title: HSB2_USP7shRNA4057_1 [SJTALL061906_C1]

source_name: Hsb-2 cell line treated with USP7 shRNA-4057

value: USP7 shRNA-4057


title: HSB2_scrambled_1 [SJTALL061905_C1]

status: Public on Mar 09 2021

type: SRA

city: Memphis

first: Timothy

middle: Isham

last: Shaw

state: TN

address: 262 Danny Thomas Pl

department: Computational Biology

country: USA

institute: St Jude Children's Research Hospital

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA
fastq files werer mapped by StrongARM, an internal mapping pipeline that performs STAR and bwa mapping.
reads were counted using htseq/0.6.1p1 with gencode.v19.annotation.gtf
htseq was used to derive the read counts with parameters -r name -a 0 -s no -m union -t exon
Genome_build: hg19
Supplementary_files_format_and_content: counts

molecule: total RNA

organism: Homo sapiens

source_name: Hsb-2 cell line treated with scrambled siRNA

extract_protocol:
Total RNA was extracted using the QIAGEN Rneasy Mini kit.
The total stranded RNA library was prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche Sequencing). RNA sequencing was performed on NovaSeq 6000 system (Illumina).

tag: cell line

tag: cell type

value: T-ALL Cancer Cell Line

tag: genotype

tag: treatment

value: scrambled siRNA

tag: molecule subtype

value: Ribo-depleted


title: HSB2_USP7shRNA4057_2 [SJTALL061906_C2]


title: Jurkat_USP7shRNA4057_2 [SJTALL061902_C2]

source_name: Jurkat cell line treated with USP7 shRNA-4057

value: Jurkat


title: HSB2_WT_1 [SJTALL061904_C1]

source_name: Wild-type Hsb-2 cell line


title: Jurkat_USP7shRNA4058_2 [SJTALL061903_C2]

source_name: Jurkat cell line treated with USP7 shRNA-4058

value: USP7 shRNA-4058


title: Jurkat_USP7shRNA4058_1 [SJTALL061903_C1]


title: HSB2_WT_2 [SJTALL061904_C2]


title: Molt4_WT_1 [SJTALL065786_C1]

source_name: Wild-type Jurkat cell line

tag: genotype/varaition

value: Wild-type


title: Partial_KO_Molt4_2 [SJTALL065786_C4]

source_name: Partial KO USP7 in Molt4

value: Partial KO USP7 in Molt4


title: Jurkat_scrambled_2 [SJTALL061901_C2]

source_name: Jurkat cell line treated with scrambled siRNA


title: Jurkat_USP7shRNA4057_1 [SJTALL061902_C1]


title: Jurkat_WT_2 [SJTALL061900_C2]


title: Jurkat_scrambled_1 [SJTALL061901_C1]


title: USP7-wild-type_3 [Hausp51.wt.S9]

data_processing:
Basecalls performed using CASAVA
fastq files werer mapped by STAR_2.4.1d_modified parameters --chimSegmentMin 20 --chimJunctionOverhangMin 20
reads were counted using htseq/0.6.1p1 with Mus_musculus.NCBIM37.67.gtf
htseq was used to derive the read counts with parameters -r name -a 0 -s no -m union -t exon
Genome_build: mm9
Supplementary_files_format_and_content: counts

organism: Mus musculus

source_name: USP7 wild-type in the hematopoeitic system

extract_protocol:
RNA samples were isolated using the RNeasy Mini Kit (QIAGEN)
The total stranded RNA library was prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche Sequencing). RNA sequencing was performed on NovaSeq 6000 system (Illumina).

treatment_protocol: Total RNA was extracted from the thymus 3 days after birth.

tag: strain background

tag: genotype/variation

tag: tissue

value: Thymus


title: USP7-wild-type_4 [Hausp56.wt.S10]

value: USP7 wild-type in the hematopoeitic system


title: homozygous-KO-3 [Hausp62.homo.S3]

source_name: Homozygous knock-out of USP7 in the hematopoeitic system


title: Subject NS1 at timepoint B

status: Public on Apr 05 2021

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

description: single-cell RNAseq

data_processing:
Raw sequencing reads were demultiplexed using Cell Ranger mkfastq pipeline to create FASTQ files.
Cell Ranger count pipeline (v3.1) was employed in order to perform alignment (using STAR), filtering, barcode counting, and UMI counting.
Seurat v3.1 pre-processing standard protocol as defined by Satija lab.
10x cellranger count filtered output data of PBMCs from thirteen healthy controls were added to that of the eighteen Covid-19 samples. Seurat package (v3.1) was used for all downstream analysis. 10x gene expression matrices for each sample were converted and combined into one Seurat object.
Cells that had mitochondrial gene percentages higher than 12% and cells with less than 200 genes were excluded from the study to filter out dead and dying cells.
Genome_build: GRCh38 (Ensembl 93)
Supplementary_files_format_and_content: Cell Ranger filtered_gene_matrix, seurat objects

source_name: PBMC

extract_protocol:
PBMCs were isolated from whole blood using density gradient centrifugation, and immediately cryopreserved. They were later thawed, DMSO was removed, cells were filtered and loaded to the 10x chromium platform
Libraries were prepared using the 10X Genomics Chromium Next GEM Chip G, according to the manufacturer’s user guide (document number CG000208, revision E, February 2020)

value: PBMC

tag: diagnosis

tag: disease severity

value: Stable

tag: tocilizumab treatment

value: No

tag: age

tag: Sex

value: F

tag: race

value: white

tag: bmi

tag: weight-kg

tag: height-m

value: No Tocilizumab

tag: time-point

value: B

tag: chronic htn

tag: htn

tag: lung disease

tag: hospital admission

value: Yes

tag: icu admission

tag: outcome

value: Discharged

tag: tocilizumab dose (mg/kg)

tag: time difference between samples a and b (d)


title: USP7-wild-type_2 [Hausp47.wt.wt.S8]

tag: strain background

tag: genotype/variation

tag: tissue

tag: molecule subtype


title: USP7-wild-type_1 [Hausp44.wt.wt.S7]


title: heterozygous_KO-3 [Hausp63.het.S6]

source_name: Heterozygous knock-out of USP7 in the hematopoeitic system


title: P2 Control female fl/fl Msi1 fl/fl Msi2

status: Public on Jan 11 2021

city: LITTLE ROCK

first: Melanie

last: MacNicol

state: Arkansas

address: 4301 W Markham St

department: Neuroscience

institute: UAMS

description: virgin, diestrous female

data_processing:
Demultiplexed fastq files were analyzed with the 10x Genomics Cell Ranger 3.1.0 count function for sequence alignment and gene counting
The UCSC mm10 reference mouse transcriptome was amended by annotating chromosome 11: 50,948,572-50,949,192 in the gene transfer file (gtf) as an artificial single exon gene on the negative strand named “Prop1L” as described by Cheung et al A custom reference was then compiled using the cellranger mkref command, and the custom reference was used for Cell Ranger/STAR alignment instead of the original UCSC mm10 transcriptome.
Seurat was used to pre-process the raw counts generated by cellranger count to filter cells with low quality cells, cell doublets, and cells with high percentage of mitochondrial genes
Filtered cells that have unique feature counts over more the 75th percentile plus 1.5 times the interquartile range (IQR) or less than the 25th percentile minus 1.5 time the IQR. Additionally, filtered cells with mitochondrial counts falling outside the same range with respect to mitochondrial gene percentage
Counts were normalized using the LogNormalize method, which normalizes the feature expression measurements for each cell by the total expression, multiplies this by a scale factor (10,000 by default), and log-transforms the result using the natural log.
The 2000 highest variable features were selected. The data was then scaled by a linear transformation and PCA performed on the scaled data. A JackStraw procedure was implemented to determine the significant PCA components that have a strong enrichment of low p-value features
A graph-based clustering approach was then applied to embed cells in a graph structure with edges drawn between cells with similar feature expression patterns, and then attempt to partition this graph into highly interconnected ‘quasi-cliques’ or ‘communities’. To this end, we employed Uniform Manifold Approximation and Projection (UMAP) (41), a non-linear dimensional reduction technique to visualize and explore the results using Seurat.
Seurat FindNeighbors and FindClusters functions were optimized to label clusters based on the visual clustering in the projections and cell types assigned
Differential expression analysis was performed using MAST, a GLM-framework that treats cellular detection rate as a covariate
Genome_build: The UCSC mm10 reference mouse transcriptome was amended by annotating chromosome 11: 50,948,572-50,949,192 in the gene transfer file (gtf) as an artificial single exon gene on the negative strand named “Prop1L” as described by Cheung et al A custom reference was then compiled using the cellranger mkref command, and the custom reference was used for Cell Ranger/STAR alignment instead of the original UCSC mm10 transcriptome.

source_name: pituitary

growth_protocol: Growth in low adherant culture for 7 days

extract_protocol:
Pituitaries from 8-week old control diestrous FVB females (n = 6) were collected and individually dispersed as previously described (14).  Following mechanical dispersion, cells were pelleted and washed once with DMEM.  Cells were pelleted again and fixed with methanol according to the 10x Genomics methanol fixation protocol.
Single cell 3’ library generation was performed using a 10X Genomics Chromium Controller and the v3 reagent kit (10x Genomics) according to the manufacturer’s protocol.  Cell suspensions were loaded on to the middle four channels of a Chromium Single Cell A Chip according to the manufacturer’s instructions, aiming for 10,000 cells per channel.  Following generation of single-cell gel bead-in-emulsions (GEM), reverse transcription, fragmentation and cDNA amplification, library preparations and bar coding were performed using the Illumina TruSeq Stranded mRNA Sample Preparation Kit v2 as per manufacturer’s instructions
200pM of each library was pooled for sequencing on the Illumina NextSeq 500 platform using a high output flow cell (100 cycles) to generate approximately 25 million 75 base reads per sample.

treatment_protocol: Pituispheres were prepared from dispersed whole female pituitaries (REF). After growth in low adherent culture for 7 days, pituispheres were fixed and dual labeled for Sox2 and Musashi1 or Sox2 and Musashi2.

value: pituitary

tag: age

value: 8-week old

tag: gender

value: female

tag: strain

value: FVB


title: P1 Control female fl/fl Msi1 fl/fl Msi2

description: virgin, diestrous female


title: shID1_3_S18

status: Public on Dec 14 2020

city: Pamplona

first: Silvestre

last: Vicent

address: Avenida Pío XII 55

department: Oncology

country: Spain

institute: Center for Applied Medical Research (CIMA)

data_processing:
The quality of the samples was verified using FastQC software.
FASTQ files were mapped to hg19 human assembly using STAR 2.5.2b using default parameters.
Gene expression quantification was carried out with featureCounts v1.5.0 using read counts of exonic gene regions.
The gene annotation reference was Gencode v19.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw count values summarized by "featureCounts v1.5.0" for each gene

molecule: polyA RNA

source_name: H1792 cell line

extract_protocol: RNAseq (Hashimshony T, Senderovich N, Avital G, Klochendler A, de Leeuw Y, Anavy L, Gennert D, Li S, Livak KJ, Rozenblatt-Rosen O, Dor Y, Regev A, Yanai I. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome biology 2016; 17: 77.)

tag: cell line

tag: cell type

value: lung adenocarcinoma

tag: treatment

value: Infection with an inducible Id1 shRNA


title: heterozygous_KO-1 [Hausp48.het.S4]

value: Heterozygous knock-out of USP7 in the hematopoeitic system

value: Thymus

value: Ribo-depleted


title: homozygous-KO-2 [Hausp57.homo.S2]

value: Homozygous knock-out of USP7 in the hematopoeitic system


title: shID1_2_S17


title: homozygous-KO-1 [Hausp50.homo.S1]


title: shGFP_2_S14

value: Infection with an inducible GFP shRNA


title: shGFP_3_S15


title: shGFP_1_S13


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d12 [d12_FNA_3]

status: Public on Aug 13 2020

data_processing:
Single cell feature counts for a single library were generated using `cellranger count` from Cell Ranger v3.1.0
Single cell feature counts for multiple libraries were pooled by subsampling to the same effective sequencing depth using `cellranger aggr` from Cell Ranger v3.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content:
matrix.mtx.gz contains a gene expression count matrix stored in the Market Exchange Format for sparse matrices
features.tsv.gz contains feature information that correspond to row indices of matrix.mtx.gz
barcodes.tsv.gz contains cellular barcodes that correspond to column indices of matrix.mtx.gz. The trailing dash and number (e.g. -12) indicates the sample from which the cell originated and corresponds the row number for that sample in aggregation.csv.
aggregation.csv contains the sample information. The order of the samples represented as rows in aggregation.cs corresponds to the numbers after the dash (e.g. -12) in barcodes.tsv.gz.

source_name: Lymph node

extract_protocol:
PBMCs were isolated from blood. Fine-needle aspiration was performed on axillary lymph nodes.
Libraries were prepared using 10x Genomics' Chromium Next GEM single cell 5' gene expression workflow

value: male

value: Lymph node

tag: time point

tag: isolate


title: Jurkat_WT_1 [SJTALL061900_C1]

value: Jurkat

value: T-ALL Cancer Cell Line

tag: genotype


title: heterozygous_KO-2 [Hausp61.het.S5]


title: scRNA-seq of Homo sapiens: adult male PBMC enriched for IgD low B cells d0 [d0_memory_B_PBMC]

value: PBMC


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d28 [d28_FNA_3]


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d60 [d60_FNA]


title: scRNA-seq of Homo sapiens: adult male PBMC enriched for IgD low B cells d12 [d12_memory_B_PBMC]


title: shID1_1_S16


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d28 [d28_FNA_2]


title: scRNA-seq of Homo sapiens: adult male whole PBMC d28 [d28_PBMC_2]


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d12 [d12_FNA]


title: scRNA-seq of Homo sapiens: adult male whole PBMC d5 [d5_PBMC]


title: scRNA-seq of Homo sapiens: adult male whole PBMC d0 [d0_PBMC_2]


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d0 [d0_FNA_2]


title: scRNA-seq of Homo sapiens: adult male whole PBMC d60 [d60_PBMC]


title: scRNA-seq of Homo sapiens: adult male PBMC enriched for IgD low B cells d60 [d60_memory_B_PBMC]


title: scRNA-seq of Homo sapiens: adult male PBMC enriched for IgD low B cells d28 [d28_memory_B_PBMC]


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d5 [d5_FNA_2]


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d0 [d0_FNA]


title: scRNA-seq of Homo sapiens: adult male PBMC enriched for IgD low B cells d5 [d5_memory_B_PBMC]


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d5 [d5_FNA]


title: TESTGEX_HHT

status: Public on Aug 03 2020

description: Control Sample

data_processing:
Base calls were converted to fastq sequences and demultiplexed using the cellranger mkfastq function from 10X Genomics 2.2.0.
Reads were aligned to the GCRhg38 genome supplied by 10X Genomics.
Sparse count matrices, barcode assignments and feature calls were made using the Cell Ranger count function.
The resulting output was loaded into Seurat v.2.3.4 for analysis.
Cells with less than 50 genes detected, or mitochondrial content above 0.2 of all transcripts were discarded.
Genome_build: GCRhg38
Supplementary_files_format_and_content: Output files from Cell Ranger (10X Genomics) were archived and compressed into a tar.gz file, one per sample. Each compressed archive contains the tab-delimited text files barcodes.tsv, features.tsv & genes.tsv. The tar.gz file also contains a feature-barcode matrix file named matrix.mtx, stored in the Market Exchange Format for sparse matrices. The matrix file contains indexes to barcodes and gene/features, as well as total UMI count per cell and gene/feature combination.

source_name: Peripheral blood

extract_protocol:
B cells were isolated from PBMCs by Human Pan B cell immunomagnetic negative selection kit (StemCell) per manufacturer’s instructions.
Libraries were prepared using the Chromium Single-cell5′ Reagent Kit (10x Genomics) for version 3 chemistry per the manufacturer’s protocol.

value: B-lymphocytes

tag: mgfa class

value: Asymptomatic


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d60 [d60_FNA_2]


title: scRNA-seq of Homo sapiens: adult male whole PBMC d12 [d12_PBMC_2]


title: MG189B_NOIGD_HHT

value: IIb


title: MG192B_NOIGHD_HHT

value: Iia


title: MG139B_NOIGHD_HHT


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d12 [d12_FNA_2]


title: D6 cells Replicate 2

status: Public on Jul 01 2020

type: RNA

city: Glendale

first: Crystal

last: Marconett

state: CA

address: 1856 Kirkby Rd

department: Translational Genomics

institute: Keck School of Medicine

description: total miRNA from D6 cells

hyb_protocol: unknown

scan_protocol: Scan date 5/13/11 10:36 using Agilent Technologies Scanner G2505C US45102918 using one-color scanning

data_processing: MicroRNA array data were processed using AgiMicroRNA package  in R. Microarray data identification of significantly affected miRNAs over the course of alveolar transdifferentiation utilized ANOVA with a Benjamini-Hochburg FDR correction.

source_name: human AT1-like (D6) cells Replicate 2

label_protocol: MiRNA expression was assessed on the Agilent MicroRNA Array v2.0 platform

growth_protocol: Primary AEC were isolated and cultured as described previously (Marconett et al., PLoS genetics 2013).

extract_protocol: RNA was harvested from each biological replicate on Day 0 (D0), D2, D4, D6, and D8. miRNA was extracted with the MirVana miRNA isolation kit (Thermo Fisher Scientific)

treatment_protocol: No Treatment

value: female

value: 49 years old

tag: race

value: caucasian


title: D6 cells Replicate 1

description: total miRNA from D6 cells

source_name: human AT1-like (D6) cells Replicate 1

value: 61 years old


title: D4 cells Replicate 2

description: total miRNA from D4 cells

source_name: human AT differentiating (D4) cells Replicate 2


title: Donor 3: intermediate cell phenotype (D2)

description: RiboZero depleted RNAseq

data_processing:
Raw reads were aligned to the genome using Tophat2.1
BAM files were used to construct BigWig files for visualization
Genome_build: hg19

source_name: primary alveolar epithelial cells taken from human remnant transplant lung

growth_protocol: PurifiedAT2 cells were harvested from a human lung donor without prior history of lung disease and differentiated in vitro for 6 days

extract_protocol:
RNA was isolated using whole-cell extract by performing RNA purification using the Illustra TriplePrep kit.
Library construction was performed at the USC Epigenome center.
Barcodes were attached;  Libraries were plated using the Illumina cBot and run on the Hi-Seq 2000 according to manufacturer’s instructions using HSCS v 1.5.15.1. Sample underwent Paired End 50 cycling. Libraries were plated using the Illumina cBot and run on the Hi-Seq 2000 according to manufacturer’s instructions using HSCS v 1.5.15.1.

value: intermediate differentiation AEC cells

tag: donor


title: D8 cells Replicate 3

description: total miRNA from D8 cells

source_name: human AT1-like (D6) cells Replicate 3

value: 47 years old


title: D8 cells Replicate 1

description: total miRNA from D8 cells


title: Donor 2: AT1-like cells (D4)

description: RiboZero depleted RNAseq

value: AT1-like cells


title: D2 cells Replicate 1

description: total miRNA from D2 cells

source_name: human AT differentiating (D2) cells Replicate 1


title: D6 cells Replicate 3

description: total miRNA from D6 cells


title: D4 cells Replicate 1

description: total miRNA from D4 cells

source_name: human AT differentiating (D4) cells Replicate 1


title: Donor 2: AT1-like cells (D6)

description: RiboZero depleted RNAseq


title: D8 cells Replicate 2

description: total miRNA from D8 cells


title: D4 cells Replicate 3

description: total miRNA from D4 cells

source_name: human AT differentiating (D4) cells Replicate 3


title: Donor 3: AT1-like cells (D4)

description: RiboZero depleted RNAseq


title: D2 cells Replicate 2

description: total miRNA from D2 cells

source_name: human AT differentiating (D2) cells Replicate 2


title: Donor 3: purified AT2 cells (D0)

description: RiboZero depleted RNAseq

value: Purified primary AT2 cells


title: Donor 3: AT1-like cells (D6)

description: RiboZero depleted RNAseq


title: Donor 1: AT1-like cells (D6)

description: RiboZero depleted RNAseq


title: Donor 2: purified AT2 cells (D0)

description: RiboZero depleted RNAseq


title: D0 cells Replicate 2

description: total miRNA from D0 cells

source_name: human AT2 (D0) cells Replicate 2


title: Donor 2: intermediate cell phenotype (D2)

description: RiboZero depleted RNAseq


title: Donor 1: intermediate cell phenotype (D2)

description: RiboZero depleted RNAseq


title: Donor 1: AT1-like cells (D4)

description: RiboZero depleted RNAseq


title: Donor 1: purified AT2 cells (D0)

description: RiboZero depleted RNAseq


title: D0 cells Replicate 1

description: total miRNA from D0 cells

source_name: human AT2 (D0) cells Replicate 1


title: D0 cells Replicate 3

description: total miRNA from D0 cells

source_name: human AT2 (D0) cells Replicate 3

value: male


title: Hi-C chl4Δ - Tension

status: Public on Jan 13 2020

city: Edinburgh

first: Daniel

last: Robertson

state: Midlothian

address: 2.28 Michael Swann Building, Kings Buildings, Mayfield Road

department: Discovery Research Platform for Hidden Cell Biology

country: United Kingdom

institute: University of Edinburgh

library_source: genomic

data_processing:
Fastq reads aligned to sacCer3 using HiC-Pro v2.11.1 , bowtie2 v2.3.4.1 (--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder), removing singleton, multi hit and duplicated reads.
Valid interaction pairs were converted into the .cool contact matrix format using cooler (1 kb resolution)
Matrixes balanced using Iterative correction
Genome_build: SacCer3
Supplementary_files_format_and_content: Cooler .cool matrix 1kb binned, balanced with iterative correction

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cells

growth_protocol: Cells were diluted to OD(600)=0.2 and arrested G1 with alpha factor for 3 hours, then released into a metaphase arrest by depletion of Cdc20 for 2 hours. "No tension" condition included addition of nocodazole and benomyl, "Tension" condition did not.

extract_protocol:
Lysates were prepared by grinding the frozen pellet in a chilled mortar with a pestle for 15 minutes and 1/10th of the initial pellet weight (~0.5 g) was taken for further processing. Restriction enzyme digestion (DpnII), filling-in, ligation, crosslink reversal, DNA concentration and purification and biotin removal were carried out as described in Schalbetter et al. (2018) doi: https://doi.org/10.1101/442038. DNA was then fragmented on a Bioruptor Plus sonication device (Diagenode) for a total of 2x 30 cycles 30 seconds on/off at High setting.
DNA end repair and A-tailing using T4 DNA polymerase, T4 Polynucleotide Kinase and Klenow fragment DNA polymerase I were carried out as in Schalbetter et al., 2018. Hi-C libraries were fractionated using Ampure XP beads as previously described in Belton et al. (2015) DOI: 10.1101/pdb.prot085209. Biotin pull-down, adapter ligation (NextFlex, Bioo Scientific) and sequencing (EMBL Core Genomics Facility, Heidelberg, Germany) were carried as in Schalbetter et al. (2018) doi: https://doi.org/10.1101/442038.

treatment_protocol: Cells were fixed and lysed as in Belton & Dekker (2015) DOI: 10.1101/pdb.prot085209. Briefly, 200 ml of cells at OD~0.6 carrying pMET-CDC20 were arrested in metaphase at 25 ˚C in the presence and absence of tension as described above, fixed with 3% formaldehyde for 20 minutes at 25 ˚C at 250 rpm and the reaction was quenched for 5 minutes by the addition of 0.35 M glycine (final concentration). Cells were washed with cold water, resuspended in 5 ml 1x NEBuffer 2 and frozen in liquid nitrogen.

tag: target

tag: cell cycle stage

value: Metaphase

value: Tension


title: D2 cells Replicate 3

description: total miRNA from D2 cells

source_name: human AT differentiating (D2) cells Replicate 3


title: scRNA-seq of Mus musculus: lymph nodes

status: Public on Jun 09 2020

data_processing:
Single cell feature counts for a single library were generated using `cellranger count` from Cell Ranger v3.1.0
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx.gz contains a gene expression count matrix stored in the Market Exchange Format for sparse matrices
Supplementary_files_format_and_content: features.tsv.gz contains feature information that correspond to row indices of matrix.mtx.gz
Supplementary_files_format_and_content: barcodes.tsv.gz contains cellular barcodes that correspond to column indices of matrix.mtx.gz

source_name: Lymph nodes

extract_protocol:
Total antibody-secreting cells (CD19+ CD4- IgDlo Fas+ CD38lo CD138+) were bulk sorted from draining lymph nodes.
Libraries were prepared using 10x Genomics' Chromium Next GEM single cell 5' gene expression workflow

treatment_protocol: Intramuscular injection of 10 microgram of the receptor-binding domain (RBD) of the spike protein was administered on Day 0. Intramuscular injection of 5 microgram of the whole spike protein was administered on Day 14, and then again on Day 24. Draining lymph nodes were harvested on Day 29.

value: 10 weeks

tag: Sex

value: Iliac and inguinal lymph nodes


title: Hi-C Wild type - No tension

description: WT-NT

value: Wild type

value: No tension (Nocodazole treatment)


title: Hi-C chl4Δ - No tension

source_name: Hi-C chl4Δ - No tension

tag: tension / no tension


title: 2102EP-C1_rep2

status: Public on Nov 11 2019

city: Urbana

first: Michael

last: Spinella

state: IL

address: 2001 S Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois at Urbana-Champaign

description:
processed data file: EP_GEO_Processed.txt
2102EP_C1_UT_2_GAATGAGA-GAGGCATT_L00M

data_processing:
fastq files were aligned to human genome assembly NCBI GRCh38.p12 using STAR aligner .
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was TMM normalized using the calcNormFactors function in R
Differentially expressed genes (³2-fold and £1% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma trend package.
Genome_build: human genome assembly NCBI GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files includeTMM normalized counts per million (CPM) values for each Sample ...

source_name: Derived from 2102EP

growth_protocol: All cells were cultured in DMEM with 10% FBS and antibiotic in incubator (5% CO2; 37°C)

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the HiSeq 4000 sequencing kit version 1, according to the manufacturer’s instructions.

value: Embryonic carcinoma

tag: tissue origin

value: testis

tag: cisplatin sensitivity

value: Cisplatin acquired resistant


title: 833K-A2_rep2

description:
processed data file: 833K_GEO_Processed.txt
833K_A2_UT_2_GTCGGAGC-GGTTATAA_L00M

source_name: Derived from 833K


title: 833K-A2_rep3

description:
processed data file: 833K_GEO_Processed.txt
833K_A2_UT_3_CTTGGTAT-CCAAGTCC_L00M


title: 833K-A2_rep1

description:
processed data file: 833K_GEO_Processed.txt
833K_A2_UT_1_ACTAAGAT-AACCGCGG_L00M


title: 833K-B4_rep1

description:
processed data file: 833K_GEO_Processed.txt
833K_B4_UT_1_GGCATTCT-CTAGCTTG_L00M


title: Hi-C Wild type - Tension


title: 2102EP-B3_rep1

description:
processed data file: EP_GEO_Processed.txt
2102EP_B3_UT_1_ATATCTCG-ATCTTAGT_L00M


title: 833K-B4_rep2

description:
processed data file: 833K_GEO_Processed.txt
833K_B4_UT_2_AATGCCTC-TCGATCCA_L00M


title: 2102EP-C1_rep1

description:
processed data file: EP_GEO_Processed.txt
2102EP_C1_UT_1_AGGCAGAG-AGAATGCC_L00M


title: 2102EP-B3_rep2

description:
processed data file: EP_GEO_Processed.txt
2102EP_B3_UT_2_GCGCTCTA-GCTCCGAC_L00M


title: 833K_rep2

description:
processed data file: 833K_GEO_Processed.txt
833K_UT_2_GCACGGAC-GTCTCGCA_L00M

source_name: Testicular embryonal carcinoma cell lines derived from metastatic site; Abdomen


title: 833K_rep1

description:
processed data file: 833K_GEO_Processed.txt
833K_UT_1_ATGTAAGT-ACTCTATG_L00M


title: 833K-B4_rep3

description:
processed data file: 833K_GEO_Processed.txt
833K_B4_UT_3_TACCGAGG-CCTGAACT_L00M


title: 2102EP-A1_rep3

description:
processed data file: EP_GEO_Processed.txt
2102EP_A1_UT_3_ATGGCATG-AAGGTACC_L00M


title: 2102EP-A1_rep1

description:
processed data file: EP_GEO_Processed.txt
2102EP_A1_UT_1_AAGATACT-ACTTACAT_L00M


title: NT2/D1-B3_rep2

description:
processed data file: NT1_GEO_Processed.txt
NT2B3_UT2_GAGATTCC-GTACTGAC_L00M

source_name: Derived from NT2/D1


title: 2102EP_rep2

description:
processed data file: EP_GEO_Processed.txt
2102EP_UT_2_CTACGACA-GAGTCCAA_L00M

source_name: Testicular embryonal carcinoma cell lines derived from retroperitoneal lymph node

value: Cisplatin sensitive


title: 2102EP_rep1

description:
processed data file: EP_GEO_Processed.txt
2102EP_UT_1_TCGTAGTG-AGACTTGG_L00M


title: 2102EP-A1_rep2

description:
processed data file: EP_GEO_Processed.txt
2102EP_A1_UT_2_GGAGCGTC-GTCCGTGC_L00M


title: NT2/D1-B3_rep3

description:
processed data file: NT1_GEO_Processed.txt
NT2B3_UT3_ATTCAGAA-TATAGCCT_L00M


title: 2102EP_rep3

description:
processed data file: EP_GEO_Processed.txt
2102EP_UT_3_TAAGTGGT-CTTAAGCC_L00M


title: 833K_rep3

description:
processed data file: 833K_GEO_Processed.txt
833K_UT_3_GGTACCTT-AAGACGTC_L00M


title: NT2/D1-B3_rep1

description:
processed data file: NT1_GEO_Processed.txt
NT2B3_UT1_GAGATTCC-CAGGACGT_L00M


title: NT2/D1-A4_rep2

description:
processed data file: NT1_GEO_Processed.txt
NT2A4_UT2_TCCGGAGA-TAATCTTA_L00M


title: NT2/D1-A4_rep1

description:
processed data file: NT1_GEO_Processed.txt
NT2A4_UT1_TCCGGAGA-AGGCGAAG_L00M


title: 2102EP-C1_rep3

description:
processed data file: EP_GEO_Processed.txt
2102EP_C1_UT_3_TGCGGCGT-CCTCGGTA_L00M


title: NT2/D1-A4_rep3

description:
processed data file: NT1_GEO_Processed.txt
NT2A4_UT3_TCCGGAGA-CAGGACGT_L00M


title: 2102EP-B3_rep3

description:
processed data file: EP_GEO_Processed.txt
2102EP_B3_UT_3_AACAGGTT-ATACCAAG_L00M


title: NT2/D1_rep2

description:
processed data file: NT1_GEO_Processed.txt
NT21_21_17_UT2_CGCTCATT-GGCTCTGA_L00M

source_name: Testicular embryonal carcinoma cell lines derived from metastatic site, Lung


title: NT2/D1_rep3

description:
processed data file: NT1_GEO_Processed.txt
NT21_21_17_UT3_CGCTCATT-AGGCGAAG_L00M


title: 7681.NORM

status: Public on Jun 22 2019

description:
Normal brain cortex of athymic nude mice
SJMMNORM016461_G1-7681
SJMMNORM016461.G1.7681.NORM

data_processing:
Basecalls performed using CASAVA
fastq files werer mapped by StrongARM, an internal mapping pipeline that performs STAR and bwa mapping.
reads were counted using an internal perl script and converted to FPKM using mm9
Genome_build: mm9
Supplementary_files_format_and_content: matrix txt file with log2FPKM for each gene symbol for each sample

source_name: normal brain cortex

extract_protocol:
RNAs were extracted by Trizol (Invitrogen) from about 20 mg aliquots of the same tumor samples for proteomics analyses.
For RNAseq, libraries were generated from ~1 µg total RNA using the Illumina Stranded Total RNA kit with the Human/Mouse/Rat Ribo-Zero Gold ribosomal reduction kit. Libraries were sequenced on an Illumina HiSeq 2500 using paired-end 100 bp sequencing chemistry.

tag: host strain

value: athymic nude mice

tag: tissue type

value: normal brain cortex


title: 7679.NORM

description:
Normal brain cortex of athymic nude mice
SJMMNORM016460_G1-7679
SJMMNORM016460.G1.7679.NORM


title: 7370.TPM3_NTRK1

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human TPM3-NTRK1 fusion along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG016450_D1-IC_7370
SJMMHGG016450.D1.IC.7370.TPM3_NTRK1

source_name: high grade glioma with TPM3-NTRK1 Fusion

tag: injection cell

value: high grade glioma


title: 7677.NORM

description:
Normal brain cortex of athymic nude mice
SJMMNORM016458_G1-7677
SJMMNORM016458.G1.7677.NORM


title: K8wt_4

status: Public on Jun 27 2019

city: Boston

first: Zhe

last: Li

state: MA

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

description: Gene expression data for wild-type YFP+ luminal mammary epithelial cells sorted from Rosa26-Stop-YFP female mouse #4 10-14 days after intraductal injection of Ad-K8-Cre

hyb_protocol: The biotinylated cDNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C

scan_protocol: Each cDNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured

data_processing:
The raw CEL files were imported and processed with genepattern AffySTExpressionFileCreator tool from Broad institiute.
Expression data was generated by AffySTExpressionFileCreator tool using the Robust Multi-array Average (RMA) algorithm as provided by the 'oligo' package in Bioconductor.

label: biotin

source_name: Wild-type YFP+ K8+ luminal mammary epithelial cells sorted from Ad-K8-Cre-injected Rosa26-Stop-YFP female mouse 4

label_protocol: Labeling, hybridization and scan were performed by the Dana-Farber Cancer Institute Molecular Biology Core Facility. The NuGEN Ovation V2 Amplification System was used to amplify and label the samples, according to manufacturer's protocol.

growth_protocol: Wild-type luminal mammary epithelial cells were sorted from Rosa26-Stop-YFP female mice after Ad-K8-Cre injection; Trp53/Brca1-null mammary tumors were collected from Trp53L/L;Brca1L/L female mice after Ad-K8-Cre injection.

extract_protocol: RNeasy kit (Qiagen, #73504) was used on wild-type luminal mammary epithelial cells or Trp53/Brca1-null mammary tumors according to manufacturer's protocol

treatment_protocol: Wild-type luminal mammary epithelial cells were obtained from Rosa26-Stop-YFP female mice 10-14 days after intraductal injection of Ad-K8-Cre; Trp53/Brca1-null mammary tumors were obtained from Trp53L/L;Brca1L/L females several months after intraductal injection of Ad-K8-Cre.

tag: tissue

value: mammary gland

tag: cell type

value: luminal mammary epithelial cells

value: wildtype


title: 7371.TPM3_NTRK1

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human TPM3-NTRK1 fusion along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG016451_D1-IC_7371
SJMMHGG016451.D1.IC.7371.TPM3_NTRK1


title: 7372.TPM3_NTRK1

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human TPM3-NTRK1 fusion along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG016452_D1-IC_7372
SJMMHGG016452.D1.IC.7372.TPM3_NTRK1


title: 1159.TPM3_NTRK1

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human TPM3-NTRK1 fusion along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG016453_D1-IC_1159
SJMMHGG016453.D1.IC.1159.TPM3_NTRK1


title: K8wt_1

description: Gene expression data for wild-type YFP+ luminal mammary epithelial cells sorted from Rosa26-Stop-YFP female mouse #1 10-14 days after intraductal injection of Ad-K8-Cre

data_processing: The raw CEL files were imported and processed with genepattern AffySTExpressionFileCreator tool from Broad institiute. Expression data was generated by AffySTExpressionFileCreator tool using the Robust Multi-array Average (RMA) algorithm as provided by the 'oligo' package in Bioconductor.

source_name: Wild-type YFP+ K8+ luminal mammary epithelial cells sorted from Ad-K8-Cre-injected Rosa26-Stop-YFP female mouse 1


title: 7672.TPM3_NTRK1

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human TPM3-NTRK1 fusion along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG015503_D1-IC_7672
SJMMHGG015503.D1.IC.7672.TPM3_NTRK1


title: Brca1Tumor_25

description: Gene expression data for Trp53/Brca1-null mammary tumor #25 developed in a Trp53L/L;Brca1L/L female mouse injected with Ad-K8-Cre

source_name: Trp53/Brca1-null mammary tumor #25 developed in a Trp53L/L;Brca1L/L female mouse injected with Ad-K8-Cre adenovirus

value: mammary tumor


title: Brca1Tumor_24

description: Gene expression data for Trp53/Brca1-null mammary tumor #24 developed in a Trp53L/L;Brca1L/L female mouse injected with Ad-K8-Cre

source_name: Trp53/Brca1-null mammary tumor #24 developed in a Trp53L/L;Brca1L/L female mouse injected with Ad-K8-Cre adenovirus


title: NT2/D1_rep1

description:
processed data file: NT1_GEO_Processed.txt
NT21_21_17_UT1_CGCTCATT-CCTATCCT_L00M

source_name: Testicular embryonal carcinoma cell lines derived from metastatic site; Lung


title: 4419.PDGFRA

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human PDGFRA D842V mutation along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG016457_D1-IC_4419
SJMMHGG016457.D1.IC.4419.PDGFRA

source_name: high grade glioma with PDGFRA D842V mutation

value: PDGFRA D842V


title: K8wt_2

description: Gene expression data for wild-type YFP+ luminal mammary epithelial cells sorted from Rosa26-Stop-YFP female mouse #2 10-14 days after intraductal injection of Ad-K8-Cre

source_name: Wild-type YFP+ K8+ luminal mammary epithelial cells sorted from Ad-K8-Cre-injected Rosa26-Stop-YFP female mouse 2


title: 7675.TPM3_NTRK1

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human TPM3-NTRK1 fusion along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG015502_D1-IC_7675
SJMMHGG015502.D1.IC.7675.TPM3_NTRK1


title: Brca1Tumor_23

description: Gene expression data for Trp53/Brca1-null mammary tumor #23 developed in a Trp53L/L;Brca1L/L female mouse injected with Ad-K8-Cre

source_name: Trp53/Brca1-null mammary tumor #23 developed in a Trp53L/L;Brca1L/L female mouse injected with Ad-K8-Cre adenovirus


title: 4412.PDGFRA

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human PDGFRA D842V mutation along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG016454_D1-IC_4412
SJMMHGG016454.D1.IC.4412.PDGFRA


title: 4418.PDGFRA

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human PDGFRA D842V mutation along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG016456_D1-IC_4418
SJMMHGG016456.D1.IC.4418.PDGFRA


title: 9444374158_R02C01

status: Public on Jun 11 2019

type: genomic

city: Newcastle upon Tyne

first: Ed

last: Schwalbe

address: Ellison Place

department: Natural Sciences

institute: Northumbria University

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 and Infinium MethylationEPIC Beadchips using standard Illumina protocol.

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

data_processing:
Arrays were imported and quality control performed using minfi.
Beta values - A correction for the type of material (FFPE/frozen) was performed by using the removeBatchEffect function of the limma package v.3.24.15. The log2-transformed intensities of the methylated and unmethylated signal were corrected individually. Beta-values were calculated from the retransformed intensities using an offset of 100 (as recommended by Illumina) and used for all downstream analyses.
GSE130051_beta_values.csv: Beta values; Rows are Samples, columns are ID_REFs.
GSE130051_transposed_beta_values.csv: Beta values; Rows are ID_REFs, columns are Samples.

label: Cy5 and Cy3

source_name: medulloblastoma

label_protocol: Standard Illumina protocol.

extract_protocol: Genomic DNA was extracted and purified from medulloblastoma samples using standard extraction protocols.

tag: cohort

value: Previously unpublished - sample from St. Jude collection

value: Medulloblastoma

tag: subgroup

tag: subtype


title: 7671.TPM3_NTRK1

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human TPM3-NTRK1 fusion along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG015501_D1-IC_7671
SJMMHGG015501.D1.IC.7671.TPM3_NTRK1


title: 7664.PDGFRA

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human PDGFRA D842V mutation along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG015500_D1-IC_7664
SJMMHGG015500.D1.IC.7664.PDGFRA


title: 7661.PDGFRA

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human PDGFRA D842V mutation along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG015498_D1-IC_7661
SJMMHGG015498.D1.IC.7661.PDGFRA


title: 9855358053_R02C02

value: Northcott et al. 2017 (PMID:28726821)


title: 9934625063_R01C02

value: MBNOS


title: 7662.PDGFRA

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human PDGFRA D842V mutation along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG015499_D1-IC_7662
SJMMHGG015499.D1.IC.7662.PDGFRA


title: 9855358064_R02C02


title: 7678.NORM

description:
Normal brain cortex of athymic nude mice
SJMMNORM016459_G1-7678
SJMMNORM016459.G1.7678.NORM


title: 4416.PDGFRA

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human PDGFRA D842V mutation along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG016455_D1-IC_4416
SJMMHGG016455.D1.IC.4416.PDGFRA


title: 9855358064_R02C01


title: 9855358048_R06C01


title: 9855358048_R06C02


title: 9829119124_R02C02


title: 9855358053_R01C01


title: 9761749012_R02C02


title: 9610361029_R03C01


title: 9610361023_R03C01


title: 9855358048_R05C02


title: 9610361023_R05C01


title: 9761749012_R03C01


title: 9741950103_R04C02


title: 9553932002_R04C01


title: 9444374147_R01C02


title: 9444374135_R02C02


title: 9444374157_R06C01


title: 9610361022_R02C02


title: 9444374135_R05C02


title: 9553932002_R01C01


title: 9379086095_R06C01


title: 9379086089_R04C01


title: 9379086089_R05C01


title: 9444374146_R05C02


title: 9305651041_R01C02


title: 9379086088_R02C02


title: 9444374135_R05C01


title: 9379086095_R05C02


title: 9379086088_R06C01


title: 9297949037_R04C01


title: 9297949037_R01C02


title: 9007217016_R03C02


title: 9379086088_R04C01


title: 9379086088_R02C01


title: 9007217016_R04C02


title: 7990895142_R04C01


title: 9297949033_R03C01


title: 7990895046_R05C01


title: 9007217108_R01C01


title: 8622007028_R05C02


title: 9296930039_R05C02


title: 8622007026_R06C01


title: 9297949037_R06C01


title: 8622007026_R04C02


title: 8622007026_R02C02


title: 6969568004_R06C02


title: 8622007028_R03C02


title: 7970376026_R04C02


title: 6929793061_R01C01


title: 7970376055_R02C02


title: 7970368168_R04C01


title: 6929718049_R02C02


title: 6929718049_R04C02


title: 6929689136_R03C01


title: 8622007026_R01C01


title: 6929689136_R01C01


title: 6929718049_R01C02


title: 6929689136_R02C01


title: 8622007026_R06C02


title: 6752625054_R05C01


title: 6229017094_R04C02


title: 6229017094_R01C02


title: 3998909137_R03C02


title: Kinetin-treated FD fibroblasts 5

status: Public on Mar 21 2019

first: Susan

last: Slaugenhaupt

state: Massachusetts

address: 185 Cambridge Street, CPZN-5254

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

description:
SEMatrix_kin_on_fd.txt
4663_KIN-A-FD

data_processing:
RNASeq reads were mapped against Ensembl GRCh37 (version 75) by STAR (version 2.4.2) allowing 5% mismatch
Number of reads covering splice junction was measured by STAR during alignment
Exon triplet index was built on Ensembl GRCh37 (version 75) where each triplet is a three-consecutive exons, namely exon 1, 2 and 3, according to the annotation
For each triplet, two values are measured. The first value is the average of number of reads connecting exon 1 and 2 and number of reads connecting exon 2 and 3. This value is an integer
The second value is the number of reads connecting exon 1 and 3, which is an integer as well.
Genome_build: Ensembl GRCh37 version 75
Supplementary_files_format_and_content: Fastq format for RNASeq reads; Tab-delimited txt format for splice junction counts

source_name: Human fibroblast

growth_protocol: Six different human FD fibroblast cell lines were obtained from Coriell Institute and cultured in Dulbecco's modified Eagle's medium (D-MEM, Gibco) with 10% fetal bovine serum (FBS, Sigma). Cells were counted and plated in order to achieve semi-confluence after eight days.

extract_protocol:
After seven days of treatment, cells were collected, and RNA was extracted using the TRI reagent procedure provided by the manufacturer.
RNA-Seq libraries were prepared by the Genomic and Technology Core (GTC) of MGH using strand-specific dUTP method. In brief, RNA sample quality (based on RNA Integrity Number, or RIN) and quantity was determined using the Agilent 2200 TapeStation and between 100-1000 ng of total RNA was used for library preparation. Each RNA sample was spiked with 1 µl of diluted (1:100) External RNA Controls Consortium (ERCC) RNA Spike-In Mix (4456740, ThermoFisher) alternating between mix 1 and mix 2 for each well in the batch. Samples were then enriched for mRNA using polyA capture, followed by stranded reverse transcription and chemical shearing to make appropriate stranded cDNA inserts. Libraries were finished by adding Y-adapters, with sample specific barcodes, followed by between 10-15 rounds of PCR amplification. Libraries were evaluated for final concentration and size distribution by Agilent 2200 TapeStation and/or qPCR, using Library Quantification Kit (KK4854, Kapa Biosystems), and multiplexed by pooling equimolar amounts of each library prior to sequencing.

treatment_protocol: Twenty-four hours after plating, the medium was changed and cells were treated with kinetin or DMSO to a final concentration of 200 µM and 0.5%, respectively. DMSO was used as vehicle and the concentration of kinetin was chosen based on our previous studies, since at this concentration kinetin induces robust splicing changes.

value: fibroblast

tag: genotype/variation

value: ELP1 mutation

tag: treatment

value: Kinetin treated


title: Kinetin-treated FD fibroblasts 6

description:
SEMatrix_kin_on_fd.txt
4899_KIN-A-FD


title: 3998909137_R06C01


title: 6229017094_R04C01


title: 6229017094_R06C01


title: Kinetin-treated FD fibroblasts 1

description:
SEMatrix_kin_on_fd.txt
0850_KIN-A-FD


title: Untreated FD fibroblasts 6

description:
SEMatrix_kin_on_fd.txt
4899_CTRL-A-FD

value: untreated


title: Untreated FD fibroblasts 5

description:
SEMatrix_kin_on_fd.txt
4663_CTRL-A-FD


title: Untreated FD fibroblasts 3

description:
SEMatrix_kin_on_fd.txt
2343_CTRL-A-FD


title: Kinetin-treated FD fibroblasts 3

description:
SEMatrix_kin_on_fd.txt
2343_KIN-A-FD


title: Untreated FD fibroblasts 4

description:
SEMatrix_kin_on_fd.txt
4589_CTRL-A-FD


title: Untreated FD fibroblasts 2

description:
SEMatrix_kin_on_fd.txt
2341_CTRL-A-FD


title: Donor 1 AT1-like cells (D6)

status: Public on Mar 18 2019

description: RiboZero depleted RNAseq

data_processing:
Raw reads were aligned to the genome using Tophat2.1
BAM files were used to construct BigWig files for visualization

source_name: AT1-like cells

extract_protocol:
RNA was isolated using whole-cell extract by performing RNA purification using the Illustra TriplePrep kit.
Library construction was performed at the USC Epigenome center.
Barcodes were attached; D0= ATGTCA, D2=CCGTCC, D4=GTCCGC, D6=GTGAAA. Libraries were plated using the Illumina cBot and run on the Hi-Seq 2000 according to manufacturer’s instructions using HSCS v 1.5.15.1. Sample underwent Paired End 50 cycling. Libraries were plated using the Illumina cBot and run on the Hi-Seq 2000 according to manufacturer’s instructions using HSCS v 1.5.15.1.

tag: individual

value: donor 1


title: Kinetin-treated FD fibroblasts 4

description:
SEMatrix_kin_on_fd.txt
4589_KIN-A-FD


title: Donor 1 AT1-like cells (D4)

description: RiboZero depleted RNAseq


title: ChIP Input AT1-like cells

description: INPUT DNA

data_processing:
fastx_toolkit_0.0.13 was used to filter low quality reads: average quality score < 30 and length < 20
bwa-0.7.7was used to perform alignment using hg19 genome, with 2 mismatches allowed, and only reads with mapping quality (MAPQ) ≥ 30 are retained using samtools-0.1.19
Duplicates were removed with picard-tools-1.107
SICERv1.1 was used to perform peak calls. Settings used were FAIRE: window size 50, gap size 50, H3K27ac: window size 100, gap size 200,and H3K4me1: window size 200, gap size 20. Fragment size set as 150 for all samples.
Genome_build: hg19
Supplementary_files_format_and_content: Peaks called via SICER (.bed files)

source_name: Alveolar epithelial cells

growth_protocol: PurifiedAT2 cells were harvested from a human lung donor without prior history of lung disease.

extract_protocol:
Chomatin of freshly isolated AT2 cells was prepared as previously described (Marconett et al., PLoS Genetics, 2013). INPUT DNA was collected after sonication and supernatant collection but before IP stage. FAIRE was performed on supernanant removed after ChIP immunoprecipiation.
ChIPseq libraries were made by the USC Epigenome Center. The NEB Ultra Kit was used for library construction according to manufacturer's reccomendations. Adapter sequences were obtained from BioScientific. Barcodes were attached. Libraries were plated using the Illumina cBot and run on the Hi-Seq 2000 according to manufacturer’s instructions using HSCS v 1.5.15.1. Sample underwent Single End 50 cycling.  Libraries were plated using the Illumina cBot and run on the Hi-Seq 2000 according to manufacturer’s instructions using HSCS v 1.5.15.1. Sample underwent Single End 50 cycling.

value: lung

value: Alveolar epithelial cells


title: Donor 1 purified AT2 cells (D0)

description: RiboZero depleted RNAseq

source_name: Purified primary AT2 cells


title: ChIP input transitional AT2->AT1 cells

description: INPUT DNA


title: Untreated FD fibroblasts 1

description:
SEMatrix_kin_on_fd.txt
0850_CTRL-A-FD


title: Purified AT2 cells- H3K27Ac ChIP

description: Histone ChIP


title: Transitional AT2->1 cells  - H3K27Ac ChIP

description: Histone ChIP


title: Donor 1 intermediate cell phenotype (D2)

description: RiboZero depleted RNAseq

source_name: intermediate differentiation AEC cells


title: Purified AT2 cells- H3K4me1 ChIP

description: Histone ChIP


title: Transitional AT2->1 cells  -H3K4me1 ChIP

description: Histone ChIP


title: Differentiated AT1-like cells - H3K4me1 ChIP

description: Histone ChIP


title: Kinetin-treated FD fibroblasts 2

description:
SEMatrix_kin_on_fd.txt
2341_KIN-A-FD


title: ChIP Input AT2 cells

description: INPUT DNA


title: Differentiated AT1-like cells - FAIREseq

description: FAIRE


title: Differentiated AT1-like cells -H3K27Ac ChIP

description: Histone ChIP


title: Purified AT2 cells- FAIREseq

description: FAIRE


title: H522 control sample 3

status: Public on Mar 01 2019

description:
H522-CMV-NEO-3
RiboZero-depleted RNA

data_processing:
FASTQ reads were trimmed to remove bases 1-12 due to lack of sequence complexity.
Reads were filtered to remove those with quality scores of less than 30 for 90% of the read.
Reads were aligned to the hg38 genome and assembled into transcripts based on Gencode annotation. BigWig files provided for visualization are hg38-based.
Transcripts with less than 10 reads across the dataset were removed due to low expression levels.
EdgeR was used for differential expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig visualization files

source_name: stably transfected H522 lung adenocarcinoma cells

growth_protocol: Human H522 LUAD cell lines were grown in RPMI with 10% FBS and 1:1000 Penicillin/Streptomycin.

extract_protocol:
RNA was isolated using the BioRad Arum RNA purification kit.
RNA library preparation was performed at the USC Epigenome Center using the RiboZero depletion protocol.

treatment_protocol: Cells were transfected with CMV-LINC00261 and selected using Puromycin. Stables were derived from monoclonal outgrowths, and verified using qRT-PCR prior to sequencing.

tag: cell line

value: LUAD

tag: transfection

value: CMV-NEO


title: H522 with CMV-LINC00261 sample 3

description:
H522-CMV-LINC00261-3
RiboZero-depleted RNA


title: H522 with CMV-LINC00261 sample 1

description:
H522-CMV-LINC00261-1
RiboZero-depleted RNA


title: H522 control sample 2

description:
H522-CMV-NEO-2
RiboZero-depleted RNA


title: H2347

description: Ribo-depleted RNA

data_processing:
FASTQ reads were trimmed to remove bases 1-12 due to lack of sequence complexity
Reads were filtered to remove those with quality scores of less than 30 for 90% of the read
Reads were aligned to the lncipedia2.1 transcriptome for differential analysis. BigWig files provided for visualization are hg19-based
Table of counts were assembled for all transcripts for all samples
Transcripts with less than 10 reads across the dataset were removed due to low expression levels
Genome_build: hg19
Supplementary_files_format_and_content: Counts per transcript for lncRNA transcriptome

source_name: human lung adenocarcinoma cell lines

growth_protocol: Primary AEC were isolated and cultured as described previously (Marconett et al., PLoS genetics 2013). Human LUAD cell lines were grown in RPMI with 10% FBS and 1:1000 Penicylin/Streptomycin.

extract_protocol:
RNA was isolated using the Illustra GE Triple Prep kit.
RNA library preparation was performed at the USC Epigenome Center using the RiboZero depletion protocol
Paired end 50bp reads were multiplexed on the Illumina HiSeq2000

value: human lung adenocarcinoma (LUAD) cell lines

value: LUAD cell line H2347


title: H1975

description: Ribo-depleted RNA

value: LUAD cell line H1975


title: PC9

description: Ribo-depleted RNA

value: LUAD cell line PC9


title: 6247004027_R05C02


title: HCC827

description: Ribo-depleted RNA

value: LUAD cell line HCC827


title: H2228

description: Ribo-depleted RNA

value: LUAD cell line H2228


title: H292

description: Ribo-depleted RNA

value: LUAD cell line H292


title: H1792

description: Ribo-depleted RNA

value: LUAD cell line H1792


title: H1944

description: Ribo-depleted RNA

value: LUAD cell line H1944


title: H1648

description: Ribo-depleted RNA

value: LUAD cell line H1648


title: H1650

description: Ribo-depleted RNA

value: LUAD cell line H1650


title: Transitional AT2->1 cells  - FAIREseq

description: FAIRE


title: H3122

description: Ribo-depleted RNA

value: LUAD cell line H3122


title: H522

description: Ribo-depleted RNA

value: LUAD cell line H522


title: AEC Donor 2

description: Ribo-depleted RNA

source_name: purified primary human alveolar epithelial cells

value: primary human alveolar epithelial cells


title: H1395

description: Ribo-depleted RNA

value: LUAD cell line H1395


title: AEC Donor 1

description: Ribo-depleted RNA

value: purified primary human alveolar epithelial cells


title: H358

description: Ribo-depleted RNA

value: LUAD cell line H358


title: AEC Donor 3

description: Ribo-depleted RNA


title: PC3

description: Ribo-depleted RNA

value: human lung adenocarcinoma (LUAD) cell lines

value: LUAD cell line PC3


title: decidua_induced abortion_rep2

status: Public on Jul 12 2018

city: Nanjing

first: Mingming

last: Yu

address: NO.818 Tianyuan East Road, Jiangning District

department: School of public health

country: China

institute: Nanjing Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19  whole genome using tophat with default parameters
Fragments Per Kilobase Of Exon Per Million Fragments Mapped (FPKM) were calculated using a protocol from Cole Trapnell  et al., Nature Protocols volume 7, pages 562–578 (2012).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: decidua samples from induced abortion patients

extract_protocol:
RNA was extracted by RNeasy Kits (Qiagen, Hilden, NRW, Germany) and treated with DNase I (Thermo Fisher Scientific, Wilmington, DE, USA) according to standard protocols. RNA-sequencing was done in Genesky using TruSeq Stranded mRNA Library Preparation (Genesky, Shanghai, China). Briefly, intact RNA was fragmented, end repaired, adapter ligation and PCR amplified following illumina protocol. Libraries were sequencing by illumins Hiseq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: decidua

tag: Stage

value: Twelve weeks before pregnancy

tag: age

value: 24 years old


title: decidua_recurrent spontaneous abortion_rep3

source_name: decidua sample from recurrent spontaneous abortion patients


title: decidua_induced abortion_rep1


title: decidua_induced abortion_rep3

value: 25 years old


title: decidua_recurrent spontaneous abortion_rep1


title: decidua_recurrent spontaneous abortion_rep2

value: 23 years old


title: Donor 2- Input DNA that underwent reverse crosslinking from purified primary AT2 cells

status: Public on Feb 07 2018

description: sonicated DNA

data_processing:
AT2 Sequencing data collection: Sequencing data for this study included that which our group generated for primary AT2 alveolar epithelial cells from Donor 1 and Donor2, described below, as well as publicly available pre-processed A549 lung adenocarcinoma ChIP-Seq data from the UCSC Genome Browser website (https://genome.ucsc.edu).  Data we generated in-house from highly pure populations of primary AT2 cells included ChIP-seq and whole-genome bisulfite sequencing (WGBS). Libraries and FASTQ files were generated at the USC Epigenome Center.
AT2 Sequencing data filtering and alignment: For single-end ChIP-seq sequencing data: we started from raw FASTQ files and used cutadapt-1.5(Martin 2011) to filter reads with a quality score below 20. Remaining high-quality reads were aligned to the reference human genome, hg19 assembly, using bowtie2 (Langmead 2012). For paired-end WGB sequencing data (WGBS), we first used cutadapt-1.5 to trim low-quality sequencing reads. Remaining reads were aligned to hg19 using bwa-0.7.7 mem (Li and Durbin 2010) with default parameters. WGBS data were aligned with BSMAP V 2.5(Xi and Li 2009).
AT2 ChIP-seq Peak calling: SICER (Zang et al. 2009) was applied with default parameters to call peaks for histone H3K27Ac & H3K4me1 ChIP-Seq. Window size and gap size for H3K27ac and H3K4me1 ChIP-seq were set to 200bp (FDR cutoff = 1 x 10-3).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files contain the read density over the entire hg19-genome. Files have been binned into 30bp windows. BED files contain H3k4me1 and H3K27ac Peaks called in SICER (Zang et al. 2009).

source_name: donor lung

growth_protocol: Human AT1 and AT2 cells were isolated from two de-identified non-smoker remnant transplant lung as previously described and were used to obtain WGBS & histone mark ChIP data.

extract_protocol:
ChIP-seq on AT2 cells was performed as previously described(Marconett et al. 2013).
ChIP-Seq of AT2 cells from Donor 1 and Donor 2 in this Study. ChIP-seq of human AT2 cells from Donor1 and Donor2 in this study: Human AT2 cells underwent ChIP-seq using a modified version of the Sigma ChIP-it kit (Sigma). Specifically, 2 million human AT2 were used per ChIPseq of H3K27Ac (Cat # 39135, ActiveMotif), H3K4me1 (Cat # 39297, ActiveMotif). All cells were crosslinked with 3.75% formaldehyde at 25C for 5 minutes with gentle nutation. Fixation was quenched with 2.5mM glycine, then cells frozen at -80C until differentiation of all time points was complete. Each sample underwent nuclei fractionation using cell lysis buffer prepared per manufacturer’s recommendations. Upon nuclei isolation, cells were sonicated into fragments (average size 300bp) using a Bioruptor2000 (Diagenode) with 30-second pulses for a total of 30 minutes of sonication (15 on, 15 off). StaphSeq (Cat # S6576, Sigma) was used for antibody binding. All ChIPs were verified for enrichment by site-specific PCR prior to sequencing using the active region of PGDH for enhancer marks. All ChIP-seq samples underwent library preparation and sequencing at the USC Epigenomic Core. Samples were multiplexed using adapter barcoding and underwent single-end 50bp sequencing using the IlluminaHiSeq2000.
Whole genome bisulfite sequencing (WGBS) of AT2 cells from Donor 1 and Donor 2 in this Study. Total DNA from 8x10^6 Donor 1 and Donor 2 AT2 cells in this study was isolated using the Illustra Triple Prep kit (GE LifeSciences, Piscataway NJ). Four μg of sample genomic DNA was sonicated using a Covaris S2 to an average molecular weight of 150 bp.   Achievement of the desired size range was verified by Bioanalyzer (Agilent) analysis. Fragmented DNA was repaired to generate blunt ends using the END-It kit (Epicentre Biotechnologies, Madison, WI) according to manufacturer’s instructions.  Following incubation, the treated DNA was purified using AmpureX beads from Agencourt.  In general, magnetic beads were employed for all nucleic acid purifications in the following protocol.  Following end repair, A-tailing was performed using the NEB dA-tailing module according to manufacturer’s instructions (New England Biolabs, Ipswich, MA). Adapters with a 3’ ‘T’ overhang were then ligated to the end-modified DNA.  For whole genome bisulfite sequencing, modified Illumina paired-end (PE) adapters were used in which cytosine bases in the adapter are replaced with 5-methylcytosine bases. Ligation was carried out using ultrapure, rapid T4 ligase (Enzymatics, Beverly, MA) according to manufacturer’s instructions.  The final product was then purified with magnetic beads to yield an adapter-ligation mix. Prior to bisulfite conversion, bacteriophage lambda DNA that had been through the same library preparation protocol described above to generate adapter-ligation mixes was combined with the genomic sample adapter ligation mix at 0.5% w/w.  Adapter-ligation mixes were then bisulfite converted using the Zymo DNA Methylation Gold kit (Zymo Research, Orange, CA) according to the manufacturer’s recommendations. Final modified product was purified by magnetic beads and eluted in a final volume of 20 ul. Amplification of one-half the adapter-ligated library was performed using Kapa HiFi-U Ready Mix for the following protocol: 98° 2’, Then six cycles of: 98° 30”, 65° 15”, 72° 60”, with a final 72° 10’ extension, in a 50 ul total volume reaction. Final library product was examined on the Agilent Bioanalyzer, then quantified using the Kapa Biosystems Library Quantification kit according to manufacturer’s instructions.   Optimal concentrations to get the right cluster density were determined empirically but tended to be higher than for non-bisulfite libraries.  Libraries were plated using the Illumina cBot and run on the Hi-Seq 2000 according to manufacturer’s instructions using HSCS v 1.5.15.1. Donor 1 samples underwent Paired End 100 cycling; Donor 2 and 3 samples underwent Paired End 75 cycling. Image analysis and basecalling were carried out using RTA 1.13.48.0, deconvolution and fastq file generation were carried out using CASAVA_v1.7.1a5. Alignment to the genome was carried out using bsmap V 2.5.
Libraries were prepared at the USC Epigenome Core as previously  described (Marconett, 2013).

value: purified primary alveolar epithelial type 2 cells


title: Donor 1- ChIPseq of H3K27Ac in purified primary AT2 cells

description: sonicated and immunoprecipitated DNA


title: Donor 1- Input DNA that underwent reverse crosslinking from purified primary AT2 cells

description: sonicated DNA


title: Donor2-WGBS library from purified primary AT2 cells

description: Bisulfite-converted DNA


title: PFC_α-Gal-A(-/0)_3

status: Public on Jul 01 2018

city: Innsbruck

first: Kai

last: Kummer

address: Schoepfstrasse 41/Eg

department: Institute of Physiology

country: Austria

institute: Medical University of Innsbruck

hyb_protocol: Following cRNA clean-up and quantification, Cyanine-3-labeled cRNA samples were fragmented and prepared for one-color-based hybridization (Gene Expression Hybridization Kit, Agilent Technologies) and hybridized at 65°C for 17 hours on Agilent SurePrint G3 Mouse GE 8x60K Microarrays. After hybridization, microarrays were washed with increasing stringency using Triton X-102 supplemented Gene Expression Wash Buffers (Agilent Technologies) followed by drying with acetonitrile (Sigma).

scan_protocol: Fluorescence signals were detected on an Agilent DNA Microarrays Scanner and extracted using feature extraction software (Agilent Technologies).

data_processing: The software tools Feature Extraction 10.7.3.1. and GeneSpring GX 13.0 were used for quality control, statistical data analysis, filtering of differentially expressed transcripts, transcript annotation and visualization.

source_name: PFC

label_protocol: For mRNA analysis, total RNA samples were spiked with in vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix, Agilent Technologies), reverse transcribed into cDNA and then converted into Cyanine-3 labeled complementary RNA (Low Input Quick-Amp Labeling Kit One-Color, Agilent Technologies) according to the manufacturer’s instructions. cRNA concentration, RNA absorbance ratio and Cyanine-3 dye concentration were recorded using a NanoDrop ND-1000 UV-VIS spectral photometer, and quality of labeled cRNA was analyzed using the RNA 6000 Nano LabChip Kit (Agilent Technologies) on a 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNA including small RNAs was isolated using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions and eluted in 40 µl RNase-free water. RNA concentration and purity was determined on a NanoDrop ND-1000 spectral photometer (Peqlab). Samples were analyzed using the RNA 6000 Nano LabChip Kit (Agilent Technologies) on a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Four adult mice per group were deeply anesthetized with isoflurane and euthanized by decapitation. Brains were removed, PFCs harvested and flash-frozen in liquid nitrogen. Sample were kept at -80°C until further processing for mRNA expression profiling.

tag: genotype

tag: strain

value: PFC

tag: Sex

value: male

value: 20-24 weeks


title: Donor 2- ChIPseq of H3K27Ac in purified primary AT2 cells

description: sonicated and immunoprecipitated DNA


title: PFC_α-Gal-A(-/0)_2


title: PFC_C57BL/6J_2

value: wildtype


title: Donor 2- ChIPseq of H3K4me1 in purified primary AT2 cells

description: sonicated and immunoprecipitated DNA


title: H23

description: Ribo-depleted RNA

value: LUAD cell line H23


title: PFC_α-Gal-A(-/0)_4


title: A549 RNAseq: 20uM Cigarette smoke condensate (CSC) treated for 2 weeks Replicate 3

data_processing:
Image analysis and basecalling were carried out using RTA 1.13.48.0, deconvolution and fastq file generation were carried out using CASAVA_v1.7.1a5.
RNAseq fastq files were aligned to the hg19  genome using tophat2-2.0.9.
Genome_build: hg19
Supplementary_files_format_and_content: Tophat FPKM values

extract_protocol:
RNA was isolated from treated A549 cells using the Illustra TriplePrep Kit from GE.
RNA was isolated from treated A549 cells grown on 15cm plates using the GE TriplePrep kit (Cat# 28-9425-44, Pittsburgh PA). 2ug of RNA was made into libraries using the Illumina (Madison WI) Ribo-Zero™ Gold Magnetic Kit (MRZG 12324) and sequenced using the Illumina HiSeq2000 at the University of Southern California Epigenome Center Core. Basecalls were converted into FASTQ files and aligned to the hg19 genome using tophat2-2.0.9 through Illumina Basespace.
2ug of RNA was made into libraries using the Illumina (Madison WI) Ribo-Zero™ Gold Magnetic Kit (MRZG 12324)

value: A549 Lung Adenocarcinoma cells

tag: stress

value: Cigarette smoke condensate (CSC)

tag: time

value: 2 weeks


title: Donor1-WGBS library from purified primary AT2 cells

description: Bisulfite-converted DNA


title: PFC_C57BL/6J_4

tag: tissue


title: PFC_C57BL/6J_3


title: PFC_α-Gal-A(-/0)_1


title: PFC_C57BL/6J_1


title: A549 RNAseq: 20uM Cigarette smoke condensate (CSC) treated for 2 weeks Replicate 2


title: A549 RNAseq: DMSO vehicle treated for 2 weeks Replicate 2

source_name: DMSO vehicle treated for 2 weeks

value: DMSO


title: A549 RNAseq: DMSO vehicle treated for 2 weeks Replicate 1


title: A549 RNAseq: 20uM Cigarette smoke condensate (CSC) treated for 48 Hours Replicate 2

value: 48 hours


title: A549 RNAseq: 20uM Cigarette smoke condensate (CSC) treated for 48 Hours Replicate 3


title: A549 RNAseq: DMSO vehicle treated for 48 Hours Replicate 3

source_name: DMSO vehicle treated for 48 Hours


title: Donor 1- ChIPseq of H3K4me1 in purified primary AT2 cells

description: sonicated and immunoprecipitated DNA

tag: cell type


title: A549 RNAseq: DMSO vehicle treated for 48 Hours Replicate 2


title: A549 RNAseq: 20uM Cigarette smoke condensate (CSC) treated for 2 weeks Replicate 1


title: A549 RNAseq: 20uM Cigarette smoke condensate (CSC) treated for 48 Hours Replicate 1


title: A549 RNAseq: DMSO vehicle treated for 2 weeks Replicate 3


title: MB_SubtypeStudy_55738_methylation

status: Public on Jun 13 2017

city: Toronto

first: Florence

middle: M G

last: Cavalli

state: Ontario

address: PGCRL, 686 Bay Street

department: Developmental and Stem Cell

country: Canada

institute: The Hospital for Sick Children

hyb_protocol: Standard Illumina Protocol

scan_protocol: Samples were processed as per manufacturer’s instructions. Raw data files (.idat) generated by the Illumina iScan array scanner

data_processing: Raw data was processed in R using the minfi (v1.6.0) and IlluminaHumanMethylation450kmanifest (v0.4.0) R Bioconductor packages. We checked all samples for unexpected genotype matches by pairwise correlation of the 65 genotyping probes on the 450k arrays, allowing us to remove remaining duplicates. We ran the detectionP function from the minfi package to identify probes and samples with low quality. Samples were removed if more than 1% of their probes had a p-value above 0.01 and probes were removed if their p-value was above 0.01 in at least 5% of samples.  We removed probes on sex chromosomes as well as those located on or close to known single nucleotide polymorphisms (SNP). We retained a total of 321,174 probes for the analysis. The data was normalized using the SWAN method (Makismovic et al., Genome Biology 2012) as implemented in the minfi package.  The matrix of normalized beta values is available on the series record.

label: Cy3 and Cy5

source_name: Fresh frozen

label_protocol: Standard Illumina Protocol

extract_protocol: Snap frozen tissue was digested overnight at 55 C with Proteinase K and SDS in TE. DNA was extracted from the digest with phenol-chloroform and precipitated with ammonium acetate and ethanol. The pellet was resuspended in TE buffer. Bisulfite conversion was carried out according to the manufacturer's instructions for the Zymo EZ DNA Methylation Kit

value: medulloblastoma

tag: type

value: primary tumor

value: SHH


title: MB_SubtypeStudy_55752_methylation

tag: subgroup


title: MB_SubtypeStudy_55741_methylation


title: MB_SubtypeStudy_55723_methylation


title: DRG_L3-L5_α-Gal-A(-/0)_4

status: Public on Jan 01 2018

source_name: DRG L3-L5

treatment_protocol: Eight adult mice per group were deeply anesthetized with isoflurane and euthanized by decapitation. Spinal cords were removed, lumbar DRGs L3-L5 harvested and flash-frozen in liquid nitrogen. The DRG tissue from two mice was pooled for the final tissue sample. Sample were kept at -80°C until further processing for mRNA expression profiling.

value: alpha-Gal A(-/0)

value: DRG L3-L5


title: MB_SubtypeStudy_55719_methylation


title: MB_SubtypeStudy_55711_methylation


title: DRG_L3-L5_C57BL/6J_4


title: DRG_L3-L5_C57BL/6J_2


title: DRG_L3-L5_α-Gal-A(-/0)_3


title: DRG_L3-L5_α-Gal-A(-/0)_2


title: MB_SubtypeStudy_55712_methylation


title: DRG_L3-L5_C57BL/6J_3


title: MB_SubtypeStudy_55709_methylation


title: MB_SubtypeStudy_55732_methylation


title: DRG_L3-L5_α-Gal-A(-/0)_1


title: MB_SubtypeStudy_55692_methylation


title: MB_SubtypeStudy_55686_methylation


title: MB_SubtypeStudy_55696_methylation


title: MB_SubtypeStudy_55704_methylation


title: MB_SubtypeStudy_55652_methylation


title: MB_SubtypeStudy_55659_methylation


title: MB_SubtypeStudy_55658_methylation


title: MB_SubtypeStudy_55690_methylation


title: MB_SubtypeStudy_55655_methylation


title: MB_SubtypeStudy_55650_methylation


title: MB_SubtypeStudy_55649_methylation


title: MB_SubtypeStudy_55749_methylation


title: MB_SubtypeStudy_55747_methylation


title: MB_SubtypeStudy_55645_methylation


title: MB_SubtypeStudy_55632_methylation


title: DRG_L3-L5_C57BL/6J_1


title: MB_SubtypeStudy_55589_methylation


title: MB_SubtypeStudy_55608_methylation


title: MB_SubtypeStudy_55634_methylation


title: MB_SubtypeStudy_55615_methylation


title: MB_SubtypeStudy_55580_methylation


title: MB_SubtypeStudy_55605_methylation


title: MB_SubtypeStudy_55623_methylation


title: MB_SubtypeStudy_55591_methylation


title: MB_SubtypeStudy_55606_methylation


title: MB_SubtypeStudy_55582_methylation


title: MB_SubtypeStudy_55587_methylation


title: MB_SubtypeStudy_55593_methylation


title: MB_SubtypeStudy_55554_methylation


title: MB_SubtypeStudy_55567_methylation


title: MB_SubtypeStudy_55572_methylation


title: MB_SubtypeStudy_55579_methylation


title: MB_SubtypeStudy_55574_methylation


title: MB_SubtypeStudy_55560_methylation


title: MB_SubtypeStudy_55612_methylation


title: MB_SubtypeStudy_55549_methylation


title: MB_SubtypeStudy_55564_methylation


title: MB_SubtypeStudy_55550_methylation


title: MB_SubtypeStudy_55558_methylation


title: MB_SubtypeStudy_55556_methylation


title: MB_SubtypeStudy_55551_methylation


title: MB_SubtypeStudy_55537_methylation


title: MB_SubtypeStudy_55547_methylation


title: MB_SubtypeStudy_55590_methylation


title: MB_SubtypeStudy_55642_methylation


title: MB_SubtypeStudy_55526_methylation


title: MB_SubtypeStudy_55532_methylation


title: MB_SubtypeStudy_55520_methylation


title: MB_SubtypeStudy_55529_methylation


title: MB_SubtypeStudy_55534_methylation


title: MB_SubtypeStudy_55477_methylation


title: MB_SubtypeStudy_55480_methylation


title: MB_SubtypeStudy_55462_methylation


title: MB_SubtypeStudy_55525_methylation


title: MB_SubtypeStudy_55469_methylation


title: MB_SubtypeStudy_55444_methylation


title: MB_SubtypeStudy_55523_methylation


title: MB_SubtypeStudy_55443_methylation


title: MB_SubtypeStudy_55500_methylation


title: MB_SubtypeStudy_55501_methylation


title: MB_SubtypeStudy_55488_methylation


title: MB_SubtypeStudy_55497_methylation


title: MB_SubtypeStudy_55437_methylation


title: MB_SubtypeStudy_55472_methylation


title: MB_SubtypeStudy_55430_methylation


title: MB_SubtypeStudy_55429_methylation


title: MB_SubtypeStudy_55493_methylation


title: MB_SubtypeStudy_55489_methylation


title: MB_SubtypeStudy_55418_methylation


title: MB_SubtypeStudy_55432_methylation


title: MB_SubtypeStudy_55394_methylation


title: MB_SubtypeStudy_55486_methylation


title: MB_SubtypeStudy_55395_methylation


title: MB_SubtypeStudy_55512_methylation


title: MB_SubtypeStudy_55436_methylation

value: WNT


title: MB_SubtypeStudy_55387_methylation


title: MB_SubtypeStudy_55427_methylation


title: MB_SubtypeStudy_55415_methylation


title: MB_SubtypeStudy_55416_methylation


title: MB_SubtypeStudy_55406_methylation


title: MB_SubtypeStudy_55375_methylation


title: MB_SubtypeStudy_55366_methylation


title: MB_SubtypeStudy_55412_methylation


title: MB_SubtypeStudy_55351_methylation


title: MB_SubtypeStudy_55407_methylation


title: MB_SubtypeStudy_55402_methylation


title: MB_SubtypeStudy_55318_methylation


title: MB_SubtypeStudy_55374_methylation


title: MB_SubtypeStudy_55316_methylation


title: MB_SubtypeStudy_55335_methylation


title: MB_SubtypeStudy_55371_methylation


title: MB_SubtypeStudy_55314_methylation


title: MB_SubtypeStudy_55286_methylation


title: MB_SubtypeStudy_55401_methylation


title: MB_SubtypeStudy_55306_methylation


title: MB_SubtypeStudy_55361_methylation


title: MB_SubtypeStudy_55349_methylation


title: MB_SubtypeStudy_55270_methylation


title: MB_SubtypeStudy_55259_methylation


title: MB_SubtypeStudy_55315_methylation


title: MB_SubtypeStudy_55326_methylation


title: MB_SubtypeStudy_55265_methylation


title: MB_SubtypeStudy_55276_methylation


title: MB_SubtypeStudy_55295_methylation


title: MB_SubtypeStudy_55397_methylation


title: MB_SubtypeStudy_55329_methylation


title: MB_SubtypeStudy_55243_methylation


title: MB_SubtypeStudy_55239_methylation


title: MB_SubtypeStudy_55231_methylation


title: MB_SubtypeStudy_55287_methylation


title: MB_SubtypeStudy_55230_methylation


title: MB_SubtypeStudy_55209_methylation


title: MB_SubtypeStudy_55211_methylation


title: MB_SubtypeStudy_55275_methylation


title: MB_SubtypeStudy_55208_methylation


title: MB_SubtypeStudy_55278_methylation


title: MB_SubtypeStudy_55280_methylation


title: MB_SubtypeStudy_55254_methylation


title: MB_SubtypeStudy_55228_methylation


title: MB_SubtypeStudy_55219_methylation


title: MB_SubtypeStudy_55216_methylation


title: MB_SubtypeStudy_55220_methylation


title: MB_SubtypeStudy_55191_methylation


title: MB_SubtypeStudy_55152_methylation


title: MB_SubtypeStudy_55155_methylation


title: MB_SubtypeStudy_55164_methylation


title: MB_SubtypeStudy_55242_methylation


title: MB_SubtypeStudy_55223_methylation


title: MB_SubtypeStudy_55101_methylation


title: MB_SubtypeStudy_55198_methylation


title: MB_SubtypeStudy_55206_methylation


title: MB_SubtypeStudy_55241_methylation


title: MB_SubtypeStudy_55192_methylation


title: MB_SubtypeStudy_55070_methylation


title: MB_SubtypeStudy_55119_methylation


title: MB_SubtypeStudy_55066_methylation


title: MB_SubtypeStudy_55063_methylation


title: MB_SubtypeStudy_55193_methylation


title: MB_SubtypeStudy_55060_methylation


title: MB_SubtypeStudy_55118_methylation


title: MB_SubtypeStudy_55049_methylation


title: MB_SubtypeStudy_55075_methylation


title: MB_SubtypeStudy_55036_methylation


title: MB_SubtypeStudy_55098_methylation


title: MB_SubtypeStudy_55031_methylation


title: MB_SubtypeStudy_55097_methylation


title: MB_SubtypeStudy_55033_methylation


title: MB_SubtypeStudy_55091_methylation


title: MB_SubtypeStudy_55057_methylation


title: MB_SubtypeStudy_55067_methylation


title: MB_SubtypeStudy_55028_methylation


title: MB_SubtypeStudy_55088_methylation


title: MB_SubtypeStudy_55064_methylation


title: MB_SubtypeStudy_55055_methylation


title: MB_SubtypeStudy_55018_methylation


title: MB_SubtypeStudy_55056_methylation


title: MB_SubtypeStudy_55020_methylation


title: MB_SubtypeStudy_55029_methylation


title: MB_SubtypeStudy_55012_methylation


title: MB_SubtypeStudy_55014_methylation


title: MB_SubtypeStudy_55017_methylation


title: MB_SubtypeStudy_55009_methylation


title: MB_SubtypeStudy_55001_methylation


title: MB_SubtypeStudy_55010_methylation


title: MB_SubtypeStudy_55006_methylation


title: MB_SubtypeStudy_55002_methylation


title: MB_SubtypeStudy_55027_methylation


title: genomic DNA from medulloblastoma_NMB905

status: Public on May 29 2017

description: medulloblastoma 392

hyb_protocol: According to the manufacturer’s instructions

scan_protocol: Illumina iScan System, according to the manufacturer’s instructions

data_processing: Arrays were processed using the R package minfi. Beta values were reported after functional normalisation. Intensity values were calculated without background subtraction and normalized to internal controls.

source_name: genomic DNA from medulloblastoma

extract_protocol: Extraction of DNA from tumor samples was carried out using Qiagen Allprep DNA/RNA/Protein Mini kit (Fresh Frozen) and Qiagen QIAamp DNA FFPE Tissue Kit (FFPE)

tag: sample type

tag: disease state

value: primary medulloblastoma

tag: gender

value: M

tag: age (yrs)

tag: pathology

value: CLA


title: genomic DNA from medulloblastoma_NMB92

description: medulloblastoma 396

label_protocol: According to the manufacturer’s instructions


title: genomic DNA from medulloblastoma_NMB89

description: medulloblastoma 384

value: F


title: genomic DNA from medulloblastoma_NMB868

description: medulloblastoma 377


title: genomic DNA from medulloblastoma_NMB910

description: medulloblastoma 395


title: H2009_FOSL1 sh1 2

status: Public on Jun 12 2017

description:
Gene expression data from FOSL1 depleted H2009 cells
H2009_Fosl1_sh3_2

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix HuGene-2_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: Affymetrix HuGene-2_0-st chip with bioconductor cdf (hugene20stv1cdf); The data were normalized with Bioconductor software using RMA algorithm.

source_name: H2009_FOSL1 shRNA

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: Cells were grown in RPMI164 medium supplemented with 10% FBS and 1% antibiotics

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: H2009 cells were infected with lentivirus carrying a FOSL1 or a control (GFP) shRNA for 2 days. Then, cells were selected for 3 days using 5ug/ml puromycin. After that, cells were counted and plated at a density of 600,000 cells/well (6-well plate) for 24h.

tag: cell line

value: mutant KRAS lung adenocarcinoma cells

tag: infected with

value: lentivirus carrying a FOSL1 shRNA


title: genomic DNA from medulloblastoma_NMB816

description: medulloblastoma 366


title: genomic DNA from medulloblastoma_NMB892

description: medulloblastoma 387

value: LCA


title: genomic DNA from medulloblastoma_NMB873

description: medulloblastoma 381

value: NOS


title: genomic DNA from medulloblastoma_NMB899

description: medulloblastoma 391


title: genomic DNA from medulloblastoma_NMB812

description: medulloblastoma 365


title: H2009_FOSL1 sh1 1

description:
Gene expression data from FOSL1 depleted H2009 cells
H2009_Fosl1_sh3_32


title: genomic DNA from medulloblastoma_NMB798

description: medulloblastoma 352

value: DN


title: genomic DNA from medulloblastoma_NMB805

description: medulloblastoma 359


title: genomic DNA from medulloblastoma_NMB766

description: medulloblastoma 329


title: genomic DNA from medulloblastoma_NMB803

description: medulloblastoma 357


title: genomic DNA from medulloblastoma_NMB769

description: medulloblastoma 332


title: genomic DNA from medulloblastoma_NMB799

description: medulloblastoma 353


title: genomic DNA from medulloblastoma_NMB756

description: medulloblastoma 319


title: genomic DNA from medulloblastoma_NMB804

description: medulloblastoma 358


title: genomic DNA from medulloblastoma_NMB760

description: medulloblastoma 323


title: H2009_Control sh 2

description:
Gene expression data from H2009 cells
H2009_GFP2

source_name: H2009_GFP shRNA

value: lentivirus carrying a GFP shRNA


title: genomic DNA from medulloblastoma_NMB762

description: medulloblastoma 325


title: genomic DNA from medulloblastoma_NMB783

description: medulloblastoma 341


title: genomic DNA from medulloblastoma_NMB807

description: medulloblastoma 361


title: genomic DNA from medulloblastoma_NMB741

description: medulloblastoma 310


title: H2009_Control sh 3

description:
Gene expression data from H2009 cells
H2009_GFP3


title: genomic DNA from medulloblastoma_NMB754

description: medulloblastoma 317


title: genomic DNA from medulloblastoma_NMB742

description: medulloblastoma 311


title: genomic DNA from medulloblastoma_NMB79

description: medulloblastoma 346


title: genomic DNA from medulloblastoma_NMB734

description: medulloblastoma 303


title: genomic DNA from medulloblastoma_NMB712

description: medulloblastoma 286


title: genomic DNA from medulloblastoma_NMB716

description: medulloblastoma 289


title: genomic DNA from medulloblastoma_NMB717

description: medulloblastoma 290


title: genomic DNA from medulloblastoma_NMB723

description: medulloblastoma 294


title: genomic DNA from medulloblastoma_NMB715

description: medulloblastoma 288


title: H2009_Control sh 1

description:
Gene expression data from H2009 cells
H2009_GFP1


title: genomic DNA from medulloblastoma_NMB726

description: medulloblastoma 297


title: H2009_FOSL1 sh1 3

description:
Gene expression data from FOSL1 depleted H2009 cells
H2009_Fosl1_sh3_3


title: genomic DNA from medulloblastoma_NMB675

description: medulloblastoma 273


title: genomic DNA from medulloblastoma_NMB690

description: medulloblastoma 279


title: genomic DNA from medulloblastoma_NMB676

description: medulloblastoma 274


title: genomic DNA from medulloblastoma_NMB70

description: medulloblastoma 280


title: genomic DNA from medulloblastoma_NMB684

description: medulloblastoma 277


title: genomic DNA from medulloblastoma_NMB673

description: medulloblastoma 271


title: genomic DNA from medulloblastoma_NMB679

description: medulloblastoma 275


title: genomic DNA from medulloblastoma_NMB671

description: medulloblastoma 270


title: genomic DNA from medulloblastoma_NMB648

description: medulloblastoma 261


title: genomic DNA from medulloblastoma_NMB658

description: medulloblastoma 264


title: genomic DNA from medulloblastoma_NMB669

description: medulloblastoma 268


title: genomic DNA from medulloblastoma_NMB633

description: medulloblastoma 255


title: genomic DNA from medulloblastoma_NMB626

description: medulloblastoma 250


title: genomic DNA from medulloblastoma_NMB666

description: medulloblastoma 266


title: genomic DNA from medulloblastoma_NMB670

description: medulloblastoma 269


title: genomic DNA from medulloblastoma_NMB612

description: medulloblastoma 240


title: genomic DNA from medulloblastoma_NMB617

description: medulloblastoma 243


title: genomic DNA from medulloblastoma_NMB608

description: medulloblastoma 237

value: MBEN


title: genomic DNA from medulloblastoma_NMB632

description: medulloblastoma 254

value: medulloblastoma


title: genomic DNA from medulloblastoma_NMB637

description: medulloblastoma 257


title: genomic DNA from medulloblastoma_NMB609

description: medulloblastoma 238


title: genomic DNA from medulloblastoma_NMB554

description: medulloblastoma 220


title: genomic DNA from medulloblastoma_NMB618

description: medulloblastoma 244


title: genomic DNA from medulloblastoma_NMB615

description: medulloblastoma 242


title: genomic DNA from medulloblastoma_NMB651

description: medulloblastoma 263


title: genomic DNA from medulloblastoma_NMB569

description: medulloblastoma 224


title: genomic DNA from medulloblastoma_NMB674

description: medulloblastoma 272


title: genomic DNA from medulloblastoma_NMB553

description: medulloblastoma 219


title: genomic DNA from medulloblastoma_NMB531

description: medulloblastoma 208


title: genomic DNA from medulloblastoma_NMB535

description: medulloblastoma 211


title: genomic DNA from medulloblastoma_NMB491

description: medulloblastoma 193


title: genomic DNA from medulloblastoma_NMB537

description: medulloblastoma 213


title: genomic DNA from medulloblastoma_NMB493

description: medulloblastoma 194


title: genomic DNA from medulloblastoma_NMB497

description: medulloblastoma 197


title: genomic DNA from medulloblastoma_NMB489

description: medulloblastoma 190


title: genomic DNA from medulloblastoma_NMB498

description: medulloblastoma 198


title: genomic DNA from medulloblastoma_NMB479

description: medulloblastoma 184


title: genomic DNA from medulloblastoma_NMB476

description: medulloblastoma 182


title: genomic DNA from medulloblastoma_NMB495

description: medulloblastoma 195


title: genomic DNA from medulloblastoma_NMB490

description: medulloblastoma 192


title: genomic DNA from medulloblastoma_NMB483

description: medulloblastoma 186


title: genomic DNA from medulloblastoma_NMB477

description: medulloblastoma 183


title: genomic DNA from medulloblastoma_NMB474

description: medulloblastoma 181


title: genomic DNA from medulloblastoma_NMB466

description: medulloblastoma 179


title: genomic DNA from medulloblastoma_NMB519

description: medulloblastoma 203


title: genomic DNA from medulloblastoma_NMB484

description: medulloblastoma 187


title: genomic DNA from medulloblastoma_NMB499

description: medulloblastoma 199


title: genomic DNA from medulloblastoma_NMB457

description: medulloblastoma 173


title: genomic DNA from medulloblastoma_NMB486

description: medulloblastoma 189


title: genomic DNA from medulloblastoma_NMB485

description: medulloblastoma 188


title: genomic DNA from medulloblastoma_NMB439

description: medulloblastoma 167


title: genomic DNA from medulloblastoma_NMB471

description: medulloblastoma 180


title: genomic DNA from medulloblastoma_NMB436

description: medulloblastoma 164


title: genomic DNA from medulloblastoma_NMB422

description: medulloblastoma 160


title: genomic DNA from medulloblastoma_NMB386

description: medulloblastoma 135


title: genomic DNA from medulloblastoma_NMB460

description: medulloblastoma 175


title: genomic DNA from medulloblastoma_NMB459

description: medulloblastoma 174


title: genomic DNA from medulloblastoma_NMB496

description: medulloblastoma 196


title: genomic DNA from medulloblastoma_NMB456

description: medulloblastoma 172


title: genomic DNA from medulloblastoma_NMB381

description: medulloblastoma 130


title: genomic DNA from medulloblastoma_NMB416

description: medulloblastoma 154


title: genomic DNA from medulloblastoma_NMB441

description: medulloblastoma 169


title: genomic DNA from medulloblastoma_NMB379

description: medulloblastoma 128


title: genomic DNA from medulloblastoma_NMB371

description: medulloblastoma 121


title: genomic DNA from medulloblastoma_NMB375

description: medulloblastoma 124


title: genomic DNA from medulloblastoma_NMB365

description: medulloblastoma 115


title: genomic DNA from medulloblastoma_NMB374

description: medulloblastoma 123


title: genomic DNA from medulloblastoma_NMB363

description: medulloblastoma 113


title: genomic DNA from medulloblastoma_NMB361

description: medulloblastoma 111


title: genomic DNA from medulloblastoma_NMB420

description: medulloblastoma 158


title: genomic DNA from medulloblastoma_NMB443

description: medulloblastoma 170


title: genomic DNA from medulloblastoma_NMB465

description: medulloblastoma 178


title: genomic DNA from medulloblastoma_NMB357

description: medulloblastoma 107


title: genomic DNA from medulloblastoma_NMB345

description: medulloblastoma 104


title: genomic DNA from medulloblastoma_NMB335

description: medulloblastoma 101


title: genomic DNA from medulloblastoma_NMB384

description: medulloblastoma 133


title: genomic DNA from medulloblastoma_NMB331

description: medulloblastoma 99


title: genomic DNA from medulloblastoma_NMB341

description: medulloblastoma 102


title: genomic DNA from medulloblastoma_NMB320

description: medulloblastoma 91


title: genomic DNA from medulloblastoma_NMB326

description: medulloblastoma 94


title: genomic DNA from medulloblastoma_NMB272

description: medulloblastoma 78


title: genomic DNA from medulloblastoma_NMB251

description: medulloblastoma 66


title: genomic DNA from medulloblastoma_NMB254

description: medulloblastoma 69


title: genomic DNA from medulloblastoma_NMB250

description: medulloblastoma 65


title: genomic DNA from medulloblastoma_NMB153

description: medulloblastoma 33


title: genomic DNA from medulloblastoma_NMB187

description: medulloblastoma 55


title: genomic DNA from medulloblastoma_NMB148

description: medulloblastoma 29


title: AT2 WGBS Donor 2 -Run2

status: Public on Nov 06 2016

description: Bisulfite-treated DNA

data_processing:
Image analysis and basecalling were carried out using RTA 1.13.48.0, deconvolution and fastq file generation were carried out using CASAVA_v1.7.1a5.
WGBS fastq files were aligned to the hg19 BS genome using BSmap2.0. ChIPseq Fastq files were aligned to the genome using BWA0.6.2.
ChIPseq data underwent .bam to .bed format conversion and peaks were called using the SICER peakcalling program.
Genome_build: hg19
Supplementary_files_format_and_content: .fastq files are raw sequence, .bw files are wiggle tracks designed to display the enrichment of ChIPseq regions, .txt peak calling files are the locations of called peaks.

source_name: Whole genome bisulfite sequencing

extract_protocol:
DNA was isolated from freshly isolated primary AT2 cells using the Illustra TriplePrep Kit.
WGBS libraries were made by the USC Epigenome Center. 4 μg of sample genomic DNA was sonicated using a Covaris S2 to an average molecular weight of 150 bp.   Achievement of the desired size range was verified by Bioanalyzer (Agilent) analysis. Fragmented DNA was repaired to generate blunt ends using the END-It kit (Epicentre Biotechnologies, Madison, WI) according to manufacturer’s instructions.  Following incubation, the treated DNA was purified using AmpureX beads from Agencourt.  In general, magnetic beads were employed for all nucleic acid purifications in the following protocol.  Following end repair, A-tailing was performed using the NEB dA-tailing module according to manufacturer’s instructions (New England Biolabs, Ipswich, MA). Adapters with a 3’ ‘T’ overhang were then ligated to the end-modified DNA.  For whole genome bisulfite sequencing, modified Illumina paired-end (PE) adapters were used in which cytosine bases in the adapter are replaced with 5-methylcytosine bases. Ligation was carried out using ultrapure, rapid T4 ligase (Enzymatics, Beverly, MA) according to manufacturer’s instructions.  The final product was then purified with magnetic beads to yield an adapter-ligation mix. Prior to bisulfite conversion, bacteriophage lambda DNA that had been through the same library preparation protocol described above to generate adapter-ligation mixes was combined with the genomic sample adapter ligation mix at 0.5% w/w.  Adapter-ligation mixes were then bisulfite converted using the Zymo DNA Methylation Gold kit (Zymo Research, Orange, CA) according to the manufacturer’s recommendations. Final modified product was purified by magnetic beads and eluted in a final volume of 20 ul. Amplification of one-half the adapter-ligated library was performed using Kapa HiFi-U Ready Mix for the following protocol: 98° 2’, Then six cycles of: 98° 30”, 65° 15”, 72° 60”, with a final 72° 10’ extension, in a 50 ul total volume reaction. Final library product was examined on the Agilent Bioanalyzer, then quantified using the Kapa Biosystems Library Quantification kit according to manufacturer’s instructions.   Optimal concentrations to get the right cluster density were determined empirically but tended to be higher than for non-bisulfite libraries.  Libraries were plated using the Illumina cBot and run on the Hi-Seq 2000 according to manufacturer’s instructions using HSCS v 1.5.15.1. Rep 1 underwent Paired End 100 cycling; rep 2 underwent Paired End 75 cycling.

value: purified AT2 cells

tag: individual

value: Donor 2


title: genomic DNA from medulloblastoma_NMB143

description: medulloblastoma 25


title: AT2 WGBS Donor 2 -Run1

description: Bisulfite-treated DNA


title: genomic DNA from medulloblastoma_NMB376

description: medulloblastoma 125


title: genomic DNA from medulloblastoma_NMB333

description: medulloblastoma 100


title: AT2 WGBS Donor 1

description: Bisulfite-treated DNA

value: Donor 1


title: genomic DNA from medulloblastoma_NMB152

description: medulloblastoma 32


title: genomic DNA from medulloblastoma_NMB17

description: medulloblastoma 39


title: genomic DNA from medulloblastoma_NMB178

description: medulloblastoma 46


title: genomic DNA from medulloblastoma_NMB128

description: medulloblastoma 13


title: genomic DNA from medulloblastoma_NMB138

description: medulloblastoma 20


title: genomic DNA from medulloblastoma_NMB378

description: medulloblastoma 127


title: genomic DNA from medulloblastoma_NMB32

description: medulloblastoma 90


title: genomic DNA from medulloblastoma_NMB364

description: medulloblastoma 114


title: genomic DNA from medulloblastoma_NMB179

description: medulloblastoma 47


title: genomic DNA from medulloblastoma_NMB330

description: medulloblastoma 98