title: CluGFP- [B05_Plate4]

description:
B05_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [B04_Plate4]

status: Public on Feb 28 2019

type: SRA

city: Toronto

first: Bibaswan

last: Ghoshal

address: 600 University Avenue

country: Canada

institute: Lunenfeld Tanenbaum Research Institute

description:
B04_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv

library_source: transcriptomic

data_processing:
Reads obtained from each cell were then aligned to the mm10 mouse genome using the STAR RNAseq aligner. A combined count matrix was generated from all 192 cells using the featurecounts function.
Data is read into Seurat with 1 minimum cell and 200 minimum genes and subsequently converted in scater for quality control and filtering based on library size, feature size and percentage of mitochondrial genes. Furthermore, normalization steps are performed and then the normalized data is transported back to Seurat. In Seurat, data is scaled and dimension reduction, cluster identification, PCA and tSNE are performed.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_data.csv: Comma-separated text files contain the raw data from the 192 cells and the normalized expression data from the filtered 166 cells that are finally used for analysis and visualization.

molecule: total RNA

organism: Mus musculus

source_name: Intestinal Epithelium

extract_protocol:
Full length scRNA-seq was performed by SMART-seq2 upon enrichment of Clu+ rSCs using BAC-CluGFP transgenic mice. In short, approximately 2000 GFP+ and GFP- FACS-isolated cells in less than 10 mL were directly processed on a Fluidigm C1 platform and 96 GFP+ and 96 GFP- healthy cells were selected and subjected to RNA extraction, library preparation and deep sequencing using the SMART-Seq_V4 Ultra Low Input RNA Kit for Sequencing as described in the manual.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: FACS sorted intestinal epithelial cells

tag: treatment

value: EpCAM+ CluGFP-

tag: strain


title: S1076_G10_G10_G001 [TF1_clones_scRNA-seq]

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

country: USA

institute: Memorial Sloan Kettering

data_processing:
RNA sequencing data was aligned to the human reference genome (GRCh37/hg19) using STAR using standard two-pass approach.
Gene were quantified using the STAR --quantMode GeneCounts flag over the Gencode v19 annotation.
Processed bams were genotyped for mitochondria using a custom python script.
Samples were filtered such that individual cells each had at least 100x coverage at 9 established heteroplasmic variants. No nuclear genome QC was performed
Genome_build: hg19
Supplementary_files_format_and_content: High confidence mitochondrial variants for 3 clones assayed by 3 separate single cell technologies

organism: Homo sapiens

source_name: ATCC

growth_protocol: RPMI, 10%FBS, Pen/Strep, 2ng/ml GM-CSF

extract_protocol:
Qiagen TCL lysis buffer
Smart-seq2
Single cell RNA-seq

tag: cell line

value: hematopoietic cell line


title: CluGFP- [B02_Plate4]

description:
B02_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [B03_Plate4]

description:
B03_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [B01_Plate4]

description:
B01_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [C09_Plate4]

description:
C09_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [A11_Plate4]

description:
A11_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1074_G10_G10_G001 [TF1_clones_scRNA-seq]


title: CluGFP- [B08_Plate4]

description:
B08_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [A12_Plate4]

description:
A12_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [A09_Plate4]

description:
A09_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [A10_Plate4]

description:
A10_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1072_G10_G10_G001 [TF1_clones_scRNA-seq]


title: S1073_G10_G10_G001 [TF1_clones_scRNA-seq]


title: S1079_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP- [A06_Plate4]

description:
A06_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [A08_Plate4]

description:
A08_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [A05_Plate4]

description:
A05_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1071_G10_G10_G001 [TF1_clones_scRNA-seq]


title: CluGFP- [A07_Plate4]

description:
A07_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1069_G10_G10_G001 [TF1_clones_scRNA-seq]


title: CluGFP- [A01_Plate4]

description:
A01_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [A02_Plate4]

description:
A02_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [A03_Plate4]

description:
A03_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1070_G10_G10_G001 [TF1_clones_scRNA-seq]


title: S1068_G10_G10_G001 [TF1_clones_scRNA-seq]


title: S1075_G10_G10_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [H10_Plate3]

description:
H10_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv

value: EpCAM+ CluGFP+


title: CluGFP+ [H11_Plate3]

description:
H11_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [H09_Plate3]

description:
H09_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [H08_Plate3]

description:
H08_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [H12_Plate3]

description:
H12_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [H07_Plate3]

description:
H07_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1065_G10_G10_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [H06_Plate3]

description:
H06_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1064_G10_G10_G001 [TF1_clones_scRNA-seq]


title: S1066_G10_G10_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [H04_Plate3]

description:
H04_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [H05_Plate3]

description:
H05_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [H02_Plate3]

description:
H02_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [A04_Plate4]

description:
A04_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1063_G10_G10_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [G12_Plate3]

description:
G12_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [H01_Plate3]

description:
H01_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [G11_Plate3]

description:
G11_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [G10_Plate3]

description:
G10_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1062_G10_G10_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [G09_Plate3]

description:
G09_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1067_G10_G10_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [G08_Plate3]

description:
G08_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1060_G10_G10_G001 [TF1_clones_scRNA-seq]


title: S1059_G10_G10_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [G04_Plate3]

description:
G04_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [G06_Plate3]

description:
G06_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [G07_Plate3]

description:
G07_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [G01_Plate3]

description:
G01_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [H03_Plate3]

description:
H03_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1058_G10_G10_G001 [TF1_clones_scRNA-seq]


title: S1057_G10_G10_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [G03_Plate3]

description:
G03_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [G05_Plate3]

description:
G05_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [F12_Plate3]

description:
F12_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [G02_Plate3]

description:
G02_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [F08_Plate3]

description:
F08_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [F07_Plate3]

description:
F07_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [F10_Plate3]

description:
F10_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1056_G10_G10_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [F11_Plate3]

description:
F11_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [F05_Plate3]

description:
F05_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1053_D6_D6_G001 [TF1_clones_scRNA-seq]


title: S1061_G10_G10_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [F03_Plate3]

description:
F03_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [F06_Plate3]

description:
F06_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1054_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [F02_Plate3]

description:
F02_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1051_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [F01_Plate3]

description:
F01_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [E11_Plate3]

description:
E11_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [E12_Plate3]

description:
E12_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [E09_Plate3]

description:
E09_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1050_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [F09_Plate3]

description:
F09_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [E07_Plate3]

description:
E07_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [E10_Plate3]

description:
E10_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [E08_Plate3]

description:
E08_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [E06_Plate3]

description:
E06_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1047_D6_D6_G001 [TF1_clones_scRNA-seq]


title: S1049_D6_D6_G001 [TF1_clones_scRNA-seq]


title: S1048_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [E03_Plate3]

description:
E03_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1046_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [F04_Plate3]

description:
F04_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [E02_Plate3]

description:
E02_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [E01_Plate3]

description:
E01_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1045_D6_D6_G001 [TF1_clones_scRNA-seq]


title: S1052_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [D10_Plate3]

description:
D10_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [D11_Plate3]

description:
D11_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1043_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [D09_Plate3]

description:
D09_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1042_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [E05_Plate3]

description:
E05_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [D08_Plate3]

description:
D08_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [D07_Plate3]

description:
D07_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [D06_Plate3]

description:
D06_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1041_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [D05_Plate3]

description:
D05_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1040_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [D02_Plate3]

description:
D02_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [D04_Plate3]

description:
D04_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [E04_Plate3]

description:
E04_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1039_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [D03_Plate3]

description:
D03_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [D01_Plate3]

description:
D01_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [C11_Plate3]

description:
C11_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1038_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [C12_Plate3]

description:
C12_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1037_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [C09_Plate3]

description:
C09_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [D12_Plate3]

description:
D12_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [C10_Plate3]

description:
C10_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [C08_Plate3]

description:
C08_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1036_D6_D6_G001 [TF1_clones_scRNA-seq]


title: S1044_D6_D6_G001 [TF1_clones_scRNA-seq]


title: S1055_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [C06_Plate3]

description:
C06_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1035_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [C05_Plate3]

description:
C05_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [C04_Plate3]

description:
C04_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [C01_Plate3]

description:
C01_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1033_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [C02_Plate3]

description:
C02_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [B09_Plate3]

description:
B09_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [B07_Plate3]

description:
B07_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1031_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [C03_Plate3]

description:
C03_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [B12_Plate3]

description:
B12_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1034_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [B11_Plate3]

description:
B11_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1030_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [B06_Plate3]

description:
B06_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1029_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [C07_Plate3]

description:
C07_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [B10_Plate3]

description:
B10_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [B05_Plate3]

description:
B05_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [B03_Plate3]

description:
B03_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1028_C9_C9_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [B02_Plate3]

description:
B02_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [A12_Plate3]

description:
A12_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [B04_Plate3]

description:
B04_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [B01_Plate3]

description:
B01_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1027_C9_C9_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [A11_Plate3]

description:
A11_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [A09_Plate3]

description:
A09_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [A10_Plate3]

description:
A10_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1025_C9_C9_G001 [TF1_clones_scRNA-seq]


title: S1032_D6_D6_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [A07_Plate3]

description:
A07_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1024_C9_C9_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [B08_Plate3]

description:
B08_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [A08_Plate3]

description:
A08_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [A06_Plate3]

description:
A06_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1023_C9_C9_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [A03_Plate3]

description:
A03_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [A04_Plate3]

description:
A04_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [A05_Plate3]

description:
A05_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP+ [A01_Plate3]

description:
A01_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1020_C9_C9_G001 [TF1_clones_scRNA-seq]


title: S1022_C9_C9_G001 [TF1_clones_scRNA-seq]


title: Crypts-Irradiated

data_processing:
Cellranger 2.0 is run on the FASTQ files to generate matrix
Data is read into Seurat with 1 minimum cell and 200 minimum genes and subsequently converted in scater for quality control and filtering based on lirary size, feature size and percentage of mitochondrial genes. Furthermore, normalization steps are performed and then the normalized data is transported back to Seurat. In Seurat, data is scaled and dimesion reduction, cluster identification, PCA and tSNE are performed.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix in .mtx format generated by cellranger filtered_bc_matrices, barcodes.tsv, genes.tsv
Supplementary_files_format_and_content: *_processed.csv: Comma-separated files contain normalized expression data from combined whole epithelium, crypts and 170 FACS sorted cells with in-depth sequencing.

extract_protocol:
To isolate single cells, whole epithelial segments or crypts were washed in PBS prior to adding fresh prewarmed Trypsin (Corning, USA) and incubated at 37°C for 50 minutes, with mixing every 20 minutes. Tissues were filtered through a 40 mm mesh cell strainer on ice and pelleted by centrifugation at 4°C and washed twice with ice cold regular medium to remove debris. A manually estimated 4500 single cells per sample were then subjected to 10X Genomics single cell RNA sequencing following manufacturer’s recommendations. Illumina HiSeq 3000 was used for deep sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: All epithelial cells

value: Whole body radiation (12 Gy)


title: Crypts-Normal


title: Whole Epithelium-Irradiated


title: S1026_C9_C9_G001 [TF1_clones_scRNA-seq]


title: Whole Epithelium-Normal


title: S1019_C9_C9_G001 [TF1_clones_scRNA-seq]


title: MSCATV-Exo-1: exosomes derived from ATV pretreated MSCs

city: Beijing

first: Peisen

last: Huang

state: Beijing

address: No.167 Bei Li Shi Road, Xicheng District

country: China

institute: Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Illumina RNA-seq was performed by the RiboBio Company (Guangzhou, China).
Quality assessment of the RNA-seq data was done using FASTX-Toolkit. Reads with >20% nucleotides with Phred quality scores <20 were removed from further analysis.
Quality-filtered reads were then aligned to the rat reference genome RGSC 6.0/rn6 using the TopHat2 aligner using default settings. Reads mapped to ribosomal RNA were removed by TopHat2. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi A, et al., Nat Methods. 2008.
GFOLD was used for ranking differentially expressed genes from RNA-seq data. Differential lncRNA expression analysis was performed using the method described by Audic S and Claverie JM., Genome Res. 1997. False discovery rate (FDR) (Benjamini Y and Hochberg Y., Journal of the Royal Statistical Society. 1995) was used to determine the p-value thresholds in multiple testing . Cutoff values of fold change >1.5 and Q value <0.001 were then used to select for differentially expressed genes between sample group comparisons.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files include RPKM values, gene type, chromosome, and strand information for each Sample.

source_name: bone-marrow derived MSCs

growth_protocol: Rat MSCs were isolated from bone marrow of 6–8 week old male SD rats. Rats were sacrificed by isoflurane inhalation and cervical dislocation. In brief, total bone marrow cells were flushed with culture medium from the femur and tibia and seeded in culture dishes containing Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 10% fetal bovine serum (FBS) and penicillin (100 U/mL)/streptomycin (100 mg/mL). Cells were incubated at 37°C in a humidified atmosphere containing 5% CO2. The first medium change was performed to remove the non-adherent cells at 24 hours. Fresh complete medium was added and replaced every 3 days. Each primary culture was sub-cultured 1:3 when MSCs grew to approximately 80% - 90% confluence. MSCs at Passages 3-4 were used.

extract_protocol:
A total of 200 ml of conditioned media of each sample was mixed with Ribo™ Exosome Isolation Reagent and exosomes isolation was performed according to the manufacturer's instructions (RiboBio, Guangzhou, China).Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).Total RNA from exosomes was used for library preparation and sequencing.
Library preparation and sequencing were performed at RiboBio.Briefly, RNA was fragmented to approximately 200 bp. Subsequently,the collected RNAs were subjected to first strand and second strand cDNA synthesis followed by adaptor ligation and enrichment with a low-cycle according to the instructions provided with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA). The purified library products were evaluated using the Agilent 2200 TapeStation (Agilent Technologies) and Qubit®2.0 (Life Technologies, USA)and then sequencing using a HiSeq30000.

treatment_protocol: For isolation of exosomes derived from MSCs, 10 15cm-dishes of MSCs were pretreated with 1 μmol/L ATV or same volume of DMSO in exosome-free IMDM for 48 h until collection of the conditioned medium. Cells and debris were removed by differential centrifugation at 300 g for 10 min, 2,000 g for 20 min respectively; and macrovesicles were removed at 13,500 g for 30 min. The supernatant continue to be ultracentrifuged at 120,000 g for 70 minutes to obtain the crude exosome pellet. The pellet was subsequently washed with phosphate buffered saline (PBS pH7.4) followed by repeat ultracentrifugation for 70 minutes at the same speed.

value: SD

tag: gender

value: male

tag: tissue

value: Mesenchymal stem cells (MSCs)

value: ATV (1μM)

tag: time

value: 24 hours

tag: sample type


title: MSC-Exo-1: exosomes derived from normal MSCs

value: exosomes derived from normal MSCs

value: DMSO (same volume of ATV)


title: MSC-Exo-2: exosomes derived from normal MSCs


title: S1016_C9_C9_G001 [TF1_clones_scRNA-seq]


title: S1017_C9_C9_G001 [TF1_clones_scRNA-seq]


title: CluGFP+ [A02_Plate3]

description:
A02_Plate3
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1014_C9_C9_G001 [TF1_clones_scRNA-seq]


title: S1013_C9_C9_G001 [TF1_clones_scRNA-seq]


title: S1021_C9_C9_G001 [TF1_clones_scRNA-seq]


title: MSCATV-Exo-2: exosomes derived from ATV pretreated MSCs


title: S1018_C9_C9_G001 [TF1_clones_scRNA-seq]


title: S1011_C9_C9_G001 [TF1_clones_scRNA-seq]


title: S1015_C9_C9_G001 [TF1_clones_scRNA-seq]


title: S1010_C9_C9_G001 [TF1_clones_scRNA-seq]


title: S1012_C9_C9_G001 [TF1_clones_scRNA-seq]


title: population_RNAseq [Mo7_GP2]

city: Heidelberg

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

country: Germany

institute: German Cancer Research Center

description:
Mo7_GP2
Gene_expression_matrix_population.xlsx

data_processing:
Basecalls performed using RTA 1.18.64
Before alignment, adapter sequences in raw reads were trimmed by Btrim64 (http://graphics.med.yale.edu/trim)
Trimmed reads were mapped to mouse genome (ENSEMBL) using STAR_2.4.0g1.
Expression level of each gene was quantified in unites by transcript per million (TPM) using RSEM rsem-1.2.18 with default parameters.
We developed custom R scripts based on FactoMineR library (http://factominer.free.fr/) performing PCA analysis on gene expression matrices.Hierarchical clustering was performed on cells and on the genes identified by PCA using Euclidean distance or correlation metric.
Genome_build: mm10
Supplementary_files_format_and_content: Gene_expression_matrices (TPM value) of each gene in each cells in CSV format and Gene_expression_matrix_population (TPM) of each gene in population in xlsx format

growth_protocol: C57BL/6 male mice of 2, 7 and 19 months of age were used. Male C57BL/6 mice were purchased from Janvier or bred in house at the DKFZ Center for Preclinical Research facility.  Animals were housed under standard conditions and fed ad libitum. All procedures were in accordance to the DKFZ guidelines and approved by the Regierungpräsidium Karlsruhe.

extract_protocol:
Animals were sacrificed by cervical dislocation and their brains immediately placed on ice. The lateral SVZ was microdissected as a whole mount as previously described. SVZs from 2 mice of 2 or 4 mice of 7 months of age were pulled per replicate. Single cell suspension was obtained using the Neural Tissue Dissociation kit with Trypsin (or Papain when staining for CD31+ and CDd11b+ cells) and Gentle MACS dissociator (Miltenyi) to maximize cell viability and recovery. Cells were stained for 20 minutes on ice in DPBS (without Ca and Mg) supplemented with 10% fetal calf serum. Combinations of the following antibodies were used: O4 APC-Cy7 (Miltenyi, 1:50), CD45 APC-Cy7 (BD, 1:200), GLAST(ACSA-1)-PE (Miltenyi, 1:20), Prom-APC, PSA-NCAM PE-Cy7 Miltenyi, 1:75), CD31-PE (BD, 1:100) and CD11b-APC (BD, 1:100). Sytox Blue (Life Technologies, 1/1000) was added to the cell suspension prior to sorting. Stained cell suspensions were sorted in a FACSAriaII (BD) using a 100um nozzle at 20psi. Cells were collected in ice-cold Neurobasal medium supplemented with L-Glutamine, B27 at a density of approx. 1cell/ul.  Immediately after sorting cells were manually picked with a thin gel-loading micropipette under continuous visual inspection in a Zeiss microscope. To ensure that only one cell was picked, we transferred sequentially 1ul of the cell suspension to the picking plate where a single cell was immediately picked in 0.3ul with another pipette before the addition of a new cell to the plate. Cells were directly transferred to ice-cold lysis buffer (0.2%Triton X-100 containing RNAse inhibitors, Clontech) and frozen at -80ºC until library preparation. For single cell RNA-seq, we sorted for CD45-O4-CD133+GLAST+, cells. Single NSCs were handpicked and libraries according to Smartseq2 were prepared. For Bulk sequencing we sorted 1000 events of different populations based on the following marker combinations: Endothelial CD45-CD31+, Microglia CD45+Cd11b+, NSCs CD45-CD133+GLAST+, Neuroblasts CD45-GLAST-PSA-NCAM+.
RNA-seq libraries were prepared using Smart-seq2 technology as previously described. Briefly, lysed cells were thawed and subject to reverse transcription using an oligo(dT) primer and a locked nucleic acid (LNA)-containing template-switching oligonucleotide (Exiqon). In a randomly selected set of samples we included ERCC Spike-Ins (Ambion) at a 1:1000000 dilution. Full-length cDNAs were amplified by 20 cycles of PCR using KAPA HiFi DNA polymerase (KAPA biosystems). Amplified cDNAs for every single cell were quantified and run on a High Sensitivity Bioanalyzer chip (Agilent). Samples containing no material or in which the cDNA appeared degraded were excluded (approx. 5-10%) from further processing. cDNAs were then converted into libraries for Illumina sequencing according to the Nextera XT Sample Preparation (Illumina) protocol with minor modifications. Specifically, we extended the tagmentation step to 8 minutes and performed a double cleanup with 0.8X AMPure XP SPRI beads (Agencourt) after PCR amplification for 9 cycles. To control for technical variability, we performed two replicate DNA libraries with cDNA from the same cell. For population studies, approx. 1ng of total RNA from 1000 cells was subject to SMARTer Ultra Low RNA kit (Clontech) according to the manufacturer’s instructions. cDNA products were quantified, run in a Bioanalyzer and subject to Illumina library preparation according to NEBNext Ultra DNA Library Preparation Kit (NEB). Libraries were quantified, pooled at equal concentrations and the multiplex was cleaned up again with 1X AMPure beads and measured in a Bioanalyzer prior to 101bp paired-end sequencing in an Illumina HiSeq 2000 or 3000.

tag: age

value: 7 MO

value: SVZ

value: Male


title: S1009_C9_C9_G001 [TF1_clones_scRNA-seq]


title: S1008_C9_C9_G001 [TF1_clones_scRNA-seq]


title: 2530

type: RNA

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: Chamber-exposed

hyb_protocol: The cRNA was hybridized to Affymetrix GeneChip Rat Genome 2.0 arrays using Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using GCS30007G scanner and Gene Chip Operating System software

data_processing: Raw CEL files were normalized using RMA in Expression Console v1.4

label: biotin

organism: Rattus norvegicus

source_name: midbrain

label_protocol: RNA was converted to single-stranded cDNA using Superscript II reverse transcriptase and the GeneChip T7 promoter primer kit (Affymetrix). The single-stranded cDNA was converted to double-stranded cDNA using DNA polymerase I, DNA ligase, and RNase H from Escherichia coli. Double-stranded cDNA was cleaned up and in vitro transcribed to biotin-labeled cRNA. 35-200-base fragments were generated by metal-induced hydrolysis and hybridized to Affymetrix Rat Genome 230 2.0 oligonucleotide arrays

extract_protocol: Total RNA was isolated from tissue using an RNeasy RNA Isolation kit (Qiagen, Valencia, CA)which included an on-column Dnase step. The integrity of isolated RNA was assessed by using a nanodrop spectrophotometer and an Agilent Bioanalyzer. RIN were between 8.5 and 10 for all samples.

treatment_protocol: Dissected midbrains were placed in RNase/DNase-free tubes and immediately flash-frozen on dry ice and maintained at -80 ºC until extraction

value: OVX ADX


title: 4123

description: Paced


title: 2541

description: Paced


title: S1006_C9_C9_G001 [TF1_clones_scRNA-seq]


title: 1954_4138_21718_Intact-6_Rat230+2

description: Chamber-exposed

value: proestruous


title: 1955_4139_21724_OVX-6_Rat230+2

description: Chamber-exposed

value: OVX


title: 4126

description: Chamber-exposed


title: 4125

description: Paced


title: 1955_4139_21720_OVX-2_Rat230+2

description: Chamber-exposed


title: 1955_4139_21719_OVX-1_Rat230+2

description: Paced


title: S1005_C9_C9_G001 [TF1_clones_scRNA-seq]

value: hematopoietic cell line


title: 4124

description: Chamber-exposed


title: population_RNAseq [Mo7_GP1]

description:
Mo7_GP1
Gene_expression_matrix_population.xlsx


title: 1955_4139_21722_OVX-4_Rat230+2

description: Chamber-exposed


title: 1954_4138_21717_Intact-5_Rat230+2

description: paced


title: 1955_4139_21721_OVX-3_Rat230+2

description: Paced


title: 1954_4138_21715_Intact-3_Rat230+2

description: paced


title: 1954_4138_21716_Intact-4_Rat230+2

description: Chamber-exposed


title: 2539

description: Chamber-exposed


title: 1954_4138_21713_Intact-1_Rat230+2

description: Paced


title: 1955_4139_21723_OVX-5_Rat230+2

description: Paced


title: 1954_4138_21714_Intact-2_Rat230+2

description: Chamber-exposed


title: 2531

description: paced


title: 2536

description: Chamber-exposed


title: S1007_C9_C9_G001 [TF1_clones_scRNA-seq]


title: S1004_C9_C9_G001 [TF1_clones_scRNA-seq]


title: S1002_C9_C9_G001 [TF1_clones_scRNA-seq]


title: S3003_G10_G10_G001 [TF1 clone RNA-seq]

data_processing:
RNA sequencing data was aligned to the human reference genome (GRCh37/hg19) using STAR using standard two-pass approach.
Gene were quantified using the STAR --quantMode GeneCounts flag over the Gencode v19 annotation.
Processed bams were genotyped for mitochondria using a custom python script.
All samples/libraries passed QC (none were filtered in downstream analyses)
Genome_build: hg19
Supplementary_files_format_and_content: Mitochondrial variants w/ heteroplasmy, coverage, and mean base quality for 3 clones for ATAC (mtDNA) and RNA (mtRNA)

extract_protocol:
Qiagen RLT lysis buffer
Smart-seq2

tag: clone id


title: S1001_C9_C9_G001 [TF1_clones_scRNA-seq]


title: S3001_C9_C9_G001 [TF1 clone RNA-seq]


title: S0069_mix2_mix_Gmix [TF1_clones_ATAC-seq]

library_source: genomic

data_processing:
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters. Paired-end reads were aligned to hg19 or mm10 using BOWTIE2 using the parameter –X2000 allowing fragments of up to 2 kb to align. Duplicates were removed using PICARD tools for reads uniquely mapping to the nuclear genome.
Reads were subsequently filtered for alignment quality of >Q20 and were required to be properly paired. We used MACS2 to call all  ATAC-seq peaks. MACS2 was used with the following parameters (--nomodel --nolambda --keep-dup all --call-summits). Peaks were filtered using the consensus excludable ENCODE blacklist (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/) and a custom blacklist, designed to remove high-signal causing repeats and mitochondrial homologues.
For all subsequent analysis we discarded peaks falling within these regions. Mitochondrial genotypes were inferred for each ATAC-seq sample using a custom python script.
All samples/libraries passed QC (none were filtered in downstream analyses)
Genome_build: hg19
Supplementary_files_format_and_content: Heteroplasmy estimations of high confidence variants for each of the TF1 libraries plus standard ATAC-seq peaks, counts in peaks, and mitochondrial QC statistics

molecule: genomic DNA

extract_protocol:
NP 40 lysis
ATAC-seq


title: S0068_mix1_mix_Gmix [TF1_clones_ATAC-seq]


title: S3002_D6_D6_G001 [TF1 clone RNA-seq]


title: single_cell_RNAseq [OGStr9]

description:
OGStr9
mRNA_with_poly_a_tail

growth_protocol: C57BL/6 male mice between 23 and 25 months of age were used for all experiments. Mice were purchased from Janvier. Animals were housed under standard conditions and fed ad libitum. All procedures were in accordance to the DKFZ guidelines and approved by the Regierungpräsidium Karlsruhe.

extract_protocol:
Animals were sacrificed by cervical dislocation and their brains immediately placed on ice. The lateral SVZ was microdissected as a whole mount as previously described. Pooled SVZ tissue (3-4 mice) was digested with trypsin and DNAse according to the Neural Tissue Dissociation kit in a Gentle MACS dissociatior (Miltenyi) to maximize cell viability and recovery. Cells were stained for 20 minutes on ice in DPBS (without Ca and Mg) supplemented with 10% fetal calf serum. Combinations of the following antibodies were used: APC and PE anti-GLAST (ACSA-1, Miltenyi, 1/40), APC anti O4 (Miltenyi, 1:40), PE-Vio770 anti PSA-NCAM (Miltenyi, 1/50), APC anti-Prominin-1 (eBioscience, 1/75), Alexa488::EGF (Life Technologies, 1/100), APC-Cy7 anti-CD45 (BD, 1/200). Sytox Blue (Life Technologies, 1/1000) was added to the cell suspension prior to sorting. Stained cell suspensions were sorted in a FACSAriaII (BD) using a 100um nozzle at 20psi. Cells were collected in ice-cold Neurobasal medium supplemented with L-Glutamine, B27 at a density of approx. 1cell/ul.  Str refers to GLASTpos CD45/O4neg cells from the striatum (SVZ was excluded). Str refers to GLASTpos CD45/O4neg from the somatosensory cortex. Immediately after sorting cells were manually picked with a thin gel-loading micropipette under continuous visual inspection in a Zeiss microscope. To ensure that only one cell was picked, we transferred sequentially 1ul of the cell suspension to the picking plate where a single cell was immediately picked in 0.3ul with another pipette before the addition of a new cell to the plate. Cells were directly transferred to ice-cold lysis buffer (0.2%Triton X-100 containing RNAse inhibitors, Clontech) and frozen at -80ºC until library preparation. Cells labeled as PSA, were sorted according to CD45negPSA-NCAMposGLASTneg; all the other cells were CD45negPSA-NCAMnegGLASTposPROM1pos.
RNA-seq libraries were prepared using Smart-seq2 technology as previously described. Briefly, lysed cells were thawed and subject to reverse transcription using an oligo(dT) primer and a locked nucleic acid (LNA)-containing template-switching oligonucleotide (Exiqon). In a randomly selected set of samples we included ERCC Spike-Ins (Ambion) at a 1:1000000 dilution. Full-length cDNAs were amplified by 20 cycles of PCR using KAPA HiFi DNA polymerase (KAPA biosystems). Amplified cDNAs for every single cell were quantified and run on a High Sensitivity Bioanalyzer chip (Agilent). Samples containing no material or in which the cDNA appeared degraded were excluded (approx. 5-10%) from further processing. cDNAs were then converted into libraries for Illumina sequencing according to the Nextera XT Sample Preparation (Illumina) protocol with minor modifications. Specifically, we extended the tagmentation step to 8 minutes and performed a double cleanup with 0.8X AMPure XP SPRI beads (Agencourt) after PCR amplification for 9 cycles. To control for technical variability we performed two replicate DNA libraries with cDNA from the same cell. For population studies, approx. 1ng of total RNA from 1000 cells was subject to SMARTer Ultra Low RNA kit (Clontech) according to the manufacturer’s instructions. cDNA products were quantified, run in a Bioanalyzer and subject to Illumina library preparation according to NEBNext  Ultra DNA Library Preparation Kit (NEB). Libraries were quantified, pooled at equal concentrations and the multiplex was cleaned up again with 1X AMPure beads and measured in a Bioanalyzer prior to 101bp paired-end sequencing in an Illumina HiSeq 2000.

value: 25 MO

value: Striatum


title: single_cell_RNAseq [OStr21]

description:
OStr21
mRNA_with_poly_a_tail


title: single_cell_RNAseq [OStr4]

description:
OStr4
mRNA_with_poly_a_tail


title: single_cell_RNAseq [OGStr8]

description:
OGStr8
mRNA_with_poly_a_tail


title: single_cell_RNAseq [OGStr30]

description:
OGStr30
mRNA_with_poly_a_tail


title: S0067_G11-B10-C11-C6-B8-E10-F9-F8_G11_G008 [TF1_clones_ATAC-seq]


title: Ezh1KO_Ezh2KO_SMARTSeq_rep1

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology

data_processing:
Sequencing reads were aligned to mouse reference genome using Bowtie with configuration -m 1
Duplicates reads were removed with picard
Peaks were called with MACS2 with the following configuration:  --nomodel and -p 1e-5
Peaks with pvalue >=10 were considered for further analyses
Genome_build: mm9
Supplementary_files_format_and_content: NarrowPeak files were generated with MACS2 (--nomodel and -p 1e-5)

source_name: mouse embrionic stem cell

extract_protocol:
1% formaldehyde cross-linked chromatin was sheared by sonication and the DNA fragments associated with the proteins of interest were selectively immunoprecipitated using specific antibodies
Libraries were prepared according to Blecher-Gonen R., et al. 2013 and sequenced on Illumina HiSeq 2000
Chip-Seq, ATAC-Seq, SMART-Seq

value: embryonic stem cell


title: Ezh2KO_SMARTSeq_rep2


title: WT_SMARTSeq_rep1


title: Ezh1KO_EZh2Y726D_SMARTSeq_rep2


title: Ezh2KO_SMARTSeq_rep1


title: Ezh1KO_Ezh2KO_SMARTSeq_rep2


title: WT_SMARTSeq_rep2


title: Ezh1KO_EZh2Y726D_SMARTSeq_rep1


title: S1003_C9_C9_G001 [TF1_clones_scRNA-seq]


title: 2543

description: Paced


title: Lef1-deficient CD4 T cells

city: Washington

first: Weiqun

last: Peng

state: DC

address: 1918 F Street, NW , DC

institute: The George Washington University

description: Used as control to generate 2052_Pvalue_-4_Lef1_peaks.bed file.

data_processing:
The sequencing quality of ChIP-Seq libraries was assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bowtie2 (v2.3.4.1, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm10 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
For ChIP-Seq libraries, MACS2 (v2.1.1, Zhang et al., Genome Biol) was used for peaks calling. We used the criteria of a P value of < 1E-4  as identified Lef1 binding peaks.
Genome_build: mm10
Supplementary_files_format_and_content: bed

source_name: all CD4 T cells

extract_protocol:
Conventional CD4+ T cells were sort-purified from WT C57BL/6 mice, and the Lef1-deficient CD4+ T cells were sorted from CD4-Cre+ Lef1 fl/fl mice. The cells were then fixed and sonicated to generate chromatin fragments, followed by immunoprecipitation with an anti-Lef1 antibody (C18A7, Cell Signaling Technology), which were then properly washed and immunoprecipitated DNA extracted.
The DNA segments from ChIP were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.

tag: genotype

value: Lef1 deficient

value: naive CD4 T cells

tag: cell phenotype

value: TCRb+, CD4+

tag: chip antibody


title: single_cell_RNAseq [OGStr29]

description:
OGStr29
mRNA_with_poly_a_tail


title: LY101-4B treated cells 2

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

institute: CRCHUL

description: MiaPaCa2 cells was analyzed after the LY101-4B treatment  50 µM for 24 h

hyb_protocol: Fifteen micrograms of fragmented cRNA were hybridized for 16 hrs at 45°C under constant rotation, using a mouse oligonucleotide array Genechip® Human Gene 1.0 ST Arrays . After hybridization, chips were processed using the Affymetrix GeneChip Fluidic Station 450 (protocol EukGE-WS2v5_450). Staining was made with streptavidin-conjugated phycoerythrin (SAPE, Molecular Probes), followed by amplification with a biotinylated anti17 streptavidin antibody (Vector Laboratories), and followed by a second round of SAPE.

scan_protocol: The arrays were scanned using the Affymetrix GCS 3000 7G and the Gene-Chip Operating Software (Affymetrix, Santa Clara, CA), to produce the intensity files. Microarray hybridization was carried out at the Microarrays Facility of the Research Center of Laval University CRCHUL.

data_processing: Background subtraction and normalization of probe set intensities were performed using the method of Robust Multiarray Analysis (RMA).

label: Biotin

source_name: MiaPaCa2 cells

label_protocol: For each sample, 400 ng of total RNA were labeled with the FlashTag Biotin HSR Labeling Kit (Affimetrix, Santa Clara, USA) and hybridized to the Genechip® Human Gene 1.0 ST Arrays  (Affymetrix).

growth_protocol: MiaPaCa2 cell lines were obtained from ATCC and maintained according to ATCC's recommendations. Briefly, cells were maintained in Dulbecco's Modified Eagle Medium (DMEM, Life Technologies, Inc., Gaithersburg, MD, USA) supplemented with 10% fetal calf serum. Cells were routinely grown in 50 ml flasks at 37°C in a humidified 5% CO2–95% air atmosphere.

extract_protocol: Total RNA was purified using TRIzol® Reagent (Gibco, Life Technologies) according to the manufacturer. RNA Integrity Number (RIN) was calculated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). RNA samples that reached a RIN over 8 were used for microarray hybridization (GeneChip; Affymetrix Inc., Santa Clara, CA).

treatment_protocol: MiaPaCa2 cells was treated with LY101-4D 25 µM, or vehicle, for 24 h.

tag: agent

value: 50 microM LY101-4B


title: Vehicle treated cells 1

description: MiaPaCa2 cells was analyzed after vehicle treatment for 24 h

value: vehicle


title: Vehicle treated cells 2


title: 2538

description: paced


title: LY101-4B treated cells 1


title: single_cell_RNAseq [OGStr28]

description:
OGStr28
mRNA_with_poly_a_tail


title: S0066_G11-B10-C11-C6-B8-E10-F9-C7_G11_G008 [TF1_clones_ATAC-seq]


title: S0065_G11-B10-C11-C6-B8-E10-F9_G11_G007 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [OGStr24]

description:
OGStr24
mRNA_with_poly_a_tail


title: single_cell_RNAseq [OGStr16]

description:
OGStr16
mRNA_with_poly_a_tail


title: single_cell_RNAseq [OGStr22]

description:
OGStr22
mRNA_with_poly_a_tail


title: 2526

description: Chamber-exposed


title: S0064_G11-B10-C11-C6-B8-E10-B10_G11_G007 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [OGStr13]

description:
OGStr13
mRNA_with_poly_a_tail


title: single_cell_RNAseq [OGStr15]

description:
OGStr15
mRNA_with_poly_a_tail


title: S0060_G11-B10-E10-E9-D9_G11_G005 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [OCx1]

description:
OCx1
mRNA_with_poly_a_tail

value: Cortex


title: S0063_G11-B10-C11-C6-B8-E10_G11_G006 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [OCx5]

description:
OCx5
mRNA_with_poly_a_tail


title: single_cell_RNAseq [OGStr1]

description:
OGStr1
mRNA_with_poly_a_tail


title: single_cell_RNAseq [OCx24]

description:
OCx24
mRNA_with_poly_a_tail


title: S0062_G11-B10-C11-C6-B8-D9_G11_G006 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [OCx19]

description:
OCx19
mRNA_with_poly_a_tail


title: S0059_G11-B10-C11-C6-G5_G11_G005 [TF1_clones_ATAC-seq]


title: CONT_SPERM_H2A.Z_Rep2

city: Atlanta

first: Yoonhee

last: Jung

state: Georgia

address: 615 Michael Street

department: Human Genetics

institute: Emory university

description: chormatin IP against H2A.Z

data_processing:
All libraries were sequenced using an Illumina Hiseq v4 sequencer and 50 bp paired-end format. Paired reads were aligned to mouse reference genome mm9 using Bowtie2 for ChIP-seq. Duplicates were removed using Samtools.  For generating wiggle files, we combined each replicates.
Genome_build: mm9

source_name: Sperm

extract_protocol:
For ChIP-seq of crosslink samples, sperm were crosslinked with 1% formaldehyde in 1x PBS for 10 min at RT, and the reaction was quenched with 125 mM glycine for 10 min at RT. After washing with PBS, crosslinked sperm were lysed with 5 mM PIPES, 85 mM KCl, 0.5% NP40 and 1x proteinase inhibitor on ice for 10 min. Then we performed a second fixation step by directly adding 1% formaldehyde to the lysis buffer on ice. After 10 min sperm were homogenized with a glass dounce homogenizer. Following quenching and washing, sperm cells were resuspended in RIPA buffer (1x PBS; 1% NP40; 0.5% sodium deoxycholate; 0.1% SDS; 1x proteinase inhibitor) and incubated on ice for 20 min. The purified sperm chromatin was sonicated to 300-1000 bp using a Diagenode Bioruptor at 25 cycles of 30 sec on and 30 sec off and the supernatant was collected. Immunoprecipitation was performed overnight at 4°C with antibodies. For ChIP-seq of Mnase samples, lysate was digested with Mnase and histone-DNA complexes were isolated with antibody.
Libraries for Illumina sequencing were constructed using the following standard protocol. The fragment end were repaired using the NEBNext End Repair Module, and adenosine was added at the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs). Precipitated DNA and input DNA were incubated with adaptors at room temperature for 1 hr with T4 DNA ligase (New England Biolabs) and amplified with Illumina primers.

tag: strain background

value: sperm

tag: chip-antibody

value: ab4174, Abcam


title: CONT_SPERM_H2A.Z_Rep1

description: chormatin IP against H2A.Z


title: CONT_SPERM_H3.3_Rep1

description: chormatin IP against H3.3

value: ab176840, Abcam


title: S0058_G11-B10-C11-C6-B8_G11_G005 [TF1_clones_ATAC-seq]


title: S0057_B3-B6-H5-D5-G6_B3_G005 [TF1_clones_ATAC-seq]


title: CONT_SPERM_AR_Rep1

description: chormatin IP against AR

value: sc-816, Santa Cruz


title: CONT_SPERM_AR_Rep2

description: chormatin IP against AR


title: CONT_SPERM_ERa_Rep1

description: chormatin IP against Era

value: sc-543, Santa Cruz


title: CONT_SPERM_ERa_Rep2

description: chormatin IP against ERa


title: S0056_B3-B6-H5-D5-C7_B3_G005 [TF1_clones_ATAC-seq]


title: CONT_SPERM_Foxa1_Rep1

description: chormatin IP against Foxa1

value: ab5089, Abcam


title: CONT_SPERM_ZNF143_Rep2

description: chormatin IP against ZNF143

value: 16618-1-AP, Proteintech


title: S0055_B3-B6-G6-C2-G4_B3_G005 [TF1_clones_ATAC-seq]

value: hematopoietic cell line


title: S0061_G11-B10-E10-E9-G9_G11_G005 [TF1_clones_ATAC-seq]


title: S0054_B3-B6-G6-C2-F4_B3_G005 [TF1_clones_ATAC-seq]


title: CONT_SPERM_ZNF143_Rep1

description: chormatin IP against ZNF143


title: CONT_SPERM_Med12_Rep2

description: chormatin IP against Med12

value: A300-774A, Bethyl laboratories


title: CONT_SPERM_Med12_Rep1

description: chormatin IP against Med12


title: S0052_G11-B10-E10-E9_G11_G004 [TF1_clones_ATAC-seq]


title: CONT_SPERM_Med12_Rep3

description: chormatin IP against Med12


title: S0053_G11-B10-E10-F9_G11_G004 [TF1_clones_ATAC-seq]


title: CONT_SPERM_RNAPIIS2p_Rep1

description: chormatin IP against RNAPIISer2p

value: ab5095, Abcam


title: S0051_G11-B10-C11-C7_G11_G004 [TF1_clones_ATAC-seq]


title: MOUSE_MII_ATACseq_Rep1

data_processing:
All libraries were sequenced using an Illumina Hiseq v4 sequencer and 50 bp paired-end format. Paired reads were aligned to mouse reference genome mm9, human reference genome hg19 and monkey reference genome rheMac8 using Bowtie2.  ATAC-seq reads were aligned using default parameters except -X 2000 -m 1. Duplicates were removed using Samtools.  To adjust for fragment size, we aligned all reads as + strands offset by +4 bp and – strands offset by -5 bp (Buenrostro et al. 2013). To separate nucleosome-free (THSS)  and  mono-nucleosome (Nucleosome) fragments, we chose reads 50-115 bp 180-247 bp in length, respectively. Mono-nucleosome reads were analyzed using DANPOS2 (Chen et al. 2013). MACS was used for peak calling with nucleosome-free reads (Liu 2014). For generating wiggle files, we combined each replicates.
Genome_build: mm9, hg19, rheMac8

extract_protocol:
After sperm cells were counted, the nuclei from 100,000 sperm were isolated with Lysis Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3mM MgCl2) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. Purified sperm nuclei pellet was then resuspended in the transposase reaction mix containing 0.05% digitonin and incubated for 30 min at 37°C. Following incubation, sperm were treated with Proteinase K at 55°C for 2 hr, and gDNA was isolated by phenol:chloroform:isoamyl alcohol and EtOH precipitation.
Library amplification was done with 2x KAPA HiFi mix and 1.25 µM indexed primers using the following PCR conditions: 72°C for 5 min; 98°C for 30 s; and 10-11 cycles at 98°C for 10 s, 63°C for 30 s, and 72°C for 1 min.

value: MII-stage oocyte


title: MOUSE_MII_ATACseq_Rep2


title: CONT_SPERM_RNAPIIS5p_Rep2

description: chormatin IP against RNAPIISer5p

value: ab5131, Abcam


title: CONT_SPERM_RNAPIIS5p_Rep1

description: chormatin IP against RNAPIISer5p


title: CONT_SPERM_RNAPIIS2p_Rep2

description: chormatin IP against RNAPIISer2p


title: MOUSE_GV_ATACseq_Rep2

value: GV-stage oocyte


title: CONT_SPERM_H3.3_Rep2

description: chormatin IP against H3.3


title: S0050_G11-B10-C11-C6_G11_G004 [TF1_clones_ATAC-seq]


title: MOUSE_SPERM_ATACseq_Rep1


title: MOUSE_SPERM_ATACseq_Rep2


title: MOUSE_GV_ATACseq_Rep1


title: S0049_D2-F7-E7-F9_D2_G004 [TF1_clones_ATAC-seq]


title: Ezh1KO_Ezh2KO-resEZH2Y731D_H3K27me3_ChipSeq

data_processing:
Sequencing reads were aligned to mouse reference genome mm9 using Bowtie with configuration -m 1
Duplicates reads were removed with picard
No peaks (heatmap only)
Genome_build: mm9

source_name: mouse embryonic stem cell

extract_protocol:
1% formaldehyde cross-linked chromatin was sheared by sonication and the DNA fragments associated with the proteins of interest were selectively immunoprecipitated using specific antibodies
Libraries were prepared according to Blecher-Gonen R., et al. 2013 and sequenced on Illumina HiSeq 2000

value: mouse embryonic stem cell

value: H3K27me3 (C36B11, Cell Signaling #9733)

tag: genotype/variation


title: E14_input

data_processing:
Sequencing reads were aligned to mouse reference genome mm9 using Bowtie with configuration -m 1
Duplicates reads were removed with picard
Genome_build: mm9


title: CONT_SPERM_Foxa1_Rep2

description: chormatin IP against Foxa1


title: S0048_D2-F7-E7-B10_D2_G004 [TF1_clones_ATAC-seq]

tag: cell type


title: Ezh1KO_Ezh2KO-resEZH2_H3K27me3_ChipSeq


title: S0046_B3-B6-H5-D5_B3_G004 [TF1_clones_ATAC-seq]


title: Ezh1KO_Ezh2KO-resEZH2_SUZ12_ChipSeq

value: SUZ12 (D39F6, Cell Signaling #3737)


title: S0045_B3-B6-G6-F2_B3_G004 [TF1_clones_ATAC-seq]


title: S0044_B3-B6-G6-C2_B3_G004 [TF1_clones_ATAC-seq]


title: Ezh1KO_EZh2Y726D_DMSO_H2AK119ub_ChipSeq

value: H2AK119ub (D27C4, Cell Signaling #8240)


title: EZh2Y726D_H3K27me3_ChipSeq

data_processing:
Sequencing reads were aligned to mouse reference genome mm9 using Bowtie with configuration -m 1
Duplicates reads were removed with picard
Peaks were called with MACS2 with the following configuration:  --nomodel and -p 1e-5
Genome_build: mm9


title: Ezh1KO_EZh2Y726D_MG132_SUZ12_ChipSeq


title: S0042_F4-E9-D10_F4_G003 [TF1_clones_ATAC-seq]


title: S0041_B5-C3-D3_B5_G003 [TF1_clones_ATAC-seq]


title: Ezh1KO_EZh2Y726D_MG132_H2AK119ub_ChipSeq


title: Ezh1KO_Ezh2KO_H3K27me3_ChipSeq


title: WT_H3K27ac_ChipSeq

value: H3K27ac (Abcam ab4729)

value: WT


title: EZh2Y726D_RING1B_ChipSeq

value: home made


title: Ezh1KO_Ezh2KO_RING1B_ChipSeq


title: Ezh2KO_RING1B_ChipSeq


title: S0039_B11-E8-G7_B11_G003 [TF1_clones_ATAC-seq]


title: S0040_B5-C3-C2_B5_G003 [TF1_clones_ATAC-seq]


title: Ezh1KO_Ezh2KO-resEZH2Y731D_SUZ12_ChipSeq


title: EZh2Y726D_SUZ12_ChipSeq


title: Ezh1KO_Ezh2KO_SUZ12_ChipSeq


title: S0038_B11-E8-B6_B11_G003 [TF1_clones_ATAC-seq]


title: WT_SUZ12_ChipSeq


title: WT_RING1B_ChipSeq


title: Ezh2KO_SUZ12_ChipSeq


title: WT_H3K27me3_ChipSeq


title: Ezh1KO_EZh2Y726D_DMSO_SUZ12_ChipSeq


title: S0043_F4-E9-F11_F4_G003 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp99]

description:
s_dot_ogp99
Gene_expression_matrix.csv

growth_protocol: C57BL/6 male mice of 2, 7, 23 and 25 months of age were used. Male C57BL/6 mice were purchased from Janvier or bred in house at the DKFZ Center for Preclinical Research facility.  Animals were housed under standard conditions and fed ad libitum. All procedures were in accordance to the DKFZ guidelines and approved by the Regierungpräsidium Karlsruhe.

extract_protocol:
Animals were sacrificed by cervical dislocation and their brains immediately placed on ice. The lateral SVZ was microdissected as a whole mount as previously described. SVZs from 2 mice of 2 or 4 mice of 22 months of age were pulled per replicate. Single cell suspension was obtained using the Neural Tissue Dissociation kit with Trypsin (or Papain when staining for CD31+ and CDd11b+ cells) and Gentle MACS dissociator (Miltenyi) to maximize cell viability and recovery. Cells were stained for 20 minutes on ice in DPBS (without Ca and Mg) supplemented with 10% fetal calf serum. Combinations of the following antibodies were used: O4 APC-Cy7 (Miltenyi, 1:50), CD45 APC-Cy7 (BD, 1:200), GLAST(ACSA-1)-PE (Miltenyi, 1:20), Prom-APC, PSA-NCAM PE-Cy7 Miltenyi, 1:75), CD31-PE (BD, 1:100) and CD11b-APC (BD, 1:100). Sytox Blue (Life Technologies, 1/1000) was added to the cell suspension prior to sorting. Stained cell suspensions were sorted in a FACSAriaII (BD) using a 100um nozzle at 20psi. Cells were collected in ice-cold Neurobasal medium supplemented with L-Glutamine, B27 at a density of approx. 1cell/ul.  Immediately after sorting cells were manually picked with a thin gel-loading micropipette under continuous visual inspection in a Zeiss microscope. To ensure that only one cell was picked, we transferred sequentially 1ul of the cell suspension to the picking plate where a single cell was immediately picked in 0.3ul with another pipette before the addition of a new cell to the plate. Cells were directly transferred to ice-cold lysis buffer (0.2%Triton X-100 containing RNAse inhibitors, Clontech) and frozen at -80ºC until library preparation. For single cell RNA-seq, we sorted for CD45-O4-CD133+GLAST+, cells. Single NSCs were handpicked and libraries according to Smartseq2 were prepared. For Bulk sequencing we sorted 1000 events of different populations based on the following marker combinations: Endothelial CD45-CD31+, Microglia CD45+Cd11b+, NSCs CD45-CD133+GLAST+, Neuroblasts CD45-GLAST-PSA-NCAM+.
RNA-seq libraries were prepared using Smart-seq2 technology as previously described. Briefly, lysed cells were thawed and subject to reverse transcription using an oligo(dT) primer and a locked nucleic acid (LNA)-containing template-switching oligonucleotide (Exiqon). In a randomly selected set of samples we included ERCC Spike-Ins (Ambion) at a 1:1000000 dilution. Full-length cDNAs were amplified by 20 cycles of PCR using KAPA HiFi DNA polymerase (KAPA biosystems). Amplified cDNAs for every single cell were quantified and run on a High Sensitivity Bioanalyzer chip (Agilent). Samples containing no material or in which the cDNA appeared degraded were excluded (approx. 5-10%) from further processing. cDNAs were then converted into libraries for Illumina sequencing according to the Nextera XT Sample Preparation (Illumina) protocol with minor modifications. Specifically, we extended the tagmentation step to 8 minutes and performed a double cleanup with 0.8X AMPure XP SPRI beads (Agencourt) after PCR amplification for 9 cycles. To control for technical variability, we performed two replicate DNA libraries with cDNA from the same cell. For population studies, approx. 1ng of total RNA from 1000 cells was subject to SMARTer Ultra Low RNA kit (Clontech) according to the manufacturer’s instructions. cDNA products were quantified, run in a Bioanalyzer and subject to Illumina library preparation according to NEBNext Ultra DNA Library Preparation Kit (NEB). Libraries were quantified, pooled at equal concentrations and the multiplex was cleaned up again with 1X AMPure beads and measured in a Bioanalyzer prior to 101bp paired-end sequencing in an Illumina HiSeq 2000 or 3000.

value: 23 MO

value: SVZ

value: Male


title: S0037_G11-B10-E10_G11_G003 [TF1_clones_ATAC-seq]


title: S0047_B3-B6-H5-E8_B3_G004 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp96]

description:
s_dot_ogp96
Gene_expression_matrix.csv


title: S0036_G11-B10-C11_G11_G003 [TF1_clones_ATAC-seq]


title: Ezh2KO_H3K27me3_ChipSeq


title: single_cell_RNAseq [s_dot_ogp92]

description:
s_dot_ogp92
Gene_expression_matrix.csv


title: S0034_D2-F7-E7_D2_G003 [TF1_clones_ATAC-seq]


title: S0033_B3-B6-H5_B3_G003 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp9]

description:
s_dot_ogp9
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp89]

description:
s_dot_ogp89
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp86]

description:
s_dot_ogp86
Gene_expression_matrix.csv


title: S0035_D2-F7-F9_D2_G003 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp83]

description:
s_dot_ogp83
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp81]

description:
s_dot_ogp81
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp80]

description:
s_dot_ogp80
Gene_expression_matrix.csv


title: S0029_D2-H9_D2_G002 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp82]

description:
s_dot_ogp82
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp7]

description:
s_dot_ogp7
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp77]

description:
s_dot_ogp77
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp75]

description:
s_dot_ogp75
Gene_expression_matrix.csv


title: S0031_G11-E10_G11_G002 [TF1_clones_ATAC-seq]


title: S0032_B3-B6-G6_B3_G003 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp71]

description:
s_dot_ogp71
Gene_expression_matrix.csv


title: S0028_D2-F7_D2_G002 [TF1_clones_ATAC-seq]


title: S0030_G11-B10_G11_G002 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp68]

description:
s_dot_ogp68
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp73]

description:
s_dot_ogp73
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp67]

description:
s_dot_ogp67
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp69]

description:
s_dot_ogp69
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp66]

description:
s_dot_ogp66
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp65]

description:
s_dot_ogp65
Gene_expression_matrix.csv


title: S0026_B3-B6_B3_G002 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp63]

description:
s_dot_ogp63
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp61]

description:
s_dot_ogp61
Gene_expression_matrix.csv


title: S0025_A9-D2_A9_G002 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp55]

description:
s_dot_ogp55
Gene_expression_matrix.csv


title: S0024_A9-B3_A9_G002 [TF1_clones_ATAC-seq]


title: S0027_B3-H5_B3_G002 [TF1_clones_ATAC-seq]


title: S0023_F4-G9_F4_G002 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp74]

description:
s_dot_ogp74
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp54]

description:
s_dot_ogp54
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp52]

description:
s_dot_ogp52
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp51]

description:
s_dot_ogp51
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp50]

description:
s_dot_ogp50
Gene_expression_matrix.csv


title: S0022_F4-E9_F4_G002 [TF1_clones_ATAC-seq]


title: S0021_B5-F2_B5_G002 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp48]

description:
s_dot_ogp48
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp94]

description:
s_dot_ogp94
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp47]

description:
s_dot_ogp47
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp5]

description:
s_dot_ogp5
Gene_expression_matrix.csv


title: S0020_B5-C3_B5_G002 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp64]

description:
s_dot_ogp64
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp45]

description:
s_dot_ogp45
Gene_expression_matrix.csv


title: S0019_B11-F6_B11_G002 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp46]

description:
s_dot_ogp46
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp43]

description:
s_dot_ogp43
Gene_expression_matrix.csv


title: S0018_B11-E8_B11_G002 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp41]

description:
s_dot_ogp41
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp40]

description:
s_dot_ogp40
Gene_expression_matrix.csv


title: S0017_G10_G10_G001 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp39]

description:
s_dot_ogp39
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp56]

description:
s_dot_ogp56
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp53]

description:
s_dot_ogp53
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp38]

description:
s_dot_ogp38
Gene_expression_matrix.csv


title: S0016_D6_D6_G001 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp37]

description:
s_dot_ogp37
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp35]

description:
s_dot_ogp35
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp36]

description:
s_dot_ogp36
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp34]

description:
s_dot_ogp34
Gene_expression_matrix.csv


title: S0014_D2_D2_G001 [TF1_clones_ATAC-seq]


title: S0012_C4_C4_G001 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp33]

description:
s_dot_ogp33
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp32]

description:
s_dot_ogp32
Gene_expression_matrix.csv


title: S0013_C10_C10_G001 [TF1_clones_ATAC-seq]


title: S0011_B9_B9_G001 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp3]

description:
s_dot_ogp3
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp31]

description:
s_dot_ogp31
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_95]

description:
s_dot_ogp2_dot_95
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_96]

description:
s_dot_ogp2_dot_96
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp4]

description:
s_dot_ogp4
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_90]

description:
s_dot_ogp2_dot_90
Gene_expression_matrix.csv


title: S0008_G11_G11_G001 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp2_dot_87]

description:
s_dot_ogp2_dot_87
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_84]

description:
s_dot_ogp2_dot_84
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_85]

description:
s_dot_ogp2_dot_85
Gene_expression_matrix.csv


title: S0015_C9_C9_G001 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp2_dot_9]

description:
s_dot_ogp2_dot_9
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_82]

description:
s_dot_ogp2_dot_82
Gene_expression_matrix.csv


title: S0006_D3_D3_G001 [TF1_clones_ATAC-seq]


title: S0009_B3_B3_G001 [TF1_clones_ATAC-seq]


title: S0007_F4_F4_G001 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp2_dot_80]

description:
s_dot_ogp2_dot_80
Gene_expression_matrix.csv


title: S0005_C7_C7_G001 [TF1_clones_ATAC-seq]


title: S0004_B11_B11_G001 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp2_dot_81]

description:
s_dot_ogp2_dot_81
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_8]

description:
s_dot_ogp2_dot_8
Gene_expression_matrix.csv


title: S0003_A9_A9_G001 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp2_dot_92]

description:
s_dot_ogp2_dot_92
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_83]

description:
s_dot_ogp2_dot_83
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_79]

description:
s_dot_ogp2_dot_79
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_74]

description:
s_dot_ogp2_dot_74
Gene_expression_matrix.csv


title: S0001_bulk1_bulk_G000 [TF1_clones_ATAC-seq]


title: S0002_bulk2_bulk_G000 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp2_dot_72]

description:
s_dot_ogp2_dot_72
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_70]

description:
s_dot_ogp2_dot_70
Gene_expression_matrix.csv


title: S0010_B5_B5_G001 [TF1_clones_ATAC-seq]


title: single_cell_RNAseq [s_dot_ogp2_dot_69]

description:
s_dot_ogp2_dot_69
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_7]

description:
s_dot_ogp2_dot_7
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_93]

description:
s_dot_ogp2_dot_93
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_67]

description:
s_dot_ogp2_dot_67
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_68]

description:
s_dot_ogp2_dot_68
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_66]

description:
s_dot_ogp2_dot_66
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_63]

description:
s_dot_ogp2_dot_63
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_59]

description:
s_dot_ogp2_dot_59
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_57]

description:
s_dot_ogp2_dot_57
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_73]

description:
s_dot_ogp2_dot_73
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_6]

description:
s_dot_ogp2_dot_6
Gene_expression_matrix.csv


title: SFN_rep1

city: Little Rock

first: Ravi

middle: W.

last: Sun

state: Arkansas

address: 4301 W Markham St

department: Department of Otolaryngology - Head and Neck Surgery

institute: University of Arkansas for Medical Sciences

data_processing:
The sequenced reads were quality checked using FastQC v0.11.7.
The adaptors and low-quality bases (Q < 20) were trimmed to a minimum of 35 base pairs using Trimmomatic v0.38.
Reads that passed quality control were aligned to the mouse mm10 reference genome (GCA_000001305.2) using TopHat 2.1.1 with the following parameters:  -p 10 --library-type=fr-firststrand --no-novel-juncs -G genes.gtf --transcriptome-index=transcriptome_data/known genome.
BAM files were imported into Blast2GO v5.0 and gene level expression counts quantified using htseq.
Genes with at least 1 CPM in a minimum of 3 libraries were retained for further analysis.
Filtered counts were TMM normalized and log2 transformed to correct for compositional bias.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file of gene level counts for each sample.

source_name: B16F10 melanoma cell line

growth_protocol: Mouse melanoma B16F10 cells were obtained from ATCC and maintained in Dulbecco's Modified Eagle Medium (DMEM) (ThermoFisher, Waltham, MA) supplied with 10% FBS (ThermoFisher, Waltham, MA) and 1% penicillin/streptomycin (ThermoFisher, Waltham, MA). Cells were checked for mycoplasma contamination and cultured at 2x10^5 cells per 10 cm dish until 90% confluent. Cells were further subcultured until ready for experiments.

extract_protocol:
RNA was extracted with the RNeasy Mini Kit (Qiagen Germantown, MD) following manufactural protocols and eluted in water. cDNA synthesis was performed with One Step iScript kit (BioRad Hercules, CA) following the manufacturer’s protocol.
For RNA-seq, the sequence library was prepared from 500 ng of total RNA using Illumina’s (San Diego, CA) TruSeq stranded mRNA Sample Preparation Kit v2 following the manufacturer’s protocol. Library fragment sizes were validated using a Fragment Analyzer and quantified by a Qubit fluorometer. Equal amounts of each library were pooled for sequencing on the NextSeq 500 platform using a high output flow cell to generate approximately 25 million 75bp SE reads per sample.

treatment_protocol:
IC50s for both drugs were determined by using CellTiter 96 AQueous One Solution Cell Proliferation kit (Promega, Madison WI ) followed the manufacturer’s protocols. In brief, cells were seeded at 1500 cells/well in a 96-well plate and were allowed to attach for 24 hours. They were then treated with 5-Aza-2′-deoxycytidine (DAC) (Sigma Aldrich, St. Louis, MO) at concentrations ranging from 6.1 nM to 25 µM for 72 hours, and sulforaphane (LKT labs, St Paul MN) at concentrations, ranging from 86 nm to 352 µM for 48 hours. Dimethyl sulfoxide (DMSO) (Sigma Aldrich, St. Louis, MO) was used in the control wells at 0.025%.
For all treatment assays, 6-well plates were seeded at 4x10^4 cells and were allowed to attach for 24 hours. For DAC single treatment, cells were treated with DAC at 25 nM for 72 hrs with a medium change at 24 hrs. For SFN single treatment, the cells were allowed to sit with no treatment for the first 24 hours after attached on the plate. They were then treated with SFN at 5 nM for another 48 hours. For combinational drug treatment, cells were treated with DAC at 25 nM for 24 hrs. The medium was removed, and fresh medium with 25 nM DAC and 5 µM SFN was added. Cells were then incubated for another 48 hrs. All cells were harvested at the end of 72 hrs for cell number counting, apoptosis, cell cycle, and RNA-seq analysis.

value: B16F10 melanoma cell line

tag: treatment

value: SFN


title: DAC_SFN_rep2

value: DAC + SFN


title: DAC_SFN_rep1


title: DAC_rep3

value: DAC


title: SFN_rep2


title: DAC_rep2


title: CON_rep3

value: DMSO control


title: single_cell_RNAseq [s_dot_ogp2_dot_54]

description:
s_dot_ogp2_dot_54
Gene_expression_matrix.csv

tag: strain


title: single_cell_RNAseq [s_dot_ogp2_dot_78]

description:
s_dot_ogp2_dot_78
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_55]

description:
s_dot_ogp2_dot_55
Gene_expression_matrix.csv


title: DAC_SFN_rep3

tag: cell line


title: DAC_rep1


title: MEFs_Alone

first: Jason

last: Moffat

state: ON

address: 686 Bay Street, Room 13.9705

department: Molecular Genetics

institute: University of Toronto

data_processing:
Sequencing was performed on an Illumina NextSeq 500 using 75 base pair single-end reads
Reads were trimmed to eliminate adaptor contamination using the Illumina bcl2fastq-conversion software (v2.20), and any reads shorter than 36bp after trimming were removed
Filtered reads were mapped to hg38/Gencode_v25 using STAR (v2.4.2a)
Filtered reads were also mapped to mm10/Gencode_vM12 using STAR (v2.4.2a)
Human and mouse BAM files were analyzed using XenofileR (v0.99.0) to remove contaminating mouse reads
Human filtered BAM files were summarized to read counts using HTSeq (v0.6.1)
Genome_build: hg38

source_name: mouse embryonic fibroblasts

growth_protocol: H1 cells (NIH code WA01, sex: male, RRID: CVCL_9771) were obtained from WiCell for research use. H1 wild-type and H1-iCas9 cells were maintained in one of two culture conditions:  “MEF culture” means culture on irradiated mouse embryonic fibroblasts (MEFs) in human embryonic stem cell (hESC) medium as described (Ditadi and Sturgeon, 2016). Briefly, hESC medium consists of DMEM/F12 (50:50; ThermoFisher) supplemented with 20% knockout serum replacement (KOSR) (Gibco), 1% penicillin/streptomycin (ThermoFisher), 2mM L-glutamine (ThermoFisher), 1% non-essential amino acids (NEAA) (ThermoFisher) and 55µM b-mercaptoethanol (Sigma). Immediately prior to use, hESC media was supplemented with 15ng/ml human basic fibroblast growth factor (hbFGF) (R&D Systems). Cells were passaged every 4-5 days using TrypLE Express (Gibco), and plated in presence of 10µM ROCK inhibitor Y-27632 (ROCKi) (Tocris) for 24 hours. Cells were cryopreserved in freezing media containing 50% hESC medium plus 40% FCS plus 10% DMSO. In feeder-free conditions, H1-iCas9 cells were maintained on tissue culture plates coated with recombinant human laminin at a concentration of 0.5mg/cm2 (rhLaminin-521, ThermoFisher; diluted in DPBS with Ca2+ and Mg2+, Gibco) or vitronectin at a concentration of 1.05mg/cm2 (STEMCELL, diluted in PBS) in mTeSR1 complete medium (STEMCELL). Cells were passaged every 4-5 days using ReLeSR enzyme-free dissociation reagent (STEMCELL) in the absence of ROCKi (only used for thawing and transduction), and cryopreserved in mFreSR medium (STEMCELL). H1 and H1-iCas9 cells were maintained in culture plates of 24-well to 10-cm size at individually optimized cell numbers. Growth media were changed daily with occasional “double-feeds” over two days. To generate the iCas9 targeting construct for the AAVS1 locus, humanized S. pyogenes Cas9 was amplified from pLCV2 (Addgene #52961) by PCR and, together with a BFP2 PCR product, was inserted into a target vector with AAVS1 homology arms (kindly provided by Ajamete Kaykas) via Gibson cloning (NEBuilder HiFi DNA Assembly Master Mix, NEB). The resulting all-in-one plasmid constitutively expresses the Tet-On 3G protein under a CAG promoter, and Cas9-P2A-BFP2 inducibly under a TRE3Gs promoter in the presence of doxycycline. Correct insertion into the AAVS1 locus yields expression of the promoterless P2A-Neomycin resistance gene fused to a splice acceptor site, resulting in cell survival upon G418 treatment.  The all-in-one plasmid was inserted into intron 1 of PPP1R12C (AAVS1 locus) of H1-hESCs by homologous recombination via co-electroporation (10-20ms, 1100/1200/1400V) with an AAVS1-targeting gRNA, similar to a previously described approach (González et al., 2014), and selected with 100µg/ml G418 for 7 days. AAVS1 T2 CRISPR in pX330 was a gift from Masato Kanemaki (Addgene plasmid #72833).  G418-resistant colonies were expanded for characterization. Sanger sequencing of clones that successfully underwent homologous recombination confirmed seamless integration of the construct at the 3’ and 5’ ends into the AAVS1 locus, and plasmid backbone-specific PCRs confirmed absence of random integration. Short tandem repeat (STR) profiles by PCR profiling of 9 regions plus Amelogenin for gender determination (GenePrint 10 System, Promega) and karyotype are consistent with parental H1 cells as determined by G-banding analysis of fixed cells. Sample preparation was performed as instructed (www.cuh.nhs.uk/sites/default/files/misc/ Tissue%20 Harvest%20Protocol%283%29.pdf) and karyotyping was performed by the Medical Genetics Service Cytogenics Laboratory, Cambridge, UK. STR profiling was performed at The Centre for Applied Genomics (TCAG) at the Hospital for Sick Children (SickKids), Toronto, Canada.

extract_protocol:
Transduced and untransduced H1-iCas9 cells were lysed on ice using RLT Plus buffer, and total RNA was extracted with the RNeasy Plus Mini Kit (Qiagen). Following lysis, supernatant was transferred to a QIAShredder spin column (Qiagen) and centrifuged at maximum speed for 2 minutes. The supernatant was transferred to RNeasy spin columns and on-column DNase digestion was performed using the RNase-Free DNase set (Qiagen). RNA extraction procedure was continued according to manufacturer’s instructions. Samples were stored at -80ºC prior to sequencing. Total RNA was quantified using Qubit RNA BR Assay fluorescent chemistry (ThermoFisher Scientific) and diluted to 1ng/µl. 1µL of the dilution stock was used to obtain RNA Integrity Number (RIN) using the Agilent Bioanalyzer RNA 6000 Pico kit (Agilent). Lowest RIN was 8.4, median RIN score was 9.7.
750ng per sample was processed according to Illumina TruSeq Stranded mRNA sample preparation protocol (Part # 15031047 Rev. E). 1µL top stock of each purified final library was run on an Agilent Bioanalyzer dsDNA High Sensitivity chip (Agilent). The libraries were quantified using Qubit dsDNA HS Assay Kit (ThermoFisher Scientific) and were pooled at equimolar ratios after size adjustment. The final pool was run on an Agilent Bioanalyzer dsDNA High Sensitivity chip and quantified using NEBNext Library Quant Kit for Illumina (NEB). The quantified pool was hybridized at a final concentration of 2.2pM and sequenced single-end on the Illumina NextSeq500 platform using high-output v2.5 75c chemistry.

treatment_protocol: gRNA transductions (DRICH1 = g15 and g16, AAVS = control) on MEF feeder cells were performed after induction with doxycycline (1.5µg/ml, Sigma) for 48 hours. Infected cells were selected with 0.5µg/ml puromycin (Sigma) for 48 hours. For gRNA experiments on laminin, H1-iCas9 cells were treated with doxycycline (1.5µg/ml, Sigma) 48 hours prior to infection with gRNAs. 24 hours prior to infection, cells were dissociated using ReLeSR and plated at optimized densities in 24-well plates in triplicate wells with 10µM ROCKi. Adherent doxycycline-treated cells were infected with target and control gRNAs with ROCKi. 24 hours post infection, mTeSR1 medium was replaced with fresh medium containing puromycin (0.5ug/ml) and cells were incubated for 48 hours. Cells were cultured on both MEFs and laminin until 4 days after infection (2 days after selection).

value: mouse embryonic fibroblasts


title: single_cell_RNAseq [s_dot_ogp2_dot_53]

description:
s_dot_ogp2_dot_53
Gene_expression_matrix.csv

tag: gender


title: single_cell_RNAseq [s_dot_ogp2_dot_50]

description:
s_dot_ogp2_dot_50
Gene_expression_matrix.csv

tag: tissue


title: single_cell_RNAseq [s_dot_ogp2_dot_52]

description:
s_dot_ogp2_dot_52
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_49]

description:
s_dot_ogp2_dot_49
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_5]

description:
s_dot_ogp2_dot_5
Gene_expression_matrix.csv


title: SFN_rep3


title: CON_rep1


title: CON_rep2


title: single_cell_RNAseq [s_dot_ogp2_dot_56]

description:
s_dot_ogp2_dot_56
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_47]

description:
s_dot_ogp2_dot_47
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_48]

description:
s_dot_ogp2_dot_48
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_46]

description:
s_dot_ogp2_dot_46
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_43]

description:
s_dot_ogp2_dot_43
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_39]

description:
s_dot_ogp2_dot_39
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_40]

description:
s_dot_ogp2_dot_40
Gene_expression_matrix.csv


title: Ezh1KO_EZh2Y726D_ATACSeq_R1

value: embryonic stem cell


title: Ezh2KO_ATACSeq_R1


title: Ezh1KOEzh2R685C_Suz12_ChipSeq


title: WT_ATACSeq_R1


title: single_cell_RNAseq [s_dot_ogp2_dot_38]

description:
s_dot_ogp2_dot_38
Gene_expression_matrix.csv


title: Ezh1KO_Ezh2KO_ATACSeq_R1


title: Yolk Sac Rep1

city: Philadelphia

first: Katherine

middle: Ann

last: Alexander

state: PA

address: 3400 Civic Center Blvd.

institute: University of Pennsylvania

data_processing:
library strategy: Precision nuclear run-on sequencing (PRO-Seq)
Adaptor sequences were removed using fastx_clipper
PCR duplicates were removed and reads collapsed using fastx_collapser
8pb barcode was removed using fastx_trimmer
The reverse complement was obtained using fastx_referse_complement
Reads were then aligned using bowtie2 using --sensitive-local
Genome_build: mm10
Supplementary_files_format_and_content: dREG_* files are bed files with the coordinants of peaks called by dREG software (https://github.com/Danko-Lab/dREG)
Supplementary_files_format_and_content: bedgraph files of the minus (mn) and plus (pl) strands were made using genomeCoverageBed, and normallized to reads per million (RPM)

source_name: PRO-seq_Yolk Sac

extract_protocol:
Liver and yolk sac were dissected from E14.5 embryos and flash frozen. Livers or yolk sac were pooled from 6 different embryos and smashed into a fine powder in liquid nitrogen using a tissue smasher. Chromatin was then isolated and flash frozen in Storage buffer (as described in Nature Protocols volume 11, pages 1455–1476 (2016))
Libraries were prepared as in Nature Protocols volume 11, pages 1455–1476 (2016), starting with Nuclear Run-On from isolated chromatin in Storage Buffer

value: Mixed C57BL/6h and CAST/EiJ

tag: developmental stage

value: Embryonic Day E14.5

tag: # pooled

value: Yolk Sac

tag: molecule subtype

value: nascentRNA


title: single_cell_RNAseq [s_dot_ogp2_dot_35]

description:
s_dot_ogp2_dot_35
Gene_expression_matrix.csv

tag: age


title: single_cell_RNAseq [s_dot_ogp2_dot_33]

description:
s_dot_ogp2_dot_33
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_37]

description:
s_dot_ogp2_dot_37
Gene_expression_matrix.csv


title: Ezh2KO_H3K27ac_ChipSeq

value: H3K27ac (Abcam ab4729)


title: single_cell_RNAseq [s_dot_ogp2_dot_31]

description:
s_dot_ogp2_dot_31
Gene_expression_matrix.csv


title: BAF170 KO CM rep5

city: San Francisco

first: Benoit

last: Bruneau

state: CA

address: 1650 Owens Street

institute: Gladstone Institute of Cardiovascular Disease

data_processing:
bigwig files
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files

source_name: cardiac myocyte

growth_protocol: Es cell were differentiated following Katman et al., 2011 and Wamstad et al., 2012 papers

extract_protocol:
We followed Corces et al., 2017 paper to perform ATACSeq
Lysed nuclei were tagmented at 37C for 45 mins for CPs and 3hrs for CMs, before purified and PCR amplified with Ad1 and Ad2 primers (corces et al., 2017)

treatment_protocol: ES cells were differentiated to cardiac precursor or cardiomyocytes before harvested for ATACseq

tag: genotype

value: BRG1-3XFLAG; BAF170 KO

value: ES cell derived cardiac myocyte


title: single_cell_RNAseq [s_dot_ogp2_dot_34]

description:
s_dot_ogp2_dot_34
Gene_expression_matrix.csv

value: 23 MO


title: single_cell_RNAseq [s_dot_ogp2_dot_44]

description:
s_dot_ogp2_dot_44
Gene_expression_matrix.csv

value: SVZ


title: BAF170 KO CM rep4


title: single_cell_RNAseq [s_dot_ogp2_dot_30]

description:
s_dot_ogp2_dot_30
Gene_expression_matrix.csv

value: Male


title: single_cell_RNAseq [s_dot_ogp2_dot_41]

description:
s_dot_ogp2_dot_41
Gene_expression_matrix.csv


title: BAF170 KO CM rep3


title: Ezh1KOEzh2KO_H3K27ac_ChipSeq


title: Ezh1KOEzh2R685C_H3K27ac_ChipSeq


title: single_cell_RNAseq [s_dot_ogp2_dot_3]

description:
s_dot_ogp2_dot_3
Gene_expression_matrix.csv


title: Liver Rep2

value: Liver


title: single_cell_RNAseq [s_dot_ogp2_dot_29]

description:
s_dot_ogp2_dot_29
Gene_expression_matrix.csv


title: Ezh1KOEzh2Y726D_H3K27ac_ChipSeq


title: single_cell_RNAseq [s_dot_ogp2_dot_36]

description:
s_dot_ogp2_dot_36
Gene_expression_matrix.csv


title: Liver Rep1


title: BAF170 KO CM rep2


title: Yolk Sac Rep2


title: BAF170 KO CM rep1


title: Ezh1KOEzh2R685C_H3K27me3_ChipSeq

value: H3K27me3 (C36B11, Cell Signaling #9733)


title: single_cell_RNAseq [s_dot_ogp2_dot_24]

description:
s_dot_ogp2_dot_24
Gene_expression_matrix.csv


title: BAF60 KO CM rep3

value: BRG1-3XFLAG; BAF60c KO


title: BAF60 KO CM rep2


title: single_cell_RNAseq [s_dot_ogp2_dot_25]

description:
s_dot_ogp2_dot_25
Gene_expression_matrix.csv


title: Ezh1KOEzh2Y726D_H3K27me2_ChipSeq

value: H3K27me2 (Cell Signaling #9728)


title: single_cell_RNAseq [s_dot_ogp2_dot_22]

description:
s_dot_ogp2_dot_22
Gene_expression_matrix.csv


title: Ezh1KOEzh2KO_H3K27me2_ChipSeq


title: single_cell_RNAseq [s_dot_ogp2_dot_21]

description:
s_dot_ogp2_dot_21
Gene_expression_matrix.csv


title: WT CM rep4


title: Ezh2KO_H3K27me2_ChipSeq


title: single_cell_RNAseq [s_dot_ogp2_dot_2]

description:
s_dot_ogp2_dot_2
Gene_expression_matrix.csv


title: AAB-N-C071

first: James

middle: C

last: Chen

state: NEW YORK

address: 1130 St Nicholas Ave

department: Systems Biology

institute: Columbia University

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming.
We map the reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm10) using STAR(2.5.2b) and featureCounts(v1.5.0-p3).
We test for differentially expressed genes under various conditions using DEseq. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Genome_build: (Human: NCBI/build37.2; Mouse: UCSC/mm10)
Supplementary_files_format_and_content: tab-delimited, FPKM

source_name: Scalp Skin

extract_protocol:
Trizol RNA extraction, manufacturer protocols
Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2500/HiSeq4000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 280-400 million reads for the whole lane.

treatment_protocol: Scalp biopsy sites were anesthatized with 1% lidocaine with epinephrine, and a 4 milimeter punch was used to incise the biopsy area. The skin sample was then extracted from the scalp using nontramautic forceps and surgical cissors.

tag: patient status

value: Normal Control


title: WT CM rep3


title: E14_H3K27me2_ChipSeq

tag: chip antibody


title: single_cell_RNAseq [s_dot_ogp2_dot_19]

description:
s_dot_ogp2_dot_19
Gene_expression_matrix.csv

data_processing:
Basecalls performed using RTA 1.18.64
Before alignment, adapter sequences in raw reads were trimmed by Btrim64 (http://graphics.med.yale.edu/trim)
Trimmed reads were mapped to mouse genome (ENSEMBL) using STAR_2.4.0g1.
Expression level of each gene was quantified in unites by transcript per million (TPM) using RSEM rsem-1.2.18 with default parameters.
We developed custom R scripts based on FactoMineR library (http://factominer.free.fr/) performing PCA analysis on gene expression matrices.Hierarchical clustering was performed on cells and on the genes identified by PCA using Euclidean distance or correlation metric.
Genome_build: mm10
Supplementary_files_format_and_content: Gene_expression_matrices (TPM value) of each gene in each cells in CSV format and Gene_expression_matrix_population (TPM) of each gene in population in xlsx format


title: Ezh1KOEzh2KO-reshEzh1_HA_ChipSeq

value: anti-HA home made


title: Ezh1KOEzh2KO_HA_ChipSeq

value: embryonic stem cell


title: WT CM rep1


title: AAB-N-C151- 1


title: single_cell_RNAseq [s_dot_ogp2_dot_18]

description:
s_dot_ogp2_dot_18
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp2_dot_17]

description:
s_dot_ogp2_dot_17
Gene_expression_matrix.csv


title: AAB-N-C069


title: WT CM rep2


title: Ezh1KOEzh2Y726D_H3K27me1_ChipSeq

value: H3K27me1 (Active Motif #61015)


title: AAB-N-C150- 1


title: BAF60 KO CM rep1


title: Ezh1KOEzh2KO_H3K27me1_ChipSeq


title: BAF170 KO CP rep1

source_name: cardiac progenitor

value: Es cell derived cardiac progenitor


title: AAB-N-C149- 1


title: BAF170 KO CP rep2


title: BAF60 KO CP rep2


title: single_cell_RNAseq [s_dot_ogp2_dot_11]

description:
s_dot_ogp2_dot_11
Gene_expression_matrix.csv


title: E14_H3K27me1_ChipSeq


title: T12-24

value: AA 24wks treatment


title: Ezh2KO_H3K27me1_ChipSeq


title: single_cell_RNAseq [s_dot_ogp2_dot_15]

description:
s_dot_ogp2_dot_15
Gene_expression_matrix.csv


title: T12-00

value: AA Pre treatment


title: BAF60 KO CP rep1


title: single_cell_RNAseq [s_dot_ogp28]

description:
s_dot_ogp28
Gene_expression_matrix.csv


title: T11-24


title: AAB-N-C070


title: WT CP Rep2


title: single_cell_RNAseq [s_dot_ogp27]

description:
s_dot_ogp27
Gene_expression_matrix.csv


title: WT CP rep1


title: T11-00


title: T10-00


title: T10-24


title: T09-00

value: AA pre treatment


title: T09-24


title: single_cell_RNAseq [s_dot_ogp22]

description:
s_dot_ogp22
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp21]

description:
s_dot_ogp21
Gene_expression_matrix.csv


title: sgNT_C

first: Elizabeth

middle: A

last: White

address: 3610 Hamilton Walk, 203C Johnson Pavilion, Mail Code 6114

department: Otorhinolaryngology

data_processing:
Raw image data file from high-throughput sequencing was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Sequenced reads were filtered to remove adapters and low-quality reads
Clean reads were mapped to hg19 using STAR (v2.5). STAR used  the method of Maximal Mappable Prefix (MMP).
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between conditions/groups was performed using the DESeq2 R package (2_1.6.3).
Genome_build: hg19
Supplementary_files_format_and_content: gene expression quantification table, calculated all genes' FPKM

molecule: polyA RNA

source_name: G5-Ep primary human forekin keratinocyte

growth_protocol: Primary human keratinocytes stably harboring retroviral expression vectors were grown to 30% confluence in keratinocyte serum-free medium with 0.5 ug/ml puromycin

extract_protocol:
RNA was isolated with Qiagen RNeasy mini kit in White Laboratory and polyA RNA was isolates using oligo dT beads at Novogene Corporation
RNA libraries were prepared for sequencing using standard Illumina protocols at Novogene Corporation

tag: retrovirus

value: Transduced with LentiCRISPRv2-sgNT-2

value: Primary human foreskin keratinocytes selected with puromycin post retroviral transduction


title: sgP14_A


title: single_cell_RNAseq [s_dot_ogp20]

description:
s_dot_ogp20
Gene_expression_matrix.csv

value: 23 MO


title: sgP14_B


title: T07-24


title: sgNT_B


title: T07-00


title: single_cell_RNAseq [s_dot_ogp19]

description:
s_dot_ogp19
Gene_expression_matrix.csv

value: SVZ


title: sgNT_A


title: T05-36

value: AA 36wks treatment


title: DLYC_C

value: Tranduced with HPV16 E7 ∆21-24 retrovirus (MSCV-IP N-HA 16E7 ∆21-24, also known as ∆DLYC)


title: single_cell_RNAseq [s_dot_ogp15]

description:
s_dot_ogp15
Gene_expression_matrix.csv

value: Male


title: single_cell_RNAseq [s_dot_ogp12]

description:
s_dot_ogp12
Gene_expression_matrix.csv


title: DLYC_B


title: single_cell_RNAseq [s_dot_ogp111]

description:
s_dot_ogp111
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp25]

description:
s_dot_ogp25
Gene_expression_matrix.csv


title: E10K_C

value: Tranduced with HPV16 E7 E10K retrovirus (MSCV-IP N-HA 16E7 E10K)


title: single_cell_RNAseq [s_dot_ogp110]

description:
s_dot_ogp110
Gene_expression_matrix.csv


title: E10K_B


title: T05-00


title: single_cell_RNAseq [s_dot_ogp109]

description:
s_dot_ogp109
Gene_expression_matrix.csv


title: E10K_A


title: single_cell_RNAseq [s_dot_ogp106]

description:
s_dot_ogp106
Gene_expression_matrix.csv


title: 16E7_C

value: Tranduced with HPV16 E7 retrovirus (MSCV-IP N-HA 16E7)