title: PBMC_severe patient_subject4

city: Hangzhou

first: Qiong

last: Zhang

address: 866 YuHangTang Rd, Medical Research Building A212, ZiJinGang Campus, Zhejiang University

institute: Zhejiang University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 15 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

source_name: PBMC, severe patient

label_protocol: Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

tag: disease

tag: group

value: severe

value: male


title: 2hH2O_37C1h_Pol2CST_AFF4AID_DLD_rep3

status: Public on Jan 15 2021

type: SRA

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University Feinberg School of Medicine

description: Pol2 ChIP-seq

library_source: genomic

data_processing:
For ChIP-seq, single-end raw reads were trimmed by Trimmomatic 0.33 (Bolger et al., 2014) and aligned to hg19 using Bowtie version 1.1.2, allowing only uniquely mapping reads with up to two mismatches within the 50 bp read. The resulting reads were extended to 150 bp toward the interior of the sequenced fragment, normalized to total reads aligned (reads per million, rpm), and formatted as bigWig-coverage tracks using GenomicRanges.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files with normalized read counts were provided for all samples.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: DLD-1 cells were cultured in DMEM (Corning) supplemented with 10% FBS (Corning), 1X GlutaMAX (Gibco), 100 U/ml Penicillin and 100 µg/ml Streptomycin (Gibco).

extract_protocol:
For ChIP-seq, 20-50 million cells were crosslinked with 1% paraformaldehyde (Electron Microscopy Sciences) in PBS for 10 min at r.t. Chromatin was sonicated with the Covaris E220 for 4 min with 10% duty cycle, 140 peak intensity power, 200 cycles per burst. Immunoprecipitations were carried out with antibodies and Protein A/G-agarose beads (Santa Cruz) or Dynabeads Protein G (Invitrogen).
For ChIP-seq, DNA libraries were prepared by the HTP Library Preparation Kit for Illimina (KAPA) and sequenced on the NextSeq 500 or NovaSeq 6000 (Illumina).

treatment_protocol: Cells were treated with 500 µM Auxin (3-indole-acetic acid sodium salt, abcam), 250 nM dBET6 (AOBIOUS), or 20 nM KL-1 (Liang et al. 2018). Heat shock treatment at 42 ˚C for 1 h was carried out as described previously (Mahat et al, 2016)

tag: cell line

value: Colorectal adenocarcinoma DLD-1

tag: genotype

value: AFF4-AID OsTIR1

tag: chip antibody

value: Rpb1 NTD (D8L4Y)


title: SUM52_GFP

type: RNA

city: Detroit

first: Zeng-Quan

last: Yang

state: MI

address: 4100 John R HWCRC 815

department: Oncology

institute: Karmanos Cancer Institute

description: SUM52 cells were infected by adenoviruses of the control GFP.

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip based on the LC Sciences service procedure. On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 mL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C. After RNA hybridization, tag-conjugating Cy3 dye was circulated through the microfluidic chip for dye staining.

scan_protocol: Fluorescence images were collected using a laser scanner and digitized using Array-Pro image analysis software (Media Cybernetics). Microarray images were carefully scanned for a balanced view. Numerical intensities are extracted for control, background, and microRNA probes.

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).

molecule: total RNA

source_name: Breast cancer line

label_protocol: Cy3 - LC Sciences service procedure.

extract_protocol: Total RNA was extracted with miRNeasy Mini kits (Qiagen, Hilden, Germany), and miRNA microarray analysis was performed by LC Sciences (Houston,TX).

tag: tissue

value: Breast


title: PBMC_severe patient_subject1

country: China

tag: gender

tag: age


title: PBMC_severe patient_subject2


title: WT 1

city: Houston

first: Peixin

last: Jiang

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data was processed and normalized using R package lumi.

label: biotin

organism: Mus musculus

source_name: wild type

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted by using the AllPrep DNA/RNA/Protein Mini kit.

tag: strain

value: TRAMP

tag: genotype/treatment

value: wild type

value: whole prostate


title: PBMC_severe patient_subject3


title: 2hH2O_37C1h_Pol2CST_AFF1AID_DLD_rep3

description: Pol2 ChIP-seq

value: AFF1-AID OsTIR1


title: WT 2


title: PBMC_mild_patient_subject5

source_name: PBMC, mild patient

value: mild

value: female


title: MDA-MB-231-PCMV6XL5-Rep1

city: Ankara

first: Hakan

last: Gurdal

address: A. Adnan Saygun Cad.

department: Faculty of Medicine

country: Turkey

institute: Ankara University

description: MDA-MB-231 cells transfected with empty PCMV6XL5 vector, biological replicate 1

hyb_protocol: 1 µg of total RNA was processed using the protocols and instruments recommended by the manufacturer.

scan_protocol: Arrays were scanned using the Affymetrix Genechip Scanner 3000 according to the manufacturer's instructions.

data_processing: The data normalised with BRB-ArrayTools v4.6.1 and JustRMA algorithm was used.

source_name: mammary gland/breas

label_protocol: standard Affymetrix protocol

growth_protocol: MDA-MB-231 human triple negative breast cancer cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) and Eagle’s minimal essential medium (EMEM), supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 5% CO2, 37˚C with 90-95 % humidity.

extract_protocol: For the RNA isolation, the cells were put into Trizol reagent (AppliChem, Darmstadt, Germany), disrupted with a homogenizer, and total RNA was isolated according to the manufacturer’s instructions. DNase treatment was performed to each RNA after RNA isolation by using DNase I (EN0521; Thermo Scientific).

treatment_protocol: DNA transfections were performed according to the manufacturer’s protocol using, for each well, 4 µl of TurboFectin Transfection 8.0 Reagent and 2µg of control nontarget DNA (Cloning vector PCMV6XL5 or PCMV6XL6), and Human βArr1cDNA or Human βArr2 cDNA. After transfection for 48 h at 37˚C, the medium was replaced, and the cells were cultured for an additional 12 h.

value: mammary gland/breast; derived from metastatic site


title: PBMC_severe patient_subject5


title: PBMC_mild_patient_subject3


title: PBMC_mild_patient_subject4


title: 2hAux_42C1h_Pol2CST_AFF4AID_DLD_rep2

description: Pol2 ChIP-seq

tag: growth temperature

value: Heat shock

tag: treatment

value: Auxin


title: SUM225_4μ8C

description: SUM225 cells were treated with 4μ8C for 2 days.


title: SUM52_4μ8C

description: SUM52  cells were treated with 4μ8C for 2 days.


title: PBMC_healthy_subject4

source_name: PBMC, HC

value: healthy


title: Vehicle 1

source_name: vehicle-treated

value: vehicle-treated

value: neuroendocrine carcinomas


title: MDA-MB-231-PCMV6XL5-Rep2

description: MDA-MB-231 cells transfected with empty PCMV6XL5 vector, biological replicate 2


title: PBMC_healthy_subject5

value: peripheral blood mononuclear cells (PBMCs)


title: 2hH2O_42C1h_Pol2CST_AFF4AID_DLD_rep2

description: Pol2 ChIP-seq

value: Colorectal adenocarcinoma DLD-1


title: 2hAux_37C1h_Pol2CST_AFF4AID_DLD_rep2

description: Pol2 ChIP-seq

value: AFF4-AID OsTIR1


title: 2hH2O_37C1h_Pol2CST_AFF4AID_DLD_rep2

description: Pol2 ChIP-seq

value: Rpb1 NTD (D8L4Y)


title: 24_Chromium_3p_v3_lymphocyte_cell line_mix

city: SOUTH SAN FRANCISCO

first: Tracy

last: Yamawaki

state: California

address: 1120 VETERANS BLVD.

institute: AMGEN, INC.

description: 1:1:1:1 mixture of Jurkat, TALL104, EL4, IVA12 cells sequenced using the 10X Chromium 3' v3 kit targeting a capture of 6000 cells.

library_source: transcriptomic

data_processing:
fastq files were downsampled using seqtk v1.3-r106
fastq files were processed with cellranger v3.0.2 for cell demultiplexing, read alignment and transcript counting
Genome_build: Data was aligned to a “cellRanger_1.2.0” reference composed of hg19 with Ensembl 82 and mm10 with Ensembl 84.
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx

organism:
Homo sapiens
Mus musculus

source_name: lymphocyte cell line mix

extract_protocol:
cell suspensions were encapsulated in cell lysis buffer with the 10X Chromium
Libraries were constructed with the 10X Genomics 3' v2, v3 or 5' v1 kits.

value: Jurkat, TALL104, EL4, IVA12 (1:1:1:1 mixture)


title: HeLa_infected_6h_3

city: Barcelona

first: Marc

last: Torrent Burgas

address: Carrer de la Vall Moronta

department: Biochemistry and Molecular Biology

country: Spain

institute: Universitat Autònoma de Barcelona

data_processing:
Illumina’s bcl2fastq2 Software v2.20.0 was used for basecalling
Quality control of RNA-Seq reads was performed with FastQC. Sequenced reads were trimmed for adaptor content with Trimmomatic. Reads were mapped to Homo sapiens reference genome (GRCh38) using STAR aligner (version 2.6.1b) with default settings.
Mapped data was transformed to gene level counts using human Gencode annotations and FeatureCounts software.
Time-series differential expression analysis was carried out for each time point, by comparing the data obtained at 2, 4 and 6 hours-post-infection to the data in the sample at  0 hours (control conditions) and using the DESeq2 Bioconductor package. Differential expressed genes (DEGs) were defined using the following criteria: |log2-fold change| >= 1 and adjusted p-val <= 0.05.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: HeLa infected

growth_protocol: HeLa cells were routinely passage each  2-3 days,  (typically  1 × 106 cells into a T75 flask)  ( Bellaterra, Spain)

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

treatment_protocol: Infected by Acinetobacter baumannii and each point infection time we clean and add trizol

value: HeLa

value: HeLa (ATCC CCL-2)

value: epithelial

tag: infection status

value: infected by Acinetobacter baumannii

tag: time


title: PBMC_mild_patient_subject1

value: mild

value: male


title: HeLa_infected_6h_2


title: MDA-MB-231-PCMV6XL5:ARRB2-Rep1

description: MDA-MB-231 cells transfected with PCMV6XL5:ARRB2 vector, biological replicate 1

value: mammary gland/breast; derived from metastatic site


title: WC_R3_240

first: Javier

last: Avalos

address: Av. Reina Mercedes sn

department: Genetics

institute: University of Seville

description: WC mutant 240 min illumination, replicate 3

data_processing:
Raw reads for all samples were trimmed, filtered and quality controlled with AfterQC (Chen et al., 2017; doi:10.1186/s12859-017-1469-3)
Read mapping to the reference genome was performed using Tophat 2.1.1 (https://ccb.jhu.edu/software/tophat/index.shtml)
Transcript assembly was performed using Cufflinks and Cuffmerge (Roberts, 2011; doi:10.1093/bioinformatics/btr355. http://cole-trapnell-lab.github.io/cufflinks/)
Mapped sequences were analyzed using SeqMonk (version 1.45.4, https://github.com/s-andrews/SeqMonk)
Quantification was performed using the RNAseq quantitation pipeline with the improved mRNA annotation generated by Cuffmerge, merging transcripts and counting reads over exons.
Deseq2 tool (Love et al., 2014; doi:10.1186/s13059-014-0550-8), implemented in SeqMonk, which needs raw counts for quantitation, was used to compare among conditions.
Genome_build: FMJU01;
https://www.ebi.ac.uk/ena/browser/view/FMJU01000001-FMJU01000086
Supplementary_files_format_and_content: Processed data are described in a single tab-delimited text file that includes raw counts for all samples, indicating probe, chromosome, start and end positions, and feature. Transcripts with no equivalent in FFUJ annotation are indicated as "null"

organism: Fusarium fujikuroi

source_name: WC mutant 240 min illumination

growth_protocol: the strains were grown in 100 ml of DG medium in 500 ml Erlenmeyer flasks, inoculated with 1000000 conidia. The flasks were kept in total darkness for three days at 30°C in an orbital shaker (150 rpm). Then, the cultures were transferred to four 25-ml Petri dishes under safe red light and kept in static conditions in the dark for 240 min. Subsequently, the Petri dishes were either kept in the dark or illuminated for 15, 60, or 240 min.

extract_protocol:
RNA samples were extracted with Trizol (Invitrogen, Paisley, UK) using the protocol described by the manufacturer
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Illumination was provided by a set of four fluorescent tubes (Philips TL-D 18 W/840) at a distance of 60 cm, yielding a light intensity of 7 W/m2.

tag: genotype/variation

value: null wcoA mutant

value: 240 min illumination

value: mycelium


title: 23_Chromium_3p_v3_lymphocyte_cell line_mix


title: 2hAux_42C1h_Pol2CST_AFF1AID_DLD_rep2

description: Pol2 ChIP-seq

value: AFF1-AID OsTIR1

value: Heat shock

value: Auxin


title: WC_R3_60

description: WC mutant 60 min illumination, replicate 3

source_name: WC mutant 60 min illumination

value: 60 min illumination


title: HeLa_infected_6h_1


title: WC_R3_15

description: WC mutant 15 min illumination, replicate 3

source_name: WC mutant 15 min illumination

value: 15 min illumination


title: SUM52_Ctrl

description: SUM52 cells without treatment.

value: Breast


title: 22_Chromium_3p_v3_lymphocyte_cell line_mix

description: 1:1:1:1 mixture of Jurkat, TALL104, EL4, IVA12 cells sequenced using the 10X Chromium 3' v3 kit targeting a capture of 3000 cells.

value: Jurkat, TALL104, EL4, IVA12 (1:1:1:1 mixture)


title: MDA-MB-231-PCMV6XL5:ARRB2-Rep2

description: MDA-MB-231 cells transfected with PCMV6XL5:ARRB2 vector, biological replicate 2


title: 2hH2O_42C1h_Pol2CST_AFF1AID_DLD_rep2

description: Pol2 ChIP-seq

value: Colorectal adenocarcinoma DLD-1

value: Rpb1 NTD (D8L4Y)


title: MDA-MB-231-PCMV6XL5:ARRB1-Rep2

description: MDA-MB-231 cells transfected with PCMV6XL5:ARRB1 vector, biological replicate 2


title: HeLa_infected_4h_3

value: HeLa

value: HeLa (ATCC CCL-2)

value: epithelial


title: 2hAux_37C1h_Pol2CST_AFF1AID_DLD_rep2

description: Pol2 ChIP-seq


title: PBMC_healthy_subject1

value: peripheral blood mononuclear cells (PBMCs)

value: healthy

value: male


title: WC_R3_0

description: WC mutant dark, replicate 3

source_name: WC mutant dark

value: null wcoA mutant

value: dark


title: 21_Chromium_3p_v3_lymphocyte_cell line_mix


title: MDA-MB-231-PCMV6XL5:ARRB1-Rep1

description: MDA-MB-231 cells transfected with PCMV6XL5:ARRB1 vector, biological replicate 1

value: mammary gland/breast; derived from metastatic site


title: SUM225_Ctrl

description: SUM225 cells without treatment.


title: PBMC_healthy_subject2


title: HeLa_infected_4h_2

value: infected by Acinetobacter baumannii


title: WC_R2_240

description: WC mutant 240 min illumination, replicate 2

value: 240 min illumination

value: mycelium


title: PBMC_mild_patient_subject2

value: mild


title: HeLa_infected_4h_1


title: 2hH2O_37C1h_Pol2CST_AFF1AID_DLD_rep2

description: Pol2 ChIP-seq

value: AFF1-AID OsTIR1


title: 6hKL1_20uM_42C1h_Pol2CST_AFF4AID_DLD_rep1

description: Pol2 ChIP-seq

value: AFF4-AID OsTIR1

value: Heat shock


title: WC_R2_60

description: WC mutant 60 min illumination, replicate 2

value: 60 min illumination


title: 6hDMSO_42C1h_Pol2CST_AFF4AID_DLD_rep1

description: Pol2 ChIP-seq

value: Colorectal adenocarcinoma DLD-1

value: Rpb1 NTD (D8L4Y)


title: HeLa_infected_2h_4

value: HeLa

value: HeLa (ATCC CCL-2)

value: epithelial


title: HeLa_infected_2h_3


title: HeLa_infected_2h_2


title: 6hKL1_20uM_37C1h_Pol2CST_AFF4AID_DLD_rep1

description: Pol2 ChIP-seq


title: WC_R2_15

description: WC mutant 15 min illumination, replicate 2

value: 15 min illumination


title: WC_R1_240

description: WC mutant 240 min illumination, replicate 1

value: null wcoA mutant


title: HeLa_control_3

source_name: HeLa control

value: not infected


title: HeLa_infected_2h_1


title: WC_R1_15

description: WC mutant 15 min illumination, replicate 1


title: 6hDMSO_37C1h_Pol2CST_AFF4AID_DLD_rep1

description: Pol2 ChIP-seq


title: 2hAux_37C1h_Pol2CST_DoubleAID_DLD_rep2

description: Pol2 ChIP-seq

value: AFF1/4-AID OsTIR1

value: Auxin


title: WC_R1_60

description: WC mutant 60 min illumination, replicate 1


title: HeLa_control_2


title: 2hAux_42C1h_Pol2CST_DoubleAID_DLD_rep2

description: Pol2 ChIP-seq


title: WC_R1_0

description: WC mutant dark, replicate 1

value: dark


title: 2hH2O_42C1h_Pol2CST_DoubleAID_DLD_rep2

description: Pol2 ChIP-seq


title: HeLa_control_1


title: ganai2_2

city: Beijing

first: Yuntao

last: Bing

address: No.49 Huayuan North Road

department: Department of General Surgery

institute: Peking University Third Hospital

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at The Agilent Feature Extraction Software (version 11.0.1.1) was used to analyze and extract array images. Quantile normalization and subsequent data processing were conducted in GeneSpring GX v12.1 software package (Agilent Technologies). Threshold defined as fold-change > 2.0 (Student’s t test, P < 0.05) was used as a volcano plot filtering for DE lncRNAs and mRNAs.

source_name: hepatocellular carcinoma

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Frozen tissues from ganai and normal patients were cryo pulverized using biopulverizer (Biospec) and homogenized with TRIzol (Invitrogen Life Technologies) by Mini-Bead-Beater-16 (Biospec). RNA was collected from each sample based on the manufacturer’s protocols.

treatment_protocol: The fresh tissues of patients were preserved at -80 degrees Celsius.

value: hepatocellular carcinoma


title: normal2_2

source_name: normal

value: normal


title: ganai2_1


title: 2hH2O_37C1h_Pol2CST_DoubleAID_DLD_rep2

description: Pol2 ChIP-seq


title: WT_R3_240

description: Wild type 240 min illumination, replicate 3

source_name: Wild type 240 min illumination

value: wild type

value: 240 min illumination

value: mycelium


title: WC_R2_0

description: WC mutant dark, replicate 2


title: ganai2_3


title: normal2_1


title: ganai1_3


title: normal2_3


title: 2hAux_42C1h_Pol2CST_DoubleAID_DLD_rep1

description: Pol2 ChIP-seq

value: Heat shock


title: SUM52-K599A

description: SUM52 cells transducted with the IRE1 dominant-negative K599A adenovirus

data_processing:
The 3' adaptor (TGGAATTCTCGGGTGCCAAGG) for sequencing was removed from the raw reads.
After removing the 3' adaptor, reads with length less than 10 were excluded. The remaining reads were mappable reads.
Mappable reads were aligned to genome using Tophat_v1.4.1.
The mRNA abundance was normalized and evaluated in Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using the Cuffdiff module of Cufflinks_v2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include test_id, nearest_ref_id, gene_locus, and FPKM values for each sample.
Supplementary_files_format_and_content: FPKM text files

source_name: Breast cancer cells

growth_protocol: SUM52 cell line is cultured in Ham's F-12 medium supplemented with 5% fetal bovine serum, fungizone (0.5 µg/mL), gentamicin (5 µg/mL), hydrocortisone (1 µg/mL) and insulin (5 µg/mL).

extract_protocol:
Total RNA was extracted with an RNeasy Plus Mini Kit in accordance with the manufacturer’s protocol (Qiagen, Hilden, Germany).
RNAs from SUM52 cells transducted with the IRE1 dominant-negative K599A, K907A, or control adenovirus were equally pooled (total 3 μg) and sequenced by LC Sciences. RNA was subjected to isolated poly(A) mRNA with poly-T oligo-attached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions were fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA). Approximately 1 µg of this RNA was prepared for Next Generation Sequencing using a version of the Illumina protocol, Directional_mRNA-Seq_SamplePrep_Guide_15018460_A.

treatment_protocol: SUM52 cells were infected by adenoviruses of the IRE1 dominant-negative K599A, K907A, or control GFP.

value: Luminal breast cancer cell line


title: ganai1_2


title: ganai1_1


title: normal1_3


title: WT_R3_15

description: Wild type 15 min illumination, replicate 3

source_name: Wild type 15 min illumination


title: SUM52-GFP

description: SUM52 cells transducted with the control GFP adenovirus


title: WT_R2_240

description: Wild type 240 min illumination, replicate 2


title: 2hH2O_42C1h_Pol2CST_DoubleAID_DLD_rep1

description: Pol2 ChIP-seq

value: Colorectal adenocarcinoma DLD-1

value: Rpb1 NTD (D8L4Y)


title: 02_Chromium_3p_v2_lymphocyte_cell line_mix

description: 1:1:1:1 mixture of Jurkat, TALL104, EL4, IVA12 cells sequenced using the 10X Chromium 3' v2 kit targeting a capture of 2000 cells.

value: Jurkat, TALL104, EL4, IVA12 (1:1:1:1 mixture)


title: normal1_1


title: WT_UV_rep1

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

description: UbH2B_Distribution_Above100kbGenes_averages.xlsx

data_processing:
Reads were aligned to the Human Genome 38 (Hg38) using bwa-mem tools (Li, 2013) during which only high-quality reads (> q30) were included in the analyses and duplicates were removed. Bam files were converted into TagDirectories using HOMER tools (Heinz et al., 2010). Binding profiles around TSSs were defined using the AnnotatePeaks.pl tool of HOMER using the default normalization to 10mln reads. Individual datasets were subsequently processed in R (Team, 2019).
Supplementary_files_format_and_content: excel tables providing averaged ubH2B binding versus distance from the TSS for genes

extract_protocol: ChIP-seq: Chromatin was sonicated to approximately 1 nucleosome using a Bioruptor waterbath sonicator (Diagenode). Chromatin of ~5x106 cells was incubated with 3ug antibody (RNAPII, rabbit polyclonal, Bethyl laboratories, A304-405A; PAF1, rabbit polyclonal, Bethyl laboratories, A300-172A) over night at 4°C, followed by a 1.5 hrs protein-chromatin pull-down with a 1:1 mix of protein A and protein G Dynabeads (Thermo Fisher; 10001D and 10003D). ChIP samples were washed extensively, followed by decrosslinking for 4 hrs at 65°C in the presence of proteinase K. DNA was purified using a Qiagen MinElute kit. Sample libraries were prepared using Hifi Kapa sample prep kit and A-T mediated ligation of Nextflex or xGen UDI-UMI adapters. Samples were sequenced using an Illumina NextSeq500 or HiSeqX, using paired-end sequencing with 42 bp or 151 bp from each end. BrU-seq: cDNA libraries were made from the Bru-labeled RNA using the Illumina TruSeq library kit and paired-end 151 bp sequenced using the Illumina NovaSeq platform at the University of Michigan DNA Sequencing Core. Only single-end sequencing data was used for downstream analyses

tag: chip-antibody

value: UbH2B (D11); Cell signalling (#5546)

tag: uv-c dose

tag: time point

value: 8 hours

value: WT


title: WT_mock_rep2

value: no UV

value: not applicable


title: 2hAux_42C1h_Pol2CST_BRD4AID_DLD_rep3

description: Pol2 ChIP-seq

value: BRD4-AID OsTIR1

value: Auxin


title: WT_UV_rep2


title: normal1_2


title: 01_Chromium_3p_v2_lymphocyte_cell line_mix

description: 1:1:1:1 mixture of Jurkat, TALL104, EL4, IVA12 cells sequenced using the 10X Chromium 3' v2 kit targeting a capture of 5000 cells.


title: WT_R1_240

description: Wild type 240 min illumination, replicate 1


title: SUM52-K907A

description: SUM52 cells transducted with the IRE1 dominant-negative K907A or control adenovirus


title: EL4

data_processing:
Gene expression data were quantified using featureCounts v1.6.3.
Genome_build: Data was aligned to a “cellRanger_1.2.0” referenced composed of hg19 with Ensembl 82 and mm10 with Ensembl 84 using STAR v2.5.1b.
Supplementary_files_format_and_content: 4cell_fpkm.csv

extract_protocol:
Qiagen RNeasy Mini kit
TruSeq Stranded mRNA


title: IVA12


title: 2hDMSO_42C1h_Pol2CST_BRD4AID_DLD_rep2

description: Pol2 ChIP-seq


title: WT_mock_rep1


title: 2hH2O_37C1h_Pol2CST_DoubleAID_DLD_rep1

description: Pol2 ChIP-seq

value: AFF1/4-AID OsTIR1


title: 2hAux_42C1h_Pol2CST_BRD4AID_DLD_rep2

description: Pol2 ChIP-seq


title: 2hAux_37C1h_Pol2CST_DoubleAID_DLD_rep1

description: Pol2 ChIP-seq


title: FAK-kd1

city: Edinburgh

first: Billie

middle: Georgina Cooper

last: Griffith

address: Crewe road south

department: IGMM, ECRC

country: United Kingdom

institute: University of Edinburgh

data_processing:
ATAC-seq reads were aligned to the mm10 genome assembly using the bcbio ATAC-seq pipeline with default settings
Peaks were called using MACS version 2.1.1 with the following parameters: -B --broad -q 0.05 --nomodel --shift -100 --extsize 200 -g 1.87e9
Genome_build: mm10
Supplementary_files_format_and_content: peak text files

source_name: Sqaumouos cell carcinoma cell

growth_protocol: FAK-/- and FAK-WT-, FAK-nls- and FAK-kd-expressing SCC cell lines were cultured at 37°C, 5% CO2, in 1× Glasgow minimum essential medium (MEM) supplemented with 10% fetal bovine serum, 1% MEM non-essential amino acids, 1% sodium pyruvate, 1% L-glutamine and 1% MEM vitamins (all from Sigma-Aldrich).

extract_protocol:
Accessible chromatin was digested with Tn5 transposase as described in Brunton et al., 2020.
DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: SCCs were induced in K14CreER FAKflox/flox FVB mice by DMBA/TPA two-stage cutaneous chemical carcinogenesis protocol (McLean et al., 2004). SCCs cells were  isolated and cultured in the presence of 4-hydroxytamoxifen to induce FAK deletion (Serrels et al., 2012). A FAK kinase-dead (FAK-kd, K454R) construct was re-expressed using retrovirial transduction.

tag: cell type

value: Cutaneous sqaumouos cell carcinoma cell

tag: driver gene

value: Ha-Ras

value: K14CreER FAKflox/flox


title: WT_R2_15

description: Wild type 15 min illumination, replicate 2

value: wild type

value: 15 min illumination

value: mycelium


title: 2hH2O_42C1h_Pol2CST_BRD4AID_DLD_rep3

description: Pol2 ChIP-seq

tag: cell line

value: Colorectal adenocarcinoma DLD-1

tag: genotype

value: Heat shock


title: FAK-kd2

value: FAK kinase-dead (FAK-kd, K454R) construct was re-expressed


title: CSB_UV_rep2

source_name: U2OS CSB-KO

value: UbH2B (D11); Cell signalling (#5546)

value: CSB-KO


title: FAK-nls2

treatment_protocol: SCCs were induced in K14CreER FAKflox/flox FVB mice by DMBA/TPA two-stage cutaneous chemical carcinogenesis protocol (McLean et al., 2004). SCCs cells were  isolated and cultured in the presence of 4-hydroxytamoxifen to induce FAK deletion (Serrels et al., 2012). A FAK nuclear localization-deficient (FAK-nls, R177A/R178A/R190A/R191A/R216A/R218A) construct was re-expressed using retroviral transduction


title: CSBKO_UV_INPUT

value: 8 hours


title: 2hAux_42C1h_Pol2CST_BRD3AID_DLD_rep2

description: Pol2 ChIP-seq

value: BRD3-AID OsTIR1

tag: chip antibody

value: Rpb1 NTD (D8L4Y)


title: CSB_UV_rep1


title: WT_R1_15

description: Wild type 15 min illumination, replicate 1

tag: tissue


title: 2hH2O_42C1h_Pol2CST_BRD4AID_DLD_rep2

description: Pol2 ChIP-seq

value: BRD4-AID OsTIR1


title: FAK-nls1

value: FAK nuclear localization-deficient (FAK-nls, R177A/R178A/R190A/R191A/R216A/R218A) construct was re-expressed


title: 2hH2O_42C1h_Pol2CST_BRD3AID_DLD_rep2

description: Pol2 ChIP-seq


title: FAK-/-1

treatment_protocol: SCCs were induced in K14CreER FAKflox/flox FVB mice by DMBA/TPA two-stage cutaneous chemical carcinogenesis protocol (McLean et al., 2004). SCCs cells were  isolated and cultured in the presence of 4-hydroxytamoxifen to induce FAK deletion (Serrels et al., 2012).

value: control


title: AM21

city: New York

first: Genome Technology Center

last: (GTC)

address: 550 First Avenue

institute: NYU Langone Health

data_processing:
Basecalling and demultiplexing were performed using the Illumina bcl2fastq software (v2.20)
Sequenced reads were mapped to the mm10 reference genomce using STAR (v2.7.3a)
featureCounts (Subread package v1.6.3) was used to generate the matrix of read counts for annotated genomic features
The DESeq2 package (R v3.6.1) in the R statistical programming environment was utilized to calculate differential gene statistical comparisons
Genome_build: mm10
Supplementary_files_format_and_content: CSV file containing normalized matrix of read counts which includes values for all features and all samples

source_name: mouse lung adenocarcinoma (subcutaneous)

extract_protocol: Automated Illumina TruSeq Stranded Total RNA Sample Prep Kit with RiboZero Gold (Cat. No. RS-122-2301)

value: KPKshEmsy


title: FAK-/-2

value: Cutaneous sqaumouos cell carcinoma cell

value: Ha-Ras


title: 2hAux_42C1h_Pol2CST_BRD2AID_DLD_rep2

description: Pol2 ChIP-seq

value: BRD2-AID OsTIR1

value: Auxin


title: AM20


title: CSB_mock_rep1

value: no UV

value: not applicable


title: FAK-WT2

treatment_protocol: SCCs were induced in K14CreER FAKflox/flox FVB mice by DMBA/TPA two-stage cutaneous chemical carcinogenesis protocol (McLean et al., 2004). SCCs cells were  isolated and cultured in the presence of 4-hydroxytamoxifen to induce FAK deletion (Serrels et al., 2012). A FAK-WT construct was re-expressed using retroviral transduction.

value: K14CreER FAKflox/flox

value: FAK-WT construct was re-expressed


title: sciMAP Mouse Ischemia

city: Portland

first: Andrew

last: Adey

state: OR

address: 3181 S.W. Sam Jackson Park Rd, RHH, L103

department: MMG

institute: Oregon Health & Science University

data_processing:
scitools fastq-dump to generate index-matched fastq files
bwa mem to align to respective genome (mm10 for mouse, hg38 for human)
scitools count to generate count matrixes
cistopic v3 for dimensionality reduction
Genome_build: mm10 for mouse, hg38 for human
Supplementary_files_format_and_content: Count matrixes in sparse matrix format with row and column files along with a triplet matrix values file
Supplementary_files_format_and_content: Aggregate metadata is a csv file with additional informaiton on all cells

source_name: Mouse whole brain - cryosectioned

extract_protocol:
Nuclei isolation using sciMAP-ATAC protocols
sci-ATAC-seq protocol
sciMAP-ATAC and sci-ATAC-seq

value: whole brain - cryosectioned

tag: region

value: Whole brain

tag: exposure

value: MCAO stroke model


title: 2hDMSO_42C1h_Pol2CST_WT_DLD_rep1

description: Pol2 ChIP-seq

value: Colorectal adenocarcinoma DLD-1

value: Heat shock


title: 2hH2O_42C1h_Pol2CST_BRD2AID_DLD_rep2

description: Pol2 ChIP-seq

value: Rpb1 NTD (D8L4Y)


title: AM19


title: AM18

value: KPKshCTRL


title: sciMAP Mouse SSp

value: SSp

tag: strain


title: FAK-WT1


title: TALL104


title: 2hH2O_42C1h_Pol2CST_WT_DLD_rep3

description: Pol2 ChIP-seq

tag: growth temperature


title: sciMAP Mouse Brain


title: Jurkat

source_name: Jurkat

value: Jurkat


title: CSB_mock_rep2

value: UbH2B (D11); Cell signalling (#5546)

value: CSB-KO


title: AM9

tag: treatment

value: KPshEmsy


title: EOM1-109

city: Baltimore

first: Dong Won

middle: Thomas

last: Kim

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

institute: Johns Hopkins University

description: bulk RNA-Seq

data_processing:
Bulk RNA-Seq (mouase): The RNA-seq reads were mapped against the mouse reference genome (build 37) using TopHat2. The aligned reads were assembled into transcripts, and gene expression was calculated using. The expression level of genes was determined based on the value of fragments per kilobase per million (FPKM), which was calculated as the number of fragments mapped to the transcripts of one gene divided by the transcript length and the number of total mapped reads in one sample. The differentially expressed genes were identified using Cufflinks (Fold change>4, FDR<0.01). Principal component analysis was carried out with the web tool ClustVis.
Bulk RNA-Seq (human): Illumina adapters of libraries after sequencing were removed using Cutadapt (v1.18)  with default parameters. Libraries were then aligned to GRCh38 using STAR (v2.42a)  with –twopassMode Basic. RSEM (v1.3.1)  was used for transcript quantification, with rsem-calculate-expression (--forwad-prob 0.5). TPM value from RSEM was used to plot white, beige, or brown adipocytes-enriched markers using ggplot (v3.32).
Genome_build: Mouse: Tophat2 mouse reference genome (build 37)
Genome_build: Human: GRCh38

source_name: Replicate 3

extract_protocol: Nine-week old CD-1 mice were euthanized and their OF, inguinal, epididymal, and brown fat isolated.  Human orbital fat was obtained using using a protocol approved by the Institutional Review Board. RNA was extracted from each fat depot using Trizol and RNeasy mini kits. RNA sequencing performed using Illumina Nextseq500.

value: Extra occular muscle

tag: age

value: 9 weeks old

tag: Sex

value: Male


title: M. albugensis + A. laibachii + SynCom Peeled Rep3

city: Cologne

first: Gunther

last: Doehlemann

address: Zülpicher Straße 47a

department: CEPLAS / Institute of Botany

country: Germany

institute: University of Cologne

data_processing:
Sequencing read quality control was performed using FastQC version 0.11.5
Sequenced reads were mapped to the genome of M. albugensis using tophat v2.0.10
Read counts per gene were extracted by using HTSeq version 0.9.0
Genome_build: Moesziomyces albugensis WT v.2 (currently in submission).
Supplementary_files_format_and_content: tab delimited .txt file with raw read counts for each predicted M. albugensis transcript, samples in columns

molecule: polyA RNA

organism:
Arabidopsis thaliana
Albugo laibachii
Moesziomyces sp. GD-2020a

source_name: Latex-peeled microbes from plant leaves, 4dpi

growth_protocol: For axenic culture samples and prior to inoculation M. albugensis was grown in liquid YEPSlight medium at 22°C and 200rpm. Bacterial SynCom member were grown in KingsB media under the same conditions. A. thaliana seedlings were grown under short day conditions (22°C/18°C 8h day/16h night).

extract_protocol:
Four weeks old A. thaliana plants were fixed and liquid latex was applied to the leaf surface. The latex was dried using the cold air option of a hair dryer, carefully peeled off  and immediately frozen in liquid nitrogen. Afterwards the frozen latex pieces were grinded with liquid nitrogen and the RNA was isolated by using Trizol® Reagent (Invitrogen) according to the manufacturer’s instructions.DNA contaminations were removed by using Turbo DNA-Free™ Kit (Ambion).
RNA libraries were prepared by the CCG (Cologne genome center) using standard Illumina protocols

treatment_protocol: 3-weeks old seedlings were spray inoculated, each with 500µl of M. albugensis/ SynCom members (OD600 0.6) solved in MgCl2. After two days plants are challenged with the oomycete pathogen A. laibachii. Therefore zoospores were harvested from infected plants, washed and set to a spore number of 16*10^4 spores/ml. 500µl are evenly sprayed to each plant. Plants that are not infected with the pathogen were sprayed with MgCl2. All samples were incubated at 4°C over night with 100% humidity and moved to the growth chamber on the next day. 24h after moving samples were harvested.

tag: host plant cultivar

tag: biotic interaction

value: M. albugensis, A. thaliana, A. laibachii, bacterial SynCom

value: Latex-peeled microbes from plant leaves


title: 2hAux_37C1h_Pol2CST_BRD4AID_DLD_rep3

description: Pol2 ChIP-seq

value: BRD4-AID OsTIR1

value: Auxin


title: M. albugensis + A. laibachii + SynCom Peeled Rep2


title: AM17


title: 2hAux_37C1h_Pol2CST_BRD4AID_DLD_rep2

description: Pol2 ChIP-seq


title: M. albugensis + A. laibachii + SynCom Peeled Rep1


title: AM16


title: 2hH2O_37C1h_Pol2CST_BRD4AID_DLD_rep2

description: Pol2 ChIP-seq


title: M. albugensis + A. laibachii Peeled Rep3

value: M. albugensis, A. thaliana, A. laibachii


title: AM8


title: OF2-914

description: bulk RNA-Seq

value: Orbital fat


title: M. albugensis + A. laibachii Peeled Rep2


title: 2hAux_37C1h_Pol2CST_BRD3AID_DLD_rep2

description: Pol2 ChIP-seq

value: Colorectal adenocarcinoma DLD-1

value: BRD3-AID OsTIR1


title: AM2

value: KPshCTRL


title: OF1-914

description: bulk RNA-Seq

source_name: Replicate 2


title: sciATAC Mouse Brain

source_name: Mouse whole brain

value: whole brain

value: Whole brain


title: OF1

description: bulk RNA-Seq

source_name: Replicate 1


title: 2hH2O_37C1h_Pol2CST_WT_DLD_rep3

description: Pol2 ChIP-seq

value: Rpb1 NTD (D8L4Y)


title: EOM2-822

description: bulk RNA-Seq


title: 2hH2O_37C1h_Pol2CST_BRD3AID_DLD_rep2

description: Pol2 ChIP-seq


title: AM1


title: AM3


title: M. albugensis + A. laibachii Peeled Rep1


title: EOM1-822

description: bulk RNA-Seq


title: IF2-920

description: bulk RNA-Seq

value: Inguinal fat


title: M. albugensis Axenic Rep3

organism: Moesziomyces sp. GD-2020a

source_name: fungal axenic culture

value: fungal axenic culture


title: 2hAux_37C1h_Pol2CST_BRD2AID_DLD_rep2

description: Pol2 ChIP-seq

value: BRD2-AID OsTIR1


title: IF2

description: bulk RNA-Seq

value: 9 weeks old


title: AM7

value: KPshEmsy


title: 2hH2O_37C1h_Pol2CST_BRD2AID_DLD_rep2

description: Pol2 ChIP-seq


title: 2hDMSO_37C1h_Pol2CST_BRD4AID_DLD_rep2

description: Pol2 ChIP-seq


title: M. albugensis Axenic Rep1


title: M. albugensis Axenic Rep2


title: EF3

description: bulk RNA-Seq

value: Epididymal fat

value: Male


title: 2hdBET6_37C1h_Pol2CST_WT_DLD_rep1

description: Pol2 ChIP-seq


title: 2hDMSO_37C1h_Pol2CST_WT_DLD_rep1

description: Pol2 ChIP-seq


title: R-23od-B: white light for 8weeks

first: Yingying

last: Wen

address: 79 Qingchun Road

department: Department of Ophthalmology

institute: First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China

data_processing:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
The RNeasy Mini Kit (Qiagen) was used to isolate RNA from tissues according to the manufacturer’s instructions
The RNA was quantified with spectrophotometry on a Nanodrop (Thermo Fisher Scientific, Grand Island, NY), and 260/280 ratios for all sample ranged from 2.11-2.13
The RNA Integrity Number (RIN = 9.0-10.0) was then evaluated on an  Agilent Bioanalyzer (Agilent, Santa Clara, CA).
the RNA-seq was performed by Genesky Biotechnologies (Shanghai, China). Briefly, 1 g of purified retinal RNA was used to construct Illumina sequencing libraries using the Illumina (San Diego, CA) TruSeq Stranded Total RNA LT kit.
Genome_build: Genome_build: cavPor3
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

organism: Cavia porcellus

source_name: retina

growth_protocol: Forty-five male tri-color guinea pigs (Dunkin-Hartley strain, 2 weeks old) were obtained from the laboratory of Zhejiang Academy of Medical Sciences.

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
The libraries were sequenced on an Illumina HiSeq 2500 (Illumina,  144 CA, USA) with paired end reads.

treatment_protocol: In this study, guinea pigs were randomly divided into 3 groups that received different lighting conditions (12:12 light cycle) for 8 weeks:

value: retina

value: 12 weeks

value: receive white light for 8weeks


title: EF2

description: bulk RNA-Seq


title: 6os: white light for 8weeks


title: EF1

description: bulk RNA-Seq


title: PAFAID_24hUV_2 nascent RNA (BrU-seq)

data_processing:
Library strategy: BrU-seq
ChIP-seq: Reads were aligned to the Human Genome 38 (Hg38) using bwa-mem tools (Li, 2013) during which only high-quality reads (> q30) were included in the analyses and duplicates were removed. Bam files were converted into TagDirectories using HOMER tools (Heinz et al., 2010). Binding profiles within selected areas of individual genes (e.g. around TSS or TTS), were defined using the AnnotatePeaks.pl tool of HOMER using the default normalization to 10mln reads. Metagene profiles were defined using the makeMetaGeneProfile.pl tool of HOMER, using default settings. Individual datasets were subsequently processed in R (Team, 2019). BrU-seq: Data was processed as previously described (Paulsen et al., 2014).  Briefly, reads were pre-filtered by alignment to the human ribosomal repeating subunit (GenBank U13369.1) and human mitochondrial genome (chrM) from the hg38 reference genome using bowtie2 v.2.3.3.1. The remaining reads were mapped to the hg38 reference genome using STAR v2.7.0f. Base coverages were used to compute read counts for features, such as genes and bins, which were then normalized to feature length and number of uniquely-mapped reads (RPKM method). Gene selection was based on the following criteria: length as indicated per figure, TSS is at least 10kb apart, expression is at least 0.05 RPKM. The median expression was calculated for each 500 bp bins from 5kb upstream until 100kb downstream of the selected genes for each time-point.
Genome_build: hg38
Supplementary_files_format_and_content: excel tables providing avearged read coverage around the TSS or normalized traverling ratios for the top 3000 genes for each individual sample, and the BrU-seq counts versus distance from the TSS for genes of 25-50Kb, 50-100Kb and >100Kb

source_name: U2OS OsTIR1 + PAF-AID14

growth_protocol: DMEM GlutaMAX +10% Fetal Calf Serum + antibiotics

extract_protocol:
ChIP-seq: Cells were plated and grown to ~90% confluency and crosslinked with 0.5 mg/mL disuccinimidyl glutarate (DSG; Thermo Fisher) in PBS for 45 min at room temperature. Cells were washed with PBS and crosslinked with 1 % PFA for 20 min at room temperature. Fixation was stopped by adding 1.25 M Glycin in PBS to a final concentration of 0.1 M for 3 minutes at room temperature. Cells were washed with cold PBS and lysed and collected in a buffer containing 0.25% Triton X-100, 10 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6). Chromatin was pelleted in 5 min at 400 g and incubated in a buffer containing 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 50 mM Hepes (pH 7.6) for 10 minutes at 4°C. Chromatin was again pelleted for 5 min at 400 g and resuspended in ChIP-buffer (0.15 % SDS, 1 % Triton X-100, 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6)) to a final concentration of 15x106 cells/ml. BrU-seq: U2OS osTIR1 or PAF1-AID cells were induced with doxycycline for 24 hrs, and subsequently with auxin for 5 hrs. After this treatment, cells were either mock-treated or irradiated with UV-C light (7 J/m2). Cells were then incubated in conditioned media for different periods of time (0, 3, 8, 24h) before being incubated with 2 mM bromouridine (Bru) at 37°C for a 30 min. The cells were then lysed in TRIzol reagent (Invitrogen) and Bru-containing RNA isolated as previously described (Andrade-Lima et al., 2015).
ChIP-seq: Chromatin was sonicated to approximately 1 nucleosome using a Bioruptor waterbath sonicator (Diagenode). Chromatin of ~5x106 cells was incubated with 3ug antibody (RNAPII, rabbit polyclonal, Bethyl laboratories, A304-405A; PAF1, rabbit polyclonal, Bethyl laboratories, A300-172A) over night at 4°C, followed by a 1.5 hrs protein-chromatin pull-down with a 1:1 mix of protein A and protein G Dynabeads (Thermo Fisher; 10001D and 10003D). ChIP samples were washed extensively, followed by decrosslinking for 4 hrs at 65°C in the presence of proteinase K. DNA was purified using a Qiagen MinElute kit. Sample libraries were prepared using Hifi Kapa sample prep kit and A-T mediated ligation of Nextflex adapters. Samples were sequenced using an Illumina NextSeq500, using paired-end sequencing with 42 bp from each end. BrU-seq: cDNA libraries were made from the Bru-labeled RNA using the Illumina TruSeq library kit and paired-end 151 bp sequenced using the Illumina NovaSeq platform at the University of Michigan DNA Sequencing Core. Only single-end sequencing data was used for downstream analyses

treatment_protocol: DNA damage was induced by irradiating cells with varying doses of UV-C as indicated per sample; samples were assayed at different time-periods after UV treatment as indicated per sample; to deplete PAF1 using the auxin-inducible degron system cells were induced with 2ug/ml doxycycline for 24 hrs and pre-treated with 500uM auxin for 5hours prior to UV-C irradiation or harversting.

tag: genotype/variation

value: OsTIR1 + PAF-AID14

tag: uv-c dose

tag: time after uv-c

value: 24 hours

tag: pre-treatment

value: 24hrs treatment with 2ug/ml Doxycycline, followed by 500uM auxin for 5-6hrs

tag: molecule subtype

value: nascent RNA (BrU-labeled)


title: 6od: white light for 8weeks


title: PBMC_healthy_subject3

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 15 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

source_name: PBMC, HC

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

tag: disease

value: healthy

tag: gender

value: male


title: PAFAID_8hUV_2 nascent RNA (BrU-seq)

value: 8 hours


title: CUG960 +dox, PN1 induction [V123V]

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

data_processing:
Fastq files were aligned to mm10 mouse reference genome (GRCm38.39) and per-gene counts quantified by RSEM (1.3.1)
based on the gene annotation Mus_musculus.GRCm38.89.chr.gtf. Differentially expressed genes are called with
false discovery rate (FRD) < 0.05 using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: txt file with read counts of genes in each sample

source_name: Ventricle

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

value: FvB

value: 10 weeks

tag: genotype

value: Female


title: CUG960 +dox, PN1 induction [V119V]


title: CUG960 +dox, PN1 induction [V120V]


title: CUG960 +dox, PN1 induction [V119A]

source_name: Atria


title: CUG960 +dox, PN1 induction [V120A]


title: MHCrtTA control +dox, PN1 induction [V334V]

value: MHCrtTA(hemi)


title: BF3

description: bulk RNA-Seq

tag: tissue

value: Brown fat

value: 9 weeks old


title: BF2

description: bulk RNA-Seq

tag: strain

value: Male


title: 32os: blue light for 8weeks

value: retina

value: 12 weeks

value: receive blue light for 8weeks


title: PAFAID_3hUV_2 nascent RNA (BrU-seq)

value: OsTIR1 + PAF-AID14

value: 3 hours


title: 32od: blue light for 8weeks


title: MHCrtTA control +dox, PN1 induction [V333V]


title: PAFAID_noUV_2 nascent RNA (BrU-seq)

value: no UV

value: not applicable

value: 24hrs treatment with 2ug/ml Doxycycline, followed by 500uM auxin for 5-6hrs

value: nascent RNA (BrU-labeled)


title: IF1

description: bulk RNA-Seq

value: Inguinal fat


title: 2R-23od: blue light for 8weeks


title: CUG960 +dox, PN1 induction [V123A]

value: FvB


title: PAFAID_24hUV_1 nascent RNA (BrU-seq)

value: 24 hours


title: 16os: green light for 8weeks

value: receive green light for 8weeks


title: MHCrtTA control +dox, PN1 induction [V334A]

value: 10 weeks

value: MHCrtTA(hemi)

value: Female


title: PAFAID_8hUV_1 nascent RNA (BrU-seq)

value: 8 hours


title: 11od: green light for 8weeks

value: retina


title: 2hH2O_37C1h_Pol2CST_BRD4AID_DLD_rep3

description: Pol2 ChIP-seq

data_processing:
For ChIP-seq, single-end raw reads were trimmed by Trimmomatic 0.33 (Bolger et al., 2014) and aligned to hg19 using Bowtie version 1.1.2, allowing only uniquely mapping reads with up to two mismatches within the 50 bp read. The resulting reads were extended to 150 bp toward the interior of the sequenced fragment, normalized to total reads aligned (reads per million, rpm), and formatted as bigWig-coverage tracks using GenomicRanges.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files with normalized read counts were provided for all samples.

extract_protocol:
For ChIP-seq, 20-50 million cells were crosslinked with 1% paraformaldehyde (Electron Microscopy Sciences) in PBS for 10 min at r.t. Chromatin was sonicated with the Covaris E220 for 4 min with 10% duty cycle, 140 peak intensity power, 200 cycles per burst. Immunoprecipitations were carried out with antibodies and Protein A/G-agarose beads (Santa Cruz) or Dynabeads Protein G (Invitrogen).
For ChIP-seq, DNA libraries were prepared by the HTP Library Preparation Kit for Illimina (KAPA) and sequenced on the NextSeq 500 or NovaSeq 6000 (Illumina).

tag: cell line

value: Colorectal adenocarcinoma DLD-1

value: BRD4-AID OsTIR1

tag: chip antibody

value: Rpb1 NTD (D8L4Y)


title: MHCrtTA control +dox, PN1 induction [V327A]

tag: age


title: Tumorsphere LM9KO_1

city: Basel

first: Mohamed

last: Bentires-Alj

address: Hebelstrasse 20

department: DBM

country: Switzerland

institute: University Hospital Basel

data_processing:
Standard Illumina software was used for base calling
Reads were aligned on the mm10 mouse genome (TxDb.Mmusculus.UCSC.mm10.knownGene package) using the STAR Aligner.
Genome_build: mm10

source_name: breast cancer cell line

growth_protocol: LM1, LM9, LM1 Nfib KO, and LM9 Nfib KO cells were plated in ultra-low attachment plates (Corning) for six days at 10,000 cells per mL in DMEM:F12 supplemented with 1x B27 (Gibco, Invitrogen), 20 ng/mL human or mouse EGF (PeproTech), 20 ng/mL basic FGF (PeproTech), and 1x penicillin/ streptomycin (Gibco, Invitrogen). Primary tumourspheres were dissociated with 0.05% trypsin and collected.

extract_protocol:
Total RNA was extracted using a Qiagene, RNeasy Plus Mini kit (cat. number 74136)
The library was prepared using Illumina TruSeq stranded mRNA-seq preparation kit (according to recommendations from the manufacturer)

tag: breast cancer model


title: 11od-B: green light for 8weeks

value: 12 weeks

tag: treatment


title: PAFAID_3hUV_1 nascent RNA (BrU-seq)

value: OsTIR1 + PAF-AID14

value: 3 hours


title: C3

city: Shanghai

first: Ningxin

last: Qin

address: 910, Hengshan Road

institute: The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China

data_processing:
Data analysis were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China). The raw data was delieved into NCBI’s Gene Expression Omnibius. Sequenced reads were trimmed for low quality sequence with skewer (v0.2.2). Data quality was checked by FastQC (v0.11.5). Clean read were mapped to the mus musculus genome with STAR (2.5.3a). The expression of the transcript was calculate by FPKM with StringTie (v1.3.1c). The differentially expression genes (DEGs) were determined using DESeq2 (v1.16.1). The thresholds for determining DEGs are P < 0.05 and absolute fold change ≥ 2.
Genome_build: mus musculus genome
Supplementary_files_format_and_content: tab-delimited text fils include FPKM values for each Sample

source_name: concieved by IVF-FET_liver

extract_protocol:
Liver tissue was removed from 20-week-old mice after 4 h of fasting.  Total RNA was isolated from livers using TRIzol reagent (Invitrogen, Carlsbad, CA, USA).
The quality of total RNA was confirmed by agarose gel electrophoresis, and RNA was used for the construction of a cDNA library. The sequencing of cDNA was conducted on an Illumina Nova6000 system and performed by Genergy biological technology Co., Ltd. (Shanghai, China).

value: 20 weeks old

value: concieved by IVF-FET

value: liver


title: Tumorsphere LM9_1


title: C4


title: MHCrtTA control +dox, PN1 induction [V327V]

value: FvB

tag: Sex


title: MHCrtTA control +dox, PN1 induction [V333A]


title: Tumorsphere LM9_3


title: TIR1_24hUV_2 nascent RNA (BrU-seq)

source_name: U2OS OsTIR1 control

tag: genotype/variation

value: OsTIR1 control

value: 24 hours

value: 24hrs treatment with 2ug/ml Doxycycline, followed by 500uM auxin for 5-6hrs

value: nascent RNA (BrU-labeled)


title: TIR1_8hUV_2 nascent RNA (BrU-seq)

tag: uv-c dose


title: Tumorsphere LM9_2


title: Tumorsphere LM1KO_3


title: ATRA-treated E-type cell line

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

description: Gene expression of E-type bladder cancer cell line treated with all-trans retinoic acid (20uM, 4days)

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: ATRA-treated E-type bladder cancer cell line

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: BOY12E, JMSU1, T24 and 5637 cell lines were cultured under supplier‐recommended conditions (for details, visit http://cell.brc.riken.jp/en/). HuB6 and HuB15 were cultured using Dulbecco's Modified Eagle Medium.

extract_protocol: Total RNA was isolated with RNA iso plus (similar to TRIzol).

treatment_protocol: Concentration of all-trans-retinoic acid against each cell line was determined by morphological change and half maximal inhibitory concentration (IC50) for cell death.

value: urothelial carcinoma

tag: emt status

value: Epithelial Retained

tag: atra treatment

value: All-trans-retinoic acid (20uM, 4days)


title: Tumorsphere LM9KO_2


title: BF1

description: bulk RNA-Seq

value: Brown fat

value: 9 weeks old

value: Male


title: B4

source_name: concieved by IVF-ET_liver

value: concieved by IVF-ET


title: HuB15RA

description: Gene expression of E-type bladder cancer cell line treated with all-trans retinoic acid (2.5uM, 6days)

value: All-trans-retinoic acid (2.5uM, 6days)


title: HuB6RA

description: Gene expression of E-type bladder cancer cell line treated with all-trans retinoic acid (5uM, 5days)

value: All-trans-retinoic acid (5uM, 5days)


title: TIR1_noUV_2 nascent RNA (BrU-seq)

value: no UV

tag: time after uv-c

value: not applicable

tag: pre-treatment

tag: molecule subtype


title: Tumorsphere LM1KO_1


title: TIR1_24hUV_1 nascent RNA (BrU-seq)

tag: cell type


title: PAFAID_noUV_1 nascent RNA (BrU-seq)

value: OsTIR1 + PAF-AID14


title: B3

value: 20 weeks old

value: liver


title: 5637

description: Gene expression of E-type bladder cancer cell line

source_name: E-type bladder cancer cell line


title: Tumorsphere LM9KO_3


title: B2


title: TIR1_8hUV_1 nascent RNA (BrU-seq)

value: OsTIR1 control

value: 8 hours


title: A5

source_name: natural conceieved_liver

value: natural conceieved


title: TIR1_noUV_1 nascent RNA (BrU-seq)

value: 24hrs treatment with 2ug/ml Doxycycline, followed by 500uM auxin for 5-6hrs

value: nascent RNA (BrU-labeled)


title: Tumorsphere LM1_2


title: HubB15

value: urothelial carcinoma

value: Epithelial Retained


title: A1


title: HuB6


title: csf1ra-A-2

status: Public on Jan 14 2021

city: Tianjin

first: Yue

last: Shang

address: Tianjin Key Laboratory of Tumor Microenvironment and Neurovascular Regulation, Department of Pathology, Nankai University School of Medicine, Tianjin 300071, China

institute: Nankai University

data_processing:
Quality Control:In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Trimmomatic (v0.30) to be high quality clean data.
Mapping:Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Expression analysis:In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis:Differential expression analysis used the DESeq Bioconductor package, a model based on the negative binomial distribution. After adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate, P-value of genes were setted <0.05 to detect differential expressed ones.
GO and KEGG enrichment analysis
:GO-TermFinder was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant p-value less than 0.05.
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances (http://en.wikipedia.org/wiki/KEGG). We used scripts in house to enrich significant differential expression gene in KEGG pathways.
Novel transcripts prediction:After assembling a transcriptome from one or more samples, Cuffcompare, a tool of Cufflinks v2.2.1, compared assembly to known transcripts. Then, novel transcripts can be predicted via results of Cuffcompare.
Alternative splicing analysis:Asprofile v1.0 is a suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data. It took a GTF transcript file created by Cufflinks as its input.
SNV analysis:Samtools v0.1.18 with command mpileup and Bcftools v0.1.19 were used to do SNV calling.
Genome_build: GRCz10.86
Supplementary_files_format_and_content: fpkm

organism: Danio rerio

source_name: embryo

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) according to the manusfacturer’s instructions and quantified by NanoDrop (Thermo Fisher Scientific). 1 μg total RNA was used to prepare the library.
RNA libraries were prepared for sequencing using standard Illumina HiSeq protocols

treatment_protocol: At 3 dpf, 30 embryos from the wild-type and csf1ra−/− groups were collected, anesthetized with 0.1% MS-222 and immediately euthanized.

tag: genotype

tag: developmental stage

value: 3 days post fertilization (dpf)


title: csf1ra-A-3


title: A6

tag: strain

tag: tissue


title: T24

description: Gene expression of M-type bladder cancer cell line

source_name: M-type bladder cancer cell line

tag: cell line

value: Mesenchymal Transition


title: csf1ra-A-1


title: Tumorsphere LM1KO_2


title: TIR1_3hUV_1 nascent RNA (BrU-seq)

value: 3 hours


title: Brain 5xFAD acute - rep 4

city: Mainz

first: Anna

last: Wierczeiko

address: Hanns-Dieter-Hüsch-Weg 15

department: Institute for Human Genetics

institute: University Medical Center, Johannes Gutenberg University Mainz

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_24_tg_C_USC_1697_S24.R1

data_processing:
Five technical replicates were merged together and the raw file from Sample 16 was down-sampled to 50 % of total reads.
Sequenced reads were trimmed using BBDuk (version 38.06) with parameters , then mapped to the UCSC mm10 reference genome provided by iGenomes using the splice-aware mapper STAR (version 2.7.0d, default options of 2-pass mapping).
The aligned reads were counted per gene and sample (based on the mm10 UCSC annotation file from iGenomes) using FeatureCounts provided by SubRead (version 1.6.2, default options for single-end reads).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Brain - Right hemisphere

growth_protocol: Male B6SJL-Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mmjax (5xFAD) mice (Jackson Lab, Bar Harbor, Maine, USA) were crossbred with female C57BL/6J mice and maintained as heterozygous transgenics on the C57BL/6J background. The animals were single-caged in type II cages with a 12h day/night cycle. Food and water were available ad libitum. The non-transgenic littermates were used as control. All procedures were performed in accordance with the European Communities Council Directive regarding care and use of animals for experimental procedures and were approved by local authorities (Landesuntersuchungsamt Rhineland-Palatinate; approval number G 14-1-087).

extract_protocol:
The right hemisphere was cut into small cubicles and incubated at RT for 20 min in RNAlater (Qiagen, Hilden, Germany) before being stored at -80°C.
NGS library preparation was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illumina’s standard protocol (Part # 15031047 Rev, E). The libraries were prepared with a starting amount of 302 ng and amplified in 12 PCR cycles, profiled in a DNA 1000 Chip on a 2100 Bioanalyzer (Agilent Technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2,0 Fluorometer (Life technologies). All 24 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC, PE for 2x 42 cycles plus 7 cycles for the index read.

treatment_protocol: Mice were randomly assigned to three groups: untrained (sedentary), access to a saucer wheel (15 cm diameter; med associates Inc.) for 30 days, or access to a saucer wheel for 18h before sacrifice. The saucer wheel contained a WLAN connection to a computer for measuring running counts. Food consumption and body weight were assessed regularly.

value: 5xFAD (C57BL/6)

value: right hemisphere

tag: age

value: 3 months

value: male

value: one day voluntary saucer wheel running

tag: treatment synonym

value: acute


title: BOY12E


title: JMSU1


title: Brain 5xFAD chronic - rep 4

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_20_tg_B_USC_1765_S20.R1

tag: treatment

value: 30 days voluntary saucer wheel running

value: chronic


title: TIR1_3hUV_2 nascent RNA (BrU-seq)

value: OsTIR1 control


title: TU-A-2

value: wild type(WT)


title: TU-A-3


title: TU-A-1


title: Brain 5xFAD acute - rep 3

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_23_tg_C_USC_1768_S23.R1

tag: Sex


title: Tumorsphere LM1_3

tag: breast cancer model


title: Brain 5xFAD acute - rep 2

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_22_tg_C_USC_1802_S22.R1


title: Brain 5xFAD acute - rep 1

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_21_tg_C_USC_1776_S21.R1


title: Brain 5xFAD sedentary - rep 4

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_16_tg_A_USC_1764_S5.R1

value: untreated

value: sedentary


title: Brain 5xFAD sedentary - rep 1

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_13_tg_A_USC_1724_S13.R1


title: Brain 5xFAD chronic - rep 3

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_19_tg_B_USC_1801_S19.R1


title: Brain 5xFAD sedentary - rep 2

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_14_tg_A_USC_1731_S14.R1


title: Brain WT acute - rep 2

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_10_wt_C_USC_1490_S10.R1

value: wild-type


title: Brain 5xFAD sedentary - rep 3

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_15_tg_A_USC_1800_S15.R1


title: Brain WT acute - rep 3

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_11_wt_C_USC_1645_S11.R1


title: Brain 5xFAD chronic - rep 1

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_17_tg_B_USC_1815_S17.R1


title: Tumorsphere LM1_1


title: Brain WT chronic - rep 1

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_05_wt_B_USC_1631_S5.R1


title: Brain WT sedentary - rep 3

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_03_wt_A_USC_1650_S3.R1


title: Brain WT sedentary - rep 2

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_02_wt_A_USC_1630_S2.R1


title: Brain 5xFAD chronic - rep 2

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_18_tg_B_USC_1775_S18.R1


title: Brain WT chronic - rep 4

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_08_wt_B_USC_1483_S8.R1


title: Brain WT acute - rep 1

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_09_wt_C_USC_1626_S9.R1


title: Brain WT sedentary - rep 1

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_01_wt_A_USC_1643_S1.R1


title: ID_NF03

city: Rome

first: Daniela

last: Laricchiuta

state: Rome

address: Via del fosso di fiorano, 64

department: Preclinical neuroscience

country: Italy

institute: IRCCS Fondazione Santa Lucia

description:
raw counts data.txt
preprocessed data arsyn.txt

data_processing:
For the processing of raw data (format conversion and de-multiplexing), Bcl2Fastq 2.20 version of the Illumina pipeline was used.
GRCm38.p6 genome was used to map the reads, and transcript abundances were estimated using Salmon v1.2
o obtain gene-level count matrices the quantification data were imported using tximport
Differences in RNA composition between samples were corrected by the Trimmed mean of M-values (TMM) normalization (Robinson and Oshlack, 2010), and filtered for low counts based on a count per million reads (CPM) criteria.
Subsequently, ARSyNseq was used to remove the technical batch effect and NOISeqBIO was used to assess differential gene expression (q>0.95, equivalent to FDR-corrected P<0.05)
Genome_build: GRCm38.p6

source_name: Amygdala

extract_protocol:
Amygdalae were punched and manual and enzymatic dissociations were performed using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec, Bergisch Gladbach, Germany). Pyramidal neurons were then sorted by using the MoFlo Astrios EQ (Beckman Coulter, California, USA) into ice-cold lysis buffer (Reliaprep RNA Cell Miniprep System, Promega, Wisconsin, USA) and then stored at -80°C until RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina PE protocols

value: Pyramidal neurons

tag: condition

value: NOT FEAR

tag: stimulation

value: OPTO


title: BL6xC-mESCs-LP-PIGA-C5-BS07005A

first: Mathew

middle: T

last: Maurano

state: NY

address: 435 E 30th St

department: Institute for Systems Genetics

description: Captured genomic DNA

data_processing:
Illumina libraries were sequenced in paired-end mode on an Illumina NextSeq 500 operated at the Institute for Systems Genetics or NovaSeq 6000 operated by the NYU Langone Health Genome Technology Center. Reads were demultiplexed with Illumina bcl2fastq v2.20 requiring a perfect match to indexing BC sequences. All WGS and Capture-Seq data were processed using a uniform mapping and peak calling pipeline. Illumina sequencing adapters were trimmed with Trimmomatic v0.39{Bolger, 2014 #3524}. Sequencing reads were aligned using BWA v0.7.17{Li, 2009 #3526} to a genome reference (GRCh38/hg38 or GRCm38/mm10) including unscaffolded contigs and alternate references, as well as independently to custom references for relevant vectors and their payloads. PCR duplicates were marked using samblaster v0.1.24{Faust, 2014 #3527}. Generation of per-base coverage depth tracks and quantification was performed using BEDOPS v2.4.35{Neph, 2012 #3540}. Data were visualized using the UCSC Genome Browser. The sequencing processing pipeline is available at https://github.com/mauranolab/mapping .
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: coverage depth track (bigwig)

growth_protocol: hESCs were grown on Geltrex-coated plates with StemFlex medium supplemented with 1% Pen-Strep and passaged in clumps using Versene. mESCs were cultured on gelatin-coated plates coated in 80/20 medium comprising 80% 2i medium and 20% mESC medium and with 1% Pen-strep.

extract_protocol:
Cells were dissociated using TryPE-Select, spun-down and media aspirate. Pellets were either processed immediately or stored at -80 deg. Genomic DNA was extracted using the DNeasy Blood & Tissue kit (QIAGEN 69506).
Double-stranded DNA libraries were prepared from sheared genomic DNA. DNA fragments were end-repaired, A-tailed, and Illumina-compatible adapters were ligated to DNA ends.
Other - DNA Capture-seq

treatment_protocol: Cells were selected combinatorially with puromycin, blasticidin, proaerolysin and ganciclovir as described in the manuscript

value: C57BL6/6J x CAST/EiJ F1 hybrid

value: C57BL6/6J x CAST/EiJ F1 hybrid mESC


title: Brain WT sedentary - rep 4

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_04_wt_A_USC_1482_S4.R1

value: right hemisphere


title: ID_NF02


title: ID_NFS2

value: SHAM


title: BL6xC-mESCs-LP-PIGA-C2-BS07004A

description: Captured genomic DNA


title: BL6xC-mESCs-LP-PIGA-G2-BS07006A

description: Captured genomic DNA


title: Brain WT acute - rep 4

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_12_wt_C_USC_1696_S12.R1

value: 3 months

value: male


title: ID_FS2

value: FEAR


title: ID_FS1


title: ID_FS3


title: ID_FO4


title: Brain WT chronic - rep 3

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_07_wt_B_USC_1634_S7.R1

value: 30 days voluntary saucer wheel running


title: ID_NFS3


title: Brain WT chronic - rep 2

description:
Raw_gene_counts_matrix.txt
imb_roignant_2018_12_06_wt_B_USC_1644_S6.R1

value: chronic


title: ID_FO3


title: ID_FO1


title: BL6xC-mESCs-Sox2-46kb-F6-BS07850A

description: Captured genomic DNA


title: BL6xC-mESCs-Sox2-46kb-MC-A4-BS07853A

description: Captured genomic DNA


title: BL6xC-mESCs-Sox2-46kb-MC-A3-BS07852A

description: Captured genomic DNA


title: ID_NFS4


title: BL6xC-mESCs-Sox2-46kb-F4-BS07849A

description: Captured genomic DNA


title: ID_NF01


title: BL6xC-mESCs-Sox2-46kb-F7-BS07851A

description: Captured genomic DNA


title: BL6xC-mESCs-Sox2-46kb-F2-BS07848A

description: Captured genomic DNA


title: BL6xC-mESCs-Sox2-46kb-E11-BS07845A

description: Captured genomic DNA


title: BL6xC-mESCs-Sox2-46kb-E12-BS07846A

description: Captured genomic DNA


title: BL6xC-mESCs-LP-PIGA2-BS07913A

description: Captured genomic DNA


title: BL6xC-mESCs-Sox2-46kb-E9-BS07844A

description: Captured genomic DNA


title: BL6xC-mESCs-Parental-BS07912A

description: Captured genomic DNA

value: delta-Piga


title: BL6xC-mESCs-Sox2-143kb-G11-BS07692A

description: Captured genomic DNA


title: BL6xC-mESCs-Sox2-46kb-MC-F9-BS04680A

description: Captured genomic DNA


title: BL6xC-mESCs-Sox2-46kb-MC-E9-BS04679A

description: Captured genomic DNA


title: Failed-BL6xC-mESCs-Sox2-46kb-MC-clone-BS03614A

description: Captured genomic DNA


title: ID_FO2


title: BL6xC-mESCs-Sox2-46kb-MC-B9-BS04676A

description: Captured genomic DNA


title: BL6xC-mESCs-Sox2-46kb-E2-BS07843A

description: Captured genomic DNA


title: BL6xC-mESCs-Sox2-46kb-MC-A9-BS04675A

description: Captured genomic DNA


title: BL6xC-mESCs-PL1-F3-BS04674A

description: Captured genomic DNA


title: BL6xC-mESCs-PL1-D3-BS04672A

description: Captured genomic DNA


title: BL6xC-mESCs-PL1-E3-BS04673A

description: Captured genomic DNA


title: BL6xC-mESCs-PL1-C3-BS04671A

description: Captured genomic DNA


title: BL6xC-mESCs-PL1-B3-BS04670A

description: Captured genomic DNA


title: BL6xC-mESCs-PL1-A3-BS04669A

description: Captured genomic DNA


title: ChIPseq-GRKO-GFP-GR-407C_PlusDEX_rep1

city: Bethesda

first: Thomas

middle: A

last: Johnson

address: 41 Medlars Dr. Room B307

department: CCR

institute: National Cancer Institute

data_processing:
RTA 2.4.11 was used for Basecalling and Bcl2fastq 2.17 was used for demultiplexing allowing 1 mismatch.
Trimmomatic 0.36 was used for adapter and quality control.
ChIP- seq alignment was performed by Bowtie2 (2.1.0) with Bowtie2 –p 8 –x bowtie2_ref/genome_prefix –U read1.fastq –S result.sam.
Peaks were called using HOMER program version 4.9 with findPeaks with following parameters; FDR<0.001, 4x fold enrichment over local background, and 4x normalized tag enrichment over NT control.
Genome_build: mm10
Supplementary_files_format_and_content: Deeptools   bamCoverage -b FILENAME.bam -o FILENAME.bigWig -of bigwig --binSize 20 --effectiveGenomeSize 2308125349 --normalizeUsing RPGC

source_name: 3617-KOGR cells, stably integrated GFP-GR-407C trunc. mutant, 100nM Dex treatment, Immunoprecipitated DNA

growth_protocol: Mouse adenocarcinoma cells were grown in Dulbecco's Modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum and 2mM L-Glutamine, and kept at 37 °C in a humidified 95% air/ 5% CO2 incubator. Mouse adenocarcinoma cells were also supplemented with 5 µg/ml of tetracycline to supress GFP-GR expression.

extract_protocol:
For ChIP-seq, lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with specified antibody.
Libraries were prepared for sequencing using standard Illumina protocols. For ChIP-seq, Illumina TruSeq Chip Sample Prep Kit.

treatment_protocol: Mouse adenocarcinoma cells were grow in steroid-depleted medium (10% charcoal stripped FBS in DMEM) for 24 h, and the cells were subsequently left untreated or treated 100 nM of dexamethasone for 1 h in ChIP-seq.

value: mouse adenocarcinoma

tag: stably expressing

value: GFP-GR-407C truncation mutant

value: Dexamethasone.

tag: concentration

tag: time

value: 1 hr.


title: ChIPseq-GRKO-GFP-GR-407C_PlusDEX_rep2


title: BL6xC-mESCs-Parental-BS06877A

description: Captured genomic DNA


title: BL6xC-mESCs-LP-PIGA-A1-BS07003A

description: Captured genomic DNA


title: ChIPseq-GRKO-GFP-GR-C428G_PlusDEX_rep1

source_name: 3617-KOGR cells, stably integrated GFP-GR-C428G pt mutant, 100nM Dex treatment, Immunoprecipitated DNA

value: GFP-GR-C428G pt mutant


title: ChIPseq-GRKO-GFP-GR-407C_noDEX_rep1

source_name: 3617-KOGR cells, stably integrated GFP-GR-407C trunc. mutant, Notreatment, Immunoprecipitated DNA


title: Failed-BL6xC-mESCs-LP-PIGA-Clone-BS03022A

description: Captured genomic DNA


title: ChIPseq-GRKO-GFP-GR-C428G_PlusDEX_rep2


title: ID_NFS1

value: Pyramidal neurons

value: NOT FEAR


title: ChIPseq-GRKO-GFP-GR-C428G_noDEX_rep1

source_name: 3617-KOGR cells, stably integrated GFP-GR-C428G pt mutant, Notreatment, Immunoprecipitated DNA


title: ChIPseq-GRKO-GFP-GR-C428G_noDEX_rep2


title: 9_6Emyo

city: Adelaide

first: Susan

last: Woods

state: Select State

address: Level 5 South, SAHMRI building, North Terrace

department: School of Medicine

country: Australia

institute: The University of Adelaide

data_processing:
KAPA adapters were trimmed off using cutadapt25,26 (V1.16; minimum-length 18, error-rate 0.2, overlap=5)
Reads were mapped to the mouse genome (mm10) using the STAR aligner2 (V2.6.1b; default parameters, read counts quantified by GeneCounts).  97%+ of reads mapped to the genome for each sequenced sample.
Genome_build: mm10
Supplementary_files_format_and_content: count table

source_name: small intestine

growth_protocol: Adult mouse small intestine (SI) was removed, opened longitudinally, and villi was mechanically scraped off. Embryonic mouse SI was collected under dissection microscope and cut into 2 mm pieces. The Intestine was incubated with chelation buffer (3mM EDTA, 0.05mM DTT (Sigma) in PBS) for 30 minutes at room temperature. The epithelial layer was removed with shaking in PBS. The remaining intestine was digested using 3.8mg/ml Collagenase XI (Sigma) and 0.1mg/ml Dispase II (Roche) for 15 minutes at 37℃. The resulting supernatant was passed through a 70 µm strainer and single cells were pelleted by centrifugation at 300g for 5 minutes and plated in RPMI1640, supplemented with 10% FBS, 2 mM L-glutamine (GIBCO), 10 mM HEPES, 1mM sodium pyruvate, 100 U/ml penicillin and 100 mg/ml streptomycin (GIBCO), 50µM β-mercaptoethanol, and 1µM Y27632 until confluent

extract_protocol:
RNeasy mini kits (Qiagen) were used to isolate RNA from cultured cells. Manufacturer's instructions were followed
RNA quality and quantity were analyzed using a NanoDrop and TapeStation. PolyA+ stranded RNA-seq libraries were prepared using the KAPA RNA Hyper Prep kit (Roche). The multiplexed libraries were sequenced on an Illumina NextSeq 500 to obtain a single-end 75 bp read

tag: Stage

value: mesenchymal cells


title: 5_8Emyo1

tag: cell type


title: BL6xC-mESCs-Sox2-46kb-MC-D9-BS04678A

description: Captured genomic DNA

value: C57BL6/6J x CAST/EiJ F1 hybrid

tag: genotype

value: C57BL6/6J x CAST/EiJ F1 hybrid mESC


title: BL6xC-mESCs-Sox2-46kb-MC-C9-BS04677A

description: Captured genomic DNA


title: 5_28Emyo1


title: 9_6Adultmyo

value: Adult


title: 5_8Adultmyo2


title: C2

value: 20 weeks old

value: concieved by IVF-FET

value: liver


title: 5_28Adultmyo2


title: MLLAF9_rep2

city: Chapel Hill

first: Gang (Greg)

last: Wang

state: NC

address: 450 West Drive, Lineberger Cancer Center

institute: UNC-Chapel Hill

data_processing:
RNA-seq reads were aligned to the mm10 mouse genome using STAR v2.4.2.
Transcript abundance for each sample was estimated with salmon v0.1.19.
Gene level counts were summed across isoforms and genes with low expression (all samples had less than 10 reads) were filtered.
DESeq2 was used to analyze differentially expressed genes between different samples.
Genome_build: mm10

source_name: MLLAF9-immortalized murine hematopoietic progenitor cells

growth_protocol: Transduced murine HSPCs were grown in the Opti-MEM base medium supplemented with 15% FBS (Invitrogen, 16000-044), 1% antibiotics, 50 μM β-mercaptoethanol, murine SCF (5% supernatant from murine SCF-producer cells) and murine Flt3 ligand (5% supernatant from murine Flt3 ligand-producing cells).

extract_protocol:
Total RNAs were extracted using RNeasy Plus kit and residual DNAs were removed using Turbo DNA-free kit.
RNA-seq libraries were generated using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II RNA library Prep kit according to manufacturer's instructions.


title: EV

source_name: EV-transduced murine hematopoietic progenitor cells


title: ChIPseq-GRKO-GFP-GR-407C_noDEX_rep2


title: ZM_long_term_rep1

source_name: ZM-immortalized murine hematopoietic progenitor cells


title: A9M_rep2

source_name: A9M-immortalized murine hematopoietic progenitor cells


title: ZM_long_term_rep2

value: ZM-immortalized murine hematopoietic progenitor cells


title: A9M_rep1

value: A9M-immortalized murine hematopoietic progenitor cells


title: ZM_short_term_rep1


title: ZM_Tip60_GFP_ChIP

description:
ZM_Tip60_GFP_ChIP_rep1
ZM_Tip60_GFP_ChIP_rep2

data_processing:
ChIP-seq reads were aligned to mouse genome build NCBI37/mm9 using STAR version 2.7.1a after quality trimming. Non-primary alignment and PCR duplicates were then removed by samtools.
Alignment files in the bam format were transformed into read coverage files (bigWig format) using DeepTools. Genomic binding profiles were generated using the deepTools “bamCompare” functions with options [--operation ratio ---pseudocount 1 -binSize 10 --extendReads 250] and normalized to the matched input.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

growth_protocol: ZM-transformed murine AML cells were grown in the Opti-MEM base medium supplemented with 15% FBS (Invitrogen, 16000-044), 1% antibiotics, 50 μM β-mercaptoethanol, murine SCF (5% supernatant from murine SCF-producer cells) and murine Flt3 ligand (5% supernatant from murine Flt3 ligand-producing cells).

extract_protocol:
Cells were fixed in PBS containing 1% formaldehyde and then subject to lysis, sonication, IP, wash, elution, reverse crosslink, Rnase and Proteinase K digestion, and DNA recover by Qiagen PCR purification kit.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L) following the manufacture’s protocol.

tag: chip antibody

value: anti-GFP (Abcam, ab290)


title: ZM_Brd4_ChIP_input

value: n/a (input)


title: ZM_H3K27ac_ChIP

value: anti-H3K27ac (Abcam, ab4729)


title: ZM_Brd4_ChIP

value: anti‐Brd4 (Bethyl, A301-985A100)


title: ZM_Tip60_GFP_ChIP_input


title: ZM_histoneChIP_input


title: ZM_H3K27me3_ChIP

value: anti‐H3K27me3 (Millipore, 07-449)


title: ZM_H4ac_ChIP

value: anti-H4ac (Millipore, 06-866)


title: ZM_short_term_rep2


title: WT2_H9_P4

city: Cambridge

middle: James

last: LaSalle

state: MA

address: 415 Main Street

institute: Broad Institute

data_processing:
FASTQ files were aligned to the NCBI Genome Reference Consortium Mouse Build 38 (mm10) using the STAR alignment algorithm.
Expression levels were computed using the RSEM tool and quantified as both raw counts and Transcripts Per Million (TPM).
We used four quality control metrics for each cell. We excluded: (1) cells expressing less than 2500 genes with three or more counts, (2) cells with less than 500,000 RNA molecules detected, (3) cells with mitochondrial gene counts exceeding 10% of total gene expression, (4) cells with an average expression of housekeeping genes with log2(TPM+1) < 6.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab-delimited text file containing raw counts for 54,247 transcripts (rows) and 284 cells (columns)

source_name: TPC single cell

growth_protocol: 8-week-old animals were treated once with DMBA, followed by repetitive treatment of TPA for more than 20 weeks.

extract_protocol:
RNA isolation and library construction was done using a modified version of the Smart-seq2 protocol as recently described (Sade-Feldman et al, Cell 2018). Briefly, 22µl of Agencourt RNAClean XP SPRI beads (Beckman Coulter, A63987) was added and mixed in the 96 well plates containing sorted single cell lysates. After 10 minutes incubation, plates were placed on a DynaMag-96 side skirted magnet (Invitrogen, 12027) for 5 minutes, followed by supernatant removal and two washes with 75% ethanol. Next, dried beads were mixed with 4µl of mix-1 containing 1µl (10µM) RT primer (IDT, DNA oligo) 5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3′; 1µl (10mM) dNTPs (Thermo-Fisher, R0192); 1µl (4U/µl) Recombinant RNase Inhibitor (Clontech, 2313B); and 1µl nuclease free water, and plates were placed in a thermocycler for 3 minutes at 72°C. After RNA denaturation, reverse transcription (RT) step was done by adding, 7µl of mix-2 containing 0.75µl nuclease free water; 2µl 5X Maxima RT buffer (Thermo-Fisher, EP0753); 2µl (5M) betaine (Sigma-Aldrich, B0300-1VL); 0.9µl (100mM) MgCl2 (Sigma-Aldrich, M1028); 1µl (10µM) TSO primer (Qiagen, RNA oligo) 5′-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3′; 0.25µl (40U/µl) Recombinant RNase Inhibitor (Clontech, 2313B); and 0.1µl (200U/µl) of Maxima H Minus Reverse Transcriptase (Thermo-Fisher, EP0753) was added and mixed followed by 90 minutes incubation at 50°C and 5 minutes incubation at 85°C. For cDNA amplification, 14µl of mix-3 containing 1µl nuclease free water; 0.5µl (10µM) ISPCR primer (IDT, DNA oligo) 5′-AAGCAGTGGTATCAACGCAGAGT-3′; and 12.5µl 2X KAPA HiFi HotStart ReadyMix (KAPA Biosystems, KK2602) was added and mixed, and plates were placed for 3 minutes at 98°C, followed by 21 cycles at [98C for 15 seconds, 67C for 20 seconds and 72C for 6 minutes] with final extension at 72C for 5 minutes. Removal of primer dimers after cDNA amplification was done by adding 20µl of Agencourt AMPureXP SPRI beads (Beckman Coulter, A63881) to each well, incubation for 5minutes, placement of plates on a DynaMag-96 side skirted magnet for 5 minutes, followed by two 75% ethanol washes and resuspension of dried beads with 20µl TE buffer (Tekanova, T0228). This step was repeated to ensure complete removal of primer dimers. Quantification of the concentration of each cell was done on the Cytation-5 plate reader (BioTek) by using the Qubit dsDNA high sensitivity assay (Invitrogen, Q32854). For each plate, representative wells were also evaluated for cDNA size distribution to ensure quality of sorted cells, using the High-sensitivity DNA Bioanalyzer kit (Agilent 5067-4626).
The Nextera XT library Prep kit (Illumina, FC-131-1096) was used to generate libraries for next-generation sequencing. After this step barcoded single cells were grouped into a single tube, followed by sequencing on a NextSeq 500 sequencer (Illumina) using the 75 cycles kit, with paired-end 38-base-reads and dual barcoding 8-base-reads.

treatment_protocol: Mice bearing skin tumors were euthanized and the tumors were collected on ice. Each tumor was cut into small pieces and incubated with 0.5% trypsin (diluted in keratinocyte serum-free medium, Gibco) on a horizontal shaker at 37°C for 1.5 hr. Using an 18G syringe, digested tumor cells were physically isolated into a single cell suspension. The trypsin was inactivated by adding chelexed FBS. After serial filtering with 70μm and 40μm strainers (BD sciences), tumor cells were centrifuged at 1200 rpm, 4°C for 10 min. Cell pellets were resuspended with PBS containing 4% chelexed FBS and then transferred into FACS tubes with a 40μm filter. Isolation of TPC cells for single cell RNA sequencing was done on a BD Aria cell sorter, by sorting cells into 96 well plates (Eppendorf) containing 10µl of lysis buffer (TCL buffer + 1% 2-mercaptoethanol). Selection of cells was done using standard cell surface staining protocols with BV421-CD34 (BD sciences, 562608, 1:50), PE-CD49f (eBiosciences, 12-0495-81, 1:200), and by gating on endogenous YFP expression in ROSA26-LSL-eYFP; Keratin14-Cre transgenic mice. The viability dye propidium iodine (Sigma, P4864, 1:1000) was used to exclude dead cells and was added after antibody labeling.  Proper isotype controls, single color controls, and FMO controls were used in every experiment to set up optimal compensation and gates. After sorting the TPCs, the 96-well plates were sealed, vortexed, spun down at 2500 rpm for 30 seconds, and immediately placed on dry ice. Plates were stored at -80C until further processing.

tag: strain

value: skin tumor

tag: mouse id

value: wild type


title: ZM_H3K36me3_ChIP

value: anti‐H3K36me3 (Abcam, ab9050)


title: WT2_H11_P4


title: WT2_H2_P4


title: WT2_H7_P4


title: WT2_G8_P4


title: WT2_G9_P4


title: WT2_H8_P4


title: MLLAF9_rep1

value: MLLAF9-immortalized murine hematopoietic progenitor cells


title: WT2_H4_P4


title: WT2_H10_P4


title: WT2_G4_P4


title: WT2_H6_P4


title: WT2_H11_P3


title: WT2_G5_P4


title: WT2_G12_P4


title: WT2_G6_P4


title: WT2_G3_P4


title: WT2_G10_P4


title: WT2_F8_P4


title: WT2_F6_P4


title: WT2_G1_P4


title: WT2_F3_P4


title: WT2_G11_P4


title: WT2_F5_P4


title: WT2_F2_P4


title: WT2_G7_P4


title: WT2_G2_P4


title: WT2_F4_P4


title: WT2_F12_P3


title: WT2_F1_P4


title: WT2_E8_P4


title: WT2_F10_P4


title: WT2_E6_P4


title: WT2_E9_P4


title: WT2_E4_P4


title: WT2_E11_P4


title: WT2_D9_P4


title: WT2_D7_P4


title: WT2_E10_P4


title: WT2_E12_P4


title: WT2_E2_P4


title: WT2_E1_P4


title: WT2_E3_P4


title: WT2_D8_P4


title: WT2_F11_P4


title: WT2_D4_P4


title: WT2_G11_P3


title: WT2_E12_P3


title: WT2_D3_P4


title: WT2_D12_P4


title: WT2_D12_P3


title: WT2_D2_P4


title: WT2_D11_P4


title: WT2_D10_P4


title: WT2_C6_P4


title: WT2_D1_P4


title: WT2_C4_P4


title: WT2_C9_P4


title: WT2_D6_P4


title: WT2_C5_P4


title: WT2_C3_P4


title: WT2_D5_P4


title: WT2_C2_P4


title: WT2_C12_P4


title: WT2_C11_P4


title: WT2_C1_P4


title: WT2_B7_P4


title: WT2_B8_P4


title: WT2_B12_P4


title: WT2_A5_P4


title: WT2_B10_P4


title: WT2_B12_P3


title: WT2_A6_P4


title: WT2_B11_P4


title: WT2_A8_P4


title: WT2_A7_P4


title: WT2_B1_P4


title: WT2_B6_P4


title: WT2_B4_P4


title: WT2_B5_P4


title: WT2_A4_P4


title: WT2_A1_P4


title: WT2_A12_P4


title: WT1_H9_P3


title: WT2_A10_P4


title: WT2_A12_P3


title: WT2_A3_P4


title: WT2_A11_P4


title: WT1_H5_P3


title: WT1_H3_P3


title: WT2_A9_P4


title: WT1_H4_P3


title: WT1_H12_P3


title: WT1_G9_P3


title: WT1_G8_P3


title: WT1_H1_P3


title: WT1_G6_P3


title: WT1_G5_P3


title: WT1_F9_P3


title: WT1_F7_P3


title: WT1_G7_P3


title: WT1_G10_P3


title: WT1_G1_P3


title: WT1_F5_P3


title: WT1_F4_P3


title: WT1_F6_P3


title: WT1_H2_P3


title: WT1_E7_P3


title: WT1_E6_P3


title: WT1_F11_P3


title: WT1_F2_P3


title: WT1_F10_P3


title: WT1_E5_P3


title: WT1_E3_P3


title: WT1_E10_P3


title: WT1_E11_P3


title: WT1_G4_P3


title: WT1_E1_P3


title: WT1_F3_P3


title: WT2_B2_P4


title: WT1_D8_P3


title: WT1_D9_P3


title: WT1_D7_P3


title: WT1_D6_P3


title: WT1_D1_P3


title: WT1_D10_P3


title: WT1_C9_P3


title: WT1_C6_P3


title: WT1_E4_P3


title: WT1_D11_P3


title: WT1_C5_P3


title: WT1_D3_P3


title: WT1_B7_P3


title: WT1_C1_P3


title: WT1_B8_P3


title: WT1_G3_P3


title: WT1_C2_P3


title: WT1_B6_P3


title: WT1_E9_P3


title: WT1_B9_P3


title: WT1_B11_P3


title: WT1_B3_P3


title: WT1_B10_P3


title: WT1_B4_P3


title: WT1_B1_P3


title: WT1_A9_P3


title: WT1_D2_P3


title: WT1_A7_P3


title: WT1_A8_P3


title: WT1_A10_P3


title: WT1_C4_P3


title: KO3_H8_P2


title: WT1_A3_P3


title: WT1_A11_P3


title: KO3_H3_P2


title: KO3_H9_P2


title: KO3_H7_P2


title: WT1_B5_P3


title: KO3_H4_P2


title: KO3_H12_P2


title: WT1_A1_P3


title: KO3_H1_P2


title: KO3_G7_P2


title: KO3_G9_P2


title: KO3_G5_P2


title: KO3_F9_P2


title: KO3_H2_P2


title: KO3_F8_P2


title: WT1_A5_P3


title: WT1_A4_P3


title: KO3_F4_P2


title: KO3_F5_P2


title: KO3_F7_P2


title: KO3_F3_P2


title: KO3_F1_P2


title: KO3_F6_P2


title: KO3_E4_P2


title: KO3_E5_P2


title: KO3_E7_P2


title: KO3_E2_P2


title: KO3_E3_P2


title: KO3_G4_P2


title: KO3_D7_P2


title: KO3_E1_P2


title: KO3_D3_P2


title: KO3_E9_P2


title: KO3_C4_P2


title: KO3_D1_P2


title: KO3_C7_P2


title: KO3_C8_P2


title: KO3_B8_P2


title: KO3_B9_P2


title: KO3_C1_P2


title: KO3_B7_P2


title: KO3_B6_P2


title: KO3_E8_P2


title: KO3_B4_P2


title: KO3_A9_P2


title: KO3_A7_P2


title: KO3_B2_P2


title: KO3_A6_P2


title: KO3_D5_P2


title: KO3_A5_P2


title: KO3_A2_P2


title: KO3_A10_P2


title: KO3_A11_P2


title: KO3_A1_P2


title: KO3_A3_P2


title: KO1_H9_P1


title: KO1_H7_P1


title: KO1_H6_P1


title: KO1_H8_P1


title: KO1_H4_P1


title: KO1_H10_P2


title: KO1_H11_P1


title: KO3_B1_P2


title: KO1_H1_P1


title: KO1_G7_P1


title: KO1_H10_P1


title: KO1_G6_P1


title: KO1_G5_P1


title: KO1_H12_P1


title: KO1_G3_P1


title: KO1_G11_P2


title: KO1_F9_P1


title: KO1_F7_P1


title: KO1_G11_P1


title: KO1_F3_P1


title: KO1_F2_P1


title: KO1_F4_P1


title: KO1_F5_P1


title: KO3_B3_P2


title: KO1_F6_P1


title: KO3_D6_P2


title: KO1_E9_P1


title: KO1_F11_P1


title: KO1_E7_P1


title: KO1_E6_P1


title: KO1_E5_P1


title: KO1_G10_P2


title: KO1_E10_P2


title: KO1_E12_P1


title: KO1_E10_P1


title: KO1_E3_P1


title: KO1_D9_P1


title: KO1_E1_P1


title: WT1_C3_P3


title: KO1_D8_P1


title: KO1_D4_P1


title: KO1_F1_P1


title: KO1_D7_P1


title: KO1_D5_P1


title: KO1_D12_P1


title: KO1_G10_P1


title: KO1_C9_P1


title: KO1_D1_P1


title: KO1_D10_P1


title: KO1_E8_P1


title: KO1_C7_P1


title: KO1_E4_P1


title: KO1_C6_P1


title: KO1_C4_P1


title: KO1_C3_P1


title: KO1_C12_P1


title: KO1_E11_P2


title: KO1_C11_P2


title: KO1_B8_P1


title: KO1_B6_P1


title: KO1_B7_P1


title: KO1_B3_P1


title: KO1_B5_P1


title: KO1_B12_P1


title: KO1_B10_P1


title: KO1_B11_P1


title: KO1_B1_P1


title: KO1_B10_P2


title: KO1_A7_P1


title: KO1_D11_P2


title: KO1_A4_P1


title: KO1_A12_P1


title: KO1_A3_P1


title: KO1_C2_P1


title: KO1_A11_P1


title: KO1_A1_P1


title: KO1_C10_P1


title: Sal003_2

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

country: Canada

institute: Lady Davis Institute for Medical Research

data_processing:
Raw reads are trimmed using Trimmomatic v0.32. First, adaptors and other Illumina-specific sequences from each read are removed using palindrome mode. Then, a four-nucleotide sliding window removes the bases once the average quality within the window falls below 30. Next, the first four bases at the start of each read are removed. Finally, reads shorter than 30 base pairs are dropped
Cleaned reads are aligned to the mouse reference genome build mm10 using STAR v2.3.0e with default settings. Reads mapping to more than 10 locations in the genome (MAPQ < 1) were discarded.
Gene expression levels were estimated by quantifying uniquely mapped reads to exonic regions (the maximal genomic locus of each gene and its known isoforms) using featureCounts (v1.4.4) and the Ensembl gene annotation set
Genome_build: mm10
Supplementary_files_format_and_content: Raw exonic counts for each sample using the mm10 Ensembl annotation set in a tab-separated value file.

source_name: diaphragm and abdominal muscle

extract_protocol:
total RNA was isolated from satellite cell cultures using the RNeasy® Micro Kit (Qiagen)
The RiboGone™-mammalian (Takara Bio) kit was subsequently used to eliminate ribosomal and mitochondrial RNA. cDNA libraries for RNA-sequencing were then prepared using the SMARTer® Stranded RNA-Seq (Takara Bio) kit. The resulting cDNA libraries were sequenced with the Illumina MiSeq system (Genome Quebec).

treatment_protocol: Satellite cells were isolated from Pax3GFP/+ adult mice and seeded at 7500 cells per 35mm plate and subsequently cultured in 10 mM sal003 (n=4) or DMSO (n=4) for 4 days.

tag: developmental stage

value: adult

value: 10 uM sal003

value: satellite cells


title: Sal003_1


title: DMSO_4

value: DMSO


title: Sal003_4


title: Sal003_3


title: DMSO_3