title: H10: T cell

city: Des Moines

first: Chunfa

last: Jie

state: IA

address: 3200 Grand Ave

institute: Des Moines University

data_processing:
The fastq files were proeduced by bcl2fastq version 2.15.0.4.
Sequenced reads were trimmed for adaptor sequence, and mapped to human genome UCSC hg19 using  bowtie version 0.12.7: bowtie -q --phred33-quals -n 1 -e 99999999 -l 25 -I 1 -X 2000 -a -m 15 --best -S -p 6.
TPM (Transcripts Per Kilobase Million) were calculated for genes using the rsem version 1.2.19: rsem-calculate-expression --estimate-rspd --paired-end -sam -p 6.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values per gene for each Sample.

source_name: T cell

extract_protocol:
Peripheral blood samples were obtained from Type 1 diabetes patient. Cell phenotypes were analyzed using a LSRII multicolor flow cytometer (BD Biosciences). Briefly, single cell suspensions were surface-stained for 20 min on ice with predetermined optimal concentrations of indicated fluorochrome-conjugated antibodies (Key resources Table of the CELL article (Ahmed, et al., 2019)) using established methods (Dai et al., 2015; Martina et al., 2015). Acquired samples (5 x 105 to 1 x 106 live events) were properly compensated using single color stains. Data analysis, gating, and graphical presentation were done using FlowJo software (TreeStar). Doublets were excluded from analysis using FSC-Height versus FSC-Width and SSC-Height versus SSC-Width plots. Multiple specificity controls were used. These included human FcR blocking reagent (Miltenyi Biotec), Fluorescence-Minus One (FMO) for CD5, CD19, TCR, IgD, dump gating, and isotype controls. In addition, when applicable, irrelevant cell types were used as internal biological controls and in the case of in vitro stimulation, we used unstimulated cultures as negative controls. As illustrated in the figure S5A of the CELL article (Ahmed, et al., 2019), the Strategy used to isolate DEs for high-throughput sequencing analysis included the gating of lymphocytes, exclusion of doublets and dead cells followed by using of CD5 and CD19 expression to divide live singlets into Bcon, Tcon cells and DE cells which were identified based on TCR expression among CD5+ CD19+ cells.
FACS sorted single cells were processed with the Smart-seq2  protocol (Picelli et al., 2014) with the following modifications. RNA purification was performed prior to reverse  transcription using RNAClean XP beads (Beckman Coulter). cDNA was amplified with 21 PCR cycles  followed by DNA cleanup with AMPure XP beads. Libraries were prepared using the Nextera XT Library Prep  kit (Illumina) using custom barcode adapters.

value: PBMC

tag: disease

value: Type 1 diabetes

tag: cell type

value: Tcon (Conventional T) cells


title: H12: T cell

status: Public on Jun 02 2019

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: H09: T cell


title: RNA-seq_A549_siNON_TNF_rep1

status: Public on Jun 03 2019

city: Kuopio

first: Einari

middle: A

last: Niskanen

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

description:
RNA-seq sample
RNA-seq_A549_siNON-vs-siIRF2BP2_EtOH-vs-dex-vs-TNF-vs-DT.txt.gz

data_processing:
The quality of raw reads was analyzed by FastQC and FASTX-toolkit was used for preprocessing raw reads (removal of artifacts, trimming reads, quality filtering and collapsing identical reads).
For RNA-seq, raw reads were trimmed using trimmomatic (v. 0.33; parameters LEADING:5 TRAILING:5 MINLEN:36) and poly-A tails were removed using HOMER (homerTools trim -3 AAAAAAAA -mis 1 -min 36). Contaminants reported in iGENOME hg19 were removed using bowtie2 and remaining reads were mapped to human hg19 transcriptome and genome with tophat2. Differential expression of genes was analyzed using edgeR and expression values (FPKM) from combined replicates using HOMER.
Genome_build: hg19
Supplementary_files_format_and_content: For RNA-seq, tables with results from the differential gene expression analysis (siNON vs siIRF2BP2, EtOH vs dex vs TNF vs DT) and expression (FPKM) are given as tab delimited text files.

molecule: polyA RNA

source_name: A549 cells

growth_protocol: Isogenic HEK293 cells (Flp-In 293, ThermoFisher Scientific) that constitutively express GR (HEK293-GR) were maintained in Dulbecco’s modified Eagle’s medium (Gibco® Invitrogen) supplemented with 10% (v/v) fetal bovine serum (FBS), 25 U/ml penicillin, 25 µg/ml streptomycin and 100 µg/ml hygromycin-B. Adenocarcinoma human alveolar basal epithelial cells (A549, ATCC) were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Gibco® Invitrogen) supplemented with 10% (v/v) fetal bovine serum (FBS), 25 U/ml penicillin and 25 µg/ml streptomycin.

extract_protocol:
For RNA-seq, RNA was extracted using RNease Plus Mini kit (Qiagen) and mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
Library preparation was done using NEBNext Ultra II kit (New England Biolabs) and sequenced using Illumina Hiseq2000 at EMBL GeneCore (Heidelberg, Germany).

treatment_protocol: For siRNA transfection, medium was changed to steroid-depleted medium (DMEM containing 2.5% (v/v) charcoal-stripped FBS). Cells were transfected with 20 nM siRNAs (Dharmacon, ON-TARGETplus SMARTpool) against IRF2BP2 (L-007177-02-0005), or non-targeting control siRNA (Dharmacon, non-targeting pool) for two (ChIP-seq) or three (RNA-seq) days using Lipofectamine RNAiMAX transfection reagent (Invitrogen). For ChIP-seq, HEK293-GR cells were treated with 100 nM dexamethasone (dex) or vehicle (EtOH, equal amount of ethanol) for 1h before fixing with formaldehyde. For RNA-seq, cells were treated for six hours with vehicle (EtOH, ethanol), 100 nM dexamethasone (dex), 10 ng/ml tumor necrosis factor alpha (TNF), or co-treated with both dex and TNF (DT), before extracting the RNA.

tag: cell line

tag: treatment 1

value: siNON transfection in steroid-depleted medium, 72h

tag: treatment 2

value: TNF, 10 ng/ml, 6h


title: H11: T cell


title: H08: T cell


title: H04: T cell


title: H05: T cell


title: H07: T cell


title: H03: T cell


title: H02: T cell


title: ND liver 2

city: Cologne

first: Ali

middle: T

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

country: Germany

institute: University of Cologne

description:
annotation_liver.csv
Liver_CDWT16_2.txt

data_processing:
All samples were sequenced on a NextSeq 500 sequencing system with the following run parameters:
26 cycles for read 1, 98 cycles for read 2, 8 cycles for index 1. Binary sequencing data were converted to the fastq format
Then the CellRanger analysis pipeline (v2.0.0) from 10x Genomics was used with standard parameters in order to
(1) align the reads and count them for each gene and each cell with cellranger count
(2) merge all liver samples with cellranger merge
(3) merge all bone marrow samples with cellranger merge
Seurat package (v 2.3.0) was used to generate a gene expression matrix for each of the merged samples (genes row wise and cell column wise)
Only Cell containing at least 50 genes and gene expressing in at least three cells were kept all others were filtered out.
Cell names ending with 1 to 4 in the liver expression matrix corresponds to sample 1 to sample 4 respectively
Cell names ending with 1 to 4 in the bone marrow expression matrix corresponds to sample 5 to sample 8 respectively
Cells were clustered and undergone cell type identification using the Seurat Package (v 2.3.0) which resulted with the annotation of each cell with a cell type.
Genome_build: mm10 (preprocessed release 84 downloaded from the website of 10x Genomics)
Supplementary_files_format_and_content: Two expression matrices in txt format containing genes row wise and cells column wise.
Supplementary_files_format_and_content: Two cell to cell type annotation files. One is for liver samples (1-4) and the other one for bone marrow samples (5-8)

organism: Mus musculus

source_name: CD45+ Ly6G- non-lymphoid

growth_protocol: mice received standard chow (normald diet) or Western diet (high-fat, high-sugar, high-cholesterol) for 24 weeks from 8 weeks of age

extract_protocol:
cells were isolated by collagenase digestion and FACS purified for CD45+ LY6G- CD3- CD4- CD19- NK11-, 50.000 cells were then resuspended in cold PBS + 0.1 % BSA and subjected to 10x single cell library generation according to manufacturers protocol
cDNA

tag: strain

tag: age

value: 24 weeks

tag: diet

value: Normald diet (ND) for 16 weeks


title: H01: T cell


title: G12: T cell


title: G11: T cell


title: G10: T cell


title: G09: T cell


title: G04: T cell


title: G07: T cell


title: G05: T cell


title: G08: T cell


title: F09: B cell

source_name: B cell

value: Bcon (Conventional B) cells


title: F11: B cell


title: G01: T cell


title: G06: T cell


title: F10: B cell


title: G03: T cell


title: F08: B cell


title: F07: B cell


title: F03: B cell


title: F06: B cell


title: F05: B cell


title: E11: B cell


title: F01: B cell


title: E12: B cell


title: E09: B cell


title: E08: B cell


title: G02: T cell


title: E04: B cell


title: E05: B cell


title: E03: B cell


title: E07: B cell


title: E01: B cell


title: D12: Dual Expressor

source_name: Dual Expressor

value: Des (Dual Expressors) cells


title: D10: Dual Expressor


title: D11: Dual Expressor


title: D09: Dual Expressor


title: C09: Dual Expressor


title: C10: Dual Expressor


title: D06: Dual Expressor


title: C08: Dual Expressor


title: RNA-WT-rep2

city: Singapore

first: Jia

last: Li

address: 8 College Road

country: Singapore

institute: Duke-NUS

data_processing:
For ChIP-seq analysis, reads were mapped by bowtie2 against human reference genome GRCh38 (Langmead and Salzberg 2012).
The resulting bam files are converted to bigWig format by bedGraphToBigWig from bedGraph generated by bedtools.
Supplementary_files_format_and_content: bigWig format
For WGBS analysis, the leading 3 bases and adaptor sequences were trimmed from paired-end reads by TrimGalore.
The resulting FASTQ files were analyzed by BISMARK.
PCR duplicates were removed by SAMtools rmdup.
Then bismark_methylation_extractor continued the extraction of the DNA methylation status on every cytosine sites.
Supplementary_files_format_and_content: txt file recoding cytosine methylation status
For RNA-seq analysis, the paired-end RNA-seq reads were trimmed for adaptor sequence by TrimGalore and then mapped by STAR to the human reference genome GRCh38 with reference gene annotation GENCODE 26
PCR duplicates were removed in the paired-end alignments by samtools rmdup.
Alignments with mapping quality < 20 were removed.
Gene expression levels in FPKM were determined by cuffdiff in the Cufflinks package
Genome_build: hg38
Supplementary_files_format_and_content: txt file recoding FPKM values

source_name: H1 human embryonic stem cell

growth_protocol: H1 cell and derivatives were cultured on hESC-qualified Matrigel (354277, Corning) coated plate and were fed with mTeSR1 (05850, Stemcell Technologies) daily. The cell were passage every 4 to 6 days.

extract_protocol:
1) ChIP-seq:Cell were fixed with 1% formaldehyde and insoluble chromatin fraction were isolated. Chromatin were sonicated to 100 to 500 base pair and protein-DNA complexes were pulled down by antbodies. 2) RNA-seq: RNA was harvested by trizol followed by DNAseI treatment and Qiagen RNA mini column for further purification. 3) WGBS: gDNA was harvested by lysing the cells in 50mM Tris-HCl pH8, 100mM NaCl, 25mM EDTA and 1%SDS buffer with 1mg/mL of proteinase K and incubate at 65C overnight.
1) ChIP-seq: Libraries were prepared using ThruPLEX DNA-seq kit (R400428) according to manufacturer's instruction. Constructed libraries were PAGE purified and only libraries with 250 to 500bp were used for sequencing 2) RNA-seq: Librarries were prepared using Scriptseq V2 RNA-seq Library preparation kit (SSV21124) according to manufacturer's instruction.  Constructed libraries were PAGE purified and only libraries with 250 to 500bp were used for sequencing. 3) WGBS library were prepared by BGI using standard Illumina WGBS protocol.

treatment_protocol: DNMT3B knock out and PWWP domain deletion was achived using CRISPR-Cas9 gene editing method.

value: human embryonic stem cell

tag: mutation

value: Wild type

tag: passage


title: RNA-WT-rep1


title: ChIP-WT-Input-rep2

library_source: genomic

molecule: genomic DNA

tag: antibody

value: Input


title: ChIP-WT-Input-rep1


title: C07: Dual Expressor


title: E10: B cell


title: C06: Dual Expressor


title: E06: B cell


title: C04: Dual Expressor


title: thyroid gland DNA methylation 383

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

data_processing:
Illumina HiSeq 2500 paired ends sequencing
Raw sequencing data were converted to fastq.gz files.
bowtie2 --sensitive alignment of the reads in fastq files to hg19 and generating SAM files
generating sorted bam files from the sam files with samtools
counting methylated CCGGG signatures and unmethylated GGG at the reads aligned to CCCGGG sites
Adjusting methylation values based on the spiked in standards. At each SmaI/XmaI site, let Xma be the number of reads corresponding to methylated CpG (i.e., reads starting with CCGGG) and Sma be the number of reads corresponding to unmethylated CpG (i.e., reads starting with GGG), the methylation value was calculated as 100%*(c*(Xma+0.5)/(c*(Xma+0.5)+Sma+0.5)), where c was the correction factor calculated based on observed and expected methylation of spiked-in standards.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are in tab-delimited text file. The columns of the file are: ID_SmaI_hg19 (CCCGGG site ID), chromosome (chromosome of the CCCGGG site), position (position of the CCCGGG site), meth_reads (observed number of reads corresponding to methylated CpG, Xma),  unmeth_reads (observed number of reads corresponding to unmethylated CpG, Sma), total_reads, raw_methylation (unadjusted methylation value), adjusted_methylation (methylation value adjusted based on the spiked in standards).

source_name: thyroid gland

extract_protocol:
Puregene Gentra DNA extraction.
Two to five micrograms of genomic DNA spiked with 2 picograms of methylation standards with defined methylation levels of 0, 25, 50, and 100% were digested with 100 units of SmaI endonuclease (NEB) for 3 hours at 25°C. Subsequently, 100 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA was purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA) and eluted in TRIS-HCl 10 mM pH 8.5 (EB). Eluted DNA was supplemented with NEB buffer #2, dCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3'→5' exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3' DNA ends created by XmaI digestion and added 3' dA tails to all fragments. Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA).

tag: gender

value: Male

tag: race

value: White

tag: ethnicity

value: Non-Spanish


title: ChIP-WT-DNMT3B-rep1

value: anti-human DNMT3B rabbit monoclonal antibody (Clone D3C8T, Cell Signaling Technologies, custom-made antibody)


title: C03: Dual Expressor


title: thyroid gland DNA methylation 324

value: Female


title: D05: Dual Expressor

value: PBMC


title: C02: Dual Expressor

value: Type 1 diabetes


title: C01: Dual Expressor


title: B12: Dual Expressor


title: testis  DNA methylation 931

source_name: testis


title: thyroid gland DNA methylation 308


title: testis  DNA methylation 10


title: B10: Dual Expressor


title: B11: Dual Expressor


title: stomach  DNA methylation 678

source_name: stomach

value: Unknown


title: B08: Dual Expressor


title: B06: Dual Expressor


title: B07: Dual Expressor


title: stomach  DNA methylation 658


title: C05: Dual Expressor


title: ChIP-WT-DNMT3B-rep2


title: prostate  DNA methylation 958

source_name: prostate

value: Puerto Rican


title: prostate  DNA methylation 549

value: Black


title: B04: Dual Expressor


title: prostate  DNA methylation 535


title: ovary  DNA methylation 943

source_name: ovary


title: B05: Dual Expressor


title: testis  DNA methylation 757


title: B02: Dual Expressor


title: ovary  DNA methylation 534


title: brain  DNA methylation nb2

source_name: brain


title: A10: Dual Expressor


title: B01: Dual Expressor


title: brain  DNA methylation nb1


title: B09: Dual Expressor


title: lung  DNA methylation 386

source_name: Lower lobe lung


title: stomach  DNA methylation 627


title: A09: Dual Expressor


title: lung  DNA methylation 268

source_name: Upper lobe lung


title: esophagus  DNA methylation 46

source_name: esophagus


title: prostate  DNA methylation 701


title: esophagus  DNA methylation 36


title: A03: Dual Expressor


title: A07: Dual Expressor


title: RNA-PWWP-rep2

value: PWWP domain knock out


title: RNA-PWWP-rep1


title: dermis  DNA methylation 392

source_name: dermis


title: A01: Dual Expressor


title: dermis  DNA methylation 309


title: B03: Dual Expressor


title: RNA-KO-rep2

value: DNMT3B knock out


title: uterine cervix  DNA methylation 402

source_name: uterine cervix


title: RNA-KO-rep1


title: bladder  DNA methylation 702

source_name: bladder


title: bladder  DNA methylation 461


title: ChIP-dPWWP-Input-rep2


title: ChIP-KO-Input-rep2


title: ChIP-dPWWP-H3K27me3

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb (9733BC, Cell Signalinf Technology, lot:10/2016)


title: adrenal gland DNA methylation 475

source_name: adrenal gland


title: adrenal gland DNA methylation 418


title: adrenal gland DNA methylation 24


title: ChIP-KO-H3K27me3


title: A08: Dual Expressor

value: Des (Dual Expressors) cells


title: ChIP-dPWWP-H3K4me3-rep2

value: human embryonic stem cell

value: Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb (9751S, Cell Signalinf Technology, lot:01/2017)


title: ChIP-KO-Input-rep1

value: Input


title: epidermis  DNA methylation 611

source_name: epidermis


title: epidermis  DNA methylation 392


title: ChIP-dPWWP-H3K4me3-rep1


title: ChIP-KO-H3K4me3-rep2


title: ChIP-dPWWP-H3K36me3-rep2

value: Rb pAb to histone H3 tri methyl K36 (ab0905, abcam, lot:GR249065-1)


title: ChIP-KO-H3K4me3-rep1


title: WGBS-KO-rep2


title: ChIP-dPWWP-H3K36me3-rep1


title: ChIP-dPWWP-DNMT3B-rep2


title: ChIP-KO-H3K36me3-rep2


title: bladder  DNA methylation 217

value: Male

value: White


title: ChIP-dPWWP-Input-rep1


title: WGBS-KO-rep1


title: ChIP-KO-H3K36me3-rep1


title: WGBS-dPWWP-rep2


title: WGBS-dPWWP-rep1


title: ChIP-dPWWP-DNMT3B-rep1

value: anti-human DNMT3B rabbit monoclonal antibody (Clone D3C8T, Cell Signaling Technologies, custom-made antibody)


title: SW620_Cytoplasmic_FullRNASeq

status: Public on Jun 01 2019

city: Cambridge

first: Harry

last: Fischl

address: Babraham Research Campus

country: United Kingdom

institute: Storm Therapeutics

description: polyadenylated RNA

data_processing: Sequences were aligned using bowtie to genome build hg19

source_name: SW620 cell line

growth_protocol: SW480 and SW620 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% (v/v) foetal calf serum (FCS), 2 mM glutamine and ampicillin (100 mg/ml). Cells were grown to 60-80% confluence before harvesting or passaging unless specified otherwise. 1CT cells were cultured as described previously (Roig et al., 2010).

extract_protocol:
Subcellular fractionation into nuclear and cytoplasmic fractions followed by RNA isolation using Triazol reagent (Neve et al., 2015)
Libraries were constructed from polyA purified RNA using the Ion Total RNA-seq kit v2

tag: subcellular fraction

value: Cytoplasmic

tag: sirna treatment


title: 1CT_Nuclear_FullRNASeq

description: polyadenylated RNA

source_name: 1CT cell line

value: Nuclear


title: 1CT_Cytoplasmic_FullRNASeq

description: polyadenylated RNA


title: SW620_Nuclear_FullRNASeq

description: polyadenylated RNA


title: SW620_Scrambledkd_C_rep3

description: polyadenylated RNA

data_processing:
Sequences were aligned using the Ion Torrent Server TMAP aligner to genome build hg19
Reads mapping to true pA sites were then extracted by using the Bedtools Intersect function to select only reads that fell within 100 nucleotides of a previously confirmed pA site. These poly(A) sites were those identified using 3’READS in HEK293 or HBL cells, or those identified using PolyA-Seq in several different human tissues under accession number GSE30198 (Derti et al., 2012). Bigwig files were generated of these extracted reads normalized to reads per million.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
Subcellular fractionation into nuclear and cytoplasmic fractions followed by RNA isolation using Triazol reagent (Neve et al., 2015)
The 3’ ends of extracted RNA were generated into libraries using the QuantSeq 3’mRNA-Seq library kit (Lexogen)
3’mRNA-seq

treatment_protocol: Scrambled negative control siRNA (ThermoFisher, 4390843) and siRNAs targetting ELAVL1 (ThermoFisher, s4609) or HNRNPC (ThermoFisher, s6721) were transfected in a reaction mix containing Opti-MEM medium (Sigma, 31985062) and Lipofectamine RNAiMAX (ThermoFisher, 13778075) when the SW620 cells reached 30% confluence. siRNA containing media was replaced by normal DMEM media 24 hours after the first transfection. Cells were transfected again 24 hours after the replacement of the normal media. RNA from nuclear and cytoplasmic subcellular fractions were extracted 24 hours after the second transfection.

value: scrambled siRNA


title: SW620_HNRNPCkd_C_rep3

value: HNRNPC siRNA


title: SW620_Scrambledkd_N_rep3

description: polyadenylated RNA


title: SW620_HNRNPCkd_N_rep3

description: polyadenylated RNA


title: CTC-MCC-41 at passage 10

type: RNA

city: Montpellier

first: Said

last: Assou

address: 80, av. Augustin Fliche

department: Institute for Regenerative Medecine and Biotherapy

country: France

institute: University Hospital of Montpellier, Inserm

description: Gene expression data from CTC-MCC-41 at passage 10

hyb_protocol: After fragmentation, the labeled antisense aRNA (12 μg) was hybridized to HG-U133 Plus 2.0 GeneChip pan-genomic oligonucleotide arrays (Affymetrix)

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

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

label: biotin

source_name: human colon

label_protocol: Biotinylated nucleotide analog was incorporated during in vitro transcription step according to the Affymetrix protocol.

growth_protocol: The CTC line was established from Circulating Tumor Cells isolated from a patient with colon cancer using the CellSearch system. Briefly, 10 mL of blood was collected in an EDTA tube and was immediately used for CTC isolation by depletion of hematopoietic CD45-positive cells using the RosetteSep Human Circulating Epithelial Tumor Cell Enrichment cocktail. The HT-29 cell line (ATCC® HTB-38™) is a human colorectal adenocarcinoma cell line that was established in 1964 by J. Fogh from the primary tumor.

extract_protocol: RNeasy Mini Kit was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: Isolated CTCs were then plated in 24-well non-adherent plates and cultured in Dulbecco’s modified Eagle’s medium/F12 with 20 ug/mL insulin, 1% N2 complement, 20 ng/mL epithelial growth factor, 2mM L-Glutamine, 10 ng/mL fibroblast growth factor-2 (FGF2) and 2% fetal calf serum (FCS). HT-29 cells were maintained in Dulbecco's modified Eagle's medium (# 31966-021, Gibco, ThermoFisher) supplemented with 10% FCS.

value: circulating tumor cells


title: hESC_3999213071_F

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

institute: Klinikum rechts der Isar – Technical University Munich

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: H9 hESC cell line

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

extract_protocol: Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) and 1 ug RNA was used for transcription using the High-capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific). Quality control was performed with Agilent Bioanalyser.

value: embryonic stem cells


title: hESC_3999213071_E

description: replicate 2


title: SW620_Scrambledkd_N_rep2

extract_protocol:
Subcellular fractionation into nuclear and cytoplasmic fractions followed by RNA isolation using Triazol reagent (Neve et al., 2015)
The 3’ ends of extracted RNA were generated into libraries using the QuantSeq 3’mRNA-Seq library kit (Lexogen)


title: SW620_Scrambledkd_C_rep1


title: iPSC_L_3999213071_C

description: replicate 3

source_name: human induced pluripotent stem cells

value: lymphocytes derived induced pluripotent stem cells


title: SW620_HNRNPCkd_N_rep2


title: CTC-MCC-41 at passage 8

description: Gene expression data from CTC-MCC-41 at passage 8


title: CTC-MCC-41 at passage 6

description: Gene expression data from CTC-MCC-41 at passage 6


title: iPSC_L_3999213071_B

description: replicate 2


title: HT-29 at passage 134

description: Gene expression data from HT-29 at passage 134

value: cell line established from a primary colon cancer


title: SW620_Scrambledkd_C_rep2


title: HT-29 at passage 130

description: Gene expression data from HT-29 at passage 130


title: HT-29 at passage 132

description: Gene expression data from HT-29 at passage 132


title: SW620_HNRNPCkd_N_rep1


title: SW620_HNRNPCkd_C_rep1


title: SW620_ELAVL1kd_N_rep1

value: ELAVL1 siRNA


title: SW620_HNRNPCkd_C_rep2


title: SW620_ELAVL1kd_N_rep2


title: SW620_Scrambledkd_N_rep1


title: SW620_ELAVL1kd_C_rep2


title: SW620_ELAVL1kd_C_rep1


title: SW620_N_rep1


title: SW620_C_rep1


title: SW620_C_rep2


title: SW480_N_rep1

source_name: SW480 cell line


title: iPSC_L_3999213071_A

description: replicate 1


title: SW480_C_rep2


title: SW480_C_rep1


title: 1CT_N_rep2


title: 1CT_C_rep2


title: 1CT_N_rep1


title: 1CT_C_rep1


title: hESC_3999213071_D

description: replicate 1


title: SW620_N_rep2


title: SW480_N_rep2


title: carotid-atherosclerotic-plaque-rep37

city: Stockholm

first: Jesper

middle: Robert

last: Gådin

address: CMM, L8:02 Karolinska Universitetessjukhuset, Solna

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

hyb_protocol: User Manual Affymetrix HTA-2_0 arrays

scan_protocol: Scanning images were generated using using Affymetrix GeneChip® Command Console Software (AGCC)

data_processing: Expression Console Software, med-polish (gc-correction, algo_rev=4, cel_out=false,scale-intensities, floor=1, low=20, high=50000, ceiling=1000000, low_pct=0, 02, high_pct=0, 98, cel_out=false,rma-bg,quant-norm, sketch=-1, bioc=true, lowprecision=false, usepm=true, target=0, doavg=false)

source_name: carotid-atherosclerotic-plaque

label_protocol: User Manual Affymetrix HTA-2_0 arrays

extract_protocol: Plaque tissues from n=40 patients were frozen at -80°C immediately after surgery and RNA was prepared using Qiazol Lysis Reagent (Qiagen, Hilden, Germany) and purified by RNeasy Mini kit (Qiagen), including DNase digestion.

value: carotid-atherosclerotic-plaque

tag: ID

tag: Sex


title: carotid-atherosclerotic-plaque-rep33

tag: tissue


title: carotid-atherosclerotic-plaque-rep40


title: carotid-atherosclerotic-plaque-rep31

value: Female


title: carotid-atherosclerotic-plaque-rep36


title: carotid-atherosclerotic-plaque-rep26


title: carotid-atherosclerotic-plaque-rep34


title: carotid-atherosclerotic-plaque-rep39


title: carotid-atherosclerotic-plaque-rep30


title: carotid-atherosclerotic-plaque-rep23


title: carotid-atherosclerotic-plaque-rep38


title: carotid-atherosclerotic-plaque-rep28


title: carotid-atherosclerotic-plaque-rep20


title: carotid-atherosclerotic-plaque-rep17


title: carotid-atherosclerotic-plaque-rep22


title: carotid-atherosclerotic-plaque-rep24


title: carotid-atherosclerotic-plaque-rep16


title: carotid-atherosclerotic-plaque-rep25


title: carotid-atherosclerotic-plaque-rep29


title: carotid-atherosclerotic-plaque-rep13


title: carotid-atherosclerotic-plaque-rep18


title: carotid-atherosclerotic-plaque-rep15


title: carotid-atherosclerotic-plaque-rep32


title: carotid-atherosclerotic-plaque-rep21


title: carotid-atherosclerotic-plaque-rep27


title: carotid-atherosclerotic-plaque-rep35


title: carotid-atherosclerotic-plaque-rep14


title: carotid-atherosclerotic-plaque-rep12


title: carotid-atherosclerotic-plaque-rep19


title: LPS-duplicate2

first: Lisa

last: Borghini

state: Singapore

address: 60 Biopolis Street, Genome, #02-01

department: Infectious Diseases

institute: GIS

data_processing:
mapping of the reads to hg19 with TopHat
Differential gene expression analysis with CuffDiff, using the Ensemble gtf file GRCh37.73 and running the treated condition against the non-treated condition (for each duplicate) bam file (cuffdiff-2.2.0 -u -o xxx GRCh37.73_+chrm.gtf no_treatment.bam treatment.bam)
Genome_build: hg19
Supplementary_files_format_and_content: For LPS samples, the 'gene_exp.diff' output file from cuffdiff against non-treated sample is given

source_name: FaDu cells

growth_protocol: FaDu cells were purchased from ATCC and cultured in RPMI medium (Gibco) supplemented with 10% fetal bovine serum performance (Gibco), 100U/ml penicillin, 100ug/ml streptomycin (Gibco) and 1mM sodium pyruvate (Gibco).

extract_protocol:
Total RNAs were extracted using the RNeasy Plus Universal kit (Qiagen) and loaded on a NanoRNA Bioanalyzer chip (Agilent) for qualification and quantification.
Libraries for RNA-seq were prepared with the TruSeq Stranded mRNA Library Prep kit (Illumina) according to the manufacturer’s instructions.  Samples were sequenced on an Illumina NextSeq-500 1x76bp

treatment_protocol: FaDu cells were treated with LPS at 1μg/mL for 80 minutes. For each experiment, a “no treatment” control consisting of a change of culture medium was processed along with the treated samples.

tag: cell line

value: FaDu

tag: treatment

value: LPS


title: Control-duplicate2


title: carotid-atherosclerotic-plaque-rep11


title: LPS-duplicate1


title: Control-duplicate1


title: carotid-atherosclerotic-plaque-rep9


title: hESC line H9 cells after 96 hours of rWnt3a treatment, biol. repl. 2

city: Neuherberg

first: Dmitry

last: Shaposhnikov

address: Ingolstädter Landstraße 1

institute: Helmholtz Center Munich

data_processing:
FASTQ generation was done automatically in Illumina BaseSpace application
reads were pseudo-aligned to human transcriptome (Ensembl version GRChg38.86) using kallisto (version 0.43.0_3)
transcript-level abundances were aggregated into counts per gene and exported using Tximport (version 1.10.1) pipeline
Genome_build: GRChg38.86
Supplementary_files_format_and_content: csv file containing raw gene counts for all samples

source_name: embryonic stem cells

growth_protocol: H9 cell line was grown on Geltrex-coated plates in mTESR1 medium

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kit according to manufacturer's instructions
Total RNA libraries were prepared from 1 µg of total RNA using Illumina TruSeq Stranded Total RNA LT kit according to manufacturer's instructions.

treatment_protocol: Cells were seeded at 100% confluency on Matrigel-coated plates. 16 hours later the medium was replaced with differentiation medium (RPMI1640 + B27 supplement without vitamin A) and either 10 µM CHIR99021, 240 ng/ml rWnt3a or 1 µg/ml doxycycline. Differentiation medium and ligands were freshly added every 24 hours.

value: recombinant Wnt3a


title: PBMC1_bulk

first: Aviv

last: Regev

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

description:
bulk RNA-Seq
full-length
HEK293_PBMC_TPM_bulk.tsv

data_processing:
For scRNA-seq and snRNA-seq data, scumi v0.1.0 (https://bitbucket.org/jerry00/scumi-dev/src/master/) was used to produce cell by gene sparse matrices (UMI count matrices for 3'-end methods and read count matrices for Smart-seq2). More specifically, STAR v2.6.1a was used for alignment except for Smart-seq2 and CEL-Seq2 data where HISAT v2.0.5 was used. featureCounts from the Subread package, v1.6.2 was used to tag each alignment with a gene tag. For bulk RNA-Seq data, reads were mapped to the reference genomes using Bowtie v0.12.9, and further quantified by RSEM v1.3.0 to generate transcripts per million values.
Genome_build: scRNA-seq data: a merged hg19 and mm10 geome for human and mouse mixture datasets, hg38 (GRCh38) for human PBMCs, and mm10 for mouse cortex data; bulk RNA-Seq data, hg38 (GRCh38) for human data and mm10 for mouse data
Supplementary_files_format_and_content: scRNA-seq data: mtx, a gene by cell count matrix in the sparse matrix market format
Supplementary_files_format_and_content: scRNA-seq data: cell.tsv, cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: scRNA-seq data: gene.tsv, gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: Bulk RNA-Seq data: TPM_bulk.tsv, tab-delimited text files of transcripts per million measurements of genes in each sample
Supplementary_files_format_and_content: mixture_hg19_mm10_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: mixture_hg19_mm10_count_matrix.mtx :A gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: mixture_hg19_mm10_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: pbmc_hg38_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: pbmc_hg38_count_matrix.mtx :A gene by cell count matrix in the matrix market format
Supplementary_files_format_and_content: pbmc_hg38_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: cortex_mm10_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: cortex_mm10_count_matrix.mtx :A gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: cortex_mm10_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: HEK293_PBMC_TPM_bulk.tsv :A matrix of transcripts per million measurements
Supplementary_files_format_and_content: NIH3T3_cortex_TPM_bulk.tsv :A matrix of transcripts per million measurements

source_name: Peripheral blood mononuclear cell

extract_protocol:
Total RNA from bulk samples was extracted using Quick-RNA Mini Prep (Zymo Research) following the vendor protocol with a DNase treatment step
For library construction methods, see SAMPLES, description: Library Construction field. For details see the Methods section in the manuscript

value: Male

tag: library construction

value: TruSeq


title: Mixture2_HEK293_bulk

source_name: Human HEK293 cell line


title: hESC line H9 cells after 120 hours of rWnt3a treatment, biol. repl. 2


title: Mixture1_HEK293_bulk


title: hESC line H9 cells after 120 hours of rWnt3a treatment, biol. repl. 1


title: carotid-atherosclerotic-plaque-rep7


title: Input DNA - Control

data_processing:
mapping of the reads to hg19 with BWA
Filtering with samtools 1.2 (samtools view -bh -F 1804 -q 20)
Peak calling with Dfilter 1.5  For RELA ChIP-seq, 2 calls were carried out against different controls: (a) against no treatment control RELA ChIP-seq and (b) against input DNA, using the following command: run_dfilter15.sh -f=bam -ks=20 -bs=50 -lpval=2 -nonzero -refine -wig. The first 100,000 most confident peaks were extracted from each call. Irreproducibility Discovery Rate (IDR) analysis was performed between calls (a) and (b). This strategy allows discovery of reproducible peaks against the 2 controls and a stringent threshold of IDR<=0.005 was applied to identify final RELA peaks in FaDu cells.  For H3K27ac ChIP-seq, a simple peak calling was performed with Dfilter 1.5 in each condition (Control no treatment and LPS treatment) against input DNA using the following command: run_dfilter15.sh -d=ChIP.bam -c=Input.bam -o=peaks -f=bam -ks=60 -bs=100 -lpval=6  A bedGraph file generated with Homer is also provided for each of the ChIP sample.
Black listed regions were removed found in wgEncodeDacMapabilityConsensusExcludable.bed (http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeMapability/) were removed from the final list of peaks using bedtools intersect command. Any peaks falling in chromosome Y was also filtered out as the cell line studied is derived from a female.
Genome_build: hg19
Supplementary_files_format_and_content: For all ChIP-seq samples, bedGraph files are provided (generated with Homer makeTagDirectory command followed by makeUCSCfile command).  A list of peaks (bed files) generated as described in data processing are also provided for Control and LPS treated H3K27ac ChIP-seq as well as LPS-induced RELA ChIP-seq.

source_name: FaDu cultured cells

extract_protocol:
After treatment, cells were crosslinked with 0.75% formaldehyde for 8 minutes and cross-linking was quenched with 180mM Glycine for 10 minutes at room temperature. Cells were then lysed with cell lysis buffer (0.25% Triton X-100, 10mM EDTA, 0.1M NaCl in 10mM Tris-HCl pH8) for 20 minutes at 4°C. Nuclei were collected by centrifugation at 4,000rpm for 10 minutes at 4°C and lysed in nuclei lysis buffer (1% NP-40, 0.5% NaDOC, 0.1% SDS in PBS) for 20 minutes at 4°C.  Chromatin shearing was performed using a sonicator (Bioruptor, Diagenode) on high setting for 40 cycles of 30 seconds ON/45 seconds OFF, leading to a fragment range of 100-250bp.
ChIP-seq libraries were built following the library-on-beads protocol from Wallerman et al. (Wallerman et al. 2015). Chromatin was incubated with antibodies bound to protein G magnetic beads (Dyanabeads protein G, Thermo Fisher scientific) prepared by mixing the antibody with the beads in PBS+0.5%BSA for 4 to 6 hours at room temperature. Four ug of anti-RELA antibody (NFKB p65 (c20): sc-372) or 5 ug of anti-H3K27ac (Active motif, reference 39138) were mixed with 40 uL or 50 uL of beads respectively.  Immunoprecipitation was performed by rotation at 4°C overnight. After immunoprecipitation, samples were washed twice with nuclei lysis buffer, twice with nuclei lysis buffer complemented with 350mM NaCl, twice with LiCl/NP-40 buffer (0.25M LiCl, 1mM EDTA, 0.5% NP-40, 0.5% NaDOC in 10mM Tris-HCl pH8) and once with PBS. Libraries on beads were then built using NEBnext DNA library prep kit (New England Biolabs) according to the manufacturer’s instructions. Due to the nature of the samples, minor adjustments were done: two washes with PBS were performed in between each step of the preparation and elution of the DNA from the beads was done after adaptor ligation. ChIP samples were eluted in Elution buffer (10mM EDTA, 1% SDS in 50mM Tris-HCl pH7.5) for 4 hours at 65°C and purified with Agencourt AMPure XP beads (Beckman Coulter). PCR reaction was performed using Phusion High-Fidelity PCR Master Mix (Thermo scientific) and custom primers for multiplexing. The following program was applied: 3 minutes at 98°C; 17x(30 seconds at 98°C, 30 seconds at 65°C, 30 seconds at 72°C); 5 minutes at 72°C. Samples were loaded on a DNA1000 bioanalyzer chip (Agilent) to check the size of the libraries as well as the concentration. As a control, 2-5% of input DNA was reverse cross-linked at 65°C for minimum 6 hours and libraries were prepared using the same library preparation kit.  Samples were sequenced on an Illumina HiSeq Rapid 2x76bp for the RELA ChIP-seq and on an Illumina NextSeq High 1x76bp for the H3K27ac ChIP-seq.

treatment_protocol: FaDu cells were treated with LPS at 1μg/mL for 60 minutes. For each experiment, a “no treatment” control consisting of a change of culture medium was processed along with the LPS treated sample.

tag: chip antibody

value: input for H3K27ac


title: Input DNA - LPS


title: H3K27ac ChIP-seq - LPS


title: H3K27ac ChIP-seq - Control


title: carotid-atherosclerotic-plaque-rep8

tag: age


title: carotid-atherosclerotic-plaque-rep6


title: PBMC2_bulk


title: carotid-atherosclerotic-plaque-rep5


title: carotid-atherosclerotic-plaque-rep1


title: Control-2, biological rep2

city: Chicago

first: Wancai

last: Yang

state: IL

address: 840 South Wood Street

department: Pathology

institute: University of Illinois at Chicago

hyb_protocol: Followed fragmentation and biotin labeling

scan_protocol: After washing and staining, the arrays were scanned by the Affymetrix Scanner 3000(Affymetrix).

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) software was used to extract raw data. Next, Expression Console (version1.3.1, Affymetrix) software offered RMA normalization for both gene and exon level analysis.

label: Biotin

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols.

growth_protocol: Human colon cancer HCT116 cells from American Type Culture Collection (ATCC) (Manassas, VA) were maintained in a complete MEM medium.

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

treatment_protocol: HCT116 cells were transiently transfected with PRSS8 expression plasmids or the vector control and collected

tag: genotype/variation

value: control


title: Test-2, biological rep2

source_name: PRSS8 OE2

value: overexpressing PRSS8


title: carotid-atherosclerotic-plaque-rep2


title: hESC line H9 cells after 72 hours of rWnt3a treatment, biol. repl. 1


title: hESC line H9 cells after 72 hours of rWnt3a treatment, biol. repl. 2


title: hESC line H9 cells after 96 hours of rWnt3a treatment, biol. repl. 1


title: hESC line H9 cells after 48 hours of rWnt3a treatment, biol. repl. 2


title: Test-1, biological rep1

source_name: PRSS8 OE1


title: hESC line H9 cells after 48 hours of rWnt3a1 treatment, biol. repl. 1


title: carotid-atherosclerotic-plaque-rep3


title: Control-1,biological rep1


title: carotid-atherosclerotic-plaque-rep10


title: undifferentiated hESC line H9 cells, biol. repl. 1 (wnt)


title: hESC line H9 cells after 48 hours of CHIR99021 treatment, biol. repl. 2


title: undifferentiated hESC line H9 cells, biol. repl. 2 (wnt)


title: hESC line H9 cells after 24 hours of rWnt3a treatment, biol. repl. 2


title: hESC line H9 cells after 48 hours of CHIR99021 treatment, biol. repl. 1


title: hESC line H9 cells after 72 hours of CHIR99021 treatment, biol. repl. 2


title: undifferentiated hESC line H9 cells, biol. repl. 2 (chir)


title: hESC line H9 cells after 8 hours of rWnt3a treatment, biol. repl. 1


title: hESC line H9 cells after 16 hours of CHIR99021 treatment, biol. repl. 1


title: hESC line H9 cells after 16 hours of CHIR99021 treatment, biol. repl. 2


title: hESC line H9 with stably integrated constitutively active beta-catenin, 72 hours of Dox treatment, biol. repl. 2

value: doxycycline


title: hESC line H9 cells after 8 hours of CHIR99021 treatment, biol. repl. 1


title: hESC line H9 cells after 24 hours of rWnt3a treatment, biol. repl. 1


title: hESC line H9 cells after 8 hours of CHIR99021 treatment, biol. repl. 2


title: undifferentiated hESC line H9 cells, biol. repl. 1 (chir)


title: hESC line H9 cells after 72 hours of CHIR99021 treatment, biol. repl. 1


title: hESC line H9 with stably integrated constitutively active beta-catenin, 72 hours of Dox treatment, biol. repl. 1


title: hESC line H9 cells after 24 hours of CHIR99021 treatment, biol. repl. 2


title: hESC line H9 with stably integrated constitutively active beta-catenin, 48 hours of Dox treatment, biol. repl. 2


title: hESC line H9 with stably integrated constitutively active beta-catenin, 48 hours of Dox treatment, biol. repl. 1


title: hESC line H9 with stably integrated constitutively active beta-catenin, 24 hours of Dox treatment, biol. repl. 2


title: hESC line H9 with stably integrated constitutively active beta-catenin, 8 hours of Dox treatment, biol. repl. 1


title: hESC line H9 with stably integrated constitutively active beta-catenin, 8 hours of Dox treatment, biol. repl. 2


title: hESC line H9 with stably integrated constitutively active beta-catenin, 16 hours of Dox treatment, biol. repl. 1


title: hESC line H9 with stably integrated constitutively active beta-catenin, 24 hours of Dox treatment, biol. repl. 1


title: hESC line H9 with stably integrated constitutively active beta-catenin, uninduced, biol. repl. 2


title: hESC line H9 with stably integrated constitutively active beta-catenin, 16 hours of Dox treatment, biol. repl. 2


title: hESC line H9 cells after 8 hours of rWnta3a treatment, biol. repl. 2


title: hESC line H9 cells after 24 hours of CHIR99021 treatment, biol. repl. 1


title: hESC line H9 with stably integrated constitutively active beta-catenin, uninduced, biol. repl. 1


title: PD10_fibroblast

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

institute: Lund University

data_processing:
Illumina bcl2fastq was used for basecalling.
RSEM (1.30) was used to generate expression estimates after alignment to the human transcriptome (Ensembl v.75)
Abundance estiamtes were combined using tximport and normalized using edgeR/limma
Genome_build: GrCH37
Supplementary_files_format_and_content: TSV of normalized counts per gene per patient

source_name: fibroblast

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen)
Libraries were prepared using Illumina truseq library kit.
150 cycles paired end RNA-seq

tag: disease state

value: Parkinsons Disease

value: Fibroblasts were kept 3 days in culture in DMEM, 10 % FBS, 1 % penicillin-streptomycin

tag: cell type

value: fibroblast


title: PD09_fibroblast


title: PD11_fibroblast


title: PD10_iN

source_name: iN

value: Fibroblasts were transduced with the pB.pA.shREST lentiviral vector (Drouin-Ouellet et al. 2017) the day following plating and allowed to be reprogrammed for 30 days.

value: iN


title: PD09_iN


title: PD08_iN


title: PD07_iN


title: PD05_fibroblast


title: PD06_fibroblast


title: PD03_fibroblast


title: PD05_iN


title: PD06_iN


title: PD03_iN


title: PD02_fibroblast


title: PD02_iN


title: PD01_fibroblast


title: C12_fibroblast

value: Control


title: C10_iN


title: PD01_iN


title: C10_fibroblast


title: C09_iN


title: C11_fibroblast


title: C09_fibroblast


title: C08_fibroblast


title: C13_fibroblast


title: C08_iN


title: C11_iN


title: C07_iN


title: C07_fibroblast


title: C02_fibroblast


title: C02_iN


title: C01_fibroblast


title: C04_iN


title: C04_fibroblast


title: C01_iN


title: MEL624 PCIF1 KO2, replicate B

city: Mexico City

first: David

last: Valle-Garcia

address: Av. Insurgentes Sur 3877, La Fama, Tlalpan

country: Mexico

institute: National Institute of Neurology and Neurosurgery

description:
MEL624-Proseq-KO2-B
processed data file:
GEO-hg38-MEL624-proseq-norm_counts.txt
hg38_MEL624_PROseq_PCIF1-KO_clone2_N3_matchnorm_dedup_F.bedGraph.gz
hg38_MEL624_PROseq_PCIF1-KO_clone2_N3_matchnorm_dedup_R.bedGraph.gz

data_processing:
library strategy: PRO-seq
Paired-end reads were trimmed to 40 nt. To remove adapter sequence and low quality 3' ends we used cutadapt 1.14, discarding reads shorter than 20 nt (-m 20 -q 10), and removing a single nucleotide from the 3' end of all trimmed reads.
Alignment against hg38 genome assembly were done with Bowtie 1.2.2 using the following parameters: up to 2 mismatches, maximum fragment length of 1000 nt, and uniquely mappable, and unmappable pairs routed to separate output files (-m1, -v2, -X1000, --un)
Uniligned read pairs were paired-end aligned to the Drosophila dm3 genome index to determine spike-normalization ratios based on uniquely mapped reads using the same setting as above. Counts of pairs mapping uniquely to spike-in RNAs (drosophila genome) were determined for each sample. In this case, the samples displayed highly comparable recovery of spike-in reads, thus only depth normalization was used for bedGraph generation
Strand-specific counts of the 3'-end mapping positions determined at single nucleotide resolution, genome-wide, and expressed in bedGraph format with “plus” and “minus” strand labels, as appropriate. Combined bedGraphs were generated after deduplication by summing counts per nucleotide of all 3 replicates for each condition. All bedgraphs were generated using in-house scripts
Read counts were calculated per gene (from transcription start site to transcription end site), in a strand-specific manner, based on default annotations (ensembl genes 93, GRCh38.p12), using featureCounts from the Rsubread package version 1.6.2
PRO-seq size factors were determined based on DESeq2 (for Control: 0.9690449, 0.8752877, 0.9008983; PCIF1-KO1: 1.1669854, 0.9802904, 1.3105898; PCIF1-KO2: 0.9866223, 1.0047620, 0.9516695). DEG genes were determined at an adjusted p-value threshold of <0.01
Genome_build: hg38, ensebml genes 93 annotation
Supplementary_files_format_and_content: Bedgraph files representing stranded read counts. Tab-delimited txt file with mean normalized counts per kb from DeSeq2

source_name: MEL624 PCIF1 KO2

growth_protocol: MEL624 cells were grown in standard DMEM media supplemented with 10% FBS and pen/strep in a 37C CO2 incubator

extract_protocol:
10 Million cells were dounced in permeabilization buffer (10mM Tris-Cl, pH 8.0, 10mM KCl, 250mM sucrose, 5mM MgCl2, 0.5mM DTT, 10% Glycerol, 0.1% Igepal) to obtain permeabilized nuclei. Nuclei were then processed for PRO-Seq as described previously by Mahat et al. (PMID: 27442863 )
Illumina sequencing libraries were prepared using the ProSeq library protocol from Mahat et al. detailed in PMID 27442863

tag: cellosaurus cell line identifier

value: Human melanoma cell line

value: PCIF1 KO

tag: molecule subtype

value: chromatin-associated RNA


title: MEL624 PCIF1 KO2, replicate A

description:
MEL624-Proseq-KO2-A
processed data file:
GEO-hg38-MEL624-proseq-norm_counts.txt
hg38_MEL624_PROseq_PCIF1-KO_clone2_N3_matchnorm_dedup_F.bedGraph.gz
hg38_MEL624_PROseq_PCIF1-KO_clone2_N3_matchnorm_dedup_R.bedGraph.gz


title: MEL624 PCIF1 KO1, replicate A

description:
MEL624-Proseq-KO1-A
processed data file:
GEO-hg38-MEL624-proseq-norm_counts.txt
hg38_MEL624_PROseq_PCIF1-KO_clone1_N3_matchnorm_dedup_F.bedGraph.gz
hg38_MEL624_PROseq_PCIF1-KO_clone1_N3_matchnorm_dedup_R.bedGraph.gz

source_name: MEL624 PCIF1 KO1


title: MEL624 PCIF1 KO1, replicate C

description:
MEL624-Proseq-KO1-C
processed data file:
GEO-hg38-MEL624-proseq-norm_counts.txt
hg38_MEL624_PROseq_PCIF1-KO_clone1_N3_matchnorm_dedup_F.bedGraph.gz
hg38_MEL624_PROseq_PCIF1-KO_clone1_N3_matchnorm_dedup_R.bedGraph.gz


title: MEL624 control cells, replicate C

description:
MEL624-Proseq-Cont-C
processed data file:
GEO-hg38-MEL624-proseq-norm_counts.txt
hg38_MEL624_PROseq_Control_N3_matchnorm_dedup_F.bedGraph.gz
hg38_MEL624_PROseq_Control_N3_matchnorm_dedup_R.bedGraph.gz

source_name: MEL624 control cells

value: Wild type + Random sgRNA


title: MEL624 control cells, replicate B

description:
MEL624-Proseq-Cont-B
processed data file:
GEO-hg38-MEL624-proseq-norm_counts.txt
hg38_MEL624_PROseq_Control_N3_matchnorm_dedup_F.bedGraph.gz
hg38_MEL624_PROseq_Control_N3_matchnorm_dedup_R.bedGraph.gz


title: MEL624 PCIF1 KO1, replicate B

description:
MEL624-Proseq-KO1-B
processed data file:
GEO-hg38-MEL624-proseq-norm_counts.txt
hg38_MEL624_PROseq_PCIF1-KO_clone1_N3_matchnorm_dedup_F.bedGraph.gz
hg38_MEL624_PROseq_PCIF1-KO_clone1_N3_matchnorm_dedup_R.bedGraph.gz


title: MEL624 control cells, replicate A

description:
MEL624-Proseq-Cont-A
processed data file:
GEO-hg38-MEL624-proseq-norm_counts.txt
hg38_MEL624_PROseq_Control_N3_matchnorm_dedup_F.bedGraph.gz
hg38_MEL624_PROseq_Control_N3_matchnorm_dedup_R.bedGraph.gz


title: MEL624 PCIF1 KO2, replicate C

description:
MEL624-Proseq-KO2-C
processed data file:
GEO-hg38-MEL624-proseq-norm_counts.txt
hg38_MEL624_PROseq_PCIF1-KO_clone2_N3_matchnorm_dedup_F.bedGraph.gz
hg38_MEL624_PROseq_PCIF1-KO_clone2_N3_matchnorm_dedup_R.bedGraph.gz


title: MEL624 KO cells, Ab6 [MEL624-m6Am-KO-Ab6]

data_processing:
Reads were aligned against hg38 genome assembly with hisat 2.0.4 using the following parameters: --no-unal --rna-strandness R
sam files were sorted and converted to bam with samtools v1.7. Reads with QS < 10 were excluded
Normalized bigWig files were generated from bam files with bamCoverage from the deepTools suite v3.0.2 with the following parameters: -bs 20 --normalizeUsing BPM --skipNAs. Reads that overlap with the blacklisted regions from ENCODE project were excluded
Average bigWig files for the biological replicates were generated using the bigwigCompare program from the deepTools suite v3.0.2
A SAF file containing the coordinates of all transcripts from TSS to +300bp from the ensembl genes 93 annotation was generated using in-house scripts
Using the SAF file from the previous step, reads that overlap with TSS were counted using featureCounts from the Rsubread package v1.22.3 in a R 3.3.3 environment
The read count table was analyzed with edgeR v3.12.1 in a R 3.3.3 environment and CPM measurements were generated. After calculating normalization factors and estimating dispersion, m6Am replicates were compared to their respective inputs to find statistically enriched genes (i.e. m6Am peaks) with a FDR < 1e-3. Finally, enriched genes in control cells were compared to KO and only genes that showed a significantly enrichement over KO cells (FDR < 1e-3) were considered to be true m6Am-enriched genes
Genome_build: hg38, ensebml genes 93 annotation
Supplementary_files_format_and_content: bigwig files depicting genome-wide normalized read coverage, tab-delimited txt with log2 CPM information (TSS+300bp) as calculated by edgeR

source_name: MEL624 KO cells, Ab6

extract_protocol:
Total RNA was extracted from ~20 million cells with Trizol, following manufacturer instructions. 200ug of total RNA were subjected to two rounds of mRNA purification using the magnetic mRNA isolation kit from NEB (#S1550S)
Illumina sequencing libraries were prepared with the NEBNext Ultra II Directional Library Prep Kit for Illumina from NEB (#E7760), following manufacture's instructions


title: MEL624 KO cells, Ab4 [MEL624-m6Am-KO-Ab4]

source_name: MEL624 KO cells, Ab4


title: MEL624 KO cells, Ab5 [MEL624-m6Am-KO-Ab5]

source_name: MEL624 KO cells, Ab5


title: MEL624 KO cells, Ab3 [MEL624-m6Am-KO-Ab3]

source_name: MEL624 KO cells, Ab3


title: MEL624 KO cells, Ab7 [MEL624-m6Am-KO-Ab7]

source_name: MEL624 KO cells, Ab7


title: MEL624 KO cells, Ab1 [MEL624-m6Am-KO-Ab1]

source_name: MEL624 KO cells, Ab1


title: MEL624 KO cells, Ab8 [MEL624-m6Am-KO-Ab8]

source_name: MEL624 KO cells, Ab8


title: MEL624 KO cells, Ab2 [MEL624-m6Am-KO-Ab2]

source_name: MEL624 KO cells, Ab2


title: MEL624 control cells, Ab8 [MEL624-m6Am-Cont-Ab8]

source_name: MEL624 control cells, Ab8


title: MEL624 KO cells [MEL624-Input-KO-RNA]

source_name: MEL624 KO cells, input


title: MEL624 control cells, Ab6 [MEL624-m6Am-Cont-Ab6]

source_name: MEL624 control cells, Ab6


title: MEL624 control cells, Ab7 [MEL624-m6Am-Cont-Ab7]

source_name: MEL624 control cells, Ab7


title: MEL624 control cells, Ab5 [MEL624-m6Am-Cont-Ab5]

source_name: MEL624 control cells, Ab5


title: MEL624 control cells, Ab3 [MEL624-m6Am-Cont-Ab3]

source_name: MEL624 control cells, Ab3


title: MEL624 control cells, Ab2 [MEL624-m6Am-Cont-Ab2]

source_name: MEL624 control cells, Ab2


title: MEL624 control cells, Ab1 [MEL624-m6Am-Cont-Ab1]

source_name: MEL624 control cells, Ab1


title: MEL624 control cells, Ab4 [MEL624-m6Am-Cont-Ab4]

source_name: MEL624 control cells, Ab4


title: PD04_fibroblast

source_name: fibroblast


title: MEL624 control cells [MEL624-Input-Cont-RNA]

source_name: MEL624 control cells, input


title: MEL624 PCIF1 KO, replicate B [MEL624-m6Am-KO-B]

description:
processed data file:
GEO-hg38-MEL624-m6Am_TSS-CPM_log2.txt
hg38-MEL624-m6Am-KO-avg.bw

source_name: MEL624 PCIF1 KO


title: MEL624 PCIF1 KO, replicate C [MEL624-Input-KO-C]

description:
processed data file:
GEO-hg38-MEL624-m6Am_TSS-CPM_log2.txt
hg38-MEL624-Input-KO-avg.bw


title: MEL624 PCIF1 KO, replicate B [MEL624-Input-KO-B]


title: MEL624 control cells, replicate C [MEL624-m6Am-Cont-C]

description:
processed data file:
GEO-hg38-MEL624-m6Am_TSS-CPM_log2.txt
hg38-MEL624-m6Am-Cont-avg.bw

source_name: MEL624 control cells


title: MEL624 PCIF1 KO, replicate A [MEL624-Input-KO-A]


title: MEL624 control cells, replicate C [MEL624-Input-Cont-C]

description:
processed data file:
GEO-hg38-MEL624-m6Am_TSS-CPM_log2.txt
hg38-MEL624-Input-Cont-avg.bw


title: MEL624 control cells, replicate B [MEL624-m6Am-Cont-B]


title: MEL624 control cells, replicate B [MEL624-Input-Cont-B]


title: MEL624 control cells, replicate A [MEL624-m6Am-Cont-A]


title: 2018-02-15-Nikita-Sharma-09-OGTi-2_S2_L002

city: Miami

first: Nikita

middle: Satish

last: Sharma

state: FL

address: 1550 NW 10th Avenue PAP 134

department: Surgery

institute: University of Miami

data_processing:
O-GlcNAc transferase or OGT is responsible for modification of a number of critical pathways that actively affect oncogenic signaling in cancer. To study the major pathways that are downregulated upon inhibition OGT, we performed a RNA-seq analysis on OGTi cells. Raw sequence data was processed through PartekFlow RNAseq pipeline (Partek Inc., St. Louis, MO) as follows- A pre-alignment QA/QC was performed and bases with Q>30 were retained for analysis. Bowtie2 was used to filter out non-human DNA, mtDNA and rDNA from the samples and STAR 2.5.3 aligner was used to map the high-quality reads to Hg19 human genome assembly. Aligned reads were quantified for differential abundance among samples using (a) Partek E/M annotation model and (b) Cufflinks algorithm using the Hg19- Ensemble transcripts release 75. Out of 13,401 identified transcripts, 43 were found to be significantly different among the two study groups. .
12 barcoded libraries were sequenced across 4 lanes.
3. 864.33 M pass filter paired-end reads (432.17 M clusters) were generated.
4. 44.8 M paired-end reads (22.4 M clusters) were unindexed.
Genome_build: hg19
Supplementary_files_format_and_content: Total Gene list

source_name: Pancreatic Cancer cells

growth_protocol: S2VP10 Pancreatic Caner cells were cultured in RPMI 1640 with 10% FBS and 1% Penecillin

extract_protocol:
RNA was extracted using the Trizol metod
Libraries were prepared using Illumina’s Truseq Stranded Total-RNA library prep kit and sequenced on a 75 bp pair-end run using the NextSeq 500 High Output Kit 150-cycle; 400 M flow cell)

treatment_protocol: Transdected cells were treatedd with 0.5Microgm/ml of puromycin and then single sorted via flow and grown into colonies

value: OGT Knockout cells


title: 2018-02-15-Nikita-Sharma-09-OGTi-2_S2_L003


title: 2018-02-15-Nikita-Sharma-09-OGTi-2_S2_L001


title: MEL624 PCIF1 KO, replicate C [MEL624-m6Am-KO-C]


title: MEL624 PCIF1 KO, replicate A [MEL624-m6Am-KO-A]


title: carotid-atherosclerotic-plaque-rep4

source_name: carotid-atherosclerotic-plaque

value: carotid-atherosclerotic-plaque

value: Male


title: 2018-02-15-Nikita-Sharma-07-OGTi-1_S10_L001


title: 2018-02-15-Nikita-Sharma-08-SC-2_S8_L002

value: Scrambled Control


title: 2018-02-15-Nikita-Sharma-11-OGTi-3_S1_L003


title: 2018-02-15-Nikita-Sharma-10-SC-3_S6_L002


title: 2018-02-15-Nikita-Sharma-08-SC-2_S8_L004


title: 2018-02-15-Nikita-Sharma-10-SC-3_S6_L003


title: 2018-02-15-Nikita-Sharma-07-OGTi-1_S10_L003


title: 2018-02-15-Nikita-Sharma-11-OGTi-3_S1_L001


title: 2018-02-15-Nikita-Sharma-11-OGTi-3_S1_L002


title: 2018-02-15-Nikita-Sharma-10-SC-3_S6_L004


title: 2018-02-15-Nikita-Sharma-11-OGTi-3_S1_L004


title: 2018-02-15-Nikita-Sharma-07-OGTi-1_S10_L004


title: 2018-02-15-Nikita-Sharma-08-SC-2_S8_L003


title: 2018-02-15-Nikita-Sharma-07-OGTi-1_S10_L002


title: 2018-02-15-Nikita-Sharma-08-SC-2_S8_L001


title: 2018-02-15-Nikita-Sharma-10-SC-3_S6_L001


title: 2018-02-15-Nikita-Sharma-06-SC-1_S11_L001


title: MEL624 control cells, replicate A [MEL624-Input-Cont-A]


title: 2018-02-15-Nikita-Sharma-06-SC-1_S11_L002


title: 2018-02-15-Nikita-Sharma-06-SC-1_S11_L003


title: 2018-02-15-Nikita-Sharma-09-OGTi-2_S2_L004


title: 8-inp1-ICI_S4

city: Oslo

first: Siv

last: Gilfillan

address: Gaustadaleen 21

department: Norwegian Center for Molecular Medicine

country: Norway

institute: University of Oslo

description: Mice treated with ICI, Input control, ie no IP

data_processing:
Reads were mapped to the human reference genome using bowtie version 1.1.2
Filtering of alignment files to identify uniquely mapping, non-duplicate reads, was performed using samtools version 1.3.1
Peak calling was performed by HOMER 4.7.2 and MACS2 (version  2.1.1.20160309), then the peaks overlapping from these two approches (bedtools v2.25.0) were used
Genome_build: hg19
Supplementary_files_format_and_content: txt file: annotated peak files from HOMER (ie peaks overlapping from HOMER and macs2)
Supplementary_files_format_and_content: excel file: from annotated peak files from HOMER (ie peaks overlapping from HOMER and macs2), with focus on distribution of peaks between Genebody, Intergenic and Promoter regions. The README file on the series record provides a description of the data on each tab.

extract_protocol:
Tumors were frozen in liquid nitrogen. For ChIP the detailed protocol from Scmidt D. et al (Methods 2009) were followed, ie samples were pulverised and x-linked in PBS with 0,5% folmaldehyde for 10 minutes, then proceeded with Lysis buffers.
Library construction: ThruPLEX (Rubicon Genomics, Ann Arbor, MI, USA) supplied by Diagenode. The manufacturer’s instructions were followed.

value: human breast cancer cells from PDX mice

tag: replicate number

value: first replicate

value: none (input)


title: 7-inpC_S3

description: Mice treated withNaCl only, Input control, ie no IP


title: 5-H-h-ICI_S1

description: Mice treated with heregulin Herceptin and ICI

value: FoxA1 rabbit ab23738 (lot GR292351-2)


title: 4-hereg-ICI_S8

description: Mice treated with heregulin and ICI

source_name: Mice treated with heregulin and ICI


title: 3-heregulin_S7

description: Mice treated with heregulin

source_name: Mice treated with heregulin


title: 2-Hercep-ICI_S6

description: Mice treated with Herceptin and ICI

source_name: Mice treated with Herceptin and ICI


title: 1-ICI_S5

description: Mice treated with ICI

source_name: Mice treated with ICI


title: 2018-02-15-Nikita-Sharma-06-SC-1_S11_L004


title: 7-mice-breast_S9

description: Only mice breast tissue

source_name: Only mice breast tissue

value: second replicate


title: 1-ICI_S1

description: Mice treated with ICI


title: 9-inp-ICI_S2

source_name: Mice treated with ICI, Input control, ie no IP


title: 10-inp-mice-breast_S4

description: Only mice breast tissue, Input control, ie no IP


title: 8-inp-C_S10

source_name: Mice treated with NaCl only, Input control, ie no IP


title: Mixture2_NIH3T3_bulk

description:
bulk RNA-Seq
full-length
NIH3T3_cortex_TPM_bulk.tsv

source_name: Mouse NIH3T3 cell line

value: TruSeq


title: Cortex2_bulk

source_name: Cortex

value: One month

tag: strain


title: 3-heregulin_S5

description: Mice treated with heregulin


title: 5-heregulin-Herceptin-ICI_S7

source_name: Mice treated with heregulin Herceptin and ICI


title: Cortex1_bulk


title: 4-heregulin-ICI_S6

description: Mice treated with heregulin and ICI


title: 6-Control-NaCl_S8

description: Mice treated with NaCl only

source_name: Mice treated with NaCl only


title: Mixture1_NIH3T3_bulk


title: 6-C_S2

description: Mice treated with NaCl only


title: Brown adipose tissue uORF-TAA rep 1

city: San Francisco

first: Phillip

middle: Anthony

last: Dumesic

state: CA

address: 513 Parnassus Ave, HSW1119

department: Diabetes Center

institute: University of California, San Francisco

data_processing:
Sequenced reads were aligned to the UCSC mm9 reference genome assembly and gene counts were quantified using STAR (v2.5.1b).
Differential gene expression testing was performed by DESeq2 (v1.10.1) and resulting fold change values were used as a pre-ranked gene list for gene set enrichment analysis.
For DESeq analysis of quadriceps, data are expressed as (uORF-TAA/WT).  For DESeq analysis of BAT, data are expressed as (WT/uORF-TAA).
Genome_build: mm9

source_name: Brown adipose tissue

growth_protocol: Mice were housed at room temperature

extract_protocol:
Muscle or brown adipose tissue were removed, flash frozen on liquid nitrogen, and total RNA was harvested using Trizol reagent and RNeasy column (QIAGEN).
Libraries were prepared using Kapa stranded mRNA Hyper Prep sample preparation kits from 500 ng of total RNA.  The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit.  Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 ith single-end 75bp reads by the DFCI Molecular Biology Core Facility

value: male

value: 10-week old

value: Brown adipose tissue

tag: genotype

value: uORF-TAA homozygous


title: Brown adipose tissue uORF-TAA rep 4


title: Brown adipose tissue Wild-type rep 2

value: Wild-type


title: Quadriceps muscle uORF-TAA rep 4

source_name: Quadriceps muscle

value: Quadriceps muscle


title: Brown adipose tissue Wild-type rep 1


title: Quadriceps muscle uORF-TAA rep 3


title: Brown adipose tissue uORF-TAA rep 2


title: Quadriceps muscle uORF-TAA rep 1


title: Brown adipose tissue uORF-TAA rep 3


title: Quadriceps muscle Wild-type rep 4


title: 2-ICI-Herceptin_S3

description: Mice treated with Herceptin and ICI


title: Quadriceps muscle uORF-TAA rep 2


title: Quadriceps muscle Wild-type rep 1


title: Quadriceps muscle Wild-type rep 2


title: Brown adipose tissue Wild-type rep 3


title: Brown adipose tissue Wild-type rep 4


title: E11.5 ventricle _Nkx Cre +/-; wt (10R-2)

city: Indianapolis

first: Anthony

last: Firulli

state: IN

address: 1044 W Walnut R4 351

department: Pediatrics - Wells Center

institute: Indiana University School of Medicine

data_processing:
Sequence reads were aligned to mouse reference genome mm10 with STAR-2.4.2a.
featureCounts (subread-1.5.0) was used to quantify gene expression (parameters applied: "“-s 2 –Q 10")
Differential expression analysis was performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited excel file includes raw counts, log2 fold change values, p-values and FDR for all samples

source_name: E11.5 ventricle

growth_protocol: Pregnant Dams where sacrifced on E11.5 Venrticles were isolated, immersed in RNA-later and processed

extract_protocol:
RNA was isolated from tissues emersed in RNA-later using and RNA was isolated by CoFactor Genomics
Library was constructed by Co Factor Genomics

treatment_protocol: No treatments were employed

value: Ventricle

value: Mixed background

value: Nkx Cre +/-; wt


title: E11.5 ventricle _Nkx Cre +/-; wt (10R-6)


title: E11.5 ventricle _Nkx Cre +/-; H1flox/flox (NT-1)

value: Nkx Cre +/-; H1flox/flox


title: E11.5 ventricle _Nkx Cre +/-; wt (83-1)


title: DRG_WT_Oxalipl_1

city: St Lucia

first: Alexander

last: Mueller

state: Queensland

address: 306 Carmody Rd

department: Institute for Molecular Bioscience

country: Australia

institute: University of Queensland

data_processing:
Alignment: STAR aligner (version star/2.3.0e) and samtools
Mapping: Mapped to Ensembl Mus musculus mm10 genome (version GRCm38)
Counts: Generated using HTSeq_count in the HTSeq package
Genome_build: mm10
Supplementary_files_format_and_content: .txt files, tab-delimited.

source_name: Dorsal root ganglia from levels L3, L4 and L5

extract_protocol:
Whole dorsal root ganglia (DRG) from levels L3, L4 and L5 (ipsilateral to the treated paws) were removed and immediately put into RNALater and cut into pieces in RNA later. DRGs from four animals were collected and pooled to obtain one biological replicate. RNA was extracted using the Rneasy Mini kit (Qiagen).
RNA libraries were prepared using TruSeq stranded total RNA library preparation.

tag: gender

value: 8-10 weeks

value: oxaliplatin 40µg cumulative intraplantar


title: DRG_WT_Oxalipl_3

value: Dorsal root ganglia from levels L3, L4 and L5


title: DRG_WT_Oxalipl_2


title: DRG_WT_veh_Ox_Cis_3

value: vehicle


title: DRG_WT_Vinc_3

value: female

value: vincristine 40µg cumulative intraplantar


title: DRG_WT_veh_vinc_2


title: DRG_WT_veh_Ox_Cis_1


title: DRG_WT_veh_vinc_3


title: Quadriceps muscle Wild-type rep 3


title: DRG_WT_veh_vinc_1


title: P60-Yap-CKO_rep3

city: Saclay

first: Jerome

middle: Eric

last: Roger

state: Please select

address: 151 Route de la Rotonde, Campus CEA Saclay - Bat 151

department: CERTO

institute: CNRS-Universite Paris Sud

data_processing:
Paired-end sequencing of 40 bases length was performed on NextSeq 500 (Illumina)
Pass-filtered reads were mapped using HISAT2 2.1.0 and aligned to Ensembl mouse reference genome GRCm38.84.
Count table of the gene features was obtained using FeatureCounts
Normalization, differential expression analysis and FPKM (fragments per kilobase of exon per million fragments mapped) values were computed using EdgeR
Genome_build: Ensembl GRCm38.84
Supplementary_files_format_and_content: tab-delimited text files include counts from FeatureCounts and List of Differentially expressed genes with FPKM values for each Sample, fold change, p-value and adjusted p-value

source_name: Yap-CKO mouse retina at age postnatal day 60

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Nucleospin RNA Plus kit, which includes DNase treatment. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for directional next-generation sequencing using a modified TruSeq RNA Sample Preparation Kit protocol as described. The protocol utilizes the labeling of the second strand of cDNA with uracil, which allows the degradation of this strand prior to sequencing.

tag: strain background

value: Yap CKO ; Rax-CreERT2

value: post natal day 60

value: Retina


title: P60-Yap-CKO_rep2


title: DRG_WT_Cispl_2

value: male

value: cisplatin 40µg cumulative intraplantar


title: P60-Yap-CKO_rep1


title: E11.5 ventricle _Nkx Cre wt; H1flox/flox (310-4)

value: Nkx Cre wt; H1flox/flox


title: E11.5 ventricle _Nkx Cre wt; H1flox/flox (NT-7)


title: DRG_WT_Cispl_3


title: E11.5 ventricle _Nkx Cre +/-; H1flox/flox (NT-6 )


title: DRG_WT_Cispl_1


title: P60-Control_rep2

source_name: Control mouse retina at age postnatal day 60

value: Yap CKO


title: P60-Control_rep1


title: S192

city: Charlestown

first: Kamil

last: Slowikowski

state: Massachusetts

address: Mailstop CNY 149-8, 149 13th Street

institute: Massachusetts General Brigham

data_processing:
kallisto version 0.43.1
Genome_build: Ensembl release 89
Supplementary_files_format_and_content: tab-separated files, estimated counts, transcripts per million (TPM)

source_name: synovium

growth_protocol: Fibroblasts were transfected with an siRNA against CUX1, LIFR, STAT3, STAT4 and ELF3 and plated on day 1 at 50,000 cells per well in 24-well plates in 10% FBS containing media. Cells were serum-starved on day 2 by changing to 1% FBS-containing media.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Micro Kit.
SMART-seq2

treatment_protocol: Cells were stimulated with TNF (0.1 ng/mL) or TNF (0.1 ng/mL) + IL-17A (1 ng/mL) on day 3 for 0, 1 ,6, 16 hours.

tag: donor

tag: sirna

tag: time

tag: stimulation

tag: plate


title: S191

value: TNF (1)


title: S189


title: DRG_WT_Vinc_1

tag: tissue

tag: treatment


title: S190


title: S185


title: DRG_WT_veh_Ox_Cis_2

tag: age


title: S184


title: DRG_WT_Vinc_2


title: S187


title: S183


title: S182


title: S180


title: S179


title: S181


title: S176


title: S177


title: S175


title: S173


title: S170


title: S171


title: S174


title: S168

value: LIFR


title: S169


title: S167


title: S172


title: S166


title: S188


title: S164


title: S163


title: S186


title: S161


title: S159


title: S160


title: S162


title: S158


title: S178


title: S152

value: Ctrl


title: S156


title: S155


title: S153


title: S149


title: S151


title: S150


title: S157


title: S148


title: S143


title: S147


title: S145


title: S142


title: S144


title: S141


title: S165


title: S140


title: S139


title: S136


title: S135


title: S134


title: S137


title: S133


title: S154


title: S131


title: S130


title: S126


title: S129


title: S127


title: S122


title: S124


title: S123


title: P60-Control_rep3

tag: genotype/variation


title: S146


title: S121


title: S119


title: S138


title: S117


title: S115


title: S116


title: S114


title: S120


title: S118


title: S112


title: S132


title: S113


title: S108


title: S111


title: S110


title: S109


title: S106


title: S107


title: S128


title: S104


title: S101


title: S102


title: S103


title: S100


title: S125


title: S96


title: S105


title: S99


title: S94


title: S92


title: S95


title: S93


title: S89


title: S90


title: S91


title: S88


title: S87


title: S86


title: S98


title: S83


title: S81


title: S80


title: S85


title: S84


title: S82


title: S79


title: S77


title: S76


title: S97


title: S74


title: S75


title: S73


title: S70


title: S71


title: S69


title: S72


title: S68


title: S65


title: S62


title: S61


title: S60


title: S66


title: S63


title: S64


title: S58


title: S56


title: S78


title: S52


title: S51


title: S53


title: S54


title: S57


title: S67


title: S49


title: S50


title: S48


title: S47


title: S46


title: S45


title: S43


title: S44


title: S40


title: S42


title: S41


title: S39


title: S59


title: S35


title: S36


title: S37


title: S38


title: S33


title: S32


title: S55


title: S34


title: S31


title: S30


title: S24


title: S26


title: S27


title: S23


title: S22


title: S21


title: S25


title: S28


title: S20


title: S18


title: S19


title: S29


title: S17


title: S15


title: S14


title: S13


title: S12


title: S16


title: S10


title: S9


title: S7


title: S8


title: S5


title: S6


title: S3


title: S4


title: S2


title: S11


title: S1


title: S99 time-course

growth_protocol: Fibroblasts were plated on day 1 at 50,000 cells per well in 24-well plates in 10% FBS containing media. Cells were serum-starved on day 2 by changing to 1% FBS-containing media.

treatment_protocol: Cells were stimulated with TNF (1 ng/mL) or TNF (1 ng/mL) + IL-17A (1 ng/mL) on day 3 for 0, 2, 4 ,6, 8, 10, 12, 18, 24 hours.

tag: well

tag: disease

value: RA


title: S95 time-course

value: OA


title: S96 time-course


title: S98 time-course


title: S97 time-course


title: S91 time-course


title: S90 time-course


title: S93 time-course


title: S92 time-course


title: S87 time-course


title: S84 time-course


title: S89 time-course


title: S88 time-course


title: S83 time-course


title: S9 time-course


title: S82 time-course


title: S81 time-course


title: S80 time-course


title: S76 time-course


title: S75 time-course


title: S73 time-course


title: S8 time-course


title: S79 time-course


title: S77 time-course


title: S74 time-course


title: S72 time-course


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title: IgG repeat 2

city: Rochester

first: Zhenkun

last: Lou

state: MN

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
RIP seq was performed using an Illumina HiSeq 2000 sequencer at the Genomic Core facility of the Mayo Clinic, Rochester, MN. Paired-end sequencing libraries were prepared using the TruSeq Stranded Total Sample Preparation kit (Illumina) by the Mayo Clinic sequencing core facilities followed by quality control, cluster generation and sequencing on the Illumina HiSeq 2000 platform. Sequence alignment was performed using Tophat 2.0.14(Kim et al., 2013)against the hg19 human reference genome. Peak calling and annotation were performed using HOMER 4.8.3 (Heinz et al., 2010).
Supplementary_files_format_and_content: processed RIP Data.xls

extract_protocol:
Crosslinked RIP was performed as previously described with minor modification(Gilbert and Svejstrup, 2006). Briefly, cells were first fixed with 0.3% formaldehyde for 10min followed by stopping crosslinking reaction with 0.2M glycine. Then the cells were lysed with FA lysis buffer (50 mM This.HCl, pH=7.5, 140 mM NaCl, 1 mM EDTA, 1% (v/v) Triton X-100, 0.1% (w/v) sodium deoxycholate) followed by sonication (10% AMP, 5s sonication, 5s pause, 10 cycles). The supernatant of the cell lysate was then mixed with antibody and protein A/G magnetic beads followed by incubation overnight at 4℃. Then the beads were washed two times of FA lysis buffer, FA500 buffer (50 mM This.HCl, pH=7.5, 500 mM NaCl, 1 mM EDTA, 1% (v/v) Triton X-100, 0.1% (w/v) sodium deoxycholate), LiCl buffer (10 mM Tris HCl, pH 8, 250 mM LiCl, 0.5% (v/v) NP-40, 0.1% (w/v) sodium deoxycholate, 1 mM EDTA), and TE/100 mM NaCl buffer (10 mM Tris HCl, pH 8, 1 mM EDTA, 100 mM NaCl). The RNA was then eluted by elution buffer (100 mM Tris⋅Cl, pH 8, 10 mM EDTA, 1% (w/v) SDS) and extracted using Trizol (invitrogen).
Paired-end sequencing libraries were prepared using the TruSeq Stranded Total Sample Preparation kit (Illumina) by the Mayo Clinic sequencing core facilities

tag: cell line

tag: antibody

value: IgG


title: IgG repeat 1


title: IgG repeat 3


title: PD-L1 repeat 3


title: siMEF2C 3

city: Poznan

first: Michał

last: Szcześniak

address: Uniwersytetu Poznanskiego 6

department: Institute of Human Biology and Evolution

country: Poland

institute: Adam Mickiewicz University

description: small RNA pool

data_processing:
Adapter clipping: fastx_clipper from FASTX-Toolkit (0.0.13.2) was used; the clipped adapter was TGGAATTCTCGGG; only reads with adapters and min. 17 nt long were kept
Quality filtering: fastq_quality_filter from FASTX-Toolkit (0.0.13.2) was used with -Q33, -p 95 and -q 20 parameters
Conversion to fasta:  fastq_to_fasta from FASTX-Toolkit (0.0.13.2) was used
Read collapsing: read redundance was removed and reads were counted with fastx_collapser from FASTX-Toolkit (0.0.13.2)
Genome_build: NA
Supplementary_files_format_and_content: Fasta files with consecutive Ids and raw read count in the header

source_name: Human Skeletal Myoblats

growth_protocol: Primary skeletal myoblasts and HSkM cells were grown in HAM F-10 medium (Lonza) supplemented with 20% FBS (BioWest), 2 mM l-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin (Invitrogen) at 37°C, 5% CO2. Upon shifting to a 2% horse serum-containing medium, HSkM myoblasts were induced to differentiate and fuse.

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen) from cells according to the manufacturer's protocol.
Total RNA was purified by 12% PAGE, and a fraction of small RNAs of 10-30 nt in length was excised. Small RNA libraries were generated using a TruSeq Small RNA kit (Illumina) according to the manufacturer’s instructions. Number of biological replicas per group: 3. To equalize the read depth, the libraries were multiplexed with four libraries sequenced per lane of Illumina HiSeq 2000.

treatment_protocol: To knock down MEF2C (MEF2C KD), the HSkM cells were transfected using Lipofectamine 2000 (Invitrogen) according to the manufacturer's protocols; 50 nM siRNA was used.

tag: differentiation

value: day 4

value: MEF2C knock-down

value: HSkM


title: PD-L1 repeat 1


title: siMEF2C 1

description: small RNA pool


title: siMEF2C 2

description: small RNA pool


title: siCTRL 3

description: small RNA pool

value: control


title: siCTRL 2

description: small RNA pool


title: hNSC_WWOX_del

city: Lodz

first: Andrzej

middle: K.

last: Bednarek

address: Zeligowskiego St. 7/9

department: Department of Molecular Carcinogenesis

institute: Medical University in Lodz

data_processing:
CAGE libraries were sequenced using Illumina HiSeq 2000 platform. Read length 100 bp. Base calling and FASTQ files were generated with bcl2fastq (1.8.4).
Barcodes used for individual samples are: hNSC – CTTCAGCAG; hNSC_WWOX_del – AGACAGCAG; neurons – GATCAGCAG; neurons_WWOX_del – ACACAGCAG
IMPORTANT NOTICE: sample specific demultiplexed FASTQ files are NOT the files used in our workflow.
Individual transcription start site extraction and genome mapping was performed using MOIRAI software (Hasegawa, et al., PMID:24884663) and human genome build hg19. Genome mapped reads were exported to BAM files, than converted to BED format using bedtools software and remapped to  human genome build hg38 using liftOver software.
Identification of transcription start sites was performed with CAGEr (Haberle, et al., PMID:25653163). Briefly, tag counts were normalized to one million tags using simple TPM and transcription start sites (TSS) were clustered using paraclu. Finally, all genome mapped TSS were cross-identified using FANTOM5 human hg38 true-TSS library (http://fantom.gsc.riken.jp/5/datafiles/reprocessed/). All above done using CAGEr.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Spreadsheet file of hg38 genome coordinates of identified TSS including TPM normalized signals of all samples and cross-identified according to FANTOM5 project: TSScoordinates_TPMexpression_all_samples_F5mapped.txt;  Gene expression was counted as a summary of all TSS of a single gene. Spreadsheet file of gene expression of all samples: TPMexpression_all_genes_all_samples merged.txt

source_name: human neural stem cells

growth_protocol: The hNSC cells were grown in Geltrex coated vessels in KnockOut DMEM/F12 supplemented with Neural Supplement (Gibco), 20 ng/mL bFGF and EGF and antibiotic-antimycotic (Amphotericin B, Penicillin, Streptomycin). The cells were cultured in 37°C in a humidified atmosphere of 6% CO2. hNSC were spontaneously differentiated into neurons by withdrawal of bFGF and EGF from culture medium.

extract_protocol:
Total RNA was extracted with TRIzol reagent.
The libraries for sequencing were prepared according to Piero Carnici’s protocol [Takahashi, et al., PMID:22362160]. Briefly, polyadenylated and non-poliadenylated RNA was reverse transcribed into cDNA with usage of random prime containing EcoP15I sequence. Next step was biotinylation of the cap site and the 3’ends of hybridized RNAs. Non-hybridized ssRNAs were digested and 5’ complete cDNAs hybridized to biotin-tagged, cap-containing RNAs were separated on streptavidin coated magnetic beads. cDNA was released from RNA and a double stranded 5’ linker with a barcode and EcoP15I sequences was ligated. Subsequently, using the biotinylated 2nd SOL primer, a second strand cDNA was synthetized. The digestion with EcoP15I allowed to cleave 27 bp fragments inside the 5’ end of the cDNA. In the 3’ end of cDNA a 3’ linker with 3’ Ilumina primer sequence was ligated. Next, constructed CAGE tags were amplified and purified. The prepared libraries were sequenced on Illumina HiSeq System.

treatment_protocol: Lentiviral transduction with shRNA gene silencing system.

tag: differentiation stage

value: undifferentiated

tag: wwox expression

value: silenced

value: nervous


title: neurons

value: differentiated

value: wild type


title: hNSC


title: MEL624 PCIF1 KO2, replicate C [input RNA-seq]

description:
MEL624-KO2-RNAseq-C
processed data file:
GEO-hg38-MEL624-RNA_seq-log2_TPM.txt
hg38-MEL624-RNA_seq-KO2-avg.bw
hg38-MEL624-m6A-KO2-avg.bw

data_processing:
library strategy: m6A MeRIP-Seq
Reads were aligned against hg38 genome assembly with hisat 2.0.4 using the following parameters: --no-unal --rna-strandness R
sam files were sorted and converted to bam with samtools v1.7. Reads with QS < 10 were excluded
Normalized bigWig files were generated from bam files with bamCoverage from the deepTools suite v3.0.2 with the following parameters: -bs 20 --normalizeUsing BPM --skipNAs. Reads that overlap with the blacklisted regions from ENCODE project were excluded
Average bigWig files for the biological replicates were generated using the bigwigCompare program from the deepTools suite v3.0.2
Read counts for the RNAseq inputs were calculated with featureCounts from the Rsubread package v1.22.3 in a R 3.3.3 environment
The read count table was analyzed with edgeR v3.12.1 in a R 3.3.3 environment and log2 TPM measurements were generated. After calculating normalization factors and estimating dispersion, DEG genes between KOs and Control cells were calculated using glm modeling with a FDR < 1e-5. A final list of DEG shared between KO1 and KO2 was generated using in-house scripts
Genome_build: hg38, ensebml genes 93 annotation
Supplementary_files_format_and_content: bigwig files depicting average normalized read coverage, tab-delimited txt with log2 TPM information from RNAseq inputs as calculated by edgeR

source_name: MEL624 PCIF1 KO2

tag: cellosaurus cell line identifier

tag: cell type

value: Human melanoma cell line

value: PCIF1 KO

tag: rip antibody

value: none (input)


title: MEL624 PCIF1 KO2, replicate B [input RNA-seq]

description:
MEL624-KO2-RNAseq-B
processed data file:
GEO-hg38-MEL624-RNA_seq-log2_TPM.txt
hg38-MEL624-RNA_seq-KO2-avg.bw
hg38-MEL624-m6A-KO2-avg.bw


title: MEL624 PCIF1 KO2, replicate B [m6A MeRIP-Seq]

description:
MEL624-KO2-m6A-B
processed data file:
GEO-hg38-MEL624-RNA_seq-log2_TPM.txt
hg38-MEL624-RNA_seq-KO2-avg.bw
hg38-MEL624-m6A-KO2-avg.bw

value: m6A antibody


title: MEL624 PCIF1 KO2, replicate A [input RNA-seq]

description:
MEL624-KO2-RNAseq-A
processed data file:
GEO-hg38-MEL624-RNA_seq-log2_TPM.txt
hg38-MEL624-RNA_seq-KO2-avg.bw
hg38-MEL624-m6A-KO2-avg.bw


title: MEL624 PCIF1 KO2, replicate A [m6A MeRIP-Seq]

description:
MEL624-KO2-m6A-A
processed data file:
GEO-hg38-MEL624-RNA_seq-log2_TPM.txt
hg38-MEL624-RNA_seq-KO2-avg.bw
hg38-MEL624-m6A-KO2-avg.bw


title: MEL624 PCIF1 KO1, replicate C [input RNA-seq]

description:
MEL624-KO1-RNAseq-C
processed data file:
GEO-hg38-MEL624-RNA_seq-log2_TPM.txt
hg38-MEL624-RNA_seq-KO1-avg.bw
hg38-MEL624-m6A-KO1-avg.bw

source_name: MEL624 PCIF1 KO1


title: MEL624 PCIF1 KO1, replicate B [input RNA-seq]

description:
MEL624-KO1-RNAseq-B
processed data file:
GEO-hg38-MEL624-RNA_seq-log2_TPM.txt
hg38-MEL624-RNA_seq-KO1-avg.bw
hg38-MEL624-m6A-KO1-avg.bw


title: MEL624 PCIF1 KO1, replicate B [m6A MeRIP-Seq]

description:
MEL624-KO1-m6A-B
processed data file:
GEO-hg38-MEL624-RNA_seq-log2_TPM.txt
hg38-MEL624-RNA_seq-KO1-avg.bw
hg38-MEL624-m6A-KO1-avg.bw


title: MEL624 PCIF1 KO1, replicate A [m6A MeRIP-Seq]

description:
MEL624-KO1-m6A-A
processed data file:
GEO-hg38-MEL624-RNA_seq-log2_TPM.txt
hg38-MEL624-RNA_seq-KO1-avg.bw
hg38-MEL624-m6A-KO1-avg.bw


title: PD-L1 repeat 2


title: MEL624 control cells, replicate C [input RNA-seq]

description:
MEL624-Cont-RNAseq-C
processed data file:
GEO-hg38-MEL624-RNA_seq-log2_TPM.txt
hg38-MEL624-RNA_seq-Cont-avg.bw
hg38-MEL624-m6A-Cont-avg.bw

source_name: MEL624 control cells

value: Wild type + Random sgRNA


title: MEL624 control cells, replicate B [input RNA-seq]

description:
MEL624-Cont-RNAseq-B
processed data file:
GEO-hg38-MEL624-RNA_seq-log2_TPM.txt
hg38-MEL624-RNA_seq-Cont-avg.bw
hg38-MEL624-m6A-Cont-avg.bw


title: MEL624 control cells, replicate B [m6A MeRIP-Seq]

description:
MEL624-Cont-m6A-B
processed data file:
GEO-hg38-MEL624-RNA_seq-log2_TPM.txt
hg38-MEL624-RNA_seq-Cont-avg.bw
hg38-MEL624-m6A-Cont-avg.bw


title: MEL624 control cells, replicate A [input RNA-seq]

description:
MEL624-Cont-RNAseq-A
processed data file:
GEO-hg38-MEL624-RNA_seq-log2_TPM.txt
hg38-MEL624-RNA_seq-Cont-avg.bw
hg38-MEL624-m6A-Cont-avg.bw


title: MEL624 control cells, replicate C [m6A MeRIP-Seq]

description:
MEL624-Cont-m6A-C
processed data file:
GEO-hg38-MEL624-RNA_seq-log2_TPM.txt
hg38-MEL624-RNA_seq-Cont-avg.bw
hg38-MEL624-m6A-Cont-avg.bw


title: MEL624 PCIF1 KO1, replicate C [m6A MeRIP-Seq]

description:
MEL624-KO1-m6A-C
processed data file:
GEO-hg38-MEL624-RNA_seq-log2_TPM.txt
hg38-MEL624-RNA_seq-KO1-avg.bw
hg38-MEL624-m6A-KO1-avg.bw


title: neurons_WWOX_del


title: siCTRL 1

description: small RNA pool


title: D14 MODY1-1B

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

institute: IMCB, A*STAR

data_processing:
Sequenced reads were trimmed for adaptor sequence using Trimmomatic-0.33, and then mapped to hg19 whole genome using tophat-2.0.14
Raw counts were calculated using HtSeq-count
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks-2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample, raw htseq counts for each sample, edgeR output

extract_protocol:
RNA was harvested from cells using the PrepEase RNA Spin Kit (Affymetrix)
mRNA was first isolated with poly dT beads from 1-10µg of total RNA. RNA-seq libraries were prepared using the NEXTflex Rapid Directional RNA-SEQ Kit (dUTP-Based) v2 as per manufacturer's direction.

tag: genotype

value: HNF4A p.Ile271fs

tag: family identifier

tag: gender

value: female


title: MEL624 PCIF1 KO2, replicate C [m6A MeRIP-Seq]

description:
MEL624-KO2-m6A-C
processed data file:
GEO-hg38-MEL624-RNA_seq-log2_TPM.txt
hg38-MEL624-RNA_seq-KO2-avg.bw
hg38-MEL624-m6A-KO2-avg.bw


title: D14 MODY1-1A


title: D14 MODY1-1C


title: RKO cells treated by control siRNA

city: shanghai

first: Qianqian

last: Wang

address: yueyang road,number 320

country: China

institute: Chinese Academy of Sciences

data_processing:
Illumina GA Pipeline v1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
The stat of mapped reads was list in MappingStatistic_SICHERP.xls and MappingStatistic_SINC.xls
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Mortazavi, 2008.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM

source_name: Control RKO cells

extract_protocol:
RKO cells 72 hours after tranfected with siRNA were collected , and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: time

value: treated for 72 hours

tag: tissue

value: colon


title: RKO cells treated by siCHERP

source_name: siCHERP treated RKO cells

tag: treatment

value: siCHERP


title: D14 Control-7A

value: Wild type

value: male


title: D14 Control-7C


title: D14 Control-13B


title: D14 Control-13A


title: MEL624 PCIF1 KO1, replicate A [input RNA-seq]

description:
MEL624-KO1-RNAseq-A
processed data file:
GEO-hg38-MEL624-RNA_seq-log2_TPM.txt
hg38-MEL624-RNA_seq-KO1-avg.bw
hg38-MEL624-m6A-KO1-avg.bw

tag: genotype/variation


title: D14 Control-7B