title: MCTP_SAMPLE_98_tissue_lung_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_98
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_262_tissue_esophageal_cancer

status: Public on May 28 2015

type: SRA

city: Ann Arbor

first: Oscar

middle: Alejandro

last: Balbin

state: Michigan

address: Comprenhensive Cancer Center

department: Pathology

country: USA

institute: University of Michigan

description:
Sample name: MCTP_SAMPLE_262
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence alignment was performed using the Tuxedo pipeline: Bowtie2 (Bowtie2/2.0.2) and Tophat2 (TopHat/2.0.4)(Kim et al., 2013). We supplied TopHat with the set of transcript models annotated in the Homo sapiens Ensembl database version 69. The option fr-firststrand was used for the strand specific RNA-seq libraries while all other parameters were used with default values. When provided with ssRNA-seq data TopHat2 annotates aligned reads with the tag XS indicating the strand of origin in the DNA.
We used Ensembl v69 as the reference transcriptome to reconstruct the longest annotation for each gene based on the transcript and exon information provided by this assembly. We only included transcript isoforms that satisfied the following criteria: gene and transcript biotypes were annotated with the same type; transcript isoform annotation level was manual or automatic followed by manual revision (annotation levels 1 or 2) and transcript isoform was not reported as a problematic in the Encode-Gencode attributes table (e.g: transcript biotype is retained_intron, to be experimentally confirmed, or disruptive_domain).  Moreover, each transcript isoform used for our gene models was annotated with their “isoform expression rank” across the tissue cohorts, and their support level (tsl) provided by the Genecode project. Tsl equal to 1 indicates that all splice junctions of that transcript are supported by at least one non-suspect mRNA; any other number suggests that the transcript is supported by suspicious ESTs. These final gene models were used as the reference loci, or features, for downstream analysis.
The final gene models in the summarized transcriptome were used to compute strand specific expression. Paired-end reads mapping to the forward or opposite strand of a feature were counted in order to quantify the raw amount of forward and opposite transcription on a particular locus.  In order to determine what DNA strand a read pair was originated from, we first used the reads’ XS tag, provided by TopHat2, to identify the strand for each read in the pair. Then, we use the fact that in our ssRNA-seq protocol the second read is complementary to original mRNA and therefore the second read has to be on the same strand than the feature, while the first read on the opposite strand. These criteria unambiguously define a read pair DNA strand of origin. We discard all pairs in which one or both reads map to multiple locations in the genome, and all read pairs in which any of the reads was improperly mapped or did not have the XS flag provided by TopHat2 to indicate the strand of origin.
Genome_build: hg19
Supplementary_files_format_and_content: Feature (e.g. gene) raw read count over sense and antisense strands.  Processed data files linked to SuperSeries record.

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA from frozen tissues or cell lines were isolated using miRNeasy mini kit (Qiagen Valencia, CA) while RNA was isolated from FFPE sections using FFPE RNAeasy kit (Qiagen).  For RNA from frozen sections and cell lines only samples with RNA integrity number (RIN) >8.0, upon 2100 Bioanalyzer analysis (Agilent Santa Clara, CA) were subjected to RNA sequencing.
Transcriptome libraries were prepared following a modified protocol previously described for generating strand specific RNASeq libraries 8.  Briefly 2.5 μg of total RNA was subjected to polyA selection using oligodT beads (Invitrogen, Carlsbad, CA).  Purified polyA RNA was fragmented and reverse transcribed using Superscipt-II (Invitrogen, Carlsbad CA).  Second strand synthesis was performed with DNA Ploymerase I (New England Biolabs, Ipswich, MA) in the presence of dNTP mix containing dUTP instead of dTTP.  The product was then subjected to end repair, A base addition and adaptor ligation steps.  Libraries were next size selected in the range of 350 bps after resolving in a 3% Nusieve 3:1 (Lonza, Basel, Switzerland) agarose gel and DNA recovered using QIAEX II gel extraction reagent (Qiagen, Valencia, CA). Libraries were barcoded during the 14-cycle PCR amplification with Phusion DNA polymerase (New England Biolabs, Ipswich, MA) and purified using AMPure XP beads (Beckman Coulter, Brea, CA).

tag: age

value: not collected

value: MCTP

tag: gender

value: tissue

tag: disease

value: cancer

value: ESOPHAGEAL


title: MCTP_SAMPLE_274_tissue_colon_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_274
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: colon

value: COLON


title: MCTP_SAMPLE_249_tissue_clear_cell_carcinoma

description:
Sample name: MCTP_SAMPLE_249
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_264_tissue_breast_metastatic_carcinoma

description:
Sample name: MCTP_SAMPLE_264
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: metastatic

value: BRCA


title: MCTP_SAMPLE_73_tissue_lung_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_73
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: lung

value: LUAD


title: MCTP_SAMPLE_60_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_60
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: breast


title: MCTP_SAMPLE_58_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_58
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_59_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_59
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_245_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_245
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_244_tissue_breast_metastatic_carcinoma

description:
Sample name: MCTP_SAMPLE_244
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_57_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_57
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_54_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_54
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_51_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_51
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_48_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_48
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_263_tissue_breast_metastatic_carcinoma

description:
Sample name: MCTP_SAMPLE_263
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_41_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_41
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_44_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_44
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_40_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_40
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_42_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_42
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_261_tissue_breast_metastatic_carcinoma

description:
Sample name: MCTP_SAMPLE_261
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_47_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_47
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_45_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_45
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_46_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_46
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_43_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_43
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_38_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_38
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_39_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_39
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_36_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_36
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_253_tissue_breast_metastatic_carcinoma

description:
Sample name: MCTP_SAMPLE_253
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_35_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_35
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_34_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_34
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_30_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_30
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_33_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_33
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_31_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_31
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_28_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_28
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_29_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_29
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_55_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_55
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_56_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_56
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_53_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_53
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_52_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_52
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_27_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_27
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_25_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_25
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_24_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_24
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_26_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_26
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_23_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_23
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_37_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_37
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_20_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_20
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_19_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_19
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_17_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_17
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_16_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_16
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_14_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_14
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_15_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_15
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_18_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_18
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_22_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_22
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_21_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_21
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_11_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_11
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_12_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_12
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_13_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_13
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_32_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_32
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_7_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_7
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_8_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_8
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_9_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_9
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_6_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_6
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_4_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_4
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_3_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_3
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_2_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_2
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_5_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_5
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_1_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_1
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_238_tissue_bladder_carcinoma

description:
Sample name: MCTP_SAMPLE_238
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: bladder

value: BLADDER


title: MCTP_SAMPLE_216_tissue_benign

description:
Sample name: MCTP_SAMPLE_216
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: benign

value: BENIGN


title: MCTP_SAMPLE_214_tissue_benign

description:
Sample name: MCTP_SAMPLE_214
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_215_tissue_benign

description:
Sample name: MCTP_SAMPLE_215
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_325_tissue_aml

description:
Sample name: MCTP_SAMPLE_325
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: aml

value: RARE


title: MCTP_SAMPLE_94_tissue_benign

description:
Sample name: MCTP_SAMPLE_94
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: not collected

value: MCTP


title: MCTP_SAMPLE_82_tissue_benign

description:
Sample name: MCTP_SAMPLE_82
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: tissue


title: MCTP_SAMPLE_92_tissue_benign

description:
Sample name: MCTP_SAMPLE_92
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_10_tissue_breast_carcinoma

description:
Sample name: MCTP_SAMPLE_10
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: cancer


title: MCTP_SAMPLE_254_tissue_adrenocortical_carcinoma

description:
Sample name: MCTP_SAMPLE_254
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: adrenocortical

value: ADRENOCORTICAL


title: lung_esophageal_oe33_cell_line_lung_esophageal_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_147
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: LUCL


title: lung_H2170_cell_line_lung_squamous_carcinoma

description:
Sample name: MCTP_SAMPLE_158
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_242_tissue_adrenocortical_carcinoma

description:
Sample name: MCTP_SAMPLE_242
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: lung_esophageal_flo_cell_line_lung_esophageal_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_145
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: lung_esophageal_het_cell_line_lung_esophageal_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_146
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_248_tissue_adrenocortical_carcinoma

description:
Sample name: MCTP_SAMPLE_248
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: MCTP_SAMPLE_67_tissue_adrenocortical_carcinoma

description:
Sample name: MCTP_SAMPLE_67
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: lung_H2228_cell_line_lung_carcinoma

description:
Sample name: MCTP_SAMPLE_159
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: lung_H827_cell_line_lung_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_167
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: YcnC_0.9_1

status: Public on Mar 20 2015

type: RNA

city: New York

first: Patrick

last: Eichenberger

email: pe19@nyu.edu, arb401@nyu.edu

state: New York

address: 12 Waverly Place

department: Center for Genomics and Systems Biology

institute: New York University

description: YcnC regulon LmrA regulon Replicate 1: PY79 vs PE2822 (ycnC::erm) grown in parallel in Difco Sporulation Medium. Samples were collected at OD600nm 0.9 and 1.4

hyb_protocol: Hybridizations were incubated at 65˚C for 17 hours. After hybridization slides were washed using Agilent's Wash Buffer 1 and 2.

scan_protocol: Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology

data_processing: Microarray data processing was performed in R (www.r-project.org) using the Bioconductor bioinformatics software package (www.bioconductor.org). Data were loaded into R using the marray package and normalized between arrays using loess normalization. Normalized log-ratios of gMedianSignal and rMedianSignal were collapsed for redundant probes taking the average.

organism: Bacillus subtilis

label_protocol: 6-10 ug of RNA was labelled using Agilent's Fairplay III Protocol for NHS-ester dye-coupling reaction to amino allyl dUTP . Cy3 and Cy5 were purchased from GE Healthcare

extract_protocol: RNA was extracted using the Hot Phenol method followed by Dnase treatment and cleaning with Qiagen's Rneasy kit

tag: strain

source_name: wildtype


title: LmrA_1.4_1

description: LmrA regulon Replicate 1: PY79 vs PE2835 (lmrA::erm) grown in parallel in Difco Sporulation Medium. Samples were collected at OD600nm 0.9 and 1.4


title: LmrA_0.9_1


title: YcnC_1.4_1


title: NtdR_T-0.5

description: NtdR regulon LmrA regulon Replicate 1: PY79 vs PE2671 (ntdR::kan) grown in parallel in Difco Sporulation Medium. Samples were collected at 0.5 hours before the onset of stationary phase and the onset of stationary phase


title: YoaUT3.5

description: YoaU regulon LmrA regulon Replicate 1: Wild-type PY79 vs PE2670 (yoaU::erm) at 3.5 and 5.5 hours post-resuspension.


title: AseR_1.4_1

description: AseR regulon Replicate 1: PY79 vs PE2836 (aseR::erm) grown in parallel in Difco Sporulation Medium. Samples were collected at OD600nm 0.9 and 1.4


title: YxaD T-1

description: YxaD regulon LmrA regulon Replicate 1: PY79 vs PE2672 (yxaD::kan) grown in parallel in Difco Sporulation Medium. Samples were collected at 1 and 0.5 hours before the onset of stationary phase

source_name: yxaD::kan yxaD::kan


title: YxaD T-0.5

source_name: YxaD


title: YdtP_T0

description: RmgR (YtdP) regulon LmrA regulon Replicate 1: PY79 vs PE2673 (rmgR::kan) grown in parallel in Difco Sporulation Medium. Samples were collected at 0.5 hours before the onset of stationary phase and the onset of stationary phase

source_name: YdtP


title: 6913 - 1135082_20111212DN-der

status: Public on Mar 27 2015

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

description: 6913 - 1135082_20111212DN-der.AVG_Signal

hyb_protocol: Per Washington University Core Facility protocol.

label: biotin

source_name: CD141-CD14- dermal cells

extract_protocol: RNA from sorted populations was purified using TRIzol. RNA was processed, amplified, labeled and hybridized at Washington University Core Facility (GTAC) with Illumina HumanHT-12 v4 Expression BeadChip. Data were background subtracted and quantile normalized.

tag: cell type

value: CD141-CD14- dermal cells


title: YoaUT5.5


title: NtdR_T0


title: 6899 - 1135065_2011171114_plus_der

description: 6899 - 1135065_2011171114_plus_der.AVG_Signal

scan_protocol: Per Washington University Core Facility protocol.

source_name: CD14+ dermal cells

value: CD14+ dermal cells


title: 6905 - 1135072_20112111DN-der

description: 6905 - 1135072_20112111DN-der.AVG_Signal

data_processing: Per Washington University Core Facility protocol.


title: 6915 - 1135136_20112812epiLCs

description: 6915 - 1135136_20112812epiLCs.AVG_Signal

source_name: epidermal Langerhan Cells

label_protocol: Per Washington University Core Facility protocol.

value: epidermal Langerhan Cells


title: 6918 - 1135133_2011281214_plus-der

description: 6918 - 1135133_2011281214_plus-der.AVG_Signal


title: 6910 - 1135077_20112311DN-der

description: 6910 - 1135077_20112311DN-der.AVG_Signal


title: 6908 - 1135075_2011231114_plus_der

description: 6908 - 1135075_2011231114_plus_der.AVG_Signal


title: 6911 - 1135078_20111212epiLCs

description: 6911 - 1135078_20111212epiLCs.AVG_Signal


title: YdtP_T0.5

source_name: rmgR::kan rmgR::kan


title: 6904 - 1135071_20112111A3_plus_der

description: 6904 - 1135071_20112111A3_plus_der.AVG_Signal

source_name: CD141+ dermal cells

value: CD141+ dermal cells


title: 6901 - 1135068_20112111epiLCs

description: 6901 - 1135068_20112111epiLCs.AVG_Signal


title: 6903 - 1135070_2011211114_plus_der

description: 6903 - 1135070_2011211114_plus_der.AVG_Signal


title: AseR_0.9_1


title: AlaR_OD 1.7

description: AlaR regulon Replicate 1: PY79 vs PE2669 (alaR::kan) grown in parallel in Difco Sporulation Medium. Samples were collected at OD600nm 0.4, 0.7, 1.0 and 1.7


title: SigF2

description: SigF regulon Replicate 1: Strain PE2689 (sigE::tet sigF::erm) vs PE126 (sigE::tet) at 2 hours post-resuspension.

source_name: sigF::erm sigE::tet


title: AlaR_OD 0.7


title: AlaR_OD 1.0


title: SigG2

description: SigG regulon Replicate 2: Strain PE452 (sigG::cat, sigK::erm) vs PE451 (sigK::erm) at 4 hours post-resuspension.

source_name: sigG::cat sigK::erm


title: 6898 - 1135063_20111711epiLCs

description: 6898 - 1135063_20111711epiLCs.AVG_Signal


title: 6909 - 1135076_20112311A3_plus_der

description: 6909 - 1135076_20112311A3_plus_der.AVG_Signal


title: 6906 - 1135073_20112311epiLCs

description: 6906 - 1135073_20112311epiLCs.AVG_Signal


title: AlaR_OD 0.4


title: 6916 - 1135137_20112812epiLCs

description: 6916 - 1135137_20112812epiLCs.AVG_Signal


title: 6912 - 1135081_20111212A3_plus_der

description: 6912 - 1135081_20111212A3_plus_der.AVG_Signal


title: 6900 - 1135067_20111711DN-der

description: 6900 - 1135067_20111711DN-der.AVG_Signal


title: SigF&E1

description: SigF and SigE regulon Replicate 1: Issue with strain construction. Results suggest wild-type vs PE2689 at 2 hours post-resuspension.


title: RemA1_T15

description: remA overexpression Replicate 1: PE2668 (remA::kan, thrC::Phyperspank-remA erm) was grown to mid-log phase in LB, split into two flasks and IPTG was added to one flask. Samples were collected at 0, 15, and 30 minutes post-addition of IPTG.

source_name: IPTG

source_name: no IPTG


title: SigD2_T30

description: sigD overexpression Replicate 2: PE2599 (sigD::tet, amyE::Phyperspank-sigD kan) was grown to mid-log phase in LB, split into two flasks and IPTG was added to one flask. Samples were collected at 0, 15, and 30 minutes post-addition of IPTG.


title: SigD2_T15


title: RemA1_T5


title: SigD2_T0


title: SigD1_T15

description: sigD overexpression Replicate 1 :  PE2599 (sigD::tet, amyE::Phyperspank-sigD kan) was grown to mid-log phase, split into two flasks and IPTG was added to one flask. Samples were collected at 0, 5, 15, and 30 minutes post-addition of IPTG.


title: SigD1_T0


title: RemA1_T30


title: YfmP3

description: YfmP regulon Replicate 3: PY79 vs PE2684 (yfmP::kan) grown in parallel in Difco Sporulation Medium at OD600nm 2.4.


title: Gin(6825vs6827)1_T3

description: Gin regulon Replicate 1: Gin regulon Strain PE2680 (gin::tet, amyE::gin spc) vs PE2682 (gin::tet, amyE::PsigF-gin spc) at 3 hours post-resupension.

source_name: PsigF-gin

source_name: Pgin-gin


title: YfmP1

description: YfmP regulon Replicate 1: PY79 vs PE2684 (yfmP::kan) grown in parallel in Difco Sporulation Medium at OD600nm 2.4.


title: Gin(6825vs6827)2_T3

description: Gin regulon Replicate 2: Strain PE2680 (gin::tet, amyE::gin spc) vs PE2682 (gin::tet, amyE::PsigF-gin spc) at 3 hours post-resupension.


title: PsigKGin1_T4.5

description: Gin regulon Replicate 1: Strain PE2680 (gin::tet, amyE::gin spc) vs PE2682 (gin::tet, amyE::PsigF-gin spc) at 4.5 hours post-resupension.


title: SigD1_T30


title: SigD1_T5


title: Gin1_T2

description: Gin regulon Replicate 1: Strain PE2679 (gin::tet) vs PE2680 (gin::tet, amyE::gin spc) at 2 hours post-resuspension.

source_name: gin::tet amyE::Pgin-gin spc


title: PsigFGin1_T4.5

description: Gin regulon Replicate 1: Strain PE2680 (gin::tet, amyE::gin spc) vs PE2681 (gin::tet, amyE::PsigK-gin spc) at 4.5 hours post-resupension.

source_name: PsigK-gin


title: Rifamp1_T30

description: Rifampicin Replicate 1: A wild-type PY79 culture was grown in LB to mid-exponential phase and then split into two flasks. Rifampicin was added to one flask to a concentration of 0.03 μg/mL. Samples were collected at 0, 5, 15, and 30 minutes post-Rifampicin addition.

source_name: Rif

source_name: No Rif


title: Gin1_T4.5

description: Gin regulon Replicate 1: Strain PE2679 (gin::tet) vs PE2680 (gin::tet, amyE::gin spc) at 4.5 hours post-resuspension.

source_name: gin::tet amyE::gin spc


title: Rifamp1_T5


title: Rifamp1_T15


title: Spec1_T15

description: Spectinomycin Replicate 1: A wild-type PY79 culture was grown in LB to mid-exponential phase and then split into two flasks. Spectinomycin was added to one flask to a concentration of 15 μg/mL. Samples were collected at 0, 5, 15, and 30 minutes post-Spectinomycin addition.

source_name: No Spec

source_name: Spec


title: Spec2_T5

description: Spectinomycin Replicate 2: A wild-type PY79 culture was grown in LB to mid-exponential phase and then split into two flasks. Spectinomycin was added to one flask to a concentration of 15 μg/mL. Samples were collected at 0, 5, 15, and 30 minutes post-Spectinomycin addition.


title: PsigKGin1_T2

description: Gin regulon Replicate 1: Strain PE2680 (gin::tet, amyE::gin spc) vs PE2682 (gin::tet, amyE::PsigF-gin spc) at 2 hours post-resupension.


title: Spec2_T30


title: PsigFGin1_T2

description: Gin regulon Replicate 1: Strain PE2680 (gin::tet, amyE::gin spc) vs PE2681 (gin::tet, amyE::PsigK-gin spc) at 2 hours post-resupension.


title: Rifamp1_T0


title: Spec2_T15


title: YfmP2

description: YfmP regulon Replicate 2: PY79 vs PE2684 (yfmP::kan) grown in parallel in Difco Sporulation Medium at OD600nm 2.4.

source_name: wildtype


title: Spec2_T0


title: Spec1_T30


title: PhoPT4_2

description: PhoP regulon Replicate 2: A wild-type PY79 and PE475 (phoP::kan) cultures were grown in parallel and resuspended in low phosphate minimal medium. Samples were collected 3 and 4 hours after resuspension


title: Spec1_T0


title: Dapt2_T30

description: Daptomycin Replicate 2: A wild-type PY79 culture was grown in LB to mid-exponential phase and then split into two flasks. Daptomycin was added to one flask to a concentration of 4 μg/mL. Samples were collected at 0, 5, 15, and 30 minutes post-Daptomycin addition.

source_name: No Dapto

source_name: Dapto


title: Dapt2_T15


title: PhoPT3_1

description: PhoP regulon Replicate 1: A wild-type PY79 and PE475 (phoP::kan) cultures were grown in parallel and resuspended in low phosphate minimal medium. Samples were collected 3 hours after resuspension


title: PhoPT3_2


title: Dapt2_T5


title: Dapt2_T0


title: Dapt1_T30

description: Daptomycin Replicate 1: A wild-type PY79 culture was grown in LB to mid-exponential phase and then split into two flasks. Daptomycin was added to one flask to a concentration of 4 μg/mL. Samples were collected at 0, 5, 15, and 30 minutes post-Daptomycin addition.


title: Dapt1_T15


title: NalAcid2_T30

description: Nalidixic acid Replicate 2: A wild-type PY79 culture was grown in LB to mid-exponential phase and then split into two flasks. Nalidixic Acid was added to one flask to a concentration of 8 μg/mL. Samples were collected at 0, 5, 15, and 30 minutes post-Nalidixic Acid addition.

source_name: No Nal Acid

source_name: Nal Acid


title: Spec1_T5


title: Dapt1_T0


title: Vanco1_T0

description: Vancomycin challenge Replicate 1: A wild-type PY79 culture was grown in LB to mid-exponential phase and then split into two flasks. Vancomycin was added to one flask to a concentration of 0.15 μg/mL. Samples were collected at 0, 5, 15, and 30 minutes post-Vancomycin addition.

source_name: No Vanco

source_name: Vanco


title: NalAcid1_T30

description: Nalidixic acid Replicate 1: A wild-type PY79 culture was grown in LB to mid-exponential phase and then split into two flasks. Nalidixic Acid was added to one flask to a concentration of 8 μg/mL. Samples were collected at 0, 5, 15, and 30 minutes post-Nalidixic Acid addition.


title: NalAcid2_T0


title: NalAcid1_T15


title: SigMXT30_2

description: SigM and SigX regulons and vancomycin challenge Replicate 2: A wild-type PY79 and PE2843 (sigM::kan sigX::erm) cultures were grown in parallel in LB to mid-log phase. Vancomycin was added to each culture to a concentration of 0.15 μg/mL. Samples were collected 30 minutes post-Vancomycin addition.


title: Vanco1_T15


title: Vanco1_T5


title: NalAcid2_T5


title: Vanco1_T30


title: NalAcid2_T15


title: Dapt1_T5


title: NalAcid1_T5


title: NalAcid1_T0


title: Vanco2_T15

description: Vancomycin challenge Replicate 2: A wild-type PY79 culture was grown in LB to mid-exponential phase and then split into two flasks. Vancomycin was added to one flask to a concentration of 0.15 μg/mL. Samples were collected at 0, 5, 15, and 30 minutes post-Vancomycin addition.


title: SigMXT30_1

description: SigM and SigX regulons and vancomycin challenge Replicate 1: A wild-type PY79 and PE2843 (sigM::kan sigX::erm) cultures were grown in parallel in LB to mid-log phase. Vancomycin was added to each culture to a concentration of 0.15 μg/mL. Samples were collected 30 minutes post-Vancomycin addition.


title: SigMT30_3

description: SigM regulon and vancomycin challenge Replicate 2: A wild-type PY79 and PE2730 (sigM::kan) cultures were grown in parallel in LB to mid-log phase. Vancomycin was added to each culture to a concentration of 0.15 μg/mL. Samples were collected 30 minutes post-Vancomycin addition.


title: SigMT30_4

description: SigM regulon and vancomycin challenge Replicate 3: A wild-type PY79 and PE2730 (sigM::kan) cultures were grown in parallel in LB to mid-log phase. Vancomycin was added to each culture to a concentration of 0.15 μg/mL. Samples were collected 30 minutes post-Vancomycin addition.


title: Vanco2_T30


title: SigW0.9_2

description: SigW regulon Replicate 2: A wild-type PY79 and PE2732 (sigW::erm) cultures were grown in parallel in Difco Sporulation Medium and samples were collected at OD600nm of 0.9 and 1.4.


title: SigW1.4_2


title: SigMT30_2

description: SigM regulon and vancomycin challenge Replicate 1: A wild-type PY79 and PE2730 (sigM::kan) cultures were grown in parallel in LB to mid-log phase. Vancomycin was added to each culture to a concentration of 0.15 μg/mL. Samples were collected 30 minutes post-Vancomycin addition.


title: SigW1.4_1

description: SigW regulon Replicate 1: A wild-type PY79 and PE2732 (sigW::erm) cultures were grown in parallel in Difco Sporulation Medium and samples were collected at OD600nm of 0.9 and 1.4.


title: SigW0.9_1


title: SigB3_T30

description: SigB regulon and EtOH challenge Replicate 3: A wild-type PY79 and PE259 (sigB::cat) cultures were grown in parallel in LB to mid-log phase. Ethanol was added to each culture to reach a final concentration of 5%. Samples were collected at 5, 15, and 30 minutes post-EtOH addition.


title: SigB3_T15


title: Vanco2_T5


title: SigB2_T30

description: SigB regulon and EtOH challenge Replicate 2: A wild-type PY79 and PE259 (sigB::cat) cultures were grown in parallel in LB to mid-log phase. Ethanol was added to each culture to reach a final concentration of 5%. Samples were collected at 5, 15, and 30 minutes post-EtOH addition.


title: SigB2_T15


title: SigB3_T5


title: SigB1_T5

description: SigB regulon and EtOH challenge Replicate 1: A wild-type PY79 and PE259 (sigB::cat) cultures were grown in parallel in LB to mid-log phase. Ethanol was added to each culture to reach a final concentration of 5%. Samples were collected at 5, 15, and 30 minutes post-EtOH addition.


title: SigB1_T30


title: SigB2_T5


title: SigB1_T15


title: SigD2_S

description: SigD regulon Replicate 2: A wild-type PY79 and sigD mutant (PE2597) cultures were grown in parallel in Difco Sporulation Medium. Samples were collected during mid-log (ML), late-log (LL), transition to stationary phase (T), and stationary phase.


title: SinR_1

description: SinR regulon Replicate 1: An epsH::tet mutant (PE2746) and sinR::cat epsH::tet double mutant (PE2748) cultures were grown in parallel in Difco Sporulation Medium. Samples were collected during mid-log phase (OD600nm of 1.0).


title: SigD1_T

description: SigD regulon Replicate 1: A wild-type PY79 and sigD mutant (PE2597) cultures were grown in parallel in Difco Sporulation Medium. Samples were collected during mid-log (ML), late-log (LL), transition to stationary phase (T), and stationary phase.


title: MSgg1_T+3.5

description: Biofilm medium (MSgg) Replicate 1: A wild-type PY79 culture was grown in MSgg Medium and samples were collected at 3.5 (OD600nm 0.6), 2.5 (OD600nm 1.3), 1.5 (OD600nm 2.0), and 0.5 (OD600nm 2.3) hours before the onset of stationary phase, and at 0.5 (OD600nm 2.8), 1.5, 2.5, and 3.5 hours after the onset of stationary phase. A common reference was made by pooling RNA from each time point.

source_name: sample

source_name: reference


title: MSgg1_T+0.5


title: MSgg1_T-0.5


title: SigD2_T


title: SinR_2

description: SinR regulon Replicate 2: An epsH::tet mutant (PE2746) and sinR::cat epsH::tet double mutant (PE2748) cultures were grown in parallel in Difco Sporulation Medium. Samples were collected during mid-log phase (OD600nm of 1.0).


title: MSgg1_T+1.5


title: SigD1_LL


title: SigD1_S


title: MSgg1_T-1.5


title: SigD1_ML


title: SigD2_LL


title: MSgg1_T+2.5


title: Vanco2_T0


title: MSgg1_T-2.5


title: MSgg1_T-3.5


title: ComK2_T1.5

description: comK mutant Replicate 2: A wild-type PY79 and comK mutant (PE31 comK::kan) cultures were grown in parallel in Competence Medium. Samples were collected at 1.5 and 2.5 hours post-onset of stationary phase.


title: ComK2_T2.5


title: ComK1_T2.5

description: comK mutant Replicate 1: A wild-type PY79 and comK mutant (PE31 comK::kan) cultures were grown in parallel in Competence Medium. Samples were collected at 1.5 and 2.5 hours post-onset of stationary phase.


title: SigD2_ML


title: ComK1_T1.5


title: Com2_T+2.5

description: Competence medium Replicate 2: A wild-type PY79 culture was grown in Competence Medium and samples were collected at 1.5 (OD600nm 0.4), 1 (OD600nm 0.4), and 0.5 (OD600nm 0.6) hours before the onset of stationary phase, the onset of stationary phase (OD600nm 0.9), and 0.5 (OD600nm 0.9), 1.5 (OD600nm 1.0), 2.5 (OD600nm 0.9), and 3.5 (O.D.600nm 1.0) hours after the onset of stationary phase. A common reference was made by pooling RNA from each time point.


title: Com2_T+3.5


title: Com2_T+1.5


title: Com2_T0


title: Com2_T+0.5


title: Com2_T-0.5


title: Com1_T+2.5

description: Competence medium Replicate 1: A wild-type PY79 culture was grown in Competence Medium and samples were collected at 1.5 (OD600nm 0.4), 1 (OD600nm 0.4), and 0.5 (OD600nm 0.6) hours before the onset of stationary phase, the onset of stationary phase (OD600nm 0.9), and 0.5 (OD600nm 0.9), 1.5 (OD600nm 1.0), 2.5 (OD600nm 0.9), and 3.5 (O.D.600nm 1.0) hours after the onset of stationary phase. A common reference was made by pooling RNA from each time point.


title: GerR_3

description: GerR regulon Replicate 3: PE316 (gerR::spc) at 5.5 hours post-resuspension.


title: Com1_T-0.5


title: GerE2

description: GerE regulon Replicate 2: Wild-type PY79 vs PE454 (gerE::cat) at 5.5 hours post-resuspension.


title: Com1_T0


title: Com1_T+1.5


title: Com1_T-1.5


title: SpoVT2

description: SpoVT regulon Replicate 2: PE2686 (spoVT::spc, sigK::erm) vs PE451 (sigK::erm) at 5 hours post-resuspension.

source_name: spoVT::spc sigK::erm


title: GerR1_T5.5

description: GerR regulon Replicate 1: PE316 (gerR::spc) at 5.5 hours post-resuspension.


title: SpoVT1

description: SpoVT regulon Replicate 1: PE2686 (spoVT::spc, sigK::erm) vs PE451 (sigK::erm) at 5 hours post-resuspension.


title: RsfA_T4_2

description: RsfA regulon Replicate 2: Strain PE2753 (rsfA::erm) vs wild type PY79 at 4 hours post-resuspension.


title: Com1_T-1.0


title: GerE1

description: GerE regulon Replicate 1: Wild-type PY79 vs PE454 (gerE::cat) at 5.5 hours post-resuspension.


title: SpoIIID1

description: SpoIIID regulon Replicate 1: Strain PE453 (spoIIID::tet, sigK::erm) vs PE451 (sigK::erm) at 3.5 hours post-resuspension.

source_name: spoIIID::tet sigK::erm


title: SpoIIID2

description: SpoIIID regulon Replicate 2: Strain PE453 (spoIIID::tet, sigK::erm) vs PE451 (sigK::erm) at 3.5 hours post-resuspension.


title: SigG3

description: SigG regulon Replicate 3 : Strain PE452 (sigG::cat, sigK::erm) vs PE451 (sigK::erm) at 4 hours post-resuspension.

source_name: sigG::cat sigK::erm


title: SigK1

description: SigK regulon Replicate 1: Strain PE455 (sigK::erm gerE::cat) vs PE454 (gerE::cat) at 4.5 hours post-resuspension.

source_name: sigK::erm gerE::cat


title: SigK2

description: SigK regulon Replicate 2: Strain PE455 (sigK::erm gerE::cat) vs PE454 (gerE::cat) at 4.5 hours post-resuspension.


title: Com2_T-1.5


title: SigE&G2

description: SigE & SigG regulons Replicate 2: Strain PE437 (sigE::erm spoIIID::tet) vs PE239 (spoIIID::tet) at 2.5 hours post-resuspension.

source_name: sigE::erm spoIIID::tet


title: SigE&G1

description: SigE & SigG regulons Replicate 1: Strain PE437 (sigE::erm spoIIID::tet) vs PE239 (spoIIID::tet) at 2.5 hours post-resuspension.


title: Com1_T+0.5


title: Com1_T+3.5


title: Com2_T-1.0


title: SigE2

description: SigE regulon Replicate 2: PE437 (sigE::erm spoIIID::tet) vs PE436 (sigG::cat spoIIID::tet) at 2.5 hours post-resuspension.

source_name: sigG::cat spoIIID::tet


title: SigFT2.5_2

description: SigF regulon (time course) Replicate 2: Strain BDR1730 (sigF::erm) and strain BDR323 (sigE:: erm) grown in parallel and resuspended in Sterlini-Mandelstam medium. Samples were collected at 2, 2.5 and 3 hours post-resuspension.


title: RsfA_T4_1

description: RsfA regulon Replicate 1: Strain PE2753 (rsfA::erm) vs wild type PY79 at 4 hours post-resuspension.


title: SigFT2.5_1

description: SigF regulon (time course) Replicate 1: Strain BDR1730 (sigF::erm) and strain BDR323 (sigE:: erm) grown in parallel and resuspended in Sterlini-Mandelstam medium. Samples were collected at 2, 2.5 and 3 hours post-resuspension.


title: SigFT3_2


title: SigFT2_2


title: SigFT2_1


title: Spo2_T7.0

description: Sporulation by resuspension Replicate 2: A wild-type PY79 culture was grown in Supplemented Lysogeny Broth until mid-log. It was then pelleted and resuspended in Sterlini-Mandelstam medium. Samples were collected at 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, and 7 hours post-resuspension. A common reference was made by pooling RNA from each time point.


title: Spo2_T4.5


title: Spo2_T6.5


title: Spo2_T4.0


title: Spo2_T5.0


title: Spo2_T3.0


title: Spo2_T6.0


title: Spo2_T5.5


title: Spo2_T3.5


title: SigE1

description: SigE regulon Replicate 1: PE437 (sigE::erm spoIIID::tet) vs PE436 (sigG::cat spoIIID::tet) at 2.5 hours post-resuspension.


title: SigG1

description: SigG regulon Replicate 1 : Strain PE452 (sigG::cat, sigK::erm) vs PE451 (sigK::erm) at 4 hours post-resuspension.


title: SigFT3_1


title: Spo2_T2.5


title: Spo2_T1.5


title: Spo2_T1.0


title: Spo3_T0.5


title: Spo1_T4.5

description: Sporulation by resuspension Replicate 1: A wild-type PY79 culture was grown in Supplemented Lysogeny Broth until mid-log. It was then pelleted and resuspended in Sterlini-Mandelstam medium. Samples were collected at 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, and 7 hours post-resuspension. A common reference was made by pooling RNA from each time point.


title: Spo1_T4.0


title: Spo1_T6.5


title: Spo1_T5.0


title: Spo1_T7.0


title: Spo1_T5.5


title: Spo1_T6.0


title: Spo1_T3.5


title: Spo1_T3.0


title: BkdR OD 1.6

description: BkdR regulon Replicate 1: PY79 vs PE2674 (bkdR::kan) grown in parallel in Difco Sporulation Medium. Samples were collected at OD600nm 0.9 and 1.7

source_name: BkdR


title: Spo2_T2.0


title: Spo1_T2.5


title: Spo1_T1.5


title: Spo1_T2.0


title: BkdR OD 0.4

description: BkdR regulon Replicate 1: PY79 vs PE2674 (bkdR::kan) grown in parallel in Difco Sporulation Medium. Samples were collected at OD600nm 0.9 and 1.6

source_name: bkdR::kan bkdR::kan


title: BkdR OD 1.4

description: BkdR regulon Replicate 1: PY79 vs PE2674 (bkdR::kan) grown in parallel in Difco Sporulation Medium. Samples were collected at OD600nm 0.9 and 1.5

source_name: wildtype


title: SigL_1.4_1

description: SigL regulon Replicate 1: A wild-type PY79 and sigL mutant (PE2830) cultures were grown in parallel in Difco Sporulation Medium and samples were collected at time-points 1-2 which correspond to OD600nm of 0.9 and 1.4, respectively.


title: BkdR OD 0.9

description: BkdR regulon Replicate 1: PY79 vs PE2674 (bkdR::kan) grown in parallel in Difco Sporulation Medium. Samples were collected at OD600nm 0.9 and 1.4


title: SigL_0.9_1


title: Spo1_T1.0


title: SigL_0.9_2

description: SigL regulon Replicate 2: A wild-type PY79 and sigL mutant (PE2830) cultures were grown in parallel in Difco Sporulation Medium and samples were collected at time-points 1-2 which correspond to OD600nm of 0.9 and 1.4, respectively.


title: CodY 1.4_2

description: CodY regulon Replicate 2: A wild-type PY79 and codY mutant (PE2752) cultures were grown in parallel in Difco Sporulation Medium and samples were collected at time-points 1-2 which correspond to OD600nm of 0.9 and 1.4, respectively.


title: CodY 0.9_2


title: SigL_1.4_2


title: CodY 1.4_1

description: CodY regulon Replicate 1: A wild-type PY79 and codY mutant (PE2752) cultures were grown in parallel in Difco Sporulation Medium and samples were collected at time-points 1-2 which correspond to OD600nm of 0.9 and 1.4, respectively.


title: Spo1_T0.5


title: ScoC_2.0_3

description: ScoC regulon Replicate 2: A wild-type PY79 and scoC mutant (PE2821) cultures were grown in parallel in Difco Sporulation Medium and samples were collected at time-points 1-2 which correspond to OD600nm of 1.4 and 2.0, respectively.


title: CodY 0.9_1


title: ScoC_1.4_3


title: ScoC_2.0_2

description: ScoC regulon Replicate 1: A wild-type PY79 and scoC mutant (PE2821) cultures were grown in parallel in Difco Sporulation Medium and samples were collected at time-points 1-2 which correspond to OD600nm of 1.4 and 2.0, respectively.


title: ScoC_1.4_1


title: SigH2_4

description: SigH regulon Replicate 2: A wild-type PY79 and sigH mutant (PE152) cultures were grown in parallel in Difco Sporulation Medium and samples were collected at time-points 1-5 which correspond to OD600nm of 0.4, 0.7, 1.1, 1.4, and 1.9, respectively.


title: SigH2_5


title: SigH1_3

description: SigH regulon Replicate 1: A wild-type PY79 and sigH mutant (PE152) cultures were grown in parallel in Difco Sporulation Medium and samples were collected at time-points 1-5 which correspond to OD600nm of 0.4, 0.7, 1.1, 1.4, and 1.9, respectively.


title: SigH1_4


title: SigH2_2


title: SigH1_5


title: SigH2_1


title: SigH2_3


title: SigH1_1


title: Spo0A2_1

description: Spo0A regulon Replicate 2: A wild-type PY79 and spo0A mutant (PE2687) cultures were grown in parallel in Difco Sporulation Medium. Samples were collected during OD600nm 1.0, 1.4, 2.2.


title: Spo0A1_3

description: Spo0A regulon Replicate 1: A wild-type PY79 and spo0A mutant (PE2687) cultures were grown in parallel in Difco Sporulation Medium. Samples were collected during OD600nm 0.8, 1.2, 2.0.


title: Spo0A1_2


title: DSM2_T+3.5

description: Growth and sporulation in DSM Replicate 2: A wild-type PY79 culture was grown in Difco Sporulation Medium. Samples were taken at 2.5 (OD600nm 0.4), 2 (OD600nm 0.6), 1.5 (OD600nm 1.3), 1 (OD600nm 1.9), and 0.5 (OD600nm 2.2) hours before the onset of stationary phase, the onset of stationary phase (OD600nm 2.4), and 0.5 (OD600nm 2.5), 1 (OD600nm 2.5), 1.5 (OD600nm 2.5), 2 (OD600nm 2.3), 2.5 (OD600nm 2.4), 3 (OD600nm 2.4), 3.5 (OD600nm 2.4), 4 (OD600nm 2.5), 4.5 (OD600nm 2.5), and 5 (OD600nm 2.8) hours after the onset of stationary phase. A common reference was made by pooling RNA from each time point.


title: Spo0A1_1


title: DSM2_T+3.0


title: DSM2_T+4.0


title: DSM2_T+4.5


title: DSM2_T+2.5


title: DSM2_T+1.5


title: DSM2_T+1.0


title: DSM2_T+2.0


title: DSM2_T+0.5


title: Spo0A2_3


title: SigH1_2


title: DSM2_T-2.5


title: DSM2_T-2.0


title: DSM2_T-1.5


title: Spo0A2_2


title: DSM2_T-1.0


title: DSM2_T+5.0


title: Germ2_T70min

description: Germination in DSM Replicate 2: A wild-type PY79 culture was grown in Difco Sporulation Medium (DSM) for 72 hours and spores were harvested. The purified spores were germinated in DSM and samples were collected at 40, 70, 90, 105, and 120 minutes. A common reference was made by pooling RNA from each time point.


title: Germ2_T120min


title: Germ2_T90min


title: DSM2_T-0.5


title: DSM1_T+5.5

description: Growth and sporulation in DSM Replicate 1: A wild-type PY79 culture was grown in Difco Sporulation Medium. Samples were taken at 1.5 (OD600nm 1.0), 1 (OD600nm 1.3), and 0.5 (OD600nm 1.7) hours before the onset of stationary phase, the onset of stationary phase (OD600nm 1.9), and 0.5 (OD600nm 1.9), 1 (OD600nm 2.3), 1.5 (OD600nm 2.2), 2.5 (OD600nm 2.3), 3.5 (OD600nm 2.0), 4 (OD600nm 2.3), 4.5 (OD600nm 2.6), 5 (OD600nm 2.7), and 5.5 (OD600nm 2.9) hours after the onset of stationary phase. A common reference was made by pooling RNA from each time point.


title: Germ2_T40min


title: DSM1_T+5.0


title: DSM1_T+4.5


title: DSM1_T+1.5


title: DSM1_T+2.5


title: DSM1_T+0.5


title: DSM1_T+1.0


title: DSM1_T0


title: DSM1_T+3.5


title: DSM2_T0


title: DSM1_T-1.0


title: DSM1_T-0.5


title: Germ2_T105min


title: Germ1_T150min

description: Germination in DSM Replicate 1: A wild-type PY79 culture was grown in Difco Sporulation Medium (DSM) for 72 hours and spores were harvested. The purified spores were germinated in DSM and samples were collected at 40, 70, 90, 120, and 150 minutes. A common reference was made by pooling RNA from each time point.


title: DSM1_T-1.5


title: Germ1_T40min


title: Germ1_T70min


title: Germ1_T90min


title: DSM1_T+4.0


title: Germ1_T120min


title: BP-2

status: Public on Feb 28 2015

city: Chicago

first: Stefani

last: Spranger

state: IL

address: 929 E 57th Street

institute: University of Chicago

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

organism: Mus musculus

source_name: Braf/PTEN

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

extract_protocol: Trizol

tag: strain background

tag: genotype/variation

value: Braf/PTEN

tag: tissue

value: melanoma


title: SK_MAC_X218

status: Public on Oct 15 2014

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

data_processing: Expression data was exported from Illlumina GenomeStudio software without background subtraction and was then quantile normalized and log (base 2) transformed in R (v. 2.15.2) using Bioconductor (v.2.18.0) lumi (v.2.10.0) package.

label_protocol: Standard labelling protocol

growth_protocol: Monocytes and dendritic cell subsets were purified by FACS sorting from primary samples for transcription analysis

extract_protocol: Total RNA was extracted using Qiagen RNeasy Micro RNA kit. Amplification was performed using Nugen Pico Ovation kit.

tag: donor id

value: Skin

tag: cell subtype

value: Macrophages


title: BBcP-3

source_name: Braf/PTEN/Bcat

value: Braf/PTEN/Bcat


title: SK_CD14_DC_X239

value: CD14+ dendritic cells (DCs)


title: BBcP-1


title: BP-1


title: SK_LC_X231

value: Langerhans cells


title: BBcP-2


title: SK_CD14_DC_X231


title: Cord_blood_Tartu_1_rehybridized

status: Public on Sep 25 2014

city: Turku

first: Essi

last: Laajala

address: Tykistökatu 6

country: Finland

institute: Turku Centre for Biotechnology

hyb_protocol: Samples were hybridized to GeneChip Human Genome U219 array plate (Affymetrix) with manufacturer´s protocols for using the GeneTitan Hybridization, Wash and Stain Kit for 3’ IVT Array Plates (Affymetrix). GeneTitan MC Instrument (Affymetrix) was used to hybridize, wash, stain, and scan the arrays.

scan_protocol: GeneTitan MC Instrument was used to scan the arrays. The probe cell intensity data was summarized with Affymetrix GeneChip Command Consol 3.1.

data_processing: The intensity data was pre-processed using robust multi-array averaging (RMA). The absent call filtering was done by determining a threshold value empirically for each sample by fitting a two-component GMM for all non-control probesets. A probeset was filtered out if it was absent in at least 50 % of the samples from Espoo, Tartu and Petrozavodsk, excluding these 15 rehybridized samples. Batch correction was done by applying the ComBat analysis method. These 15 rehybridized samples were utilized for the batch correction of the 113 samples (in a separate data set).

source_name: Cord blood

label_protocol: 50 ng of total RNA was processed to cDNA with Ovation RNA amplification system v2, including the Ovation whole blood reagent (NuGEN Technologies). The amplified cDNA was subsequently biotin-labelled and fragmented with Encore biotin module (NuGEN Technologies).

growth_protocol: Umbilical cord blood was drawn into Tempus Blood RNA tubes according to the manufacturer´s protocol and then stored in −70 °C until analyzed.

extract_protocol: Total whole-blood RNA was extracted from the samples using Tempus Spin RNA isolation kit (Applied Biosystems) according to manufacturer's instructions. RNA quality and quantity was determined using NanoDrop ND-2000 (Thermo Scientific) and Experion Automated Electrophoresis System (Bio-Rad Laboratories).

tag: country

value: Estonia

tag: sample month

value: January

value: Male

tag: hla risk category (np=neutral/protective, m=medium, h=high, vh=very high)

value: VH

tag: gestational week

tag: hybridization batch


title: BP-3


title: BP-4


title: SK_LC_X221


title: SK_MAC_X312


title: BBcP-4


title: SK_MAC_X231


title: Cord_blood_Petrozavodsk_5_rehybridized

value: Russia

value: February

value: Female

value: NP


title: SK_CD14_DC_X213


title: Cord_blood_Petrozavodsk_32_rehybridized

value: April


title: Cord_blood_Petrozavodsk_15_rehybridized

value: March


title: Cord_blood_Tartu_20_rehybridized


title: Cord_blood_Petrozavodsk_40_rehybridized

value: May


title: Cord_blood_Petrozavodsk_20_rehybridized


title: Cord_blood_Tartu_17_rehybridized


title: Cord_blood_Tartu_24_rehybridized

value: M


title: SK_CD14_DC_X221

value: Skin


title: Cord_blood_Petrozavodsk_9_rehybridized


title: SK_LC_X239


title: Cord_blood_Petrozavodsk_19_rehybridized


title: Cord_blood_Espoo_44_rehybridized

value: Finland

value: H


title: SK_MAC_X221

value: Macrophages


title: Blood_LPS+IVIg_rep.3

status: Public on Jul 01 2014

city: Jena

first: S.

last: Lambeck

address: Erlanger Allee 101

country: Germany

institute: JUH

description: in vivo

hyb_protocol: Hybridization was in agreement with the Whole-Genome Gene Expression protocol from Illumina.

scan_protocol: Illumina mouseRef8 V2 chips were scanned using the BeadArray Reader 500 X  from Illumina.

data_processing: Raw data were obtained using GenomeStudio (v 1.9.0)  and annotation by MouseRef-8_V2_0_R3_11278551_A.bgx.xml. Robust spline normalization (rsn) and detection filtering were performed via the lumi package within Bioconductor and R. Each organ was processed separately. One sample from kidney and one samples from blood did not pass quality control and were removed. Filtering of differentially expressed genes was conducted by linear model approaches with LIMMA and its moderated t-statistics (empirical Bayes).

source_name: Blood WBC, LPS, IVIg

label_protocol: Amplification and biotinylation of RNA were carried out using the TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip® (Epicentre).

growth_protocol:
Animal experiments were carried out after approval of the local ethics committee.
Animal experiments were carried out after approval of the local ethics committee. Male 20 to 30 weeks old C57BL/6 Jackson mice were used.

extract_protocol:
Standard
Liver and kidney homogenates were obtained by standard protocols. Blood was processed with the RNeasy® Mini Kit from Qiagen in accordance to the Purification of Total RNA from Animal Cells Using Spin Technology protocol and the Purification of Total RNA from Animal Tissues protocol, respectively. RNA concentration and purity were determined and quality control was performed with the automated electrophoresis system ExperionTM (Bio-Rad Laboratories) according to the manufacturer’s specifications.

treatment_protocol:
LPS + IVIg
Mice subjected to LPS and (mod)IVIg or vehicle controls.

value: WBC

value: male

tag: treatment

value: LPS + IVIg


title: Blood_LPS+modIVIg_rep.1

description: in vivo

source_name: Blood WBC, LPS, modIVIg

treatment_protocol:
LPS + modIVIg
Mice subjected to LPS and (mod)IVIg or vehicle controls.

value: LPS + modIVIg


title: Blood_LPS+vehicle_rep.2

description: in vivo

source_name: Blood WBC, LPS

treatment_protocol:
LPS
Mice subjected to LPS and (mod)IVIg or vehicle controls.

value: LPS


title: Blood_LPS+IVIg_rep.1

description: in vivo


title: Blood_LPS+modIVIg_rep.2

description: in vivo


title: Kidney_LPS+modIVIg_rep.3

description: in vivo

source_name: Kidney tissue, LPS, modIVIg

value: kidney


title: Blood_LPS+IVIg_rep.2

description: in vivo


title: Cord_blood_Espoo_29_rehybridized

value: February


title: Kidney_LPS+modIVIg_rep.4

description: in vivo


title: Cord_blood_Espoo_37_rehybridized

value: Female

value: VH


title: Blood_LPS+vehicle_rep.3

description: in vivo


title: Kidney_LPS+modIVIg_rep.1

description: in vivo


title: Kidney_LPS+IVIg_rep.2

description: in vivo

source_name: Kidney tissue, LPS, IVIg


title: Kidney_LPS+vehicle_rep.2

description: in vivo

source_name: Kidney tissue, LPS


title: Blood_LPS+vehicle_rep.1

description: in vivo


title: Kidney_LPS+IVIg_rep.4

description: in vivo


title: Kidney_LPS+IVIg_rep.1

description: in vivo


title: Liver_LPS+IVIg_rep.2

description: in vivo

source_name: liver tissue, LPS, IVIg

value: liver


title: Kidney_LPS+vehicle_rep.1

description: in vivo


title: Kidney_LPS+modIVIg_rep.2

description: in vivo


title: Liver_LPS+IVIg_rep.3

description: in vivo


title: Kidney_LPS+vehicle_rep.3

description: in vivo


title: Liver_LPS+modIVIg_rep.2

description: in vivo

source_name: liver tissue, LPS, modIVIg


title: Kidney_LPS+IVIg_rep.3

description: in vivo


title: Liver_LPS+modIVIg_rep.4

description: in vivo


title: Cord_blood_Espoo_13_rehybridized

value: January

value: NP


title: Liver_LPS+modIVIg_rep.3

description: in vivo


title: Liver_LPS+modIVIg_rep.1

description: in vivo


title: Liver_LPS+IVIg_rep.1

description: in vivo


title: Liver_LPS+vehicle_rep.4

description: in vivo

source_name: liver tissue, LPS


title: PCBM1662, Passage 7, Technical Replicate 3

status: Public on Apr 01 2014

city: Silver Spring

first: Raj

middle: K

last: Puri

state: Maryland

address: 10903 New Hampshire Ave

institute: FDA

description: {PCBM1662_P7_3} Cy5/Cy3 [PCBM1662|P3star]

hyb_protocol: Hyper5 and Cy3 labeled samples were mixed and hybridized on he Maui hybridization system for 16 hours at 42C

scan_protocol: Microarray slides were scanned using the 4000B GenePix Axon Scanner.  PMT voltages of both channels were adjusted such that their intensity histograms overlap.

data_processing: LOESS/Linear normalization was performed using ArrayTrack software (FDA) with no background subtraction

source_name: PCBM1662_MSCs_passage 7

label_protocol: Individual RNA material was labeled with Hyper5 and reference material (P3star or P3*) was labeled with Cy3.  See manuscript for more detailed description

growth_protocol: MSCs were grown in alpha minimum essential media with 10% FBS, 1% L-gluatmine & 1% penicillin G and streptomycin under humidified atmosphere of 5% CO2 at 37C

extract_protocol: Total RNA was extracted by the Qiagen Rneasy Mini kit

treatment_protocol: MSCs were passaged after reaching 80% confluency as determined by one sole cell biologist

value: human multipotent stromal cells (MSCs) derived from bone marrow

tag: passage

value: passage 7

source_name: pooled reference (P3star)

tag: sample type

value: Pooled reference Sample

tag: rna source

value: equal portions of total RNA from 6 donors (PCBM1641 P3, PCBM1632 P3, PCBM1662 P3, 8F3560 P3, 167696 P3, 110877 P3).


title: Liver_LPS+vehicle_rep.2

description: in vivo

tag: gender


title: Liver_LPS+vehicle_rep.1

description: in vivo

tag: strain


title: PCBM1662, Passage 5, Technical Replicate 2

description: {PCBM1662_P5_2} Cy5/Cy3 [PCBM1662|P3star]

source_name: PCBM1662_MSCs_passage 5

tag: cell type

value: passage 5


title: Liver_LPS+vehicle_rep.3

description: in vivo


title: PCBM1662, Passage 5, Technical Replicate 3

description: {PCBM1662_P5_3} Cy5/Cy3 [PCBM1662|P3star]


title: PCBM1662, Passage 7, Technical Replicate 2

description: {PCBM1662_P7_2} Cy5/Cy3 [PCBM1662|P3star]


title: PCBM1662, Passage 5, Technical Replicate 1

description: {PCBM1662_P5_1} Cy5/Cy3 [PCBM1662|P3star]


title: PCBM1662, Passage 7, Technical Replicate 1

description: {PCBM1662_P7_1} Cy5/Cy3 [PCBM1662|P3star]


title: PCBM1662, Passage 3, Technical Replicate 3

description: {PCBM1662_P3_3} Cy5/Cy3 [PCBM1662|P3star]

source_name: PCBM1662_MSCs_passage 3

value: passage 3


title: PCBM1662, Passage 3, Technical Replicate 1

description: {PCBM1662_P3_1} Cy5/Cy3 [PCBM1662|P3star]


title: PCBM1662, Passage 3, Technical Replicate 2

description: {PCBM1662_P3_2} Cy5/Cy3 [PCBM1662|P3star]


title: 8F3560, Passage 3, Technical Replicate 3

description: {8F3560_P3_3} Cy5/Cy3 [8F3560|P3star]

source_name: 8F3560_MSCs_passage 3


title: 8F3560, Passage 7, Technical Replicate 3

description: {8F3560_P7_3} Cy5/Cy3 [8F3560|P3star]

source_name: 8F3560_MSCs_passage 7


title: 167696, Passage 7, Technical Replicate 2

description: {167696_P7_2} Cy5/Cy3 [167696|P3star]

source_name: 167696_MSCs_passage 7


title: 167696, Passage 5, Technical Replicate 1

description: {167696_P5_1} Cy5/Cy3 [167696|P3star]

source_name: 167696_MSCs_passage 5


title: 8F3560, Passage 5, Technical Replicate 2

description: {8F3560_P5_2} Cy5/Cy3 [8F3560|P3star]

source_name: 8F3560_MSCs_passage 5


title: 8F3560, Passage 7, Technical Replicate 1

description: {8F3560_P7_1} Cy5/Cy3 [8F3560|P3star]


title: 167696, Passage 5, Technical Replicate 2

description: {167696_P5_2} Cy5/Cy3 [167696|P3star]


title: 8F3560, Passage 7, Technical Replicate 2

description: {8F3560_P7_2} Cy5/Cy3 [8F3560|P3star]


title: 8F3560, Passage 5, Technical Replicate 3

description: {8F3560_P5_3} Cy5/Cy3 [8F3560|P3star]


title: 167696, Passage 7, Technical Replicate 3

description: {167696_P7_3} Cy5/Cy3 [167696|P3star]


title: 8F3560, Passage 3, Technical Replicate 1

description: {8F3560_P3_1} Cy5/Cy3 [8F3560|P3star]


title: 8F3560, Passage 3, Technical Replicate 2

description: {8F3560_P3_2} Cy5/Cy3 [8F3560|P3star]


title: 167696, Passage 5, Technical Replicate 3

description: {167696_P5_3} Cy5/Cy3 [167696|P3star]


title: 167696, Passage 7, Technical Replicate 1

description: {167696_P7_1} Cy5/Cy3 [167696|P3star]


title: 8F3560, Passage 5, Technical Replicate 1

description: {8F3560_P5_1} Cy5/Cy3 [8F3560|P3star]


title: 167696, Passage 3, Technical Replicate 3

description: {167696_P3_3} Cy5/Cy3 [167696|P3star]

source_name: 167696_MSCs_passage 3


title: 167696, Passage 3, Technical Replicate 1

description: {167696_P3_1} Cy5/Cy3 [167696|P3star]


title: 110877, Passage 5, Technical Replicate 1

description: {110877_P5_1} Cy5/Cy3 [110877|P3star]

source_name: 110877_MSCs_passage 5

value: Male


title: 110877, Passage 7, Technical Replicate 3

description: {110877_P7_3} Cy5/Cy3 [110877|P3star]

source_name: 110877_MSCs_passage 7


title: 110877, Passage 7, Technical Replicate 1

description: {110877_P7_1} Cy5/Cy3 [110877|P3star]


title: PCBM1632, Passage 7, Technical Replicate 2

description: {PCBM1632_P7_2} Cy5/Cy3 [PCBM1632|P3star]

source_name: PCBM1632_MSCs_passage 7


title: 110877, Passage 3, Technical Replicate 2

description: {110877_P3_2} Cy5/Cy3 [110877|P3star]

source_name: 110877_MSCs_passage 3


title: 167696, Passage 3, Technical Replicate 2

description: {167696_P3_2} Cy5/Cy3 [167696|P3star]


title: PCBM1632, Passage 7, Technical Replicate 3

description: {PCBM1632_P7_3} Cy5/Cy3 [PCBM1632|P3star]


title: 110877, Passage 5, Technical Replicate 3

description: {110877_P5_3} Cy5/Cy3 [110877|P3star]


title: 110877, Passage 3, Technical Replicate 1

description: {110877_P3_1} Cy5/Cy3 [110877|P3star]


title: 110877, Passage 7, Technical Replicate 2

description: {110877_P7_2} Cy5/Cy3 [110877|P3star]


title: 110877, Passage 3, Technical Replicate 3

description: {110877_P3_3} Cy5/Cy3 [110877|P3star]


title: 110877, Passage 5, Technical Replicate 2

description: {110877_P5_2} Cy5/Cy3 [110877|P3star]


title: PCBM1632, Passage 5, Technical Replicate 3

description: {PCBM1632_P5_3} Cy5/Cy3 [PCBM1632|P3star]

source_name: PCBM1632_MSCs_passage 5


title: PCBM1632, Passage 3, Technical Replicate 3

description: {PCBM1632_P3_3} Cy5/Cy3 [PCBM1632|P3star]

source_name: PCBM1632_MSCs_passage 3


title: PCBM1632, Passage 3, Technical Replicate 1

description: {PCBM1632_P3_1} Cy5/Cy3 [PCBM1632|P3star]


title: PCBM1641, Passage 7, Technical Replicate 2

description: {PCBM1641_P7_2} Cy5/Cy3 [PCBM1641|P3star]

source_name: PCBM1641_MSCs_passage 7


title: PCBM1641, Passage 3, Technical Replicate 2

description: {PCBM1641_P3_2} Cy5/Cy3 [PCBM1641|P3star]

source_name: PCBM1641_MSCs_passage 3


title: PCBM1632, Passage 5, Technical Replicate 1

description: {PCBM1632_P5_1} Cy5/Cy3 [PCBM1632|P3star]

source_name: pooled reference (P3star)


title: PCBM1641, Passage 5, Technical Replicate 3

description: {PCBM1641_P5_3} Cy5/Cy3 [PCBM1641|P3star]

source_name: PCBM1641_MSCs_passage 5


title: PCBM1632, Passage 3, Technical Replicate 2

description: {PCBM1632_P3_2} Cy5/Cy3 [PCBM1632|P3star]


title: PCBM1641, Passage 7, Technical Replicate 1

description: {PCBM1641_P7_1} Cy5/Cy3 [PCBM1641|P3star]


title: PCBM1641, Passage 7, Technical Replicate 3

description: {PCBM1641_P7_3} Cy5/Cy3 [PCBM1641|P3star]


title: PCBM1632, Passage 5, Technical Replicate 2

description: {PCBM1632_P5_2} Cy5/Cy3 [PCBM1632|P3star]


title: PCBM1641, Passage 5, Technical Replicate 2

description: {PCBM1641_P5_2} Cy5/Cy3 [PCBM1641|P3star]


title: PCBM1641, Passage 3, Technical Replicate 3

description: {PCBM1641_P3_3} Cy5/Cy3 [PCBM1641|P3star]


title: PCBM1641, Passage 5, Technical Replicate 1

description: {PCBM1641_P5_1} Cy5/Cy3 [PCBM1641|P3star]


title: PCBM1632, Passage 7, Technical Replicate 1

description: {PCBM1632_P7_1} Cy5/Cy3 [PCBM1632|P3star]


title: Liver_LPS+IVIg_rep.4

description: in vivo

source_name: liver tissue, LPS, IVIg

value: male

value: LPS + IVIg


title: WT Dermis P5, steady-state, replicate 3

status: Public on Nov 04 2013

city: Marseille

first: Marc

last: DALOD

address: Parc scientifique de Luminy, Case 906

department: Dendritic cells and antiviral defense

country: France

institute: Center of Immunology of Marseille Luminy (CIML)

description: WT Dermal P5 from steady state B6 mice, FACS sorted as: live, CD11b+ CD24- CD64+ Ly6C- CCR2- MHCII+

hyb_protocol: Following fragmentation, 2 µg of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Gene 1.0 ST . GeneChips were washed and stained in the Affymetrix Fluidics Station 450 .

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

data_processing: The data were RMA normalized in R and Bioconductor, using the affy package.

label_protocol: Biotinylated double strand cDNA targets were prepared, from 5 ng to 20 ng of total RNA depending on the amount available per individual samples, using the NuGEN Ovation Pico WTA System V2 kit (Cat # 3302) and the NuGEN Encore Biotin Module kit (Cat # 4200) according to NuGEN recommendations.

extract_protocol: Total RNA was extracted from between 5x10E3 and 1x10E4 cells for each leukocyte subset with the Qiagen micro RNAeasy kit, according to the manufacturer protocol.

treatment_protocol: Inflammation was induced by application of 10µl of a 0.5% of DNFB diluted in acetone/olive oil (4:1). Ears and skin draining lymph nodes were harvested from untreated animals or 3 days post inflammation. Ear skin tissue was digested by dispase and collagenase 4 treatment, cells were enriched by percoll gradient and resuspended in PBS 2%FCS, EDTA 5mM before sorting by flow cytometry. Cutaneous lymph nodes were digested by collagenase 2 treatment, cells were enriched by optiprep gradient and resuspended in PBS 2%FCS, EDTA 5mM before sorting by flow cytometry.

value: WT

tag: tissue origin

value: Dermis

value: Macrophage

tag: cell phenotype

value: CD11b+ CD64+ Ly6C- CCR2- MHCII+

tag: inflammation

value: female

tag: age

value: 6 weeks-old


title: WT CLN CD11b+ migDC,  steady-state, replicate 2

description: WT migratory CD11b+ Dermal DC from steady state B6 mice, FACS sorted as: live, CD11c+ MHCIIhi CD11b+ CD24- Ly6C- CD64-

tag: genotype/variation

value: CLN

value: Migratory Dermal DC

value: CD11c+ MHCIIhi CD11b+ CD24- CD64-


title: PCBM1641, Passage 3, Technical Replicate 1

description: {PCBM1641_P3_1} Cy5/Cy3 [PCBM1641|P3star]

tag: donor id

value: human multipotent stromal cells (MSCs) derived from bone marrow


title: WT CLN CD11b+ migDC,  steady-state, replicate 1


title: WT Dermis CD11b+ DC, steady-state, replicate 2

description: WT CD11b+ Dermal DC from steady state B6 mice, FACS sorted as: live, CD11b+ CD24- Ly6C- CD64- MHCII+

value: Dermal DC

value: CD11b+ CD24- CD64- MHCII+


title: Col-0 biological rep2

status: Public on Jan 16 2014

city: Higashi-Hiroshima

first: Atsushi

last: Sakamoto

address: 1-3-1 Kagamiyama

department: Graduate School of Science

country: Japan

institute: Hiroshima University

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridized for 16 h at 45C on ATH1 microarrays (Affymetrix) in the Affymetrix GeneChip hybridization oven. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: Image data were normalized with MAS5 statistical algorithms using GeneSpring GX software ver. 11 (Agilent technology), and the normalized gene expression data were used to identify enrich gene ontology (GO) using GeneSpring GX ver. 11 (Agilent technology).

organism: Arabidopsis thaliana

source_name: Col-0, 2-week-old seedlings

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 nanograms of total RNA using GeneChip 3' IVT Express Kit (Affymetrix).

growth_protocol: Seeds were germinated and the seedlings were grown aseptically on solid 1/2MS media plus 1% sucrose at 22C under long-day (16 h light / 8 h darkness) photoperiodic conditions.

extract_protocol: Guanidinium thiocyanate extraction of total RNA followed by spin column purification was performed using NucleoSpin RNA II (Macherey-Nagel).

treatment_protocol: Aerial parts of the seedlings were harvested 2 weeks after germination.

value: wild type

tag: tissue

value: Aerial part of seedlings

tag: developmental stage

value: 2 weeks after germination

tag: genetic background


title: aln-1 biological rep1

source_name: aln-1, 2-week-old seedlings

value: aln-1 mutant


title: WT Dermis P5, steady-state, replicate 1


title: WT Dermis CD11b+ DC, steady-state, replicate 1


title: WT Dermis P4, steady-state, replicate 3

description: WT Dermal P4 from steady state B6 mice, FACS sorted as: live, CD11b+ CD24- CD64+ Ly6C- CCR2- MHCII-

value: CD11b+ CD64+ Ly6C- CCR2- MHCII-


title: WT Dermis P5, steady-state, replicate 2

value: WT


title: WT Dermis P3, steady-state, replicate 1

description: WT Dermal P3 from steady state B6 mice, FACS sorted as: live, CD11b+ CD24- CD64+ Ly6Clow CCR2+ MHCII+

value: Dermis

value: Monocyte

value: CD11b+ CD64+ Ly6Clow CCR2+ MHCII+


title: Col-0 biological rep1


title: WT Dermis P1, steady-state, replicate 2

description: WT Dermal P1 from steady state B6 mice, FACS sorted as: live, CD11b+ CD24-CD64low Ly6Chigh CCR2+ MHCII-

value: CD11b+ CD64low Ly6Chigh CCR2+ MHCII-

value: female


title: aln-1 biological rep2


title: WT Dermis P3, steady-state, replicate 3

value: 6 weeks-old


title: WT Dermis CD11b+ DC, steady-state, replicate 3


title: WT Dermis P3, steady-state, replicate 2


title: WT Dermis P2, steady-state, replicate 1

description: WT Dermal P2 from steady state B6 mice, FACS sorted as: live, CD11b+ CD24- CD64+ Ly6Chigh CCR2+ MHCII+

value: CD11b+ CD64+ Ly6Chigh CCR2+ MHCII+


title: WT Blood Ly6C monocyte, steady-state, replicate 1

description: WT Ly6Chi Blood monocyte from steady state B6 mice, FACS sorted as: live, Ly6Chi CD11b+

value: Blood

value: CD11b+ Ly6Chigh


title: WT CLN CD11b+ migDC,  steady-state, replicate 3

value: CLN

value: Migratory Dermal DC

value: CD11c+ MHCIIhi CD11b+ CD24- CD64-


title: WT Dermis P4, steady-state, replicate 2

value: Macrophage


title: WT Blood Ly6C monocyte, steady-state, replicate 2


title: WT Dermis P1, steady-state, replicate 1


title: WT Blood Ly6C monocyte, steady-state, replicate 3


title: WT Dermis P4, steady-state, replicate 1


title: WT Dermis P2, steady-state, replicate 3


title: WT Dermis P2, steady-state, replicate 2


title: WT Dermis P1, steady-state, replicate 3


title: ES_TRA(+)_2

status: Public on Jul 01 2013

city: Kyoto

first: Kazutoshi

last: Takahashi

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

description: Human embryonic stem cell line 2

hyb_protocol: Manufature's protocol

scan_protocol: Slides were scanned on the G2565CA Microarray Scanner System (Agilent).

data_processing: GeneSpring GX. Signals were normalized to percentile.

source_name: Sorted TRA-1-60 (+) cells Human embryonic stem cell line 2

label_protocol: Manufature's protocol

growth_protocol: DMEM containing 10% fetal bovine serum (by day 7) or Primate ESC medium (ReproCELL) supplemented with 4 ng/ml bFGF (from day 8 to 28) at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the miRNeasy Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Human somatic cells were transduced with OCT3/4, SOX2, KLF4 and c-MYC using retrovirus. From day 7 to 28, we collected TRA-1-60 positive cells as nascent reprogrammed cells.

value: Sorted TRA-1-60 (+) cells from Human embryonic stem cells


title: iPS_TRA(+)_2

source_name: Sorted TRA-1-60 (+) cells from Human induced pluripotent stem cell line 2

value: Sorted TRA-1-60 (+) cells Human induced pluripotent stem cell line


title: ES_TRA(+)_3

description: Human embryonic stem cell line 3

source_name: Sorted TRA-1-60 (+) cells Human embryonic stem cell line 3


title: skin-cd14-dc-4

status: Public on Jul 12 2012

first: Pavandip Singh

last: Wasan

address: 8A Biomedical Grove, #03-06, Immunos

department: Bioinformatics

description:
SK_X_CD14_DC
healthy donor, dendritic cell, CD14,Homo sapiens,skin,dendritic cell,CD14,total RNA,biotin

hyb_protocol: According to BeadChip array manufacturer's protocol.

data_processing: Array data were extracted at the probeset level with no background correction using Illumina's BeadStudio software. These raw data were normalised using the Loess method within the LUMI package in R/Bioconductor v2.13.1. Resulting p-values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate, and probesets with corrected p-value less than 0.05 were considered.

source_name: healthy donor, dendritic cell, CD14

label_protocol: Total RNA samples were amplified and biotinylated using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX).

growth_protocol: Monocytes and dendritic cell subsets were purified by FACS sorting from primary samples for transcription analysis.

extract_protocol: RNA was extracted from monocytes using an RNeasy Mini Kit (Qiagen) as per manufacturer's specifications. Extracted RNA was runned and quantified on a Bioanalyser (Agilent) for quality control and used subsequently in a microarray assay.

treatment_protocol: None.

value: skin

value: dendritic cell

tag: cell subtype

tag: disease state

value: healthy


title: skin-cd141-dc-2

description:
SK_X_CD141_DC
healthy donor, dendritic cell, CD141,Homo sapiens,skin,dendritic cell,CD141,total RNA,biotin

scan_protocol: According to BeadChip array manufacturer's protocol.

source_name: healthy donor, dendritic cell, CD141


title: skin-cd14-dc-3

description:
SK_IX_CD14_DC
healthy donor, dendritic cell, CD14,Homo sapiens,skin,dendritic cell,CD14,total RNA,biotin


title: ES_TRA(+)_1

description: Human embryonic stem cell line 1

source_name: Sorted TRA-1-60 (+) cells Human embryonic stem cell line 1


title: skin-cd1c-dc-3

description:
SK_VII_CD1c_DC
healthy donor, dendritic cell, CD1c,Homo sapiens,skin,dendritic cell,CD1c,total RNA,biotin

source_name: healthy donor, dendritic cell, CD1c


title: skin-cd1c-dc-2

description:
SK_X_CD1c_DC
healthy donor, dendritic cell, CD1c,Homo sapiens,skin,dendritic cell,CD1c,total RNA,biotin


title: skin-cd141-dc-4

description:
SK_VIII_CD141_DC
healthy donor, dendritic cell, CD141,Homo sapiens,skin,dendritic cell,CD141,total RNA,biotin


title: skin-cd1c_cd141-dc-1

description:
SK_IX_CD1c_CD141_DC
healthy donor, dendritic cell, CD1c_CD141,Homo sapiens,skin,dendritic cell,CD1c_CD141,total RNA,biotin


title: blood-cd1c-dc-5

description:
BD_CD1c_DC_IV
healthy donor, dendritic cell, CD1c,Homo sapiens,blood,dendritic cell,CD1c,total RNA,biotin

value: blood


title: blood-cd16-mono-2

description:
BD_CD16_Mono_V
healthy donor, monocyte, CD16,Homo sapiens,blood,monocyte,CD16,total RNA,biotin

source_name: healthy donor, monocyte, CD16

value: monocyte


title: skin-cd1c_cd141-dc-4

description:
SK_VII_CD1c_CD141_DC
healthy donor, dendritic cell, CD1c_CD141,Homo sapiens,skin,dendritic cell,CD1c_CD141,total RNA,biotin


title: skin-cd1c-dc-4

description:
SK_VIII_CD1c_DC
healthy donor, dendritic cell, CD1c,Homo sapiens,skin,dendritic cell,CD1c,total RNA,biotin


title: skin-cd141-dc-3

description:
SK_VII_CD141_DC
healthy donor, dendritic cell, CD141,Homo sapiens,skin,dendritic cell,CD141,total RNA,biotin


title: iPS_TRA(+)_1

source_name: Sorted TRA-1-60 (+) cells from Human induced pluripotent stem cell line 1


title: blood-cd16-mono-5

description:
BD_CD16_Mono_III
healthy donor, monocyte, CD16,Homo sapiens,blood,monocyte,CD16,total RNA,biotin


title: skin-cd1c_cd141-dc-3

description:
SK_VIII_CD1c_CD141_DC
healthy donor, dendritic cell, CD1c_CD141,Homo sapiens,skin,dendritic cell,CD1c_CD141,total RNA,biotin