title: Esophageal squamous carcinoma UROC84Nsp

description:
UROC84Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC84


title: Esophageal squamous carcinoma UROC125Nsp

status: Public on Apr 07 2020

type: genomic

city: Johannesburg

first: Jacqueline

last: Brown

state: Gauteng

address: 7 York Rd Parktown

department: Molecular Medicine and Haematology

country: South Africa

institute: National Health Laboratory Services

description:
UROC125Nsp
Hybridized to 250K Nsp SNP array.

hyb_protocol: As per manufacturer (Affymetrix) in GeneChip 640 ovens.

scan_protocol: The arrays were washed using Affymetrix GeneChip 450 Fluidics Stations, and scanned using the GeneChip Scanner 3000 7G.

data_processing: CEL files were generated using the Affymetrix algorithm and were then imported into Partek Genomics Suite for DNA copy number analysis. The copy number data were segmented using the circular binary algorithm in GenePattern (Broad Institute) To assess the significance of gains and losses, the segmentation file was analysed using GISTIC 2.0 (Genomic Identification of Significant Targets in Cancer).

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: esophageal squamous carcinoma UROC125

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: DNA was extracted using a phenol/chloroform protocol from 80% tumour cells that were macrodissected from the tissue blocks. The reference samples were also extracted in the same way. DNA quality was assessed using the Nanodrop, standard gel electrophoresis and a multiplex PCR.

tag: disease state

value: esophageal squamous carcinoma

tag: tissue

value: esophageal squamous epithelium

tag: gender

value: male

tag: age

tag: sample identifier


title: Esophageal squamous carcinoma UROC87Nsp

description:
UROC87Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC87

value: female


title: Normal tissue URCONT41Nsp

description:
URCONT41Nsp
Hybridized to 250K Nsp SNP array.

source_name: normal tissue URCONT41

value: normal

value: esophagus


title: Esophageal squamous carcinoma UROC130Nsp

description:
UROC130Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC130


title: Esophageal squamous carcinoma UROC65Nsp

description:
UROC65Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC65


title: Esophageal squamous carcinoma UROC70Nsp

description:
UROC70Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC70


title: Esophageal squamous carcinoma UROC67Nsp

description:
UROC67Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC67


title: Esophageal squamous carcinoma UROC62Nsp

description:
UROC62Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC62


title: Esophageal squamous carcinoma UROC53Nsp

description:
UROC53Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC53


title: Esophageal squamous carcinoma UROC63Nsp

description:
UROC63Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC63


title: Esophageal squamous carcinoma UROC55Nsp

description:
UROC55Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC55


title: Esophageal squamous carcinoma UROC60Nsp

description:
UROC60Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC60


title: Esophageal squamous carcinoma UROC59Nsp

description:
UROC59Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC59


title: NMuMG BC030870  anti-H3K27Ac_3

type: SRA

city: Milano

first: gabriele

last: bucci

state: MI

address: via olgettina 58

department: CTGB

country: Italy

institute: IRCCS Ospedale San Raffaele

library_source: genomic

data_processing:
basecall CASAVA 1.8
demultiplexing with bcl2fastq v.2
low quality bases and adapter removal made with bbduk
reads were aligned to mouse genome in single end with bwa mem
duplicates were marked with sambamba markdup -p -t 10
mapped reads were quantified by tranforming in BigWig with Deeptools bamCoverage 2.4.0
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files obtained from aligned reads and quantified by a binsize of 10bp with Deeptools bamCoverage

organism: Mus musculus

source_name: NMuMG cells

growth_protocol: Both NMuMG mock cells and overexpressing BC030870 were cultured in DMEM+10%FCS+10 microgram/ml insulin up to a 70% confluence

extract_protocol:
Cells were extracted according to the Magna-ChIP (Millipore) protocol
Libraries were constructed using the ChIP Elute Kit and DNA SMART ChIP-Seq Kit (Illumina) sequencing library preparation from low-input DNA templates, 75nt paired-end

treatment_protocol: Cell fixation according to the Magna-ChIP (Millipore) protocol

tag: cell line

value: NMuMG

tag: genotype/variation

value: overexpressing BC030870

tag: chip antibody

value: anti-H3K27Ac (Abcam, ab4729)


title: NMuMG BC030870  anti-H3K27Ac_2


title: Esophageal squamous carcinoma UROC98Nsp

description:
UROC98Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC98


title: Esophageal squamous carcinoma UROC48Nsp

description:
UROC48Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC48


title: Esophageal squamous carcinoma UROC69Nsp

description:
UROC69
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC69


title: Esophageal squamous carcinoma UROC54Nsp

description:
UROC54
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC54

value: unknown


title: NMuMG BC030870  anti-H3K4me3_3

value: anti-H3K4me3 (Abcam, ab8580)


title: Esophageal squamous carcinoma UROC40Nsp

description:
UROC40Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC40


title: NMuMG BC030870  anti-H3K27Ac_1


title: Esophageal squamous carcinoma UROC47Nsp

description:
UROC47Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC47


title: Esophageal squamous carcinoma UROC31Nsp

description:
UROC31Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC31


title: NMuMG BC030870  anti-H3K4me3_2


title: NMuMG BC030870  anti-H3K4me3_1


title: Esophageal squamous carcinoma UROC37Nsp

description:
UROC37Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC37


title: Esophageal squamous carcinoma UROC103Nsp

description:
UROC103Nsp_2
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC103


title: NMuMG mock anti-H3K27Ac_3

value: mock


title: NMuMG mock anti-H3K27Ac_2


title: Esophageal squamous carcinoma UROC33Nsp

description:
UROC33Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC33


title: NMuMG mock anti-H3K4me3_3


title: Esophageal squamous carcinoma UROC20Nsp

description:
UROC20Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC20


title: Esophageal squamous carcinoma UROC71Nsp

description:
UROC71Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC71


title: Esophageal squamous carcinoma UROC29Nsp

description:
UROC29Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC29


title: NMuMG mock anti-H3K4me3_2


title: Esophageal squamous carcinoma UROC22Nsp

description:
UROC22Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC22


title: Esophageal squamous carcinoma UROC42Nsp

description:
UROC42Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC42


title: Esophageal squamous carcinoma UROC16Nsp

description:
UROC16Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC16


title: Esophageal squamous carcinoma UROC30Nsp

description:
UROC30Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC30


title: NMuMG mock input

source_name: NMuMG cells

value: none (input)


title: Young CM rep2

city: Frankfurt

first: David

last: John

state: Hessen

address: Theodor-Stern-Kai 7

country: Germany

institute: Institute for Cardiovascular Regeneration

library_source: transcriptomic

data_processing:
Reads were mapped by tophat2 (v.2.0.9) to GRCm38. Afterwards Cufflinks was utilized with the default attributes for gene quantification.
Genome_build: GRCm38
Supplementary_files_format_and_content: genes.fpkm_tracking, Gene_expression_english_03.04.20.tsv

molecule: polyA RNA

source_name: young cardiomyocytes

growth_protocol: Mice were kept in individually ventilated cages at 12:12 hour-light/dark cycles at 21-24°C and 45-60% humidity and fed a normal chow diet

extract_protocol:
All samples were prepared using miRNeasy Kit (Qiagen) including DNase treatment.
500ng of total RNA was used as input for whole transcriptome RNA-seq library preparation (TruSeq RNA, Illumina) following low throughput protocol. Sequencing was performed on Nextseq 500 (Illumina) using V2 chemistry and 75bp single-end setup.

value: 8-weeks old

tag: cell type

value: cardiomyocytes


title: Young CM rep1


title: Young Rest rep3

source_name: young non-cardiomyocytes

value: non-cardiomyocytes


title: Young Rest rep2


title: Old CM rep2

source_name: old cardiomyocytes

value: 18-months old


title: Esophageal squamous carcinoma UROC46Nsp

description:
UROC46Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC46

value: esophageal squamous carcinoma


title: Young CM rep3


title: Old Rest rep3

source_name: old non-cardiomyocytes


title: Young Rest rep1


title: Old CM rep1


title: Esophageal squamous carcinoma UROC86Nsp

description:
UROC86Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC86

value: esophageal squamous epithelium


title: Old Rest rep1

value: male


title: Old Rest rep2


title: Esophageal squamous carcinoma UROC26Nsp

description:
UROC25Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC26


title: Gem-resistant MIA PaCa2_CM03_24h_Rep3

city: London

first: Stephen

last: Neidle

address: Brunswick Square

department: School of Pharmacy

country: United Kingdom

institute: UCL

data_processing:
Illumina run data were demultiplexed and converted to fastq files using Illumina’s bcl2fastq Conversion Software (v2.19).
Fastq files were pre-processed to remove adapter contamination and poor quality sequences using the program Trimmomatic (v0.36)
Duplication levels were estimated using JE-Suite50
Reads per transcript were counted using the program FeatureCounts51 (v1.4.6p5)
Genome_build: Mapped to a recent human genome build (UCSC hg38: https://genome.ucsc.edu/) using the RNA-seq alignment tool STAR (v2.5b: https://github.com/alexdobin/STAR)
Supplementary_files_format_and_content: Excel format, contains differential expression data for 6 h and 24 h CM03 exposure

molecule: total RNA

source_name: pancreatic cancer

growth_protocol: GemMIA-R3 cells were seeded in 100 mm plates (6 h = 2.5 × 10^6 and 24 h = 1.0 × 10^6 cells/well) and incubated overnight

extract_protocol:
Total RNA was extracted from 2 - 4 x 10^6 cells using the RNeasy mini kit (Qiagen, cat no. 74104) and on-column DNase1 digestion (Qiagen, cat no. 79254)
RNA-seq libraries were generated using the NEBNext mRNA Ultra II with IDT xGen UMI adapters kit

treatment_protocol: Cells were treated with 0.40 µM CM03 or vehicle (PBS) for 6 h and 24 h

tag: source

value: derived from ATCC cell line

value: Gem-resistant MIA PaCa2

value: pancreas ductal adenocarcinoma cell line


title: MIA PaCa2 cell line_control_24h_Rep1

value: ATCC cell line

value: MIA PaCa2

value: Untreated/control_24 h


title: MIA PaCa2 cell line_control_24h_Rep3


title: Gem-resistant MIA PaCa2_control_24h_Rep3


title: Gem-resistant MIA PaCa2_control_24h_Rep1


title: Gem-resistant MIA PaCa2_control_24h_Rep2


title: MIA PaCa2 cell line_control_24h_Rep2


title: Gem-resistant MIA PaCa2_CM03_24h_Rep2


title: MIA PaCa2 cell line_control_6h_ Rep2

value: Untreated/control_6 h


title: Gem-resistant MIA PaCa2_CM03_6h_Rep1


title: Gem-resistant MIA PaCa2_CM03_6h_Rep3


title: Esophageal squamous carcinoma UROC124Nsp

description:
UROC124Nsp
Hybridized to 250K Nsp SNP array.

source_name: esophageal squamous carcinoma UROC124

value: female


title: Gem-resistant MIA PaCa2_control_6h_Rep3


title: Gem-resistant MIA PaCa2_CM03_6h_Rep2


title: Gem-resistant MIA PaCa2_control_6h_Rep1


title: Gem-resistant MIA PaCa2_CM03_24h_Rep1


title: OPM-1 gFBXW7 + gKMT2D - rep2

city: Philadelphia

first: Luca

last: Busino

state: PA

address: 421 Curie Blvd, 705 BRB II/III

department: Cancer Biology

country: USA

institute: Luca Busino

data_processing:
reads were aligned to GRCh38 with STAR
Reads were followed by read trimming using “Trimmomatic” to remove adaptors and low-quality reads. “FeatureCounts” calculated how many reads map to each gene/feature with the parameters ‘-C’ (without reads whose pairs mapped to different chromosomes), ‘-M’ (with multi-mapped reads) and ‘-t exon’ (within exon region).
Differential expression was determined with the R package DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: Table of counts and normalized RPKM values for all genes

source_name: OPM-1 cells

growth_protocol: RPMI + 10% FBS

extract_protocol:
RNA was extracted using RNeasy Mini Kit (QIAGEN, #74104) and polyA+ transcripts were isolated with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #7490S).
RNA-Seq libraries were prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB, #E7760S).
Strand-specific RNA-seq (dUTP)

tag: genotype

value: WT

tag: treatment

value: gFBXW7 + gKMT2D


title: OPM-1 gFBXW7 + gKMT2D - rep3


title: OPM-1 gFBXW7 + gKMT2D - rep1


title: OPM-1 gFBXW7 - rep3


title: OPM-1 gFBXW7 - rep2


title: OPM-1 gLuc - rep3

value: gLuc


title: OPM-1 gFBXW7 - rep1


title: OPM-1 gLuc - rep2


title: MIA PaCa2 cell line_control_6h_ Rep3


title: OPM-1 gLuc - rep1


title: Day_3_FSHD2_2_R2_H8

city: Irvine

first: Ali

last: Mortazavi

state: CA

address: 2300E Biological Sciences 3

institute: UC Irvine

description: poly-A+ RNA

data_processing:
Raw data converted to fastq using bcl2fastq v2.18.0.12 from Illumina.
Reads were mapped to hg38 by STAR (version 2.5.1b) using defaults except with a maximum of 10 mismatches per pair, a ratio of mismatches to read length of 0.07, and a maximum of 10 multiple alignments.
Quantitation was performed using RSEM (version 1.2.31) by defaults with gene annotations from GENCODE v28, and results were output in transcripts per million (TPM).
Genome_build: hg38
Supplementary_files_format_and_content: RSEM output tab-delimited text files with abundance measures in counts and TPM

source_name: Primary myotube nuclei

extract_protocol:
Day 0 myoblasts were lifted from plates using trypsin, washed, and captured on medium IFCs (10-17 um). Day 3 myotube single nuclei were isolated from mononucleated cells (MNCs) by washing a 6 cm dish once with trypsin, then adding trypsin for about 5 min until myotubes lifted off the plate and MNCs were still attached. Cells were initially pelleted at 2000 rpm for 2 min and resuspended in lysis buffer with 0.02% IGEPAL CA-630. Lysis was done for 3 minutes, filtered and spun at 4000 rpm for 1 minute. Nuclei were captured on medium IFCs (10-17 um) at a density between 340 and 640 nuclei/ul in a volume of 10 ul.
cDNA was normalized to approximately 0.1 ng/ul for tagmentation and library prep (Illumina, FC-131-1096). Libraries were sequenced on the Illumina NextSeq500 platform using paired-end 75 bp mode with 1-3 million reads per sample for full length RNA-seq single-cell and single-nucleus libraries.

tag: individual

tag: day of differentiation

value: Day 3

tag: fshd status

tag: cell or nucleus

value: nucleus


title: Day_3_FSHD2_2_R2_H7

description: poly-A+ RNA


title: Old CM rep3

value: 18-months old

value: cardiomyocytes


title: Day_3_FSHD2_2_R2_H6

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_H4

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_H3

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_H5

description: poly-A+ RNA


title: MIA PaCa2 cell line_control_6h_ Rep1


title: Day_3_FSHD2_2_R2_H1

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_G8

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_G7

description: poly-A+ RNA


title: Gem-resistant MIA PaCa2_control_6h_Rep2


title: Day_3_FSHD2_2_R2_G5

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_G6

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_G4

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_G3

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_F8

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_G1

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_G2

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_F6

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_F7

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_F3

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_F2

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_F1

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_H2

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_E7

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_E6

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_E5

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_E8

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_D8

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_E3

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_E1

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_D7

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_D5

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_D3

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_D6

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_F5

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_F4

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_D4

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_D2

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_C2

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_C1

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_C3

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_B4

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_B5

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_C5

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_B8

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_E4

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_C7

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_C8

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_E2

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_B3

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_B2

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_A8

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_B1

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_D1

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_A7

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_A6

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_C6

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_A5

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_A2

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_H7

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_H6

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_A1

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_H5

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_H8

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_H4

description: poly-A+ RNA


title: NMuMG mock anti-H3K27Ac_1

value: NMuMG

value: mock

value: anti-H3K27Ac (Abcam, ab4729)


title: Day_3_FSHD2_2_R1_H3

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_H11

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_H12

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_H2

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_G9

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_H10

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_G8

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_G6

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_G5

description: poly-A+ RNA


title: Day_3_FSHD2_2_R2_A3

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_G2

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_H1

description: poly-A+ RNA


title: NMuMG mock anti-H3K4me3_1

value: anti-H3K4me3 (Abcam, ab8580)


title: Day_3_FSHD2_2_R1_G11

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_G10

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_F8

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_F7

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_F9

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_F3

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_F4

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_F2

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_F5

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_F6

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_F12

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_F11

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_G3

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_G4

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_E6

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_G7

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_G12

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_E10

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_E5

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_E12

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_E9

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_D9

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_D8

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_E11

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_D7

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_D6

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_E4

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_D5

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_D4

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_D3

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_D11

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_D10

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_C9

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_C8

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_D2

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_D12

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_C7

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_C6

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_E3

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_C3

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_C2

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_C4

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_C12

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_B9

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_C10

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_C11

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_B6

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_B7

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_B4

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_B11

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_B12

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_B5

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_B3

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_B1

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_A6

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_A5

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_A1

description: poly-A+ RNA


title: Day_3_Control_3_R3_G9_3

description: poly-A+ RNA

value: Control


title: Day_3_Control_3_R3_H10_3

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_A11

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_A10

description: poly-A+ RNA


title: Day_3_Control_3_R3_H8_3

description: poly-A+ RNA


title: Day_3_Control_3_R3_G11_3

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_A12

description: poly-A+ RNA


title: Day_3_Control_3_R3_G10_1

description: poly-A+ RNA


title: Day_3_Control_3_R3_E9_3

description: poly-A+ RNA


title: Day_3_Control_3_R3_D11_2

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_B2

description: poly-A+ RNA


title: Day_3_Control_3_R3_F9_3

description: poly-A+ RNA


title: Day_3_Control_3_R3_D10_3

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_B10

description: poly-A+ RNA


title: Day_3_FSHD2_2_R1_A3

description: poly-A+ RNA


title: Day_3_Control_3_R3_B9_3

description: poly-A+ RNA


title: Day_3_Control_3_R3_A9_2

description: poly-A+ RNA


title: Day_3_Control_3_R3_A12_3

description: poly-A+ RNA


title: Day_3_Control_3_R3_F11_2

description: poly-A+ RNA


title: Day_3_Control_3_R3_A10_3

description: poly-A+ RNA


title: Day_3_Control_3_R2_H7

description: poly-A+ RNA


title: Day_3_Control_3_R2_F1

description: poly-A+ RNA


title: Day_3_Control_3_R3_D10_2

description: poly-A+ RNA


title: Day_3_Control_3_R2_F6

description: poly-A+ RNA


title: Day_3_Control_3_R2_E2

description: poly-A+ RNA


title: Day_3_Control_3_R2_F4

description: poly-A+ RNA


title: Day_3_Control_3_R2_D9

description: poly-A+ RNA


title: Day_3_Control_3_R2_D8

description: poly-A+ RNA


title: Day_3_Control_3_R3_A9_3

description: poly-A+ RNA


title: Day_3_Control_3_R2_D3

description: poly-A+ RNA


title: Day_3_Control_3_R2_E8

description: poly-A+ RNA


title: Day_3_Control_3_R1_H9_1

description: poly-A+ RNA


title: Day_3_Control_3_R1_H9_2

description: poly-A+ RNA


title: Day_3_Control_3_R2_B9

description: poly-A+ RNA


title: Day_3_Control_3_R2_A6

description: poly-A+ RNA


title: Day_3_Control_3_R2_A7

description: poly-A+ RNA


title: Day_3_Control_3_R2_C7

description: poly-A+ RNA


title: Day_3_Control_3_R1_G9_2

description: poly-A+ RNA


title: Day_3_Control_3_R1_H11_2

description: poly-A+ RNA


title: Day_3_Control_3_R1_H11_1

description: poly-A+ RNA


title: Day_3_Control_3_R1_H10_2

description: poly-A+ RNA


title: Day_3_Control_3_R1_H10_1

description: poly-A+ RNA


title: Day_3_Control_3_R1_G9_1

description: poly-A+ RNA


title: Day_3_Control_3_R1_G12_2

description: poly-A+ RNA


title: RIP using strain containing no tags

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

description:
Untagged-GFP RIPseq
PIR2_RIP_untagged_subtracted_forward.bedgraph
PIR2_RIP_untagged_subtracted_reverse.bedgraph

data_processing:
Alignment was done using Tophat.
Reads Per Kilobase of transcript, per Million mapped reads (RPKM) values were obtained using Deeptools suite.
Alignments were strand separated using Samtools
RPKM Normalized Untagged RIPseq was subtracted from RPKM normalized Pir2-GFP RIPseq using deeptools-bamCompare.
Genome_build: asm294v2.28
Supplementary_files_format_and_content: bedgraph

organism: Schizosaccharomyces pombe

source_name: log. growing cells

growth_protocol: Standard conditions were used for logarithmically growing cultures in rich media (YEA). Cultures were grown at 32C overnight.

extract_protocol:
Cells were fixed with 1% formaldehyde at room temperature for 20 minutes. Cells were lysed and were sonicated using bioruptor. Immunoprecipitations were performed using GFP antibodies (ab290). Reverse crosslinking was performed overnight at 65˚C and protein was degraded using proteinase K. RNAase free DNAase I (Thermo Fisher, am2222) was used to degrade DNA fragments and RNA was purified using phenol-chloroform and ethanol precipitation.
NEB Ultra Directional RNA Library Prep kit (NEB, E7420S) was used according to manufacturer's recommendation.
Libraries were analyzed using an Agilent 4200 TapeStation system (Agilent) and sequenced on the Illumina NextSeq 500 platform.

tag: growth stage

value: log. growing cells

value: wild type cells

tag: rip antibody

value: GFP antibodies (Abcam, ab290, Lot#:GR306215-1)


title: ChIPseq of Pir2

description: Pir2-GFP ChIPseq

data_processing:
Alignment was done using Bowtie2.
Reads Per Kilobase of transcript, per Million mapped reads (RPKM) values were obtained using Deeptools-bamCoverage suite and plotted as bedgraphs.
Genome_build: asm294v2.29
Supplementary_files_format_and_content: bedgraph

growth_protocol: Standard conditions were used for logarithmically growing cultures in rich media (YEA). Cultures were grown at 32˚C.

extract_protocol:
Cells were crosslinked with 1% formaldehyde at room temperature for 20 minutes. Cells were lysed and sonicated using Bioruptor. Immunoprecipitations were performed using GFP antibodies (ab290). Crosslink was reversed overnight at 65˚C, and treated with with RNase A and proteinase K. QIAquick PCR purification kit (cat. no. 28014) was used to purify the DNA.
NEBNext Ultra II DNA Library Prep kit (NEB, E7645S) was used according to manufacturer's recommendation.
Libraries were analyzedanalyzed using an Agilent 4200 TapeStation system (Agilent) and sequenced on the Illumina NextSeq 500 platform.


title: Day_3_Control_3_R1_G11_2

description: poly-A+ RNA


title: RIP using strain containing Pir2-GFP

description:
Pir2-GFP RIPseq
PIR2_RIP_untagged_subtracted_forward.bedgraph
PIR2_RIP_untagged_subtracted_reverse.bedgraph


title: Day_3_Control_3_R1_G11_1

description: poly-A+ RNA


title: Day_3_Control_3_R1_G10_1

description: poly-A+ RNA


title: Day_3_Control_3_R1_G10_2

description: poly-A+ RNA


title: REF 11b

city: Amherst

first: Tianfa

last: Xie

state: Massachusetts

address: 240 Thatcher Way

department: Mechanical and Industrial Engineering

institute: University of Massachusetts Amherst

data_processing:
Validation of sequence quality was performed using the BaseSpace cloud computing service supported by Illumina (BaseSpace Sequence Hub, https://basespace.illumina.com/home/index).
RNA-seq reads were aligned to the rat reference genome (Rattus norvegicus UCSC rn5) using TopHat Alignment.
Then, the differential gene expression analyses were performed by Cufflinks Assembly & DE using previous alignment results produced by the TopHat app as input.
Shortlists of significantly differentially expressed genes were identified by applying thresholds of 2-fold differential expression and false discovery rate q ≤ 0.05.
Genome_build: Rattus norvegicus UCSC rn5
Supplementary_files_format_and_content: the spreadsheet file include RPKM values for each sample

organism: Rattus norvegicus

source_name: Rat Embryonic Fibroblast

growth_protocol: Cells were cultured at 37 °C and 5% CO2.

extract_protocol:
Total RNA was extracted from REF subclones 2c and 11b using the Aurum Total RNA Mini Kit (Bio-rad) following manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment.

value: Fibroblast

tag: passages

tag: clone


title: Day_3_Control_3_R1_F12_2

description: poly-A+ RNA


title: Day_3_Control_3_R1_F9_2

description: poly-A+ RNA


title: REF 2c


title: Day_3_Control_3_R1_F9_1

description: poly-A+ RNA


title: Contusion SCI_Soleus, Replicate 3

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Illumina BaseSpace FastQ v1.0.0 used for basecalling
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
The sequences were directly aligned to the Rattus norvegicus reference genome assembly (Rn6) using Star version 2.6.
Read counts for gene regions were obtained with HTSeq using Ensembl annotations (Rn6 version 93).
The annotation file was parsed to exclude mitochondria genes in an effort to reduce non-relevant variation in subsequent steps of the analysis. The resulting annotation file tested 24,613 gene locations.
Genome_build: rn6
Supplementary_files_format_and_content: Expression data tracks in UCSC Genome Browser bigwig format were generated for each sample.

source_name: Contusion SCI

growth_protocol: All rats were housed initially in standard cages and maintained in a continuous 12h-light/dark cycle. Tap water and a standard rodent diet were available to all rats ad libitum.

extract_protocol:
Animals were perfused with PBS supplemented with 20% RNAlater (Ambion, Life Technologies). Soleus muscle tissue was retrieved and collected in QIAzol (Qiagen). Total RNA from each sample was isolated with RNeasy Lipid Tissue Mini Kit (Qiagen).
Libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit- Set A (Cat# RS-122-2101) and Set B (Cat# RS-122-2102) with poly-A enrichment.

treatment_protocol: Animals were given either T2 complete transection SCI, T2 contusion SCI, or no SCI. A subset of contused SCI animals were exposed to either swimming or shallow water walking exercise.

tag: strain

value: Sprague-Dawley

tag: injury type

value: T2 Contusion

tag: time

value: 11.5 weeks after injury

tag: tissue

value: soleus muscle


title: Contusion SCI_Soleus, Replicate 2


title: Day_3_Control_3_R1_F11_2

description: poly-A+ RNA

value: Day 3


title: No SCI_Soleus, Replicate 4

source_name: No SCI

value: No SCI


title: Day_3_Control_3_R1_F11_1

description: poly-A+ RNA

value: nucleus


title: No SCI_Soleus, Replicate 3


title: No SCI_Soleus, Replicate 2


title: No SCI_Soleus, Replicate 1


title: Contusion SCI_Soleus, Replicate 4


title: Day_3_Control_3_R1_E11_2

description: poly-A+ RNA


title: Day_3_Control_3_R1_E10_2

description: poly-A+ RNA


title: Complete transection SCI_Soleus, Replicate 3

source_name: Complete transection SCI

value: T2 Complete transection

value: 8.5 weeks after injury


title: Day_3_Control_3_R1_E9_2

description: poly-A+ RNA


title: Complete transection SCI_Soleus, Replicate 4


title: Day_3_Control_3_R1_E10_1

description: poly-A+ RNA


title: Complete transection SCI_Soleus, Replicate 2


title: Day_3_Control_3_R1_D9_2

description: poly-A+ RNA


title: Day_3_Control_3_R1_D12_2

description: poly-A+ RNA


title: Complete transection SCI_Soleus, Replicate 1


title: Contusion SCI + SWW_Soleus, Replicate 4

source_name: Contusion SCI + SWW

tag: exercise

value: SWW

value: 13.5 weeks after injury


title: Day_3_Control_3_R1_D11_2

description: poly-A+ RNA


title: Contusion SCI + SWW_Soleus, Replicate 3


title: Day_3_Control_3_R1_F10_1

description: poly-A+ RNA


title: Day_3_Control_3_R1_F10_2

description: poly-A+ RNA


title: Day_3_Control_3_R1_D11_1

description: poly-A+ RNA


title: Day_3_Control_3_R1_D10_2

description: poly-A+ RNA


title: Day_3_Control_3_R1_D10_1

description: poly-A+ RNA


title: Contusion SCI + SWW_Soleus, Replicate 1


title: Contusion SCI + SWW_Soleus, Replicate 2


title: Day_3_Control_3_R1_C9_2

description: poly-A+ RNA


title: Day_3_Control_3_R1_C11_2

description: poly-A+ RNA


title: Contusion SCI + SWIM_Soleus, Replicate 3

source_name: Contusion SCI + SWIM

value: SWIM


title: Contusion SCI + SWIM_Soleus, Replicate 2


title: Contusion SCI + SWIM_Soleus, Replicate 1


title: Day_3_Control_3_R1_C11_1

description: poly-A+ RNA

value: Control


title: Day_3_Control_3_R1_C10_2

description: poly-A+ RNA


title: Day_3_Control_3_R1_B12_2

description: poly-A+ RNA


title: Contusion SCI + SWIM_Soleus, Replicate 4


title: Day_3_Control_3_R1_B11_1

description: poly-A+ RNA


title: Day_3_Control_3_R1_B12_1

description: poly-A+ RNA


title: Day_3_Control_3_R1_B9_2

description: poly-A+ RNA


title: Day_3_Control_3_R1_B10_2

description: poly-A+ RNA


title: Day_3_Control_3_R1_A9_2

description: poly-A+ RNA


title: Day_3_Control_3_R1_B10_1

description: poly-A+ RNA


title: Day_3_Control_3_R1_A12_1

description: poly-A+ RNA


title: Day_3_Control_3_R1_A11_2

description: poly-A+ RNA


title: Day_3_Control_3_R1_A10_1

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_H4

description: poly-A+ RNA

source_name: Primary myoblasts

value: Day 0

value: cell


title: Day_3_Control_3_R1_A10_2

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_H2

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_H7

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_G9

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_H11

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_G6

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_H1

description: poly-A+ RNA


title: Day_3_Control_3_R1_B11_2

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_G2

description: poly-A+ RNA


title: Day_3_Control_3_R1_C10_1

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_G8

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_G5

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_F10

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_E4

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_D7

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_D8

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_F7

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_E7

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_D6

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_F1

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_D2

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_E3

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_C7

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_D10

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_C2

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_C10

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_C1

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_C11

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_B8

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_B9

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_B2

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_B4

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_B1

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_B5

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_B12

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_F9

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_D1

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_C8

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_B11

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_D11

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_B10

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_C5

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_A4

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_A2

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_A8

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_A6

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_A12

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_A1

description: poly-A+ RNA


title: Day_0_FSHD2_2_R1_A11

description: poly-A+ RNA


title: Day_0_Control_3_R1_H8

description: poly-A+ RNA


title: Day_0_Control_3_R1_H6

description: poly-A+ RNA


title: Day_0_Control_3_R1_H9

description: poly-A+ RNA


title: Day_0_Control_3_R1_H7

description: poly-A+ RNA


title: Contusion SCI_Soleus, Replicate 1


title: Day_0_Control_3_R1_H5

description: poly-A+ RNA


title: Day_0_Control_3_R1_H3

description: poly-A+ RNA


title: Day_0_Control_3_R1_H4

description: poly-A+ RNA


title: ozs3 at 4°C, biological replicate 2

type: RNA

city: Bayreuth

first: Michael

last: Weber

address: Universitätsstrasse 30

department: Plant Physiology

institute: University of Bayreuth

description: Gene expression in roots of ozs3 at 4°C

hyb_protocol: Following fragmentation, 12.5 µg of cRNA were hybridized for 16 hr at 45°C on Affymetrix Arabidopsis Genome ATH1 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station

scan_protocol: GeneChips were scanned using a GeneChipTM Scanner

data_processing: Data were analyzed using R  (BioConductor library tools). Data were RMA normalized (Robust Multi-chip Analysis).

organism: Arabidopsis thaliana

source_name: ozs3, 4°C, root

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA

growth_protocol: plants were cultivated for 4 weeks in hydroponic culture at short day conditions (8h light, 16 h dark) at 23°C in an Arabidopsis growth chamber (Percival)

extract_protocol: total RNA was extracted using RNeasy Plant Mini Kit from Qiagen (according to the manufacturer's instructions).

treatment_protocol: plants were transfered to 4°C for 24h, control plants remained at 23°C for 24h

value: root

tag: genetic background

tag: age

value: 4 week old plants

tag: cultivation system

value: hydroponic culture

tag: duration of treatment

tag: temperature treatment


title: Day_0_Control_3_R1_H2

description: poly-A+ RNA

tag: individual

tag: day of differentiation


title: Day_0_Control_3_R1_G5

description: poly-A+ RNA

tag: fshd status

tag: cell or nucleus


title: Day_0_Control_3_R1_H10

description: poly-A+ RNA


title: ozs3 at 4°C, biological replicate 3

description: Gene expression in roots of ozs3 at 4°C

tag: genotype


title: Day_0_Control_3_R1_G4

description: poly-A+ RNA


title: Day_0_Control_3_R1_G3

description: poly-A+ RNA


title: Day_0_Control_3_R1_G2

description: poly-A+ RNA


title: Day_0_Control_3_R1_F3

description: poly-A+ RNA


title: Day_0_Control_3_R1_F6

description: poly-A+ RNA


title: Day_0_Control_3_R1_F7

description: poly-A+ RNA


title: Day_0_Control_3_R1_F2

description: poly-A+ RNA


title: Day_0_Control_3_R1_F1

description: poly-A+ RNA


title: Col-0 at 4°C, biological replicate 2

description: Gene expression in roots of Col-0 at 4°C

source_name: Col-0, 4°C, root

value: wildtype


title: Day_0_Control_3_R1_F5

description: poly-A+ RNA


title: Day_0_Control_3_R1_F10

description: poly-A+ RNA


title: P53ki-3

city: Tianjin

first: Ling

last: Shuai

address: 38 Tong Yan Road, Jinnan district

department: State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy

country: China

institute: Nankai University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: embryonic stem cells

extract_protocol:
ESCs were collected and RNA was harvested using Trizol reagent. NEB Next® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °Cbefore PCR. Then PCR was performed with Phusion High -Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: cell type

value: embryonic stem cells

value: P53 - haploid


title: Day_0_Control_3_R1_F12

description: poly-A+ RNA


title: Day_0_Control_3_R1_E9

description: poly-A+ RNA


title: Day_0_Control_3_R1_E6

description: poly-A+ RNA


title: ozs3 at 4°C, biological replicate 1

description: Gene expression in roots of ozs3 at 4°C


title: P53ki-2


title: Col-0 at 4°C, biological replicate 3


title: P53ki-1


title: Day_0_Control_3_R1_E4

description: poly-A+ RNA


title: ozs3 at RT, biological replicate 1

description: Gene expression in roots of ozs3 at RT

source_name: ozs3, control (=RT), root

value: control (23degC)


title: Col-0 at RT, biological replicate 3

description: Gene expression in roots of Col-0 at RT

source_name: Col-0, control (=RT), root


title: Col-0 at 4°C, biological replicate 1


title: ozs3 at RT, biological replicate 2

description: Gene expression in roots of ozs3 at RT


title: Col-0 at RT, biological replicate 2

description: Gene expression in roots of Col-0 at RT


title: Col-0 at RT, biological replicate 1

description: Gene expression in roots of Col-0 at RT


title: WT-haESC-T3-1-3

value: wild type haploid


title: ozs3 at RT, biological replicate 3

description: Gene expression in roots of ozs3 at RT


title: Day_0_Control_3_R1_D8

description: poly-A+ RNA


title: Day_0_Control_3_R1_G10

description: poly-A+ RNA


title: WT-haESC-T3-1-2


title: Day_0_Control_3_R1_E3

description: poly-A+ RNA


title: Day_0_Control_3_R1_C7

description: poly-A+ RNA


title: Day_0_Control_3_R1_D5

description: poly-A+ RNA


title: Day_0_Control_3_R1_D11

description: poly-A+ RNA


title: 7657_patient_diagnosis

city: Lublin

first: Monika

last: Szelest

address: ul. Antoniego Gębali 6

department: Laboratory of Genetic Diagnostics

country: Poland

institute: Medical University of Lublin

hyb_protocol: The 250 ng of genomic DNA from the leukemic cells was subjected to microarray examination according to the manufacturer's protocols as follows: i) Digestion with the restriction enzyme NspI; ii) adapter ligation, polymerase chain reaction (PCR) amplification and magnetic bead purification; iii) fragmentation and end-labeling with biotin; iv) washing and staining using a GeneChip ® Fluidics Station 450; and v) scanning using an Affymetrix GeneChip Scanner 3000 7G (Affymetrix). Scanned data files were generated using Affymetrix GeneChip Command Console Software,  and analyzed with Affymetrix Chromosome Analysis Suite v 3.3 (Affymetrix).

data_processing:
To calculate the copy number of altered regions, the data were normalized to baseline reference intensities using NA 32.3 FFPE v.2 reference model (Affymetrix). The hidden Markov model available within the software package was used to determine the copy number states (CN) and their breakpoints. Thresholds of log 2 ratio ≥0.58 and ≤1 were used to categorize altered regions as CN variation (CNV) gains (amplifications) and copy number losses (deletions), respectively. To prevent the detection of false-positive CNVs arising due to microarray unspecific signals, only regions that involved at least 50 consecutive probes were considered in the analysis of gains or losses in this study. Amplificationsand deletions were analyzed separately. To exclude aberrations representing common normal CNVs, all the identified CNVs were compared with those reported in the Database of Genomic Variants ( http://projects.tcag.ca/variation/ ). To identify the genes involved in the CNVs further, the UCSC database ( http://genome.ucsc.edu) and Ensemble (http://www.ensembl.org) were used.
Gene annotation and gene overlap were determined using the human genome build 19 and NetAffx (http://www.affymetrix.com).The obtained data were analyzed based on two different criteria: genome-wide CNVs and leukaemia-associated region/gene-specific CNAs (leukaemia genes_all_20150505; Fullerton Overlap Map_hg19).

label: biotin

source_name: patient with Nijmegen breakage syndrome

growth_protocol: Karyotypes are prepared from mitotic cells that have been arrested in the metaphase or prometaphase portion of the cell cycle, when chromosomes assume their most condensed conformations. For cancer diagnoses, typical specimens include bone marrow samples. The process of generating a karyotype begins with the short-term culture of cells derived from a specimen. After a period of cell growth and multiplication, dividing cells are arrested in metaphase by addition of colchicine, which poisons the mitotic spindle. The cells are next treated with a hypotonic solution that causes their nuclei to swell and the cells to burst. The nuclei are then treated with a chemical fixative, dropped on a glass slide, and treated with various stains that reveal structural features of the chromosomes.

extract_protocol: The researched material was the genomic DNA extracted from bone marrow samples using the QIAamp DNA Blood Mini Kit (Qiagen, Hilden, Germany).

tag: disease

value: non-Hodgkin lymphoma

value: blast cells

tag: gender

value: male


title: Day_0_Control_3_R1_D10

description: poly-A+ RNA


title: Day_0_Control_3_R1_C6

description: poly-A+ RNA


title: Day_0_Control_3_R1_C4

description: poly-A+ RNA


title: Day_0_Control_3_R1_D4

description: poly-A+ RNA


title: Day_0_Control_3_R1_C3

description: poly-A+ RNA


title: Day_0_Control_3_R1_C2

description: poly-A+ RNA


title: Day_0_Control_3_R1_E12

description: poly-A+ RNA


title: stimulating liver tissue from mouse1 WGBS

city: Xi’an

first: Yi

last: Wu

state: Shaanxi

address: No.28, Xianning West Road

institute: Xi'an Jiaotong University

data_processing:
The raw data were subject to quality control with trimmmomatic/0.39 and sickle/1.33
Alignment to Genome using hisat2/2.1.0 for RNAseq, bismark/0.19.0(bowtie2/2.3.5.1) for GWBS
samtools/1.7 for file transformation or sorting
picard/2.9.2 for removing duplications of PCR
the counts were extracted using htseq/0.9.1 for RNAseq; bismark(bismark_methylation_extractor) for GWBS
Genome_build: GRCh38.p13 for human; GRCm38.p6 for mouse
Supplementary_files_format_and_content: ht.counts for RNAseq; cytosine_report results for GWBS

source_name: liver

growth_protocol: Hep3B was obtained from ATCC and cultured using DMEM with 10% FBS

extract_protocol: RNA / DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hep3B cells with or without IL-6 and IL-1β treatment for 24 h;100ul turpentine was subcutaneously injected to the mouse every hind limb for 2 days.

tag: strain

value: liver

tag: treated

value: turpentine


title: resting liver tissue from mouse2 WGBS

tag: tissue


title: Day_0_Control_3_R1_C1

description: poly-A+ RNA


title: resting liver tissue from mouse1 WGBS


title: Day_0_Control_3_R1_C10

description: poly-A+ RNA


title: Day_0_Control_3_R1_B8

description: poly-A+ RNA


title: stimulating liver tissue from mouse2 RNAseq


title: Day_0_Control_3_R1_B7

description: poly-A+ RNA


title: Day_0_Control_3_R1_B4

description: poly-A+ RNA


title: stimulating liver tissue from mouse2 WGBS


title: Day_0_Control_3_R1_B2

description: poly-A+ RNA


title: Day_0_Control_3_R1_B3

description: poly-A+ RNA


title: resting liver tissue from mouse2 RNAseq


title: stimulating liver tissue from mouse1 RNAseq


title: Day_0_Control_3_R1_B10

description: poly-A+ RNA


title: Day_0_Control_3_R1_A5

description: poly-A+ RNA


title: Day_0_Control_3_R1_A7

description: poly-A+ RNA


title: resting liver tissue from mouse1 RNAseq


title: Day_0_Control_3_R1_A6

description: poly-A+ RNA


title: Day_0_Control_3_R1_A3

description: poly-A+ RNA


title: Day_0_Control_3_R1_A2

description: poly-A+ RNA


title: Day_0_Control_3_R1_C11

description: poly-A+ RNA


title: Day_0_Control_3_R1_A11

description: poly-A+ RNA


title: DNMT3AB_E6.5_ExE

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

description: Whole-genome bisulfite sequencing of Dnmt3a KO E6.5 mouse extraembryonic tissues

data_processing:
Raw base call (BCL) files generated by Illumina sequencers were demultiplexed into FASTQ files using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("mkfastq" pipeline, version 1.3.1, default parameters).
For each experiment FASTQ files were aligned, filtered, barcode and UMI counted using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("count pipeline", version 1.3.1, default parameters). The count pipeline was run jointly on multiple sequencing runs of the same experiment. Genomic reference: "refdata-cellranger-mm10-1.2.0", prepared by 10x Genomics.
For experiments with multiple libraries, all libraries were aggregated using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("aggr pipeline", version 1.3.1, default parameters). The output of Cell Ranger "count" was aggregated and normalized to the same sequencing depth and then the gene-barcode matrices were recomputed on the combined data. Sample aggregation was evaluated with normalizing for sequencing depth differences in the libraries. Normalized UMI counts used the 'mapped' normalization mode. Analysis of the data was based on the normalized UMI counts.
Genome_build: mm10
Supplementary_files_format_and_content: For all samples there is one tar gz archive containing the gene-barcode matrices as produced by the Cell Ranger pipeline. They contain the MEX-formatted UMI count matrices of each sample, or if multiple libraries where sequence, the aggregated gene-barcode matrix. Samples names consist of genotype (KO), developmental state (E6.5, E7.5, E8.5, experiment number (1, 2) with respect to genotype and stage and, if aggregated, library number (a, b). 10x Genomics explains their MEX-formatted UMI counts as follows: "The cellranger pipeline generates a gene-barcode matrix... Each matrix is stored in Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively." More information on the formatting can be found at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices.
Bisulfite-converted reads were quality filtered and adapter trimmed using cutadapt (v2.4), followed by alignment to the mm10 reference genome with bsmap using the following parameter: -v 0.01 -s 16 -w 100 -S 1 -R -u -q 20. Duplicate reads were removed using GATK MarkDuplicates (v4.1.0.0).
Methylation rates were called using mcall using default parameter and subsequently filtered for coverage (min 10 reads).
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bigWig file of 10X coverage filtered methylation rate BED file (<chr> <start> <end> <methylation rate>)

source_name: Extraembryonic Ectoderm

growth_protocol: Preimplantation embryos were cultured in pre-gassed 25 ul KSOM supplemented with 1/2 amino acids (Millipore) under mineral oil at 37ºC and 5% CO2.  After ~84 hours post-fertilization, cavitated blastocysts were transferred into the uterine horns of pseudopregnant females in clutches of 10-15 per horn.

extract_protocol:
Preparation of samples was performed as described in Smith, Chan, et. al, Nature 2014. The decidua of mated female mice were isolated on the morning of E6.5 and the conceptus removed. Then, under a stereomicroscope, the embryo was carefully bisected along the extraembryonic/embryonic axis, removing the ectoplacental cone from the extraembryonic ectoderm when apparent. After separation, Epiblast and extraembryonic ectoderm incubated for 15 min at 4ºC in 0. 5% Trypsin, 2.5% Pancreatin dissolved in PBS and filtered through a 0.2 mm syringe filter and allowed to rest for 5-10 minutes in KSOM at room temperature. Finally, visceral endoderm was removed by drawing the embryo through a narrow, flame drawn glass capillary and only embryo fragments with no apparent contamination were collected. On average, matched ExE and Epiblast from ~10 embryos were collected per assay. Samples were snap frozen in minimal volume prior to extraction and next-generation library synthesis.
Genomic DNA for Whole Genome Bisulfite Sequencing was isolated according to Smith, Chan et. al, Nature, 2012 using a lysis buffer containing 300 ug/mL Proteinase K, followed by phenol:chloroform extraction and ethanol precipitation. Libraries were prepared using the Accel-NGS™ Bisulfite DNA library kit (Swift Biosciences) according to the manufacturers protocol. Final libraries were generated from 8-9 PCR cycles.

treatment_protocol: B6D2F1 oocytes were isolated from 5-10 week old female mice ~12h after a hormone priming superovulation regime (5 IU PSMG and 5IU hCG delivered 46 hours afterwards) and stored in 25 ul droplets of pregassed KSOM media with 1/2 amino acids (Millipore) at 37ºC and 5%C02 .  Zygotes were generated either by intracytoplasmic sperm injection of decapitated B6/CAST F1 strain sperm (RNA-seq) or natural mating with B6D2F1 males (Bisulfite-seq) and cultured to E3.5 blastoycsts prior to uterine transfer into pseudopregnant CD-1 strain females (~25-35 g).  Post-implantation embryos were isolated according to the embryonic day with a 24 hour offset to accommodate developmental delay as a result of uterine transfer (see extract protocol).  Experimental samples were additionally injected with a cocktail of 3-4 discrete gRNA's targeted to exons of respective KO gene and Cas9 mRNA synthesized by in vitro transcription at concentrations of 33.3 ng/ul per gRNA and 200 ng/ul for Cas9.  gRNA/Cas9 injections occurred within 6-8 hours post fertilization, followed by equivalent culture in KSOM media to the blastocyst stage as the control.

value: B6D2F1 maternal strain crossed with B6D2F1 males

value: Extraembryonic Ectoderm

tag: developmental stage

value: Dnmt3a + Dnmt3b DKO


title: Day_0_Control_3_R1_A1

description: poly-A+ RNA

value: Day 0

value: Control

value: cell


title: Day_0_Control_3_R1_B9

description: poly-A+ RNA


title: Day_0_Control_3_R1_A10

description: poly-A+ RNA


title: Quad_Control-4_Day_5_Rep_2

description: poly-A+ RNA

data_processing:
Raw data converted to fastq using bcl2fastq v2.18.0.12 from Illumina.
Reads were mapped to hg38 by STAR (version 2.5.1b) using defaults except with a maximum of 10 mismatches per pair, a ratio of mismatches to read length of 0.07, and a maximum of 10 multiple alignments.
Quantitation was performed using RSEM (version 1.2.31) by defaults with gene annotations from GENCODE v28, and results were output in transcripts per million (TPM).
Protein coding and long non-coding RNA genes with greater than 5 TPM in both replicates in at least one timepoint and with greater than 1 TPM for both reps for both cell lines of the same disease and day were kept. Genes were TMM normalized using edgeR (version 3.18.1) and log2-transformed.
Batch correction was performed using ComBat from sva (version 3.32.1) and scaled for two batches which used different library prep kits; control-3, control-4, FSHD2-2 for one batch, and control-1, control-2, FSHD2-1 for the second.
Genome_build: hg38
Supplementary_files_format_and_content: RSEM output tab-delimited text files with abundance measures in counts and TPM; Supplementary file contains comma-separated file with expression values normalized as described in data processing.

source_name: Primary myoblasts from quadricep biopsy

extract_protocol:
Cells were lifted using trypsin. Total RNA was extracted by using the RNeasy kit (QIAGEN).
Between 19 and 38 ng of RNA were converted to cDNA using the Smart-Seq 2 protocol (Picelli, et al., Nat. Protoc., 2014). Libraries were constructed with the Nextera DNA Library Prep Kit (FC-121-1030, Illumina) for control-3, control-4, and FSHD2-2 libraries, and the Nextera DNA Flex Library Prep Kit (20018704, Illumina) for control-1, control-2 and FSHD2-1 libraries. Libraries were sequenced on the Illumina NextSeq500 platform using paired-end 43 bp mode.

value: Day 5

tag: muscle source

value: quadricep

tag: library prep kit


title: Quad_Control-4_Day_5_Rep_1

description: poly-A+ RNA

value: Nextera DNA Library Prep Kit (FC-121-1030, Illumina)


title: DNMT3AB_E6.5_Epi

description: Whole-genome bisulfite sequencing of Dnmt3a KO E6.5 mouse embryonic tissues

source_name: proximal Epiblast

value: proximal Epiblast


title: Quad_Control-4_Day_4_Rep_2

description: poly-A+ RNA

value: Day 4


title: DNMT1_E6.5_ExE

description: Whole-genome bisulfite sequencing of Dnmt1 KO E6.5 mouse extraembryonic tissues

value: Dnmt1 KO


title: DNMT3A_E6.5_Epi

value: Dnmt3a KO


title: DNMT3A_E6.5_ExE


title: Quad_Control-4_Day_3_Rep_2

description: poly-A+ RNA

value: Day 3


title: Quad_Control-4_Day_4_Rep_1

description: poly-A+ RNA


title: Quad_Control-4_Day_3_Rep_1

description: poly-A+ RNA


title: Quad_Control-4_Day_2_Rep_2

description: poly-A+ RNA

value: Day 2


title: Quad_Control-4_Day_1_Rep_2

description: poly-A+ RNA

value: Day 1


title: Quad_Control-4_Day_2_Rep_1

description: poly-A+ RNA


title: DNMT3A_E8.5_1b

description: Single-cell RNA-sequencing of 10 Dnmt3a KO E8.5 mouse embryos (library b)

source_name: whole embryo

extract_protocol:
Respective gene null (KO) embryos were isolated from surrogate mice. Outermost extraembryonic tissues (yolk sac, trophectoderm derived tissues) were preserved if possible. The 7-12 embryos isolated per experiment were washed in 1xPBS/0.4%BSA, pooled without pre-selection and subjected to tissue dissociation in 200 µl TrypLE Express (Gibco) for 40-60 minutes at 37ºC, with pipetting in 5 minute intervals. The cell suspension was filtered using Scienceware Flowmi Cell Strainers, 40 µM. Cells were washed twice with 1ml 1xPBS/0.4%BSA and centrifugation for 5 minutes at 1200 rpm. The cell concentration was determined using a hemocytometer and cells were subjected to single-cell RNA sequencing (10x Genomic, Chromium™ Single Cell 3’ v3).
Single-cell libraries were generated following the manual instructions of 10x Genomic (Chromium™ Single Cell 3’ v2 or v3), with the exception of fewer PCR cycles in cDNA amplification and sample index PCR than recommended in order to increase complexity of libraries. Libraries were sequenced with a minimum of 230 Mio paired end reads and parameters as described in the manual.

value: B6D2F1 maternal strain crossed with B6/CAST F1 males

value: embryo


title: DNMT3A_E8.5_1a

description: Single-cell RNA-sequencing of 10 Dnmt3a KO E8.5 mouse embryos (library a)


title: Quad_Control-4_Day_1_Rep_1

description: poly-A+ RNA


title: Quad_Control-4_Day_0_Rep_1

description: poly-A+ RNA


title: DNMT1_E8.5_1b

description: Single-cell RNA-sequencing of 12 Dnmt1 KO E8.5 mouse embryos (library b)

extract_protocol:
Respective gene null (KO) embryos were isolated from surrogate mice. Outermost extraembryonic tissues (yolk sac, trophectoderm derived tissues) were preserved if possible. The 7-12 embryos isolated per experiment were washed in 1xPBS/0.4%BSA, pooled without pre-selection and subjected to tissue dissociation in 200 µl TrypLE Express (Gibco) for 40-60 minutes at 37ºC, with pipetting in 5 minute intervals. The cell suspension was filtered using Scienceware Flowmi Cell Strainers, 40 µM. Cells were washed twice with 1ml 1xPBS/0.4%BSA and centrifugation for 5 minutes at 1200 rpm. The cell concentration was determined using a hemocytometer and cells were subjected to single-cell RNA sequencing (10x Genomic, Chromium™ Single Cell 3’ v2).
Single-cell libraries were generated following the manual instructions of 10x Genomic (Chromium™ Single Cell 3’ v2 or v3), with the exception of fewer PCR cycles in cDNA amplification and sample index PCR than recommended in order to increase complexity of libraries. Libraries were sequenced with a minimum of 230 Mio paired end reads and parameters as described in the manual.


title: Quad_Control-3_Day_5_Rep_2

description: poly-A+ RNA


title: Quad_Control-3_Day_3_Rep_2

description: poly-A+ RNA


title: Quad_Control-3_Day_4_Rep_1

description: poly-A+ RNA


title: Quad_Control-3_Day_4_Rep_2

description: poly-A+ RNA


title: Quad_Control-3_Day_2_Rep_2

description: poly-A+ RNA


title: Quad_Control-3_Day_3_Rep_1

description: poly-A+ RNA


title: ChIP_HSPC_total_PolII_WT_rep2

city: Kyoto

first: Yotaro

last: Ochi

address: Yoshida-Konoe-cho

department: Department of Pathology and Tumor Biology

country: Japan

institute: Kyoto Univiersity

data_processing:
The sequencing reads were aligned to the reference genome (hg19 or mm9) using bowtie (v1.2.2) following trimming of adapters and read tails to a total length of 50 base pairs using cutadapt.
Duplicates and reads on blacklisted regions (ENCODE) were removed by Picard and bedtools, respectively.
Peaks were called using MACS (v2.1.1) for each replicate individually with a p value threshold of 1 x 10–3.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: Peaks were called using MACS (v2.1.1) for each replicate individually with a p value threshold of 1 x 10–3.

source_name: bone marrow

extract_protocol:
ChIP-seq experiments were performed using c-Kit+ HSPCs or HL-60 cell lines.
Cells were fixed in PBS with 1% formaldehyde (Thermo Fisher Scientific) for 10 min at room temperature with gentle mixing.  The reaction was stopped by adding glycine solution (10x) (Cell Signaling Technology) and incubating for 5 minutes at room temperature, and the cells were washed in cold PBS twice.  The cells were then processed with SimpleChIP Plus Sonication Chromatin IP Kit (Cell Signaling Technology) and Covaris E220 (Covaris) according to the manufacturer’s protocol.  The antibodies used for ChIP are as follows: STAG1 (Protein Tech, 14015-1-AP), STAG2 (Novus, NBP1-30472), SMC1 (Abcam, ab9262), CTCF (Cell Signaling Technology, D31H2), RUNX1 (Abcam, 23980), total Pol II (CST, D8L4Y), Ser5-P Pol II (Abcam, ab5408), H3K27ac (Cell Signaling Technology, D5E4), H3K27me3 (Cell Signaling Technology, C36B11), H3K4me1 (Cell Signaling Technology, D1A9), or H3K4me3 (Cell Signaling Technology, C42D8).  ChIP-seq libraries were constructed using ThruPLEX DNA-seq kit (Takara) according to the manufacturer’s protocol, and then subjected to sequencing using HiSeq 2500 or NovaSeq 6000 (Illumina).

value: HSPC

value: bone marrow

value: WT


title: DNMT1_E6.5_Epi

description: Whole-genome bisulfite sequencing of Dnmt1 KO E6.5 mouse embryonic tissues

value: B6D2F1 maternal strain crossed with B6D2F1 males


title: ChIP_HSPC_total_PolII_WT_rep1


title: Quad_Control-3_Day_2_Rep_1

description: poly-A+ RNA

value: Control


title: Quad_Control-3_Day_1_Rep_1

description: poly-A+ RNA


title: Quad_Control-3_Day_0_Rep_2

description: poly-A+ RNA

value: Day 0


title: 2-1002124: Splenic Tetramer+ WGBS

city: memphis

first: yiping

last: fan

state: tn

address: 262 Danny Thomas Place

institute: st jude children's hospital

data_processing:
Basecalling was performed using Illumina RealTimeAnalysis software
FASTQ sequences adapter trimmed (trimglore) and mapped to the hg19 and mm10 genome by BSMAP
CpGs were extracted by the methratio.py in the BSMAP package
Genome_build: mm10 (mouse WGBS), hg19 (human WGBS)
Supplementary_files_format_and_content: methylation ratio are in bed formats that contains methylation ratio for each CpG

source_name: Splenic Tetramer+

extract_protocol:
DNA was extracted followed by bisulfite treatment for library prepration. Nuclei were exteacted for ATAC-Seq.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA Methylation Kit (Part# EGMK81312). Briefly, Bisulfite converted DNA was annealed with random hexamer with tagging sequence. DNA copy was synthesized using TruSeq DNA Methyl Polymerase. Then Exonuclease I was used to digest excess random primer.  The 3’ ends of the strands are then selectively tagged with a second specific sequence tag to generate di-tagged DNA using DNA polymerase. The di-tagged DNA with known sequence tags at both ends was cleaned up by the AMPureXP Beads. The dsDNA library was generated by PCR amplification with Illumina primers for 10 cycles and library fragments of ~350 bp (insert plus adaptor and PCR primer sequences). The library was purified by the AMPureXP Beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2500 following the manufacturer's protocols. For ATAC-Seq, nuclei were isolated from FACS purified tetramer+ beta cell-specific CD8 T cells and polyclonal Tem and naive CD8 T cells from T1D donors using the Low Cell Input Nuclei Isolation protocol from 10x Genomics. The transposition reaction was then performed on the bulk nuclei. The transposed nuclei were partitioned into nanoliter-scale barcoded Gel Beads-in-emulsion (GEMs) after running the loaded Chromium microfluidic Chip E on the Chromium Controller, and the transposed DNA was uniquely indexed and barcoded for each individual nucleus per manufacturer’s instructions (10x Genomics). Libraries were generated and sequenced using Illumina Hiseq system following the manufacturer's protocols. For each sample, the single cell ATAC data were mapped to hg38 using the Cell Ranger ATAC pipeline.  We then used SnapATAC (https://github.com/r3fang/SnapATAC) to combine multiple samples, i.e. the fragment.tsv files generated by Cell Ranger ATAC pipeline, and performed the clustering analysis.

value: Tetramer+ CD8 T cells


title: 2-1002123: Splenic Tetramer+ WGBS


title: 2-1002125: Splenic Tetramer+ WGBS


title: Quad_Control-3_Day_0_Rep_1

description: poly-A+ RNA

value: quadricep

value: Nextera DNA Library Prep Kit (FC-121-1030, Illumina)


title: TA_FSHD2-1_Day_5_Rep_2

description: poly-A+ RNA

source_name: Primary myoblasts from tibialis anterior biopsy

value: Day 5

value: tibialis anterior

value: Nextera DNA Flex Library Prep Kit (20018704, Illumina)


title: 2-1002122: Pancreatic Tetramer+ WGBS

source_name: Pancreatic Tetramer+


title: TA_FSHD2-1_Day_5_Rep_1

description: poly-A+ RNA


title: TA_FSHD2-1_Day_4_Rep_1

description: poly-A+ RNA

value: Day 4


title: Quad_Control-4_Day_0_Rep_2

description: poly-A+ RNA


title: DNMT1_E8.5_1a

description: Single-cell RNA-sequencing of 12 Dnmt1 KO E8.5 mouse embryos (library a)

value: Dnmt1 KO


title: TA_FSHD2-1_Day_4_Rep_2

description: poly-A+ RNA


title: 2-1002120: Pancreatic LN Tetramer+ WGBS

source_name: Pancreatic LN Tetramer+


title: Quad_Control-3_Day_5_Rep_1

description: poly-A+ RNA


title: TA_FSHD2-1_Day_3_Rep_2

description: poly-A+ RNA

value: Day 3


title: TA_FSHD2-1_Day_3_Rep_1

description: poly-A+ RNA


title: TA_FSHD2-1_Day_2_Rep_2

description: poly-A+ RNA

value: Day 2


title: TA_FSHD2-1_Day_1_Rep_2

description: poly-A+ RNA

value: Day 1


title: BS-seq_KMT2B_E6.5_ExE

description: Whole-genome bisulfite sequencing of Kmt2b KO E6.5 mouse extraembryonic tissues

data_processing:
Bisulfite-converted reads were quality filtered and adapter trimmed using cutadapt (v2.4), followed by alignment to the mm10 reference genome with bsmap using the following parameter: -v 0.01 -s 16 -w 100 -S 1 -R -u -q 20. Duplicate reads were removed using GATK MarkDuplicates (v4.1.0.0).
Methylation rates were called using mcall using default parameter and subsequently filtered for coverage (min 10 reads).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig file of 10X coverage filtered methylation rate BED file (<chr> <start> <end> <methylation rate>)

value: Extraembryonic Ectoderm

value: Kmt2b KO


title: TA_FSHD2-1_Day_2_Rep_1

description: poly-A+ RNA


title: Quad_Control-3_Day_1_Rep_2

description: poly-A+ RNA


title: TA_FSHD2-1_Day_0_Rep_2

description: poly-A+ RNA


title: TA_FSHD2-1_Day_1_Rep_1

description: poly-A+ RNA


title: BS-seq_KMT2A_E6.5_ExE

description: Whole-genome bisulfite sequencing of Kmt2a KO E6.5 mouse extraembryonic tissues

value: Kmt2a KO


title: TA_FSHD2-1_Day_0_Rep_1

description: poly-A+ RNA


title: BS-seq_KMT2A_E6.5_Epi

description: Whole-genome bisulfite sequencing of Kmt2a KO E6.5 mouse embryonic tissues

value: B6D2F1 maternal strain crossed with B6D2F1 males

value: proximal Epiblast


title: TA_FSHD2-2_Day_5_Rep_2

description: poly-A+ RNA


title: Acod1-KO OI+PM rep1

city: Chicago

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

data_processing:
Raw sequencing QC assessement: FastQC v0.11.5
Alignment: STAR v2.5.3a
Post alignement QC assessment: RSeQC and Picard tools v2.9.0
Gene transcripts assembly: featureCounts
Differentially expressed genes analysis: DESeq2
Genome_build: GENCODE human genome model: GRCm38 v11
Supplementary_files_format_and_content: tab-delimited text files include gene features raw counts values summarized by featureCouts for each Sample.

source_name: Bone Marrow Derived Macrophages

growth_protocol: Hematopoetic cells were isolated from mouse bone marrow and cultured in vitro with M-CSF to generate bone marrow derived macrophages (BMDMs).

extract_protocol:
RNA was harvested with Trizol reagent using Zymo Direct-zol RNA kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDMs were treated with 4-Octyl Itaconate (OI, 0.25 mM, 2 hours pretreatment) and/or PM (20ug/cm2) for 24 hours.

value: Bone Marrow Derived Macrophages


title: Acod1-KO OI+PM rep2


title: Acod1-KO PM rep2


title: TA_FSHD2-2_Day_5_Rep_1

description: poly-A+ RNA


title: BS-seq_G9A_E6.5_ExE

description: Whole-genome bisulfite sequencing of G9a KO E6.5 mouse extraembryonic tissues

value: G9a KO


title: BS-seq_DNMT3B_E6.5_ExE

description: Whole-genome bisulfite sequencing of Dnmt3b KO E6.5 mouse extraembryonic tissues

value: Dnmt3b KO


title: BS-seq_G9A_E6.5_Epi

description: Whole-genome bisulfite sequencing of G9a KO E6.5 mouse embryonic tissues


title: TA_FSHD2-2_Day_4_Rep_2

description: poly-A+ RNA

value: Nextera DNA Library Prep Kit (FC-121-1030, Illumina)


title: Acod1-KO PM rep1


title: BS-seq_DNMT3B_E6.5_Epi

description: Whole-genome bisulfite sequencing of Dnmt3b KO E6.5 mouse embryonic tissues


title: TA_FSHD2-2_Day_4_Rep_1

description: poly-A+ RNA


title: Acod1-KO Control rep2


title: Acod1-KO Control rep1


title: TA_FSHD2-2_Day_3_Rep_2

description: poly-A+ RNA


title: BS-seq_L3MBTL2_E6.5_ExE

description: Whole-genome bisulfite sequencing of L3mbtl2 KO E6.5 mouse extraembryonic tissues

value: L3mbtl2 KO


title: BS-seq_KMT2B_E6.5_Epi

description: Whole-genome bisulfite sequencing of Kmt2b KO E6.5 mouse embryonic tissues


title: BS-seq_KDM2B_E6.5_ExE

description: Whole-genome bisulfite sequencing of Kdm2B KO E6.5 mouse extraembryonic tissues

value: Kdm2b KO


title: BS-seq_KDM2B_E6.5_Epi

description: Whole-genome bisulfite sequencing of Kdm2B KO E6.5 mouse embryonic tissues


title: WT OI+PM rep2

value: WT


title: WT PM rep2


title: TA_FSHD2-2_Day_2_Rep_1

description: poly-A+ RNA

value: tibialis anterior


title: BS-seq_RNF2_E6.5_ExE

description: Whole-genome bisulfite sequencing of Rnf2 KO E6.5 mouse extraembryonic tissues

value: Rnf2 KO


title: TA_FSHD2-2_Day_1_Rep_1

description: poly-A+ RNA


title: WT Control rep2


title: BS-seq_RNF2_E6.5_Epi

description: Whole-genome bisulfite sequencing of Rnf2 KO E6.5 mouse embryonic tissues


title: TA_FSHD2-2_Day_1_Rep_2

description: poly-A+ RNA


title: BS-seq_EED_E6.5_ExE_rep2

description: Whole-genome bisulfite sequencing of Eed KO E6.5 mouse extraembryonic tissues

value: Eed KO


title: BS-seq_EED_E6.5_ExE_rep1


title: WT Control rep1


title: TA_FSHD2-2_Day_0_Rep_2

description: poly-A+ RNA

value: Day 0


title: BS-seq_L3MBTL2_E6.5_Epi

description: Whole-genome bisulfite sequencing of L3mbtl2 KO E6.5 mouse embryonic tissues


title: EED.CDKN2A_E8.5_1a

description:
Single-cell RNA-sequencing of 9 Eed Cdkn2a DKO E8.5 mouse embryos (library a)
EED.CDKN2A_E8.5_1ab.tar.gz

data_processing:
Raw base call (BCL) files generated by Illumina sequencers were demultiplexed into FASTQ files using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("mkfastq" pipeline, version 1.3.1, default parameters).
For each experiment FASTQ files were aligned, filtered, barcode and UMI counted using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("count pipeline", version 1.3.1, default parameters). The count pipeline was run jointly on multiple sequencing runs of the same experiment. Genomic reference: "refdata-cellranger-mm10-1.2.0", prepared by 10x Genomics.
For experiments with multiple libraries, all libraries were aggregated using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("aggr pipeline", version 1.3.1, default parameters). The output of Cell Ranger "count" was aggregated and normalized to the same sequencing depth and then the gene-barcode matrices were recomputed on the combined data. Sample aggregation was evaluated with normalizing for sequencing depth differences in the libraries. Normalized UMI counts used the 'mapped' normalization mode. Analysis of the data was based on the normalized UMI counts.
Genome_build: mm10
Supplementary_files_format_and_content: For all samples there is one tar gz archive containing the gene-barcode matrices as produced by the Cell Ranger pipeline. They contain the MEX-formatted UMI count matrices of each sample, or if multiple libraries where sequence, the aggregated gene-barcode matrix. Samples names consist of genotype (KO), developmental state (E6.5, E7.5, E8.5, experiment number (1, 2) with respect to genotype and stage and, if aggregated, library number (a, b). 10x Genomics explains their MEX-formatted UMI counts as follows: "The cellranger pipeline generates a gene-barcode matrix... Supplementary_files_format_and_content: Each matrix is stored in Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively." More information on the formatting can be found at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices.

extract_protocol:
Respective gene null (KO) embryos were isolated from surrogate mice. Outermost extraembryonic tissues (yolk sac, trophectoderm derived tissues) were preserved if possible. The 7-11 embryos isolated per experiment were washed in 1xPBS/0.4%BSA, pooled without pre-selection and subjected to tissue dissociation in 200 µl TrypLE Express (Gibco) for 40-60 minutes at 37ºC, with pipetting in 5 minute intervals. The cell suspension was filtered using Scienceware Flowmi Cell Strainers, 40 µM. Cells were washed twice with 1ml 1xPBS/0.4%BSA and centrifugation for 5 minutes at 1200 rpm. The cell concentration was determined using a hemocytometer and cells were subjected to single-cell RNA sequencing (10x Genomic, Chromium™ Single Cell 3’ v2).
Single-cell libraries were generated following the manual instructions of 10x Genomic (Chromium™ Single Cell 3’ v2 or v3), with the exception of fewer PCR cycles in cDNA amplification and sample index PCR than recommended in order to increase complexity of libraries. Libraries were sequenced with a minimum of 230 Mio paired end reads and parameters as described in the manual.

value: B6D2F1 maternal strain crossed with B6/CAST F1 males

value: embryo

value: Eed Cdkn2a DKO

tag: chromium single cell 3' chemistry version


title: TA_FSHD2-2_Day_0_Rep_1

description: poly-A+ RNA


title: BS-seq_EED_E6.5_Epi_rep2

description: Whole-genome bisulfite sequencing of Eed KO E6.5 mouse embryonic tissues


title: CDKN2A_E8.5_1b

description:
Single-cell RNA-sequencing of 11 Cdkn2a KO E8.5 mouse embryos (library b)
CDKN2A_E8.5_1ab.tar.gz

value: Cdkn2a KO


title: TA_Control-2_Day_5_Rep_2

description: poly-A+ RNA

value: Day 5

value: Control

value: Nextera DNA Flex Library Prep Kit (20018704, Illumina)


title: TA_Control-2_Day_5_Rep_1

description: poly-A+ RNA


title: EED.CDKN2A_E8.5_1b

description:
Single-cell RNA-sequencing of 9 Eed Cdkn2a DKO E8.5 mouse embryos (library b)
EED.CDKN2A_E8.5_1ab.tar.gz


title: BS-seq_WT_E6.5_ExE_rep2

description: Whole-genome bisulfite sequencing of wild-type KO E6.5 mouse extraembryonic tissues

value: B6D2F1 maternal strain crossed with B6D2F1 males

value: Extraembryonic Ectoderm

value: wild-type


title: TA_FSHD2-2_Day_3_Rep_1

description: poly-A+ RNA

value: Day 3

value: Nextera DNA Library Prep Kit (FC-121-1030, Illumina)


title: TA_FSHD2-2_Day_2_Rep_2

description: poly-A+ RNA

value: Day 2


title: CDKN2A_E8.5_1a

description:
Single-cell RNA-sequencing of 11 Cdkn2a KO E8.5 mouse embryos (library a)
CDKN2A_E8.5_1ab.tar.gz


title: BS-seq_EED_E6.5_Epi_rep1

value: proximal Epiblast


title: WT OI+PM rep1

value: Bone Marrow Derived Macrophages

value: WT


title: TA_Control-2_Day_4_Rep_2

description: poly-A+ RNA

value: Day 4

value: tibialis anterior


title: WT PM rep1


title: DNMT3B_E8.5_1b

description:
Single-cell RNA-sequencing of 8 Dnmt3b KO E8.5 mouse embryos (library b)
DNMT3B_E8.5_1ab.tar.gz

value: B6D2F1 maternal strain crossed with B6/CAST F1 males

value: embryo

value: Dnmt3b KO


title: TA_Control-2_Day_4_Rep_1

description: poly-A+ RNA


title: BS-seq_WT_E6.5_Epi_rep2

description: Whole-genome bisulfite sequencing of wild-type KO E6.5 mouse embryonic tissues


title: BS-seq_WT_E6.5_ExE_rep1


title: DNMT3B_E8.5_1a

description:
Single-cell RNA-sequencing of 8 Dnmt3b KO E8.5 mouse embryos (library a)
DNMT3B_E8.5_1ab.tar.gz


title: TA_Control-2_Day_3_Rep_2

description: poly-A+ RNA


title: BS-seq_WT_E6.5_Epi_rep1


title: KMT2B_E8.5_1b

description:
Single-cell RNA-sequencing of 10 Kmt2b KO E8.5 mouse embryos (library b)
KMT2B_E8.5_1ab.tar.gz

extract_protocol:
Respective gene null (KO) embryos were isolated from surrogate mice. Outermost extraembryonic tissues (yolk sac, trophectoderm derived tissues) were preserved if possible. The 7-11 embryos isolated per experiment were washed in 1xPBS/0.4%BSA, pooled without pre-selection and subjected to tissue dissociation in 200 µl TrypLE Express (Gibco) for 40-60 minutes at 37ºC, with pipetting in 5 minute intervals. The cell suspension was filtered using Scienceware Flowmi Cell Strainers, 40 µM. Cells were washed twice with 1ml 1xPBS/0.4%BSA and centrifugation for 5 minutes at 1200 rpm. The cell concentration was determined using a hemocytometer and cells were subjected to single-cell RNA sequencing (10x Genomic, Chromium™ Single Cell 3’ v3).
Single-cell libraries were generated following the manual instructions of 10x Genomic (Chromium™ Single Cell 3’ v2 or v3), with the exception of fewer PCR cycles in cDNA amplification and sample index PCR than recommended in order to increase complexity of libraries. Libraries were sequenced with a minimum of 230 Mio paired end reads and parameters as described in the manual.

value: Kmt2b KO


title: KMT2B_E8.5_1a

description:
Single-cell RNA-sequencing of 10 Kmt2b KO E8.5 mouse embryos (library a)
KMT2B_E8.5_1ab.tar.gz


title: EED_E8.5_1b

description:
Single-cell RNA-sequencing of 10 Eed KO E8.5 mouse embryos (library b)
EED_E8.5_1ab.tar.gz

value: Eed KO


title: TA_Control-2_Day_2_Rep_2

description: poly-A+ RNA

value: Control

value: Nextera DNA Flex Library Prep Kit (20018704, Illumina)


title: TA_Control-2_Day_3_Rep_1

description: poly-A+ RNA


title: EED_E8.5_1a

description:
Single-cell RNA-sequencing of 10 Eed KO E8.5 mouse embryos (library a)
EED_E8.5_1ab.tar.gz


title: TA_Control-2_Day_2_Rep_1

description: poly-A+ RNA


title: KMT2A_E8.5_1b

description:
Single-cell RNA-sequencing of 11 Kmt2a KO E8.5 mouse embryos (library b)
KMT2A_E8.5_1ab.tar.gz

value: Kmt2a KO


title: G9A_E8.5_1b

description:
Single-cell RNA-sequencing of 11 G9a KO E8.5 mouse embryos (library b)
G9A_E8.5_1ab.tar.gz

value: G9a KO


title: EED_E7.5_1

description:
Single-cell RNA-sequencing of 7 Eed KO E7.5 mouse embryos
EED_E7.5_1.tar.gz


title: EED_E6.5_1

description:
Single-cell RNA-sequencing of 9 Eed KO E6.5 mouse embryos
EED_E6.5_1.tar.gz


title: TA_Control-2_Day_1_Rep_1

description: poly-A+ RNA

value: Day 1


title: G9A_E8.5_1a

description:
Single-cell RNA-sequencing of 11 G9a KO E8.5 mouse embryos (library a)
G9A_E8.5_1ab.tar.gz


title: KMT2A_E8.5_1a

description:
Single-cell RNA-sequencing of 11 Kmt2a KO E8.5 mouse embryos (library a)
KMT2A_E8.5_1ab.tar.gz


title: TA_Control-2_Day_1_Rep_2

description: poly-A+ RNA


title: Tranduced control Rep4

city: San Francisco

first: Alex

last: Lee

address: 1550 Fourth St.

institute: UCSF

description:
tumor cells derived from a lung cancer model of Kras-induced oncogenesis
AG18

data_processing:
Raw reads ( bcl files ) were demultiplex into FASTQs using Illumina’s bcl2fastq software
Samples were trimmed for adaptor sequence and remove for low-quality sequence using Trimmomatic 0.38,  then mapped to mm10 whole genome using  STAR 2.5.1b and counts were computed using the parameter --quantMode and gtf from genecode ( vM13)
Sequences were imported into R , scaled, filter for low counts ( < 1 cpm) and  TMM normalized using the edgeR package.
log2 ( cpm ) were derived by further transfomring the normalized counts using the limma package, voom
Genome_build: mm10
Supplementary_files_format_and_content: single tab delimited file containing TMM-voom-normalized ( cpm log2 ) counts: genes as rows and one sample per column

source_name: KLA

growth_protocol: KLA mut/mut and wt/wt cells were grown in 10% serum DMEM

extract_protocol:
RNA from cells were extracted using trizol reagent and cleaned up with Qiagen columns.
Libraries  created with TruSeq Stranded mRNA kit (Illumina, RS-122-2101) following manufacturer's instructions and sequenced on an Illumina 4000

treatment_protocol: KLA mut/mut and wt/wt cells were treated with adCre for 48 hours and then cultured in fresh medium for 24 additional hours before RNA was harvested

value: adCre to deplete endogenous mir181ab1 expression, transduced with a control plasmid

tag: transduction

value: control


title: EED_E6.5_2

description:
Single-cell RNA-sequencing of 8 Eed KO E6.5 mouse embryos
EED_E6.5_2.tar.gz


title: TA_Control-2_Day_0_Rep_2

description: poly-A+ RNA

value: Day 0


title: Tranduced control Rep3

description:
tumor cells derived from a lung cancer model of Kras-induced oncogenesis
AG17


title: KDM2B_E8.5_1b

description:
Single-cell RNA-sequencing of 10 Kdm2b KO E8.5 mouse embryos (library b)
KDM2B_E8.5_1ab.tar.gz

value: Kdm2b KO


title: Tranduced control Rep1

description:
tumor cells derived from a lung cancer model of Kras-induced oncogenesis
AG15


title: TA_Control-1_Day_4_Rep_2

description: poly-A+ RNA


title: Tranduced mir181ab1 Rep4

description:
tumor cells derived from a lung cancer model of Kras-induced oncogenesis
AG10

value: adCre to deplete endogenous mir181ab1 expression, transduced with plasmid expressing exogenous mir181ab1


title: TA_Control-2_Day_0_Rep_1

description: poly-A+ RNA


title: Tranduced control Rep2

description:
tumor cells derived from a lung cancer model of Kras-induced oncogenesis
AG16


title: L3MBTL2_E8.5

description:
Single-cell RNA-sequencing of 10 L3mbtl2 KO E8.5 mouse embryos
L3MBTL2_E8.5_1.tar.gz

value: L3mbtl2 KO


title: TA_Control-1_Day_4_Rep_1

description: poly-A+ RNA

value: Day 4

value: tibialis anterior


title: TA_Control-1_Day_5_Rep_1

description: poly-A+ RNA

value: Day 5


title: RNF2_E8.5_1a

description:
Single-cell RNA-sequencing of 11 Rnf2 KO E8.5 mouse embryos (library a)
RNF2_E8.5_1ab.tar.gz

value: B6D2F1 maternal strain crossed with B6/CAST F1 males

value: embryo

value: Rnf2 KO


title: KDM2B_E8.5_1a

description:
Single-cell RNA-sequencing of 10 Kdm2b KO E8.5 mouse embryos (library a)
KDM2B_E8.5_1ab.tar.gz


title: TA_Control-1_Day_5_Rep_2

description: poly-A+ RNA

value: Control


title: RNF2_E8.5_1b

description:
Single-cell RNA-sequencing of 11 Rnf2 KO E8.5 mouse embryos (library b)
RNF2_E8.5_1ab.tar.gz


title: Tranduced mir181ab1 Rep2

description:
tumor cells derived from a lung cancer model of Kras-induced oncogenesis
AG8


title: WT-haESC-T3-1-1

value: embryonic stem cells

value: wild type haploid


title: TA_Control-1_Day_3_Rep_1

description: poly-A+ RNA

value: Day 3

value: Nextera DNA Flex Library Prep Kit (20018704, Illumina)


title: TA_Control-1_Day_3_Rep_2

description: poly-A+ RNA


title: TA_Control-1_Day_2_Rep_2

description: poly-A+ RNA

value: Day 2


title: TTAATC_Control

city: Munich

first: Enric

last: Redondo Monte

state: Bavaria

address: Max-Lebsche-Platz 30

department: Internal Medicine 3

institute: Ludwig-Maximilians University Munich

data_processing:
Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017)
cDNA reads were aligned to the Human Genome (hg38) with STAR 2.6.0a
Quantification was done with ENSEMBL gene models (GRCh38.84)
Genome_build: Human: hg38, Ensembl 84
Supplementary_files_format_and_content: sample (columns) and gene (rows) -wise UMI expression table

extract_protocol:
Cells were Counted, pelletized and dissolved in the lysis buffer.
Libraries were constructed using a bulk adjusted SCRB-seq protocol.

tag: cell line


title: TA_Control-1_Day_2_Rep_1

description: poly-A+ RNA

tag: individual


title: TGTTTA_KO

value: KO


title: Tranduced mir181ab1 Rep1

description:
tumor cells derived from a lung cancer model of Kras-induced oncogenesis
AG7


title: TTATTG_KO


title: GR siRNA + DEX

city: New Haven

first: Julie

last: Goodwin

address: 333 Cedar St

institute: Yale University

data_processing:
The reads were trimmed for quality.
The reads were aligned to the reference mm10 genome using bwa mem. The alignment files were sorted and index.
We used macs2 --callPeaks for peak detection.  The Input and IgG files were used a controls, and pull-down files were used a treatments.
Genome_build: mm10
Supplementary_files_format_and_content: bw

source_name: mouse lung endothelial cells

growth_protocol: Cells were cultured in EBM-2 and 10% serum.

extract_protocol: Lysates were clarified from sonicated nuclei and chromatin-DNA complexes were isolated with antibody.

treatment_protocol: Cells were treated with control or GR siRNA ofr 48 hours with and without dexamethasone 100 nM for 1 hour.

tag: strain background

value: mouse lung endothelial cells

tag: treatment

value: GR siRNA + DEX

tag: chip antibody

value: GR (Abcam3578)


title: TTAGTT_KO

tag: genotype


title: input DNA

tag: cell type


title: IgG control


title: TCTGCA_Control


title: Tranduced mir181ab1 Rep3

description:
tumor cells derived from a lung cancer model of Kras-induced oncogenesis
AG9

value: adCre to deplete endogenous mir181ab1 expression, transduced with plasmid expressing exogenous mir181ab1


title: TA_Control-1_Day_1_Rep_1

description: poly-A+ RNA

tag: day of differentiation

value: Day 1

tag: fshd status


title: TTGAAA_Control


title: TA_Control-1_Day_1_Rep_2

description: poly-A+ RNA

value: tibialis anterior


title: control siRNA + DEX

value: control siRNA + DEX


title: control siRNA

value: control siRNA


title: TACTAT_Control


title: TAATGA_KO


title: TA_Control-1_Day_0_Rep_2

description: poly-A+ RNA

value: Day 0


title: TAAAGT_KO


title: TA_Control-1_Day_0_Rep_1

description: poly-A+ RNA


title: Day_5_Control_2_R2

description: poly-A+ RNA

data_processing:
Raw data converted to fastq using bcl2fastq v2.18.0.12 from Illumina.
Reads were demultiplexed using ddSeekR (Romagnoli, et al., BMC Genomics, 2019).
Nuclei with at least 500 UMIs detected were mapped using STAR (version 2.5.1b) [38] and quantitated using RSEM (version 1.2.31) [39] with the rsem-calculate-expression with options --star and --estimate-rspd. We kept nuclei with ≥150 genes detected and <20% mitochondrial reads. Genes detected in at least 5 nuclei were kept for downstream analysis.
The data was loaded into Seurat (version 3.1.0) and normalized using the SCTransform function (Butler, et al., Nat. Biotechnol., 2018; Hafemeister & Satija, bioRxiv, 2019).
Genome_build: hg38
Supplementary_files_format_and_content: Abundance files for nuclei with ≥150 genes detected;Supplemental table includes Seurat normalized counts for nuclei used in analysis

source_name: Primary myoblasts

extract_protocol:
Myotubes from day 3 or day 5 of differentiation were isolated from mononucleated cells (MNCs) by washing a 35 mm dish once with trypsin, then adding trypsin for about 5 min until myotubes lifted off the plate and MNCs were still attached. Cells were washed once in 1X PBS + 0.1% BSA, and the nuclei were prepared according to Illumina (Document # 1070-2016-014-C) with the following modifications. We used 0.2 U/ul RNasin Plus RNase Inhibitor (Promega) for the cell lysis buffer and nuclei storage buffer, and nuclei were filtered through a 40 um filter (Falcon) after isolation. Nuclear isolation and quality were assessed by staining with ethidium homodimer.
Nuclei were loaded onto the ddSeq Single Cell Isolator (BioRad) for droplet generation, and libraries were prepared using the SureCell WTA 3’ Library Prep Kit (Illumina). Libraries were sequenced on the Illumina NextSeq500 platform using PE 68 bp for read 1 and 75 bp for read 2 with a custom primer with around 370 million reads for four samples.

value: Day 5

tag: cell or nucleus

value: nucleus


title: Day_5_FSHD2_2_R2

description: poly-A+ RNA

value: FSHD


title: TLA_GFP_u4

city: Lausanne

first: Gustavo

middle: Agustín

last: Ruiz Buendía

state: Vaud

address: University of Lausanne

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

description: TLA library created with HEK293-derived cells that contain the ectopic CAG repeat locus within a GFP reporter construct. This TLA library was generated with a viewpoint located 4 kb upstream from the CAG repeats.

data_processing:
Demultiplexed reads were mapped using a custom TLA analysis pipeline using the BWA mapping software (v 0.7.17) (Li & Durbin, 2010). First, reads were mapped to the human genome GRCh38. Then, unaligned sequences were digested in-silico with the NlaIII restriction site and remapped to the genome. The combined mapping results were used to determine the integration site.
Genome_build: hg38
Supplementary_files_format_and_content: BAM files that resulted from aligning the TLA library reads to the GRCh38 human reference genome were used to identify the insertion site of the GFP construct. The precise mapping of an insertion site was determined by PCR-amplifying an amplicon with a forward primer on the GFP construct and a reverse primer on human chr12. This amplicon was Sanger-sequenced with both the F and R primers. The corresponding fasta sequence and Sanger sequencing traces are included.

source_name: HEK293-derived GFP(CAG) cells

growth_protocol: The GFP(CAG)270 and GFP(CAG)15 cell lines were maintained at 37°C and 5% CO2 in DMEM with Glutamax, 1% penicillin-streptomycin, 15 μg/mL blasticidine, and 150 μg/mL hygromycin.

extract_protocol:
Samples of 10 million cells were crosslinked in 2% formaldehyde for 10 minutes at room temperature and quenched with glycine to a final concentration of 275 mM. Cell were lysed for 5 minutes at room temperature in lysis buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, 1x protease inhibitors). Crosslinked samples were digested at 37ºC overnight with 400 U NlaIII (NEB) followed by NlaIII heat inactivation. Samples were ligated at room temperature for 2 hours with 20 U T4 DNA ligase (Thermo Scientific) in 500 µL. Ligated samples were de-crosslinked with 5 µL Proteinase K (10 mg/mL) at 65ºC overnight followed by RNAse A treatment and phenol-chloroform purification. Samples then digested overnight at 37ºC with 50 U NspI (NEB) followed by NspI inactivation. The second ligation was performed overnight at 16ºC with 100 U T4 DNA ligase in 14 mL. The resulting TLA circularized templates were purified with the QIAquick PCR purification kit.
TLA libraries were generated by amplifying 800 ng of purified TLA template with TLA viewpoint primers. 2 x 150 bp paired-end sequencing of pooled TLA libraries was performed on Illumina HiSeq 4000.

treatment_protocol: Cells were treated with DMSO or doxycycline at a final concentration of 2 µg/mL for five days to induce transcription of the GFP mini-gene.

value: HEK293 T-Rex Flp-In


title: GTTTAT_Control

value: Control


title: GGGATT_Control


title: GTTCGA_KO


title: Day_5_FSHD2_2_R1

description: poly-A+ RNA


title: GR siRNA

value: GR siRNA


title: Day_3_Control_2_R2

description: poly-A+ RNA

value: Day 3


title: GGCGTC_KO

value: KO


title: Day_3_Control_2_R1

description: poly-A+ RNA


title: GGCCAC_KO


title: GGAGCC_KO


title: Day_3_FSHD2_2_R1

description: poly-A+ RNA


title: GCTCGC_KO


title: TLA_GFP_d3

description: TLA library created with HEK293-derived cells that contain the ectopic CAG repeat locus within a GFP reporter construct. This TLA library was generated with a viewpoint located 3 kb downstream from the CAG repeats.


title: GCTAGA_KO