected, progesterone-estrodiol-cyclic AMP treated, rep1 [L001]

description: Library name: FOXC1-1-PEC [L001]


title: Ishikawa cells, Foxc1 transfected, rep1 [L001]

description: Library name: FOXC1-1 [L001]


title: DAP_myod-myod_d1_rep1_3037

value: mESC


title: DAP_myod-myod_d1_rep2_3037

value: DNMT1-/-; DNMT3a-/-; DNMT3b-/-


title: Equinox day samples at Zeitgeber time 04 h replicate C

description: Library name: EquinoxDay_ZT04_Rep_C


title: IEL, WT, rep7

description: Library name: IEL7

value: female


title: Equinox day samples at Zeitgeber time 04 h replicate B

description: Library name: EquinoxDay_ZT04_Rep_B


title: Ishikawa cells, Foxc1 and Six1 transfected, rep4 [L001]

description: Library name: FOXC1+SIX1-4 [L001]

value: Foxc1 and Six1 transfected


title: Ishikawa cells, Foxc1 and Six1 transfected, progesterone-estrodiol-cyclic AMP treated, rep4 [L001]

description: Library name: FOXC1+SIX1-4-PEC [L001]

value: Foxc1 and Six1 transfected, Progesterone, estrodiol, cyclic AMP


title: ChIPseq_NGN2mut_6h_ctrl_KD_3404

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for single-read experiments. Illumina RTA 2.4.11 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for paired-read experiments. ChIP-seq samples were aligned to the mm10 assembly of the mouse genome using QuasR (Gaidatzis et al, Bioinformatics 2015), which internally uses Bowtie (Langmead, Genome Biology 2009). Bowtie was run with QuasR default parameters.
Assembly: mm10
Supplementary files format and content: ExportWig function from the QuasR package was employed to generate the wig files with default parameters except scaling=1e6 and setting shift to 80 as the average of all samples after quantifying the estimated fragment length (half).

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were grown for several passages at 37℃ 7% CO2 seeded on plates coated with 0.2% gelatin (Sigma) and maintained in serum/LIF (Dulbecco’s modified Eagle medium (DMEM, Invitrogen), supplemented with 15% fetal calf serum (Invitrogen),L-glutamine (Gibco), nonessential amino acids (Gibco), 0.001% 2-Mercaptoethanol (Sigma) and leukemia inhibitory factor (produced in-house).

extract_protocol:
DNA was purified with AmpureXP beads
Immunoprecipitated DNA was subjected to library preparation (NEBNext Ultra II DNA Library Prep Kit, Illumina).

treatment_protocol: To induce expression with TETON system, cells were washed with PBS and treated with 1 μg/ml doxycycline (Sigma, no. D989) in induction media, also referred as N2B27w/oVitA, (DMEM/F12/Glutamax (LifeTech, no. 31331-028), 1× B27 without vitamin A (LifeTech, no. 12587-010), 1× N2 supplement (LifeTech, no. 17502-048), ) or in serum/LIF media as indicated.

value: 6 hours N2B27(w/oVitA)+dox

value: Streptavidin (Thermo Fisher, 11205D)


title: Equinox day samples at Zeitgeber time 04 h replicate A

description: Library name: EquinoxDay_ZT04_Rep_A


title: ChIPseq_NGN2_6h_TCF12_KD_3404


title: IEL, Het, rep6

description: Library name: IEL6

value: Primary cells

value: Sorted Mast Cells

value: IgE Het


title: IEL, Het, rep5

description: Library name: IEL5

value: BALB/cJ


title: Ishikawa cells, Foxc1 and Six1 transfected, progesterone-estrodiol-cyclic AMP treated, rep3 [L001]

description: Library name: FOXC1+SIX1-3-PEC [L001]


title: Equinox day samples at Zeitgeber time 24 h replicate B

description: Library name: EquinoxDay_ZT24_Rep_B

value: Whole seedlings

value: Columbia 0


title: IEL, WT, rep3

description: Library name: IEL3

value: WT


title: ChIPseq_NGN2_6h_TCF3_KD_3404


title: IEL, WT, rep8

description: Library name: IEL8

value: Small Intestine, intraepithelial fraction

value: OVA


title: Ishikawa cells, Foxc1 and Six1 transfected, rep3 [L001]

description: Library name: FOXC1+SIX1-3 [L001]

value: Ishikawa cells


title: IEL, WT, rep4

description: Library name: IEL4


title: ChIPseq_NGN2_6h_TCF4_KD_3404

value: embryonic stem cells

value: mESC


title: IEL, WT, rep2

description: Library name: IEL2

value: female


title: Long day samples at Zeitgeber time 20 h replicate C

description: Library name: LongDay_ZT20_Rep_C

value: Long day


title: Equinox day samples at Zeitgeber time 24 h replicate A

description: Library name: EquinoxDay_ZT24_Rep_A

value: Equinox day


title: ChIPseq_NGN2_6h_ctrl_KD_3404

value: 6 hours N2B27(w/oVitA)+dox


title: Ishikawa cells, Foxc1 and Six1 transfected, progesterone-estrodiol-cyclic AMP treated, rep2 [L001]

description: Library name: FOXC1+SIX1-2-PEC [L001]

value: Foxc1 and Six1 transfected, Progesterone, estrodiol, cyclic AMP


title: Long day samples at Zeitgeber time 20 h replicate B

description: Library name: LongDay_ZT20_Rep_B


title: Control P5 barrel cortex 10

description:
counttab_2.txt
21R_UB

source_name: Barrel cortex female

extract_protocol:
The brain tissue was thawed in an ice-cold  glass homogenizer containing 1 mL cell-lysis buffer. After manually homogenizing the samples with 3-5 gentle strokes, samples were  homogenized in a motor-driven overhead stirrer. A post-nuclear supernatant was prepared by centrifugation. Post-mitochondrial supernatant was prepared by centrifugation after NP40 and DHPC treatment. GFP-antibod-coated beads were added to each supernatant. After overnight incubation, the polysome-bound beads were washed with the high-salt buffer. RNA clean-up was performed using RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.
RNA integrity was assayed using an RNA Pico chip on a Bioanalyzer 2100 (Agilent, Santa Clara, CA), and only samples with RIN>9 were considered for subsequent analysis. Double-stranded cDNA was generated from 1-5 ng of RNA using the Nugen Ovation V2 kit (NuGEN, San Carlos, CA) following the manufacturer’s instructions. Libraries for sequencing were prepared using Nextera XT kit (Illumina, San Diego, CA, USA) following the manufacturer’s instructions. The quality of the libraries was assessed by 2200 TapeStation (Agilent).

treatment_protocol: To activate Tamoxifen-inducible Cre (CreErt2), Cx3cr1CreER/+ (Litt); Eef1a1LSL.eGFPL10a/+ mice were orally administered 50 µg tamoxifen (T5648, Sigma, St. Louis, MO) dissolved 10 mg/mL in corn oil (C8267, Sigma) once daily at ages P1, P2, and P3. Aldh1l1EGFP-L10a/+ mice were not injected with tamoxifen. Unilateral whisker lesioning was performed at P4. Mice were euthanized at P5 with CO2, and the barrel cortex region was dissected and flash-frozen for TRAP.

value: Barrel cortex

value: whole tissue

value: Mice were treated with Tamoxifen at P1-3, whiskers on the right side were cauterized at P4.


title: Ishikawa cells, Foxc1 and Six1 transfected, rep2 [L001]

description: Library name: FOXC1+SIX1-2 [L001]

value: Foxc1 and Six1 transfected


title: PU.1-low Cortex microglia rep 6

extract_protocol:
Cortices were dissected from animals and frozen. Frozen cortices were lysed and microglial mRNAs were isolated using the TRAP protocol
cDNA was generated using Nugen Ovation V2 kit. Libraries were produced using TruSeq DNA Sample kit.
Multiplexed libraries were directly loaded on NextSeq 500 (Ilumina) with High Output single read sequencing for 75 cycles for RNA seq.

value: Cortical microglia

value: Black 6

value: Female

value: 6 month old


title: Equinox day samples at Zeitgeber time 24 h replicate C

description: Library name: EquinoxDay_ZT24_Rep_C

value: Whole seedlings

value: Columbia 0


title: Long day samples at Zeitgeber time 20 h replicate A

description: Library name: LongDay_ZT20_Rep_A


title: PU.1-low Cortex microglia rep 5

value: Male


title: Deprived P5 barrel cortex 10

description:
counttab_2.txt
17R_UB


title: Equinox day samples at Zeitgeber time 08 h replicate B

description: Library name: EquinoxDay_ZT08_Rep_B


title: Long day samples at Zeitgeber time 16 h replicate C

description: Library name: LongDay_ZT16_Rep_C


title: Ishikawa cells, empty vector control, rep4 [L001]

description: Library name: EV-4 [L001]

value: Ishikawa cells

value: empty vector control


title: Long day samples at Zeitgeber time 16 h replicate A

description: Library name: LongDay_ZT16_Rep_A

value: Long day


title: Long day samples at Zeitgeber time 16 h replicate B

description: Library name: LongDay_ZT16_Rep_B


title: 5xFAD Cortex microglia rep 6


title: Ishikawa cells, empty vector control, progesterone-estrodiol-cyclic AMP treated, rep4 [L001]

description: Library name: EV-4_PEC [L001]

value: empty vector control, Progesterone, estrodiol, cyclic AMP


title: Ishikawa cells, empty vector control, progesterone-estrodiol-cyclic AMP treated, rep3 [L001]

description: Library name: EV-3_PEC [L001]


title: IEL, WT, rep1

description: Library name: IEL1

value: Small Intestine, intraepithelial fraction

value: female

value: Primary cells

value: Sorted Mast Cells

value: WT

value: BALB/cJ

value: PBS


title: Ishikawa cells, empty vector control, rep3 [L001]

description: Library name: EV-3 [L001]


title: Ishikawa cells, Foxc1 and Six1 transfected, progesterone-estrodiol-cyclic AMP treated, rep1 [L001]

description: Library name: FOXC1+SIX1-1-PEC [L001]

value: Foxc1 and Six1 transfected, Progesterone, estrodiol, cyclic AMP


title: 5xFAD Cortex microglia rep 5

value: Cortical microglia

value: Black 6

value: Female


title: Deprived P5 barrel cortex 8

description:
counttab_2.txt
15L_UB

source_name: Barrel cortex male

value: Barrel cortex

value: male

value: whole tissue

value: Mice were treated with Tamoxifen at P1-3, whiskers on the right side were cauterized at P4.


title: Long day samples at Zeitgeber time 12 h replicate C

description: Library name: LongDay_ZT12_Rep_C

value: Whole seedlings

value: Columbia 0

value: Long day


title: Control Cortex microglia rep 6

value: Male

value: 6 month old


title: 5xFAD Cortex microglia rep 4


title: Control P5 barrel cortex 9

description:
counttab_2.txt
21L_UB

value: female


title: Control P5 barrel cortex 7

description:
counttab_2.txt
14R_UB


title: Ishikawa cells, empty vector control, progesterone-estrodiol-cyclic AMP treated, rep2 [L001]

description: Library name: EV-2_PEC [L001]

value: Ishikawa cells

value: empty vector control, Progesterone, estrodiol, cyclic AMP


title: Long day samples at Zeitgeber time 12 h replicate A

description: Library name: LongDay_ZT12_Rep_A


title: Ishikawa cells, Foxc1 and Six1 transfected, rep1 [L001]

description: Library name: FOXC1+SIX1-1 [L001]

value: Foxc1 and Six1 transfected


title: Deprived P5 barrel cortex 7

description:
counttab_2.txt
14L_UB


title: Ishikawa cells, empty vector control, rep2 [L001]

description: Library name: EV-2_L001 [L001]

value: empty vector control


title: PU.1-low Cortex microglia rep 4

value: Cortical microglia


title: Deprived P5 barrel cortex 9

description:
counttab_2.txt
17L_UB


title: Long day samples at Zeitgeber time 08 h replicate C

description: Library name: LongDay_ZT08_Rep_C


title: Control P5 barrel cortex microglia 4

description:
counttab_2.txt
21R

value: Microglia


title: Control P5 barrel cortex 8

description:
counttab_2.txt
15R_UB


title: Long day samples at Zeitgeber time 08 h replicate B

description: Library name: LongDay_ZT08_Rep_B


title: Control Cortex microglia rep 4

value: Black 6


title: Ishikawa cells, empty vector control, rep1 [L001]

description: Library name: EV-1 [L001]


title: Control P5 barrel cortex microglia 3

description:
counttab_2.txt
21L

value: Barrel cortex


title: Long day samples at Zeitgeber time 12 h replicate B

description: Library name: LongDay_ZT12_Rep_B


title: Long day samples at Zeitgeber time 08 h replicate A

description: Library name: LongDay_ZT08_Rep_A


title: Renal carcinoma tissue, Shaking Dissociation,3

city: Tianjin

first: Yang

last: Bai

address: Tianjin

institute: Tianjin University

description:
Library name: D
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using Cell Ranger (v6.1.2) with default parameters. Reads were aligned to the human genome (GRCh38) and unique molecular identifiers (UMIs) were counted to generate feature-barcode matrices.
Filtering and normalization of gene expression matrices were performed using Seurat (v4.0.5). Cells with fewer than 200 expressed genes or high mitochondrial content were removed.
Dimensionality reduction, clustering, and differential expression analysis were conducted using Seurat with PCA, UMAP, and FindMarkers functions.
Differential gene expression analysis was performed using edgeR (v3.36.0) for comparisons between the S and D groups.
Assembly: Human genome reference: GRCh38
Supplementary files format and content: Processed gene expression matrices in CSV format. Metadata annotations in TXT format.

source_name: Renal carcinoma

growth_protocol: Not applicable (human patient samples were used).

extract_protocol:
Single-cell suspensions were obtained according to the 10X Genomics Cell Preparation Guide. Cells were washed, counted, and loaded into 10X Chromium microfluidic chips.
Single-cell RNA libraries were prepared using the 10X Genomics Chromium Single Cell 3’ v3 kit. Reverse transcription and cDNA amplification followed the manufacturer’s protocol.

treatment_protocol: Samples were dissociated using either acoustic streaming-based dissociation (S group) or enzymatic digestion with a shaker (D group).

value: Renal carcinoma

value: Mixed tumor microenvironment

value: Enzymatic dissociation (shaker-based)


title: Long day samples at Zeitgeber time 04 h replicate C

description: Library name: LongDay_ZT04_Rep_C

value: Whole seedlings


title: 5xFAD+CSF1Ri Cortex microglia rep 2

value: Female

tag: diet

value: 4-6 weeks on CSF1Ri diet (1200 ppm)

value: Cx3cr1CreErt2/+(Litt);5xFAD;Eef1a1LSL.eGFPL10a/+ mice fed CSF1Ri diet for 4-6 weeks


title: Control Cortex microglia rep 5

value: 6 month old


title: iCas9 KPL-1 cells, sgSETD1A, RNAP2_rep2

description: Library name: iCas9_KPL-1_sgSETD1A_Dox_day7_RNAP2_rep2

extract_protocol:
Cells were fixed with 2 mM DSG for 30 min, followed by 1% formaldehyde for 10 min, and treated with 0.125 M glycine for 5 min. The fixed cells were washed twice with cold PBS. Washed cells were resuspended in ChIP lysis buffer and centrifuged at 3200 rpm for 5 min at 4ºC to collect the nuclei pellet. The pellet was washed with ChIP wash buffer and resuspended in ChIP Shearing Buffer, and then frozen at -80ºC. Nuclear samples were shredded using a Picoruptor (Diagenode) and pre-cleared using Dynabeads protein G (Thermo Fisher Scientific) for 60 min at 4ºC with gentle rotation. Appropriate amounts of antibodies were added to chromatin and incubated overnight at 4ºC.
ChIP-seq libraries were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems).

value: breast cancer cell line

value: SETD1A knockout


title: 5xFAD+CSF1Ri Cortex microglia rep 1


title: Deprived P5 barrel cortex microglia 2

description:
counttab_2.txt
15L

value: male

value: Mice were treated with Tamoxifen at P1-3, whiskers on the right side were cauterized at P4.


title: Ishikawa cells, empty vector control, progesterone-estrodiol-cyclic AMP treated, rep1 [L001]

description: Library name: EV-1_PEC [L001]

value: Ishikawa cells

value: empty vector control, Progesterone, estrodiol, cyclic AMP


title: iCas9 KPL-1 cells, sgEmpty, RNAP2_rep2

description: Library name: iCas9_KPL-1_sgEmpty_Dox_day7_RNAP2_rep2

value: WT


title: Control P5 barrel cortex microglia 1

description:
counttab_2.txt
14R

value: female

value: Microglia


title: PU.1-high Cortex microglia rep 4

value: Cortical microglia

value: Black 6

value: Male


title: iCas9 KPL-1 cells, sgSETD1A, SETD1A

description: Library name: iCas9_KPL-1_sgSETD1A_Dox_day7_SETD1A


title: Deprived P5 barrel cortex microglia 4

description:
counttab_2.txt
17R

value: Barrel cortex


title: Long day samples at Zeitgeber time 24 h replicate C

description: Library name: LongDay_ZT24_Rep_C

value: Whole seedlings

value: Columbia 0

value: Long day


title: 5xFAD+CSF1Ri Cortex microglia rep 4

value: 6 month old

value: 4-6 weeks on CSF1Ri diet (1200 ppm)

value: Cx3cr1CreErt2/+(Litt);5xFAD;Eef1a1LSL.eGFPL10a/+ mice fed CSF1Ri diet for 4-6 weeks


title: iCas9 KPL-1 cells, sgEmpty, SETD1A

description: Library name: iCas9_KPL-1_sgEmpty_Dox_day7_SETD1A

value: breast cancer cell line


title: Deprived P5 barrel cortex microglia 1

description:
counttab_2.txt
14L

value: Mice were treated with Tamoxifen at P1-3, whiskers on the right side were cauterized at P4.


title: 5xFAD+CSF1Ri Cortex microglia rep 3


title: Deprived P5 barrel cortex microglia 3

description:
counttab_2.txt
17L


title: Long day samples at Zeitgeber time 24 h replicate B

description: Library name: LongDay_ZT24_Rep_B


title: Renal carcinoma tissue, Acoustic Streaming Dissociation,3

description:
Library name: S
10x Genomics

value: Renal carcinoma

value: Mixed tumor microenvironment

value: Acoustic streaming dissociation


title: Control P5 barrel cortex microglia 2

description:
counttab_2.txt
15R

value: male


title: Long day samples at Zeitgeber time 24 h replicate A

description: Library name: LongDay_ZT24_Rep_A


title: Deprived P5 barrel cortex 5

description:
counttab_1.txt
Dori-AC22

value: whole tissue

value: Whiskers on the right side were cauterized at P4.


title: PU.1-high Cortex microglia rep 1

value: Cortical microglia

value: Black 6

value: Female


title: Long day samples at Zeitgeber time 04 h replicate B

description: Library name: LongDay_ZT04_Rep_B

value: Whole seedlings


title: MCF7, scramble RNA, ERalpha, ChIP

extract_protocol:
Cells were fixed using 1% formaldehyde for 10 mins at room temperature on an orbital shaker. After 10mins, formaldehyde was quenched using 0.125M glycine for 5mins at room temperature on the orbital shaker. The cells were washed with cold 1XPBS and scraped. The cells were pelleted down at 3000rpm for 5mins at 4°C. The pellets were stored at -80°C. 10 million cells were resuspended in 1 ml of nuclear lysis buffer (NLB) (50mM Tris-HCl pH 7.4, 1% SDS, 10mM EDTA pH 8.0, and 1X PIC) and incubated in ice for 10mins. After nuclear lysis, cells were sonicated using Bioruptor pico for 28cycles with 30secs ON and 30secs OFF settings. The lysate was then spun at 12000rpm for 12mins at 4°C to clear off the cell debris. 100μg of chromatin was used for IP, further 3μg of sonicated S2 chromatin was added as spike-in for only H3K27ac ChIP. The IP was diluted 2.5 times with dilution buffer (20mM Tris-HCl pH 7.4, 100mM NaCl, 2mM EDTA pH 8.0, 0.5% Triton X-10, and 1X PIC). IP was set in a volume of 500μl. Additionally, 50μl was taken out and labelled as 10% input. For IP, main as well spike-in antibody was added in their respective amounts (ERα (sc-8002, Santa Cruz Biotech) 1μg, anti-PolII (Diagenode C15200004) 2μg, H3K27ac (ab4729, Abcam) 1μg and spike-in H2av 0.3ug (61686, Active Motif)). IP was incubated with antibodies overnight at 4°C at constant rotation of 12rpm. After incubation, 15μl of Protein G beads pre-blocked in BSA were added to the mix. It was incubated for 4 hours at 4°C on the rotor. After incubation, the beads were washed with wash buffers I, II, III and 1XTE sequentially (Li et al., 2013). The DNA-protein complexes were eluted from the beads by resuspending the beads in (100mM NaHCO3, 1%SDS, 2μg of RNaseA) at 37°C in a thermomixer with 1400rpm for 30mins. The crosslinked DNA-protein complexes were reverse-crosslinked over night at 65°C by the addition of NaCl. After that 2μl of Proteinase K (20mg/ml) was added to the mix and incubated for 2hours at 45°C. The ChIP DNA was then purified using PCI (Phenol:Chloroform:Isoamylalcohol) and ethanol precipitation. The pellet was resuspended in 10μl of NFW.
library preparation was done using NEBNext Ultra II DNA library Prep kit with Sample Purification Beads (E7103L).

value: Breast, mammary gland

value: epithelial cell

tag: chip antibody

value: Estrogen Receptor alpha Antibody (F-10), sc-8002, scbt

value: exosc3 knockdown, 17beta-estradiol (1hr)


title: Long day samples at Zeitgeber time 04 h replicate A

description: Library name: LongDay_ZT04_Rep_A

value: Columbia 0

value: Long day


title: PU.1-low Cortex microglia rep 3

value: 6 month old


title: Control P5 barrel cortex 5

description:
counttab_1.txt
Dori-AC21

value: Barrel cortex


title: HFD-ARM2

city: Changsha

first: Hu

last: Wanyu

address: 长沙市芙蓉区人民中路139号

institute: 中南大学湘雅二医院

description: HFD gene_expression.xls

data_processing:
Total RNAs of ARMs and NARMs were isolated and followed by RNA-seq analysis in the company (The Beijing Genomics Institute, Shenzhen, China) using the Illumina high-throughput sequencing platforms. The differential expression of genes was selected by Log2FC > 0.6 or Log2FC < -0.6 and P < 0.05.
Assembly: mm10
Supplementary files format and content: FPKM, TPM, read count

source_name: ewat

extract_protocol:
Trizol was used to extract RNA from cells, 200 ng RNA was used for sequencing.
Total RNA of ARM/SM that were purified via FACS sorting was extracted by Trizol (Life Technologies, Cat#15596026) according to the manufacturer’s protocol.

value: ewat

value: WT

value: HFD diet


title: PU.1-high Cortex microglia rep 3


title: MCF7, exosc3 knockdown, ERalpha, ChIP

source_name: Breast, mammary gland

value: scr knockdown, 17beta-estradiol (1hr)


title: Deprived P5 barrel cortex 4

description:
counttab_1.txt
Dori-AC20

value: female

value: whole tissue

value: Whiskers on the right side were cauterized at P4.


title: Control P5 barrel cortex 4

description:
counttab_1.txt
Dori-AC19


title: HFD-NARM2

address: 长沙市芙蓉区人民中路139号

description: HFD gene_expression.xls


title: PU.1-high Cortex microglia rep 2

value: Cortical microglia

value: Black 6

value: Female


title: PU.1-low Cortex microglia rep 2


title: PU.1-low Cortex microglia rep 1

value: Male


title: HFD-ARM1

address: 长沙市芙蓉区人民中路139号

description: HFD gene_expression.xls


title: Deprived P5 barrel cortex 3

description:
counttab_1.txt
Dori-AC18


title: Control P5 barrel cortex 3

description:
counttab_1.txt
Dori-AC17


title: 5xFAD Cortex microglia rep 3


title: HFD-NARM1

address: 长沙市芙蓉区人民中路139号

description: HFD gene_expression.xls