title: D17-188009: ATF6f/XBP1s 37C, Rep3

description: Sample 9 ATF6f/XBP1s 37C, Rep3


title: D17-188002: Basal 37C, Rep2

status: Public on Sep 10 2018

type: SRA

city: Cambridge

first: Matthew

middle: D

last: Shoulders

state: MA

address: 77 Massachusetts Avenue

department: Chemistry

country: USA

institute: Massachusetts Institute of Technology

description: Sample 2 Basal 37C, Rep2

library_source: transcriptomic

data_processing:
Illumina Offline BaseCaller1.9.3  software used for basecalling.
Quality control: Reads were aligned against hg19 (Feb. 2009) using bwa mem v. 0.7.12-r1039 with flags –t 16 –f and mapping rates, fraction of multiply-mapping reads, number of unique 20-mers at the 5’ end of the reads, insert size distributions and fraction of ribosomal RNAs were calculated using dedicated perl scripts and bedtools v. 2.25.0.64 In addition, each resulting bam file was randomly down-sampled to a million reads, which were aligned against hg19 and read density across genomic features were estimated for RNA-Seq-specific quality control metrics.
RNA-Seq mapping and quantitation: Reads were aligned against hg38 / ENSEMBL 89 annotation using STAR v. 2.5.3a with flags --runThreadN 8 --runMode alignReads  --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFileNamePrefix D17-188001 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM   with --genomeDir pointing to a 75nt-junction hg38 STAR suffix array.
Gene expression was quantitated using RSEM v. 1.3.0 with the following flags for all libraries: rsem-calculate-expression --calc-pme --alignments -p 8  --forward-prob 0 against an annotation matching the STAR SA reference. Posterior mean estimates (pme) of counts and estimated RPKM were retrieved.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file containing log2-transformed RPKM values for all hg38 annotated genes (ENSEMBL 89) in each sample (RSEM pme_RPKM output).

molecule: total RNA

organism: Homo sapiens

source_name: Human Embryonic Kidney (HEK) 293T-Rex Cells

growth_protocol: Low passage cells were plated at a density of 750,000 cells/well in 12 well plates.

extract_protocol:
Cells were trypsinized and RNA was extracted using the Qiagen RNeasy Plus Mini Kit and QIAshredder homogenization columns.
For RNAseq, RNA integrity and concentration were checked on a Fragment Analyzer (Advanced Analytical) and libraries were prepared using the Kapa HyperPrep RNAseq kit (Roche). Libraries were quantified using the Fragment Analyzer (Advanced Analytical) and qPCR before being loaded for single-end sequencing using the Illumina HiSeq 2500 for 40 nucleotides.
polyA-based mRNA capture using Kapa Hyperprep strand-specific strategy.

treatment_protocol: At the time of plating, cells were treated with either 0.01% DMSO, 1 ug/mL Doxycycline, or 1 ug/mL Doxycycline + 1 uM TMP, at both 37C and 39C (24 hour treatment).

tag: tissue

value: Adult-derived epithelial cell line

tag: cell line

value: Human Embryonic Kidney (HEK) 293T-Rex

tag: genotype

value: Clonal; stably expressing DHFR.ATF6, Tet-XBP1s, and the tetracycline repressor

tag: condition

value: 24h 0.01% DMSO treatment, 37C


title: PAH P2

status: Public on Oct 08 2019

type: RNA

city: Bethesda

first: Gabriela

middle: A

last: Ferreyra

state: MD

address: 9000 Rockville Pike - Building 10 room 4D03

department: CCMD

institute: Clinical Center

description: PBMC Gene expression data from IPAH patient

hyb_protocol: 2,3 ug of fragmented biotin labeled cRNA was used on hybridization cocktails on GeneChip Human Gene 1.0 ST Array (Affymetrix) following manufacturer protocols.

scan_protocol: Affymetrix GeneChip Human Gene 1.0 ST Array chips were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: Raw signal intensity values (mas 5 algorithm) are provided in the matrix file.

label: Biotin

source_name: PBMC

label_protocol: Affymetrix GeneChip WT Expression kit  was used for the synthesis of cDNA and cRNA an biotin-labeled cRNA. 150 ng of tRNA was utilized as starting material following manufacturer protocol.

growth_protocol: PBMCs were isolated from whole blood using BD Vacutainer CPT cell preparation tubes. Following PBMC isolation, citospined samples were used to confirm sample purity manually (> 97% lymphocytes and monocytes).

extract_protocol: Purified PBMCs were lysed in buffer RLT and, passed through Qiashredder columns.  Total RNA was purified using RNeasy mini kits and quantified with a NanoDrop spectrophotometer. Quality of total RNA was evaluated using RNA 6000 Nano LabChip

tag: gender

value: female


title: PAH P11


title: D17-188001: Basal 37C, Rep1

description: Sample 1 Basal 37C, Rep1


title: Sample_1124979_06

status: Public on Jul 24 2018

city: La Jolla

first: Sunil

last: Kurian

state: CA

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized, washed and stained in the Affymetrix Gene Titan MC

scan_protocol: GeneChips were scanned in the Affymetrix Gene Titan MC

data_processing: From the CEL files, data was generated by correction and normalization parameters using frozen RMA (fRMA). Technical batches were then adjusted using ComBat using the surrogate variable analysis (SVA) package

label: biotin

source_name: Human Peripheral Blood

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

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

tag: phenotype

value: subclinical acute rejection

value: peripheral blood


title: Sample_1124951_06


title: Sample_1124267_04


title: Sample_1131609_04


title: Sample_1130242_04


title: Sample_1122530_04


title: Sample_1123765_06


title: Sample_1117046_04


title: Control P2

description: PBMC Gene expression data from Healthy Volunteer


title: Sample_1117054_05


title: Sample_1126940_04


title: Sample_1131598_04


title: Sample_1126487_04


title: Sample_1133100_04


title: Sample_1127878_04


title: Sample_1119051_06


title: Sample_1123271_04_2


title: Sample_1128861_04


title: Sample_1124251_04


title: Sample_1122218_04


title: Sample_1123023_06


title: Sample_1120289_05


title: Sample_1124371_04


title: Sample_1124254_05


title: Sample_1121519_04


title: Sample_1116089_04


title: Sample_1116366_06


title: Sample_1114721_04


title: Breast Cancer Array_Patient ID_ 115_S

status: Public on Apr 13 2020

city: st louis

first: Cynthia

last: Ma

state: Missouri

address: 4515 Mckinley, 4515 Mckinley

department: Medical Oncology

institute: Washington University

description: POL

hyb_protocol: Agilent 60-mer oligo microarray processing protocol

scan_protocol: Microarrays were scanned with an Agilent Scanner.

data_processing: txt files from Agilent Feature Extraction software were loaded into the UNC-CH Microarray Database. Final loess, normalized log2 ratios (Cy5-sample/Cy3-control) for each probe were retrieved after applying default quality control filters.

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

label_protocol: Agilent Low Input Linear Amplification Kit and protocol

extract_protocol: Trizol extractions followed by Dnase treatment and column purification.

tag: reference

value: Total RNA from 10 human cell lines:1_Adenocarcinoma, mammary gland 2_Hepatoblastoma, liver 3_Adenocarcinoma, cervix 4_Embryonal carcinoma, testis 5_Glioblastoma, brain 6_Melanoma 7_Liposarcoma 8_Histiocytic Lymphoma; macrophage; histocyte 9_ Lymphoblastic leukemia, T lymphoblast 10_Plasmacytoma; myeloma; B lymphocyte.  Also, mRNA spiked in from MCF7 and ME16C.

source_name: Primary Breast Tumor_Patient ID_ 115_S

growth_protocol: patient biopsies were frozen and stored in oct compound

tag: test

value: oct blocks from fine needle biopsies which contained at least 50 percent tumor cellularity


title: Sample_1113513_04


title: Sample_1112548_05


title: Sample_1110965_04


title: Sample_1111869_04


title: Sample_1113026_06


title: Sample_1114715_04


title: Sample_1108705_05


title: Sample_1109293_04


title: Sample_1112061_05


title: Sample_1114001_04


title: Sample_1114017_04


title: Sample_1003265_06


title: Sample_1105152_06


title: Sample_1107553_04


title: Sample_1105153_06


title: Sample_1106417_04


title: Sample_1136185_04

value: Transplant eXcellence


title: Sample_1134571_04


title: Sample_1116615_04


title: Sample_1112456_04


title: Sample_1134586_04


title: Sample_1112550_04


title: Sample_1134584_04


title: Sample_1131595_04


title: Sample_1133779_04


title: Sample_1131592_04


title: Sample_1107538_05


title: Sample_1131615_04


title: Sample_1133109_04


title: Sample_1129891_04


title: Sample_1111872_04


title: Sample_1129681_04


title: Sample_1129212_04


title: Sample_1129215_04


title: Sample_1129703_04


title: Sample_1128877_04


title: Sample_1129216_04


title: Sample_1125904_04


title: Sample_1125795_04


title: Sample_1128865_04


title: Sample_1127728_04


title: Sample_1124759_04


title: Sample_1123658_04


title: Sample_1125792_04


title: Sample_1124253_04


title: Sample_1124085_04


title: Sample_1128585_05


title: Sample_1127208_04


title: Sample_1124245_04


title: Sample_1124364_04


title: Sample_1124885_04


title: Sample_1124720_04


title: Sample_1123534_04


title: Sample_1123654_04


title: Sample_1127503_04


title: Sample_1123655_04


title: Sample_1123660_04


title: Sample_1123947_04


title: Sample_1122532_04


title: Sample_1123067_04


title: Sample_1123263_04


title: Sample_1124246_04


title: Sample_1123022_05


title: Sample_1121663_04


title: Sample_1121661_04


title: Sample_1122219_04


title: Sample_1121658_06


title: Sample_1121518_04


title: Sample_1121271_04


title: Sample_1121521_04


title: Sample_1123657_04


title: Sample_1120921_04


title: Sample_1120663_06


title: Sample_1120649_04


title: Sample_1120019_05


title: Sample_1119861_04


title: Sample_1121525_04


title: Sample_1119742_04


title: Sample_1121112_04


title: Sample_1119860_06


title: Sample_1119052_04


title: Sample_1118189_04


title: Sample_1117855_04


title: Sample_1119072_06


title: Sample_1117179_04


title: Sample_1118600_04


title: Sample_1117048_04


title: Sample_1118089_06


title: Sample_1117854_04


title: Sample_1117174_04


title: Sample_1117040_04


title: Sample_1117176_06


title: Sample_1117852_04


title: Sample_1116931_04


title: Sample_1119869_04


title: Sample_1117182_04


title: Sample_1116616_04


title: Sample_1116617_04


title: Sample_1117043_06


title: Sample_1117038_04


title: Sample_1116372_04


title: Sample_1116367_04


title: Sample_1116094_04


title: Sample_1116093_04


title: Sample_1116087_04


title: Sample_1116095_04


title: Sample_1115281_04


title: Sample_1115733_04


title: Sample_1115016_04


title: Sample_1114350_04


title: Sample_1114354_04


title: Sample_1114718_04


title: Sample_1115731_04


title: Sample_1115282_04


title: Sample_1114714_04


title: Sample_1114351_04


title: Sample_1113997_04


title: Sample_1113512_04


title: Sample_1113998_04


title: Sample_1115734_04


title: Sample_1112643_04


title: Sample_1113332_04


title: Sample_1118086_06


title: Sample_1115735_04


title: Sample_1112553_04


title: Sample_1115005_04


title: Sample_1112642_04


title: Sample_1112544_05


title: Sample_1112545_04


title: Sample_1112542_04


title: Sample_1114000_04


title: Sample_1114204_05


title: Sample_1112453_04


title: Sample_1112069_04


title: Sample_1112053_04


title: Sample_1111870_04


title: Sample_1112066_04


title: Sample_1112068_04


title: Sample_1112057_04


title: Sample_1111867_04


title: Sample_1110785_04


title: Sample_1112052_05


title: Sample_1110321_04


title: Sample_1110968_04


title: Sample_1111864_06


title: Sample_1110792_04


title: Sample_1110320_06


title: Sample_1112256_04


title: Sample_1112259_04


title: Sample_1110275_04


title: Sample_1110268_04


title: Sample_1110674_04


title: Sample_1109801_04


title: Sample_1110313_04


title: Sample_1110971_06


title: Sample_1108914_04


title: Sample_1108906_04


title: Sample_1108905_04


title: Sample_1108911_04


title: Sample_1108497_05


title: Sample_1108687_04


title: Sample_1108496_04


title: Sample_1108899_05


title: Sample_1108704_04


title: Sample_1107495_05


title: Sample_1107535_04


title: Sample_1106755_04


title: Sample_1107042_05


title: Sample_1109290_04


title: Sample_1106743_04


title: Sample_1106737_04


title: Sample_1106512_04


title: Sample_1109291_04


title: Sample_1106506_04


title: Sample_1106238_04


title: Sample_1106420_04


title: Sample_1106232_04


title: Sample_1106240_04


title: Sample_1113516_04


title: Sample_1106745_05


title: Sample_1106511_04


title: Sample_1104905_04


title: Sample_1103713_06


status: Public on May 29 2018

type: protein

description:
BKM120 most sensitive
CM_93_93.2
4-V4-564

hyb_protocol: Protein lysate from each sample was spotted to glass slides and probed with 204 antibodies.  Slides were incubated with primary antibody and primary antibody was then detected using a biotinylated secondary antibody followed by streptavidin-conjugated IRDye 680 fluorophore (LI-COR Biosciences).

scan_protocol: Fluorescence-labeled slides were scanned on a GenePix AL4200 scanner, each slide, along with its accompanying negative control slide, is scanned at an appropriate PMT to obtain optimal signal for this specific set of samples. The images were analyzed with GenePix Pro 7.0 (Molecular Devices).

data_processing:
Raw data file contains: raw total fluorescent signal intensity before background subtraction or total protein normalization.
Data normalization: signal for each spot is subtracted by the corresponding negative control signal for that spot and followed by total protein normalization.

label: antibody

molecule: protein

source_name: WU PDX WHIM4_50hr control_bioreplicate3_technical replicate2

extract_protocol: Protein lysates were prepared with modified tissue protein extraction reagent (TPER; Pierce) and a cocktail of protease and phosphatase inhibitors (Roche Life Science).

value: pulverized tumor tissue from human:mouse xenograft

tag: bkm120 sensitivity

value: BKM120 most sensitive


description:
BKM120 most sensitive
CM_95_95.1
4-B5-567

source_name: WU PDX WHIM4_50hr washout_bioreplicate2_technical replicate1

label_protocol: Protein lysate from each sample was spotted to glass slides and probed with 204 antibodies.  Slides were incubated with primary antibody and primary antibody was then detected using a biotinylated secondary antibody followed by streptavidin-conjugated IRDye 680 fluorophore (LI-COR Biosciences).


description:
BKM120 most sensitive
CM_95_95.3
4-B5-567

source_name: WU PDX WHIM4_50hr washout_bioreplicate2_technical replicate3


description:
BKM120 most sensitive
CM_96_96.1
4-B5-568

source_name: WU PDX WHIM4_50hr washout_bioreplicate3_technical replicate1


description:
BKM120 most sensitive
CM_94_94.3
4-B5-566

source_name: WU PDX WHIM4_50hr washout_bioreplicate1_technical replicate3


description:
BKM120 most sensitive
CM_96_96.3
4-B5-568

source_name: WU PDX WHIM4_50hr washout_bioreplicate3_technical replicate3


title: Sample_1104897_04


title: Sample_1103475_06


title: Sample_1003266_04


title: Sample_1108900_06


description:
BKM120 most sensitive
CM_95_95.2
4-B5-567

source_name: WU PDX WHIM4_50hr washout_bioreplicate2_technical replicate2


title: Sample_1003264_06


title: Sample_1105677_04


title: Sample_1105461_04


description:
BKM120 most sensitive
CM_92_92.3
4-V4-562

source_name: WU PDX WHIM4_50hr control_bioreplicate2_technical replicate3


description:
BKM120 most sensitive
CM_94_94.1
4-B5-566

source_name: WU PDX WHIM4_50hr washout_bioreplicate1_technical replicate1


description:
BKM120 most sensitive
CM_96_96.2
4-B5-568

source_name: WU PDX WHIM4_50hr washout_bioreplicate3_technical replicate2


description:
BKM120 most sensitive
CM_92_92.1
4-V4-562

source_name: WU PDX WHIM4_50hr control_bioreplicate2_technical replicate1


description:
BKM120 most sensitive
CM_92_92.2
4-V4-562

source_name: WU PDX WHIM4_50hr control_bioreplicate2_technical replicate2


description:
BKM120 most sensitive
CM_93_93.3
4-V4-564

source_name: WU PDX WHIM4_50hr control_bioreplicate3_technical replicate3


description:
BKM120 most sensitive
CM_91_91.3
4-V4-561

source_name: WU PDX WHIM4_50hr control_bioreplicate1_technical replicate3


description:
BKM120 most sensitive
CM_93_93.1
4-V4-564

source_name: WU PDX WHIM4_50hr control_bioreplicate3_technical replicate1


description:
BKM120 most sensitive
CM_91_91.2
4-V4-561

source_name: WU PDX WHIM4_50hr control_bioreplicate1_technical replicate2


description:
BKM120 most sensitive
CM_90_90.3
4-B3-560

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate4_technical replicate3


description:
BKM120 most sensitive
CM_90_90.2
4-B3-560

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate4_technical replicate2


description:
BKM120 most sensitive
CM_90_90.1
4-B3-560

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate4_technical replicate1


description:
BKM120 most sensitive
CM_89_89.3
4-B3-559

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate3_technical replicate3


description:
BKM120 most sensitive
CM_88_88.2
4-B3-557

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate2_technical replicate2


description:
BKM120 most sensitive
CM_88_88.3
4-B3-557

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate2_technical replicate3


description:
BKM120 most sensitive
CM_89_89.2
4-B3-559

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate3_technical replicate2


description:
BKM120 most sensitive
CM_88_88.1
4-B3-557

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate2_technical replicate1


description:
BKM120 most sensitive
CM_87_87.3
4-B3-556

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate1_technical replicate3


description:
BKM120 most sensitive
CM_87_87.2
4-B3-556

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate1_technical replicate2


description:
BKM120 most sensitive
CM_89_89.1
4-B3-559

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate3_technical replicate1


description:
BKM120 most sensitive
CM_91_91.1
4-V4-561

source_name: WU PDX WHIM4_50hr control_bioreplicate1_technical replicate1


description:
BKM120 most sensitive
CM_86_86.3
4-B2-554

source_name: WU PDX WHIM4_2hr Buparlisib treatment_bioreplicate2_technical replicate3


description:
BKM120 most sensitive
CM_87_87.1
4-B3-556

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate1_technical replicate1


description:
BKM120 most sensitive
CM_86_86.2
4-B2-554

source_name: WU PDX WHIM4_2hr Buparlisib treatment_bioreplicate2_technical replicate2


description:
BKM120 most sensitive
CM_86_86.1
4-B2-554

source_name: WU PDX WHIM4_2hr Buparlisib treatment_bioreplicate2_technical replicate1


description:
BKM120 most sensitive
CM_85_85.3
4-B2-551

source_name: WU PDX WHIM4_2hr Buparlisib treatment_bioreplicate1_technical replicate3


description:
BKM120 most sensitive
CM_85_85.1
4-B2-551

source_name: WU PDX WHIM4_2hr Buparlisib treatment_bioreplicate1_technical replicate1


description:
BKM120 most sensitive
CM_84_84.3
4-V1-549

source_name: WU PDX WHIM4_2hr control_bioreplicate3_technical replicate3


description:
BKM120 most sensitive
CM_85_85.2
4-B2-551

source_name: WU PDX WHIM4_2hr Buparlisib treatment_bioreplicate1_technical replicate2


description:
BKM120 most sensitive
CM_83_83.2
4-V1-548

source_name: WU PDX WHIM4_2hr control_bioreplicate2_technical replicate2


description:
BKM120 most sensitive
CM_83_83.3
4-V1-548

source_name: WU PDX WHIM4_2hr control_bioreplicate2_technical replicate3


description:
BKM120 most sensitive
CM_84_84.2
4-V1-549

source_name: WU PDX WHIM4_2hr control_bioreplicate3_technical replicate2


description:
BKM120 most sensitive
CM_84_84.1
4-V1-549

source_name: WU PDX WHIM4_2hr control_bioreplicate3_technical replicate1


description:
BKM120 most sensitive
CM_82_82.3
4-V1-546

source_name: WU PDX WHIM4_2hr control_bioreplicate1_technical replicate3


description:
BKM120 most sensitive
CM_83_83.1
4-V1-548

source_name: WU PDX WHIM4_2hr control_bioreplicate2_technical replicate1


title: Sample_1104985_04

source_name: Human Peripheral Blood


description:
BKM120 most sensitive
CM_82_82.2
4-V1-546

source_name: WU PDX WHIM4_2hr control_bioreplicate1_technical replicate2


description:
BKM120 most sensitive
CM_82_82.1
4-V1-546

source_name: WU PDX WHIM4_2hr control_bioreplicate1_technical replicate1


description:
BKM120 most resistant
CM_81_81.3
21-B5-545

source_name: WU PDX WHIM21_50hr washout_bioreplicate3_technical replicate3

value: BKM120 most resistant


description:
BKM120 most resistant
CM_81_81.1
21-B5-545

source_name: WU PDX WHIM21_50hr washout_bioreplicate3_technical replicate1


description:
BKM120 most resistant
CM_81_81.2
21-B5-545

source_name: WU PDX WHIM21_50hr washout_bioreplicate3_technical replicate2


description:
BKM120 most resistant
CM_80_80.1
21-B5-543

source_name: WU PDX WHIM21_50hr washout_bioreplicate2_technical replicate1


description:
BKM120 most resistant
CM_80_80.2
21-B5-543

source_name: WU PDX WHIM21_50hr washout_bioreplicate2_technical replicate2


description:
BKM120 most resistant
CM_78_78.1
21-V4-540

source_name: WU PDX WHIM21_50hr control_bioreplicate3_technical replicate1


description:
BKM120 most resistant
CM_77_77.2
21-V4-539

source_name: WU PDX WHIM21_50hr control_bioreplicate2_technical replicate2


description:
BKM120 most resistant
CM_78_78.3
21-V4-540

source_name: WU PDX WHIM21_50hr control_bioreplicate3_technical replicate3


description:
BKM120 most resistant
CM_79_79.2
21-B5-542

source_name: WU PDX WHIM21_50hr washout_bioreplicate1_technical replicate2


description:
BKM120 most resistant
CM_79_79.3
21-B5-542

source_name: WU PDX WHIM21_50hr washout_bioreplicate1_technical replicate3


description:
BKM120 most resistant
CM_76_76.3
21-V4-538

source_name: WU PDX WHIM21_50hr control_bioreplicate1_technical replicate3


description:
BKM120 most resistant
CM_77_77.3
21-V4-539

source_name: WU PDX WHIM21_50hr control_bioreplicate2_technical replicate3


description:
BKM120 most resistant
CM_78_78.2
21-V4-540

source_name: WU PDX WHIM21_50hr control_bioreplicate3_technical replicate2


description:
BKM120 most resistant
CM_76_76.2
21-V4-538

source_name: WU PDX WHIM21_50hr control_bioreplicate1_technical replicate2


description:
BKM120 most resistant
CM_76_76.1
21-V4-538

source_name: WU PDX WHIM21_50hr control_bioreplicate1_technical replicate1


description:
BKM120 most resistant
CM_74_74.3
21-B3-535

source_name: WU PDX WHIM21_50hr Buparlisib treatment_bioreplicate2_technical replicate3


description:
BKM120 most resistant
CM_74_74.2
21-B3-535

source_name: WU PDX WHIM21_50hr Buparlisib treatment_bioreplicate2_technical replicate2


description:
BKM120 most resistant
CM_75_75.1
21-B3-537

source_name: WU PDX WHIM21_50hr Buparlisib treatment_bioreplicate3_technical replicate1


description:
BKM120 most resistant
CM_80_80.3
21-B5-543

source_name: WU PDX WHIM21_50hr washout_bioreplicate2_technical replicate3


description:
BKM120 most resistant
CM_75_75.3
21-B3-537

source_name: WU PDX WHIM21_50hr Buparlisib treatment_bioreplicate3_technical replicate3


description:
BKM120 most resistant
CM_73_73.2
21-B3-534

source_name: WU PDX WHIM21_50hr Buparlisib treatment_bioreplicate1_technical replicate2


description:
BKM120 most resistant
CM_73_73.3
21-B3-534

source_name: WU PDX WHIM21_50hr Buparlisib treatment_bioreplicate1_technical replicate3


description:
BKM120 most resistant
CM_74_74.1
21-B3-535

source_name: WU PDX WHIM21_50hr Buparlisib treatment_bioreplicate2_technical replicate1


description:
BKM120 most resistant
CM_75_75.2
21-B3-537

source_name: WU PDX WHIM21_50hr Buparlisib treatment_bioreplicate3_technical replicate2


description:
BKM120 most resistant
CM_72_72.3
21-B2-533

source_name: WU PDX WHIM21_2hr Buparlisib treatment_bioreplicate3_technical replicate3


description:
BKM120 most resistant
CM_72_72.2
21-B2-533

source_name: WU PDX WHIM21_2hr Buparlisib treatment_bioreplicate3_technical replicate2


description:
BKM120 most resistant
CM_79_79.1
21-B5-542

source_name: WU PDX WHIM21_50hr washout_bioreplicate1_technical replicate1


description:
BKM120 most resistant
CM_71_71.2
21-B2-530

source_name: WU PDX WHIM21_2hr Buparlisib treatment_bioreplicate2_technical replicate2


description:
BKM120 most resistant
CM_71_71.3
21-B2-530

source_name: WU PDX WHIM21_2hr Buparlisib treatment_bioreplicate2_technical replicate3


description:
BKM120 most resistant
CM_77_77.1
21-V4-539

source_name: WU PDX WHIM21_50hr control_bioreplicate2_technical replicate1


description:
BKM120 most resistant
CM_72_72.1
21-B2-533

source_name: WU PDX WHIM21_2hr Buparlisib treatment_bioreplicate3_technical replicate1


description:
BKM120 most resistant
CM_71_71.1
21-B2-530

source_name: WU PDX WHIM21_2hr Buparlisib treatment_bioreplicate2_technical replicate1


description:
BKM120 most resistant
CM_73_73.1
21-B3-534

source_name: WU PDX WHIM21_50hr Buparlisib treatment_bioreplicate1_technical replicate1


description:
BKM120 most resistant
CM_70_70.1
21-B2-529

source_name: WU PDX WHIM21_2hr Buparlisib treatment_bioreplicate1_technical replicate1


description:
BKM120 most resistant
CM_68_68.2
21-V1-526

source_name: WU PDX WHIM21_2hr control_bioreplicate2_technical replicate2


description:
BKM120 most resistant
CM_70_70.3
21-B2-529

source_name: WU PDX WHIM21_2hr Buparlisib treatment_bioreplicate1_technical replicate3


description:
BKM120 most resistant
CM_68_68.3
21-V1-526

source_name: WU PDX WHIM21_2hr control_bioreplicate2_technical replicate3


description:
BKM120 most resistant
CM_70_70.2
21-B2-529

source_name: WU PDX WHIM21_2hr Buparlisib treatment_bioreplicate1_technical replicate2


description:
BKM120 most resistant
CM_69_69.2
21-V1-527

source_name: WU PDX WHIM21_2hr control_bioreplicate3_technical replicate2


description:
BKM120 most resistant
CM_66_66.1
6-B5-429

source_name: WU PDX WHIM6_50hr washout_bioreplicate4_technical replicate1


description:
BKM120 most resistant
CM_69_69.3
21-V1-527

source_name: WU PDX WHIM21_2hr control_bioreplicate3_technical replicate3


description:
BKM120 most resistant
CM_68_68.1
21-V1-526

source_name: WU PDX WHIM21_2hr control_bioreplicate2_technical replicate1


description:
BKM120 most resistant
CM_67_67.2
21-V1-525

source_name: WU PDX WHIM21_2hr control_bioreplicate1_technical replicate2


description:
BKM120 most resistant
CM_67_67.1
21-V1-525

source_name: WU PDX WHIM21_2hr control_bioreplicate1_technical replicate1


description:
BKM120 most resistant
CM_67_67.3
21-V1-525

source_name: WU PDX WHIM21_2hr control_bioreplicate1_technical replicate3


description:
BKM120 most resistant
CM_66_66.2
6-B5-429

source_name: WU PDX WHIM6_50hr washout_bioreplicate4_technical replicate2


description:
BKM120 most resistant
CM_66_66.3
6-B5-429

source_name: WU PDX WHIM6_50hr washout_bioreplicate4_technical replicate3


description:
BKM120 most resistant
CM_65_65.3
6-B5-428

source_name: WU PDX WHIM6_50hr washout_bioreplicate3_technical replicate3


description:
BKM120 most resistant
CM_65_65.2
6-B5-428

source_name: WU PDX WHIM6_50hr washout_bioreplicate3_technical replicate2


description:
BKM120 most resistant
CM_65_65.1
6-B5-428

source_name: WU PDX WHIM6_50hr washout_bioreplicate3_technical replicate1


description:
BKM120 most resistant
CM_64_64.2
6-B5-426

source_name: WU PDX WHIM6_50hr washout_bioreplicate2_technical replicate2


description:
BKM120 most resistant
CM_64_64.1
6-B5-426

source_name: WU PDX WHIM6_50hr washout_bioreplicate2_technical replicate1


description:
BKM120 most sensitive
CM_94_94.2
4-B5-566

source_name: WU PDX WHIM4_50hr washout_bioreplicate1_technical replicate2


description:
BKM120 most resistant
CM_63_63.3
6-B5-424

source_name: WU PDX WHIM6_50hr washout_bioreplicate1_technical replicate3


description:
BKM120 most resistant
CM_62_62.3
6-V4-434

source_name: WU PDX WHIM6_50hr control_bioreplicate3_technical replicate3


description:
BKM120 most resistant
CM_63_63.1
6-B5-424

source_name: WU PDX WHIM6_50hr washout_bioreplicate1_technical replicate1


description:
BKM120 most resistant
CM_62_62.2
6-V4-434

source_name: WU PDX WHIM6_50hr control_bioreplicate3_technical replicate2


description:
BKM120 most resistant
CM_63_63.2
6-B5-424

source_name: WU PDX WHIM6_50hr washout_bioreplicate1_technical replicate2


description:
BKM120 most resistant
CM_69_69.1
21-V1-527

source_name: WU PDX WHIM21_2hr control_bioreplicate3_technical replicate1


description:
BKM120 most resistant
CM_61_61.2
6-V4-433

source_name: WU PDX WHIM6_50hr control_bioreplicate2_technical replicate2


description:
BKM120 most resistant
CM_62_62.1
6-V4-434

source_name: WU PDX WHIM6_50hr control_bioreplicate3_technical replicate1


description:
BKM120 most resistant
CM_61_61.3
6-V4-433

source_name: WU PDX WHIM6_50hr control_bioreplicate2_technical replicate3


description:
BKM120 most resistant
CM_64_64.3
6-B5-426

source_name: WU PDX WHIM6_50hr washout_bioreplicate2_technical replicate3


description:
BKM120 most resistant
CM_60_60.3
6-V4-430

source_name: WU PDX WHIM6_50hr control_bioreplicate1_technical replicate3


description:
BKM120 most resistant
CM_61_61.1
6-V4-433

source_name: WU PDX WHIM6_50hr control_bioreplicate2_technical replicate1


description:
BKM120 most resistant
CM_60_60.1
6-V4-430

source_name: WU PDX WHIM6_50hr control_bioreplicate1_technical replicate1


description:
BKM120 most resistant
CM_60_60.2
6-V4-430

source_name: WU PDX WHIM6_50hr control_bioreplicate1_technical replicate2


description:
BKM120 most resistant
CM_58_58.3
6-B3-417

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate3_technical replicate3


description:
BKM120 most resistant
CM_58_58.2
6-B3-417

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate3_technical replicate2


description:
BKM120 most resistant
CM_59_59.2
6-B3-418

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate4_technical replicate2


description:
BKM120 most resistant
CM_59_59.3
6-B3-418

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate4_technical replicate3


description:
BKM120 most resistant
CM_57_57.2
6-B3-415

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate2_technical replicate2


description:
BKM120 most resistant
CM_59_59.1
6-B3-418

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate4_technical replicate1


description:
BKM120 most resistant
CM_57_57.3
6-B3-415

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate2_technical replicate3


description:
BKM120 most resistant
CM_56_56.3
6-B3-414

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate1_technical replicate3


description:
BKM120 most resistant
CM_57_57.1
6-B3-415

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate2_technical replicate1


description:
BKM120 most resistant
CM_58_58.1
6-B3-417

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate3_technical replicate1


description:
BKM120 most resistant
CM_56_56.1
6-B3-414

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate1_technical replicate1


description:
BKM120 most resistant
CM_56_56.2
6-B3-414

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate1_technical replicate2


description:
BKM120 most resistant
CM_55_55.1
6-B2-413

source_name: WU PDX WHIM6_2hr Buparlisib treatment_bioreplicate3_technical replicate1


description:
BKM120 most resistant
CM_55_55.3
6-B2-413

source_name: WU PDX WHIM6_2hr Buparlisib treatment_bioreplicate3_technical replicate3


description:
BKM120 most resistant
CM_54_54.1
6-B2-411

source_name: WU PDX WHIM6_2hr Buparlisib treatment_bioreplicate2_technical replicate1


description:
BKM120 most resistant
CM_54_54.2
6-B2-411

source_name: WU PDX WHIM6_2hr Buparlisib treatment_bioreplicate2_technical replicate2


description:
BKM120 most resistant
CM_54_54.3
6-B2-411

source_name: WU PDX WHIM6_2hr Buparlisib treatment_bioreplicate2_technical replicate3


description:
BKM120 most resistant
CM_53_53.3
6-B2-410

source_name: WU PDX WHIM6_2hr Buparlisib treatment_bioreplicate1_technical replicate3


description:
BKM120 most resistant
CM_53_53.2
6-B2-410

source_name: WU PDX WHIM6_2hr Buparlisib treatment_bioreplicate1_technical replicate2


description:
BKM120 most resistant
CM_53_53.1
6-B2-410

source_name: WU PDX WHIM6_2hr Buparlisib treatment_bioreplicate1_technical replicate1


description:
BKM120 most resistant
CM_52_52.3
6-V1-422

source_name: WU PDX WHIM6_2hr control_bioreplicate3_technical replicate3


description:
BKM120 most resistant
CM_52_52.1
6-V1-422

source_name: WU PDX WHIM6_2hr control_bioreplicate3_technical replicate1


description:
BKM120 most resistant
CM_51_51.3
6-V1-421

source_name: WU PDX WHIM6_2hr control_bioreplicate2_technical replicate3


description:
BKM120 most resistant
CM_51_51.2
6-V1-421

source_name: WU PDX WHIM6_2hr control_bioreplicate2_technical replicate2


description:
BKM120 most resistant
CM_55_55.2
6-B2-413

source_name: WU PDX WHIM6_2hr Buparlisib treatment_bioreplicate3_technical replicate2


description:
BKM120 most resistant
CM_50_50.2
6-V1-419

source_name: WU PDX WHIM6_2hr control_bioreplicate1_technical replicate2


description:
BKM120 most resistant
CM_50_50.3
6-V1-419

source_name: WU PDX WHIM6_2hr control_bioreplicate1_technical replicate3


description:
BKM120 most resistant
CM_51_51.1
6-V1-421

source_name: WU PDX WHIM6_2hr control_bioreplicate2_technical replicate1


description:
BKM120 most resistant
CM_49_49.3
12-B5-474

source_name: WU PDX WHIM12_50hr washout_bioreplicate4_technical replicate3


description:
BKM120 most resistant
CM_49_49.1
12-B5-474

source_name: WU PDX WHIM12_50hr washout_bioreplicate4_technical replicate1


description:
BKM120 most resistant
CM_48_48.1
12-B5-473

source_name: WU PDX WHIM12_50hr washout_bioreplicate3_technical replicate1


description:
BKM120 most resistant
CM_47_47.3
12-B5-472

source_name: WU PDX WHIM12_50hr washout_bioreplicate2_technical replicate3


description:
BKM120 most resistant
CM_48_48.2
12-B5-473

source_name: WU PDX WHIM12_50hr washout_bioreplicate3_technical replicate2


description:
BKM120 most resistant
CM_48_48.3
12-B5-473

source_name: WU PDX WHIM12_50hr washout_bioreplicate3_technical replicate3


description:
BKM120 most resistant
CM_52_52.2
6-V1-422

source_name: WU PDX WHIM6_2hr control_bioreplicate3_technical replicate2


description:
BKM120 most resistant
CM_46_46.2
12-B5-470

source_name: WU PDX WHIM12_50hr washout_bioreplicate1_technical replicate2


description:
BKM120 most resistant
CM_46_46.1
12-B5-470

source_name: WU PDX WHIM12_50hr washout_bioreplicate1_technical replicate1


description:
BKM120 most resistant
CM_47_47.1
12-B5-472

source_name: WU PDX WHIM12_50hr washout_bioreplicate2_technical replicate1


description:
BKM120 most resistant
CM_47_47.2
12-B5-472

source_name: WU PDX WHIM12_50hr washout_bioreplicate2_technical replicate2


description:
BKM120 most resistant
CM_45_45.2
12-V4-484

source_name: WU PDX WHIM12_50hr control_bioreplicate3_technical replicate2


description:
BKM120 most resistant
CM_44_44.2
12-V4-483

source_name: WU PDX WHIM12_50hr control_bioreplicate2_technical replicate2


description:
BKM120 most resistant
CM_44_44.1
12-V4-483

source_name: WU PDX WHIM12_50hr control_bioreplicate2_technical replicate1


description:
BKM120 most resistant
CM_45_45.3
12-V4-484

source_name: WU PDX WHIM12_50hr control_bioreplicate3_technical replicate3


description:
BKM120 most resistant
CM_44_44.3
12-V4-483

source_name: WU PDX WHIM12_50hr control_bioreplicate2_technical replicate3


description:
BKM120 most resistant
CM_43_43.3
12-V4-481

source_name: WU PDX WHIM12_50hr control_bioreplicate1_technical replicate3


description:
BKM120 most resistant
CM_43_43.2
12-V4-481

source_name: WU PDX WHIM12_50hr control_bioreplicate1_technical replicate2


description:
BKM120 most resistant
CM_43_43.1
12-V4-481

source_name: WU PDX WHIM12_50hr control_bioreplicate1_technical replicate1


description:
BKM120 most resistant
CM_50_50.1
6-V1-419

source_name: WU PDX WHIM6_2hr control_bioreplicate1_technical replicate1


description:
BKM120 most resistant
CM_46_46.3
12-B5-470

source_name: WU PDX WHIM12_50hr washout_bioreplicate1_technical replicate3


description:
BKM120 most resistant
CM_42_42.3
12-B3-480

source_name: WU PDX WHIM12_50hr Buparlisib treatment_bioreplicate3_technical replicate3


description:
BKM120 most resistant
CM_49_49.2
12-B5-474

source_name: WU PDX WHIM12_50hr washout_bioreplicate4_technical replicate2


description:
BKM120 most resistant
CM_41_41.2
12-B3-478

source_name: WU PDX WHIM12_50hr Buparlisib treatment_bioreplicate2_technical replicate2


description:
BKM120 most resistant
CM_45_45.1
12-V4-484

source_name: WU PDX WHIM12_50hr control_bioreplicate3_technical replicate1


description:
BKM120 most resistant
CM_41_41.3
12-B3-478

source_name: WU PDX WHIM12_50hr Buparlisib treatment_bioreplicate2_technical replicate3


description:
BKM120 most resistant
CM_41_41.1
12-B3-478

source_name: WU PDX WHIM12_50hr Buparlisib treatment_bioreplicate2_technical replicate1


description:
BKM120 most resistant
CM_42_42.1
12-B3-480

source_name: WU PDX WHIM12_50hr Buparlisib treatment_bioreplicate3_technical replicate1


title: WHIM12_50hr Buparlisib treatment_bioreplicate1_technical replicate2b

description:
BKM120 most resistant
CM_40_40.2
12-B3-477

source_name: WU PDX WHIM12_50hr Buparlisib treatment_bioreplicate1_technical replicate2


title: WHIM12_50hr Buparlisib treatment_bioreplicate1_technical replicate3a

description:
BKM120 most resistant
CM_39_39.3
12-B3-475

source_name: WU PDX WHIM12_50hr Buparlisib treatment_bioreplicate1_technical replicate3


title: WHIM12_50hr Buparlisib treatment_bioreplicate1_technical replicate1b

description:
BKM120 most resistant
CM_40_40.1
12-B3-477

source_name: WU PDX WHIM12_50hr Buparlisib treatment_bioreplicate1_technical replicate1


description:
BKM120 most resistant
CM_38_38.3
12-B2-468

source_name: WU PDX WHIM12_2hr Buparlisib treatment_bioreplicate3_technical replicate3


description:
BKM120 most resistant
CM_36_36.3
12-B2-465

source_name: WU PDX WHIM12_2hr Buparlisib treatment_bioreplicate1_technical replicate3


description:
BKM120 most resistant
CM_37_37.2
12-B2-467

source_name: WU PDX WHIM12_2hr Buparlisib treatment_bioreplicate2_technical replicate2


description:
BKM120 most resistant
CM_35_35.3
12-V1-464

source_name: WU PDX WHIM12_2hr control_bioreplicate3_technical replicate3


description:
BKM120 most resistant
CM_38_38.1
12-B2-468

source_name: WU PDX WHIM12_2hr Buparlisib treatment_bioreplicate3_technical replicate1


title: WHIM12_50hr Buparlisib treatment_bioreplicate1_technical replicate2a

description:
BKM120 most resistant
CM_39_39.2
12-B3-475


description:
BKM120 most resistant
CM_42_42.2
12-B3-480

source_name: WU PDX WHIM12_50hr Buparlisib treatment_bioreplicate3_technical replicate2


description:
BKM120 most resistant
CM_37_37.1
12-B2-467

source_name: WU PDX WHIM12_2hr Buparlisib treatment_bioreplicate2_technical replicate1


description:
BKM120 most resistant
CM_37_37.3
12-B2-467

source_name: WU PDX WHIM12_2hr Buparlisib treatment_bioreplicate2_technical replicate3


description:
BKM120 most resistant
CM_38_38.2
12-B2-468

source_name: WU PDX WHIM12_2hr Buparlisib treatment_bioreplicate3_technical replicate2


title: WHIM12_50hr Buparlisib treatment_bioreplicate1_technical replicate1a

description:
BKM120 most resistant
CM_39_39.1
12-B3-475


description:
BKM120 most resistant
CM_35_35.1
12-V1-464

source_name: WU PDX WHIM12_2hr control_bioreplicate3_technical replicate1


description:
BKM120 most resistant
CM_33_33.3
12-V1-461

source_name: WU PDX WHIM12_2hr control_bioreplicate1_technical replicate3


description:
BKM120 most resistant
CM_34_34.2
12-V1-463

source_name: WU PDX WHIM12_2hr control_bioreplicate2_technical replicate2


description:
BKM120 most resistant
CM_34_34.3
12-V1-463

source_name: WU PDX WHIM12_2hr control_bioreplicate2_technical replicate3


description:
BKM120 most resistant
CM_36_36.1
12-B2-465

source_name: WU PDX WHIM12_2hr Buparlisib treatment_bioreplicate1_technical replicate1


description:
BKM120 most resistant
CM_33_33.2
12-V1-461

source_name: WU PDX WHIM12_2hr control_bioreplicate1_technical replicate2


title: WHIM12_50hr Buparlisib treatment_bioreplicate1_technical replicate3b

description:
BKM120 most resistant
CM_40_40.3
12-B3-477

source_name: WU PDX WHIM12_50hr Buparlisib treatment_bioreplicate1_technical replicate3


description:
BKM120 most resistant
CM_34_34.1
12-V1-463

source_name: WU PDX WHIM12_2hr control_bioreplicate2_technical replicate1


description:
BKM120 most resistant
CM_33_33.1
12-V1-461

source_name: WU PDX WHIM12_2hr control_bioreplicate1_technical replicate1


description:
BKM120 most resistant
CM_36_36.2
12-B2-465

source_name: WU PDX WHIM12_2hr Buparlisib treatment_bioreplicate1_technical replicate2


description:
BKM120 most sensitive
CM_32_32.2
30-B5-523

source_name: WU PDX WHIM30_50hr washout_bioreplicate3_technical replicate2


description:
BKM120 most resistant
CM_35_35.2
12-V1-464

source_name: WU PDX WHIM12_2hr control_bioreplicate3_technical replicate2


description:
BKM120 most sensitive
CM_32_32.3
30-B5-523

source_name: WU PDX WHIM30_50hr washout_bioreplicate3_technical replicate3


description:
BKM120 most sensitive
CM_31_31.2
30-B5-521

source_name: WU PDX WHIM30_50hr washout_bioreplicate2_technical replicate2


description:
BKM120 most sensitive
CM_31_31.3
30-B5-521

source_name: WU PDX WHIM30_50hr washout_bioreplicate2_technical replicate3


description:
BKM120 most sensitive
CM_32_32.1
30-B5-523

source_name: WU PDX WHIM30_50hr washout_bioreplicate3_technical replicate1


description:
BKM120 most sensitive
CM_31_31.1
30-B5-521

source_name: WU PDX WHIM30_50hr washout_bioreplicate2_technical replicate1


description:
BKM120 most sensitive
CM_30_30.2
30-B5-520

source_name: WU PDX WHIM30_50hr washout_bioreplicate1_technical replicate2


description:
BKM120 most sensitive
CM_30_30.3
30-B5-520

source_name: WU PDX WHIM30_50hr washout_bioreplicate1_technical replicate3


description:
BKM120 most sensitive
CM_30_30.1
30-B5-520

source_name: WU PDX WHIM30_50hr washout_bioreplicate1_technical replicate1


description:
BKM120 most sensitive
CM_29_29.3
30-V4-518

source_name: WU PDX WHIM30_50hr control_bioreplicate3_technical replicate3


description:
BKM120 most sensitive
CM_29_29.2
30-V4-518

source_name: WU PDX WHIM30_50hr control_bioreplicate3_technical replicate2


description:
BKM120 most sensitive
CM_29_29.1
30-V4-518

source_name: WU PDX WHIM30_50hr control_bioreplicate3_technical replicate1


description:
BKM120 most sensitive
CM_28_28.3
30-V4-517

source_name: WU PDX WHIM30_50hr control_bioreplicate2_technical replicate3


description:
BKM120 most sensitive
CM_28_28.1
30-V4-517

source_name: WU PDX WHIM30_50hr control_bioreplicate2_technical replicate1


description:
BKM120 most sensitive
CM_28_28.2
30-V4-517

source_name: WU PDX WHIM30_50hr control_bioreplicate2_technical replicate2


title: WHIM6_50hr washout

description:
BKM120 most resistant
BKM120_6-B5-426

data_processing: txt files from Agilent Feature Extraction software were loaded into the UNC-CH Microarray Database. Final loess, normalized log2 ratios (Cy5-sample/Cy3-control) for each probe were retrieved.

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

value: 10 human cell lines:1_Adenocarcinoma, mammary gland 2_Hepatoblastoma, liver 3_Adenocarcinoma, cervix 4_Embryonal carcinoma, testis 5_Glioblastoma, brain 6_Melanoma 7_Liposarcoma 8_Histiocytic Lymphoma; macrophage; histocyte 9_ Lymphoblastic leukemia, T lymphoblast 10_Plasmacytoma; myeloma; B lymphocyte.  Also, mRNA spiked in from MCF7 and ME16C.

source_name: WU PDX WHIM6_50hr washout

tag: pdx breast cancer model


description:
BKM120 most sensitive
CM_27_27.1
30-V4-515

source_name: WU PDX WHIM30_50hr control_bioreplicate1_technical replicate1


description:
BKM120 most sensitive
CM_27_27.2
30-V4-515

source_name: WU PDX WHIM30_50hr control_bioreplicate1_technical replicate2


description:
BKM120 most sensitive
CM_27_27.3
30-V4-515

source_name: WU PDX WHIM30_50hr control_bioreplicate1_technical replicate3


description:
BKM120 most sensitive
CM_26_26.3
30-B3-513

source_name: WU PDX WHIM30_50hr Buparlisib treatment_bioreplicate3_technical replicate3


title: WHIM6_50hr control

description:
BKM120 most resistant
BKM120_6-V4-430

source_name: WU PDX WHIM6_50hr control


title: WHIM4_2hr control

description:
BKM120 most sensitive
BKM120_4-V1-546

source_name: WU PDX WHIM4_2hr control


title: WHIM6_50hr Buparlisib treatment

description:
BKM120 most resistant
BKM120_6-B3-415

source_name: WU PDX WHIM6_50hr Buparlisib treatment


title: WHIM30_50hr Buparlisib treatment

description:
BKM120 most sensitive
BKM120_30-B3-510

source_name: WU PDX WHIM30_50hr Buparlisib treatment


title: WHIM6_2hr Buparlisib treatment

description:
BKM120 most resistant
BKM120_6-B2-411

source_name: WU PDX WHIM6_2hr Buparlisib treatment


description:
BKM120 most sensitive
CM_26_26.2
30-B3-513

source_name: WU PDX WHIM30_50hr Buparlisib treatment_bioreplicate3_technical replicate2


title: WHIM30_50hr control

description:
BKM120 most sensitive
BKM120_30-V4-515

source_name: WU PDX WHIM30_50hr control


title: WHIM21_2hr control

description:
BKM120 most resistant
BKM120_21-V1-525

source_name: WU PDX WHIM21_2hr control


description:
BKM120 most sensitive
CM_25_25.3
30-B3-512

source_name: WU PDX WHIM30_50hr Buparlisib treatment_bioreplicate2_technical replicate3


description:
BKM120 most sensitive
CM_25_25.2
30-B3-512

source_name: WU PDX WHIM30_50hr Buparlisib treatment_bioreplicate2_technical replicate2


description:
BKM120 most sensitive
CM_26_26.1
30-B3-513

source_name: WU PDX WHIM30_50hr Buparlisib treatment_bioreplicate3_technical replicate1


title: WHIM4_50hr washout

description:
BKM120 most sensitive
BKM120_4-B5-567

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: WU PDX WHIM4_50hr washout


title: WHIM4_2hr Buparlisib treatment

description:
BKM120 most sensitive
BKM120_4-B2-551

source_name: WU PDX WHIM4_2hr Buparlisib treatment


description:
BKM120 most sensitive
CM_24_24.1
30-B3-510

source_name: WU PDX WHIM30_50hr Buparlisib treatment_bioreplicate1_technical replicate1


title: WHIM30_2hr Buparlisib treatment_bioreplicate3_technical replicate3

description:
BKM120 most sensitive
CM_23_23.3
30-B2-508

source_name: WU PDX WHIM30_2hr Buparlisib treatment_bioreplicate2_technical replicate3


description:
BKM120 most sensitive
CM_24_24.2
30-B3-510

source_name: WU PDX WHIM30_50hr Buparlisib treatment_bioreplicate1_technical replicate2


description:
BKM120 most sensitive
CM_25_25.1
30-B3-512

source_name: WU PDX WHIM30_50hr Buparlisib treatment_bioreplicate2_technical replicate1


description:
BKM120 most sensitive
CM_24_24.3
30-B3-510

source_name: WU PDX WHIM30_50hr Buparlisib treatment_bioreplicate1_technical replicate3


title: WHIM6_2hr control

description:
BKM120 most resistant
BKM120_6-V1-419

source_name: WU PDX WHIM6_2hr control


title: WHIM30_50hr washout

description:
BKM120 most sensitive
BKM120_30-B5-520

source_name: WU PDX WHIM30_50hr washout


title: WHIM21_50hr control

description:
BKM120 most resistant
BKM120_21-V4-540

source_name: WU PDX WHIM21_50hr control


title: WHIM30_2hr Buparlisib treatment_bioreplicate3_technical replicate2

description:
BKM120 most sensitive
CM_23_23.2
30-B2-508

source_name: WU PDX WHIM30_2hr Buparlisib treatment_bioreplicate2_technical replicate2


title: WHIM30_2hr Buparlisib treatment_bioreplicate3_technical replicate1

description:
BKM120 most sensitive
CM_23_23.1
30-B2-508

source_name: WU PDX WHIM30_2hr Buparlisib treatment_bioreplicate2_technical replicate1


title: WHIM30_2hr Buparlisib treatment_bioreplicate2_technical replicate3

description:
BKM120 most sensitive
CM_22_22.3
30-B2-506


title: WHIM2_50hr Buparlisib treatment

description:
BKM120 most resistant
BKM120_2-B3-446

source_name: WU PDX WHIM2_50hr Buparlisib treatment


title: WHIM12_50hr control

description:
BKM120 most resistant
BKM120_12-V4-481

source_name: WU PDX WHIM12_50hr control


title: WHIM2_50hr control

description:
BKM120 most resistant
BKM120_2-V4-440

source_name: WU PDX WHIM2_50hr control


title: WHIM12_50hr Buparlisib treatment

description:
BKM120 most resistant
BKM120_12-B3-475

source_name: WU PDX WHIM12_50hr Buparlisib treatment


title: WHIM21_50hr Buparlisib treatment

description:
BKM120 most resistant
BKM120_21-B3-534

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: WU PDX WHIM21_50hr Buparlisib treatment


title: WHIM2_50hr washout

description:
BKM120 most resistant
BKM120_2-B5-435

source_name: WU PDX WHIM2_50hr washout


title: WHIM21_2hr Buparlisib treatment

description:
BKM120 most resistant
BKM120_21-B2-530

source_name: WU PDX WHIM21_2hr Buparlisib treatment


description:
BKM120 most sensitive
CM_20_20.1
30-V1-503

source_name: WU PDX WHIM30_2hr control_bioreplicate3_technical replicate1


title: WHIM12_2hr control

description:
BKM120 most resistant
BKM120_12-V1-461

source_name: WU PDX WHIM12_2hr control


description:
BKM120 most sensitive
CM_19_19.3
30-V1-502

source_name: WU PDX WHIM30_2hr control_bioreplicate2_technical replicate3


title: WHIM12_2hr Buparlisib treatment

description:
BKM120 most resistant
BKM120_12-B2-465

source_name: WU PDX WHIM12_2hr Buparlisib treatment


description:
BKM120 most sensitive
CM_20_20.2
30-V1-503

source_name: WU PDX WHIM30_2hr control_bioreplicate3_technical replicate2


description:
BKM120 most sensitive
CM_20_20.3
30-V1-503

source_name: WU PDX WHIM30_2hr control_bioreplicate3_technical replicate3


description:
BKM120 most resistant
CM_16_16.2
2-B5-438

source_name: WU PDX WHIM2_50hr washout_bioreplicate3_technical replicate2


description:
BKM120 most resistant
CM_16_16.3
2-B5-438

source_name: WU PDX WHIM2_50hr washout_bioreplicate3_technical replicate3


description:
BKM120 most sensitive
CM_22_22.1
30-B2-506

source_name: WU PDX WHIM30_2hr Buparlisib treatment_bioreplicate2_technical replicate1


description:
BKM120 most resistant
CM_17_17.1
2-B5-439

source_name: WU PDX WHIM2_50hr washout_bioreplicate4_technical replicate1


description:
BKM120 most sensitive
CM_19_19.1
30-V1-502

source_name: WU PDX WHIM30_2hr control_bioreplicate2_technical replicate1


description:
BKM120 most sensitive
CM_18_18.3
30-V1-501

source_name: WU PDX WHIM30_2hr control_bioreplicate1_technical replicate3


description:
BKM120 most sensitive
CM_21_21.1
30-B2-505

source_name: WU PDX WHIM30_2hr Buparlisib treatment_bioreplicate1_technical replicate1


description:
BKM120 most sensitive
CM_19_19.2
30-V1-502

source_name: WU PDX WHIM30_2hr control_bioreplicate2_technical replicate2


description:
BKM120 most sensitive
CM_21_21.2
30-B2-505

source_name: WU PDX WHIM30_2hr Buparlisib treatment_bioreplicate1_technical replicate2


description:
BKM120 most sensitive
CM_22_22.2
30-B2-506

source_name: WU PDX WHIM30_2hr Buparlisib treatment_bioreplicate2_technical replicate2


description:
BKM120 most sensitive
CM_21_21.3
30-B2-505

source_name: WU PDX WHIM30_2hr Buparlisib treatment_bioreplicate1_technical replicate3


title: WHIM4_50hr Buparlisib treatment

description:
BKM120 most sensitive
BKM120_4-B3-557

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: WU PDX WHIM4_50hr Buparlisib treatment


title: WHIM30_2hr Buparlisib treatment

description:
BKM120 most sensitive
BKM120_30-B2-505

source_name: WU PDX WHIM30_2hr Buparlisib treatment


title: WHIM21_50hr washout

description:
BKM120 most resistant
BKM120_21-B5-543

source_name: WU PDX WHIM21_50hr washout


description:
BKM120 most resistant
CM_15_15.2
2-B5-437

source_name: WU PDX WHIM2_50hr washout_bioreplicate2_technical replicate2


description:
BKM120 most resistant
CM_15_15.1
2-B5-437

source_name: WU PDX WHIM2_50hr washout_bioreplicate2_technical replicate1


title: WHIM12_50hr washout

description:
BKM120 most resistant
BKM120_12-B5-470

source_name: WU PDX WHIM12_50hr washout


description:
BKM120 most sensitive
CM_18_18.2
30-V1-501

source_name: WU PDX WHIM30_2hr control_bioreplicate1_technical replicate2


description:
BKM120 most resistant
CM_17_17.3
2-B5-439

source_name: WU PDX WHIM2_50hr washout_bioreplicate4_technical replicate3


description:
BKM120 most resistant
CM_17_17.2
2-B5-439

source_name: WU PDX WHIM2_50hr washout_bioreplicate4_technical replicate2


description:
BKM120 most resistant
CM_16_16.1
2-B5-438

source_name: WU PDX WHIM2_50hr washout_bioreplicate3_technical replicate1


description:
BKM120 most resistant
CM_15_15.3
2-B5-437

source_name: WU PDX WHIM2_50hr washout_bioreplicate2_technical replicate3


description:
BKM120 most resistant
CM_14_14.3
2-B5-435

source_name: WU PDX WHIM2_50hr washout_bioreplicate1_technical replicate3


title: WHIM4_50hr control

description:
BKM120 most sensitive
BKM120_4-V4-562

source_name: WU PDX WHIM4_50hr control


description:
BKM120 most sensitive
CM_18_18.1
30-V1-501

source_name: WU PDX WHIM30_2hr control_bioreplicate1_technical replicate1


title: WHIM30_2hr control

description:
BKM120 most sensitive
BKM120_30-V1-503

source_name: WU PDX WHIM30_2hr control


title: WHIM2_2hr control

description:
BKM120 most resistant
BKM120_2-V1-455

source_name: WU PDX WHIM2_2hr control


title: WHIM2_2hr Buparlisib treatment

description:
BKM120 most resistant
BKM120_2-B2-450

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: WU PDX WHIM2_2hr Buparlisib treatment


description:
BKM120 most resistant
CM_14_14.1
2-B5-435

source_name: WU PDX WHIM2_50hr washout_bioreplicate1_technical replicate1


description:
BKM120 most resistant
CM_13_13.3
2-V4-444

source_name: WU PDX WHIM2_50hr control_bioreplicate3_technical replicate3


description:
BKM120 most resistant
CM_12_12.1
2-V4-443

source_name: WU PDX WHIM2_50hr control_bioreplicate2_technical replicate1


description:
BKM120 most resistant
CM_13_13.2
2-V4-444

source_name: WU PDX WHIM2_50hr control_bioreplicate3_technical replicate2


description:
BKM120 most resistant
CM_13_13.1
2-V4-444

source_name: WU PDX WHIM2_50hr control_bioreplicate3_technical replicate1


description:
BKM120 most resistant
CM_12_12.2
2-V4-443

source_name: WU PDX WHIM2_50hr control_bioreplicate2_technical replicate2


description:
BKM120 most resistant
CM_14_14.2
2-B5-435

source_name: WU PDX WHIM2_50hr washout_bioreplicate1_technical replicate2


description:
BKM120 most resistant
CM_11_11.1
2-V4-440

source_name: WU PDX WHIM2_50hr control_bioreplicate1_technical replicate1


description:
BKM120 most resistant
CM_11_11.2
2-V4-440

source_name: WU PDX WHIM2_50hr control_bioreplicate1_technical replicate2


description:
BKM120 most resistant
CM_11_11.3
2-V4-440

source_name: WU PDX WHIM2_50hr control_bioreplicate1_technical replicate3


description:
BKM120 most resistant
CM_10_10.1
2-B3-449

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate4_technical replicate1


description:
BKM120 most resistant
CM_10_10.2
2-B3-449

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate4_technical replicate2


description:
BKM120 most resistant
CM_10_10.3
2-B3-449

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate4_technical replicate3


description:
BKM120 most resistant
CM_9_9.2
2-B3-448

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate3_technical replicate2


description:
BKM120 most resistant
CM_9_9.1
2-B3-448

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate3_technical replicate1


description:
BKM120 most resistant
CM_12_12.3
2-V4-443

source_name: WU PDX WHIM2_50hr control_bioreplicate2_technical replicate3


description:
BKM120 most resistant
CM_9_9.3
2-B3-448

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate3_technical replicate3


description:
BKM120 most resistant
CM_8_8.2
2-B3-446

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate2_technical replicate2


description:
BKM120 most resistant
CM_8_8.1
2-B3-446

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate2_technical replicate1


description:
BKM120 most resistant
CM_7_7.3
2-B3-445

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate1_technical replicate3


description:
BKM120 most resistant
CM_7_7.2
2-B3-445

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate1_technical replicate2


description:
BKM120 most resistant
CM_8_8.3
2-B3-446

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate2_technical replicate3


description:
BKM120 most resistant
CM_7_7.1
2-B3-445

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate1_technical replicate1


description:
BKM120 most resistant
CM_5_5.2
2-B2-452

source_name: WU PDX WHIM2_2hr Buparlisib treatment_bioreplicate2_technical replicate2


description:
BKM120 most resistant
CM_5_5.3
2-B2-452

source_name: WU PDX WHIM2_2hr Buparlisib treatment_bioreplicate2_technical replicate3


description:
BKM120 most resistant
CM_6_6.3
2-B2-454

source_name: WU PDX WHIM2_2hr Buparlisib treatment_bioreplicate3_technical replicate3


description:
BKM120 most resistant
CM_6_6.1
2-B2-454

source_name: WU PDX WHIM2_2hr Buparlisib treatment_bioreplicate3_technical replicate1


description:
BKM120 most resistant
CM_3_3.1
2-V1-458

source_name: WU PDX WHIM2_2hr control_bioreplicate3_technical replicate1


description:
BKM120 most resistant
CM_3_3.2
2-V1-458

source_name: WU PDX WHIM2_2hr control_bioreplicate3_technical replicate2


description:
BKM120 most resistant
CM_4_4.3
2-B2-450

source_name: WU PDX WHIM2_2hr Buparlisib treatment_bioreplicate1_technical replicate3


description:
BKM120 most resistant
CM_4_4.2
2-B2-450

source_name: WU PDX WHIM2_2hr Buparlisib treatment_bioreplicate1_technical replicate2


description:
BKM120 most resistant
CM_6_6.2
2-B2-454

source_name: WU PDX WHIM2_2hr Buparlisib treatment_bioreplicate3_technical replicate2


description:
BKM120 most resistant
CM_3_3.3
2-V1-458

source_name: WU PDX WHIM2_2hr control_bioreplicate3_technical replicate3


title: H3K27me3 ChIP 1

status: Public on Mar 07 2018

city: Piscataway

first: Kelvin

middle: Y.

last: Kwan

state: NJ

address: 604 Allison Rd.

department: Cell Biology & Neuroscience

institute: Rutgers University

description: H3K27me3 ChIP biological replicate 1

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly.
peaks were called using the MACS2 narrow peak algorithm with a cutoff of q value <0.05
Genome_build: mm9
Supplementary_files_format_and_content: begraph with enrichment normalized to input

molecule: genomic DNA

organism: Mus musculus

source_name: iMOP cells

growth_protocol: Cells were cultured in the DMEM/F12 containing B27 and 20 ng/ml of bFGF in suspension as floating otospheres

extract_protocol:
iMOP cells were harvested by gravity sedimentation. Cells were lysed and nuclei enriched.  Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: iMOP cells grown in suspension with DMEM/F12 containing B27 and 20 ng/ml of bFGF. Depending on treatments, small molecules were added to the cultures.

tag: cell type

value: iMOP

tag: chip antibody

value: H3K27me3 (Upstate, Cat#05-851)


title: H3K4me3 ChIP 2

description: H3K4me3 ChIP biological replicate 2

value: H3K4me3 (Active Motif, Cat#39159)


description:
BKM120 most resistant
CM_2_2.3
2-V1-457

source_name: WU PDX WHIM2_2hr control_bioreplicate2_technical replicate3


title: H3K4me3 ChIP 1

description: H3K4me3 ChIP biological replicate 1


title: E17.5_KO2

status: Public on Mar 05 2018

city: ILLKIRCH

first: Delphine

last: Duteil

address: 1 rue Laurent Fries

country: France

institute: IGBMC

data_processing:
We aligned these reads to the mm10 build of the mouse genome using TopHat version 2
The aligned reads were counted with the homer software (analyze RNA) and DEG’s were identified using EdgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab files on samples records contain the raw read counts from Homer. Tab files on series record contain raw counts from all samples for each developmental stage.

source_name: Epidermis

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files).

tag: differentiation stage

value: Nir KO

value: epidermis


description:
BKM120 most resistant
CM_2_2.1
2-V1-457

source_name: WU PDX WHIM2_2hr control_bioreplicate2_technical replicate1


description:
BKM120 most resistant
CM_1_1.1
2-V1-455

source_name: WU PDX WHIM2_2hr control_bioreplicate1_technical replicate1


description:
BKM120 most resistant
CM_1_1.3
2-V1-455

source_name: WU PDX WHIM2_2hr control_bioreplicate1_technical replicate3


title: E17.5_KO1


title: E17.5_CT1

value: Control


description:
BKM120 most resistant
CM_1_1.2
2-V1-455

source_name: WU PDX WHIM2_2hr control_bioreplicate1_technical replicate2


title: E17.5_CT2


title: E15.5_KO2


description:
BKM120 most resistant
CM_5_5.1
2-B2-452

source_name: WU PDX WHIM2_2hr Buparlisib treatment_bioreplicate2_technical replicate1


title: E15.5_KO1


title: H3K27me3 ChIP 2

description: H3K27me3 ChIP biological replicate 2


title: E15.5_CT2


title: E15.5_CT1


description:
BKM120 most resistant
CM_4_4.1
2-B2-450

source_name: WU PDX WHIM2_2hr Buparlisib treatment_bioreplicate1_technical replicate1


description:
BKM120 most resistant
CM_2_2.2
2-V1-457

source_name: WU PDX WHIM2_2hr control_bioreplicate2_technical replicate2


title: Repleted 1

status: Public on Jan 18 2018

data_processing:
Illumina Offline BaseCaller1.9.3  software used for basecalling.
Quality control: Reads were aligned against hg19 (Feb. 2009) using bwa mem v. 0.7.12-r1039 [https://github.com/lh3/bwa] with flags –t 16 –f. Mapping rates, fraction of multiply-mapping reads, number of unique 20-mers at the 5ʹ end of the reads, insert size distributions, and fraction of ribosomal RNAs were calculated using dedicated perl scripts and bedtools v. 2.25.0.3 In addition, each resulting bam file was randomly down-sampled to a million reads, which were then aligned against hg19 and read density across genomic features was estimated for RNA-Seq-specific quality control metrics.
Reads were aligned against an hg19 / ENSEMBL GRCh37 75 annotation (without added polyA) using rsem v. 1.2.6 / bowtie v. 1.0.1 with the following flags: -p 4 --output-genome-bam --calc-ci --bowtie-chunkmbs 1024.4-5 Counts and RPKM were retrieved
Genome_build: Homo sapiens hg19 / ENSEMBL 75
Supplementary_files_format_and_content: comma-delimited text files with log2(RPKM+1) data from RSEM

molecule: polyA RNA

source_name: HEK293 Freestyle Cells

growth_protocol: Prior to beginning the experiment, HEK293 Freestyle cells were suspended at a density of 1,000,000 cells/mL in a total volume of 40 mL Freestyle medium for at least 18 h.

extract_protocol:
36 h later, RNA was harvested with a Qiagen RNeasy Plus kit after homogenization of cells with a QIAshredder. The experiment was performed in biological triplicate. Total RNA was submitted to the MIT BioMicroCenter for library preparation and sequencing.
RNA integrity and concentration were checked on a Fragment Analyzer (Advanced Analytical). The mRNA was purified by polyA-tail enrichment, fragmented, and reverse transcribed into cDNA (Illumina TruSeq). cDNA samples were then end-repaired and adaptor-ligated using the SPRI-works Fragment Library System I (Beckman Coulter Genomics) and indexed during amplification. Libraries were quantified using the Fragment Analyzer (Advanced Analytical) and qPCR before being loaded for single-end sequencing using the Illumina HiSeq 2000.

treatment_protocol: A  portion of cells was then washed with PBS 3× and brought to a density of 4,000,000 cells/mL in PBS before being plated into a 12-well plate containing either untreated Freestyle Medium, Zinc-Depleted Freestyle Medium, or Repleted Freestyle Medium that had been washed with 500 M EDTA then three times with PBS.

tag: culture medium

value: Zn(II) Depleted Freestyle Medium repleted with Zn(II)


title: Repleted 3


title: Repleted 2


title: Depleted 2

value: Zn(II) Depleted Freestyle Medium


title: Depleted 3


title: Full 2

value: Untreated Freestyle Medium


title: Depleted 1


title: Sample 19 DHFR.YFP +10 uM TMP 24h

status: Public on Nov 15 2017

data_processing:
Illumina Offline BaseCaller1.9.3  software used for basecalling.
Quality control: Reads were aligned against canFam3 (Sept. 2011) using bwa mem v. 0.7.12-r1039 with flags –t 16 –f and mapping rates, fraction of multiply-mapping reads, number of unique 20-mers at the 5’ end of the reads, insert size distributions and fraction of ribosomal RNAs were calculated using dedicated perl scripts and bedtools v. 2.25.0.64 In addition, each resulting bam file was randomly down-sampled to a million reads, which were aligned against canFam3 and read density across genomic features were estimated for RNA-Seq-specific quality control metrics.
RNA-Seq mapping and quantitation: Reads were aligned against canFam3 / ENSEMBL 86 annotation using STAR v. 2.5.3a with flags -runThreadN 8 --runMode alignReads  --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM with --genomeDir pointing to a 75nt-junction canFam3 STAR suffix array.
Gene expression was quantitated using RSEM v. 1.3.0 with the following flags for all libraries: rsem-calculate-expression --calc-pme --alignments -p 8  --forward-prob 0 against an annotation matching the STAR SA reference. Posterior mean estimates (pme) of counts and estimated RPKM were retrieved.
Genome_build: canFam3
Supplementary_files_format_and_content: Tab-delimited text file containing log2-transformed RPKM values for all canFam3 annotated genes (ENSEMBL 86) in each sample (RSEM pme_RPKM output).

organism: Canis lupus familiaris

source_name: DHFR.YFP +10 uM TMP 24h

growth_protocol: Low passage cells were plated at a density of 200,000 cells/well in 6 well plates.

extract_protocol:
Cells were trypsinized and RNA was extracted using the Qiagen RNeasy Plus Mini Kit and QIAshredder homogenization columns.
For RNAseq, RNA integrity and concentration were checked on a Fragment Analyzer (Advanced Analytical) and libraries were prepared using the Illumina NeoPrep RNAseq kit. Libraries were quantified using the Fragment Analyzer (Advanced Analytical) and qPCR before being loaded for single-end sequencing using the Illumina HiSeq 2000 for 50 nucleotides.
polyA-based mRNA capture using Neoprep with TruSeq strand-specific strategy.

treatment_protocol: At the time of plating, cells were treated with either 0.1% DMSO, 10 µM TMP, or 10 nM STA-9090 (24 hour treatment).

value: Madin-Darby Canine Kidney (MDCK) cells

tag: genotype/variation

value: Clonal; stably expressing DHFR.YFP

tag: developmental stage

value: Adult-derived epithelial cell line

tag: treated with

value: 10uM Trimethroprim (TMP) for 24hrs


title: Sample 7 DHFR.cHSF1 +10 uM TMP 24h

source_name: DHFR.cHSF1 +10 uM TMP 24h

value: Clonal; stably expressing DHFR.cHSF1


title: Sample 15 DHFR.YFP DMSO 24h

source_name: DHFR.YFP DMSO 24h

value: 0.1% DMSO for 24hrs


title: Sample 3 DHFR.cHSF1 DMSO 24h

source_name: DHFR.cHSF1 DMSO 24h


title: Sample 12 DHFR.cHSF1 +10 nM STA 24h

source_name: DHFR.cHSF1 +10 nM STA 24h

value: 10 nM STA-9090 for 24hrs


title: Sample 8 DHFR.cHSF1 +10 uM TMP 24h


title: Sample 4 DHFR.cHSF1 DMSO 24h


title: Sample 2 DHFR.cHSF1 DMSO 24h


title: Sample 11 DHFR.cHSF1 +10 nM STA 24h


title: Sample 13 DHFR.YFP DMSO 24h


title: Sample 6 DHFR.cHSF1 +10 uM TMP 24h


title: Sample 20 DHFR.YFP +10 uM TMP 24h


title: Sample 14 DHFR.YFP DMSO 24h


title: Sample 10 DHFR.cHSF1 +10 nM STA 24h


title: Full 3


title: Full 1


title: Sample 18 DHFR.YFP +10 uM TMP 24h


title: 356_KO_6weeks

status: Public on Aug 22 2017

data_processing:
We aligned these reads to the mm10 build of the mouse genome using TopHat version 2
The aligned reads were counted with the homer software (analyze RNA) and DEG’s were identified using EdgeR
Genome_build: mm10

source_name: ingWAT

tag: tissue

value: inguinal white adipose tissue (ingWAT)

value: Lsd1 KO


title: Heat Shocked and Wounded Sample 2

status: Public on Sep 08 2017

description: CCL130911_ALI_HS-W S2b

hyb_protocol: Hybridization Cocktails were incubated  at 45°C and 60 rpm for 18 hours. Arrays were washed and stained in Affymetrix Fluidics Station 450 using manufacturer's protocol.

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

data_processing: Gene expression was preprocessed by the Robust Multichip Analysis (RMA) algorithm using Affymetrix Expression Console

source_name: Heat Shocked and Wounded A549 cells

label_protocol: 100 ng of total RNA was processed for GeneChip analysis using the 3’ IVT Express kit and the PrimeView microarray chip (Affymetrix) following the manufacturer’s directions

growth_protocol: A549 cells were purchased from American Type Culture Collection Manassas, VA. A549 cells were maintained in RPMI 1640 supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 10 mM HEPES buffer, pH 7.3, and 10% defined fetal bovine serum (all from Gibco Life Technologies, Grand Island, NY).  Cells were cultured on uncoated plastic for maintenance and wounding assays.

extract_protocol: A549 monolayers were lysed in Trizol (Thermo Fisher; Waltham, MA) and total RNA was isolated using the manufacturer’s protocol. Total RNA concentration was measured by the Nanodrop ND-1000 spectophotometer (NanoDrop Technologies, Wilmington, DE)

treatment_protocol: Control and heat shocked (2 hours treatment) and subsequently wounded or wounded alone (for 4 hours) A549 monolayers were used for analysis of gene expression.

tag: cell line

tag: treatment

value: Heat Shocked and Wounded


title: Wounded Sample 3

description: CCL130911_ALI_W S3a

source_name: Wounded A549 cells

value: Wounded


title: Heat Shocked and Wounded Sample 1

description: CCL130911_ALI_HS-W S2a


title: 359_KO_6weeks

tag: genotype


title: 360_KO_6weeks


title: 518_CT_6weeks


title: Wounded Sample 2

description: CCL130911_ALI_W S2b


title: 358_CT_6weeks


title: 361_KO_6weeks


title: 357_CT_6weeks


title: 517_CT_6weeks


title: Control Sample 3

description: CCL130911_ALI_BL S3a

source_name: Control A549 cells


title: Control Sample 2

description: CCL130911_ALI_BL S2b


title: Heat Shocked Sample 3

description: CCL130911_ALI_HS S3a

source_name: Heat Shocked A549 cells

value: Heat Shocked


title: Control Sample 1

description: CCL130911_ALI_BL S2a


title: Heat Shocked and Wounded Sample 3

description: CCL130911_ALI_HS-W S3a


title: Heat Shocked Sample 1

description: CCL130911_ALI_HS S2a


title: Heat Shocked Sample 2

description: CCL130911_ALI_HS S2b


title: Wounded Sample 1

description: CCL130911_ALI_W S2a


title: ARDS 3064 D3

hyb_protocol: Hybridization Cocktail (130 ul) per array was incubated  at 48°C and 60 rpm for 18 hours. Arrays were washed and stained in Affymetrix Fluidics Station 450 using protocol FS450_0003.

scan_protocol: Affymetrix  GeneChip miRNA 3.0 Arrays were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: Raw data were normalized using RMA in Affymetrix Expression Console and presented as log transformed signal intensity. The probe set results were all within bounds.

source_name: during methylprednisolone therapy_Day 3

label_protocol: Total RNA (500 ng including miRNA) was labeled with Poly (A) tail and biotinylated tag (Flashtag Biotin HSR Kit, Affymetrix) as per the manufacture’s instructions.

growth_protocol: Blood leukocytes were isolated by centrifugation of 30 ml of heparinized whole blood at 500 g for 10 min. The buffy coat was obtained and cells were then incubated with erytrocytes lysing buffer and washed with PBS.Thawed blood leukocytes were washed 3 times with 10 ml PBS and then lysed (Qiazol, Qiagen, Valencia, CA). Total RNA, including miRNA was isolated (miRNeasy Mini Kit) as per manufacturer’s instructions.

extract_protocol: Thawed blood leukocytes were washed 3 times with 10 ml PBS and then lysed. Total RNA, including miRNA was isolated (miRNeasy Mini Kit) as per manufacturer’s instructions.

tag: gender

value: Female

tag: age

value: 68 years old

tag: disease status

value: pneumonia

tag: treatment group

value: during methylprednisolone therapy

tag: timepoint

value: Day 3

value: blood leukocytes


title: ARDS 3076 D0

source_name: pre methylprednisolone _Day 0

value: Male

value: 35 years old

value: pre methylprednisolone

value: Day 0


title: ARDS 3084 D3

source_name: usual care_Day 3

value: 69 years old

value: usual care


title: ARDS 3076 D3


title: ARDS 3084 D0

source_name: usual care_Day 0


title: ARDS 3070 D3

value: 52 years old


title: ARDS 3014 D0

value: female

value: 45 years old


title: ARDS 3057 D0

value: 75 years old


title: ARDS 3062 D0

value: 63 years old


title: ARDS 3061 D3

value: Female

value: 48 years old


title: ARDS 3061 D0

value: pneumonia


title: ARDS 3062 D3

value: during methylprednisolone therapy


title: ARDS 3064 D0

value: 68 years old


title: ARDS 3057 D3

description:
CCL130702_ARDS_3057_D2_NS
Please note that the CEL file was mislabeled as D2 during the chip scanning process.

value: Day 3

value: blood leukocytes


title: ARDS 3014 D3


title: ARDS 3070 D0

value: Male


title: Breast Cancer Array_Patient ID_130_C1D15

status: Public on Apr 07 2017

description:
pd991
Sample name: 130_C1D15
Generated labeled cRNA.

hyb_protocol: Agilent 60-mer oligo microarray processing protocol.

data_processing:
Text files from Agilent Feature Extraction software were loaded into the UNC-CH Microarray Database. Final Loess, normalized log2 ratios (Cy5-sample/Cy3-control) for each probe were retrieved after applying default quality control filters.
Probes were excluded if the microarray spot: a) was not found in either channel, b) is a non-uniform outlier, c) background is a non-uniform outlier, d) is a non-uniform outlier for the population, e) background is a non-uniform outlier for the population, or f) is not a positive and significant signal in either channel.

source_name: Stratagene Human Universal Reference spiked with MCF7 and ME16C mRNA

label_protocol: Agilent Low Input Linear Amplification Kit and protocol.

extract_protocol: Trizol extractions followed by DNase treatment and column purification.

value: 10 human cell lines (1_Adenocarcinoma, mammary gland; 2_Hepatoblastoma, liver; 3_Adenocarcinoma, cervix; 4_Embryonal carcinoma, testis; 5_Glioblastoma, brain; 6_Melanoma; 7_Liposarcoma; 8_Histiocytic Lymphoma; macrophage; histocyte; 9_ Lymphoblastic leukemia, T lymphoblast; 10_Plasmacytoma; myeloma; B lymphocyte). Also, mRNA spiked in from MCF7 and ME16C.

tag: sample type

value: reference

source_name: Primary Breast Tumor_Patient ID_130_C1D15

growth_protocol: Patient biopsies were frozen and stored in oct compound.

treatment_protocol: The treatment time course is BL - C1D1 - C1D15 - Surgery.

tag: disease state

value: breast cancer

value: oct blocks from fine needle breast tumor biopsies which contained at least 50% tumor cellularity

tag: patient id


title: Breast Cancer Array_Patient ID_133_C1D1

description:
pd991
Sample name: 133_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_133_C1D1


title: Breast Cancer Array_Patient ID_134_Surg

description:
pd991
Sample name: 134_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_134_Surg

value: Surgery


title: Breast Cancer Array_Patient ID_131_C1D15

description:
pd991
Sample name: 131_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_131_C1D15


title: Breast Cancer Array_Patient ID_133_Surg

description:
pd991
Sample name: 133_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_133_Surg


title: Breast Cancer Array_Patient ID_133_C1D15

description:
pd991
Sample name: 133_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_133_C1D15


title: Breast Cancer Array_Patient ID_134_BL

description:
pd991
Sample name: 134_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_134_BL

value: Baseline


title: Breast Cancer Array_Patient ID_131_Surg

description:
pd991
Sample name: 131_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_131_Surg


title: Breast Cancer Array_Patient ID_130_Surg

description:
pd991
Sample name: 130_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_130_Surg


title: Breast Cancer Array_Patient ID_134_C1D15

description:
pd991
Sample name: 134_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_134_C1D15


title: Breast Cancer Array_Patient ID_130_C1D1

description:
pd991
Sample name: 130_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_130_C1D1


title: Breast Cancer Array_Patient ID_134_C1D1

description:
pd991
Sample name: 134_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_134_C1D1


title: Breast Cancer Array_Patient ID_133_BL

description:
pd991
Sample name: 133_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_133_BL


title: Breast Cancer Array_Patient ID_129_C1D15

description:
pd991
Sample name: 129_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_129_C1D15


title: Breast Cancer Array_Patient ID_128_C1D15

description:
pd991
Sample name: 128_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_128_C1D15


title: Breast Cancer Array_Patient ID_124_C1D1

description:
pd991
Sample name: 124_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_124_C1D1


title: Breast Cancer Array_Patient ID_124_C1D15

description:
pd991
Sample name: 124_C1D15
Generated labeled cRNA.

source_name: Stratagene Human Universal Reference spiked with MCF7 and ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_124_C1D15


title: Breast Cancer Array_Patient ID_128_Surg

description:
pd991
Sample name: 128_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_128_Surg


title: Breast Cancer Array_Patient ID_131_C1D1

description:
pd991
Sample name: 131_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_131_C1D1


title: Breast Cancer Array_Patient ID_129_C1D1

description:
pd991
Sample name: 129_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_129_C1D1


title: Breast Cancer Array_Patient ID_127_C1D1

description:
pd991
Sample name: 127_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_127_C1D1


title: Breast Cancer Array_Patient ID_126_Surg

description:
pd991
Sample name: 126_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_126_Surg


title: Breast Cancer Array_Patient ID_128_BL

description:
pd991
Sample name: 128_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_128_BL


title: Breast Cancer Array_Patient ID_128_C1D1

description:
pd991
Sample name: 128_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_128_C1D1


title: Breast Cancer Array_Patient ID_126_BL

description:
pd991
Sample name: 126_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_126_BL


title: Breast Cancer Array_Patient ID_126_C1D1

description:
pd991
Sample name: 126_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_126_C1D1


title: Breast Cancer Array_Patient ID_123_C1D15

description:
pd991
Sample name: 123_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_123_C1D15


title: Breast Cancer Array_Patient ID_123_C1D1

description:
pd991
Sample name: 123_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_123_C1D1


title: Breast Cancer Array_Patient ID_123_BL

description:
pd991
Sample name: 123_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_123_BL


title: Breast Cancer Array_Patient ID_121_Surg

description:
pd991
Sample name: 121_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_121_Surg


title: Breast Cancer Array_Patient ID_119_Surg

description:
pd991
Sample name: 119_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_119_Surg


title: Breast Cancer Array_Patient ID_119_C1D1

description:
pd991
Sample name: 119_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_119_C1D1


title: Breast Cancer Array_Patient ID_120_BL

description:
pd991
Sample name: 120_BL
Generated labeled cRNA.

source_name: Stratagene Human Universal Reference spiked with MCF7 and ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_120_BL


title: Breast Cancer Array_Patient ID_123_Surg

description:
pd991
Sample name: 123_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_123_Surg


title: Breast Cancer Array_Patient ID_117_C1D15

description:
pd991
Sample name: 117_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_117_C1D15


title: Breast Cancer Array_Patient ID_118_BL

description:
pd991
Sample name: 118_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_118_BL


title: Breast Cancer Array_Patient ID_118_C1D15

description:
pd991
Sample name: 118_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_118_C1D15


title: Breast Cancer Array_Patient ID_119_BL

description:
pd991
Sample name: 119_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_119_BL


title: Breast Cancer Array_Patient ID_121_C1D1

description:
pd991
Sample name: 121_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_121_C1D1


title: Breast Cancer Array_Patient ID_124_BL

description:
pd991
Sample name: 124_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_124_BL


title: Breast Cancer Array_Patient ID_125_C1D1

description:
pd991
Sample name: 125_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_125_C1D1


title: Breast Cancer Array_Patient ID_116_C1D1

description:
pd991
Sample name: 116_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_116_C1D1


title: Breast Cancer Array_Patient ID_114_C1D1

description:
pd991
Sample name: 114_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_114_C1D1


title: Breast Cancer Array_Patient ID_117_C1D1

description:
pd991
Sample name: 117_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_117_C1D1


title: Breast Cancer Array_Patient ID_115_BL

description:
pd991
Sample name: 115_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_115_BL


title: Breast Cancer Array_Patient ID_118_C1D1

description:
pd991
Sample name: 118_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_118_C1D1


title: Breast Cancer Array_Patient ID_113_BL

description:
pd991
Sample name: 113_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_113_BL


title: Breast Cancer Array_Patient ID_112_C1D15

description:
pd991
Sample name: 112_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_112_C1D15


title: Breast Cancer Array_Patient ID_112_S

description:
pd991
Sample name: 112_S
Generated labeled cRNA.

source_name: Stratagene Human Universal Reference spiked with MCF7 and ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_112_S


title: Breast Cancer Array_Patient ID_110_Surg

description:
pd991
Sample name: 110_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_110_Surg


title: Breast Cancer Array_Patient ID_112_BL

description:
pd991
Sample name: 112_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_112_BL


title: Breast Cancer Array_Patient ID_111_BL

description:
pd991
Sample name: 111_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_111_BL


title: Breast Cancer Array_Patient ID_112_C1D1

description:
pd991
Sample name: 112_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_112_C1D1


title: Breast Cancer Array_Patient ID_108_Surg

description:
pd991
Sample name: 108_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_108_Surg


title: Breast Cancer Array_Patient ID_108_C1D15

description:
pd991
Sample name: 108_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_108_C1D15


title: Breast Cancer Array_Patient ID_110_BL

description:
pd991
Sample name: 110_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_110_BL


title: Breast Cancer Array_Patient ID_107_C1D1

description:
pd991
Sample name: 107_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_107_C1D1


title: Breast Cancer Array_Patient ID_104_C1D15

description:
pd991
Sample name: 104_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_104_C1D15


title: Breast Cancer Array_Patient ID_108_BL

description:
pd991
Sample name: 108_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_108_BL


title: Breast Cancer Array_Patient ID_107_BL

description:
pd991
Sample name: 107_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_107_BL


title: Breast Cancer Array_Patient ID_106_BL

description:
pd991
Sample name: 106_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_106_BL


title: Breast Cancer Array_Patient ID_104_C1D1

description:
pd991
Sample name: 104_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_104_C1D1


title: Breast Cancer Array_Patient ID_102_C1D1

description:
pd991
Sample name: 102_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_102_C1D1


title: Breast Cancer Array_Patient ID_105_C1D1

description:
pd991
Sample name: 105_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_105_C1D1


title: Breast Cancer Array_Patient ID_104_BL

description:
pd991
Sample name: 104_BL
Generated labeled cRNA.

source_name: Stratagene Human Universal Reference spiked with MCF7 and ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_104_BL


title: Breast Cancer Array_Patient ID_107_Surg

description:
pd991
Sample name: 107_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_107_Surg


title: Breast Cancer Array_Patient ID_101_C1D15

description:
pd991
Sample name: 101_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_101_C1D15


title: Breast Cancer Array_Patient ID_103_BL

description:
pd991
Sample name: 103_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_103_BL


title: Breast Cancer Array_Patient ID_403_Surg

description:
pd991
Sample name: 403_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_403_Surg


title: Breast Cancer Array_Patient ID_102_C1D15

description:
pd991
Sample name: 102_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_102_C1D15


title: Breast Cancer Array_Patient ID_106_C1D15_Redo

description:
pd991
Sample name: 106_C1D15_Redo
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_106_C1D15_Redo


title: Breast Cancer Array_Patient ID_105_BL

description:
pd991
Sample name: 105_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_105_BL


title: Breast Cancer Array_Patient ID_103_C1D15

description:
pd991
Sample name: 103_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_103_C1D15


title: Breast Cancer Array_Patient ID_103_C1D1

description:
pd991
Sample name: 103_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_103_C1D1


title: Breast Cancer Array_Patient ID_101_C1D1

description:
pd991
Sample name: 101_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_101_C1D1


title: Breast Cancer Array_Patient ID_101_BL

description:
pd991
Sample name: 101_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_101_BL


title: Breast Cancer Array_Patient ID_403_BL

description:
pd991
Sample name: 403_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_403_BL


title: Breast Cancer Array_Patient ID_403_C1D15

description:
pd991
Sample name: 403_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_403_C1D15


title: Breast Cancer Array_Patient ID_102_BL

description:
pd991
Sample name: 102_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_102_BL


title: Breast Cancer Array_Patient ID_402_C1D1

description:
pd991
Sample name: 402_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_402_C1D1


title: Breast Cancer Array_Patient ID_402_C1D15

description:
pd991
Sample name: 402_C1D15
Generated labeled cRNA.

source_name: Stratagene Human Universal Reference spiked with MCF7 and ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_402_C1D15


title: Breast Cancer Array_Patient ID_401_C1D15

description:
pd991
Sample name: 401_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_401_C1D15


title: Breast Cancer Array_Patient ID_402_BL

description:
pd991
Sample name: 402_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_402_BL


title: Breast Cancer Array_Patient ID_401_C1D1

description:
pd991
Sample name: 401_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_401_C1D1


title: Breast Cancer Array_Patient ID_302_BL

description:
pd991
Sample name: 302_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_302_BL


title: Breast Cancer Array_Patient ID_303_BL

description:
pd991
Sample name: 303_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_303_BL


title: Breast Cancer Array_Patient ID_208_C1D15

description:
pd991
Sample name: 208_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_208_C1D15


title: Breast Cancer Array_Patient ID_305_C1D15

description:
pd991
Sample name: 305_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_305_C1D15


title: Breast Cancer Array_Patient ID_209_C1D1

description:
pd991
Sample name: 209_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_209_C1D1


title: Breast Cancer Array_Patient ID_304_C1D15

description:
pd991
Sample name: 304_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_304_C1D15


title: Breast Cancer Array_Patient ID_301_Surg

description:
pd991
Sample name: 301_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_301_Surg


title: Breast Cancer Array_Patient ID_303_C1D15

description:
pd991
Sample name: 303_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_303_C1D15


title: Breast Cancer Array_Patient ID_209_Surg

description:
pd991
Sample name: 209_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_209_Surg


title: Breast Cancer Array_Patient ID_305_C1D1

description:
pd991
Sample name: 305_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_305_C1D1


title: Breast Cancer Array_Patient ID_206_C1D1

description:
pd991
Sample name: 206_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_206_C1D1


title: Breast Cancer Array_Patient ID_304_BL

description:
pd991
Sample name: 304_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_304_BL


title: Breast Cancer Array_Patient ID_207_C1D15

description:
pd991
Sample name: 207_C1D15
Generated labeled cRNA.

source_name: Stratagene Human Universal Reference spiked with MCF7 and ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_207_C1D15


title: Breast Cancer Array_Patient ID_207_BL

description:
pd991
Sample name: 207_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_207_BL


title: Breast Cancer Array_Patient ID_302_C1D15

description:
pd991
Sample name: 302_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_302_C1D15


title: Breast Cancer Array_Patient ID_203_Surg

description:
pd991
Sample name: 203_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_203_Surg


title: Breast Cancer Array_Patient ID_207_Surg

description:
pd991
Sample name: 207_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_207_Surg


title: Breast Cancer Array_Patient ID_303_C1D1

description:
pd991
Sample name: 303_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_303_C1D1


title: Breast Cancer Array_Patient ID_208_Surg

description:
pd991
Sample name: 208_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_208_Surg


title: Breast Cancer Array_Patient ID_305_BL

description:
pd991
Sample name: 305_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_305_BL


title: Breast Cancer Array_Patient ID_209_C1D15

description:
pd991
Sample name: 209_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_209_C1D15


title: Breast Cancer Array_Patient ID_302_Surg

description:
pd991
Sample name: 302_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_302_Surg


title: Breast Cancer Array_Patient ID_208_BL

description:
pd991
Sample name: 208_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_208_BL


title: Breast Cancer Array_Patient ID_207_C1D1

description:
pd991
Sample name: 207_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_207_C1D1


title: Breast Cancer Array_Patient ID_204_C1D15

description:
pd991
Sample name: 204_C1D15
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_204_C1D15


title: Breast Cancer Array_Patient ID_208_C1D1

description:
pd991
Sample name: 208_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_208_C1D1


title: Breast Cancer Array_Patient ID_206_Surg

description:
pd991
Sample name: 206_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_206_Surg


title: Breast Cancer Array_Patient ID_401_BL

description:
pd991
Sample name: 401_BL
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_401_BL


title: Breast Cancer Array_Patient ID_204_Surg

description:
pd991
Sample name: 204_Surg
Generated labeled cRNA.

source_name: Stratagene Human Universal Reference spiked with MCF7 and ME16C mRNA

source_name: Primary Breast Tumor_Patient ID_204_Surg


title: Breast Cancer Array_Patient ID_111_Surg

description:
pd991
Sample name: 111_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_111_Surg


title: Breast Cancer Array_Patient ID_203_C1D1

description:
pd991
Sample name: 203_C1D1
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_203_C1D1


title: Breast Cancer Array_Patient ID_201_Surg

description:
pd991
Sample name: 201_Surg
Generated labeled cRNA.

source_name: Primary Breast Tumor_Patient ID_201_Surg


title: Breast Cancer Array_Patient ID_18197_w2

status: Public on Jan 04 2017

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

tag: rna source

value: Total RNA from 10 human cell lines:1_Adenocarcinoma, mammary gland 2_Hepatoblastoma, liver 3_Adenocarcinoma, cervix 4_Embryonal carcinoma, testis 5_Glioblastoma, brain 6_Melanoma 7_Liposarcoma 8_Histiocytic Lymphoma; macrophage; histocyte 9_ Lymphoblastic leukemia, T lymphoblast 10_Plasmacytoma; myeloma; B lymphocyte.  Also, mRNA spiked in from MCF7 and ME16C.

source_name: Primary Breast Tumor_Patient ID_18197_w2

value: breast cancer tissue

tag: biopsy type

value: oct blocks from fine needle biopsies which contained at least 50% tumor cellularity

tag: study id

tag: studynum

tag: bl  ki67

tag: eot ki67

tag: endocrine therapy response group

value: sensitive

tag: treatment course

value: continue AI


title: Breast Cancer Array_Patient ID_21009_w2

source_name: Primary Breast Tumor_Patient ID_21009_w2

tag: tissue


title: Breast Cancer Array_Patient ID_18189_w2

source_name: Primary Breast Tumor_Patient ID_18189_w2


title: Breast Cancer Array_Patient ID_21072_BL

source_name: Primary Breast Tumor_Patient ID_21072_BL


title: Breast Cancer Array_Patient ID_18182_w2

source_name: Primary Breast Tumor_Patient ID_18182_w2


title: Breast Cancer Array_Patient ID_18182_BL

source_name: Primary Breast Tumor_Patient ID_18182_BL


title: Breast Cancer Array_Patient ID_21080_W2

source_name: Primary Breast Tumor_Patient ID_21080_W2

value: resistant

value: switch to NAC


title: Breast Cancer Array_Patient ID_203_BL

description:
pd991
Sample name: 203_BL
Generated labeled cRNA.

tag: cell line

source_name: Primary Breast Tumor_Patient ID_203_BL

tag: treatment


title: Breast Cancer Array_Patient ID_18183_W2

source_name: Primary Breast Tumor_Patient ID_18183_W2


title: Breast Cancer Array_Patient ID_21080_BL

source_name: Primary Breast Tumor_Patient ID_21080_BL


title: Breast Cancer Array_Patient ID_18184_BL

source_name: Primary Breast Tumor_Patient ID_18184_BL