title: CheRNASeq_multiH1sh_Untreated_r1

library_source: other

molecule: other

extract_protocol:
Chromatin-enriched RNA (CheRNA) fraction was extracted. Briefly, 40x106 T47D cells were lysed in 800 µL ice-cold Lysis Buffer A (10 mM Tris pH 7.5, 0.1% NP-40, 150 mM NaCl) for 5 min on ice. A sucrose cushion (24% sucrose in lysis buffer A) was used to collect nuclei upon centrifugation (200g, 4ºC,10min). Pellet was washed with pre-chilled PBS + 1mM EDTA, and resuspended in 500µL ice-cold Glycerol Buffer (20 mM Tris pH 7.9, 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT, 0.125 mM PMSF, 50% glycerol). Nuclei were lysed by adding ice-cold Lysis Buffer B (10 mM HEPES pH 7.6, 1mM DTT, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3M NaCl, 1M urea, 1% NP-40) and kept on ice for 10 min, with periodic vortex shaking. Pellet containing chromatin was obtained by centrifugation (14000g, 4ºC,2 min), washed twice with pre-chilled PBS+1mM EDTA, and finally resuspended in 100 µL PBS. Che-RNA were purified using TRIZOL reagent (Invitrogen), following the manufacturer’s instructions.
Strand-Specific Transcriptome Library Construction Protocol (DNBSEQ). According to the manufacturer’s instructions, the first step involves the removal of ribosomal RNA (rRNA) using target-specific oligos and RNase H reagents to deplete both cytoplasmic (5S rRNA, 5.8S rRNA, 18S rRNA, and 28S rRNA) and mitochondrial ribosomal RNA (12S rRNA and 16S rRNA) from total RNA preparations. Following SPRI beads purification, the RNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first-strand cDNA using reverse transcriptase and random primers, followed by second-strand cDNA synthesis using DNA Polymerase I and RNase H. This process removes the RNA template and synthesizes a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. After UDG treatment, the incorporation of dUTP quenches the second strand during amplification. The products are enriched with PCR to create the final cDNA library. The libraries’ quality and quantity were assessed in two methods: check the distribution of the fragment size using the Agilent 2100 bioanalyzer and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). The qualified libraries were sequenced pair end on the BGISEQ-500/ MGISEQ-2000 System (BGI-Shenzhen, China).

treatment_protocol: Initially, a cell line expressing the Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) was generated. Then, this cell line was infected with viruses for expression of the different H1 variants shRNAs (pLVTHM). The inducible knocked-down cell lines were sorted in a FACSvantageSE (Becton Dickinson) for RedFP-positive and GFP-positive fluorescence after 3 days of Doxycycline treatment. Then cells were amplified in the absence of Dox until an experiment was performed and the resulting cell line was used to perform two replicates of cheRNA-Seq experiments under Untreated conditions (i.e. no induction of the shRNA, no Dox-induced depletion of any H1).


title: CheRNASeq_multiH1sh_Untreated_r2

status: Public on Jan 09 2024

type: SRA

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

country: Spain

institute: IBMB-CSIC

data_processing:
RNA-Seq reads were mapped to the reference genome (GRCh37/hg19) using HISAT2 v2.2.1 with default parameters and specifying strand-specific information (--rna-strandness RF).
SAMtools v1.11 was used to sort BAM files and filter for properly paired-end reads (-f 2).
Aligned reads were mapped to the Ensembl GRCh37.87 gene annotation with TEtranscripts v2.1.4 (--sortByPos --mode multi --stranded reverse).
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw read counts for the Ensembl GRCh37.87 gene annotation (hg19).

organism: Homo sapiens

growth_protocol: Cells were grown in RPMI 1640 medium, supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin, and 100µg/ml streptomycin.

tag: cell line

tag: cell type

value: Breast cancer cell line

tag: genotype

value: Multi-H1sh (shRNA not induced)

tag: treatment

value: Untreated


title: ChIPSeq_H1X_HCT116

library_source: genomic

data_processing:
All samples were treated as single-end data to homogenize the processing protocol. Single-end reads were aligned to the human GRCh37/hg19 reference genome using Bowtie2 (v2.3.5.1) with default options.
SAMtools (v1.9) were used to filter out the low-quality alignments using the flag 3844.
Input and H1 variants genome coverage was calculated and normalized by reads per million (genomecov -bga -scale) with BEDTools (v2.28.0).
MACS2 (v2.1.2) was used to calculate input-subtracted ChIP-Seq signal coverage tracks (bdgcmp -m subtract).
Assembly: hg19
Supplementary files format and content: bigWig files include input-subtracted ChIP-Seq signal.

molecule: genomic DNA

growth_protocol: HeLa, SK-N-SH, HCT-116, and SK-MEL-147 cells were grown in DMEMGlutaMax medium, supplemented with 10% FBS, 100 U/ml penicillin, and 100µg/ml streptomycin. MCF-7 cells were grown in MEM medium containing 10% FBS, 1% penicillin/streptomycin, 1% non-essential aminoacids, 1% sodium pyruvate, and 1% Glutamine

extract_protocol:
Library construction and sequencing were performed under BGI (Beijing Genomic Institution) ChIP-seq protocols, using combinatorial Probe-Anchor Synthesis (cPAS) and DNA nanoball sequencing.
Cells were fixed using 1% formaldehyde, chromatin was extracted and sonicated using a Diagenode Bioruptor to generate fragments between 200 and 500 bp. 30 µg of chromatin was immunoprecipitated overnight using the indicated antibody. Rabbit IgG (Milipore 12-370) was used as a nonspecific control. Input was prepared with 10% of the chromatin material used for an immunoprecipitation. Immunocomplexes were recovered using Protein A magnetic beads from Millipore. Beads with bound antibody/protein/DNA complexes were washed, decross-linked at 65ºC overnight, and immunoprecipitated DNA was recovered using the IPure Kit from Diagenode.
Library construction and sequencing were performed under Illumina or BGI ChIP-Seq protocols, depending on the sample.

treatment_protocol: Some samples (indicated above) were cell-cycle synchronized in G1/S using standard double thymidine block treatment, to homogenize cell population. If not, no treatment was performed.

value: Colorectal cancer cell line

value: WT

value: G1/S synchronization by standard double Thymidine block treatment

tag: chip antibody

value: anti-H1X (Abcam, ab31972)


title: ChIPSeq_Input_HCT116

value: Input sample


title: ChIPSeq_Input_SKMEL147

value: Melanoma cell line


title: ChIPSeq_H1X_SKNSH

source_name: SK-N-SH

value: SK-N-SH

value: Neuroblastoma cell line


title: B12_20956

status: Public on Jan 10 2024

type: RNA

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

institute: Hospital del Mar Research Institute

hyb_protocol: Performed according to protocol GeneChip WT PLUS Reagent kit (P/N 703174 2017) and hybridized to Human Clariom S Array (Thermo Fisher Scientific).

scan_protocol: Performed according to protocol GeneChip WT PLUS Reagent kit (P/N 703174 2017).

data_processing: R programming (Version 3.4.3) Bioconductor and the Comprehensive R Archive Network (CRAN 2017) packages were used. Samples were background corrected, quantile-normalized and summarized to a gene-level using the robust multi-chip average (RMA).

label: Biotin

molecule: total RNA

source_name: Breast carcinoma

extract_protocol: Total RNA was isolated according to protocol of RNeasy® Micro Kit (Qiagen).

tag: tumour-infiltrating nk cell status

value: Positive

tag: til score

tag: tumour-infiltrating nk cells

tag: g

tag: t

tag: er status

tag: status

value: DF

tag: age

tag: cdi

value: CDI


title: RNASeq_H1Xsh_+Dox_r1

library_source: transcriptomic

data_processing:
RNA-Seq reads were mapped to the reference genome (GRCh37/hg19) using HISAT2 v2.2.1 with default parameters and specifying strand-specific information (--rna-strandness RF).
SAMtools v1.11 was used to sort BAM files and filter for properly paired-end reads (-f 2).
Aligned reads were mapped to the Ensembl GRCh37.87 gene annotation with TEtranscripts v2.1.4 (--sortByPos --mode multi --stranded reverse).
DESeq2 v1.26.0 was used to identify differentially expressed genes between control and H1X KD cells. Gene expression changes were considered significantly different if the absolute value of the log2(FC) was higher than 1.4 and the adjusted p-value was lower than 0.05.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw read counts for the Ensembl GRCh37.87 gene annotation (hg19).

extract_protocol:
Total RNA of T47D-MTVL H1Xsh Untreated or 6-days-Dox-treated cells was extracted with High Pure RNA Isolation kit (Roche)
Strand-Specific Transcriptome Library Construction Protocol (DNBSEQ). According to the manufacturer’s instructions, the first step involves the removal of ribosomal RNA (rRNA) using target-specific oligos and RNase H reagents to deplete both cytoplasmic (5S rRNA, 5.8S rRNA, 18S rRNA, and 28S rRNA) and mitochondrial ribosomal RNA (12S rRNA and 16S rRNA) from total RNA preparations. Following SPRI beads purification, the RNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first-strand cDNA using reverse transcriptase and random primers, followed by second-strand cDNA synthesis using DNA Polymerase I and RNase H. This process removes the RNA template and synthesizes a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. After UDG treatment, the incorporation of dUTP quenches the second strand during amplification. The products are enriched with PCR to create the final cDNA library. The libraries’ quality and quantity were assessed in two methods: check the distribution of the fragment size using the Agilent 2100 bioanalyzer and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). The qualified libraries were sequenced pair end on the BGISEQ-500/ MGISEQ-2000 System (BGI-Shenzhen, China).

treatment_protocol: Initially, T47D-MTVL cell line expressing the Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) was generated. Then, this cell line was infected with viruses for expression of H1X shRNA (pLVTHM). The inducible knocked-down cell line was sorted in a FACSvantageSE (Becton Dickinson) for RedFP-positive and GFP-positive fluorescence after 3 days of Dox treatment. Then cells were amplified in the absence of Dox until an experiment was performed. Dox (Sigma) was added at 2.5 µg/ml when indicated and treated for 6 days.

value: H1X knock-down

value: Treated with Dox (6 days)


title: RNASeq_H1Xsh_+Dox_r2


title: Venom gland, milked, 4 days before dissection, rep1

city: Aberdeen

first: Centre for Genome-Enabled Biology and Medicine

last: on behalf of listed contributors

state: Aberdeenshire

address: 23 St Machar Drive

department: CGEBM

country: United Kingdom

institute: University of Aberdeen

description: Raw shotgun whole transcriptome sequencing data and respective annotation

data_processing:
Raw read quality was assessed before and after pre-processing with FastQC (version 0.11.8) (Andrews et al., 2010) and MultiQC (version 1.7) (Ewels et al., 2016).
Raw reads were pre-processed using Trim Galore! (Version 0.6.4) (Krueger et al., 2021) to trim low-quality bases (<Q30) and adapters, and excluding short trimmed reads (<20bp), before de novo transcriptome assembly with Trinity (version 2.8.5) (Grabherr et al., 2011; Haas et al., 2013).
Assembly quality was assessed with BUSCO (version 4.0.6) with the arthropod lineage dataset, arthropoda_odb10 (Manni et al., 2021), rnaQUAST (version 2.2.0) (Bushmanova et al., 2016) and GeneMarkS-T (version 5.1) gene prediction (Tang et al., 2015).
The assembly was annotated using Trinotate software (version 3.2.1) (Bryant et al., 2017).
Assembly: FASTA file available at the foot of this record.
Supplementary files format and content: Trinotate-based annotation converted to Excel format (.xlsx) and with included bespoke "transcript_nt_length" and "peptide_aa_length" columns (for further filtering purposes when applicable).

organism: Androctonus amoreuxi

source_name: telson

growth_protocol: Crude venom was extracted using electrical stimulation (12-16 V; 10 s) and the milked venom was collected and centrifuged for 20 min at 13,000 rpm/4 °C. Clear supernatants were pooled, freeze-dried and stored at − 20 °C until use

extract_protocol:
Total RNA was extracted in TRIzol (Thermo Scientific, UK) and purified on RNeasy micro columns with on column DNase digestion (Qiagen, CA), according to the manufacturer’s instructions. Total RNA was quantified by fluorimetry (Qubit, Thermo Scientific, UK) and quality (RIN 9.1) was assessed on a Tapestation 4200 (Agilent, CA).
Unique dual indexed stranded TruSeq mRNAseq libraries were prepared from 500 ng total RNA, according to the manufacturer’s instructions (Illumina, CA). Libraries were quantified by qPCR with SYBR green (Kapa Library Quantification Complete Universal, Roche, CH) on the QuantStudio 6 Flex (ThermoFisher Scientific, UK) and average library size of 291 bp determined on the Tapestation 4200 (Agilent, CA) prior to sequencing and base calling on an Illumina NextSeq500 with v2.5 chemistry and 75 bp paired-end reads, with 14.3 Gb sequence output

treatment_protocol: RNA was extracted from telsons dissected from five adult scorpions and stored in RNAlater® at -80°C. Telsons were shipped on dry-ice and stored on receipt at -80°C until processing. Scorpions were anesthetized before telson dissection by putting them in a freezer at -20°C for ~4-5 minutes. Venom was milked 4 days before dissection. Telsons were combined, washed in ice-cold PBS to remove RNAlater® and homogenized in 1 mL TRIzol reagent (Thermo Scientific, UK) with 2 x 3mm tungsten carbide beads in a TissueLyser II (Qiagen, CA).

tag: tissue

value: telson


title: ChIPSeq_Input_SKNSH


title: ChIPSeq_H1X_MCF7_r2

value: Breast cancer cell line


title: ChIPSeq_Input_MCF7_r2


title: B09_18176

label_protocol: Performed according to protocol GeneChip WT PLUS Reagent kit (P/N 703174 2017).


title: RNASeq_H1Xsh_Untreated_r1


title: B07_10496


title: B14_4019

value: Negative


title: PP, replicate 3, bulk RNA-seq

city: HOUSTON

first: Zhongming

last: Zhao

state: Texas

address: 7000 Fannin St

department: School of Biomedical Informatics

country: USA

institute: UTHealth

data_processing:
The raw sequenced files were mapped to the mouse reference genome mm10 using HISAT2. StringTie was used to quantify the counts. We then used R package DESeq2 (version 1.30.1) to perform the differential gene expression tests.
Assembly: mm10
Supplementary files format and content: tab file: contains gene expression profile

organism: Mus musculus

source_name: Posterior palate

extract_protocol:
The anterior (n=3) and posterior (n=3) 1/3 palatal shelves of E14.0 C57BL/6J mice were microdissected, isolated, and then subjected to bulk RNA-seq.
The bulk RNA-seq library construction involves steps such as RNA isolation, cDNA synthesis, adapter ligation, and PCR amplification.

value: Posterior palate

tag: strain

tag: developmental stage


title: B12_24370


title: Control, replicate 1, snRNAseq

city: La Jolla

first: Colin

last: Kern

state: CA

address: 9500 Gilman Dr

institute: UC San Diego

library_source: transcriptomic single cell

data_processing:
The raw reads were processed with Cellranger v6.0.2
Assembly: mm10
Supplementary files format and content: Cell by gene tables in the cellranger h5 format

molecule: nuclear RNA

source_name: Hippocampus

extract_protocol:
30 mg dounce homogenized hippocampus tissue was resuspended in 500 µL of nuclei permeabilization buffer (0.1% Triton-X-100 (Sigma-Aldrich, T8787), 1X protease inhibitor, 1 mM DTT, and 0.2 U/µL RNase inhibitor (Promega, N211B), 2% BSA (Sigma-Aldrich, SRE0036) in PBS). Sample was incubated on a rotator for 5 min at 4°C and then centrifuged at 500 rcf for 5 min (4°C, run speed 3/3). Supernatant was removed and pellet was resuspended in 400 µL of sort buffer (1 mM EDTA 0.2 U/µL RNase inhibitor (Promega, N211B), 2% BSA (Sigma-Aldrich, SRE0036) in PBS) and stained with DRAQ7 (1:100; Cell Signaling, 7406). 75,000 nuclei were sorted using a SH800 sorter (Sony) into 50 µL of collection buffer consisting of 1 U/µL RNase inhibitor in 5% BSA; the FACS gating strategy sorted based on particle size and DRAQ7 fluorescence. Sorted nuclei were then centrifuged at 1000 rcf for 15 min (4°C, run speed 3/3) and supernatant was removed. Nuclei were resuspended in 35 µL of reaction buffer (0.2 U/µL RNase inhibitor (Promega, N211B), 2% BSA (Sigma-Aldrich, SRE0036) in PBS) and counted on a hemocytometer. 12,000 nuclei were loaded onto a Chromium Controller (10x Genomics)
Libraries were generated using the Chromium Single-Cell 5' HT Library Construction Kit v2 with the Chromium Single-Cell B Chip Kit (10x Genomics, 1000153) and the Chromium i7 Multiplex Kit for sample indexing (10x Genomics, 120262) according to manufacturer specifications. CDNA was amplified for 12 PCR cycles. SPRISelect reagent (Beckman Coulter, B23319) was used for size selection and clean-up steps. Final library concentration was assessed by Qubit dsDNA HS Assay Kit (Thermo-Fischer Scientific) and fragment size was checked using Tapestation High Sensitivity D1000 (Agilent) to ensure that fragment sizes were distributed normally about 500 bp. Libraries were sequenced using the NextSeq500 and a NovaSeq6000 (Illumina) with these read lengths: 28 + 8 + 91 (Read1 + Index1 + Read2).

value: Hippocampus

value: 1 year


title: PP, replicate 1, bulk RNA-seq


title: AP, replicate 3, bulk RNA-seq

source_name: Anterior palate

value: Anterior palate


title: AP, replicate 2, bulk RNA-seq


title: Control, replicate 2, snRNAseq


title: Control, replicate 3, snRNAseq


title: PP, replicate 2, bulk RNA-seq


title: RNASeq_H1Xsh_Untreated_r2

tag: cell line

value: WT

value: Untreated


title: AP, replicate 1, bulk RNA-seq


title: M2_ARV825-2

city: Shenzhen

first: Difei

last: Li

address: No. 1017, Dongmen North Road, Luohu District

country: China

institute: Shenzhen People's Hospital

data_processing:
Raw reads were removed with the help of Trimmomatic  v0.39, and aligned to the mm10 mouse genome by Bowtie2 v2.2.5. Duplicate sequences were removed using MarkDuplicates v3.0.0 in Picard software. Quantification of genes was performed by featureCounts v2.0.03 followed by normalization in edgeR v3.32.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

source_name: Alveolar macrophage

extract_protocol:
total RNA was extracted from AMs using a UNIQ-10 Column Total RNA extraction Kit (IA24KA6842, Sangon Biotech, China)
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). (Refer to RNA quality inspection report for specific instruments).Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.

tag: cell type

value: Alveolar macrophage


title: M2_ARV825_1

tag: genotype


title: X15B7616

value: Relapse


title: M2-1

tag: treatment


title: M2-3


title: M2_DMSO-3


title: M0-c


title: M2-2


title: M2_ZL0420_1


title: M2_DMSO-2


title: M0-b


title: M2_JQ1-2


title: M2_DMSO-1


title: M2_ARV825-3


title: M2_ZL0420_3


title: M2_JQ1-3


title: M2_ZL0420_2


title: M2_JQ1-1


title: CMT93

city: Utsunomiya

first: Naoyuki

last: Toyota

state: Tochigi

country: Japan

institute: Tochigi Cancer Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse430_2 array following the manufacturer’s instructions.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: normal CMT-93 cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All cells were cultured and maintained in Dulbecco’s modified Eagle’s medium (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 10% fetal bovine serum (v/v), 10,000 units/mL penicillin, 10,000 μg/mL streptomycin, and 25 μg/mL Gibco amphotericin B (Thermo Fisher Scientific, Tokyo, Japan) at a temperature of 37℃ with 5% CO2.

extract_protocol: Total RNAs were extracted from CMT-93 and CMT-93PM1 cells using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: CMT-93 cells (CCL-223; ATCC, Manassas, VA, USA) were injected into the tail veins of six-week-old female C57BL/6 mice. Eight weeks after the tail vein injection, the mice were euthanized, and the lung metastatic tumors were visually identified. Tumor tissues were recovered and used for primary tissue culture.

value: normal CMT-93 cell


title: M0-a


title: M1_ZL0420_3


title: M1_ZL0420_1


title: M1_JQ1_3


title: M1_ZL0420_2


title: B13_41327

value: Positive


title: a1 IRF4

data_processing:
Removal of raw reads and alignment to mm10 mouse genome was performed as aforementioned. SEACR peak caller v1.3 with default parameters was employed to identify binding sites, and annotated by ChIPseeker v1.34.1. Reads coverage per genome bin was quantified and normalized as counts per million (CPM) using bamCoverage of deepTools v3.5.1 . Further, R v4.1.0 was employed to construct heatmaps enriched around transcription start sites (TSS), and visualized in EnrichedHeatmap v1.28.1. A binding density plot of gene body and enhancer regions was generated using ngsplot v2.61. Super-enhancers (SEs) were identified by first merging H3K27ac and BRD4 binding peaks using mergeBed, and enriched H3K27ac signals were calculated inside 12.5 kb windows of merged binding sites using the ROSE algorithm. By ranking these stitched enhancer regions based on the H3K27ac signal, SEs were identified, and associated target genes were annotated. Genomic signal tracks of desired genes were visualized in IGV browser v2.15.4.
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

extract_protocol:
In order to investigate the potential binding of BRD4, H3k27ac, IRF4, CUT&Tag-seq was performed using NovoNGS CUT&Tag 2.0 High-Sensitivity Kit for Illumina (Novoprotein Scientific Inc., Cat# N259-YH01-01A).
DNA was isolated by NovoNGS DNA Clean Beads and dissolved in TE-RA-Buffer. DNA was amplified with N5 and N7 primers and purified with NovoNGS DNA Clean Beads for high-throughput sequencing.

tag: chip antibody


title: a2 IRF4


title: Hom-7-Tail

city: Acton

first: Zhi-Ping

last: Feng

state: ACT

address:
131 Garran Road, John Curtin School Of Medical Research Building (Level 3, Stage 1)
, The Australian National University

country: Australia

institute: JCSMR

data_processing:
quality check with FastQC
alignment using HIsat2(v2.1.0)
alignment reads were sorted using samtools
aligned reads were assigned using FeatureCounts (v1.4) based on NCBI refseq gene models
differential gene expression analysis using limma_voom
Assembly: mm10
Supplementary files format and content: count matrix in txt format

source_name: Skin - Tail

extract_protocol:
Skin from ears and tail of each mouse was taken and snap froze in liquid nitrogen. Samples were defrosted in RNA protect reagent, and mechanically cut into smaller pieces of 3-4 mm. We used Monarch total RNA extraction kit to isolate total RNA from the samples. Briefly: 300 ul of RNA protection samples added to each sample followed by 45ul of Prot K Reaction buffer plus Prot K and incubated at 55 C for 30 minutes.  Samples were vortex and spun at 16000 xg for 2 minutes and supernatant transferred to fresh microfuge tubes. Equal volume of RNA Lysis buffer was added and transferred samples to gDNA removal column, spun at 16000xg for 1 minute. equal volume 95% ethanol was added to flow through and transferred to purification column and spun at 16000xg for 1 minute. discarded flow through, added 500 ul RNA wash buffer to the column and spun for 30 seconds, then 80 ul of DNases plus DNase I reaction buffer was added to the column and incubated for 15 minutes at room temperature. 500 ul RNA priming buffer was added and spun for 30 seconds, discarded flow through, and wash the column with 500ul of Wash buffer twice. added 40 ul Nuclease free water to the column and spun for 30 seconds to collect the total RNA in fresh nuclease-free microfuge tubes.
NEB Ultra II Directional RNA Prep kit was used for library preperation

value: Skin - Tail

value: Homozygous IKBKB


title: M1_DMSO-2


title: M1_ARV825_2


title: M1_DMSO-1


title: M1-3


title: M1_ARV825_1


title: M1_JQ1_1


title: Hom-23-Tail


title: M0-3

value: no


title: M0-1


title: sham peritoneum rep1

city: Manhasset

first: Ping

last: Wang

state: New York

address: 350 Community Dr

department: Center for Immunology and Inflammation

institute: The Feinstein Institutes for Medical Research

description: 10X Genomics

data_processing:
The Cell Ranger count pipeline (v6.0.0, 10X Genomics) was used to align FASTQs to the mouse reference genome (gex-mm10-2020-A, 10X Genomics) and produce digital gene-cell counts matrices
Assembly: gex-mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: peritoneum

extract_protocol:
Single-cell RNA sequencing (scRNA-seq) using the 10X Genomics Chromium platform
Library preparation was conducted according to the recommended protocol for the NextGEM Single-Cell 3’ Library Kit v3.1 (#1000121; 10X Genomics)

treatment_protocol: sham procedure or cecal ligation and puncture (CLP)

value: peritoneum

value: primary cells

value: sham surgery


title: CLP spleen rep1

description: 10X Genomics

source_name: spleen

value: spleen

value: cecal ligation and puncture


title: CLP peritoneum rep1

description: 10X Genomics


title: M1_ARV825_3


title: M0-2


title: RNAseq_cDiet_Ing_dNT_rep3

city: Madrid

first: Tirso

last: Pons

state: Madrid

address: C/ Darwin 3

department: Inmunology and Oncology

institute: Centro Nacional de Biotecnologia

description: White Adipose Tissue (WAT)

data_processing:
Sequenced reads were mapped to mm10 whole genome using BWA-MEM 0.7.15 with parameters mem -M -t 4 mm10bwaidx file_1.fastq file_2.fastq
Transcripts per Million of library size (TPM) were calculated using StringTie version 1.3.3 with parameters -e -v -p 32 -G knownGene_UCSC_mm10.gtf
The expression level of all genes was estimated by DESeq2 1.40.1 in RStudio 2023.03.1+446
Assembly: GRCm38/mm10 assembly
Supplementary files format and content: tab-delimited text files include cov, FPKM, and TPM values for each Sample (*.gtf)
Supplementary files format and content: Matrix table with TPM values for every transcript and every sample (*.csv)

source_name: Epididymal (eWAT)

growth_protocol: Mixed genetic background dNT mice were generated as described (Fütterer, et al., 2005; doi:10.1172/JCI24177) and backcrossed more than 10 times on a C57BL/6 background.

extract_protocol:
Total RNA was purified with the Split RNA Extraction Kit (Lexogen, Austria). Triplicate RNA probes from wild-type and Dido1_dNT mutant were sequenced.
RNA libraries for epididymal WAT were prepared by the servicio de genomica at the Parque Cientifico de Madrid using standard Illumina protocols. RNA libraries for inguinal WAT were prepared by BGI Genomics (China).

treatment_protocol: Mice were maintained at 22º on a normal diet (ND) (SAFE150) composed of 12.6% fat, on a 12/12-h light/dark cycle with ad libitum access to food and water. A control diet (CD) / high fat diet (HFD) pair, was used as recommended by manufacturer. CD (Ssniff E15748) composed of 4.1% fat. HFD (Ssniff E15744) composed of 45% fat was used to induce obesity.

value: Epididymal (eWAT)

value: Dido1_dNT mutant


title: M1_JQ1_2


title: CMT93-PM1

source_name: CMT-93cells recovered from lung metastasis lesion and cultured primarily


title: M1_DMSO-3


title: M1-2


title: M1-1


title: Hom-7-Ears

source_name: Skin - Ears

value: Skin - Ears


title: sham spleen rep1

description: 10X Genomics


title: m2 IRF4


title: Hom-13-Tail


title: WT-8-Tail

value: Wild type IKBKB


title: Hom-13-Ears


title: WT-8-Ears


title: c2 IRF4


title: B10_26106

tag: tumour-infiltrating nk cell status

value: Negative

value: CDI


title: RNAseq_cDiet_Ing_WT_rep2

description: White Adipose Tissue (WAT)

value: wild type


title: RNAseq_cDiet_Ing_dNT_rep1

description: White Adipose Tissue (WAT)


title: WT-1-Tail


title: WT-18-Tail


title: Mouse 11, PBS

city: Freiburg im Breisgau

first: Julian

last: Rapp

address: Killianstraße 5

country: Germany

institute: University Medical Center Freiburg

data_processing:
NextSeq 2000 Control Software (NCS) v1.2.0.36376
Aligned to GRCm39 by STAR aligner
Assigned to genes by featureCounts
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: sorted retinal endothelial cells

growth_protocol: Standard OIR model

extract_protocol:
RNeasy Plus Micro Kit (Cat#: 74034, Qiagen). 500 pg pf RNA was used for downstream application
SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Cat#: 634893, Takara), Illumina Nextera XT Sample Preparation Guide (Cat#: FC-131-1024, Illumina)

treatment_protocol: 0.5µL of 100 ng/µL OSM or 0.5µL PBS intravitreal injection at P12

tag: disease state

value: OIR model

value: sorted retinal endothelial cells

value: PBS


title: RNAseq_cDiet_Ing_dNT_rep4

description: White Adipose Tissue (WAT)


title: Hom-23-Ears

value: Homozygous IKBKB


title: c1 IRF4

value: Alveolar macrophage

value: no


title: WT-1-Ears


title: a1 H3K27ac


title: a2 H3K27ac


title: Mouse 9, OSM

value: OSM


title: RNAseq_cDiet_Ing_WT_rep1

description: White Adipose Tissue (WAT)


title: RNAseq_cDiet_Epi_dNT_rep3

description: White Adipose Tissue (WAT)


title: Mouse 10, PBS


title: m1 IRF4


title: WT-18-Ears


title: m2 H3K27ac


title: Mouse 8, PBS


title: Mouse 7, PBS


title: RNAseq_cDiet_Ing_WT_rep3

description: White Adipose Tissue (WAT)


title: m1 H3K27ac


title: RNAseq_cDiet_Epi_dNT_rep1

description: White Adipose Tissue (WAT)


title: RNAseq_cDiet_Epi_WT_rep3

description: White Adipose Tissue (WAT)


title: Mouse 6, OSM


title: RNAseq_cDiet_Ing_dNT_rep2

description: White Adipose Tissue (WAT)


title: Mouse 4, PBS


title: c2 H3K27ac


title: Mouse 3, PBS


title: RNAseq_cDiet_Epi_dNT_rep2

description: White Adipose Tissue (WAT)


title: Mouse 2, OSM


title: RNAseq_cDiet_Epi_WT_rep2

description: White Adipose Tissue (WAT)


title: Mouse 1, OSM


title: RNAseq_cDiet_Epi_WT_rep1

description: White Adipose Tissue (WAT)


title: RNAseq_WAT_Dido1_MUT_rep3

data_processing:
Sequenced reads were mapped to mm10 whole genome using BWA-MEM 0.7.15 with parameters mem -M -t 4 mm10bwaidx file_1.fastq file_2.fastq
Transcripts per Million of library size (TPM) were calculated using StringTie version 1.3.3 with parameters -e -v -p 32 -G knownGene_UCSC_mm10.gtf
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include cov, FPKM, and TPM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with TPM values for every transcript and every sample

source_name: White Adipose Tissue (WAT)

growth_protocol: Animals were maintained on a normal diet (ND) at 22ºC on a 12/12-h light/dark cycles with ad libitum access to food and water.

extract_protocol:
Total RNA was performed with a SPLIT RNA extraction kit (Lexogen, Austria). Triplicate RNA probes from wild-type and Dido1_dNT mutant were sequenced.
RNA libraries for epididymal WAT were prepared by the servicio de genomica at the Parque Cientifico de Madrid using standard Illumina protocols. RNA libraries for cells differentiated into adipocytes were prepared by BGI Genomics (China).

treatment_protocol: A high fat diet (HFD), made of 45% fat, 20% proteins and 35% carbohydrates (energy 4615 Kcal/kg; Ssniff E15744) was used to induce obesity in mice. MEF cells were from Trachana et al., 2007 (DOI 10.1073/pnas.0611132104) and differentiated precisely following the protocol described in Aune et al., 2013 (DOI 10.3791/50191).

value: Epididymal WAT

tag: source

value: tissue

tag: wild type


title: RNAseq_WAT_Dido1_MUT_rep2


title: B12_1485

tag: til score

tag: tumour-infiltrating nk cells

tag: g

tag: t

value: Positive


title: a2 BRD4


title: a1 BRD4


title: RNAseq_WAT_Dido1_WT_rep4


title: RNAseq_WAT_Dido1_WT_rep3


title: m2 BRD4


title: Mouse 5, OSM


title: RNAseq_WAT_Dido1_WT_rep1


title: RNAseq_WAT_Dido1_WT_rep2


title: c2 BRD4


title: c1 H3K27ac


title: m1 BRD4


title: c1 BRD4


title: T2-3, replicate 2, scRNAseq

city: shenyang

first: sun

middle: yuan

last: yuan

address: 沈北新区蒲河路77号

institute: China Medical University

description: 10x Genomics

data_processing:
Reads were processed using the Cell Ranger 2.1.0 pipeline with default and recommended parameters. FASTQs generated from Illumina sequencing output were aligned to the human genome, version GRCh38, using the STAR algorithm.Next, Gene-Barcode matrices were generated for each individual sample by counting UMIs and filtering non-cell associated barcodes. Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts. This output was then imported into the Seurat (v2.3.0) R toolkit for quality control and downstream analysis of our single cell RNAseq data. All functions were run with default parameters, unless specified otherwise. We excluded cells with fewer than 200 or more than 6000 detected genes (where each gene had to have at least one UMI aligned in at least three cells). The expression of mitochondria genes was calculated using PercentageFeatureSet function of the seurat package.To remove low activity cells, cells with more than 10 percent expression of mitochondria genes were excluded. The normalized data (NormalizeData function in Seurat package) was performed for extracting a subset of variable genes. Variable genes were identified while controlling for the strong relationship between variability and average expression. Next, we integrated data from different samples after identifying ‘anchors’ between datasets using FindIntegrationAnchors and IntegrateData in the seurat package.Then we performed principal component analysis (PCA) and reduced the data to the top 30 PCA components after scaled the data. We visualized the clusters on a 2D map produced with t-distributed stochastic neighbor embedding (t-SNE).
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: larynx

extract_protocol:
Tissues were transported in sterile culture dish with 10 ml 1x Dulbecco's Phosphate-Buffered Saline (DPBS; Thermo Fisher, Cat. no. 14190144) on ice to remove the residual tissue storage solution, then minced on ice. We used dissociation enzyme 0.25% Trypsin (Thermo Fisher, Cat. no. 25200-072) and 10 ug/mL lDNase I (Sigma, Cat. no. 11284932001) dissolved in PBS with 5% Fetal Bovine Serum (FBS; Thermo Fisher, Cat. no. SV30087.02) to digest the tissues. Tissues were dissociated at 37 ℃ with a shaking speed of 50 r.p.m for about 40 min.We repeatedly collected the dissociated cells at interval of 20 min to increase cell yield and viability. Cell suspensions were filtered using a 40 um nylon cell strainer and red blood cells were removed by 1X Red Blood Cell Lysis Solution (Thermo Fisher, Cat. no. 00-4333-57) . Dissociated cells were washed with 1x DPBS containing 2% FBS. Cells were stained with 0.4% Trypan blue (Thermo Fisher, Cat. no. 14190144) to check the viability on Countess® II Automated Cell Counter (Thermo Fisher)
Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a Gel Beads-in-emulsion(GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification.Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (CG000206 Rev D).

value: larynx

tag: tissue type

value: laryngeal cancer tissue


title: RNAseq_WAT_Dido1_MUT_rep1

tag: tissue

value: Dido1_dNT mutant


title: Uninjured-Lane 2-2

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

data_processing:
Samples were sequenced on NovaSeq 6000 or NextSeq 500 platform at UCLA Technology Center for Genomics and Bioinformatics.
Cellranger-7.0.1 from 10x Genomics was used for alignment and quantification
Assembly: mm10-2020-A
Supplementary files format and content: For each sample: barcodes, features, and count matrix, in the forms of tab-separated and market exchange format, respectively

source_name: spinal cord, healthy

growth_protocol: adult mice (3 months old)

extract_protocol:
Tissue samples were collected from n=4 uninjured mice and n=4 mice at 28d after crush SCI. Mice were perfused with ice cold heparinized saline that was prepared using RNAse- and DNAse- free water and 10X PBS for 2 minutes at 7ml/min for blood clearance. Spinal cords were rapidly dissected on ice chilled blocks. For SCI samples, the lesion core center was identified and a tissue block of 1 mm rostral and caudal was then rapidly removed. Anatomically equivalent regions of spinal cord were taken from uninjured mice. Tissue samples were rapidly snap frozen in microcentrifuge tubes maintained in a dry ice bath and stored at -80°C until further processing. To avoid potential batch effects, frozen tissue samples were all processed at the same time. To enrich for astrocyte nuclei, we used Sox9 antibody-binding and magnet-assisted nuclear immunoprecipitation (MAN-IP) using well characterized procedures{Krishnaswami, 2016 #5364;Bhattacharyya, 2019 #5615;Batiuk, 2017 #5624} as follows. Tissue samples were first gently dissociated by trituration and pelleted by centrifugation. Nuclei were extracted from cell pellets by gentle resuspension in ice-cold lysis buffer (10mM Tris buffer, 10mM NaCl, 3 mM MgCl2, 0.1% Nonidet P40 Substitute). Nuclei were pelleted by centrifugation (500RPM (Model 5415R, Eppendorf) for 5 min at 4°C) and then resuspended in Nuclei Wash and Resuspension Buffer (NWRB) (1xPBS, 1% BSA, 0.2U/uL RNAse inhibitor) before being washed once more in NWRB and then filtered using a 5 mL Polystyrene Round-Bottom Tube with 35 µm Cell-Strainer Cap and concentrated to a nuclei concentration of 1000 nuclei/µL (1 x 106 nuclei/mL), resuspended and incubated with Sox9 rabbit monoclonal antibody (ThermoFisher, Cat#72016) for 30 minute and then centrifuged at 700g for 10 minutes. Pellets were resuspended in 80μl of MACS Buffer composed of 1X PBS (Tissue Culture grade; Ca2+, Mg2+ free), 0.5% Nuclease free Bovine Serum Albumin (BSA), and 2mM EDTA, and then incubated with anti-Rabbit IgG Microbeads (Miltenyi, Cat# 130-048-602) for 20 minutes at 4°C. After washing with 1ml of MACS buffer at 300g for 10 minutes at 4 ̊C, immunolabeled nuclei were enriched by magnetic separation using MACS MS columns (Miltenyi Cat# 30-042-201, 130-042-102 and 130-042-303). Pellets were resuspended in an appropriate volume of Resuspension Buffer to achieve a final concentration of 1000 nuclei/µL (1 x 106 nuclei/mL) and immediately processed for Library preparation using Chromium Next GEM Single Cell 3' v3.1 kits using manufacturer’s instructions. Eight library samples were then processed simultaneously for RNA-Sequencing on 2 lanes (Lane 1: injured-1, injured-2, uninjured-1, uninjured-2; Lane 2: injured-3, injured-4, uninjured-3; uninjured-4) of Illumina NovaSeq S4 with at least 300M reads per library sample, conducted in house by the UCLA Technology Center for Genomics & Bioinformatics using pair end reads (2x100).
The library preparation and sequencing were performed following 10X Genomics Chromium protocols.

treatment_protocol: spinal cord injury

value: Spinal cord

value: uninjured


title: ChIPSeq_H1X_MCF7_r1

extract_protocol:
DNA libraries were prepared for sequencing using standard Illumina protocols.
Cells were fixed using 1% formaldehyde, chromatin was extracted and sonicated using a Diagenode Bioruptor to generate fragments between 200 and 500 bp. 30 µg of chromatin was immunoprecipitated overnight using the indicated antibody. Rabbit IgG (Milipore 12-370) was used as a nonspecific control. Input was prepared with 10% of the chromatin material used for an immunoprecipitation. Immunocomplexes were recovered using Protein A magnetic beads from Millipore. Beads with bound antibody/protein/DNA complexes were washed, decross-linked at 65ºC overnight, and immunoprecipitated DNA was recovered using the IPure Kit from Diagenode.
Library construction and sequencing were performed under Illumina or BGI ChIP-Seq protocols, depending on the sample.

value: Breast cancer cell line

value: WT

value: Untreated

value: anti-H1X (Abcam, ab31972)


title: T2-2, replicate 1, scRNAseq

description: 10x Genomics


title: ChIPSeq_Input_MCF7_r1

value: Input sample


title: Uninjured-Lane 2-1


title: Uninjured-Lane 1-2


title: T2-4, replicate 3, scRNAseq

description: 10x Genomics


title: Uninjured-Lane 1-1


title: HBL1_H3K27Ac_ChIP

city: Cold Spring Harbor

first: Christopher

middle: R.

last: Vakoc

state: NY

address: 1 Bungtown road

institute: Cold Spring Harbor Laboratory

data_processing:
Sequencing reads were mapped to the human genome (hg38) using Bowtie2 (2.4.4). Duplicate read removal and sorting was performed using SAMtools (1.14). Peaks were called using MACS2 (2.2.7.1) broad peak (H3K27ac) or narrow peak (p50, OCT2, option using FDR cut off 5%. Big wig files were generated using DeepTools (3.5.1).
Assembly: hg38
Supplementary files format and content: peaks

source_name: Blood

extract_protocol: For each ChIP, 20 million cells were used. Cells were cross-linked with 1% formaldehyde for 10 min at room temperature with agitation and quenched with 0.125 M glycine for 5 min at room temperature. After washing twice with PBS, cells were incubated in 1 ml cell lysis buffer (10 mM Tris-HCl (pH 8.0), 10 mM NaCl, 0.2% NP-40 with protease inhibitor) for 15 min on ice. Nuclei were isolated by centrifugation at 600×g for 30 s, resuspended in 1 ml nuclear lysis buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 1% SDS with protease inhibitor) and sonicated using a Bioruptor Pico (Diagenode) (30s on/off, 10 cycles). In all cases, the chromatin was centrifuged at maximum speed in a tabletop centrifuge for 15 min at 4 °C. The supernatant was mixed with 7 ml IP dilution buffer (20 mM Tris-HCl (pH 8.0), 2 mM EDTA, 150  mM NaCl, 1% Triton X-100), and incubated with the 2.5 µg of the indicated antibody for 2 h. Protein A/G magnetic beads (25 µl, Dynabeads, Thermo Fisher Scientific) were washed twice with PBS and added to the antibody–chromatin mixture at 4 °C overnight. The beads were washed once with IP wash 1 buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 50 mM NaCl, 1% Triton X-100, 0.1% SDS), twice with high salt buffer (20 mM Tris-HCl (pH 8.0), 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.01% SDS), once with IP wash 2 buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate) and twice with TE (pH 8.0). Chromatin DNA was eluted, and cross-linking was reversed in 200 µl nuclear extraction buffer with 12 µl of 5 M NaCl and 1 µg /mL RNase A at 65 °C overnight. The beads were then discarded. The DNA-containing supernatant was treated with 4 µg /mL proteinase K at 56 °C for 20 min and purified using the QIAquick PCR purification kit (QIAGEN) in 60 μl water.

value: Blood

value: Tumor Cells

value: Genomic DNA

tag: antibody

value: Abcam, ab4729, 2 µg


title: HBL1_OCT2_abcam_ChIP

value: Abcam, ab178679, 5 µg


title: HBL1_IkBz_17139_ChIP

value: Invitrogen Cat #PA5-17139, 10 µg


title: HBL1_IkBz_CST_ChIP


title: HBL1_OCT2_proteintech_ChIP

value: Proteintech 10867, 5 µg


title: ChIPSeq_H1X_HeLa_r2

data_processing:
All samples were treated as single-end data to homogenize the processing protocol. Single-end reads were aligned to the human GRCh37/hg19 reference genome using Bowtie2 (v2.3.5.1) with default options.
SAMtools (v1.9) were used to filter out the low-quality alignments using the flag 3844.
Input and H1 variants genome coverage was calculated and normalized by reads per million (genomecov -bga -scale) with BEDTools (v2.28.0).
MACS2 (v2.1.2) was used to calculate input-subtracted ChIP-Seq signal coverage tracks (bdgcmp -m subtract).
Assembly: hg19
Supplementary files format and content: bigWig files include input-subtracted ChIP-Seq signal.

source_name: HeLa

value: HeLa

value: Cervical cancer cell line


title: HBL1,Input


title: ChIPSeq_Input_HeLa


title: G01 GQIcombi control, K2, Day 10

city: Moscow

first: Varvara

last: Kolesnikova

state: Russian Federation

address: Moscow, Butlerova st., 5A

country: Russia

institute: IHNA&NPh RAS

data_processing:
STAR version 2.7.9a
Reads were mapped to GRCh38 genome using STAR 2.7.9a (parameter --outFilterMismatchNmax 3)
Gene annotation provided byEnsembl
RNA-seq data was analized by DESeq2.0
Differentially expressed genes with padj less than 0.01 were found
Assembly: GRCh38
Supplementary files format and content: excel file includes raw counts for each sample
Supplementary files format and content: excel file includes differential expression for each sample

source_name: tumor biopsy

growth_protocol: G01 glioblastoma cells were maintained in DMEM/F12 supplemented with 10 fetal bovine serum (FBS) and 1% L-glutamine in humidifies atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated from cell lysate using Trisol reagent (Thermo Fisher Scientific according to the protocol for this reagent. Quality and quantity of allocated total RNA was tested using a BioAnalyser and an RNA 6000 NanoKit (Agilent). Next, total RNA was used to obtain the polyA fraction using oligoT magnetic beads Dynabeads® mRNAPurificationKit (Ambion) according to the protocol for this kit.
RNA libraries for RNA-seq were prepaired using NEBNext® RNA UltraII (NEB) following manufacturer's protocol.

treatment_protocol: Neural differentiation was induced by treatment of 1- day seeded G01 cells with sequently added GQIcombi factors

value: tumor biopsy

value: glioblastoma cell culture G01

tag: tumor stage

value: IV Grade

value: no treatment

tag: time

value: Day 10


title: G01 GQIcombi control, K1, Day 10

tag: cell type


title: ChIPSeq_H1X_HeLa_r1

tag: cell line

tag: genotype

value: WT

value: Untreated


title: OB3A_NU_2D, Day 21

city: Bern

first: Daniel

middle: Walter

last: Hanhart

state: Bern

address: Murtenstrasse 24

department: Department for BioMedical Research (DBMR)

country: Switzerland

institute: UroGenus

data_processing:
Sequencing reads were analyzed using the rnaseq pipeline from nf-core (version 3.7)
Adapter sequences were removed with trimgalore (version 0.6.7)
Alignment to the reference genome (GRCh38) was performed using STAR (version 2.7.10a)
Transcript quantification was done using Salmon (version 1.5.2)
The count matrix was loaded into R (version 4.1.2) with the tximport (version 1.20.0) package.
Assembly: GRCh38
Supplementary files format and content: File containing raw counts.

source_name: Bone

extract_protocol:
For RNA extraction from cultured cells, 300,000 cells from the cell suspension used for differentiation were pelleted, washed in PBS and resuspended in 1 ml of TriPure. Differentiated OPC were gently washed twice with PBS and harvested with 1 ml of TriPure. RNA was then extracted according to the manufacturer’s instructions. Genomic DNA was eliminated by using the RNeasy MinElute Cleanup kit (Qiagen). RNA integrity of the samples from cultured cells was checked with the Qubit RNA IQ Assay kit (Thermo Fischer Scientific), that of tissue samples was assessed by using the RNA 6000 Nano kit and following manufacturer’s instructions (Agilent)
Specimens were prepared for RNA sequencing using the “NEBNext Ultra II Directional RNA Library Prep Kit for Illumina” (NEB #E7760S/L). For batch_3, library was prepared using the Illumina TruSeq v2 mRNA protocol. The mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp). Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used.

value: Bone

value: Osteoprogenitor cells

tag: Sex

value: M

tag: type

value: Nonunion

tag: fracture site

value: Femur

tag: age patient

tag: nonunion type

value: Oligotrophic

tag: age fracture

value: 18 months

tag: batch

value: Day 21


title: OB3A_NU_2D, Day 0

value: Day 0


title: Injured-Lane 2-2

source_name: spinal cord, injured

value: Spinal cord

tag: treatment

value: full crush SCI


title: B06_8414

data_processing: R programming (Version 3.4.3) Bioconductor and the Comprehensive R Archive Network (CRAN 2017) packages were used. Samples were background corrected, quantile-normalized and summarized to a gene-level using the robust multi-chip average (RMA).

source_name: Breast carcinoma

extract_protocol: Total RNA was isolated according to protocol of RNeasy® Micro Kit (Qiagen).

tag: tumour-infiltrating nk cell status

value: Negative

tag: til score

tag: tumour-infiltrating nk cells

tag: g

tag: t

tag: er status

value: Positive

tag: status

value: Relapse

tag: age

tag: cdi

value: CDI


title: LNCaP, oeSTAT5A_1 (ATAC-seq)

city: shanghai

first: jing

state: shanghai

address: Rm 1515, Bldg 17, 160 Pujian Rd, Shanghai 200127, China

institute: Shanghai jiaotong university

data_processing:
Raw Reads were filtered to remove adapters and low quality reads (including Reads with N ratio greater than 10% were removed, and Reads with bases quality value Q<=10 accounting for more than 50% of the entire Read were removed), and then high-quality Clean Reads provided in FASTQ format were obtained for subsequent information analysis. The libraries were sequenced on an Illumina NovaSeq platform to generate 150 bp paired-end reads, according to the manufacturer’s instructions.
The Bowtie2 software was used to compare the high-quality Reads obtained from the sequencing of each sample with the reference genome to obtain the alignment efficiency of the sample Reads and the position information of the Reads on the genome. DeepTools v2.07 was used to map the density distribution of sequencing Read in the 3 kb of interval upstream and downstream of the TSS of each gene, and the results were presented as heat maps.
Use the STAR alignment tool to align sequencing reads to the reference genome. Upon alignment, calculate the genome coverage at each position using the aligned sequence data. Utilize the 'wigToBigWig' tool to convert the coverage data from WIG format to BigWig format based on the coverage information.
MACS2 v2.1.1 software was used to perform peak extraction.MACS2 contained four steps:(1) removing redundant Reads；(2) adjusting the Read position；(3) calculating Peak enrichment；(4) estimating the empirical false detection rate (FDR)；Finally, FDR<0.05(default) was selected as the identified peak.
Assembly: The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Supplementary files format and content: tab-delimited text file includes raw counts and TPMs for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: prostate

growth_protocol: LNCaP cells were cultured in RPMI-1640 medium  supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. DU145 cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10%  FBS and 1% penicillin/streptomycin.

extract_protocol:
For RNA-seq, 1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit. 1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR. Sequencing was performed using 12pM hybridization to a 2x100 paired end flow cell. For the ATAC-seq assay, 50000 cells were centrifuged at 500 g for 5 min at 4℃, and the supernatant was removed. Cells were washed once with cold PBS. Subsequently, the cells were again centrifuged at 500 g for 5 min at 4℃ and the supernatant was removed. The cells were then suspended in cold lysis buffer. Next, the cells were again centrifuged at 500 g for 10 min at 4℃ and the supernatant was removed. The transposition reaction system was performed using Tn5 transposase. The cell nuclear content was added to the transposing reaction system mixture, and the DNA were purified after incubation at 37℃ for 30 min. The PCR system was performed with purified DNA, and PCR amplification was performed. For ATAC-seq, 40 000 nuclei were pelleted and resuspended with transposase, for 30 minutes at 37 ℃. The transposed DNA fragments were purified immediately after with a MinElute PCR Purification Kit (Qiagen). After Samples were PCR-amplified using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligoattached magnetic beads.First strand cDNA was synthesized and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. ATAC was performed according to ATAC-seq protocol by Biomarker Technologies Biotechnology Ltd. In brief, native nuclei were purified from cell as previously described (Buenrostro et al.,2015). The Nextera DNA Library Preparation Kit (Illumina) was used to perform the transposition according to the manufacturer’s manual. 40 000 nuclei were pelleted and resuspended with transposase, for 30 minutes at 37 ℃. The transposed DNA fragments were purified immediately after with a MinElute PCR Purification Kit (Qiagen). After Samples were PCR-amplified using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA). Subsequent libraries were purified with the MinElute PCR Purification Kit (Qiagen) and subjected to sequencing on Illumina Novaseq 6000 using PE150

treatment_protocol: All cells were incubated at 37°C in 5% CO2. An LNCaP_ENZ cell line was cultured further in the continuous presence of 20 µM enzalutamide  to maintain enzalutamide resistance.

tag: tissue

value: prostate

tag: cell line

value: LNCaP

tag: cell type

value: Human prostate cancer

tag: genotype

value: STAT5A overexpression


title: LNCaP, oeSTAT5A_2 (ATAC-seq)


title: LNCaP, oePAX6_2 (ATAC-seq)

value: PAX6 overexpression


title: LNCaP, oePAX6_1 (ATAC-seq)


title: OB2B_HB_2D, Day 21

value: Bone

value: Osteoprogenitor cells

tag: Sex

value: M

tag: type

value: Healthy

tag: fracture site

value: Iliac crest

tag: age patient

value: 0 month

tag: time


title: B04_8728

tag: tumour-infiltrating nk cell status

tag: til score


title: OB2B_HB_2D, Day 14

tag: age fracture

tag: batch

value: Day 14


title: Injured-Lane 2-1

value: Spinal cord

tag: treatment

value: full crush SCI


title: G01 GQIcombi, G01_DNRT1, Day 10

value: tumor biopsy

value: glioblastoma cell culture G01

tag: tumor stage

value: IV Grade

value: GQIcombi

value: Day 10


title: G01 GQIcombi, G01_DNRT2, Day 10


title: LNCaP, con_2 (ATAC-seq)

value: prostate

value: LNCaP

value: Human prostate cancer

value: WT


title: OB2B_HB_2D, Day 7

value: Bone

value: Osteoprogenitor cells

value: Day 7


title: OB3A_NU_2D, Day 14

value: M

value: Nonunion

value: Femur

tag: nonunion type

value: Oligotrophic

value: 18 months


title: Injured-Lane 1-2

value: Spinal cord

value: full crush SCI


title: OB2B_HB_2D, Day 0

value: Healthy

value: Iliac crest

value: 0 month

value: Day 0


title: Injured-Lane 1-1


title: OB3A_NU_2D, Day 7


title: DU145, shPAX6_3 (RNA-seq)

description:
SHPAX6-3
DU145_shCON__DU145_shPAX6.txt

value: prostate

value: PAX6 knockdown


title: OB1_CA_2D, Day 21

value: F

value: Callus

value: Wrist

value: 3 month

value: Day 21


title: Bone marrow FOXP3-GFP+ sorted Tregs - GEX Sample3

description: 10x Genomics-gene expresssion

data_processing:
alignment and create feature-barcode matrics using cellranger-6.0.1
data clean and filte low quality cells using SoupX_1.5.2
to filtering low quality cells, normalizing the data, identification of highly variable genes,  performing linear dimensional reduction(PCA), cluster cells, running non-linear dimensional reduction (UMAP/tSNE), finding cluster biomarkers using Seurat_4.0.1
To Intergrade all processedsamplesbased on archers, renormalize all the data, identification of grouping highly variable genes, performing linear dimensional reduction(PCA), cluster cells, running non-linear dimensional reduction (UMAP/tSNE), finding cluster biomarkers for each group and each sample  using Seurat_4.0.1 .
To perform gene set enrichment and pathway analysis
Assembly: mm10
Supplementary files format and content: bam files contain raw R2 sequencing reads and alignment details for each sample
Supplementary files format and content: .h5 files contain feature verse barcode matrix

source_name: Bone marrow

extract_protocol: FACS-sorted FOXP3-GFP+ Tregs from bone marrow and spleen of wild type and IkbkbV203I homozygous mice. Single gene expression libraries were preprared by the Biomolecular Resource Facility at JCSMR, ANU using Chromium Next GEM Single cell 5' kit v2 Dual Index (10X Genomics) according to manufacturer's instructions. The library was sequenced in S1 Flowcell with 2x50bp paired-end reads by NovaSeq 6000 sequencer (Illumina). The 10X Cell ranger package (10X Genomics, v6.0.1) was used to process data and align to mouse genome (mm10).

value: Bone marrow

value: FACS-purified FOXP3-GFP+ Tregs

value: IkbkbV203I mut/mut

value: No treatment


title: OB1_CA_2D, Day 14

value: Bone

value: Osteoprogenitor cells

value: Day 14


title: DU145, shPAX6_1 (RNA-seq)

description:
SHPAX6-1
DU145_shCON__DU145_shPAX6.txt

value: Human prostate cancer


title: DU145, shPAX6_2 (RNA-seq)

description:
SHPAX6-2
DU145_shCON__DU145_shPAX6.txt


title: LNCaP, con_1 (ATAC-seq)

value: LNCaP

value: WT


title: OB1_CA_2D, Day 0

value: Day 0


title: DU145, shCON_3 (RNA-seq)

description:
NC3
DU145_shCON__DU145_shPAX6.txt

value: prostate


title: Spleen FOXP3-GFP+ sorted Tregs - GEX Sample3

description: 10x Genomics-gene expresssion

source_name: Spleen

value: Spleen


title: Spleen FOXP3-GFP+ sorted Tregs - GEX Sample1

description: 10x Genomics-gene expresssion

value: IkbkbV203I +/+


title: DU145, shCON_2 (RNA-seq)

description:
NC2
DU145_shCON__DU145_shPAX6.txt


title: cKO2

city: Beijing

first: Jiali

last: Liu

address: 2 West Yuanmingyuan Road

institute: China Agricultural University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 v2.0.5
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: testis

growth_protocol: All mice were bred and housed under specific pathogen-free conditions with controlled temperature (22 ± 1℃) and exposed to a constant 12-hour light-dark cycle in the animal facilities of China Agricultural University. All experiments were conducted following the guidelines and with the approval of the Institutional Animal Care and Use Committee of China Agricultural University

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Conditional knockout

value: testis

value: Germ cell

value: STRA8+ cell

value: Srsf1 knockout


title: Control3

value: Cre


title: cKO3


title: cKO1


title: Bone marrow FOXP3-GFP+ sorted Tregs - GEX Sample1

description: 10x Genomics-gene expresssion

value: Bone marrow

value: FACS-purified FOXP3-GFP+ Tregs


title: Control2


title: Control1


title: LNCaP, ENZ cells (RNA-seq)

description:
LNCAP_ENZ
LNCAP_control__LNCAP_ENZ30.txt

value: enzalutamide (20uM)

tag: phenotype

value: enzalutamide resistant


title: C3

city: Jinan

first: Peichao

state: Shangdong

address: The Second Hospital of Shandong University

department: thoracic surgery department

institute: Shandong University

data_processing:
Raw data (fastq) were processed using in-house perl scripts to remove any remaining adaptors and ambiguous nucleotides.
The trimmed sequence files were mapped to the reference genome, Homo Sapiens (GRCh38/hg38), using HISAT2 (v2.0.5).
Gene expression levels were quantified as Fragments Per Kilobase of transcript per Millions base pairs sequenced.
Differential expression analysis of MOF knockdown (si-MOF#1, si-MOF#2) and control (si-NC) groups was performed using DESeq2 R package (1.16.1).
Differentially expressed genes (DEGs) were identified according to the criteria of |log2(foldchange)| ≥1 and adjusted P value < 0.05. Finally, GO enrichment analysis for 430 shared DEGs was performed using the analysis tool NovoMagic by Novogene.
Assembly: Homo Sapiens (GRCh38/hg38)
Supplementary files format and content: Tab-delimited text file inckude raw counts for each sample
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample

source_name: esophagus mucosa

growth_protocol: RPM1640,10%FBS,1%Antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol reagent.
Briefly, libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, E7530)

treatment_protocol: transfected with siRNA

tag: tissue

value: esophagus mucosa

value: esophageal squamous cell carcinoma cells

value: treated with siMOF-2


title: LNCaP, control cells (RNA-seq)

description:
LNCAP_control
LNCAP_control__LNCAP_ENZ30.txt

tag: cell line

value: LNCaP

value: Human prostate cancer

value: WT


title: OB1_CA_2D, Day 7

value: Bone

tag: cell type

value: Osteoprogenitor cells

value: F

value: Callus

value: Wrist

value: 3 month

value: Day 7


title: C2


title: DU145, shCON_1 (RNA-seq)

description:
NC1
DU145_shCON__DU145_shPAX6.txt

value: prostate

tag: genotype


title: C1


title: B3

value: treated with siMOF-1


title: Ocs_EoS4

city: Erlangen

first: Darja

last: Andreev

address: Glückstraße 6

department: Medicine 3

institute: Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen

data_processing:
Clustering of the index-coded samples was completed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina), according to the manufacturer’s instructions.
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N  sequences and reads with low quality from raw data. All the downstream analyses were based on the clean data with high quality.
Reference genome (mm10) and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5. and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Feature counts v1.5.0-p3 was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Osteoclasts (day 3) differentiated from bone marrow-derived monocytes

growth_protocol: Bone marrow-derived monocytes (BMMs) were isolated from the femur and tibia of BALB/c wildtype mice. BMMs were differentiated into osteoclasts within 3 days. BMMs were cultured in a concentration of 1x10^6 cells/mL in osteoclast differentiation medium (αMEM and GlutaMAX with 10% FCS and 1% penicillin/streptomycin) supplemented with 5 ng/µL M-CSF and 10ng/µL RANKL at 37°C and 5.5% CO2. Medium was changed on day 2.

extract_protocol:
RNA of osteoclasts at day 3 of differentiation was purified with the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: BMMs were stimulated with sorted eosinophils (from IL-5tg/4get mice; BMMs/Eos ration of 1:2) or with eosinophil supernatant (1:2 dilution) at day 0 of cultivation for 48h as compared with unstimulated BMMs. After 48h the stimuli were removed, the cells were washed and the medium was replaced with freh osteoclast differentiation medium with supplements. Osteoclasts were harvested at day 3 of differentiation.

tag: strain

value: BALB/c

value: stimulation with eosinophil supernatant (1:2 dilution)


title: Ocs_EoS3

value: Osteoclasts (day 3) differentiated from bone marrow-derived monocytes


title: B2

value: esophagus mucosa

value: esophageal squamous cell carcinoma cells


title: Ocs_EoS2


title: Ctrl HT1080-6

city: bethesda

first: David

last: Peeney

state: MD

address: 10 Center Drive, Building 10, 6B05

institute: NCI

description: HT1080_ConA_treatment_Normalization_Normalized_counts.txt

data_processing:
Partek Flow
Read contaminants and low-quality reads (Phred score <20) were removed using Bowtie 2.
Trimmed reads were aligned to the mouse (mm10) genome using STAR and annotated to RefSeq transcripts using Partek’s expectation-maximization algorithm.
Counts were subjected to median ratio normalization prior to cluster analysis and differential expression analysis (DEseq2).
Assembly: hg19
Supplementary files format and content: tab-delimited text files contain the median ratio normalized counts for all samples

source_name: Connective Tissue

growth_protocol: Cells were seeded at 1,000,000 cells per 10cm dish in biotin depleted full media (DMEM 10% FBS).

extract_protocol:
Rneasy kit (Qiagen)
PolyA selection was used to enrich for mRNA and RNA sequencing was performed by Azenta Life Science.

treatment_protocol: 3 days after seeding, the cells were switched to low-serum biotin depleted media (1% FBS) and treated with 40nM PMA or 40ug/mL ConA for 24 hours.

value: Connective Tissue

value: Fibrosarcoma

value: wt

value: Control


title: A3

value: treated with si-NC


title: Ctrl HT1080-5


title: Ocs_Eo3

value: WT

value: stimulation with eosinophils (BMMs/Eos ratio of 1:2)


title: A2


title: Ocs_EoS1


title: Ocs_Eo4


title: Ocs_Eo2


title: Ctrl HT1080-4


title: ConA treated HT1080-3

value: 40ug/mL ConA (24h)


title: Ocs_Eo1


title: A1


title: TPK_25_T_NU

extract_protocol:
For RNA extraction from tissues, snap-frozen tissues were homogenized in a TissueLyser II (Qiagen) in 2ml tubes with a 4 mm metallic bead for 2 cycles of 2 minutes each at 25 Hz, using the RNeasy Plus Universal Mini kit (Qiagen) and following manufacturer’s instructions, including the step to remove genomic DNA contaminations. RNA integrity of the samples from cultured cells was checked with the Qubit RNA IQ Assay kit (Thermo Fischer Scientific), that of tissue samples was assessed by using the RNA 6000 Nano kit and following manufacturer’s instructions (Agilent)
Specimens were prepared for RNA sequencing using the “NEBNext Ultra II Directional RNA Library Prep Kit for Illumina” (NEB #E7760S/L). For tissue samples, total RNA was used, after removal of ribosomal and globin RNA. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp). Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used.

value: Bone

tag: Sex

value: F

tag: type

value: Nonunion

value: Humerus

value: Hyper

tag: age fraction

value: 180 months


title: TPK_30_T_NU

tag: fracture site

value: Femur

tag: age patient

value: 21 months


title: ConA treated HT1080-2


title: B1

value: esophagus mucosa

value: esophageal squamous cell carcinoma cells

value: treated with siMOF-1


title: Ocs_Ctr2

value: BALB/c

value: Osteoclasts (day 3) differentiated from bone marrow-derived monocytes

value: untreated


title: Ocs_Ctr4

value: WT


title: ConA treated HT1080-1

value: Connective Tissue

value: Fibrosarcoma

value: wt


title: TPK_39_T_NU

value: Bone

value: M

value: Oligo

value: 28 months


title: TPK_3_T_NU

value: Nonunion

value: Tibia

value: Hyper

value: 95 months


title: PMA treated HT1080, 3

description: HT1080_PMA_treatment_Normalization_Normalized_counts.txt

value: 40nM PMA (24h)


title: TPK_29_T_NU

value: Femur

value: 35 months


title: PMA treated HT1080, 2


title: Ocs_Ctr1

value: BALB/c

value: Osteoclasts (day 3) differentiated from bone marrow-derived monocytes


title: PMA treated HT1080, 1


title: Control HT1080, 3

value: Control


title: TPK_16_T_NU

value: F

value: 22 months


title: TPK_43_T_NU

value: 27 months


title: Control HT1080, 2

value: Connective Tissue

value: Fibrosarcoma

value: wt


title: TPK_33_T_NU

value: Bone

value: M

value: 25 months


title: Control HT1080, 1


title: 2-LR-ET10

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

data_processing:
The adapter sequences were trimmed using TrimGalore (https://www.bioinformatics.babraham.ac.uk/).
The trimmed reads were aligned to the reference genome (GRCh38) using STAR (v2.7.3a).
The expression value per gene was estimated as a read count or the number of transcripts per kilobase million (TPM) value calculated using RSEM (v1.3.3) with the human gene annotation GRCh38.104.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes expected_count, TPM, FPKM

growth_protocol: The lung cancer cell line H3122 was maintained in complete RPMI-1640 medium (Welgene, Korea). H3122 cells were cultured with increasing concentrations of ceritinib starting at the IC30 value. Resistant cells were derived after approximately 6 mo of culture with continuous 1 μM ceritinib treatment.

extract_protocol:
Total RNA samples were isolated using RNeasy Plus Mini Kit (QIAGEN, Germany) according to the manufacturer's instructions including gDNA Eliminator.
The RNA-seq library was prepared using the TruSeq Stranded mRNA Kit (Illumina, CA), and sequencing was performed using the Illumina Novaseq platform to generate 150-bp paired-end reads.
Read length: 151

treatment_protocol: H3122-LR cells treated with vehicle (DMSO) and 10 nM Emetine (ET10) for 72 h.

value: Non-Small Cell Lung Cancer

value: Emetine, 10nM

tag: time


title: Ocs_Ctr3

value: WT

value: untreated


title: Patient34 20100-Nivo

city: Bangalore

first: Nandini

middle: Pal

last: Basak

state: Karnataka

address: Hosur road

department: R&D

country: India

institute: Farcast Biosciences

hyb_protocol: Manufacturer's protocol was followed

scan_protocol: Digital analyser is used for the scanning of  catridge.

data_processing: nSolver software was used to normalise the data against the selected 5 specific housekeeping genes DNAJC14, GUSB, NRDE2, TFRC, UBB.

source_name: HNSCC

growth_protocol: Ex vivo culture for 72 hours

extract_protocol: RNA was extracted from FFPE blocks.

treatment_protocol: Samples were either untreated (Control), Nivolumab treated (Nivo) or Nivolumab+Ipilimumab treated (N+I)

tag: gender

value: Male

tag: age (years)

tag: site

value: Tongue

tag: sample type

value: Primary

tag: therapy

value: Naive

tag: cancer grade

tag: cancer stage

value: III

tag: cohort

tag: treatment in culture

value: Nivolumab


title: TPK_41_T_NU

tag: tissue

value: F

value: Nonunion

value: Humerus

tag: nonunion type

value: Oligo

tag: batch

value: 13 months


title: Patient35 20104-Nivo

value: Female

value: Buccal Mucosa


title: 1-LR-ET10

tag: cell line

tag: cell type

value: Non-Small Cell Lung Cancer

tag: treatment


title: TPK_37_T_NU

value: Bone

tag: Sex

tag: type

tag: fracture site

tag: age patient

tag: age fraction


title: TPK_35_T_NU

value: M

value: Ulna

value: Hyper


title: 2-LR-DMSO

value: DMSO

tag: time


title: 1-LR-DMSO


title: TPK_32_T_NU

value: Tibia


title: TPK_18_T_NU

value: 21 months


title: TPK_31_T_NU

value: Femur

value: 8 months


title: Patient33 20020-Nivo

tag: gender

value: Male

tag: age (years)

tag: site

tag: sample type

value: Primary

tag: therapy

value: Naive

value: III

value: Nivolumab


title: TPK_17_T_NU

tag: tissue

value: F

value: Nonunion

value: Humerus

value: Oligo

value: 18 months


title: TPK_23_T_NU

value: Bone

value: M

tag: nonunion type

value: 7 months


title: TPK_27_T_NU

tag: batch


title: TPK_24_T_NU

value: 6 months


title: Patient21-20100

value: Tongue

tag: cancer grade

tag: cancer stage

tag: cohort


title: Patient22-20104

value: Female

value: Buccal Mucosa


title: Patient35 20104-Control

tag: treatment in culture

value: Control


title: Patient32 10005-Nivo

value: Alveolus

value: Primary

value: IVA


title: Patient23-20113

value: Naive

value: II


title: Patient34 20100-Control

value: Male

value: III


title: TPK_12_T_NU

tag: Sex

value: F

tag: type

value: Nonunion

value: Humerus

value: Oligo

value: 5 months


title: DIO-Hypothelamus-PF+CS 2

city: Boston

first: dongxian

last: guan

state: MA

address: Children's Hospital 300 Longwood Ave

institute: Boston Children's Hospital

data_processing:
CLC genomics workbench v 11.0.1
sequence reads were trimmed for adapyor sequence/low-quality sequency using CLC genomics benchwork (papameter-quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm 10 using CLC genomic benchwork (parameter-mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similaryty fraction: 0.8)
Reads count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm 10
Supplementary files format and content: tab-delimited excel file includes raw counts for each sample
Supplementary files format and content: tab-delimited excel file includes normalized expression value for each sample

source_name: Hypothelamus

growth_protocol: The WT mice were fed with high fat diet to indiuce obese.

extract_protocol:
RNAs were extracted using Rneasy mini plus kit(Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq werer prepared using SMARTER mRNA-seq Library Prep Kit following manufacture's protocols.

treatment_protocol: DIO mice were acclimated with DMSO with daily i.p. injections for 1 week and then randomly divided into 4 groups for a subsequent 4-day treatment. 1) Vehicle (Veh), treated with DMSO and ad libitum access to food, 2) CS, treated with Celastrol (100μg/kg/day, i.p.) and ad libitum access to food, 3) PF, pair-fed to Celastrol-treated group, in which 0.5g high fat diet per mice per day was given (0.34g for dark cycle and 0.16g for light cycle) (a little bit less than 0.8g, the average amount of diet Celastrol-treated mice consumed), 4) PF/CS, treated with Celastrol and given the same amount of food and at the same intervals as the PF group. On the fourth day around 8:00 am, all mice received a final injection and 6 hours later blood glucose (mg/dl) levels were measured before tissue collection.

value: Hypothelamus

tag: genotype

tag: treatment

value: Celastrol  and pair-fed


title: DIO-Hypothelamus-PF+CS 3


title: TPK_20_T_CA

value: Bone

value: M

value: Callus

tag: fracture site

value: Ulna

tag: age patient

tag: age fraction

value: 3 months


title: DIO-Hypothelamus-PF+CS 4


title: DIO-Hypothelamus-CS 3

value: Celastrol


title: DIO-Hypothelamus-CS 2


title: TPK_19_T_CA

value: Radius

value: 2 months


title: DIO-Hypothelamus-CS 1


title: TPK_15_T_CA

value: Wrist


title: Patient32 10005-Control

tag: gender

value: Female

tag: age (years)

tag: site

value: Alveolus

value: Primary

value: Naive

value: IVA

value: Control


title: Patient33 20020-Control

value: Male

value: Buccal Mucosa

tag: sample type

tag: therapy

value: III


title: DIO-Hypothelamus-PF+CS 1

tag: tissue

value: Hypothelamus

value: Celastrol  and pair-fed


title: TPK_13_T_CA

value: Bone

value: F

value: Callus

value: Ulna

tag: batch


title: DIO-Hypothelamus-CS 4

value: Celastrol


title: DIO-Hypothelamus-PF 4

value: Vehiclen and pair-fed


title: DIO-Hypothelamus-PF 2


title: TPK_42A_T_CA

value: M

value: Wrist

value: 0.6 month


title: DIO-Hypothelamus-PF 1


title: TPK_7_T_CA

value: Tibia

value: 0.65 month


title: DIO-Hypothelamus-Veh 4

value: Vehicle


title: TPK_4_T_CA

value: Ulnca

value: 0.5 month


title: Patient27 10006-N+I

value: Male

value: Tongue

value: Primary

value: Naive

tag: cancer grade

tag: cancer stage

value: IVA

value: Nivolumab+Ipilimumab


title: DIO-Hypothelamus-Veh 3

value: Hypothelamus


title: Patient28 L0042-N+I

value: Female

value: II

tag: cohort

tag: treatment in culture


title: TPK_34_T_HB

value: Bone

tag: Sex

value: M

tag: type

value: Healthy

value: Iliac crest

value: 0 month


title: TPK_28_T_HB


title: DIO-Hypothelamus-Veh 2

tag: genotype

tag: treatment

value: Vehicle


title: Patient26 10002-N+I

value: Alveolus

value: Neoadjuvant CT/RT


title: Patient22 20085-N+I

value: Buccal Mucosa

value: III


title: DIO-Hypothelamus-PF 3

value: Vehiclen and pair-fed


title: TPK_9_T_HB

tag: fracture site

tag: age patient


title: DIO-Hypothelamus-Veh 1


title: Patient24 20114-N+I

tag: gender

value: Male

value: Submindibular region

value: Primary

value: Naive

value: IV


title: AlphaToxin_NonClonal_U2OS_lib7

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

description:
combined-non-clonal.csv
lib3749-15757749_R1

data_processing:
Sequences were pre-processed (Trimmomatic v. 0.33) to remove Illumina adaptor sequences, filter out sequences < 40 bp and crop longer sequences to 50 bp.
Sequences were then aligned to human genome hg38 (Bowtie v. 2.1.0). Sequences that did not map to unique sites or showed significant mismatch or error (edit distance >2 over 50bp) were excluded from further analysis
Finally, reads were mapped and filtered to a known PiggyBac consensus insertion site (TTAA) at their start.
Common insertion sites (CIS) were identified using the Poisson Regression Insertion Model (PRIM) published by Bergemann et al 2012
The PRIM model was run using a p-value cutoff of 0.01 and Bonferroni correction on both selected, unselected, and in silico-generated libraries based on known TTAA sites in the genome, using window sizes of 10 kb, 25 kb, 50 kb, 75 kb, and 100 kb. CIS in experimental libraries that were also found in unselected or in silico generated libraries were excluded
Assembly: hg38
Supplementary files format and content: processed clonal data contain chromosome,mappingStart,mappingEnd,width,strand,libid,cpm,annotation,geneStart,geneEnd,geneLength,geneId,geneSymbol,normCpm,cpmRank
Supplementary files format and content: processed non clonal data contain CIS summary information and BED tracks

growth_protocol: U2OS cells were co-transfected with piggyBac plasmid pPB-SB-CMV-puro-SD3 and p-hyPBASE using Fugene 6 transfection reagent (Promega, Madison WI, USA). For each library, between 107 - 108 cells were transfected, cultured with the addition of 3 µg/ml puromycin (Gibco) for one week to select cells that had incorporated the transposon, and then used for screens of alpha-toxin resistance with minimal further expansion. Un-mutagenized U2OS cells were treated with alpha-toxin under the same conditions to confirm that no resistance was seen in the absence of transposon mutagenesis.

extract_protocol:
genomic DNA (gDNA) was isolated from 5-10 X 106 cells
4 mg of gDNA were digested with BfaI or CviQI (New England Biolabs, Ipswich MA, USA) and purified (QIAquick PCR purification kits, Qiagen, Hilden, Germany) then ligated with barcoded P7-side adaptors using T4 DNA Ligase (New England BioLabs). Ligated gDNA fragments were then combined and amplified by nested PCR. The first round of PCR used primers corresponding to transposon sequence (KS15) and the P7-side adaptor (LP1). A second round of PCR (primers P2A and LP22) added the full Illumina P5 and P7 sequences. Sequencing was performed by the BRI Genomics platform using a HiScan or HiSeq platform (Illumina, San Diego CA, USA) with a custom sequencing primer (Rd1SeqP.ipdC) to generate 50 or 100 bp single end reads.
described in Bruchez et al 2020

treatment_protocol: Cells were treated twice with alpha-toxin (500 ng/ml) for 48h to ensure the selection of only highly resistant cells.

tag: cell line

value: mutagenized U2OS cells

value: alpha-toxin


title: Patient25 10001-N+I

value: Female

tag: age (years)

tag: site

value: IVA

value: Nivolumab+Ipilimumab


title: TPK_5_T_HB

value: Bone

value: M

value: Healthy

value: Iliac crest

tag: age fraction

value: 0 month


title: TPK_36_T_HB

tag: tissue

value: F


title: AlphaToxin_NonClonal_U2OS_lib6

description:
combined-non-clonal.csv
lib3739-15756745_R1


title: Patient20 20057-N+I

value: Buccal Mucosa

tag: sample type

tag: therapy

value: III


title: OB39_NU_2D, Day 21

tag: cell type

value: Osteoprogenitor cells

value: Nonunion

value: Humerus

tag: nonunion type

value: Oligotrophic

tag: age fracture

value: 5 months

tag: batch

tag: time

value: Day 21


title: Patient16 20025-N+I

value: Male

value: Primary

value: Naive

tag: cancer grade

tag: cancer stage

tag: cohort

tag: treatment in culture


title: Patient17 20026-N+I

tag: gender

value: GBS

value: Nivolumab+Ipilimumab


title: OB39_NU_2D, Day 14

value: Bone

tag: Sex

tag: type

tag: fracture site

tag: age patient

value: Day 14


title: Patient19-20026

tag: age (years)

tag: site


title: Patient17-20020

tag: sample type

tag: therapy


title: Patient18 20043-N+I

value: IVb


title: Patient15-10005

value: Female

value: Alveolus

value: IVA


title: Patient20-20043

value: Buccal Mucosa


title: Patient18-20023

value: III


title: Patient16-10108

value: Tongue

value: Radiotherapy


title: OB39_NU_2D, Day 7

tag: tissue

tag: cell type

value: Osteoprogenitor cells

value: F

value: Nonunion

value: Humerus

tag: nonunion type

value: Oligotrophic

value: 5 months

value: Day 7


title: Patient15 20023-N+I

value: Primary

value: Naive

value: Nivolumab+Ipilimumab


title: AlphaToxin_U2OS_clone11

tag: cell line

tag: genotype

value: mutagenized U2OS cells

tag: treatment

value: alpha-toxin


title: AlphaToxin_NonClonal_U2OS_lib5

description:
combined-non-clonal.csv
lib3737-15945041_R1


title: AlphaToxin_U2OS_clone18


title: OB39_NU_2D, Day 0

value: Bone

tag: age fracture

tag: batch

tag: time

value: Day 0


title: AlphaToxin_U2OS_clone15


title: AlphaToxin_U2OS_clone14


title: Patient14 20019-N+I

tag: gender

value: Male

value: Oral Cavity

tag: cancer grade

tag: cancer stage

value: III

tag: cohort

tag: treatment in culture


title: OB39_NU_2D, Day 28

value: Osteoprogenitor cells

tag: Sex

tag: type

tag: fracture site

tag: age patient

value: Day 28


title: Patient13 20015-N+I

value: Female

tag: age (years)

tag: site

tag: sample type

tag: therapy

value: II


title: OB40_HB_2D, Day 21

tag: tissue

tag: cell type

value: F

value: Healthy

value: Iliac crest

value: 0 month

value: Day 21


title: Patient19 20047-N+I

value: Buccal Mucosa

value: Primary

value: Naive

value: Nivolumab+Ipilimumab


title: Patient12 20012-N+I

value: Local Recurrent

value: Prior treatment:CT/RT

value: IVA


title: AlphaToxin_U2OS_clone10

tag: cell line

tag: genotype

value: mutagenized U2OS cells

tag: treatment

value: alpha-toxin


title: OB40_HB_2D, Day 28

value: Bone

value: Osteoprogenitor cells

tag: age fracture

tag: batch

tag: time

value: Day 28


title: OB40_HB_2D, Day 14

value: F

value: Day 14


title: AlphaToxin_U2OS_clone17


title: Patient11 20006-N+I

tag: gender

value: Female

value: Radiotherapy

tag: cancer grade

tag: cancer stage

tag: cohort

tag: treatment in culture


title: OB40_HB_2D, Day 7

tag: Sex

tag: type

value: Healthy

tag: fracture site

value: Iliac crest

tag: age patient

value: 0 month

value: Day 7


title: OB32_CA_2D, Day 28

tag: tissue

value: Callus

value: Humerus

value: 1 month


title: AlphaToxin_U2OS_clone8


title: OB40_HB_2D, Day 0

tag: cell type

value: Day 0


title: OB32_CA_2D, Day 14


title: OB32_CA_2D, Day 21

value: Day 21


title: OB32_CA_2D, Day 7


title: OB32_CA_2D, Day 0


title: Patient3 10035-N+I

tag: age (years)

tag: site

value: Larynx

tag: sample type

value: Primary

tag: therapy

value: Naive

value: IVb

value: Nivolumab+Ipilimumab


title: Patient6 10078-N+I

value: Male

value: Lip

value: Local Recurrent

value: Prior treatment:CT/RT

value: IVA


title: Patient30 L0041-Nivo

value: Female

value: RMT

value: III

value: Nivolumab


title: Patient9 10100-N+I

value: Tongue

value: II


title: Patient7 10091-N+I

value: IVB


title: OB24_NU_2D, Day 0

value: Bone

value: Osteoprogenitor cells

value: M

value: Nonunion

value: Femur

tag: nonunion type

value: Hypertrophic

tag: age fracture

value: 34 months

tag: batch

value: Day 0


title: Patient29 K0038-Nivo

tag: gender

value: Lip

value: Primary

value: Naive

tag: cancer grade


title: OB10_NU_2D, Day 0

value: 19 months

tag: time


title: Patient8 10093-N+I

value: Male

value: Supra Glottis

tag: cancer stage

value: III

tag: cohort

tag: treatment in culture

value: Nivolumab+Ipilimumab


title: Patient28 K0037-Nivo

value: Female

value: Mouth

value: IVA

value: Nivolumab


title: Patient10 10108-N+I

value: Tongue

value: Radiotherapy


title: OB23_CA_2D, Day 0

value: Bone

value: Osteoprogenitor cells

tag: Sex

value: M

tag: type

value: Callus

tag: fracture site

value: Clavicle

value: 0.5 month


title: Patient27 10006-Nivo

value: Primary

value: Naive


title: AlphaToxin_U2OS_clone9

tag: cell line

tag: genotype

value: mutagenized U2OS cells

tag: treatment

value: alpha-toxin


title: AlphaToxin_U2OS_clone4


title: AlphaToxin_U2OS_clone19


title: AlphaToxin_U2OS_clone20


title: AlphaToxin_U2OS_clone6


title: AlphaToxin_U2OS_clone22


title: AlphaToxin_U2OS_clone7


title: AlphaToxin_U2OS_clone16


title: AlphaToxin_U2OS_clone23


title: AlphaToxin_U2OS_clone24


title: OB21_CA_2D, Day 0

tag: tissue

tag: cell type

value: Scapula

tag: age patient

value: Day 0


title: Patient26 10002-Nivo

value: Female

tag: age (years)

tag: site

value: Alveolus

tag: sample type

tag: therapy

value: Neoadjuvant CT/RT


title: Patient25 10001-Nivo

tag: gender

value: Buccal Mucosa

tag: cancer grade

value: IVA

value: Nivolumab


title: OB20_CA_2D, Day 0

value: Bone

value: Osteoprogenitor cells

value: Radius

tag: age fracture

tag: batch

tag: time


title: AlphaToxin_U2OS_clone21


title: AlphaToxin_U2OS_clone5


title: AlphaToxin_U2OS_clone12


title: OB16_NU_2D, Day 21

tag: Sex

value: M

tag: type

value: Nonunion

value: Tibia

tag: nonunion type

value: Hypertrophic

value: 8 months

value: Day 21


title: AlphaToxin_U2OS_clone1

tag: cell line

tag: genotype

value: mutagenized U2OS cells

value: alpha-toxin


title: OB16_NU_2D, Day 14

tag: tissue

tag: fracture site

value: Day 14


title: Patient22 20085-Nivo

value: Female

value: Primary

value: Naive

tag: cancer stage

value: III

tag: cohort

tag: treatment in culture


title: OB16_NU_2D, Day 28

tag: cell type

tag: age patient

value: Day 28


title: AlphaToxin_U2OS_clone13

tag: treatment


title: Patient23 20113-Nivo

tag: gender

tag: age (years)

tag: site

value: Buccal Mucosa

tag: sample type

tag: therapy

tag: cancer grade

value: II

value: Nivolumab


title: OB16_NU_2D, Day 7

value: Bone

value: Osteoprogenitor cells

tag: Sex

value: M

tag: type

tag: nonunion type

tag: age fracture

tag: batch

tag: time

value: Day 7


title: OB4_HB_2D, Day 21

tag: tissue

value: F

value: Healthy

tag: fracture site

value: Iliac crest

value: 0 month


title: Patient20 20057-Nivo

tag: cancer stage

tag: cohort

tag: treatment in culture


title: OB4_HB_2D, Day 14

tag: cell type

tag: age patient

value: Day 14


title: OB4_HB_2D, Day 7


title: Patient16 20025-Nivo

tag: gender

value: Male

tag: age (years)

tag: site


title: Patient18 20043-Nivo

tag: sample type

value: Primary

tag: therapy

tag: cancer grade

value: IVb


title: 1% DMS treated HIV1 RRE

first: Gabriel

middle: A

last: Romero Agosto

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

data_processing:
Data was processed using the DREEM software (https://github.com/rouskinlab/DREEM) .
Assembly: For PANDA the NCBI Reference Sequence is NR_109836.1. For the RRE the GenBank accession number is MN989412.1
Supplementary files format and content: The filw format is a .csv file that can be opened as a data table using excell. It provides the number of mutations per position of the entire population of RNA molecules that aligned to the referecne sequence.
Library strategy: DMS-MaPseq

organism: synthetic construct

source_name: g-block of HIV1 RRE

extract_protocol:
All RNA was acquired from in-vitro transcription of PCR amplified cDNA or gene-blockes.
The libraies for the HIV-1 RRE were prepared using the NEBnext RNA library prep kit. The libraries for the lncRNA PANDA were prepared using the Broad range RNA Xgen kit form IDT. The reverse transcriptase was changed to the Induro RT from NEB for the purposes of our experiment.

tag: cell line

tag: treatment

value: 1% DMS


title: 1.5% DMS treated HIV1 RRE


title: untreated HIV1 RRE

value: untreated


title: Patient24 20114-Nivo

value: Submindibular region

value: Naive

value: IV


title: Patient19 20047-Nivo

value: Buccal Mucosa

value: III

value: Nivolumab


title: OB15_CA_2D, Day 28

value: Bone

value: Osteoprogenitor cells

tag: Sex

value: M

tag: type

value: Callus

value: Femur

tag: age fracture

value: 1 month

tag: batch

value: Day 28


title: 1% DMS treated HIV1 RRE replicate

tag: tissue


title: Patient15 20023-Nivo

value: Female

value: Primary

tag: cancer stage

tag: cohort


title: Patient17 20026-Nivo

value: Male

value: GBS

tag: treatment in culture


title: RNAseq_HFD_Ing_MUT_rep4

first: Tirso

address: C/ Darwin 3

institute: Centro Nacional de Biotecnologia

description: White Adipose Tissue (WAT)

data_processing:
Sequenced reads were mapped to mm10 whole genome using BWA-MEM 0.7.15 with parameters mem -M -t 4 mm10bwaidx file_1.fastq file_2.fastq
Transcripts per Million of library size (TPM) were calculated using StringTie version 1.3.3 with parameters -e -v -p 32 -G knownGene_UCSC_mm10.gtf
The expression level of all genes was estimated by DESeq2 1.40.1 in RStudio 2023.03.1+446
Assembly: GRCm38/mm10 assembly
Supplementary files format and content: tab-delimited text files include cov, FPKM, and TPM values for each Sample (*.gtf)
Supplementary files format and content: Matrix table with TPM values for every transcript and every sample (*.csv)

source_name: Inguinal (iWAT)

extract_protocol:
Total RNA was purified with the Split RNA Extraction Kit (Lexogen, Austria). Triplicate RNA probes from wild-type and Dido1_dNT mutant were sequenced.
RNA libraries for epididymal WAT were prepared by the servicio de genomica at the Parque Cientifico de Madrid using standard Illumina protocols. RNA libraries for inguinal WAT were prepared by BGI Genomics (China).

value: Inguinal (iWAT)

tag: genotype

value: Dido1_dNT mutant

tag: strain


title: OB15_CA_2D, Day 21

tag: cell type

tag: fracture site

tag: age patient

tag: time

value: Day 21


title: OB15_CA_2D, Day 14

value: Day 14


title: OB4_HB_2D, Day 28

value: F

value: Healthy

value: Iliac crest

value: 0 month


title: Patient21 20074-Nivo

tag: gender

tag: age (years)

tag: site

value: Alveolus

tag: sample type

tag: therapy

value: Naive

tag: cancer grade

value: IVa

value: Nivolumab


title: Patient14 20019-Nivo

value: Oral Cavity

value: III


title: AlphaToxin_U2OS_clone3

tag: cell line

value: mutagenized U2OS cells

tag: treatment

value: alpha-toxin


title: AlphaToxin_U2OS_clone2


title: RNAseq_HFD_Ing_MUT_rep3

description: White Adipose Tissue (WAT)

tag: tissue


title: OB15_CA_2D, Day 7

value: Bone

value: Osteoprogenitor cells

tag: Sex

value: M

tag: type

value: Callus

value: Femur

tag: age fracture

value: 1 month

tag: batch

value: Day 7


title: RNAseq_HFD_Ing_MUT_rep2

description: White Adipose Tissue (WAT)

value: Inguinal (iWAT)

tag: genotype

value: Dido1_dNT mutant

tag: strain


title: OB16_NU_2D, Day 0

tag: cell type

value: Nonunion

tag: fracture site

value: Tibia

tag: age patient

tag: nonunion type

value: Hypertrophic

value: 8 months

value: Day 0


title: Patient13 20015-Nivo

tag: gender

value: Female

tag: age (years)

tag: site

value: Oral Cavity

value: Primary

value: Naive

tag: cancer stage

value: II

tag: cohort

tag: treatment in culture

value: Nivolumab


title: RNAseq_HFD_Ing_MUT_rep1

description: White Adipose Tissue (WAT)

tag: tissue