title: 5DayWound_fibroblast_Act_rep1

status: Public on Apr 14 2020

city: Chicago

first: Mateusz

middle: S

last: Wietecha

address: 801 S Paulina St

department: Oral Biology

institute: University of Illinois Chicago

data_processing:
Sequence alignment to the Mus musculus reference genome (build GRCm38) and transcript expression quantification of the resulting high-quality reads was performed using the CLC Genomics Workbench (Qiagen). Quality control via CLC Genomics Workbench excluded one sample (rep2) from the Act_5DW group; all other samples generated 20-40 million reads, showed high (82.3-95.7%) mapping rates to the mouse reference genome, high (93.7-97.5%) mapping rates to genes and low (0.2-6.1%) rRNA mapping rates.
Numbers of RNA transcripts were determined on the gene level and normalized to reads per kilobase of transcript, per million mapped reads (RPKM). Principal component analysis (PCA) was performed to evaluate grouping of samples. Differential expression analysis was performed across all group comparisons using the edgeR exact test as implemented in the CLC Genomics Workbench (Qiagen), and differentially expressed genes (DEGs) were determined and compared.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited table format containing gene names (annotated by HGNC-approved gene symbol) and nomalized RPKM values for all samples.

source_name: Fibroblast

extract_protocol:
Total RNA was isolated using the RNeasy Micro Kit (Qiagen). RNA was analyzed via TapeStation (Agilent), and samples with RIN>6.8 were adjusted to 100 ng (back skin) or 200 ng (5-day wounds).
Extracted RNA samples were subjected to the RNA sequencing protocol via poly-A enrichment, True-Seq library preparation, and stranded 100bp sequencing on an Illumina HiSeq 2500 instrument. Quality control via CLC Genomics Workbench excluded one sample (rep2) from the Act_5DW group; all other samples generated 20-40 million reads, showed high (82.3-95.7%) mapping rates to the mouse reference genome, high (93.7-97.5%) mapping rates to genes and low (0.2-6.1%) rRNA mapping rates.

treatment_protocol: Back skin and 5-day wounds were harvested, minced with scissors, and digested with 0.25 mg/ml Liberase TL (Roche) in DMEM for 1 h at 37°C. Following digestion, the cell suspension was filtered through a 70  µm nylon strainer, centrifuged at 300g at 4°C for 10 min, and resuspended in FACS buffer. Back skin and 5-day excisional wound fibroblasts were enriched by FACS sorting of CD45-negative/CD140a-positive (CD45-CD140a+) cells. CD3, CD11b and F4/80 were used as additional negative markers. Dead cells were excluded by Sytox Green staining. Cells were sorted into cold empty Eppendorf tubes with FACS buffer containing RNAase inhibitor and centrifuged for total RNA extraction.

tag: strain

tag: cell type/source

value: FACS-sorted CD45-CD140a+ live cells

value: 5-day excisional wounds

value: 9-12 weeks


title: 5DayWound_fibroblast_Act_rep3

type: SRA

state: IL

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype

tag: age


title: 5DayWound_fibroblast_WT_rep2

value: Wt


title: HEK293T, ChIP Input - rep2

status: Public on Apr 30 2020

city: Los Angeles

first: Weiya

middle: Stephanie

last: Ni

state: California

address: 1450 Biggy Street

institute: University of Southern California

library_source: genomic

data_processing:
Sequencing results were aligned to hg19 using bwa
Peaks were called using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: peak files with quantitative data

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HEK293T cells were grown according to ATCC protocol

extract_protocol:
Chromatins were prepared using the protocol previously published (PMID: 29429977). Briefly, cells were crosslinked by 1%formedelhyde for 10 mins and lysised into nuclei. Nuclei were sonicated using BioRuptor to break into chromatin fragments.
Librarys were prepared using KAPA Hyper Prep Kit (Kapa #KK8505) according to provided protocol

tag: cell line

value: kidney cell line HEK293T

tag: factor

value: Input


title: HEK293T, ChIP Input - rep1


title: 5DayWound_fibroblast_WT_rep3


title: BackSkin_fibroblast_Act_rep1

value: Back skin


title: BackSkin_fibroblast_Act_rep3


title: 5DayWound_fibroblast_WT_rep1


title: BackSkin_fibroblast_Act_rep2


title: BackSkin_fibroblast_WT_rep3


title: BackSkin_fibroblast_WT_rep2


title: BackSkin_fibroblast_WT_rep1


title: 133C scRNAseq

status: Public on May 12 2020

city: New Haven

first: Naftali

last: Kaminski

state: CT

address: 300 Cedar Street

department: PCCSM

institute: Yale School of Medicine

data_processing:
Demultiplex and basecall to fastq with cellranger mkfastq
Trimming of Read 2 for TSO and poly(A) with cutadapt
filtering, alligning, and barcode collapsing with zUMIs 2.0 (STAR 2.6.0 for alignment)
Cells filtered with > 12% of transcriptome from intron-spanning reads; < 20% mitochondrial origin; at least 1000 unique genes
ensembl gene IDs translated to HGNC only when a 1:1 translation was feasible using the R package biomaRt with the "Oct 2018" ensembl archive
Genome_build: GRCh38 Release 91
Supplementary_files_format_and_content:
RawCounts_sparse.mtx.gz: gunzipped, gene expression UMI count matrix of all intron and exon spanning transcripts are in sparse matrix format, generated with R package 'Matrix' and writeMM() function; 312,928 cells x 45,947 genes
AllCells.GeneIDs.txt: tab delimited table of corresponding gene identities for the count matrix. 2 columns: Ensembl_GeneID is the original gene ensembl IDs, HGNC_EnsemblAlt_GeneID is the mixed HGNC/ensemblIDs used for analysis in the manuscript.
AllCells.cellBarcodes.txt: tab delimited list of corresponding cell barcode identities for the count matrix
Cell_MetaData.txt: MetaData to describe all 312,928 cells; including subject and library source, disease status and cell-type identities we assigned in our study
Sample-Associated .rds files: R object files specific to each sequenced library, representing gene expression count data per cell, formatted with ensembl gene IDs. These are the primary data outputs by the processing program zUMIs 2.0. Each one is a nested list of intron spanning, exon spanning and combined intron and exon spanning UMI and read counts for the top 8,000-10,000 cell barcodes in each library ranked by total number of reads

source_name: Whole Lung Dissociate

extract_protocol:
Thawed Cells were rinsed with 10% FBS; passed through 40 uM strainer
10X Genomics 3 prime v2

treatment_protocol: Enzymatic and Mechanical Digestion; Cryopreservation in 10% DMSO

value: Whole Lung Dissociate

tag: disease

value: Control

tag: Sex

value: F


title: Q38_2_RNA-seq

status: Public on Apr 10 2020

city: Omaha

first: Pranita

last: Atri

state: NE

address: S 42nd and Emile St

department: Biochemistry

institute: UNIVERSITY OF NEBRASKA MEDICAL CENTER

data_processing:
Illumina sequencing
FastQ raw reads alligned to Hg38 using bowtie bases TopHat
Genome_build: Hg38
Supplementary_files_format_and_content: Counts

source_name: Brain

extract_protocol:
RecoverAll total RNA extraction
Illumina TruSeq (as per manufacturer intructions)

value: Brain

tag: disease state

value: Medulloblastoma

tag: subgroup

value: Group 4

value: deceased

tag: histology

value: CLASSIC

tag: metastasis

value: NO

tag: recurrence

value: YES


title: Q38_3_RNA-seq


title: Q37_1_RNA-seq

value: SHH

value: alive

value: DESMOPLASTIC


title: Q8_2_RNA-seq

value: M


title: Q37_4_RNA-seq


title: Q8_3_RNA-seq


title: Q8_4_RNA-seq


title: Q49_4_RNA-seq

value: UNKNOWN


title: Q37_3_RNA-seq


title: Q49_3_RNA-seq


title: Q49_1_RNA-seq


title: Q38_4_RNA-seq


title: Q37_2_RNA-seq


title: Q8_1_RNA-seq


title: Q7_4_RNA-seq


title: Q7_3_RNA-seq


title: Q7_2_RNA-seq


title: Q7_1_RNA-seq


title: Q6_4_RNA-seq

value: LARGE CELL/ANAPLASTIC


title: Q6_3_RNA-seq


title: Q49_2_RNA-seq


title: Q5_3_RNA-seq


title: Q5_4_RNA-seq


title: Q6_2_RNA-seq


title: Q5_2_RNA-seq


title: Q5_1_RNA-seq


title: Q4_4_RNA-seq


title: Q38_1_RNA-seq


title: Q6_1_RNA-seq


title: Q4_3_RNA-seq


title: Q4_2_RNA-seq


title: Q4_1_RNA-seq


title: Q34_3_RNA-seq

value: Group 3


title: Q34_4_RNA-seq


title: Q34_2_RNA-seq


title: Q30_3_RNA-seq


title: Q33_1_RNA-seq


title: Q33_2_RNA-seq


title: Q32_2_RNA-seq


title: Q31_4_RNA-seq


title: Q31_3_RNA-seq


title: Q33_3_RNA-seq


title: Q32_1_RNA-seq


title: Q31_1_RNA-seq


title: Q30_1_RNA-seq


title: Q3_3_RNA-seq


title: Q3_2_RNA-seq


title: Q34_1_RNA-seq


title: Q30_4_RNA-seq


title: Q30_2_RNA-seq


title: Q33_4_RNA-seq


title: Q32_4_RNA-seq


title: Q31_2_RNA-seq


title: Q3_1_RNA-seq


title: Q29_2_RNA-seq


title: Q29_3_RNA-seq


title: Q29_4_RNA-seq


title: Q29_1_RNA-seq


title: Q32_3_RNA-seq


title: Q27_4_RNA-seq


title: Q27_3_RNA-seq


title: Q27_1_RNA-seq


title: Q27_2_RNA-seq


title: Q26_4_RNA-seq


title: Q3_4_RNA-seq


title: Q26_2_RNA-seq


title: Q24_2_RNA-seq


title: Q25_2_RNA-seq


title: Q23_1_RNA-seq


title: Q23_3_RNA-seq


title: Q26_1_RNA-seq


title: Q22_4_RNA-seq


title: Q25_3_RNA-seq


title: Q23_4_RNA-seq


title: Q23_2_RNA-seq


title: Q25_4_RNA-seq


title: Q25_1_RNA-seq


title: Q24_4_RNA-seq


title: Q24_3_RNA-seq


title: Q26_3_RNA-seq


title: Q22_1_RNA-seq


title: Q21_4_RNA-seq


title: Q22_3_RNA-seq


title: Q21_1_RNA-seq


title: Q24_1_RNA-seq


title: Q21_2_RNA-seq


title: Q22_2_RNA-seq


title: Q21_3_RNA-seq


title: Q2_4_RNA-seq


title: Q2_3_RNA-seq


title: Q2_1_RNA-seq


title: Q2_2_RNA-seq


title: Q18_2_RNA-seq


title: Q18_4_RNA-seq


title: Q18_1_RNA-seq


title: Q15_4_RNA-seq


title: NC6_1_RNA-seq

value: Healthy Control

value: not collected

value: Normal adult


title: NC6_4_RNA-seq

value: Brain


title: Q15_3_RNA-seq

value: Medulloblastoma


title: Q15_1_RNA-seq


title: NC6_2_RNA-seq


title: NC6_3_RNA-seq


title: NC5_4_RNA-seq


title: NC5_2_RNA-seq


title: Q15_2_RNA-seq


title: NC5_1_RNA-seq


title: NC4_1_RNA-seq


title: NC4_4_RNA-seq


title: NC4_3_RNA-seq


title: NC5_3_RNA-seq


title: NC25_4_RNA-seq

value: F

value: Normal pediatric


title: NC25_2_RNA-seq


title: NC25_3_RNA-seq


title: Q18_3_RNA-seq

value: deceased

value: CLASSIC


title: NC25_1_RNA-seq


title: NC24_4_RNA-seq


title: NC24_2_RNA-seq


title: NC24_1_RNA-seq


title: Q11_2_RNA-seq

value: YES

value: NO


title: Q11_4_RNA-seq


title: NC23_4_RNA-seq


title: Q11_1_RNA-seq


title: Q11_3_RNA-seq


title: NC24_3_RNA-seq


title: NC20_3_RNA-seq


title: NC20_4_RNA-seq


title: NC23_1_RNA-seq


title: NC4_2_RNA-seq


title: NC21_1_RNA-seq


title: NC20_1_RNA-seq


title: NC18_2_RNA-seq


title: NC18_3_RNA-seq


title: NC16_3_RNA-seq


title: NC23_2_RNA-seq


title: NC16_2_RNA-seq


title: NC20_2_RNA-seq


title: NC16_4_RNA-seq


title: NC16_1_RNA-seq


title: NC21_3_RNA-seq


title: NC21_4_RNA-seq


title: NC23_3_RNA-seq


title: NC15_3_RNA-seq


title: NC18_1_RNA-seq


title: NC15_2_RNA-seq


title: NC15_1_RNA-seq


title: NC14_4_RNA-seq


title: NC13_4_RNA-seq

value: 2 mo


title: NC14_1_RNA-seq


title: NC14_3_RNA-seq


title: NC13_3_RNA-seq


title: NC21_2_RNA-seq


title: NC18_4_RNA-seq


title: NC1_2_RNA-seq


title: NC13_2_RNA-seq


title: NC1_4_RNA-seq


title: NC1_1_RNA-seq


title: NC13_1_RNA-seq


title: NC1_3_RNA-seq


title: UACC812-LTR

status: Public on Apr 04 2020

city: Houston

first: Xiaoyong

last: Fu

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description:
anti-HER2-resistant
processed data file: MVA_fpkm_genelevel_GEO_submission_5-28-19.txt

data_processing:
Analysis was performed with the ALEXA-seq software package (http://www.alexaplatform.org/alexa_seq/) as previously described by Griffith et al., in Nature Methods, 2010.
Creation of a database of expression and alternative expression sequence “features” (genes, transcripts, exons, junctions, boundaries, introns, and intergenic sequences) based on Ensembl (53_36o) gene models.
Alignment of short paired-end sequence reads to these features using BWA (0.5.8a) and BLAST (2.2.18).
Identification of features that are expressed above background while taking into account locus-by-locus noise.
Assignment of FPKM-like values for each feature type, normalized to feature size and total library coverage.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: MVA_fpkm_genelevel_GEO_submission_5-28-19.txt: Tab-delimited text file includes hg19 gene symbols and gene-level FPKM values across all P and R models.

source_name: human breast cancer cells

growth_protocol: AU-565 cells were cultured in RPMI 1640 with 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin-streptomycin-glutamine (PSG). SKBR3 cells were grown in McCoy's 5A with 10% heat-inactivated FBS and 1% PSG. UACC-812 cells were maintained in Dulbecco's modified Eagle medium (DMEM) supplemented with 10% heat-inactivated FBS and 1% PSG.

extract_protocol:
Total RNA was isolated using an RNeasy Mini Kit (Qiagen), using manufacturer's protocol.
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina) and Agilent Automation NGS system according to manufacturers’ instructions.

treatment_protocol: HER2+ breast cancer cells resistant to HER2-targeted therapy were generated by long term culture of the parental (P) cells in their original media with increasing concentrations of lapatinib (0.1 to 1 μM), or lapatinib (0.1 to 1 μM) plus trastuzumab (1 to 50 μg/ml). Responsive cells were cultured with their respective treatments until growth resumed. The time to the development of resistant growth varied from 3 to 12 months. P cells were also treated for 24 h with lapatinib (1 µM) or lapatinib plus trastuzumab (L: 1 µM, T: 50 µg/ml).

tag: cell model

tag: anti-her2 resistance

value: Resistant

tag: treatment

value: Lapatinib plus trastuzumab, long-term


title: SKBR3-LR

value: Lapatinib, long-term


title: UACC812-P L

description:
anti-HER2 sensitive
processed data file: MVA_fpkm_genelevel_GEO_submission_5-28-19.txt

value: Sensitive

value: Lapatinib, 24h


title: UACC812-P LT

value: Lapatinib plus trastuzumab, 24h


title: NC15_4_RNA-seq

value: Healthy Control

value: not collected


title: UACC812-P

value: None (parental)


title: UACC812-LR


title: SKBR3-P LT


title: SKBR3-LTR


title: SKBR3-P L


title: SKBR3-P


title: NC14_2_RNA-seq

value: Brain

value: Normal adult


title: AU565-LTR


title: AU565-LR


title: AU565-P


title: AU565-P L


title: AU565-P LT


title: 25BPI.2

status: Public on Apr 01 2020

city: Boston

first: Annie

last: Kathuria

state: MA

address: 185 cambridge street

institute: Mass Gen Hospital

data_processing:
Analysis was performed by DNA Link USA, Inc.
Sequence quality was assessed using FASTQC
Sequences were trimmed using cutadapt v 1.18, paired-end reads mode -u 7 -u -3 -U 7 -U -3
Trimmed reads were aligned to the reference genome using TopHat v2.1.1 (--no-coverage-search, -G refseqhg38p9.gtf)
Bam files were merged using samptools v 1.9 for samples with techincal replicates.
FPKM calulcation done using cufflinks v2.2.1 using annotation from RefSeq assembly hg38 p9 which was modified according UCSC-style-name
Pairwise differential expression analysis was performed using cuffdiff v2.2.1
Genome_build: Homo sapience hg38 (UCSC tophat version as downloaded May 2017)
Supplementary_files_format_and_content: tab-delimited w/ the following columns: tracking_id, gene_id, gene_short_name, locus, FPKM for each sample

source_name: cerebral organoids

extract_protocol:
Tissue was dissolved in Trizol and RNA was extracted using qiagen rneasy kit
RNA libraries were prepared for sequencing using Truseq Stranded Total RNA H/M/R

tag: diagnosis

value: Bipolar Disorder

tag: cell type

value: Human iPSC derived cerebral organoids

tag: state

value: 6 months of differention


title: 136BPI.1


title: 68BPI


title: 151BPI


title: 81BPI.2


title: 92BPI


title: 136BPI.2


title: 81BPI.1


title: 45BPI


title: siRNA CYP2J2 rep_2

status: Public on Mar 07 2020

city: Seattle

first: Sina

last: Gharib

state: WA

address: 850 Republican St.

department: Medicine

institute: University of Washington

data_processing:
Sequencing was performed using an Illumina HiSeq 4000 instrument using paired end 75 bp lanes. Base calls were generated in real-time on the HiSeq instrument, and RTA-generated BCL files were converted to FASTQ files. Sequence read and base quality were checked using the FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) and FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and adaptor and low-quality bases were trimmed. Sequences were aligned to GRCh38 with reference transcriptome Gencode release 26 (GRCh38.p10) using STAR (v2.5.3a). Transcript abundances were quantified using Kallisto (v0.43.1)
Differential gene expression between IRI and sham conditions was determined using DESeq2 package in R environment
Genome_build: GRCh38
Supplementary_files_format_and_content: abundance count

source_name: Adult human cardiomyocyte

extract_protocol:
Cell culture materials including adult derived primary human cardiomyocytes (cat #36044-15), media (complete growth media, cat #M36044-15S), and extracellular matrix pre-coated flasks and plates (cat #E36044-15) were obtained from Celprogen Inc. (San Pedro, CA, USA). Media were further sterile filtered using a vacuum filter through a 0.22 μm polyethersulfone (PES) filter. Celprogen’s protocols were followed for culture and passage of adult human ventricular cardiomyoctes. Experiments were performed between passages 6 and 8, where passage numbers were determined by number of times cells were treated with trypsin since receipt from Celprogen which was designated passage 1 for the purposes of these experiments. Briefly, cells were cultured and expanded using Celprogen pre-coated flasks and complete growth media with serum. Cells used for RNA isolation and subsequent experiments were harvested by washing the cells still attached to the plate with 1X PBS. After washing, all liquid was aspirated from the wells and the entire plate was stored in -80 °C until RNA extraction and purification. CYP2J2 gene expression was silenced using the RNAiMAX lipofectamine (Thermo Fisher Scientific, Waltham MA) and the CYP2J2 Trilencer siRNA or scrambled siRNA (Origene, Rockville, MD), using the manufacturer’s suggested protocols. Silencing of the HPRT1 gene using the Origene siRNA served as positive control. Lipofectamine was delivered using a reverse transfection protocol.  siRNA was reconstituted to a stock concentration of 20 μM per the manufacturer protocols and prepared with the lipofectamine using OptiMEM reduced serum media (Thermo Fisher Scientific, Waltham, MA) by diluting to a concentration of 50 nM. Cells were washed with warm (37 °C) PBS and harvested using trypsin. Following trypsinization, cells were pelleted and resuspended and diluted to a concentration of 200,000 cells/mL in complete media. The lipofectamine/siRNA stocks were added to each well to a final concentration of 10 nM siRNA (250 μL volume of 50 nM siRNA/lipofectamine in OptiMEM), followed by the cells (1 mL of cell suspension) for a final volume of 1250 μL in each well. The cells were incubated with the lipofectamine/siRNA for 72 hours.
Total RNA was extracted using the MagMax 96 Total RNA Isolation kit (Thermo Fisher Scientific, Waltham MA). Initial RNA quality (A260/A280) and quantity was determined using a Synergy HTX Multi-Mode Reader (BioTek, Winooski VT).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sirna

value: Treated with CYP2J2 siRNA

tag: tissue

value: Adult human cardiomyocyte


title: 25BPI.1


title: 97BPI


title: siRNA CYP2J2 rep_1


title: siRNA Scramble rep_3

value: Treated with scrambled siRNA


title: siRNA Scramble rep_2


title: siRNA Scramble rep_1


title: Wt_Wt_rep3

status: Public on Mar 01 2020

data_processing:
The raw reads were first cleaned by removing adapter sequences, trimming low quality ends (four bases from read start and read end), and filtering reads with low quality (phred quality <20) using Trimmomatic
Sequence alignment and isoform expression quantification of the resulting high-quality reads to the Mus musculus reference genome (build GRCm38) was performed with the RSEM algorithm (version 1.2.18) with the following parameters: trimAdapter=TRUE, trimLeft=3, trimRight=0, minTailQuality=20
To detect differentially expressed genes we applied the count based negative binomial model implemented in the software package edgeR (version: 3.10.2), in which the normalization factor was calculated by the trimmed mean of M values (TMM) method.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tabular format of Ensembl-annotated transcripts containing TPM and FPKM values, as well as the expected counts ("transcriptCount" column) produced by RSEM.

extract_protocol:
Total RNA was isolated immediately after sorting using the RNeasy Micro Kit (Qiagen, Hilden, Germany) and stored at -80°C. RNA was analyzed via TapeStation (Agilent), and samples with RIN>7 were adjusted to 100 ng and subjected to the RNA sequencing protocol via poly-A enrichment, True-Seq library preparation, and stranded 100bp sequencing on an Illumina HiSeq 2500 instrument. Quality control via FastQC showed rRNA mapping rates of <5% and over 30 million reads for all samples.
RNA libraries were prepared for sequencing using standard Illumina protocols (poly-A enrichment, True-Seq library preparation)

treatment_protocol: Dorsal and ventral parts of the mouse ears were separated, minced with scissors, and digested with 0.25 mg/ml Liberase TL (Roche) in DMEM for 1 h at 37°C. Following digestion, the cell suspension was filtered through a 70  µm nylon strainer, centrifuged at 300g at 4°C for 10 min, and resuspended in FACS buffer. Ear skin fibroblasts were enriched by FACS sorting of CD45-Cd140a+ cells from the non-cancerous ear skin of 12-15 week- old mice. For each replicate, ear skin from 3-6 mice per genotype was pooled. CD3, CD11b and F4/80 were used as additional negative markers. Dead cells were excluded by Sytox Green staining. Cells were sorted into cold empty Eppendorf tubes and centrifuged for total RNA extraction.

tag: strain

tag: cell type/source

value: FACS-sorted CD45-CD140a+ live cells

value: Ear skin

tag: genotype

value: Wt/Wt

tag: age

value: 12-16 weeks


title: siRNA CYP2J2 rep_3


title: Act_HPV8_rep2

value: Pre-cancerous ear skin


title: Act_Wt_rep1

value: Hyperplastic ear skin


title: Wt_HPV8_rep1


title: Act_HPV8_rep1


title: Wt_Wt_rep2


title: Act_Wt_rep2


title: Wt_HPV8_rep3


title: Act_Wt_rep3


title: Wt_Wt_rep1


title: Wt_HPV8_rep2


title: Brx121_1_SC3_120913

status: Public on Feb 07 2020

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

data_processing:
Color space reads were aligned using tophat version 2.0.4 and bowtie1 version 0.12.7 with the no-novel-juncs argument set with human genome version hg19 and transcriptome defined by the hg19 knownGene table from genome.ucsc.edu.
Reads that did not align or aligned to multiple locations in the genome were discarded.
The hg19 table knownToLocusLink from genome.ucsc.edu was used to map, if possible, each aligned read to the gene who's exons the read had aligned to. The reads count for each gene was the number of reads that were so mapped to that gene.
The read count was divided by the total number of reads that were mapped to any gene and multiplied by one million to form the reads-per-million (rpm) count.
Genome_build: hg19
Supplementary_files_format_and_content: The readCounts.xls file gives the read counts described above for each sample (columns) and gene (rows). See platform.xls for a description of the IDs in readCounts.xls

source_name: CTCs

extract_protocol:
RNA was extracted as previously described (Tang, F., Barbacioru, C., Nordman, E., Li, B., Xu, N., Bashkirov, V.I., Lao, K., and Surani, M.A. (2010). RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5, 516-535).
Libraries were constructed as previously described (Tang, F., Barbacioru, C., Nordman, E., Li, B., Xu, N., Bashkirov, V.I., Lao, K., and Surani, M.A. (2010). RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5, 516-535). Briefly, to generate cDNA, samples were treated with reverse transcription master mix (0.05 uL RNase inhibitor, 0.07uL T4 gene 32 protein, and 0.33uL SuperScript III Reverse Transcriptase per 1X volume) and incubated on thermocycler at 50C for 30 minutes and 70C for 15 minutes. To remove free primer, 1.0uL of EXOSAP mix was added to each sample, which was incubated at 37C for 30 minutes and inactivated at 80C for 25 minutes. Next, a 3'-poly-A tail was added to the cDNA in each sample by incubating in master mix (0.6uL 10X PCR Buffer II, 0.36uL 25mM MgCl2, 0.18uL 100mM dATP, 0.3uL Terminal Transferase, 0.3uL RNase H, and 4.26uL H2O per 1X volume) at 37C for 15 minutes and inactivated at 70C for 10 minutes. A second strand cDNA was synthesis by dividing each sample into 4 and incubating in master mix (2.2uL 10X High Fidelity PCR Buffer, 1.76uL 2.5mM each dNTP, 0.066uL UP2 Primer at 100uM, 0.88uL 50mM MgSO4, 0.44uL Platinum Taq DNA Polymerase, and 13.654uL H2O per 1X volume) at 95C for 3 minutes, 50C for 2 minutes, and 72C for 10 minutes. DNA was sheared using a Covaris S2 system and then prepared for ABI 5500XL library construction with end polishing, size selection of 200-500 bp using AMPure XP, ABI barcode adaptor ligation, amplification and purification with AMPure XP, and then pooling of barcoded samples for emulsion PCR wiht template beads preparation.  Samples were then loaded per protocol on the ABI 5500XL.
RNA-Seq using oligo-dT cDNA synthesis and amplification of cDNA libraries using custom universal PCR primers

treatment_protocol: Patients with a diagnosis of ER and/or PR positive metastatic breast cancer provided informed consent for de-identified blood collection, as per institutional review board approved protocol (DF/HCC 05-300) at Massachusetts General Hospital. Approximately 6-12 mL of fresh whole blood was processed through the microfluidic CTC-iChip as previously described [PMID: 24577360] within 4 hours from the blood draw. Before processing, whole blood samples were incubated with biotinylated antibodies against CD45 (R&D Systems, clone 2D1), CD66b (AbD Serotec, clone 80H3) and followed by incubation with Dynabeads MyOne Streptavidin T1 (Invitrogen) to achieve magnetic labelling of white blood cells. This mixture was processed through the CTC-iChip. To identify CTCs, the CTC-enriched product was stained with Alexa Fluor 488-conjugated antibodies against EpCAM (Cell Signaling Technology, #5198), Cadherin 11 (R&D Systems, FAB17901G), and HER2 (BioLegend, #324410). To identify contaminating white blood cells the product was stained with TexasRed-conjugated antibodies against CD45 (BD Biosciences, BDB562279), CD14 (BD Biosciences, BDB562334), and CD16 (BD Biosciences, BDB562320). The stained product was viewed under a fluorescent microscope where single CTCs were identified based on intact cellular morphology, Alexa Fluor 488-positive staining and lack of TexasRed staining. Cells of interest were individually micromanipulated with a 10 mm transfer tip on an Eppendorf Transfer-Man NK 2 micromanipulator and lysed.

tag: patient

tag: overall survival days

tag: overall survival event


title: Reanalysis Br29_1_012913


title: Brx130_1_SC2_011714


title: Brx116_1_SC1_120213


title: Brx164_1_SC2_091814


title: Brx134_1_SC2_021914


title: Brx109_1_CL1_121613


title: Brx126_1_SC3_021214


title: Brx117_1_SC2_120613


title: Brx107_1_SC2_092013


title: Reanalysis Brx66_2_CL1_012913


title: Brx122_1_SC1_121213


title: Reanalysis Brx53_CL1_011513


title: Reanalysis Brx98_1_SC3_072313


title: Act_HPV8_rep3


title: Reanalysis Brx73_1_SC2_032013


title: Reanalysis Brx74_1_SC2_032813


title: Reanalysis Brx83_1_SC1_051613


title: Reanalysis Brx97_1_SC1_072313


title: Brx86_1_SC2_052313


title: Brx100_1_SC3_080113


title: Reanalysis Br21_1_SC1_052113


title: Reanalysis Brx10_1_SC1_041113


title: Reanalysis BrTr08_1_CL1_012913


title: Brx35_1_SC1_091213


title: BrTr11_1_SC2_022513


title: Reanalysis Brx87_1_SC1_062113


title: Reanalysis Brx78_1_05102013


title: Brx90_1_SC1_062713


title: Brx95_1_SC1_071713


title: Reanalysis Brx50_2_031113


title: Reanalysis Brx71_SC1_031413


title: eHCC-8

status: Public on Jan 10 2020

type: RNA

city: Suwon, Korea

first: Jung Woo

last: Eun

state: Korea

address: Department of Gastroenterology

country: South Korea

institute: Ajou University of Korea

description: SAMPLE 27

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with GenPlex 3.0

label: biotin

source_name: Mouse liver tissue

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

growth_protocol: Male C3H/He N mice were purchased from Central Lab Animal, Inc. (Seoul, Korea), and handled according to the guidelines for the care and use of laboratory animals.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen). RNA quality control was performed with Bio-Rad Experion.

treatment_protocol: Diethylnitrosamine (DEN; Sigma) was administered twice by intraperitoneal injections at a dose of 5 mg/kg of body weight at 14 days of age and of 75 mg/kg of body weight at 20 weeks of age. The mice were sacrifice at 15, 20, 36, and 42 weeks after treatment. Blood and liver samples were collected after the mice were sacrificed under ether anesthesia.

tag: Stage

value: eHCC


title: eHCC-2

description: SAMPLE 21

value: Diethylnitrosamine (DEN; Sigma) was administered twice by intraperitoneal injections at a dose of 5 mg/kg of body weight at 14 days of age and of 75 mg/kg of body weight at 20 weeks of age.


title: A-6

description: SAMPLE 18

value: Adenoma


title: aHCC-3

description: SAMPLE 33

value: aHCC


title: eHCC-11

description: SAMPLE 30


title: aHCC-6

description: SAMPLE 36


title: A-1

description: SAMPLE 13


title: A-3

description: SAMPLE 15


title: N-12

description: SAMPLE 12

value: saline solution

value: Control


title: eHCC-5

description: SAMPLE 24


title: aHCC-1

description: SAMPLE 31


title: aHCC-4

description: SAMPLE 34


title: eHCC-9

description: SAMPLE 28


title: A-4

description: SAMPLE 16


title: eHCC-6

description: SAMPLE 25


title: A-7

description: SAMPLE 19


title: eHCC-3

description: SAMPLE 22


title: aHCC-7

description: SAMPLE 37


title: aHCC-5

description: SAMPLE 35


title: N-11

description: SAMPLE 11


title: eHCC-1

description: SAMPLE 20


title: A-5

description: SAMPLE 17


title: A-2

description: SAMPLE 14


title: eHCC-10

description: SAMPLE 29


title: eHCC-4

description: SAMPLE 23


title: FFPE tumor 13

status: Public on Dec 31 2019

city: Shoham

first: jasmine

last: Jacob

state: -Select-

address: haChevel 33

country: Israel

institute: Sheba Medical Center at Tel HaShomer

hyb_protocol: Affymetrix 3' IVT labeling protocol  https://www.affymetrix.com/support/downloads/manuals/3_ivt_express_kit_manual.pdf

data_processing: RMA (PARTEK)

source_name: FFPE tumor

label_protocol: FlashTag Biotin HSR RNA labeling kit (Affymetrix 901910)

extract_protocol: Total RNA was extracted according to the miRNeasy kit manufacturer's protocol.

treatment_protocol: For normal fallopian tube epithelial cell harvest : Normal  resected fallopian tube fimbriae tissues were incubated in dissociation medium (DMEM, Biological Industries) supplemented with 1.4mg/ml Pronase (Roche Applied Science) and 0.1mg/ml DNase (Sigma-Aldrich) for 48 hours at 4ºc with constant mild agitation. The dissociated epithelial cells were harvested by centrifugation. For FFPE material: 4X10 micron thick sections were cut and subjected to RNA extraction.

value: HG serous papillary carcinoma


title: Fresh frozen tumor 4

scan_protocol: Affymetrix 3' IVT labeling protocol  https://www.affymetrix.com/support/downloads/manuals/3_ivt_express_kit_manual.pdf

source_name: Fresh frozen tumor


title: eHCC-7

description: SAMPLE 26


title: Fresh frozen tumor 5


title: Fresh frozen tumor 6


title: FFPE tumor 12


title: FFPE tumor 11


title: N-10

description: SAMPLE 10


title: N-9

description: SAMPLE 9


title: N-8

description: SAMPLE 8


title: aHCC-2

description: SAMPLE 32


title: N-7

description: SAMPLE 7


title: N-6

description: SAMPLE 6


title: N-2

description: SAMPLE 2


title: Normal fallopian tube epithelium 2

source_name: Normal fallopian tube epithelium

value: Normal fallopian tube epithelium


title: Normal fallopian tube epithelium 6


title: Fresh frozen tumor 3


title: Normal fallopian tube epithelium 5


title: N-5

description: SAMPLE 5


title: N-3

description: SAMPLE 3


title: N-4

description: SAMPLE 4


title: N-1

description: SAMPLE 1


title: Normal fallopian tube epithelium 4


title: FFPE tumor 9


title: FFPE tumor 10


title: Fresh frozen tumor 2


title: FFPE tumor 8


title: FFPE tumor 6


title: FFPE tumor 3


title: FFPE tumor 4


title: FFPE tumor 5


title: FFPE tumor 7


title: FFPE tumor 2


title: Normal fallopian tube epithelium 1


title: Fresh frozen tumor 1


title: OSA Subject before CPAP 1046b

status: Public on Dec 21 2019

description:
OSA Subject before CPAP
STUDY GROUP 2

hyb_protocol: Affymetrix standard protocol

scan_protocol: GeneChip Operating System (GCOS)

data_processing: RMA algorithm with quantile normalization and background correction

label: Biotin

source_name: Subcutaneous Fat Tissue

label_protocol: Affymetrix standard protocol

extract_protocol: Total RNA was isolated from subcutaneous fat tissue using RNeasy Lipid Tissue Mini Kit with DNase treatment  (Qiagen, Valencia, CA)

tag: Sex

value: F

tag: bmi


title: FFPE tumor 1


title: OSA Subject before CPAP 5028b

description:
OSA Subject before CPAP
STUDY GROUP 2

value: M


title: OSA Subject after CPAP 1089c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 1046c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject before CPAP 1089b

description:
OSA Subject before CPAP
STUDY GROUP 2


title: OSA Subject before CPAP 5030b

description:
OSA Subject before CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 1038c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject before CPAP 1038b

description:
OSA Subject before CPAP
STUDY GROUP 2


title: OSA Subject before CPAP 5031b

description:
OSA Subject before CPAP
STUDY GROUP 2


title: OSA Subject before CPAP 5032b

description:
OSA Subject before CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 5031c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 5030c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject before CPAP 5026b

description:
OSA Subject before CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 5026c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject before CPAP 5022b

description:
OSA Subject before CPAP
STUDY GROUP 2


title: OSA Subject before CPAP 5025b

description:
OSA Subject before CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 5022c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 5032c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 5028c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 5020c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject before CPAP 5021b

description:
OSA Subject before CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 5018c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 5017c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 5021c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject before CPAP 5018b

description:
OSA Subject before CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 5025c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject before CPAP 5017b

description:
OSA Subject before CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 5016c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 5015c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject before CPAP 5016b

description:
OSA Subject before CPAP
STUDY GROUP 2


title: OSA Subject before CPAP 5015b

description:
OSA Subject before CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 5011c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 5006c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 5009c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 5012c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject before CPAP 5011b

description:
OSA Subject before CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 5004c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject before CPAP 5012b

description:
OSA Subject before CPAP
STUDY GROUP 2


title: OSA Subject before CPAP 5006b

description:
OSA Subject before CPAP
STUDY GROUP 2


title: OSA Subject before CPAP 5009b

description:
OSA Subject before CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 5003c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject after CPAP 5001c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject 14-S-A

description:
OSA Subject
STUDY GROUP 1


title: OSA Subject 26-S-A

description:
OSA Subject
STUDY GROUP 1


title: OSA Subject before CPAP 5001b

description:
OSA Subject before CPAP
STUDY GROUP 2


title: OSA Subject 15-S-A

description:
OSA Subject
STUDY GROUP 1


title: OSA Subject 11-S-A

description:
OSA Subject
STUDY GROUP 1


title: OSA Subject after CPAP 5002c

description:
OSA Subject after CPAP
STUDY GROUP 2


title: OSA Subject 16-S-A

description:
OSA Subject
STUDY GROUP 1


title: OSA Subject 3-S-A

description:
OSA Subject
STUDY GROUP 1


title: OSA Subject 6-S-A

description:
OSA Subject
STUDY GROUP 1


title: OSA Subject before CPAP 5003b

description:
OSA Subject before CPAP
STUDY GROUP 2


title: MCF7L-TamR_siHIF-2α_seq2 rep3

status: Public on Dec 18 2019

description: processed data file: Cuffdiff_TamR_siNS_siEPAS1-3.txt

data_processing:
Raw reads were mapped to the human reference genome (hg38) using Bowtie 2 v2.3.4.1.
Relative transcript abundance was calculated by Fragments Per Kilobase of transcript per Million mapped reads (FPKMs) using Cufflinks v2.2.1. FPKMs were scaled via the median of the geometric means of fragment counts across all libraries, as described in Anders and Huber (Genome Biology, 2010).
Differential gene expression was calculated using Cuffdiff program of Cufflinks v2.2.1, by modeling dispersion in a global model for all conditions.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for comparisons between control knockdown and HIF-2α knockdown.

source_name: breast cancer MCF7 cells

growth_protocol: Tamoxifen-resistant MCF7L cells were kept in phenol-red free (PRF) medium supplemented with 10% heat-inactivated charcoal-stripped (CS)-FBS and 1% PSG, with the addition of 100 nM 4-OH-tamoxifen (H7904, Sigma).

extract_protocol:
Total RNA isolation was performed using the RNeasy Mini Kit (Qiagen). DNA was degraded on columns with DNase I (Qiagen).
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina) adapted for use on the Sciclone (Perkin-Elmer) liquid handler.

treatment_protocol: Transient reverse-phase siRNA (ordered from Ambion) transfection was performed using RNAiMAX reagent, 3 days before harvesting for RNA.

value: breast cancer

tag: cell line

tag: genotype/variation

value: Tamoxifen-resistant derivative


title: OSA Subject before CPAP 5002b

description:
OSA Subject before CPAP
STUDY GROUP 2


title: OSA Subject 24-S-A

description:
OSA Subject
STUDY GROUP 1


title: MCF7L-TamR_siHIF-2α_seq2 rep2


title: OSA Subject 7-S-A

description:
OSA Subject
STUDY GROUP 1


title: MCF7L-TamR_siHIF-2α_seq1 rep3

description: processed data file: Cuffdiff_TamR_siNS_siEPAS1-2.txt


title: MCF7L-TamR_siHIF-2α_seq2 rep1


title: Normal Subject 12-S-N

description:
Normal Subject
STUDY GROUP 1


title: Normal Subject 21-S-N

description:
Normal Subject
STUDY GROUP 1


title: MCF7L-TamR_siHIF-2α_seq1 rep2


title: Normal Subject 19-S-N

description:
Normal Subject
STUDY GROUP 1


title: Normal Subject 22-S-N

description:
Normal Subject
STUDY GROUP 1


title: MCF7L-TamR_siNS rep3


title: MCF7L-TamR_siNS rep1


title: OSA Subject 2-S-A

description:
OSA Subject
STUDY GROUP 1


title: MCF7L-TamR_siNS rep2


title: Normal Subject 13-S-N

description:
Normal Subject
STUDY GROUP 1


title: OSA Subject before CPAP 5004b

description:
OSA Subject before CPAP
STUDY GROUP 2


title: Normal Subject 10-S-N

description:
Normal Subject
STUDY GROUP 1


title: MCF7L-TamR_siHIF-2α_seq1 rep1


title: MCF7L-TamR_input

data_processing:
Raw fastq reads were aligned separately to the reference genomes of human (hg19) and Drosophila melanogaster (dm3) using Bowtie 2 v2.3.4.1. Uniquely mapped reads with up to 2 mismatches were used for subsequent peak calling.
We used HOMER v4.9.1 to call peaks for FOXA1 (FDR < 0.001, DESeq FDR < 0.05 for duplicates), using the input DNA as background control. For H3K27ac and H3K4me1 ChIP-seq, we used HOMER to call peaks (FDR < 0.001) with the parameters of “-size 1000 -minDist 2500”. Differential peaks were analyzed using merged peaks with the cutoff P-value < 10^-10 and fold-change > 4.
FOXA1 ChIP-Seq BAM files were downsampled for spike-in normalization using Picard v2.17.8 (Broad Institute). Scaling factors were calculated based on the spiked-in chromatin reads aligned to the reference genome of Drosophila melanogaster (dm3).
Genome_build: hg19
Genome_build: dm3
Supplementary_files_format_and_content: We used HOMER v4.9.1 makeUCSCfile command to create bedGraph files, and used ENCODE bedGraphToBigWig tool to covert bedGraph to bigwig files.

growth_protocol: MCF7L-P cells were maintained in RPMI/1640 medium, supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin/streptomycin/glutamine (PSG). Tamoxifen-resistant cells were kept in phenol-red free (PRF) medium supplemented with 10% heat-inactivated charcoal-stripped (CS)-FBS and 1% PSG, with the addition of 100 nM 4-OH-tamoxifen (H7904, Sigma). The isogenic MCF7L-P line with doxycycline (Dox)-inducible FOXA1 overexpression was maintained in the presence of 200 μg/ml Geneticin (Invitrogen).

extract_protocol:
Breast cancer cells were grown to 85% confluence in 15-cm plates and cross-linked with 1% formaldehyde (10 min) followed by quenching (125 mM glycine). Cells were washed in cold PBS and harvested by cell scraper in cold PBS with protease inhibitors (Roche). Cells were centrifuged at 3,220g for 5 min, snap-frozen, and stored at -80°C at 1×10^7 cells per pellet. Pellets were resuspended in cytosolic and then nuclear lysis buffer, and chromatin was sheared at 4°C using a water-bath sonicator (Bioruptor, Diagenode) for 20 min at high output (30 s on, 30 s off). Sonicated lysates were cleared by centrifuging at 20,000g for 10 min and diluted 4 times before pre-incubation with protein-A/G beads (Santa Cruz) for 30 min at 4°C. ChIP was performed by overnight incubation at 4°C with antibody against human FOXA1 (Abcam, ab23738), H3K27ac (Active Motif, #39134), or H3K4me1 (Abcam, ab176877), or Drosophila melanogaster histone variant H2Av (Active Motif, # 61752), followed by an additional 1 h incubation with protein-A/G beads. Beads were washed consecutively with low and high salt wash buffer, once with LiCl wash buffer, and once with TE buffer. DNA was eluted in elution buffer (50 mM NaHCO3 and 1% SDS) and then supplemented with 300 mM NaCl. Cross-links were reversed overnight at 67°C. RNA was digested at 37°C with 0.1 mg/ml RNase A for 30 min. DNA was purified with a PCR purification kit (Qiagen).
Indexed libraries were prepared from ChIP DNA using the KAPA Hyper Library Preparation Kit (Kapa Biosystems). Libraries were amplified by 12 cycles of PCR, and then assessed for size distribution using the 4200 TapeStation High Sensitivity D1000 ScreenTape (Agilent Technologies) and quantified using the Qubit dsDNA HS Assay Kit (ThermoFisher). The indexed libraries were multiplexed, 10 libraries per pool. The pool was quantified by qPCR using the KAPA Library Quantification Kit (KAPA Biosystems) and then sequenced on the Illumina HiSeq 2000.

treatment_protocol: MCF7L-P cells constructed with Dox-inducible FOXA1 overexpression were incubated with 1 μg/ml Dox for 5 days before fixation for chromatin extraction.

tag: chip antibody

value: none (input)


title: MCF7L-TamR_H3K27ac_ChIPSeq


title: FOXA1-Dox_input

value: Parental


title: MCF7L-P_H3K27ac_ChIPSeq


title: FOXA1-Dox_H3K4me1_ChIPSeq


title: MCF7L-P_input


title: FOXA1+Dox_input


title: FOXA1+Dox_H3K4me1_ChIPSeq


title: FOXA1+Dox_H3K27ac_ChIPSeq


title: FOXA1-Dox_H3K27ac_ChIPSeq


title: Normal Subject 18-S-N

description:
Normal Subject
STUDY GROUP 1


title: FOXA1+Dox_FOXA1_ChIPSeq rep1


title: FOXA1+Dox_FOXA1_ChIPSeq rep2


title: FOXA1-Dox_FOXA1_ChIPSeq


title: 05_Panobinostat_rep1

status: Public on Jun 11 2019

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

description: 005_RNA_Smalley_CICPT1094_Combined.counts

data_processing:
Basecalling and quality scoring are performed on the NextSeq instrument with the Real-Time Analysis (RTA) v2 software
READ TRIMMING were performed.
Read alignment using TopHat v2.0.13
Abundance (Reads Per Kilobase of exon per Megabase of library size --RPKM) calculation using cufflinks v2.2.1
Differential expression calculation using DESeq2
Genome_build: hs375d
Supplementary_files_format_and_content: Tab delimited text file containing gene symbols (first column) and normalized count for the four samples (columns two through five)

growth_protocol: 92.1 uveal melanoma cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and 1% of penicillin and streptomycin (pen/strep).

extract_protocol:
Samples were trypsinized, washed in PBS 2x and the pellect was harvested using Trizol reagent. Then, the RNA extraction procedure was conducted with RNEasy Qiagen Kit (#74104) and 1 ug of total RNA for the construction of sequencing libraries.
RNA-Seq was performed using the NuGEN Ovation Human RNA-Seq FFPE kit

treatment_protocol: 92.1 uveal melanoma cells were treated for 24h with 10nM of Trametinib or Panobinostat or vehicle (DMSO- Control group).

tag: cell type

value: Uveal melanoma cells

tag: treatment

value: panobinostat (MEKi) (10nM, 24 hr)


title: 06_Panobinostat_rep2

description: 006_RNA_Smalley_CICPT1094_Combined.counts


title: 08_Trametinib+Panobinostat_rep2

description: 008_RNA_Smalley_CICPT1094_Combined.counts

value: trametinib+panobinostat (MEKi) (10nM, 24 hr)


title: WT-4

status: Public on Jun 16 2019

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Base calls from Illumina HiSeq 4000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (version: Schizosaccharomyces_pombe.ASM294v2.28) using HISAT2_2.1.0
resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Genome_build: Schizosaccharomyces_pombe.ASM294v2.28.dna.genome.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/OLD/20150909/Schizosaccharomyces_pombe.ASM294v2.28.dna.genome.fa.gz)
Supplementary_files_format_and_content: Matrix file for raw HTSeq counts; individual files for DESeq2 for comparison of each mutant with WT

molecule: polyA RNA

organism: Schizosaccharomyces pombe

source_name: WT

growth_protocol: log phase cultures, 30ºC, YES medium

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

tag: lab strain number

value: JS 77

tag: growth conditions

value: log phase culture, YES medium

tag: developmental stage

value: vegetative growth


title: 07_Trametinib+Panobinostat_rep1

description: 007_RNA_Smalley_CICPT1094_Combined.counts


title: WT-6


title: WT-5


title: PC3: input_DNA_control  DMSO

status: Public on May 21 2019

city: Oslo

first: Alfonso

last: Urbanucci

state: Oslo

address: Trondheimsveien 8

country: Norway

institute: Oslo University Hospital

data_processing:
The raw reads were mapped with novoalign  to the human reference genome (build hg19) with default parameters.  Only reads with q>20 and a maximum of 5 read duplicates per genomic location were allowed by filtering.
note that files from input DNA from three biological replicates ChIP assay were "pooled" together using the cat command.
Peak detection (i.e., binding site detection)  was performed with MACS1.4 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: bwig files

growth_protocol: LNCaP and PC3 cells were maintained in RPMI media supplemented with 10% FBS.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed from ~20x106 cells by first cross-linking cells with 1% para-formaldehyde (pFa) in room temperature for 10 minutes. PFa was quenched by addition of 125mM glycine for 10 minutes and cells were washed twice in ice-cold PBS. Next, cells were solubilized into ChIP lysis buffer (0.1% SDS, 1% Triton X-100, 0.15M NaCl, 1mM EDTA, 20mM Tris pH8.0), and samples were sonicated using Bioruptor (Diagenode) to obtain DNA fragments of 200-500 based pairs in length (this was confirmed for every experiment). After sonication, samples were centrifuged and supernatant was used for ChIP. Antibodies for ChIP: RL2 #ab2739 (Abcam) and MYC AF3696 (R&D systems). ChIP was performed over-night in +4˚C, and beads were washed as follows: 2x in wash buffer 1 (0.1% SDS, 0.1% Na-deoxycholate, 1% Triton X-100, 0.15M NaCl, 1mM EDTA, 20mM HEPES pH8.0), 1x in wash buffer 2 (0.1% SDS, 0.1% Na-deoxycholate, 1% Triton X-100, 0.5M NaCl, 1mM EDTA, 20mM HEPES pH8.0), 1x in wash buffer 3 (0.25M LiCl, 0.5% Na-deoxycholate, 0.5% NP-40, 1mM EDTA, 20mM HEPES pH8.0) and 2x in wash buffer 4 (10mM EDTA, 20mM HEPES). After this, DNA was extracted using phenol-chloroform extraction and used for sequencing.
Libraries were prepared according Illumina's instructions accompanying the TruSeq library preparation kit.

treatment_protocol: cells were treated for 4 hours with DMSO or 40 micromolar of the OGT inhibitor OSMI-2

tag: tissue

value: prostate cancer

tag: antibody

value: no antibody

value: DMSO


title: PC3: O-GlcNAc_3 OSMI-2

value: anti-RL2 #ab2739 (Abcam)


title: PC3: O-GlcNAc_1 OSMI-2


title: PC3: O-GlcNAc_2 OSMI-2


title: PC3: O-GlcNAc_2 DMSO


title: PC3: IgG_1  DMSO

value: anti-IgG (scbt-816X)


title: 02_Control_rep2

description: 002_RNA_Smalley_CICPT1094_Combined.counts

data_processing:
Basecalling and quality scoring are performed on the NextSeq instrument with the Real-Time Analysis (RTA) v2 software
READ TRIMMING were performed.
Read alignment using TopHat v2.0.13
Abundance (Reads Per Kilobase of exon per Megabase of library size --RPKM) calculation using cufflinks v2.2.1
Gene is excluded if the sum of raw count across 4 samples is 0.
Differential expression calculation using R/3.1.1 package DESeq2
Genome_build: hs375d (ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz)
Supplementary_files_format_and_content: Tab delimited text file containing gene symbols (first column) and normalized count for the four samples (columns two through five)

source_name: Uveal melanoma cells

treatment_protocol: 92.1 uveal melanoma cells were treated for 24h with 10nM of Trametinib or vehicle (DMSO- Control group).

value: cells treated with vehicle


title: 01_Control_rep1

description: 001_RNA_Smalley_CICPT1094_Combined.counts


title: 03_Trametinib_rep1

description: 003_RNA_Smalley_CICPT1094_Combined.counts

value: cells treated with trametinib (MEKi) (10nM, 24 hr)


title: 04_Trametinib_rep2

description: 004_RNA_Smalley_CICPT1094_Combined.counts


title: Normal fallopian tube epithelium 3

value: Normal fallopian tube epithelium


title: LNCaP: O-GlcNAc_3 OSMI-2

source_name: LNCaP

value: LNCaP


title: PC3: O-GlcNAc_3 DMSO


title: LNCaP: O-GlcNAc_2 OSMI-2


title: LNCaP: O-GlcNAc_1 OSMI-2


title: LNCaP: IgG OSMI-2


title: PC3: O-GlcNAc_1 DMSO


title: Combo_24h_Rep2

description: Salmon_counts.txt and Salmon_abundance_TPM.txt

data_processing:
raw reads were trimmed with Trimgalore (v.0.4.1) and aligned to the transcriptome (UCSC .gtf hg19) using Salmon (v.0.9.1) with  default parameter and --gcBias. Read counts and transcripts per Million bases (TPM) were retreaved.
Genome_build: hg19
Supplementary_files_format_and_content: Salmon was used to retrieve read counts and transcripts per Million bases (TPM).

growth_protocol: LNCaP cells were maintained in RPMI media supplemented with 10% FBS.

extract_protocol:
RNA was isolated using an illustraMiniSpin kit (GE Healthcare) according to the manufacturer's instructions
Libraries were prepared according Illumina's instructions accompanying the TruSeq library preparation kit.

treatment_protocol: Cells were treated for the indicated amount of hours with the indicated compounds (OSMI2, Doxycycline, or a combination of both (combo)).

value: Combo 24h


title: Doxycycline_24h_Rep2

value: Doxycycline 24h


title: DMSO_24h_Rep2

value: DMSO 24h


title: OSMI2_24h_Rep2

value: OSMI2 24h


title: Combo_4h_Rep2

value: Combo 4h


title: OSMI2_4h_Rep2

value: OSMI2 4h


title: DMSO_4h_Rep2

value: DMSO 4h


title: Combo_24h_Rep1


title: Doxycycline_24h_Rep1


title: OSMI2_4h_Rep1


title: Doxycycline_4h_Rep1

value: Doxycycline 4h


title: Combo_4h_Rep1

value: prostate cancer


title: DMSO_24h_Rep1


title: DMSO_4h_Rep1


title: easyCLIP PCBP1-100Q Replicate 4 [Exp71_PCBP1-100Q_hpGTCGTC_TCA]

status: Public on May 17 2019

city: Stanford

first: Douglas

last: Porter

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford

description:
Exp71_PCBP1-100Q_hpGTCGTC_TCA
processed data file: ann_counts.txt

data_processing:
library strategy: CLIP-seq
Custom processing scripts used at every stage except:
Mapping with STAR (2.5.4b) using all default parameters
After adapters and read-internal barcodes removed with custom scripts, cutadapt v. 2.0 was run to clean up any remaining adapter using the parameters -A CTATACTACCCTTCGCTTCACACACACAAG -a CTTGTGTGTGTGAAGCGAAGGGTAGTATAG
Genome_build: Human GRCh38 Gencode release 28 and a custom chromosome made of repetitive elements
Supplementary_files_format_and_content: Tab separated text file of raw reads per element. Elements beginning with '>' denote repetitive elements not in GRCh38. Introns and exons are listed separately.

source_name: HCT116_easyCLIP PCBP1-100Q

growth_protocol: 293Ts grown in DMEM 10% FBS, HCT116s grown in McCoy's 5A 10% FBS

extract_protocol:
easyCLIP, a flavor of CLIP-seq
easyCLIP, a flavor of CLIP-seq

treatment_protocol: UV cross-linked at 253 nm on plates.

tag: cell line background

tag: expression

value: FLAG-HA-HIS tagged ORF CRISPR targetted to AAVS1 safe harbor locus with Puro selection

tag: sample type

value: Library from RNA UV cross-linked to the indicated protein


title: LNCaP: MYC_1 DMSO

data_processing:
The raw reads were mapped with novoalign  to the human reference genome (build hg19) with default parameters.  Only reads with q>20 and a maximum of 5 read duplicates per genomic location were allowed by filtering.
note that fils from input DNA from three biological replicates ChIP assay were "pooled" together using the cat command.
Peak detection (i.e., binding site detection)  was performed with MACS1.4 with default parameters using the input file as control in each peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: bwig files

value: anti-MYC AF3696 (R&D systems)

value: DMSO


title: LNCaP: IgG_1 DMSO

value: anti-IgG (scbt-816X)


title: LNCaP: O-GlcNac_1 DMSO

value: anti-RL2 #ab2739 (Abcam)


title: LNCaP: input_DNA_control DMSO

value: no antibody


title: LNCaP: MYC_3 DMSO

value: LNCaP


title: easyCLIP PCBP1-100Q Replicate 3 [Exp71_PCBP1-100Q_hpGTCGTC_AGT]

description:
Exp71_PCBP1-100Q_hpGTCGTC_AGT
processed data file: ann_counts.txt


title: LNCaP: O-GlcNac_2 DMSO


title: easyCLIP CELF1 Replicate 1 [Exp71_CELF1_hpGCGGAC_AGT]

description:
Exp71_CELF1_hpGCGGAC_AGT
processed data file: ann_counts.txt

source_name: HEK293T_easyCLIP CELF1

value: FLAH-HA-HIS tagged ORF expressed from pLEX with a uORF in front of CDS to lower expression levels


title: OSMI2_24h_Rep1


title: easyCLIP PCBP1-dKH Replicate 3 [Exp71_PCBP1-dKH_hpCTGATC_AGT]

description:
Exp71_PCBP1-dKH_hpCTGATC_AGT
processed data file: ann_counts.txt

source_name: HCT116_easyCLIP PCBP1-dKH


title: Doxycycline_4h_Rep2


title: easyCLIP PCBP1-dKH Replicate 1 [Exp61_PCBP1-dKH_hpATCGTG_AGT]

description:
Exp61_PCBP1-dKH_hpATCGTG_AGT
processed data file: ann_counts.txt


title: easyCLIP PCBP1-dKH Replicate 2 [Exp61_PCBP1-dKH_hpATCGTG_TCA]

description:
Exp61_PCBP1-dKH_hpATCGTG_TCA
processed data file: ann_counts.txt


title: easyCLIP PCBP1-100P Replicate 2 [Exp71_PCBP1-100P_hpCCACTC_TCA]

description:
Exp71_PCBP1-100P_hpCCACTC_TCA
processed data file: ann_counts.txt

source_name: HCT116_easyCLIP PCBP1-100P


title: easyCLIP HCT116 Replicate 2 [Exp61_HCT116_hpGTAGCC_TCA]

description:
Exp61_HCT116_hpGTAGCC_TCA
processed data file: ann_counts.txt

source_name: HCT116_easyCLIP HCT116

value: Unmodified cells, immunopurified with anti-HA but without epitope


title: LNCaP: MYC_2 DMSO


title: easyCLIP PCBP1-dKH Replicate 4 [Exp71_PCBP1-dKH_hpCTGATC_TCA]

description:
Exp71_PCBP1-dKH_hpCTGATC_TCA
processed data file: ann_counts.txt


title: easyCLIP PCBP1-100Q Replicate 2 [Exp61_PCBP1-100Q_hpAGCTAG_TCA]

description:
Exp61_PCBP1-100Q_hpAGCTAG_TCA
processed data file: ann_counts.txt


title: LNCaP: O-GlcNac_3 DMSO


title: easyCLIP PCBP1 Replicate 2 [Exp61_PCBP1_hpCGATTA_TCA]

description:
Exp61_PCBP1_hpCGATTA_TCA
processed data file: ann_counts.txt

source_name: HCT116_easyCLIP PCBP1


title: easyCLIP HCT116 Replicate 1 [Exp61_HCT116_hpGTAGCC_AGT]

description:
Exp61_HCT116_hpGTAGCC_AGT
processed data file: ann_counts.txt


title: easyCLIP PCBP1 Replicate 1 [Exp61_PCBP1_hpCGATTA_AGT]

description:
Exp61_PCBP1_hpCGATTA_AGT
processed data file: ann_counts.txt


title: easyCLIP Rbfox1 Replicate 2 [Exp73_Rbfox1_rbCTGATC_AGT]

description:
Exp73_Rbfox1_rbCTGATC_AGT
processed data file: ann_counts.txt

source_name: HEK293T_easyCLIP Rbfox1


title: easyCLIP PCBP1-100Q Replicate 1 [Exp61_PCBP1-100Q_hpAGCTAG_AGT]

description:
Exp61_PCBP1-100Q_hpAGCTAG_AGT
processed data file: ann_counts.txt


title: easyCLIP CELF1 Replicate 2 [Exp71_CELF1_hpGCGGAC_TCA]

description:
Exp71_CELF1_hpGCGGAC_TCA
processed data file: ann_counts.txt


title: easyCLIP Rbfox1 Replicate 3 [Exp73_Rbfox1_rbCTGATC_AAC]

description:
Exp73_Rbfox1_rbCTGATC_AAC
processed data file: ann_counts.txt


title: easyCLIP hnRNPD Replicate 2 [Exp73_hnRNPD_rbCGATTA_AGT]

description:
Exp73_hnRNPD_rbCGATTA_AGT
processed data file: ann_counts.txt

source_name: HEK293T_easyCLIP hnRNPD


title: easyCLIP hnRNPD Replicate 1 [Exp73_hnRNPD_rbCGATTA_TCA]

description:
Exp73_hnRNPD_rbCGATTA_TCA
processed data file: ann_counts.txt


title: easyCLIP PCBP1-100P Replicate 1 [Exp71_PCBP1-100P_hpCCACTC_AGT]

description:
Exp71_PCBP1-100P_hpCCACTC_AGT
processed data file: ann_counts.txt


title: easyCLIP UBA2 Replicate 3 [Exp33_UBA2_17TGAGTG_AGT]

description:
Exp33_UBA2_17TGAGTG_AGT
processed data file: ann_counts.txt

source_name: HEK293T_easyCLIP UBA2

value: FLAG-HA-HIS tagged ORF transiently expressed from pLEX vector 2 days without selection


title: OSA Subject before CPAP 5020b

description:
OSA Subject before CPAP
STUDY GROUP 2

tag: age

value: M


title: easyCLIP Rbfox2 Replicate 3 [Exp73_Rbfox2_rbAGCTAG_TCA]

description:
Exp73_Rbfox2_rbAGCTAG_TCA
processed data file: ann_counts.txt

source_name: HEK293T_easyCLIP Rbfox2

value: Immunopurified endogenous protein (unmodified cells)


title: easyCLIP Rbfox2 Replicate 1 [Exp73_Rbfox2_rbGTCGTC_TCA]

description:
Exp73_Rbfox2_rbGTCGTC_TCA
processed data file: ann_counts.txt


title: easyCLIP Rbfox1 Replicate 1 [Exp73_Rbfox1_rbCTGATC_TCA]

description:
Exp73_Rbfox1_rbCTGATC_TCA
processed data file: ann_counts.txt


title: easyCLIP hnRNPD Replicate 3 [Exp73_hnRNPD_rbCGATTA_AAC]

description:
Exp73_hnRNPD_rbCGATTA_AAC
processed data file: ann_counts.txt


title: Normal Subject 25-S-N

description:
Normal Subject
STUDY GROUP 1

value: F


title: easyCLIP UBA2 Replicate 1 [Exp31_UBA2_05TGAGTG_AAC]

description:
Exp31_UBA2_05TGAGTG_AAC
processed data file: ann_counts.txt


title: easyCLIP TPGS2 Replicate 1 [Exp31_TPGS2_05CCACTC_AAC]

description:
Exp31_TPGS2_05CCACTC_AAC
processed data file: ann_counts.txt

source_name: HEK293T_easyCLIP TPGS2


title: easyCLIP UBA2 Replicate 2 [Exp32_UBA2_05TGAGTG_TCA]

description:
Exp32_UBA2_05TGAGTG_TCA
processed data file: ann_counts.txt


title: easyCLIP SF3B1 Replicate 2 [Exp28_SF3B1_17AGCTAG_TCA]

description:
Exp28_SF3B1_17AGCTAG_TCA
processed data file: ann_counts.txt

source_name: HEK293T_easyCLIP SF3B1

value: 3X FLAG tagged SF3B1 expressed from pLEX vector for 2 days without selection


title: easyCLIP SF3B1 Replicate 1 [Exp28_SF3B1_17AGCTAG_AGT]

description:
Exp28_SF3B1_17AGCTAG_AGT
processed data file: ann_counts.txt


title: easyCLIP ITPA Replicate 2 [Exp32_ITPA_05GCCTAA_TCA]

description:
Exp32_ITPA_05GCCTAA_TCA
processed data file: ann_counts.txt

source_name: HEK293T_easyCLIP ITPA


title: easyCLIP hnRNPC Replicate 2 [Exp16_hnRNPC_24TGAGTG_AAC]

description:
Exp16_hnRNPC_24TGAGTG_AAC
processed data file: ann_counts.txt

source_name: HEK293T_easyCLIP hnRNPC


title: easyCLIP ITPA Replicate 1 [Exp32_ITPA_05GCCTAA_AGT]

description:
Exp32_ITPA_05GCCTAA_AGT
processed data file: ann_counts.txt


title: easyCLIP FBL Replicate 1 [Exp15_FBL_24AGCTAG_TCA]

description:
Exp15_FBL_24AGCTAG_TCA
processed data file: ann_counts.txt

source_name: HEK293T_easyCLIP FBL


title: easyCLIP IDE Replicate 1 [Exp33_IDE_17GCTCAT_TCA]

description:
Exp33_IDE_17GCTCAT_TCA
processed data file: ann_counts.txt

source_name: HEK293T_easyCLIP IDE


title: easyCLIP ETS2 Replicate 1 [Exp33_ETS2_17TGCCGA_AGT]

description:
Exp33_ETS2_17TGCCGA_AGT
processed data file: ann_counts.txt

source_name: HEK293T_easyCLIP ETS2


title: easyCLIP hnRNPC Replicate 1 [Exp15_hnRNPC_24TGAGTG_TCA]

description:
Exp15_hnRNPC_24TGAGTG_TCA
processed data file: ann_counts.txt


title: easyCLIP Rbfox2 Replicate 2 [Exp73_Rbfox2_rbGTCGTC_AGT]

description:
Exp73_Rbfox2_rbGTCGTC_AGT
processed data file: ann_counts.txt


title: easyCLIP CHMP3 Replicate 2 [Exp33_CHMP3_17TGTTGG_TCA]

description:
Exp33_CHMP3_17TGTTGG_TCA
processed data file: ann_counts.txt

source_name: HEK293T_easyCLIP CHMP3


title: easyCLIP EPB41L5 Replicate 2 [Exp56_EPB41L5_tcAGCTAG_AGT]

description:
Exp56_EPB41L5_tcAGCTAG_AGT
processed data file: ann_counts.txt

source_name: HEK293T_easyCLIP EPB41L5


title: easyCLIP CCIN Replicate 2 [Exp56_CCIN_tcCTGATC_AGT]

description:
Exp56_CCIN_tcCTGATC_AGT
processed data file: ann_counts.txt

source_name: HEK293T_easyCLIP CCIN


title: easyCLIP CHMP3 Replicate 1 [Exp33_CHMP3_17TGTTGG_AGT]

description:
Exp33_CHMP3_17TGTTGG_AGT
processed data file: ann_counts.txt


title: easyCLIP DCTN6 Replicate 1 [Exp33_DCTN6_17GCTGTA_TCA]

description:
Exp33_DCTN6_17GCTGTA_TCA
processed data file: ann_counts.txt

source_name: HEK293T_easyCLIP DCTN6


title: easyCLIP EPB41L5 Replicate 1 [Exp56_EPB41L5_tcAGCTAG_TCA]

description:
Exp56_EPB41L5_tcAGCTAG_TCA
processed data file: ann_counts.txt


title: easyCLIP CDK4 Replicate 2 [Exp32_CDK4_05GCCATG_TCA]

description:
Exp32_CDK4_05GCCATG_TCA
processed data file: ann_counts.txt

source_name: HEK293T_easyCLIP CDK4


title: easyCLIP TPGS2 Replicate 2 [Exp31_TPGS2_05CCACTC_CAG]

description:
Exp31_TPGS2_05CCACTC_CAG
processed data file: ann_counts.txt


title: easyCLIP FBL Replicate 2 [Exp15_FBL_24AGCTAG_AGT]

description:
Exp15_FBL_24AGCTAG_AGT
processed data file: ann_counts.txt


title: easyCLIP ETS2 Replicate 2 [Exp33_ETS2_17TGCCGA_TCA]

description:
Exp33_ETS2_17TGCCGA_TCA
processed data file: ann_counts.txt


title: 13-Baloh-7505_S3

status: Public on Apr 03 2019

first: Shaughn

last: Bell

address: 8700 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

data_processing:
fastq reads were aligned to the mouse genome (mm10) with the Tophat app v1.0.0 on Illumina Basespace using default parameters
bam files were annotated using Partek software v7.17.0918 to generate RPKM numbers for each Refseq annotated gene
Genome_build: mm10
Supplementary_files_format_and_content: tab-deliminated text file containing RPKM values for each sample

source_name: spinal cord

growth_protocol: Mouse lumbar spinal cords were collected at 10 months

extract_protocol:
The lumbar regions of the spinal cords were dissected away from the rest of the spinal cord and flash frozen on dry ice.  RNA was harvested using standard Trizol protocol.  Total RNA was isolated using the PureLink RNA Mini Kit (Catalog # 12183018A), and RNA integrity was determined using the Agilent 2100 Bioanalyzer.  2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were constructed and indexed in parallel using the Illumina TruSeq Stranded mRNA Library Prep Kit v2 (standard protocol).  Library integrities were determined using the Agilent 2100 Bioanalyzer, quantified using Qubit fluorometric quantitation, and pooled for sequencing.

tag: strain

value: lumbar spinal cord

tag: genotype


title: 05-Baloh-7498_S8

value: nTg


title: 04-Baloh-7496_S6


title: 16-Baloh-7478_S9


title: 07-Baloh-7399_S13


title: 12-Baloh-7502_S4


title: 18-Baloh-7501_S5


title: 06-Baloh-7438_S10


title: 14-Baloh-7507_S12


title: 15-Baloh-7398_S2


title: 19-Baloh-7503_S1


title: easyCLIP CDK4 Replicate 1 [Exp31_CDK4_05GCCATG_AAC]

description:
Exp31_CDK4_05GCCATG_AAC
processed data file: ann_counts.txt


title: Human AM from ARDS day 8 [AM_B3_32]

status: Public on Mar 31 2019

hyb_protocol: Samples were hybridized to the Illumina HumanRef-8 BeadChip v3.

scan_protocol: Illumina iScan system.

data_processing: Microarray data was assessed for quality, followed by variance stabilization and quantile normalization of log-transformed values using the Bioconductor package "lumi." The normalized intensities were converted into natural scale.

source_name: Human alveolar macrophage

label_protocol: High quality RNA samples were converted to cDNA and biotin-labeled. MessageAmp II-96 Kit, Version C amplification Kit (Applied Biosciences, Foster City, CA).

growth_protocol: Human bronchoalveolar lavage fluid (BALF) was collected from ARDS patients and AMs were isolated by antibody-based negative selection via magnetic autoMacs columns (Miltenyi).

extract_protocol: Total RNA was isolated by ABI Prism 6100 Nucleic Acid PrepStation (Applied Biosciences, Foster City, CA).

tag: disease state

value: Acute respiratory distress syndrome

tag: patient identification number

value: ARDS patient number 32

tag: gender

value: Female

value: alveolar macrophages

tag: time point

value: Day 8

tag: ventilator-free days (vfd)


title: Human AM from ARDS day 8 [AM_B3_42]

value: ARDS patient number 42

tag: cell type


title: Human AM from ARDS day 8 [AM_B3_44]

value: ARDS patient number 44


title: Human AM from ARDS day 8 [AM_B3_28]

value: ARDS patient number 28

value: Male


title: Human AM from ARDS day 8 [AM_B3_8]

value: ARDS patient number 8


title: Human AM from ARDS day 8 [AM_B3_22]

value: ARDS patient number 22


title: Human AM from ARDS day 8 [AM_B3_10]

value: ARDS patient number 10


title: Human AM from ARDS day 8 [AM_B3_1]

value: ARDS patient number 1


title: Human AM from ARDS day 8 [AM_B3_40]

value: ARDS patient number 40


title: Human AM from ARDS day 8 [AM_B3_43]

value: ARDS patient number 43


title: Human AM from ARDS day 4 [AM_B2_8]

value: Day 4


title: Human AM from ARDS day 8 [AM_B3_3]

value: ARDS patient number 3


title: Human AM from ARDS day 8 [AM_B3_5]

value: Acute respiratory distress syndrome

value: ARDS patient number 5


title: Human AM from ARDS day 8 [AM_B3_23]

value: ARDS patient number 23

value: Female


title: Human AM from ARDS day 4 [AM_B2_9]

value: ARDS patient number 9

value: alveolar macrophages


title: Human AM from ARDS day 4 [AM_B2_45]

value: ARDS patient number 45


title: Human AM from ARDS day 4 [AM_B2_44]

value: ARDS patient number 44


title: Human AM from ARDS day 4 [AM_B2_5]

value: Male


title: Human AM from ARDS day 4 [AM_B2_48]

value: ARDS patient number 48


title: Human AM from ARDS day 4 [AM_B2_32]

value: ARDS patient number 32


title: Human AM from ARDS day 8 [AM_B3_19]

value: ARDS patient number 19

value: Day 8


title: Human AM from ARDS day 4 [AM_B2_36]

value: ARDS patient number 36


title: Human AM from ARDS day 4 [AM_B2_43]

value: ARDS patient number 43


title: easyCLIP CCIN Replicate 1 [Exp56_CCIN_tcCTGATC_TCA]

description:
Exp56_CCIN_tcCTGATC_TCA
processed data file: ann_counts.txt

value: FLAG-HA-HIS tagged ORF transiently expressed from pLEX vector 2 days without selection

value: Library from RNA UV cross-linked to the indicated protein


title: Human AM from ARDS day 8 [AM_B3_36]

value: Acute respiratory distress syndrome


title: Human AM from ARDS day 4 [AM_B2_42]

value: ARDS patient number 42

value: Day 4


title: Human AM from ARDS day 4 [AM_B2_40]

value: ARDS patient number 40


title: Human AM from ARDS day 4 [AM_B2_39]

value: ARDS patient number 39


title: Human AM from ARDS day 4 [AM_B2_47]

value: ARDS patient number 47

value: alveolar macrophages


title: Human AM from ARDS day 4 [AM_B2_15]

value: ARDS patient number 15


title: Human AM from ARDS day 4 [AM_B2_3]

value: ARDS patient number 3

value: Male


title: Human AM from ARDS day 4 [AM_B2_23]

value: ARDS patient number 23

value: Female


title: Human AM from ARDS day 8 [AM_B3_46]

value: ARDS patient number 46

value: Day 8


title: Human AM from ARDS day 1 [AM_B1_43]

value: ARDS patient number 43

value: Day 1


title: Human AM from ARDS day 1 [AM_B1_47]


title: Human AM from ARDS day 4 [AM_B2_11]

value: ARDS patient number 11


title: Human AM from ARDS day 4 [AM_B2_14]

value: Acute respiratory distress syndrome

value: ARDS patient number 14


title: Human AM from ARDS day 1 [AM_B1_8]

value: ARDS patient number 8


title: Human AM from ARDS day 4 [AM_B2_24]

value: ARDS patient number 24

value: Day 4


title: Human AM from ARDS day 1 [AM_B1_9]

value: ARDS patient number 9


title: Human AM from ARDS day 1 [AM_B1_42]

value: ARDS patient number 42

value: alveolar macrophages


title: Human AM from ARDS day 1 [AM_B1_34]

value: ARDS patient number 34


title: Human AM from ARDS day 1 [AM_B1_44]

value: ARDS patient number 44


title: Human AM from ARDS day 4 [AM_B2_10]

value: ARDS patient number 10


title: Human AM from ARDS day 4 [AM_B2_19]

value: ARDS patient number 19

value: Male


title: Human AM from ARDS day 1 [AM_B1_49]

value: ARDS patient number 49


title: Human AM from ARDS day 1 [AM_B1_40]

value: ARDS patient number 40


title: Human AM from ARDS day 1 [AM_B1_41]

value: ARDS patient number 41

value: Female

value: Day 1


title: Human AM from ARDS day 1 [AM_B1_37]

value: Acute respiratory distress syndrome

value: ARDS patient number 37


title: Human AM from ARDS day 1 [AM_B1_3]

value: ARDS patient number 3


title: Human AM from ARDS day 1 [AM_B1_39]

value: ARDS patient number 39


title: Human AM from ARDS day 1 [AM_B1_46]

value: ARDS patient number 46


title: Human AM from ARDS day 1 [AM_B1_33]

value: ARDS patient number 33


title: Human AM from ARDS day 4 [AM_B2_28]

value: ARDS patient number 28

value: alveolar macrophages

value: Day 4


title: Human AM from ARDS day 1 [AM_B1_36]

value: ARDS patient number 36


title: Human AM from ARDS day 1 [AM_B1_28]


title: Human AM from ARDS day 1 [AM_B1_32]

value: ARDS patient number 32


title: Human AM from ARDS day 1 [AM_B1_38]

value: ARDS patient number 38

value: Male


title: 5456_NAcc_pos (ATAC-Seq)

status: Public on Dec 17 2018

city: Baltimore

first: Andrew

middle: P.

last: Feinberg

state: MD

address: 855 N. Wolfe St

institute: Johns Hopkins University School of Medicine

data_processing:
We trimmed reads of their adapter sequences using trimadap (v0.1) with the following parameters: trimadap-mt -3 CTGTCTCTTATACACATCTCCGAGCCCACGAGA ${READ1}; trimadap-mt -3 CTGTCTCTTATACACATCTGACGCTGCCGACGA ${READ2}. We then aligned these trimmed reads to the hg19 build of the human genome (including autosomes, sex chromosomes, mitochondrial sequence, unplaced sequence, and unlocalized sequence) using Bowtie214 (v2.2.5) with alignment parameters: bowtie2 -X 2000 --local --dovetail. Potential PCR duplicate reads were marked using MarkDuplicates from the Picard library (v2.2.1).
Peaks were called using MACS (v2.1.0) on a metasample formed by combining all non-duplicate-marked reads with a mapping quality > 30 from the 22 samples: macs2 callpeaks --nomodel --nolambda --call-summits -t ${BAMS[@]}. We excluded those peaks overlapping the ENCODE mappability consensus blacklist regions (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/) and the blacklist for ATAC-seq created by Buenrostro et al. (https://sites.google.com/site/atacseqpublic/atac-seq-analysis-methods/mitochondrialblacklists-1). We extended +/- 250 bp from the summit of peak and merged overlapping peaks to form our initial set of peaks.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: Matrix of read count data for each genome location for all samples.

source_name: NeuN positive nuclei sorted from nucleus accumbens (NAcc)

extract_protocol: Nextera DNA library prep kit (cat #:FC-121-1031, Illumina)

treatment_protocol: ATAC-seq was performed as described in Buenrostro et al. 2015 using 100,000 neuronal and non-neuronal nuclei isolated from nucleus accumbens and prefrontal cortex (BA9) tissues (for samples with "_pos" or "_neg" at end of sample ID) and sorted via FACS based on NeuN staining as in Montano et al. 2013.

value: NeuN pos

value: nucleus accumbens (NAcc)

tag: individual id


title: Human AM from ARDS day 1 [AM_B1_29]

value: ARDS patient number 29


title: Human AM from ARDS day 1 [AM_B1_23]

value: ARDS patient number 23

value: Female

value: Day 1


title: Human AM from ARDS day 1 [AM_B1_18]

value: Acute respiratory distress syndrome

value: ARDS patient number 18


title: Human AM from ARDS day 1 [AM_B1_25]

value: ARDS patient number 25


title: Human AM from ARDS day 1 [AM_B1_15]

value: ARDS patient number 15


title: Human AM from ARDS day 1 [AM_B1_11]

value: ARDS patient number 11


title: Human AM from ARDS day 1 [AM_B1_10]

value: ARDS patient number 10

value: alveolar macrophages


title: Human AM from ARDS day 1 [AM_B1_16]

value: ARDS patient number 16


title: Human AM from ARDS day 1 [AM_B1_24]

value: ARDS patient number 24


title: Human AM from ARDS day 1 [AM_B1_19]

value: ARDS patient number 19


title: Human AM from ARDS day 1 [AM_B1_1]

value: ARDS patient number 1

value: Male


title: MDM from CF patient 5 stimulated with apoptotic PMNs

status: Public on Sep 30 2018

description: CF_Patient 5_apop PMN

hyb_protocol: Hybridization to microarrays were performed per Illumina protocols.

scan_protocol: Illumina iScan system

data_processing: Microarray data was assessed for quality, followed by variance stabilization and quantile normalization using the Bioconductor package lumi.

source_name: Human monoctye-derived macrophage

label_protocol: High quality RNA samples were converted to cDNA and biotin-labaled

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated from whole blood by density gradient centrifugation using Lymphoprep (StemCell Technologies, Vancouver, BC, Canada), followed by three PBS washes and removal of erythrocytes with RBC Lysis Buffer (eBioscience, San Diego, CA). PBMC were immediately enriched for monocytes using the Dynabeads Untouched Human Monocytes Kit (Life Technologies, Carlsbad, CA), per manufacturer instructions. Monocyte enrichment was confirmed by flow cytometry, using CD14 FITC antibody (eBioscience, San Diego, CA). Monocytes were plated at a density of 1.1x103 cells/mm2 and differentiated for 7 days in RPMI 1640 supplemented with 10% FBS, 2mM L-glutamine, 1mM sodium pyruvate, 0.15% w/v sodium bicarbonate, 10mM HEPES, 1% penicillin-streptomycin, and 100 ng/ml human M-CSF (PeproTech, Rocky Hill, NJ) to generate monocyte-derived macrophages (MDMs). After 7 days of differentiation, non-adherent cells were removed, and remaining MDMs were considered to be in a non-polarized, M0 state.

extract_protocol: Total RNA from macrophages was isolated and purified using the RNeasy Micro Kit (Qiagen, Valencia, CA).

treatment_protocol: Initially, M1 polarization was achieved by treating M0 MDM with culture media containing E. Coli O111:B4 LPS (100 ng/ml; Sigma-Aldrich, St. Louis, MO) for 24 h, at which LPS media was aspirated, and MDMs were rinsed three times with PBS to remove residual LPS. M1 MDMs were then cultured in MDM media alone (no treatment) or supplemented with IL-4 (10 ng/ml), IL-10 (50 ng/ml), methylprednisolone (100 nM), azithromycin (30μm), or apoptotic PMNs (5:1) for 24 h to repolarize MDMs towards an M2 state.

value: CF patient 5


title: MDM from CF patient 1 stimulated with azithromycin

description: CF_Patient 1_AZM

value: CF patient 1


title: MDM from CF patient 1 stimulated with methylprednisolone

description: CF_Patient 1_MP


title: MDM from CF patient 3 stimulated with methylprednisolone

description: CF_Patient 3_MP

value: CF patient 3


title: MDM from CF patient 5 stimulated with azithromycin

description: CF_Patient 5_AZM


title: MDM from CF patient 2 stimulated with apoptotic PMNs

description: CF_Patient 2_apop PMN

value: CF patient 2


title: MDM from CF patient 3 stimulated with azithromycin

description: CF_Patient 3_AZM

value: Female


title: MDM from CF patient 1 stimulated with apoptotic PMNs

description: CF_Patient 1_apop PMN


title: MDM from CF patient 3 stimulated with apoptotic PMNs

description: CF_Patient 3_apop PMN


title: MDM from CF patient 5 stimulated with methylprednisolone

description: CF_Patient 5_MP


title: MDM from CF patient 4 stimulated with azithromycin

description: CF_Patient 4_AZM

value: CF patient 4


title: MDM from CF patient 6 stimulated with azithromycin

description: CF_Patient 6_AZM

value: CF patient 6


title: MDM from CF patient 6 stimulated with IL10

description: CF_Patient 6_IL10


title: MDM from CF patient 2 stimulated with IL10

description: CF_Patient 2_IL10


title: MDM from CF patient 2 stimulated with azithromycin

description: CF_Patient 2_AZM


title: MDM from CF patient 3 stimulated with IL4

description: CF_Patient 3_IL4


title: MDM from CF patient 6 stimulated with methylprednisolone

description: CF_Patient 6_MP


title: MDM from CF patient 5 stimulated with IL10

description: CF_Patient 5_IL10


title: MDM from CF patient 3 stimulated with IL10

description: CF_Patient 3_IL10


title: MDM from CF patient 6 stimulated with IL4

description: CF_Patient 6_IL4


title: MDM from CF patient 4 stimulated with methylprednisolone

description: CF_Patient 4_MP


title: MDM from CF patient 5 stimulated with IL4

description: CF_Patient 5_IL4


title: MDM from CF patient 1 stimulated with IL10

description: CF_Patient 1_IL10


title: MDM from CF patient 4 stimulated with apoptotic PMNs

description: CF_Patient 4_apop PMN


title: MDM from CF patient 2 stimulated with IL4

description: CF_Patient 2_IL4


title: MDM from CF patient 2 stimulated with methylprednisolone

description: CF_Patient 2_MP


title: MDM from CF patient 6 stimulated with apoptotic PMNs

description: CF_Patient 6_apop PMN


title: MDM from CF patient 4 stimulated with IL10

description: CF_Patient 4_IL10


title: MDM from CF patient 1 stimulated with IL4

description: CF_Patient 1_IL4


title: MDM from CF patient 4 stimulated with IL4

description: CF_Patient 4_IL4


title: MDM from CF patient 4 cultured in media alone

description: CF_Patient 4_No Tx


title: MDM from CF patient 1 cultured in media alone

description: CF_Patient 1_No Tx


title: MDM from CF patient 2 cultured in media alone

description: CF_Patient 2_No Tx


title: MDM from CF patient 5 cultured in media alone

description: CF_Patient 5_No Tx


title: MDM from non CF subject 4 stimulated with apoptotic PMNs

description: nonCF_Subject 4_apop PMN

value: Non CF subject 4


title: MDM from non CF subject 5 stimulated with apoptotic PMNs

description: nonCF_Subject 5_apop PMN

value: Non CF subject 5


title: MDM from non CF subject 3 stimulated with apoptotic PMNs

description: nonCF_Subject 3_apop PMN

value: Non CF subject 3


title: MDM from non CF subject 5 stimulated with azithromycin

description: nonCF_Subject 5_AZM


title: MDM from non CF subject 3 stimulated with methylprednisolone

description: nonCF_Subject 3_MP


title: MDM from non CF subject 1 stimulated with methylprednisolone

description: nonCF_Subject 1_MP

value: Non CF subject 1


title: MDM from non CF subject 2 stimulated with azithromycin

description: nonCF_Subject 2_AZM

value: Non CF subject 2


title: MDM from non CF subject 6 stimulated with methylprednisolone

description: nonCF_Subject 6_MP

value: Non CF subject 6


title: MDM from non CF subject 4 stimulated with methylprednisolone

description: nonCF_Subject 4_MP


title: MDM from non CF subject 5 stimulated with IL10

description: nonCF_Subject 5_IL10


title: MDM from non CF subject 5 stimulated with methylprednisolone

description: nonCF_Subject 5_MP


title: MDM from non CF subject 1 stimulated with apoptotic PMNs

description: nonCF_Subject 1_apop PMN


title: MDM from non CF subject 2 stimulated with methylprednisolone

description: nonCF_Subject 2_MP


title: MDM from CF patient 6 cultured in media alone

description: CF_Patient 6_No Tx


title: MDM from non CF subject 3 stimulated with IL10

description: nonCF_Subject 3_IL10


title: MDM from non CF subject 3 stimulated with azithromycin

description: nonCF_Subject 3_AZM


title: MDM from non CF subject 1 stimulated with azithromycin

description: nonCF_Subject 1_AZM


title: MDM from non CF subject 4 stimulated with IL10

description: nonCF_Subject 4_IL10


title: MDM from non CF subject 6 stimulated with IL10

description: nonCF_Subject 6_IL10


title: MDM from non CF subject 4 stimulated with azithromycin

description: nonCF_Subject 4_AZM


title: MDM from non CF subject 6 stimulated with azithromycin

description: nonCF_Subject 6_AZM


title: MDM from non CF subject 2 stimulated with apoptotic PMNs

description: nonCF_Subject 2_apop PMN


title: MDM from non CF subject 2 stimulated with IL10

description: nonCF_Subject 2_IL10


title: MDM from non CF subject 6 stimulated with apoptotic PMNs

description: nonCF_Subject 6_apop PMN


title: MDM from non CF subject 5 stimulated with IL4

description: nonCF_Subject 5_IL4


title: MDM from non CF subject 1 stimulated with IL10

description: nonCF_Subject 1_IL10


title: MDM from non CF subject 6 stimulated with IL4

description: nonCF_Subject 6_IL4


title: MDM from non CF subject 4 stimulated with IL4

description: nonCF_Subject 4_IL4


title: H1_day6_INN_1 (RNA-Seq)

status: Public on Aug 28 2018

city: Clemson

first: Qing

last: Liu

state: SC

address: Jordan Hall

department: Biological Sciences

institute: Clemson University

description: biological replicate 1

data_processing:
RNA-seq fastq data were aligned with Tophat (version 2.0.9) to GRCh39/hg19 Homo sapiens reference genome from the UCSC Genome Browser.
The human gene symbols and their raw counts were calculated using HTSeq (version 0.6.1p1) package in Python with GRCh39/hg19 Homo sapiens gtf file.
Differential gene-expression analysis was performed using edgeR package in R, and the normalization was performed using a trimmed mean of M-values (TMM)method.
Genome_build: hg19
Supplementary_files_format_and_content: fastq

source_name: hESC-derived cells

growth_protocol: Both hESCs and hiPSCs  were grown in Matrigel (Corning)-coated 12-well plates with Essential 8™ Medium (Thermo Fisher Scientific).

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Qiagen), and RNA was then subjected to DNase I digestion and purified using a RNeasy Mini spin column (Qiagen) according to the manufacturer’s instructions.
RNA-seq libraries were constructed using ScriptSeq™ v2 RNA-Seq Library Preparation kit (Epicentre Biotechnologies) according to the manufacturer’s instructions. . All RNA-seq libraries were sequenced by HiSeq 4000 sequencers (Illumina) with 2 x 101 cycles.

treatment_protocol: The cardiomyocyte differentiation was initiated using a monolayer differentiation method with PSC Cardiomyocyte Differentiation kit (Thermo Fisher Scientific).

value: hESC-derived cells

tag: cell line

tag: treatment

value: INN-treatment

tag: differentiation time (days)


title: H1_day6_INN_2 (RNA-Seq)

description: biological replicate 2


title: MDM from non CF subject 2 stimulated with IL4

description: nonCF_Subject 2_IL4


title: MDM from non CF subject 3 stimulated with IL4

description: nonCF_Subject 3_IL4


title: MDM from non CF subject 1 stimulated with IL4

description: nonCF_Subject 1_IL4


title: MDM from non CF subject 6 cultured in media alone

description: nonCF_Subject 6_No Tx


title: MDM from non CF subject 5 cultured in media alone

description: nonCF_Subject 5_No Tx


title: H1_day2_INN_2 (RNA-Seq)

description: biological replicate 2


title: H1_day0_INN_2 (RNA-Seq)

description: biological replicate 2

source_name: hESC

value: hESC


title: H1_day6_C_2 (RNA-Seq)

description: biological replicate 2

value: Control


title: H1_day2_C_2 (RNA-Seq)

description: biological replicate 2


title: H1_day0_INN_1 (RNA-Seq)

description: biological replicate 1


title: H1_day6_C_1 (RNA-Seq)

description: biological replicate 1


title: H1_day2_INN_1 (RNA-Seq)

description: biological replicate 1


title: MDM from non CF subject 3 cultured in media alone

description: nonCF_Subject 3_No Tx


title: H1_day0_C_2 (RNA-Seq)

description: biological replicate 2


title: C15_day2_INN_1 (RNA-Seq)

description: biological replicate 1

source_name: hiPSC-derived cells

value: hiPSC-derived cells


title: H1_day0_C_1 (RNA-Seq)

description: biological replicate 1


title: C15_day6_INN_2 (RNA-Seq)

description: biological replicate 2


title: H1_day2_C_1 (RNA-Seq)

description: biological replicate 1


title: C15_day2_INN_2 (RNA-Seq)

description: biological replicate 2


title: C15_day0_INN_2 (RNA-Seq)

description: biological replicate 2

source_name: hiPSC

value: hiPS cell


title: MDM from non CF subject 2 cultured in media alone

description: nonCF_Subject 2_No Tx

value: Male


title: C15_day6_C_2 (RNA-Seq)

description: biological replicate 2


title: C15_day0_INN_1 (RNA-Seq)

description: biological replicate 1


title: MDM from non CF subject 4 cultured in media alone

description: nonCF_Subject 4_No Tx


title: C15_day6_INN_1 (RNA-Seq)

description: biological replicate 1


title: MDM from non CF subject 1 cultured in media alone

description: nonCF_Subject 1_No Tx


title: C15_day6_C_1 (RNA-Seq)

description: biological replicate 1


title: C15_day2_C_2 (RNA-Seq)

description: biological replicate 2


title: C15_day0_C_2 (RNA-Seq)

description: biological replicate 2


title: C15_day2_C_1 (RNA-Seq)

description: biological replicate 1


title: H1_day6_INN_2 (ATAC-Seq)

description: biological replicate 2

data_processing:
The raw data was then trimmed to remove the adapter sequences (CTGTCTCTTATACACATCT) with in house script.  The trimmed files were mapped to the human genome (hg19 GRCh37) using Bowtie2 (2.1.0) with default parameters.  Read pairs, which aligned concordantly to the genome and had a mapping quality greater than 10, were kept for following analysis. Read pairs mapped to mitochondria DNA were discarded. Redundancy read pairs from PCR amplification were also removed afterward using Picard tools (version 1.79). The finally filtered bam files were converted into normalized BigWig files using Bedtools (2.25.0) for visualization of the peaks.
Open accessible-regions for each library were defined by the peaks called by MACS2 (2.1.0) with the parameters “-g hs --nomodel --shift 0 –q 0.01”.  Peaks located at blacklist genomics regions were removed using bedtools (2.25.0).
Genome_build: hg19
Supplementary_files_format_and_content: bed/peak

growth_protocol: Both hESCs and hiPSCs were grown in Matrigel (Corning)-coated 12-well plates with Essential 8™ Medium (Thermo Fisher Scientific).

extract_protocol:
About 50,000 cells were collected and pelleted by centrifugation for 15 min at 500 g and 4°C. Cell pellets were washed once with ice-cold 1x PBS and then pelleted again by centrifugation at the previous settings. Cell pellets were re-suspended in 25 μl of ice-cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630), and nuclei were pelleted by centrifugation for 30 min at 500g, 4°C
The nuclei were re-suspended in 50 μl reaction buffer (2 μl of Tn5 transposase and 12.5 μl of TD buffer from a Nextera DNA Library Prep Kit from Illumina, and 22.5 μl nuclease-free H2O). The reaction was incubated at 37°C for 30 min, and subsequently the reaction mixture was purified using MinElute PCR Purification Kit (Qiagen). The purified transposed DNA was amplified with NEBNext High-Fidelity 2 X PCR Master Mix (New England Biolabs) and custom-designed primers with barcodes (Buenrostro et al. 2013). Gel electrophoresis was used to remove primer dimers from the PCR products with 2% E-Gel EX Agarose Gels (Thermo Fisher Scientific), and then the PCR products were purified using QIAquick PCR Purification Kit (Qiagen). DNA concentration was measured with a Qubit Fluorometer (Thermo Fisher Scientific) and library sizes were determined using Agilent High Sensitivity DNA kit on Agilent 2100 Bioanalyzer. The ATAC-seq libraries were sequenced with a HiSeq 4000 sequencer (Illumina) with 2 X101 cycles.

treatment_protocol: Cardiomyocyte differentiation was performed using a monolayer differentiation method with a PSC Cardiomyocyte Differentiation kit (Thermo Fisher Scientific) according to the instruction, and the cells were exposed to 25 nM of isotretinoin (0.1% DMSO) through the differentiation process. At days 0, 2, and 6 during the differentiation period (before the medium-change on that day), cells were collected using Accutase (Thermo Fisher Scientific).


title: H1_day6_INN_1 (ATAC-Seq)

description: biological replicate 1


title: H1_day2_INN_2 (ATAC-Seq)

description: biological replicate 2


title: H1_day2_INN_1 (ATAC-Seq)

description: biological replicate 1


title: H1_day0_INN_1 (ATAC-Seq)

description: biological replicate 1


title: H1_day2_C_2 (ATAC-Seq)

description: biological replicate 2


title: H1_day6_C_2 (ATAC-Seq)

description: biological replicate 2


title: H1_day0_INN_2 (ATAC-Seq)

description: biological replicate 2


title: C15_day2_C_1 (ATAC-Seq)

description: biological replicate 1


title: C15_day2_C_2 (ATAC-Seq)

description: biological replicate 2


title: H1_day0_C_1 (ATAC-Seq)

description: biological replicate 1


title: H1_day0_C_2 (ATAC-Seq)

description: biological replicate 2


title: C15_day2_INN_2 (ATAC-Seq)

description: biological replicate 2


title: C15_day0_INN_1 (ATAC-Seq)

description: biological replicate 1


title: C15_day0_INN_2 (ATAC-Seq)

description: biological replicate 2


title: C15_day6_INN_1 (ATAC-Seq)

description: biological replicate 1


title: H1_day2_C_1 (ATAC-Seq)

description: biological replicate 1


title: C15_day6_INN_2 (ATAC-Seq)

description: biological replicate 2


title: C15_day0_C_1 (ATAC-Seq)

description: biological replicate 1


title: H1_day6_C_1 (ATAC-Seq)

description: biological replicate 1


title: C15_day2_INN_1 (ATAC-Seq)

description: biological replicate 1


title: C15_day6_C_1 (ATAC-Seq)

description: biological replicate 1


title: C15_day6_C_2 (ATAC-Seq)

description: biological replicate 2


title: C15_day0_C_1 (RNA-Seq)

description: biological replicate 1


title: m6A-IP from BrU-labeled non-fragmented nascent RNA; 30 min chase; supernatant rep A

status: Public on Jun 19 2018

city: Heraklion

first: Evgenia

last: Ntini

address: Nik. Plastira 100

country: Greece

institute: IMBB-FORTH

description:
m6A-depleted nascent RNA
m6A-IP was performed subsequently to the BrU-IP (from the purified BrU-labeled—and—30 min chased, nascent RNA). This sample is the m6A-IP supernatant.

data_processing:
Reads were mapped to GRCh37/hg19 using STAR version 2.4.2a
Only uniquely aligned reads were kept.
bigWig files were generated with WigToBigWig from UCSC utilities
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bigWig

growth_protocol: HEK293T were grown in DMEM supplemented with 10% FBS

extract_protocol:
Trizol
Libraries were prepared according to TruSeq Stranded mRNA Library Preparation Kit instructions.

treatment_protocol: Cells were incubated with 2 mM bromouridine for 15 min and chased with 20 mM uridine for 0 min or 30 min.

tag: bru labeling time

tag: uridine chase time

tag: anti-brdu

value: BrU-IP (purified nascent RNA non-fragmented)

value: m6A-IP supernatant

tag: rip antibody (anti-brdu)

value: anti-BrdU (mouse monoclonal from BD Pharmigen)

tag: rip antibody (anti-m6a)

value: anti-m6A (rabbit polyclonal from Synaptic Systems)

tag: rip antibody (anti-brdu) vendor

value: BD Pharmigen

tag: rip antibody (anti-m6a) vendor

value: Synaptic Systems

tag: rip antibody (anti-brdu) cat. nr.

tag: rip antibody (anti-m6a) cat. nr.

tag: rip antibody (anti-brdu) lot #

tag: rip antibody (anti-m6a) lot #


title: m6A-IP from BrU-labeled non-fragmented nascent RNA; 30 min chase; supernatant rep B


title: C15_day0_C_2 (ATAC-Seq)

description: biological replicate 2


title: MDM from CF patient 3 cultured in media alone

description: CF_Patient 3_No Tx

tag: patient identification number

value: CF patient 3

tag: age

tag: gender

value: Female


title: Hep3B_Mock-2

status: Public on Jun 30 2018

hyb_protocol: This protocol uses directly isolated RNA without RNA target amplification, and ultimately reflects the cellular microRNA molar ratio, thus providing for the reliability of hybridization signals. The streptavidin conjugated dye stain (SA-S Dye) and the staining buffer (Buffer S) reagents are also included in this kit. Their preparation and use in the post-hybridization staining procedure is described below in the hybridization assay section.

scan_protocol: The SA-S dye stain signal can be detected using the GenePix 4000B scanner 635 nm wavelength (Cy5) channel.

data_processing: The arrays with hybridized targets were scanned using an Axon scanner and the scanned images were analyzed using GenePix Pro 5.0 software (Axon Instruments) and spots of poor quality determined by visual inspection were also removed from further analysis. The resulting data, the average of 3 mean fluorescence signal intensities for each probe, collected from each array was submitted to the GenePlex 3.0 (Istech Inc. Seoul, Korea) database. Data were normalized using the method of quantile normalization and class-specific filtering.

source_name: human HCC cell line

label_protocol: This procedure is used to attach a biotin label to the 5' ends of RNA molecules.Total 10ug amount of RNA used.

growth_protocol: Cell line was grown in RPMI1640 or DMEM medium supplemented with 10 % fetal bovine serum (FBS; Sigma, St Louis, MO), 100 units/ml of penicillin and streptomycin. Cultures were incubated at 37 °C in a humidified incubator at 5% CO2.

extract_protocol: For each the experimental conditions, total RNA was extracted from three independent sets of the corresponding cell lines using TRIzol Reagent (Invitrogen), followed by clean up on Ambion columns (Illumina Total-Prep RNA Amplification Kit, Ambion). For each experimental condition, an RNA pool was then obtained by mixing equal quantities of total RNA from each of the three independent RNA extractions. RNA quality control was performed with Bio-Rad Experion.

treatment_protocol: The cells were harvested by Trypsin/EDTA, replated at 1.5 x 10^5 cells in a 60mm2 dish, and allowed to grow overnight at 37 °C in a humidified incubator at 5% CO2. After 16~18 hr of plating, the cells were tranfected with empty mock and pcDNA_HDAC6 in Opti-MEM (Invitrogen). Transfection was carried out using lipofectamine 2000 reagent (Invitrogen) according to the manufecturer's specifications. After 4~6 hr of transfection, the medium was replaced by new fresh RPMI 1640 medium supplemented with 10% FBS.

tag: cell line

tag: transfection

value: Mock


title: Hep3B_Mock-3


title: Hep3B_HDAC6-1


title: Hep3B_Mock-1


title: Hep3B_HDAC6-2


title: Hep3B_HDAC6-3


title: m6A-IP from BrU-labeled non-fragmented nascent RNA; 0 min; m6A-IP eluate rep B

description:
m6A-enriched nascent RNA
m6A-IP was performed subsequently to the BrU-IP (from the purified BrU-labeled, 0min chase, nascent RNA). This sample is the m6A-IP eluate.

value: BrU-IP (purified BrU-labeled nascent RNA, non-fragmented)

value: m6A-IP eluate


title: m6A-IP from BrU-labeled non-fragmented nascent RNA; 30 min chase; m6A-IP eluate rep B

description:
m6A-enriched nascent RNA
m6A-IP was performed subsequently to the BrU-IP (from the purified BrU-labeled—and—30 min chased, nascent RNA). This sample is the m6A-IP eluate.


title: BrU-labeled nascent RNA; non-fragmented; 30 min chase; Input rep B

description:
Nascent RNA (non-fragmented)
BrU-IP was performed from the 15min BrU-labeled—and—30 min chased total RNA. The BrU-IP eluate (purified nascent non-fragmented RNA) is the Input to the subsequent m6A-IP.


title: m6A-IP from BrU-labeled non-fragmented nascent RNA; 0 min; m6A-IP eluate rep A


title: m6A-IP from BrU-labeled non-fragmented nascent RNA; 30 min chase; m6A-IP eluate rep A