title: Control 1706

description:
H9_1706_35d_ctrl
salmon-TPM-day35-all-samples.csv

data_processing:
[Bulk RNA-seq]
FASTQ sequence read files were aligned to the hg38 transcriptome (with decoy sequences) and quantified using salmon v0.14.1 applying both a sequence bias correction and a GC bias correction with a mean fragment length of 300 bp and a standard deviation of 50 bp.
Salmon quantification files containing Transcripts Per Million (TPM) estimates were imported into R using tximport v1.16.1 and DESeq2 v1.28.
Prior to analysis, a non-parametric empirical Bayesian batch-correction was applied to the data using the function ‘ComBat’ in sva v3.36.0.
[Single-cell RNA-seq]
Raw sequencing output was converted to the standard fastq format by bcl2fastq, before running through CellRanger Count (version 3.1.0, 10X Genomics) which also performed read alignment using STAR with GRCh38 human reference genome.
The filtered feature barcode matrix for each sample was then analysed further with the Seurat v3 R package by first merging the matrices, followed by removal of cells with mitochondrial percentage >10%, and removal of likely doublets based on nCount_RNA, resulting in a total dataset of 6,899 cells.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: For bulk RNA-seq: Matrix file output (.txt file) from DESeq2.
Supplementary_files_format_and_content: For single-cell RNA-seq: Expression matrix (.txt file) for RNA assay of the processed Seurat object.

tag: tissue

tag: treatment

value: Control


title: Tnfr2-/-_CD4+ T

status: Public on Nov 06 2021

type: SRA

city: Bethesda

first: Jonathan

middle: D

last: Ashwell

state: MD

address: Room 3002, Bldg. 37, 9000 Rockville Pike

department: Laboratory of Immune Cell Development

country: USA

institute: NIH

library_source: transcriptomic

data_processing:
FASTQ demultiplexing with CellRanger v3.1.0
Read alignment and single cell data parsing with CellRanger v3.1.0
Genome_build: mm10 (refdata-cellranger-mm10-3.0.0)
Supplementary_files_format_and_content: 10x Genomics filtered h5 files

molecule: total RNA

organism: Mus musculus

source_name: CNS infiltrated CD4+ T cells

growth_protocol: WT or Tnfr2-/- mice were immunized with MOG(35-55) peptide and CD4+ T cells were isolated at day 15 from the CNS of WT and Tnfr2-/- mice followed by single cell RNA sequencing by 10X genomics.

extract_protocol:
CNS infiltrated CD4+ T cells were purified by flow cytometry sorting and performed single cell sequencing.
10x Genomics Chromium Single Cell 3' v3

treatment_protocol: Mice were immunized with MOG emulsion (Hookie kit, Cat#EK-2160) subcutaneously 0.1 ml each in both upper and lower back. 3 hrs after immunization pertussis toxin was injected intraperitoneally.

tag: cell type

value: CD4+ T cells isolated from spinal cord

tag: strain

tag: genotype


title: IMCD negreplete

city: St. Louis

first: Leslie

middle: Stuart

last: Gewin

state: MO

address: 660 S Euclid Ave, McDonnell Science Building, Rm 718

department: Medicine (Nephrology)

institute: Washington University in St. Louis

data_processing:
RNAseq raw reads were aligned against MM10 reference using TOPHAT2 followed by gene quantification into FPKM using Cufflinks. .
Differential expression analyses were performed using cuffdiff from Cufflink packages.
p values were adjusted using Benjamini-Hochberg method.
Supplementary_files_format_and_content: Processed data are comparisons between different samples in Excel files

source_name: IMCD (inner medullary collecting duct) cells

growth_protocol: IMCD cells immortalized with psv40 as detailed and characterized in JASN manuscript, PMID 20576806

extract_protocol:
RNA isolation performed with Qiagen Rneasy Kit plus DNAse step
performed by Vanderbilt VANTAGE Core
RNAseq with Hiseq 2500 with 50 bp, 30 million reads

treatment_protocol: Cells were either kept in serum containing media or serum starved prior to isolation

value: C57B/l mice with Tgfbr2 floxed

tag: cre treatment

value: Untreated

tag: tgfbr2 expression

tag: media conditions

value: Serum replete


title: SF3B1_mutant-2

city: NewYork

first: Zhaoqi

last: Liu

state: New York

address: ICRC Building 8th Floor, Office 803B 1130 St. Nicholas Ave

department: Systems Biology

institute: Columbia university

description:
SY064_CAGATC
60 million paired-end reads performed at Columbia University Genome Center

data_processing:
Raw data were aligned to hg19 using the STAR alignment package
Unique junction counts as determined by STAR are output to a tabular file
Genome_build: hg19 for human samples
Supplementary_files_format_and_content: Raw junction counts for each sample as output by STAR

molecule: polyA RNA

organism: Homo sapiens

extract_protocol: NOT PROVIDED; REQUESTED

tag: cell line

value: SF3B1 K700E


title: NN-Veh-02

type: RNA

city: Hamamatsu city

first: Misako

last: SUZUKI

state: Shizuoka, Japan

address: Higashi-ku 1-20-1 Handayama

country: Japan

institute: Hamamatsu University School of Medicine.

description: Gene expression data from adipose tisssue

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChipTM Hybridization Oven 645(Thermo Fisher Scientific,Inc.). GeneChips were washed and stained in the GeneChipTM Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChipTM Scanner 3000 7G(Thermo Fisher Scientific, Inc.)

data_processing: The data were analyzed with Transcriptome Analysis Console(TAC)software version 4.0 using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: mouse adipose tissue of group NN-Veh

label_protocol: Fragmented and Labeled cRNA were prepared according to the GeneChipTM WT PLUS Reagent Kit User Manual(Thermo Fisher Scientific,Inc.)

growth_protocol: Pregnant C57Bl/6 mice were divided into two groups(NN: fed ad libitum with regular chow, UN:restricted to 60% of the energies). In UN dams, the number of pups was adjysted to 4 per litter for the purpose of inducing rapid infantile growth(RG) during lactation period. After weaning, HFD was supplied to all pups from 9 to 17 wks.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: TUDCA  or Vehicle was orally administered between 11 and 16.5 wks.

value: adipose tissue

tag: maternal diet

value: fed ad libitum with regular chow

value: vehicle

tag: Sex

value: male


title: IMCD crex5replete

value: Treated with adeno-Cre

value: IMCD (inner medullary collecting duct) cells


title: NN-Veh-01


title: NN-TUDCA-05

source_name: mouse adipose tissue of group NN-RG-TU

value: TUDCA


title: HM7_iron_replete_rep3

city: Ann Arbor

first: Arwen

last: Frick-Cheng

state: Michigan

address: 1150 W. Medical Center Dr.

department: Microbiology and Immunology

institute: University of Michigan Medical School

data_processing:
Raw sequencing data was preprocessed using BBTools (38.18)
BBDuk was used to remove Illumina adapter sequences, and to quality trim and filter the reads (minlength=20, trimq=14, maq=20, maxns=1)
reads were aligned to the HM7 genome using BWA
The resulting alignment files were filtered (mapping quality > 10) using samtools (1.11)
counts for each feature were generated using htseq-count (0.13.5)
Genome_build: SRR16639093, FASTA and GFF inlcuded on the series record.
Supplementary_files_format_and_content: normalized abundance files are normalized vst counts generated from DEseq2 analysis along with accompanying p values, adjusted pvalues, and fold change values.  Files are comma delimited. There is also the FASTA file of genome HM7 as well as the accompanying annotation file (.gff)

organism: Escherichia coli

source_name: uropathogenic e coli

growth_protocol: E. coli HM7 was cultured overnight in M9 medium, supplemented with 0.4% glucose, shaking at 37°C. Overnight cultures were diluted 1:100 in M9 medium with 0.4% glucose supplemented with either 36 μM FeCl3 (Sigma), or 150 μM 2,2’ Dipyridyl (Sigma) and grown to mid-log phase (0.4-0.6 OD600).

extract_protocol:
bacterial pellets were treated with lysozyme (Sigma, final concertation: 1 mg/mL) and proteinaseK (Qiagen, final concertation: 1.81 μg/mL) in RNAse-free Tris-EDTA buffer (Corning), for five minutes with continual vortexing. Total RNA was extracted using RNeasy mini kit (Qiagen). Genomic DNA was removed with Turbo DNA-free kit (Invitrogen). Bacterial rRNA was removed with the RiboMinus Transcriptome Isolation Kit, Bacteria (Invitrogen).
rRNA was depleted using ThermoFisher's Ribominus Bacteria 2.0 Transcriptome Isolation kit. Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit as per manufacter's instructions

treatment_protocol: Cultures were treated with Bacterial RNA Protect (Qiagen), harvested by centrifugation and the pellets stored at -80°C.

tag: growth medium

value: minimal m9 medium + 0.4% glucose+36 uM FeCl3


title: HM7_iron_limited_rep3

value: minimal m9 medium + 0.4% glucose+150 uM 2,2'-dipyridyl


title: HM7_iron_limited_rep1


title: HM7_iron_replete_rep1


title: HM7_iron_replete_rep2


title: HM7_iron_limited_rep2


title: NN-Veh-03


title: IMCD crex5deprived

value: Serum deplete for 4 days


title: ATACseq_CXCR6_4

status: Public on Nov 05 2021

city: Boston

first: Linglin

last: Huang

state: MA

address: 60 Fenwood Road, HBTM 10016F

department: Neurology

institute: Brigham and Women’s Hospital

library_source: genomic

data_processing:
Base-calling was performed by RTA v2.4.11, and the BCL files were translated to fastqs using bcl2fastq2 v2.20.0.
RNA-seq: Paired reads were mapped to mouse annotation mm10 using HISAT2, and sequencing depth normalized TPM values were computed using RSEM with default parameters for each lane. TPM values from lanes for the sample were summed up. Data for samples in the same experiment were then column combined into a matrix (samples with low quality were excluded, see Method Details section in paper).
ATAC-seq: Reads were aligned to reference mouse annotation mm10 using Bowtie2, and filtered for duplicated and mitochondrial reads. Peak-calling was performed using MACS2. Read counts per peak were computed using bedtools multicov tool for each sample and then column combined into a matrix.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: comma-separated values (CSV) files include TPM values for each gene in each sample.
Supplementary_files_format_and_content: ATAC-seq: tab-delimited text file include read counts per peak values for each peak in each sample.

molecule: genomic DNA

source_name: Il17CreTdtomato+ cells from spleen

growth_protocol: To generate conditional IL-23 receptor knockout mice (named Il23rfl/fl) we took advantage of a recently established ES cell resource. ES cell clone EPD0812_2_C11 with a targeted IL-23 receptor allele (containing a neomycin selectable marker flanked by frt sites) with conditional potential was acquired from EuMMCR (European Mouse Mutant Cell Repository; www.eummcr.org) within EUCOMM (European Conditional Mouse Mutagenesis Program). This ES cell clone was used for blastocyst injections. Faithful targeting of the IL-23 receptor allele was confirmed in the ES clone prior to blastocyst injections by Southern blot analysis. Chimeric mice were bred to C57Bl/6 mice and offspring screened for germline transmission by PCR for the neomycin selectable marker cassette. Offspring harboring the targeted IL-23 receptor neo+ allele were then bred to Flpo deleter mice. Offspring carrying the final conditional IL-23 receptor allele (2lox) were bred to C57Bl/6 to remove the Flpo transgene. The IL-23 receptor conditional allele was bred to homozygosity and then to various Cre strains to obtain tissue/cell-type specific deletion of IL-23 receptor. The primers TCCAGAGACGCCTGTACTCA and CACCAAGCTTTTCTCCTCCTC are used for routine genotyping (wt=414bp and 2lox=577bp). For experiments, mice were sex- and age- matched  and littermates were used as controls. Mice were housed under specific-pathogen-free conditions (SPF) at the Brigham and Women’s Hospital mouse facility in Boston. Tissue Th17 cells were collected when mice were 8-12 weeks old.

extract_protocol:
To harvest tissues, mice were perfused intracardially with cold PBS. Spleen was harvested and smashed through 40 um sterile strainers. ACK lysis (Buffer from Lonza) was performed with the spleen for 5 min at RT. For bulk RNA-seq, 1,000 living cells were sorted by FACS and immediately lysed in TCL buffer (QIAGEN) supplemented with 1% ß-mercaptoethanol (Sigma Aldrich). For bulk ATAC-seq, 6,000 living cells were sorted by FACS and stored at -80°C in BambankerTM cell freezing medium (LYMPHOTEC Inc.).
For bulk RNA-seq, full-length RNA-seq libraries were prepared following a modified SMART-Seq2 protocol as previously described. The cDNA concentration was measured using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific) and normalized to 0.25ng/ul. The cDNA libraries were prepared using the Nextera XT DNA Library Preparation kit (Illumina). Final libraries were confirmed to have a size of 500 bp using a Bioanalyzer (Agilent). Prior to sequencing, the uniquely barcoded libraries were pooled, normalized to 2 nM, and denatured using 0.1 N NaOH. Flow cell cluster amplification and sequencing were performed according to the manufacturer’s protocols using the paired-end Illumina sequencing (38bp X 2) with 75 cycle Nextseq 500 high output V2 kit (Illumina).  For bulk ATAC-seq, cells were thawed at 37°C. Subsequently, cells were lysed and tagmented in 1X TD Buffer, 0.2l TDE1 (Illumina), 0.01% digitonin, and 0.3X PBS at 37°C for 30 min at 300 rpm, as previously described [86]. DNA purification was performed with the MinElute PCR purification kit (QIAGEN). The complete eluate was pre-amplified with 5 PCR cycles using indexed primers with NEBNext High-Fidelity 2X PCR Master Mix (NEB) and the number of additional cycles was determined by SYBR Green quantitative PCR. After DNA purification, library quantification and quality control were performed with the Kapa Library Quantification Kit (Kapa Biosystems) and a Qubit dsDNA HS Assay kit (Invitrogen). Libraries were sequenced on an Illumina NextSeq 550 system with paired-end reads of 37 base pairs in length.

treatment_protocol: For active induction of EAE, mice were immunized subcutaneously in the flanks with the myelin oligodendrocyte glycoprotein (MOG) peptide MOG35-55 (100 g/mouse, Genemed Synthesis), emulsified in complete Freund’s adjuvant (CFA) (200 l/mouse, Becton Dickinson), and supplemented with Mycobacterium tuberculosis H37Ra extract (5 mg/ml, Becton Dickinson). Pertussis toxin (100 ng/mouse, List Biological Laboratories) was administered intravenously into the tail vein on day 0 and day 2 post immunization.  Disease course was monitored daily, and mice were assigned a clinical score as follows: 0, healthy; 1, limp tail; 2, hind limb weakness or impaired righting reflex; 3, hind limb paralysis; 4, hind and front limb paralysis; 5, moribund or dead. Mice with a clinical score >4 were euthanized.

value: spleen

tag: disease state

value: EAE


title: ATACseq_CXCR6_5


title: ATACseq_CXCR6_3


title: ATACseq_CXCR6_1


title: ATACseq_SLAMF6_5


title: ATACseq_CXCR6_2


title: ATACseq_SLAMF6_4


title: ATACseq_SLAMF6_3


title: RNAseq_SLAMF6_Il23rKO_4

value: Il17aCre Il23rfl/fl


title: RNAseq_SLAMF6_Il23rKO_3


title: ATACseq_SLAMF6_1


title: RNAseq_SLAMF6_Il23rKO_2


title: RNAseq_CXCR6_Il23rKO_1


title: RNAseq_CXCR6_Il23rKO_2


title: RNAseq_SLAMF6_Il23rKO_1


title: RNAseq_SLAMF6_WT_4

value: Il17aCre Il23rWT


title: RNAseq_CXCR6_WT_3


title: RNAseq_CXCR6_WT_4


title: RNAseq_CXCR6_WT_1


title: RNAseq_CXCR6_3


title: RNAseq_CXCR6_4


title: RNAseq_SLAMF6_WT_3


title: RNAseq_CXCR6_WT_2


title: RNAseq_CXCR6_2


title: RNAseq_SLAMF6_WT_2


title: RNAseq_CXCR6_1


title: ATACseq_SLAMF6_2


title: RNAseq_SLAMF6_4


title: RNAseq_SLAMF6_3


title: RNAseq_CXCR6_Il23rKO_4


title: RNAseq_CXCR6_Il23rKO_3


title: RNAseq_SLAMF6_2


title: RNAseq_SLAMF6_1


title: SCZ_NeuN-_input

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

data_processing:
Sequencing reads were trimmed by trim galore v0.6.5 with default parameters. Trimmed ChIP-seq reads were mapped to the hg38 genome with bowtie2 v2.4.1. Peaks were called using MACS2 v2.2.7.1 (q < 0.05). Mapped reads from ChIP and input samples were extended by 100 bp on either side (250 bp total) and a normalized signal was calculated. For visualization in IGV v2.8.12 (Broad Institute), the signal was calculated in 100bp windows over the entire genome and output as a bigWig file.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files are converted by wigToBigWig. Raw counts of sequencing reads were generated by featureCounts.

source_name: glial nuclei from Brodmann area 9 (BA9) of postmortem brain tissue

extract_protocol:
Nuclei extraction: All steps were conducted on ice, and all centrifugation was conducted at 4 °C. One piece of frozen tissues (never fixed) of postmortem prefrontal cortex (PFC) Brodnabb Area 9 (BA9) (~20 mg) was placed in 3 ml of ice-cold nuclei extraction buffer (NEB) [0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM tris-HCl, and 0.1%(v/v) Trition X-100] with freshly added 30 µl of protease inhibitor cocktail (PIC, Sigma-Aldrich), 3 µl of 100 mM phenylmethylsulfonyl fluoride (PMSF, Sigma-Aldrich) in Isopropyl alcohol, 3 µl of 1 M dithiothreitol (DTT, Sigma-Aldrich), and 4.5 µl of ribonuclease (RNase) inhibitor (2313A,Takara Bio). The tissue was homogenized in tissue grinder (D9063, Sigma-Aldrich). The homogenate was filtered with a 40 µm cell strainer (22-363-547, Thermo Fisher Scientific) and collected in a 15-ml centrifuge tube. The cell suspension was centrifuged at 1000 RCF for 10 min. The supernatant was discarded, and the pellet was resuspended in 0.5 ml of ice-cold NEB with freshly added 5 µl of PIC, 0.5 µl of PMSF, 0.5 µl of DTT, and 0.75 µl of RNase inhibitor. 500 µl of the sample was mixed with 750 µl of 50%(w/v) iodixanol (made by mixing 4 ml of OptiPrepTM gradient (Sigma-Aldrich) and 0.8 ml of diluent [150 mM KCl, 30 mM MgCl2, and 120 mM tris-HCl]). The mixture was centrifuged at 10,000 RCF for 20 min. Then, the supernatant was removed and 300 µl of 2%(w/v) normal goat serum (50062Z, Life technologies) in Dulbecco’s PBS (DPBS, Life technologies) was added to resuspend the nuclei pellet. To separate NeuN+ and NeuN- fractions, 6 µl of 2 ng/µl anti-NeuN antibody conjugated with Alexa 488 (MAB377X, Millipore) in DPBS was added into the nuclei suspension. The suspension was mixed well and incubated at 4 °C for 1 h on a rotator mixer (Labnet). After incubation, the sample was sorted into NeuN+ and NeuN- fractions using a BD FACSAriaTM cell sorter (BD Biosciences). The sorted NeuN+/NeuN- nuclei were directly used for RNA-seq experiment. 200 µl of sorted NeuN+/NeuN- nuclei suspension, containing ~26,000 nuclei, was added into 800 µl of ice-cold PBS for ChIP-seq experiment. 200 µl of 1.8 M sucrose solution, 10 µl of 1 M CaCl2, and 3 µl of 1 M Mg(Ac)2 were added into the mixture. The solution was mixed well and incubated on ice for 15 min. Then, the sample was centrifuged at 1800 RCF at 4 °C for 15 min. The supernatant was discarded and the pellet was resuspended in 60 µl of PBS with freshly added 0.6 µl of PIC and 0.6 µl of PMSF and stored on ice until use for ChIP-seq.
ChIP-seq library construction: ~10,000 NeuN+/NeuN- nuclei were used to produce each ChIP-seq library and two technical replicates were generated for each brain sample. One input per sample was generated using ~4,000 nuclei. ChIP was carried out using multiplexed MOWChIP-seq with MNase digestion for chromatin fragmentation and anti-H3K27ac (39135, Active Motif) antibody, following a published protocol (Zhu et al., Nature Protocols 14 (2019) 3366-3394.). RNA-seq library construction: ~5000 NeuN+/NeuN- nuclei were used to produce each RNA-seq library and two technical replicates were generated for each brain sample. RNA extraction from 50 µl of nuclei suspension from FACS (containing 5000 sorted NeuN+/NeuN- nuclei) was conducted using RNeasy Mini Kit (74104, Qiagen) and RNase-Free DNase Set (79254, Qiagen), following the manufacturer’s instruction. Extracted mRNA in 30-µl volume was concentrated by ethanol precipitation and resuspended in 4.6 µl of RNase-free water. cDNA was prepared using SMART-seq2 protocol (Picelli et al., Nature Protocols 9 (2014) 171–181.) with minor modification. ~2 ng of mRNA in 4.6 µl of water was mixed with 2 µl of 100 µM oligo-dT primer and 2 µl of 10 mM dNTP mix. After being denatured at 72 °C for 3 min, the mRNA solution was immediately placed on ice. 11.4 µl of reverse transcript mix [made from 1 µl of SuperScript II reverse transcriptase (200 U/µl), 0.5 µl of RNAse inhibitor (40 U/µl), 4 µl of Superscript II first-strand buffer, 1 µl of DTT (100mM), 4 µl of 5 M Betaine, 0.12 µl of 1 M MgCl2, 0.2 µl of TSO (100 µM), 0.58 µl of nuclease-free water] was mixed with the mRNA solution and the mixture was incubated at 42 °C for 90 min, followed by 10 cycles of (50 °C for 2 min, 42 °C for 2 min). The reaction was finally inactivated at 70 °C for 15 min. 20 µl of first-strand mixture was then mixed with 25 µl of KAPA HiFi HotStart ReadyMix, 0.5 µl of (100 µM) IS PCR primers, 0.5 µl of Evagreen dye, and 4 µl of nuclease-free water. Generated cDNA was amplified by incubated at 98 °C  for 1 min, followed by 9-11 cycles of (98 °C 15 s, 67 °C 30 s, 72 °C 6 min). After PCR amplification, 50 µl of PCR mix was purified by using 50 µl of SPRIselect beads. ~600 pg of purified cDNA was used to produce a RNA-seq library using Nextera XT DNA Library Preparation kit (FC-131-1024, Illumina), following the manufacturer instructions.
MOWChIP-seq and Smart-seq2

tag: age

value: 24 years

value: SCZ

tag: sample type

value: glial nuclei

tag: chip antibody


title: Control_NeuN+_input

source_name: neuronal nuclei from Brodmann area 9 (BA9) of postmortem brain tissue

value: 22 years

value: Control

value: neuronal nuclei


title: SCZ_NeuN+_input


title: Control_29_NeuN-_RNA_R1

value: 41 years


title: Control_NeuN-_input


title: Control_28_NeuN-_RNA_R1

value: 36 years


title: Control_28_NeuN-_RNA_R2


title: Chondrocytes, NC (circRNA-Seq)

city: Guangzhou

first: li

middle: hao

last: yuan

address: International Biotech Island

country: China

institute: Forevergen Biosciences Co.,Ltd

description: one sample from  chondrocytes of male rat

data_processing:
fastqc do QC
Sequenced reads were filter by SOAPnuke1.4.1(-f AGATCGGAAGAGC -r AGATCGGAAGAGC -A 0.62 -l 5 -q 0.25 -Q 2)
fastqc do cleandata QC
bwa-0.7.12 Compare to the reference genome ;CIRI_v2.0.5 get circ sequence
Transcripts Per Kilobase of exon model per Million mapped reads(TPM)
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include TPM  values for each Sample

organism: Rattus norvegicus

source_name: chondrocytes

growth_protocol: Cell was cultured in GIBCO DMEM/F12 (1:1) medium (No.: C11330500BT), supplemented with 10% fetal bovine plasma (FBS; Gibco) and 1% penicillin and streptomycin (Sigma Aldrich).

extract_protocol:
Briefly, total RNA samples were extracted from chondrocytes after the indicated treatments. The RNA integrity was evaluated using an Agilent 2100 Bioanalyzer. The fragment size of RNA was determined by agarose gel electrophoresis. The rRNA components were removed from the RNA samples using the Qiagen RiboMinus Eukaryote Kit, according to the manufacturer’s instructions.
The RNA library for sequencing was established from the mixed RNA samples (from three independent experiments) using the NEBNext Ultra II RNA Library Prep Kit (#E7770S; NEB, United States) according to the protocol provided by the manufacturer. Finally, the constructed RNA library was sequenced using a Hiseq 2000 instrument (Illumina,United States).

treatment_protocol: Chondrocytes within P3 generation were used in this study.Rat chondrocytes were treated with recombinant rat IL-1β (cat. No. I2393; Sigma Aldrich; 10 ng/ml) for 24 h to establish an in vitro OA cellular model as previously described (Huang et al., 2019). Chondrocytes cultured under normal conditions without IL-1β were set as normal control (NC) group.

value: chondrocytes

value: male

value: untreated


title: RNAseq_SLAMF6_WT_1


title: Chondrocytes, NC (mRNA-Seq)

data_processing:
fastqc do QC
filter using SOAPnuke（1.6.5）
HISAT2（2.1.0）  Compare to the reference genome rn6
Comparison sorts  the results BAM file use SAMtools（1.6）
RNASeQC (2.3.4) quantified the expression and obtained the expression matrix
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include RPKM  values for each Sample


title: Control_27_NeuN-_RNA_R2


title: Control_27_NeuN-_RNA_R1


title: Control_25_NeuN-_RNA_R2

value: 60 years


title: Control_26_NeuN-_RNA_R1

value: 54 years


title: Control_25_NeuN-_RNA_R1


title: Control_24_NeuN-_RNA_R1

value: 50 years


title: Control_24_NeuN-_RNA_R2


title: Control_23_NeuN-_RNA_R1

value: 42 years


title: Chondrocytes, IL-1β (circRNA-Seq)

value: IL-1β treated


title: Chondrocytes, IL-1β (mRNA-Seq)


title: Control_21_NeuN-_RNA_R1

value: 48 years


title: Control_21_NeuN-_RNA_R2


title: Control_20_NeuN-_RNA_R1

value: 56 years


title: Control_22_NeuN-_RNA_R1

value: 34 years


title: Control_19_NeuN-_RNA_R2

value: 52 years

value: glial nuclei


title: Control_20_NeuN-_RNA_R2

value: Control


title: Control_29_NeuN-_RNA_R2


title: Control_23_NeuN-_RNA_R2


title: Control_19_NeuN-_RNA_R1


title: Control_17_NeuN-_RNA_R2

value: 26 years


title: Control_22_NeuN-_RNA_R2


title: Control_16_NeuN-_RNA_R2

value: 32 years


title: Control_18_NeuN-_RNA_R2

value: 36 years


title: Control_15_NeuN-_RNA_R2

value: 74 years


title: Control_26_NeuN-_RNA_R2


title: Control_16_NeuN-_RNA_R1


title: Control_15_NeuN-_RNA_R1


title: Control_14_NeuN-_RNA_R2

value: 71 years


title: Control_14_NeuN-_RNA_R1


title: Control_13_NeuN-_RNA_R2

value: 49 years


title: Control_12_NeuN-_RNA_R2

value: 44 years


title: Control_13_NeuN-_RNA_R1


title: Control_12_NeuN-_RNA_R1


title: Control_11_NeuN-_RNA_R2

value: 33 years


title: Control_11_NeuN-_RNA_R1


title: Control_10_NeuN-_RNA_R1

value: 51 years


title: Control_10_NeuN-_RNA_R2


title: Control_9_NeuN-_RNA_R1


title: Control_8_NeuN-_RNA_R2

value: 66 years


title: Control_9_NeuN-_RNA_R2


title: Control_7_NeuN-_RNA_R2

value: 25 years


title: Control_8_NeuN-_RNA_R1


title: Control_18_NeuN-_RNA_R1


title: Control_6_NeuN-_RNA_R1

value: 28 years


title: Control_7_NeuN-_RNA_R1


title: Control_6_NeuN-_RNA_R2


title: Control_2_NeuN-_RNA_R1

value: 21 years


title: Control_4_NeuN-_RNA_R2


title: Control_5_NeuN-_RNA_R1


title: Control_29_NeuN+_RNA_R2

value: 41 years

value: neuronal nuclei


title: Control_5_NeuN-_RNA_R2

value: glial nuclei


title: Control_17_NeuN-_RNA_R1

value: Control


title: Control_29_NeuN+_RNA_R1


title: Control_2_NeuN-_RNA_R2


title: Control_3_NeuN-_RNA_R1

value: 18 years


title: Control_1_NeuN-_RNA_R1

value: 22 years


title: Control_4_NeuN-_RNA_R1

value: 32 years


title: Control_28_NeuN+_RNA_R2

value: 36 years


title: Control_1_NeuN-_RNA_R2


title: Control_27_NeuN+_RNA_R2


title: Control_27_NeuN+_RNA_R1


title: Control_28_NeuN+_RNA_R1


title: Control_26_NeuN+_RNA_R2

value: 54 years


title: Control_25_NeuN+_RNA_R2

value: 60 years


title: Control_26_NeuN+_RNA_R1


title: Control_24_NeuN+_RNA_R2

value: 50 years


title: Control_23_NeuN+_RNA_R2

value: 42 years


title: Control_22_NeuN+_RNA_R2

value: 34 years


title: Control_25_NeuN+_RNA_R1


title: Control_23_NeuN+_RNA_R1


title: Control_21_NeuN+_RNA_R2

value: 48 years


title: Control_21_NeuN+_RNA_R1


title: Control_20_NeuN+_RNA_R2

value: 56 years


title: Control_22_NeuN+_RNA_R1


title: Control_3_NeuN-_RNA_R2


title: Control_17_NeuN+_RNA_R2

value: 26 years


title: Control_20_NeuN+_RNA_R1


title: Control_19_NeuN+_RNA_R1

value: 52 years


title: Control_19_NeuN+_RNA_R2


title: Control_15_NeuN+_RNA_R1

value: 74 years


title: Control_14_NeuN+_RNA_R1

value: 71 years

value: neuronal nuclei


title: Control_14_NeuN+_RNA_R2

value: Control


title: Control_16_NeuN+_RNA_R1


title: Control_15_NeuN+_RNA_R2


title: Control_13_NeuN+_RNA_R1

value: 49 years


title: Control_24_NeuN+_RNA_R1


title: Control_12_NeuN+_RNA_R1

value: 44 years


title: Control_13_NeuN+_RNA_R2


title: Control_12_NeuN+_RNA_R2


title: Control_11_NeuN+_RNA_R2

value: 33 years


title: Control_11_NeuN+_RNA_R1


title: Control_10_NeuN+_RNA_R2

value: 51 years


title: Control_10_NeuN+_RNA_R1


title: Control_8_NeuN+_RNA_R2

value: 66 years


title: Control_9_NeuN+_RNA_R2


title: Control_9_NeuN+_RNA_R1


title: Control_6_NeuN+_RNA_R2

value: 28 years


title: Control_6_NeuN+_RNA_R1


title: Control_8_NeuN+_RNA_R1


title: Control_7_NeuN+_RNA_R1

value: 25 years


title: Control_18_NeuN+_RNA_R1

value: 36 years


title: Control_16_NeuN+_RNA_R2

value: 32 years


title: Control_18_NeuN+_RNA_R2


title: Control_5_NeuN+_RNA_R2


title: Control_17_NeuN+_RNA_R1


title: Control_4_NeuN+_RNA_R2


title: Control_5_NeuN+_RNA_R1


title: Control_4_NeuN+_RNA_R1


title: Control_2_NeuN+_RNA_R1

value: 21 years


title: Control_3_NeuN+_RNA_R2

value: 18 years


title: Control_2_NeuN+_RNA_R2


title: Control_1_NeuN+_RNA_R2

value: 22 years


title: Control_3_NeuN+_RNA_R1


title: Control_1_NeuN+_RNA_R1


title: SCZ_29_treated_NeuN-_RNA_R2

value: 42 years

value: SCZ

value: antipsychotic medications

value: glial nuclei


title: SCZ_29_treated_NeuN-_RNA_R1


title: SCZ_28_treated_NeuN-_RNA_R2


title: SCZ_28_treated_NeuN-_RNA_R1


title: SCZ_27_treated_NeuN-_RNA_R2

value: 41 years


title: SCZ_26_treated_NeuN-_RNA_R2

value: 56 years


title: Control_7_NeuN+_RNA_R2

value: Control

value: neuronal nuclei


title: SCZ_25_treated_NeuN-_RNA_R2

value: 60 years


title: SCZ_26_treated_NeuN-_RNA_R1


title: SCZ_25_treated_NeuN-_RNA_R1


title: SCZ_23_treated_NeuN-_RNA_R2

value: 43 years


title: SCZ_24_treated_NeuN-_RNA_R1

value: 50 years


title: SCZ_22_treated_NeuN-_RNA_R2

value: 34 years


title: SCZ_23_treated_NeuN-_RNA_R1


title: SCZ_24_treated_NeuN-_RNA_R2


title: SCZ_22_treated_NeuN-_RNA_R1


title: SCZ_21_treated_NeuN-_RNA_R2

value: 52 years


title: SCZ_21_treated_NeuN-_RNA_R1


title: SCZ_20_treated_NeuN-_RNA_R1

value: 58 years


title: SCZ_20_treated_NeuN-_RNA_R2


title: SCZ_19_treated_NeuN-_RNA_R2

value: 51 years


title: SCZ_19_treated_NeuN-_RNA_R1


title: SCZ_18_treated_NeuN-_RNA_R2

value: 35 years


title: SCZ_18_treated_NeuN-_RNA_R1


title: SCZ_17_treated_NeuN-_RNA_R1

value: 26 years


title: SCZ_15_untreated_NeuN-_RNA_R1

value: 74 years

value: untreated


title: SCZ_16_treated_NeuN-_RNA_R2

value: 32 years

value: SCZ

value: antipsychotic medications


title: SCZ_15_untreated_NeuN-_RNA_R2

value: glial nuclei


title: SCZ_17_treated_NeuN-_RNA_R2


title: SCZ_16_treated_NeuN-_RNA_R1


title: SCZ_14_untreated_NeuN-_RNA_R2

value: 70 years


title: SCZ_27_treated_NeuN-_RNA_R1

value: 41 years


title: SCZ_13_untreated_NeuN-_RNA_R2

value: 49 years


title: SCZ_14_untreated_NeuN-_RNA_R1


title: SCZ_12_untreated_NeuN-_RNA_R2

value: 43 years


title: SCZ_10_untreated_NeuN-_RNA_R1

value: 53 years


title: SCZ_9_untreated_NeuN-_RNA_R2

value: 34 years


title: SCZ_8_untreated_NeuN-_RNA_R2

value: 67 years


title: SCZ_8_untreated_NeuN-_RNA_R1


title: SCZ_10_untreated_NeuN-_RNA_R2


title: SCZ_11_untreated_NeuN-_RNA_R1


title: SCZ_11_untreated_NeuN-_RNA_R2


title: SCZ_7_untreated_NeuN-_RNA_R2

value: 25 years


title: SCZ_9_untreated_NeuN-_RNA_R1


title: SCZ_12_untreated_NeuN-_RNA_R1


title: SCZ_7_untreated_NeuN-_RNA_R1


title: SCZ_6_untreated_NeuN-_RNA_R2

value: 27 years


title: SCZ_13_untreated_NeuN-_RNA_R1


title: SCZ_6_untreated_NeuN-_RNA_R1


title: SCZ_4_untreated_NeuN-_RNA_R2

value: 31 years


title: SCZ_4_untreated_NeuN-_RNA_R1


title: SCZ_5_untreated_NeuN-_RNA_R1

value: 28 years


title: SCZ_2_untreated_NeuN-_RNA_R2

value: 21 years


title: SCZ_29_treated_NeuN+_RNA_R2

value: 42 years

value: neuronal nuclei


title: SCZ_1_untreated_NeuN-_RNA_R1

value: 24 years

value: SCZ

value: untreated


title: SCZ_3_untreated_NeuN-_RNA_R1

value: 18 years

value: glial nuclei


title: SCZ_2_untreated_NeuN-_RNA_R1


title: SCZ_3_untreated_NeuN-_RNA_R2


title: SCZ_29_treated_NeuN+_RNA_R1

value: antipsychotic medications


title: SCZ_1_untreated_NeuN-_RNA_R2


title: SCZ_5_untreated_NeuN-_RNA_R2


title: SCZ_28_treated_NeuN+_RNA_R2

value: 36 years


title: SCZ_27_treated_NeuN+_RNA_R1

value: 41 years


title: SCZ_27_treated_NeuN+_RNA_R2


title: SCZ_26_treated_NeuN+_RNA_R2

value: 56 years


title: SCZ_26_treated_NeuN+_RNA_R1


title: SCZ_24_treated_NeuN+_RNA_R2

value: 50 years


title: SCZ_25_treated_NeuN+_RNA_R2

value: 60 years


title: SCZ_23_treated_NeuN+_RNA_R2

value: 43 years


title: SCZ_24_treated_NeuN+_RNA_R1


title: SCZ_23_treated_NeuN+_RNA_R1


title: SCZ_22_treated_NeuN+_RNA_R2

value: 34 years


title: SCZ_25_treated_NeuN+_RNA_R1


title: SCZ_22_treated_NeuN+_RNA_R1


title: SCZ_21_treated_NeuN+_RNA_R2

value: 52 years


title: SCZ_20_treated_NeuN+_RNA_R2

value: 58 years


title: SCZ_21_treated_NeuN+_RNA_R1


title: SCZ_19_treated_NeuN+_RNA_R1

value: 51 years


title: SCZ_19_treated_NeuN+_RNA_R2

value: neuronal nuclei


title: SCZ_28_treated_NeuN+_RNA_R1


title: SCZ_18_treated_NeuN+_RNA_R1

value: 35 years


title: SCZ_14_untreated_NeuN+_RNA_R2

value: 70 years

value: SCZ


title: SCZ_20_treated_NeuN+_RNA_R1


title: SCZ_18_treated_NeuN+_RNA_R2


title: SCZ_17_treated_NeuN+_RNA_R2

value: 26 years


title: SCZ_13_untreated_NeuN+_RNA_R2

value: 49 years

value: untreated


title: SCZ_17_treated_NeuN+_RNA_R1

value: antipsychotic medications


title: SCZ_16_treated_NeuN+_RNA_R2

value: 32 years


title: SCZ_16_treated_NeuN+_RNA_R1


title: SCZ_14_untreated_NeuN+_RNA_R1


title: SCZ_12_untreated_NeuN+_RNA_R1


title: SCZ_12_untreated_NeuN+_RNA_R2


title: SCZ_13_untreated_NeuN+_RNA_R1


title: SCZ_11_untreated_NeuN+_RNA_R2


title: SCZ_15_untreated_NeuN+_RNA_R1

value: 74 years


title: SCZ_8_untreated_NeuN+_RNA_R2

value: 67 years


title: SCZ_8_untreated_NeuN+_RNA_R1


title: SCZ_7_untreated_NeuN+_RNA_R2

value: 25 years


title: SCZ_9_untreated_NeuN+_RNA_R2


title: SCZ_11_untreated_NeuN+_RNA_R1


title: SCZ_9_untreated_NeuN+_RNA_R1


title: SCZ_6_untreated_NeuN+_RNA_R1

value: 27 years


title: SCZ_10_untreated_NeuN+_RNA_R1

value: 53 years


title: SCZ_10_untreated_NeuN+_RNA_R2


title: SCZ_15_untreated_NeuN+_RNA_R2


title: SCZ_4_untreated_NeuN+_RNA_R1

value: 31 years


title: SCZ_5_untreated_NeuN+_RNA_R2

value: 28 years


title: SCZ_6_untreated_NeuN+_RNA_R2


title: SCZ_5_untreated_NeuN+_RNA_R1


title: SCZ_7_untreated_NeuN+_RNA_R1


title: SCZ_3_untreated_NeuN+_RNA_R1

value: 18 years


title: SCZ_3_untreated_NeuN+_RNA_R2

value: neuronal nuclei


title: SCZ_4_untreated_NeuN+_RNA_R2


title: SCZ_2_untreated_NeuN+_RNA_R1

value: 21 years


title: SCZ_1_untreated_NeuN+_RNA_R1

value: 24 years


title: SCZ_1_untreated_NeuN+_RNA_R2

value: SCZ


title: Control_29_NeuN-_H3K27ac_R2

value: 41 years

value: Control

value: glial nuclei


title: Control_28_NeuN-_H3K27ac_R2

value: 36 years


title: Control_29_NeuN-_H3K27ac_R1


title: Control_27_NeuN-_H3K27ac_R1


title: Control_28_NeuN-_H3K27ac_R1


title: Control_26_NeuN-_H3K27ac_R2

value: 54 years


title: Control_26_NeuN-_H3K27ac_R1


title: Control_25_NeuN-_H3K27ac_R1

value: 60 years


title: Control_24_NeuN-_H3K27ac_R2

value: 50 years


title: Control_25_NeuN-_H3K27ac_R2


title: Control_24_NeuN-_H3K27ac_R1


title: Control_23_NeuN-_H3K27ac_R1

value: 42 years


title: Control_22_NeuN-_H3K27ac_R2

value: 34 years


title: Control_21_NeuN-_H3K27ac_R2

value: 48 years


title: Control_21_NeuN-_H3K27ac_R1


title: Control_20_NeuN-_H3K27ac_R2

value: 56 years


title: Control_19_NeuN-_H3K27ac_R2

value: 52 years


title: SCZ_2_untreated_NeuN+_RNA_R2

value: untreated


title: Control_18_NeuN-_H3K27ac_R2


title: Control_19_NeuN-_H3K27ac_R1


title: Control_18_NeuN-_H3K27ac_R1


title: Control_17_NeuN-_H3K27ac_R1

value: 26 years


title: Control_16_NeuN-_H3K27ac_R1

value: 32 years


title: Control_27_NeuN-_H3K27ac_R2


title: Control_14_NeuN-_H3K27ac_R2

value: 71 years


title: Control_15_NeuN-_H3K27ac_R2

value: 74 years


title: Control_12_NeuN-_H3K27ac_R2

value: 44 years


title: Control_13_NeuN-_H3K27ac_R2

value: 49 years

value: Control


title: Control_13_NeuN-_H3K27ac_R1

value: glial nuclei


title: Control_14_NeuN-_H3K27ac_R1


title: Control_11_NeuN-_H3K27ac_R1

value: 33 years


title: Control_9_NeuN-_H3K27ac_R2


title: Control_10_NeuN-_H3K27ac_R1

value: 51 years


title: Control_22_NeuN-_H3K27ac_R1


title: Control_10_NeuN-_H3K27ac_R2


title: Control_23_NeuN-_H3K27ac_R2


title: Control_20_NeuN-_H3K27ac_R1


title: Control_9_NeuN-_H3K27ac_R1


title: Control_8_NeuN-_H3K27ac_R2

value: 66 years


title: Control_7_NeuN-_H3K27ac_R1

value: 25 years


title: Control_17_NeuN-_H3K27ac_R2


title: Control_7_NeuN-_H3K27ac_R2


title: Control_8_NeuN-_H3K27ac_R1


title: Control_16_NeuN-_H3K27ac_R2


title: Control_6_NeuN-_H3K27ac_R2

value: 28 years


title: Control_5_NeuN-_H3K27ac_R1


title: Control_4_NeuN-_H3K27ac_R2


title: Control_5_NeuN-_H3K27ac_R2


title: Control_4_NeuN-_H3K27ac_R1


title: Control_15_NeuN-_H3K27ac_R1


title: Control_6_NeuN-_H3K27ac_R1


title: Control_12_NeuN-_H3K27ac_R1


title: Control_3_NeuN-_H3K27ac_R2

value: 18 years


title: Control_2_NeuN-_H3K27ac_R2

value: 21 years


title: Control_3_NeuN-_H3K27ac_R1


title: Control_1_NeuN-_H3K27ac_R1

value: 22 years


title: Control_29_NeuN+_H3K27ac_R2

value: 41 years

value: neuronal nuclei


title: Control_2_NeuN-_H3K27ac_R1


title: Control_28_NeuN+_H3K27ac_R2

value: 36 years


title: Control_28_NeuN+_H3K27ac_R1


title: Control_26_NeuN+_H3K27ac_R2

value: 54 years


title: Control_26_NeuN+_H3K27ac_R1


title: Control_27_NeuN+_H3K27ac_R2


title: Control_11_NeuN-_H3K27ac_R2


title: Control_25_NeuN+_H3K27ac_R2

value: 60 years


title: Control_29_NeuN+_H3K27ac_R1


title: Control_24_NeuN+_H3K27ac_R2

value: 50 years


title: Control_22_NeuN+_H3K27ac_R1

value: 34 years


title: Control_22_NeuN+_H3K27ac_R2

value: Control


title: Control_23_NeuN+_H3K27ac_R2

value: 42 years


title: Control_23_NeuN+_H3K27ac_R1


title: Control_24_NeuN+_H3K27ac_R1


title: Control_21_NeuN+_H3K27ac_R2

value: 48 years


title: Control_25_NeuN+_H3K27ac_R1


title: Control_20_NeuN+_H3K27ac_R2

value: 56 years


title: Control_19_NeuN+_H3K27ac_R2

value: 52 years


title: Control_18_NeuN+_H3K27ac_R2


title: Control_19_NeuN+_H3K27ac_R1


title: Control_21_NeuN+_H3K27ac_R1


title: Control_17_NeuN+_H3K27ac_R1

value: 26 years


title: Control_18_NeuN+_H3K27ac_R1


title: Control_1_NeuN-_H3K27ac_R2

value: glial nuclei


title: Control_16_NeuN+_H3K27ac_R2

value: 32 years


title: Control_17_NeuN+_H3K27ac_R2


title: Control_27_NeuN+_H3K27ac_R1


title: Control_15_NeuN+_H3K27ac_R2

value: 74 years


title: Control_15_NeuN+_H3K27ac_R1


title: Control_14_NeuN+_H3K27ac_R1

value: 71 years


title: Control_13_NeuN+_H3K27ac_R2

value: 49 years


title: Control_13_NeuN+_H3K27ac_R1

value: neuronal nuclei


title: Control_12_NeuN+_H3K27ac_R2

value: 44 years


title: Control_11_NeuN+_H3K27ac_R2

value: 33 years


title: Control_12_NeuN+_H3K27ac_R1


title: Control_10_NeuN+_H3K27ac_R1

value: 51 years


title: Control_10_NeuN+_H3K27ac_R2


title: Control_20_NeuN+_H3K27ac_R1


title: Control_8_NeuN+_H3K27ac_R2

value: 66 years


title: Control_9_NeuN+_H3K27ac_R1

value: 34 years


title: Control_8_NeuN+_H3K27ac_R1

value: Control


title: Control_9_NeuN+_H3K27ac_R2


title: Control_6_NeuN+_H3K27ac_R1

value: 28 years


title: Control_6_NeuN+_H3K27ac_R2


title: Control_4_NeuN+_H3K27ac_R1


title: Control_5_NeuN+_H3K27ac_R2


title: Control_5_NeuN+_H3K27ac_R1


title: Control_2_NeuN+_H3K27ac_R2

value: 21 years


title: Control_4_NeuN+_H3K27ac_R2


title: Control_16_NeuN+_H3K27ac_R1


title: Control_3_NeuN+_H3K27ac_R2

value: 18 years


title: Control_29_NeuN-_H3K4me3_R2

value: 41 years


title: Control_11_NeuN+_H3K27ac_R1


title: Control_3_NeuN+_H3K27ac_R1


title: Control_29_NeuN-_H3K4me3_R1


title: Control_14_NeuN+_H3K27ac_R2


title: Control_2_NeuN+_H3K27ac_R1


title: Control_27_NeuN-_H3K4me3_R1


title: Control_26_NeuN-_H3K4me3_R2

value: 54 years


title: Control_1_NeuN+_H3K27ac_R1

value: 22 years


title: Control_26_NeuN-_H3K4me3_R1

value: glial nuclei


title: Control_7_NeuN+_H3K27ac_R2

value: 25 years


title: Control_24_NeuN-_H3K4me3_R2

value: 50 years


title: Control_25_NeuN-_H3K4me3_R2

value: 60 years


title: Control_28_NeuN-_H3K4me3_R2

value: 36 years


title: Control_25_NeuN-_H3K4me3_R1


title: Control_28_NeuN-_H3K4me3_R1


title: Control_23_NeuN-_H3K4me3_R2

value: 42 years


title: Control_27_NeuN-_H3K4me3_R2


title: Control_7_NeuN+_H3K27ac_R1

value: neuronal nuclei


title: Control_24_NeuN-_H3K4me3_R1


title: Control_22_NeuN-_H3K4me3_R2


title: Control_23_NeuN-_H3K4me3_R1


title: Control_1_NeuN+_H3K27ac_R2


title: Control_22_NeuN-_H3K4me3_R1


title: Control_21_NeuN-_H3K4me3_R2

value: 48 years


title: Control_20_NeuN-_H3K4me3_R2

value: 56 years


title: Control_21_NeuN-_H3K4me3_R1


title: Control_19_NeuN-_H3K4me3_R2

value: 52 years


title: Control_19_NeuN-_H3K4me3_R1

value: Control


title: Control_18_NeuN-_H3K4me3_R1


title: Control_16_NeuN-_H3K4me3_R2

value: 32 years


title: Control_18_NeuN-_H3K4me3_R2


title: Control_17_NeuN-_H3K4me3_R1

value: 26 years


title: Control_16_NeuN-_H3K4me3_R1


title: Control_15_NeuN-_H3K4me3_R2

value: 74 years


title: Control_15_NeuN-_H3K4me3_R1


title: Control_14_NeuN-_H3K4me3_R2

value: 71 years


title: Control_14_NeuN-_H3K4me3_R1


title: Control_13_NeuN-_H3K4me3_R2

value: 49 years


title: Control_13_NeuN-_H3K4me3_R1


title: Control_12_NeuN-_H3K4me3_R2

value: 44 years


title: Control_12_NeuN-_H3K4me3_R1

value: glial nuclei


title: Control_11_NeuN-_H3K4me3_R1

value: 33 years


title: Control_11_NeuN-_H3K4me3_R2


title: Control_9_NeuN-_H3K4me3_R1

value: 34 years


title: Control_9_NeuN-_H3K4me3_R2


title: Control_20_NeuN-_H3K4me3_R1


title: Control_10_NeuN-_H3K4me3_R1

value: 51 years


title: Control_8_NeuN-_H3K4me3_R2

value: 66 years


title: Control_7_NeuN-_H3K4me3_R2

value: 25 years


title: Control_8_NeuN-_H3K4me3_R1


title: Control_17_NeuN-_H3K4me3_R2


title: Control_3_NeuN-_H3K4me3_R2

value: 18 years


title: Control_7_NeuN-_H3K4me3_R1


title: Control_5_NeuN-_H3K4me3_R1

value: 28 years


title: Control_6_NeuN-_H3K4me3_R1


title: Control_4_NeuN-_H3K4me3_R2


title: Control_4_NeuN-_H3K4me3_R1


title: Control_5_NeuN-_H3K4me3_R2


title: Control_1_NeuN-_H3K4me3_R1

value: 22 years


title: Control_2_NeuN-_H3K4me3_R2

value: 21 years


title: Control_29_NeuN+_H3K4me3_R1

value: 41 years

value: Control

value: neuronal nuclei


title: Control_27_NeuN+_H3K4me3_R2


title: Control_6_NeuN-_H3K4me3_R2


title: Control_28_NeuN+_H3K4me3_R2

value: 36 years


title: Control_25_NeuN+_H3K4me3_R1

value: 60 years


title: Control_3_NeuN-_H3K4me3_R1


title: Control_10_NeuN-_H3K4me3_R2


title: Control_2_NeuN-_H3K4me3_R1


title: Control_27_NeuN+_H3K4me3_R1


title: Control_26_NeuN+_H3K4me3_R2

value: 54 years


title: Control_26_NeuN+_H3K4me3_R1


title: Control_24_NeuN+_H3K4me3_R2

value: 50 years


title: Control_24_NeuN+_H3K4me3_R1


title: Control_22_NeuN+_H3K4me3_R2


title: Control_28_NeuN+_H3K4me3_R1


title: Control_23_NeuN+_H3K4me3_R2

value: 42 years


title: Control_29_NeuN+_H3K4me3_R2


title: Control_23_NeuN+_H3K4me3_R1


title: Control_1_NeuN-_H3K4me3_R2

value: glial nuclei


title: GRA6_TINT_4

city: Berkeley

first: Zoë

last: Steier

state: CA

address: 378 Stanley Hall

institute: UC Berkeley

description:
T intermediate cell biological replicate 3
GRA6-4B

data_processing:
Sequencing reads were processed with Trimmomatic (v0.32) to remove adapter sequences and trim low-quality bases. Reads were aligned to the mm10 genome using Bowtie2 (v2.3.2) and transcripts were quantified using RSEM (v1.2.31).
Genome_build: mm10
Supplementary_files_format_and_content: txi_rsem_transcript_counts.rds: R object including transcript counts, abundance, and gene lengths as quantified by RSEM for all genes and for each sample.
Supplementary_files_format_and_content: normalized_counts.csv: Matrix of normalized counts for all genes and for each sample (normalized by DESeq2 median of ratios method).

source_name: spleen

extract_protocol:
RNA was harvested using a Quick-RNA Microprep Kit from Zymo Research (Cat. No. R1050) according to the manufacturer’s instructions. RNA integrity was confirmed via Bioanalyzer and Qbit.
RNA was sent to BGI Genomics for library generation and RNA sequencing. RNA was sequenced on an Illumina-HiSeq2500/4000 to a depth of 20 million reads.

treatment_protocol: Spleens were removed from mice infected with T. gondii for six weeks and dissociated into single cell suspensions in FACS buffer. Splenocytes were surface stained with B220, CD4, CD8, GRA6 Tetramer, CXCR3, and KLRG1 and sorted into memory cells (TMEM: B220- CD4- CD8+ Tetramer+ CXCR3+ KLRG1-), intermediate cells (TINT: B220- CD4- CD8+ Tetramer+ CXCR3+ KLRG1+), and effector cells (TEFF: B220- CD4- CD8+ Tetramer+ CXCR3- KLRG1+). Populations were sorted using a BD FACSAria Fusion sorter.

value: C57/BL6 x B6.C-H2d/bByJ

tag: sort population

value: CD8+ T intermediate


title: GRA6_TEFF_2

description:
T effector biological replicate 2
GRA6-2C

value: CD8+ T effector


title: GRA6_TEFF_3

description:
T effector biological replicate 3
GRA6-3C


title: GRA6_TEFF_1

description:
T effector biological replicate 1
GRA6-1C


title: GRA6_TEFF_4

description:
T effector biological replicate 4
GRA6-4C


title: GRA6_TINT_1

description:
T intermediate cell biological replicate 1
GRA6-1B


title: GRA6_TMEM_2

description:
T memory cell biological replicate 2
GRA6-2A

value: CD8+ T memory


title: GRA6_TMEM_4

description:
T memory cell biological replicate 3
GRA6-4A


title: GRA6_TINT_3

description:
T intermediate cell biological replicate 2
GRA6-3B


title: P10_wt2_ctx_S2_L004_R1_001

city: San Francisco

first: Kenneth

last: Lim

department: Psychiatry

institute: UCSF

data_processing:
ATACseq and Histone ChIPseq were aligned to mm9 (UCSC) genome assembly using BWA mem (v0.7.17). CUT&RUN reads were aligned to mm9 genome assembly using Bowtie2 default mode. RNA-seq reads were mapped to mm9 genome assembly using HISAT2 (v2.0.5).
Bigwig files were generated using deepTools bamCoverage (v3.4.3)
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files generated using deepTools.

source_name: medial prefrontal cortex

growth_protocol:
PROTOCOL 1: Cerebral cortex or basal ganglia tissue was dissected from WT or mutant E13.5 littermate embryos.
PROTOCOL 2: Cerebral cortex tissue was dissected from WT or mutant E13.5 embryos.
PROTOCOL 3: Cerebral cortex tissue was dissected from WT or POGZ mutant mice.
PROTOCOL 4: Whole Telencephalon was dissected from WT E13.5 mice.

extract_protocol:
PROTOCOL 1: Intact nuclei were isolated by pipetting up and down twenty times in ice cold 0.5 mL Buffer 1 (300mM sucrose, 60mM KCl, 15mM NaCl, 15mM Tris-HCl, pH 7.5, 5mM MgCl2, 0.1mM EGTA, 1mM DTT, 1.1mM PMSF, Protease inhibitors), and then lysed on ice for 10 minutes after adding 0.5 mL Buffer 2 (300mM sucrose, 60mM KCl, 15mM NaCl, 15mM Tris-HCl, pH 7.5, 5mM MgCl2, 0.1mM EGTA, 0.1% NP-40, 1mM DTT, 1.1mM PMSF, Protease inhibitors). During these ten minutes, nuclei were counted using trypan blue and 50,000 nuclei were spun down at 7,000rpm for ten minutes at 4C.
PROTOCOL 1: Nuclei were resuspended in 25uL Tagmentation buffer, 22.5 uL Nuclease Free H20, and 2.5 uL Tagmentation Enzyme from Nextera DNA Library Prep Kit, gently mixed, and placed in 37C water bath for thirty minutes. The tagmentation reaction was stopped by MinElute PCR purification and DNA was eluted in 10uL Nuclease Free water. ATAC-seq library generation was performed using Illumina barcode oligos as described (Buenrostro et al 2015), for 8-11 cycles PCR using NEBNext High Fidelity 2x PCR master mix. The number of cycles was empirically determined for each library by qPCR. Libraries were bioanalyzed using Agilent High Sensitivity DNA Kit, pooled together and sequenced on Hiseq 2500.
PROTOCOL 2: Intact nuclei were isolated by pipetting up and down twenty times in ice cold 0.5 mL Buffer 1 (300mM sucrose, 60mM KCl, 15mM NaCl, 15mM Tris-HCl, pH 7.5, 5mM MgCl2, 0.1mM EGTA, 1mM DTT, 1.1mM PMSF, 50mM Sodium Butyrate, EDTA-free Protease inhibitors), and then lysed on ice for 10 minutes after adding 0.5 mL Buffer 2 (300mM sucrose, 60mM KCl, 15mM NaCl, 15mM Tris-HCl, pH 7.5, 5mM MgCl2, 0.1mM EGTA, 0.1% NP-40, 1mM DTT, 1.1mM PMSF, 50mM Sodium Butyrate,  EDTA-free Protease inhibitors). During this ten minutes, nuclei were counted using trypan blue and 500,000 nuclei were spun down at 7,000rpm for ten minutes at 4C.  Nuclei were resuspended in 0.250mL MNase buffer  (320mM sucrose, 50mM Tris-HCl, pH 7.5, 4mM MgCl2, 1mM CaCl2, 1.1mM PMSF, 50mM Sodium Butyrate) and incubated in a 37C water bath with 2 microliters Micrococcal Nuclease enzyme (NEB) for eight minutes.  Micrococcal Nuclease digestion was stopped by adding 10 microliters 0.5M EDTA, and chromatin was spun down for 10 minutes 10,000rpm 4C.  Soluble fraction “S1” supernatant was saved at 4C overnight, and “S2” fraction was dialyzed overnight in 250uL dialysis buffer at 4C (1mm Tris-HCl pH 7.5, 0.2mM EDTA, 0.1mM PMSF, 50mM Sodium Butyrate, Protease Inhibitors).  Next day S1 and S2 fractions were combined, 50 microliters were saved as input, and Chromatin immunoprecipitation was set up in ChIP buffer: 50mM Tris, pH 7.5, 10mM EDTA, 125 mM NaCl1, 0.1% Tween. 250m M Sodium Butyrate was supplemented for H3K27ac ChIPs.  1 microliter of antibody was added to 1mL chromatin in ChIP buffer and incubated overnight at 4C rotating.  Protein A and Protein G beads (10 microliters for each ChIP) were blocked overnight in 700uL ChIP buffer, 20 uL yeast tRNA (20mg/mL), and 300uL BSA (10mg/mL). Beads were washed three times for five minutes on ice in Wash buffer 1 (50 mM Tris, pH 7.5 , 10mM EDTA , 125mM NaCl, 0.1% Tween-20, with protease inhibitors and 5mM sodium butyrate) and three times in Wash buffer 2 (50 mM Tris, pH 7.5 , 10mM EDTA , 175mM NaCl, 0.1% NP-40, with protease inhibitors and 5mM sodium butyrate), and ChIP DNA was eluted in elution buffer at 37C and purified by phenol chloroform extraction and ethanol precipitation.
PROTOCOL 2: Sequencing libraries were made using Nugen Ovation Ultralow V2 kit and quantified by Agilent High Sensitivity DNA kit on the Agilent bioanalyzer.
PROTOCOL 3: From each dissection, RNA was isolated using QIAGEN RNeasy mini columns. RNA was treated with Turbo DNAse and inactivated.  RNA quality was assessed using Agilent Bioanalyzer RNA Nano kit, and samples with RNA Integrity Number values greater than 9.0 were used for subsequent profiling.
PROTOCOL 3: RNA-seq libraries were generated using Nugen’s Ovation Mouse RNA-seq kit and amplified for 15 cycles.  Libraries were quantified using Agilent Bioanalyzer High Sensitivity DNA kit, and sequenced on Hiseq 2500 using paired end sequencing.
PROTOCOL 4: After spinning down nuclei at 7,000rpm for ten minutes at 4C, we methodically followed the protocol for CUT &RUN (Skene, Henikoff, and Henikoff 2018), starting at step 6 “Resuspend in 1mL of wash buffer at RT by gentle pipetting”. Antibodies were used at the following dilutions: POGZ 1:500, ADNP 1:13, Hp1g 1:500, IgG 1:1000. For the final DNA extraction step, we performed phenol-chloroform extraction and ethanol precipitation.
PROTOCOL 4: We generated libraries using Nugen’s Ovation Ultralow V2 kit, and amplified libraries for 16 cycles, and bioanalyzed libraries using the Agilent High Sensitivity DNA kit and sequenced libraries on the Hiseq 2500.

treatment_protocol: PROTOCOL 4: From each dissection of E13.5 telencephalon, intact nuclei were isolated using Buffer 1 and Buffer 2 as for ChIP-seq and ATAC-seq above.

tag: experiment

value: RNAseq

tag: tissue

value: medial prefrontal cortex

tag: replicate

value: POGZ +/+

tag: strain background

tag: protocol used

value: Protocol 3


title: GRA6_TMEM_1

description:
T memory cell biological replicate 1
GRA6-1A

tag: genotype

tag: strain

tag: cell type


title: P10_wt9_ctx_S14_L006_R1_001


title: Control_25_NeuN+_H3K4me3_R2


title: P10_het7_ctx_S9_L005_R1_001

value: POGZ +/-


title: P0_wt6_ctx_S11_L005_R1_001

source_name: rostral cerebral cortex

value: rostral cerebral cortex


title: P10_het8_ctx_S13_L006_R1_001


title: P10_het5_ctx_S7_L005_R1_001


title: P10_het1_ctx_S1_L004_R1_001


title: P0_wt2_ctx_S5_L004_R1_001


title: P0_wt1_ctx_S4_L004_R1_001


title: P0_het4_ctx_S10_L005_R1_001


title: mPFC_P28_3wt_S122_L008_R1_001


title: P0_het8_ctx_S15_L006_R1_001


title: mPFC_P28_12wt_S127_L008_R1_001


title: mPFC_P28_2wt_S121_L008_R1_001


title: mPFC_P28_13het_S128_L008_R1_001


title: mPFC_P28_5het_S124_L008_R1_001


title: mPFC_P28_11wt_S126_L008_R1_001


title: P10_wt6_ctx_S8_L005_R1_001


title: mPFC_P28_1het_S120_L008_R1_001


title: e13_BG_ko7_S3_L007_R1_001

source_name: basal ganglia

value: basal ganglia

value: POGZ -/-


title: e13_BG_WT3_S1_L007_R1_001


title: e13_BG_WT4_S2_L007_R1_001


title: e13_BG_KO9_S46_R1_001


title: ko11_ctx_e13_S45_R1_001

source_name: cerebral cortex

value: Cortex


title: e13_BG_WT12_S44_R1_001


title: wt12_ctx_e13_S42_R1_001


title: ko9_ctx_e13_S44_R1_001


title: e13_BG_KO11_S4_L007_R1_001


title: ko7_ctx_e13_S43_R1_001


title: wt4_ctx_e13_S41_R1_001


title: wt3_ctx_e13_S40_R1_001


title: 7WT_pogz_ak27_S203_L008_R1_001

data_processing:
library strategy: HistoneChIPseq
ATACseq and Histone ChIPseq were aligned to mm9 (UCSC) genome assembly using BWA mem (v0.7.17). CUT&RUN reads were aligned to mm9 genome assembly using Bowtie2 default mode. RNA-seq reads were mapped to mm9 genome assembly using HISAT2 (v2.0.5).
Bigwig files were generated using deepTools bamCoverage (v3.4.3)
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files generated using deepTools.

value: HistoneChIPseq

value: anti-H3K27ac Clone CMA309 (Millipore, Cat# 05-1334)

value: Protocol 2


title: 5KO_pogz_ak27_S201_L008_R1_001


title: 6WT_pogz_ak27_S202_L008_R1_001


title: P0_het3_ctx_S6_L004_R1_001


title: 4WT_pogz_ak27_S200_L008_R1_001


title: 3KO_pogz_ak27_S199_L008_R1_001


title: KO11_bg_atac_S10_L002_R1_001

value: ATACseq

value: Protocol 1


title: KO9_bg_atac_S9_L002_R1_001


title: 2KO_pogz_ak27_S198_L008_R1_001


title: WT3_bg_atac_S5_L002_R1_001


title: KO7_bg_atac_S8_L002_R1_001


title: WT4_bg_atac_S6_L002_R1_001


title: mPFC_P28_4het_S123_L008_R1_001


title: WT12_bg_atac_S7_L002_R1_001


title: e13_KO7_atac_S12_L002_R1_001


title: e13_WT3_atac_S9_L002_R1_001


title: e13_WT4_atac_S10_L002_R1_001


title: e13_KO11_atac_S14_L002_R1_001


title: RP2

city: Charlottesville

first: Golam

last: Mohi

state: Virginia

address: 1340 Jefferson Park Ave

department: Biochemistry and Molecular Genetics

institute: University of Virginia

data_processing:
Raw reads were adapter trimmed and >Q30 quality filtered with fastp 0.20.0
Trimmed reads were aligned using HISAT2 2.0.1 to Mus musculus GRCm38
Aligned reads were converted to BAM via Samtools 1.10
Gene counts were generated using featureCounts 2.0.0
Differential gene expression was done using DESeq2
Genome_build: GRCm38

source_name: BMT LSK cells

extract_protocol:
Bone marrow cells were harvested and lineage depleted by MACS mouse lineage depletion kit then sorted by flow cytometry.
Library prep was done according to protocol of NEB polyA-RNA magnetic isolation kit and then NEBNext Ultra II RNA Library Prep Kit for Illumina

value: Bone Marrow

value: Homozygous JAK2V617F

tag: treatment

value: Palbociclib & Ruxolitinib


title: e13_WT12_atac_S11_L002_R1_001


title: RP3


title: e13_KO9_atac_S13_L002_R1_001


title: R1

value: Ruxolitinib


title: R2


title: P2

value: Palbociclib


title: RP1


title: P3


title: P1


title: R3


title: V3

value: Vehicle


title: V2


title: V1


title: PFC-HDAC2-100K-1

description: nMOWChIP-seq data. Name format: Sample-target-cell/nuclei number-replicate number

data_processing:
Raw reads were trimmed with TrimGalore 0.4.1
Trimmed reads were aligned using bowtie 1.1.2. Uniquely mapped reads were filtered for known blacklisted genome regions using Samtools55 and bedtools56 to remove ChIP-seq artifacts.
Reads were extended by 100 bp on either ends
Sample was normalized and input subtracted. The reference genome was then divided into 100-bp bins and ChIP-seq signal for each bin was counted for both ChIP and input samples.
Sample was converted to BigWig format
Genome_build: hg38, mm10
Supplementary_files_format_and_content: Normalized ChIP-seq signal in BigWig format

source_name: C57BL/6J brain

growth_protocol: GM12878 cells were obtained from Coriell Institute for Medical Research. Cells were cultured in RPMI-1640 medium (30-2001, ATCC) with 15% fetal bovine serum (16000-044, Gibco) and 1% pen-strep (Invitrogen) at 37°C, 5% CO2. Cells were subcultured every 3 d to maintain exponential growth. C57BL/6J mice were purchased from Jackson Laboratory and maintained in the animal facility with 12-h light/12-h dark cycles and food and water ad libitum. 8-week old male mice were sacrificed by compressed CO2 followed by cervical dislocation. Mouse brains were rapidly dissected, frozen on dry ice and stored at -80°C. This study was approved by the Institutional Animal Care and Use Committee (IACUC) at Virginia Tech.

extract_protocol:
GM12878 protocol: Cells were centrifuged at 1,600 g for 5 min and resuspended in DPBS. Our experiments usually started with 4×10^5 cells/nuclei suspended in 100 µl of DPBS. 1 µl of PIC, 1 µl of 100 mM PMSF and 100 µl lysis buffer [4% Triton X-100, 100 mM tris-HCl, 100 mM NaCl, and 30 mM MgCl2] were added, mixed by vortexing and incubated at room temperature for 10 min. 10 µl of 100 mM CaCl2 and 2.5 µl 100U MNase (88216, Thermo Fisher Scientific) were added, mixed by vortexing and incubated at room temperature for 10 min. 22 µl of 0.5 M EDTA was then added, mixed by vortexing and incubated on ice for 10 min. The solution was centrifuged at 16,100g for 5 min at 4°C. Supernatant containing fragmented chromatin was collected into a new 1.5 ml tube and placed on ice. Chromatin volume equal to the stated number of cells per assay was taken and used for nMOWChIP, diluted to 60 µl loading volume with IP buffer if needed. Mouse protocol: A mouse brain was put on ice and PFC and cerebellum were dissected for nuclei isolation. The following steps are performed on ice and centrifugation performed at 4°C. Tissue was placed in 3 ml of ice-cold nuclei extraction buffer [0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM tris-HCl, and 0.1% Triton X-100, with 30 µl of PIC (P8340, Sigma-Aldrich), 3 µl of 100 mM PMSF, and 3 µl of 1 M dithiothreitol added before use]. Tissue was homogenized in the grinder set (D9063, Sigma-Aldrich) by slowly douncing 15 times with pestle A and 25 times with pestle B. Homogenate was filtered through a 40 µm cell strainer into a 15 ml tube and centrifuged at 1000g for 10 min. The supernatant was removed and the pellet was resuspended in 500 µl nuclei extraction buffer and transferred to a 1.5 ml tube. 750 µl of 50% iodixanol, 7.5 µl of PIC, 0.75 µl of 100 mM PMSF and 0.75 µl of 1M dithiothreitol were added and mixed by pipetting. The mixture was centrifuged at 10,000g for 20 min and the supernatant was removed. If mixed nuclei (without separation of neurons and glia) were used for MOWChIP directly, the nuclei pellet was resuspended in 200 µl of Dulbecco's phosphate-buffered saline (DPBS). If nuclei labeling and FACS sorting were conducted, 500 µl of 2% normal goat serum (50062Z, Life Technologies) in DPBS was added to the nuclei pellet and incubated for 10 min before resuspending. Anti-NeuN antibody conjugated with Alexa 488 (MAB377X, EMD Millipore) was diluted with DPBS to 2 ng/µl. 8 µl of anti-NeuN was added to each 500 µl of nuclei suspension and incubated at 4°C for 1 h on a rotator. The labeled nuclei were then sorted using FACS (BD FACSAria, BD Biosciences). 8 µl of non-labeled nuclei were saved as unstained control prior to addition of anti-NeuN antobody. The concentration of nuclei suspension after FACS was typically low (~1.2×10^5/ml). The nuclei were re-concentrated by adding 200 µl of 1.8 M sucrose, 5 µl of 1M CaCl2 and 3 µl of 1M Mg(Ac)2 to 1 ml of the nuclei suspension. The mixture was incubated on ice for 15 min and centrifuged at 1800g for 15 min. Supernatant was removed and the nuclei pellet was resuspended in DPBS. Nuclei were digested using the same steps as GM12878 cells.
Antibody information: anti-Pol II-total (Abcam, ab817, lot GR3271868-2),anti-Pol II-S5 (Abcam, ab5131, lot GR3202335-5), anti-EGR1 (Santa Cruz, sc-101033, lot A1618), anti-MEF2C (Santa Cruz, sc-365862, lot B0818), anti-HDAC2 (Abcam, ab124974, lot GR97402-7)
Libraries were constructed using Accel-NGS 2S Plus DNA Library kit (Swift Biosciences) following the manufacturer’s instructions. 1× EvaGreen dye (Biotium) was added to the amplification mixture to monitor the PCR amplification. Library was eluted to 7 µl of low EDTA TE buffer. Library fragment size was examined using TapeStation (Agilent) and the concentration was quantified with KAPA Library Quantification kit (Kapa Biosystems). Libraries were pooled accordingly for sequencing by Illumina HiSeq 4000 SR50 mode.

value: PFC


title: PFC-HDAC2-100K-2


title: PFC-HDAC2-NeuN+-80K-1


title: PFC-HDAC2-NeuN+-80K-2


title: Cerebellum-MEF2C-100K-2

value: Cerebellum


title: Cerebellum-MEF2C-100K-1


title: Cerebellum-EGR1-100K-2


title: Cerebellum-EGR1-100K-1


title: PFC-MEF2C-100K-2


title: wildtype control replicate 1

city: Nashville

first: Paul

middle: Brent

last: Ferrell

state: TN

address: 777 Preston Research Bldg., 2220 Pierce Ave.

department: Medicine

institute: Vanderbilt University Medical Center

data_processing:
biological (all 54 bp)
technical -- part 1 of cell barcode (all 8bp)
technical -- library barcode (though files are already demultiplexed; all 8bp)
technical -- part 2 of cell barcode (1-8bp) and UMI (9-14bp)
Raw sequencing data were processed using the previously described (Zilionis et al., Nature Protocols 2017) inDrops.py bioinformatics pipeline, available at https://github.com/indrops/indrops, using library version "v3".
The cDNA read was trimmed using Trimomatic (5) (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:30).
Barcodes for each read were matched against a list of the pre-determined barcodes, and errors of up to two nucleotides mismatch were corrected. Reads with a barcode separated by more than two nucleotides from the reference list were discarded. The reads were then split into barcode-specific files for mapping and UMI filtering.
The trimmed reads were aligned using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 200 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (GRCm38.90) including all annotations with ""Transcript Support Levels"" of 1, 2, or NA (only accepted for protein coding genes).
A custom Python and PySAM script to process mapped reads into counts of UMI-filtered transcripts per gene, as previously described (Zilionis et al., Nature Protocols 2017).
Genome_build: GRCm38
Supplementary_files_format_and_content: mtx, barcodes, genes

source_name: Acute Myeloid Leukemia Cells

growth_protocol: Cells were grown per manufacturer's protocol and harvested at similar titers to ensure no additional variability.

extract_protocol:
Cells were washed out of PBS prior to extraction. Using inDrops, cells were encapsulated into 4-nL droplets on ice and lysed using a final concentration of 0.4% NP-40. Single-cell lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015).
Libraries were prepared as in Zilionis et al., Nat. Protoc. 2017, with modifications summarized in Supplementary Table 7 of Tusi et al., Nature 2018.

treatment_protocol: PBS or IL-1β (20ng/mL) incubation for 3 hours

value: wtIDH

tag: group

value: control

tag: biological replicate

tag: agent

value: PBS


title: wildtype control  replicate 2


title: Wildtype stimulated replicate 1

value: stimulated


title: Wildtype stimulated replicate 2


title: Mutant stimulated replicate 2


title: PFC-EGR1-100K-1


title: Cerebellum-Pol2-total-10K-2


title: PFC-EGR1-100K-2


title: Cerebellum-Pol2-total-50K-1


title: Cerebellum-Pol2-total-50K-2


title: Cerebellum-Pol2-total-10K-1


title: PFC-MEF2C-100K-1


title: PFC-Pol2-total-10K-1


title: PFC-Pol2-total-10K-2


title: PFC-Pol2-total-50K-1


title: Mutant control replicate 2


title: Mutant stimulated replicate 1


title: Control_22_NeuN+_H3K4me3_R1

value: 34 years

tag: disease state

value: Control

value: neuronal nuclei


title: Mutu-LCL cell line, olaparib treated, replicate 1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
Briefly, 75-bp paired reads were separately aligned to the EBV genome (V01555.2) using Bowtie2 (version 2.2.9) with iterative alignment strategy.  Redundant paired reads derived from a PCR bias, reads aligned to repetitive sequences, and reads with low mapping quality (MapQ < 30) were removed.  Reads potentially derived from self-ligation and undigested products were also discarded. EBV genome were divided into 5 kb windows with 1 kb sliding. Raw contact matrices were constructed by counting paired reads assigned to two 5 kb windows. Hi-C biases in contact matrices were corrected using the ICE method
Genome_build: EBV V01555.2
Supplementary_files_format_and_content: ICE normalized interaction matrix for 5kb resolution

source_name: Mutu-LCL cell line

extract_protocol:
After 72 hour incubation with or without olaparib, five million cells per condition were collected for in situ Hi-C as per Rao et al. Cell 2014.
Libraries of total ligation products were produced using Ultralow Library Systems V2 (Tecan Genomics, part no. 0344NB-32) as per manufacturer’s protocol

tag: cell line

value: Mutu LCL

value: olaparib


title: Mutu-LCL cell line, control condition, replicate 2


title: PFC-Pol2-total-50K-2


title: Control_21_NeuN+_H3K4me3_R1

tag: age

value: 48 years

tag: sample type


title: Mutant control replicate 1


title: Mutu-LCL cell line, control condition, replicate 1


title: Mutu I Burkitt Lymphoma cell line, olaparib treated, replicate 1

source_name: Mutu I Burkitt Lymphoma cell line

value: Mutu I


title: Control_20_NeuN+_H3K4me3_R2

value: 56 years

tag: chip antibody


title: Control_20_NeuN+_H3K4me3_R1


title: Control_19_NeuN+_H3K4me3_R2

value: 52 years


title: Mutu I Burkitt Lymphoma cell line, control condition, replicate 1


title: Control_19_NeuN+_H3K4me3_R1


title: Control_18_NeuN+_H3K4me3_R2

value: 36 years


title: Mutu-LCL cell line, olaparib treated, replicate 2


title: Control_15_NeuN+_H3K4me3_R2

value: 74 years


title: Control_13_NeuN+_H3K4me3_R1

value: 49 years


title: Control_14_NeuN+_H3K4me3_R2

value: 71 years


title: Control_13_NeuN+_H3K4me3_R2


title: Control_17_NeuN+_H3K4me3_R1

value: 26 years


title: Control_16_NeuN+_H3K4me3_R1

value: 32 years


title: Control_16_NeuN+_H3K4me3_R2


title: Control_15_NeuN+_H3K4me3_R1


title: Control_11_NeuN+_H3K4me3_R1

value: 33 years


title: Control_12_NeuN+_H3K4me3_R2

value: 44 years


title: Control_17_NeuN+_H3K4me3_R2


title: Control_21_NeuN+_H3K4me3_R2


title: Control_9_NeuN+_H3K4me3_R2

value: 34 years


title: Control_10_NeuN+_H3K4me3_R1

value: 51 years

value: Control


title: Control_11_NeuN+_H3K4me3_R2

value: neuronal nuclei


title: Control_10_NeuN+_H3K4me3_R2


title: Control_9_NeuN+_H3K4me3_R1


title: Control_8_NeuN+_H3K4me3_R2

value: 66 years


title: Control_14_NeuN+_H3K4me3_R1


title: Control_4_NeuN+_H3K4me3_R2


title: Control_6_NeuN+_H3K4me3_R1

value: 28 years


title: Control_8_NeuN+_H3K4me3_R1


title: Control_12_NeuN+_H3K4me3_R1


title: Control_7_NeuN+_H3K4me3_R2

value: 25 years


title: Control_18_NeuN+_H3K4me3_R1


title: Control_7_NeuN+_H3K4me3_R1


title: Control_3_NeuN+_H3K4me3_R2

value: 18 years


title: Control_6_NeuN+_H3K4me3_R2


title: Control_5_NeuN+_H3K4me3_R2


title: Control_4_NeuN+_H3K4me3_R1


title: Control_1_NeuN+_H3K4me3_R2

value: 22 years


title: Control_3_NeuN+_H3K4me3_R1


title: Control_1_NeuN+_H3K4me3_R1


title: SCZ_29_treated_NeuN-_H3K27ac_R1

value: 42 years

value: SCZ

value: antipsychotic medications

value: glial nuclei


title: SCZ_29_treated_NeuN-_H3K27ac_R2


title: SCZ_27_treated_NeuN-_H3K27ac_R1

value: 41 years


title: SCZ_27_treated_NeuN-_H3K27ac_R2


title: SCZ_28_treated_NeuN-_H3K27ac_R1

value: 36 years


title: SCZ_24_treated_NeuN-_H3K27ac_R2

value: 50 years


title: Control_2_NeuN+_H3K4me3_R1

value: 21 years


title: SCZ_26_treated_NeuN-_H3K27ac_R2

value: 56 years


title: Control_5_NeuN+_H3K4me3_R1


title: SCZ_23_treated_NeuN-_H3K27ac_R2

value: 43 years


title: SCZ_25_treated_NeuN-_H3K27ac_R1

value: 60 years


title: SCZ_25_treated_NeuN-_H3K27ac_R2


title: SCZ_23_treated_NeuN-_H3K27ac_R1


title: SCZ_21_treated_NeuN-_H3K27ac_R1

value: 52 years


title: SCZ_26_treated_NeuN-_H3K27ac_R1


title: SCZ_22_treated_NeuN-_H3K27ac_R1

value: 34 years


title: SCZ_20_treated_NeuN-_H3K27ac_R2

value: 58 years


title: Control_2_NeuN+_H3K4me3_R2

value: Control

value: neuronal nuclei


title: SCZ_18_treated_NeuN-_H3K27ac_R2

value: 35 years


title: SCZ_19_treated_NeuN-_H3K27ac_R2

value: 51 years


title: SCZ_19_treated_NeuN-_H3K27ac_R1

value: SCZ


title: SCZ_22_treated_NeuN-_H3K27ac_R2

value: antipsychotic medications


title: SCZ_17_treated_NeuN-_H3K27ac_R2

value: 26 years

value: glial nuclei


title: SCZ_28_treated_NeuN-_H3K27ac_R2

value: 36 years


title: SCZ_24_treated_NeuN-_H3K27ac_R1

value: 50 years


title: SCZ_15_untreated_NeuN-_H3K27ac_R2

value: 74 years

value: untreated


title: SCZ_14_untreated_NeuN-_H3K27ac_R1

value: 70 years


title: SCZ_21_treated_NeuN-_H3K27ac_R2


title: SCZ_15_untreated_NeuN-_H3K27ac_R1


title: SCZ_14_untreated_NeuN-_H3K27ac_R2


title: SCZ_16_treated_NeuN-_H3K27ac_R1

value: 32 years


title: SCZ_12_untreated_NeuN-_H3K27ac_R2

value: 43 years


title: SCZ_13_untreated_NeuN-_H3K27ac_R1

value: 49 years


title: Input_Dnmt_cTKO_EpiLC

city: Vancouver

first: Kentaro

last: Mochizuki

state: BC

address: 2350 Health Sciences Mall

department: Medical Genetics

country: Canada

institute: University of British Columbia

data_processing:
ChIP-seq: Reads were aligned to the mouse genome (mm10) using bwa (Li and Durbin 2009). PCR duplicates were removed by Picard-tools (http://broadinstitute.github.io/picard) and remaining reads with low mapping quality (MAPQ < 5) were excluded by Samtools (http://www.htslib.org/). Smoothed bigWig files were generated by deeptools (Ramírez et al., 2014) with BINSIZE=100 and SMOOTHLENGTH=1000 options.
Aligned reads were converted to bigWig format using bedtools (Quinlan et al., 2010) and bedGraphToBigWig (UCSC).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: EpiLC

extract_protocol:
EpiLC induction was performed essentially as described previously (Hayashi et al., Cell, 2011) with minor modifications. Briefly, pESCs were adapted to 2i (PD0325901, CHIR99021) + LIF feeder-free culture conditions to transit to nESCs. The EpiLCs were induced by plating nESCs in a well coated with human plasma fibronectin (Millipore) in N2B27 medium containing Activin A (R&D), bFGF (Gibco) and KnockOut Serum Replacement (KSR; Gibco). For cKO cells, 4-hydroxytamoxifen (4OHT; Sigma, dissolved in ethanol) at a final concentration of 100 nM was added to culture medium to induce Cre recombinase activity.
ULI-N-ChIP-seq protocol (Brind'Amour et al., Nat Commun, 2015) was used for generating ChIP-seq libraries with some modifications. Briefly, chromatin was fragmentated by MNase (NEB), diluted in native ChIP buffer (20 mM Tris-HCl pH 8.0; 2 mM EDTA; 150 mM NaCl; 0.1% Triton X-100) containing 1 mM PMSF and EDTA-free protease inhibitor cocktail (Roche) and sonicated 5 second sonication cycles for 3 times with low power (Diagenode Bioruptor). Following pre-clearing of chromatin fragments with protein A and G beads (ThermoFisher Scientific), chromatin fragments were split and incubated with each of the histone methylation antibodies at 4 degree for overnight. Following purification of ChIPed DNA by AMPure XP beads, end repair and A-tailing were performed using NEBNext UltraII End Repair/dA-Tailing Module (NEB) and ligation was carried out using NEBNext Ultra II Ligation Module (NEB) with an in-house adaptor which is compatible with Illumina sequencers. After purification of adaptor-ligated products by AMPure XP beads, libraries were amplified with unique indexing primers for 14 cycles. Following purification of the amplified libraries by AMPure XP beads, libraries were pooled, run on 2% E-Gel EX Gel (ThermoFisher Scientific) and the fragments from 200-600 bp was excised and purified by Zymoclean Gel DNA Recovery Kit (Zymo Research).

tag: developmental stage

value: EpiLC

value: Dnmt cTKO


title: SCZ_18_treated_NeuN-_H3K27ac_R1


title: H2AK119ub1_Dnmt_cTKO_nESC

source_name: nESC

value: nESC


title: Input_Dnmt_cTKO_nESC


title: SCZ_11_untreated_NeuN-_H3K27ac_R1


title: SCZ_17_treated_NeuN-_H3K27ac_R1


title: SCZ_10_untreated_NeuN-_H3K27ac_R1

value: 53 years


title: H3K9me3_Dnmt_cTKO_nESC

value: H3K9me3 (Active Motif, 39161)


title: SCZ_16_treated_NeuN-_H3K27ac_R2

value: SCZ


title: SCZ_20_treated_NeuN-_H3K27ac_R1

value: 58 years

value: antipsychotic medications


title: H2AK119ub1_Dnmt_cTKO_EpiLC


title: SCZ_11_untreated_NeuN-_H3K27ac_R2

value: glial nuclei


title: SCZ_9_untreated_NeuN-_H3K27ac_R2

value: 34 years


title: SCZ_13_untreated_NeuN-_H3K27ac_R2


title: Input_Dnmt_WT_EpiLC

value: Dnmt WT


title: H3K9me3_Dnmt_WT_EpiLC


title: H3K9me3_Dnmt_cTKO_EpiLC


title: SCZ_10_untreated_NeuN-_H3K27ac_R2


title: SCZ_12_untreated_NeuN-_H3K27ac_R1


title: H2AK119ub1_Dnmt_WT_nESC


title: Input_Dnmt_WT_nESC


title: H3K9me3_Dnmt_WT_nESC


title: H2AK119ub1_Dnmt_WT_EpiLC


title: SCZ_8_untreated_NeuN-_H3K27ac_R2

value: 67 years


title: SCZ_8_untreated_NeuN-_H3K27ac_R1

value: untreated


title: SCZ_6_untreated_NeuN-_H3K27ac_R2

value: 27 years


title: SCZ_6_untreated_NeuN-_H3K27ac_R1


title: SCZ_7_untreated_NeuN-_H3K27ac_R2

value: 25 years


title: SCZ_5_untreated_NeuN-_H3K27ac_R2

value: 28 years


title: time_release_ATAC_24H_3

city: Madison

first: Melissa

middle: M

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

data_processing:
Adapter sequences were trimmed from raw sequence reads using NGmerge
Reads were aligned to the D. melanogaster genome (version dm6) using Bowtie2 using the following parameters: --very-sensitive, --no-mixed, --no-discordant, -X 5000, -k 2
Aligned reads were filtered to include only reads with a mapping quality score > 30. Reads aligning to scaffolds or the mitochondrial genome were discarded. To identify fragments that likely originated from nucleosome-free regions, fragments were filtered to include only those < 100 bp.
To call peaks on accessible fragments, accessible fragments from all replicates of all time points were merged and MACS2 was used with the following parameters: -f BAMPE, --keep-dup all, -g 1.2e8, --call-summits
Genome_build: dm6
Supplementary_files_format_and_content: Merged peaks are provided as BED files. For each individual sample, a bigWig file is provided representing sequencing depth across the genome.

organism: Drosophila melanogaster

source_name: larval brain

growth_protocol: standard fly food at 25°C

extract_protocol: Nextera DNA Library Preparation Kit (Illumina, San Diego, CA, Cat #FC1211030)

treatment_protocol: Larvae were grown at 25°C and then transferred to 33°C to induce synchronous differentiation of type II neuroblasts (as described in Rives-Quinto et al., 2020)

value: brat11/Df(2L)Exel8040, tub-Gal80TS; UAS-InsbFL-mcy/Wor-Gal4, ase-Gal80

value: L3 larvae

tag: time point


title: time_release_ATAC_24H_2


title: time_release_ATAC_24H_1


title: SCZ_4_untreated_NeuN-_H3K27ac_R2

value: 31 years


title: SCZ_7_untreated_NeuN-_H3K27ac_R1


title: time_release_ATAC_18H_2


title: SCZ_4_untreated_NeuN-_H3K27ac_R1


title: SCZ_3_untreated_NeuN-_H3K27ac_R2

value: 18 years


title: time_release_ATAC_18H_1


title: time_release_ATAC_12H_3


title: SCZ_3_untreated_NeuN-_H3K27ac_R1


title: SCZ_9_untreated_NeuN-_H3K27ac_R1


title: time_release_ATAC_12H_1


title: time_release_ATAC_6H_1


title: time_release_ATAC_0H_3


title: SCZ_2_untreated_NeuN-_H3K27ac_R2

value: 21 years


title: SCZ_2_untreated_NeuN-_H3K27ac_R1


title: SCZ_29_treated_NeuN+_H3K27ac_R2

value: 42 years

value: neuronal nuclei


title: time_release_ATAC_6H_2


title: time_release_ATAC_12H_2


title: time_release_ATAC_0H_1


title: SCZ_1_untreated_NeuN-_H3K27ac_R1

value: 24 years

value: SCZ


title: SCZ_28_treated_NeuN+_H3K27ac_R1

value: 36 years

value: antipsychotic medications


title: SCZ_28_treated_NeuN+_H3K27ac_R2


title: SCZ_29_treated_NeuN+_H3K27ac_R1


title: SCZ_5_untreated_NeuN-_H3K27ac_R1

value: glial nuclei


title: SCZ_26_treated_NeuN+_H3K27ac_R2

value: 56 years


title: SCZ_26_treated_NeuN+_H3K27ac_R1


title: hp1gamma_cr_e13_wt_rep1_R1

data_processing:
library strategy: CUT&RUN
ATACseq and Histone ChIPseq were aligned to mm9 (UCSC) genome assembly using BWA mem (v0.7.17). CUT&RUN reads were aligned to mm9 genome assembly using Bowtie2 default mode. RNA-seq reads were mapped to mm9 genome assembly using HISAT2 (v2.0.5).
Bigwig files were generated using deepTools bamCoverage (v3.4.3)
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files generated using deepTools.

source_name: whole telencephalon

tag: experiment

value: CUT&RUN

tag: tissue

value: whole telencephalon

value: anti-HP1gamma (Abcam, Cat# ab10480)

tag: replicate

value: POGZ +/+

value: Protocol 4


title: hp1gamma_cr_e13_wt_rep2_R1

tag: genotype

tag: strain background

tag: protocol used


title: adnp_cr_e13_wt_rep2_R1

value: anti-ADNP (Invitrogen, Cat# PA5-47792)


title: SCZ_1_untreated_NeuN-_H3K27ac_R2

source_name: glial nuclei from Brodmann area 9 (BA9) of postmortem brain tissue

tag: treatment

value: untreated


title: IgG_cr_e13_wt_rep2

value: anti-IgG (Stem Cell Technologies, Cat# 60129AV)


title: SCZ_24_treated_NeuN+_H3K27ac_R2

source_name: neuronal nuclei from Brodmann area 9 (BA9) of postmortem brain tissue

value: 50 years


title: SCZ_27_treated_NeuN+_H3K27ac_R2

value: 41 years


title: SCZ_25_treated_NeuN+_H3K27ac_R1

value: 60 years

value: neuronal nuclei


title: SCZ_25_treated_NeuN+_H3K27ac_R2

value: SCZ


title: SCZ_24_treated_NeuN+_H3K27ac_R1


title: IgG_cr_e13_wt_rep1


title: time_release_ATAC_0H_2

value: brat11/Df(2L)Exel8040, tub-Gal80TS; UAS-InsbFL-mcy/Wor-Gal4, ase-Gal80

value: L3 larvae


title: SCZ_23_treated_NeuN+_H3K27ac_R2

value: 43 years

value: antipsychotic medications


title: SCZ_23_treated_NeuN+_H3K27ac_R1


title: pogz_cr_e13_ko_rep1

value: CUT&RUN

value: anti-POGZ (Abcam, Cat# ab171934)

value: POGZ -/-


title: SCZ_22_treated_NeuN+_H3K27ac_R2

value: 34 years


title: pogz_cr_e13_wt_rep1

value: whole telencephalon

value: POGZ +/+

value: Protocol 4


title: SCZ_21_treated_NeuN+_H3K27ac_R2

value: 52 years


title: SCZ_22_treated_NeuN+_H3K27ac_R1


title: SCZ_27_treated_NeuN+_H3K27ac_R1


title: SCZ_21_treated_NeuN+_H3K27ac_R1


title: SCZ_20_treated_NeuN+_H3K27ac_R2

value: 58 years


title: SCZ_20_treated_NeuN+_H3K27ac_R1


title: SCZ_18_treated_NeuN+_H3K27ac_R2

value: 35 years


title: adnp_cr_e13_wt_rep1_R1

value: anti-ADNP (Invitrogen, Cat# PA5-47792)


title: SCZ_19_treated_NeuN+_H3K27ac_R2

value: 51 years

value: neuronal nuclei


title: SCZ_19_treated_NeuN+_H3K27ac_R1

value: SCZ


title: SCZ_18_treated_NeuN+_H3K27ac_R1


title: SCZ_17_treated_NeuN+_H3K27ac_R1

value: 26 years


title: SCZ_16_treated_NeuN+_H3K27ac_R2

value: 32 years


title: SCZ_16_treated_NeuN+_H3K27ac_R1

value: antipsychotic medications


title: H4K20me3_cr_e13_wt_R1

value: CUT&RUN

value: anti-H4K20me3 (Abcam, Cat# ab9053)


title: AF29

city: Rome

first: Linda

last: Quatrini

address: Via San Paolo 15

department: Immunology

country: Italy

institute: IRCCS Bambino Gesù Pediatric Hospital

description:
NormCount.xlsx
RawCount.xlsx

data_processing:
RNA sequencing was performed with a NextSeq 500 (Illumina; paired-end reads 2 × 75 with 30 M reads per sample)
The fastq files were assessed with the fastqc program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc)
Cutadapt (https://journal.embnet.org/index.php/embnetjournal/article/view/200) was used to remove the adapter sequence (if present) and the very short reads (reads length < 20)
Genome_build: The samples were mapped on reference Homo Sapiens genome (HG38)
Supplementary_files_format_and_content: the number of reads mapped to each gene was determined with featureCounts

source_name: peripheral blood mononuclear cells

extract_protocol:
RNA was extracted with an RNeasy Plus Micro Kit (Qiagen)
The DNA libraries were generated with the TruSeq stranded mRNA prep kit (Illumina)

tag: cell subset

value: CD34+ HSC

tag: in vitro colture

value: 10 days with SCF+FLT3L+IL15 +IL7+ vehicle (DMSO)


title: SCZ_17_treated_NeuN+_H3K27ac_R2


title: AF29DEX

description:
NormCount.xlsx
RawCount.xlsx

value: 10 days with SCF+FLT3L+IL15 +IL7+ Dexamethasone


title: AF26

description:
NormCount.xlsx
RawCount.xlsx


title: AF26DEX

description:
NormCount.xlsx
RawCount.xlsx


title: AF25DEX

description:
NormCount.xlsx
RawCount.xlsx


title: pogz_cr_e13_wt_rep2

value: whole telencephalon

value: anti-POGZ (Abcam, Cat# ab171934)

value: POGZ +/+


title: SCZ_15_untreated_NeuN+_H3K27ac_R1

value: 74 years

value: untreated


title: SCZ_15_untreated_NeuN+_H3K27ac_R2


title: pogz_cr_e13_ko_rep2_R1

value: POGZ -/-

value: Protocol 4


title: SCZ_14_untreated_NeuN+_H3K27ac_R1

value: 70 years

value: neuronal nuclei


title: AF25

description:
NormCount.xlsx
RawCount.xlsx


title: SCZ_13_untreated_NeuN+_H3K27ac_R1

value: 49 years

value: SCZ


title: SCZ_13_untreated_NeuN+_H3K27ac_R2


title: SCZ_12_untreated_NeuN+_H3K27ac_R2

value: 43 years


title: IgG in Mutu I cell line

data_processing:
CHIP-seq data was aligned using bowtie against NC_007605 version of the EBV genome
Genome_build: EBV NC_007605
Supplementary_files_format_and_content: CHIP-seq signal in bigwig format

extract_protocol:
25 million cells per immunoprecipitation were collected and fixed with 1% formaldehyde to preserve all DNA-protein interactions for 15 minutes and then quenched with .25M glycine for 5 minutes on ice. Pellet was resuspended after centrifugation in 10mL each of a series of three lysis buffers before fragmentation in Qsonica sonicator (90AMP, 25 sonication cycles, 30 seconds on/30 seconds off) to generate chromatin fragments roughly 200-500bp in size. Chromatin was centrifuged to clear of debris and a sample of this cleared chromatin (1% of total material) was kept as a standard input for comparison against immunoprecipitations
Libraries for sequencing were made NEBNext® Ultra™ II DNA Library Prep Kit

tag: celline

value: Mutu I Burkitt Lymphoma cell line

tag: antibody

value: IgG

tag: antibody vendon/catalog

value: Jackson ImmunoResearch, Product No. 111-005-003


title: SCZ_12_untreated_NeuN+_H3K27ac_R1

tag: age

tag: disease state


title: 2D cells 1

city: Plovdiv

first: Yordan

last: Sbirkov

address: 15 A Vassil Aprilov Blvd

department: Medical Biology

country: Bulgaria

institute: Medical University of Plovdiv

data_processing:
First 5 steps were carried out by Novogene UK. Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling)
Filter the raw reads and obtain the clean reads - (1)Remove reads with adaptor contamination. (2)Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). (3)Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
HISAT2 is selected to map the filtered sequenced reads to the reference genome.
Gene expression level is estimated by the abundance of transcripts (count of sequencing) that mapped to genome or exon. Read counts is proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments (Mortazavi et al. 2008)
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (Anders et al., 2010). It provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. Therefore, if the readcount of the i-th gene in j-th sample is Kij, there is: Kij ～ NB(μij,σij2) And the resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.
GO analysis with BinGO in Cytoscape and GSEA analysis with GSEA Software (Broad Institute)
Genome_build: ensembl_homo_sapiens_grch38_p12
Supplementary_files_format_and_content: Processed data is in text matrix format (DEG_3DBP_vs_2D_fpkm.xlsx). This is the gene list used for GO and GSEA analysis with differentially expressed genes (DEG) at 1.5 FC and adj p-value<0.05). The file contains Gene ID, log2Fold Change, padj values, gene_name, as well as  columns with FPKM values for each sample  - BP_3D1, BP_3D2 for 3DBP cells, and Ctrl_2D1 and Ctrl_2D2 for 2D cultured cells.

source_name: Caco-2 cells – colorectal cancer

growth_protocol: DMEM/F12 with 10% FCS and 0.5% Pen/Strep

extract_protocol:
Rneasy kit (Qiagen)
Sequencing was outsourced to Novogene UK -  NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used for library preparation with AMPure XP beads (Beckman Coulter, Beverly, USA) for size selection and PCR purification steps, both performed as instructed by the manufacturers.

treatment_protocol: 30uM of Atovaquone for 3 days

tag: cell line

tag: tumour

value: Colorectal cancer

tag: origin

value: Colon carcinoma

tag: condition

value: 3D bioprint


title: 3DBP cells 1

value: 2D monolayer


title: 3DBP cells 2


title: 2D cells 2


title: batch9_hashed_UT_mouse2_VDJ

description: cells pooled from multiple tissues of 1 mouse

data_processing:
Library strategy: VDJ-seq
Basecalls performed by RTA v2.4.11.
Fastq files were generated from bcl with CellRanger v3.0.2 with default parameters.
For scRNA-seq (GEX library), reads were mapped to mm10 and UMI count matrices were computed by CellRanger v3.0.2. Default parameters were used except that "chemistry" was set to "SC3Pv2" for batch 1-5, and "fiveprime" for batch 6-9.
To obtain the expression of Il17-GFP, reads were mapped to a custom reference transcriptome built with the CellRanger mkref command that included the Il17aGFP transcript (Il17aGFP and mm10 chr19). UMI counts computed in the same way as for the whole mm10 reference.
For hashtags (ADT library), reads were mapped to hashtag oligo sequences and UMI count matrices were computed by CellRanger v3.0.2. DemuxEM v0.1.5 with default parameters was then applied to identify hashtag labels for each cell.
For scTCR-seq (VDJ library), paired reads were mapped to GRCm38 V(D)J sequences (build from Ensembl Mus_musculus.GRCm38.90.chr_patch_hapl_scaff.gtf) and UMI counts were computed using CellRanger v3.0.2 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz, features.tsv.gzand matrix.mtx.gzfiles together define a matrix of raw UMI counts
Supplementary_files_format_and_content: metadata_demuxEM.csv contains the tissue labels of cells inferred by demuxEM
Supplementary_files_format_and_content: all_contig_annotations.csv contains the information (e.g. V(D)J genes, CDR3 sequences, UMI counts) for all TCR contigs identified in the sample.

source_name: Il17CreTdtomato+ cells from mutliple tissue

growth_protocol: Mice were housed under specific-pathogen-free conditions (SPF) at the Brigham and Women’s Hospital mouse facility in Boston. Tissue Th17 cells were collected when mice are 8-12 weeks old.

extract_protocol:
For tissue harvest, mice were perfused intracardially with cold PBS. Lymphoid tissues, spleen and mesenteric lymph nodes were harvested and smashed through 40 um sterile strainers. ACK lysis (Buffer from Lonza) was performed with the spleen for 5 min at RT. Peyer’s patches were digested for 20 min at 37C in a water bath in digestion buffer (5% fetal bovine serum, 50 g/ml DNase I (Sigma Aldrich), 1 mg/ml Collagenase Type VIII (Sigma Aldrich), 2 mM CaCl2 (Sigma Aldrich), 5 mM MgCl2 (Sigma Aldrich) in RPMI 1640 medium (Thermo Fisher Scientific)) and smashed through a 40 um sterile strainer. To isolate cells from the small intestine and the colon, intestinal tissues were harvested and cleaned. Epithelial cells and intraepithelial lymphocytes were removed by incubating the tissues for 20 min at 37C with constant stirring at 350 rpm in extraction buffer (5% fetal bovine serum, 1 mM DTT (Thermo Fischer Scientific), 5 mM EDTA (Thermo Fisher Scientific) in RPMI 1640 medium (Thermo Fisher Scientific)). Tissues were minced and incubated in digestion buffer for 40 min at 37C with constant stirring at 550 rpm and smashed through a 40 um sterile strainer. To isolate CNS-infiltrating lymphocytes from EAE mice, brain and spinal cord were flushed out with PBS by hydrostatic pressure. The CNS was minced and digested in 2.5 mg/ml Collagenase D (Roche Diagnostics) in RPMI 1640 medium (Thermo Fisher Scientific) for 20 min at 37C. Cells were smashed through a 40 um sterile cell strainer and mononuclear cells were enriched on a discontinuous (37% and 70%) Percoll gradient (Cytiva). After tissue cell isolation, cells were stained for flow cytometry.   Single-cell suspensions were stained in flow buffer (2% fetal bovine serum in PBS) with antibodies for surface proteins. Viable CD4+ TCR+ tdTomato+ tissue Th17 cells were sorted by FACS for sequencing. Cell hashing was performed with samples for scRNA/TCR-Seq in order to process all tissues of one mouse together in one 10x channel. After the sort, cells were resuspended in flow buffer with the TotalSeqTM-antibody pool (Biolegend) at 1:1000 final dilution for each antibody, followed by incubation for 30 min on ice. Next, cells were washed for a total of three washes with flow buffer. Samples for scRNA/TCR-Seq with 5' feature barcoding were then separated into droplet emulsions using the Chromium Single Cell 5' V2 Solution, according to manufacturer’s instructions (10x Genomics). For samples that did not include scTCR-seq and 5' feature barcoding, sorted cells were separated into droplet emulsions using the Chromium Single Cell 3′ Solution (v2 or v3) according to manufacturer’s instructions (10x Genomics).
ScRNA-seq, scTCR-seq and 5' feature barcoding library preparations were performed according to manufacturer’s instructions (10x Genomics). Single Cell 3' v2 chemistry was used for non-cell-hashing samples (batch 1-5), and Single Cell 5' chemistry was used for cell-hashing samples (batch6-9).

treatment_protocol: For active induction of EAE, mice were immunized subcutaneously in the flanks with the myelin oligodendrocyte glycoprotein (MOG) peptide MOG35-55 (100 mg/mouse, Genemed Synthesis), emulsified in complete Freund’s adjuvant (CFA) (200 ml/mouse, Becton Dickinson), and supplemented with Mycobacterium tuberculosis H37Ra extract (5 mg/ml, Becton Dickinson). Pertussis toxin (100 ng/mouse, List Biological Laboratories) was administered intravenously into the tail vein on day 0 and day 2 post immunization.  Disease course was monitored daily, and mice were assigned a clinical score as follows: 0, healthy; 1, limp tail; 2, hind limb weakness or impaired righting reflex; 3, hind limb paralysis; 4, hind and front limb paralysis; 5, moribund or dead. Mice with a clinical score >4 were euthanized.

tag: tissue

value: SPL, MLN, PP, SI, COL

tag: cell type

value: Homeostasis


title: batch9_hashed_UT_mouse1_VDJ


title: SCZ_11_untreated_NeuN+_H3K27ac_R2

data_processing:
Sequencing reads were trimmed by trim galore v0.6.5 with default parameters. Trimmed ChIP-seq reads were mapped to the hg38 genome with bowtie2 v2.4.1. Peaks were called using MACS2 v2.2.7.1 (q < 0.05). Mapped reads from ChIP and input samples were extended by 100 bp on either side (250 bp total) and a normalized signal was calculated. For visualization in IGV v2.8.12 (Broad Institute), the signal was calculated in 100bp windows over the entire genome and output as a bigWig file.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files are converted by wigToBigWig. Raw counts of sequencing reads were generated by featureCounts.

value: 32 years

value: untreated

tag: sample type

tag: chip antibody


title: SCZ_11_untreated_NeuN+_H3K27ac_R1


title: SCZ_10_untreated_NeuN+_H3K27ac_R2

value: 53 years


title: batch8_hashed_UT_mouse2_ADT

data_processing:
Library strategy: ADT-seq
Basecalls performed by RTA v2.4.11.
Fastq files were generated from bcl with CellRanger v3.0.2 with default parameters.
For scRNA-seq (GEX library), reads were mapped to mm10 and UMI count matrices were computed by CellRanger v3.0.2. Default parameters were used except that "chemistry" was set to "SC3Pv2" for batch 1-5, and "fiveprime" for batch 6-9.
To obtain the expression of Il17-GFP, reads were mapped to a custom reference transcriptome built with the CellRanger mkref command that included the Il17aGFP transcript (Il17aGFP and mm10 chr19). UMI counts computed in the same way as for the whole mm10 reference.
For hashtags (ADT library), reads were mapped to hashtag oligo sequences and UMI count matrices were computed by CellRanger v3.0.2. DemuxEM v0.1.5 with default parameters was then applied to identify hashtag labels for each cell.
For scTCR-seq (VDJ library), paired reads were mapped to GRCm38 V(D)J sequences (build from Ensembl Mus_musculus.GRCm38.90.chr_patch_hapl_scaff.gtf) and UMI counts were computed using CellRanger v3.0.2 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz, features.tsv.gzand matrix.mtx.gzfiles together define a matrix of raw UMI counts
Supplementary_files_format_and_content: metadata_demuxEM.csv contains the tissue labels of cells inferred by demuxEM
Supplementary_files_format_and_content: all_contig_annotations.csv contains the information (e.g. V(D)J genes, CDR3 sequences, UMI counts) for all TCR contigs identified in the sample.


title: batch8_hashed_UT_mouse2_VDJ


title: SCZ_10_untreated_NeuN+_H3K27ac_R1


title: SCZ_14_untreated_NeuN+_H3K27ac_R2

value: 70 years


title: EgAGL9_input

city: Hainan

first: zhang

last: qing

address: 58 renmin avenue

department: Department of Biotechnology, College of Tropical Crops Hainan University, Haikou 570228, Hainan, China

institute: hainan university

description: Elaeis guineensis Jacq

data_processing:
Quality distribution plot and base content distribution were generated by FASTQC. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences.
Paired-end ChIP-Seq reads were aligned using BWA mem (v.0.7.8) (Li and Durbin, 2009) against the Elaeis_guineensis_Jacq genome assembly with default settings.
For peak calling, MACS2 callpeak (v2.1.1) (Zhang et al., 2008) were called on individual replicates for each ChIP (treatment) and Input (control) pair, using q value < 0.05.
The HOMER's findMotifsGenome.pl tool was used for Motif analysis.
Peaks were annotated by the function of annotatePeak of ChIPseeker.
Genome_build: Elaeis_guineensis_Jacq
Supplementary_files_format_and_content: Eg-F1-IPVSEg-F1-INPUT_peaks.narrowPeak: Peak text file.
Supplementary_files_format_and_content: *.bw: bigwig files were generated using MACS2.

organism: Elaeis guineensis

source_name: Fruit Elaeis guineensis Jacq

growth_protocol:
Temperature: The annual average temperature is above 18°C, and the temperature must not change significantly.
Rainfall: If the rainy season is only about 8 months, the annual rainfall needs 1500 mm.
Sunshine: Oil palm likes sunshine, and the rainy season should not be too long.
Soil: Oil palm has low requirements on soil and can grow in unsuitable cultivation.
Terrain: Undulating, well-drained terrain is the best.

extract_protocol: Libraries were prepared following the NEB/NEBNext® Library Quant Kit for Illumina® (E7630S).

treatment_protocol: No treatment. EgAGL9 overexpression in oil palm fruit.

tag: cultivar

value: Jacq

tag: genotype

value: EgAGL9 overexpression

value: Fruit


title: batch8_hashed_UT_mouse2_GEX

data_processing:
Basecalls performed by RTA v2.4.11.
Fastq files were generated from bcl with CellRanger v3.0.2 with default parameters.
For scRNA-seq (GEX library), reads were mapped to mm10 and UMI count matrices were computed by CellRanger v3.0.2. Default parameters were used except that "chemistry" was set to "SC3Pv2" for batch 1-5, and "fiveprime" for batch 6-9.
To obtain the expression of Il17-GFP, reads were mapped to a custom reference transcriptome built with the CellRanger mkref command that included the Il17aGFP transcript (Il17aGFP and mm10 chr19). UMI counts computed in the same way as for the whole mm10 reference.
For hashtags (ADT library), reads were mapped to hashtag oligo sequences and UMI count matrices were computed by CellRanger v3.0.2. DemuxEM v0.1.5 with default parameters was then applied to identify hashtag labels for each cell.
For scTCR-seq (VDJ library), paired reads were mapped to GRCm38 V(D)J sequences (build from Ensembl Mus_musculus.GRCm38.90.chr_patch_hapl_scaff.gtf) and UMI counts were computed using CellRanger v3.0.2 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz, features.tsv.gzand matrix.mtx.gzfiles together define a matrix of raw UMI counts
Supplementary_files_format_and_content: metadata_demuxEM.csv contains the tissue labels of cells inferred by demuxEM
Supplementary_files_format_and_content: all_contig_annotations.csv contains the information (e.g. V(D)J genes, CDR3 sequences, UMI counts) for all TCR contigs identified in the sample.