title: E7.5_Plate4_E2 (scBS-Seq)


title: E7.5_Plate4_E1 (scBS-Seq)

status: Public on Sep 30 2019

type: SRA

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: genomic

data_processing:
Libraries were sequenced on the Illumina Nextseq 500 platform using the default RTA analysis software.
BS-seq libraries were aligned to the bisuflite converted GRCm38 mouse genome using Bismark (v0.19.1) in single-end nondirectional mode. Following the removal of PCR duplicates, we retained a mean of 1.6 million reads per cell. Methylation calling and separation of endogenous methylation (from A-C-G and T-C-G trinucleotides) and chromatin accessibility (G-C-A, G-C-C and G-C-T trinucleotides) was performed with Bismark using the --NOMe option of the coverage2cytosine script.
Following our previous approach, individual CpG or GpC sites in each cell were modelled using a binomial distribution where the number of successes is the number of reads that support methylation and the number of trials is the total number of reads. A CpG methylation or GpC accessibility rate for each site and cell was calculated by maximum likelihood. The rates were subsequently rounded to the nearest integer (0 or 1).
Genome_build: GRCm38
Supplementary_files_format_and_content: [Accessibility file]  A table of format  <chromosome><position><methylated_reads><nonmethylated_reads><binary_accessibility_status>
Supplementary_files_format_and_content: [Methylation file]  A table of format  <chromosome><position><methylated_reads><nonmethylated_reads><binary_methylation_status>

molecule: genomic DNA

organism: Mus musculus

source_name: Early embryo

extract_protocol: Single-cells were sorted either manually (E4.5, E5.5) or using flow cytometry (E6.5, E7.5) into 96 well PCR plates containing 2.5μl of methylase reaction buffer (1 × M.CviPI Reaction buffer (NEB), 2 U M.CviPI (NEB), 160 μM S-adenosylmethionine (NEB), 1 U μl−1 RNasein (Promega), 0.1% IGEPAL (Sigma)). Samples were incubated for 15 minutes at 37°C to methylate accessible chromatin before the reaction was stopped with the addition of RLT plus buffer (Qiagen) and samples frozen down and stored at -80°C prior to processing. Poly-A RNA was captured on oligo-dT conjugated to magnetic beads and amplified cDNA was prepared according to the G&T-seq and Smartseq2 protocols. The lysate containing gDNA was purified on AMPureXP beads before bisulfite-seq libraries were prepared according to the scBS-seq protocol.

tag: strain

tag: developmental stage

tag: sample type

value: single cell


title: E7.5_Plate4_E12 (scBS-Seq)


title: E7.5_Plate4_F2 (scBS-Seq)


title: E7.5_Plate4_E10 (scBS-Seq)


title: E7.5_Plate4_D8 (scBS-Seq)


title: E7.5_Plate4_D7 (scBS-Seq)


title: E7.5_Plate4_D9 (scBS-Seq)


title: E7.5_Plate4_E11 (scBS-Seq)


title: E7.5_Plate4_D4 (scBS-Seq)


title: E7.5_Plate4_D2 (scBS-Seq)


title: E7.5_Plate4_D5 (scBS-Seq)


title: E7.5_Plate4_C8 (scBS-Seq)


title: E7.5_Plate4_D11 (scBS-Seq)


title: E7.5_Plate4_C9 (scBS-Seq)


title: E7.5_Plate4_D12 (scBS-Seq)


title: E7.5_Plate4_D10 (scBS-Seq)


title: E7.5_Plate4_D1 (scBS-Seq)


title: E7.5_Plate4_C7 (scBS-Seq)


title: E7.5_Plate4_C6 (scBS-Seq)


title: E7.5_Plate4_C5 (scBS-Seq)


title: E7.5_Plate4_F7 (scBS-Seq)


title: E7.5_Plate4_C4 (scBS-Seq)


title: E7.5_Plate4_C2 (scBS-Seq)


title: E7.5_Plate4_C11 (scBS-Seq)


title: E7.5_Plate4_C1 (scBS-Seq)


title: E7.5_Plate4_C12 (scBS-Seq)


title: E7.5_Plate4_D3 (scBS-Seq)


title: E7.5_Plate4_C10 (scBS-Seq)


title: E7.5_Plate4_B7 (scBS-Seq)


title: E7.5_Plate4_B9 (scBS-Seq)


title: E7.5_Plate4_B6 (scBS-Seq)


title: E7.5_Plate4_B8 (scBS-Seq)


title: E7.5_Plate4_E9 (scBS-Seq)


title: E7.5_Plate4_D6 (scBS-Seq)


title: E7.5_Plate4_B5 (scBS-Seq)


title: E7.5_Plate4_F4 (scBS-Seq)


title: E7.5_Plate4_B2 (scBS-Seq)


title: E7.5_Plate4_B12 (scBS-Seq)


title: E7.5_Plate4_B4 (scBS-Seq)


title: E7.5_Plate4_B3 (scBS-Seq)


title: E7.5_Plate4_C3 (scBS-Seq)


title: WT-ctx-1

city: Lexington

first: Hualin

last: Xi

state: Massachusetts

address: 34 webb st

country: USA

institute: AbbVie

library_source: transcriptomic

data_processing:
aligned to hg19 reference genome using STAR v2.4
count uniquely aligned reads per gene using FeatureCount from Subread package and gencode v19 as the gene model annotation

molecule: total RNA

source_name: Frontal Cortex

extract_protocol:
3-month-old GFAP-IL6 homozygous or wild-type mice were euthanized by cervical dislocation followed by decapitation. Frontal cortex was dissected and snap-frozen in RNAse-free tubes on dry ice. Total RNA was isolated by Trizol-chloroform extraction, followed by RNeasy clean-up.
Illumina TruSeq mRNA library preparation

tag: tissue

value: Frontal Cortex

tag: age

value: 3 month post-natal

tag: genotype

value: WT


title: E7.5_Plate4_B1 (scBS-Seq)


title: E7.5_Plate4_A8 (scBS-Seq)


title: E7.5_Plate4_B11 (scBS-Seq)


title: E7.5_Plate4_B10 (scBS-Seq)


title: E7.5_Plate4_A9 (scBS-Seq)


title: E7.5_Plate4_A7 (scBS-Seq)


title: E7.5_Plate4_A6 (scBS-Seq)


title: E7.5_Plate4_A5 (scBS-Seq)


title: E7.5_Plate4_A4 (scBS-Seq)


title: E7.5_Plate4_A11 (scBS-Seq)


title: E7.5_Plate3_H8 (scBS-Seq)


title: E7.5_Plate4_A12 (scBS-Seq)


title: E7.5_Plate4_A2 (scBS-Seq)


title: E7.5_Plate3_H5 (scBS-Seq)


title: E7.5_Plate4_A1 (scBS-Seq)


title: E7.5_Plate3_H9 (scBS-Seq)


title: E7.5_Plate3_H3 (scBS-Seq)


title: E7.5_Plate3_H4 (scBS-Seq)


title: E7.5_Plate3_H2 (scBS-Seq)


title: E7.5_Plate3_H7 (scBS-Seq)


title: E7.5_Plate4_A10 (scBS-Seq)


title: E7.5_Plate3_H12 (scBS-Seq)


title: E7.5_Plate3_H6 (scBS-Seq)


title: E7.5_Plate3_H1 (scBS-Seq)


title: E7.5_Plate4_A3 (scBS-Seq)


title: E7.5_Plate3_H11 (scBS-Seq)


title: E7.5_Plate3_G8 (scBS-Seq)


title: E7.5_Plate3_G5 (scBS-Seq)


title: E7.5_Plate3_H10 (scBS-Seq)


title: E7.5_Plate3_G9 (scBS-Seq)


title: E7.5_Plate3_G4 (scBS-Seq)


title: E7.5_Plate3_G6 (scBS-Seq)


title: E7.5_Plate3_G1 (scBS-Seq)


title: E7.5_Plate3_G3 (scBS-Seq)


title: E7.5_Plate3_G2 (scBS-Seq)


title: E7.5_Plate3_G11 (scBS-Seq)


title: E7.5_Plate3_G10 (scBS-Seq)


title: E7.5_Plate3_G7 (scBS-Seq)


title: E7.5_Plate3_F6 (scBS-Seq)


title: E7.5_Plate3_F7 (scBS-Seq)


title: E7.5_Plate3_F8 (scBS-Seq)


title: E7.5_Plate4_E3 (scBS-Seq)


title: E7.5_Plate3_F5 (scBS-Seq)


title: E7.5_Plate3_F3 (scBS-Seq)


title: E7.5_Plate3_F1 (scBS-Seq)


title: E7.5_Plate3_F2 (scBS-Seq)


title: E7.5_Plate3_F4 (scBS-Seq)


title: E7.5_Plate3_E8 (scBS-Seq)


title: E7.5_Plate3_E6 (scBS-Seq)


title: E7.5_Plate3_E3 (scBS-Seq)


title: E7.5_Plate3_E9 (scBS-Seq)


title: E7.5_Plate3_F10 (scBS-Seq)


title: E7.5_Plate3_E4 (scBS-Seq)


title: E7.5_Plate3_F11 (scBS-Seq)


title: E7.5_Plate3_E5 (scBS-Seq)


title: E7.5_Plate3_E7 (scBS-Seq)


title: E7.5_Plate3_G12 (scBS-Seq)


title: E7.5_Plate3_D9 (scBS-Seq)


title: E7.5_Plate3_E2 (scBS-Seq)


title: E7.5_Plate3_E12 (scBS-Seq)


title: E7.5_Plate3_E11 (scBS-Seq)


title: E7.5_Plate3_D7 (scBS-Seq)


title: E7.5_Plate3_F9 (scBS-Seq)


title: E7.5_Plate3_D6 (scBS-Seq)


title: E7.5_Plate3_D8 (scBS-Seq)


title: E7.5_Plate3_F12 (scBS-Seq)


title: E7.5_Plate3_D5 (scBS-Seq)


title: E7.5_Plate3_D3 (scBS-Seq)


title: E7.5_Plate3_D4 (scBS-Seq)


title: E7.5_Plate3_E1 (scBS-Seq)


title: E7.5_Plate3_D2 (scBS-Seq)


title: E7.5_Plate3_E10 (scBS-Seq)


title: E7.5_Plate3_D11 (scBS-Seq)


title: E7.5_Plate3_D1 (scBS-Seq)


title: E7.5_Plate3_C1 (scBS-Seq)


title: E7.5_Plate3_C12 (scBS-Seq)


title: E7.5_Plate3_C3 (scBS-Seq)


title: E7.5_Plate3_C6 (scBS-Seq)


title: E7.5_Plate3_C8 (scBS-Seq)


title: E7.5_Plate3_C5 (scBS-Seq)


title: E7.5_Plate3_C2 (scBS-Seq)


title: E7.5_Plate3_C9 (scBS-Seq)


title: E7.5_Plate3_C4 (scBS-Seq)


title: E7.5_Plate3_C11 (scBS-Seq)


title: E7.5_Plate3_B8 (scBS-Seq)


title: E7.5_Plate3_C10 (scBS-Seq)


title: E7.5_Plate3_B9 (scBS-Seq)


title: E7.5_Plate3_C7 (scBS-Seq)


title: E7.5_Plate3_B6 (scBS-Seq)


title: E7.5_Plate3_B4 (scBS-Seq)


title: E7.5_Plate3_B3 (scBS-Seq)


title: E7.5_Plate3_B2 (scBS-Seq)


title: E7.5_Plate3_B1 (scBS-Seq)


title: E7.5_Plate3_B12 (scBS-Seq)


title: E7.5_Plate3_B5 (scBS-Seq)


title: E7.5_Plate3_D12 (scBS-Seq)


title: E7.5_Plate3_B11 (scBS-Seq)


title: E7.5_Plate3_D10 (scBS-Seq)


title: E7.5_Plate3_A9 (scBS-Seq)


title: E7.5_Plate3_B10 (scBS-Seq)


title: E7.5_Plate3_A8 (scBS-Seq)


title: E7.5_Plate3_A7 (scBS-Seq)


title: E7.5_Plate3_A6 (scBS-Seq)


title: E7.5_Plate3_A5 (scBS-Seq)


title: E7.5_Plate3_A4 (scBS-Seq)


title: E7.5_Plate3_A3 (scBS-Seq)


title: E7.5_Plate3_A1 (scBS-Seq)


title: E7.5_Plate3_A11 (scBS-Seq)


title: E7.5_Plate3_A2 (scBS-Seq)


title: E7.5_Plate2_H6 (scBS-Seq)


title: E7.5_Plate3_A10 (scBS-Seq)


title: E7.5_Plate2_H8 (scBS-Seq)


title: E7.5_Plate2_H9 (scBS-Seq)


title: E7.5_Plate2_H7 (scBS-Seq)


title: E7.5_Plate2_H5 (scBS-Seq)


title: E7.5_Plate3_B7 (scBS-Seq)


title: E7.5_Plate2_H4 (scBS-Seq)


title: E7.5_Plate2_H3 (scBS-Seq)


title: E7.5_Plate2_G8 (scBS-Seq)


title: E7.5_Plate2_H12 (scBS-Seq)


title: E7.5_Plate2_G7 (scBS-Seq)


title: E7.5_Plate2_H1 (scBS-Seq)


title: E7.5_Plate2_H2 (scBS-Seq)


title: E7.5_Plate2_H10 (scBS-Seq)


title: E7.5_Plate2_H11 (scBS-Seq)


title: E7.5_Plate3_A12 (scBS-Seq)


title: E7.5_Plate2_G6 (scBS-Seq)


title: E7.5_Plate2_G9 (scBS-Seq)


title: E7.5_Plate2_G5 (scBS-Seq)


title: E7.5_Plate2_G3 (scBS-Seq)


title: E7.5_Plate2_G2 (scBS-Seq)


title: E7.5_Plate2_G4 (scBS-Seq)


title: E7.5_Plate2_G12 (scBS-Seq)


title: E7.5_Plate2_F9 (scBS-Seq)


title: E7.5_Plate2_F7 (scBS-Seq)


title: E7.5_Plate2_F4 (scBS-Seq)


title: E7.5_Plate2_F1 (scBS-Seq)


title: E7.5_Plate2_F2 (scBS-Seq)


title: E7.5_Plate2_F5 (scBS-Seq)


title: E7.5_Plate2_F3 (scBS-Seq)


title: E7.5_Plate2_F12 (scBS-Seq)


title: E7.5_Plate2_F6 (scBS-Seq)


title: E7.5_Plate2_F10 (scBS-Seq)


title: E7.5_Plate2_E9 (scBS-Seq)


title: E7.5_Plate2_E8 (scBS-Seq)


title: E7.5_Plate2_E7 (scBS-Seq)


title: E7.5_Plate2_E5 (scBS-Seq)


title: E7.5_Plate2_E6 (scBS-Seq)


title: E7.5_Plate2_G1 (scBS-Seq)


title: E7.5_Plate2_E4 (scBS-Seq)


title: E7.5_Plate2_E3 (scBS-Seq)


title: E7.5_Plate2_G11 (scBS-Seq)


title: E7.5_Plate2_E11 (scBS-Seq)


title: E7.5_Plate2_F8 (scBS-Seq)


title: E7.5_Plate2_E1 (scBS-Seq)


title: E7.5_Plate2_E2 (scBS-Seq)


title: E7.5_Plate2_E10 (scBS-Seq)


title: E7.5_Plate2_G10 (scBS-Seq)


title: E7.5_Plate2_E12 (scBS-Seq)


title: E7.5_Plate2_D9 (scBS-Seq)


title: E7.5_Plate2_D7 (scBS-Seq)


title: E7.5_Plate2_F11 (scBS-Seq)


title: E7.5_Plate2_D8 (scBS-Seq)


title: E7.5_Plate2_D1 (scBS-Seq)


title: E7.5_Plate2_D4 (scBS-Seq)


title: E7.5_Plate2_D5 (scBS-Seq)


title: E7.5_Plate2_D3 (scBS-Seq)


title: E7.5_Plate2_D11 (scBS-Seq)


title: E7.5_Plate2_D10 (scBS-Seq)


title: E7.5_Plate2_C7 (scBS-Seq)


title: E7.5_Plate2_C8 (scBS-Seq)


title: E7.5_Plate2_C9 (scBS-Seq)


title: E7.5_Plate2_C6 (scBS-Seq)


title: E7.5_Plate2_C5 (scBS-Seq)


title: E7.5_Plate2_C3 (scBS-Seq)


title: E7.5_Plate2_C2 (scBS-Seq)


title: E7.5_Plate2_C1 (scBS-Seq)


title: E7.5_Plate2_C12 (scBS-Seq)


title: E7.5_Plate2_C10 (scBS-Seq)


title: E7.5_Plate2_B8 (scBS-Seq)


title: E7.5_Plate2_B6 (scBS-Seq)


title: E7.5_Plate2_B7 (scBS-Seq)


title: E7.5_Plate2_B9 (scBS-Seq)


title: E7.5_Plate2_D6 (scBS-Seq)


title: E7.5_Plate2_B4 (scBS-Seq)


title: E7.5_Plate2_B2 (scBS-Seq)


title: E7.5_Plate2_B1 (scBS-Seq)


title: E7.5_Plate2_A8 (scBS-Seq)


title: E7.5_Plate2_B11 (scBS-Seq)


title: E7.5_Plate2_B3 (scBS-Seq)


title: E7.5_Plate2_B5 (scBS-Seq)


title: E7.5_Plate2_A9 (scBS-Seq)


title: E7.5_Plate2_D2 (scBS-Seq)


title: E7.5_Plate2_C4 (scBS-Seq)


title: E7.5_Plate2_A7 (scBS-Seq)


title: E7.5_Plate2_C11 (scBS-Seq)


title: E7.5_Plate2_B10 (scBS-Seq)


title: E7.5_Plate2_A4 (scBS-Seq)


title: E7.5_Plate2_A6 (scBS-Seq)


title: E7.5_Plate2_A5 (scBS-Seq)


title: E7.5_Plate2_A3 (scBS-Seq)


title: E7.5_Plate2_A1 (scBS-Seq)


title: E7.5_Plate2_A2 (scBS-Seq)


title: E7.5_Plate2_A12 (scBS-Seq)


title: E7.5_Plate1_H3 (scBS-Seq)


title: E7.5_Plate2_A10 (scBS-Seq)


title: E7.5_Plate2_A11 (scBS-Seq)


title: E7.5_Plate1_G2 (scBS-Seq)


title: E7.5_Plate1_F5 (scBS-Seq)


title: E7.5_Plate1_D7 (scBS-Seq)


title: E7.5_Plate1_A3 (scBS-Seq)


title: E7.5_Plate2_B12 (scBS-Seq)


title: E7.5_Plate1_B10 (scBS-Seq)


title: E7.5_Plate2_D12 (scBS-Seq)


title: E6.75_Plate2_H8 (scBS-Seq)


title: E6.75_Plate2_H9 (scBS-Seq)


title: E7.5_Plate1_D2 (scBS-Seq)


title: E6.75_Plate2_H7 (scBS-Seq)


title: E6.75_Plate2_H5 (scBS-Seq)


title: E6.75_Plate2_H4 (scBS-Seq)


title: E6.75_Plate2_H6 (scBS-Seq)


title: E6.75_Plate2_H12 (scBS-Seq)


title: E6.75_Plate2_H2 (scBS-Seq)


title: E6.75_Plate2_G9 (scBS-Seq)


title: E6.75_Plate2_H11 (scBS-Seq)


title: E6.75_Plate2_G6 (scBS-Seq)


title: E6.75_Plate2_H3 (scBS-Seq)


title: E6.75_Plate2_G8 (scBS-Seq)


title: E6.75_Plate2_G7 (scBS-Seq)


title: E7.5_Plate1_A5 (scBS-Seq)


title: E6.75_Plate2_G11 (scBS-Seq)


title: E6.75_Plate2_G12 (scBS-Seq)


title: E6.75_Plate2_G3 (scBS-Seq)


title: E6.75_Plate2_H10 (scBS-Seq)


title: E6.75_Plate2_G10 (scBS-Seq)


title: E6.75_Plate2_G5 (scBS-Seq)


title: E6.75_Plate2_F7 (scBS-Seq)


title: E6.75_Plate2_G2 (scBS-Seq)


title: E6.75_Plate2_F6 (scBS-Seq)


title: E6.75_Plate2_F9 (scBS-Seq)


title: E6.75_Plate2_F5 (scBS-Seq)


title: E6.75_Plate2_F3 (scBS-Seq)


title: E6.75_Plate2_F4 (scBS-Seq)


title: E6.75_Plate2_H1 (scBS-Seq)


title: E6.75_Plate2_F1 (scBS-Seq)


title: E6.75_Plate2_G1 (scBS-Seq)


title: E6.75_Plate2_F11 (scBS-Seq)


title: E6.75_Plate2_F10 (scBS-Seq)


title: E6.75_Plate2_F12 (scBS-Seq)


title: E6.75_Plate2_G4 (scBS-Seq)


title: E6.75_Plate2_F2 (scBS-Seq)


title: E6.75_Plate2_E9 (scBS-Seq)


title: E6.75_Plate2_E6 (scBS-Seq)


title: E6.75_Plate2_E5 (scBS-Seq)


title: E6.75_Plate2_F8 (scBS-Seq)


title: E6.75_Plate2_E4 (scBS-Seq)


title: E6.75_Plate2_E2 (scBS-Seq)


title: E6.75_Plate2_E1 (scBS-Seq)


title: E6.75_Plate2_E12 (scBS-Seq)


title: E6.75_Plate2_D9 (scBS-Seq)


title: E6.75_Plate2_E10 (scBS-Seq)


title: E6.75_Plate2_D7 (scBS-Seq)


title: E6.75_Plate2_D6 (scBS-Seq)


title: E6.75_Plate2_E11 (scBS-Seq)


title: E6.75_Plate2_D5 (scBS-Seq)


title: E6.75_Plate2_D8 (scBS-Seq)


title: E6.75_Plate2_D1 (scBS-Seq)


title: E6.75_Plate2_D2 (scBS-Seq)


title: E6.75_Plate2_D12 (scBS-Seq)


title: E6.75_Plate2_D3 (scBS-Seq)


title: E6.75_Plate2_E8 (scBS-Seq)


title: E6.75_Plate2_D11 (scBS-Seq)


title: E6.75_Plate2_D10 (scBS-Seq)


title: E6.75_Plate2_C8 (scBS-Seq)


title: E6.75_Plate2_C5 (scBS-Seq)


title: E6.75_Plate2_C6 (scBS-Seq)


title: E6.75_Plate2_C9 (scBS-Seq)


title: E6.75_Plate2_D4 (scBS-Seq)


title: E6.75_Plate2_C4 (scBS-Seq)


title: E6.75_Plate2_C2 (scBS-Seq)


title: E6.75_Plate2_C3 (scBS-Seq)


title: E6.75_Plate2_C7 (scBS-Seq)


title: E6.75_Plate2_C1 (scBS-Seq)


title: E6.75_Plate2_C11 (scBS-Seq)


title: E6.75_Plate2_B8 (scBS-Seq)


title: E6.75_Plate2_E7 (scBS-Seq)


title: E6.75_Plate2_B9 (scBS-Seq)


title: E6.75_Plate2_B4 (scBS-Seq)


title: E6.75_Plate2_B2 (scBS-Seq)


title: E6.75_Plate2_B5 (scBS-Seq)


title: E6.75_Plate2_B12 (scBS-Seq)


title: E6.75_Plate2_E3 (scBS-Seq)


title: E6.75_Plate2_B3 (scBS-Seq)


title: E6.75_Plate2_B11 (scBS-Seq)


title: E6.75_Plate2_B10 (scBS-Seq)


title: E6.75_Plate2_A8 (scBS-Seq)


title: E6.75_Plate2_A9 (scBS-Seq)


title: E6.75_Plate2_C10 (scBS-Seq)


title: E6.75_Plate2_A4 (scBS-Seq)


title: E6.75_Plate2_C12 (scBS-Seq)


title: E6.75_Plate2_A5 (scBS-Seq)


title: E6.75_Plate2_A2 (scBS-Seq)


title: E6.75_Plate2_A1 (scBS-Seq)


title: E6.75_Plate2_A12 (scBS-Seq)


title: E6.75_Plate2_B1 (scBS-Seq)


title: E6.75_Plate2_B6 (scBS-Seq)


title: E6.75_Plate2_A11 (scBS-Seq)


title: E6.75_Plate2_B7 (scBS-Seq)


title: E6.75_Plate1_B6 (scBS-Seq)


title: E6.5_Plate3_H9 (scBS-Seq)


title: E6.75_Plate2_A6 (scBS-Seq)


title: E6.5_Plate3_H8 (scBS-Seq)


title: E6.5_Plate3_H5 (scBS-Seq)


title: E6.5_Plate3_H6 (scBS-Seq)


title: E6.5_Plate3_H4 (scBS-Seq)


title: E6.5_Plate3_H3 (scBS-Seq)


title: E6.5_Plate3_H2 (scBS-Seq)


title: E6.5_Plate3_H11 (scBS-Seq)


title: E6.5_Plate3_H7 (scBS-Seq)


title: E6.5_Plate3_H10 (scBS-Seq)


title: E6.75_Plate2_A3 (scBS-Seq)


title: E6.75_Plate2_A7 (scBS-Seq)


title: E6.5_Plate3_H12 (scBS-Seq)


title: E6.5_Plate3_G9 (scBS-Seq)


title: E6.5_Plate3_G8 (scBS-Seq)


title: E6.5_Plate3_G7 (scBS-Seq)


title: E6.5_Plate3_G3 (scBS-Seq)


title: E6.5_Plate3_G2 (scBS-Seq)


title: E6.5_Plate3_G12 (scBS-Seq)


title: E6.5_Plate3_G11 (scBS-Seq)


title: E6.5_Plate3_G1 (scBS-Seq)


title: E6.5_Plate3_G6 (scBS-Seq)


title: E6.5_Plate3_G5 (scBS-Seq)


title: E6.5_Plate3_G4 (scBS-Seq)


title: E6.75_Plate2_A10 (scBS-Seq)


title: E6.5_Plate3_F8 (scBS-Seq)


title: E6.5_Plate3_H1 (scBS-Seq)


title: E6.5_Plate3_F9 (scBS-Seq)


title: E6.5_Plate3_G10 (scBS-Seq)


title: E6.5_Plate3_F7 (scBS-Seq)


title: E6.5_Plate3_F5 (scBS-Seq)


title: E6.5_Plate3_F6 (scBS-Seq)


title: E6.5_Plate3_F4 (scBS-Seq)


title: E6.5_Plate3_F1 (scBS-Seq)


title: E6.5_Plate3_F11 (scBS-Seq)


title: E6.5_Plate3_F10 (scBS-Seq)


title: E6.5_Plate3_E9 (scBS-Seq)


title: E6.5_Plate3_E6 (scBS-Seq)


title: E6.5_Plate3_F12 (scBS-Seq)


title: E6.5_Plate3_E8 (scBS-Seq)


title: E6.5_Plate3_E3 (scBS-Seq)


title: E6.5_Plate3_E5 (scBS-Seq)


title: E6.5_Plate3_E7 (scBS-Seq)


title: E6.5_Plate3_E11 (scBS-Seq)


title: E6.5_Plate3_E2 (scBS-Seq)


title: E6.5_Plate3_E1 (scBS-Seq)


title: E6.5_Plate3_E4 (scBS-Seq)


title: E6.5_Plate3_E10 (scBS-Seq)


title: E6.5_Plate3_D9 (scBS-Seq)


title: E6.5_Plate3_D8 (scBS-Seq)


title: E6.5_Plate3_F3 (scBS-Seq)


title: E6.5_Plate3_E12 (scBS-Seq)


title: E6.5_Plate3_F2 (scBS-Seq)


title: E6.5_Plate3_D2 (scBS-Seq)


title: E6.5_Plate3_D6 (scBS-Seq)


title: E6.5_Plate3_D5 (scBS-Seq)


title: E6.5_Plate3_D4 (scBS-Seq)


title: E6.5_Plate3_D1 (scBS-Seq)


title: E6.5_Plate3_D3 (scBS-Seq)


title: E6.5_Plate3_C8 (scBS-Seq)


title: E6.5_Plate3_C7 (scBS-Seq)


title: E6.5_Plate3_C5 (scBS-Seq)


title: E6.5_Plate3_D7 (scBS-Seq)


title: E6.5_Plate3_C3 (scBS-Seq)


title: E6.5_Plate3_C12 (scBS-Seq)


title: E6.5_Plate3_C10 (scBS-Seq)


title: E6.5_Plate3_C4 (scBS-Seq)


title: E6.5_Plate3_C11 (scBS-Seq)


title: E6.5_Plate3_C9 (scBS-Seq)


title: E6.5_Plate3_B9 (scBS-Seq)


title: E6.5_Plate3_D10 (scBS-Seq)


title: E6.5_Plate3_C6 (scBS-Seq)


title: E6.5_Plate3_C2 (scBS-Seq)


title: E6.5_Plate3_D11 (scBS-Seq)


title: E6.5_Plate3_D12 (scBS-Seq)


title: E6.5_Plate3_B6 (scBS-Seq)


title: E6.5_Plate3_B4 (scBS-Seq)


title: E6.5_Plate3_B7 (scBS-Seq)


title: E6.5_Plate3_B1 (scBS-Seq)


title: E6.5_Plate3_B11 (scBS-Seq)


title: E6.5_Plate3_B2 (scBS-Seq)


title: E6.5_Plate3_B12 (scBS-Seq)


title: E6.5_Plate3_B10 (scBS-Seq)


title: E6.5_Plate3_A9 (scBS-Seq)


title: E6.5_Plate3_A8 (scBS-Seq)


title: E6.5_Plate3_B8 (scBS-Seq)


title: E6.5_Plate3_A7 (scBS-Seq)


title: E6.5_Plate3_A6 (scBS-Seq)


title: E6.5_Plate3_A2 (scBS-Seq)


title: E6.5_Plate3_A1 (scBS-Seq)


title: E6.5_Plate3_A3 (scBS-Seq)


title: E6.5_Plate3_A5 (scBS-Seq)


title: E6.5_Plate3_B5 (scBS-Seq)


title: E6.5_Plate3_B3 (scBS-Seq)


title: E6.5_Plate3_C1 (scBS-Seq)


title: E4.5-5.5_new_Plate4_H08 (scBS-Seq)


title: E6.5_Plate3_A10 (scBS-Seq)


title: E6.5_Plate2_G6 (scBS-Seq)


title: E4.5-5.5_new_Plate4_H10 (scBS-Seq)


title: E4.5-5.5_new_Plate4_H04 (scBS-Seq)


title: E4.5-5.5_new_Plate4_H07 (scBS-Seq)


title: E4.5-5.5_new_Plate4_H02 (scBS-Seq)


title: E4.5-5.5_new_Plate4_H09 (scBS-Seq)


title: E4.5-5.5_new_Plate4_H03 (scBS-Seq)


title: E4.5-5.5_new_Plate4_H06 (scBS-Seq)


title: E4.5-5.5_new_Plate4_H01 (scBS-Seq)


title: E4.5-5.5_new_Plate4_G12 (scBS-Seq)


title: E4.5-5.5_new_Plate4_G11 (scBS-Seq)


title: E4.5-5.5_new_Plate4_G09 (scBS-Seq)


title: E4.5-5.5_new_Plate4_G08 (scBS-Seq)


title: E4.5-5.5_new_Plate4_H12 (scBS-Seq)


title: E4.5-5.5_new_Plate4_G07 (scBS-Seq)


title: E4.5-5.5_new_Plate4_G04 (scBS-Seq)


title: E4.5-5.5_new_Plate4_G06 (scBS-Seq)


title: E6.5_Plate3_A12 (scBS-Seq)


title: E4.5-5.5_new_Plate4_G05 (scBS-Seq)


title: E4.5-5.5_new_Plate4_G02 (scBS-Seq)


title: E4.5-5.5_new_Plate4_H11 (scBS-Seq)


title: E4.5-5.5_new_Plate4_G10 (scBS-Seq)


title: E4.5-5.5_new_Plate4_G01 (scBS-Seq)


title: E4.5-5.5_new_Plate4_F12 (scBS-Seq)


title: E4.5-5.5_new_Plate4_F11 (scBS-Seq)


title: E4.5-5.5_new_Plate4_F08 (scBS-Seq)


title: E4.5-5.5_new_Plate4_F06 (scBS-Seq)


title: E4.5-5.5_new_Plate4_F10 (scBS-Seq)


title: E4.5-5.5_new_Plate4_F05 (scBS-Seq)


title: E4.5-5.5_new_Plate4_F04 (scBS-Seq)


title: E4.5-5.5_new_Plate4_F03 (scBS-Seq)


title: E4.5-5.5_new_Plate4_E11 (scBS-Seq)


title: E4.5-5.5_new_Plate4_E10 (scBS-Seq)


title: E4.5-5.5_new_Plate4_F01 (scBS-Seq)


title: E4.5-5.5_new_Plate4_E09 (scBS-Seq)


title: E4.5-5.5_new_Plate4_G03 (scBS-Seq)


title: E4.5-5.5_new_Plate4_E08 (scBS-Seq)


title: E4.5-5.5_new_Plate4_E12 (scBS-Seq)


title: E4.5-5.5_new_Plate4_F02 (scBS-Seq)


title: E4.5-5.5_new_Plate4_F07 (scBS-Seq)


title: E4.5-5.5_new_Plate4_E05 (scBS-Seq)


title: E4.5-5.5_new_Plate4_D12 (scBS-Seq)


title: E4.5-5.5_new_Plate4_E07 (scBS-Seq)


title: E4.5-5.5_new_Plate4_E04 (scBS-Seq)


title: E4.5-5.5_new_Plate4_D11 (scBS-Seq)


title: E4.5-5.5_new_Plate4_D09 (scBS-Seq)


title: E4.5-5.5_new_Plate4_E01 (scBS-Seq)


title: E4.5-5.5_new_Plate4_F09 (scBS-Seq)


title: E4.5-5.5_new_Plate4_D08 (scBS-Seq)


title: E4.5-5.5_new_Plate4_E03 (scBS-Seq)


title: E4.5-5.5_new_Plate4_E06 (scBS-Seq)


title: E4.5-5.5_new_Plate4_D03 (scBS-Seq)


title: E4.5-5.5_new_Plate4_D04 (scBS-Seq)


title: E4.5-5.5_new_Plate4_D02 (scBS-Seq)


title: E4.5-5.5_new_Plate4_D06 (scBS-Seq)


title: E4.5-5.5_new_Plate4_D05 (scBS-Seq)


title: E4.5-5.5_new_Plate4_C11 (scBS-Seq)


title: E4.5-5.5_new_Plate4_C09 (scBS-Seq)


title: E4.5-5.5_new_Plate4_D01 (scBS-Seq)


title: E4.5-5.5_new_Plate4_C08 (scBS-Seq)


title: E4.5-5.5_new_Plate4_C07 (scBS-Seq)


title: E4.5-5.5_new_Plate4_C06 (scBS-Seq)


title: E4.5-5.5_new_Plate4_C05 (scBS-Seq)


title: E4.5-5.5_new_Plate4_C12 (scBS-Seq)


title: E4.5-5.5_new_Plate4_C10 (scBS-Seq)


title: E4.5-5.5_new_Plate4_H05 (scBS-Seq)


title: E4.5-5.5_new_Plate4_C03 (scBS-Seq)


title: E4.5-5.5_new_Plate4_C02 (scBS-Seq)


title: E4.5-5.5_new_Plate4_D07 (scBS-Seq)


title: E4.5-5.5_new_Plate4_C04 (scBS-Seq)


title: E4.5-5.5_new_Plate4_C01 (scBS-Seq)


title: E4.5-5.5_new_Plate4_B12 (scBS-Seq)


title: E4.5-5.5_new_Plate4_B09 (scBS-Seq)


title: E4.5-5.5_new_Plate4_B11 (scBS-Seq)


title: E4.5-5.5_new_Plate4_D10 (scBS-Seq)


title: E4.5-5.5_new_Plate4_B10 (scBS-Seq)


title: E4.5-5.5_new_Plate4_B08 (scBS-Seq)


title: E4.5-5.5_new_Plate4_B04 (scBS-Seq)


title: E4.5-5.5_new_Plate4_B07 (scBS-Seq)


title: E4.5-5.5_new_Plate4_B01 (scBS-Seq)


title: E4.5-5.5_new_Plate4_B02 (scBS-Seq)


title: E4.5-5.5_new_Plate4_A12 (scBS-Seq)


title: E4.5-5.5_new_Plate4_A11 (scBS-Seq)


title: E4.5-5.5_new_Plate4_A08 (scBS-Seq)


title: E4.5-5.5_new_Plate4_A07 (scBS-Seq)


title: E4.5-5.5_new_Plate4_B05 (scBS-Seq)


title: E4.5-5.5_new_Plate4_B03 (scBS-Seq)


title: E4.5-5.5_new_Plate4_A10 (scBS-Seq)


title: E4.5-5.5_new_Plate4_A09 (scBS-Seq)


title: E4.5-5.5_new_Plate4_E02 (scBS-Seq)


title: E4.5-5.5_new_Plate4_A06 (scBS-Seq)


title: E4.5-5.5_new_Plate4_A03 (scBS-Seq)


title: E4.5-5.5_new_Plate4_A04 (scBS-Seq)


title: E4.5-5.5_new_Plate4_A02 (scBS-Seq)


title: E4.5-5.5_new_Plate4_B06 (scBS-Seq)


title: E4.5-5.5_new_Plate3_H05 (scBS-Seq)


title: E4.5-5.5_new_Plate3_H09 (scBS-Seq)


title: E4.5-5.5_new_Plate3_H02 (scBS-Seq)


title: E4.5-5.5_new_Plate3_G10 (scBS-Seq)


title: E4.5-5.5_new_Plate3_H03 (scBS-Seq)


title: E4.5-5.5_new_Plate3_H04 (scBS-Seq)


title: E4.5-5.5_new_Plate3_G09 (scBS-Seq)


title: E4.5-5.5_new_Plate3_G07 (scBS-Seq)


title: E4.5-5.5_new_Plate3_F07 (scBS-Seq)


title: E4.5-5.5_new_Plate3_F01 (scBS-Seq)


title: E4.5-5.5_new_Plate4_A05 (scBS-Seq)


title: E4.5-5.5_new_Plate3_G06 (scBS-Seq)


title: E4.5-5.5_new_Plate3_E09 (scBS-Seq)


title: E4.5-5.5_new_Plate3_F02 (scBS-Seq)


title: E4.5-5.5_new_Plate4_A01 (scBS-Seq)


title: E4.5-5.5_new_Plate3_E12 (scBS-Seq)


title: E4.5-5.5_new_Plate3_H10 (scBS-Seq)


title: E4.5-5.5_new_Plate3_E02 (scBS-Seq)


title: E4.5-5.5_new_Plate3_E04 (scBS-Seq)


title: E4.5-5.5_new_Plate3_E10 (scBS-Seq)


title: E4.5-5.5_new_Plate3_D05 (scBS-Seq)


title: E4.5-5.5_new_Plate3_C07 (scBS-Seq)


title: E4.5-5.5_new_Plate3_C05 (scBS-Seq)


title: E4.5-5.5_new_Plate3_G08 (scBS-Seq)


title: E4.5-5.5_new_Plate3_C04 (scBS-Seq)


title: E4.5-5.5_new_Plate3_B09 (scBS-Seq)


title: E4.5-5.5_new_Plate3_B07 (scBS-Seq)


title: E4.5-5.5_new_Plate3_B01 (scBS-Seq)


title: E4.5-5.5_new_Plate3_B03 (scBS-Seq)


title: E4.5-5.5_new_Plate3_A12 (scBS-Seq)


title: E4.5-5.5_new_Plate3_B02 (scBS-Seq)


title: E4.5-5.5_new_Plate3_A10 (scBS-Seq)


title: E4.5-5.5_new_Plate3_G01 (scBS-Seq)


title: E4.5-5.5_new_Plate3_A07 (scBS-Seq)


title: E4.5-5.5_new_Plate3_E03 (scBS-Seq)


title: E4.5-5.5_new_Plate3_A02 (scBS-Seq)


title: E4.5-5.5_new_Plate3_A04 (scBS-Seq)


title: E4.5-5.5_new_Plate2_H12 (scBS-Seq)


title: E4.5-5.5_new_Plate2_H11 (scBS-Seq)


title: E4.5-5.5_new_Plate3_E01 (scBS-Seq)


title: E4.5-5.5_new_Plate3_A06 (scBS-Seq)


title: E4.5-5.5_new_Plate2_H10 (scBS-Seq)


title: E4.5-5.5_new_Plate2_H07 (scBS-Seq)


title: E4.5-5.5_new_Plate2_H06 (scBS-Seq)


title: E4.5-5.5_new_Plate2_H05 (scBS-Seq)


title: E4.5-5.5_new_Plate2_H08 (scBS-Seq)


title: E4.5-5.5_new_Plate2_H03 (scBS-Seq)


title: E4.5-5.5_new_Plate2_H04 (scBS-Seq)


title: E4.5-5.5_new_Plate2_H09 (scBS-Seq)


title: E4.5-5.5_new_Plate2_H01 (scBS-Seq)


title: E4.5-5.5_new_Plate2_G11 (scBS-Seq)


title: E4.5-5.5_new_Plate2_G10 (scBS-Seq)


title: E4.5-5.5_new_Plate2_G09 (scBS-Seq)


title: E4.5-5.5_new_Plate2_G08 (scBS-Seq)


title: E4.5-5.5_new_Plate2_G12 (scBS-Seq)


title: E4.5-5.5_new_Plate2_G07 (scBS-Seq)


title: E4.5-5.5_new_Plate2_G06 (scBS-Seq)


title: E6.5_Plate3_A11 (scBS-Seq)


title: E4.5-5.5_new_Plate2_G05 (scBS-Seq)


title: E4.5-5.5_new_Plate2_G03 (scBS-Seq)


title: E4.5-5.5_new_Plate2_F12 (scBS-Seq)


title: E4.5-5.5_new_Plate2_G04 (scBS-Seq)


title: E4.5-5.5_new_Plate2_H02 (scBS-Seq)


title: E4.5-5.5_new_Plate2_G01 (scBS-Seq)


title: E4.5-5.5_new_Plate2_G02 (scBS-Seq)


title: E4.5-5.5_new_Plate2_F10 (scBS-Seq)


title: E4.5-5.5_new_Plate2_F07 (scBS-Seq)


title: E4.5-5.5_new_Plate2_F09 (scBS-Seq)


title: E4.5-5.5_new_Plate2_F06 (scBS-Seq)


title: E4.5-5.5_new_Plate2_F04 (scBS-Seq)


title: E4.5-5.5_new_Plate2_F03 (scBS-Seq)


title: E4.5-5.5_new_Plate2_F08 (scBS-Seq)


title: E4.5-5.5_new_Plate2_E11 (scBS-Seq)


title: E4.5-5.5_new_Plate2_F11 (scBS-Seq)


title: E4.5-5.5_new_Plate2_F01 (scBS-Seq)


title: E6.5_Plate2_H3 (scBS-Seq)


title: E4.5-5.5_new_Plate2_E10 (scBS-Seq)


title: E4.5-5.5_new_Plate2_E08 (scBS-Seq)


title: E4.5-5.5_new_Plate2_E09 (scBS-Seq)


title: E4.5-5.5_new_Plate2_F05 (scBS-Seq)


title: E4.5-5.5_new_Plate2_F02 (scBS-Seq)


title: E4.5-5.5_new_Plate2_E06 (scBS-Seq)


title: E4.5-5.5_new_Plate2_E07 (scBS-Seq)


title: E4.5-5.5_new_Plate2_E05 (scBS-Seq)


title: E4.5-5.5_new_Plate2_E04 (scBS-Seq)


title: E4.5-5.5_new_Plate2_E03 (scBS-Seq)


title: E4.5-5.5_new_Plate2_D11 (scBS-Seq)


title: E4.5-5.5_new_Plate2_D12 (scBS-Seq)


title: E4.5-5.5_new_Plate2_D10 (scBS-Seq)


title: E4.5-5.5_new_Plate2_D08 (scBS-Seq)


title: E4.5-5.5_new_Plate2_D09 (scBS-Seq)


title: E4.5-5.5_new_Plate2_D05 (scBS-Seq)


title: E4.5-5.5_new_Plate2_E12 (scBS-Seq)


title: E4.5-5.5_new_Plate2_D03 (scBS-Seq)


title: E4.5-5.5_new_Plate2_D07 (scBS-Seq)


title: E4.5-5.5_new_Plate2_D06 (scBS-Seq)


title: E4.5-5.5_new_Plate2_D02 (scBS-Seq)


title: E4.5-5.5_new_Plate2_D01 (scBS-Seq)


title: E4.5-5.5_new_Plate2_C11 (scBS-Seq)


title: E4.5-5.5_new_Plate2_C09 (scBS-Seq)


title: E4.5-5.5_new_Plate2_C08 (scBS-Seq)


title: E4.5-5.5_new_Plate2_C12 (scBS-Seq)


title: E6.5_Plate3_A4 (scBS-Seq)


title: E4.5-5.5_new_Plate2_C07 (scBS-Seq)


title: E4.5-5.5_new_Plate2_C05 (scBS-Seq)


title: E4.5-5.5_new_Plate2_C03 (scBS-Seq)


title: E4.5-5.5_new_Plate2_C04 (scBS-Seq)


title: E4.5-5.5_new_Plate2_C02 (scBS-Seq)


title: E4.5-5.5_new_Plate2_E02 (scBS-Seq)


title: E4.5-5.5_new_Plate2_E01 (scBS-Seq)


title: E4.5-5.5_new_Plate2_B11 (scBS-Seq)


title: E4.5-5.5_new_Plate2_C01 (scBS-Seq)


title: E4.5-5.5_new_Plate2_B12 (scBS-Seq)


title: E4.5-5.5_new_Plate2_D04 (scBS-Seq)


title: E4.5-5.5_new_Plate2_B09 (scBS-Seq)


title: E4.5-5.5_new_Plate2_B08 (scBS-Seq)


title: E4.5-5.5_new_Plate2_B06 (scBS-Seq)


title: E4.5-5.5_new_Plate2_B10 (scBS-Seq)


title: E4.5-5.5_new_Plate2_B07 (scBS-Seq)


title: E4.5-5.5_new_Plate2_B05 (scBS-Seq)


title: E4.5-5.5_new_Plate2_B04 (scBS-Seq)


title: E4.5-5.5_new_Plate2_B03 (scBS-Seq)


title: E4.5-5.5_new_Plate2_B02 (scBS-Seq)


title: E4.5-5.5_new_Plate2_B01 (scBS-Seq)


title: E4.5-5.5_new_Plate2_C10 (scBS-Seq)


title: E4.5-5.5_new_Plate2_C06 (scBS-Seq)


title: E4.5-5.5_new_Plate2_A01 (scBS-Seq)


title: E4.5-5.5_new_Plate2_A09 (scBS-Seq)


title: E4.5-5.5_new_Plate2_A04 (scBS-Seq)


title: E4.5-5.5_new_Plate2_A03 (scBS-Seq)


title: E4.5-5.5_new_Plate2_A10 (scBS-Seq)


title: E4.5-5.5_new_Plate2_A06 (scBS-Seq)


title: E4.5-5.5_new_Plate1_H09 (scBS-Seq)


title: E4.5-5.5_new_Plate1_H08 (scBS-Seq)


title: E4.5-5.5_new_Plate2_A05 (scBS-Seq)


title: E4.5-5.5_new_Plate2_A08 (scBS-Seq)


title: E4.5-5.5_new_Plate1_G08 (scBS-Seq)


title: E4.5-5.5_new_Plate2_A02 (scBS-Seq)


title: E4.5-5.5_new_Plate1_G09 (scBS-Seq)


title: E4.5-5.5_new_Plate1_F03 (scBS-Seq)


title: E4.5-5.5_new_Plate1_E09 (scBS-Seq)


title: E4.5-5.5_new_Plate1_E11 (scBS-Seq)


title: E4.5-5.5_new_Plate1_E05 (scBS-Seq)


title: E4.5-5.5_new_Plate1_E08 (scBS-Seq)


title: E4.5-5.5_new_Plate2_A12 (scBS-Seq)


title: E4.5-5.5_new_Plate1_G07 (scBS-Seq)


title: E4.5-5.5_new_Plate2_A11 (scBS-Seq)


title: E4.5-5.5_new_Plate1_E03 (scBS-Seq)


title: E4.5-5.5_new_Plate1_D11 (scBS-Seq)


title: E4.5-5.5_new_Plate1_D05 (scBS-Seq)


title: E4.5-5.5_new_Plate1_D03 (scBS-Seq)


title: E4.5-5.5_new_Plate1_H02 (scBS-Seq)


title: E4.5-5.5_new_Plate1_C11 (scBS-Seq)


title: E4.5-5.5_new_Plate1_B11 (scBS-Seq)


title: E4.5-5.5_new_Plate1_C02 (scBS-Seq)


title: E4.5-5.5_new_Plate1_B08 (scBS-Seq)


title: E4.5-5.5_new_Plate1_C05 (scBS-Seq)


title: E4.5-5.5_new_Plate1_B12 (scBS-Seq)


title: E4.5-5.5_new_Plate1_C09 (scBS-Seq)


title: E4.5-5.5_new_Plate1_C03 (scBS-Seq)


title: E4.5-5.5_new_Plate1_B07 (scBS-Seq)


title: E4.5-5.5_new_Plate1_B02 (scBS-Seq)


title: E4.5-5.5_new_Plate1_A12 (scBS-Seq)


title: E4.5-5.5_new_Plate1_B01 (scBS-Seq)


title: E4.5-5.5_new_Plate1_A09 (scBS-Seq)


title: E4.5-5.5_new_Plate1_A07 (scBS-Seq)


title: E4.5-5.5_new_Plate1_A08 (scBS-Seq)


title: E4.5-5.5_new_Plate1_E02 (scBS-Seq)


title: E4.5-5.5_new_Plate1_A04 (scBS-Seq)


title: E4.5-5.5_new_Plate1_A05 (scBS-Seq)


title: E4.5-5.5_new_Plate1_A03 (scBS-Seq)


title: E4.5-5.5_new_Plate1_A02 (scBS-Seq)


title: E4.5-5.5_new_Plate1_C08 (scBS-Seq)


title: E7.5_Plate4_H4 (scRNA-Seq)

data_processing:
Libraries were sequenced on the Illumina Nextseq 500 platform using the default RTA analysis software.
RNA-seq libraries were aligned to the GRCm38 mouse genome build using HiSat270 (v2.1.0) using options --dta --sp 1000,1000 --no-mixed --no-discordant, yielding a mean of 611,000 aligned reads per cell.
Subsequently, gene expression counts were quantified from the mapped reads using featureCounts with the Ensembl gene annotation (version 87). Only protein-coding genes matching canonical chromosomes were considered. The read counts were log-transformed and size-factor adjusted.
Genome_build: GRCm38
Supplementary_files_format_and_content: A table of genes (rows) x cells (columns). The first column is the ensembl gene ID.  RNAseq quantitation file.

molecule: polyA RNA


title: E7.5_Plate4_H6 (scRNA-Seq)


title: E7.5_Plate4_H8 (scRNA-Seq)


title: E7.5_Plate4_H5 (scRNA-Seq)


title: E7.5_Plate4_H9 (scRNA-Seq)


title: E7.5_Plate4_H3 (scRNA-Seq)


title: E7.5_Plate4_H1 (scRNA-Seq)


title: E7.5_Plate4_H2 (scRNA-Seq)


title: E7.5_Plate4_H12 (scRNA-Seq)


title: E7.5_Plate4_H11 (scRNA-Seq)


title: E7.5_Plate4_H10 (scRNA-Seq)


title: E4.5-5.5_new_Plate1_A11 (scBS-Seq)


title: E7.5_Plate4_G9 (scRNA-Seq)


title: E7.5_Plate4_G5 (scRNA-Seq)


title: E7.5_Plate4_G4 (scRNA-Seq)


title: E7.5_Plate4_G3 (scRNA-Seq)


title: E7.5_Plate4_G2 (scRNA-Seq)


title: E7.5_Plate4_G1 (scRNA-Seq)


title: E7.5_Plate4_G12 (scRNA-Seq)


title: E7.5_Plate4_G10 (scRNA-Seq)


title: E7.5_Plate4_G11 (scRNA-Seq)


title: E7.5_Plate4_F8 (scRNA-Seq)


title: E7.5_Plate4_F9 (scRNA-Seq)


title: E7.5_Plate4_H7 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_A07 (scBS-Seq)


title: E7.5_Plate4_F7 (scRNA-Seq)


title: E7.5_Plate4_G8 (scRNA-Seq)


title: E7.5_Plate4_F5 (scRNA-Seq)


title: E7.5_Plate4_F6 (scRNA-Seq)


title: E7.5_Plate4_F2 (scRNA-Seq)


title: E7.5_Plate4_F3 (scRNA-Seq)


title: E7.5_Plate4_G7 (scRNA-Seq)


title: E7.5_Plate4_F4 (scRNA-Seq)


title: E7.5_Plate4_F1 (scRNA-Seq)


title: E7.5_Plate4_F11 (scRNA-Seq)


title: E7.5_Plate4_F10 (scRNA-Seq)


title: E7.5_Plate4_F12 (scRNA-Seq)


title: E7.5_Plate4_E8 (scRNA-Seq)


title: E7.5_Plate4_E7 (scRNA-Seq)


title: E7.5_Plate4_E5 (scRNA-Seq)


title: E7.5_Plate4_E6 (scRNA-Seq)


title: E7.5_Plate4_E3 (scRNA-Seq)


title: E7.5_Plate4_G6 (scRNA-Seq)


title: E7.5_Plate4_E4 (scRNA-Seq)


title: E7.5_Plate4_E1 (scRNA-Seq)


title: E7.5_Plate4_E12 (scRNA-Seq)


title: E7.5_Plate4_E11 (scRNA-Seq)


title: E7.5_Plate4_E10 (scRNA-Seq)


title: E7.5_Plate4_D9 (scRNA-Seq)


title: E7.5_Plate4_D8 (scRNA-Seq)


title: E7.5_Plate4_D7 (scRNA-Seq)


title: E7.5_Plate4_D6 (scRNA-Seq)


title: E7.5_Plate4_D5 (scRNA-Seq)


title: E7.5_Plate4_D4 (scRNA-Seq)


title: E7.5_Plate4_E9 (scRNA-Seq)


title: E7.5_Plate4_D3 (scRNA-Seq)


title: E7.5_Plate4_D12 (scRNA-Seq)


title: E7.5_Plate4_D10 (scRNA-Seq)


title: E7.5_Plate4_D11 (scRNA-Seq)


title: E7.5_Plate4_C9 (scRNA-Seq)


title: E7.5_Plate4_C8 (scRNA-Seq)


title: E7.5_Plate4_E2 (scRNA-Seq)


title: E7.5_Plate4_D2 (scRNA-Seq)


title: E7.5_Plate4_C4 (scRNA-Seq)


title: E7.5_Plate4_C5 (scRNA-Seq)


title: E7.5_Plate4_C3 (scRNA-Seq)


title: E7.5_Plate4_C1 (scRNA-Seq)


title: E7.5_Plate4_C7 (scRNA-Seq)


title: E7.5_Plate4_C12 (scRNA-Seq)


title: E7.5_Plate4_C11 (scRNA-Seq)


title: E7.5_Plate4_C10 (scRNA-Seq)


title: E7.5_Plate4_B6 (scRNA-Seq)


title: E7.5_Plate4_B9 (scRNA-Seq)


title: E7.5_Plate4_B5 (scRNA-Seq)


title: E7.5_Plate4_B8 (scRNA-Seq)


title: E7.5_Plate4_B7 (scRNA-Seq)


title: E7.5_Plate4_B4 (scRNA-Seq)


title: E7.5_Plate4_B3 (scRNA-Seq)


title: E7.5_Plate4_D1 (scRNA-Seq)


title: E7.5_Plate4_B2 (scRNA-Seq)


title: E7.5_Plate4_B1 (scRNA-Seq)


title: E7.5_Plate4_B12 (scRNA-Seq)


title: E7.5_Plate4_B10 (scRNA-Seq)


title: E7.5_Plate4_A9 (scRNA-Seq)


title: E7.5_Plate4_C6 (scRNA-Seq)


title: E7.5_Plate4_A7 (scRNA-Seq)


title: E7.5_Plate4_C2 (scRNA-Seq)


title: E7.5_Plate4_B11 (scRNA-Seq)


title: E7.5_Plate4_A8 (scRNA-Seq)


title: E7.5_Plate4_A4 (scRNA-Seq)


title: E7.5_Plate4_A6 (scRNA-Seq)


title: E7.5_Plate4_A3 (scRNA-Seq)


title: E7.5_Plate4_A12 (scRNA-Seq)


title: E7.5_Plate4_A2 (scRNA-Seq)


title: E7.5_Plate4_A11 (scRNA-Seq)


title: E7.5_Plate4_A10 (scRNA-Seq)


title: E7.5_Plate3_H8 (scRNA-Seq)


title: E7.5_Plate3_H3 (scRNA-Seq)


title: E7.5_Plate3_H6 (scRNA-Seq)


title: E7.5_Plate4_A5 (scRNA-Seq)


title: E7.5_Plate3_H7 (scRNA-Seq)


title: E7.5_Plate3_H5 (scRNA-Seq)


title: E7.5_Plate3_H4 (scRNA-Seq)


title: E7.5_Plate3_H1 (scRNA-Seq)


title: E7.5_Plate3_H2 (scRNA-Seq)


title: E7.5_Plate3_H12 (scRNA-Seq)


title: E7.5_Plate3_H11 (scRNA-Seq)


title: E7.5_Plate3_H10 (scRNA-Seq)


title: E7.5_Plate3_G9 (scRNA-Seq)


title: E7.5_Plate3_G8 (scRNA-Seq)


title: E7.5_Plate3_G7 (scRNA-Seq)


title: E7.5_Plate3_G5 (scRNA-Seq)


title: E7.5_Plate4_A1 (scRNA-Seq)


title: E7.5_Plate3_G3 (scRNA-Seq)


title: E7.5_Plate3_G6 (scRNA-Seq)


title: E7.5_Plate3_G4 (scRNA-Seq)


title: E7.5_Plate3_G2 (scRNA-Seq)


title: E7.5_Plate3_G1 (scRNA-Seq)


title: E7.5_Plate3_G12 (scRNA-Seq)


title: E7.5_Plate3_F9 (scRNA-Seq)


title: E7.5_Plate3_F8 (scRNA-Seq)


title: E7.5_Plate3_G11 (scRNA-Seq)


title: E7.5_Plate3_H9 (scRNA-Seq)


title: E7.5_Plate3_F7 (scRNA-Seq)


title: E7.5_Plate3_F5 (scRNA-Seq)


title: E7.5_Plate3_F6 (scRNA-Seq)


title: E7.5_Plate3_F3 (scRNA-Seq)


title: E7.5_Plate3_F2 (scRNA-Seq)


title: E7.5_Plate3_F4 (scRNA-Seq)


title: E7.5_Plate3_F1 (scRNA-Seq)


title: E7.5_Plate3_F11 (scRNA-Seq)


title: E7.5_Plate3_F12 (scRNA-Seq)


title: E7.5_Plate3_F10 (scRNA-Seq)


title: E7.5_Plate3_E9 (scRNA-Seq)


title: E7.5_Plate3_E7 (scRNA-Seq)


title: E7.5_Plate3_E6 (scRNA-Seq)


title: E7.5_Plate3_E8 (scRNA-Seq)


title: E7.5_Plate3_E5 (scRNA-Seq)


title: E7.5_Plate3_E4 (scRNA-Seq)


title: E7.5_Plate3_E2 (scRNA-Seq)


title: E7.5_Plate3_E10 (scRNA-Seq)


title: E7.5_Plate3_G10 (scRNA-Seq)


title: E7.5_Plate3_E3 (scRNA-Seq)


title: E7.5_Plate3_E12 (scRNA-Seq)


title: E7.5_Plate3_D8 (scRNA-Seq)


title: E7.5_Plate3_D9 (scRNA-Seq)


title: E7.5_Plate3_D5 (scRNA-Seq)


title: E7.5_Plate3_D7 (scRNA-Seq)


title: E7.5_Plate3_D6 (scRNA-Seq)


title: E7.5_Plate3_D4 (scRNA-Seq)


title: E7.5_Plate3_D12 (scRNA-Seq)


title: E7.5_Plate3_D11 (scRNA-Seq)


title: E7.5_Plate3_E11 (scRNA-Seq)


title: E7.5_Plate3_C8 (scRNA-Seq)


title: E7.5_Plate3_C6 (scRNA-Seq)


title: E7.5_Plate3_D3 (scRNA-Seq)


title: E7.5_Plate3_D10 (scRNA-Seq)


title: E4.5-5.5_new_Plate1_G03 (scBS-Seq)


title: E7.5_Plate3_C4 (scRNA-Seq)


title: E7.5_Plate3_C5 (scRNA-Seq)


title: E7.5_Plate3_C3 (scRNA-Seq)


title: E7.5_Plate3_E1 (scRNA-Seq)


title: E7.5_Plate3_C1 (scRNA-Seq)


title: E7.5_Plate3_C2 (scRNA-Seq)


title: E7.5_Plate3_C12 (scRNA-Seq)


title: E7.5_Plate3_C10 (scRNA-Seq)


title: E7.5_Plate3_C11 (scRNA-Seq)


title: E7.5_Plate3_B8 (scRNA-Seq)


title: E7.5_Plate3_B7 (scRNA-Seq)


title: E7.5_Plate3_B9 (scRNA-Seq)


title: E7.5_Plate3_D1 (scRNA-Seq)


title: E7.5_Plate3_D2 (scRNA-Seq)


title: E7.5_Plate3_B4 (scRNA-Seq)


title: E7.5_Plate3_B5 (scRNA-Seq)


title: E7.5_Plate3_B3 (scRNA-Seq)


title: E7.5_Plate3_C9 (scRNA-Seq)


title: E7.5_Plate3_B6 (scRNA-Seq)


title: E7.5_Plate3_B12 (scRNA-Seq)


title: E7.5_Plate3_C7 (scRNA-Seq)


title: E7.5_Plate3_B2 (scRNA-Seq)


title: E7.5_Plate3_B11 (scRNA-Seq)


title: E7.5_Plate3_A9 (scRNA-Seq)


title: E7.5_Plate3_B10 (scRNA-Seq)


title: E7.5_Plate3_A7 (scRNA-Seq)


title: E7.5_Plate3_A6 (scRNA-Seq)


title: E7.5_Plate3_A5 (scRNA-Seq)


title: E7.5_Plate3_A8 (scRNA-Seq)


title: E7.5_Plate3_A3 (scRNA-Seq)


title: E7.5_Plate3_A4 (scRNA-Seq)


title: E7.5_Plate3_A2 (scRNA-Seq)


title: E7.5_Plate3_B1 (scRNA-Seq)


title: E7.5_Plate3_A12 (scRNA-Seq)


title: E7.5_Plate3_A10 (scRNA-Seq)


title: E7.5_Plate3_A1 (scRNA-Seq)


title: E7.5_Plate3_A11 (scRNA-Seq)


title: E7.5_Plate2_H9 (scRNA-Seq)


title: E7.5_Plate2_H7 (scRNA-Seq)


title: E7.5_Plate2_H8 (scRNA-Seq)


title: E7.5_Plate2_H6 (scRNA-Seq)


title: E7.5_Plate2_H3 (scRNA-Seq)


title: E7.5_Plate2_H5 (scRNA-Seq)


title: E7.5_Plate2_H4 (scRNA-Seq)


title: E7.5_Plate2_H2 (scRNA-Seq)


title: E7.5_Plate2_H1 (scRNA-Seq)


title: E7.5_Plate2_H11 (scRNA-Seq)


title: E7.5_Plate2_G9 (scRNA-Seq)


title: E7.5_Plate2_G6 (scRNA-Seq)


title: E7.5_Plate2_G7 (scRNA-Seq)


title: E7.5_Plate2_H10 (scRNA-Seq)


title: E7.5_Plate2_G8 (scRNA-Seq)


title: E7.5_Plate2_G4 (scRNA-Seq)


title: E7.5_Plate2_G3 (scRNA-Seq)


title: E7.5_Plate2_G1 (scRNA-Seq)


title: E7.5_Plate2_G2 (scRNA-Seq)


title: E7.5_Plate2_G12 (scRNA-Seq)


title: E7.5_Plate2_G10 (scRNA-Seq)


title: E7.5_Plate2_G11 (scRNA-Seq)


title: E7.5_Plate2_F9 (scRNA-Seq)


title: E7.5_Plate2_F7 (scRNA-Seq)


title: E7.5_Plate2_F3 (scRNA-Seq)


title: E7.5_Plate2_F8 (scRNA-Seq)


title: E7.5_Plate2_F1 (scRNA-Seq)


title: E7.5_Plate2_F4 (scRNA-Seq)


title: E7.5_Plate2_F5 (scRNA-Seq)


title: E7.5_Plate2_F2 (scRNA-Seq)


title: E7.5_Plate2_F12 (scRNA-Seq)


title: E7.5_Plate2_H12 (scRNA-Seq)


title: E7.5_Plate2_F11 (scRNA-Seq)


title: E7.5_Plate2_F10 (scRNA-Seq)


title: E7.5_Plate2_E9 (scRNA-Seq)


title: E7.5_Plate2_E8 (scRNA-Seq)


title: E7.5_Plate2_G5 (scRNA-Seq)


title: E7.5_Plate2_E5 (scRNA-Seq)


title: E7.5_Plate2_E7 (scRNA-Seq)


title: E7.5_Plate2_E6 (scRNA-Seq)


title: E7.5_Plate2_E1 (scRNA-Seq)


title: E7.5_Plate2_E12 (scRNA-Seq)


title: E7.5_Plate2_E10 (scRNA-Seq)


title: E7.5_Plate2_D8 (scRNA-Seq)


title: E7.5_Plate2_F6 (scRNA-Seq)


title: E7.5_Plate2_D7 (scRNA-Seq)


title: E7.5_Plate2_D6 (scRNA-Seq)


title: E7.5_Plate2_D9 (scRNA-Seq)


title: E7.5_Plate2_E11 (scRNA-Seq)


title: E7.5_Plate2_D2 (scRNA-Seq)


title: E7.5_Plate2_D1 (scRNA-Seq)


title: E7.5_Plate2_D11 (scRNA-Seq)


title: E7.5_Plate2_D3 (scRNA-Seq)


title: E7.5_Plate2_D12 (scRNA-Seq)


title: E7.5_Plate2_E4 (scRNA-Seq)


title: E7.5_Plate2_C9 (scRNA-Seq)


title: E7.5_Plate2_D5 (scRNA-Seq)


title: E7.5_Plate2_E3 (scRNA-Seq)


title: E7.5_Plate2_C8 (scRNA-Seq)


title: E7.5_Plate2_C4 (scRNA-Seq)


title: E7.5_Plate2_C3 (scRNA-Seq)


title: E7.5_Plate2_C6 (scRNA-Seq)


title: E7.5_Plate2_C2 (scRNA-Seq)


title: E7.5_Plate2_C12 (scRNA-Seq)


title: E7.5_Plate2_E2 (scRNA-Seq)


title: E7.5_Plate2_C5 (scRNA-Seq)


title: E7.5_Plate2_C7 (scRNA-Seq)


title: E7.5_Plate2_C1 (scRNA-Seq)


title: E7.5_Plate2_C11 (scRNA-Seq)


title: E7.5_Plate2_C10 (scRNA-Seq)


title: E7.5_Plate2_B9 (scRNA-Seq)


title: E7.5_Plate2_D4 (scRNA-Seq)


title: E7.5_Plate2_B7 (scRNA-Seq)


title: E7.5_Plate2_B8 (scRNA-Seq)


title: E7.5_Plate2_B4 (scRNA-Seq)


title: E7.5_Plate2_B5 (scRNA-Seq)


title: E7.5_Plate2_B3 (scRNA-Seq)


title: E7.5_Plate2_D10 (scRNA-Seq)


title: E7.5_Plate2_B6 (scRNA-Seq)


title: E7.5_Plate2_B2 (scRNA-Seq)


title: E7.5_Plate2_B12 (scRNA-Seq)


title: E7.5_Plate2_B11 (scRNA-Seq)


title: E7.5_Plate2_A7 (scRNA-Seq)


title: E7.5_Plate2_B10 (scRNA-Seq)


title: E7.5_Plate2_A8 (scRNA-Seq)


title: E7.5_Plate2_A9 (scRNA-Seq)


title: E7.5_Plate2_B1 (scRNA-Seq)


title: E7.5_Plate2_A5 (scRNA-Seq)


title: E7.5_Plate2_A6 (scRNA-Seq)


title: E7.5_Plate2_A4 (scRNA-Seq)


title: E7.5_Plate2_A11 (scRNA-Seq)


title: E7.5_Plate2_A10 (scRNA-Seq)


title: E7.5_Plate1_H3 (scRNA-Seq)


title: E7.5_Plate2_A3 (scRNA-Seq)


title: E7.5_Plate2_A1 (scRNA-Seq)


title: E7.5_Plate2_A2 (scRNA-Seq)


title: E7.5_Plate2_A12 (scRNA-Seq)


title: E7.5_Plate1_F5 (scRNA-Seq)


title: E7.5_Plate1_A5 (scRNA-Seq)


title: E7.5_Plate1_B10 (scRNA-Seq)


title: E7.5_Plate1_A3 (scRNA-Seq)


title: E7.5_Plate1_D2 (scRNA-Seq)


title: E7.5_Plate1_D7 (scRNA-Seq)


title: E6.75_Plate2_H7 (scRNA-Seq)


title: E6.75_Plate2_H8 (scRNA-Seq)


title: E6.75_Plate2_H5 (scRNA-Seq)


title: E6.75_Plate2_H6 (scRNA-Seq)


title: E6.75_Plate2_H4 (scRNA-Seq)


title: E6.75_Plate2_H3 (scRNA-Seq)


title: E6.75_Plate2_H2 (scRNA-Seq)


title: E6.75_Plate2_H1 (scRNA-Seq)


title: E6.75_Plate2_H11 (scRNA-Seq)


title: E6.75_Plate2_G4 (scRNA-Seq)


title: E6.75_Plate2_G7 (scRNA-Seq)


title: E6.75_Plate2_H10 (scRNA-Seq)


title: E6.75_Plate2_G5 (scRNA-Seq)


title: E6.75_Plate2_G3 (scRNA-Seq)


title: E7.5_Plate1_G2 (scRNA-Seq)


title: E6.75_Plate2_G1 (scRNA-Seq)


title: E6.75_Plate2_H9 (scRNA-Seq)


title: E6.75_Plate2_G8 (scRNA-Seq)


title: E6.75_Plate2_G12 (scRNA-Seq)


title: E6.75_Plate2_G10 (scRNA-Seq)


title: E6.75_Plate2_F8 (scRNA-Seq)


title: E6.75_Plate2_G9 (scRNA-Seq)


title: E6.75_Plate2_F5 (scRNA-Seq)


title: ATAC_RA

city: Berlin

first: Laura

middle: V

last: Glaser

address: Ihnestraße 63-73

department: Computational Molecular Biology

country: Germany

institute: Max Planck Institute for Molecular Genetics

data_processing:
RNA-seq: Raw sequencing reads were mapped to mm10 reference genome using Burrows-Wheeler Alignment tool (BWA-MEM algorithm, PMID: 19451168), processing fastq to bam files. Mapped reads were sorted using SAMtools (PMID: 19505943) and DESeq2 (PMID: 25516281) was applied for differential gene expression analysis using ENSEMBL gene annotation (Mus_musculus.GRCm38.90).
ChIP-seq: Each ChIP library was sequenced in two separate sequencing runs. Raw sequencing reads were mapped to mm10 reference genome using STAR Alignment tool (STAR_2.5.1b_modified, PMID: 23104886), allowing a maximum intron size of 1 to adjust for non-spliced input data. Subsequently reads from the same library were merged into one file.
ATAC-seq: We processed fastq to bam files using the Burrows-Wheeler Alignment tool (BWA) (PMID: 19451168) for mapping and SAMtools (PMID: 19505943) for filtering, sorting and removing duplicates.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: The DESeq2 derived final data file contains all genes with an adjusted p-value below 0.1 (padj < 0.1).
Supplementary_files_format_and_content: ChIP-seq: Mapped reads were converted to bigwig coverage tracks using the bam2bigwig script (https://github.com/milospjanic/bam2bigwig).
Supplementary_files_format_and_content: ATAC-seq: We called peaks on the alignment results using MACS2 (PMID: 18798982) and converted bam files to bigwig format using the bamToBigWig tool from the bioinformatics library Gonetics (P. Benner. Gonetics. https://github.com/pbenner/gonetics).

source_name: Embryonic stem cells

growth_protocol: E14 mouse embryonic stem cells (mESCs) were cultured under feeder-free conditions and routinely passaged every two days in ES medium plus LIF: Glasgow Minimum Essential Medium (Sigma-Aldrich) supplemented with 17% FBS (HycloneTM, SV30160.03, GE Healthcare), 2 mM GlutaMAXTM (Gibco), 100 U/ml Penicillin-Streptomycin (Gibco), 1x MEM Non-Essential Amino Acid Solution (Gibco), 1 mM Sodium Pyruvate (Gibco), 0.5 mM 2-Mercaptoethanol (Gibco), and recombinantly expressed LIF.

extract_protocol:
2x105 low passage (< 10) E14 cells were plated per 10 cm culture dish and cultivated for 48 h in regular ES medium containing LIF. 4 h prior to harvest cells were treated with LIF or RA as described in the treatment protocol. 75,000 cells per treatment were subjected to transposition reaction and PCR amplification of accessible regions by Omni-ATAC-seq as described previously by Corces et al. (PMID: 28846090).
Sequencing libraries were constructed using Omni-ATAC-seq ) (Corces et al., PMID: 28846090), a modified version of the Nextera DNA Sample prep kit (Illumina, FC-121-1030).

treatment_protocol: E14 mESC cells were cultured in the presence of leukemia inhibitory factor (LIF) in order to maintain the pluripotent state of the cells. To exit from pluripotency and push the cells towards differentiation, LIF was withdrawn and retinoic acid (RA, Sigma, R2625) was added to the medium to a final concentration of 1 µM. For all experiments, 4h prior to harvest, cell culture medium was removed, cells washed twice with PBS and fresh ES medium was added containing either LIF or RA.

tag: cell line

value: E14 ES cells

tag: treatment

value: RA


title: E6.75_Plate2_F4 (scRNA-Seq)


title: E6.75_Plate2_F9 (scRNA-Seq)


title: E6.75_Plate2_G11 (scRNA-Seq)


title: E6.75_Plate2_G2 (scRNA-Seq)


title: E6.75_Plate2_F2 (scRNA-Seq)


title: ATAC_LIF

value: LIF


title: E6.75_Plate2_H12 (scRNA-Seq)


title: E6.75_Plate2_G6 (scRNA-Seq)


title: E6.75_Plate2_F11 (scRNA-Seq)


title: E6.75_Plate2_F1 (scRNA-Seq)


title: E6.75_Plate2_E9 (scRNA-Seq)


title: E6.75_Plate2_F10 (scRNA-Seq)


title: E6.75_Plate2_E8 (scRNA-Seq)


title: E6.75_Plate2_F6 (scRNA-Seq)


title: E6.75_Plate2_F7 (scRNA-Seq)


title: E6.75_Plate2_E5 (scRNA-Seq)


title: E6.75_Plate2_E6 (scRNA-Seq)


title: E6.75_Plate2_E4 (scRNA-Seq)


title: E6.75_Plate2_E11 (scRNA-Seq)


title: E6.75_Plate2_E3 (scRNA-Seq)


title: E6.75_Plate2_E12 (scRNA-Seq)


title: E6.75_Plate2_E1 (scRNA-Seq)


title: E6.75_Plate2_E2 (scRNA-Seq)


title: E6.75_Plate2_F3 (scRNA-Seq)


title: E6.75_Plate2_E7 (scRNA-Seq)


title: E6.75_Plate2_D7 (scRNA-Seq)


title: E6.75_Plate2_E10 (scRNA-Seq)


title: E6.75_Plate2_D8 (scRNA-Seq)


title: E6.75_Plate2_D9 (scRNA-Seq)


title: E6.75_Plate2_F12 (scRNA-Seq)


title: E6.75_Plate2_D4 (scRNA-Seq)


title: E6.75_Plate2_D3 (scRNA-Seq)


title: E6.75_Plate2_D1 (scRNA-Seq)


title: E6.75_Plate2_D2 (scRNA-Seq)


title: E6.75_Plate2_D12 (scRNA-Seq)


title: E6.75_Plate2_D5 (scRNA-Seq)


title: E6.75_Plate2_C9 (scRNA-Seq)


title: E6.75_Plate2_D11 (scRNA-Seq)


title: E6.75_Plate2_C8 (scRNA-Seq)


title: E6.75_Plate2_C6 (scRNA-Seq)


title: E6.75_Plate2_C7 (scRNA-Seq)


title: E6.75_Plate2_C5 (scRNA-Seq)


title: E6.75_Plate2_D6 (scRNA-Seq)


title: E6.75_Plate2_C1 (scRNA-Seq)


title: E6.75_Plate2_C4 (scRNA-Seq)


title: E6.75_Plate2_C2 (scRNA-Seq)


title: E6.75_Plate2_C10 (scRNA-Seq)


title: E6.75_Plate2_C3 (scRNA-Seq)


title: E6.75_Plate2_B7 (scRNA-Seq)


title: E6.75_Plate2_B9 (scRNA-Seq)


title: E6.75_Plate2_B4 (scRNA-Seq)


title: E6.75_Plate2_B6 (scRNA-Seq)


title: E6.75_Plate2_C12 (scRNA-Seq)


title: E6.75_Plate2_B8 (scRNA-Seq)


title: E6.75_Plate2_B3 (scRNA-Seq)


title: E6.75_Plate2_B1 (scRNA-Seq)


title: E6.75_Plate2_B12 (scRNA-Seq)


title: E6.75_Plate2_B2 (scRNA-Seq)


title: E6.75_Plate2_D10 (scRNA-Seq)


title: E6.75_Plate2_B10 (scRNA-Seq)


title: E6.75_Plate2_A9 (scRNA-Seq)


title: E6.75_Plate2_A8 (scRNA-Seq)


title: E6.75_Plate2_B11 (scRNA-Seq)


title: E6.75_Plate2_A7 (scRNA-Seq)


title: E6.75_Plate2_A6 (scRNA-Seq)


title: E6.75_Plate2_A5 (scRNA-Seq)


title: E6.75_Plate2_A3 (scRNA-Seq)


title: E6.75_Plate2_A4 (scRNA-Seq)


title: E6.75_Plate2_C11 (scRNA-Seq)


title: E6.75_Plate2_B5 (scRNA-Seq)


title: E6.75_Plate2_A1 (scRNA-Seq)


title: E6.75_Plate2_A12 (scRNA-Seq)


title: E6.5_Plate3_H8 (scRNA-Seq)


title: E6.5_Plate3_H4 (scRNA-Seq)


title: E6.5_Plate3_H9 (scRNA-Seq)


title: E6.5_Plate3_H6 (scRNA-Seq)


title: E6.5_Plate3_H5 (scRNA-Seq)


title: E6.75_Plate2_A10 (scRNA-Seq)


title: E6.5_Plate3_G9 (scRNA-Seq)


title: E6.5_Plate3_H10 (scRNA-Seq)


title: E6.5_Plate3_H7 (scRNA-Seq)


title: E6.5_Plate3_H2 (scRNA-Seq)


title: E6.75_Plate1_B6 (scRNA-Seq)


title: E6.75_Plate2_A11 (scRNA-Seq)


title: E6.5_Plate3_H12 (scRNA-Seq)


title: E6.5_Plate3_H11 (scRNA-Seq)


title: E6.5_Plate3_G6 (scRNA-Seq)


title: E6.5_Plate3_G8 (scRNA-Seq)


title: E6.5_Plate3_H3 (scRNA-Seq)


title: E6.5_Plate3_G4 (scRNA-Seq)


title: E6.5_Plate3_G5 (scRNA-Seq)


title: E6.5_Plate3_G3 (scRNA-Seq)


title: E6.75_Plate2_A2 (scRNA-Seq)


title: E6.5_Plate3_G7 (scRNA-Seq)


title: E6.5_Plate3_G1 (scRNA-Seq)


title: E6.5_Plate3_G2 (scRNA-Seq)


title: E6.5_Plate3_G11 (scRNA-Seq)


title: E6.5_Plate3_G12 (scRNA-Seq)


title: E6.5_Plate3_G10 (scRNA-Seq)


title: E6.5_Plate3_F9 (scRNA-Seq)


title: E6.5_Plate3_F8 (scRNA-Seq)


title: E6.5_Plate3_H1 (scRNA-Seq)


title: E6.5_Plate3_F7 (scRNA-Seq)


title: E6.5_Plate3_F6 (scRNA-Seq)


title: E6.5_Plate3_F2 (scRNA-Seq)


title: E6.5_Plate3_F4 (scRNA-Seq)


title: E6.5_Plate3_F3 (scRNA-Seq)


title: E6.5_Plate3_F11 (scRNA-Seq)


title: E6.5_Plate3_F10 (scRNA-Seq)


title: E6.5_Plate3_E9 (scRNA-Seq)


title: E6.5_Plate3_F1 (scRNA-Seq)


title: E6.5_Plate3_E7 (scRNA-Seq)


title: E6.5_Plate3_F5 (scRNA-Seq)


title: E6.5_Plate3_E3 (scRNA-Seq)


title: E6.5_Plate3_E6 (scRNA-Seq)


title: E6.5_Plate3_E4 (scRNA-Seq)


title: E6.5_Plate3_E8 (scRNA-Seq)


title: E6.5_Plate3_E5 (scRNA-Seq)


title: E6.5_Plate3_E2 (scRNA-Seq)


title: E6.5_Plate3_D9 (scRNA-Seq)


title: E6.5_Plate3_E1 (scRNA-Seq)


title: E6.5_Plate3_E12 (scRNA-Seq)


title: E6.5_Plate3_E11 (scRNA-Seq)


title: E6.5_Plate3_D8 (scRNA-Seq)


title: E6.5_Plate3_D6 (scRNA-Seq)


title: E6.5_Plate3_D7 (scRNA-Seq)


title: E6.5_Plate3_D5 (scRNA-Seq)


title: E6.5_Plate3_D4 (scRNA-Seq)


title: E6.5_Plate3_D1 (scRNA-Seq)


title: E6.5_Plate3_C9 (scRNA-Seq)


title: E6.5_Plate3_D10 (scRNA-Seq)


title: E6.5_Plate3_D2 (scRNA-Seq)


title: E6.5_Plate3_D3 (scRNA-Seq)


title: E6.5_Plate3_C6 (scRNA-Seq)


title: E6.5_Plate3_F12 (scRNA-Seq)


title: E6.5_Plate3_C4 (scRNA-Seq)


title: E6.5_Plate3_D12 (scRNA-Seq)


title: E6.5_Plate3_C7 (scRNA-Seq)


title: E6.5_Plate3_C8 (scRNA-Seq)


title: E6.5_Plate3_D11 (scRNA-Seq)


title: E6.5_Plate3_E10 (scRNA-Seq)


title: E6.5_Plate3_C5 (scRNA-Seq)


title: E6.5_Plate3_C1 (scRNA-Seq)


title: E6.5_Plate3_C12 (scRNA-Seq)


title: E6.5_Plate3_B9 (scRNA-Seq)


title: E6.5_Plate3_C11 (scRNA-Seq)


title: E6.5_Plate3_B8 (scRNA-Seq)


title: E6.5_Plate3_C2 (scRNA-Seq)


title: E6.5_Plate3_B7 (scRNA-Seq)


title: E6.5_Plate3_C10 (scRNA-Seq)


title: E6.5_Plate3_B4 (scRNA-Seq)


title: E6.5_Plate3_B5 (scRNA-Seq)


title: E6.5_Plate3_B2 (scRNA-Seq)


title: E6.5_Plate3_B1 (scRNA-Seq)


title: E6.5_Plate3_B12 (scRNA-Seq)


title: E6.5_Plate3_A9 (scRNA-Seq)


title: E6.5_Plate3_A5 (scRNA-Seq)


title: E6.5_Plate3_C3 (scRNA-Seq)


title: E6.5_Plate3_A6 (scRNA-Seq)


title: E6.5_Plate3_A7 (scRNA-Seq)


title: E6.5_Plate3_A8 (scRNA-Seq)


title: E6.5_Plate3_A3 (scRNA-Seq)


title: E6.5_Plate3_A4 (scRNA-Seq)


title: E6.5_Plate3_B10 (scRNA-Seq)


title: E6.5_Plate3_A2 (scRNA-Seq)


title: E6.5_Plate3_A1 (scRNA-Seq)


title: E6.5_Plate3_A12 (scRNA-Seq)


title: E6.5_Plate3_B6 (scRNA-Seq)


title: E6.5_Plate3_A10 (scRNA-Seq)


title: E6.5_Plate3_A11 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_H12 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p205

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

data_processing:
Quality check of raw reads by FastQC
Raw sequencing data in. fastq format were processed using RNA-seq aligner STAR v2. GenCode v24 was used for transcriptome annotation
The abundance of transcripts was summarized into CPM (Counts per Million mapped reads).
Genes with a value of CPM > 0.5 in at least two samples were included for downstream analysis
The filtered raw read data were transformed to log2-counts per million (logCPM) and normalized with the associated precision weights using "voom" and "TMM" normalization implemented in R/Bioconductor packages, including "limma" and "edgeR"
Genome_build: hg38
Supplementary_files_format_and_content: aligned.readCounts.txt

organism: Homo sapiens

source_name: Ideopathic pulmonary disease, PBMCs

extract_protocol: PBMC samples were obtained by density centrifugation. RNA was extracted with TRIzol (Invitrogen) and was re-precipitated by sodium acetate/ethanol. RNA quality and integrity were confirmed by Nanodrop (A260/A280 ratios between 1.7 and 2.2) and Bio-Analyzer mini-gel assay (Agilent, Santa Clara, CA). All RNA samples displayed a RNA Integrity Number (RIN) > 7 were proceeded to cDNA library preparation at the Genomics Core Facility of the University of Chicago (https://fgf.uchicago.edu/). Total RNA in the amount of 1μg per sample was depleted of ribosomal RNA using the Ribo-Zero kit (Epicentre, Madison, WI). The directional (first strand) cDNA libraries were prepared following the guide of TruSeq Stranded Total RNA Sample Preparation kit. RNA was fragmented at 94°C for 6 min, followed by the first strand cDNA generation. Deoxy-UTP was incorporated in second strand synthesis in order to effectively quench the second strand during PCR amplification. After adenylation of the 3' end and ligation of adapters, fragments were selected and enriched with 10 cycles of PCR amplification. Clusters were generated by bridge amplification within paired-end flow cells using Illumina HiSeq PE Cluster Kit v4 cBot according to manufacturer’s instructions (Illumina, San Diego, CA). The clusters on flow cells were then sequenced on the Illumina HiSeq4000 using HiSeq SBS Kit V4.

tag: disease state

value: Ideopathic pulmonary disease

tag: Sex

value: M

tag: ethnicity

value: Caucasian

tag: cell type

value: Peripheral blood mononuclear cells

tag: patient id

tag: blood draw time (month)

tag: timecourse

tag: pair

tag: tobacco history


title: Ideopathic pulmonary disease, PBMCs, p213


title: E6.5_Plate3_B3 (scRNA-Seq)

tag: strain


title: E6.5_Plate2_G6 (scRNA-Seq)

tag: developmental stage


title: E4.5-5.5_new_Plate4_H11 (scRNA-Seq)

tag: sample type


title: E6.5_Plate3_B11 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_H10 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p154

value: F

value: Other


title: Ideopathic pulmonary disease, PBMCs, p150


title: E4.5-5.5_new_Plate4_H09 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p145


title: Ideopathic pulmonary disease, PBMCs, p128


title: E4.5-5.5_new_Plate4_H07 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_H05 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_H06 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p115


title: E4.5-5.5_new_Plate4_H03 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p127


title: Ideopathic pulmonary disease, PBMCs, p123


title: E4.5-5.5_new_Plate4_H08 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p192


title: E6.5_Plate2_H3 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p108


title: Ideopathic pulmonary disease, PBMCs, p103


title: E4.5-5.5_new_Plate4_H01 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p118


title: Ideopathic pulmonary disease, PBMCs, p098


title: E4.5-5.5_new_Plate4_H04 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_G12 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_G11 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p094


title: E4.5-5.5_new_Plate4_H02 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_G10 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p090


title: E4.5-5.5_new_Plate4_G09 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p077


title: Ideopathic pulmonary disease, PBMCs, p089


title: Ideopathic pulmonary disease, PBMCs, p078


title: E4.5-5.5_new_Plate4_G08 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_G03 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_F10 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_G07 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p066


title: Ideopathic pulmonary disease, PBMCs, p063


title: Ideopathic pulmonary disease, PBMCs, p065


title: E4.5-5.5_new_Plate4_G01 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p069


title: Ideopathic pulmonary disease, PBMCs, p083


title: Ideopathic pulmonary disease, PBMCs, p081


title: E4.5-5.5_new_Plate4_F11 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_G04 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_G05 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p075


title: E4.5-5.5_new_Plate4_G06 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p073


title: E4.5-5.5_new_Plate4_G02 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_F12 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p068


title: Ideopathic pulmonary disease, PBMCs, p056


title: Ideopathic pulmonary disease, PBMCs, p093


title: E4.5-5.5_new_Plate4_F08 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_F04 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_F09 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p058


title: E4.5-5.5_new_Plate4_F05 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p055


title: Ideopathic pulmonary disease, PBMCs, p064


title: E4.5-5.5_new_Plate4_F02 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_F01 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_F03 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p051


title: Ideopathic pulmonary disease, PBMCs, p041


title: Ideopathic pulmonary disease, PBMCs, p052


title: E4.5-5.5_new_Plate4_E12 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p034


title: E4.5-5.5_new_Plate4_E10 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p047


title: Ideopathic pulmonary disease, PBMCs, p050


title: E4.5-5.5_new_Plate4_E09 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_E07 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_E08 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p028


title: Ideopathic pulmonary disease, PBMCs, p027


title: Ideopathic pulmonary disease, PBMCs, p026


title: Ideopathic pulmonary disease, PBMCs, p030


title: E4.5-5.5_new_Plate4_F07 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p059


title: E4.5-5.5_new_Plate4_E04 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_E06 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_F06 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_E05 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_E03 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p021


title: E4.5-5.5_new_Plate4_E02 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_E01 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_D12 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_E11 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p019


title: Ideopathic pulmonary disease, PBMCs, p014


title: Ideopathic pulmonary disease, PBMCs, p036


title: Ideopathic pulmonary disease, PBMCs, p012


title: Ideopathic pulmonary disease, PBMCs, p011


title: E4.5-5.5_new_Plate4_D09 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p022


title: E4.5-5.5_new_Plate4_D08 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p003


title: Ideopathic pulmonary disease, PBMCs, p001


title: E4.5-5.5_new_Plate4_D10 (scRNA-Seq)


title: Ideopathic pulmonary disease, PBMCs, p017


title: E4.5-5.5_new_Plate4_D07 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_D11 (scRNA-Seq)


title: RCC19: IRCR_RCC16_190

city: Seongnam-si

first: Je-Gun

last: Joung

address: 335, Pangyo-ro, Bundang-gu

country: South Korea

institute: CHA University

data_processing:
For cluster generation, the library is loaded into a flow cell where fragments are captured on a lawn of surface-bound oligos complementary to the library adapters. Each fragment is then amplified into distinct, clonal clusters through bridge amplification. When cluster generation is complete, the templates are ready for sequencing.
Illumina SBS technology utilizes a proprietary reversible terminator-based method that detects single bases as they are incorporated into DNA template strands. As all 4 reversible, terminator-bound dNTPs are persent during each sequencing cycle, natural competition minimizes incorporation bias and greatly reduces raw error rates compared to other technologies. The result is highly accurate base-by-base sequencing that virtually eliminates sequence-context-specific errors, even within repetitive sequence regions and homopolymers.
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file include TPM values for samples

source_name: clear cell renal cell carcinoma

extract_protocol:
For library construction, DNA/RNA is extracted from a sample. After performing quality control (QC), qualified samples proceed to library construction.
The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.

value: clear cell renal cell carcinoma


title: RCC18: IRCR_RCC16_178


title: E4.5-5.5_new_Plate4_D06 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_D05 (scRNA-Seq)


title: RCC15: IRCR_RCC13_126


title: E4.5-5.5_new_Plate4_D04 (scRNA-Seq)


title: Combinatorial_library_plasmid_rep2

city: Cleveland

first: Kenneth

last: Matreyek

state: OH

address: 2103 Cornell Rd

department: Pathology

institute: Case Western Reserve University

description:
Library and barcode cassette sequencing from DNA
Combination_indices.csv
Plasmid_reseq

data_processing:
Libraries were sequenced on NextSeq 500 instruments (Illumina) and base called using the instruments' Real Time Analysis software.
Sequencing reads were converted to fastq format and de-multiplexed with bcl2fastq. R1 and R2 were trimmed to the first 16 nucleotides,which includes both the eight nucleotides of known sequence serving as a transgene identifier, as well as the flanking four degenerate nucleotides serving as unique plasmid identifier sequences. These datafiles were used to identify each unique plasmid molecule which had been recombined. In subsequent analyses only looking at the eight nucleotides serving as a transgene identifier, the initial fastq files were trimmed such that only nucleotides 5-12 remained. Both steps were performed using custom python scripts which are posted on the lab Github page.
The properly trimmed fastq files were concatenated to create a single sequence denoting the paired transgene combination. The resulting fastq file was entered into Enrich2, and Log2 enrichment scores for each transgene combination was calculated for each replicate experiment. Scores from replicate experiments were averaged to obtain a single average enrichment score, as well as its standard error.
Genome_build: NONE
Supplementary_files_format_and_content: The "Combination_indices.csv" files lists the indices that denote which transgene is present based on the Illumina sequencing data. The "Enrichment_scores.csv" file is the final result of running the Illumina fastq files through trimming (described above) for the indices, Enrich, and associating the enrichment scores for each index combination back to the transgenes they represent. In this file, the number following "e" represents the replicate number. Columns with the letter "s" following the number are columns containing the enrichment score for that replicate. Columns with the letter "e" contain the standard error for that replicate.

molecule: other

organism: Escherichia coli

source_name: Synthetic sequence

growth_protocol: HEK 293T LLP-rEF1alpha cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 100 U/mL penicillin, 0.1 mg/mL streptomycin

extract_protocol:
Cells were transferred into a microfuge tube, pelleted and stored at -20˚C. Genomic DNA was prepared using the GentraPrep kit (Qiagen) or Dneasy kit (Qiagen).
40 ng of plasmid DNA was mixed with 0.333 µM of forward primer, 0.333 µM of reverse primer, and 2x Kapa Hifi added as half the volume (Supplementary table 1). The mixtures were cycled 12 times in a thermocycler. 1 µl of DPNI enzyme (20 units) was added to each tube, and incubated at 37◦C for 2 hours. 15 µl of product was mixed with 3 µl of (6x gel loading dye), and run on a 0.8 percent agarose gel in TBE. Bands were cut, position 1 bands and position 2 bands were pooled separately, and extracted using the Qiagen Gel Extraction kit. Position 1 and position 2 DNA were eluted in 10 µl nuclease-free water. 5 µl of each eluate were mixed together with 10 µl 2x Gibson mix and incubated at 50◦C for 30 minutes. After incubation, the product was eluted in 5 µl, and 4 µl of library was electroporated into 10-beta cells (NEB) using 0.1 µm cuvettes (Bio-Rad) according to manufacturer instructions. Approximately 2.16 million colony forming units of transformants were grown in 200 ml Luria Broth overnight, and plasmid DNA was extracted with a Qiagen Midiprep Kit (Qiagen). 320 ng of library DNA was mixed with 2x Kapa Hifi Readymix and a final concentration of 0.333 µM KAM2311 and 0.333 µM KAM2312, with 30 µl distributed into 8 replicate tubes. 160 ng of rIP2M_attB_GFP plasmid was mixed with 2x Kapa Hifi and a final concentration of 0.333 µM KAM2313 and 0.333 µM KAM2314, with 30 µl distributed into 4 replicate tubes. Both sets of tubes were amplified over 18 cycles. 1 µl (20 units) of DPNI enzyme was added to each tube, and incubated at 37◦C for 2 hours. After incubation, the rIP2M_attB_GFP amplicon was gel extracted from a 0.8% agarose gel and eluted in 10 µl, whereas the library amplicon was cleaned and concentrated (Zymo), and eluted in 5 µl. 4 µl of each were mixed together with 8 µl of 2x Gibson mix and incubated at 50◦C for 30 minutes. The product was clean-and-concentrated, eluted in 5 µl, and electroporated in 10-beta cells using 0.1 µm cuvettes (Bio-Rad) according to manufacturer's instructions. Approximately 0.5 million colony forming units were amplified in 200 ml Luria Broth overnight, and extracted using the Qiagen Midiprep kit. Sanger sequencing of 8 colonies revealed 6 to be intended library members. This library was called attB-TSPCR.

treatment_protocol: Cells harboring variant libraries, prepared as described above, were grown in the presence of 2 μg/mL doxycycline, incuding expression of the variant library. Cells were passaged over approximately two weeks, with a subset of cells collected and frozen for genomic extraction and sequencing after each replicate was complete.


title: Combinatorial_library_plasmid_rep1

description:
Library and barcode cassette sequencing from DNA
Combination_indices.csv
Plasmid


title: RCC17: IRCR_RCC15_165


title: RCC14: IRCR_RCC13_118


title: RCC13: IRCR_RCC13_114


title: RCC11: IRCR_RCC12_107


title: E4.5-5.5_new_Plate4_D01 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_C11 (scRNA-Seq)


title: RCC12: IRCR_RCC13_111


title: E4.5-5.5_new_Plate4_D03 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_C10 (scRNA-Seq)


title: RCC09: IRCR_RCC12_072


title: RCC08: IRCR_RCC12_071


title: E4.5-5.5_new_Plate4_C09 (scRNA-Seq)


title: ck_FL_Somatopleure_15

city: Boston

first: John

last: Young

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

data_processing:
RNA-seq reads were mapped using STAR to reference genomes (galGal4 or droNov1)
Quantification via FeatureCounts
Differential gene expression was determined using DESeq.
Genome_build: galGal4 for chick or droNov1 for emu
Supplementary_files_format_and_content: Tab delimited .txt files with transcript counts generated from featureCounts

organism: Gallus gallus

source_name: Embryonic tissue

extract_protocol:
RNA was harvested using PicoPure columns
libraries were synthesized from 50ng of total RNA by automation using Kappa reagents followed by 15 cycles of replication.

tag: tissue

value: Somatorpleure at the forelimb leve

tag: Stage


title: ck_FL_Splancnopleure_61

value: Splanchnopleure at the forelimb level


title: ck_FL_Somatopleure_60


title: ck_FL_Splancnopleure_50


title: ck_FL_Splancnopleure_64


title: RCC07: IRCR_RCC12_067


title: ck_FL_Somatopleure_63


title: E4.5-5.5_new_Plate4_C12 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_C08 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_C07 (scRNA-Seq)


title: ck_FL_LPM_31

value: Undifferentiated lateral plate mesoderm at the forelimb level


title: RCC16: IRCR_RCC13_130


title: ck18K3

extract_protocol:
RNA was harvested via lysis in Trizol followed by isolation using RNeasy micro columns.
Libraries were synthesized from 200ng total RNA using the stranded TruSeq kit (Illumina) followed by 15 cycles of amplification.

value: Flank somatopleure


title: ck18K4


title: ck_FL_LPM_30


title: RCC06: IRCR_RCC12_066


title: E4.5-5.5_new_Plate4_C06 (scRNA-Seq)

value: single cell


title: RCC10: IRCR_RCC12_094


title: RCC05: IRCR_RCC11_059


title: E4.5-5.5_new_Plate4_D02 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_C05 (scRNA-Seq)


title: ck18k2


title: ck18K1


title: RCC04: IRCR_RCC11_056


title: E4.5-5.5_new_Plate4_C04 (scRNA-Seq)


title: ck18HL3

value: Hindlimb somatopleure


title: RCC03: IRCR_KN11_046


title: ck_FL_LPM_32


title: ck18HL2


title: RCC02: IRCR_KN11_013


title: RCC01: IRCR_KN11_008


title: E4.5-5.5_new_Plate4_C03 (scRNA-Seq)


title: ck18HL1


title: ck18FL2

value: Forelimb somatopleure


title: ck18FL1


title: Both 3

first: Abby

last: Olsen

address: 60 Fenwood Rd

department: Neurology

institute: Brigham and Women's Hospital

description: Ribosomal depleted RNA

data_processing:
The four raw sequence (.fastq) files generated by the NextSeq were concatenated for each library, then analyzed with FastQC (Babraham Bioinformatics).
Count matrices were generated in R Studio Version 1.1.423 using the Bioconductor (Huber et al., 2015) package called bcbioRNAseq, an open source python framework that aggregates other best-practice pipelines for RNA-seq analysis developed by the Harvard Chan Bioinformatics Core in the Harvard Chan School of Public Health (Steinbaugh MJ, Pantano L, Kirchner RD, Barrera V, Chapman BA, Piper ME, Mistry M, Khetani RS, Rutherford KD, Hofmann O, Hutchinson JN, Sui SH, 2018).
Within the bcbioRNAseq package, STAR (Dobin et al., 2013) was used to align the sequence reads to the Drosophila melanogaster Release 6 reference genome (BDGP6), and Salmon (Patro, Duggal, Love, Irizarry, & Kingsford, 2017) and featureCounts (Y. Liao, Smyth, & Shi, 2014) were used to generate counts associated with known genes. Gene annotations were obtained from Ensembl.
Quality of the RNA-seq data was assessed with MultiQC (Ewels, Magnusson, Lundin, & Käller, 2016).
Principle component analysis demonstrated strongest clustering by genotype (accounting for 43% of the variance). Based on the clustering analysis, 1 sample each from the Control, Glia, and Neuron conditions was excluded from further analysis, leaving a minimum of 3 remaining biological replicates per genotype.
Transcript quantification files produced by Salmon were imported into the DESeq2 package (Love, Huber, & Anders, 2014) and pair-wise differential expression across conditions was analyzed using a generalized linear model implemented in DESeq2. A pseudo count of 1 was added to all genes with an expression count of 0.
Genome_build: Drosophila melanogaster Release 6 reference genome (BDGP6)

organism: Drosophila melanogaster

source_name: Head

growth_protocol: Flies were aged to 10 days post eclosion. Each biological replicate contains 6 flies (3 males and 3 females).

extract_protocol:
Flies were snap frozen on dry ice followed by dissection of heads. Heads were homogenized in trizol and phase separated. The aqueous phase was then purified using the Qiagen Rneasy kit per the manufacturer's protocol.
Stranded libraries for next-generation sequencing were prepared in the Harvard Biopolymers core facility by depleting total RNA of ribosomal RNA using the Directional RNA-Seq Wafergen system (Wafergen). All RNA samples were run on Agilent 2100 TapeStation D1000 High Sensitivity ScreenTape to assess concentration and size distribution prior to library creation and again after library creation. Libraries were also subjected to qPCR analysis for quality control. Libraries were then paired-end sequenced on an Illumina NextSeq 500 instrument.

value: glia and neurons

value: Head

tag: batch

tag: genotype

value: SybQF2, RepoGAL4, QUASSyn/UAS-Syn


title: Both 2

description: Ribosomal depleted RNA


title: Both 4

description: Ribosomal depleted RNA


title: E4.5-5.5_new_Plate4_B12 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_B11 (scRNA-Seq)


title: ck18HL4


title: Neuron 4

description: Ribosomal depleted RNA

value: neurons

value: SybQF2, RepoGAL4, QUAS-Syn/+


title: Neuron 2

description: Ribosomal depleted RNA


title: Both 1

description: Ribosomal depleted RNA


title: E4.5-5.5_new_Plate4_B10 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_B09 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_C02 (scRNA-Seq)


title: ck18FL3


title: Glia 4

description: Ribosomal depleted RNA

value: glia

value: SybQF2, RepoGAL4/UAS-Syn


title: Glia 3

description: Ribosomal depleted RNA


title: Neuron 3

description: Ribosomal depleted RNA


title: Glia 1

description: Ribosomal depleted RNA


title: Control 4

description: Ribosomal depleted RNA

value: SybQF2, RepoGAL4/+


title: E4.5-5.5_new_Plate4_C01 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_B08 (scRNA-Seq)


title: Control 2

description: Ribosomal depleted RNA


title: ck18FL4


title: E4.5-5.5_new_Plate4_B07 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_B06 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_B05 (scRNA-Seq)


title: Control 3

description: Ribosomal depleted RNA


title: Glia 2

description: Ribosomal depleted RNA


title: E4.5-5.5_new_Plate4_A10 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_B03 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_B04 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_A12 (scRNA-Seq)


title: Control 1

description: Ribosomal depleted RNA


title: E4.5-5.5_new_Plate4_B02 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_B01 (scRNA-Seq)


title: Neuron 1

description: Ribosomal depleted RNA


title: E4.5-5.5_new_Plate4_A01 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_A11 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_A07 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_A08 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_H09 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_A06 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_A04 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_A03 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_H03 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_A02 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_H05 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_H02 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_G09 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_G08 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_G06 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_G01 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_G10 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_G07 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_E12 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_F01 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_A09 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_H04 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_F02 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_F07 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_E10 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_H10 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_E09 (scRNA-Seq)


title: E4.5-5.5_new_Plate4_A05 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_D05 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_C07 (scRNA-Seq)


title: HCT116 GROseq, rep2

city: Stockholm

first: Rolf

last: Ohlsson

address: Solnavägen 30, 171 64

department: Department of Oncology-Pathology

country: Sweden

institute: Karolinska Institutet

description: Processed data file: EnsembleGenes75_GROseq-500_raw.txt

data_processing:
Library strategy: GRO-Seq
Reads were aligned to GRCh37.75 using Bowtie 2 under default conditions. Resulting sam-files were loaded into Seqmonk (0.31.1). Probes were defined according to Ensembl GRCh37 release 75. For raw read count quantification, duplicated reads were counted only once and only reads that mapped to the same strand as the probe. Also, regions 500 bp downstream the transcription start sites were excluded from the quantification.
Genome_build: Ensembl GRCh37 release 75
Supplementary_files_format_and_content: Tab-delimited text file includes raw counts for each sample.

growth_protocol: Human colon cancer cells (HCT116) were maintained in McCoy’s 5A modified medium (Life Technologies, 16600-082) supplemented with 10% Fetal Bovine Serum (FBS), penicillin (Life Technologies) and streptomycin (Life Technologies). Normal colon cells (HCEC, ScienCell, 2950) were maintained in Colonic Epithelial Cell Medium (ScienCell, 2951). Both cells were cultured under 5% CO2 circumstance at 37 C.

extract_protocol:
Cells of 1 to 3 million at 50-70% confluency were lysed by loading 1 ml of Tripure Isolation Reagent (Roche Diagnostics, 1667157). Two biological replica were prepared separately in each cell line. Total RNA was extracted by following manufacturer’s instruction. The extracted RNA was subjected on Bioanalyzer 2100 (Agilent Technologies) and RNA integrity number was confirmed as > 8. 10 ug each of total RNA was proceeded for capturing nascent transcript using Click-iT Nascent RNA capture kit (Life Technology, C10365) following manufacturer’s instruction. Briefly, rRNA was removed by Ribominus Eukaryote system v2 (Life Technology, A15020). Etynyl Uridine was crosslinked with azide modified biotin (PEG4 carboxiamide-6-azidohexanyl biotin) and recovered by streptavidin-coated magnetic beads.
cDNA was prepared from EU labeled RNA by SuperScript VILO cDNA Synthesis Kit (Life Technology, 11754050). The sequence library was prepared using Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101). The quality and quantity of the library were assessed on Bioanalyzer 2100 and Qubit (Life Technologies).

treatment_protocol: Cells were incubated with 0.2 mM EU (Ethynyl Uridine, Thermo Fisher Scientific, E10345) for 1 hour at growing condition before RNA extraction.

tag: cell line

value: human colorectal carcinoma cell line


title: E4.5-5.5_new_Plate3_E04 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_E01 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_E03 (scRNA-Seq)


title: HCT116 GROseq, rep1


title: E4.5-5.5_new_Plate3_C05 (scRNA-Seq)


title: HCEC GROseq, rep2

source_name: HCEC

value: HCEC

value: human colonic epithelial cell line


title: E4.5-5.5_new_Plate3_E02 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_C04 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_B07 (scRNA-Seq)


title: HCEC GROseq, rep1


title: E4.5-5.5_new_Plate3_B03 (scRNA-Seq)


title: HCT116 RNAseq, rep1

description: Processed data file: EnsembleGenes75_RNAseq-500_raw.txt

data_processing:
Reads were aligned to GRCh37.75 using Bowtie 2 under default conditions. Resulting sam-files were loaded into Seqmonk (0.31.1). Probes were defined according to GRCh37.75. For raw read count quantification, duplicated reads were counted only once and only reads that mapped to the same strand as the probe. Also, regions 500 bp downstream the transcription start sites were excluded from the quantification.
Genome_build: Ensembl GRCh37 release 75
Supplementary_files_format_and_content: Tab-delimited text file includes raw counts for each sample.

growth_protocol: Human colon cancer cells (HCT116) were maintained in McCoy's 5A modified medium (Life Technologies, 16600-082) supplemented with 10% Fetal Bovine Serum (FBS), penicillin (Life Technologies) and streptomycin (Life Technologies). Normal colon cells (HCEC, ScienCell, 2950) were maintained in Colonic Epithelial Cell Medium (ScienCell, 2951). Both cells were cultured under 5% CO2 circumstance at 37 C.

extract_protocol:
Cells of 1 to 3 million at 50-70% confluency were lysed by loading 1 ml of Tripure Isolation Reagent (Roche Diagnostics, 1667157). Two biological replica were prepared separately in each cell line. Total RNA was extracted by following manufacturer’s instruction. The extracted RNA was subjected on Bioanalyzer 2100 (Agilent Technologies) and RNA integrity number was confirmed as > 8.
4 ug each of total RNA was proceeded for sequence library preparation using Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101). The quality and quantity of the library were assessed on Bioanalyzer 2100 and Qubit (Life Technologies). Total 4 libraries (2 x replica of HCEC, 2 x replica of HCT116) were pooled and sequenced on Illumina MiSeq using MiSeq Reagent Kit v2 (Illumina, MS-102-2002) generating 150 bp single-end read.


title: E4.5-5.5_new_Plate3_B02 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_B01 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_A12 (scRNA-Seq)


title: HCEC RNAseq, rep1


title: E4.5-5.5_new_Plate3_A10 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_A07 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_A02 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_A04 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_H12 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_H11 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_H10 (scRNA-Seq)


title: E4.5-5.5_new_Plate3_B09 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_H09 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_H04 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_H07 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_H08 (scRNA-Seq)


title: HCT116 RNAseq, rep2


title: E4.5-5.5_new_Plate2_H06 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_H05 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_G12 (scRNA-Seq)


title: 11.5 R1 +M_R3

type: RNA

city: Guildford

first: Fernando

middle: O

last: Martinez Estrada

state: Surrey

address: Stag Hill

department: Faculty of Health & Medical Sciences

institute: University of Surrey

description: Wt1GFP+ Cells at day 11.5

hyb_protocol: Hybridization and washing were performed according to the Illumina Manual “Direct Hybridization Assay Guide”

scan_protocol: Scanning was performed on the Illumina iScan (Illumina, Inc., San Diego, CA, U.S.A.).

data_processing: Image analysis and extraction of raw expression data was performed with Illumina GenomeStudio v2011.1 Gene Expression software with default settings (no background substraction and no normalization)

label: biotin

source_name: enzymatically disaggregated embryonic heart ventricles into single cells from Wt1GFPKI mice

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Austin,  TX, U.S.A.) according to the manufacturer’s specifications with an input of 200 ng total RNA.

growth_protocol: cells were extracted from enzymatically disaggregated embryonic heart ventricles into single cells and used directly for mRNA studies.

extract_protocol: Rneasy Total RNA isolation

treatment_protocol: Samples were FACS sorted and RNA lysis buffer was added post sorting to avoid mRNA changes

tag: stage of development


title: 16.5 R1 +M_R3

description: Wt1GFP+ Cells at day 16.5


title: E4.5-5.5_new_Plate3_A06 (scRNA-Seq)


title: 13.5 R1 +M_R3

description: Wt1GFP+ Cells at day 13.5


title: 15.5 R1 +M_R3

description: Wt1GFP+ Cells at day 15.5


title: 14.5 R1 +M_R3

description: Wt1GFP+ Cells at day 14.5


title: E4.5-5.5_new_Plate2_H03 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_G11 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_H01 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_G08 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_H02 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_G09 (scRNA-Seq)


title: 15.5 R1 +M_R2

description: Wt1GFP+ Cells at day 15.5


title: E4.5-5.5_new_Plate2_G06 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_G10 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_G07 (scRNA-Seq)


title: 13.5 R1 +M_R2

description: Wt1GFP+ Cells at day 13.5


title: E4.5-5.5_new_Plate2_G05 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_G04 (scRNA-Seq)


title: 16.5 R1 +M_R2

description: Wt1GFP+ Cells at day 16.5


title: E4.5-5.5_new_Plate2_G03 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_G02 (scRNA-Seq)


title: 15.5 R1 +M_R1

description: Wt1GFP+ Cells at day 15.5


title: 11.5 R1 +M_R2

description: Wt1GFP+ Cells at day 11.5


title: 16.5 R1 +M_R1

description: Wt1GFP+ Cells at day 16.5


title: E4.5-5.5_new_Plate2_G01 (scRNA-Seq)


title: 13.5 R1 +M_R1

description: Wt1GFP+ Cells at day 13.5


title: E4.5-5.5_new_Plate2_F09 (scRNA-Seq)


title: 11.5 R1 +M_R1

description: Wt1GFP+ Cells at day 11.5


title: E4.5-5.5_new_Plate2_F11 (scRNA-Seq)


title: 12.5 R1 +M_R1

description: Wt1GFP+ Cells at day 12.5


title: 14.5 R1 +M_R2

description: Wt1GFP+ Cells at day 14.5


title: 15.5 R1 +HI_R3

description: Wt1GFP++ Cells at day 15.5


title: 16.5 R1 +HI_R3

description: Wt1GFP++ Cells at day 16.5


title: 13.5 R1 +HI_R3

description: Wt1GFP++ Cells at day 13.5


title: E4.5-5.5_new_Plate2_F12 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_F10 (scRNA-Seq)


title: 12.5 R1 +HI_R3

description: Wt1GFP++ Cells at day 12.5


title: 16.5 R1 +HI_R2

description: Wt1GFP++ Cells at day 16.5


title: E4.5-5.5_new_Plate2_F07 (scRNA-Seq)


title: 14.5 R1 +M_R1

description: Wt1GFP+ Cells at day 14.5


title: 12.5 R1 +M_R2

description: Wt1GFP+ Cells at day 12.5


title: 14.5 R1 +HI_R3

description: Wt1GFP++ Cells at day 14.5


title: 11.5 R1 +HI_R3

description: Wt1GFP++ Cells at day 11.5


title: 14.5 R1 +HI_R2

description: Wt1GFP++ Cells at day 14.5


title: 12.5 R1 +M_R3

description: Wt1GFP+ Cells at day 12.5


title: E4.5-5.5_new_Plate2_F08 (scRNA-Seq)


title: 13.5 R1 +HI_R2

description: Wt1GFP++ Cells at day 13.5


title: E4.5-5.5_new_Plate2_F06 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_F05 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_F03 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_E06 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_E12 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_E04 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_E07 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_E10 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_F01 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_E11 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_E03 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_E01 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_F02 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_E08 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_E05 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_E09 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_D11 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_E02 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_D10 (scRNA-Seq)


title: 15.5 R1 +HI_R2

description: Wt1GFP++ Cells at day 15.5


title: 12.5 R1 +HI_R2

description: Wt1GFP++ Cells at day 12.5


title: 16.5 R1 +HI_R1

description: Wt1GFP++ Cells at day 16.5


title: 11.5 R1 +HI_R2

description: Wt1GFP++ Cells at day 11.5


title: 13.5 R1 +HI_R1

description: Wt1GFP++ Cells at day 13.5


title: E4.5-5.5_new_Plate2_D09 (scRNA-Seq)


title: 11.5 R1 +HI_R1

description: Wt1GFP++ Cells at day 11.5


title: 15.5 R1 +HI_R1

description: Wt1GFP++ Cells at day 15.5


title: E4.5-5.5_new_Plate2_D08 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_D05 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_D07 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_F04 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_D02 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_D06 (scRNA-Seq)


title: 14.5 R1 +HI_R1

description: Wt1GFP++ Cells at day 14.5


title: E4.5-5.5_new_Plate2_D01 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_D03 (scRNA-Seq)


title: 12.5 R1 +HI_R1

description: Wt1GFP++ Cells at day 12.5


title: L2N7 [Ect2]

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

institute: University of Pennsylvania

data_processing:
Basecalling- CASAVA 1.8.2
trimReads.py (https://github.com/safisher/ngs/blob/master/trimReads.py) - adaptor trimming, low quality base masking, polyA/T trimming
alignment to reference genome - STAR 2.4.0j  (--outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 30 --outFilterMismatchNmax 100 --outFilterMismatchNoverLmax 0.3 --outFilterMatchNminOverLread 0.4)
Quantification- Uniquely mapped reads quantifed with HTSeq v0.6.1p1 (--mode=intersection-strict --stranded=no --type=exon --idattr=gene_id)
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq gene counts

source_name: Freshly isolated heart cell

extract_protocol:
Ventricular cardiac cells were dissociated by enzymatic digestion from Azami green geminin (mAG-Geminin) transgenic mice and sorted by FACS. Following cell lysis, mRNA was reverse transcribed into 1st strand cDNA. Single cell cDNA was subjected to quality control using PCR for the cardiomyocytespecific marker, troponin T2 (Tnnt2). Potential contamination from non-cardiomyocytes (i.e. cardiac fibroblasts and endothelial cells) was detected by PCR for platelet derived growth factor receptor ß (Pdgfrb).Single cells showing Tnnt2 positive and Pdgfrb negative were considered as confirmed cardiomyocytes.
library preparation using the Illumina TruSeq RNA sample preparation kit according to the manufacturer's protocol

value: postnatal days 5

value: single cardiomyocytes

tag: group

value: mAG-hGem negative


title: L2N9 [Ect2]


title: E4.5-5.5_new_Plate2_C12 (scRNA-Seq)

value: single cell


title: HCEC RNAseq, rep2


title: L2N12 [Ect2]


title: L2N10 [Ect2]


title: E4.5-5.5_new_Plate2_C11 (scRNA-Seq)


title: L1N3 [Ect2]


title: E4.5-5.5_new_Plate2_C10 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_C09 (scRNA-Seq)


title: L2P12 [Ect2]

value: mAG-hGem positive


title: L2P10 [Ect2]


title: E4.5-5.5_new_Plate2_C08 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_C06 (scRNA-Seq)


title: L2P7 [Ect2]


title: E4.5-5.5_new_Plate2_C07 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_D04 (scRNA-Seq)


title: L2P8 [Ect2]


title: L2P3 [Ect2]


title: E4.5-5.5_new_Plate2_C05 (scRNA-Seq)


title: L2N4 [Ect2]


title: E4.5-5.5_new_Plate2_C03 (scRNA-Seq)


title: N30 [Ect2]

value: embryonic days 14.5


title: L1P5 [Ect2]


title: N28 [Ect2]


title: N24 [Ect2]


title: E4.5-5.5_new_Plate2_B12 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_B11 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_B10 (scRNA-Seq)


title: N25 [Ect2]


title: N23 [Ect2]


title: E4.5-5.5_new_Plate2_B08 (scRNA-Seq)


title: N10 [Ect2]


title: E4.5-5.5_new_Plate2_B07 (scRNA-Seq)


title: N8 [Ect2]


title: E4.5-5.5_new_Plate2_B06 (scRNA-Seq)


title: N5 [Ect2]


title: N7 [Ect2]


title: CD34+ selected HSPCs from MDS-MSC 775 AZA co-culture

city: Singapore

first: Zhiyong

last: Poon

address: 20 College Road

country: Singapore

institute: Singapore General Hospital

description: HSPC (HR775 AZA)

data_processing:
Paired end raw data fastq files were imported into Partek Flow 7.0. The sequences were aligned to hg19 using STAR version 2.5.3a default parameters. Transcript abundance was determined using Partek E/M algorithm based on Ensembl Transcripts release 751. Raw read count were generated and normalized for sequence depth –RPM, a small offset of 0.0001 were added to each value to deal with 0s. Low expression genes are indistinguishable from noise, so genes with total raw counts less than or equal 10 were removed during quantification. After normalization, another filter was performed so that only genes with geometric average greater than or equal to 1 are used for the downstream analysis. Partek GSA were used to detect differential expressed genes between treated vs not treatment groups. The default setting for GSA is LIMMA2. p < 0.05 were considered significant.
Genome_build: hg19

source_name: co-culture with 5-azacitidine-treated mesenchymal stromal cells from patients with myelodyplastic syndrome

growth_protocol: For MSCs, the culture reagents used were: Dulbecco’s Modified Eagle’s Medium (DMEM) - low glucose (Gibco) supplemented with 10% fetal bovine serum (FBS) (Hyclone) and 50 U/ml penicillin and streptomycin (Gibco), subsequently referred to as D10 media. To derive MSCs, 2.0 - 3.0 × 105 cells/cm2 of BM derived mononuclear cells were inoculated in D10 media that was changed completely after 3 days and subsequently replaced twice a week until confluence and cryopreserved for experiments at P1. MDS patient derived mononuclear cells (1.0 × 106 – 1.0 × 107 cells/ml) were also inoculated in D10 media in a T75 flask. Non-adherent cells were removed after 3 days with subsequent media change twice a week. MDS-MSCs were further expanded, frozen down and all experiments were carried out using MSCs derived from P1 - P2.

extract_protocol:
CD34+ HSPCs were isolated using the CD34+ MicroBead Kit and magnetic-activated cell sorting (MACS) (Miltenyi Biotec).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 5-azacitidine treated or untreated MDS-MSCs were plated at a near confluent density of 2.0 × 104 cells/cm2 in DMEM with 10% FBS. 24 h later, healthy CD34+ HSPCs were seeded in contact with the MSC feeder layer at a density of 2.0 × 103 cells/cm2 in hematopoietic media and cultured for 14-21 days with replacement of media after 7 days. On the last day, CD34+ HSPCs were flow sorted for RNA extraction and subsequent sequencing.

tag: mds-msc 5-aza treatment

value: Yes

tag: co-culture with mds derived mscs

value: Healthy bone marrow CD34+ hematopoietic stem and progenitor cells


title: E4.5-5.5_new_Plate2_B09 (scRNA-Seq)


title: N3 [Ect2]

tag: cell type


title: G29 [Ect2]


title: E4.5-5.5_new_Plate2_B05 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_C02 (scRNA-Seq)


title: G28 [Ect2]


title: E4.5-5.5_new_Plate2_B04 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_B03 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_B02 (scRNA-Seq)


title: CD34+ selected HSPCs from MDS-MSC 627 AZA co-culture

description: HSPC (HR627 AZA)


title: G27 [Ect2]


title: N21 [Ect2]


title: CD34+ selected HSPCs from MDS-MSC 261 AZA co-culture

description: HSPC (HR261 AZA)


title: CD34+ selected HSPCs from MDS-MSC 613 AZA co-culture

description: HSPC (HR613 AZA)


title: E4.5-5.5_new_Plate2_B01 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_A12 (scRNA-Seq)


title: G25 [Ect2]


title: CD34+ selected HSPCs from MDS-MSC 775 UT co-culture

description: HSPC (HR775 UT)

source_name: co-culture with untreated mesenchymal stromal cells from patients with myelodyplastic syndrome

value: No


title: CD34+ selected HSPCs from MDS-MSC 613 UT co-culture

description: HSPC (HR613 UT)


title: E4.5-5.5_new_Plate2_A11 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_A10 (scRNA-Seq)


title: G8 [Ect2]


title: CD34+ selected HSPCs from MDS-MSC 261 UT co-culture

description: HSPC (HR261 UT)


title: E4.5-5.5_new_Plate2_A09 (scRNA-Seq)


title: G5 [Ect2]


title: E4.5-5.5_new_Plate2_C04 (scRNA-Seq)


title: CD34+ selected HSPCs from MDS-MSC 325 UT co-culture

description: HSPC (HR325 UT)


title: G2 [Ect2]


title: E4.5-5.5_new_Plate2_A06 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_A07 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_A05 (scRNA-Seq)


title: G10 [Ect2]


title: G1 [Ect2]


title: E4.5-5.5_new_Plate2_A04 (scRNA-Seq)


title: ago4-3_NaCl_Rep1

city: Cuernavaca

first: Veronica

last: Jimenez-Jacinto

state: Morelos

address: Av. Universidad 2001. Col. chamilpa

department: Unidad Universitaria de Secuenciación Masiva y Bioinformática

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

description:
ColNaClvsago43NaCl.txt
ago43MSvsago43NaCl.txt
ago42NaClvsago43NaCl.txt

data_processing:
Sequencing control software: HCSv2.2
Alignment: smalt VN:0.7.6, with deafult parameters
converse sam to bam: samtools view  0.1.19-96b5f2294a
MarkDuplicates: VN:1.114 picard.sam.MarkDuplicates. Parameters: REMOVE_DUPLICATES=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25
calculation of coverages: bamtools coverge bed
Analisys Differential Expresion: DESeq package R, NOISeq package R, EdgeR package R
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include: col1: gene_id, col2: logFC; col3: logCPM; col4: Pvalue; col5: FDR; col6,col7,col8,col9: rawcounts for each Sample with replica; col10,col11,col12,col13: normalizated counts for each Sample and Replica; col14: DiffExp=100-FDR; col15: Regulation;  For each paired comparation.

organism: Arabidopsis thaliana

source_name: Germinating seeds

growth_protocol: Seeds were sown in MS media and germinated under 16/8 light/dark photoperiod at 21ºC and 100uE of light intensity

extract_protocol: RNA was extracted using the mini hot phenol method for plant seeds

treatment_protocol: MS 1X was used as control medium while for salinity we added 100 mM of NaCl to MS

tag: ecotype

tag: condition

value: Salinity


title: E4.5-5.5_new_Plate2_A03 (scRNA-Seq)


title: G6 [Ect2]


title: ago4-3_Control_Rep1

description:
ago43MSvsago43NaCl.txt
ago42MSvsago43MS.txt
ColMSvsago43MS.txt

value: control


title: E4.5-5.5_new_Plate2_A02 (scRNA-Seq)


title: ago4-2_NaCl_Rep2

description:
ago42MSvsago42NaCl.txt
ColNaClvsago42NaCl.txt
ago42NaClvsago43NaCl.txt


title: E4.5-5.5_new_Plate2_A08 (scRNA-Seq)


title: E4.5-5.5_new_Plate2_A01 (scRNA-Seq)


title: E4.5-5.5_new_Plate1_H09 (scRNA-Seq)


title: ago4-2_NaCl_Rep1


title: ago4-3_NaCl:Rep2


title: ago4-2_Control_Rep2

description:
ago42MSvsago42NaCl.txt
ago42MSvsago43MS.txt
ColMSvsago42MS.txt


title: E4.5-5.5_new_Plate1_H08 (scRNA-Seq)


title: Col-0_NaClRep1

description:
ColMSvsColNaCl.txt
ColNaClvsago43NaCl.txt
ColNaClvsago42NaCl.txt


title: E4.5-5.5_new_Plate1_G09 (scRNA-Seq)


title: ago4-2_Control_Rep1


title: E4.5-5.5_new_Plate1_G08 (scRNA-Seq)


title: ago4-3_Control_Rep2


title: E4.5-5.5_new_Plate1_H02 (scRNA-Seq)