title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_D8_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_D9_AD007_indexed

status: Public on Aug 27 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: MOs

tag: Sex

value: male

tag: age

tag: strain


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_D9_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_D7_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_D8_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_D8_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_D7_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_D7_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_D7_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_D8_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_D8_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_E10_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_D8_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_D7_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_D6_AD008_indexed


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title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_C4_AD012_indexed


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title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_C12_AD012_indexed


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title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_A12_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_A10_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_A10_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_A12_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_A1_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H8_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_A10_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_A10_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H9_AD006_indexed


title: Tempus xO assay DNA sequencing [19_T]

city: Chicago

first: Pedram

last: Gerami

state: Illinois

address: 420 E Superior St

institute: Northwestern University

description:
19-AST
Skin
19_AST.vcf
19-AST.soma.pindel.vcf

data_processing:
Library strategy: DNA-seq
FASTQ files containing raw sequencing data were generated using BCL2FASTQ version 2.17 from Illumina Inc.
NovoAlign version 3.05.00 was used for reference sequence alignment.
Variant calls were performed using Freebayes version 1.0.2.58-g054b257.
Indel calls were performed using Pindel version 0.2.5.b9.
RNA fusion calls were performed using P.ARC version 2.5.2.
RNA expression analysis was conducted with CRISP version 1.4.2.4.
Variants were filtered using proprietary Tempus VCF filtering code.
Genome_build: GRCh37, GRCh38, 1000 genomes human reference, HG19, ExAC Database V 0.3.1, Tempus Knowledge database (KDB) V.0.1 COSMIC database version 79 GRCh37
Supplementary_files_format_and_content: .txt files containing RNA counts were generated from FASTQ files using CRISP version 1.4.2.4.
Supplementary_files_format_and_content: VCF files containing DNA variants were generated using Freebayes version 1.0.2.58-g054b257.

organism: Homo sapiens

source_name: Sptitz Tumor

extract_protocol:
Tumor total nucleic acid was extracted from at least ten 5-micron FFPE tissue sections with tumor cellularity > 20% by a Chemagic360 instrument (PerkinElmer, MA) using a source-specific magnetic bead protocol and digested with proteinase K. Nucleic acid is quantified by a Quant-iT picogreen dsDNA reagent Kit or Quant-iT Ribogreen RNA Kit (Life Technologies, CA). A Covaris ultrasonicator mechanically sheared 100 nanograms of DNA from each tumor and normal sample to an average size of 200 base pairs (bp).
Libraries were prepared with KAPA Hyper Prep Kit (Kapa Biosystems, MA). DNA underwent enzymatic end-repair and A-tailing, adapter ligation, bead-based size selection, PCR and probe hybridization. KAPA HiFi HotStart ReadyMix (Kapa Biosystems, MA) was used to amplify captured DNA targets which were then sequenced to an average depth of 500X on the Illumina HiSeq 4000 System (Illumina, Inc., CA) utilizing patterned flow cell technology. One hundred nanograms of RNA per tumor sample was fragmented in the presence of magnesium to an average size of 200 bp. The RNA then underwent first strand cDNA synthesis using random primers, followed by combined second strand synthesis and A-tailing, adapter ligation, bead-based cleanup and library amplification. Samples were then hybridized with the IDT xGEN Exome Research Panel (IDT Inc., CA) and sequenced to obtain > 50 million reads on the Illumina HiSeq 4000 System (Illumina, Inc., San Diego, CA) utilizing patterned flow cell technology.
Next-generation sequencing (DNA with 1711 gene panel and whole transcriptome RNA sequencing).

tag: tissue

value: Sptitz Tumor (tumor)


title: Tempus xO assay DNA sequencing [1_T]

description:
1-AST
Skin
1_AST.vcf
1-AST.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [19_N]

value: Sptitz Tumor (normal)


title: Tempus xO assay DNA sequencing [199_T]

description:
199-SN
Skin
199_SN.vcf
199-SN.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_A2_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_A10_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H9_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_A1_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H9_AD010_indexed


title: Tempus xO assay DNA sequencing [197_T]

description:
197-SN
Skin
197_SN.vcf
197-SN.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [195_T]

description:
195-AST
Skin
195_AST.vcf
195-AST.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_A10_AD001_indexed


title: Tempus xO assay DNA sequencing [194_T]

description:
194-AST
Skin
194_AST.vcf
194-AST.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [193_T]

description:
193-SN
Skin
193_SN.vcf
193-SN.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H9_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H9_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H7_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H8_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H6_AD012_indexed


title: NL16_Normal_Skin

city: San Francisco

first: Margaret

last: Lowe

address: 513 Parnassus Avenue, HSW1201B

institute: UCSF

library_source: transcriptomic

data_processing:
Following clipping of adapter sequences, reads were aligned to Ensembl hg19 GRCh37.75 with kallisto (v 0.46.0) with the bootstrap=40 setting
Transcripts were quantified from the abundance.h5 file using GenomicFeatures makeTxDbFromGFF command
Genome_build: hg19
Supplementary_files_format_and_content: csv file containing raw read counts for each gene

molecule: total RNA

source_name: Normal Skin

extract_protocol:
Total RNA was extracted using Qiagen miRNeasy Kits
cDNA was created from 100ng of input RNA using theTruSeq Stranded mRNA input kit, sequencing 50 bp paired end stranded

tag: donor sex

value: F

value: whole skin

tag: tissue type

value: Normal Skin

tag: batch


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H9_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H9_AD002_indexed


title: NL15_Normal_Skin


title: NL14_Normal_Skin


title: Tempus xO assay DNA sequencing [192_T]

description:
192-AST
Skin
192_AST.vcf
192-AST.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [191_T]

description:
191-AST
Skin
191_AST.vcf
191-AST.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [18_N]

description:
18-AST
Skin
18_AST.vcf
18-AST.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [189_T]

description:
189-SN
Skin
189_SN.vcf
189-SN.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [18_T]


title: Tempus xO assay DNA sequencing [188_T]

description:
188-AST
Skin
188_AST.vcf
188-AST.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H7_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H8_AD007_indexed


title: Tempus xO assay DNA sequencing [187_T]

description:
187-SN
Skin
187_SN.vcf
187-SN.soma.pindel.vcf


title: NL13_Normal_Skin


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_3_CEMBA180501_3B_4_A3_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H8_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H6_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H9_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H7_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H7_AD004_indexed


title: Tempus xO assay DNA sequencing [186_T]

description:
186-SN
Skin
186_SN.vcf
186-SN.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H7_AD002_indexed


title: NL11_Normal_Skin


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H6_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H6_AD006_indexed


title: Tempus xO assay DNA sequencing [186_N]


title: NL10_Normal_Skin


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H7_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H6_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H8_AD004_indexed


title: Tempus xO assay DNA sequencing [185_T]

description:
185-SN
Skin
185_SN.vcf
185-SN.soma.pindel.vcf


title: 228_Lesional_PRE

source_name: Lesional_PRE-TNF-alpha inhibitor

value: M

value: Lesional

tag: treatment category

value: PRE-TNF-alpha inhibitor

tag: response

value: Yes


title: Tempus xO assay DNA sequencing [184_T]

description:
184-SN
Skin
184_SN.vcf
184-SN.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H5_AD012_indexed


title: NL12_Normal_Skin

value: Unknown


title: 198_Lesional_PRE


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H6_AD002_indexed


title: 208_Lesional_PRE


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H6_AD010_indexed


title: Tempus xO assay DNA sequencing [183_T]

description:
183-SN
Skin
183_SN.vcf
183-SN.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H5_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H4_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H5_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H6_AD001_indexed


title: Tempus xO assay DNA sequencing [181_T]

description:
181-SN
Skin
181_SN.vcf
181-SN.soma.pindel.vcf


title: 72_Lesional_ON

source_name: Lesional_ON-TNF-alpha inhibitor

value: ON-TNF-alpha inhibitor

value: No


title: 182_Lesional_PRE


title: Tempus xO assay DNA sequencing [182_T]

description:
182-AST
Skin
182_AST.vcf
182-AST.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H5_AD007_indexed


title: Tempus xO assay DNA sequencing [180_T]

description:
180-AST
Skin
180_AST.vcf
180-AST.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H5_AD001_indexed


title: 138_Lesional_ON


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H4_AD006_indexed


title: 181_Lesional_PRE


title: Tempus xO assay DNA sequencing [17_T]

description:
17-AST
Skin
17_AST.vcf
17-AST.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H5_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H5_AD006_indexed


title: 172_Lesional_PRE


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H4_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H4_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H4_AD004_indexed


title: 171_Lesional_ON

source_name: Lesional_ONTNF-alpha inhibitor

value: ONTNF-alpha inhibitor


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H3_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H3_AD010_indexed


title: Tempus xO assay DNA sequencing [177_T]

description:
177-SN
Skin
177_SN.vcf
177-SN.soma.pindel.vcf


title: 115_Lesional_ON

value: Partial


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H4_AD002_indexed


title: Tempus xO assay DNA sequencing [176_T]

description:
176-AST
Skin
176_AST.vcf
176-AST.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H4_AD001_indexed


title: 120_Lesional_ON


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H4_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H3_AD006_indexed


title: Tempus xO assay DNA sequencing [175_T]

description:
175-AST
Skin
175_AST.vcf
175-AST.soma.pindel.vcf


title: 122_Lesional_ON


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H2_AD008_indexed


title: Tempus xO assay DNA sequencing [175_N]


title: Tempus xO assay DNA sequencing [17_N]


title: Tempus xO assay DNA sequencing [172_T]

description:
172-SN
Skin
172_SN.vcf
172-SN.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H2_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H3_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H3_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H3_AD001_indexed


title: Tempus xO assay DNA sequencing [171_T]

description:
171-MWS
Skin
171_MWS.vcf
171-MWS.soma.pindel.vcf

source_name: Melanoma with Spitzoid Features

value: Melanoma with Spitzoid Features (tumor)


title: Tempus xO assay DNA sequencing [178_T]

description:
178-AST
Skin
178_AST.vcf
178-AST.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H2_AD001_indexed

value: MOs


title: NL08_Normal_Skin

source_name: Normal Skin_Normal Skin


title: Tempus xO assay DNA sequencing [170_T]

description:
170-MWS
Skin
170_MWS.vcf
170-MWS.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H2_AD002_indexed

value: male


title: NL07_Normal_Skin


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H1_AD012_indexed


title: NL06_Normal_Skin


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H1_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H1_AD004_indexed


title: Tempus xO assay DNA sequencing [169_T]

description:
169-MWS
Skin
169_MWS.vcf
169-MWS.soma.pindel.vcf


title: NL05_Normal_Skin


title: Tempus xO assay DNA sequencing [16_T]

description:
16-AST
Skin
16_AST.vcf
16-AST.soma.pindel.vcf

value: Sptitz Tumor (tumor)


title: 116_Lesional_ON


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H2_AD006_indexed


title: NL09_Normal_Skin


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H12_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H12_AD012_indexed


title: NL04_Normal_Skin


title: Tempus xO assay DNA sequencing [167_T]

description:
167-MWS
Skin
167_MWS.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H1_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H3_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H1_AD002_indexed


title: NL02_Normal_Skin


title: NL03_Normal_Skin


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H1_AD008_indexed


title: Tempus xO assay DNA sequencing [166_T]

description:
166-MWS
Skin
166_MWS.vcf
166-MWS.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [167_N]

description:
167-MWS
Skin
167_MWS.vcf
167-MWS.soma.pindel.vcf

value: Melanoma with Spitzoid Features (normal)


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H12_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H12_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H2_AD004_indexed


title: NL01_Normal_Skin


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H12_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H11_AD006_indexed


title: Tempus xO assay DNA sequencing [165_T]

description:
165-MWS
Skin
165_MWS.vcf
165-MWS.soma.pindel.vcf


title: 138_Nonlesional_PRE

source_name: Non-lesional_PRE-TNF-alpha inhibitor

value: F

value: Non-lesional


title: Tempus xO assay DNA sequencing [168_T]

description:
168-AST
Skin
168_AST.vcf
168-AST.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H11_AD008_indexed


title: 138_Lesional_PRE

value: whole skin


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H11_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H11_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H12_AD002_indexed


title: Tempus xO assay DNA sequencing [164_N]

description:
164-MWS
Skin
164_MWS.vcf
164-MWS.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H11_AD012_indexed


title: Tempus xO assay DNA sequencing [163_T]

description:
162-SM
Skin
163_MWS.vcf
163-MWS.soma.pindel.vcf


title: 82_Lesional_ON


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H11_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H10_AD008_indexed


title: 82_Nonlesional_ON

source_name: Non-lesional_ONTNF-alpha inhibitor


title: 124_Nonlesional_TxNaive

source_name: Non-lesional_TNF-alpha inhibitor NAIVE

value: TNF-alpha inhibitor NAIVE


title: Tempus xO assay DNA sequencing [162_T]

description:
162-SM
Skin
162_SM.vcf

source_name: Spitzoid Melanoma

value: Spitzoid Melanoma (tumor)


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H10_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H11_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H10_AD004_indexed


title: Tempus xO assay DNA sequencing [160_T]

description:
160-MWS
Skin
160_MWS.vcf
160-MWS.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H10_AD002_indexed


title: Tempus xO assay DNA sequencing [162_N]

description:
162-SM
Skin
162_SM.vcf
162-SM.soma.pindel.vcf

value: Spitzoid Melanoma (normal)


title: 122_Nonlesional_PRE

value: M

value: PRE-TNF-alpha inhibitor

value: Yes


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H10_AD001_indexed


title: 124_Lesional_TxNaive

source_name: Lesional_TNF-alpha inhibitor NAIVE

value: Lesional


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G9_AD004_indexed


title: 122_Lesional_PRE

value: yes


title: Tempus xO assay DNA sequencing [15_T]

description:
15-AST
Skin
15_AST.vcf
15-AST.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [164_T]


title: Tempus xO assay DNA sequencing [15_N]

value: Sptitz Tumor (normal)


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G9_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H10_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G9_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G9_AD006_indexed


title: Tempus xO assay DNA sequencing [157_T]

description:
157-SM
Skin
157_SM.vcf
157-SM.soma.pindel.vcf


title: 120_Nonlesional_PRE

value: No


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G8_AD012_indexed

value: MOs


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G8_AD010_indexed

value: male


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G8_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_H11_AD004_indexed


title: 115_Lesional_PRE

value: Partial


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G8_AD002_indexed


title: 120_Lesional_PRE


title: Tempus xO assay DNA sequencing [154_T]

description:
154-SM
Skin
154_SM.vcf
154-SM.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G9_AD007_indexed


title: 80_Nonlesional_TxNaive


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G9_AD001_indexed


title: 37_Nonlesional_ON

source_name: Non-lesional_ON-TNF-alpha inhibitor

value: ON-TNF-alpha inhibitor


title: Tempus xO assay DNA sequencing [152_T]

description:
152-MWS
Skin
152_MWS.vcf
152-MWS.soma.pindel.vcf

value: Melanoma with Spitzoid Features (tumor)


title: Tempus xO assay DNA sequencing [151_T]

description:
151-MWS
Skin
151_MWS.vcf
151-MWS.soma.pindel.vcf


title: 115_Nonlesional_PRE

value: Non-lesional


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G7_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G7_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G8_AD006_indexed


title: 101_Nonlesional_ON

value: F

value: whole skin

value: ONTNF-alpha inhibitor


title: Tempus xO assay DNA sequencing [150_T]

description:
150-SM
Skin
150_SM.vcf
150-SM.soma.pindel.vcf

value: Spitzoid Melanoma (tumor)


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G9_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G8_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G7_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G7_AD007_indexed


title: Tempus xO assay DNA sequencing [149_T]

description:
149-SM
Skin
149_SM.vcf
149-SM.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [13_T]

description:
13-AST
Skin
13_AST.vcf
13-AST.soma.pindel.vcf

value: Sptitz Tumor (tumor)


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G7_AD012_indexed


title: Tempus xO assay DNA sequencing [14_N]

description:
14-AST
Skin
14_AST.vcf
14_AST.soma.pindel.vcf


title: 37_Lesional_ON


title: Tempus xO assay DNA sequencing [14_T]


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G7_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G7_AD001_indexed


title: 101_Lesional_ON


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G6_AD007_indexed


title: 97_Nonlesional_TxNaive

value: TNF-alpha inhibitor NAIVE


title: Tempus xO assay DNA sequencing [13_N]


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G6_AD012_indexed


title: 80_Lesional_TxNaive


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G7_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G6_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G5_AD012_indexed


title: Tempus xO assay DNA sequencing [131_T]

description:
131-SM
Skin
131_SM.vcf
131-SM.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [130_T]

description:
130-MWS
Skin
130_MWS.vcf
130-MWS.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G6_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G5_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G8_AD001_indexed


title: Tempus xO assay DNA sequencing [12_T]

description:
12-AST
Skin
12_AST.vcf
12-AST.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [130_N]

value: Melanoma with Spitzoid Features (normal)


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G5_AD004_indexed


title: 54_Lesional_ON

value: Lesional


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G5_AD007_indexed


title: Tempus xO assay DNA sequencing [129_T]

description:
129-MWS
Skin
129_MWS.vcf
129-MWS.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G4_AD008_indexed


title: 76_Lesional_ON

value: M

value: Yes


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G4_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G5_AD001_indexed


title: 76_Nonlesional_ON


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G4_AD010_indexed


title: Tempus xO assay DNA sequencing [127_T]

description:
127-SM
Skin
127_SM.vcf
127-SM.soma.pindel.vcf


title: 6_Nonlesional_ON


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G4_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G4_AD006_indexed


title: Tempus xO assay DNA sequencing [11_T]

description:
11-ASN
Skin
11_ASN.vcf
11-ASN.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [11_N]

value: Sptitz Tumor (normal)


title: 54_Nonlesional_ON

value: No


title: 6_Lesional_ON


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G4_AD001_indexed

value: MOs

value: male


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G4_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G3_AD004_indexed


title: 97_Lesional_TxNaive


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G3_AD012_indexed


title: Tempus xO assay DNA sequencing [10_T]

description:
10-AST
Skin
10_AST.vcf
10-AST.soma.pindel.vcf


title: 78_Lesional_TxNaive


title: Tempus xO assay DNA sequencing [10_N]


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G3_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G4_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G3_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G3_AD010_indexed


title: 76_Nonlesional_PRE

value: PRE-TNF-alpha inhibitor


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G3_AD002_indexed


title: 72_Nonlesional_PRE


title: shYY1-2+PDS-1

city: Riverside

first: LIN

last: LI

state: California

address: 501 Big Springs Road, University of California at Riverside

department: Department of chemistry

institute: UC, riverside

data_processing:
For RNA-seq analysis, the sequencing results were first aligned to human hg19 reference genome using the HISAT2 for RNA-seq data. FeatureCounts was used to assembe the aligned reads and DESeq2 was used to analyze differential expressed genes among different treatment.
Genome_build: hg38
Supplementary_files_format_and_content: For RNA-seq,xlsx files were generated using Microsoft Office software. Gene expressing transcripts per million (TPM) files were included.

source_name: HEK293T cells

growth_protocol: Cells were cultured at 37 oC in a humidified incubator with 5% CO2.

extract_protocol:
RNA was extracted with Omega Total RNA Kit I (Omega).NEBNext rRNA Depletion Kit was used to remove the rRNA.
Libraries were conducted following the instructions for NEBNext® Ultra™ II RNA Library Prep Kit for Illumina.

tag: shRNA

tag: agent

value: PDS

tag: cell type

value: Human embryonic kidney cells

tag: cell lline

value: HEK293T cells


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G2_AD006_indexed


title: shYY1-2+PDS-2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G5_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G3_AD001_indexed


title: shYY1-2-2


title: 78_Nonlesional_TxNaive

value: F

value: whole skin

value: Non-lesional


title: 72_Lesional_PRE


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G2_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G2_AD007_indexed


title: 27_Nonlesional_ON

value: ON-TNF-alpha inhibitor


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G2_AD001_indexed


title: shYY1-1+PDS-2


title: shYY1-2-1


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G1_AD008_indexed


title: 76_Lesional_PRE


title: shYY1-1+PDS-1


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G1_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G1_AD010_indexed


title: 27_Lesional_ON


title: 62_Nonlesional_TxNaive

value: TNF-alpha inhibitor NAIVE


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G1_AD004_indexed


title: shYY1-1-2


title: 62_Lesional_TxNaive


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G1_AD006_indexed


title: shYY1-1-1


title: 55_Nonlesional_PRE

value: Partial


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G1_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G2_AD004_indexed


title: 55_Lesional_PRE

value: Lesional


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G12_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G12_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G12_AD012_indexed


title: shCtrl+PDS-1

value: shCtrl


title: 52_Nonlesional_ON

value: M

value: ONTNF-alpha inhibitor

value: Yes


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G11_AD001_indexed

value: MOs


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G11_AD012_indexed

value: male


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G11_AD008_indexed


title: 52_Lesional_ON


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G11_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G11_AD004_indexed


title: shCtrl-2


title: shCtrl-1


title: 50_Lesional_TxNaive


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G11_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G10_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G1_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G10_AD006_indexed


title: 50_Nonlesional_TxNaive


title: P53-1

city: Shijiazhuang

first: Zhan

last: Yang

state: Hebei

address: 215 Heping W Rd

country: China

institute: The Second Hospital of Hebei Medical University

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8).
Sequence quality was examined using the FastQC software. The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 software(v2.0.4).
The transcript abundances for each sample was estimated with StringTie (v1.2.3), and the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0).
The differentially expressed genes and transcripts were filtered using R package Ballgown. The novel genes and transcripts were predicted from assembled results by comparing to the reference annotation using StringTie and Ballgown.
Principle Component Analysis (PCA) and correlation analysis were based on gene expression level, Hierarchical Clustering, Gene Ontology, Pathway analysis, scatter plots and volcano plots were performed with the differentially expressed genes in R, Python or shell environment for statistical computing and graphics.
Genome_build: Hg19
Supplementary_files_format_and_content: the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)

source_name: prostate cancer cell line

growth_protocol: PC3 (CRL-1435; ATCC) grown and maintained in RPMI 1640 medium (Gibco, USA) containing penicillin (100 units/ml) and streptomycin (100 µg/ml). Cultures were incubated in a humidified environment at 5% CO2 and 37°C.

extract_protocol:
RNA extraction was performed with the miRNeasy Mini Kit (217004; Qiagen) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In brief, PC3 cells were transfected with constructs expressing Cas9-D10A (Nickase) and control sgRNAs or sgRNAs targeting p53 exon 3 (sc-437281 for control; sc-416469-NIC for targeting p53). After 48 h of transfection, cells were suspended, diluted and re-seeded to make sure single clone formation. GFP positive clones were picked up, and the expression of p53 in each single clone was evaluated by Western blotting with p53 (sc-126) antibody. The stable clones were seeded again in 10-cm plates at 3–5 days after culture, when the cells reached 50% confluency, the cells were washed with ice-cold PBS twice and RNA extraction was performed with the miRNeasy Mini Kit (217004; Qiagen) according to the manufacturer's instructions.

tag: cell line

value: prostate cancer

tag: gender

tag: passages

tag: genotype


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G10_AD012_indexed

tag: brain region

tag: Sex


title: shCtrl+PDS-2

value: PDS


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G10_AD002_indexed

tag: age

tag: strain


title: P53-2

tag: tissue


title: 49_Nonlesional_PRE

tag: donor sex

tag: tissue type

value: PRE-TNF-alpha inhibitor


title: con-1

value: wild type


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F9_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F9_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F9_AD008_indexed


title: 49_Lesional_PRE

value: F

tag: treatment category

tag: batch


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F9_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F9_AD007_indexed


title: w1118 ChIP-seq rep2

city: Geneva

first: Federico

last: Miozzo

address: 30 Quai Ernest-Ansermet, CH-1211

country: Switzerland

institute: University of Geneva

data_processing:
ChIP-seq reads were aligned to the dm3 genome assembly using Bowtie2 with default settings
Peaks were called using MACS2 with default settings (q-value=0.05) by comparing each Fer2::GFP::V5 ChIP sample (N=2) to each w1118 ChIP sample (N=2; negative control). The 267 shared peaks overlapping in all the four FER2 ChIP vs w1118 ChIP comparisons were selected as confident peaks.
Genome_build: dm3
Supplementary_files_format_and_content: peak text files generated by MACS2

organism: Drosophila melanogaster

source_name: fly heads

growth_protocol: Flies were maintained on standard cornmeal-agar food at 25 °C in a 12 h:12 h light-dark cycle and under controlled humidity.

extract_protocol:
~8000 14-day-old flies per sample were collected 2 h before lights-on (ZT22), frozen in liquid nitrogen and maintained at -80 °C until processed. Heads were collected using metal sieves, and then, 1 ml of heads was ground in liquid nitrogen and homogenized 30 times in NE Buffer with 1% PFA. Lysates were clarified from sonicated nuclei and Fer2-DNA complexes were isolated with antibody.
Libraries were prepared with 0,5 to 0,7 ng of ChIP-enriched DNA as starting material and processed using the Illumina TruSeq ChIP kit according to the manufacturer’s specifications, at the iGE3 Genomics Platform in Geneva. The libraries were validated on a Tapestation 2200 (Agilent) and a Qubit fluorometer (Invitrogen - Thermo Fisher Scientific). Single reads of 50 bp were generated using the TruSeq SBS HS v3 chemistry on an Illumina HiSeq 2500 sequencer.

value: day 14

tag: antibody

value: anti-V5 (Sigma A7345)


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F8_AD008_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: w1118 ChIP-seq rep1


title: Fer2::GFP::V5 ChIP-seq rep2

value: w;;Fer2::GFP::V5, Fer21


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F9_AD004_indexed


title: 39_Nonlesional_TxNaive

value: whole skin

value: Non-lesional

value: TNF-alpha inhibitor NAIVE

tag: response


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F8_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F8_AD006_indexed


title: 25_Lesional_ON

value: Lesional

value: ON-TNF-alpha inhibitor


title: 39_Lesional_TxNaive

value: M


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F8_AD012_indexed


title: con-2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F9_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F8_AD004_indexed


title: Fer2::GFP::V5 ChIP-seq rep1


title: 25_Nonlesional_ON

value: Yes


title: ctrl_48h_2

data_processing:
Sequencing reads were mapped to the dm3 genome assembly using TopHat with default settings.
Differentially expressed genes (DEG) analysis was performed using Cufflinks, Cuffmerge and Cuffdiff, to compare flies who received the heat shock treatment with untreated flies. The same analysis was performed on hs-GAL4 flies not carrying the UAS-Fer2::FLAG transgene (ctrl), to identify the genes which responded to heat irrespective of Fer2 induction. These heat-responsive genes were subtracted from DEG identified in the hs>Fer2::FLAG experiment.
Genome_build: dm3
Supplementary_files_format_and_content: table files including relative abundance for each group

extract_protocol:
50 flies per replicate were frozen in liquid nitrogen and kept at -80 °C until processed. Fly heads were collected using metal sieves. Total RNA was isolated from fly heads using Trizol according to the manufacturer’s instructions and treated with Turbo DNase for 30 min at 37 °C.
Libraries were prepared at the iGE3 Genomics Platform in Geneva. Single reads of 50 bp were generated using an Illumina HiSeq 2500 sequencer.

treatment_protocol: hs-GAL4, UAS-Fer2::FLAG flies (hs>Fer2::FLAG) were heat-shocked at 37 °C for 3 h, or maintained at 25 °C (untreated), and collected 12 h or 48 h later (N=3 replicates per group). The same procedure was also applied to flies carrying hs-GAL4 but not the UAS-Fer2::FLAG transgene (ctrl), in order to identify and exclude from our analysis the genes that responded to heat irrespective of Fer2 induction.

tag: treatment

value: 48h heat-shock


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_G10_AD001_indexed

value: MOs

value: male


title: ctrl_48h_3


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F8_AD007_indexed


title: 35_Nonlesional_PRE


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F7_AD006_indexed


title: 37_Lesional_PRE


title: ctrl_48h_1


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F7_AD008_indexed


title: 35_Lesional_PRE


title: ctrl_12h_3

value: 12h heat-shock


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F6_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F7_AD001_indexed


title: ctrl_12h_2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F7_AD010_indexed


title: 37_Nonlesional_PRE

value: PRE-TNF-alpha inhibitor


title: 13_Nonlesional_PRE


title: 13_Lesional_PRE


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F7_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F8_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F6_AD010_indexed


title: 27_Nonlesional_PRE

value: No


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F6_AD004_indexed


title: ctrl_12h_1


title: ctrl_untreated_2

value: untreated


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F8_AD001_indexed


title: 27_Lesional_PRE

value: F


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F5_AD008_indexed


title: ctrl_untreated_1

value: day 14


title: 25_Nonlesional_PRE


title: ctrl_untreated_3


title: 25_Lesional_PRE


title: OE_48h_3

value: hs-GAL4, UAS-Fer2::FLAG


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F7_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F5_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F5_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F4_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F5_AD004_indexed


title: OE_48h_2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F4_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F7_AD007_indexed


title: CBC-3

city: Wuhan

first: Peng

last: Zhao

address: Luojia Hill

department: College of Life Sciences

institute: Wuhan University

description:
Col (♀)× Ler (♂)
Amplified with SMART-Seq Ultra Low Input RNA Kit

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to arabidopsis genome TAIR10 using tophat2(v2.1.1) with parameters tophat2 -G ref.gff --library-type fr-unstranded -i 20 -I 500000 -o outdir genome_index fq1 fq2
Expression level are quantified by a software package: RSEM (RNASeq by Expectation Maximization v1.3.0).
Genome_build: Arabidopsis thaliana genome TAIR10
Supplementary_files_format_and_content: FPKM

organism: Arabidopsis thaliana

source_name: Basal cell of hybrid proembryo (Col × Ler)

growth_protocol: In greenhouse under long-day conditions (16 h light/8 h dark) at 22 °C

extract_protocol:
mRNA was extracted with Dynabeads® mRNA DIRECT™ Micro Kit. And SMART-Seq  Ultra Low Input RNA Kit was used to generate cDNA library for sequencing
Libraries were constructed using Nextera XT Library Prep Kit or NEBNext Ultra DNA Library Prep Kit

value: Basal cell

tag: developmental stage

value: 2-celled embryo

tag: corss type

value: Col (female)x Ler (male)


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F4_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F4_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F4_AD010_indexed


title: OE_12h_3


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F3_AD010_indexed


title: LBC-2

description:
Ler (♀)× Col (♂)
Amplified with SMART-Seq Ultra Low Input RNA Kit

source_name: Basal cell of hybrid proembryo (Ler × Col)

value: Ler (female)x Col (male)


title: OE_12h_2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F4_AD004_indexed


title: LBC-3


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F3_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F5_AD007_indexed


title: OE_12h_1


title: C32S-2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to arabidopsis genome TAIR10 using tophat2(v2.1.1) with parameters tophat2 -G ref.gff --library-type fr-unstranded -i 20 -I 500000 -o outdir genome_index fq1 fq2
Expression level are quantified by a software package: RSEM (RNASeq by Expectation Maximization v1.3.0).
Genome_build: Arabidopsis thaliana genome TAIR10
Supplementary_files_format_and_content: FPKMs

source_name: Suspensor of hybrid embryos at 32-celled embryo stage  (Col × Ler)

extract_protocol:
mRNA was extracted with Dynabeads® mRNA DIRECT™ Micro Kit. And SMART-Seq v4 Ultra Low Input RNA Kit was used to generate cDNA library for sequencing
Amplified with SMART-Seq Ultra Low Input RNA Kit
Libraries were constructed using Nextera XT Library Prep Kit

value: Suspensor

value: 32-celled embryo

tag: cross type

value: Col (♀)× Ler (♂)


title: C32S-3

description: Amplified with SMART-Seq Ultra Low Input RNA Kit


title: OE_untreated_3


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F4_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F3_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F4_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F3_AD007_indexed


title: OE_untreated_2


title: L32S-1

source_name: Suspensor of hybrid proembryo at 32-celled embryo stage (Ler × Col)


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F6_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F3_AD002_indexed


title: L32S-3

source_name: Suspensor of hybrid embryos at 32-celled embryo stage (Ler × Col)

value: Ler (♀)× Col (♂)


title: OE_untreated_1


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F3_AD001_indexed

value: MOs


title: L32S-2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F3_AD012_indexed

value: male


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F3_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F2_AD012_indexed


title: C32E-3

source_name: Embro proper of hybrid embryos at 32-celled embryo stage  (Col × Ler)

value: Embryo proper


title: Subject_F_totalCD27-_ATAC

city: San Antonio

first: Justin

last: Moroney

state: Texas

address: 7703 Floyd Curl Drive; Medical Building, Rm #5.011V

department: Microbiology, Immunology and Molecular Genetics

institute: UT Health San Antonio

description:
Accessible Chromatin
ATAC_Peak_Counts_TotalCD27-andTotalCD27+.txt
ATAC_DARs_Peaks_TotalCD27-andTotalCD27+.txt

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Hisat2-2.1.0
Abundance measurements were otained using HTSeq-0.11.2
Peak calling was performed using HOMER-4.10
Genome_build: UCSC hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene or miRNA

source_name: Human PBMCs

growth_protocol: Human IgD+ naïve B cells were purified by negative selection from healthy donor PBMCs using the EasySep Human Naïve B Cell Enrichment Kit (19254, STEMCELL Technologies).  Naïve B cells were then cultured in FCS-RPMI and stimulated with trimeric CD154 (10 U ml-1), IL-4 (20 ng ml-1, R&D Systems) and IL-21 (50 ng ml-1, R&D Systems) or CD154 (10 U ml-1), IL-21 (50 ng ml-1) and TGF-β (0.5 ng ml-1) in the presence of nil, butyrate ((1000 M)) for 60 hours.

extract_protocol:
Total RNA was extracted using Direct-zol RNA Miniprep Plus kit (Zymo Research) following manufacturer's instructions. Nuclear chromatin was prepared using the Omni-ATAC protocol (Corces et al., 2017, Nature Methods)
Libraries were prepared for sequencing using standard Illumina TruSeq protocol

tag: cell type

value: CD27- B cell

tag: subject id


title: Subject_F_totalCD27+_ATAC

value: CD27+ B cell


title: Subject_E_totalCD27+_ATAC


title: C32E-2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F2_AD004_indexed

tag: brain region


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F2_AD010_indexed

tag: Sex


title: OE_48h_1

tag: age

tag: genotype

value: 48h heat-shock


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F1_AD012_indexed

tag: strain


title: C32E-1

tag: tissue


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F2_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F1_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F1_AD007_indexed


title: Subject_D_totalCD27+_ATAC


title: Subject_E_totalCD27-_ATAC


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F1_AD006_indexed


title: L32E-2

source_name: Embro proper of hybrid embryos at 32-celled embryo stage (Ler × Col)


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F2_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F1_AD010_indexed


title: Subject_D_totalCD27-_ATAC


title: Subject_A_totalCD27+_ATAC


title: CBC-2

source_name: Basal cell of hybrid embryos (Col × Ler)


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F2_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F1_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F2_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F1_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F12_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F12_AD008_indexed


title: Subject_F_totalCD27+_mRNA

description:
Total RNA
Sample_CD27-vCD27+_Genes_ReadCount_mRNA.txt


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F1_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F10_AD010_indexed


title: Subject_F_totalCD27-_mRNA


title: CBC-1


title: L32E-3


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F12_AD007_indexed


title: CAC-3

source_name: Apical cell of hybrid embryos (Col × Ler)

value: Apical cell


title: Subject_E_totalCD27+_mRNA


title: CAC-2


title: Subject_E_totalCD27-_mRNA


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F12_AD002_indexed


title: L32E-1


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F11_AD010_indexed


title: CAC-1


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F11_AD008_indexed


title: LAC-3

source_name: Apical cell of hybrid embryos (Ler × Col)


title: Subject_A_totalCD27-_ATAC


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F11_AD006_indexed


title: Subject_D_totalCD27-_mRNA


title: LBC-1

source_name: Basal cell of hybrid embryos (Ler × Col)


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F11_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F10_AD008_indexed


title: LAC-2


title: LAC-1


title: Subject_A_totalCD27+_mRNA


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E8_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E9_AD010_indexed


title: Subject_A_totalCD27-_mRNA


title: R317-TAC

city: Vancouver

first: James

last: Johnson

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

country: Canada

institute: University of British Columbia

data_processing:
Sample quality control was performed using the Agilent 2100 Bioanalyzer. Qualifying samples were then prepped following the standard protocol for the NEBNext Ultra II Stranded mRNA (New England Biolabs).
Sequencing was performed on the Illumina NextSeq 500 with Paired End 42bp × 42bp reads.
Sequencing data was demultiplexed using Illumina's bcl2fastq2.
De-multiplexed read sequences were then aligned to the Mus Musculous mm10 reference sequence using STAR aligner (https://www.ncbi.nlm.nih.gov/ pubmed/23104886).
Assembly was estimated using Cufflinks (http://cole-trapnell-lab.github.io/cufflinks/) through bioinformatics apps available on Illumina Sequence Hub using default settings
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts for each sample

source_name: Islets of Langerhans

growth_protocol: Human Islets were cultured for 48 hours at 37°C and 5% C02 in RPMI 1640 medium (Thermo Fisher Scientific) supplemented with 5.5 mmol glucose, 10% FBS, and 100 units/ml penicillin/streptomycin

extract_protocol: Total RNA were extracted with Qiagen Rneasy Kit.

treatment_protocol: 100 human islets were cultured as per the above conditions with either DMSO (1/1000), Voclosporin (60 ng/ml) or Tacrolius (30 ng/ml). After 48 hours of incubation islets were flash frozen and stored at -80°C.

tag: concentration

value: 30 ng/ml


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E8_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F11_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F10_AD007_indexed


title: Tempus xO assay DNA sequencing [8_T]

description:
8-SM
Skin
8_SM.vcf
8-SM.soma.pindel.vcf

source_name: Spitzoid Melanoma

value: Spitzoid Melanoma (tumor)


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F12_AD001_indexed


title: Tempus xO assay DNA sequencing [85_T]

description:
85-AST
Skin
85_AST.vcf
85-AST.soma.pindel.vcf

source_name: Sptitz Tumor

value: Sptitz Tumor (tumor)


title: R316-TAC


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F10_AD002_indexed


title: Subject_D_totalCD27+_mRNA


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E8_AD012_indexed


title: R314-TAC


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E9_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F12_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E9_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E8_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_F10_AD012_indexed


title: Tempus xO assay DNA sequencing [83_T]

description:
83-SN
Skin
83_SN.vcf
83-SN.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E9_AD004_indexed


title: Tempus xO assay DNA sequencing [82_T]

description:
82-SN
Skin
82_SN.vcf
82-SN.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E9_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E9_AD012_indexed


title: Tempus xO assay DNA sequencing [83_N]

value: Sptitz Tumor (normal)


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E8_AD006_indexed


title: R305-TAC


title: Tempus xO assay DNA sequencing [82_N]


title: R310-TAC


title: R302-TAC


title: C32S-1


title: Tempus xO assay DNA sequencing [80_T]

description:
80-SN
Skin
80_SN.vcf
80-SN.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E8_AD007_indexed


title: R309-TAC


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E8_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E6_AD012_indexed


title: Tempus xO assay DNA sequencing [7_T]

description:
7-SM
Skin
7_SM.vcf
7-SM.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E7_AD001_indexed


title: R317-VCS

value: 60 ng/ml


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E6_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E7_AD010_indexed


title: R314-VCS


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E7_AD012_indexed


title: Tempus xO assay DNA sequencing [79_T]

description:
79-MWS
Skin
79_MWS.vcf
79-MWS.soma.pindel.vcf

source_name: Melanoma with Spitzoid Features

value: Melanoma with Spitzoid Features (tumor)


title: Tempus xO assay DNA sequencing [84_T]

description:
84-SN
Skin
84_SN.vcf
84-SN.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E7_AD007_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: R310-VCS


title: R316-VCS


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E7_AD002_indexed


title: Tempus xO assay DNA sequencing [76_T]

description:
76-AST
Skin
76_AST.vcf
76-AST.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E6_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E7_AD004_indexed


title: Tempus xO assay DNA sequencing [78_T]

description:
78-AST
Skin
78_AST.vcf
78-AST.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E6_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E6_AD001_indexed


title: Tempus xO assay DNA sequencing [75_T]

description:
75-ASN
Skin
75_ASN.vcf
75-ASN.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [73_T]

description:
73-SN
Skin
73_SN.vcf
73-SN.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E5_AD004_indexed


title: R309-VCS


title: R302-VCS


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E5_AD006_indexed


title: R316-DMSO


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E5_AD010_indexed


title: Tempus xO assay DNA sequencing [75_N]


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E6_AD004_indexed


title: R317-DMSO


title: Tempus xO assay DNA sequencing [73_N]


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E5_AD001_indexed


title: R314-DMSO


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E5_AD008_indexed


title: Tempus xO assay DNA sequencing [71_T]

description:
71-AST
Skin
71_AST.vcf
71-AST.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E6_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E6_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E4_AD007_indexed


title: R305-VCS


title: Tempus xO assay DNA sequencing [6_T]

description:
6-SM
Skin
6_SM.vcf
6-SM.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E4_AD010_indexed


title: R309-DMSO


title: R310-DMSO


title: Tempus xO assay DNA sequencing [69_T]

description:
69-SM
Skin
69_SM.vcf
69-SM.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E4_AD006_indexed


title: R305-DMSO


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E4_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E4_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E4_AD004_indexed


title: Tempus xO assay DNA sequencing [69_N]

value: Spitzoid Melanoma (normal)


title: Tempus xO assay DNA sequencing [67_T]

description:
67-SM
Skin
67_SM.vcf
67-SM.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [68_T]

description:
68-SN
Skin
68_SN.vcf
68-SN.soma.pindel.vcf


city: Cambridge

first: Nir

last: Hacohen

state: MA

address: 415 Main St

institute: Broad Institute of MIT and Harvard

description:
RTF2-Rescued_24h IFN and 16h IAV_40h harvest_rep 3
F9

data_processing:
Short sequencing reads were aligned to the hg38 genome (GENCODE v21) using STAR v2.6
Genomic coordinates were then converted to transcriptomic coordinates, and transcript abundances were quantified using RSEM v1.3.1
Transcript abundances were then aggregated to gene abundances
Genome_build: hg38
Supplementary_files_format_and_content: counts, TPMs

source_name: RTF2-Rescued A549

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol.
The Smart-Seq2 protocol (Picelli, Nat Protoc, 2014) was employed to perform transcriptomic analyses of the different cells. The cDNA was synthesized from 1ng of total RNA using SuperScript II reverse transcription, followed by PCR amplification and quality check using high-sensitivity DNA Bioanalyzer chip (Agilent). 0.15 ng of cDNA was then used for the tagmentation reaction carried out with the Nextera XT DNA sample preparation kit (Illumina) and further PCR amplification.

tag: cell line

value: IFN 24h 200U/ml

tag: infection

value: IAV PR8 MOI 5 for 16h

tag: harvest time


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E3_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E3_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E3_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E3_AD010_indexed


title: R302-DMSO


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E4_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E2_AD008_indexed


title: Tempus xO assay DNA sequencing [66_T]

description:
66-AST
Skin
66_AST.vcf
66-AST.soma.pindel.vcf


description:
RTF2-Rescued_24h IFN and 16h IAV_40h harvest_rep 1
F7


description:
RTF2-Rescued_24h IFN and 16h IAV_40h harvest_rep 2
F8


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E3_AD001_indexed


description:
RTF2-KO_24h IFN and 16h IAV_40h harvest_rep 3
F6

source_name: RTF2-KO A549


title: Tempus xO assay DNA sequencing [64_T]

description:
64-SM
Skin
64_SM.vcf
64-SM.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E3_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E2_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E2_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E3_AD012_indexed


title: Tempus xO assay DNA sequencing [62_T]

description:
62-AST
Skin
62_AST.vcf
62-AST.soma.pindel.vcf


description:
RTF2-KO_24h IFN and 16h IAV_40h harvest_rep 2
F5


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E1_AD012_indexed


title: Tempus xO assay DNA sequencing [58_T]

description:
58-SM
Skin
58_SM.vcf
58-SM.soma.pindel.vcf


description:
RTF2-KO_24h IFN and 16h IAV_40h harvest_rep 1
F4


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E2_AD012_indexed


description:
WT A549_24h IFN and 16h IAV_40h harvest_rep 3
F3

source_name: WT A549

value: WT


title: Tempus xO assay DNA sequencing [5_T]

description:
5-AST
Skin
5_AST.vcf
5-AST.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E2_AD004_indexed

value: MOs


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E1_AD008_indexed

value: male


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E1_AD010_indexed


title: Tempus xO assay DNA sequencing [48_T]

description:
48-AST
Skin
48_AST.vcf
48-AST.soma.pindel.vcf


description:
WT A549_24h IFN and 16h IAV_40h harvest_rep 1
F1


title: Tempus xO assay DNA sequencing [4_T]

description:
4-AST
Skin
4-AST.vcf
4-AST.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E1_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E1_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E12_AD010_indexed


title: Tempus xO assay DNA sequencing [48_N]


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E2_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E4_AD008_indexed


title: RTF2-Rescued_16h IAV_40h harvest_rep 3

description:
RTF2-Rescued_16h IAV_40h harvest_rep 3
E9


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E2_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E1_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E2_AD002_indexed


title: Tempus xO assay DNA sequencing [46_T]

description:
46-AST
Skin
46_AST.vcf
46-AST.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [47_T]

description:
47-AST
Skin
47_AST.vcf
47-AST.soma.pindel.vcf


title: RTF2-Rescued_16h IAV_40h harvest_rep 2

description:
RTF2-Rescued_16h IAV_40h harvest_rep 2
E8


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E1_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E12_AD008_indexed


title: RTF2-Rescued_16h IAV_40h harvest_rep 1

description:
RTF2-Rescued_16h IAV_40h harvest_rep 1
E7


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E12_AD007_indexed


title: Tempus xO assay DNA sequencing [46_N]


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E12_AD004_indexed


description:
WT A549_24h IFN and 16h IAV_40h harvest_rep 2
F2


title: RTF2-KO_16h IAV_40h harvest_rep 3

description:
RTF2-KO_16h IAV_40h harvest_rep 3
E6


title: RTF2-KO_16h IAV_40h harvest_rep 2

description:
RTF2-KO_16h IAV_40h harvest_rep 2
E5


title: Tempus xO assay DNA sequencing [44_N]

description:
44-AST
Skin
44_AST.vcf
44-AST.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [44_T]


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E11_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E11_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E11_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E12_AD001_indexed


title: RTF2-KO_16h IAV_40h harvest_rep 1

description:
RTF2-KO_16h IAV_40h harvest_rep 1
E4


title: WT A549_16h IAV_40h harvest_rep 3

description:
WT A549_16h IAV_40h harvest_rep 3
E3


title: Tempus xO assay DNA sequencing [42_N]

description:
42-AST
Skin
42_AST.vcf
42-AST.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E11_AD007_indexed


title: WT A549_16h IAV_40h harvest_rep 2

description:
WT A549_16h IAV_40h harvest_rep 2
E2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E10_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E11_AD004_indexed


title: Tempus xO assay DNA sequencing [41_T]

description:
41-AST
Skin
41_AST.vcf
41-AST.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E10_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E10_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E10_AD007_indexed


title: WT A549_16h IAV_40h harvest_rep 1

description:
WT A549_16h IAV_40h harvest_rep 1
E1


title: Tempus xO assay DNA sequencing [41_N]


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E10_AD001_indexed


title: Tempus xO assay DNA sequencing [40_T]

description:
40-AST
Skin
40_AST.vcf
40-AST.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D9_AD012_indexed


description:
RTF2-Rescued_24h IFN treatment_40h harvest_rep 3
D9


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D9_AD010_indexed


description:
RTF2-Rescued_24h IFN treatment_40h harvest_rep 2
D8


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D9_AD007_indexed


title: Tempus xO assay DNA sequencing [40_N]


title: Tempus xO assay DNA sequencing [42_T]


description:
RTF2-Rescued_24h IFN treatment_40h harvest_rep 1
D7


description:
RTF2-KO_24h IFN treatment_40h harvest_rep 3
D6


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E10_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D9_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E10_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E11_AD002_indexed


title: Tempus xO assay DNA sequencing [39_T]

description:
39-AST
Skin
39_AST.vcf
39-AST.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D9_AD008_indexed


title: Tempus xO assay DNA sequencing [3_T]

description:
3-AST
Skin
3_AST.vcf
3-AST.soma.pindel.vcf


description:
RTF2-KO_24h IFN treatment_40h harvest_rep 2
D5


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D9_AD001_indexed


title: Tempus xO assay DNA sequencing [39_N]


description:
RTF2-KO_24h IFN treatment_40h harvest_rep 1
D4


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D8_AD012_indexed


title: Tempus xO assay DNA sequencing [38_T]

description:
38-AST
Skin
38_AST.vcf
38-AST.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D9_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D8_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D8_AD006_indexed


title: Tempus xO assay DNA sequencing [38_N]


description:
WT A549_24h IFN treatment_40h harvest_rep 3
D3


description:
WT A549_24h IFN treatment_40h harvest_rep 2
D2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D8_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D8_AD010_indexed


description:
WT A549_24h IFN treatment_40h harvest_rep 1
D1


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D5_AD007_indexed


title: Tempus xO assay DNA sequencing [37_N]

description:
37-AST
Skin
37_AST.vcf
37-AST.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [37_T]


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_E10_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D9_AD002_indexed


title: Tempus xO assay DNA sequencing [33_T]

description:
33-SN
Skin
33_SN.vcf
33-SN.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D5_AD006_indexed


title: Tempus xO assay DNA sequencing [33_N]


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D5_AD012_indexed


description:
RTF2-Rescued_no treatment_40h harvest_rep 3
C9


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D4_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D8_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D5_AD004_indexed


title: Tempus xO assay DNA sequencing [32_T]

description:
32-SN
Skin
32_SN.vcf
32-SN.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D8_AD004_indexed


description:
RTF2-Rescued_no treatment_40h harvest_rep 2
C8


description:
RTF2-Rescued_no treatment_40h harvest_rep 1
C7


title: RTF2-KO_no treatment_40h harvest_rep 3

description:
RTF2-KO_no treatment_40h harvest_rep 3
C6


title: Tempus xO assay DNA sequencing [32_N]


title: RTF2-KO_no treatment_40h harvest_rep 2

description:
RTF2-KO_no treatment_40h harvest_rep 2
C5


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D4_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D3_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D4_AD008_indexed


title: Tempus xO assay DNA sequencing [30_T]

description:
30-SN
Skin
30_SN.vcf
30-SN.soma.pindel.vcf


title: RTF2-KO_no treatment_40h harvest_rep 1

description:
RTF2-KO_no treatment_40h harvest_rep 1
C4


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D5_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D4_AD002_indexed


title: Tempus xO assay DNA sequencing [2_T]

description:
2-AST
Skin
2_AST.vcf
2-AST.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [29_T]

description:
29-SM
Skin
29_SM.vcf
29-SM.soma.pindel.vcf


title: WT A549_no treatment_40h harvest_rep 3

description:
WT A549_no treatment_40h harvest_rep 3
C3


title: Tempus xO assay DNA sequencing [27_T]

description:
27-AST
Skin
27_AST.vcf
27-AST.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D3_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D1_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D3_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D4_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D5_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D2_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D3_AD004_indexed


title: WT A549_no treatment_40h harvest_rep 2

description:
WT A549_no treatment_40h harvest_rep 2
C2


title: Tempus xO assay DNA sequencing [26_T]

description:
26-AST
Skin
26_AST.vcf
26-AST.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D4_AD001_indexed


title: WT A549_no treatment_40h harvest_rep 1

description:
WT A549_no treatment_40h harvest_rep 1
C1


description:
RTF2-Rescued_24h IFN treatment_24h harvest_rep 2
B8


title: Tempus xO assay DNA sequencing [26_N]


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D2_AD006_indexed


description:
RTF2-Rescued_24h IFN treatment_24h harvest_rep 1
B7


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D2_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D4_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D3_AD002_indexed


title: Tempus xO assay DNA sequencing [25_T]

description:
25-AST
Skin
25_AST.vcf
25-AST.soma.pindel.vcf


description:
RTF2-KO_24h IFN treatment_24h harvest_rep 3
B6


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D2_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D3_AD012_indexed


title: Tempus xO assay DNA sequencing [25_N]


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D2_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D2_AD004_indexed


description:
RTF2-KO_24h IFN treatment_24h harvest_rep 2
B5


title: Tempus xO assay DNA sequencing [27_N]