title: Heart_DM1_9

source_name: Heart

value: Heart


title: Quad_Control_4

status: Public on Sep 29 2016

type: SRA

city: Gainesville

first: Eric

middle: T

last: Wang

state: FL

address: 2033 Mowry Rd

country: USA

institute: University of Florida

library_source: transcriptomic

data_processing:
Used standard Hiseq 2000 software.
Reads were mapped using Hisat2.
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] Alternative splicing events were quantitated using MISO software.

molecule: total RNA

organism: Homo sapiens

source_name: Quadriceps muscle

extract_protocol:
Frozen tissue samples were lysed using a homogenizer in Trizol. Chloroform was added and mixed, and the aqueous layer was added to isopropanol to precipitate RNA. The RNA was then cleaned up on RNeasy columns (Qiagen) with on column DNase treatment.
Strand-specific libraries (using dUTP incorporation during reverse transcription, and USER treatment prior to PCR) were prepared using standard protocols. RNA was first fragmented, and then ribosomal RNA was subtracted using ribo-zero beads from Epicentre Biotechnologies. Reverse transcription was performed using random primers, followed by 2nd strand cDNA synthesis, end repair, adenylation, and ligation of adapters. Products were run on agarose, size selected, and then subjected to 14-18 cycles of PCR.

treatment_protocol: Autopsy and biopsy samples were frozen at -80 until RNA extraction.

tag: source

value: biopsy

tag: anonymized patient identifier

tag: anonymized center identifier

value: B

tag: disease classification

tag: tissue

value: Quadriceps muscle


title: Heart_DM1_8

value: autopsy

value: C

value: myotonic dystrophy type 1


title: Heart_DM1_7


title: Heart_DM1_19

value: D


title: Heart_DM1_14


title: Heart_DM1_11


title: Heart_DM1_13


title: Heart_DM1_10


title: Heart_Control_2


title: Gastroc_Duchenne_4

source_name: Gastrocnemius muscle

value: Duchenne muscular dystrophy

value: Gastrocnemius muscle


title: Quad_Control_2


title: Quad_Control_12


title: Heart_Control_3


title: Heart_Control_1


title: Diaphragm_DM1_1

source_name: Diaphragm muscle

value: Diaphragm muscle


title: Gastroc_DM1_1


title: Digitorum_DM1_1

source_name: Digitorum muscle

value: Digitorum muscle


title: Heart_DM2_20


title: Deltoid_DM1_3

source_name: Deltoid muscle

value: Deltoid muscle


title: Diaphragm_DM1_3


title: Deltoid_DM1_2


title: Deltoid_DM1_1


title: Bicep_DM1_4

source_name: Bicep muscle

value: Bicep muscle


title: Bicep_Duchenne_5


title: Bicep_DM1_3


title: Heart_DM1_15


title: Bicep_DM1_2


title: Heart_DM1_12


title: EPCs Protocol I

city: Singapore

first: Xiaoran

last: Chai

state: Singapore

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

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Illumina Casava1.9 software used for basecalling
Sequenced reads were trimmed for adaptor sequence,, then mapped to hg19 whole genome using tophat-2.0.9 with parameters --bowtie-n
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks-2.1.1 with parameters -b -u --max-bundle-frags 100000000
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: hESCs-derived endothelial progenitor cells, from protocol I, CD31+ purification on Day 7 of differentiation

extract_protocol:
Total RNA from HUVECs and hESCs-derived cells at different time points was purified using RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions.
RNAseq libraries were prepared using Illumina Tru-Seq Stranded Total RNA with Ribo-Zero Gold kit protocol, according to the manufacturer’s instructions (Illumina, San Diego, California, USA). Libraries were validated with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA), diluted and applied to an Illumina flow cell using the Illumina Cluster Station. Sequencing was performed on Illumina HiSeq2000 sequencer at the Duke-NUS Genome Biology Facility with the paired-end 100 bp read option


title: EPCs Protocol II

source_name: hESCs-derived endothelial progenitor cells, from protocol II, CD31+ purification on Day 11 of differentiation


title: Input_2

city: Jerusalem

first: Eran

last: Meshorer

address: Edmond J. Safra Campus

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

library_source: genomic

data_processing:
Raw reads that passed the quality controls were  aligned to human genome assembly hg19 using Bowtie 0.12.7 (Langmead et al. Genome Biol., 2009), taking only uniquely aligned reads with no more than 2 mismatches.
Significant peaks of H3K4me3 and H3K27me3 were extracted using MACS 1.4 (Zhang et al., 2008), using a minimal p-value cutoff of 10E-5 and a fold change for model building of 30.
Peak detection for H1.0 and H1.4 was performed using in house scriots. In short, reads were counted within 50 bp windows. The median was calculated for each three bins and normalized by the sum of the reads.  To effectively capture local biases in the genome, the Log2 ratio between the ChIP samples and the input genomic DNA was calculated. Peaks were defined as regions with log2 ratio of ChIP DNA over Input DNA > 2 within six neighbouring windows, and average number of reads > 15.
Genome_build: hg19
Supplementary_files_format_and_content: bed format

molecule: genomic DNA

source_name: in vitro transformed human skin fibroblasts

growth_protocol: Cells were grown in minimum essential medium (MEM) containing 15% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin, at 37 °C in 5% CO2

extract_protocol:
Cells were harvested with trypsin and ChIP was performed as previously described (Sailaja et al., Methods in molecular biology, 2012).
Library construction was carried out as published (Blecher-Gonen et al., 2013, Nat Prot). Paired end libraries were constructed using standard Illumina protocols, with some modifications. Agencourt AMPure XP (Beckman Coulter) at 0.8x ratio were used to size select out adapter dimers. The Illumina Phusion enzyme was replaced by Kapa HiFi HotStart ready mix (Kapa Biosystems). An Invitrogen SizeSelect R-gel system (Life Technologies) was used to size select following PCR amplification.

tag: cell type

tag: chip antibody


title: HUVECs

source_name: Primary cells isolated from umbilical cords

value: Human umbilical vein endothelial cells


title: H3K27me3ChIPseq_2

description: ChIP-seq

data_processing:
Raw reads that passed the quality controls were  aligned to human genome assembly hg19 using Bowtie 0.12.7 (Langmead et al. Genome Biol., 2009), taking only uniquely aligned reads with no more than 2 mismatches.
Significant peaks of H3K4me3 and H3K27me3 were extracted using MACS 1.4 (Zhang et al., 2008), using a minimal p-value cutoff of 10E-5 and a fold change for model building of 30.
Peak detection for H1.0 and H1.4 was performed using in house scripts. In short, reads were counted within 50 bp windows. The median was calculated for each three bins and normalized by the sum of the reads.  To effectively capture local biases in the genome, the Log2 ratio between the ChIP samples and the input genomic DNA was calculated. Peaks were defined as regions with log2 ratio of ChIP DNA over Input DNA > 2 within six neighbouring windows, and average number of reads > 15.
Genome_build: hg19
Supplementary_files_format_and_content: bed format

value: in vitro transformed human skin fibroblasts

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


title: Gastroc_DM2_3


title: Gastroc_DM1_2


title: hESCs (H1)

source_name: Human embryonic stem cells

value: Human embryonic stem cells (H1 cell line)


title: H3K4me3ChIPseq_2

description: ChIP-seq

value: anti-H3K4me3 (ab8580, Abcam)


title: H3K27me3ChIPseq_1

description: ChIP-seq


title: Diaphragm_DM1_2


title: H3K4me3ChIPseq_1

description: ChIP-seq


title: PLP_PH

city: Baltimore

middle: W

last: Mills

state: Maryland

address: 725 N. Wolfe St

institute: Johns Hopkins University School of Medicine

data_processing:
Basecalls were made using CASAVA 1.8
rRNA-derived reads were subtracted using Bowtie 2 version 2.2.6
non-rRNA Reads were aligned to hg19 using TopHat v2.0.10
Relative 3´UTR occupancy was calculated by utr3 FP density divided by the cds FP density
Genome_build: hg19
Supplementary_files_format_and_content: Primary_PLT_Ribo.txt: coding sequence ribosome  footprints and relative 3´UTR occupancy from resting and thrombin treated platelets
Supplementary_files_format_and_content: Primary_Retic_Ribo.txt: coding sequence ribosome  footprints and relative 3´UTR occupancy from reticulocytes
Supplementary_files_format_and_content: K562_HeminTimeCourse.txt: coding sequence ribosome  footprints and relative 3´UTR occupancy from 50 micromolar hemin-induced K562 cells at 0, 2, and 10 days
Supplementary_files_format_and_content: Meg01_PLP.txt: coding sequence ribosome  footprints and relative 3´UTR occupancy from Meg01, platelet-like particles, and high salt washed platelet-like particles
Supplementary_files_format_and_content: K562_ABCE1_exp.txt: meta-analysis of ribosome footprints around the stop codon in GFP or PELO/HBS1L overexpressing K562 cells with or without ABCE1 knockdown
Supplementary_files_format_and_content: K562_PELO-HBS1L_exp.txt: coding sequence ribosome  footprints and relative 3´UTR occupancy from 50 micromolar hemin-induced GFP or PELO/HBS1L overexpressing K562 cells at 0, 2, 4, and 6 days
Supplementary_files_format_and_content: Meg01_PLP_PH.txt: coding sequence ribosome  footprints and relative 3´UTR occupancy from GFP or PELO/HBS1L overexpressing Meg01 and platelet-like particles.

source_name: Meg01 cells

extract_protocol:
Samples were extracted as described previously in Ingolia et al., 2014
Ribosome profiling libraries were prepared as described previously in Ingolia et al., 2014

value: cell line

tag: rrna depletion

value: RiboZero-Gold rRNA depletion


title: H1.4ChIPseq_1

description: ChIP-seq

value: anti-H1.4 (Millipore, 05-457)


title: Meg01_PH


title: H1.4ChIPseq_2

description: ChIP-seq


title: Meg01_GFP


title: K562_PH_4d

source_name: K562 cells

tag: drug treatment

value: 50 micromolar hemin - 4 days


title: H1.0ChIPseq_2

description: ChIP-seq

value: anti-H1.0 (Millipore, 05-629)


title: H1.0ChIPseq_1

description: ChIP-seq


title: K562_PH_2d

value: 50 micromolar hemin - 2 days


title: Bicep_DM1_1

value: autopsy

value: C

value: myotonic dystrophy type 1


title: K562_GFP_6d

value: 50 micromolar hemin - 6 days


title: K562_PH_0d

value: untreated - 0 days


title: K562_GFP_2d


title: K562_GFP_4d


title: Input_1

description: ChIP-seq


title: K562_GFP_0d


title: K562_GFP_shCtrl


title: K562_PH_shCtrl


title: K562_GFP_shABCE1


title: K562_PH_shABCE1


title: flowcell276_lane3_pair1_GCAGCT.fastq.tar.gz

value: 50 micromolar hemin - replicate 1


title: flowcell276_lane3_pair1_CGACGT.fastq.tar.gz

value: 50 micromolar hemin - replicate 2


title: PLP_GFP


title: flowcell276_lane3_pair1_CAGCAT.fastq.tar.gz


title: Meg01_Ribo


title: PLP_highsalt_Ribo


title: PLP_Ribo


title: flowcell276_lane3_pair1_TACGAT.fastq.tar.gz


title: K562_PH_6d


title: Retic_Ribo_Globin_rep1

source_name: reticulocyte

value: primary cell type

value: Globin RNA depletion


title: flowcell276_lane3_pair1_ACGACT.fastq.tar.gz

value: untreated - 0 days - replicate 1


title: Retic_Ribo_Globin_rep2


title: Primary_PLT_Ribo_Rest

source_name: platelet

value: vehicle


title: Primary_PLT_Ribo_Thr2

value: 0.01U/ml thrombin for 60 min at 37C - replicate 2


title: 50CSN

city: Rasht

first: Misagh

last: Moridi

address: Rasht-Qazvin highway

department: Animal Science

country: Iran

institute: University of Guilan

data_processing:
RAW datasets were aligned using Tophat2 Version 2.0.9
Transcripts were assembled using Cufflinks version 2.2.1.0
Assembled files were mereged together using Cuffmerge version 2.2.1.0
Differential expression testing were performed using Cuffdiff2 version 2.2.1.3
Genome_build: bosTau4
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample and differential expression testing results

organism: Bos taurus

source_name: crossbreds

extract_protocol:
At least 4 ml blood was used for RNA extraction from each sample. First, buffy coat of blood samples was isolated by centrifugation at 2000 ×g for 10 min at 4 0C, then white blood cells (WBC) were washed with red blood cell (RBC) lysis buffer (1X) twice and centrifuged at 2000 ×g for 10 min at 4 0C to obtain white pellet of WBC. Total RNA was extracted using Trizol reagent method.
Total RNA was digested by DNaseІ (NEB) and purified by oligo-dT beads (Dyna beads mRNA purification kit, Invitrogen, USA), then poly (A)-containing mRNA were fragmented into 130 bp with first strand buffer. First-strand cDNA was synthesized using N6 primer, first strand master mix, and super script II reverse transcription (Invitrogen, USA). Reaction condition: 25°C for 10 min; 42°C for 40 min; 70°C for 15 min. The second strand master mix was added to synthesize the second-strand cDNA (16°C for 1h). The cDNA was Purified using Agencourt® AMPure® XP PCR purification kit (Agencourt, USA). The final library was quantitated in two ways for validation: the average of molecule length was determined using the Agilent 2100 Bioanalyzer instrument (Agilent DNA 1000 Reagents), and quantification of the library was performed by real-time quantitative PCR (qPCR) using TaqMan Probes. The qualified libraries were amplified on cBot to generate the cluster on the flow cell (TruSeq PE cluster kit V3–cBot–HS, Illumina). The amplified flow cell was sequenced, pair ended, on the HiSeq 2000 device (TruSeq SBS KIT-HS V3, Illumina) with read length of 100 base pair.

tag: breed

value: crossbreds

value: Peripheral blood

value: Leukocytes


title: 75C


title: 50CSH


title: H

source_name: purebred H

value: purebred H


title: dKO_LK_rep3

city: Cincinnati

first: Daniel

last: Starczynowski

state: OH

address: 3333 Burnet Ave

department: Experimental Hematology

institute: CCHMC

data_processing:
Paired-end reads were aligned to UCSC mm10 genome (downloaded from Illumina’s iGenomes repository; https://support.illumina.com/sequencing/sequencing_software /igenome.html) using TopHat and mouse mm10-refseq gene GTF file
FeatureCounts was used for read counting.
Data was normalized into log2 CPM using Voom package
Genome_build: mm10
Supplementary_files_format_and_content: text file with log2 CPM from voom.

organism: Mus musculus

source_name: TIFAB-/-;miR-146a-/- (DKO) LK BM cells

growth_protocol: Animals were bred and housed in the Association for Assessment and Accreditation of Laboratory Animal Care-accredited animal facility of Cincinnati Children’s Hospital Medical Center.

extract_protocol:
Total RNA was extracted and purified with Quick-RNA MiniPrep Kit from Zymo Research (Cat#R1054) according to the manufacturer's instructions.
Total RNA was amplified using the Ovation RNA-Seq System v2 (NuGEN) according to the manufacturer’s protocol. The libraries were prepared with the Nextera XT DNA Sample Preparation kit (Illumina Technologies). 1 ng of cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Amplicon Tagment Mix), incubating at 55C for 10 min. NT Buffer was then added to neutralize the samples. Libraries were prepared by PCR with the Nextera PCR Master Mix, and 2 Nextera Indexes (N7XX, and N5XX) according to the following program: one cycle of 72C for 3min, one cycle of 98C for 30s, 12 cycles of 95C for 10s, 55C for 30s, and 72C for 1min, and one cycle of 72C for 5min.

treatment_protocol: Sorted LK isolated from 2-5 month-old mice transplanted with TIFAB+/+;miR-146a+/+ (WT), TIFAB-/-;miR-146a+/+ (TIFAB KO), TIFAB+/+;miR-146a-/- (miR-146a KO) or TIFAB-/-;miR146a-/- (DKO) BM cells (n = 3 mice/group) were injected i.v. into lethally-radiated (7.0 Gy and 4.75 Gy after 3 hours) syngeneic recipient Boy/J mice.

tag: genotype

value: bone marrow

value: LK


title: dKO_LK_rep4


title: dKO_LK_rep2


title: dKO_LK_rep1


title: miR-146a_KO_LK_rep3

source_name: TIFAB+/+;miR-146a-/- (miR-146a KO) LK BM cells


title: miR-146a_KO_LK_rep2


title: TIFAB_KO_LK_rep3

source_name: TIFAB-/-;miR-146a+/+ (TIFAB KO) LK BM cells


title: miR-146a_KO_LK_rep1


title: flowcell276_lane3_pair1_ATCAGT.fastq.tar.gz

value: cell line

value: untreated - 0 days - replicate 2

value: RiboZero-Gold rRNA depletion


title: Retic_Ribo_Gold_rep2


title: Retic_Ribo_Gold_rep1


title: TIFAB_KO_LK_rep1


title: TIFAB_KO_LK_rep2


title: WT_LK_rep3

source_name: TIFAB+/+;miR-146a+/+ (WT) LK BM cells


title: WT_LK_rep2


title: WT_LK_rep1


title: N

source_name: purebred N

value: purebred N


title: Primary_PLT_Ribo_Thr1

value: 0.01U/ml thrombin for 60 min at 37C - replicate 1


title: RNASeq_LDHA-KO-1

city: New York

first: Ming

last: Li

state: NY

address: 408 East 69th Street

department: Immunology

institute: Memorial Sloan-Kettering Cancer Center

data_processing:
Chipseq: Reads were first trimmed using Trimmomatic (v0.33). Reads were trimmed if first/last 3 nucleotides had phread quality score of < 15 or at the point where a sliding window of 4 nucleotides averaged a phred quality score < 15. Illumina adapters were also removed. The reads were then aligned using bowtie2 (v 2.2.6, options –fr --no-discordant). Multimapping reads were removed after alignment.
RNAseq: Quality Control of raw reads was done using FastQC (v0.11.2) to make sure there were no major flaws in sequencing. They were then mapped to mm10 genome using STAR (v2.3.0e_r291) and default parameters. The mapped reads were counted using htseq-count (v0.6.0, parameters –t exon) and gene models from Ensembl (Mus_musculus.GRCm38.75.gtf).
Genome_build: mm10
Supplementary_files_format_and_content: For RNAseq, raw read counts. For Chipseq, bigWig track file

source_name: Th1 cells

growth_protocol: Naïve CD4+ T cells were activated by plate-bound anti-CD3 (5 μg/ml)  and soluble anti-CD28 (2 μg/ml) in T cell medium (RPMI/1640, 10% fetal bovine serum, 2 mM glutamine, 1 mM sodium pyruvate, 1x non-essential amino acid, 10 mM HEPES, 55 μM 2-mercaptoethanol, 100 U/ml penicillin, 100 mg/ml streptomycin) supplemented with and 100 U/ml IL-2, 10 μg/ml anti-IL-4 and 10 ng/ml IL-12 for 3 days. cells were stimulated with 50ng/ml phorbol 12-myristate 13-acetate  and 1μM ionomycin in the presence of GolgiStop  for 4h.

extract_protocol:
Total RNA was extracted with RNeasy kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary mouse T cells

tag: culture

value: Th1 condition for 3 days

tag: background strain

tag: genotype/variation

value: LDHA-KO


title: RNASeq_WT-1

value: Wild-type


title: RNASeq_LDHA-KO-2


title: RNASeq_WT-2


title: Input_ChIPSeq_LDHA-KO-1

growth_protocol: Naïve CD4+ T cells were activated by plate-bound anti-CD3 (5 μg/ml)  and soluble anti-CD28 (2 μg/ml) in T cell medium (RPMI/1640, 10% fetal bovine serum, 2 mM glutamine, 1 mM sodium pyruvate, 1x non-essential amino acid, 10 mM HEPES, 55 μM 2-mercaptoethanol, 100 U/ml penicillin, 100 mg/ml streptomycin) supplemented with and 100 U/ml IL-2, 10 μg/ml anti-IL-4 and 10 ng/ml IL-12 for 3 days.

extract_protocol:
Chromatin immunoprecipitations were performed with SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling) according to manufacturer’s instructions.
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: antibody


title: Input_ChIPSeq_WT-1


title: Input_ChIPSeq_WT-2


title: H3K9Ac_ChIPSeq_LDHA-KO-2

value: H3K9Ac (Abcam, ab4441)


title: Input_ChIPSeq_LDHA-KO-2


title: H3K9Ac_ChIPSeq_WT-1


title: H3K9Ac_ChIPSeq_LDHA-KO-1


title: Ly6Clo mouse 1

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

institute: Singapore Immunology Network

description: Sample name: RMB3448

data_processing:
50bp paired end reads from Illumina HiSeq 2500 were obtained and mapped to the mouse genome build mm10 using the STAR alignment software.
The mapped reads were counted using featureCounts (part of the Subread package) using mouse GENCODE version M9 with exons as the feature summarized to the gene level.
edgeR running in R version 3.1.2 was used to normalize the raw gene counts to normalized RPKM values.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files containing raw gene counts as well as normalized log2 RPKM values

source_name: bone marrow

growth_protocol: Following cell sorting, cells were incubated in RPMI + 10%FCS for 3hours and were then subjected to RNA extraction.

extract_protocol:
Total RNA was extracted using Arcturus PicoPure RNA Isolation kit according to manufacturer's protocol.
cDNA libraries were prepared using 2ng of total RNA using SMARTSeq v2 protocol (Picelli et al., 2014) except for the following modifications: 1. Use of 20µM TSO, 2. Use of 250pg of cDNA with 1/5 reaction of Illumina Nextera XT kit

value: monocyte

tag: monocyte subset

tag: mouse number

tag: strain

tag: age

value: 7 weeks old


title: Ly6Clo mouse 2

description: Sample name: RMB3451


title: Ly6Clo mouse 3

description: Sample name: RMB3454


title: CXCR4lo mouse 2

description: Sample name: RMB3442


title: H3K9Ac_ChIPSeq_WT-2


title: CXCR4lo mouse 1

description: Sample name: RMB3439


title: CXCR4lo mouse 3

description: Sample name: RMB3445


title: CXCR4hi mouse 3

description: Sample name: RMB3436


title: CXCR4hi mouse 2

description: Sample name: RMB3433


title: cMoP mouse 3

description: Sample name: RMB3427

value: cMoP


title: CXCR4hi mouse 1

description: Sample name: RMB3430


title: cMoP mouse 1

description: Sample name: RMB3421


title: cMoP mouse 2

description: Sample name: RMB3424


title: PyMTElp3cKO2

city: LIEGE

first: Sylvain

last: Delaunay

state: BELGIQUE

address: Avenue de l'hôpital 1

department: Molecular biology of diseases

country: Belgium

institute: University of Liège

description: same size PyMT tumor extracted from 7weeks old mouse female.

data_processing:
HiSeq2000
ChIP-seq reads were aligned to the mm10 genome assembly using Tophat version 2.0.9
Cufflinks 2.1.1 suite was used to normalize data and generate FPKM values and
CuffDiff was used to identify significantly differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: breast tumor

growth_protocol: mice were sacrificed at 7weeks old and same size breast tumors were extracted in both conditions

extract_protocol:
Tumor organoids were extracted from PyMT tumors of similar size, in three different mice for each experimental condition and use for the generation of unicellular suspension. The organoid pellets were then trypsinized in 2ml of Trypsin-EDTA 0,25% for 5 minutes, centrifuged and resuspended in pre-warmed Dispase 5mg/ml and 0.2ml of DNase I 1mg/ml (Stemcell technologies). The samples were then centrifuged and resuspended in DMEM-F12 FBS 10% to form unicellular suspension. The EasySepTM Mouse Mammary Epithelial Cell Enrichment Kit (Stemcell technologies) was used to select epithelial cells. Total RNAs from mammary epithelial tumor cells were extracted using TRIzol (Life Technologies), according to the manufacturer's protocol.
RNA integrity was verified on the Bioanalyser 2100 with RNA 6000 Nano chips and RIN scores were >9 for all samples. The Illumina Truseq RNA Sample Preparation kit V2 was used to prepare libraries from 500 nanograms of total RNAs. PolyA RNAs were purified with polyT-coated magnetic beads, chemically fragmented and used as template for cDNA synthesis using random hexamers. cDNA ends were subsequently end-blunted, adenylated at 3'OH extremities and ligated to indexed adaptors. Finally, the adapters ligated library fragments were enriched by PCR following Illumina's protocol and purified. Libraries were validated on the Bioanalyser DNA 1000 chip and quantified by qPCR using the KAPA library quantification kit. Sequencing was performed on HiSeq2000 in paired-end 2x100 base protocol.

value: FVBN

tag: gender

value: Female


title: PyMTElp3cKO3


title: PyMTWT3


title: PyMTWT1


title: PyMTElp3cKO1


title: PyMTWT2


title: 2459-JG-0015

city: Athens

first: Janet

last: Grimes

state: GA

address: 2200 College Station Road

department: Small Animal Medicine and Surgery

institute: University of Georgia College of Veterinary Medicine

data_processing:
Post processing of the sequencing reads from miRNA-seq experiments from each sample was performed as per unique in-house pipelines. Briefly, quality control checks on raw sequence data from each sample was performed using FastQC (Babraham Bioinformatics, London, UK). Raw reads were imported on a commercial data analysis platform CLCbio v 6.5.1 (Qiagen Inc., Valencia, CA, USA). Adapter trimming (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT) was done to remove ligated adapters from the 3' end of the sequenced reads with only one mismatch allowed; poorly aligned 3' ends were also trimmed. Sequences shorter than 15 nucleotides length were excluded from further analysis. Trimmed reads with low qualities (base quality score less than 30, alignment score less than 95, mapping quality less than 40) were removed. Filtered reads were used to extract and count the small RNA that were annotated with Canis familaris miRNAs from the miRBase release 20 database. The quantification operation carried out measurement at both the gene level and at the active region level. Active region quantification considered only reads whose 5' end matched the 5' end of the mature miRNA annotation. Samples were grouped as patient and control identifiers, and differential expression of miRNA was calculated on the basis of their fold change observed between individual patients and averaged control samples. The p-value of differentially expressed miRNAs was estimated by implementing t-tests with Benjamini Hochberg false discovery rate corrections of 0.05.
Genome_build: canFam3 (UCSC)
Supplementary_files_format_and_content: excel file contains normalized expressions for each sample

organism: Canis lupus familiaris

source_name: Spleen

growth_protocol: Splenic mass samples: Samples were collected from spleens removed from client-owned animals undergoing splenectomy for a splenic mass.  After removal of the spleen, the mass was trimmed to obtain two samples: one for the study and an adjacent piece of tissue for histopathologic evaluation to confirm a diagnosis and ensure that representative tissue was present in the sample.  Samples to be used for the study were flash frozen with liquid nitrogen within 30 minutes of splenectomy and stored in a -80°C freezer until further use.  Only masses confirmed to contain tissue from hemangiosarcoma or nodular hyperplasia were used for the study.  Five samples in each category (hemangiosarcoma and nodular hyperplasia) were collected. Normal spleen samples: Archived fresh frozen tissue samples were utilized to analyze normal splenic tissue.  Samples were collected within 30 minutes of splenectomy, flash frozen in liquid nitrogen, and stored in a -80°C freezer.  Histopathology of adjacent tissue performed at the time of sample collection confirmed these spleens to be normal.  Five normal spleens were collected.

extract_protocol:
The Qiagen miRNeasy kit (Qiagen Inc., Valencia, CA, USA) was utilized to extract RNA from the frozen tissue sections.  Extraction was performed according to manufacturer protocol using the Bullet Blender (Next Advance Inc., Averill Park, NY, USA) for homogenization, and one modification to the protocol, where the Buffer RWT step was repeated for a second time.  The NanoDrop (ThermoScientific, Wilmington, DE, USA) was used to confirm an appropriate 260/280 and 260/230 ratio for the sample (>1.8 in each case).
RNA samples were sent to the Genomic Services Laboratory at the HudsonAlpha Institute for Biotechnology for miRNA-sequencing analysis. NEBNext® Small RNA Library Prep Set for Illumina® (New England BioLabs Inc., Ipswich, MA, USA) was utilized. 3` adapters were ligated to total input RNA followed by hybridization of multiplex SR RT primers and ligation of multiplex 5` SR adapters. Reverse Transcription (RT) was done using SuperScript III RT (Life Technologies, Grand Island, NY, USA) for 1 hour at 50°C. Immediately after RT reaction, indexed primers were added to uniquely barcode each sample and PCR amplification was done for 12 cycles using LongAmp Taq 2X master mix. Post PCR material was then purified using QIAquick PCR purification kit (Qiagen Inc., Valencia, CA, USA). Post PCR yield and concentration of the prepared libraries was assessed using Qubit® 2.0 Fluorometer and DNA 1000 chip on Agilent 2100 Bioanalyzer. Size selection of small RNA libraries with a target size range of 140 base pairs was done on a 3% agarose gel using Pipin prep instrument (Sage Sceince, Boston, MA, USA).  Accurate quantification for sequencing applications was performed using the qPCR-based KAPA Biosystems Library Quantification kit. Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering.   Single End (SE) sequencing was performed on an Illumina HiSeq2000, running HiSeq Control Software (HCS) v1.5.15.1, using a 50 cycle TruSeq SBS HS v3 reagent kit.

value: spleen

tag: disease state

value: Hemangiosarcoma

tag: sample identifier

value: Gunner 1

tag: replicate number

value: Biological replicate 5


title: 2459-JG-0012

tag: tissue

value: Buddy 4

value: Biological replicate 2


title: 2459-JG-0014

value: Shug 1

value: Biological replicate 4


title: 2459-JG-0011

value: Kirra 2

value: Biological replicate 1


title: 2459-JG-0008

value: Nodular Hyperplasia

value: Sheema 2

value: Biological replicate 3


title: 2459-JG-0009

value: Skye 1


title: 2459-JG-0007

value: Oz 2


title: 2459-JG-0010

value: Delilah 1


title: 3074-CAW-0006

city: Nashville

middle: P

last: Skaar

state: TN

address: 1161 21st Avenue South Medical Center North RM# A5104

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt University School of Medicine

data_processing:
Post processing of the sequencing reads from RNA-seq experiments from each sample was performed as per our unique in-house pipeline. Briefly, quality control checks on raw sequence data from each sample were performed using FastQC (Babraham Bioinformatics, London, UK). Raw reads were imported on to CLC Genomics workbench (Qiagen) and the expression level were identified using following parameters. Reference type = One reference sequence per transcript; Reference sequence = NC_008463; Mismatch cost = 2;  Insertion cost = 3; Deletion cost = 3; Length fraction = 0.8; Similarity fraction = 0.8; Global alignment = No; Auto-detect paired; distances = Yes; Strand specific = Both; Maximum number of hits for a read = 10; Count paired reads as two = No; Expression value = RPKM; Calculate RPKM for genes without transcripts = Yes; Create report = Yes; Create fusion gene table = No; Create list of unmapped reads = No. Differential expression of genes was calculated on the basis of fold change (using default cut-off ≥ ±2.0) observed between defined conditions, and the p-value of the differentially expressed gene list was estimated by t-test with Benjamini Hochberg False discovery rate (FDR) correction of 0.05 (Benjamini, 1995).
Genome_build: NC_008463
Supplementary_files_format_and_content: excel file contains normalized expressions for each sample

organism: Pseudomonas aeruginosa PA14

source_name: Pseudomonas aeruginosa PA14_0.25 mg/mL calprotectin

growth_protocol: Experimental cultures were inoculated with 1:100 dilution of an overnight culture. Samples were inoculated in 5 mL of 60% TSB; 40% calprotectin buffer +/- 0.25 mg/mL calprotectin. Experimental cultures were grown aerobically for 18 hours prior to sample collection.

extract_protocol:
Upon completion of growth, samples were pelleted and RNA was harvested from pellets using a standard organic extraction involving a combination of LETS  buffer (0.1 M LiCl; 10 mM EDTA; 10 mM Tris-HCl pH 7.4; 1% SDS) and TRI Reagent as previously described (Wakeman et al., 2014 Journal of Bacteriology)
Approximately 500ng of total RNA was required for proceeding to downstream RNA-seq applications. First, ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold kit (Epicenter, Madison, WI) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit.Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and custom adapter ligation. Post-ligated materials were individually barcoded with unique in-house Genomic Services Lab (GSL) primers and amplified through 12 cycles of PCR. Library quantity was assessed by Qubit 2.0 Fluorometer, and the library quality was estimated by utilizing a DNA 1000 chip on an Agilent 2100 Bioanalyzer. Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Paired-End (PE) sequencing  was performed using on an Illumina HiSeq2500 sequencer (Illumina, Inc.). Directional RNA-seq with Ribosomal reduction

treatment_protocol: Samples were either treated with 40% calprotectin buffer (100 mM NaCl, 3 mM CaCl2 10 mM β-mercaptoethanol, 20 mM Tris, pH 7.5)  or 40% calprotectin buffer + 0.25 mg/mL calprotectin.

tag: treatment

value: 0.25 mg/mL calprotectin


title: 2459-JG-0013

value: spleen

value: Rerun 1


title: 3074-CAW-0005


title: 2459-JG-0006

value: Punk 2


title: 2459-JG-0005

value: Normal Spleen

value: Biological replicate 5


title: 3074-CAW-0004


title: 3074-CAW-0003

source_name: Pseudomonas aeruginosa PA14_calprotectin buffer

value: calprotectin buffer


title: 2459-JG-0004


title: Sp9_OB_Input

city: Shanghai

first: Jiwen

address: NO. 138 Yixueyuan Road

country: China

institute: Fudan University

data_processing:
Basecalls performed using Illumina RTA2
ChIP-seq reads were aligned to mouse genome (UCSC mm9) using bowtie2 software (v2.2.4) with default parameters.
Peak calling was performed with MACS (version 1.4.2) software
The enriched peaks were then annotated with the latest UCSC RefSeq database to connect the peak information with the gene annotation.
Genome_build: mm9
Supplementary_files_format_and_content: Txt file includes chromsome, start, end, peak score and gene name of the peak shared in duplicate ChIP-seq experiments ; bedGraph files provide the results of alignment of the calling peaks.

source_name: olfactory bulb

extract_protocol:
The lysate was sheared into 200- to 1000-bp fragments and Sp9-DNA complex was isolated with specific Sp9 antibody.
The yield of ChIP DNA was determined via Quant IT fluorescence assay (Life Technologies) and enrichment efficiencies of ChIP reaction were evaluated by qPCR. Illumina sequencing libraries were generated with NEBNext® Ultra™ DNA Library Prep Kit (New England Biolabs) by following the manufacturer's manual. The library quality was determined by using Agilent 2100 Bioanalyzer(Agilent), and then, subjected to high-throughput 150 base paired-end sequencing on Illumina Hiseq sequencer according to the manufacturer’s recommended protocol.

treatment_protocol: Neonatal CD1 olfactory bulbs were dissected in ice-cold HBSS. Dissected OBs were fixed in 1% formaldehyde for 10 min and neuralized with glycine. We harvested fixed cells by centrifugation and washed twice with 1X PBS. The harvested pellet was lysed in SDS Lysis Buffer (Millipore) with protease inhibitor PMSF.

value: postnatal day 0-2

value: olfactory bulb

tag: chip antibody


title: 3074-CAW-0002

value: Biological replicate 2


title: 2459-JG-0003


title: Sp9_OB_IP_1

value: Sp9 (homemade antibody)


title: 3074-CAW-0001

value: Biological replicate 1


title: 2459-JG-0002


title: 2459-JG-0001


title: Sp9_OB_IP_2


title: S3 [miRNA-seq]

status: Public on Sep 28 2016

first: Ze-Guang

last: Han

address: 800 Dongchuan Road

department: Shanghai Center for Systems Biomedicine

institute: Shanghai Jiao Tong University

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
Reads obtained from the sequencing machines included dirty reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get clean tags, raw reads were further filtered according to the following rules:(1) Removing low quality reads containing more than one low quality (Q-value≤20) base or containing unknown nucleotides(N);(2) Removing reads without 3'adapters;(3) Removing reads containing 5'adapters;(4) Removing reads containing 3' and 5' adapters but no small RNA fragment;(5) Removing reads containing ployA in small RNA fragment;6) Removing reads shorter than 18nt (not include adapters).
Alignment of small RNA:(1)Alignment with small RNA in GeneBank. All of the clean tags were aligned with small RNAs in GeneBank database(Release 209.0) to identify and remove rRNA,scRNA,snoRNA,snRNA and tRNA;(2)Alignment with small RNA in Rfam. Meanwhile, all of the clean tags were aligned with small RNAs in Rfam database(11.0) to identify and remove rRNA,scRNA,sonRNA,snRNA and tRNA; (3) Alignment with Genome (exon, intron, repeat sequences). All of the clean tags were also aligned with reference genome. Those mapped to exons or introns might be fragments from mRNA degradation, so these tags were removed. The tags mapped to repeat sequences were also removed.
Identification of small RNA:(1)Identification of exist miRNA. All of the clean tags were then searched against miRBase database(Release 21) to identify known  miRNAs (exist miRNAs).(2)Identification of known miRNA. So far the miRNA sequences of some species were still not included in miRBase database. For those species, the miRNAs alignment with other species was a dependable way to identify the known miRNAs.(3)All of the unannotated tags were aligned with reference genome. According to their genome positions and hairpin structures predicted by software Mireap_v0.2, the novel miRNA candidates were identified.
Total miRNA consists of exist miRNA, known miRNA and novel miRNA. Based on their reads in each sample, the miRNA expression level was calculated and normalized to transcripts per million (TPM).
Genome_build: C_idella_female_genemodels.v1.0.gz(http://www.ncgr.ac.cn/grasscarp/)
Supplementary_files_format_and_content: The tab-delimited text files include all miRNAs' expression profile in each sample.

organism: Ctenopharyngodon idella

source_name: Susceptible CIK cells

growth_protocol: CIK cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco) at 28 °C with 5% CO2.

extract_protocol:
Total RNA was harvested using Trizol reagent, and RNA Integrity was measured by Agilent Bioanalyzer 2100.
The RNA molecules in a size range of 18–30nt were enriched by polyacrylamide gel electrophoresis(PAGE). Then the 3’ adapters and 5’ adapters were ligated to the RNAs. The ligation products were reverse transcripted by PCR amplification, and the 140-160bp size of PCR products were enriched to generate a cDNA library and sequenced using Illumina HiSeqTM 2500.

treatment_protocol: To obtain single CIK cell, CIK cell line were digested by 0.5% tyrisin, then passed through a 150 μM nylon mesh filter twice to guarantee CIK cells singly suspended in phosphate-buffered saline (PBS). 100 μL DMEM supplemented with 7% FBS, 100 U/mL of penicillin, 100 U/mL of streptomycin sulfate and 5 μL/mL insulin (Gibco) were added to each well of the 96-well culture plates beforehand, the single cell ultimately instilled in a row utilizing the BD FACSAria™ III Cell Sorter (USA). The sorted single cells were similarly maintained at 28 °C with 5% CO2 and sub-cultured up to being the monoclonal cells.

value: Kidney

value: CIK

tag: component

value: Susceptible CIK cells:S1501, S1519, S1523


title: C1 [miRNA-seq]

source_name: CIK cells

value: General CIK cells


title: R2 [miRNA-seq]

source_name: Resistant CIK cells

value: Resistant CIK cells:S1517, S1536, S1558


title: S3 [RNA-seq]

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
Reads obtained from the sequencing machines include raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads would be further filtered according to the following rules:(1) removing reads containing adapters;(2) removing reads containing more than 10% of unknown nucleotides (N);(3) removing low quality reads (Q-value≤20).
Short reads alignment tool Bowtie2  was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.0.3.12), respectively. The alignment parameters were as follows:(1) Maximum read mismatch is 2;(2) The distance between mate-pair reads is 50bp;(3) The error of distance between mate-pair reads is ±80bp.
Gene abundances were quantified by software RSEM.
Genome_build: C_idella_female_genemodels.v1.0.gz(http://www.ncgr.ac.cn/grasscarp/)
Supplementary_files_format_and_content: The tab-delimited text file includes RNA expression profile in each sample.

extract_protocol:
Total RNA was harvested using Trizol reagent, and RNA Integrity was measured by Agilent Bioanalyzer 2100.
mRNA was enriched by Oligo(dT) magnetic beads, and ribosomal RNA (rRNA) was removed by Ribo-ZeroTM Magnetic Kit (Epicentre, USA). Then the enriched mRNA was fragmented into short pieces (200-500 bp) and reversely transcribed into cDNA with random primers. cDNA fragments were purified by QiaQuick PCR extraction kit (Qiagen, Germany), end repaired, poly (A) added, and ligated to Illumina sequencing adapters. The products were size selected by AGE, PCR amplified, and paired-end (2×125 bp) sequenced using Illumina HiSeqTM 2500.


title: R2 [RNA-seq]


title: C1 [MeDIP-seq]

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
The fastx-toolkit program was used to filter off low quality sequences from raw sequencing data.
Sequences were aligned with Grass carp genome using SOAP(Release 2.21).
MeDIP-seq peaks were called with the Model-based Analysis of MeDIP-Seq (MACS) software(1.4.0) with default parameters with alignment results.
The three peak sets generated by MACS(1.4.0) were merged using Bedtools for peaks with at least 1bp overlap to get a reference peak set (REF) for following analysis.
Genome_build: "C_idella_female_genemodels.v1.0.gz"(http://www.ncgr.ac.cn/grasscarp/)
Supplementary_files_format_and_content: The tab-delimited text files include peaks' information in each sample.

extract_protocol:
DNA extraction was extracted by the classical phenol and chloroform method. The concentration of extracted DNA was measured using the Qubit instrument and the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Cleveland, OH, USA).
Genome DNA was fragmented to 100-500bp by sonication. DNA-end was repaired to overhang a 3'-dA, then adapters were ligated to the end of DNA fragments. Double-stranded DNA was denatured. Then DNA fragments were immunoprecipitated by 5mC antibody. Real-time PCR was used to validate the quality of immunoprecipitation. DNA fragments with proper size (220-320bp) were selected after PCR amplification. Finally we got qualified library for sequencing.


title: S3 [MeDIP-seq]


title: C1 [RNA-seq]


title: R2 [MeDIP-seq]


title: T38-CXCR6n

city: London

first: Victoria

last: Male

state: Not Applicable (Outside of US and Canada)

address: Metabolism, Digestion and Reproduction, Imperial College London, Chelsea and Westminster Hospital Campus, 369 Fulham Road

country: United Kingdom

institute: Imperial College London

data_processing:
Basecalls were made using Illumina BaseSpace TrueSeq Amplicon 2.0
Alignments were performed against Homo sapiens/hg19 (RefSeq) using Illumina BaseSpace TopHat v2.1.0
Regularized log transformed normalization was performed using Illumina DESeq2 v1.0.0
Genome_build: hg19
Supplementary_files_format_and_content: csv files contain raw and normalized reads for each sample

source_name: Healthy liver leukocytes

extract_protocol:
Total RNA was extracted from sorted cells using an RNeasy Micro Kit (Qiagen, Manchester, UK) and cDNA amplified using a SMART-Seq Ultra Low Input RNA kit for sequencing (Takara Bio Europe/Clontech, Saint-Germain-en-Laye, France).
Amplified cDNA (200 pg) was used as input for library preparation using Nextera XT DNA Library Preparation Kit (Illumina, Essex, UK) with 12 cycles of PCR.

treatment_protocol: Leukocytes were isolated from the perfusion fluid of healthy human livers destined for transplant by density gradient centrifugation. Live Eomes- NK cells (propidium iodide negative, CD3-, CD56+, CXCR6-, CD16+) and Eomes+ NK cells (propidium iodide negative, CD3-, CD56+, CXCR6+) were sorted on a BD Aria

tag: individual

value: patient T38

tag: cell type

value: Eomes negative NK cells


title: T35-CXCR6p

value: patient T35

value: Eomes positive NK cells


title: TB-CXCR6n

value: patient TB


title: T35-CXCR6n


title: T36-CXCR6p

value: patient T36


title: T36-CXCR6n


title: TB-CXCR6p


title: T34-CXCR6p

value: patient T34


title: T34-CXCR6n


title: Breast_Normal_Fibroblast_1

city: Boston

first: Muhammad

middle: B

last: Ekram

state: MA

address: 450 Brookline Avenue, DA 740A

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
RNA-Seq: Basecalls were performed using CASAVA version 1.8.2
RNA-Seq: Quality check of the called bases of the reads were performed using the FastQC tool (Babraham Bioinformatics)
RNA-Seq: The datasets were aligned to the human reference GRCh37/hg19 genome using the STAR RNA-Seq aligner (version 2.3.1) using the default parameters.
RNA-Seq: The read counts for individual genes were generated using the htseq-count script of the HTSeq framework (version 0.6.1p1) using the default parameters and the hg19 refGene annotation file available at the UCSC Genome Browser.
processed data files format and content: RNA-Seq: Tab-separated file of the raw read counts of each samples for each gene.
Genome_build: hg18

source_name: Fibroblast from normal breast tissue

growth_protocol: Fibroblasts were expanded in 50/50 mixture of DMEM-F12, 10% FBS/MEGM with supplements.

extract_protocol:
mRNA was extracted using the uMACS mRNA Isolation (Columns) kit (130-075-201). RNA concentrations were measured and quality controlled on a Bioanalyzer
RNAseq libraries were generated by Center for Cancer Computational Biology (CCCB) at Dana-Farber Cancer Institute following manufacture protocol.

tag: tissue of origin

value: breast (normal)


title: Breast_Tumor_Fibroblast_1

source_name: Fibroblast from breast tumor

value: breast tumor


title: Breast_Normal_Fibroblast_2


title: Brain_Metastasis_Fibroblast_2

source_name: Fibroblast from breast metastasis in brain

value: breast metastatic site in brain


title: Brain_Metastasis_Fibroblast_4


title: Brain_Metastasis_Fibroblast_3


title: Brain_Metastasis_Fibroblast_5


title: Brain_Metastasis_Fibroblast_1


title: Normal_Human_Astrocytes_1

source_name: Human astrocyte

value: central nervous system


title: T38-CXCR6p


title: LR2

city: Lanzhou

first: Yan

last: Qiao

state: Gansu Province

address: No. 1 Yingmen village, Anning District

department: College of Agronomy

institute: Gansu Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
After discarding low quality reads , clean reads were mapped  to the potato reference genome using tophat package(Trapnell et al. 2012).
To estimate transcript abundance,the aligned reads in BAM format files were processed by GFOLD V1.1.1 program (Feng et al. 2012).The value of 0.25 RPKM was set as a threshold to determine the expressed gene. Differentially expressed genes were identified using GFOLD V1.1.1 program, which could provide more consistent and more biologically meaningful gene ranking than other commonly approach for RNA-seq experiment without biological replicates. Therefore, DEGs were identified by stringent threshold(｜log2(Ratio)｜>1 and｜GFOLD (0.01) >1｜) .
Genome_build: The potato reference genome sequence (PGSC v4.03 pseudomolecules) and genome annotation V3.4 were used in our research.
The PGSC v4.03 pseudomolecules and potato genome annotation V3.4  were released by Potato Genome Sequencing Consortium in September 4, 2013. (http://potato.plantbiology.msu.edu/pgsc_download.shtml)
Genome_build: Potato Genome Sequencing Consortium 2011, Genome sequence and analysis of the tuber crop potato. Nature 475: 189–195.
Supplementary_files_format_and_content: tab-delimited text file include read count and RPKM values for each sample.
the identifier are searchable in these databases:
http://potato.plantbiology.msu.edu/pgsc_download.shtml
http://plants.ensembl.org/Solanum_tuberosum/Info/Index
https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Stuberosum

organism: Solanum tuberosum

source_name: potato leaf

growth_protocol: Plantlets were cultured in MS medium at 22℃ under long-day photoperiod (16 h light/8h dark) condition.To induce microtubers, eight-week-old plantlets were added to 20 ml liquid MS medium containing 8% sucrose. These plantlets grew in growth cabinet at 19℃ under darkness condition. After eight weeks, in vitro generated microtubers were harvested.

extract_protocol:
Total RNA was isolated from leaves and tuber’s peel with TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s procedure. Equal amounts of each RNA samples were pooled at 12, 24 and 48 h time points and the quality were checked by Agilent 2100 bioanalyzer.
RNA libraries preparation were performed using True-seq RNA sample preparation kit following the manufactures’instructions.RNA-seq libraries were subjected to deep sequencing with Illumina HiSeq 2000 at LC Sciences (Hangzhou, China).

treatment_protocol: Eight-week-old plantlets were shifted to the dark 3 day and subsequently reexposed to red light (～19.7μmol m−2s−1, 630 nm). Then, the leaves of plantlets were harvested after 12, 24, and 48 h, respectively. Dark-grown plantlets were collected as the control. The leaves were collected and immediately frozen in liquid nitrogen.In vitro generated microtubers were treated under the same conditions as described previously.

tag: cultivar

value: Solanum tuberosum L. cv.Zhuangshu No.3

value: leaf

tag: growth condition

value: Plantlets were shifted to the dark for 3 days and exposed to red light for 12,24,and 48 h


title: TR2

source_name: potato tuber

value: tuber

value: Microtubers were exposed to red light for 12, 24, and 48 h


title: TM2 [miRNA]

description: processed data file: tuber_miRNAs.txt

data_processing:
Using the UEA sRNA workbench Filter Tool (Stocks et al. 2012), sRNA reads were mapped onto plant t/rRNAs sequences obtained from RFAM version 10, the Genomic tRNA Database and EMBL release 95, then the matched sequences were discarded.
To identify the isoforms of known miRNA, the miRProf tool was run with clean sRNA reads. The reads were mapped with at most 1 nt mismatch to known Viridiplantae mature miRNA annotated in miRBase 21.
To identify novel miRNAs and their precursors, the unique reads were submitted to the miRCat pipeline and default plant parameters were defined. miRCat maps sRNA sequence to the potato reference genome (PGSC DM v4.03 pseudomolecules) using PatMaN(Prufer et al. 2008).
Supplementary_files_format_and_content: tab-delimited text file include read count and RPM values for each sample.

extract_protocol:
Total RNA was isolated from leaves and tuber’s peel with TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s procedure. Equal amounts of each RNA samples were pooled at 12, 24 and 48 h time points and the quality were checked by Agilent 2100 bioanalyzer.
Small RNAs (18-30 nt) were isolated from total RNA by polyacrylamide gel electrophoresis, and ligated to 3‘illumina adapter. The adapter-ligated sRNA were transcribed into cDNA by Super-script II Reverse Transcriptase (Invitrogen) to generate sRNA libraries. Small RNA libraries were subjected to deep sequencing with Illumina HiSeq 2000 at LC Sciences (Hangzhou, China).

treatment_protocol: Eight-week-old plantlets were shifted to the dark 3 day and subsequently re-exposed to red light (～19.7μmol m−2s−1, 630 nm). Then, the leaves of plantlets were harvested after 12, 24, and 48 h, respectively. Dark-grown plantlets were collected as the control. The leaves were collected and immediately frozen in liquid nitrogen.In vitro generated microtubers were treated under the same conditions as described previously.

value: Eight-week-old


title: Breast_Tumor_Fibroblast_3


title: TR1

value: Microtubers grown under dark conditions


title: TM1 [miRNA]

description: processed data file: tuber_miRNAs.txt


title: LM2 [miRNA]

description: processed data file: leaf_miRNAs.txt


title: LR1

value: Plantlets were shifted to the dark for 3 days


title: LM1 [miRNA]

description: processed data file: leaf_miRNAs.txt


title: Breast_Tumor_Fibroblast_2


title: T980097 [RNA-seq]

first: Aditi

last: Qamra

institute: GIS

data_processing:
RNA-seq reads were aligned to the human genome (hg19) using TopHat2-2.0.12
Transcript abundances at the gene level were estimated by cufflinks
Gene expression from primary samples showing variation greater than zero were corrected for potential batch effects using ComBat
Genome_build: hg19
Supplementary_files_format_and_content: the genomic intervals followed by sequencing coverage.

source_name: Gastric Primary Tissue

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini Kit according to the manufacturer’s protocol.
Sequencing libraries were prepared using Illumina TruSeq RNA Sample Prep Kit v2 according to manufacturer’s protocol.

tag: tissuetype

value: Gastric primary tumor tissue

tag: histology

value: mixed


title: T980417 [RNA-seq]

value: diffuse


title: T20020720 [RNA-seq]

value: intestinal


title: T2000877 [RNA-seq]


title: 3277_Control1_CAGATC

city: Badalona

first: Miguel

middle: A.

last: Peinado

address: Can Ruti Campus

country: Spain

institute: IGTP

data_processing:
Paired-end reads were mapped with tophat v2.1.0  with the –b2-sensitive flag against the ENSEMBL GRCh37 69 human reference genome plus the ERCC92 RNA Spike-In Mix (Thermo Fischer Scientific)
Accepted hits were marked for duplicates using picard v2.0.1
To assign each uniquely mapped read to transcripts and repeats, we retrieved the annotations from ENSEMBL GRCh37 69 and the rmsk table from the hg19 assembly hosted at UCSC, respectively, as GTF/GFF files.Feature counting was run on each GTF independently; we ignored sequencing duplicates, multimappers and ambiguous reads using featureCounts from subread v1.5.0-p1
Genome_build: GRCh37 69
Supplementary_files_format_and_content: featureCounts counting outputs

molecule: polyA RNA

source_name: Colon tumor cell line

growth_protocol: DMEM:F12 + 10%FBS + 100uM pyruvate + 200uM Glutamine

extract_protocol:
RNA was extracted with the miRNAeasy Mini Kit Qiagen, Venlo, Netherlands) according to manufacturer’s instructions from two independent cultures of the  HCT116 cell line, which were processed separately.
PolyA selected RNA libraries were prepared for sequencing using the HiSeq Sequencing Kit Truseq v3.
Paired-end RNA-Seq

value: Cell line

tag: cell line


title: N2000877 [RNA-seq]

value: Gastric primary non-malignant tissue

value: not applicable


title: N980437 [RNA-seq]


title: lane1_HCT116_Control


title: N20020720 [RNA-seq]


title: Normal_Human_Astrocytes_2


title: T980437 [RNA-seq]


title: N980417 [RNA-seq]


title: N2000721 [RNA-seq]


title: T2000721 [RNA-seq]


title: T2000986 [RNA-seq]


title: N2000986 [RNA-seq]


title: T2000639 [RNA-seq]


title: YCC-7 [RNA-seq]

source_name: Gastric cancer cell line

value: Gastric cancer cell line

value: Adenocarcinoma


title: N2000639 [RNA-seq]


title: YCC-22 [RNA-seq]


title: RERF-GC-1B [RNA-seq]

value: Adenocarcinoma;


title: YCC-3 [RNA-seq]

value: Poorly differentiated


title: OCUM-1 [RNA-seq]

value: poorly differentiated adenocarcinoma containing signet ring cells;


title: CHG314

data_processing:
Sequencing reads were trimmed (10bp from front and back) and mapped against human genome reference hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.6.2) 'mem' algorithm.
We filtered reads based on their mapping quality (MAPQ) and used uniquely mapped reads to perform peak calling using CCAT v3.0 [local FDR < 0.05]
Genome_build: hg19
Supplementary_files_format_and_content: interval format for ucsc genome browser, including 8 columns: "chromosome" "position of the peak" "start of region" "end of region" "read counts in ChIP library" "read counts in control library" "fold-change score" "local FDR"

source_name: Gastric Primary Sample

extract_protocol:
Fresh-frozen cancer and normal tissues were dissected using a razor blade in liquid nitrogen to obtain ~5mg sized pieces for each ChIP. Tissue pieces were fixed in 1% formaldehyde/PBS buffer for 10 min at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Tissue pieces were washed 3 times with TBSE buffer. For cell lines, 1 million fresh harvested cells were fixed in 1% formaldehyde/medium buffer for 10 minutes (min) at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Fixed cells were washed 3 times with TBSE buffer, and centrifuged (5,000 r.p.m., 5 min). Pelleted cells and pulverized tissues were lysed in 100 µl 1% SDS lysis buffer and sonicated to 300-500bp using a Bioruptor (Diagenode). ChIP was performed using the following antibodies: H3K4me3 (07-473, Millipore); H3K4me1 (ab8895, Abcam); H3K27ac (ab4729, Abcam).
library construction protocol: 30ng of amplified DNA was used for each sequencing library preparation (New England Biolabs). 8 libraries were multiplexed (New England Biolabs) and sequenced on 2 lanes of a Hiseq2500 sequencer (Illumina) to an average depth of 20-30 million reads per library.

tag: tissue type

value: T

value: Input


title: CHG274


title: CHG320

value: N


title: N980097 [RNA-seq]


title: GCC133

source_name: Gastric Cancer Line


title: GCC139


title: GCC140

value: KATO-III (rep2)


title: CHG025_mem

value: Gastric Primary Sample

tag: primary sample type (t=tumor, n=normal)

value: none (input)


title: CHG033_mem


title: CHG037_mem


title: CHG090_mem


title: NCC-59 [RNA-seq]

value: Moderately differentiated tubular adenocarcinoma


title: CHG094_mem


title: CHG021_mem


title: MKN7 [RNA-seq]


title: CHG029_mem


title: CHG098_mem


title: CHG017_mem


title: CHG093_mem


title: CHG083_mem


title: CHG086_mem


title: CHG079_mem


title: CHG091_mem


title: CHG275


title: CHG035_mem


title: FU97 [RNA-seq]

value: Diffuse adenocarcinoma;poorly differentiated; Lymph node metastasis and pancreatic metastasis were observed


title: CHG027_mem


title: CHG031_mem


title: CHG023_mem


title: GCC134


title: CHG101_mem


title: CHG039_mem


title: CHG089_mem


title: CHG019_mem


title: CHG082_mem


title: CHG080_mem


title: CHG099_mem


title: CHG078_mem


title: CHG081_mem


title: CHG038_mem


title: CHG022_mem


title: CHG034_mem


title: GCC101_mem


title: GCC099_mem


title: GCC102_mem


title: CHG030_mem


title: GCC100_mem


title: CHG026_mem


title: GCC093_mem


title: GCC095_mem


title: GCC094_mem


title: GCC092_mem


title: GCC096_mem


title: GCC091_mem


title: GCC097_mem


title: GCC089_mem


title: CHG092_mem


title: GCC088_mem


title: GCC086_mem


title: GCC084_mem


title: CHG018_mem


title: GCC082_mem


title: GCC081_mem


title: GCC087_mem


title: GCC080_mem


title: GCC098_mem


title: GCC079_mem


title: GCC075_mem


title: GCC074_mem


title: GCC077_mem


title: GCC090_mem


title: GCC072_mem


title: GCC073_mem


title: GCC065_mem

value: Gastric Cancer Line


title: GCC071_mem


title: GCC053_mem


title: GCC083_mem


title: GCC052_mem


title: GCC085_mem


title: GCC045_mem


title: GCC076_mem


title: GCC043_mem


title: GCC078_mem


title: GCC041_mem


title: GCC051_mem


title: GCC040_mem


title: GCC038_mem


title: GCC039_mem


title: GCC061_mem


title: GCC036_mem


title: GCC037_mem


title: GCC034_mem


title: GCC035_mem


title: GCC032_mem


title: GCC029_mem


title: GCC030_mem


title: GCC033_mem


title: GCC028_mem


title: GCC027_mem


title: GCC026_mem


title: GCC025_mem


title: GCC023_mem


title: GCC024_mem


title: GCC021_mem


title: GCC018_mem


title: GCC022_mem


title: GCC017_mem


title: GCC016_mem


title: GCC012_mem


title: GCC014_mem


title: GCC011_mem


title: GCC015_mem


title: GCC020_mem


title: GCC008_mem


title: GCC009_mem


title: GCC019_mem


title: GCC007_mem


title: GCC005_mem


title: GCC003_mem


title: GCC006_mem


title: GCC001_mem


title: GCC002_mem


title: CHG451_mem


title: GCC031_mem


title: CHG452_mem


title: CHG448_mem


title: GCC013_mem


title: CHG444_mem


title: CHG445_mem


title: CHG447_mem


title: GCC010_mem


title: CHG441_mem


title: GCC004_mem


title: CHG440_mem


title: CHG434_mem


title: CHG432_mem


title: CHG443_mem


title: CHG431_mem


title: CHG424_mem


title: CHG428_mem


title: CHG427_mem


title: CHG449_mem


title: CHG422_mem


title: CHG423_mem


title: CHG421_mem


title: CHG417_mem


title: CHG429_mem


title: CHG374_mem


title: CHG437_mem


title: CHG324_mem


title: CHG371_mem


title: CHG323_mem


title: CHG419_mem


title: CHG436_mem


title: CHG318_mem


title: CHG439_mem


title: CHG426_mem


title: CHG245_mem


title: CHG279_mem


title: CHG284_mem


title: CHG244_mem


title: CHG242_mem


title: CHG232_mem


title: CHG233_mem


title: CHG236_mem


title: CHG227_mem


title: CHG226_mem


title: CHG230_mem


title: CHG100_mem


title: CHG376_mem


title: CHG215_mem


title: CHG214_mem


title: CHG212_mem


title: CHG208_mem


title: CHG209_mem


title: CHG238_mem


title: CHG218_mem


title: GCC096

data_processing:
Sequencing reads were trimmed (10bp from front and back) and mapped against human genome reference hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.6.2) ‘aln’ algorithm.
We filtered reads based on their mapping quality (MAPQ) and used uniquely mapped reads to perform peak calling using CCAT v3.0 [local FDR < 0.05]
Genome_build: hg19
Supplementary_files_format_and_content: interval format for ucsc genome browser, including 8 columns: "chromosome" "position of the peak" "start of region" "end of region" "read counts in ChIP library" "read counts in control library" "fold-change score" "local FDR"


title: GCC097


title: GCC099


title: GCC098


title: GCC100


title: GCC095


title: GCC101


title: GCC090


title: GCC091


title: GCC092


title: GCC094


title: GCC093


title: GCC089


title: GCC083


title: GCC084


title: GCC077


title: GCC078


title: GCC102


title: GCC081


title: GCC088


title: GCC087


title: GCC082


title: GCC073


title: GCC086


title: GCC076


title: GCC071


title: GCC085


title: GCC075


title: GCC063_mem


title: GCC074


title: GCC072


title: GCC065


title: GCC045


title: GCC055


title: GCC051


title: GCC055_mem


title: GCC053


title: GCC063


title: GCC061


title: GCC079


title: GCC052


title: GCC043


title: GCC040


title: GCC036


title: GCC037


title: GCC034


title: GCC035


title: GCC038


title: GCC041


title: GCC039


title: GCC030


title: GCC029


title: GCC031


title: GCC027


title: GCC033


title: GCC026


title: GCC028


title: GCC023


title: MI_day 13_32C_sample 5 [re-analysis]

city: Sydney

first: Rachel

last: Levin

state: New South Wales

address: UNSW

country: Australia

institute: University of New South Wales

description:
processed data files: day13_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872193

data_processing:
Illumina Truseq (TruSeq3-SE) adapters were removed from sequence reads using Trimmomatic.
Prinseq was used to remove poly-A tails (min 6-A tail) and to filter short (min length 60 bases), low quality (min mean quality score 20, 4 base window, 1 base step), and low complexity sequences (dust method threshold 7).
Genome_build: RNA sequences from the 24 samples per population (four replicates, two temperature treatments, three time points) were combined for de novo assembly of the SM and MI transcriptomes using Trinity (version: 2.0.6).
Genome_build: SM_min250_nr.fasta;South Molle population de novo transcriptome, non redundant transcripts ≥ 250 bp
Genome_build: MI_min250_nr.fasta; Magnetic Island population de novo transcriptome, non redundant transcripts ≥ 250 bp
Genome_build: transcript annotation is provided in the *annotation_report.complete.5.xls
transcripts shorter than 250 bp were removed from the assembeled transcriptomes
redundant transcripts (similarity ≥ 99%) were removed from the assembled transcriptomes using cd-hit-est
Supplementary_files_format_and_content: tab-delimited text files include expression matrices for fpkm and counts of each sample at each time point

organism: Cladocopium sp. C1

source_name: MI_day 13_32C

growth_protocol: The thermal sensitive South Molle (SM) Symbiodinium population and thermal tolerant Magnetic Island (MI) Symbiodinium population were cultured in filtered seawater supplemented with Daigo IMK (Wako Pure Chemical Industries, Ltd.). For this study, 5x107 cells (1.5x106 cells/ml) of each population were added to eight replicate culture flasks per population. Light was provided at an intensity of 30 µmol quanta m-2 s-1 with a 12:12 h light:dark cycle.

extract_protocol:
Precisely after six hours of light exposure, 2-4 x 106 cells per population were immediately snap frozen in liquid nitrogen within 10 s of removal from experimental incubators and stored at -80°C. Snap frozen cells were thawed at room temperature and pelleted at 4°C (3,000 x g, 5 min). Media was removed, and pellets were lysed in buffer RLT (RNeasy plant mini kit, Qiagen) containing β-mercaptoethanol by bead beating with 0.3 g of 710-1,180 µm acid-washed glass beads (Sigma) using a TissueLyser II (Qiagen) for 90 s at 30 Hz. RNA was extracted and purified using the RNeasy plant mini kit (Qiagen) with an added on-column DNase I treatment (Qiagen).
Total RNA (150-500 ng) of each sample was sent to the Australian Genome Research Facility for confirmation of high quality RNA on an Agilent 2100 bioanalyzer, polyA-purification, Illumina TruSeq stranded library preparation, and sequencing on an Illumina HiSeq2500 (single end 100 bp, ~107 reads per sample)

treatment_protocol: Two flasks per population were randomly assigned to each of four experimental incubators and acclimated at 27°C for two weeks. Transcriptomes were sampled on day -1 to confirm that there were no significant pre-experimental differentially expressed genes before heating. Two incubators were ramped on day 0 at 0.5°C/h to 32°C for the heat stress temperature treatment, while two incubators remained at 27°C. Transcriptomes were sampled on day 9 and day 13.

tag: population source

value: Magnetic Island, Great Barrier Reef

tag: sample type

value: cell culture

tag: medium

value: filtered sea water + IMK nutrient supplement

tag: coral host from which it was isolated

value: Acropora tenuis

tag: sampling time point

value: day 13

tag: temperature treatment

tag: incubator

value: incubator 3


title: MI_day 13_32C_sample 6 [re-analysis]

description:
processed data files: day13_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872194


title: GCC021

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

tag: tissue

tag: chip antibody


title: MI_day 13_27C_sample 8 [re-analysis]

description:
processed data files: day13_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872196

source_name: MI_day 13_27C

value: incubator 4


title: GCC025


title: MI_day 13_27C_sample 3 [re-analysis]

description:
processed data files: day13_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872191

value: incubator 2


title: GCC024


title: MI_day 13_27C_sample 7 [re-analysis]

description:
processed data files: day13_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872195


title: MI_day 13_32C_sample 2 [re-analysis]

description:
processed data files: day13_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872190

value: incubator 1


title: GCC022


title: GCC032

value: Input


title: MI_day 13_27C_sample 4 [re-analysis]

description:
processed data files: day13_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872192


title: GCC020

value: T


title: MI_day 13_32C_sample 1 [re-analysis]

description:
processed data files: day13_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872189


title: GCC018


title: MI_day 9_27C_sample 7 [re-analysis]

description:
processed data files: day9_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872187

source_name: MI_day 9_27C

value: day 9


title: MI_day 9_32C_sample 6 [re-analysis]

description:
processed data files: day9_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872186

source_name: MI_day 9_32C


title: GCC017

value: Gastric Primary Sample


title: GCC016

value: N


title: MI_day 9_27C_sample 8 [re-analysis]

description:
processed data files: day9_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872188


title: MI_day 9_32C_sample 5 [re-analysis]

description:
processed data files: day9_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872185


title: GCC015


title: MI_day 9_32C_sample 1 [re-analysis]

description:
processed data files: day9_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872181


title: MI_day 9_32C_sample 2 [re-analysis]

description:
processed data files: day9_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872182


title: MI_day 9_27C_sample 4 [re-analysis]

description:
processed data files: day9_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872184


title: GCC013


title: GCC014


title: MI_day -1_27C_sample 6 [re-analysis]

description:
processed data files: day-1_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872178

source_name: MI_day -1_27C

value: day -1


title: MI_day -1_27C_sample 7 [re-analysis]

description:
processed data files: day-1_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872179


title: MI_day 9_27C_sample 3 [re-analysis]

description:
processed data files: day9_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872183


title: MI_day -1_27C_sample 4 [re-analysis]

description:
processed data files: day-1_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872176


title: GCC007


title: GCC010


title: MI_day -1_27C_sample 8 [re-analysis]

description:
processed data files: day-1_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872180


title: GCC011


title: GCC006


title: MI_day -1_27C_sample 3 [re-analysis]

description:
processed data files: day-1_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872175


title: GCC005


title: MI_day -1_27C_sample 5 [re-analysis]

description:
processed data files: day-1_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872177


title: GCC008


title: GCC019


title: GCC012


title: MI_day -1_27C_sample 1 [re-analysis]

description:
processed data files: day-1_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872173


title: GCC009


title: SM_day 13_27C_sample 8 [re-analysis]

description:
processed data files: day13_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872172

source_name: SM_day 13_27C

value: South Molle Island, Great Barrier Reef


title: GCC002


title: SM_day 13_27C_sample 7 [re-analysis]

description:
processed data files: day13_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872171


title: MI_day -1_27C_sample 2 [re-analysis]

description:
processed data files: day-1_MI_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872174


title: GCC003


title: CHG452


title: SM_day 13_32C_sample 5 [re-analysis]

description:
processed data files: day13_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872169

source_name: SM_day 13_32C


title: CHG448


title: SM_day 13_27C_sample 3 [re-analysis]

description:
processed data files: day13_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872167


title: SM_day 13_32C_sample 2 [re-analysis]

description:
processed data files: day13_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872166


title: CHG449


title: SM_day 13_32C_sample 6 [re-analysis]

description:
processed data files: day13_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872170


title: SM_day 13_27C_sample 4 [re-analysis]

description:
processed data files: day13_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872168


title: CHG445


title: CHG443


title: CHG451


title: GCC004


title: CHG439


title: CHG444


title: SM_day 9_27C_sample 7 [re-analysis]

description:
processed data files: day9_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872163

source_name: SM_day 9_27C


title: SM_day 13_32C_sample 1 [re-analysis]

description:
processed data files: day13_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872165


title: SM_day 9_27C_sample 8 [re-analysis]

description:
processed data files: day9_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872164


title: CHG437


title: CHG436

value: Gastric Cancer Line


title: CHG434


title: CHG432


title: SM_day 9_32C_sample 6 [re-analysis]

description:
processed data files: day9_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872162

source_name: SM_day 9_32C


title: SM_day 9_32C_sample 5 [re-analysis]

description:
processed data files: day9_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872161


title: Hu_Female_rep2

city: Beijing

first: Jiaxue

last: Cao

state: Beijing

address: Yuanmingyuan West Road 2#

institute: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ovis aries Oar_v3.1 whole genome using SOAP aligner v 2.21  with parameters -s  34  -p  4  -v  2
Peaks were called using MACs 1.4.0
Genome_build: Ovis aries Oar_v3.1
Supplementary_files_format_and_content: wig files were generated using MACs.1.4.0

organism: Ovis aries

source_name: Blood

extract_protocol:
Blood genomic DNA was isolated according to the manufacturer’s protocol of TIANamp Blood DNA Kit (DP318, TIANGEN, Beijing)
Adaptor-ligated DNA was used for MeDIP enrichment based on the manufacturer’s recommendation of Magnetic Methylated DNA Immunoprecipitation kit (Diagenod, Liège, Belgium), MeDIP libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Hu sheep

tag: gender

value: Female

value: Venous blood

tag: age

value: post natal day 364


title: Hu_Female_rep1

value: post natal day 361


title: StH_Female_rep2

value: Small-tailed-Han sheep

value: post natal day 375


title: CHG441


title: SM_day 9_27C_sample 4 [re-analysis]

description:
processed data files: day9_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872160

value: cell culture

value: filtered sea water + IMK nutrient supplement

value: Acropora tenuis

value: incubator 2


title: CHG440

value: T

value: Input


title: StH_Female_rep1

value: post natal day 386


title: Tan_Female_rep2

value: Tan sheep

value: post natal day 348


title: CHG431

value: Gastric Cancer Line


title: CHG429


title: SM_day 9_27C_sample 3 [re-analysis]

description:
processed data files: day9_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872159

value: South Molle Island, Great Barrier Reef

value: day 9


title: SM_day 9_32C_sample 1 [re-analysis]

description:
processed data files: day9_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872157

value: incubator 1


title: J48-1

city: Chongqing

first: Xuejiao

last: Liu

state: Chongqing

address: Tiansheng

institute: Southwest university

data_processing:
Samples were sequenced on Ion proton platform, the original image data is transferred into sequence data via base calling and saved as BAM file
Duplication sequences, adaptor sequences and low-quality reads were removed from the raw data, then the clean reads were mapped to Tetranychus urticae whole genome using TMAP with an maxium mismatch of 2 bases
Genes expression level are quantified by a software package: Sailfish. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated and used for downstream differentially expression analysis
We mapped our reads to the whole genome of Tetranychus urticae and the sequence identifier in the RPKM data files (e.g. tetur03g01320,tetur30g01560, tetur28g00430, etc.) is the Gene ID in the reference genome. Here is the web link (http://bioinformatics.psb.ugent.be/orcae/overview/Tetur) from which you can track and query them.
Genome_build: Tetranychus urticae
Supplementary_files_format_and_content: BAM file for all the reads data and excel files for RPKM values for each sample

organism: Tetranychus cinnabarinus

source_name: adult tissue

growth_protocol: T. cinnabarinus was reared on cowpea seedlings (Vigna unguiculata) in an artificial climate chamber at 26±1°C, 60-80% relative humidity, with a 14/10 h light/dark photoperiod.

extract_protocol:
At 24 h post treatment and 48 h post treatment, all the alive mites from each treatment were collected and frozen immediately in liquid nitrogen. Total RNA of each sample was extracted using the RNeasy® plus Micro Kit (Tiangen, Beijing, China) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: mites treated with curcumin(2.64 mg/mL) for 48 h

tag: strain

value: susceptible strain

value: 2-day old adult mite


title: J24-2

value: mites treated with curcumin(2.64 mg/mL) for 24 h


title: SM_day 9_32C_sample 2 [re-analysis]

description:
processed data files: day9_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872158

value: cell culture


title: J24-1


title: CHG428

city: Singapore

tag: cell line


title: CHG447

value: Gastric Primary Sample


title: CHG427


title: CK48-2

value: solvent control for 48h


title: Tan_Female_rep1

value: Female

tag: tissue type

value: Venous blood

value: post natal day 343


title: UQ_Male_rep2

value: Ujumqin sheep

value: Male

value: post natal day 371


title: UQ_Female_rep2

value: post natal day 357


title: J48-2


title: CHG426

value: Gastric Cancer Line

value: Input


title: GCC001

tag: primary sample type (t=tumor, n=normal)

value: T


title: SM_day -1_27C_sample 8 [re-analysis]

description:
processed data files: day-1_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872156

source_name: SM_day -1_27C

tag: population source

value: South Molle Island, Great Barrier Reef

value: filtered sea water + IMK nutrient supplement

value: Acropora tenuis

value: day -1

value: incubator 4


title: UQ_Male_rep1

value: post natal day 372


title: CHG424


title: CHG423


title: SM_day -1_27C_sample 6 [re-analysis]

description:
processed data files: day-1_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872154

tag: sample type

value: cell culture

value: incubator 3


title: CK24-2

value: solvent control for 24h

value: susceptible strain

value: 2-day old adult mite


title: CK24-1


title: Liver_CP2

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

country: Germany

institute: Helmholtz Zentrum München

description: Lane 2 - Barcode Solid 8

data_processing:
Lifescope mapping
Htseq-Count Galaxy
Genome_build: mm10
Supplementary_files_format_and_content: htseq counts, feature: genes

source_name: Liver

extract_protocol:
Qiagen RNA elute kit.
Lexogen plus strand synthesis

treatment_protocol: Hormonal treatment of mice

value: Liver

value: Cp


title: Liver_CP3

description: Lane 3 - Barcode Solid 12


title: SM_day -1_27C_sample 5 [re-analysis]

description:
processed data files: day-1_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872153

tag: medium


title: SM_day -1_27C_sample 3 [re-analysis]

description:
processed data files: day-1_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872151

tag: coral host from which it was isolated

value: incubator 2


title: Liver_CP1

description: Lane 1 - Barcode Solid 4


title: Liver_GT4

description: Lane 4 - Barcode Solid 3


title: CHG421

value: Gastric Cancer Line


title: SM_day -1_27C_sample 1 [re-analysis]

description:
processed data files: day-1_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872149

tag: sampling time point

value: incubator 1


title: SM_day -1_27C_sample 2 [re-analysis]

description:
processed data files: day-1_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872150

tag: temperature treatment


title: CHG417


title: SM_day -1_27C_sample 7 [re-analysis]

description:
processed data files: day-1_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872155

tag: incubator


title: Liver_GT3

description: Lane 3 - Barcode Solid 11

tag: tissue


title: CHG371

tag: chip antibody


title: CHG374


title: UQ_Female_rep1

tag: breed

value: Ujumqin sheep

value: Female

value: Venous blood

value: post natal day 359


title: Liver_GT2

description: Lane 2 - Barcode Solid 7


title: CHG324

value: Gastric Primary Sample

value: N


title: Liver_GT1

description: Lane 1 - Barcode Solid 3


title: Liver_CP4

description: Lane 4 - Barcode Solid 4


title: Liver_T4

description: Lane 5 - Barcode Solid 8


title: CHG422


title: CHG323


title: Liver_T2

description: Lane 5 - Barcode Solid 6


title: CHG284


title: CHG376

value: Input


title: CHG279

value: T


title: Liver_G4

description: Lane 4 - Barcode Solid 2

value: Gluc


title: Liver_T1

description: Lane 5 - Barcode Solid 5


title: CHG242


title: CHG244


title: Liver_G3

description: Lane 3 - Barcode Solid 10


title: CHG245


title: Intestine and colon, tumor pool#3 (n=3 donors)

city: Québec

first: Chantal

last: Guillemette

state: Québec

address: 2705 blvd Laurier

department: Faculty of Pharmacy

country: Canada

institute: Laval University

description: UGT sequences were enriched from cDNA librairies with capture probes (NimbleGen SeqCap EZ choice) spanning genomic sequences of UGT1 and UGT2 loci including introns, intergenic sequences and 50 000 bp on both side of each UGT locus.

data_processing:
Illumina CASAVA software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and then mapped to Hg19 whole genome and UGT reference transcriptome (Tourancheau, The Pharmacogenomics Journal, 2016; 16:60-70)  using tophat v2.0.13 (parameters: --no-novel-juncs) and bowtie v1.0.0-1 (Trapnell, Nat Biotechnol. 2013;31:46-53)
The aligned reads were assembled by Cufflinks program to produce transcripts annotated to the same reference genome. The tool Cuffdiff of Cufflinks was utilized to quantify the transcriptomes and compare them across calcified and normal tricuspid valves  (Trapnell, Nat Biotechnol. 2013;31:46-53).
Genome_build: hg19
Supplementary_files_format_and_content: genes FPKM; isoforms FPKM

source_name: Intestine and colon_tumor_tissue biopsy

extract_protocol:
RNA was extracted from 1 ug of each tissue using TriReagent followed by RNA cleanup using QIAGEN RNeasy Mini Kit with DNAse I. Equal amount of RNA from 3 tissue samples were pooled and 1 ug total RNA from each pool was used to prepare sequencing librairies with Illumina TruSeq RNA Sample Prep Kit
UGT CaptureSeq; RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: pooled male and female

value: Intestine and colon

value: tumoral


title: Liver_G2

description: Lane 2 - Barcode Solid 6

value: Liver


title: Intestine and colon, tumor, pool#2 (n=3 donors)


title: CHG318


title: GCC080


title: Liver_G1

description: Lane 1 - Barcode Solid 2


title: Intestine and colon, tumor, pool#1 (n=3 donors)


title: CHG236


title: CHG238


title: Liver_C4

description: Lane 4 - Barcode Solid 1

value: Control


title: SM_day -1_27C_sample 4 [re-analysis]

description:
processed data files: day-1_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872152

value: South Molle Island, Great Barrier Reef

value: cell culture

value: filtered sea water + IMK nutrient supplement

value: Acropora tenuis

value: day -1

value: incubator 2


title: Liver_C3

description: Lane 3 - Barcode Solid 9


title: 5075_WT_RNA-seq

city: Richardson

first: Joseph

middle: Michael

last: Boll

state: TX

address: 800 W Campbell

department: Biological Sciences

institute: University of Texas at Dallas

description: Whole cell RNA

data_processing:
Reads were imported into CLC Genomics Workbench.
Reads were aligned to annotated genome with mismatch, insertion, and deletion cost of 3. Length and Similarity fraction were set to 0.95. The alignment files were ATCC17978 (ASM1542v1), ATCC19606 (ASM16229v1), Ab5075 (ASM96381v1), and AYE (ASM6924v1).
Expression was reported as RPKM value.
LOS-deficient RPKM expression values were compared to WT RPKM expression values to indicate fold change in transcripts.
Genome_build: ATCC17978: ASM1542v1
Genome_build: ATCC19606: ASM16229v1
Genome_build: Ab5075: ASM96381v1
Genome_build: AYE: ASM6924v1
Supplementary_files_format_and_content: Excel files were generated by exporting the gene name, fold change relative to wild type, and KEGG pathway annotation. Scores represent the fold change of the transcript in LOS-deficient A. baumannii relative to wild type.

organism: Acinetobacter baumannii

growth_protocol: A. baumannii strains were grown to OD600 = 0.7 in 5 ml of LB broth at 37 degrees with shaking.

extract_protocol:
Trizol extraction and zymo RNA isolation.
NEBNext Ultra RNA library prep kit for Illumina.

tag: strain/background

tag: genotype/variation

value: WT

tag: growth phase

value: OD600 0.7 mid-log phase

tag: growth media

value: Luria-Bertani (LB) broth


title: Intestine and colon, normal, pool#3 (n=5 donors)

source_name: Intestine and colon_normal_tissue biopsy

tag: tissue type

value: normal


title: AYE_WT_RNA-seq

description: Whole cell RNA

source_name: AYE, WT

value: AYE


title: CHG232

source_name: Gastric Cancer Line

tag: cell line

value: Gastric Cancer Line

value: Input


title: CHG233


title: Liver_C2

description: Lane 2 - Barcode Solid 5

tag: treatment


title: Intestine and colon, normal, pool#2 (n=5 donors)

value: pooled male and female

value: Intestine and colon


title: Intestine and colon, normal, pool#1 (n=5 donors)


title: 19606_WT_RNA-seq

description: Whole cell RNA

source_name: ATCC 19606, WT


title: 17978_WT_RNA-seq

description: Whole cell RNA

source_name: ATCC 17978, WT


title: Liver_C1

description: Lane 1 - Barcode Solid 1

value: Liver


title: CHG227


title: CHG230


title: Kidney, tumor, pool#3 (n=3 donors)

source_name: Kidney_tumor_tissue biopsy

value: Kidney

value: tumoral


title: Kidney, tumor, pool#2 (n=3 donors)


title: CHG218


title: 5075_LOS-_RNA-seq

description: Whole cell RNA

value: LOS-


title: Kidney, tumor, pool#1 (n=3 donors)


title: AYE_LOS-_RNA-seq

description: Whole cell RNA

source_name: AYE, LOS-


title: Kidney, normal, pool#3 (n=3 donors)

source_name: Kidney_normal_tissue biopsy


title: Kidney, normal, pool#2 (n=3 donors)


title: Neu tumor n3

city: Dunedin

first: Sarah

middle: D

last: Diermeier

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

description: polyA+ RNA

data_processing:
Illumina Casava software used for basecalling.
The quality of the raw data was evaluated using FastQC.
The reads were mapped to mm10 using STAR.
The GENCODE mV5 annotation set was used as a reference and the reads per gene record were counted using the HTSeq package.
Differential gene expression was performed with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads (generated with HTSeq-count) for each sample.

source_name: mammary tumor

growth_protocol: Organoids from MMTV-PyMT tumors were prepared as described previously (Ewald AJ et al, Cold Spring Harbor Protocols, 2013) and cultured in matrigel in the presence of FGF2 for 6 days. For day 0 datasets, RNA was extratced directly after organoid preparation. For tumor sections, RNA was extratced from a homogenous, 30 µm cryo-section.

extract_protocol:
Total RNA was extracted using TRIzol reagent from both organoids and homogenized tumor tissue.
Libraries for polyA+ RNA-Sequencing were prepared from 1 μg RNA per sample using TruSeq chemistry (Illumina)

tag: strain

value: FVB

tag: genotype

value: MMTV-Cre;Flox-Neo-Neu-NT

tag: processing

value: tumor section

tag: culture time


title: CHG214


title: Neu tumor n2

description: polyA+ RNA


title: 17978_LOS-_RNA-seq

description: Whole cell RNA

source_name: ATCC 17978, LOS-


title: Liver_T3

description: Lane 5 - Barcode Solid 7


title: CHG215


title: Neu organoids n2

description: polyA+ RNA

value: MMTV-Neu-NDL

value: organoids

value: 6 days


title: Neu organoids n3

description: polyA+ RNA


title: 17978_dPonA_RNA-seq

description: Whole cell RNA

source_name: ATCC 17978, dPonA

value: dPonA

value: OD600 0.7 mid-log phase

value: Luria-Bertani (LB) broth


title: CHG212

value: Gastric Cancer Line


title: CK48-1

value: solvent control for 48h

value: susceptible strain

tag: age

value: 2-day old adult mite


title: PyMT organoids n2

description: polyA+ RNA

value: MMTV-PyMT


title: Neu organoids n1

description: polyA+ RNA


title: CHG226

value: Input


title: CHG208


title: Neu tumor n1

description: polyA+ RNA


title: CHG209


title: Liver, normal, pool#2 (n=3 donors)

source_name: Liver_normal_tissue biopsy

value: pooled male and female

value: Liver

value: normal


title: 630E-24H_rep2

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using AlienTrimmer_0.4.0. Only sequence with a minimum length of 30 were considered.
Sequenced were mapped to Peptoclostridium difficile 630 whole genome sequence complemented by the known ncRNA using bowtie v1.0.1 with parameter -k 2000
MAP2COV was used for counting genes with parameters -t RNA -b YES
Statistical analyses were performed using R version 3 and Bioconductor packages.
The whole dataset was first normalized using the normalization function of DESeq2 and with default parameters.
The statistical test function of DESeq2 was then applied on each strand coverage count with the 6 h value as a reference for reporting the expression data of 14 and 24 h.
Genome_build: Peptoclostridium difficile 630 (NC_009089.1) complemented by the known ncRNA (PMID: 23675309)
Supplementary_files_format_and_content: Genome annotation (Gene ID, Gene Name), Raw Counts (630, 630Derm, 630E, 6H, 14H, 24H), Normalized Counts (630, 630Derm, 630E, 6H, 14H, 24H), Statistics (FC, pvalue, significant)

organism: Clostridioides difficile

source_name: Erythromycin-sensitive strain 630E

growth_protocol: Strains were grown aerobically in TY at 37°C for 6, 14 and 24 H)

extract_protocol:
Total RNA was extracted using phenol, Trizol reagent and chloroform/isoamylalcohol.
RNA libraries were prepared for sequencing using standard Illumina protocols
Truseq stranded RNA seq kit

tag: strain provider

value: Rood laboratory

tag: phenotype

value: Erythromycin-sensitive


title: 19606_LOS-_RNA-seq

description: Whole cell RNA

source_name: ATCC 19606, LOS-

value: LOS-


title: Liver, normal, pool#3 (n=3 donors)

tag: tissue


title: 630E-24H_rep1


title: PyMT organoids day6 n3

description: polyA+ RNA

value: FVB

value: organoids


title: G1 Ribo-Seq Exp2 Rep1

city: Tel Aviv-Yafo

first: Tamir

last: Tuller

department: Biomedical Engineering

institute: Tel Aviv University

description: 'G1 RP Rep4' column in RC_Data.xlsx

data_processing:
library strategy: Ribo-seq
Reference transcriptome, rRNAs, and tRNAs, were assembled from BioMart (GRCh37.p11).
The 3’end adapter CTGTAGGCACCATCAAT was removed from the 51nt long reads using Cutadapt v1.6, retaining only reads with a minimum length of 24nt.
These reads were then initially mapped against the rRNA and tRNA databases, using Bowtie v0.12.8: -a --best --strata -n 2 --seedlen 24 --tryhard. Throughout the analysis the Bowtie mapping is executed as described. Reads which mapped against the rRNA and tRNA databases were removed.
The remaining reads are mapped against the assembled transcriptome using Bowtie as described.
Please see our paper for multi-read handling documentation.
Genome_build: GRCh37.p11
Supplementary_files_format_and_content: Excel file containing per gene read counts for each sample.

source_name: HeLa S3_G1_Ribo-Seq Exp2

extract_protocol:
Total mRNA and ribosome-protected fragments were analyzed essentially as described in [PMID:22836135]. In brief, 5x106 HeLa S3 cells synchronized to either G1 or M phase were treated with 100 ug/mL cycloheximide for 5 min, harvested on ice and washed twice in ice-cold PBS. Following cell lysis and removal of nuclei by centrifugation, one tenth of the lysate was removed for total mRNA extraction and the rest was digested with 60 units RNase I (Ambion) for 45 min at room temp. Digestion was terminated with SuperaseIN (Ambion) and monosomes were pelleted by ultracentrifugation on a sucrose cushion. Footprint fragments were purified using a 15% polyacrylamide urea gel, and rRNA fragments were removed using Ribo-Zero Magnetic Gold Kit (Epicentre) according to the manufacturer’s instructions. In parallel, mRNA was purified using Oligo (dT) cellulose (Ambion) according to the manufacturer’s instructions and fragmented for 25 min at 94°C.
Both mRNA and ribosome-protected fragments were dephosphorylated with T4 polynucleotide kinase and ligated to Universal miRNA Cloning Linker (NEB). RNA was reverse transcribed using SuperScript III and cDNA was circularized using CircLigase (both Epicentre). Libraries were amplified using indexed Illumina primers, size selected on a 1% agarose gel and extracted using High Pure PCR Purification Kit (Roche).

tag: cell type

value: HeLa S3 cells

tag: cell cycle phase

value: G1 phase

tag: molecule subtype

value: ribosome-protected fragments  (Ribo-seq)


title: Liver, normal, pool#1 (n=3 donors)

tag: Sex


title: 630E-6H_rep2


title: 630E-14H_rep1


title: PyMT organoids day6 n2

description: polyA+ RNA

value: 6 days


title: SUM149PT_co-culture

description: co-cultured with cancer-associated fibroblasts (CAFs)

data_processing:
Library strategy: SAGE-Seq
SAGE-Seq: Basecalls were performed using CASAVA version 1.8.2
SAGE-Seq: The sequencing tags were mapped and normalized as described in Wu et al., Genome Research, 2010 (PMID: 21045080). Tag counts used were the sums of all sense SAGE-Seq tags uniquely mapped to the same gene.
processed data files format and content: SAGE-Seq: Tab-separated file of the normalized tag counts of each samples for each gene.
Genome_build: hg18

growth_protocol: All the epithelial and fibroblast cell lines were grown in media representing 50/50 mixture of DMEM-F12, 10% FBS/MEGM with supplements, as this media fully supported growth and viability of both epithelial cells and fibroblasts. Matrigel 3d culture experiments were performed using on-top method as described in Lee et al., Nature Methods, 2007 (PMID: 17396127).

extract_protocol:
DsRED labeled carcinoma cell lines and GFP expressing primary CAFs were cultured either separately or in co-cultures for 17 hours. Colonies were released from Matrigel by 30 min incubation in PBS/EDTA, at which point separately cultured cells were combined to control for cross-contamination. Cell mixtures were washed with PBS, trypsinized for 7 min, quenched with serum containing media, washed and spun down. Epithelial cells were selected using Epithelial Enrich dynabeads (Life Technologies) following manufacturer’s protocol. Microscopic examination of captured cells revealed no detectable CAF contamination.
From each sample 5E5 cells were used to prepare SAGE-Seq (serial analysis of gene expression combined with the Illumina/Solexa 1G platform) libraries according to a detailed protocol available at http://polyaklab.dfci.harvard.edu/index.php/science/protocols

tag: tissue of origin

value: breast tumor

tag: cell line type

value: cancer cell line

tag: sub-type

value: triple-negative


title: G1 Ribo-Seq Exp1 Rep2

description: 'G1 RP Rep2' column in RC_Data.xlsx

source_name: HeLa S3_G1_Ribo-Seq Exp1


title: PyMT organoids day6 n1

description: polyA+ RNA

value: MMTV-PyMT


title: SUM149PT_separate_culture

description: cultured seperately and mixed with cancer-associated fibroblasts (CAFs)

tag: cell line


title: 630E-6H_rep1


title: PyMT organoids day0 n3

description: polyA+ RNA

value: 0 days


title: Kidney, normal, pool#1 (n=3 donors)

value: pooled male and female

value: Kidney

tag: tissue type


title: G1 Ribo-Seq Exp1 Rep1

description: 'G1 RP Rep1' column in RC_Data.xlsx


title: G1 RNA-Seq Exp2 Rep1

description: 'G1 mRNA Rep4' column in RC_Data.xlsx

data_processing:
Reference transcriptome, rRNAs, and tRNAs, were assembled from BioMart (GRCh37.p11).
The 3’end adapter CTGTAGGCACCATCAAT was removed from the 51nt long reads using Cutadapt v1.6, retaining only reads with a minimum length of 24nt.
These reads were then initially mapped against the rRNA and tRNA databases, using Bowtie v0.12.8: -a --best --strata -n 2 --seedlen 24 --tryhard. Throughout the analysis the Bowtie mapping is executed as described. Reads which mapped against the rRNA and tRNA databases were removed.
The remaining reads are mapped against the assembled transcriptome using Bowtie as described.
Please see our paper for multi-read handling documentation.
Genome_build: GRCh37.p11
Supplementary_files_format_and_content: Excel file containing per gene read counts for each sample.

source_name: HeLa S3_G1_RNA-Seq Exp2

value: Total mRNA (RNA-seq)


title: 630∆erm-24H_rep2

source_name: Erythromycin-sensitive strain 630∆erm

value: Mullany laboratory

tag: strain