title: CT_LCG_6

city: Shenyang

first: yu

last: zhang

address: Dongling Street

institute: Shenyang Agricultural University

data_processing:
Library strategy: Ribo-seq
Poly-N, adapter and low-quality were removed by in-house perl scripts ，Quality control analysis was performed by ng_qc.
Quantification of mapped results to gene level was carried out using HTSeq
Ribo-seq used TopHat2 for genome map
For samples with biological replicates, DESeq2 R package (1.14.1) was used for differential expression analysis
Genome_build: Capra hircus NCBI genome GCA_001704415.1
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...

organism: Capra hircus

source_name: skin

extract_protocol: To digest the RNA other than RPFs, cell or tissue lysate was treated with unspecific endoribonuclease RNase ǀ.  Isolation of monosomes was performed by size-exclusion chromatography with MicroSpin S-400 HR columns. The RNA samples were then treated with rRNA depletion kit to deplete the samples of as much rRNA  contamination as possible before PAGE purification of the relatively short (20~38 nt) RPFs. Following PAGE  purification, the both ends of RPF were phosphorylated and ligated with 5’ and 3’ adapters respectively. Then the  fragments were reversely transcribed to the cDNAs and amplified by PCR.

tag: phenotype

value: coarse Liaoning cashmere


title: CT_LCG_4

status: Public on Nov 05 2021

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA


title: CT_LCG_5


title: batch8_hashed_UT_mouse1_VDJ

city: Boston

first: Linglin

last: Huang

state: MA

address: 60 Fenwood Road, HBTM 10016F

department: Neurology

country: USA

institute: Brigham and Women’s Hospital

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.

organism: Mus musculus

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

tag: disease state

value: Homeostasis


title: FT_LCG_2

value: fine Liaoning cashmere


title: SCZ_9_untreated_NeuN+_H3K27ac_R1

city: Blacksburg

first: Chang

last: Lu

state: VA

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

department: Chemical Engineering

institute: Virginia Tech

library_source: genomic

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.

molecule: genomic DNA

organism: Homo sapiens

source_name: neuronal 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: 34 years

value: SCZ

tag: treatment

value: untreated

tag: sample type

value: neuronal nuclei

tag: chip antibody


title: CTCF in Mutu I cell line

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

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

source_name: Mutu I Burkitt Lymphoma cell line

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: CTCF

tag: antibody vendon/catalog

value: Active Motif Catalog No. 61311


title: FT_LCG_1


title: SCZ_9_untreated_NeuN+_H3K27ac_R2


title: batch7_hashed_EAE_mouse2_VDJ

value: SPL, MLN, PP, SI, COL, CNS, DLN

value: EAE


title: FT_LCG_3


title: SCZ_8_untreated_NeuN+_H3K27ac_R2

value: 67 years


title: sfGFP-Zld_aGFP_input_1

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:
Adapters and low-quality bases were removed using Trimmomatic-0.39
Reads were mapped to the dm6 genome assembly using Bowtie 2
Unmapped, multiply aligning, mitochondrial, and scaffold reads were removed using SAMtools
MACS2 was used with an m-fold range of 3 to 50 to call peaks.
Genome_build: dm6
Supplementary_files_format_and_content: ChIP-seq or ATAC-seq 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: Type II neuroblasts

growth_protocol: standard fly food at 25°C

extract_protocol: NEB Next Ultra II DNA library kit (New England BioLabs Inc, Ipswich, MA, Cat #E7645S)

tag: genotype

tag: developmental stage

value: L3 larvae


title: sfGFP-Zld_aGFP_ChIP_1

value: α-GFP (Abcam, Cambridge, UK, Cat #ab290)


title: batch7_hashed_EAE_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: typeII_NB_ATAC_1

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 both replicates 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: ChIP-seq or ATAC-seq peaks are provided as BED files. For each individual sample, a bigWig file is provided representing sequencing depth across the genome.

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


title: Zld_aZld_ChIP_2

data_processing:
Adapters and low-quality bases were removed using Trimmomatic-0.39
Reads were mapped to the dm6 genome assembly using Bowtie 2
Unmapped, multiply aligning, mitochondrial, and scaffold reads were removed using SAMtools
MACS2 was used with default parameters to call ChIP peaks.
Genome_build: dm6
Supplementary_files_format_and_content: ChIP-seq or ATAC-seq peaks are provided as BED files. For each individual sample, a bigWig file is provided representing sequencing depth across the genome.

value: α-Zelda (Harrison et al., 2011)


title: batch7_hashed_EAE_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.


title: EgAGL9_IP

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

value: EgAGL9 overexpression

value: Fruit


title: SCZ_7_untreated_NeuN+_H3K27ac_R2

value: 25 years


title: SCZ_7_untreated_NeuN+_H3K27ac_R1


title: Zld_aZld_input_1


title: Zld_aZld_input_2


title: Zld_aZld_ChIP_1


title: batch7_hashed_EAE_mouse1_VDJ


title: batch7_hashed_EAE_mouse1_ADT


title: SCZ_6_untreated_NeuN+_H3K27ac_R1

value: 27 years


title: typeII_NB_ATAC_2

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 both replicates 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: ChIP-seq or ATAC-seq peaks are provided as BED files. For each individual sample, a bigWig file is provided representing sequencing depth across the genome.


title: SCZ_8_untreated_NeuN+_H3K27ac_R1

value: SCZ


title: SCZ_5_untreated_NeuN+_H3K27ac_R2

value: 28 years

value: untreated


title: SCZ_5_untreated_NeuN+_H3K27ac_R1

value: neuronal nuclei


title: batch7_hashed_EAE_mouse1_GEX


title: batch6_hashed_EAE_mouse2_VDJ


title: SCZ_4_untreated_NeuN+_H3K27ac_R2

value: 31 years


title: batch6_hashed_EAE_mouse1_VDJ


title: 12 weeks Smoke 2

type: RNA

city: Ultimo

first: Philip

last: Hansbro

address: 15 Broadway

country: Australia

institute: University of Technology Sydney

description: miRNA expression (12 weeks; smoke)

hyb_protocol: Samples were reconstituted with 18μL of nuclease-free water and blocked with 4.5μL of kit-supplied 10X gene expression and supplied with 22.5μL of Hi-RPM hybridisation buffer. Samples were later heated and cooled for 5 mins at 100°C and on ice and then then hybridised to the microarray chips (55°C for 20 hours). Hybridised microarrays chips were washed with the supplied wash buffers and scanned with an Agilent microarray scanner.

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Scanner (G2505C) using one color scan setting for 8 x 15k array slides.

data_processing:
Raw microarray data was extracted using the scanner software’s feature extraction function.
Signals were background corrected and normalized with quantile method by using the rmaMicroRna function of AgiMicroRna package. The measured itensities are log2 transformed. The microRNAs that did not reach a minimum of quality were filtered out. After processing, the expression set was saved as processed data for further analysis.

source_name: Lung

label_protocol: 100ng of total RNA was incubated with 2μL of calf intestinal alkaline phosphatase (CIP) master mix2 and 2.8μL of dimethyl sulfoxide (DMSO) was added and denaturation was carried at 100°C for 5 minutes. These denatured samples were incubated with 4.5μL of ligation master mix to label them 3’ end. These labelled samples were supplemented with nuclease-free water and purified from DMSO and free Cyanine3-pCp by elution through Micro Bio-Spin 6 columns (1000xg for 2 minutes) followed by drying with a vacuum concentrator for 50°C for 1 hour.

extract_protocol: RNA was iprepared using TRizol (Invitrogen) extraction method following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Mice were exposed to cigarette smoke (or room air) for 4, 6, 8, 12 weeks, lungs were excised, and total RNA isolated.

value: Lung

tag: gender

value: Female

tag: strain

value: BALB/c

value: 12 weeks Smoke


title: 12 weeks Smoke 3

description: miRNA expression (12 weeks; smoke)


title: 12 weeks Control 3

description: miRNA expression (12 weeks; control)

value: 12 weeks Control


title: 8 weeks Smoke 4

description: miRNA expression (8 weeks; smoke)

value: 8 weeks Smoke


title: 12 weeks Control 2

description: miRNA expression (12 weeks; control)


title: 12 weeks Control 1

description: miRNA expression (12 weeks; control)


title: batch4_CNS_EAE

description: cells pooled from 2 mice

source_name: Il17CreTdtomato+ cells from CNS

value: CNS

value: EAE


title: 12 weeks Smoke 1

description: miRNA expression (12 weeks; smoke)


title: SCZ_6_untreated_NeuN+_H3K27ac_R2


title: 8 weeks Smoke 3

description: miRNA expression (8 weeks; smoke)


title: batch4_COL_EAE

description: cells pooled from 2 mice

source_name: Il17CreTdtomato+ cells from colon

value: colon


title: 8 weeks Smoke 2

description: miRNA expression (8 weeks; smoke)


title: SCZ_3_untreated_NeuN+_H3K27ac_R2

value: 18 years


title: batch4_COL_UT

description: cells pooled from 2 mice

value: Homeostasis


title: batch4_SI_EAE

description: cells pooled from 2 mice

source_name: Il17CreTdtomato+ cells from small intestine

value: small intestine


title: 8 weeks Smoke 1

description: miRNA expression (8 weeks; smoke)


title: 8 weeks Control 3

description: miRNA expression (8 weeks; control)

value: 8 weeks Control


title: 8 weeks Control 2

description: miRNA expression (8 weeks; control)


title: 8 weeks Control 4

description: miRNA expression (8 weeks; control)


title: 12 weeks Control 4

description: miRNA expression (12 weeks; control)


title: SCZ_3_untreated_NeuN+_H3K27ac_R1

value: SCZ


title: SCZ_2_untreated_NeuN+_H3K27ac_R2

value: 21 years

value: untreated


title: batch4_SI_UT

description: cells pooled from 2 mice


title: 8 weeks Control 1

description: miRNA expression (8 weeks; control)


title: SCZ_4_untreated_NeuN+_H3K27ac_R1

value: 31 years

value: neuronal nuclei


title: 6 weeks Smoke 4

description: miRNA expression (6 weeks; smoke)

value: Lung

value: Female

value: 6 weeks Smoke


title: SCZ_2_untreated_NeuN+_H3K27ac_R1


title: batch3_CNS_EAE

description: cells pooled from 2 mice


title: SCZ_1_untreated_NeuN+_H3K27ac_R2

value: 24 years


title: batch4_PP_UT

description: cells pooled from 2 mice

source_name: Il17CreTdtomato+ cells from peyers patches

value: Peyer's patches


title: 6 weeks Smoke 3

description: miRNA expression (6 weeks; smoke)

value: BALB/c


title: batch4_MLN_UT

description: cells pooled from 2 mice

source_name: Il17CreTdtomato+ cells from mesenteric lymph nodes

value: mesenteric lymph nodes


title: batch3_COL_EAE

description: cells pooled from 2 mice

value: colon

value: EAE


title: 6 weeks Control 2

description: miRNA expression (6 weeks; control)

value: 6 weeks Control


title: 6 weeks Control 1

description: miRNA expression (6 weeks; control)


title: 6 weeks Smoke 2

description: miRNA expression (6 weeks; smoke)


title: 6 weeks Control 3

description: miRNA expression (6 weeks; control)


title: 6 weeks Control 4

description: miRNA expression (6 weeks; control)


title: 6 weeks Smoke 1

description: miRNA expression (6 weeks; smoke)


title: SCZ_29_treated_NeuN-_H3K4me3_R1

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

value: 42 years

value: antipsychotic medications

value: glial nuclei


title: 4 weeks Smoke 4

description: miRNA expression (4 weeks; smoke)

value: 4 weeks Smoke


title: SCZ_1_untreated_NeuN+_H3K27ac_R1

value: SCZ

value: untreated


title: 4 weeks Smoke 2

description: miRNA expression (4 weeks; smoke)


title: 4 weeks Smoke 3

description: miRNA expression (4 weeks; smoke)


title: SCZ_29_treated_NeuN-_H3K4me3_R2


title: 4 weeks Smoke 1

description: miRNA expression (4 weeks; smoke)


title: batch3_SI_EAE

description: cells pooled from 2 mice

value: small intestine


title: SCZ_28_treated_NeuN-_H3K4me3_R2

value: 36 years


title: 4 weeks Control 3

description: miRNA expression (4 weeks; control)

value: Lung

value: Female

value: 4 weeks Control


title: batch3_COL_UT

description: cells pooled from 2 mice

value: Homeostasis


title: 4 weeks Control 4

description: miRNA expression (4 weeks; control)

value: BALB/c


title: batch3_SI_UT

description: cells pooled from 2 mice


title: SCZ_28_treated_NeuN-_H3K4me3_R1


title: 4 weeks Control 2

description: miRNA expression (4 weeks; control)


title: Colon_DSS

data_processing:
Basecalls performed by RTA v2.4.11.
Fastq files were generated from bcl with CellRanger v2.1.0 with default parameters.
Reads were mapped to mm10 and UMI count matrices were computed by CellRanger v2.1.0 with default parameters,
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz files together define a matrix of raw UMI counts

extract_protocol:
For tissue harvest, mice were perfused intracardially with cold PBS. To isolate cells from the colon, intestinal tissues were harvested and cleaned. Epithelial cells and intraepithelial lymphocytes were removed by incubating the tissues for 20 min at 37ºC 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 37ºC with constant stirring at 550 rpm and smashed through a 40 um sterile strainer. Viable CD4+ TCR+ tdTomato+ tissue Th17 cells were sorted by FACS for sequencing.
ScRNA-seq library preparations were performed according to manufacturer’s instructions (10x Genomics, Single Cell 3' v2 chemistry)

treatment_protocol: Colitis was induced by adding 2% DSS (Affymetrix) to the drinking water on days 0-7, followed by a two-day recovery period with normal drinking water. The disease progression was monitored by measurement of the body weight.

value: DSS-induced colitis


title: 4 weeks Control 1

description: miRNA expression (4 weeks; control)


title: batch3_SPL_EAE

description: cells pooled from 2 mice

source_name: Il17CreTdtomato+ cells from spleen

value: Spleen


title: batch9_hashed_UT_mouse2_ADT

value: SPL, MLN, PP, SI, COL


title: SCZ_27_treated_NeuN-_H3K4me3_R2

value: 41 years


title: Colon_UT

value: colon


title: batch9_hashed_UT_mouse2_GEX


title: SCZ_25_treated_NeuN-_H3K4me3_R2

value: 60 years

value: antipsychotic medications


title: SCZ_27_treated_NeuN-_H3K4me3_R1

value: glial nuclei


title: batch2_CNS_EAE

description: cells pooled from 2 mice

value: CNS

value: EAE


title: SCZ_26_treated_NeuN-_H3K4me3_R2

value: 56 years

value: SCZ


title: batch2_COL_EAE

description: cells pooled from 2 mice


title: batch9_hashed_UT_mouse1_ADT


title: batch9_hashed_UT_mouse1_GEX


title: batch6_hashed_EAE_mouse1_ADT

value: SPL, MLN, PP, SI, COL, CNS, DLN


title: SCZ_26_treated_NeuN-_H3K4me3_R1


title: batch8_hashed_UT_mouse1_GEX


title: batch6_hashed_EAE_mouse2_ADT


title: batch6_hashed_EAE_mouse1_GEX


title: batch2_COL_UT

description: cells pooled from 2 mice


title: batch6_hashed_EAE_mouse2_GEX


title: batch5_PP_EAE

description: cells pooled from 2 mice

value: Peyer's patches


title: SCZ_25_treated_NeuN-_H3K4me3_R1


title: batch2_PP_EAE

description: cells pooled from 2 mice


title: batch5_PP_UT

description: cells pooled from 2 mice


title: batch2_SI_EAE

description: cells pooled from 2 mice

value: small intestine


title: batch5_MLN_EAE

description: cells pooled from 2 mice

value: mesenteric lymph nodes


title: batch3_SPL_UT

description: cells pooled from 2 mice

value: Homeostasis


title: SCZ_24_treated_NeuN-_H3K4me3_R2

value: 50 years


title: SCZ_24_treated_NeuN-_H3K4me3_R1


title: batch5_MLN_UT

description: cells pooled from 2 mice


title: batch8_hashed_UT_mouse1_ADT


title: batch2_PP_UT

description: cells pooled from 2 mice


title: Beta hCG transgenic-2

city: New Delhi

first: Rahul

last: Pal

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Immunology

data_processing:
HISAT2 which is a splice aligner was used to align the high quality data to the reference genome with the default parameters. Reads are classified into aligned reads (which align to the reference genome) and unaligned reads.
HTSeq was used to estimate and calculate gene abundance. Absolute counts for each gene were identified which were used in differential expression calculations.
DESeq was used to calculate the differentially expressed genes. Genes were categorized into UP, on the log2fold change cutoff of 1 value.
Genome_build: Mus musculus GRCm38.p6
Supplementary_files_format_and_content: counts.csv: Comma-delimited text file containing gene counts per sample and corresponding analysis results.

source_name: Lewis Lung Carcinoma cells

extract_protocol:
Tissue samples were homogenized in TOMY Microsmash in presence of liquid nitrogen. TRIZOL reagent (Ambion#15596018) was added and incubated at room temperature for 5 minute, lysate was centrifuged at 13500 rpm for 10 minutes to remove debris followed by phase separation by Chloroform. Aqueous phase was separated and RNA was precipitated with Ethanol. Rest of the protocol was followed as per manufacturer’s guidelines including on column DNase treatment. RNA was eluted in Nuclease free water (Ambion, USA). The quantification and quality of the genomic DNA was assessed using Nanodrop2000 (Thermo Scientific, USA) , Qubit (Thermo Scientific, USA) and Bioanalyzer 2100 (Agilent, USA).
RNA sequencing libraries were prepared with Illumina-compatible NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England BioLabs, MA, USA) at Genotypic Technology Pvt. Ltd., Bangalore, India. 500 ng of Qubit quantified total RNA was taken for mRNA isolation, fragmentation and priming. Fragmented and primed mRNA was further subjected to first strand CDNA synthesis followed by second strand synthesis. The double stranded cDNA was purified using HighPrep Beads (Magbio, Cat # AC-60050). Purified cDNA was end-repaired, adenylated and ligated to Illumina multiplex barcode adapters as per NEBNext® Ultra™ II Directional RNA Library Prep protocol followed by second strand excision using USER enzyme at 37 ˚C for 15mins. Adapter ligated cDNA was purified using HighPrep Beads and was subjected to 11 cycles for Indexing- (98˚C for 30 sec, cycling (98˚C for 10sec, 65˚C for 75sec) and 65˚C for 5min to enrich the adapter-ligated fragments. Final PCR product (sequencing library) was purified with HighPrep Beads, followed by library quality control check. Illumina-compatible sequencing library was quantified by Qubit fluorometer (Thermo Fisher Scientific, MA, USA).

tag: implanted cells

value: LLC1 cells (ATCC CRL-1642)

tag: transgenic animal

value: Outcross of CB57BL/6 female with beta-hCG transgenic FVB male


title: Beta hCG transgenic-1


title: SCZ_23_treated_NeuN-_H3K4me3_R2

value: 43 years


title: SCZ_23_treated_NeuN-_H3K4me3_R1


title: Ovx beta hCG transgenic Vehicle treated-1

tag: condition

value: Ovariectomized

value: Vehicle


title: Ovx beta hCG transgenic Progesterone treated-2

value: Progesterone


title: Ovx beta hCG transgenic Vehicle treated-2


title: Ovx beta hCG transgenic Progesterone treated-1


title: batch2_SPL_UT

description: cells pooled from 2 mice

tag: tissue

value: spleen

tag: cell type


title: SCZ_22_treated_NeuN-_H3K4me3_R1

tag: age

value: 34 years

tag: disease state

value: antipsychotic medications

value: glial nuclei


title: SCZ_22_treated_NeuN-_H3K4me3_R2

value: SCZ

tag: treatment

tag: sample type


title: batch2_SPL_EAE

description: cells pooled from 2 mice

value: EAE


title: SCZ_21_treated_NeuN-_H3K4me3_R2

value: 52 years

tag: chip antibody


title: batch1_SI_UT

description: cells pooled from 1 mouse

value: small intestine


title: batch1_COL_UT

description: cells pooled from 1 mouse

value: colon


title: PD-12H

city: Seattle

first: Chengxiang

last: Qiu

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description: sci-RNA-seq3 library

data_processing:
Base calls were converted to fastq format using Illumina’s bcl2fastq/v2.20 and demultiplexed based on PCR i5 and i7 barcodes using maximum likelihood demultiplexing package deML (Renaud et al. 2015) with default settings. Downstream sequence processing and single cell digital expression matrix generation were similar to sci-RNA-seq (Cao et al. 2017) except that RT index was combined with hairpin adaptor index, and thus the mapped reads were split into constituent cellular indices by demultiplexing reads using both the RT index and ligation index (Levenshtein edit distance (ED) < 2, including insertions and deletions).
Briefly, demultiplexed reads were filtered based on RT index and ligation index (ED < 2, including insertions and deletions) and adaptor-clipped using trim_galore/v0.6.5 with default settings. Trimmed reads were mapped to the mouse reference genome (mm10) for mouse embryo nuclei, using STAR/v2.6.1d (Dobin et al. 2013) with default settings and gene annotations (GENCODE VM12 for mouse). Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, hairpin ligation adaptor index and read 2 end-coordinate (i.e. reads with UMI sequence less than 2 edit distance, RT index, ligation adaptor index and tagmentation site were considered duplicates).
Finally, mapped reads were split into constituent cellular indices by further demultiplexing reads using the RT index and ligation hairpin (ED < 2, including insertions and deletions). To generate digital expression matrices, we calculated the number of strand-specific UMIs for each cell mapping to the exonic and intronic regions of each gene with python/v2.7.13 HTseq package (Anders, Pyl, and Huber 2015). For multi-mapped reads, reads were assigned to the closest gene, except in cases where another intersected gene fell within 100 bp to the end of the closest gene, in which case the read was discarded. For most analyses we included both expected-strand intronic and exonic UMIs in per-gene single-cell expression matrices.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files include a cell annotation csv  file, gene annotation csv file, and a gene count sparse matrix file

molecule: polyA RNA

source_name: mouse embryos

growth_protocol: We set up C57BL/6J timed mouse breeding pairs; evidence of vaginal plug is counted as embryonic day 0.5. 16 days later, the dam was sacrificed. E16.5 embryos were then dissected and briefly rinsed in 1xPBS; the excess liquid was wicked away by Kimwipe before immediately flash freezing in LN2. Mice had ad libitum access to standard chow and water and were housed in the University of Washington Animal Research and Care Facility on a standard 12 hr light cycle. All procedures were approved by the UW IACUC (protocol number PROTO201800017). E16.5 embryos were stored in a foil pouch in LN2 storage tank until ready for dissociation.

extract_protocol:
Nuclei were isolated from a single E16.5 mouse with a hypotonic, phosphate-based, lysis buffer containing sucrose and DEPC, and fixed with a combination of DSP and methanol.
Nuclei were washed and resuspended in SPBSTM buffer. ~4 million of these nuclei were processed with 2 plates of RT indexes, 2 plates of ligation indexes, and 3.5 plates of PCR indexes, as per the protocol described above. About 2000 nuclei per well were distributed into the final PCR plates. All 3.5 plates of PCR reactions were pooled and sequenced on an Illumina NovaSeq 6000 with dual index reads using the S4-200 kit and standard primers (Read1 34 cycles, Index1 10 cycles, Index2 10 cycles, Read2 100 cycles), resulting in about 7.15 billion reads in total, or 4.34 billion after removal of PCR duplicates.

value: mouse embryo (E16.5)


title: PD-12G

description: sci-RNA-seq3 library


title: PD-12D

description: sci-RNA-seq3 library


title: PD-12C

description: sci-RNA-seq3 library


title: PD-12E

description: sci-RNA-seq3 library


title: PD-12F

description: sci-RNA-seq3 library


title: SCZ_21_treated_NeuN-_H3K4me3_R1


title: PD-12B

description: sci-RNA-seq3 library


title: SCZ_20_treated_NeuN-_H3K4me3_R2

value: 58 years


title: batch1_MLN_UT

description: cells pooled from 1 mouse

value: mesenteric lymph nodes

value: Homeostasis


title: PD-11H

description: sci-RNA-seq3 library


title: batch1_SPL_UT

description: cells pooled from 1 mouse


title: PD-11G

description: sci-RNA-seq3 library


title: SCZ_20_treated_NeuN-_H3K4me3_R1


title: PD-11F

description: sci-RNA-seq3 library


title: PD-11E

description: sci-RNA-seq3 library


title: ex-vivo Ubc9-inhibited mouse morula, replicate 6

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were then mapped to the mouse genome mm10 using STAR method. Followed by quantification with RefSeq annotated genes. Counting was performed using HTSeq.
Normalization of the counts was done using DESeq2. Raw P-values were adjusted for multiple testing using Benjamini and Hochberg.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include counts.

source_name: mouse pre-implantation embryos that were cultured ex vivo

growth_protocol: Mouse E0.5 embryos were recovered by flushing the oviduct. Then, embryos were cultured for 3 days under KSOM conditions.

extract_protocol:
Embryos were directly lysed in lysis buffer.
cDNA synthesis and library preparation using SMART-Seq2 as described previously (Picelli et al., 2014) with minor modifications.

treatment_protocol: UBC9 inhibition was achieved by 2D08 (50 µM), and DMSO was used as control.

value: Morula

value: UBC9 inhibition


title: ex-vivo Ubc9-inhibited mouse morula, replicate 7


title: SCZ_19_treated_NeuN-_H3K4me3_R2

value: 51 years


title: SCZ_19_treated_NeuN-_H3K4me3_R1


title: ex-vivo Ubc9-inhibited mouse morula, replicate 5


title: PD-11C

description: sci-RNA-seq3 library


title: batch1_PP_UT

description: cells pooled from 1 mouse

value: Peyer's patches


title: PD-11B

description: sci-RNA-seq3 library


title: PD-10H

description: sci-RNA-seq3 library


title: PD-11A

description: sci-RNA-seq3 library


title: SCZ_18_treated_NeuN-_H3K4me3_R2

value: 35 years


title: ex-vivo Ubc9-inhibited mouse morula, replicate 4


title: SCZ_18_treated_NeuN-_H3K4me3_R1


title: SCZ_17_treated_NeuN-_H3K4me3_R2

value: 26 years


title: PD-12A

description: sci-RNA-seq3 library


title: PD-10D

description: sci-RNA-seq3 library


title: ex-vivo Ubc9-inhibited mouse morula, replicate 3


title: ex-vivo Ubc9-inhibited mouse morula, replicate 2


title: PD-10C

description: sci-RNA-seq3 library


title: PD-10G

description: sci-RNA-seq3 library


title: PD-11D

description: sci-RNA-seq3 library


title: PD-10B

description: sci-RNA-seq3 library


title: ex-vivo mouse morula in DMSO, replication 7

value: DMSO


title: SCZ_17_treated_NeuN-_H3K4me3_R1

value: antipsychotic medications

value: glial nuclei


title: PD-10E

description: sci-RNA-seq3 library


title: PD-10A

description: sci-RNA-seq3 library


title: PD-10F

description: sci-RNA-seq3 library


title: SCZ_16_treated_NeuN-_H3K4me3_R2

value: 32 years

value: SCZ


title: ex-vivo mouse morula in DMSO, replication 6


title: PD-09G

description: sci-RNA-seq3 library


title: PD-09F

description: sci-RNA-seq3 library


title: PD-09E

description: sci-RNA-seq3 library


title: SCZ_15_untreated_NeuN-_H3K4me3_R2

value: 74 years

value: untreated


title: PD-09D

description: sci-RNA-seq3 library

value: mouse embryo (E16.5)


title: PD-09H

description: sci-RNA-seq3 library


title: ex-vivo mouse morula in DMSO, replication 5


title: PD-09C

description: sci-RNA-seq3 library


title: PD-09A

description: sci-RNA-seq3 library


title: SCZ_14_untreated_NeuN-_H3K4me3_R2

value: 70 years


title: SCZ_14_untreated_NeuN-_H3K4me3_R1


title: PD-08F

description: sci-RNA-seq3 library


title: PD-08E

description: sci-RNA-seq3 library


title: PD-08D

description: sci-RNA-seq3 library


title: PD-08G

description: sci-RNA-seq3 library


title: SCZ_16_treated_NeuN-_H3K4me3_R1


title: PD-08C

description: sci-RNA-seq3 library


title: CD11b- BM "macrophage" - rep3

city: Woolloongabba

first: Susan

last: Millard

state: QLD

address: 37 Kent St

department: Translational Research Institute

institute: Mater Research Institute - The University of Queensland

data_processing:
Reads were mapped to the mouse genome (mm9) using Tophat2 with default parameters.
Transcript counts were generated with HTseq (version 0.10.0; doi:10.1093/bioinformatics/btu638).
Differential expression testing and CPM were generated with DESeq2 (doi:10.1186/s13059-014-0550-8).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *_FPKM.txt: Tab-delimited text files include FPKM values for each Sample.
Supplementary_files_format_and_content: CPM_gene_count_matrix.txt: Matrix table with abundance measurement (CPM) for every gene and every sample.

source_name: Sorted CD11b-F4/80+GFP+VCAM1+ bone marrow cells

growth_protocol: Animals were maintained under specific pathogen-free conditions, fed standard chow with ad libitum water access and simulated diurnal cycle.

extract_protocol:
Femoral bone marrow (BM) was collected by flushing the BM cavity with 2%FCS/PBS. Following staining with fluorochrome labelled antibodies, BM cell populations were sorted into 50% FCS/RPMI media, washed with 2%FCS/PBS and cell pellets snap frozen. RNA was harvested using Trizol reagent followed by QIAGEN RNeasy mini kit.
RNA libraries were prepared for sequencing using SmartSeq2 (https://doi.org/10.1038/nprot.2014.006).

treatment_protocol: No treatment prior to euthanasia.

tag: transgene

value: CD11b- BM "macrophage"


title: SCZ_13_untreated_NeuN-_H3K4me3_R2

value: 49 years


title: CD11b- BM "macrophage" - rep4


title: CD11b- BM "macrophage" - rep2


title: PD-08H

description: sci-RNA-seq3 library


title: PD-08B

description: sci-RNA-seq3 library


title: SCZ_12_untreated_NeuN-_H3K4me3_R2

value: 43 years


title: CD11b+ BM "macrophage" - rep4

source_name: Sorted CD11b+F4/80+Ly6G-GFPloVCAM1+ bone marrow cells

value: CD11b+ BM "macrophage"


title: batch2_MLN_EAE

description: cells pooled from 2 mice

value: mesenteric lymph nodes

value: EAE


title: ex-vivo mouse morula in DMSO, replication 1

value: Morula


title: CD11b+ BM "macrophage" - rep3


title: PD-07H

description: sci-RNA-seq3 library


title: SCZ_15_untreated_NeuN-_H3K4me3_R1


title: PD-07G

description: sci-RNA-seq3 library


title: PD-07F

description: sci-RNA-seq3 library


title: CD11b+ BM "macrophage" - rep2


title: SCZ_11_untreated_NeuN-_H3K4me3_R2


title: CD11b- BM "macrophage" - rep1


title: SCZ_12_untreated_NeuN-_H3K4me3_R1


title: PD-07D

description: sci-RNA-seq3 library


title: CD11b+ BM "macrophage" - rep1


title: SCZ_11_untreated_NeuN-_H3K4me3_R1


title: PD-09B

description: sci-RNA-seq3 library


title: PD-07C

description: sci-RNA-seq3 library


title: PD-07B

description: sci-RNA-seq3 library


title: SCZ_13_untreated_NeuN-_H3K4me3_R1


title: PD-08A

description: sci-RNA-seq3 library


title: PD-06H

description: sci-RNA-seq3 library


title: PD-07A

description: sci-RNA-seq3 library


title: PD-06G

description: sci-RNA-seq3 library


title: SCZ_10_untreated_NeuN-_H3K4me3_R2

value: 53 years


title: SCZ_10_untreated_NeuN-_H3K4me3_R1


title: PD-06F

description: sci-RNA-seq3 library


title: PD-06E

description: sci-RNA-seq3 library


title: PD-06D

description: sci-RNA-seq3 library


title: RNA_Setdb1Ring1b_cDKO_EpiLC1

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:
Reads were aligned to the mouse genome (mm10) and transcripts using STAR (Dobin et al., 2013) with --sjdbGTFfile and --twopassMode Basic 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.
Total RNA was extracted from 10 K cells by using RNeasy micro kit (Qiagen) with on-column DNaseⅠ treatment. rRNA was depleted by NEBNext rRNA Depletion Kit (NEB) and cDNA was synthesized by NEBNext UltraII RNA First Strand Synthesis Module (NEB) and double-stranded using NEBNext UltraII Directional RNA Second Strand Synthesis Module (NEB). Following purification of double-stranded DNA by AMPure XP beads, library was constructed as described previously with modifications (Brind'Amour et al., Nat Commun, 2015). Briefly, 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 12 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).

value: EpiLC

value: Setdb1/Ring1b cDKO


title: SCZ_9_untreated_NeuN-_H3K4me3_R1

value: 34 years

value: glial nuclei


title: SCZ_9_untreated_NeuN-_H3K4me3_R2

value: SCZ


title: RNA_Setdb1Ring1b_cDKO_EpiLC2


title: PD-06B

description: sci-RNA-seq3 library


title: Left Nodose

city: Durham

first: Winston

last: Liu

state: NC

address: MSRB1 217, 203 Research Drive

department: Neurobiology

institute: Duke University

data_processing:
Cellranger 2.1.1 was used to convert base calls to fastq, map, and count genes
Seurat 3.1.0 was used to merge the data sets, and project data onto existing atlases for the nodose ganglia
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of raw transcript counts for every gene and cell
Supplementary_files_format_and_content: Metadata matching barcode to predicted cell type and original location of origin

source_name: Nodose neurons

extract_protocol:
Left (N = 6) and right (N = 5) nodose ganglia adult from adult C57 BL/6J wild-type euthanized mice were dissected and separated into two distinct tubes.  Dissections were completed in tandem by three lab members, and all nodose were dissected within 30 minutes. Ganglia were immediately placed into 500 μL of ganglia dissociation solution containing 10 mM HEPES, 1x Glutamax, 1x N2 supplement, 1x B27 supplement, 0.5 μg/mL NGF, and 55 μg/mL of Liberase (Roche, 5401054001) in Advanced DMEM/f12. Following 30 minutes of digestion, ganglia were rinsed twice with PBS, mechanically dissociated in dissociation solution, and filtered through a 70 μm cell strainer. The dissociated solution was then carefully laid upon a density gradient of 500 μL 12% and 500 μL 28% Percoll (Sigma) and centrifuged for 10 minutes at 2,900 x g at room temperature.  Once centrifugation was complete, the top 700 μL was removed, and 700 μL of fresh dissociation solution was added.  Cells were then centrifuged for 15 mins at 2,900 x g, and the final pellet was resuspended in 500 μL of PBS + 0.04% BSA
Capturing of single cells was performed using Chromium Single-cell 3’ v2.  cDNA synthesis with PCR and library preparation were done according to standard Illumina protocols.

value: nodose ganglion

tag: location

value: left


title: Right Nodose

value: right


title: SCZ_8_untreated_NeuN-_H3K4me3_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: 67 years

value: untreated


title: PD-06A

description: sci-RNA-seq3 library

value: mouse embryo (E16.5)


title: PD-05G

description: sci-RNA-seq3 library


title: PD-05H

description: sci-RNA-seq3 library


title: SCZ_8_untreated_NeuN-_H3K4me3_R1


title: PD-05F

description: sci-RNA-seq3 library


title: PD-05D

description: sci-RNA-seq3 library


title: SCZ_7_untreated_NeuN-_H3K4me3_R2

value: 25 years


title: PD-05E

description: sci-RNA-seq3 library


title: RNA_Setdb1Ring1b_WT_EpiLC1

tag: genotype

value: Setdb1/Ring1b WT


title: RNA_Setdb1Ring1b_WT_EpiLC2

tag: developmental stage


title: SCZ_6_untreated_NeuN-_H3K4me3_R2

value: 27 years


title: PD-06C

description: sci-RNA-seq3 library


title: RNA_Setdb1Ring1b_WT_nESC2

source_name: nESC

value: nESC


title: PD-05B

description: sci-RNA-seq3 library


title: PD-05A

description: sci-RNA-seq3 library


title: PD-04F

description: sci-RNA-seq3 library


title: RNA_Setdb1Ring1b_cDKO_nESC2


title: RNA_Setdb1Ring1b_WT_nESC1


title: RNA_Ring1b_cKO_EpiLC2

value: Ring1b cKO


title: PD-04E

description: sci-RNA-seq3 library


title: SCZ_6_untreated_NeuN-_H3K4me3_R1


title: PD-04G

description: sci-RNA-seq3 library


title: PD-04D

description: sci-RNA-seq3 library


title: RNA_Ring1b_cKO_EpiLC1


title: SCZ_5_untreated_NeuN-_H3K4me3_R2

value: 28 years


title: RNA_Setdb1Ring1b_cDKO_nESC1


title: SCZ_5_untreated_NeuN-_H3K4me3_R1


title: PD-04B

description: sci-RNA-seq3 library


title: PD-04C

description: sci-RNA-seq3 library


title: SCZ_4_untreated_NeuN-_H3K4me3_R2

value: 31 years


title: PD-04A

description: sci-RNA-seq3 library


title: RNA_Ring1b_cKO_nESC2


title: RNA_Ring1b_cKO_nESC1


title: SCZ_4_untreated_NeuN-_H3K4me3_R1


title: PD-03G

description: sci-RNA-seq3 library


title: PD-04H

description: sci-RNA-seq3 library


title: SCZ_7_untreated_NeuN-_H3K4me3_R1


title: PD-03D

description: sci-RNA-seq3 library


title: RNA_Ring1b_WT_EpiLC2

value: EpiLC

value: Ring1b WT


title: PD-03F

description: sci-RNA-seq3 library


title: PD-05C

description: sci-RNA-seq3 library


title: PD-03E

description: sci-RNA-seq3 library


title: SCZ_3_untreated_NeuN-_H3K4me3_R2

value: 18 years

value: glial nuclei


title: PD-03C

description: sci-RNA-seq3 library


title: PD-03B

description: sci-RNA-seq3 library


title: SCZ_2_untreated_NeuN-_H3K4me3_R2

value: 21 years

value: SCZ


title: PD-03A

description: sci-RNA-seq3 library


title: RNA_Ring1b_WT_EpiLC1


title: SCZ_3_untreated_NeuN-_H3K4me3_R1


title: PD-02H

description: sci-RNA-seq3 library


title: RNA_Ring1b_WT_nESC2


title: RNA_Ring1b_WT_nESC1


title: SCZ_2_untreated_NeuN-_H3K4me3_R1


title: PD-02F

description: sci-RNA-seq3 library


title: PD-02E

description: sci-RNA-seq3 library


title: PD-03H

description: sci-RNA-seq3 library


title: SCZ_1_untreated_NeuN-_H3K4me3_R2

value: 24 years


title: RNA_Pcgf6_cKO_EpiLC2

value: Pcgf6 cKO


title: PD-02D

description: sci-RNA-seq3 library


title: SCZ_1_untreated_NeuN-_H3K4me3_R1

value: untreated


title: PD-02C

description: sci-RNA-seq3 library

value: mouse embryo (E16.5)


title: PD-02B

description: sci-RNA-seq3 library


title: SCZ_29_treated_NeuN+_H3K4me3_R2

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

value: 42 years

value: antipsychotic medications

value: neuronal nuclei


title: PD-02A

description: sci-RNA-seq3 library


title: PD-01F

description: sci-RNA-seq3 library


title: PD-01G

description: sci-RNA-seq3 library


title: PD-01H

description: sci-RNA-seq3 library


title: RNA_Pcgf6_WT_EpiLC2

value: Pcgf6 WT


title: RNA_Pcgf6_cKO_EpiLC1


title: RNA_Pcgf6_cKO_nESC2

value: nESC


title: SCZ_28_treated_NeuN+_H3K4me3_R2

value: 36 years


title: PD-01D

description: sci-RNA-seq3 library


title: PD-01C

description: sci-RNA-seq3 library


title: PD-02G

description: sci-RNA-seq3 library


title: SCZ_28_treated_NeuN+_H3K4me3_R1


title: RNA_Pcgf6_WT_EpiLC1


title: RNA_Pcgf6_WT_nESC2


title: PD-01A

description: sci-RNA-seq3 library


title: SCZ_27_treated_NeuN+_H3K4me3_R2

value: 41 years


title: PC-12H

description: sci-RNA-seq3 library


title: SCZ_27_treated_NeuN+_H3K4me3_R1


title: RNA_Pcgf6_WT_nESC1


title: PC-12G

description: sci-RNA-seq3 library


title: PC-12F

description: sci-RNA-seq3 library


title: RNA_Setdb1_cKO_EpiLC2

value: EpiLC

value: Setdb1 cKO


title: RNA_Pcgf6_cKO_nESC1


title: SCZ_26_treated_NeuN+_H3K4me3_R2

value: 56 years


title: SCZ_29_treated_NeuN+_H3K4me3_R1


title: PD-01E

description: sci-RNA-seq3 library


title: SCZ_25_treated_NeuN+_H3K4me3_R2

value: 60 years


title: RNA_Setdb1_cKO_EpiLC1


title: RNA_Setdb1_cKO_nESC2


title: RNA_Setdb1_cKO_nESC1


title: SCZ_26_treated_NeuN+_H3K4me3_R1


title: PC-12B

description: sci-RNA-seq3 library


title: PC-12D

description: sci-RNA-seq3 library


title: PC-12C

description: sci-RNA-seq3 library


title: PC-12A

description: sci-RNA-seq3 library


title: SCZ_25_treated_NeuN+_H3K4me3_R1


title: PC-11G

description: sci-RNA-seq3 library


title: PC-11E

description: sci-RNA-seq3 library


title: SCZ_24_treated_NeuN+_H3K4me3_R2

value: 50 years


title: PC-11C

description: sci-RNA-seq3 library


title: PD-01B

description: sci-RNA-seq3 library


title: SCZ_24_treated_NeuN+_H3K4me3_R1

value: SCZ


title: PC-11B

description: sci-RNA-seq3 library


title: PC-11A

description: sci-RNA-seq3 library


title: RNA_Setdb1_WT_nESC2

value: Setdb1 WT


title: PC-11H

description: sci-RNA-seq3 library


title: SCZ_23_treated_NeuN+_H3K4me3_R2

value: 43 years


title: RNA_Setdb1_WT_EpiLC2


title: PC-10H

description: sci-RNA-seq3 library


title: RNA_Setdb1_WT_nESC1


title: PC-11F

description: sci-RNA-seq3 library


title: PC-10F

description: sci-RNA-seq3 library


title: PC-10G

description: sci-RNA-seq3 library


title: PC-12E

description: sci-RNA-seq3 library


title: PC-10D

description: sci-RNA-seq3 library


title: RNA_Mga_∆HLH_EpiLC2

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).
Total RNA was extracted from 10 K cells by using RNeasy micro kit (Qiagen) with on-column DNaseⅠ treatment. rRNA was depleted by NEBNext rRNA Depletion Kit (NEB) and cDNA was synthesized by NEBNext UltraII RNA First Strand Synthesis Module (NEB) and double-stranded using NEBNext UltraII Directional RNA Second Strand Synthesis Module (NEB). Following purification of double-stranded DNA by AMPure XP beads, library was constructed as described previously with modifications (Brind'Amour et al., Nat Commun, 2015). Briefly, 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 12 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).

value: Mga-<delta>HLH


title: PC-11D

description: sci-RNA-seq3 library

value: mouse embryo (E16.5)


title: RNA_Setdb1_WT_EpiLC1


title: SCZ_22_treated_NeuN+_H3K4me3_R2

value: 34 years


title: PC-10E

description: sci-RNA-seq3 library


title: PC-10A

description: sci-RNA-seq3 library


title: PC-10C

description: sci-RNA-seq3 library


title: RNA_Mga_∆HLH_nESC2


title: PC-10B

description: sci-RNA-seq3 library


title: RNA_Mga_∆HLH_EpiLC1


title: SCZ_23_treated_NeuN+_H3K4me3_R1

value: antipsychotic medications


title: SCZ_21_treated_NeuN+_H3K4me3_R2

value: 52 years

value: neuronal nuclei


title: PC-09H

description: sci-RNA-seq3 library


title: SCZ_20_treated_NeuN+_H3K4me3_R2

value: 58 years


title: SCZ_21_treated_NeuN+_H3K4me3_R1


title: RNA_Mga_∆HLH_nESC1

value: nESC


title: PC-09F

description: sci-RNA-seq3 library


title: PC-09G

description: sci-RNA-seq3 library


title: RNA_Mga_WT_EpiLC2

value: Mga WT


title: PD-07E

description: sci-RNA-seq3 library


title: PC-09D

description: sci-RNA-seq3 library


title: PC-09E

description: sci-RNA-seq3 library


title: PC-09C

description: sci-RNA-seq3 library


title: RNA_Mga_WT_EpiLC1

value: EpiLC


title: SCZ_22_treated_NeuN+_H3K4me3_R1


title: SCZ_20_treated_NeuN+_H3K4me3_R1


title: RNA_Mga_WT_nESC2


title: PC-09B

description: sci-RNA-seq3 library


title: PC-09A

description: sci-RNA-seq3 library


title: PC-08H

description: sci-RNA-seq3 library


title: SCZ_19_treated_NeuN+_H3K4me3_R2

value: 51 years


title: RNA_Mga_WT_nESC1


title: PC-08F

description: sci-RNA-seq3 library


title: PC-08G

description: sci-RNA-seq3 library


title: SCZ_19_treated_NeuN+_H3K4me3_R1


title: RNA_Dnmt_cTKO_EpiLC2

value: Dnmt cTKO


title: SCZ_18_treated_NeuN+_H3K4me3_R1

value: 35 years


title: SCZ_18_treated_NeuN+_H3K4me3_R2


title: PC-08E

description: sci-RNA-seq3 library


title: PC-08D

description: sci-RNA-seq3 library


title: PC-08B

description: sci-RNA-seq3 library


title: PC-08C

description: sci-RNA-seq3 library


title: PC-08A

description: sci-RNA-seq3 library


title: PC-07H

description: sci-RNA-seq3 library


title: RNA_Dnmt_cTKO_nESC2


title: RNA_Dnmt_cTKO_EpiLC1


title: SCZ_17_treated_NeuN+_H3K4me3_R2

value: 26 years


title: RNA_Dnmt_cTKO_nESC1


title: SCZ_17_treated_NeuN+_H3K4me3_R1

value: SCZ


title: RNA_Dnmt_WT_EpiLC2

value: Dnmt WT


title: PC-07F

description: sci-RNA-seq3 library


title: PC-07E

description: sci-RNA-seq3 library


title: SCZ_16_treated_NeuN+_H3K4me3_R2

value: 32 years


title: PC-07D

description: sci-RNA-seq3 library


title: SCZ_16_treated_NeuN+_H3K4me3_R1


title: PC-07C

description: sci-RNA-seq3 library


title: RNA_Dnmt_WT_nESC2


title: RNA_Dnmt_WT_EpiLC1


title: PC-07A

description: sci-RNA-seq3 library


title: SCZ_15_untreated_NeuN+_H3K4me3_R2

value: 74 years

value: untreated


title: PC-06H

description: sci-RNA-seq3 library

value: mouse embryo (E16.5)


title: RNA_Dnmt_WT_nESC1


title: SCZ_15_untreated_NeuN+_H3K4me3_R1


title: PC-06G

description: sci-RNA-seq3 library


title: Input_Pcgf6_cKO_EpiLC

data_processing:
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

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).

value: Pcgf6 cKO


title: PC-06F

description: sci-RNA-seq3 library


title: PC-07G

description: sci-RNA-seq3 library


title: SCZ_14_untreated_NeuN+_H3K4me3_R2

value: 70 years


title: PC-06D

description: sci-RNA-seq3 library


title: PC-06E

description: sci-RNA-seq3 library


title: PC-06B

description: sci-RNA-seq3 library


title: PC-06A

description: sci-RNA-seq3 library


title: PC-06C

description: sci-RNA-seq3 library


title: SCZ_13_untreated_NeuN+_H3K4me3_R2

value: 49 years

value: neuronal nuclei


title: PC-07B

description: sci-RNA-seq3 library


title: SCZ_14_untreated_NeuN+_H3K4me3_R1


title: SCZ_13_untreated_NeuN+_H3K4me3_R1


title: Input_Pcgf6_cKO_nESC

value: nESC


title: H2AK119ub1_Pcgf6_cKO_EpiLC


title: PC-05F

description: sci-RNA-seq3 library


title: PC-05G

description: sci-RNA-seq3 library


title: SCZ_12_untreated_NeuN+_H3K4me3_R2

value: 43 years


title: H2AK119ub1_Pcgf6_cKO_nESC


title: H3K9me3_Pcgf6_cKO_nESC

value: H3K9me3 (Active Motif, 39161)


title: SCZ_12_untreated_NeuN+_H3K4me3_R1


title: PC-05B

description: sci-RNA-seq3 library


title: PC-05C

description: sci-RNA-seq3 library


title: SCZ_11_untreated_NeuN+_H3K4me3_R2


title: PC-04H

description: sci-RNA-seq3 library


title: PC-05D

description: sci-RNA-seq3 library


title: PC-04G

description: sci-RNA-seq3 library


title: H3K9me3_Pcgf6_cKO_EpiLC

value: EpiLC


title: Input_Pcgf6_WT_EpiLC

value: Pcgf6 WT


title: SCZ_11_untreated_NeuN+_H3K4me3_R1


title: PC-04F

description: sci-RNA-seq3 library


title: H2AK119ub1_Pcgf6_WT_EpiLC


title: PC-04E

description: sci-RNA-seq3 library


title: PC-04C

description: sci-RNA-seq3 library


title: PC-04D

description: sci-RNA-seq3 library


title: SCZ_10_untreated_NeuN+_H3K4me3_R1

value: 53 years


title: Input_Pcgf6_WT_nESC


title: SCZ_10_untreated_NeuN+_H3K4me3_R2


title: PC-04B

description: sci-RNA-seq3 library


title: PC-04A

description: sci-RNA-seq3 library


title: PC-03H

description: sci-RNA-seq3 library


title: PC-05E

description: sci-RNA-seq3 library


title: SCZ_9_untreated_NeuN+_H3K4me3_R2

value: 34 years


title: PC-03G

description: sci-RNA-seq3 library


title: H3K9me3_Pcgf6_WT_nESC


title: PC-05H

description: sci-RNA-seq3 library


title: SCZ_9_untreated_NeuN+_H3K4me3_R1

value: SCZ


title: PC-05A

description: sci-RNA-seq3 library


title: H3K9me3_Pcgf6_WT_EpiLC


title: PC-03F

description: sci-RNA-seq3 library


title: H2AK119ub1_Setdb1_cKO_EpiLC

value: Setdb1 cKO


title: PC-03E

description: sci-RNA-seq3 library


title: SCZ_8_untreated_NeuN+_H3K4me3_R2

value: 67 years


title: PC-03D

description: sci-RNA-seq3 library


title: PC-03C

description: sci-RNA-seq3 library


title: SCZ_8_untreated_NeuN+_H3K4me3_R1


title: PC-03B

description: sci-RNA-seq3 library


title: H3K9me3_Setdb1_cKO_EpiLC


title: Input_Setdb1_cKO_nESC


title: SCZ_7_untreated_NeuN+_H3K4me3_R2

value: 25 years


title: PC-03A

description: sci-RNA-seq3 library


title: H2AK119ub1_Setdb1_cKO_nESC


title: PC-02H

description: sci-RNA-seq3 library


title: PC-02G

description: sci-RNA-seq3 library


title: PC-02F

description: sci-RNA-seq3 library


title: SCZ_7_untreated_NeuN+_H3K4me3_R1

value: untreated


title: H2AK119ub1_Pcgf6_WT_nESC


title: PC-02E

description: sci-RNA-seq3 library

value: mouse embryo (E16.5)


title: SCZ_6_untreated_NeuN+_H3K4me3_R2

value: 27 years


title: PC-02C

description: sci-RNA-seq3 library


title: PC-02D

description: sci-RNA-seq3 library


title: SCZ_6_untreated_NeuN+_H3K4me3_R1


title: PC-02B

description: sci-RNA-seq3 library


title: H2AK119ub1_Setdb1_WT_EpiLC

value: Setdb1 WT


title: H3K9me3_Setdb1_WT_EpiLC


title: H3K9me3_Setdb1_cKO_nESC


title: PC-02A

description: sci-RNA-seq3 library


title: Input_Setdb1_WT_nESC


title: SCZ_5_untreated_NeuN+_H3K4me3_R2

value: 28 years


title: SCZ_5_untreated_NeuN+_H3K4me3_R1

value: neuronal nuclei


title: PC-01F

description: sci-RNA-seq3 library


title: H3K9me3_Setdb1_WT_nESC

value: nESC


title: PC-01D

description: sci-RNA-seq3 library


title: SCZ_4_untreated_NeuN+_H3K4me3_R2

value: 31 years


title: SCZ_4_untreated_NeuN+_H3K4me3_R1


title: PC-01E

description: sci-RNA-seq3 library


title: PC-01C

description: sci-RNA-seq3 library


title: PC-01A

description: sci-RNA-seq3 library


title: Input_Mga_∆HLH_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).
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).

value: Mga-<delta>HLH


title: SCZ_3_untreated_NeuN+_H3K4me3_R1

value: 18 years


title: PB-12G

description: sci-RNA-seq3 library


title: PB-12H

description: sci-RNA-seq3 library


title: PB-12F

description: sci-RNA-seq3 library


title: PC-01H

description: sci-RNA-seq3 library


title: Input_Mga_∆HLH_nESC


title: PB-12D

description: sci-RNA-seq3 library


title: PC-01G

description: sci-RNA-seq3 library


title: SCZ_2_untreated_NeuN+_H3K4me3_R2

value: 21 years


title: PB-12C

description: sci-RNA-seq3 library


title: SCZ_2_untreated_NeuN+_H3K4me3_R1


title: H2AK119ub1_Setdb1_WT_nESC


title: PB-12A

description: sci-RNA-seq3 library


title: PB-11H

description: sci-RNA-seq3 library


title: SCZ_1_untreated_NeuN+_H3K4me3_R2

value: 24 years


title: H2AK119ub1_Mga_∆HLH_nESC


title: SCZ_3_untreated_NeuN+_H3K4me3_R2


title: PC-01B

description: sci-RNA-seq3 library


title: PB-11G

description: sci-RNA-seq3 library


title: H2AK119ub1_Mga_∆HLH_EpiLC

value: EpiLC


title: H3K9me3_Mga_∆HLH_nESC

value: H3K9me3 (Active Motif, 39161)


title: SCZ_1_untreated_NeuN+_H3K4me3_R1

value: SCZ


title: PB-11D

description: sci-RNA-seq3 library


title: PB-11F

description: sci-RNA-seq3 library


title: GM12878-Pol2-S5-100K-cl-2

description: crosslinked MOWChIP-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: GM12878 cell line

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.
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.

tag: cell line


title: PB-11E

description: sci-RNA-seq3 library


title: H2AK119ub1_Mga_WT_d4PGCLC

extract_protocol:
EpiLC-PGCLC 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). The PGCLCs were induced under floating aggregation culture conditions by plating EpiLCs in a well of a low-cell-binding U-bottom 96-well plate (Nunc) in GMEM-based serum-free medium in the presence of the cytokines BMP4 (R&D), LIF (ESGRO; Chemicon), SCF (R&D) and EGF (R&D). Cell aggregates including d4 PGCLCs were dissociated with TrypLE (10 min., 37℃ ) and incubated with anti-SSEA1 antibody (BioLegend) and anti-CD61 antibody (BioLegend) conjugated with Phycoerythrin (PE) and Alexa Fluor 647, respectively. Cells were washed with FACS buffer (0.1% BSA/PBS) and passed through a 35 μm cell strainer. FACS was carried out on a BD Influx. Following removal of doublet/triplet cells, double positive PGCLCs were sorted.
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).

value: Mga WT


title: PB-11C

description: sci-RNA-seq3 library


title: Input_Mga_WT_d4PGCLC


title: PB-11B

description: sci-RNA-seq3 library


title: PB-12E

description: sci-RNA-seq3 library


title: H3K9me3_Mga_∆HLH_EpiLC


title: H3K9me3_Mga_WT_d4PGCLC


title: PB-10H

description: sci-RNA-seq3 library


title: GM12878-Pol2-S5-100K-cl-1


title: PB-10G

description: sci-RNA-seq3 library


title: Input_Mga_WT_EpiLC


title: PB-12B

description: sci-RNA-seq3 library


title: GM12878-EGR1-5K-2

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

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.


title: GM12878-EGR1-5K-1


title: PB-10E

description: sci-RNA-seq3 library


title: H2AK119ub1_Mga_WT_EpiLC


title: PB-10F

description: sci-RNA-seq3 library


title: PB-11A

description: sci-RNA-seq3 library


title: H3K9me3_Mga_WT_EpiLC


title: PB-10D

description: sci-RNA-seq3 library


title: PB-10C

description: sci-RNA-seq3 library


title: PB-10B

description: sci-RNA-seq3 library


title: PB-10A

description: sci-RNA-seq3 library


title: GM12878-EGR1-10K-1


title: GM12878-EGR1-50K-2


title: PB-09G

description: sci-RNA-seq3 library


title: PB-09F

description: sci-RNA-seq3 library


title: H3K9me3_Mga_WT_nESC


title: PB-09E

description: sci-RNA-seq3 library


title: GM12878-EGR1-50K-1


title: PB-09D

description: sci-RNA-seq3 library


title: H3K9me3_E9.5_PGC

source_name: E9.5 primordial germ cells

extract_protocol:
The hindgut endoderm regions that contained PGCs were isolated and incubated at 37℃ for 5-8 minutes in 0.25% trypsin/0.5 mM EDTA/PBS with serial pipetting to obtain single cell suspensions. After quenching the reaction with fetal bovine serum (FBS), cells were washed once with FACS buffer (0.1% BSA/PBS), stained with Propidium Iodide (PI) and passed through a 35 μm cell strainer (Falcon). FACS was carried out on a BD Influx. Following removal of doublet/triplet cells, OCT3/4-EGFP+ (PI-) cells were sorted.
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).

value: embryonic day 9.5

value: WT


title: GM12878-EGR1-100K-2


title: PB-09B

description: sci-RNA-seq3 library

value: mouse embryo (E16.5)


title: PB-09C

description: sci-RNA-seq3 library


title: GM12878-EGR1-100K-1


title: PB-09A

description: sci-RNA-seq3 library


title: PB-08H

description: sci-RNA-seq3 library


title: GM12878-EGR1-10K-2


title: PB-08G

description: sci-RNA-seq3 library


title: PB-08F

description: sci-RNA-seq3 library


title: PB-08E

description: sci-RNA-seq3 library


title: GM12878-Pol2-S5-2K-2


title: Input_Mga_WT_nESC


title: PB-08B

description: sci-RNA-seq3 library


title: GM12878-Pol2-S5-2K-1


title: PB-08D

description: sci-RNA-seq3 library


title: PB-09H

description: sci-RNA-seq3 library


title: PB-08C

description: sci-RNA-seq3 library


title: GM12878-Pol2-S5-10K-st-2


title: PB-08A

description: sci-RNA-seq3 library


title: PB-07G

description: sci-RNA-seq3 library


title: PB-07H

description: sci-RNA-seq3 library


title: GM12878-Pol2-S5-10K-st-1


title: H2AK119ub1_Mga_WT_nESC


title: PB-07F

description: sci-RNA-seq3 library


title: GM12878-Pol2-S5-1K-2


title: GM12878-Pol2-S5-10K-2


title: PB-07D

description: sci-RNA-seq3 library


title: PB-07C

description: sci-RNA-seq3 library


title: PB-07B

description: sci-RNA-seq3 library


title: GM12878-Pol2-S5-1K-1


title: GM12878-Pol2-S5-10K-1


title: PB-07A

description: sci-RNA-seq3 library


title: PB-06H

description: sci-RNA-seq3 library


title: GM12878-Pol2-S5-50K-2


title: PB-06G

description: sci-RNA-seq3 library


title: PB-06E

description: sci-RNA-seq3 library


title: PB-06C

description: sci-RNA-seq3 library


title: GM12878-Pol2-S5-50K-1


title: GM12878-Pol2-total-50K-2


title: PB-07E

description: sci-RNA-seq3 library


title: PB-06B

description: sci-RNA-seq3 library


title: YH25005-3

city: Yangling

first: Chengyu

last: Yu

state: Shaanxi

address: 3 Taicheng Road

department: College of Agronomy

institute: Northwest A&F University

data_processing:
Bcl2fastq Conversion software (v2.20) was used for basecalling.
The raw data was trimmed with strict standards as followsd:(1) Trimmed Reads with adapter seq;(2) Trimmed low quality bases(Reads would be discarded if percent of N base is greater than 10% or percent of low quality bases is greater than 50%).
We mapped the clean data against the reference genome of Darmor-bzh (http://www.genoscope.cns.fr/brassicanapus/data/). HISAT2 (https://cloud.biohpc.swmed.edu/index.php/s/hisat2-220-source/download) is used as an alignment software for RNA-seq. Based on mapped data, we carried out library insert size check, sequencing randomness check, gene expression quantification analysis, alternative splicing analysis, novel genes detection and genes structure optimization.
Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped (FPKM).
Differential expression analysis of two sample groups was performed using the DEseq2. Fold Change(FC)≥2 and FDR<0.01 were used as the screening criteria to identify differentially expressed genes.
Genome_build: Darmor-bzh (http://www.genoscope.cns.fr/brassicanapus/data/)
Supplementary_files_format_and_content: Tab-delimited text files include count number and fragments per kilobase of transcript per million fragments mapped (FPKM) values for each sample.

organism: Brassica napus

source_name: Unmatured seeds

growth_protocol: The plants of the four genotypes were cultivated in the experimental field of Northwest A&F University.

extract_protocol:
The 24-days-old emboys of the four genotypes were collected and put into liquid nitrogen. Total RNAs were extracted using the Trizol® Reagent (Invitrogen, USA). The total RNA quantity and purity were analyed by using of Bioanalyzer 2100 (Agilent, CA, USA). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
Based on sequencing-by-synthesis (Sequencing By Synthesis, SBS) technology, the cDNA libraries were sequenced on Illumina Novaseq6000 platform with flow cell type PE150. Raw Data for each sequencing sample included two FASTQ files contain all cDNA fragments were measured at both ends of reads.

treatment_protocol: When the plants were flowering, the flowers opened in the same days were marked and the inflorescences were bagged to get selfing-pollinated seeds.

value: Unmatured seeds

tag: development stage

value: 24 days old after pollination


title: PB-06D

description: sci-RNA-seq3 library

tag: strain


title: PB-06A

description: sci-RNA-seq3 library


title: PB-05H

description: sci-RNA-seq3 library