title: ChIP STAG3 RPE/STAG3

description: bigWig: chr1-22,X

source_name: retina, eye

value: RPE epithelial cells immortalized with hTERT

value: pigmented epithelium


title: ChIP-2 SMC1B K562/SMC1B

status: Public on Sep 30 2022

type: SRA

city: Guangzhou

first: Alexander

middle: V.

last: Strunnikov

state: Guangdong

address: 190 Kai Yuan Avenue

country: China

institute: GIBH

description: bigWig: chr1-22,X

library_source: genomic

data_processing:
the original image data was transferred into sequence data via base calling, producing raw reads and saved as FASTQ files.
reads trimmed of adapters and  low quality reads using fastp (doi.org/10.1093/bioinformatics/bty560)
clean FASTQ files  generated.
paired end reads (R1 and R2 FASTQ files) were treated as single reads. R1 and R2 reads were combined and aligned using bowtie-1.2.2 software with parameters: -best -m 5 -v 3
peak calling was done with MACS2-2.1.1. software using a corresponding chromatin input file as a control
peak calling was applied to the full genome assembly, including assembled chromosomes, and both placed and unplaced fragments
bedgraph files were converted to bigWig files using bedGraphToBigWig script (ucsC utilities), excluding chromsome fragments
Genome_build: hg38 (GRCh38.p12, NCBI Assembly ID: 5800238)
Supplementary_files_format_and_content: bigWig file is an indexed binary format file that displays continuous signal data as a graph.

molecule: genomic DNA

organism: Homo sapiens

source_name: bone marrow

growth_protocol: K562, hTERT RPE-1, or DLD-1 cells and stably infected derivatives were grown in IMDM with 10% or 20% Tet-On certified FBS. Cells infected with lentivirus stock were selected for 4 weeks or more in media supplemented with 600µg/ml G418, 300 µg/ml zeocin, 1 µg/ml puromycin, or 200 µg/ml hygromycin B, dependent on the vector's marker, followed by the selection of individual clones.

extract_protocol:
Cells were fixed at 1% formaldehyde for 10 min at room temperature and quenched with 0.125 mM glycine for 5 min. For some experiments a dual crosslinking was used, by incubating the cells in 1.5 mM ethylene glycol bis(succinimidyl succinate) (EGS) (Sigma) in PBS for 45 min at RT under gentle shaking. Then, 1% formaldehyde was added and the incubation left to proceed for 20 min, after which the fixation was quenched with 0.125 mM glycine for 5 min at RT. Cells were centrifuged, resuspended in PBS/1 x proteinase inhibitor cocktail /10% glycerol, and kept at -80 degrees C. A modified ChIP version named ChEP (chromatin enriched for proteomics) was used to precipitate proteins of interest with specific antibodies.
DNA fragments were end-repaired and A-tailed according to Illumina protocol, and then ligated with adapters. DNA fragments that have adapter molecules on both ends were amplified by PCR. DNA concentration of the resulting sequencing libraries was measured with the Qubit 2.0 fluorometer dsDNA HS Assay (Thermo Fisher Scientific), and the size distribution was analyzed using Agilent BioAnalyzer 2100 (Agilent). Paired-end sequencing was performed using an Illumina system with Illumina-provided protocols for paired-end sequencing

treatment_protocol: For ChIP-seq experiments, stable Tet-On transgenic cells and the control replicates were plated at 40% to 50% confluence in 10 cm plates, and induced by 200 ng/ml of doxycycline for 72 hours

tag: cell line

value: lymphoblast  tumor cells K-562

tag: cell type

value: chronic myelogenous leukemia

tag: chip antibody

value: custom rabbit polyclonal anti-SMC1B


title: ChIP-2 STAG3 K562/STAG3

description: bigWig: chr1-22,X

value: custom rabbit polyclonal anti-STAG3


title: ChIP-1 SMC1B K562/SMC1B

description: bigWig: chr1-22,X


title: POR_PC_77_2

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description:
S273_20200619120606_16
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi

library_source: transcriptomic

data_processing:
The reads were trimmed to remove adapter sequences and low-quality ends and reads mapping to contaminating sequences (e.g., ribosomal RNA, phIX control) were filtered-out.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include raw counts for each Sample.

molecule: total RNA

source_name: RNA isolated from Melanoma biopsy

extract_protocol:
RNA was quantified and mixed at 10ng/µl.
For RNA-seq analysis, libraries were prepared according to manufacturer's instructions (QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen GmbH) starting from 250ng of total RNA.
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NovaSeq6000 (Illumina) with a read length of 100 bp.

treatment_protocol: Patients with mutant BRAFV600-positive metastatic melanoma were treated with either a BRAF inhibitor, or a combination of BRAF and MEK inhibitors (for patient characteristics see Table S1). All patients consented for tissue acquisition as per an institutional-review-board-approved protocol (Office for Human Research Studies, Dana-Farber/Harvard Cancer Center). Tumor biopsies were obtained at time of progression if applicable. The study was conducted according to the guidelines of the Declaration of Helsinki and approved by the Ethics Committee of Istituto Nazionale Tumori-IRCCS-Fondazione "G. Pascale", Naples, Italy (date of registration 18/01/2018; project identification code n° 33/17 oss, 2018). Total RNA from FFPE tissues was isolated using Maxwell RSC RNA FFPE kit (Promega, Madison, WI, USA) and processed with Maxwell RSC Instrument (Promega, Madison, WI, USA) as described in (Barbato et al., 2021a).

tag: diagnosis

value: Melanoma

tag: tissue

value: Melanoma biopsy

tag: phenotype

value: Responder to MAPKi

tag: gender

value: not collected


title: POR_PC_36_POST_1

description:
S273_20200127164454_16
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi

value: Resistant to MAPKi


title: POR_PC_78_2

description:
S273_20200619120606_17
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: POR_PC_76_2

description:
S273_20200619120606_15
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: POR_PC_35_POST_1

description:
S273_20200127164454_15
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: ChIP-1 SMC3 DLD-1/RAD21L+STAG3+SMC1B

description: bigWig: chr1-22,X,Y

source_name: colon epithelium

value: epithelial tumor cells DLD-1

value: colorectal adenocarcinoma

value: rabbit polyclonal anti-SMC3, Abcam ab9263


title: POR_PC_34_POST_1

description:
S273_20200127164454_14
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: POR_PC_75_2

description:
S273_20200619120606_14
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: POR_PC_33_POST_1

description:
S273_20200127164454_13
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: H3-K27Ac ChIP Monkey 1610

description: bigWig: chr1-20,X

data_processing:
Paired end reads (R1 and R2 FASTQ files) were treated as single reads
R1 and R2 reads were cleaned using fastp application (github..com/OpenGene/fastp.git) . Reads were combined and aligned using bowtie-1.2.2 software with parameters: -best -m 5 -v 3
Peak calling was done with MACS2-2.1.1. software using a corresponding chromatin input file as a control
Peak calling was applied to the full genome assembly, including assembled chromosomes, and both placed and unplaced fragments
Bedgraph files were converted to bigWig files using bedGraphToBigWig script (ucsC utilities), excluding chromosome fragments
Genome_build: macFas5 (June 2013), Accession GCA_000364345.1 , NCBI Assembly 704988.
Supplementary_files_format_and_content: bigWig file is an indexed binary format file that displays continuous signal data as a graph.

organism: Macaca fascicularis

source_name: dissected testis

extract_protocol:
Testis fractionation: Testis samples were placed on ice and cut into pieces with sterile scalpel. Homogenates were individually filtered through two mesh wire gauzes to remove large pieces of tissue fragments and the cells of stroma. Cells in filtered homogenates were extensively washed with cold PBS and fixed with 1% EM-grade formaldehyde/PBS for 15 min. Crosslinking was quenched with glycine (0.125M final concentration). Cells were centrifuged, resuspended in PBS/1 x proteinase inhibitor cocktail /10% glycerol, and kept at -80 degrees C. A modified ChIP version named ChEP (chromatin enriched for proteomics) was used to precipitate proteins of interest with specific antibodies.
DNA fragments were end-repaired and A-tailed according to Illumina protocol, and then ligated with adapters. DNA fragments that have adapter molecules on both ends were amplified by PCR. DNA concentration of the resulting sequencing libraries was measured with the Qubit 2.0 fluorometer dsDNA HS Assay (Thermo Fisher Scientific), while the size distribution was analyzed using Agilent BioAnalyzer 2100 (Agilent). Paired-end sequencing was performed using an Illumina HiSeq system with Illumina-provided protocols for paired-end sequencing.

value: testis

value: male germline cells

tag: antibody

value: Diagenode, anti-H3K27Ac C15410196


title: POR_PC_31_POST_1

description:
S273_20200127164454_11
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: POR_PC_72_2

description:
S273_20200619120606_11
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: POR_PC_74_2

description:
S273_20200619120606_13
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: POR_PC_30_POST_1

description:
S273_20200127164454_10
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: POR_PC_30_POST_2

description:
S273_20200619120606_10
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: POR_PC_70_POST_2

description:
S273_20200619120606_8
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: PRDM9 ChIP Monkey 1610

description: bigWig: chr1-20,X

value: Sigma, anti-PRDM9 SAB1300161


title: POR_PC_71_POST_2

description:
S273_20200619120606_9
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: H3-K27Ac ChIP Monkey 38

description: bigWig: chr1-20,X


title: POR_PC_36_POST_2

description:
S273_20200619120606_7
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: PRDM9 ChIP Monkey 38

description: bigWig: chr1-20,X


title: POR_PC_34_POST_2

description:
S273_20200619120606_6
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: POR_PC_69_PRE_2

description:
S273_20200619120606_3
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: POR_PC_25_PRE_1

description:
S273_20200127164454_5
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: POR_PC_22_PRE_2

description:
S273_20200619120606_5
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: POR_PC_21_PRE_2

description:
S273_20200619120606_4
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: POR_PC_68_PRE_2

description:
S273_20200619120606_2
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: POR_PC_22_PRE_1

description:
S273_20200127164454_2
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: POR_PC_23_PRE_1

description:
S273_20200127164454_3
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: POR_PC_67_PRE_2

description:
S273_20200619120606_1
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: POR_PC_21_PRE_1

description:
S273_20200127164454_1
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: C. elegans, no bacteria, 9h, rep3

status: Public on Sep 29 2022

first: Friedrich

last: Preusser

address: Hannoversche Str. 26

department: Berlin Institute For Molecular Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

data_processing:
Raw sequencing basecalls were demultiplexed and converted to FASTQ format using custom python scripts.
RNA-seq reads were mapped to the ce11/WBcel235 genome assembly using STAR_2.7.3a (Dobin et al., 2013), annotated using Rsubread (Liao et al., 2019) and count matrices were generated using custom python scripts.
Assembly: ce11/WBcel235
Supplementary files format and content: .csv files of read counts per gene

organism: Caenorhabditis elegans

source_name: Head

growth_protocol: Worms were maintained at 15°C on nematode growth medium (NGM) with Escherichia Coli OP50 as food source as previously described. Dauer formation was induced by transferring a mixed population of ca. 50-100 worms to 6cm NGM plates seeded with E. coli OP50. Plates were then incubated for at least 7-10 days at 25°C. Next, worms were washed off with M9, washed twice to eliminate remaining bacteria and 1% SDS solution was added. The mixture was incubated for 30 mins at room temperature (Cassada and Russell, 1975). After an additional washing step with M9 to eliminate SDS, worms were transferred to an unseeded NGM plate. After 30 mins, once the drop of M9 dried out, dauers, which can survive SDS treatment (unlike all other C. elegans stages), crawled out of the mix of dead worms and were collected.

extract_protocol:
For each time point 10 heads were pooled into a pre-cooled Eppendorf tube on dry ice, containing 500 µl trizol and 1 µl GlycoBlue. Samples were frozen at -80°C for storage and later subjected to RNA sequencing according to the Tomo-Seq protocol (Holler and Junker, 2019) with minor modifications. Briefly, after thawing, samples were mixed thoroughly and incubated for 5 min at room temperature. Subsequently, 100 µl of chloroform were added to each sample, mixed well and incubated for 5 min. Samples were then centrifuged at 12,000 g for 15 min at 4°C. Next, the aqueous phase was carefully transferred to an Eppendorf LoBind containing 250 µl isopropanol and precipitated overnight at -20°C. Samples were centrifuged for 10 min at 12,000 g and at 4°C. Next, the supernatant was removed and the RNA pellet was washed with 75% freshly prepared ethanol. After washing, the pellet was dried and, once completely dry, resuspended in 2 µl molecular grade water. 1 µl of the sample was transferred to a fresh low binding PCR tube containing barcoded oligo(dT) primer. Reverse transcription was performed with the Superscript II kit according to (Holler and Junker, 2019). First strand synthesis was performed for 1 h at 42°C. Second strand synthesis was performed for 1 h at 16°C. Next, samples were pooled and purified with Agencourt AMPureXP beads. IVT was performed for 16h at 37°C. After fragmentation and purification, RNA was reverse transcribed with superscript II and amplified by PCR.
Concentration and size distribution of the resulting cDNA were measured with Qubit and Tapestation. mRNA Libraries were sequenced on a NextSeq500 in paired end mode with 150 cycles.

treatment_protocol: For time point 0, dauers were directly collected from the unseeded NGM plate. Dauers assigned to “no bacteria” condition were always collected first and “with bacteria” condition second (10-20 mins later). Assay conditions were the same as for the timelapse imaging experiments and both conditions (no bacteria and + OP50) were processed in parallel. Every hour, a fraction of dauers was washed off the assay plates and anesthetized with 1mM tetramisole. Under a dissecting microscope, the worm’s head was cut off just below the terminal bulb of the pharynx.

value: Head

tag: time point

tag: replicate

tag: genotype

tag: treatment

value: no bacteria


title: C. elegans, no bacteria, 3h, rep3


title: C. elegans, no bacteria, 6h, rep3


title: C. elegans, no bacteria, 0h, rep3


title: C. elegans, no bacteria, 6h, rep2


title: C. elegans, no bacteria, 3h, rep2


title: C. elegans, no bacteria, 0h, rep2


title: POR_PC_27_PRE_1

description:
S273_20200127164454_7
Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi


title: C. elegans, no bacteria, 3h, rep1


title: C. elegans, no bacteria, 0h, rep1


title: C. elegans, no bacteria, 6h, rep1


title: C. elegans, with bacteria, 0h, rep4

value: with bacteria


title: C. elegans, with bacteria, 3h, rep4


title: C. elegans, with bacteria, 9h, rep3


title: C. elegans, no bacteria, 9h, rep1


title: C. elegans, with bacteria, 9h, rep4


title: C. elegans, with bacteria, 6h, rep3


title: C. elegans, with bacteria, 3h, rep3


title: C. elegans, with bacteria, 9h, rep2


title: C. elegans, with bacteria, 0h, rep3


title: C. elegans, with bacteria, 0h, rep2


title: C. elegans, with bacteria, 6h, rep2


title: C. elegans, with bacteria, 9h, rep1


title: C. elegans, with bacteria, 3h, rep2


title: C. elegans, with bacteria, 3h, rep1


title: C. elegans, no bacteria, 9h, rep2


title: MLLT3-MLL positive AML 2

city: Heidelberg

first: Linda

middle: Christina

last: Schuster

address: Im Neuenheimer Feld 280

department: Chromatin Networks

institute: German Cancer Research Center (DKFZ)

description:
p1002
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using  Cell Ranger version 3.1.0 (10x Genomics).
Filtering was performed using the Seurat package in R
Assembly: GRCh38-1.2.0_premrna

source_name: blood

extract_protocol:
The samples were enriched for mononuclear cells (MNCs) via ficoll-hypaque and depleted from CD3+ cells via autoMACS (Miltenyi Biotec)
Library was performed according to the manufacter’s instructions with PBMCs on the Chromium platform with the single cell 3’ library and gel bead kit v2 (10x Genomics)

value: blood

tag: Sex

value: F

tag: age

tag: aml type

value: De-novo AML, thus no MDS phase

tag: prior aml_treatment

tag: karyotype

tag: timepoint of_cell_sampling

value: Diagnosis


title: MLL-ELL positive AML

description:
p1072
10x Genomics

value: t-AML (after RCTx for ovarian cancer), no MDS phase


title: MLLT3-MLL positive AML 1

description:
p1001
10x Genomics

value: t-AML (after RCTx for Hodgkins lymphoma), no MDS phase


title: C. elegans, with bacteria, 6h, rep4


title: K562_DAC_96h_4

city: Xiamen

first: Xi

last: Zeng

state: Fujian

address: No.422, Siming South Road

institute: Xiamen University

data_processing:
Raw data for sequencing were filtered by Trim Galore! (Version 0.6.6) in RRBS mode.
Reads were aligned to the hg19 gene by Bismark(http://www.bioinformatics.bbsrc.ac.uk/projects/bismark/) and Bowtie2(http://bowtie bio.sourceforge.net/bowtie2/index.shtml).
The coverage was calculated by methylKit(https://github.com/al2na/methylKit)
Lambda DNA was used as an internal reference to calculate the conversion rate by methylextract39 (https://github.com/bioinfoUGR/methylextract).
CpG island, CpG shores and promoters were obtained from UCSC database, other gene areas were annotated by annovar40 (https://annovar.openbioinformatics.org/en/latest/).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include methylation information of CpG sites for each sample

growth_protocol: GM12878 cells were cultured in RPMI 1640 medium plus 15% fetal bovine serum and 100 U/ml penicillin–streptomycin at 37 °C in a humidified incubator with 5% CO2. K562 cells were cultured in IMDM medium supplemented with 10% fetal bovine serum and 100 U/ml penicillin–streptomycin at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Single cells were isolated with the digital microfluidics chip. After cell lysis, genomic DNA were obotained for methylome libraries construction.
All of the following procedures are successively performed on the digital microfluidics chip: single-cell isolation; release of genomic DNA; spike unmethylated λ-DNA; digestion of the genome by MspI enzyme; repair and addition of an A-tail to the digested fragments; ligation of T-tail adapters; and bisulfite conversion of the ligated fragments. Subsequently, sufficient amplifiable DNA is purified and recovered from the chip, and sequencing libraries are generated after PCR amplification and fragment selection.

treatment_protocol: K562 cells were treated with decitabine in a final concentration of 300 nM for 48 hours and 96 hours to induce demethylation.

tag: cell line

tag: cell type

value: chronic myeloid leukemia cells

value: decitabine treatment


title: K562_DAC_96h_2


title: K562_DAC_96h_5


title: K562_DAC_48h_6


title: K562_DAC_48h_3


title: K562_DAC_96h_1


title: K562_DAC_48h_5


title: K562_DAC_96h_3


title: C. elegans, with bacteria, 6h, rep1


title: K562_DAC_48h_1


title: K562_DAC_48h_4


title: K562_sc_7


title: K562_sc_6


title: C. elegans, with bacteria, 0h, rep1


title: K562_sc_5


title: K562_sc_2


title: MLL-EDC4 positive AML

description:
p1000
10x Genomics

value: Secondary AML evolving from MDS (no prior CTx)

value: Decitabine

value: Before 4th cycle of decitabine (blast persistence)


title: K562_sc_1


title: GM12878_10ng_1

value: B lymphocytes


title: K562_sc_4


title: GM12878_0.3ng_1


title: GM12878_3ng_1


title: GM128781_1ng_1


title: GM12878_3ng_2


title: GM12878_10ng_2


title: GM128781_1ng_2


title: K562_DAC_48h_7


title: K562_DAC_48h_2


title: K562_sc_8


title: GM12878_4cells


title: GM12878_sc_tube_2


title: GM12878_20cells


title: GM12878_3cells


title: GM12878_sc_tube_1


title: K562_sc_3


title: GM12878_10cells


title: GM12878_15cells


title: GM12878_sc_5


title: GM12878_2cells


title: GM12878_sc_4


title: GM12878_sc_7


title: GM12878_sc_3


title: GM12878_sc_2


title: RNAseq_forelimb_E115_mm10_DLAD3BKO_Rep-2-1_L26138

city: Berlin

first: Michael

middle: I

last: Robson

address: Max Planck Institut für molekulare Genet, Ihnestrasse 63-73

institute: Max Planck Institute for Molecular Genetics

data_processing:
Single-end, 100 bp reads from Illumina sequencing were mapped to the reference genome (mm10) using the STAR mapper (splice junctions based on RefSeq; options: ‐‐alignIntronMin20 ‐‐alignIntronMax500000 ‐‐outFilterMismatchNmax 10).
Differential gene expression was ascertained using the DESeq2 package (Love et al., 2014). The cut-off for significantly altered gene expression was an adjusted P value of 0.05.
Assembly: mm10
Supplementary files format and content: bigwig

organism: Mus musculus

source_name: limb

growth_protocol: Isolated ESCs were trypsinized, heavily feeder depleted, centrifuged and snap frozen. E11.5 forelimb buds were microdissected from wildtype and mutant embryos in cold PBS and immediately snap-frozen for storage at −80°C. In all cases, mutants were generated using CRISPR.

extract_protocol:
Total RNAs were extracted using the RNeasy Mini Kit according to the manufacturer’s instructions.
Samples were poly-A enriched, prepared into libraries using  the Kapa HyperPrep Kit.

value: limb


title: GM12878_0.3ng_2


title: GM12878_sc_tube_3


title: RNAseq_forelimb_E115_mm10_DLAD3BKO_Rep-2-2_L26139


title: CD11c+ lung cells pooled from 2 untreated male mice

city: San Francisco

first: Xin-Zi

last: Tang

address: 555 Mission Bay Boulevard S

department: CVRI

country: USA

institute: UCSF

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v2.1.1. Aggregation of both samples was done using Cell Ranger v5.0.1. (10x Genomics)
Assembly: mm10
Supplementary files format and content: gene matrix .h5 file

source_name: Dissociated whole lung

extract_protocol:
Lungs were excised from four naive mice (two males and two females) into DMEM media supplemented with HEPES (Gibco), Penicillin, Streptomycin and L-Glutamine (Life Technologies). For lung digestion, 25 ug of DNase I (Sigma) and 0.28 Wunitz Units of Liberase TM (Roche) were added to each mL of digest. Lungs were snipped into small pieces with scissors in a 1.7 mL eppendorf tube and incubated on a 37°C shaker for 30-45 min at 700 rpm on a ThermoMixer F1.5 (Eppendorf). The digestion reaction was quenched by adding FBS and EDTA to a final concentration of 5% FBS and 10 mM EDTA. Digested lungs were then gently dissociated and passed through a 70 um strainer to yield single cell suspensions that were then centrifuged and resuspended in DMEM supplemented with 5% FBS, HEPES, Penicillin, Streptomycin and L-Glutamine. Single cell suspensions of two lung samples from mice of the same sex were pooled and washed with a 2X volume of ACK Lysing Buffer (Quality Biological) as above to lyse red blood cells and then were resuspended in PBS with 0.5% BSA (Roche) and 2 mM EDTA (Gibco) (MACS buffer). Cells were depleted of B cells and partially depleted of AMs and cells that had lost membrane integrity by first incubating with anti-IgD Biotin (Southern Biotech) and anti-Siglec-F Biotin, as well as 0.25 mM of NHS-Biotin (Life Technologies, freshly reconstituted in PBS), for 30 min on ice. Cells were washed in MACS buffer and incubated with 50 ml of MyOne Streptavidin T1 Dynabeads (Thermo Fisher) for 30 min, during which tubes were inverted and rotated at 4°C. Tubes were placed in a Dynamag-2 magnet (Thermo Fisher) for 2 min for bead isolation and the negative fraction containing unlabeled cells was collected and diluted with MACS buffer to 5 ml. To further enrich for macrophages and DCs and to remove stromal cells, 3ml of 14% OptiprepTM (Axis-Shield) was layered below the cell suspension, and cells were centrifuged at 600 g for 20 min with no brake at 8°C. Cells at the interface were collected and washed in MACS buffer. Finally, CD11c+ cells were enriched by incubating with CD11c Mojosort Nanobeads (Biolegend) for 15 min at 4°C. Bead-labeled cells were purified with the Mojosort magnet (Biolegend) according to the manufacturer’s instructions. Bead-labeled cells were washed in PBS with 0.5% BSA (Roche), washed, and submitted to the UCSF Institute for Human Genetics for single cell RNA sequencing using 10x Genomics Chromium technology.
Libraries were prepared by UCSF Institute for Human Genetics, according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)

value: Dissociated whole lung

value: male

value: CD11c+ enriched cells

value: MacBlue

value: untreated


title: CD11c+ lung cells pooled from 2 untreated female mice

description: 10x Genomics

value: female


title: ATAC-seq__limb_HH22_wt_chicken_Rep-1

data_processing:
Raw sequencing fastq files were processed using cutadapt (Martin, 2011) for adapter trimming, Bowtie2 (Langmead and Salzberg, 2012) for mapping, SAMtools (Li et al., 2009) for filtering, sorting and removing duplicates, and deepTools (Ramirez et al., 2016) for generating coverage tracks.
Genome_build: mm10 galgal6 and mondom5
Supplementary_files_format_and_content: bigwig files

organism: Gallus gallus

source_name: forelimb

growth_protocol: Chicken, opossum and mouse limb buds were microdissected from embryos in cold PBS. Isolated limbs were then trypsinised 5 minutes at 37°C with continuous agitation with a P1000 pipette until no visible clumps remained. Limb cell suspensions were then passed through a 40 µm filter, centrifuged at 250 g for 5 min. Supernatants were then removed from isolated ESCs or limb cells which could then be used for downstream applications.

extract_protocol:
Resulting DNA was then purified using MinElute Reaction Clean up  kit, eluted in 11 µl of elution buffer and stored in -20° C, if not immediately processed further.
Barcoded adapters were added to the transposed fragments by PCR. To avoid saturation in our PCR, we initially performed 5 cycles and extracted a 5 µl aliquot for qPCR to identify the number of cycles required without overamplification. Nextera qPCR primers were used for the amplification. The remaining 45 µl of the PCR reaction were  then amplified for the desired number of cycles which never exceeded 12. Finally, samples were purified on AMPure XP beads and eluted in 20 µl. Concentration was measured with Qubit and the quality of the samples was estimated by Bioanalyzer analysis. ATAC-seq samples were sequenced yielding for 50 million 75 bp paired-end reads and each experiment was performed in duplicate.

treatment_protocol: ATAC-seq was performed as described previously (Buenrostro et al., 2015). Briefly, 1x105 isolated limb cells were employed per biological replicate. Cells were washed in cold PBS, lysed in fresh lysis buffer (10mM TrisCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% (v/v) Igepal CA-630) for 2 min on ice, and finally pelleted for 10 min at 500 x g and 4°C. Following supernatant aspiration, nuclei-containing pellets were subjected to transposition using Tn5 Transposase for 30 min at 37° C.

tag: Stage

value: wt


title: RNAseq_forelimb_E115_mm10_DLAD3BKO_Rep-1-1_L26136

tag: tissue


title: RNAseq_forelimb_E115_mm10_Fat1enhKO_Rep-4_L25647


title: RNAseq_forelimb_E115_mm10_DLAD3BKO_Rep-1-2_L26137


title: RNAseq_forelimb_E115_mm10_Fat1enhKO_Rep-3_L25646


title: GM12878_sc_8


title: RNAseq_forelimb_E115_mm10_Fat1enhKO_Rep-1_L25644


title: GM12878_sc_6


title: RNAseq_forelimb_E115_mm10_Fat1enhKO_Rep-2_L25645


title: cHiC_ limb_E115_deltaD1_mouse_Rep-1

data_processing:
Fastq files were processed with the Juicer pipeline v1.5.6 (Durand et al., 2016) (CPU version) using bwa v0.7.17 (Li and Durbin, 2010) for mapping short reads to the reference genomes mm10 (mouse), hg19 (human), galGal6 (chicken), monDom5 (opossum), susScr11.1 (pig), and AmexG_v6.0-DD (axolotl), respectively.
Replicates were merged after the mapping, filtering and deduplication steps of the Juicer pipeline. Juicer tools v1.7.5 (Durand et al., 2016) were used to generate binned and KR normalized HiC maps from read pairs with MAPQ≥30.
For compartment analysis, hic-files were converted at 100kb bin size to the cool format using hic2cool (v0.8.2) (https://github.com/4dn-dcic/hic2cool) and balanced using cooler (v0.8.5) (Abdennur and Mirny, 2020). Afterwards, compartment analysis was performed using cooltools (v0.3.0) (https://github.com/open2c/cooltools) and using the GC content as reference track.  TADs were identified by applying TopDom v.0.0.228 on 50-kb binned and KR-normalized maps using a window size of 10 (Shin et al., 2016).
Assembly: mondom5 and galgal6
Supplementary files format and content: .hic

growth_protocol: Embryonic limb cells were isolated from chicken or opossum embryos through limb dissection, trypsinization, filtration (100 µm) and centrifugation.

extract_protocol: A S-Series 220 Covaris was used to shear the DNA to fragments of 300–600 bp for library preparation, and biotin-filled DNA fragments were pulled down using Dynabeads MyOne Streptavidin T1 beads. DNA ends were subsequently repaired using T4 DNA polymerase and the Klenow fragment of DNA polymerase I and phosphorylated with T4 Polynucleotide Kinase NK. DNA was further prepared for sequencing by ligating adaptors to DNA fragments, using the NEBNext Multiplex Oligos for Illumina kit. Indexes were added via PCR amplification (4–8 cycles) using the NEBNext Ultra II Q5 Master Mix. PCR purification and size selection were carried out using Agencourt AMPure XP beads. Libraries were sequenced on a x platform yielding x bp paired-end reads. For each sample, the HiC library was created by pooling a total of four technical replicates generated from two different cell isolations cultures in order to ensure higher complexity of the sequencing library

treatment_protocol: HiC libraries were prepared as described in a previously published in situ protocol (Melo et al., 2020; Rao et al., 2014). Briefly, ∼1 million cells were fixed in 2% formaldehyde, lysed, and stored at -80°C.

value: DNMT3B KO


title: cHiC__ESC_G4_deltaPromoterRex1_mouse_Rep-1

source_name: ESC

value: ESC


title: RNA-seq__limb_E115_detlaD1-D2_mouse_Rep-4

data_processing:
Single-end, 100 bp reads from Illumina sequencing were mapped to the reference genome (mm10) using the STAR mapper (splice junctions based on RefSeq; options: ‐‐alignIntronMin20 ‐‐alignIntronMax500000 ‐‐outFilterMismatchNmax 10).
Differential gene expression was ascertained using the DESeq2 package (Love et al., 2014). The cut-off for significantly altered gene expression was an adjusted P value of 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

tag: strain

tag: condition


title: ATAC-seq__limb_stg30_wt_opossum_Rep-2

organism: Monodelphis domestica


title: cHiC__ESC_G4_deltaPromoterRex1-Triml_mouse_Rep-1


title: GM12878_sc_1


title: ATAC-seq__limb_stg30_wt_opossum_Rep-1


title: RNA-seq__ESC_G4_detlaD1-D2_mouse_Rep-2

value: G4 (XY, 129S6/SvEvTac x C57BL/6Ncr F1 hybrid)


title: RNA-seq__ESC_G4_detlaD1-D2_mouse_Rep-3


title: RNA-seq__ESC_G4_detlaD1-D2_mouse_Rep-1


title: RNA-seq__ESC_G4_deltaD2_mouse_Rep-3


title: RNA-seq__ESC_G4_deltaD1_mouse_Rep-3


title: RNA-seq__ESC_G4_deltaRex1_mouse_Rep-3


title: RNA-seq__ESC_G4_deltaD1_mouse_Rep-1


title: RNA-seq__ESC_G4_deltaD1_mouse_Rep-2


title: RNA-seq__ESC_G4_deltaRex1_mouse_Rep-1


title: RNA-seq__ESC_G4_wt_mouse_Rep-3


title: RNA-seq__ESC_G4_deltaRex1_mouse_Rep-2


title: RNA-seq__ESC_G4_wt_mouse_Rep-2


title: RNA-seq__limb_E115_detlaD1-D2_mouse_Rep-3


title: RNA-seq__ESC_G4_deltaD2_mouse_Rep-2


title: RNA-seq__ESC_G4_deltaD2_mouse_Rep-1


title: cHiC__ESC_E14Tg2a_depletionCTCF_mouse_Rep-1

data_processing:
Raw fastq files had read lengths of 75bp and 100bp, respectively. In a preprocessing step, fastq files with 100 bp read length were trimmed to 75bp to achieve comparable initial read lengths for all samples.
Fastq files were processed with the HiCUP pipeline v0.8.1 (no size selection, Nofill: 1, Format: Sanger) for mapping, filtering and deduplication steps (Wingett et al., 2015). The pipeline was set up with Bowtie 2.4.2 for mapping short reads to reference genome mm10 (Langmead and Salzberg, 2012). If replicates were available, they were merged after the processing with the HiCUP pipeline. Binned and KR normalized cHiC maps (Knight and Ruiz, 2012; Rao et al., 2014) were generated using Juicer tools v1.19.02 (Durand et al., 2016). Only read pairs for region chr8:39,030,001-48,000,000 and with MAPQ≥30 were considered for the generation of cHiC maps.
Additional to the original cHiC maps, custom reference genomes were derived from mm10  for the three deletions (ΔD1, ΔD2, ΔD1+2), considering the respective deletions and cHiC data was processed correspondingly. cHiC maps were displayed as heatmaps in which very high values were truncated to improve the visualization.
Genome_build: mm10 and custom mutant genomes
Supplementary_files_format_and_content: .hic .mutants are mapped on both wt and corresponding mutant mm10 genomes (see description for each sample)

growth_protocol: Mouse G4 ESCs (XY, 129S6/SvEvTac x C57BL/6Ncr F1 hybrid) were grown as described previously on a mitomycin-inactivated CD1 mouse embryonic fibroblast feeder monolayer on gelatinised dishes  at 37oC, 7.5% CO2 (Andrey and Spielmann, 2017; George et al., 2007). ESCs were cultured in ESC medium containing knockout DMEM with 4,5 mg/ml glucose and sodium pyruvate supplemented with 15% FCS, 10 mM Glutamine, 1x penicillin/streptomycin, 1x non-essential amino acids, 1x nucleosides, 0.1 mM beta-Mercaptoethanol and 1000 U/ml LIF. Medium was changed every day while G4-cells were split every 2-3 days or were frozen at 1x 106 cells/cryovial in ESC medium containing 20% FCS and 10% DMSO. ESCs and feeder cells were tested for Mycoplasma contamination using the MycoAlert detection kit and MycoAlert Assay Control Set.    E11.5 forelimb cells were isolated from C57BL/6 embryonic limbs through trypsinization, filtration (100 µm) and centrifugation.

extract_protocol:
3C libraries were prepared from fixed nuclei as described previously (Kragesteen et al, 2018). Briefly, lysis buffer was removed by centrifugation at 400 g for 5 min at 4 °C, followed by supernatant aspiration, snap-freezing, and pellet storage at − 80 °C. Later, nuclei pellets were thawed on ice, resuspended in 520 μl 1× DpnII buffer, and then incubated with 7.4 μl 20% SDS shaking at 900 rpm. at 37 °C for 1 h. Next, 75 μl 20% Triton X-100 was added and the pellet was left shaking at 900 rpm at 37°C for 1 h. A 15-μl aliquot was taken as a control for undigested chromatin (stored at − 20°C). The chromatin was digested using 40 μl 10 U/μl DpnII buffer shaking at 900 rpm at 37°C for 6 h; 40 μl of DpnII was added and samples were incubated overnight, shaking at 900 rpm. at 37°C. On day three, 20 μl DpnII buffer was added to the samples followed by shaking for an additional 5 h at 900 rpm. at 37 °C. DpnII subsequently was inactivated at 65 °C for 25 min and a 50-μl aliquot was taken to test digestion efficiency (stored at − 20 °C). Next, digested chromatin was diluted in 5.1 ml H2O, 700 μl 10× ligation buffer, 5 μl 30 U/μl T4 DNA ligase and incubated at 16°C for 4 h while rotating. Ligated samples were incubated for a further 30 min at room temperature. Chimeric chromatin products and test aliquots were de-cross-linked overnight by adding 30 μl and 5 μl proteinase K, respectively, and incubated at 65 °C overnight. On the fourth day, 30 μl or 5 μl of 10 mg ml−1 RNase was added to the samples and aliquots, respectively, and incubated for 45 min at 37°C. Next, chromatin was precipitated by adding 1 volume phenol-chloroform to the samples and aliquots, vigorously shaking them, followed by centrifugation at 4,000 rpm at room temperature for 15 min. To precipitate aliquot chromatin, 1 volume 100% ethanol and 0.1 volume 3M NaAc, pH 5.6 was added and the aliquots placed at -80°C for 30 min. DNA was then precipitated by centrifugation at 5,000 rpm. for 45 min at 4°C followed by washing with 70% ethanol, and resuspension in 20 μl with 10 mM Tris-HCl, pH 7.5. To precipitate samples, extracted sample aqueous phases were mixed with 7 ml H2O, 1 ml 3M NaAc, pH 5.6, and 35 ml 100% ethanol. Following incubation at −20°C for at least 3 h, precipitated chromatin was isolated by centrifugation at 5,000 rpm for 45 min at 4 °C. The chromatin pellet was washed with 70% ethanol and further centrifuged at 5,000 rpm for 15 min at 4 °C. Finally, 3C library chromatin pellets were dried at room temperature and resuspended in 10 mM Tris-HCl, pH 7.5. To check the 3C library, 600 ng were loaded on a 1% gel together with the undigested and digested aliquots.
The 3C library was then sheared using a Covaris sonicator (duty cycle: 10%; intensity: 5; cycles per burst: 200; time: 6 cycles of 60 s each; set mode: frequency sweeping; temperature: 4–7 °C). Adaptors were added to the sheared DNA and amplified according to the manufacturer’s instructions for Illumina sequencing (Agilent). The library was hybridised to the custom designed SureSelect beads and indexed for sequencing (75–100 bp paired-end) following the manufacturer’s instructions (Agilent).

treatment_protocol: Disassociated ESCs and limb cells were transferred to a 50-ml falcon tube and complemented with 10% FCS/PBS. 37% formaldehyde was added to a final concentration of 2% and cells were fixed for 10 min at room temperature. Crosslinking was quenched by adding glycine (final concentration; 125 mM). Fixed cells were washed twice with cold PBS and lysed using fresh lysis buffer (10 mM Tris, pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA with protease inhibitor) to isolate nuclei. Cell lysis was assessed microscopically after 10-min incubation in ice. Nuclei were centrifuged for 5 min at 480g, washed once with PBS and snap frozen in liquid N2.

tag: group

value: depletionCTCF


title: cHiC__ESC_E14Tg2a_depletionRad21_mouse_Rep-1


title: cHiC__limb_E115_detlaD1-D2_mouse_Rep-1

description: del chr8:41457521-43108935 + chr8:43402062-44932011


title: RNA-seq__ESC_G4_wt_mouse_Rep-1


title: ChIP-seq_CTCF_OEF_cultured_wt_mouse_Rep-1

data_processing:
Raw sequencing fastq files were processed using STAR (Dobin et al., 2013) for mapping, SAMtools (Li et al., 2009) for filtering, sorting and removing duplicates, and deepTools (Ramirez et al., 2016) for generating coverage tracks.
Genome_build: mm10 and mondom5
Supplementary_files_format_and_content: bigwig

source_name: OEF

growth_protocol: Mouse G4 ESCs (XY, 129S6/SvEvTac x C57BL/6Ncr F1 hybrid) were grown as described previously on a mitomycin-inactivated CD1 mouse embryonic fibroblast feeder monolayer on gelatinised dishes  at 37oC, 7.5% CO2 (Andrey and Spielmann, 2017; George et al., 2007). ESCs were cultured in ESC medium containing knockout DMEM with 4,5 mg/ml glucose and sodium pyruvate supplemented with 15% FCS, 10 mM Glutamine, 1x penicillin/streptomycin, 1x non-essential amino acids, 1x nucleosides, 0.1 mM beta-Mercaptoethanol and 1000 U/ml LIF. Medium was changed every day while G4-cells were split every 2-3 days or were frozen at 1x 106 cells/cryovial in ESC medium containing 20% FCS and 10% DMSO. ESCs and feeder cells were tested for Mycoplasma contamination using the MycoAlert detection kit and MycoAlert Assay Control Set.    OEFs were isolated from Stage 30 opossum embryos following head removal by trypsinization, filtration (100 µm) and centrifugation. When cultured in vitro, OEFs were grown on gelatine-coated plates at 37oC in 5.0% CO2  in ESGRO Complete Basal Medium with supplement.

extract_protocol:
Chromatin was sheared using a Bioruptor until reaching a fragment size of 200–500 base pairs. Afterwards, samples were processed with the iDeal ChIP-seq kit according to the manufacturer’s instructions. For each Histone ChIP 5 μg chromatin was used in combination with antibodies against H3K4me1 (1 µg) H3K4me3 (1 µg), H3K27ac (1 µg) and H3K27me3 (1 µg).
Libraries were prepared for sequencing using the KAPA HyperPrep kit and their quality confirmed by Bioanalyzer analysis. ChIP-seq libraries were finally sequenced at 100 bp paired-end reads with all samples analyzed in biological duplicates.

treatment_protocol: ChIP-seq was performed using the iDeal ChIP-seq kit for histones with several modifications. Briefly, ESCs were fixed in 1% paraformaldehyde (PFA)/10% FCS/PBS for 10 min with rotation at room temperature. Fixation was stopped by glycine after which cells were pelleted by centrifugation (8 min, 250 x g, 4°C). Cells were lysed in Lysis buffer (50 mM Tris, pH 7.5; 150 mM NaCl; 5 mM EDTA; 0.5% NP-40; 1.15% Triton X-100; protease inhibitors) for 10 min on ice. Nuclei were resuspended in sonication buffer (10 mM Tris–HCl, pH 8.0; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0,1% Na-deoxycholate; 0.5% N-lauroylsarcosine; protease inhibitors).

value: cultured

tag: histone mark

value: CTCF


title: ChIP-seq_H3K27ac_ESC_G4_wt_mouse_Rep-1


title: ChIP-seq_H3K27ac_ESC_G4_wt_mouse_Rep-2


title: Wierman_94

type: RNA

city: AURORA

first: Katja

last: Kiseljak-Vassiliades

state: Colorado

address: 12801  E 17TH AVE, RC1SOUTH, ENDOCRINOLOGY MS8106

institute: UNIVERSITY OF COLORADO

hyb_protocol: An Affymetrix Human Gene 1.1 ST array plate (Thermo Fisher Scientific) was hybridized with 2.3 µg of fragmented and labeled single-stranded complementary DNA (cDNA).

scan_protocol: Hybridization and scanning were done on the Affymetrix GeneTitan instrument.

data_processing: Hybridization intensities were quantified and normalized across all arrays using the robust multichip average algorithm available as an array processing tool on Partek Genomics Suite software (Partek, St. Louis, MO).

label: biotin

source_name: GH tumor

label_protocol: Microarray targets were prepared and labeled from 150 ng of total RNA using the Ambion WT (Thermo Fisher Scientific, Waltham, MA) expression kit following the manufacturer’s instructions.

extract_protocol: Our cohort consisted of 21 GH tumors (11 DG and 10 SG) and 20 samples of normal human pituitary. Total RNA was isolated using TRIzol method (Invitrogen, Carlsbad, CA), followed by clean-up with a QIAGEN Bioinformatics RNeasy mini kit (Redwood City, CA). RNA was quantified by spectrophotometry, and RNA integrity was verified using the Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: disease

value: GH tumor

tag: granulations

value: Sparse


title: Wierman_93

value: Dense


title: Wierman_95

source_name: Normal pituitary

value: Normal pituitary


title: Wierman_88


title: Wierman_87


title: Wierman_91


title: Wierman_77


title: ChIP-seq_H3K4me3_ESC_G4_wt_mouse_Rep-2

tag: genotype


title: Wierman_75


title: Wierman_85


title: Wierman_9


title: Wierman_70


title: Wierman_67


title: Wierman_64


title: Wierman_60


title: Wierman_6


title: Wierman_57


title: Wierman_63


title: ChIP-seq_H3K4me3_ESC_G4_wt_mouse_Rep-1


title: ChIP-seq_H3K4me1_ESC_G4_wt_mouse_Rep-2


title: Wierman_54


title: ChIP-seq_H3K4me1_ESC_G4_wt_mouse_Rep-1


title: Wierman_74


title: RNA-seq__limb_E115_deltaDNMT3B_mouse_Rep-2


title: Wierman_81


title: RNA-seq__limb_E115_detlaD1-D2_mouse_Rep-1


title: Wierman_49


title: RNA-seq__limb_E115_deltaDNMT3B_mouse_Rep-1


title: Wierman_53


title: RNA-seq__limb_E115_detlaD1-D2_mouse_Rep-2


title: RNA-seq__limb_E115_wt_mouse_Rep-6


title: RNA-seq__limb_E115_deltaRex1_mouse_Rep-2


title: RNA-seq__limb_E115_wt_mouse_Rep-5


title: Wierman_42


title: RNA-seq__limb_E115_deltaD2_mouse_Rep-2


title: RNA-seq__limb_E115_deltaD2_mouse_Rep-1


title: Wierman_48


title: Wierman_39


title: Wierman_29


title: Wierman_36


title: 200054I_hyh_bm

city: Tianjin

first: yingying

last: chen

state: Tianjin

address: 154 Anshan Street

institute: Department of Hemataology,Tianjin Medical University General Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow

extract_protocol:
20 mL of heparin anticoagulant PB and BM from SAA patients or HCs were collected to separate mononuclear cells with lymphocyte separation medium (Amersham Bioscience, UK) under sterile conditions. Mononuclear cells were washed with sterile phosphate-buffered saline, The percentage of NK cells was determined by flow cytometry (Calibur, BD Biosciences, USA) using CD3-PerCP (347344, BD Biosciences, USA), CD56-PE (555516, BD Biosciences, USA), or isotype control antibody (BD Biosciences, USA). The remaining cells were suspended in 1ml of sterile magnetic bead sorting buffer and counted. Negative magnetic beads (130-092-657, Miltenyi Biotec, USA) were used to sort NK cells, and the NK cells was washed with sterile phosphate-buffered saline, suspended, and counted. The cell suspension was adjusted to 300-600 cells/μL, and cell viability was analyzed with Countstar Rigel S2. Sequencing analysis was carried out after passing quality inspection.
According to the manufacturer’s instructions, single-cell RNA-seq libraries were constructed using the Single Cell 3′ Library and Gel Bead Kit v3.1. The libraries were sequenced in an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with a paired-end 150-bp reading strategy (performed by CapitalBio Technology, Beijing).

value: NK cells

value: Bone marrow

tag: gender

value: Female

tag: disease state

value: SAA

value: 51 years old


title: Wierman_21


title: RNA-seq__limb_E115_deltaD1_mouse_Rep-2


title: Wierman_46


title: RNA-seq__limb_E115_deltaD1_mouse_Rep-1


title: 200054H_wje_pb

description: 10x Genomics

value: healthy control

tag: age

value: 38 years old


title: Wierman_35


title: RNA-seq__limb_E115_deltaRex1_mouse_Rep-1


title: Wierman_3


title: 200054H_wje_bm

description: 10x Genomics


title: Wierman_27


title: RNA-seq__limb_E115_wt_mouse_Rep-4

value: wt


title: RNA-seq__limb_E115_wt_mouse_Rep-1


title: RNA-seq__limb_E115_wt_mouse_Rep-3


title: 200054H_sn_pb

description: 10x Genomics

value: 35 years old


title: WGBS__ESC_G4_wt_mouse_Rep-2

data_processing:
Raw reads were subjected to adapter and quality trimming using cutadapt (version 2.4; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 nucleotides from the 5’ end of the first read, 15 nucleotides from the 5’ end of the second read and 5 nucleotides from the 3’ end of both reads (Kechin et al., 2017).
The trimmed reads were aligned to the mouse genome (mm10) using BSMAP (version 2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R) (Xi and Li, 2009).
Duplicates were removed using the ‘MarkDuplicates’ command from GATK (version 4.1.4.1; --VALIDATION_STRINGENCY=LENIENT --REMOVE_DUPLICATES=true) (McKenna et al., 2010).
Methylation rates were called using mcall from the MOABS package (version 1.3.2; default parameters) (Sun et al., 2014). All analyses were restricted to autosomes and only CpGs covered by at least 10 reads and at most 150 reads were considered for downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
Genomic DNA was extracted from ESCs and E11.5 limb buds using the PureLink Genomic DNA Mini Kit following manufacturer’s instructions. gDNA was then sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes. Next, the sheared gDNA was purified with the Zymo DNA Clean & Concentrator according to manufacturer’s instructions. Purified DNA was then bisulfite converted using the EZ DNA Methylation-Gold Kit.
WGBS libraries were processed using the Accel-NGS Methyl-seq DNA library kit following manufacturer’s recommendations for each. Libraries were prepared and cleaned using Agencourt AMPure XP beads. The absence of adapters from the final libraries was verified using the Agilent TapeStation.

value: G4 (XY, 129S6/SvEvTac x C57BL/6Ncr F1 hybrid)


title: RNA-seq__limb_E115_wt_mouse_Rep-2


title: Wierman_25


title: Wierman_26


title: 200054H_sn_bm

description: 10x Genomics


title: WGBS__limb_E115_deltaDNMT3B_mouse_Rep-2


title: 200054G_LX_PB

description: 10x Genomics

source_name: Peripheral blood

value: Peripheral blood

value: 53 years old


title: 200054J_hyh_pb

description: 10x Genomics

source_name: NK cells


title: WGBS__ESC_G4_wt_mouse_Rep-1


title: Wierman_18


title: WGBS__limb_E115_wt_mouse_Rep-1


title: Wierman_10


title: JD-YX-2020-0054-JSFU-02

description: 10x Genomics

value: male

value: 56 years old


title: Wierman_17

value: GH tumor


title: JD-YX-2020-0054-JSFU-04

description: 10x Genomics

value: 40 years old


title: Wierman_15

value: Normal pituitary


title: 200054G_LX_BM

description: 10x Genomics

value: NK cells


title: JD-YX-2020-0054-JSFU-03

description: 10x Genomics


title: WGBS__limb_E115_deltaDNMT3B_mouse_Rep-1


title: WGBS__limb_E115_wt_mouse_Rep-2


title: ATAC-seq__limb_E115_wt_mouse_Rep-2


title: ATAC-seq__limb_E115_wt_mouse_Rep-1


title: LPS-3

city: Changsha

first: Ludong

last: Yuan

address: Department of Pathophysiology, Xiangya School of Medicine, Central South University,

institute: Central south university

description: tsRNA expression after 24 h LPS stimulation in mouse heart

hyb_protocol: 22.5 uL 2X Hybridization buffer (Agilent) was mixed with the completed labeling reaction to a final volume of 45 uL. The mixture was heated at 100°C for 5 min and chilled immediately to 0°C. 45 uL labeled sample mix was hybridized onto a microarray at 55°C for 20 hrs. The slides were washed at room temperature in 6X SSC with 0.005% Triton X-102 for 10 min, then in 0.1X SSC with 0.005% Triton X-102 for 5 min. The slides were scanned on an Agilent G2505C microarray scanner.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. The raw intensities were log2 transformed and quantile normalized. After normalization, the probe signals having Present (P) or Marginal (M) QC flags in a certain proportion were retained. Multiple probes from the same small RNA (miRNA/tsRNA/pre-miRNA/tRNA/ snoRNA) were averaged and consolidated into one RNA level. Differentially expressed small RNAs between two comparison groups were identified by filtering at the indicated fold change (FC) and statistical significance (p-value) thresholds. Hierarchical clustering, scatter plots, and volcano plots were generated by R software.

organism: Mus

source_name: heart,Intraperitoneal LPS 10mg/kg,24h

label_protocol: For Small RNA Microarray profiling, 100 ng total RNA was firstly dephosphorylated with 3 units T4 polynucleotide kinase (T4 PNK) at 37°C for 40 min to remove both (P) and (cP) chemical groups from the 3' end of RNAs to form a 3-OH end. The reaction was terminated at 70°C for 5 min and cooled immediately to 0°C. 7 uL of DMSO was added and heated to 100°C for 3 min to denature the RNAs and chilled immediately to 0°C. RNA end labeling was performed by adding ligase buffer, BSA, final 50 mM pCp-Cy3, and 15 units T4 RNA ligase in a 28 uL reaction at 16°C overnight.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen). RNA quantity was measured by using NanoDrop ND-1000 spectrophotometer and RNA integrity (quality) was assessed by Bioanalyzer 2100 or denaturing gel electrophoresis.

value: 10 weeks

tag: treatment

value: Intraperitoneal LPS 10mg/kg,24h

value: heart


title: CONTROL-3

description: tsRNA expression after 24 h saline stimulation in mouse heart

source_name: heart,Intraperitoneal saline,24h

value: Intraperitoneal saline,24h


title: VADHBEMA003FG_Dapi_plus

status: Public on Sep 28 2022

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description: VADHBEMA003FG Dapi plus

data_processing:
Cell Ranger from 10x Genomics was used for alignment and quantification
Assembly: GRCh38
Supplementary files format and content: There are 3 files for each sample: barcodes, features, and count matrix, in the forms of tab-separated values and market exchange format, respectively

extract_protocol:
Mitroi et al. J Cell Mol Med . 2022 Jun;26(11):3183-3195. doi: 10.1111/jcmm.17315.
Single cell suspension from mouse brain tissues were prepared using 10x Genomics Chromium Single Cell 3’ Reagent Kits v2 and v3 (10X Genomics) according to manufacture’s protocol. Quantity and quality of cDNA were assessed by Agilent 2100 expert High Sensitivity DNA Assay. cDNA samples were sequenced on NovaSeq 6000 or NextSeq 500 platform at UCLA Technology Center for Genomics and Bioinformatics.
10X Genomics Chromium

value: Dapi plus

tag: Sex

value: M

tag: sample type

value: VAD adj WM Dapi


title: CONTROL-2


title: VADHBEMA003FG_ERG_plus

description: VADHBEMA003FG ERG plus

value: ERG plus

value: VAD adj WM ERG


title: JD-YX-2020-0054-JSFU-01

description: 10x Genomics

value: Peripheral blood

value: SAA


title: CONTROL-1

value: male


title: C_4582_F_Neg

description: C 4582 F Neg

value: Neg

value: Control Frontal Dapi


title: VADHBEMA001F_Dapi_plus

description: VADHBEMA001F Dapi plus

value: VAD Dapi


title: LPS-2


title: VADHBEMA001F_ERG_plus

description: VADHBEMA001F ERG plus

value: VAD ERG


title: VADFGoodUCLA_ERG

description: VADFGoodUCLA ERG

value: ERG

value: F


title: LPS-1

value: 10 weeks

value: Intraperitoneal LPS 10mg/kg,24h


title: Wierman_11

value: Normal pituitary


title: VADFGoodUCLA_Dapi

description: VADFGoodUCLA Dapi

value: Dapi


title: VAD4143FG_ERG_plus

description: VAD4143FG ERG plus

value: M


title: Wierman_1


title: VAD_FUCLA_Dapi

description: VAD FUCLA Dapi


title: VAD_FUCLA_ERG

description: VAD FUCLA ERG


title: VAD4143FG_Dapi_plus

description: VAD4143FG Dapi plus

value: Dapi plus

value: VAD adj WM Dapi


title: VAD4143F_ERG_plus

description: VAD4143F ERG plus

value: ERG plus


title: VAD3761FG_ERG_plus

description: VAD3761FG ERG plus

value: VAD adj WM ERG


title: VAD4143F_Dapi_plus

description: VAD4143F Dapi plus


title: VAD3761F_Dapi_plus

description: VAD3761F Dapi plus


title: VAD3505FG_Dapi_plus

description: VAD3505FG Dapi plus


title: VAD3505FG_ERG_plus

description: VAD3505FG ERG plus


title: VAD3761FG_Dapi_plus

description: VAD3761FG Dapi plus


title: C4621F_Dapi_plus

description: C4621F Dapi plus


title: C4621F_ERG_plus

description: C4621F ERG plus

value: Control Frontal ERG


title: C_4858_F_Erg_pos_MED

description: C 4858 F Erg pos MED

value: ERG pos MED


title: C_4582_F_Erg_pos_MED

description: C 4582 F Erg pos MED


title: C2526F_Dapi_plus

description: C2526F Dapi plus


title: VAD3761F_ERG_plus

description: VAD3761F ERG plus


title: C2526F_ERG_plus

description: C2526F ERG plus


title: VAD3505F_Dapi_plus

description: VAD3505F Dapi plus


title: CCLP1 SB 16h rep2

city: Shanghai

first: Yuanyuan

last: Shi

address: changhailu 168

institute: the First Affiliated Hospital of Naval Medical University

data_processing:
For RNA-seq analysis, 2 × 150 bp paired-end sequencing (PE150) was generated on an Illumina Novaseq 6000 (LC-Bio Technology CO., Ltd.).
The fastp software (https://github.com/OpenGene/fastp) was used to remove the reads that contained adaptor contamination, low-quality bases, and undetermined bases with default parameters.
HISAT2 (https://ccb.jhu.edu/software/hisat2) was used to map reads to the reference genome of Homo sapiens GRCh38.
StringTie was used to perform expression levels for mRNAs by calculating FPKM (fragments per kilobase of exon model per million mapped fragments).
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

extract_protocol:
CCLP1 cells were treated with SB743921 or vehicle control for 8 and 16 hours. RNA extraction was performed following the standard protocol, and 500 ng of total RNA was used for input to library preparation. For RNA-seq analysis, 2 × 150 bp paired-end sequencing (PE150) was generated on an Illumina Novaseq 6000 (LC-Bio Technology CO., Ltd.).
RNA library were prepared for sequencing using standard lllumina protocols.

tag: cell line

value: cholangiocarcinoma cell line

value: 10 nM SB743921 for 16 hours


title: CCLP1 SB 8h rep1

tag: cell type

value: 10 nM SB743921 for 8 hours


title: CCLP1 SB 16h rep1


title: CCLP1 control rep2

value: saline


title: CCLP1 SB 8h rep2


title: C4320F_Dapi_plus

description: C4320F Dapi plus

value: Control Frontal Dapi


title: VAD3505F_ERG_plus

description: VAD3505F ERG plus

value: F

value: VAD ERG


title: C4320F_ERG_plus

description: C4320F ERG plus


title: CCLP1 control rep1


title: Periodontal ligament cells - batch 2 rep10

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

country: Japan

institute: Osaka university

data_processing:
Sequencing outputs were demultiplexed using bcl2fastq2 (https://jp.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html)
files were aligned to Mus musculus GRCm38 reference using STAR aligner (2.7.6a; https://github.com/alexdobin/STAR)
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tar-archived STAR output directory (Solo.out).
Supplementary_files_format_and_content: Tar-archived directory (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)

source_name: Periodontal ligament cells

extract_protocol:
Dissected teeth were treated with Liberase TM to obtain a PDL cell suspension
Cells were sorted into 384-well plates with barcoded oligo dT primer for each well (1 cell / well). After reverse transcription in each well, cDNA was pre-amplified using the Accel-NGS 1S Plus DNA Library Kit (Swift Biosciences). Purified cDNAs were subjected to tagmentation reaction with Amplicon Tagment enzyme (Illumina), and then amplified by PCR for library construction using NEBNext High-Fidelity 2× PCR Master Mix (NEB).

tag: cell sorting

value: Sytox-

tag: batch

value: Batch 2


title: Periodontal ligament cells - batch 2 rep7

tag: strain


title: Periodontal ligament cells - batch 2 rep8


title: Periodontal ligament cells - batch 2 rep9


title: Periodontal ligament cells - batch 2 rep5


title: Periodontal ligament cells - batch 2 rep3


title: Periodontal ligament cells - batch 2 rep6


title: Periodontal ligament cells - batch 1 rep10

value: Batch 1


title: C_4858F_Neg

description: C 4858F Neg

value: Neg


title: Periodontal ligament cells - batch 2 rep4


title: Periodontal ligament cells - batch 2 rep2


title: Periodontal ligament cells - batch 2 rep1


title: Periodontal ligament cells - batch 1 rep9


title: Periodontal ligament cells - batch 1 rep8


title: Periodontal ligament cells - batch 1 rep6


title: Periodontal ligament cells - batch 1 rep7


title: Periodontal ligament cells - batch 1 rep3


title: Periodontal ligament cells - batch 1 rep4


title: Periodontal ligament cells - batch 1 rep2


title: Periodontal ligament cells - batch 1 rep5


title: Periodontal ligament cells - batch 1 rep1


title: 4.12_UPS F-8

city: NEW HAVEN

first: Arie

last: Kaffman

state: CT

address: 300 GEORGE ST. SUITE 901, SUITE 901

institute: YALE UNIVERSITY

description: NS_Mm_Glial_v1.0 (1)

hyb_protocol: Complexes were hybridized at 65C for 16hrs.

scan_protocol: Using in the nCounter Digital analyzer.

data_processing: Counts were normalized using all 13 housekeeping genes available on the mouse Glia panel and genes with counts greater then negative control (> 20) were considered present. Preliminary MANOVA analysis of the 524 expressed genes revealed that the vast majority of the differentially regulated genes (DRGs) were regulated by rearing (87 DRGs) with relatively few genes regulated by sex (13 DRG) and only 5 DRGs showing significant interaction between rearing and sex. Based on the prominent rearing effect, advanced-analysis was conducted using the nSolver software to identify DRG between CTL and LB group, CTL and UPS, and LB and UPS with batch as a covariance to correct for differences noted in one of the batches used in this experiment.

label: nanostring fluorescence barcode

source_name: UPS female

label_protocol: Five uL of lysate were used  for hybridization setup and mRNA counting using the nCounter manufacturer protocol. Samples from 8 pups (from 4-5 independent litters) per rearing and sex group were ran in 4 batches of 12 reactions each (total of 48 reactions).

extract_protocol: 17-day old pups were rapidly processed to harvest 60,000 microglia from the hippocampus using Percoll gradient followed by flow cytometry. Purified microglial cells were spun down at 400g for 8min at 4C, the supernatant was discarded and the pellet resuspended in 5ul of 1/3RLT buffer (cat. No. 79216, Qiagen) and frozen at -80C until further genomic analysis using the mouse Glia panel (Nanostring, Cat # XT- CSO-M-Glial-12).

treatment_protocol: Mouse pups were exposed to CTL, LB and UPS conditions as described previously (PMID: 33259286, PMID: 29463821).

value: Balbc/Byj

value: female

tag: rearing

value: UPS

tag: brain region

value: hippocampus

value: microglia


title: 4.8_LB F-8

description: NS_Mm_Glial_v1.0 (1)

source_name: LB female

value: LB


title: 4.9_UPS M-7

description: NS_Mm_Glial_v1.0 (1)

source_name: UPS male

value: male


title: 4.7_LB M-8

description: NS_Mm_Glial_v1.0 (1)

source_name: LB male


title: 4.11_UPS M-8

description: NS_Mm_Glial_v1.0 (1)


title: 4.10_UPS F-7

description: NS_Mm_Glial_v1.0 (1)


title: 4.6_LB F-7

description: NS_Mm_Glial_v1.0 (1)


title: 4.1_CTL M-7

description: NS_Mm_Glial_v1.0 (1)

source_name: Control male

value: control


title: 4.2_CTL F-7

description: NS_Mm_Glial_v1.0 (1)

source_name: Control female


title: 3.10_UPS F-5

description: NS_Mm_Glial_v1.0 (1)


title: 3.9_UPS M-5

description: NS_Mm_Glial_v1.0 (1)


title: 3.12_UPS F-6

description: NS_Mm_Glial_v1.0 (1)


title: 3.11_UPS M-6

description: NS_Mm_Glial_v1.0 (1)


title: 4.4_CTL F-8

description: NS_Mm_Glial_v1.0 (1)


title: 4.3_CTL M-8

description: NS_Mm_Glial_v1.0 (1)


title: 3.8_LB F-6

description: NS_Mm_Glial_v1.0 (1)


title: 3.6_LB F-5

description: NS_Mm_Glial_v1.0 (1)


title: 3.5_LB M-5

description: NS_Mm_Glial_v1.0 (1)


title: 3.7_LB M-6

description: NS_Mm_Glial_v1.0 (1)


title: 3.4_CTL F-6

description: NS_Mm_Glial_v1.0 (1)


title: 3.2_CTL F-5

description: NS_Mm_Glial_v1.0 (1)


title: 3.3_CTL M-6

description: NS_Mm_Glial_v1.0 (1)


title: 3.1_CTL M-5

description: NS_Mm_Glial_v1.0 (1)


title: 2.10_UPS F-3

description: NS_Mm_Glial_v1.0 (1)


title: 2.11_UPS M-4

description: NS_Mm_Glial_v1.0 (1)


title: 2.12_UPS F-4

description: NS_Mm_Glial_v1.0 (1)


title: 4.5_LB M-7

description: NS_Mm_Glial_v1.0 (1)


title: 2.9_UPS M-3

description: NS_Mm_Glial_v1.0 (1)


title: 2.8_LB F-4

description: NS_Mm_Glial_v1.0 (1)


title: 2.7_LB M-4

description: NS_Mm_Glial_v1.0 (1)


title: 2.6_LB F-3

description: NS_Mm_Glial_v1.0 (1)


title: 2.5_LB M-3

description: NS_Mm_Glial_v1.0 (1)


title: 2.3_CTL M-4

description: NS_Mm_Glial_v1.0 (1)


title: 2.4_CTL F-4

description: NS_Mm_Glial_v1.0 (1)


title: 2.2_CTL F-3

description: NS_Mm_Glial_v1.0 (1)


title: 2.1_CTL M-3

description: NS_Mm_Glial_v1.0 (1)


title: 1.11_UPS M-2

description: NS_Mm_Glial_v1.0 (1)


title: 1.7_LB M-2

description: NS_Mm_Glial_v1.0 (1)


title: 1.9_UPS M-1

description: NS_Mm_Glial_v1.0 (1)


title: Teg41D3' 9h C (wt teg41)

city: Athens

first: Ronan

middle: Kevin

last: Carroll

state: OHIO

address: 107 Irvine Hall

department: Biological Sciences

institute: Ohio University

data_processing:
Raw data files (.fastq) were imported into the CLC Genomics Workbench software platform for analysis
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Replicate data sets were grouped and normalized using "quantile normalization"
Normalized expression values were exported into excel files
Assembly: The reference genome used for the analysis was based on NC_007793 and included annotations for sRNA genes (https://dx.doi.org/10.6084/m9.figshare.2061132.v1)
Supplementary files format and content: Expression values for each gene were initially calculated as RPKM values. The RPKM values were then normalized and the "Normalized expression values" are presented in the excel files

organism: Staphylococcus aureus

source_name: Bacterial cells

growth_protocol: Strains were grown in TSB medium at 37°C with shaking

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free
Library construction was performed using the Illumina TruSeq Stranded mRNA Sample Prep Kit

treatment_protocol: Samples were stored at -80°C prior to RNA extraction

tag: tissue

value: Bacterial cells

tag: growth medium

value: TSB

tag: timepoint

value: 9 h


title: 1.8_LB F-2

description: NS_Mm_Glial_v1.0 (1)


title: 1.10_UPS F-1

description: NS_Mm_Glial_v1.0 (1)


title: Teg41D3' 9h B (wt teg41)


title: 1.5_LB M-1

description: NS_Mm_Glial_v1.0 (1)


title: 1.6_LB F-1

description: NS_Mm_Glial_v1.0 (1)


title: 1.4_CTL F-2

description: NS_Mm_Glial_v1.0 (1)


title: WT 9h C (wt teg41)

value: AH1263 WT


title: Teg41D3' 9h A (wt teg41)


title: WT 9h B (wt teg41)


title: WT 9h A (wt teg41)


title: Teg41D3' 6h C (wt teg41)

value: 6 h


title: Teg41D3' 6h A (wt teg41)


title: 1.3_CTL M-2

description: NS_Mm_Glial_v1.0 (1)


title: WT 6h B (wt teg41)


title: 1.2_CTL F-1

description: NS_Mm_Glial_v1.0 (1)


title: 1.1_CTL M-1

description: NS_Mm_Glial_v1.0 (1)


title: WT 6h C (wt teg41)


title: WT 6h A (wt teg41)


title: Teg41D3' 3h C (wt teg41)

value: 3 h


title: 1.12_UPS F-2

description: NS_Mm_Glial_v1.0 (1)


title: Teg41D3' 3h A (wt teg41)


title: Teg41D3' 6h B (wt teg41)


title: WT 3h C (wt teg41)


title: WT 3h B (wt teg41)


title: Teg41D3' 3h B (wt teg41)


title: WT 3h A (wt teg41)


title: Wierman_33

tag: disease

value: Normal pituitary


title: Teg41D3' 6h B (teg41 psm)


title: Teg41D3' 6h A (teg41 psm)


title: Dpsm mutant 6h B (teg41 psm)

value: AH1263 Dpsm


title: Teg41D3' 6h C (teg41 psm)


title: WT OvxP 3

status: Public on Sep 22 2022

city: Montreal

first: Annik

last: PRAT

state: QC

address: 110 Pine Avenue West, Biochemical Neuroendocrinology

country: Canada

institute: IRCM (Montreal)

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to the reference mouse genome version GRCm38 (gene annotation Ensembl v84) using STAR version 2.5
Gene expressions are obtained with featureCounts v1.5
DESeq2 was used to normalize raw counts and compute differential expression
Assembly: GRCm38
Supplementary files format and content: normalized count matrix from DESeq2

source_name: Adult liver

growth_protocol: mice were on a regular laboratory diet

extract_protocol:
Liver pieces (~30 mg; 3 per genotype/condition) were homogenized (Polytron) in 1 mL of TriZol on ice. After addition of 0.2 mL of chloroform, and centrifugation, the upper phase was collected. Contaminating DNA was digested with DNAse I and RNA was purified on Zymo-Spin IIICG columns (ZymoResearch, Irvin, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice underwent sham surgery (sham) or Ovx at 8 weeks of age under 2% isoflurane anesthesia (CDMV, Quebec, QC) as described previously,18 except that stainless steel autoclips were used (Becton Dickinson). Two days post-Ovx, mice were re-anesthetized and a pellet delivering either placebo (P) or ~1 mg/day of E2 (E-121, Innovative Research of America, Sarasota, FL) was inserted subcutaneously between the ear and shoulder. The skin was closed with a running 4-0 nylon PDS suture (Ethicon, Bridgewater, NJ) and mice were analyzed 10 to 20 days later.

value: liver

tag: genotype

value: WT

value: C57BL/6J (>12 backcrosses)

value: subcutaneous pellet:1ug placebo/day

value: 11 weeks of age


title: WT OvxP 2

value: female


title: WT OvxP 1


title: WT female 3

value: 3 months of age


title: WT female 2


title: WT male 3

value: male


title: WT male 2


title: WT female 1


title: WT OvxE2 3

value: subcutaneous pellet:1ug E2/day


title: PCSK9 KO OvxP 1

value: PCSK9 KO


title: PCSK9 KO OvxP 3


title: PCSK9 KO OvxP 2


title: PCSK9 KO male 3


title: WT OvxE2 1


title: PCSK9 KO male 1


title: WT OvxE2 2


title: PCSK9 KO OvxE2 3


title: Dpsm mutant 6h C (teg41 psm)

value: Bacterial cells

value: TSB


title: PCSK9 KO male 2


title: Dpsm mutant 6h A (teg41 psm)


title: PCSK9 KO female 3


title: PCSK9 KO female 1


title: PCSK9 KO OvxE2 2


title: PCSK9 KO OvxE2 1


title: S6_Control

status: Public on Sep 19 2022

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

data_processing:
Sample de-multiplexing, alignment, filtering, and UMI counting was performed with 10x Genomics Cell Ranger (v3.1) pipeline.
The reads were mapped to the human reference genome (GRCh38.98).
The UMI counts were filtered with DropletUtils to remove empty droplets, mouse cells and mouse transcripts from the data.
The filtered counts were analyzed with Seurat.
Genome_build: GRCh38.98
Supplementary_files_format_and_content: Single cell read count matrix (matrix.mtx), cell barcode (barcodes.tsv), and gene names (features.tsv).
Supplementary_files_format_and_content: UMAP and clustering metadata (csv), and Seurat DE analysis results for simple and complex cell type annotations (csv).

molecule: polyA RNA

source_name: iPS derived pancreatic cells

growth_protocol: Human embryonic cell line H1 was cultured on Matrigel-coated plates in E8 medium and passaged using EDTA. To prepare the differentiation experiments, near-confluent plates of stem cells were dissociated using EDTA and seeded on new Matrigel coated plates in E8 supplemented with 0.5-uM Rho-Associated kinase inhibitor to achieve confluent plates.

extract_protocol:
SC-islets were incubated with 1:1 mix of TrypLe and 10x Trypsin – EDTA for 10 min in +37°C. Disassociation media was neutralized by adding 3x volume 0.5% FBS in PBS and strained through a 30-um filter to remove cell clusters. Finally, the cells were resuspended in PBS+0.04% BSA, washed, counted and diluted to a 1x10^6 cells/ml concentration for encapsulation.
10x Genomics Chromium Single Cell 3’RNAseq platform using the Chromium Next GEM Single Cell 3' Gene Expression (version 3.1 chemistry).

treatment_protocol: To start the differentiations, the medium was changed to D0 medium 24h post-seeding. The differentiation was carried out using a 7-stage protocol combined from several publications (Pagliuca 2014, Rezania 2014, Nostro 2015, patent WO2017222879A1), with stage 7 medium containing CMRL1066 supplemented with BSA, sodium pyruvate, glutmax, ITS-X, ZnSO4, heparin, Trace elements A and B and lipid concentrate with added aurora kinase inhibitor ZM447439 (ZM), tri-iodothyronine (T3) and N-acetyl cysteine (NAC). On the 3rd day of S4 culture, the planar pancreatic epithelium was dissociated using TrypLE and seeded to microwells (AggreWell 400, Stemcell technologies) at a density of 800-1000 cells per microwell. On the 1st day of S6 culture the SC-islets were transferred from the microwells to suspension culture placed on rotator spinning at 95 RPM. Media changes were performed daily until the 1st day of S6 culture and every two to three days thereafter.

tag: developmental stage

value: endocrine cells

value: control


title: S6_TYK2_KO_IFNa24h

value: TYK2 KO

value: IFNa 24h


title: S6_Control_IFNa24h


title: S6_TYK2_KO


title: WT male 1

tag: age


title: HUVECs, EndMT

status: Public on Sep 20 2022

city: Leipzig

first: Jes-Niels

last: Boeckel

address: Johannisalle 30

department: Klinik und Poliklinik für Kardiologie

institute: Universitätsklinikum Leipzig

description:
10x Genomics
SID15932

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0
Assembly: hg38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: HUVEC

extract_protocol:
After treatment cells were harvested using trypsin. Cells were diluted in PBS+0.04% BSA to an concentration of 1200 cells / μl.
Using the 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 the cells were transferred into oil droplets containing barcoded gel beads. Thereafter, beads are dissolved and reverse transcription into cDNA was done to obtain barcoded full-length cDNA from poly-adenylated mRNA. The obtained cDNA was amplified and used for sequencing.

value: HUVEC

tag: treatment

value: 10 ng/ml TGF-β2


title: S5_TYK2_KO

value: endocrine progenitor


title: HUVECs, Control

description:
10x Genomics
SID15931

value: no treatment


title: primary myoblasts, myogenic differentiation, DM2

status: Public on Sep 15 2022

city: guangzhou

first: Shuai Zhang

last: Shuai Zhang

address: Wushan Street, Tianhe District

institute: South China Agricultural University

data_processing:
remove low quailty reads and adapter (software:cutadapt, fastqc)
Mapping (software:hisat2)
Back spilcing identify (software:tophat_fusing)
transcript assembly (software:StringTie)
Difference analysis (software:edgeR)
Assembly: AnsCyg
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Anser cygnoides

source_name: muscle

growth_protocol: primary myoblasts were maintained in DMEM supplemented with 15% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from each goose tissue/cell using MagZol Reagent (Magen, Guangzhou, China)
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA HT Sample Prep Kit(Illumina RS-122-2203)

treatment_protocol: myogenic differentiation was induced by treatment of 2% horse serum, , and then cultured for 2 - 4 days to induce cells to differentiate into myotubes.

value: muscle

value: primary myoblasts

value: myoblasts

value: WT

value: myogenic differentiation


title: primary myoblasts, myogenic differentiation, DM3


title: primary myoblasts, myogenic differentiation, DM1


title: PCSK9 KO female 2

value: liver

tag: Sex

value: female

value: C57BL/6J (>12 backcrosses)

value: 3 months of age


title: primary myoblasts, GM3


title: primary myoblasts, GM1


title: primary myoblasts, GM2


title: ‘Fuding Dabaicha’,As2-3,Day15

status: Public on Sep 09 2022

city: Guiyang

first: yunfeng

last: wei

address: Huaxi District, Guiyang City

institute: Guizhou University

description: ‘Fuding Dabaicha’,As2-3,Day15

data_processing:
Tea Plant Information Archive (TPIA) database (http://tpdb.shengxin.ren) was used to download the genome sequence and corresponding annotations of C. sinensis.
The HMA (PF00403) domain HMM (Hidden Markov Model) profile, obtained from the Pfam database, was used to identify the candidate CsHIPP family genes from C. sinensis genome using the HMMER3 software package .
The distribution of CsHIPP genes was plotted using MapInspect software (http://mapinspect.software.informer.com/).
Gene Structure Display Server (GSDS) was used to visualize the intron/exon structures of genes using the C. sinensis genome annotation information.
The conserved motifs of CsHIPPs were identified using the MEME suite (http://meme-suite.org/tools/meme).
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Camellia sinensis

source_name: Root

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cultivar

value: Fuding Dabaicha

value: Root

value: As processing

tag: time

value: day 15


title: ‘Fuding Dabaicha’,Cd2-3,Day15

description: ‘Fuding Dabaicha’,Cd2-3,Day15

value: Cd processing


title: ‘Fuding Dabaicha’,As1-3,Day15

description: ‘Fuding Dabaicha’,As1-3,Day15


title: ‘Fuding Dabaicha’,Cd1-3,Day15

description: ‘Fuding Dabaicha’,Cd1-3,Day15


title: ‘Fuding Dabaicha’,As2-1,Day15

description: ‘Fuding Dabaicha’,As2-1,Day15


title: ‘Fuding Dabaicha’,As2-2,Day15

description: ‘Fuding Dabaicha’,As2-2,Day15


title: ‘Fuding Dabaicha’,Cd2-1,Day15

description: ‘Fuding Dabaicha’,Cd2-1,Day15


title: ‘Fuding Dabaicha’,As1-1,Day15

description: ‘Fuding Dabaicha’,As1-1,Day15


title: ‘Fuding Dabaicha’,Cd1-1,Day15

description: ‘Fuding Dabaicha’,Cd1-1,Day15


title: ‘Fuding Dabaicha’,As1-2,Day15

description: ‘Fuding Dabaicha’,As1-2,Day15


title: ‘Fuding Dabaicha’,Cd2-2,Day15

description: ‘Fuding Dabaicha’,Cd2-2,Day15


title: HUVECs, EndMT + Leptin

description:
10x Genomics
SID15933

tag: cell type

value: HUVEC

value: 10 ng/ml TGF-β2 + 200 ng/ml leptin


title: ‘Fuding Dabaicha’,CK1-3,Day15

description: ‘Fuding Dabaicha’,CK1-3,Day15

value: No processing


title: ‘Fuding Dabaicha’,Cd1-2,Day15

description: ‘Fuding Dabaicha’,Cd1-2,Day15


title: ‘Fuding Dabaicha’,CK1-2,Day15

description: ‘Fuding Dabaicha’,CK1-2,Day15


title: S5_Control

value: endocrine progenitor

value: control


title: SLE1.2.3 mouse 2, Th17 cells

status: Public on Sep 07 2022

city: Nashville

first: Kelsey

last: Voss

state: TN

address: 21st Ave

department: PMI

institute: Vanderbilt University Medical Center

description: SLE1.2.3 mouse 2

data_processing:
FASTQ analysis was conducted by Vanderbilt Technologies for Advanced Genomics Analysis and Research Design (VANGARD)
Cutadapt v2.10, DESeq2 v1.24.0, WebGestaltR v0.4.4, FastQC v0.11.9, STAR v2.7.3a, and featureCounts v2.0.0.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: CD4 T cells

growth_protocol: Isolated naïve CD4 T cells were stimulated with anti-CD3/28 coated plates for 5 days.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Th17 differentiation conditions: anti-IL4 (10μg/mL), anti-IFNγ (10μg/mL), TGFβ1 (1ng/mL), IL-23 (10ng/mL), IL-6 (50ng/mL), and IL-1β (10ng/mL).

value: CD4 T cells

value: Th17 differentiated

value: Day 5


title: SLE1.2.3 mouse 1, Th17 cells

description: SLE1.2.3 mouse 1


title: Control mouse 2, Th17 cells

description: Control mouse 2

value: WT


title: Control mouse 1, Th17 cells

description: Control mouse 1


title: MENI-TB106: WHO Grade-1 histology

status: Public on Sep 06 2022

city: New York

first: Prabhjot

middle: Singh

last: Mundi

state: NY

address: 1130 St. Nicholas Avenue

department: Medicine; Systems Biology

institute: COLUMBIA UNIVERSITY HEALTH SCIENCES

data_processing:
Alignment with STARv2.5.3 to GRCh38.
Gene-level raw counts summarization with STARv2.5.3 quant-mode.
Assembly: GRCh38.v90
Supplementary files format and content: Tab delimited text output of raw counts from STAR alignment and gene count quantification.

source_name: CUIMC Meningioma Patient Tumor Sequencing Project

extract_protocol:
RNAs were extracted using polyA selection kits, TruSeq
RNA Sequencing was performed on an Illumina NextSeq 500.

value: meningioma tumor


title: MENI-TB105: WHO Grade-1 histology


title: MENI-TB104: WHO Grade-2 histology


title: MENI-TB103: WHO Grade-2 histology


title: MENI-TB101: WHO Grade-2 histology


title: MENI-TB100: WHO Grade-2 histology


title: MENI-TB098: WHO Grade-2 histology


title: MENI-TB102: WHO Grade-2 histology


title: MENI-TB097: WHO Grade-1 histology


title: MENI-TB090: WHO Grade-1 histology


title: MENI-TB099: WHO Grade-2 histology


title: MENI-TB094: WHO Grade-2 histology


title: MENI-TB092: WHO Grade-1 histology


title: MENI-TB089: WHO Grade-1 histology


title: MENI-TB091: WHO Grade-1 histology


title: MENI-TB088: WHO Grade-1 histology


title: MENI-TB093: WHO Grade-2 histology


title: MENI-TB086: WHO Grade-2 histology


title: ‘Fuding Dabaicha’,CK1-1,Day15

description: ‘Fuding Dabaicha’,CK1-1,Day15


title: MENI-TB087: WHO Grade-1 histology


title: SLE1.2.3 mouse 3, Th17 cells

description: SLE1.2.3 mouse 3


title: Control mouse 3, Th17 cells

description: Control mouse 3


title: MENI-TB083: WHO Grade-2 histology


title: MENI-TB084: WHO Grade-2 histology


title: MENI-TB085: WHO Grade-2 histology


title: MENI-TB082: WHO Grade-2 histology


title: MENI-TB107: WHO Grade-1 histology


title: MENI-TB079: WHO Grade-2 histology


title: MENI-TB078: WHO Grade-2 histology


title: MENI-TB096: WHO Grade-1 histology


title: MENI-TB095: WHO Grade-1 histology


title: MENI-TB077: WHO Grade-1 histology


title: MENI-TB074: WHO Grade-1 histology


title: MENI-TB073: WHO Grade-1 histology


title: MENI-TB068: WHO Grade-1 histology


title: MENI-TB071: WHO Grade-1 histology


title: MENI-TB072: WHO Grade-1 histology


title: MENI-TB069: WHO Grade-1 histology


title: MENI-TB065: WHO Grade-1 histology


title: MENI-TB070: WHO Grade-1 histology


title: MENI-TB064: WHO Grade-1 histology


title: MENI-TB067: WHO Grade-1 histology


title: MENI-TB066: WHO Grade-1 histology


title: MENI-TB060: WHO Grade-1 histology


title: MENI-TB063: WHO Grade-1 histology


title: MENI-TB062: WHO Grade-1 histology


title: MENI-TB059: WHO Grade-1 histology


title: MENI-TB081: WHO Grade-2 histology


title: MENI-TB057: WHO Grade-1 histology


title: MENI-TB080: WHO Grade-2 histology


title: MENI-TB058: WHO Grade-1 histology


title: MENI-TB054: WHO Grade-1 histology


title: MENI-TB056: WHO Grade-1 histology


title: MENI-TB055: WHO Grade-1 histology


title: MENI-TB050: WHO Grade-2 histology


title: MENI-TB076: WHO Grade-1 histology


title: MENI-TB075: WHO Grade-1 histology


title: MENI-TB051: WHO Grade-2 histology


title: MENI-TB052: WHO Grade-2 histology


title: MENI-TB049: WHO Grade-2 histology


title: MENI-TB048: WHO Grade-2 histology


title: MENI-TB044: WHO Grade-2 histology


title: MENI-TB046: WHO Grade-2 histology


title: MENI-TB043: WHO Grade-2 histology


title: MENI-TB047: WHO Grade-2 histology


title: MENI-TB041: WHO Grade-2 histology


title: MENI-TB042: WHO Grade-2 histology


title: MENI-TB061: WHO Grade-1 histology


title: MENI-TB040: WHO Grade-2 histology


title: MENI-TB037: WHO Grade-2 histology


title: MENI-TB045: WHO Grade-2 histology


title: MENI-TB038: WHO Grade-2 histology


title: MENI-TB033: WHO Grade-1 histology


title: MENI-TB039: WHO Grade-2 histology


title: MENI-TB036: WHO Grade-2 histology


title: MENI-TB034: WHO Grade-2 histology


title: MENI-TB035: WHO Grade-2 histology


title: MENI-TB031: WHO Grade-1 histology


title: MENI-TB028: WHO Grade-1 histology


title: MENI-TB053: WHO Grade-2 histology


title: MENI-TB030: WHO Grade-1 histology


title: MENI-TB029: WHO Grade-1 histology


title: MENI-TB027: WHO Grade-1 histology


title: MENI-TB025: WHO Grade-1 histology


title: MENI-TB026: WHO Grade-1 histology


title: MENI-TB024: WHO Grade-1 histology


title: MENI-TB022: WHO Grade-1 histology


title: MENI-TB023: WHO Grade-1 histology


title: MENI-TB020: WHO Grade-1 histology


title: MENI-TB019: WHO Grade-1 histology


title: MENI-TB014: WHO Grade-3 histology


title: MENI-TB017: WHO Grade-3 histology


title: MENI-TB015: WHO Grade-3 histology


title: MENI-TB013: WHO Grade-3 histology


title: MENI-TB010: Not Classified


title: MENI-TB032: WHO Grade-1 histology


title: MENI-TB009: Not Classified


title: MENI-TB011: Not Classified


title: MENI-TB008: Not Classified


title: MENI-TB007: Not Classified


title: MENI-TB004: Not Classified


title: human PBMCs, WT, Rm group_3

status: Public on Sep 02 2022

city: Hangzhou

first: QIXIA

last: SHEN

state: Zhejiang

address: Qinchun Rd.79, Hangzhou

institute: The first affiliated hospital, Hangzhou, China

data_processing:
sequence reads were aligned to the genome using HISAT2 first.
Then, Stringtie was used to assemble and quantify expressed genes and transcripts.
Then, differential expression analysis was performed by the ballgown package of R software.
Transcripts and genes statistically different between groups were identified by stattest using R 266 software.
Assembly: mm10
Supplementary files format and content: .csv files comparing the differentially expressed genes between two groups (Rm versus Rc group, Rc versus HC group, Rc versus Hc group, Rm versus Hc group)

source_name: human PBMCs, WT, Rm group

extract_protocol:
PBMCs were isolated from 5 to 10 ml peripheral blood of KTx recipients and healthy individuals by Ficoll–Hypaque density gradient centrifugation at diagnosis of FSGS and stored at −20°C for future use. The TRIzol Reagent (Invitrogen) and the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) were used for total RNA extraction. A NanoDropTM 2000 (Thermo Scientific, Waltham, MA) spectrophotometer was used for a purity check, followed by agarose gel electrophoresis for degradation and contamination.  216 monitoring. A total amount of DNA of >700 ng or RNA >1 mg  217 was at least required for library preparation and sequencing.
For RNA extracted, the first and second strand cDNA and NEBNext Adaptor hybridization were performed, successively. Then, the AMPure XP system (Beckman Coulter, Beverly, USA) was used for fragment purification. A cBot Cluster Generation System using a HiSeq 2500 PE Cluster Kit (Illumina) was used for cluster generation.
The library sequencing was performed by the Illumina. Hiseq 2500 platform (Illumina Inc., San Diego, CA, USA). Paired-end reads of 125 bp/150 bp were generated for RNA sequencing.

value: whole blood

value: peripheral blood mononuclear cells

tag: disease state

value: FSGS with remission


title: human PBMCs, WT, HC group_1

source_name: human PBMCs, WT, HC group

value: healthy


title: human PBMCs, WT, HC group_2


title: human PBMCs, WT, RC group_2

source_name: human PBMCs, WT, RC group

value: FSGS with recurrence


title: MENI-TB021: WHO Grade-1 histology


title: human PBMCs, WT, Rm group_2


title: human PBMCs, WT, RC group_3


title: Mouse cortex, plate-based snFFPE-Seq with SMART-Seq2, batch 3

status: Public on Aug 31 2022

city: Cambridge

first: Hattie

last: Chung

state: MA

address: 415 Main St

institute: Broad Institute

data_processing:
Demultiplexing and construction of gene counts matrices were conducted with zUMIs pipeline version 2.4.5b
Assembly: hg19_and_mm10_premrna
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Mouse cortex

extract_protocol:
Nuclei were extracted from 50µm scrolls of FFPE mouse brain. Scrolls were first deparaffinized with mineral oil with heat, xylene with heat, or xylene at room temperature, then rehydrated with graded ethanol washes. Tissue were then lysed for nuclei extraction, and individual nuclei were sorted into 96-well plates.
Library was constructed using SCRB-seq or SMART-Seq2, as described in the paper
scRNA-seq via SMART-Seq2 and SCRB-Seq

value: Mouse cortex

value: 8-12 weeks old


title: MENI-TB018: WHO Grade-3 histology


title: Mouse cortex, FFPE deparaffinization comparison, bulk SMART-Seq2


title: MENI-TB012: Not Classified


title: MENI-TB016: WHO Grade-3 histology


title: Mouse cortex, plate-based snFFPE-Seq with SMART-Seq2, batch 2


title: Mouse cortex, FFPE deparaffinization comparison, bulk SCRB-Seq

description: SCRB-Seq


title: human PBMCs, WT, Rm group_1


title: Mouse cortex, plate-based snFFPE-Seq with SMART-Seq2, batch 1


title: Mouse cortex, droplet-based snFFPE-Seq on 10X platform

description: 10x Genomics


title: BB6_DLPFC_N_ATAC

status: Public on Aug 25 2022

first: Panos

last: Roussos

address: 1470 madison ave

institute: Icahn school of medicine at mount sinai

description:
neuron_DLPFC-includes-blacklisted-regions_peaks.narrowPeak
neuron_DLPFC.bw

data_processing:
The raw reads were trimmed with Trimmomatic and then mapped to the human reference genome GRCh38 analysis set reference genome with the pseudoautosomal region masked on chromosome Y with the STAR aligner.
To correct for allelic bias resulting from individual-specific genome variation, we ran STAR with enabled WASP module as we provide both ATAC-seq FASTQ file and WGS file of the corresponding individual.
This yielded for each sample a BAM file of mapped paired-end reads sorted by genomic coordinates. From these files, reads that mapped to multiple loci or to the mitochondrial genome were removed using samtools and duplicated reads were removed with PICARD. Quality control metrics were reported with phantompeakqualtools and Picard.
The samples from the same brain region and cell type were subsampled and merged.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01 and parameters "--shift -100 --extsize 200"
bigWig files were generated using the genomeCoverageBed from bedtools
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

source_name: Dorsolateral Prefrontal Cortex

extract_protocol:
ATAC-seq reactions were performed on Neuronal (NeuN+) and non-neuronal (NeuN-) nuclei isolated by FANS from 149 tissue dissections from 25 brain regions
Where available, 100,000 sorted nuclei were centrifuged at 500 × g for 10 min, 4°C. Pellets were resuspended in the transposase reaction mix and libraries were generated using an established protocol.

tag: group

value: neuron

value: DLPFC

value: Forebrain

tag: age of_death

value: Female


title: BB2_CN_N_ATAC

description:
neuron_CN-includes-blacklisted-regions_peaks.narrowPeak
neuron_CN.bw

source_name: Caudate Nucleus

value: CN

value: BasalGanglia

value: Male


title: BB6_DLPFC_G_ATAC

description:
glia_DLPFC-includes-blacklisted-regions_peaks.narrowPeak
glia_DLPFC.bw

value: non-neuron


title: BB5_ITC_N_ATAC

description:
neuron_ITC-includes-blacklisted-regions_peaks.narrowPeak
neuron_ITC.bw

source_name: Inferior Temporal Cortex

value: ITC


title: BB3_EC_N_ATAC

description:
neuron_EC-includes-blacklisted-regions_peaks.narrowPeak
neuron_EC.bw

value: EC


title: BB2_RMTG_G_ATAC

description:
glia_RMTG-includes-blacklisted-regions_peaks.narrowPeak
glia_RMTG.bw

source_name: Rostromedial Tegmental Nucl

value: RMTG

value: Midbrain


title: BB6_INS_G_ATAC

description:
glia_INS-includes-blacklisted-regions_peaks.narrowPeak
glia_INS.bw

source_name: Insula

value: INS


title: BB2_DRN_G_ATAC

description:
glia_DRN-includes-blacklisted-regions_peaks.narrowPeak
glia_DRN.bw

source_name: Dorsal Raphe Nucleus

value: DRN


title: BB2_VTA_G_ATAC

description:
glia_VTA-includes-blacklisted-regions_peaks.narrowPeak
glia_VTA.bw

source_name: Ventral Tegmental Area

value: VTA


title: BB5_PSC_N_ATAC

description:
neuron_PSC-includes-blacklisted-regions_peaks.narrowPeak
neuron_PSC.bw

source_name: Primary Somatosensory Cortex

value: PSC


title: BB2_CN_G_ATAC

description:
glia_CN-includes-blacklisted-regions_peaks.narrowPeak
glia_CN.bw


title: BB2_CRBLM_G_ATAC

description:
glia_CRBLM-includes-blacklisted-regions_peaks.narrowPeak
glia_CRBLM.bw

source_name: Cerebellum

value: CRBLM

value: Hindbrain


title: BB2_ITC_N_ATAC

value: neuron


title: BB2_ITC_G_ATAC

description:
glia_ITC-includes-blacklisted-regions_peaks.narrowPeak
glia_ITC.bw

value: Forebrain


title: BB5_PSC_G_ATAC

description:
glia_PSC-includes-blacklisted-regions_peaks.narrowPeak
glia_PSC.bw


title: BB2_MDT_G_ATAC

description:
glia_MDT-includes-blacklisted-regions_peaks.narrowPeak
glia_MDT.bw

source_name: Mediodorsal Thalamus

value: MDT


title: BB2_PSTC_N_ATAC

description:
neuron_PSTC-includes-blacklisted-regions_peaks.narrowPeak
neuron_PSTC.bw

source_name: Posterior Superior Temporal Cortex

value: PSTC


title: BB2_CRBLM_N_ATAC

description:
neuron_CRBLM-includes-blacklisted-regions_peaks.narrowPeak
neuron_CRBLM.bw


title: BB2_PVC_N_ATAC

description:
neuron_PVC-includes-blacklisted-regions_peaks.narrowPeak
neuron_PVC.bw

source_name: Primary Visual Cortex

value: PVC


title: BB2_GP_N_ATAC

description:
neuron_GP-includes-blacklisted-regions_peaks.narrowPeak
neuron_GP.bw

source_name: Globus Pallidus

value: GP

value: BasalGanglia

value: Male


title: BB2_GP_G_ATAC

description:
glia_GP-includes-blacklisted-regions_peaks.narrowPeak
glia_GP.bw

value: non-neuron


title: BB2_PSC_N_ATAC


title: BB2_PVC_G_ATAC

description:
glia_PVC-includes-blacklisted-regions_peaks.narrowPeak
glia_PVC.bw


title: human PBMCs, WT, HC group_3

value: whole blood

value: peripheral blood mononuclear cells

value: WT

value: healthy


title: BB2_PSTC_G_ATAC

description:
glia_PSTC-includes-blacklisted-regions_peaks.narrowPeak
glia_PSTC.bw


title: BB2_MDT_N_ATAC

description:
neuron_MDT-includes-blacklisted-regions_peaks.narrowPeak
neuron_MDT.bw

value: Midbrain


title: BB2_PSC_G_ATAC

value: PSC


title: BB2_DLPFC_N_ATAC

description:
neuron_DLPFC-includes-blacklisted-regions_peaks.narrowPeak
neuron_DLPFC.bw

value: DLPFC


title: BB2_NAC_N_ATAC

description:
neuron_NAC-includes-blacklisted-regions_peaks.narrowPeak
neuron_NAC.bw

source_name: Nucleus Accumbens

value: NAC


title: BB2_INS_N_ATAC

description:
neuron_INS-includes-blacklisted-regions_peaks.narrowPeak
neuron_INS.bw

value: neuron

value: INS


title: BB2_INS_G_ATAC

description:
glia_INS-includes-blacklisted-regions_peaks.narrowPeak
glia_INS.bw

value: Forebrain


title: BB2_HAB_N_ATAC

description:
neuron_HAB-includes-blacklisted-regions_peaks.narrowPeak
neuron_HAB.bw

source_name: Habenula

value: HAB


title: BB2_EC_G_ATAC

description:
glia_EC-includes-blacklisted-regions_peaks.narrowPeak
glia_EC.bw

value: EC


title: BB2_OFC_N_ATAC

description:
neuron_OFC-includes-blacklisted-regions_peaks.narrowPeak
neuron_OFC.bw

source_name: Orbital Frontal Cortex

value: OFC


title: BB2_NAC_G_ATAC

description:
glia_NAC-includes-blacklisted-regions_peaks.narrowPeak
glia_NAC.bw

value: BasalGanglia


title: BB2_VLPFC_G_ATAC

description:
glia_VLPFC-includes-blacklisted-regions_peaks.narrowPeak
glia_VLPFC.bw

source_name: Ventrolateral Prefrontal Cortex

value: VLPFC

value: Male


title: BB2_AMY_G_ATAC

description:
glia_AMY-includes-blacklisted-regions_peaks.narrowPeak
glia_AMY.bw

source_name: Amygdaloid Complex

value: non-neuron

value: AMY


title: BB2_AMY_N_ATAC

description:
neuron_AMY-includes-blacklisted-regions_peaks.narrowPeak
neuron_AMY.bw


title: BB2_VLPFC_N_ATAC

description:
neuron_VLPFC-includes-blacklisted-regions_peaks.narrowPeak
neuron_VLPFC.bw


title: BB2_PVPC_G_ATAC

description:
glia_PVPC-includes-blacklisted-regions_peaks.narrowPeak
glia_PVPC.bw

source_name: Posteroventral (Inferior) Parietal Cortex

value: PVPC


title: BB2_EC_N_ATAC

description:
neuron_EC-includes-blacklisted-regions_peaks.narrowPeak
neuron_EC.bw


title: BB2_PAC_G_ATAC

description:
glia_PAC-includes-blacklisted-regions_peaks.narrowPeak
glia_PAC.bw

source_name: Primary Auditory Cortex

value: PAC


title: BB2_PVPC_N_ATAC

description:
neuron_PVPC-includes-blacklisted-regions_peaks.narrowPeak
neuron_PVPC.bw


title: BB2_OFC_G_ATAC

description:
glia_OFC-includes-blacklisted-regions_peaks.narrowPeak
glia_OFC.bw


title: BB2_DLPFC_G_ATAC

description:
glia_DLPFC-includes-blacklisted-regions_peaks.narrowPeak
glia_DLPFC.bw

source_name: Dorsolateral Prefrontal Cortex


title: BB2_ARC_N_ATAC

description:
neuron_ARC-includes-blacklisted-regions_peaks.narrowPeak
neuron_ARC.bw

source_name: Arcuate Nucleus

value: ARC

value: Midbrain


title: BB1_PAC_G_ATAC

value: Female


title: BB2_ARC_G_ATAC

description:
glia_ARC-includes-blacklisted-regions_peaks.narrowPeak
glia_ARC.bw


title: BB1_PVC_N_ATAC

description:
neuron_PVC-includes-blacklisted-regions_peaks.narrowPeak
neuron_PVC.bw

value: PVC


title: BB1_PAC_N_ATAC

description:
neuron_PAC-includes-blacklisted-regions_peaks.narrowPeak
neuron_PAC.bw

value: neuron


title: BB1_ITC_N_ATAC

description:
neuron_ITC-includes-blacklisted-regions_peaks.narrowPeak
neuron_ITC.bw

source_name: Inferior Temporal Cortex

value: ITC


title: BB1_PVC_G_ATAC

description:
glia_PVC-includes-blacklisted-regions_peaks.narrowPeak
glia_PVC.bw

value: Forebrain


title: BB2_HIPP_N_ATAC

description:
neuron_HIPP-includes-blacklisted-regions_peaks.narrowPeak
neuron_HIPP.bw

source_name: Hippocampus

value: HIPP


title: BB1_PMC_G_ATAC

description:
glia_PMC-includes-blacklisted-regions_peaks.narrowPeak
glia_PMC.bw

source_name: Primary Motor Cortex

value: PMC


title: BB1_DLPFC_G_ATAC

value: DLPFC