title: dVHL_clone44

source_name: VHL inactivated, clone44


title: H295R_AngII_control_0_rep1

status: Public on Jun 01 2021

type: SRA

city: NEW YORK

first: RUI

last: FU

state: NY

address: 101 6th Ave

department: Computational Biology

country: USA

institute: New York Genome Center

library_source: transcriptomic

data_processing:
Reads were mapped using Salmon with custom index containing ERCC spike-ins and precursor transcripts. Settings for salmon quant: -l A --allowDovetail --validateMappings
Genome_build: GRCh38
Supplementary_files_format_and_content: Salmon output quant.sf files, tab-delimited text file of read counts and TPM for each sample

molecule: total RNA

organism: Homo sapiens

source_name: H295R cells

growth_protocol: H295R cells cultured in DMEM/F12 with 1% ITS and 10% CCS; cadeveric human adrenocortical cells were isolated and cultured as previously (PMC4475723)

extract_protocol:
H295R cells were washed and treated with TRIzol and RNA was extracted using ZYMO DirectZol RNA Miniprep kit. rRNA was depleted using ribozero gold; RNA from human adrenocortical cells was polyA-selected. For samples treated with 4-thiouridine, labeled RNA was biotinylated and purified using streptavidin as described previously (Methods Mol Biol. 2013;1064:91-100. doi: 10.1007/978-1-62703-601-6_6).
All RNA was made into cDNA libraries using Kappa HyperPrep kit an sequenced on Nova-seq.

treatment_protocol: 24 hours prior to stimulation of H295R cells wiht 10 nM AngII media was replaced with low sera media (DMEM/F12 with 0.1% CCS, 1% ITS); human adrenocortical cells were treated with 10 nM and 10uM of AngII and ACTH respectively.

tag: cell line

tag: treatment

value: control, unstimulated


title: Mouse_brain_ONT_cDNA

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

data_processing:
short-read RNA-seq: Sequencing data were quality controlled and adapter trimmed using Trim Galore
short-read RNA-seq: Filtered data were mapped to the relevant genome using TopHat2
short-read RNA-seq: CircRNA detection was performed using primarily using CIRI2 and secondarily using find_circ.
ONT_DNA: Nanopore data was basecalled using Guppy (v 3.4.5)
ONT_DNA: Basecalled fastq files were mapped to the relevant genome using FLAIR v1.4
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: For short-read RNA-seq: Tab-delimited text files list all detected circRNAs, including genomic coordinates, number of reads spanning backsplice junction (BSJ), host gene that circRNAs originates from and circRNA ID from circBase, circAtlas and CIRCpedia. For ONT cDNA: bigWig files show genome mapping of reads

organism: Mus musculus

source_name: Mouse total brain

extract_protocol:
Total human brain RNA was derived from post mortem cortex and provided by Agilent (Agilent Technologies, cat: 540143). For the preparation of mouse brain RNA, a male mouse (strain 129S2/SV) was sacrificed, and the entire brain was harvested and grained in Trizol (Thermo Fisher Scientific). Total RNA was obtained according to the manufacture’s protocol.
ONT cDNA sequencing libraries were prepared according to the protocol, SQK-PCS108, version PCS_9035_v108_revF_26Jun2017

tag: strain

tag: tissue

value: total brain

tag: genotype

value: wild type

tag: age

value: 8 weeks


title: Caki1_3

city: Vienna

first: Artem

middle: V

last: Artemov

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

library_source: genomic

data_processing:
Sequenced bcl files were converted to fastq files with cellranger 3.0.1
Reads were mapped to hg19 reference genome with Bismark software
To estimate the efficacy of C-to-T conversion, lambda phage genome was added to the reference genome. Low DNA methylation levels at cytosines in lambda phage DNA indicate good bisulfite conversion. Additionally, we estimated DNA methylation level at C positions outside the CpG context.
Differential methylation analysis was performed by MethPipe/RADmeth software package
Custom scripts were used to iterate through bisulfite bam files and estimate global DNA methylation, per-chromosome methylation levels. To find out how DNA methylation changed in individual CpG islands, we calculated the total number of methylated and unmethylated CpG's in bisulfite reads at each CpG position within the CpG island. Beta-binomial test was applied to estimate if the DNA methylation of a given CpG island significantly differed between two groups of samples.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-separated table, for each CpG island (identified by chr, start, end columns), the number of methylated and umnethylated CpG's in the bisulfite reads at positions overlapping with the island is provided (two columns for each sample)

molecule: genomic DNA

source_name: Caki1 cell line, wildtype VHL

growth_protocol: Caki-1 and HEK293t cell lines were grown in Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, and 2 mM L-glutamine.

extract_protocol:
VHL mutant: Human pre-natal tissue was retrieved from clinical routine abortions with oral and written consent from the patient. All procedures regarding the acquisition of human pre-natal tissue for research was approved by the Swedish Ethical Research Authority and the National Board of Health and Welfare. Post-conception age was determined using measurement of crown-rump-length (CRL) and anatomical landmarks. After identifying the adrenal glands, this tissue was retrieved and placed in ice-cold PBS pending dissociation. Tissue was chopped into 1 mm pieces and placed in 500 ul 0.05% Trypsin/0.02% EDTA (Sigma, 59417-C) and incubated at 37°C for 15 min with careful mix every 5 min. Following this, the tissue was triturated slowly and carefully with a P-1000, then P-200 pipette until complete dissociation. 500 ul 10% FBS in PBS was added to cell suspension for trypsin inactivation. Cell suspension was centrifuged at 500 rcf for 5 min at 4°C, followed by two washes with 1000 uL PBS. Cell suspension was pass though the 35 um cell strainer (Falcon, 352235 ) and spin down at 500 rcf for 5 min at 4°C. Cell pellet was resuspended in 100 ul 0.04% BSA in PBS and 400 ul of ice cold methanol was added for methanol fixation of the cells for storage. Cells suspension in cryotubes were placed in Mister Frosty (Thermo Scientific) and at -80°C for controlled cooling. Exogenous VHL: VHL-HA was subcloned to pCDF1-MCS2-EF1-Puro vector (System BioSciences). HEK293t cells were transfected with pCDF-VHL-HA, pVSV-G and pFiv-34N vectors. Viral supernatant was collected after 48 and 60 hrs, filtered through a 40um filter. Virus was precipitated by 12,5% PEG 8000 at +40C overnight followed by centrifugation at 4200g during 40 minutes at+4C. Pellet was resuspended in 300 mkl of OPTI-MEM and stored at -80C. Infections were carried out in 4ml medium using polybrene diluted 1:2,000. 100ul of viral concentrate were used per 60-mm cell plate for 12 hrs. Infected cells were selected by puromycine (2 mkg/ml).
DNA methylation was profiled by whole genome bisulfite sequencing (WGBS). Two micrograms of genomic DNA from every cell line and 4 ng of lambda phage DNA were sonicated to average size 250 bp with Covaris S2. The end repair  and an adenine was added to the 3′ end of the DNA fragments according to NebNext DNA  UltraII  protocol (NEB, USA). Preannealed forked Illumina adaptors containing 5′-methylcytosine instead of cytosine were ligated to both ends of DNA fragments using standard NEB adaptor ligation protocol (NEB, USA). Ligated fragments were treated with the sodium bisulfite and subsequent clean-up was performed with the EZ DNA MethylationTM Kit (ZymoResearch, USA) according to the manufacturer’s instructions. The bisulfite-treated DNA fragments were amplified using PCR and the following reaction: 5 µl of eluted DNA, 1 µl of NEB PE PCR two primers (1.0 and 2.0), and EpiMark® Hot Start Taq DNA Polymerase (NEB, USA). The amplification conditions were as follows: 5 min at 95 °C, 30 s at 98 °C then 15 (10 s at 98 °C, 30 s at 65 °C, 30 s at 72 °C), followed by 5 min at 72 °C. The PCR reaction was purified with AMPure XP beads (Beckman Coulter, USA), and final reduced representation bisulfite library was eluted in 30 µl EB buffer. The concentration of the final library was measured using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA). The library was sequenced on Illumina 2500 platform according to standard Illumina cluster generation and sequencing protocols.

treatment_protocol: CRISPR/CAS9–based editing was performed as described in ref. (Ran et al. 2013). Briefly, Caki1 cells were seeded on a 12-well plate. Cells were transfected with Lipofectamine 3000 with PX459-VHL plasmid  to generate frame shift which led to a stop loss in the C-terminal alpha domain of VHL (Zhigalova et al. 2017). Puromycin was applied after 24 h at a concentration of 2 μg ml−1. Cells were incubated for 72 h, passaged into a 96-well plate at a density of 1 cell per 2 wells on medium without puromycin. For further study, we have chosen three clones for each experiment. The frame shift was confirmed by Sanger sequencing of the corresponding amplicons obtained from PCR with genomic DNA.

value: VHL wildtype


title: dVHL_clone12

source_name: VHL inactivated, clone12

value: VHL mutant


title: circNick-LRS_mouse_brain

data_processing:
Nanopore data was basecalled using Guppy (v 3.4.5)
filtered using NanoFilt (v 2.6.0) allowing only reads with average base quality of 7 or more and a read length of 250 bp or more
mapped to the human genome (hg19) or mouse genome (mm10) using a parallelized version of  Blat
Detetion of circular RNA (circRNA) using custom scripts
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: Tab-delimited text files list all detected circRNAs, including genomic coordinates, number of reads spanning backsplice junction (BSJ), host gene that circRNAs originates from and circRNA ID from circBase, circAtlas and CIRCpedia.

extract_protocol:
Total human brain RNA was derived from post mortem cortex and provided by Agilent (Agilent Technologies, cat: 540143). For the preparation of mouse brain RNA, a male mouse (strain 129S2/SV) was sacrificed, and the entire brain was harvested and grained in Trizol (Thermo Fisher Scientific). Total RNA was obtained according to the manufacture’s protocol.
After rRNA and linear RNA depletion the enriched circRNA linearized and polyadenylated. Later, the protocol, SQK-PCS108, version PCS_9035_v108_revF_26Jun2017, provided by ONT was applied to prepare  the library and run it on the MinION flow cells.
Sequencing of circular RNA

tag: molecule subtype

value: enriched circRNA


title: Caki1_2


title: 3_LPS_Mse_BMDM [nanopore]

city: Santa Cruz

first: Sergio

last: Covarrubias

state: CA

address: Thimann Receiving/Department Carpenter Lab/Biomed 125, 1156 High St., Thimann Labs

department: MCD

institute: UCSC

data_processing:
ONT albacore version 2.1.0 was used to baseball Nanopore direct RNA raw signal
We used minimap2 with default parameters to align reads to the mm10 mouse genome reference
We used SAMtools to filter-out reads with mapping quality (MAPQ) less than 30
Genome_build: mm10

molecule: polyA RNA

source_name: Primary Bone Marrow Derived Macrophages, Day 8

growth_protocol: Harvest bone marrow from mice, lyse all red blood cells and differentiate hematopoietic stem cells for 8 days using MCSF from L929 cell line. Grow cells in DMEM 10% FCS 10%MCSF, Pen/strep

extract_protocol: Remove all media, pipette in 400ul of TriReagent into cell culture dish. Isolate RNA using Zimogen kit.

treatment_protocol: Treat cells with 100ng/ml LPS for 6hrs.

tag: cell type

value: Primary BMDM

value: 100ng/ml LPS for 6hrs

value: 10 weeks


title: 2_LPS_Mse_BMDM [nanopore]


title: Caki1_1


title: bm_old_2_scRNA-seq

city: St. Louis

first: Marco

last: Colonna

state: MO

address: 660 S. Euclid Ave.

institute: Washington University in St. Louis

data_processing:
Cell Ranger Software Suite (v3.1.0) from 10X Genomics was used for sample demultiplexing, barcode processing, and single-cell counting. Cell Ranger count was used to align samples to the reference genome GRCm38 (mm10), quantify reads, and filter reads and barcodes. Downstream analysis was performed using the Seurat package.
Genome_build: mm10
Supplementary_files_format_and_content: raw aligned barcode and feature count matrices from cellranger count (.h5)

source_name: bone marrow

extract_protocol: Library preparation was performed using the 10X Chromium VDJ + 5' Gene expression v.1 platform, up to 17,500 cells were partitioned into nanoliter Gel-bead-in-Emulsions (GEMs) droplets. Each GEM undergoes retro-transcriptase reaction to generate single-cell cDNA and receives a unique 12 nt cell barcode and unique molecular identifier (UMI). GEM cDNA was amplified for 11 cycles before being purified using SPRIselect beads. 10μl of purified cDNA was used to 5 generate the library for RNA sequencing. Libraries were sequenced on a NovaSeq S4 (Illumina, 300 cycle kit) flow cell, targeting 50K read pairs/cell.

value: aged

value: bone marrow


title: H295R_AngII_siBTG2_0_rep1

value: siBTG2, unstimulated


title: 1_LPS_Mse_BMDM [nanopore]


title: bm_old_1_scRNA-seq


title: TAD-treated HeLa cells rep2

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

country: China

institute: Beijing Institute of Radiation Medicine

data_processing:
Sequencing data were mapped GRCh38 reference genome using  STAR seperately
Gene expression was quantified as fragments per kilobase of transcript per million mapped reads (FPKM) using HTSeq (v0.10.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: plain txt file for illumina RNA-seq data, each file contain 2 column, the first column represents the gene id and the second column represents the raw count of each gene.

source_name: TAD-treated HeLa cells

growth_protocol: HeLa cells were seeded in 10-cm dishes and cultured in Dulbecco’s modified Eagle’s medium (DMEM, Thermo Fisher Scientific) supplemented with 10% FBS (Bi) and penicillin–streptomycin at 37 °C with 5% CO2.

extract_protocol:
For RNA-seq, about 1000,000 cells (top 5% GFP signal) were collected and RNA was extracted according to the standard protocol.
For library construction, mRNAs were fragmented and converted to cDNA using random hexamers or oligo(dT) primers.
High-throughput mRNA sequencing was carried out  on Illumina NovaSeq 6000 platform with a 150-bp paired-end module.

treatment_protocol: Cells were transfected with 30 μg plasmids using Lipofectamine 3000 (Thermo Fisher Scientific). Three days after transfection, cells were digested with 0.05% trypsin and prepared for FACS. GFP-positive cells were sorted and kept in Trizol (Solarbio).

value: HeLa

value: TAD-treated


title: TAD-treated HeLa cells rep3


title: 3_Ctl_Mse_BMDM [nanopore]


title: BEM_rep2: Human brain extracellular matrix

city: Seoul

first: Ann-Na

last: Cho

address: Yonsei-ro 50

country: South Korea

institute: Yonsei university

data_processing:
Illumina Casava1.8.2 software used for basecalling.(Hiseq 2500 sample), bcl2fastq2 v2.20(Novaseq 6000 sample)
Sequence reads were mapped by TopHat with paramters-p 8 -G genes.gtf genome read1.fastq read2.fastq.
Mapped reads were assembled by Cufflinks and FPKM value was calculated by Cufflnorm.
Genome_build: hg19

source_name: Brain organoid

growth_protocol: Human brain organoids were cultured in differentiation medium comprising DMEM/F12 and Neurobasal (1:1) ratio supplemented with 1:200 (v/v) N2 supplement, 1:100 (v/v) B27 supplement, 1:100 (v/v) Glutamax, 1:200 (v/v) NEAA, 1:4000 (v/v) insulin, and 3.5 μl/ml β-mercaptoethanol until day 75.

extract_protocol:
RNA extraction kit(Takara) were applied on brain organoids to extract total RNA.
RNA was enriched using an Illumina Truseq stranded mRNA library prep kit, mRNA was enriched by poly-T oligo-attached magnetic beads, fragments of cleaved RNA were reverse-transcribed into the first strand of cDNA using reverse transcriptase, a single ‘A’ nucleotide was attached to the 3’ ends of the cDNA fragments, and the adapter was subsequently ligated.

treatment_protocol: Brain organoids were washed with PBS for twice.

value: Human induced pluripotent stem cell derived

tag: developmental stage

value: Organoid

tag: region

value: Brain


title: BEM_rep1: Human brain extracellular matrix


title: bm_young_3_scRNA-seq

value: young


title: 2_Ctl_Mse_BMDM [nanopore]

value: wild type


title: bm_young_2_scRNA-seq


title: dura_young_2_scRNA-seq

source_name: dura

value: dura


title: dura_young_1_scRNA-seq


title: MAT_rep3: Matrigel


title: H295R_AngII_siBTG2_0_rep2


title: MAT_rep2: Matrigel


title: 1_Ctl_Mse_BMDM [nanopore]


title: blood_old_7_scRNA-seq

source_name: peripheral blood

value: peripheral blood


title: BE3-treated HeLa cells rep1

source_name: BE3-treated HeLa cells


title: bm_old_3_scRNA-seq


title: bm_young_1_scRNA-seq


title: GFP-treated HeLa cells rep3

source_name: GFP-treated HeLa cells

value: GFP-treated


title: MAT_rep1: Matrigel


title: BE3-treated HeLacells rep2

source_name: BE3-treated HeLacells


title: TAD-treated HeLa cells rep1


title: GFP-treated HeLa cells rep2


title: BEM_rep3: Human brain extracellular matrix


title: blood_old_5_scRNA-seq


title: GFP-treated HeLa cells rep1


title: ATAC_19: rb1_osi_3

city: New York

first: Eric

middle: Edison

last: Gardner

state: New York

address: 413 East 69th Street, BRB-1352

department: Medicine

institute: Weill Cornell Medicine

description: clone 3

data_processing:
Alignment and identification of open chromatin regions The data was processed following the recommendations of the ENCODE consortium (The ENCODE Consortium, n.d.): Reads were aligned to the human reference genome (version GRCh38) with BWA-backtrack (Heng Li and Durbin 2009). Post-alignment filtering was done with samtools and Picard tools (Li et al. 2009, Broad Institute (2015)) to remove unmapped reads, improperly paired reads, non-unique reads, and duplicates. To identify regions of open chromatin represented by enrichments of reads, peak calling was performed with MACS2 (Liu 2014). For every replicate, the narrowpeak results of MACS2 were used after filtering for adjusted p-values smaller than 0.01.
Coverage files Individual coverage files per replicate normalized for differences in sequencing depths between the different samples were generated with bamCoverage of the deepTools suite (Ramìrez et al. 2016) using the following parameters: -bs 10 --normalizeUsing RPGC --blackListFileName hg38.blacklist --ignoreForNormalization chrX chrY --ignoreDuplicates --minFragmentLength 40 -p 1.  Version 1 blacklist files were retrieved from https://sites.google.com/site/anshulkundaje/projects/blacklists.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: BigWig files for each sample

growth_protocol: Cells were seeded at 50% confluence in 100mm tissue culture plates. 24 hours following plating, cells were used for experiments

extract_protocol:
Culture media was removed, cells were washed 1X with cold PBS/2% FBS and then removed using TrypLE. Samples were processed using the Omni-ATAC protocol (MR Corces, et al.) by the WCM Epigenomics Core
NEB Nextera kit using the original ATAC-seq library prep protocol (JD Buenrostro, et al.) by the WCM Epigenomics Core
balanced block design

treatment_protocol: Cells were treated with vehicle (DMSO) or 1uM kinase inhibitor for 12 hours in complete culture media prior to collection

tag: crispr ko

value: osimertinib

tag: duration

value: 12 hours


title: blood_old_4_scRNA-seq


title: ATAC_18: rb1_osi_2

description: clone 2


title: HEK293T_APOBEC1-treated cells rep2 (3.5μg)

source_name: HEK293T_APOBEC1-treated cells (3.5μg)

growth_protocol: HEK293T cells were seeded in 10-cm dishes and cultured in Dulbecco’s modified Eagle’s medium (DMEM, Thermo Fisher Scientific) supplemented with 10% FBS (Bi) and penicillin–streptomycin at 37 °C with 5% CO2.

value: APOBEC1 (3.5μg)


title: blood_old_3_scRNA-seq


title: ATAC_17: rb1_osi_1

description: clone 1


title: blood_old_2_scRNA-seq


title: ATAC_16: rb1_4

description: clone 4

value: vehicle


title: blood_young_7_scRNA-seq


title: blood_old_1_scRNA-seq

value: aged


title: HEK293T_APOBEC1-treated cells rep2 (2.5μg)

source_name: HEK293T_APOBEC1-treated cells (2.5μg)

value: APOBEC1 (2.5μg)


title: ATAC_14: rb1_2

description: clone 2


title: HEK293T_APOBEC1-treated cells rep2 (1.5μg)

source_name: HEK293T_APOBEC1-treated cells (1.5μg)

value: APOBEC1 (1.5μg)


title: ATAC_15: rb1_3

description: clone 3


title: blood_young_4_scRNA-seq


title: blood_old_6_scRNA-seq


title: ATAC_20: rb1_osi_4

description: clone 4


title: HEK293T_APOBEC1-treated cells rep1 (1.5μg)


title: ATAC_13: rb1_1

description: clone 1


title: ATAC_12: safe_osi_4

description: clone 4

value: SAFE


title: blood_young_6_scRNA-seq


title: ATAC_11: safe_osi_3

description: clone 3


title: blood_young_2_scRNA-seq


title: blood_young_3_scRNA-seq


title: HEK293T_Tad-treated cells rep3 (3.5μg)

source_name: HEK293T_Tad-treated cells (3.5μg)

value: Tad (3.5μg)


title: blood_young_1_scRNA-seq


title: HEK293T_Tad-treated cells rep1 (3.5μg)


title: HEK293T_APOBEC1-treated cells rep1 (3.5μg)


title: ATAC_8: safe_4

description: clone 4


title: HEK293T_Tad-treated cells rep3 (2.5μg)

source_name: HEK293T_Tad-treated cells (2.5μg)

value: Tad (2.5μg)


title: HEK293T_APOBEC1-treated cells rep1 (2.5μg)


title: HEK293T_APOBEC1-treated cells rep3 (1.5μg)


title: ATAC_7: safe_3

description: clone 3


title: HEK293T_Tad-treated cells rep2 (2.5μg)


title: shScram_Pre_Rep1

city: nanjing

first: Zhang

last: Jun

state: jiangsu

address: longmiandadao

institute: China Pharmaceutical University

description: preadipocytes

data_processing:
Trim Galore (v.0.6.5) was initially used to trim the low quality sequences and retain paired reads under -length 100 -paired parameters.
The paired-end reads were aligned to mouse genome (GRCm38) with HISAT2 aligner (v2.1.0) with default parameters and Ensemble genes (GRCm38.102) transcriptome annotation.
Then gene expression were quantified using stringtie (v2.1.4), and differentially expressed genes were identifified using DESeq2 (v1.30.1). The FoldChange > 2 or < 0.5 and p-value < 0.05 genes were considered as differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

growth_protocol: Cells were seeded and cultured until a confluency of 100% was reached. Two days after complete confluency, cells were fed with MDI induction media. Three days later, cells were replenished with media supplied with 10% FBS, 1% PS and 10 μg/ml insulin every 2-3 days until fully diffenretiated adipocyte-like cells were obtained.

extract_protocol:
Total RNA was extracted using TRIzol Reagent and MeRIP-seq samples were immunoprecipitated by m6A antibody.
Samples were first dephosporylated and 40-60nt region was selected according to 15% polyacrylamide TBE-urea gel separation. Desired RNA species were excised and soaked overnight followed by ethanol precipitation. the purified RNA was processed for Poly-(A) tailing reaction and reverse transcription afterwards. Eventually, PCR amplification was proceeded using Phusion High-Fidelity DNA Polymerase.

treatment_protocol: One sample was treated by 20 μM Rhein and DMSO from DAY0 to DAY3.

value: fibroblast

value: knockdown control


title: shScram_MCE_Rep2

description: preadipocytes at the mitotic clonal expansion stage


title: HEK293T_Tad-treated cells rep1 (2.5μg)


title: HEK293T_Tad-treated cells rep3 (1.5μg)

source_name: HEK293T_Tad-treated cells (1.5μg)

value: Tad (1.5μg)


title: EZH2_WT_H3K27me3_ChIP-Rx

city: Dublin 2

first: Craig

last: Monger

state: Ireland

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

data_processing:
ChIP-RX data were aligned to a metagenome of the combined Human hg38 and mouse mm10 reference genomes (with 'mm10_' appended as a prefix of mouse chromosome names) using bowtie2 (v2.3.4.1) with the --no_unal parameter
Samtools (v1.7) was used to convert SAM to BAM files, sort them, remove duplicates and remove multimappers with the samtools view -q 2 parameter.
Aligned reads were seperated into those uniquely aligning to either the human or mouse genome by using grep for chromosome names containing 'mm10_'.
ChIP-RX normalisation factors were generated by counting the number of reads aligned to the human and mouse reference genomes with samtools flagstat and using the formula 1/(spike-in counts/1000000).
Bigwig files were generated using bamCoverage (deeptools v3.3.0) with the -of bigwig -bs10 parameters and scaled for the ChIP-RX normalisation factor with --scalefactor.
Peaks were called using Homer (v4.10.4) findPeaks and average plots generated using deeptools computeMatrix and plotProfile.
genome build: mm10
processed data files format and content: bigWig files contain ChIP-RX RRPM scaled librarys.

source_name: Embryonic stem cells

growth_protocol: Mouse embryonic stem cells were grown on gelatin in media containing serum, LIF and 2i.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone/protein-DNA complexes were isolated using antibodies.
Libraries were constructed using the Rubicon Genomics DNA ThruPlex library preparation kit, catalog number R400427, in accordance with the manufacturers instructions.

treatment_protocol: Ezh2 +/- mouse embryonic stem cells were engineered to exogenously express wild-type hEZH2.

value: Embryonic stem cells

value: EZH +/- + WT EZH2

tag: chip antibody


title: ATAC_6: safe_2

description: clone 2


title: HEK293T_Tad-treated cells rep2 (3.5μg)


title: ATAC_5: safe_1

description: clone 1


title: ATAC_10: safe_osi_2

description: clone 2


title: EZH2_WT_Input_ChIP-Rx


title: EZH2_WT_H3K27Ac_ChIP-Rx


title: shScram_MCE_Rep1


title: shScram_Diff_Rep1

description: mature adipocytes

value: Fto knockdown


title: shScram_Diff_Rep2

description: mature adipocytes


title: shFTO_Pre_Rep2

description: preadipocytes


title: ATAC_4: bulk_4

description: replicate 2

value: high passage


title: EZH2_WT_H3K27me2_ChIP-Rx


title: ATAC_3: bulk_3

description: replicate 1


title: ATAC_9: safe_osi_1

description: clone 1

value: osimertinib


title: shScram_Pre_Rep2

description: preadipocytes


title: ATAC_2: bulk_2

description: replicate 2

value: low passage


title: Ezh2_Het_Input_ChIP-Rx

value: EZH +/-


title: HEK293T_GFP only-treated cells rep6

source_name: HEK293T_GFP only-treated cells

value: GFP only


title: shFTO_Pre_Rep1

description: preadipocytes


title: HEK293T_GFP only-treated cells rep5


title: ATAC_1: bulk_1

description: replicate 1


title: Ezh2_Het_H3K27me3_ChIP-Rx


title: shFTO_MCE_Rep2


title: HEK293T_Tad-treated cells rep2 (1.5μg)


title: HEK293T_Tad-treated cells rep1 (1.5μg)


title: Ezh2_Het_H3K27me2_ChIP-Rx


title: HEK293T_GFP only-treated cells rep4


title: shFTO_MCE_Rep1


title: HEK293T_GFP only-treated cells rep3


title: Ezh2_Het_H3K27Ac_ChIP-Rx


title: HEK293T_GFP only-treated cells rep2


title: HEK293T_GFP only-treated cells rep1


title: shFTO_Diff_Rep1

description: mature adipocytes


title: FT110 siFOXL2 B1

city: Jerusalem

first: Rotem

last: Karni

address: Hadassah Ein-Kerem

country: Israel

institute: Hebrew University of Jerusalem

data_processing:
Library strategy: CEL-seq
Raw reads were processed with cutadapt, v1.12, with parameters -e 0 -q 10 -a "A\{100\}" -a "A\{15\}N\{100\}" -a GATCGTCGGACT -n 3 -m 28.
Trimmed reads were aligned with Tophat2, v2.0.14, using parameters -N 2 --read-edit-dist 2 -G genes.gtf. The GTF file was taken from Ensembl release 84, together with data for the ERCC genes.
Counting was done with htseq-count, v0.6.0, with default parameters.
Raw counts were normalized and differential expression was calculated with DESeq2, v1.12.4.
Genome_build: GRCh38
Supplementary_files_format_and_content: An Excel file with column headers that explain the content. The file includes columns for gene details, such as symbol and location, normalized counts and the results of the DESeq2 analysis.

source_name: patient derived immortal fallopian tube cells

growth_protocol: FT109 and FT110  are patient-derived cell lines of immortalized human benign fallopian tube secretory epithelial cells (by retroviral infection with hTERT (pBABE-puro-hTERT, Addgene #1771) and SV40 TAg (pBABE-puro SV40 LT, Addgene #13970) expression vectors. The cells were developed by Dr. Keren Levanon’s lab, Sheba Medical Center, Ramat Gan, Israel. The cells were grown in DMEM F-12 supplemented with 10% (v/v) FCS, 1% L-glutamine, penicillin and streptomycin.

extract_protocol: Total RNA was extracted with TRI Reagent (Sigma)

value: FOXL2 knock down

value: Fallopian tube cells


title: FT110 siFOXL2 B2


title: exvivo_ACTH_24_rep3 [NM2019_0070]

value: primary/isolated adrenocortical cells

value: ACTH, 24hr


title: FT110 control B2

value: Wild type


title: FT109 siFOXL2 B1


title: exvivo_ACTH_24_rep1 [NM2019_0068]


title: m1PVneg_cSNAIL_rep2

city: Pittsburgh

first: Alyssa

middle: J

last: Lawler

state: PA

address: 4400 Fifth Ave

institute: Carnegie Mellon University

description:
transposase-accessible DNA
M1PVneg2

data_processing:
ATAC-seq alignment: Reads were mapped to the mm10 genome with Bowtie2 using the ENCODE ATAC-seq pipeline (https://github.com/kundajelab/atac_dnase_pipelines) with default parameters.
ATAC-seq filtering: Duplicate reads, mitochondrial reads, and blacklist region reads were filtered out as a part of the ENCODE ATAC-seq pipeline.
ATAC-seq peak calling: Peaks were called on each sample individually using MACS2 within the ENCODE ATAC-seq pipeline workflow and reproducible peaks were determined on biological replicates with an IDR threshold of 0.1.
Generation of ATAC-seq count matrix: The IDR peaks across all biological replicates were merged to create the genomic ranges of interest. Read counts per sample in these regions were computed with Rsubread featureCounts version 1.28.1 on the filtered bam alignments.
Other: More information on all data processing and conclusions can be found in the publication.
Genome_build: mm10
Supplementary_files_format_and_content: peak; ATAC-seq peaks called in each sample
Supplementary_files_format_and_content: bigWig; MACS2 pval signal tracks for each sample in bigwig format
Supplementary_files_format_and_content: supplementary file countData_CortexPVvsPVneg.txt; count matrix for cSNAIL Cortex PV+ and PV- samples
Supplementary_files_format_and_content: supplementary file countData_PVSNAILevaluations.txt; count matrix for bulk, cSNAIL, and SNAIL samples in cortex, striatum, and GPe

extract_protocol:
We used an affinity purification approach to isolate PV neurons from the mouse isocortex, as described in Lawler et al., J Neurosci (2020). Briefly, mice were overdosed with isoflurane, decapitated, and rapidly dissected. Fresh brain tissue was sectioned coronally on a vibratome for precision, and we dissected brain regions relevant to the specific experiment to be processed as separate samples. All dissections took place in cold, oxygenated artificial cerebrospinal fluid (aCSF). After dissection, we isolated nuclei from the samples by 30 strokes of dounce homogenization with the loose pestle (0.005 in clearance) in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). The nuclei were filtered through a 70µm strainer and pelleted with 10 minutes of centrifugation at 2,000 x g at 4°C. We resuspended the nuclei pellets in wash buffer (0.25M Sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine with KOH to pH 7.8, and 0.4% IGEPAL) for the affinity purification steps. The suspension was incubated with anti-GFP antibody (Invitrogen, #G10362) in wash buffer for 30 minutes at 4°C with end-to-end rotation. After this period, we added Protein G Dynabeads  (Thermo Fisher, cat. 10004D) to the reaction and incubated again for 20 minutes. We separated the Sun1GFP+ fraction from the Sun1GFP- fraction on a magnetic bead rack. Sun1GFP- nuclei in the supernatant were centrifuged at 2000 x g for 10 minutes to pellet nuclei, washed one time, and filtered with a 40µm cell strainer. The Sun1GFP+ nuclei attached to the beads were washed 3-4 times with 800µL wash buffer by resuspending the sample, letting it settle onto the magnet, and removing the buffer. Where cell yield was not a concern, we also performed a large volume wash with 10 mL wash buffer and filtered through a 20µm cell strainer. All nuclei preparations were resuspended in water for the ATAC-seq reaction.
For each sample, a small aliquot was stained with DAPI (Thermo Scientific, cat. 62248) and the concentration of nuclei was determined by counting DAPI+ nuclei with a hemocytometer. Next, we combined 50,000 nuclei, 25 µL Tagment DNA Buffer, and 2.5 µL Tagment DNA Enzyme I (Illumina cat. 20034198) into 50 µL total for the transposition reaction. The reaction incubated at 37°C for 30 minutes with 300 rpm mixing. Samples containing beads were gently resuspended every 5-10 minutes throughout the incubation to prevent the beads from staying settled at the bottom. Immediately following incubation, the DNA was column purified with the Qiagen MinElute PCR Purification kit (Qiagen, cat. 28004). Libraries were amplified to ⅓ saturation with dual-indexed Illumina primers. We ensured that samples had the characteristic periodic fragment length distribution of high quality ATAC-seq using Agilent TapeStation assessment. Successful samples were sequenced at low depth on the Illumina Miseq system to determine appropriate library pooling and sequencing depth, then paired-end sequenced for 2 x 150 cycles with the Novaseq 6000.

treatment_protocol: Animals were injected with cSNAIL or SNAIL AAV-PHP.eB viruses to enable the isolation of tagged nuclei. Injections were retro-orbital and the total virus injected per animal was 4 x 10^11 vector genomes.

value: primary motor cortex

tag: celltype

value: PVneg

tag: assay

value: cSNAIL ATAC-seq

tag: virus

tag: Sex

value: F

tag: individual


title: m1PVneg_cSNAIL_rep1

description:
transposase-accessible DNA
M1PVneg1


title: gpePV_SC2SNAIL_rep2

description:
transposase-accessible DNA
SS5B

value: gpe

value: PV

value: SNAIL ATAC-seq

value: M


title: gpePV_SC2SNAIL_rep3

description:
transposase-accessible DNA
SS5C


title: exvivo_ACTH_24_rep2 [NM2019_0069]

tag: treatment


title: FT109 control B2


title: m1PVneg_cSNAIL_rep3

description:
transposase-accessible DNA
M1PVneg3

tag: strain


title: FT109 control B1

tag: tissue


title: ctxPVneg_cSNAIL_rep3

description:
transposase-accessible DNA
CTXPVneg3

value: cortex


title: shFTO_Diff_Rep2

description: mature adipocytes

value: fibroblast

value: Fto knockdown


title: ctxPVneg_cSNAIL_rep2

description:
transposase-accessible DNA
CTXPVneg2


title: FT109 siFOXL2 B2

tag: genotype


title: strPV_SC2SNAIL_rep3

description:
transposase-accessible DNA
SS3C

value: striatum

tag: age


title: FT110 control B1


title: FT110 siFOXL2 A2

value: FOXL2 knock down


title: exvivo_AngII_24_rep1 [NM2019_0065]

value: AngII, 24hr


title: ctxPV_cSNAIL_rep3

description:
transposase-accessible DNA
CTXPVpos3


title: FT110 control A2

value: Fallopian tube cells


title: exvivo_AngII_24_rep3 [NM2019_0067]

value: primary/isolated adrenocortical cells


title: exvivo_basal_24_rep3 [NM2019_0064]

value: basal media, 24hr


title: ctxPVneg_cSNAIL_rep1

description:
transposase-accessible DNA
CTXPVneg1


title: gpePV_SC2SNAIL_rep1

description:
transposase-accessible DNA
SS5A


title: ctxPV_cSNAIL_rep1

description:
transposase-accessible DNA
CTXPVpos1


title: ctxPV_cSNAIL_rep2

description:
transposase-accessible DNA
CTXPVpos2


title: strPV_SC2SNAIL_rep1

description:
transposase-accessible DNA
SS3A


title: ctxPV_SC2SNAIL_rep3

description:
transposase-accessible DNA
SS1C


title: strPV_SC2SNAIL_rep2

description:
transposase-accessible DNA
SS3B


title: FT110 control A1

value: Wild type


title: exvivo_basal_24_rep2 [NM2019_0063]


title: ctxPV_SC2SNAIL_rep2

description:
transposase-accessible DNA
SS1B


title: (ChIPSeq) input

city: Birmingham

first: Eddy

last: Yang

state: AL

address: 1700 6th Avenue South

department: Department of Radiation Oncology

institute: University of Alabama at Birmingham

data_processing:
ChIP-Seq reads were aligned to mm10 with BWA version 0.7.12 with default setting.
Samples were normalized by randomly sampling the reads to the same number.
Peaks were called with MACS2 version 2.1.0 with input as control and these options: -g 1.87e9 -f BAM --nomodel -p 0.05  --extsize 200
Read depth was generated by Deeptools bamCoverage version 3.3.0 at bin of 50bp.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files generated by Deeptools bamCoverage, tab-delimited annotated peak files generated by MACS2

source_name: Breast tumor tissue

growth_protocol: Dulbecco’s Modified Eagle’s Medium (DMEM)/Hams F-12 50/50 Mix (Corning, Cat# 10-090-CV) supplemented with 10% Fetal Bovine Serum (FBS) (MilliporeSigma, Cat# 12306C), and 10 units of Penicillin and 10 µg/mL Streptomycin (GE, Cat# SV30010), and 50 µg/mL Geneticin (ThermoFisher Scientific, Cat# 10131035)

extract_protocol:
Lysates were clarified from sonicated nuclei and Rnf2-DNA complexes were isolated with antibody
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

value: Breast Cancer (Triple Negative)

value: WT

value: BALB/c

tag: antibody


title: FT109 siFOXL2 A2


title: ctxPV_SC2SNAIL_rep1

description:
transposase-accessible DNA
SS1A

value: F


title: exvivo_AngII_24_rep2 [NM2019_0066]

tag: cell type


title: (ChIPSeq) RNF2 Replicate #2


title: FT110 siFOXL2 A1


title: FT109 siFOXL2 A1


title: exvivo_basal_24_rep1 [NM2019_0062]


title: (ChIPSeq) RNF2 Replicate #1


title: exvivo_ACTH_3_rep3 [NM2019_0043]

value: ACTH, 3hr


title: gpePV_SC1SNAIL_rep3

description:
transposase-accessible DNA
SF5C

value: gpe

value: PV

value: SNAIL ATAC-seq


title: exvivo_ACTH_3_rep2 [NM2019_0042]


title: PparDA.High Fat rep4

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
NextSeq 500 using v3 chemistry. Software: Control v2.2.58, RTA 2.11.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
3’ DGE FASTQ sequencing reads were collapsed to one representative read per unique molecular identifier using a custom python script.
Gene expression was quantified using salmon v1.1.0 using a transcriptome prepared from the mouse mm10 primary genome assembly and the ensembl version 101 annotation. The resulting counts were summarized to the gene level using R (version 4.0.2) running tximport (version 1.16.1, Soneson et al., 2015) and counts per million (cpm) were calculated using utilities implement in edgeR (version 3.30.2, Chen et al., 2014). The cpm values with a +1 offset were transformed to log2 space
Genome_build: mm10 with ensembl v101annotation
Supplementary_files_format_and_content: mmana_200923Yil_intCt.txt.gz is a text file of integer count data
Supplementary_files_format_and_content: mmana_200923Yil_l2cpm.txt.gz is a text file of log2 cpm data with a plus 1 offset

source_name: Intestinal stem cell (GFP-hi)

growth_protocol: Following crypt isolation, ISCs were trypsinized, filtered, stained with CD326-eFluor450 and DAPI, and isolated by flow cytometry. GFP-Hi ISCs were sorted directly into TRI reagent.

extract_protocol:
Sigma Aldrich TRI reagent
High Throughput 3'DGE

tag: diet

value: High Fat

value: Ppard-fl/fl; Ppara-null


title: FT109 control A2


title: FT109 control A1


title: PparDA.Control rep4

value: Control


title: gpePV_SC1SNAIL_rep2

description:
transposase-accessible DNA
SF5B

value: M


title: PparA.High Fat rep4

value: Ppara-null


title: OCI-LY-18 72 hour KDM5i 3

city: London

first: James

last: Heward

state: England

address: Haemato Oncology, Barts Cancer Institute, Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute

description:
RNA
KDM5i_RNA_seq_DE_data

data_processing:
For ChIP seq analysis - Input FASTQ files were mapped to hg19 using Bowtie, whilst H3K4me3 FASTQ files were mapped to hg19 and dm3. The number of reads mapping to the dm3 genome were used to calculate a scaling factor and sequencing reads were randomly removed from samples requiring normalization using SAMtools (samtools view -b -s <scaling.factor> <filename.bam>  > <scaled.bam>). Peaks were identified using the broad source option in MACS2 (macs2 callpeak -t <filename.bam> -c <input.bam> --broad -n <filename> -g hs --broad-cutoff 0.1 -q 0.05) and regions known to result in poor quality sequencing (https://www.encodeproject.org/annotations/ENCSR636HFF/) removed using BEDtools
For KDM5i RNA-seq analysis - mRNA isolation and strand-specific cDNA libraries were prepared using the Illumina TruSeq stranded mRNA Prep kit according to the manufactures instructions. For SU-DHL-6 and OCI-LY-18, two hundred cycles of sequencing on the Illumina HiSeq 2500 instrument were performed to generate 2x100bp paired-end sequencing reads. HT libraries were sequenced by 300 cycles of sequencing on the HiSeq 4000 to generate 2x150bp paired-end sequencing reads. Raw data was aligned to hg19 using STAMPY and BWA. The number of uniquely aligned reads (quality score q > 10) aligned to the exonic region of each gene were counted using HTSeq based on the Ensembl annotation (version 75). Only genes that achieved at least one read per million reads (CPM) in at least 3 samples were kept. Aligned reads numbers were further normalised using the ‘cqn’ method, accounting for gene length and GC content. Differential expression (DE) analysis was then performed using the edgeR R package, employing the generalised linear model (GLM) approach, for the treated versus control pairwise matched comparisons.
For FL patient RNA-seq analysis - 14 FL RNA samples  with a RIN value > 6 were isolated from fresh frozen biopsies and sequenced on the HiSeq 2000. 100bp reads were aligned to the reference genome hg19 using Tophat2 and analysed as above using the ‘cqn’ method to obtain RPKM values for all filtered genes.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files of ChIP seq data and data matrix of analysed RNA-seq data.

source_name: OCI-LY-18 cells

growth_protocol: Cells were cultured in RPMI-1640 media at 37°C 5% CO2

extract_protocol:
mRNA was extracted using QIAGEN Rneasy kits. ChIP was performed using a modied version of the Active Motif ChIP-IT High Sensitivity Kit protocol.
RNA-seq libraries were prepared using the TruSeq stranded mRNA Prep kit and ChIP-seq libraries prepared using the NEBNext Ultra II kit .

treatment_protocol: Cells were treated with DMSO or 1μM GS-701644 for 24 or 72 hours

tag: sample type

tag: time

value: 72 hours


title: gpePV_SC1SNAIL_rep1

description:
transposase-accessible DNA
SF5A


title: exvivo_ACTH_3_rep1 [NM2019_0041]

value: primary/isolated adrenocortical cells


title: exvivo_AngII_3_rep3 [NM2019_0040]

value: AngII, 3hr


title: strPV_SC1SNAIL_rep2

description:
transposase-accessible DNA
SF3B

value: striatum


title: strPV_SC1SNAIL_rep3

description:
transposase-accessible DNA
SF3C


title: OCI-LY-18 72 hour DMSO 3

description:
RNA
KDM5i_RNA_seq_DE_data

value: DMSO


title: exvivo_AngII_3_rep2 [NM2019_0039]


title: PparA.Control rep4


title: strPV_SC1SNAIL_rep1

description:
transposase-accessible DNA
SF3A


title: OCI-LY-18 24 hour KDM5i 3

description:
RNA
KDM5i_RNA_seq_DE_data

value: 24 hours


title: PparD.High Fat rep4

value: Ppard-fl/fl


title: ctxPV_SC1SNAIL_rep3

description:
transposase-accessible DNA
SF1C

value: cortex


title: exvivo_AngII_3_rep1 [NM2019_0038]


title: exvivo_basal_3_rep3 [NM2019_0037]

value: basal media, 3hr


title: PparD.Control rep4


title: exvivo_basal_3_rep2 [NM2019_0036]


title: OCI-LY-18 72 hour DMSO 2

description:
RNA
KDM5i_RNA_seq_DE_data


title: OCI-LY-18 72 hour KDM5i 2

description:
RNA
KDM5i_RNA_seq_DE_data


title: WT.Control rep4

value: Wildtype


title: ctxPV_SC1SNAIL_rep2

description:
transposase-accessible DNA
SF1B

value: PV


title: exvivo_basal_3_rep1 [NM2019_0035]


title: ctxPV_SC1SNAIL_rep1

description:
transposase-accessible DNA
SF1A

value: SNAIL ATAC-seq

value: F


title: WT.High Fat rep4

value: High Fat


title: H295R_AngII_24_rep2 [NM2019_0024]

tag: cell line

value: steroid-producing adrenocortical cell line

value: AngII, 24hr


title: OCI-LY-18 24 hour DMSO 2

description:
RNA
KDM5i_RNA_seq_DE_data


title: PparDA.Control rep3

value: Control

value: Ppard-fl/fl; Ppara-null


title: gpeGFPneg_Ef1aSNAIL_rep2

description:
transposase-accessible DNA
SE6B

value: gpe

value: GFPneg


title: PparDA.High Fat rep3


title: gpeGFPneg_Ef1aSNAIL_rep1

description:
transposase-accessible DNA
SE6A

value: M


title: OCI-LY-18 24 hour KDM5i 2

description:
RNA
KDM5i_RNA_seq_DE_data


title: OCI-LY-18 72 hour KDM5i 1

description:
RNA
KDM5i_RNA_seq_DE_data

value: 72 hours


title: H295R_AngII_8_rep2 [NM2019_0023]

value: AngII, 8hr


title: H295R_AngII_6_rep2 [NM2019_0022]

value: AngII, 6hr


title: OCI-LY-18 24 hour DMSO 3

description:
RNA
KDM5i_RNA_seq_DE_data

value: DMSO

value: 24 hours


title: PparA.High Fat rep3

value: Ppara-null


title: PparA.Control rep3


title: gpeGFP_Ef1aSNAIL_rep2

description:
transposase-accessible DNA
SE5B

value: GFP


title: OCI-LY-18 24 hour KDM5i 1

description:
RNA
KDM5i_RNA_seq_DE_data


title: strGFPneg_Ef1aSNAIL_rep2

description:
transposase-accessible DNA
SE4B

value: striatum

value: SNAIL ATAC-seq


title: H295R_AngII_4_rep2 [NM2019_0021]

value: AngII, 4hr


title: gpeGFP_Ef1aSNAIL_rep1

description:
transposase-accessible DNA
SE5A


title: OCI-LY-18 72 hour DMSO 1

description:
RNA
KDM5i_RNA_seq_DE_data


title: OCI-LY-18 24 hour DMSO 1

description:
RNA
KDM5i_RNA_seq_DE_data


title: strGFPneg_Ef1aSNAIL_rep1

description:
transposase-accessible DNA
SE4A


title: PparD.High Fat rep3

value: High Fat

value: Ppard-fl/fl


title: PparD.Control rep3

value: Control


title: SU-DHL-6 72 hour KDM5i 3

description:
RNA
KDM5i_RNA_seq_DE_data

source_name: SU-DHL-6 cells


title: H295R_AngII_2_rep2 [NM2019_0019]

value: steroid-producing adrenocortical cell line

value: AngII, 2hr


title: H295R_AngII_3_rep2 [NM2019_0020]

value: AngII, 3hr


title: WT.High Fat rep3

value: Wildtype


title: strGFP_Ef1aSNAIL_rep2

description:
transposase-accessible DNA
SE3B

value: F


title: H295R_AngII_1.5_rep2 [NM2019_0018]

value: AngII, 1.5hr


title: strGFP_Ef1aSNAIL_rep1

description:
transposase-accessible DNA
SE3A

value: M


title: H295R_AngII_1_rep2 [NM2019_0017]

value: AngII, 1hr


title: SU-DHL-6 72 hour DMSO 3

description:
RNA
KDM5i_RNA_seq_DE_data

value: DMSO

value: 72 hours


title: WT.Control rep3


title: PparDA.High Fat rep2

value: Ppard-fl/fl; Ppara-null


title: ctxGFPneg_Ef1aSNAIL_rep2

description:
transposase-accessible DNA
SE2B

value: cortex

value: GFPneg


title: SU-DHL-6 24 hour DMSO 3

description:
RNA
KDM5i_RNA_seq_DE_data

value: 24 hours


title: SU-DHL-6 24 hour KDM5i 3

description:
RNA
KDM5i_RNA_seq_DE_data


title: H295R_AngII_0.75_rep2 [NM2019_0016]

value: AngII, 0.75hr


title: ctxGFPneg_Ef1aSNAIL_rep1

description:
transposase-accessible DNA
SE2A

value: SNAIL ATAC-seq


title: PparDA.Control rep2

value: Control


title: SU-DHL-6 72 hour KDM5i 2

description:
RNA
KDM5i_RNA_seq_DE_data


title: H295R_AngII_0.5_rep2 [NM2019_0015]

value: steroid-producing adrenocortical cell line

value: AngII, 0.5hr


title: H295R_AngII_0.25_rep2 [NM2019_0014]

value: AngII, 0.25hr


title: PparA.High Fat rep2

value: High Fat

value: Ppara-null


title: SU-DHL-6 72 hour DMSO 2

description:
RNA
KDM5i_RNA_seq_DE_data


title: ctxGFP_Ef1aSNAIL_rep2

description:
transposase-accessible DNA
SE1B

value: GFP

value: F


title: ctxGFP_Ef1aSNAIL_rep1

description:
transposase-accessible DNA
SE1A

value: M


title: H295R_AngII_0_rep2 [NM2019_0013]

value: Unstimulated


title: PparA.Control rep2


title: gpePVneg_cSNAIL_rep1

description:
transposase-accessible DNA
SC6B

value: gpe

value: PVneg

value: cSNAIL ATAC-seq


title: SU-DHL-6 24 hour KDM5i 2

description:
RNA
KDM5i_RNA_seq_DE_data


title: PparD.High Fat rep2

value: Ppard-fl/fl


title: H295R_AngII_24_rep1 [NM2019_0012]

value: AngII, 24hr


title: SU-DHL-6 24 hour DMSO 2

description:
RNA
KDM5i_RNA_seq_DE_data

value: DMSO

value: 24 hours


title: strPVneg_cSNAIL_rep2

description:
transposase-accessible DNA
SC4B

value: striatum


title: H295R_AngII_8_rep1 [NM2019_0011]

value: steroid-producing adrenocortical cell line

value: AngII, 8hr


title: PparD.Control rep2

value: Control


title: strPVneg_cSNAIL_rep1

description:
transposase-accessible DNA
SC4A


title: SU-DHL-6 72 hour KDM5i 1

description:
RNA
KDM5i_RNA_seq_DE_data

value: 72 hours


title: H295R_AngII_6_rep1 [NM2019_0010]

value: AngII, 6hr


title: H295R_AngII_3_rep1 [NM2019_0008]

value: AngII, 3hr


title: SU-DHL-6 72 hour DMSO 1

description:
RNA
KDM5i_RNA_seq_DE_data


title: WT.Control rep2

value: Wildtype


title: SU-DHL-6 24 hour KDM5i 1

description:
RNA
KDM5i_RNA_seq_DE_data


title: ctxPVneg_cSNAIL_rep4

description:
transposase-accessible DNA
SC2A

value: cortex

value: M


title: H295R_AngII_4_rep1 [NM2019_0009]

value: AngII, 4hr


title: ctxPVneg_cSNAIL_rep5

description:
transposase-accessible DNA
SC2B

value: PVneg

value: F


title: SU-DHL-6 24 hour DMSO 1

description:
RNA
KDM5i_RNA_seq_DE_data


title: PparDA.High Fat rep1

value: High Fat

value: Ppard-fl/fl; Ppara-null


title: PparDA.Control rep1


title: H295R_AngII_1_rep1 [NM2019_0005]

value: AngII, 1hr


title: PparA.High Fat rep1

value: Ppara-null


title: H295R_AngII_0.75_rep1 [NM2019_0004]

value: AngII, 0.75hr


title: PparD.High Fat rep1

value: Ppard-fl/fl


title: H295R_AngII_2_rep1 [NM2019_0007]

value: steroid-producing adrenocortical cell line

value: AngII, 2hr


title: CD4_ACT_TI_rep2

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

country: Switzerland

institute: EPFL

data_processing:
Alignement for ChIP-seqs: bowtie2 v2.2.1 with --sensitive-local parameter. For RNA-seq: tophat2 v. 2.0.11 with -g 1 --no-novel-juncs --no-novel-indels --b2-sensitive
Peak calling for ChIP-seqs were done using MACS v.1.4.2.1 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: A bed file containing the output of the peak called by MACS is provided.

growth_protocol: Primary CD4+ lymphocytes obtained from adult healthy donors were maintained in X-VIVO 15 medium (Lonza), supplemented with 10% fetal calf serum, penicillin and streptomycin at 5 mM (Gibco) and 2 mM glutamine (Gibco) at 37°C with 5% CO2. Cells were cultured at a density of 1 to 2 million cells/ml for the indicated time.

extract_protocol:
Total inputs and ChIPed samples were prepared for libraries using 10ng of material. Aliquots of the samples were tested in qPCR using the KAPA SYBR FAST qPCR Master Mix (KAPA Biosystems, KK4604) to determine the optimal number of PCR cycles needed to amplify each library without reaching saturation. Libraries were amplified with KAPA HiFi Hotstart Readymix polymerase (KAPA Biosystems, KK2602), size-selected using Ampure XP beads (Beckman Coulter) and always quality checked on Bioanalyser DNA high sensitivity chip (Agilent) and quantified by picogreen (Qubit® 2.0 Fluorometer, Invitrogen).
Chromatin was prepared from 10 million cells as previously described (Rowe et al., 2013b).

treatment_protocol: Activation was performed by addition of Dynabeads Human T-Activator CD3/CD28 (25 ul/0.5 million cells; Life Technologies), along with IL-2 (20 U/ml; Sigma).

value: peripheral blood

value: CD4+ T lymphocytes

tag: culture condition

value: 3-day culture in activating condition (anti-CD3, anti-CD28, IL-2)


title: CD4_REST_H3K9me3_rep2

value: no treatment

tag: chip antibody

value: H3K9me3 (Diagenode, pAb-056-050)


title: CD4_REST_TI_rep2


title: CD4_ACT_H3K9me3_rep2


title: H295R_AngII_0.5_rep1 [NM2019_0003]

data_processing:
Reads were mapped using Salmon with custom index containing ERCC spike-ins and precursor transcripts. Settings for salmon quant: -l A --allowDovetail --validateMappings
Genome_build: GRCh38
Supplementary_files_format_and_content: Salmon output quant.sf files, tab-delimited text file of read counts and TPM for each sample

extract_protocol:
H295R cells were washed and treated with TRIzol and RNA was extracted using ZYMO DirectZol RNA Miniprep kit. rRNA was depleted using ribozero gold; RNA from human adrenocortical cells was polyA-selected. For samples treated with 4-thiouridine, labeled RNA was biotinylated and purified using streptavidin as described previously (Methods Mol Biol. 2013;1064:91-100. doi: 10.1007/978-1-62703-601-6_6).
All RNA was made into cDNA libraries using Kappa HyperPrep kit an sequenced on Nova-seq.

value: AngII, 0.5hr


title: H295R_AngII_0.25_rep1 [NM2019_0002]

value: AngII, 0.25hr


title: WT.High Fat rep2

value: Wildtype


title: WT.High Fat rep1


title: CD4_REST_KAP1_rep2

value: KAP1 (custom rabbit polyclonal)


title: H295R_AngII_0_rep1 [NM2019_0001]

value: Unstimulated


title: CD4_ACT_KAP1_rep2


title: WT.Control rep1

source_name: Intestinal stem cells (GFP-hi)

value: Control


title: PparD.Control rep1


title: H295R_AngII_1.5_rep1 [NM2019_0006]

value: AngII, 1.5hr


title: CD4_REST_KAP1_rep1


title: 2884: IVS snRNA-seq

city: Boston

first: Michael

last: Chin

address: 15 Kneeland St

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

data_processing:
Demultiplexing, read alignment, and read counting, and nuclei calls were done with Cellranger 3.0
Quality control (QC) filtering, clustering, dimensionality reduction, visualization, and differential gene expression was performed using the development version of the R package Seurat in R 3.5.0
Genome_build: GRCh38-1.2.0
Supplementary_files_format_and_content: tab separated values files with barcode sequences corresponding to column indices, features corresponding to row indices.  For each feature, its feature ID and names are stored in the first and second column of the features.tsv file.  The third column of this file indentifies that it is a gene expression feature.  The actual gene cell matrix, .mtx file, is stored in the Market Exchange Format (MEX) for sparse matrices.

source_name: Adult human interventricular septum

extract_protocol:
Nuclei were released from the tissue via dounce homogenization and then nuclei were processed using 10x genomics Chromium Single Cell 3' reagent V2 kit
10x Genomics Chromium Single Cell 3' reagent v2 kit

tag: developmental stage

value: adult

tag: gender

value: Female

tag: age (years)

value: interventricular septum

tag: molecule subtype

value: nuclear RNA


title: 2880: IVS snRNA-seq

value: Male


title: CD4_REST_H3K9me3_rep1

value: peripheral blood


title: CD4_ACT_TI_rep1

value: CD4+ T lymphocytes


title: PparA.Control rep1

value: Ppara-null


title: S17_Cre_2d

city: Glasgow

first: Ania

last: Wilczynska

address: Switchback Road

institute: Beatson Insistute for Cancer Research

data_processing:
BCL files were converted to fastq using bcl2fastq
reads were aligned to the mouse genome using HISAT2 v2.1.0 with parameters -q -p 24 --phred33
resulting sam files were converted to bam using samtools
read counts were generated using featurecounts () with parameters -T 20 -s 2 -t exon -g gene_id
Genome_build: GRCm38.84 with addition of AAV8-Cre and AAV8-null viral sequence
Supplementary_files_format_and_content: counts text files

source_name: liver

extract_protocol:
The caudate lobe of the liver was snap frozen in liquid nitrogen and then stored in -80 until the day of the extraction. All 27 samples were extracted on the same day. Livers were homogenized in a Precellys Evolution homogenizer (Cat. Number P000062-PEVO0-A, “MET” programme) in 600µl buffer RLT/1% β-mercaptoethanol and RNA was extracted using the Rneasy kit from Qiagen (Dnase step included). The RNA concentration was determined by Nanodrop.
1μg RNA in 50μl Rnase-free water were used to prepare libraries using the TruSeq Stranded mRNA Kit.

treatment_protocol: The mice were either injected with AAV8-TBG-null (Addgene, 105536-AAV8, 2x10^11 genetic copies in 100μl sterile PBS) or injected with AAV8-TBG-Cre (Addgene, 107787-AAV8, 2x10^11 genetic copies in 100μl sterile PBS) or not injected at all (uninduced). They were then culled either immediately (Uninduced, day 0) or at day 2, 4 or 7 post injection.

value: liver

value: WT

tag: aav genotype

value: Cre

tag: timepoint


title: 2879: IVS snRNA-seq

tag: tissue


title: S19_Cre_2d

tag: strain

tag: genotype


title: S20_Cre_2d


title: 2867: IVS snRNA-seq


title: S28_null_7d


title: TAD-treated cells rep3

source_name: HEK293T cells

extract_protocol:
For RNA-seq, about 1000,000 cells (top 5% GFP signal) were collected and RNA was extracted according to the standard protocol.
For library construction, mRNAs were fragmented and converted to cDNA using random hexamers or oligo(dT) primers.

tag: treatment

value: TAD


title: CD4_ACT_H3K9me3_rep1

tag: cell type

value: 3-day culture in activating condition (anti-CD3, anti-CD28, IL-2)

value: H3K9me3 (Diagenode, pAb-056-050)


title: TAD-treated cells rep2


title: S13_null_4d


title: CD4_ACT_15

data_processing:
tophat2 v. 2.0.11 with -g 2 --no-novel-juncs --no-novel-indels --b2-sensitive
Multimapped reads were removed.
Counts of reads on genes were computed using HTseq-count v0.6.1 with default parameters
Counts of read on TEs were generated using bedtools multicov with options: -split.
Genome_build: hg19
Supplementary_files_format_and_content: The .txt files contain reads count for genes and the .txt files contain read counts for TEs

extract_protocol:
TruSeq stranded RNA sample preparation kit (Illumina).
Total RNA was extracted using TRIzol reagent (Invitrogen), purified using miRNeasy kit (Qiagen) and treated with RNase-Free DNase (Qiagen) according to manufacturers instructions.

treatment_protocol: Activation was performed by addition of Dynabeads Human T-Activator CD3/CD28 (25 ul/0.5 million cells; Life Technologies), along with IL-2 (20 U/ml; Sigma). Where indicated, 24h after addition of the beads CD4+ cells were transduced with lentiviral vectors (LV)-expressing small hairpin RNAs (shRNAs) targeting either TRIM28 (shTRIM28b or shTRIM28d) or Luciferase (shLUC) and encoding for green fluorescent protein (GFP), at a multiplicity of infection (MOI; determined in 293T cells) of 20. GFP-positive cells were sorted 3 days after transduction. Alternatively, transduction was performed at MOI 40 after 4 days of treatment with IL-7 (25 ng/ml; Lubioscience). Cells were cultured for 4 additional days in presence of IL-7 or rested for one more week in medium containing IL-2, prior to sorting GFP-positive cells.

tag: subject status

value: adult healthy donor

tag: subject id

value: subject 15

tag: genotype/variation

value: Untransduced

value: activated (anti-CD3, anti-CD28, IL-2)

tag: time point

value: day 3 after activation

tag: batch


title: CD4_ACT_KAP1_rep1

tag: culture condition

tag: chip antibody

value: KAP1 (custom rabbit polyclonal)


title: TAD-treated cells rep1

tag: cell line


title: S22_Cre_4d


title: CD4_ACT_13

value: subject 13


title: CD4_Unstim_15

value: no treatment

value: day 0


title: BE3-treated cells rep3


title: CD4_REST_TI_rep1

value: peripheral blood

value: CD4+ T lymphocytes


title: S11_null_2d

value: liver


title: S12_null_2d

value: WT


title: CD4_Unstim_13


title: S9_null_2d


title: CD4_IL7_shLUC_104

value: subject 104

value: LV sh-LUC transduced

value: IL-7 treated

value: day 4 after LV-sh transduction


title: CD4_IL7_shLUC_105

value: adult healthy donor

value: subject 105


title: GFP-treated cells rep2

value: GFP


title: S18_Cre_2d

value: Cre


title: BE3-treated cells rep1


title: GFP-treated cells rep3


title: CD4_IL7_shLUC_103

value: subject 103


title: CD4_IL7_shKAP1d_105

value: LV sh-TRIM28d transduced


title: S10_null_2d


title: S6_uninduced_0

value: uninduced


title: GFP-treated cells rep1


title: S26_uninduced_0


title: S27_null_7d


title: endometrium, S3

city: Hong Kong

first: William

last: Yeung

address: Pokfulam

department: Department of Obstetrics and Gynecology

institute: The University of Hong Kong

description: single cell RNA

data_processing:
cellranger pipeline v3.0.2 for alignment, cell calling and quantification
cellranger aggr  for sample aggregation to generate processed data  4S3M.barcodes.tsv.gz,4S3M.features.tsv.gz,4S3M.matrix.mtx.gz
Taking cellranger aggr output processed data, R package Seurat V3.1 was used to generate the count data table and meta data table. Briefly, cells with 3MAD deviation in total UMIs, number of detected genes, mitochondrial/ribosomal genes were filtered. Genes with expression less than 1% of total cells were removed. Ribosomal and mitochondrial genes were also removed. After filtering, cells were clustered using Seurat after removing cell cycle effect (regression in Seurat) and donor variation (FastMNN was used).
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: aggregated expression file for different groups, and UMI count table and metadata table for each group samples.
emsc_count.csv: expression count table
emsc_meta_data.csv: metadata table that includes information for samples

source_name: endometrium

extract_protocol:
Stromal cells were isolated from fresh endometrium. Stromal cells cultured for two weeks. eMSCs were isolated from the cultured stromal cells and subjected to single cell encapsulation and library construction.
RNA libraries were prepared for sequencing using standard 10X Genmics and Illumina protocols

tag: age

tag: menstrual cycle

value: secretory

value: in vitro cultured eMSCs


title: S25_null_7d

tag: aav genotype


title: BE3-treated cells rep2


title: CD4_IL7_shKAP1d_103

value: peripheral blood


title: endometrium, S1

description: single cell RNA


title: endometrium, S2

description: single cell RNA


title: S8_uninduced_0

tag: timepoint


title: CD4_IL7_shKAP1d_104

tag: tissue

value: CD4+ T lymphocytes


title: MMAB_ASO_4

city: New Haven

first: Alberto

last: Canfrán-Duque

state: CT

address: 10 Amistad

department: Comparative Medicine

institute: Yale University

data_processing:
Using the PartekFlow® software, version 8.0.19.0405 (Partek, Inc., St. Louis, MO) the reads were aligned with the STAR algorithm to the mouse genome mmu10.
To estimate the transcript expression abundance we used Quantify to annotation model (Partek E/M) algorithm.
Counts were normalized using the recommended methods (Total count, Add 0.0001, Log2) from PartekFlow®
Genome_build: mmu10
Supplementary_files_format_and_content: MMAB_Liver_Normalize_counts.txt

source_name: Mouse liver

extract_protocol:
Total RNA from liver samples of mice treated with 50 mg/kg Control ASO or MMAB ASO  was extracted and purified using the RNeasy isolation Kit (Qiagen) according to the manufacturer’s instructions and treated with DNAse to remove genomic contamination (RNA MinElute Cleanup, Qiagen).
rRNA was depleted from RNA samples using Ribo-Zero rRNA Removal Kit (Illumina). RNA libraries were performed using TrueSeq Small RNA Library preparation (Illumina).
Libraries were sequenced for 45 cycles on Illumina NovaSeq 6000 (1 x 100bp read length).

treatment_protocol: Mice received one i.p. injection per week of 50 mg/kg Control ASO or MMAB ASO for 6 weeks. 48 hours after the last injection animals were sacrificed and liver sample were collected.

tag: strain

value: Liver

value: MMAB ASO


title: endometrium, M2

description: single cell RNA

value: menstrual


title: S30_null_7d

value: liver

tag: genotype

value: WT


title: MMAB_ASO_2

tag: treatment


title: MMAB_ASO_1


title: Control_ASO_4

value: Control ASO


title: CD4_IL7_shKAP1b_105

value: adult healthy donor

tag: cell type

value: LV sh-TRIM28b transduced

value: IL-7 treated

value: day 4 after LV-sh transduction


title: endometrium, M1

description: single cell RNA


title: CD4_IL7_shKAP1b_104

tag: subject status

value: subject 104


title: S1_Cre_7d

value: Cre


title: CD4_IL7_shKAP1b_103

tag: subject id

value: subject 103


title: S3_Cre_7d


title: endometrium, M3

description: single cell RNA


title: Device_rep3: New established device culture

source_name: Brain organoid

extract_protocol:
RNA extraction kit(Takara) were applied on brain organoids to extract total RNA.
RNA was enriched using an Illumina Truseq stranded mRNA library prep kit, mRNA was enriched by poly-T oligo-attached magnetic beads, fragments of cleaved RNA were reverse-transcribed into the first strand of cDNA using reverse transcriptase, a single ‘A’ nucleotide was attached to the 3’ ends of the cDNA fragments, and the adapter was subsequently ligated.

value: Human induced pluripotent stem cell derived

tag: developmental stage

value: Organoid

tag: region

value: Brain


title: CD4_REST_shLUC_105

value: subject 105

value: peripheral blood

value: CD4+ T lymphocytes

tag: genotype/variation

value: LV sh-LUC transduced

value: IL-7 treated and rested

tag: time point

value: 10 days after LV-sh transduction

tag: batch


title: S2_Cre_7d

value: liver

value: WT


title: CD4_REST_shLUC_104

value: adult healthy donor

tag: culture condition


title: ATAC PVT Polg rep2

city: Wako

first: Emilie

middle: Kristine

last: Bagge

state: Saitama

address: 2-1 Hirosawa

department: Center for Brain Science

country: Japan

institute: RIKEN

data_processing:
Reads were filtered using bbduk.sh using default settings
Reads were mapped using STAR
Peakcalling was performed with HMMRATAC for ATAC and Homer for H3K27Ac
Reads were counted with featureCounts
Differential analysis was performed with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: RNA_raw_counts.txt: reads were counted by Subread featureCounts (mm10) as raw counts
Supplementary_files_format_and_content: ATAC+H3K27Ac: After peak calling, reads in each peak were counted using featureCounts from Rsubread as raw counts

source_name: PVT

extract_protocol:
Illumina Nextera + NEB Next
ATAC + ChIP: Brain was removed, cut on brain matrix and brain regions of interest isolated and snap-frozen. Nuclei were extracted by douncing in homogenization buffer, stained with NeuN-AlexaFluor488 antibody and FACS sorted prior to the assay.

value: Brain, paraventricular thalamic nucleus

tag: age

value: Adult

tag: chip antibody


title: S15_null_4d

tag: aav genotype


title: ATAC PVT Polg rep1


title: CD4_REST_shLUC_103


title: Device_rep1: New established device culture

data_processing:
Illumina Casava1.8.2 software used for basecalling.(Hiseq 2500 sample), bcl2fastq2 v2.20(Novaseq 6000 sample)
Sequence reads were mapped by TopHat with paramters-p 8 -G genes.gtf genome read1.fastq read2.fastq.
Mapped reads were assembled by Cufflinks and FPKM value was calculated by Cufflnorm.
Genome_build: hg19


title: S21_Cre_4d

tag: timepoint


title: CD4_REST_shKAP1d_105

tag: tissue

value: LV sh-TRIM28d transduced


title: Bulk_rep3: Conventional bulk culture


title: ATAC PVT WT rep2

tag: strain


title: ATAC PVT WT rep1

tag: genotype


title: CD4_REST_shKAP1d_104

value: subject 104


title: RNA PVT Polg dep COX- rep4

extract_protocol:
Nugen Ovation SoLo
ATAC + ChIP: Brain was removed, cut on brain matrix and brain regions of interest isolated and snap-frozen. Nuclei were extracted by douncing in homogenization buffer, stained with NeuN-AlexaFluor488 antibody and FACS sorted prior to the assay.

tag: behavioural state

value: Depressive

tag: cox staining

value: Negative


title: Control_ASO_2

value: Liver

tag: treatment

value: Control ASO


title: Bulk_rep1: Conventional bulk culture

tag: cell type

value: Human induced pluripotent stem cell derived

value: Organoid

value: Brain


title: S24_Cre_4d

value: Cre


title: Control_ASO_1


title: S7_uninduced_0

value: uninduced


title: RNA PVT Polg dep COX- rep3


title: T11.WGS

city: Shenzhen,Guangdong Province,China

first: Yayan

last: Feng

state: --- Select a state ---

address: No. 7 pengfei road, dapeng new district, shenzhen

institute: Chinese Academy of Agricultural Sciences

data_processing:
Library strategy: WGS
FastQC (v0.11.7) was used to assess the quality of sequence reads.
Adapters and low-quality reads were removed from raw sequencing reads by Trimmomatic (v0.36) using following paramaters: LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, MINLEN:75
Clean reads from each species were mapped to respective reference genome after quality control, and then conduct SNP calling using GATK workflow.
MUMmer (v3.0) was used to examine all the single nucleotide polymorphism (SNPs) between reference genomes of T. pseudospiralis and other eleven Trichinella species. SNPs from uniquely aligned regions and with homozygous genotypes constituted the final set of SNVs.
Genome_build: The genomic data resources of the twelve Trichinella species were downloaded from NCBI BioProject database with the following accession codes: PRJNA12603 for T. spiralis,  PRJNA451013 for T. pseudospiralis, and PRJNA257433 for other ten Trichinella species.

organism: Trichinella zimbabwensis

source_name: T. zimbabwensis

extract_protocol:
DNA was extracted using the phenol chloroform extraction method.
High molecular DNA from 12 Trichinella genotypes were extracted from freshly collected muscle larvae. Qubit Fluorometer dsDNA HS Kit (Invitrogen) was used to determine total DNA amounts, followed by measurement of integrity by by agarose gel electrophoresis and using a BioAnalyzer (2100, Agilent). Paired-end sequencing libraries with insert size of 300 bp were conducted on the HiSeq 2,500 platform, according to instructions provided by Illumina.

tag: passages

value: Muscle larvae


title: Device_rep2: New established device culture

tag: developmental stage

tag: region


title: S16_null_4d

value: liver


title: RNA PVT Polg dep COX- rep2


title: RNA PVT Polg dep COX- rep1


title: CD4_REST_shKAP1b_104

tag: subject status

tag: subject id

value: peripheral blood

value: CD4+ T lymphocytes

tag: genotype/variation

value: LV sh-TRIM28b transduced

value: IL-7 treated and rested

tag: time point

value: 10 days after LV-sh transduction


title: CD4_REST_shKAP1b_105

value: adult healthy donor

value: subject 105

tag: culture condition

tag: batch


title: T4.WGS

organism: Trichinella pseudospiralis

source_name: T. pseudospiralis


title: S29_null_7d

value: WT

tag: aav genotype

tag: timepoint


title: S14_null_4d

tag: tissue

tag: strain


title: T2.WGS

organism: Trichinella nativa

source_name: T. nativa


title: S23_Cre_4d

tag: genotype


title: RNA PVT Polg dep COX+ rep4

value: Brain, paraventricular thalamic nucleus

tag: behavioural state

value: Depressive

tag: cox staining

value: Positive

tag: age

value: Adult

tag: chip antibody


title: RNA PVT Polg dep COX+ rep3


title: virus male avpv input replicate 2

city: Houston

first: Jonathan

middle: Carter

last: Bean

state: TX

address: 1100 Bates Ave

department: Pediatrics

institute: Baylor College of Medicine

description:
total RNA
virus_m_avpv_n2_AH

data_processing:
Basecalls performed by Real-Time Analysis software RTA v2
BCL files converted to fastq and demultiplexing performed by bcl2fastq v2.20.0.422 using options --minimum-trimmed-read-length 0 --mask -short-adapter-reads 0 –no-lane-splitting
The first 5 base calls were then trimmed and low quality reads filtered out using FASTX-Toolkit v0.0.14 with  zcat original_file.fastq.gz | fastx_trimmer -f 6 -v -Q33 | fastq_quality_filter -q 25 -p 80 -v -Q33 -z -o filtered_file.fastq.gz; done
trimmed and filtered fastq files were aligned using Tophat2 v2.1.1 to create bam files
Bam files were used to calculate raw counts, scaled counts, and FPKMs using cuffnorm from cufflinks v2.2.1 using options --no-update-check --output-format cuffdiff
Genome_build: UCSC mm10
Supplementary_files_format_and_content: raw counts, scaled counts, FPKMs in tab delimited text file

source_name: input avpv hypothalamus brain

extract_protocol:
Circular 2 mm-punches containing the RP3V area or the ARC from groups of four RiboTag expressing mice were pooled and homogenized in 1 ml of buffer as described previously (Sanz et al., 2019; Sanz et al., 2015). Briefly, 4 μl of anti-HA antibody (Clone 16B12, BioLegend) were added to 800 μl of the cleared lysate and incubated for 4 h at 4°C. A sample of total lysate (80 μl) was saved as an input. After incubation, 200 μl of protein A/G magnetic beads (Thermo Fisher Scientific) were added and incubated overnight at 4°C with rotation. Immunoprecipitates (IPs) were washed in high salt buffer and RNA from inputs and IPs extracted using the RNeasy micro kit (Qiagen).
NuGEN Ovation RNA-Seq System V2 (Catalog # 7102)(NuGEN, San Carlos, CA) in combination with Ovation Ultralow Library Systems (Catalog #s 0330, 0331) (NuGEN) and 2-10ng of total RNA were used to make cDNA libraries. Libraries were quantified with NEBNext Library Quant Kit for Illumina (Catalog # E7630, New England BioLabs, Ipswich, MA) before sequencing them on a NextSeq500 (Illumina, San Diego, CA) using NextSeq500 High-Output v2 75 cycles consumables (FC-404-2005; Illumina). Libraries were sequenced 75 cycles using single-ended reads with 6 additional reads for barcodes.

tag: Sex

value: male

tag: treatment

value: AAV-DIO-Rpl22-HA injection

tag: target of treatment

value: AVPV of hypothalamus of brain


title: Bulk_rep2: Conventional bulk culture

city: Seoul

first: Ann-Na

last: Cho

institute: Yonsei university

tag: cell type

value: Human induced pluripotent stem cell derived

tag: developmental stage

value: Organoid

tag: region

value: Brain


title: CD4_ACT_shLUC_73

tag: subject status

tag: subject id

value: subject 73

value: peripheral blood

value: CD4+ T lymphocytes

tag: genotype/variation

value: LV sh-LUC transduced

tag: culture condition

value: activated (anti-CD3, anti-CD28, IL-2)

tag: time point

value: day 3 after LV-sh transduction


title: RNA PVT Polg dep COX+ rep2

tag: strain

tag: tissue


title: virus male avpv input replicate 1

description:
total RNA
virus_m_avpv_n1_AH

tag: genotype


title: CD4_ACT_shLUC_71

value: adult healthy donor

value: subject 71

tag: batch


title: CD4_ACT_shKAP1d_73

value: LV sh-TRIM28d transduced


title: CD4_ACT_shKAP1d_72

value: subject 72


title: RNA PVT Polg eu COX- rep4

value: Brain, paraventricular thalamic nucleus

tag: behavioural state

value: Euthymic

tag: cox staining

value: Negative

tag: age

value: Adult


title: RNA PVT Polg dep COX+ rep1

value: Depressive

value: Positive

tag: chip antibody


title: CD4_REST_shKAP1d_103

value: subject 103

value: IL-7 treated and rested

value: 10 days after LV-sh transduction


title: CD4_REST_shKAP1b_103

value: peripheral blood

value: CD4+ T lymphocytes

value: LV sh-TRIM28b transduced


title: virus male avpv IP replicate 1

description:
total RNA enriched for translating mRNA in Kiss1 neurons
virus_m_avpv_ip1_AH

source_name: IP avpv hypothalamus brain

tag: Sex

value: male

tag: treatment

value: AAV-DIO-Rpl22-HA injection

tag: target of treatment

value: AVPV of hypothalamus of brain


title: virus female avpv input replicate 1

description:
total RNA
virus_f_avpv_n1_AH

value: female


title: CD4_ACT_shLUC_72

value: adult healthy donor

value: subject 72

tag: cell type

value: LV sh-LUC transduced

value: activated (anti-CD3, anti-CD28, IL-2)

value: day 3 after LV-sh transduction


title: virus female avpv IP replicate 2

description:
total RNA enriched for translating mRNA in Kiss1 neurons
virus_f_avpv_ip2_AH


title: CD4_ACT_shKAP1b_73

tag: subject status

value: subject 73


title: CD4_ACT_shKAP1b_72

tag: subject id


title: RNA PVT Polg eu COX- rep1

value: Brain, paraventricular thalamic nucleus

value: Euthymic

value: Negative

value: Adult


title: virus male avpv IP replicate 2

description:
total RNA enriched for translating mRNA in Kiss1 neurons
virus_m_avpv_ip2_AH


title: RNA PVT Polg eu COX+ rep4

value: Positive


title: CD4_ACT_shKAP1b_71

value: subject 71

value: peripheral blood

value: CD4+ T lymphocytes

tag: genotype/variation


title: RNA PVT Polg eu COX- rep3


title: virus female avpv input replicate 2

description:
total RNA
virus_f_avpv_n2_AH

value: AAV-DIO-Rpl22-HA injection


title: RNA PVT Polg eu COX+ rep3


title: virus female avpv IP replicate 1

description:
total RNA enriched for translating mRNA in Kiss1 neurons
virus_f_avpv_ip1_AH

value: ARC of hypothalamus of brain

value: AVPV of hypothalamus of brain


title: virus male arc input replicate 1

description:
total RNA
virus_m_arc_n1_AH

source_name: input arc hypothalamus brain

value: male


title: RNA PVT Polg eu COX+ rep2


title: RNA PVT Polg eu COX- rep2


title: CD4_ACT_shKAP1d_71

value: adult healthy donor

value: LV sh-TRIM28d transduced

tag: culture condition


title: virus male arc IP replicate 2

description:
total RNA enriched for translating mRNA in Kiss1 neurons
virus_m_arc_ip2_AH

source_name: IP arc hypothalamus brain


title: RNA PVT Polg eu COX+ rep1


title: virus male arc IP replicate 1

description:
total RNA enriched for translating mRNA in Kiss1 neurons
virus_m_arc_ip1_AH


title: RNA PVT WT eu COX+ rep4

value: WT


title: Sesquia2_EoN_Bio3

city: Oeiras

first: Jingtao

last: Lilue

state: Lisbon

address: Rua da Quinta Grande, 6

department: Bioinformatics facility

country: Portugal

institute: Instituto Gulbenkian de Ciencia

data_processing:
BGI used internal software for cleaning up the raw files (SOAPnuke version1.5.5; parameters: -n 0.001 -l 20 -q 0.4)
SOAPnuke can be found at: https://github.com/BGI-flexlab/SOAPnuke
Reads with adaptor sequences, and reads in which unknown bases (N) are more than 0,1% were both removed (parameters: -n 0,001)
Removed low quality reads (parameters: -l 20 -q 0.4)
Clean reads were aligned to the Arabidopsis genome (TAIR10), without storage of the intermediate .sam files, using Hisat2 and samtools (for x in $(ls|grep_1.fq.gz); do hisat2 -x Arabidopsis_thaliana.TAIR10.dna.toplevel.hisat2 -U $x | samtools view -Sb - | samtools sort - -o ${x}.sorted.bam; samtools index ${x}.sorted.bam; done)
A single table of counts was generated and annotated with the "Arabidopsis thaliana TAIR10.43.gtf" file, using featureCounts (featureCounts -a Arabidopsis_thaliana.TAIR10.43.gtf -o SnRK1_RNASeq_Allsamples.feature.counts *.bam)
Genome_build: TAIR10
Supplementary_files_format_and_content: edgeR expression count

organism: Arabidopsis thaliana

source_name: Whole 20d-old rosette

growth_protocol: Col-0 and SnRK1α1 plants were sown directly on soil and kept under a 12:12 photoperiod under a 22ºC/18ºC (light/dark) temperature and 160µmol light intensity. ColB and sesquiα2 plants were pre-selected on BASTA plates (0,5x MS no sugar) for 6 days before transfer to soil (all other growth conditions were similar to those of Col-0 and SnRK1α1 plants)

extract_protocol:
Total RNA was extracted from 50mg of finely ground tissue with the Qiagen RNeasy® Plant Mini Kit
Libraries were prepared by BGI Tech Solutions (Hongkong), according to the BGISEQ-500 platform. Briefly, poly-T oligo-attached mRNA was fragmented using divalent cations under elevated temperature and RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H and cDNA fragments were 3´adenylated and ligated to adapters. Products were enriched with PCR amplification and purified. The double stranded PCR products were heat denatured and circularized by a splint oligo sequence, generating the final library. The library was amplified with phi29 to make DNA nanoballs (DNB; around 300 copies per DNA molecule). The DNBs were loaded into the patterned nanoarray and paired-end 150 bp reads were read through the BGISEQ-500 platform.

treatment_protocol: No treatment; whole rosettes were directly harvested at ZT12 and ZT24

value: rosette

value: sesqui_alpha2 (GABI_579E09 (-/-) x WiscDsLox384F5 (+/-))

tag: harvest time

value: End of dark period (ZT24)

value: 20 days-old (after sowing)


title: virus male arc input replicate 2

description:
total RNA
virus_m_arc_n2_AH

tag: strain


title: RNA PVT WT eu COX+ rep3

tag: tissue

value: Brain, paraventricular thalamic nucleus

value: Euthymic


title: virus female arc input replicate 2

description:
total RNA
virus_f_arc_n2_AH

value: female

tag: genotype


title: Sesquia2_EoD_Bio2

value: End of light period (ZT12)


title: virus female arc input replicate 1

description:
total RNA
virus_f_arc_n1_AH


title: Sesquia2_EoN_Bio2


title: RNA PVT WT eu COX+ rep2

value: Positive

value: Adult


title: Sesquia2_EoN_Bio1


title: Sesquia2_EoD_Bio1


title: virus female arc IP replicate 2

description:
total RNA enriched for translating mRNA in Kiss1 neurons
virus_f_arc_ip2_AH

value: AAV-DIO-Rpl22-HA injection


title: Sesquia2_EoD_Bio3


title: SnRK1a1-OE_EoN_Bio3

tag: background ecotype


title: virus female arc IP replicate 1

description:
total RNA enriched for translating mRNA in Kiss1 neurons
virus_f_arc_ip1_AH

value: ARC of hypothalamus of brain


title: Input NAC

source_name: NAC

extract_protocol:
NEB Next Ultra II
ATAC + ChIP: Brain was removed, cut on brain matrix and brain regions of interest isolated and snap-frozen. Nuclei were extracted by douncing in homogenization buffer, stained with NeuN-AlexaFluor488 antibody and FACS sorted prior to the assay.

value: Brain, nucleus accumbens


title: mouse castrated male avpv input replicate 2

description:
total RNA
mouse_castr_m_avpv_n2_AH

value: male

value: castration

value: testicles

value: AVPV of hypothalamus of brain


title: SnRK1a1-OE_EoN_Bio1

value: rosette


title: SnRK1a1-OE_EoN_Bio2


title: Input CP

source_name: CP

value: Brain, caudate putamen


title: mouse castrated male avpv input replicate 1

description:
total RNA
mouse_castr_m_avpv_n1_AH


title: RNA PVT WT eu COX+ rep1

value: WT

tag: behavioural state


title: Input COR

source_name: COR

value: Brain, cortex


title: mouse castrated male avpv IP replicate 2

description:
total RNA enriched for translating mRNA in Kiss1 neurons
mouse_castr_m_avpv_ip2_AH


title: SnRK1a1-OE_EoD_Bio3

value: 20 days-old (after sowing)


title: Input PVT

value: Brain, paraventricular thalamic nucleus


title: mouse castrated male avpv IP replicate 1

description:
total RNA enriched for translating mRNA in Kiss1 neurons
mouse_castr_m_avpv_ip1_AH


title: SnRK1a1-OE_EoD_Bio2


title: SnRK1a1-OE_EoD_Bio1


title: H3K27Ac NAC Polg rep1


title: Col0_EoN_Bio3

value: wildtype

value: End of dark period (ZT24)


title: mouse male avpv input replicate 1

description:
total RNA
mouse_m_avpv_n1_AH


title: mouse male avpv input replicate 2

description:
total RNA
mouse_m_avpv_n2_AH


title: H3K27Ac NAC Polg rep2


title: Col0_EoN_Bio2


title: H3K27Ac NAC WT rep2


title: mouse male avpv IP replicate 2

description:
total RNA enriched for translating mRNA in Kiss1 neurons
mouse_m_avpv_ip2_AH


title: H3K27Ac NAC WT rep1


title: H3K27Ac CP Polg rep2


title: Individual 32 203752100072_R05C01

type: genomic

city: Hanover

first: Nasim

last: Azizgolshani

state: NH

address: Dartmouth College

department: Christensen Lab

institute: Dartmouth College

description:
203752100072_R05C01 is theBS treated version  and 203752110002_R06C01 is the BS treated version of the same sample from Individual 32
Individual 32

hyb_protocol: BS and oxBS conversions were performed with 1.2 -1.4 _g of DNA according to the TrueMethyl protocol. ssDNA was recovered and quantified with Qubit and processed on Illumina EPIC methylation arrays at the Diagenode Genomics Facility using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: We extracted signal intensity from both BS (5hmC and 5mC beta values) and OxBS files (5mC only),  minfi funnorm used,  Fortin et al Bioinformatics 2016, for normalization. In our literature, these beta values were used to calculate 5hmC levels (BS-OxBS)

label: Cy5 and Cy3

source_name: non-tumor brain tissue

label_protocol: Standard Illumina Protocol

growth_protocol: human fresh frozen brain tissue

extract_protocol: Tumor DNA was extracted with the QIAmp DNeasy tissue kit (Qiagen) according to the manufacturer instructions

tag: subject

value: no

tag: slide

tag: array

tag: age (years)

value: F

tag: vital status(alive=1)

tag: duration of clinical follow up (years)

tag: fresh frozen (ff)

value: FF

tag: sample brain region

value: infratentorial

tag: sample brain lobe location

tag: condition

value: BS

tag: sample label

value: Non-Tumor


title: Individual 32 203752100072_R01C01

description:
203752100072_R01C01 is theOxBS treated version  and 203752100072_R05C01 is the BS treated version of the same sample from Individual 32
Individual 32

tag: Sex

value: OxBS


title: mouse male avpv IP replicate 1

description:
total RNA enriched for translating mRNA in Kiss1 neurons
mouse_m_avpv_ip1_AH

tag: strain

value: male

tag: treatment

tag: target of treatment


title: Col0_EoN_Bio1

tag: tissue

tag: genotype

tag: background ecotype

tag: harvest time

tag: age


title: Individual 30 203723060072_R05C01

description:
203723060072_R05C01 is theBS treated version  and 203723060072_R03C01 is the BS treated version of the same sample from Individual 30
Individual 30

source_name: tumor tissue

tag: subject

tag: slide

tag: array

tag: age (years)

value: M

value: left temporal resection


title: Individual 29 203752110071_R04C01

description:
203752110071_R04C01 is theOxBS treated version  and 203723060072_R05C01 is the BS treated version of the same sample from Individual 29
Individual 29

tag: vital status(alive=1)

tag: duration of clinical follow up (years)

tag: fresh frozen (ff)

tag: sample brain region

value: SPINAL CORD

value: Ependymoma


title: mouse female avpv input replicate 2

description:
total RNA
mouse_f_avpv_n2_AH

tag: Sex

value: female

value: AVPV of hypothalamus of brain


title: Col0_EoD_Bio2

value: rosette

value: End of light period (ZT12)

value: 20 days-old (after sowing)


title: Col0_EoD_Bio3

value: wildtype


title: Individual 33 203752110002_R06C01

description:
203752110002_R06C01 is theBS treated version  and 203752110002_R03C01 is the BS treated version of the same sample from Individual 33
Individual 33

value: no

value: F

tag: sample brain lobe location

tag: condition

tag: sample label


title: Individual 31 203751380056_R04C01

description:
203751380056_R04C01 is theOxBS treated version  and 203752100072_R01C01 is the BS treated version of the same sample from Individual 31
Individual 31

value: FF

value: infratentorial

value: Hippocampus, brain


title: H3K27Ac CP Polg rep1

tag: strain

tag: tissue

value: Brain, caudate putamen

value: Adult

tag: chip antibody


title: Individual 26 203723180102_R06C01

description:
203723180102_R06C01 is theBS treated version  and 203752110071_R01C01 is the BS treated version of the same sample from Individual 26
Individual 26

value: M

value: POSTERIOR FOSSA

value: BS

value: Glioma


title: Individual 30 203723060072_R03C01

description:
203723060072_R03C01 is theOxBS treated version  and 203751380056_R03C01 is the BS treated version of the same sample from Individual 30
Individual 30

value: left temporal resection

value: OxBS

value: Non-Tumor


title: Individual 27 203752110071_R05C01

description:
203752110071_R05C01 is theOxBS treated version  and 203723050029_R01C01 is the BS treated version of the same sample from Individual 27
Individual 27

value: Embryonal


title: Individual 33 203752110002_R03C01

description:
203752110002_R03C01 is theOxBS treated version  and 203752110002_R06C01 is the BS treated version of the same sample from Individual 33
Individual 33


title: H3K27Ac CP WT rep1

tag: genotype

value: WT


title: mouse female avpv IP replicate 1

description:
total RNA enriched for translating mRNA in Kiss1 neurons
mouse_f_avpv_ip1_AH

value: female

tag: treatment

tag: target of treatment

value: AVPV of hypothalamus of brain


title: Individual 27 203752110071_R01C01

description:
203752110071_R01C01 is theBS treated version  and 203752110071_R05C01 is the BS treated version of the same sample from Individual 27
Individual 27

tag: subject

value: no

tag: slide


title: Individual 28 203723050029_R01C01

description:
203723050029_R01C01 is theBS treated version  and 203723050029_R06C01 is the BS treated version of the same sample from Individual 28
Individual 28

tag: array

tag: age (years)

value: FF

value: LATERAL VENTRICLE


title: H3K27Ac COR Polg rep2

value: Brain, cortex

tag: age


title: Individual 31 203751380056_R03C01

description:
203751380056_R03C01 is theBS treated version  and 203751380056_R04C01 is the BS treated version of the same sample from Individual 31
Individual 31

value: F

tag: vital status(alive=1)

tag: duration of clinical follow up (years)

tag: fresh frozen (ff)

value: infratentorial

value: Hippocampus, brain


title: H3K27Ac CP WT rep2

value: Brain, caudate putamen

value: Adult


title: Individual 26 203723180102_R05C01

description:
203723180102_R05C01 is theOxBS treated version  and 203723180102_R06C01 is the BS treated version of the same sample from Individual 26
Individual 26

tag: Sex

value: M

tag: sample brain region

tag: sample brain lobe location

value: POSTERIOR FOSSA

value: Glioma


title: mouse female avpv input replicate 1

description:
total RNA
mouse_f_avpv_n1_AH

tag: strain


title: Individual 28 203723050029_R06C01

description:
203723050029_R06C01 is theOxBS treated version  and 203752110071_R08C01 is the BS treated version of the same sample from Individual 28
Individual 28

tag: condition

value: OxBS

tag: sample label


title: mouse castrated male arc input replicate 2

description:
total RNA
mouse_castr_m_arc_n2_AH

value: male

tag: genotype

value: castration

value: testicles

tag: tissue

value: ARC of hypothalamus of brain


title: H3K27Ac COR Polg rep1

tag: chip antibody


title: Individual 23 203752100011_R04C01

description:
203752100011_R04C01 is theOxBS treated version  and 203723180102_R02C01 is the BS treated version of the same sample from Individual 23
Individual 23

tag: subject

value: no

value: 4TH VENTRICLE

value: Ependymoma


title: Individual 22 203752100072_R07C01

description:
203752100072_R07C01 is theBS treated version  and 203752100011_R06C01 is the BS treated version of the same sample from Individual 22
Individual 22

tag: slide

value: FF

value: BS


title: LNCaPabl-Enza_Dex_rep3

type: RNA

city: Innsbruck

first: Martin

last: Puhr

address: Anichstrasse 35

department: Department of Urology

institute: Medical University of Innsbruck

description: gene expression profiling of treated prostate cancer cell lines

hyb_protocol: The generated target RNA was loaded onto the Affymetrix Clariom S human array cartridge and hybridized for 16 hours at 45°C using GeneTitan Hybridization modul

scan_protocol: Array were scanned in the GeneChip Scanner 7G. The image files were imported into the Affymetrix Expression Console software.

data_processing: Preprocessing were performed with Affymetrix Expression Console software and RMA was used for background modeling, quantile normalization, and probe summarization. Analysis were performed on the gene level (with Refseq annotation) and differentially expressed genes were identified using moderated t-test with limma R package.

label: biotin

source_name: Epithelial prostate cancer cell line (LNCaPabl-Enza) treated with Dex

label_protocol: A target preparation of 150 ng RNA was used for cDNA synthesis, in vitro transcription and terminal labeling utilizing the WT PLUS reagent kit (Affymetrix).

growth_protocol: LNCaP were cultured in RPMI 1640 supplemented with 10% fetal calf serum (FCS) (Biowest, MI, USA), 1% penicillin/streptomycin (Szabo Scandic, Vienna, Austria), and 1x glutamax (ThermoFisher Scientific, Vienna).

extract_protocol: Total RNA from cell lines was isolated with the EXTRACTME TOTAL RNA KIT (DNA-Gdansk) according to manufacturer’s instructions. Quality and amount of isolated RNA were determined on a Nanodrop2000 system (ThermoFisher Scientific).

treatment_protocol: 5 Mio epithelial LNCaPabl-Abi/Enza were seeded into T175 tissue flasks. On the next day specific treatments were performed as followed. Epitelial cells : Group 1: vehicle Ctrl was treated with DMSO for 24h. Group 2: 100 nM dexamethasone for 24h.

tag: treatment

value: Dexamethasone

tag: concentration

value: 100nM (Dex)


title: Individual 29 203752110071_R08C01

description:
203752110071_R08C01 is theBS treated version  and 203752110071_R04C01 is the BS treated version of the same sample from Individual 29
Individual 29

tag: array

tag: age (years)

value: F

value: infratentorial

value: SPINAL CORD


title: Individual 23 203752100011_R06C01

description:
203752100011_R06C01 is theBS treated version  and 203752100011_R04C01 is the BS treated version of the same sample from Individual 23
Individual 23

value: M

tag: vital status(alive=1)

tag: duration of clinical follow up (years)


title: LNCaPabl-Enza_Dex_rep2


title: mouse castrated male arc input replicate 1

description:
total RNA
mouse_castr_m_arc_n1_AH

tag: Sex

tag: target of treatment


title: mouse female avpv IP replicate 2

description:
total RNA enriched for translating mRNA in Kiss1 neurons
mouse_f_avpv_ip2_AH

value: female

value: AVPV of hypothalamus of brain


title: Individual 24 203723180102_R07C01

description:
203723180102_R07C01 is theBS treated version  and 203723180102_R05C01 is the BS treated version of the same sample from Individual 24
Individual 24

tag: fresh frozen (ff)

tag: sample brain region

tag: sample brain lobe location

value: Embryonal


title: Col0_EoD_Bio1

value: rosette

value: wildtype

tag: background ecotype

tag: harvest time

value: End of light period (ZT12)

tag: age

value: 20 days-old (after sowing)


title: H3K27Ac COR WT rep1

tag: strain

tag: genotype

value: WT

tag: tissue

value: Brain, cortex

value: Adult

tag: chip antibody


title: mouse castrated male arc IP replicate 2

description:
total RNA enriched for translating mRNA in Kiss1 neurons
mouse_castr_m_arc_ip2_AH

value: male

tag: treatment

value: castration

value: testicles

value: ARC of hypothalamus of brain


title: H3K27Ac COR WT rep2


title: LNCaPabl-Enza_Ctrl_rep3

source_name: Epithelial prostate cancer cell line (LNCaPabl-Enza) treated with DMSO

value: DMSO

tag: concentration

value: Control


title: mouse castrated male arc IP replicate 1

description:
total RNA enriched for translating mRNA in Kiss1 neurons
mouse_castr_m_arc_ip1_AH


title: Individual 22 203752100072_R03C01

description:
203752100072_R03C01 is theOxBS treated version  and 203752100072_R07C01 is the BS treated version of the same sample from Individual 22
Individual 22

tag: subject

value: no

tag: slide

tag: array

tag: age (years)

value: F

value: FF

value: infratentorial

value: POSTERIOR FOSSA

tag: condition

value: OxBS

tag: sample label

value: Glioma


title: H3K27Ac PVT Polg rep2

value: Brain, paraventricular thalamic nucleus


title: Individual 24 203723180102_R02C01

description:
203723180102_R02C01 is theOxBS treated version  and 203723180102_R07C01 is the BS treated version of the same sample from Individual 24
Individual 24

tag: Sex

value: M

tag: vital status(alive=1)

tag: duration of clinical follow up (years)

tag: fresh frozen (ff)

tag: sample brain region

value: 4TH VENTRICLE

value: Embryonal


title: H3K27Ac PVT Polg rep1

tag: strain

tag: age

value: Adult


title: mouse male arc input replicate 1

description:
total RNA
mouse_m_arc_n1_AH

value: male

tag: genotype

tag: target of treatment

tag: tissue


title: H3K27Ac PVT WT rep2

value: WT

tag: chip antibody


title: LNCaPabl-Enza_Ctrl_rep2

tag: treatment

tag: concentration


title: LNCaPabl-Enza_Ctrl_rep1


title: mouse male arc IP replicate 2

description:
total RNA enriched for translating mRNA in Kiss1 neurons
mouse_m_arc_ip2_AH

value: ARC of hypothalamus of brain


title: H3K27Ac PVT WT rep1


title: LNCaPabl-Abi_Dex_rep3

source_name: Epithelial prostate cancer cell line (LNCaPabl-Abi) treated with Dex

value: Dexamethasone

value: 100nM (Dex)


title: LNCaPabl-Abi_Dex_rep2


title: mouse male arc IP replicate 1

description:
total RNA enriched for translating mRNA in Kiss1 neurons
mouse_m_arc_ip1_AH


title: Individual 21 203752100011_R01C01

description:
203752100011_R01C01 is theOxBS treated version  and 203752100072_R03C01 is the BS treated version of the same sample from Individual 21
Individual 21

tag: subject

value: no

tag: slide

tag: array

tag: sample brain lobe location

value: SUPRASELLAR


title: mouse male arc input replicate 2

description:
total RNA
mouse_m_arc_n2_AH

tag: Sex


title: FPI Astro rep 5

city: Iowa City

middle: S

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

data_processing:
Reads were demultiplexed and converted to fastq format using Illumina's 'bcl2fastq'.  Fastq rna-seq data were processed using the 'bcbio-nextgen.py' pipeline.
bcbio-nextgen.py' (v1.0.8) was run in "RNA-seq" mode with reference genome set to "mm10" referencing the Ensembl GRCm38.p6 v94 build.  'hisat2' (v2.1.0) in soft-clipping mode was used for full alignment and 'featureCounts' was used to generate processed "counts" tables.  "salmon" (v0.9.1) was also used for quantification against the transcriptome.
Genome_build: "mm10" (Ensembl GRCm38.p6 v94 / GENCODE M19)
Supplementary_files_format_and_content: text format (counts from FeatureCounts)

source_name: Ipsilateral forebrain

extract_protocol:
Microglia and astrocytes were isolated by FACS sorting, mRNA was extracted using the Qiagen RNAeasy Plus Micro kit.
Sequencing libraries were prepared using the Clontech SMARTer Stranded Total RNA-Seq Kit v2- Pico Input Mammalian Kit following the manufacturer’s recommendations. All libraries were sequenced on the NovaSeq S4 2x150-bp flow cell.

tag: cell type

value: Astrocyte

tag: protocol

value: traumatic brain injury

tag: time point

value: 7-days post sham/FPI


title: mouse female arc input replicate 2

description:
total RNA
mouse_f_arc_n2_AH

value: female


title: LNCaPabl-Enza_Dex_rep1


title: LNCaPabl-Abi_Dex_rep1


title: FPI Astro rep 3


title: FPI Astro rep 4


title: mouse female arc input replicate 1

description:
total RNA
mouse_f_arc_n1_AH


title: LNCaPabl-Abi_Ctrl_rep2

source_name: Epithelial prostate cancer cell line (LNCaPabl-Abi) treated with DMSO

value: DMSO

value: Control


title: LNCaPabl-Abi_Ctrl_rep3