title: 156560566_1_D12_CTCTCTAC-AGAGTAGA_L004


title: ISPY2_677910

status: Public on May 25 2022

type: RNA

city: San Francisco

first: Denise

middle: M

last: Wolf

state: CA

address: 2340 Sutter st

country: USA

institute: University of California, San Francisco

hyb_protocol: Hybridization was performed by Agendia Inc (Irvine, CA). This company is referenced by the platforms used: GPL20078 and GPL30494 (updated version of GPL16233).

scan_protocol: Scanning was performed by Agendia Inc (Irvine, CA).

data_processing:
For each array, gnormalized signal (log2) data, as provided in the raw files on each patient, was extracted and aligned to its 75th quantile by Agendia as per the manufacturer’s data processing recommendations. All values indicated for non-conformity, as indicated by the 'gIsFeatNonUnifOL' column in the raw files, are NA'd out; and a fixed value of 9.5 was added to avoid negative values. Probeset level data per array were mean-collapsed to the gene level, and genes common to the two platforms identified. Expression data from the first ~900 I-SPY2 patients distributed over the two platforms GPL30494 (updated version of GPL16233; n=334) and GPL20078 (n=545) were combined into a single gene-level dataset after batch-adjusting using ComBat [PMID:16632515]. Linear adjustment factors were derived from the ComBat transformation, per platform, which can be used to batch correct raw files. The subsequent ~100 samples, assayed on GPL20078, were batch corrected using these factors and added to the original set, yielding a normalized expression dataset comprising 988 samples (987 unique patients) x 19,134 (common) genes. The linear adjustment factors and updated probe annotation files per platform are provided, as is the ComBat-normalized data we used in our analysis (supplemental file "ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt").
ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt: Normalized, gene-level, batch-/platform- adjusted pre-treatment Agilent 44K expression data for patients from 10 arms of the neoadjuvant I-SPY 2 platform trial for early stage, aggressive breast cancer (n=988 samples for 987 patients). This is the dataset we used in our pan-arm analysis, and constitutes part of the I-SPY2-990 mRNA/RPPA Data Resource. To derive this matrix, probeset level expression data from the first ~900 I-SPY2 patients distributed over the two platforms GPL30494 (updated version of GPL16233; n=334) and GPL20078 (n=545) were mean-collapsed by gene and combined into a single gene-level dataset after batch-adjusting using ComBat [PMID:16632515]. Linear adjustment factors were derived from the ComBat transformation, per platform, which can be used to batch correct new files. The subsequent ~100 samples, assayed on GPL20078, were batch corrected using these factors and added to the original set, yielding the resulting normalized expression dataset comprising 988 samples (987 unique patients) x 19,134 (common) genes.
ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL20078_ProbeLevel_n654.txt: Normalized probeset level pre-treatment gene expression data from Agilent 44K expression arrays Agendia32627_DPv1.14_SCFGplus [with annotation GPL20078 (n=654)] from the I-SPY 2 platform trial for early stage, aggressive breast cancer. Each column represents a patient sample. Per column, green-channel (Cy3) normalized signal intensity (log2) data, as provided in the raw files on each patient, was extracted and aligned to its (within-array) 75th quantile by Agendia as per the manufacturer’s data processing recommendations. All values indicated for non-conformity are NA'd out; and a fixed value of 9.5 was added to avoid negative values.
ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL30493.wasGPL16233_ProbeLevel_n334.txt: Normalized probeset level pre-treatment gene expression data from Agilent 44K expression arrays Agilent_human_DiscoverPrint_15746 [with annotation GPL30493 (update of GPL16233; n=334)] from the I-SPY 2 platform trial for early stage, aggressive breast cancer. Each column represents a patient sample. Per column, green-channel (Cy3) normalized signal intensity (log2) data, as provided in the raw files on each patient, was extracted and aligned to its (within-array) 75th quantile by Agendia as per the manufacturer’s data processing recommendations. All values indicated for non-conformity are NA'd out; and a fixed value of 9.5 was added to avoid negative values.
ISPY2_LinearFit_forCombiningExp_20078.txt: This file contains linear adjustment factors (intercept and linear coefficient) derived from the ComBat transformation combining data (~900 samples) from GPL20078 and GPL30493 that can be used to batch-/platform- correct new Agilent 44K expression arrays of the type Agendia32627_DPv1.14_SCFGplus [gene-collapsed using annotation GPL20078] for inclusion in the larger normalized dataset. Application of this transformation to columns from ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL20078_ProbeLevel_n654.txt, once mean-collapsed to gene level using GPL20078, results in values nearly identical to those in ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt, the normalized expression matrix in the I-SPY2-990 data resource.
ISPY2_LinearFit_forCombiningExp_GPL30493_wasGPL16233.txt: This file contains linear adjustment factors (intercept and linear coefficient) derived from the ComBat transformation combining data (~900 samples) from GPL20078 and GPL30493 that can be used to batch-/platform- correct new Agilent 44K expression arrays of the type Agilent_human_DiscoverPrint_15746 [with annotation GPL30493 (update of GPL16233)] for inclusion in the larger normalized dataset. Application of this transformation to columns from ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL30493.wasGPL16233_ProbeLevel_n334.txt, once mean-collapsed to gene level using GPL20078, results in values nearly identical to those in ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt.
ProbeAnnotation_ISPY2Edit_GPL30493_wasGPL16233.txt: This is the probeset annotation file for GPL30493, a minor update of GPL16233. For each probeset ID (row), the associated gene name, systematic name and DNA sequence is described (columns).

molecule: total RNA

organism: Homo sapiens

source_name: Breast cancer biopsy (pre-treatment)

label_protocol: Labeling was performed by Agendia Inc (Irvine, CA).

extract_protocol: Extraction was performed by Agendia Inc (Irvine, CA).

tag: patient id

tag: tissue

value: Breast cancer biopsy (pre-treatment)

tag: hr

tag: mp

tag: pcr

tag: arm

value: Paclitaxel + AMG 386

tag: adjustment method

value: ComBat Adjust


title: ISPY2_676630

value: Paclitaxel + Ganitumab


title: 156560566_1_D11_TAGGCATG-AGAGTAGA_L004

type: SRA

city: Seattle

first: Yuan

last: Tian

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

library_source: transcriptomic

data_processing:
Fastq files were processed with Kallisto v0.45.0 (9), and gene-level counts were generated from abundances scaled using the average transcript length, averaged over samples and to library size (lengthScaledTPM), using the tximport package v1.16.1 (10). Subsequent analysis was performed using a typical Bioconductor workflow (11). Briefly, the count matrix was imported of into R to create a SingleCellExperiment object. Cells with a library size of < 30,000 reads were removed from the analysis. After QC metric filtering, a total of 689 cells were kept for downstream analysis. The logNormCounts() function from the scater  package v1.16.2 (12) was used to generate log-transformed normalized expression values. PCA was performed using the top 4000 highly variable genes, and tSNE (13) and UMAP (14) was subsequently performed using the top 30 principal components for data visualization. The top 30 principal components were also used to build a shared nearest-neighbour (SNN) graph, and cell clusters were identified using the walktrap algorithm from the igraph package v1.2.5 (15). Differentially expressed genes between groups were identified using MAST v1.14.0 (16). Genes with a false discovery rate (FDR) of < 0.05 and a fold change of > 1.25 or < −1.25 were considered significantly differentially expressed between groups.
Supplementary_files_format_and_content: CSV and raw counts

source_name: PBMC

extract_protocol:
Samples were single-cell sorted into 96-well PCR plates containing 5 µL of DNA Suspension Buffer (Teknova) with 1% BSA (Sigma-Aldrich) per well. Plates were sealed and briefly vortexed before being spun at 800 × g for 1 minute and immediately transferred to dry ice. Plates were stored at -80°C for at least overnight before proceeding. Once ready to proceed, the plates were thawed on ice and spun at 800 × g for 1 minute to collect all liquid. We used a modified version of a previously published method to amplify the whole transcriptome (8). In brief, the reverse transcriptase that is used to make cDNA has a terminal transferase activity. Then, a “template‐switch” primer incorporates a second universal priming sequence yielding cDNA with two universal priming sequences.  Custom primers were synthesized by IDT using sequences published by Trombetta, et al. (8). In brief, reverse transcription occurred in two steps.  The initial step was conducted in 5 µL of the lysed cell, 2.4 µM 3’ SMART CDS Primer II A (IDT), 2.4 mM each dNTP mix (GeneAmp) and 6.32 U RNaseOUT (Invitrogen).  The samples were incubated at room temperature for 1 minute, 72°C for 3 minutes and held on ice before beginning the second step.  The next step was conducted with SuperScript II Reverse Transcriptase Kit (Invitrogen), using 7 µL of the step 1 product, 1× First Strand Buffer, 2.5 mM DTT, 110 U SuperScript II and an additional 11 U RNaseOUT, as well as 1 µM SMARTer II Oligonucleotide (IDT) and molecular-grade water to 11 µL. The samples were incubated at 42°C for 90 min, followed by a limited cycle amplification of 10 cycles at 50°C for 2 min and 42°C for 2 min, concluding with a final extension at 72°C for 15 minutes.
Whole transcriptome amplification (WTA) immediately proceeded with the 11 µL of the reverse transcription product, using 1× KAPA HiFi HotStart Ready Mix (Roche) and 0.5 µM IS PCR Primer (IDT).  Amplification parameters were 98°C for 3 min and 22 cycles of 98°C for 15 sec, 67°C for 20 sec and 72°C for 6 min, followed by a final extension of 72°C for 5 min.  The WTA product was cleaned using AMPure XP beads (Beckman Coulter).  The PCR product was incubated at room temperature for 5 min with 0.8 volumes of XP beads before being placed on a magnet.  The beads were washed three times with 100 µL of 80% ethanol.  After briefly drying, the beads were resuspended in 20 µL of 1× TE Buffer (Sigma Aldrich) and 18 µL of supernatant were was transferred to a new 96-well PCR plate. Quality and quantitation were measured by TapeStation using a High Sensitivity D5000 ScreenTape (Agilent).  Samples with a concentration ≥200 pg/µL were carried forward for sequencing according to the Nextera XT DNA Library Preparation Kit (Illumina) protocol.  Samples were dual-indexed using the Nextera Index XT Kit (Illumina) and a scheme that would allow for eight pools without overlapping indices. After pooling, the concentration of each pool was measured by Qubit dsDNA HS Assay Kit (Invitrogen) and sizing was determined by Fragment Analyzer HS Small Fragment Kit (Agilent).  A smear analysis was conducted in the range of 150 to 1000 bp, and the average peak size along with the Qubit results were used to determine the molarity.  Each pool was then diluted to a concentration of 2 nM.  The samples were sequenced on the Illumina HiSeq 2500 using PE50 on a high-output 8-lane flow cell with one pool per lane.

treatment_protocol: PBMCs were thawed RPMI media containing 10% FBS, L-Glut, Pen-Strep and rested overnight (16-18 hours). The cells were incubated with purified anti-CD40 monoclonal antibody (Miltenyi Biotec) for 10 minutes before being stimulated (Frentsch, M. et al Nat Med 2005).  The CD40L-PE-Cy7 antibody was added along with 1 μg/mL anti-human CD28/CD49d co-stimulatory antibody and either 2 g/mL vaccine-matched 92TH023-Env peptide pool or with peptide diluent (DMSO) only for 5 hours at 37C 5% CO2. PBMCs were then incubated with a mix of equal parts IFN- Catch Reagent (Miltenyi Biotec), IL-2 Catch Reagent (Miltenyi Biotec), IL-4 Catch Reagent (Miltenyi Biotec) on ice for 15 mins. R10 was added and PBMCs were incubated rotating at 37C 5% CO2 for 1 hour. Samples were washed with buffer (1x PBS, 2 mM EDTA, 0.5% BSA) and stained on ice with aqua viability dye followed by an antibody cocktail containing phenotyping markers as well as cytokine detection antibodies (Table 1). Live CD14- CD19- CD56- CD8- single cytokine+ CD154+, IFN-+, IL-2+ or CD154+IL2+ CD4+ T lymphocytes were single-cell sorted  with a FACSAria II cell sorter. PolyfunctionalityFull functional profiles wasere determined post-sorting using analysis usingof the individual cell level flow cytometry data (acquired by indexing).

value: PBMC

tag: cell type

value: CD4 T cells

tag: vaccination

value: RV144 vaccine regimen


title: UA03-S-01

type: genomic

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchips using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner settings

data_processing:
Data was processed with the minfi package in R
Normalization was performed with the Noob method, followed by the Quantile method (minfi)

label: Cy3, Cy5

molecule: genomic DNA

source_name: synovial fluid

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from monocytes using the Maxwell RSC Cell DNA kit (Promega) according to standard instructions

tag: donor

tag: age

tag: Sex

value: M

tag: diagnosis baseline

value: UA

tag: prognosis

value: Poor

value: Synovial fluid

value: monocytes


title: UA05-S-01

value: F


title: 156560566_1_D10_GGACTCCT-AGAGTAGA_L004


title: ISPY2_683896


title: UA19-B-04

source_name: peripheral blood

value: Peripheral blood


title: 156560566_1_C9_CAGAGAGG-TATCCTCT_L004


title: UA17-B-04

value: Good


title: UA20-B-04


title: tumor_EP2-/-_male_T99

city: Göteborg

first: Britt-Marie

last: Iresjö

address: Forskningsmottagning Kirurgi, Vita Stråket 12, plan 2, Sahlgrenska Universitetssjukhuset

department: Inst. of Clinical sciences/Dep. of Surgery

country: Sweden

institute: University of Gothenburg

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions.

scan_protocol: Slides were scanned immediately after washing on Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel set to Green, PMT set to 100%).

data_processing:
Scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
normalized signal intensities after processing in Genespring GX software v. 14.9.1. Normalized values are; log 2, 75 percentile shift, baseline transformed to median of all samples (in respective tissue).

organism: Mus musculus

source_name: tumor

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng Total RNA using the LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).

extract_protocol: RNA was prepared using qiagen Rneasy fibrous tissue kit. RIN values were above 7 for all samples.

treatment_protocol: MCG 101 tumor cells were implanted in EP2 Wildtype and EP2 knockout mice

tag: genotype

value: knock

value: male

value: tumor


title: Healthy donor, CL04

value: HD


title: 156560566_1_C8_CTCTCTAC-TATCCTCT_L004


title: tumor_EP2-/-_male_T95


title: UA02-S-01


title: UA18-B-04


title: UA16-B-04


title: UA09-B-04


title: tumor_EP2-/-_male_T81


title: UA08-B-04


title: UA06-B-04


title: UA11-B-04


title: UA15-B-04


title: 156560566_1_C6_GGACTCCT-TATCCTCT_L004


title: tumor_EP2-/-_male_T15


title: UA10-B-04


title: UA02-B-04


title: tumor_EP2+/+_male_T82

value: wildtype


title: UA14-B-04


title: UA12-B-04


title: 156560566_1_C4_AGGCAGAA-TATCCTCT_L004


title: UA05-B-04


title: UA03-B-04


title: 156560566_1_C7_TAGGCATG-TATCCTCT_L004


title: Healthy donor, CL01


title: UA13-B-04


title: 156560566_1_C3_CGTACTAG-TATCCTCT_L004


title: tumor_EP2+/+_male_T9


title: UA04-B-04


title: UA18-B-01


title: 156560566_1_C2_TAAGGCGA-TATCCTCT_L004


title: UA01-B-04


title: tumor_EP2+/+_male_T4


title: UA07-B-04


title: 156560566_1_C1_GTAGAGGA-CTCTCTAT_L004


title: UA15-B-01


title: 156560566_1_C12_AAGAGGCA-TATCCTCT_L004


title: UA17-B-01


title: tumor_EP2-/-_female_T59B

value: female


title: tumor_EP2-/-_female_T51


title: UA19-B-01


title: 156560566_1_C5_TCCTGAGC-TATCCTCT_L004

value: PBMC


title: 156560566_1_C11_CGAGGCTG-TATCCTCT_L004

value: CD4 T cells


title: tumor_EP2-/-_female_T149


title: 156560566_1_C10_GCTACGCT-TATCCTCT_L004

value: RV144 vaccine regimen


title: tumor_EP2+/+_male_T65


title: UA16-B-01


title: tumor_EP2+/+_female_T68


title: UA13-B-01


title: tumor_EP2+/+_female_T45


title: UA12-B-01

value: M


title: tumor_EP2-/-_female_T12


title: 156560566_1_B11_CGAGGCTG-CTCTCTAT_L004


title: LF ATF4 KO, biological rep 3

city: Philadelphia

first: Constantinos

last: Koumenis

state: PA

address: 13400 Civic Center Blvd

department: Radiation Oncology

institute: University of Pennsylvania

description: Gene expression data from LFBD/D at passage 2

hyb_protocol: Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99 °C for 5 min and hybridized for 16 h at 45 °C to Clariom D Mouse Arrays  using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: Cel files were imported to TAC software (v4, ThermoFisher) and normalized with RMA using the default values.

label: biotin

source_name: LFBD/D, p2

label_protocol: 250ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

growth_protocol: The isolated LFBwt/wt and LFBD/D were cultured until they reached passage 2.

extract_protocol: Total RNA isolation was performed using Macherey-Nagel and according to the manufacturer's instructions.

treatment_protocol: ATF4 WT and ATF4 KO

value: Lung

tag: gender

value: Both genders

tag: passage


title: UA14-B-01

value: UA

value: Poor


title: 156560566_1_B7_CAGAGAGG-CTCTCTAT_L004


title: LF ATF4 KO, biological rep 2


title: UA10-B-01

value: monocytes


title: 156560566_1_B10_GCTACGCT-CTCTCTAT_L004


title: tumor_EP2+/+_female_T5


title: 156560566_1_A8_TAGGCATG-CTCTCTAT_L004


title: LF ATF4 WT, biological rep 1

description: Gene expression data from LFBwt/wt at passage 2

source_name: LFBwt/wt, p2


title: LF ATF4 WT, biological rep 3


title: UA09-B-01

value: F

value: Peripheral blood


title: stroma_EP2-/-_male_S99

source_name: tumor stroma

value: knock

value: tumor stroma


title: LF ATF4 WT, biological rep 2


title: UA11-B-01

value: Good


title: 156560566_1_A7_GGACTCCT-CTCTCTAT_L004


title: L ATF4 KO, biological rep 4

description: Gene expression data from lungs of Atf4D/D mouse at 4 weeks post tamoxifen treatment

source_name: lung, 4 weeks post tamoxifen treatment

growth_protocol: Lungs from Atf4wt/wt and Atf4D/D mice were harvested at 4 weeks post tamoxifen treatment.

value: Male

value: 13 weeks


title: LF ATF4 KO, biological rep 1


title: tumor_EP2+/+_female_T1

value: wildtype

value: female

value: tumor


title: 156560566_1_A6_TCCTGAGC-CTCTCTAT_L004

value: PBMC

value: CD4 T cells

value: RV144 vaccine regimen


title: 156560566_1_A5_AGGCAGAA-CTCTCTAT_L004


title: UA06-B-01

value: M


title: L ATF4 KO, biological rep 2

value: Lung

value: Female


title: L ATF4 KO, biological rep 3


title: L ATF4 KO, biological rep 1


title: UA03-B-01

value: UA

value: Poor

value: monocytes


title: stroma_EP2-/-_male_S81

value: knock

value: male


title: L ATF4 WT, biological rep 3

description: Gene expression data from lungs of Atf4wt/wt mouse at 4 weeks post tamoxifen treatment


title: L ATF4 WT, biological rep 2


title: UA20-B-01

value: F

value: Good

value: Peripheral blood


title: UA05-B-01


title: GMCSF_C

description: GM-CSF macrophage

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylationEPIC Beadchips using standard Illumina protocol.

extract_protocol: Genomic DNA was extracted and purified from monocytes or macrophages using the Maxwell RSC Cell DNA kit (Promega) according to standard instructions

value: B

tag: condition

value: GMCSF

value: peripheral blood

value: macrophage


title: stroma_EP2-/-_male_S95

tag: tissue

value: tumor stroma


title: 156560566_1_A4_CGTACTAG-CTCTCTAT_L004

value: PBMC

value: CD4 T cells

value: RV144 vaccine regimen


title: WT_3_9 hrs auxin

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

data_processing:
Following sequencing, Illumina Primary Analysis version RTA 1.18.61 and Secondary Analysis bcl2fastq2 v2.17 were run to demultiplex reads from all libraries and generate FASTQ files.
Reads were aligned to version sacCer3 of the Saccharomyces cerevisiae genome  with gene models from Ensembl 94 using STAR with --quantMode GeneCounts. The resulting read counts to genes were analyzed in R. Bioconductor package edgeR was used to perform differential expression analysis.
Expression levels in TPM were estimated using RSEM.
Assembly: sacCer3
Supplementary files format and content: tab-delimited text file of TPM gene values for each Sample

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Scc2 degron strains carrying pRS413(HIS) plasmid with SCC2-WT, R787G, G1242V or empty vector (null) were cultured in triplicate (except for null strain in duplicate) overnight in SD-HIS.

extract_protocol:
Cells were pelleted and RNA was extracted using SDS and hot acid phenol, followed by chloroform. RNA was recovered by and ethanol precipitation. RNA integrity was checked on a 1.2% agarose gel and run on an Agilent Technologies 2100 Bioanalyzer. Samples were ribo-depleted with TruSeq Stranded Yeast Ribo-Zero Gold Kit (Illumina, MRZY1324) per manufacturer’s instructions.
Illumina libraries were generated using the TruSeq Stranded RNA LT kit with Ribo-Zero Gold, 48; Set A (Illumina, RS-122-2301). Libraries were normalized and pooled together with an average base pair size of 290 and sequenced as 50 bp single reads on the HiSeq 2500 (Illumina) using HiSeq Control Software v2.2.58.

treatment_protocol: The following day, strains were diluted to ~OD600 = 0.1 in SD-HIS, after 90 minutes, 3-indoleacetic acid (IAA) was added to a concentration of 1mM and cells were cultured for an additional 9 hours to OD600 range of 0.4 – 0.8. Cells were pelleted and RNA was extracted.

value: yeast cells

tag: strain

tag: plasmid

value: MATa ade2-1 his3-11,15 trp1-1 leu2-3,112 can1-100 ura3-1::ADH1-OsTIR1(pMK200,URA3) SCC2-AID*-6FLAG-HYG

tag: mutation

value: WT

tag: replicate

tag: treatment

value: 9 hrs auxin

tag: lims ids

value: MOLNG-2790, mma6


title: GMCSF_B

description: GM-CSF macrophage

value: A

tag: cell type


title: stroma_EP2-/-_male_S15

value: knock

value: male


title: L ATF4 WT, biological rep 4

value: Lung

value: Male

value: 13 weeks


title: WT_2_9 hrs auxin


title: L ATF4 WT, biological rep 1


title: WT_1_9 hrs auxin


title: 156560566_1_A3_TAAGGCGA-CTCTCTAT_L004

tag: vaccination


title: UA08-B-01

tag: donor

tag: age

value: M

value: UA

value: Good

value: Peripheral blood

value: monocytes


title: UA04-B-01

tag: Sex

tag: diagnosis baseline

value: Poor


title: R787G_3_9 hrs auxin

value: yeast cells

tag: genotype


title: 156560566_1_A2_GTAGAGGA-GCGTAAGA_L004

value: PBMC

value: CD4 T cells

value: RV144 vaccine regimen


title: R787G_2_9 hrs auxin

value: MATa ade2-1 his3-11,15 trp1-1 leu2-3,112 can1-100 ura3-1::ADH1-OsTIR1(pMK200,URA3) SCC2-AID*-6FLAG-HYG

value: 9 hrs auxin

value: MOLNG-2790, mma6


title: UA02-B-01

value: F

tag: prognosis


title: UA07-B-01


title: stroma_EP2+/+_male_S82

value: wildtype

value: male

value: tumor stroma


title: NULL_2_9 hrs auxin


title: 156560566_1_A1_AAGAGGCA-GCGTAAGA_L004


title: stroma_EP2+/+_male_S65


title: MCSF_A

description: M-CSF macrophage

value: A

value: MCSF

value: peripheral blood

value: macrophage


title: UA01-B-01

value: UA

value: Good

value: Peripheral blood

value: monocytes


title: G1242V_3_9 hrs auxin

value: yeast cells


title: 156560566_1_A12_CTCTCTAC-CTCTCTAT_L004

value: PBMC

value: CD4 T cells

value: RV144 vaccine regimen


title: stroma_EP2+/+_male_S4


title: G1242V_2_9 hrs auxin

value: MATa ade2-1 his3-11,15 trp1-1 leu2-3,112 can1-100 ura3-1::ADH1-OsTIR1(pMK200,URA3) SCC2-AID*-6FLAG-HYG

value: 9 hrs auxin

value: MOLNG-2790, mma6


title: NULL_1_9 hrs auxin


title: G1242V_1_9 hrs auxin


title: WT_3_3 hrs auxin

treatment_protocol: The following day, strains were diluted to ~OD600 = 0.1 in SD-HIS, after 90 minutes, 3-indoleacetic acid (IAA) was added to a concentration of 1mM and cells were cultured for an additional 3 hours to OD600 range of 0.4 – 0.8. Cells were pelleted and RNA was extracted.

value: WT

value: 3 hrs auxin

value: MOLNG-2652, mma5


title: 156560262_3_H8_CTCTCTAC-GTAAGGAG_L002


title: 156560262_3_H9_CTCTCTAC-TATCCTCT_L001


title: MCSF_B

description: M-CSF macrophage

value: B

value: MCSF


title: WT_2_3 hrs auxin


title: 156560262_3_H7_CTCTCTAC-AGAGTAGA_L001


title: 156560262_3_H5_CTCTCTAC-GCGTAAGA_L001


title: WT_1_3 hrs auxin


title: Mo_B

description: Peripheral blood monocytes

value: Mo

value: peripheral blood

value: monocyte


title: R787G_2_3 hrs auxin


title: GMCSF_A

description: GM-CSF macrophage

value: C

value: GMCSF

value: macrophage


title: Mo_C

description: Peripheral blood monocytes


title: 156560262_3_H10_CTCTCTAC-AGAGTAGA_L002

value: PBMC


title: NULL_3_3 hrs auxin

value: yeast cells


title: stroma_EP2-/-_female_S51

value: knock

value: female

value: tumor stroma


title: NULL_2_3 hrs auxin

value: MATa ade2-1 his3-11,15 trp1-1 leu2-3,112 can1-100 ura3-1::ADH1-OsTIR1(pMK200,URA3) SCC2-AID*-6FLAG-HYG


title: Mo_A

description: Peripheral blood monocytes

value: A


title: R787G_3_3 hrs auxin

value: 3 hrs auxin


title: NULL_1_3 hrs auxin

value: MOLNG-2652, mma5


title: MCSF_C

description: M-CSF macrophage


title: stroma_EP2-/-_female_S12


title: stroma_EP2-/-_female_S59B


title: stroma_EP2-/-_female_S49


title: G1242V_2_3 hrs auxin


title: stroma_EP2+/+_male_S9

value: wildtype

value: male


title: stroma_EP2+/+_female_S68


title: R787G_1_3 hrs auxin


title: 156560262_3_G3_GTAGAGGA-CTAAGCCT_L008

value: CD4 T cells

value: RV144 vaccine regimen


title: 156560262_3_G9_CTCTCTAC-AAGGAGTA_L001


title: ISPY2_676365

tag: patient id

value: Breast cancer biopsy (pre-treatment)

tag: hr

tag: mp

tag: pcr

tag: arm

value: Paclitaxel + Ganetespib

tag: adjustment method

value: ComBat Adjust


title: G1242V_1_3 hrs auxin

tag: mutation

tag: replicate

tag: strain

tag: plasmid


title: 156560262_3_G10_CTCTCTAC-ACTGCATA_L001

tag: tissue

tag: cell type

tag: vaccination


title: 156560262_3_G11_CTCTCTAC-TATCCTCT_L002


title: ISPY2_674897

value: Paclitaxel


title: ISPY2_668752

value: Paclitaxel + Pembrolizumab

value: Linear Adjustment Factor


title: stroma_EP2+/+_female_S45

tag: Sex


title: G1242V_3_3 hrs auxin

value: yeast cells

tag: treatment

tag: lims ids


title: 156560262_3_F1_AAGAGGCA-CTCTCTAT_L001

value: PBMC


title: stroma_EP2+/+_female_S1

tag: genotype

value: female

value: tumor stroma


title: stroma_EP2+/+_female_S5


title: ISPY2_666715

tag: patient id


title: Normoxia_rep1

city: Daegu

first: Sehyun

last: Chae

address: 61, Cheomdan-ro

department: Neurovascular Unit Research Group

country: South Korea

institute: Korea Brain Research Institute

description:
Normoxia
Sample 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: The arrays were scanned according to the Illumina's standard scanning protocol using the Illumina Bead Array Reader Confocal Scanner.

data_processing: The log2-intensities of the probes from the arrays were normalized using the quantile normalization method with MATLAB

source_name: adipocyte-derived stem cells (hADSCs)

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

growth_protocol: Human Adipose-Derived Stem Cells were purchased from Invitrogen (Carlsbad, CA), which are isolated from human adipose tissue collected during liposuction procedures.

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

treatment_protocol: The hADSCs were treated with hypoxia (0.5% O2, 48 hours) or clioquinol (50 μM, 48 hours).

value: adipocyte-derived stem cells (hADSCs)

value: Normoxia (21% O2)


title: Hypoxia_rep1

description:
Hypoxia
Sample 3


title: CQ_rep2

description:
CQ treatment
Sample 6

value: Clioquinol (50 uM, 48 h)


title: CQ_rep1

description:
CQ treatment
Sample 5


title: Prdm16-null Neural Stem Cells

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

library_source: genomic

data_processing:
Base-calling software with HCS1.5.15.1+RTA1.13.48+OLB1.9.4
Data filtering with BGI in-house tool
Read alignment with BSMAP v2.74
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files were generated with BSMAP v2.74

source_name: E14.5 Forebrain

extract_protocol:
Genomic DNA was isolated with QIAamp DNA Mini Kit (QIAGEN)
a. Genome DNA were cut by Restriction Enzyme; b. DNA-end repair, 3'-dA overhang; c. Select the 40-220bp fragment; d. Bisulfite treatment by ZYMO EZ DNA Methylation-Gold kit; e. PCR amplification; f. Qualified library for sequencing.

value: Neural Stem Cell


title: Wild Type Neural Stem Cell-derived Neurons

value: Neural Stem Cell-derived Neurons

value: Wild Type


title: Prdm16-overexpressing Neural Stem Cells


title: ISPY2_664658

tag: hr


title: Wild Type Neural Stem Cells


title: Hypoxia_rep2

description:
Hypoxia
Sample 4


title: Normoxia_rep2

description:
Normoxia
Sample 2


title: 156560262_3_F2_AAGAGGCA-CTAAGCCT_L001

value: CD4 T cells

value: RV144 vaccine regimen


title: 828199

type: protein

data_processing: These samples were assayed on three different RPPA arrays (RPPA.1, RPPA.2 and RPPA.3) under GPL28470.  Each individual array (containing hundreds of samples) was standardized as follows: (1) sample w/out replacement 5000 times, maintaining a receptor subtype balance equal to that of the first ~1000 patients (HR+HER2-: 0.384, TN:0.368, HR+HER2+:0.158, HR-HER2+:0.09); (2) calculate the mean(mean) and mean(sd) for each RPPA endpoint over the samples; (3) standardize each endpoint of the array, as y=(x-mean(mean))/mean(sd).  Standardized data from the different arrays was then combined.  This procedure resulted in removal of batch effects, without 'warping' due to mismatches in subtype prevalence.

molecule: protein

source_name: breast cancer biopsy

extract_protocol: Reverse phase protein array (RPPA)

value: Paclitaxel + Neratinib

tag: arm (short name)

value: N

tag: rppa array (normalization key)


title: 156560262_3_F11_CTCTCTAC-CTCTCTAT_L002


title: ISPY2_664111

value: Breast cancer biopsy (pre-treatment)

tag: mp

tag: pcr

tag: arm

value: Paclitaxel + MK-2206

value: ComBat Adjust


title: 156560262_3_F10_CTCTCTAC-GCGTAAGA_L002


title: ISPY2_666147

value: Paclitaxel + Ganitumab

tag: adjustment method


title: 156560262_3_E5_AAGAGGCA-CTAAGCCT_L008

value: PBMC


title: 152197

value: Paclitaxel + Pembrolizumab

value: Pembro


title: 697871

value: Paclitaxel + ABT 888 + Carboplatin

value: VC


title: 156560262_3_F12_AAGAGGCA-GTAAGGAG_L001


title: ISPY2_663197

value: Linear Adjustment Factor


title: 584561

value: Paclitaxel + Pertuzumab + Trastuzumab

value: Pertuzumab


title: 515105


title: 960963

description: same as GSM4552526

value: Paclitaxel + MK-2206 + Trastuzumab


title: 442637

value: Paclitaxel + Trastuzumab

value: Control

value: RPPA.1 & RPPA.2 (ave)


title: 156560262_3_E1_AAGAGGCA-AGAGTAGA_L001

value: CD4 T cells

value: RV144 vaccine regimen


title: 156560262_3_E12_AAGAGGCA-TATCCTCT_L001


title: 156560262_3_D9_GCTACGCT-CTAAGCCT_L008


title: 677915

value: Paclitaxel


title: 790397

value: T-DM1 + Pertuzumab


title: 168044


title: 149654


title: R787G_1_9 hrs auxin

value: yeast cells

tag: strain

value: MATa ade2-1 his3-11,15 trp1-1 leu2-3,112 can1-100 ura3-1::ADH1-OsTIR1(pMK200,URA3) SCC2-AID*-6FLAG-HYG

tag: mutation

tag: replicate

value: 9 hrs auxin

value: MOLNG-2790, mma6


title: ISPY2_660534

tag: tissue

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel + Pembrolizumab


title: ISPY2_655795

value: Linear Adjustment Factor


title: ISPY2_663144

value: Paclitaxel + Ganitumab

value: ComBat Adjust


title: ISPY2_658541


title: ISPY2_661730

value: Paclitaxel + AMG 386


title: 535415

description: same as GSM4552544

value: Paclitaxel + MK-2206 + Trastuzumab


title: 341238

value: Pembro


title: 156560262_3_D3_TAGGCATG-AAGGAGTA_L002

value: PBMC

tag: cell type

tag: vaccination


title: 905264

description: same as GSM4552545


title: 220925


title: 300724

value: Control


title: 156560262_3_E11_TAGGCATG-CTAAGCCT_L002

value: CD4 T cells

value: RV144 vaccine regimen


title: 156560262_3_D11_AAGAGGCA-GCGTAAGA_L001


title: ISPY2_655128


title: ISPY2_654064

value: Paclitaxel + MK-2206


title: 156560262_3_D8_CAGAGAGG-CTAAGCCT_L008


title: 963604

value: Paclitaxel + AMG-386


title: 156560262_3_D10_CGAGGCTG-CTAAGCCT_L008


title: 572444

value: Paclitaxel + Neratinib

value: N


title: 386664


title: 896939


title: 733962


title: ISPY2_654021

value: Paclitaxel


title: ISPY2_653325

value: Breast cancer biopsy (pre-treatment)


title: ISPY2_652480


title: 156560262_3_C9_TAGGCATG-ACTGCATA_L002


title: 782334

value: RPPA.1 & RPPA.2 (ave)


title: ISPY2_651401

value: Paclitaxel + Pembrolizumab

value: Linear Adjustment Factor


title: 156560262_3_C8_AAGAGGCA-AAGGAGTA_L001


title: 635632

description: same as GSM4552588


title: 156560262_3_C3_CTCTCTAC-CTAAGCCT_L008


title: 273745


title: 319324

description: same as GSM4552590


title: 573586

value: Paclitaxel + Trastuzumab


title: 350331


title: 156560262_3_C1_GGACTCCT-CTAAGCCT_L001


title: 156560262_3_C7_AAGAGGCA-ACTGCATA_L001


title: 923968


title: 901807


title: 720065


title: 363669

description: same as GSM4552614


title: ISPY2_653927

value: ComBat Adjust


title: ISPY2_651145


title: 651145

description: same as GSM4552613


title: 156560262_3_B9_TAGGCATG-AGAGTAGA_L002


title: 156560262_3_C11_TAGGCATG-GTAAGGAG_L002


title: ISPY2_646600

value: Paclitaxel + Ganetespib


title: ISPY2_649198

value: Paclitaxel + Pertuzumab + Trastuzumab


title: 282644


title: 578975

description: same as GSM4552618


title: 141782


title: 422454

description: same as GSM4552610


title: ISPY2_641977

value: Paclitaxel + AMG 386


title: ISPY2_644609


title: 156560262_3_B5_GGACTCCT-GTAAGGAG_L001

value: PBMC


title: 156560262_3_B4_GGACTCCT-CTCTCTAT_L001

value: CD4 T cells


title: 156560262_3_B6_TAGGCATG-CTCTCTAT_L002

value: RV144 vaccine regimen


title: ISPY2_644186


title: 156560262_3_B8_TAGGCATG-TATCCTCT_L002


title: 160120

value: Paclitaxel + ABT 888 + Carboplatin

value: VC


title: ISPY2_641697


title: 156560262_3_B3_GGACTCCT-TATCCTCT_L001


title: 357017

description: same as GSM4552517

value: Control


title: 650589

value: Paclitaxel + AMG-386


title: 664658

value: Pembro


title: 808714

description: same as GSM4552647

value: Paclitaxel


title: 129837


title: 303685


title: ISPY2_640043

value: Breast cancer biopsy (pre-treatment)


title: 156560262_3_B2_GGACTCCT-AGAGTAGA_L001


title: 575372


title: 156560262_3_B12_TAGGCATG-GCGTAAGA_L002


title: 941191

value: Paclitaxel + Neratinib

value: N


title: ISPY2_639663

value: Paclitaxel + MK-2206


title: ISPY2_637566

value: ComBat Adjust


title: 417654


title: 263143

description: same as GSM4552578

value: Paclitaxel + MK-2206 + Trastuzumab


title: 611662


title: 156560262_3_B10_GGACTCCT-GCGTAAGA_L001


title: 683173

value: Paclitaxel + Pembrolizumab


title: 156560262_3_A9_GGACTCCT-AAGGAGTA_L002


title: 353318


title: 655795


title: ISPY2_637051

value: Paclitaxel + Ganetespib


title: ISPY2_635632


title: 156560262_3_A4_TAGGCATG-CTAAGCCT_L008

value: PBMC


title: ISPY2_631337


title: 655703


title: 755914

description: same as GSM4552563


title: 991818

value: Paclitaxel + Pertuzumab + Trastuzumab

value: Pertuzumab


title: 748583

description: same as GSM4552609


title: 637566

description: same as GSM4552550


title: 156560262_2_H2_GGACTCCT-ACTGCATA_L001

value: CD4 T cells

value: RV144 vaccine regimen


title: 188511

value: Paclitaxel + ABT 888 + Carboplatin

value: VC


title: ISPY2_631299


title: 156560262_2_H9_GGACTCCT-AAGGAGTA_L001


title: 728182

value: Paclitaxel + AMG-386


title: ISPY2_636424

value: Paclitaxel

value: Linear Adjustment Factor


title: 156560262_2_H12_GGACTCCT-CTAAGCCT_L008


title: 640043

value: Pembro


title: 568953


title: 652480


title: 156560262_3_B11_GGACTCCT-CTAAGCCT_L002


title: ISPY2_628823

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel + Ganitumab


title: 700549

description: same as GSM4552539

value: Paclitaxel + MK-2206


title: ISPY2_629371

value: Paclitaxel + MK-2206 + Trastuzumab

value: ComBat Adjust


title: ISPY2_629606-GPL20078


title: 156560262_2_G7_GGACTCCT-GTAAGGAG_L002


title: 988443


title: ISPY2_624777

value: T-DM1 + Pertuzumab


title: 156560262_2_G8_GGACTCCT-ACTGCATA_L002

value: PBMC


title: 378885


title: ISPY2_625854

value: Paclitaxel + Pembrolizumab


title: ISPY2_628788


title: 156560262_2_G9_CGAGGCTG-CTAAGCCT_L001


title: 938719

description: same as GSM4552571

value: Control


title: 384830

description: same as GSM4552573


title: 749097


title: ISPY2_623569

value: Paclitaxel + Ganetespib


title: 156560262_2_G6_CGAGGCTG-GTAAGGAG_L001

value: CD4 T cells

value: RV144 vaccine regimen


title: 889225


title: 156560262_2_E3_CGAGGCTG-TATCCTCT_L001


title: 420523

value: Paclitaxel + Neratinib

value: N


title: 724293


title: 342996

value: Paclitaxel


title: ISPY2_622688

value: Linear Adjustment Factor


title: 953885


title: 183831

description: same as GSM4552535


title: 834418

description: same as GSM4552585

value: RPPA.2 & RPPA.3 (ave)


title: 156560262_2_G4_GGACTCCT-AGAGTAGA_L002


title: 689480

value: Paclitaxel + AMG-386


title: 146987


title: ISPY2_621179

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel + AMG 386


title: 156560262_2_D7_CGAGGCTG-GCGTAAGA_L001


title: 823618


title: 900959

value: Paclitaxel + Pertuzumab + Trastuzumab

value: Pertuzumab


title: 373346


title: ISPY2_618717

value: ComBat Adjust


title: 531672


title: 156560262_2_E6_GGACTCCT-TATCCTCT_L002

value: PBMC


title: 156560262_2_G12_CGAGGCTG-CTCTCTAT_L001


title: 156560262_2_D4_GGACTCCT-CTCTCTAT_L002


title: 972307

value: Paclitaxel + ABT 888 + Carboplatin

value: VC


title: 607047


title: 156560262_2_D3_CGAGGCTG-AAGGAGTA_L001


title: 156560262_2_E1_CGAGGCTG-AGAGTAGA_L001


title: 128051

value: T-DM1 + Pertuzumab


title: 156560262_2_D2_GGACTCCT-GCGTAAGA_L002

value: CD4 T cells


title: ISPY2_618860

value: Paclitaxel + Ganitumab


title: 103939

value: Control


title: 654064

description: same as GSM4552597

value: Paclitaxel + MK-2206


title: ISPY2_622315


title: 240957


title: 156560262_2_D1_TCCTGAGC-ACTGCATA_L002

value: RV144 vaccine regimen


title: 885590

value: Paclitaxel


title: ISPY2_616994

value: Linear Adjustment Factor


title: ISPY2_613961

value: Paclitaxel + Ganetespib


title: ISPY2_618240

value: Breast cancer biopsy (pre-treatment)


title: 156560262_2_D11_TCCTGAGC-CTAAGCCT_L002


title: ISPY2_614434

value: Paclitaxel + MK-2206 + Trastuzumab


title: ISPY2_609642


title: 994987


title: 422450

value: Paclitaxel + Neratinib

value: N


title: ISPY2_609151

value: ComBat Adjust


title: 156560262_2_D10_TCCTGAGC-AAGGAGTA_L002

value: PBMC


title: 199115

value: Paclitaxel + AMG-386


title: 492612


title: 766301


title: 156560262_1_H9_CGAGGCTG-ACTGCATA_L001


title: 618717

value: Paclitaxel + Pertuzumab + Trastuzumab

value: Pertuzumab


title: ISPY2_607843


title: 156560262_1_H7_AGGCAGAA-CTAAGCCT_L001

value: CD4 T cells


title: 156560262_1_H11_AGGCAGAA-GTAAGGAG_L001


title: ISPY2_604326


title: 982505


title: 122579


title: 495440


title: 572235


title: 570148


title: 522140


title: 156560262_1_G11_TCCTGAGC-GTAAGGAG_L002


title: ISPY2_602451


title: 139973


title: 375455

value: Paclitaxel + Trastuzumab


title: 156560262_1_F7_AGGCAGAA-CTCTCTAT_L001


title: ISPY2_601489


title: ISPY2_598835

value: T-DM1 + Pertuzumab


title: 701790

value: Paclitaxel + Pembrolizumab

value: Pembro


title: 156560262_1_F3_TCCTGAGC-AGAGTAGA_L002

value: RV144 vaccine regimen


title: 478055

value: Paclitaxel

value: Control


title: 166412


title: 156560262_1_F1_AGGCAGAA-TATCCTCT_L001


title: 156560262_1_F2_TCCTGAGC-TATCCTCT_L002


title: 155171

value: Paclitaxel + ABT 888 + Carboplatin

value: VC


title: 473365


title: ISPY2_597873

value: Breast cancer biopsy (pre-treatment)

value: Linear Adjustment Factor


title: ISPY2_597907

value: Paclitaxel + AMG 386

value: ComBat Adjust


title: ISPY2_591810

value: Paclitaxel + MK-2206


title: 301289


title: 494296


title: 517446


title: 156560262_1_E5_AGGCAGAA-AGAGTAGA_L001

value: PBMC


title: 156560262_1_D6_AGGCAGAA-GCGTAAGA_L001


title: ISPY2_604199


title: ISPY2_590299


title: 703401


title: ISPY2_591079

value: Paclitaxel + Ganetespib


title: 924071

value: Paclitaxel + AMG-386


title: 866660


title: 741535


title: 125385


title: 157463


title: ISPY2_587691


title: 957408


title: 477816

value: RPPA.1 & RPPA.2 (ave)


title: 156560262_1_D2_TCCTGAGC-CTAAGCCT_L008

value: CD4 T cells


title: 845147

description: same as GSM4552641


title: 607843


title: 156560124_2_G9_CGAGGCTG-GCGTAAGA_L004


title: ISPY2_587604


title: 156560124_2_G5_GCTACGCT-GCGTAAGA_L004


title: 437968

value: Paclitaxel + Neratinib

value: N


title: 144302

value: Paclitaxel + Pertuzumab + Trastuzumab

value: Pertuzumab


title: 156560262_1_B3_AGGCAGAA-ACTGCATA_L001

value: RV144 vaccine regimen


title: ISPY2_586207


title: 903880


title: 790070


title: 156560124_2_G3_CAGAGAGG-GCGTAAGA_L004


title: ISPY2_589502


title: ISPY2_586091

value: Paclitaxel + Pembrolizumab


title: 156560262_1_B5_AGGCAGAA-AAGGAGTA_L001


title: 831702

value: T-DM1 + Pertuzumab


title: 156560124_2_F9_CGTACTAG-CTAAGCCT_L001


title: 395379

value: Paclitaxel

value: Control


title: 901705


title: 752372

description: same as GSM4552604


title: ISPY2_584561

value: Breast cancer biopsy (pre-treatment)


title: 156560124_2_F1_CGTACTAG-GTAAGGAG_L001


title: 646233


title: 198891


title: ISPY2_581180

value: Linear Adjustment Factor


title: 963303

description: same as GSM4552625


title: 423979


title: 156560124_2_F1_CTCTCTAC-GCGTAAGA_L004


title: ISPY2_580541

value: ComBat Adjust


title: 455828


title: 156560124_2_F11_TCCTGAGC-CTCTCTAT_L002

value: PBMC


title: 604199

description: same as GSM4552622

value: Paclitaxel + MK-2206


title: 174904

value: Paclitaxel + AMG-386


title: ISPY2_575457


title: ISPY2_574091


title: 328160


title: 653325


title: 156560124_2_F10_TCCTGAGC-GCGTAAGA_L002


title: ISPY2_573605


title: 999733

description: same as GSM4552600


title: 156560124_2_E8_TAGGCATG-GCGTAAGA_L004


title: 156560124_2_E8_AGGCAGAA-CTAAGCCT_L002


title: 311316


title: ISPY2_572793


title: 698094

description: same as GSM4552645


title: 250274


title: 156560124_2_E5_CGTACTAG-CTCTCTAT_L001


title: 355942

value: RPPA.2 & RPPA.3 (ave)


title: 504838


title: 987995


title: ISPY2_572016

value: Paclitaxel + Ganetespib


title: ISPY2_571995

value: Paclitaxel + AMG 386


title: ISPY2_571276


title: 156560124_2_E1_GGACTCCT-GCGTAAGA_L004

value: CD4 T cells


title: ISPY2_570966

value: Paclitaxel + AMG 386 + Trastuzumab


title: 223030


title: 695521


title: 156560124_2_E11_AGGCAGAA-GTAAGGAG_L002


title: 329076


title: ISPY2_570685

value: Paclitaxel + Pertuzumab + Trastuzumab


title: 156560124_2_D9_CGTACTAG-TATCCTCT_L001

value: RV144 vaccine regimen


title: 688291


title: 879224

description: same as GSM4552598


title: 882553


title: ISPY2_568953


title: 462582


title: 156560124_2_E4_AGGCAGAA-AAGGAGTA_L002


title: 107700

description: same as GSM4552528

value: Paclitaxel + MK-2206 + Trastuzumab


title: 922872


title: ISPY2_567907

value: Paclitaxel + Ganitumab


title: 987914

value: Paclitaxel


title: ISPY2_567201


title: 728149

value: T-DM1 + Pertuzumab


title: 156560124_2_D12_CGTACTAG-AGAGTAGA_L001


title: 856159

description: same as GSM4552624

value: Paclitaxel + Trastuzumab

value: Control


title: 156560124_2_D11_AGGCAGAA-GCGTAAGA_L002


title: 688955

description: same as GSM4552628


title: 208265

value: Paclitaxel + ABT 888 + Carboplatin

value: VC


title: 433144


title: 156560124_2_B1_TCCTGAGC-GCGTAAGA_L004

value: PBMC


title: 156560124_2_D7_AGGCAGAA-TATCCTCT_L002


title: ISPY2_564701

value: Breast cancer biopsy (pre-treatment)

value: ComBat Adjust


title: ISPY2_563681


title: 156560124_2_A9_CGTACTAG-GCGTAAGA_L004


title: 570685

value: Pertuzumab


title: ISPY2_559263


title: 349330

value: Paclitaxel + AMG-386


title: 478484

value: Paclitaxel + Neratinib

value: N


title: 142688


title: 156560124_2_D3_AGGCAGAA-CTCTCTAT_L002

value: CD4 T cells


title: 156560124_2_A8_TAAGGCGA-GCGTAAGA_L004

value: RV144 vaccine regimen


title: ISPY2_559021


title: 728714


title: 847753

value: Paclitaxel + Pembrolizumab

value: Pembro


title: 405717

value: Paclitaxel


title: ISPY2_555214

value: Paclitaxel + AMG 386 + Trastuzumab


title: 156560124_2_A7_GTAGAGGA-CTAAGCCT_L003


title: ISPY2_554577

value: Paclitaxel + Ganetespib


title: 616994

value: Control


title: 156560124_2_A12_AGGCAGAA-GCGTAAGA_L004


title: 721099

value: Paclitaxel + Pertuzumab + Trastuzumab


title: 196064


title: 228192


title: 343898

description: same as GSM4552642

value: Paclitaxel + MK-2206


title: 418593


title: ISPY2_553012

value: Linear Adjustment Factor


title: ISPY2_552549

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel + AMG 386


title: 156560124_1_H9_CAGAGAGG-CTAAGCCT_L003

value: PBMC


title: 306127

value: Paclitaxel + ABT 888 + Carboplatin

value: VC


title: 169918

value: Paclitaxel + AMG-386


title: 156560124_1_H8_CTCTCTAC-CTAAGCCT_L003

value: CD4 T cells


title: ISPY2_551795

value: ComBat Adjust


title: 580541

description: same as GSM4552562


title: 156560124_1_H7_TAGGCATG-CTAAGCCT_L003

value: RV144 vaccine regimen


title: ISPY2_550421


title: 156560124_2_A8_CGTACTAG-GCGTAAGA_L001


title: 323721

description: same as GSM4552564


title: 179369

description: same as GSM4552583


title: 484867

value: Paclitaxel + Neratinib

value: N


title: ISPY2_550157

value: Paclitaxel


title: 156560124_1_H6_GGACTCCT-CTAAGCCT_L003


title: ISPY2_547892

value: Paclitaxel + Ganitumab


title: 156560124_1_H5_TCCTGAGC-CTAAGCCT_L003


title: 156560124_1_H4_AGGCAGAA-CTAAGCCT_L003


title: 820348

value: Control


title: 462605

value: Paclitaxel + Pertuzumab + Trastuzumab

value: Pertuzumab


title: 156560124_1_H3_CGTACTAG-CTAAGCCT_L003


title: 408692


title: ISPY2_547405

value: Paclitaxel + MK-2206


title: 342959

description: same as GSM4552631


title: 622078


title: ISPY2_543795

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel + Pembrolizumab

value: Linear Adjustment Factor


title: 215932

value: Paclitaxel + AMG-386 + Trastuzumab


title: ISPY2_542392


title: 156560124_1_H2_TAAGGCGA-CTAAGCCT_L003

value: PBMC


title: 156560124_1_H12_AAGAGGCA-CTAAGCCT_L003


title: 575457


title: 687288

value: T-DM1 + Pertuzumab


title: 824350


title: 156560124_1_H1_GTAGAGGA-AAGGAGTA_L003

value: CD4 T cells


title: 159284


title: ISPY2_539904

value: Paclitaxel + Trastuzumab

value: ComBat Adjust


title: 228340

value: Paclitaxel + Neratinib


title: 982086


title: ISPY2_539876

value: Paclitaxel + Ganetespib


title: 527581


title: 494022


title: ISPY2_536253


title: 227881

value: N


title: 551795


title: 156560124_1_H11_CGAGGCTG-CTAAGCCT_L003

value: RV144 vaccine regimen


title: ISPY2_535779

value: Paclitaxel + Ganitumab


title: 156560124_1_H10_GCTACGCT-CTAAGCCT_L003


title: ISPY2_535569


title: 156560124_1_H10_CGTACTAG-ACTGCATA_L001


title: 590220

description: same as GSM4552532


title: 451482

value: Paclitaxel + AMG-386


title: 765671


title: ISPY2_535415

value: Paclitaxel + MK-2206 + Trastuzumab


title: 840501


title: 156560124_1_G9_GCTACGCT-AAGGAGTA_L003


title: 156560124_1_G8_CAGAGAGG-AAGGAGTA_L003


title: 174903


title: ISPY2_531988


title: 600536


title: 156560124_1_H11_CGTACTAG-AAGGAGTA_L001


title: 729270


title: ISPY2_532183

value: Paclitaxel


title: 383456


title: 489973


title: 815421


title: 632408


title: ISPY2_530095

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel + AMG 386


title: 266509


title: 156560124_1_G7_CTCTCTAC-AAGGAGTA_L003


title: 829491


title: 237158


title: ISPY2_528479


title: 246134

value: Control


title: 156560124_1_G6_CGTACTAG-AGAGTAGA_L002


title: 887594

description: same as GSM4552560

value: Paclitaxel + MK-2206


title: 299840


title: ISPY2_527581

value: Paclitaxel + Pertuzumab + Trastuzumab


title: 156560124_1_G5_GGACTCCT-AAGGAGTA_L003

value: PBMC


title: 706418

value: T-DM1 + Pertuzumab


title: ISPY2_524170


title: 156560124_1_G4_TCCTGAGC-AAGGAGTA_L003

value: CD4 T cells


title: 156560124_1_G7_CGTACTAG-GTAAGGAG_L002


title: ISPY2_521860

value: ComBat Adjust


title: 156560124_1_G3_AGGCAGAA-AAGGAGTA_L003


title: 581648

value: RPPA.2 & RPPA.3 (ave)


title: ISPY2_528833

value: Paclitaxel + AMG 386 + Trastuzumab


title: ISPY2_522140


title: 913527


title: 845079


title: 814299

value: Paclitaxel + Neratinib

value: N


title: 264678


title: ISPY2_520986


title: 156560124_1_G2_CGTACTAG-AAGGAGTA_L003

value: RV144 vaccine regimen


title: 156560124_1_G6_TAGGCATG-AAGGAGTA_L003


title: 378401

value: Paclitaxel + AMG-386


title: 156560124_1_G1_TAAGGCGA-AAGGAGTA_L003


title: 789497


title: 496205


title: ISPY2_518576

value: Paclitaxel + Ganetespib


title: 549172

description: same as GSM4552644

value: Paclitaxel


title: 491526


title: 156560124_1_G12_AAGAGGCA-AAGGAGTA_L003


title: 179568


title: 156560124_1_G11_CGAGGCTG-AAGGAGTA_L003


title: ISPY2_518000

value: Breast cancer biopsy (pre-treatment)


title: 192548

value: Paclitaxel + ABT 888 + Carboplatin

value: VC


title: 689452

value: Control


title: 156560124_1_F9_GCTACGCT-ACTGCATA_L003


title: ISPY2_516834

value: Paclitaxel + Ganitumab


title: ISPY2_516763


title: 156560124_1_F8_CAGAGAGG-ACTGCATA_L003

value: PBMC


title: 156560124_1_F6_TAGGCATG-ACTGCATA_L003


title: 625854

value: Paclitaxel + Pembrolizumab

value: Pembro


title: 156560124_1_F7_CTCTCTAC-ACTGCATA_L003

value: CD4 T cells


title: 605713


title: 460776


title: 391942


title: ISPY2_515284

value: ComBat Adjust


title: ISPY2_515281


title: 153327


title: 712276

description: same as GSM4552542

value: Paclitaxel + MK-2206


title: 597907


title: 235995

value: Paclitaxel + Pertuzumab + Trastuzumab

value: Pertuzumab


title: 156560124_1_F5_GGACTCCT-ACTGCATA_L003

value: RV144 vaccine regimen


title: ISPY2_517870


title: 894128

value: Paclitaxel + AMG-386


title: 111674


title: 203060


title: 156560124_1_F3_AGGCAGAA-ACTGCATA_L003


title: 930853


title: 104384


title: ISPY2_507249


title: 327142

value: Paclitaxel + Neratinib

value: N


title: 156560124_1_F2_CGTACTAG-ACTGCATA_L003


title: 962472


title: ISPY2_510543

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel + Ganetespib


title: ISPY2_506623


title: ISPY2_504838

value: Paclitaxel


title: 233191

description: same as GSM4552543

value: Control


title: 541165


title: 597253


title: 156560124_1_F1_TAAGGCGA-ACTGCATA_L003


title: 156560124_1_F12_GTAGAGGA-ACTGCATA_L003


title: 156560124_1_F4_TCCTGAGC-ACTGCATA_L003


title: 819622


title: 507198


title: ISPY2_503034


title: ISPY2_502486

value: Linear Adjustment Factor


title: 783578

value: Paclitaxel + ABT 888 + Carboplatin

value: VC


title: 833536


title: 255078


title: 706943


title: ISPY2_509012

value: Paclitaxel + Ganitumab


title: 156560124_1_F10_CGAGGCTG-ACTGCATA_L003

value: PBMC

value: CD4 T cells


title: ISPY2_501303

value: Paclitaxel + Trastuzumab

value: ComBat Adjust


title: 197942


title: 156560124_1_E9_GCTACGCT-GTAAGGAG_L003


title: 598835

value: T-DM1 + Pertuzumab


title: ISPY2_500826

value: Paclitaxel + Pembrolizumab


title: 156560124_1_E8_CAGAGAGG-GTAAGGAG_L003

value: RV144 vaccine regimen


title: 156560124_1_F11_AAGAGGCA-ACTGCATA_L003


title: ISPY2_498985

value: Paclitaxel + AMG 386 + Trastuzumab


title: ISPY2_498024


title: 156560124_1_E7_CTCTCTAC-GTAAGGAG_L003


title: 708387


title: 156163

value: Paclitaxel + AMG-386


title: 156560124_1_E6_TAGGCATG-GTAAGGAG_L003


title: 156560124_1_E5_GGACTCCT-GTAAGGAG_L003


title: ISPY2_494296

value: Breast cancer biopsy (pre-treatment)


title: ISPY2_494946


title: 635862


title: 399478


title: 156560124_1_E4_TCCTGAGC-GTAAGGAG_L003


title: 134526

value: Paclitaxel + Neratinib

value: N


title: 636424

value: Paclitaxel

value: Control


title: ISPY2_497010

value: Linear Adjustment Factor


title: 227055

value: Paclitaxel + AMG-386 + Trastuzumab


title: 202539


title: 156560124_1_E3_AGGCAGAA-GTAAGGAG_L003


title: 944536


title: ISPY2_494022


title: 162562

description: same as GSM4552551


title: 629371

description: same as GSM4552548

value: Paclitaxel + MK-2206 + Trastuzumab


title: 629210


title: 767934


title: 614434

description: same as GSM4552587


title: ISPY2_493775

value: Paclitaxel + Ganetespib


title: 156560124_1_E1_TAAGGCGA-GTAAGGAG_L003

value: PBMC

value: CD4 T cells


title: 962153


title: 490023

description: same as GSM4552629


title: 284443


title: ISPY2_493472

value: ComBat Adjust


title: 156560124_1_E12_GTAGAGGA-GTAAGGAG_L003


title: ISPY2_493519


title: 156560124_1_E10_CGAGGCTG-GTAAGGAG_L003


title: 156560124_1_E2_CGTACTAG-GTAAGGAG_L003


title: ISPY2_492612


title: ISPY2_491779

value: T-DM1 + Pertuzumab


title: ISPY2_490023


title: 946927

description: same as GSM4552534


title: 539904

description: same as GSM4552576

value: Paclitaxel + Trastuzumab


title: 156560124_1_C8_CAGAGAGG-AGAGTAGA_L003

value: RV144 vaccine regimen


title: ISPY2_490805


title: 204939

value: Paclitaxel + Pertuzumab + Trastuzumab

value: Pertuzumab


title: 779739

description: same as GSM4552621


title: 981461


title: 771443

description: same as GSM4552617


title: 255388

description: same as GSM4552533


title: 555214


title: 156560124_1_C6_TAGGCATG-AGAGTAGA_L003


title: 156560124_1_C7_CTCTCTAC-AGAGTAGA_L003


title: 109980


title: ISPY2_489194

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel + Pembrolizumab


title: 799149


title: 402265


title: 625800

value: Paclitaxel + Neratinib

value: N


title: 156560124_1_C9_GCTACGCT-AGAGTAGA_L003


title: 388581


title: 666450


title: 156560124_1_C5_GGACTCCT-AGAGTAGA_L003


title: ISPY2_484894

value: Paclitaxel


title: 795996


title: ISPY2_485637

value: Linear Adjustment Factor


title: 268937


title: 156560124_1_C3_AGGCAGAA-AGAGTAGA_L003


title: ISPY2_483667


title: 273691


title: ISPY2_483910


title: 156560124_1_C12_GTAGAGGA-AGAGTAGA_L003


title: 156560124_1_C11_AAGAGGCA-AGAGTAGA_L003


title: 156560124_1_C1_TAAGGCGA-AGAGTAGA_L003


title: ISPY2_478655


title: 349639


title: 156560124_1_C2_CGTACTAG-AGAGTAGA_L003


title: 413211


title: 375954

description: same as GSM4552552


title: 920479


title: 397505


title: 156560124_1_C4_TCCTGAGC-AGAGTAGA_L003


title: ISPY2_477994


title: 156560124_1_C10_CGAGGCTG-AGAGTAGA_L003


title: 786753

description: same as GSM4552557


title: 151230


title: 851180


title: 835137

description: same as GSM4552521


title: 156560124_1_B8_CGTACTAG-CTCTCTAT_L002


title: ISPY2_473505


title: 415039


title: 154293


title: 156560124_1_A9_GCTACGCT-TATCCTCT_L003


title: ISPY2_473468


title: ISPY2_474874


title: ISPY2_478055


title: 824234

description: same as GSM4552607

value: Control


title: 303947


title: 453596


title: 156560124_1_A8_CAGAGAGG-TATCCTCT_L003


title: ISPY2_472799


title: 654956


title: ISPY2_473365


title: 145513

description: same as GSM4552530

value: Paclitaxel + MK-2206 + Trastuzumab


title: 960029


title: 156560124_1_A7_CTCTCTAC-TATCCTCT_L003


title: 335091


title: 738041


title: 760011


title: 797499


title: ISPY2_467686

value: Paclitaxel + Ganitumab


title: 156560124_1_A6_TAGGCATG-TATCCTCT_L003

value: PBMC


title: 862244


title: 138425


title: ISPY2_467622


title: 767081


title: 156560124_1_A5_GGACTCCT-TATCCTCT_L003

value: CD4 T cells


title: 128675


title: 592535

value: Paclitaxel + ABT 888 + Carboplatin

value: VC


title: ISPY2_465008

value: ComBat Adjust


title: ISPY2_466267

value: Paclitaxel + Ganetespib


title: 156560124_1_A4_TCCTGAGC-TATCCTCT_L003

value: RV144 vaccine regimen


title: 503034

value: Paclitaxel + Pertuzumab + Trastuzumab

value: Pertuzumab


title: ISPY2_462605

value: Breast cancer biopsy (pre-treatment)


title: ISPY2_464547

value: T-DM1 + Pertuzumab


title: 955953

description: same as GSM4552531


title: 131961


title: 825363


title: 474874


title: 156560069_3_H8_AGGCAGAA-CTAAGCCT_L008


title: 156560069_3_H4_CGTACTAG-CTAAGCCT_L008


title: 156560124_1_A12_GTAGAGGA-TATCCTCT_L003


title: 156560124_1_A10_CGAGGCTG-TATCCTCT_L003


title: 213913


title: ISPY2_462581


title: 490805


title: 889721


title: 253531


title: 831848


title: ISPY2_462582


title: 202535

value: Paclitaxel + AMG-386 + Trastuzumab


title: 156560124_1_A11_AAGAGGCA-TATCCTCT_L003


title: ISPY2_460642


title: ISPY2_460812


title: 156560069_3_H3_TAAGGCGA-CTAAGCCT_L008


title: 624777


title: ISPY2_458196

value: Paclitaxel


title: 296841


title: ISPY2_459311


title: ISPY2_456506

value: Paclitaxel + Pembrolizumab

value: Linear Adjustment Factor


title: ISPY2_456432


title: ISPY2_455828


title: 146033


title: 127791


title: 552313

value: Paclitaxel + Neratinib

value: N


title: 443444


title: 396723


title: 981664


title: 285339


title: ISPY2_454808

value: Paclitaxel + Ganitumab


title: 156560069_3_D6_TAAGGCGA-AAGGAGTA_L002

value: PBMC

value: CD4 T cells


title: 156560069_3_G3_TAAGGCGA-CTAAGCCT_L001


title: 156560069_3_D3_TAAGGCGA-TATCCTCT_L001


title: 156560069_3_H1_CGTACTAG-GCGTAAGA_L002


title: 156560069_3_G2_TAAGGCGA-GTAAGGAG_L001


title: 156560069_3_E2_AAGAGGCA-AAGGAGTA_L008


title: 329941


title: 464547


title: 111881


title: 644609


title: ISPY2_453596


title: 947398


title: 539291


title: 516763


title: 604326


title: 156560069_3_G11_TAAGGCGA-CTCTCTAT_L001


title: 108939


title: 156560069_3_F9_GTAGAGGA-AAGGAGTA_L008


title: 156560069_3_D2_TAAGGCGA-GTAAGGAG_L002


title: 895653


title: ISPY2_452703


title: 324021


title: 896852


title: ISPY2_442669


title: 491779


title: 156560069_3_C11_TAAGGCGA-CTCTCTAT_L002


title: 723918


title: 356684


title: 788149


title: ISPY2_446263


title: ISPY2_442981


title: 156560069_3_C5_TAAGGCGA-AGAGTAGA_L001


title: 156560069_3_C9_GCTACGCT-AAGGAGTA_L008


title: 156560069_3_C12_CGAGGCTG-AAGGAGTA_L008


title: 587691


title: 786003


title: 255535


title: ISPY2_435279


title: ISPY2_439489


title: 156560069_3_B7_CAGAGAGG-AAGGAGTA_L008


title: ISPY2_437162


title: 156560069_2_H5_GGACTCCT-AAGGAGTA_L008


title: 156560069_3_B2_CTCTCTAC-AAGGAGTA_L008


title: 287961

description: same as GSM4552603

value: Paclitaxel + MK-2206 + Trastuzumab


title: 995480


title: 156560069_2_G2_TCCTGAGC-AAGGAGTA_L008


title: 649198


title: 432114


title: ISPY2_431061


title: ISPY2_432114

value: ComBat Adjust


title: ISPY2_436371


title: 839274

description: same as GSM4552594


title: 156560069_3_A10_TAGGCATG-AAGGAGTA_L008


title: 122287


title: 156560069_2_E9_TAAGGCGA-GCGTAAGA_L001


title: 477994

description: same as GSM4552615


title: 125130


title: ISPY2_430441


title: 156560069_2_F7_AGGCAGAA-AAGGAGTA_L008


title: 275034


title: 683374


title: ISPY2_424541


title: 108969


title: 156560069_2_E11_TAAGGCGA-ACTGCATA_L001


title: ISPY2_423979


title: 519738


title: ISPY2_429220


title: ISPY2_425173


title: 201873


title: 156560069_1_H5_TAAGGCGA-AAGGAGTA_L008


title: ISPY2_422454

value: Paclitaxel + MK-2206


title: 863161

description: same as GSM4552643


title: 211408


title: 891645


title: 156560069_2_E8_TAAGGCGA-AAGGAGTA_L001

value: RV144 vaccine regimen


title: 156560069_1_H4_CGTACTAG-TATCCTCT_L003


title: 609151

description: same as GSM4552541


title: 169536


title: 872188


title: 641246


title: 287300


title: 156560069_2_E2_CGTACTAG-AAGGAGTA_L008


title: 416434

description: same as GSM4552555


title: 316996


title: ISPY2_419590

value: Paclitaxel + Ganetespib


title: ISPY2_421917


title: 156560069_1_G9_AAGAGGCA-CTCTCTAT_L003


title: 123660

description: same as GSM4552554

value: Paclitaxel + Trastuzumab

value: Control

value: RPPA.2 & RPPA.3 (ave)


title: 501303

description: same as GSM4552636


title: 990443

value: Pembro


title: 220471

description: same as GSM4552626


title: ISPY2_418593

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel


title: ISPY2_417474


title: ISPY2_421829

value: Linear Adjustment Factor


title: 156560069_1_G8_CGAGGCTG-CTCTCTAT_L003


title: 156560069_1_G12_TAAGGCGA-TATCCTCT_L003


title: 254273

value: T-DM1 + Pertuzumab


title: 724384


title: 209397

value: Paclitaxel + Pembrolizumab


title: 111004


title: ISPY2_416434


title: ISPY2_414971


title: ISPY2_414256


title: 242370


title: 156560069_1_F9_GGACTCCT-CTCTCTAT_L003


title: 896621


title: 654021


title: ISPY2_414844


title: 507249

value: Paclitaxel + Pertuzumab + Trastuzumab

value: Pertuzumab


title: 156560069_1_G1_GCTACGCT-CTCTCTAT_L003

value: PBMC

value: CD4 T cells


title: 865416


title: 156560069_1_F7_AGGCAGAA-CTCTCTAT_L003


title: 442981


title: 836983

value: Paclitaxel + Neratinib

value: N


title: 156560069_1_F5_TAAGGCGA-CTCTCTAT_L003

value: RV144 vaccine regimen


title: 156560069_1_G11_GTAGAGGA-CTCTCTAT_L003


title: 156560069_1_F6_CGTACTAG-CTCTCTAT_L003


title: 705381


title: 208650


title: ISPY2_413211

value: ComBat Adjust


title: 916645


title: ISPY2_412772

value: Paclitaxel + Ganitumab


title: 349225

value: Control


title: 156560069_1_F8_TCCTGAGC-CTCTCTAT_L003


title: 156560069_1_H10_AGGCAGAA-TATCCTCT_L003


title: 899692


title: 752469

description: same as GSM4552574


title: 472799


title: 156560069_1_F4_GTAGAGGA-GCGTAAGA_L003


title: 572731

value: Paclitaxel + ABT 888 + Carboplatin

value: VC


title: 156560069_1_F12_CAGAGAGG-CTCTCTAT_L003


title: ISPY2_411950

value: Breast cancer biopsy (pre-treatment)


title: 380239


title: 974618

value: Paclitaxel + AMG-386


title: ISPY2_413961

value: Paclitaxel + MK-2206


title: 266840

description: same as GSM4552639

value: Paclitaxel + Trastuzumab

value: RPPA.2 & RPPA.3 (ave)


title: ISPY2_410083

value: T-DM1 + Pertuzumab


title: 156560069_1_F10_TAGGCATG-CTCTCTAT_L003


title: 924812


title: ISPY2_411008

value: Paclitaxel + AMG 386


title: 156560069_1_F11_CTCTCTAC-CTCTCTAT_L003

value: PBMC


title: 241998

value: Paclitaxel


title: ISPY2_411806

value: Paclitaxel + Ganetespib


title: 437162


title: 156560069_1_E2_AAGAGGCA-GCGTAAGA_L003

value: CD4 T cells


title: 130892

description: same as GSM4552601


title: 601489

description: same as GSM4552580

value: Paclitaxel + MK-2206 + Trastuzumab


title: 498985

value: Paclitaxel + AMG-386 + Trastuzumab


title: 366120


title: ISPY2_409288

value: ComBat Adjust


title: 156560069_1_E1_CGAGGCTG-GCGTAAGA_L003

value: RV144 vaccine regimen


title: 178815

value: Paclitaxel + Neratinib

value: N


title: 156560069_1_D3_CAGAGAGG-GCGTAAGA_L003


title: ISPY2_402384

value: Breast cancer biopsy (pre-treatment)


title: 356399

value: Control


title: 726381


title: ISPY2_408692


title: 156560069_1_D1_TAGGCATG-GCGTAAGA_L003


title: 683896

value: Paclitaxel + AMG-386


title: ISPY2_401215


title: 809037

description: same as GSM4552525

value: RPPA.1 & RPPA.2 (ave)


title: 156560069_1_D11_GCTACGCT-GCGTAAGA_L003


title: ISPY2_407539

value: Paclitaxel + Ganitumab


title: 156560069_1_D2_CTCTCTAC-GCGTAAGA_L003


title: ISPY2_397505

value: T-DM1 + Pertuzumab


title: 579881


title: ISPY2_399478

value: Paclitaxel + AMG 386


title: 906042


title: 156560069_1_A9_AGGCAGAA-GCGTAAGA_L003

value: PBMC


title: 317402

description: same as GSM4552623

value: Paclitaxel + MK-2206


title: ISPY2_396723


title: 156560069_1_B12_GGACTCCT-GCGTAAGA_L003


title: ISPY2_395249

value: Paclitaxel + Ganetespib


title: 156560069_1_A8_CGTACTAG-GCGTAAGA_L003

value: CD4 T cells


title: 775346

description: same as GSM4552520

value: Paclitaxel


title: 422013


title: 944419

value: Paclitaxel + ABT 888 + Carboplatin

value: VC


title: 913225


title: 156560069_1_A7_TAAGGCGA-GCGTAAGA_L003

value: RV144 vaccine regimen


title: 290413

value: Paclitaxel + AMG-386 + Trastuzumab


title: 929980

description: same as GSM4552637

value: Paclitaxel + MK-2206 + Trastuzumab


title: 685182

value: Paclitaxel + Pertuzumab + Trastuzumab

value: Pertuzumab


title: ISPY2_384830

value: Breast cancer biopsy (pre-treatment)

value: ComBat Adjust


title: ISPY2_391942

value: Paclitaxel + Pembrolizumab

value: Linear Adjustment Factor


title: 188091

value: Paclitaxel + Neratinib

value: N


title: 234272


title: 628692


title: 382853

value: Paclitaxel + Trastuzumab

value: Control


title: ISPY2_383456

value: Paclitaxel + AMG 386


title: ISPY2_378885


title: 771813

description: same as GSM4552529

value: Paclitaxel

value: RPPA.1 & RPPA.2 (ave)


title: ISPY2_380972

value: Paclitaxel + Ganetespib


title: 728287


title: Set1 mycelia 7 days rep1

city: Hangzhou

first: Chuyu

last: Lin

state: Zhejiang

address: 866#, Yuhangtang Road

department: College of Agriculture and Biotechnology

country: China

institute: Zhejiang University

data_processing:
RNAs were sequenced with Illumina Hiseq X-Ten with Hiseq-PE150 strategy by Novogene Corporation (Beijing, China).
The obtained reads were mapped to the Ustilaginoidea virens (UV-8b) genome using Hisat2 (version 2.1.0) with default settings and sorted by SAMtools (Version 1.9).
R v4.0.3 package DESeq2 (version 1.30.1) was used to identify genes that were differentially expressed between the WT and ∆Uvkmt2 mutant. Genes with at least a 2-fold change in expression level (log2Fold Change ≥ 1, P < 0.05) between the ∆Uvkmt2 mutant and WT were considered to be differentially expressed.
Assembly: UV-8b
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Ustilaginoidea virens

source_name: mycelia

growth_protocol: The WT and all transformed strains derived from the WT were cultured on PSA (potato sucrose agar, potato 200 g/L, sucrose 20 g/L and agar 20 g/L) plates at 28°C under dark conditions.

extract_protocol:
Total RNA was isolated from mycelia cultured in liquid PS for 7 d using the TRIzol (Invitrogen) reagent. Subsequently, cDNAs were synthesized with a reversely transcribed kit (TAKARA) according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: mutant

tag: developmental stage

value: mycelia

tag: time

value: 7 days


title: 238790


title: 527320


title: WT mycelia 7 days rep3

tag: genotype

value: wild type


title: 572793

description: same as GSM4552540

value: Paclitaxel + MK-2206


title: Set1 mycelia 7 days rep2


title: 974181

value: Paclitaxel + AMG-386


title: ISPY2_377460

tag: patient id

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel + Pertuzumab + Trastuzumab

value: ComBat Adjust


title: 156560069_1_A10_TCCTGAGC-GCGTAAGA_L003

value: PBMC

value: CD4 T cells

value: RV144 vaccine regimen


title: Set1 mycelia 7 days rep3


title: 641977

tag: hr


title: 685753

tag: arm (short name)


title: WT mycelia 7 days rep1


title: ISPY2_376676

value: Paclitaxel + Ganitumab


title: 373672

value: Control

tag: rppa array (normalization key)


title: 485637

value: Paclitaxel + Pembrolizumab

value: Pembro


title: 892390


title: WT mycelia 7 days rep2


title: mycelia - H3K4me3_set1_rep2_input

data_processing:
High-throughput sequencing was carried out using Illumina Hiseq-PE150 by Novogene Corporation (Beijing, China) for Illumina (Langmead et al., 2009).
The clean read pairs were mapped to the reference genome with Bowtie2 (Version 2.3.5) (Langmead and Salzberg, 2012) , and reads with low mapping quality or multiple positions on the genome were identified and removed by SAMtools (Version 1.9).
Enriched peaks were called by HOMER (Version 4.9.1) with default parameters (Heinz, 2010).
Assembly: UV-8b
Supplementary files format and content: peak text files
Supplementary files format and content: bedGraph

extract_protocol:
After the cross-linking was stopped with 125 mM glycine, the mycelia were ground in liquid nitrogen and suspended with the nuclei isolating buffer (10 mM Tris pH 8.0, 10 mM sodium butyrate, 400 mM sucrose, 0.1 mM PMSF, 5 mM β-mercaptoethanol and 1 × proteinase inhibitors). The precipitated nuclei were treated with 1 mL lysis buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 10 mM sodium butyrate, 0.1% deoxycholate, 1% Triton X-100, 0.1% SDS, 1mM PMSF and 1 × Roche protease inhibitor cocktail) and broken into DNA fragments between 200 -500 bp using Diagenode Vioruptor. After pretreating with 10 μL protein A beads (Thermofisher, 10001D), the supernatant was incubated with anti-H3K4me3 antibody (Abcam, ab1012) for 1 h. Then 20 μL protein A beads were added into the above reaction system to bind anti-H3K4me3 antibody. Two biological repeats were conducted.
The purified DNA was used as libraries construction with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L).

treatment_protocol: The mycelia were crosslinked with 1% formaldehyde for 20 mins and stopped with 125 mM glycine for 5 mins at room temperature.

tag: isolate

value: mutant UvKmt2

value: potato sucrose agar

tag: treatment

value: input


title: mycelia - H3K4me3_set1_rep2_IP


title: ISPY2_375342

tag: mp

tag: pcr

tag: arm


title: 132463

description: same as GSM4552549

value: Paclitaxel + MK-2206 + Trastuzumab


title: 425173


title: mycelia - H3K4me3_set1_rep1_IP


title: 587388

value: Paclitaxel + ABT 888 + Carboplatin

value: VC


title: ISPY2_369040

value: Paclitaxel

tag: adjustment method

value: Linear Adjustment Factor


title: 568331

value: Paclitaxel + AMG-386


title: 105513


title: ISPY2_362150

value: Breast cancer biopsy (pre-treatment)

value: ComBat Adjust


title: 231633


title: ISPY2_375954


title: ISPY2_366120

value: T-DM1 + Pertuzumab


title: 139771

value: Paclitaxel + Neratinib

value: N


title: 293142

description: same as GSM4552572

value: Control


title: mycelia - H3K4me3_WT_rep2_input

value: wild type


title: 284593

description: same as GSM4552611

value: Paclitaxel + MK-2206


title: ISPY2_371528

value: Paclitaxel + Pembrolizumab


title: mycelia - H3K4me3_WT_rep2_IP

value: potato sucrose agar


title: 697098


title: 506623

description: same as GSM4552570


title: ISPY2_361701


title: 812089


title: ISPY2_363669


title: mycelia - H3K4me3_set1_rep1_input

value: mutant UvKmt2

value: input


title: 615873


title: 794428


title: 318569


title: mycelia - H3K4me3_WT_rep1_IP


title: 889049

value: Paclitaxel + Trastuzumab


title: mycelia - H3K4me3_WT_rep1_input


title: ISPY2_357034

value: Paclitaxel + Ganetespib


title: 159352

description: same as GSM4552612

value: Paclitaxel + MK-2206 + Trastuzumab


title: ISPY2_356684

value: Paclitaxel + AMG 386 + Trastuzumab


title: 218503

description: same as GSM4552650


title: Control empy vector rep 3 [EV7]

city: Kiryat Shmona

first: Rachel

last: Amir

address: Tarshis 2

department: Plant Science

country: Israel

institute: Migal

description: hairy roots having an empty vector

data_processing:
fastq files were generated by the usage bcl2fastq-v2.17.1.14 (basecalling)
Reads were trimmed using cutadapt
Reads were aligned to the  genomepomegranate (Punica granatum L.) using STAR (2.4.2a).
Counting reads on reference pomegranate (Punica granatum L.) genome, GCA_007655135.2, was done with HTSeq-count (version 0.6.1p1)
Differential analysis was carried out using DESeq2 (1.10.1)
Genome_build: GCA_007655135.2
Supplementary_files_format_and_content: Excel file includes the raw counts, genereted by HTSeq-count
Supplementary_files_format_and_content: Excel file includes the normalized counts (DESeq Normalization)

organism: Punica granatum

source_name: Control empy vector_hairy roots

growth_protocol: Plants with roots that showed the presence of GFP, were transferred to pots with samll particles of limestone in the presence of a  quarter of Hogland solution for three months in a greenhouse.

extract_protocol:
The RNA was extracted using the Spectrum plant total RNA kit (Sigma).
RNA-Seq (3' Prime End Sequencing); TranSeq mRNA

tag: cultivar

value: young hairy roots

tag: cells

value: All the cells found in the roots


title: Rabies Infected V1 Cortical Nuclei

city: LA JOLLA

first: Edward

middle: M.

last: Callaway

address: 10010 N Torrey Pines Rd

department: SNL-C

institute: Salk Institute

data_processing:
3' polyA RNA-Seq (10X Genomics, chemistry v3.1)
CellRanger 5.0 (reference genome: mm10). Fastqs from both Illumina NextSeq550 and NovaSeq6000 were combined and used as input for CellRanger.
The gene count matrices were loaded into Seurat v4. Nuclei with more than 0.5% mitochondrial transcript reads, less than 500 genes, or more than 8000 genes were filtered out. Doublets were removed using DoubletFinder.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are gene count matrices as output by CellRanger.

molecule: polyA RNA

source_name: mouse primary visual cortex V1 neurons

growth_protocol: All experimental procedures were approved by the Salk Institute Animal Care and Use Committee. C57BL/6J mice were used as wild-type. Homozygous Gad2-Cre and R26-LSL-TVA-LacZ (Seidler et al., 2008) mice were bred to produce Gad2-Cre; R26-LSL-TVA-LacZ. Mice were housed with a 12-hour light and 12-hour dark cycle and ad libitum access to food and water. Both male and female mice were used for RNA sequencing experiments.

extract_protocol: Single nuclei preparations were performed as follows: the frozen brain tissues were transferred to pre-chilled dounce homogenizers with 1ml NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10ul of protease inhibitor (Sigma P8340), 1.5ul of RNasin Plus RNase inhibitor (Promega, N2611)), 0.1% Triton X-100, and 10 uM DAPI, and gently homogenized on ice with ice-cold pestles 10 - 15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 3000 rpm for 8 min at 4°C to pellet the nuclei. The supernatant was aspirated, the pellet gently resuspended in ice-cold 1ml NIM buffer, and again centrifuged at 3000 rpm for 8 min at 4°C. The pellet was then resuspended in 450ul of nuclei storage buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through a 40μM cell strainer. The sample was incubated with 50ul of nuclease-free BSA to prevent nuclei clumping. Fluorescence-activated nuclei sorting of single nuclei was performed using a BD Influx sorter with a 70 μM nozzle at 22.5 PSI sheath pressure. DAPI+/mCherry+ rabies-infected nuclei were sorted into 1.5ml Eppendorf tubes and immediately loaded onto the 10X Genomics Chromium Controller. For 10x processing, we used Chromium Next GEM single-cell 3’ Kit v3.1 (10x Genomics, PN-1000128). We followed the manufacturer’s instructions for single-cell capture, barcoding, reverse transcription, cDNA amplification, and library construction. We targeted sequencing depth of 100,000 reads per cell. Libraries were sequenced on both Illumina NextSeq550 and NovaSeq6000 and raw read (fastq) files from both sequencing platforms were combined and aligned to the mouse pre-mRNA reference transcriptome (mm10) using the 10x Genomics CellRanger pipeline (version 5.0.). Intronic reads were included in expression quantification using the include-introns parameter

treatment_protocol: To collect large numbers of rabies-infected neurons for transcriptomic experiments, 150 nl of unpseudotyped G+RVdG-H2BmCherry (9.59E+09 IU/ml) was injected into the center of V1 of P60-P75 C57BL/6 mice 0.5–0.7 mm ventral from the pia. To bias infection to inhibitory neurons 150 nl of EnvA+RVdG-H2BmCherry (1.09E+08 IU/ml) was injected into P65-P85 Gad2-Cre; R26-LSL-TVA mice. For HCR experiments 100 nl of diluted AAV8-nef-AO-66/71-TVA950 (5.25E+11 GC/mL) was injected into V1 of Sst-Cre; INTACT mice. Two weeks after AAV helper virus injection, 200 nl of EnvA+RVdG-H2BmCherry (7.43E+07 IU/ml) was injected into the same site in V1. Ten days after rabies injection, brains were extracted and immediately submerged in ice-cold slicing solution. Coronal brain slices (400um thick) were cut using VF-300 CompresstomeTM (Precisionary Instruments, Greenville,NC) and submerged in ice-cold slicing solution. Subregions of V1 containing mCherry+ nuclei in brain slices were micro-dissected out under a fluorescent dissection microscope (Olympus SZX6).

tag: strain

value: C57BL/6J and Gad2-Cre; R26-LSL-TVA-LacZ

tag: cell type

value: primary visual cortex V1 neurons


title: ISPY2_356431

tag: tissue

value: Breast cancer biopsy (pre-treatment)

value: T-DM1 + Pertuzumab

value: ComBat Adjust


title: 543795

value: Pembro


title: 103693


title: ISPY2_356399

value: Paclitaxel

value: Linear Adjustment Factor


title: Control empy vector rep 2 [EV6]

description: hairy roots having an empty vector

value: Control


title: Control empy vector rep 1 [EV4]

description: hairy roots having an empty vector


title: ISPY2_355292


title: Transgnic line R2R3 Myb Pg308-like rep 2 [9658-3]

description: hairy roots overexpressing the accession number: AIO09658.1

source_name: Transgnic line R2R3 Myb Pg308-like_hairy roots

value: transgenic line over-expressing the R2R3 PgMyb308-like


title: 502486


title: 597873

value: Paclitaxel + Pembrolizumab


title: 318438

value: RPPA.1 & RPPA.2 (ave)


title: ISPY2_355942

source_name: Breast cancer biopsy (pre-treatment)


title: 181442


title: 320538


title: Transgnic line R2R3 Myb Pg308-like rep 3 [9658-4]


title: 294176

value: Paclitaxel + Neratinib

value: N


title: 104268


title: ISPY2_353318


title: Transgnic line R2R3 Myb Pg308-like rep 1   [9658-10]


title: 851223

value: Paclitaxel + AMG-386


title: 690089


title: Transgnic line 1712 rep 2 [1712-6]

description: hairy roots overexpressing the accession number: KM881712.1

source_name: Transgnic line 1712_hairy roots

value: transgenic line over-expressing the R2R3 PgMyb308

value: young hairy roots


title: 692885


title: ISPY2_345907

value: Paclitaxel + MK-2206


title: ISPY2_349330

value: Paclitaxel + AMG 386


title: 778527

description: same as GSM4552577


title: Transgnic line 1712 rep 1 [1712-1]

value: All the cells found in the roots


title: ISPY2_347516

value: Breast cancer biopsy (pre-treatment)


title: ISPY2_997702

value: Paclitaxel + ABT 888 + Carboplatin

value: ComBat Adjust


title: 361701

description: same as GSM4552627


title: 680881

description: same as GSM4552522


title: ISPY2_994987


title: ISPY2_345483

value: Paclitaxel + Ganitumab


title: 622688

value: Pembro


title: ISPY2_988443


title: 267306

value: VC


title: 644186

value: Paclitaxel

value: Control


title: ISPY2_345460


title: ISPY2_342996


title: 489194

value: Paclitaxel + Pembrolizumab


title: ISPY2_974618


title: 953262

value: Paclitaxel + Neratinib


title: 883886

value: N


title: 830958


title: 446263


title: ISPY2_973837


title: 883696


title: 832056


title: ISPY2_342959


title: ISPY2_972307


title: 494946


title: ISPY2_342142

value: Paclitaxel + Ganetespib


title: 848371


title: ISPY2_962827


title: 942017

description: same as GSM4552515


title: ISPY2_343898


title: ISPY2_341238

value: Linear Adjustment Factor


title: ISPY2_962472


title: 640927


title: ISPY2_961350


title: 151481

value: RPPA.1 & RPPA.2 (ave)


title: 803677

description: same as GSM4552538

value: Paclitaxel + MK-2206


title: 333145


title: ISPY2_333145


title: ISPY2_960963

value: Paclitaxel + MK-2206 + Trastuzumab


title: 725455

value: Paclitaxel + Trastuzumab


title: 613188

value: Paclitaxel + AMG-386


title: ISPY2_332655

value: Breast cancer biopsy (pre-treatment)


title: 111344


title: 517870

description: same as GSM4552648

value: RPPA.2 & RPPA.3 (ave)


title: ISPY2_330134

value: Paclitaxel + Ganitumab

value: ComBat Adjust


title: ISPY2_959366

value: Paclitaxel + ABT 888 + Carboplatin


title: 528833

value: Paclitaxel + AMG-386 + Trastuzumab


title: 930172


title: ISPY2_329941

value: T-DM1 + Pertuzumab


title: 660534

value: Paclitaxel + Pembrolizumab

value: Pembro


title: 500826


title: 520986

description: same as GSM4552581


title: ISPY2_955953


title: ISPY2_329076

value: Paclitaxel + AMG 386


title: ISPY2_953262

value: Paclitaxel + Neratinib


title: ISPY2_335536


title: ISPY2_328160

value: Paclitaxel


title: 369040

value: Control


title: 178649

value: N


title: 630758

value: VC


title: ISPY2_944536


title: 663197


title: ISPY2_957408


title: ISPY2_327917


title: 177795


title: ISPY2_944419


title: 999264

value: Paclitaxel + Pertuzumab + Trastuzumab

value: Pertuzumab


title: ISPY2_326202

value: Breast cancer biopsy (pre-treatment)

value: Linear Adjustment Factor


title: 929391

description: same as GSM4552649


title: ISPY2_942017


title: 602943


title: 406190


title: ISPY2_324021


title: 473505


title: 746731


title: 841336


title: ISPY2_323721

value: Paclitaxel + MK-2206


title: 327133


title: ISPY2_320538

value: ComBat Adjust


title: ISPY2_946927

value: Paclitaxel + MK-2206 + Trastuzumab


title: ISPY2_934459

value: Paclitaxel + ABT 888 + Carboplatin


title: 112606

description: same as GSM4552518

value: Paclitaxel + Trastuzumab


title: ISPY2_326433


title: 229824


title: ISPY2_319324


title: 456506

value: Paclitaxel + Pembrolizumab


title: 553012

value: Pembro


title: ISPY2_318407

value: Paclitaxel + Ganitumab


title: ISPY2_930172

value: Paclitaxel + Neratinib


title: 591810

description: same as GSM4552635


title: ISPY2_941191


title: ISPY2_930853

value: Paclitaxel + AMG 386


title: ISPY2_932200

value: Paclitaxel


title: 803514

value: Control

value: RPPA.1 & RPPA.2 (ave)


title: ISPY2_318293


title: 709559


title: ISPY2_317641


title: ISPY2_925691


title: 395076

description: same as GSM4552516


title: ISPY2_924812


title: 802778

value: VC


title: ISPY2_317402


title: 711476

description: same as GSM4552634


title: 756412


title: ISPY2_922433


title: 598798


title: ISPY2_920479


title: ISPY2_317131


title: ISPY2_313672

value: Paclitaxel + Ganetespib


title: 484894


title: 483667

value: Paclitaxel + Pertuzumab + Trastuzumab

value: Pertuzumab


title: 845663


title: 229144


title: ISPY2_916645

value: Breast cancer biopsy (pre-treatment)


title: ISPY2_913225

value: ComBat Adjust


title: ISPY2_311455

value: Linear Adjustment Factor


title: 899381


title: ISPY2_313243


title: ISPY2_910706

value: Paclitaxel + ABT 888 + Carboplatin


title: ISPY2_906042


title: ISPY2_311316

value: T-DM1 + Pertuzumab


title: 311455


title: 573881

value: N


title: 371528

value: Paclitaxel + Pembrolizumab

value: Pembro


title: 802105


title: ISPY2_904269


title: 706169

description: same as GSM4552569

value: RPPA.2 & RPPA.3 (ave)


title: 200222

description: same as GSM4552546

value: Paclitaxel + MK-2206


title: ISPY2_306401

value: Paclitaxel + AMG 386


title: 552549

value: Paclitaxel + AMG-386


title: 116165


title: ISPY2_309830


title: ISPY2_903880

value: Paclitaxel + Neratinib


title: 414844

value: Paclitaxel

value: Control


title: ISPY2_303685


title: 240432


title: ISPY2_894491


title: ISPY2_301968


title: 458196


title: ISPY2_894128


title: 424541


title: ISPY2_301665

value: Paclitaxel + AMG 386 + Trastuzumab


title: 317641

description: same as GSM4552633


title: 941926


title: ISPY2_301289


title: ISPY2_890414


title: 676048

value: VC


title: ISPY2_889225

value: Breast cancer biopsy (pre-treatment)


title: 257735


title: ISPY2_299962

value: Paclitaxel + Ganitumab

value: ComBat Adjust


title: 790722

value: Paclitaxel + ABT 888 + Carboplatin


title: 461824


title: 735673


title: ISPY2_889049

value: Paclitaxel + Trastuzumab


title: 835658

value: N


title: ISPY2_885590


title: 275626


title: 114087

value: Paclitaxel + Pembrolizumab


title: 220664


title: ISPY2_296841

value: Paclitaxel + Pertuzumab + Trastuzumab


title: ISPY2_891645


title: 116603

description: same as GSM4552651

value: RPPA.2 & RPPA.3 (ave)


title: ISPY2_883886


title: ISPY2_296123


title: ISPY2_883696


title: ISPY2_300724


title: ISPY2_294739


title: 202956


title: 732137

description: same as GSM4552566

value: Paclitaxel + MK-2206


title: 520258

description: same as GSM4552519


title: ISPY2_876511


title: ISPY2_299840

value: Linear Adjustment Factor


title: 515565

description: same as GSM4552523

value: RPPA.1 & RPPA.2 (ave)


title: ISPY2_294265


title: 345907

description: same as GSM4552595


title: ISPY2_872188

value: Paclitaxel + Neratinib


title: 848003

value: Paclitaxel + AMG-386


title: 563856


title: ISPY2_293142

value: Paclitaxel


title: 679787

description: same as GSM4552575

value: Control


title: ISPY2_290413

value: Paclitaxel + AMG 386 + Trastuzumab


title: ISPY2_851180

value: Breast cancer biopsy (pre-treatment)


title: 436371


title: 127675


title: 213328


title: ISPY2_849605


title: 345574

value: VC


title: 970839

description: same as GSM4552567


title: 614044


title: ISPY2_845663

value: ComBat Adjust


title: ISPY2_287961

value: Paclitaxel + MK-2206 + Trastuzumab


title: 748611

description: same as GSM4552558


title: ISPY2_840501

value: Paclitaxel + AMG 386


title: 348009

value: Paclitaxel + ABT 888 + Carboplatin


title: 932200


title: ISPY2_859699

value: Paclitaxel + Trastuzumab


title: 129973


title: ISPY2_836114


title: ISPY2_836983


title: ISPY2_285339

value: Paclitaxel + Pertuzumab + Trastuzumab


title: 950131


title: ISPY2_289420

value: Paclitaxel + Ganitumab


title: ISPY2_284443


title: 218249


title: 801641

description: same as GSM4552606

value: Paclitaxel + MK-2206


title: ISPY2_835658


title: ISPY2_289107

value: Paclitaxel + Pembrolizumab

value: Linear Adjustment Factor


title: 639663

description: same as GSM4552579


title: 521860


title: ISPY2_282777

value: Paclitaxel + Ganetespib


title: 247641


title: ISPY2_835137


title: ISPY2_280375


title: 291515


title: 712785


title: ISPY2_833536


title: 658541


title: 965265

value: Paclitaxel + AMG-386


title: ISPY2_828199

value: Paclitaxel + Neratinib


title: ISPY2_283070


title: 997702


title: 904269


title: 111038


title: 152090

value: Paclitaxel

value: Control


title: ISPY2_277888

value: Breast cancer biopsy (pre-treatment)


title: ISPY2_275626


title: ISPY2_814299


title: ISPY2_819622


title: 653927


title: ISPY2_815421


title: ISPY2_273691


title: 201831


title: ISPY2_812089


title: 340186

value: VC


title: ISPY2_809649

value: ComBat Adjust


title: ISPY2_279902


title: 574091

value: Pembro


title: 147139


title: ISPY2_266840


title: 423619

value: N


title: 117424


title: ISPY2_275034

value: Paclitaxel + AMG 386 + Trastuzumab


title: 172168

description: same as GSM4552565


title: 570966

value: Paclitaxel + AMG-386 + Trastuzumab


title: ISPY2_266509

value: Paclitaxel + AMG 386


title: ISPY2_268937

value: T-DM1 + Pertuzumab


title: ISPY2_269899


title: 618240


title: ISPY2_800710


title: 547405

description: same as GSM4552652

value: Paclitaxel + MK-2206


title: 409288


title: ISPY2_809037


title: 573605

description: same as GSM4552630


title: 402384

description: same as GSM4552586


title: 857165

value: Paclitaxel + Pembrolizumab


title: 591180


title: ISPY2_803514


title: ISPY2_797427

value: Paclitaxel + Trastuzumab


title: ISPY2_261304

value: Paclitaxel + Ganitumab


title: S23 Parhyale embryo RNA-Seq, replicate C

city: Woods Hole

first: Nipam

middle: H

last: Patel

state: MA

address: 7 Mbl Street

institute: Marine Biological Laboratory

description:
Trinity_S23.fasta
Trinity_S23.sorted.gff
Trinity_S23.fasta.gene_trans_map

data_processing:
Reads were quality trimmed using trim_galore (FASTQC + cutadapt)
Trimmed reads were assembled into de novo transcriptomes using Trinity
A genome-guided transcriptome was also assembled after mapping reads to the genome using hisat2
A combined short- & long-read transcriptome was generated using StringTie2
FPKM quantification was performed using kallisto + RSEM via the Trinity pipeline
Differential expression analysis was performed using Trinity
Transcriptomes were merged with the previous genome annotation using Mikado
Mikado and MAKER annotations were functionally annotated using eggNOG
Mikado and MAKER annotations were compared to the Drosophila proteome using OrthoFinder
Assembly: phaw_5.0
Supplementary files format and content: DAS.mikado.loci.fasta and DAS.mikado.loci.fasta.gene_trans_map are the final Mikado merged transcriptome files
Supplementary files format and content: The files beginning with "Orthogroups" are the output from OrthoFinder. The output for Mikado does not have an additional suffix, whereas the output for MAKER has the suffix "_MAKER"
Supplementary files format and content: The files in the format "S##_vs_S##_RNASeq_Results.csv" are pairwise differential expression comparisions made using DESeq2
Supplementary files format and content: The files beginning with "Sall_peaktypes" are summarized gene models containing useful information (such as categories of nearby genes and peaks)
Supplementary files format and content: The files beginning with "Omni_vs_RNA_" are peak-gene pairs from differential expression and accessibility analysis between timepoints. CC pairs are concordant; DC pairs are discordant; all peaks are found in the "peak" file whereas inferred promoter peaks are found in the "pro" file
Supplementary files format and content: The "portcullis" files are the predicted splice junctions from the Mikado pipeline
Supplementary files format and content: The "FASTA_metadata.csv" file contains additional descriptions of the transcriptomes included in this dataset
Supplementary files format and content: The "Sun_annotations…" and "Blondel_annotations…" files contain the eggNOG-assigned gene annotations for the Mikado and MAKER annotations, respectively

organism: Parhyale hawaiensis

source_name: whole embryo

extract_protocol:
RNA was isolated using the Zymo Direct-Zol Miniprep Plus kit
Libraries were prepared using the TaKaRa SMART-Seq v4 Ultra Low-Input kit

value: whole embryo

value: Chicago F Isogenic


title: ISPY2_263143

value: Paclitaxel + MK-2206 + Trastuzumab


title: ISPY2_264305


title: S23 Parhyale embryo RNA-Seq, replicate B


title: ISPY2_802778

value: Paclitaxel + ABT 888 + Carboplatin


title: S23 Parhyale embryo RNA-Seq, replicate A


title: ISPY2_791944

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel + Neratinib


title: ISPY2_257735

value: Paclitaxel

value: Linear Adjustment Factor


title: ISPY2_259899

value: ComBat Adjust


title: 768214

value: Paclitaxel + AMG-386


title: 660915

value: N


title: ISPY2_790070


title: S21 Parhyale embryo RNA-Seq, replicate C

description:
Trinity_S21.fasta
Trinity_S21.sorted.gff
Trinity_S21.fasta.gene_trans_map


title: ISPY2_789497

value: Paclitaxel + AMG 386


title: ISPY2_790722


title: 651541


title: 664111

description: same as GSM4552602


title: S21 Parhyale embryo RNA-Seq, replicate A


title: ISPY2_254273

value: T-DM1 + Pertuzumab


title: 233832

value: VC


title: ISPY2_783578


title: 800710

value: Control


title: S19 Parhyale embryo RNA-Seq, replicate B

description:
Trinity_S19.fasta
Trinity_S19.sorted.gff
Trinity_S19.fasta.gene_trans_map


title: ISPY2_794428


title: 604380


title: 243836


title: ISPY2_782334


title: 553141


title: ISPY2_254060


title: S19 Parhyale embryo RNA-Seq, replicate A


title: ISPY2_252748


title: ISPY2_255577


title: ISPY2_781335


title: S21 Parhyale embryo RNA-Seq, replicate B


title: ISPY2_778020


title: ISPY2_253531


title: ISPY2_247641


title: S19 Parhyale embryo RNA-Seq, replicate C


title: S13 Parhyale embryo RNA-Seq, replicate C

description:
Trinity_S13.fasta
Trinity_S13.sorted.gff
Trinity_S13.fasta.gene_trans_map


title: ISPY2_250274


title: S13 Parhyale embryo RNA-Seq, replicate B


title: 347516

value: Paclitaxel + Pembrolizumab

value: Pembro


title: 282082

value: RPPA.1 & RPPA.2 (ave)


title: S13 Parhyale embryo RNA-Seq, replicate A

value: whole embryo

value: Chicago F Isogenic


title: ISPY2_242370


title: ISPY2_775346


title: ISPY2_771813


title: 478655


title: 792412