title: FUSCCTNBC341_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC341, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC341 fresh frozen primary tumor tissue


title: FUSCCTNBC330_FrozenPrimaryTumorTissue

status: Public on Mar 09 2019

type: genomic

city: Shanghai

first: Zhi-Ming

last: Shao

address: 270 Dong An Road, Build 7, RM304

country: China

institute: Fudan University Shanghai Cancer Center

description: Copy number profiling of patient FUSCCTNBC330, fresh frozen primary tumor tissue

hyb_protocol: Genome-wide copy number analysis was performed using an OncoScan CNV Assay Kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s recommendations. Briefly, a total of 80 ng of DNA from each tumor sample was processed. Molecular inversion probes (MIPs) were added to the sample DNA and annealed at 58°C overnight. The annealed DNA was divided into two equal parts and incubated with AT or GC gap-fill master mixes for ligation. Then, the unincorporated, non-circularized MIPs and the remains of the genomic template were removed through exonuclease treatment. The circularized MIPs were linearized with a cleavage enzyme, and the first PCR amplification was performed, followed by a second amplification. The amplified products were digested with HaeIII, and the small fragments containing the specific SNP genotype were hybridized onto arrays.

scan_protocol: The arrays were washed and stained using GeneChip Fluidics Station 450 (Affymetrix, Inc.) and scanned in GeneChip Scanner 3000 7G (Affymetrix, Inc.). The fluorescence of clusters was measured to generate a DAT file. Cluster intensity values were automatically calculated using a built-in algorithm from DAT files using GeneChip Command Console software (Affymetrix, Inc.), and a CEL file was generated.

data_processing:
An analysis of Affymetrix OncoScan CNV SNP probe assays was performed with OncoScan Console (v1.3) software (Affymetrix, Inc.). BioDiscovery Nexus ExpressTM for OncoScan 3 software was used to assess recurrent germline/potential false-positive calls by using a reference cohort of DNA from 23 white blood cell samples (regions altered in 12 or more patients were defined as recurrent germline/potential false-positive calls which would be removed later).  Probe-level output from OncoScan Console were analyzed using ASCAT (v2.4.2)(Van Loo et al., 2010) to obtain segmented copy number calls, estimated tumor ploidy as well as estimated tumor purity.
Primary data description: Output (probe level) of OncoScan Console (v1.3): Log2Ratio, WeightedLog2Ratio, AllelicDifference, NormalDiploid, BAF (B allele frequency)

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Patient FUSCCTNBC330 fresh frozen primary tumor tissue

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Tumor tissues were macrodissected to avoid the influence of stromal tissues (< 10% stromal). The percentage of tumor cells was confirmed to be 50% or more in all the breast cancer specimens. Total DNA was isolated from 485 fresh frozen TNBC samples using TGuide M24 (Tiangen, Beijing, China). The purity and quantity of total DNA were estimated by measuring absorbance at 260 nm (A260) and 280 nm (A280) using a NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). The extracted DNA was considered pure and suitable for future experiments when the A260/A280 ratio was within 1.6-1.9

tag: patient id

tag: tissue

value: Primary triple negative breast cancer


title: FUSCCTNBC331_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC331, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC331 fresh frozen primary tumor tissue


title: FUSCCTNBC327_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC327, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC327 fresh frozen primary tumor tissue


title: FUSCCTNBC328_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC328, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC328 fresh frozen primary tumor tissue


title: FUSCCTNBC325_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC325, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC325 fresh frozen primary tumor tissue


title: FUSCCTNBC326_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC326, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC326 fresh frozen primary tumor tissue


title: FUSCCTNBC342_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC342, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC342 fresh frozen primary tumor tissue


title: FUSCCTNBC318_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC318, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC318 fresh frozen primary tumor tissue


title: FUSCCTNBC316_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC316, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC316 fresh frozen primary tumor tissue


title: FUSCCTNBC320_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC320, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC320 fresh frozen primary tumor tissue


title: FUSCCTNBC317_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC317, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC317 fresh frozen primary tumor tissue


title: FUSCCTNBC334_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC334, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC334 fresh frozen primary tumor tissue


title: FUSCCTNBC313_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC313, peripheral white blood cell

source_name: Patient FUSCCTNBC313 peripheral white blood cell

value: Peripheral white blood cell


title: FUSCCTNBC315_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC315, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC315 fresh frozen primary tumor tissue


title: FUSCCTNBC311_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC311, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC311 fresh frozen primary tumor tissue


title: FUSCCTNBC310_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC310, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC310 fresh frozen primary tumor tissue


title: FUSCCTNBC312_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC312, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC312 fresh frozen primary tumor tissue


title: FUSCCTNBC309_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC309, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC309 fresh frozen primary tumor tissue


title: FUSCCTNBC308_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC308, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC308 fresh frozen primary tumor tissue


title: FUSCCTNBC305_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC305, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC305 fresh frozen primary tumor tissue


title: FUSCCTNBC329_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC329, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC329 fresh frozen primary tumor tissue


title: FUSCCTNBC306_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC306, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC306 fresh frozen primary tumor tissue


title: FUSCCTNBC306_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC306, peripheral white blood cell

source_name: Patient FUSCCTNBC306 peripheral white blood cell


title: FUSCCTNBC307_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC307, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC307 fresh frozen primary tumor tissue


title: FUSCCTNBC304_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC304, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC304 fresh frozen primary tumor tissue


title: FUSCCTNBC305_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC305, peripheral white blood cell

source_name: Patient FUSCCTNBC305 peripheral white blood cell


title: FUSCCTNBC303_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC303, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC303 fresh frozen primary tumor tissue


title: FUSCCTNBC324_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC324, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC324 fresh frozen primary tumor tissue


title: FUSCCTNBC313_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC313, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC313 fresh frozen primary tumor tissue


title: FUSCCTNBC302_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC302, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC302 fresh frozen primary tumor tissue


title: FUSCCTNBC299_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC299, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC299 fresh frozen primary tumor tissue


title: FUSCCTNBC301_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC301, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC301 fresh frozen primary tumor tissue


title: FUSCCTNBC298_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC298, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC298 fresh frozen primary tumor tissue


title: FUSCCTNBC322_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC322, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC322 fresh frozen primary tumor tissue


title: FUSCCTNBC323_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC323, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC323 fresh frozen primary tumor tissue


title: FUSCCTNBC297_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC297, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC297 fresh frozen primary tumor tissue


title: FUSCCTNBC296_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC296, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC296 fresh frozen primary tumor tissue


title: FUSCCTNBC296_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC296, peripheral white blood cell

source_name: Patient FUSCCTNBC296 peripheral white blood cell


title: FUSCCTNBC295_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC295, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC295 fresh frozen primary tumor tissue


title: FUSCCTNBC291_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC291, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC291 fresh frozen primary tumor tissue


title: FUSCCTNBC293_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC293, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC293 fresh frozen primary tumor tissue


title: FUSCCTNBC290_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC290, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC290 fresh frozen primary tumor tissue


title: FUSCCTNBC290_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC290, peripheral white blood cell

source_name: Patient FUSCCTNBC290 peripheral white blood cell


title: FUSCCTNBC288_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC288, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC288 fresh frozen primary tumor tissue


title: FUSCCTNBC289_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC289, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC289 fresh frozen primary tumor tissue


title: FUSCCTNBC283_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC283, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC283 fresh frozen primary tumor tissue


title: FUSCCTNBC282_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC282, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC282 fresh frozen primary tumor tissue


title: FUSCCTNBC287_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC287, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC287 fresh frozen primary tumor tissue


title: FUSCCTNBC285_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC285, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC285 fresh frozen primary tumor tissue


title: FUSCCTNBC300_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC300, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC300 fresh frozen primary tumor tissue


title: FUSCCTNBC274_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC274, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC274 fresh frozen primary tumor tissue


title: FUSCCTNBC275_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC275, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC275 fresh frozen primary tumor tissue


title: FUSCCTNBC272_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC272, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC272 fresh frozen primary tumor tissue


title: FUSCCTNBC272_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC272, peripheral white blood cell

source_name: Patient FUSCCTNBC272 peripheral white blood cell


title: FUSCCTNBC273_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC273, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC273 fresh frozen primary tumor tissue


title: FUSCCTNBC277_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC277, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC277 fresh frozen primary tumor tissue


title: FUSCCTNBC292_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC292, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC292 fresh frozen primary tumor tissue


title: FUSCCTNBC271_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC271, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC271 fresh frozen primary tumor tissue


title: FUSCCTNBC276_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC276, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC276 fresh frozen primary tumor tissue


title: FUSCCTNBC264_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC264, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC264 fresh frozen primary tumor tissue


title: FUSCCTNBC265_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC265, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC265 fresh frozen primary tumor tissue


title: FUSCCTNBC267_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC267, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC267 fresh frozen primary tumor tissue


title: FUSCCTNBC263_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC263, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC263 fresh frozen primary tumor tissue


title: FUSCCTNBC263_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC263, peripheral white blood cell

source_name: Patient FUSCCTNBC263 peripheral white blood cell


title: FUSCCTNBC284_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC284, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC284 fresh frozen primary tumor tissue


title: FUSCCTNBC262_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC262, peripheral white blood cell

source_name: Patient FUSCCTNBC262 peripheral white blood cell


title: FUSCCTNBC262_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC262, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC262 fresh frozen primary tumor tissue


title: FUSCCTNBC281_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC281, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC281 fresh frozen primary tumor tissue


title: FUSCCTNBC261_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC261, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC261 fresh frozen primary tumor tissue


title: FUSCCTNBC259_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC259, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC259 fresh frozen primary tumor tissue


title: FUSCCTNBC260_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC260, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC260 fresh frozen primary tumor tissue


title: FUSCCTNBC268_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC268, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC268 fresh frozen primary tumor tissue


title: FUSCCTNBC261_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC261, peripheral white blood cell

source_name: Patient FUSCCTNBC261 peripheral white blood cell


title: FUSCCTNBC257_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC257, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC257 fresh frozen primary tumor tissue


title: FUSCCTNBC418_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC418, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC418 fresh frozen primary tumor tissue


title: FUSCCTNBC256_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC256, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC256 fresh frozen primary tumor tissue


title: FUSCCTNBC278_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC278, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC278 fresh frozen primary tumor tissue


title: FUSCCTNBC256_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC256, peripheral white blood cell

source_name: Patient FUSCCTNBC256 peripheral white blood cell


title: FUSCCTNBC255_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC255, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC255 fresh frozen primary tumor tissue


title: FUSCCTNBC252_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC252, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC252 fresh frozen primary tumor tissue


title: FUSCCTNBC266_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC266, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC266 fresh frozen primary tumor tissue


title: FUSCCTNBC248_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC248, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC248 fresh frozen primary tumor tissue


title: FUSCCTNBC245_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC245, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC245 fresh frozen primary tumor tissue


title: FUSCCTNBC243_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC243, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC243 fresh frozen primary tumor tissue


title: FUSCCTNBC247_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC247, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC247 fresh frozen primary tumor tissue


title: FUSCCTNBC240_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC240, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC240 fresh frozen primary tumor tissue


title: FUSCCTNBC249_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC249, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC249 fresh frozen primary tumor tissue


title: FUSCCTNBC246_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC246, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC246 fresh frozen primary tumor tissue


title: FUSCCTNBC250_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC250, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC250 fresh frozen primary tumor tissue


title: FUSCCTNBC244_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC244, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC244 fresh frozen primary tumor tissue


title: FUSCCTNBC258_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC258, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC258 fresh frozen primary tumor tissue


title: FUSCCTNBC238_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC238, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC238 fresh frozen primary tumor tissue


title: FUSCCTNBC230_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC230, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC230 fresh frozen primary tumor tissue


title: FUSCCTNBC233_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC233, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC233 fresh frozen primary tumor tissue


title: FUSCCTNBC234_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC234, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC234 fresh frozen primary tumor tissue


title: FUSCCTNBC229_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC229, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC229 fresh frozen primary tumor tissue


title: FUSCCTNBC227_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC227, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC227 fresh frozen primary tumor tissue


title: FUSCCTNBC228_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC228, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC228 fresh frozen primary tumor tissue


title: FUSCCTNBC225_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC225, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC225 fresh frozen primary tumor tissue


title: FUSCCTNBC226_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC226, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC226 fresh frozen primary tumor tissue


title: FUSCCTNBC224_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC224, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC224 fresh frozen primary tumor tissue


title: FUSCCTNBC251_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC251, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC251 fresh frozen primary tumor tissue


title: FUSCCTNBC222_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC222, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC222 fresh frozen primary tumor tissue


title: FUSCCTNBC223_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC223, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC223 fresh frozen primary tumor tissue


title: FUSCCTNBC220_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC220, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC220 fresh frozen primary tumor tissue


title: FUSCCTNBC239_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC239, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC239 fresh frozen primary tumor tissue


title: FUSCCTNBC236_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC236, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC236 fresh frozen primary tumor tissue


title: FUSCCTNBC237_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC237, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC237 fresh frozen primary tumor tissue


title: FUSCCTNBC219_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC219, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC219 fresh frozen primary tumor tissue


title: FUSCCTNBC216_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC216, peripheral white blood cell

source_name: Patient FUSCCTNBC216 peripheral white blood cell


title: FUSCCTNBC216_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC216, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC216 fresh frozen primary tumor tissue


title: FUSCCTNBC212_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC212, peripheral white blood cell

source_name: Patient FUSCCTNBC212 peripheral white blood cell


title: FUSCCTNBC215_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC215, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC215 fresh frozen primary tumor tissue


title: FUSCCTNBC211_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC211, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC211 fresh frozen primary tumor tissue


title: FUSCCTNBC212_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC212, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC212 fresh frozen primary tumor tissue


title: FUSCCTNBC218_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC218, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC218 fresh frozen primary tumor tissue


title: FUSCCTNBC208_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC208, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC208 fresh frozen primary tumor tissue


title: FUSCCTNBC209_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC209, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC209 fresh frozen primary tumor tissue


title: FUSCCTNBC206_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC206, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC206 fresh frozen primary tumor tissue


title: FUSCCTNBC210_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC210, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC210 fresh frozen primary tumor tissue


title: FUSCCTNBC207_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC207, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC207 fresh frozen primary tumor tissue


title: FUSCCTNBC203_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC203, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC203 fresh frozen primary tumor tissue


title: FUSCCTNBC204_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC204, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC204 fresh frozen primary tumor tissue


title: FUSCCTNBC203_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC203, peripheral white blood cell

source_name: Patient FUSCCTNBC203 peripheral white blood cell


title: FUSCCTNBC202_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC202, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC202 fresh frozen primary tumor tissue


title: FUSCCTNBC201_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC201, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC201 fresh frozen primary tumor tissue


title: FUSCCTNBC201_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC201, peripheral white blood cell

source_name: Patient FUSCCTNBC201 peripheral white blood cell


title: FUSCCTNBC340_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC340, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC340 fresh frozen primary tumor tissue


title: FUSCCTNBC198_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC198, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC198 fresh frozen primary tumor tissue


title: FUSCCTNBC197_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC197, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC197 fresh frozen primary tumor tissue


title: FUSCCTNBC221_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC221, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC221 fresh frozen primary tumor tissue


title: FUSCCTNBC200_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC200, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC200 fresh frozen primary tumor tissue


title: FUSCCTNBC195_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC195, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC195 fresh frozen primary tumor tissue


title: FUSCCTNBC196_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC196, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC196 fresh frozen primary tumor tissue


title: FUSCCTNBC214_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC214, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC214 fresh frozen primary tumor tissue


title: FUSCCTNBC191_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC191, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC191 fresh frozen primary tumor tissue


title: FUSCCTNBC194_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC194, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC194 fresh frozen primary tumor tissue


title: FUSCCTNBC195_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC195, peripheral white blood cell

source_name: Patient FUSCCTNBC195 peripheral white blood cell


title: FUSCCTNBC192_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC192, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC192 fresh frozen primary tumor tissue


title: FUSCCTNBC184_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC184, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC184 fresh frozen primary tumor tissue


title: FUSCCTNBC205_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC205, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC205 fresh frozen primary tumor tissue


title: FUSCCTNBC186_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC186, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC186 fresh frozen primary tumor tissue


title: FUSCCTNBC189_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC189, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC189 fresh frozen primary tumor tissue


title: FUSCCTNBC188_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC188, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC188 fresh frozen primary tumor tissue


title: FUSCCTNBC185_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC185, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC185 fresh frozen primary tumor tissue


title: FUSCCTNBC181_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC181, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC181 fresh frozen primary tumor tissue


title: FUSCCTNBC183_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC183, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC183 fresh frozen primary tumor tissue


title: FUSCCTNBC232_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC232, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC232 fresh frozen primary tumor tissue


title: FUSCCTNBC179_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC179, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC179 fresh frozen primary tumor tissue


title: FUSCCTNBC182_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC182, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC182 fresh frozen primary tumor tissue


title: FUSCCTNBC180_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC180, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC180 fresh frozen primary tumor tissue


title: FUSCCTNBC178_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC178, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC178 fresh frozen primary tumor tissue


title: FUSCCTNBC199_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC199, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC199 fresh frozen primary tumor tissue


title: FUSCCTNBC176_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC176, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC176 fresh frozen primary tumor tissue


title: FUSCCTNBC177_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC177, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC177 fresh frozen primary tumor tissue


title: FUSCCTNBC177_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC177, peripheral white blood cell

source_name: Patient FUSCCTNBC177 peripheral white blood cell


title: FUSCCTNBC175_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC175, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC175 fresh frozen primary tumor tissue


title: FUSCCTNBC173_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC173, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC173 fresh frozen primary tumor tissue


title: FUSCCTNBC172_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC172, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC172 fresh frozen primary tumor tissue


title: FUSCCTNBC171_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC171, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC171 fresh frozen primary tumor tissue


title: FUSCCTNBC190_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC190, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC190 fresh frozen primary tumor tissue


title: FUSCCTNBC170_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC170, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC170 fresh frozen primary tumor tissue


title: FUSCCTNBC169_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC169, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC169 fresh frozen primary tumor tissue


title: FUSCCTNBC174_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC174, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC174 fresh frozen primary tumor tissue


title: FUSCCTNBC165_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC165, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC165 fresh frozen primary tumor tissue


title: FUSCCTNBC166_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC166, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC166 fresh frozen primary tumor tissue


title: FUSCCTNBC167_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC167, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC167 fresh frozen primary tumor tissue


title: FUSCCTNBC168_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC168, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC168 fresh frozen primary tumor tissue


title: FUSCCTNBC160_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC160, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC160 fresh frozen primary tumor tissue


title: FUSCCTNBC159_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC159, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC159 fresh frozen primary tumor tissue


title: FUSCCTNBC155_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC155, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC155 fresh frozen primary tumor tissue


title: FUSCCTNBC157_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC157, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC157 fresh frozen primary tumor tissue


title: FUSCCTNBC154_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC154, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC154 fresh frozen primary tumor tissue


title: FUSCCTNBC153_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC153, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC153 fresh frozen primary tumor tissue


title: FUSCCTNBC161_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC161, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC161 fresh frozen primary tumor tissue


title: FUSCCTNBC152_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC152, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC152 fresh frozen primary tumor tissue


title: FUSCCTNBC148_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC148, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC148 fresh frozen primary tumor tissue


title: FUSCCTNBC150_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC150, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC150 fresh frozen primary tumor tissue


title: FUSCCTNBC149_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC149, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC149 fresh frozen primary tumor tissue


title: FUSCCTNBC147_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC147, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC147 fresh frozen primary tumor tissue


title: FUSCCTNBC146_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC146, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC146 fresh frozen primary tumor tissue


title: FUSCCTNBC145_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC145, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC145 fresh frozen primary tumor tissue


title: FUSCCTNBC144_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC144, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC144 fresh frozen primary tumor tissue


title: FUSCCTNBC139_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC139, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC139 fresh frozen primary tumor tissue


title: FUSCCTNBC141_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC141, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC141 fresh frozen primary tumor tissue


title: FUSCCTNBC163_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC163, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC163 fresh frozen primary tumor tissue


title: FUSCCTNBC142_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC142, peripheral white blood cell

source_name: Patient FUSCCTNBC142 peripheral white blood cell


title: FUSCCTNBC138_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC138, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC138 fresh frozen primary tumor tissue


title: FUSCCTNBC150_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC150, peripheral white blood cell

source_name: Patient FUSCCTNBC150 peripheral white blood cell


title: FUSCCTNBC140_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC140, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC140 fresh frozen primary tumor tissue


title: FUSCCTNBC142_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC142, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC142 fresh frozen primary tumor tissue


title: FUSCCTNBC131_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC131, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC131 fresh frozen primary tumor tissue


title: FUSCCTNBC134_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC134, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC134 fresh frozen primary tumor tissue


title: FUSCCTNBC137_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC137, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC137 fresh frozen primary tumor tissue


title: FUSCCTNBC135_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC135, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC135 fresh frozen primary tumor tissue


title: FUSCCTNBC136_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC136, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC136 fresh frozen primary tumor tissue


title: FUSCCTNBC128_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC128, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC128 fresh frozen primary tumor tissue


title: FUSCCTNBC130_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC130, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC130 fresh frozen primary tumor tissue


title: FUSCCTNBC156_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC156, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC156 fresh frozen primary tumor tissue


title: FUSCCTNBC127_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC127, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC127 fresh frozen primary tumor tissue


title: FUSCCTNBC126_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC126, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC126 fresh frozen primary tumor tissue


title: FUSCCTNBC129_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC129, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC129 fresh frozen primary tumor tissue


title: FUSCCTNBC124_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC124, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC124 fresh frozen primary tumor tissue


title: FUSCCTNBC132_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC132, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC132 fresh frozen primary tumor tissue


title: FUSCCTNBC121_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC121, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC121 fresh frozen primary tumor tissue


title: FUSCCTNBC122_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC122, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC122 fresh frozen primary tumor tissue


title: FUSCCTNBC123_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC123, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC123 fresh frozen primary tumor tissue


title: FUSCCTNBC120_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC120, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC120 fresh frozen primary tumor tissue


title: FUSCCTNBC118_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC118, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC118 fresh frozen primary tumor tissue


title: FUSCCTNBC119_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC119, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC119 fresh frozen primary tumor tissue


title: Sample_T9-7

type: SRA

city: San Francisco

first: Charles

last: Chiu

state: CA

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

country: USA

institute: University of California, San Francisco

description: processed data file: FES_isoforms_FPKM.txt

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Reads were mapped to hg19 RefSeq annotation using Bowtie 2 version 2.2.2 as part of Tophat 2.
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks 2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: FES_isoforms_FPKM.txt: Tab-delimited text file includes gene isoforms abundance normalized as FPKM.

molecule: total RNA

source_name: whole blood

extract_protocol:
Whole blood (2.5 mL) from cases and controls was drawn into a PAXgene Blood RNA Tube (Qiagen, Valencia, CA) to stabilize RNA prior to extraction and stored at -20C. Total RNA was extracted using the PAXgene Blood RNA Kit (Qiagen, Valencia, CA) and all samples were lyophilized in RNAstable reagent (Biomatrica, San Diego, CA) for shipment at room temperature and long-term storage.
The Ovation Human blood RNA-seq kit (Nugen, San Carlos, CA) was used to generate strand-specific RNA-seq libraries depleted for reads derived from rRNA (12S, 16S, 18S and 28S genes) and globin (HBA1, HBA2, HBB and HBD genes) according to the manufacturer's protocol. Briefly, 100ng RNA extract, as measured by Qubit RNA high sensitivity kit (Thermo Fisher, South San Francisco), were DNased and cDNA was prepared from extracted total RNA by reverse transcription using a mixture of random and poly(T) primers. Successive steps of end-repair, adaptor ligation, strand selection via nucleotide analog-targeted degradation, insert-dependent adaptor cleavage for targeted depletion of rRNA and globin reads, PCR amplification, and bead-based purification were then used to construct cDNA libraries for RNA-seq analysis.

value: Whole blood

tag: disease state

value: Control

tag: treatment

value: Cardiopulmonary exercise

tag: timepoint (day)

tag: individual identifier


title: FUSCCTNBC117_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC117, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC117 fresh frozen primary tumor tissue


title: FUSCCTNBC116_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC116, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC116 fresh frozen primary tumor tissue


title: Sample_T9-3


title: FUSCCTNBC115_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC115, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC115 fresh frozen primary tumor tissue


title: Sample_T9-1


title: Sample_T9-2


title: Sample_T6-7


title: FUSCCTNBC113_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC113, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC113 fresh frozen primary tumor tissue


title: Sample_T6-3


title: FUSCCTNBC112_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC112, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC112 fresh frozen primary tumor tissue


title: FUSCCTNBC114_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC114, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC114 fresh frozen primary tumor tissue


title: Sample_T6-2


title: FUSCCTNBC158_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC158, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC158 fresh frozen primary tumor tissue


title: FUSCCTNBC110_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC110, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC110 fresh frozen primary tumor tissue


title: FUSCCTNBC108_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC108, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC108 fresh frozen primary tumor tissue


title: Sample_T14-7


title: Sample_T6-1


title: Sample_T14-1


title: FUSCCTNBC107_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC107, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC107 fresh frozen primary tumor tissue


title: FUSCCTNBC109_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC109, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC109 fresh frozen primary tumor tissue


title: Sample_T14-3


title: FUSCCTNBC107_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC107, peripheral white blood cell

source_name: Patient FUSCCTNBC107 peripheral white blood cell


title: Sample_T13-2


title: FUSCCTNBC105_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC105, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC105 fresh frozen primary tumor tissue


title: Sample_T13-3


title: FUSCCTNBC106_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC106, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC106 fresh frozen primary tumor tissue


title: Sample_T13-7


title: Sample_T13-1


title: FUSCCTNBC104_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC104, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC104 fresh frozen primary tumor tissue


title: FUSCCTNBC103_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC103, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC103 fresh frozen primary tumor tissue


title: Sample_T11-7

description: processed data file: FES_isoforms_FPKM.txt

source_name: whole blood


title: FUSCCTNBC100_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC100, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC100 fresh frozen primary tumor tissue


title: Sample_T11-1


title: FUSCCTNBC111_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC111, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC111 fresh frozen primary tumor tissue


title: Sample_T11-2


title: Sample_T11-3


title: FUSCCTNBC101_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC101, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC101 fresh frozen primary tumor tissue


title: FUSCCTNBC102_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC102, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC102 fresh frozen primary tumor tissue


title: Sample_T14-2


title: Sample_T10-3


title: Sample_T10-2


title: Sample_T10-1


title: FUSCCTNBC098_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC098, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC098 fresh frozen primary tumor tissue


title: FUSCCTNBC097_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC097, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC097 fresh frozen primary tumor tissue


title: FUSCCTNBC092_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC092, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC092 fresh frozen primary tumor tissue


title: FUSCCTNBC094_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC094, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC094 fresh frozen primary tumor tissue


title: FUSCCTNBC099_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC099, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC099 fresh frozen primary tumor tissue


title: Sample_P8-7

value: ME/CFS


title: Sample_P8-3


title: FUSCCTNBC089_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC089, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC089 fresh frozen primary tumor tissue


title: Sample_P8-2


title: Sample_P7-7


title: FUSCCTNBC091_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC091, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC091 fresh frozen primary tumor tissue


title: Sample_T10-7


title: FUSCCTNBC088_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC088, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC088 fresh frozen primary tumor tissue


title: Sample_P7-3


title: Sample_P8-1


title: FUSCCTNBC086_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC086, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC086 fresh frozen primary tumor tissue


title: FUSCCTNBC087_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC087, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC087 fresh frozen primary tumor tissue


title: Sample_P7-2


title: FUSCCTNBC085_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC085, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC085 fresh frozen primary tumor tissue


title: FUSCCTNBC093_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC093, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC093 fresh frozen primary tumor tissue


title: FUSCCTNBC083_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC083, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC083 fresh frozen primary tumor tissue


title: FUSCCTNBC082_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC082, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC082 fresh frozen primary tumor tissue


title: FUSCCTNBC081_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC081, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC081 fresh frozen primary tumor tissue


title: Sample_P7-1

description: processed data file: FES_isoforms_FPKM.txt

source_name: whole blood


title: Sample_P6-7


title: Sample_P6-3


title: Sample_P6-2


title: Sample_P6-1


title: FUSCCTNBC078_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC078, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC078 fresh frozen primary tumor tissue


title: FUSCCTNBC077_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC077, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC077 fresh frozen primary tumor tissue


title: Sample_P5-7


title: FUSCCTNBC080_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC080, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC080 fresh frozen primary tumor tissue


title: FUSCCTNBC076_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC076, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC076 fresh frozen primary tumor tissue


title: Sample_P5-3


title: FUSCCTNBC075_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC075, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC075 fresh frozen primary tumor tissue


title: Sample_P5-2


title: Sample_P5-1


title: FUSCCTNBC074_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC074, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC074 fresh frozen primary tumor tissue


title: FUSCCTNBC073_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC073, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC073 fresh frozen primary tumor tissue


title: Sample_P3-7


title: FUSCCTNBC072_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC072, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC072 fresh frozen primary tumor tissue


title: FUSCCTNBC070_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC070, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC070 fresh frozen primary tumor tissue


title: Sample_P3-2


title: Sample_P3-3


title: Sample_P3-1


title: FUSCCTNBC069_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC069, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC069 fresh frozen primary tumor tissue


title: FUSCCTNBC066_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC066, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC066 fresh frozen primary tumor tissue


title: FUSCCTNBC068_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC068, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC068 fresh frozen primary tumor tissue


title: Sample_P14-7


title: Sample_P14-2


title: FUSCCTNBC064_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC064, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC064 fresh frozen primary tumor tissue


title: progressor 11

type: RNA

city: Madrid

first: Monica

last: Martinez-Fernandez

address: Avda Complutense 40

country: Spain

institute: CIEMAT

hyb_protocol: Following fragmentation, 5.5 ug of fragmented and labeled ss-DNA were hybridized for 16 hr at 45ºC at 60 rpm on Hybridization Oven 640 de Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 7G de Affymetrix

data_processing: Expression data were normalized, background-and batch corrected using the Guanine Cytosine Count Normalization (GCCN) and Signal Space Transformation (SST), and prior to summarizing using the Robust Multi-Array Average (RMA) algorithm implemented in the Affymetrix Expression Console software. In order to combine the different microarray data sets, possible batch effects were corrected by using the Bioconductor Combat package in R environment (Johnson et al., 2007)

source_name: progressor

label_protocol: cRNA is converted to biotinylated sense-strand DNA prepared according to the standard Affymetrix protocol from 12 ngs total RNA (GeneChip Whole Trasncript WT Expression Arrays, Affymetrix).

extract_protocol: Total RNA was extracted from ten serial sections (10µm) of each tumor sample using the miRNeasy FFPE Kit (Qiagen, Venlo, Netherlands) according to the manufacturer’s recommendations

treatment_protocol: All subjects received pembrolizumab 200 mg every three weeks until disease progression or until completion of 2 years of therapy regardless of PD-L1 status

value: bladder cancer

value: pembrolizumab

tag: treatment response

value: progressor

value: Bladder


title: FUSCCTNBC063_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC063, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC063 fresh frozen primary tumor tissue


title: Sample_P14-1


title: Maresi_Roots_Drought_repl1

city: Katowice

first: Agnieszka

last: Janiak

address: Jagiellonska 28

department: Department of Genetics

country: Poland

institute: University of Silesia in Katowice

description:
Gene expression in roots of Maresi barley breeding line in mild drought
P_Mar_R_d_46

hyb_protocol: 55 µl of 2x the GE Hybridization mix (Agilent GE Hybridization Kit) was added to the fragmented cRNA and 110 was loaded onto the Agilent 4x44k Barley Array within a gasket array slide sandwich. Arrays were hybridised in a rotisserie hybridisation oven at 65°C for 17 hours (Agilent p/n G2545a Hybridization Oven). After 17 hours, the slides were removed from the oven and washed with Agilent Wash Buffers containing Triton X.

scan_protocol: After the wash, the slides were taken to be scanned on an Agilent High Resolution Scanner using the green dye channel at a resolution of a 5 µm single pass scan with no extended dynamic range

data_processing: Scanned images were analysed using Agilent Feature extraction software version 10.7.3.1.

organism: Hordeum vulgare

source_name: Maresi, roots, 10-days mild drought, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of RNA using the the Agilent Low Input Quick Amp Kit according to the manufacturer's instructions, followed by Qiagen RNeasy Mini Kit column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Grains of CamB and Maresi genotypes were sterilized and initially 20 grains were placed in the Double-walled Kick-Brauckman’s pots of 10 dm3 capacity. After germination, the number of plants was reduced to 10. The pots were filled with a mixture of sandy loam and sand (7:2, w/w).

extract_protocol: Total RNA was isolated using an RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions. After isolation, RNA was purified using precipitation in 1M lithium chloride. Each RNA precipitate was dissolved in nuclease-free H2O. The yield and purity of the RNA was determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). The integrity of the RNA was checked using denaturation agarose gel electrophoresis using pre-cast gels and FlashGel RNA System (Lonza, Basel, Switzerland).

treatment_protocol: The analysis of water retention curve for the soil substrate (sandy loam:sand, 7:2, w/w) showed that a pF range of 2.2-3.0 indicated easily available water. At the pF 3.0-4.2 water was less available, creating the conditions of a drought stress and the pF > 4.2 was a permanent wilting point. Two water regimes were used: control conditions with the pF range of pF 2.2-3.0 and a mild drought with pF value kept at the range of 3.4-3.6, which was applied at the 3-leaf seedling stage and lasted for 10 days.

tag: genotype

value: Maresi

tag: phenotype

value: more drought-susceptible

value: Drought

value: whole root system


title: progressor 10


title: progressor 7


title: progressor 9


title: Sample_P14-3

source_name: whole blood


title: Sample_P11-7


title: progressor 8


title: Maresi_Roots_Control_repl1

description:
Gene expression in roots of Maresi barley breeding line in control conditions
P_Mar_R_c_43

source_name: Maresi, roots, control conditions, replicate 1


title: Sample_P11-3

description: processed data file: FES_isoforms_FPKM.txt


title: responder to therapy 4

source_name: responder to therapy

value: responder to therapy


title: Maresi_Roots_Control_repl3

description:
Gene expression in roots of Maresi barley breeding line in control conditions
P_Mar_R_c_45

source_name: Maresi, roots, control conditions, replicate 3


title: FUSCCTNBC061_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC061, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC061 fresh frozen primary tumor tissue


title: FUSCCTNBC060_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC060, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC060 fresh frozen primary tumor tissue


title: Maresi_Roots_Drought_repl2

description:
Gene expression in roots of Maresi barley breeding line in mild drought
P_Mar_R_d_47

source_name: Maresi, roots, 10-days mild drought, replicate 2


title: Maresi_Leaf_Drought_repl3

description:
Gene expression in leaf of Maresi barley breeding line in mild drought
P_Mar_L_d_42

source_name: Maresi, leaf no.2, 10-days mild drought, replicate 3

value: second leaf


title: Maresi_Roots_Drought_repl3

description:
Gene expression in roots of Maresi barley breeding line in mild drought
P_Mar_R_d_48

source_name: Maresi, roots, 10-days mild drought, replicate 3


title: responder to therapy 5


title: responder to therapy 6


title: Sample_P11-2


title: FUSCCTNBC059_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC059, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC059 fresh frozen primary tumor tissue


title: LRRK2_WT

city: Maastricht

first: Silvia

last: Bolognin

state: -- None selected --

address: Universiteitssingel 40,

country: Netherlands

institute: Maastricht University

description: Day 0 = stem cells, Days 10, 14, 42 = DA neurons

data_processing:
Bcl2fastq ver 2.0 was used for the base calling
Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Dropseq implementation (Macosko et al; 2015), the reads were demultiplexed for the cell barcode and UMI. The genes mapped to hg19 whole genome using STAR genome aligner - with default parameters
Barcode and UMI are in R1 and as in the original Dropseq paper (Mackoso et al., 2015): barcode 1-12 basepairs and UMI 13-20.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts

source_name: IPSC

growth_protocol: as described in Reinhardt et al., 2013 Plos ONE doi.org/10.1371/journal.pone.0059252

extract_protocol: Single cell RNA seq using Dropseq - 3' bead based enrichment technique, using SMART synthesis (Macosko et al, 2015 doi: 10.1016/j.cell.2015.05.002)

tag: cell type

value: stem cells and DA neurons


title: FUSCCTNBC058_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC058, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC058 fresh frozen primary tumor tissue

value: Primary triple negative breast cancer


title: Maresi_Leaf_Drought_repl1

description:
Gene expression in leaf of Maresi barley breeding line in mild drought
P_Mar_L_d_40

source_name: Maresi, leaf no.2, 10-days mild drought, replicate 1


title: Sample_P11-1


title: responder to therapy 2


title: scRNA data of lung cells from naive mouse_sample 4_K8

city: Pittsburgh

first: Zhe

last: Sun

state: PA

address: 130 DeSoto Street

institute: University of Pittsburgh

description: scRNA data from lung cells

data_processing:
Standard 10X Genomics CellRanger pipeline
Genome_build: mm10
In our multiple fastq files, R1 read is biological, R2 is 14bp GemCode barcode, R3 is 10bp UMI and I1 is 8bp sample index.
Supplementary_files_format_and_content: for each sample, there are one mtx file with filtered gene expressing UMI counts for each sample; a tsv file containing gene names; a tsv file with cell barcodes.

organism: Mus musculus

source_name: lung

extract_protocol:
Sorted cells were loaded into the Single Cell Chip and processed through the 10X controller for droplet generation, resulting in droplets containing a single cell and bead per droplet
Chromium Single Cell 3' RNA-seq libraries were prepared for sequencing using standard 10X Genomics protocols

tag: strain

value: lung

tag: agent

value: Naïve


title: responder to therapy 3


title: scRNA data of lung cells from streptococcus pneumonia (SP) infected mouse_sample 2_K6

description: scRNA data from lung cells

value: streptococcus pneumonia (SP) infected


title: Sample_P10-3

value: Whole blood

value: Cardiopulmonary exercise


title: Maresi_Leaf_Drought_repl2

description:
Gene expression in leaf of Maresi barley breeding line in mild drought
P_Mar_L_d_41

source_name: Maresi, leaf no.2, 10-days mild drought, replicate 2


title: FUSCCTNBC056_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC056, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC056 fresh frozen primary tumor tissue


title: responder to therapy 1

value: bladder cancer


title: Maresi_Leaf_Control_repl2

description:
Gene expression in leaf of Maresi barley breeding line in control conditions
P_Mar_L_c_38

source_name: Maresi, leaf no.2, control conditions, replicate 2

value: Control


title: Maresi_Leaf_Control_repl3

description:
Gene expression in leaf of Maresi barley breeding line in control conditions
P_Mar_L_c_39

source_name: Maresi, leaf no.2, control conditions, replicate 3


title: Maresi_Leaf_Control_repl1

description:
Gene expression in leaf of Maresi barley breeding line in control conditions
P_Mar_L_c_37

source_name: Maresi, leaf no.2, control conditions, replicate 1


title: Sample_P10-2

source_name: whole blood

value: ME/CFS


title: Sample_P10-7


title: FUSCCTNBC057_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC057, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC057 fresh frozen primary tumor tissue


title: scRNA data of lung cells from streptococcus pneumonia (SP) infected mouse_sample 1_K5

description: scRNA data from lung cells

data_processing:
Standard 10X Genomics CellRanger pipeline
In our multiple fastq files, R1 read is biological, R2 is 14bp GemCode barcode, R3 is 10bp UMI and I1 is 8bp sample index.
Genome_build: mm10
Supplementary_files_format_and_content: for each sample, there are one mtx file with filtered gene expressing UMI counts for each sample; a tsv file containing gene names; a tsv file with cell barcodes.


title: FUSCCTNBC054_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC054, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC054 fresh frozen primary tumor tissue


title: Sample_P10-1

description: processed data file: FES_isoforms_FPKM.txt


title: Maresi_Roots_Control_repl2

description:
Gene expression in roots of Maresi barley breeding line in control conditions
P_Mar_R_c_44

source_name: Maresi, roots, control conditions, replicate 2


title: FUSCCTNBC053_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC053, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC053 fresh frozen primary tumor tissue


title: CamB_Roots_Drought_repl1

description:
Gene expression in roots of CamB barley breeding line in mild drought
P_Cam_R_d_34

source_name: CamB, roots, 10-days mild drought, replicate 1

value: CamB

value: less drought-susceptible


title: LRRK2_G2019S


title: CamB_Roots_Drought_repl3

description:
Gene expression in roots of CamB barley breeding line in mild drought
P_Cam_R_d_36

source_name: CamB, roots, 10-days mild drought, replicate 3


title: CamB_Roots_Drought_repl2

description:
Gene expression in roots of CamB barley breeding line in mild drought
P_Cam_R_d_35

source_name: CamB, roots, 10-days mild drought, replicate 2


title: Nontumor_FBXL5KO_2820_rep5

city: St. Louis

first: Yoshiharu

last: Muto

state: MO

address: 660. S Euclid Ave., CB 8118

department: Medicine / Nephrology

institute: Washington University in St. Louis

description:
liver_fbxl5_fpkm.csv
Sample 22

data_processing:
The total amount of each transcript was calculated with the use of a series of programs including TopHat2 and Cufflinks.
RNA-seq reads were mapped against the mouse (mm10) genome.
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated values (csv) files include FPKM values for each Sample ...

source_name: Liver

extract_protocol:
TRIzol Plus RNA Purification Kit (Life Technologies)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A single dose (25 mg/kg) of diethylnitrosamine (Sigma) was injected intraperitoneally in mice at 15 days of age

value: mixed genetic background (C57BL/6;129/Sv)

value: liver (nontumor tissue)


title: scRNA data of lung cells from naive mouse_sample 3_K7

description: scRNA data from lung cells


title: Nontumor_FBXL5KO_2820_rep4

description:
liver_fbxl5_fpkm.csv
Sample 21


title: CamB_Roots_Control_repl2

description:
Gene expression in roots of CamB barley breeding line in control conditions
P_Cam_R_c_32

source_name: CamB, roots, control conditions, replicate 2

value: whole root system


title: Sample_K7-7


title: FUSCCTNBC055_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC055, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC055 fresh frozen primary tumor tissue


title: Nontumor_FBXL5KO_2820_rep3

description:
liver_fbxl5_fpkm.csv
Sample 20


title: Sample_K7-2


title: Sample_K7-3


title: Nontumor_FBXL5KO_2820_rep1

description:
liver_fbxl5_fpkm.csv
Sample 18


title: Nontumor_FBXL5KO_2820_rep2

description:
liver_fbxl5_fpkm.csv
Sample 19


title: FUSCCTNBC050_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC050, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC050 fresh frozen primary tumor tissue


title: FUSCCTNBC051_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC051, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC051 fresh frozen primary tumor tissue


title: Sample_K4-7


title: Sample_K7-1


title: Sample_K4-3


title: Nontumor_control_2822_rep2

description:
liver_fbxl5_fpkm.csv
Sample 16

value: control


title: Sample_K4-2


title: FUSCCTNBC052_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC052, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC052 fresh frozen primary tumor tissue


title: Sample_K4-1


title: FUSCCTNBC047_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC047, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC047 fresh frozen primary tumor tissue


title: FUSCCTNBC046_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC046, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC046 fresh frozen primary tumor tissue


title: Sample_K2-7


title: FUSCCTNBC049_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC049, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC049 fresh frozen primary tumor tissue


title: Nontumor_control_2821_rep3

description:
liver_fbxl5_fpkm.csv
Sample 14


title: Nontumor_control_2822_rep3

description:
liver_fbxl5_fpkm.csv
Sample 17


title: Nontumor_control_2821_rep2

description:
liver_fbxl5_fpkm.csv
Sample 13


title: CamB_Leaf_Drought_repl1

description:
Gene expression in leaf of CamB barley breeding line in mild drought
P_Cam_L_d_28

source_name: CamB, leaf no.2, 10-days mild drought, replicate 1

value: Drought

value: second leaf


title: Sample_K2-3

source_name: whole blood


title: CamB_Roots_Control_repl1

description:
Gene expression in roots of CamB barley breeding line in control conditions
P_Cam_R_c_31

source_name: CamB, roots, control conditions, replicate 1


title: CamB_Leaf_Drought_repl3

description:
Gene expression in leaf of CamB barley breeding line in mild drought
P_Cam_L_d_30

source_name: CamB, leaf no.2, 10-days mild drought, replicate 3


title: CamB_Leaf_Control_repl3

description:
Gene expression in leaf of CamB barley breeding line in control conditions
P_Cam_L_c_27

source_name: CamB, leaf no.2, control conditions, replicate 3


title: CamB_Leaf_Drought_repl2

description:
Gene expression in leaf of CamB barley breeding line in mild drought
P_Cam_L_d_29

source_name: CamB, leaf no.2, 10-days mild drought, replicate 2


title: FUSCCTNBC044_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC044, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC044 fresh frozen primary tumor tissue

value: Primary triple negative breast cancer


title: CamB_Leaf_Control_repl2

description:
Gene expression in leaf of CamB barley breeding line in control conditions
P_Cam_L_c_26

source_name: CamB, leaf no.2, control conditions, replicate 2


title: FUSCCTNBC048_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC048, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC048 fresh frozen primary tumor tissue


title: AM: 6720_REP1

city: Potsdam-Golm

first: Tegan

last: Armarego-Marriott

address: Am Muehlenberg, 1

country: Germany

institute: Max Planck Institute of Molecular Plant Physiology

data_processing:
Quality control: Quality of obtained Illumina single-end sequences was tested with FastQC v0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). As no overrepresented sequences were detected, an additional 3'-trimming step was skipped.
Mapping: To reduce complexity, and because the project aimed to defined and identify evolutionarily conserved features, we mapped to the tobacco maternal (Renny-Byfield et al., 2011) progenitor N. sylvestris, as opposed to N. tabacum (Sierro et al., 2014). Mapping was undertaken using BWA v0.70 in aln mode with default parameters (Li and Durbin, 2009). Samtools v1.0 was used to create, sort and index the alignment data in BAM format and calculate transcript counts (Li et al., 2009).
Read counting: Samtools v1.0 was used to create, sort and index the alignment data in BAM format and calculate transcript counts (Li et al., 2009).
Genome_build: N. sylvestris (ftp://ftp.ncbi.nlm.nih.gov/genomes/Nicotiana_sylvestris/RNA/rna.fa.gz; file date 10/24/14
Supplementary_files_format_and_content: Read count output files (ASCII format): NCBI GI identifier, Read count

molecule: polyA RNA

organism: Nicotiana tabacum

source_name: pool of two youngest leaves from each of three replica plants

growth_protocol: Nicotiana tabacum plants were grown on soil until near maturity under long day (16 hours light, 350 uE/m2/s), and subjected to extended dark treatment.

extract_protocol:
Leaf harvests at day 3 were done at 10 h and 15 h after dawn and at day 4 at 9 h after dawn. Frozen leaf tissue (40 - 100 mg) from three independent replicates each of bacteria-primed and mock treated plants was ground (2 x 45 s, maximum frequency) by a Retsch mill (MM 400, Retsch, Haan, Germany). Each harvest was a single young systemic leaf from a single rosette. The harvested systemic leaves were all developmentally younger than the previously locally infected leaves. RNA was extracted with the RNeasy Plant Mini Kit according to the manual (QIAGEN GmbH, Hilden, Germany). RNA was quantified with a Qubit® RNA HS Assay Kit (ThermoFisher Scientific Life Technologies GmbH, Darmstadt, Germany) and RNA quality was further assessed by agarose gel electrophoresis.
RNA samples were sequenced at the Max Planck Genome Centre (MP-GC, Cologne, Germany), with an Illumina HiSeq2500 (Illumina, San Diego, CA). Single end, 100 bp reads to a minimum of 30 million (± 10%) reads per sample were undertaken using a TruSeq RNA library prepared by the MP-GC.

treatment_protocol: Whole plants were submitted to extended dark treatment. Young growing leaves were pale (etiolated). Leaf tissue was taken following return to the light (t=0) to observe de-etiolation. Samples were taken the middle section (excluding leaf-tip and basal region) of two leaves of each of three replica plants. These samples were pooled to make one biological repeat.

value: de-etiolating tobacco leaves

value: Extended dark

tag: harvest time after treatment

value: 6720 minutes


title: AK: 2400_REP1

value: 2400 minutes


title: AL: 3840_REP1

value: 3840 minutes


title: CamB_Roots_Control_repl3

description:
Gene expression in roots of CamB barley breeding line in control conditions
P_Cam_R_c_33

source_name: CamB, roots, control conditions, replicate 3


title: Sample_K2-2

description: processed data file: FES_isoforms_FPKM.txt

value: Whole blood

value: Cardiopulmonary exercise


title: FUSCCTNBC040_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC040, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC040 fresh frozen primary tumor tissue


title: CamB_Leaf_Control_repl1

description:
Gene expression in leaf of CamB barley breeding line in control conditions
P_Cam_L_c_25

source_name: CamB, leaf no.2, control conditions, replicate 1

value: Control


title: Tumor_FBXL5KO_2820_T5

description:
liver_fbxl5_fpkm.csv
Sample 11

source_name: Liver

value: liver (tumor tissue)


title: AI: 0480_REP1

value: 0480 minutes


title: Sample_K2-1


title: FUSCCTNBC045_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC045, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC045 fresh frozen primary tumor tissue


title: FUSCCTNBC039_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC039, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC039 fresh frozen primary tumor tissue


title: AH: 0240_REP1

value: 0240 minutes


title: AJ: 0960_REP1

value: 0960 minutes


title: Tumor_FBXL5KO_2820_T3

description:
liver_fbxl5_fpkm.csv
Sample 9

value: mixed genetic background (C57BL/6;129/Sv)


title: FUSCCTNBC038_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC038, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC038 fresh frozen primary tumor tissue


title: Sample_K12-7


title: Sample_K12-3


title: Nontumor_control_2821_rep1

description:
liver_fbxl5_fpkm.csv
Sample 12

value: liver (nontumor tissue)

value: control


title: FUSCCTNBC037_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC037, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC037 fresh frozen primary tumor tissue


title: Tumor_FBXL5KO_2820_T4

description:
liver_fbxl5_fpkm.csv
Sample 10


title: Tumor_FBXL5KO_2820_T2

description:
liver_fbxl5_fpkm.csv
Sample 8


title: Sample_K12-2

source_name: whole blood


title: AF: 0060_REP1

value: 0060 minutes


title: Sample_K12-1


title: Tumor_control_2822_T2

description:
liver_fbxl5_fpkm.csv
Sample 5


title: Tumor_FBXL5KO_2820_T1

description:
liver_fbxl5_fpkm.csv
Sample 7


title: Sample_K1-7


title: FUSCCTNBC036_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC036, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC036 fresh frozen primary tumor tissue

value: Primary triple negative breast cancer


title: FUSCCTNBC034_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC034, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC034 fresh frozen primary tumor tissue


title: Sample_K1-3


title: AC: 0005_REP1

value: de-etiolating tobacco leaves

value: 0005 minutes


title: AD: 0010_REP1

value: Extended dark

value: 0010 minutes


title: AE: 0030_REP1

value: 0030 minutes


title: Nontumor_control_2822_rep1

description:
liver_fbxl5_fpkm.csv
Sample 15


title: AB: 0000_REP1

value: 0000 minutes


title: AG: 0120_REP1

value: 0120 minutes


title: Tumor_control_2822_T1

description:
liver_fbxl5_fpkm.csv
Sample 4


title: AA: Control_REP1

value: control (no darkness)

value: Control minunts


title: FUSCCTNBC030_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC030, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC030 fresh frozen primary tumor tissue


title: FUSCCTNBC032_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC032, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC032 fresh frozen primary tumor tissue


title: Z: 6720_REP2

value: 6720 minutes


title: Sample_K1-1

value: Whole blood

value: Control

value: Cardiopulmonary exercise


title: Sample_G9-7

value: ME/CFS


title: Tumor_control_2821_T3

description:
liver_fbxl5_fpkm.csv
Sample 3

value: mixed genetic background (C57BL/6;129/Sv)

value: liver (tumor tissue)

value: control


title: FUSCCTNBC033_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC033, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC033 fresh frozen primary tumor tissue

value: Primary triple negative breast cancer


title: FUSCCTNBC029_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC029, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC029 fresh frozen primary tumor tissue


title: Tumor_control_2821_T1

description:
liver_fbxl5_fpkm.csv
Sample 1


title: Tumor_control_2821_T2

description:
liver_fbxl5_fpkm.csv
Sample 2


title: FUSCCTNBC031_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC031, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC031 fresh frozen primary tumor tissue


title: Sample_G9-2


title: FUSCCTNBC028_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC028, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC028 fresh frozen primary tumor tissue


title: FUSCCTNBC027_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC027, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC027 fresh frozen primary tumor tissue


title: X: 2400_REP2

source_name: pool of two youngest leaves from each of three replica plants

value: de-etiolating tobacco leaves

value: 2400 minutes


title: Sample_G9-3


title: Y: 3840_REP2

value: Extended dark

value: 3840 minutes


title: FUSCCTNBC026_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC026, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC026 fresh frozen primary tumor tissue


title: Sample_K1-2

description: processed data file: FES_isoforms_FPKM.txt


title: macaque8_ICD

city: Davis

first: Samuel

middle: Taler

last: Westreich

address: 1 Shields Ave

department: Genome Center

institute: University of California, Davis

data_processing:
Paired-end alignment with PEAR software
Cleanup & low-quality sequence removal with Trimmomatic
Removal of ribosomal sequences with SortMeRNA
Annotation with DIAMOND against RefSeq Bacteria database (release 102, 22 December 2015)
Aggregation by genus with SAMSA2 pipeline script
Normalization with R and DESeq2 package
Supplementary_files_format_and_content: Processed data files contain annotation results against RefSeq bacterial complete database for either best organism match (top 1) or best function match (top 1) per read.  Results are normalized across all samples, done using the DESeq package.

organism: Macaca mulatta

source_name: feces

extract_protocol:
Total RNA was extracted using Qiagen's RNeasy Micro kit, with RNA concentration and integrity verified by BioAnalyzer
Ribodepletion was performed using Illumina Ribo-Zero Gold (Epidemiology) kit, then cDNA libraries were prepared for PE100 sequencing

treatment_protocol: feces were frozen at -80 degrees Celsius and preserved in RNAlater

tag: diagnosis

value: ICD

tag: ribodepletion

value: ribodepleted


title: macaque9_ICD


title: V: 0480_REP2

value: 0480 minutes


title: FUSCCTNBC025_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC025, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC025 fresh frozen primary tumor tissue


title: Sample_G4-7


title: macaque6_ICD


title: FUSCCTNBC024_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC024, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC024 fresh frozen primary tumor tissue


title: Sample_G4-3


title: macaque7_ICD


title: macaque5_ICD


title: U: 0240_REP2

value: 0240 minutes


title: Sample_G4-2


title: T: 0120_REP2

value: 0120 minutes


title: FUSCCTNBC023_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC023, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC023 fresh frozen primary tumor tissue


title: macaque4_ICD


title: W: 0960_REP2

value: 0960 minutes


title: S: 0060_REP2

value: 0060 minutes


title: Sample_G9-1

value: Whole blood

value: Cardiopulmonary exercise


title: Sample_G2-7

value: ME/CFS


title: macaque2_ICD


title: R: 0030_REP2

value: 0030 minutes


title: Q: 0010_REP2

value: 0010 minutes


title: FUSCCTNBC021_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC021, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC021 fresh frozen primary tumor tissue

value: Primary triple negative breast cancer


title: Sample_G2-2

source_name: whole blood


title: P: 0005_REP2

value: de-etiolating tobacco leaves

value: 0005 minutes


title: Sample_G4-1


title: macaque24_control

value: control


title: Tumor_control_2822_T3

description:
liver_fbxl5_fpkm.csv
Sample 6

source_name: Liver

value: mixed genetic background (C57BL/6;129/Sv)

value: liver (tumor tissue)


title: macaque23_control

value: ribodepleted


title: O: 0000_REP2

value: Extended dark

value: 0000 minutes


title: Sample_G2-1


title: FUSCCTNBC022_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC022, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC022 fresh frozen primary tumor tissue


title: Sample_G13-7


title: macaque21_control


title: M: 6720_REP3

value: 6720 minutes


title: N: Control_REP2

value: control (no darkness)

value: Control minunts


title: macaque22_control


title: macaque3_ICD

value: ICD


title: FUSCCTNBC018_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC018, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC018 fresh frozen primary tumor tissue


title: FUSCCTNBC017_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC017, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC017 fresh frozen primary tumor tissue


title: FUSCCTNBC016_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC016, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC016 fresh frozen primary tumor tissue


title: FUSCCTNBC015_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC015, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC015 fresh frozen primary tumor tissue


title: FUSCCTNBC019_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC019, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC019 fresh frozen primary tumor tissue


title: macaque20_control


title: Sample_G2-3

value: Whole blood

value: Cardiopulmonary exercise


title: Sample_G13-2

value: ME/CFS


title: Sample_G13-3


title: FUSCCTNBC013_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC013, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC013 fresh frozen primary tumor tissue


title: L: 3840_REP3

value: 3840 minutes


title: macaque19_control


title: J: 0960_REP3

value: 0960 minutes


title: FUSCCTNBC012_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC012, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC012 fresh frozen primary tumor tissue

value: Primary triple negative breast cancer


title: K: 2400_REP3

source_name: pool of two youngest leaves from each of three replica plants

value: de-etiolating tobacco leaves

value: 2400 minutes


title: Sample_G12-3


title: FUSCCTNBC011_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC011, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC011 fresh frozen primary tumor tissue


title: macaque18_control

source_name: feces

value: control


title: Sample_G12-2


title: FUSCCTNBC010_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC010, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC010 fresh frozen primary tumor tissue


title: macaque17_control


title: FUSCCTNBC009_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC009, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC009 fresh frozen primary tumor tissue


title: H: 0240_REP3

value: 0240 minutes


title: I: 0480_REP3

value: 0480 minutes


title: G: 0120_REP3

value: Extended dark

value: 0120 minutes


title: Sample_G1-7


title: F: 0060_REP3

value: 0060 minutes


title: Sample_G1-3


title: macaque15_control

value: ribodepleted


title: FUSCCTNBC007_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC007, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC007 fresh frozen primary tumor tissue


title: macaque1_ICD


title: FUSCCTNBC006_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC006, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC006 fresh frozen primary tumor tissue


title: E: 0030_REP3

value: 0030 minutes


title: macaque14_control


title: macaque13_control


title: FUSCCTNBC008_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC008, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC008 fresh frozen primary tumor tissue


title: Sample_G1-1

description: processed data file: FES_isoforms_FPKM.txt

source_name: whole blood


title: D: 0010_REP3

value: 0010 minutes


title: Sample_G1-2

value: Whole blood


title: C: 0005_REP3

value: 0005 minutes


title: FUSCCTNBC004_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC004, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC004 fresh frozen primary tumor tissue


title: FUSCCTNBC005_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC005, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC005 fresh frozen primary tumor tissue


title: macaque12_ICD

value: ICD


title: macaque11_ICD


title: FUSCCTNBC002_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC002, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC002 fresh frozen primary tumor tissue


title: Sample_G12-1

value: ME/CFS

value: Cardiopulmonary exercise


title: B: 0000_REP3

value: 0000 minutes


title: macaque10_ICD


title: A: Control_REP3

value: de-etiolating tobacco leaves

value: control (no darkness)

value: 0000 minutes (no treatment)


title: FUSCCTNBC001_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC001, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC001 fresh frozen primary tumor tissue

value: Primary triple negative breast cancer