title: 2d_GATA4_(20181121_MM_HsSc_768_1113)

description: CUT&RUN for GATA4 in 2 day cells using AutoCUT&RUN; Rb anti-Ms 2* ab differentiated for 2 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)


title: 2d_CTCF_auto_(20181004_MPM_HsSc_678_0926)

status: Public on Jun 25 2019

type: SRA

city: Chapel Hill

first: Michael

last: Meers

state: NC

address: 250 Bell Tower Dr.

country: USA

institute: UNC Chapel Hill

description: CUT&RUN for CTCF in 2 day cells using AutoCUT&RUN differentiated for 2 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

library_source: genomic

data_processing:
Genome_build: UCSC hg19
1. We used Bowtie2 2.2.5 with options "--local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to hg19 of Homo sapiens genomic sequence obtained from UCSC. 2. We extracted properly paired reads from Homo sapiens alignments to generate a bed files <chr> <start> <stop> <length> (Supplementary file .bed).

molecule: genomic DNA

organism: Homo sapiens

source_name: CUT&Run

extract_protocol:
Janssens_protocols.docx
PMID 25827087

tag: antibody

value: Rb anti-CTCF Millipore cat# 07-729

tag: cell type

value: H1 (WA01) human embryonic stem cell line (WiCell)

tag: Stage

value: 2 days


title: 2d_ATACseq_(20181017_MM_Hs_0705MPM512)

description: ATAC-seq in 2 day cells

source_name: ATAC-Seq

extract_protocol:
MeersEtAl2019.ATACseq.txt
PMID 25827087


title: 2d_POU5F1_std_(20181220_MM_HsSc_1213MPM843)

description: CUT&RUN for POU5F1 in 2 day cells using Standard CUT&RUN differentiated for 2 days using the StemDiff Definitive Endoderm kit (STEMCELL Technologies)

value: Rb anti-POU5F1 Abcam cat# ab109183


title: ASXL1_WT_ChIPSeq

status: Public on Dec 08 2018

city: Tianjin

first: Caiying

last: Zhu

address: Heping District, Nanjing Road, 288

country: China

institute: Institute of Hematology and Blood Disease Hospital

data_processing:
Basecalls performed using Illumina NextSeq 500
ChIP-Seq reads were aligned to the mm10 genome assembly using the BWA algorithm with default settings
Data were filtered using the following specifications:only reads that pass Illumina's purity filter,aligned with no more than 2 mismatches,and map uniquely to the genome were used in the subsequent analysis,than duplicate reads were removed.
peaks were called using SICER version 1.1 with the following setting:Threshold for redundancy allowed for ChIP reads(1),window size(200bp) ,FDR cutoff(1E-10)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file format,it contains peaks position imformation such as chromosome,peaks start and end positions.

organism: Mus musculus

source_name: WT_BM-derived MSPCs

growth_protocol: Bone marrow–derived mesenchymal stem/progenitor cells were cultured with MSC medium (MesenCult basal media plus 20% of MesenCult Supplemental), and replated when the cultures reached 80-90% confluency.

extract_protocol:
MSPCs were fixed with 1% formaldehyde, lysates were sonicated and the DNA was sheared to an average length of 300 to 500 bp. Histone-DNA complexes were isolated with specific histone modification antibodies.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced.

tag: strain background

tag: genotype/variation

value: Wild type

value: BM-derived Mesenchymal stem/progenitor cells (MSPCs)

value: BM-derived MSPCs

tag: passages

tag: chip antibody

value: ASXL1 (Santa Cruz sc-85283)


title: INPUT_ChIPSeq

source_name: BM-derived MSPCs


title: H3K27me3_WT_ChIPSeq

value: H3K27me3 (Millipore 07-449)


title: H3K4me3_WT_ChIPSeq

value: H3K4me3 (Active Motif 39159)


title: H3K4me2_KO_ChIPSeq

source_name: Asxl1-/-_BM-derived MSPCs

value: H3K4me2 (Active Motif 39141)


title: H3K4me2_WT_ChIPSeq


title: Patient 15 tumor

status: Public on Dec 05 2018

city: Los Angeles

first: Willy

last: Hugo

state: California

address: 10833 Le Conte Ave

department: Medicine

institute: University of California, Los Angeles

description: mRNA from fresh surgical samples

library_source: transcriptomic

data_processing:
The reads are first mapped to Grch38 using HISAT2
Gene level raw read counts are quantified using htseq-count
Ensemble ID to HUGO gene mapping using biomaRt R package
Gene set enrichment analysis using GSVA R package
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene level raw count matrix

molecule: total RNA

source_name: Recurrent glioblastoma

extract_protocol:
QIAGEN Rneasy Mini Kit without Dnase
NUGEN mRNA PLUS kit (stranded)

tag: therapy

value: adjuvant pembrolizumab


title: Patient 24 tumor

description: mRNA from fresh surgical samples


title: Patient 29 tumor

description: mRNA from fresh surgical samples


title: Patient 17 tumor

description: mRNA from fresh surgical samples


title: Patient 20 tumor

description: mRNA from fresh surgical samples


title: Patient 22 tumor

description: mRNA from fresh surgical samples


title: Patient 35 tumor

description: mRNA from fresh surgical samples


title: Patient 31 tumor

description: mRNA from fresh surgical samples


title: Patient 34 tumor

description: mRNA from fresh surgical samples


title: Patient 30 tumor

description: mRNA from fresh surgical samples


title: Patient 21 tumor

description: mRNA from fresh surgical samples


title: Patient 10 tumor

description: mRNA from fresh surgical samples


title: Patient 27 tumor

description: mRNA from fresh surgical samples

value: neoadjuvant pembrolizumab


title: Patient 33 tumor

description: mRNA from fresh surgical samples


title: Patient 28 tumor

description: mRNA from fresh surgical samples


title: Patient 14 tumor

description: mRNA from fresh surgical samples


title: Patient 2 tumor

description: mRNA from fresh surgical samples


title: Patient 11 tumor

description: mRNA from fresh surgical samples


title: H3K27me3_KO_ChIPSeq


title: H3K4me3_KO_ChIPSeq


title: Patient 26 tumor

description: mRNA from fresh surgical samples


title: Patient 23 tumor

description: mRNA from fresh surgical samples


title: Patient 19 tumor

description: mRNA from fresh surgical samples


title: Patient 16 tumor

description: mRNA from fresh surgical samples


title: Patient 5 tumor

description: mRNA from fresh surgical samples


title: Patient 4 tumor

description: mRNA from fresh surgical samples


title: Patient 6 tumor

description: mRNA from fresh surgical samples


title: Patient 8 tumor

description: mRNA from fresh surgical samples


title: Patient 12 tumor

description: mRNA from fresh surgical samples


title: Patient 3 tumor

description: mRNA from fresh surgical samples


title: Patient 25 tumor

description: mRNA from fresh surgical samples


title: Y1.7-BRAFi-aPDL2-small-1

status: Public on Sep 13 2017

description: YUMM1.7 melanoma tumor, on BRAFi+aPD-L2 treatment, residual, 1st tumor (batch 2)

data_processing:
FASTQ files were mapped by Tophat2
Tophat BAMs were quantified and normalized using Cuffnorm, DGE were called by cuffdiff
Genome_build: mm9
Supplementary_files_format_and_content: The normalized expression levels in FPKM called by cuffnorm

molecule: polyA RNA

extract_protocol:
mirVana RNA extraction kit
TruSeq RNA Sample Preparation Kit v2, unstranded
Poly A transcript enrichment, paired end RNAseq

tag: tissue

value: tumor biopsy

tag: mapki treatment

value: on-treatment

tag: mapki type


title: Y1.7-BRAFi-aPDL2-small-2

description: YUMM1.7 melanoma tumor, on BRAFi+aPD-L2 treatment, residual, 2nd tumor (batch 2)


title: Y1.7-BRAFi-aPDL2-large-1

description: YUMM1.7 melanoma tumor, BRAFi+aPD-L2 resistant, 1st tumor (batch 2)

value: resistant


title: Y1.7-BRAFi-Prog-3

description: YUMM1.7 melanoma tumor, BRAFi resistant, 3rd tumor  (batch 2)

value: BRAFi


title: Y1.7-BRAFi-Prog-1

description: YUMM1.7 melanoma tumor, BRAFi resistant, 1st tumor (batch 2)


title: Ramos EBV pos

status: Public on Jan 17 2018

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Sequencing reads were aligned to the GrCh37 (hg19) build of the human genome using TopHat and Bowtie2 with Ensembl52 RNA transcript annotations as a guide. In parallel, these data were aligned to the EBV genome (NCBI).
For allelic analysis, sequencing reads were aligned to the GrCh37 (hg19) build of the human genome using Hisat2. Differential expression analysis was performed using Cufflinks.
Genome_build: hg19
Supplementary_files_format_and_content: EBV-Ramos.txt (TPM values)

source_name: Ramos cell line

extract_protocol:
TRUseq RNA sample kit  (Illumina)
RNA was isolated from Ramos cell lines with and without EBV infection using the mirVANA Isolation Kit (Ambion). RNA sequencing targeting 150 million mappable 125 basepair reads from paired-end polyA enriched libraries was performed at the CCHMC DNA Sequencing and Genotyping Core Facility at CCHMC.

value: cKit+ splenocytes

tag: infection

value: with EBV


title: M249DDR5-offdrug6h

status: Public on Nov 28 2017

description: M249DDR5 after 6 hours of BRAFi/MEKi withdrawal

data_processing:
FASTQ files were mapped by Tophat2
Tophat BAMs were quantified and normalized using Cuffquant and Cuffnorm
Genome_build: hg19
Supplementary_files_format_and_content: The normalized FPKM levels by cuffnorm

source_name: melanoma cell line

extract_protocol:
mirVana RNA extraction kit
TruSeq RNA Sample Preparation Kit v2

treatment_protocol: BRAFi: Vemurafenib 1uM, MEKi: Selumetinib 1uM

tag: cell line

tag: brafi/meki treatment

value: withdrawal for 6 hr


title: SKMEL28DDR1-offdrug24h

description: SKMEL28DDR1 after 24 hours of BRAFi/MEKi withdrawal

value: withdrawal for 24 hr


title: SKMEL28DDR1-offdrug6h

description: SKMEL28DDR1 after 6 hours of BRAFi/MEKi withdrawal


title: SKMEL28DDR1-ondrug6h

description: SKMEL28DDR1 after 6 hours of BRAFi/MEKi treatment

value: treated for 6 hr


title: M249DDR5-offdrug24h

description: M249DDR5 after 24 hours of BRAFi/MEKi withdrawal


title: Y1.7-Prog-3

description: YUMM1.7 melanoma tumor, BRAFi resistant, 3rd tumor


title: Y1.7-Prog-4

description: YUMM1.7 melanoma tumor, BRAFi resistant, 4th tumor


title: Y1.7-Prog-2

description: YUMM1.7 melanoma tumor, BRAFi resistant, 2nd tumor


title: Y1.7-Prog-1

description: YUMM1.7 melanoma tumor, BRAFi resistant, 1st tumor


title: Y1.7-Res-5

description: YUMM1.7 melanoma tumor, on BRAFi treatment, residual/cytostatic, 5th tumor


title: Ramos EBV neg

value: without EBV


title: Y1.7-BRAFi-aPDL2-large-2

description: YUMM1.7 melanoma tumor, BRAFi+aPD-L2 resistant, 2nd tumor (batch 2)


title: Y1.7-Prog-5

description: YUMM1.7 melanoma tumor, BRAFi resistant, 5th tumor


title: Y1.7-Res-4

description: YUMM1.7 melanoma tumor, on BRAFi treatment, residual/cytostatic, 4th tumor


title: M249DDR5-ondrug6h

description: M249DDR5 after 6 hours of BRAFi/MEKi treatment


title: Y1.7-Res-3

description: YUMM1.7 melanoma tumor, on BRAFi treatment, residual/cytostatic, 3rd tumor


title: Y1.7-Reg-4

description: YUMM1.7 melanoma tumor, on BRAFi treatment, regressing, 4th tumor


title: Y1.7-BRAFi-Prog-2

description: YUMM1.7 melanoma tumor, BRAFi resistant, 2nd tumor  (batch 2)


title: Y1.7-Res-1

description: YUMM1.7 melanoma tumor, on BRAFi treatment, residual/cytostatic, 1st tumor


title: Y1.7-Reg-3

description: YUMM1.7 melanoma tumor, on BRAFi treatment, regressing, 3rd tumor


title: Y1.7-Veh2

description: YUMM1.7 melanoma tumor, pre BRAFi treatment, 2nd tumor


title: Y1.7-Reg-1

description: YUMM1.7 melanoma tumor, on BRAFi treatment, regressing, 1st tumor


title: Y1.7-Veh4

description: YUMM1.7 melanoma tumor, pre BRAFi treatment, 4th tumor


title: Y1.7-NSG-Pdl2OE-BRAFi-3

status: Public on Sep 12 2017

description: YUMM1.7 melanoma tumor with PD-L2 overexpression in NSG mice, BRAFi treated, 3rd tumor

extract_protocol:
QIAGEN RNeasy micro kit
TruSeq RNA Sample Preparation Kit v2, unstranded
Poly A transcript enrichment, paired end RNAseq

value: YUMM1.7 melanoma

tag: pd-l2 overexpression

value: yes


title: Y1.7-P-Cd45neg-3

description: Sorted CD45- cell fraction of YUMM1.7 melanoma tumor, pre BRAFi treatment, 3rd tumor

source_name: CD45- fraction of YUMM1.7 melanoma

value: YUMM1.7 melanoma tumor


title: Y1.7-NSG-Ctrl-DMSO-3

description: YUMM1.7 melanoma tumor in NSG mice, vehicle treated, 3rd tumor

value: no


title: Y1.7-NSG-Ctrl-DMSO-2

description: YUMM1.7 melanoma tumor in NSG mice, vehicle treated, 2nd tumor


title: Y1.7-NSG-Ctrl-BRAFi-2

description: YUMM1.7 melanoma tumor in NSG mice, BRAFi treated, 2nd tumor


title: Y1.7-NSG-Pdl2OE-DMSO-2

description: YUMM1.7 melanoma tumor with PD-L2 overexpression in NSG mice, vehicle treated, 2nd tumor


title: Y1.7-NSG-Pdl2OE-DMSO-3

description: YUMM1.7 melanoma tumor with PD-L2 overexpression in NSG mice, vehicle treated, 3rd tumor


title: Y1.7-NSG-Ctrl-BRAFi-3

description: YUMM1.7 melanoma tumor in NSG mice, BRAFi treated, 3rd tumor


title: Y1.7-NSG-Pdl2OE-BRAFi-2

description: YUMM1.7 melanoma tumor with PD-L2 overexpression in NSG mice, BRAFi treated, 2nd tumor


title: Y1.7-Res-Cd45neg-2

description: Sorted CD45- cell fraction of YUMM1.7 melanoma tumor, on BRAFi treatment, residual, 2nd tumor

source_name: CD45- fraction of YUMM1.7 melanoma_on-treatment


title: Y1.7-NSG-Pdl2OE-DMSO-1

description: YUMM1.7 melanoma tumor with PD-L2 overexpression in NSG mice, vehicle treated, 1st tumor


title: Y1.7-NSG-Ctrl-BRAFi-1

description: YUMM1.7 melanoma tumor in NSG mice, BRAFi treated, 1st tumor


title: Y1.7-NSG-Ctrl-DMSO-1

description: YUMM1.7 melanoma tumor in NSG mice, vehicle treated, 1st tumor


title: Y1.7-P-Cd45neg-2

description: Sorted CD45- cell fraction of YUMM1.7 melanoma tumor, pre BRAFi treatment, 2nd tumor


title: Y1.7-Res-2

description: YUMM1.7 melanoma tumor, on BRAFi treatment, residual/cytostatic, 2nd tumor


title: M229DDR-PD1-STP20-D2

description: M229 DDR cultured with PD-1+ 293T, STP 20 mins, d2

data_processing:
FASTQ files were mapped by Tophat2
Tophat BAMs were quantified and normalized using Cuffnorm, DGE were called by cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: The normalized expression levels in FPKM called by cuffnorm

source_name: Melanoma cell line

extract_protocol:
QIAGEN RNeasy micro kit
KAPA Stranded mRNA-Seq Kits
Poly A transcript enrichment, single end RNAseq

value: Melanoma cell line

tag: gene overexpressed in hek293t cells

tag: staurosporine treatment

value: 20 min of STP, 0.5 uM

tag: treatment duration

value: 2 day


title: Y1.7-Res-Cd45neg-3

description: Sorted CD45- cell fraction of YUMM1.7 melanoma tumor, on BRAFi treatment, residual, 3rd tumor


title: Y1.7-Reg-2

description: YUMM1.7 melanoma tumor, on BRAFi treatment, regressing, 2nd tumor

value: tumor biopsy


title: M229DDR-Ctrl-STP20-D2

description: M229 DDR cultured with PD-1+ 293T, no STP, d2

tag: cell type

value: GFP


title: M229DDR-PD1-STP0-D1

description: M229 DDR cultured with Control 293T, STP 20 mins, d1

value: 1 day


title: M229DDR-PD1-STP20-D1

description: M229 DDR cultured with PD-1+ 293T, STP 20 mins, d1


title: Y1.7-Veh1

description: YUMM1.7 melanoma tumor, pre BRAFi treatment, 1st tumor


title: Y1.7-P-Cd45neg-1

description: Sorted CD45- cell fraction of YUMM1.7 melanoma tumor, pre BRAFi treatment, 1st tumor


title: M229DDR-PD1-STP0-D2

description: M229 DDR cultured with Control 293T, STP 20 mins, d2


title: M229DDR-Ctrl-STP20-D1

description: M229 DDR cultured with PD-1+ 293T, no STP, d1


title: Y1.7-Res-Cd45neg-1

description: Sorted CD45- cell fraction of YUMM1.7 melanoma tumor, on BRAFi treatment, residual, 1st tumor

value: on-treatment

value: BRAFi


title: Y1.7-NSG-Pdl2OE-BRAFi-1

description: YUMM1.7 melanoma tumor with PD-L2 overexpression in NSG mice, BRAFi treated, 1st tumor


title: Y1.7-Veh3

description: YUMM1.7 melanoma tumor, pre BRAFi treatment, 3rd tumor


title: M229DDR-Ctrl-STP0-D1

description: M229 DDR cultured with Control 293T, no STP, d1


title: M229DDR-Ctrl-STP0-D2

description: M229 DDR cultured with Control 293T, no STP, d2


title: M229SDR-Ctrl-STP0-D1

description: M229 SDR cultured with Control 293T, no STP, d1


title: M229SDR-PD1-STP0-D1

description: M229 SDR cultured with Control 293T, STP 20 mins, d1


title: M229SDR-Ctrl-STP0-D2

description: M229 SDR cultured with Control 293T, no STP, d2


title: M229SDR-PD1-STP0-D2

description: M229 SDR cultured with Control 293T, STP 20 mins, d2


title: M229SDR-PD1-STP20-D2

description: M229 SDR cultured with PD-1+ 293T, STP 20 mins, d2


title: M229SDR-PD1-STP20-D1

description: M229 SDR cultured with PD-1+ 293T, STP 20 mins, d1


title: M229SDR-Ctrl-STP20-D2

description: M229 SDR cultured with PD-1+ 293T, no STP, d2


title: M229SDR-Ctrl-STP20-D1

description: M229 SDR cultured with PD-1+ 293T, no STP, d1


title: M395 DTPP

description: Melanoma cell line

source_name: Melanoma cell line M395, treated with BRAFi (PLX4320 1uM), DTPP population

extract_protocol:
mirVana RNA extraction kit
KAPA Stranded mRNA-Seq Kits
Poly A transcript enrichment, paired end RNAseq

value: resistant


title: M397 DTPP

description: Melanoma cell line

source_name: Melanoma cell line M397, treated with BRAFi (PLX4320 1uM), DTPP population

extract_protocol:
mirVana RNA extraction kit
KAPA Stranded mRNA-Seq Kits
Poly A transcript enrichment, single end RNAseq


title: M397 P2

description: Melanoma cell line

source_name: Melanoma cell line M397, parental, MAPKi sensitive, DMSO treated for 2 days


title: M249 BRAFi2D

description: Melanoma cell line

source_name: Melanoma cell line M249, treated with BRAFi (PLX4320 1uM) for 2 days


title: SKMEL28 P2

description: Melanoma cell line

source_name: Melanoma cell line SKMEL28, parental, MAPKi sensitive, DMSO treated for 2 days


title: M397 BRAFi2D

description: Melanoma cell line

source_name: Melanoma cell line M397, treated with BRAFi (PLX4320 1uM) for 2 days


title: M395 P3

description: Melanoma cell line

source_name: Melanoma cell line M395, parental, MAPKi sensitive, DMSO treated for 2 days


title: SKMEL28 DTP

description: Melanoma cell line

source_name: Melanoma cell line SKMEL28, treated with BRAFi (PLX4320 1uM), DTP population


title: M249 DTP

description: Melanoma cell line

source_name: Melanoma cell line M249, treated with BRAFi (PLX4320 1uM), DTP population


title: M249 P2

description: Melanoma cell line

source_name: Melanoma cell line M249, parental, MAPKi sensitive, DMSO treated for 2 days


title: M395 DTP

description: Melanoma cell line

source_name: Melanoma cell line M395, treated with BRAFi (PLX4320 1uM), DTP population


title: M395 BRAF2D

description: Melanoma cell line

source_name: Melanoma cell line M395, treated with BRAFi (PLX4320 1uM) for 2 days


title: M249 DTPP

description: Melanoma cell line

source_name: Melanoma cell line M249, treated with BRAFi (PLX4320 1uM), DTPP population


title: SKMEL28 BRAFi2D

description: Melanoma cell line

source_name: Melanoma cell line SKMEL28, treated with BRAFi (PLX4320 1uM) for 2 days


title: M397 P1

status: Public on Sep 08 2017

description:
Melanoma cell line M397, parental, MAPKi sensitive, DMSO treated for 2 days
CellLine.FPKM.batch2.xlsx

extract_protocol:
Qiagen RNeasy Mini kit (cat #: 74104)
TruSeq RNA Sample Preparation Kit v2, unstranded
Poly A transcript enrichment, paired end RNAseq


title: M397 DTP

description: Melanoma cell line

source_name: Melanoma cell line M397, treated with BRAFi (PLX4320 1uM), DTP population


title: M395 SDR2

description:
Melanoma cell line M395, BRAFi resistant (PLX4320 1uM) subline of M395 (developed separately at Ribas lab)
CellLine.FPKM.batch2.xlsx


title: M395 P2

description:
Melanoma cell line M395, parental, MAPKi sensitive, DMSO treated for 2 days  (developed separately at Ribas lab)
CellLine.FPKM.batch2.xlsx


title: M395 SDR1

description:
Melanoma cell line M395, BRAFi resistant (PLX4320 1uM) subline of M395
CellLine.FPKM.batch2.xlsx


title: M263 SDR

description:
Melanoma cell line M263, BRAFi resistant (PLX4320 1uM) subline of M263 (clone R3)
CellLine.FPKM.batch2.xlsx


title: M229-DDR

description:
Melanoma cell line M229DDR, BRAFi+MEKi resistant  subline of M229, polyclonal
CellLine.FPKM.batch1.xlsx

value: BRAFi+MEKi


title: M263 P

description:
Melanoma cell line M263, parental, MAPKi sensitive, DMSO treated for 2 days
CellLine.FPKM.batch2.xlsx


title: M397 SDR

description:
Melanoma cell line M397, BRAFi resistant (PLX4320 1uM) subline of M395
CellLine.FPKM.batch2.xlsx


title: SKMel28-DDR

description:
Melanoma cell line SKMEL28DDR1, BRAFi+MEKi resistant  subline of SKMEL28 (clone DDR1)
CellLine.FPKM.batch1.xlsx


title: SKMEL28-P

description:
Melanoma cell line SKMEL28, parental, MAPKi sensitive, DMSO treated for 2 days
CellLine.FPKM.batch1.xlsx


title: Pt9-D15-B

description:
Patient 9 melanoma, during BRAFi and MEKi treatment, day 15, 2nd biopsy
PatientFPKM.batch3.xlsx

source_name: tumor biopsy

extract_protocol:
mirVana RNA extraction kit
KAPA Stranded mRNA-Seq Kits, stranded
Poly A transcript enrichment, paired end RNAseq


title: Pt9-D15-A

description:
Patient 9 melanoma, during BRAFi and MEKi treatment, day 15, 1st biopsy
PatientFPKM.batch3.xlsx


title: Pt9-baseline

description:
Patient 9 melanoma, pre MAPKi treatment, 1st biopsy
PatientFPKM.batch3.xlsx


title: M395 P1

description:
Melanoma cell line M395, parental, MAPKi sensitive, DMSO treated for 2 days
CellLine.FPKM.batch2.xlsx

source_name: Melanoma cell line


title: M249-DDR4

status: Public on Sep 07 2017

description:
Melanoma cell line M249 DDR4, BRAFi+MEKi resistant subline of M249 (clone DDR4)
CellLine.FPKM.batch1.xlsx


title: M249-P1

description:
Melanoma cell line M249, parental, MAPKi sensitive, DMSO treated for 2 days
CellLine.FPKM.batch1.xlsx


title: M249-DDR5

description:
Melanoma cell line M249 DDR5, BRAFi+MEKi resistant subline of M249 (clone DDR5)
CellLine.FPKM.batch1.xlsx


title: M238-SDR-2

status: Public on Sep 05 2017

description:
Melanoma cell line M238R1, BRAFi resistant  subline of M238 (clone R1), Rep 2
CellLine.FPKM.batch1.xlsx

extract_protocol:
mirVana RNA extraction kit
TruSeq RNA Sample Preparation Kit v2
Poly A transcript enrichment, paired end RNAseq


title: M238-SDR-1

description:
Melanoma cell line M238R1, BRAFi resistant  subline of M238 (clone R1), Rep 1
CellLine.FPKM.batch1.xlsx


title: M238-DTP-2

description:
Melanoma cell line M238, treated with BRAFi , DTP population, Rep 2
CellLine.FPKM.batch1.xlsx


title: M238-DTP-1

description:
Melanoma cell line M238, treated with BRAFi , DTP population, Rep 1
CellLine.FPKM.batch1.xlsx


title: M238-DTPP-2

description:
Melanoma cell line M238, treated with BRAFi , DTPP population, Rep 2
CellLine.FPKM.batch1.xlsx


title: M229-SDR-2

description:
Melanoma cell line M229R5, BRAFi resistant  subline of M229 (clone R5), Rep 2
CellLine.FPKM.batch1.xlsx


title: M238-P-2

description:
Melanoma cell line M238, parental, MAPKi sensitive, DMSO treated for 2 days, Rep 2
CellLine.FPKM.batch1.xlsx


title: M238-BRAFi2D-1

description:
Melanoma cell line M238, treated with BRAFi  for 2 days, Rep 1
CellLine.FPKM.batch1.xlsx


title: M238-BRAFi2D-2

description:
Melanoma cell line M238, treated with BRAFi  for 2 days, Rep 2
CellLine.FPKM.batch1.xlsx


title: SKMEL28 DTPP

description: Melanoma cell line

source_name: Melanoma cell line SKMEL28, treated with BRAFi (PLX4320 1uM), DTPP population


title: SKMel28-SDR

description:
Melanoma cell line SKMEL28R1, BRAFi resistant  subline of SKMEL28 (clone R1)
CellLine.FPKM.batch1.xlsx


title: M229-SDR-1

description:
Melanoma cell line M229R5, BRAFi resistant  subline of M229 (clone R5), Rep 1
CellLine.FPKM.batch1.xlsx


title: M229-BRAFi2D-1

description:
Melanoma cell line M229, treated with BRAFi for 2 days, Rep 1
CellLine.FPKM.batch1.xlsx


title: M229-DTPP-1

description:
Melanoma cell line M229, treated with BRAFi , DTPP population, Rep 1
CellLine.FPKM.batch1.xlsx


title: M229-DTP-1

description:
Melanoma cell line M229, treated with BRAFi , DTP population, Rep 1
CellLine.FPKM.batch1.xlsx


title: M229-DTP-2

description:
Melanoma cell line M229, treated with BRAFi , DTP population, Rep 2
CellLine.FPKM.batch1.xlsx


title: M229-P-2

description:
Melanoma cell line M229, parental, MAPKi sensitive, DMSO treated for 2 days, Rep 2
CellLine.FPKM.batch1.xlsx


title: M229-BRAFi2D-2

description:
Melanoma cell line M229, treated with BRAFi  for 2 days, Rep 2
CellLine.FPKM.batch1.xlsx


title: M229-P-1

description:
Melanoma cell line M229, parental, MAPKi sensitive, DMSO treated for 2 days, Rep 1
CellLine.FPKM.batch1.xlsx


title: M238-DTPP-1

description:
Melanoma cell line M238, treated with BRAFi , DTPP population, Rep 1
CellLine.FPKM.batch1.xlsx


title: Pt8 D22

description:
Patient 8 melanoma, during BRAFi and MEKi treatment, day 22, 1st biopsy
PatientFPKM.xlsx


title: Pt7 D15B

description:
Patient 7 melanoma, during MEKi treatment, day 15, 2nd biopsy
PatientFPKM.xlsx

value: MEKi


title: Pt7 baseline

description:
Patient 7 melanoma, pre MAPKi treatment, 1st biopsy
PatientFPKM.xlsx


title: Pt5-baseline.replicate1

type: RNA

description: Patient 5 melanoma, pre MAPKi treatment, 1st biopsy, replicate

hyb_protocol: GeneAtlas at 48C for 24 hours

scan_protocol: GeneAtlas scanner

data_processing:
CEL files are loaded using oligo R package. Probe set definition is based on pd.hugene.1.0.st.v1 R package. Gene level raw expression values is computed by fitProbeLevelModel function using the 'target=core' argument. Expression values is then RMA normalized.
probe group file: pd.hugene.1.0.st.v1 R package

label: biotin

label_protocol: Ambion GeneChip® WT PLUS Reagent Kit (4411974)

extract_protocol: Qiagen RNeasy Mini kit (cat #: 74104)

tag: mapki sensitivity

value: sensitive


title: Pt5-baseline.replicate2

description: Patient 5 melanoma, pre MAPKi treatment, 1st biopsy, replicate 2


title: Pt6 D12

description:
Patient 6 melanoma, during BRAFi and MEKi treatment, day 12, 1st biopsy
PatientFPKM.xlsx


title: Pt5-D15

description: Patient 5 melanoma, BRAFi on-Tx D15, 1st biopsy

value: On-treatment, responding to BRAFi


title: Pt5-D15.replicate2

description: Patient 5 melanoma, BRAFi on-Tx D15, 1st biopsy, replicate 2


title: Pt6 D6

description:
Patient 6 melanoma, during BRAFi treatment, day 15, 1st biopsy
PatientFPKM.xlsx


title: Pt5-baseline

description: Patient 5 melanoma, pre MAPKi treatment, 1st biopsy


title: M238-P-1

description:
Melanoma cell line M238, parental, MAPKi sensitive, DMSO treated for 2 days, Rep 1
CellLine.FPKM.batch1.xlsx


title: Pt3 D22

description:
Patient 3 melanoma, during BRAFi and MEKi treatment, day 22, 1st biopsy
PatientFPKM.xlsx


title: Pt4 baseline

description:
Patient 4 melanoma, pre MAPKi treatment, 1st biopsy
PatientFPKM.xlsx


title: Pt5-D15.replicate1

description: Patient 5 melanoma, BRAFi on-Tx D15, 1st biopsy, replicate


title: Pt8 baseline

description:
Patient 8 melanoma, pre MAPKi treatment, 1st biopsy
PatientFPKM.xlsx


title: M229-DTPP-2

description:
Melanoma cell line M229, treated with BRAFi , DTPP population, Rep 2
CellLine.FPKM.batch1.xlsx


title: Pt2 baseline

description:
Patient 2 melanoma, pre MAPKi treatment, 1st biopsy
PatientFPKM.xlsx


title: Pt1 D85

description:
Patient 1 melanoma, during BRAFi treatment, day 85, 1st biopsy
PatientFPKM.xlsx


title: Pt7 D15A

description:
Patient 7 melanoma, during MEKi treatment, day 15, 1st biopsy
PatientFPKM.xlsx


title: Pt1 baseline

description:
Patient 1 melanoma, pre MAPKi treatment, 1st biopsy
PatientFPKM.xlsx


title: Pt6 D15

description:
Patient 6 melanoma, during BRAFi and MEKi treatment, day 15 (using a combination of two different BRAFi and MEKi), 1st biopsy
PatientFPKM.xlsx


title: Pt6 baseline

description:
Patient 6 melanoma, pre MAPKi treatment, 1st biopsy
PatientFPKM.xlsx


title: Pt4 RD261

description:
Patient 4 melanoma, during BRAFi and MEKi treatment, day 261, 1st biopsy
PatientFPKM.xlsx


title: Pt4 D15

description:
Patient 4 melanoma, during BRAFi and MEKi treatment, day 15, 1st biopsy
PatientFPKM.xlsx


title: Pt3 baseline

description:
Patient 3 melanoma, pre MAPKi treatment, 1st biopsy
PatientFPKM.xlsx


title: Pt2 D726

description:
Patient 2 melanoma, during BRAFi treatment, day 726, 1st biopsy
PatientFPKM.xlsx


title: Pt7 D15C

description:
Patient 7 melanoma, during MEKi treatment, day 15, 3rd biopsy
PatientFPKM.xlsx


title: AFX023_muscle_6weeks

status: Public on Aug 31 2017

city: Washington

first: Yi-Wen

last: Chen

state: DC

address: 111 Michigan Ave NW

institute: Children's Research Institute

hyb_protocol: Biotin-labelled and fragmented cRNAs were hybridized to the Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 800.

source_name: medial gastrocnemius, immobilization

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA.

extract_protocol: Total RNA was extracted according to the standard Affymetrix protocol including Trizol extraction and Rneasy column cleanup.

tag: rehabilitation

value: high responder

tag: immobolization

tag: time point

value: 6 weeks after rehabilitation

tag: gender

value: male


title: AFX025_muscle_immobolization

value: immobilization

value: female


title: AFX024_muscle_immobolization


title: AFX024_muscle_4months

source_name: medial gastrocnemius, uninvolved leg

value: 4 months after rehabilitation


title: AFX031_muscle_6weeks


title: AFX022_muscle_immobolization


title: AFX026_muscle_immobolization


title: AFX024_muscle_6weeks


title: AFX021_muscle_3weeks

value: low responder

value: 3 weeks after rehabilitation


title: AFX025_muscle_3weeks


title: AFX023_muscle_4months


title: AFX023_muscle_immobolization


title: AFX026_muscle_3weeks


title: AFX026_muscle_6weeks


title: AFX023_muscle_3weeks


title: AFX021_muscle_immobolization


title: AFX022_muscle_4months


title: AFX024_muscle_3weeks


title: AFX021_muscle_6weeks


title: AFX020_muscle_4months


title: AFX022_muscle_3weeks


title: AFX022_muscle_6weeks


title: AFX021_muscle_4months


title: AFX019_muscle_immobolization


title: AFX020_muscle_6weeks


title: AFX019_muscle_6weeks


title: AFX020_muscle_immobolization


title: AFX020_muscle_3weeks


title: AFX019_muscle_4months


title: AFX017_muscle_immobolization


title: AFX016_muscle_4months


title: AFX013_muscle_4months


title: AFX017_muscle_6weeks


title: AFX013_muscle_6weeks


title: AFX018_muscle_immobolization


title: AFX014_muscle_6weeks


title: AFX015_muscle_6weeks


title: AFX016_muscle_6weeks


title: AFX015_muscle_immobolization


title: AFX017_muscle_3weeks


title: AFX012_muscle_immobolization


title: AFX014_muscle_3weeks


title: AFX019_muscle_3weeks


title: AFX014_muscle_immobolization


title: AFX012_muscle_6weeks


title: AFX015_muscle_4months


title: AFX013_muscle_immobolization


title: AFX016_muscle_3weeks


title: AFX012_muscle_4months


title: AFX015_muscle_3weeks


title: AFX010_muscle_6weeks


title: AFX010_muscle_4months


title: AFX011_muscle_3weeks


title: AFX017_muscle_4months


title: AFX012_muscle_3weeks


title: AFX013_muscle_3weeks


title: AFX009_muscle_6weeks


title: AFX011_muscle_4months


title: AFX007_muscle_4months


title: AFX011_muscle_6weeks


title: TapeStrip_FAIRE_3

status: Public on Aug 28 2017

data_processing:
Illumina Off-Line Basecaller(OLB) v1.9.4 software used for basecalling
The quality of FASTQ files was assessed with FASTQC
reads were aligned to human genome assembly hg19 using Bowtie2 with default parameters
bam files of the same sample type were merged with BamTools Merge
bigwig files were generated using merged bam files as input with DeepTools bamCoverage 2.5.0 with a 50bp bin size, minimum mapping quality of 25, and minimum fragment length of 25
bed files were generated using merged bam files as input with Homer findPeaks  with -tbp 1 -size 200 -fdr 0.05 -L 0
Specialized peak files were generated by performing BedTools intersect with >25% overlap on the bed files for sample types of interest, and then BedTools subtract to remove peaks with >10% overlap with selected background files.  FAIRE peaks identified in ENCODE non-keratinocyte cell types were also subracted.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files include signal values for a the coverage of a given bam file across the genome
Supplementary_files_format_and_content: bed files were generated with Homer findPeaks and represent distinct regions of DNA whose sequences are enriched compared with the genome in general.
Supplementary_files_format_and_content: specialized peak files (linked as Series supplementary files) include: Epidermal peaks- Keratinocyte, ESS, Graft, and Tape Strip intersect; ThreeD-ESS, Graft, and TapeStrip intersect with Keratinocytes subtracted; Stable- Graft and TapeStrip intersect with ESS and Keratinocytes subtracted; IntactBarrier-Graft with ESS and TapeStrip subtracted; BarrierDeficient- ESS and TapeStrip intersect with Graft subtracted.

extract_protocol:
DNA was recovered from fixed tissue sonicated in 5% SDS followed by phenol-chloroform extraction
DNA fragments underwent end repair with T4 DNA polymerase, Klenow DNA Polymerase , and T4 polynucleotide kinase. Following purification with Agencourt AmPure XP DNA-binding beads in polyethylene glycol (PEG) at a 1.9:1 bead: DNA volume ratio, adenine bases were added to the ends of each fragment with Klenow exonuclease. Pre-annealed Illumina adaptors were ligated overnight at 16°C with T4 DNA ligase. Unligated adaptors and adaptor dimers were removed with an AMPure XP bead purification (1.2:1 bead: DNA) performed twice. PCR following adaptor ligation was performed with Phusion High-Fidelity DNA Polymerase (ThermoScientific F-530L) using unique Illumina TruSeq DNA LT indexing primers for 12-14 amplification cycles. Following PCR, amplified DNA underwent a final AmPure XP bead purification at a 1.1:1 or 1:1 PEG to DNA volume ratio.

tag: sample type

value: ESS grafted to nude mouse

tag: passage

tag: growth media

tag: treatment

value: tape-stripping


title: TapeStrip_FAIRE_4


title: AFX007_muscle_6weeks


title: AFX010_muscle_3weeks


title: AFX006_muscle_6weeks


title: AFX007_muscle_3weeks


title: AFX009_muscle_3weeks


title: AFX008_muscle_4months


title: AFX007_muscle_immobolization


title: AFX009_muscle_4months


title: AFX006_muscle_4months


title: TapeStrip_FAIRE_2


title: Graft_FAIRE_4


title: Graft_FAIRE_3


title: Graft_FAIRE_Merge

description: bamMerge Graft FAIRE 1-4


title: ESS_FAIRE_6

value: engineered skin substitute (ESS)

value: UCDM-1 (Boyce, et al., 2017)


title: TapeStrip_FAIRE_1


title: ESS_FAIRE_5


title: Keratinocyte_FAIRE_3

value: primary epidermal keratinocytes

value: MCDB 153 (Boyce, et al., 1995)


title: Keratinocyte_FAIRE_Merge

description: bamMerge Keratinocyte FAIRE 1-5


title: AFX006_muscle_immobolization


title: TapeStrip_FAIRE_Merge

description: bamMergeTapeStrip FAIRE 1-4


title: Keratinocyte_FAIRE_1


title: Graft_FAIRE_2


title: Keratinocyte_FAIRE_2


title: AFX006_muscle_3weeks


title: Graft_FAIRE_1


title: ESS_FAIRE_Merge

description: bamMerge ESS FAIRE 1-6


title: ESS_FAIRE_4


title: ESS_FAIRE_2


title: ESS_FAIRE_3


title: Pt4_OnTx

status: Public on May 09 2017

description: Patient 4 melanoma, on anti-PD-1 treatment

source_name: on-anti-PD-1 treatment_tumor biopsy

tag: subject status/id

value: melanoma patient 4

value: on-treatment

tag: tissue

value: Melanoma biopsy


title: ESS_FAIRE_1


title: Pt2_baseline

description: Patient 2 melanoma, pre anti-PD-1 treatment

source_name: baseline_tumor biopsy

value: melanoma patient 2

value: pre-treatment


title: Pt4_baseline

description: Patient 4 melanoma, pre anti-PD-1 treatment


title: Keratinocyte_FAIRE_5


title: Pt5_OnTx

description: Patient 5 melanoma, on anti-PD-1 treatment

value: melanoma patient 5


title: Pt5_baseline

description: Patient 5 melanoma, pre anti-PD-1 treatment


title: KO897

status: Public on Jun 30 2016

data_processing:
aligement use Tophat:tophat-2.0.3.Linux_x86_64 with parameters -p 4 -G   --splice-mismatches 2 --max-multihits 1 --min-intron-length 20  --library-type fr-unstranded
abundance measurements use cufflinks:cufflinks-2.2.1.Linux_x86_64 with parameters -p 4 -v -u   -G
differential expression use cuffdiff:versions cufflinks-2.2.1.Linux_x86_64/cuffdiff ,with parameters -p 5 --library-type fr-unstranded  -m 400
DAVID functional annotation use differential expression gene between WT and KO
Gene set enrichment anslysis(GSEA) use gene profiling generated from cofflinks.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample,differentiation experssion gene between WT and KO

source_name: Asxl1-/-_BM-derived MSPCs

extract_protocol:
2x10^6 MSPCs were harvested and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

value: BM-derived Mesenchymal stem/progenitor cells (MSPCs)

tag: passages


title: Mouse-CtrlD2

status: Public on Jul 29 2016

data_processing:
FASTQ files were mapped by Tophat2
Tophat BAMs were quantified and normalized using Cuffnorm, DGE were called by cuffdiff
Genome_build: mm9
Supplementary_files_format_and_content: The normalized expression levels by cuffnorm

source_name: Mouse Tissue with Incisional Wound, Day 2, no treatment

extract_protocol:
See Methods
Poly A tail enriching, single end RNAseq

treatment_protocol: See Methods

value: skin

tag: background strain

tag: day


title: WT532

source_name: WT_BM-derived MSPCs

value: Wild type

tag: cell type


title: Pt2_OnTx

description: Patient 2 melanoma, on anti-PD-1 treatment


title: Pt38

status: Public on Mar 18 2016

description: Patient 38 melanoma, pre anti-PD-1 treatment, 1st biopsy

data_processing:
FASTQ files were mapped by Tophat2
Tophat BAMs were quantified and normalized using Cuffnorm (for gene analysis) and by htseq-count followed by edgeR's log CPM (for gene-set analysis)
Genome_build: hg19
Supplementary_files_format_and_content: The normalized expression levels by cuffnorm

source_name: tumor biopsy_Partial Response

extract_protocol:
mirVana RNA extraction kit
TruSeq RNA Sample Preparation Kit v2 (unstranded) and KAPA stranded RNA kit (stranded)
Poly A transcript enrichment, paired end RNAseq

tag: patient id

tag: anti-pd-1 response

value: Partial Response

tag: study site

value: VIC

value: F

tag: age (yrs)

tag: disease status

tag: overall survival (days)

tag: vital status

value: Alive

tag: previous mapki

value: Y

tag: anatomical location

value: Cervical, LN

value: Pembrolizumab

tag: biopsy time

value: Melanoma biopsies

tag: stranded/unstranded rnaseq

value: stranded


title: Keratinocyte_FAIRE_4

tag: sample type

value: primary epidermal keratinocytes

tag: passage

tag: growth media

value: MCDB 153 (Boyce, et al., 1995)

tag: treatment


title: Pt3_OnTx

description: Patient 3 melanoma, on anti-PD-1 treatment

tag: subject status/id

value: melanoma patient 3

value: on-treatment

tag: tissue

value: Melanoma biopsy


title: Pt3_baseline

description: Patient 3 melanoma, pre anti-PD-1 treatment

value: pre-treatment


title: Mouse-CtrlD14

source_name: Mouse Tissue with Incisional Wound, Day 14, no treatment

value: skin

tag: background strain

tag: day


title: Mouse-VemD14

source_name: Mouse Tissue with Incisional Wound, Day 14, Vemurafenib treated once every other day


title: Pt1_baseline

description: Patient 1 melanoma, pre anti-PD-1 treatment

value: melanoma patient 1


title: Pt1_OnTx

description: Patient 1 melanoma, on anti-PD-1 treatment


title: Mouse-VemD6

source_name: Mouse Tissue with Incisional Wound, Day 6, Vemurafenib treated once every other day


title: Pt31

description: Patient 31 melanoma, pre anti-PD-1 treatment, 1st biopsy

source_name: tumor biopsy_Progressive Disease

tag: patient id

tag: anti-pd-1 response

value: Progressive Disease

tag: study site

tag: gender

value: M

value: N

value: Sigmoid colon

tag: braf


title: Mouse-CtrlD6

source_name: Mouse Tissue with Incisional Wound, Day 6, no treatment


title: Pt28

description: Patient 28 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: Partial Response

value: UCLA

tag: age (yrs)

tag: disease status

tag: overall survival (days)

tag: vital status

value: Dead

tag: previous mapki

value: Scalp, SC

value: unstranded


title: Pt23

description: Patient 23 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: Y

tag: anatomical location

value: Left Leg, SC

value: Pembrolizumab

tag: biopsy time

value: Melanoma biopsies

tag: stranded/unstranded rnaseq


title: Pt27B

description: Patient 27 melanoma, pre anti-PD-1 treatment, 2nd biopsy

source_name: tumor biopsy_Complete Response

value: Complete Response

value: Alive

value: R upper back

tag: nras

tag: treatment

value: stranded


title: Pt37

description: Patient 37 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: VIC

value: F

value: Small bowel

value: pre-treatment

tag: tissue


title: Mouse-VemD2

source_name: Mouse Tissue with Incisional Wound, Day 2, Vemurafenib treated once every other day

value: skin

tag: background strain

tag: day


title: KO511

tag: strain background

tag: genotype/variation

tag: cell type

value: BM-derived Mesenchymal stem/progenitor cells (MSPCs)

tag: passages


title: WT535

value: Wild type


title: Pt32

description: Patient 32 melanoma, pre anti-PD-1 treatment, 1st biopsy

tag: patient id

tag: anti-pd-1 response

value: Progressive Disease

tag: study site

tag: gender

value: M

tag: age (yrs)

value: Dead

value: Abdominal wall

tag: braf


title: Pt35

description: Patient 35 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: Partial Response

tag: disease status

tag: overall survival (days)

tag: vital status

tag: previous mapki

value: Y

tag: anatomical location

value: Flank

value: Pembrolizumab

tag: biopsy time


title: Pt19

description: Patient 19 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: UCLA

value: Alive

value: N

value: Chest, SC

tag: nras

tag: treatment

tag: tissue

value: Melanoma biopsies

tag: stranded/unstranded rnaseq

value: unstranded


title: Pt15

description: Patient 15 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: R clavicle, LN

value: pre-treatment


title: Pt14

description: Patient 14 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: F

value: R neck, SC


title: Pt29

description: Patient 29 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: Progressive Disease

value: M

value: Lung


title: Pt25

description: Patient 25 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: Dead

value: L Outer Inguinal


title: Pt27A

description: Patient 27 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: Complete Response

value: R upper arm

value: stranded


title: Pt9

description: Patient 9 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: UCLA

value: Alive

value: L forearm, SC

value: Pembrolizumab


title: Pt7

description: Patient 7 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: N

value: Crown/scalp, SC

value: Melanoma biopsies

value: unstranded


title: Pt22

description: Patient 22 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: Left Flank, SC

value: pre-treatment


title: Pt6

description: Patient 6 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: Partial Response

value: M

value: Y


title: Pt20

description: Patient 20 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: Progressive Disease

value: F

value: Dead

value: L clavicle

value: K615K Splice Site


title: Pt13

description: Patient 13 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: Complete Response

value: UCLA

value: Alive

value: Lower back, SC


title: Pt10

description: Patient 10 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: Neck, SC

value: Pembrolizumab


title: Pt8

description: Patient 8 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: N

value: R leg, SC

value: Melanoma biopsies

value: unstranded


title: Pt5

description: Patient 5 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: Partial Response

value: M

value: L Chestwall, SC

value: pre-treatment


title: Pt16

description: Patient 16 melanoma, on-anti-PD-1 treatment, 1st biopsy

value: Progressive Disease

value: Dead

value: Y

value: Lung

value: on-treatment


title: Pt12

description: Patient 12 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: UCLA

value: L lower abdomen, SC


title: Pt2

description: Patient 2 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: Alive

value: Frame_Shift_Ins H31fs, Splice_Site


title: Pt1

description: Patient 1 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: F

value: N

value: L post. Thigh, inf., SC

value: Pembrolizumab


title: Pt4

description: Patient 4 melanoma, pre anti-PD-1 treatment, 1st biopsy

value: Partial Response

value: Adrenal

value: Melanoma biopsies

value: unstranded


title: SKMel28R1-PLX-1

status: Public on Sep 15 2015

type: genomic

description: Melanoma cell line SKMel28, BRAFi resistant subline

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: To identify the differentially methylated CpG sites, we analyze the Illumina 450K Methylation array output data using R-package minfi (Aryee et al., 2014). Raw image IDAT files were loaded into the R statistical computing environment using minfi, and the data was normalized using the SWAN function. This output a matrix of methylation indices (beta values), which were continuous values between 0 and 1 representing the ratio/fraction of the intensity of the methylated-probe signal to the total signal intensity for each probed CpG site. For each site, the methylation change was measured by the percent methylation difference (Δbeta) from paired baseline to DP/DD-DP samples. Minfi function dmpFinder was then applied to calculate the p-value of the logit transformed differential methylation. The p-values were corrected for multiple hypothesis testing with false discovery rates (FDR) q-values. We then used a cutoff of q-value ≤ 0.05 to define differential methylation

label: Cy5 and Cy3

source_name: tumor cell line

label_protocol: Not provided

extract_protocol: genomic DNA

tag: cell type

value: melanoma

tag: mapki sensitivity

value: resistant

tag: mapki treatment

value: BRAFi


title: SKMel28-DMSO-2

description: Melanoma cell line SKMel28, parental, MAPKi sensitive in DMSO, rep 2

value: sensitive


title: SKMel28DDR1-PLXAZD-1

description: Melanoma cell line SKMel28, BRAF+MEKi resistant subline

value: BRAFi+MEKi


title: M229-DMSO2D-3

description: Melanoma cell line M229, parental, MAPKi sensitive in DMSO, rep 3


title: SKMel28DDR1-PLXAZD-2

description: Melanoma cell line SKMel28, BRAF+MEKi resistant subline, rep 2


title: M238-DMSO2D-2

description: Melanoma cell line M238, parental, MAPKi sensitive in DMSO, rep 2


title: M238-DMSO2D-1

description: Melanoma cell line M238, parental, MAPKi sensitive in DMSO


title: M229-DMSO2D-2

description: Melanoma cell line M229, parental, MAPKi sensitive in DMSO, rep 2


title: M238R1-PLX-2

description: Melanoma cell line M238, BRAFi resistant subline, rep 2


title: M238R1-PLX-1

description: Melanoma cell line M238, BRAFi resistant subline


title: M229R5-PLX-2

description: Melanoma cell line M229, BRAFi resistant subline, rep 2


title: SKMel28R1-PLX-2

description: Melanoma cell line SKMel28, BRAFi resistant subline, rep 2


title: Pt22-DD-DP1-2

description: Patient 22 melanoma, post BRAFi+MEKi resistance, 1st biopsy, replicate

source_name: tumor biopsy


title: Pt23-DD-DP1-1

description: Patient 23 melanoma, post BRAFi+MEKi resistance, 1st biopsy


title: Pt22-DD-DP3-2

description: Patient 22 melanoma, post BRAFi+MEKi resistance, 3rd biopsy, replicate


title: Pt23-baseline-1

description: Patient 23 melanoma, pre MAPKi treatment, 1st biopsy


title: M229R5-PLX-3

description: Melanoma cell line M229, BRAFi resistant subline, rep 3


title: Pt22-baseline1-1

description: Patient 22 melanoma, pre MAPKi treatment, 1st biopsy


title: M229R5-PLX-1

description: Melanoma cell line M229, BRAFi resistant subline


title: M229DDRpoly-PLXAZD-1

description: Melanoma cell line M229, BRAF+MEKi resistant subline


title: SKMel28R1-PLX

description: Melanoma cell line SKMel28, BRAFi resistant subline

data_processing:
FASTQ files were mapped by Tophat2
Tophat BAMs were quantified and normalized using Cuffnorm, DGE were called by cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: The normalized expression levels by cuffnorm

source_name: Melanoma cell line

extract_protocol:
Poly A tail enriching, paired end RNAseq
TruSeq RNA Sample Preparation Kit v2


title: M229DDRpoly-PLXAZD-2

description: Melanoma cell line M229, BRAF+MEKi resistant subline, rep 2


title: Pt22-DD-DP1-1

description: Patient 22 melanoma, post BRAFi+MEKi resistance, 1st biopsy


title: M229-DMSO2D-1

description: Melanoma cell line M229, parental, MAPKi sensitive in DMSO


title: SKMel28-DMSO

description: Melanoma cell line SKMel28, parental, MAPKi sensitive in DMSO


title: Pt22-DD-DP3-1

description: Patient 22 melanoma, post BRAFi+MEKi resistance, 3rd biopsy


title: Pt23-DD-DP1-2

description: Patient 23 melanoma, post BRAFi+MEKi resistance, 1st biopsy, replicate


title: SKMel28-DMSO-1


title: M238R1-PLX

description: Melanoma cell line M238, BRAFi resistant subline


title: M229DDRpoly-PLXAZD


title: M229R5-PLX


title: Pt23-baseline-2

description: Patient 23 melanoma, pre MAPKi treatment, 1st biopsy, replicate


title: Pt22-DD-DP2-2

description: Patient 22 melanoma, post BRAFi+MEKi resistance, 2nd biopsy, replicate


title: Pt24-DDP1

description: Patient 24 melanoma, post BRAFi+MEKi resistance, 1st biopsy


title: Pt24-baseline

description: Patient 24 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt23-DDP1

description: Patient 23 melanoma, post BRAFi+MEKi resistance, 1st biopsy


title: M238-DMSO2D

description: Melanoma cell line M238, parental, MAPKi sensitive in DMSO


title: Pt22-DDP3

description: Patient 21 melanoma, post BRAFi+MEKi resistance, 3rd biopsy


title: M229-DMSO2D


title: Pt22-baseline1-2

description: Patient 22 melanoma, pre MAPKi treatment, 1st biopsy, replicate


title: Pt22-DD-DP2-1

description: Patient 22 melanoma, post BRAFi+MEKi resistance, 2nd biopsy


title: Pt22-DDP1

description: Patient 21 melanoma, post BRAFi+MEKi resistance, 1st biopsy


title: Pt23-baseline

description: Patient 23 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt21-DP2

description: Patient 21 melanoma, post BRAFi resistance, 2nd biopsy (surrogate reference for BRAFi+MEKi resistant tumors)


title: Pt22-DDP2

description: Patient 21 melanoma, post BRAFi+MEKi resistance, 2nd biopsy


title: Pt21-DDP2


title: Pt22-baseline

description: Patient 22 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt21-DDP1


title: Pt20-DP1

description: Patient 20 melanoma, post BRAFi+MEKi resistance, 2nd biopsy


title: Pt20-DDP1

description: Patient 20 melanoma, post BRAFi+MEKi resistance, 1st biopsy


title: Pt21-DP2-2

description: Patient 21 melanoma, post BRAFi resistance, 2nd biopsy, replicate (surrogate baseline for BRAFi+MEKi tumors)


title: Pt20-baseline

description: Patient 20 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt19-DDP2

description: Patient 19 melanoma, post BRAFi+MEKi resistance, 2nd biopsy


title: Pt21-DD-DP1-2

description: Patient 21 melanoma, post BRAFi+MEKi resistance, 1st biopsy, replicate


title: Pt19-DDP1

description: Patient 19 melanoma, post BRAFi+MEKi resistance, 1st biopsy


title: Pt21-DD-DP1-1


title: Pt18-DDP1

description: Patient 18 melanoma, post BRAFi+MEKi resistance, 1st biopsy


title: Pt19-baseline

description: Patient 19 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt21-DP2-1

description: Patient 21 melanoma, post BRAFi resistance, 2nd biopsy (surrogate baseline for BRAFi+MEKi tumors)


title: Pt20-DP1-2

description: Patient 20 melanoma, post BRAFi resistance, 1st biopsy, replicate


title: Pt18-baseline

description: Patient 18 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt20-DD-DP1-2

description: Patient 20 melanoma, post BRAFi+MEKi resistance, 1st biopsy, replicate


title: Pt20-baseline-2

description: Patient 20 melanoma, pre MAPKi treatment, 1st biopsy, replicate


title: Pt17-DP2

description: Patient 17 melanoma, post BRAFi resistance, 2nd biopsy


title: SKMel28DDR1-PLXAZD

description: Melanoma cell line SKMel28, BRAF+MEKi resistant subline


title: Pt20-DP1-1

description: Patient 20 melanoma, post BRAFi resistance, 1st biopsy


title: Pt20-baseline-1


title: Pt19-baseline-1


title: Pt17-DP1

description: Patient 17 melanoma, post BRAFi resistance, 1st biopsy


title: Pt18-DD-DP1-1


title: Pt18-DD-DP1-2

description: Patient 18 melanoma, post BRAFi+MEKi resistance, 1st biopsy, replicate


title: Pt18-baseline-1


title: Pt17-baseline

description: Patient 17 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt16-DP1

description: Patient 16 melanoma, post BRAFi resistance, 1st biopsy


title: Pt16-baseline

description: Patient 16 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt19-baseline-2

description: Patient 19 melanoma, pre MAPKi treatment, 1st biopsy, replicate


title: Pt18-baseline-2

description: Patient 18 melanoma, pre MAPKi treatment, 1st biopsy, replicate


title: Pt15-DP2

description: Patient 15 melanoma, post BRAFi resistance, 2nd biopsy


title: Pt17-baseline-2

description: Patient 17 melanoma, pre MAPKi treatment, 1st biopsy, replicate


title: Pt19-DD-DP1-2

description: Patient 19 melanoma, post BRAFi+MEKi resistance, 1st biopsy, replicate


title: Pt17-DP1-1


title: Pt15-DP1

description: Patient 15 melanoma, post BRAFi resistance, 1st biopsy


title: Pt15-baseline

description: Patient 15 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt20-DD-DP1-1

description: Patient 20 melanoma, post BRAFi+MEKi resistance, 1st biopsy


title: Pt10-DP9

description: Patient 10 melanoma, post BRAFi resistance, 9th biopsy


title: Pt17-DP2-1

description: Patient 17 melanoma, post BRAFi resistance, 2nd biopsy


title: Pt10-DP8

description: Patient 10 melanoma, post BRAFi resistance, 8th biopsy


title: Pt10-DP7

description: Patient 10 melanoma, post BRAFi resistance, 7th biopsy


title: Pt17-baseline-1


title: Pt10-DP6

description: Patient 10 melanoma, post BRAFi resistance, 6th biopsy


title: Pt17-DP2-2

description: Patient 17 melanoma, post BRAFi resistance, 2nd biopsy, replicate


title: Pt21-DD-DP2-2

description: Patient 21 melanoma, post BRAFi+MEKi resistance, 2nd biopsy, replicate


title: Pt21-DD-DP2-1

description: Patient 21 melanoma, post BRAFi+MEKi resistance, 2nd biopsy


title: Pt10-DP5

description: Patient 10 melanoma, post BRAFi resistance, 5th biopsy


title: Pt19-DD-DP1-1

description: Patient 19 melanoma, post BRAFi+MEKi resistance, 1st biopsy


title: Pt17-DP1-2

description: Patient 17 melanoma, post BRAFi resistance, 1st biopsy, replicate


title: Pt10-DP4

description: Patient 10 melanoma, post BRAFi resistance, 4th biopsy


title: Pt10-DP3

description: Patient 10 melanoma, post BRAFi resistance, 3rd biopsy


title: Pt10-DP2

description: Patient 10 melanoma, post BRAFi resistance, 2nd biopsy


title: Pt10-DP1

description: Patient 10 melanoma, post BRAFi resistance, 1st biopsy


title: Pt10-baseline

description: Patient 10 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt16-baseline-2

description: Patient 16 melanoma, pre MAPKi treatment, 1st biopsy, replicate


title: Pt9-DP1

description: Patient 9 melanoma, post BRAFi resistance, 1st biopsy


title: Pt15-DP2-1

description: Patient 15 melanoma, post BRAFi resistance, 2nd biopsy


title: Pt9-DP2

description: Patient 9 melanoma, post BRAFi resistance, 2nd biopsy


title: Pt9-baseline

description: Patient 9 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt16-baseline-1

description: Patient 16 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt8-DP3

description: Patient 8 melanoma, post BRAFi resistance, 3rd biopsy


title: Pt8-DP2

description: Patient 8 melanoma, post BRAFi resistance, 2nd biopsy


title: Pt15-DP2-2

description: Patient 15 melanoma, post BRAFi resistance, 2nd biopsy, replicate


title: Pt8-DP1

description: Patient 8 melanoma, post BRAFi resistance, 1st biopsy


title: Pt15-DP1-1

description: Patient 15 melanoma, post BRAFi resistance, 1st biopsy


title: Pt15-baseline-1

description: Patient 15 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt8-baseline

description: Patient 8 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt15-DP1-2

description: Patient 15 melanoma, post BRAFi resistance, 1st biopsy, replicate


title: Pt14-DP1-1

description: Patient 14 melanoma, post BRAFi resistance, 1st biopsy


title: Pt6-DP2

description: Patient 6 melanoma, post BRAFi resistance, 2nd biopsy


title: Pt6-baseline

description: Patient 6 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt16-DP1-2

description: Patient 16 melanoma, post BRAFi resistance, 1st biopsy, replicate


title: Pt5-DP3

description: Patient 5 melanoma, post BRAFi resistance, 3rd biopsy


title: Pt14-DP1-2

description: Patient 14 melanoma, post BRAFi resistance, 1st biopsy, replicate


title: Pt10-DP8-2

description: Patient 10 melanoma, post BRAFi resistance, 8th biopsy, replicate


title: Pt14-baseline-1

description: Patient 14 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt5-DP2

description: Patient 5 melanoma, post BRAFi resistance, 2nd biopsy


title: Pt6-DP1

description: Patient 6 melanoma, post BRAFi resistance, 1st biopsy


title: Pt15-baseline-2

description: Patient 15 melanoma, pre MAPKi treatment, 1st biopsy, replicate


title: Pt5-DP1

description: Patient 5 melanoma, post BRAFi resistance, 1st biopsy


title: Pt16-DP1-1

description: Patient 16 melanoma, post BRAFi resistance, 1st biopsy


title: Pt5-baseline

description: Patient 5 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt4-DP1

description: Patient 4 melanoma, post BRAFi resistance, 1st biopsy


title: Pt4-baseline

description: Patient 4 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt10-DP6-2

description: Patient 10 melanoma, post BRAFi resistance, 6th biopsy, replicate


title: Pt10-DP7-2

description: Patient 10 melanoma, post BRAFi resistance, 7th biopsy, replicate


title: Pt10-DP7-1

description: Patient 10 melanoma, post BRAFi resistance, 7th biopsy


title: Pt10-DP6-1

description: Patient 10 melanoma, post BRAFi resistance, 6th biopsy


title: Pt3-DP2

description: Patient 3 melanoma, post BRAFi resistance, 2nd biopsy


title: Pt10-DP9-1

description: Patient 10 melanoma, post BRAFi resistance, 9th biopsy


title: Pt10-DP5-1

description: Patient 10 melanoma, post BRAFi resistance, 5th biopsy


title: Pt3-baseline

description: Patient 3 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt10-DP3-1

description: Patient 10 melanoma, post BRAFi resistance, 3rd biopsy


title: Pt3-DP1

description: Patient 3 melanoma, post BRAFi resistance, 1st biopsy


title: Pt2-DP1

description: Patient 2 melanoma, post BRAFi resistance, 1st biopsy


title: Pt10-DP4-2

description: Patient 10 melanoma, pre MAPKi treatment, 4th biopsy, replicate


title: Pt2-DP2

description: Patient 2 melanoma, post BRAFi resistance, 2nd biopsy


title: Pt10-DP9-2

description: Patient 10 melanoma, post BRAFi resistance, 9th biopsy, replicate


title: Pt10-DP5-2

description: Patient 10 melanoma, post BRAFi resistance, 5th biopsy, replicate


title: Pt10-baseline2-2

description: Patient 10 melanoma, pre MAPKi treatment, 1st biopsy, replicate


title: Pt14-baseline-2

description: Patient 14 melanoma, pre MAPKi treatment, 1st biopsy, replicate


title: Pt2-baseline

description: Patient 2 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt1-DP1

description: Patient 1 melanoma, post BRAFi resistance, 1st biopsy


title: Pt1-baseline

description: Patient 1 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt10-DP2-1

description: Patient 10 melanoma, post BRAFi resistance, 2nd biopsy


title: Pt3-DP3

description: Patient 3 melanoma, post BRAFi resistance, 3rd biopsy


title: Pt10-DP2-2

description: Patient 10 melanoma, post BRAFi resistance, 2nd biopsy, replicate


title: Pt10-DP1-1

description: Patient 10 melanoma, post BRAFi resistance, 1st biopsy


title: Pt10-DP3-2

description: Patient 10 melanoma, post BRAFi resistance, 3rd biopsy, replicate


title: Pt10-DP4-1

description: Patient 10 melanoma, pre MAPKi treatment, 4th biopsy


title: Pt10-baseline2-1

description: Patient 10 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt9-DP2-1

description: Patient 9 melanoma, post BRAFi resistance, 2nd biopsy


title: Pt9-DP1-2

description: Patient 9 melanoma, post BRAFi resistance, 1st biopsy, replicate


title: Pt10-DP1-2

description: Patient 10 melanoma, post BRAFi resistance, 1st biopsy, replicate


title: Pt9-baseline-1

description: Patient 9 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt9-DP2-2

description: Patient 9 melanoma, post BRAFi resistance, 2nd biopsy, replicate


title: Pt8-DP2-2

description: Patient 8 melanoma, post BRAFi resistance, 2nd biopsy, replicate


title: Pt9-baseline-2

description: Patient 9 melanoma, pre MAPKi treatment, 1st biopsy, replicate


title: Pt8-DP3-2

description: Patient 8 melanoma, post BRAFi resistance, 3rd biopsy, replicate


title: Pt7-DP1-1

description: Patient 7 melanoma, post BRAFi resistance, 1st biopsy


title: Pt10-DP8-1

description: Patient 10 melanoma, post BRAFi resistance, 8th biopsy


title: Pt8-DP2-1

description: Patient 8 melanoma, post BRAFi resistance, 2nd biopsy


title: Pt8-DP1-1

description: Patient 8 melanoma, post BRAFi resistance, 1st biopsy


title: Pt8-baseline-2

description: Patient 8 melanoma, pre MAPKi treatment, 1st biopsy, replicate


title: Pt7-DP1-2

description: Patient 7 melanoma, post BRAFi resistance, 1st biopsy, replicate


title: Pt6-DP2-2

description: Patient 6 melanoma, post BRAFi resistance, 2nd biopsy, replicate


title: Pt8-DP1-2

description: Patient 8 melanoma, post BRAFi resistance, 1st biopsy, replicate


title: Pt6-baseline-1

description: Patient 6 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt6-baseline-2

description: Patient 6 melanoma, pre MAPKi treatment, 1st biopsy, replicate


title: Pt6-DP2-1

description: Patient 6 melanoma, post BRAFi resistance, 2nd biopsy


title: Pt6-DP1-1

description: Patient 6 melanoma, post BRAFi resistance, 1st biopsy


title: Pt8-DP3-1

description: Patient 8 melanoma, post BRAFi resistance, 3rd biopsy


title: Pt7-baseline-2

description: Patient 7 melanoma, pre MAPKi treatment, 1st biopsy, replicate


title: Pt9-DP1-1

description: Patient 9 melanoma, post BRAFi resistance, 1st biopsy


title: Pt6-DP1-2

description: Patient 6 melanoma, post BRAFi resistance, 1st biopsy, replicate


title: Pt5-DP2-2

description: Patient 5 melanoma, post BRAFi resistance, 2nd biopsy, replicate


title: Pt5-DP1-2

description: Patient 5 melanoma, post BRAFi resistance, 1st biopsy, replicate


title: Pt5-DP2-1

description: Patient 5 melanoma, post BRAFi resistance, 2nd biopsy


title: Pt4-DP1-2

description: Patient 4 melanoma, post BRAFi resistance, 1st biopsy, replicate


title: Pt5-baseline-2

description: Patient 5 melanoma, pre MAPKi treatment, 1st biopsy, replicate


title: Pt7-baseline-1

description: Patient 7 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt5-DP3-1

description: Patient 5 melanoma, post BRAFi resistance, 3rd biopsy


title: Pt5-baseline-1

description: Patient 5 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt3-DP3-2

description: Patient 3 melanoma, post BRAFi resistance, 3rd biopsy, replicate


title: Pt4-baseline-1

description: Patient 4 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt5-DP3-2

description: Patient 5 melanoma, post BRAFi resistance, 3rd biopsy, replicate


title: N1 ChIP

status: Public on Aug 01 2015

description: Illumina next-generation sequencing

data_processing:
SpDamID-seq enriched segments were identified using Poisson model comparing against DAM library and for the triplicates only segments called in 2 out of 3 replicates were retained
N1 ChIP enriched segments were identified by requiring over 10 fold more reads than in the input and segments mapping to repeat regions were masked
Total FAIRE sites were identified using MAC peak calling of N1wt FAIRE compared against input and requiring that the same site must be present in all 3 N1wt vs input FAIRE comparisons
Notch1-dependent FAIRE sites were identified using MAC peak calling of N1wt FAIRE compared against Control FAIRE and requiring that the same site must have been called in all 3 N1wt vs Control FAIRE comparisons
Genome_build: mm9

extract_protocol:
SpDamID used Dneasy extraction kit, DpnI digestion, and ligation mediated PCR to generate libraries that are in turn sonicated and ligated to bar-coded Illumina sequencing adaptors; FAIRE was performed by sonicating formaldehyde cross-linked nuclei and phenol:chloroform extraction of open chromatin compared to input DNA extracted after cross-link reversal, ChIP used myc-epitope tag to immunoprecipitate bound DNA from sonicated cross-linked DNA
Illumina library construction protocol

tag: strain

tag: cell line


title: Pt7-baseline

data_processing:
CEL files are loaded using oligo R package. Probe set definition is based on pd.hugene.2.1.st R package. Gene level raw expression values is computed by fitProbeLevelModel function using the 'target=core' argument. Expression values is then RMA normalized.
pd.hugene.2.1.st R package

extract_protocol: total RNA


title: Pt3-DP1-2

description: Patient 3 melanoma, post BRAFi resistance, 1st biopsy, replicate


title: Pt4-baseline-2

description: Patient 4 melanoma, pre MAPKi treatment, 1st biopsy, replicate


title: N1wt FAIRE_2

description: Illumina next-generation sequencing


title: Pt7-DP1

description: Patient 7 melanoma, post BRAFi resistance, 1st biopsy


title: Pt3-DP1-1

description: Patient 3 melanoma, post BRAFi resistance, 1st biopsy


title: Pt3-DP3-1

description: Patient 3 melanoma, post BRAFi resistance, 3rd biopsy


title: ChIP input

description: Illumina next-generation sequencing


title: Pt3-DP2-1

description: Patient 3 melanoma, post BRAFi resistance, 2nd biopsy


title: Pt3-baseline-2

description: Patient 3 melanoma, pre MAPKi treatment, 1st biopsy, replicate


title: Pt7-DP1.replicate

description: Patient 7 melanoma, post BRAFi resistance, 1st biopsy, replicate


title: Mef2c-D/p300-AM-Ert2

description: Illumina next-generation sequencing

data_processing:
Library strategy: SpDamID-seq
SpDamID-seq enriched segments were identified using Poisson model comparing against DAM library and for the triplicates only segments called in 2 out of 3 replicates were retained
N1 ChIP enriched segments were identified by requiring over 10 fold more reads than in the input and segments mapping to repeat regions were masked
Total FAIRE sites were identified using MAC peak calling of N1wt FAIRE compared against input and requiring that the same site must be present in all 3 N1wt vs input FAIRE comparisons
Notch1-dependent FAIRE sites were identified using MAC peak calling of N1wt FAIRE compared against Control FAIRE and requiring that the same site must have been called in all 3 N1wt vs Control FAIRE comparisons
Genome_build: mm9


title: N1wt_FAIRE input

description: Illumina next-generation sequencing


title: Pt8-baseline-1

description: Patient 8 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt2-baseline-1

description: Patient 2 melanoma, pre MAPKi treatment, 1st biopsy


title: Pt1-DP1-1

description: Patient 1 melanoma, post BRAFi resistance, 1st biopsy


title: Control FAIRE_2

description: Illumina next-generation sequencing


title: Mef2c-D/MAML-AM-Ert2

description: Illumina next-generation sequencing


title: N1-D/N1-AM-Ert2_1

description: Illumina next-generation sequencing


title: N1wt FAIRE_1

description: Illumina next-generation sequencing


title: Control FAIRE_1

description: Illumina next-generation sequencing


title: N1-D/p300-AM-Ert2_3

description: Illumina next-generation sequencing


title: Pt2-DP2-2

description: Patient 2 melanoma, post BRAFi resistance, 2nd biopsy, replicate


title: Pt2-DP1-1

description: Patient 2 melanoma, post BRAFi resistance, 1st biopsy


title: N1-D/p300-AM-Ert2_2

description: Illumina next-generation sequencing


title: N1-D/MAML-AM-Ert2_3

description: Illumina next-generation sequencing


title: Pt4-DP1-1

description: Patient 4 melanoma, post BRAFi resistance, 1st biopsy


title: N1-D/MAML-AM-Ert2_1

description: Illumina next-generation sequencing


title: N1-D/RBP-AM-Ert2_2

description: Illumina next-generation sequencing


title: N1-D/MAML-AM-Ert2_2

description: Illumina next-generation sequencing


title: N1-D/RBP-AM-Ert2_3

description: Illumina next-generation sequencing


title: Pt7-baseline.replicate

description: Patient 7 melanoma, pre MAPKi treatment, 1st biopsy, replicate


title: N1-D/p300-AM-Ert2_1

description: Illumina next-generation sequencing


title: Pt2-baseline-2

description: Patient 2 melanoma, pre MAPKi treatment, 1st biopsy, replicate


title: N1-D/N1-AM-Ert2_2

description: Illumina next-generation sequencing


title: DAM_3

description: Illumina next-generation sequencing


title: DAM_2

description: Illumina next-generation sequencing


title: Mef2c-D/p300-AM-Ert2_3_vs_DPNII

description: promoter array analysis

hyb_protocol: Nimblegen hybridization protocol performed by MoGene Inc

scan_protocol: performed by MoGene Inc

data_processing:
Signal was mapped to DpnI fragments and compared against signal produced by D/AM controls
Experimental signal was compared against D/AM control signal and scored based on anova analysis of replicates to identify DpnI fragments showing enrichment over control

label_protocol: Nimblegen labeling protocol performed by MoGene Inc.

extract_protocol: Dneasy extraction kit, Dpn1 digestion, adaptor ligation, and adaptor mediated PCR for library generation

source_name: DpnII background


title: DAM_1

description: Illumina next-generation sequencing


title: Control FAIRE_3

description: Illumina next-generation sequencing


title: N1-D/RBP-AM-Ert2_1

description: Illumina next-generation sequencing


title: Mef2c-D/MAML-AM-Ert2_3_vs_DPNII

description: promoter array analysis


title: Pt2-DP1-2

description: Patient 2 melanoma, post BRAFi resistance, 1st biopsy, replicate


title: Mef2c-D/MAML-AM-Ert2_2_vs_DPNII

description: promoter array analysis


title: Pt5-DP1-1

description: Patient 5 melanoma, post BRAFi resistance, 1st biopsy


title: Mef2c-D/MAML-AM-Ert2_1_vs_DPNII

description: promoter array analysis


title: Pt3-baseline-1

description: Patient 3 melanoma, pre MAPKi treatment, 1st biopsy


title: N1-D/N1-AM-Ert2_2_vs_DPNII

description: promoter array analysis


title: Mef2c-D/p300-AM-Ert2_2_vs_DPNII

description: promoter array analysis


title: N1-D/p300-AM-Ert2_3_vs_DPNII

description: promoter array analysis


title: N1-D/p300-AM-Ert2_1_vs_DPNII

description: promoter array analysis


title: Pt2-DP2-1

description: Patient 2 melanoma, post BRAFi resistance, 2nd biopsy


title: N1-D/MAML-AM-Ert2_1_vs_DPNII

description: promoter array analysis


title: N1-D/p300-AM-Ert2_2_vs_DPNII

description: promoter array analysis


title: N1-D/MAML-AM-Ert2_2_vs_DPNII

description: promoter array analysis


title: N1-D/RBP-AM-Ert2+Dox_3_vs_DPNII

description: promoter array analysis


title: N1-D/RBP-AM-Ert2+Dox_2_vs_DPNII

description: promoter array analysis


title: Pt3-DP2-2

description: Patient 3 melanoma, post BRAFi resistance, 2nd biopsy, replicate


title: N1-D/RBP-AM-Ert2+Dox_1_vs_DPNII

description: promoter array analysis


title: N1Dram-D/RBP-AM-Ert2+Dox_3_vs_DPNII

description: promoter array analysis


title: N1-D/RBP-AM-Ert2_3_vs_DPNII

description: promoter array analysis


title: N1-D/MAML-AM-Ert2_3_vs_DPNII

description: promoter array analysis


title: N1Dram-D/RBP-AM-Ert2+Dox_2_vs_DPNII

description: promoter array analysis


title: N1Dram-D/RBP-AM-Ert2+Dox_1_vs_DPNII

description: promoter array analysis


title: N1-D/RBP-AM-Ert2_2_vs_DPNII

description: promoter array analysis


title: DAM_3_vs_DPNII

description: promoter array analysis


title: DAM_1_vs_DPNII

description: promoter array analysis


title: N1-D/RBP-AM-Ert2_1_vs_DPNII

description: promoter array analysis


title: DAM_2_vs_DPNII

description: promoter array analysis


title: Pt1-DP1-2

description: Patient 1 melanoma, post BRAFi resistance, 1st biopsy, replicate


title: Pt1-baseline-2

description: Patient 1 melanoma, pre MAPKi treatment, 1st biopsy, replicate


title: Pt1-baseline-1

description: Patient 1 melanoma, pre MAPKi treatment, 1st biopsy


title: N1wt FAIRE_3

description: Illumina next-generation sequencing


title: N1-D/N1-AM-Ert2_1_vs_DPNII

description: promoter array analysis


title: rat SCI14d, rep2

status: Public on Jun 30 2015

description: Gene expression profile of rat soleus muscle

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard G2500A Gene Array Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Rattus norvegicus

source_name: rat soleus, 14 days after SCI, rep2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

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

treatment_protocol: Rat soleus of total 36 samples including  controls; 3, 8 and 14 days after SCI; 8 and 14 days after SCI with locomotor treadmill training.  N=6

tag: time point

value: 14 days after SCI

tag: tm (locomotor treadmill training)

value: No


title: Mef2c-D/p300-AM-Ert2_1_vs_DPNII

description: promoter array analysis


title: rat SCI8d, TM, rep2

source_name: rat soleus, 8 days after SCI, with locomotor treadmill training, rep2

value: 8 days after SCI

value: Yes


title: rat SCI8d, TM, rep6

source_name: rat soleus, 8 days after SCI, with locomotor treadmill training, rep6


title: rat SCI8d, TM, rep5

source_name: rat soleus, 8 days after SCI, with locomotor treadmill training, rep5


title: rat SCI14d, TM, rep2

source_name: rat soleus, 14 days after SCI, with locomotor treadmill training, rep2


title: rat SCI8d, TM, rep3

source_name: rat soleus, 8 days after SCI, with locomotor treadmill training, rep3


title: rat SCI14d, TM, rep1

source_name: rat soleus, 14 days after SCI, with locomotor treadmill training, rep1


title: rat SCI14d, rep5

source_name: rat soleus, 14 days after SCI, rep5


title: rat SCI14d, TM, rep5

source_name: rat soleus, 14 days after SCI, with locomotor treadmill training, rep5


title: rat SCI3d, rep5

source_name: rat soleus, 3 days after SCI, rep5

value: 3 days after SCI


title: rat SCI8d, rep6

source_name: rat soleus, 8 days after SCI, rep6


title: rat SCI14d, rep4

source_name: rat soleus, 14 days after SCI, rep4


title: rat SCI8d, rep5

source_name: rat soleus, 8 days after SCI, rep5


title: rat SCI3d, rep3

source_name: rat soleus, 3 days after SCI, rep3


title: rat SCI8d, rep1

source_name: rat soleus, 8 days after SCI, rep1


title: rat SCI8d, rep3

source_name: rat soleus, 8 days after SCI, rep3


title: rat SCI8d, rep4

source_name: rat soleus, 8 days after SCI, rep4


title: rat SCI14d, TM, rep4

source_name: rat soleus, 14 days after SCI, with locomotor treadmill training, rep4


title: rat SCI14d, rep3

source_name: rat soleus, 14 days after SCI, rep3


title: rat SCI8d, TM, rep4

source_name: rat soleus, 8 days after SCI, with locomotor treadmill training, rep4


title: rat SCI14d, rep1

source_name: rat soleus, 14 days after SCI, rep1


title: rat SCI3d, rep2

source_name: rat soleus, 3 days after SCI, rep2


title: rat SCI14d, TM, rep3

source_name: rat soleus, 14 days after SCI, with locomotor treadmill training, rep3


title: rat SCI8d, rep2

source_name: rat soleus, 8 days after SCI, rep2


title: rat SCI14d, TM, rep6

source_name: rat soleus, 14 days after SCI, with locomotor treadmill training, rep6


title: rat SCI8d, TM, rep1

source_name: rat soleus, 8 days after SCI, with locomotor treadmill training, rep1


title: rat SCI3d, rep6

source_name: rat soleus, 3 days after SCI, rep6


title: rat SCI14d, rep6

source_name: rat soleus, 14 days after SCI, rep6


title: rat SCI3d, rep4

source_name: rat soleus, 3 days after SCI, rep4


title: rat Control, rep6

source_name: rat soleus, control, rep6

value: Pre


title: rat Control, rep4

source_name: rat soleus, control, rep4


title: LSK_Aspp1-/-

status: Public on May 20 2015

city: Memphis

first: Masayuki

last: Yamashita

state: TN

address: 262 Danny Thomas Place

department: Division of Experimental Hematology, Department of Hematology

institute: St. Jude Children's Research Hospital

hyb_protocol: For each hybridization, 0.60 μg of Cy3 labeled cRNA were fragmented and hybridized to an Agilent SurePrint Mouse GE 8x60K Microarray (Design ID: 028005) at 65°C for 17 h.

scan_protocol: After washing, microarrays were scanned using an Agilent DNA microarray scanner.

data_processing: Intensity values of each scanned feature were quantified using Agilent feature extraction software version 10.7.3.1, which performs background subtractions. Normalization was performed using Agilent GeneSpring version 12.6.1. (per chip: normalization to 75 percentile shift; per gene: normalization to median of all samples).

source_name: Aspp1-/- LSK cells

label_protocol: Total RNA was amplified and labeled with Cyanine 3 (Cy3) using Agilent Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies) following the manufacturer’s instructions. Labeled cRNAs were purified using Qiagen’s RNeasy mini spin columns and eluted in 30 μl of nuclease-free water. After amplification and labeling, cRNA quantity and cyanine incorporation were determined using a Nanodrop ND-1000 spectrophotometer and an Agilent Bioanalyzer.

extract_protocol: Total RNA was further purified using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions. RNA quantity and quality were determined using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, USA) and an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), as recommended.

treatment_protocol: 8-week-old WT, Aspp1-/-, Mx1-Cre(+)p53flox/flox and Mx1-Cre(+)Aspp1-/-p53flox/flox mice were intraperitoneally administered with 400 μg pIpC five times every other day to obtain WT, Aspp1-/-, p53-/- and Aspp1-/-p53-/- bone marrow. 4 weeks after pIpC treatment, bone marrow lineage(-) Sca-1(+) cKit(+) cells were isolated.

tag: strain background

tag: gender

value: male

tag: age

tag: genotype/variation

tag: treated with

value: 401 μg pIpC five times every other day

value: bone marrow


title: rat Control, rep5

source_name: rat soleus, control, rep5


title: rat SCI3d, rep1

source_name: rat soleus, 3 days after SCI, rep1


title: rat Control, rep2

source_name: rat soleus, control, rep2


title: LSK_Aspp1-/-p53-/-

source_name: Aspp1-/-p53-/- LSK cells

value: 403 μg pIpC five times every other day

value: bone marrow lineage(-) Sca-1(+) cKit(+) cells


title: C2C12 cells transfected with pCIneo, biological rep3

status: Public on Apr 08 2013

description: Gene expression data from C2C12 cells transfected with pCIneo

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 and Mouse 430 Plus 2.0 arrays for human and mouse samples respectively. Gene Chips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: C2C12 cells transfected with pCIneo (insertless vector)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400 ng total RNA.

growth_protocol: The cell culture and transfection experiments of both the RD and C2C12 cells were conducted in parallel under the same conditions. A total of 1 x 105 cells were seeded and cultured to 60% confluence in Dulbecco’s modified Eagle’s medium containing 10% heat inactivated fetal bovine serum (Sigma-Aldrich) and 1% penicillin-streptomycin in 25 cm2 flasks at 37 °C, 5% CO2.

treatment_protocol: The cells were transfected with 6.25 ug pCIneo-DUX4 expression vector (n=4) using Lipofectamine LTX (Life Technologies) according to the manufacturer’s protocol, and cells collected 16 hours afterwards.

value: mouse C2C12 myoblast cells

value: control


title: RD cells transfected with pCIneo-DUX4, biological rep1

description: Gene expression data from RD cells transfected with pCIneo-DUX4

source_name: RD cells transfected with pCIneo-DUX4

value: human rhabdmyosarcoma cancer cells

value: DUX4 ectopic expression


title: C2C12 cells transfected with pCIneo, biological rep1


title: C2C12 cells transfected with pCIneo-DUX4, biological rep1

description: Gene expression data from C2C12 cells transfected with pCIneo-DUX4


title: C2C12 cells transfected with pCIneo, biological rep4


title: rat Control, rep1

source_name: rat soleus, control, rep1


title: RD cells transfected with pCIneo-DUX4, biological rep4


title: LSK_p53-/-

source_name: p53-/- LSK cells

value: 402 μg pIpC five times every other day


title: C2C12 cells transfected with pCIneo-DUX4, biological rep4


title: LSK_WT

description: WT

source_name: WT LSK cells

value: wild type

value: 400 μg pIpC five times every other day


title: C2C12 cells transfected with pCIneo-DUX4, biological rep2


title: RD cells transfected with pCIneo, biological rep1

description: Gene expression data from RD cells transfected with pCIneo

source_name: RD cells transfected with pCIneo (insertless vector)


title: rat Control, rep3

source_name: rat soleus, control, rep3

value: No


title: RD cells transfected with pCIneo-DUX4, biological rep2


title: C2C12 cells transfected with pCIneo-DUX4, biological rep3


title: RD cells transfected with pCIneo, biological rep2


title: RD cells transfected with pCIneo-DUX4, biological rep3


title: RD cells transfected with pCIneo, biological rep3


title: C2C12 cells transfected with pCIneo, biological rep2


title: RD cells transfected with pCIneo, biological rep4


title: Muscle, regular-muscle [TG40886]

status: Public on Feb 19 2013

description: From HR line #8

hyb_protocol: Biotin-labelled and fragmented cRNAs were hybridized to the Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA).

source_name: left or right gastrocnemius muscles of regular-muscle mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

growth_protocol: Male mice were used from an animal model of selectively bred for high voluntary wheel-running behaviour (HR) and lines bred without intentional selection.  Animals used in the current work were sampled from generation 37 at a mean age of 84 days (range = 79-86).  We used gastrocnemius muscles (including both lateral and medial portions) from the mice described above for HRmini line #3 and HRnormal line #8 (n = 6, in each group).  To obtain sufficient RNA, gastrocnemius samples of HRmini were pooled from left and right limbs from each animal, whereas HRnormal gastrocnemius was sampled from either left or right limb only.

value: left or right gastrocnemius muscles


title: Muscle, mini-muscle [TG40804]

description: From HR line #3

source_name: left and right gastrocnemius muscles of mini-muscle mouse

value: left and right gastrocnemius muscles


title: Muscle, regular-muscle [TG40457]

description: From HR line #8


title: Muscle, mini-muscle [TG40592]

description: From HR line #3


title: Muscle, mini-muscle [TG40805]

description: From HR line #3


title: Muscle, regular-muscle [TG40146]

description: From HR line #8


title: Muscle, regular-muscle [TG40449]

description: From HR line #8


title: Muscle, regular-muscle [TG40708]

description: From HR line #8


title: Muscle, regular-muscle [TG40160]

description: From HR line #8


title: Muscle, mini-muscle [TG40190]

description: From HR line #3


title: Muscle, mini-muscle [TG40062]

description: From HR line #3


title: 10-muscle_SCI_Day5

status: Public on Oct 23 2010

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 plus2  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip  Scanner 3000.

source_name: vastus lateralis, SCI

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted according to the standard Affymetrix protocol including Trizol extraction and Rneasy column cleanup

treatment_protocol: Nine male patients and one female patient with spinal cord injury (SCI) (Mean ± SEM = 43.9 ± 6.7 yrs) were recruited for this study.

tag: human sci

value: Day 5

value: vastus lateralis


title: Muscle, mini-muscle [TG40077]

description: From HR line #3

value: male


title: 10-muscle_SCI_Day2

value: Day 2


title: 6-muscle_SCI_Day5


title: 7-muscle_SCI_Day5


title: 5-muscle_SCI_Day2


title: 2-muscle_SCI_Day2


title: 8-muscle_SCI_Day5


title: 8-muscle_SCI_Day2


title: 2-muscle_SCI_Day5


title: 6-muscle_SCI_Day2


title: 3-muscle_SCI_Day2


title: 3-muscle_SCI_Day5


title: 5-muscle_SCI_Day5


title: 4-muscle_SCI_Day2


title: 9-muscle_SCI_Day2


title: 4-muscle_SCI_Day5


title: 1-muscle_SCI_Day2


title: 9-muscle_SCI_Day5


title: 7-muscle_SCI_Day2


title: 1-muscle_SCI_Day5


title: 1-Muscle_Unloading_0h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 plus2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

source_name: vastus lateralis, control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

treatment_protocol: Seven sedentary men (n = 7, mean age ± S.D = 22.1 ± 3.7 yr) following 48h unloading (UL) via unilateral lower limb suspension and 24h reloading (RL).

tag: protocol

tag: time

value: 0 hour


title: 1-Muscle_Reloading_24h

source_name: vastus lateralis, reloading

tag: tissue

value: reloading

value: 24 hour


title: 1-Muscle_Unloading_48h

source_name: vastus lateralis, unloading

value: unloading

value: 48 hour


title: 2-Muscle_Unloading_48h


title: 2-Muscle_Reloading_24h


title: 2-Muscle_Unloading_0h

value: control


title: 3-Muscle_Unloading_0h


title: 4-Muscle_Unloading_48h


title: 3-Muscle_Unloading_48h


title: 4-Muscle_Unloading_0h


title: 6-Muscle_Unloading_0h


title: 3-Muscle_Reloading_24h


title: 6-Muscle_Unloading_48h


title: 7-Muscle_Unloading_0h


title: 4-Muscle_Reloading_24h


title: 5-Muscle_Unloading_0h


title: 7-Muscle_Unloading_48h


title: 5-Muscle_Unloading_48h


title: 6-Muscle_Reloading_24h


title: 7-Muscle_Reloading_24h


title: Muscle_AQM_Treatment S 3

status: Public on Aug 31 2009

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

organism: Sus scrofa

source_name: biceps femoris, treated with Sepsis

treatment_protocol: Sixteen female domestic piglets (Sus scrofa, average body weight 26.5 kg) were used in this study. All piglets were immobilized by anesthesia and mechanically ventilated (Servo 900C, Siemens-Elema, Solna, Sweden). The first m. biceps femoris biopsies (day 1)  were obtained from all animals, after administering anesthetics. During the five day study period, four  animals were sedated using isoflurane inhalation (Abbott Laboratories, Chicago, Il, USA, 0.8 – 1.3% end-tidal concentration) supplemented by intravenous bolus doses of morphine and ketamine as needed. Biopsies from the m. biceps femoris were obtained on two further separate occasions (days 3 and 5) in these animals. Core body temperature (blood) was maintained in the range of 38.5 – 40°C by a servocontrolled heating pad.  The animals received intravenous crystalloid fluid (Ringer’s acetate) to maintain stable blood pressure and urinary output and a glucose infusion (Rehydrex, Fresenius Kabi, Stockholm, Sweden, 25 mg glucose /mL) in the range of 0.5 – 1.5 mg/kg/minute to decrease the effects of catabolism.  Each animal received prophylactic streptomycin 750 mg/d and benzylpenicillin 600 mg/d (Streptocillin Vet, Boeringer-Ingelheim, Hellerup, Denmark). Arterial blood gas analysis as well as electrolytes and blood glucose levels were monitored regularly and kept in the normal range throughout the study period.

tag: disease

value: acute quadriplegic myopathy (porcine AQM)

value: Day 1


title: Muscle_AQM_Control D5 3

source_name: biceps femoris, control


title: Muscle_AQM_Control D3 2

value: Day 3


title: Muscle_AQM_Control D3 1


title: Muscle_AQM_Control D3 3


title: Muscle_AQM_Treatment S 4


title: Muscle_AQM_Control D5 2


title: Muscle_AQM_Control D3 4


title: Muscle_AQM_Control D5 1


title: Muscle_AQM_Control D5 4


title: Muscle_AQM_Treatment N CS S 2

source_name: biceps femoris, treated with non-depolarizing neuromuscular blocking agents(NMBA),Corticosteroids(CS) and sepsis


title: Muscle_AQM_Treatment N CS S 1


title: Muscle_AQM_Treatment N CS S 4


title: Muscle_AQM_Control D1 2


title: Muscle_AQM_Treatment S 1


title: Muscle_AQM_Treatment CS 3

source_name: biceps femoris,treated with corticosteroids


title: Muscle_AQM_Treatment CS 1


title: Muscle_AQM_Treatment S 2


title: Muscle_AQM_Control D1 3


title: Muscle_AQM_Treatment CS 4


title: Muscle_AQM_Treatment N CS S 3


title: Muscle_AQM_Control D1 1


title: Muscle_AQM_Treatment CS 2


title: Muscle_AQM_Control D1 4


title: 5-Muscle_Reloading_24h


title: Muscle JDM (YJD-JDM-8UA-s2)

status: Public on Jul 18 2008

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133A  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

source_name: skeletal muscle, long duration

tag: duration of untreated disease in month:105.6

tag: age at onset:2.6


title: Muscle JDM (YJD-JDM-6UA-s2)

tag: duration of untreated disease in month:3.2

tag: age at onset:8.4


title: Muscle control (YJD-JDM-54UA-s2)

source_name: skeletal muscle, normal control

tag: control


title: Muscle control (YJD-JDM-50UA-s2)


title: Muscle JDM (YJD-JDM-3UA-s2)

tag: duration of untreated disease in month:7.7

tag: age at onset:1.6


title: Muscle control (YJD-JDM-51UA-s2)


title: Muscle control (YJD-JDM-48UA-s2)


title: Muscle JDM (YJD-JDM-5UA-s2)

tag: duration of untreated disease in month:2.1

tag: age at onset:8.3


title: Muscle JDM (YJD-JDM-30UA-s2)

tag: duration of untreated disease in month:30.6

tag: age at onset:1.0


title: Muscle JDM (YJD-JDM-9UA-S2)

tag: duration of untreated disease in month:4.9


title: Muscle JDM (YJD-JDM-25UA-s2)

tag: duration of untreated disease in month:13.6

tag: age at onset:2.5


title: Muscle JDM (YJD-JDM-23UA-s2)

tag: duration of untreated disease in month:2.2

tag: age at onset:7.2


title: Muscle JDM (YJD-JDM-2UA-s2)

source_name: skeletal muscle, short duration

tag: duration of untreated disease in month:1.1

tag: age at onset:4.7


title: Muscle JDM (YJD-JDM-1UA-s2)

tag: age at onset:6.8


title: Muscle JDM (YJD-JDM-21UA-s2)

tag: duration of untreated disease in month:2.6

tag: age at onset:8.8


title: Muscle JDM (YJD-JDM-19UA-s2)

tag: duration of untreated disease in month:6.1

tag: age at onset:1.8


title: Muscle JDM (YJD-JDM-18UA-s2)

tag: duration of untreated disease in month:16.1

tag: age at onset:3.9


title: Muscle JDM (YJD-JDM-13UA-s2)

tag: duration of untreated disease in month:8.5

tag: age at onset:4.5


title: Muscle JDM (YJD-JDM-15UA-s2)

tag: duration of untreated disease in month:6.6

tag: age at onset:6.1


title: Muscle JDM (YJD-JDM-14UA-s2)

tag: duration of untreated disease in month:6.5

tag: age at onset:7.7


title: Muscle JDM (YJD-JDM-16UA-s2)

tag: duration of untreated disease in month:0.6

tag: age at onset:5.5


title: Muscle JDM (YJD-JDM-12UA-s2)

tag: duration of untreated disease in month

tag: age at onset


title: Muscle JDM (YJD-JDM-10UA-S2)