title: Donor 2, Timepoint 20, Replicate C

city: Saarbrücken

first: Tim

last: Kehl

address: Campus E2.1, P.O. box 151150

department: Center for Bioinformatics

institute: Saarland University

description: miRNA expression after T cell activation (Timepoint 20)

hyb_protocol: miRNA labeling and hybridization to the Human SurePrint G3 Unrestricted miRNA 8x60k Microarrays (Release 21.0, G4872A;  Agilent Technologies, Santa Clara, California, United States) was performed using the miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara, California, United States) following the manufacturer’s protocol.

scan_protocol: Arrays were scanned with a resolution of 3 µm. Raw data was extracted using Feature Extraction software (Agilent Technologies, Santa Clara, California, United States).

data_processing: Raw expression values were background corrected, quantile normalized and log2 transformed using the limma R-package (method = normexp, offset = 16).

growth_protocol: Venous blood samples were obtained from two age and gender matched volunteers (female; Donor 1: Age 26 years; Donor 2: Age 23 years). Samples were collected using lithium heparin containing vacutainer collection tubes (S-Monovette®, Sarstedt AG& Co. KG, Numbrecht, Germany). PBMCs were isolated by Ficoll density gradient centrifugation. CD4+ T cells were isolated by negative selection (Human CD4+ T cell Isolation Kit, Miltenyi Biotech, Bergisch Gladbach, Germany). Cells were resolved and cultured in RPMI 1640 medium (Life Technologies GmbH, Darmstadt, Germany), supplemented with 10 % heat inactivated fetal bovine serum (Biochrom GmbH, Berlin, Germany), penicillin (100 U/mL) and streptomycin (100 μg/mL)

extract_protocol: Total RNA was extracted in a semi-automated procedure, using QIAcube robot systems and following the manufacturers` instructions for miRNeasy Micro Kit (Qiagen, Hilden, Germany). The RNA was quantified by Qubit® Fluorometer using Qubit® RNA HS Assay Kit (Thermo Fisher Scientific Inc., Waltham, Massachusetts, United States). RNA integrity was verified using Agilent 2100 Bioanalyzer instrument and RNA Pico Kit (Agilent Technologies, Santa Clara, California, United States). To determine miRNA expression profiles, 75 ng total RNA of each sample was utilized for miRNA labeling and hybridization to Human SurePrint G3 Unrestricted miRNA 8x60K arrays (Release 21.0, G4872A, Agilent Technologies, Santa Clara, California, United States) following the instructions of miRNA Complete Labeling and Hyb Kit.

treatment_protocol: 3.5x105 cells/well of the freshly isolated CD4+ cells were seeded into 100 µl of medium within a 96-well plate by using a multichannel pipette. Cells were subsequently activated in separate wells by αCD2/αCD3/αCD28 MACSiBead™ particles (T cell activation/expansion kit, human, Miltenyi Biotec GmbH, Bergisch Gladbach, Germany). Sampling during a total time period of 24 h was conducted, collecting cells of each donor from three separate wells at intervals of 2 h. Cells were pelleted and lysed immediately by QIAzol® Lysis Reagent from miRNeasy Micro Kit (Qiagen, Hilden, Germany). Samples were frozen (-70 °C) for less than 2 months before RNA extraction.

tag: gender

value: female


title: Donor 2, Timepoint 24, Replicate C

status: Public on Sep 04 2020

type: RNA

country: Germany

description: miRNA expression after T cell activation (Timepoint 24)

molecule: total RNA

organism: Homo sapiens

label_protocol: miRNA labeling and hybridization to the Human SurePrint G3 Unrestricted miRNA 8x60k Microarrays (Release 21.0, G4872A;  Agilent Technologies, Santa Clara, California, United States) was performed using the miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara, California, United States) following the manufacturer’s protocol.


title: x034_b1_p1_B05_1c_M_S34: Mouse embryonic stomach at E13.5 Batch1

type: SRA

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

institute: Institute of Molecular Biology, Mainz

library_source: transcriptomic

data_processing:
Reads were demultiplexed and fastq files were generated with Illumina bcl2fastq-1.8.4
Fastq files were mapped with STAR_2.5.2b onto Ensembl 88 GRCm38 reference
Secondary alignments were filtered with samtools 1.5
Counts for every gene were calculated with Subread’s FeatureCounts (version 1.5.1) using the gene model provided with Ensembl 88 GRCm38 reference
Genome_build: Ensembl 88 GRCm38
Supplementary_files_format_and_content: tab separated file containing counts per gene

organism: Mus musculus

source_name: stomach cells

extract_protocol:
Single EpCAM+ and EpCAM- embryonic gastric cells were isolated by FACS directly in 96 well plates supplemented with buffer (Takara, Clontech). ERCC RNA Spike-In Mix (ThermoFisher) were added for quality and normalization controls. Plates were stored at -80°C.
50ng of total RNA was used for cDNA synthesis using Ovation v2.0 kit (NuGEN) according to manufacturer’s instructions. After cDNA fragmentation (Covaris), libraries were prepared using NEBNext v2.0 kit (NEB) according to manufacturer’s instructions.

treatment_protocol: Stomachs were dissected from mouse embryos at indicated stages, cut in pieces of 2 mm and incubated for 10 min with 0.15mg/ml collagenase (Sigma) in PBS at 37°C with shaking at 800 rpm. Single cell suspensions were collected by centrifugation at 200g for 3 min, washed twice and resuspended in PBS supplemented with 2% foetal calf serum. Cells were stained with APC–conjugated anti-EpCAM 1:1000 (eBioscience) for 30 min at room temperature. Living cells were gated by DAPI dye exclusion. Embryonic gastric epithelial cells were isolated as EpCAM+DAPI−, mesenchymal cells were EpCAM-DAPI-. Fluorescence-activated cell sorting was performed using BD FACS Aria III SORP cell sorter (100 μM nozzle)

tag: strain

value: mixed C57BL/6 CD1

tag: tissue

value: stomach

tag: age

value: embryonic day 13.5


title: x032_b2_p4_H04_1c_E_S32: Mouse embryonic stomach at E13.5 Batch2


title: ATMhTERT_24hr_R2_HiC

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: TN

address: 1311 Cumberland Ave

department: BCMB

country: USA

institute: University of Tennessee,Knoxville

library_source: genomic

data_processing:
Sequenced reads were mapped to the hg19 genome using bowtie2
Filtering was carried out using the dekkerlab-cMapping pipeline available on github
Iterative correction was performed using method described by Imakaev et al.
All processed Hi-C contact maps were scaled to a sum of 1 million
Genome_build: hg19
Supplementary_files_format_and_content: each .tar file contains the iteratively corrected and raw matrix.gz files for 40 kb, 250 kb, and 2.5 Mb in their respective directories

molecule: genomic DNA

growth_protocol: Fibroblast lines were grown to confluency prior to X-ray exposure. For the GM12878 suspension cell line, cells were passaged at a density around 500,000 cells per 1 mL of medium. For irradiation experiments, GM12878 cells were grown to a density of 1 million cells per 1 mL of medium prior to X-ray exposure.

extract_protocol:
Briefly, 5-20 million cells were fixed with 1% formaldehyde, suspended in cell lysis buffer for permeabilization, and homogenized by douncing. Crosslinked chromatin was digested overnight with HindIII. Sticky ends were filled in with biotin-dCTP, and the blunt ends of interacting fragments were ligated together. DNA was purified by two phenol-chloroform extractions and ethanol precipitation. Biotin-dCTP at unligated ends was removed, and the DNA was sheared to a target size of 200-400 bp by a Covaris sonicator
Biotinylated DNA was pulled down using streptavidin coated magnetic beads and prepared for multiplex sequencing on an Illumina platform using the NEBNext Ultra II kit (NEB). All end preparation, adaptor ligation, and PCR amplification steps were carried out on bead bound DNA libraries.

treatment_protocol: Treated cells were X-rayed using 5 Gy X-rays and fixed for Hi-C after 30 mins, 24 hours, or split after 24 hours and allowed to recover for 5 days. The treated cells and their control counterparts were then fixed for Hi-C. ATM inhibitor treated cells were subjected to 10um KU-55933 for 1 hour before experiment began. ATMiC was subjected to KU-55933, but not IR.

tag: cell line

value: ATMhTERT

tag: cell type

value: Skin fibroblast

tag: condition

tag: media


title: YueLab-RNA-Seq-Kidney-rep1

city: CHICAGO

first: Yu

last: Luan

state: Illinois

address: 303 E. Superior Simpson Querrey 7-518

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
RNA-seq reads were aligned to zv10 genome assembly using STAR;
ChIP-seq and ATAC-seq reads were aligned to zv10 genome assembly using BWA
HiC reads were aligned to zv10 genome assembly using Bowtie2
The TPM value of gene expression was caculated using RSEM
ChIP-seq and ATAC-seq peaks were called using MACS2 with the following  setting: ChIP-seq q-value <10e-2, p-value<10e-5, Change>1,FC>2. ATAC-seq: q-value<10e-2 and p-value<10e-5
HiC matrix was generated using HiC-Pro
Genome_build: zv10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi-C for each Sample.**All replicates were merged

molecule: polyA RNA

organism: Danio rerio

source_name: Tissue

growth_protocol: Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions

extract_protocol:
For each RNA-seq experiment, the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk, ten 1-dpf fish were dechorionated with pronase and trunk were cut off for RNA-seq. For embryonic neuron, green cells from Tg(Huc:Kaede) cells were sorted by FACS and approxinately 20,000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol (Invitrogen).
The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit (Agilent) according to the manufacturer’s protocol. Briefly, polyA RNA was purified from 1000 ng of total RNA using oligo (dT) beads (Invitrogen). Extracted RNA was first fragmented, then followed by reverse transcription, end repair, adenylation, adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent) and Kapa Library Quantification Kit (Kapa Biosystems) and then followed by pair-end 2X 50 bp high-throughput sequencing using HiSeq 2500 (Illumina).

value: Tuebingen

value: Kidney


title: Donor 2, Timepoint 18, Replicate C

description: miRNA expression after T cell activation (Timepoint 18)


title: x032_b1_p1_H04_1c_E_S32: Mouse embryonic stomach at E13.5 Batch1


title: Donor 2, Timepoint 16, Replicate C

description: miRNA expression after T cell activation (Timepoint 16)


title: YueLab-RNA-Seq-Intestine-rep2

description: YueLab-RNA-seq-embryonic-Trunk_merged.TPM.txt

value: Intestine


title: BJ1_Control_R1_HiC

value: Foreskin fibroblast

value: Control

value: 4:1DMEM:Medium199,10%FBS, 0.01mgHygroB


title: Donor 2, Timepoint 22, Replicate C

description: miRNA expression after T cell activation (Timepoint 22)


title: YueLab-RNA-Seq-Colon-rep2

value: Colon


title: YueLab-RNA-Seq-Colon-rep1


title: x030_b2_p4_F04_1c_E_S30: Mouse embryonic stomach at E13.5 Batch2


title: YueLab-RNA-Seq-Heart-rep2

description: YueLab-RNA-seq-embryonic-Brain_merged.TPM.txt

value: Heart


title: YueLab-RNA-Seq-Intestine-rep1


title: x033_b1_p1_A05_1c_M_S33: Mouse embryonic stomach at E13.5 Batch1


title: x031_b2_p4_G04_1c_E_S31: Mouse embryonic stomach at E13.5 Batch2


title: x031_b1_p1_G04_1c_E_S31: Mouse embryonic stomach at E13.5 Batch1


title: x030_b1_p1_F04_1c_E_S30: Mouse embryonic stomach at E13.5 Batch1


title: x028_b2_p4_D04_1c_E_S28: Mouse embryonic stomach at E13.5 Batch2


title: YueLab-RNA-Seq-Heart-rep1


title: x029_b1_p1_E04_1c_E_S29: Mouse embryonic stomach at E13.5 Batch1


title: Donor 2, Timepoint 10, Replicate C

description: miRNA expression after T cell activation (Timepoint 10)


title: YueLab-RNA-Seq-Brain-rep2

value: Brain


title: Donor 2, Timepoint 4, Replicate C

description: miRNA expression after T cell activation (Timepoint 4)


title: Donor 2, Timepoint 12, Replicate C

description: miRNA expression after T cell activation (Timepoint 12)


title: S18-5874TUCR (S18-5874)

city: Bologna

first: Luca

last: Morandi

address: via Altura 3

department: DIBINEM

country: Italy

institute: University of Bologna

data_processing:
Reads were mapped by BWAmeth generating the .bam file which was processed by MethylDackel using hg38 for human samples, Felis_catus_9.0 for feline samples as a reference;
EPIC-TABSAT web-tool
Methylation Plotter Webtool
ClustVis webtool
EasyROC
Genome_build: hg38
Supplementary_files_format_and_content: Table 1: Clinical details of mammalian species other than human included in this study:
Supplementary_files_format_and_content: Table 2: genomic regions investigated in this study (reference genome: hg38; gene annotations were retrieved from UCNE database[2] and from Bajerano database[1]):
Supplementary_files_format_and_content: Table 3: Best and worst AUC values for all the seven UCNEs; the number indicates the position on the genome taking into account hg38 as a reference:
Supplementary_files_format_and_content: Table S1: Summary Table with the mean, the standard deviation, the minimum, the maximum and p value of the Kruskal-Wallis test for each position and group of samples comparing all SCC from all the species together vs normal samples and feline stomatitis
Supplementary_files_format_and_content: Table S2: Summary Table comparing human normal donors vs SCC
Supplementary_files_format_and_content: Table S3: Summary Table with the mean, the standard deviation, the minimum, the maximum and p value of the Kruskal-Wallis test for feline SCC vs feline normal samples and feline stomatitis
Supplementary_files_format_and_content: TUCRDataFinalJuly2020: methylation level of each CpG for all cases

organism: Hystrix cristata

source_name: oral mucosa

extract_protocol:
MasterPure DNA purification kit or QuickExtract FFPE DNA Extraction kit
Locus-specific amplicon libraries were generated with tagged primers in two steps: a first PCR amplification for target enrichment, and a second shorter amplification session (8 cycles) to allow the barcoding of the template-specific amplicons obtained from the first amplification step using the Nextera™ Index Kit (Illumina, San Diego, CA, USA)

treatment_protocol: Formali Fixed Paraffin Embedded Tissue or oral brushing specimens

tag: disease state

value: SCC

value: FFPE

tag: tnm

value: Squamous Cell Carcinoma


title: x028_b1_p1_D04_1c_E_S28: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1


title: Donor 2, Timepoint 2, Replicate C

description: miRNA expression after T cell activation (Timepoint 2)

value: female


title: Donor 2, Timepoint 6, Replicate C

description: miRNA expression after T cell activation (Timepoint 6)


title: YueLab-RNA-Seq-Brain-rep1


title: x027_b1_p1_C04_1c_E_S27: Mouse embryonic stomach at E13.5 Batch1

value: stomach

value: embryonic day 13.5


title: x029_b2_p4_E04_1c_E_S29: Mouse embryonic stomach at E13.5 Batch2


title: Donor 2, Timepoint 0, Replicate C

description: miRNA expression after T cell activation (Timepoint 0)


title: BJ5ta_ATMiX_R1_HiC

source_name: Skin fibroblast


title: BJ5ta_ATMiC_R1_HiC


title: x027_b2_p4_C04_1c_E_S27: Mouse embryonic stomach at E13.5 Batch2


title: BADGER (BADGER)

organism: Meles meles

value: Normal

value: oral brush

value: unknown

value: Normal oral mucosa


title: S17-3828TUCR (S17-3828)


title: Donor 2, Timepoint 14, Replicate C

description: miRNA expression after T cell activation (Timepoint 14)


title: x026_b1_p1_B04_1c_E_S26: Mouse embryonic stomach at E13.5 Batch1


title: Donor 2, Timepoint 24, Replicate B


title: Donor 2, Timepoint 8, Replicate C

description: miRNA expression after T cell activation (Timepoint 8)


title: x026_b2_p4_B04_1c_E_S26: Mouse embryonic stomach at E13.5 Batch2


title: x025_b1_p1_A04_1c_E_S25: Mouse embryonic stomach at E13.5 Batch1


title: Donor 2, Timepoint 20, Replicate B


title: Donor 2, Timepoint 22, Replicate B


title: BJ5ta_Recovery_R1_HiC

value: Foreskin fibroblast

value: Recovery


title: x025_b2_p4_A04_1c_E_S25: Mouse embryonic stomach at E13.5 Batch2


title: Donor 2, Timepoint 18, Replicate B


title: BJ5ta_Recovery_R2_HiC

value: 4:1DMEM:Medium199,10%FBS, 0.01mgHygroB


title: Donor 2, Timepoint 16, Replicate B


title: x024_b1_p1_H03_1c_M_S24: Mouse embryonic stomach at E13.5 Batch1


title: CD4+ T cells, healthy donor 20

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

hyb_protocol: Hybridisation was performed using GeneChip® High Throughput Pico Kit (Affymatrix) according to manufacturers' instructions

scan_protocol: Scanning was performed using GeneChip® High Throughput Pico Kit (Affymatrix) according to manufacturers' instructions

data_processing: Raw data were process using the R language. First, background normalisation was performed using Robust Microarray Analysis (RMA) normalisation provided by oligo package. Each probe was then annotated using clariomshumantranscriptcluster.db package, and the average expression level was calculated if more than one probe was mapped to the same gene.

label: biotin

source_name: CD4+ T cells isolated from PBMCs of healthy donor

label_protocol: Labelling was performed using GeneChip® High Throughput Pico Kit (Affymatrix) according to manufacturers' instructions

growth_protocol: 15 ml of peripheral blood was collected from 16 healthy donors and 48 SSc patients in Lithium Heparin tubes

extract_protocol: RNA was extracted utilizing the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, Hilden, Germany) according to manufacturers’ instructions.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were separated by laying on Lymphocytes Isolation Solution (Rafer, Zaragoza, Spain) and centrifuged without braking. PBMCs were stained with fluorochrom-conjugated antibody against CD4-APC (BD Pharmingen, New Jersey, USA) in staining buffer (PBS with 2 mM of EDTA and 4 % FBS) for 20 mins. Gating strategies were employed to eliminate doublets, cell debris and DAPI+ cells. Lymphocytes were separated by forward and side scatter, in which CD4+ cells were separated by positive selection.

tag: donor

value: Healthy donor

value: F

tag: skin disease

value: HD

tag: lung disease


title: CD4+ T cells, healthy donor 26

value: M


title: CD4+ T cells, healthy donor 25


title: CD4+ T cells, healthy donor 19


title: Donor 2, Timepoint 14, Replicate B


title: Donor 2, Timepoint 6, Replicate B


title: Donor 2, Timepoint 8, Replicate B


title: x024_b2_p4_H03_1c_M_S24: Mouse embryonic stomach at E13.5 Batch2


title: ATMhTERT_Recovery_R1_HiC

value: ATMhTERT

value: Skin fibroblast


title: x023_b2_p4_G03_1c_M_S23: Mouse embryonic stomach at E13.5 Batch2

value: mixed C57BL/6 CD1


title: Donor 2, Timepoint 12, Replicate B

value: female


title: x022_b2_p4_F03_1c_M_S22: Mouse embryonic stomach at E13.5 Batch2

value: stomach


title: Donor 2, Timepoint 10, Replicate B


title: x023_b1_p1_G03_1c_M_S23: Mouse embryonic stomach at E13.5 Batch1

value: embryonic day 13.5


title: BJ5ta_Control_R1_HiC

value: Control


title: ATMhTERT_Recovery_R2_HiC


title: CD4+ T cells, healthy donor 18


title: CD4+ T cells, SSc patient 48

source_name: CD4+ T cells isolated from PBMCs of SSc patient

value: Systemic sclerosis

value: lcSSc

value: PAH


title: x022_b1_p1_F03_1c_M_S22: Mouse embryonic stomach at E13.5 Batch1


title: x020_b2_p4_D03_1c_M_S20: Mouse embryonic stomach at E13.5 Batch2


title: CD4+ T cells, healthy donor 17


title: AP768 (AP768)

organism: Felis catus

value: SCC

value: FFPE

value: Squamous Cell Carcinoma


title: x020_b1_p1_D03_1c_M_S20: Mouse embryonic stomach at E13.5 Batch1


title: AP18102 (AP18102)


title: CD4+ T cells, SSc patient 46

value: ssSSc


title: CD4+ T cells, SSc patient 47

value: F


title: Donor 2, Timepoint 4, Replicate B


title: ATMhTERT_Control_R1_HiC


title: Donor 2, Timepoint 2, Replicate B


title: AP8694 (AP8694)


title: x019_b1_p1_C03_1c_M_S19: Mouse embryonic stomach at E13.5 Batch1


title: CD4+ T cells, SSc patient 45

value: Initial


title: x021_b2_p4_E03_1c_M_S21: Mouse embryonic stomach at E13.5 Batch2


title: CAT-6 (CAT17967)

value: Normal

value: Normal oral mucosa


title: CD4+ T cells, SSc patient 41


title: x019_b2_p4_C03_1c_M_S19: Mouse embryonic stomach at E13.5 Batch2


title: Donor 2, Timepoint 24, Replicate A


title: CD4+ T cells, SSc patient 43


title: CAT-5 (CAT17951)


title: Donor 2, Timepoint 16, Replicate A


title: x018_b1_p1_B03_1c_M_S18: Mouse embryonic stomach at E13.5 Batch1


title: Donor 2, Timepoint 18, Replicate A


title: x021_b1_p1_E03_1c_M_S21: Mouse embryonic stomach at E13.5 Batch1


title: CAT-7 (CAT17979)


title: Donor 2, Timepoint 22, Replicate A


title: Donor 2, Timepoint 20, Replicate A


title: CD4+ T cells, SSc patient 42


title: x017_b2_p4_A03_1c_M_S17: Mouse embryonic stomach at E13.5 Batch2


title: Donor 2, Timepoint 0, Replicate B


title: CD4+ T cells, SSc patient 44

value: dcSSc


title: CD4+ T cells, SSc patient 38


title: CD4+ T cells, SSc patient 40

value: ILD


title: AP17714 (AP17714)


title: AP17595 (AP17595)


title: Donor 2, Timepoint 14, Replicate A

value: female


title: x017_b1_p1_A03_1c_M_S17: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1

value: stomach


title: Donor 2, Timepoint 12, Replicate A


title: AP17076 (AP17076)

value: Stomatitis


title: CD4+ T cells, SSc patient 39

value: Systemic sclerosis


title: CD4+ T cells, SSc patient 37


title: x016_b2_p4_H02_1c_E_S16: Mouse embryonic stomach at E13.5 Batch2

value: embryonic day 13.5


title: x016_b1_p1_H02_1c_E_S16: Mouse embryonic stomach at E13.5 Batch1


title: Donor 2, Timepoint 8, Replicate A


title: Donor 2, Timepoint 6, Replicate A


title: x018_b2_p4_B03_1c_M_S18: Mouse embryonic stomach at E13.5 Batch2


title: CD4+ T cells, SSc patient 36

value: M


title: AP13806 (AP13806)

value: SCC


title: CD4+ T cells, SSc patient 35


title: CAT-3 (CAT13583)

value: FFPE


title: x015_b2_p4_G02_1c_E_S15: Mouse embryonic stomach at E13.5 Batch2


title: AP7692 (AP7692)


title: Donor 2, Timepoint 10, Replicate A


title: x014_b2_p4_F02_1c_E_S14: Mouse embryonic stomach at E13.5 Batch2


title: CD4+ T cells, SSc patient 34


title: Donor 2, Timepoint 4, Replicate A


title: Donor 2, Timepoint 2, Replicate A


title: CAT-4 (CAT15073)


title: AP498 (AP498)


title: CD4+ T cells, SSc patient 33


title: CD4+ T cells, SSc patient 31


title: x014_b1_p1_F02_1c_E_S14: Mouse embryonic stomach at E13.5 Batch1


title: Donor 2, Timepoint 0, Replicate A


title: AP2115 (AP2115)


title: Donor 1, Timepoint 24, Replicate C


title: AP18404 (AP18404)


title: x015_b1_p1_G02_1c_E_S15: Mouse embryonic stomach at E13.5 Batch1


title: CD4+ T cells, SSc patient 32


title: x013_b2_p4_E02_1c_E_S13: Mouse embryonic stomach at E13.5 Batch2


title: CD4+ T cells, SSc patient 30


title: Donor 1, Timepoint 22, Replicate C


title: AP18136 (AP18136)


title: x013_b1_p1_E02_1c_E_S13: Mouse embryonic stomach at E13.5 Batch1


title: x012_b2_p4_D02_1c_E_S12: Mouse embryonic stomach at E13.5 Batch2


title: AP17936 (AP17936)


title: CD4+ T cells, SSc patient 28

value: lcSSc

value: PAH


title: CD4+ T cells, SSc patient 29

value: F


title: Donor 1, Timepoint 18, Replicate C


title: x012_b1_p1_D02_1c_E_S12: Mouse embryonic stomach at E13.5 Batch1


title: x011_b2_p4_C02_1c_E_S11: Mouse embryonic stomach at E13.5 Batch2


title: Donor 1, Timepoint 16, Replicate C


title: AP17845 (AP17845)

value: Squamous Cell Carcinoma


title: CD4+ T cells, SSc patient 26

value: ssSSc


title: Donor 1, Timepoint 14, Replicate C


title: AP17827 (AP17827)


title: CAT-2 (CAT17664)

value: Normal

value: Normal oral mucosa


title: AP17919 (AP17919)


title: Donor 1, Timepoint 12, Replicate C


title: CD4+ T cells, SSc patient 24

value: ILD


title: x010_b1_p1_B02_1c_E_S10: Mouse embryonic stomach at E13.5 Batch1


title: Donor 1, Timepoint 20, Replicate C

value: female


title: CD4+ T cells, SSc patient 25

value: dcSSc


title: Donor 1, Timepoint 10, Replicate C


title: CAT-1 (CAT17663)


title: Donor 1, Timepoint 8, Replicate C


title: CD4+ T cells, SSc patient 27


title: x010_b2_p4_B02_1c_E_S10: Mouse embryonic stomach at E13.5 Batch2

value: mixed C57BL/6 CD1

value: stomach


title: CD4+ T cells, SSc patient 23

value: Systemic sclerosis


title: Donor 1, Timepoint 6, Replicate C


title: x009_b1_p1_A02_1c_E_S9: Mouse embryonic stomach at E13.5 Batch1

value: embryonic day 13.5


title: AP16102 (AP16102)

value: Stomatitis


title: x011_b1_p1_C02_1c_E_S11: Mouse embryonic stomach at E13.5 Batch1


title: CD4+ T cells, SSc patient 22


title: x008_b2_p4_H01_1c_M_S8: Mouse embryonic stomach at E13.5 Batch2


title: Donor 1, Timepoint 4, Replicate C


title: Donor 1, Timepoint 2, Replicate C


title: AP2633 (AP2633)


title: x007_b2_p4_G01_1c_M_S7: Mouse embryonic stomach at E13.5 Batch2


title: CD4+ T cells, SSc patient 20


title: x009_b2_p4_A02_1c_E_S9: Mouse embryonic stomach at E13.5 Batch2


title: AP10728 (AP10728)


title: CD4+ T cells, SSc patient 19


title: AP9960 (AP9960)

value: SCC


title: x006_b2_p4_F01_1c_M_S6: Mouse embryonic stomach at E13.5 Batch2


title: Donor 1, Timepoint 24, Replicate B


title: Donor 1, Timepoint 0, Replicate C


title: AP9641 (AP9641)

value: FFPE


title: Donor 1, Timepoint 22, Replicate B


title: AP847 (AP847)


title: CD4+ T cells, SSc patient 18

value: Initial


title: Donor 1, Timepoint 20, Replicate B


title: AP4925 (AP4925)


title: CD4+ T cells, SSc patient 21

value: M

value: lcSSc


title: AP5978 (AP5978)


title: CD4+ T cells, SSc patient 16

value: F


title: x005_b2_p4_E01_1c_M_S5: Mouse embryonic stomach at E13.5 Batch2


title: x008_b1_p1_H01_1c_M_S8: Mouse embryonic stomach at E13.5 Batch1


title: CD4+ T cells, SSc patient 17


title: AP18369 (AP18369)

value: Squamous Cell Carcinoma


title: x005_b1_p1_E01_1c_M_S5: Mouse embryonic stomach at E13.5 Batch1


title: x007_b1_p1_G01_1c_M_S7: Mouse embryonic stomach at E13.5 Batch1


title: AP18349 (AP18349)


title: Donor 1, Timepoint 14, Replicate B


title: AP18329 (AP18329)


title: CD4+ T cells, SSc patient 13


title: x006_b1_p1_F01_1c_M_S6: Mouse embryonic stomach at E13.5 Batch1


title: x004_b1_p1_D01_1c_M_S4: Mouse embryonic stomach at E13.5 Batch1


title: CD4+ T cells, SSc patient 14


title: AP15289TUCR (AP15289)


title: Donor 1, Timepoint 12, Replicate B


title: CAT11306 (CAT11306)


title: AP8012TUCR (AP8012)


title: x003_b1_p1_C01_1c_M_S3: Mouse embryonic stomach at E13.5 Batch1


title: Donor 1, Timepoint 16, Replicate B


title: Donor 1, Timepoint 18, Replicate B


title: CD4+ T cells, SSc patient 15

value: ssSSc


title: Donor 1, Timepoint 10, Replicate B


title: CD4+ T cells, SSc patient 11


title: CD4+ T cells, SSc patient 12


title: Donor 1, Timepoint 8, Replicate B


title: Donor 1, Timepoint 6, Replicate B


title: CD4+ T cells, SSc patient 9


title: x002_b2_p4_B01_1c_M_S2: Mouse embryonic stomach at E13.5 Batch2


title: CD4+ T cells, SSc patient 10


title: Donor 1, Timepoint 4, Replicate B


title: AP11378TUCR (AP11378)


title: x001_b2_p4_A01_1c_M_S1: Mouse embryonic stomach at E13.5 Batch2


title: x003_b2_p4_C01_1c_M_S3: Mouse embryonic stomach at E13.5 Batch2


title: CD4+ T cells, SSc patient 8


title: CD4+ T cells, SSc patient 7


title: DOG5 (DOG5)

organism: Canis lupus familiaris

value: Normal

value: oral brush

value: Normal oral mucosa


title: x002_b1_p1_B01_1c_M_S2: Mouse embryonic stomach at E13.5 Batch1


title: CD4+ T cells, SSc patient 6


title: Donor 1, Timepoint 2, Replicate B

value: female


title: Donor 1, Timepoint 0, Replicate B


title: DOG4 (DOG4)


title: x004_b2_p4_D01_1c_M_S4: Mouse embryonic stomach at E13.5 Batch2

value: mixed C57BL/6 CD1


title: DOG3 (DOG3)


title: Fosl2 Ko 3

city: Zurich

first: Oliver

last: Distler

address: Gloriastrasse 25

department: Department of Rheumatology

country: Switzerland

institute: University Hospital Zurich

data_processing:
The “TopHat” algorithm was used to align the reads to the mm10 genome
BAM files were further analyzed using the Cufflinks suite of programs (running consecutively: Cufflinks, Cuffcompare, Cuffdiff)
Genome_build: mm10
Supplementary_files_format_and_content: xlsx, contains FPKM of all genes in sheet 1, differently expressed genes in sheet 2

source_name: Naive CD4+ T cells

extract_protocol:
T cells were collected, washed in PBS and RNA was extracted using Qiagen’s RNeasy Mini Kit. RIN values ranged from 8.1 to 10.0
Directional Poly-A RNA-seq libraries were prepared

treatment_protocol: Naive T cells were stimulated for 24 hours with anti-CD3 and anti-CD28.

value: Sorted CD4+CD62LhighCD44low

tag: stimulation

value: 24 hours stimulation with anti-CD3 and anti-CD28

tag: genotype/variation

value: Fosl2fl/fl CD4-cre+


title: x001_b1_p1_A01_1c_M_S1: Mouse embryonic stomach at E13.5 Batch1

value: stomach

value: embryonic day 13.5


title: Fosl2 Ko 2


title: DOG1 (DOG1)


title: Fosl2 Ko 1


title: Donor 1, Timepoint 24, Replicate A


title: CD4+ T cells, SSc patient 5

value: Systemic sclerosis


title: Donor 1, Timepoint 20, Replicate A


title: Donor 1, Timepoint 18, Replicate A


title: AP16359TUCR (AP16359)

value: SCC

value: FFPE


title: Donor 1, Timepoint 22, Replicate A


title: CD4+ T cells, SSc patient 4

value: lcSSc

value: ILD


title: CD4+ T cells, healthy donor 13

value: Healthy donor

value: M

value: HD


title: CD4+ T cells, SSc patient 2

value: F


title: Fosl2 Tg 3

value: Fosl2 Tg


title: Fosl2 Tg 2


title: CD4+ T cells, SSc patient 3

value: dcSSc


title: Fosl2 Tg 1


title: CD4+ T cells, SSc patient 1


title: Donor 1, Timepoint 14, Replicate A

value: female


title: Control 3

value: Sorted CD4+CD62LhighCD44low

value: wt


title: AP16030TUCR (AP16030)

value: Squamous Cell Carcinoma


title: Donor 1, Timepoint 16, Replicate A


title: DOG2 (DOG2)

value: Normal

value: oral brush

value: Normal oral mucosa


title: YY1-Rep2

city: Durham

first: Bryan

middle: J

last: Venters

state: NC

address: 6 Davis Drive

institute: EpiCypher

description: CUT&RUN YY1 500K Nuclei_bioRep2

data_processing:
Library strategy: CUT&RUN
Base-calling: illumina software
Adapter Trimming: TBD
Alignment: TBD
Filtering: TBD
Peak Calliing: TBD
Genome_build: hg19
Supplementary_files_format_and_content: PCRP_Metadata.xlsx: contains one excel sheet

source_name: K562 human immortalised myelogenous leukemia cell line

growth_protocol: K562 cells were maintained (1–10 × 10^5 cell/ml) in T25 flasks in IMDM + 10% FBS  +  1% Pen/Strep

extract_protocol:
Nuclei were extracted by incubating cells on ice for 10 min in Nuclei Extraction buffer (NE: 20 mM HEPES–KOH, pH 7.9; 10 mM KCl; 0.1% Triton X-100; 20% Glycerol; 0.5mM spermidine; 1x complete protease inhibitor [Roche # 11836170001]), collecting by centrifugation (600 g, 3 min, 4C), discarding the supernatant, and resuspending at [100 µl / 500K nuclei] sample in NE buffer. CUTANA protocol v1.5.1; optimized version of PMID: 29651053
NEBNext Ultra II DNA Library Prep kit (New England Biolabs #E7645S)
Cleavage under targets and Release using nuclease

treatment_protocol: Native cells used for Nuclei extraction

tag: antibody


title: Donor 1, Timepoint 10, Replicate A


title: USF2-Rep2

description: CUT&RUN USF2 500K Nuclei_bioRep2


title: CD4+ T cells, healthy donor 12


title: NRF1-Rep2

description: CUT&RUN NRF1 500K Nuclei_bioRep2


title: CD4+ T cells, healthy donor 11


title: Control 2

value: 24 hours stimulation with anti-CD3 and anti-CD28


title: AP17735TUCR (AP17735)

value: SCC

value: FFPE


title: Control 1


title: Mouse IgG

description: CUT&RUN Mouse IgG 500K Nuclei

value: Mouse IgG Invitrogen Cat# 10400C, lot VD293456


title: USF1-Rep2

description: CUT&RUN USF1 500K Nuclei_bioRep2


title: CTCF-Rep2

description: CUT&RUN CTCF 500K Nuclei_bioRep2

value: anti-CTCF Millipore Cat # 07-729, lot 3205452


title: Donor 1, Timepoint 8, Replicate A


title: Donor 1, Timepoint 6, Replicate A


title: CD4+ T cells, healthy donor 8

value: Healthy donor


title: STF9 rep3

status: Public on Sep 03 2020

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: STF_raw_counts; DESeq2_STF9_vs_T4A

data_processing:
Base calls from Illumina NovaSeq 6000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Genome_build: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary_files_format_and_content: Matrix file for raw HTSeq counts; individual files for DESeq2 for comparison of each suppressor mutant with parent strain

organism: Schizosaccharomyces pombe

growth_protocol: log phase cultures, 30ºC, YES medium

extract_protocol:
hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina HiSeq 4000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).
Stranded polyA+ RNA Seq

tag: lab strain number

value: BS 11

tag: growth conditions

value: log phase culture, YES medium

tag: developmental stage

value: vegetative growth


title: STF6 rep3

description: STF_raw_counts; DESeq2_STF6_vs_T4A

value: BS 8


title: Donor 1, Timepoint 4, Replicate A

tag: gender

value: female


title: STF9 rep2

description: STF_raw_counts; DESeq2_STF9_vs_T4A


title: CD4+ T cells, healthy donor 9

value: F

value: HD


title: CD4+ T cells, healthy donor 10


title: STF9 rep1

description: STF_raw_counts; DESeq2_STF9_vs_T4A


title: Donor 1, Timepoint 2, Replicate A


title: Rabbit IgG

description: CUT&RUN Rabbit IgG 500K Nuclei_bioRep2

value: CUTANA™ Rabbit IgG CUT&RUN Negative Control Antibody EpiCypher 13-0042, lot 20036001-52


title: STF6 rep2

description: STF_raw_counts; DESeq2_STF6_vs_T4A


title: STF6 rep1

description: STF_raw_counts; DESeq2_STF6_vs_T4A


title: CD4+ T cells, healthy donor 6


title: Donor 1, Timepoint 0, Replicate A


title: Donor 1, Timepoint 12, Replicate A


title: CD4+ T cells, healthy donor 5


title: TAM062119_007

city: Madison

first: Owen

middle: James

last: Tamplin

state: WI

address: 1111 Highland Ave

department: Cell and Regenerative Biology

institute: University of Wisconsin-Madison

data_processing:
Gene expression quantification: Raw reads were aligned to reference genome mm10 using STAR (Dobin et al., 2013). ENSEMBL genes were quantified using FeatureCounts (Liao, Smyth, & Shi, 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Table of raw counts per gene – tabular text file

source_name: Gabbr1 null_sorted mouse bone marrow HSPCs (~12,000 cell/LSK population)

extract_protocol:
HSPCs (~12,000 cell/LSK population) from P15 wild-type (n=4) or Gabbr1 null (n=4) BM were sorted (MoFlo Astrios) and collected in Trizol LS (Invitrogen). Volumes were adjusted to a final ratio of 3:1 for Trizol LS and nuclease-free water. Samples were stored at -80°C until total RNA was isolated. Then samples were thawed, equilibrated to room temperature, and divided into 800 μl aliquots. 5 μg of Sigma “GenElute” linear polyacrylamide (LPA; Cat. No. 56575-1ML), diluted in nuclease-free water, was added to each aliquot and vortexed for 30 seconds. Chloroform extraction and 3 ethanol washes were performed as per the Trizol product insert (Invitrogen protocol Cat. No. 10296-010). The pellet was resuspended in 6 μl RNAse-free water.
RNA samples were quantified and purity and integrity were checked using NanoDrop™ One Spectrophotometer (Thermo Scientific) and Agilent 4200 TapeStation. NGS library preparation was completed using NuGen’s Ovation® SoLo RNA-Seq Systems, per their User Guide M01406 v4, including a targeted depletion with SoLo AnyDeplete Mouse Probe Mix. RNA input into library preparation was between 3.6 - 5 ng. The number of cycles for the first library PCR amplification were optimized using qPCR, as outlined in the SoLo User Guide, with the Prime Pro 48 Real-Time PCR system (Techne).
Completed libraries were quantified using Qubit fluorometer (Invitrogen) and size was determined using TapeStation. Libraries were pooled based on Qubit dsDNA concentration and run on MiSeq for index balancing. The second pool, with corrected library inputs based on the %Reads Identified (PF) results from the MiSeq run, was purified with 1:1 Agencourt AMPure XP beads. The final, purified pool was quantified using Qubit and pool size was determined using TapeStation. Sequencing was run on a NovaSeq6000 SP flow cell, 2x50 bp, two lanes, at the University of Illinois Roy J. Carver Biotechnology Center High-Throughput Sequencing and Genotyping Unit.

tag: strain background

value: Gabbr1 null mutant

value: hematopoietic stem and progenitor cells (HSPCs)


title: CD4+ T cells, healthy donor 7


title: TAM062119_004

source_name: WT_sorted mouse bone marrow HSPCs (~12,000 cell/LSK population)

value: WT


title: TAM062119_005


title: TAM062119_006


title: CD4+ T cells, healthy donor 4

value: M


title: TAM062119_003


title: Nanos2RFP-Positive germ cells

city: Houston

first: Nicholas

last: Webster

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
Single-cell data were aligned to the murine reference genome (mm10) using CellRanger from 10X Genomics and processed using Seurat v.3.1.1
cells with >5% mitochondrial expression counts or expressing less than 1,000 or more than 5,000 unique genes were removed from further analysis.
For each of the samples, Seurat employed a global-scaling normalization method to normalize the gene expression for each cell by multiplying by 10,000 and log transforming the resulting expression levels.
Data were then scaled prior to dimensional reduction using the top 2,000 most variable features. Cells from each sample were then clustered using the default Louvain algorithm with a resolution parameter equal to 0.5
Differential gene analysis was performed using the Seurat “FindAllMarkers” function. Clusters of interest were compared and genes with an absolute natural log fold change >= 0.25 and Bonferroni adjusted p.value < 0.05 were reported. Pathways analysis was performed using Gene Set Enrichment Analysis
Each gene set was analyzed using the “Compute Overlap” feature and pathways with an FDR < 0.05 were reported.
Genome_build: mm10
Supplementary_files_format_and_content: the raw and filtered barcodes, features, and matrix files

source_name: Embryonic germ cells

extract_protocol:
Germ cells were sorted, single cell suspension loaded on a Chromium controller (10x Genomics) to generate single cell GEMS (Gel Beads-In-Emulsions) where full length cDNA was synthesized and barcoded.
Subsequently the GEMS are broken and cDNA from each single cell are pooled. Following cleanup using Dynabeads MyOne Silane Beads (Thermo Fisher, 370020), cDNA is amplified by PCR.  The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. Final library was generated by amplification

tag: strain

tag: tissue

value: Embryonic germ cell


title: Nanos2RFP-Negative germ cells


title: PDAC_#211

city: Shinjuku

first: Yohei

last: Masugi

state: Tokyo

address: 35 Shinanomachi

department: Pathology

country: Japan

institute: Keio University School of Medicine

description: Gene expression data from pancreatic ductal adenocarcinoma, case #211.

hyb_protocol: Fragmented and labeled ss-cDNA were hybridized for 16 hr at 45°C on GeneChip Clariom D Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: CEL files were summarized using the SST RMA algorithm in Transcriptome Analysis Console v4.0.2.15 (Affymetrix)

source_name: Pancreatic ductal adenocarcinoma, case #211

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 2 ng total RNA (GeneChip WT Pico Reagent Kit User Guide, Thermo Fisher Scientific Applied Biosystems). Biotinylated ss-cDNA yield were checked with the NanoDrop ND-2000c Spectrophotometer.

extract_protocol: Total RNA was extracted from the frozen tissue of pancreatic ductal adenocarcinoma using RNeasy RNA Purification Kit.

value: Pancreatic ductal adenocarcinoma

tag: stroma type

value: A-stroma


title: PDAC_#132

description: Gene expression data from pancreatic ductal adenocarcinoma, case #132.

source_name: Pancreatic ductal adenocarcinoma, case #132

value: C-stroma


title: PDAC_#223

description: Gene expression data from pancreatic ductal adenocarcinoma, case #223.

source_name: Pancreatic ductal adenocarcinoma, case #223

value: F-stroma


title: Irradiated_VC

city: Nanjing

first: Shentong

last: Fang

address: Longmian Avenue

country: China

institute: China Pharmaceutical University

description: Sample 4

data_processing:
The Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3’ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
Reads were aligned to mouse reference genome mm10
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx

source_name: bone marrow

extract_protocol:
the mice were injected intravenously with VE-Cadherin A647 (BioLegend, CA). WBM plug was obtained by flushing tibias and digestion with Collagenase I (Worthington Biochemical Corporation, NJ), Dispase II (Roche Applied Science, Swizerland) and DNase I (Sigma-Aldrich) in HBSS with calcium and magnesium. The digested marrow was pooled with staining buffer (HBSS +2% FBS +2mM EDTA) to stop the enzymatic reaction. The red cell-depleted WBM cells were stained with antibodies against CD45 eFluor 450, Ter119 eFluor 450, and biotinylated LepR (1:100, R&D Systems, CA) on ice for 30 minutes followed by streptavidin PE-Cy5 on ice for 15 minutes.
use the Chromium Single-Cell 3′RNA-sequencing system (10x Genomics, Pleasanton, CA) with the Reagent Kit v3.1 according to the manufacturer’s instructions
Sample libraries were sequenced on the Illumina NovaSeq 6000 system using S2 flow cell (Illumina)

treatment_protocol:
For sample 1-3, mice received tamoxifen via gavage.
Five consecutive intragastric doses of tamoxifen were administered to Vegfcflox/flox  and Rosa26-CreERT2; Vegfcflox/flox  mice at 7-8 weeks old. Two weeks later, three VciΔR26 and three Vcfl/fl mice received a sub-lethal dose (4Gy) of total body irradiation.Seven days later, isolated DAPI-Lin- CD45-Ter119- cells from the non-irradiated VciΔR26 mice (pooled from 3 mice), non-irradiated Vcfl/fl mice (pooled from 3 mice), irradiated VciΔR26 (pooled from 2 mice) and, irradiated Vcfl/fl mice (pooled from 2 mice) were resuspended in 0,04% bovine serum albumin and HBSS; and analyzed using the Chromium Single-Cell 3′RNA-sequencing system (10x Genomics, Pleasanton, CA) with the Reagent Kit v3.1.

value: bone marrow

tag: genotype

value: RosaCreERT2;Vegfc flox/flox

tag: treatment

value: Irradiated


title: Irradiated_Control

description: Sample 3

value: Vegfc flox/flox


title: PDAC_#225

description: Gene expression data from pancreatic ductal adenocarcinoma, case #225.

source_name: Pancreatic ductal adenocarcinoma, case #225

tag: disease state


title: Non_irradiated_VC

description: Sample 2


title: PDAC_#283

description: Gene expression data from pancreatic ductal adenocarcinoma, case #283.

source_name: Pancreatic ductal adenocarcinoma, case #283


title: primary osteoblast culture, patient 18

city: Auckland

first: Dorit

last: Naot

address: Private Bag 92019

department: Medicine

country: New Zealand

institute: University of Auckland

description: Gene expression data from osteoblast cultured from bone obtained from a patient of European ancestry

hyb_protocol: cRNA samples were hybridized to GeneChip® PrimeView™ Human Gene Expression Arrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: The GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Transcriptome Analysis Console 4.0.2 (Affymetrix, Inc., Thermo Fisher Scientific), using the default settings.

source_name: primary osteoblast culture, patient 18

label_protocol: Biotinylated, fragmented cRNA was prepared from 210 ng of total RNA using the GeneChip® 3′ IVT Express Kit (Affymetrix).

growth_protocol: Bone fragments were cultured in DMEM/10% FBS and 5 μg/mL l-ascorbic acid 2-phosphate to allow outgrowth of osteoblastic cells. Cell were harvested when they reached 90-100% confluence.

extract_protocol: RNA was extracted from cells using the RNeasy Mini-prep kit with in-column DNase digestion (Qiagen)

treatment_protocol: No treatment was used.

tag: disease

value: osteoarthritis

tag: cell type

value: osteoblasts

tag: ancestry

value: European


title: PDAC_#220

description: Gene expression data from pancreatic ductal adenocarcinoma, case #220.

source_name: Pancreatic ductal adenocarcinoma, case #220


title: primary osteoblast culture, patient 19

source_name: primary osteoblast culture, patient 19


title: PDAC_#293

description: Gene expression data from pancreatic ductal adenocarcinoma, case #293.

source_name: Pancreatic ductal adenocarcinoma, case #293


title: PDAC_#282

description: Gene expression data from pancreatic ductal adenocarcinoma, case #282.

source_name: Pancreatic ductal adenocarcinoma, case #282


title: primary osteoblast culture, patient 20

source_name: primary osteoblast culture, patient 20


title: PDAC_#241

description: Gene expression data from pancreatic ductal adenocarcinoma, case #241.

source_name: Pancreatic ductal adenocarcinoma, case #241


title: PDAC_#249

description: Gene expression data from pancreatic ductal adenocarcinoma, case #249.

source_name: Pancreatic ductal adenocarcinoma, case #249


title: PDAC_#238

description: Gene expression data from pancreatic ductal adenocarcinoma, case #238.

source_name: Pancreatic ductal adenocarcinoma, case #238


title: primary osteoblast culture, patient 17

source_name: primary osteoblast culture, patient 17


title: PDAC_#288

description: Gene expression data from pancreatic ductal adenocarcinoma, case #288.

source_name: Pancreatic ductal adenocarcinoma, case #288


title: PDAC_#325

description: Gene expression data from pancreatic ductal adenocarcinoma, case #325.

source_name: Pancreatic ductal adenocarcinoma, case #325


title: PDAC_#192

description: Gene expression data from pancreatic ductal adenocarcinoma, case #192.

source_name: Pancreatic ductal adenocarcinoma, case #192


title: PDAC_#226

description: Gene expression data from pancreatic ductal adenocarcinoma, case #226.

source_name: Pancreatic ductal adenocarcinoma, case #226


title: PDAC_#153

description: Gene expression data from pancreatic ductal adenocarcinoma, case #153.

source_name: Pancreatic ductal adenocarcinoma, case #153


title: primary osteoblast culture, patient 15

description: Gene expression data from osteoblast cultured from bone obtained from a patient of Polynesian ancestry

source_name: primary osteoblast culture, patient 15

value: Polynesian


title: PDAC_#296

description: Gene expression data from pancreatic ductal adenocarcinoma, case #296.

source_name: Pancreatic ductal adenocarcinoma, case #296


title: PDAC_#323

description: Gene expression data from pancreatic ductal adenocarcinoma, case #323.

source_name: Pancreatic ductal adenocarcinoma, case #323


title: PDAC_#138

description: Gene expression data from pancreatic ductal adenocarcinoma, case #138.

source_name: Pancreatic ductal adenocarcinoma, case #138


title: primary osteoblast culture, patient 12

source_name: primary osteoblast culture, patient 12


title: PDAC_#229

description: Gene expression data from pancreatic ductal adenocarcinoma, case #229.

source_name: Pancreatic ductal adenocarcinoma, case #229


title: Drought_T

city: Brno

first: Vivek

middle: Kumar

last: Raxwal

address: building A26, Kamenice 753/5

department: Plant Molecular Biology

country: Czech Republic

institute: Central European Institute of Technology

data_processing:
FASTQC for quality control
Bowtie2/Tophat2 for mapping to TAIR 10
Samtools for pre-processing
MACS2 for peak calling
Cufflink, cummerband for RNA-seq
Genome_build: TAIR10
Supplementary_files_format_and_content: narrow peak containing coordinates of the open chromatin region with tag density

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Pants were grown on 1/2MS plate with 3% sucrose for 10 days before giving stress

extract_protocol:
For RNA-seq, total RNA was extracted with Qiagen plant RNA extraction kit. For Dnase-seq, Nuclei were extracted using protocol deescribed by Dorweiler et al 2000 followed by Dnase I digestion as described by He et al 2012. For FAIRE-seq, seedlings were fixed with formaldehyde before extracting nuclei and chromatin was extracted as described by Giresi et al 2007.
DNA library were prepared with NEB kit whereas RNA-seq was prepared as per protocol of Illumina TruSeq RNA sample preparation kit.
50 bp single end on Illumina HiSeq 2000

treatment_protocol: heat (38C for 6h), cold (4C for 24h), salt (250mM Nacl for 6h) and drought(air dry 1h)

tag: genetic accession

value: Columbia-0 (Col-0)

tag: abiotic stress

value: Drought

tag: age

value: 10 day old


title: primary osteoblast culture, patient 13

source_name: primary osteoblast culture, patient 13


title: primary osteoblast culture, patient 9

description: Gene expression data from osteoblast cultured from bone obtained from a patient of European ancestry

source_name: primary osteoblast culture, patient 9


title: primary osteoblast culture, patient 14

source_name: primary osteoblast culture, patient 14


title: primary osteoblast culture, patient 11

source_name: primary osteoblast culture, patient 11


title: primary osteoblast culture, patient 2

source_name: primary osteoblast culture, patient 2


title: primary osteoblast culture, patient 10

source_name: primary osteoblast culture, patient 10


title: CHC326N [non-tumor liver tissue]

type: genomic

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

country: France

institute: Ligue Contre Le Cancer

description: SAMPLE 270

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing:
Standard Illumina protocol. Beta values exported from Illumina Beadstudio software.
(provide the normalization method) Average Beta
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

label_protocol: Standard Illumina protocol

growth_protocol: Not applicable

extract_protocol: DNA was extracted from 3 mm3 frozen tumor samples using high salt precipitation (as described in PMID: 3344216).

treatment_protocol: Not applicable

tag: age at sampling

value: M

value: non-tumor liver tissue


title: CHC302N [non-tumor liver tissue]

description: SAMPLE 272


title: CHC313N [non-tumor liver tissue]

description: SAMPLE 274

value: F


title: CHC306N [non-tumor liver tissue]

description: SAMPLE 273


title: CHC051N [non-tumor liver tissue]

description: SAMPLE 271


title: Drought_F_R3


title: Drought_F_R2


title: primary osteoblast culture, patient 1

source_name: primary osteoblast culture, patient 1


title: primary osteoblast culture, patient 4

source_name: primary osteoblast culture, patient 4


title: primary osteoblast culture, patient 7

source_name: primary osteoblast culture, patient 7


title: primary osteoblast culture, patient 5

source_name: primary osteoblast culture, patient 5


title: primary osteoblast culture, patient 3

source_name: primary osteoblast culture, patient 3


title: primary osteoblast culture, patient 8

source_name: primary osteoblast culture, patient 8


title: CHC789N [non-tumor liver tissue]

description: SAMPLE 269


title: primary osteoblast culture, patient 6

source_name: primary osteoblast culture, patient 6


title: CHC1069N [non-tumor liver tissue]

description: SAMPLE 267


title: CHC1162N [non-tumor liver tissue]

description: SAMPLE 268


title: CHC1062N [non-tumor liver tissue]

description: SAMPLE 266


title: CHC1055N [non-tumor liver tissue]

description: SAMPLE 265


title: Drought_F_R1


title: CHC1044N [non-tumor liver tissue]

description: SAMPLE 263


title: CHC1052N [non-tumor liver tissue]

description: SAMPLE 264


title: Drought_D_R2

data_processing:
Library strategy: Dnase-seq
FASTQC for quality control
Bowtie2/Tophat2 for mapping to TAIR 10
Samtools for pre-processing
MACS2 for peak calling
Cufflink, cummerband for RNA-seq
Genome_build: TAIR10
Supplementary_files_format_and_content: narrow peak containing coordinates of the open chromatin region with tag density


title: Drought_D_R3


title: primary osteoblast culture, patient 16

source_name: primary osteoblast culture, patient 16


title: CHC203N [non-tumor liver tissue]

description: SAMPLE 261


title: Salt_T

value: Salt


title: CHC1040N [non-tumor liver tissue]

description: SAMPLE 262


title: Salt_F_R3


title: CHC1196N [non-tumor liver tissue]

description: SAMPLE 260


title: CHC934N [non-tumor liver tissue]

description: SAMPLE 259


title: CHC173N [non-tumor liver tissue]

description: SAMPLE 257


title: Salt_D_R3


title: Salt_F_R2


title: Heat_T

value: Heat


title: Salt_D_R1


title: CHC043N [non-tumor liver tissue]

description: SAMPLE 258


title: CHC081N [non-tumor liver tissue]

description: SAMPLE 255


title: CHC168N [non-tumor liver tissue]

description: SAMPLE 256


title: CHC046N [non-tumor liver tissue]

description: SAMPLE 254


title: Heat_F_R2


title: Salt_D_R2


title: CHC239N [non-tumor liver tissue]

description: SAMPLE 252


title: CHC226N [non-tumor liver tissue]

description: SAMPLE 253


title: CHC333N [non-tumor liver tissue]

description: SAMPLE 251


title: Heat_F_R1


title: Salt_F_R1


title: Drought_D_R1


title: Heat_D_R3


title: Heat_D_R1


title: Heat_D_R2


title: CHC229N [non-tumor liver tissue]

description: SAMPLE 247


title: Cold_T

value: Cold


title: CHC469N [non-tumor liver tissue]

description: SAMPLE 246


title: Cold_F_R1


title: Cold_D_R2


title: CHC591N [non-tumor liver tissue]

description: SAMPLE 244


title: CHC898N [non-tumor liver tissue]

description: SAMPLE 242


title: CHC152N [non-tumor liver tissue]

description: SAMPLE 245


title: CHC013N [non-tumor liver tissue]

description: SAMPLE 241


title: Cold_D_R1


title: CHC235N [non-tumor liver tissue]

description: SAMPLE 243


title: CHC014N [non-tumor liver tissue]

description: SAMPLE 240


title: Control_F_R3

value: Control


title: Control_F_R1


title: CHC2691T [hepatocellular carcinoma]

description: SAMPLE 239

value: hepatocellular carcinoma


title: Control_F_R2


title: Control_D_R3


title: CHC2443T [hepatocellular carcinoma]

description: SAMPLE 238


title: CHC245N [non-tumor liver tissue]

description: SAMPLE 250


title: Control_D_R2


title: CHC028N [non-tumor liver tissue]

description: SAMPLE 248


title: CHC2538T [hepatocellular carcinoma]

description: SAMPLE 237


title: Control_D_R1


title: CHC566N [non-tumor liver tissue]

description: SAMPLE 249


title: Cold_F_R2


title: CHC2135T [hepatocellular carcinoma]

description: SAMPLE 234


title: CHC2706T [hepatocellular carcinoma]

description: SAMPLE 235


title: Control_T


title: CHC2697T [hepatocellular carcinoma]

description: SAMPLE 233


title: CHC2210T [hepatocellular carcinoma]

description: SAMPLE 236


title: CHC2558T [hepatocellular carcinoma]

description: SAMPLE 232


title: Non_irradiated_Control

description: Sample 1

source_name: bone marrow

value: bone marrow


title: CHC2491T [hepatocellular carcinoma]

description: SAMPLE 231


title: GATA6-AS1 shRNA Day5_Replicate 2

city: ATLANTA

first: Dong

last: Li

state: GEORGIA

address: 2015 UPPERGATE DR

department: Pediatrics

institute: Emory University

description: DESeq_GATA6-AS1_shRNA_vs._Control_shRNA_Day5.txt

data_processing:
Total RNA reads were aligned to the reference human genome using gencode v28.
Per sample read counts were calculated with htseq-count, mode: union, feature type: exon, id attribute: gene_id, and all other defaults. Data analyses were carried out in R v3.4.0.
Normalized read count abundance was estimated and differential expression was calculated with DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing raw or normalized read counts for each sample (in columns) and each annotated transcript (in rows).

source_name: Cardiac progenitor cells

extract_protocol:
Cardiac differentiation was induced on IMR90 hiPSCs transfected with GATA6-AS1 shRNA or control shRNA using a growth factor-guided protocol. RNA samples from cells at differentiation day 2 and day 5 were prepared using Bio-Rad RNA extraction kit and 1 µg of total RNA/sample was used for the construction of sequencing libraries using Illumina TruSeq RNA Sample Prep Kit.
Libraries were generated using the Illumina standard TruSeq protocol and next-generation sequencing was done through an Illumina HiSeq 2500, 75bp paired end sequencing.

value: IMR90 iPSC derived cardiac progenitor cells

tag: developmental

value: Day 5 differentiated cells

value: GATA6-AS1 shRNA lentiviral transduced


title: GATA6-AS1 shRNA Day5_Replicate 3


title: CHC2132T [hepatocellular carcinoma]

description: SAMPLE 230


title: CHC2560T [hepatocellular carcinoma]

description: SAMPLE 229


title: CHC2207T [hepatocellular carcinoma]

description: SAMPLE 228


title: CHC2686T [hepatocellular carcinoma]

description: SAMPLE 227


title: GATA6-AS1 shRNA Day2_Replicate 2

description: DESeq_GATA6-AS1_shRNA_vs._Control_shRNA_Day2.txt

value: Day 2 differentiated cells


title: Control shRNA Day5_Replicate 2

value: Control shRNA lentiviral transduced


title: CHC1606T [hepatocellular carcinoma]

description: SAMPLE 225


title: GATA6-AS1 shRNA Day2_Replicate 1


title: GATA6-AS1 shRNA Day2_Replicate 3


title: CHC2539T [hepatocellular carcinoma]

description: SAMPLE 226


title: Control shRNA Day5_Replicate 1


title: CHC2707T [hepatocellular carcinoma]

description: SAMPLE 224


title: Control shRNA Day2_Replicate 3


title: CHC2448T [hepatocellular carcinoma]

description: SAMPLE 222


title: CHC2687T [hepatocellular carcinoma]

description: SAMPLE 223


title: CHC2415T [hepatocellular carcinoma]

description: SAMPLE 221


title: Control shRNA Day2_Replicate 2


title: GATA6-AS1 shRNA Day5_Replicate 1


title: CHC2695T [hepatocellular carcinoma]

description: SAMPLE 220


title: Control shRNA Day2_Replicate 1


title: Control shRNA Day5_Replicate 3


title: CHC2449T [hepatocellular carcinoma]

description: SAMPLE 219


title: CHC1592T [hepatocellular carcinoma]

description: SAMPLE 218


title: noDox_RBM4 replicate 3

city: Bethesda

first: Stefan

middle: A

last: Muljo

state: MD

address: 10 CENTER DR RM 11N306

institute: NIH/NIAID

data_processing:
The PAR-CLIP sequencing data were processed by the PARpipe pipeline (https://ohlerlab.mdc-berlin.de/software/PARpipe_119/).
Adapters were trimmed using Cutadapt 1.8.3 and reads were aligned to the hg38 (GRCh38.p5) genome using Bowtie v1.1.2 allowing for 2 mismatches, and keeping up to 3600 multi-mapping alignments tied for the best alignment score (parameters: -v 2 -a -m 3600 --best --strata). This was done to account for the highly repetitive nature of HERVs among other transposable elements. The coverage of these reads was evenly divided across all genomic positions which were tied for the best alignment score. The identifiers for the alignments of each read to each distinct genomic position were processed using in-house scripts to be unique and passed into PARalyzer v1.5 for clustering and annotation (see Methods section for PARalyzer parameters used).
Reads, groups and clusters were annotated to the features in the Gencode v24 annotation file for reference chromosomes, scaffolds, assembly patches and alternative loci, with introns given higher precedence in the annotation rank as compared to coding regions.
Genome_build: hg38
Supplementary_files_format_and_content: The *.clusters.tsv files contain, for each cluster called by PARalyzer, the genomic coordinates, clusterID, annotated feature, annotated gene (if applicable), nucleotide sequence, read count, T2C location/counts and T2C fraction.

source_name: KBM-7 derived near-haploid cell line

growth_protocol: The cell lines were cultured in IMDM medium (Quality Biological)  supplemented with 10% (v/v) Tet System Approved fetal calf serum (Takara Bio/previously Clontech), 100 U/mL penicillin, 100 µg/mL streptomycin (Pen/Strep) (Thermo Fisher Scientific), at 37°C in an incubator containing 5% CO2. 500-600 x 10^6 HAP1 RBM4 KO with FLAG-HA-tagged RBM4 cells grown in 15 cm plates were used for each biological replicate

extract_protocol:
UV-crosslinked cells were scraped off the dishes, lysed, Rnase T1 treated, and then immunoprecipitated using anti-FLAG magnetic beads. Beads were washed and resuspended in immunoprecipitation wash buffer. RNA residing in the immprecipitate was further trimmed with RNase T1, washed three more times in high-salt lysis buffer, and finally resuspended in one bead volume of dephosphorylation buffer. (see Methods section for exact amounts, concentrations and timings used)
3' ends of RNA fragments were dephosphorylated in calf intestinal phosphatase and RNA was radioactively 5' end-labeled using T4 polynucleotide kinase and P-32-gamma-ATP. Protein-RNA complexes were separated by SDS-PAGE, transferred to nitrocellulose and visualized with autoradiography. Radioactive bands corresponding to the FLAG/HA-RBM4 rbionucleoprotein complex were recovered, and protein was removed via proteinase K digestion. RNA was then isolated by acidic phenol/chloroform extraction and ethanol precipitation. The recovered RNA was converted into a cDNA library using a standard small RNA library protocol (Hafner et al., Methods 2008) and sequenced on an Illumina HiSeq2500 instrument. (see Methods section for exact amounts, concentrations and timings used)
RIP-seq (PAR-CLIP)

treatment_protocol: 24 hours before UV-crosslinking, expression of the FLAG-HA-tagged RBM4 transgene was induced by addition of 200 ng/mL doxycycline (Takara) and 16 hours (or 1 hours) before UV-crosslinking 100 µM 4SU was added. After washing with ice-cold PBS cells were crosslinked (irradiation with 312 nm UV light, 5 min). (see Methods section for exact amounts, concentrations and timings used)

tag: cell line

value: no Dox


title: noDox_RBM4 replicate 4


title: CHC1556T [hepatocellular carcinoma]

description: SAMPLE 216

tag: gender


title: CHC1085T [hepatocellular carcinoma]

description: SAMPLE 215


title: CHC1534T [hepatocellular carcinoma]

description: SAMPLE 212


title: CHC902T [hepatocellular carcinoma]

description: SAMPLE 211


title: CHC923T [hepatocellular carcinoma]

description: SAMPLE 214


title: noDox_RBM4 replicate 2


title: myocardial tissues from mice, diabetes mellitus+high-dose angiotensin IV, rep4

city: jinan

first: meng

last: zhang

address: Jinan 250012, Shandong, China

institute: Shandong University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: myocardial tissues from mice, FBG≥16.7mM, 6 months + high-dose AngIV treatment for 4 months

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

growth_protocol: Diabetes was induced in mice via intraperitoneal injection of streptozotocin  for 5 days consecutively. Two weeks after STZ injection, mice with fasting blood glucose (FBG) ≥16.7mM were chosen for subsequent experiments.In the NC group, mice were intraperitoneally injected with vehicle daily for 5 days.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: High-dose AngIV (2.88 mg/kg/day) was infused in the treatment group of mice from the end of 8 weeks to the end of 24 weeks.

value: diabetes mellitus

value: high-dose angiotensin IV

value: myocardium


title: noDox_RBM4 replicate 1


title: myocardial tissues from mice, diabetes mellitus+high-dose angiotensin IV, rep3


title: myocardial tissues from mice, diabetes mellitus+high-dose angiotensin IV, rep1


title: myocardial tissues from mice, diabetes mellitus+high-dose angiotensin IV, rep2


title: RBM4 replicate 4

value: treated with doxycycline (RBM4 induced)


title: CHC1753T [hepatocellular carcinoma]

description: SAMPLE 210

value: M


title: CHC1530T [hepatocellular carcinoma]

description: SAMPLE 209


title: CHC1750T [hepatocellular carcinoma]

description: SAMPLE 208


title: CHC1081T [hepatocellular carcinoma]

description: SAMPLE 207


title: RBM4 replicate 3


title: CHC1775T [early hepatocellular carcinoma]

description: SAMPLE 217

value: early hepatocellular carcinoma


title: CHC1738T [hepatocellular carcinoma]

description: SAMPLE 206

value: F


title: CHC1774T [early hepatocellular carcinoma]

description: SAMPLE 213


title: Heat_F_R3

source_name: seedlings

value: Columbia-0 (Col-0)

value: Heat

value: 10 day old


title: myocardial tissues from mice, diabetes mellitus, rep1

source_name: myocardial tissues from mice, FBG≥16.7mM, 6 months

value: untreated


title: myocardial tissues from mice, diabetes mellitus, rep2


title: CHC1210T [hepatocellular carcinoma]

description: SAMPLE 205

value: hepatocellular carcinoma


title: CHC1737T [hepatocellular carcinoma]

description: SAMPLE 204


title: myocardial tissues from mice, negative control, rep4

source_name: myocardial tissues from mice, negative control, 6 months

value: negative control


title: CHC2362T [early hepatocellular carcinoma]

description: SAMPLE 203


title: myocardial tissues from mice, diabetes mellitus, rep4


title: CHC1714T [hepatocellular carcinoma]

description: SAMPLE 202


title: CHC1180T [hepatocellular carcinoma]

description: SAMPLE 201


title: myocardial tissues from mice, diabetes mellitus, rep3


title: myocardial tissues from mice, negative control, rep3


title: myocardial tissues from mice, negative control, rep2


title: RsmI-bound RNA biol. replica 3

city: Granada

first: Manuel

last: Espinosa-Urgel

address: Profesor Albareda, 1

department: Environmental Protection

institute: Estacion Experimental del Zaidin. CSIC

data_processing:
libraries were analyzed for quality and replicas below standards (RsmA1 and RsmI2) were discarded
Filtered reads were aligned to reference genome with Bowtie v2
Alignment.sam file was analyzed using MACS v14 to identify reads-enriched regions in the genome.
pvalue cutoff = 1,00e-05
Genome_build: NC_002947.3
Supplementary_files_format_and_content: wig files

organism: Pseudomonas putida

source_name: bacterial culture

growth_protocol: Overnight cultures (10 ml) of KT2440 harbouring each construct were inoculated in 500 ml of LB medium, and incubated at 30°C under shaking to an OD660 of 0.8. At that point, expression of His-tagged-Rsm proteins was induced for 6 h by the addition of IPTG to a final concentration of 0.5 mM. 3 biological replicas

extract_protocol:
Total RNA and RNA from Rsm-RNA complex was extracted using RNA isolation kit (Macherey-Nagel) following the manufacturer´s instructions. RNA samples were subsequently treated with RNase-free DNase I (Turbo DNA-free kit, Ambion) to remove DNA traces, as specified by the supplier.
Total RNA quality was assessed using Agilent RNA 6000 Nano Kit (Agilent Technologies) in the Agilent 2100 Bioanalyzer. RNA concentration was measured using Qubit RNA BR assay kit (Life Technologies). 1µg of RNA was used for rRNA depletion using Ribo-Zero rRNA Removal Kit (Illumina). The generation of cDNA libraries was carried out using NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB). Dual Index Primers Set 1 was used to generate bar-coded multiplex libraries (NEB). Library QC was performed using bioanalyser HS kit (Agilent biotechnologies). cDNA libraries were quantified using qPCR (Kapa Biosystems). Libraries were pooled at the desired concentrations, denatured and loaded for sequencing according to manufacturer’s instructions.
RAP-Seq (RNA seq after affinity purification of RNA-protein complexes)

treatment_protocol: Aliquots of 1.5 ml were harvested by centrifugation, instantly frozen with liquid nitrogen and stored at -80C for total RNA purification. Cells from the remaining cultures were also harvested and cell pellets stored at -80C. His-tagged Rsm-RNA complex purification were isolated using Ni-NTA Fast Start Kit (Qiagen).

tag: plasmid


title: total RNA biol. replica 5

tag: strain


title: myocardial tissues from mice, negative control, rep1

tag: tissue


title: CHC1177T [hepatocellular carcinoma]

description: SAMPLE 198


title: RBM4 replicate 2


title: CHC1712T [hepatocellular carcinoma]

description: SAMPLE 199


title: total RNA biol. replica 4


title: CHC1601T [hepatocellular carcinoma]

description: SAMPLE 194


title: CHC1053T [hepatocellular carcinoma]

description: SAMPLE 192


title: CHC1596T [hepatocellular carcinoma]

description: SAMPLE 195


title: CHC1595T [hepatocellular carcinoma]

description: SAMPLE 193


title: CHC1719T [hepatocellular carcinoma]

description: SAMPLE 189


title: CHC2200T [hepatocellular carcinoma]

description: SAMPLE 191


title: CHC1591T [hepatocellular carcinoma]

description: SAMPLE 190


title: RBM4 replicate 1


title: CHC2358T [early hepatocellular carcinoma]

description: SAMPLE 200


title: total RNA biol. replica 2


title: CHC1611T [hepatocellular carcinoma]

description: SAMPLE 188


title: CHC1743T [hepatocellular carcinoma]

description: SAMPLE 186


title: CHC2351T [early hepatocellular carcinoma]

description: SAMPLE 197


title: CHC2216T [hepatocellular carcinoma]

description: SAMPLE 184


title: total RNA biol. replica 1


title: CHC1624T [early hepatocellular carcinoma]

description: SAMPLE 196


title: RsmE-bound RNA biol. replica3


title: RsmI-bound RNA biol.replica 1


title: CHC2111T [hepatocellular carcinoma]

description: SAMPLE 182


title: RsmE-bound RNA biol. replica2


title: RsmE-bound RNA biol. replica1


title: total RNA biol. replica 3


title: CHC2103T [hepatocellular carcinoma]

description: SAMPLE 180


title: CHC2208T [hepatocellular carcinoma]

description: SAMPLE 185


title: total RNA biol. replica3


title: RsmA-bound RNA biol. replica3


title: CHC2202T [hepatocellular carcinoma]

description: SAMPLE 179


title: CHC2206T [hepatocellular carcinoma]

description: SAMPLE 181


title: CHC2098T [hepatocellular carcinoma]

description: SAMPLE 177


title: CHC2141T [hepatocellular carcinoma]

description: SAMPLE 176


title: total RNA biol. replica2


title: CHC2052T [hepatocellular carcinoma]

description: SAMPLE 175


title: RsmA-bound RNA biol. replica2


title: CHC1569T [hepatocellular carcinoma]

description: SAMPLE 187


title: CHC2048T [hepatocellular carcinoma]

description: SAMPLE 173


title: CHC2128T [hepatocellular carcinoma]

description: SAMPLE 172


title: CHC2211T [hepatocellular carcinoma]

description: SAMPLE 183


title: RBM4 KO 1B6 (PacBio)

data_processing:
All reads were mapped to hg38  using minimap2 (Li, Bioinformatics 2018) using the following parameters:  -ax splice -uf --secondary=no -C5  Homo_sapiens.GRCh38.dna.primary_assembly.fa
The resulting bam files were then filtered for mapping quality and unique mapping using samtools view -F 256 -q 20,
Genome_build: hg38
Supplementary_files_format_and_content: Binary alignment map (bam) and corresponding index files filtered for mapping quality (MAPQ>20) and unique mapping (SAM flag = 256)

growth_protocol: The cell lines were cultured in IMDM medium (Quality Biological)  supplemented with 10% (v/v) Tet System Approved fetal calf serum (Takara Bio/previously Clontech), 100 U/mL penicillin, 100 µg/mL streptomycin (Pen/Strep) (Thermo Fisher Scientific), at 37°C in an incubator containing 5% CO2

extract_protocol:
Total RNA was cleaned via Agencourt RNA Clean XP (Beckman Coulter) beads and resuspended in Buffer EB (Qiagen). Quality and quantity was assessed via BioPhotometer (Eppendorf) and Agilent RNA 6000 Pico kit on the 2100 Bioanalyzer (Agilent Technologies).
SMRTbell libraries were generated using Pacific Bioscience’s no-size selection Iso-Seq Template Preparation guide following the manufacture’s recommendations. Input amounts for generating cDNA (Takara Bio) was 1000ng and PCR was optimized at 10 cycles for subsequent large-scale PCR. Fraction 1 and 2 of the cleaned-up products were quantified via Qubit (Thermo Fisher Scientific) fluorometric assay and equal molar quantities were combined resulting in over 1 µg cDNA going forward. Final SMRTbell libraries were quantified using Qubit and qualitative and quantitative analyses were performed using BioAnalyzer DNA 12000 kit (Agilent Technologies), and Fragment Analyzer Large-Fragment kit (Agilent Technologies). Pacific Biosciences stand-alone Excel template was followed for primer and polymerase addition/cleanup and sequence data for each library was generated using MagBead loading on three independent SMRTcells on the Sequel (Pacific Biosciences) at 50, 65, and 75 pM respectively. Movie collection time was set at 10 hours with a pre-extension time of 120 minutes.

value: RBM4 KO


title: Wild Type (PacBio)

value: wild type


title: CHC2043T [hepatocellular carcinoma]

description: SAMPLE 171


title: CHC2127T [hepatocellular carcinoma]

description: SAMPLE 170


title: CHC2115T [hepatocellular carcinoma]

description: SAMPLE 169


title: CHC2099T [hepatocellular carcinoma]

description: SAMPLE 178


title: CHC2034T [hepatocellular carcinoma]

description: SAMPLE 168


title: CHC2215T [hepatocellular carcinoma]

description: SAMPLE 167


title: CHC2113T [hepatocellular carcinoma]

description: SAMPLE 166


title: CHC2112T [hepatocellular carcinoma]

description: SAMPLE 164


title: CHC2029T [hepatocellular carcinoma]

description: SAMPLE 165


title: CHC1757T [hepatocellular carcinoma]

description: SAMPLE 162


title: CHC2025T [hepatocellular carcinoma]

description: SAMPLE 163


title: cat2_stress_PAK_2

city: Wageningen

first: Tom

last: van der Meer

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University

description: Grown in liquid 1/2 MS in 96 well translucent plates

data_processing:
Illumina Casava 1.8 software used for basecalling.
Quality trimming with Trim Galore v0.3.3 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), retaining high-quality reads of at least 50 bp in length
Genome alignment TAIR10 Arabidopsis by TopHat2 (v2.1.0).
Gene quantification using featureCounts function of the Subread package (v1.4.6).
Genome_build: TAIR10
Supplementary_files_format_and_content: Matrix table with log2FC and statistics for the pairwise comparisons, and CPM data per treatment

source_name: plant leaf

growth_protocol: Arabidopsis thaliana catalase2-2 plants were grown in liquid 1/2 MS media in translucent 96 well plates (5 plants per well) for 7 days at long day conditions (16h light/8h dark, 100 µmol m-2 s-1 light intensity, 21 oC, 70% relative humidity).

extract_protocol:
Total RNA was extracted from leaf material (100 mg fresh leaf material/sample) using the SpectrumTM Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO, USA) using the standard provided protocol.
approx. 30 million 75 bp single end reads per sample were generated. Adapter sequences and low-quality base pairs (length below 20 bp) were trimmed with Trim Galore v0.3.3 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), retaining high-quality reads of at least 50 bp in length. Quality-filtered reads were aligned to the TAIR10 Arabidopsis reference genome using the spliced aligner TopHat2 v2.1.0. The number of reads per gene was quantified with the feature ‘Counts’ function as implemented in the Subread package v1.4.6. Reads mapping to genes annotated as rRNA, tRNA, and other RNA forms (TAIR10 annotation) were not considered for further analysis

treatment_protocol: After 7 days, the media was replaced by 1/2 MS media containing pakerine (10 μM) or equal amounts of DMSO (mock-treatment). Control samples were harvested after 4 days incubation in LD conditions and in the presence of DMSO. Pakerine treated samples were harvested after two days of photorespiratory inducing conditions (Sealed plates with 2 layers Parafilm and 24 hour light treatment) following four days of incubation at LD conditions.

value: leaf

tag: growth condition

value: Photorespiratory stress (2 days)

tag: chemical treatment

value: Pakerine (10 μM, dissolved in DMSO)


title: cat2_stress_PAK_1

tag: genotype


title: CHC1715T [hepatocellular carcinoma]

description: SAMPLE 160


title: CHC1742T [hepatocellular carcinoma]

description: SAMPLE 161


title: CHC2134T [hepatocellular carcinoma]

description: SAMPLE 174


title: TU3401 ash-2

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

institute: Graduate School of Biostudies, Kyoto University

hyb_protocol: Fragmented and labelled cDNA was hybridised to GeneChip C. elegans Gene 1.0 ST Array (Affymetrix).

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The probe set signals were calculated with the robust multi-array average (RMA) algorithm implemented in GeneSpring GX 11.0.2 (Agilent Technologies).

organism: Caenorhabditis elegans

source_name: ash-2 RNAi in neuron

label_protocol: Ambion WT cDNA Expression Kit was used according to the protocol.

growth_protocol: All strains were maintained at 20 °C on nematode growth medium (NGM) plates seeded with Escherichia coli OP50 as previously described.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) in N2, VP303, NR350, TU3401 worms under Control RNAi and ash-2 RNAi conditions.

treatment_protocol: N2, VP303, NR350 or TU3401 worms were subjected to control or ash-2 RNAi for 3 days from egg stage to young adult stage.

tag: strain/background

value: neuron

tag: RNAi


title: cat2_stress_DMSO_3

value: control


title: NR350 ash-2

source_name: ash-2 RNAi in muscle

value: muscle


title: cat2_stress_DMSO_1


title: N2 control

source_name: Control RNAi in whole body

value: whole body

value: Control


title: NR350 control

source_name: Control RNAi in muscle


title: CHC1603T [hepatocellular carcinoma]

description: SAMPLE 159

value: M

tag: disease


title: VP303 control

source_name: Control RNAi in intestine

value: intestine


title: CHC1566T [hepatocellular carcinoma]

description: SAMPLE 158


title: TU3401 control

source_name: Control RNAi in neuron


title: N2 ash-2

source_name: ash-2 RNAi in whole body


title: cat2_ctrl_PAK_2

value: DMSO (mock)


title: CHC1079T [hepatocellular carcinoma]

description: SAMPLE 157


title: CHC1741T [hepatocellular carcinoma]

description: SAMPLE 155


title: cat2_ctrl_PAK_1


title: cat2_ctrl_DMSO_3


title: cat2_ctrl_PAK_3


title: CHC1756T [hepatocellular carcinoma]

description: SAMPLE 156


title: cat2_ctrl_DMSO_2


title: cat2_ctrl_DMSO_1


title: CHC1754T [hepatocellular carcinoma]

description: SAMPLE 152


title: CHC1602T [hepatocellular carcinoma]

description: SAMPLE 154


title: CHC1190T [hepatocellular carcinoma]

description: SAMPLE 153

value: F


title: CHC1189T [hepatocellular carcinoma]

description: SAMPLE 149


title: CHC1028T [hepatocellular carcinoma]

description: SAMPLE 148


title: CHC1545T [hepatocellular carcinoma]

description: SAMPLE 150


title: cat2_stress_PAK_3


title: cat2_stress_DMSO_2


title: CHC1600T [hepatocellular carcinoma]

description: SAMPLE 146


title: CHC1708T [hepatocellular carcinoma]

description: SAMPLE 147


title: CH8: DDX3X control (shNS)

city: Washington

first: Hyeongjwa

last: Choi

state: DC

address: 3970 Reservoir Road NW

department: Oncology

institute: Georgetown University

description: shRNA were delivered to cells by transduction of lentiviral particles.

data_processing:
The alignment was doen using LifeScope.
The read numbers for mRNA were counted using "HTSeq".
mRNAs with read counts lower than 20 in all samples were filtered out.
"DESeq2" was used for the differentially expressed gene analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes DESeq2 normalized count for each sample

source_name: MCF7 Breast cancer cell line

growth_protocol: Cells were grown in DMEM supplemented with 10% heat-inactivated FBS, 1% Pen-Strep, and 2 ug/ml of puromycin.

extract_protocol:
RNA was extracted using QIAGEN Rneasy kits according to manufacturer's instructions.
RNA libraries were prepared for SOLiDTM sequencing using whole transcriptome library preparation (part num: 4409491)

tag: cell type

value: Breast cancer

tag: shRNA

value: Non-specific shRNA


title: CH9: DDX3X control (shNS)


title: VP303 ash-2

source_name: ash-2 RNAi in intestine


title: CH7: DDX3X control (shNS)


title: CHC1186T [hepatocellular carcinoma]

description: SAMPLE 144

value: hepatocellular carcinoma


title: CHC1539T [hepatocellular carcinoma]

description: SAMPLE 145


title: CH17: DDX3X control (shNS)


title: TTCCTC_AML491_M55980_nLRC_1000

city: Munich

first: Tobias

last: Herold

address: Marchioninistr. 15

department: Department of Internal Medicine III

institute: University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)

description:
sample name:
GGCGTC

data_processing:
Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017)
cDNA reads were aligned to the concatenated Human (hg38) and Mouse (mm10) Genome with STAR 2.6.0a
Quantification was done with ENSEMBL gene models (GRCh38.84/GRCm38.75)
Genome_build: Human: hg38, Ensembl 84; Mouse: mm10, Ensembl 75
Supplementary_files_format_and_content: sample (columns) and gene (rows) -wise UMI expression table

source_name: nLRC

growth_protocol: AML PDX cells were isolated from a donor mouse, stained with CFSE, and 1E7 cells were re-injected into four recipient mice per sample. Ten (AML-393) or 14 (AML-491) days later, AML PDX cells were re-isolated from bone marrow.

extract_protocol:
AML PDX cells were re-isolated from murine bone marrow using a mortar and pistil, washed once in PBS. Murine cells were depleted using mouse cell depletion kit from Miltenyi. PDX cells were dissolved in PBS, and sorted according to the CFSE content as LRC or nLRC population (see Figure 1 for details of cell harvesting).
Libraries were constructed using a bulk adjusted SCRB-seq protocol.

treatment_protocol: AML PDX cells were stained with CFSE before injection into experimental mice.

value: acute myeloid leukemia

tag: pdx

tag: mouse

value: nLRC

tag: cell number


title: D: post-transfection MDA-MB-231/CDDP

city: Harbin

first: Bolin

last: Wu

state: Heilongjiang Province

address: No.150, Haping Road, Nangang District

institute: Harbin Medical University Cancer Hospital

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perl  scripts. In this step, clean data(clean reads) were obtained by removing reads  containing adapter, reads on containing ploy-N and low quality reads from raw data.  At the same time, Q20, Q30 and GC content of the clean data were calculated. All the  down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using bowtie2 v2.2.8 and  paired-end clean reads were aligned to the reference genome using HISAT2(Langmead,  B.et al) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set  as default.
The mapped reads of each sample were assembled by StringTie (v1.3.1) (Mihaela  Pertea.et al. 2016) in a reference-based approach. StringTie uses a novel network flow  algorithm as well as an optional de novo assembly step to assemble and quantitate full-  length transcripts representing multiple splice variants for each gene locus.
CNCI (Coding-Non-Coding-Index) (v2) profiles adjoining nucleotide triplets to  effectively distinguish protein-coding and non-coding sequences independent of  known annotations (Sun et al. 2013). We use CNCI with default parameters.
CPC (Coding Potential Calculator) (0.9-r2) mainly through assess the extent and  quality of the ORF in a transcript and search the sequences with known protein  sequence database to clarify the coding and non-coding transcripts (Kong et al.  2007). We used the NCBI eukaryotes' protein database and set the e-value ‘1e-10’  in our analysis.
Phast (v1.3) is a software package contains much of statistical programs, most used in  phylogenetic analysis (Siepel, et al. 2005), and phastCons is a conservation scoring and  identificating program of conserved elements. We used phyloFit to compute  phylogenetic models for conserved and non-conserved regions among species and then  gave the model and HMM transition parameters to phyloP to compute a set of  conservation scores of lncRNA and coding genes.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in  each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the  FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of  exon per million fragments mapped, calculated based on the length of the fragments  and reads count mapped to this fragment.
The Ballgown suite includes functions for interactive exploration of the transcriptome  assembly, visualization of transcript structures and feature-specific abundances for  each locus, and post-hoc annotation of assembled features to annotated features(Alyssa  C. Frazee et al.2014). Transcripts with an P-adjust <0.05 were assigned as differentially  expressed.  Cuffdiff provides statistical routines for determining differential expression in digital  transcript or gene expression data using a model based on the negative binomial  distribution (Trapnell, C. et al. 2010). Transcripts with an P-adjust <0.05 were assigned  as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes or lncRNA  target genes were implemented by the GOseq R package, in which gene length bias  was corrected(Young, M. D.et al.2010). GO terms with corrected Pvalue less than 0.05  were considered significantly enriched by differential expressed genes.  KEGG is a database resource for understanding high-level functions and utilities of the  biological system(Kanehisa, M.et al.2008), such as the cell, the organism and the  ecosystem, from molecular-level information, especially large-scale molecular datasets  generated by genome sequencing and other high-throughput experimental technologies  (http://www.genome.jp/kegg/). We used KOBAS software to test the statistical  enrichment of differential expression genes or lncRNA target genes in KEGG  pathways(Mao, X.et al.1995).
PPI analysis of differentially expressed genes was based on the STRING database,  which known and predicted Protein-Protein Interactions. For the species existing in the  database, we construct the networks by extract the target gene list from the database;  Otherwise, Blastx (v2.2.28) was used to align the target gene sequences to the selected  reference protein sequences, and then the networks was built according to the known  interaction of selected reference species.
Alternative splicing events were classified to 12 basic types by the software Asprofile  v1.0. The number of AS events in each sample was estimated, separately.
Picard-tools v1.96 and samtools v0.1.18 were used to sort, mark duplicated reads and  reorder the bam alignment results of each sample. GATK2 software was used to  perform SNP calling(McKenna, A.et al.2010).
Genome_build: homo_sapiens_Ensembl_94

source_name: post-transfection MDA-MB-231/CDDP

extract_protocol:
A total amount of 3 μg RNA per sample was used as input material for the RNA sample  preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA  Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol  precipitation.
Subsequently, sequencing libraries were generated using the rRNA-  depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®  (NEB, USA) following manufacturer’s recommendations. Briefly, fragmentation was  carried out using divalent cations under elevated temperature in NEBNext First Strand  Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random  hexamer primer and M-MuLV Reverse Transcriptase(RNaseH-). Second strand cDNA  synthesis was subsequently performed using DNA Polymerase I and RNase H. In the  reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were  converted into blunt ends via exonuclease/polymerase activities. After adenylation of  3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated  to prepare for hybridization. In order to select cDNA fragments of preferentially  150~200 bp in length, the library fragments were purified with AMPure XP system  (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used  with size-selected, adaptor-ligated cDNA at 37° C for 15 min followed by 5 min at  95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were  purified (AMPure XP system) and library quality was assessed on the Agilent  Bioanalyzer 2100 system.

value: Triple negative breast cancer

value: female


title: CHC1705T [hepatocellular carcinoma]

description: SAMPLE 141

tag: age at sampling


title: TTCAAT_AML491_M55971_nLRC_1000

description:
sample name:
GGCCAC


title: CHC1736T [hepatocellular carcinoma]

description: SAMPLE 142


title: CHC1598T [hepatocellular carcinoma]

description: SAMPLE 140


title: TTATAC_AML491_M55971_LRC_1000

description:
sample name:
GGAGCC

source_name: LRC

value: LRC


title: C: pre-transfection MDA-MB-231/CDDP

source_name: pre-transfection MDA-MB-231/CDDP

tag: cell line


title: B: post-transfection MDA-MB-231 cells

source_name: post-transfection MDA-MB-231 cells

tag: gender


title: CHC1531T [hepatocellular carcinoma]

description: SAMPLE 139


title: TTACAT_AML393_M55782_nLRC_1000

description:
sample name:
GCTCGC


title: TTAAAG_AML393_M55782_LRC_1000

description:
sample name:
GCTAGA


title: CHC1185T [hepatocellular carcinoma]

description: SAMPLE 138


title: CHC1739T [hepatocellular carcinoma]

description: SAMPLE 151


title: CHC1734T [hepatocellular carcinoma]

description: SAMPLE 137


title: A: pre-transfection MDA-MB-231 cells

source_name: pre-transfection MDA-MB-231 cells


title: CHC1751T [hepatocellular carcinoma]

description: SAMPLE 143


title: TAATTC_AML491_M55981_nLRC_2000

description:
sample name:
CTGCGG


title: TAAGTA_AML491_M55981_LRC_2000

description:
sample name:
CGTGGG


title: Blood_mo3

city: Amsterdam

first: Benjamin

last: Nota

state: Noord Holland

address: Plesmanlaan 125

department: Research Facilities

institute: Sanquin

data_processing:
Alignment of reads was done using STAR (v2.5.3a)
For each gene all reads were counted that aligned to exonic regions using featureCounts (v1.5.2) with Homo_sapiens.GRCh38.87.gtf annotation from Ensembl
Genes that had more than 1 CPM in 3 or more samples were kept for further analysis. Differentially expression analysis was done in R limma trend (v3.34.9), taking the donor as batch factor in the model. Groups (cell type) were compared in contrasts and genes with an FDR-adjusted p-value < 0.05 were considered significant.
Genome_build: hg38
Supplementary_files_format_and_content: Raw read count per gene
Supplementary_files_format_and_content: TopTable results from limma trend

source_name: Blood

extract_protocol:
QIAamp RNA Blood Mini Kit
Illumina Truseq RNA library prep

value: Blood Monocyte

tag: donor


title: Spleen_mo3

source_name: Spleen

value: Spleen Monocyte


title: Spleen_ma3

value: Spleen Macrophage


title: CHC1597T [hepatocellular carcinoma]

description: SAMPLE 135


title: TAAATG_AML393_M55785_nLRC_2000

description:
sample name:
CGGTGG


title: Blood_mo2


title: CHC1704T [hepatocellular carcinoma]

description: SAMPLE 136


title: CHC1183T [hepatocellular carcinoma]

description: SAMPLE 134


title: GTTTTA_AML393_M55785_LRC_2000

description:
sample name:
CCGGAC


title: Spleen_ma2


title: Spleen_mo2


title: GTACAC_AML393_M55784_nLRC_1000

description:
sample name:
CCCTGG


title: CHC1732T [hepatocellular carcinoma]

description: SAMPLE 132


title: Spleen_mo1


title: CHC1749T [hepatocellular carcinoma]

description: SAMPLE 133


title: GCTTAC_AML393_M55784_LRC_1000

description:
sample name:
CCCCGT


title: CCGGCA_AML491_M55981_nLRC_1000

description:
sample name:
CCCACG


title: Spleen_ma1


title: CCGAGG_AML491_M55981_LRC_1000

description:
sample name:
CCAACC


title: TAGTGG_AML491_M55980_LRC_1000

description:
sample name:
GACCGC


title: Blood_mo1


title: CHC1211T [hepatocellular carcinoma]

description: SAMPLE 130


title: CHC801T [hepatocellular carcinoma]

description: SAMPLE 129


title: CCCCTG_AML393_M55785_nLRC_1000

description:
sample name:
ATTCTA


title: CHC1747T [hepatocellular carcinoma]

description: SAMPLE 128


title: CHC1700T [hepatocellular carcinoma]

description: SAMPLE 131


title: CHC1731T [hepatocellular carcinoma]

description: SAMPLE 127


title: CCCAGC_AML393_M55785_LRC_1000

description:
sample name:
ATTACT


title: ATTAGA_AML491_M55980_nLRC_2000

description:
sample name:
ATGAAT


title: CHC1594T [hepatocellular carcinoma]

description: SAMPLE 125


title: ATGATA_AML491_M55980_LRC_2000

description:
sample name:
ATCAAA


title: ATCATT_AML393_M55783_nLRC_2000

description:
sample name:
ATATAG


title: CHC1629T [hepatocellular carcinoma]

description: SAMPLE 126


title: MDA-MB-468 DMSO 7 days (replicate 2)

city: Melbourne

first: Shom

last: Goel

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description: MCF7-2_M453_M468_DMSOvsAbema_7d_RNA-seq_readcounts.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using STAR.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using the VIPER pipeline; tab delimited text files of gene counts from STAR alignment

source_name: Breast carcinoma cell line

growth_protocol: Cells were cultured in sterile dishes in media as described. Cells were plated at densities such that final density at time of RNA-seq was between 60-70%.

extract_protocol:
Total RNA was isolated from cell lines using a Nucleospin RNA Plus kit (Macherey-Nagel).
NEBNext® Ultra™ RNA Library Prep Kit for Illumina

treatment_protocol: Abemaciclib (500 nM) or DMSO for 7 days for all cell lines.

value: MDA-MB-468 breast carcinoma cell line

tag: treamtent

value: DMSO

tag: treatment length

value: 7 days


title: MDA-MB-468 Abemaciclib 7 days (replicate 2)

value: abemaciclib


title: MDA-MB-468 DMSO 7 days (replicate 3)


title: MDA-MB-468 Abemaciclib 7 days (replicate 3)


title: CHC1209T [hepatocellular carcinoma]

description: SAMPLE 124

value: M


title: MDA-MB-468 DMSO 7 days (replicate 1)


title: CHC1746T [hepatocellular carcinoma]

description: SAMPLE 123


title: MCF7_shRB1-3_LY500nM_2

description: MCF7-2_shRB_DMSOvsAbema_7d_RNA-seq_readcounts.txt

value: MCF7 breast carcinoma cell line


title: CHC1725T [hepatocellular carcinoma]

description: SAMPLE 122

value: F


title: AAGTAT_AML491_M55971_nLRC_2000

description:
sample name:
AAGATT

tag: tissue


title: MCF7_shRB1-3_LY500nM_1


title: AACAAT_AML491_M55971_LRC_2000

description:
sample name:
AAATTG


title: CHC1626T [hepatocellular carcinoma]

description: SAMPLE 121


title: CHC1207T [hepatocellular carcinoma]

description: SAMPLE 120


title: MCF7_shRB1-3_DMSO_1


title: AAATAC_AML393_M55782_nLRC_2000

description:
sample name:
AAAGTT


title: MCF7_shRB1-3_DMSO_2


title: CHC432T [hepatocellular carcinoma]

description: SAMPLE 119


title: AAAATC_AML393_M55782_LRC_2000

description:
sample name:
AAAACT


title: MCF7 LY500_3


title: MDA-MB-468 Abemaciclib 7 days (replicate 1)


title: CHC1745T [hepatocellular carcinoma]

description: SAMPLE 118


title: MCF7 LY500_2


title: CHC1720T [hepatocellular carcinoma]

description: SAMPLE 117