title: Cpeb3_KO_rep1

description:
IWHH_2
norm_counts.tsv


title: MCF10A-ha-fus-tfcp2-r3-H3K27ac

status: Public on Nov 06 2023

type: SRA

city: Heidelberg

first: Claudia

last: Scholl

address: Im Neuenheimer Feld 581

country: Germany

institute: German Cancer Research Center (DKFZ)

description: ACT-Seq of MCF10A cells transduced with FUS-TFCP2 targeting H3K27ac, replicate 3

library_source: genomic

data_processing:
nf-core ATAC-seq v1.2.1 in broad peak mode for calling histone marks
nf-core ChIP-seq v1.2.1 in narrow peak mode for calling FUS/EWSR1-TFCP2 and wild-type TFCP2/FUS/EWSR1 binding sites
Assembly: hs37d5 + PhiX
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Homo sapiens

source_name: breast

extract_protocol:
MinElute Kit (Qiagen, #28004)
To generate sequencing libraries, real-time PCR was performed in a total volume of 50 µl using 25 µl NEBNext High Fidelity 2x Mix (New England Biolabs, #M0541), 0.5 µl 100x SYBR Green, 19.5 µl tagmented eluate, and 5 µl of Nextera UDI primer (replicates R1, R3, and R4) or 2.5 µl primer T5McP1n and 2.5 µl barcode primer (replicate R2) for each sample with the following program: 72°C, 5 minutes (gap repair); 98 °C, 30 seconds (initial melting); 98°C, 10 seconds; 63°C, 10 seconds; 72°C, 10 seconds (cycling). The reaction was stopped after an increase of five or more fluorescence units. Libraries were purified using AMPure XP beads with a bead-to-DBA ratio of 1.4:1 and 12 µl elution buffer for single-phase purification (anti-HA antibodies and IgG) and with bead-to-DBA ratios of 0.5:1 and 1.4:1 for biphasic purification (anti-H3K27me3 and anti-H3K27ac).
ACT-Seq, paired-end

tag: tissue

value: breast

tag: cell line

tag: cell type

value: mammary gland cell line

tag: genotype

value: Case

tag: treatment


title: WaGa, DMSO control, 6h, 2 [WD6h2]

city: Tucson

first: Jiawen

last: Yang

state: Arizona

address: 1515 N Campbell Ave

department: University of Arizona Cancer Center

country: USA

institute: The University of Arizona

library_source: transcriptomic

data_processing:
Ran fastqc to check the quality of raw data
Trimmed the adapter sequence from raw sequencing data by using trimmomatic-0.39
Performed data alignment by using STAR 2.7.10a with a hg38 reference genome (“GDC.h38.d1.vd1 STAR2 Index Files (v36)” downloaded from https://gdc.cancer.gov/about-data/gdc-data-processing/gdc-reference-files)
The aligned data were mapped to the same reference genome by using Rsubread package.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts for individual sample
Supplementary files format and content: tab-delimited text files include read count matrix for all samples

molecule: total RNA

source_name: Merkel cell carcinoma

growth_protocol: MKL1 and WaGa cells were cultured in RPMI-1640 medium, containing 10% fetal bovine serum (FBS), 1% glutaMAX, 10 U/ml penicillin, and 10 mg/ml streptomycin, at 37 ℃ under 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen）
Total RNA was sent to Novogene CO.for mRNA library preparation and sequencing.

treatment_protocol: MKL1 and WaGa cells were resuspended in 5 ml RPMI culture medium and seeded in 25 cm^2 flasks. 5 μL DMSO were added for vehicle control group and 5 μL 1 mM pyrvinium pamoate (dissolved in DMSO) were added for drug treated group. The cells were collected at 6 hours and 24h hours after treatment.

value: Merkel cell carcinoma

value: WaGa

value: suspension cells

value: WT

value: DMSO


title: WaGa, DMSO control, 6h, 3 [WD6h3]


title: MCF10A-ev-r4-H3K27ac

description: ACT-Seq of MCF10A cells transduced with empty vector targeting H3K27ac, replicate 4

value: Control


title: MCF10A-ev-r3-H3K27ac

description: ACT-Seq of MCF10A cells transduced with empty vector targeting H3K27ac, replicate 3


title: CN1_d75

city: New York

first: Hyein

middle: Sophia

last: Cho

state: NY

address: 430 E 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description: ribo-depleted total RNA

data_processing:
Transcriptome alignment by STAR 2.6.0
Gene quantification by HTSeq 0.9.1
Differential expression by DESeq2 1.16.1
Genome_build: hg19
Supplementary_files_format_and_content: txt, gene quantifcation of raw counts

source_name: hPSC-derived neurons, day 75, replicate 1

growth_protocol: WA09 (H9) hPSC line was cultured in Essential 8 on Vitronectin coated dishes and expanded by dissociation with 0.5mM EDTA. Neural induction was completed using the dual SMAD inhibition protocol and WNT inhibition on Matrigel coated dishes. hPSC for differentiation and neuronal progenitors were dissociated using Accutase. Neurons were maintained on poly-L-ornithine and Laminin/ Fibronectin coated plates in Neurobasal medium supplemented with B27, L-glutamine, BDNF, GDNF, cAMP, AA. DAPT was added to the neuronal maintenance medium from day20 to day30 of differentiation.

extract_protocol:
Illumina TruSeq Stranded Total RNA Library Prep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Neurons


title: MCF10A-ev-r2-H3K27ac

description: ACT-Seq of MCF10A cells transduced with empty vector targeting H3K27ac, replicate 2


title: CN1_d25

description: ribo-depleted total RNA

source_name: hPSC-derived neurons, day 25, replicate 1


title: WaGa, DMSO control, 24h, 3 [WD24h3]


title: WaGa, DMSO control, 6h, 1 [WD6h1]


title: MCF10A-ev-r1-H3K27ac

description: ACT-Seq of MCF10A cells transduced with empty vector targeting H3K27ac, replicate 1


title: WaGa, DMSO control, 24h, 2 [WD24h2]


title: CN1_NPC

description: ribo-depleted total RNA

source_name: hPSC-derived neural progenitor cells, replicate 1

value: Neural progenitor cells


title: MCF10A-ha-tfcp2-wt-r3-HA-santacruz-sc-7392

description: ACT-Seq of MCF10A cells transduced with wild-type TFCP2 targeting HA using SantaCruz antibody, replicate 3


title: pseudolymphoma patient13

type: RNA

city: Kiel

first: Julia

last: Richter

address: Arnold-Heller Straße 3, Haus U33

department: Department of Pathology, Hematopathology Section

institute: University Hospital Schleswig-Holstein

description:
total RNA extracted from FFPE biopsie
Pseudo13

hyb_protocol: See manufacturer's website (http://www.nanostring.com)

data_processing: raw data were processed using nSolver 4.0 and included background thresholding and normalization

source_name: primary skin tissue

growth_protocol: FFPE biopsy

extract_protocol: total RNA was extracted from FFPE tissue using the AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. 200ng RNA were used for the initial hybridization step and the manufacturer´s protocol was followed.

tag: age

tag: gender

value: female

value: primary skin tissue


title: pseudolymphoma patient16

description:
total RNA extracted from FFPE biopsie
Pseudo16

scan_protocol: See manufacturer's website (http://www.nanostring.com)


title: WaGa, DMSO control, 24h, 1 [WD24h1]


title: pseudolymphoma patient14

description:
total RNA extracted from FFPE biopsie
Pseudo14

label_protocol: See manufacturer's website (http://www.nanostring.com)

value: male


title: CN1_ESC

description: ribo-depleted total RNA

source_name: hPSC, replicate 1

value: hPSC


title: pseudolymphoma patient27

description:
total RNA extracted from FFPE biopsie
Pseudo27


title: MCF10A-ha-tfcp2-wt-r2-HA-santacruz-sc-7392

description: ACT-Seq of MCF10A cells transduced with wild-type TFCP2 targeting HA using SantaCruz antibody, replicate 2


title: pseudolymphoma patient28

description:
total RNA extracted from FFPE biopsie
Pseudo28


title: CN1_d50

description: ribo-depleted total RNA

source_name: hPSC-derived neurons, day 50, replicate 1


title: WaGa, empty control, 24h, 2 [Wcon2]

value: no treatment


title: MCF10A-ha-tfcp2-wt-r1-HA-santacruz-sc-7392

description: ACT-Seq of MCF10A cells transduced with wild-type TFCP2 targeting HA using SantaCruz antibody, replicate 1


title: WaGa, empty control, 24h, 3 [Wcon3]


title: MCF10A-ha-fus-tfcp2-r4-HA-santacruz-sc-7392

description: ACT-Seq of MCF10A cells transduced with FUS-TFCP2 targeting HA using SantaCruz antibody, replicate 4


title: MKL1, pyrvinium pamoate, 6h, 3 [MP6h3]

value: pyrvinium pamoate 1 μM


title: MCF10A-ha-fus-tfcp2-r3-HA-santacruz-sc-7392

description: ACT-Seq of MCF10A cells transduced with FUS-TFCP2 targeting HA using SantaCruz antibody, replicate 3

value: breast


title: Villi VDR ChIP-seq Replicate 4

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

data_processing:
Adapter removal: The ATAC-seq FASTQ files were adapter-trimmed using CutAdapt v1.9.1. The ChIP-seq FASTQ files were adapter-trimmed using NGmerge v0.3.
Genome alignment: The adapter-trimmed FASTQ files were aligned to the mouse (mm9) genome using Bowtie2 v2.2.6. The SAM files were converted into BAM files using SAMtools v0.1.19 samtobam. The BAM files sorted using SAMtools v0.1.19 sortbam. Mitochondrial peaks were removed from the BAM files using SAMtools v0.1.19.
Replicate merging: Each set of replicate BAM files were merged into a single BAM file using SAMtools v0.1.19 merge.
BigWig coverage: A BigWig file was generated for each sorted BAM file using deeptools v2.4.2-4-99ec5c bamcoverage with the following parameters: “-bs 10 --normalizeUsing RPKM --effectiveGenomeSize 2620329765 --ignoreForNormalization chrX --centerReads --extendReads”. ENCODE blacklisted regions were excluded from the generated BigWig files.
Peak calling: ATAC-seq BAM files: A BED file was generated from each sorted BAM file using the BAMtoBED utility included in bedtools v2.17.0. The median insert size of each BED file was determined using the CollectInsertSizeMetrics utility included in the Picard v2.18.27 suite. Statistically significant enriched genomic regions (“peaks”) were identified from the BED files using MACS2 v2.1.0.20150731 with a 5’ shift of one-half the median insert length for each BED file. ENCODE blacklisted regions and mitochondrial regions were removed from the BED file. Each peak was re-centered on its summit. ChIP-seq BAM files: Statistically significant enriched genomic regions (“peaks”) were identified from the BED files using MACS2 v2.1.0.20150731. ENCODE blacklisted regions and mitochondrial regions were removed from the BED file. Each peak was re-centered on its summit.
Differential binding analysis: The BAM file generated by Bowtie2 and the peaks BED file generated by MACS2 for each sample were analyzed using DiffBind. Pairwise-comparisons were conducted between samples of the same tissue at different ages (tissue-constant comparisons) and between samples of different tissues at the same age (age-constant comparisons). For each pairwise comparison, DiffBind generated a set of differentially accessible peaks and their associated significance values. Any peak in the set of peaks generated by DiffBind that had a significance value < 2×10^-5 was counted as a significant differentially accessible peak. Any peak in the set of peaks generated by DiffBind that had a significance value ≥ 2×10^-5 was counted as a non-significant differentially accessible peak. The set of significant differentially accessible peaks was divided into a set of peaks that were more accessible in the first condition being compared and a set of peaks that were more accessible in the second condition being compared. The two sets of significant differentially accessible peaks were written to a BED file.
Genome_build: mm9
Supplementary_files_format_and_content: Processed FASTQ files have had adapter content removed. Processed BigWig files have had ENCODE blacklist and mitochondrial content removed. Excel spreadsheet files were generated by MACS2. Processed MACS2 BED files have had ENCODE blacklist and mitochondrial content removed. Differential XLS and BED files were generated by DiffBind.

organism: Mus musculus

source_name: duodenum villi

extract_protocol:
For optimal crypts and villi isolation, the isolation was performed in the laboratory at 12-15°C with extreme care and all the tubes containing the crypts and villi were pre-coated with 0.1% BSAin 1XPBS. Before harvesting, three C57BL/6J mice were treated with 1,25(OH)2D3 for 1 hour. After 1 hour of injection, the whole intestine was harvested and placed on top of 150mm petri plate on ice. Much of the adipose tissue was removed from the intestine and about 15 cm of the proximal half of the small intestine were used for the duodenum crypts and villi samples. After flushing with cold 1XPBS, the intestines were opened longitudinally, cut into 1-2 cm pieces in cold 1XPBS for washing, and then incubated in 10 ml of cold 3mM EDTA/1XPBS in rotator for 5 minutes at 4°C. The supernatant was discarded and the tissues were incubated with fresh 10ml of cold 3mM EDTA/PBS in rotator for 10 minutes at 4°C. After shaking the tubes for 10 times, the intestinal pieces were transferred to new tubes prepare with 10ml of cold 3mM EDTA/1XPBS, rotated for 30 minutes at 4°C, and then were semi-vigorously shaken 30 times. The supernatant containing crypts and villi were collected and spun down at 200 rcf for 3 minutes at 4°C. The pellet was re-suspended with cold 1XPBS, and the villi were separated from crypts by passing the whole epithelium solution throμgh 70 μm FisherbrandTM Sterile Cell Strainers (Fisher Scientific, Cat. No. 22-363-548). The flow-throμgh containing the crypts was collected in 50 ml tubes while the villi were collected on top of the 70 μm filter. The villi were transferred from the 70 μm filter to 50 ml tubes using 1XPBS and a 5ml serological pipet pre-coated with 0.5% BSA in 1XPBS. The tubes containing the crypts and villi were filled with 50mlof 1XPBS and spun down at 170 rcf for 3 minutes at 4°C. Afterwards, the supernatant was removed and the crypts and villi pellets were incubated in 1.5% formaldehyde made from 36.5-38% formaldehyde solution, (Sigma-Aldrich, Cat. No. F8775-25ML), GibcoTM Advanced DMEM/F-12 (ThermoFisher Scientific, Cat. No. 12634010), and 1XPBS in rotator for 15 minutes at 4°C and 40 minutes at 25°C. Upon completion of fixation, the supernatants were discarded and washed with 1XPBS twice for 3 minutes at 200 rcf at 4°C. The fixed crypts and villi samples were pooled together according to their respective groups and then aliquoted to 1.5ml tubes. All samples were centrifμged at 200 rcf for 3 mins at 4°C and at 300 rcf for 30 seconds at 4°C in order to remove any residual PBS. The samples were frozen on dry ice for 5 minutes before storage in the -80°C freezer. The colon was harvested from the same group of C57BL/6J mice as the crypts and villi isolation at the same time. The entire colon tissues from the terminal cecum to rectum were used for colon samples. After flushing with cold 1XPBS, the colon was opened longitudinally and laid on clean 100 mm petri plate with villi facing up. Two histological glass slides were used to remove the epithelial mucosa by scraping: one to hold down the intestine and the other to scrape2. The colon was scraped until the colon became transparent. The colon whole epithelium was washed with 1XPBS twice and incubated in 1.5% formaldehyde solution in rotator for 15 minutes at 4°C and 40 minutes at 25°C. Upon completion of fixation, the supernatants were discarded, washed with 1XPBS twice for 3 minutes at 200 rcf at 4°C, and spun down at 300 rcf for 30 seconds at 4°C in order to remove any residual PBS. The samples were frozen on dry ice for 5 minutes before storage in the -80°C freezer.
For chromatin immunoprecipitation (ChIP) assays, two types of anti-VDR antibody were obtained from Santa Cruz Biotechnology (Dallas, TX): (1) a mouse monoclonal IgG2a VDR antibody D-6 (Cat. No. sc-13133), which was raised against amino acids 344-424 of VDR of human origin (https://www.scbt.com/p/vdr-antibody-d-6) and (2) a rabbit polyclonal IgG VDR antibody C-20 (Cat. No. sc-1008), which has been discontinued (https://www.scbt.com/p/vdr-antibody-c-20).ChIP The villi, crypts, and colon whole epithelium pellets that were stored in -80°C were thawed on ice and mixed with 3-4 times the volume of the lysis buffer composed of 1% SDS, 2% 0.5 M EDTA pH 8.0, 5% 1M Tris pH 8.0, and 10% 100X ProteaseArrestTM for Mammalian [100X] (G-Biosciences, Cat. No. 786-433) dissolved in MilliQ water. After the addition of the lysis buffer, the lysate containing the tissues were incubated at RT for 10 minutes, aliquoted at volumes between 300-400 uL, and sonicated in colduLtrasonication water bath for intervals of 10 minutes. Once the samples were sonicated, 5uL of the lysate was mixed with 100 uL of the reverse cross-linking buffer (10% 1M NaHCO3, 1% SDS, and MilliQ water) and incubated overnight in 65°C or for 15 minutes at 95°C. The DNA was purified from the lysate using QIAquick PCR Purification Kit (50) (Qiagen, Cat. No. 28104) and ran on a 2% agarose gel to check the whole chromatin size of the lysate. If the whole chromatin size was not between 200-500bp, the lysate was sonicated more. But if the whole chromatin size was between 200-500bp, then the lysate was spun down at 15,000 rpm for 10 minutes at 8°C, the supernatant was transferred to a new tube, and 5uLof the supernatant was placed into the input tube. For immunoprecipitation, mixture of 15uL of InvitrogenTM DynabeadsTM Protein A (ThermoFisher Scientific, Cat. No. 10008D) and 15uLof InvitrogenTM DynabeadsTM Protein G (ThermoFisher Scientific, Cat. No. 10009D) were blocked in 1 ml of blocking buffer (10% 10X BSA, 10% 10X PBS, and MilliQ water) in rotator for an hour at 4°C. The first set of 6 VDR ChIP samples were incubated with 4μg of VDR D-6X (2ul) (Santa Cruz Biotechnology, Cat. No. sc-13133, Lot. K0912 and Lot. B0918) and 2μg of VDR C-20 (10uL) (SCB, Cat. No. sc-1008, Lot. H1216) whereas the second set of 6 VDR ChIP samples were incubated with 2μg of VDR D-6X (1ul) (SCB, Cat. No. sc-13133, Lot. B0918) and4μg of VDR C-20 (20uL) (SCB, Cat. No. sc-1008, Lot. D0914 and Lot. H1216). The bead-antibody mixture was incubated in rotator for 4-6 hours at 4°C. After a quick wash of removing the supernatant by placing the tubes in the magnetic tube holder, the bead-antibody mixture was incubated in rotator for another hour at 4°C. After incubation, the blocking buffer was removed from the bead-antibody mixture. Then, the sonicated lysate and the supernatant dilution buffer (1% of 100X ProteaseArrestTM for Mammalian [100X], 2% 1M Tris pH 8, 3% 5M NaCl, 0.4% 0.5M EDTA, 5% of 20% Triton X, and MilliQ water) were mixed together at a ratio that would give a concentration of 0.22-0.24% SDS. The sample lysates mixed with the beads, VDR antibody, and the supernatant dilution buffer were incubated in rotator overnight at 4°C. After immunoprecipitation, the samples were washed with 1 ml of RIPA buffer (5% 1M HEPES pH 7.6, 0.2% 0.5M EDTA, 7% of 10% Na Deoxycholate, 10% of 10% NP40, 12.5% 4M LiCl, and MilliQ water) in rotator for five times for 5 minutes each at 4°C. The RIPA buffer was removed by placing tubes in the magnetic tube holder. After the RIPA buffer wash, the samples were washed with 1 ml of TE buffer (0.1 mM EDTA, 10 mM Tris) by rotating the tube 180° in the magnetic tube holder and removing the TE buffer. The samples were then mixed with 100uL of reverse cross-linking buffer and incubated for 6 hours or overnight at 65°C. After incubation, the supernatant was transferred to a new tube. The DNA was purified using QIAquick PCR Purification Kit and quantified using InvitrogenTM Quant-iTTM PicoGreenTM dsDNA Reagent (ThermoFisher Scientific, Cat. No. P7581) standards.DNA Library Preparation for ChIP-seq ChIP DNA was used to prepare ChIP-seq libraries using the Takara Bio USA ThruPLEX DNA-seq Kit (R400427/R400428/R40048), fragment size was selected using Pippin Prep and sequenceon Illumina NextSeq (2x75-bp reads; paired end; ~14-18 M reads).

value: duodenum villi

tag: strain

value: 4–6 weeks

tag: antibody

value: anti-VDR antibody


title: Villi VDR ChIP-seq Replicate 3


title: MKL1, pyrvinium pamoate, 6h, 2 [MP6h2]

value: Merkel cell carcinoma


title: WaGa, empty control, 24h, 1 [Wcon1]

value: WaGa

value: suspension cells


title: MCF10A-ha-fus-tfcp2-r2-HA-santacruz-sc-7392

description: ACT-Seq of MCF10A cells transduced with FUS-TFCP2 targeting HA using SantaCruz antibody, replicate 2

value: mammary gland cell line

value: Case


title: PCSM-LPD patient29

description:
total RNA extracted from FFPE biopsie
Case29


title: PCSM-LPD patient34

description:
total RNA extracted from FFPE biopsie
Case34


title: PCSM-LPD patient32

description:
total RNA extracted from FFPE biopsie
Case32


title: Villi VDR ChIP-seq Replicate 2


title: MKL1, pyrvinium pamoate, 6h, 1 [MP6h1]

value: WT


title: MCF10A-ev-r4-HA-santacruz-sc-7392

description: ACT-Seq of MCF10A cells transduced with empty vector targeting HA using SantaCruz antibody, replicate 4

value: Control


title: Crypt VDR ChIP-seq Replicate 4

source_name: duodenum crypts

value: duodenum crypts


title: PCSM-LPD patient19

description:
total RNA extracted from FFPE biopsie
Case19

value: primary skin tissue


title: MCF10A-ha-fus-tfcp2-r1-HA-santacruz-sc-7392

description: ACT-Seq of MCF10A cells transduced with FUS-TFCP2 targeting HA using SantaCruz antibody, replicate 1


title: MKL1, pyrvinium pamoate, 24h, 3 [MP24h3]


title: PCSM-LPD patient27

description:
total RNA extracted from FFPE biopsie
Case27

value: female


title: PCSM-LPD patient16

description:
total RNA extracted from FFPE biopsie
Case16


title: Crypt VDR ChIP-seq Replicate 3


title: MCF10A-ev-r3-HA-santacruz-sc-7392

description: ACT-Seq of MCF10A cells transduced with empty vector targeting HA using SantaCruz antibody, replicate 3


title: Villi VDR ChIP-seq Replicate 1


title: MKL1, pyrvinium pamoate, 24h, 1 [MP24h1]


title: PCSM-LPD patient14

description:
total RNA extracted from FFPE biopsie
Case14


title: MCF10A-ev-r2-HA-santacruz-sc-7392

description: ACT-Seq of MCF10A cells transduced with empty vector targeting HA using SantaCruz antibody, replicate 2


title: Crypt VDR ChIP-seq Replicate 2


title: Crypt VDR ChIP-seq Replicate 1


title: PCSM-LPD patient12

description:
total RNA extracted from FFPE biopsie
Case12


title: MKL1, pyrvinium pamoate, 24h, 2 [MP24h2]


title: MCF10A-ev-r1-HA-santacruz-sc-7392

description: ACT-Seq of MCF10A cells transduced with empty vector targeting HA using SantaCruz antibody, replicate 1


title: MKL1, DMSO control, 6h, 2 [MD6h2]

value: DMSO


title: MKL1, DMSO control, 6h, 3 [MD6h3]


title: Colon VDR ChIP-seq Replicate 3

source_name: colon epithelium

value: colon epithelium


title: Colon VDR ChIP-seq Replicate 4


title: MCF10A-ha-tfcp2-wt-r2-HA-cellsignaling-3724

description: ACT-Seq of MCF10A cells transduced with wild-type TFCP2 targeting HA using CellSignaling antibody, replicate 2


title: isoseq_48H_activated_2Div_WT

city: Basel

first: Denis

last: Seyres

address: Hebelstrasse 20

country: Switzerland

institute: UniversitatSpital Basel

data_processing:
Consensus sequences (.ccs) were generated from your raw subread data by using ccs (--min-rq 0.9). Full-length reads were generated after primer removal and demultiplexing using lima --ccs.
Then we removed polyA tails and artificial concatemers with isoseq3 refine (--require-polya --min-polya-length 20) and clustered consensus sequences to generate transcriptome fastas with isoseq3 cluster (--use-qvs).
High-Quality Full-Length Polished Isoforms were mapped to the genome and collapsed into transcripts based on genomic mapping using pbmm2 align (--preset ISOSEQ).
We then used isoseq3 collapse to generate fastq and gff files. Transcripts were annotated using SQANTI3 (v0.1) (Tardaguila et al., 2018) (--aligner_choice minimap2) and providing liste of mouse polyA motifs retrieved from PolyASite database (https://polyasite.unibas.ch/atlas), transcript abundance from isoseq3 output and CAGE peaks from Fantom5 (https://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_latest/extra/CAGE_peaks/).
Assembly: mm10 / Mus_musculus.GRCm38.94
Supplementary files format and content: gtf files containing collapsed transcripts

source_name: Spleens and lymph nodes

extract_protocol:
Trizol isolated high-quality RNA samples (>500 ng total RNA)
Three SMRTbell libraries (Naive, 48h activated 0 division and 2 divisions) from Trizol isolated high-quality RNA samples (>500 ng total RNA) were sequenced on a Sequel SMRT Cells 1M for a general survey of full-length isoforms in a transcriptome with moderate to high expression levels.

value: Spleens and lymph nodes

tag: Sex

value: male

tag: cell division

tag: time


title: PCSM-LPD patient3

description:
total RNA extracted from FFPE biopsie
Case3


title: MKL1, DMSO control, 6h, 1 [MD6h1]


title: Colon VDR ChIP-seq Replicate 2


title: isoseq_48H_activated_noDiv_WT


title: Colon VDR ChIP-seq Replicate 1


title: PCSM-LPD patient6

description:
total RNA extracted from FFPE biopsie
Case6


title: MCF10A-ha-tfcp2-wt-r1-HA-cellsignaling-3724

description: ACT-Seq of MCF10A cells transduced with wild-type TFCP2 targeting HA using CellSignaling antibody, replicate 1

value: breast


title: MKL1, DMSO control, 24h, 2 [MD24h2]


title: isoseq_naive_WT

value: Naive


title: Villi ATAC-seq Replicate 3

value: duodenum villi

value: 90 days


title: MKL1, DMSO control, 24h, 1 [MD24h1]

value: Merkel cell carcinoma


title: MCF10A-ha-tfcp2-wt-r3-HA-cellsignaling-3724

description: ACT-Seq of MCF10A cells transduced with wild-type TFCP2 targeting HA using CellSignaling antibody, replicate 3


title: BS-IFN-2

city: Seoul

first: Jeonghwan

last: Kim

address: 369 Sangdo-Ro, Entrepreneurship & Small Business Center 612

country: South Korea

institute: Soongsil University

description:
shDRG2-IFN-2
BS-IFN-2

data_processing:
The raw sequencing reads were filtered and trimmed using Trim Galore0.6.7.
The filtered reads were aligned to the reference genome mm10 using the Spliced Transcripts Alignment to a Reference (STAR) software tool version 2.6.1d with the parameter 2pass.
Transcript abundance was estimated using the quasi-mapping method and gene-level counts were generated using Salmon version 1.5.2.
Assembly: mm10

source_name: Murine Melanoma B16F10

extract_protocol:
We performed RNA-Seq on total RNA samples (RIN above 8.5) from B16F10-pLKO and B16F10-shDRG2 cells stimulated with 5 ng/ml recombinant mouse IFN-γ (PeproTech, 315-05) for 24 h.
The cDNA library was prepared with 1.0 μg of total RNA following manufacturer’s recommendations of TrueSeq RNA library Preparation Kit (Illumina, San Diego, CA, USA), followed by paired-end sequencing (2 × 100 bp) using the HiSeq1500 platform (Illumina, San Diego, CA, USA).  cDNAs were amplified according to the RNAseq protocol provided by Illumina and sequenced using an Illumina HiSeq 2500 system to obtain 150-bp paired-end reads.

value: melanoma

value: IFN-gamma


title: BS-NO-1

description:
shDRG2-NO-1
BS-NO-1


title: Villi ATAC-seq Replicate 1


title: MKL1, empty control, 24h, 3 [Mcon3]

value: suspension cells

value: no treatment


title: MCF10A-ha-fus-tfcp2-r3-HA-cellsignaling-3724

description: ACT-Seq of MCF10A cells transduced with FUS-TFCP2 targeting HA using CellSignaling antibody, replicate 3

value: mammary gland cell line

value: Case


title: Villi ATAC-seq Replicate 2


title: Crypt ATAC-seq Replicate 3

value: duodenum crypts


title: MCF10A-ha-fus-tfcp2-r1-HA-cellsignaling-3724

description: ACT-Seq of MCF10A cells transduced with FUS-TFCP2 targeting HA using CellSignaling antibody, replicate 1


title: MKL1, empty control, 24h, 2 [Mcon2]

value: WT


title: MCF10A-ha-fus-tfcp2-r2-HA-cellsignaling-3724

description: ACT-Seq of MCF10A cells transduced with FUS-TFCP2 targeting HA using CellSignaling antibody, replicate 2


title: MKL1, empty control, 24h, 1 [Mcon1]


title: BP-NO-2

description:
pLKO-NO-2
BP-NO-2

value: pLKO


title: BS-IFN-1

description:
shDRG2-IFN-1
BS-IFN-1


title: MKL1, DMSO control, 24h, 3 [MD24h3]

value: DMSO


title: Crypt ATAC-seq Replicate 1


title: Crypt ATAC-seq Replicate 2


title: Tonsil 2, rep1, scRNAseq

city: Huddinge

first: Christopher

middle: Thomas

last: Stamper

address: Alfred Nobels Allè 8

department: Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tonsil

extract_protocol:
Freshly resected tonsil tissue was washed in PBS, any visible signs of pus, blood, or burns were cut away and then tissue was further cut into smaller pieces before being mechanically disrupted by grinding and filtering. The filtered cell suspension was washed in 50 ml PBS, pelleted by centrifugation and resuspended in 20mL PBS and layered onto 30mL Ficoll (Cytiva) and centrifuged. The lymphocyte layer was harvested and washed with 50mL PBS before being pelleted by centrifugation and resuspended in 50mL PBS. 500 million cells were stained with Fc Block (Miltenyi Biotec) for 15 minutes, washed, and then stained with Miltenyi MACS anti-CD19 magnetic beads according to manufacturer’s instructions. After staining cells were washed and B cells were depleted using Miltenyi MACS LD columns to deplete B cells according to manufacturer’s instructions. , cells were incubated with live/dead cell marker (DCM; Invitrogen) and surface protein antibodies at 4 °C for 30 min, washed with PBS and resuspended in FACS buffer (PBS with 2% FBS). Cells were sorted into eppendorf tubes containg Sort Buffer (PBS with 0.2% BSA and 5mM EDTA). Cells were sorted on a FACSAria III sorter (BD Biosciences), with FACS Diva version 9 software.
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics)

value: Tonsil

value: ILCs, NKs, T cells


title: BP-NO-1

description:
pLKO-NO-1
BP-NO-1


title: MCF10A-ev-r3-HA-cellsignaling-3724

description: ACT-Seq of MCF10A cells transduced with empty vector targeting HA using CellSignaling antibody, replicate 3

value: breast

value: Control


title: MCF10A-ev-r4-HA-cellsignaling-3724

description: ACT-Seq of MCF10A cells transduced with empty vector targeting HA using CellSignaling antibody, replicate 4


title: MCF10A-ha-fus-tfcp2-r4-HA-cellsignaling-3724

description: ACT-Seq of MCF10A cells transduced with FUS-TFCP2 targeting HA using CellSignaling antibody, replicate 4


title: Colon ATAC-seq Replicate 3

value: colon epithelium


title: MCF10A-ev-r2-HA-cellsignaling-3724

description: ACT-Seq of MCF10A cells transduced with empty vector targeting HA using CellSignaling antibody, replicate 2


title: BP-IFN-2

description:
pLKO-IFN-2
BP-IFN-2


title: BS-NO-2

description:
shDRG2-NO-2
BS-NO-2


title: Tonsil 1, rep1, scRNAseq

description: 10x Genomics


title: Colon ATAC-seq Replicate 2

value: 90 days


title: H9_43_d27

first: Ryan

last: Walsh

institute: MSKCC

description: 10x Genomics

data_processing:
Cellranger v6.1.2 was used for demultiplexing and generation of a count matrix
Assembly: GRCh38
Supplementary files format and content: comma separated count matrix

source_name: cell culture

extract_protocol:
Monolayer cortical differentiation cultures were dissociated with accutase and papain to obtain a single cell suspension. Dissociated neurons were then washed, filtered and resuspended in 0.04% BSA/PBS + Ribolock RNase inhibitor
Libraries were constructed with the Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics) according to the manufacturer's protocol. In brief, single cell suspensions were loaded onto a Chromium Next GEM Chip G for GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 7,000-15,000 cells. cDNA amplification included 11-12 cycles and 30-240 ng of the material were used to prepare sequencing libraries with 10-16 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/88 run using the NovaSeq 6000 S1 or S4 Reagent Kit (100 or 200 cycles) (Illumina).

value: cell culture

value: Neurons

value: Cortical Differentiation


title: MCF10A-ev-r1-HA-cellsignaling-3724

description: ACT-Seq of MCF10A cells transduced with empty vector targeting HA using CellSignaling antibody, replicate 1


title: Colon ATAC-seq Replicate 1


title: BP-IFN-1

description:
pLKO-IFN-1
BP-IFN-1

value: melanoma

value: IFN-gamma


title: con.005

status: Public on Nov 05 2023

city: St. Louis

first: Jeannine

middle: M

last: Basta

state: MO

department: Internal Medicine/Nephrology

institute: Washington University in St. Louis

data_processing:
Basecalling was performed by Torrent Suite version 4 and 5 software using the default settings
Alignment to mus musculus genome mm10 sequence was performed using TMAP map4 algorithm with 5' and 3' softclipping and a minimum seed length of 20 nt
The total sequencing base pair coverage in all exons was summed for all annotated genes in each sample and normalized to total coverage using bedtools and custom R scripts as described in Wu et al. 2015 PLoS Genetics 11:e1005655.
Average expression values of three wild type replicates were compared to the average of three mutant replicates.
Assembly: mus musculus mm10
Supplementary files format and content: Microsoft Excel File with normalized sequencing coverage of all annotated expressed genes and statistical comparison of expression in wild type kidney to mutant kidney.

source_name: kidney

growth_protocol: In utero mouse kidney growth to E17.

extract_protocol:
Total RNA was isolated from three E17 kidneys for each genotype using an RNeasy Mini Kit (Qiagen 74104) with on the column DNAse I treatment. Ribosomal RNA was depleted from 1 μg of total RNA using Ribominus Eukaryote System v2 (Life Technologies).
Construction of barcoded sequencing libraries was performed using the Ion Total RNA-seq v2 kits (Life Technologies) according to the manufacturer’s instructions.

treatment_protocol: Fresh kidney tissue harvested.

value: kidney

tag: developmental stage


title: Mutant 3489

growth_protocol: Mouse kidney growth to 2 months old.

extract_protocol:
Total RNA was isolated from four kidneys for each genotype using an RNeasy Mini Kit (Qiagen 74104) with on the column DNAse I treatment. Ribosomal RNA was depleted from 1 μg of total RNA using Ribominus Eukaryote System v2 (Life Technologies).
Construction of barcoded sequencing libraries was performed using the Ion Total RNA-seq v2 kits (Life Technologies) according to the manufacturer’s instructions.

value: 2 month

value: Six2Cre Mta2flx/flx


title: con.007


title: GRG_12h_3

city: Haikou

first: tian

last: jiang

address: 58 of Ren min Road

country: China

institute: Hainan University

data_processing:
The de novo assembly was performed on cleaned reads using Trinity (Grabherr et al., 2011). Before assembly, raw reads were trimmed by removing adaptor sequences and ambiguous nucleotides. Reads with quality scores less than 20 and length below 30 bp were all trimmed. The resulting high-quality sequences were used in subsequent assembly. Briefly, the raw reads were assembled into the unique sequences of transcripts in Inchworm via greedy K-mer extension (k-mer 25).
After mapping of reads to Inchworm contig bundles, Chrysalis incorporated reads into de Bruijn graphs. Butterfly then processed the individual graphs in parallel, reporting full-length transcripts and paralogous genes. After assembly, the open reading frame (ORF) of each unisequence was predicted by using Trinity software. Unisequences were used for BLAST search and annotation against the NR, NT, STRING (http://string-db.org/) (Franceschini et al., 2013), COG (http://www.ncbi.nlm.nih.gov/COG/), KEGG (http://www.genome.jp/kegg/) databases using an E-value cut-off of 10-5 (Camacho et al., 2009). Functional annotation by gene ontology (GO, http://www.geneontology.org) terms was analysed by using BLAST2GO software (NCBI) (Conesa et al., 2005).
Supplementary_files_format_and_content: Identified mRNAs in each library with count reads and normalized data

molecule: polyA RNA

organism: Trachinotus blochii

growth_protocol: The amount of 500 fish were randomly transferred to three indoor tanks with a circulating water filtration system (each tank has a volume of 3000 L) for one week. During the holding period, the fish were fed once a day, the amount of feed is controlled at 2 % of the total weight of the 500 fish. What's more, the water qualities were monitored twice a day and maintained as follows: temperature (27.1-29.3 ℃), pH (8.0), and ammonia (0.6), dissolved oxygenation (6.59 - 7.05 mg/L).

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After hypoxia challenge for 0 h and 12 h, the liver of three fish at each sampling time points were collected in the control group and hypoxic group, named normoxia_0h, normoxia_12h, hypoxia_0h, hypoxia_12h, respectively. Upon reoxygenation period, after different reoxygenation methods for 3h and 12h,the liver of three fish at each sampling time points were collected in the RRG group and GRG group,named RRG_3h, RRG_12h, GRG_3h, GRG_12h, respectively. First, the experimental fish was anesthetized with MS-222, the spine of the fish was severed and immediately dissected to collect gill tissues. All samples were collected in 2 mL cryotubes and rapidly frozen in liquid nitrogen and stored at -80 °C until total RNA was isolated.

tag: treatement

value: liver


title: Control 3486


title: Control 3586


title: GRG_12h_2


title: Control 3401


title: mut.009


title: Mutant 3387


title: mut.006


title: con.011


title: Mutant 3487


title: Control 3587


title: GRG_3h_3


title: GRG_12h_1


title: ChIP-Seq B cells, LPS+IL21, anti-IKZF1

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: ChIP-Seq B cells, LPS+IL21, anti-IKZF1

data_processing:
Sequenced reads (50 bp, single end) were obtained with the Illumina CASAVA pipeline and mapped to the mouse genome mm10 (GRCm38, December 2011) using Bowtie 2.2.6.
The mapped outputs were converted to browser-extensible data files, which were then converted to binary tiled data files (TDFs) using IGVTools 2.4.13 for viewing on the IGV browser (https://software.broadinstitute.org/software/igv/). Peak calling was performed by MACS 1.4.2 relative to an IgG library as input control and the p-value threshold was set as 1e-10. Only non-redundant reads were analyzed for peak calling. ChIP-Seq binding intensity heat maps were analyzed and visualized using deepTools. ChIP-Seq co-localization analysis was performed using R package “ChIPseeker”, and Reactome pathway analysis was performed using R package “ClusterProfiler”.
Assembly: mm10 (GRCm38)
Supplementary files format and content: bigwig

source_name: spleen

growth_protocol: Mouse splenic B cells were isolated using the EasySepTM Mouse B cell isolation Kit (STEMCELL technologies, 19854) according to the manufacturer’s protocol. Primary mouse B cells were cultured in RPMI-1640 medium containing 10% FBS, 1% penicillin-streptomycin and 50 mM 2-mercaptoethanol (Gibco, 21985023). LPS (Escherichia coli O111:B4) was purchased from Sigma-Aldrich (L3012). Recombinant human and mouse IL-21 protein was purchased from R & D systems.

extract_protocol:
Immunoprecipitation was performed overnight at 4oC using antibodies to cJUN (Cell Signaling Technologies, 9165S), IKZF1 (Active Motif, 39291), normal mouse IgG (Santa Cruz, sc-2025), or normal rabbit IgG (Cell Signaling Technologies, 2729S). ChIP-Seq DNA libraries were prepared with the KAPA LTP Library Preparation Kit and barcoded with NEXTflex DNA barcodes, quantified, and sequenced on an Illumina HiSeq 3000 system.
PCR products were barcoded (indexed) and sequenced on Illumina HiSeq 3000 platform.

treatment_protocol: For ChIP-Seq experiments, 8-10 million B cells were treated with either LPS (1 mg ml-1) or LPS + mouse IL-21 (100 ng ml-1) for 3 hours.

value: spleen

value: Wild-type

value: primary B cells

tag: chip antibody


title: ChIP-Seq B cells, LPS+IL21, anti-cJUN

description: ChIP-Seq B cells, LPS+IL21, anti-cJUN

value: anti-cJUN


title: ChIP-Seq B cells, LPS, anti-IKZF1

description: ChIP-Seq B cells, LPS, anti-IKZF1

value: LPS


title: mut.008


title: RRG_12h_3


title: RRG_12h_2


title: GRG_3h_1


title: ChIP-Seq B cells, untreated, anti-IKZF1

description: ChIP-Seq B cells, untreated, anti-IKZF1

value: untreated


title: RRG_12h_1


title: Mutant 3382


title: ChIP-Seq B cells, untreated, anti-cJUN

description: ChIP-Seq B cells, untreated, anti-cJUN


title: ChIP-Seq B cells, LPS, anti-cJUN

description: ChIP-Seq B cells, LPS, anti-cJUN


title: ChIP-Seq B cells, IgG

description: ChIP-Seq B cells, IgG

value: IgG


title: RRG_3h_3


title: GRG_3h_2


title: RRG_3h_2


title: hypoxia_12h_2


title: hypoxia_12h_1


title: hypoxia_0h_3


title: hypoxia_12h_3


title: EX30_Triple-_S1

type: genomic

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

country: United Kingdom

institute: University of Exeter

description:
Triple-
205096370087_R04C01

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing:
Data was imported and preprocessed using the R package bigmelon. Data was then  normalised by cell type using the dasen function.
Normalised beta value

label: Cy3, cy5

source_name: Triple-

label_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit  (Zymo Research) according to the manufacturer’s standard protocol.

extract_protocol: Genomic DNA was extracted from Fluorescence-Activated Nuclei Sorting (FANS) sorted prefrontal cortex tissue using a standard cell lysis, proteinase K digestion, phenol/chloroform, ethanol precipitation method.

value: F

value: Post-mortem prefrontal cortex


title: EX15_Triple-_S1

description:
Triple-
203991460047_R07C01

value: M


title: EX44_Sox10+_S1

description:
Sox10+
201118840110_R07C01


title: EX11_Triple-_S1

description:
Triple-
203991450090_R03C01


title: EX7_Sox10+_S1

description:
Sox10+
203205080216_R06C01


title: EX12_Triple-_S1

description:
Triple-
203991450109_R06C01


title: EX14_Triple-_S1

description:
Triple-
203991450140_R06C01


title: EX40_Triple-_S1

description:
Triple-
205862290057_R05C01


title: EX13_Triple-_S1

description:
Triple-
203991450123_R07C01


title: normoxia_12h_3


title: hypoxia_0h_1


title: normoxia_12h_2


title: EX43_Sox10+_S1

description:
Sox10+
205862290091_R05C01


title: hypoxia_0h_2


title: normoxia_12h_1


title: EX42_Sox10+_S1

description:
Sox10+
205862290079_R01C01


title: normoxia_0h_3


title: EX41_Sox10+_S1

description:
Sox10+
205862290072_R03C01


title: normoxia_0h_2


title: EX40_Sox10+_S1

description:
Sox10+
205862290057_R01C01


title: RRG_3h_1


title: normoxia_0h_1


title: EX4_Sox10+_S1

description:
Sox10+
203205080214_R02C01


title: EX6_Sox10+_S1

description:
Sox10+
203205080216_R02C01


title: EX39_Sox10+_S1

description:
Sox10+
205862290047_R07C01


title: EX38_Sox10+_S1

description:
Sox10+
205862290015_R03C01


title: EX37_Sox10+_S1

description:
Sox10+
205862290014_R07C01


title: EX21_Sox10+_S1

description:
Sox10+
201194010019_R06C01


title: EX3_Sox10+_S1

description:
Sox10+
203205080202_R06C01


title: EX35_Sox10+_S2

description:
Sox10+
205854150117_R06C01


title: EX23_Sox10+_S1

description:
Sox10+
201194010025_R06C01


title: H.HepG2.40k.RBFOX2.StrongRNase.30nt.rep2

city: Chicago

first: Yanming

last: Chen

address: 929 E 57th Street

institute: The University of Chicago

description: Strong RNase treatment

data_processing:
The adaptor sequences were trimmed with Cutadapt (v4.2) using the parameter cutadapt --nextseq-trim=20 -a AGATCGGAAGAGCACACGTCTGAACTCCAG; the 8-nt UMI sequences were moved and add to the read name for the further deduplication. Especially for libraries in Groups D-G with 8-nt inline barcodes at the 5'-end of the 3'-end adaptors, extra 8 nts should be trimmed after adapter sequence removal. For all libraries, extra 4 nts at the reads’ 3-end were removed from the adapter-free sequence to minimize mapping mismatch caused by the imperfect paired sequence in the random primer.
The reads were first mapped to the corresponding rRNA sequences using Bowtie2 (v2.4.4) with parameters: --seedlen=15, and the mapped reads were discarded to avoid rRNA contamination.
The remaining unmapped reads were mapped to the corresponding genome using STAR (v2.7.9a) with parameters: --readFilesCommand zcat --alignEndsType EndToEnd --genomeLoad NoSharedMemory --quantMode TranscriptomeSAM --alignMatesGapMax 15000 --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outSAMprimaryFlag AllBestScore --outSAMattributes All --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --outFilterMatchNmin 24.
Uniquely mapped reads were deduplicated to get the usable reads using UMI-tools with the parameter, --method unique (v1.1.2).
Assembly: GRCh38.p13, GRCm39
Supplementary files format and content: bigWig files for  ARTR-seq libraries were generated by bamCoverage with the parameters-normalizeUsing BPM --binSize 1. The tab-delimited text files include read counts for sodium arsenite-treated samples counted by featureCounts.

source_name: Liver cancer cell line

growth_protocol: HeLa or HepG2 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics. K562 cells were cultured in RPMI 1640 medium supplementec with 10% FBS, 2mM L-glutamine and antibiotics. All cells were placed in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were fixed with 1.5 % paraformaldehyde for 10 minutes, quenched with 125 mM glycine at room temperature for 5 min, and permeabilized with 0.5% Triton X-100 on ice for 10min. For samples with RNase treatment, RNase I was added and samples were incubated at 37C for 5 min. Samples were blocked with 1 mg/ml BSA, followed by staining with primary antibody, secondary antibody and protein A/G-reverse transcriptase. For samples with strong RNase treatment, RNase I was added and samples were incubated at 37C for an additional 5 min. Then, the in-situ reverse transcription was preformed at 37C for 30min. Cells were digested with proteinase K at 37C for 2h, and total nucleic acids were extracted with phenol-chloroform extraction and concentrated by ethanol precipitation.
Biotinylated cDNA were enriched by strepavidin beads. 3' cDNA adapter (5′Phos-NNNNNNNNAGATCGGAAGAGCGTCGTGT-3′SpC3) was ligated by T4 RNA ligase 1 by incubating at 25 °C for 16 h. cDNA was recovered from beads. Then, the library can be obtained by PCR amplification with NGS sequencing primer and gel purification of size between 180bp and 400bp.
OTHER: ARTR-seq (an Assay of Reverse Transcription-based RBP binding sites Sequencing)

treatment_protocol: For stress treatment, HeLa cells were changed into fresh pre-warmed medium supplemented with 5mM sodium arsenite and incubated at 37C, 5% CO2.

value: Liver cancer cell line

value: Liver cancer cells

value: WT

value: Rich Medium

tag: cell number

value: RBFOX2(Proteintech, #12498-1-AP)


title: H.HepG2.40k.RBFOX2.noRNase.30nt.rep2


title: H.HepG2.40k.RBFOX2.noRNase.3nt.rep1


title: H.HepG2.40k.RBFOX2.noRNase.13nt.rep1


title: H.HepG2.40k.RBFOX2.noRNase.13nt.rep2


title: H.HepG2.40k.RBFOX2.StrongRNase.30nt.rep1

description: Strong RNase treatment


title: EX22_Sox10+_S1

description:
Sox10+
201194010025_R02C01


title: H.HepG2.40k.RBFOX2-noSecAnti.noRNase.30nt.rep2

description: Without secondary antibody


title: H.HepG2.40k.RBFOX2.noRNase.30nt.rep1


title: H.HepG2.40k.RBFOX2.WeakRNase.30nt.rep2

description: Weak RNase treatment


title: EX2_Sox10+_S1

description:
Sox10+
203205080202_R02C01


title: EX19_Sox10+_S1

description:
Sox10+
204001350069_R04C01


title: H.HepG2.40k.RBFOX2.WeakRNase.30nt.rep1

description: Weak RNase treatment


title: H.HepG2.40k.Input.noRNase.30nt.rep2


title: EX18_Sox10+_S1

description:
Sox10+
204001350068_R01C01


title: H.HepG2.40k.Input.noRNase.30nt.rep1


title: H.HepG2.40k.RBFOX2-noSecAnti.noRNase.30nt.rep1

description: Without secondary antibody


title: EX17_Sox10+_S1

description:
Sox10+
204001350047_R01C01


title: EX16_Sox10+_S1

description:
Sox10+
204001350046_R05C01


title: H.HepG2.40k.Input.noRNase.13nt.rep2


title: EX36_Sox10+_S1

description:
Sox10+
205862290012_R06C01


title: H.HepG2.40k.Input.noRNase.13nt.rep1


title: H.HepG2.40k.RBFOX2.noRNase.3nt.rep2


title: EX33_Sox10+_S1

description:
Sox10+
205097260049_R06C01


title: H.HepG2.40k.Input.noRNase.3nt.rep1


title: EX25_SATB2+_S1

description:
SATB2+
205061420101_R02C01


title: EX15_SATB2+_S1

description:
SATB2+
203991450159_R06C01


title: EX14_SATB2+_S1

description:
SATB2+
203991450134_R06C01


title: 25_SIINFEKL

city: Seattle

first: Martin

last: Prlic

state: WA

address: 1100 Fairview Ave, Mail stop E5-110

institute: Fred Hutchinson Cancer Center

description: low input bulk RNAseq

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads.
Reads were processed using workflows managed on the Galaxy platform. Reads were trimmed by 1 base at the 3′ end then trimmed from both ends until base calls had a minimum quality score of at least 30. Any remaining adapter sequence was removed as well.
To align the trimmed reads, STAR aligner (v2.4.2a) was used with the GRCm38 reference genome.
Gene counts were generated using HTSeq-count (v0.4.1).
Assembly: GRCm38
Supplementary files format and content: comma-separated values file includes raw counts for each Sample

source_name: lymphoid organs (lymph nodes and spleen)

growth_protocol: To enrich bulk T cells from single cell suspensions, we used a mouse-specific T cell negative isolation MACS (STEMCELL Technologies, Canada). We plated 0.5–1 × 106 T cells per well in 96-well V-bottom tissue culture plates. We cultured cells in mouse RP10 media (RPMI 1640 supplemented with 10% FBS, 2mM L-glutamine, 100 U/mL penicillin-streptomycin, 1mM sodium pyruvate, 0.05mM β mercaptoethanol, and 1mM HEPES) at 37°C with 5% CO2.

extract_protocol:
None. 500 OT-I T cells were sorted directly into the lysis buffer of the SMART-Seq v4 Ultra Low Input RNA Kit (Takara).
RNAseq libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara) per the manufacturer's guidelines.

treatment_protocol: Cells were cultured in conditions of 2 hours no stimulation, 2 hours stimulation with 100ng/mL TGF-β, 24 hours stimulation with 100nM N4 (SIINFEKL), and 24 hours stimulation with 100nM N4 (SIINFEKL) and 100ng/mL TGF-β.

value: FACS:Live/Dead -, CD45.1+, CD8a+ (OT-I T cells)

value: SIINFEKL


title: EX13_SATB2+_S1

description:
SATB2+
203991460077_R07C01


title: 27_SIINFEKL

description: low input bulk RNAseq

value: lymphoid organs (lymph nodes and spleen)


title: EX12_SATB2+_S1

description:
SATB2+
203991450121_R04C01


title: EX1_Sox10+_S1

description:
Sox10+
203205080172_R06C01


title: 26_SIINFEKL_and_TGFb

description: low input bulk RNAseq


title: 23_SIINFEKL

description: low input bulk RNAseq


title: 22_SIINFEKL_and_TGFb

description: low input bulk RNAseq


title: 21_SIINFEKL

description: low input bulk RNAseq


title: 28_SIINFEKL_and_TGFb

description: low input bulk RNAseq


title: EX11_SATB2+_S1

description:
SATB2+
203991450094_R04C01


title: 24_SIINFEKL_and_TGFb

description: low input bulk RNAseq


title: EX26_SATB2-_S1

description:
SATB2-
205061420101_R06C01


title: 20_TGFb

description: low input bulk RNAseq

value: TGFb


title: EX24_SATB2+_S1

description:
SATB2+
205061420089_R04C01


title: EX15_SATB2-_S1

description:
SATB2-
203991450159_R07C01


title: EX14_SATB2-_S1

description:
SATB2-
203991450134_R07C01


title: 19_none

description: low input bulk RNAseq


title: EX13_SATB2-_S1

description:
SATB2-
203991460077_R08C01


title: H.HepG2.40k.Input.noRNase.3nt.rep2


title: EX9_SATB2+_S1

description:
SATB2+
203973690080_R06C01


title: EX12_SATB2-_S1

description:
SATB2-
203991450121_R08C01


title: EX8_SATB2+_S1

description:
SATB2+
203962710030_R03C01


title: 16_TGFb

description: low input bulk RNAseq


title: EX7_NeuN+_S1

description:
NeuN+
203205080216_R05C01

source_name: NeuN+


title: 15_none

description: low input bulk RNAseq


title: EX11_SATB2-_S1

description:
SATB2-
203991450094_R08C01


title: EX6_NeuN+_S1

description:
NeuN+
203205080216_R01C01


title: EX5_NeuN+_S1

description:
NeuN+
203205080214_R05C01


title: EX43_NeuN+_S1

description:
NeuN+
205862290091_R04C01


title: EX44_NeuN+_S1

description:
NeuN+
201118840110_R06C01


title: EX41_NeuN+_S1

description:
NeuN+
205862290072_R04C01


title: 13_none

description: low input bulk RNAseq


title: 11_SIINFEKL

description: low input bulk RNAseq


title: 12_SIINFEKL_and_TGFb

description: low input bulk RNAseq


title: 8_SIINFEKL_and_TGFb

description: low input bulk RNAseq


title: 10_SIINFEKL_and_TGFb

description: low input bulk RNAseq


title: EX42_NeuN+_S1

description:
NeuN+
205862290079_R02C01


title: 9_SIINFEKL

description: low input bulk RNAseq


title: 18_TGFb

description: low input bulk RNAseq


title: 7_SIINFEKL

description: low input bulk RNAseq


title: 17_none

description: low input bulk RNAseq


title: EX39_NeuN+_S1

description:
NeuN+
205862290047_R06C01


title: EX4_NeuN+_S1

description:
NeuN+
203205080214_R01C01


title: EX38_NeuN+_S1

description:
NeuN+
205862290015_R06C01


title: 5_none

description: low input bulk RNAseq


title: 6_TGFb

description: low input bulk RNAseq


title: 4_TGFb

description: low input bulk RNAseq


title: EX35_NeuN+_S2

description:
NeuN+
205854150117_R05C01


title: EX35_NeuN+_S1

description:
NeuN+
205854150118_R03C01


title: EX36_NeuN+_S1

description:
NeuN+
205862290012_R05C01


title: 3_none

description: low input bulk RNAseq


title: EX34_NeuN+_S1

description:
NeuN+
205854150087_R06C01


title: 2_TGFb

description: low input bulk RNAseq


title: 14_TGFb

description: low input bulk RNAseq


title: EX30_NeuN+_S1

description:
NeuN+
205096370087_R07C01


title: 1_none

description: low input bulk RNAseq


title: EX28_NeuN+_S1

description:
NeuN+
205096370073_R03C01


title: EX22_NeuN+_S1

description:
NeuN+
201194010025_R01C01


title: EX27_NeuN+_S1

description:
NeuN+
205096370002_R05C01


title: EX21_NeuN+_S1

description:
NeuN+
201194010019_R05C01


title: 24_26_SIINFEKL and TGFb

description: bulk ATACseq

data_processing:
Fastq data processed with ENCODE ATAC-seq pipeline v1.7 except MACS2 input limited to a maximum 50 million mapped reads per replicate
MACS2 output for each replicate was filtered for peaks with q-value less than 0.0001
Bedtools merge was used to consolidate peaks from all replicates to a common peak set
Peaks were resized to a uniform size of 500 bp
Reads overlapping peaks were computed for all replicates and normalized with limma/voom
Peaks limited to those with a mean of at least 6 normalized counts per million mapped reads in at least 1 biological group
Assembly: GRCm38
Supplementary files format and content: tab-seperated values containing voom normalized ATAC-seq counts per peak

extract_protocol: ATAC-seq was performed on pools of 40,000 to 50,000 sort-purified OT-I T cells pooled from 2 to 3 mice. Extraction and library constuction was performed according to (Buenrostro JD et. al 2015, https://doi.org/10.1002/0471142727.mb2129s109).

value: SIINFEKL and TGFb


title: 23_25_SIINFEKL

description: bulk ATACseq


title: 22_28_SIINFEKL and TGFb

description: bulk ATACseq


title: EX23_NeuN+_S1

description:
NeuN+
201194010025_R05C01


title: 14_20_TGFb

description: bulk ATACseq


title: 16_18_TGFb

description: bulk ATACseq


title: 13_19_none

description: bulk ATACseq


title: 15_17_none

description: bulk ATACseq


title: 8_10_12_SIINFEKL and TGFb

description: bulk ATACseq


title: EX20_NeuN+_S1

description:
NeuN+
201194010019_R01C01


title: EX18_NeuN+_S1

description:
NeuN+
204001350068_R02C01


title: 7_9_11_SIINFEKL

description: bulk ATACseq


title: EX17_NeuN+_S1

description:
NeuN+
204001350047_R04C01


title: EX16_NeuN+_S1

description:
NeuN+
204001350046_R02C01


title: EX19_NeuN+_S1

description:
NeuN+
204001350069_R01C01


title: 1_3_5_none

description: bulk ATACseq


title: EX10_NeuN+_S1

description:
NeuN+
203977090072_R05C01


title: 2_4_6_TGFb

description: bulk ATACseq


title: G.HeLa_Trt60.40k.Input.rep2

data_processing:
The adaptor sequences were trimmed with Cutadapt (v4.2) using the parameter cutadapt --nextseq-trim=20 -a AGATCGGAAGAGCACACGTCTGAACTCCAG; the 8-nt UMI sequences were moved and add to the read name for the further deduplication. Especially for libraries in Groups D-G with 8-nt inline barcodes at the 5'-end of the 3'-end adaptors, extra 8 nts should be trimmed after adapter sequence removal. For all libraries, extra 4 nts at the reads’ 3-end were removed from the adapter-free sequence to minimize mapping mismatch caused by the imperfect paired sequence in the random primer.
The reads were first mapped to the corresponding rRNA sequences using Bowtie2 (v2.4.4) with parameters: --seedlen=15, and the mapped reads were discarded to avoid rRNA contamination.
The remaining unmapped reads were mapped to the corresponding genome using STAR (v2.7.9a) with parameters: --readFilesCommand zcat --alignEndsType EndToEnd --genomeLoad NoSharedMemory --quantMode TranscriptomeSAM --alignMatesGapMax 15000 --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outSAMprimaryFlag AllBestScore --outSAMattributes All --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --outFilterMatchNmin 24.
Uniquely mapped reads were deduplicated to get the usable reads using UMI-tools with the parameter, --method unique (v1.1.2).
Assembly: GRCh38.p13, GRCm39
Supplementary files format and content: bigWig files for  ARTR-seq libraries were generated by bamCoverage with the parameters-normalizeUsing BPM --binSize 1. The tab-delimited text files include read counts for sodium arsenite-treated samples counted by featureCounts.
Library strategy: ARTR-seq (an Assay of Reverse Transcription-based RBP binding sites Sequencing)

source_name: Cervical cancer cell line

extract_protocol:
Cells were fixed with 1.5 % formaldehyde for 10 minutes, quenched with 125 mM glycine at room temperature for 5 min, and permeabilized with 0.5% Triton X-100 on ice for 10min. Samples were blocked with 1 mg/ml BSA, followed by staining with primary antibody, secondary antibody and protein A/G-reverse transcriptase. Then, the in-situ reverse transcription was preformed at 37C for 30min. RT-primer Cells were digested with proteinase K at 37C for 2h, and total nucleic acids were extracted with phenol-chloroform extraction and concentrated by ethanol precipitation.
Biotinylated cDNA were enriched by strepavidin beads. 3' cDNA adapter (5′Phos-NNNNNNNNAGATCGGAAGAGCGTCGTGT-3′SpC3) was ligated by T4 RNA ligase 1 by incubating at 25 °C for 16 h. cDNA was recovered from beads. Then, the library can be obtained by PCR amplification with NGS sequencing primer and gel purification of size between 180bp and 400bp.

value: Cervical cancer

value: HeLa

value: Cervical cancer cells

value: Sodium Arsenite 60 min


title: EX43_IRF8+_S1

description:
IRF8+
205862290091_R01C01


title: G.HeLa_Trt60.40k.G3BP1.rep2

value: G3BP1(BD Bioscience, #611126)


title: G.HeLa_Trt60.40k.Input.rep1


title: EX42_IRF8+_S1

description:
IRF8+
205862290079_R05C01

value: F

value: Post-mortem prefrontal cortex


title: 21_27_SIINFEKL

description: bulk ATACseq


title: EX3_NeuN+_S1

description:
NeuN+
203205080202_R05C01


title: EX40_IRF8+_S1

description:
IRF8+
205862290057_R04C01

value: M


title: G.HeLa_Trt60.40k.G3BP1.rep1


title: G.HeLa_Trt20.40k.Input.rep2

value: Sodium Arsenite 20 min


title: EX39_IRF8+_S1

description:
IRF8+
205862290047_R04C01


title: EX2_NeuN+_S1

description:
NeuN+
203205080202_R01C01


title: EX36_IRF8+_S1

description:
IRF8+
205862290012_R08C01


title: EX30_IRF8+_S1

description:
IRF8+
205096370087_R06C01


title: EX35_IRF8+_S2

description:
IRF8+
205854150117_R01C01


title: G.HeLa_Trt20.40k.G3BP1.rep1

value: WT


title: G.HeLa_Trt20.40k.Input.rep1


title: G.HeLa_Trt10.40k.Input.rep2

value: Sodium Arsenite 10 min


title: EX27_IRF8+_S1

description:
IRF8+
205096370002_R04C01


title: G.HeLa_Trt10.40k.G3BP1.rep2


title: EX29_IRF8+_S1

description:
IRF8+
205096370073_R08C01


title: EX18_IRF8+_S1

description:
IRF8+
204001350068_R05C01


title: G.HeLa_Trt10.40k.G3BP1.rep1


title: EX17_IRF8+_S1

description:
IRF8+
204001350047_R05C01


title: G.HeLa_Trt0.40k.Input.rep2

value: Sodium Arsenite 0 min


title: EX16_IRF8+_S1

description:
IRF8+
204001350046_R01C01


title: G.HeLa_Trt0.40k.G3BP1.rep2


title: EX14_IRF8+_S1

description:
IRF8+
203991450140_R07C01


title: EX12_IRF8+_S1

description:
IRF8+
203991450109_R05C01


title: EX13_IRF8+_S1

description:
IRF8+
203991450123_R05C01


title: E.HepG2.20.PTBP1.rep2

value: Liver cancer

value: Liver cancer cells

value: Rich Medium


title: E.HepG2.20.PTBP1.rep1


title: EX37_IRF8+_S1

description:
IRF8+
205862290014_R04C01


title: G.HeLa_Trt20.40k.G3BP1.rep2


title: EX11_IRF8+_S1

description:
IRF8+
203991450090_R02C01


title: EX7_Double-_S1

description:
Double-
203205080216_R08C01

source_name: Double-


title: EX5_Double-_S1

description:
Double-
203205080214_R08C01


title: G.HeLa_Trt10.40k.Input.rep1


title: E.HepG2.50.PTBP1.rep2


title: EX44_Double-_S1

description:
Double-
201118840110_R08C01


title: E.HepG2.100.PTBP1.rep2


title: E.HepG2.100.PTBP1.rep1


title: EX43_Double-_S1

description:
Double-
205862290091_R03C01


title: EX39_Double-_S1

description:
Double-
205862290047_R03C01


title: EX4_Double-_S1

description:
Double-
203205080214_R04C01


title: E.HepG2.500.PTBP1.rep2


title: EX38_Double-_S1

description:
Double-
205862290015_R07C01


title: G.HeLa_Trt0.40k.Input.rep1


title: EX37_Double-_S1

description:
Double-
205862290014_R03C01


title: G.HeLa_Trt0.40k.G3BP1.rep1


title: E.HepG2.200.PTBP1.rep2


title: E.HepG2.1k.PTBP1.rep2


title: EX35_Double-_S1

description:
Double-
205854150118_R02C01


title: E.HepG2.500.PTBP1.rep1


title: E.HepG2.2k.PTBP1.rep2


title: EX36_Double-_S1

description:
Double-
205862290012_R04C01


title: E.HepG2.1k.PTBP1.rep1


title: EX35_Double-_S2

description:
Double-
205854150117_R04C01


title: E.HepG2.2k.PTBP1.rep1


title: E.HepG2.50.PTBP1.rep1


title: EX34_Double-_S1

description:
Double-
205854150087_R04C01


title: EX30_Double-_S1

description:
Double-
205096370087_R05C01


title: E.HepG2.5k.PTBP1.rep1


title: E.HepG2.5k.PTBP1.rep2


title: EX20_Double-_S1

description:
Double-
201194010019_R04C01


title: EX22_Double-_S1

description:
Double-
201194010025_R04C01


title: EX3_Double-_S1

description:
Double-
203205080202_R08C01


title: D.K562.5k.PTBP1.rep1

source_name: Leukemia cell line

value: Leukemic bone marrow

value: Leukemia cells


title: EX2_Double-_S1

description:
Double-
203205080202_R04C01


title: E.HepG2.200.PTBP1.rep1


title: D.K562.5k.PTBP1.rep2


title: C.HepG2_siPTBP1-2.40k.PTBP1.rep1


title: EX18_Double-_S1

description:
Double-
204001350068_R04C01


title: EX17_Double-_S1

description:
Double-
204001350047_R02C01


title: EX19_Double-_S1

description:
Double-
204001350069_R05C01


title: C.HepG2_siPTBP1-1.40k.PTBP1.rep1


title: C.HepG2_siPTBP1-1.40k.PTBP1.rep2


title: C.HepG2_siCtrl.40k.PTBP1.rep2

value: siCtrl


title: EX16_Double-_S1

description:
Double-
204001350046_R03C01


title: C.HepG2_siCtrl.40k.PTBP1.rep1


title: Mesenchymal, biological replicate 3

city: Crawley

first: Jessica

last: King

address: 35 Stirling Hwy

department: School of Molecular Sciences

country: Australia

institute: University of Western Australia

data_processing:
Initial quality control was conducted using FASTQC.
RNA-seq reads were aligned to the human reference genome (hg38) using STAR.
Read quantification was performed using HTSeq-count.
Subsequent processing of count data was conducted using R 4.1.2 via RStudio.
Variance stabilizing transformation and principal component analysis were conducted as quality control prior to differential gene expression analysis.
Assembly: Human reference genome hg38
Supplementary files format and content: Comma-delimited text files indicate raw gene counts for each Sample.

source_name: mesHMLE

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen, #74104), with DNA removal using RNase-Free DNase kit (Qiagen, #79254).
Library preparation and RNA sequencing were conducted by Macrogen Oceania Pty Ltd using Illumina TruSeq stranded mRNA library kit and Novaseq 6000 150 bp PE at depth 6 Gb, 40 × 10^6 reads.

value: mesHMLE

value: HMLE-derived mesenchymal

value: wt

value: Untreated

value: 0 d


title: Mesenchymal, biological replicate 2


title: C.HepG2_siPTBP1-1.40k.Input.rep2


title: C.HepG2_siPTBP1-2.40k.Input.rep1


title: C.HepG2_siPTBP1-2.40k.Input.rep2


title: TGF-β-treated 20 d, biological replicate 4

source_name: HMLE

value: HMLE

value: Human mammary luminal epithelial

value: TGF-beta


title: C.HepG2_siCtrl.40k.Input.rep2


title: C.HepG2_siPTBP1-1.40k.Input.rep1


title: Mesenchymal, biological replicate 1


title: Docetaxel-treated 20 d, biological replicate 4

value: Docetaxel


title: C.HepG2_siCtrl.40k.Input.rep1


title: C.HepG2_siPTBP1-2.40k.PTBP1.rep2


title: Spontaneous EMT 20 d, biological replicate 4

value: Spontaneous EMT


title: B.HeLa.40k.YTHDF2.rep2

value: Cervical cancer

value: HeLa

value: Cervical cancer cells

value: WT

value: YTHDF2(Abcam, #ab220163)


title: Untreated 0 d, biological replicate 4


title: Untreated 0 d, biological replicate 3


title: Docetaxel-treated 20 d, biological replicate 3


title: B.HeLa.40k.YTHDF1.rep2

value: Rich Medium

value: YTHDF1(Abcam, #ab220162)


title: B.HeLa.40k.YTHDF2.rep1


title: TGF-β-treated 20 d, biological replicate 3


title: Spontaneous EMT 20 d, biological replicate 3


title: B.HeLa.40k.YTHDF1.rep1


title: B.HeLa.40k.YTHDC1.rep2

value: YTHDC1(Abcam, #ab122340)


title: Untreated 20 d, biological replicate 2


title: TGF-β-treated 20 d, biological replicate 2


title: B.HeLa.40k.YTHDC1.rep1


title: Untreated 0 d, biological replicate 2


title: Docetaxel-treated 20 d, biological replicate 2


title: B.HeLa.40k.Input.rep3


title: B.HeLa.40k.PTBP1.rep1


title: B.HeLa.40k.Input.rep2


title: B.HeLa.40k.Input.rep1


title: A.HepG2.40k.RBFOX2.rep2

value: Liver cancer

value: Liver cancer cells

value: RBFOX2(Proteintech, #12498-1-AP)


title: A.HepG2.40k.RBFOX2.rep1


title: A.HepG2.40k.PTBP1.rep1


title: A.HepG2.40k.PTBP1.rep2


title: A.HepG2.40k.HNRNPC.rep1

value: HNPNPC (Santa Cruz, #sc-32308)


title: Osteoclast day 2 in vitro Donor 8

city: Odense

first: Alexander

last: Rauch

address: Campusvej 55

department: Department of Clinical Research

country: Denmark

institute: University of Southern Denmark and Odense University Hospital

data_processing:
RNA-seq reads were aligned to GRCh38 genome using STAR aligner and default settings.
Gene expression was quantified using HOMER (Heinz S, et al. 2010. Molecular Cell 38: 576-589) with the options -count exons -condenseGenes -noCondensing -noadj. Normalization and differential expression analysis was performed using DEseq2 (Love M I,  et al. 2014. Genome Biology 15: 550) comparing all time points against each including Donor information in the model.
Assembly: GRCh38
Supplementary files format and content: RNAcounts_Differentiation.txt, tab delimited text file, contains HOMER based raw tag counts at the gene body level (RefSeqID GRCh38).
Supplementary files format and content: Counts.txt, tab delimited text file, contains DEseq2 normalized counts that are not normalized for gene length and gene length information.
Supplementary files format and content: Diff_ctr.txt, tab delimited text file, contains  DEseq2 derived  rlog transformed counts as well as adjusted p values and logFC  comparing each time point against each other and for each time point against resorption activity of the mature cells.

source_name: CD14+ monocytes derived osteoclasts in vitro

growth_protocol: Primary human osteoclasts were differentiated from human CD14+ monocytes isolated from buffy coats obtained from anonymous blood donations as previously described (Herrild D M H, et al. 2015. Bone Research 3: 15032). Monocytes were seeded in T75 cell culture flasks (5 x 106 cells/flask) in α-minimal essential medium (αMEM, Gibco) with 10% fetal bovine serum (FBS, Gibco), 1% penicillin/streptomycin (Gibco) and stimulated with 25 ng/mL macrophage colony-stimulating factor (MCSF, R&D Systems). After two days, media was replaced with fresh media containing MCSF and receptor activator of nuclear κB (RANKL) (25 ng/mL each, R&D Systems), and media refreshed every 2-3 days thereafter until a total of seven days stimulation with RANKL. Microscopic validation of the presence of multinucleated cells was performed before cells were used for experiments. All cells were maintained at 37oC, 5% CO2.

extract_protocol:
RNA was extracted from cultured cells using Trizol combined with Econo Spin columns (Epoch Life Sciences).
RNA-seq was performed according to manufacturer’s instructions (TruSeq 2, Illumina) using 1 µg RNA for preparation of cDNA libraries.

treatment_protocol: Cells were harvested using TRIzol right after isolation of CD14+ cells (day 0) and after 2, 5 and 9 days of differentiation.

tag: time point

value: day 2


title: Osteoclast day 5 in vitro Donor 8

value: CD14+ monocytes derived osteoclasts in vitro

value: day 5


title: A.HepG2.40k.HNRNPC.rep2

tag: tissue


title: Osteoclast day 9 in vitro Donor 8

value: day 9


title: A.HepG2.40k.Input.rep2

tag: cell line


title: B.HeLa.40k.PTBP1.rep2

tag: cell type


title: Osteoclast day 9 in vitro Donor 6


title: Osteoclast day 5 in vitro Donor 6


title: Osteoclast day 2 in vitro Donor 6


title: Osteoclast day 2 in vitro Donor 7


title: Osteoclast day 5 in vitro Donor 7


title: A.HepG2.40k.Input.rep1

tag: genotype


title: Osteoclast day 5 in vitro Donor 5


title: Osteoclast day 0 in vitro Donor 6

value: day 0


title: Osteoclast day 2 in vitro Donor 5


title: Osteoclast day 9 in vitro Donor 4


title: Osteoclast day 5 in vitro Donor 4


title: Osteoclast day 9 in vitro Donor 7


title: Osteoclast day 2 in vitro Donor 4


title: TP0-baseline-PCR1

city: Melbourne

first: Dane

middle: Aaron McKay

last: Vassiliadis

address: Parkville VIC 3000

institute: Peter MacCallum Cancer Centre

description: DNA barcode amplicon sequencing of MLL-AF9 cells cultured in vitro

data_processing:
Raw sequence data from population-based dose-escalation were processed using BARtab v1.3 with the following parameters: --mode “single-bulk”, --upconstant “CGATTGACTA”, --downconstant “TGCTAATGCG”, --alnmismatches 1, --minqual 20, --pctqual 80, --constants “up”, --constantmismatches 0.1, --barcode_length 60. Count files were imported into R v4.2 and further analysed with bartools v0.2.5.
Assembly: SPLINTR BFP V1 reference barcode list (Addgene #179776)
Supplementary files format and content: tab delimited text file contains raw counts per barcode for each sample

source_name: in vitro

growth_protocol: Mouse MLL-AF9 leukaemia cells were generated from the bone marrow of female C56BL6/J mice as previously described (Fennell & Vassiliadis, Nature, 2022) and cultured in RPMI-1640 medium supplemented with mouse IL-3 (10 ng ml−1), human IL-6 (10 ng ml−1), mouse SCF (50 ng ml−1) 20% fetal bovine serum, streptomycin (100 µg ml−1), penicillin (100 U ml−1) and 2 mM GlutaMAX (Thermo Fisher Scientific) in 5% CO2 at 37 °C

extract_protocol:
5x10^5 cells were lysed in 40 µl Viagen lysis buffer containing 0.5 mg ml−1 proteinase K (Invitrogen) and split into technical replicates.
Barcode libraries were constructed using a two step PCR strategy using Q5 polymerase (NEB).
dual indexed PCR amplicon

treatment_protocol: Dose escalation cultures were supplemented with either 0.1% v/v DMSO, 400nM IBET or 300nM AraC. For the high dose arms, liquid cultures were supplemented with 800nM IBET or 700nM AraC. Drugs were replenished every three days by replating in fresh medium with drug. For the dose escalation, every 7 days, 5×10^5 cells were replated into fresh medium supplemented with an increased concentration of IBET (TP1 - 400nM, TP-2 - 600nM, TP-3 – 800nM and TP-4 - 1000nM), AraC (TP1 - 300nM, TP-2 - 300nM, TP-3 – 300nM and TP-4 - 500nM) or maintained in 0.1% v/v DMSO.

value: in vitro

value: mouse leukaemia MLL-AF9

value: C57BL6/J background

tag: treatment


title: TP0-baseline-PCR2


title: IBET-highdose-TR2-PCR2-08119


title: IBET-highdose-TR2-PCR2-221119


title: IBET-highdose-TR2-PCR2-04119


title: Osteoclast day 0 in vitro Donor 4


title: A.HepG2.40k.Input.rep3

value: WT


title: Osteoclast day 9 in vitro Donor 5


title: Osteoclast day 9 in vitro Donor 3


title: Osteoclast day 5 in vitro Donor 3


title: Osteoclast day 2 in vitro Donor 3


title: Osteoclast day 0 in vitro Donor 3


title: IBET-highdose-TR2-PCR1-04119


title: IBET-highdose-TR2-PCR1-221119


title: IBET-highdose-TR2-PCR1-08119


title: Osteoclast day 5 in vitro Donor 2


title: IBET-highdose-TR1-PCR2-221119


title: Osteoclast day 9 in vitro Donor 2


title: IBET-highdose-TR2-PCR1-01119


title: IBET-highdose-TR1-PCR2-011119


title: Osteoclast day 2 in vitro Donor 2


title: Osteoclast day 0 in vitro Donor 2


title: IBET-highdose-TR1-PCR2-081119


title: IBET-highdose-TR1-PCR2-041119


title: Osteoclast day 9 in vitro Donor 1


title: Osteoclast day 2 in vitro Donor 1


title: Osteoclast day 5 in vitro Donor 1


title: Osteoclast day 0 in vitro Donor 1


title: HeLa cells, TAK-931 treat, 72 h-2

city: Kashiwa

first: Akihiro

last: Ohashi

state: Chiba

address: 6-5-1 Kashiwanoha

department: Exploratory Oncology Research and Clinical Center

country: Japan

institute: National Cancer Center Japan

description:
H72h_T2
H72h_combined_featureCounts

data_processing:
Sequence read was mapped to human genome using STAR (v2.6.1c).
Multimapped reads were removed.
Assembly: hg38
Supplementary files format and content: tab-delimited text file including expression level for each sample (featureCounts)

source_name: Cervix

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% Fetal Bovine Serum and penicillin/Streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy Mini kit (QIAGEN).
RNA-seq was performed by Filgen, Inc.

treatment_protocol: HeLa cells were treated with DMSO or TAK-931 (300 nM) for 24 h, 48 h, or 72 h.

value: Cervix

value: HeLa cells

value: epithelial cell


title: IBET-highdose-TR1-PCR1-041119


title: IBET-highdose-TR1-PCR1-011119


title: IBET-highdose-TR2-PCR2-01119


title: IBET-gradual-TR2-PCR2-221119


title: IBET-highdose-TR1-PCR1-081119


title: IBET-gradual-TR2-PCR2-151119


title: IBET-gradual-TR2-PCR2-081119


title: HeLa cells, TAK-931 treat, 48 h-1

description:
H48h_T1
H48h_combined_featureCounts


title: IBET-gradual-TR2-PCR2-041119


title: HeLa cells, TAK-931 treat, 72 h-1

description:
H72h_T1
H72h_combined_featureCounts


title: IBET-gradual-TR2-PCR1-221119


title: HeLa cells, TAK-931 treat, 24 h-1

description:
H24h_T1
H24h_combined_featureCounts


title: IBET-gradual-TR2-PCR2-011119


title: IBET-gradual-TR2-PCR1-151119


title: HeLa cells, TAK-931 treat, 48 h-2

description:
H48h_T2
H48h_combined_featureCounts


title: HeLa cells, DMSO treat, 48 h-2

description:
H48h_D2
H48h_combined_featureCounts

value: DMSO


title: HeLa cells, DMSO treat, 72 h-1

description:
H72h_D1
H72h_combined_featureCounts


title: IBET-gradual-TR1-PCR2-221119


title: IBET-gradual-TR2-PCR1-041119


title: IBET-gradual-TR2-PCR1-081119


title: HeLa cells, DMSO treat, 48 h-1

description:
H48h_D1
H48h_combined_featureCounts


title: IBET-gradual-TR2-PCR1-011119


title: IBET-highdose-TR1-PCR1-221119


title: HeLa cells, DMSO treat, 72 h-2

description:
H72h_D2
H72h_combined_featureCounts


title: IBET-gradual-TR1-PCR2-151119


title: HeLa cells, DMSO treat, 24 h-1

description:
H24h_D1
H24h_combined_featureCounts


title: 293T,3days, rep2_3

city: Shenzhen

first: Weilong

last: Yang

state: Guangdong

address: No. 1088 Xueyuan Avenue, Nanshan District

institute: Southern University of Science and Technology

data_processing:
*library strategy: GUIDE-seq
GUIDE-seq was analysed using an open-source guideseq software:
https://github.com/aryeelab/guideseq
Assembly: hg38

growth_protocol: DMEM supplemented with 10% (v/v) fetal bovine serum  and 1% Penicillin‒Streptomycin  at 37°C with 5% CO2.

extract_protocol: the sequencing data were collected and analyzed by DIATRE, Shanghai.

treatment_protocol: 4.5 μg all-in-one plasmid for each target site, expressing Cas-SF01 and designed crRNA, and 1 nM of annealed GUIDE-seq oligonucleotides were transfected into HEK293T cells (2×106) by electroporation (Lonza, V4XC-2012). The electroporation was performed by 4D-Nucleofector™ Core Unit with program CM-130, and each sample was repeated three times and then cultured into one plate. Cells were then collected at approximately 90% confluency after transfection and stored at -80°C after liquid nitrogen flash freezing.

value: Human embryonic kidney

value: Wild type

value: Nucleofection


title: 293T,3days, rep2_4


title: IBET-gradual-TR1-PCR2-041119


title: HeLa cell, TAK-931DMSO, Day3

data_processing:
cellranger-6.0.0
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix file

extract_protocol:
Freshly collected DMSO or TAK-931 treated HeLa cells were filtlated with 35 mm niron mesh. After centrifugation, supernatant discarded and suspended in 10% FBS/PBS.
Library was performed according to the manufacter's instructions (Single Cell 3’ GEM v3.1, 10x Genomics).

treatment_protocol: HeLa cells were treated with DMSO or TAK-931 (300 nM) for 72 h.

value: Day 3


title: HeLa cell, DMSO, Day3


title: IBET-gradual-TR1-PCR2-011119


title: HeLa cells, TAK-931 treat, 24 h-2

description:
H24h_T2
H24h_combined_featureCounts


title: IBET-gradual-TR1-PCR1-221119


title: 293T,3days, rep2_2


title: 293T,3days, rep2_1


title: IBET-gradual-TR1-PCR1-081119


title: HeLa cells, DMSO treat, 24 h-2

description:
H24h_D2
H24h_combined_featureCounts


title: IBET-gradual-TR1-PCR1-151119


title: 293T,3days, rep1_4


title: IBET-gradual-TR1-PCR1-041119


title: IBET-gradual-TR1-PCR1-011119


title: 293T,3days, rep1_2


title: 293T,3days, rep1_3


title: DMSO-TR2-PCR2-221119


title: DMSO-TR2-PCR2-081119


title: 293T,3days, rep1_1


title: RNA-H9-C8-5i-1

city: Shanghai

first: Gufa

last: Lin

address: 1239 Siping road Tongji university

department: Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University

institute: Tongji University

data_processing:
The raw paired end reads were trimmed and quality controlled by Trimmomatic with parameters (SLIDINGWINDOW:4:15 MINLEN:75) (version 0.36)
clean reads were separately aligned to reference genome with orientation mode using bowtie2
MACS2  for peak calling : The candidate peak region was extended to be long enough for modeling. Dynamic Possion Distribution was used to calculated p-value of the specific region based on the unique mapped reads. The region would be defined as a peak when p-value < le-03.
For RNA-seq, clean reads were separately aligned to reference genome with orientation mode using hisat2.The quality assessment of these data were taken by qualimap_v2.2.1.Use htseq to count each gene reads.
Genome_build: mm10 for R1 cell line
Genome_build: hg38 for H9 cell line
Supplementary_files_format_and_content: bdg and bw files were used for represent RIP-seq data
Supplementary_files_format_and_content: xlsx file with raw gene counts for every gene and every sample

source_name: human embryo stem cell

growth_protocol: H9 hESCs were cultured using mTeSR medium (Stemcell technologies, Cambridge, USA). Cells were cultured on Matrigel (Fisher Scientific) -coated culture dishes, with daily medium change. H9 hESCs were passaged as small cluster using Versene solution (Thermo Fisher Scientific, USA). R1 mESCs were cultured on mouse embryonic fibroblast feeder cells inactivated with mitomycin-C (Sigma-Aldrich), using mouse ESC (mESC) medium (knockout DMEM, Life Technologies, Carlsbad, CA, USA) supplemented with 15% knockout serum replacer (Life Technologies, Carlsbad, CA, USA), 1×GlutaMAX (Life Technologies, Carlsbad, CA, USA), 1×Anti-Anti (Life Technologies, Carlsbad, CA, USA), 1% MEM non-essential amino acids (Life Technologies, Carlsbad, CA, USA), 0.1 mM 2-Mercaptoethanol (Sigma-Aldrich, St. Louis, MO, USA) and 1000 Units/ml ESGRO-mLIF (Millipore, Burlington, MA, USA), at 37˚C in 5% CO2. R1 mESCs were passaged as single cell using 0.05%-trypsin-EDTA (Life Technologies, Carlsbad, CA, USA).   H9 cells were induced to the naïve state using the 5i method (Theunissen et al., 2014). Briefly, H9 cells maintained on Matrigel were seeded onto feeder cells for two generations for acclimation with mTeSR medium, and were dissociated into single cells using Accutase (Thermo Fisher, USA). Dissociated H9 cells (2 × 105, for one well of a 12-well plate) were cultured with mTeSR supplemented with 10 μM Y27632 (Stemcell technologies, Cambridge, USA) for one day before switching to the 5i medium (DMEM/F12 : Neural basal = 1:1 mix, 1×N, 1× B27, 1×GlutaMAX, 1% NEAA, 0.1 mM BME, 1 μM PD0325901, 3 μM Chir99021, 0.5 μM SB590885, 1 μM  WH-4-023, 10 μM Y27632, 20 ng/mL hLIF, 20 ng/mL Activin  A, 8 ng/mL FGF2). Induced naïve state colonies with translucent edges were visible after 10 days of culture, and passaged using Accutase (Thermo Fisher, USA).

extract_protocol:
For RNA-seq, total RNA was extracted from the cells using TRIzol® Reagent (Invitrogen) and genomic DNA was removed using DNase I (TaKara). For RIP-sequencing, RNA was extracted from RNA precipitation preparations. Then RNA quality was determined using 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). High-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) is used to construct sequencing library.  For RIP-seq,RNA immunoprecipitation was performed with reversible cross-linking of the cells, as previously described (Niranjanakumari et al., 2002). In brief, 1×107 cells were washed three times with pre-chilled PBS and resuspended in 10 mL of PBS, cells were fixed with 1% formaldehyde (diluted from 37% HCHO/10% methanol stock solution, Sigma-Aldrich) at room temperature for 10 minutes with slow mixing. Crosslinking reactions was quenched by the addition of glycine (pH 7.0) to a final concentration of 0.25 M, followed by incubation at room temperature for 5 minutes. The cells were harvested by centrifugation and washed twice with ice-chilled PBS. Fixed cells were resuspended in 2 mL of RIPA buffer containing protease inhibitors (Roche) and RNAase inhibitors (Ambion), and sonication was used to solubilize RNPs. Insoluble material was removed by centrifugation at 16,000g for 10 minutes at 4 °C. The supernatant was mixed with the antibody and incubated overnight at 4˚C with rotation, followed by incubation with protein A/G beads. The beads were collected by centrifugation at 6000 rpm for 30s and washed five times with wash buffer (50 mM Tris–Cl, pH 7.5, 1% NP-40, 1% sodium deoxycholate, 0.1% sodium dodecyl sulfate (SDS), 1 mM EDTA, 1 M NaCl and 0.2 mM PMSF). The beads containing the immunoprecipitated samples are collected and resuspended in resuspended buffer (50 mM Tris–Cl, pH 7.0, 5 mM EDTA, 10 mM DTT and 1% SDS). Samples (resuspended beads) are incubated at 70°C for 45 minutes to reverse the crosslinks. The RNA was extracted from these samples using Trizol reagent (Invitrogen) and used for RIP-Seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: culture medium

value: MSI1 RRM Knockout

tag: rip antibody


title: RNA-H9-WT-5i-1

value: wild type


title: IBET-gradual-TR1-PCR2-081119


title: DMSO-TR2-PCR1-221119


title: DMSO-TR2-PCR2-041119


title: DMSO-TR2-PCR2-011119


title: RNA-H9-WT-5i-2


title: DMSO-TR2-PCR1-151119


title: RNA-H9-C8-1


title: DMSO-TR2-PCR1-041119


title: DMSO-TR2-PCR1-081119


title: DMSO-TR2-PCR1-011119


title: RNA-H9-MSI1FL-OE

data_processing:
The raw paired end reads were trimmed and quality controlled by Trimmomatic with parameters (SLIDINGWINDOW:4:15 MINLEN:75) (version 0.36)
clean reads were separately aligned to reference genome with orientation mode using bowtie2
MACS2  for peak calling : The candidate peak region was extended to be long enough for modeling. Dynamic Possion Distribution was used to calculated p-value of the specific region based on the unique mapped reads. The region would be defined as a peak when p-value < le-03.
For RNA-seq, clean reads were separately aligned to reference genome with orientation mode using hisat2.The quality assessment of these data were taken by qualimap_v2.2.1.Use htseq to count each gene reads.
RIP-seq_gene_FPKM_data_and_RNA-seq_DEG_LogFC_data_.xlsx: the DEG_logFC were generated form RNA sequencing data from MSI1 (273-362), MSI1 (139-362) and MSI1-FL compared to the Vector group analyzed using edgeR, We screened genes with FC <= -1 or >= 1 and p-value < 0.05. The RIP-FPKM were generated form RIP-seq data.
Genome_build: mm10 for R1 cell line
Genome_build: hg38 for H9 cell line
Supplementary_files_format_and_content: bdg and bw files were used for represent RIP-seq data
Supplementary_files_format_and_content: xlsx file with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: RIP-seq_gene_FPKM_data_and_RNA-seq_DEG_LogFC_data_.xlsx

value: MSI1 Full length overexpression


title: RNA-H9-MSI1V138-OE

value: MSI1-C (138-362) variant  overexpression


title: RNA-H9-MSI1V272-OE

value: MSI1-C (272-362) variant  overexpression


title: DMSO-TR1-PCR2-221119

value: in vitro


title: RNA-H9-Vector-OE

value: empty vector control


title: DMSO-TR1-PCR2-081119

value: mouse leukaemia MLL-AF9

value: C57BL6/J background


title: DMSO-TR2-PCR2-151119


title: DMSO-TR1-PCR2-151119


title: RNA-H9-C8-5i-2


title: RNA-H9-WT-2


title: DMSO-TR1-PCR2-041119


title: RIP-H9-MSI1FL-Flag

value: Anti-Flag (Invitrogen, PA1-984B)


title: DMSO-TR1-PCR2-011119


title: DMSO-TR1-PCR1-221119


title: DMSO-TR1-PCR1-151119


title: IgG-control

value: IgG isotype control(abcam, ab172730)


title: DMSO-TR1-PCR1-081119


title: DMSO-TR1-PCR1-041119


title: DMSO-TR1-PCR1-011119


title: RNA-H9-C8-2


title: RIP-H9-MSI1-2

value: Anti-MSI1(abcam, ab52865)


title: ARAC-high-dose-TR2-PCR2-041119

value: Cytarabine


title: Streptomyces lividans, 3,4-dihydroxybenzoate, replicate 1

city: Bielefeld

first: Christian

last: Ruckert-Reed

address: Sequenz 1

department: Medical School OWL

institute: Bielefeld University

data_processing:
Basecalls were performed using RTA v 1.18.66.3
Sequenced reads were mapped to the CP111182.1 whole genome using bowtie2 v2.3.2 with parameters -X 600
Raw read counts per gene were calculated using featureCounts v2.0.0 with parameters -O -M -t gene -g locus_tag -s 1
Read cound normalization and data analysis were performed using DESeq2
Assembly: CP111182.1
Supplementary files format and content: tab-delimited matrix table with raw read counts for every gene and every sample
Supplementary files format and content: tab-delimited matrix table with normalized read counts derived via DESeq2 for each gene

organism: Streptomyces lividans

source_name: liquid culture

growth_protocol: Liquid cultures of S. lividans involved two sequential precultures, followed by the main culture. Tryptic soy broth (30 g L-1, TSB, Sigma-Aldrich) was used for the first precultivation. The second precultivation and the main cultivation were conducted in minimal medium, containing 200 mM potassium phosphate buffer (pH 7.8): 15 g of (NH4)2SO4, 1 g of NaCl, 200 mg of MgSO4·7H2O, 55 mg of CaCl2, 20 mg of FeSO4·7H2O, 2 mg of FeCl3·6H2O, 2 mg of MnSO4·H2O, 0.5 mg of ZnSO4·H2O, 0.2 mg of CuCl2·2H2O, 0.2 mg of Na2B4O7·10H2O, 0.1 mg of (NH4)6Mo7O24·4H2O, 1 mg of riboflavin, 1 mg of nicotinamide, 0.5 mg of thiamine hydrochloride, 0.5 mg of pyridoxine hydrochloride, 0.2 mg of biotin, and 0.1 mg of p-aminobenzoate per liter. Cultivations were conducted in 500 mL baffled shake flasks, filled with 50 mL medium and 30 g soda-lime glass beads (5 mm, Sigma-Aldrich) on an orbital shaker (230 rpm, 28 °C, 75% relative humidity, 5 cm shaking diameter, Multitron, Infors AG, Bottmingen, Switzerland). For bottromycin production, 10^7 spores of the corresponding producer were inoculated into TSB medium and incubated for 48 hours. Then, cells were harvested (8000 × g, 2 min, 25 °C), and transferred to the second preculture in minimal medium, containing 10 g L-1 of mannitol as carbon source, followed by incubation over 72 hours, harvesting, and inoculation of the main culture, which contained either 30 mM mannitol, 4-hydroxybenzoate, or 3,4-dihydroxybenzoate.

extract_protocol:
Total RNA was isolated using the Quick-RNA Miniprep Plus kit (Zymo Research, Freiburg, Germany). After DNase treatment, the obtained RNA was purified (RNA Clean & Concentrator-5 kit, Zymo Research) and quantified (DropSense 16, Trinean NV, Gent, Belgium).
To construct whole transcriptome cDNA libraries, 2.5 μg of total RNA each was depleted of rRNA (Ribo-Zero rRNA Removal Kit (Bacteria), Illumina, San Diego, CA, USA). Successful rRNA removal was validated (Agilent RNA Pico 6000 kit, Agilent 2100 Bioanalyzer, Agilent Technologies). The obtained mRNA was converted into a cDNA library according to the TruSeq Stranded mRNA Sample Preparation guide (Illumina). Appropriate cDNA quality and quantity was validated (Agilent High Sensitivity DNA kit, Agilent 2100 Bioanalyzer, Agilent Technologies). Sequencing was performed on an Illumina NextSeq 500 instrument using 75 bases read length (Illumina).

value: liquid culture


title: RIP-H9-MSI1-1


title: Streptomyces lividans, 3,4-dihydroxybenzoate, replicate 3


title: Streptomyces lividans, 3,4-dihydroxybenzoate, replicate 2


title: RNA-H9-WT-1


title: Streptomyces lividans, 4-hydroxybenzoate, replicate 3


title: RIP-H9-MSI1V138-Flag


title: ARAC-high-dose-TR2-PCR1-011119


title: ARAC-high-dose-TR2-PCR2-011119


title: Streptomyces lividans, 4-hydroxybenzoate, replicate 2


title: RIP-H9-MSI1V272-Flag


title: ARAC-high-dose-TR1-PCR2-011119


title: Streptomyces lividans, 4-hydroxybenzoate, replicate 1


title: mRNA_146

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

institute: Monash University

data_processing:
Read alignment using STAR v2.5.2b
featureCounts from subread v1.5.1 for gene quantification
Differential Gene Expression analysis using Degust (DOI: 10.5281/zenodo.3258932)
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Gene counts table

source_name: Primary Lung Fibroblasts, Apex

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS and antibiotics (growth media) in 5% CO2 at 37°C in a humidified atmosphere. Cells at passages 3-4 were used in all experiments. In experiments, growth media is substituted with DMEM and antibiotics without serum (0% FBS).

extract_protocol:
After 24 hours, cells were lysed in RNA lysis buffer (Qiagen, Aus) and stored at -80°C until further extraction for transcriptomic analyses. RNA was extracted using the Quick-RNA MiniPrep Kit (Zymo, Australia) according to manufacturer’s instructions. RNA was extracted in groups of two patient samples per group per round to reduce batch effects. RNA was eluted into 30 μL RNase-free water and 24 μL was sent for sequencing
NEBNext® Ultra Directional RNA Library Prep Kit for Illumina®

treatment_protocol: Cells were plated at 100,000 cells per mL in growth media and incubated overnight. Following quiescing in 0% FBS media for 24 hours, cells were stimulated with growth media in the presence/absence of the drug ACT001.

tag: participant id

tag: age

tag: gender

value: M

tag: smoking history

tag: fvc%

tag: dlco%

tag: disease state

value: Normal

tag: drug treatment

tag: drug concentration


title: mRNA_62

value: F


title: ARAC-high-dose-TR1-PCR1-041119


title: ARAC-high-dose-TR1-PCR1-011119


title: mRNA_34


title: ARAC-gradual-TR2-PCR2-151119


title: Streptomyces lividans, manitol, replicate 3

value: manitol


title: Streptomyces lividans, manitol, replicate 2


title: ARAC-gradual-TR2-PCR2-081119


title: mRNA_230


title: ARAC-gradual-TR2-PCR2-041119


title: Streptomyces lividans, manitol, replicate 1


title: ARAC-high-dose-TR2-PCR1-041119


title: Zbtb7a_rep2_9463

data_processing:
Reads were aligned to the mm10 mouse genome using the Bowtie2 read aligner.
RPKM noralized Bigwig files were made using Deeptools bamCoverage.
Genome coverage was calculated for ChIP and input samples using Deeptools bamCoverage.
ChIP peaks were called using Macs2 standard peak calling parameters using input samples as control.
Called peaks were assigned to genomic features (promoters, enhancers, introns, or exons) using Bedtools based on peak overlap with a defined feature. Genomic features (active/inactive promoters and predicted enhancers) were defined using published ENCODE (50) datasets for H3K4me3 (ENCSR000CAN), H3K27ac (ENCSR000CDG), H3K4me1 (ENCSR000CAF) and DNase-seq (ENCSR000CNG).
Assembly: mus musculus mm10
Supplementary files format and content: Merged (rep1 and rep2) BigWig files for each antibody (Mta2, Mbd3, Zbtb7a).
Supplementary files format and content: Merged (rep1 and rep2) narrowPeak files for each antibody (except Input).

source_name: kidney cortex

extract_protocol:
Chromatin was extracted from isolated nuclei and sheared to 100-1000bp. Primary antibody was incubated overnight for ChIP reactions. Crosslinks were reversed by adding NaCl and heating at 65 °C for 15 h, RNase A was added and incubated for 2 h at 37 °C, and Proteinase K added and incubated 2 h at 63 °C. DNA was isolated using the MinElute PCR Purification Kit (Qiagen 28004).
Libraries were made using NEBNext Ultra II Library Kit (E7645) and sequenced on an Illumina Nova Seq at a depth of 100 million paired end reads.

treatment_protocol: Two month old kidneys (2 biological replicates) were harvested and isolated kidney cortex was cross-linked with 2 mM Di (N succinimidyl) glutarate (DSG, Proteo Chem C1104) in PBS for 30 min followed incubation in 1% formaldehyde (Thermo Scientific 28906) for an additional 10 min at room temperature and quenched with 125 mM glycine for 5 min.

value: kidney cortex

tag: developmental stage

value: 2 month


title: mRNA_202


title: ARAC-gradual-TR2-PCR2-011119

tag: tissue


title: ARAC-high-dose-TR1-PCR2-041119

tag: cell line


title: ARAC-gradual-TR2-PCR1-221119

tag: cell type


title: Zbtb7a_rep1_9462

tag: genotype


title: ARAC-gradual-TR2-PCR1-151119

tag: treatment


title: mRNA_118


title: PWAT, Sedentary; Bulk_P43

city: College Station

first: James

last: Cai

state: TX

address: 4458 TAMU

department: Veterinary Intergrative Biosciences

institute: Texas A&M University

data_processing:
Bulk RNA-seq: QC Reports completed with: FastQC v0.11.9. Mapping performed using Bowtie2 version 2.3.5.1 64-bit with default settings. Counting performed using htseq-count version 2.0.2. Data was normalized using upperquartile method. DE analysis preformed in R using edgeR version 3.34.1 and limma 3.48.3.
scRNA-seq: Sample demultiplexing, STAR alignment to the Landrace_pig_v1 transcriptome, filtering, and UMI counting were achieved using Cell Ranger 3.0.1 (10X Genomics)44.
Assembly: Sscrofa11.1
Supplementary files format and content: HDF5 files include filtered counts for scRNA-seq samples
Supplementary files format and content: comma-delimited text files include raw counts for Bulk RNA-seq samples

organism: Sus scrofa

source_name: PWAT, Sedentary

extract_protocol:
Total RNA was extracted using TRIzol® (Thermofisher Scientific, Waltham, MA) for Bulk RNA-seq and
cDNA libraries for Bulk RNA-seq were prepared, and sequencing was performed at the Molecular Genomics Core, Texas A&M University. Single nuclei 3` sequencing libraries were generated following the 10x Genomics dual index manual preparation v3.1 reagent kit with a target nuclei recovery of approximately 5,000 – 10,000 nuclei for each reaction.

treatment_protocol: Animals were divided into two exercise (sedentary vs exercised) and two coronary artery (non-occluded and occluded) treatment groups. Surgeries were performed to place an ameroid constrictor (2.5-3.5 mm) around the proximal left circumflex artery.

value: Pericardial White Adipose Tissue

value: Sedentary


title: PWAT, Exercise; Bulk_P46

source_name: PWAT, Exercise

value: Exercise


title: Mbd3_rep2_9463


title: mRNA_90


title: ARAC-gradual-TR2-PCR2-221119

value: in vitro


title: mRNA_132

value: Idiopathic Pulmonary Fibrosis (IPF)


title: ARAC-gradual-TR2-PCR1-081119

value: mouse leukaemia MLL-AF9

value: C57BL6/J background


title: PWAT, Exercise; Bulk_P42


title: ARAC-gradual-TR2-PCR1-041119


title: Mbd3_rep1_9462


title: Mta2_rep2_9463


title: mRNA_104

value: Never


title: PWAT, Exercise; Bulk_P39


title: Mta2_rep1_9462


title: PWAT, Sedentary; Bulk_P53


title: PWAT, Sedentary; Bulk_P38


title: mRNA_216


title: ARAC-gradual-TR1-PCR2-221119


title: ARAC-gradual-TR2-PCR1-011119


title: Input_rep2_9463


title: PWAT, Exercise; Bulk_P55


title: mRNA_174


title: ARAC-gradual-TR1-PCR2-151119


title: EAT, Sedentary, Occluded; O2_Landrace

source_name: EAT, Sedentary, Occluded

value: Epicardial Adipose Tissue

value: Sedentary, Occluded


title: mRNA_188


title: ARAC-gradual-TR1-PCR2-081119

value: Cytarabine


title: EAT, Exercise, Occluded; O1_Landrace

source_name: EAT, Exercise, Occluded

value: Exercise, Occluded


title: Input_rep1_9462


title: mRNA_76


title: ARAC-gradual-TR1-PCR2-041119