title: RPE-Cas9-p53KD_KO5-d4


title: COAD.ct-563

status: Public on Jan 01 2020

type: SRA

city: La Jolla

first: Kang

last: Zhang

address: 9500 Gilman Dr

country: USA

institute: UCSD

library_source: genomic

data_processing:
unique molecular identifiers were extracted from each read using custom script
reads were adaptor and quality trimmed using Trim-galore and Cutadapt 1.4.1 with parameters -e 0.1 -q 20 -O 1
BisReadMapper1.3 (D.Diep, K.Zhang) using Bowtie2 was used to align reads to in-silico bisulfite-converted genome sequence
C and Ts were extracted from reads at the targeted positions using only reads with unique identifiers using custom scripts (BamExtractor, D.Diep, K.Zhang)
methylation frequencies were calculated by binning data into 100bp regions and aggregating methylated and non-methylated cytosines within 100bp bins
Genome_build: hg19
Supplementary_files_format_and_content: text file containing beta values for all samples at all analyzed 100bp genomic regions

molecule: genomic DNA

organism: Homo sapiens

source_name: blood serum

extract_protocol:
cfDNA extraction from 1.5 ml of serum samples was performed using QIAamp cfDNA Kit (Qiagen) according to manufacturer’s recommendations
10 ng of cfDNA was bisulfite-converted using EZ DNA Methylation-Lightning™ Kit (Zymo). Bis-DNA specific "padlock" probes (molecular inversion probes, MIPS) were used to capture genomic regions and provide adaptors for NGS library construction. Nextera-XT compatible barcoding primers were used to amplify DNA for sequencing. Library (~300bp) was purified using AMPure beads.
custom-made libraries were sequenced on HiSeq2500 using 150PE reads

tag: sample type

value: cell-free DNA


title: WT_12F2_LP1

city: Jerusalem

first: Matan

last: Sorek

address: Edmond J. Safra Campus

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

description:
human embryonic stem cells- and induced pluripotenet stem cells-derived striatal GABAergic neurons
all_raw_counts.txt
all_normalized_RPM_counts.txt

library_source: transcriptomic

data_processing:
Raw reads that passed the quality controls were aligned to human genome assembly hg19 using STAR (Dobin et al. ,2013, Bioinformatics) with parameters alignIntronMax=1000 and alignMatesGapMax=1000.
unmapped and low quality read were removed
multiple reads that were mapped to the same location in the genome with the same UMI in the same sample were removed
Filtered reads were passed to the End Sequence Analysis Toolkit (ESAT, Derr et al., 2016, Genome Research)  with parameters wLen=400, wOlap=50, wExt=2000 and sigTest=0.05.
Reads Per Megabase of library size (RPM) were calculated, and further normalized according to DE-Seq (Anders et al., 2010, Genome Biology). In short, each sample is normalized by a factor which corresponds to the median ratio of expression of genes in the sample and the geometric mean of genes in all samples
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized RPM values for each sample

molecule: total RNA

source_name: striatal GABAergic neurons

growth_protocol: hESCs (Bradley et al., 2011), and hiPSCs were cultured as described (Takahashi et al., 2007). For neuronal induction, hiPSC colonies were induced for neuronal lineage differentiation using dual SMAD inhibition by blocking BMP and TGF. hiPSC colonies were separated and seeded on Matrigel as single cells and incubated with human induction media [DMEM/F12, Neurobasal, N2, B27] supplemented with 2 SMADi (20 M SB, 100 nM LDN) and 1 μM XAV-939 for 10 days. From day 10 to 20 of differentiation, cells were incubated with neural induction media supplemented with 50 nM SAG and 1 μM XAV-939, inducing the cells to become neural progenitor cells (NPCs). For terminal differentiation, the cells were re-seeded on PLO/laminin coated plates at 75,000 cells/cm2, and exposed to neural terminal differentiation medium supplemented with 20 ng/ml BDNF, 0.5 mM dbcAMP, and 0.5 mM Valpromide.

extract_protocol:
RNA was extracted from neurons using Qiagene 96-well kit according to the manufacturer's instructions.
library construction was carried out as published (Soumillion et al., 2014)

treatment_protocol: For progerin induced samples, HEK293T cells were transduced with the target lentiviral vector (either lenti-GFP- LMNA or lenti-GFP-progerin) and packaging vectors deltaR8.9 and VSV- G (2th generation) using TransIT-LT1 (Mirus) transfection reagent. Before transfection, HEK293T medium was replaced with neural medium (w/o neuro-factors). 24 and 48-hours post transfection, Polybrene (8 μg/ml) and neurofactors were added to filtered-medium containing-virions. From each well containing neurons, 2/3 of the volume was replaced with media containing virions. For the drugs GSK-J4 and UNC1999, they were added in day 39 of the differentiation protocol, in concentrations of 10 μM and  5 μM, respectively.

tag: cell type

value: striatal GABAergic neurons

tag: derived from hesc or ipsc

value: iPSC

tag: genotype

value: WT

tag: progerin

value: Yes


title: COAD.ct-562


title: HD_090_LP3

value: ESC

value: HD


title: HD_090_LP2


title: COAD.ct-558


title: COAD.ct-559


title: HD_089_LP3


title: COAD.ct-557


title: COAD.ct-560


title: HD_090_LP1


title: COAD.ct-566


title: COAD.ct-556


title: HD_020_LP2


title: COAD.ct-555


title: HD_020_LP3


title: HD_089_LP1


title: COAD.ct-553


title: HD_16F2_LP2


title: COAD.ct-554


title: HD_018_LP3


title: HD_018_LP2


title: HD_020_LP1


title: COAD.ct-561


title: COAD.ct-550


title: WT_019_LP6


title: WT_019_LP5


title: WT_019_LP4


title: HD_089_LP2


title: COAD.ct-548


title: COAD.ct-547


title: WT_019_LP3


title: WT_019_LP2


title: COAD.ct-546


title: COAD.ct-545


title: WT_019_LP1


title: WT_022_LP3


title: COAD.ct-543


title: COAD.ct-544


title: COAD.ct-551


title: COAD.ct-552


title: COAD.ct-542


title: COAD.ct-540


title: COAD.ct-541


title: HD_018_LP1


title: COAD.ct-539


title: COAD.ct-549


title: COAD.ct-538


title: WT_029_LP2_469


title: HD_090_LP2_469


title: COAD.ct-537


title: COAD.ct-536


title: COAD.ct-535


title: HD_090_LP1_469


title: WT_022_LP1


title: WT_029_LG2_469

value: No


title: HD_090_LG1_469


title: HD_090_LG2_469


title: WT_029_LG1_469


title: COAD.ct-532


title: WT_022_LP2


title: RPE-Cas9-p53KD_KO3-d22

city: Baltimore

first: Daniel

last: Ardeljan

address: 733 N Broadway, MRB 432

institute: Johns Hopkins University School of Medicine

description:
sgRNA DNA library
KDscreen_MAGeCK_NTCnorm_counts.txt

data_processing:
Library strategy: CRISPR KO screen
CRISPR KO reads aligned to Brunello Index using Bowtie.
CRISPR KO counts processed with MAGeCK.
RNAseq reads aligned with STAR (hg38), counted with HTSeq, and differential expression was performed with DESeq2.
Genome_build: hg38 or Brunello Index (https://www.addgene.org/pooled-library/broadgpp-human-knockout-brunello/). Brunello citation PMID: 26780180
Supplementary_files_format_and_content: All are .txt files. The DESeq2 file contains differential expression data for cells expressing LINE-1 vs. Luciferase that is standard output from the DESeq2 program. The 'htseq_output_with_stat_summary.txt' file includes the RNA-seq differential expression analysis table to accompany the reads. The MAGeCK files contain screen count data normalized to non-target-controls, as generated by the MAGeCK program.

growth_protocol: RPE cell lines are grown in DMEM/F12 supplemented with sodium bicarbonate and 10% FBS at 37C and 5% CO2. Tet-Free FBS is used in Tet-On expression systems. Tet-On expression systems also require 400 ug/ml G418 and Cas9-expressing cells require 10 ug/ml Blasticidin.

extract_protocol: genomic DNA was collected by lysing in SDS and treating with proteinase K and RNase A. gDNA was purified with Ethanol precipitation. CRISPR sequencing libraries were created using primers to amplify the sgRNA sequences. The primers encoded adaptors P5 and P7 for use in Illumina sequencing machines.

tag: passages

tag: expression method

value: Tet-On LINE-1

tag: treatment

value: cells were transduced with the Brunello Knockout Library and doxycycline was added to induce expression of LINE-1 or Luciferase


title: COAD.ct-533


title: COAD.ct-531


title: SOX4noDOX

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

country: Netherlands

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

data_processing:
Truseq nano DNA sample preparation kit 10 (Illumina) was used for End-repair, A-tailing, and ligation of sequence adaptors. Samples were subsequently PCR amplified after which the libraries were size selected to remove adapter dimers and select fragments in the 200-500bp range. Barcoded libraries were sequenced on Illumina NextSeq500 sequencer (75bp, single-end, Utrecht DNA sequencing facility).
Genome_build: hg19
Supplementary_files_format_and_content: peak list in *.cod format (rank chromosome start end strand peak_length FDR left_peakboundary right_peakboundary peak_summit bound_center bound_width maxT maxT_pos max_log2FC maxFC_pos minuslog10_minPoisP minPoisP_pos  )

growth_protocol: Immortalized human mammary epithelial cells (HMLE) (kindly provided by dr. R.A. Weinberg) and were cultured in human mammary epithelial growth media (cc- 3150, Lonza).

extract_protocol:
ChIP was performed as described previously (PMID:23832113) using the following antibodies: 10μg of SOX4 antibody (CS-129-100, Diagenode), 5μg H3K4me3, H3K27ac, (ab8580, ab4729, Abcam), 5μg anti-RBP1 (PB-7C2, RNAPII) antibody (Euromedex), and 5μg H3K27me3 (39157, Active Motif).
Truseq nano DNA sample preparation kit 10 (Illumina) was used for End-repair, A-tailing, and ligation of sequence adaptors. Samples were subsequently PCR amplified after which the libraries were size selected to remove adapter dimers and select fragments in the 200-500bp range. Barcoded libraries were sequenced on Illumina NextSeq500 sequencer (75bp, single-end, Utrecht DNA sequencing facility).

treatment_protocol: Prior to chromatin immunoprecipitation (ChIP) and sequencing HMLE-S4 cells were grown in the absence or presence of 1μg/ml of doxycycline for 16h.

tag: cell line

value: DOX-

tag: ip


title: H3K4noDOX


title: COAD.ct-530


title: POL2noDOX

value: RNAPII


title: COAD.ct-529


title: COAD.ct-527


title: COAD.ct-528


title: COAD.ct-526


title: SOX4DOX1

value: DOX+


title: POL2DOX


title: WT_029_LP1_469


title: H3K4DOX1


title: COAD.ct-525


title: H3K27menoDOX


title: KPC_rep4

city: St Louis

first: Samarth

last: Hegde

state: MO

address: 660 South Euclid Avenue, Campus Box 8069

department: Internal Medicine

institute: Washington University in St. Louis

data_processing:
Total basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program.
Single-reads aligned to Ensembl release 76 top-level assembly with STAR (version 2.0.4b). Gene counts derived from the number of uniquely aligned unambiguous reads.
Isoform expression of known Ensembl transcripts estimated with Sailfish (version 0.6.13).  Ribosomal fraction, known junction saturation, and read distribution over known gene models  quantified with RSeQC (version 2.3).
Gene counts imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million (cpm) were excluded from further analysis.
TMM size factors and matrix of counts imported into Limma and differential expression analyses performed.
Genome_build: Ensembl_R76
Supplementary_files_format_and_content: tab-delimited text files include bias-corrected RPKM values

organism: Mus musculus

source_name: Pancreas

extract_protocol:
Pancreas were extracted after perfusion, flash frozen in liquid nitrogen and stored at -80C. Total RNA was extracted after pulverization using an E.Z.N.A.® Total RNA Kit (OMEGA) according to manufacturer’s instructions, and banked as aliquots in -80C until use.
RNA libraries were prepared for sequencing using standard Illumina protocols after ribosomal depletion

tag: strain

tag: tissue

value: pancreas

tag: age

value: post natal day 42

tag: genotype/variation


title: H3K27acnoDOX


title: OG_rep3


title: OG_rep1


title: H3K27meDOX


title: OG_rep2


title: COAD.ct-523


title: OG_rep4


title: KPC_rep1


title: COAD.ct-522


title: KPC_rep3


title: KPC_rep2


title: Na2SeO3+CYP rep3

city: Hefei

first: Kan

last: He

state: Anhui

address: 111 Jiulong Road

department: School of life sciences

country: China

institute: Anhui University

description:
gene_exp_with_symbol.txt
processed data column header: f3

data_processing:
BGISEQ500 platform used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using HISAT software
Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by Cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include the expression values of this transcript  for each Sample ..

source_name: liver tissue

extract_protocol:
RNA was harvested using Trizol reagent.TruSeq® RNA LT Sample Prep Kit v2  was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGISEQ500 protocols

value: 40mg/kg [beta]-CYP and 50μg/kg Na2SeO3

value: liver

value: Swiss

tag: ages

value: weeks 10-12


title: Na2SeO3+CYP rep2

description:
gene_exp_with_symbol.txt
processed data column header: f2


title: Input

value: input


title: H3K27acDOX


title: CYP rep3

description:
gene_exp_with_symbol.txt
processed data column header: e3

value: 40mg/kg [beta]-CYP


title: Na2SeO3+CYP rep1

description:
gene_exp_with_symbol.txt
processed data column header: f1


title: COAD.ct-521

value: cell-free DNA


title: HTGTS_PB_VK1_117_CRISPR_NO_STI

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

institute: Bar-Ilan University

data_processing:
Library strategy: HTGTS
Reads were aligned to the GRCm38p2/mm10 and GRCh37/hg19 genome assembly
Sites that underwent chromosomal translocations to the bait sites were identified as described (Hu et al., 2016).
Genome_build: GRCm38p2/mm10, GRCh37/hg19
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig . Supplementary_files_format_and_content: tlx files were generated using HTGTS pipeline (Hu et al. 2016)

source_name: Abelson-transformed pre-B cell

growth_protocol: Abelson pre-B cell lines were cultured DMEM supplemented 10% FBS, with 2 mM L-glutamine, 1 mM Sodium piruvate, non-essential amino acids, 0.05 mM β-mercaptoethanol, penicillin (100 U/ml) and streptomycin (100 U/ml) (Invitrogen).

extract_protocol:
10 million of Abelson pre-B cells, primary mouse bone marrow pre-B cells, splenic IgM positive B cells, and human PBMC B cells were used for HTGTS analyses. Primary mouse bone marrow pre-B cells were obtained from 6-12 week old wild-type, C57BL/6 mice with flow cytometry cell sorting on a FACSAria II cell sorter (BD Biosciences) using a combination of anti-B220, anti-CD43, anti-CD24 and anti-IgM antibodies (ThermoFisher/eBioscience) (Lin et al., 2016). IgM positive mature resting B cells were isolated from C57BL/6 mice spleen with anti-CD43 MicroBeads (Miltenyi Biotech). Human peripheral blood B cells were isolated from deidentified, donated PBMC using human B cell isolation kit (STEMCELL Technologies 17954).
HTGTS was performed as described (Hu et al., 2015). Genomic DNA was extracted from splenic B cells, isolated B cells from human PBMC, or  v-Abl cells arrested in G1 for 2 days by treatment with 3 mM of STI-571. Briefly, 20-50 ug of DNA was fragmented via sonication on a Diagenode bioruptor and subjected to linear PCR amplification with a biotinylated primer. Single-stranded PCR products were purified via Dynabeads MyONE C1 streptavidin beads (Life Technologies, 65002) and ligated to bridge adaptors. Adaptor-ligated products were amplified via nested PCR with indexed locus-specific primers and primer annealed to adaptor. The PCR products were further tagged with Illumina sequencing adaptor sequences, size-selected (fragment size 500 – 1,000 bp) via gel extraction and loaded to Illumina MiSeq for paired-end 250 bp sequencing. For translocation analysis, the standard LAM-HTGTS bioinformatic pipeline was used (Hu et al., 2015).

treatment_protocol: Abelson pre-B cells were arrested in G1 by treatment with 3 mM imatinib for 48 hours and harvested for HTGTS. For detecting translocation from Cas9/gRNA DSBs, gRNA was design to generate DSBs 654 bp downstream of the Vk1-117 bRSS breakage site. HTGTS primer was design that allowed 5' broken ends of these DSBs to be used as a bait. WT abelson pre-B cells were treated with 3 μM imatinib at a concentration of 5x105 cells/ml for 30 hours followed by nucleofection of pX330-Cas9-Vk1-117-CRSPR plasmid (15μg) into 20 million G1-arrested cells (2 reactions; 10 million cells each reaction) using X-001 program of Amaxa Nucleofector II (Lonza) with Human B cell Nucleofector kit (Lonza). Transfected cells were cultured in DMEM medium with 15% (v/v) FBS plus 3 μM imatinib for 3 more days before harvested for genomic DNA.

value: Abelson-transformed pre-B cell

value: WT


title: HTGTS_PB_VK1_117_CRISPR_REP3


title: COAD.ct-519


title: CYP rep2

description:
gene_exp_with_symbol.txt
processed data column header: e2


title: HTGTS_PB_VK1_117_CRISPR_REP2


title: CYP rep1

description:
gene_exp_with_symbol.txt
processed data column header: e1


title: COAD.ct-534


title: COAD.ct-524


title: HTGTS_PB_VK1_117_CRISPR_REP1


title: COAD.ct-518


title: Control rep2

description:
gene_exp_with_symbol.txt
processed data column header: a2

value: control


title: Control rep3

description:
gene_exp_with_symbol.txt
processed data column header: a3


title: Nsmce1-pb rep2 (N32)

source_name: hippocampal cells

growth_protocol: HT-22 were routinely maintained in the conventional mouseEagle's medium

value: Nsmce1 overeexpression

value: hippocampal neuron


title: Control rep1

description:
gene_exp_with_symbol.txt
processed data column header: a1


title: HTGTS_PB_VK1_117_ART_clone2

value: ART-/-


title: Nsmce1-pb rep1 (N31)

value: passage 21-24


title: COAD.ct-517


title: COAD.ct-520


title: HTGTS_PB_VK1_117_ART_clone1


title: COAD.ct-516


title: WT rep2 (PBIP2)

value: wild type


title: COAD.ct-515


title: HTGTS_BMPB_VK1_117_REP1

source_name: Primary BM pre-B cell

value: Primary BM pre-B cell


title: HTGTS_BMPB_VK1_117_REP2


title: WT rep1 (PBIP1)


title: COAD.ct-514


title: HTGTS_PB_VK1_117_LIG4


title: Week25_stimulated_DFC3_AE

city: Cambridge

first: Alex

last: Shalek

state: MA

address: 45 Carleton Street

department: Chemistry

institute: MIT

description: Transcriptome of single cells

data_processing:
Illumina bcl2fastq2.17.1.14 was used to generate fastqs from bcl files
Read 1 contains the barcode (bp 1-12) and UMI (13-18); Read 2 contains the biological sequence.
STAR was used to align the scRNA-seq data
Regression analysis was done as described in manuscript
Genome_build: mmul_8.0.1
Supplementary_files_format_and_content: Filtered UMI-collapsed Matrix

organism: Macaca mulatta

extract_protocol: high-throughput single-cell mRNA sequencing by Seq-Well was performed on single-cell suspensions obtain from NHP BAL. 15,000 vialble cells per sample were applied directly to the surface of a Seq-Well device. At each time point after BCG, 2 arrays were run for each sample - one unstimulated and one stimulated overnight with 20 ug/mL of PPD in R10.

treatment_protocol: PPD-Stimulated == Tuberculin Protein Purified Derivative-Stimulated

tag: time after bcg vaccination

value: Week 25

tag: stimulation

value: PPD-Stimulated Cells

value: Bronchoalveolar Lavage

tag: vaccination route

value: Aerosol

tag: vaccination dose

value: 5x10e7 CFU


title: Week25_stimulated_O6T_IV

description: Transcriptome of single cells

value: Intravenous


title: HTGTS_Spl_B_VK1_117_REP3

source_name: Primary splenic B cell

tag: cell type

value: Primary splenic B cell


title: Week25_stimulated_OVN_IDHigh

description: Transcriptome of single cells

value: Intradermal


title: Week25_stimulated_DF4E_Naive

description: Transcriptome of single cells

value: Naive

value: 0 CFU


title: Week25_stimulated_OC6_Naive

description: Transcriptome of single cells


title: COAD.ct-513

tag: sample type

value: cell-free DNA


title: Week25_stimulated_DG44_IDLow

description: Transcriptome of single cells

value: 5x10e5 CFU


title: Week25_stimulated_DF4N_Naive

description: Transcriptome of single cells


title: HTGTS_Spl_B_VK1_117_REP2

tag: genotype

value: WT


title: COAD.ct-512


title: Week25_stimulated_OLB_IDHigh

description: Transcriptome of single cells


title: Week25_stimulated_OPH_AE

description: Transcriptome of single cells


title: HTGTS_Spl_B_VK1_117_REP1


title: Week25_stimulated_DFW7_IV

description: Transcriptome of single cells


title: Week25_stimulated_DFT3_IDHigh

description: Transcriptome of single cells


title: Week25_stimulated_DF8P_AE

description: Transcriptome of single cells


title: COAD.ct-509


title: COAD.ct-510


title: HTGTS_Spl_B_JK1


title: HTGTS_PB_VK8_34_DELJK_REP3

value: Abelson-transformed pre-B cell

value: DJK


title: Week25_stimulated_DFF3_IV

description: Transcriptome of single cells


title: COAD.ct-508


title: Week25_stimulated_DF16_IDLow

description: Transcriptome of single cells


title: COAD.ct-507


title: HTGTS_PB_VK8_34_DELJK_REP1


title: HTGTS_PB_VK8_34_WT_REP6


title: Week25_unstimulated_OVN_IDHigh

description: Transcriptome of single cells

value: Unstimulated cells


title: Week25_unstimulated_DG44_IDLow

description: Transcriptome of single cells


title: HTGTS_PB_VK8_34_DELJK_REP2


title: Week25_unstimulated_O6T_IV

description: Transcriptome of single cells


title: Week25_unstimulated_DFC3_AE

description: Transcriptome of single cells


title: COAD.ct-506


title: COAD.ct-511


title: Week25_unstimulated_DF4N_Naive

description: Transcriptome of single cells


title: HTGTS_PB_VK8_34_WT_REP5


title: Week25_unstimulated_OLB_IDHigh

description: Transcriptome of single cells


title: COAD.ct-504


title: Week25_stimulated_HBZ_IDLow

description: Transcriptome of single cells


title: COAD.ct-505


title: HTGTS_PB_VK8_34_WT_REP4


title: Week25_unstimulated_OPH_AE

description: Transcriptome of single cells


title: COAD.ct-503


title: Week25_unstimulated_DFW7_IV

description: Transcriptome of single cells


title: Week25_unstimulated_HBZ_IDLow

description: Transcriptome of single cells


title: Week25_unstimulated_DFT3_IDHigh

description: Transcriptome of single cells


title: COAD.ct-502


title: HTGTS_PB_VK8_34_WT_REP3


title: Week25_unstimulated_DF4E_Naive

description: Transcriptome of single cells


title: Week25_unstimulated_DF8P_AE

description: Transcriptome of single cells


title: COAD.ct-501


title: HTGTS_PB_VK8_34_WT_REP1


title: Week25_unstimulated_DF16_IDLow

description: Transcriptome of single cells


title: Week25_unstimulated_DFF3_IV

description: Transcriptome of single cells


title: Week25_unstimulated_OC6_Naive

description: Transcriptome of single cells


title: COAD.ct-500


title: HTGTS_PB_VK1_117_RAG1


title: Week13_stimulated_OVN_IDHigh

description: Transcriptome of single cells

value: Week 13


title: Week13_stimulated_OC6_Naive

description: Transcriptome of single cells


title: HTGTS_PB_VK1_117_DELJK_REP6


title: COAD.ct-499


title: Week13_stimulated_DFC3_AE

description: Transcriptome of single cells


title: Week13_stimulated_O6T_IV

description: Transcriptome of single cells


title: Week13_stimulated_DF4E_Naive

description: Transcriptome of single cells


title: COAD.ct-497


title: HTGTS_PB_VK1_117_DELJK_REP4


title: Week13_stimulated_OLB_IDHigh

description: Transcriptome of single cells


title: HTGTS_PB_VK8_34_WT_REP2


title: Week13_stimulated_DFW7_IV

description: Transcriptome of single cells


title: Week13_stimulated_HBZ_IDLow

description: Transcriptome of single cells


title: HTGTS_PB_VK1_117_DELJK_REP2


title: HTGTS_PB_VK1_117_DELJK_REP3


title: Week13_stimulated_DFT3_IDHigh

description: Transcriptome of single cells


title: COAD.ct-494


title: Week13_stimulated_DF4N_Naive

description: Transcriptome of single cells


title: Week13_stimulated_DF8P_AE

description: Transcriptome of single cells


title: COAD.ct-493


title: HTGTS_PB_VK1_117_DELJK_REP1


title: Week13_stimulated_DFF3_IV

description: Transcriptome of single cells


title: HTGTS_PB_VK1_117_DELJK_REP5


title: COAD.ct-492


title: HTGTS_PB_VK1_117_WT_REP6


title: Week13_unstimulated_DF4E_Naive

description: Transcriptome of single cells


title: Week13_stimulated_DF16_IDLow

description: Transcriptome of single cells


title: Week13_unstimulated_OVN_IDHigh

description: Transcriptome of single cells


title: Week13_stimulated_OPH_AE

description: Transcriptome of single cells


title: COAD.ct-490


title: Week13_unstimulated_DFC3_AE

description: Transcriptome of single cells


title: Week13_unstimulated_OC6_Naive

description: Transcriptome of single cells


title: HTGTS_PB_VK1_117_WT_REP4


title: COAD.ct-496


title: COAD.ct-491


title: Week13_stimulated_DG44_IDLow

description: Transcriptome of single cells


title: HTGTS_PB_VK1_117_WT_REP5


title: Week13_unstimulated_DF4N_Naive

description: Transcriptome of single cells


title: COAD.ct-495


title: Week13_unstimulated_O6T_IV

description: Transcriptome of single cells


title: COAD.ct-489


title: Week13_unstimulated_OLB_IDHigh

description: Transcriptome of single cells


title: Week13_unstimulated_OPH_AE

description: Transcriptome of single cells


title: COAD.ct-488


title: Week13_unstimulated_DG44_IDLow

description: Transcriptome of single cells


title: HTGTS_PB_VK1_117_WT_REP3


title: Week13_unstimulated_HBZ_IDLow

description: Transcriptome of single cells


title: HTGTS_PB_VK1_117_WT_REP2


title: Week13_unstimulated_DFT3_IDHigh

description: Transcriptome of single cells


title: Week13_unstimulated_DF8P_AE

description: Transcriptome of single cells


title: Week13_unstimulated_DFF3_IV

description: Transcriptome of single cells


title: COAD.ct-486


title: COAD.ct-487


title: HTGTS_PB_JK1_WT_REP2


title: HTGTS_PB_VK1_117_WT_REP1


title: COAD.ct-498


title: HTGTS_PB_JK1_WT_REP1


title: COAD.ct-484


title: Week13_unstimulated_DFW7_IV

description: Transcriptome of single cells


title: COAD.ct-483


title: COAD.ct-482


title: HTGTS_PB_JK1_WT_REP3


title: COAD.ct-480


title: COAD.ct-485


title: COAD.ct-479


title: COAD.ct-478


title: COAD.ct-477


title: Week13_unstimulated_DF16_IDLow

description: Transcriptome of single cells


title: CTCF siRNA 144hrs Rep2

type: RNA

city: Darlinghurst

first: Amanda

last: Khoury

state: NSW

address: 384 Victoria St.

country: Australia

institute: Garvan Institute

hyb_protocol: As per standard Affymetrix protocol for the Human 2.0ST arrays

data_processing:
Analysis of Affymetrix expression arrays was performed using R version 3.2.5. Raw CEL files were read in, background corrected, quantile normalised and median-polished using RMA (Irizarry et al., 2003) as implemented in the oligo bioconductor package (Carvalho & Irizarry, 2010).Quality control plots (intensity distributions, RLE and NUSE plots) were generated and visually inspected to ensure data was of consistent quality across the experiment. Probesets from the HuGene array were annotated with Ensembl gene and transcript identifiers using biomaRt (Durinck et al., 2009). Differential expression analysis was performed using limma (Ritchie et al., 2015). The design matrix used in linear model fitting included the siRNAs used (CTCF or control), the time point after siRNA addition (24, 72 or 144 hours) and the paired nature of the biological replicates in the time course. The contrast matrix was constructed to detect differences in gene expression between the CTCF and non-targeting siRNA samples at each time point using moderated t-statistics. Genes were deemed as significantly up- or down-regulated if the Benjamini-Hochberg adjusted P-value was < 0.05.
Bioconductor package pd.hugene.2.0.st

label: biotin

source_name: LNCaP Prostate Cancer Cells

growth_protocol: LNCaP were cultured under ATCC recommended conditions at 37°C and 5% CO2.

extract_protocol: Total RNA extraction was performed using Trizol Reagent  (invitrogen) following manufacturer's instructions

treatment_protocol: LNCaP cells were transfected with 20nM of Dhamacon ON-TARGET plus pooled Non-targeting siRNA or 20nM of Dhamacon ON-TARGET plus pooled CTCF siRNA (containing sequences GAUGAAGACUGAAGUAAUG, GGAGAAAGAAGAAGAGUA, GAAGAUGCCUGCCACUUAC, GAACAGCCCAUAAACAUAG) according to the manufacturer-supplied protocol. Following 72hrs of transfection, cells were split and reverse transfected for a further 72hrs (144hrs).

value: prostate

value: LNCaP Prostate Cancer Cells

value: 20nM CTCF siRNA pool

tag: time


title: CTCF siRNA 24hrs Rep2

scan_protocol: As per standard Affymetrix protocol for the Human 2.0ST arrays


title: COAD.ct-476


title: Control siRNA 144hrs Rep2

label_protocol: As per standard Affymetrix protocol for the Human 2.0ST arrays

value: 20nM Non-Target siRNA pool


title: CTCF siRNA 24hrs Rep1


title: CTCF siRNA 72hrs Rep1


title: Control siRNA 144hrs Rep1


title: CTCF siRNA 72hrs Rep2


title: COAD.ct-473


title: COAD.ct-471


title: COAD.ct-475


title: COAD.ct-481


title: COAD.ct-472


title: Control siRNA 24hrs Rep1


title: Control siRNA 24hrs Rep2


title: Control siRNA 72hrs Rep1


title: Control siRNA 72hrs Rep2


title: CTCF siRNA 144hrs Rep1


title: COAD.ct-469


title: Untransfected Rep2


title: COAD.ct-474


title: COAD.ct-467


title: COAD.ct-466


title: 9973_C13

city: Philadelphia

first: Blanca

middle: E

last: Himes

state: PA

address: 423 Guardian Dr

department: Department of Biostatistics, Epidemiology and Informatics

institute: University of Pennsylvania

description: Gene expression data from peripheral blood samples of children without fever

hyb_protocol: standard Affymetrix protocol

scan_protocol: Genome-wide gene expression measures were obtained using the Affymetrix Human Gene 2.0 ST Array, scanned with an Affymetrix scanner.

data_processing: Raw intensity data was analyzed with steps that included obtaining quality metrics of raw intensity data using outlier scoring methods adapted from the arrayQualityMetrics R package, considering microarray scan date as a batch variable via principal component analysis, and processing raw intensities using robust multi-array average (RMA) with the oligo R package.

source_name: Whole peripheral blood

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

extract_protocol: Whole peripheral blood RNA was extracted using Tempus Spin RNA Isolation Kit (Thermo Fisher Scientific).

value: Whole peripheral blood

value: control

tag: Sex

value: male

value: white


title: 9973_C9

value: female


title: CTR_D0_2

type: genomic

city: Lyon

first: Zdenko

last: Herceg

address: 25 avenue Tony Garnier CS 90627

department: EGM

country: France

institute: IARC

hyb_protocol: 250 ng of bisulphite converted DNA were hybridised to Illumina Infinium HumanMethylation EPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged with standard recommended Illumina scanner settings

data_processing: Idat files were loaded into R and analyzed with R/Bioconductor packages (minfi, limma)

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

growth_protocol: For maintainance, cells were cultured in DMEM/F-12 supplemented with 10% (v/v) charcoal-stripped fetal bovine serum, 1% nonessential amino acids, sodium pyruvate and penicillin/streptomycin and with a daily addition of 10nM E2 in 0.1% DMSO

extract_protocol: AllPrep DNA/RNA Mini kit (Qiagen)

treatment_protocol: 10nM 17β-estradiol in 0.1% DMSO (CTR and ReSt) or only 0.1% DMSO (E2D)

value: MCF-7 HTB22 (ATCC)

tag: treatment

value: CTR

tag: time point


title: Untransfected Rep1

tag: cell line


title: E2D_D4_2


title: Rest_D14_1

value: ReSt


title: CTR_D4_2


title: COAD.ct-463

value: cell-free DNA


title: COAD.ct-470


title: COAD.ct-468


title: CTR_D14_2


title: Rest_D14_3


title: E2D_D14_3


title: Rest_D14_2


title: E2D_D4_3


title: COAD.ct-460


title: E2D_D14_2


title: COAD.ct-465


title: E2D_D4_1


title: COAD.ct-464


title: CTR_D4_1


title: HTGTS_PBMC_B_JK1

source_name: Human PBMC B cell

value: PBMC B cell


title: 9973_C11


title: COAD.ct-458


title: 9973_C2


title: 9973_C10

value: black


title: 9973_C4

value: Hispanic


title: CTR_D14_1


title: 9973_C14


title: COAD.ct-457


title: COAD.ct-462


title: CTR_D0_3


title: COAD.ct-461


title: HTGTS_PBMC_B_VK3_20


title: E2D_D14_1


title: HTGTS_PBMC_B_VK2_28


title: CTR_D0_1


title: COAD.ct-454


title: CTR_D14_3


title: 9973_C7


title: 9973_C12


title: 9973_C6


title: COAD.ct-453


title: CTR_D4_3


title: COAD.ct-455


title: 9973_C3


title: 9973_225

description: Gene expression data from peripheral blood samples of children with suspected sepsis.

value: bacterial

value: Asian


title: 9973_C1


title: COAD.ct-452


title: COAD.ct-451


title: 9973_223


title: 9973_226

value: shock


title: COAD.ct-450


title: 9973_221


title: COAD.ct-449


title: 9973_222


title: 9973_220

value: viral


title: 9973_216


title: 9973_218


title: COAD.ct-448


title: COAD.ct-456


title: 9973_224


title: Baseline_Residual_Platelet_Reactivity

city: Chengdu

first: Mao

last: Chen

address: 37 Guoxue Street

institute: West China Hospital

description: Gene expression of the mixed platelet with baseline residual platelet reactivity

hyb_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide.

scan_protocol: The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 2 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a mixture of oligo(dT) and random primers (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

extract_protocol: RNA quantity and quality were measured by NanoDrop ND-1000, and amplified by using TargetAmpTM 1-Round aRNA Amplification Kit (Epicentre).

tag: disease state

value: coronary heart disease (CHD)

value: platelet

tag: reactivity

value: baseline


title: 9973_215

tag: tissue

value: Whole peripheral blood


title: High_Residual_Platelet_Reactivity

description: Gene expression of the mixed platelet with high residual platelet reactivity

value: high platelet reactivity (HPR)


title: GBE HCC 3 [Methylation]

city: Research Triangle Park

first: Deepak

last: Mav

state: NC

address: 2 Davis Drive

institute: Sciome LLC

description: Methylation Signal for GBE HCC 3

hyb_protocol: The labeling of WGA IP and input DNA, microarray hybridization, and scanning were performed at the Florida State University genomics core laboratory following the described protocol (Roche NimbleGen (2010)).

scan_protocol: Data were extracted from scanned images using NimbleScan 2.4 extraction software (NimbleGen Systems, Inc., Madison, WI)

data_processing: The probe-level log2(Cy5/Cy3) values were normalized using Lowess curve fitting conditioning on GC content as described in BMC Bioinformatics 2009, 10:173. These signal values were further quantile normalized to adjust for between sample variations.   DETAILS: The GC Lowess method utilizes both 'Cy3' and 'Cy5' values as following:  * Classify probes into bins according to CG content (proportion of number of C and G nucleotides in probe sequence)  * For each CG content bin (k), we fit lowess regression to predict log2(Cy5/Cy3)_k value using log2(sqrt(Cy3*Cy5))_k value  * Compute normalized value = sigma_bar *(observed log2(Cy5/Cy3)_k - predicted log2(Cy5/Cy3)_k)/sigma_k, where sigma_k is mean absolute deviation of (observed log2(Cy5/Cy3)_k - predicted log2(Cy5/Cy3)_k) and sigma_bar is geometric mean of all sigma_k's.  This normalization corrects for both dye bias and CG bias simultaneously.

source_name: input DNA from GBE HCC 3

label_protocol: The high molecular weight genomic DNA was sonicated to generate 200-500bp sized DNA fragments using a Bioruptor sonicator® (Diagenode, Denville, NJ) using cycle conditions of 30 sec on/90 sec off for a total duration of 12.5 minutes. Methylated DNA molecules were enriched by binding to the MBD2B/MBD3L1 complex using the MethylCollector Ultra kit® (Active Motif, Carlsbad, CA) according to the manufacturer’s protocol. Input and enriched methylated-DNA fragments from the same sample were whole genome amplified (WGA) using a WGA2 kit® (Sigma-Aldrich, St. Louis, MO) according to the manufacturer’s protocol

extract_protocol: DNA were isolated from these selected samples using the DNeasy kit® (Qiagen, Valencia, CA) and Invitrogen PureLink Mini Kit® (Life Technologies Corporation, Carlsbad, CA), respectively, and stored at -80C. DNA were quantified by using a NanoDrop® (ThermoScientific, Wilmington, MA),

treatment_protocol: 2000 mg/kg of GBE by oral gavage for 2 years

tag: cohort

value: GBE HCC

tag: replicate

tag: fraction

value: input DNA

source_name: methylated DNA from GBE HCC 3

value: methylated DNA


title: COAD.ct-447


title: GBE HCC 5 [Methylation]

description: Methylation Signal for GBE HCC 5

source_name: input DNA from GBE HCC 5

source_name: methylated DNA from GBE HCC 5


title: G464

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

hyb_protocol: Labeled cDNA was hybridized at 48°C to Affymetrix Human Gene ST 2.1 array plates, which were then washed, stained and scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515) with the assistance of the University of Michigan DNA Sequencing Core.

data_processing: R bioconduct was used to process the data, and RMA was used to summarize and normalize the expression values

source_name: Skin

label_protocol: Complementary DNA was prepared and biotinylated using the NuGEN Encore Biotin Module (Encore Biotin Module Manual, P/N M01111 v6).

extract_protocol: RNA was isolated from 10μm sections of formalin-fixed paraffin embedded blocks of identified skin biopsies. RNA was extracted using the E.N.Z.A. FFPE RNA Kit (Omega Bio-tek).

tag: condition

value: NN


title: G463

scan_protocol: Labeled cDNA was hybridized at 48°C to Affymetrix Human Gene ST 2.1 array plates, which were then washed, stained and scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515) with the assistance of the University of Michigan DNA Sequencing Core.


title: COAD.ct-459

value: cell-free DNA


title: 9973_214

value: male

value: white


title: G462


title: G461


title: GBE HCC 2 [Methylation]

description: Methylation Signal for GBE HCC 2

source_name: input DNA from GBE HCC 2

source_name: methylated DNA from GBE HCC 2


title: G459

value: HYPERTROPHIC LP


title: G458


title: COAD.ct-445

source_name: blood serum


title: COAD.ct-446


title: 9973_213

value: female


title: SPNT HCC 5 [Methylation]

description: Methylation Signal for SPNT HCC 5

source_name: input DNA from SPNT HCC 5

treatment_protocol: Vehicle control by oral gavage for 2 years

value: SPNT HCC

source_name: methylated DNA from SPNT HCC 5


title: GBE HCC 4 [Methylation]

description: Methylation Signal for GBE HCC 4

source_name: input DNA from GBE HCC 4

source_name: methylated DNA from GBE HCC 4


title: 9973_210

value: shock

value: bacterial

value: Hispanic


title: SPNT HCC 4 [Methylation]

description: Methylation Signal for SPNT HCC 4

source_name: input DNA from SPNT HCC 4

source_name: methylated DNA from SPNT HCC 4


title: SPNT HCC 3 [Methylation]

description: Methylation Signal for SPNT HCC 3

source_name: input DNA from SPNT HCC 3

source_name: methylated DNA from SPNT HCC 3


title: GBE HCC 1 [Methylation]

description: Methylation Signal for GBE HCC 1

source_name: input DNA from GBE HCC 1

source_name: methylated DNA from GBE HCC 1


title: COAD.ct-443


title: SPNT HCC 1 [Methylation]

description: Methylation Signal for SPNT HCC 1

source_name: input DNA from SPNT HCC 1

source_name: methylated DNA from SPNT HCC 1


title: COAD.ct-442


title: CNTL 1 [Methylation]

description: Methylation Signal for CNTL 1

source_name: input DNA from CNTL 1

value: CNTL

source_name: methylated DNA from CNTL 1


title: G454

source_name: Skin


title: COAD.ct-441


title: G443


title: G453


title: 9973_206

source_name: Whole peripheral blood

value: vasopressor-responsive

value: black


title: COAD.ct-440

source_name: blood serum


title: G455


title: SPNT HCC 2 [Methylation]

description: Methylation Signal for SPNT HCC 2

source_name: input DNA from SPNT HCC 2

source_name: methylated DNA from SPNT HCC 2


title: G456


title: 9973_205

value: Whole peripheral blood

value: viral


title: G452


title: 9973_198


title: G451


title: G440


title: G441


title: 9973_203


title: CNTL 3 [Methylation]

description: Methylation Signal for CNTL 3

source_name: input DNA from CNTL 3

value: input DNA

source_name: methylated DNA from CNTL 3


title: G438


title: G442


title: G439


title: CNTL 4 [Methylation]

description: Methylation Signal for CNTL 4

source_name: input DNA from CNTL 4

source_name: methylated DNA from CNTL 4

value: methylated DNA


title: CNTL 5 [Methylation]

description: Methylation Signal for CNTL 5

source_name: input DNA from CNTL 5

source_name: methylated DNA from CNTL 5


title: CNTL 2 [Methylation]

description: Methylation Signal for CNTL 2

source_name: input DNA from CNTL 2

source_name: methylated DNA from CNTL 2


title: G437

value: NN


title: COAD.ct-439

value: cell-free DNA


title: 9973_209


title: COAD.ct-435


title: G429

value: LICHEN PLANUS


title: G432


title: G426


title: COAD.ct-444


title: COAD.ct-438


title: G431


title: G423


title: COAD.ct-437


title: COAD.ct-434


title: G421


title: G419


title: COAD.ct-436


title: G418


title: 9973_191

value: Asian


title: 9973_197

value: male

value: white


title: G417


title: G416


title: 9973_195


title: G422


title: 9973_190

value: female


title: COAD.ct-432


title: G415


title: COAD.ct-433


title: 9973_192


title: 9973_196


title: G420


title: 9973_188


title: COAD.ct-430


title: COAD.ct-431


title: COAD.ct-429


title: COAD.ct-428


title: COAD.ct-427


title: 9973_185

value: shock


title: G414


title: 9973_184


title: G413


title: 9973_174

value: bacterial


title: G411

value: HYPERTROPHIC LP


title: COAD.ct-426


title: COAD.ct-425


title: G412


title: 9973_176


title: 9973_175

value: Hispanic


title: G405


title: G408


title: G406


title: 9973_172


title: G407


title: COAD.ct-424


title: G403


title: G399


title: 9973_169


title: G410


title: G402


title: G401


title: 9973_171


title: G395


title: COAD.ct-423


title: G396


title: G409


title: 9973_168


title: COAD.ct-422


title: COAD.ct-421


title: 9973_166


title: COAD.ct-420


title: COAD.ct-419


title: COAD.ct-418


title: COAD.ct-417


title: G394


title: CD133-CD15-MUG-CHOR1(2)

city: Istanbul

first: Emre Can

last: Tüysüz

address: Ibrahimaga Mah.

country: Turkey

institute: Yeditepe University

description: Gene expression data from CD133-CD15- chordoma cells

hyb_protocol: 943 ng of ss-cDNA were hybridized for 20 hr at 48C on Human Gene 2.1 ST Array. Array strpis were washed and stained in the GeneAtlas Fluidics station (Affymetrix)

scan_protocol: GeneChips were scanned using the GeneAtlas Array scanner

data_processing: The resulting data were analyzed with Transcriptome Analysis Console 3 software and DAVID online tool and IPA

source_name: CD133-CD15- chordoma cells

label_protocol: Fragmented and Labeled ss-cDNA were prepared according to WT PLUS Reagent Kit from 500 ng total RNA

growth_protocol: Chordoma cells were cultured in IMDM: RPMI (4/1) supplemented with %10 FBS  %1 PS

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

treatment_protocol: Not Applicable

value: chordoma

tag: cell markers


title: COAD.ct-416


title: CD133-CD15- MUG-CHOR1


title: Day15_Rep2_Vvri

city: Geneva

first: Alisson

last: Kovaleski

state: NY

address: 630 W. North Street

institute: Cornell University

data_processing:
Barcode spltting: Fastx_Barcode_splitter.pl.  Raw data files were split based on custom 6bp nucleotides
Reads were quality filtered using fastq_quality_filter (-Q33 -q 25 -p 25)
Barcodes removed from each bin using fastx_trimmer  (-Q33 -f 7)
Adapter removal: cutadapt (--minimum-len 25 -O 3)
Alignment: STAR using default parameters, the 12xV2 grapevine genome and the V3 annotation file (Vitis_vinifera_gene_annotation_on_V2_v20.gff3)
Feature counting: ht-seq count (-f sam -s no -t gene)
Differential gene expression: DESeq2
Pathway Enrichment: VitisPathways
Genome_build: 12xV2 grapevine genome: https://urgi.versailles.inra.fr/Species/Vitis
Supplementary_files_format_and_content: Counts files are the output gene counts produced by htseq-count.

organism: Vitis vinifera

growth_protocol: Two clonal vines of Vitis amurensis and Vitis riparia are maintained under standard vineyard conditions in the USDA cold hardy grapevine germplasm repository.  Vitis vinifera vines are grown in a commercial vineyard under standard vineyard conditions.

extract_protocol:
RNA was isolated from pulverized tissue using the Sigma Spectrum Plant total RNA isolation kit.
Libraries were constructed following a modified protocol based on Borodina et al 2011.  Methods were modified by adding 3% w/v PVP40 to the lysis buffer to help reduce extraction inhibitors.

treatment_protocol: Dormant canes were pruned from the vineyard.  Day0 buds (3 replicate buds) were cut from the cane and plunged into liquid nitrogen.  Canes were pruned to single node cuttings and placed in cups of water. Cups were placed at room temperature.  Each subsequent day, replicate buds were cut from the canes and flash frozen.  Five replicate collections were conducted on each collection day.  Buds were collected until evidence of budburst was observed for each genotype.

value: Dormant Bud

value: Riesling


title: Day14_Rep3_Vvri


title: Day15_Rep1_Vvri


title: CD133+CD15+ JHC7 (2)

description: Gene expression data from CD133+CD15+ chordoma cells

source_name: CD133+CD15+ chordoma cells


title: CD133+CD15+ MUG-CHOR1


title: Day15_Rep3_Vvri


title: 9973_157

value: Whole peripheral blood

value: viral


title: CD133-CD15- JHC7


title: Day14_Rep1_Vvri


title: 9973_165

value: vasopressor-responsive

value: black


title: 9973_158


title: COAD.ct-415

value: cell-free DNA


title: 9973_164


title: 9973_160


title: CD133+CD15+ JHC7


title: CD133-CD15- JHC7 (2)


title: 9973_156


title: 9973_155


title: CD133-CD15-U1 (2)


title: CD133+CD15+ U1


title: CD133+CD15+ MUG-CHOR1(2)


title: Day14_Rep2_Vvri


title: Day13_Rep2_Vvri


title: Day13_Rep3_Vvri


title: COAD.ct-414


title: 9973_154


title: CD133-CD15- U1


title: Day13_Rep1_Vvri


title: Day12_Rep3_Vvri


title: Day12_Rep2_Vvri


title: CD133+CD15+ U1(2)


title: Day12_Rep1_Vvri


title: Day11_Rep3_Vvri


title: COAD.ct-412


title: Day11_Rep2_Vvri


title: Day11_Rep1_Vvri


title: COAD.ct-411


title: G397

value: LICHEN PLANUS


title: Day10_Rep3_Vvri


title: Day10_Rep2_Vvri


title: Day10_Rep1_Vvri


title: Day9_Rep3_Vvri


title: COAD.ct-409


title: 9973_153


title: Day9_Rep1_Vvri


title: 9973_148


title: COAD.ct-410


title: COAD.ct-408


title: COAD.ct-413


title: Day9_Rep2_Vvri


title: COAD.ct-407


title: Day8_Rep5_Vvri


title: COAD.ct-406


title: Day8_Rep4_Vvri


title: Day7_Rep3_Vvri


title: Day8_Rep1_Vvri


title: COAD.ct-405


title: Day8_Rep2_Vvri


title: Day8_Rep3_Vvri


title: 9973_152


title: 9973_149

value: Asian


title: 9973_134

value: male


title: 9973_145


title: 9973_139


title: 9973_138


title: 9973_136

value: white


title: Day7_Rep1_Vvri


title: Day6_Rep1_Vvri


title: Day6_Rep3_Vvri


title: COAD.ct-402


title: COAD.ct-403


title: Day5_Rep2_Vvri


title: Day5_Rep1_Vvri


title: 9973_132

value: female


title: Day7_Rep2_Vvri


title: COAD.ct-404


title: COAD.ct-401


title: 9973_124


title: COAD.ct-400


title: 9973_126


title: Day6_Rep4_Vvri


title: Day4_Rep3_Vvri


title: 9973_120

value: shock


title: COAD.ct-399


title: Day4_Rep2_Vvri


title: Day4_Rep1_Vvri


title: Day3_Rep2_Vvri


title: Day3_Rep3_Vvri


title: Day4_Rep5_Vvri


title: COAD.ct-398


title: Day6_Rep2_Vvri


title: 9973_118


title: COAD.ct-397


title: 9973_123


title: 9973_119


title: Day2_Rep3_Vvri


title: Day4_Rep4_Vvri


title: COAD.ct-396


title: Day3_Rep1_Vvri


title: Day2_Rep1_Vvri


title: COAD.ct-395


title: Day2_Rep2_Vvri


title: Day1_Rep1_Vvri


title: Day1_Rep2_Vvri


title: COAD.ct-394


title: COAD.ct-393


title: Day0_Rep3_Vvri


title: COAD.ct-392


title: Day0_Rep2_Vvri


title: 9973_113


title: Day17_Rep3_Vvcs

value: Cabernet Sauvignon


title: Day17_Rep2_Vvcs


title: COAD.ct-391


title: Day0_Rep1_Vvri


title: Day17_Rep1_Vvcs


title: Day1_Rep3_Vvri


title: 9973_112


title: 9973_110


title: Day16_Rep3_Vvcs


title: 9973_117

value: bacterial


title: 9973_111


title: COAD.ct-390


title: 9973_104


title: 9973_105

value: Hispanic


title: 9973_102


title: Day16_Rep2_Vvcs


title: Day15_Rep3_Vvcs


title: COAD.ct-389


title: Day16_Rep1_Vvcs


title: COAD.ct-388


title: Day15_Rep1_Vvcs


title: Day15_Rep2_Vvcs


title: Day14_Rep3_Vvcs


title: COAD.ct-387


title: Day14_Rep2_Vvcs


title: 9973_98


title: Day14_Rep1_Vvcs


title: Day13_Rep3_Vvcs


title: 9973_96


title: COAD.ct-386


title: Day13_Rep2_Vvcs


title: COAD.ct-385


title: Day12_Rep3_Vvcs


title: COAD.ct-383


title: COAD.ct-384


title: Day12_Rep2_Vvcs


title: Day12_Rep1_Vvcs


title: COAD.ct-382


title: Day11_Rep3_Vvcs


title: Day11_Rep1_Vvcs


title: Day11_Rep2_Vvcs


title: COAD.ct-381


title: Day10_Rep3_Vvcs


title: COAD.ct-380


title: Day13_Rep1_Vvcs


title: COAD.ct-379


title: 9973_95


title: COAD.ct-378


title: 9973_93


title: COAD.ct-377


title: Day8_Rep2_Vvcs


title: Day9_Rep3_Vvcs


title: Day8_Rep3_Vvcs


title: Day9_Rep2_Vvcs


title: Day10_Rep2_Vvcs


title: Day8_Rep1_Vvcs


title: Day7_Rep3_Vvcs


title: 9973_88


title: Day7_Rep5_Vvcs


title: Day9_Rep1_Vvcs


title: COAD.ct-376


title: 9973_86


title: 9973_87


title: 9973_89


title: Day7_Rep2_Vvcs


title: Day7_Rep1_Vvcs


title: Day6_Rep4_Vvcs


title: COAD.ct-375


title: 9973_82


title: 9973_80


title: 9973_84


title: Day6_Rep3_Vvcs


title: 9973_75


title: 9973_79


title: 9973_78


title: Day6_Rep2_Vvcs


title: Day5_Rep5_Vvcs


title: Day5_Rep4_Vvcs


title: COAD.ct-373


title: COAD.ct-371


title: COAD.ct-372


title: 9973_73


title: COAD.ct-374


title: Day5_Rep3_Vvcs


title: 9973_72


title: Day5_Rep1_Vvcs


title: Day4_Rep4_Vvcs


title: 9973_70


title: COAD.ct-370


title: Day5_Rep2_Vvcs


title: Day4_Rep3_Vvcs


title: Day4_Rep2_Vvcs


title: COAD.ct-369


title: Day6_Rep1_Vvcs


title: Day4_Rep1_Vvcs


title: Day3_Rep3_Vvcs


title: Day3_Rep2_Vvcs


title: Day3_Rep1_Vvcs


title: COAD.ct-368


title: 9973_69


title: COAD.ct-367


title: COAD.ct-366


title: Day2_Rep3_Vvcs


title: Day1_Rep3_Vvcs


title: Day2_Rep2_Vvcs


title: COAD.ct-365


title: Day1_Rep2_Vvcs


title: Day0_Rep2_Vvcs


title: Day0_Rep3_Vvcs


title: Day1_Rep1_Vvcs


title: 9973_62


title: 9973_68


title: COAD.ct-363


title: 9973_63


title: 9973_54


title: 9973_61


title: 9973_53


title: Day0_Rep1_Vvcs


title: 9973_50


title: 9973_52


title: mixed Sample 1

city: Stanford

first: Ricardo

middle: A

last: Fernandes

state: California

address: 279 Campus Drive

department: Molecular and Cellular Physiology

institute: Stanford University

data_processing:
Alignment of Forward and reverse reads using pandaseq
Raw sequences were converted to clustal
Sequence files were parsed for sequences containning the plasmid backbone sequences: GTTTTG and GGCGGTGG
DNA sequences were translated to amino acid format
Stop sequences were removed
The number of reads per peptide sequence was determined as described in Birnbaum M., et al, Cell, 2014 and Gee, M., et al., Cell, 2018
Genome_build: NA
Supplementary_files_format_and_content: Excel/csv; Number of counts for each unique peptide identified for each round of selection and Naive, pre-TCR selected library.

organism: synthetic construct

source_name: Synthetic DNA/peptide library

growth_protocol: Yeast were grown in SDCAA and pMHC was induced in SGCAA

extract_protocol:
Zymoprep was used to extract the plasmid containing the gene for the peptide-MHC
peptide library was encoded in an appropriate oligo using degenerate oligos (e.g. NNK) where appropriate and as described in the manuscrip
The naive library and round 1, 2 and 3 were incubated with magnetic-streptavidin beads coated with TCR of interest at 400 nM. After incubation for 3 hours at 4C, the fraction of TCR bound beads was isolated using LS magnetic columns (Miltenyi). For round 4 of the Pmhc selection a TCR-streptavidin tetramer was used iin place of the streptavidin-beads.

treatment_protocol: Yeast were selected after binding to TCR of interest. Unbound fraction was discarded. TCR bound yeast were isolated and expanded.

value: Isolated from Yeast


title: CIP-5h rep3

city: Montes de Oca

first: Jose

middle: Arturo

last: Molina-Mora

state: San Jose

address: Sede Universitaria Rodrigo Facio

department: Facultad de Microbiología

country: Costa Rica

institute: Universidad de Costa Rica

description:
CIP-5h
Sample C3

data_processing:
Quality control: FastQC v0.11.7 and Trimmomatic v0.38
Mapping and quantification: EDGEPro v1.3.1
Differential expression analisys: DESeq2 v1.26.0
Genome_build: Pseudomonas aeruginosa AG1
Supplementary_files_format_and_content: "EDGEpro_counts_AG1" tab-delimited text files include raw counts values, and "DESeq-ntd-normalized-counts-ALL-genes" are the normalized values by DESeq2 function

organism: Pseudomonas aeruginosa

source_name: Clinical isolate

growth_protocol: LB medium

extract_protocol:
RNeasy Protect Bacteria Mini Kit - QIAGEN; Epicentre RiboZero Gold (Epidemiology Kit) Part#RZE1224
Illumina TruSeq Stranded Total RNA: 1ug was used as input and library amplification was 13 PCR cycles.

treatment_protocol: 12.5 ug/mL Ciprofloxacin

tag: strain

tag: time point (after_exposure)

tag: antibiotic

value: Ciprofloxacin


title: 9973_49


title: Day2_Rep1_Vvcs

value: Dormant Bud

tag: genotype


title: CIP-5h rep1

description:
CIP-5h
Sample C1


title: COAD.ct-364

city: La Jolla

first: Kang

last: Zhang

address: 9500 Gilman Dr

institute: UCSD

data_processing:
unique molecular identifiers were extracted from each read using custom script
reads were adaptor and quality trimmed using Trim-galore and Cutadapt 1.4.1 with parameters -e 0.1 -q 20 -O 1
BisReadMapper1.3 (D.Diep, K.Zhang) using Bowtie2 was used to align reads to in-silico bisulfite-converted genome sequence
C and Ts were extracted from reads at the targeted positions using only reads with unique identifiers using custom scripts (BamExtractor, D.Diep, K.Zhang)
methylation frequencies were calculated by binning data into 100bp regions and aggregating methylated and non-methylated cytosines within 100bp bins
Genome_build: hg19
Supplementary_files_format_and_content: text file containing beta values for all samples at all analyzed 100bp genomic regions

extract_protocol:
cfDNA extraction from 1.5 ml of serum samples was performed using QIAamp cfDNA Kit (Qiagen) according to manufacturer’s recommendations
10 ng of cfDNA was bisulfite-converted using EZ DNA Methylation-Lightning™ Kit (Zymo). Bis-DNA specific "padlock" probes (molecular inversion probes, MIPS) were used to capture genomic regions and provide adaptors for NGS library construction. Nextera-XT compatible barcoding primers were used to amplify DNA for sequencing. Library (~300bp) was purified using AMPure beads.
custom-made libraries were sequenced on HiSeq2500 using 150PE reads

tag: sample type


title: COAD.ct-360


title: mixed Sample 2

tag: cell type


title: CIP-2.5h rep1

description:
CIP-2.5h
Sample B1


title: CIP-0h rep3

description:
CIP-0h
Sample A3


title: COAD.ct-359


title: CIP-2.5h rep2

description:
CIP-2.5h
Sample B2


title: 9973_45

value: Whole peripheral blood

tag: Sex


title: 9973_51

value: viral


title: 9973_42


title: COAD.ct-358


title: CIP-0h rep2

description:
CIP-0h
Sample A2


title: CIP-0h rep1

description:
CIP-0h
Sample A1


title: CIP-5h rep2

description:
CIP-5h
Sample C2


title: COAD.ct-357


title: sham control  rep2

city: shanghai

first: zhibin

last: zhou

address: 415 Fengyang Road

department: orthopedics

institute: changzheng hospital

data_processing:
Basecalls performed using CASAVA version 1.8.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Seqtk.
Reads were aligned to the Rnor_6.0 genome assembly using BWA-MEM
Circular RNA were identified by CIRI(https://sourceforge.net/projects/ciri/) and quantified by SRPBM(back-spliced reads (support for circRNA) by read   length and number of mapped reads (spliced reads per billion   mapping.
Differential expression were analysed  using edgeR.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files include back-spliced reads values and SRPBM

organism: Rattus norvegicus

source_name: sciatic nerve tissue

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Pairedend libraries were synthesized by using the VAHTS Total RNA-Seq（H/M/R) Library PrepKit（Vazyme NR603-02） for Illumina following  Sample Preparation Guide.

value: Sprague-Dawley rats

value: sciatic nerve tissue

tag: age

value: post natal week 6


title: COAD.ct-361

value: cell-free DNA


title: COAD.ct-356


title: CIP-2.5h rep3

description:
CIP-2.5h
Sample B3


title: sciatic nerve injury model  rep2


title: sciatic nerve injury model  rep1


title: COAD.ct-355


title: eds4 nuclear rep 2

city: CABA

first: Marcelo

last: Yanovsky

address: Av. Patricias Argentinas

country: Argentina

institute: FIL/IIBBA-CONICET

description:
RNA was extracted from nuclei obtained by FACS-based nuclear sorting
eds_N_vs_T_counts.tab
eds_N_2

data_processing:
Base-calling by default setting of Illumina HiSeq 1500
Aligment to to Arabidopsis thaliana TAIR10 genome using TopHat v2.1.1
Generation of BAM files with SAMtools V1.3
Data analysis with ASpli R-package 1.6.0
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: All processed data files are .txt count tables containing the number of raw counts in each sample for all the sequenced gene transcripts of Arabidopsis thaliana genome.

molecule: nuclear RNA

organism: Arabidopsis thaliana

source_name: isolated nuclei

growth_protocol: Seeds were sown onto Murashige and Skoog medium containing 0.8% agarose, stratified for 4 d in the dark at 4°C, and then grown at 22°C in continuous light (50 μmol·m−2·s−1 of white light). Whole plants were harvested after 10-14 days.

extract_protocol:
In the transcriptional profiling assay total RNA was extracted with RNeasy Plant Mini Kit (Qiagen) following the manufacturer’s protocols. For the distribution of transcripts assay RNA was phenol-extracted, precipitated in sodium acetate, ethanol, and glycogen, washed in 80% ethanol and re-suspended in RNase-free water.
Libraries were prepared following the TruSeq RNA Sample Preparation Guide (Illumina). Briefly, 3 μg of total RNA was polyA-purified and fragmented, first-strand cDNA synthesized by reverse transcriptase (SuperScript III; Invitrogen) using random hexamers. This was followed by RNA degradation and second-strand cDNA synthesis. End repair process and addition of a single A nucleotide to the 3′ends allowed ligation of multiple indexing adapters. Then, an enrichment step of 12 cycles of PCR was performed. Library validation included size and purity assessment with the Agilent 2100 Bioanalyzer and the Agilent DNA1000 kit (Agilent Technologies). Samples were pooled to create 12 multiplexed DNA libraries, which were pair-end sequenced with an Illumina HiSeq 1500.

value: 2 weeks old

tag: developmental stage

value: seedling

tag: growth conditions

value: Continuous white light 22°C

tag: rna extracted from


title: 9973_40

source_name: Whole peripheral blood

tag: tissue

value: male

value: white


title: wt nuclear rep 2

description:
RNA was extracted from nuclei obtained by FACS-based nuclear sorting
ctrl_N_vs_T_counts.tab
ctrl_N_2

tag: ecotype

value: wt


title: eds4 nuclear rep 1

description:
RNA was extracted from nuclei obtained by FACS-based nuclear sorting
eds_N_vs_T_counts.tab
eds_N_1


title: eds4 total rep 2

description:
RNA was extracted from whole seedlings
eds_N_vs_T_counts.tab
eds_T_2

molecule: polyA RNA

source_name: whole seedlings

value: whole seedlings


title: 9973_39

value: female

value: black


title: COAD.ct-354

source_name: blood serum


title: eds4 total rep 1

description:
RNA was extracted from whole seedlings
eds_N_vs_T_counts.tab
eds_T_1


title: 9973_38


title: sham control  rep1


title: COAD.ct-353


title: 9973_36

value: vasopressor-responsive

value: shock


title: wt total rep 2

description:
RNA was extracted from whole seedlings
ctrl_N_vs_T_counts.tab
ctrl_T_2


title: wt total rep 1

description:
RNA was extracted from whole seedlings
ctrl_N_vs_T_counts.tab
ctrl_T_1


title: 9973_35

value: Whole peripheral blood

value: Hispanic


title: COAD.ct-351


title: 9973_30


title: eds4 mutant rep 2

description:
RNA was extracted from whole seedlings
eds4_vs_wt_counts.tab
eds4_2


title: eds4 mutant rep 3

description:
RNA was extracted from whole seedlings
eds4_vs_wt_counts.tab
eds4_3


title: COAD.ct-350


title: wt nuclear rep 1

description:
RNA was extracted from nuclei obtained by FACS-based nuclear sorting
ctrl_N_vs_T_counts.tab
ctrl_N_1


title: wt Col-0 rep 3

description:
RNA was extracted from whole seedlings
eds4_vs_wt_counts.tab
wt_3


title: wt Col-0 rep 4

description:
RNA was extracted from whole seedlings
eds4_vs_wt_counts.tab
wt_4


title: wt Col-0 rep 2

description:
RNA was extracted from whole seedlings
eds4_vs_wt_counts.tab
wt_2


title: 9973_25

description: Gene expression data from peripheral blood samples of children with suspected sepsis.

value: viral


title: wt Col-0 rep 1

description:
RNA was extracted from whole seedlings
eds4_vs_wt_counts.tab
wt_1


title: RNA Polymerase II Hydra Replicate II

city: Pune

first: Krishanpal

last: Karmodiya

state: Maharashtra

address: Dr. Homi Bhabha Road

department: Center of Excellence in Epigenetics

country: India

institute: Indian Institute of Science Education and Research

description: Chromatin IP using specific antibody

data_processing:
For the SOLiD 4 System, high-quality reads were matched to individual samples based on the barcode tag and using default parameters in SOLiD Experimental Tracking Software (SETS) v4.0.1.
Reads were mapped using the Bowtie, color-space program.
Bed files were generated using BedTools
Genome_build: Hydra_vulg_ind_pune, h7
Supplementary_files_format_and_content: bed

organism: Hydra vulgaris

source_name: Complete Polyp

growth_protocol: Hydra vulgaris were grown using standard protocol.

extract_protocol:
Lysates  were clarified from sonicated nuclei and histone H3-DNA and RNA polymerase II-DNA complexes were isolated with antibody.
Standard ChIP protocols was followed to obatin chromatin from Hydra vulgaris. The ChIP-seq libraries have been prepared according to the Life Technologies protocol, SOLiD ChIP-seq kit guide (A12066). The quality of the libraries has been checked with the Bioanalyser DNA High sensitivity and by ChIP-qPCR. The sequencing was performed with the AB SOLiD 4 System  sequencer.

value: Hydra vulgaris Ind-Pune

tag: chip antibody

value: Pol II CTD monoclonal antibody 7G5


title: COAD.ct-348

value: cell-free DNA


title: COAD.ct-352


title: COAD.ct-347


title: RNA Polymerase II Hydra Replicate I

description: Chromatin IP using specific antibody


title: 9973_21


title: 9973_24


title: eds4 mutant rep 1

description:
RNA was extracted from whole seedlings
eds4_vs_wt_counts.tab
eds4_1

value: 2 weeks old


title: Histone H3 Hydra Replicate II

description: Chromatin IP using specific antibody

value: HIstone H3 (Ab1791, abcam)


title: 9973_19

value: Asian


title: 9973_18

value: bacterial


title: COAD.ct-346


title: 9973_28

value: white


title: 9973_22


title: Input_hydra Replicate II

description: Input


title: Input_hydra Replicate I

description: Input


title: Histone H3 Hydra Replicate I

description: Chromatin IP using specific antibody

value: Histone H3 (Ab1791, abcam)


title: COAD.ct-345


title: COAD.ct-344


title: COAD.ct-349


title: Btheta VPI-5482 grown in vitro, Ribose_Rep_2

first: Eric

middle: C

last: Martens

address: 1150 West Medical Center Drive, 6751 Medical Science BLDG II

department: Microbiology and Immunology

data_processing:
Data was analyzed using Arraystar software (DNASTAR, Inc.)
Reads Per Kilobase of reads per Megabase of library, RPKM normalization with default parameters
Gene expression in ribose was compared to gene expression in a glucose reference
Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >5-fold and with at least 2/3 biological replicates with a normalized expression level >1% of the overall average RPKM expression level in either glucose or ribose, and a p-value < 0.05 (t test with Benjamini-Hochberg correction)
Genome_build: NC_004663.1
[RNAseq_Ribose_Over_Glucose_Btheta_VPI_5482.txt] Tab-delimited text file includes RPKM values for each sample as well as the fold change of Ribose over Glucose grown cells, the p-values, and T-values.
[RNAseq_Btheta_VPI_5482_Ribose_over_Glucose_genes_matching_cutoffs_only.txt]  Tab-delimited text file includes the fully processed data according to our specified cutoffs listed in the summary methods information above showing the 81 genes significantly altered when Bacteroides thetaiotaomicron was growin in ribose compared to glucose in vitro.

organism: Bacteroides thetaiotaomicron

source_name: Ribose

growth_protocol: Bacteroides thetaiotaomicron cells were grown overnight in rich TYG media then transferred to fresh MM containing either 5 mg/ml glucose or 5 mg/ml ribose. Cells were then grown until mid-log phase (absorbance between 0.6-0.8)

extract_protocol:
Total RNA was extracted using the RNeasy mini kit buffers (Qiagen) and purified on RNA-binding spin columns (Epoch), treated with TURBO DNaseI (Ambion) or DNase I (NEB) after elution and purified again using a second RNeasy mini kit isolation column. Total RNA was then rRNA depleted using the Ribo-Zero Bacterial rRNA Removal Kit (Illumina Inc.) and concentrated with the RNA Clean and Concentrator-5 kit (Zymo Research Corp, Irvine, CA).
Samples were multiplexed for sequencing on the Illumina HiSeq 2500 platform at the University of Michigan Sequencing Core.

treatment_protocol: Two volumes of RNA Protect (Qiagen) were added to cells and frozen at -80C until RNA was extracted

value: Wild-type

tag: growth phase

value: Mid-Log, exponential growth

tag: growth medium

value: Ribose


title: Btheta VPI-5482 grown in vitro, Glucose_Rep_3

source_name: Glucose

value: Glucose


title: Btheta VPI-5482 grown in vitro, Ribose_Rep_1


title: 9973_12

value: male


title: COAD.ct-343


title: COAD.ct-342


title: Btheta VPI-5482 grown in vitro, Glucose_Rep_1


title: 9973_17

value: Whole peripheral blood

value: female


title: 9973_11

value: Hispanic


title: COAD.ct-341


title: Whole worms, S1_T5_R3

city: Santa Barbara

first: Erik

last: Spickard

state: CA

address: UCSB

department: MCDB

institute: University of California Santa Barbara

data_processing:
Data processing was performed in Galaxy (usegalaxy.org) using a custom workflow.
Raw fastq files were concatenated for each sample and trimmed using Trimmomatic (Galaxy Version 0.36.3) with the parameters:  -threads 1 -phred33 fastq_in.fastqsanger fastq_out.fastqsanger ILLUMINACLIP:/TruSeq3-SE.fa:2:30:10 SLIDINGWINDOW:4:10 LEADING:5 TRAILING:5 MINLEN:50 AVGQUAL:20 for single reads and:  -threads 1 -phred33 fastq_r1.fastqsanger fastq_r2.fastqsanger fastq_out_r1_paired.fastqsanger fastq_out_r1_unpaired.fastqsanger fastq_out_r2_paired.fastqsanger fastq_out_r2_unpaired.fastqsanger ILLUMINACLIP:/TruSeq3-PE.fa:2:30:10 MINLEN:100 AVGQUAL:20 SLIDINGWINDOW:4:10 LEADING:5 TRAILING:5 for paired-end reads.
Pseudoalignment and abundance quantification of RNA-seq reads was performed using Salmon (Galaxy Version 0.8.2) to the C. elegans WS263 reference transcriptome.
Genome_build: WS263
Supplementary_files_format_and_content: Processed data: Salmon output files are plain-text tab-delimited format and contain gene-level quantification of expression. Data columns contain: (1) WormBase gene names, (2) length of target transcript in nucleotides, (3) the computed effective length of the target transcript, (4) mRNA transcript relative abundances given as Transcripts Per Million (TPM) used for downstream analysis, (5) the estimated number of reads mapping to each transcript that was quantified.

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: C. elegans strains were grown at 20 C on NGM media seeded with OP50 bacteria.

extract_protocol:
Whole worm populations were rinsed in M9 solution, pelleted, resuspended in TriReagent, and flash frozen in liquid nitrogen. Total RNA was extracted by rapidly freeze-thawing samples 3-4 times followed by purification using a Zymo Research Direct-zol RNA Mini Prep kit (cat no: R2050).
Sequencing libraries were built using an Illumina TruSeq Stranded mRNA sample prep kit following the LS protocol using 1-4 ug of total RNA input.

treatment_protocol: Control and experimental strains were given identical treatments. Synchronized cultures of approximately 2,000 worms were grown to early L4 stage and then exposed to heat shock for 30 minutes at 33 C. Samples were collected immediately before heat shock and 3, 6, 12, and 30 hours post heat shock.

tag: time

value: 3 hours post heat shock


title: Whole worms, S1_T5_R4

tag: strain


title: COAD.ct-340


title: Whole worms, S2_T5_R4


title: Whole worms, S2_T5_R3


title: COAD.ct-339


title: Whole worms, S2_T5_R2


title: 9973_9

value: viral

value: black


title: Btheta VPI-5482 grown in vitro, Glucose_Rep_2


title: Whole worms, S2_T5_R1


title: 9973_7


title: 9973_8


title: 9973_6

value: shock


title: Whole worms, S2_T4_R3

value: 30 hours post heat shock


title: Whole worms, S1_T5_R2


title: Whole worms, S1_T5_R1


title: Whole worms, S2_T4_R1


title: Whole worms, S1_T4_R3


title: Whole worms, S2_T4_R2


title: COAD.ct-338

value: cell-free DNA


title: Whole worms, S1_T4_R2


title: 9973_3


title: COAD.ct-336


title: 9973_10

value: vasopressor-responsive


title: COAD.ct-335


title: Whole worms, S1_T4_R1


title: COAD.ct-334


title: Whole worms, S2_T3_R1

value: 12 hours post heat shock


title: Whole worms, S2_T3_R2


title: COAD.ct-337


title: COAD.ct-333


title: 9973_1

value: white


title: Whole worms, S1_T3_R2


title: Whole worms, S1_T3_R3


title: COAD.ct-362


title: Whole worms, S2_T2_R2

value: 6 hours post heat shock


title: COAD.ct-331


title: Whole worms, S2_T2_R3


title: Whole worms, S2_T3_R3


title: Whole worms, S1_T2_R3


title: COAD.ct-332


title: Whole worms, S1_T2_R1


title: 9973_2


title: amygdala HR2965

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

country: Germany

institute: FBN

description: Gene expression data from amygdala of adult pig, high-reactive coping pattern

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42 C on Affymetrix Porcine Snowball Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

organism: Sus scrofa

source_name: amygdala

label_protocol: biotin-labeled cRNAs were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

value: amygdala

tag: breed

value: German Landrace

value: adult

tag: coping pattern

value: high-reactive


title: amygdala HR2915


title: COAD.ct-330


title: Whole worms, S2_T1_R3

value: 0 hours post heat shock

tag: genotype


title: amygdala HR2900


title: Whole worms, S1_T3_R1


title: Whole worms, S2_T1_R1


title: COAD.ct-328

tag: sample type


title: Whole worms, S1_T1_R3


title: Whole worms, S2_T1_R2


title: amygdala HR2894


title: Whole worms, S2_T2_R1


title: Whole worms, S1_T1_R1


title: amygdala HR2978


title: 9973_4

value: Whole peripheral blood

value: female


title: COAD.ct-327


title: COAD.ct-326


title: amygdala HR2857


title: COAD.ct-325


title: Whole worms, S1_T1_R2


title: COAD.ct-324


title: amygdala HR2835


title: amygdala HR2897


title: amygdala HR2797


title: amygdala LR2793

description: Gene expression data from amygdala of adult pig, low-reactive coping pattern

value: low-reactive


title: COAD.ct-323


title: amygdala HR2593


title: COAD.ct-322


title: Whole worms, S1_T2_R2


title: VK2_EstrogenPretreatment_Flagellin_24hr_rep3 [102403-24]

city: Newcastle Upon Tyne

first: Judith

last: Hall

state: Tyne & Wear

address: Medical School, Framlington Place, Newcastle University

department: ICaMB

country: United Kingdom

institute: Newcastle University

description: replicate 3

hyb_protocol: The ServiceXS protocol that describes the method for hybridization, wash and staining of BeadChip arrays as well as the scanning procedure, was adapted from the Illumina protocol: ”Whole-Genome Gene Expression Direct Hybridization Assay”. The samples were scanned using the Illumina iScan array scanner. There were no deviations from the Illumina protocol and all experiments were performed in compliance with ServiceXS Standard Operating Procedures (SOPs).

scan_protocol: Scanning was performed on the Illumina iScan (Illumina, Inc., San Diego, CA, U.S.A.). Image analysis and extraction of raw expression data was performed with Illumina GenomeStudio v2011.1 Gene Expression software with default settings (no background subtraction and no normalization).

data_processing:
Normalisation of data was carried out in GenomeStudio v.2011.1 using the quantile normalisation method
Primary gene expression analysis of the scanned BeadChip arrays was performed using Illumina’s GenomeStudio v.2011.1 software with the default settings advised by Illumina. BeadChip arrays have internal quality control features, consisting of spiked-in sample independent controls and sample dependent controls. This allows us to closely monitor if differences between samples are sample dependent or independent and to exclude technical variation.

label: Biotin

source_name: VK2 E6/E7 vaginal cell line, 7 day estrogen pretreament (4nM), E.coli Flagellin exposure (50ng/ml), 24hour timepoint

label_protocol: The Illumina TotalPrep-96 RNA Amplification Kit was used to generate Biotin labeled (Biotin-16-UTP),  amplified cRNA starting from 200 ng total RNA. 750 ng of the obtained biotinylated cRNA samples was  hybridized onto the Illumina HumanHT-12 v4.

growth_protocol: VK2 E6/E7 cells were maintained in  Keratinocyte-Serum Free medium (GIBCO-BRL 17005-042) with 0.1 ng/ml human recombinant EGF, 0.05 mg/ml bovine pituitary extract, and additional calcium chloride 44.1 mg/L (final concentration 0.4 mM). Cells were passaged every 7 days and were seeded at 1x10^5 in 6-well plates for experimental purposes, grown for 3 days.

extract_protocol: Total RNA was extracted using the Promega SV Total RNA Isolation Kit following manufacturer's instructions (this includes a DNase step)

treatment_protocol: Estrogen pretreatment with cyclodextrin-encapsulated estrogen at 4nM was applied for cells for 7 days prior to flagellin challenge beginning.

tag: cell line

value: VK2 E6/E7

tag: cell type

value: immortalised vaginal cell line

tag: treatment

value: Estrogen (encapsulated in cyclodextrin) pretreatment for 7 days proir to the experiment commencing, plus flagellin exposure (50ng/ml, from E.coli) for 24 hours


title: COAD.ct-321


title: amygdala LR2790

tag: developmental stage


title: VK2_EstrogenPretreatment_Flagellin_24hr_rep1 [102403-22]

description: replicate 1


title: amygdala LR2639


title: VK2_Flagellin_24hr_rep3 [102403-21]

description: replicate 3

source_name: VK2 E6/E7 vaginal cell line, E.coli Flagellin exposure (50ng/ml), 24hour timepoint

value: Flagellin exposure (50ng/ml, from E.coli) for 24 hours


title: VK2_Flagellin_24hr_rep2 [102403-20]

description: replicate 2


title: COAD.ct-320

value: cell-free DNA


title: VK2_Flagellin_24hr_rep1 [102403-19]

description: replicate 1


title: COAD.ct-319


title: VK2_EstrogenPretreatment_24hr_rep3 [102403-18]

description: replicate 3

source_name: VK2 E6/E7 vaginal cell line, 7 day estrogen pretreament (4nM), 24hour timepoint

value: Estrogen (encapsulated in cyclodextrin) pretreatment for 7 days proir to the experiment commencing


title: COAD.ct-318


title: VK2_EstrogenPretreatment_24hr_rep1 [102403-16]

description: replicate 1


title: VK2_Control_24hr_rep2 [102403-14]

description: replicate 2

source_name: VK2 E6/E7 vaginal cell line, control (vehicle only), 24hour timepoint

value: Vehicle only (PBS)


title: amygdala LR2611


title: amygdala LR2789


title: VK2_Control_24hr_rep3 [102403-15]

description: replicate 3


title: VK2_Control_24hr_rep1 [102403-13]

description: replicate 1


title: COAD.ct-317


title: amygdala LR2635


title: VK2_EstrogenPretreatment_24hr_rep2 [102403-17]

description: replicate 2


title: VK2_EstrogenPretreatment_Flagellin_12hr_rep2 [102403-11]

description: replicate 2

source_name: VK2 E6/E7 vaginal cell line, 7 day estrogen pretreament (4nM), E.coli Flagellin exposure (50ng/ml), 12hour timepoint

value: Estrogen (encapsulated in cyclodextrin) pretreatment for 7 days proir to the experiment commencing, plus flagellin exposure (50ng/ml, from E.coli) for 12 hours


title: COAD.ct-316


title: amygdala LR2562


title: VK2_Flagellin_12hr_rep2 [102403-08]

description: replicate 2

source_name: VK2 E6/E7 vaginal cell line, E.coli Flagellin exposure (50ng/ml), 12hour timepoint

value: Flagellin exposure (50ng/ml, from E.coli) for 12 hours


title: amygdala LR2579

value: amygdala


title: VK2_Flagellin_12hr_rep1 [102403-07]

description: replicate 1


title: VK2_EstrogenPretreatment_Flagellin_12hr_rep1 [102403-10]

description: replicate 1


title: amygdala LR2594

value: German Landrace


title: amygdala LR2016

value: adult


title: Btheta VPI-5482 grown in vitro, Ribose_Rep_3

value: Wild-type

value: Mid-Log, exponential growth

value: Ribose


title: VK2_EstrogenPretreatment_Flagellin_12hr_rep3 [102403-12]

description: replicate 3


title: VK2_Flagellin_12hr_rep3 [102403-09]

description: replicate 3


title: COAD.ct-315


title: COAD.ct-314


title: VK2_EstrogenPretreatment_12hr_rep2 [102403-05]

description: replicate 2

source_name: VK2 E6/E7 vaginal cell line, 7 day estrogen pretreament (4nM), 12hour timepoint


title: COAD.ct-313


title: VK2_EstrogenPretreatment_12hr_rep3 [102403-06]

description: replicate 3


title: VK2_Control_12hr_rep3 [102403-03]

description: replicate 3

source_name: VK2 E6/E7 vaginal cell line, control (vehicle only), 12hour timepoint


title: VK2_EstrogenPretreatment_12hr_rep1 [102403-04]

description: replicate 1


title: COAD.ct-311


title: COAD.ct-310


title: VK2_Control_12hr_rep1 [102403-01]

description: replicate 1


title: COAD.ct-312


title: M_20_1_360

city: Wageningen

first: Juri

last: Matualatupauw

address: PO Box 17

department: Human Nutrition

institute: Wageningen University

hyb_protocol: The amount of biotinylated cRNA which was hybridized onto the Illumina HumanHt12-v4 Expression Beadchip was 750 ng.

scan_protocol: The samples were scanned using the Illumina iScan array scanner according to the manufacturer's protocol.

data_processing:
Illumina’s Genomestudio v1.1.1 software with the default settings advised by Illumina was used for Gene Expression analysis.
Microarray QC and pre-processing were performed using Arrayanalysis.org. Three samples did not pass QC-criteria and were left out of further analysis. Probe expression values were calculated using the neqc algorithm from the limma package, which performs background correction, quantile normalization and log2-transformation of the data. We filtered out low expressing probes by selecting only the probes with a detection p-value < 0.01  in at least 5 arrays for further analysis.

label_protocol: The Illumina® TotalPrep™ RNA Amplification Kit (Ambion, art.No.AM-IL1791) was used to synthesize biotin labeled cRNA starting with 500 ng total RNA.

growth_protocol: Men aged between 35 and 65 years were recruited from a pool of volunteers from the Netherlands Organisation for Applied Scientific Research (TNO) database and with the assistance of a recruitment agency. In total, 20 men participated in the study. Of these men, 10 were presumably healthy, and 10 had two or more characteristics of MetS. Inclusion criteria for the healthy men were age 35–65 yr, BMI 23–30 kg/m2, normal Dutch eating habits and eating without restriction, defined as a score of <3.25 on the Dutch Restrained Eating Questionnaire. Inclusion criteria for the MetS group were age 35–65 yr, BMI 23–40 kg/m2, normal Dutch eating habits , and 2 or more cardiometabolic risk factors, defined as waist circumference ≥ 94 cm, TGs ≥ 1.7 mM, HDL cholesterol < 0.9 mM, systolic blood pressure ≥ 130 mm Hg and diastolic blood pressure ≥ 85 mm Hg and fasting glucose ≥ 5.6 mM. Exclusion criteria for both groups were a history of medical or surgical events that may significantly affect the study outcome, including medication for diabetes, cholesterol-lowering medication, eating disorders, food allergy, smoking, consuming more than 28 U/wk of alcohol, and exercising more than 3 h/wk.

extract_protocol: Total RNA was extracted using glass beads and RNAzol (Campro Scientific, Veenendaal, The Netherlands). RNA integrity was examined using the RNA 6000 Nano Lab-on-a-Chip kit and a bioanalyzer 2100 (Agilent Technologies, Amstelveen, The Netherlands).

treatment_protocol: The healthy subjects underwent a 4 week high-fat high-calorie dietary intervention. The intervention diet consisted of a fixed amount of commercially available foods high in fat, sugar, or both and was consumed on top of their habitual diet (see below for details). Before and after the 4 week intervention period, the healthy subjects underwent a high-fat challenge consisting of whipping cream, water and a bit of sugar (see below for details). The MetS subjects underwent the high-fat challenge once.

tag: disease

value: Metabolic Syndrome

tag: subject id

tag: day

tag: time point

value: Whole blood


title: M_20_1_0

source_name: Metabolic Syndrome_subject20_day1_0min

tag: tissue


title: Uninfected MSC rep3

city: New Delhi

first: Dhiraj

last: Kumar

state: New Delhi

address: Aruna Asaf Ali Marg

department: Cellular Immunology

institute: ICGEB, New Delhi

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Adipose tissue

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Mesenchymal stem cell

tag: age

value: Day 6

value: Primary cells

value: uninfected


title: hippocampus HR2915

description: Gene expression data from hippocampus of adult pig, high-reactive coping pattern

source_name: hippocampus

value: hippocampus

value: high-reactive


title: hippocampus HR2900


title: VK2_EstrogenPretreatment_Flagellin_24hr_rep2 [102403-23]

description: replicate 2

value: VK2 E6/E7

value: immortalised vaginal cell line

value: Estrogen (encapsulated in cyclodextrin) pretreatment for 7 days proir to the experiment commencing, plus flagellin exposure (50ng/ml, from E.coli) for 24 hours


title: hippocampus HR2857


title: Mtb infected MSC rep1

value: Mtb infected


title: M_20_1_120


title: H_3_1_0

value: Healty


title: Uninfected MSC rep2


title: VK2_Control_12hr_rep2 [102403-02]

description: replicate 2

value: Vehicle only (PBS)


title: hippocampus HR2835

value: German Landrace

value: adult


title: Mtb infected MSC rep3


title: hippocampus HR2894


title: H_3_1_120


title: COAD.ct-307

source_name: blood serum

value: cell-free DNA


title: Mtb infected MSC rep2


title: Uninfected MSC rep1


title: COAD.ct-306


title: COAD.ct-305


title: COAD.ct-329


title: COAD.ct-304


title: COAD.ct-303


title: hippocampus HR2965


title: COAD.ct-302


title: H_3_1_360


title: COAD.ct-308


title: COAD.ct-301


title: M_14_1_120

value: Metabolic Syndrome


title: H_3_29_120

value: Whole blood


title: M_14_1_0

source_name: Metabolic Syndrome_subject14_day1_0min


title: H_6_29_0


title: hippocampus HR2897


title: M_16_1_360


title: H_6_1_120


title: M_14_1_360


title: hippocampus HR2797


title: H_6_29_360


title: H_6_1_360


title: H_6_29_120


title: hippocampus HR2593


title: M_16_1_120


title: H_3_29_360


title: hippocampus LR2793

description: Gene expression data from hippocampus of adult pig, low-reactive coping pattern

value: low-reactive


title: H_3_29_0


title: H_6_1_0


title: hippocampus LR2789


title: hippocampus LR2639


title: hippocampus LR2790


title: M_16_1_0

source_name: Metabolic Syndrome_subject16_day1_0min


title: hippocampus LR2611


title: COAD.ct-299


title: M_11_1_360


title: COAD.ct-298


title: COAD.ct-297


title: M_11_1_120


title: COAD.ct-296


title: COAD.ct-295


title: COAD.ct-300


title: H_1_1_120


title: hippocampus LR2635


title: M_11_1_0

source_name: Metabolic Syndrome_subject11_day1_0min


title: COAD.ct-294


title: H_10_1_0


title: COAD.ct-309


title: H_1_1_0


title: H_1_1_360


title: hippocampus LR2594


title: H_10_1_360


title: H_10_29_360


title: hippocampus HR2978


title: hippocampus LR2579


title: hippocampus LR2562


title: H_1_29_0


title: H_10_29_120


title: H_1_29_360


title: H_10_29_0


title: H_10_1_120


title: COAD.ct-293


title: hippocampus LR2016


title: H_1_29_120


title: COAD.ct-292


title: hypothalamus HR2965

description: Gene expression data from hypothalamus of adult pig, high-reactive coping pattern

source_name: Hypothalamus from adult pig

value: hypothalamus


title: COAD.ct-291


title: hypothalamus HR2915


title: COAD.ct-290


title: COAD.ct-289


title: hypothalamus HR2978


title: COAD.ct-288


title: H_7_1_120


title: COAD.ct-286


title: H_7_1_0


title: H_7_29_0


title: H_7_29_120


title: hypothalamus HR2900


title: hypothalamus HR2897


title: M_15_1_360


title: M_15_1_0

source_name: Metabolic Syndrome_subject15_day1_0min


title: H_8_1_360


title: M_15_1_120


title: COAD.ct-287


title: H_7_29_360


title: H_8_1_120


title: M_17_1_120


title: H_8_1_0


title: hypothalamus HR2857


title: M_17_1_0

source_name: Metabolic Syndrome_subject17_day1_0min


title: hypothalamus HR2835


title: M_17_1_360


title: COAD.ct-284


title: H_7_1_360


title: hypothalamus HR2593


title: COAD.ct-285


title: hypothalamus HR2797


title: hypothalamus HR2894


title: COAD.ct-283


title: hypothalamus LR2793

description: Gene expression data from hypothalamus of adult pig, low-reactive coping pattern


title: COAD.ct-282


title: H_5_29_0


title: COAD.ct-281


title: H_5_29_360


title: H_5_1_360


title: H_5_29_120


title: H_8_29_360


title: COAD.ct-280


title: hypothalamus LR2790


title: COAD.ct-279


title: hypothalamus LR2789


title: H_8_29_120


title: H_5_1_0


title: H_5_1_120


title: hypothalamus LR2639


title: COAD.ct-278


title: M_18_1_120


title: M_18_1_0

source_name: Metabolic Syndrome_subject18_day1_0min


title: H_8_29_0


title: H_2_1_120


title: COAD.ct-277


title: hypothalamus LR2611


title: COAD.ct-276


title: hypothalamus LR2579


title: M_12_1_360


title: hypothalamus LR2635


title: M_12_1_120


title: H_2_29_120


title: COAD.ct-275


title: COAD.ct-274


title: H_2_1_360


title: M_18_1_360


title: COAD.ct-273


title: H_2_29_360


title: adrenal gland HR2965

description: Gene expression data from adrenal gland of adult pig, high-reactive coping pattern

source_name: Adrenal gland from adult pig

value: adrenal gland


title: hypothalamus LR2016


title: hypothalamus LR2594


title: adrenal gland HR2978


title: hypothalamus LR2562


title: adrenal gland HR2915


title: COAD.ct-271


title: COAD.ct-270


title: COAD.ct-272


title: M_13_1_360


title: H_9_1_0


title: adrenal gland HR2900


title: COAD.ct-269


title: H_9_1_360


title: M_13_1_120


title: H_2_29_0


title: M_13_1_0

source_name: Metabolic Syndrome_subject13_day1_0min


title: M_19_1_120


title: H_9_29_0


title: M_19_1_0

source_name: Metabolic Syndrome_subject19_day1_0min


title: H_9_29_120


title: M_19_1_360


title: adrenal gland HR2897


title: COAD.ct-267


title: adrenal gland HR2857


title: adrenal gland HR2894


title: COAD.ct-266


title: COAD.ct-268


title: COAD.ct-264


title: COAD.ct-263


title: adrenal gland HR2835


title: P493_mst_24h-2

city: Singapore

first: Julius

last: Müller

address: 61 Biopolis Drive

department: IMCB

country: Singapore

institute: A*Star Singapore

description: replicate 2

data_processing: The data were normalized using quantile normalization with beadarray in R

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: time (release)


title: P493_mst_24h-3

description: replicate 3


title: P493_mst_8h-3

description: replicate 3


title: Cells at timepoint Day 3, repeat 3

city: St. Louis

first: Jinsheng

last: Yu

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

description:
MSC177_D3
miRNA
Mitochondrial miRNA expression data.

hyb_protocol: The standard Affymetrix chip hybridization protocol was followed to hybridize the labeled miRNAs onto Affymtrix miRNA array 4.0 in the hybridization oven at 48 C and 60 rpm for 18 hours.

scan_protocol: After washing and staining, the chips were scanned using the Affymetrix 7G scanner with standard settings to capture the signal intensities for the miRNAs.

data_processing: The raw signal data were loaded into Affymetrix Expression Console (v1.4) and subjected to RMA background correction, median summarization of multiple probes, and quantile normalization. This was done only within the probes for Human miRNAs on chip.

source_name: Cells treated with osteogenic induction medium at day 3

label_protocol: 400 ng of miRNAs were first subjected to poly-A tailing with Poly A Polymerase and substrate ATP. Then the FlashTag Ligation Mix and ligase were added to carry out the ligation reaction so that the Biotin-labeled, dendritic structutre of 3DNAs were ligated onto miRNA molecules to archieve the miRNA labeling and the amplification of detection signals.

growth_protocol: MSCs were cultured and expanded in growth medium containing DMEM (low glucose), 10% fetal bovine serum, 2mM L-glutamine, 100U/ml penicillin, 100µg/ml streptomycin and 1ng/ml basic FGF.

extract_protocol: Mitochondria were extracted from MSCs or differentiated MSCs using the human Mitochondria Isolation Kit (Milteny Biotec) which involves the use of magnetically-labeled anti-TOM22 microbeads. Total RNA was isolated from purified mitochondria extracts using the Norgen Total RNA purification kit. For both isolation of mitochondrial or RNA, the manufacturer's recommended protocol was followed carefully.

treatment_protocol: MSCs were cultured in MSC growth medium (described above) and used as controls. The treatment (differentiation) protocol involved culturing MSCs in the presence of osteogenic induction (differentiation) medium containing aMEM base medium, 10% fetal bovine serum, 2mM L-glutamine, 100U/ml penicillin, 100µg/ml streptomycin, 10mM β-glycerol phosphate, 50µM ascorbic acid and 10µM dexamethasone.

value: Mesenchymal stem/stromal cells (MSCs)

value: Osteogenic induction medium

tag: subcellular compartment

value: Mitochondria

tag: repeat id


title: Cells at timepoint Day 14, repeat 3

description:
MSC177_D14
miRNA
Mitochondrial miRNA expression data.

source_name: Cells treated with osteogenic induction medium at day 14


title: COAD.ct-265


title: Cells at timepoint Day 7, repeat 3

description:
MSC177_D7
miRNA
Mitochondrial miRNA expression data.

source_name: Cells treated with osteogenic induction medium at day 7


title: P493_mst_24h-1

description: replicate 1


title: P493_mst_8h-1

description: replicate 1


title: COAD.ct-262


title: adrenal gland HR2593

tag: breed


title: adrenal gland HR2797


title: adrenal gland LR2790

description: Gene expression data from adrenal gland of adult pig, low-reactive coping pattern


title: P493_mst_0h-2

description: replicate 2


title: P493_mst_4h-3

description: replicate 3


title: P493_mst_4h-2

description: replicate 2


title: P493_mst_0h-3

description: replicate 3


title: P493_wt_24h-3

description: replicate 3


title: P493_mst_4h-1

description: replicate 1


title: P493_mst_8h-2

description: replicate 2


title: P493_mst_0h-1

description: replicate 1


title: COAD.ct-261


title: Cells at timepoint Day 0, repeat 3

description:
MSC177_D0
miRNA
Mitochondrial miRNA expression data.

source_name: Cells treated with growth medium at day 0

value: Growth medium


title: adrenal gland LR2639


title: P493_wt_24h-2

description: replicate 2


title: adrenal gland LR2793


title: COAD.ct-260


title: adrenal gland LR2789


title: COAD.ct-259


title: COAD.ct-258


title: COAD.ct-257


title: adrenal gland LR2635


title: Cells at timepoint Day 14, repeat 2

description:
MSC139_D14
miRNA
Mitochondrial miRNA expression data.


title: Cells at timepoint Day 7, repeat 2

description:
MSC139_D7
miRNA
Mitochondrial miRNA expression data.


title: P493_wt_24h-1

description: replicate 1


title: Cells at timepoint Day 3, repeat 2

description:
MSC139_D3
miRNA
Mitochondrial miRNA expression data.


title: adrenal gland LR2611


title: P493_wt_8h-2

description: replicate 2


title: Cells at timepoint Day 14, repeat 1

description:
MSC049_D14
miRNA
Mitochondrial miRNA expression data.


title: P493_wt_8h-3

description: replicate 3


title: adrenal gland LR2562


title: COAD.ct-254


title: adrenal gland LR2594


title: adrenal gland LR2579