title: NAc_ZT13_Ctrl_3

first: Qian

last: Gao

state: hubei

address: Luoyu Road 1037 Huazhong University of Science and Technology

department: College of Life Science and Technology

description: NAc, nucleus accumbens;Zeitgeber Time 13h (ZT0 is defined as the time of lights on);rep3

data_processing:
The raw reads were filtered to produce clean data by excluding sequencing adaptors and low quality reads, including reads containing over 5% “N” and those containing >50% bases with quality value less than 10. The quality assessment of clean data was performed using FastQC v0.11.9.
Sequencing reads were then aligned to the mouse mm10 reference genome using HISAT2 and the gene expressions (FPKM) were qualified by Stringtie.
The differential expression analysis was performed by DESeq2 with default parameters. The significance threshold of P<0.05 was applied. The number of differentially expressed genes (DEGs) and the number of genes that exhibited a fold-change >2 in each brain tissue at each time point were displayed in the different expression gene dataset file
Genome_build: mm10
Supplementary_files_format_and_content: table with FPKM  counts for every gene and every sample

source_name: NAc

growth_protocol: 12 hour light, 12 hour dark

extract_protocol:
Total RNA was extracted using RNA isolater (Vazyme, China). RNA integrity was assessed with RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Alilent Technologies, USA) before the samples were sent for RNA-seq.
The sequencing libraries were generated using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, NR601) following manufacturer’s recommendations.

treatment_protocol: For chronic jet lag, lights on and off times were advanced by 6 hours every 2 days whereas for control they remain unchanged. After CJL for 10 days, the brain tissues (PFC and NAc) of mice were harvested.

tag: brain region

value: nucleus accumbens

value: no chronic jet lag

tag: sampling time


title: NAc_ZT13_Ctrl_2

status: Public on Oct 01 2020

type: SRA

city: Wuhan

country: China

institute: Huazhong University of Science and Technology

description: NAc, nucleus accumbens;Zeitgeber Time 13h (ZT0 is defined as the time of lights on);rep2

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: treatment


title: NAc_ZT13_Ctrl_1

description: NAc, nucleus accumbens;Zeitgeber Time 13h (ZT0 is defined as the time of lights on);rep1


title: NAc_ZT1_CJL_2

description: NAc, nucleus accumbens;CJL, chronic jet lag;Zeitgeber Time 1h; rep2

value: chronic jet lag


title: NAc_ZT1_CJL_3

description: NAc, nucleus accumbens;CJL, chronic jet lag;Zeitgeber Time 1h; rep3


title: NAc_ZT13_CJL_2

description: NAc, nucleus accumbens;CJL, chronic jet lag ;Zeitgeber Time 13h (ZT0 is defined as the time of lights on);rep2


title: NAc_ZT13_CJL_3

description: NAc, nucleus accumbens;CJL, chronic jet lag ;Zeitgeber Time 13h (ZT0 is defined as the time of lights on);rep3


title: NAc_ZT13_CJL_1

description: NAc, nucleus accumbens;CJL, chronic jet lag ;Zeitgeber Time 13h (ZT0 is defined as the time of lights on);rep1


title: NAc_ZT1_Ctrl_3

description: NAc, nucleus accumbens;ZT1, Zeitgeber Time 1h; rep3


title: NAc_ZT1_Ctrl_2

description: NAc, nucleus accumbens;ZT1, Zeitgeber Time 1h; rep2


title: PFC_ZT1_CJL_3

description: PFC, prefrontal cortex; CJL, chronic jet lag;Zeitgeber Time 1h; rep3

source_name: PFC

value: prefrontal cortex


title: PFC_ZT13_Ctrl_1

description: PFC, prefrontal cortex; Zeitgeber Time 13h (ZT0 is defined as the time of lights on);rep1


title: PFC_ZT13_Ctrl_3

description: PFC, prefrontal cortex; Zeitgeber Time 13h (ZT0 is defined as the time of lights on);rep3


title: Brain_KO2

city: Guangzhou

first: shuibin

last: lin

state: Guangdong

address: Nonglin street

department: Center for Translational Medicine

institute: The First Affiliated Hospital of Sun Yat-sen University

data_processing:
SOAPnuke software used for filtering.
Sequenced reads mapped to mm10 whole genome using Bowtie2 to obtain the alignment results. Then RSEM was used to calculate gene and transcript expression levels.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include FPKM values for each sample

molecule: total RNA

source_name: Brain

extract_protocol:
Brains were removed and RNA was harvested using Trizol reagent.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces and then cDNA was generated using random hexamer-primed reverse transcription and amplified by PCR for construction of sequencing libraries.

tag: strain

tag: tissue

value: brain

tag: age

value: post natal day 28

tag: genotype


title: PFC_ZT13_CJL_1

description: PFC, prefrontal cortex; CJL, chronic jet lag ;Zeitgeber Time 13h (ZT0 is defined as the time of lights on);rep1


title: PFC_ZT1_Ctrl_3

description: PFC, prefrontal cortex; ZT1, Zeitgeber Time 1h; rep3


title: PFC_ZT1_CJL_2

description: PFC, prefrontal cortex; CJL, chronic jet lag;Zeitgeber Time 1h; rep2


title: PFC_ZT13_CJL_3

description: PFC, prefrontal cortex; CJL, chronic jet lag ;Zeitgeber Time 13h (ZT0 is defined as the time of lights on);rep3


title: PFC_ZT1_Ctrl_2

description: PFC, prefrontal cortex; ZT1, Zeitgeber Time 1h; rep2


title: PFC_ZT1_CJL_1

description: PFC, prefrontal cortex; CJL, chronic jet lag;Zeitgeber Time 1h; rep1


title: AO356_17800_4

city: Berkeley

first: Alexey

last: Kazakov

state: CA

address: 1 Cyclotron Road

department: Environmental Genomics and Systems Biology Division

country: USA

institute: Lawrence Berkeley National Laboratory

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated AO356_17800
AO356_17800_4_S83_L002

library_source: genomic

data_processing:
library strategy: DAP-seq
Read trimming using Trimmomatic
Alignment using Bowtie
Peak calling using SPP
Closest features were called using dap-seq-utils(https://github.com/novichkov-lab/dap-seq-utils)
Genome_build: GCF_000327065.1, GCF_001623525.1, GCF_000007565.2, GCF_001307275.1
Supplementary_files_format_and_content: wig

molecule: genomic DNA

organism: Pseudomonas fluorescens

source_name: purified genomic DNA from liquid cultures

growth_protocol: Pseudomonas strains were cultured in either LB or minimal media.

extract_protocol:
Genomic DNA was extracted with Promega wizard genomic kit according to the manufacturers protocols for gram negative bacteria. 6XHIS-tagged DNA-binding response regulator proteins were heterologously expressed in E. coli, purified with metal affinity resin, and mixed with 60 uL DNA binding buffer before elution. DNA binding buffer contained  0.4 ng/uL sheared adapter-ligated Pseudomonas genomic DNA, 10 mM imidazole, 0.1% Tween20 with or without 50 mM acetyl phosphate in TBS buffer pH 7.4. To enrich for specific protein-DNA interactions, resin bound protein-DNA was washed in a low concentration of imidazole before elution in a high concentration of imidazole. DNA was then amplified with index primers and sequenced with Illumina NovaSeq 6000.
DNA libraries were prepared for sequencing using a protocol from Chiniquy et al., BMC Genomics, 2020.

value: 50 mM acetyl phosphate

tag: protein


title: NAc_ZT1_CJL_1

description: NAc, nucleus accumbens;CJL, chronic jet lag;Zeitgeber Time 1h; rep1


title: WT6

city: La Jolla

first: Paul

middle: A

last: Insel

address: 9500 Gilman Drive

department: Pharmacology

institute: UC San Diego

data_processing:
Inspection via FASTQC
Adapter trimming via BBDUK
Quantification via Kallisto
Gene-level quantification via Tximport
Differential Expression analysis via EdgeR
Genome_build:   GRCm38 - mm10
Supplementary_files_format_and_content: Excel file containing gene-level expression in TPM and estimated Counts for each sample

source_name: CD11c+ve Bone marrow-derived dendritic cells

growth_protocol: Bone marrow was isolated from murine femurs and tibiae and cultured with GM-CSF for 6 days. CD11c+ cells were isolated with magnetic beads.

extract_protocol:
Total RNA was isolated via Qiagen Rneasy spin columns, with on-column digestion via Dnase-1
Illumina Truseq stranded mRNA, with standard Illumina protocols

value: WT

tag: Sex

value: Female


title: WT4

value: Male


title: WT5


title: GNAS_KO_6


title: GNAS_KO_7


title: PFC_ZT1_Ctrl_1

description: PFC, prefrontal cortex; ZT1, Zeitgeber Time 1h; rep1


title: PFC_ZT13_Ctrl_2

description: PFC, prefrontal cortex; Zeitgeber Time 13h (ZT0 is defined as the time of lights on);rep2


title: WT7


title: WT3


title: GNAS_KO_3


title: Tomato Knockout 3D Culture Condition Replicate 3

city: New York

first: Alec

last: Kimmelman

address: 550 1st Avenue

department: Department of Radiation Oncology, Perlmutter Cancer Center

institute: NYU School of Medicine

data_processing:
Illumina Casava software used for basecalling (performed by Novogene)
Sequencing reads were mapped using STAR v2.5 with a mismatch parameter of m=2 (performed by Novogene), reads with adaptor contamination were removed, reads with uncertain nucleotids for more than 10% of either read were removed, reads with low quality nucleotides (base quality < 20) for more than 50% of read were removed
FPKM values were generated from these count values (performed by Novogene)
Differential gene expression was performed using DESeq2_1.24.0 using the raw counts matrix
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: comma separated file of DESeq2 rlog transformed read counts
Supplementary_files_format_and_content: tab-delimited text files with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: table of raw read counts from HTSeq/STAR aligner

source_name: Pancreatic Cancer

growth_protocol: 2D culture collected 3 days after plating grown in DMEM, 10%fbs, 1%p/s.  3D culture collected 3 days after plating grown in DMEM, 10%fbs, 1% p/s, 5% matrigel.  Tumors were collected from orthotopic injections collected at endpoint of experiment.

extract_protocol:
RNA harvested using trizol extraction and Invitrogen purelink mRNA kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth condition

tag: cell line

value: KrasG12D-driven autochthonous PDA model


title: Tomato Knockout Tumor Culture Condition Replicate 2

value: Tumor


title: Tomato Knockout Tumor Culture Condition Replicate 1


title: Tomato Knockout 3D Culture Condition Replicate 2


title: Tomato Knockout 2D Culture Condition Replicate 3


title: Tomato Knockout 2D Culture Condition Replicate 2


title: FDFT1 Knockout 2 Tumor Culture Condition Replicate 1


title: Tomato Knockout 2D Culture Condition Replicate 1


title: FDFT1 Knockout 2 Tumor Culture Condition Replicate 2


title: FDFT1 Knockout 2 Tumor Culture Condition Replicate 3


title: FDFT1 Knockout 2 3D Culture Condition Replicate 3


title: FDFT1 Knockout 2 3D Culture Condition Replicate 2


title: GNAS_KO_4


title: FDFT1 Knockout 2 2D Culture Condition Replicate 3


title: FDFT1 Knockout 2 3D Culture Condition Replicate 1


title: FDFT1 Knockout 2 2D Culture Condition Replicate 2


title: FDFT1 Knockout 2 2D Culture Condition Replicate 1


title: NAc_ZT1_Ctrl_1

description: NAc, nucleus accumbens;ZT1, Zeitgeber Time 1h; rep1


title: Tomato Knockout Tumor Culture Condition Replicate 3


title: FDFT1 Knockout 1 3D Culture Condition Replicate 3


title: FDFT1 Knockout 1 Tumor Culture Condition Replicate 3


title: FDFT1 Knockout 1 Tumor Culture Condition Replicate 2


title: FDFT1 Knockout 1 2D Culture Condition Replicate 3


title: FDFT1 Knockout 1 2D Culture Condition Replicate 2


title: FDFT1 Knockout 1 3D Culture Condition Replicate 2


title: FDFT1 Knockout 1 2D Culture Condition Replicate 1


title: Tomato Knockout 3D Culture Condition Replicate 1


title: FDFT1 Knockout 1 3D Culture Condition Replicate 1


title: 10uM BPDP 24h rep4

city: Montreal

first: Barbara

middle: F.

last: Hales

state: QC

address: 3655 Prom. Sir William Osler, room 110

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

data_processing:
Base calling was performed using Illumina CASAVA (v1.8)
Sequences were filtered for reads containing adaptor or of low quality, then mapped to mm10 using STAR (v2.5, mismatch=2)
Quantification was performed using HTSeq (v0.6.1, -m union)
Differential analysis was performed using DESeq2 (v2_1.6.3, q-value < 0.05)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table containing raw count and FPKM value of each gene for each sample, plus normalized abundance output from DESeq2 of each gene for each treatment group

source_name: Embryonic forelimb

extract_protocol:
Cultured limb buds were preserved in RNAlater (Qiagen) and RNA was extracted using the Qiagen RNeasy Plus Mini Kit
mRNA was purified from 1ug of total RNA using poly-T oligo-attached magnetic beads and fragmented randomly in a fragmentation buffer. First-strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-); second-strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. Double-stranded cDNA was purified using AMPure XP beads. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3' ends of DNA fragments, NEBNext Adaptor was ligated to prepare for hybridization. The library fragments were purified with AMPure XP system. The final library was obtained by PCR amplification and purification of PCR products using AMPure XP beads.

tag: gestation day

value: GD 13

value: limb bud

value: 10uM BPDP

tag: treatment length

value: 24 hours


title: 10uM BPDP 24h rep3


title: 10uM BPDP 24h rep2


title: 1uM BPDP 24h rep3

value: 1uM BPDP


title: 1uM BPDP 24h rep2


title: 10uM BPDP 24h rep1


title: 1uM BPDP 24h rep4


title: snRNAseq_AR6_Gfap-Cre_Wlsfl+_RP2

city: Baltimore

first: Amir

last: Rattner

state: MD - Maryland

address: 725 North Wolfe St.

institute: Johns Hopkins University

data_processing:
RNA-Seq: Read alignment to the mm10 reference mouse genome sequence was performed with the RSEM-1.3.0 program (Li and Dewey, 2011) using the Bowtie2-2.2.9 aligner (Langmead and Salzberg, 2012).  Differential gene expression analysis was performed with EBseq 1.24.0 (Leng et al., 2013).
snRNA-Seq: Reads were aligned to a mm10 pre-mRNA index using Cellranger version 3.1.0.  Libraries were merged using Cellranger and data was analyzed using both the Monocle 3 (Qiu et al., 2017).

source_name: Adult control hippocampus

extract_protocol: both hippocampi of a single male mouse were rapidly dissected in ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH).  The tissue was minced with a razor blade and Dounce homogenized using a loose-fitting pestle in 5 ml of homogenization buffer supplemented with 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, and EDTA-free protease inhibitor (Roche 11 836 170 001), and 60 U/mL RNasin Plus RNase Inhibitor (Promega N2611).  A 5% IGEPAL-630 solution was added to bring the homogenate to 0.3% IGEPAL-630, and the homogenate was further homogenized with five strokes of a tight-fitting pestle.  The sample was filtered through a 50 μm filter (CellTrix, Sysmex, 04-004-2327), underlayed with solutions of 30% and 40% iodixanol in homogenization buffer (Sigma D1556), and centrifuged at 10,000 x g for 18 minutes in a swinging bucket centrifuge at 4°C.  Nuclei were collected at the 30%-40% interface, diluted with 2 volumes of homogenization buffer and concentrated by centrifugation for 10 min at 0.5 x g at 4°C.  snRNA-seq sequencing libraries were constructed using the 10X Genomics Chromium single cell 3’ v3 kit.

value: hippocampus

value: Gfap-Cre;Wlsfl/+


title: snRNAseq_AR5_Gfap-Cre_Wlsfl-_RP2

source_name: Adult mutant hippocampus

value: Gfap-Cre;Wlsfl/-


title: snRNAseq_AR1_Gfap-Cre_Wlsfl-_RP1


title: 1uM BPDP 24h rep1


title: Control 24h rep4

value: DMSO


title: Control 24h rep2


title: Control 24h rep3


title: Control 24h rep1


title: 10uM BPDP 3h rep4

value: 3 hours


title: snRNAseq_AR2_Gfap-Cre_Wlsfl+_RP1


title: 1uM BPDP 3h rep4


title: 10uM BPDP 3h rep2


title: Control 3h rep3


title: 1uM BPDP 3h rep2


title: 10uM BPDP 3h rep1


title: 1uM BPDP 3h rep1


title: 1uM BPDP 3h rep3


title: Control 3h rep4


title: Control 3h rep1


title: Control 3h rep2


title: EpCAM+ Zeb1-/- 1 [PS_KO_1]

city: AlDawadmi

first: Alhomidi

last: Almotiri

address: King Abdulaziz Rd

country: Saudi Arabia

institute: Shaqra University

data_processing:
The quality of raw reads was first assessed using an in-house script. Clean reads were obtained for future analysis after removing reads with low quality, adapter sequences and those sequences containing multiple ‘N’ bases
Reads were aligned to the mouse genome (Mus_musculus, GRCm38.p6) with STAR (v2.6.1d). The read numbers mapped to each gene was quantified with FeatureCounts (v1.5.0-p3). Fragments Per Kilobase of transcript per Million mapped reads (FPKM) of each gene was calculated based on gene length and mapped read counts.
Differential gene expression analysis was performed using the DESeq2 package (v1.20.0) for samples with bio-replicate. Resulting P values were adjusted using the Benjamini and Hochberg approach to control the false discovery rate (FDR, adjusted P value). Genes with an adjusted P < 0.05 were deemed differentially expressed.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text file containing: ensemble gene ID, gene name, chromosome, start and end locations, strand, gene length, biotype and description, read counts, transcription factor family, and fpkm for all the samples.

source_name: EpCAM+ Zeb1-/-

extract_protocol:
Cells were resuspended in RLT Plus buffer (Qiagen) and stored at -80 degrees. Total RNA was isolated from EpCAM+ and EpCAM- Zeb1-/- LSK cells 14 days after the last dose of pIpC (n= 4 mice per genotype) using the RNeasy Mini Kit™ (Qiagen) according to the manufacturer’s instructions. Total RNA stored in RNase-free water was amplified using SMART-Seq™ v4 Ultra™ Low Input RNA Kit for Sequencing (Takara Bio USA, Inc., Mountain View, USA) with the double strand cDNA (ds-cDNA) being synthesized. Then, ds-cDNA is purified with AMPure XP beads and quantified with Qubit (Life TechnologiesTM).
1 ng cDNA per sample was used as input to construct 250~300 bp insert cDNA libraries using NEBNext® UltraTM RNA Library Prep Kit (New England Biolabs, Ipswich, USA) following the manufacturer’s recommendations. Libraries were sequenced by Novogene, as 150-bp paired-end reads on an Illumina Novaseq 6000 platform.

tag: strain background

value: EpCAM+ Zeb1-/-

value: bone marrow

tag: immunophenotype

value: Lin- C-KIT+ SCA-1+ EpCAM+


title: mESCs_M5_KO_1

data_processing:
The original image files obtained by high-throughput sequencing undergo base recognition and error filtering to obtain Raw Data, stored in the compressed FASTQ format.
MeRIP-seq reads were aligned to the mm10 genome assembly using HISAT2.
Peaks were called using exomePeak and then used wto the following analysis: Motif search (HOMER), Peak annotation,Differential Peak annotation.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include annotated m6A peak for each sample

source_name: Embryonic stem cells

growth_protocol: 105 cells were seeded in 100 mm tissue culture dishes of the Mettl5 knockout and wildtype mESCs

extract_protocol:
Total RNA was harvested by phenol chloroform method.
Total RNA was randomly fragmented to size around 200 nucleotides at an appropriate temperature and then subjected to immunoprecipitation (IP) with anti-m6A antibody (Sigma-Aldrich, cat. no ABE572), Dynabeads Protein A (Invitrogen™, cat. no 10002D) and Dynabeads Protein G (Invitrogen™, cat. no 10004D). The immunoprecipitation RNAs were recovered and library was synthesized by SMART principle into the first strand cDNA, amplified and enriched by PCR, and purified by DNA from magnetic bead library fragments to obtain ultrafine RNA methylation of m6A.
m6A MeRIP-Seq

treatment_protocol: For spontaneous differentiation of mESCs, the cell culture dishes were coated with Poly (2-hydroxyethyl methacrylate) to prevent cell attachment. Then 5 × 106 mESCs were cultured with LIF (-) medium in the Poly 2-pre-coated dishes to induce embryoid body formation for 6 days. To induce the neural lineage differentiation of mESCs, 5 × 105 mESCs were cultured in N2B27 medium for 6 days.

tag: merip-chip antibody

value: Anti-m6A antibody (Sigma-Aldrich, cat. no ABE572)


title: PFC_ZT13_CJL_2

description: PFC, prefrontal cortex; CJL, chronic jet lag ;Zeitgeber Time 13h (ZT0 is defined as the time of lights on);rep2

value: prefrontal cortex

value: chronic jet lag


title: EpCAM- Zeb1-/- 1 [NG_KO_1]

source_name: EpCAM- Zeb1-/-

value: EpCAM- Zeb1-/-

value: Lin- C-KIT+ SCA-1+ EpCAM-


title: EpCAM- Zeb1-/- 4 [NG_KO_4]


title: EpCAM+ Zeb1-/- 4 [PS_KO_4]


title: mESCs_WT

value: wild type


title: mESCs_Ctr


title: EpCAM+ Zeb1-/- 3 [PS_KO_3]


title: EpCAM- Zeb1-/- 2 [NG_KO_2]


title: 10uM BPDP 3h rep3

value: GD 13

value: limb bud

value: 10uM BPDP


title: NUP98-NSD1 + NRASG12D  replicate 3

city: Halle

first: Razif

last: Gabdoulline

state: Sachsen-Anhalt

address: Ernst-Grube-Straße 40

department: Innere Medizin IV Haematologie und Onkologie

country: Germany

institute: Universitätsklinikum Halle

description: Sequenced as paired-end reads each 50bp (PE100)

data_processing:
Sequences are aligned to mouse genome GRCm38 with alignment program STAR_2.7.2a
Mapping to the transcriptome and gene expression analysis done with Cufflinks v2.2.1  using Gencode release M22.
Gene expression quantified by FPKM (Fragments Per Kilobase per Million).
Genome_build: mouse genome GRCm38.p6
Supplementary_files_format_and_content: For each Gene: Ensembl_ID, Gene_symbol, Locus (chr:start-end), FPKM

source_name: 5 Fluro-Uracil treated mouse bone marrow cells

growth_protocol: Cells were grown in Dulbecco’s modified Eagle medium (DMEM) (STEM cell Technologies, Cologne, Germany) supplemented with 15% fetal bovine serum (FBS) (Sigma-Aldrich, Munich, Germany), 10 ng/mL human interleukin-6 (hIL-6), 6 ng/mL murine interleukin-3 (mIL-3), and 20 ng/mL murine stem cell factor (mSCF; all from PeproTech, Hamburg, Germany).

extract_protocol: AllPrep DNA/RNA mini kit (Qiagen, Hilden, Germany).

tag: sample type


title: NUP98-NSD1 replicate 2


title: NUP98-NSD1 + NRASG12D replicate 1


title: NUP98-NSD1 replicate 3


title: NRASG12D  replicate 2


title: FDFT1 Knockout 1 Tumor Culture Condition Replicate 1

value: Tumor

value: KrasG12D-driven autochthonous PDA model


title: NRASG12D replicate 3


title: NUP98-NSD1 replicate 1


title: cKO PTH

city: Shen Zhen

first: Guozhi

last: Xiao

state: Guang Dong

address: No. 1088, Xueyuan Road

department: Biology

institute: Southern University of Science and Technology

data_processing:
Raw sequencing data was processed with Cell Ranger (v3.0.1)
Genome_build: mm10
Supplementary_files_format_and_content: feature barcode matrices were generated using Cell Ranger (v3.0.1)

source_name: bone marrow non-hematopoietic cell

extract_protocol:
Bones (femur and tibia) were harvested. Muscle and tendon tissue was removed and bone marrow was flushed. Stromal cells from bone marrow fraction were isolated. Bone marrow stromal cells were enriched by FACS.
Libraries were constructed according to 10X Chromium Single Cell 3ʹ Reagent Kits v3 protocols

treatment_protocol: Control and Kindlin-2 knockout mice were treated with or without PTH for 28d.


title: control PTH


title: control veh


title: cKO veh


title: NRASG12D replicate 1


title: EpCAM+ Zeb1-/- 2 [PS_KO_2]


title: EpCAM- Zeb1-/- 3 [NG_KO_3]


title: pancreas-in-vitro-SHP099-6

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were adapter- and quality-trimmed with Trimmomatic.
The sequencing reads were aligned to the mouse genome (build mm10/GRCm38) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.

source_name: PDAC CELL LINE

extract_protocol:
RNA was extracted from frozen tumors using the miRNeasy Mini Kit (Qiagen), according to the manufacturer's instructions.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit.

value: pancreatic ductal adenocarcinoma (PDAC) cell line

tag: duration


title: pancreas-in-vitro-SHP099-5


title: pancreas-in-vitro-SHP099-4


title: mESCs_M5_KO_2


title: pancreas-in-vitro-COMBO-11


title: pancreas-in-vitro-COMBO-12


title: NUP98-NSD1 + NRASG12D replicate 2


title: pancreas-in-vitro-ARS1620-8


title: pancreas-in-vitro-COMBO-10


title: pancreas-in-vitro-ARS1620-9


title: pancreas-in-vitro-DMSO-2

value: DMSO


title: pancreas-in-vitro-DMSO-3


title: pancreas-in-vitro-ARS1620-7


title: pancreas-in-vivo-shp099-6

source_name: PDAC

value: pancreatic ductal adenocarcinoma (PDAC)

value: 3 days


title: pancreas-in-vivo-shp099-5


title: pancreas-in-vivo-shp099-4


title: pancreas-in-vivo-ctrl-1

value: Vehicle


title: pancreas-in-vivo-ctrl-3


title: pancreas-in-vivo-ars1620-9


title: pancreas-in-vivo-combo-10


title: pancreas-in-vivo-combo-12


title: pancreas-in-vivo-ars1620-7


title: lung-in-vivo-SHP099-6

source_name: NSCLC

value: non-small cell lung cancer (NSCLC)


title: pancreas-in-vivo-ars1620-8


title: pancreas-in-vivo-combo-11


title: lung-in-vivo-CTRL-2


title: lung-in-vivo-CTRL-1


title: lung-in-vivo-SHP099-5


title: lung-in-vivo-CTRL-3


title: lung-in-vivo-COMBO-12


title: pancreas-in-vitro-DMSO-1


title: lung-in-vivo-COMBO-11


title: lung-in-vivo-COMBO-10


title: lung-in-vivo-ARS1620-9


title: WT 2

city: Cincinnati

first: Samantha

last: Brugmann

state: OH

address: Department of Developmental Biology, DK 1 BLDG R, 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

data_processing:
BAM files were loaded into Strand NGS, RNA-seq analysis
The mouse reference genome mm10 was selected
Data Interpretation was set to program defaults
Quality inspection was performed and data proved of good quality
For quantification, partial reads were considered and the detection of novel genes and exons was allowed for. Counts were normalized to one, with the baseline median to all samples. All entities were filtered on expression, with at least one sample having a value within the defined range. DeSeq2 was used for quantification.
The Audic Claverie test (no correction) was used to identify differentially expressed genes in between wild-type and mutant samples with a p-value ≤ 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: text files include transcript counts for each sample

source_name: mandibular prominence

growth_protocol: Timed matings were recorded and embryonic day 0.5 was counted to be noon of the day on which a copulation plug was discovered.

extract_protocol:
Dissected mandibular prominences were removed, flash frozen on dry ice, and RNA was harvested using RNAqueous-micro Total RNA Isolation Kit (Cat#AM1931).
RNA libraries were prepared for sequencing using standard Illumina sequencing protocols

value: mandibular prominence

value: embryonic day 10.5

value: Wild-type


title: lung-in-vivo-ARS1620-8


title: lung-in-vivo-ARS1620-7


title: WT 4


title: Hand2;Wnt1-Cre Mutant 1

value: Hand2 f/f; Wnt1-Cre+


title: Hand2;Wnt1-Cre Mutant 2


title: Hand2;Wnt1-Cre Mutant 3


title: WT 1


title: Gli2;Gli3;Wnt1-Cre Mutant 2

value: Gli2 f/f; Gli3 f/f; Wnt1-Cre+


title: Gli2;Gli3;Wnt1-Cre Mutant 3


title: Gli2;Gli3;Wnt1-Cre Mutant 1


title: lung-in-vivo-SHP099-4


title: Cortex, cKO rep1

first: Lichao

last: Xu

address: luojiashan

institute: Wuhan University

data_processing:
Cutadapt (version 1.16, http:// cutadapt.readthedocs.io/en/stable/guide.html) was used for adaptor sequence remove with the parameters -u 0 -u -30 -U 0 -U -30 -m 30
Cleaned reads were mapped to the mouse reference genome (mm10) using TopHat (version 2.1.1, http://ccb.jhu.edu/software/tophat/index.shtml) with default settings.
The gene expression level was calculated by Cufflinks (version 2.2.1, http://cole-trapnell-lab.github.io/ cufflinks) and normalized by fragments per kilobase of bin per million mapped reads (FPKM).
Principal component analysis (PCA) of the quality control matrices was employed to determine the presence of RNA-Seq sample outliers.
Differentially expressed genes are defined as ones with the false discovery rate (FDR) less than 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts and FPKM values for each Sample.

source_name: cortex

extract_protocol:
RNA isolation was performed using the TRIZOL reagent (Invitrogen) according to manufacturer’s instructions. Tissue or cells were homogenized using a glass-Teflon in 1 ml or 500 µl TRIZOL reagent on ice and phase separation was achieved with 200 µl or 100 µl chloroform. After centrifugation at 12,000× g for 15 min at 4°C, RNA was precipitated by mixing aqueous phase with equal volumes of isopropyl alcohol and 0.5 µl 20 mg/ml glycogen. Precipitation were dissolved in DNase/RNase-free water (not diethylpyrocarbonate treated, Ambion).
Total RNA was extracted as described above. The concentration and quality of RNA was measured with Nanodrop 2000c (Thermo Fisher Scientific) and an Agilent 2100 Bioanalyzer (Agilent Technologies), respectively. RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111). Briefly, mRNA was extracted by poly-A selected with magnetic beads with poly-T and transformed into cDNA by first and second strand synthesis. Newly synthesized cDNA was purified by AMPure XP beads (1:1) and eluted in 50 μl nucleotide-free water. RNA-seq libraries were sequenced by Illumina NovaSeq 6000 platform with pair-end reads of 150 bp. The sequencing depth was 60 million reads per library.

value: cortex

value: Embryo 13.5

value: Emx1 cKO


title: Cortex, cKO rep3


title: Cortex, control rep3

value: control


title: Cortex, cKO rep2


title: Cortex, control rep2


title: WT 3


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H9_ad010

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

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

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: CP

value: male


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H9_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H9_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H9_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H9_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H8_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H8_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H8_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H8_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H8_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H8_ad004


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H8_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H7_ad010


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H7_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H7_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H7_ad004


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H7_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H6_ad012


title: Cortex, control rep1


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H6_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H6_ad004


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H6_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H9_ad004


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H5_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H6_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H5_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H7_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H4_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H4_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H4_ad004


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H4_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H4_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H3_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H3_ad010


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H4_ad010


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H4_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H3_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H3_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H4_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H2_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H3_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H3_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H2_ad010


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H6_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H2_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H5_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H2_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H2_ad004


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H3_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H12_ad010


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H12_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H12_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H12_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H12_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H11_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H11_ad010


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H11_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H11_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H11_ad004


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H11_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H11_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H10_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H1_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H1_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H10_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H10_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H1_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H1_ad004


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H12_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H1_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G9_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H1_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G9_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G9_ad010


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G9_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G9_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G8_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G8_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H11_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G8_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H10_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G8_ad010


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G8_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G8_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H10_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H1_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G7_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H1_ad010


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G7_ad010


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G7_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G6_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G7_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G7_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G6_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G6_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G6_ad010


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G6_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G6_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G5_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G8_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G8_ad004


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G5_ad010


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G7_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G5_ad004


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G4_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G4_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G5_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G4_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G5_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G4_ad004


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G5_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G3_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G3_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G3_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G3_ad004


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G3_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G6_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G2_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G3_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G5_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G2_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G2_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G2_ad010


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G2_ad004


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G2_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G2_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G12_ad010


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G5_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G2_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G12_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G12_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_H7_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G12_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G12_ad004


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G12_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G12_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G11_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G11_ad010


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G11_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G11_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G11_ad004


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G11_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G10_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G10_ad010


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G10_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G10_ad004


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G10_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G10_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G1_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G1_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F9_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G1_ad004


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G1_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G1_ad010


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G1_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F9_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F9_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F9_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F9_ad004


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F8_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F8_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F8_ad010


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F8_ad004


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F8_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F7_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F7_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F7_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F7_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F6_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F7_ad004


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F7_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F6_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F7_ad010


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F9_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F6_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_G1_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F6_ad010


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F5_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F5_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F6_ad004


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F8_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F5_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F6_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F6_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F5_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F6_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F8_ad008


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F4_ad012


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F4_ad001


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F7_ad006


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F5_ad002


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F4_ad007


title: CEMBA190207_5J_3_CEMBA190207_5J_4_F4_ad010


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title: CEMBA190207_5J_1_CEMBA190207_5J_2_E10_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_E1_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_E1_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_E10_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_E1_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_E10_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_E2_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_E1_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_E1_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_E11_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_E11_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D9_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D8_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D9_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_E1_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D9_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D9_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D9_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D8_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D8_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D8_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_E1_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D7_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D7_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D7_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D7_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D7_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D7_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D7_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D7_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_E1_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D6_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D6_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D6_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D6_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D6_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D6_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D5_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D8_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D8_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D4_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D5_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D4_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D5_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D5_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D5_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D3_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D5_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D3_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D5_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D3_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D4_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D4_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D4_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D4_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D3_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D3_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D2_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D2_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D2_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D2_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D3_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D2_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D2_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D12_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D12_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D2_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D12_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_E5_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D12_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D12_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D12_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D3_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D11_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D11_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D11_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D11_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D11_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D10_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C9_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C9_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D10_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D10_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D10_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D10_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_D10_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C9_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C9_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C9_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C9_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C9_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C9_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C8_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C8_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C8_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C8_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C8_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C8_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C7_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C7_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C7_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C7_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C6_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C6_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C6_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C5_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C5_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C6_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C6_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C5_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C5_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C5_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C6_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C4_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C4_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C4_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C4_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C4_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C3_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C4_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C3_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C3_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C2_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C8_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C2_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C5_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C2_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C4_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C2_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C5_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C2_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C2_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C12_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C11_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C12_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C11_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C4_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C12_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C3_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C11_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C3_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C11_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C11_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C11_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C10_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C10_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C11_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C2_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C10_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C10_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C10_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C12_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C11_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C12_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C10_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C12_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C1_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C10_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C1_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C1_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B9_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C1_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C1_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C1_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B9_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B8_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B9_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B8_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B9_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B8_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B8_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B8_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B8_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C12_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B8_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C1_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B7_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B7_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B7_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B6_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B6_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B7_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B7_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B6_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B6_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B6_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B5_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B5_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B5_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B5_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B5_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B5_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B4_ad010


title: Nlrp12-KO Tumor-4

city: Dallas

first: Hasan

last: Zaki

address: 6000 Harry Hines Blvd

department: Pathology

institute: UT Southwestern Medical Center

data_processing:
RNA sequencing was performed by commercial vendor Novogene (CA).
Quality control of RNA-seq data was performed by removing reads containing adapters, low quality (Qscore<= 5) and N > 10% (N represents the base cannot be determined).
Sequencing Reads were mapped to mm10 using STAR and then gene expression levels for each sample were calculated by RSEM with default setting.
Differential Expression Analysis was conducted by EBSeq with FDR=0.05.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file for each sample

source_name: Nlrp12-KO tumor

extract_protocol:
Colorectal tumors were removed, frozen in liquid nitrogen and stored at -80C. RNA was isolated from the tumor tissue with  Trizol reagent.
Standard Illumina protocols were used to prepare RNA libraries.

value: 20 weeks

value: Colorectal tumor


title: Nlrp12-KO Tumor-1


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B4_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B3_ad012


title: WT-Tumor -3

source_name: WT-tumor


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B4_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B3_ad001


title: WT-Tumor -2


title: WT-Tumor -1


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B3_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B3_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B3_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B6_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B3_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B3_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B5_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B4_ad012


title: Nlrp12-KO Tumor-2


title: Nlrp12-KO Tumor-3


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B2_ad012


title: WT-Tumor -4


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B2_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B2_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B2_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B2_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B2_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B2_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B2_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B12_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B12_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B12_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B12_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_C6_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B12_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B11_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B12_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B12_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B11_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B11_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B11_ad004


title: T470_patient_sample_1

type: genomic

city: Luxembourg

first: Ann-Christin

last: Hau

address: 1, Rue Louis Rech

department: National Center of Pathology

country: Luxembourg

institute: Laboratoire National de sante

hyb_protocol: Similarly treated amounts of reference; Female or Male gDNA pool (Promega) were processed as sample genomic DNAs and hybridized with the Agilent Oligo aCGH Hybridization Kit to the corresponding platform array at 65°C for 24h or 48h respectively.

scan_protocol: Microarray slides were scanned using an Agilent 2565C DNA scanner

data_processing:
The tif images were analyzed with Agilent Feature Extraction version 12.5, using default settings
normalised log ratio Cy5/Cy3 representing test/reference; transformed logratio matrix with 0 - unaltered, 1 - gain, -1 - loss, 2 - amplification, -2 - deletion

organism: Homo sapiens

source_name: Primary patient sample

label_protocol: For Agilent-021529 platform 2µg, for Agilent-021850 and Agilent-028081 platform 1µg, for Agilent-030587 platform 500ng and for Agilent-021924 platform 250ng of genomic DNA  were digested with RSA1 and Alu1 (Agilent) to generate 200-500bp large fragments. The BioPrime aCGH Genomic labeling Kit (Life Technologies) and Cy3 and Cy5 dyes (GE Healthcare) were used following standard protocols for Agilent aCGH (CGH enzymatic protocol v6.2; Ref # G4410-90010).

growth_protocol: patient specimen were: 1) flash frozen on dry ice after surgical removal or 2) mechanically cut, seeded on agar coated flasks (0.85%) and allowed to form spheroids for up to 2 weeks at 37°C under 5% CO2 and atmospheric oxygen in DMEM medium, 10% FBS, 2mM L-Glutamine, 0.4mM NEAA and 100U/ml Pen-Strep (all from Lonza).  Spheroids (generation 0) with a diameter of 300-1000 µm were then implanted in the brain of immunodeficient mice (NOD/Scid, Nude or NSG; 6 spheroids per mice). Cell lines were derived from xenotransplanted mice by papain-based enzymatic digestion of PDOX tissue and cultured in serum-free medium based on  Neurobasal® base medium (Life Technologies) supplemented with 1 x B27 (Life Technologies) 2 mM L-Glutamine, 30 U/ml Pen-Step, 1 U/ml Heparin (Sigma), 20 ng/ml bFGF (Miltenyi, 130-093-841) and 20 ng/ml EGF (Provitro, 1325950500).

extract_protocol: Genomic DNA was isolated from patient tissue, spheroid cultures or cell lines using the AllPrep DNA/RNA Mini Kit® (Qiagen) following manufacturer’s instructions for “Simultaneous purification of genomic DNA and total RNA from animal tissues”.

value: Primary patient sample

tag: gender

value: Male

source_name: Reference DNA

value: Reference DNA

value: Female

tag: catalog no


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B11_ad002

tag: strain


title: T470_Xenograft_Generation_3

source_name: Xenotransplant

value: Xenotransplant


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B11_ad001

tag: age


title: T407_cell-line_passage_6

source_name: Cell Line

value: Cell Line


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B10_ad012


title: T434_patient_sample_1


title: T394_Xenograft_Generation_4


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B10_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B10_ad008


title: T239_patient_sample_1


title: T361_Xenograft_Generation_1


title: T394_patient_sample_1


title: T186_patient_sample_1


title: T251_patient_sample_1


title: T239_Xenograft_Generation_2


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B1_ad012


title: T361_patient_sample_1


title: T394_cell-line_passage_5


title: T188_patient_sample_1


title: T238_patient_sample_1


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B1_ad006


title: T192_patient_sample_2


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B1_ad007


title: T347_Xenograft_Generation_2


title: T233_Xenograft_Generation_1


title: T233_patient_sample_1


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B10_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B1_ad004


title: T341_patient_sample_1


title: T331_patient_sample_1


title: T188_patient_sample_2


title: T192_Xenograft_Generation_3


title: T188_Xenograft_Generation_2


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B1_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A9_ad012


title: T16_cell-line_passage_8


title: T347_patient_sample_1


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A9_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A9_ad010


title: T185_Xenograft_Generation_1


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A9_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A9_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A9_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_B1_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A8_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A8_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A8_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A8_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A8_ad006


title: T185_patient_sample_2


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A8_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A8_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A8_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A7_ad012


title: T16_patient_sample_2