title: SK-N-BE-2C [43_total_run329_G2_JQ1]


title: SAMPLE 19 BE.BE

status: Public on Jan 01 2019

type: genomic

city: Seattle

first: Sean

last: Maden

state: WA

address: 1100 Fairview Ave N

department: Clinical Research

country: USA

institute: Fred Hutch

description: nondysplastic Barrett's sample from Barrett's patient

hyb_protocol: Illumina Infinium HD Methylation protocol

scan_protocol: Imaged with iScan+ using Methylation NXT scan setting

data_processing: GenomeStudio v2011.1 with Methylation Module v1.9.0

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Tissue core or slide

extract_protocol: DNA from formalin fixed paraffin-embedded (FFPE) cores or tissue sections

value: non-dysplastic

tag: age

tag: gender

value: male


title: SAMPLE 29 BE.BE

label_protocol: Illumina Infinium HD Methylation protocol


title: SK-N-BE-2C [42_total_run329_F12]

type: SRA

city: Ghent

first: Celine

last: Everaert

address: De Pintelaan 185

country: Belgium

institute: University Ghent

library_source: transcriptomic

data_processing:
Alligment with STAR v2.5.3 :STAR --runThreadN 10 --outFileNamePrefix outdir --readFilesIn sample.fastq --genomeDir star_index --sjdbGTFfile gtf_index --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --twopassMode Basic --outSAMmultNmax 1 --outSAMprimaryFlag AllBestScore --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0
Quantification with Kallisto v0.43.1. For polyA: kallisto quant -t 10 -i kallisto_index --single -l 200 -s 20 -o outdir sample.fastq; For total: kallisto quant -t 10 -i kallisto_index –rf-stranded --single -l 200 -s 20 -o outdir sample.fastq
Genome_build: hg38
Supplementary_files_format_and_content: abundance.tsv output for kallisto

molecule: total RNA

source_name: cell line

extract_protocol:
Cells were lysed and cDNA was synthesized according to the SMARTer single cell total RNA sequencing protocol on script hub (Fluidigm).
polyA+ RNA-seq libraries were generated using the SMART-seq ultra low input RNA kit for the Fluidigm C1 system. Total RNA-seq libraries were generated using a single cell adapted SMARTer stranded total RNA-seq v2 kit pico input mammalian protocol.

tag: treatment

value: vehicle

tag: cell line

tag: mrna seq

value: total


title: SAMPLE 24 BE.BE


title: SK-N-BE-2C [41_total_run329_F11]


title: SAMPLE 16 BE.BE

value: female


title: SAMPLE 21 BE.BE


title: H3K27ac ChIP-seq in H1299 WT

city: Irvine

first: Jiejun

last: Shi

state: CA

address: 5270 California Ave

department: School of Medicine

institute: University of California Irvine

library_source: genomic

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie v1.1.0
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq bigWig files were generated using MACS-1.4.2; Scores represent the ChIP-seq tag numbers

growth_protocol: Human H1299 cells (ATCC) were cultured in RPMI 1640 with 10% FBS (Cellgro) supplemented with 10% fetal bovine serum (Sigma), 5% CO2, 37 oC.

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.
For ChIP-seq, sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using single-end sequencing technology on Illumina HiSeq 3000 platform.

treatment_protocol: For virus packaging, 293T cells were co-transfected with pMD2.G and pPAX2 (Addgene) together with pCDH-FLAG-p300BRPHZT constructs or the control vector. Viral supernatants were harvested after 48 hrs. For infections, H1299 cells were incubated with viral supernatants in the presence of 8 µg/ml polybrene. After 48 hrs, blasticidin (2 µg/ml) was added to the medium. Cells were grown with selection for 8-10 days to select for stable cells.

value: FLAG-tagged WT p300-BRPHZT

tag: antibody

value: Abcam Ab4729


title: H3K18ac ChIP-seq in H1299 WT

value: Active Motif 39755


title: SK-N-BE-2C [40_total_run329_F9_JQ1]


title: SAMPLE 13 BE.BE


title: SAMPLE 12 BE.BE


title: Flag-p300 ChIP-seq in H1299 WT

value: Sigma F1804


title: Input

value: no treatment


title: H3K27ac ChIP-seq in H1299 with control vector

value: control vector


title: SAMPLE 17 BE.BE


title: SAMPLE 15 BE.BE


title: SK-N-BE-2C [38_total_run329_F5]


title: SAMPLE 20 BE.BE


title: H3K18ac ChIP-seq in H1299 with control vector


title: SAMPLE 10 BE.BE


title: Skin_Fibro_Veh5

type: RNA

city: Baltimore

first: Theresa

middle: K

last: Hodges

state: MD

address: 801 W. Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

description:
Gene expression data from fibroblasts treated with DMSO 1μM daily for three days
Human, adult, dermal fibroblasts (ATCC® PCS-201-012™)

hyb_protocol: Following fragmentation, biotinylated cRNA were hybridized for 16 hr on GeneChip® Human Genome U133 Plus 2.0 array.

scan_protocol: The arrays were washed and stained in the Affymetrix fluidics station and scanned in a 3000 7G scanner.

data_processing: Probe level analysis was performed on the Affymetrix raw data (.cel files) with the Robust Multi-Array Average (RMA) method implemented in the Bioconductor package 'affy' to obtain a log2 expression value for each gene probe set.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Human, adult, dermal fibroblasts (ATCC® PCS-201-012™) were seeded in cell culture flasks treated with poly-L-lysine hydrobromide and grown under standard culture conditions.

extract_protocol: Total RNA was extracted on the fourth day of the experiment using a standard TRIzol®-based extraction method.

treatment_protocol: Cells were transferred to 35mm cell culture dishes, grown to confluence, and then treated once daily for three days with erlotinib 100nM (n = 5), erlotinib 1μM (n = 5), vehicle 1μM (DMSO) (n = 5), or no treatment (n = 5).

tag: cell type

value: dermal fibroblasts

tag: tissue

value: skin

value: DMSO


title: Flag-p300 ChIP-seq in H1299 with control vector


title: SK-N-BE-2C [36_total_run329_F2]


title: H3K27ac ChIP-seq in D1690A

value: FLAG-tagged D1690A p300-BRPHZT


title: SK-N-BE-2C [35_total_run329_E12_JQ1]


title: SAMPLE 22 BE.BE


title: SK-N-BE-2C [37_total_run329_F4_JQ1]


title: SAMPLE 18 BE.BE


title: Skin_Fibro_Veh1

source_name: Gene expression data from fibroblasts treated with DMSO 1μM daily for three days


title: Skin_Fibro_Veh2


title: SK-N-BE-2C [34_total_run329_E11]


title: Skin_Fibro_Veh4


title: Flag-p300 ChIP-seq in D1690A


title: SAMPLE 5 BE.BE


title: H3K27ac ChIP-seq in N1671A

value: FLAG-tagged N1671A p300-BRPHZT


title: SK-N-BE-2C [32_total_run329_E6_JQ1]


title: SAMPLE 8 BE.BE


title: SAMPLE 11 BE.BE


title: SK-N-BE-2C [33_total_run329_E7]


title: SAMPLE 9 BE.BE


title: H3K18ac ChIP-seq in N1671A


title: SAMPLE 7 BE.BE


title: SAMPLE 3 BE.BE


title: SAMPLE 4 BE.BE


title: Skin_Fibro_No_Treatment3

description:
Gene expression data from fibroblasts not treated
Human, adult, dermal fibroblasts (ATCC® PCS-201-012™)


title: SAMPLE 6 BE.BE


title: SK-N-BE-2C [31_total_run329_E5]


title: Skin_Fibro_No_Treatment4

source_name: Gene expression data from fibroblasts not treated


title: GcKO_G

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

country: China

institute: Life Sciences Institute, Zhejiang University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequencing reads were mapped to the mouse genome (mm9) with TopHat v2.0.11 coupled with Bowtie v2.1.0. The mapped reads were subjected to Cufflinks v2.2.1 with the reference annotation (UCSC gene models) to calculate the FPKM values of each gene.
Genome_build: mm9
Supplementary_files_format_and_content: the processed data files contain the FPKM values of each gene (gene id, chromosome, strand, TSS, TES, description, FPKM value)

molecule: polyA RNA

organism: Mus musculus

source_name: 14-day-old mouse oocyte

growth_protocol: Oocytes were released by puncturing follicles with a fine needle in 37℃ pre-warmed M2 medium (Sigma-Aldrich).Growing oocytes were obtained from the ovaries of 13.5~14.5-days-old female mice. Fully grown oocytes were obtained from the ovaries of 3-week-old female mice 48 h after intraperitoneal injection of 5 IU of PMSG (Ningbo Sansheng Pharmaceutical Co., Ltd., China).

extract_protocol:
Each sample (10 oocytes per sample) was added with 4 μl lysis buffer (consisting of 0.2% TritonX-100, RNase inhibitor, dNTPs and oligo-dT primers) and immediately processed into cDNA using Smart-seq2 protocol with slight modification.
RNA-seq libraries were constructed from 500 pg of pre-amplified cDNA using a DNA library preparation kit (TruePrep DNA Library Prep Kit V2 for Illumina, Vazyme) which is based on Tn5 transposase.

tag: strain background

tag: genotype/variation

tag: Stage

value: growing oocyte stage

value: oocyte


title: SK-N-BE-2C [30_total_run329_E4]


title: SK-N-BE-2C [29_total_run329_E1]


title: SK-N-BE-2C [39_total_run329_F7_JQ1]


title: SAMPLE 1 BE.BE

value: non-dysplastic

value: male


title: SK-N-BE-2C [28_total_run329_D12_JQ1]

value: total


title: WT_F

description: Fully grown oocytes were obtained from the ovaries of 3-week-old female mice 48 h after intraperitoneal injection of 5 IU of PMSG (Ningbo Sansheng Pharmaceutical Co., Ltd., China).

source_name: 23-day-old mouse oocyte

value: fully grown oocyte stage


title: Skin_Fibro_No_Treatment1


title: SK-N-BE-2C [27_total_run329_D11_JQ1]


title: GcKO_F


title: SAMPLE 14 BE.BE


title: Skin_Fibro_Erlot100nM5

description:
Gene expression data from fibroblasts treated with erlotinib 100nM daily for three days
Human, adult, dermal fibroblasts (ATCC® PCS-201-012™)

value: erlotinib


title: WT_G

description: Growing oocytes were obtained from the ovaries of 13.5~14.5-days-old female mice.


title: Skin_Fibro_Erlot100nM4

source_name: Gene expression data from fibroblasts treated with erlotinib 100nM daily for three days


title: SK-N-BE-2C [26_total_run329_D10_JQ1]


title: rbm48-umu2 +/+ (WT) Rep3

city: Gainesville

first: William

middle: Bradley

last: Barbazuk

state: Florida

address: UF-CGRC Room 407 2033 Mowry Rd

department: Biology

institute: University of Florida

description:
rbm48-umu2-WT-rep-3_CAGATC_L003
WT seed form the same cob segregating with rbm48 mutant seeds from which umu2 sample 3 was obtained
processed data file:
RBM48-umu2_DESeq2_DEAnalysis.csv

data_processing:
Illumina casava 1,8 for basecalling
Raw RNA-seq data were screened to remove adapter sequences using Cutadapt v1.1 with the following parameters: error-rate=0.1, times=1, overlap=5, and minimum-length=0. Adapter trimmed sequences were quality trimmed with Trimmomatic v0.22 using parameters (HEADCROP:0, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, and MINLEN:40) to truncate reads for base quality <15 within 4 base windows and kept only reads ≥40 bases after trimming.
Reads were uniquely aligned the B73 RefGen_v2 maize genome assembly with GSNAP (Version 2013-07-20) using the following parameters: --orientation=FR --batch=5 --suboptimal-levels=0 --novelsplicing=1 --localsplicedist=8000 --local-splice-penalty=0     --distant-splice-penalty=4 --quality-protocol=sanger --npaths=1 --quiet-if-excessive --max-mismatches=0.02 --nofails --format=sam --sam-multiple-primaries --pairmax-rna=8000 --pairexpect=200 --pairdev=150 --nthreads=4. The --use-splicing argument was implemented to guide GSNAP by the ZmB73_5b Filtered Gene Set annotations but was permitted to discover novel splicing events
raw counts were enumerated using the HTSeq-Count utility in the HTSeq package. DEGs were identified usind DESeq
reads falling into introns or spanning junctions were identified by creating 3 bed format files: One that held the coordinates of the intron, one that held the coordinate of the last base of the exon preceeding the intron, and one that defined the coordinate of the first base of the exon after the intron. BEDtools ws used to intersect these with BAM alignment files.  Reads identified in the intersect with the BED file defining the last base of the upstream exon and the BAM file defining the first base of the downstream exon, but not intersecting with the intron BED file, defined junction reads. Any read intersecting with the intron BED file was considered an intron read and the intron coordinates are the 0-start, half-open (0-based) convention.
Genome_build: APGv2
Supplementary_files_format_and_content:
csv files contain the output for DESeq2, files of counts to genes (for DESeq2) or intron/junction read counts are tab delimited.
HTSeq-out.txt: Counts per gene
upstream_exon_downstream_exon-spanning_reads_rbm48-*-TABLE.txt: Junction read counts
INTRON_READS_COUNT_rbm48-*-table.txt: Intron read counts
Please note that the identifiers are available in the public maizeGDB database (https://www.maizegdb.org) which also has a genome browser.
The latest version is APGv4 (http://plants.ensembl.org/Zea_mays/Info/Index).
There is a conversion tool that places the AGPv2 identifies onto the AGPv4 framework
http://plants.ensembl.org/Zea_mays/Tools/AssemblyConverter?db=core
AGPv2 is also available as a standard genome in IGV and at the public USCS browser resource (http://www.genomaize.org/).

organism: Zea mays

source_name: rbm48-umu2 +/+ (WT)_endospern 16-18 DAP

extract_protocol:
Endosperm tissue from 16-18 DAP normal and rbm48 kernels in the W22 genetic background was dissected and frozen in liquid nitrogen. Total RNA was isolate using TRIzol reagent followed by a clean up with the Qiagen Rneasy kit.
Non-strand specific TruSeqTM (Illumina) cDNA libraries were prepared from 1 µg total RNA input with a 200 bp median insert length.

tag: cultivar background

value: WT

value: endosperm


title: Skin_Fibro_Erlot100nM3


title: rbm48-umu2 +/+ (WT) Rep4

description:
rbm48-umu2-WT-rep-4_AGTCAA_L003
WT seed form the same cob segregating with rbm48 mutant seeds from which umu2 sample 4 was obtained
processed data file:
RBM48-umu2_DESeq2_DEAnalysis.csv


title: Skin_Fibro_Erlot100nM2


title: rbm48-umu2 +/+ (WT) Rep2

description:
rbm48-umu2-WT-rep-2_ACAGTG_L003
WT seed form the same cob segregating with rbm48 mutant seeds from which umu2 sample 2 was obtained
processed data file:
RBM48-umu2_DESeq2_DEAnalysis.csv


title: SK-N-BE-2C [25_total_run329_D9_JQ1]


title: Skin_Fibro_Erlot100nM1


title: SK-N-BE-2C [24_total_run329_D7]

value: vehicle


title: Skin_Fibro_Erlot1uM5

description:
Gene expression data from fibroblasts treated with erlotinib 1μM daily for three days
Human, adult, dermal fibroblasts (ATCC® PCS-201-012™)


title: rbm48-umu2 +/+ (WT) Rep1

description:
rbm48-umu2-WT-rep-1_CGATGT_L003
WT seed form the same cob segregating with rbm48 mutant seeds from which umu2 sample 1 was obtained
processed data file:
RBM48-umu2_DESeq2_DEAnalysis.csv


title: SK-N-BE-2C [23_total_run329_D6_JQ1]


title: rbm48-umu2 -/- Rep4

description:
rbm48-umu2-MUT-rep-4_AGTTCC_L003
processed data file:
RBM48-umu2_DESeq2_DEAnalysis.csv

source_name: rbm48-umu2 -/-_endospern 16-18 DAP

value: rbm48 umu2 -/-


title: SK-N-BE-2C [22_total_run329_D5_JQ1]


title: rbm48-umu2 -/- Rep3

description:
rbm48-umu2-MUT-rep-3_CTTGTA_L003
processed data file:
RBM48-umu2_DESeq2_DEAnalysis.csv


title: rbm48-umu2 -/- Rep2

description:
rbm48-umu2-MUT-rep-2_GCCAAT_L003
processed data file:
RBM48-umu2_DESeq2_DEAnalysis.csv


title: SK-N-BE-2C [21_total_run329_D4]


title: SK-N-BE-2C [19_total_run329_C11_JQ1]


title: 10456SD0094: DRG_Sham_63d_T+16_7

city: Edinburgh

first: Dale

middle: Andrew

last: Sandercock

state: Midlothian

address: Roslin Institute Building

department: Animal and Veterinary Science

country: United Kingdom

institute: Scotland's Rural College (SRUC)

hyb_protocol: ~3ug of fragmented, labelled cDNA were hybridized on the Porcine 1.1 ST-96 array on the Gene Titan MC Instrument (Affymetrix)

scan_protocol: Scanning of the hybridised, washed array was carried out within the Gene Titan MC Instrument.

data_processing: Initial QC was carried out in Expression Console (Affymetrix) using GC-RMA normalisation.  Further Gene Expression analysis was carried out in Partek Genomics Suite (Partek Inc)

label: Biotin

organism: Sus scrofa

source_name: pig caudal DRG

label_protocol: Single-stranded cDNA were prepared according to the Ambion WT Expression Kit method, using 500ng of total RNA as input.  This was then fragmented and biotinylated using the Affymetrix Terminal Labelling Kit, according to manufacturer's instructions.

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

treatment_protocol: Tail amputation of neonatal pigs at 3 days of age using hot docking iron and surgical tail amputation of juvenile pigs at 63 days of age (under anaesthesia) using Liston bone cutters

value: pig caudal dorsal root ganglia (DRG)

value: Sham

tag: treatment age

tag: time after treatment


title: 10456SD0095: DRG_Sham_63d_T+16_8


title: Skin_Fibro_Erlot1uM4

source_name: Gene expression data from fibroblasts treated with erlotinib 1μM daily for three days

value: dermal fibroblasts

value: skin


title: 10456SD0093: DRG_Sham_63d_T+16_6


title: 10456SD0092: DRG_Sham_63d_T+16_5


title: Skin_Fibro_Erlot1uM3


title: Skin_Fibro_Erlot1uM2


title: SK-N-BE-2C [18_total_run329_C10_JQ1]


title: Skin_Fibro_No_Treatment5


title: SK-N-BE-2C [20_total_run329_D2_JQ1]


title: rbm48-umu1 +/+ (WT) Rep4

description:
rbm48-umu1-WT-rep-4_AGTCAA_L002
WT seed form the same cob segregating with rbm48 mutant seeds from which umu1 sample 4 was obtained
processed data file:
RBM48-umu1_DESeq2_DEAnalysis.csv

source_name: rbm48-umu1 +/+ (WT)_endospern 16-18 DAP


title: rbm48-umu1 +/+ (WT) Rep3

description:
rbm48-umu1-WT-rep-3_CAGATC_L002
WT seed form the same cob segregating with rbm48 mutant seeds from which umu1 sample 3 was obtained
processed data file:
RBM48-umu1_DESeq2_DEAnalysis.csv


title: SK-N-BE-2C [17_total_run329_C9]


title: SAMPLE 2 BE.BE


title: rbm48-umu1 +/+ (WT) Rep2

description:
rbm48-umu1-WT-rep-2_ACAGTG_L002
WT seed form the same cob segregating with rbm48 mutant seeds from which umu1 sample 2 was obtained
processed data file:
RBM48-umu1_DESeq2_DEAnalysis.csv


title: rbm48-umu2 -/- Rep1

description:
rbm48-umu2-MUT-rep-1_TGACCA_L003
processed data file:
RBM48-umu2_DESeq2_DEAnalysis.csv


title: 10456SD0089: DRG_Sham_63d_T+16_2


title: 10456SD0091: DRG_Sham_63d_T+16_4


title: 10456SD0090: DRG_Sham_63d_T+16_3


title: SK-N-BE-2C [15_total_run329_C6_JQ1]


title: SK-N-BE-2C [16_total_run329_C7]


title: rbm48-umu1 -/- Rep4

description:
rbm48-umu1-MUT-rep-4_AGTTCC_L002
processed data file:
RBM48-umu1_DESeq2_DEAnalysis.csv

source_name: rbm48-umu1 -/-_endospern 16-18 DAP

value: rbm48 umu1 -/-


title: SK-N-BE-2C [14_total_run329_B10_JQ1]


title: rbm48-umu1 +/+ (WT) Rep1

description:
rbm48-umu1-WT-rep-1_CGATGT_L002
WT seed form the same cob segregating with rbm48 mutant seeds from which umu1 sample 1 was obtained
processed data file:
RBM48-umu1_DESeq2_DEAnalysis.csv


title: rbm48-umu1 -/- Rep3

description:
rbm48-umu1-MUT-rep-3_CTTGTA_L002
processed data file:
RBM48-umu1_DESeq2_DEAnalysis.csv


title: rbm48-umu1 -/- Rep2

description:
rbm48-umu1-MUT-rep-2_GCCAAT_L002
processed data file:
RBM48-umu1_DESeq2_DEAnalysis.csv


title: 10456SD0088: DRG_Sham_63d_T+16_1


title: SK-N-BE-2C [13_total_run329_B9_JQ1]


title: Control-IP_experiment

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

description: Control Immunoprecipitation in 293T cell lines

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix HG-U133 plus 2.0 arrays.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: RMA processing was used to generate expression levels for the probesets. It includes quantile normalization and log2 transformation (R Affy package). MAS5 was used as well to return 'Present/Absent/Marginal' flags and p-values on each probeset, which can be used for filtering ('pam' and 'pvalue' in the data table).

source_name: 293T cells - miR-941 overexpression

label_protocol: Labeling was performed according to standard Affymetrix protocols.

growth_protocol: 293T was cultured in DMEM/HIGH GLUCOSE (HyClone,SH30243.018), supplemented with 10％ heat-inactivated fetal calf serum (hyclone，SH30070),100U/ml penicillin, 100ug/ml streptomycin.

extract_protocol: Total RNA were extracted with Trizol reagent (Invitrogen).

treatment_protocol: Ago2 Immunoprecipitation (Ago2-IP) experiments after miR-941 overexpression were conducted in 293T cell line. Briefly, All transfections were performed using human 293T cells cultured in 6-well tissue culture plates. Lipofectamine 2000 (Invitrogen) was used for a Synthetic miR-941 or a scrambled oligo transfection, at 30 nmol/l each (final concentration) per 1x106 cells/well of a 6-well plate using DharmaFECT (GE Healthcare). Total 5x106 cells were collected and subjected to Ago2 immunoprecipitation (Ago2-IP) using the RNA isolation kit Mouse Ago2 (Wako Chemicals) according to the manufacturer's instructions. For a negative control, immunoprecipitation was performed using nonimmune IgG beads prepared with the antibody immobilization bead kit (Wako Chemicals). The IP pull down RNA was used as template for an “in vitro” transcription reaction generating biotin-labeled antisense cRNA. The cRNA was analyzed on affymetrix Human Genome U133 Plus 2.0 arrays following the manufacturer’s instructions.

value: Human embryonic kidney cell line


title: SK-N-BE-2C [12_total_run329_B6]


title: 10456SD0086: DRG_Amputated_63d_T+16_7

value: Amputated


title: 10456SD0084: DRG_Amputated_63d_T+16_5


title: CF099

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression data from UPN727 cells stimulated with cystic fibrosis (CF) plasma

hyb_protocol: The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log ratios. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

source_name: UPN727 cells stimulated with CF099 plasma

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN727 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

extract_protocol: Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of autologous, unrelated healthy control (uHC), or cystic fibrosis (CF) plasma.  Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: responder cells

value: UPN727 cells


title: rbm48-umu1 -/- Rep1

description:
rbm48-umu1-MUT-rep-1_TGACCA_L002
processed data file:
RBM48-umu1_DESeq2_DEAnalysis.csv


title: CF102

source_name: UPN727 cells stimulated with CF102 plasma


title: 10456SD0082: DRG_Amputated_63d_T+16_3


title: SK-N-BE-2C [11_total_run329_B5]


title: SK-N-BE-2C [10_total_run329_B2]


title: 10456SD0083: DRG_Amputated_63d_T+16_4


title: Skin_Fibro_Erlot1uM1


title: 10456SD0085: DRG_Amputated_63d_T+16_6


title: SK-N-BE-2C [8_total_run329_A12]


title: 10456SD0087: DRG_Amputated_63d_T+16_8


title: CF101

source_name: UPN727 cells stimulated with CF101 plasma


title: CF098

source_name: UPN727 cells stimulated with CF098 plasma


title: CF103

source_name: UPN727 cells stimulated with CF103 plasma


title: 10456SD0081: DRG_Amputated_63d_T+16_2


title: SK-N-BE-2C [7_total_run329_A11_JQ1]

source_name: cell line


title: Ago2-IP_experiment

description: AGO2  Immunoprecipitation  in 293T cell lines


title: 10456SD0079: DRG_Amputated_63d_T+8_8


title: CF100

source_name: UPN727 cells stimulated with CF100 plasma


title: SK-N-BE-2C [6_total_run329_A10]


title: CF095

source_name: UPN727 cells stimulated with CF095 plasma


title: CF096

source_name: UPN727 cells stimulated with CF096 plasma


title: Flag-p300 ChIP-seq in N1671A

value: FLAG-tagged N1671A p300-BRPHZT

value: Sigma F1804


title: SK-N-BE-2C [9_total_run329_B1]

value: total


title: CF092

source_name: UPN727 cells stimulated with CF092 plasma


title: SK-N-BE-2C [5_total_run329_A9]


title: CF093

source_name: UPN727 cells stimulated with CF093 plasma


title: SK-N-BE-2C [3_total_run329_A5]


title: 10456SD0078: DRG_Amputated_63d_T+8_7


title: 10456SD0080: DRG_Amputated_63d_T+16_1


title: SK-N-BE-2C [2_total_run329_A2]


title: CF094

source_name: UPN727 cells stimulated with CF094 plasma


title: 10456SD0075: DRG_Amputated_63d_T+8_4

source_name: pig caudal DRG


title: SK-N-BE-2C [1_total_run329_A1]


title: 10456SD0076: DRG_Amputated_63d_T+8_5


title: 10456SD0077: DRG_Amputated_63d_T+8_6


title: SHSY5Y-MYCN-TR [run255_H8]

data_processing:
Alligment with STAR v2.5.3 :STAR --runThreadN 10 --outFileNamePrefix outdir --readFilesIn sample.fastq.gz --genomeDir star_index --sjdbGTFfile gtf_index --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --twopassMode Basic --outSAMmultNmax 1 --outSAMprimaryFlag AllBestScore --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0
Quantification with Kallisto v0.43.1. For polyA: kallisto quant -t 10 -i kallisto_index --single -l 200 -s 20 -o outdir sample.fastq.gz; For total: kallisto quant -t 10 -i kallisto_index –rf-stranded --single -l 200 -s 20 -o outdir sample.fastq.gz
Genome_build: hg38
Supplementary_files_format_and_content: abundance.tsv output for kallisto


title: CF097

source_name: UPN727 cells stimulated with CF097 plasma


title: CF091

source_name: UPN727 cells stimulated with CF091 plasma


title: CF090

source_name: UPN727 cells stimulated with CF090 plasma


title: 10456SD0071: DRG_Sham_63d_T+8_8


title: 10456SD0073: DRG_Amputated_63d_T+8_2


title: 10456SD0072: DRG_Amputated_63d_T+8_1


title: SHSY5Y-MYCN-TR [run255_H7]


title: CF088

source_name: UPN727 cells stimulated with CF088 plasma


title: 10456SD0074: DRG_Amputated_63d_T+8_3


title: CF087

source_name: UPN727 cells stimulated with CF087 plasma


title: CF086

source_name: UPN727 cells stimulated with CF086 plasma


title: H3K18ac ChIP-seq in D1690A

value: FLAG-tagged D1690A p300-BRPHZT

value: Active Motif 39755


title: 10456SD0070: DRG_Sham_63d_T+8_7


title: CF089

source_name: UPN727 cells stimulated with CF089 plasma


title: CF085

source_name: UPN727 cells stimulated with CF085 plasma


title: SK-N-BE-2C [4_total_run329_A7]


title: SHSY5Y-MYCN-TR [run255_H2]


title: Macrophage_PPVL 10 day_P10-3

city: New Haven

first: Masatake

last: Tanaka

state: CT

address: 300 Cedar Street

department: Internal Medicine

institute: Yale School of Medicine

description: Gene expression data in hepatic macrophages from rat with PPVL surgery for 10 days.

hyb_protocol: Following fragmentation, 3.5 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip® Rat Gene 2.0 ST Array.  GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: GeneChips were scanned using the the GeneChip® Scanner 3000 (Thermo Fisher Scientific).

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) 4.0 using Affymetrix default analysis settings and the Robust Multiarray Average (RMA) algorithm was used for normalization of the data to generate single expression value for each probe set.

organism: Rattus norvegicus

source_name: Hepatic macrophage from PPVL 10day rat P10-3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 50-500 ng total RNA.

growth_protocol: Approximately 3x10^6 hepatic macrophages were isolated from each rat liver.

treatment_protocol: After midline abdominal incision under anesthesia, the portal vein was separated from the surrounding tissue in three rats.  A ligature (silk gut 3–0) was placed around a 20-gauge blunt tipped needle lying along the portal vein.  Subsequent removal of the needle yielded a calibrated stenosis of the portal vein.  Hepatic macrophages were collected three days (n = 3) or ten days (n = 3) after ligation.  In sham-operated rats (n = 3), the same operation was performed, but no ligature was placed.

value: 10 days after partial portal vein ligation (PPVL) surgery

value: hepatic macrophage

tag: strain

value: Sprague-Dawley


title: SHSY5Y-MYCN-TR [run255_H3]

source_name: cell line

value: vehicle


title: 10456SD0069: DRG_Sham_63d_T+8_6

value: pig caudal dorsal root ganglia (DRG)


title: SHSY5Y-MYCN-TR [run255_G9]

value: Doxycyclin


title: SHSY5Y-MYCN-TR [run255_G8]


title: Macrophage_PPVL 10 day_P10-2

source_name: Hepatic macrophage from PPVL 10day rat P10-2


title: SHSY5Y-MYCN-TR [run255_F8]


title: 10456SD0067: DRG_Sham_63d_T+8_4

value: Sham


title: 10456SD0068: DRG_Sham_63d_T+8_5


title: CF083

source_name: UPN727 cells stimulated with CF083 plasma


title: CF082

source_name: UPN727 cells stimulated with CF082 plasma


title: 10456SD0066: DRG_Sham_63d_T+8_3


title: CF084

source_name: UPN727 cells stimulated with CF084 plasma


title: CF081

source_name: UPN727 cells stimulated with CF081 plasma


title: Macrophage_PPVL 10 day_P10-1

source_name: Hepatic macrophage from PPVL 10day rat P10-1


title: Macrophage_PPVL 3 day_P3-2

description: Gene expression data in hepatic macrophages from rat with PPVL surgery for 3 days.

source_name: Hepatic macrophage from PPVL 3day rat P3-2

value: 3 days after partial portal vein ligation (PPVL) surgery


title: 10456SD0065: DRG_Sham_63d_T+8_2

source_name: pig caudal DRG


title: Macrophage_PPVL 3 day_P3-1

source_name: Hepatic macrophage from PPVL 3day rat P3-1


title: 10456SD0064: DRG_Sham_63d_T+8_1


title: Macrophage_sham_N3

description: Gene expression data in hepatic macrophages from sham rat.

source_name: Hepatic macrophage from sham rat N3

value: sham


title: SHSY5Y-MYCN-TR [run255_F7]


title: CF080

source_name: UPN727 cells stimulated with CF080 plasma


title: SHSY5Y-MYCN-TR [run255_G3]


title: Macrophage_sham_N2

source_name: Hepatic macrophage from sham rat N2


title: CF077

source_name: UPN727 cells stimulated with CF077 plasma


title: 10456SD0063: DRG_Sham_63d_T+1_8


title: 10456SD0062: DRG_Sham_63d_T+1_7


title: CF078

source_name: UPN727 cells stimulated with CF078 plasma


title: 10456SD0061: DRG_Sham_63d_T+1_6


title: SHSY5Y-MYCN-TR [run255_F3]


title: OCI-ly19 RNA_rep3

city: Shenyang

first: Wei

last: Yang

state: Liaoning

address: Huaxiang Road 39

department: Hematology

institute: Shengjing Hospital of China Medical University

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

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

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, lncRNAs and mRNAs that had flags in 3 out of 9 samples or more in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed lncRNAs and mRNAs with statistical significance between GCB DLBCL and benign B-cell groups were identified with P-value/FDR filtering. Differentially expressed lncRNAs and mRNAs between the two groups were identified with Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: OCI-ly19 RNA, replicate 3

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

extract_protocol: Total RNA was isolated from each sample using Trizol reagent (Invitrogen, CA, USA) and quantified using a NanoDrop ND-1000 spectrophotometer. The integrity of RNA was assessed by standard denaturing agarose gel electrophoresis, and the purity was evaluated by the ratio of absorbance at 260~280nm.


title: CF076

source_name: UPN727 cells stimulated with CF076 plasma


title: SHSY5Y-MYCN-TR [run255_F2]

source_name: cell line


title: SHSY5Y-MYCN-TR [run255_E11]


title: SHSY5Y-MYCN-TR [run255_E9]


title: SHSY5Y-MYCN-TR [run255_F1]


title: Macrophage_PPVL 3 day_P3-3

source_name: Hepatic macrophage from PPVL 3day rat P3-3


title: 10456SD0060: DRG_Sham_63d_T+1_5


title: OCI-ly19 RNA_rep1

source_name: OCI-ly19 RNA, replicate 1


title: 10456SD0059: DRG_Sham_63d_T+1_4


title: CF074

source_name: UPN727 cells stimulated with CF074 plasma


title: Macrophage_sham_N1

source_name: Hepatic macrophage from sham rat N1


title: CF073

source_name: UPN727 cells stimulated with CF073 plasma


title: CF079

source_name: UPN727 cells stimulated with CF079 plasma


title: CF075

source_name: UPN727 cells stimulated with CF075 plasma


title: OCI-ly1 RNA_rep2

source_name: OCI-ly1 RNA, replicate 2


title: SHSY5Y-MYCN-TR [run255_E8]


title: OCI-ly19 RNA_rep2

source_name: OCI-ly19 RNA, replicate 2


title: OCI-ly1 RNA_rep3

source_name: OCI-ly1 RNA, replicate 3


title: 10456SD0056: DRG_Sham_63d_T+1_1

source_name: pig caudal DRG


title: SHSY5Y-MYCN-TR [run255_E7]


title: SHSY5Y-MYCN-TR [run255_E4]


title: 10456SD0058: DRG_Sham_63d_T+1_3


title: SHSY5Y-MYCN-TR [run255_E5]


title: SHSY5Y-MYCN-TR [run255_E2]


title: Ssl2aa with rapa rep 1

city: Göttingen

first: Christian

last: Dienemann

address: Am Faßberg 11

country: Germany

institute: MPI Göttingen

data_processing:
Acquisition of data obtained from 4tU-Seq experiments was performed as described (Schulz et al., 2013), with minor modifications. Briefly, paired-end 50 base reads with additional 6 base reads of barcodes were obtained for labeled RNA. Reads were demultiplexed and aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using STAR (version 2.3.0) (Dobin et al., 2013). SAMTools was used to quality filter SAM files (Li et al., 2009). Alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f163) were selected. Further processing of the data was carried out using R/Bioconductor (Gentleman et al., 2004; Ihaka and Gentleman, 1996).
We used a spike-in (RNAs) normalization strategy essentially as described before in (Schwalb et al., 2016) to allow observation of global shifts in 4sU-seq signal. Read counts for all spike-ins necessary to that end were calculated using HTSeq (Anders et al., 2015). Those size factors were used to correct for library size and sequencing depth variations.
Piled-up counts for every genomic position were summed up over replicates, using fragment coverage i.e. counting both sequenced bases covered by reads and unsequenced bases spanned between proper mate-pair reads.
Genome_build: S. cerevisiae genome (sacCer3, Version R64-1-1, released 03Feb2011, http://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-1-1_20110203.tgz)
Supplementary_files_format_and_content: tabular containing read counts according to Sc.cerevisiae.feature.anno_Steinmetz_2013.gtf

organism: Saccharomyces cerevisiae

growth_protocol: inoculate strain from O/N culture at OD600 0.1, grow at 30C in YPD to OD600 0.8, label with 5mM 4thiouracil final conc. for 6 minutes, spin 1 min, discard supernatant, freeze in lN2

extract_protocol:
add spike-ins before cell lysis, extract total RNA with phenol/chloroform, purify labeled RNA
using NUGen Ovation Universal RNA-Seq System starting with 100 ng RNA input

tag: genotype

value: Y40343 Ssl2-FRB::kanMX6

tag: group

value: with rapa


title: Ssl2aa with rapa rep 2

treatment_protocol: label with 5mM 4thiouracil final conc. for 6 minutes


title: 10456SD0055: DRG_Amputated_63d_T+1_8

value: Amputated


title: SHSY5Y-MYCN-TR [run255_E1]


title: Ssl2aa no rapa rep 2

value: no rapa


title: SHSY5Y-MYCN-TR [run255_D12]


title: Ssl2aa no rapa rep 1


title: 10456SD0053: DRG_Amputated_63d_T+1_6


title: CF068

source_name: UPN727 cells stimulated with CF068 plasma

value: UPN727 cells


title: CF071

source_name: UPN727 cells stimulated with CF071 plasma


title: SHSY5Y-MYCN-TR [run255_D11]

value: total


title: CF072

source_name: UPN727 cells stimulated with CF072 plasma


title: CF066

source_name: UPN727 cells stimulated with CF066 plasma


title: CF069

source_name: UPN727 cells stimulated with CF069 plasma


title: 492R_TBP

city: Geneva

first: Slawomir

last: Kubik

address: quai Ernest-Ansermet 30

department: Molecular Biology Department

country: Switzerland

institute: University of Geneva

data_processing:
Raw reads were aligned to the sacCer3 genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800".
Data were filtered to retain only the mapped reads with at most 5 hits in the reference.
For nucleosome occupancy tracks each paired-end read was trimmed by 15 bp at each end to improve separation of nucleosome peaks.
For ChEC-seq experiments the mapped reads were extended by 1 bp only to indicate cut sites and then, the signal for each protein tested was normalized to the signal of free MNase using a Bayesian approach
For ChIP-seq the reads were shifted by 150 bp and extended by 50 bp
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were obtained using HTSStation (http://htsstation.epfl.ch)

source_name: whole organism

extract_protocol: ChIP-seq ibraries were prepared according to manufactrer's instructions (Illumina)

treatment_protocol: 30 minutes auxin (3-IAA)

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 SPT15-FLAG-HphMX; INO80-aid*-9myc-HphNT Padh1-Os.TIR1

value: ANTI-FLAG M2 (Sigma F3165)


title: SHSY5Y-MYCN-TR [run255_D8]

source_name: cell line


title: 492V_TBP

treatment_protocol: no auxin


title: 10456SD0054: DRG_Amputated_63d_T+1_7


title: 10456SD0057: DRG_Sham_63d_T+1_2


title: 10456SD0051: DRG_Amputated_63d_T+1_4


title: CF065

source_name: UPN727 cells stimulated with CF065 plasma


title: CD19-positive B cells RNA_rep3

source_name: CD19-positive B cell RNA, replicate 3

value: CD19-positive B cell


title: SHSY5Y-MYCN-TR [run255_D6]


title: CF064

source_name: UPN727 cells stimulated with CF064 plasma


title: 492R_Pol

value: Anti-RNA polymerase II CTD repeat YSPTSPS (Abcam ab5131)


title: CF070

source_name: UPN727 cells stimulated with CF070 plasma


title: CF067

source_name: UPN727 cells stimulated with CF067 plasma


title: CF063

source_name: UPN727 cells stimulated with CF063 plasma


title: 10456SD0050: DRG_Amputated_63d_T+1_3


title: 10456SD0052: DRG_Amputated_63d_T+1_5


title: SHSY5Y-MYCN-TR [run255_D5]


title: OCI-ly1 RNA_rep1

source_name: OCI-ly1 RNA, replicate 1


title: CD19-positive B cells RNA_rep1

source_name: CD19-positive B cell RNA, replicate 1


title: 10456SD0048: DRG_Amputated_63d_T+1_1


title: 426V_TBP

treatment_protocol: no rapamycin

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 SNF2-FRB-KanMX; SPT15-13xmyc-KanMX

value: Anti-Myc (homemade)


title: CF062

source_name: UPN727 cells stimulated with CF062 plasma


title: 426R_TBP

treatment_protocol: 60 minutes rapamycin


title: CD19-positive B cells RNA_rep2

source_name: CD19-positive B cell RNA, replicate 2


title: SHSY5Y-MYCN-TR [run255_C12]


title: 426R_Pol


title: SHSY5Y-MYCN-TR [run255_C11]


title: 492V_Pol


title: 10456SD0049: DRG_Amputated_63d_T+1_2

source_name: pig caudal DRG

value: pig caudal dorsal root ganglia (DRG)


title: SHSY5Y-MYCN-TR [run255_C10]

value: Doxycyclin


title: SHSY5Y-MYCN-TR [run255_D1]


title: 10456SD0046: DRG_Amputated_3d_T+16_6


title: CF058

source_name: UPN727 cells stimulated with CF058 plasma


title: SHSY5Y-MYCN-TR [run255_C9]


title: 10456SD0044: DRG_Amputated_3d_T+16_4


title: CF060

source_name: UPN727 cells stimulated with CF060 plasma


title: CF061

source_name: UPN727 cells stimulated with CF061 plasma


title: 426V_Pol

extract_protocol:
ChIP-seq was performed as described previously (Ribaud et al., 2012) (PMID: 21952045)
ChIP-seq ibraries were prepared according to manufactrer's instructions (Illumina)


title: Chd1_1m_ChEC

data_processing:
Library strategy: ChEC-seq
Raw reads were aligned to the sacCer3 genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800".
Data were filtered to retain only the mapped reads with at most 5 hits in the reference.
For nucleosome occupancy tracks each paired-end read was trimmed by 15 bp at each end to improve separation of nucleosome peaks.
For ChEC-seq experiments the mapped reads were extended by 1 bp only to indicate cut sites and then, the signal for each protein tested was normalized to the signal of free MNase using a Bayesian approach
For ChIP-seq the reads were shifted by 150 bp and extended by 50 bp
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were obtained using HTSStation (http://htsstation.epfl.ch)

extract_protocol: libraries were prepared as described in Zentner et al., 2015 (PMID: 26490019)

treatment_protocol: 1 minute of 2.5 mM calcium

value: W303 CHD1-3xFLAG-MNase-HphMX


title: Isw1_1m_ChEC

value: W303 ISW1-3xFLAG-MNase-HphMX


title: SHSY5Y-MYCN-TR [run255_C8]

value: vehicle


title: 10456SD0043: DRG_Amputated_3d_T+16_3


title: CF059

source_name: UPN727 cells stimulated with CF059 plasma


title: Isw2_1m_ChEC

source_name: whole organism

value: W303 ISW2-3xFLAG-MNase-HphMX


title: SHSY5Y-MYCN-TR [run255_C6]

source_name: cell line


title: SHSY5Y-MYCN-TR [run255_C7]


title: 10456SD0042: DRG_Amputated_3d_T+16_2


title: Swi3_1m_ChEC

value: W303 SWI3-3xFLAG-MNase-HphMX


title: SHSY5Y-MYCN-TR [run255_C2]


title: SHSY5Y-MYCN-TR [run255_C3]


title: Ino80_1m_ChEC

value: W303 INO80-3xFLAG-MNase-HphMX


title: SHSY5Y-MYCN-TR [run255_C1]


title: Rsc8_1m_ChEC

growth_protocol: cells were grown at 30 degrees in YPD to OD600=0.7

extract_protocol:
DNA was prepared as described in Zentner et al., 2015 (PMID: 26490019)
libraries were prepared as described in Zentner et al., 2015 (PMID: 26490019)

value: W303 RSC8-3xFLAG-MNase-HphMX


title: SHSY5Y-MYCN-TR [run255_B12]


title: 443R_high

data_processing:
Raw reads were aligned to the sacCer3 genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800".
Data were filtered to retain only the mapped reads with at most 5 hits in the reference.
For nucleosome occupancy tracks each paired-end read was trimmed by 15 bp at each end to improve separation of nucleosome peaks.
For ChEC-seq experiments the mapped reads were extended by 1 bp only to indicate cut sites
For ChIP-seq the reads were shifted by 100 bp and extended by 50 bp
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were obtained using HTSStation (http://htsstation.epfl.ch)

growth_protocol: cells were grown at 30 degrees i YPD to mid-log phase before treatment

extract_protocol:
Chromatin for MNase digestion was prepared essentially as described in Kubik et al., 2015 (GSE73337) (PMID: 26545077)
Libraries were prepared essentially as described in Henikoff et al., 2011 (GSE30551) (PMID: 22025700)

value: whole organism

value: W303 CHD1-FRB-KanMX tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 ADE2


title: 443R_low


title: 443V_high


title: SHSY5Y-MYCN-TR [run255_B11]

value: total


title: 443V_low


title: SHSY5Y-MYCN-TR [run255_B10]


title: 419R_high


title: 10456SD0047: DRG_Amputated_3d_T+16_7

value: Amputated


title: 10456SD0037: DRG_Sham_3d_T+16_5

value: Sham


title: 10456SD0038: DRG_Sham_3d_T+16_6


title: CF050

source_name: UPN727 cells stimulated with CF050 plasma

value: UPN727 cells


title: CF047

source_name: UPN727 cells stimulated with CF047 plasma


title: CF053

source_name: UPN727 cells stimulated with CF053 plasma


title: 10456SD0040: DRG_Sham_3d_T+16_8


title: 10456SD0041: DRG_Amputated_3d_T+16_1


title: 10456SD0034: DRG_Sham_3d_T+16_2


title: CF048

source_name: UPN727 cells stimulated with CF048 plasma


title: CF051

source_name: UPN727 cells stimulated with CF051 plasma


title: CF057

source_name: UPN727 cells stimulated with CF057 plasma


title: CF054

source_name: UPN727 cells stimulated with CF054 plasma


title: 10456SD0031: DRG_Amputated_3d_T+8_7


title: SHSY5Y-MYCN-TR [run255_B9]


title: 10456SD0039: DRG_Sham_3d_T+16_7


title: 10456SD0036: DRG_Sham_3d_T+16_4


title: SHSY5Y-MYCN-TR [run255_B8]


title: CF056

source_name: UPN727 cells stimulated with CF056 plasma


title: 10456SD0032: DRG_Amputated_3d_T+8_8


title: CF055

source_name: UPN727 cells stimulated with CF055 plasma


title: 10456SD0033: DRG_Sham_3d_T+16_1


title: 419V_high


title: 10456SD0035: DRG_Sham_3d_T+16_3


title: CF049

source_name: UPN727 cells stimulated with CF049 plasma


title: 10456SD0045: DRG_Amputated_3d_T+16_5

source_name: pig caudal DRG


title: CF045

source_name: UPN727 cells stimulated with CF045 plasma


title: 419R_low


title: SHSY5Y-MYCN-TR [run255_B6]


title: CF052

source_name: UPN727 cells stimulated with CF052 plasma


title: 419V_low


title: CF046

source_name: UPN727 cells stimulated with CF046 plasma


title: SHSY5Y-MYCN-TR [run255_B7]


title: SHSY5Y-MYCN-TR [run255_B5]


title: 396R_low


title: 396V_high


title: 396R_high


title: SHSY5Y-MYCN-TR [run255_B4]


title: SHSY5Y-MYCN-TR [run255_A12]


title: 396V_low


title: 10456SD0030: DRG_Amputated_3d_T+8_6


title: SHSY5Y-MYCN-TR [run255_A11]


title: SHSY5Y-MYCN-TR [run255_B1]


title: 10456SD0029: DRG_Amputated_3d_T+8_5


title: 10456SD0028: DRG_Amputated_3d_T+8_4


title: SHSY5Y-MYCN-TR [run255_A9]


title: 173R_high

value: W303 ISW2-FRB-HIS3MX tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 ADE2


title: 173V_high


title: 10456SD0024: DRG_Sham_3d_T+8_8


title: SHSY5Y-MYCN-TR [run255_A8]


title: 10456SD0026: DRG_Amputated_3d_T+8_2


title: 10456SD0025: DRG_Amputated_3d_T+8_1


title: 10456SD0027: DRG_Amputated_3d_T+8_3


title: SHSY5Y-MYCN-TR [run255_A7]


title: 173V_low


title: CF041

source_name: UPN727 cells stimulated with CF041 plasma


title: CF037

source_name: UPN727 cells stimulated with CF037 plasma


title: CF043

source_name: UPN727 cells stimulated with CF043 plasma


title: CF038

source_name: UPN727 cells stimulated with CF038 plasma


title: CF040

source_name: UPN727 cells stimulated with CF040 plasma


title: 173R_low

source_name: whole organism


title: CF042

source_name: UPN727 cells stimulated with CF042 plasma


title: 387R_high

value: W303 SNF2-FRB-KanMX tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1


title: 387V_high


title: 387R_low


title: 10456SD0022: DRG_Sham_3d_T+8_6

value: pig caudal dorsal root ganglia (DRG)


title: SHSY5Y-MYCN-TR [run255_A5]

source_name: cell line


title: SHSY5Y-MYCN-TR [run255_A4]

value: Doxycyclin


title: CF039

source_name: UPN727 cells stimulated with CF039 plasma


title: SHSY5Y-MYCN-TR [run255_A3]


title: CF044

source_name: UPN727 cells stimulated with CF044 plasma


title: SHSY5Y-MYCN-TR [run255_A6]


title: 387V_low


title: 10456SD0020: DRG_Sham_3d_T+8_4


title: CF035

source_name: UPN727 cells stimulated with CF035 plasma


title: 10456SD0021: DRG_Sham_3d_T+8_5


title: SHSY5Y-MYCN-TR [run255_A2]


title: RASMC_RNA_PDGF_JQ1_2H_H

city: Houston

first: Charles

middle: Yang

last: Lin

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
alignment: HiSat using default settings
expression levels: Gene-level expression measurements for RefSeq genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples. FPKM values were ERCC normalized. See methods for further details
Genome_build: rn6
Supplementary_files_format_and_content: rasmc_rna_all_fpkm_exprs_raw.txt: Tab-delimited text file matix containing raw FPKM values for each transcript; rasmc_rna_all_fpkm_exprs_norm.txt:  Tab-delimited text file matix containing ERCC cell count normalized FPKM values for each transcript

source_name: RNA-Seq for RASMC 2 hours after PDGF and JQ1 treatment

growth_protocol: Rat aortic smooth muscle cells (RASMCs), obtained from Lonza, were cultured in DMEM:F12 media supplemented with 10% v/v FBS, 100 U/ml penicillin-streptomycin, and 2 mM L-glutamine at 37 °C in a humidified atmosphere of 95% air and 5% CO2 incubator. Cells were starved in serum free media for 24 hours before starting any treatment.

extract_protocol:
RNA was isolated using the High Pure RNA Isolation Kit (Roche 11828665001). RNA samples were spiked with ERCC RNA Spike-In Mix (Ambion, Life Technologies) as per the manufacturer’s instructions. The dilution of spike-ins was proportional to the amount of RNA from 500k cells per group. RNA was sent to WIGTC for NGS library preparation (Illumina TruSeq) and sequencing (HiSeq 2500).
TruSeq Stranded mRNA Library Prep Kit (Cat. No. RS-122-2101, RS-122-2102, and RS-122-2103) was used according to manufacturer's instructions
polyA RNA-seq with 40bp single end reads

treatment_protocol: RASMCs were pretreated with JQ1 (500nM) for 3 hour followed by PDGF (925ng/ml) treatment for 2 hour and 24 hour.

value: RASMC

value: Rat aortic smooth muscle cells

tag: bar code

value: AGTCAA


title: 10456SD0019: DRG_Sham_3d_T+8_3

tag: treatment


title: RASMC_RNA_PDGF_JQ1_2H_G

tag: cell line

value: ACTTGA


title: SHSY5Y-MYCN-TR [run255_A1]

tag: mrna seq


title: CF036

source_name: UPN727 cells stimulated with CF036 plasma


title: 10456SD0018: DRG_Sham_3d_T+8_2

source_name: pig caudal DRG


title: CF032

source_name: UPN727 cells stimulated with CF032 plasma


title: 147_NGP_total_H12

value: vehicle

value: NGP


title: CF034

source_name: UPN727 cells stimulated with CF034 plasma


title: CF031

source_name: UPN727 cells stimulated with CF031 plasma


title: CF033

source_name: UPN727 cells stimulated with CF033 plasma


title: RASMC_RNA_PDGF_JQ1_2H_E

value: TTAGGC


title: 146_NGP_total_H9

value: nutlin


title: 10456SD0023: DRG_Sham_3d_T+8_7


title: RASMC_RNA_PDGF_JQ1_24H_H

source_name: RNA-Seq for RASMC 24 hours after PDGF and JQ1 treatment

value: ATGTCA


title: 10456SD0017: DRG_Sham_3d_T+8_1


title: 145_NGP_total_H8

value: total


title: RASMC_RNA_PDGF_JQ1_24H_F

value: TAGCTT


title: CF029

source_name: UPN727 cells stimulated with CF029 plasma


title: RASMC_RNA_PDGF_JQ1_24H_E

value: ACAGTG


title: 10456SD0016: DRG_Amputated_3d_T+1_8

value: Amputated


title: 143_NGP_total_H1


title: RASMC_RNA_PDGF_2H_D

source_name: RNA-Seq for RASMC 2 hours after PDGF treatment

value: CTTGTA


title: 10456SD0012: DRG_Amputated_3d_T+1_4


title: CF028

source_name: UPN727 cells stimulated with CF028 plasma

value: UPN727 cells


title: 142_NGP_total_G9


title: 141_NGP_total_G8


title: CF030

source_name: UPN727 cells stimulated with CF030 plasma


title: CF027

source_name: UPN727 cells stimulated with CF027 plasma


title: RASMC_RNA_PDGF_2H_B

value: CGATGT


title: CF026

source_name: UPN727 cells stimulated with CF026 plasma


title: 10456SD0014: DRG_Amputated_3d_T+1_6

value: pig caudal dorsal root ganglia (DRG)


title: 144_NGP_total_H2

source_name: cell line


title: 10456SD0013: DRG_Amputated_3d_T+1_5


title: 140_NGP_total_G3


title: RASMC_RNA_PDGF_24H_D

source_name: RNA-Seq for RASMC 24 hours after PDGF treatment

value: RASMC

value: AGTTCC


title: RASMC_RNA_PDGF_2H_C

value: Rat aortic smooth muscle cells

value: CAGATC


title: 10456SD0015: DRG_Amputated_3d_T+1_7


title: 139_NGP_total_G2


title: 10456SD0011: DRG_Amputated_3d_T+1_3


title: CF024

source_name: UPN727 cells stimulated with CF024 plasma


title: 138_NGP_total_G1


title: 10456SD0007: DRG_Sham_3d_T+1_7

value: Sham


title: CF025

source_name: UPN727 cells stimulated with CF025 plasma


title: 10456SD0009: DRG_Amputated_3d_T+1_1


title: 10456SD0006: DRG_Sham_3d_T+1_6


title: 10456SD0008: DRG_Sham_3d_T+1_8


title: 10456SD0005: DRG_Sham_3d_T+1_5


title: RASMC_RNA_PDGF_24H_A

value: TGACCA


title: 10456SD0010: DRG_Amputated_3d_T+1_2


title: CF023

source_name: UPN727 cells stimulated with CF023 plasma


title: 137_NGP_total_F11

value: vehicle

value: NGP


title: RASMC_RNA_0H_B

source_name: RNA-Seq for unstimulated RASMC at 0 hours

value: GCCAAT


title: 136_NGP_total_F9

value: total


title: RASMC_RNA_0H_A

value: ATCACG


title: RASMC_RNA_PDGF_24H_B

value: GATCAG


title: 135_NGP_total_F8

value: nutlin


title: CF022

source_name: UPN727 cells stimulated with CF022 plasma


title: RASMC_ATAC_UNSTIM_REP2

data_processing:
Paired end reads were aligned to RN6 referenece genome using bowtie2 with the following parameters: --end-to-end --sensitive --no-unal --no-discordant --mm
Aligned bams were filtered and sorted using samtools by removing chrM, filtering against the ENCODE blacklist, and removing discordant reads.
Peaks were called using MACS1.4 with  p-val =1e-9
Genome_build: rn6
Supplementary_files_format_and_content: Processed ATAC data files are in wiggle format

source_name: ATAC-Seq of RASMC under unstimulated conditions at 0 hours

extract_protocol:
Samples for ATAC-Seq were prepared as described by Buenrostro J.D. et.al. PMID: 24097267. Transposition reaction was performed for 60min at 37oC. PCR product for library amplification was amplified for the total of 9 cycles.
We used Ad1_noMX and Ad2.1 to Ad2.10 primers published in Buenrostro J.D. et.al. 2013 (PMID: 24097267).
ATAC-seq paired end sequencing with 100bp reads

treatment_protocol: For PDGF treatment, cells were treated with PDGF-BB (25ng/ml)  for 24 hours

value: Rat aortic smooth muscle cell

tag: barcode


title: CF021

source_name: UPN727 cells stimulated with CF021 plasma

value: UPN727 cells


title: AH1263_Teg41_3

city: Athens

first: Ronan

middle: Kevin

last: Carroll

state: OHIO

address: 107 Irvine Hall

department: Biological Sciences

institute: Ohio University

description:
total RNA, rRNA-depleted
474_C

data_processing:
Raw data files (.fastq) were imported into the CLC Genomics Workbench software platform for analysis
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Expression values were exported into excel files
Genome_build: The reference genome used for the analysis was based on NC_007793 and included annotations for sRNA genes (https://dx.doi.org/10.6084/m9.figshare.2061132.v1)
Supplementary_files_format_and_content: Expression values calculated for each gene are presented as RPKM values in excel format

organism: Staphylococcus aureus

source_name: Bacterial cells, pelleted

growth_protocol: Strains were grown in TSB medium at 37°C with shaking

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free
Library construction was performed using the Illumina TruSeq Stranded mRNA Sample Prep Kit

treatment_protocol: Samples were stored at -80°C prior to RNA extraction

value: wild-type overproducing Teg41

tag: growth medium

value: TSB

tag: growth conditions


title: AH1263_Teg41_2

description:
total RNA, rRNA-depleted
474_B


title: 134_NGP_total_F7

data_processing:
Alligment with STAR v2.5.3 :STAR --runThreadN 10 --outFileNamePrefix outdir --readFilesIn sample.fastq --genomeDir star_index --sjdbGTFfile gtf_index --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --twopassMode Basic --outSAMmultNmax 1 --outSAMprimaryFlag AllBestScore --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0
Quantification with Kallisto v0.43.1. For polyA: kallisto quant -t 10 -i kallisto_index --single -l 200 -s 20 -o outdir sample.fastq; For total: kallisto quant -t 10 -i kallisto_index –rf-stranded --single -l 200 -s 20 -o outdir sample.fastq
Genome_build: hg38
Supplementary_files_format_and_content: abundance.tsv output for kallisto

extract_protocol:
Cells were lysed and cDNA was synthesized according to the SMARTer single cell total RNA sequencing protocol on script hub (Fluidigm).
polyA+ RNA-seq libraries were generated using the SMART-seq ultra low input RNA kit for the Fluidigm C1 system. Total RNA-seq libraries were generated using a single cell adapted SMARTer stranded total RNA-seq v2 kit pico input mammalian protocol.


title: 10456SD0004: DRG_Sham_3d_T+1_4

source_name: pig caudal DRG

tag: tissue

value: pig caudal dorsal root ganglia (DRG)


title: AH1263_Teg41_1

description:
total RNA, rRNA-depleted
474_A


title: RASMC_ATAC_UNSTIM_REP1

value: RASMC


title: RASMC_ATAC_PDGF_JQ1_2H_REP1

source_name: ATAC-Seq of RASMC under addition of PDGF and JQ1 at 2 hours


title: 132_NGP_total_F3


title: AH1263_3

description:
total RNA, rRNA-depleted
72_C

value: wild-type


title: 131_NGP_total_F1


title: 133_NGP_total_F4


title: RASMC_ATAC_PDGF_JQ1_24H_REP2

source_name: ATAC-Seq of RASMC under addition of PDGF and JQ1 at 24 hours


title: CF017

source_name: UPN727 cells stimulated with CF017 plasma


title: AH1263_2

description:
total RNA, rRNA-depleted
72_B


title: 130_NGP_total_E11


title: RASMC_ATAC_PDGF_JQ1_2H_REP2


title: CF019

source_name: UPN727 cells stimulated with CF019 plasma


title: CF018

source_name: UPN727 cells stimulated with CF018 plasma


title: CF020

source_name: UPN727 cells stimulated with CF020 plasma


title: AH1263_1

description:
total RNA, rRNA-depleted
72_A


title: 129_NGP_total_E8

source_name: cell line


title: RASMC_ATAC_PDGF_2H_REP2

source_name: ATAC-Seq of RASMC under addition of PDGF at 2 hours


title: 128_NGP_total_E7


title: RASMC_ATAC_PDGF_2H_REP1


title: 127_NGP_total_E6


title: RASMC_ATAC_PDGF_JQ1_24H_REP1


title: CF014

source_name: UPN727 cells stimulated with CF014 plasma


title: 10456SD0001: DRG_Sham_3d_T+1_1


title: 126_NGP_total_E5


title: 124_NGP_total_E1


title: RASMC_ATAC_PDGF_24H_REP2

source_name: ATAC-Seq of RASMC under addition of PDGF at 24 hours


title: 122_NGP_total_D9


title: 125_NGP_total_E2


title: 121_NGP_total_D8


title: CF016

source_name: UPN727 cells stimulated with CF016 plasma


title: CF015

source_name: UPN727 cells stimulated with CF015 plasma


title: 120_NGP_total_D7


title: 119_NGP_total_D5


title: CF011

source_name: UPN727 cells stimulated with CF011 plasma


title: CF013

source_name: UPN727 cells stimulated with CF013 plasma


title: CF008

source_name: UPN727 cells stimulated with CF008 plasma


title: 118_NGP_total_D4


title: CF010

source_name: UPN727 cells stimulated with CF010 plasma


title: RASMC_WCE_PDGF_24H_NEW

data_processing:
Sequenced reads were aligned to RN6 referenece genome using bowtie2 with default parameters with the exception of '-k 1'
Peaks were called using MACS1.4.2 with  p-val =1e-9 and background datasets as described in characteristic: input
Genome_build: rn6
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in wiggle format

source_name: Whole cell extract input control  in RASMC under PDGF stimulation at 24 hours

extract_protocol:
ChIP was performed as described previously (PMID: 27425608). Briefly, cells were fixed with 1% formaldehyde for 10min, quenched with 0.125M glycine for 5min and washed with ice cold PBS containing protease inhibitor. Cell pellets were snap frozen in liquid nitrogen and saved in -80oC. Cells were lysed in lysis buffer as described here PMID: 27425608 and chromatin was sheared using Diagenode Bioruptor plus (16 min, 30 sec on/30 sec off, setting high). Immunoprecipitation was performed using 25 million cells for each H3k27Ac (Abcam, ab4729, 5µg per IP) and RNA Pol II (Biolegend 920102 Clone 8WG16, 5µl per IP). 75 million cells and 5µg antibody was used for Brd4 IP (Bethyl A301-985A). IP Samples were reverse cross linked and DNA was purified using phenol:chloroform:isoamyl alcohol. Purified DNA samples were sent to WIGTC for NGS library preparation and sequencing.
TruSeq ChIP library preparation kit was used according to manufacturer's instructions (https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-chip.html)
ChIP-Seq with single end 40bp sequencing

tag: input

value: PDGF (25ng/ml) for 24 hours

value: ATGTCA

tag: antibody

tag: antibody maker

tag: antibody catalog number


title: RASMC_WCE_PDGF_2H_POOLED

source_name: Whole cell extract input control  in RASMC under PDGF stimulation at 2 hours

value: PDGF (25ng/ml) for 2 hours


title: RASMC_WCE_UNSTIM_NEW

source_name: Whole cell extract input control  in RASMC without stimulation

value: CTTGTA


title: RASMC_WCE_PDGF_JQ1_24H_NEW

source_name: Whole cell extract input control  in RASMC under PDGF stimulation and JQ1 treatment at 24 hours

value: JQ1 (500nM) pre-treatment for 3 hours followed by PDGF (25ng/ml) for 24 hours

value: CCGTCC


title: RASMC_WCE_UNSTIM_POOLED

value: ACTTGA


title: RASMC_ATAC_PDGF_24H_REP1


title: RASMC_WCE_PDGF_JQ1_2H_NEW

source_name: Whole cell extract input control  in RASMC under PDGF stimulation and JQ1 treatment at 2 hours

value: JQ1 (500nM) pre-treatment for 3 hours followed by PDGF (25ng/ml) for 2 hours

value: AGTTCC


title: RASMC_WCE_PDGF_2H_NEW

value: AGTCAA


title: 123_NGP_total_D10

value: nutlin

value: NGP

value: total


title: 10456SD0003: DRG_Sham_3d_T+1_3

source_name: pig caudal DRG

value: Sham

tag: treatment age

tag: time after treatment


title: CF007

source_name: UPN727 cells stimulated with CF007 plasma

tag: responder cells

value: UPN727 cells


title: CF005

source_name: UPN727 cells stimulated with CF005 plasma


title: CF002

source_name: UPN727 cells stimulated with CF002 plasma


title: RASMC_WCE_BRD4_UNSTIM_NEW

source_name: Whole cell extract input control for Brd4 ChIP-Seq in RASMC without stimulation

value: RASMC

value: Rat aortic smooth muscle cell

value: GTTTCG


title: CF004

source_name: UPN727 cells stimulated with CF004 plasma


title: CF001

source_name: UPN727 cells stimulated with CF001 plasma


title: RASMC_WCE_PDGF_24H_POOLED

value: PDGF (25ng/ml) for 24 hours

value: TAGCTT


title: CF009

source_name: UPN727 cells stimulated with CF009 plasma


title: CF012

source_name: UPN727 cells stimulated with CF012 plasma


title: 10456SD0002: DRG_Sham_3d_T+1_2

value: pig caudal dorsal root ganglia (DRG)


title: CF006

source_name: UPN727 cells stimulated with CF006 plasma


title: RASMC_WCE_BRD4_PDGF_2H_NEW

source_name: Whole cell extract input control for Brd4 ChIP-Seq in RASMC under PDGF stimulation at 24 hours

value: PDGF (25ng/ml) for 2 hours

value: CGTACG


title: uHC31

description: Gene expression data from UPN727 cells stimulated with unrelated healthy control (uHC) plasma

source_name: UPN727 cells stimulated with uHC31 plasma


title: CF003

source_name: UPN727 cells stimulated with CF003 plasma


title: 116_NGP_total_D2

source_name: cell line

value: vehicle


title: RASMC_POL2_UNSTIM_NEW

source_name: ChIP-Seq for RNA Polymerase II in RASMC under no stimulation at 0 hours

value: CAGATC

value: RNA Pol II

value: Biolegend


title: RASMC_POL2_PDGF_2H_NEW

source_name: ChIP-Seq for RNA Polymerase II in RASMC under PDGF stimulation at 2 hours

value: ACTTGA


title: 114_NGP_total_C11

value: nutlin

value: NGP


title: 113_NGP_total_C10

value: total


title: uHC30

source_name: UPN727 cells stimulated with uHC30 plasma

value: UPN727 cells


title: RASMC_POL2_PDGF_2H_JQ1_NEW

source_name: ChIP-Seq for RNA Polymerase II in RASMC under PDGF stimulation and JQ1 treatment at 2 hours

value: RASMC

value: JQ1 (500nM) pre-treatment for 3 hours followed by PDGF (25ng/ml) for 2 hours

value: GATCAG


title: uHC29

source_name: UPN727 cells stimulated with uHC29 plasma


title: RASMC_WCE_BRD4_PDGF_24H_NEW

source_name: Whole cell extract input control for Brd4 ChIP-Seq for Brd4 in RASMC under PDGF stimulation at 24 hours

value: Rat aortic smooth muscle cell

value: PDGF (25ng/ml) for 24 hours

value: GAGTGG


title: RASMC_POL2_PDGF_24H_NEW

source_name: ChIP-Seq for RNA Polymerase II in RASMC under PDGF stimulation at 24 hours

value: TAGCTT


title: 111_NGP_total_C8


title: 110_NGP_total_C7


title: 117_NGP_total_D3


title: 109_NGP_total_C6


title: 115_NGP_total_C12


title: RASMC_BRD4_UNSTIM_REP1

source_name: ChIP-Seq for Brd4 in RASMC under no stimulation at 0 hours

value: CGATGT

value: Brd4 IP

value: Bethyl


title: RASMC_BRD4_UNSTIM_NEW

value: GTCCGC


title: 107_NGP_total_C4

value: vehicle


title: uHC28

source_name: UPN727 cells stimulated with uHC28 plasma


title: RASMC_POL2_PDGF_24H_JQ1_NEW

source_name: ChIP-Seq for RNA Polymerase II in RASMC under PDGF stimulation and JQ1 treatment at 24 hours

value: JQ1 (500nM) pre-treatment for 3 hours followed by PDGF (25ng/ml) for 24 hours

value: GGCTAC

value: RNA Pol II

value: Biolegend


title: RASMC_BRD4_PDGF_2H_REP2

source_name: ChIP-Seq for Brd4 in RASMC under PDGF stimulation at 2 hours

value: PDGF (25ng/ml) for 2 hours

value: ACAGTG


title: 106_NGP_total_C3

value: NGP

value: total


title: 105_NGP_total_C2


title: RASMC_BRD4_PDGF_2H_NEW

value: RASMC

value: Rat aortic smooth muscle cell

value: GTGAAA


title: 104_NGP_total_B11


title: uHC25

source_name: UPN727 cells stimulated with uHC25 plasma

value: UPN727 cells


title: RASMC_BRD4_PDGF_24H_NEW

source_name: ChIP-Seq for Brd4 in RASMC under PDGF stimulation at 24 hours

value: PDGF (25ng/ml) for 24 hours

value: GTGGCC


title: 103_NGP_total_B10


title: 108_NGP_total_C5


title: uHC27

source_name: UPN727 cells stimulated with uHC27 plasma


title: uHC24

source_name: UPN727 cells stimulated with uHC024 plasma


title: 112_NGP_total_C9

value: nutlin


title: RASMC_WCE_UNSTIM_REP2

data_processing:
Sequenced reads were aligned to a custom reference bowtie2 index combining the RN6 and DM6 genome builds
ChIP_RX scaling factors were determined as in Orlando et al., 2014, "Quantitative ChIP-Seq normalization reveals global modulation of the epigenome", PMID 25437568
Peaks were called using MACS1.4.2 with  p-val =1e-9 and background datasets as described in characteristic: input
Genome_build: rn6:dm6
Supplementary_files_format_and_content: Processed ChIP-Rx datasets are provided in a cell count normalized scaled and unscaled wig format. File RN6_RASMC_NEW_CHIPRX_SCALE_FACTORS.txt contains ChIP-Rx scale factors for each dataset

source_name: Spike in normalized ChIP-Seq for H3k27ac in RASMC, unstimulated at 0hr

extract_protocol:
ChIP was performed as described previously (PMID: 27425608). Briefly, cells were fixed with 1% formaldehyde for 10min, quenched with 0.125M glycine for 5min and washed with ice cold PBS containing protease inhibitor. Cell pellets were snap frozen in liquid nitrogen and saved in -80oC. Cells were lysed in lysis buffer as described here PMID: 27425608 and chromatin was sheared using Diagenode Bioruptor plus (16 min, 30 sec on/30 sec off, setting high). Immunoprecipitation was performed using 25 million cells for each H3k27Ac (Abcam, ab4729, 5µg per IP) and RNA Pol II (Biolegend 920102 Clone 8WG16, 5µl per IP). 75 million cells and 5µg antibody was used for Brd4 IP (Bethyl A301-985A). IP Samples were reverse cross linked and DNA was purified using phenol:chloroform:isoamyl alcohol. Purified DNA samples were sent to WIGTC for NGS library preparation and sequencing.
TruSeq ChIP library preparation kit was used according to manufacturer's instructions (https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-chip.html)
ChIP-Rx (PMID:25437568) with single end 40bp sequencing

value: CTTGTA


title: 102_NGP_total_B9

source_name: cell line


title: RASMC_WCE_UNSTIM_NEW


title: uHC22

source_name: UPN727 cells stimulated with uHC22 plasma


title: uHC19

source_name: UPN727 cells stimulated with uHC19 plasma


title: uHC21

source_name: UPN727 cells stimulated with uHC21 plasma


title: RASMC_WCE_PDGF_JQ1_2H_REP2

source_name: Spike in normalized ChIP-Seq for H3k27ac in RASMC, 2hr after PDGF and JQ1 treatment

value: AGTTCC


title: RASMC_BRD4_PDGF_24H_REP2

value: CAGATC

value: Brd4 IP

value: Bethyl


title: 100_NGP_total_B6

value: vehicle


title: RASMC_WCE_PDGF_JQ1_2H_NEW


title: 99_NGP_total_B5


title: 98_NGP_total_B4


title: uHC20

source_name: UPN727 cells stimulated with uHC20 plasma


title: uHC26

source_name: UPN727 cells stimulated with uHC26 plasma


title: uHC23

source_name: UPN727 cells stimulated with uHC023 plasma


title: uHC18

source_name: UPN727 cells stimulated with uHC18 plasma


title: uHC16

source_name: UPN727 cells stimulated with uHC16 plasma


title: uHC17

source_name: UPN727 cells stimulated with uHC17 plasma


title: uHC15

source_name: UPN727 cells stimulated with uHC15 plasma


title: 97_NGP_total_B3


title: uHC14

source_name: UPN727 cells stimulated with uHC14 plasma


title: RASMC_WCE_PDGF_JQ1_24H_NEW

source_name: Spike in normalized ChIP-Seq for H3k27ac in RASMC, 24hr after PDGF and JQ1 treatment

value: CCGTCC


title: uHC12

source_name: UPN727 cells stimulated with uHC12 plasma


title: RASMC_WCE_PDGF_2H_REP2

source_name: Spike in normalized ChIP-Seq for H3k27ac in RASMC, 2hr after PDGF treatment

value: AGTCAA


title: uHC10

source_name: UPN727 cells stimulated with uHC10 plasma


title: 101_NGP_total_B7

source_name: cell line

value: NGP


title: RASMC_WCE_PDGF_2H_NEW


title: 96_NGP_total_B2

value: total


title: uHC11

source_name: UPN727 cells stimulated with uHC11 plasma


title: 94_NGP_total_A11


title: RASMC_WCE_PDGF_24H_REP2

source_name: Spike in normalized ChIP-Seq for H3k27ac in RASMC, 24hr after PDGF treatment

value: RASMC

value: ATGTCA


title: RASMC_WCE_PDGF_24H_NEW

source_name: Spike in normalized ChIP-Seq for H3k27ac in RASMC, whole cell extract 24hr after PDGF treatment

value: Rat aortic smooth muscle cell


title: RASMC_WCE_PDGF_JQ1_24H_REP2


title: 93_NGP_total_A10


title: mouse8

city: GALVESTON

first: Kamil

last: Khanipov

address: 301 University Blvd

institute: University of Texas Medical Branch

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed by 14 bases from the 5' end, reads containing nucleotides with a phred quality score below 15 were removed.
CLC Genomics Workbench 9.0.1 RNA Seq Analysis tool was used to map all of the reads to the Noncode v4 lncRNA allowing up to 2 mismatches
Genome_build: mm9
Supplementary_files_format_and_content: Excel file with read counts and coverage for each lncRNA from Noncode v4

source_name: lung tissue

extract_protocol:
Total RNA from lung tissues was extracted using TRIzol reagent according to the manufacturer’s instructions (Invitrogen).
RNA samples were subjected to treatment with DNaseI (NEB) to remove any contaminating DNA and then enriched with Ribo-Zero rRNA Removal kit (Illumina). Concentration of RNA in sample preparations using the MultiSkan Go UV/Vis instrument for microsample analysis (Thermo Scientific) and the quality of RNA was evaluated on a bioanalyzer (Agilent Technologies). The samples with an RNA integrity number (RIN) of >9 were subjected to RNA-sequencing (Chowdhury et al., 2017). Briefly, RNA fragments of 50 bases were generated by incubating purified total RNA in a fragmentation buffer (Ambion) and fragmented RNA was then 140 ligated with 5′ and 3′-adaptors using a T4 RNA ligase (NEB). Adaptor-ligated RNAs were reverse transcribed and subjected to PCR amplification with barcoded primers (Illumina) (Narra et al., 2016; Schroeder et al., 2016). Finally, amplified cDNA libraries were purified using standard gel purification procedures.
RNA sequencing was performed on an Illumina HiSeq 1500 equipment at the Next Generation Sequencing Core facility at the UTMB. Briefly, 50 base long reads were obtained from the RNA derived from the lungs of R. conorii-infected and uninfected control (n=3 for each) mice.

tag: strain

tag: infection

value: R. conorii

value: lung


title: RASMC_H3K27AC_UNSTIM_REP1

source_name: Spike in normalized ChIP-Seq for H3k27ac in RASMC, unstimulated at 0hr

value: TTAGGC

value: Abcam


title: mouse7


title: mouse5


title: uHC13

source_name: UPN727 cells stimulated with uHC13 plasma

value: UPN727 cells


title: RASMC_H3K27AC_UNSTIM_NEW

value: CGATGT


title: mouse3

value: uninfected control


title: 92_NGP_total_A9


title: uHC08

source_name: UPN727 cells stimulated with uHC08 plasma


title: uHC09

source_name: UPN727 cells stimulated with uHC09 plasma


title: 90_NGP_total_A7

value: nutlin


title: RASMC_H3K27AC_PDGF_JQ1_2H_REP2

source_name: Spike in normalized ChIP-Seq for H3k27ac in RASMC, 2hr after PDGF and JQ1 treatment

value: ACAGTG


title: 95_NGP_total_A12

value: vehicle


title: RASMC_H3K27AC_PDGF_JQ1_2H_NEW

value: TGACCA


title: uHC06

source_name: UPN727 cells stimulated with uHC06 plasma


title: mouse1b


title: 89_NGP_total_A6


title: RASMC_H3K27AC_PDGF_JQ1_24H_REP2

value: GGCTAC


title: RASMC_H3K27AC_PDGF_JQ1_24H_NEW

value: GCCAAT


title: mouse1a


title: 88_NGP_total_A5

value: NGP

value: total


title: 91_NGP_total_A8


title: 87_NGP_total_A4


title: uHC04

source_name: UPN727 cells stimulated with uHC04 plasma


title: RASMC_H3K27AC_PDGF_2H_REP2

value: RASMC


title: 86_NGP_total_A3


title: 85_NGP_total_A2


title: RASMC_H3K27AC_PDGF_2H_NEW

value: Rat aortic smooth muscle cell


title: 84_NGP_total_A1


title: RASMC_H3K27AC_PDGF_24H_REP2

value: ACTTGA


title: uHC05

source_name: UPN727 cells stimulated with uHC05 plasma


title: 82_NGP_pA_H11

value: polyA+


title: uHC03

source_name: UPN727 cells stimulated with uHC03 plasma


title: AsCas12a - T gRNA

city: Raleigh

first: Chase

last: Beisel

state: NC

address: 840 Main Campus Drive

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

data_processing:
see the following website: https://bitbucket.org/csmaxwell/crispr-txtl-pam-counting-script/overview
Real Time Analysis for basecalling
Supplementary_files_format_and_content: counts .csv files

organism: synthetic construct

source_name: plasmid DNA

extract_protocol:
myTXTL extract purchased from Arbor Biosciences.
The samples were PCR amplified twice. The 1st PCR involved attachment of unique adapters that provided a landing site for the 2nd PCR. The 2nd PCR involved attachment of i5 and i7 Nextera low plex pooling indices.

treatment_protocol: Prior to library construction, the TXTL reaction should be diluted 1:10 for successful amplification using a high-fidelity polymerase.

tag: in vitro environment

value: myTXTL from Arbor Biosciences

tag: grna

value: Targets the randomized PAM library


title: uHC02

source_name: UPN727 cells stimulated with uHC02 plasma

value: UPN727 cells


title: 83_NGP_pA_H12

tag: treatment

tag: cell line


title: 81_NGP_pA_H10

tag: mrna seq


title: uHC07

source_name: UPN727 cells stimulated with uHC07 plasma


title: 80_NGP_pA_H9

source_name: cell line


title: uHC01

source_name: UPN727 cells stimulated with uHC01 plasma


title: 79_NGP_pA_H8


title: Tsku knockout biological rep1

city: Ann Arbor

first: QIUYU

last: WANG

state: MI

address: 210 Washtenaw Ave

institute: Life sciences institute

description: Gene expression data from KO mice biological rep1

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on Mouse Gene ST 2.1 arrays, and were washed and stained using the Affymetrix GeneTitan system (software version 4.3.0.1592)

scan_protocol: Arrays were scanned using the Affymetrix GeneTitan system (software version 4.3.0.1592)

data_processing: Data was analyzed using the limma and oligo Bioconductor packages implemented in the R-statistical language version 3.3.0. RMA was used to fit log2 transformed expression values

source_name: BAT

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA.

extract_protocol: mouse BAT was extracted, immediately frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.

treatment_protocol: WT and KO mice was fed with chow diet

tag: age

value: 4 months

tag: gender

value: male

value: BAT

tag: genotype

value: KO


title: Wild type biological rep2

description: Gene expression data from wild type mice biological rep2

tag: tissue

value: WT


title: 77_NGP_pA_H4

city: Ghent

first: Celine

last: Everaert

address: De Pintelaan 185

institute: University Ghent

value: vehicle


title: AsCas12a - NT gRNA

value: Non-targeting gRNA


title: 78_NGP_pA_H6


title: 76_NGP_pA_H3


title: 75_NGP_pA_H2


title: 74_NGP_pA_G12

value: nutlin


title: Wild type biological rep1

description: Gene expression data from wild type mice biological rep1


title: GIST44_DMET

city: Bologna

first: Gloria

last: Ravegnini

state: BO

address: via irnerio 48

department: PHARMACY AND BIOTECHNOLOGY

country: Italy

institute: UNIVERSITY OF BOLOGNA

description: GIST KIT exon 11 mutant

hyb_protocol: Labeled DNA products were hybridized onto DMET Plus arrays at 49°C and 35 rpm for 16 h. Subsequent to hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Scanned in an Affymetrix GeneChip Scanner 3000 7G

data_processing:
Data extraction was done by the Affymetrix Command Console v1.3. Algorithm is Fixed Genotype Boundaries version 2 that is built in Command Console.
Data were produced by Affymetrix Command Console Analysis Software. CHP files contain probe set analysis results.

label_protocol: Genomic DNA fragments were biotinylated at 3' end using terminal deoxynucleotidyl transferase according to the standard Affymetrix protocol.

extract_protocol: Genomic DNA was extracted from from peripheral blood  using the Qiagen DNA Blood Mini Kit. DNA concentratuion was measured with Picogreen

tag: disease

value: GIST

value: peripheral blood

tag: agent

value: imatinib

tag: imatinib responder

value: Yes


title: 73_NGP_pA_G11

value: NGP


title: 6_w_osa-IR_Mlut24h_C

city: TAMPERE

first: Mika

last: Ramet

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: sequencing was done in 1 lane

data_processing:
The base calling was done using bcl2fastq (v. 1.8.4)
Read alignment was done using TopHat (2.0.10) to BDGP6 assembly of Drosophila melanogaster genome reference
Genewise read counts were calculated using subread (v1.5.0)
Genome_build: Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part # 15031047)
Supplementary_files_format_and_content: RNA-seq

organism: Drosophila melanogaster

source_name: whole organism

extract_protocol:
total RNAs were extracted with TRI reagent according to the manufacturers protocol (ThermoFisher Scientific) and the resulting RNAs treated with the RapidOut DNA Removal Kit (ThermoFisher Scientific).
Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part # 15031047)

tag: infect

value: Micrococcus luteus

tag: infection time

value: 24 hours


title: GIST43_DMET

description: GIST KIT exon 11 mutant

value: No


title: 5_w_osa-IR_Mlut24h_B

description: sequencing was done in 1 lane


title: 4_w_osa-IR_Mlut24h_A

description: sequencing was done in 1 lane


title: GIST42_DMET

description: GIST KIT exon 11 mutant


title: 3_w_osa-IR_C

description: sequencing was done in 1 lane

value: 0 hours


title: bts +Fe Root biorep3

city: Hanover

first: Maria

middle: Noelle

last: Hindt

state: NH

address: 78 College St. Rm 130 HB6044

institute: Dartmouth College

description: Gene expression in roots of plants exposed to 72 hrs Fe sufficiency

hyb_protocol: 5.5ug of labelled cRNA went into the fragmentation and hybridization protocol which is done using the Affymetrix Hybridization, Wash and Stain kit (affy cat#900720) according to directions.

scan_protocol: The arrays used were the Arabidopsis 1.0ST arrays.  The were washed and stained using the Affymetrix  Fluidics 450 station and scanned using the GeneChip Scanner 3000.

data_processing: Raw data was RMA normalized using Affymetrix Expression Console software and downstream analyses were performed using BRB-Array Tools Version 4.2.1. Differentially expressed genes were identified among two classes using a random-variance t-test with a p-value cutoff of 0.01.

organism: Arabidopsis thaliana

source_name: Root 72 hr+Fe bts-3

label_protocol: 100 ng RNA used for labeling. The Ambion WT Expression kit ( Ambion cat@4411974) and the Affymetrix GeneChip WT Terminal Labelling kit (Affy cat# 901524) were used according to directions

growth_protocol: Plants were grown for 2 weeks on B5 medium and transferred to either +Fe or -Fe medium for 3 days (72 hours) before RNA extraction

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

treatment_protocol: Before RNA extraction, root and shoot tissue were separated and flash frozen in liquid nitrogen immediately

value: Root


title: bts -Fe Root biorep3

description: Gene expression in roots of plants exposed to 72 hrs Fe deficiency

source_name: Root 72 hr-Fe bts-3


title: WT -Fe Root biorep2

source_name: Root 72 hr -Fe WT

value: WT (Col)


title: 71_NGP_pA_G9

value: polyA+


title: bts -Fe Root biorep1


title: WT -Fe Root biorep1


title: bts +Fe Root biorep2


title: GIST40_DMET

description: GIST KIT exon 11 mutant


title: 70_NGP_pA_G8


title: GIST41_DMET

description: GIST KIT exon 11 mutant

value: Severe Toxicity


title: bts +Fe Root biorep1


title: 2_w_osa-IR_B

description: sequencing was done in 1 lane


title: bts -Fe Root biorep2


title: WT +Fe Root biorep2

source_name: Root 72 hr +Fe WT


title: 68_NGP_pA_G5


title: 72_NGP_pA_G10


title: GIST38_DMET

description: GIST KIT exon 11 mutant


title: w1118_w1118_rep3

city: Bethesda

first: Brian

last: Oliver

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description:
FBgn0014387; FBgn0029899
ERCC subpool: 78B
Analysis group: sov control

data_processing:
RNAseq librarires were sequenced on an Illumina HiSeq 2500 machine with base calling by CASAVA software (version 1.8.2, Illumina, San Diego, CA, USA).
RNAseq reads were mapped to the Drosophila melanogaster FlyBase r6.21 genome with Hisat2 (version 2.0.5., PMID: 25751142, -k 1 --rna-strandness R --dta).
Read counts for each attribute of the Drosophila melanogaster FlyBase r6.21 GTF file were determined with HTSeq-count (version 0.7.2., PMID:25260700). Spike-in ERCC and transposable element sequence locations were added to the FlyBase r6.21 GTF file. Transposable element sequence locations were extracted from the UCSC Genome Browser RepeatMasker track (PMID:29106570; Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-4.0.).
Genome_build: Drosophila melanogaster FlyBase release 6.21 genome.
Supplementary_files_format_and_content: txt files contain total read counts for each attribute of the Drosophila melanogaster FlyBase release 6.21 GTF file.

source_name: ovary

growth_protocol: Flies were raised on Fly Food B with 0.4% propionic acid and 0.15% tegosept (Labexpress, Ann Arbor, MI) at 25°C and constant light. Females of the desired genotype were collected post-eclosion and aged 4-5 days before tissue extraction.

extract_protocol:
15 ovaries were dissected in PBS and immediately transferred to ice cold PBS for each sample. Total RNA was extracted with a Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) according to manufacturer’s protocol.
PolyA RNA was isolated from 200 ng of total RNA and used to create RNAseq libraries according to PMID: 27599372. 10 pg of ERCC spike-in control RNAs (pools 78A or 78B) were added to each sample during library preparation (PMID: 21816910, PMID:22859977, PMID:27342544, PMID: 27512518).

value: 4-5 days post-eclosion

tag: age cv

tag: tissue cv

tag: Sex

value: Female

tag: sex cv

tag: developmental stage

value: Adult

tag: developmental stage cv

tag: fertility phenotype

value: Fertile


title: GIST39_DMET

description: GIST KIT exon 11 mutant

value: GIST


title: 69_NGP_pA_G6

tag: treatment

value: vehicle

tag: cell line

tag: mrna seq


title: w1118_w1118_rep2

description:
FBgn0014387; FBgn0029899
ERCC subpool: 78A
Analysis group: sov control

tag: age

tag: genotype


title: GIST37_DMET

description: GIST KIT exon 11 mutant

tag: disease

tag: tissue

value: peripheral blood

value: imatinib


title: 67_NGP_pA_G4

value: nutlin

value: NGP


title: GIST36_DMET

description: GIST KIT exon 11 mutant

tag: agent

tag: imatinib responder


title: Tsku knockout biological rep2

description: Gene expression data from KO mice biological rep2

tag: strain

value: 4 months

tag: gender

value: male

value: BAT

value: KO


title: GIST35_DMET

description: GIST KIT exon 11 mutant

value: Yes


title: w1118_w1118_rep1

tag: age cv

tag: tissue cv


title: 1_w_osa-IR_A

description: sequencing was done in 1 lane

tag: infect

tag: infection time

value: 0 hours


title: w1118_sov2_rep2

tag: Sex

tag: sex cv

tag: developmental stage

tag: developmental stage cv


title: GIST34_DMET

description: GIST KIT exon 11 mutant


title: 65_NGP_pA_G2

tag: treatment

tag: cell line

tag: mrna seq

value: polyA+


title: 66_NGP_pA_G3


title: w1118_sov2_rep1

tag: age

value: 4-5 days post-eclosion

tag: genotype

tag: fertility phenotype


title: 64_NGP_pA_G1


title: 63_NGP_pA_F11


title: GIST33_DMET

description: GIST KIT exon 11 mutant

tag: disease

tag: tissue

tag: agent

tag: imatinib responder

value: No


title: Progressive 17

city: London

first: Vitor

middle: H

last: Teixeira

address: 5 University Street

department: Medicine

institute: University College London

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw gene expression data were expressed as log2 ratios of fluorescence intensities of the experimental samples. Quantile normalization was applied. Differential expression analysis was performed using the significance analysis of microarrays method as implemented in the samr Bioconductor package. Raw p-values were adjusted by the Benjamini-Hochberg procedure to give a FDR. A significance threshold of FDR < 0.01 was used to select differentially expressed genes.

source_name: Human preinvasive lung squamous cell carcinoma lesions_progressive

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

extract_protocol: Laser-capture micro-dissection (LCM) was used to selectively isolate CIS cells for molecular analysis, reducing the extent of contamination by stromal cells. RNA was extracted using the High Pure FFPE RNA Kit (Roche Applied Science, West Sussex, UK) according to manufacturer’s protocol. Quantification was carried out using the Quant-iT RNA assay kit and the Qubit® 2.0 fluorometer (Life Technologies, Paisley, UK).

value: Preinvasive lung squamous cell carcinoma lesions

tag: lesion outcome

value: progression


title: w1118_NP6070_rep3

tag: age cv

tag: tissue cv

value: Female

value: Adult

value: Fertile


title: 62_NGP_pA_F10

value: vehicle


title: w1118_NP6070_rep2

tag: Sex


title: Progressive 14


title: WT +Fe Root biorep1

value: Root

value: WT (Col)


title: Progressive 15


title: Progressive 16


title: GIST31_DMET

description: GIST KIT exon 11 mutant

value: GIST

value: peripheral blood

value: imatinib


title: w1118_sov2_rep3

tag: sex cv


title: GIST30_DMET

description: GIST KIT exon 11 mutant


title: 61_NGP_pA_F9

value: nutlin

value: NGP


title: w1118_NP6070_rep1

tag: developmental stage


title: 60_NGP_pA_F8


title: GIST29_DMET

description: GIST KIT exon 11 mutant


title: Progressive 10


title: GIST28_DMET

description: GIST KIT exon 11 mutant

value: Yes


title: w1118_KG00226_rep3

tag: developmental stage cv


title: w1118_KG00226_rep2


title: 59_NGP_pA_F7

tag: treatment

value: polyA+


title: Progressive 13


title: Progressive 11


title: 58_NGP_pA_F6

tag: cell line


title: Progressive 12


title: GIST26_DMET

description: GIST KIT exon 11 mutant


title: GIST25_DMET

description: GIST KIT exon 11 mutant


title: tj-Gal4_sov-RNAi_rep3

description:
FBgn0014387; FBgn0029899
ERCC subpool: 78A
Analysis group: sov RNAi

value: 4-5 days post-eclosion

value: Sterile


title: 56_NGP_pA_F4

tag: mrna seq


title: Progressive 8

value: Preinvasive lung squamous cell carcinoma lesions


title: w1118_KG00226_rep1

tag: age


title: Progressive 7

value: progression


title: tj-Gal4_sov-RNAi_rep2

value: Female

tag: genotype


title: GIST24_DMET

description: GIST KIT exon 11 mutant

value: No


title: Progressive 6


title: GIST23_DMET

description: GIST KIT exon 11 mutant


title: 55_NGP_pA_F3


title: RASMC_H3K27AC_PDGF_24H_NEW

source_name: Spike in normalized ChIP-Seq for H3k27ac in RASMC, 24hr after PDGF treatment

value: RASMC

value: Rat aortic smooth muscle cell

tag: input

tag: barcode

value: ACAGTG

tag: antibody

tag: antibody maker

value: Abcam

tag: antibody catalog number


title: tj-Gal4_sov-RNAi_rep1

value: Adult

tag: fertility phenotype


title: 54_NGP_pA_F2

value: vehicle


title: Progressive 9

tag: tissue

tag: lesion outcome


title: GIST22_DMET

description: GIST KIT exon 11 mutant

tag: disease

value: GIST

value: peripheral blood

tag: agent

value: imatinib

tag: imatinib responder


title: tj-Gal4_mCherry-RNAi_rep3

description:
FBgn0014387; FBgn0029899
ERCC subpool: 78A
Analysis group: control RNAi

tag: age cv

tag: tissue cv

tag: Sex

tag: sex cv

tag: developmental stage

tag: developmental stage cv

value: Genotype:y[*] w[*]/y[1] sc[*] v[1]; P{ww[+mC]=GawB}NP1624; P{y[+t7.7] v[+t1.8]=VALIUM20-mCherry}attP2

value: Fertile


title: GIST21_DMET

description: GIST KIT exon 11 mutant


title: 53_NGP_pA_F1

tag: treatment

tag: cell line

value: NGP

tag: mrna seq

value: polyA+


title: GIST19_DMET

description: GIST KIT exon 11 mutant


title: 57_NGP_pA_F5


title: GIST18_DMET

description: GIST KIT exon 11 mutant

value: Yes


title: tj-Gal4_mCherry-RNAi_rep1

description:
FBgn0014387; FBgn0029899
ERCC subpool: 78B
Analysis group: control RNAi

tag: age

value: 4-5 days post-eclosion

tag: genotype


title: tj-Gal4_mCherry-RNAi_rep2

value: Female

tag: fertility phenotype


title: GIST17_DMET

description: GIST KIT exon 11 mutant

tag: tissue

value: No


title: 50_NGP_pA_E9

value: nutlin


title: Progressive 4

value: Preinvasive lung squamous cell carcinoma lesions

tag: lesion outcome

value: progression


title: sovML150_w1118_rep2


title: GIST16_DMET

description: GIST KIT exon 11 mutant

tag: disease

value: Severe Toxicity


title: sovML150_w1118_rep3

value: Adult


title: Progressive 5


title: Progressive 1


title: Progressive 2


title: sovML150_w1118_rep1


title: Regressive 16

source_name: Human preinvasive lung squamous cell carcinoma lesions_regressive

value: regression


title: Regressive 15


title: GIST15_DMET

description: GIST KIT exon 11 mutant

value: GIST

tag: agent


title: sovML150_sov2_rep3

description:
FBgn0014387; FBgn0029899
ERCC subpool: 78B
Analysis group: sov mutant

value: Sterile


title: Progressive 3


title: 48_NGP_pA_E7


title: 49_NGP_pA_E8

value: vehicle


title: Regressive 13


title: GIST14_DMET

description: GIST KIT exon 11 mutant

value: peripheral blood

value: imatinib

tag: imatinib responder


title: 52_NGP_pA_E12

value: NGP


title: Regressive 12


title: sovML150_sov2_rep2

description:
FBgn0014387; FBgn0029899
ERCC subpool: 78A
Analysis group: sov mutant

tag: age cv


title: 51_NGP_pA_E11

value: polyA+


title: Regressive 11


title: GIST13_DMET

description: GIST KIT exon 11 mutant


title: 46_NGP_pA_E5


title: Regressive 10


title: GIST12_DMET

description: GIST KIT exon 11 mutant

value: Yes


title: GIST11_DMET

description: GIST KIT exon 11 mutant


title: sovML150_KG00226_rep3

value: 4-5 days post-eclosion

tag: tissue cv


title: sovML150_sov2_rep1

tag: Sex

value: Female


title: Regressive 14


title: sovML150_KG00226_rep2

tag: sex cv


title: 43_NGP_pA_E2


title: 47_NGP_pA_E6


title: Regressive 9


title: GIST10_DMET

description: GIST KIT exon 11 mutant

value: No


title: sovEA42_w1118_rep2

tag: developmental stage

value: Fertile


title: sovML150_KG00226_rep1

tag: developmental stage cv


title: sovEA42_w1118_rep3


title: GIST09_DMET

description: GIST KIT exon 11 mutant


title: GIST06_DMET

description: GIST KIT exon 11 mutant


title: 41_NGP_pA_D11

tag: treatment


title: Regressive 8

value: Preinvasive lung squamous cell carcinoma lesions


title: Regressive 6


title: 45_NGP_pA_E4

tag: cell line


title: Regressive 7


title: sovEA42_w1118_rep1


title: 40_NGP_pA_D10

tag: mrna seq


title: 44_NGP_pA_E3


title: 39_NGP_pA_D9


title: GIST05_DMET

description: GIST KIT exon 11 mutant


title: GIST04_DMET

description: GIST KIT exon 11 mutant


title: 42_NGP_pA_D12

value: nutlin


title: sovEA42_sov2_rep3

tag: age

value: Genotype:sov[EA42]/y[1] cv[1] sov[2] v[1] f[1]


title: Regressive 4


title: 38_NGP_pA_D8


title: Regressive 5


title: sovEA42_sov2_rep2

value: Adult

tag: genotype


title: Regressive 3

value: regression


title: 37_NGP_pA_D5


title: GIST01_DMET

description: GIST KIT exon 11 mutant

value: GIST


title: 36_NGP_pA_D4


title: sovEA42_KG00226_rep3

tag: fertility phenotype

value: Sterile


title: Regressive 1

tag: tissue


title: 35_NGP_pA_D3

value: vehicle


title: Regressive 2

tag: lesion outcome


title: 34_NGP_pA_D2


title: sovEA42_KG00226_rep1


title: 33_NGP_pA_D1


title: sov2_w1118_rep3


title: 32_NGP_pA_C12


title: GIST02_DMET

description: GIST KIT exon 11 mutant

tag: disease

value: peripheral blood


title: sov2_w1118_rep2


title: 31_NGP_pA_C11


title: Mucinous cancer cell_control siRNA_rep3

first: Takeshi

last: Hisamatsu

state: Texas

address: 1515 Holcombe Boulevard

department: Gynecologic Oncology and Reproductive Medicine

institute: The University of Texas MD Anderson Cancer Center

hyb_protocol: 100ng of total RNA was used for hybridization to each chip and incubated for 12 hours. Hybridization assays were left at 65°C until ready for processing and did not exceed 30 hours.

scan_protocol: After sample processing and hybridization were completed, samples were inserted into the Prep Station for purification and immobilization onto the internal surface of each sample cartridge (3 hours). The Digital Analyzer, a multi-channel epifluorescence scanner configured specifically for use with NanoString’s sample cartridges, was used for all scanning (~4.5 hours) (nCounter Dx Analysis System User Manual).

data_processing:
The Digital Analyzer for data imaging and processing (nCounter Dx Analysis System User Manual) and nSolver2 for data analysis (nCounter Expression Data Analysis Guide).
A two-sided t-test was applied to determine significantly different miRNAs between samples.

label_protocol: 100ng of each total RNA sample was labeled with a Reporter CodeSet according to NanoString. protocols (nCounter miRNA Expression Assay User Manual).

growth_protocol: RMUG-S-ip1 mucinous ovarian cancer cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and 0.1% gentamicin at 37°C in 5% CO2 and 95% air.

extract_protocol: Total RNA was extracted from the RMUG-S-ip1 cells under normal or silencing PRKRA conditions using the mirVana RNA Isolation kit.

treatment_protocol: siPRKRA or control siRNA transfections were performed using RNAiMAX reagent with the forward transfection protocol from the manufacturer. Media was changed 6 hours after transfection to minimize toxicity.

tag: cell type

value: mucinous ovarian cancer cells

tag: genotype/variation

value: control siRNA


title: Mucinous cancer cell_siPRKRA_rep2

value: siPRKRA


title: sovEA42_sov2_rep1

tag: age cv


title: Mucinous cancer cell_siPRKRA_rep1


title: Mucinous cancer cell_siPRKRA_rep3


title: 30_NGP_pA_C10

value: NGP

value: polyA+


title: sovEA42_KG00226_rep2

value: 4-5 days post-eclosion

tag: tissue cv

value: Female


title: sov2_w1118_rep1

tag: Sex

value: Fertile


title: Mucinous cancer cell_control siRNA_rep2


title: Mucinous cancer cell_control siRNA_rep1


title: sov2_NP6070_rep3

tag: sex cv


title: sov2_NP6070_rep2

tag: developmental stage


title: 28_NGP_pA_C8