title: MB-E105-Wt-Mm-cHiC-1

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

description:
processed data file: MB-E105-Wt-Mm-cHiC-merged.hicup.MAPQ30.KR_5kb.WashU.txt
processed data file: WT-MB_vs_WT-FL_diff_diagnorm_5kb_MAPQ30_KR.txt

data_processing:
Library strategy: HiC
Preprocessing and mapping of paired-end sequencing data, as well as filtering of mapped di-tags was performed with the HiCUP pipeline v.0.5.8 (Wingett et al. 2015) (Nofill: 1, no size selection, Format: Sanger). The pipeline used Bowtie2 v.2.2.6 (Langmead and Salzberg 2012) for mapping short reads to reference genome (NCBI37/mm9). Replicates were combined after mapping and filtering. Filtered di-tags were further processed with Juicebox command line tools to bin di-tags (5 and 10 kb bins) and to normalize the map by Knight-Ruiz (KR) matrix balancing (Lieberman-Aiden et al. 2009; Knight and Ruiz 2013; Durand et al. 2016)+ (Durand et al, Cell Systems 3(1), 2016.). For this, only reads with a MAPQ ≥30 were considered. The DNA-capturing step enriches genomic region chr13:53,400,001-57,300,000 on mm9 leading to three different regimes in the cHi-C map: (i) enriched versus enriched, (ii) enriched versus non-enriched, and (iii) non-enriched versus non- enriched. For binning and normalization only di-tags in regime (i) were considered. Therefore di-tags were filtered for the enriched region and mm9 coordinates were shifted by 53,400,000 bp. For Juicebox, a custom chromosome sizes file containing only the enriched region on chr13 (length 3900000 bp) was used. After binning and normalization, coordinates were shifted back to their original values. All maps were processed on the WT reference genome to work with the same genomic coordinates across all samples. To account for differences between maps in their distance dependent signal decay, maps were scaled pairwise by the sum of their sub-diagonals. Therefore, each sub-diagonal vector in one matrix is divided by its sum and multiplied by the average of the sums of both matrices. To normalize for sequencing depth, each map was additionally converted to reads per million (RPM). To avoid copy number biases, a region spanning all tested deletions (chr13:55,730,001-56,500,000) was not considered for the computation of scaling factors, for the diagonal normalization as well as for the RPM normalization. cHi-C maps of count values and subtraction maps were visualized as heat maps truncating all values above the 99-th percentile for visualization purposes. The percentile was determined from absolute values within the same region used for normalisation.
Differential interactions were determined from the pairwise subtraction of normalized maps. For diagonal and RPM normalization, as well as for the computation of P-values, individual regions spanning the corresponding deletions were excluded. To avoid artefacts from KR normalization due to low coverage, maps were analysed on 10 kb resolution and a single row with very low coverage (chr1:54,450,001-54,460,000) was excluded. To account for the distance dependence of the magnitude of differences, each difference value was subtracted by the mean and divided by the standard deviation of the corresponding sub-diagonal. For the computation of mean and variance per sub-diagonal, values above the 99.5-th percentile were not included. P-values for the z-transformed difference values were computed using a standard normal distribution and further corrected for multiple testing with false discovery rate (Benjamini and Hochberg 1995). In histograms the distributions of z-scores do not fit the normal distribution perfectly, but show as well a bell-like shape.
To obtain more fine-grained interaction profiles, we generated virtual Capture-C-like profiles based on the same filtered BAM files also used for the cHi-C maps and defined several virtual viewpoints of 10 kb size. A read pair was considered in the profile, when one mate mapped to the defined viewpoint region and the other one outside of it. Reads were counted per restriction fragment and binned further to a regular 1kb grid. In case a fragment spanned more than one bin, the count value was distributed proportionally to the overlaps. Afterwards, the profiles were smoothed by averaging over a sliding window of 5 bins. For coverage normalization the profiles were divided by sum of counts on chr13 and multiplied with 103. The region ± 5kb around the viewpoint as well as the regions in Tab. XX_DEL were mutually excluded from the computation of the scaling factor in pairwise comparisons. The profiles were generated with custom Java code using htsjdk v1.139 (https://samtools.github.io/htsjdk/).
Genome_build: NCBI37/mm9 (MGSCv37)
Supplementary_files_format_and_content: HL-E115-Inv1-Mm-cHiC-merged.hicup.MAPQ30.KR_5kb.WashU.txt: Pairwise interactions
Supplementary_files_format_and_content: MB-E105-Wt-Mm-cHiC-merged.hicup.MAPQ30.KR_5kb.WashU.txt: Pairwise interactions
Supplementary_files_format_and_content: Inv1-FL_vs_Inv1-HL_diff_diagnorm_5kb_MAPQ30_KR.txt: Subtracted interactions
Supplementary_files_format_and_content: WT-MB_vs_WT-FL_diff_diagnorm_5kb_MAPQ30_KR.txt: Subtracted interactions

source_name: Embryonic Midbrain

growth_protocol: Midbrains were micro-dissected from E10.5 mouse embryos.

extract_protocol:
3C-libraries were prepared from wild type midbrain tissues as described previously (Hagege et al. 2007). cHi-C experiments were performed as  duplicates. Per biological replicate, 8-10 midbrains (ca. 3 ×10^6 cells) were micro dissected in PBS at room temperature (RT). A single cell suspension was obtained by incubating the tissue in 500 µl Trypsin-EDTA 0.05 % (Gibco) at 37°C for 10 minutes shaking at 900 RPM. The cells were resuspended and homogenised using a 0.40 µm cell strainer (Falcon) and diluted in 10% FCS/PBS. Cells were fixed by adding 650 µl 37% formaldehyde (Sigma-Aldrich) with a final concentration of 2% and mixed for 10 minutes at room temperature. Fixation was quenched using 1.425 M glycine (Merck) on ice and immediately centrifuged at 260 g for 8 minutes. Supernatant was removed, the pellet resuspended in lysis buffer (final concentration of 10 mM Tris pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 M EGTA, and 1x Complete protease inhibitors (Roche)) and incubated on ice for 10 minutes. Removal of lysis buffer was done by centrifugation at 400 g for 5 minutes at 4°C, followed by removal of supernatant, snap-freezing and storage at -80°C. On the next day, the pellet was resuspended in 520 µl 1x DpnII buffer (Thermo Fisher Scientific), and incubated with 7.4 µl 20% SDS shaking at 900 RPM at 37°C for 1 hour. Next, 75 µl 20% x-100 Triton was added and left shaking at 900 RPM at 37°C for 1 hour. A 15 µl aliquot was taken as a control for undigested chromatin (stored at -20°C). The chromatin was digested using 40 µl 10 U/µl DpnII (Thermo Fisher Scientific) shaking at 900 RPM at 37°C for 6 hours. 40 µl of DpnII was added and samples were incubated overnight shaking at 900 RPM at 37°C. On the third day, 20 µl DpnII was added to the samples shaking 5 more hours at 900 RPM at 37°C. DpnII restriction enzyme was inactivated at 65°C for 25 minutes. A 50 µl aliquot was taken to test digestion efficiency (stored at -20°C). Next, the digested chromatin was diluted and re-ligated in 5.1 ml H2O, 700 µl 10x ligation buffer (Fermentas), 5 µl 30 U/µl T4-ligase (Fermentas), incubated at 16°C for 4 hours and shake manually 3 times. The ligated samples were incubated further 30 minutes at RT. The chimeric chromatin products and test aliquots were de-crosslinked o.n. by adding 30 µl and 5 µl Proteinase K, respectively, and incubated at 65°C overnight. On the fourth day, 30 µl or 5 µl of 10 mg/ml RNase was added to the samples and aliquots, respectively, and incubated for 45 minutes at 37°C. Next, chromatin was precipitated by adding 1 volume phenol-chloroform to the samples and aliquots, vigorously shaking them, followed by centrifugation at 4000 RPM at RT for 15 minutes. The upper phase containing the chromatin was transferred to a new tube. To the aliquots, 100% ethanol was added and the samples were frozen for 30 minutes, centrifuged at 5000 RPM for 45 minutes at 4°C, washed with 70% ethanol and resuspended in 20 µl 10 mM Tris-HCl pH 7.5. To the samples, 7 ml H2O, 1 ml 3M NaAc pH 5.6 and 35 ml 100% ethanol was added. The samples were frozen at -20°C for 3 hours. The precipitated chromatin was isolated by centrifugation at 5000 RPM for 45 minutes at 4°C. The chromatin pellet was washed with 70% ethanol, and further centrifuged at 5000 RPM for 15 minutes at 4°C. Finally, the 3C-library chromatin pellet was dried at RT and resuspended in 10 mM Tris-HCl pH 7.5. To check the 3C-library, 600ng was loaded on a 1% gel together with the undigested and digested aliquots.
The 3C-library was then sheared using a Covaris sonicator (duty cycle: 10%, intensity: 5, cycles per burst: 200, time: 6 cycles of 60 s each, set mode: frequency sweeping, temperature: 4 to 7 °C). Adaptors were added to the sheared DNA and amplified according to Agilent instructions for Illumina sequencing. The library was hybridized to the custom-designed sure-select beads and indexed for sequencing (50 to 100 bp paired-end) following Agilent instructions.

value: Midbrain

tag: developmental stage

tag: genotype

value: wild type


title: MB-E105-Wt-Mm-cHiC-2

status: Public on Oct 01 2018

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: strain

tag: tissue


title: SH_TS_BC_C3

city: Chapel Hill

first: Zhiyuan

last: Hu

state: NC

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

country: USA

institute: University of North Carolina at Chapel Hill

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC_C3

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling and sequencing data were demultiplexed based on dual indexes.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, demultiplexed and then only read 1 in each sample were mapped to known Targeted regions of human genomes for counts using R package "ShortRead".
Raw counts of all samples were imported to edgeR for normalization by the size of the transcripts and by the size of the library and then calculation of CPM per sample as a gene expression matrix
Gene expression CPM dataset were median-centered and column-standardized using DWD
DWD dataset were used for iRDM data analysis including subtype classification, iRDM risks,  immunity scores, and proliferation scores.
Genome_build: hg19
Supplementary_files_format_and_content: csv files were generated including raw counts and normalized gene expression data

molecule: total RNA

organism: Homo sapiens

source_name: Breast cancer

extract_protocol:
FFPE tissues total RNA extraction was routinely performed using Roche FFPE RNA extraction kit according to the manufacturer’s protocol.
The Illumina TruSeq Targeted RNA expression kit was used to build libraries of the targeted 72-genes. To synthesize cDNA, 200 to 800 nanograms of purified FFPE RNA in a total volume of 3 µl was mixed with 4.0 µl RCS1, 2.0 µl ProtoScrip II Reverse Transcriptase, 1.0 µl 10mM DTT at 42OC for 30 min and 94OC for 10 min. The cDNA was hybridized with custom oligo pools in a thermal cycler programed to gradually decrease temperature from 70 OC to 30 OC in 30 minutes. The RNA/Oligo hybrid products were washed, extended and ligated. The ligated DNA was amplified by DNA polymerase on the thermal cycler with 35 PCR cycles of 98 OC for 30 seconds, 62 OC for 30 seconds and 72 OC for 60 seconds. The PCR products were purified with AMPure XP beads and eluted in 15 µl of buffer, measured using Agilent Bioanalyzer2100 and DNA1000 chips, pooled with equal amounts of DNA from each sample’s library, and finally diluted to 4 nM, denatured, and loaded to Nextseq500 according to the manufacturer’s protocol.
Libraries were multiplexed and sequenced on Illumina Nextseq500  to generate 75bp single read R1.

tag: gender

value: female

tag: dmfs time

tag: dmfs event

tag: sample type

value: Solid tumor

tag: irdm subtype

tag: pam50 subtype

value: Basal

tag: immunity group

value: istrong

tag: proliferation group

value: low

tag: er status rna

value: ER-

tag: pr status rna

value: PR-


title: SH_TS_BC010_1

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC010_1

value: Immuno

value: ER+

value: PR+


title: HL-E115-Inv1-Mm-cHiC-1

description:
processed data file: HL-E115-Inv1-Mm-cHiC-rep1.hicup.MAPQ30.KR_5kb.WashU.txt
processed data file: HL-E115-Inv1-Mm-cHiC-merged.hicup.MAPQ30.KR_5kb.WashU.txt
processed data file: Inv1-FL_vs_Inv1-HL_diff_diagnorm_5kb_MAPQ30_KR.txt

data_processing:
Library strategy: HiC
Preprocessing and mapping of paired-end sequencing data, as well as filtering of mapped di-tags was performed with the HiCUP pipeline v.0.5.8 (Wingett et al. 2015) (Nofill: 1, no size selection, Format: Sanger). The pipeline used Bowtie2 v.2.2.6 (Langmead and Salzberg 2012) for mapping short reads to reference genome (NCBI37/mm9). Replicates were combined after mapping and filtering. Filtered di-tags were further processed with Juicebox command line tools to bin di-tags (5 and 10 kb bins) and to normalize the map by Knight-Ruiz (KR) matrix balancing (Lieberman-Aiden et al. 2009; Knight and Ruiz 2013; Durand et al. 2016)+ (Durand et al, Cell Systems 3(1), 2016.). For this, only reads with a MAPQ ≥30 were considered. The DNA-capturing step enriches genomic region chr13:53,400,001-57,300,000 on mm9 leading to three different regimes in the cHi-C map: (i) enriched versus enriched, (ii) enriched versus non-enriched, and (iii) non-enriched versus non- enriched. For binning and normalization only di-tags in regime (i) were considered. Therefore di-tags were filtered for the enriched region and mm9 coordinates were shifted by 53,400,000 bp. For Juicebox, a custom chromosome sizes file containing only the enriched region on chr13 (length 3900000 bp) was used. After binning and normalization, coordinates were shifted back to their original values. All maps were processed on the WT reference genome to work with the same genomic coordinates across all samples. To account for differences between maps in their distance dependent signal decay, maps were scaled pairwise by the sum of their sub-diagonals. Therefore, each sub-diagonal vector in one matrix is divided by its sum and multiplied by the average of the sums of both matrices. To normalize for sequencing depth, each map was additionally converted to reads per million (RPM). To avoid copy number biases, a region spanning all tested deletions (chr13:55,730,001-56,500,000) was not considered for the computation of scaling factors, for the diagonal normalization as well as for the RPM normalization. cHi-C maps of count values and subtraction maps were visualized as heat maps truncating all values above the 99-th percentile for visualization purposes. The percentile was determined from absolute values within the same region used for normalisation.
Differential interactions were determined from the pairwise subtraction of normalized maps. For diagonal and RPM normalization, as well as for the computation of P-values, individual regions spanning the corresponding deletions were excluded. To avoid artefacts from KR normalization due to low coverage, maps were analysed on 10 kb resolution and a single row with very low coverage (chr1:54,450,001-54,460,000) was excluded. To account for the distance dependence of the magnitude of differences, each difference value was subtracted by the mean and divided by the standard deviation of the corresponding sub-diagonal. For the computation of mean and variance per sub-diagonal, values above the 99.5-th percentile were not included. P-values for the z-transformed difference values were computed using a standard normal distribution and further corrected for multiple testing with false discovery rate (Benjamini and Hochberg 1995). In histograms the distributions of z-scores do not fit the normal distribution perfectly, but show as well a bell-like shape.
To obtain more fine-grained interaction profiles, we generated virtual Capture-C-like profiles based on the same filtered BAM files also used for the cHi-C maps and defined several virtual viewpoints of 10 kb size. A read pair was considered in the profile, when one mate mapped to the defined viewpoint region and the other one outside of it. Reads were counted per restriction fragment and binned further to a regular 1kb grid. In case a fragment spanned more than one bin, the count value was distributed proportionally to the overlaps. Afterwards, the profiles were smoothed by averaging over a sliding window of 5 bins. For coverage normalization the profiles were divided by sum of counts on chr13 and multiplied with 103. The region ± 5kb around the viewpoint as well as the regions in Tab. XX_DEL were mutually excluded from the computation of the scaling factor in pairwise comparisons. The profiles were generated with custom Java code using htsjdk v1.139 (https://samtools.github.io/htsjdk/).
Genome_build: NCBI37/mm9 (MGSCv37)
Supplementary_files_format_and_content: HL-E115-Inv1-Mm-cHiC-rep1.hicup.MAPQ30.KR_5kb.WashU.txt
Supplementary_files_format_and_content: HL-E115-Inv1-Mm-cHiC-merged.hicup.MAPQ30.KR_5kb.WashU.txt: Pairwise interactions
Supplementary_files_format_and_content: MB-E105-Wt-Mm-cHiC-merged.hicup.MAPQ30.KR_5kb.WashU.txt: Pairwise interactions
Supplementary_files_format_and_content: Inv1-FL_vs_Inv1-HL_diff_diagnorm_5kb_MAPQ30_KR.txt: Subtracted interactions
Supplementary_files_format_and_content: WT-MB_vs_WT-FL_diff_diagnorm_5kb_MAPQ30_KR.txt: Subtracted interactions

source_name: Embryonic Limb Bud

growth_protocol: Forelimb and hindlimb buds were micro-dissected from E11.5 mouse embryos.

extract_protocol:
3C-libraries were prepared from homozygous E11.5 forelimb and hindlimb buds as described previously (Hagege et al. 2007). cHi-C experiments were performed as quadruplets (WT) or duplicates (mutants). Per biological replicate, 5-6 pairs of limb buds (ca. 3 ×10^6 cells) were micro dissected in PBS at room temperature (RT). A single cell suspension was obtained by incubating the tissue in 500 µl Trypsin-EDTA 0.05 % (Gibco) at 37°C for 10 minutes shaking at 900 RPM. The cells were resuspended and homogenised using a 0.40 µm cell strainer (Falcon) and diluted in 10% FCS/PBS. Cells were fixed by adding 650 µl 37% formaldehyde (Sigma-Aldrich) with a final concentration of 2% and mixed for 10 minutes at room temperature. Fixation was quenched using 1.425 M glycine (Merck) on ice and immediately centrifuged at 260 g for 8 minutes. Supernatant was removed, the pellet resuspended in lysis buffer (final concentration of 10 mM Tris pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 M EGTA, and 1x Complete protease inhibitors (Roche)) and incubated on ice for 10 minutes. Removal of lysis buffer was done by centrifugation at 400 g for 5 minutes at 4°C, followed by removal of supernatant, snap-freezing and storage at -80°C. On the next day, the pellet was resuspended in 520 µl 1x DpnII buffer (Thermo Fisher Scientific), and incubated with 7.4 µl 20% SDS shaking at 900 RPM at 37°C for 1 hour. Next, 75 µl 20% x-100 Triton was added and left shaking at 900 RPM at 37°C for 1 hour. A 15 µl aliquot was taken as a control for undigested chromatin (stored at -20°C). The chromatin was digested using 40 µl 10 U/µl DpnII (Thermo Fisher Scientific) shaking at 900 RPM at 37°C for 6 hours. 40 µl of DpnII was added and samples were incubated overnight shaking at 900 RPM at 37°C. On the third day, 20 µl DpnII was added to the samples shaking 5 more hours at 900 RPM at 37°C. DpnII restriction enzyme was inactivated at 65°C for 25 minutes. A 50 µl aliquot was taken to test digestion efficiency (stored at -20°C). Next, the digested chromatin was diluted and re-ligated in 5.1 ml H2O, 700 µl 10x ligation buffer (Fermentas), 5 µl 30 U/µl T4-ligase (Fermentas), incubated at 16°C for 4 hours and shake manually 3 times. The ligated samples were incubated further 30 minutes at RT. The chimeric chromatin products and test aliquots were de-crosslinked o.n. by adding 30 µl and 5 µl Proteinase K, respectively, and incubated at 65°C overnight. On the fourth day, 30 µl or 5 µl of 10 mg/ml RNase was added to the samples and aliquots, respectively, and incubated for 45 minutes at 37°C. Next, chromatin was precipitated by adding 1 volume phenol-chloroform to the samples and aliquots, vigorously shaking them, followed by centrifugation at 4000 RPM at RT for 15 minutes. The upper phase containing the chromatin was transferred to a new tube. To the aliquots, 100% ethanol was added and the samples were frozen for 30 minutes, centrifuged at 5000 RPM for 45 minutes at 4°C, washed with 70% ethanol and resuspended in 20 µl 10 mM Tris-HCl pH 7.5. To the samples, 7 ml H2O, 1 ml 3M NaAc pH 5.6 and 35 ml 100% ethanol was added. The samples were frozen at -20°C for 3 hours. The precipitated chromatin was isolated by centrifugation at 5000 RPM for 45 minutes at 4°C. The chromatin pellet was washed with 70% ethanol, and further centrifuged at 5000 RPM for 15 minutes at 4°C. Finally, the 3C-library chromatin pellet was dried at RT and resuspended in 10 mM Tris-HCl pH 7.5. To check the 3C-library, 600ng was loaded on a 1% gel together with the undigested and digested aliquots.
The 3C-library was then sheared using a Covaris sonicator (duty cycle: 10%, intensity: 5, cycles per burst: 200, time: 6 cycles of 60 s each, set mode: frequency sweeping, temperature: 4 to 7 °C). Adaptors were added to the sheared DNA and amplified according to Agilent instructions for Illumina sequencing. The library was hybridized to the custom-designed sure-select beads and indexed for sequencing (50 to 100 bp paired-end) following Agilent instructions.

value: Hindlimb


title: SH_TS_BC_C11

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC_C11

value: Mixed

value: high


title: SH_TS_BC01

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC01

value: LumA


title: SH_TS_BC_C1

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC_C1

value: iweak


title: U2OS SMF R1

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

data_processing:
Adapters trimmed with Sythe and Sickle (RNA-seq)
Alignment was done with Tophat2 v. 2.1.0 (RNA-seq) or BWA v. 0.7.5a (ChIP-exo) with default options
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v. 1.3.1
Mapped reads were de-duplicated with Picard (ChIP-exo)
Peak calling was performed with MACS v. 1.3.7.1 (ChIP-exo)
RNA-seq differential expression was performed with HTseq and DESeq2.
Bigwig files were generated with the bedGraphToBigWig script
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

source_name: RNA-seq_U2OS Flag-SETMAR cell line

growth_protocol: U2OS cells were maintained in DMEM with 10% fetal bovine serum and antibiotics.

extract_protocol:
RNA extracted with the High Pure RNA isolation kit (Roche Applied Science), following manufacturer's instructions
Libraries were prepared using Illumina's TruSeq RNA Sample Preparation V2 according to manufacturer's instructions

tag: cell line

tag: chip antibody


title: U2OS SMF R2


title: U2OS Control R1

source_name: RNA-seq_U2OS control line


title: SH_TS_BC103

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC103


title: Co_As_rep2

city: Buffalo

first: Hai

last: Wang

state: NY

address: Elm and Carlton Streets, MRC 328

department: Molecular and Cellular Biology

institute: Roswell Park Cancer Institute

data_processing:
Illumina Nextseq 500 automatically used bcl2fastq2 (version 2.17) for basecalling. FASTQ files were downloaded from BaseSpace.
RNA-seq NGS reads derived from cocultures containing a mixture of human and mouse reads were separated using Xenome (version 1.0.1).
RNA-seq NGS reads were mapped using STAR RNA-seq aligner (version 2.4.1d).
RSEM (version 1.2.28) was used to quantify gene and isoform expression.
DEseq2 R package is used to normalize the gene/isoform expression matrix.
Genome_build: GRCh38.83 and GRCm38.83
Supplementary_files_format_and_content: CoAs.RData (includes RSEM read counts and DESeq2 normalized gene expression values) and CoAs.csv (includes only the DESeq2 normalized gene expression values).

organism:
Homo sapiens
Mus musculus

source_name: MCF7-MSC organoids

growth_protocol: 2E5/well MCF-7 cells are cultured in DMEM with 10% FBS and then cocultured with 2E5/well mouse MSC in serum-free DMEM/F12 media in 6-well low attachment plates, treated with 5uM Arsenic trioxide or PBS (Vehicle) for <48h

extract_protocol:
After centrifuge, total RNA were extracted by Direct-zol RNA miniprep kit. . The first and second strand cDNA were prepared by SuperScript III First-Strand Synthesis System and NEBNext mRNA Second Strand Synthesis Module from at least 200ng total RNA for each sample. Illumina Nextera XT DNA Sample Prep Kit  was used with 1 ng of dsDNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using nextera Illumina protocols

value: human breast cancer cell line MCF-7

tag: cell type

value: mouse MSC cells

tag: growth protocol

value: MCF-7 cells cocultured with MSCs in 3D culture

tag: passage

tag: reporter gene

value: Firefly Luciferase (MCF-7)

tag: treatment

value: ATO


title: Pax5 preB input control

city: La Jolla

first: Salvatore

last: Loguercio

state: California

address: 10550 North Torrey Pines Rd

department: MB

institute: TSRI

data_processing:
Duplicated reads were removed before mapping.
Experimental and input control fastaq tags were aligned to the mouse reference genome (mm9) using Bowtie 0.12.9. Alignment parameters used:-a -v 2 -m 3 --best --strata
All reads mapping with their best alignment score at more than 3 sites in the genome were discarded.
Confident peaks were called using MACS (version 1.4.2), with FDR<= 1% and the default p value (1E-5).
Genome_build: mm9
Supplementary_files_format_and_content: file format: bed; content: confident peaks (as called by MACS).

source_name: RAG-/-µ+ pre-B cells

growth_protocol: Bone marrow and spleen cells were isolated from 6 to 14 wk old C57BL/6 mice, including both males and females.

extract_protocol:
For bone marrow subset purification we used B6 RAG-/- µ+ mice bearing a rearranged IgM transgene were used to obtain pre-B cells.
For each sample 1 - 10 ng of IP material or input control sample was prepared into sequencing libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina following manufacturers protocol. Samples were amplified using 18 cycles of PCR and then size selected on 2% EX agarose gels (Thermo Fisher) and bands cut at 300bps (+ 25 bps) and cleaned up using DNA Clean & Concentrator-25  (Zymo Research). The prepared libraries were loaded onto an Illumina HiSeq2000 for single-end base reads with 7 bases of the index read. Data was processed to generate Fastq files using CASAVA 1.8 and demultiplexed based on index sequences.

tag: strain

tag: tissue

value: Pre-B cells


title: U2OS SMF-N210A R1

source_name: RNA-seq_U2OS Flag-SETMAR N210A cell line


title: SH_TS_BC_C15

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC_C15

tag: gender

value: female

tag: dmfs time

tag: dmfs event

value: Solid tumor

value: istrong


title: human_liver_adult_male4

city: Cambridge

first: Francesco Nicola

last: Carelli

address: Henry Wellcome Building of Cancer and Developmental Biology,  Tennis Court Road

institute: University of Cambridge

description: sample id: 5563sTS

data_processing:
RNA-seq reads were aligned to the assembled genomes of their corresponding species using STAR (version 2.2.1) using the 2-pass mapping mode and standard settings.
Aligned reads from all replicates of each organ were used to reconstruct transcripts through a genome-guided de novo transcriptome assembly using StringTie (version 1.3.4d) with the following parameters: -j 5 –g 50.
Assembled transcripts from each organ were then merged using Cuffmerge to define a unique set of transcripts. Expression levels (measured in FPKM) of the assembled transcripts were calculated with Cuffnorm (version 2.2.1) with --library-norm-method classic-fpkm.
Genome_build: human: hg38; macaque: rheMac8; marmoset: calJac3; mouse: mm10; rat: rn6; rabbit: oryCun2
Supplementary_files_format_and_content: *sample_name*.Signal.UniqueMultiple.str*N*.out.bw: STAR-generated bigWig tracks of the RPM-normalized read coverage from each sample. Files represent reads mapped on the forward (N=1) or reverse (N=2) strand.

molecule: polyA RNA

source_name: Adult liver

extract_protocol:
QIAGEN RNeasy Kit
Single-end strand-specific RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA LT kit according to manufacturer instructions. Libraries were sequenced using the Illumina HiSeq 2500.

value: liver

tag: Sex

value: male

tag: developmenta stage

value: adult


title: H3K4Me3 pre-B ChIP-seq


title: Pax5 preB ChIP-seq


title: H3K27Ac pre-B input control


title: H3K27Ac pre-B ChIP-seq


title: Co_veh_rep3

value: control


title: Co_veh_rep1


title: human_kidney_adult_male1

description: sample id: 5821sTS

source_name: Adult kidney

value: kidney


title: H3K4Me3 pre-B input control


title: Co_As_rep3


title: human_heart_adult_male2

description: sample id: 5822sTS

source_name: Adult heart

value: heart


title: Co_veh_rep2


title: human_heart_adult_female1

description: sample id: 5828sTS


title: Co_As_rep1


title: human_heart_adult_male1

description: sample id: 5839sTS


title: human_heart_adult_female2

description: sample id: 5843sTS


title: U2OS Control R2


title: U2OS SMF-N210A R2


title: human_brain_adult_male2

description: sample id: 5574sTS

source_name: Adult brain

value: brain


title: human_brain_adult_male3

description: sample id: 5896sTS


title: human_brain_adult_male4

description: sample id: 5895sTS


title: HL-E115-Inv1-Mm-cHiC-2

description:
processed data file: HL-E115-Inv1-Mm-cHiC-merged.hicup.MAPQ30.KR_5kb.WashU.txt
processed data file: Inv1-FL_vs_Inv1-HL_diff_diagnorm_5kb_MAPQ30_KR.txt

value: Hindlimb

tag: developmental stage

tag: genotype


title: Adult Non-IBD 31

first: Terry

last: Furey

address: 5022 Genetic Medicine Building

department: Department of Genetics

institute: The University of North Carolina at Chapel Hill

description:
31
Small RNA
processed data file: adult_Colon.txt

data_processing:
miRquant 2.0 used for 3' adapter trimming (Cutadapt), two tier read alignment (Bowtie and SHRiMP), and miRNA annotation (miRBase, GtRNAdb, and GENCODE).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Data matrix of raw reads normalised to total microRNA reads; Reads Per Million Mapped to miRs Count Matrix.

source_name: Ascending colon mucosal biopsy

growth_protocol: CD patients from the adult IBD Center at University of North Carolina were included in this study.

extract_protocol:
Total RNA was isolated from flash-frozen tissue samples (mucosal not whole tissue) from surgical resections using the Qiagen RNeasy kit following the manufacturer’s protocol.
Small RNA libraries were generated using Illumina TruSeq Small RNA Sample Preparation Kit (San Diego, CA).
Single-end (50 bp) sequencing was performed on the Illumina HiSeq 2500 platform.

tag: age

value: Adult

value: Ascending colon mucosa

tag: phenotypic status

value: Non-IBD


title: Adult Non-IBD 39

description:
39
Small RNA
processed data file: adult_Colon.txt


title: human_kidney_adult_female1

description: sample id: 5844sTS


title: human_brain_adult_male1

description: sample id: 5543sTS


title: Adult Non-IBD 30

description:
30
Small RNA
processed data file: adult_Colon.txt


title: Adult Non-IBD 48

description:
48
Small RNA
processed data file: adult_Colon.txt


title: Adult CD 424

description:
424
Small RNA
processed data file: adult_Colon.txt

value: Crohn's disease

tag: cd group

value: Ileum-like CD


title: Adult Non-IBD 50

description:
50
Small RNA
processed data file: adult_Colon.txt


title: Adult Non-IBD 27

description:
27
Small RNA
processed data file: adult_Colon.txt


title: human_liver_adult_male2

description: sample id: 5558sTS


title: Adult Non-IBD 23

description:
23
Small RNA
processed data file: adult_Colon.txt


title: Adult Non-IBD 49

description:
49
Small RNA
processed data file: adult_Colon.txt


title: Adult Non-IBD 32

description:
32
Small RNA
processed data file: adult_Colon.txt


title: Adult Non-IBD 36

description:
36
Small RNA
processed data file: adult_Colon.txt


title: Adult CD 64

description:
64
Small RNA
processed data file: adult_Colon.txt


title: Adult CD 29

description:
29
Small RNA
processed data file: adult_Colon.txt


title: Adult CD 21

description:
21
Small RNA
processed data file: adult_Colon.txt


title: Adult CD 25

description:
25
Small RNA
processed data file: adult_Colon.txt


title: Adult Non-IBD 43

description:
43
Small RNA
processed data file: adult_Colon.txt


title: Adult Non-IBD 22

description:
22
Small RNA
processed data file: adult_Colon.txt


title: Adult CD 20

description:
20
Small RNA
processed data file: adult_Colon.txt


title: human_liver_adult_male3

description: sample id: 5551sTS


title: Adult CD 450

description:
450
Small RNA
processed data file: adult_Colon.txt


title: Adult CD 422

description:
422
Small RNA
processed data file: adult_Colon.txt


title: Adult CD 63

description:
63
Small RNA
processed data file: adult_Colon.txt

value: Colon-like CD


title: Adult CD 413

description:
413
Small RNA
processed data file: adult_Colon.txt


title: Adult CD 62

description:
62
Small RNA
processed data file: adult_Colon.txt


title: MCF-7 KLHDC7B overexpression

type: genomic

city: Ilsan

first: Juyeon

last: Ham

address: 32, Dongguk-ro

country: South Korea

institute: Dongguk University

description: SAMPLE 2

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina HumanHT-12   Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader  Confocal  Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

label: biotin

source_name: RNA from MCF-7 transfected KLHDC7B ORF vector

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep   RNA Amplification Kit (Ambion, Austin,TX).

growth_protocol: RPMI1640 medium supplemented with 10% FBS and 1% Penicillin-Streptomycin at 37℃ containing 5% CO2

extract_protocol: RNA was extracted and purified from MCF-10A using ZR Dyet DNA/RNA kit (Zymo research) according to standard instructions

treatment_protocol: transfection using lipofectamin 3000

tag: cell line

tag: cell type

value: breast cancer

value: female

value: adenocarcinoma


title: MCF-7 LOC100128098 siRNA knockdown

description: SAMPLE 2

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufactur

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

source_name: RNA from MCF-7 transfected LOC100128098 siRNA

label_protocol:
MCF-7 was grown in RPMI1640 medium with 10% FBS and 2% penicillin/streptomycin.
Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

extract_protocol: RNA was extracted and purified from MCF-7 using ZR Dyet DNA/RNA kit (Zymo research) according to standard instructions

treatment_protocol: LOLOC100128098  siRNA and siRNA Negative Control are transfected into MCF-7 using Lipofectamine RNAiMAX(Invitrogen, Carlsbad, CA, USA)


title: Adult CD 51

description:
51
Small RNA
processed data file: adult_Colon.txt


title: MCF-7 KLHDC7B overexpression control

description: SAMPLE 1

source_name: RNA from MCR-7 transfected negative control vector


title: MCF-7 KLHDC7B siRNA knockdown

description: SAMPLE 2

source_name: RNA from MCF-7 transfected KLHDC7B's siRNA

treatment_protocol: transfection using lipofectamin and siRNA


title: MCF-7 LOC100128098 siRNA control

description: SAMPLE 1

source_name: RNA from MCF-7 transfected LOC100128098 siRNA Negative Control


title: MCF-7 KLHDC7B siRNA knockdown control

description: SAMPLE 1

source_name: RNA from MCR-7 transfected siRNA Negative control


title: PC3 cells, transfected with DAB2IP siRNA (siDAB2IP), replica 1

type: RNA

city: Baltimore

first: Luigi

last: Marchionni

state: MD

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

institute: Johns Hopkins University

description: Hybridization for sample siDAB2IP_rep1

hyb_protocol: cRNA was hybridized  using standard Illumina protocols onto each array (three replicates for each condition) and then labeled with Cy3-streptavidin (Amersham Biosciences).

scan_protocol: After hybridization, all slides were washed using standard Illumina protocols and then scanned using a BeadStation 500 system (Illumina).

data_processing: The probe intensities were calculated using GenomeStudio Data Analysis Software’s Gene Expression Module (GSGX) Version 1.9 (Illumina). Further data processing was performed in the R computing environment (R-3.2.2) using BioConductor packages. Probe level expression summaries were quantile-normalized across samples without background correction.

label_protocol: Total RNA (2ug) was reverse transcribed and amplified according to standard protocols and in vitro transcription was then carried out to generate cRNA.

extract_protocol: Total RNA was extracted with QIAzol (Qiagen) following manufacturer’s instructions.


title: PC3 cells, transfected with miR-149-3p mimic (miR149), replica 1

description: Hybridization for sample miR149_rep1


title: Adult CD 54

description:
54
Small RNA
processed data file: adult_Colon.txt


title: Adult CD 429

description:
429
Small RNA
processed data file: adult_Colon.txt


title: PC3 cells, transfected with miR-149-3p mimic (miR149), replica 2

description: Hybridization for sample miR149_rep2


title: Adult CD 420

description:
420
Small RNA
processed data file: adult_Colon.txt


title: PC3 cells, control, replica 2

description: Hybridization for sample siC_rep2

source_name: PC3 cells, control, replica 2"

value: Control


title: PC3 cells, transfected with DAB2IP siRNA (siDAB2IP), replica 2

description: Hybridization for sample siDAB2IP_rep2


title: Adult CD 431

description:
431
Small RNA
processed data file: adult_Colon.txt


title: PC3 cells, control, replica 1

description: Hybridization for sample siC_rep1

source_name: PC3 cells, control


title: D_mk26

city: New Brunswick

first: SAURABH

middle: V

last: LADDHA

state: NEW JERSEY

address: 195 Little Albany Street

department: Center for Systems and Computational Biology

institute: Rutgers Cancer Institute of New Jersey

description:
Gene Expression Data from Human PanNETs
D_mk26

hyb_protocol: Hybridization were done using the standard Affymetrix protocol

scan_protocol: Scanning of all samples were done using GeneArray Scanner (Affymetrix)

data_processing: The raw affymetrix CEL files were loaded in R and normalized using GCRMA method and collapsed all probes to respective genes using CollapseRow

source_name: DAXX mutated PanNET

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

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

value: Pancreatic neuroendocrine tumors (PanNETs)

value: DAXX

tag: pannet subtype

value: A-D-M Mutant PanNETs


title: DM1_ls7

description:
Gene Expression Data from Human PanNETs
DM1_ls7

source_name: DAXX and MEN1 mutated PanNET

value: DAXX and MEN1


title: A_mk4

description:
Gene Expression Data from Human PanNETs
A_mk4

source_name: ATRX mutated PanNET

value: ATRX


title: DM1_mk45

description:
Gene Expression Data from Human PanNETs
DM1_mk45


title: DM1_mk44

description:
Gene Expression Data from Human PanNETs
DM1_mk44


title: A_mk12

description:
Gene Expression Data from Human PanNETs
A_mk12


title: DM1_mk38

description:
Gene Expression Data from Human PanNETs
DM1_mk38


title: A_mk11

description:
Gene Expression Data from Human PanNETs
A_mk11


title: Adult CD 407

description:
407
Small RNA
processed data file: adult_Colon.txt


title: Adult CD 405

description:
405
Small RNA
processed data file: adult_Colon.txt


title: DM1_mk52

description:
Gene Expression Data from Human PanNETs
DM1_mk52


title: DM1_mk17

description:
Gene Expression Data from Human PanNETs
DM1_mk17


title: D_mk34

description:
Gene Expression Data from Human PanNETs
D_mk34


title: DM1_ls5

description:
Gene Expression Data from Human PanNETs
DM1_ls5


title: AM1_mk36

description:
Gene Expression Data from Human PanNETs
AM1_mk36

source_name: ATRX and MEN1 mutated PanNET

value: ATRX and MEN1


title: WT_mk46

description:
Gene Expression Data from Human PanNETs
WT_mk46

source_name: WT PanNET for ATRX / DAXX and MEN1

value: WT for ATRX/DAXX/MEN

value: A-D-M WT PanNETs


title: WT_mk8

description:
Gene Expression Data from Human PanNETs
WT_mk8


title: WT_mk49

description:
Gene Expression Data from Human PanNETs
WT_mk49


title: WT_mk19

description:
Gene Expression Data from Human PanNETs
WT_mk19


title: WT_mk39

description:
Gene Expression Data from Human PanNETs
WT_mk39


title: WT_mk15

description:
Gene Expression Data from Human PanNETs
WT_mk15


title: WT_mk50

description:
Gene Expression Data from Human PanNETs
WT_mk50


title: WT_mk41

description:
Gene Expression Data from Human PanNETs
WT_mk41


title: AM1_mk53

description:
Gene Expression Data from Human PanNETs
AM1_mk53


title: WT_mk16

description:
Gene Expression Data from Human PanNETs
WT_mk16


title: WT_mk27

description:
Gene Expression Data from Human PanNETs
WT_mk27


title: WT_mk29

description:
Gene Expression Data from Human PanNETs
WT_mk29


title: WT_ls65

description:
Gene Expression Data from Human PanNETs
WT_ls65


title: WT_mk21

description:
Gene Expression Data from Human PanNETs
WT_mk21


title: tid134286_mTORMouse87_LP_M_Liver

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

hyb_protocol: All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.

scan_protocol: Scanned images were subjected to visual inspection and a chip quality report was generated by the Affymetrix's GeneChip Operating System (GCOS) and Expression console (Affymetrix).

data_processing: The image data was processed using the Affymetrix GCOS algorithm utilizing quantile normalization or the Robust Multiarray method (RMA) to determine the specific hybridizing signal for each gene.

source_name: liver

label_protocol: All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome 430 2.0 arrays.

extract_protocol: Qiazol with homogenization followed by Rneasy spin columns with option Dnase per manufacturers protocol

tag: maternal diet

value: low-protein

value: male

value: 10 months


title: WT_mk13

description:
Gene Expression Data from Human PanNETs
WT_mk13


title: WT_LS39

description:
Gene Expression Data from Human PanNETs
WT_LS39


title: M1_mk5

description:
Gene Expression Data from Human PanNETs
M1_mk5

source_name: MEN1 mutated PanNET


title: WT_LS27

description:
Gene Expression Data from Human PanNETs
WT_LS27


title: tid134287_mTORMouse88_LP_M_Liver


title: tid134269_mTORMouse70_LP_M_Liver


title: WT_LS35

description:
Gene Expression Data from Human PanNETs
WT_LS35


title: M1_mk14

description:
Gene Expression Data from Human PanNETs
M1_mk14


title: tid134266_mTORMouse67_LP_M_Liver


title: tid134268_mTORMouse69_LP_M_Liver


title: M1_mk3

description:
Gene Expression Data from Human PanNETs
M1_mk3


title: M1_mk10

description:
Gene Expression Data from Human PanNETs
M1_mk10


title: M1_LS53

description:
Gene Expression Data from Human PanNETs
M1_LS53


title: tid134285_mTORMouse86_LP_M_Liver


title: M1_LS23

description:
Gene Expression Data from Human PanNETs
M1_LS23


title: M1_LS1

description:
Gene Expression Data from Human PanNETs
M1_LS1


title: D_mk42

description:
Gene Expression Data from Human PanNETs
D_mk42


title: M1_mk6

description:
Gene Expression Data from Human PanNETs
M1_mk6


title: tid134253_mTORMouse54_LP_M_Liver


title: D_mk32

description:
Gene Expression Data from Human PanNETs
D_mk32


title: D_mk51

description:
Gene Expression Data from Human PanNETs
D_mk51


title: D_mk9

description:
Gene Expression Data from Human PanNETs
D_mk9


title: D_mk18

description:
Gene Expression Data from Human PanNETs
D_mk18


title: D_LS21

description:
Gene Expression Data from Human PanNETs
D_LS21


title: tid134252_mTORMouse53_LP_M_Liver


title: A_mk47

description:
Gene Expression Data from Human PanNETs
A_mk47


title: D_LS33

description:
Gene Expression Data from Human PanNETs
D_LS33


title: tid134254_mTORMouse55_LP_M_Liver


title: tid134251_mTORMouse52_LP_M_Liver


title: tid134250_mTORMouse51_LP_M_Liver


title: tid134249_mTORMouse50_LP_M_Liver


title: tid134247_mTORMouse48_LP_M_Liver


title: WKY RVLM 5

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

institute: University of Bristol

description: Sample represents the rostral ventrolateral medulla from 5 WKY animals

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: GCOS version 1.2

label: MessageAmpII aRNA Amplification kit (Ambion)

organism: Rattus norvegicus

source_name: WKY Rostral ventrolateral medulla

label_protocol: Protocol available at http://www.AMBION.com/catalog/CatNum.php?1753

extract_protocol: Tissue was dissected in an RNase free manner and stored in RNAlater (Ambion) at -20C for no more than 1 month. Homogenisation in QIAzol was conducted mechanically and the aqueous phase separated using a PLG column (Eppendorf). RNA was further purified using RNeasy minelute cleanup kit (Qiagen). RNA quality was confirmed using nanodrop and bioanylizer 2100 (Agilent).

tag: Strain

value: WKY

tag: Gender

value: Male

tag: Age

value: 10-13 weeks

tag: Tissue

value: Rostral ventrolateral medulla


title: WKY RVLM 3


title: tid134248_mTORMouse49_LP_M_Liver

tag: strain


title: SHR RVLM 3

description: Sample represents the rostral ventrolateral medulla from 5 SHR animals

source_name: SHR rostral ventrolateral medulla

value: SHR


title: WKY RVLM 2


title: SHR RVLM


title: SHR RVLM 4


title: SHR RVLM 5


title: WKY RVLM


title: SHR RVLM 2


title: WKY RVLM 4


title: tid134294_mTORMouse95_HP_M_Liver

value: high-protein


title: tid134293_mTORMouse94_HP_M_Liver


title: tid134292_mTORMouse93_HP_M_Liver


title: SHR SON 3

description: Sample represents the supraoptic nucleus from 5 SHR animals

source_name: SHR Supraoptic nucleus

value: Supraoptic nucleus


title: tid134290_mTORMouse91_HP_M_Liver


title: tid134273_mTORMouse74_HP_M_Liver


title: SHR PVN 4

description: Sample represents the paraventricular nucleus from 5 SHR animals

source_name: SHR Paraventricular nucleus

value: Paraventricular nucleus


title: SHR PVN 2


title: SHR NIL 5

description: Sample represents the neurointermediate lobe from 5 SHR animals

source_name: SHR Neurointermediate lobe of the pituitary

value: Neurointermediate lobe of the pituitary


title: tid134291_mTORMouse92_HP_M_Liver


title: tid134288_mTORMouse89_HP_M_Liver


title: SHR SON 2


title: SHR PVN


title: SHR PVN 5


title: tid134271_mTORMouse72_HP_M_Liver


title: SHR PVN 3


title: SHR NIL 2

tag: gender

value: 10-12 weeks

tag: tissue

value: Neurointermediate Lobe of the Pituitary


title: tid134289_mTORMouse90_HP_M_Liver

tag: Sex


title: SHR NIL 3


title: SHR SON 4


title: SHR SON


title: tid134270_mTORMouse71_HP_M_Liver


title: SHR NIL


title: APO-IWAT

city: Kasugai

first: Hitoshi

last: Yamashita

address: 1200 Matsumoto-cho

department: Biomedical Sciences

country: Japan

institute: Chubu University

description:
Gene expression data from IWAT of ApoE-KO mice fed high-fat diet
PF081111_02

hyb_protocol: The labeled DNA were hybridized to Mouse Gene ST 1.0 array.

scan_protocol: GeneChip was scanned by GeneChip 3000 Scanner.

data_processing: rma-gene-default-Signal.  The data were analyzed using Affymetrix software.

source_name: ApoE-KO

label_protocol: Fragmented DNA was labeled using WT Sense Targeting Labelling kit (Affymetrix).

growth_protocol: Ucp1-/-;ApoE-/- (DKO) mice were bred from Ucp1-/- (UCP1-KO) and ApoE-/- (ApoE-KO) mice on C57BL/6J background (The Jackson Laboratory, Bar Harbor, ME). Mice were maintained at 23ºC and provided a standard chow (CE-2, CLEA Japan, Inc.) and tap water ad libitum.

treatment_protocol: At 9 weeks of age, mice were fed a high-fat diet (B15040, CLEA Japan, Inc.) for 9 weeks.

value: inguinal white adipose tissue

tag: genotype/variation

value: ApoE-KO

tag: protocol

value: fed high-fat diet


title: SHR NIL 4


title: DKO-IWAT

description:
Gene expression data from IWAT of DKO mice fed high-fat diet
PF081111_01

value: DKO


title: Male transgenerational offspring (F2) of DMSO exposed fish, biological rep4

city: Gainesville

first: Tracie

middle: R

last: Baker

state: FL

institute: University of Florida

description:
Zebrafish_F2DM-4
Gene expression data from the F2-lineage of  zebrafish exposed to DMSO (control)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Zebrafish Gene 1.0 ST Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GC3000 G7.

data_processing:
The data was extracted and processed using Affymetrix Command Console version 3.2.4.1515W
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

organism: Danio rerio

source_name: Zebrafish adult testicular tissue of DMSO exposed F2 lineage

label_protocol: All samples were end-terminus labeled following the guidelines of the Affymetrix GeneChip WT terminal labeling an hybridization user manual target (P/N 702808 Rev. 7)

growth_protocol: Zebrafish embryos (AB strain) were kept at 27-30 °C in lightly buffered water with a standard 14-h/10-h light/dark cycle as described by Westerfield (2000).

extract_protocol: Rneasy lipid tissue mini kit extraction of total RNA and was performed according to the manufacturer's instructions.

treatment_protocol: Fo zebrafish were exposed for 1 hour to waterborne TCDD at 50 pg/ml or vehicle (DMSO) at both 3 and 7 wpf (weeks post fertilization; during sexual differentiation and gonad maturation). The next two generations were not exposed but were raised to adulthood and assessed.

value: AB

value: wild type

tag: age

value: 1 year old (adult)

tag: generation/lineage

tag: exposed to

value: 1 hour to vehicle (DMSO) at both 3 and 7 wpf

value: testicular tissue


title: Male transgenerational offspring (F2) of DMSO exposed fish, biological rep5

description:
Zebrafish_F2DM-5
Gene expression data from the F2-lineage of  zebrafish exposed to DMSO (control)


title: Male transgenerational offspring (F2) of DMSO exposed fish, biological rep3

description:
Zebrafish_F2DM-3
Gene expression data from the F2-lineage of  zebrafish exposed to DMSO (control)


title: tid134272_mTORMouse73_HP_M_Liver

value: male

value: 10 months


title: Male transgenerational offspring (F2) of DMSO exposed fish, biological rep2

description:
Zebrafish_F2DM-2
Gene expression data from the F2-lineage of  zebrafish exposed to DMSO (control)


title: Male transgenerational offspring (F2) of DMSO exposed fish, biological rep1

description:
Zebrafish_F2DM-1
Gene expression data from the F2-lineage of  zebrafish exposed to DMSO (control)


title: tid134256_mTORMouse57_HP_M_Liver

value: high-protein


title: Male transgenerational offspring (F2) of TCDD exposed fish, biological rep5

description:
Zebrafish_F2TM-5
Gene expression data from the F2-lineage of zebrafish exposed to TCDD

source_name: Zebrafish adult testicular tissue of TCDD exposed F2 lineage

value: 1 hour to waterborne TCDD at 50 pg/ml at both 3 and 7 wpf


title: Male transgenerational offspring (F2) of TCDD exposed fish, biological rep1

description:
Zebrafish_F2TM-1
Gene expression data from the F2-lineage of zebrafish exposed to TCDD


title: tid134306_mTORMouse107_Chow_M_Liver

value: chow


title: Male transgenerational offspring (F2) of TCDD exposed fish, biological rep2

description:
Zebrafish_F2TM-2
Gene expression data from the F2-lineage of zebrafish exposed to TCDD


title: Male offspring (F1) of TCDD exposed fish, biological rep3

description:
Zebrafish_F1TM-3
Gene expression data from the F1-lineage of zebrafish exposed to TCDD

source_name: Zebrafish adult testicular tissue of TCDD exposed F1 lineage


title: Male offspring (F1) of DMSO exposed fish, biological rep2

description:
Zebrafish_F1DM-2
Gene expression data from the F1-lineage of  zebrafish exposed to DMSO (control)

source_name: Zebrafish adult testicular tissue of DMSO exposed F1 lineage


title: tid134258_mTORMouse59_HP_M_Liver


title: Male offspring (F1) of DMSO exposed fish, biological rep4

description:
Zebrafish_F1DM-4
Gene expression data from the F1-lineage of  zebrafish exposed to DMSO (control)


title: tid134275_mTORMouse76_Chow_M_Liver


title: tid134257_mTORMouse58_HP_M_Liver


title: Male offspring (F1) of TCDD exposed fish, biological rep4

description:
Zebrafish_F1TM-4
Gene expression data from the F1-lineage of zebrafish exposed to TCDD


title: tid134305_mTORMouse106_Chow_M_Liver


title: tid134276_mTORMouse77_Chow_M_Liver


title: tid134255_mTORMouse56_HP_M_Liver


title: Male offspring (F1) of DMSO exposed fish, biological rep3

description:
Zebrafish_F1DM-3
Gene expression data from the F1-lineage of  zebrafish exposed to DMSO (control)


title: tid134307_mTORMouse108_Chow_M_Liver


title: Male offspring (F1) of DMSO exposed fish, biological rep1

description:
Zebrafish_F1DM-1
Gene expression data from the F1-lineage of  zebrafish exposed to DMSO (control)


title: Male transgenerational offspring (F2) of TCDD exposed fish, biological rep3

description:
Zebrafish_F2TM-3
Gene expression data from the F2-lineage of zebrafish exposed to TCDD


title: Male offspring (F1) of DMSO exposed fish, biological rep5

description:
Zebrafish_F1DM-5
Gene expression data from the F1-lineage of  zebrafish exposed to DMSO (control)


title: Male offspring (F1) of TCDD exposed fish, biological rep5

description:
Zebrafish_F1TM-5
Gene expression data from the F1-lineage of zebrafish exposed to TCDD


title: Male offspring (F1) of TCDD exposed fish, biological rep2

description:
Zebrafish_F1TM-2
Gene expression data from the F1-lineage of zebrafish exposed to TCDD


title: Male transgenerational offspring (F2) of TCDD exposed fish, biological rep4

description:
Zebrafish_F2TM-4
Gene expression data from the F2-lineage of zebrafish exposed to TCDD


title: Male offspring (F1) of TCDD exposed fish, biological rep1

description:
Zebrafish_F1TM-1
Gene expression data from the F1-lineage of zebrafish exposed to TCDD


title: tid134274_mTORMouse75_Chow_M_Liver


title: tid134269_mTORMouse70_LP_M_Hypo

source_name: hypothalamus

value: low-protein


title: tid134268_mTORMouse69_LP_M_Hypo


title: tid134287_mTORMouse88_LP_M_Hypo


title: tid134264_mTORMouse65_Chow_M_Liver


title: tid134263_mTORMouse64_Chow_M_Liver


title: tid134262_mTORMouse63_Chow_M_Liver


title: tid134285_mTORMouse86_LP_M_Hypo


title: tid134265_mTORMouse66_Chow_M_Liver


title: tid134286_mTORMouse87_LP_M_Hypo


title: tid134267_mTORMouse68_LP_M_Hypo


title: tid134266_mTORMouse67_LP_M_Hypo


title: tid134254_mTORMouse55_LP_M_Hypo


title: tid134253_mTORMouse54_LP_M_Hypo


title: HEK293T_560+198ZNF830_alt-splice_rep1

city: Philadelphia

first: Tara

last: Davis

state: PA

department: Biochemistry and Molecular Biology

institute: Drexel University College of Medicine

hyb_protocol: Hybridization was conducted by the Molecular Profiling Facility at the University of Pennsylvania. Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Human Transcriptome 2.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: Scanning was conducted by the Molecular Profiling Facility at the University of Pennsylvania. A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: Probeset and gene normalized data was calculated from cel files in Affymetrix Expression Console software using RMA with default parameters.

label_protocol: Labeling was conducted by the Molecular Profiling Facility at the University of Pennsylvania. All protocols were conducted as described in the Affymetrix WT Plus Reagent Kit Manual and the Affymetrix GeneChip Expression Analysis Technical Manual. Briefly, 250ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

growth_protocol: HeLa cells were transduced with titered lentivirus containing either shRNA from the MISSION library or with scrambled shRNA. Puromycin was used to select for incorporation. Cells were grown to 80% confluency and harvested.

extract_protocol: total RNA was extracted and purified using the Bioline ISOLATE II kit according to manufacturer's instructions.

treatment_protocol: Cells were washed with 1X PBS before freezing in preparation for RNA extraction.

tag: cell line

value: ZNF830 knockdown


title: HEK293T_560+198ZNF830_alt-splice_rep3


title: HEK293T_165PPWD1_alt-splice_rep1

source_name: HEK293T, 165PPWD1, rep1

growth_protocol: HEK293T cells were transduced with titered lentivirus containing either shRNA from the MISSION library or with scrambled shRNA. Puromycin was used to select for incorporation. Cells were grown to 80% confluency and harvested.

value: PPWD1 knockdown


title: HEK293T_560+198ZNF830_alt-splice_rep2


title: HEK293T_755+769PRPF4_alt-splice_rep2

value: PRPF4 knockdown


title: HEK293T_470PPIL1_alt-splice_rep2

source_name: HEK293T, 470PPIL1, rep2

value: PPIL1 knockdown


title: HEK293T_475PPIL2_alt-splice_rep2

source_name: HEK293T, 475PPIL2, rep2

value: PPIL2 knockdown


title: HEK293T_5191SCR_alt-splice_rep2

source_name: HEK293T, SCR, rep2

value: SCR control


title: HEK293T_5104SCR_alt-splice_rep3

source_name: HEK293T, SCR, rep3


title: HEK293T_165PPWD1_alt-splice_rep2

source_name: HEK293T, 165PPWD1, rep2


title: HEK293T_5191SCR_alt-splice_rep1

source_name: HEK293T, SCR, rep1


title: HEK293T_470PPIL1_alt-splice_rep3

source_name: HEK293T, 470PPIL1, rep3


title: HEK293T_5104SCR_alt-splice_rep2


title: HEK293T_470PPIL1_alt-splice_rep1

source_name: HEK293T, 470PPIL1, rep1


title: HEK293T_755+769PRPF4_alt-splice_rep1


title: tid134252_mTORMouse53_LP_M_Hypo


title: rat_liver_adult_male3

description: sample id: 1969sTS

source_name: Adult liver

value: liver

tag: developmenta stage

value: adult


title: rat_liver_adult_male1

description: sample id: 2359sTS


title: HEK293T_475PPIL2_alt-splice_rep3

source_name: HEK293T, 475PPIL2, rep3


title: HEK293T_755+769PRPF4_alt-splice_rep3


title: tid134249_mTORMouse50_LP_M_Hypo


title: HEK293T 368PPIL3 alt-splice rep3

source_name: HEK293T, 185PPIL3, rep3

value: PPIL3 knockdown


title: rat_kidney_adult_male4

description: sample id: 2856sTS

source_name: Adult kidney

value: kidney


title: rat_liver_adult_male4

description: sample id: 1973sTS


title: tid134247_mTORMouse48_LP_M_Hypo


title: rat_kidney_adult_male2

description: sample id: 5360sTS


title: rat_kidney_adult_male3

description: sample id: 2743sTS


title: HEK293T 368PPIL3 alt-splice rep1

source_name: HEK293T, 185PPIL3, rep1


title: HEK293T_368PPIG_alt-splice_rep2

source_name: HEK293T, 368PPIG, rep2


title: HEK293T_165PPWD1_alt-splice_rep3

source_name: HEK293T, 165PPWD1, rep3


title: tid134248_mTORMouse49_LP_M_Hypo

source_name: hypothalamus


title: tid134251_mTORMouse52_LP_M_Hypo


title: rat_heart_adult_male4

description: sample id: 2751sTS

source_name: Adult heart

value: heart


title: rat_liver_adult_male2

description: sample id: 2370sTS

value: male


title: rat_heart_adult_male3

description: sample id: 2742sTS


title: rat_kidney_adult_male1

description: sample id: 2748sTS


title: rat_heart_adult_male1

description: sample id: 2747sTS


title: rat_brain_adult_male3

description: sample id: 1875sTS

source_name: Adult brain

value: brain


title: tid134250_mTORMouse51_LP_M_Hypo

value: 10 months


title: tid134292_mTORMouse93_HP_M_Hypo

value: high-protein


title: HEK293T 368PPIL3 alt-splice rep2

source_name: HEK293T, 185PPIL3, rep2


title: tid134293_mTORMouse94_HP_M_Hypo


title: rat_brain_adult_male2

description: sample id: 2367sTS


title: HEK293T_368PPIG_alt-splice_rep3

source_name: HEK293T, 368PPIG, rep3


title: rat_brain_adult_male1

description: sample id: 2356sTS


title: WT_p30_skeletal muscle

city: Shanghai

first: Yuguo

last: Liu

address: 320 Yue Yang Road

department: Institute for Nutritional Sciences, SIBS

country: China

institute: Chinese Academy of Sciences

description:
1yueKO
WGC033158_NBC-1_1yueWT_combined

data_processing:
Illumina GA Pipeline v1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie MapSplice version 2.1.7.
The stat of mapped reads was list in MappingStatistic_1yueWT and MappingStatistic_1yueKO
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi, 2008.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: skeletal muscle

extract_protocol:
RNA from p30 WT and SRSF1-MKO hindlimb muslce were extracted by standard Trizol methods.
RNA libraries were prepared for sequencing using standard Lifetech protocol.

tag: strain background

value: postnatal day 30

value: WT

value: skeletal muscle


title: SRSF1-MKO_p30_skeletal muscle

description:
1yueWT
WGC033158_NBC-1_1yueKO_combined


title: HEK293T_368PPIE_alt-splice_rep3

source_name: HEK293T, 368PPIE, rep3


title: tid134290_mTORMouse91_HP_M_Hypo

tag: maternal diet


title: tid134289_mTORMouse90_HP_M_Hypo


title: tid134294_mTORMouse95_HP_M_Hypo


title: tid134288_mTORMouse89_HP_M_Hypo


title: rat_brain_adult_male4

description: sample id: 1971sTS


title: KYSE410 cells were treated with PBS

city: Beijing

first: Jie

last: Chen

address: No. 52 Fucheng Road Haidian District Beijing

institute: Peking University Cancer Hospital

hyb_protocol: Hybridization was performed in NimbleGen Hybridization System.

scan_protocol: After washing, slides were scanned with Axon GenePix 4000B scanner.

data_processing: Data was extracted and normalized using NimbleScan v2.5 software. Further Data analysis was performed using Agilent GeneSpring GX v11.5.1 software.

source_name: KYSE410 cells were treated with PBS for 24h

label_protocol: NimbleGen One-Color DNA Labeling Kit was used for sample labeling.

growth_protocol: KYSE410 cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), penicillin (100U/ml), and streptomycin (100 μg/ml).

extract_protocol: Total RNA was reversely transcripted into first-strand cDNA using Superscript Frist-Strand cDNA Synthesis Kit (Invitrogen).

treatment_protocol: KYSE410 cells were respectively treated with PBS (control solvent), TNFα, IL1β, and LPS.

tag: agent

value: PBS


title: tid134291_mTORMouse92_HP_M_Hypo


title: KYSE410 cells were treated with TNFα

source_name: KYSE410 cells were treated with TNFα for 24h

value: TNFα


title: tid134272_mTORMouse73_HP_M_Hypo


title: Nourin No.2_nodule 24h_5 mM nitrate_rep1

city: Tokyo

first: Takuji

last: Ohyama

address: 1-1-1 Sakuragaoka, Setagaya-ku

department: Department of Applied Biology and Chemistry

institute: Tokyo University of Agriculture

description: Gene expression of soybean nodules treated with 5 mM nitrate

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes and hybridized to Agilent G. max (Soybean) Oligo Microarray 4x44K (arrayID:016772) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: After hybridization, the microarray slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides at two laser power settings (100% and 10%).

data_processing:
The scanned images were analyzed with Agilent’s Feature Extraction Software (v 9.5.1) to obtain background subtracted and spatially detrended Processed Signal intensities.
The data were then normalized subjected to 75 percentile normalization and log2 transformation using data analysis tools Subio Basic Plug-in.

organism: Glycine max

source_name: Nourin No.2_nodule 24h_5 mM nitrate_replicate 1

label_protocol: Each RNA sample (0.5 ug) was labeled with Cyanine-3 (Cy3) fluorescent dye, using Agilent’s Quick Amp Labeling Kit, one color*3. The cRNA was produced by in vitro transcription.

growth_protocol: Seeds of soybean (Glycine max L. cv. Nourin No. 2) were inoculated with rhizobia (Bradyrhizobium diazoefficiens USDA110) and sown in vermiculite. Five days after planting, each seedling was hydroponically cultivated in an 800-ml glass bottle with continuous aeration. under controlled conditions with nitrogen free culture solution.

extract_protocol: total RNA was extracted with RNA isoPlus (Fruit-mate for RNA purification, Takara Bio Ltd.), following the manufacturer's instructions. RNA samples were visualized and quantified on Agilent’s 2100 Bioanalyzer to check for degradation and to determine the concentration.

treatment_protocol: At 19 days after planting, 5 mM nitrate treatment and the control treatment with N free solution were imposed for 24-hours. At the end of the treatment, the lower half of the root system without visible nodules was collected in order to eliminate nodule mRNA, and the nodules attached to the upper half of the root with a diameter larger than 3 mm were collected.

value: nodules


title: tid134271_mTORMouse72_HP_M_Hypo


title: KYSE410 cells were treated with LPS

source_name: KYSE410 cells were treated with LPS for 24h

value: LPS


title: Nourin No.2_nodule 24h_5 mM nitrate_rep2

source_name: Nourin No.2_nodule 24h_5 mM nitrate_replicate 2


title: rat_heart_adult_male2

description: sample id: 2749sTS


title: Nourin No.2_nodule 24h_5 mM nitrate_rep3

source_name: Nourin No.2_nodule 24h_5 mM nitrate_replicate 3


title: HEK293T_368PPIE_alt-splice_rep2

source_name: HEK293T, 368PPIE, rep2


title: tid134270_mTORMouse71_HP_M_Hypo


title: HEK293T_368PPIG_alt-splice_rep1

source_name: HEK293T, 368PPIG, rep1


title: Nourin No.2_nodule 24h_cont_rep3

description: Gene expression of control soybean npodules treated with N free medium

source_name: Nourin No.2_nodule 24h_control_replicate 3


title: UNC_TGS_BC_Y90_R1

first: Zhiyuan

last: Hu

institute: University of North Carolina at Chapel Hill

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_Y90_R1

data_processing:
Illumina Casava1.7 software used for basecalling and sequencing data were demultiplexed based on dual indexes.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, demultiplexed and then only read 1 in each sample were mapped to known Targeted regions of human genomes for counts using R package "ShortRead".
Raw counts of all samples were imported to edgeR for normalization by the size of the transcripts and by the size of the library and then calculation of CPM per sample as a gene expression matrix
Gene expression CPM dataset were median-centered and column-standardized using DWD
DWD dataset were used for iRDM data analysis including subtype classification, iRDM risks,  immunity scores, and proliferation scores.
Genome_build: hg19
Supplementary_files_format_and_content: csv files were generated including raw counts and normalized gene expression data

source_name: Breast cancer

extract_protocol:
FFPE tissues total RNA extraction was routinely performed using Roche FFPE RNA extraction kit according to the manufacturer’s protocol.
The Illumina TruSeq Targeted RNA expression kit was used to build libraries of the targeted 72-genes. To synthesize cDNA, 200 to 800 nanograms of purified FFPE RNA in a total volume of 3 µl was mixed with 4.0 µl RCS1, 2.0 µl ProtoScrip II Reverse Transcriptase, 1.0 µl 10mM DTT at 42OC for 30 min and 94OC for 10 min. The cDNA was hybridized with custom oligo pools in a thermal cycler programed to gradually decrease temperature from 70 OC to 30 OC in 30 minutes. The RNA/Oligo hybrid products were washed, extended and ligated. The ligated DNA was amplified by DNA polymerase on the thermal cycler with 35 PCR cycles of 98 OC for 30 seconds, 62 OC for 30 seconds and 72 OC for 60 seconds. The PCR products were purified with AMPure XP beads and eluted in 15 µl of buffer, measured using Agilent Bioanalyzer2100 and DNA1000 chips, pooled with equal amounts of DNA from each sample’s library, and finally diluted to 4 nM, denatured, and loaded to Nextseq500 according to the manufacturer’s protocol.
Libraries were multiplexed and sequenced on Illumina Nextseq500  to generate 75bp single read R1.

value: female

tag: dmfs time

tag: dmfs event

tag: sample type

value: Solid tumor

tag: irdm subtype

tag: pam50 subtype

tag: immunity group

value: iweak

tag: proliferation group

value: high

tag: er status rna

value: ER-

tag: pr status rna

value: PR+


title: Nourin No.2_nodule 24h_cont_rep2

description: Gene expression of control soybean nodules treated with N free medium

source_name: Nourin No.2_nodule 24h_control_replicate 2

tag: tissue


title: tid134273_mTORMouse74_HP_M_Hypo

source_name: hypothalamus

tag: strain

tag: Sex

value: male

tag: age


title: UNC_TGS_BC_Y90

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_Y90

tag: gender

value: PR-


title: tid134256_mTORMouse57_HP_M_Hypo

value: 10 months


title: Nourin No.2_root 24h_5 mM nitrate_rep2

description: Gene expression of soybean roots treated with 5 mM nitrate

source_name: Nourin No.2_root 24h_5 mM nitrate_replicate 2

value: roots


title: UNC_TGS_BC_Y23_R1

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_Y23_R1

value: Basal

value: istrong


title: Nourin No.2_root 24h_5 mM nitrate_rep1

source_name: Nourin No.2_root 24h_5 mM nitrate_replicate1


title: Nourin No.2_nodule 24h_cont_rep1

source_name: Nourin No.2_nodule 24h_control_replicate 1


title: Nourin No.2_root 24h_5 mM nitrate_rep3

source_name: Nourin No.2_root 24h_5 mM nitrate_replicate 3


title: Nourin No.2_root 24h_cont_rep3

description: Gene expression of control soybean roots treated with N free medium

source_name: Nourin No.2_root 24h_control_replicate 3


title: tid134258_mTORMouse59_HP_M_Hypo

value: high-protein


title: tid134255_mTORMouse56_HP_M_Hypo


title: tid134257_mTORMouse58_HP_M_Hypo


title: UNC_TGS_BC_Y23

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_Y23


title: Nourin No.2_root 24h_cont_rep2

source_name: Nourin No.2_root 24h_control_replicate 2


title: tid134307_mTORMouse108_Chow_M_Hypo

value: chow


title: Nourin No.2_root 24h_cont_rep1


title: UNC_TGS_BC_99

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_99


title: UNC_TGS_BC_97

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_97

value: LumA

value: low

value: ER+


title: tid134306_mTORMouse107_Chow_M_Hypo


title: UNC_TGS_BC_96

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_96

value: female


title: KYSE410 cells were treated with IL1β

source_name: KYSE410 cells were treated with IL1β for 24h

tag: cell line


title: UNC_TGS_BC_95

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_95

value: Solid tumor


title: tid134305_mTORMouse106_Chow_M_Hypo

tag: maternal diet


title: HEK293T_368PPIE_alt-splice_rep1

source_name: HEK293T, 368PPIE, rep1


title: UNC_TGS_BC_89

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_89

value: Normal

value: iweak


title: UNC_TGS_BC_93

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_93

value: LumB

value: high


title: UNC_TGS_BC_88

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_88

value: PR+


title: UNC_TGS_BC_87

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_87


title: UNC_TGS_BC_83

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_83

value: ER-

value: PR-


title: UNC_TGS_BC_85

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_85


title: UNC_TGS_BC_9m

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_9m

value: Immuno


title: UNC_TGS_BC_92

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_92


title: HEK293T_475PPIL2_alt-splice_rep1

source_name: HEK293T, 475PPIL2, rep1

tag: genotype/variation

value: PPIL2 knockdown


title: UNC_TGS_BC_82

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_82

tag: dmfs time


title: HEK293T_SCR_alt-splice_rep1

source_name: HEK293T, SCR, rep1

value: SCR control


title: UNC_TGS_BC_80

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_80

tag: dmfs event


title: UNC_TGS_BC_81

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_81

tag: sample type

value: Basal


title: HEK293T_5191SCR_alt-splice_rep3

source_name: HEK293T, SCR, rep3


title: UNC_TGS_BC_78

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_78

tag: irdm subtype


title: UNC_TGS_BC_79

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_79

tag: pam50 subtype


title: UNC_TGS_BC_8

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_8

tag: immunity group


title: UNC_TGS_BC_76_R1

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_76_R1

value: Mixed

tag: proliferation group


title: HEK293T_SCR_alt-splice_rep3


title: HEK293T_5104SCR_alt-splice_rep1


title: UNC_TGS_BC_76

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_76

value: LumA

tag: er status rna


title: HEK293T_139CWC27_alt-splice_rep1


title: UNC_TGS_BC_74

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_74

tag: pr status rna


title: HEK293T_SCR_alt-splice_rep2

source_name: HEK293T, SCR, rep2


title: tid134275_mTORMouse76_Chow_M_Hypo

value: chow

value: male

value: 10 months


title: UNC_TGS_BC_71

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_71

value: female

value: Solid tumor

value: low

value: ER+


title: UNC_TGS_BC_72

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_72

value: istrong

value: high


title: tid134274_mTORMouse75_Chow_M_Hypo


title: UNC_TGS_BC_77

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_77

value: iweak

value: ER-


title: tid134263_mTORMouse64_Chow_M_Hypo


title: HEK293T_139CWC27_alt-splice_rep2


title: tid134265_mTORMouse66_Chow_M_Hypo


title: HEK293T_139CWC27_alt-splice_rep3


title: tid134276_mTORMouse77_Chow_M_Hypo


title: UNC_TGS_BC_68

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_68

value: PR+


title: UNC_TGS_BC_7

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_7

value: PR-


title: UNC_TGS_BC_69m

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_69m

value: Immuno


title: UNC_TGS_BC_67

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_67

value: Normal


title: tid134262_mTORMouse63_Chow_M_Hypo


title: UNC_TGS_BC_66m

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_66m

value: Basal


title: MB_794

city: Heidelberg

first: Kwong Leong

last: Wong

state: Germany (DEU)

address: Im Neuenheimer Feld 280

department: Molecular genetics

country: Germany

institute: DKFZ

description: Tumor Tissue

hyb_protocol: Array experiment performed at the core facility of DKFZ.

data_processing: the R library `affy` was used to process the raw CEL files of the Affymetrix Mouse 430 v2.0 expression array

source_name: Medulloblastoma

tag: tissue

value: Brain

tag: cell type

value: Medulloblastoma


title: tid134264_mTORMouse65_Chow_M_Hypo

tag: strain

value: chow

tag: Sex

value: male


title: MB_1224

description: Tumor Tissue

scan_protocol: Array experiment performed at the core facility of DKFZ.


title: MB_630

description: Tumor Tissue

label_protocol: Array experiment performed at the core facility of DKFZ.


title: UNC_TGS_BC_66

city: Chapel Hill

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_66

tag: gender

value: female


title: MB_706

description: Tumor Tissue


title: UNC_TGS_BC_63

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_63

value: Solid tumor

value: LumB


title: UNC_TGS_BC_60

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_60

value: ER+


title: UNC_TGS_BC_6

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_6

value: Mixed

value: low


title: UNC_TGS_BC_69

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_69

value: LumA

value: istrong


title: UNC_TGS_BC_58

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_58

value: iweak

value: PR+


title: UNC_TGS_BC_62

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_62

value: high

value: ER-


title: UNC_TGS_BC_55

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_55


title: UNC_TGS_BC_57

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_57

value: PR-


title: UNC_TGS_BC_59

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_59


title: UNC_TGS_BC_54

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_54


title: UNC_TGS_BC_56

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_56


title: MB_1207

description: Tumor Tissue

value: Brain


title: MB_1187

description: Tumor Tissue

value: Medulloblastoma


title: UNC_TGS_BC_50

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_50

value: Normal


title: MB_1206

description: Tumor Tissue


title: UNC_TGS_BC_49

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_49


title: UNC_TGS_BC_48

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_48


title: UNC_TGS_BC_61

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_61


title: MB_1197

description: Tumor Tissue


title: UNC_TGS_BC_47

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_47

value: Immuno


title: WC_2646

description: Normal Tissue

source_name: Whole Cerebellum

value: Whole Cerebellum


title: UNC_TGS_BC_46m

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_46m

source_name: Breast cancer

value: female

value: Solid tumor

value: Basal


title: UNC_TGS_BC_46

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_46


title: CGNP_2705

description: Normal Tissue

source_name: Cerebellar Granule Progenitor Cells

value: Cerebellar Granule Progenitor Cells


title: UNC_TGS_BC_45

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_45

value: LumB

value: ER+


title: WC_2647

description: Normal Tissue


title: UNC_TGS_BC_44

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_44

value: istrong

value: low


title: UNC_TGS_BC_43m

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_43m

value: iweak

value: PR+


title: UNC_TGS_BC_43

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_43

value: high


title: CGNP_2698

description: Normal Tissue


title: UNC_TGS_BC_42_R1

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_42_R1

value: ER-

value: PR-


title: UNC_TGS_BC_42

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_42


title: UNC_TGS_BC_4

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_4


title: UNC_TGS_BC_40

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_40


title: UNC_TGS_BC_64

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_64

value: LumA


title: UNC_TGS_BC_37

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_37


title: UNC_TGS_BC_39

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_39


title: UNC_TGS_BC_345

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_345


title: UNC_TGS_BC_38

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_38


title: UNC_TGS_BC_346

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_346


title: UNC_TGS_BC_341

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_341


title: UNC_TGS_BC_340

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_340


title: UNC_TGS_BC_344

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_344


title: UNC_TGS_BC_333

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_333

value: Mixed


title: UNC_TGS_BC_36

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_36

value: Immuno


title: UNC_TGS_BC_35

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_35


title: UNC_TGS_BC_75

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_75


title: Liver, PPE-containing diet administrated for 8 weeks, biological rep2

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

description: No additional information

hyb_protocol: Following fragmentation, 12.5 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were quantified with theModel based expression index (MBEI), using the statistical language R (R-2.7.2) and Bioconductor 2.2.

source_name: Liver, fed persimmon peel extract containing diet for 8 weeks

label_protocol: biotinylated cRNA was obtained from 100 ng of purified total RNA using a GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen Life Technologies Corp.), then purified with an RNeasy mini kit (Qiagen K.K., Tokyo, Japan).

treatment_protocol: Excised liver sample was immediately immersed in RNAlater and treated according to the manufacturer's protocol.

value: Male

value: KK-Ay

value: liver

tag: age

value: 14 weeks

tag: diet

value: persimmon peel extract


title: Liver, control AIN93G diet administrated for 8 weeks, biological rep3

description: No additional information

source_name: Liver, fed control AIN93G diet for 8 weeks

value: control AIN93G


title: Liver, control AIN93G diet administrated for 8 weeks, biological rep1

description: No additional information


title: Liver, control AIN93G diet administrated for 8 weeks, biological rep4

description: No additional information


title: N9_72Q_4

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

description: Microglial cells expressing 72Q htt.

hyb_protocol: The standard hybridization protocol was used as recommended by Affymterix.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.

data_processing: R/Bioconductor GC-RMA normalization log2

source_name: microglial cells, 72Q htt

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays according to the manufacturer’s instructions.

growth_protocol:
Plating: The microglial cell line N9 was plated in 24-well plates at a density of 1 x 104 cells per well. Viral particles were added to the wells 1 day after plating. To generate clonal cell lines from N9 cells that stably expressed 25Q and 72Q htt, transduced cells with similar GFP fluorescent intensities were singly sorted into 96-well plates by flow cytometry (FACS-DIVA, Becton Dickinson), monitored daily for clonal populations, and expanded into clonal cell lines.
Culture: Three individual N9-25Q and three N9-72Q clones were grown in DMEM 10% FBS with Penicillin/Streptomycin until 80% confluence in Primaria 35 mm dishes (Falcon, BD Biosciences, San Jose, CA). Righi M, Mori L, De Libero G, Sironi M, Biondi A, Mantovani A, Donini SD, Ricciardi-Castagnoli P (1989) Monokine production by microglial cell clones. Eur J Immunol 19:1443-1448.

extract_protocol: RNA was extracted with the RNeasy micro kit (Qiagen, Valencia, CA).

tag: cell line

value: microglial cells

tag: express

value: 72Q htt


title: UNC_TGS_BC_326

address: 450 West Dr

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_326

value: female

tag: dmfs time

tag: dmfs event

value: Solid tumor

value: istrong

value: ER+


title: Liver, PPE-containing diet administrated for 8 weeks, biological rep3

description: No additional information


title: UNC_TGS_BC_328

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_328

tag: sample type

tag: irdm subtype

value: low

value: PR+


title: UNC_TGS_BC_325

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_325

value: LumA

tag: pam50 subtype

tag: immunity group


title: UNC_TGS_BC_329

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_329

tag: proliferation group

tag: er status rna

value: ER-

value: PR-


title: UNC_TGS_BC_324

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_324

value: Basal

value: high

tag: pr status rna


title: UNC_TGS_BC_323

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_323


title: UNC_TGS_BC_322

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_322


title: Liver, control AIN93G diet administrated for 8 weeks, biological rep2

description: No additional information

value: Male

value: KK-Ay

tag: tissue

value: liver


title: Liver, PPE-containing diet administrated for 8 weeks, biological rep1

description: No additional information

tag: strain

value: 14 weeks

value: persimmon peel extract


title: Liver, PPE-containing diet administrated for 8 weeks, biological rep4

description: No additional information


title: UNC_TGS_BC_33

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_33


title: UNC_TGS_BC_32

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_32

value: Mixed

value: iweak


title: N9_25Q_1

description: Microglial cells expressing 25Q htt.

source_name: microglial cells, 25Q htt

tag: cell type

value: microglial cells

value: 25Q htt


title: LFD_liver_6

city: Aberdeen

first: Claus

last: Mayer

address: Greenburn Road

institute: Biomathematics & Statistics Scotland

hyb_protocol: Labelled cRNA was hybridized using the Hi-RPM Gene Expression Hybridization Kit (cat no: 5188-5242), rotating at 65°C degrees for 17 hours. Washing was conducted using the Gene Expression Wash Buffer Kit (Cat no: 5188-5327)

scan_protocol: SureScan High Resolution Scanner (Agilent Technologies).

data_processing: The raw one-channel data (only Cy3 was used in this experiment) were normalised by the cyclicloess method within the Bioconductor library limma. This normalisation was applied to the Caecum and Liver data seperately.

source_name: liver low fat diet 8 weeks

label_protocol: Low Input Quick Amp Labeling Kit (Cat no: 5190-2305) using 100ng total RNA and a two step labelling process to generate cyanine 3-labeled cRNA for oligo microarrays. Steps include converting mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT, followed by amplifying sample using T7 RNA Polymerase, resulting in labelled anti-sense cRNA.

extract_protocol: RNA was extracted from 20 mg cecum (n = 6) using an RNeasy Mini Kit (Qiagen, Crawley, UK) incorporating DNase digestion, followed by quantification using a NanoDrop Spectrophotometer (NanoDrop Technologies). Quality was assessed using an Agilent Bioanalyser (Agilent Technologies).

treatment_protocol: Following 8 weeks consuming the experimental diets mice were killed under terminal anaesthesia. Cecal contents were removed and weighed. Cecum were weighed, frozen on dry ice and stored at -80°C prior to RNA extraction.

tag: Sex

value: male

value: 20 weeks


title: MESO1-USP22 shRNA vs. MESO1-control

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: normalized log ratio(MESO1 cells USP22 shRNA/MESO1 cells control)

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: Scan Array was used for scanning. Images were quantified using genePixpro.

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: MESO1 cells control

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: MESO1 cells were cultured on RPMI-1640 containing 10% FCS.

extract_protocol: Total RNA was isolated from liver samples using miRNeasy kit (QIAGEN).

treatment_protocol: MESO1 cells were transfected with USP22shRNA, or CtrshRNA.

tag: transfected with

value: Control shRNA

source_name: MESO1 USP22 shRNA

value: USP22 shRNA


title: N9_72Q_5

description: Microglial cells expressing 72Q htt.

value: 72Q htt


title: UNC_TGS_BC_320

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_320

tag: gender

value: female

value: Solid tumor

value: Normal

value: istrong

value: low

value: ER-

value: PR+


title: N9_25Q_2

description: Microglial cells expressing 25Q htt.

tag: cell line


title: UNC_TGS_BC_317

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_317

value: LumA

value: ER+


title: UNC_TGS_BC_313

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_313


title: UNC_TGS_BC_315

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_315

value: LumB

value: high


title: UNC_TGS_BC_310

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_310

value: Basal

value: PR-


title: LFD_liver_3

value: liver

value: male

tag: age

value: 20 weeks


title: UNC_TGS_BC_314

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_314

tag: dmfs time


title: UNC_TGS_BC_311

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_311

tag: dmfs event

value: iweak


title: LFD_liver_5


title: UNC_TGS_BC_308

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_308

value: female

tag: sample type


title: UNC_TGS_BC_318

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_318

value: Solid tumor

tag: irdm subtype

value: Immuno


title: LFD_liver_4


title: UNC_TGS_BC_309

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_309

tag: pam50 subtype


title: UNC_TGS_BC_307

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_307

tag: immunity group


title: UNC_TGS_BC_312

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_312

value: istrong

tag: proliferation group


title: UNC_TGS_BC_306

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_306

value: low

tag: er status rna


title: LFD_liver_2


title: UNC_TGS_BC_304

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_304

value: ER-

tag: pr status rna


title: UNC_TGS_BC_30

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_30

value: Normal


title: LFD_liver_1

tag: tissue


title: UNC_TGS_BC_3

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_3

value: LumA

value: PR+


title: HFD + Inulin Propionate and -butyrate_liver_5

source_name: liver inulin propionate and -butyrate esters 8 weeks

tag: strain


title: UNC_TGS_BC_297

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_297

value: ER+


title: HFD + Inulin Propionate and -butyrate_liver_6


title: UNC_TGS_BC_296

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_296

value: high


title: HFD + Inulin Propionate and -butyrate_liver_4


title: UNC_TGS_BC_295

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_295

value: Mixed


title: HFD + Inulin Propionate and -butyrate_liver_3


title: HFD + Inulin Propionate and -butyrate_liver_1


title: UNC_TGS_BC_292

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_292

value: Basal

value: PR-


title: UNC_TGS_BC_293

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_293


title: UNC_TGS_BC_286

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_286

value: LumB


title: UNC_TGS_BC_287

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_287


title: UNC_TGS_BC_285

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_285


title: UNC_TGS_BC_29

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_29


title: HFD + Inulin Propionate and -butyrate_liver_2

value: liver

value: male

value: 20 weeks


title: HFD + inulin_liver_5

source_name: liver inulin 8 weeks


title: UNC_TGS_BC_280

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_280

value: female

value: Solid tumor


title: UNC_TGS_BC_284

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_284

value: iweak


title: HFD + inulin_liver_6


title: UNC_TGS_BC_281

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_281

value: low


title: UNC_TGS_BC_27m

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_27m

value: istrong


title: UNC_TGS_BC_290

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_290


title: UNC_TGS_BC_27low

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_27low


title: HFD + inulin_liver_3


title: UNC_TGS_BC_274

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_274


title: UNC_TGS_BC_276

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_276

value: ER-


title: UNC_TGS_BC_278

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_278

value: LumA


title: UNC_TGS_BC_275

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_275

value: PR+


title: UNC_TGS_BC_273

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_273


title: HFD + inulin_liver_1


title: HFD_liver_5

source_name: liver high fat diet 8 weeks


title: HFD + inulin_liver_2


title: HFD_liver_3


title: HFD + inulin_liver_4


title: HFD_liver_6


title: UNC_TGS_BC_266

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_266

value: ER+


title: HFD_liver_4


title: UNC_TGS_BC_265

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_265

value: Normal


title: UNC_TGS_BC_25m

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_25m

value: high


title: UNC_TGS_BC_260

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_260


title: UNC_TGS_BC_262

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_262

value: Immuno

value: Basal


title: HFD_liver_2


title: UNC_TGS_BC_258

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_258


title: UNC_TGS_BC_259

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_259

value: Mixed


title: HFD_liver_1

value: liver


title: UNC_TGS_BC_27

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_27

value: PR-


title: UNC_TGS_BC_270

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_270


title: UNC_TGS_BC_254

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_254


title: UNC_TGS_BC_255

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_255


title: UNC_TGS_BC_251

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_251


title: UNC_TGS_BC_263

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_263


title: UNC_TGS_BC_250

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_250


title: UNC_TGS_BC_25

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_25

value: LumB


title: LFD_cecum_5

source_name: cecum low fat diet 8 weeks

value: cecum

value: male

value: 20 weeks


title: UNC_TGS_BC_245

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_245

value: female

value: Solid tumor

value: low


title: UNC_TGS_BC_249

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_249

value: iweak


title: LFD_cecum_4


title: LFD_cecum_2


title: UNC_TGS_BC_248

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_248

value: LumA

value: istrong


title: LFD_cecum_1


title: UNC_TGS_BC_247

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_247

value: ER+

value: PR+


title: HFD + Inulin Propionate and -butyrate_cecum_5

source_name: cecum inulin propionate and -butyrate esters 8 weeks


title: LFD_cecum_3


title: UNC_TGS_BC_246

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_246


title: UNC_TGS_BC_24

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_24

value: high


title: UNC_TGS_BC_234

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_234

value: ER-


title: UNC_TGS_BC_237

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_237

value: Basal


title: UNC_TGS_BC_234b

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_234b


title: UNC_TGS_BC_244

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_244

value: Normal

value: Mixed


title: UNC_TGS_BC_238

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_238

value: LumB

value: PR-


title: UNC_TGS_BC_235

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_235


title: HFD + Inulin Propionate and -butyrate_cecum_4

value: cecum

value: male


title: UNC_TGS_BC_232

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_232

value: female


title: UNC_TGS_BC_243

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_243

value: Solid tumor

value: Immuno


title: UNC_TGS_BC_240

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_240

value: low


title: UNC_TGS_BC_231

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_231

value: LumA


title: UNC_TGS_BC_225

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_225

value: istrong


title: UNC_TGS_BC_22

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_22

value: ER+


title: UNC_TGS_BC_217

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_217


title: UNC_TGS_BC_218

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_218

value: PR+


title: UNC_TGS_BC_220

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_220

value: iweak

value: high


title: UNC_TGS_BC_215

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_215

value: Basal

value: ER-


title: UNC_TGS_BC_214

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_214

value: Normal


title: UNC_TGS_BC_21

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_21

value: Mixed


title: UNC_TGS_BC_210

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_210


title: UNC_TGS_BC_209

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_209


title: UNC_TGS_BC_316

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_316