title: MSC-EVs biopsia 3

city: Valencia

first: Imelda

last: Ontoria-Oviedo

address: Avda Fernando Abril Martorell 106

department: Regeneration and Heart transplantation Unit

institute: Instituto de Investigación Sanitaria La Fe

description: miRNA

data_processing:
The quality of sequencing data, consisting of fasta files, was evaluated using FastQC
To ensure the precision of subsequent analyses, we employed the Atria software for automatic adapter detection within the raw data
The detected adapters were then meticulously trimmed using the Cutadapt tool
The reads were aligned against the human mature miRNA database sourced from miRNABase.org, utilizing the capabilities of bowtie2
Data processing included the exclusion of reads with a MAPQ score below 1, achieved through Samtools. We then processed the alignment files to count the occurrence of each miRNA by their identifiers.
Assembly: GRCh38, NCBI_Assembly: GCA_000001405.15
Supplementary files format and content: Matrix table with raw miRNA counts for every miRNA and every sample

source_name: mesenchymal stem cells

growth_protocol: Dental pulp MSC immortalized by transducing the lentiviral vector pLV-hTERT-IRES-hygro were maintained in DMEM low glucose supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 and 37ºC

extract_protocol:
Small RNA was isolated from MSC-EVs using the miRNeasy Mini Kit (Qiagen)
Libraries were prepared using the NEBNext® Small RNA Library Prep Set (Illumina®, E7330), according to manufacturer instructions. 5 ng of total RNA was used to construction of sequencing libraries. Final libraries were analyzed using Agilent Bioanalyzer to estimate the quantity and check size distribution

treatment_protocol: To obtain EVs, MSCs were cultured for 48 hours in an extraction medium consisting of DMEM supplemented with 20% EVs-depleted FBS and antibiotics. To extract MSC-EVs, a combined method based on tangential flow filtration (TFF) followed by size exclusion chromatography (SEC) was used (TFF-SEC).

value: mesenchymal stem cells


title: CRC Adjacent normal N071

status: Public on Jun 12 2024

type: SRA

city: Camden

first: Jean-Pierre

middle: J

last: Issa

state: NJ

address: 403 Haddon Avenue

department: Research Labs

country: USA

institute: Coriell Institute for Medical Research

library_source: genomic

data_processing:
library strategy: 16S rRNA gene sequencing
Illumina MiSeq paired-end sequencing
Raw sequencing data were converted to fastq.gz files.
The 16S rRNA sequencing data were trimmed using cutadapt
DADA2 was used to filter, trim, estimate error profiles, merge paired end reads, and construct an amplicon sequence variant (ASV) table. DADA2 was also used to remove chimeras from the denoised ASVs and assign taxonomy by fitting ASV sequences to a pre-trained naïve bayes classifier built from the Silva v138 database
Species assignments were made by exact string matching to DADA2-formatted Silva v138 reference sequences.
Assembly: Silva v138 reference sequences
Supplementary files format and content: The processed data are in tab-delimited text file. The columns of the file are amplicon sequence variants and the rows are the sample IDs.

molecule: genomic DNA

organism: Homo sapiens

source_name: colon

extract_protocol:
tissues were lysed in 2% SDS and 25 mM EDTA overnight. Ammonium acetate (10M) was added to make the precipitate of SDS with proteins and was removed by centrifugation at 12,000 rpm. Next, DNA was precipitated using isopropanol, washed with 70% ethanol, and dissolved in dissolved in LTET (Tris 10 mM, EDTA, 0.1 mM + Tween 20,0.1% )
The 16S rRNA gene V3-V4 hypervariable region was amplified using the selected universal primers (Forward 5’-NNNNCCTACGGGNGGCWGCAG-3′, Reverse 5′- GACTACHVGGGTATCTAATCC-3′) that contained overhang nucleotide sequences (Forward 5’ TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-[locus specific sequence]-3’, Reverse 5’- GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG-[locus specific sequence]-3’) for Illumina barcode indexes.

tag: tissue

value: colon

tag: tissue type

value: CRC Adjacent normal


title: MSC-EVs biopsia 2

country: Spain

description: miRNA

library_source: transcriptomic

molecule: total RNA

tag: cell type

tag: genotype

value: WT


title: CRC Adjacent normal N069


title: MSC-EVs biopsia 1

description: miRNA


title: MSC-EVs-T biopsia 3

description: miRNA

value: immortalized with TERT


title: CRC Adjacent normal N063


title: MSC-EVs-T biopsia 1

description: miRNA


title: CRC Adjacent normal N081


title: CRC Adjacent normal N065


title: MSC-EVs-T biopsia 2

description: miRNA


title: KO_T4_nobrg1i_ctrl_1

city: Heidelberg

first: Christoph

last: Plass

address: Im Neueneimer Feld 280

department: Division of Cancer Epigenomics

country: Germany

institute: DKFZ (German Cancer Research Center)

data_processing:
The data was processd using the pipe4C pipeline.
Assembly: GRCh37
Supplementary files format and content: bigwig tracks
Library strategy: 4C-seq

source_name: AID-DivA

extract_protocol:
Cells were harvested and cross-linked with 2% formaldehyde for 10 min at room temperature, lysed and digested with MboI (New England Biolabs, Cat# R0147L) for three rounds of 4h each. Then first ligation step was performed by T4 DNA ligase (New England Biolabs, Cat# M0202L), and ligated DNA was decrosslinked and purified.  A second digestion step was performed with NlaIII overnight (New England Biolabs, Cat# R0125L). Afterwards, a second ligation step was performed. DNA was purified and measured by Qubit.
5ng of DNA were amplified in PCR using the viewpoint primers. Three viewpoints were used: one close to HR-prone DSB (DSB2), one close to NHEJ-prone DSB (DSB3), and one with no adjacent DSB (ctrl). The PCR products were purified by AMPure XP beads and measured by Qubit. For 4C–seq library preparation, a final qPCR using 2ng DNA was performed with the inverse primers including the Illumina adaptor sequences and a unique index for each condition. DNA libraries were purified by AMPure XP beads and measured by Qubit. Fragment size was checked by Tape station. Libraries were pooled and subjected to 75-bp paired-end sequencing on a Nextseq550 platform at DKFZ Next Generation Sequencing Core Facility.

treatment_protocol: We used both WT AID-DivA cells and AID-DivA cells with an ARID1A knock-out. Cells were either untreated (UT) or treated with 300 nM 4-hydroxytamoxifen (4OHT) and incubated for 4h. Then treated with Auxin to stop the enzymatic generation of the double-strand breaks. Cells were collected immediately after auxin treatment (T0) or 4h after addition of auxin (T4). In addition, cells were either treated with BRG1 inhibitors (brg1i) or not (nobrg1i).

tag: cell line

value: AID-DivA

value: osteosarcoma

value: ARID1A KO

tag: treatment

tag: viewpoint

value: ctrl

tag: replicate


title: CRC Adjacent normal N059


title: CRC Adjacent normal N055


title: CRC Adjacent normal N057


title: WT_UT_IgG_2

data_processing:
The fastq files were processed with the nfcore/cutandrun v2.0 pipeline.
Reads were trimmed using Trim Galore!
Reads were aligned to the reference genome using bowtie 2.
Bigwig tracks were generated using a BPM normalization (bins per million).
Assembly: GRCh37
Supplementary files format and content: bigwig tracks
Library strategy: ACT-seq

extract_protocol:
E. coli (C3013, New England Biolabs) was transformed with plasmid pET15bpATnp (#121137, Addgene), the pA‐Tn5ase protein was isolated. The pA‐Tn5ase was mixed with Tn5ME‐A+B load adaptor mix in complex formation buffer (CB) to form the pA‐Tn5 transposome (pATn5ome). For every reaction, the pA‐Tn5ome‐antibody (pATn5ome‐ab) complex was formed by mixing 1 μL pA‐Tn5ome with 0.8 μL CB and 0.8μL antibody solution. The antibodies used in this study were: Rabbit polyclonal anti-acetyl-Histone H3 (Lys27) (ab4729, Abcam), Rabbit polyclonal anti-acetyl-Histone H2A (Lys118) (PTM-173, PTM BIO), and rabbit IgG (cat #pp64 Millipore, Burlington, MA, USA). Approximately 50,000 nuclei of cell were used for pA‐Tn5ome‐ab complex binding and tagmentation.
For normalization of sequence reads between biological replicates, approximately 3000 permeabilized nuclei of yeast Saccharomyces cerevisiae were prepared, incubated with pATn5ome‐ ab complex targeting yeast H2B, and were spiked into each mix of cells and pATn5ome‐ab complex. Tagmented DNA was purified with a MinElute kit (#28004, Qiagen, Hilden, Germany) and eluted with 20 μL elution buffer (EB). Sequencing libraries were generated under real‐time conditions with a LightCycler 480 (Roche, Basel, Switzerland) in a reaction mix consisted of tagmented DNA eluate, NEBNext High Fidelity 2X Mix (#M0541, New England Biolabs), 100X SYBRGreen, primer Tn5McP1n, and Custom Nextera PCR Barcode. Libraries were purified with AMPure XP beads (#A63880, Beckman, Brea, CA, USA) with a bead:DNA ratio of 1.4:1. Quantity and fragment size of the libraries were determined with a Qubit dsDNA HS assay kit (#Q32854, ThermoFisher and a TapeStation 4150 with D1000 High Sensitivity Assay (#5067‐ 5585, Agilent, Santa Clara, CA, USA), respectively.

treatment_protocol: We used both WT AID-DivA cells and AID-DivA cells with an ARID1A knock-out. Cells were either untreated (UT) or treated with 300 nM 4-hydroxytamoxifen (4OHT) and incubated for 4h. Then treated with Auxin to stop the enzymatic generation of the double-strand breaks. Cells were collected immediately after auxin treatment (T0) or 4h after addition of auxin (T4).

value: untreated

tag: antibody

value: IgG


title: CRC Adjacent normal N051


title: CRC Adjacent normal N061


title: CRC Adjacent normal N053


title: WT_UT_H3K27ac_1


title: KO_T4_nobrg1i_ctrl_4


title: CRC Adjacent normal N047


title: WT_UT_IgG_1


title: CRC Adjacent normal N049


title: WT_UT_IgG_3


title: CRC Adjacent normal N073


title: CRC Adjacent normal N045


title: CRC Adjacent normal N067


title: WT_UT_H2AK118ac_3


title: CRC Adjacent normal N043


title: CRC Adjacent normal N041


title: CRC Adjacent normal N039


title: WT_UT_H3K27ac_2


title: CRC Adjacent normal N037


title: WT_T4_IgG_2

value: 4h after auxin treatment


title: WT_UT_H2AK118ac_2


title: WT_T4_IgG_1


title: WT_UT_H2AK118ac_1


title: WT_T4_H3K27ac_2


title: CRC Adjacent normal N035


title: CRC Adjacent normal N033


title: WT_T4_H2AK118ac_3


title: WT_T4_H3K27ac_1


title: CRC Adjacent normal N027


title: CRC Adjacent normal N031


title: WT_T0_IgG_3

value: 0h after auxin treatment


title: WT_T4_H2AK118ac_2


title: CRC Adjacent normal N029


title: CRC Adjacent normal N025


title: CRC Adjacent normal N021


title: WT_T0_IgG_1


title: WT_T4_IgG_3


title: CRC Adjacent normal N023


title: WT_T0_IgG_2


title: CRC Adjacent normal N157


title: CRC Adjacent normal N019


title: CRC Adjacent normal N017


title: WT_T0_H3K27ac_1


title: WT_T0_H2AK118ac_3


title: WT_T0_H2AK118ac_2


title: CRC Adjacent normal N013


title: CRC Adjacent normal N015


title: WT_T0_H2AK118ac_1


title: CRC Adjacent normal N011


title: KO_UT_IgG_3


title: WT_T4_H2AK118ac_1


title: CRC Adjacent normal N007


title: KO_UT_IgG_2


title: KO_UT_H3K27ac_2


title: KO_UT_IgG_1


title: CRC Adjacent normal N005


title: urine, HFD, miR 1275

city: Sant Joan Despí

first: Maruja

last: Navarro-Díaz

state: Barcelona

address: Oriol Martorell, 12

department: Nephrology

institute: Hospital Sant Joan Despí Moisès Broggi

data_processing:
Quality assessment of RNA using TapeStation 2200 and Bioanalyzer
Removal of genomic DNA using DNase I.
Trimming of adapter sequences from reads using Cutadapt.
Mapping and quantification of transcripts using Salmon and Subread/Rsubread.
Summarization and quantification of small RNA transcripts using annotations from miRBase v22 and Ensembl release 102.
Quality control checks including multi-dimensional scaling plot analysis and Euclidean distances between samples.
Differential expression testing using DESeq2 v1.24.0 Bioconductor’s package.
Cataloging miRNA target sites using multiMiR Bioconductor’s package.
Upregulation/downregulation classification of miRNAs based on adjusted p-value and Log2 fold change.
Assembly: Rnor6.0 genome
Supplementary files format and content: Text files includes raw counts for each sample

organism: Rattus norvegicus

source_name: Urine

extract_protocol:
RNA was obtained from frozen tissue blocks using Trizol Reagent (Invitrogen, Thermo Fisher). Genomic DNA was removed by incubation with DNase I for 10 minutes (Invitrogen) and QC was assessed in a TapeStation 2200 (Agilent, Santa Clara, USA). Half of RNA were used for RNA-Seq experiments and the rest were used for qPCR purposes. SmallRNAs from tissue were purified using 1mg of total isolated RNA following an enrichment protocol with SPRIselect beads (Bee Na Lee, Beckman Coulter, California, USA). qPCR validations were done . The urine samples were collected and 500ml (total cell-free and exosomal RNA) used for smallRNA obtention following the instructions of the ZR Urine RNA Isolation Kit (Zymo Research Corp, CA, USA). In both cases, assessment of QC was done in a Bioanalyzer using a High Sensitivity chip (Agilent).
RNA-seq Libraries were prepared from 1mg of total isolated RNA with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, NEB, Massachusetts, USA), run in a HighSeq 2500 System (Illumina, CA, USA) and 40-50M of reads per sample were obtained. The quality of reads was assessed using the FastQC tool and a trimming step was applied to remove the adapters using the Cutadapt tool. Salmon tool was used to map and quantify the aligned transcripts to the Rnor6.0 genome. DESeq2 v1.24.0 Bioconductor’s package has been used for differential expression testing and the analysis of biological significance has been based on Gene Set Enrichment Analysis (GSEA) performed over two annotation databases: Gene Ontology (GO) and the Reactome Pathway Knowledge base. smallRNA libraries were prepared following the instructions of the NebNext Small RNA Library Prep Set for Illumina (NEB). Size selection of fragments was done in a 6% Polyacrylamide Gel (Invitrogen) and QC of libraries in a TapeStation 2200 using a HighSens D1000 screentape (Agilent). Libraries were sequenced in a HighSeq 2500 System (Illumina) and 12-15M reads per sample were obtained and analyzed. The quality of reads was assessed using the FastQC tool and a trimming step was applied to remove the adapters using the Cutadapt tool. The Subread/Rsubread package was used to map and quantify the aligned transcripts to the Rnor6.0 genome. For summarization/quantification step, annotations were obtained from different databases depending on the small RNA class: miRNA precursor and mature annotation was derived from miRBase v22 (http://www.mirbase.org/ftp.shtml), whereas annotations for other non-coding smallRNAs described in rat were derived from Ensembl release 102 (https: //www.ensembl.org/info/data/ftp/index.html). smallRNA libraries were prepared following the instructions of the NebNext Small RNA Library Prep Set for Illumina (NEB). Size selection of fragments was done in a 6% Polyacrylamide Gel (Invitrogen) and QC of libraries in a TapeStation 2200 using a HighSens D1000 screentape (Agilent). Libraries were sequenced in a HighSeq 2500 System (Illumina) and 12-15M reads per sample were obtained and analyzed. The quality of reads was assessed using the FastQC tool and a trimming step was applied to remove the adapters using the Cutadapt tool. The Subread/Rsubread package was used to map and quantify the aligned transcripts to the Rnor6.0 genome. For summarization/quantification step, annotations were obtained from different databases depending on the small RNA class: miRNA precursor and mature annotation was derived from miRBase v22 (http://www.mirbase.org/ftp.shtml), whereas annotations for other non-coding smallRNAs described in rat were derived from Ensembl release 102 (https: //www.ensembl.org/info/data/ftp/index.html). Different types of quality controls were also conducted (multi-dimensional scaling plot analysis, Euclidean distances between samples) to ensure the normalized data are appropriate for the differential expression analysis; as a result, no outliers or batch effects were detected. DESeq2 v1.24.0, a Bioconductor package, was utilized for the differential expression testing. miRNA target sites were cataloged in databases based on experimental validation and computational prediction using the multiMiR Bioconductor package (http://multimir.ucdenver.edu). DESeq2 v1.24.0 Bioconductor’s package was used for differential expression testing. miRNA target sites have been catalogued in databases based on experimental validation and computational prediction using the multiMiR Bioconductor’s package (http://multimir.ucdenver.edu).

value: Urine

value: Wistar rats

value: High Fat Diet


title: CRC Adjacent normal N003


title: KO_UT_H2AK118ac_2


title: KO_UT_H3K27ac_1


title: urine, HFD, miR 1271


title: CRC Adjacent normal N009


title: urine, HFD, miR 1267


title: KO_T4_IgG_3


title: urine, HFD, miR 1259


title: urine, HFD, miR 1274


title: KO_UT_H2AK118ac_1


title: WT_T0_H3K27ac_2


title: KO_T4_IgG_2


title: urine, HFD, miR 1256


title: KO_T4_IgG_1


title: KO_T4_H3K27ac_2


title: KO_T4_H3K27ac_1


title: urine, HFD, miR 1252


title: urine, SD, miR 1251

value: Standard Diet


title: urine, SD, miR 1250


title: KO_T4_H2AK118ac_2


title: urine, SD, miR 1249


title: urine, SD, miR 1248


title: KO_UT_H2AK118ac_3


title: KO_T0_IgG_3


title: urine, SD, miR 1247


title: KO_T0_IgG_2


title: KO_T4_H2AK118ac_1


title: KO_T0_H3K27ac_2


title: KO_T0_H2AK118ac_3


title: KO_T0_IgG_1


title: KO_T0_H2AK118ac_1


title: urine, SD, miR 1244


title: KO_T0_H3K27ac_1


title: kidney, HFD, miR 1274

source_name: kidney

value: kidney


title: KO_UT_nobrg1i_DSB3_8

data_processing:
The data was processed using the pipe4C pipeline.
Assembly: GRCh37
Supplementary files format and content: bigwig tracks
Library strategy: 4C-seq

extract_protocol:
Cells were harvested and cross-linked with 2% formaldehyde for 10 min at room temperature, lysed and digested with MboI (New England Biolabs, Cat# R0147L) for three rounds of 4h each. Then first ligation step was performed by T4 DNA ligase (New England Biolabs, Cat# M0202L), and ligated DNA was decrosslinked and purified. A second digestion step was performed with NlaIII overnight (New England Biolabs, Cat# R0125L). Afterwards, a second ligation step was performed. DNA was purified and measured by Qubit.
5ng of DNA were amplified in PCR using the viewpoint primers. Three viewpoints were used: one close to HR-prone DSB (DSB2), one close to NHEJ-prone DSB (DSB3), and one with no adjacent DSB (ctrl). The PCR products were purified by AMPure XP beads and measured by Qubit. For 4C–seq library preparation, a final qPCR using 2ng DNA was performed with the inverse primers including the Illumina adaptor sequences and a unique index for each condition. DNA libraries were purified by AMPure XP beads and measured by Qubit. Fragment size was checked by Tape station. Libraries were pooled and subjected to 75-bp paired-end sequencing on a Nextseq550 platform at DKFZ Next Generation Sequencing Core Facility.


title: KO_T0_H2AK118ac_2


title: kidney, HFD, miR 1275


title: kidney, HFD, miR 1267


title: kidney, HFD, miR 1271


title: urine, HFD, miR 1255


title: KO_UT_nobrg1i_DSB3_7


title: KO_T4_H2AK118ac_3


title: kidney, HFD, miR 1256


title: KO_UT_nobrg1i_DSB3_2


title: kidney, HFD, miR 1259


title: kidney, HFD, miR 1252


title: KO_T4_nobrg1i_DSB3_8


title: urine, SD, miR 1245


title: urine, SD, miR 1246


title: KO_T4_nobrg1i_DSB3_7


title: KO_T4_nobrg1i_DSB3_2


title: KO_T4_nobrg1i_DSB3_1


title: kidney, SD, miR 1249


title: kidney, SD, miR 1248


title: kidney, SD, miR 1247


title: KO_T0_nobrg1i_DSB3_8


title: kidney, SD, miR 1244


title: KO_T0_nobrg1i_DSB3_7


title: KO_UT_nobrg1i_DSB3_1


title: kidney, SD, miR 1245


title: KO_T0_nobrg1i_DSB3_2


title: WT_UT_nobrg1i_DSB3_2


title: WT_UT_nobrg1i_DSB3_3


title: WT_UT_nobrg1i_DSB3_1


title: WT_UT_nobrg1i_DSB3_7


title: WT_UT_nobrg1i_DSB3_8


title: kidney, HFD, miR 1255


title: WT_T4_nobrg1i_DSB3_2


title: KO_T0_nobrg1i_DSB3_1


title: WT_UT_nobrg1i_DSB3_9


title: WT_T4_nobrg1i_DSB3_1


title: WT_T4_nobrg1i_DSB3_8


title: kidney, SD, RNA 1251


title: kidney, SD, RNA 1249


title: kidney, SD, miR 1251


title: kidney, SD, RNA 1250


title: kidney, SD, RNA 1248


title: WT_T0_nobrg1i_DSB3_9


title: kidney, SD, miR 1250


title: WT_T0_nobrg1i_DSB3_8


title: kidney, SD, RNA 1247


title: kidney, SD, RNA 1245


title: kidney, SD, RNA 1246


title: KO_UT_brg1i_DSB3_6


title: WT_T0_nobrg1i_DSB3_2


title: kidney, SD, RNA 1244


title: WT_T0_nobrg1i_DSB3_3


title: KO_UT_brg1i_DSB3_5


title: WT_T4_nobrg1i_DSB3_7


title: KO_UT_brg1i_DSB3_2


title: KO_UT_brg1i_DSB3_3


title: KO_UT_brg1i_DSB3_1


title: KO_T4_brg1i_DSB3_6


title: KO_T4_brg1i_DSB3_4


title: KO_T4_brg1i_DSB3_2


title: KO_T4_brg1i_DSB3_3


title: KO_T4_brg1i_DSB3_5


title: KO_T0_brg1i_DSB3_5


title: KO_T0_brg1i_DSB3_6


title: KO_T0_brg1i_DSB3_2


title: KO_T0_brg1i_DSB3_3


title: KO_T0_brg1i_DSB3_4


title: KO_UT_brg1i_DSB3_4


title: KO_T4_brg1i_DSB3_1


title: 4sUseq, INTS11-AID cells, INTS11, +IAA 1

city: Kunming City

first: Jiangyang Li

last: Jingyang Li

state: Yunnan Province

address: School of Life Science, Yunnan University, Chenggong District

department: School of Life Science

country: China

institute: Yunnan Universiity

description:
IAA_rep_1
4sUseq.txt

data_processing:
Raw reads were processed with Trim Galore (v0.6.6) to remove adaptors and low-quality reads with the parameter “-q30
Ribosomal RNA contaminations were removed using Bowtie (v1.3.0) with “-un”.
Remaining reads were aligned to the human genome (UCSC hg38) with STAR (v2.7.9a), whose results were converted to BAM file with SAMtools (v1.7).
Gene expression quantification was performed with featureCounts tool of Subread (v2.0.1). Differential expression analysis was performed using DESeq2 R package (v1.34.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized counts for each samples

growth_protocol: DMEM, 10% fetal bovine serum. Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
Chromatin was extracted by Chromatin RNA separation and chromatin RNA was extracted by Trizol. Construction of chromatin RNA libraries. After 1h treatment with IAA, PBS was washed away for three times and replaced with fresh medium for 7h culture, and chromatin RNA was extracted to construct library 4sU-seq and TT-seq and data processing Detailed procedures of 4sU-seq and TT-seq followed previously pub- lished papers69,70. For 4sU-seq, cells were treated with 4-thiouridine (4sU) at a final concentration of 2 mM for 15 min, and total RNA was extracted by TRIzol (Invitrogen, 15596018). A mixture of 80 μg of total RNA and 2 μg of 4sU-labeled RNA from Drosophila S2 cells (as spike-in) was biotinylated in 4sU-seq biotinylation mix at room temperature for 2 h. Subsequently, RNA was purified by chloroform extraction twice and precipitated with isopropanol. After denaturation for 10 min at 65 °C, RNA was incubated with 50 μl of prewashed streptavidin mag- netic C1 beads (Invitrogen, 65002), with gentle rotation for 15 min at room temperature. Beads were washed five times with bead wash buffer (1 M NaCl, 5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 0.05% Tween 20). The 4sU-labeled RNA was eluted with 100 mM DTT and purified by a kit (Zymo Research, R1016). The RNA libraries were constructed with VAHTS Universal V8 RNA-seq Library Prep kit for MGI (Vazyme, NRM605-02). The quality of libraries was monitored by Bio-Fragment Analyzer (Bioptic, c100001) and the libraries were sequenced with MGI 2000 instrument (MGI-SEQ, BGI). For TT-seq, cells were treated with 2 mM 4sU for 7 min and quenched with direction RNA extraction by TRIzol reagent (Invitrogen, 15596018). The mixture of 80 μg total RNA and 2 μg 4sU-labeled RNA of Drosophila S2 cells (as spike-in) was fragmented using 20 μl 1 M NaOH for 23 min on ice and neutralized with 80 μl 1 M Tris-HCl (pH 6.8). RNA was biotinylated in TT-seq biotinylation mix for 30 min at room temperature.
Library Construction using universal RNA-seq library prep kit (Vazyme, NRM605-02). 500ng of Chromatin RNA was used for the construction of sequencing libraries.
Chromatin RNA-seq, 4sU-seq, TT-seq

treatment_protocol: FBS-free DNEM was treated for 14h, 500uM IAA for 1h, 100ng/ul EGF Protein, Human, recombinant Protein (ECD)(Solarbio,10605-HNAE) for 30min, and 2000U IFN-beta Protein(Sino Biological Inc.,50708-mccH) for 1h

value: colon cancer cell

value: auxin(IAA)

tag: time

tag: fraction

value: 4sU RNA


title: TTseq, INTS11-AID cells, ASO, 5'U1 ASO 1

description:
5U1_rep_1
TTseq_U1ASO.txt

value: 5'U1 ASO


title: TTseq, INTS11-AID cells, ASO, 5'U1 ASO 2

description:
5U1_rep_2
TTseq_U1ASO.txt


title: TTseq, INTS11-AID cells, ASO, Control 1

description:
CTRL_rep_1
TTseq_U1ASO.txt

value: DMSO


title: 4sUseq, INTS11-AID cells, INTS11, +IAA 2

description:
IAA_rep_2
4sUseq.txt


title: 4sUseq, INTS11-AID cells, INTS11, Control 2

description:
CTRL_rep_2
4sUseq.txt


title: KO_T0_brg1i_DSB3_1

value: AID-DivA

value: osteosarcoma


title: 4sUseq, INTS11-AID cells, INTS11, Control 1

description:
CTRL_rep_1
4sUseq.txt


title: WT_UT_brg1i_DSB3_6

value: WT


title: TTseq, INTS11-AID cells, INTS11, +IAA 2

description:
IAA_rep_2
TTseq_INTS11.txt


title: WT_UT_brg1i_DSB3_5

value: untreated


title: TTseq, INTS11-AID cells, INTS11, +IAA 1

description:
IAA_rep_1
TTseq_INTS11.txt


title: TTseq, INTS11-AID cells, ASO, Control 2

description:
CTRL_rep_2
TTseq_U1ASO.txt


title: WT_UT_brg1i_DSB3_4


title: WT_UT_brg1i_DSB3_2


title: NCI_H1650Re, post-SCLC, rep3

city: Shenyang

first: cheng

last: yang

address: wenhua street  number 103

institute: Shenyang Pharmaceutical University

data_processing:
Sequencing data was filtered with SOAPnuke
The clean reads were mapped to the reference genome using HISAT2
Bowtie2 was applied to align the clean reads to the gene set
Expression level of gene was calculated by RSEM
differential expression analysis was performed using the DESeq2
Assembly: mm10
Supplementary files format and content: Processed data files include FPKM values for each sample

molecule: polyA RNA

source_name: lung

extract_protocol:
RNA was extracted using a miRNeasy Tissue/Cells Advanced Mini Kit(Qiagen,217604)
RNA libranes was constructed using a Optimal Dual-mode mRNA Library Prep Kit(BGI, LR00R96)

value: lung

value: lung cell line

tag: time point

value: post-SCLC


title: WT_UT_brg1i_DSB3_1


title: NCI_H1650Re, post-SCLC, rep2


title: WT_T4_brg1i_DSB3_4

value: 4h after auxin treatment


title: WT_T4_brg1i_DSB3_6


title: NCI_H1650Re, post-SCLC, rep1


title: NCI_H1650, pre-LUAD, rep2

value: pre-LUAD


title: NCI_H1650, pre-LUAD, rep3


title: WT_UT_brg1i_DSB3_3


title: WT_T4_brg1i_DSB3_3


title: NCI_H1650, pre-LUAD, rep1


title: WT_T4_brg1i_DSB3_5


title: WT_T4_brg1i_DSB3_2


title: WT_T4_brg1i_DSB3_1


title: WT_T0_brg1i_DSB3_6

value: 0h after auxin treatment


title: WT_T0_brg1i_DSB3_3


title: WT_T0_brg1i_DSB3_1


title: KO_UT_nobrg1i_DSB2_6

value: ARID1A KO


title: KO_UT_nobrg1i_DSB2_3


title: WT_T0_brg1i_DSB3_4


title: KO_UT_nobrg1i_DSB2_4


title: KO_UT_nobrg1i_DSB2_5


title: s6_p20-2

type: RNA

city: Taipei

first: Hung-Cheng

last: Lai

address: No.250, Wuxing St.

department: Department of Obstetrics and Gynecology, School of Medicine, College of Medicine,

country: Taiwan

institute: Taipei Medical University

description: replicate 2

hyb_protocol: HumanHT-12 v4 - Standard Illumina hybridization protocol

scan_protocol: HumanHT-12 v4 - Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

source_name: cell line: CP70

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays (HumanHT-12 v4 - Standard Illumina labeling protocol)

growth_protocol: CP70 cells were propagated in RPMI1640 supplemented with 10% FBS, and 50 units/ml of P/S.

extract_protocol: RNA extraction was performed using TriZol reagent according to the manufactuerer’s protocol.

treatment_protocol: CP70 cells were transfected with pcDNA3.1/SMAD7- plasmid or empty vector using LipofectamineTM 2000, followed by selection with 400μg/ml Geneticin

tag: group


title: c1_p20-1

description: replicate 1

value: Control


title: s6_p20-1

description: replicate 1


title: TTseq, INTS11-AID cells, INTS11, Control 1

description:
CTRL_rep_1
TTseq_INTS11.txt

value: colon cancer cell


title: KO_T4_nobrg1i_DSB2_5


title: KO_UT_nobrg1i_DSB2_1


title: KO_T4_nobrg1i_DSB2_4


title: c1_p20-2

description: replicate 2


title: KO_T4_nobrg1i_DSB2_2


title: KO_UT_nobrg1i_DSB2_2


title: TTseq, INTS11-AID cells, INTS11, Control 2

description:
CTRL_rep_2
TTseq_INTS11.txt


title: KO_T4_nobrg1i_DSB2_1


title: KO_T0_nobrg1i_DSB2_5


title: TRIM24-MET-r_P2

type: genomic

city: Memphis

first: Jared

last: Andrews

state: Tennessee

address: 262 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description:
Methylation data from recurrent post-chemotherapy, pre cabozantinib patient tumor, piece 2
205113580179_R03C01

hyb_protocol: Illumina protocol

scan_protocol: Illumina HiScan System according to the manufacturer's protocol

data_processing: Raw IDAT files from the human patient tumors and cell lines were assessed for quality control and pre-processed with the sesame R package (v1.14.2) with the default QCDPB preprocessing steps. Noob normalization was applied to all samples to derive beta values.

label: bioton/DNP

source_name: Recurrent post-chemotherapy, pre cabozantinib patient tumor, piece 2

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

tag: gender

value: male


title: TRIM24-MET-r_P3

description:
Methylation data from recurrent post-chemotherapy, pre cabozantinib patient tumor, piece 3
205113580179_R04C01

source_name: Recurrent post-chemotherapy, pre cabozantinib patient tumor, piece 3


title: KO_T0_nobrg1i_DSB2_3


title: KO_T0_nobrg1i_DSB2_2


title: KO_T0_nobrg1i_DSB2_6


title: TRIM24-MET-r_P1

description:
Methylation data from recurrent post-chemotherapy, pre cabozantinib patient tumor, piece 1
205113580179_R02C01

source_name: Recurrent post-chemotherapy, pre cabozantinib patient tumor, piece 1


title: TRIM24-MET-i_line

description:
Methylation data from PDOX-derived cell line formed after transplantation of primary tumor cells.
205130650065_R03C01


title: WT_UT_nobrg1i_DSB2_3


title: WT_UT_nobrg1i_DSB2_6


title: TRIM24-MET-i_P3

description:
Methylation data from initial pre-treatment patient tumor, piece 3.
205113580083_R08C01

source_name: Initial pre-treatment patient tumor, piece 3

value: Initial pre-treatment patient tumor


title: TRIM24-MET-i_P4

description:
Methylation data from initial pre-treatment patient tumor, piece 4.
205113580179_R01C01

source_name: Initial pre-treatment patient tumor, piece 4


title: TRIM24-MET-i_P2

description:
Methylation data from initial pre-treatment patient tumor, piece 2.
205113580083_R07C01

source_name: Initial pre-treatment patient tumor, piece 2


title: TRIM24-MET-r_line

description:
Methylation data from cell line derived directly from surgical sample of recurrent patient tumor.
205130650065_R04C01

source_name: Cell line derived directly from surgical sample of recurrent patient tumor


title: iPSC_SC_64Kpa_Donor3

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

hyb_protocol: standard Illumina Protocols

scan_protocol: standard Illumina Protocols

data_processing: The data was analyzed with the minfi R package and normalized using ssNoob. CpG sites on XY chromosomes, non-CG probes, and SNP associated CpGs were removed. In addition, the detection P of the remaining CpGs were evaluated using SeSAMe package and CpG sites with detection P > 0.05 were removed.

label: Cy3, Cy5

label_protocol: standard Illumina Protocols

growth_protocol: iPSCs were cultured regularly on tissue culture plastic (TCP) coated with vitronectin (0.5 µg/cm2) in StemMACS iPS-Brew (Miltenyi Biotec, Bergish Gladbach, Germany) and passaged regularly using intermittent Ethylenediaminetetraacetic acid (EDTA) treatment.

extract_protocol: Genomic DNA was isolated using the NucleoSpin Tissue Kit (Macherey-Nagel) and quantified on a NanoDrop ND-1000 spectrophotometer (Thermo Scientific). 1.2 µg of DNA were bisulfite converted.

treatment_protocol: To investigate the impact of substrate elasticity, iPSCs were dissociated with Accutase (STEMCELL Technologies, Vancouver, Canada) and seeded (2-3×106 cells/cm2) on either PDMS with different Young´s modulus (0.2 kPa, 16 kPa, or 64 kPa; Advanced Biomatrix, Carlsbad, CA, USA) or TCP (approximately 1 GPa; TPP, Trasadingen, Switzerland), with Matrigel coating. Differentiation towards endoderm, mesoderm was carried out for 5 days and ectoderm for 7 days using STEMdiff Trilineage Differentiation Kit (STEMCELL Technologies).

tag: lineage

value: SC

value: female

tag: age

tag: substrate_elasticity (kpa


title: iPSC_ENDO_64Kpa_Donor3

value: ENDO


title: WT_UT_nobrg1i_DSB2_5

value: AID-DivA

value: osteosarcoma


title: iPSC_MESO_64Kpa_Donor3

value: MESO


title: TRIM24-MET-i_P1

description:
Methylation data from initial pre-treatment patient tumor, piece 1
203723050066_R02C01

source_name: Initial pre-treatment patient tumor, piece 1

tag: tissue


title: WT_UT_nobrg1i_DSB2_1

value: WT

value: untreated


title: WT_T4_nobrg1i_DSB2_6


title: WT_T4_nobrg1i_DSB2_4


title: iPSC_ECTO_16Kpa_Donor3

value: ECTO


title: WT_T4_nobrg1i_DSB2_3

value: 4h after auxin treatment


title: WT_T0_nobrg1i_DSB2_6


title: iPSC_ECTO_64Kpa_Donor3


title: iPSC_ENDO_16Kpa_Donor3


title: WT_T4_nobrg1i_DSB2_1


title: iPSC_ECTO_0.2Kpa_Donor3


title: iPSC_SC_0.2Kpa_Donor3


title: WT_T0_nobrg1i_DSB2_5


title: iPSC_MESO_16Kpa_Donor3


title: WT_UT_nobrg1i_DSB2_4


title: iPSC_SC_16Kpa_Donor3


title: WT_T0_nobrg1i_DSB2_3


title: iPSC_MESO_64Kpa_Donor2


title: H3K9ac-ChRD-PET-rep2

city: Wuhan

first: guoting

last: chen

address: 1 Shizishan Street, Hongshan District

institute: National Key Laboratory of Crop Genetic Improvement

data_processing:
Raw reads were filtered for adapter and low quality reads by Trimmomatic
Splitting data into DNA-end and RNA-end data, mapping DNA-end data to the reference genome by BWA
RNA-end data to the reference genome by HISAT2 and Bowtie2
Extracting the uniquely matched reads
Converting bam files to BigWig files
Genome build by BWA and assembly by HISAT2 and Bowtie2
The hic format file was converted by juicer_tools
Assembly: Download the genome from http://rice.hzau.edu.cn/
Supplementary files format and content: The bedpe files provide processed RNA-DNA interaction data.
Library strategy: ChRD-PET

molecule: nuclear RNA

organism: Oryza sativa Indica Group

source_name: mature leaf

growth_protocol: Human K562 cells (ATCC) were cultured in DMEM containing 10% FBS (Gibco) and 1% penicillin-streptomycin (Gibco) and growing at 37 °C and 5% CO2 in a cellmate CO2 incubator (Esco Scientific). Cells were cross-linked with 1% formaldehyde (Sigma-Aldrich) in 1×PBS (Thermo Fisher) for 10 min with rotation at room temperature, followed by quenching with 0.2M glycine for 5 min at room temperature with rotation. Cells were washed three times with 1×PBS and stored at -80 °C. Rice Xian/indica cv. Minghui 63 (MH63) seeds were used and sown in May. Germinated seedlings were transplanted into a paddy field (Huazhong Agricultural University at Wuhan, China), and grown under normal agricultural conditions. Mature leaves were collected on July, and were immediately single cross-linked with 1% formaldehyde and stored at -80 °C.

extract_protocol:
Approximately 1×10^6- 1×10^7 crosslinked cells were used per replicate. Cell nuclei were isolated in 1 mL lysis buffer (10mM Tris pH 7.5, 10mM NaCl, 0.2% NP40, 1×protease inhibitors, 0.2 U/μl RiboLock RNase) (Thermo Fisher), and incubated for 10min on ice followed by centrifugation for 3min at 2500g and 4°C. The nuclei were washed twice with 300µl 1×wash buffer A (20mM HEPES pH 7.6, 150mM NaCl, 0.5mM Spermidine, 1×protease inhibitors, 0.2U/μl RiboLock RNase) (Thermo Fisher), and nuclei were collected by centrifugation for 3min at 2500g and 4 °C. Nuclei were then resuspended in Antibody buffer (495μl 1×wash buffer A, 5μl 5% digitonin, 2μl 0.5M EDTA, 1.6μl 30%BSA, 10μg antibody (H3K4me3, Abcam, ab8580; H3K9ac, Abcam, ab10812; CTCF, Abcam, ab188408), and incubated at 4°C for 2h with rotation. Nuclei were pelleted for 3 min at 2500g and washed five times with 300μl 1×wash buffer A, resuspended 500µl 1×transposase incubation buffer (20mM HEPES pH 7.6, 300mM NaCl, 0.5mM Spermidine, 0.01% digitonin, 1×protease inhibitors, 0.2U/μl RiboLock RNase) (Thermo Fisher), followed by adding 5μl TTE Mix, and incubated at 4°C for 1h with rotation. Nuclei were collected and washed five times with 300µl 1×transposase incubation buffer and resuspended in tagmentation buffer (500µl 1×transposase incubation buffer, 5µl 1M MgCl2), and incubated at 37°C for 1h. Next, 500µl of 40mM EDTA (Thermo Fisher) was added to stop the reaction. The isolated nuclei were washed twice with 500µl 1×PBS (Thermo Fisher) and then incubated in 200µl permeabilization buffer (190µl nuclease-free water, 10µl 10% SDS) (Thermo Fisher) at 62°C for 10min, and immediately quenched the SDS reaction by adding add 580μl of nuclease-free water and 100μl of 10% (vol/vol) Triton X-100 (Sigma-aldrich), and incubated at 37°C for 15min with rotation. The isolated nuclei were washed twice with 500µl 1×wash buffer B (20mM Tris-HCl, pH 7.5, 10mM MgCl2 and 0.2% Tween 20) and resuspended in 500µl 1× CutSmart buffer (NEB), followed by adding 1.6µl RNase If (NEB) with dilution tenfold in 1× PBS, and incubated at 37°C for 3min with rotation followed by incubation for 5min on ice. Nuclei were collected by centrifugation, then resuspended by 400µl PNK solution containing 1×T4 PNK reaction buffer, 1mM ATP, 1U/μl RiboLock RNase and 1U/μl T4 PNK (Thermo Fisher) at 37°C for 40min with rotation. The specific bridge linker was designed containing 5ʹ phosphorylation [5Phos] and Internal Biotin dT [ibiodT] chemical modifications. The forward strand is: 5′-[5APP]CCTCGATAC/iBIOdT/TGAGCTGAC-3′, and reverse strand is 5′-[5Phos]GTCAGC/iBIOdT/CAAGTATCGAG-3′. The 5′App ends of forward strand was treated by using a DNA 5′ Adenylation Kit (NEB). The isolated nuclei were washed twice with 500µl 1×wash buffer B and resuspended in 400µl of RNA ligation solution (1×T4 RNA ligase reaction buffer, 1U/μl RiboLock RNase, 10U/μl T4 RNA Ligase 2 truncated, 1.5pmol/μl bridge linker, 15% (w/v) PEG 8000, 0.1% Triton X-100) (NEB), and incubated overnight at 16 °C with rotation. The nuclei were pelleted by centrifugation, resuspended in 400 μl reverse transcription solution (1×MMLV buffer, 0.5mM dNTP, 8U/μl MMLV (RNase H-), 1U/μl RiboLock RNase) (Promega), and then incubated at 42 °C for 1 h. The isolated nuclei were washed five times with 500μl 1×wash buffer B, resuspended in T4 DNA ligation solution (1×DNA ligase reaction buffer with 10mM ATP, 4U/μl T4 DNA ligase, 0.1% (vol/vol) Triton X-100 and 0.1 mg/mLBSA) (NEB), incubated overnight at 16 °C with rotation. The isolated nuclei were resuspended in proteinase K solution (50 mM Tris-HCl, pH 7.5, 1% SDS, 100mM NaCl, 1mM EDTA and 1mg/mL proteinase K) at 65 °C for 3h with shaking at 800 rpm. RNA/DNA complex was extracted and dissolved in nuclease-free water (Thermo Fisher). The purified RNA/DNA complexes were incubated with gap-filling solution (10×NEBuffer r2.1,1mM dNTP and 0.18U/μl T4 DNA polymerase) (NEB) at room temperature for 40min to repair the pG-Tn5 transposition gap, followed by second-strand cDNA synthesis.
DNA-cDNA complexes were converted to DNA library according to the TruePrep DNA Library Prep Kit for Illumina (Vazyme, cat. no. TD501). The fragments containing biotinylated bridge-linker were enriched by M280 beads (Thermo Fisher) before PCR, and enriched library DNA is size-selected by using AMPure XP beads (Beckman), and sequenced (2×150 bp) using Illumina Hiseq X-Ten (Annoroad Gene Technology).

tag: cultivar

value: Minghui 63

value: mature leaf


title: H3K9ac-ChRD-PET-rep1


title: WT_UT_brg1i_DSB2_6

tag: cell type


title: WT_T0_nobrg1i_DSB2_2

tag: genotype

value: 0h after auxin treatment


title: iPSC_ECTO_64Kpa_Donor2


title: H3k9ac_TaDRIM-Seq-PM-rep2

data_processing:
Raw reads were filtered for adapter and low quality reads by Trimmomatic
Splitting data into DNA-end and RNA-end data, mapping DNA-end data to the reference genome by BWA
RNA-end data to the reference genome by HISAT2 and Bowtie2
Extracting the uniquely matched reads
Converting bam files to BigWig files
Genome build by BWA and assembly by HISAT2 and Bowtie2
The hic format file was converted by juicer_tools
Assembly: Download the genome from http://rice.hzau.edu.cn/
Supplementary files format and content: The bedpe files provide processed RNA-DNA interaction data.
Library strategy: TaDRIM-Seq


title: iPSC_MESO_16Kpa_Donor2


title: WT_UT_nobrg1i_DSB2_2

tag: cell line


title: WT_UT_brg1i_DSB2_5

tag: treatment


title: iPSC_ENDO_16Kpa_Donor2


title: iPSC_ENDO_64Kpa_Donor2


title: iPSC_MESO_0.2Kpa_Donor3


title: iPSC_ENDO_0.2Kpa_Donor3


title: H3k9ac_TaDRIM-Seq-PM-rep1


title: WT_UT_brg1i_DSB2_4

tag: viewpoint


title: NC2h_3

city: shenyang

first: quangang

last: liu

state: liao ning

address: maguanqiao

department: Forestry College

institute: Shenyang Agricultural University

description: Bloom stage,pistil

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. 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, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)；Nt (NCBI non-redundant nucleotide sequences)；Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO (Gene Ontology).
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK2 or Samtools software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters ( clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD < 5.0 or HRun > 5), and only SNPs with distance > 5 were retained.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Supplementary files format and content: Analysis Name: Prunus sibirica F106 Whole Genome v1.0 Assembly & Annotation.  Source: (F106) PacBio,BioNano and Hi-C.
Supplementary files format and content: All_gene_fpkm.list include FPKM values for each sample.

organism: Prunus sibirica

source_name: Floral organ; pistil

extract_protocol:
Flower  were grinned under liquid nitrogen to fine powder using cooled mortar and pestle. Samples were placed in Eppendorf tubes. Total RNA was extracted from flower buds by EASYspin Plant microRNA Kit.
The thirty RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Floral organ; pistil

tag: clone

value: weak freezing resistance clone (NC_371)

value: Treat at -4℃ for 2h


title: WT_UT_brg1i_DSB2_3

tag: replicate


title: NC2h_2

description: Bloom stage,pistil


title: NC2h_1

description: Bloom stage,pistil


title: S.pombe-spt4D-rep2

city: Kobe

first: Atsushi

last: Matsuda

address: 588-2, Iwaoka, Iwaoka-cho, Nishi-ku

country: Japan

institute: National Institute of Information and Communications Technology

hyb_protocol: 50 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/micro-g cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 micro-l containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 micro-l of 2x GE hybridization buffer HI-RPM (Agilent) was added to the fragmentation mixture and hybridized to Agilent custom microarrays (8 x 15k format) 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.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8 x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5 micro-m, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software (ver 10.7.3.1, Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 028936_D_F_20100615) to obtain background subtracted and spatially detrended Processed Signal intensities.
5589 probes (including 60 control probes) are spotted multiply to fill 15744 spots in each array. A geometric mean of the gProcessedsignals of the spots for each probe was calculated to make a data set for 5589 probes. The geometric mean was normalized by the 75 percentile method (the value at 75% was set to 2500.) to get the value in the Matrix sheet. ID_REF in the Matrix sheet match the identifiers in the SPOT ID column in the 028936_D_GEO_20110527.txt file. When the average of the gIsWellAboveBG of the spots for each probe is higher than 0.55, the probe signal is considered more than the detection limit, ranked with “a” in the Rank columns.

organism: Schizosaccharomyces pombe

source_name: spt4 deleted cells at exponentially-growing phase replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit, one-color including Cy3-CTP (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated as follows: the cell pellet was frozen with liquid nitrogen and thawed on ice. Cells were washed once with pre-chilled water. The cell pellet was resuspended in 720 micro-l of TES(10mM Tris pH7.5, 10mM EDTA pH8, 0.5% SDS) on ice. 720 micro-l of acidic phenol-chloroform was added to the cell suspension and mixed immediately. The sample was incubated at 65°C for 1 hour, and then placed on ice for 1 min. The sample was centrifuged for 15 min. at 14000rpm at 4°C. 700 micro-l of water phase of the sample was added to 700 micro-l of acidic phenol-chloroform prepared in a phase lock tube (MaXtractTM HighDensity 2ml Qiagen), then mixed. The sample was centrifuged for 5min at 14000rpm at 4°C. 700 micro-l of water phase of the sample was added to 700 micro-l of chloroform prepared in a new phase lock tube, then mixed. The tube was centrifuged for 5 min at 14000rpm at 4°C. Total RNA from the 500 micro-l of the water phase was purified by ethanol precipitation.

treatment_protocol: A single colony of S. pombe cells on a YES plate was inoculated into YES liquid medium. Cells were incubated at 30°C and collected with filtration when they reached a density of 5x106 cells/ml.

value: spt4 deleted

value: exponentially-growing phase

tag: medium

value: YES

tag: temperature


title: iPSC_ECTO_16Kpa_Donor2

value: male


title: NC1h_3

description: Bloom stage,pistil

value: Treat at -4℃ for 1h


title: S.pombe-spt4D-rep1

source_name: spt4 deleted cells at exponentially-growing phase replicate 1


title: WT_UT_brg1i_DSB2_2

source_name: AID-DivA

value: AID-DivA

value: osteosarcoma


title: NC1h_2

description: Bloom stage,pistil


title: WT_UT_brg1i_DSB2_1

value: WT


title: NC1h_1

description: Bloom stage,pistil


title: NC30min_2

description: Bloom stage,pistil

value: Treat at -4℃ for 30min


title: S.pombe-pob3D-rep2

source_name: pob3 deleted cells at exponentially-growing phase replicate 2

value: pob3 deleted


title: WT_T4_brg1i_DSB2_6

value: 4h after auxin treatment


title: iPSC_SC_64Kpa_Donor2

value: SC


title: NC30min_1

description: Bloom stage,pistil


title: S.pombe-pob3D-rep1

source_name: pob3 deleted cells at exponentially-growing phase replicate 1


title: S.pombe-nhp6D-rep2

source_name: nhp6 deleted cells at exponentially-growing phase replicate 2

value: nhp6 deleted


title: iPSC_ENDO_0.2Kpa_Donor2

value: ENDO


title: NC15min_3

description: Bloom stage,pistil

value: Floral organ; pistil

value: Treat at -4℃ for 15min


title: WT_T4_brg1i_DSB2_4


title: NC15min_2

description: Bloom stage,pistil

value: weak freezing resistance clone (NC_371)


title: WT_T4_brg1i_DSB2_3


title: NC0h_2

description: Bloom stage,pistil

value: Treat at -4℃ for 0h


title: S.pombe-nhp6D-rep1

source_name: nhp6 deleted cells at exponentially-growing phase replicate 1

value: exponentially-growing phase


title: WT_T4_brg1i_DSB2_1


title: NC0h_3

description: Bloom stage,pistil


title: NC15min_1

description: Bloom stage,pistil


title: S.pombe-wildtype-for-rep3

source_name: wildtype  at exponentially-growing phase replicate 3

value: wildtype

value: YES


title: NC30min_3

description: Bloom stage,pistil


title: WT_T0_brg1i_DSB2_6

value: 0h after auxin treatment


title: S.pombe-wildtype-for-rep1

source_name: wildtype  at exponentially-growing phase replicate 1


title: S.pombe-wildtype-for-rep2

source_name: wildtype  at exponentially-growing phase replicate 2


title: CR2h_2

description: Bloom stage,pistil

value: strong frost resistance clone No. CR_453 (treatment group)

value: Treat at -4℃ for 2h


title: iPSC_ECTO_0.2Kpa_Donor2

value: ECTO

value: male


title: CR2h_1

description: Bloom stage,pistil


title: CR1h_3

description: Bloom stage,pistil

value: Treat at -4℃ for 1h


title: iPSC_ECTO_16Kpa_Donor1

value: female


title: iPSC_SC_16Kpa_Donor2

value: SC


title: WT_T0_brg1i_DSB2_5

value: AID-DivA

value: osteosarcoma

value: WT


title: iPSC_SC_16Kpa_Donor1


title: WT_SM_C_S6_L001

city: SEATTLE

first: Lakshmi

last: Mahendrawada

state: WA

address: 1100 FAIRVIEW AVE N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and S. pombe reference genome (ASM294v2.20) with Bowtie2 using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
SAM files for S. cerevisiae data were used as an input for HTseq-count with default settings. The GFF file with S. cerevisiae genomic features was downloaded from the Ensembl website.
HTSeq output files are used as input files for differential analysis using DESeq2 (using defaults settings)
Assembly: sacCer3 (S. cerevisiae), ASM294v2.20 (S. pombe)
Supplementary files format and content: Raw output files obtained fromHTSeq analysis

organism: Saccharomyces cerevisiae

source_name: MAT{alpha} ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0

growth_protocol: 30 degrees in a synthetic complete (SC) medium to mid-log phase.

extract_protocol:
Experiments were done as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Ovation Universal RNA-seq System kit (Tecan) was used for library construction.

treatment_protocol: Newly synthesized RNA molecules were labeled for 5 minute with 4TU.For experiments conductions under specific stress conditions,  selected samples were treated with SM, Galactose.

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0

value: SM starvation


title: iPSC_ENDO_0.2Kpa_Donor1

value: ENDO


title: iPSC_SC_0.2Kpa_Donor1


title: iPSC_MESO_0.2Kpa_Donor2

value: MESO


title: WT_T0_brg1i_DSB2_3


title: CR30min_3

description: Bloom stage,pistil

value: Floral organ; pistil

value: Treat at -4℃ for 30min


title: WT_SM_A_S4_L001


title: CR30min_1

description: Bloom stage,pistil


title: iPSC_SC_64Kpa_Donor1


title: CR1h_1

description: Bloom stage,pistil


title: WT_SM_B_S5_L001


title: WT_gal_C_S33_L001

value: Galactose induction


title: iPSC_SC_0.2Kpa_Donor2


title: WT_T0_brg1i_DSB2_2

value: 0h after auxin treatment


title: CR30min_2

description: Bloom stage,pistil

value: strong frost resistance clone No. CR_453 (treatment group)


title: iPSC_ECTO_0.2Kpa_Donor1

value: ECTO


title: KO_UT_brg1i_DSB2_6

value: ARID1A KO

value: untreated


title: CR2h_3

description: Bloom stage,pistil

value: Treat at -4℃ for 2h


title: CR1h_2

description: Bloom stage,pistil

value: Treat at -4℃ for 1h


title: iPSC_ENDO_64Kpa_Donor1

value: female


title: iPSC_ECTO_64Kpa_Donor1


title: CR0h_3

description: Bloom stage,pistil

value: Treat at -4℃ for 0h


title: KO_UT_brg1i_DSB2_5

value: AID-DivA

value: osteosarcoma


title: CR15min_2

description: Bloom stage,pistil

value: Treat at -4℃ for 15min


title: CR15min_1

description: Bloom stage,pistil


title: CR15min_3

description: Bloom stage,pistil


title: WT_gal_A_S31_L001

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0


title: iPSC_MESO_64Kpa_Donor1

value: MESO


title: KO_UT_brg1i_DSB2_3


title: WT_C_S15_L001


title: CR0h_2

description: Bloom stage,pistil

value: Floral organ; pistil


title: KO_UT_brg1i_DSB2_4


title: iPSC_ENDO_16Kpa_Donor1

value: ENDO


title: iPSC_MESO_0.2Kpa_Donor1


title: CR0h_1

description: Bloom stage,pistil


title: WT_B_S14_L001


title: KO_T4_brg1i_DSB2_6

value: 4h after auxin treatment


title: KO_UT_brg1i_DSB2_1


title: WT_A_S13_L001


title: KO2

city: Fuchu-shi

first: Jun

last: Kambe

state: Tokyo

address: -5-8 Saiwai-cho

department: Agriculture

institute: Kentaro Nagaoka

hyb_protocol: Fragmented and labeled ss-cDNA were hybridized for 16 hr at 45°C on GeneChip Clariom S Array, mouse in a rotating Hybridization Oven. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: Arrays were stained and washed in Affymetrix Fluidics Stations according to Affymetrix automated procedures. GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Transcriptome Analysis　Console (TAC) 4.0.2 using default analysis settings and global scaling as normalization method (sst-RMA). Normalized CHP files were analyzed with TAC 4.0.2.

label: Biotin

organism: Mus musculus

source_name: Mouse hippocampus

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip WT PLUS Reagent Kit User Guide, Thermo Fisher Scientific Applied Biosystems).

extract_protocol: Total RNA from hippocampus was extracted by ISOGENII (Nippon Gene Co., Ltd.). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2200 TapeStation.

tag: tisuue

value: hippocampus

tag: postnatal day

value: Day 10

tag: Sex

value: Male

tag: mother genotype

value: LAO1 KO


title: HiChIP_EC-23_H3K27ac_18351X2_Seq_combined_DMSO_rep2

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 2000 circle of hope drive

department: Oncological Sciences

institute: University of Utah

data_processing:
Paired-end Illumina sequencing reads from Illumina NovaSeq 6000 were aligned to the human Hg19 reference genome using HiC-Pro pipeline.
Hi-ChIP was analyzed using Hichipper to perform restriction site bias-aware modeling of the output from HiC-Pro and to call interaction loops.
Interaction loops were filtered where loops with at least one or more reads in both biological replicates of a particular treatment (E2 or DMSO) were kept and used for downstream analyses
Chromatin interactions that significantly change upon 1 hour of E2 induction were identified using DESeq2 with an adjusted p-value cutoff of 0.05
Assembly: Hg19
Supplementary files format and content: Paired end bed  (.bedpe) containing discovered loops
Library strategy: Hi-ChIP

growth_protocol: Ishikawa and HCI-EC-23 cells were grown in full media: RPMI 1640 medium (ThermoFisher) supplemented with 10% fetal bovine serum (FBS) (ThermoFisher) and 1% penicillin-streptomycin (ThermoFisher) and were incubated at 37°C with 5% CO2. Cells were transferred and maintained in hormone-depleted media consisting of phenol red-free RPMI 1640 (ThermoFisher) supplemented with 10% charcoal-dextran FBS (Sigma Aldrich) and 1% penicillin-streptomycin (ThermoFisher) for 5 days prior to E2 treatment

extract_protocol:
Chromatin was crosslinked with 1% formaldehyde in growth media and isolated using Hi-C lysis buffer supplemented with protease inhibitor. Antibody (Abcam, ab4729) against H3K27ac was used to pull down crosslinked chromatin associated with H3K27ac overnight at 4C.
Hi-ChIP as previously described by M. R. Mumbach et al.,.Nat Methods 13, 919-922 (2016).

treatment_protocol: Ishikawa and HCI-EC-23 maintained in estrogen deprived media for 5 days  were treated with either 10 nM E2 or DMSO for 1 hour

value: endometrioid adenocarcinoma

tag: chip antibody'

value: anti-H3K27ac (Abcam, ab4729)

value: 1 hour 0.1% DMSO


title: RAP1_C_S18_L001

source_name: MAT{alpha} ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 RAP1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 RAP1-MNase::TRP1


title: HiChIP_EC-23_H3K27ac_18351X3_Seq_combined_E2_rep1

value: 1 hour 10 nM E2


title: iPSC_MESO_16Kpa_Donor1

tag: lineage

tag: gender

value: female

tag: age

tag: substrate_elasticity (kpa


title: KO1

tag: genotype


title: HiChIP_EC-23_H3K27ac_18351X4_Seq_combined_E2_rep2

tag: cell line

tag: cell type


title: KO3


title: KO_T4_brg1i_DSB2_5

value: AID-DivA

value: osteosarcoma

value: ARID1A KO

tag: treatment

tag: viewpoint


title: KO_UT_brg1i_DSB2_2

value: untreated

tag: replicate


title: KO_T4_brg1i_DSB2_4


title: RAP1_B_S17_L001


title: WT3

value: WT


title: RAP1_A_S16_L001


title: WT1


title: HiChIP_Ishi_H3K27ac_18537X3_Seq_Combined_E2_rep1

source_name: Ishikawa

value: Ishikawa


title: HiChIP_EC-23_H3K27ac_18351X1_Seq_combined_DMSO_rep1


title: WT2


title: GCN4_SM_C_S12_L001

source_name: MAT{alpha} ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 GCN4-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 GCN4-MNase::TRP1

value: SM starvation


title: HiChIP_Ishi_H3K27ac_18537X4_Seq_CombinedE2_rep2


title: HiChIP_Ishi_H3K27ac_18537X1_Seq_Combined_DMSO_rep1


title: HiChIP_Ishi_H3K27ac_18537X2_Seq_Combined_DMSO_rep2


title: KO_T4_brg1i_DSB2_2

value: 4h after auxin treatment


title: KO_T4_brg1i_DSB2_3


title: KO_T4_brg1i_DSB2_1


title: NPR5

city: Shanghai

first: Xuebo

last: Liu

address: 389 Xincun Road,Putuo District

department: Department of Cardiology

institute: Tongji Hospital of Tongji University

description: 10× Genomics

library_source: transcriptomic single cell

data_processing:
Single-cell expression data, including de-multiplexing, genome alignment (GRCh38), barcode counting, and unique molecular identifier (UMI) counting, were processed using the Cell Ranger pipeline (v3.0.1, 10× Genomics). Seurat (V3.0.2) was used to analyze the gene barcode matrix and data integration of UMI counting.
This output was then imported into Seurat (v3.0.2) R for subsequent quality control and downstream analysis of single-cell RNA sequencing data (15). The PercentFeatureSet function of the Seurat software package was used to calculate the mitochondrial gene expression (16). Cells with >25% UMIs from the mitochondrial genome were removed through quality control. The integrated matrix was then scaled and the ﬁrst 30 dimensions from principal component analysis (PCA) were used for t-distributed stochastic neighbor embedding (t-SNE) visualization. We applied the same procedure of scaling, dimensionality reduction, and clustering to the specific sets of sub-clustering. We used the Wilcoxon rank-sum test to ﬁnd signiﬁcantly differentially expressed genes (DEGs) in each cluster by comparing other clusters. SingleR and cardinal marker genes were used to identify cell types (17).
Assembly: hg18
Supplementary files format and content: Tab-separated values files and  matrix files

source_name: PBMC

extract_protocol:
We continuously collected peripheral arterial blood samples of patients with PR and NPR before coronary angiography within six hours of symptom onset. The samples were collected in EDTA-coated tubes before heparin or any contrast agent was administered.
We processed all blood samples within 2 h of collection. We used a Ficoll–Plaque medium to separate peripheral blood mononuclear cells (PBMCs). Cell viability exceeded 90% as determined by trypan blue staining. Chromium Next GEM Single Cell 3’ v3 (10× Genomics) was used for single cell capture and library construction according to the specifications of the manufacturer. Sequencing was performed on the Illumina NovaSeq platform.

tag: tissue

value: PBMC

tag: subject status

value: AMI patients without plaque rupture


title: NC0h_1

description: Bloom stage,pistil

source_name: Floral organ; pistil

value: Floral organ; pistil

tag: clone

value: weak freezing resistance clone (NC_371)

value: Treat at -4℃ for 0h


title: NPR4

description: 10× Genomics


title: NPR3

description: 10× Genomics


title: NPR1

description: 10× Genomics


title: KO_T0_brg1i_DSB2_4

value: 0h after auxin treatment


title: Gal4_gal_C_S39_L001

source_name: MAT{alpha} ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 GAL4-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 GAL4-MNase::TRP1

value: Galactose induction


title: Gal4_gal_B_S38_L001


title: PR3

description: 10× Genomics

value: AMI patients with plaque rupture


title: PR4

description: 10× Genomics


title: PR2

description: 10× Genomics


title: Gal4_gal_A_S37_L001


title: GCN4_SM_B_S11_L001


title: CYC8_C_S21_L001

source_name: MAT{alpha} ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 CYC8-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 CYC8-MNase::TRP1


title: PR1

description: 10× Genomics


title: TTC466,iERG562,rep4

city: Columbus

first: Cenny

last: Taslim

address: 700 Children's Drive

institute: Nationwide Children's Hospital

data_processing:
Low quality and adapter sequences were trimmed using Trim_galore
Trimmed sequences were mapped to hg38 using STAR with 2-pass approach
Reads were assigned to features using featureCounts
Normalization, differential analysis and statistical reports were done using DESeq2 and SARTools
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw and normalized counts for each sample generated by DESeq2
Supplementary files format and content: tab-delimited text file include log2FoldChange, p-values adjusted and other the statistics generated by DESeq2 for each sample

growth_protocol: A673 cells were grown in DMEM + 10% FBS + PSQ + 1% Sodium Pyruvate. TTC466, 402-91, 1765-92, SUCCS1 and DTC1 cells were grown in RPMI-1640 + 10% FBS + PSQ. DL221 cells were grown in DMEM + 10% FBS + PSQ. JN-DSRCT and BER cells were grown in DMEM/F12 + 10% FBS + PSQ.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen). 300ng of total RNA was used for library prep.
NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: Cells were seeded at 30% confluency and left to adhere overnight. After 24 hours, cells were dosed with DMSO or Seclidemstat equating calculated IC90 for that cell line. Cells were harvested for RNA extraction after 48 hours.

value: Ewing sarcoma

value: knockdown/rescue with EWSR1::ERG (562) construct


title: TTC466,iERG562,rep3


title: GCN4_SM_A_S10_L001


title: NPR2

description: 10× Genomics


title: CYC8_B_S20_L001


title: TTC466,iERG197,rep4

value: knockdown/rescue with empty vector (197)


title: MSN2_37_C

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and D. melanogaster reference genome (release 6.06) with Bowtie2 (Langmead and Salzberg, 2012) using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
For each base pair in the genome, we counted the number of paired-end fragments aligned over it.
Signal per base pair was normalized by the number of all D. melanogaster reads mapped for the sample and multiplied by 10000 (arbitrarily chosen number).
Assembly: sacCer3 (S. cerevisiae), release 6.06 (D. melanogaster)
Supplementary files format and content: Processed data is provided in a bigwig format and contains spike-in normalized signal per base pair.
Library strategy: ChEC-seq

source_name: MATα {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 MSN2-MNase::TRP1

extract_protocol:
ChEC-seq was performed as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Sequencing libraries were constructed as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.

treatment_protocol: For experiments conductions under specific stress conditions,  selected samples were treated with either DMSO or SM, no heat shock (30°C) or heat shock (37°C)

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 MSN2-MNase::TRP1

value: heat shock


title: MSN2_37_B


title: CYC8_A_S19_L001


title: Oleacein pretreated and LPS induced group_rep2

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: Tennodai 1-1-1

institute: University of Tsukuba

description:
Gene expression data from mice hippocampus: mice were orally administered 10 mg/kg body weight oleacein daily for 10 consecutive days. On the 10th day of oral administration, mice received a single intraperitoneal injection of 0.85 mg/kg body weight LPS. Twenty-four hours following the intraperitoneal injection, the tail suspension test (TST) was conducted. After the completion of the TST, all mice were euthanized via cervical dislocation, and their brain hippocampus samples were collected
SST-RMA

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S array, Mouse; ThermoFisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (ThermoFisher Scientific).

data_processing:
The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. Further, gene-level analysis was performed using the Limma Bioconductor package. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above background (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7.
Signal intensity of all the samples derived from Transcriptome analysis console software (sheet 2 ). For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CEL files). filter criteria was set as p value < 0.05 (one-way between-subjects ANOVA) and fold change > 2 (in linear space)
signal space transformation robust multi-chip analysis (SST-RMA) algorithm (Transcriptome Analysis Console, version 4)

source_name: mice hippocampus, 10 mg/kg body weight oleacein daily for 10 days, a single intraperitoneal injection of 0.85 mg/kg body weight LPS, TST

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol (ThermoFisher Scientific) from 100 ng/ uL total RNA

growth_protocol: For the in vivo study, microarray analysis was performed on RNA samples extracted from the mice hippocampus of the following groups: saline-administered control, saline-administered and LPS-injected (LPS), and OC-administered and LPS-injected (Oleacein+LPS) groups

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: 8-week-old male ICR mice were obtained from Jackson Laboratory Japan (Kanagawa, Japan). They were housed individually in cages and kept under controlled environmental conditions, including a room temperature maintained at 21-23°C, a 12-hour light/dark cycle, humidity levels ranging from 50-55%, and ad libitum access to food and water. After a one-week acclimation period to the laboratory conditions, the experimental procedures began. After the acclimation period, the mice were orally given saline, fluoxetine (Flux) at a dose of 10 mg/kg body weight (obtained from FUJIFILM Wako Pure Chemical Corporation) as a positive control, or OC at a dose of 10 mg/kg body weight daily for 10 consecutive days. On the 10th day of oral administration, half of the saline-treated group received a single intraperitoneal injection of saline (control group), while the other half received a single intraperitoneal injection of LPS at a dose of 0.85 mg/kg body weight (LPS group). Similarly, OC groups received the LPS injection (Olecein+LPS group) on the 10th day following the start of oral administration. Twenty-four hours following the intraperitoneal injection of LPS into the ICR mice, the tail suspension test (TST) was conducted. After the completion of the TST, all ICR mice were euthanized via cervical dislocation, and their brain hippocampus samples were collected.

tag: sample type

value: Male 8-week-old ICR mice hippocampus


title: SUCCS1,IC90,48h,Rep2

description: IC90_48h_SUCCS1vsDMSO_48h_SUCCS1.complete.txt

value: clear cell sarcoma

value: wildtype

tag: time


title: TTC466,iERG562,rep1


title: LPS induced group_rep2

description:
Gene expression data from mice hippocampus: mice were orally administered 10 mg/kg body weight saline daily for 10 consecutive days. On the 10th day of oral administration, mice received a single intraperitoneal injection of 0.85 mg/kg body weight LPS. Twenty-four hours following the intraperitoneal injection, the tail suspension test (TST) was conducted. After the completion of the TST, all mice were euthanized via cervical dislocation, and their brain hippocampus samples were collected
SST-RMA

source_name: mice hippocampus, 10 mg/kg body weight saline daily for 10 days, a single intraperitoneal injection of 0.85 mg/kg body weight LPS, TST


title: Oleacein pretreated and LPS induced group_rep1


title: TTC466,iERG197,rep3


title: TTC466,iERG197,rep1


title: SUCCS1,IC90,48h,Rep1


title: VAT, obese, 4

city: Newark

first: Shawn

middle: William

last: Polson

state: DE

institute: University of Delaware

description: O4V.raw, O4V.cpm

data_processing:
Analysis was performed by the University of Delaware Bioinformatics Data Science Core Facility (RRID:SCR_017696) using a modified MAPRseq pipeline implemented on the BioMix compute cluster at the Center for Bioinformatics and Computational Biology/Delaware Biotechnology Institute
Sequence quality was assessed using FASTQC v 0.11.9
Sequences were end-trimmed (Q30) and filtered (no ambiguous nucleotides, 75bp minimum length after trimming) using Trim Galore (v0.6.6)
Trimmed reads were aligned to the reference genome using HiSat v2.2.0
Mapping quality was assessed using RSeQC v4.0.0 and metrics extracted from BedTools v2.29.2 and SamTools v1.11
Feature counts were extracted using HtSeq v0.13.5
Differential expression analysis was performed on features with >1 cpm in at least 3 samples with generalized linear modeling using EdgeR v 3.34.0
Assembly: GRCm39 refseq Annotation 109
Supplementary files format and content: tab-delimited text file containing two columns per sample: raw count (xxx.raw) and counts per million (xxx.cpm) and 1 row for each gene feature

source_name: Visceral adipose tissue

extract_protocol:
SAT and VAT was isolated from mice and RNA extraction was performed with the Qiagen RNeasy Universal kit as per manufacturer's guidelines.
RNAseq library preparation was done using Perkin Elmer NEXTFLEX Rapid Directional RNAseq 2.0 and NEXTFLEX Poly(A) Beads 2.0 library preparation kits as per manufacturer's guidelines.  1ug of total RNA was used as library preparation input.

value: Visceral adipose tissue

value: WT

value: High fat dier(42% kcal saturated fat, 0.2% cholesterol; Envigo, TD88137).


title: SUCCS1,DMSO,48h,Rep3

value: DMSO


title: WT_gal_B_S32_L001

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0


title: TTC466,iERG197,rep2


title: SUCCS1,DMSO,48h,Rep2


title: SUCCS1,DMSO,48h,Rep1


title: PR5

description: 10× Genomics

value: PBMC


title: LPS induced group_rep1


title: MSN2_37_A


title: JNDSRCT,IC90,48h,Rep3

description: IC90_48h_JNDSRCTvsDMSO_48h_JNDSRCT.complete.txt

value: desmoplastic small round cell tumor (DSRCT)


title: VAT, obese, 3

department: Center for Bioinformatics and Computational Biology

description: O3V.raw, O3V.cpm


title: Saline administered group_rep1

description:
Gene expression data from mice hippocampus: mice were orally administered 10 mg/kg body weight saline daily for 10 consecutive days. On the 10th day of oral administration, mice received a single intraperitoneal injection of 0.85 mg/kg body weight saline. Twenty-four hours following the intraperitoneal injection, the tail suspension test (TST) was conducted. After the completion of the TST, all mice were euthanized via cervical dislocation, and their brain hippocampus samples were collected
SST-RMA

source_name: mice hippocampus, 10 mg/kg body weight saline daily for 10 days, a single intraperitoneal injection of 0.85 mg/kg body weight saline, TST


title: TTC466,iERG562,rep2


title: SUCCS1,IC90,48h,Rep3


title: MSN2_30_C


title: Saline administered group_rep2


title: VAT, lean, 4

description: L4V.raw, L4V.cpm

value: Laboratory normal diet


title: JNDSRCT,DMSO,48h,Rep3


title: KO_T0_brg1i_DSB2_6

city: Heidelberg

first: Christoph

last: Plass

institute: DKFZ (German Cancer Research Center)

data_processing:
The data was processed using the pipe4C pipeline.
Assembly: GRCh37
Supplementary files format and content: bigwig tracks
Library strategy: 4C-seq

source_name: AID-DivA

extract_protocol:
Cells were harvested and cross-linked with 2% formaldehyde for 10 min at room temperature, lysed and digested with MboI (New England Biolabs, Cat# R0147L) for three rounds of 4h each. Then first ligation step was performed by T4 DNA ligase (New England Biolabs, Cat# M0202L), and ligated DNA was decrosslinked and purified. A second digestion step was performed with NlaIII overnight (New England Biolabs, Cat# R0125L). Afterwards, a second ligation step was performed. DNA was purified and measured by Qubit.
5ng of DNA were amplified in PCR using the viewpoint primers. Three viewpoints were used: one close to HR-prone DSB (DSB2), one close to NHEJ-prone DSB (DSB3), and one with no adjacent DSB (ctrl). The PCR products were purified by AMPure XP beads and measured by Qubit. For 4C–seq library preparation, a final qPCR using 2ng DNA was performed with the inverse primers including the Illumina adaptor sequences and a unique index for each condition. DNA libraries were purified by AMPure XP beads and measured by Qubit. Fragment size was checked by Tape station. Libraries were pooled and subjected to 75-bp paired-end sequencing on a Nextseq550 platform at DKFZ Next Generation Sequencing Core Facility.

value: AID-DivA

value: osteosarcoma

value: ARID1A KO

value: 0h after auxin treatment


title: VAT, obese, 2

description: O2V.raw, O2V.cpm


title: JNDSRCT,DMSO,48h,Rep1


title: HSF1_37_B

source_name: MATα {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 HSF1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 HSF1-MNase::TRP1


title: DTC1,IC90,48h,Rep2

description: IC90_48h_DTC1vsDMSO_48h_DTC1.complete.txt


title: JNDSRCT,IC90,48h,Rep2


title: MSN2_30_B

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 MSN2-MNase::TRP1


title: MSN2_30_A


title: VAT, obese, 1

description: O1V.raw, O1V.cpm


title: VAT, lean, 3

description: L3V.raw, L3V.cpm


title: HSF1_37_C

value: heat shock


title: HSF1_37_A


title: JNDSRCT,DMSO,48h,Rep2


title: JNDSRCT,IC90,48h,Rep1


title: DTC1,IC90,48h,Rep3

value: clear cell sarcoma


title: BER,IC90,48h,Rep1

source_name: BER

value: BER

value: wildtype


title: DTC1,DMSO,48h,Rep2


title: VAT, lean, 1

description: L1V.raw, L1V.cpm

value: Visceral adipose tissue

value: WT


title: HSF1_30_B


title: DTC1,DMSO,48h,Rep3

value: DMSO


title: VAT, lean, 2

description: L2V.raw, L2V.cpm


title: BER,DMSO,48h,Rep2


title: HSF1_30_C


title: BER,IC90,48h,Rep2


title: BER,DMSO,48h,Rep3


title: HSF1_30_A


title: BER,DMSO,48h,Rep1


title: SAT, obese, 4

description: O4S.raw, O4S.cpm

source_name: Subcutaneous adipose tissue

value: Subcutaneous adipose tissue

value: High fat dier(42% kcal saturated fat, 0.2% cholesterol; Envigo, TD88137).


title: SAT, obese, 2

description: O2S.raw, O2S.cpm


title: gcn4_ncAD_SM_C

source_name: MATα {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 gcn4 delta::NatMX pRS315-gcn4-ncAD-MNase::LEU2

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 gcn4 delta::NatMX pRS315-gcn4-ncAD-MNase::LEU2

value: SM starvation


title: SAT, obese, 1

description: O1S.raw, O1S.cpm


title: TTC466,IC90,48h,Rep2

description: IC90_48h_TTC466vsDMSO_48h_TTC466.complete.txt

value: Ewing sarcoma


title: gcn4_ncAD_SM_B


title: TTC466,DMSO,48h,Rep3


title: TTC466,DMSO,48h,Rep2


title: DL221,IC90,48h,Rep2

description: IC90_48h_DL221vsDMSO_48h_DL221.complete.txt

value: myxoid liposarcoma


title: BER,IC90,48h,Rep3

value: desmoplastic small round cell tumor (DSRCT)


title: SAT, lean, 3

description: L3S.raw, L3S.cpm

value: Laboratory normal diet


title: DL221,IC90,48h,Rep1


title: SAT, obese, 3

description: O3S.raw, O3S.cpm


title: DL221,DMSO,48h,Rep2


title: DL221,DMSO,48h,Rep3


title: gcn4_nAD_SM_B

source_name: MATα {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 gcn4 delta::NatMX pRS315-gcn4-nAD-MNase::LEU2

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 gcn4 delta::NatMX pRS315-gcn4-nAD-MNase::LEU2


title: gcn4_ncAD_C


title: gcn4_nAD_SM_C


title: cKO3

first: Jingjing

last: Qi

address: South Chongqing Road No.280

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
The raw reads were aligned to the mouse reference genome (mm10) using Tophat2 RNASeq alignment software HISAT2.
The raw reads alignment files were processed using Hisat SAMtools and HTSeq to generate read counts for every gene.
The read counts were then normalized using R package DESeq2. The normalized read counts were then centered and scaled for each gene, generating z-scores. The z-scores basically represent how many standard deviations one particular count is from the average count for that gene. P-values obtained from multiple tests were adjusted using Benjamini-Hochberg correction.
Assembly: mm10
Supplementary files format and content: csv file containing read count for each gene

source_name: Germinal center B cells

extract_protocol:
GC B cells (B220+ CD38- FAS+)  from  WT and cKO mice at day 14 after immunization were FACS-sorted and total RNA was harvested using Rneasy plus micro kit (QIAGEN, 74034).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 6-8-week old paired Senp1flox/flox (WT) and Senp1flox/flox Cγ1-Cre (cKO) mice were immunized with NP-CGG. 14 days later, splenn from WT and cKO mice were obtained for further processing.

tag: strain

value: Spleen

value: Senp1flox/flox Cgamma1-Cre

value: 100 microg NP-CGG immunization intraperitoneally


title: SAT, lean, 2

description: L2S.raw, L2S.cpm


title: gcn4_ncAD_B


title: DL221,DMSO,48h,Rep1


title: 402-91,IC90,48h,Rep2

description: IC90_48h_402-91vsDMSO_48h_402-91.complete.txt


title: 402-91,IC90,48h,Rep3


title: KO, snRNAseq

city: Zurich

first: Zheng

last: Fan

address: Winterthurerstrasse 190

department: Anatomy Institute

country: Switzerland

institute: University of Zurich

description: 10x Genomics

data_processing:
RNA velocity was estimated by velocity python module ((La Manno et al., 2018)). Briefly, to generate loom files, spliced and unspliced reads were annotated by velocyto.py with CellRanger (version 7.0.1) output files. The loom files were then loaded to jupyter notebook (Python version 3.9.13). The calculation of RNA velocity values for each cell and embedding RNA velocity vector to UMAP were done by following the scvelo python pipeline.
Assembly: mm10
Supplementary files format and content: loom, CellRanger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Colon

extract_protocol:
To isolate single nuclei from mouse colon, Sigma’s Nuclei EZ Prep Kit (Sigma, Cat #NUC-101) was used. Briefly, snap frozen mouse colon samples were firstly cut into 2mm pieces and homogenized using gentleMACS Dissociator (m_intestine_01 mode 2x, C Tubes) in 4 ml of ice-cold EZ Prep buffer (supplemented with 0.2 U/µl RNAse inhibitor, Clontech #2313A) and incubated on ice for 5 min. subsequently, nuclei were filtered through a 20-μm Pre-Separation Filter (Miltenyi Biotech, 130-101-812) and centrifuged at 500 × g for 5 min at 4 °C. After centrifugation, the nuclei were washed in 4 ml suspension buffer (1× PBS supplemented with 0.01% BSA and 0.2 U/µl RNase inhibitor (Clontech, Cat #2313A)). Isolated nuclei were resuspended in 1 ml suspension buffer, filtered through a 20-μm Pre-Separation Filter (Miltenyi Biotech, 130-101-812) and counted. A final concentration of 1000 nuclei per µl was used for 10x Genomics Chromium loading. Considering a 10–20% loss, we pipetted 9.9 μl single nuclei suspension (concentration of ~1000 nuclei/μl, ~9,900 nuclei), targeting the recovery of ~6,000 nuclei. A single nuclei suspension targeting 6000 cells per sample was loaded into 10x Genomics Chromium Single Cell Controller and barcoded with unique molecular identifiers.
Single-nuclei RNA-seq libraries were obtained following the 10x Genomics recommended protocol, using the reagents included in the Chromium Single Cell 3′v3.1 Reagent Kit Libraries.

value: Colon

value: all cell nuclei from colon

value: Ncr1cre+ Hif-1{alpha}fl+/fl+ (KO)


title: WT, snRNAseq

description: 10x Genomics

value: wild type (WT)


title: TTC466,IC90,48h,Rep3

value: wildtype


title: SAT, lean, 4

description: L4S.raw, L4S.cpm

value: Subcutaneous adipose tissue

value: WT


title: DL221,IC90,48h,Rep3


title: 402-91,DMSO,48h,Rep3

value: DMSO


title: cKO1


title: gcn4_nAD_C


title: 402-91,DMSO,48h,Rep1


title: gcn4_nAD_B


title: gcn4_ncAD_SM_A

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 gcn4 delta::NatMX pRS315-gcn4-ncAD-MNase::LEU2

value: SM starvation


title: gcn4_ncAD_A


title: SAT, lean, 1

description: L1S.raw, L1S.cpm


title: WT3


title: 1765-92,IC90,48h,Rep3

description: IC90_48h_1765-92vsDMSO_48h_1765-92.complete.txt

value: myxoid liposarcoma


title: gcn4_nAD_SM_A


title: gcn4_nAD_A


title: 1765-92,IC90,48h,Rep1


title: WT2


title: cKO2


title: 1765-92,DMSO,48h,Rep1


title: 1765-92,DMSO,48h,Rep3


title: WT1


title: 1765-92,DMSO,48h,Rep2


title: P0102, Post, scRNAseq

city: Guangzhou

first: Hao

last: Jin

state: Guangdong

address: No.72 of Second Zhongshan Road

institute: Sun Yat Sen Memorial Hospital

data_processing:
Raw sequencing data were processed using the 10X Genomics Cell Ranger v3.0.2 pipeline to generate FASTQ files
Sequences were aligned to GRCh38 genome to gene expression count using CellRanger's default settings
Gene expression level of Refseq coding genes were quantified using CellRanger's default settings
Assembly: GRCh38
Supplementary files format and content: Tap-separated values files and matrix files

source_name: triple-negative breast cancer

extract_protocol:
Freshly biopsied tumor tissues were flushed with 1×HBSS (Mg2+ Ca2+ free supplemented with 0.04% BSA) to remove any residual blood. Tumor-infiltrating cells isolation was performed by adding digestion buffer into tissues (1 mg/ml Collagenase I, 1mg /ml neutral protease, 0.2 mg/ml DNase I, and 0.01 % Hyaluronidase) in a shaking incubator at 37°C for 30 - 100 minutes. The isolated cells were resuspended with 1 × red blood cell removal solution and placed on ice for five minutes. Cells were washed and re-suspended in PBS then stained with a Viability Dye. The cell suspension was diluted with 1 × HBSS till a concentration of 700 - 1200 cells/μL was reached.
Library was constructed according to the manufacter's instructions (single-cell 3' v2 protocol, 10×Genomics). Briefly, tumor-infiltrating cells were resuspended in the master mix; they were then loaded with partioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate in every single GEM was retrotranscripted to DNA, which contained lumina R1 primer sequence, Unique Molecular Identifier (UMI), and the 10×barcode. The pooled barcoded cDNA was then cleaned up with Silane Dynabeads and amplified by PCR; the appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction, lumina R2 primer sequence, paired-end constructs with P5 +P7 sequences and a sample index were added.

value: triple-negative breast cancer

tag: tumor stage

value: post treatment


title: 402-91,DMSO,48h,Rep2


title: 402-91,IC90,48h,Rep1


title: gcn4_cAD_SM_B_S26_L001

source_name: MATα {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 gcn4 delta::NatMX pRS315-gcn4-cAD-MNase::LEU2

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 gcn4 delta::NatMX pRS315-gcn4-cAD-MNase::LEU2


title: gcn4_cAD_SM_A_S25_L001


title: Isogenic ATXN1-corrected SCA1 disease iPSC-MN sample 2

city: Suwon

first: Dongmin

last: Gim

address: 2066 Sueobu-Ro

department: School of Pharmacy

country: South Korea

institute: Sungkyunkwan University

data_processing:
STAR aligner (v.2.7.10b) was used to generate a genome index and perform mapping to the reference.
Read quality was checked for each sample using FastQC (v.0.12.1)
Raw read count extraction was perfomed by featureCounts (v.2.0.6)
Assembly: GRCh38.p.14
Supplementary files format and content: text file includes raw read counts for each sample.

growth_protocol: All the iPSCs were maintained in Essential 8 medium (gibco) contained 1X Penicillin-Streptomycin (welgene) onto coated with Matrigel-Matrix (Corning) in humidified atmosphere with 5% CO2 at 37C. For the replating, iPSCs were treated with 0.5 mM EDTA (invitrogen) and incubated at 37C for 5 min and collected with Essential 8 medium containing 10 uM Y-27632 (biogems).  When the iPSCs are reach at 70~90% confluency, we change the media with Motor Neuron Differentiation Medium (MNDM, Neurobasal Medium [gibco] + DMEM/F12 [WELGENE] + B27 supplement [gibco] + N2 supplement [gibco] + 1X GlutaMax [gibco] + 1X Penicillin-Streptomycin + 1.5 uM Ascorbic Acid [merck]) containing 3 uM CHIR99021 (Tocris), 10 uM SB431542 (Tocris) and 2 uM DHM1 (Tocris). The cells cultured under this condition for 6 days with daily media change. On the day 6 of differentiation, the cells cultured with MNDM containing 10 uM SB431542, 2 uM DMH1, 1.5 uM Retinoic Acid (Peprotech), 0.2 uM Purmorphamine (Tocris) for 8 days with daily media change. On day 14 of differentiation, the cells were dissociated with Dispase (Stemcell Tech.) and replated and expanded at a ratio of 1:8 onto Matrigel-coated plate and cultured with 3 uM CHIR99021, 10 uM SB431542, 2 uM DMH1, 0.1 uM Retinoic Acid, 0.5 uM Purmorphamine, 0.5 mM Valproic acid (Tocris) and 10 uM Y-27632. The following days, the cells were replace with same medium without Y-27632 and performed media change every otherday. When the cells reach at 70~90% confluency, the cells were passaged or replated for further differentiation. For mature Motor Neuron differentiation, the cells were dissociated with 10X TrypLE Select Enzyme (gibco) and replated at a ratio of 1:8 onto Matrigel-coated plate with MNDM containing 1.5 uM Retinoic Acid, 0.2 uM Purmorphamine, and 10 uM Y-27632. The cells cultured under this condition for 6 days with daily media change. On the day 6` of mature differentiation, the cells were cultured with MNDM containg 1.5 uM Retinoic Acid, 0.2 uM Purmorphamine, 2 uM Y-27632 and 2 uM Compound E (EMD Millipore) for 2 days. On the day 8` of mature differentiation, the cells were dissociated with 10X TrypLE select Enzyme and replated onto 0.1% polyethyleneimine (merck) and Matrigel-Matrix coated plate with MNDM contained 1.5 uM Retinoic Acid, 0.2 uM Purmorphamine, 2 uM Y-27632 and 2 uM Compound E for 2 days.

extract_protocol:
RNA was extracted using miRneasy kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina RNA library prep kit (NEB) following manufacturer`s protocols.

treatment_protocol: When the MNs differentiated at day 10`, we replace the medium with MNDM containing 30 nM DHT (Sigma). We change the medium every other day until day 7 of treatment.

value: Motor Neuron

value: ATXN1 CAG*6&29

value: 30 nM DHT


title: P0102, Pre, scRNAseq

value: pre treatment


title: Isogenic ATXN1-corrected SCA1 disease iPSC-MN sample 1


title: risk allele 3

city: Baltimore

first: Dimitrios

last: Avramopoulos

state: Maryland

address: 733 North Broadway

department: Genetic Medicine

institute: Johns Hopkins University

data_processing:
Hisat 2 (version 2.2.1)
SAMtools (version 1.1.4)
stringtie (version 2.1.7)
Bioconductor package DESeq2
Assembly: hg38
Supplementary files format and content: csv format, normalized read counts table

source_name: hiPSC differentiated to neural precursor cells

growth_protocol: half DMEM/F12 and half Neurobasal Media (Thermo #21103049) with 2% B27 supplement without vitamin A, 1% GlutaMAX, 1% N2, 1% MEM NEAA and 1:100 BME. FGF2, 10ng/ml EGF (Peprotech #100-47-10ug) and Roc inhibitor

extract_protocol:
Quick RNA MiniPrep Kit (Zymo Research #R1054)
250-300 bp insert, strand specific libraries with RNA removal
Fragmentation, reverse transcription, second strand RNA synthesis, End repair, A-tailing, adapter ligation, size selection, PCR amplification


title: risk allele 2

value: hiPSC differentiated to neural precursor cells


title: gcn4_cAD_B_S23_L001


title: risk allele 1


title: risk allele 4


title: Reference allele 6


title: SCA1 disease iPSC-MN sample 1

value: ATXN1 CAG*52&29


title: gcn4_cAD_SM_C_S27_L001


title: 1765-92,IC90,48h,Rep2


title: gcn4_cAD_A_S22_L001


title: Tumors expressing HUNK knockkdown cells replica 3

city: Indianapolis

first: Elizabeth

middle: S

last: Yeh

state: Indiana

address: 635 Barnhill Drive MS A418

department: Pharmacology and Toxicology

institute: Indiana University School of Medicine

data_processing: NanoString nSolver 4.0 software was used for analysis of gene expression values

source_name: Tumor cells expresing HUNK knockdown

growth_protocol: Cells grown in RPMI (Corning 10-041-CV) supplemented with 10% fetal bovine serum, 200 nM glutamine (Thermo Scientific), and penicillin/streptomycin (Thermo Scientific).

extract_protocol: GenJET  RNA purification kit (K0732) to isolated RNA from cells

treatment_protocol: No treatment

value: Female

value: Balbc


title: Isogenic AR-corrected SBMA disease iPSC-MN sample 2

value: AR CAA*8


title: Reference allele 4


title: Tumors expressing HUNK knockkdown cells replica 2


title: Isogenic AR-corrected SBMA disease iPSC-MN sample 1


title: Reference allele 3


title: Tumors expressing HUNK knockkdown cells replica 1


title: SBMA disease iPSC-MN sample 2

value: AR CAG*51


title: gcn4_cAD_C_S24_L001


title: Reference allele 2


title: Control Tumors expressing HUNK replica 2

source_name: Tumors cells expressing HUNK


title: Reference allele 1


title: Control Tumors expressing HUNK replica 1


title: PBMC, Type 2 diabetes, scBCR, batch9

city: Seoul

first: Do-eon

last: GU

state: Korea

address: 81 Irwon-Ro, Gangnam-gu

description: 10X Genomics

data_processing:
Barcoded processing, gene coungting were made using the Cell Ranger software v5.0.0.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
Whole blood samples were collected using BD Vacutainer CPTTM Tubes containing sodium heparin (Cat. No. 362753). PBMCs were isolated from blood samples collected in CPT tubes (maintained at room temperature) within 2¬–24 hours after blood collection for optimal results. PBMC isolation utilized Ficoll-Paque density gradient centrifugation.
For each batch, samples from four controls were pooled. The library preparation utilized a Chromium Next GEM Single Cell 5’Kit v2 (10x Genomics), with a cell recovery target of 4,000 per patient, following the manufacturer’s instructions. Libraries were processed according to the manufacturer’s recommendations (10x Genomics) and sequenced on a HiSeq 2500 system with 100-bp paired-end sequencing. Raw sequencing reads underwent processing using CellRanger (version 5.0.1) (10x Genomics) with default parameter values. The human reference sequence (version GRCh38) and annotation (version GENCODE v32) were employed, utilizing pre-built reference packages provided by 10x Genomics (version 2020-A).

value: PBMC


title: PBMC, Type 2 diabetes, scRNA-seq, batch10

description: 10X Genomics


title: Control Tumors expressing HUNK replica 3


title: PBMC, Type 2 diabetes, scBCR, batch10

description: 10X Genomics


title: SBMA disease iPSC-MN sample 1


title: SF3B3 overexpression, repeat3

first: Zhan

last: Ding

address: 300 Feng Lin Road

institute: CAS Center for Excellence in Molecular Plant Sciences

description: SF3B3-oe rep3

data_processing:
The adapter sequences were removed from raw reads by cutadapt (version 1.15).
Clean reads from RNA-seq were quality filtered, and then mapped to the human genome (hg38) and Drosophila melanogaster genome (dm6) by STAR.
Assembly: dm6, hg38
Supplementary files format and content: tab-delimited text files include TPM values for mRNA samples.

extract_protocol:
Total RNAs from the human and Drosophila cells and tissues were isolated by TRIzol (Sigma) and treated with RNase-free DNase I (Invitrogen). For RT-PCR, reverse transcription was performed using PrimeScript RT reagent Kit with gDNA Eraser (TaKaRa) and the obtained cDNA was amplified by 2×Hieff PCR Master Mix (Yeasen). the construction of cDNA libraries and sequencing were performed using Illumina HiseqXten-PE150 by Novogene.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human embryonic kidney

value: SF3B3 overexpression


title: SCA1 disease iPSC-MN sample 2


title: PBMC, Type 2 diabetes, scRNA-seq, batch9

description: 10X Genomics


title: Targeted Bisulfite-Seq PBMC_day0_s456

city: Los Angeles

first: Matteo

last: Pellegrini

state: California

address: 610 Charles E. Young Drive South TLSB room 5146, Pellegrini Lab

department: Molecular, Cell, and Developmental Biology

institute: University of California, Los Angeles

data_processing:
BSBolt (v1.3.0) was used to align the reads to the reference GRCh38 genome
Samtools was used to remove PCR duplicates using the markdup function
methylation calling was performed using the BSBolt CallMethylaiton function
Assembly: grch38 genome
Supplementary files format and content: csv, day 0 (pre-vaccination) methylation calling matrix
Supplementary files format and content: csv, day 28 (post-vaccination) methylation calling matrix

source_name: blood

extract_protocol:
the standard phenol-chloroform extraction method for blood samples
For the TBS-seq library preparation, adapter ligation and dA-tailing were performed using the NEBNext Ultra II Library prep kit and custom pre-methylated adapters (IDT). Purified libraries were then hybridized to the biotinylated probes. Under the following conditions: 2 min at 98°C; 14 cycles of (98°C for 20 sec; 60°C for 30 sec; 72°C for 30 sec); 72°C for 5 minutes; hold at 4°C, PCR amplification was performed after bisulfite treatment on captured DNA using KAPA HiFi Uracil+. Library quality control was conducted on the high-sensitivity D1000 assay on a 2200 Agilent TapeStation.
Targeted Bisulfite Sequencing
Adapter sequences were removed using cutadapt (v2.10) for the demultiplexed FastQ files

value: blood

value: pre-vaccination


title: Targeted Bisulfite-Seq PBMC_day28_s456

value: post-vaccination


title: PBMC, Type 2 diabetes, scTCR, batch10

description: 10X Genomics