title: a6

city: Wuhan

first: Feng

last: Chenzhao

address: No.1095 Jiefang Road

institute: Huazhong University of Science and Technology

description: stage 1/2

data_processing:
Clean fastq files were then mapped against human reference genome CRh38 using STAR (v2.9.6a) 2 pass mode
HTSeq-count was used to count the reads numbers mapped to each gene with the annotation file gencode.v38.annotation.gtf
Raw counts of gene expressions were transformed into TPM values for further analysis
Genome_build: CRh38
Supplementary_files_format_and_content: csv file include TPM values for each sample

source_name: Neuroblastoma

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR.
Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Neuroblastoma

tag: organism

value: Homo sapiens

tag: Stage

value: stage 1/2


title: NKDim 3

status: Public on Sep 10 2021

type: SRA

city: Paris

first: James

last: Di Santo

address: 28 Rue du Dr Roux

department: Immunology

country: France

institute: Institut Pasteur

description: NKDim 3  Freshly isolated by FACS.  mRNA  Single read (read2 used to read sample barcodes and UMI only).

library_source: transcriptomic

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7, followed by UMI of size 8.
Alignment: hisat 0.1.5 with default parameters.
Filter PCR amplification bias using alignment break site and UMI barcode (size 8).
Create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/).
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl rna hg19 -d <List of tag dir> -count 3utr -condenseGenes -strand + -norm 1e7
Genome_build: Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Supplementary_files_format_and_content: 20213108_Surace_exons_homer.txt

molecule: total RNA

organism: Homo sapiens

source_name: Healthy adult, CD56Dim, donor 3

extract_protocol:
Total RNA was extracted. Dynabeads mRNA Direct Purification Kit (Ambion).  Modified Mars-Seq (Jaitin et al., Science 2014).
library source transcriptomic. Library selection cDNA.

treatment_protocol: Whole blood was donated by healthy individuals. Mononuclear cells were isolated by Ficoll centrifugation gradient. Lineage (CD3 CD4 CD19 CD14 CD123) cells were deleted by MACS column. Cells were stained for surface antibody and the interested population were isolated by FACS.

tag: age

value: Adult

tag: disease state

value: Healthy

tag: tissue

value: peripheral blood

tag: selection markers

value: Viable CD45+ Lin- CD7+ CD56dim

tag: treatment

value: unstimulated

tag: donor


title: NKDim 1

description: NKDim 1  Freshly isolated by FACS.  mRNA  Single read (read2 used to read sample barcodes and UMI only)

source_name: Healthy adult, CD56Dim, donor 1


title: NKDim 2

description: NKDim 2  Freshly isolated by FACS.  mRNA  Single read (read2 used to read sample barcodes and UMI only)

source_name: Healthy adult, CD56Dim, donor 2


title: Delta-tocotrienol 1

city: Piscataway

first: Hong

last: Wang

state: NJ

address: 164 Frelinghuysen

department: Chemical Biology

country: USA

institute: Rutgers the State Univesrity of New Jersey

description:
Delta-tocotrienol treatment
T1

data_processing:
Firstly, we filter the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads. We mapped clean reads to reference using Bowtie2 and then calculate gene expression level with RSEM. Finally, we identify DEGs (differentially expressed genes) between samples.
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step
Genome_build: mm10
Supplementary_files_format_and_content: fpkm and read count

organism: Mus musculus

source_name: Prostate dorsal-lateral-ventral glands

extract_protocol:
RNA was extracted using Qiagen Rneasy kit.
After extracting the total RNA from the tissues, mRNA is then enriched by using the oligo (dT) magnetic beads from the total RNA. By using the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and poly (A) addition. Finally, sequencing adapters are ligated to the fragments. The fragments are purified by Agarose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis via BGISEQ-500.

treatment_protocol: In this study, male prostate-specific Pten-/- mice at the age of 6 weeks were separated randomly into 3 groups (6 per group), the control group (fed AIN93M diet), the metabolic syndrome group (fed 60% kcal high-fat diet), and the treatment group (fed AIN93M diet containing 0.05% delta-tocotrienol).  The fasting blood glucose and insulin levels measured at the age of 6 (before the use of the different diet), 10, and 20 weeks. All mice were sacrficed at 20 weeks of age after an 8 hour day timr fasting. Prostate dorsal-lateral-ventral glands were separated under dissection microscope for extracting the total RNA for quantification sequencing.

tag: strain

value: Fvb

tag: genotype

value: prostate-specific Pten-/-

value: Prostate dorsal-lateral-ventral glands

tag: pathology

value: High-grade prostatic intraepithelial neoplasia (HG-PIN)


title: Delta-tocotrienol 2

description:
Delta-tocotrienol treatment
T2


title: a8

country: China

description: stage 3/4/4S

value: stage 3/4/4S


title: ILC2 3

description: ILC2 3  Freshly isolated by FACS.  mRNA  Single read (read2 used to read sample barcodes and UMI only).

source_name: Healthy adult, ILC2, donor 3

value: Viable CD45+ Lin- CD7+ CD127+ CD117-CRTh2+


title: ILC2 2

description: ILC2 2  Freshly isolated by FACS.  mRNA  Single read (read2 used to read sample barcodes and UMI only).

source_name: Healthy adult, ILC2, donor 2


title: Sample1 TRICOV19_A [RNA-seq]

city: Birmingham

first: Graham

last: Taylor

address: Vincent Drive

department: Institute of Immunology and Immunotherapy

country: United Kingdom

institute: University of Birmingham

description: Sample1_GEXFB_filtered_feature_bc_matrix.h5

data_processing:
Processing of raw reads including 10X barcode-aware demultiplexing from BCL to FASTQ files, transcriptome alignment to human genome assembly GRCh38 and unique molecular identifier (UMI) counting were performed using the 10X Cell Ranger pipeline version 3.1.0 with GRCh38-version 3.0.0 as the reference.
Seurat v3.1.5 S6 was used for sample merging, quality control (QC), clustering and reporting.
Both gene expression (RNA) and antibody-derived tag (ADT) assays were loaded from the CellRanger count platform into a Seurat object for each sample excluding cells with less than 200 genes and features detected in less than 3 cells.
The four samples were then merged to create a single aggregated object. QC was conducted on both assays separately.
For the RNA assay, to mitigate the influence of sex on clustering and differential expression, the XIST and RSP4Y1 genes were removed.
Cells with a number of features between 200 and 600, counts of greater than 1000 and mitochondrial percentage less than 15% were kept for further processing.
The gene expression data was normalised using the ‘LogNormalize’ method with the scale.factor set to the default 10000. 1500 variable features were identified using the ‘vst’ method of the ‘FindVariableFeatures’ function.
The assay was finally scaled with the number of counts and mitochondrial percentage variables regressed.
The ADT assay was first used to identify dead cells or cell doublets by removing double positive instances of lineage markers according to the following criteria: CD14 > 60 & CD19 > 50, CD19 > 40 & CD3 > 40, CD14 > 80 & CD3 > 50 and CD3 < 50 & gamma-delta > 400.
The assay was then centred log-ratio (CLR) normalised and scaled with default parameters. The remaining object comprised 10,031 cells with 17,583 features.
Both the RNA and ADT assays were used to compute 50 principal components. These principal components were then used as input into the ‘FindNeighbours’ function and subsequently the ‘FindClusters’ function with resolution set to the default value of 1, resulting in 19 clusters which were visualised using tSNE.
The clusters were manually annotated from expression of lineage markers both at the transcript (RNA) and protein (ADT) levels.
Genome_build: GRCh38
Supplementary_files_format_and_content: Feature matrix in H5 format.

source_name: Peripheral Blood Mononuclear Cells

extract_protocol: Single cell libraries were constructed using 10X Genomics Single Cell 3' Reagents Kits v3 according to manufacturer’s instructions and sequenced on an Illumina NextSeq 500 platform.

treatment_protocol: Cryopreserved PBMCs were recovered and feature barcoded using Biolegend CITE-seq antibodies. All four samples were processed at the same time.

tag: diagnosis

value: MIS-C

tag: timepoint

value: Acute (pre-treatment)

tag: cell type

value: Peripheral Blood Mononuclear Cells

tag: donor id


title: a5

description: stage 3/4/4S

value: Neuroblastoma


title: NTF3

city: Guangzhou

first: Liping

state: Guangdong

address: No. 232, Outer Ring East Road, Guangzhou University Town, Panyu District

institute: Guangzhou University of Chinese Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: non-tumor tissue of female Abcb11-/- mice

extract_protocol:
livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 3 μg of RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: Sex

value: female

value: 52 weeks post natal


title: ILC2 1

description: ILC2 1  Freshly isolated by FACS.  mRNA  Single read (read2 used to read sample barcodes and UMI only)

source_name: Healthy adult, ILC2, donor 1

value: Adult

value: Healthy


title: a4

description: stage 1/2

value: Homo sapiens

value: stage 1/2


title: a7

description: stage 3/4/4S


title: Delta-tocotrienol 4

description:
Delta-tocotrienol treatment
T4

value: Fvb


title: p53 null hiPSC 4hr (p53 null-4)

city: Daejeon

first: Sang-Min

last: Park

address: Youseong-Daero

department: College of Pharmacy

country: South Korea

institute: Chungnam National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2.
Read count extraction and FPKM calculation were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Fibroblast

growth_protocol: Human iPSCs were cultured in mTeSR1 medium (STEMCELL Technologies) on a Mat-rigel-coated cell culture dish or feeder layer. ReLeSRTM (STEMCELL Technologies) was used to passage hiPSCs.

extract_protocol:
Total RNAs were purified from iPSCs using Trizol according to manufacturer in-structions (Thermo Fisher Scientific, Rockford, IL, USA). After quality assessment of the RNA by 2100 Bioanalyzer Instrument (Agilent, Santa Clara, CA, USA), only samples with an RNA integrity number >7.0 were included in the QuantSeq analysis. From 500 ng total RNA, double-stranded cDNA library was prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Vienna, Austria), amplified by polymerase chain reaction and then subjected to sequencing using Illumina NextSeq 500 system (Illumina, CA, USA).
Libraries were prepared according to TruSeq Stranded Total RNA LT sample prep kit (Gold). Briefly, Genomic DNA was removed by Dnase treatment. RNA was purified by ribo-zero rRNA removal kit. The purified RNAs were fragmented to do sequencing by short read. The cDNAs were synthesized from the fragmented RNA, and then were ligated with adapter in the flanking ends. The aquisition of insert ranging 200-400 bp was sequenced through paired-end sequencing.

treatment_protocol: Each iPSC line was doxorubicin treated for 2 or 4 hours.

value: human iPSC

value: p53 null

value: 0.2 uM doxorubicin for 4 hr


title: a3

description: stage 1/2


title: High-fat 6

description:
Hig-fat diet induced metabolic syndrome
O6

value: prostate-specific Pten-/-

value: Prostate dorsal-lateral-ventral glands

value: High-grade prostatic intraepithelial neoplasia (HG-PIN)


title: WTM1

source_name: liver tissue of male C57BL/6J mice

value: male

value: wild type


title: NTF1


title: Abcb11F3

source_name: tumor tissue of female Abcb11-/- mice


title: High-fat 4

description:
Hig-fat diet induced metabolic syndrome
O4


title: p53 null hiPSC 2hr (p53 null-2)

value: 0.2 uM doxorubicin for 2 hr


title: p53 null hiPSC control (p53 null-0)

value: DMSO as control


title: a23

description: stage 1/2

value: Neuroblastoma


title: Abcb11F2

value: liver

value: female

value: 52 weeks post natal


title: High-fat 3

description:
Hig-fat diet induced metabolic syndrome
O3


title: High-fat 2

description:
Hig-fat diet induced metabolic syndrome
O2


title: R72 hiPSC 4hr (R72-4)

value: Arginine 72


title: High-fat 5

description:
Hig-fat diet induced metabolic syndrome
O5


title: R72 hiPSC 2hr (R72-2)


title: High-fat 1

description:
Hig-fat diet induced metabolic syndrome
O1


title: a22

description: stage 1/2

value: Homo sapiens

value: stage 1/2


title: NTF2


title: Abcb11F1


title: a24

description: stage 1/2


title: R72 hiPSC control (R72-0)

value: human iPSC


title: a17

description: stage 1/2


title: P72 hiPSC 4hr (P72-4)

value: Proline 72


title: Control 6

description:
Control
C6

value: Fvb


title: a21

description: stage 1/2


title: Control 4

description:
Control
C4

value: prostate-specific Pten-/-


title: NPC H3K27me3 ICeChIP

city: Chicago

first: Rohan

middle: Nishant

last: Shah

state: IL

address: CLSC 856, 920 E. 58th Street

institute: University of Chicago

description: ICeChIP conducted on NPCs for H3K27me3

library_source: genomic

data_processing:
Briefly, reference genome was modified to contain sequences of semi-synthetic nucleosome barcodes. Reads were mapped to GRCm38/mm10+barcodes reference genome, using Bowtie2, end-to-end, sensitive preset.
Subsequently, SAM files were filtered to reject unmapped and unpaired reads, as well as fragments with length > 200bp and Phred quality score < 20. Paired reads were merged into single interval of the fragment.
BEDTools were used to calculate bedgraphs of the genome coverage. IP and input bedgraphs of genome coverage were subsequently merged into multiple entry interval file of genome coverage. Number of DNA fragments coming from semi-synthetic nucleosome standards were counted for each barcode and IP efficiency was calculated for each histone mark.
Genomic browser views were made using IGV. Heatmaps and gene ontology analysis was made using Homer Software.
Further data sectioning and analysis was conducted in R using the R code provided at https://www.github.com/shah-rohan/bivalency.
Genome_build: mm10_bar_Ca_1-17 (GRCm38/mm10 appended by synthetic DNA barcodes used with semisynthetic nucleosome standards)
Supplementary_files_format_and_content: Bedgraph files all have the form <chromosome> <start> <end> <value>, where the fourth field represents the value of the measurement. Bigwig files are bedgraph files in binary format, appropriate for viewing on a genome browser. Bed files all have the form <chromosome> <start> <end> and represent a list of intervals.
Supplementary_files_format_and_content: Fasta file (with extension .fa) represents the reference genome used in this study, with the mouse genome (GRCm38/mm10) appended by the DNA barcode sequences used for the semisynthetic nucleosome standards.
Supplementary_files_format_and_content: Tab file represents tab delimited file outlining the barcodes used for each semisynthetic nucleosome.

molecule: genomic DNA

source_name: Cell culture

growth_protocol: To initiate the differentiation process to neuronal progenitor cells (NPCs; Day 0), cells were split onto a gelatinized 6 cm plate at 1 x 104 cells/cm2 and allowed to grow for 24 hours. On Day 1, the media was switched to RHB-A (Takara, Y40001) and was subsequently changed every other day. On day 4, cells were split and plated onto Poly-L-Ornithine, laminin-treated 6-cm plates. Prior to cell seeding the plates were treated with 0.01% Poly-L-Ornithine (Millipore, A004C) for at least 20 min, followed by 5 ug/cm2 of laminin (Fisher, CB40232) resuspended in basal RHB-A medium (Takara, Y40000). After washing off this treatment, cells were seeded in fresh RHB-A, supplemented with 10 ng/mL of bFGF (PeproTech, 100-18B) and EGF (PeproTech, 315-09). Cells were then split every 4 days at ≥ 20,000 cells/cm2 until an appropriate amount of NPCs were cultured for ICeChIP.

extract_protocol:
ICeChIP has been done as previously described88,92. Briefly, 10^7-10^8 plate adherent cells were released using Accutase (Millipore), quenched with complete medium and collected (500 rcf, 5 min., 4°C). Subsequent steps have been done on ice, cells after each wash were collected by centrifugation (500 rcf, 5 min., 4°C). Cells were washed twice with 10 ml PBS, twice with 5ml buffer N (15 mM Tris pH 7.5, 15 mM NaCl, 60 mM KCl, 8.5% (w/v) Sucrose, 5 mM MgCl2, 1 mM CaCl2 1 mM DTT, 1x RL Protease Inhibitor Cocktail). Cells’ membranes was lysed by adding 1 volume of the 2x Lysis Buffer (Buffer N supplemented with 0.6% NP-40 substitute (Sigma)) to the single cell suspension resuspended in 2 PCVs (packed cell volumes) of Buffer N. After 10 minutes incubation on ice, nuclei were collected by centrifugation and resuspended in at least 6 PNV (packed nuclei volumes) of buffer N. Subsequently, nuclei were layered over 7.5 ml Sucrose Cushion N (15 mM Tris pH 7.5, 15 mM NaCl, 60 mM KCl, 30% (w/v) Sucrose, 5 mM MgCl2, 1 mM CaCl2 1 mM DTT, 1x RL Protease Inhibitor Cocktail, 50 µg/mL BSA(NEB)) in a 50 ml centrifuge tube. Nuclei were spun through the sucrose cushion in swinging bucket rotor at 500 rcf for 12 min., 4°C. Nuclei were resuspended in 2 PNVs of buffer N, total nuclei acid content was measured spectroscopically at 260 nm by Nanodrop (Thermo Scientific) (1A260 = 50 ng/µl), prior to measurement, DNA was stripped from chromatin by adding 18 μl – 98 μl of 2 M NaCl and DNA was fragmented by vortexing and water bath sonication. The quality and quantity of nuclei was measured using a hemocytometer. The apparent concentration of chromatin was adjusted to 1 μg/μl with Buffer N. The following semi‑synthetic standards were then spiked in: symmetrical H3K4me3, H3K9me3, H3K27me3, H3K36me3, H3K79me2, H3K4me3-K27me3 cis‑bivalent, asymmetrical H3K4me3, H3K4me3-K27me3 trans-bivalent. To fragment the DNA, we aliquoted 100 µg of chromatin and added 1 Worthington unit of Micrococcal nuclease (Worthington) per 4.785 µg of chromatin (measured at 260nm, 1A260 = 50 ng/µl) and incubated at 37°C for 12 minutes. Digestion was stopped by adding 1/10 volume of 11x MNase stop buffer (110 mM EGTA, 110 mM EDTA pH 8.0). Subsequently, nuclei were lysed by slowly adding 5 M NaCl while mixing on a vortex (lowest setting) to the final concentration of 600 mM NaCl. Insoluble material has been spun down at 18000 rcf, 1min., 4°C. Hydroxyapatite (HAP) chromatography has been done as described in92. Briefly, 66 mg of HAP resin (Bio-Rad Macro-Prep® Ceramic Hydroxyapatite Type I 20 μm) was rehydrated with 200 μl of HAP buffer 1 (3.42 mM Na2HPO4 and 1.58 mM NaH2PO4 final pH 7.2, 600 mM NaCl, 1 mM EDTA, 200 μM PMSF). Subsequently, 100 µg of digested soluble chromatin was added to the rehydrated resin and incubated for 10 minutes at 4°C on a rotator. Afterwards, resin slurry was transferred to the centrifugal filter unit (Millipore Ultrafree MC–HV Centrifugal Filter 0.45 μm). Resin was washed 4 times with 200 μl of HAP buffer 1, 4 times with 200 μl of HAP buffer 2 (3.42 mM Na2HPO4 and 1.58 mM NaH2PO4 final pH 7.2, 100 mM NaCl, 1 mM EDTA, 200 μM PMSF), and eluted 3 times with 50 µl HAP elution buffer (342 mM Na2HPO4 and 158 mM NaH2PO4 final pH 7.2, 100 mM NaCl, 1 mM EDTA, 200 μM PMSF), each wash/elution step was accompanied by centrifugation step (600 rcf, 30 sec., 4°C). Concentration of the chromatin was evaluated spectroscopically by Nanodrop (Thermo Scientific) (1A260 = 50 ng/µl). Apparent concentration of the chromatin was adjusted to 20 ng/µl with ChIP buffer 1 with BSA (25 mM Tris pH 7.5, 5 mM MgCl2, 100 mM KCl, 10% (v/v) glycerol, 0.1% (v/v) NP-40 substitute, 100 µg/ml BSA(NEB)).
ICeChIP was performed as previously described88 with following modifications: α-H3K4me3 ChIP- 5 µg chromatin, 2 µg 304M3B-1xHRV3C93, 40µl Streptavidin M-280 Dynabeads (Invitrogen). α-H3K9me3 ChIP- 3 µg chromatin, 0.5 µg 309M3B93, 10 µl Streptavidin M-280 Dynabeads (Invitrogen). α-H3K27me3 ChIP - 0.8 µg chromatin, 0.6 µg CST C36B11 lot 8, 5 µl Protein G Dynabeads (Invitrogen). Aforementioned volumes of magnetic beads were washed twice with 200 µl ChIP buffer 1 with BSA. Antibodies were resuspended in 100 µl of ChIP buffer 1 with BSA; subsequently, magnetic beads were collected using magnetic rack, supernatant was removed, and magnetic beads were resuspended with the antibody solution and incubated for at least 1 hr, 4°C, on a rotator. Afterwards unbound antibody was washed away with two 200 µl washes of ChIP buffer 1 with BSA. Streptavidin beads were additionally washed twice with 200 µl of ChIP buffer 1 with BSA supplemented with 5 µM biotin for 10 min, at 4°C, on a rotator for each wash, followed by wash with 200 µl ChIP buffer 1 with BSA. Supernatant was removed on a magnetic rack and specific amount of chromatin, mentioned at the beginning of this chapter, was used to resuspend the magnetic beads. Chromatin was incubated with antibody-beads conjugates for 10-15 minutes, at 4°C, on a rotator.
Subsequently, magnetic beads were washed two times with 200 µl ChIP buffer 2 (25 mM Tris pH 7.5, 5 mM MgCl2, 300 mM KCl, 10% (v/v) glycerol, 0.1% (v/v) NP-40 substitute, 100 µg/ml BSA(NEB)), and one time with 200 µl ChIP buffer 3 (10 mM Tris pH 7.5, 250 mM LiCl, 1 mM EDTA, 0.5% Na•Deoxycholate, 0.5%(v/v) NP 40 substitute, 100 µg/ml BSA(NEB)), 10 minutes, at 4°C, on a rotator with tube change after each wash. These washes were followed by quick 200 µl ChIP buffer 1 (without BSA) wash, and 200µl TE wash (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Chromatin was released from the resin using 50 µl ChIP elution buffer (50 mM Tris pH 7.5, 1 mM EDTA, 1% (w/v) SDS) at 55°C, for 5 minutes. Elution was supplemented with 200 mM NaCl, 10 mM EDTA, 10 µg of Proteinase K (Roche) and incubated at 55°C for 2 hours. DNA was isolated using 3 volumes of Serapure HD (1 mg/ml of 1 µm, hydrophobic, carboxylated, Sera-Mag SpeedBeads (GE 65152105050250), 20% PEG-8000, 2.5 M NaCl, 10 mM Tris pH 7.5, 1 mM EDTA, 0.05% Tween-20, filter sterilized prior to addition of magnetic beads), incubated for 5 minutes at room temperature, collected with magnetic rack and washed twice with >200 µl of 75% ethanol, on a magnetic rack without disturbing the magnetic beads. Subsequently, ethanol was carefully removed, and DNA was eluted by resuspending beads in 50 µl of TE buffer, magnetic beads were collected using magnetic rack and supernatant was moved to a new tube. In order to limit DNA loss, all operations have been performed using 250 µl siliconized tubes.
reICeChIP was performed in the same manner as described above with following changes. For the primary IP we have used 5 µg of HAP purified chromatin, 2 µg 304M3B-1xHRV3C – HRV 3C cleavable, biotinylated, αH3K4me3 Fab (PDB:4YHZ)93, immobilized on 40 µl Streptavidin M-280 Dynabeads (Invitrogen). After 10 minutes incubation of chromatin with antibody-resin conjugate, resin was washed three times with 200 µl ChIP buffer 1 with 100 µg/ml BSA, each wash consisted of 10 minutes incubation at 4°C, on a rotator, followed by tube change. Subsequently, resin was briefly washed with 200 μl ChIP buffer 1 with 100µg/ml BSA, and chromatin was released from the resin with 20 µl of ChIP buffer 1 supplemented with 100 µg/ml BSA and 4 µg HRV3C incubated (GE Healthcare) on ice for 60 minutes, elution step was repeated one more time and both elutions were combined. HRV 3C endoprotease efficiently cleaves at its target sites at 4°C46 and has a wide range of chemical tolerance94, but it highly-specific for its cognate cleavage sequence95 permitting facile use in ChIP under conditions which preserve nucleosomes. Primary elution was added to 0.6 µg CST C36B11, αH3K27me3 mAb, immobilized on 5 µl of Protein G Dynabeads(Invitrogen) for 10 minutes, at 4°C, on a rotator. Subsequently, magnetic beads were washed two t

value: Neuronal precursor cells

tag: chip antibody

value: CST C36B11, lot 8

tag: amplification cycles


title: a14

description: stage 3/4/4S

tag: organism

tag: Stage

value: stage 3/4/4S


title: P72 hiPSC control (P72-0)


title: Control 3

description:
Control
C3

value: Prostate dorsal-lateral-ventral glands

value: High-grade prostatic intraepithelial neoplasia (HG-PIN)


title: NPC Bivalency ICeChIP

description: ICeChIP conducted on NPCs for bivalency

value: 304M3B-1xHRV3C and CST C36B11, lot 8


title: NPC H3K9me3 ICeChIP

description: ICeChIP conducted on NPCs for H3K9me3


title: C_mut_120

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

institute: Queen Mary University of London

data_processing:
RNA-Seq reads were mapped to the human genome (hg19, Genome Reference Consortium GRCh37)  using BWA mem (version 0.7.15-r1140) as part of the Oxford Genomics Centre pipeline.
Number of reads aligned to the exonic region of each gene were counted using htseq-count based on the Ensembl annotation.
Genes that achieved at least one read count per million reads (CPM) in at least 25% of the samples were kept.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files includes read counts for each sample

growth_protocol: Fibroblast line was obtained from a DMD patient carrying the DMD c.10141C>T (p.Arg3381X) mutation from the MRC Centre for Neuromuscular Diseases Biobank, under appropriate ethical approval (REC reference 06/Q0406/33). We used a six-factor based reprogramming protocol and a recently developed expanded potential stem cell medium (EPSCM) (Wilkinson et al. 2019; Yang et al. 2017) to generate DMD-R3381X pluripotent stem cells (PSCs). The isogenic control PSCs (CORR-R3381X) were generated by precisely correcting the DMD c.10141C>T mutation in the DMD-R3381X PSCs using CRISPR/Cas9-mediated genome editing technology. Myogenic progenitor cells (MPCs) were generated from the isogenic pair of DMD-R3381X and CORR-R3381X PSCs as described (Chal et al. 2016). To induce secondary myogenic differentiation, MPCs were cultured in growth medium (Promocell, C-23060) and then switched to N2 based differentiation medium as described (Chal et al. 2016).

extract_protocol:
Total RNA was extracted from at least 5x105 cells using RNeasy Plus Mini Kit (Qiagen, 74134) following the manufacturer’s instructions and eluted in 10 ul of DNase/RNase free water. The concentration was determined using Qubit™ RNA HS Assay Kit (Invitrogen, Q32852) and the Qubit™ Fluorometer according to the company’s protocol
Extracted RNA samples were sent to the Barts and The London Genome Centre at Queen Mary University of London for processing. Library preps were made using ribosomal depletion.

tag: sample type

value: myogenic


title: a1

description: stage 1/2

tag: tissue

value: Neuroblastoma


title: NPC Input

description: NPC ICeChIP Input


title: Control 2

description:
Control
C2


title: a19

description: stage 3/4/4S


title: NPC H3K4me3 ICeChIP

description: ICeChIP conducted on NPCs for H3K4me3


title: Control 1

description:
Control
C1


title: a13

description: stage 3/4/4S


title: P72 hiPSC 2hr (P72-2)

value: 0.2 uM doxorubicin for 2 hr


title: Control 5

description:
Control
C5


title: dCas12a-VPR_crTet_Rep2

city: Menlo Park

first: Stephen

last: Shang

state: California

address: 297 Jane Stanford Way

institute: Stanford University

data_processing:
STAR aligner; --quant-mode
downstream TPM normalization in R code
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited files that are the Gene Counts output of quantmode from STAR alignment

source_name: HEK293T cells

growth_protocol: Cells were grown in complete DMEM containing 10%FBS.

extract_protocol:
Total RNA was isolated using RNeasy Plus Mini Kit (Qiagen)
After the QC procedures, mRNA from eukaryotic organisms is extracted using oligo(dT) beads. Then, the mRNA is fragmented randomly by adding fragmentation buffer, followed by cDNA synthesis with random hexamer primers, a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. After a series of end repair, A tailing and sequencing adaptor ligation, the double-stranded library is completed through size selection and PCR enrichment.

treatment_protocol: The TRE3G-GFP HEK293T reporter cell line was transfected with the dCasMINI-VPR or dCas12a-VPR and sgRNA or crRNA plasmids and sorted based on the expression of fluorescence proteins (mCherry and BFP) 2 days post-transfection using a Sony SH800 Cell Sorter.

tag: cell line

value: Human Embryonic Kidney cells


title: C_mut_0


title: C_mut_24


title: a16

description: stage 1/2


title: Primed mESC H3K9me3 ICeChIP

description: ICeChIP conducted on primed mESCs for H3K9me3

growth_protocol: Primed mESCs were grown from the mESC E14 cell line (129/Ola background)86 in high glucose DMEM (Invitrogen), supplemented with 15%(v/v) FBS (Gibco), 1%(v/v) non‑essential amino acids (Gibco), 1x penicillin/streptomycin (Gibco), 0.1 mM 2‑mercaptoethanol (Gibco), 2mM L-glutamine (Gibco), 1000 U/mL LIF (ESG1107 Millipore), sterilized using 0.1 µm filter flask (Millipore), stored up to 1 week in 4°C. Primed mESCs were grown on plates coated with 0.1% bovine gelatin (Sigma), grown to 70 90% confluence and passaged daily at a 1:3 ratio, with a media change 3 hours before passaging, supplemented with 1 vol. of fresh media 8 hours after passaging.

value: Primed E14 mESCs (LIF/serum)


title: Primed mESC H3K27me3 ICeChIP

description: ICeChIP conducted on primed mESCs for H3K27me3


title: EF60: EtOH 60

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

data_processing:
Adapters were trimmed during demultiplexing by the core facility and trimmed reads were aligned to the genome using RNA-Seq Alignment version 1.1.1 (Illumina BaseSpace software application). The application uses Tophat 2 for alignment to the mouse genome (UCSC mm10) and RNAReadCounter to generate count tables.
Differential expression analysis of count tables was performed using the default settings of DESeq2 (1.6.3, Benjamini-Hochberg FDR correction).
Genome_build: mm10
Supplementary_files_format_and_content: Microsoft Excel Worksheet (.xlsx), contains unnormalized counts for each sample generated by RNAReadCounter. The raw counts were used by DESeq2 for differential expression analysis.

source_name: gastrocnemius and plantaris muscle

growth_protocol: Male 12-week-old C57BL/6 mice (Charles River Breeding Laboratories; Cambridge, MA) were individually housed in shoe-box cages with corn cob bedding under environmental controlled conditions (22 ± 1 °C; 12 h; 12-h light/dark cycle). Mice were provided standard rodent chow (Envigo Global no. 8604 diet) and water ad libitum.  All mice were fasted beginning at approximately 1800 h but continued to have free access to water. After ~16h of fasting EtOH mice received an IP injection of ethanol (dose: 3g/kg) or equal volume of 0.9% saline (control).  Tissues were collected 1 hour later.  Mice remained fasted after IP injection.

extract_protocol:
Muscle was dissected while mouse was under isoflurane, immediately frozen in liquid nitrogen and stored at -80C until RNA isolation. RNA was extracted from the gastrocnemius-plantaris complex using the miRNeasy minikit (Qiagen) as per the manufacturer’s instructions.  mRNA was isolated from the total RNA using an NEBNext Poly(A) mRNA Magnetic Isolation Module as per instructions (New England Biolabs).
cDNA libraries were generated from the isolated mRNA using an NEBNext Ultra RNA library prep kit for Illumina (New England Biolabs) and 8 nucleotide i7 and i5 dual-index primers (NEBNext multiplex oligos for Illumina, Dual Index Primers) were incorporated into each sample.  The library construction was done according to NEB instructions, modified for use with a Beckman Biomek 4000 at the Florida State University Biological Sciences core lab.  The unique dual-index (barcode) primers were added to each library to multiplex the ten libraries. The multiplexed sample was quantified with qPCR (Kapa Biosystems) specific for Illumina sequencing primers and the average fragment size was determined with a Bioanalyzer high sensitivity DNA chip (Agilent Technologies).  The pooled sample was sequenced, with single end, 100 base reads on an Illumina NovaSeq 6000 located in the Translational Science Laboratory at the College of Medicine, Florida State University.  The pooled data were demultiplexed into individual sample data.

value: male

value: gastrocnemius and plantaris muscle

tag: treatment

value: EtOH


title: TG_17-med-am-RNA

city: Heidelberg

first: Joschka

last: Hey

state: Deutschland

address: Im Neuenheimer Feld 280

department: Cancer epigenomics

institute: DKFZ

data_processing:
RNA-seq data was processed with the nf-core RNA-seq pipeline (Ewels et al., 2020) (v. 1.2). Default parameters were used unless mentioned otherwise. Sequences were aligned to the mouse reference genome mm10 by application of the software HISAT2, with --unstranded option. For single-end data the -singleEnd option was applied. Transcripts were assembled using StringTie and gene code gene annotation release M20 (Frankish et al., 2019). Gene counts were generated with Stringties prepDE.py script (setting: -eb).
For the identification of differentially expressed genes, the R package DESeq2 was used (Love, Huber, & Anders, 2014). For group-wise comparison of baseline replicates, the littermate was included in the design formula to adjust for batch effects. For the LPS stimulation experiment the date of library preparation was included. The adjusted p-value as well as log2 fold change required to fulfil statistical significance is mentioned in the figure legends.
Genome_build: mm10
Supplementary_files_format_and_content: Count file as tab-delimited text file. Excel-file with differentially expressed genes;  Scnn1b-transgene vs wildtype upon LPS and medium treatment (RNA_Treat_DEG.xlsx)
Supplementary_files_format_and_content: Excel-file with differentially expressed genes; multi-factor model including treatment and genotype covariate (RNA_Treat_DEG_Model.xlsx)

source_name: airway macrophages

growth_protocol: Mice were anesthetized by intraperitoneal injection of 120 mg/kg ketamine and 16 mg/kg xylazin (Sigma-Aldrich, Darmstadt, Germany) and exsanguinated. Primary AMs were collected by flushing the lungs 3 times with 800  ml of PBS supplemented with 5 mM EDTA (Sigma-Aldrich, Darmstadt, Germany). The lavage was repeated twice.

extract_protocol:
 I thought we ended up using FACS sorted AM
For the paired-end baseline as well as LPS- and medium-treated replicates of wt- and tg-AM, sequencing libraries were prepared by the DKFZ Genomics and Proteomics Core Facility from total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit according to the manufacturer’s instructions. For sequencing, samples were sequenced on a HiSeq 2000 v4, paired-end, 125 bp platform (Illumina). Single-end baseline replicates were prepared by the EMBL Genomics Core Facility from total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.  Sequencing was performed on a Next Seq 500, single-end, 75 bp platform.

treatment_protocol: For LPS and mucus treatment, lavages from 3-4 animals were pooled to obtain sufficient numbers of AMs . For baseline gene expression individual lavages were used. Collected cells were seeded into a flat-bottom 96-well plate in complete DMEM (1g/L D-Glucose, L-Glutamine, Pyruvat; Gibco, Dreieich, Germany) containing 10 % heat-inactivated FCS (Gibco, Dreieich, Germany), 1x penicillin-streptomycin (Gibco, Dreieich, Germany) 2 mM L-glutamine (Gibco, Dreieich, Germany) to a final count of 1x105 AMs/well, for LPS treatment, according to cell composition determined by cytospin. For baseline gene expression all cells were seeded. After 1 hr incubation at 37 °C, 5 % CO2, the non-adherent cells were gently washed from the plate with prewarmed PBS. For baseline gene expression, adherent cells were resuspended in 200 ml Trizol (Thermo Fisher Scientific GmbH, Dreieich, Germany). For LPS treatment, adherent cells were exposed to 100 ng/ml LPS from P. aeruginosa (Sigma-Aldrich, Darmstadt, Germany) for 6, 12, and 24 hrs or complete DMEM as control. For mucus treatment AMs were exposed to different concentrations of bovine submaxillary gland mucus (Merck Millipore, Darmstadt, Germany). Supernatants were collected and the cells were resuspended in 200 ml Trizol for RNA extraction.

value: lung

value: airway macrophages

tag: batch

value: medium


title: C_ctrl_24


title: C_ctrl_120


title: EF59: EtOH 59

treatment_protocol: After ~16h of fasting EtOH mice received an IP injection of ethanol (dose: 3g/kg) or equal volume of 0.9% saline (control).

tag: strain


title: Primed mESC Bivalency ICeChIP

description: ICeChIP conducted on primed mESCs for bivalency


title: dCas12a-VPR_crTet_Rep1


title: EF62: EtOH 62


title: dCas12a-VPR_crNT_Rep1


title: dCas12a-VPR_crNT_Rep2


title: EF57: EtOH 57


title: C_ctrl_0


title: Primed mESC Input

description: Primed mESC ICeChIP Input


title: WT_9

city: Oxford

first: A Marieke

last: Oudelaar

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

description:
processed data files:
nanog_WT_merged_uniq_chimeric.txt
oct4_WT_merged_uniq_chimeric.txt
prdm14_WT_merged_uniq_chimeric.txt
sox2_WT_merged_uniq_chimeric.txt

data_processing:
Library strategy: Tiled-Micro-Capture-C
MCC pipeline (https://github.com/jojdavies/Micro-Capture-C)
ICE normalization (Imakaev et al. Nature Methods 2012)
Genome_build: mm10
Supplementary_files_format_and_content: chimeric junctions files: tab-delimited text files listing the locations of the identified valid junctions

source_name: E14 mouse embryonic stem cells

growth_protocol: Cells were grown, treated and processed as described in the Methods section of the paper.

extract_protocol: Tiled-Micro-Capture-C (Tiled-MCC) combines Micro-Capture-C (MCC) library preparation with oligonucleotide capture enrichment for deep, targeted sequencing of chromatin interactions within regions of interest. Details are described in the Methods section of the paper.

tag: genetic modification

value: wild type

value: E14 mouse embryonic stem cells


title: dCasMINI-VPR_sgTet_Rep1


title: WT_7


title: dCasMINI-VPR_sgNT_Rep2


title: CF38: Con 38

value: Saline control


title: EF51: EtOH 51


title: dCasMINI-VPR_sgNT_Rep1


title: CF39: Con 39


title: WT_6


title: WT_5


title: scRNA-seq of liver metastases of colorectal cancer:COL18 PBMC

first: liheng

last: che

address: Xin gang road

institute: Sun Yat sen university

data_processing:
The raw base call (BCL) files were demultiplexed into FASTQ file by bsl2fastq.
Droplet-based sequencing data were qualified by FastQC software. Then reads were aligned against GRCh38 human reference genome provided by Cell Ranger (version 2.0, 10x Genomics).
The raw gene expression matrix generated from each sample were aggregated using CellRanger (version 2.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: barcodes.tsv.gz (barcode_#, where # corresponds to patient sample name); features.tsv.gz; matrix.mtx.gz. The files contain aggregated information about unique barcodes, features and gene-cell matrix.

molecule: polyA RNA

source_name: the tumor microenvironment of liver metastases of CRC

extract_protocol:
Fresh biopsies of the primary colorectal cancer and the matched liver metastases were collected during surgery. Venous blood was collected before surgery in EDTA anticoagulant tubes and used to isolate PBMC immediately. Once the specimens were separated from body, they were processed for scRNA-seq immediately.
10x single-cell RNA libraries were prepared for sequencing using standard Illumina protocols.

value: PBMC

tag: age

value: Male

tag: tumor stage

value: IVA

value: treated


title: WT_4


title: scRNA-seq of liver metastases of colorectal cancer:COL18 liver metastases

value: matched liver metastases


title: dCasMINI-VPR_sgTet_Rep2


title: WT_3


title: WT_8


title: scRNA-seq of liver metastases of colorectal cancer:COL18 primary CRC

value: primary colorectal cancer


title: Primed mESC H3K4me3 ICeChIP

description: ICeChIP conducted on primed mESCs for H3K4me3


title: CF36: Con 36


title: CF32: Con 32


title: WT_2


title: scRNA-seq of liver metastases of colorectal cancer:COL17 PBMC

value: Female


title: B_mut_0

value: myogenic


title: B_mut_120


title: B_ctrl_0


title: A_mut_24


title: B_ctrl_120


title: B_mut_24


title: A_mut_120


title: scRNA-seq of liver metastases of colorectal cancer:COL17 liver metastases


title: WT_1


title: CF34: Con 34

value: male


title: B_ctrl_24


title: A_mut_0


title: scRNA-seq of liver metastases of colorectal cancer:COL17 primary CRC


title: A_ctrl_120


title: scRNA-seq of liver metastases of colorectal cancer:COL16 liver metastases

value: treatment-naïve


title: A_ctrl_24


title: scRNA-seq of liver metastases of colorectal cancer:COL16 primary CRC


title: scRNA-seq of liver metastases of colorectal cancer:COL15 primary CRC


title: scRNA-seq of liver metastases of colorectal cancer:COL12 PBMC


title: scRNA-seq of liver metastases of colorectal cancer:COL12 liver metastases


title: A_ctrl_0


title: scRNA-seq of liver metastases of colorectal cancer:COL12 primary CRC


title: WT2

city: Marseille

first: Laurent

last: Fasano

address: Parc Scientifique de Luminy

institute: CNRS-AMU

description: Fasano_Cmutant_vs_Ccontrole_Raw_Counts_RNA-Seq.txt

data_processing:
The quality of the data was assessed using FastQC from the Babraham Institute. Potential contaminants were investigated with the FastQ Screen software from the Babraham Institute.
RNA-seq 50nt reads were aligned to the mouse genome (UCSC mm10) with a set of gene model annotations (genes.gtf downloaded from UCSC on March 6 2013), using the splice junction mapper TopHat v2.0.13 (with bowtie 2.2.3). Final read alignments having more than 3 mismatches were discarded. Gene counting was performed using HTSeq-count 0.6.1p1 (union mode). Since data come from a strand-specific assay, the read has to be mapped to the opposite strand of the gene. Before statistical analysis, genes with less than 15 reads (cumulating all the analysed samples) were filtered out.
Genome_build: mm10
Supplementary_files_format_and_content: Text file (tab delimited) with a first column for gene identification. The next columns correspond to the raw counts (non-normalized) for each sample.

source_name: mouse cerebral cortex

extract_protocol:
1 µg of total RNA from wild-type (WT) and Tshz3 mutant (KO) neocortex at postnatal day 34 (P34) was prepared using Rneasy Plus Universal Mini Kit gDNA eliminator (Qiagen ™). Three independent replicates, each containing cortices from 3-4 mice (P34), were prepared for analysis.
RNA-seq libraries were prepared  with the "Truseq stranded mRNA sample preparation kit" (low throughput protocol) from Illumina.

value: Postnatal day 34 (P34)

tag: genotype/variation


title: KO3

value: Tshz3 mutant


title: KO2


title: WT3


title: WT1


title: scRNA-seq of liver metastases of colorectal cancer:COL15 liver metastases


title: tra1-AA repl3

city: Montpellier

first: Dominique

last: Helmlinger

address: 1919 route de Mende

department: CRBM

institute: CNRS

data_processing:
Basecalling pipeline at Fasteris: HiSeq Control Software HD 3.4.0.38; RTA 2.7.7; bcl2fastq2.17 v2.17.1.14
Sequenced reads were trimmed for adaptor sequence using FastQ Groomer and mapped to Schizosaccharomyces_pombe_1.1 reference genome using HISAT2 v2.1.0 with strand-specific information (--rna-strandness R) and otherwise default options
Reads were then counted for gene and exon features using htseq-count v0.9.1 in union mode (--mode union), reverse stranded (--stranded Reverse), and a minimum alignment quality of 10 (--minaqual 10)
Variance-mean dependence was estimated from count tables and tested for differential expression based on a negative binomial distribution, using DESeq2 v1.18.1. Pairwise comparison or one-way analysis of variance were run with a parametric fit and genotype as the source of variation (factor: ‘mutant’ or ‘control’)
Genome_build: Schizosaccharomyces_pombe_1.1
Supplementary_files_format_and_content: Tab-delimited txt files were merged into one Excel spreadsheet, in which each sheet includes Gene ID, Log2 fold-change and normalized P values (P-adj) for each DESeq2 analysis.

organism: Schizosaccharomyces pombe

source_name: Liquid cultures

growth_protocol: Yeast grown to mid-logarithmic phase

extract_protocol:
RNA was extracted from 50 mL of exponentially growing cells RNA using TRIzol. DNA was removed by DNase I digestion, using the TURBO DNA-free™ kit. RNA was cleaned using the RNeasy Mini kit. Total RNA quality and concentration was determined using an Agilent Bioanalyzer. Transcripts were purified by polyA-tail selection.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA Library prep kit

tag: genotype

tag: growth conditions

value: YES

tag: strain number


title: tra1D repl1 (re-analysis)


title: WT repl3 (re-analysis)

value: WT


title: WT repl2 (re-analysis)


title: tra1-AA repl2


title: tra1-AA repl1


title: WT repl1 (re-analysis)


title: tra1D repl2 (re-analysis)


title: tra1D repl3 (re-analysis)


title: F_MAFA WT 5

city: Nashville

first: Xin

last: Tong

state: TN

address: 2213 Garland Ave

institute: Vanderbilt University

data_processing:
Genialis Expression software
reads are preprocessed by BBDuk which removes adapters, trims reads for quality from the 3'-end, and discards reads that are too short after trimming
preprocessed reads are aligned by STAR aligner
quantification of reads is done using featureCounts
FastQC reports, alignment statistics and rRNA/globin depletion rate QC information is automatically summarized by the MultiQC tool
differential gene expression analyses performed with DESeq2 (Love et al., 2014) with a log2(fold change) threshold of 1 and FDR<0.05.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: pancreatic islets

growth_protocol: normal chow

extract_protocol:
RNA was isolated from isolated whole islets using the RNAqueous total RNA isolation kit (Ambion; Thermo Fisher), and then analyzed on an Agilent 2100 Bioanalyzer. Only samples with an RNA Integrity Number >8.0 were used for library preparation
cDNA libraries were constructed and paired-end sequencing of 4-5 replicates was performed on an Illumina NovaSeq6000 (150 nucleotide reads).

value: isolated whole islets

value: 5 weeks old

tag: Sex

value: wildtype


title: F_MAFA WT 4


title: F_MAFA S64FHET 1

value: MafA-S64F heterozygous


title: F_MAFA WT 1


title: F_MAFA S64FHET 4


title: F_MAFA WT 2


title: F_MAFA S64FHET 3


title: F_MAFA S64FHET 5


title: F_MAFA WT 3


title: F_MAFA S64FHET 2


title: WT Normoxia-2

type: RNA

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

description: Cells published in PMID: 22225988

hyb_protocol: Illumina Total Prep (Ambion)

scan_protocol: Standard Illumina protocol

data_processing: Illumina Beadstudio data were quantile normalized using Bioconductor's Limma package

source_name: PyMT mammary tumor epithelial cells

label_protocol: Standard Illumina protocol

growth_protocol: Cells were maintained as described in PMID: 22225988, standard growth medium was DMEM/F12 supplemented with 2% FBS (cat. #16000044)

extract_protocol: Cells were lysed on the plate with RNABee reagent (Tel-Test, Friendswood, TX) and total RNA prepared as per manufacturer instructions

treatment_protocol: Cells were grown in replicates in 6-well standard tissue culture plates in DMEM/F12 + 2% FBS to ~80% confluence then left at normoxia or exposed to hypoxia (0.5% oxygen) for 6h prior to washing and cell harvest

tag: protocol

value: Normoxia

tag: cell type

value: late-stage tumor ER-negative epithelial cells


title: M_MAFA S64FHET 3

value: Male


title: M_MAFA S64FHET 4


title: scRNA-seq of liver metastases of colorectal cancer:COL07 primary CRC

value: IVA


title: scRNA-seq of liver metastases of colorectal cancer:COL07 liver metastases

value: matched liver metastases


title: KO1


title: M_MAFA S64FHET 2


title: TSC2-/- kidney organoids-rep 3

city: Boston

first: Dario

last: Lemos

address: 4 Blackfan Circle

institute: Brigham and Women's Hospital

data_processing:
Illumina Casava software used for basecalling
Fastq data were aligned to the reference genome and bam files were generated using the STAR aligner (v2.5)
Genome_build: hg19
Supplementary_files_format_and_content: Tables with raw gene counts for every gene and every sample

source_name: hiPSC-derived kidney organoid

growth_protocol: Organoids were generated following the protocol reported in Morizane R et al Nat. Biotechnol. 2015 Nov;33(11):1193-200.

extract_protocol:
For each sample, total RNA was extracted from 5 organoids using the RNeasy Plus MiniKit (Qiagen). Purity was determined byA260–A280. RNA Integrity Number or RNA Quality Number were determined using a Agilent Bioanalyzer and a Fragment Analyzer respectively. Copy DNA (cDNA) library preparation and sequencing was performed at the Molecular Biology Core Facilities at Dan- Farber Cancer Institute
RNA libraries were prepared for sequencing using the Roche Kapa mRNA Hyper Prep

value: hiPSC-derived kidney organoid


title: M_MAFA S64FHET 1


title: serum-HC-rep3

city: Zhengzhou

first: Junwei

last: Zhao

state: Henan

address: Jianshe Road

institute: Zhengzhou University

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 48C on GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: Raw data from the generated .CEL files were imported into Affymetrix Expression Console using the RMA method.

label: biotin

source_name: serum,HC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)

extract_protocol: Extraction of serum，then total RNA was extracted using a miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

tag: gender

tag: disease state

value: healthy controls


title: TSC2+/+ kidney organoids-rep 1

tag: tissue


title: TSC2+/- kidney organoids-rep 3


title: TSC2-/- kidney organoids-rep 1


title: TSC2+/+ kidney organoids-rep 2


title: TSC2+/+ kidney organoids-rep 3


title: TSC2-/- kidney organoids-rep 2


title: M_MAFA WT 4


title: serum-HC-rep4

value: female


title: TSC2+/- kidney organoids-rep 1


title: M_MAFA WT 1


title: M_MAFA WT 2


title: RNA-seq-ENO1 KD

city: Hefei

first: Tong

last: Zhang

address: huangshan road 443

institute: USTC

data_processing:
raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reads were alligned to the human genome hg19 with BOWTIE2 v2.2.6 and clean reads were aligned to the reference genome using TopHat2 v2.1.0.
Cuffdiff v2.2.1 was used to count the reads numbers mapped to each gene.
Genome_build: hg19

source_name: human hepatocellular carcinoma PLC cells

growth_protocol: Human hepatocellular carcinoma PLC cells were cultured in DMEM (GIBCO) with 10%FBS. Cells were maintained in a water-jacketed incubator with 5% CO2 in 37 °C.

extract_protocol:
total RNA was extracted using TRIZOL Reagent (Life technologies) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100.Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA-sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: We treated PLC cells expressing NTC or ENO1 shRNA, respectively. After 72h, we performed RNA extraction and followed by RNA-seq.

tag: expression

value: ENO1 shRNA


title: TSC2+/- kidney organoids-rep 2


title: RNA-seq-NTC

value: human hepatocellular carcinoma PLC cells

value: NTC shRNA


title: serum-HC-rep2


title: serum-HC-rep1


title: serum-DS-TB-rep4

source_name: serum,DS-TB

value: male

value: drug-sensitive tuberculosis


title: serum-DS-TB-rep3


title: serum-DS-TB-rep1


title: M_MAFA WT 3

value: isolated whole islets


title: serum-DS-TB-rep2


title: Mouse-Cortex -Mock Rep2

status: Public on Sep 09 2021

city: Jerusalem

first: Sebastian

last: Kadener

address: SIlberman Institute of Life Sciences, Edmund J. Safra Campus

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
alignemnets to the genomes were done with STAR_2.6.1a_08-27
back spliced and linear reads was done using SRCP
Genome_build: hg38
Genome_build: mm10
Genome_build: rheMac10
Genome_build: rn5
Genome_build: dm6
Supplementary_files_format_and_content: Tables with  back-spliced reads and linear spliced reads.

source_name: Brandeis University

extract_protocol:
RNA purchase/extraction:  Human Adult Normal Brain Total RNA (R1234035-50), Human Adult Normal Cerebellum Total RNA (R1234039-50), Rat Brain Total RNA (R1434035-50), Monkey(Rh) Brain (R1534035-50) Total RNA was obtained by BioChain. Human Blood Total RNA (HR-705) was obtained from Zyagen.One C57BL/6 male and one female were sacrificed at p21, different brain regions were harvested (cerebellum, cortex, olfactory bulb, brain stem and, thalamus) by the Nelson’s lab at Brandeis University. The RNA was extracted with TRI reagent (Sigma, Aldrich) , followed by Zymo RNA cleaning and concentrator -25 Kit (Zymo), according to the manufactures’ instruction. We collected and dissected 10 days old D. melanogaster (Canton-S) heads and brains. Total RNA was  extracted with TRI reagent (Sigma, Aldrich), followed by DNase (DnaseI, NEB) treatment.
Recovered RNA was used to prepare a total RNA library, adapting the protocol from Shishkin et al. , Nature 2015. Specifically, we prepared one library for the RNAseR treated samples and one for the Mock ones. Briefly, RNA was fragmented for 3 min at 92°C in FAstAP 2X buffer (ThermoFisher). Subsequently, samples were dephosphorylated with FastAP enzyme (ThermoFisher), the first linker was ligated, and samples belonging to the same library were pulled together. Retro-transcription was performed using Affinity Script (Agilent). After second ligation, we performed PCR to add the external barcode. For Human Blood RNA samples and D. melanogaster samples, libraries were prepared using the NEXTFLEX® Rapid Directional RNA-Seq Kit 2.0 by PerkinElmer, following the manufacturer’s instructions.
RnaseR vs Mock ribodepleted total RNA library
The samples were sequenced by Novogene Corporation Inc.(8801 Folsom BLVD, Suite 290, Sacramento, CA 95826)- HiSeq 1% PhiX with HiSeq-4000sequencer

treatment_protocol:
ribodepletion:  For mammalian RNA, ribodepletion was performed on 5ug of Total RNA with Ribo-Zero Gold rRNA Removal Kit according to the manufacturer’s instruction. Degradation of rRNA was checked by TapeStation. For Drosophila RNA, ribodepletion was performed with an homemade protocol. Briefly, rRNA was hybridized with specific DNA probes and degraded with RNasH , followed by DNase treatment for removing the DNA probes from the sample.
RNaseR:  From the collected ribodepleted RNA, 2/5 of the volume was treated with 6Units of RNAseR (Lucigen) or with buffer only (Mock) for 15 min at 37°C. The RNA was immediately extracted with TRI reagent (Sigma, Aldrich) according to the manufacture’s instruction.

value: pooled male and female

tag: treatments

value: ribodepletion, mock


title: Mouse-olfactory bulb, brain stem, and thalamus-RNaseR

description: Male and Female mixed, p21

data_processing:
Alignments to the genomes were done with STAR_2.6.1a_08-27.
Back spliced and linear reads was done using SRCP.
Genome_build: Human hg38 (GRCh38)
Genome_build: Mouse mm10 (GRCm38)
Genome_build: Rhesus rheMac10 (Mmul_10)
Genome_build: Rat rn5 (Rnor_5.0)
Supplementary_files_format_and_content: *.txt: Tables with back-spliced reads and linear spliced reads.

extract_protocol:
RNA purchase/extraction: Human Adult Normal Brain Total RNA (R1234035-50), Human Adult Normal Cerebellum Total RNA (R1234039-50), Rat Brain Total RNA (R1434035-50), Monkey(Rh) Brain (R1534035-50) Total RNA was obtained by BioChain. Human Blood Total RNA (HR-705) was obtained from Zyagen. One C57BL/6 male and one female mouse were sacrificed at p21, different brain regions were harvested (cerebellum, cortex, olfactory bulb, brain stem and thalamus) by the Nelson’s lab at Brandeis University. The RNA was extracted with TRI reagent (Sigma, Aldrich), followed by Zymo RNA cleaning and concentrator -25 Kit (Zymo), according to the manufacturers’ instruction.
Recovered RNA was used to prepare a total RNA library, adapting the protocol from Shishkin et al., Nature 2015. Specifically, we prepared one library for the RNaseR treated samples and one for the Mock ones. Briefly, RNA was fragmented for 3 min at 92°C in FAstAP 2X buffer (ThermoFisher). Subsequently, samples were dephosphorylated with FastAP enzyme (ThermoFisher), the first linker was ligated, and samples belonging to the same library were pulled together. Retro-transcription was performed using Affinity Script (Agilent). After second ligation, we performed PCR to add the external barcode.
RNaseR vs. Mock ribodepleted total RNA library.
The samples were sequenced by Novogene Corporation Inc. (8801 Folsom BLVD, Suite 290, Sacramento, CA 95826) - HiSeq 1% PhiX.

treatment_protocol:
Ribodepletion: Ribodepletion was performed on 5ug of Total RNA with Ribo-Zero Gold rRNA Removal Kit according to the manufacturer’s instruction. Degradation of rRNA was checked by TapeStation.
RNaseR: From the collected ribodepleted RNA, 2/5 of the volume was treated with 6 Units of RNAseR (Lucigen) or with buffer only (Mock) for 15 min at 37°C. The RNA was immediately extracted with TRI reagent (Sigma, Aldrich) according to the manufacturer's instruction.

value: Olfactory bulb, brain stem, thalamus

value: Pooled male and female

tag: treatment

value: Ribodepletion, RNaseR


title: surem-MDR-TB-rep2

source_name: serum,MDR-TB

value: Multidrug resistant tuberculosis


title: Mouse-olfactory bulb, brain stem, and thalamus-Mock Rep2

tag: strain


title: Mouse-Cerebellum -Mock Rep2


title: surem-MDR-TB-rep1


title: surem-MDR-TB-rep3


title: Mouse-olfactory bulb, brain stem, and thalamus-Mock

description: Male and Female mixed, p21

value: Ribodepletion, mock


title: Mouse-Cortex-Mock

description: Male and Female mixed, p21

value: Cortex


title: Mouse-Cerebellum-RNaseR

description: Male and Female mixed, p21

value: Cerebellum


title: SPOPmut_EtOH_sgNT_rep.4

city: New York

first: Ivana

last: Grbesa

address: 413 E 69th St

department: Urology

institute: Weill Cornell Medicine

data_processing:
Reads were aligned to mouse genome  with Bowtie2 v.2.3.4.1.
Duplicates and mitochondrial reads were removed with Samtools v1.8.
Peaks were called with Genrich (https://github.com/jsh58/Genrich) in ATAC-seq mode.
Genome_build: mm10 genome
Supplementary_files_format_and_content: peaks

source_name: SPOPmut_EtOH_sgNT_prostate organoids

growth_protocol: Murine organoids were grown in mouse organoid media as per standard protocol.

extract_protocol:
Samples were processed as previously described in Grbesa I, et al. J Vis Exp 2017. PMID 29155775
Libraries were made as described previously in Grbesa I, et al. J Vis Exp 2017. PMID 29155775

treatment_protocol: Organoids were treated for 24h with 10 nM DHT or EtOH in mouse organoid media without mEGF.

value: SPOP-mutant with sgNT

tag: tissue/cell type

value: prostate organoids

value: EtOH


title: SPOPmut_EtOH_sgNT_rep.3


title: SPOPmut_EtOH_sgNT_rep.2


title: Mouse-Cortex-RNaseR

description: Male and Female mixed, p21

tag: age


title: SPOPmut_DHT_sgNT_rep.3

source_name: SPOPmut_DHT_sgNT_prostate organoids

value: 10 nM DHT


title: SPOPmut_EtOH_sgNT_rep.1


title: Mouse-Cerebellum-Mock

description: Male and Female mixed, p21


title: Control_EtOH_sgNT_rep.2

source_name: Control_EtOH_sgNT_prostate organoids

value: control with sgNT


title: surem-MDR-TB-rep4

value: male


title: SPOPmut_DHT_sgNT_rep.4


title: Control_EtOH_sgNT_rep.3


title: SPOPmut_DHT_sgNT_rep.1


title: Control_EtOH_sgNT_rep.4


title: Control_DHT_sgNT_rep.4

source_name: Control_DHT_sgNT_prostate organoids


title: Control_DHT_sgNT_rep.3


title: Control_EtOH_sgNT_rep.1


title: Control_DHT_sgNT_rep.2


title: input_H3K4me2_SPOPmut_EtOH_rep2

description: input H3K4me2 ChIP-seq

data_processing:
Samples were processed with Encode ChIP-seq Pipeline in Histone mode (for H3K4me2) or Transcription Factor mode (for AR and FOXA1).
Genome_build: mm10 genome
Supplementary_files_format_and_content: peak and bigwig

source_name: prostate organoids

growth_protocol: Murine organoids were grown as per standard protocol.

extract_protocol:
ChIP was prepared as per standard protocol.
Libraries were prepared according to NEBNext Ultra II DNA Library Prep kit instructions.

tag: chip-seq antibody

value: none (input)


title: SPOPmut_DHT_sgNT_rep.2

tag: genotype/variation


title: input_H3K4me2_SPOPmut_DHT_rep1

description: input H3K4me2 ChIP-seq


title: Control_DHT_sgNT_rep.1


title: input_H3K4me2_Control_EtOH_rep2

description: input H3K4me2 ChIP-seq


title: input_H3K4me2_Control_EtOH_rep1.

description: input H3K4me2 ChIP-seq


title: input_H3K4me2_Control_DHT_rep2

description: input H3K4me2 ChIP-seq


title: input_FOXA1_SPOPmut_DHT_rep.2

description: input for FOXA1 ChIP-seq


title: input_AR_SPOPmut_DHT_rep.2

description: input for AR ChIP-seq


title: input_H3K4me2_SPOPmut_EtOH_rep1

description: input H3K4me2 ChIP-seq


title: input_FOXA1_Control_DHT_rep.2

description: input for FOXA1 ChIP-seq


title: input_H3K4me2_SPOPmut_DHT_rep2

description: input H3K4me2 ChIP-seq


title: input_FOXA1_Control_EtOH_rep.1

description: input for FOXA1 ChIP-seq


title: input_FOXA1_SPOPmut_EtOH_rep.2

description: input for FOXA1 ChIP-seq


title: input_AR_Control_DHT_rep.1

description: input for AR ChIP-seq


title: input_AR_Control_DHT_rep.2

description: input for AR ChIP-seq


title: input_FOXA1_Control_DHT_rep.1

description: input for FOXA1 ChIP-seq


title: input_FOXA1_SPOPmut_DHT_rep.1

description: input for FOXA1 ChIP-seq


title: input_FOXA1_Control_EtOH_rep.2

description: input for FOXA1 ChIP-seq


title: input_AR_SPOPmut_DHT_rep.1

description: input for AR ChIP-seq


title: H3K4me2_SPOPmut_EtOH_rep1

description: H3K4me2 ChIP-seq

value: Anti-H3K4me2 - ChIP Grade (ab7766)


title: input_FOXA1_SPOPmut_EtOH_rep.1

description: input for FOXA1 ChIP-seq


title: H3K4me2_Control_EtOH_rep1

description: H3K4me2 ChIP-seq


title: H3K4me2_SPOPmut_DHT_rep1

description: H3K4me2 ChIP-seq


title: H3K4me2_Control_DHT_rep2

description: H3K4me2 ChIP-seq


title: H3K4me2_SPOPmut_DHT_rep2

description: H3K4me2 ChIP-seq


title: input_H3K4me2_Control_DHT_rep1

description: input H3K4me2 ChIP-seq


title: H3K4me2_Control_DHT_rep1

description: H3K4me2 ChIP-seq


title: FOXA1_SPOPmut_EtOH_rep.2

description: FOXA1 ChIP-seq

value: Anti-FOXA1 antibody - ChIP Grade (ab23738)


title: FOXA1_SPOPmut_EtOH_rep.1

description: FOXA1 ChIP-seq


title: H3K4me2_Control_EtOH_rep2

description: H3K4me2 ChIP-seq


title: FOXA1_SPOPmut_DHT_rep.2

description: FOXA1 ChIP-seq


title: FOXA1_SPOPmut_DHT_rep.1

description: FOXA1 ChIP-seq


title: FOXA1_Control_EtOH_rep.2

description: FOXA1 ChIP-seq


title: FOXA1_Control_DHT_rep.2

description: FOXA1 ChIP-seq


title: FOXA1_Control_DHT_rep.1

description: FOXA1 ChIP-seq


title: AR_SPOPmut_DHT_rep.1

description: AR ChIP-seq


title: AR_Control_DHT_rep.1

description: AR ChIP-seq


title: AR_SPOPmut_DHT_rep.2

description: AR ChIP-seq


title: cKO_2 H3K9m3 ChIP

city: Palo Alto

first: Ling

last: Liu

address: 300 Pasteur Drive

description: H3K9me3 ChIP-seq

data_processing:
Reads were adapter- and quality-trimmed with trim_galore.
Trimmed reads were mapped to mm10 mouse genome with Bowtie2.
Mapped reads were sorted and duplicates were removed with Picard.
Peak detection was performed by Model-based Analysis of ChIP-Seq (MACS) with the broadpeak option.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: hindlimb muscles

growth_protocol: MuSCs were FACS-purified from hindlimb muscle of mice at 4-5 months of age.

extract_protocol:
For ChIP-seq, FACS-sorted cells were crosslinked with 1% formaldehyde at room temperature with gentle agitation for 10 minutes. The crosslink was terminated by Glycine at a final concentration of 0.125 M. Cells were then washed three times with ice-cold PBS and stored at -80°C until a sufficient number of cells had been obtained. ChIP was performed following standard ChIP protocols with the following major modifications: 10E6 cells were resuspended in 200 ml lysis buffer and sonicated to obtain DNA fragments from 150 to 500 bp in size. Each ChIP reaction was performed with 10E6 cells and 5 g of antibody. For ATAC-seq, transposed genomic DNA was generated with Illumina Nextera DNA Library Prep Kit and purified with Qiagen MinElute Reaction Cleanup Kit.
ChIP-seq libraries were generated with Nugen Ovation Ultralow System v2. ATAC-seq libraries were constructed with NEBNext High-Fidelity 2x PCR Master Mix in the presence of specific barcoding primers.

value: 4-5 months

tag: sorting markers

value: muscle stem cells


title: Ctrl input

description: ChIP input


title: Ctrl_2 ATAC

description: ATAC-seq


title: cKO_1 ATAC

description: ATAC-seq


title: Ctrl_1 H3K9m3 ChIP

description: H3K9me3 ChIP-seq


title: cKO input

description: ChIP input


title: cKO_2 ATAC

description: ATAC-seq


title: Ctrl_2 H3K9m3 ChIP

description: H3K9me3 ChIP-seq


title: cKO_1

description: processed data file: edgeR_results_HrQSC.txt

data_processing:
Reads were adapter- and quality-trimmed with trim_galore (quality cutoff 20, adaptor stringency 1, final length filter 50).
Trimmed reads were mapped to mm10 mouse genome with STAR (mismatch cutoff 4% of read length, no non-canonical junction alignments).
Exonic reads uniquely mapped were summarized over genes with the featureCounts module of the Subread package.
Raw counts were analyzed with edgeR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: edgeR_results_HrQSC.txt

extract_protocol:
Total RNA was extracted from FACS-purified MuSCs with Qiagen RNeasy Plus Micro Kit.
Reverse transcription was performed with 10ng of total RNA with Clontech SMART-SEQ v4 Ultra Low Input RNA Kit for Sequencing. Sequencing libraries were generated with Nugen Ovation Ultralow System v2.

tag: strain/background

value: Conditional Hairless knockout


title: cKO_1 H3K9m3 ChIP

description: H3K9me3 ChIP-seq


title: Ctrl_2

value: Control


title: Ctrl_1


title: FOXA1_Control_EtOH_rep.1

description: FOXA1 ChIP-seq


title: Ctrl_1 ATAC

description: ATAC-seq


title: H3K4me2_SPOPmut_EtOH_rep2

description: H3K4me2 ChIP-seq


title: cKO_2


title: Control_1

city: Philadelphia

first: Benjamin

middle: C.

last: Reiner

state: PA

address: 125 S 31st St

institute: University of Pennsylvania

data_processing:
10x Genomics Cell Ranger v3.1
Genome_build: Referecne created from Ensembl Rattus_norvegicus.Rnor_6.0.101
Supplementary_files_format_and_content: Cell Ranger raw feature barcode matrix

molecule: nuclear RNA

organism: Rattus norvegicus

source_name: area postrema and nucleus tractus solitarius

extract_protocol:
Nuclei were captured with the 10x Genomics Chromium controller for 3' gene expression assay (v3.1) according to manufacturer protocols
Libraries were prepared according to 10x Genomics manufacturer protocols

value: Sprague Dawley

value: frozen postmortem brain

value: Male


title: Control_3


title: Ctrl_3 ATAC

description: ATAC-seq


title: AR_Control_DHT_rep.2

description: AR ChIP-seq


title: cKO_3 ATAC

description: ATAC-seq


title: Control_4


title: TCPMOH rep 4

city: East Lansing

first: Karilyn

middle: E

last: Sant

state: MI

address: 1355 Bogue St., Life Science B440

department: Pharmacology & Toxicology

institute: Michigan State University

data_processing:
Imported into Galaxy, FastQC used for read quality assessment
Cutadapt used for trimming: settings for paired-end reads, a minimum filter length of 20, and a quality cutoff of 20
Alignment and annotation using Spliced Transcripts Alignment to a Reference (STAR) software, Read counts from featureCounts software
DEseq2 used to assess differential expression
Lrpath's RNA-Enrich function was used for pathway analysis (KEGG)
Genome_build: Genome build and transcription annotation files obtained from the Lawson Lab, Umass Medical School (v. 4.3.2) - https://www.umassmed.edu/lawson-lab/reagents/zebrafish-transcriptome/
Supplementary_files_format_and_content: DEseq2 results (mean, fold change, p-values)

organism: Danio rerio

source_name: Embryos, 100 hpf (n=8-10 embryos per sample)

extract_protocol:
Thermo GeneJet RNA kits, per manufacturer instructions for tissues
Illumina Stranded mRNA Prep Kit following manufacturer instructions

treatment_protocol: Zebrafish embryos were exposed from 96-100 hpf to respective treatments. At 100 hpf, embryos were quickly rinsed in clean 0.3X Danieau's medium, and transferred into Eppendorf tubes in pools of 8-10 embryos. Embryos were placed into RNA later and stored at -20 degrees Celsius until RNA isolation

value: AB strain (wild-type)

value: TCPMOH, 50 nM

tag: exposure

value: waterborne, 96-100 hpf

value: embryo


title: TCPMOH rep 5


title: Control_2

tag: Sex


title: TCPMOH rep 3


title: TCPMOH rep 1


title: A2058_PHEN_R3

city: Gifu

first: Kazuki

last: Heishima

address: Yanagido 1-1

country: Japan

institute: Gifu University

description: Gene expression in A2058 cells treated for 8hr with phenformin 50 µM

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE microarray 8x60K Version 3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: A2058, 8hr, phenformin, replicate 3

label_protocol: Labeling was performed with Agilent Low input Amp Labeling Kit (Cat. #5190-2305, Agilent).

growth_protocol: EMEM supplemented with 10%FBS

extract_protocol: After 2 washes with PBS, the cells were lysed with 400 µL of Homogenization Solution containing 4 µL of 1-Thioglycerol. Subsequently, 200μl of Lysis Buffer was added to 200 µL of 1-Thioglycerol/Homogenization Solution containing lysed cells. After vigorous vortex for 15 seconds, all 400 μL of the lysate was transferred to Maxwell RSC Cartridge. After 5 μL of the DNase I Solution had been added to the cartridge, the cartridge was applied to the Promega Maxwell RSC instrument, and total RNA was purified. The RNA integrities of the samples were checked by using Agilent 2100 Bioanalyzer (Agilent, CA, USA).

treatment_protocol: A2058 cells were treated for 8 hours with NP, Met, Phen, DMSO, or water.

tag: tumor type

value: Malignant melanoma

tag: tissue/cell line

value: cell line

tag: cell line

value: 8hr with phenformin 50 µM


title: BLF3-O2

city: Rochester

first: Yang

state: NY

address: 60 Crittenden Blvd, Apt1240

department: Biology

institute: University of Rochester

data_processing:
raw fastq reads files were cleaned by Trimmomatic-0.36
cleaned reads were mapped to the genome by  STAR_2.5.2b
gene expression (TPM and reads counts) were calculated by salmon 1.4.0
regions of differential methylation were called by edgeR package in 100 window resolution (R version 3.3.2)
Genome_build: Mouse (Mus musculus): mm10
Genome_build: Blind mole rat (Spalax ehrenbergi):GCF_000622305.1_S.galili_v1.0

organism: Nannospalax ehrenbergi

source_name: Fibroblasts

growth_protocol: Fibroblasts were maintained at 37 °C incubator in an atmosphere of 5% CO2 and 3% O2 on treated polystyrene culture dishes (Corning) in EMEM media (ATCC) with 15% (vol/vol) fetal bovine serum (FBS).

extract_protocol:
For RNAseq, was extracted using a Quick-RNA MiniPrep Kit (Zymo), with a DNase I on column digestion to remove genomic DNA contamination; For MeDIP, genomic DNA was extracted using a Zymo Quick-DNA Miniprep Plus Kit.
For RNAseq, the RNA samples were processed with the Illumina TruSeq stranded total RNA RiboZero Gold kit and then subjected to Illumina HiSeq 4000 paired-end 150bp sequencing; For MeDIP, genomic DNA samples were processed using the NEBNext UltraII DNA Library Prep kit.

treatment_protocol: No treatment

value: Wild-caught

value: Fibroblasts


title: TCPM rep 5

value: TCPM, 50 nM


title: BLF3-O1


title: BLF3-Y1


title: A2058_PHEN_R2

source_name: A2058, 8hr, phenformin, replicate 2


title: TCPM rep 3


title: TCPM rep 2


title: A2058_PHEN_R1

source_name: A2058, 8hr, phenformin, replicate 1


title: TCPM rep 4


title: A2058_MET_R3

description: Gene expression in A2058 cells treated for 8hr with metformin 5 mM

source_name: A2058, 8hr, metformin, replicate 3

value: 8hr with metformin 5 mM


title: A2058_NP_R1

description: Gene expression in A2058 cells treated for 8hr with NP 3 µM

source_name: A2058, 8hr, NP, replicate 1

value: 8hr with NP 3 µM


title: A2058_MET_R1

source_name: A2058, 8hr, metformin, replicate 1


title: A2058_DMSO_R1

description: Gene expression in A2058 cells treated for 8hr with DMSO

source_name: A2058, 8hr, DMSO, replicate 1

value: 8hr with DMSO


title: A2058_NP_R2

source_name: A2058, 8hr, NP, replicate 2


title: A2058_W_R2

description: Gene expression in A2058 cells treated for 8hr with water

source_name: A2058, 8hr, water, replicate 2

value: 8hr with water


title: A2058_W_R1

source_name: A2058, 8hr, water, replicate 1


title: TCPMOH rep 2


title: A2058_DMSO_R2

source_name: A2058, 8hr, DMSO, replicate 2


title: TCPM rep 1


title: A2058_DMSO_R3

source_name: A2058, 8hr, DMSO, replicate 3


title: A2058_NP_R3

source_name: A2058, 8hr, NP, replicate 3


title: DMSO rep 1


title: BLF3-Y2


title: PBS3

city: Jinan

first: Xixi

last: Cui

address: 44 Wenhua Xilu

institute: Shandong University

data_processing:
After Illumina HiSeq 4000 sequencer sequencing, image analysis, base identification and quality control, raw reads (Raw Data) are generated. First use Q30 for quality control. Then, use cutadapt software (v1.9.2) to remove the connectors, remove low-quality reads, and obtain high-quality reads.
Use STAR software to compare these reads to the reference genome/transcriptome, use DCC software for circular RNA detection and identification, and use circBase database , circ2Trait disease database to identify the The circular RNA is annotated.
Use the total number of reads to normalize the original splicing reads (junction reads) of each sample, and log2 conversion. Use ttest to identify the differential circular RNAs of the two samples, and use the fold change to identify the differential circular RNAs between the two samples.
Genome_build: HG19
Supplementary_files_format_and_content: circRNAs identified by DCC

source_name: gastric cancer cell line AGS

extract_protocol:
After Hp26695-infected AGS cells were infected at a multiplicity of infection (MOI)  = 100:1 for 12 h, RNA was harvested using Trizol reagent. The control group used PBS for the same amount of time.Pretreat 5 μg total RNA, and use CircRNA Enrichment Kit (Cloud-seq, USA) to enrich circular RNA.
Use TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) to preprocess RNA and construct a sequencing library; Use BioAnalyzer 2100 instrument (Agilent Technologies, USA) for library quality control and quantification. According to the Illumina sequencing instructions, the library was denatured into single-stranded DNA molecules, captured on an Illumina flowcell, amplified into clusters in situ, and 150 cycle sequencing was performed on an Illumina HiSeq sequencer.

value: AGS

value: stomach

value: treated with PBS

tag: molecule subtype

value: circRNA


title: HP5

tag: tissue

value: treated with Helicobacter pylori


title: HP4


title: A2058_W_R3

source_name: A2058, 8hr, water, replicate 3


title: DMSO rep 3

source_name: Embryos, 100 hpf (n=8-10 embryos per sample)

value: AB strain (wild-type)

value: waterborne, 96-100 hpf


title: DMSO rep 4

value: embryo


title: DMSO rep 5


title: HP6


title: DMSO rep 2


title: 148_screen_Blast_190712

city: Chapel Hill

first: Jonathan

middle: S

last: Serody

state: NC

address: 125 Mason Farm Rd.

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
[RNA-seq Quant]
Map paired end fastq reads to hg38 using STAR (https://github.com/alexdobin/STAR/archive/STAR_2.4.2a.tar.gz).
Quantify with Salmon (https://github.com/COMBINE-lab/salmon/releases/download/v0.6.0/SalmonBeta-0.6.0_DebianSqueeze.tar.gz).
Sort and index bam output from STAR using samtools (https://github.com/samtools/samtools/releases/download/1.7/samtools-1.7.tar.bz2).
QC using picard (/picard-tools-1.86/).
Calculate max read length (samtools).
Used biomaRt to interface with BioMart databases (biomaRt version 2.38.0); from ImPro Analysis Suite version 0.4-71. (biomaRt values used in query: unique ensembl_transcript_id from Salmon output (quant.sf) with version numbers removed (e.g. ENST00000456328.2 > ENST00000456328)).
[mixcr (TCR)]
Analyze TCR fastq data using mixcr (https://github.com/milaboratory/mixcr/releases/download/v2.1.9/mixcr-2.1.9.zip).
QC using fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.7.zip).
Quantify diversity metrics using vdjtools (https://github.com/mikessh/vdjtools/releases/download/1.1.7/vdjtools-1.1.7.zip).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: TCR diversity metrics (tab-delimited); RNA gene expression file (tab-delimited).

source_name: Bone Marrow aspirate AML leukemia blasts

extract_protocol:
CD8 T cell RNA from PBMC and Blast RNA from Bone Marrow were isolated by Qiagen RNeasy® Plus Micro Kit.
TCR profiling using the SMARTer Human TCR a/b Profiling Kit (Takara Bio USA, Inc., Cat. No 63516); Illumina TruSeq RNA Access.

tag: cell type

value: Pre-treatment with High dose Cytarabine and Pembrolizumab

tag: timepoint

value: Screening Timepoint


title: 151_screen_Blast_191212

value: Bone Marrow aspirate AML leukemia blasts

tag: treatment


title: 145_screen_Blast_190712


title: 140_screen_Blast_190614


title: PBS2


title: PBS1


title: 130_screen_Blast_190111


title: 121_screen_Blast_180125


title: 157_screen_Blast_200306


title: 158_screen_Blast_200428


title: 153_screen_Blast_200306


title: 152_screen_Blast_191212


title: 147_screen_Blast_190712


title: 110_screen_Blast_190205


title: 125_screen_Blast_190111


title: 109_screen_Blast_180125


title: 107_screen_Blast_180125


title: 108_screen_Blast_180125


title: 142_screen_Blast_190111


title: A2058_MET_R2

source_name: A2058, 8hr, metformin, replicate 2

value: Malignant melanoma

value: cell line


title: 119_screen_Blast_190612


title: 118_screen_Blast_190111


title: 102_screen_Blast_180125


title: Human-total Brain-Mock Rep2

source_name: Human Adult Normal Brain Total RNA (R1234035-50) BioChain

value: Male

tag: treatments

value: ribodepletion, mock


title: Human-Blood-RnaseR Rep2

source_name: Human Blood Total RNA (HR-705)  Zyagen

value: Not Available

value: ribodepletion, RNaseR


title: 123_screen_Blast_190712


title: Human-Cerebellum-Mock Rep2

source_name: Human Adult Normal Cerebellum Total RNA (R1234039-50) BioChain


title: Human-Blood-Mock

description: Not Available

source_name: Human Blood Total RNA (HR-705) Zyagen

value: Blood

value: Not determined

value: Ribodepletion, mock


title: Human-Blood-RNaseR

description: Not Available

value: Ribodepletion, RNaseR


title: Human-Blood-Mock Rep2


title: 113_screen_Blast_180125


title: 4_H9_Hypo_S381

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

institute: University of Oxford

data_processing:
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/cgat-developers)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using hisat2 v2.1.0 with parameters --score-min L,0.0,-0.2
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files of read counts for each sample

extract_protocol:
Full length RNA-seq (Smartseq2)
Libraries were constructed using the smartseq2 protocol accoring to manufacturers instructions

tag: lane

tag: plate-position

tag: condition

value: hypoxia

tag: sample-identity


title: Human-total Brain-RNaseR

description: Male, 29 y.o.

value: Brain

tag: age

value: 29 yr


title: 4_H7_Hypo_S379


title: 4_H5_Norm_S359

value: Norm


title: 4_H4_Norm_S358


title: U_U_BLANK_S384

value: U

value: BLANK


title: 4_H8_Hypo_S380


title: Human-total Brain-Mock

description: Male, 29 y.o.


title: 4_H6_Norm_S360


title: 4_H3_Norm_S357


title: 4_H2_Norm_S356


title: 4_H14_Hypo_S383


title: 4_G7_Hypo_S331


title: 4_H10_Hypo_S382


title: 4_G9_Hypo_S333


title: 4_G4_Norm_S310


title: Human-Cerebellum-Mock

description: Male, 29 y.o.

value: Cerebellum


title: 4_G5_Norm_S311


title: Human-Cerebellum-RNaseR

description: Male, 29 y.o.


title: 4_H1_Norm_S355


title: AF16/HK104 hybrid rep1 cold treatment

city: Novato

first: Rachel

last: Brem

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

data_processing:
Low quality reads removed with FASTX toolkit, adapters removed with cutadapt
reads aligned to AF16 and HK104 reference genome with Hisat2 2.2.0
mapped reads input into Htseq 0.11.1 to calculate raw counts for each gene
raw counts from Htseq inputted into edgeR for differential expression analysis
PCA analysis using edgeR p<0.01
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCA_000004555.3
Supplementary_files_format_and_content: tab delimited file with raw counts for each gene and sample
Supplementary_files_format_and_content: tab delimited file with gene name, logFC, and p-value as outputed from EdgeR

organism: Caenorhabditis briggsae

source_name: whole worm

growth_protocol: synchronized mid/late L4 staged worms grown at 20C for 24 hrs, control worms collected immediately

extract_protocol:
Collected worms were homogenized in 1 ml Tri-reagent for 30 min at room temperature. 0.1 mL of BCP was added to the sample and mixed well. The sample was then spun at 12,000 g 15 min at 4°C and the aqueous phase was transferred to a new tube. 0.5 ml Isopropanol was added to the sample, incubated at room temperature for 10 min and spun at 12,000 g 10 min. The RNA pellet was washed twice with 75% EtOH and dissolved in water. The RNA sample was then was then purified to remove DNA using RNeasy Mini Kit (Qiagen)
The protocol for library preparation was using KAPA RNA hyper prep kit (Roche)

treatment_protocol: worms in treatment group collected after 4C for 60 hrs

tag: strain

value: AF16/HK104 hybrid

tag: genotype

value: WT

value: 4C 60 hrs


title: 4_G3_Norm_S309


title: 4_G6_Norm_S312


title: 4_G8_Hypo_S332


title: AF16/HK104 hybrid rep1 control

value: control


title: 4_G11_Hypo_S335


title: HK104 rep2 cold treatment


title: HK104 rep1 cold treatment


title: 4_G2_Norm_S308


title: HK104 rep2 control


title: 4_G12_Hypo_S336


title: AF16 rep2 cold treatment


title: 4_F9_Hypo_S285


title: 4_G10_Hypo_S334


title: AF16 rep1 control


title: HK104 rep1 control


title: AF16 rep1 cold treatment


title: 4_G1_Norm_S307


title: 4_F7_Hypo_S283


title: 4_F8_Hypo_S284


title: 4_F6_Norm_S264


title: Guard cells, pro17_1_pro∆17

city: Rehovot

first: David

last: Weiss

address: Hertzel st.

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the Solanum Lycopersicum reference genome using STAR  v2.4.2a (using options outFilterMismatchNoverLmax 0.04 and alignEndsType EndToEnd)
Counting proceeded over genes annotated in ITAG release 3.2, using htseq-count
Normalization was performed using DESeq2
Genome_build: Solanum Lycopersicum reference genome, release SL3.00
Supplementary_files_format_and_content: Excel file includes the normalized counts and DESEq2 differential expression analysis

organism: Solanum lycopersicum

source_name: Leaves

growth_protocol: All plants were grown in a growth room set to a photoperiod of 12/12-h night/days, light intensity )cool-white bulbs) of ~250 μmol m-2 s-1, and 25°C.  Tomato Solanum lycopersicum cv M82 (sp-/sp ) plants were used throughout this study.

extract_protocol:
Guard cells from tomato leaves were isolated according to Araújo et al. (2011)  With some modifications. Briefly, four fully expanded leaves without the veins  were ground twice in a blender in 100 mL cold distilled water, each time for 60 sec. The blended mixture was poured onto a 100-mm mesh (Sefar) and the remaining epidermal peels were rinsed thoroughly with deionized water.
Inhouse poly A based RNA seq

value: Leaves

value: Guard cells


title: 4_F4_Norm_S262


title: AF16 rep2 control


title: Guard cells, pro17_3_pro∆19


title: Guard cells, pro17_2_pro∆18


title: Guard cells, pro_2_pro

value: pro


title: Guard cells, pro_3_pro


title: Guard cells, pro_1_pro


title: 4_F2_Norm_S260


title: 4_F3_Norm_S261


title: 4_F11_Hypo_S287


title: 4_F12_Hypo_S288


title: 4_F10_Hypo_S286


title: Guard cells, M82_3_WT


title: Guard cells, M82_2_WT


title: 4_F1_Norm_S259


title: 4_E8_Hypo_S236


title: 4_E9_Hypo_S237


title: Guard cells, M82_1_WT


title: Y-3_S9_L002

source_name: Fibroblasts

value: Wild-caught

value: Fibroblasts


title: 4_F5_Norm_S263


title: 4_E6_Norm_S216


title: Y-2_S8_L002


title: Y-1_S7_L002


title: MCF10A_MinION-dRNA

city: Montpellier

first: Lucile

last: Broseus

address: 141, rue de la Cardonille

data_processing:
Base-calling for Nanopore Sequencing: Oxford Nanopore basecaller, Albacore v2.3.3
Hybrid Long Read Correction was performed using TALC (version 1.0)
Long Reads were aligned using Minimap2 (version 2.11-r797) and quantified using featureCount
Short Reads were aligned using Hisat2 (version 2.1.0) and quantified using featureCount
Genome_build: hg38
Supplementary_files_format_and_content: txt files containing read counts per gene were generated from featureCount. Genes are those annotated in Ensembl 94.

source_name: MCF10a-Snail-ER cells

growth_protocol: Human mammary epithelial MCF10a-Snail-ER cells, which stably express the epithelial repressor Snaill fused to the estrogen receptor, were cultured as previously described (Reference: Javaid S et al. Dynamic chromatin modification sustains epithelial-mesenchymal transition following inducible expression of Snail-1. Cell Reports 5, 1679–1689 (2013). ) Briefly, the cells were grown in DMEM/F-12 (Sigma) supplemented with 5% horse serum (Thermofisher), 20 ng/ml EGF (Sigma), 0.5 µg/ml hydrocortisone (Sigma), 100 ng/ml cholera toxin (Sigma), 10 µg/ml insulin (Sigma), 2mM L-Glutamine (Thermofisher) and 1x Pen./Strep. (Sigma)

extract_protocol:
Direct RNA kit SQK RNA01 from Oxford Nanopore Technologies
MinION direct RNA
After resuspending cell pellets in Trizol (Life technologies), total RNA was extracted by addition of chloroform and isopropanol precipitation, followed by RNA clean-up using the GeneJET RNA purification kit (Thermofisher).

treatment_protocol: To induce epithelial-to-mesenchymal transition initiation, MCF10-Snail-ER cells were treated with 100 nM tamoxifen (Sigma) for 1 day. Importantly, parental MCF10a cells did not show any differences in cell morphology or transcriptional and splicing patterns upon the same treatment. All cell lines were regularly tested for mycoplasma presence.


title: O-1_S10_L002


title: 4_E4_Norm_S214


title: O-3_S12_L002


title: 4_E5_Norm_S215


title: 4_E11_Hypo_S239


title: 4_E12_Hypo_S240


title: 4_E3_Norm_S213


title: BMR5_Muscle_S72

source_name: Muscle

value: Muscle


title: O-2_S11_L002


title: 4_E2_Norm_S212


title: 4_D8_Hypo_S188

value: hypoxia


title: BMR5_WAT_S82

source_name: White adipose tissue

value: White adipose tissue


title: 4_E10_Hypo_S238


title: 4_D7_Hypo_S187


title: BMR4_WAT_S81


title: BMR5_Spleen_S62

source_name: Spleen

value: Spleen


title: BMR5_Intestine_S77

source_name: Intestine

value: Intestine


title: 4_E1_Norm_S211

value: Norm


title: 4_D6_Norm_S168


title: BMR5_Skin_S57

source_name: Skin

value: Skin


title: BMR5_Lung_S67

source_name: Lung

value: Lung


title: 4_E7_Hypo_S235


title: BMR4_Muscle_S71


title: 4_D9_Hypo_S189


title: BMR4_Skin_S56


title: 4_D3_Norm_S165


title: BMR5_Liver_S47

source_name: Liver

value: Liver


title: BMR4_Lung_S66


title: BMR5_Kidney_S52

source_name: Kidney

value: Kidney


title: 4_D11_Hypo_S191


title: 4_D5_Norm_S167


title: BMR4_Kidney_S51


title: BMR4_Intestine_S76


title: 4_D4_Norm_S166


title: 4_D12_Hypo_S192


title: BMR4_Liver_S46


title: 4_C9_Hypo_S141


title: 4_D1_Norm_S163


title: BMR3_Spleen_S60


title: BMR4_Spleen_S61


title: 4_D2_Norm_S164


title: 4_C8_Hypo_S140


title: 4_C7_Hypo_S139


title: 4_D10_Hypo_S190


title: BMR3_Lung_S65


title: 4_C5_Norm_S119


title: BMR3_Kidney_S50


title: BMR3_Liver_S45


title: 4_C4_Norm_S118


title: 4_C6_Norm_S120


title: 4_C2_Norm_S116


title: BMR2_WAT_S79


title: BMR3_WAT_S80


title: BMR3_Intestine_S75


title: 4_C3_Norm_S117


title: 4_C11_Hypo_S143


title: BMR2_Skin_S54


title: BMR2_Spleen_S59


title: BMR2_Muscle_S69


title: 4_B9_Hypo_S93


title: BMR2_Lung_S64


title: BMR2_Liver_S44


title: 4_C1_Norm_S115


title: 4_C10_Hypo_S142


title: 4_B8_Hypo_S92


title: BMR3_Skin_S55


title: BMR2_Kidney_S49


title: 4_B7_Hypo_S91


title: BMR2_Intestine_S74


title: BMR3_Muscle_S70


title: 4_B6_Norm_S72


title: BMR1_WAT_S78


title: 4_B5_Norm_S71


title: BMR1_Spleen_S58


title: BMR1_Skin_S53


title: 4_B2_Norm_S68


title: 4_B3_Norm_S69


title: 4_B4_Norm_S70


title: BMR1_Muscle_S68


title: 4_B10_Hypo_S94


title: 4_B11_Hypo_S95


title: BMR1_Lung_S63


title: BMR1_Liver_S43


title: BMR1_Kidney_S48


title: 4_C12_Hypo_S144


title: 4_B12_Hypo_S96


title: 4_B1_Norm_S67


title: BMR1_Intestine_S73


title: SPOPmut_DHT_sgAr_rep.3

data_processing:
Reads were aligned to mouse genome  with Bowtie2 v.2.3.4.1.
Duplicates and mitochondrial reads were removed with Samtools v1.8. or as part of the ENCODE ATAC-seq pipeline
Peaks were called with Genrich (https://github.com/jsh58/Genrich) in ATAC-seq mode.
Genome_build: mm10 genome
Supplementary_files_format_and_content: peaks

source_name: SPOPmut_sgAR_prostate organoids

treatment_protocol: sgAr = sgRNA targeting AR exon 2 of NM_013476.4

tag: genotype/variation

value: :SPOP-mutant with sgAr

tag: tissue/cell type

value: prostate

value: 1 nM DHT


title: 4_A8_Hypo_S44


title: SPOPmut_DHT_sgAr_rep.1


title: Control_DHT_sgAr_rep.3

source_name: Control_DHT_sgAr_prostate organoids

value: :control with sgAr


title: 4_A9_Hypo_S45


title: 4_A6_Norm_S24


title: SPOPmut_DHT_sgAr_rep.2


title: Control_DHT_sgAr_rep.1


title: abc_3

city: Seville

first: Francisco

middle: Javier

last: Cejudo

state: Seville

address: Americo Vespucio 49

department: Institute for Plant Biochemistry and Photosynthesis

country: Spain

institute: University of Sevilla

data_processing:
Quality control  was performed using the software packges FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read mapping to the reference genome was performed using HISAT2 (http://daehwankimlab.github.io/hisat2/)
Transcript assembly was performed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Gene expression level measured in FPKM (fragments per kilobase of exon and million of mapped reads) was perfomed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Subsequent data analysis and visualization was performed using the R bioconductor package ballgown (https://www.bioconductor.org/packages/release/bioc/html/ballgown.html)
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Arabidopsis thaliana

source_name: Young rosette leaves

extract_protocol:
RNA extraction was performed using Qiagen-RNAesy mini-kit, following the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ntrc-2cpab triple mutant

value: 8 weeks


title: 4_A5_Norm_S23


title: 4_A4_Norm_S22


title: 4_A3_Norm_S21


title: abc_2


title: 4_A12_Hypo_S48


title: ab_3

value: 2cpab double mutant


title: abc_1


title: 4_A11_Hypo_S47


title: ab_1


title: wt3

value: Wild Type


title: ab_2


title: 4_A1_Norm_S19


title: 3_H9_Hypo_S375

value: hypoxia


title: 4_A7_Hypo_S43


title: wt2


title: 3_H6_Norm_S354


title: 11970X4, IECs - WT

city: Salt Lake City

first: W. Zac

last: Stephens

state: UT

address: 15 N. Medical Drive, EEJMRB 4208, EEJMRB 4208

department: Pathology

institute: University of Utah

data_processing:
Reads were aligned with novoalign
Counts matrices generated with Useq DefinedRegionDifferentialSeq
Genome_build: mm10
Supplementary_files_format_and_content: A tab-separated file with raw counts for each sample and genes as features is provided.

source_name: Ileum intestinal epithelial cells

extract_protocol:
400,000 Live, CD45-, EpCAM+ cells from the ileum were sorted and resuspended in Trizol then RNA was extracted with ZymoResearch Direct-zol RNA microprep kits.
Illumina TruSeq stranded RNA kit with RiboZero gold (human, mouse, rat) was used to construct libraries.

value: Ileum

value: H2-Ab1 fl/fl; Villin:Cre-

value: Live, CD45-, EpCAM+ sorted intestinal epithelial cells

tag: Sex

value: male


title: 3_H8_Hypo_S374

tag: cell line


title: 3_H7_Hypo_S373


title: wt1


title: 3_H2_Norm_S350

value: Norm


title: 11970X8, IECs - WT

value: female