title: HeLa_NicE-C_rep2

description:
HeLa_NicE-C.hic
HeLa_NicE-C.bw

value: AACCGGATCCGGTT


title: Patient 1 CMV-tet+ CD8+ T and NK cells day 60 transcriptome

status: Public on Jan 18 2022

type: SRA

city: Seattle

first: Martin

last: Prlic

state: WA

address: 1100 Fairview Ave, Mail stop E5-110

country: USA

institute: Fred Hutch

description: 3' Transcriptome

library_source: transcriptomic

data_processing:
Samples were processed using CellRanger pipline version 2.1.1 or 3.0.2
FASTQ files were processed with CellRanger software v2.1.1 or v3.0.2 and corresponding sample sheet
Genome_build: GRCh38
Supplementary_files_format_and_content: comma separated values with abundance measurements for each target.

molecule: total RNA

organism: Homo sapiens

source_name: PBMCs

extract_protocol:
RNA was extracted using 10x genomics protocols
RNA was extracted using 10x genomics protocols

treatment_protocol: 10^6 PBMCs  cells were stimulated for 18 hours at 37C with either DMSO control, pp65 peptide pool, or IE-1 peptide pool

tag: phenotype

tag: donors

value: Patient 1

tag: time point


title: HeLa_RNA_seq_rep1

city: HeFei

first: Zhengyu

last: Luo

state: AnHui

address: Huangshan street

country: China

institute: USTC

data_processing:
For HiC and NicE-C, raw HiC data were processed through the HiC-Pro (2.10.0) pipeline (PMID: 26619908). *.hic files were generated using HiC-Pro (2.10.0) script: hicpro2juicebox.sh.
For RNA-seq, reads were aligned to the hg19 or mm9 genome assembly using hisat2 version 2.1.0. Data were sorted using Samtools v1.7. BedGraph files were generated using  homer version 4.9. Counts were getting using featureCounts v1.5.0-p1.
For NicE-seq and NicE-C, reads were aligned to the hg19 or mm9 genome assembly using Bowtie2 version 2.2.5 with the following configurations: -3 120. Data were filtered using the following specifications: Samtools v1.7 was used to remove duplicate reads and chromosome M. Peaks were called using Macs2 version 2.1.0. BedGraph files were generated using  homer version 4.9.
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: bigwig files were generated using  bedGraphToBigWig
Supplementary_files_format_and_content: hic files contain the HiC contact matrix at different resolution

source_name: HeLa cells

growth_protocol: HeLa cells, HeLa-S3 cells and IMR90 cells were grown in DMEM medium containing 10% fetal bovine serum (FBS) at 37°C and 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. Cells were croseelinked with 1% formaldehyde for 10 minutes at room temperature. For Hi-C, we followed in-situ Hi-C protocol, the cells were lysed. Then the lysed cells were digested by MboI overnight at 37℃. DNA fragment ends were filled and labeled with dCTP, dGTP, dTTP and biotin-dATP. Proximity ligation was performed at room temperature for 4 hours. Then the DNA were de-crosslinked at 65°C overnight with Proteinase K and DNA were purified. For NicE-seq, the cells were lysed and then digested by Nt.CviPII and DNA polemerase I (Ecoli)  with dGTP, dTTP, biotin-dATP, biotin-dCTP and 5-methyl-dCTP for 20 min at 37℃. Then the DNA were de-crosslinked at 65°C overnight with Proteinase K and DNA were purified. For NicE-C,  the cells were lysed and then digested by Nt.CviPII and DNA polemerase I (Ecoli)  with dGTP, dTTP, dATP and 5-methyl-dCTP for 20 min at 37℃. DNA fragment ends were filled with dNTP and dA-tailing was performed. Proximity ligation by bridge-linker was performed at room temperature for 4 hours. Then the DNA were de-crosslinked at 65°C overnight with Proteinase K and DNA were purified.
Hi-C, NicE-C and NicE-seq DNA were sonicated and binding to M280 beads, then end-repair, dA-tailing and adapter ligation on beads. After PCR amplification and DNA purification, the libraries were sequenced on Illumina NovaSeq 6000 using 150bp paired-end reads. RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cultured HeLa-S3 cells were washed once with 1X PBS, then add fresh DMEM medium supplemented with final 10 ng/ml TNFα or water.

tag: cell line

value: HeLa


title: 125d Heart Mutant rep3

city: New York

first: Nicole

last: Sayles

address: 407 East 61st Street

institute: Weill Cornell

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw sequence reads were processed using the BBDuk program in the BBMap package
Trimmed readsd were aligned to the mouse genome assembly GRCm38.p6 using the STAR aligner (version2.5.0a).
SAM files were converted to BAM to read overlapping reads per gene using HTseq-count (version 0.6.1)
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: raw counts

organism: Mus musculus

source_name: Heart

extract_protocol:
Hearts were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent and Qiagen RNeasy Mini Kit (Cat# 74104). The Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: Heart

tag: age

value: post natal day 125

tag: genotype


title: HeLa_NicE-C_rep1

description:
HeLa_NicE-C.hic
HeLa_NicE-C.bw

library_source: genomic

molecule: genomic DNA

tag: sequence of bridge linker


title: 125d Heart Mutant rep2


title: Patient 1 CMV-tet+ CD8+ T and NK cells day 30 transcriptome

description: 3' Transcriptome


title: MS-22-CD19 RNA-Seq

city: San Francisco

first: Qin

last: Ma

state: CA

address: 675 Nelson Rising Ln

institute: University of California, San Francisco

data_processing:
The low quality reads were filtered by Trimmomatic, the sequencing reads were then aligned to the human reference (hg38) using hisat2.
The htseq-count tool and human gtf file from Ensembl were used to count aligned reads for each gene.
The raw counts were then normalized to counts per million (CPM) using cpm function in edgeR package.
Genome_build: hg38
Supplementary_files_format_and_content: The normalized CPM values for each sample.

source_name: peripheral blood

extract_protocol:
Total RNA was extracted using Quick-RNA Microprep Kit (Zymo Research).
The poly(A) selected paired-end sequencing libraries were constructed using the mRNA Hyper Prep Kit (KAPA), following the manufacturer’s instructions.

tag: disease status

value: Multiple sclerosis

value: peripheral blood

tag: cell type

value: CD19+ B cells


title: HeLa_Hi-C_rep2


title: HeLa_Hi-C_rep1


title: 125d Heart Mutant rep1


title: HC-10-CD14 BS-Seq

data_processing:
The low quality reads were filtered by Trimmomatic, then the reads were uniquely mapped to the reference genome (hg38, UCSC) using the Bismark software. The bisulfite conversion rates were calculated using the lambda DNA.
Genome_build: hg38
Supplementary_files_format_and_content: Methylation level for each CpG covered by a minimum of 3 reads. We counted the number of 'C' bases from sequencing reads as  methylated (denoted as NC) and the number of 'T' bases as unmodified (denoted as NT). The methylation level was estimated as NC/(NC + NT) in each CpG site. For each CpG there are four columns of data including chromosome name, location of the left CpG sits, location of the right CpG site, methylation level.

extract_protocol:
Genomic DNA from FACS isolated cells was extracted using Zymo Research Quick DNA kit.
Genomic DNA was fragmented, end-repaired, A-tailed, and ligated to methylated adaptors. Ligated fragments were then processed for bisulfite conversion using the EZ DNA Methylation Gold kit (Zymo Research) and amplified using the KAPA HiFi HotStart Uracil+ ReadyMix PCR Kit.

value: Healthy control

value: CD14+ monocytes


title: HC-9-CD14 BS-Seq


title: Patient 2 CMV-tet+ CD8+ T and NK cells day 90 transcriptome

description: 3' Transcriptome

value: Patient 2


title: 125d Heart WT rep6

value: wild type


title: Patient 4 CD8+ T cells day 90 transcriptome

description: 5' Transcriptome

value: Patient 4


title: HC-8-CD14 BS-Seq


title: Patient 4 CD8+ T cells day 60 transcriptome

description: 5' Transcriptome


title: Patient 2 CMV-tet+ CD8+ T and NK cells day 60 transcriptome

description: 3' Transcriptome


title: 225d Heart WT rep1

value: post natal day 225


title: HC-7-CD14 BS-Seq


title: Patient 4 CD8+ T cells day 30 transcriptome

description: 5' Transcriptome


title: HC-6-CD14 BS-Seq


title: Patient 3 CD8+ T cells day 90 transcriptome

description: 5' Transcriptome

value: Patient 3


title: 125d Heart WT rep5


title: 125d Heart WT rep4


title: HC-3-CD14 BS-Seq


title: Patient 3 CD8+ T cells day 60 transcriptome

description: 5' Transcriptome


title: HC-1-CD14 BS-Seq


title: HC-2-CD14 BS-Seq


title: 125d Heart WT rep3


title: Patient 3 CD8+ T cells day 30 transcriptome

description: 5' Transcriptome


title: 125d Heart WT rep2


title: Patient 2 CD8+ T cells day 90 transcriptome

description: 5' Transcriptome


title: MS-10-CD14 BS-Seq


title: 75d Heart Mutant rep5

value: post natal day 75


title: MS-9-CD14 BS-Seq


title: MS-7-CD14 BS-Seq


title: 75d Heart Mutant rep4


title: Patient 2 CD8+ T cells day 60 transcriptome

description: 5' Transcriptome


title: 75d Heart Mutant rep3


title: MS-8-CD14 BS-Seq


title: Patient 1 CD8+ T cells day 90 transcriptome

description: 5' Transcriptome


title: MS-4-CD14 BS-Seq


title: Patient 2 CD8+ T cells day 30 transcriptome

description: 5' Transcriptome


title: MS-3-CD14 BS-Seq


title: MS-5-CD14 BS-Seq


title: Patient 1 CD8+ T cells day 60 transcriptome

description: 5' Transcriptome


title: MS-2-CD14 BS-Seq


title: HC-4-CD14 BS-Seq


title: HC-5-CD14 BS-Seq


title: MS-6-CD14 BS-Seq


title: MS-1-CD14 BS-Seq


title: HC-12-CD8 BS-Seq

value: CD8+ T cells


title: 75d Heart Mutant rep1


title: MS-12-CD14 BS-Seq


title: Patient 1 CD8+ T cells day 30 transcriptome

description: 5' Transcriptome


title: HC-10-CD8 BS-Seq


title: 75d Heart WT rep5


title: HC-11-CD8 BS-Seq


title: shYTHDF1-2_m6A_INPUT

city: Toronto

first: Housheng

middle: Hansen

last: He

state: ON

address: 101 College St

country: Canada

institute: UHN

description:
m6A MeRIP-seq
shYTHDF1-2_m6A_peaks.bed

data_processing:
Library strategy: MeRIP-seq
RNA-seq, RIP-seq and m6A MeRIP-seq reads were aligned to the hg38 genome assembly using STAR2 version 2.4.2a.
Raw read were counted by HTSeq version 0.6.1 and m6A peaks were called using MeTpeak.
Genome_build: hg38
Supplementary_files_format_and_content: CSV file is for raw read counts and BED files are for m6A peaks

source_name: HCT116 cells line

growth_protocol: Human CRC cancer cell line HCT116 was maintained in McCoy's 5a medium with 10% fetal bovine serum.

extract_protocol:
For RNA-seq and m6A MeRIP-seq, total RNA from cells in culture was extracted using Trizol reagent, and then treated with DNase I to remove DNA contamination. m6A MeRIP were next performed and the m6A-enriched fragmented RNA was purified using RNeasy Mini Kit as IP. For RIP-seq, HCT116 cells were harvested after 24 h transfection of Flag-tagged YTHDF1 plasmid. The protein was extracted with RIP lysis buffer. YTHDF1-RNA complex was captured by FLAG antibody-immobilized-protein A/G magnetic beads and enriched RNAs were extracted by TRIzol as IP.
For RNA-seq, RNA libraries were constructed with TruSeq Stranded mRNA Library Prep kit. For RIP-seq and m6A MeRIP-seq, RNA libraries were prepared using SMARTer Stranded Total RNA-Seq Kit version 2-Pico Input Mammalian.

treatment_protocol: For RNA-seq and m6A MeRIP-seq, HCT116 cells were transduced with lentivirus shControl and shYTHDF1. For YTHDF1 RIP-seq, HCT116 cells were transfected with FLAG tagged YTHDF1 overexpressing plasmid.

tag: ip antibody

tag: shRNA


title: 125d Heart WT rep1


title: HC-9-CD8 BS-Seq


title: MS-11-CD14 BS-Seq


title: shYTHDF1-2_m6A_IP

description:
m6A MeRIP-seq
shYTHDF1-2_m6A_peaks.bed

value: anti-m6A(ABE572, Millipore)


title: 75d Heart WT rep4


title: HC-7-CD8 BS-Seq


title: HC-8-CD8 BS-Seq


title: shYTHDF1-1_m6A_IP

description:
m6A MeRIP-seq
shYTHDF1-1_m6A_peaks.bed


title: 75d Heart WT rep2


title: 75d Heart WT rep1


title: HC-6-CD8 BS-Seq


title: 75d Heart WT rep3


title: HC-5-CD8 BS-Seq


title: HC-3-CD8 BS-Seq


title: shCtrl_m6A_INPUT

description:
m6A MeRIP-seq
shCtrl_m6A_peaks.bed

value: shCtrl


title: HC-2-CD8 BS-Seq


title: 75d Heart Mutant rep2


title: MS-17-CD8 BS-Seq


title: shYTHDF1-1_m6A_INPUT

description:
m6A MeRIP-seq
shYTHDF1-1_m6A_peaks.bed


title: HC-1-CD8 BS-Seq


title: 30d Heart Mutant rep2

value: post natal day 30


title: MS-12-CD8 BS-Seq


title: MS-16-CD8 BS-Seq


title: HC-4-CD8 BS-Seq


title: MS-15-CD8 BS-Seq


title: 30d Heart Mutant rep1

value: Heart


title: shYTHDF1-2

description:
RNA-seq
htseq_raw_read_counts.csv

data_processing:
RNA-seq, RIP-seq and m6A MeRIP-seq reads were aligned to the hg38 genome assembly using STAR2 version 2.4.2a.
Raw read were counted by HTSeq version 0.6.1 and m6A peaks were called using MeTpeak.
Genome_build: hg38
Supplementary_files_format_and_content: CSV file is for raw read counts and BED files are for m6A peaks


title: shCtrl_m6A_IP

description:
m6A MeRIP-seq
shCtrl_m6A_peaks.bed


title: YTHDF1_RIP_INPUT

description:
RIP-seq
htseq_raw_read_counts.csv


title: 30d Heart Mutant rep3


title: YTHDF1_RIP_IP

description:
RIP-seq
htseq_raw_read_counts.csv

value: anti-FLAG (F1804, MilliporeSigma)


title: MS-13-CD8 BS-Seq

value: Multiple sclerosis


title: 30d Heart WT rep3


title: MS-11-CD8 BS-Seq

value: peripheral blood


title: shYTHDF1-1

description:
RNA-seq
htseq_raw_read_counts.csv


title: MS-8-CD8 BS-Seq


title: shCtrl-2

description:
RNA-seq
htseq_raw_read_counts.csv


title: MS-7-CD8 BS-Seq


title: 30d Heart WT rep2


title: 30d Heart WT rep1


title: Mouse peri-ovarian white adipose 03-1

city: Boston

first: NORC

last: Boston

state: MA

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

description:
processed data file:
Mm10X.counts.mtx.gz
Mm10X.counts.barcodes.tsv.gz
Mm10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Mm_POV_03-1

data_processing:
Raw sequencing reads were demultiplexed to FASTQ format files using bcl2fastq (Illumina; version 2.20.0).
Digital expression matrices were generated from the FASTQ files using the Drop-Seq tools <https://github.com/broadinstitute/Drop-seq> pipeline (version 2.3.0). Adjustments were made to the cell-tagging functions of this pipeline to account for the structure of the 10X barcode read: “BASE_RANGE=1-16” and “BASE_RANGE=17-28”, for the cell and UMI barcodes, respectively. The 10X TSO was provided to the starting sequence trimmer (“SEQUENCE=AAGCAGTGGTATCAACGCAGAGTACATGGG”); this is a minor deviation from the assumed TSO. Reads from were aligned with STAR (version 2.7.3) against the GRCm38 and GRCh38 genome assemblies for mouse and human, respectively. Gene counts were obtained, per-droplet, by summarizing the unique read alignments across exons and introns (Drop-Seq tools “Digital Expression” option: “LOCUS_FUNCTION_LIST=INTRONIC”) in release 16 of the GENCODE mouse annotation or release 27 of the human annotation.
CellBender (Fleming, et. al 2019) version 0.2.0 was used to remove background/ambient signal from the mouse DGE matrices.
In 10X Chromium Single Cell 5’ Solution (v3.x) data, the cDNA read is single-ended (read 2); read 1 contains cell and UMI barcodes pertaining to the read
Genome_build: GRCh38 or GRCm38
Supplementary_files_format_and_content: Digital gene expression matrices (“dge.tsv.gz” files): gene-by-cell UMI counts. Species-wise gene expression matrices in matrix market format: “Hs10X.counts.mtx.gz” and “Mm10X.counts.mtx.gz”. Row (feature) and column (barcode) for the combined expression matrices.

molecule: polyA RNA

source_name: peri-ovarian fat pad

extract_protocol:
Nuclei were isolated from frozen mouse and human adipose tissue samples for 10x snRNA-seq using a slightly modified approach to what was previously described50–52. Samples were kept frozen on dry ice until immediately before nuclei isolation, and all sample handling steps were performed on ice. Each flash-frozen adipose tissue sample was placed into a gentleMACS C tube (Miltenyi Biotec) with 2 mL freshly prepared TST buffer (0.03% Tween 20 [Bio-Rad], 0.01% Molecular Grade BSA [New England Biolabs], 146 mM NaCl [ThermoFisher Scientific], 1 mM CaCl2 [VWR International], 21 mM MgCl2 [Sigma Aldrich], and 10 mM Tris-Hcl pH 7.5 [ThermoFisher Scientific] in Ultrapure water [ThermoFisher Scientific]) with or without 0.2 U/ µL of Protector RNase Inhibitor (Sigma Aldrich). gentleMACS C tubes were then placed on the gentleMACS Dissociator (Miltenyi Biotec) and tissue was dissociated by running the program “mr_adipose_01” twice, and then incubated on ice for 10 minutes. Lysate was passed through a 40 µm nylon filter (CellTreat) and collected into a 50 mL conical tube (Corning). Filter was rinsed with 3 mL of freshly prepared ST buffer buffer (146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2; 10 mM Tris-Hcl pH 7.5) with or without 0.2 U/µL RNase Inhibitor, and collected into the same tube. Flow-through was centrifuged at 500 x g for 5 minutes at 4ºC with brake set to low. Following centrifugation, supernatant was removed, and the nuclear pellet was resuspended in 50 - 200 µl PBS pH 7.4 (ThermoFisher Scientific) with 0.02% BSA, with or without 0.2U/µL RNase Inhibitor. In order to reduce ambient mRNA, the nuclear pellets of some samples were washed 1-3 times with 5 mL of PBS-0.02% BSA before final resuspension. An aliquot of nuclei from each sample was stained with NucBlue (Thermofisher Scientific), counted in a hemocytometer using fluorescence to identify intact nuclei, and then immediately loaded on the 10x Chromium controller (10x Genomics) according to the manufacturer’s protocol.
For each sample, 10,000-16,500 nuclei were loaded in one channel of a Chromium Chip (10x Genomics). The Single Cell 3’ v3.1 chemistry was used to process all samples. cDNA and gene expression libraries were generated according to the manufacturer's instructions (10x Genomics). cDNA and gene expression library fragment sizes were assessed with a DNA High Sensitivity Bioanalyzer Chip (Agilent).
cDNA and gene expression libraries were quantified using the Qubit dsDNA High Sensitivity assay kit (ThermoFisher Scientific). Gene expression libraries were multiplexed and sequenced on the Nextseq 500 (Illumina) with a 75-cycle kit and the following read structure: Read 1: 28 cycles, Read 2: 55 cycles, Index Read 1: 8 cycles.
10X Chromium Single-Cell 3’ (v3 Chemistry);

value: white adipose tissue

tag: mouse strain

tag: Sex

value: female

tag: diet

value: HFD


title: MS-14-CD8 BS-Seq


title: MS-5-CD8 BS-Seq


title: Mouse peri-ovarian white adipose 02-1

description:
processed data file:
Mm10X.counts.mtx.gz
Mm10X.counts.barcodes.tsv.gz
Mm10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Mm_POV_02-1

value: NCD


title: MS-6-CD8 BS-Seq


title: MS-1-CD8 BS-Seq


title: UC-3

city: Hefei

first: Longlong

last: Wang

state: Anhui

address: No. 130, Changjiang West Road

department: School of Agronomy

institute: Anhui Agricultural University

data_processing:
All sequencing reads from 8 samples were mapped to Lotus MG-20 V3.0 genome (http://www.kazusa.or.jp/lotus/).
Two IC samples (IC-1/2) and four UC samples (UC-1/2/3/4) with above 50% mapping rate were used for further analysis, except two IC samples with a low mapping rate of less than 50%
The clean reads were mapped to the reference genome using HISAT2 v2.0.5 with default parameters.
Reads mapped to the exon regions of each gene were counted by FeatureCounts (Subread v2.0.3) with assigning reads to all their overlapping meta-features and then counts were calculated.
Genome_build: MG-20 V3.0
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM values for every gene and every sample

organism: Lotus japonicus

source_name: Root nodule

growth_protocol: For inoculation assay, five-day-old seedlings were planted in pots containing sterile perlite:vermiculite (1:3) supplemented with B&D medium containing 0.5 mM KNO3 and grown in a greenhouse at 24°C under 16/8 h day/night cycle. Ten-day-old seedlings were inoculated with Mesorhizobium loti MAFF303099.

extract_protocol:
Seperated cells were immidately transferred into the lysis buffer. Then RNA was released into the solution.
Library construction followed the Smart-Seq2 method.

value: Root nodule

tag: infection

value: uninfected cells

tag: Stage

value: mature root nodule at 4 weeks post-inoculation

value: MG-20 (wild type)


title: Mouse peri-ovarian white adipose 04-1

description:
processed data file:
Mm10X.counts.mtx.gz
Mm10X.counts.barcodes.tsv.gz
Mm10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Mm_POV_04-1


title: MS-3-CD8 BS-Seq


title: MS-4-CD8 BS-Seq


title: shCtrl-1

description:
RNA-seq
htseq_raw_read_counts.csv


title: HC-12-CD4 BS-Seq

value: Healthy control

value: CD4+ T cells


title: MS-2-CD8 BS-Seq

value: CD8+ T cells


title: Mouse peri-ovarian white adipose 01-1

description:
processed data file:
Mm10X.counts.mtx.gz
Mm10X.counts.barcodes.tsv.gz
Mm10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Mm_POV_01-1


title: HC-11-CD4 BS-Seq


title: UC-4


title: MS-10-CD8 BS-Seq


title: UC-2


title: Mouse inguinal white adipose 24-1

description:
processed data file:
Mm10X.counts.mtx.gz
Mm10X.counts.barcodes.tsv.gz
Mm10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Mm_ING_24-1

source_name: inguinal fat pad

value: male


title: MS-9-CD8 BS-Seq


title: first-episode schizophrenia [P227_158]

type: RNA

city: Barcelona

first: Sergi

last: Mas

state: BARCELONA

address: Casanova 143, Unidad Farmacologia, Facultad de Medicina, Barcelona

department: Pharmacology Unit

country: Spain

institute: University of Barcelona

description: first-episode schizophrenia

hyb_protocol: A total of 1 μg of purified RNA from each of the samples was submitted to the Kompetenzzentrum für Fluoreszente Bioanalytik Microarray Technology (KFB, BioPark Regensburg GmbH, Regensburg, Germany) for labelling and hybridization to the Clariom S Human Array (Affymetrix, Santa Clara, CA, USA), following the manufacturer’s protocols.

data_processing: Microarray data preprocessing was performed using the Oligo R package . The data were standardized using robust multichip analysis.

label: biotin

source_name: Whole Blood

growth_protocol: not applicable

extract_protocol: Peripheral blood were collected at baseline in PAXgene Blood RNA tubes and total RNA was isolated (PAXgene Blood RNA kit, PreAnalytiX Gmbh, Switzerland). The purity and integrity of RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). The mean RNA integrity number (RIN) was 7.77± 0.70, ranging from 6.5 to 8.7.  No sample was discarded due to low RIN number.

treatment_protocol: not applicable

tag: gender

value: Male

tag: age at onset

tag: ethnicity


title: UC-1


title: HC-10-CD4 BS-Seq


title: first-episode schizophrenia [P227_156]

description: first-episode schizophrenia

scan_protocol: A total of 1 μg of purified RNA from each of the samples was submitted to the Kompetenzzentrum für Fluoreszente Bioanalytik Microarray Technology (KFB, BioPark Regensburg GmbH, Regensburg, Germany) for labelling and hybridization to the Clariom S Human Array (Affymetrix, Santa Clara, CA, USA), following the manufacturer’s protocols.

value: Female


title: first-episode schizophrenia [P227_141]

description: first-episode schizophrenia

label_protocol: A total of 1 μg of purified RNA from each of the samples was submitted to the Kompetenzzentrum für Fluoreszente Bioanalytik Microarray Technology (KFB, BioPark Regensburg GmbH, Regensburg, Germany) for labelling and hybridization to the Clariom S Human Array (Affymetrix, Santa Clara, CA, USA), following the manufacturer’s protocols.


title: Mouse inguinal white adipose 22-1

description:
processed data file:
Mm10X.counts.mtx.gz
Mm10X.counts.barcodes.tsv.gz
Mm10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Mm_ING_22-1


title: first-episode schizophrenia [P227_154]

description: first-episode schizophrenia


title: IC-4

value: infected cells


title: HC-9-CD4 BS-Seq


title: Mouse inguinal white adipose 19-1

description:
processed data file:
Mm10X.counts.mtx.gz
Mm10X.counts.barcodes.tsv.gz
Mm10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Mm_ING_19-1


title: HC-8-CD4 BS-Seq


title: IC-3


title: HC-7-CD4 BS-Seq


title: IC-1


title: Mouse inguinal white adipose 16-1

description:
processed data file:
Mm10X.counts.mtx.gz
Mm10X.counts.barcodes.tsv.gz
Mm10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Mm_ING_16-1


title: HC-5-CD4 BS-Seq


title: Mouse inguinal white adipose 17-1

description:
processed data file:
Mm10X.counts.mtx.gz
Mm10X.counts.barcodes.tsv.gz
Mm10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Mm_ING_17-1


title: IC-2


title: Case 3

city: Los Angeles

first: Evanthia

last: Roussos-Torres

address: 1441 Eastlake Ave

institute: USC Keck School of Medicine

data_processing:
Salmon-0.8.2 alignment with the following options -l A -p 4
tximport_1.2.0 R package for transcript level summarization
Genome_build: gencode_vm10_ref_index
Supplementary_files_format_and_content: text, normalized and raw counts

source_name: J774M cell line

growth_protocol: 1x105 J774M cells were seeded into 96-well plates in serum-reduced media (2.5% FBS) at 37°C and 5% CO2.

extract_protocol:
Total RNA isolation
NEBNext Ultra II non-directional RNA Library Pet kit

treatment_protocol: Cells were treated with 0.5 micromolar Entinostat or DMSO.

tag: class

value: Case

tag: cell line


title: Mouse inguinal white adipose 18-1

description:
processed data file:
Mm10X.counts.mtx.gz
Mm10X.counts.barcodes.tsv.gz
Mm10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Mm_ING_18-1

tag: tissue

tag: age


title: Mouse inguinal white adipose 09-2

description:
processed data file:
Mm10X.counts.mtx.gz
Mm10X.counts.barcodes.tsv.gz
Mm10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Mm_ING_09-2


title: HC-6-CD4 BS-Seq

value: peripheral blood


title: first-episode schizophrenia [P227_143]

description: first-episode schizophrenia


title: Case 2


title: first-episode schizophrenia [P227_137]

description: first-episode schizophrenia


title: Mouse inguinal white adipose 08-3

description:
processed data file:
Mm10X.counts.mtx.gz
Mm10X.counts.barcodes.tsv.gz
Mm10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Mm_ING_08-3

value: white adipose tissue


title: first-episode schizophrenia [P227_139]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_133]

description: first-episode schizophrenia


title: Case 1


title: HC-4-CD4 BS-Seq


title: 8_BWA-9

city: St. Louis

first: Brian

middle: Jesse

last: DeBosch

state: MO

address: 660 S. Euclid Ave, Box 8208

department: Pediatrics and Cell Biology & Physiology

institute: Washington University School of Medicine

data_processing:
Sequenced data were processed with the Cell Ranger ATAC software, with alignment to the mouse (mm10) genome.
The Cell Ranger output files were used as input to Active Motif’s proprietary analysis program.
Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality > 1) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 10-7, without control file, and with the –nomodel option.
Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Signal maps and peak locations were used as input data to Active Motif’s proprietary analysis program.
Genome_build: Ensembl GRCm38 (mm10)
Supplementary_files_format_and_content: Excel tables containing detailed information on cluster-specific peak locations, gene annotations, and motif enrichment.

source_name: Liver

growth_protocol: Littermate Becn1+/+ and Becn1+/- mice on C57BL/6 background were fed a Western diet for 12 weeks and treatment started for 4 weeks while continuously on Western diet.

extract_protocol:
Tissues were prepared as described by 10X Genomics Demonstrated Protocol – Nuclei Isolation from Mouse Brain Tissue for Single Cell ATAC Sequencing Rev B with some modifications.
Isolated nuclei were then used as input following the 10X Genomics Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 manual. Targeting a 5,000 nuclei recovery, samples were added to the tagmentation reaction, loaded into the Chromium Controller for nuclei barcoding, and prepared for library construction following manufacturer’s protocol (10X Genomics PN-1000175).

treatment_protocol: Mice were injected with vehicle or ADI-PEG 20 every week for 4 weeks.

tag: strain

value: Liver

tag: genotype

tag: treatment

value: ADI-PEG 20


title: Control 3

value: Control


title: Control 2


title: first-episode schizophrenia [P227_132]

description: first-episode schizophrenia


title: 7_BWA-8


title: HC-2-CD4 BS-Seq

tag: disease status

tag: cell type


title: Control 1


title: HC-1-CD4 BS-Seq


title: 6_BWS-35

value: Vehicle


title: 5_BWS-34


title: MS-17-CD4 BS-Seq

value: Multiple sclerosis


title: Liver, arcA_8

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts with CPM and RPKM in tab-delimitted text format

growth_protocol: Littermate db/db mice were grown to ~5wks of age

extract_protocol:
Trizol reagent was used to isolate total RNA, performed exactly per manufacturer protocol on 50-100mg liver tissue homogenate
oligo-dT

treatment_protocol: Mice were injected with AAV8 encoding GFP or arcA

value: db/db

value: arcA overexpression


title: MS-16-CD4 BS-Seq


title: 4_WWA-22


title: Liver, arcA_7


title: 3_WWA-6


title: HC-3-CD4 BS-Seq

value: Healthy control


title: MS-15-CD4 BS-Seq

value: CD4+ T cells


title: Liver, arcA_6


title: MS-14-CD4 BS-Seq


title: first-episode schizophrenia [P227_129_2]

description: first-episode schizophrenia


title: Liver, arcA_5


title: 1_WWS-31


title: MS-13-CD4 BS-Seq


title: first-episode schizophrenia [P227_134]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_135]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_126]

description: first-episode schizophrenia


title: 5_4247Michigan_C39E-2

city: Ann Abor

first: Maureen

last: Sartor

address: 100 Washtenaw Ave.

institute: University of Michigan

description: ATRX.WT

data_processing:
FASTQC was employed to assess overall quality of each sample followed by TrimGalore processing to trim low-quality bases and adapter sequences.
The trimmed reads were aligned to mm9 genome by STAR (version 2.5.3a) (Dobin et al., 2013), and assembled to exons by HTSeq (version 0.11.2) (Anders et al., 2015) with the following parameters: “--mode=union --stranded=no”.
The differential expression analysis between ATRX-KO  and ATRX-WT groups was performed using the R package edgeR (version 3.20.9) (Robinson et al., 2010) and the generalized linear model (GLM) method. Genes with an absolute fold change greater than 2 and FDR less than 0.05 were reported.
Gene set enrichment testing was performed by the RNA-Enrich method (http://lrpath.ncibi.org).
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited csv files include log2(RPKM) values for each Sample

source_name: mouse GBM neurosphere cell line with wild type ATRX

growth_protocol: Mouse GBM neurospheres were generated from GBMs dissociated from immune-competent mice (C57BL/6 or FVB) injected with Sleeping Beauty plasmids encoding: (1) a short hairpin against p53 (shp53), (2) a plasmid over-expressing NRAS, and (3) with or without a plasmid expressing a short hairpin against ATRX (shATRX) into the ventricles of neonatal mice.  Mouse GBM primary cell cultures were maintained in neural stem-cell medium [DMEM/F12 with L-glutamine (Gibco, 11320-033), B-27 supplement (Gibco 12587-010), N-2 supplement (Gibco 17502-048), penicillin-streptomycin (Cellgro 30-001-CI), and Normocin (Invivogen)]. FGF and EGF (Shenandoah Biotech 100-26, 100-146) supplementation was performed two times per week at 1:l (20 ng/uL each) per 1 ml medium.

extract_protocol:
Total RNA was isolated from the cells using the Qiagen RNeasy Mini Kit (Qiagen, cat# 74104).
For each sample, 4 ug of total RNA was then used in Illumina’s TruSeq Stranded mRNA Library kit (Cat# 20020594). Libraries were sequenced on Illumina NextSeq 500 as paired-end 42-nt reads.

value: ATRX wild type

value: GBM neurosphere cell line


title: Liver, arcA_4


title: Liver, arcA_3


title: MS-11-CD4 BS-Seq


title: first-episode schizophrenia [P227_124]

description: first-episode schizophrenia

value: Male


title: Liver, arcA_2


title: first-episode schizophrenia [P227_122]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_120]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_118]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_116]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_131]

description: first-episode schizophrenia

value: Female


title: 4_4247Michigan_C39E-1

description: ATRX.WT


title: first-episode schizophrenia [P227_112]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_114]

description: first-episode schizophrenia


title: 3_4247Michigan_C54B-3

description: ATRX.KO

source_name: mouse GBM neurosphere cell line with ATRX knockout

value: ATRX knockout


title: Liver, arcA_1


title: 2_WWS-33


title: Liver, GFP_8

value: control


title: first-episode schizophrenia [P227_110]

description: first-episode schizophrenia


title: MS-9-CD4 BS-Seq

value: peripheral blood


title: 6_4247Michigan_C39E-3

description: ATRX.WT


title: first-episode schizophrenia [P227_109]

description: first-episode schizophrenia


title: Liver, GFP_7


title: MS-12-CD4 BS-Seq


title: 2_4247Michigan_C54B-2

description: ATRX.KO


title: MS-7-CD4 BS-Seq


title: Liver, GFP_6


title: RNA_Day6_H33K27A_B2 November 3,2020

city: Philadelphia

first: Peder

middle: J

last: Lund

state: PA

address: 3400 Civic Center Blvd, Smilow 9-176

institute: University of Pennsylvania

description:
RNA_Day6_H33K27A_B2
Supplementary_Table8_H33K27A_RNAseq.xlsx
YK12-Day6-H33K27A-B2mm10.alignAligned.out.bw
YK12-Day6-H33K27A-B2mm10.alignAligned.out.align1.sortedName.htseq.counts.txt

data_processing:
Single-end sequencing (75 bp) was performed on a NextSeq 500 platform (Illumina).
For ChIP-seq, FASTQ files from separate single-end sequencing runs were filtered for a Q score of at least 30 and then concatenated for alignment to the mm10 genome with STAR (v2.5.2a) with default settings except --outFilterMultimapNmax 20 --outFilterMismatchNmax 999.  Alignments were filtered for uniquely mapping reads.  BigWig files, normalized to sequencing depth (RPM), were generated for display in the UCSC genome browser.  MACS2 was used to call peaks from BED files with settings -g mm --no lambda --nomodel -p 1e-2 --min-length 1000 --max-gap 5000 --call-summits --cutoff-analysis.  Peak sets were then filtered for pileup <= 50, fold-enrichment >= 2, and -log10 pvalue >= 3.  Peaks from ChrM and ChrUn were excluded.  These filtered peak sets were used for quantitative analysis of indexed bam files with DiffBind.  Profile plots and heatmaps were generated with DeepTools.
For RNA-seq data analysis, FASTQ files were aligned to the mm10 genome with STAR with default settings except --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMax 1000000.  After filtering for uniquely mapping reads, alignments were analyzed by HTSeq (-f sam -r name -s reverse -t exon -i gene_id --nonunique none --secondary-alignments ignore --supplementary-alignments ignore) and DESEQ2.  Genes were pre-ranked by log2(d6/d0) for analysis by GSEA.
Genome_build: mm10

source_name: embryoid bodies

growth_protocol: mESC were cultured at 37°C in a 5% CO2 atmosphere on 10 cm plates coated with 0.1% gelatin in Dulbecco’s Modified Eagle Medium with L-glutamine, high glucose (4.5g/L), and sodium pyruvate (Corning) plus 1% Glutamax, 1% Non-essential amino acids, 15% characterized fetal bovine serum (Hyclone), 0.1 mM 2-mercaptoethanol (Gibco, Thermo Fisher Scientific 21985023), and supplemented with ESGRO leukemia inhibitory factor (LIF) (Millipore) to maintain stem cell pluripotency.

extract_protocol:
RNA was extracted using a RNAeasy kit (Qiagen 74014) following the manufacturer’s guidelines. Treatment with DNAse for 15 minutes was included in order to degrade genomic DNA.
Libraries were prepared using NEBNext Poly(A) mRNA magnetic isolation module and NEB Ultra Directional RNA Library kit for Illumina (New England Biolabs).

treatment_protocol: Upon 70% confluency, mESC were differentiated to embryoid bodies using 10 uM all-trans retinoic acid (Sigma) on 10 cm petri dishes in the absence of LIF. Differentiating cells were kept with constant rotation.

value: mESC-derived embryoid bodies

tag: chip target

tag: sequencing date

value: November 3,2020


title: 1_4247Michigan_C54B-1

description: ATRX.KO


title: MS-5-CD4 BS-Seq


title: RNA_Day6_H33K27A_B1 November 3,2020

description:
RNA_Day6_H33K27A_B1
Supplementary_Table8_H33K27A_RNAseq.xlsx
YK11-Day6-H33K27A-B1mm10.alignAligned.out.bw
YK11-Day6-H33K27A-B1mm10.alignAligned.out.align1.sortedName.htseq.counts.txt


title: Liver, GFP_5

value: Liver


title: MS-6-CD4 BS-Seq


title: Liver, GFP_4


title: MS-10-CD4 BS-Seq


title: RNA_Day6_H33AKO_B2 November 3,2020

description:
RNA_Day6_H33AKO_B2
Supplementary_Table8_H33K27A_RNAseq.xlsx
YK10-Day6-H33AKO-B2mm10.alignAligned.out.bw
YK10-Day6-H33AKO-B2mm10.alignAligned.out.align1.sortedName.htseq.counts.txt

value: H3.3A knockout


title: Liver, GFP_3


title: RNA_Day6_H33AKO_B1 November 3,2020

description:
RNA_Day6_H33AKO_B1
Supplementary_Table8_H33K27A_RNAseq.xlsx
YK9-Day6-H33AKO-B1mm10.alignAligned.out.bw
YK9-Day6-H33AKO-B1mm10.alignAligned.out.align1.sortedName.htseq.counts.txt


title: MS-3-CD4 BS-Seq


title: Liver, GFP_2


title: MS-2-CD4 BS-Seq


title: RNA_Day6_WT_B2 November 3,2020

description:
RNA_Day6_WT_B2
Supplementary_Table8_H33K27A_RNAseq.xlsx
YK8-Day6-WT-B2mm10.alignAligned.out.bw
YK8-Day6-WT-B2mm10.alignAligned.out.align1.sortedName.htseq.counts.txt

value: wild-type


title: MS-8-CD4 BS-Seq

value: Multiple sclerosis


title: RNA_Day6_WT_B1 November 3,2020

description:
RNA_Day6_WT_B1
Supplementary_Table8_H33K27A_RNAseq.xlsx
YK7-Day6-WT-B1mm10.alignAligned.out.bw
YK7-Day6-WT-B1mm10.alignAligned.out.align1.sortedName.htseq.counts.txt


title: Liver, GFP_1

value: db/db


title: first-episode schizophrenia [P227_106]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_107]

description: first-episode schizophrenia


title: MS-1-CD4 BS-Seq


title: first-episode schizophrenia [P227_105]

description: first-episode schizophrenia


title: eWAT Cachexia 3

city: hefei

first: dong

last: wang

address: shushan district

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. Clean data were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two groups was performed using the DESeq2 R package (1.16.1). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: mm9
Supplementary_files_format_and_content: eWAT_cachexiavseWAT_control_deg.txt (text file includes FPKM values and raw counts for each sample)
Supplementary_files_format_and_content: eWAT_cachexia_vs_eWAT_control_all_gene_count (raw counts)
Supplementary_files_format_and_content: eWAT_cachexia_vs_eWAT_control_all_gene_fpkm (raw fpkm)

source_name: eWAT

extract_protocol:
eWAT was removed and RNA was harvested using using miRNeasy Mini Kits and treated with DEPC-treated water.
RNA libraries were prepared for sequencing using NEBNext UltraTM RNA Library Prep Kit (Illumina).

tag: disease state

value: Cachexia

value: eWAT


title: first-episode schizophrenia [P227_104]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_101]

description: first-episode schizophrenia


title: HC-24-CD19 BS-Seq

value: Healthy control

value: CD19+ B cells


title: RNA_Day0_H33K27A_B2 November 3,2020

description:
RNA_Day0_H33K27A_B2
Supplementary_Table8_H33K27A_RNAseq.xlsx
YK6-Day0-H33K27A-B2mm10.alignAligned.out.bw
YK6-Day0-H33K27A-B2mm10.alignAligned.out.align1.sortedName.htseq.counts.txt

source_name: mouse embryonic stem cells

value: mouse embryonic stem cells


title: first-episode schizophrenia [P227_103]

description: first-episode schizophrenia

value: Male


title: MS-4-CD4 BS-Seq

value: CD4+ T cells


title: first-episode schizophrenia [P227_100]

description: first-episode schizophrenia

value: Female


title: first-episode schizophrenia [P227_099]

description: first-episode schizophrenia


title: eWAT Cachexia 1


title: HC-22-CD19 BS-Seq


title: eWAT Cachexia 2


title: first-episode schizophrenia [P227_098]

description: first-episode schizophrenia


title: RNA_Day0_H33AKO_B1 November 3,2020

description:
RNA_Day0_H33AKO_B1
Supplementary_Table8_H33K27A_RNAseq.xlsx
YK3-Day0-H33AKO-B1mm10.alignAligned.out.bw
YK3-Day0-H33AKO-B1mm10.alignAligned.out.align1.sortedName.htseq.counts.txt


title: first-episode schizophrenia [P227_097]

description: first-episode schizophrenia


title: RNA_Day0_H33K27A_B1 November 3,2020

description:
RNA_Day0_H33K27A_B1
Supplementary_Table8_H33K27A_RNAseq.xlsx
YK5-Day0-H33K27A-B1mm10.alignAligned.out.bw
YK5-Day0-H33K27A-B1mm10.alignAligned.out.align1.sortedName.htseq.counts.txt


title: RNA_Day0_H33AKO_B2 November 3,2020

description:
RNA_Day0_H33AKO_B2
Supplementary_Table8_H33K27A_RNAseq.xlsx
YK4-Day0-H33AKO-B2mm10.alignAligned.out.bw
YK4-Day0-H33AKO-B2mm10.alignAligned.out.align1.sortedName.htseq.counts.txt


title: HC-23-CD19 BS-Seq


title: eWAT Control 3

value: control


title: HC-21-CD19 BS-Seq

value: peripheral blood


title: RNA_Day0_WT_B2 November 3,2020

description:
RNA_Day0_WT_B2
Supplementary_Table8_H33K27A_RNAseq.xlsx
YK2-Day0-WT-B2mm10.alignAligned.out.bw
YK2-Day0-WT-B2mm10.alignAligned.out.align1.sortedName.htseq.counts.txt


title: eWAT Control 2


title: HC-20-CD19 BS-Seq


title: RNA_Day6_B1 March 28,2019

description:
RNA_Day6_B1
mESC-Day6_vs_mESC-Day0.csv
Day6-r1-ykAligned.out.bw
Day6-r1-ykAligned.out.align1.sortedName.htseq.out

value: mESC-derived embryoid bodies


title: HC-18-CD19 BS-Seq


title: RNA_Day6_B2 March 28,2019

description:
RNA_Day6_B2
mESC-Day6_vs_mESC-Day0.csv
Day6-r2-ykAligned.out.bw
Day6-r2-ykAligned.out.align1.sortedName.htseq.out


title: first-episode schizophrenia [P227_096]

description: first-episode schizophrenia


title: Mice_kidney_18m_NicE-C_rep1

description:
Mice_kidney_18m_NicE-C.hic
Mice_kidney_18m_NicE-C.bw

data_processing:
Library strategy: NicE-C
For HiC and NicE-C, raw HiC data were processed through the HiC-Pro (2.10.0) pipeline (PMID: 26619908). *.hic files were generated using HiC-Pro (2.10.0) script: hicpro2juicebox.sh.
For RNA-seq, reads were aligned to the hg19 or mm9 genome assembly using hisat2 version 2.1.0. Data were sorted using Samtools v1.7. BedGraph files were generated using  homer version 4.9. Counts were getting using featureCounts v1.5.0-p1.
For NicE-seq and NicE-C, reads were aligned to the hg19 or mm9 genome assembly using Bowtie2 version 2.2.5 with the following configurations: -3 120. Data were filtered using the following specifications: Samtools v1.7 was used to remove duplicate reads and chromosome M. Peaks were called using Macs2 version 2.1.0. BedGraph files were generated using  homer version 4.9.
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: bigwig files were generated using  bedGraphToBigWig
Supplementary_files_format_and_content: hic files contain the HiC contact matrix at different resolution

source_name: kidney

value: kidney

value: 18 month

tag: sequence of bridge linker

value: ATGCAAGCTTGCAT


title: first-episode schizophrenia [P227_093]

description: first-episode schizophrenia


title: eWAT Control 1


title: HC-19-CD19 BS-Seq


title: first-episode schizophrenia [P227_094]

description: first-episode schizophrenia


title: Mice_kidney_18m_NicE-C_rep2

value: ACATGGATCCATGT


title: RNA_Day0_B1 March 28,2019

description:
RNA_Day0_B1
mESC-Day6_vs_mESC-Day0.csv
Day0-r1-YkAligned.out.bw
Day0-r1-YkAligned.out.align1.sortedName.htseq.out

value: wild-type


title: RNA_Day3_B2 March 28,2019

description:
RNA_Day3_B2
Day3-r2-ykAligned.out.bw
Day3-r2-ykAligned.out.align1.sortedName.htseq.out


title: HC-14-CD19 BS-Seq


title: Day6_H3_B2 March 16,2020

description:
Day6_H3_B2
report_full_d6_v_d0_h31_total_annotated.csv
peaks_s16_filtered_peaks.bed
S16_d6_h31_b2_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S16_d6_h31_b2_qc_cat3.mm10.Aligned.out.bw

extract_protocol:
Samples were prepared for ChIP-seq as previously described (Lin-Shiao et al, 2018). Briefly, 2x107 mESC (day 0 pluripotent cells and day 6 embryoid bodies) were fixed in 1% formaldehyde in PBS for 5 minutes, and was quenched using 125 mM glycine incubating for 5 minutes. Two replicates were conducted per ChIP. Chromatin was sonicated in the Covaris AFA Ultrasonicator (Fisher Scientific Sonic Dismembrator Model 100) for 15 minutes at 200 power (with duty set to 5 and cycles set as 200) at 4°C. All ChIPs were performed using 600ug of sonicated lysate and 5 ug of antibody.  Antibodies were conjugated to 30 uL of Protein G Magnetic Beads (Dynabeads, Thermo Fisher Scientific 10-003-D), per ChIP. Eluted samples were reverse crosslinked overnight at 65°C, and DNA was purified after treatment with RNAse A (Thermo Fisher Scientific) and Proteinase K (Thermo Fisher Scientific).
Sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs).


title: HC-17-CD19 BS-Seq


title: HC-16-CD19 BS-Seq


title: RNA_Day3_B1 March 28,2019

description:
RNA_Day3_B1
Day3-r1-ykAligned.out.bw
Day3-r1-ykAligned.out.align1.sortedName.htseq.out


title: Mice_kidney_2m_NicE-C_rep2

description:
Mice_kidney_2m_NicE-C.hic
Mice_kidney_2m_NicE-C.bw

value: 2 month


title: Mice_kidney_2m_NicE-C_rep1


title: first-episode schizophrenia [P227_089]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_090]

description: first-episode schizophrenia


title: Mice_kidney_18m_RNA-seq_rep1


title: RNA_Day0_B2 March 28,2019

description:
RNA_Day0_B2
mESC-Day6_vs_mESC-Day0.csv
Day0-r2-ykAligned.out.bw
Day0-r2-ykAligned.out.align1.sortedName.htseq.out


title: first-episode schizophrenia [P227_087]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_083]

description: first-episode schizophrenia


title: HC-13-CD19 BS-Seq


title: HC-15-CD19 BS-Seq


title: Mice_kidney_2m_RNA-seq_rep2


title: Mice_kidney_18m_RNA-seq_rep2


title: Day6_H3_B1 March 16,2020

description:
Day6_H3_B1
report_full_d6_v_d0_h31_total_annotated.csv
peaks_s15_filtered_peaks.bed
S15_d6_h31_b1_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S15_d6_h31_b1_qc_cat3.mm10.Aligned.out.bw


title: Mice_kidney_2m_RNA-seq_rep1


title: first-episode schizophrenia [P227_082]

description: first-episode schizophrenia


title: Mice_kidney_NicE-C_rep2

description:
Mice_kidney_NicE-C.hic
Mice_kidney_NicE-C.bw

value: adult, 6 month

value: ATGCGGATCCGCAT


title: first-episode schizophrenia [P227_092]

description: first-episode schizophrenia


title: HC-11-CD19 BS-Seq

value: Healthy control


title: HC-10-CD19 BS-Seq

value: CD19+ B cells


title: first-episode schizophrenia [P227_080]

description: first-episode schizophrenia


title: Day6_H3K27me3_B1 March 16,2020

description:
Day6_H3K27me3_B1
Supplementary_Table5_ChIPseq_report_full_day6_H33K27me3_v_H3K27me3.xls
Supplementary_Table4_ChIPseq_report_full_day0_H33K27me3_v_H3K27me3.xls
report_full_D6_v_D0_h31k27me3_annotated.csv
peaks_s13_filtered_peaks.bed
S13_d6_h31k27me3_b1_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S13_d6_h31k27me3_b1_qc_cat3.mm10.Aligned.out.bw

value: H3K27me3 (Active Motif 39155)


title: Mice_kidney_NicE-C_rep1


title: Day6_H33_B2 March 16,2020

description:
Day6_H33_B2
report_full_d6_v_d0_h33_total_annotated.csv
peaks_s12_filtered_peaks.bed
S12_d6_h33_b2_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S12_d6_h33_b2_qc_cat3.mm10.Aligned.out.bw

value: H3.3 (Invitrogen RM190)


title: first-episode schizophrenia [P227_085]

description: first-episode schizophrenia

value: Male


title: Day6_H33_B1 March 16,2020

description:
Day6_H33_B1
report_full_d6_v_d0_h33_total_annotated.csv
peaks_s11_filtered_peaks.bed
S11_d6_h33_b1_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S11_d6_h33_b1_qc_cat3.mm10.Aligned.out.bw


title: HC-8-CD19 BS-Seq


title: HC-7-CD19 BS-Seq


title: Day6_H33K27me3_B2 March 16,2020

description:
Day6_H33K27me3_B2
Supplementary_Table5_ChIPseq_report_full_day6_H33K27me3_v_H3K27me3.xls
Supplementary_Table4_ChIPseq_report_full_day0_H33K27me3_v_H3K27me3.xls
Supplementary_Table3_ChIPseq_report_full_Day6_v_Day0_H33K27me3.xls
peaks_s10_filtered_peaks.bed
S10_d6_h33k27me3_b2_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S10_d6_h33k27me3_b2_qc_cat3.mm10.Aligned.out.bw

value: H3.3K27me3 (custom, Proteintech)


title: first-episode schizophrenia [P227_078]

description: first-episode schizophrenia

value: Female


title: Day6_H33K27me3_B1 March 16,2020

description:
Day6_H33K27me3_B1
Supplementary_Table5_ChIPseq_report_full_day6_H33K27me3_v_H3K27me3.xls
Supplementary_Table4_ChIPseq_report_full_day0_H33K27me3_v_H3K27me3.xls
Supplementary_Table3_ChIPseq_report_full_Day6_v_Day0_H33K27me3.xls
peaks_s09_filtered_peaks.bed
S09_d6_h33k27me3_b1_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S09_d6_h33k27me3_b1_qc_cat3.mm10.Aligned.out.bw


title: Day6_H3K27me3_B2 March 16,2020

description:
Day6_H3K27me3_B2
Supplementary_Table5_ChIPseq_report_full_day6_H33K27me3_v_H3K27me3.xls
Supplementary_Table4_ChIPseq_report_full_day0_H33K27me3_v_H3K27me3.xls
report_full_D6_v_D0_h31k27me3_annotated.csv
peaks_s14_filtered_peaks.bed
S14_d6_h31k27me3_b2_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S14_d6_h31k27me3_b2_qc_cat3.mm10.Aligned.out.bw


title: HC-12-CD19 BS-Seq

value: peripheral blood


title: first-episode schizophrenia [P227_079]

description: first-episode schizophrenia


title: HC-6-CD19 BS-Seq


title: first-episode schizophrenia [P227_076]

description: first-episode schizophrenia


title: EPC_B1

description:
aggr_barcodes.tsv
aggr_features.tsv
aggr_matrix.mtx

data_processing:
cellranger 3.0.2
Monocle 3
Genome_build: mm10

source_name: NeuN NT2.5

growth_protocol: NT2.5 implanted into NeuN  mammary fat pads.

extract_protocol:
To obtain single-cell suspensions from breast tumors, tumors were harvested, weighed, diced, and then dissociated using a tumor dissociation kit (Miltenyi Biotec, cat. 130-096-730) and the OctoDissociator (Miltenyi Biotec) per the manufacturer’s instructions. The 37C_m_TDK_2 program was used to dissociate tumors per the manufacturer’s instructions. Samples were filtered using a 40 mm cell strainer and red blood cells were lysed using ACK lysis buffer (Quality Biological, cat. 118-156-721). The resulting single-cell suspensions were used for subsequent isolation of specific immune cell types or flow cytometry as described below, or for scRNAseq following an additional step of dead cell removal using the MACS Dead Cell Removal Kit (Miltenyi Biotec).
Library construction from the single cell suspensions were performed using the 10X Genomics Chromium Single Cell 3' Reagent Kit v2, following manufacturer's instructions.

treatment_protocol: Mice treated with vehicle control or entinostat alone or entinostat + aCTLA4, or entinostat + aPD1, or entinostat + aCTLA4 + aPD1.

value: EPC


title: V_B

value: V


title: first-episode schizophrenia [P227_075]

description: first-episode schizophrenia


title: EP_B2

value: EP


title: first-episode schizophrenia [P227_074]

description: first-episode schizophrenia


title: Day0_H3_B2 March 16,2020

description:
Day0_H3_B2
report_full_d6_v_d0_h31_total_annotated.csv
peaks_s08_filtered_peaks.bed
S08_d0_h31_b2_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S08_d0_h31_b2_qc_cat3.mm10.Aligned.out.bw

value: mouse embryonic stem cells


title: HC-9-CD19 BS-Seq


title: Day0_H3_B1 March 16,2020

description:
Day0_H3_B1
report_full_d6_v_d0_h31_total_annotated.csv
peaks_s07_filtered_peaks.bed
S07_d0_h31_b1_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S07_d0_h31_b1_qc_cat3.mm10.Aligned.out.bw


title: HC-5-CD19 BS-Seq


title: first-episode schizophrenia [P227_073]

description: first-episode schizophrenia


title: EP_B1


title: HC-4-CD19 BS-Seq


title: first-episode schizophrenia [P227_071]

description: first-episode schizophrenia


title: HC-3-CD19 BS-Seq


title: first-episode schizophrenia [P227_068]

description: first-episode schizophrenia


title: HC-2-CD19 BS-Seq


title: EPC_B2


title: first-episode schizophrenia [P227_069]

description: first-episode schizophrenia


title: Day0_H3K27me3_B1 March 16,2020

description:
Day0_H3K27me3_B1
Supplementary_Table5_ChIPseq_report_full_day6_H33K27me3_v_H3K27me3.xls
Supplementary_Table4_ChIPseq_report_full_day0_H33K27me3_v_H3K27me3.xls
report_full_D6_v_D0_h31k27me3_annotated.csv
peaks_s05_filtered_peaks.bed
S05_d0_h31k27me3_b1_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S05_d0_h31k27me3_b1_qc_cat3.mm10.Aligned.out.bw


title: EC_B1

value: EC


title: Day0_H33_B2 March 16,2020

description:
Day0_H33_B2
report_full_d6_v_d0_h33_total_annotated.csv
peaks_s04_filtered_peaks.bed
S04_d0_h33_b2_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S04_d0_h33_b2_qc_cat3.mm10.Aligned.out.bw

value: wild-type


title: HC-1-CD19 BS-Seq


title: E_B

value: E


title: Day0_H33_B1 March 16,2020

description:
Day0_H33_B1
report_full_d6_v_d0_h33_total_annotated.csv
peaks_s03_filtered_peaks.bed
S03_d0_h33_b1_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S03_d0_h33_b1_qc_cat3.mm10.Aligned.out.bw


title: MS-29-CD19 BS-Seq

value: Multiple sclerosis


title: MS-28-CD19 BS-Seq


title: Day0_H33K27me3_B2 March 16,2020

description:
Day0_H33K27me3_B2
Supplementary_Table5_ChIPseq_report_full_day6_H33K27me3_v_H3K27me3.xls
Supplementary_Table4_ChIPseq_report_full_day0_H33K27me3_v_H3K27me3.xls
Supplementary_Table3_ChIPseq_report_full_Day6_v_Day0_H33K27me3.xls
peaks_s02_filtered_peaks.bed
S02_d0_h33k27me3_b2_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S02_d0_h33k27me3_b2_qc_cat3.mm10.Aligned.out.bw


title: EPC_A2


title: V_A


title: Day0_H33K27me3_B1 March 16,2020

description:
Day0_H33K27me3_B1
Supplementary_Table5_ChIPseq_report_full_day6_H33K27me3_v_H3K27me3.xls
Supplementary_Table4_ChIPseq_report_full_day0_H33K27me3_v_H3K27me3.xls
Supplementary_Table3_ChIPseq_report_full_Day6_v_Day0_H33K27me3.xls
peaks_s01_filtered_peaks.bed
S01_d0_h33k27me3_b1_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S01_d0_h33k27me3_b1_qc_cat3.mm10.Aligned.out.bw


title: Day0_H3K27me3_B2 March 16,2020

description:
Day0_H3K27me3_B2
Supplementary_Table5_ChIPseq_report_full_day6_H33K27me3_v_H3K27me3.xls
Supplementary_Table4_ChIPseq_report_full_day0_H33K27me3_v_H3K27me3.xls
report_full_D6_v_D0_h31k27me3_annotated.csv
peaks_s06_filtered_peaks.bed
S06_d0_h31k27me3_b2_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S06_d0_h31k27me3_b2_qc_cat3.mm10.Aligned.out.bw


title: first-episode schizophrenia [P227_062]

description: first-episode schizophrenia


title: MS-27-CD19 BS-Seq


title: EC_B2


title: Day6_H3_B2 March 9,2020

description:
Day6_H3_B2
report_full_d6_v_d0_h31_total_annotated.csv
peaks_s16_filtered_peaks.bed
S16_d6_h31_b2_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S16_d6_h31_b2_qc_cat3.mm10.Aligned.out.bw

value: mESC-derived embryoid bodies


title: first-episode schizophrenia [P227_060]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_064]

description: first-episode schizophrenia


title: EP_A2


title: EPC_A1


title: MS-26-CD19 BS-Seq


title: Day6_H3_B1 March 9,2020

description:
Day6_H3_B1
report_full_d6_v_d0_h31_total_annotated.csv
peaks_s15_filtered_peaks.bed
S15_d6_h31_b1_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S15_d6_h31_b1_qc_cat3.mm10.Aligned.out.bw


title: MS-25-CD19 BS-Seq


title: EP_A1


title: MS-24-CD19 BS-Seq


title: EC_A1


title: EC_A2


title: Day6_H3K27me3_B1 March 9,2020

description:
Day6_H3K27me3_B1
Supplementary_Table5_ChIPseq_report_full_day6_H33K27me3_v_H3K27me3.xls
Supplementary_Table4_ChIPseq_report_full_day0_H33K27me3_v_H3K27me3.xls
report_full_D6_v_D0_h31k27me3_annotated.csv
peaks_s13_filtered_peaks.bed
S13_d6_h31k27me3_b1_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S13_d6_h31k27me3_b1_qc_cat3.mm10.Aligned.out.bw


title: Day6_H33_B2 March 9,2020

description:
Day6_H33_B2
report_full_d6_v_d0_h33_total_annotated.csv
peaks_s12_filtered_peaks.bed
S12_d6_h33_b2_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S12_d6_h33_b2_qc_cat3.mm10.Aligned.out.bw


title: first-episode schizophrenia [P227_054]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_056]

description: first-episode schizophrenia


title: E_A


title: MS-21-CD19 BS-Seq


title: MS-22-CD19 BS-Seq


title: first-episode schizophrenia [P227_058]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_066]

description: first-episode schizophrenia


title: MS-23-CD19 BS-Seq


title: V_p2


title: first-episode schizophrenia [P227_050]

description: first-episode schizophrenia


title: MS-20-CD19 BS-Seq


title: E_p2


title: first-episode schizophrenia [P227_044]

description: first-episode schizophrenia


title: Day6_H3K27me3_B2 March 9,2020


title: Day6_H33K27me3_B1 March 9,2020


title: first-episode schizophrenia [P227_048]

description: first-episode schizophrenia


title: MS-19-CD19 BS-Seq


title: first-episode schizophrenia [P227_052]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_046]

description: first-episode schizophrenia


title: Day0_H3_B2 March 9,2020


title: first-episode schizophrenia [P227_042]

description: first-episode schizophrenia


title: MS-18-CD19 BS-Seq


title: Day0_H3_B1 March 9,2020


title: E_p1


title: Day6_H33_B1 March 9,2020

description:
Day6_H33_B1
report_full_d6_v_d0_h33_total_annotated.csv
peaks_s11_filtered_peaks.bed
S11_d6_h33_b1_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S11_d6_h33_b1_qc_cat3.mm10.Aligned.out.bw


title: MS-17-CD19 BS-Seq


title: MS-16-CD19 BS-Seq


title: V_p1


title: Day0_H3K27me3_B2 March 9,2020


title: Day0_H3K27me3_B1 March 9,2020


title: Day6_H33K27me3_B2 March 9,2020

description:
Day6_H33K27me3_B2
Supplementary_Table5_ChIPseq_report_full_day6_H33K27me3_v_H3K27me3.xls
Supplementary_Table4_ChIPseq_report_full_day0_H33K27me3_v_H3K27me3.xls
Supplementary_Table3_ChIPseq_report_full_Day6_v_Day0_H33K27me3.xls
peaks_s10_filtered_peaks.bed
S10_d6_h33k27me3_b2_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S10_d6_h33k27me3_b2_qc_cat3.mm10.Aligned.out.bw


title: first-episode schizophrenia [P227_040]

description: first-episode schizophrenia


title: Day0_H33_B2 March 9,2020


title: MS-15-CD19 BS-Seq


title: 5P-kin28is_dmso-rep2

city: Madison

first: Aseem

last: Ansari

state: WI

address: 440 Henry Mall

department: Biochemistry and The Genome Center

institute: University of Wisconsin-Madison

description:
5'P-Seq
5'P RNA
HLCLLBGX2_Ansari15_16s006635-1-2

data_processing:
Base calls were performed with CASAVA-1.8.2.
For RNA-Seq (i.e. TT-Seq), reads were clipped of adapter sequences (GATCGGAAGAGCACACGTCTGAACTCCAGTCA) and aligned to a concatenated sacCer3 and S. pombe genome using STAR (v2.4.2a). Reads mapping to more than one position were filtered to prevent ambiguous alignment of sequences shared between species. Aligned reads were sorted and indexed with SAMtools and counted with HTSeq (0.6.0). S. cerevisiae read counts were normalized with loess regression using S. pombe read counts to fit the loess as described previously (Rodriguez-Molina et al., 2016). Alignments were scaled and converted to bigwig files with deepTools 2 and visualized in IGV.
For 5'P-Seq, UMI-tools was used to move the unique molecular identifier (UMI) into the read header before alignment to sacCer3 with STAR; clipped 5′ reads were filtered with –alignEndsType Extend5pOfRead1. Aligned reads with a quality score over 30 were sorted and indexed with SAMtools. UMI-tools was used to de-duplicate reads. The 5′ nucleotide was plotted with --Offset 1 and scaled with --normalizeUsingRPKM during conversion to the bigwig format with deepTools 2.
Genome_build: SacCer3 and ASM294v.2.23
Supplementary_files_format_and_content: bigWig files (http://genome.ucsc.edu/goldenPath/help/bedgraph.html) covering the Watson- and Crick-oriented direction.

organism: Saccharomyces cerevisiae BY4741

source_name: yeast BY4741

growth_protocol: Yeast were grown in His-dropout media + 2% dextrose at 30 °C in a shaking incubator from an OD600 of 0.1 to mid-log phase OD600 of 0.4 to 1.

extract_protocol:
RNA was extracted using a standard hot acidic phenol approach and treated with DNase I (Ambion, #AM1906).
As starting material, 50 ug of RNA was used. The Ribo-Zero Magnetic Gold Kit (Epicentre) was used to deplete rRNA, and libraries were generated as previously described (PMID: 23295673). Libraries were sequenced (single-end, 100 bp) using an Illumina HiSeq 2000. Reads contain a unique molecular identifier (UMI) that is 8 nucleotides long followed by the 5' sequence. RNA fragments shorter than 100 bp may container adapter sequences that may be trimmed (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC).

treatment_protocol: Cells were treated with 5 uM of inhibitor CMK or an equivalent volume of solvent control (DMSO) at mid-log phase (50 mL, OD600 0.4 to 1) for 1 hr.

tag: genotype/variation

value: DMSO


title: 5P-kin28is_cmk-rep2

description:
5'P-Seq
5'P RNA
HFJGJBGX2_Ansari-16_16s006636-1-2

value: CMK


title: 5P-WT_dmso-rep2

description:
5'P-Seq
5'P RNA
HCMNMBGX2_Ansari-13_16s006633-1-1


title: first-episode schizophrenia [P227_039]

description: first-episode schizophrenia

tag: gender


title: MS-14-CD19 BS-Seq

value: CD19+ B cells


title: Day0_H33_B1 March 9,2020

value: H3.3 (Invitrogen RM190)


title: MS-13-CD19 BS-Seq


title: first-episode schizophrenia [P227_035]

description: first-episode schizophrenia

value: Male

tag: age at onset


title: 5P-WT_cmk-rep2

description:
5'P-Seq
5'P RNA
HCMNMBGX2_Ansari-14_16s006634-1-1


title: 5P-kin28is_dmso-rep1

description:
5'P-Seq
5'P RNA
HCMNMBGX2_Ansari-7_16s006627-1-1


title: 5P-kin28is_cmk-rep1

description:
5'P-Seq
5'P RNA
HCMNMBGX2_Ansari-8_16s006628-1-1


title: first-episode schizophrenia [P227_033]

description: first-episode schizophrenia

tag: ethnicity


title: Day0_H33K27me3_B2 March 9,2020

value: H3.3K27me3 (custom, Proteintech)


title: first-episode schizophrenia [P227_037]

description: first-episode schizophrenia


title: MS-12-CD19 BS-Seq


title: Day0_H33K27me3_B1 March 9,2020


title: 5P-WT_cmk-rep1

description:
5'P-Seq
5'P RNA
HCMNMBGX2_Ansari-6_16s006626-1-1


title: MS-11-CD19 BS-Seq


title: 5P-WT_dmso-rep1

description:
5'P-Seq
5'P RNA
HCMNMBGX2_Ansari-5_16s006625-1-1


title: Day6_H3_B2 January 31,2020

value: January 31,2020


title: Day6_H3_B1 January 31,2020


title: MS-10-CD19 BS-Seq

value: peripheral blood


title: MS-9-CD19 BS-Seq


title: n_RNA-kin28is_cmk-rep2

description:
TT-Seq
Nascent RNA
n_is-CMK-2_ACTTGA

extract_protocol:
Total RNA was extracted using a standard hot acidic phenol approach. Prior to lysis, S. pombe cells were added in a 1:6 pombe-to-cerevisiae cellular ratio. Pombe cells were also labeled with 4-thiouracil. RNA was treated with DNase I (Ambion, #AM1906). For nascent RNA extraction, 100 ug of total RNA was biotinylated with 10 ug of MTSEA-biotin XX (Biotium, #90066-10mg), and the labeled RNA was purified using Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher Scientific, #65001).
Both total and nascent RNA were ribosomal RNA-depleted and prepared for sequencing using the Yeast ScriptSeq Complete Gold Kit (Epicentre, BGY1324). DNA was sequenced on an Illumina HiSeq 2000 generating single-end reads of 100 bp length using standard Illumina protocols.

treatment_protocol: Cells were treated with 5 uM of inhibitor CMK or an equivalent volume of solvent control (DMSO) at mid-log phase (50 mL, OD600 0.4 to 1) for 1 hr. Six minutes before harvest, cells were labeled with 5 mM 4-thiouracil.


title: MS-8-CD19 BS-Seq


title: n_RNA-WT_cmk-rep2

description:
TT-Seq
Nascent RNA
n_WT-CMK-2_GCCAAT


title: MS-7-CD19 BS-Seq


title: n_RNA-WT_dmso-rep2

description:
TT-Seq
Nascent RNA
n_WT-dmso-2_ACAGTG


title: MS-6-CD19 BS-Seq


title: n_RNA-kin28is_cmk-rep1

description:
TT-Seq
Nascent RNA
n_is-CMK-1_TGACCA


title: Day6_H33_B2 January 31,2020


title: Day6_H3K27me3_B2 January 31,2020

description:
Day6_H3K27me3_B2
Supplementary_Table5_ChIPseq_report_full_day6_H33K27me3_v_H3K27me3.xls
Supplementary_Table4_ChIPseq_report_full_day0_H33K27me3_v_H3K27me3.xls
report_full_D6_v_D0_h31k27me3_annotated.csv
peaks_s14_filtered_peaks.bed
S14_d6_h31k27me3_b2_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S14_d6_h31k27me3_b2_qc_cat3.mm10.Aligned.out.bw

value: H3K27me3 (Active Motif 39155)


title: Day6_H33_B1 January 31,2020


title: Day6_H3K27me3_B1 January 31,2020


title: first-episode schizophrenia [P227_029]

description: first-episode schizophrenia


title: MS-5-CD19 BS-Seq


title: n_RNA-kin28is_dmso-rep1

description:
TT-Seq
Nascent RNA
n_is-dmso-1_TTAGGC


title: Day6_H33K27me3_B2 January 31,2020


title: MS-4-CD19 BS-Seq


title: first-episode schizophrenia [P227_031]

description: first-episode schizophrenia


title: Day6_H33K27me3_B1 January 31,2020

description:
Day6_H33K27me3_B1
Supplementary_Table5_ChIPseq_report_full_day6_H33K27me3_v_H3K27me3.xls
Supplementary_Table4_ChIPseq_report_full_day0_H33K27me3_v_H3K27me3.xls
Supplementary_Table3_ChIPseq_report_full_Day6_v_Day0_H33K27me3.xls
peaks_s09_filtered_peaks.bed
S09_d6_h33k27me3_b1_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S09_d6_h33k27me3_b1_qc_cat3.mm10.Aligned.out.bw


title: n_RNA-WT_cmk-rep1

description:
TT-Seq
Nascent RNA
n_WT-CMK-1_CGATGT


title: MS-3-CD19 BS-Seq


title: first-episode schizophrenia [P227_027]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_025]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_024]

description: first-episode schizophrenia

value: Female


title: first-episode schizophrenia [P227_019]

description: first-episode schizophrenia


title: n_RNA-kin28is_dmso-rep2

description:
TT-Seq
Nascent RNA
n_is-dmso-2_CAGATC


title: Day0_H3_B2 January 31,2020

description:
Day0_H3_B2
report_full_d6_v_d0_h31_total_annotated.csv
peaks_s08_filtered_peaks.bed
S08_d0_h31_b2_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S08_d0_h31_b2_qc_cat3.mm10.Aligned.out.bw


title: first-episode schizophrenia [P227_021]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_018]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_026]

description: first-episode schizophrenia


title: MS-2-CD19 BS-Seq


title: first-episode schizophrenia [P227_023]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_017]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_015]

description: first-episode schizophrenia


title: RNA-kin28is_cmk-rep2

description:
TT-Seq
is-CMK-2_CCGTCC


title: Day0_H3_B1 January 31,2020

description:
Day0_H3_B1
report_full_d6_v_d0_h31_total_annotated.csv
peaks_s07_filtered_peaks.bed
S07_d0_h31_b1_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S07_d0_h31_b1_qc_cat3.mm10.Aligned.out.bw


title: MS-1-CD19 BS-Seq


title: Day0_H3K27me3_B2 January 31,2020

description:
Day0_H3K27me3_B2
Supplementary_Table5_ChIPseq_report_full_day6_H33K27me3_v_H3K27me3.xls
Supplementary_Table4_ChIPseq_report_full_day0_H33K27me3_v_H3K27me3.xls
report_full_D6_v_D0_h31k27me3_annotated.csv
peaks_s06_filtered_peaks.bed
S06_d0_h31k27me3_b2_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S06_d0_h31k27me3_b2_qc_cat3.mm10.Aligned.out.bw


title: IE-1 CD137+ V(D)J

description: 5' V(D)J

data_processing:
Samples were processed using CellRanger pipline version 2.1.1 or 3.0.2
FASTQ files were processed with CellRanger software v2.1.1 or v3.0.2 and corresponding sample sheet
Genome_build: GRCh38
Supplementary_files_format_and_content: comma separated values with abundance measurements for each target.

source_name: PBMCs

extract_protocol:
RNA was extracted using 10x genomics protocols
RNA was extracted using 10x genomics protocols

tag: phenotype

tag: donors

value: Patient 3

tag: time point


title: RNA-WT_cmk-rep2

description:
TT-Seq
WT-CMK-2_AGTTCC


title: pp65 CD137+ V(D)J

description: 5' V(D)J


title: Day0_H3K27me3_B1 January 31,2020

description:
Day0_H3K27me3_B1
Supplementary_Table5_ChIPseq_report_full_day6_H33K27me3_v_H3K27me3.xls
Supplementary_Table4_ChIPseq_report_full_day0_H33K27me3_v_H3K27me3.xls
report_full_D6_v_D0_h31k27me3_annotated.csv
peaks_s05_filtered_peaks.bed
S05_d0_h31k27me3_b1_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S05_d0_h31k27me3_b1_qc_cat3.mm10.Aligned.out.bw

value: mouse embryonic stem cells

tag: cell line


title: Day0_H33_B2 January 31,2020

description:
Day0_H33_B2
report_full_d6_v_d0_h33_total_annotated.csv
peaks_s04_filtered_peaks.bed
S04_d0_h33_b2_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S04_d0_h33_b2_qc_cat3.mm10.Aligned.out.bw


title: DMSO CD137- V(D)J

description: 5' V(D)J


title: first-episode schizophrenia [P227_010]

description: first-episode schizophrenia

tag: age


title: first-episode schizophrenia [P227_012]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_013]

description: first-episode schizophrenia


title: n_RNA-WT_dmso-rep1

description:
TT-Seq
Nascent RNA
n_WT-dmso-1_ATCACG


title: Day0_H33_B1 January 31,2020

description:
Day0_H33_B1
report_full_d6_v_d0_h33_total_annotated.csv
peaks_s03_filtered_peaks.bed
S03_d0_h33_b1_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S03_d0_h33_b1_qc_cat3.mm10.Aligned.out.bw


title: RNA-kin28is_cmk-rep1

description:
TT-Seq
is-CMK-1_CTTGTA


title: IE-1 CD137+

description: 5' Transcriptome


title: RNA-kin28is_dmso-rep1

description:
TT-Seq
is-dmso-1_GGCTAC


title: first-episode schizophrenia [P227_008]

description: first-episode schizophrenia


title: pp65 CD137+

description: 5' Transcriptome


title: Day0_H33K27me3_B2 January 31,2020

description:
Day0_H33K27me3_B2
Supplementary_Table5_ChIPseq_report_full_day6_H33K27me3_v_H3K27me3.xls
Supplementary_Table4_ChIPseq_report_full_day0_H33K27me3_v_H3K27me3.xls
Supplementary_Table3_ChIPseq_report_full_Day6_v_Day0_H33K27me3.xls
peaks_s02_filtered_peaks.bed
S02_d0_h33k27me3_b2_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S02_d0_h33k27me3_b2_qc_cat3.mm10.Aligned.out.bw


title: first-episode schizophrenia [P227_007]

description: first-episode schizophrenia


title: Day0_H33K27me3_B1 January 31,2020

description:
Day0_H33K27me3_B1
Supplementary_Table5_ChIPseq_report_full_day6_H33K27me3_v_H3K27me3.xls
Supplementary_Table4_ChIPseq_report_full_day0_H33K27me3_v_H3K27me3.xls
Supplementary_Table3_ChIPseq_report_full_Day6_v_Day0_H33K27me3.xls
peaks_s01_filtered_peaks.bed
S01_d0_h33k27me3_b1_qc_cat3.mm10.Aligned.out.macs_parameters12_peaks.xls
S01_d0_h33k27me3_b1_qc_cat3.mm10.Aligned.out.bw


title: DMSO CD137-

description: 5' Transcriptome


title: RNA-kin28is_dmso-rep2

description:
TT-Seq
is-dmso-2_ATGTCA


title: first-episode schizophrenia [P227_005]

description: first-episode schizophrenia


title: treatment rep3

status: Public on Jan 17 2022

city: Jena

first: Clabe

middle: Simiyu

last: Wekesa

address: Dornburgerstr. 159

department: Plant physiology

country: Germany

institute: FSU

description:
CountMatrix.csv
DiffExpr.csv

data_processing:
Illumina Casava1.8 software used for basecalling.
Low quality reads and those with adaptors  were filtered out with Trimmomatic v0.39
Reads were aligned to Rhizobium phaseoli with bowtie2 v2.4.4 with default parameters.
Reads per gene were counted with bedtools v2.30 to form the count matrix
Count normalization and differential expression were performed in DESeq2 v1.34
Genome_build: GCA_001664385.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with differential expression for every gene

organism: Rhizobium phaseoli

source_name: bacteria cell

growth_protocol: bacteria grown in a shacker for 24 hours at 30 deg. Celcius

extract_protocol:
24 hour cultures were harvested by centrifugation and RNA extracted by Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: treated with 0 mM Al (control) or 0.01 mM Al (treated)

tag: source

value: Phaseolus vulgaris

tag: tissue

value: nodules

value: 0.1 mM aluminium


title: treatment rep1

description:
CountMatrix.csv
DiffExpr.csv

tag: treatment


title: RNA-WT_dmso-rep1

description:
TT-Seq
WT-dmso-1_GATCAG

value: wild-type


title: control rep3

description:
CountMatrix.csv
DiffExpr.csv

value: untreated


title: control rep2

description:
CountMatrix.csv
DiffExpr.csv


title: control rep1

description:
CountMatrix.csv
DiffExpr.csv


title: RNA-WT_dmso-rep2

description:
TT-Seq
WT-dmso-2_AGTCAA

value: DMSO


title: first-episode schizophrenia [P227_001]

description: first-episode schizophrenia


title: first-episode schizophrenia [P227_003]

description: first-episode schizophrenia


title: B6xSPRET-input-B1

first: Marty

middle: G

last: Yang

address: 615 Charles E Young Dr S

department: Biological Chemistry

institute: University of California, Los Angeles

data_processing:
Reads were trimmed with the paired-end option and with SLIDINGWINDOW:5:30 using Trimmomatic (Bolger et al., 2014).
Paired-end reads that survived trimming were re-paired using the bbmap utility (Bushnell 2014). Both unpaired and paired reads were concurrently mapped to the C57BL/6J and appropriate pseudogenome with bowtie2 using default parameters (Langmead and Salzberg, 2012).
Mapped reads were converted to .bam format with samtools view (Li et al., 2009) using the following options -h -b -F 3844 -q 10 and sorted by coordinate. Reads initially mapped to each pseudogenome were converted back to C57BL/6J coordinates by running Lapels (Huang et al., 2014).
For visualization purposes, mapped reads in .bam format were also converted to .bed format and unique reads were retained (with sort -k1,1 -k2,2n -k3,3n -u) and extended by 150 bp with bedtools slop -l 0 -r 150.
All samples were normalized to a depth of 10 million reads and read coverage was calculated by bedtools genomeCoverageBed. The output .bedgraph file was then converted with UCSC’s bedGraphtobigWig utility and all tracks displayed were visualized with the UCSC Genome Browser (GRCm38/mm10).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files of histograms normalized to 10 million mapped and in silico extended reads.

source_name: Primary mouse embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts (MEFs) were grown in DMEM with 10% CCS.

extract_protocol:
Media was aspirated from MEFs and 2 mL or 15 mL crosslinking buffer (10 mM HEPES pH 7.5, 100 mM NaCl, 1 mM EDTA, 1 mM EGTA) with 1% formaldehyde was added for 6-well or 15 cm dishes respectively. Cells were crosslinked by shaking gently for 10 min at room temperature. Crosslinking was quenched by adding glycine to a final concentration of 125mM and incubating for 5 min at room temperature while shaking. Cells were washed once in 2 mL or 15 mL PBS for 6-well or 15 cm dishes respectively. Cells were scraped and collected in 1 mL or 5 mL cold PBS for 6-well or 15 cm dishes respectively and pelleted by spinning at 1,000 g for 5 min at 4oC. Crosslinked MEFs per protocol above from 15 cm dishes were resuspended in 1 mL L1 buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, 0.25% Triton X-100, 0.5% NP-40, 10% glycerol, 10 mM sodium butyrate) per 15 cm dish starting material and rotated for 10 min at 4oC to lyse cells. Nuclei were pelleted by spinning at 1,350 g for 5 min at 4oC and resuspended in 1 mL L2 buffer (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 10 mM sodium butyrate) per 15 cm dish starting material and rotated for 10 min at room temperature. Nuclei were pelleted by spinning at 1,350 g for 5 min at 4oC and resuspended in 300 uL LB3 buffer (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine, 10 mM sodium butyrate) per 15 cm dish starting material. Chromatin was sonicated with a Bioruptor Plus (Diagenode (Denville, NJ, USA)) on “high” power setting with an “on” interval of 30 sec and “off” interval of 45 sec for 36 cycles). DNA concentration was determined by taking 100 uL aliquot of sonicated chromatin, decrosslinking at 95oC for 15 min, and purifying with QIAquick PCR Purification Kit (QIAGEN 28104) and quantifying by Nanodrop. 1 ug of purified chromatin in 10% glycerol was run on 2% agarose gel and stained with ethidium bromide for 30 min to validate fragment size (typically within ~200-1,000 bp). The remainder of the sonicated chromatin was transferred to 1.5 mL tubes and centrifuged at 16,000 g for 10 min at 4oC to pellet insoluble debris. Triton X-100 was added to soluble chromatin to a final 1% concentration. Protein A Dynabeads (Thermo Fisher 10008D) were washed twice in 1 mL cold block solution (0.5% BSA (w/v), 1% Triton X-100, diluted in LB3 buffer). For coupling antibodies to beads, 15 uL bead slurry per IP were resuspended in 1.5 mL cold block solution and the appropriate amount of antibody (0.5 ug for anti-H3K27ac (Abcam (Waltham, MA, USA) ab4729), 0.5 ug for anti-H3K4me1 (Abcam ab8895), 0.5 ug for anti-H3K4me2 (Abcam ab7766), 0.5ug for anti-H3K4me3 (Abcam ab8580), 2 ug for anti-Fos (in-house generated antibody and Santa Cruz Biotechnology (Dallas, TX, USA) sc-7202X), 2 ug for anti-Tead1 (Abcam ab133533), 2 ug for anti-CTCF (Active Motif (Carlsbad, CA, USA) 61312), and 2 ug for anti-JunD (Santa Cruz Biotechnology sc74)) was added before rotating beads for >2 hrs at 4oC. For pre-clearing chromatin, 15 uL bead slurry was added to appropriate amount of chromatin (40 ug for histone modifications, 80 ug for transcription factors) and additional cold LB3 buffer with 1% Triton X-100 was added such that all samples had a final volume of 1.5 mL before rotating samples for > 2 hrs at 4oC. Pre-cleared chromatin was added to antibody-coupled beads and additional cold LB3 buffer with 1% Triton X-100 was added such that all samples had a final volume of 1.8 mL before rotating samples overnight at 4oC. 50 uL of pre-cleared chromatin was stored at -20oC for making input libraries. For all wash steps listed below, samples were rinsed with 1 mL cold wash buffer and rotated for 5 min at 4oC before separating beads with magnet and discarding supernatant. Samples were washed sequentially twice in low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), twice in high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl), twice in LiCl buffer (250 mM LiCl, 1% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0), and once in TE buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA). Samples were eluted from beads by addition of 200 uL TE buffer with 1% SDS and incubating at 65oC for 30 min with brief vortexing every 10 min to mix. IP samples were placed on magnet and supernatant was transferred to new tubes. Input samples were also thawed and 150 uL TE buffer with 1% SDS was added. Both IP and input samples were decrosslinked by incubating at 65oC overnight. 10 ug RNase A (Sigma Aldrich (St. Louis, MO, USA) R6513) was added and samples were incubated at 37oC for 1 hr to digest RNA. 7 uL 20 ug/uL proteinase K (New England Biolabs P8107) was added and samples were incubated at 55oC for 2 hr to digest protein. DNA was extracted with 1 volume of 25:24:1 phenol-chloroform-isoamyl alcohol and purified with QIAquick PCR Purification Kit (QIAGEN 28104).
Libraries were prepared with the Ovation Ultralow V2 DNA-Seq Library Preparation Kit (NuGEN (Redwood City, CA, USA) 0344NB-32) per manufacturer’s instructions. Libraries were sequenced on an Illumina NextSeq 500 with 150 bp paired-end reads.

treatment_protocol: MEFs were starved for 26 hours in DMEM with 0.5% CCS and serum stimulated for the indicated times at a final concentration of 15% CCS.

tag: cell type

value: Primary mouse embryonic fibroblasts

tag: strain

value: C57BL/6J x SPRET/EiJ F1 hybrid

tag: genotype

value: 90m stimulation with 15% CCS MEF media

tag: passage

tag: chip antibody

tag: experiment

value: ChIP-seq


title: B6xSPRET-JunD-0m-B1

value: starved with 0.5% CCS MEF media

value: Santa Cruz sc-74


title: B6xSPRET-JunD-90m-B1


title: B6xSPRET-Tead1-90m-B2

value: Abcam ab133535


title: B6xSPRET-input-B3


title: RNA-WT_cmk-rep1

description:
TT-Seq
WT-CMK-1_TAGCTT

tag: genotype/variation

value: CMK


title: B6xSPRET-Tead1-90m-B1


title: B6xSPRET-input-B2


title: B6xSPRET-H3K4me3-90m-B2

value: Abcam ab8580


title: B6xSPRET-Tead1-0m-B2


title: B6xSPRET-Tead1-0m-B1


title: B6xSPRET-H3K4me3-0m-B2


title: B6xSPRET-JunD-0m-B2


title: B6xSPRET-H3K4me3-90m-B1


title: B6xSPRET-H3K4me2-cycling-B3

value: Abcam ab7766


title: B6xSPRET-H3K4me3-0m-B1


title: B6xSPRET-H3K4me2-cycling-B2


title: B6xSPRET-H3K4me2-cycling-B1


title: B6xSPRET-H3K4me1-90m-B2

value: Abcam ab8895


title: treatment rep2

description:
CountMatrix.csv
DiffExpr.csv

value: Phaseolus vulgaris


title: B6xSPRET-H3K4me1-90m-B1


title: B6xSPRET-H3K4me1-0m-B2


title: B6xSPRET-H3K27ac-90m-B4

value: Abcam ab4729


title: B6xSPRET-H3K27ac-90m-B1


title: B6xSPRET-H3K27ac-10m-B3

value: 10m stimulation with 15% CCS MEF media


title: B6xSPRET-JunD-90m-B2

value: wild-type


title: B6xSPRET-H3K27ac-10m-B1


title: B6xSPRET-Fos-90m-B2

value: Santa Cruz sc-7202X


title: B6xSPRET-H3K27ac-10m-B2


title: B6xPWK-Tead1-0m-B2

value: C57BL/6J x PWK/PhJ F1 hybrid


title: B6xSPRET-CTCF-cycling-B1

value: Primary mouse embryonic fibroblasts

value: Active Motif 61312


title: B6xPWK-input-B1

value: 90m stimulation with 15% CCS MEF media


title: B6xPWK-input-B2

value: ChIP-seq


title: B6xSPRET-CTCF-cycling-B2

value: C57BL/6J x SPRET/EiJ F1 hybrid


title: B6xPWK-input-B4


title: B6xSPRET-H3K27ac-0m-B3

value: starved with 0.5% CCS MEF media


title: B6xPWK-input-B3


title: B6xSPRET-H3K27ac-0m-B2


title: B6xPWK-Tead1-90m-B1

value: Abcam ab133535


title: B6xSPRET-H3K27ac-0m-B4


title: B6xPWK-Tead1-90m-B2


title: B6xSPRET-Fos-0m-B1


title: B6xPWK-H3K4me3-0m-B2


title: B6xPWK-H3K4me3-0m-B1


title: B6xPWK-H3K4me2-cycling-B2


title: B6xPWK-H3K4me3-90m-B2


title: B6xPWK-Tead1-0m-B1


title: B6xSPRET-H3K4me1-0m-B1


title: B6xPWK-H3K4me1-0m-B2


title: B6xPWK-H3K4me1-0m-B1


title: B6xPWK-H3K4me3-90m-B1


title: B6xSPRET-H3K27ac-90m-B3


title: B6xPWK-H3K27ac-90m-B2


title: B6xPWK-H3K27ac-90m-B3


title: B6xPWK-H3K27ac-90m-B1


title: B6xPWK-H3K27ac-10m-B2


title: B6xPWK-H3K27ac-10m-B1


title: B6xPWK-H3K27ac-0m-B3


title: B6xPWK-H3K27ac-0m-B2


title: B6xMOLF-H3K4me3-0m-B2

value: C57BL/6J x MOLF/EiJ F1 hybrid


title: B6xMOLF-H3K4me3-90m-B1

value: Abcam ab8580


title: B6xMOLF-Tead1-0m-B1


title: B6xMOLF-input-B1


title: B6xMOLF-H3K4me3-90m-B2


title: B6xMOLF-input-B2


title: B6xMOLF-Tead1-90m-B1


title: B6xMOLF-H3K4me1-90m-B1


title: B6xMOLF-H3K4me2-cycling-B2

value: Abcam ab7766


title: B6xMOLF-Tead1-90m-B2


title: B6xPWK-H3K4me2-cycling-B1


title: B6xMOLF-H3K4me1-0m-B2

value: Abcam ab8895


title: B6xMOLF-H3K4me1-90m-B2


title: B6xPWK-H3K4me1-90m-B2


title: B6xPWK-H3K27ac-0m-B1


title: B6xMOLF-H3K27ac-90m-B2


title: B6xMOLF-Tead1-0m-B2


title: B6xPWK-Fos-90m-B1


title: B6xMOLF-H3K4me2-cycling-B1


title: B6xMOLF-H3K27ac-90m-B1


title: B6xMOLF-H3K27ac-0m-B2


title: B6xMOLF-H3K27ac-10m-B1


title: B6xMOLF-H3K27ac-0m-B1


title: B6xMOLF-Fos-90m-B2


title: B6xPWK-CTCF-cycling-B2


title: B6xPWK-Fos-90m-B2


title: B6xMOLF-CTCF-cycling-B1


title: B6xMOLF-Fos-90m-B1


title: B6xCAST-Tead1-90m-B2

value: C57BL/6J x CAST/EiJ F1 hybrid


title: B6xCAST-Tead1-90m-B1


title: B6xCAST-Tead1-0m-B1


title: B6xCAST-input-B2


title: B6xMOLF-CTCF-cycling-B2


title: B6xMOLF-H3K4me1-0m-B1


title: B6xCAST-H3K4me3-90m-B1


title: B6xCAST-input-B1


title: B6xCAST-H3K4me3-0m-B2


title: B6xCAST-H3K27ac-90m-B1

value: Abcam ab4729


title: B6xCAST-H3K27ac-90m-B2


title: B6xCAST-H3K4me1-0m-B2


title: B6xCAST-Tead1-0m-B2


title: B6xCAST-H3K27ac-0m-B2


title: B6xCAST-H3K4me2-cycling-B2


title: B6xCAST-H3K27ac-10m-B1

value: 10m stimulation with 15% CCS MEF media


title: B6xCAST-H3K4me1-90m-B1

value: wild-type


title: B6xCAST-H3K4me3-0m-B1


title: B6xCAST-H3K27ac-0m-B1


title: B6xCAST-H3K4me3-90m-B2


title: B6xCAST-H3K4me1-0m-B1


title: B6xCAST-Fos-90m-B2

value: Santa Cruz sc-7202X


title: B6xCAST-Fos-90m-B1


title: B6xCAST-CTCF-cycling-B1


title: B6xCAST-H3K4me2-cycling-B1


title: KPN flox Primary Tumour Rep 3

city: Glasgow

first: Andrew

last: Campbell

address: Switchback Road

country: United Kingdom

institute: CRUK Beatson Institute

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Genome_build: GRCm38.98
Supplementary_files_format_and_content: Matrix of raw counts

source_name: Small Intestine

growth_protocol: Grown in full growth ADF media supplemented with Noggin and EGF.

extract_protocol:
Piece of intestine or tumour tissue was collected and dissociated using Precyllis homogeniser in b-ME in RLT buffer. RNA was extracted using Qiagen RNA extraction kit following manufacturer's instructions.
Libraries for cluster generation and DNA sequencing were prepared following a previously described method (Fisher et al. 2011) using TruSeq RNA sample prep kit v2 (Illumina)
The libraries were run on Illumina Next Seq using the High Output 75 cycles kit (2x36 cycles, paired end reads, single index)

value: Small Intestine

tag: genetic background

value: VilCreER KrasG12D/fl p53fl/fl Notch1Tg/+

tag: sample type

value: Primary Tumour


title: KPN Primary Tumour Rep 4

value: VilCreER KrasG12D/+ p53fl/fl Notch1Tg/+


title: KPN Primary Tumour Rep 3


title: KPN flox Primary Tumour Rep 1


title: KPN flox Tumour Organoid Rep 1

value: Organoid from Primary Tumour


title: B6xCAST-H3K27ac-10m-B2

value: Primary mouse embryonic fibroblasts

value: ChIP-seq


title: KPN flox Primary Tumour Rep 4


title: KPN flox Primary Tumour Rep 2


title: KPN flox Tumour Organoid Rep 3


title: KPN Tumour Organoid Rep 4


title: B6xCAST-H3K4me1-90m-B2

value: 90m stimulation with 15% CCS MEF media


title: Kras flox Adjacent Normal Mouse B Rep 2

value: VilCreER KrasG12D/fl

value: Adjacent Normal


title: KPN flox Tumour Organoid Rep 2


title: KPN Tumour Organoid Rep 2


title: Kras flox Adjacent Normal Mouse B Rep 3


title: KPN Tumour Organoid Rep 3


title: Kras flox Adjacent Normal Mouse A Rep 2


title: Kras flox Tumour Mouse A Rep 2


title: Kras flox Tumour Mouse B Rep 3


title: Kras flox Tumour Mouse B Rep 1


title: Kras flox Tumour Mouse B Rep 2


title: KPN Tumour Organoid Rep 1


title: Kras flox Tumour Mouse A Rep 1


title: Kras flox Adjacent Normal Mouse A Rep 1


title: SPRET-ATAC-90m-B2

extract_protocol:
MEFs from 6-well dish were washed twice in 1 mL cold PBS and pelleted each time by spinning at 300 g for 5 min at 4oC. 50,000 MEFs were resuspended in 50 uL cold ATAC lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40 0.1% Tween 20, 0.01% digitonin) and incubated for 3 min on ice.  Lysed cells were washed once in 1 mL ATAC wash buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20) by gently inverting the tube 3 times and pelleted by spinning at 500 g for 10 min at 4oC.
Pelleted nuclei were resuspended in 50 uL transposition mix (25 uL 2x TD Buffer (Illumina (San Diego, CA, USA) 20034197), 2.5 uL TDE1 transposase (Illumina 20034197), 0.5 uL 10% Tween 20, 0.5% 1% digitonin, 16.5 uL PBS, 5 uL NF-H2O) and incubated for 30 min at 37oC with a Thermomixer set to 1,000 rpm. Samples were purified with MinElute PCR Purification Kit (QIAGEN 28004) per manufacturer’s instructions and eluted in 13 uL NF-H2O. Libraries were amplified by adding the following to 10 uL purified DNA: 2.5 uL 25 uM Ad1 universal primer, 2.5 uL 25 uM Ad2.* indexing primer, 25 uL NEBNext Hi-Fi 2x PCR Master Mix (NEB (Ipswich, MA, USA) M0541S), 10 uL NF-H2O. After an initial 5 PCR cycles, libraries were quantified by qPCR by adding the following to 5 uL partially amplified DNA: 0.5 uL 25 uM Ad1 universal primer, 0.5 uL 25 uM Ad2.* indexing primer, 5 uL NEBNext Hi-Fi 2x PCR Master Mix, 0.15 uL 1x SYBR Green I (Thermo Fisher S7563), 3.85 uL NF-H2O. All primer sequences referenced are described in Buenrostro et al., 2015. The number of additional PCR cycles required for amplifying remaining libraries was determined by number of qPCR cycles needed to reach 1/3 of the maximum SYBR green signal. Libraries were purified with AMPure XP beads (0.5x volume; Beckman Coulter (Indianapolis, IN, USA) A63881) and the supernatant was retained to remove large fragments. Primer dimers were removed by a subsequent cleanup with AMPure XP beads (1.3x initial volume) and libraries were eluted in 20 uL NF-H2O. Libraries were sequenced on an Illumina NextSeq 500 with 40 bp paired-end reads.

value: SPRET/EiJ

value: ATAC-seq


title: KPN Primary Tumour Rep 1


title: KPN Primary Tumour Rep 2


title: SPRET-ATAC-90m-B1


title: SPRET-ATAC-10m-B2


title: SPRET-ATAC-0m-B2

value: starved with 0.5% CCS MEF media


title: Kras flox Adjacent Normal Mouse B Rep 1


title: PWK-ATAC-90m-B2

value: PWK/PhJ


title: PWK-ATAC-0m-B1


title: PWK-ATAC-10m-B1

value: 10m stimulation with 15% CCS MEF media


title: PWK-ATAC-0m-B2

value: wild-type


title: PWK-ATAC-10m-B2


title: B6xMOLF-ATAC-90m-B1

value: C57BL/6J x MOLF/EiJ F1 hybrid


title: Russula_sir3-8-EcoGII_90min

city: Berkeley

first: Molly

last: Brothers

address: UC Berkeley 440 Barker Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

description: mat∆::KanMX, sir3-8-M.ECOGII-NatMX

data_processing:
Reads were basecalled and demultiplexed using guppy and guppy_barcoder. Read IDs were extracted using a custom python script and used to demultiplex fast5 files.
Reads were basecalled (including modified bases) and aligned to the SacCer3 genome (modified to include mat∆) using Megalodon and the all-context model (https://github.com/nanoporetech/rerio, res_dna_r941_min_modbases-all-context_v001.cfg) with the options --mod-motif “Y A 0”, --files_out “basecalls mod_mappings per_read_mods” and --read-ids-filename “barcodeXX_readIDs.txt” (the file that contained the extracted list of readIDs for a given barcode).
Data from the .db file were aggregated using Megalodon "megalodon_extras aggregate run".
Genome_build: SacCer3 (modified)
Supplementary_files_format_and_content: All experiments include a .bed file (bedMethyl format) aggregated using Megalodon (https://github.com/nanoporetech/megalodon "megalodon_extras aggregate run"). Experiments where single reads were analyzed include a .db file (SQLite database) generated using Megalodon. These .db files can be converted to .txt files using Megalodon "megalodon_extras per_read_text modified_bases".

organism: Saccharomyces cerevisiae

growth_protocol: Yeast were cultured at 30°C in YPD unless otherwise noted under "conditions" for each experiment/sample.

extract_protocol:
DNA was extracted using the Zymo YeaStar genomic DNA Kit (Genesee Scientific, Cat #11-323). DNA was sheared to 15-25kb using a Covaris gTUBE and then concentrated and purified using 1X v/v SPRI Select beads (Beckman-Coulter B23317).
Oxford Nanopore Ligation Sequencing Kit (SQK-LSK109) with Native Barcode Expansion (EXP-NBD104).

tag: condition

value: 90min after temperature switch from 37C to 25C; YPD


title: B6xMOLF-ATAC-90m-B2


title: B6xMOLF-ATAC-10m-B1


title: Russula_sir3-8-EcoGII_60min

description: mat∆::KanMX, sir3-8-M.ECOGII-NatMX

value: 60min after temperature switch from 37C to 25C; YPD


title: B6xMOLF-ATAC-10m-B2


title: CAST-ATAC-90m-B2

value: CAST/EiJ


title: B6xMOLF-ATAC-0m-B1


title: B6xMOLF-ATAC-0m-B2


title: Russula_sir3-8-EcoGII_15min

description: mat∆::KanMX, sir3-8-M.ECOGII-NatMX

value: 15min after temperature switch from 37C to 25C; YPD


title: CAST-ATAC-10m-B2


title: Russula_sir3-8-EcoGII_30min

description: mat∆::KanMX, sir3-8-M.ECOGII-NatMX

value: 30min after temperature switch from 37C to 25C; YPD


title: Russula_sir3-8-EcoGII_45min

description: mat∆::KanMX, sir3-8-M.ECOGII-NatMX

value: 45min after temperature switch from 37C to 25C; YPD


title: Russula_sir3-8-EcoGII_0min

description: mat∆::KanMX, sir3-8-M.ECOGII-NatMX

value: 0min after temperature switch from 37C to 25C; YPD


title: CAST-ATAC-90m-B1

value: Primary mouse embryonic fibroblasts

value: 90m stimulation with 15% CCS MEF media


title: CAST-ATAC-10m-B1


title: Amanita_sir3-8-EcoGII_90min

description: mat∆::KanMX, sir3-8-M.ECOGII-NatMX


title: Amanita_sir3-8-EcoGII_60min

description: mat∆::KanMX, sir3-8-M.ECOGII-NatMX


title: CAST-ATAC-0m-B2


title: SPRET-ATAC-10m-B1


title: SPRET-ATAC-0m-B1


title: PWK-ATAC-90m-B1


title: CAST-ATAC-0m-B1


title: Amanita_sir3-8-EcoGII_45min

description: mat∆::KanMX, sir3-8-M.ECOGII-NatMX


title: Amanita_sir3-8-EcoGII_30min

description: mat∆::KanMX, sir3-8-M.ECOGII-NatMX


title: B6xNOD-ATAC-90m-B3

value: C57BL/6J x NOD/ShiLtJ F1 hybrid


title: B6xNOD-ATAC-90m-B2


title: Ocular_sir3-8-EcoGII_37C

description: mat∆::KanMX, sir3-8-M.ECOGII-NatMX

value: Cycling in YPD at 37C


title: Amanita_sir3-8-EcoGII_15min

description: mat∆::KanMX, sir3-8-M.ECOGII-NatMX


title: B6xNOD-ATAC-90m-B1

value: ATAC-seq


title: Ocular_sir3-8-EcoGII_25C

description: mat∆::KanMX, sir3-8-M.ECOGII-NatMX

value: Cycling in YPD at 25C


title: B6xNOD-ATAC-0m-B1

value: starved with 0.5% CCS MEF media


title: B6xDBA-ATAC-90m-B3

value: C57BL/6J x DBA/2J F1 hybrid


title: Amanita_sir3-8-EcoGII_0min

description: mat∆::KanMX, sir3-8-M.ECOGII-NatMX


title: B6xDBA-ATAC-90m-B2

value: wild-type


title: TakeFive_SIR3-EcoGII_overexpression

description: mat∆::K.l.LEU2, SIR3-M.ECOGII-NatMX, [pJR3526: SIR3-M.ECOGII URA3 2micron]

value: Cycling in CSM-Ura

value: mat<delta>::K.l.LEU2, SIR3-M.ECOGII-NatMX, [pJR3526:SIR3-M.ECOGII URA3 2micron]


title: TakeFive_empty-vector

description: mat∆::K.l.LEU2, SIR3-M.ECOGII-NatMX, [pJR42: URA3 2micron]

value: mat<delta>::K.l.LEU2, SIR3-M.ECOGII-NatMX, [pJR42:URA3 2micron]


title: B6xDBA-ATAC-90m-B1


title: Bonus_SIR3-EcoGII_overexpression


title: B6xDBA-ATAC-0m-B3


title: B6xDBA-ATAC-0m-B2


title: B6xDBA-ATAC-0m-B1


title: Ashby_sir3-bahD-EcoGII

description: mat∆::KanMX, sir3-bah∆-M.ECOGII-NatMX

value: Cycling in YPD


title: B6xBALB-ATAC-90m-B3

value: C57BL/6J x BALB/cJ F1 hybrid


title: B6xBALB-ATAC-90m-B2


title: Ashby_SIR3-EcoGII

description: mat∆::K.l.LEU2, SIR3-M.ECOGII-NatMX


title: B6xBALB-ATAC-90m-B1


title: Doudna_SIR3-EcoGII

description: mat∆::HphMX, SIR3-M.ECOGII-NatMX

value: mat<delta>::HphMX, SIR3-M.ECOGII-NatMX


title: Fireworks_sir3D-EcoGII

description: mat∆::HphMX, sir3∆::M.ECOGII-NatMX


title: B6xBALB-ATAC-0m-B1


title: B6xBALB-ATAC-0m-B3


title: B6xBALB-ATAC-0m-B2


title: Fireworks_sir3-bahD-EcoGII

description: mat∆::KanMX, sir3-bah∆-M.ECOGII-NatMX


title: Fireworks_SIR3-EcoGII

description: mat∆::HphMX, SIR3-M.ECOGII-NatMX


title: B6xAJ-ATAC-90m-B1

value: C57BL/6J x A/J F1 hybrid


title: Turkey_sir3D-EcoGII

description: mat∆::K.l.LEU2, sir3∆::M.ECOGII-NatMX


title: B6xAJ-ATAC-90m-B2


title: B6xAJ-ATAC-90m-B3


title: B6xAJ-ATAC-0m-B3


title: Gorgonzola_SIR2-EcoGII

description: mat∆::hygMX, SIR2-M.ECOGII-NatMX

value: mat<delta>::hygMX, SIR2-M.ECOGII-NatMX


title: B6xAJ-ATAC-0m-B2

value: Primary mouse embryonic fibroblasts


title: Bonus_empty-vector


title: B6x129-ATAC-90m-B2

value: C57BL/6J x 129S1/SvImJ F1 hybrid

value: 90m stimulation with 15% CCS MEF media


title: Turkey_SIR3-EcoGII

description: mat∆::HphMX, SIR3-M.ECOGII-NatMX


title: B6x129-ATAC-90m-B1