title: Retina_1month_rep1


title: RPE_2month_rep3

status: Public on Apr 09 2022

type: SRA

city: Singapore

first: Xinyi

last: Su

address: 61 Biopolis Drive

country: Singapore

institute: IMCB

library_source: transcriptomic

data_processing:
Sequenced paired-end reads were trimmed and mapped to hg19 reference genome using HISAT2.
Read counts per gene estimated using htseq-count
Read count normalisation and differential expresssion analysis performed using DESeq2
Assembly: GRCh38/hg38
Supplementary files format and content: comma delimited text file containing read counts per gene.

molecule: polyA RNA

organism: Oryctolagus cuniculus

source_name: Retinal Pigment Epithelium

extract_protocol:
Retina and Retinal Pigment Epithelium were lyzed with RLT buffer (Qiagen, cat. no. 79216), extracted and purified with Rneasy Mini Kit (Qiagen, cat no. 74106) following manufacturer's recommended protocol.
Illumina sequencing libraries were constructed using NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB, cat.  no. E7765)

treatment_protocol: Vitreous substitution using multiblock thermogelling polymer (PMID: 30962587)

tag: tissue

value: Retinal Pigment Epithelium

tag: Sex

value: Male

tag: age

value: 4 to 6 months

tag: treatment

value: vitreous substitution


title: RPE_2month_rep1


title: RPE_1month_rep3


title: RPE_1month_rep2


title: RPE_nonoperated_rep2

value: non-operated


title: RPE_1month_rep1


title: RPE_nonoperated_rep1


title: TNT + Polymer (24h) rep3

status: Public on Mar 09 2022

description: gene_count_matrix.csv --D3_24h

data_processing:
Sequenced paired-end reads were trimmed and mapped to hg19 reference genome using HISAT2.
Read counts per gene estimated using htseq-count
Read count normalisation and differential expresssion analysis performed using DESeq2
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Tab delimited text file containing read counts per gene.

molecule: total RNA

organism: Homo sapiens

source_name: Retinal pigment epithelial cell

growth_protocol: hESC-derived retinal pigment epithelial cells were differentiated based on a modified protocol (PMID:29155780). The experiment was conduced using passage 3 RPE cells that were replated and incubated for 24 hours before exposing to the different conditions.

extract_protocol:
RPE cells were lyzed with RLT buffer (Qiagen, cat. no. 79216), extracted and purified with Rneasy Mini Kit (Qiagen, cat no. 74106) following manufacturer's recommended protocol.
Illumina sequencing libraries were constructed using NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB, cat.  no. E7765)

treatment_protocol: RPE cells were treated with polymer alone, TNT alone or TNT + polymer for 8 and 24 hours before collecting the RNA. Media only served as the untreated control at the respective timings.

tag: cell type

value: hESC-derived

value: TNT + Polymen 24h

tag: passage

tag: culture age

value: 1 to 3 months


title: TNT + Polymer (8h) rep3

description: gene_count_matrix.csv --D3_8h

value: TNT + Polymen 8h


title: TNT + Polymer (24h) rep1

description: gene_count_matrix.csv --D1_24h


title: D7_hiPSC1_NT_1

status: Public on Jun 14 2022

city: Bethesda

first: Zachary

middle: A

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

country: USA

institute: NIH

data_processing:
Reads passing the Illumina chastity filter were demultiplexed then trimmed to remove low quality bases and adapters using Trimmomatic v0.36.
Reads were aligned to the human transcriptome (GRCH38.p13, Ensembl 98) and quantified to the transcript-level using Kallisto v0.45.0.
Transcript counts were summarized to the gene level using tximport 1.14.2 with the lengthScaledTPM option and TMM normalized using edgeR v3.28.1.
Genes with at least 1 count per million reads (CPM) in both replicates of at least one group (e.g., both D4 HiPSC3 samples) were retained for downstream analysis.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Kallisto abundance files are raw abundance tsv outputs from Kallisto for each sample
Supplementary_files_format_and_content: Adundance measurements are summarized gene and transcript abundance data for all samples

source_name: Retinal Organoid

extract_protocol:
Total RNAs were extracted from retinal organoid samples using RNAeasy Plus Mini kit (Qiagen, Germantown, MD).
Quality of isolated RNAs was assessed using Bioanalyszer RNA 6000 nano assays and only high-quality RNAs (RNA integration number (RIN) > 8) were used for construction of mRNA sequencing library. 100ng of total RNA were used to construct the strand-specific libraries using TruSeq RNA Sample Prep Kit-v2 (Illumina, San Diego, CA).

value: Retinal Organoid

tag: time

value: Control

tag: source line


title: TNT + Polymer (8h) rep2

description: gene_count_matrix.csv --D2_8h


title: TNT + Polymer (8h) rep1

description: gene_count_matrix.csv --D1_8h


title: TNT alone (24h) rep3

description: gene_count_matrix.csv --C3_24h

value: TNT alone 24h


title: TNT + Polymer (24h) rep2

description: gene_count_matrix.csv --D2_24h


title: TNT alone (24h) rep1

description: gene_count_matrix.csv --C1_24h


title: TNT alone (8h) rep2

description: gene_count_matrix.csv --C2_8h

value: TNT alone 8h


title: RPE_nonoperated_rep3


title: Polymer alone (24h) rep2

description: gene_count_matrix.csv --B2_24h

value: polymer alone 24h


title: TNT alone (8h) rep1

description: gene_count_matrix.csv --C1_8h


title: Polymer alone (8h) rep3

description: gene_count_matrix.csv --B3_8h

value: polymer alone 8h


title: Media only control (24h) rep3

description: gene_count_matrix.csv --A3_24h

value: media only 24h


title: Polymer alone (24h) rep1

description: gene_count_matrix.csv --B1_24h


title: Utx-Ko [scRNA-seq]

status: Public on Aug 04 2022

city: Madison

first: Jeffrey

last: Dilworth

state: Wisconsin

address: 1111 Highland Ave

institute: University of Wisconsin

description: Single-cell RNA-Seq

data_processing:
Performed on 10X Cell Ranger pipeline.
cellranger mkfastq  v2.1.1
cellranger count v2.1.1
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.tar archives include barcodes.tsv, features.tsv, and matrix.mtx files; single-cell gene expression matrix.

organism: Mus musculus

source_name: Satellite Stem cells

extract_protocol: Muscle satellite stem cells were isolated from indicated muscles by mincing and straining, which were further collected in microfuge tubes by fluorescence activated cell sorting.

treatment_protocol: Cardiotoxin Injections into the tibialis anterior and gastrocnemius muscle of hind limb.

tag: strain

tag: genotype

value: Utx KO

value: Cardiotoxin injury

value: Tibialis Anterior and Gastrocnemius muscles

value: Satellite Stem cells

tag: development stage

value: Adult


title: Polymer alone (24h) rep3

description: gene_count_matrix.csv --B3_24h


title: Media only control (24h) rep2

description: gene_count_matrix.csv --A2_24h


title: Media only control (8h) rep3

description: gene_count_matrix.csv --A3_8h

value: media only 8h


title: Media only control (8h) rep1

description: gene_count_matrix.csv --A1_8h

value: hESC-derived


title: TNT alone (8h) rep3

description: gene_count_matrix.csv --C3_8h


title: Media only control (24h) rep1

description: gene_count_matrix.csv --A1_24h


title: Control_S2_S7_GPR101_TSS

status: Public on Feb 23 2022

city: Pieve Emanuele

first: Giampaolo

last: Trivellin

state: Lombardy

address: Via Rita Levi Montalcini 4

country: Italy

institute: Humanitas University

library_source: genomic

data_processing:
Library strategy: 4C-seq
Sequencing data were demultiplexed and mapped to human reference genome (GRCh37/hg19). Reads located in restriction fragments flanked by restriction recognition sites of the same enzyme, in fragments smaller than 40 bp or within a window of 10 kb around the viewpoint were filtered out. Mapped reads were then converted to read counts per restriction fragment of first restriction enzyme.
For visualization, all samples were normalized for million mapped reads (reads per million, RPM) for a given genomic region (chrX:135,000,000-137,000,000, hg19) and smoothened using a 10-fragment running window algorithm.
To compare interaction profiles of patients to control, subtraction of normalized reads was applied. To reduce variability among control samples, an average profile from three independent control samples was used for subtraction.
Genome_build: human genome GRCh37/hg19

molecule: genomic DNA

source_name: Blood

extract_protocol:
4C-seq libraries were prepared following the published protocol (van de Werken et al., 2012). For GPR101 and S6 breakpoint viewpoints, Csp6 and DpnII were used for the first and second digestion, repsectively. For RBMX and VGLL1 viewpoints, DpnII and Csp6 were used for the first and second digestion, repsectively. Parallel PCR reactions were performed to amplify from a total of 1 µg template per 4C library and viewpoint. PCR reactions were pooled and purified using 1.8x volume of AMPure XP beads (Agencourt, A63881).
Samples were indexed and sequenced with Ilumina Hi-Seq technology according to standard procedures.

treatment_protocol: Approximately, 1 × 106 to 2.5 × 106 cells from cultured lymphoblastoid cells or nucleated cell isolates from peripheral blood samples were used as input material for 3C library preparation. Trypsinized or disaggregated cells were filtered through 40 µm cell strainer and pelleted by centrifugation at 500x g. Cells were fixed in 5 ml of 2 % formaldehyde in 10 % FCS/ PBS and incubated for 10 minutes at room temperatures to cross-link chromatin. The reaction was quenched with glycine at a final concentration of 0.125 M and incubation at room temperature for 5 minutes. Cells were pelleted by centrifugation for 5 minutes at 500x g at 4ºC and washed on ice twice with 1x PBS. Cell pellets were either snap frozen in liquid nitrogen or processed for nuclei extraction. For nuclei extraction, fixed cells were resuspended in 2 ml freshly prepared lysis buffer (50 mM Tris pH7.5; 150 mM NaCl; 5 mM EDTA; 0.5 % NP-40; 1.15 % Triton X-100; 1x Roche Complete protease inhibitors) and incubated for 10 minutes on ice. Nuclei were pelleted by centrifugation for 5 minutes, 800x g at 4ºC and washed with 1x PBS.

value: Blood

tag: clinical phenotype

value: healthy control

tag: viewpoint

value: GPR101 TSS


title: Control_S2_S7_VGLL1_TSS

value: VGLL1 TSS


title: Media only control (8h) rep2

description: gene_count_matrix.csv --A2_8h

value: 1 to 3 months


title: S17_GPR101_TSS

value: X-linked acrogigantism


title: TNT alone (24h) rep2

description: gene_count_matrix.csv --C2_24h

value: TNT alone 24h


title: RPE_2month_rep2

value: Retinal Pigment Epithelium

value: Male

value: 4 to 6 months

value: vitreous substitution


title: Control_S2_S7_RBMX_TSS

value: RBMX TSS


title: SupT1 2 ug/mL Dox + 10 uM TMP Rep1

status: Public on Jan 30 2022

city: Cambridge

first: Matthew

middle: D

last: Shoulders

state: MA

address: 77 Massachusetts Avenue

department: Chemistry

institute: Massachusetts Institute of Technology

description:
D17-195037
XBP1s and ATF6 transcription activation
Expression_data.txt

data_processing:
Base calling was performed using Illumina's HiSeq Control Software v. 2.5.58 and RTA v. 1.18.64.
Reads were aligned against hg19 (Feb., 2009) using bwa mem v. 0.7.12-r1039 with flags –t 16 –f and mapping rates, fraction of multiply-mapping reads, number of unique 20-mers at the 5´ end of the reads, insert size distributions and fraction of ribosomal RNAs were calculated using bedtools v. 2.25.0. In addition, each resulting bam file was randomly down-sampled to a million reads, which were aligned against hg19 and read density across genomic features were estimated for RNA-Seq-specific quality control metrics.
For mapping and quantitation, reads were aligned against GRCh38/ENSEMBL 89 annotation using STAR v. 2.5.3a with the following flags -runThreadN 8 –runMode alignReads –outFilter-Type BySJout –outFilterMultimapNmax 20 –alignSJoverhangMin 8 –alignSJDBoverhangMin 1 –outFilterMismatchNmax 999 –alignIntronMin 10 –alignIntronMax 1000000 –alignMatesGapMax1000000 –outSAMtype BAM SortedByCoordinate –quantMode TranscriptomeSAM with –genomeDir pointing to a 75nt-junction GRCh38 STAR suffix array. Gene expression was quantitated using RSEM v. 1.3.0 with the following flags for all libraries: rsem-calculate-expression –calc-pme –alignments -p 8 –forward-prob 0 against an annotation matching the STAR SA reference. Posterior mean estimates (pme) of counts and estimated RPKM were retrieved.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Expression_data.txt: For each sample and each gene, corresponding official gene symbol, ENSEMBL gene and transcript IDs, gene length, effective gene lengths and log2-transformed posterior mean estimates (pme) of RPKMs (pseudocount of 0.1) are reported in a tab-delimited format.

growth_protocol: Low passage cells were plated at a density of 50,000 cells/well in 6W plate in RPMI media supplemented with 10% FBS, 1% penicillin/streptomycin/glutamine and cultured at 37C with 5% CO2.

extract_protocol:
Cellular RNA was harvested using the RNeasy Plus Mini Kit with QIAshredder homogenization columns (Qiagen).
RNA-seq libraries were prepared using the Kapa mRNA HyperPrep RNA-seq library construction kit (Kapa/Roche), with 6 min fragmentation at 94 °C and 9 PCR cycles of final amplification and duplex barcoding. Libraries were quantified using the Fragment Analyzer and qPCR before being sequenced on an Illumina HiSeq 2000 using 40-bp single-end reads in High Output mode.

treatment_protocol: At the time of plating, cells were treated with either 1) 0.1% DMSO, 2) 2 ug/mL Dox, 3) 10 uM TMP, or 4) 2 ug/mL Dox and 10 uM TMP for 24 hours.

value: Human T lymphoblast

value: Clonal; stably expressing tetR, XBP1s (under control of tetR), and DHFR.ATF6

value: 24 hr 2 ug/mL Doxycycline (Dox) + 10 uM Trimethoprim (TMP)


title: SupT1 10 uM TMP Rep2

description:
D17-195034
ATF6 transcription activation
Expression_data.txt

value: 24 hr 10 uM Trimethoprim (TMP)


title: SupT1 10 uM TMP Rep3

description:
D17-195035
ATF6 transcription activation
Expression_data.txt


title: SupT1 2 ug/mL Dox + 10 uM TMP Rep2

description:
D17-195038
XBP1s and ATF6 transcription activation
Expression_data.txt


title: Polymer alone (8h) rep1

description: gene_count_matrix.csv --B1_8h

value: hESC-derived

value: polymer alone 8h


title: SupT1 2 ug/mL Dox Rep4

description:
D17-195032
XBP1s transcription activation
Expression_data.txt

value: 24 hr 2 ug/mL Doxycycline (Dox)


title: SupT1 10 uM TMP Rep1

description:
D17-195033
ATF6 transcription activation
Expression_data.txt


title: SupT1 2 ug/mL Dox Rep3

description:
D17-195031
XBP1s transcription activation
Expression_data.txt


title: SupT1 2 ug/mL Dox + 10 uM TMP Rep4

description:
D17-9077
XBP1s and ATF6 transcription activation
Expression_data.txt


title: SupT1 0.1% DMSO Rep1

description:
D17-195025
Vehicle treatment
Expression_data.txt

value: 24 hr 0.1% DMSO


title: SupT1 2 ug/mL Dox Rep1

description:
D17-195029
XBP1s transcription activation
Expression_data.txt


title: SupT1 0.1% DMSO Rep2

description:
D17-195026
Vehicle treatment
Expression_data.txt


title: SupT1 0.1% DMSO Rep3

description:
D17-195027
Vehicle treatment
Expression_data.txt


title: SupT1 0.1% DMSO Rep4

description:
D17-195028
Vehicle treatment
Expression_data.txt


title: SupT1 2 ug/mL Dox + 10 uM TMP Rep3

description:
D17-195040
XBP1s and ATF6 transcription activation
Expression_data.txt


title: ChIP-seq in zebrafish ctcf-/- embryos at 48hpf, replicate 2

status: Public on Aug 02 2021

city: Seville

first: José

middle: M.

last: Santos-Pereira

address: Avda. Manuel Siurot s/n

country: Spain

institute: IBiS, Universidad de Sevilla-CSIC

description: ChIP-seq

data_processing:
Reads were aligned using Bowtie
Peaks were called using MACS2 software with  q<0.001
Genome_build: Zebrafish September 2014 (GRCz10/danRer10)
Supplementary_files_format_and_content: Called peaks in narrowPeak format

organism: Danio rerio

source_name: whole embryo

growth_protocol: Embryos were cultivated at 28°C in E3 medium until desired developmental stage

extract_protocol:
Embryos were fixed in 1% paraformaldehide and quenched with 0.125M Glycine. Nuclei were extracted and lysed, and chromatin sonicated in a Covaris M220 sonicator to an average of 300bp fragments. Sonicated chromatin was divided in 6 aliquots and incubated overnight at 4ºC with 2µg of antibody per aliquiot. Immunoprecipitated chromatin was then incubated with magnetic beads, washed, TAGmented with Tn5 transposase (Schmidl et al., 2015) and eluted from beads. Then, chromatin was decrosslinked and DNA was purified using Minelute kit (Qiagen)
Preparation of ChIPmentation libraries was performed as described for ATAC-seq assays in Buenrostro et al., 2015

tag: developmental stage

value: 48 hpf

value: ctcf-/-


title: ChIP-seq in zebrafish ctcf-/- embryos at 48hpf, replicate 1

description: ChIP-seq


title: HiC in zebrafish wild-type embryos at 24hpf, replicate 1

description:
Hi-C
HiC_24h_wt_comb.hic

data_processing:
Reads from biological replicates were pooled and aligned using BWA
Ligation events were detected using Pairtools and filtered for non-ligated and self-ligated events
Binary multiresolution hic files were generated using Juicer Tools Pre
Genome_build: Zebrafish September 2014 (GRCz10/danRer10)
Supplementary_files_format_and_content: multiresolution hic files

extract_protocol:
Embryos were fixed in 1% paraformaldehyde and quenched with 0.125M Glycine. Cell were lyses and extracted nuclei were processed for in-situ HiC preparation as previously described (Rao et al. 2014). Briefly, chromatin was digested with DpnII, fragment-ends were blunted and marked with dATP-biotin, followed by proximity ligation. DNA was extracted after cross-link reversal and sonicated in a Covaris M220 sonicator for fragments between 150-600 bp. Proximity ligation products were enriched using Streptavidin-coated beads.
End-repair, A-tailing and ligation of TruSeq indexing adapters followed standard procedure for Illumina library preparations for paired-end sequencing. Final library was prepared using NEBNext High-Fidelity 2X PCR Master Mix (NEB) and standard TruSeq Primer 1.0 (P5) and TruSeq Primer 2.0 (P7).

value: 24 hpf

value: WT


title: HiC in zebrafish wild-type embryos at 24hpf, replicate 2

description:
Hi-C
HiC_24h_wt_comb.hic


title: ChIP-seq in zebrafish wild-type embryos at 24hpf, replicate 2

description: ChIP-seq


title: MR42D_Washout_Veh_1

status: Public on Jun 22 2021

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

data_processing:
Aligned to hg19 using STAR 2.5.3a
RSEM v1.2.31 for quantification of expressed genes annotated by gencode v19
DESeq2 for differential expression analysis, FDR < 0.05
Genome_build: hg19
Supplementary_files_format_and_content: raw_counts

growth_protocol: Grown in RPMI + 10% FBS

extract_protocol:
Trizol (Life Technologies) extraction, RNEasy (Qiagen) purifcation
Aligent SureSelect Strand-Specific mRNA Library Prep

tag: cell line

value: prostate carcinoma cell line

value: Enzalutamide-resistant

value: Vehicle


title: MR42D_Washout_MDV_3

value: Enzalutamide


title: SupT1 10 uM TMP Rep4

description:
D17-195036
ATF6 transcription activation
Expression_data.txt


title: MR42D_Washout_MDV_1


title: SupT1 2 ug/mL Dox Rep2

description:
D17-195030
XBP1s transcription activation
Expression_data.txt


title: HiC in zebrafish wild-type embryos at 48hpf, replicate 2


title: Sample 2 CEM.cHSF1 water 18h

description:
18h water treatment
D17-190017

data_processing:
Illumina HiSeq Control Software 2.2.58 and RTA 1.18.64 software used for basecalling.
Quality control: Reads were aligned against hg19 using bwa mem v. 0.7.12-r1039 with flags –t 16 –f and mapping rates, fraction of multiply-mapping reads, number of unique 20-mers at the 5’ end of the reads, insert size distributions and fraction of ribosomal RNAs were calculated using dedicated perl scripts and bedtools v. 2.25.0.64 In addition, each resulting bam file was randomly down-sampled to a million reads, which were aligned against hg19 and read density across genomic features were estimated for RNA-Seq-specific quality control metrics.
RNA-Seq mapping and quantitation: Reads were aligned against GRCh38 / ENSEMBL 89 annotation using STAR v. 2.5.3a with flags -runThreadN 8 --runMode alignReads  --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM with --genomeDir pointing to a 75nt-junction GRCh38 STAR suffix array.
Gene expression was quantitated using RSEM v. 1.3.0 with the following flags for all libraries: rsem-calculate-expression --calc-pme --alignments -p 8  --forward-prob 0 against an annotation matching the STAR SA reference. Posterior mean estimates (pme) of counts and estimated RPKM were retrieved.
Genome_build: hg38 / GRCh38
Supplementary_files_format_and_content: Tab-delimited text file containing RPKM values for all hg38 annotated genes (ENSEMBL 89) in each sample (RSEM pme_RPKM output).

source_name: CEM clonal T cells

growth_protocol: The cells were cultured in RPMI-1640 medium (Corning) supplemented with 10% heat-inactivated fetal bovine serum (FBS; CellGro), 1% penicillin/streptomycin/glutamine (CellGro) at 37 °C with 5% CO2(g).

extract_protocol:
Cellular RNA was extracted using the Qiagen RNeasy Plus Mini Kit and QIAshredder homogenization columns.
For RNAseq, RNA integrity and concentration were checked on a Fragment Analyzer (Advanced Analytical) and RNA-seq libraries were prepared using the Kapa mRNA HyperPrep RNA-seq library construction kit (Kapa/Roche), with 7 min fragmentation at 94 °C and 15 PCR cycles of final amplification and duplex barcoding. Libraries were quantified using the Fragment Analyzer (Advanced Analytical) and qPCR before being loaded for single-end sequencing using the Illumina HiSeq 2000 for 40 nucleotides in High Output mode.
polyA-based mRNA capture using RNA-Kapa with TruSeq strand-specific strategy.

treatment_protocol: The cells were treated with either 1ug/ml doxycycline or water for 18h prior to harvesting and RNA extraction.

value: Adult-derived single clonal T cell cell line

value: Bearing dox-inducible cHSF1 transgene

tag: agent

value: water


title: Sample 1 CEM.cHSF1 dox 18h

description:
18h 1 ug/ml Doxycycline (dox) treatment
D17-190020

value: 1 ug/ml Doxycycline


title: Sample 2 CEM.cHSF1 dox 18h

description:
18h 1 ug/ml Doxycycline (dox) treatment
D17-190021


title: Sample 4 CEM.cHSF1 dox 18h

description:
18h 1 ug/ml Doxycycline (dox) treatment
D17-190023


title: Sample 4 CEM.cHSF1 water 18h

description:
18h water treatment
D17-190019


title: MR42D_Washout_Veh_3


title: Sample 3 CEM.cHSF1dox 18h

description:
18h 1 ug/ml Doxycycline (dox) treatment
D17-190022


title: Sample 3 CEM.cHSF1 water 18h

description:
18h water treatment
D17-190018


title: Sample 1 CEM.cHSF1 water 18h

description:
18h water treatment
D17-190016


title: H3K27me3

status: Public on Apr 10 2021

city: ILLKIRCH

first: Delphine

last: Duteil

address: 1 rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Only uniquely mapped reads were retained for further analysis. Peak calling was performed with MACS2 with a qval less than 0.01
Genome_build: mm10
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b). Bed files were obtained from MACS2 peak calling.

source_name: ChIP-seq

extract_protocol:
Nuclei were extracted as described in Joshi 2017
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7  cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

tag: chip antibody

value: H3K27me3 (Active Motif, 39133)

tag: tissue

value: skeletal muscle

value: 10-12 weeks


title: ChIP-seq in zebrafish wild-type embryos at 24hpf, replicate 1

value: CTCF


title: MR42D_Washout_MDV_2


title: Input

description: Input related to GR KO

value: GR(i)skm-/-

tag: age


title: AR

value: AR (C-terminal, IGBMC)


title: MR42D_Washout_Veh_2

tag: treatment


title: Input 2

description: Input related to AR, H3K27me3 and IgG


title: Nelfb-WT_A

status: Public on Mar 18 2021

data_processing:
cellranger mkfastq  v2.1.1; performed on 10X Cell ranger pipeline
cellranger count v2.1.1
Genome_build: mm10
Supplementary_files_format_and_content: .mtx, .tsv: Processed contains single-cell gene expression matrix

source_name: Muscle satellite cells

growth_protocol: Myoblasts were harvested from muscle 72h post injury and immediately purified by FACS (TdTomato+, Alpha-integrin 7+). Myoblasts were kept on ice when possible.

extract_protocol:
Myoblasts were prepared for single-cell RNA-sequencing using a 10 X genomics Chromium Single Cell 3' Reagent kit (cat. No. pn-1000075), according to the manufacturer protocol
Sequencing library were constructed using the 10 X genomics Chromium Single cell 3'v2.2 and 3'v3 Reagent kit (cat. No. pn-1000075), according to the manufacturer protocol

treatment_protocol: Mice were induced with tamoxifen, then skeletal muscle damage through acute intramuscular cardiotoxin injection.

tag: tissue type

value: Skeletal Muscle

tag: cell type

value: Myogenic progenitor (TdT+, ITGA7+)


title: WT_ZF_Embryos_24hpf

status: Public on Apr 05 2021

city: Salt Lake City

first: Bradley

middle: R

last: Cairns

state: UT

address: 2000 Cir of Hope Dr

department: oncological Sciences

institute: Huntsman Cancer institute/HHMI

data_processing:
Reads were aligned to a merged zv10 (chromosomes were labeled 1-25) and dm6 (chromosomes were labeled 2L, 2R, 3L, 3R, 4D, XD, YD) genome using bwa mem (V 0.7.15-r1140, http://bio-bwa.sourceforge.net/bwa.shtml) using the following options -A 1 -B 4 -E 50 -L 0.
HiCexplorer (V3.3, https://hicexplorer.readthedocs.io/en/latest/) hicBuildMatrix was used to create matrix at 10kb, 25kb, 100kb resolutions, using the option --outBam, to extract valid Hi-C reads.
The bam file from the 25kb built matrices replicates were merged using Samtools merge (V1.8, http://www.htslib.org/doc/samtools-merge.html) and that file was further processed to text file with bamToBed using bedtools (V2.22.1, https://bedtools.readthedocs.io/en/latest/)
Genome_build: zv10 & dm6
Supplementary_files_format_and_content: txt.gz bed file format of all valid pairs used in creating HiC contact matrix. This format is useful for anyone to quickly import into other publicially available HiC contact matrice programs (example:juicer)

source_name: WT Tubingen

growth_protocol: Standard zebrafish growth conditions.

extract_protocol:
Embryos were dechorionated with 0.3 mg/ml pronase and then deyolked using deyolking buffer (55 mM NaCl, 3.6 mM KCl, and 1.25 mM NaHCO3). Whole embryos were cross-linked with 1% formaldehyde. Separately, Drosophila S2 spike-in control cells were collected. Washed twice in 1xPBS and cross-linked with 1% formaldehyde. Cell lysis for both was performed on ice with Cell Lysis buffer (10 mM Tris-Cl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630). Drosophila nuclei was spiked into zebrafish embryo nuclei calibrated to represent ~5% of total reads. HiC was performed as origionally described Rao et al., 2014 modified for small cell HIC as described in Diaz et al., 2018.
Samples Ran on Hiseq utilized: library prep was performed using Tn5 tagmentation on DNA according to Picelli, et al. Genome Research 2014 Samples ran on Novaseq utilized: NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (E6240) with NEBNext® Multiplex Oligos for Illumina (Dual Index Primers Set, E7600S)

treatment_protocol: Untreated - Embryos Incubated 28C; Drug treatments: 4hrs DMSO treatment - Embryos inc. 28C - 0.1 percent; 4hrs Flavopiridol treatment - Embryos inc. 28C - 1.5 μM;  4hrs SGC-p300 treatment - Embryos inc. 28C - 20 μg/mL

value: Embryo

value: Untreated


title: Nelfb-WT_1

value: WT


title: GR KO

value: GR (C-terminal, IGBMC, 3249)


title: HiC in zebrafish wild-type embryos at 48hpf, replicate 1

value: 48 hpf


title: Nelfb-KO_B

value: Nelfb-KO


title: Nelfb-KO_3


title: KO2-IgG

data_processing:
Library strategy: CUT&Tag
Nextera adapters were trimmed from sequenced reads with Cutadapt 2.6 (Python 3.7.4);
Trimmed sequences were aligned to mm10 using Bowtie2 version 2.3.4.1 with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700;
Trimmed sequences were aligned to spike-in DNA (Amp - pBluescript II SK(+)) using Bowtie2 version 2.3.4.1 with the following parameters: --very-sensitive ;
Duplicates, non-uniquely aligned reads were filtered from BAMs using Samtools v1.10 (htslib 1.10). Retained mapped and properly paired reads.
Spike-in normalized genome coverage was calculated using bamCoverage v3.3.2 (Deeptools v3.3.2)
Genome_build: mm10

source_name: Muscle Satellite cells

growth_protocol: Myoblasts were cultured in vitro on Matrigel-coated tissue culture sterile dish during progenitor expansion and 4-hydroxy-tamoxifen induction. Myoblasts were maintianed at low confluence throughout in vitro culturing, to avoid cell-cell contacts.

extract_protocol:
Whole cells were bound to concanavalin A beads and permeablized with 0.1% digitonin for faclitating antibody binding. Protein-A tagged Tn5 was added for targeted Clevage and Tagmentation.
Libraries were prepared as recommended in the CUT & Tag protocol by using 21 µl DNA of purified DNA and 2 µl each of uniquely barcoded i5 and i7 universal primers. Libraries were amplified using NEBNext® High-Fidelity 2X PCR Master Mix  (M0541L). Conditions for PCR amplifcation were followed as recommended in the protocol.

treatment_protocol: Ex vivo knockout was induced using 4-hydroxy-tamoxifen, supplemented in growth medium for 72 hours.

value: NELF-BscKO (KO)

value: Myoblasts from Satellite cells

tag: antibody

value: Phospho-Rpb1 CTD (Ser5) (D9N5I) Rabbit mAb #13523 (Cell Sig.Tech Sampler Kit Cat # 54020)


title: KO2-S5


title: KO1-S5


title: EE-Ko2-nE

data_processing:
Library strategy: CUT&Tag
Nextera adapters were trimmed from sequenced reads with Cutadapt 2.6 (Python 3.7.4);
Trimmed sequences were aligned to mm10 using Bowtie2 version 2.3.4.1 with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700;
Trimmed sequences were aligned to spike-in DNA (U00096.3) using Bowtie2 version 2.3.4.1 with the following parameters: --end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant --phred33 -I 10 -X 700;
Duplicates, non-uniquely aligned reads were filtered from BAMs using Samtools v1.10 (htslib 1.10). Retained mapped and properly paired reads.
Spike-in normalized genome coverage was calculated using bamCoverage v3.3.2 (Deeptools v3.3.2)
Genome_build: mm10
Supplementary_files_format_and_content: Normalized genome coverage bigWig for every sample

value: NelfE(Proteintech, Cat#10705-1-AP) + NelfE(F-9) (Santacruz, Cat#SC - 377052) (Mixed 1:1 (Concentration)


title: Wt1-S5

value: Wildtype (WT)


title: KO1-IgG


title: ED-Ko1-nE


title: EA-Wt1-nE


title: EB-Wt2-nE


title: DR-JF-Ott_KO3

data_processing:
Reads aligned with STAR 2.6.0a
featureCounts -s2 v1.6.1 was used for summarization of counts
DESeq2 v1.26.0 was used for Differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: tabluar format with DESeq2 output

source_name: FACS-sorted myogenic progenitor cells from hindlimb skeletal muscle

growth_protocol: Hindlimb skeletal muscle was damaged with cardiotoxin, and provided a 48-hour in vivo recovery period. Skeletal muscle was isolated, mechanically and enzymatically digested, and myogenic progenitor cells FACS-sorted based on TdTomato expression (endogenous expression to all Pax7-expressing adult tissues), and Alpha-Integrin 7 expression. Purified myogenic progenitors  immediately  underwent RNA extraction. At all steps, myogenic progenitors were stored on ice.

extract_protocol:
Total RNA was isolated using a total RNA isolation kit (ThermoFisher cat. No. 12183020) on FACS-purified myogenic progenitor cells (TdT+, AI7+) at the specified timepoint
Total RNA (approx. 350 ng per sample) underwent rRNA depletion with a Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat) (Illumina cat. No. MRZG12324). RNA library preparation proceeded with a KAPA stranded RNA-seq kit (roche 07962169001-KAPA KK8401). Fragmentation/1st strand / 2nd strand end-repair and A-tailing steps proceeded, followed with ligation to  Illumina TruSeq LT Indexes (Illumina FC-121-2001 / FC-121-2002) followed by 8 cycles of PCR enrichment.

treatment_protocol: Skeletal muscle from the hindlimbs was damaged in vivo with cardiotoxin

value: Skeletal muscle (hindlimbs)

value: Myogenic progenitor cells

value: Cardiotoxin


title: EJ-K4me3-Ko

value: H3K4me3(EMD Millipore Cat No. 07-473)


title: Nelfb-WT_B

value: Skeletal Muscle


title: DR-JF-Ott_KO2


title: DR-JF-Ott_KO1


title: EI-K4me3-Wt


title: EF-Ko3-nE


title: DR-JF-Ott_WT3


title: DR-JF-Ott_WT2


title: Nelfb-WT_rep2

data_processing:
Reads aligned with STAR 2.6.0a
featureCounts -s2 v1.6.1 was used for summarization of counts
DESeq2 v1.26.0 was used for Differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: FeatureCount Table

growth_protocol: Myoblasts were harvested from muscle 5-days post injury and immediately purified by FACS (TdTomato+, Alpha-integrin 7+). Myoblasts were kept on ice when possible.

extract_protocol:
Total RNA was isolated using a total RNA isolation kit (ThermoFisher cat. No. 12183020) on FACS-purified myoblasts (TdT+, AI7+) derived from regenerating skeletal muscle 5 days post-injury.
Total RNA (approx. 430 ng per sample) underwent rRNA depletion with a Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat) (Illumina cat. No. MRZG12324). RNA library preparation proceeded with a KAPA stranded RNA-seq kit (roche 07962169001-KAPA KK8401). Fragmentation/1st strand / 2nd strand end-repair and A-tailing steps proceeded, followed with ligation to  Illumina TruSeq LT Indexes (Illumina FC-121-2001 / FC-121-2002) followed by 8 cycles of PCR enrichment.

treatment_protocol: Mice were induced with tamoxifen, then skeletal muscle damage induced with an acute intramuscular cardiotoxin injection.

value: Myogenic progenitor (TdT+, ITGA7+)

value: Adult


title: DR-JF-Ott_WT1


title: Nelfb-KO_rep2


title: Nelfb-KO_rep3


title: Nelfb-KO_rep1


title: Nelfb-WT_rep1


title: Wt1-IgG


title: Ctrl-PolII-S5

data_processing:
Mapping: Satellite cells/Myoblasts
PeakCalling: Uniquely mapped reads were used for peak calling using MACS2
Visualization: Mapped reads were converted to bigWigs with RPKM normalization
Peak calls were converted to bigBed files
Genome_build: MM10
Supplementary_files_format_and_content: narrowPeak [peak information, location]

source_name: Satellite cells/Myoblasts

growth_protocol: Satellite cells isolated from mice muscle tissue were cultured in F10 media with 20% BGS and bFGF (2.5 ng/ml)

extract_protocol:
Cells were fixed with 1% formaldehyde for 20 min and quenched for 10 min in 125 mM glycine. Cells were sonicated in 1% SDS containing sonication buffer for extracting sonicated chromatin
Library was constructed using KAPA HyperPrep Kit (Roche 07962363001-KAPA KK8504 ). End Repair/A-tailing step then ligation of IDT for Illumina TruSeq UD Indexes (Illumina-20022370) followed by dual SPRI size selection Left  1.0 - 0.52 Right and 11 cycles of PCR enrichment.

treatment_protocol: Satellite cells were treated with 4-OHT for 72 hrs for CreERT2 activation. Before proceeding for experiment cells were cultured in 4-OHT free media for 24 hrs

value: PolII-S5 (Abcam Cat.No.ab5131)

value: Satellite cells


title: Ctrl-Pan-PolII

value: Pan-PolII (Millipore Cat.No.05-623)


title: Wt2-S5


title: EC-Wt3-nE


title: Wt2-IgG


title: TGF-beta-Hela-3

status: Public on Feb 17 2021

city: jinan

first: Xuewu

last: You

address: wenhua xi road

country: China

institute: shandong university

data_processing:
1.Basecalling
2.Reads map to the hg19 genome by SOAP to analyze their expression and distribution on the genome.
3.Tags align to miRBase database using blast，indentify known miRNA.
4.Novel miRNA prediction: sRNAs which map to antisense exon、intron or intergenic region of genome and don't map to any other RNA have a prediction of novel miRNAs. The miRNA hairpins are mostly located in intergenic regions,introns or reverse repeat sequence of coding sequence. The characteristic hairpin structure of miRNA precursor can be used to predict novel miRNA. We developed a prediction software mireap(animal/plant) or mirdeep(animal) to predict novel miRNA by exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the unannotated small RNA reads which could be mapped to genome.
5.Statistic the all miRNA expression. Differential expression analysis with DEGseq of known miRNA. Target prediction of known miRNA with miranda and Targetscan.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...
Supplementary_files_format_and_content: tab-delimited text files include Tags number for each Sample ...

source_name: Hela cells

growth_protocol: HeLa cells were cultured in DMEM (Gibco, CA, USA)medium supplemented with 10% fetal bovine serum (FBS, Biological Industries, CT, USA). All cell lines were cultured in a humidified incubator with standard culture conditions (5% CO2, 37°C).

extract_protocol:
The supernatant was collected to isolate exosomes and extract a total of 1 μg RNA as input material for RNA sample preparation.
The library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (Q-PCR) (TaqMan Probe). The final ligation PCR products were sequenced using the BGISEQ-500 platform.

treatment_protocol: HeLa cells were seeded in a 10 cm diameter dish and cultured overnight, exosome-free serum medium with or without 10 ng/ml TGF-β1 was used to continue the culture for another 24 hours.

value: HeLa

value: TGF-beta


title: Hela-3

value: control


title: TGF-beta-Hela-1


title: Hela-2


title: Hela-1


title: Calveolin KD - Vehicle 3

status: Public on Feb 24 2021

type: RNA

first: Gabriela

last: Ferreyra

address: 9000 Rockville Pike - Building 10 room 4D03

department: CCMD

institute: Clinical Center

hyb_protocol: Fragmented labeled cRNA (65 ug per sample) were hybridized for 16 hr at 45C on PrimeView Human Gene  Expression  Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 400 following manufacturer protocols.

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

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

label: Biotin

label_protocol: Total RNA (150 ng) was used as starting material for the synthesis of cDNA and cRNA in vitro transcription and labelling following manufacturer's directions (GeneChip 3′ IVT PLUS Reagent kit, Affymetrix, Santa Clara, CA). The resulting cRNA was fragmented for hybridization

growth_protocol: Human Pulmonary Arterial Endothelial Cells (PAECs) (Lonza Walkersville, MD) were seeded on type I collagen coated plates and cultured in endothelial basal media-2 (EBM-2) supplemented with growth factors (EGM™-2 SingleQuot kit) and 2% FBS (Lonza).

extract_protocol: After stimulation PAECs were lysed in RLT buffer and total RNA was isolated using RNeasy miniprep kits (Qiagen) and quality was evaluated using RNA 6000 Nano LabChip. KD efficiency was evaluated by qRTPCR (80 to 90% efficiency).

treatment_protocol: PAECs (Passage 1)  were transfected with non-targeting siRNA control pool (ON-TARGET plus Non-targeting pool; Dharmacon) or 10 nM siRNA (ON-TARGET plus CAV1; Dharmacon, Lafayette, CO) with DharmaFECT1 transfecting reagent (Dharmacon) as described in the manufacture’s protocol for 48 h follow by 4 h stimulation with or without TNF-alpha 0.5 ng/ml (Sigma, St. Louis, MO). Five complete independent experiments were performed.

tag: Sex

value: Female

value: Pulmonary Arterial Endothelial Cells


title: Calveolin KD - TNF 0.5 ng/ml 4

source_name: siCAV-1 with TNF-alpha stimulation

value: siCAV-1 with TNF-alpha stimulation


title: Ctrl SI - TNF 0.5 ng/ml 5

source_name: siControl with TNF-alpha stimulation

value: siControl with TNF-alpha stimulation


title: Polymer alone (8h) rep2

description: gene_count_matrix.csv --B2_8h

data_processing:
Sequenced paired-end reads were trimmed and mapped to hg19 reference genome using HISAT2.
Read counts per gene estimated using htseq-count
Read count normalisation and differential expresssion analysis performed using DESeq2
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Tab delimited text file containing read counts per gene.

extract_protocol:
RPE cells were lyzed with RLT buffer (Qiagen, cat. no. 79216), extracted and purified with Rneasy Mini Kit (Qiagen, cat no. 74106) following manufacturer's recommended protocol.
Illumina sequencing libraries were constructed using NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB, cat.  no. E7765)

value: hESC-derived

value: polymer alone 8h

tag: passage

tag: culture age

value: 1 to 3 months


title: TGF-beta-Hela-2


title: Ctrl SI - TNF 0.5 ng/ml 3


title: Calveolin KD - TNF 0.5 ng/ml 5


title: Calveolin KD - TNF 0.5 ng/ml 2


title: Ctrl SI - TNF 0.5 ng/ml 4


title: Ctrl SI - Vehicle4

source_name: siControl

value: siControl


title: Ctrl SI - TNF 0.5 ng/ml 1


title: Calveolin KD - Vehicle 5


title: Calveolin KD - Vehicle 4


title: Calveolin KD - Vehicle 2


status: Public on Jan 27 2021

type: protein

city: st louis

first: Cynthia

last: Ma

state: Missouri

address: 4515 Mckinley, 4515 Mckinley

department: Medical Oncology

institute: Washington University

description:
WHIM10_50hr Buparlisib treatment_bioreplicate3_technical replicate3
CM_45_128.3 10-B3-423
xenograft

hyb_protocol: Protein lysate from each sample was spotted to glass slides and probed with over 200 antibodies.  Slides were incubated with primary antibody and primary antibody was then detected using a biotinylated secondary antibody followed by streptavidin-conjugated IRDye 680 fluorophore (LI-COR Biosciences).

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

data_processing:
Raw Data Matrix: raw total fluorescent signal intensity before background subtraction or total protein normalization.
Normalized Data Matrix: signal for each spot is subtracted by the corresponding negative control signal for that spot and followed by total protein normalization.
COMBAT Matrix: Normalized data from each of the 3 RPPA batches (RPPA016, RPPA024, and RPPA027) were read in and merged on overlapping antibodies.  The merged data were then standardized such that each protein has a mean 0 and a unit SD and subjected for batch effect adjustment using COMBAT.

label: antibody

molecule: protein

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

value: pulverized tumor tissue from human:mouse xenograft


description:
WHIM10_50hr Buparlisib treatment_bioreplicate3_technical replicate2
CM_45_128.2 10-B3-423
xenograft

label_protocol: Protein lysate from each sample was spotted to glass slides and probed with over 200  antibodies.  Slides were incubated with primary antibody and primary antibody was then detected using a biotinylated secondary antibody followed by streptavidin-conjugated IRDye 680 fluorophore (LI-COR Biosciences).


title: Calveolin KD - TNF 0.5 ng/ml 3


title: Ctrl SI - Vehicle5


title: Ctrl SI - Vehicle3


title: Calveolin KD - Vehicle 1


title: Ctrl SI - Vehicle2


title: Ctrl SI - Vehicle1


title: Ctrl SI - TNF 0.5 ng/ml 2


description:
WHIM10_50hr Buparlisib treatment_bioreplicate2_technical replicate3
CM_44_127.3 10-B3-429
xenograft


description:
WHIM10_50hr Buparlisib treatment_bioreplicate3_technical replicate1
CM_45_128.1 10-B3-423
xenograft


description:
WHIM10_50hr Buparlisib treatment_bioreplicate2_technical replicate2
CM_44_127.2 10-B3-429
xenograft


description:
WHIM10_50hr Buparlisib treatment_bioreplicate2_technical replicate1
CM_44_127.1 10-B3-429
xenograft


title: Nelfb-WT_rep3

value: Skeletal Muscle

value: Myogenic progenitor (TdT+, ITGA7+)

tag: genotype

value: WT


description:
WHIM10_50hr Buparlisib treatment_bioreplicate1_technical replicate3
CM_43_126.3 10-B3-441
xenograft


description:
WHIM10_50hr Buparlisib treatment_bioreplicate1_technical replicate1
CM_43_126.1 10-B3-441
xenograft


description:
WHIM10_50hr Buparlisib treatment_bioreplicate1_technical replicate2
CM_43_126.2 10-B3-441
xenograft


description:
WHIM10_50hr control_bioreplicate2_technical replicate2
CM_38_121.2 10-C-428
xenograft


title: Calveolin KD - TNF 0.5 ng/ml 1


description:
WHIM10_50hr control_bioreplicate1_technical replicate1
CM_37_120.1 10-C-426
xenograft


description:
WHIM10_50hr control_bioreplicate1_technical replicate2
CM_37_120.2 10-C-426
xenograft


description:
WHIM10_50hr control_bioreplicate3_technical replicate3
CM_39_122.3 10-C-437
xenograft


description:
WHIM10_50hr control_bioreplicate3_technical replicate2
CM_39_122.2 10-C-437
xenograft


description:
WHIM48_50hr Buparlisib treatment_bioreplicate3_technical replicate1
CM_75_158.1 48-B3-601
xenograft


description:
WHIM10_50hr control_bioreplicate2_technical replicate3
CM_38_121.3 10-C-428
xenograft


description:
WHIM48_50hr Buparlisib treatment_bioreplicate3_technical replicate2
CM_75_158.2 48-B3-601
xenograft


description:
WHIM10_50hr control_bioreplicate2_technical replicate1
CM_38_121.1 10-C-428
xenograft


description:
WHIM48_50hr Buparlisib treatment_bioreplicate3_technical replicate3
CM_75_158.3 48-B3-601
xenograft


description:
WHIM10_50hr control_bioreplicate3_technical replicate1
CM_39_122.1 10-C-437
xenograft


description:
WHIM48_50hr Buparlisib treatment_bioreplicate2_technical replicate2
CM_74_157.2 48-B3-586
xenograft


description:
WHIM48_50hr Buparlisib treatment_bioreplicate1_technical replicate3
CM_73_156.3 48-B3-582
xenograft


description:
WHIM10_50hr control_bioreplicate1_technical replicate3
CM_37_120.3 10-C-426
xenograft


description:
WHIM48_50hr control_bioreplicate3_technical replicate2
CM_72_155.2 48-V-597
xenograft


description:
WHIM48_50hr Buparlisib treatment_bioreplicate1_technical replicate2
CM_73_156.2 48-B3-582
xenograft


description:
WHIM48_50hr control_bioreplicate3_technical replicate3
CM_72_155.3 48-V-597
xenograft


description:
WHIM48_50hr control_bioreplicate2_technical replicate1
CM_71_154.1 48-V-594
xenograft


description:
WHIM48_50hr control_bioreplicate1_technical replicate3
CM_70_153.3 48-V-587
xenograft


description:
WHIM48_50hr control_bioreplicate2_technical replicate2
CM_71_154.2 48-V-594
xenograft


description:
WHIM48_50hr Buparlisib treatment_bioreplicate2_technical replicate3
CM_74_157.3 48-B3-586
xenograft


description:
WHIM48_50hr control_bioreplicate1_technical replicate2
CM_70_153.2 48-V-587
xenograft


description:
WHIM48_50hr Buparlisib treatment_bioreplicate1_technical replicate1
CM_73_156.1 48-B3-582
xenograft


description:
WHIM48_50hr control_bioreplicate1_technical replicate1
CM_70_153.1 48-V-587
xenograft


description:
WHIM5_50hr Buparlisib treatment_bioreplicate3_technical replicate3
CM_69_152.3 5-B3-566
xenograft


description:
WHIM5_50hr Buparlisib treatment_bioreplicate3_technical replicate1
CM_69_152.1 5-B3-566
xenograft


description:
WHIM5_50hr Buparlisib treatment_bioreplicate2_technical replicate1
CM_68_151.1 5-B3-565
xenograft


description:
WHIM48_50hr control_bioreplicate3_technical replicate1
CM_72_155.1 48-V-597
xenograft


description:
WHIM5_50hr Buparlisib treatment_bioreplicate2_technical replicate2
CM_68_151.2 5-B3-565
xenograft


description:
WHIM5_50hr Buparlisib treatment_bioreplicate1_technical replicate3
CM_67_150.3 5-B3-551
xenograft


description:
WHIM48_50hr control_bioreplicate2_technical replicate3
CM_71_154.3 48-V-594
xenograft


description:
WHIM5_50hr Buparlisib treatment_bioreplicate2_technical replicate3
CM_68_151.3 5-B3-565
xenograft


description:
WHIM48_50hr Buparlisib treatment_bioreplicate2_technical replicate1
CM_74_157.1 48-B3-586
xenograft


description:
WHIM5_50hr control_bioreplicate3_technical replicate1
CM_66_149.1 5-V-563
xenograft


description:
WHIM5_50hr Buparlisib treatment_bioreplicate1_technical replicate2
CM_67_150.2 5-B3-551
xenograft


description:
WHIM5_50hr control_bioreplicate3_technical replicate2
CM_66_149.2 5-V-563
xenograft


description:
WHIM5_50hr Buparlisib treatment_bioreplicate1_technical replicate1
CM_67_150.1 5-B3-551
xenograft


description:
WHIM5_50hr control_bioreplicate2_technical replicate1
CM_65_148.1 5-V-562
xenograft


description:
WHIM5_50hr control_bioreplicate2_technical replicate3
CM_65_148.3 5-V-562
xenograft


description:
WHIM5_50hr control_bioreplicate3_technical replicate3
CM_66_149.3 5-V-563
xenograft


description:
WHIM5_50hr control_bioreplicate2_technical replicate2
CM_65_148.2 5-V-562
xenograft


description:
WHIM5_50hr control_bioreplicate1_technical replicate1
CM_64_147.1 5-V-557
xenograft


description:
WHIM5_50hr control_bioreplicate1_technical replicate3
CM_64_147.3 5-V-557
xenograft


description:
WHIM5_50hr Buparlisib treatment_bioreplicate3_technical replicate2
CM_69_152.2 5-B3-566
xenograft


description:
WHIM5_50hr control_bioreplicate1_technical replicate2
CM_64_147.2 5-V-557
xenograft


description:
WHIM36_50hr Buparlisib treatment_bioreplicate3_technical replicate2
CM_63_146.2 36-B3-507^
xenograft


description:
WHIM36_50hr Buparlisib treatment_bioreplicate3_technical replicate3
CM_63_146.3 36-B3-507^
xenograft


description:
WHIM36_50hr Buparlisib treatment_bioreplicate3_technical replicate1
CM_63_146.1 36-B3-507^
xenograft


description:
WHIM36_50hr Buparlisib treatment_bioreplicate2_technical replicate3
CM_62_145.3 36-B3-501
xenograft


description:
WHIM36_50hr Buparlisib treatment_bioreplicate1_technical replicate3
CM_61_144.3 36-B3-499
xenograft


description:
WHIM36_50hr Buparlisib treatment_bioreplicate2_technical replicate1
CM_62_145.1 36-B3-501
xenograft


description:
WHIM36_50hr control_bioreplicate3_technical replicate1
CM_60_143.1 36-V-503
xenograft


description:
WHIM36_50hr control_bioreplicate2_technical replicate3
CM_59_142.3 36-V-498
xenograft


description:
WHIM36_50hr control_bioreplicate3_technical replicate3
CM_60_143.3 36-V-503
xenograft


description:
WHIM36_50hr Buparlisib treatment_bioreplicate1_technical replicate1
CM_61_144.1 36-B3-499
xenograft


description:
WHIM36_50hr control_bioreplicate3_technical replicate2
CM_60_143.2 36-V-503
xenograft


description:
WHIM36_50hr control_bioreplicate2_technical replicate2
CM_59_142.2 36-V-498
xenograft


description:
WHIM36_50hr control_bioreplicate2_technical replicate1
CM_59_142.1 36-V-498
xenograft


description:
WHIM36_50hr control_bioreplicate1_technical replicate3
CM_58_141.3 36-V-494
xenograft


description:
WHIM36_50hr control_bioreplicate1_technical replicate2
CM_58_141.2 36-V-494
xenograft


description:
WHIM36_50hr control_bioreplicate1_technical replicate1
CM_58_141.1 36-V-494
xenograft


description:
WHIM4_50hr Buparlisib treatment_bioreplicate3_technical replicate3
CM_22_64.3 4-B3-560
xenograft


description:
WHIM4_50hr Buparlisib treatment_bioreplicate3_technical replicate2
CM_22_64.2 4-B3-560
xenograft


description:
WHIM4_50hr Buparlisib treatment_bioreplicate2_technical replicate3
CM_21_63.3 4-B3-559
xenograft


description:
WHIM4_50hr Buparlisib treatment_bioreplicate1_technical replicate3
CM_19_62.3 4-B3-556
xenograft


description:
WHIM4_50hr Buparlisib treatment_bioreplicate3_technical replicate1
CM_22_64.1 4-B3-560
xenograft


description:
WHIM36_50hr Buparlisib treatment_bioreplicate2_technical replicate2
CM_62_145.2 36-B3-501
xenograft


description:
WHIM4_50hr Buparlisib treatment_bioreplicate2_technical replicate1
CM_21_63.1 4-B3-559
xenograft


description:
WHIM4_50hr Buparlisib treatment_bioreplicate2_technical replicate2
CM_21_63.2 4-B3-559
xenograft


description:
WHIM4_50hr Buparlisib treatment_bioreplicate1_technical replicate2
CM_19_62.2 4-B3-556
xenograft


description:
WHIM4_50hr Buparlisib treatment_bioreplicate1_technical replicate1
CM_19_62.1 4-B3-556
xenograft


description:
WHIM4_50hr control_bioreplicate2_technical replicate3
CM_16_61.3 4-V4-564
xenograft


description:
WHIM36_50hr Buparlisib treatment_bioreplicate1_technical replicate2
CM_61_144.2 36-B3-499
xenograft


description:
WHIM4_50hr control_bioreplicate2_technical replicate1
CM_16_61.1 4-V4-564
xenograft


description:
WHIM4_50hr control_bioreplicate2_technical replicate2
CM_16_61.2 4-V4-564
xenograft


description:
WHIM4_50hr control_bioreplicate1_technical replicate3
CM_14_60.3 4-V4-561
xenograft


description:
WHIM4_50hr control_bioreplicate1_technical replicate1
CM_14_60.1 4-V4-561
xenograft


description:
WHIM34_50hr Buparlisib treatment_bioreplicate4_technical replicate3
CM_59_101.3 34-B3-478
xenograft


description:
WHIM34_50hr Buparlisib treatment_bioreplicate3_technical replicate3
CM_58_100.3 34-B3-470
xenograft


description:
WHIM34_50hr Buparlisib treatment_bioreplicate3_technical replicate1
CM_58_100.1 34-B3-470
xenograft


description:
WHIM34_50hr Buparlisib treatment_bioreplicate4_technical replicate1
CM_59_101.1 34-B3-478
xenograft


description:
WHIM34_50hr Buparlisib treatment_bioreplicate2_technical replicate3
CM_57_99.3 34-B3-468
xenograft


description:
WHIM34_50hr Buparlisib treatment_bioreplicate3_technical replicate2
CM_58_100.2 34-B3-470
xenograft


description:
WHIM34_50hr Buparlisib treatment_bioreplicate1_technical replicate2
CM_56_98.2 34-B3-463
xenograft


description:
WHIM34_50hr Buparlisib treatment_bioreplicate2_technical replicate1
CM_57_99.1 34-B3-468
xenograft


description:
WHIM34_50hr Buparlisib treatment_bioreplicate1_technical replicate1
CM_56_98.1 34-B3-463
xenograft


description:
WHIM34_50hr Buparlisib treatment_bioreplicate2_technical replicate2
CM_57_99.2 34-B3-468
xenograft


description:
WHIM34_50hr control_bioreplicate4_technical replicate3
CM_55_97.3 34-V4-466
xenograft


description:
WHIM34_50hr Buparlisib treatment_bioreplicate4_technical replicate2
CM_59_101.2 34-B3-478
xenograft


description:
WHIM4_50hr control_bioreplicate1_technical replicate2
CM_14_60.2 4-V4-561
xenograft


description:
WHIM34_50hr control_bioreplicate3_technical replicate3
CM_54_96.3 34-V4-461
xenograft


description:
WHIM34_50hr control_bioreplicate4_technical replicate2
CM_55_97.2 34-V4-466
xenograft


description:
WHIM34_50hr control_bioreplicate4_technical replicate1
CM_55_97.1 34-V4-466
xenograft


description:
WHIM34_50hr control_bioreplicate3_technical replicate2
CM_54_96.2 34-V4-461
xenograft


description:
WHIM34_50hr control_bioreplicate2_technical replicate3
CM_53_95.3 34-V4-458
xenograft


description:
WHIM34_50hr control_bioreplicate3_technical replicate1
CM_54_96.1 34-V4-461
xenograft


description:
WHIM34_50hr control_bioreplicate1_technical replicate3
CM_52_94.3 34-V4-452
xenograft


description:
WHIM34_50hr control_bioreplicate1_technical replicate1
CM_52_94.1 34-V4-452
xenograft


description:
WHIM34_50hr control_bioreplicate2_technical replicate2
CM_53_95.2 34-V4-458
xenograft


description:
WHIM34_50hr control_bioreplicate1_technical replicate2
CM_52_94.2 34-V4-452
xenograft


description:
WHIM31_50hr Buparlisib treatment_bioreplicate3_technical replicate3
CM_51_93.3 31-B3-338
xenograft


description:
WHIM34_50hr control_bioreplicate2_technical replicate1
CM_53_95.1 34-V4-458
xenograft


description:
WHIM31_50hr Buparlisib treatment_bioreplicate3_technical replicate1
CM_51_93.1 31-B3-338
xenograft


description:
WHIM31_50hr Buparlisib treatment_bioreplicate2_technical replicate1
CM_50_92.1 31-B3-337
xenograft


description:
WHIM34_50hr Buparlisib treatment_bioreplicate1_technical replicate3
CM_56_98.3 34-B3-463
xenograft


description:
WHIM31_50hr Buparlisib treatment_bioreplicate1_technical replicate2
CM_49_91.2 31-B3-336
xenograft


description:
WHIM31_50hr Buparlisib treatment_bioreplicate3_technical replicate2
CM_51_93.2 31-B3-338
xenograft


description:
WHIM31_50hr Buparlisib treatment_bioreplicate2_technical replicate2
CM_50_92.2 31-B3-337
xenograft


description:
WHIM31_50hr control_bioreplicate3_technical replicate3
CM_48_90.3 31-V4-335
xenograft


description:
WHIM31_50hr control_bioreplicate3_technical replicate2
CM_48_90.2 31-V4-335
xenograft


description:
WHIM31_50hr Buparlisib treatment_bioreplicate1_technical replicate1
CM_49_91.1 31-B3-336
xenograft


description:
WHIM31_50hr Buparlisib treatment_bioreplicate2_technical replicate3
CM_50_92.3 31-B3-337
xenograft


description:
WHIM31_50hr control_bioreplicate2_technical replicate2
CM_47_89.2 31-V4-316
xenograft


description:
WHIM31_50hr control_bioreplicate3_technical replicate1
CM_48_90.1 31-V4-335
xenograft


description:
WHIM31_50hr control_bioreplicate1_technical replicate3
CM_46_88.3 31-V4-315
xenograft


description:
WHIM31_50hr control_bioreplicate2_technical replicate1
CM_47_89.1 31-V4-316
xenograft


description:
WHIM31_50hr Buparlisib treatment_bioreplicate1_technical replicate3
CM_49_91.3 31-B3-336
xenograft


description:
WHIM31_50hr control_bioreplicate1_technical replicate2
CM_46_88.2 31-V4-315
xenograft


description:
WHIM31_50hr control_bioreplicate1_technical replicate1
CM_46_88.1 31-V4-315
xenograft


description:
WHIM31_50hr control_bioreplicate2_technical replicate3
CM_47_89.3 31-V4-316
xenograft


description:
WHIM29_50hr Buparlisib treatment_bioreplicate1_technical replicate3
CM_43_85.3 29-B3-312
xenograft


description:
WHIM29_50hr Buparlisib treatment_bioreplicate1_technical replicate3
CM_45_87.3 29-B3-314
xenograft


description:
WHIM29_50hr control_bioreplicate3_technical replicate3
CM_42_84.3 29-V4-311
xenograft


description:
WHIM29_50hr Buparlisib treatment_bioreplicate2_technical replicate2
CM_44_86.2 29-B3-313
xenograft


description:
WHIM29_50hr Buparlisib treatment_bioreplicate2_technical replicate3
CM_44_86.3 29-B3-313
xenograft


description:
WHIM29_50hr Buparlisib treatment_bioreplicate1_technical replicate1
CM_45_87.1 29-B3-314
xenograft


description:
WHIM29_50hr control_bioreplicate2_technical replicate1
CM_41_83.1 29-V4-300
xenograft


description:
WHIM29_50hr control_bioreplicate1_technical replicate3
CM_40_82.3 29-V4-291
xenograft


description:
WHIM25_50hr Buparlisib treatment_bioreplicate2_technical replicate3
CM_39_81.3 25-B3-185
xenograft


description:
WHIM29_50hr Buparlisib treatment_bioreplicate1_technical replicate2
CM_43_85.2 29-B3-312
xenograft


description:
WHIM29_50hr control_bioreplicate2_technical replicate3
CM_41_83.3 29-V4-300
xenograft


description:
WHIM29_50hr control_bioreplicate3_technical replicate2
CM_42_84.2 29-V4-311
xenograft


description:
WHIM29_50hr control_bioreplicate3_technical replicate1
CM_42_84.1 29-V4-311
xenograft


description:
WHIM29_50hr control_bioreplicate1_technical replicate1
CM_40_82.1 29-V4-291
xenograft


description:
WHIM29_50hr control_bioreplicate2_technical replicate2
CM_41_83.2 29-V4-300
xenograft


description:
WHIM29_50hr control_bioreplicate1_technical replicate2
CM_40_82.2 29-V4-291
xenograft


description:
WHIM25_50hr Buparlisib treatment_bioreplicate2_technical replicate2
CM_39_81.2 25-B3-185
xenograft


description:
WHIM29_50hr Buparlisib treatment_bioreplicate1_technical replicate1
CM_43_85.1 29-B3-312
xenograft


description:
WHIM29_50hr Buparlisib treatment_bioreplicate1_technical replicate2
CM_45_87.2 29-B3-314
xenograft


description:
WHIM29_50hr Buparlisib treatment_bioreplicate2_technical replicate1
CM_44_86.1 29-B3-313
xenograft


description:
WHIM25_50hr Buparlisib treatment_bioreplicate1_technical replicate3
CM_38_80.3 25-B3-184
xenograft


description:
WHIM25_50hr Buparlisib treatment_bioreplicate2_technical replicate1
CM_39_81.1 25-B3-185
xenograft


description:
WHIM25_50hr Buparlisib treatment_bioreplicate1_technical replicate2
CM_38_80.2 25-B3-184
xenograft


description:
WHIM25_50hr control_bioreplicate1_technical replicate1
CM_36_78.1 25-V4-182
xenograft


description:
WHIM25_50hr control_bioreplicate2_technical replicate1
CM_37_79.1 25-V4-183
xenograft


description:
WHIM14_50hr Buparlisib treatment_bioreplicate4_technical replicate3
CM_35_77.3 14-B3-388
xenograft


description:
WHIM25_50hr Buparlisib treatment_bioreplicate1_technical replicate1
CM_38_80.1 25-B3-184
xenograft


description:
WHIM14_50hr Buparlisib treatment_bioreplicate4_technical replicate1
CM_35_77.1 14-B3-388
xenograft


description:
WHIM14_50hr Buparlisib treatment_bioreplicate3_technical replicate3
CM_34_76.3 14-B3-387
xenograft


description:
WHIM25_50hr control_bioreplicate2_technical replicate2
CM_37_79.2 25-V4-183
xenograft


description:
WHIM14_50hr Buparlisib treatment_bioreplicate3_technical replicate1
CM_34_76.1 14-B3-387
xenograft


description:
WHIM25_50hr control_bioreplicate1_technical replicate3
CM_36_78.3 25-V4-182
xenograft


description:
WHIM14_50hr Buparlisib treatment_bioreplicate4_technical replicate2
CM_35_77.2 14-B3-388
xenograft


description:
WHIM25_50hr control_bioreplicate1_technical replicate2
CM_36_78.2 25-V4-182
xenograft


description:
WHIM14_50hr Buparlisib treatment_bioreplicate2_technical replicate3
CM_33_75.3 14-B3-386
xenograft


description:
WHIM14_50hr Buparlisib treatment_bioreplicate2_technical replicate2
CM_33_75.2 14-B3-386
xenograft


description:
WHIM14_50hr Buparlisib treatment_bioreplicate3_technical replicate2
CM_34_76.2 14-B3-387
xenograft


description:
WHIM14_50hr control_bioreplicate4_technical replicate2
CM_31_73.2 14-V4-384
xenograft


description:
WHIM14_50hr control_bioreplicate4_technical replicate1
CM_31_73.1 14-V4-384
xenograft


description:
WHIM14_50hr control_bioreplicate3_technical replicate2
CM_30_72.2 14-V4-383
xenograft


description:
WHIM14_50hr Buparlisib treatment_bioreplicate2_technical replicate1
CM_33_75.1 14-B3-386
xenograft


description:
WHIM14_50hr control_bioreplicate3_technical replicate3
CM_30_72.3 14-V4-383
xenograft


description:
WHIM14_50hr control_bioreplicate3_technical replicate1
CM_30_72.1 14-V4-383
xenograft


description:
WHIM14_50hr control_bioreplicate1_technical replicate3
CM_28_70.3 14-V4-381
xenograft


description:
WHIM14_50hr control_bioreplicate4_technical replicate3
CM_31_73.3 14-V4-384
xenograft


description:
WHIM14_50hr Buparlisib treatment_bioreplicate1_technical replicate3
CM_32_74.3 14-B3-385
xenograft


description:
WHIM14_50hr Buparlisib treatment_bioreplicate1_technical replicate2
CM_32_74.2 14-B3-385
xenograft


description:
WHIM14_50hr control_bioreplicate1_technical replicate2
CM_28_70.2 14-V4-381
xenograft


description:
WHIM14_50hr control_bioreplicate2_technical replicate3
CM_29_71.3 14-V4-382
xenograft


description:
WHIM25_50hr control_bioreplicate2_technical replicate3
CM_37_79.3 25-V4-183
xenograft


description:
WHIM14_50hr Buparlisib treatment_bioreplicate1_technical replicate1
CM_32_74.1 14-B3-385
xenograft


description:
WHIM13_50hr Buparlisib treatment_bioreplicate2_technical replicate1
CM_27_69.1 13-B3-290
xenograft


description:
WHIM14_50hr control_bioreplicate2_technical replicate2
CM_29_71.2 14-V4-382
xenograft


description:
WHIM13_50hr Buparlisib treatment_bioreplicate1_technical replicate3
CM_26_68.3 13-B3-289
xenograft


description:
WHIM13_50hr Buparlisib treatment_bioreplicate1_technical replicate2
CM_26_68.2 13-B3-289
xenograft


description:
WHIM13_50hr control_bioreplicate3_technical replicate3
CM_25_67.3 13-V4-288
xenograft


description:
WHIM13_50hr control_bioreplicate3_technical replicate2
CM_25_67.2 13-V4-288
xenograft


description:
WHIM14_50hr control_bioreplicate2_technical replicate1
CM_29_71.1 14-V4-382
xenograft


description:
WHIM13_50hr control_bioreplicate2_technical replicate2
CM_24_66.2 13-V4-273
xenograft


description:
WHIM13_50hr control_bioreplicate1_technical replicate3
CM_23_65.3 13-V4-268
xenograft


description:
WHIM13_50hr control_bioreplicate1_technical replicate2
CM_23_65.2 13-V4-268
xenograft


description:
WHIM13_50hr Buparlisib treatment_bioreplicate1_technical replicate1
CM_26_68.1 13-B3-289
xenograft


description:
WHIM13_50hr Buparlisib treatment_bioreplicate2_technical replicate2
CM_27_69.2 13-B3-290
xenograft


description:
WHIM13_50hr Buparlisib treatment_bioreplicate2_technical replicate3
CM_27_69.3 13-B3-290
xenograft


description:
WHIM13_50hr control_bioreplicate2_technical replicate3
CM_24_66.3 13-V4-273
xenograft


description:
WHIM3_50hr Buparlisib treatment_bioreplicate4_technical replicate3
CM_9_58.3 3-B3-416
xenograft


description:
WHIM3_50hr Buparlisib treatment_bioreplicate5_technical replicate2
CM_10_59.2 3-B3-417
xenograft


description:
WHIM3_50hr Buparlisib treatment_bioreplicate5_technical replicate3
CM_10_59.3 3-B3-417
xenograft


description:
WHIM3_50hr Buparlisib treatment_bioreplicate5_technical replicate1
CM_10_59.1 3-B3-417
xenograft


description:
WHIM3_50hr Buparlisib treatment_bioreplicate4_technical replicate2
CM_9_58.2 3-B3-416
xenograft


description:
WHIM14_50hr control_bioreplicate1_technical replicate1
CM_28_70.1 14-V4-381
xenograft


description:
WHIM3_50hr Buparlisib treatment_bioreplicate3_technical replicate2
CM_8_57.2 3-B3-415
xenograft


description:
WHIM3_50hr Buparlisib treatment_bioreplicate3_technical replicate1
CM_8_57.1 3-B3-415
xenograft


description:
WHIM3_50hr Buparlisib treatment_bioreplicate3_technical replicate3
CM_8_57.3 3-B3-415
xenograft


description:
WHIM3_50hr Buparlisib treatment_bioreplicate2_technical replicate3
CM_7_56.3 3-B3-414
xenograft


description:
WHIM3_50hr Buparlisib treatment_bioreplicate1_technical replicate3
CM_6_55.3 3-B3-413
xenograft


description:
WHIM3_50hr Buparlisib treatment_bioreplicate1_technical replicate1
CM_6_55.1 3-B3-413
xenograft


description:
WHIM3_50hr Buparlisib treatment_bioreplicate4_technical replicate1
CM_9_58.1 3-B3-416
xenograft


description:
WHIM3_50hr Buparlisib treatment_bioreplicate1_technical replicate2
CM_6_55.2 3-B3-413
xenograft


description:
WHIM13_50hr control_bioreplicate3_technical replicate1
CM_25_67.1 13-V4-288
xenograft


description:
WHIM3_50hr control_bioreplicate5_technical replicate3
CM_5_54.3 3-V4-412
xenograft


description:
WHIM3_50hr Buparlisib treatment_bioreplicate2_technical replicate1
CM_7_56.1 3-B3-414
xenograft


description:
WHIM13_50hr control_bioreplicate2_technical replicate1
CM_24_66.1 13-V4-273
xenograft


description:
WHIM3_50hr Buparlisib treatment_bioreplicate2_technical replicate2
CM_7_56.2 3-B3-414
xenograft


description:
WHIM3_50hr control_bioreplicate4_technical replicate2
CM_4_53.2 3-V4-411
xenograft


description:
WHIM3_50hr control_bioreplicate4_technical replicate3
CM_4_53.3 3-V4-411
xenograft


description:
WHIM3_50hr control_bioreplicate3_technical replicate3
CM_3_52.3 3-V4-410
xenograft


description:
WHIM13_50hr control_bioreplicate1_technical replicate1
CM_23_65.1 13-V4-268
xenograft


description:
WHIM3_50hr control_bioreplicate2_technical replicate1
CM_2_51.1 3-V4-409
xenograft


description:
WHIM3_50hr control_bioreplicate3_technical replicate1
CM_3_52.1 3-V4-410
xenograft


description:
WHIM3_50hr control_bioreplicate1_technical replicate2
CM_1_50.2 3-V4-408
xenograft


description:
WHIM4_50hr control_bioreplicate3_technical replicate3
CM_93_93.3   4-V4-564
xenograft
GSM2687170

source_name: WU PDX WHIM4_50hr control_bioreplicate3_technical replicate3


description:
WHIM3_50hr control_bioreplicate5_technical replicate2
CM_5_54.2 3-V4-412
xenograft


description:
WHIM3_50hr control_bioreplicate1_technical replicate1
CM_1_50.1 3-V4-408
xenograft


description:
WHIM4_50hr control_bioreplicate3_technical replicate1
CM_93_93.1   4-V4-564
xenograft
GSM2687168

source_name: WU PDX WHIM4_50hr control_bioreplicate3_technical replicate1


description:
WHIM3_50hr control_bioreplicate4_technical replicate1
CM_4_53.1 3-V4-411
xenograft


description:
WHIM4_50hr control_bioreplicate2_technical replicate3
CM_92_92.3      4-V4-562
xenograft
GSM2687167

source_name: WU PDX WHIM4_50hr control_bioreplicate2_technical replicate3


description:
WHIM3_50hr control_bioreplicate2_technical replicate3
CM_2_51.3 3-V4-409
xenograft


description:
WHIM3_50hr control_bioreplicate3_technical replicate2
CM_3_52.2 3-V4-410
xenograft


description:
WHIM4_50hr control_bioreplicate1_technical replicate3
CM_91_91.3     4-V4-561
xenograft
GSM2687164

source_name: WU PDX WHIM4_50hr control_bioreplicate1_technical replicate3


description:
WHIM4_50hr Buparlisib treatment_bioreplicate4_technical replicate1
CM_90_90.1   4-B3-560
xenograft
GSM2687159

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate4_technical replicate1


description:
WHIM4_50hr Buparlisib treatment_bioreplicate4_technical replicate2
CM_90_90.2   4-B3-560
xenograft
GSM2687160

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate4_technical replicate2


description:
WHIM4_50hr control_bioreplicate1_technical replicate1
CM_91_91.1   4-V4-561
xenograft
GSM2687162

source_name: WU PDX WHIM4_50hr control_bioreplicate1_technical replicate1


description:
WHIM3_50hr control_bioreplicate2_technical replicate2
CM_2_51.2 3-V4-409
xenograft


description:
WHIM3_50hr control_bioreplicate1_technical replicate3
CM_1_50.3 3-V4-408
xenograft


description:
WHIM4_50hr Buparlisib treatment_bioreplicate3_technical replicate2
CM_89_89.2   4-B3-559
xenograft
GSM2687157

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate3_technical replicate2


description:
WHIM4_50hr Buparlisib treatment_bioreplicate2_technical replicate2
CM_88_88.2   4-B3-557
xenograft
GSM2687154

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate2_technical replicate2


description:
WHIM4_50hr control_bioreplicate3_technical replicate2
CM_93_93.2   4-V4-564
xenograft
GSM2687169

source_name: WU PDX WHIM4_50hr control_bioreplicate3_technical replicate2


description:
WHIM4_50hr Buparlisib treatment_bioreplicate1_technical replicate3
CM_87_87.3   4-B3-556
xenograft
GSM2687152

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate1_technical replicate3


description:
WHIM4_50hr Buparlisib treatment_bioreplicate1_technical replicate2
CM_87_87.2   4-B3-556
xenograft
GSM2687151

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate1_technical replicate2


description:
WHIM21_50hr control_bioreplicate2_technical replicate3
CM_77_77.3   21-V4-539
xenograft
GSM2687122

source_name: WU PDX WHIM21_50hr control_bioreplicate2_technical replicate3


description:
WHIM21_50hr control_bioreplicate3_technical replicate1
CM_78_78.1   21-V4-540
xenograft
GSM2687123

source_name: WU PDX WHIM21_50hr control_bioreplicate3_technical replicate1


description:
WHIM21_50hr control_bioreplicate3_technical replicate2
CM_78_78.2   21-V4-540
xenograft
GSM2687124

source_name: WU PDX WHIM21_50hr control_bioreplicate3_technical replicate2


description:
WHIM21_50hr control_bioreplicate3_technical replicate3
CM_78_78.3   21-V4-540
xenograft
GSM2687125

source_name: WU PDX WHIM21_50hr control_bioreplicate3_technical replicate3


description:
WHIM3_50hr control_bioreplicate5_technical replicate1
CM_5_54.1 3-V4-412
xenograft


description:
WHIM4_50hr control_bioreplicate2_technical replicate2
CM_92_92.2     4-V4-562
xenograft
GSM2687166

source_name: WU PDX WHIM4_50hr control_bioreplicate2_technical replicate2


description:
WHIM21_50hr control_bioreplicate1_technical replicate2
CM_76_76.2   21-V4-538
xenograft
GSM2687118

source_name: WU PDX WHIM21_50hr control_bioreplicate1_technical replicate2


description:
WHIM4_50hr Buparlisib treatment_bioreplicate4_technical replicate3
CM_90_90.3   4-B3-560
xenograft
GSM2687161

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate4_technical replicate3


description:
WHIM4_50hr control_bioreplicate2_technical replicate1
CM_92_92.1   4-V4-562
xenograft
GSM2687165

source_name: WU PDX WHIM4_50hr control_bioreplicate2_technical replicate1


description:
WHIM4_50hr Buparlisib treatment_bioreplicate3_technical replicate1
CM_89_89.1   4-B3-559
xenograft
GSM2687156

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate3_technical replicate1


description:
WHIM4_50hr Buparlisib treatment_bioreplicate3_technical replicate3
CM_89_89.3   4-B3-559
xenograft
GSM2687158

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate3_technical replicate3


description:
WHIM21_50hr Buparlisib treatment_bioreplicate3_technical replicate2
CM_75_75.2   21-B3-537
xenograft
GSM2687115

source_name: WU PDX WHIM21_50hr Buparlisib treatment_bioreplicate3_technical replicate2


description:
WHIM21_50hr Buparlisib treatment_bioreplicate3_technical replicate3
CM_75_75.3   21-B3-537
xenograft
GSM2687116

source_name: WU PDX WHIM21_50hr Buparlisib treatment_bioreplicate3_technical replicate3


description:
WHIM21_50hr Buparlisib treatment_bioreplicate2_technical replicate2
CM_74_74.2   21-B3-535
xenograft
GSM2687112

source_name: WU PDX WHIM21_50hr Buparlisib treatment_bioreplicate2_technical replicate2


description:
WHIM21_50hr Buparlisib treatment_bioreplicate1_technical replicate2
CM_73_73.2   21-B3-534
xenograft
GSM2687109

source_name: WU PDX WHIM21_50hr Buparlisib treatment_bioreplicate1_technical replicate2


description:
WHIM4_50hr Buparlisib treatment_bioreplicate2_technical replicate3
CM_88_88.3   4-B3-557
xenograft
GSM2687155

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate2_technical replicate3


description:
WHIM21_50hr Buparlisib treatment_bioreplicate1_technical replicate3
CM_73_73.3   21-B3-534
xenograft
GSM2687110

source_name: WU PDX WHIM21_50hr Buparlisib treatment_bioreplicate1_technical replicate3


description:
WHIM21_50hr Buparlisib treatment_bioreplicate1_technical replicate1
CM_73_73.1   21-B3-534
xenograft
GSM2687108

source_name: WU PDX WHIM21_50hr Buparlisib treatment_bioreplicate1_technical replicate1


description:
WHIM21_50hr control_bioreplicate1_technical replicate1
CM_76_76.1   21-V4-538
xenograft
GSM2687117

source_name: WU PDX WHIM21_50hr control_bioreplicate1_technical replicate1


description:
WHIM6_50hr control_bioreplicate3_technical replicate2
CM_62_62.2     6-V4-434
xenograft
GSM2687076

source_name: WU PDX WHIM6_50hr control_bioreplicate3_technical replicate2


description:
WHIM6_50hr control_bioreplicate3_technical replicate3
CM_62_62.3      6-V4-434
xenograft
GSM2687077

source_name: WU PDX WHIM6_50hr control_bioreplicate3_technical replicate3


description:
WHIM4_50hr Buparlisib treatment_bioreplicate1_technical replicate1
CM_87_87.1   4-B3-556
xenograft
GSM2687150

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate1_technical replicate1


description:
WHIM4_50hr control_bioreplicate1_technical replicate2
CM_91_91.2   4-V4-561
xenograft
GSM2687163

source_name: WU PDX WHIM4_50hr control_bioreplicate1_technical replicate2


description:
WHIM21_50hr Buparlisib treatment_bioreplicate2_technical replicate1
CM_74_74.1   21-B3-535
xenograft
GSM2687111

source_name: WU PDX WHIM21_50hr Buparlisib treatment_bioreplicate2_technical replicate1


description:
WHIM21_50hr control_bioreplicate2_technical replicate2
CM_77_77.2   21-V4-539
xenograft
GSM2687121

source_name: WU PDX WHIM21_50hr control_bioreplicate2_technical replicate2


description:
WHIM21_50hr control_bioreplicate2_technical replicate1
CM_77_77.1   21-V4-539
xenograft
GSM2687120

source_name: WU PDX WHIM21_50hr control_bioreplicate2_technical replicate1


description:
WHIM21_50hr control_bioreplicate1_technical replicate3
CM_76_76.3   21-V4-538
xenograft
GSM2687119

source_name: WU PDX WHIM21_50hr control_bioreplicate1_technical replicate3


description:
WHIM6_50hr Buparlisib treatment_bioreplicate4_technical replicate2
CM_59_59.2   6-B3-418
xenograft
GSM2687067

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate4_technical replicate2


description:
WHIM6_50hr Buparlisib treatment_bioreplicate4_technical replicate3
CM_59_59.3   6-B3-418
xenograft
GSM2687068

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate4_technical replicate3


description:
WHIM4_50hr Buparlisib treatment_bioreplicate2_technical replicate1
CM_88_88.1   4-B3-557
xenograft
GSM2687153

source_name: WU PDX WHIM4_50hr Buparlisib treatment_bioreplicate2_technical replicate1


description:
WHIM21_50hr Buparlisib treatment_bioreplicate3_technical replicate1
CM_75_75.1   21-B3-537
xenograft
GSM2687114

source_name: WU PDX WHIM21_50hr Buparlisib treatment_bioreplicate3_technical replicate1


description:
WHIM6_50hr Buparlisib treatment_bioreplicate3_technical replicate2
CM_58_58.2   6-B3-417
xenograft
GSM2687064

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate3_technical replicate2


description:
WHIM21_50hr Buparlisib treatment_bioreplicate2_technical replicate3
CM_74_74.3   21-B3-535
xenograft
GSM2687113

source_name: WU PDX WHIM21_50hr Buparlisib treatment_bioreplicate2_technical replicate3


description:
WHIM6_50hr Buparlisib treatment_bioreplicate2_technical replicate3
CM_57_57.3   6-B3-415
xenograft
GSM2687062

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate2_technical replicate3


description:
WHIM12_50hr control_bioreplicate3_technical replicate2
CM_45_45.2   12-V4-484
xenograft
GSM2687025

source_name: WU PDX WHIM12_50hr control_bioreplicate3_technical replicate2


description:
WHIM12_50hr control_bioreplicate3_technical replicate3
CM_45_45.3   12-V4-484
xenograft
GSM2687026

source_name: WU PDX WHIM12_50hr control_bioreplicate3_technical replicate3


description:
WHIM12_50hr control_bioreplicate2_technical replicate3
CM_44_44.3   12-V4-483
xenograft
GSM2687023

source_name: WU PDX WHIM12_50hr control_bioreplicate2_technical replicate3


description:
WHIM12_50hr control_bioreplicate2_technical replicate2
CM_44_44.2   12-V4-483
xenograft
GSM2687022

source_name: WU PDX WHIM12_50hr control_bioreplicate2_technical replicate2


description:
WHIM12_50hr control_bioreplicate2_technical replicate1
CM_44_44.1   12-V4-483
xenograft
GSM2687021

source_name: WU PDX WHIM12_50hr control_bioreplicate2_technical replicate1


description:
WHIM6_50hr control_bioreplicate3_technical replicate1
CM_62_62.1   6-V4-434
xenograft
GSM2687075

source_name: WU PDX WHIM6_50hr control_bioreplicate3_technical replicate1


description:
WHIM6_50hr control_bioreplicate1_technical replicate2
CM_60_60.2   6-V4-430
xenograft
GSM2687070

source_name: WU PDX WHIM6_50hr control_bioreplicate1_technical replicate2


description:
WHIM6_50hr control_bioreplicate2_technical replicate1
CM_61_61.1   6-V4-433
xenograft
GSM2687072

source_name: WU PDX WHIM6_50hr control_bioreplicate2_technical replicate1


description:
WHIM6_50hr control_bioreplicate1_technical replicate1
CM_60_60.1   6-V4-430
xenograft
GSM2687069

source_name: WU PDX WHIM6_50hr control_bioreplicate1_technical replicate1


description:
WHIM12_50hr control_bioreplicate1_technical replicate2
CM_43_43.2   12-V4-481
xenograft
GSM2687019

source_name: WU PDX WHIM12_50hr control_bioreplicate1_technical replicate2


description:
WHIM6_50hr Buparlisib treatment_bioreplicate3_technical replicate3
CM_58_58.3   6-B3-417
xenograft
GSM2687065

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate3_technical replicate3


description:
WHIM6_50hr Buparlisib treatment_bioreplicate4_technical replicate1
CM_59_59.1   6-B3-418
xenograft
GSM2687066

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate4_technical replicate1


description:
WHIM12_50hr Buparlisib treatment_bioreplicate3_technical replicate3
CM_42_42.3      12-B3-480
xenograft
GSM2687017

source_name: WU PDX WHIM12_50hr Buparlisib treatment_bioreplicate3_technical replicate3


description:
WHIM6_50hr Buparlisib treatment_bioreplicate3_technical replicate1
CM_58_58.1   6-B3-417
xenograft
GSM2687063

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate3_technical replicate1


description:
WHIM12_50hr Buparlisib treatment_bioreplicate3_technical replicate2
CM_42_42.2     12-B3-480
xenograft
GSM2687016

source_name: WU PDX WHIM12_50hr Buparlisib treatment_bioreplicate3_technical replicate2


description:
WHIM12_50hr Buparlisib treatment_bioreplicate2_technical replicate1
CM_41_41.1   12-B3-478
xenograft
GSM2687012

source_name: WU PDX WHIM12_50hr Buparlisib treatment_bioreplicate2_technical replicate1


description:
WHIM6_50hr control_bioreplicate2_technical replicate3
CM_61_61.3     6-V4-433
xenograft
GSM2687074

source_name: WU PDX WHIM6_50hr control_bioreplicate2_technical replicate3


description:
WHIM6_50hr control_bioreplicate2_technical replicate2
CM_61_61.2   6-V4-433
xenograft
GSM2687073

source_name: WU PDX WHIM6_50hr control_bioreplicate2_technical replicate2


description:
WHIM6_50hr Buparlisib treatment_bioreplicate2_technical replicate1
CM_57_57.1   6-B3-415
xenograft
GSM2687060

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate2_technical replicate1


description:
WHIM6_50hr Buparlisib treatment_bioreplicate1_technical replicate3
CM_56_56.3   6-B3-414
xenograft
GSM2687059

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate1_technical replicate3


description:
WHIM6_50hr Buparlisib treatment_bioreplicate2_technical replicate2
CM_57_57.2   6-B3-415
xenograft
GSM2687061

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate2_technical replicate2


description:
WHIM6_50hr Buparlisib treatment_bioreplicate1_technical replicate2
CM_56_56.2   6-B3-414
xenograft
GSM2687058

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate1_technical replicate2


description:
WHIM12_50hr Buparlisib treatment_bioreplicate1_technical replicate1
CM_40_40.1   12-B3-477
xenograft
GSM2687009

source_name: WU PDX WHIM12_50hr Buparlisib treatment_bioreplicate1_technical replicate1


description:
WHIM6_50hr Buparlisib treatment_bioreplicate1_technical replicate1
CM_56_56.1   6-B3-414
xenograft
GSM2687057

source_name: WU PDX WHIM6_50hr Buparlisib treatment_bioreplicate1_technical replicate1


description:
WHIM12_50hr control_bioreplicate3_technical replicate1
CM_45_45.1   12-V4-484
xenograft
GSM2687024

source_name: WU PDX WHIM12_50hr control_bioreplicate3_technical replicate1


description:
WHIM6_50hr control_bioreplicate1_technical replicate3
CM_60_60.3   6-V4-430
xenograft
GSM2687071

source_name: WU PDX WHIM6_50hr control_bioreplicate1_technical replicate3


description:
WHIM12_50hr Buparlisib treatment_bioreplicate1_technical replicate3
CM_39_39.3   12-B3-475
xenograft
GSM2687008

source_name: WU PDX WHIM12_50hr Buparlisib treatment_bioreplicate1_technical replicate3


description:
WHIM12_50hr Buparlisib treatment_bioreplicate1_technical replicate2
CM_39_39.2   12-B3-475
xenograft
GSM2687007

source_name: WU PDX WHIM12_50hr Buparlisib treatment_bioreplicate1_technical replicate2


description:
WHIM12_50hr control_bioreplicate1_technical replicate1
CM_43_43.1   12-V4-481
xenograft
GSM2687018

source_name: WU PDX WHIM12_50hr control_bioreplicate1_technical replicate1


description:
WHIM30_50hr control_bioreplicate2_technical replicate1
CM_28_28.1   30-V4-517
xenograft
GSM2686973

source_name: WU PDX WHIM30_50hr control_bioreplicate2_technical replicate1


description:
WHIM12_50hr Buparlisib treatment_bioreplicate3_technical replicate1
CM_42_42.1   12-B3-480
xenograft
GSM2687015

source_name: WU PDX WHIM12_50hr Buparlisib treatment_bioreplicate3_technical replicate1


description:
WHIM30_50hr control_bioreplicate1_technical replicate2
CM_27_27.2   30-V4-515
xenograft
GSM2686971

source_name: WU PDX WHIM30_50hr control_bioreplicate1_technical replicate2


description:
WHIM12_50hr Buparlisib treatment_bioreplicate2_technical replicate3
CM_41_41.3     12-B3-478
xenograft
GSM2687014

source_name: WU PDX WHIM12_50hr Buparlisib treatment_bioreplicate2_technical replicate3


description:
WHIM30_50hr Buparlisib treatment_bioreplicate3_technical replicate3
CM_26_26.3   30-B3-513
xenograft
GSM2686969

source_name: WU PDX WHIM30_50hr Buparlisib treatment_bioreplicate3_technical replicate3


description:
WHIM12_50hr Buparlisib treatment_bioreplicate1_technical replicate2
CM_40_40.2   12-B3-477
xenograft
GSM2687010


description:
WHIM12_50hr Buparlisib treatment_bioreplicate1_technical replicate3
CM_40_40.3   12-B3-477
xenograft
GSM2687011


description:
WHIM12_50hr control_bioreplicate1_technical replicate3
CM_43_43.3   12-V4-481
xenograft
GSM2687020

source_name: WU PDX WHIM12_50hr control_bioreplicate1_technical replicate3


description:
WHIM30_50hr Buparlisib treatment_bioreplicate3_technical replicate2
CM_26_26.2   30-B3-513
xenograft
GSM2686968

source_name: WU PDX WHIM30_50hr Buparlisib treatment_bioreplicate3_technical replicate2


description:
WHIM30_50hr Buparlisib treatment_bioreplicate3_technical replicate1
CM_26_26.1   30-B3-513
xenograft
GSM2686967

source_name: WU PDX WHIM30_50hr Buparlisib treatment_bioreplicate3_technical replicate1


description:
WHIM30_50hr Buparlisib treatment_bioreplicate2_technical replicate2
CM_25_25.2   30-B3-512
xenograft
GSM2686965

source_name: WU PDX WHIM30_50hr Buparlisib treatment_bioreplicate2_technical replicate2


description:
WHIM30_50hr Buparlisib treatment_bioreplicate2_technical replicate1
CM_25_25.1   30-B3-512
xenograft
GSM2686964

source_name: WU PDX WHIM30_50hr Buparlisib treatment_bioreplicate2_technical replicate1


description:
WHIM2_50hr control_bioreplicate3_technical replicate1
CM_13_13.1   2-V4-444
xenograft
GSM2686928

source_name: WU PDX WHIM2_50hr control_bioreplicate3_technical replicate1


description:
WHIM2_50hr control_bioreplicate3_technical replicate2
CM_13_13.2   2-V4-444
xenograft
GSM2686929

source_name: WU PDX WHIM2_50hr control_bioreplicate3_technical replicate2


description:
WHIM30_50hr control_bioreplicate3_technical replicate3
CM_29_29.3   30-V4-518
xenograft
GSM2686978

source_name: WU PDX WHIM30_50hr control_bioreplicate3_technical replicate3


description:
WHIM12_50hr Buparlisib treatment_bioreplicate1_technical replicate1
CM_39_39.1   12-B3-475
xenograft
GSM2687006

source_name: WU PDX WHIM12_50hr Buparlisib treatment_bioreplicate1_technical replicate1


description:
WHIM30_50hr control_bioreplicate3_technical replicate1
CM_29_29.1   30-V4-518
xenograft
GSM2686976

source_name: WU PDX WHIM30_50hr control_bioreplicate3_technical replicate1


description:
WHIM30_50hr control_bioreplicate3_technical replicate2
CM_29_29.2   30-V4-518
xenograft
GSM2686977

source_name: WU PDX WHIM30_50hr control_bioreplicate3_technical replicate2


description:
WHIM12_50hr Buparlisib treatment_bioreplicate2_technical replicate2
CM_41_41.2   12-B3-478
xenograft
GSM2687013

source_name: WU PDX WHIM12_50hr Buparlisib treatment_bioreplicate2_technical replicate2


description:
WHIM30_50hr control_bioreplicate1_technical replicate3
CM_27_27.3   30-V4-515
xenograft
GSM2686972

source_name: WU PDX WHIM30_50hr control_bioreplicate1_technical replicate3


description:
WHIM30_50hr control_bioreplicate1_technical replicate1
CM_27_27.1   30-V4-515
xenograft
GSM2686970

source_name: WU PDX WHIM30_50hr control_bioreplicate1_technical replicate1


description:
WHIM30_50hr control_bioreplicate2_technical replicate2
CM_28_28.2   30-V4-517
xenograft
GSM2686974

source_name: WU PDX WHIM30_50hr control_bioreplicate2_technical replicate2


description:
WHIM30_50hr Buparlisib treatment_bioreplicate2_technical replicate3
CM_25_25.3   30-B3-512
xenograft
GSM2686966

source_name: WU PDX WHIM30_50hr Buparlisib treatment_bioreplicate2_technical replicate3


description:
WHIM30_50hr Buparlisib treatment_bioreplicate1_technical replicate3
CM_24_24.3   30-B3-510
xenograft
GSM2686963

source_name: WU PDX WHIM30_50hr Buparlisib treatment_bioreplicate1_technical replicate3


description:
WHIM2_50hr control_bioreplicate1_technical replicate3
CM_11_11.3     2-V4-440
xenograft
GSM2686924

source_name: WU PDX WHIM2_50hr control_bioreplicate1_technical replicate3


description:
WHIM30_50hr Buparlisib treatment_bioreplicate1_technical replicate2
CM_24_24.2   30-B3-510
xenograft
GSM2686962

source_name: WU PDX WHIM30_50hr Buparlisib treatment_bioreplicate1_technical replicate2


description:
WHIM2_50hr control_bioreplicate1_technical replicate1
CM_11_11.1   2-V4-440
xenograft
GSM2686922

source_name: WU PDX WHIM2_50hr control_bioreplicate1_technical replicate1


description:
WHIM30_50hr Buparlisib treatment_bioreplicate1_technical replicate1
CM_24_24.1   30-B3-510
xenograft
GSM2686961

source_name: WU PDX WHIM30_50hr Buparlisib treatment_bioreplicate1_technical replicate1


description:
WHIM30_50hr control_bioreplicate2_technical replicate3
CM_28_28.3   30-V4-517
xenograft
GSM2686975

source_name: WU PDX WHIM30_50hr control_bioreplicate2_technical replicate3


description:
WHIM2_50hr Buparlisib treatment_bioreplicate2_technical replicate2
CM_8_8.2   2-B3-446
xenograft
GSM2686914

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate2_technical replicate2


description:
WHIM2_50hr Buparlisib treatment_bioreplicate3_technical replicate1
CM_9_9.1   2-B3-448
xenograft
GSM2686916

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate3_technical replicate1


description:
WHIM2_50hr control_bioreplicate2_technical replicate3
CM_12_12.3      2-V4-443
xenograft
GSM2686927

source_name: WU PDX WHIM2_50hr control_bioreplicate2_technical replicate3


description:
WHIM2_50hr control_bioreplicate2_technical replicate2
CM_12_12.2     2-V4-443
xenograft
GSM2686926

source_name: WU PDX WHIM2_50hr control_bioreplicate2_technical replicate2


description:
WHIM2_50hr Buparlisib treatment_bioreplicate4_technical replicate2
CM_10_10.2   2-B3-449
xenograft
GSM2686920

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate4_technical replicate2


description:
WHIM2_50hr Buparlisib treatment_bioreplicate4_technical replicate3
CM_10_10.3   2-B3-449
xenograft
GSM2686921

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate4_technical replicate3


description:
WHIM2_50hr control_bioreplicate3_technical replicate3
CM_13_13.3   2-V4-444
xenograft
GSM2686930

source_name: WU PDX WHIM2_50hr control_bioreplicate3_technical replicate3


description:
WHIM2_50hr Buparlisib treatment_bioreplicate4_technical replicate1
CM_10_10.1   2-B3-449
xenograft
GSM2686919

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate4_technical replicate1


description:
WHIM2_50hr control_bioreplicate1_technical replicate2
CM_11_11.2   2-V4-440
xenograft
GSM2686923

source_name: WU PDX WHIM2_50hr control_bioreplicate1_technical replicate2


description:
WHIM2_50hr Buparlisib treatment_bioreplicate1_technical replicate1
CM_7_7.1   2-B3-445
xenograft
GSM2686910

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate1_technical replicate1


description:
WHIM2_50hr Buparlisib treatment_bioreplicate3_technical replicate2
CM_9_9.2   2-B3-448
xenograft
GSM2686917

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate3_technical replicate2


description:
WHIM2_50hr Buparlisib treatment_bioreplicate3_technical replicate3
CM_9_9.3   2-B3-448
xenograft
GSM2686918

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate3_technical replicate3


description:
WHIM2_50hr Buparlisib treatment_bioreplicate2_technical replicate3
CM_8_8.3   2-B3-446
xenograft
GSM2686915

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate2_technical replicate3


description:
WHIM2_50hr Buparlisib treatment_bioreplicate1_technical replicate3
CM_7_7.3   2-B3-445
xenograft
GSM2686912

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate1_technical replicate3


description:
WHIM2_50hr Buparlisib treatment_bioreplicate2_technical replicate1
CM_8_8.1   2-B3-446
xenograft
GSM2686913

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate2_technical replicate1


description:
WHIM2_50hr Buparlisib treatment_bioreplicate1_technical replicate2
CM_7_7.2   2-B3-445
xenograft
GSM2686911

source_name: WU PDX WHIM2_50hr Buparlisib treatment_bioreplicate1_technical replicate2


title: WHIM31B: whim31_passage B

status: Public on Dec 31 2020

hyb_protocol: Agilent 60-mer oligo microarray processing protocol

scan_protocol: Microarrays were scanned with an Agilent Scanner.

data_processing: Raw Agilent 4x44K gene expression data were normalized using the BioConductor “limma” package sequentially through background subtraction, loess within-array normalization and quantile between-array normalization. The probe level gene expression data were collapsed to gene level by median expression. ComBat was applied using the R package “sva” to the normalized gene expression data to correct for potential human/mouse batch effect.

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

label_protocol: Agilent Low Input Linear Amplification Kit and protocol

growth_protocol: Tumors from xenograft models were cryopreserved.  Tumors from patient samples were frozen and stored in OCT compound.

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

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

source_name: xenograft tumor_whim31_passage B

value: xenograft tumor

value: cryopreserved tissue


title: WHIM31Hu: human counterpart tumor_whim31

source_name: human counterpart tumor_whim31

value: human counterpart tumor

value: oct block


title: WHIM29A: whim29_passage A

source_name: xenograft tumor_whim29_passage A


title: WHIM30B: whim30_passage B

source_name: xenograft tumor_whim30_passage B


title: WHIM21Hu: human counterpart tumor_whim21

source_name: human counterpart tumor_whim21


title: WHIM30A: whim30_passage A

source_name: xenograft tumor_whim30_passage A


description:
WHIM2_50hr control_bioreplicate2_technical replicate1
CM_12_12.1   2-V4-443
xenograft
GSM2686925

source_name: WU PDX WHIM2_50hr control_bioreplicate2_technical replicate1


title: WHIM29B: whim29_passage B

source_name: xenograft tumor_whim29_passage B


title: WHIM21B: whim21_passage B

source_name: xenograft tumor_whim21_passage B


title: WHIM34Hu: human counterpart tumor_whim34

source_name: human counterpart tumor_whim34


title: WHIM29Hu: human counterpart tumor_whim29

source_name: human counterpart tumor_whim29


title: WHIM31A: whim31_passage A

source_name: xenograft tumor_whim31_passage A


title: WHIM21A: whim21_passage A

source_name: xenograft tumor_whim21_passage A


title: WHIM48Hu: human counterpart tumor_whim48

source_name: human counterpart tumor_whim48


title: WHIM6E: whim6_passage E

source_name: xenograft tumor_whim6_passage E


title: WHIM6Hu: human counterpart tumor_whim6

source_name: human counterpart tumor_whim6


title: WHIM5E: whim5_passage E

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

source_name: xenograft tumor_whim5_passage E


title: WHIM48A: whim48_passage A

source_name: xenograft tumor_whim48_passage A


title: WHIM5A: whim5_passage A

source_name: xenograft tumor_whim5_passage A


title: WHIM6A: whim6_passage A

source_name: xenograft tumor_whim6_passage A


title: WHIM5Hu: human counterpart tumor_whim5

source_name: human counterpart tumor_whim5


title: WHIM6C: whim6_passage C

source_name: xenograft tumor_whim6_passage C


title: WHIM5C: whim5_passage C

source_name: xenograft tumor_whim5_passage C


title: WHIM34A: whim34_passage A

source_name: xenograft tumor_whim34_passage A


title: WHIM4E: whim4_passage E

source_name: xenograft tumor_whim4_passage E


title: WHIM4D: whim4_passage D

source_name: xenograft tumor_whim4_passage D


title: WHIM4Hu: human counterpart tumor_whim4

source_name: human counterpart tumor_whim4


title: WHIM34E: whim34_passage E

source_name: xenograft tumor_whim34_passage E


title: WHIM4C: whim4_passage C

source_name: xenograft tumor_whim4_passage C


title: WHIM3C: whim3_passage C

source_name: xenograft tumor_whim3_passage C


title: WHIM3A: whim3_passage A

source_name: xenograft tumor_whim3_passage A


title: WHIM3E: whim3_passage E

source_name: xenograft tumor_whim3_passage E


title: WHIM36Hu: human counterpart tumor_whim36

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

source_name: human counterpart tumor_whim36


title: WHIM4A: whim4_passage A

source_name: xenograft tumor_whim4_passage A


title: WHIM2E: whim2_passage E

source_name: xenograft tumor_whim2_passage E


title: WHIM3B: whim3_passage B

source_name: xenograft tumor_whim3_passage B