title: ChIA-PET, CTCF

city: San Juan de Alicante

first: Sergio

last: Niñerola

state: Alicante

address: Avenida Santiago Ramon y Cajal, s/n

department: Molecular Neurobiology and Neuropathology

country: Spain

institute: CSIC-Instituto de Neurociencias de Alicante

data_processing:
For RNA, adapters were trimmed using cutadapt v1.18 selecting reads longer than 25 bp.  HISAT2 (Kim et al., 2015) (v2.1.0) was used for reads alignment to the mouse genome (GRCm38.89, mm10) and reads with mapq > 30 and that mapped to nuclear chromosomes were quantified using HTSeq v0.11.1 (Anders et al., 2015). Data processing was performed with custom R scripts (v3.5.1, 2018), Samtools v1.9 (Li et al., 2009), Bedtools v2.27.1 (Quinlan and Hall, 2010), and DeepTools v3.5.0 (Ramírez et al., 2016). Whole genome alignments were normalized to 10× RPM (read per 10 million sequenced reads).
For ChIPs, Adapters were trimmed using TrimGalore v 0.6.4_dev (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), and the reads obtained were mapped to the mouse genome (mm10) with Bowtie2 (v2.3.4.3) (Langmead and Salzberg, 2012). Only those reads with a mapq > 30 were selected. Data was processed using Samtools v1.10 (Li et al., 2009), Deeptools v 3.5.0 (Ramírez et al., 2016), and Bedtools v2.25.0 (Quinlan and Hall, 2010). For BigWigs, ChIP-seq reads were normalized by reads per genomic content with Deeptools (Ramírez et al., 2016).
ChIA-PET, was processed by the ChIA-PIPE pipeline (Lee et al., 2020) using mm10 as a reference genome and default parameters. The resulting *hic file for 2D contact maps and *bigwig file for protein binding coverage were used for visualizing on Juicebox (Durand et al., 2016) Within ChIA-PIPE, peaks were called via MACS2 without input control and only those with the maximum coverage greater than 50 (which is twice the median of all peaks) were kept by pybedgraph (Zhang et al., 2020), resulting in 34,885 confident peaks. Using these peaks, the loops reported in *bedpe format with 7th column denoting PET counts are further filtered to have PET count greater than or equal to 3 and to have both left and right anchors to overlap with at least one peak.
For 4C-seq analysis all samples were trimmed to 75 bp. The wig and peaks were calculated using pipe4C and peakC as mentioned in (Krijger et al., 2020).
Assembly: mm10
Supplementary files format and content: For RNA tab-delimited text file contains raw counts data for each sample, BigWig files
Supplementary files format and content: BigWig files for ChIP-seq data
Supplementary files format and content: BigWig, Bedgraph and hic files for ChIAPet data
Library strategy: ChIAPet

source_name: Camk2a+ neurons from hippocampus

extract_protocol:
For RNA, total RNA was extracted from hippocampal tissue with TRI reagent (Sigma-Aldrich) as recommended by the manufacturer.  Subsequently, genomic DNA was eliminated by a treatment with DNAse I (Qiagen) for 30 min at 25ºC. Followed by precipitation with phenol-chloroform-isoamyl alcohol (Sigma-Aldrich).
ChIPs were performed as previously described in detail (Galvão-Ferreira et al., 2017) with minor modifications. Briefly, 3 μg of antibody were incubated with Dynabeads coated to Protein G (Invitrogen) in RIPA-150 buffer (50 mM Tris-HCl, 150 mM NaCl, 1 mM, EDTA, 0.1% SDS, 1% Triton X-100, and 0.1% sodium deoxycholate; pH 8) for 6-18 h at 4°C in agitation. Nuclei from hippocampal cells were extracted in a dounce homogenizer as explained for the FANS method. Samples were fixed with 1% formaldehyde (Sigma-Aldrich) for 10 min at room temperature followed by 0.1 M glycine for 5 min to stop the fixation. Nuclei were centrifuged at 1,5 G, and the pellet was resuspended in 100 μL of SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris; pH 8) prior to its sonication in a Bioruptor Pico (Diagenode) for 12 cycles of 15 s on/30 s off. After 6 min of centrifugation at 13000 rpm, the supernatant containing isolated chromatin was collected. Samples were diluted in 900 μL of ChIP Dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, 167 mM NaCl; pH 8) and incubated overnight at 4°C with the antibody-Dynabeads mix. Beads were thoroughly rinsed at 4ºC as follows: two washes in RIPA-150 buffer, three washes in RIPA-500 buffer (50mM Tris-HCl, 500 mM NaCl, 1 mM, EDTA, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate; pH 8), two washes in RIPA LiCl buffer (50 mM Tris-HCl, 1 mM EDTA, 1% NP-40, 0.7%, sodium deosycholate, 500 mM LiCl2), and two final washes in TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA; pH 8.0), five minutes each. Samples were resuspended in 200 μl Elution buffer (10 mM Tris-HCl, 5 mM EDTA, 300 mM NaCl, 0.5% SDS; pH 8) and treated with 1 μl of 10 mg/mL RNase A (Fermentas) overnight at 65°C in agitation for crosslink reversion. Samples were treated with 3 μl of 20 mg/mL Proteinase K (Thermo Scientific) for 2 hours at 55°C in agitation. Last, DNA precipitation was performed by phenol-chloroform-isoamyl alcohol (Sigma-Aldrich). For Kdm1a ChIP, some modification were applied as in (Lipinski et al., 2020). In brief, samples required a stronger fixation treatment in 1% PFA for 30 min at 37ºC. To fragment these highly fixed samples, 43 cycles of sonication (30 s On, 30 s Off) were applied in a Bioruptor Pico (Diagenode). SDS lysis buffer was modified to RIPA buffer (0.1% SDS, 1% IGEPAL, and 0.5% sodium deoxycholate).
Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) using a CTCF-specific antibody (Abclonal Cat # ab70303) was performed as described in the in situ ChIA-PET protocol (Wang et al., 2021) on approximately 10 million nuclei of hippocampal excitatory neurons sorted by FANS as described above.
4C-seq, was performed as previously described (Krijger et al., 2020) with minimal changes. Approximately 5 million hippocampal nuclei were fixed at 1 % with PFA. The restriction enzyme cutting order was Dpn II as the primary enzyme and Csp6I as the secondary enzyme. Ligated chromatin was phenol-chloroform extracted and ethanol precipitated. Reactions were then further purified with Ampure XP beads with a 0.8x ratio of bead solution to library following the manufactures instructions. Samples were then quantified with Qubit and 4C-seq libraries were sequenced using an Illumina high-throughput sequencing equip.
For RNA three mice were used per genotype (Kdm1a-ifKO and their control littermates) and Poly-A libraries were generated. For RNA and ChIPseq,  libraries were generated for each independent sample and single-end sequenced in a HiSeq 2500 apparatus from Illumina. For ChIAPet, librearies were generated and paired end and 150 pb were sequenced and emrged from Miseq, Nextseq 500/550 and Hiseq 3000/4000 aparatus.
PolyA RNAseq, ChIP-seq, 4C-seq and ChIAPet

value: Camk2a+ neurons from hippocampus

value: Tamoxifen


title: C32.RTX.T15.Cold4

status: Public on Dec 04 2023

type: SRA

city: Riverside

first: Dawn

last: Nagel

state: CA

address: 900 University Avenue

country: USA

institute: UC Riverside Department of Botany and Plant Sciences

library_source: transcriptomic

data_processing:
Sequencing reads were not trimmed and mapped on the Sbicolor_454_v3.1.1 genome using Hisat2 and the SystemPipeR pipeline (genome downloaded from Phytozome: https://data.jgi.doe.gov/refine-download/phytozome?organism=Sbicolor&expanded=45).
Read counting was performed with the summarizeOverlaps function from the GenomicRanges Package, and using the Sbicolor_454_v3.1.1.gene.gff3.gz file for the annotation.
Normalized transcript abundance was then calculated using the rlog function from the R package ‘DESeq2’ (Love et al., 2014, 10.1186/s13059-014-0550-8)
Assembly: Sbicolor_454_v3.0.1
Supplementary files format and content: tab-delimited text file includes raw count values for each Sample

molecule: polyA RNA

organism: Sorghum bicolor

source_name: RTX430, Cold stress, ZT15, replicate 4

extract_protocol:
Between ~2 and ~40 ug of total RNA was extracted from three biological replicates of sorghum samples for each genotype and treatment (control, heat, cold stress) using GeneJET Plant RNA Extraction Kit (Thermofisher K0801) followed by DNAse I treatment (Thermofisher EN0521). Total mRNAs were isolated using biotinylated oligo(dT) and streptavidin magnetic beads (New England Biolabs) as previously described (Wang et al., 2011, 10.1371/journal.pone.0026426)
Purified mRNAs were used for library preparation as previously described with the following modifications. In the final enrichment step, indexed adapter enrichment primers were used (Townsley et al., 2015, 10.3389/fpls.2015.00366) and 12 cycles were performed to amplify the libraries. The libraries were quantified using a Qubit 2.0 Fluorescence Reader (Thermo Fisher Scientific) and quality was verified using a Bioanalyzer 2100 (Agilent Genomics). Final libraries were multiplexed and sequenced on the NextSeq 500 (Illumina) at the UC Riverside (UCR) Institute for Integrated Genome Biology (IIGB) Genomics Core facility to obtain 75 nt single-end reads.

treatment_protocol: Plants were grown under controlled (30/20°C; day/night) conditions and then subjected to 1 h of cold (10°C) or 1 h of heat (42°C) at four times of the day (ZT0, ZT6, ZT9, and ZT15).

tag: experiment

value: Cold stress

tag: tissue

value: leaves

tag: genotype

tag: treatment

tag: time of_day

tag: replicate


title: Panc02, parental, rep2

city: Atlanta

first: Tenzin

last: Passang

state: Georgia

address: 1365 Clifton Road NE

department: Hematology and Medical Oncology

institute: Emory University

data_processing:
The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the Control software. Raw sequence data (.bcl files) generated by the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove adapter sequences. The trimmed reads were mapped to the mouse reference genome GRCm38 available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes. Genes with adjusted p-values < 0.05 and absolute log2 fold changes > 1 were called as differentially expressed genes for each comparison. A PCA analysis was performed using the "plotPCA" function within the DESeq2 R package. The plot shows the samples in a 2D plane spanned by their first two principal components. The top 500 genes, selected by highest row variance, were used to generate the plot.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample
Supplementary files format and content: tab-delimited text files includes RPKM value for each sample

organism: Mus musculus

source_name: pancreas

growth_protocol: Panc02 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% HEPES with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from frozen cell pellet samples using Qiasymphony RNA kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles.The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: No treatment

value: pancreas

tag: cell line

tag: cell type

value: ductal adenocarcinoma cells

value: Wild type


title: 3448_Striatonigral-medium-spiny-neuron_BEB18116_CTRL

city: New York

first: Kert

last: Matlik

state: NY

address: 1230 York Avenue

institute: Rockefeller University

description:
3448
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

data_processing:
Sequence and transcript coordinates for human hg38 UCSC genome and gene models were retrieved from the BSgenome.Hsapiens.UCSC.hg38 Bioconductor package (version 1.4.1) and TxDb.Haspiens.UCSC.hg38.knownGene (version 3.4.0) Bioconductor libraries respectively. FANSseq reads were aligned to the genome using Rsubread's subjunc method (version 1.30.6).
Aligned reads were exported as bigWigs normalized to reads per million using the rtracklayer package (version 1.40.6).
Aligned reads in genes were counted using the featurecounts function within the Rsubread package against gene exons.
Assembly: BSgenome.Hsapiens.UCSC.hg38
Supplementary files format and content: BigWig files, Counts files

molecule: nuclear RNA

organism: Homo sapiens

source_name: Anterior caudate

extract_protocol:
RNA extraction was carried out with AllPrep DNA/RNA FFPE Kit (Qiagen, #80234).
RNA-seq libraries were prepared with Trio RNA-Seq™ library preparation kit (Tecan, #0506-A01) and pooled for sequencing on NovaSeq6000 (SP 2 x 150bp).

treatment_protocol: Nuclei were isolated from fresh-frozen post-mortem human caudate nucleus and putamen, labeled with cell type-specific probes and separated by FACS as described by Matlik et al. 2023.

value: Anterior caudate

value: Striatonigral medium spiny neuron

tag: donor

tag: age

tag: Sex

value: Male

tag: pmi (hrs)

tag: disease

value: CTRL


title: C31.RTX.T15.Cold3

source_name: RTX430, Cold stress, ZT15, replicate 3


title: Panc02, parental, rep1


title: 3453_Striatopallidal-medium-spiny-neuron_BEB19051_CTRL

description:
3453
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

source_name: Posterior caudate

value: Posterior caudate

value: Striatopallidal medium spiny neuron


title: Col6a2_25W_M_Rep4

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

data_processing:
Quality inspection of the reads was accomplished using the FastQC tool (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC tool (https://multiqc.info/) which showed a high quality of sequencing indicated by a GC content peak around 50%, an ambiguity base content of nearly 0%, and an average PHRED score near 40 for all libraries.
The Trimmomatic tool (http://www.usadellab.org/cms/?page=trimmomatic) was used (HEADCROP:13, TRAILING:20, SLIDINGWINDOW:4:20, MINLEN:15) to clip Illumina adaptors and trim/remove low quality nucleotides.
Surviving Intact read pairs post trimming were reference mapped to the Mouse genome (http://daehwankimlab.github.io/hisat2/download/#m-musculus) using HISAT2 (http://daehwankimlab.github.io/hisat2/) under specific conditions (-rna-strandness RF, --fr, --no-discordant, --no-mixed).
The returned alignment files were sorted and indexed using samtools (http://www.htslib.org/). Enumeration per gene (Mus_musculus.GRCm38.92.gtf) for each alignment file was accomplished using Stringtie (http://ccb.jhu.edu/software/stringtie/), producing coverage estimation per gene and expression per gene in in both Fragments per kilo base per million mapped reads (FPKM) and Transcript Per Million (TPM) units.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

molecule: total RNA

source_name: quadriceps muscle

growth_protocol: The mouse strain used for this research project, C57BL/6N-Col6a2tm1(KOMP)Vlcg/MbpMmucd, RRID:MMRRC_047168-UCD, was obtained from the Mutant Mouse Resource and Research Center (MMRRC) at University of California at Davis, an NIH-funded strain repository, and was donated to the MMRRC by The KOMP Repository, University of California, Davis, originating from Kent Lloyd, UC Davis Mouse Biology Program.

extract_protocol:
The RNA was isolated and purified as previously described (PMID: 20516177). RNA quality was analyzed using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Samples that had a RIN/RINe ≥ 8 were used for RNA-Seq library construction.
Libraries were prepared according to the manufactirer's protocol for the Illumina TruSeq RNA Sample Prep Kit.  Starting amount of total RNA used was 150ng. The cDNA produced was fragmented using a Covaris E210 and amplified using 12-15 cycles.
Paired-end sequencing of the libraries for 150bp per read was performed using the Illumina MiSeq platform with a target depth of 100 million reads per library. Sequences returned were processed via RTA and deplexed using CASAVA (http://www.illumina.com/software).

treatment_protocol:
The Col6a2 tm1(KOMP)Vlcg mice were backcrossed 5 generations onto a C57BL/6J background, and maintained at the intramural NIH Bldg 35 vivarium. Regular light–dark cycles (12 hour) were maintained. The room temperature was maintained at 20–25°C, with a relative humidity of 40–65%. Untreated drinking water and chow was provided ad libitum for the duration of the study. Heterozygous (Col6a2+/-) breeders were used to generate wildtype (WT) controls, Col6a2+/- controls/breeders, and homozygous Col6a2 tm1(KOMP)Vlcg (Col6a2 -/-) transgenic animals.
10 μm cryosections of quadriceps muscle snap frozen in liquid nitrogen were collected in QIAzole (Qiagen Cat#79306). Four male and four female WT and Col6a2-/- mice were included at two different age groups (5 weeks and 25 weeks old).

value: quadriceps muscle

tag: gender

value: 25 weeks


title: Col6a2_25W_M_Rep3


title: Col6a2_25W_M_Rep2


title: 3446_Striatonigral-medium-spiny-neuron_BEB18117_CTRL

description:
3446
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)


title: Lung, D21, rep 1

city: Palo Alto

first: Audrey

last: Lee

address: 240 Pasteur Dr. 1500 BMI

institute: Stanford University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
scRNA-seq data obtained on the 10x genomics platform was pre-processed using Cell Ranger software (10x Genomics)
Assembly: mm10
Supplementary files format and content: Tab-separated value files
Supplementary files format and content: Matrix files

source_name: Lungs

extract_protocol:
Murine lungs were llavaged with digestion medium containing RPMI 1640, elastase (Worthington), dispase II (Sigma) and DNase I (Sigma). Lungs were then harvested and incubated in the digestion medium for 45 min at 37°C. After incubation, lungs were cut into small pieces using scissors and incubated with RPMI 1640 containing liberase (Sigma) and DNase I for 30 min at 37°C. Dissociated cells were then passed through a 70mm strainer and RBCs lysed using ACK lysis buffer.
Cells were partitioned into Gel Beads-in-emulsion (GEMs) using the 10x Chromium 3′ V3 chemistry system (10x Genomics). The released RNA was reverse transcribed in the C1000 touch PCR instrument (Bio-Rad). Barcoded cDNA was extracted from the GEMs by post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was subjected to 0.6x SPRI beads cleanup (Beckman, B23318). 25% of the amplified cDNA was used to perform enzymatic fragmentation, end-repair, A tailing, adapter ligation, and 10X specific sample indexing as per manufacturer’s protocol.

value: Lungs

value: Immune and epithelial cells

value: BCG-vaccinated


title: Lung, D0, rep 1

description: 10x Genomics

value: Control


title: 3452_Striatonigral-medium-spiny-neuron_BEB19051_CTRL

description:
3452
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)


title: C27.RTX.T9.Cold3

source_name: RTX430, Cold stress, ZT9, replicate 3

value: Cold stress


title: 3445_Striatopallidal-medium-spiny-neuron_BEB18116_CTRL

description:
3445
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

source_name: Posterior putamen

value: Posterior putamen


title: Col6a2_25W_M_Rep1


title: C23.RTX.T6.Cold3

source_name: RTX430, Cold stress, ZT6, replicate 3

value: leaves


title: 3444_Striatonigral-medium-spiny-neuron_BEB18116_CTRL

description:
3444
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)


title: C22.RTX.T6.Cold2

source_name: RTX430, Cold stress, ZT6, replicate 2


title: 3443_Striatopallidal-medium-spiny-neuron_BEB18117_CTRL

description:
3443
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)


title: Col6a2_25W_F_Rep3

value: Female


title: CD4+ T lymphocytes, zr2533_4

city: Blacksburg

first: Zhuang

last: Wang

state: VA

address: 1739 Autumn Splendor Way

institute: VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY

library_source: genomic

data_processing:
FastQC and Cutadapt for raw sequence quality control and processing
Bismark for alignment
Differential methylation sites and regions analysis performed with Bioconductor packages in R
Assembly: GRCm39
Supplementary files format and content: MRLvsMRL-lpr_DMR_anno.xlsx (meanMethy1 is the average value of the control group (MRL-28, MRL-29, MRL-30) and meanMethy2 is the average value of the experiment group (lpr-8, lpr-24, lpr-25))  (Compared to "sheet1", the locations of each DMR at different genomic features are annotated in "sheet1(2)".)
Supplementary files format and content: MRLvsMRL-lpr_DMS_anno.xlsx (the results are used to generate figures for manuscript)
Supplementary files format and content: EGR2_annotated_DMR.xlsx
Supplementary files format and content: EGR2_annotated_DMS.xlsx

molecule: genomic DNA

source_name: CD4+ T lymphocytes

extract_protocol:
DNeasy Blood and Tissue Kit (Qiagen)
Methyl-MiniSeq Library Construction by Zumo Research DNA Clean&Concentrator-5 (Cat#: D4003)
Methyl_MiniSeq

value: CD4+ T lymphocytes

value: MRL Faslpr/lpr


title: C19.RTX.T1.Cold3

source_name: RTX430, Cold stress, ZT1, replicate 3


title: Col6a2_25W_F_Rep2


title: 3442_Striatonigral-medium-spiny-neuron_BEB18117_CTRL

description:
3442
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

value: Striatonigral medium spiny neuron


title: 3447_Striatopallidal-medium-spiny-neuron_BEB18117_CTRL

description:
3447
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

value: Anterior caudate

value: Male


title: C18.RTX.T1.Cold2

source_name: RTX430, Cold stress, ZT1, replicate 2


title: CD4+ T lymphocytes, zr2533_2

value: MRL WT


title: 3441_Astrocyte_HCT-17-HFG_CTRL

description:
3441
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

value: Astrocyte

value: CTRL


title: CD4+ T lymphocytes, zr2533_3


title: Col6a2_25W_F_Rep1

value: quadriceps muscle

value: 25 weeks


title: C28.RTX.T9.Cold4

source_name: RTX430, Cold stress, ZT9, replicate 4


title: C14.RTX.T15.Cont2

source_name: RTX430, Control, ZT15, replicate 2


title: C15.RTX.T15.Cont3

source_name: RTX430, Control, ZT15, replicate 3


title: Col6a2_5W_M_Rep4

value: 5 weeks


title: Col6a2_5W_M_Rep3


title: CD4+ T lymphocytes, zr2533_6


title: 3440_Microglia_HCT-17-HFG_CTRL

description:
3440
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)

value: Microglia


title: CD4+ T lymphocytes, zr2533_5


title: HS_ZM323_VEGF [S38 ]

city: Los Angeles

first: Karolina Elzbieta

middle: Kaczor

last: Urbanowcz

address: 10833 Le Conte Avenue

institute: UCLA

data_processing:
Data mapping using STAR version 2.3.1
Assembly: hg38
Supplementary files format and content: raw counts with merged technical replicates

source_name: HUVEC

growth_protocol: HUVECs cultured in MCDB-131 (VEC Technologies) with 10% FBS in a humidified incubator at 37°C with 5% CO2 and atmospheric oxygen.

extract_protocol:
Total RNA was extracted and purified using RNeasy mini kit (Qiagen) according to manufacturer’s instructions.
RNA libraries were prepared using the Illumina TruSeq Total RNA library prep kit according to manufacturer’s instructions.
Following barcoding, 18 samples per lane were sequenced on a HiSeq3000 using 50 bp single-end protocol.

treatment_protocol: After washing cells once with serum-free media cells were serum starved overnight followed by addition of DMSO or ZM323 (Tocris) directly to media incubated for 1h followed by application of vehicle or VEGF at a final concentration of 100 ng/mL for 1h.

value: HUVEC

value: endothelial cells

value: donor 3

value: VEGF


title: Col6a2_5W_M_Rep2


title: CD4+ T lymphocytes, zr2533_1


title: HS_ZM323_VEGF [S37 ]


title: Col6a2_25W_F_Rep4

value: Female


title: 3374_Striatopallidal-medium-spiny-neuron_BEB19051_CTRL

description:
3374
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

value: Posterior putamen

value: Striatopallidal medium spiny neuron


title: C11.RTX.T9.Cont3

source_name: RTX430, Control, ZT9, replicate 3

value: Cold stress

value: leaves

value: Control


title: C10.RTX.T9.Cont2

source_name: RTX430, Control, ZT9, replicate 2


title: Col6a2_5W_M_Rep1

value: Male


title: 3373_Striatonigral-medium-spiny-neuron_BEB19051_CTRL

description:
3373
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

value: Striatonigral medium spiny neuron


title: HS_ZM323_CTRL [S35 ]

value: vehicle


title: HS_ZM323_CTRL [S36 ]


title: C7.RTX.T6.Cont3

source_name: RTX430, Control, ZT6, replicate 3


title: C6.RTX.T6.Cont2

source_name: RTX430, Control, ZT6, replicate 2


title: 3372_Striatopallidal-medium-spiny-neuron_BEB19051_CTRL

description:
3372
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

source_name: Anterior putamen

value: Anterior putamen

value: CTRL


title: 3371_Striatonigral-medium-spiny-neuron_BEB19051_CTRL

description:
3371
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)


title: 3439_Oligodendrocyte_BEB19025_CTRL

description:
3439
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)

value: Oligodendrocyte


title: HS_DMSO_VEGF [S34 ]

value: DMSO


title: HS_DMSO_CTRL [S32 ]

value: HUVEC


title: GH_ZM323_VEGF [S54 ]

value: endothelial cells

value: donor 2


title: C2.RTX.T1.Cont2

source_name: RTX430, Control, ZT1, replicate 2


title: 3370_Striatopallidal-medium-spiny-neuron_BEB19025_CTRL

description:
3370
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

source_name: Anterior caudate

value: Anterior caudate


title: WT_25W_M_Rep3

source_name: quadriceps muscle

value: quadriceps muscle

value: WT

value: 25 weeks


title: 3369_Striatonigral-medium-spiny-neuron_BEB19025_CTRL

description:
3369
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)


title: 3368_Striatopallidal-medium-spiny-neuron_HCT-17-HFG_CTRL

description:
3368
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

value: Striatopallidal medium spiny neuron


title: Col6a2_5W_F_Rep2

value: Female

value: 5 weeks


title: GH_ZM323_VEGF [S53 ]

value: VEGF


title: WT_25W_M_Rep4

value: Male


title: Col6a2_5W_F_Rep1


title: H62.Macia.T15.H2

source_name: Macia, Heat stress, ZT15, replicate 2

value: Heat stress

value: leaves

value: Macia


title: WT_25W_M_Rep2


title: HS_DMSO_CTRL [S31 ]

value: donor 3

value: vehicle


title: HS_DMSO_VEGF [S33 ]

value: HUVEC

value: DMSO


title: C3.RTX.T1.Cont3

source_name: RTX430, Control, ZT1, replicate 3

value: Cold stress

value: Control


title: 3367_Striatonigral-medium-spiny-neuron_HCT-17-HFG_CTRL

description:
3367
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

value: Anterior putamen

value: Striatonigral medium spiny neuron

value: CTRL


title: WT_25W_M_Rep1

value: quadriceps muscle

value: WT

value: 25 weeks


title: H54.RTX.T15.H2

source_name: RTX430, Heat stress, ZT15, replicate 2


title: GH_ZM323_CTRL [S52 ]

value: endothelial cells

value: donor 2


title: H57.Macia.T15.C1

source_name: Macia, Control, ZT15, replicate 1

value: Heat stress


title: Col6a2_5W_F_Rep3

value: Female

value: 5 weeks


title: Col6a2_5W_F_Rep4


title: 3366_Striatopallidal-medium-spiny-neuron_BEB18135_CTRL

description:
3366
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

value: Striatopallidal medium spiny neuron

value: Male


title: WT_25W_F_Rep4


title: 3365_Striatonigral-medium-spiny-neuron_BEB18135_CTRL

description:
3365
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)


title: 3364_Striatopallidal-medium-spiny-neuron_BEB19025_CTRL

description:
3364
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

source_name: Posterior putamen

value: Posterior putamen


title: H61.Macia.T15.H1

source_name: Macia, Heat stress, ZT15, replicate 1

value: leaves

value: Macia


title: H58.Macia.T15.C2

source_name: Macia, Control, ZT15, replicate 2

value: Control


title: H53.RTX.T15.H1

source_name: RTX430, Heat stress, ZT15, replicate 1


title: GH_DMSO_VEGF [S50 ]

source_name: HUVEC

value: HUVEC

value: DMSO

value: VEGF


title: 3363_Striatonigral-medium-spiny-neuron_BEB19025_CTRL

description:
3363
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

value: Striatonigral medium spiny neuron

value: CTRL


title: H50.RTX.T15.C2

source_name: RTX430, Control, ZT15, replicate 2


title: H46.Macia.T9.H2

source_name: Macia, Heat stress, ZT9, replicate 2


title: GH_DMSO_CTRL [S47 ]

value: vehicle


title: GH_ZM323_CTRL [S51 ]

value: endothelial cells


title: 3360_Striatopallidal-medium-spiny-neuron_HCT-17-HFG_CTRL

description:
3360
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)


title: GH_DMSO_CTRL [S48 ]

value: donor 2


title: WT_25W_F_Rep3

value: quadriceps muscle

value: WT

value: 25 weeks


title: WT_25W_F_Rep1

value: Female


title: 3362_Striatopallidal-medium-spiny-neuron_BEB18135_CTRL

description:
3362
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

value: Anterior caudate

value: Striatopallidal medium spiny neuron

value: Male


title: H49.RTX.T15.C1

source_name: RTX430, Control, ZT15, replicate 1

value: Heat stress

value: leaves


title: ER_ZM323_VEGF [S46 ]

value: HUVEC

value: donor 1


title: 3361_Striatonigral-medium-spiny-neuron_BEB18135_CTRL

description:
3361
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)


title: GH_DMSO_VEGF [S49 ]

value: DMSO

value: VEGF


title: WT_5W_M_Rep3

value: 5 weeks


title: 3358_Striatopallidal-medium-spiny-neuron_HCT-17-HFG_CTRL

description:
3358
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

value: CTRL


title: WT_5W_M_Rep2


title: H45.Macia.T9.H1

source_name: Macia, Heat stress, ZT9, replicate 1

value: Macia


title: WT_5W_M_Rep1


title: 3357_Striatonigral-medium-spiny-neuron_HCT-17-HFG_CTRL

description:
3357
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

value: Striatonigral medium spiny neuron


title: ER_ZM323_CTRL [S44 ]

value: endothelial cells

value: vehicle


title: H38.RTX.T9.H2

source_name: RTX430, Heat stress, ZT9, replicate 2


title: WT_25W_F_Rep2

value: quadriceps muscle

value: WT

value: 25 weeks


title: WT_5W_M_Rep4


title: HeLa-4G8-IgG

city: Shenzhen

first: Zengqi

last: Wen

state: Guangdong

address: No 66, Gongchang Road, Guangming District

department: School of Medicine

country: China

institute: Sun Yat-sen University

data_processing:
Paired-end fastq reads were trimmed for adaptor sequence and filtered for low quality bases using cutadapt (V1.18) (Martin 2011) with parameters: -e 0.1 -n 2 -m 35 -q 30 –pairfilter= any, and parameter: -a GTCTCTTATACACATCT -A GTCTCTTATACACATCT for CUT&Tag or parameter: -a GAAGAGCACACGTCTGAACTCCAGTCAC -A GAAGAGCGTCGTGTAGGGAAAGAGTGT for BrdU-IP-seq and SNS-seq. Then the trimmed reads were mapped to a merged reference of human (hg38) and mouse (mm9) using Bowtie2 (V2.3.5.1) (Langmead, Trapnell et al. 2009) with parameters: -I 10 -X 1000 -3 5 --local --no-mixed --no-discordant --no-unal. Duplicate reads were marked by picard (V2.26.10) MarkDuplicates (http://broadinstitute.github.io/picard/). Duplicated reads and low mapping quality reads were filtered out with samtools (V1.14) (Li, Handsaker et al. 2009) with parameters: -f 2 -F 1024 -q 10. Bigwig files normalized by “RPM” were generated by bamCoverage from deeptools (V3.5.1) (Ramírez, Ryan et al. 2016) with parameters: --normalizeUsing CPM --exactScaling --extendReads --samFlagInclude 64. Bigwig files normalized by “RRPM” were generated by bamCoverage from deeptools (V3.5.1) with parameters: --normalizeUsing CPM --exactScaling --extendReads --samFlagInclude 64 –scaleFactor N. The scale factor N is calculated by dividing 1,000,000 by the number of spike-in reads. H4K20me2 peaks are called using MACS2 (V2.2.7.1) (Zhang, Liu et al. 2008) with parameters as: -f BAMPE -g hs -q 0.05 --broad --fix-bimodal --nolambda. Peaks overlapping the blacklist of human genome (hg38-blacklist.v2.bed)(Amemiya, Kundaje et al. 2019) were filtered out with Bedtools (V2.30.0) (Quinlan and Hall 2010). Heatmap matrixes were generate by computeMatrix from deeptools (V3.5.1) with “reference-point” mode for H4K20me2, and “scale-regions” mode for BrdU. Heatmaps were plotted with plotHeatmap from deeptools (V3.5.1). getDifferentialPeaks (parameter: -F 2 -P 0.01) from HOMER (V4.11) (Heinz, Benner et al. 2010) was used to find the H4K20me2 peaks with significantly decreased signal after H2A.Z knockdown or SUV420H1 mutation.
Assembly: hg19, mm10
Supplementary files format and content: bigwig

source_name: Uterus; Cervix

extract_protocol:
SNS-seq and BrdU-seq libraries were prepared as described in Haizhen Long, et al.  Nature 577, 576–581 (2020) (PMID: 31875854). CUT&Tag libraries were prepared as Kaya-Okur HS, et. al. Nature Communications 2019  (PMID:31036827).
SNS-seq, BrdU-seq, CUT&Tag

value: Uterus; Cervix

value: HeLa

value: epithelial cell

value: SUV420H1 K219A/R220A mutation


title: H37.RTX.T9.H1

source_name: RTX430, Heat stress, ZT9, replicate 1

value: Heat stress

value: leaves


title: ER_ZM323_CTRL [S43 ]

value: HUVEC

value: donor 1


title: H42.Macia.T9.C2

source_name: Macia, Control, ZT9, replicate 2

value: Control


title: WT_5W_F_Rep4

source_name: quadriceps muscle

value: Female

value: 5 weeks


title: 3359_Striatonigral-medium-spiny-neuron_HCT-17-HFG_CTRL

description:
3359
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

value: Posterior putamen

value: Striatonigral medium spiny neuron

value: Male

value: CTRL


title: ER_ZM323_VEGF [S45 ]

value: endothelial cells

value: VEGF


title: ER_DMSO_VEGF [S42 ]

value: DMSO


title: HeLa-4G8-H4K20me2-rep2

value: Uterus; Cervix

value: HeLa


title: HeLa-4G11-IgG

value: epithelial cell

value: SUV420H1 K219A/R220A mutation


title: WT_5W_F_Rep3

value: quadriceps muscle

value: WT


title: H41.Macia.T9.C1

source_name: Macia, Control, ZT9, replicate 1

value: Heat stress

value: leaves

value: Macia


title: HeLa-4G8-H4K20me2-rep1


title: ER_DMSO_CTRL [S40 ]

value: HUVEC

value: donor 1

value: vehicle


title: ER_DMSO_VEGF [S41 ]


title: H34.RTX.T9.C2

source_name: RTX430, Control, ZT9, replicate 2

value: Control


title: H30.Macia.T6.H2

source_name: Macia, Heat stress, ZT6, replicate 2


title: HeLa-4G11-H4K20me2-rep2


title: H33.RTX.T9.C1

source_name: RTX430, Control, ZT9, replicate 1


title: H29.Macia.T6.H1

source_name: Macia, Heat stress, ZT6, replicate 1


title: TmlLs-3

city: Xining

first: Delin

last: Qi

address: No. 251, Ningda Road

institute: Qinghai university

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2 2) Disables the coverage based search for junctions 3) The distance between mate-pair reads is 50bp 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: Oncorhynchus mykiss Omyk_1.1
Supplementary files format and content: tab-delimited text files include FPKM and TPM values for each Sample

organism: Oncorhynchus mykiss

source_name: liver tissues

extract_protocol:
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver tissues

value: hypoxia stress

tag: phenotype

value: wild-type


title: ER_DMSO_CTRL [S39 ]

value: endothelial cells

value: DMSO


title: WT_5W_F_Rep1

value: Female

value: 5 weeks


title: H26.Macia.T6.C2

source_name: Macia, Control, ZT6, replicate 2


title: Mmusculus_MesLN_MAIT

city: Paris

first: Martin

last: MESTDAGH

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mesenteric LNs

extract_protocol:
Mesenteric lymph nodes were mashed over 40 mm nylon mesh to create single cell suspensions. Ileum and colon samples were flushed with PBS, opened longitudinally and cut into approximately 0.5 cm pieces. Dissociation of epithelial cells was performed by incubation with constant stirring in HBSS w/o Ca/Mg (Life Technologies) containing 5 mM EDTA (Thermo Fisher Scientific), 1 mM DTT (Euromedex), and 5% FCS twice for 20 min at 37 °C. After each step, samples were vortexed and the epithelial fraction discarded. Tissue fragments were then washed in HBSS (Thermo Fisher Scientific) and enzymatic digestion was performed in CO2-independent medium (Life Technologies) containing collagenase D (1 mg/ml; Roche), liberase TM (0.17 U/ml; Roche) and DNase I (100 µg/ml; Roche) on a shaker for 30 min at 37 °C. Colon fragments were then dissociated with a gentleMACS dissociator according to the manufacturer’s instructions (Miltenyi). Lymphocytes were collected at the interface of a 40%/80% Percoll gradient (GE Healthcare).  Cells from mesenteric lymph nodes, ileum and colon were stained for 30 min at room temperature with PE-labeled mouse MR1:5-OP-RU tetramer, then washed with FACS buffer and stained for 30 min at 4°C with the following antibodies: Anti-TCRb PECy5 (clone H57-597, BD 553173), anti-CD11c AF700 (clone N418, Biolegend 117320), anti-CD19 AF700 (clone 6D5, Biolegend 115528), anti-B220 AF700 (clone RA3-6B2, Invitrogen 56-0452-82), anti-CD44 APC-Cy7 (clone IM7, Biolegend 103028). Cells were then washed with FACS buffer and stained with DAPI.  DAPI- Tetramer+ TCRb+ CD11c- B220- CD19- cells were flow-sorted (Aria III, BD) into PBS supplemented with 0.35% BSA (Sigma). Sorted cells were centrifuged, counted and 5,000 – 10,000 cells were loaded onto the Chromium 3’ chip. Reverse transcription, library preparation and sequencing were performed according to manufacturer’s recommendations (10x Genomics).
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: MAIT

value: mesenteric LNs

tag: condition

value: Steady State

tag: strain


title: Mmusculus_Ileum_MAIT

description: 10x Genomics

source_name: Ileum

value: Ileum


title: HeLa-4G11-H4K20me2-rep1

value: Uterus; Cervix

value: HeLa

value: epithelial cell

value: SUV420H1 K219A/R220A mutation


title: Mmusculus_Colon_MAIT

description: 10x Genomics

source_name: Colon

extract_protocol:
Mesenteric lymph nodes were mashed over 40 mm nylon mesh to create single cell suspensions. Ileum and colon samples were flushed with PBS, opened longitudinally and cut into approximately 0.5 cm pieces. Dissociation of epithelial cells was performed by incubation with constant stirring in HBSS w/o Ca/Mg (Life Technologies) containing 5 mM EDTA (Thermo Fisher Scientific), 1 mM DTT (Euromedex), and 5% FCS twice for 20 min at 37 °C. After each step, samples were vortexed and the epithelial fraction discarded. Tissue fragments were then washed in HBSS (Thermo Fisher Scientific) and enzymatic digestion was performed in CO2-independent medium (Life Technologies) containing collagenase D (1 mg/ml; Roche), liberase TM (0.17 U/ml; Roche) and DNase I (100 µg/ml; Roche) on a shaker for 30 min at 37 °C. Colon fragments were then dissociated with a gentleMACS dissociator according to the manufacturer’s instructions (Miltenyi). Lymphocytes were collected at the interface of a 40%/80% Percoll gradient (GE Healthcare).   Cells from mesenteric lymph nodes, ileum and colon were stained for 30 min at room temperature with PE-labeled mouse MR1:5-OP-RU tetramer, then washed with FACS buffer and stained for 30 min at 4°C with the following antibodies: Anti-TCRb PECy5 (clone H57-597, BD 553173), anti-CD11c AF700 (clone N418, Biolegend 117320), anti-CD19 AF700 (clone 6D5, Biolegend 115528), anti-B220 AF700 (clone RA3-6B2, Invitrogen 56-0452-82), anti-CD44 APC-Cy7 (clone IM7, Biolegend 103028). Cells were then washed with FACS buffer and stained with DAPI.    DAPI- Tetramer+ TCRb+ CD11c- B220- CD19- cells were flow-sorted (Aria III, BD) into PBS supplemented with 0.35% BSA (Sigma). Sorted cells were centrifuged, counted and 5,000 – 10,000 cells were loaded onto the Chromium 3’ chip. Reverse transcription, library preparation and sequencing were performed according to manufacturer’s recommendations (10x Genomics).
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Colon


title: TmlLs-2


title: WT_5W_F_Rep2

value: quadriceps muscle

value: WT


title: ChIP_KDM1a_2

data_processing:
For RNA, adapters were trimmed using cutadapt v1.18 selecting reads longer than 25 bp.  HISAT2 (Kim et al., 2015) (v2.1.0) was used for reads alignment to the mouse genome (GRCm38.89, mm10) and reads with mapq > 30 and that mapped to nuclear chromosomes were quantified using HTSeq v0.11.1 (Anders et al., 2015). Data processing was performed with custom R scripts (v3.5.1, 2018), Samtools v1.9 (Li et al., 2009), Bedtools v2.27.1 (Quinlan and Hall, 2010), and DeepTools v3.5.0 (Ramírez et al., 2016). Whole genome alignments were normalized to 10× RPM (read per 10 million sequenced reads).
For ChIPs, Adapters were trimmed using TrimGalore v 0.6.4_dev (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), and the reads obtained were mapped to the mouse genome (mm10) with Bowtie2 (v2.3.4.3) (Langmead and Salzberg, 2012). Only those reads with a mapq > 30 were selected. Data was processed using Samtools v1.10 (Li et al., 2009), Deeptools v 3.5.0 (Ramírez et al., 2016), and Bedtools v2.25.0 (Quinlan and Hall, 2010). For BigWigs, ChIP-seq reads were normalized by reads per genomic content with Deeptools (Ramírez et al., 2016).
ChIA-PET, was processed by the ChIA-PIPE pipeline (Lee et al., 2020) using mm10 as a reference genome and default parameters. The resulting *hic file for 2D contact maps and *bigwig file for protein binding coverage were used for visualizing on Juicebox (Durand et al., 2016) Within ChIA-PIPE, peaks were called via MACS2 without input control and only those with the maximum coverage greater than 50 (which is twice the median of all peaks) were kept by pybedgraph (Zhang et al., 2020), resulting in 34,885 confident peaks. Using these peaks, the loops reported in *bedpe format with 7th column denoting PET counts are further filtered to have PET count greater than or equal to 3 and to have both left and right anchors to overlap with at least one peak.
For 4C-seq analysis all samples were trimmed to 75 bp. The wig and peaks were calculated using pipe4C and peakC as mentioned in (Krijger et al., 2020).
Assembly: mm10
Supplementary files format and content: For RNA tab-delimited text file contains raw counts data for each sample, BigWig files
Supplementary files format and content: BigWig files for ChIP-seq data
Supplementary files format and content: BigWig, Bedgraph and hic files for ChIAPet data

source_name: Hippocampus

value: Hippocampus

value: Male


title: TmlLs-1

value: liver tissues

value: hypoxia stress

value: wild-type


title: HeLa-WT-H4K20me2-rep2

value: wild type


title: H22.RTX.T6.H2

source_name: RTX430, Heat stress, ZT6, replicate 2

tag: experiment

value: Heat stress

value: leaves


title: H25.Macia.T6.C1

source_name: Macia, Control, ZT6, replicate 1

tag: tissue

value: Macia

value: Control


title: HeLa-WT-H4K20me2-rep1

source_name: Uterus; Cervix

value: Uterus; Cervix

tag: genotype


title: H21.RTX.T6.H1

source_name: RTX430, Heat stress, ZT6, replicate 1

tag: treatment


title: ChIP_KDM1a


title: H18.RTX.T6.C2

source_name: RTX430, Control, ZT6, replicate 2

tag: time of_day


title: HeLa-4G8-BrdU-IP-rep1

value: HeLa


title: H17.RTX.T6.C1

source_name: RTX430, Control, ZT6, replicate 1

tag: replicate


title: ClLs-1

value: control


title: HeLa-WT-IgG

tag: cell line

value: epithelial cell


title: ChIP_H3k27ac_ifKO, rep2

value: ifKO

value: Tamoxifen


title: HeLa-4G8-BrdU-Input-rep2

tag: cell type

value: SUV420H1 K219A/R220A mutation


title: PC12 cells, 200 μM Sal, 24h, rep3

city: Beijing

first: Xuechai

last: Chen

address: 100 Ping Le Yuan, Chaoyang District

institute: Beijing University of Technology

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (RN5) with hisat2 software (v2.0.4).
Then, HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization, then differentially expressed mRNAs were identified by p-value and fold change.
GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Assembly: RN5
Supplementary files format and content: excel file includes raw counts for each Sample
Supplementary files format and content: excel file includes Normalized counts for each Sample

organism: Rattus norvegicus

extract_protocol:
Total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions.
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions.

value: WT

value: 200 μM Sal, 24h


title: H14.Macia.T1.H2

source_name: Macia, Heat stress, ZT1, replicate 2


title: ChIP_H3k27ac_ifKO, rep1

value: Hippocampus

value: Male


title: HeLa-4G8-BrdU-IP-rep2


title: HeLa-4G8-BrdU-Input-rep1


title: H13.Macia.T1.H1

source_name: Macia, Heat stress, ZT1, replicate 1


title: ChIP_H3k27ac_ifKO, rep3


title: PC12 cells, 200 μM Sal, 24h, rep2


title: ChIP_H3k27ac_WT, rep2


title: HeLa-4G11-BrdU-IP-rep2


title: PC12 cells, 200 μM Sal, 24h, rep1


title: H10.Macia.T1.C2

source_name: Macia, Control, ZT1, replicate 2


title: ClLs-2

value: liver tissues

value: wild-type


title: PC12 cells, ctrl, 24h, rep3


title: HeLa-4G11-BrdU-IP-rep1


title: ClLs-3


title: ChIP_H3k27ac_WT, rep1


title: H9.Macia.T1.C1

source_name: Macia, Control, ZT1, replicate 1

value: Heat stress


title: PC12 cells, ctrl, 24h, rep2


title: H6.RTX.T1.H2

source_name: RTX430, Heat stress, ZT2, replicate 2

value: leaves


title: ChIP_H3k27me3_ifKO, rep2

description: ifKOLSD1_H3K27me3.mapq30.bam.SCALESIZEFACTORS.bw


title: PC12 cells, ctrl, 24h, rep1


title: H5.RTX.T1.H1

source_name: RTX430, Heat stress, ZT1, replicate 1


title: ChIP_H3k27ac_WT, rep3


title: ChIP_H3k27me3_WT, rep2

description: WTLSD1_H3K27me3.mapq30.bam.SCALESIZEFACTORS.bw


title: HeLa-WT-BrdU-IP-rep1

value: wild type


title: H2.RTX.T1.C2

source_name: RTX430, Control, ZT1, replicate 2

value: Control


title: H1.RTX.T1.C1

source_name: RTX430, Control, ZT1, replicate 1


title: RNA-Seq of Triticum aestivum :His control_2

city: Hefei

first: zhao

middle: xiao

last: zhen

address: Anhui Agricultural University, 130 Changjiangxilu, Shushan District, Hefei, Anhui Province, China

institute: Anhui Agricultural University

data_processing:
For RNA-seq analysis, all of the raw reads were filtered by Fastp (version 0.18.0) software to remove adapters and low quality reads (quality score≤20).
Clean reads were aligned to the Fg reference genome using Hisat2 (v1.3.3).
Expression levels for each sample were quantified to TPM
Assembly: reference genome of F. graminearum strain PH-1 GCA_900044135.1
Supplementary files format and content: Genes displaying log2 [fold change] ≥ 1.5 and an adjusted (false discovery rate) p value < 0.05 were classified as differentially expressed genes (DEGs) by using DESeq2 package.

organism: Triticum aestivum

source_name: seedling leaves

extract_protocol:
total RNA extraction using TRIZOL reagent following the manufacturer’s instructions.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT)  beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic  Kit (Epicentre, Madison, WI, USA). Then the enriched mRNA was fragmented into short  fragments using fragmentation buffer and reverse transcripted into cDNA with random  primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and  buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen,  Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing  adapters.

value: seedling leaves

tag: time

value: 24 hour post-inoculation


title: HeLa-WT-BrdU-IP-rep2

value: Uterus; Cervix

value: HeLa


title: RNA-Seq of Triticum aestivum :His control_3


title: RNA-Seq of Triticum aestivum :His control_1


title: C61.SC224.T15.Cold1

source_name: SC224, Cold stress, ZT15, replicate 1

value: Cold stress


title: ChIP_H3k27me3_WT, rep1

source_name: Hippocampus

value: Tamoxifen


title: ChIP_H3k4me1_ifKO, rep3

value: ifKO


title: ChIP_H3k4me1_ifKO, rep2


title: HeLa-WT-BrdU-Input-rep1

value: epithelial cell


title: HeLa-4G8-SNS-rep2

value: SUV420H1 K219A/R220A mutation


title: RNA-Seq of Triticum aestivum :BCG1_3

value: WT


title: RNA-Seq of Triticum aestivum :BCG1_2


title: ChIP_H3k4me1_ifKO, rep1

value: Hippocampus

value: Male


title: C53.SC224.T6.Cold1

source_name: SC224, Cold stress, ZT6, replicate 1


title: HeLa-4G11-BrdU-Input-rep2


title: C57.SC224.T9.Cold1

source_name: SC224, Cold stress, ZT9, replicate 1


title: HeLa-4G8-SNS-rep1

source_name: Uterus; Cervix


title: ChIP_H3k27me3_ifKO, rep1


title: HeLa-4G11-BrdU-Input-rep1


title: ChIP_H3k4me1_WT, rep3


title: C49.SC224.T1.Cold1

source_name: SC224, Cold stress, ZT1, replicate 1


title: ChIP_H3k4me1_WT, rep2


title: C45.SC224.T15.Cont1

source_name: SC224, Control, ZT15, replicate 1


title: RNA-Seq of Triticum aestivum :BCG1_1


title: HeLa-4G8-RNA-SNS-rep2


title: HeLa-WT-BrdU-Input-rep2


title: ChIP_H3k4me1_WT, rep1


title: HeLa-4G11-SNS-rep2


title: HeLa-4G8-RNA-SNS-rep1


title: C37.SC224.T6.Cont1

source_name: SC224, Control, ZT6, replicate 1


title: Foxj1b Mutant R3

city: Trondheim

first: Nathalie

last: Jurisch-Yaksi

address: Erling Skjalgsons gate 1

country: Norway

institute: NTNU

data_processing:
In order to analyze the RNA-Sequencing data, the paired-end sequencing reads were aligned to the Zebrafish genome (GRCz11) using and read counts per gene were determined by using featureCounts using GTF file from Ensembl version 106.
The raw read counts were used as input for DESeq2 for Differentially expressed genes. Genes with abs(log2 fold change) > 2 and p-adj < 0.1 were assumed as significantly expressed genes.
Assembly: GRCz11/ensembl 106
Supplementary files format and content: tab-delimited raw read counts

organism: Danio rerio

source_name: whole embryo

growth_protocol: Embryonic, larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 °C, 14/10 light/dark cycle.

extract_protocol:
To isolate RNA for sequencing, 4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples, 500μL trizol was added and the euthanized larvae were homogenized through a 27-gauge needle until the mixture looked uniform. After adding another 500μL trizol, the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform, and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. After centrifugation, the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column (Qiagen) and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme (Qiagen) in RDD buffer (10μL DNase+ 70μL RDD buffer per tube) for 45mins at room temperature. After incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice, and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column, 30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA.
The library construction and sequencing was done by BGI’s DNBSEQTM Technology.

value: whole embryo

value: Foxj1b Knockout


title: C41.SC224.T9.Cont1

source_name: SC224, Control, ZT9, replicate 1

value: leaves


title: ChIP_H3k4me3_ifKO, rep3

description: S3K_merged.mapq30.bam.SCALESIZEFACTORS.bw


title: Foxj1b Control R3

value: Wild Type


title: Foxj1a Control R3


title: HeLa-4G11-SNS-rep1


title: HeLa-4G11-RNA-SNS-rep2


title: ChIP_H3k4me3_ifKO, rep1


title: C33.SC224.T1.Cont1

source_name: SC224, Control, ZT1, replicate 1

value: Control


title: Foxj1b Mutant R2


title: C29.RTX.T15.Cold1

source_name: RTX430, Cold stress, ZT15, replicate 1


title: Foxj1b Control R2


title: ChIP_H3k4me3_WT, rep2

description: S3W_merged.mapq30.bam.SCALESIZEFACTORS.bw


title: HeLa-4G11-RNA-SNS-rep1


title: C25.RTX.T9.Cold1

source_name: RTX430, Cold stress, ZT9, replicate 1


title: HeLa-WT-SNS-rep2

value: wild type


title: ChIP_H3k4me3_WT, rep1


title: Foxj1a Mutant_R2

value: Foxj1a Knockout


title: HeLa-WT-SNS-rep1

value: Uterus; Cervix


title: Foxj1a Mutant_R3


title: Foxj1a Control R2


title: C21.RTX.T6.Cold1

source_name: RTX430, Cold stress, ZT6, replicate 1


title: C17.RTX.T1.Cold1

source_name: RTX430, Cold stress, ZT1, replicate 1


title: Foxj1b Mutant R1


title: RNA_Kdm1a_ifKO, rep1

description:
KDM1a_1
raw_counts.txt
KDM1a_merge.bam.RPKM.bw


title: Foxj1b Control R1


title: RNA_Kdm1a_ifKO, rep3

description:
KDM1a_3
raw_counts.txt
KDM1a_merge.bam.RPKM.bw


title: HeLa-WT-RNA-SNS-rep1

value: HeLa


title: C9.RTX.T9.Cont1

source_name: RTX430, Control, ZT9, replicate 1

value: Cold stress


title: C13.RTX.T15.Cont1

source_name: RTX430, Control, ZT15, replicate 1


title: RNA_WT, rep3

description:
KDM1a_wt_3
raw_counts.txt
KDM1a_wt_merge.bam.RPKM.bw

value: Tamoxifen


title: HeLa-WT-RNA-SNS-rep2


title: RNA_Kdm1a_ifKO, rep2

description:
KDM1a_2
raw_counts.txt
KDM1a_merge.bam.RPKM.bw

value: ifKO


title: HeLaS3_ChIPGNL3

city: Montpellier

first: Cyril

last: Ribeyre

address: 141 rue de la cardonille

institute: CNRS

data_processing:
Sequencing data were processed and analyzed using the online Galaxy platform (https://usegalaxy.org/)
Reads were aligned on human reference genome using Bowtie2 tool with default parameters
Peaks were discovered using MACS2 callpeak tool using input as control file with a q-value<0.005
Genome_build: GRCh37/Hg19
Supplementary_files_format_and_content: bigwig
Supplementary_files_format_and_content: peaks.bed

growth_protocol: HeLa S3 are grown in DMEM supplemented with 10% fetal bovine serum and penicillin/streptomycin

extract_protocol: Cell were fixed with 1% formaldehyde and lysed with True-ChIP kit (Covaris) and sonicated with a Covaris E220evolution. After IP DNA were purified using DNA Prep Adem kit (Ademtech). 3 independent experiments were pooled prior to library construction.

value: HeLa S3

tag: chip antibody

value: GNL3 (Bethyl A300-600A)


title: Foxj1a Mutant_R1


title: RNA_WT, rep2

description:
KDM1a_wt_2
raw_counts.txt
KDM1a_wt_merge.bam.RPKM.bw

tag: Sex

value: WT


title: C5.RTX.T6.Cont1

source_name: RTX430, Control, ZT6, replicate 1


title: HeLaS3_INPUT

value: input


title: C1.RTX.T1.Cont1

source_name: RTX430, Control, ZT1, replicate 1


title: Foxj1a Control R1


title: RNA_WT, rep1

description:
KDM1a_wt_1
raw_counts.txt
KDM1a_wt_merge.bam.RPKM.bw

source_name: Hippocampus

value: Hippocampus

value: Male


title: MTA Treated, Breast Fibroblasts, rep4

status: Public on Dec 03 2023

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

data_processing:
Reads were aligned to the human reference genome (hg38) using STAR (version_2.7.5c) in two-pass mode following STAR best practices and recommendations [Dobin et al]. The quality of the data was evaluated using STAR (version 2.7.5c) [Dobin et al] and samtools (version 1.15) [Danecek et al and Bonfield et al]. PCR duplicates were removed from aligned bam files using samtools (version 1.15) [Bonfield et al]. Read counts were extracted from the aligned bam files using subread’s FeatureCounts (version 2.0.3) [Liao et al]. Normalisation of read counts for analysis was done according to EdgeR recommendations using the Ratio of the Variance method which accounts for inter-sample variance and the differential expression analysis of the normalised read counts between the sample groups was performed following best practices and recommendations of EdgeR [Robinson et al, McCarthy et al, Chen et al] and Limma [Ritchie et al] on R environment (version 3.6.0).
Assembly: hg38
Supplementary files format and content: Tab separated raw reads values

source_name: Breast

growth_protocol: Human breast fibroblasts (HBF) cells were regularly grown in Dulbecco's modified Eagle media (DMEM) with 10% fetal bovine serum (FBS) and 1% Penicillin-Streptomycin.

extract_protocol:
Using the Maxwell® RSC simplyRNA Cells Kit and the Maxwell® RSC 48 Instrument, RNA was extracted.
TruSeq Stranded mRNA Sample Preparation Guide (Part # 15031058 Rev. E), using “TruSeq® Stranded mRNA Library Prep” kit  (Illumina Inc. Cat. # 20020594) and TruSeq RNA Single Indexes (Illumina Inc. Cat. # 20020492 and 20020493)
Stranded mRNA library

treatment_protocol: 10 µm MTA for 24 hours

value: Breast

value: Human Breast Fibroblasts

value: mesenchymal cell

value: 10 µm MTA for 24 hours


title: MTA Treated, Breast Fibroblasts, rep3


title: ChIP_H3k4me3_ifKO, rep2

extract_protocol:
For RNA, total RNA was extracted from hippocampal tissue with TRI reagent (Sigma-Aldrich) as recommended by the manufacturer.  Subsequently, genomic DNA was eliminated by a treatment with DNAse I (Qiagen) for 30 min at 25ºC. Followed by precipitation with phenol-chloroform-isoamyl alcohol (Sigma-Aldrich).
ChIPs were performed as previously described in detail (Galvão-Ferreira et al., 2017) with minor modifications. Briefly, 3 μg of antibody were incubated with Dynabeads coated to Protein G (Invitrogen) in RIPA-150 buffer (50 mM Tris-HCl, 150 mM NaCl, 1 mM, EDTA, 0.1% SDS, 1% Triton X-100, and 0.1% sodium deoxycholate; pH 8) for 6-18 h at 4°C in agitation. Nuclei from hippocampal cells were extracted in a dounce homogenizer as explained for the FANS method. Samples were fixed with 1% formaldehyde (Sigma-Aldrich) for 10 min at room temperature followed by 0.1 M glycine for 5 min to stop the fixation. Nuclei were centrifuged at 1,5 G, and the pellet was resuspended in 100 μL of SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris; pH 8) prior to its sonication in a Bioruptor Pico (Diagenode) for 12 cycles of 15 s on/30 s off. After 6 min of centrifugation at 13000 rpm, the supernatant containing isolated chromatin was collected. Samples were diluted in 900 μL of ChIP Dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, 167 mM NaCl; pH 8) and incubated overnight at 4°C with the antibody-Dynabeads mix. Beads were thoroughly rinsed at 4ºC as follows: two washes in RIPA-150 buffer, three washes in RIPA-500 buffer (50mM Tris-HCl, 500 mM NaCl, 1 mM, EDTA, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate; pH 8), two washes in RIPA LiCl buffer (50 mM Tris-HCl, 1 mM EDTA, 1% NP-40, 0.7%, sodium deosycholate, 500 mM LiCl2), and two final washes in TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA; pH 8.0), five minutes each. Samples were resuspended in 200 μl Elution buffer (10 mM Tris-HCl, 5 mM EDTA, 300 mM NaCl, 0.5% SDS; pH 8) and treated with 1 μl of 10 mg/mL RNase A (Fermentas) overnight at 65°C in agitation for crosslink reversion. Samples were treated with 3 μl of 20 mg/mL Proteinase K (Thermo Scientific) for 2 hours at 55°C in agitation. Last, DNA precipitation was performed by phenol-chloroform-isoamyl alcohol (Sigma-Aldrich). For Kdm1a ChIP, some modification were applied as in (Lipinski et al., 2020). In brief, samples required a stronger fixation treatment in 1% PFA for 30 min at 37ºC. To fragment these highly fixed samples, 43 cycles of sonication (30 s On, 30 s Off) were applied in a Bioruptor Pico (Diagenode). SDS lysis buffer was modified to RIPA buffer (0.1% SDS, 1% IGEPAL, and 0.5% sodium deoxycholate).
Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) using a CTCF-specific antibody (Abclonal Cat # ab70303) was performed as described in the in situ ChIA-PET protocol (Wang et al., 2021) on approximately 10 million nuclei of hippocampal excitatory neurons sorted by FANS as described above.
4C-seq, was performed as previously described (Krijger et al., 2020) with minimal changes. Approximately 5 million hippocampal nuclei were fixed at 1 % with PFA. The restriction enzyme cutting order was Dpn II as the primary enzyme and Csp6I as the secondary enzyme. Ligated chromatin was phenol-chloroform extracted and ethanol precipitated. Reactions were then further purified with Ampure XP beads with a 0.8x ratio of bead solution to library following the manufactures instructions. Samples were then quantified with Qubit and 4C-seq libraries were sequenced using an Illumina high-throughput sequencing equip.
For RNA three mice were used per genotype (Kdm1a-ifKO and their control littermates) and Poly-A libraries were generated. For RNA and ChIPseq,  libraries were generated for each independent sample and single-end sequenced in a HiSeq 2500 apparatus from Illumina. For ChIAPet, librearies were generated and paired end and 150 pb were sequenced and emrged from Miseq, Nextseq 500/550 and Hiseq 3000/4000 aparatus.
PolyA RNAseq, ChIP-seq, 4C-seq and ChIAPet


title: Control, Breast Fibroblasts, rep3

value: Untreated


title: Control, Breast Fibroblasts, rep4


title: Control, Breast Fibroblasts, rep1


title: Control, Breast Fibroblasts, rep2


title: MTA Treated, Breast Fibroblasts, rep1


title: MTA Treated, Breast Fibroblasts, rep2


title: scRNAseq, GEX library 3

city: Seoul

first: Minji

last: Kang

address: 103 daehak-ro

department: biomedical sciences

country: South Korea

institute: Seoul National University graduate school

description: 10X Genomics

data_processing: The Cell Ranger (version 7.0.1, 10X Genomics) was utilized to demultiplex cellular barcodes

source_name: PBMC

extract_protocol:
Blood samples were collected using CPT Mononuclear Cell Preparation Tubes. Samples underwent centrifugation at 1800g for 20 min at 20 ℃.
scRNA-seq analysis were performed following the manufacturer’s guidelines (10X Genomics, Chromium Next GEM Single Cell 5’ HT Reagent Kits v2, CG000424). Gel Bead-in-emulsions (GEMs) were generated by combining PBMCs samples and Gel Beads onto Chromium Next GEM Chip N.

value: PBMC


title: scRNAseq, GEX library 1

description: 10X Genomics


title: scRNAseq, TCR library 1

description: 10X Genomics


title: spatial transcriptomics, ROI23

description: FFPE spatial transcriptome analysis

data_processing:
Fastq files were converted into DCC files by GeoMxNGSPipeline software
GeoMx DSP Analysis Suite (GEOMX-0094, v2.4.2.2) was utilized to analyze the spatial transcriptomic data. Target genes with 5% of the segment above the threshold were retained in the datasets and gene expressions with lower than the limit of quantitation were initially excluded.
Library strategy: Spatial Transcriptomics

source_name: Kidney biopsy tissue

extract_protocol: 5-um thickness kidney biopsy sections were mounted on charged slides

value: Kidney biopsy tissue


title: scRNAseq, TCR library 3

description: 10X Genomics


title: scRNAseq, Hash tag oligo library 2

description: 10X Genomics


title: scRNAseq, GEX library 2

description: 10X Genomics


title: scRNAseq, Hash tag oligo library 1

description: 10X Genomics


title: scRNAseq, Hash tag oligo library 3

description: 10X Genomics


title: spatial transcriptomics, ROI20

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics, ROI18

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics, ROI14

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics, ROI15

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics, ROI16

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics, ROI21

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics, ROI17

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics, ROI24

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics, ROI22

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics, ROI13

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics, ROI11

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics, ROI10

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics, ROI12

description: FFPE spatial transcriptome analysis


title: scRNAseq, TCR library 2

description: 10X Genomics


title: spatial transcriptomics, ROI7

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics, ROI4

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics, ROI5

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics, ROI9

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics, ROI8

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics, ROI6

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics, ROI2

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics, ROI19

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics, ROI3

description: FFPE spatial transcriptome analysis


title: C03399-plasma-EVs

city: St. John's

first: Sherri

middle: Lynn

last: Christian

state: Newfoundland and Labrador

address: 45 Arctic Avenue

department: Biochemistry

country: Canada

institute: Memorial University of Newfoundland and Labrador

description: total RNA

data_processing:
Raw reads from RNASeq were processed using Illumina's basespace sequence downloader hub (v 2.2.1.6, https://basespace.illumina.com/dashboard, accessed on April 22, 2022), which runs on the Illumina sequence hub platform 2017.
Adaptor sequences were removed and size filtered using Cutadapt (v4.0).
QC was done using FastQC (v0.11.9) and MultiQC (v1.13.10).
Alignment to a reference genome was conducted with Bowtie 2 (v2.4.5)47(49), followed by indexing using Samtools (v1.16.1)
Assembly: GrCh38
Supplementary files format and content: Count data was obtained from sorted Bam files using featurecounts ®.

source_name: Peripheral blood

extract_protocol:
RNA was isolated from EVs using miRVana
The library was prepared using 10ng RNA input or less with a library normalized for all samples and the NEXTFLEX Small RNA-Seq Kit v3 (Perkin Elmer, NOVA-5132-24) following the manufacturer’s instructions. First, QIAseq miRNA Library QC Spike-Ins (Qiagen, 331535) was diluted 1/2 and then added to the samples resulting in a final dilution of 1/42. NEXTFLEX 3’ 4N adenylated adapters were ligated to samples using a 1/4 adapter dilution and a 16°C overnight incubation. The adaptor-ligated samples were purified with NEXTFLEX cleanup beads, and excess adapters were inactivated. Next, NEXTFLEX 5’ 4N adapters were added to samples using a 1/4 adapter dilution followed by reverse transcription first strand synthesis. Reverse transcribed samples were subjected to a bead clean-up without any size selection. For the PCR enrichment, a different unique dual index (Perkin Elmer, NOVA-5132-24) was added to each sample, and 22 PCR cycles were used. Amplified libraries were purified without any size selection initially; however, due to high molecular weight templates, a final size selection was performed to obtain the final library. The quality of the library was assessed as follows; size distribution was determined with the D1000 assay on the Tapestation (Agilent, 5067-5582 and 5067-5583). The KAPA Library Quantification Kit (Roche, KK4824) was used to evaluate the concentration.
Equimolar amounts of libraries were first sequenced on the iSeq 100 instrument (Illumina) using single-end sequencing of 1X100 to assess both library and pooling qualities. Libraries’ inputs were rebalanced following Illumina’s recommendations to ensure an equal representation of each sample. Libraries were then sequenced using the Novaseq 6000 instrument (Illumina). Samples were loaded on an S1 flow cell, and a single-end sequencing of 1X101 was used.

treatment_protocol: Extracellular vesicles (EV) was isolated from plasma using synthetic peptide Vn96

tag: cohort

value: pediatric B-ALL

value: Peripheral blood

tag: biofluid

value: plasma


title: C04894-plasma-EVs

description: total RNA


title: C04353-plasma-EVs

description: total RNA


title: B-ALL-Sample-10

description: total RNA


title: C03701-plasma-EVs

description: total RNA


title: C01442-plasma-EVs

description: total RNA


title: C04395-plasma-EVs

description: total RNA


title: C01874-plasma-EVs

description: total RNA


title: HD5-C04311-Plasma-EVs

description: total RNA

value: Non-cancer donor


title: HD4-C02365-Plasma-EVs

description: total RNA


title: lung_ adenocarcinoma_matched_paired_brain_metastasis_10

type: RNA

city: Rotterdam

first: Shiva

last: Najjary

address: Dr. Molewaterplein 40

country: Netherlands

institute: Erasmus University Medical Center

hyb_protocol: For each sample, 300 ng of good quality RNA, with a maximum of 7 μL was used for hybridization with the PanCancer IO 360™  probes for 17 hours at 67⁰C, following the manufacturing procedure (NanoString Technologies Inc., Seattle, WA, USA).

scan_protocol: The nCounter FLEX platform was used and genes were counted by scanning 490 Fields-of-view (FOV).

data_processing: Data analysis was performed using the advanced analysis module (version 2.0) of nSolver software (version 4.0, NanoString Technology).

extract_protocol: Tissue sections of 5 μm were stained with hematoxylin and eosin (H&E), and examined by a pathologist. Total RNA was extracted from 10-12 sections of 10 μm thickness. RNA was stored in RNase/DNase-free water at -80°C. The nCounter® PanCancer IO 360™ Panel was used for NanoString targeted gene expression analysis. The total RNA was isolated from tumor tissue using the RNeasy® FFPE isolation kit (Qiagen, Hilden, Germany). The RNA quantity and quality were measured using the Agilent 2100 BioAnalyzer (Santa Clara, CA, USA), RNA degradation was calculated using percentages of fragments of 300-4000 nucleotides. The 300 ng of good quality RNA, with a maximum of 7 μL was used for hybridization with the panel probes for 17 hours at 65°C using a SimpliAmp Thermal Cycler (Applied Biosystems, Foster City, CA, USA).

tag: age at diagnosis

value: male

tag: histology

value: adenocaricnoma

tag: smoking status

value: smoker

tag: treatment after surgery of bm

value: Radiotherapy


title: lung_ adenocarcinoma_matched_paired_brain_metastasis_8

value: former-smoker

value: SRT


title: HD6-C04611-Plasma-EVs

description: total RNA


title: lung_ adenocarcinoma_matched_paired_brain_metastasis_9

value: female

value: unknown

value: WBRT


title: lung_ adenocarcinoma_matched_paired_brain_metastasis_7


title: lung_ adenocarcinoma_matched_paired_brain_metastasis_11

value: former-roker


title: lung_ adenocarcinoma_matched_paired_brain_metastasis_6


title: lung_ adenocarcinoma_matched_paired_brain_metastasis_5

value: Never smoking

value: No treatment


title: HD3-C04620-Plasma-EVs

description: total RNA


title: spatial transcriptomics, ROI1

description: FFPE spatial transcriptome analysis

value: Kidney biopsy tissue


title: HD1-C04665-Plasma-EVs

description: total RNA


title: RNA-seq_FH_rep3

first: ji

last: yiliang

address: No. 10 right outside the Western headlines

department: Department of Immunology

institute: Capital Medical University

data_processing:
RNA-seq : the RNA-seq  data were mapped to the Homo sapiens (hg38) using hisat2 with the default parameters.
Assembly: hg38
Supplementary files format and content: txt

source_name: Breast; Mammary gland

growth_protocol: MDA-MB-231 cells were infected with lentivirus, and stable cell lines were generated by puromycin (1 μg/mL) selection

extract_protocol:
The total RNA was extracted with TRIzol reagent (Invitrogen, 15596026) according to the manufacturer’s instruction.
The poly(A) RNA-seq libraries were prepared according to the Illumina TruSeq protocol and sequenced using Illumina Novaseq6000

value: Breast; Mammary gland

value: breast cancer

value: overexpress FH


title: lung_ adenocarcinoma_matched_paired_brain_metastasis_2


title: lung_ adenocarcinoma_matched_paired_brain_metastasis_3


title: lung_ adenocarcinoma_matched_paired_brain_metastasis_1

value: Other


title: RNA-seq_FH_rep2


title: primary_LUAD_11

source_name: primary LUAD

value: male

value: surgery & Radiochemotherapy


title: RNA-seq_FH_rep1


title: RNA-seq_FOXA1_rep3

value: overexpress FOXA1


title: RNA-seq_FOXA1_rep1


title: RNA-seq_FOXA1_rep2


title: primary_LUAD_10

value: adenocaricnoma

value: smoker

value: Surgery & Chemotherapy & Radiotherapy


title: primary_LUAD_9

value: female

value: surgery


title: lung_ adenocarcinoma_matched_paired_brain_metastasis_4

value: Radiotherapy


title: HD2-C02938-Plasma-EVs

description: total RNA

value: Non-cancer donor

value: Peripheral blood

value: plasma


title: primary_LUAD_8

value: former-smoker

value: surgery & Radiotherapy


title: RNA-seq_vector_rep2

value: Breast; Mammary gland

value: breast cancer

value: vector


title: RNA-seq_vector_rep1


title: RNA-seq_vector_rep3


title: ATAC-seq_FH_rep2

data_processing:
ATAC-seq : the ChIP-seq data were mapped to the Homo sapiens (hg38) using bowtie2 with the default parameters.
Assembly: hg38
Supplementary files format and content: WIG

extract_protocol:
50,000 viable cells were subjected to ATAC-seq protocol directly as previously described56. Briefly, the cell viabilities and counted were assessed by counter (Thermo). After a wash step in PBS, cells were disrupted in cold resuspension buffer for 2 min on ice. The lysis reaction was stopped with the addition of 1 mL wash buffer. After a centrifugation step at 500g for 10 min, pelleted nuclei were resuspended in 50 μL of transposition buffer (25 μL 2× TD buffer, 2.5 μL transposase (100 nM final), 16.5 μL PBS, 2×TD Buffer for 30 min at 37 ℃ with 1000 rpm mixing. DNA was purified on AMPure XP beads. Freshly eluted DNA was amplified using NEB Next High Fidelit 2 × PCR Master Mix to generate a library with PCR program
Quality control of the libraries was performed and then pooled at equimolar concentration and were sequenced multiplexed on the Illumina Novaseq6000 with 150-bp paired-ends.

value: overexpress FH


title: primary_LUAD_6

value: surgery & Radiochemotherapy


title: primary_LUAD_5

value: Never smoking


title: ATAC-seq_FOXA1_rep2

value: overexpress FOXA1


title: ATAC-seq_FOXA1_rep1


title: ATAC-seq_vector_rep2


title: primary_LUAD_2

value: male

value: adenocaricnoma


title: breast_cancer_matched_paired_brain_metastasis_11

value: female

value: ER- PR- HER2+

value: Radiotherapy & Chemoterapy


title: primary_LUAD_3

value: surgery


title: primary_LUAD_1

value: surgery + chemotherapy


title: breast_cancer_matched_paired_brain_metastasis_10

value: ER+ PR- HER2-

value: Radiotherapy


title: ATAC-seq_vector_rep1


title: breast_cancer_matched_paired_brain_metastasis_9

value: ER- PR+ HER2-


title: breast_cancer_matched_paired_brain_metastasis_8

value: Other


title: ChIP-seq_FOXA1_H3K4me3_rep1

data_processing:
ChIP-seq: the ChIP-seq data were mapped to the Homo sapiens (hg38)  and D. melanogaster genome assembly (dm6) using bowtie2 with the default parameters.
Assembly: hg38
Supplementary files format and content: WIG

extract_protocol:
cells were crosslinked in adherent conditions with 1% formaldehyde for 15 minutes at room temperature and quenched with glycine to a final concentration of 125 nM. Fixed cells were lysed in nuclei lysis buffer to extract nuclei and sheared by sonication to 300-500-bp-sized fragments. Sheared chromatin was incubated with antibodies and protein A/G-Dynabeads for 12 hours at 4 ℃. The beads were washed with RIPA150, RIPA500, RIPA-LiCl and TE buffer , respectively. The beads were resuspended with NLB buffer. After de-crosslinked at 65 ℃ for 6 hours, DNA fragments were digested with RNase A and proteinase K. Purified DNA fragments were generated libraries followed by high throughput sequencing using Illumina Novaseq6000
Purified DNA fragments were generated libraries followed by high throughput sequencing using Illumina Novaseq6000.

value: Breast; Mammary gland

value: breast cancer

tag: antibody


title: primary_LUAD_7

value: smoker


title: ChIP-seq_FOXA1_H3K4me1_rep2

tag: tissue


title: ChIP-seq_vector_H3K4me3_rep1

tag: genotype

value: vector


title: ATAC-seq_FH_rep1

value: overexpress FH


title: breast_cancer_matched_paired_brain_metastasis_6

value: TNBC


title: breast_cancer_matched_paired_brain_metastasis_4

value: ER+ PR+ HER2-


title: primary_LUAD_4

value: adenocaricnoma

value: surgery & Radiotherapy


title: ChIP-seq_FOXA1_H3K4me1_rep1

value: overexpress FOXA1


title: ChIP-seq_vector_H3K4me1_rep1


title: breast_cancer_matched_paired_brain_metastasis_5

value: female


title: ChIP-seq_vector_H3K4me1_rep2


title: breast_cancer_matched_paired_brain_metastasis_3

value: Unknown

value: Chemoterapy


title: ChIP-seq_FH_H3K9me3_rep2


title: breast_cancer_matched_paired_brain_metastasis_2

value: ER+ PR- HER2-

value: Radiotherapy & Chemoterapy


title: ChIP-seq_FOXA1_H3K4me3_rep2


title: ChIP-seq_FH_H3K9me3_rep1


title: ChIP-seq_FOXA1_H3K9me3_rep1


title: ChIP-seq_FOXA1_H3K9me3_rep2


title: primary_breast_cancer_11

source_name: primary breast

value: ER+ PR-HER2+

value: surgery + chemotherapy + Radiotherapy


title: breast_cancer_matched_paired_brain_metastasis_1


title: primary_breast_cancer_10

value: surgery + chemotherapy


title: ChIP-seq_vector_H3K4me3_rep2

value: Breast; Mammary gland

value: breast cancer


title: ChIP-seq_vector_H3K9me3_rep2

value: vector


title: primary_breast_cancer_9

value: surgery + chemotheapy + Radiotherapy


title: primary_breast_cancer_7

value: TNBC


title: breast_cancer_matched_paired_brain_metastasis_7

value: ER- PR+ HER2-

value: Radiotherapy


title: ChIP-seq_vector_H3K9me3_rep1


title: ChIP-seq_FOXA1_H3K27ac_rep2


title: primary_breast_cancer_8

value: ER- PR- HER2+

value: surgery + chemotherpy + Radiotherapy


title: primary_breast_cancer_6

value: female

value: surgery +  chemotherapy + Radiotherapy


title: primary_breast_cancer_5

value: surgery


title: cytarabine resistance HL60 cells [array]

city: Kaohsiung

first: Yu-Hsin

last: Tseng

address: No.100, Tzyou 1st Rd., Sanmin Dist.

department: Department of Pediatrics

country: Taiwan

institute: Kaohsiung Medical University Hospital

hyb_protocol: Correspondingly fragmented and labeled cRNA was pooled and hybridized to a SurePrint G3 Human Gene Expression 8x60K Microarray (Agilent Technologies) at 65 ◦C for 17 h.

scan_protocol: The Cy3 microarray was scanned at 535 nm with a microarray scanner (Agilent Technologies, Santa Clara, CA, USA).

data_processing:
The scans were analyzed using Feature Extraction 10.7.3.1 software (Agilent Technologies, Santa Clara, CA, USA).
The data were normalized by quantile normalization.
The normalized_data.txt file includes normalized signal intensities.

source_name: AML cell line

label_protocol: Total RNA (200 ng) was amplified using a Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) and labeled using fluorescent Cy3 dye (Agilent Technologies, Santa Clara, CA, USA). After incubation with fragmentation buffer at 60°C for 30 min, 0.6 µg Cy3-labeled cRNA was fragmented to an average size of 50–100 nucleotides.

growth_protocol: Cells are maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% antibiotic–antimycotic reagents under a humidified atmosphere of 5% CO2 at 37 °C.

extract_protocol: Total RNA was extracted from HL60 and R-HL60 cells using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA, USA) and according to the instruction manual. The RNA samples were submitted to Welgene Biotech. Co., Ltd. (Taipei, Taiwan, R.O.C) for gene expression array analysis. RNA quantity was determined using an ND-1000 spectrophotometer (Nanodrop Technology, Wilmington, DE, USA) and RNA quality was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: The R-HL60 cell line was established through the continuous treatment of parental HL60 cells with increasing concentrations of cytarabine.

value: AML cell line

tag: treatment

value: Cytarabine

tag: phenotype

value: Cytarabine resistant


title: parental HL60 cells [array]

value: No treatment

value: Parental


title: ChIP-seq_vector_H3K27ac_rep1

value: Breast; Mammary gland


title: ChIP-seq_vector_H3K27ac_rep2

value: breast cancer


title: primary_breast_cancer_4

value: ER+ PR+ HER2-


title: SAP30BP knockdown rep 2

city: Hirakata

first: Rei

last: Yoshimoto

state: Osaka

address: 45-1 Nagaotoge-cho

department: Faculty of Agriculture

country: Japan

institute: Setsunan University

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using HISAT2
bedgraph files were generated using bedtools genomecov
Assembly: hg19

source_name: HEK293 cells

growth_protocol: HeLa  cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Wako) supplemented  with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNAs were prepared with RNeasy Mini Kit (QIAGEN).
rRNA depletion was performed with NEBNext rRNA Depletion Kit v2 (NEB) The preparation of RNA libraries were performed using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs).

value: HEK293 cells

value: SAP30BP knockdown


title: SPF45 knockdown rep 1

value: SPF45 knockdown


title: primary_breast_cancer_3

value: Unknown

value: surgery + chemotherapy + Radiotherapy


title: SAP30BP knockdown rep 1


title: primary_breast_cancer_2

value: surgery +  chemotherpy + Radiotherapy


title: Control biol rep 2 (SAP30BP and SPF45 control)

value: WT


title: ATAC-seq_NIH-3T3_FH_rep1

data_processing:
ATAC-seq : the ATAC-seq data were mapped to the Mus musculus (mm10)  using bowtie2 with the default parameters.
Assembly: mm10
Supplementary files format and content: WIG

source_name: Embryo

growth_protocol: NIH-3T3 cells were transiently transfected  with plasmid.

value: Embryo

value: Fibroblast

value: overexpress FH


title: ChIP-seq_FOXA1_rep1

value: overexpress FOXA1


title: primary_breast_cancer_1

value: female

value: TNBC

value: surgery + chemotherpy


title: ATAC-seq_NIH-3T3_FOXA1_rep2


title: Control biol rep 1 (SAP30BP and SPF45 control)


title: WT

city: ILLKIRCH Cedex

first: Norbert

middle: B

last: GHYSELINCK

state: CU STRASBOURG

address: 1 rue Laurent Fries BP10144

department: Functional Genomics & Cancer

institute: Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)

data_processing:
Image analysis, base calling and demultiplexing were performed using RTA 2.7.7 and Cell Ranger 3.0.2 mkfastq.
Alignment, barcode and UMI filtering and counting were performed using Cell Ranger 3.1.0 count on a reference composed of mm10 assembly (GRCm38 Ensembl release 99) and YFP sequence.
Assembly: mm10 + YFP sequence
Supplementary files format and content: Filtered (contains only detected cellular barcodes) feature-barcode matrix (each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)) in Market Exchange Format (MEX) and gzipped.
Supplementary files format and content: Gzipped tsv files with feature and barcode sequences corresponding respectively to row and column indices from the matrix.

source_name: testis

extract_protocol:
Freshly collected testicular cells at E14.5 from 12 controls and 16 Nr5a1 Sertoli cell deficient mutants. The testes were incubated for 10 minutes at 37°C in 350 μl of trypsin/EDTA 0.05% (w/v), phenol red solution (Gibco Ref 25300), filtered through a 40 μm cell strainer to generate single cell suspensions, centrifuged at 3000g and suspended in 300 µl PBS.
Cell number and viability were determined by a Trypan Blue exclusion assay on a Bürker Chamber. Samples consisted of > 90 percent viable cells were processed on the Chromium Controller from 10X Genomics (Leiden, The Netherlands). 10000 total cells were loaded per well to yield approximately 6000 captured cells into nanoliter-scale Gel Beads-in-Emulsion (GEMs). Single cell 3 prime mRNA seq library were generated using Chromium Single Cell 3 prime Reagent Kits v3 (10X Genomics). Briefly, GEMs were generated by combining barcoded gel beads, a RT master mix containing cells, and partitioning oil onto Chromium Chip B. Following full length cDNA synthesis and barcoding from poly-adenylated RNAs, GEM were broken and pooled before cDNA amplification by PCR using 11 cycles. After enzymatic fragmentation and size selection, sequencing library were constructed by adding P5 and P7 primers (Illumina, San Diego, USA) as well as sample index via end-repair, A-tailing, adaptor ligation and PCR amplification with 10 cycles. Library quantification and quality control was performed using Bioanalyzer 2100 (Agilent Technologies, Santa Clara CA).

value: testis

value: fresh testes cells


title: ChIP-seq_FH_V5_rep2

value: Breast; Mammary gland

value: breast cancer


title: ATAC-seq_NIH-3T3_FH_rep2


title: ATAC-seq_NIH-3T3_FOXA1_rep1


title: HCC38_CD44high.104Low_2

city: Darlinghurst

first: Heloisa

middle: Helena

last: Milioli

state: NSW

address: 384, Victoria St

department: Cancer

country: Australia

institute: Garvan Institute of Medical Research

description:
Human (hg19)
Library preparation and QC validation complete
Qiagen miRNeasy Micro Kit

data_processing:
The next generation sequencing data was processed on the Illumina System.
Genome-guided alignment to a human reference (GRCh38) was performed using Rsubread.
Feature counts were computed in R using the package Rsubread.
The differential gene expression analysis was conducted with edgeR and limma packages in the R environment.
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: Cell line

extract_protocol:
MCF7 cells (Michigan Cancer Foundation) and ZR75-1 cells (American Type Culture Collection) lines were verified through short tandem repeat profiling and tested negative for mycoplasma contamination. Parental cell lines were cultured in RPMI 1640 media (Thermo Fisher) supplemented with 10% fetal bovine serum (GE Healthcare) and 20 mM HEPES (Thermo Fisher). HMEC cells were purchased from ATCC and transformed into HMLER cells by the sequential addition of hTERT, SV40-ER and RAS as previously described21. Cells were cultured in serum-free mammary epithelial growth medium (MEGM) and MEGM Single Quots (Lonza, cat no. CC-4136: 1 ml bovine pituitary extract (BPE), 0.5 ml GA-1000 (30 mg/ml Gentamicin and 15 µg/ml Amphotericin), 0.5 ml insulin, 0.5 ml hydrocortisone and 0.5 ml hEGF). Cells were maintained at 37oC with 5% CO2. HCC38 cells were purchased from ATCC and cultured in RPMI containing 10% FBS containing penicillin/streptomycin (PS; 5.000 units penicillin and 5 mg streptomycin/ml in H2O, Sigma Aldrich, cat no. P4333). All cell lines were routinely tested to confirm the absence of mycoplasma contamination.
Cells were grown in P150 plates for 48h-72h, depending on growth kinetics, till plates reached 80% confluence. At harvest time, cells were washed twice with cold PBS1x (Invitrogen), scraped and collected in eppendorfs. Cells were spun down, washed once more with cold PBS1x, removing the supernatant, followed by snap freezing in liquid nitrogen. Frozen cell pellets (1 x 10^6 cells) were used for RNA extraction of RNA using the commercial RNeasy Kit (Qiagen). Quality of RNA was assessed using a bioanalyzer Eukaryote Total RNA Nano chip. Samples that scored above RIN:9 were used to generate the mRNA library, using a  TruSeq Stranded mRNA LT - Set A kit (Illumina:   RS-122-2101). CD44-low versus CD44-high cell lines: MCF-7, ZR75-1, HMLER and HCC38. Samples were submitted for depth pair-end sequencing (Illumina HiSeq 2500 v4.0) at the Garvan Molecular Genetics.
Samples were submitted for depth pair-end sequencing (Illumina HiSeq 2500 v4.0) at the Garvan Molecular Genetics. The next-generation sequencing data were processed on the Illumina System.

tag: condition

tag: volume (ul)

tag: concentration (ng/ul)


title: ChIP-seq_FOXA1_rep2

tag: cell line

tag: cell type


title: ChIP-seq_FH_V5_rep1


title: HCC38_CD44high.104Low_3


title: HCC38_CD44high.104Low_1


title: ChIP-seq_FOXA1_H3K27ac_rep1


title: ChIP-seq_vector_V5_rep2

value: vector


title: HCC38_CD44high.104Med_3


title: SPF45 knockdown rep 2

value: HEK293 cells

value: SPF45 knockdown


title: KO

value: Nr5a1 lost in Sertoli cells


title: ATAC-seq_NIH-3T3_vector_rep2


title: ATAC-seq_NIH-3T3_vector_rep1


title: HCC38_CD44high.104Med_1


title: ChIP-seq_NIH-3T3_FH_H3K9me3_rep2

data_processing:
ChIP-seq: the ChIP-seq data were mapped to Mus musculus (mm10) and D. melanogaster genome assembly (dm6) using bowtie2 with the default parameters.
Assembly: mm10
Supplementary files format and content: WIG


title: HCC38_CD44low_2


title: HCC38_CD44low_1


title: HCC38-veh-N2

description: Human (hg38)

source_name: Cell line HCC38

growth_protocol: HCC38 cells were purchased from ATCC and cultured in RPMI containing 10% FBS containing penicillin/streptomycin (PS; 5.000 units penicillin and 5 mg streptomycin/ml in H2O, Sigma Aldrich, cat no. P4333). All cell lines were routinely tested to confirm the absence of mycoplasma contamination. HCC38 CD44Hi cells treated with control siRNA or two different siRNAs targeting AR (AR ex1, AR ex7). HCC38 CD44Hi cells also followed treatment with AR antagonists vehicle (DMSO), Seviteronel, Abiraterone or Enzalutamide.

extract_protocol:
Cells were grown in P150 plates and treated with AR antagonists. At harvest time, cells were washed twice with cold PBS1x (Invitrogen), scraped and collected in eppendorfs. Cells were spun down, washed once more with cold PBS1x, removing the supernatant, followed by snap freezing in liquid nitrogen. Frozen cell pellets (1 x 10^6 cells) were used for RNA extraction using the commercial RNeasy Kit (Qiagen). The quality of RNA was assessed using a bioanalyzer  Eukaryote Total RNA Nano chip. Samples that scored above RIN:9 were used to generate the mRNA library.
Samples were submitted for pair-end sequencing at Macrogen Oceania PL. The next-generation sequencing data were processed on the Illumina System.

value: Vehicle (DMSO)


title: HCC38-veh-N1

description: Human (hg38)


title: HCC38-siCT-N2

description: Human (hg38)

value: siControl


title: ChIP-seq_NIH-3T3_FOXA1_H3K9me3_rep2

value: Embryo


title: HMLER_CD44high.104High_3

value: HMLER


title: HMLER_CD44high.104High_1


title: HMLER_CD44high.104Med_1


title: HMLER_CD44high.104Med_2


title: HMLER_CD44low_3


title: HMLER_CD44high.104Med_3


title: HCC38-siCT-N1

description: Human (hg38)


title: HCC38_CD44high.104Med_2


title: HMLER_CD44low_2


title: ChIP-seq_NIH-3T3_vector_H3K9me3_rep2

value: Fibroblast


title: ChIP-seq_NIH-3T3_FOXA1_H3K9me3_rep1

value: overexpress FOXA1


title: HCC38-siAR-N1

description: Human (hg38)

value: siAR


title: HMLER_CD44low_1


title: HCC38-Sev-N2

description: Human (hg38)

value: Seviteronel


title: ChIP-seq_vector_V5_rep1


title: MCF7_1


title: ChIP-seq_NIH-3T3_vector_H3K9me3_rep1


title: ChIP-seq_NIH-3T3_FH_V5_rep2

value: overexpress FH


title: MCF7_3


title: HCC38-Sev-N1

description: Human (hg38)


title: ZR751_2


title: ZR751_3


title: ChIP-seq_NIH-3T3_FH_H3K9me3_rep1


title: HMLER_CD44high.104High_2


title: HCC38-siAR-N2

description: Human (hg38)


title: ZR751_1


title: HCC38-Enz-N2

description: Human (hg38)

value: Enzalutamide


title: HCC38-Enz-N1

description: Human (hg38)


title: ChIP-seq_NIH-3T3_FOXA1_V5_rep1


title: HCC38-Abi-N2

description: Human (hg38)

value: Abiraterone