title: mdOrg2_B2_hOrg_ESC_reg2_53d

description:
Single cell B2 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_B2_hOrg_ESC_reg2_53d


title: mdOrg2_B3_hOrg_ESC_reg2_53d

status: Public on Dec 07 2015

type: SRA

city: Leipzig

first: Gray

last: Camp

address: Deutscher Pl. 6

department: Evolutionary Genetics

country: Germany

institute: Max Planck Institute for Evolutionary Anthropology

description:
Single cell B3 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_B3_hOrg_ESC_reg2_53d

library_source: transcriptomic

data_processing:
"freeIbis" was used as an efficient basecaller with calibrated quality scores for Illumina sequencers. (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.)
"leeHom" was used to trim adapters and merge Illumina sequencing reads. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.)
"deML" was used for robust demultiplexing of Illumina sequences using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.)
Reads were aligned against the human genome (build GRCh38.77 from ENSEMBLE) using TopHat v2.0.14. The genome was indexed using Bowtie v2.2.6
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks v2.2.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Master data frame including sample name, gene ID, and FPKM values for each single cell.

molecule: total RNA

organism: Homo sapiens

source_name: ESC H9

growth_protocol: Cerebral organoids were generated using the same protocol as described Lancaster et al. Nature Protocols 2014, with the exception that mTESR1 (Stem Cell Technologies) was used during embryoid body formation.

extract_protocol:
Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions at a dilution of 1:40,000.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

treatment_protocol: Whole cerebral organoids and microdisseccted ventricles were dissociated in 2 ml of Accutase (StemPro) containing 0.2 U/µl Dnase I (Roche) for approximately 45 minutes. Dissociated cells were filtered through 40, 30, and 20 μm diameter strainers to create a single cell suspension.

tag: Stage

value: 53 days

tag: tissue

value: Microdissected cortical-like ventricle from cerebral organoid


title: mdOrg2_C10_hOrg_ESC_reg2_53d

description:
Single cell C10 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_C10_hOrg_ESC_reg2_53d


title: mdOrg2_B4_hOrg_ESC_reg2_53d

description:
Single cell B4 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_B4_hOrg_ESC_reg2_53d


title: mdOrg2_A5_hOrg_ESC_reg2_53d

description:
Single cell A5 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_A5_hOrg_ESC_reg2_53d


title: mdOrg2_A7_hOrg_ESC_reg2_53d

description:
Single cell A7 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_A7_hOrg_ESC_reg2_53d


title: mdOrg2_A2_hOrg_ESC_reg2_53d

description:
Single cell A2 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_A2_hOrg_ESC_reg2_53d


title: mdOrg1_H1_hOrg_ESC_reg1_53d

description:
Single cell H1 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_H1_hOrg_ESC_reg1_53d


title: mdOrg1_G7_hOrg_ESC_reg1_53d

description:
Single cell G7 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_G7_hOrg_ESC_reg1_53d


title: mdOrg1_G5_hOrg_ESC_reg1_53d

description:
Single cell G5 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_G5_hOrg_ESC_reg1_53d


title: mdOrg1_G11_hOrg_ESC_reg1_53d

description:
Single cell G11 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_G11_hOrg_ESC_reg1_53d


title: mdOrg1_F9_hOrg_ESC_reg1_53d

description:
Single cell F9 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_F9_hOrg_ESC_reg1_53d


title: mdOrg1_H3_hOrg_ESC_reg1_53d

description:
Single cell H3 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_H3_hOrg_ESC_reg1_53d


title: mdOrg1_H7_hOrg_ESC_reg1_53d

description:
Single cell H7 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_H7_hOrg_ESC_reg1_53d


title: mdOrg1_H9_hOrg_ESC_reg1_53d

description:
Single cell H9 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_H9_hOrg_ESC_reg1_53d


title: mdOrg1_G6_hOrg_ESC_reg1_53d

description:
Single cell G6 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_G6_hOrg_ESC_reg1_53d


title: mdOrg1_G12_hOrg_ESC_reg1_53d

description:
Single cell G12 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_G12_hOrg_ESC_reg1_53d


title: mdOrg1_G4_hOrg_ESC_reg1_53d

description:
Single cell G4 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_G4_hOrg_ESC_reg1_53d


title: mdOrg2_D1_hOrg_ESC_reg2_53d

description:
Single cell D1 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_D1_hOrg_ESC_reg2_53d


title: mdOrg2_A1_hOrg_ESC_reg2_53d

description:
Single cell A1 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_A1_hOrg_ESC_reg2_53d


title: mdOrg3_F10_hOrg_iPSC_reg3_58d

description:
Single cell F10 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_F10_hOrg_iPSC_reg3_58d

source_name: iPSC 409B2

value: 58 days


title: mdOrg1_F1_hOrg_ESC_reg1_53d

description:
Single cell F1 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_F1_hOrg_ESC_reg1_53d


title: mdOrg2_B10_hOrg_ESC_reg2_53d

description:
Single cell B10 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_B10_hOrg_ESC_reg2_53d


title: mdOrg1_E7_hOrg_ESC_reg1_53d

description:
Single cell E7 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_E7_hOrg_ESC_reg1_53d


title: mdOrg1_F8_hOrg_ESC_reg1_53d

description:
Single cell F8 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_F8_hOrg_ESC_reg1_53d


title: mdOrg3_C12_hOrg_iPSC_reg3_58d

description:
Single cell C12 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_C12_hOrg_iPSC_reg3_58d


title: mdOrg1_E4_hOrg_ESC_reg1_53d

description:
Single cell E4 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_E4_hOrg_ESC_reg1_53d


title: mdOrg1_F10_hOrg_ESC_reg1_53d

description:
Single cell F10 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_F10_hOrg_ESC_reg1_53d


title: mdOrg1_F11_hOrg_ESC_reg1_53d

description:
Single cell F11 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_F11_hOrg_ESC_reg1_53d


title: mdOrg1_C9_hOrg_ESC_reg1_53d

description:
Single cell C9 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_C9_hOrg_ESC_reg1_53d


title: mdOrg1_E3_hOrg_ESC_reg1_53d

description:
Single cell E3 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_E3_hOrg_ESC_reg1_53d


title: mdOrg1_F4_hOrg_ESC_reg1_53d

description:
Single cell F4 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_F4_hOrg_ESC_reg1_53d


title: mdOrg1_E10_hOrg_ESC_reg1_53d

description:
Single cell E10 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_E10_hOrg_ESC_reg1_53d


title: mdOrg1_C8_hOrg_ESC_reg1_53d

description:
Single cell C8 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_C8_hOrg_ESC_reg1_53d


title: mdOrg1_E11_hOrg_ESC_reg1_53d

description:
Single cell E11 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_E11_hOrg_ESC_reg1_53d


title: mdOrg1_C7_hOrg_ESC_reg1_53d

description:
Single cell C7 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_C7_hOrg_ESC_reg1_53d


title: mdOrg1_C5_hOrg_ESC_reg1_53d

description:
Single cell C5 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_C5_hOrg_ESC_reg1_53d


title: mdOrg1_C6_hOrg_ESC_reg1_53d

description:
Single cell C6 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_C6_hOrg_ESC_reg1_53d


title: mdOrg1_D9_hOrg_ESC_reg1_53d

description:
Single cell D9 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_D9_hOrg_ESC_reg1_53d


title: mdOrg1_E1_hOrg_ESC_reg1_53d

description:
Single cell E1 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_E1_hOrg_ESC_reg1_53d


title: mdOrg1_D3_hOrg_ESC_reg1_53d

description:
Single cell D3 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_D3_hOrg_ESC_reg1_53d


title: mdOrg1_E5_hOrg_ESC_reg1_53d

description:
Single cell E5 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_E5_hOrg_ESC_reg1_53d


title: mdOrg1_E12_hOrg_ESC_reg1_53d

description:
Single cell E12 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_E12_hOrg_ESC_reg1_53d


title: mdOrg1_C12_hOrg_ESC_reg1_53d

description:
Single cell C12 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_C12_hOrg_ESC_reg1_53d


title: mdOrg1_C1_hOrg_ESC_reg1_53d

description:
Single cell C1 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_C1_hOrg_ESC_reg1_53d


title: mdOrg1_B8_hOrg_ESC_reg1_53d

description:
Single cell B8 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_B8_hOrg_ESC_reg1_53d


title: mdOrg1_B5_hOrg_ESC_reg1_53d

description:
Single cell B5 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_B5_hOrg_ESC_reg1_53d


title: mdOrg1_B12_hOrg_ESC_reg1_53d

description:
Single cell B12 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_B12_hOrg_ESC_reg1_53d


title: mdOrg1_B9_hOrg_ESC_reg1_53d

description:
Single cell B9 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_B9_hOrg_ESC_reg1_53d


title: mdOrg1_C2_hOrg_ESC_reg1_53d

description:
Single cell C2 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_C2_hOrg_ESC_reg1_53d


title: mdOrg1_B7_hOrg_ESC_reg1_53d

description:
Single cell B7 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_B7_hOrg_ESC_reg1_53d


title: mdOrg1_A8_hOrg_ESC_reg1_53d

description:
Single cell A8 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_A8_hOrg_ESC_reg1_53d


title: mdOrg1_A6_hOrg_ESC_reg1_53d

description:
Single cell A6 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_A6_hOrg_ESC_reg1_53d


title: mdOrg2_A11_hOrg_ESC_reg2_53d

description:
Single cell A11 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_A11_hOrg_ESC_reg2_53d


title: mdOrg1_A3_hOrg_ESC_reg1_53d

description:
Single cell A3 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_A3_hOrg_ESC_reg1_53d


title: mdOrg1_A4_hOrg_ESC_reg1_53d

description:
Single cell A4 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_A4_hOrg_ESC_reg1_53d


title: whOrg5_H9_hOrg65d

description:
Single cell H9 from human cerebral organoid experiment at 65d
whOrg5_H9_hOrg65d

value: 65 days

value: Dissociated whole cerebral organoid


title: whOrg5_H7_hOrg65d

description:
Single cell H7 from human cerebral organoid experiment at 65d
whOrg5_H7_hOrg65d


title: mdOrg1_A10_hOrg_ESC_reg1_53d

description:
Single cell A10 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_A10_hOrg_ESC_reg1_53d


title: mdOrg1_A12_hOrg_ESC_reg1_53d

description:
Single cell A12 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_A12_hOrg_ESC_reg1_53d


title: whOrg5_H4_hOrg65d

description:
Single cell H4 from human cerebral organoid experiment at 65d
whOrg5_H4_hOrg65d


title: whOrg5_H3_hOrg65d

description:
Single cell H3 from human cerebral organoid experiment at 65d
whOrg5_H3_hOrg65d


title: whOrg5_H12_hOrg65d

description:
Single cell H12 from human cerebral organoid experiment at 65d
whOrg5_H12_hOrg65d


title: whOrg5_G8_hOrg65d

description:
Single cell G8 from human cerebral organoid experiment at 65d
whOrg5_G8_hOrg65d


title: whOrg5_H11_hOrg65d

description:
Single cell H11 from human cerebral organoid experiment at 65d
whOrg5_H11_hOrg65d


title: whOrg5_H1_hOrg65d

description:
Single cell H1 from human cerebral organoid experiment at 65d
whOrg5_H1_hOrg65d


title: whOrg5_G9_hOrg65d

description:
Single cell G9 from human cerebral organoid experiment at 65d
whOrg5_G9_hOrg65d


title: whOrg5_G7_hOrg65d

description:
Single cell G7 from human cerebral organoid experiment at 65d
whOrg5_G7_hOrg65d


title: whOrg5_G6_hOrg65d

description:
Single cell G6 from human cerebral organoid experiment at 65d
whOrg5_G6_hOrg65d


title: mdOrg1_A9_hOrg_ESC_reg1_53d

description:
Single cell A9 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_A9_hOrg_ESC_reg1_53d


title: mdOrg1_B1_hOrg_ESC_reg1_53d

description:
Single cell B1 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_B1_hOrg_ESC_reg1_53d


title: whOrg5_G4_hOrg65d

description:
Single cell G4 from human cerebral organoid experiment at 65d
whOrg5_G4_hOrg65d


title: whOrg5_G2_hOrg65d

description:
Single cell G2 from human cerebral organoid experiment at 65d
whOrg5_G2_hOrg65d


title: whOrg5_G11_hOrg65d

description:
Single cell G11 from human cerebral organoid experiment at 65d
whOrg5_G11_hOrg65d


title: whOrg5_G10_hOrg65d

description:
Single cell G10 from human cerebral organoid experiment at 65d
whOrg5_G10_hOrg65d


title: whOrg5_G12_hOrg65d

description:
Single cell G12 from human cerebral organoid experiment at 65d
whOrg5_G12_hOrg65d


title: whOrg5_F9_hOrg65d

description:
Single cell F9 from human cerebral organoid experiment at 65d
whOrg5_F9_hOrg65d


title: mdOrg1_B11_hOrg_ESC_reg1_53d

description:
Single cell B11 from human cerebral organoid experiment micro-dissected region 1 53d
mdOrg1_B11_hOrg_ESC_reg1_53d


title: whOrg5_H6_hOrg65d

description:
Single cell H6 from human cerebral organoid experiment at 65d
whOrg5_H6_hOrg65d


title: whOrg5_F8_hOrg65d

description:
Single cell F8 from human cerebral organoid experiment at 65d
whOrg5_F8_hOrg65d


title: whOrg5_F4_hOrg65d

description:
Single cell F4 from human cerebral organoid experiment at 65d
whOrg5_F4_hOrg65d


title: whOrg5_F11_hOrg65d

description:
Single cell F11 from human cerebral organoid experiment at 65d
whOrg5_F11_hOrg65d


title: whOrg5_F5_hOrg65d

description:
Single cell F5 from human cerebral organoid experiment at 65d
whOrg5_F5_hOrg65d


title: whOrg5_F3_hOrg65d

description:
Single cell F3 from human cerebral organoid experiment at 65d
whOrg5_F3_hOrg65d


title: whOrg5_F12_hOrg65d

description:
Single cell F12 from human cerebral organoid experiment at 65d
whOrg5_F12_hOrg65d


title: whOrg5_E4_hOrg65d

description:
Single cell E4 from human cerebral organoid experiment at 65d
whOrg5_E4_hOrg65d


title: whOrg5_G1_hOrg65d

description:
Single cell G1 from human cerebral organoid experiment at 65d
whOrg5_G1_hOrg65d


title: whOrg5_G5_hOrg65d

description:
Single cell G5 from human cerebral organoid experiment at 65d
whOrg5_G5_hOrg65d


title: whOrg5_E5_hOrg65d

description:
Single cell E5 from human cerebral organoid experiment at 65d
whOrg5_E5_hOrg65d


title: whOrg5_E8_hOrg65d

description:
Single cell E8 from human cerebral organoid experiment at 65d
whOrg5_E8_hOrg65d


title: whOrg5_F10_hOrg65d

description:
Single cell F10 from human cerebral organoid experiment at 65d
whOrg5_F10_hOrg65d


title: whOrg5_D4_hOrg65d

description:
Single cell D4 from human cerebral organoid experiment at 65d
whOrg5_D4_hOrg65d


title: whOrg5_E11_hOrg65d

description:
Single cell E11 from human cerebral organoid experiment at 65d
whOrg5_E11_hOrg65d


title: whOrg5_D6_hOrg65d

description:
Single cell D6 from human cerebral organoid experiment at 65d
whOrg5_D6_hOrg65d


title: whOrg5_D3_hOrg65d

description:
Single cell D3 from human cerebral organoid experiment at 65d
whOrg5_D3_hOrg65d


title: whOrg5_F7_hOrg65d

description:
Single cell F7 from human cerebral organoid experiment at 65d
whOrg5_F7_hOrg65d


title: whOrg5_E10_hOrg65d

description:
Single cell E10 from human cerebral organoid experiment at 65d
whOrg5_E10_hOrg65d


title: whOrg5_D2_hOrg65d

description:
Single cell D2 from human cerebral organoid experiment at 65d
whOrg5_D2_hOrg65d


title: whOrg5_E2_hOrg65d

description:
Single cell E2 from human cerebral organoid experiment at 65d
whOrg5_E2_hOrg65d


title: whOrg5_D8_hOrg65d

description:
Single cell D8 from human cerebral organoid experiment at 65d
whOrg5_D8_hOrg65d


title: whOrg5_C9_hOrg65d

description:
Single cell C9 from human cerebral organoid experiment at 65d
whOrg5_C9_hOrg65d


title: whOrg5_D12_hOrg65d

description:
Single cell D12 from human cerebral organoid experiment at 65d
whOrg5_D12_hOrg65d


title: whOrg5_D10_hOrg65d

description:
Single cell D10 from human cerebral organoid experiment at 65d
whOrg5_D10_hOrg65d


title: whOrg5_D7_hOrg65d

description:
Single cell D7 from human cerebral organoid experiment at 65d
whOrg5_D7_hOrg65d


title: whOrg5_F2_hOrg65d

description:
Single cell F2 from human cerebral organoid experiment at 65d
whOrg5_F2_hOrg65d


title: whOrg5_C8_hOrg65d

description:
Single cell C8 from human cerebral organoid experiment at 65d
whOrg5_C8_hOrg65d


title: whOrg5_C7_hOrg65d

description:
Single cell C7 from human cerebral organoid experiment at 65d
whOrg5_C7_hOrg65d


title: whOrg5_E9_hOrg65d

description:
Single cell E9 from human cerebral organoid experiment at 65d
whOrg5_E9_hOrg65d


title: whOrg5_C4_hOrg65d

description:
Single cell C4 from human cerebral organoid experiment at 65d
whOrg5_C4_hOrg65d


title: whOrg5_D11_hOrg65d

description:
Single cell D11 from human cerebral organoid experiment at 65d
whOrg5_D11_hOrg65d


title: whOrg5_D1_hOrg65d

description:
Single cell D1 from human cerebral organoid experiment at 65d
whOrg5_D1_hOrg65d


title: whOrg5_C12_hOrg65d

description:
Single cell C12 from human cerebral organoid experiment at 65d
whOrg5_C12_hOrg65d


title: whOrg5_C3_hOrg65d

description:
Single cell C3 from human cerebral organoid experiment at 65d
whOrg5_C3_hOrg65d


title: whOrg5_C1_hOrg65d

description:
Single cell C1 from human cerebral organoid experiment at 65d
whOrg5_C1_hOrg65d


title: whOrg5_E3_hOrg65d

description:
Single cell E3 from human cerebral organoid experiment at 65d
whOrg5_E3_hOrg65d


title: whOrg5_C11_hOrg65d

description:
Single cell C11 from human cerebral organoid experiment at 65d
whOrg5_C11_hOrg65d


title: whOrg5_C10_hOrg65d

description:
Single cell C10 from human cerebral organoid experiment at 65d
whOrg5_C10_hOrg65d


title: whOrg5_B9_hOrg65d

description:
Single cell B9 from human cerebral organoid experiment at 65d
whOrg5_B9_hOrg65d


title: whOrg5_B7_hOrg65d

description:
Single cell B7 from human cerebral organoid experiment at 65d
whOrg5_B7_hOrg65d


title: whOrg5_B4_hOrg65d

description:
Single cell B4 from human cerebral organoid experiment at 65d
whOrg5_B4_hOrg65d


title: whOrg5_C2_hOrg65d

description:
Single cell C2 from human cerebral organoid experiment at 65d
whOrg5_C2_hOrg65d


title: whOrg5_B3_hOrg65d

description:
Single cell B3 from human cerebral organoid experiment at 65d
whOrg5_B3_hOrg65d


title: whOrg5_B12_hOrg65d

description:
Single cell B12 from human cerebral organoid experiment at 65d
whOrg5_B12_hOrg65d


title: whOrg5_B1_hOrg65d

description:
Single cell B1 from human cerebral organoid experiment at 65d
whOrg5_B1_hOrg65d


title: whOrg5_B6_hOrg65d

description:
Single cell B6 from human cerebral organoid experiment at 65d
whOrg5_B6_hOrg65d


title: whOrg5_B11_hOrg65d

description:
Single cell B11 from human cerebral organoid experiment at 65d
whOrg5_B11_hOrg65d


title: whOrg5_A9_hOrg65d

description:
Single cell A9 from human cerebral organoid experiment at 65d
whOrg5_A9_hOrg65d


title: whOrg5_B10_hOrg65d

description:
Single cell B10 from human cerebral organoid experiment at 65d
whOrg5_B10_hOrg65d


title: whOrg5_A6_hOrg65d

description:
Single cell A6 from human cerebral organoid experiment at 65d
whOrg5_A6_hOrg65d


title: whOrg5_C6_hOrg65d

description:
Single cell C6 from human cerebral organoid experiment at 65d
whOrg5_C6_hOrg65d


title: whOrg5_A5_hOrg65d

description:
Single cell A5 from human cerebral organoid experiment at 65d
whOrg5_A5_hOrg65d


title: whOrg5_A7_hOrg65d

description:
Single cell A7 from human cerebral organoid experiment at 65d
whOrg5_A7_hOrg65d


title: whOrg5_C5_hOrg65d

description:
Single cell C5 from human cerebral organoid experiment at 65d
whOrg5_C5_hOrg65d


title: whOrg5_A1_hOrg65d

description:
Single cell A1 from human cerebral organoid experiment at 65d
whOrg5_A1_hOrg65d


title: whOrg5_A4_hOrg65d

description:
Single cell A4 from human cerebral organoid experiment at 65d
whOrg5_A4_hOrg65d


title: whOrg5_A8_hOrg65d

description:
Single cell A8 from human cerebral organoid experiment at 65d
whOrg5_A8_hOrg65d


title: whOrg5_A12_hOrg65d

description:
Single cell A12 from human cerebral organoid experiment at 65d
whOrg5_A12_hOrg65d


title: whOrg5_A10_hOrg65d

description:
Single cell A10 from human cerebral organoid experiment at 65d
whOrg5_A10_hOrg65d


title: whOrg5_A2_hOrg65d

description:
Single cell A2 from human cerebral organoid experiment at 65d
whOrg5_A2_hOrg65d


title: whOrg5_A11_hOrg65d

description:
Single cell A11 from human cerebral organoid experiment at 65d
whOrg5_A11_hOrg65d


title: whOrg4_H3_hOrg41d

description:
Single cell H3 from human cerebral organoid experiment at 41d
whOrg4_H3_hOrg41d

value: 41 days


title: whOrg4_H8_hOrg41d

description:
Single cell H8 from human cerebral organoid experiment at 41d
whOrg4_H8_hOrg41d


title: whOrg5_B5_hOrg65d

description:
Single cell B5 from human cerebral organoid experiment at 65d
whOrg5_B5_hOrg65d


title: whOrg4_H7_hOrg41d

description:
Single cell H7 from human cerebral organoid experiment at 41d
whOrg4_H7_hOrg41d


title: whOrg4_H10_hOrg41d

description:
Single cell H10 from human cerebral organoid experiment at 41d
whOrg4_H10_hOrg41d


title: whOrg4_H2_hOrg41d

description:
Single cell H2 from human cerebral organoid experiment at 41d
whOrg4_H2_hOrg41d


title: whOrg4_G9_hOrg41d

description:
Single cell G9 from human cerebral organoid experiment at 41d
whOrg4_G9_hOrg41d


title: whOrg4_G7_hOrg41d

description:
Single cell G7 from human cerebral organoid experiment at 41d
whOrg4_G7_hOrg41d


title: whOrg4_G4_hOrg41d

description:
Single cell G4 from human cerebral organoid experiment at 41d
whOrg4_G4_hOrg41d


title: whOrg4_G3_hOrg41d

description:
Single cell G3 from human cerebral organoid experiment at 41d
whOrg4_G3_hOrg41d


title: whOrg4_G1_hOrg41d

description:
Single cell G1 from human cerebral organoid experiment at 41d
whOrg4_G1_hOrg41d


title: whOrg4_G11_hOrg41d

description:
Single cell G11 from human cerebral organoid experiment at 41d
whOrg4_G11_hOrg41d


title: whOrg4_G10_hOrg41d

description:
Single cell G10 from human cerebral organoid experiment at 41d
whOrg4_G10_hOrg41d


title: whOrg4_F7_hOrg41d

description:
Single cell F7 from human cerebral organoid experiment at 41d
whOrg4_F7_hOrg41d


title: whOrg4_F8_hOrg41d

description:
Single cell F8 from human cerebral organoid experiment at 41d
whOrg4_F8_hOrg41d


title: whOrg4_F2_hOrg41d

description:
Single cell F2 from human cerebral organoid experiment at 41d
whOrg4_F2_hOrg41d


title: whOrg4_F1_hOrg41d

description:
Single cell F1 from human cerebral organoid experiment at 41d
whOrg4_F1_hOrg41d


title: whOrg4_F3_hOrg41d

description:
Single cell F3 from human cerebral organoid experiment at 41d
whOrg4_F3_hOrg41d


title: whOrg4_F12_hOrg41d

description:
Single cell F12 from human cerebral organoid experiment at 41d
whOrg4_F12_hOrg41d


title: whOrg4_F6_hOrg41d

description:
Single cell F6 from human cerebral organoid experiment at 41d
whOrg4_F6_hOrg41d


title: whOrg4_F11_hOrg41d

description:
Single cell F11 from human cerebral organoid experiment at 41d
whOrg4_F11_hOrg41d


title: whOrg4_F10_hOrg41d

description:
Single cell F10 from human cerebral organoid experiment at 41d
whOrg4_F10_hOrg41d


title: whOrg4_E9_hOrg41d

description:
Single cell E9 from human cerebral organoid experiment at 41d
whOrg4_E9_hOrg41d


title: whOrg4_E7_hOrg41d

description:
Single cell E7 from human cerebral organoid experiment at 41d
whOrg4_E7_hOrg41d


title: whOrg4_E4_hOrg41d

description:
Single cell E4 from human cerebral organoid experiment at 41d
whOrg4_E4_hOrg41d


title: whOrg4_G8_hOrg41d

description:
Single cell G8 from human cerebral organoid experiment at 41d
whOrg4_G8_hOrg41d


title: whOrg4_E3_hOrg41d

description:
Single cell E3 from human cerebral organoid experiment at 41d
whOrg4_E3_hOrg41d


title: whOrg4_E6_hOrg41d

description:
Single cell E6 from human cerebral organoid experiment at 41d
whOrg4_E6_hOrg41d


title: whOrg4_E1_hOrg41d

description:
Single cell E1 from human cerebral organoid experiment at 41d
whOrg4_E1_hOrg41d


title: whOrg4_D9_hOrg41d

description:
Single cell D9 from human cerebral organoid experiment at 41d
whOrg4_D9_hOrg41d


title: whOrg4_G12_hOrg41d

description:
Single cell G12 from human cerebral organoid experiment at 41d
whOrg4_G12_hOrg41d


title: whOrg4_F4_hOrg41d

description:
Single cell F4 from human cerebral organoid experiment at 41d
whOrg4_F4_hOrg41d


title: whOrg4_D6_hOrg41d

description:
Single cell D6 from human cerebral organoid experiment at 41d
whOrg4_D6_hOrg41d


title: whOrg4_D4_hOrg41d

description:
Single cell D4 from human cerebral organoid experiment at 41d
whOrg4_D4_hOrg41d


title: whOrg4_D5_hOrg41d

description:
Single cell D5 from human cerebral organoid experiment at 41d
whOrg4_D5_hOrg41d


title: whOrg4_D2_hOrg41d

description:
Single cell D2 from human cerebral organoid experiment at 41d
whOrg4_D2_hOrg41d


title: whOrg4_D12_hOrg41d

description:
Single cell D12 from human cerebral organoid experiment at 41d
whOrg4_D12_hOrg41d


title: whOrg4_G5_hOrg41d

description:
Single cell G5 from human cerebral organoid experiment at 41d
whOrg4_G5_hOrg41d


title: whOrg4_D10_hOrg41d

description:
Single cell D10 from human cerebral organoid experiment at 41d
whOrg4_D10_hOrg41d


title: whOrg4_C9_hOrg41d

description:
Single cell C9 from human cerebral organoid experiment at 41d
whOrg4_C9_hOrg41d


title: whOrg4_D7_hOrg41d

description:
Single cell D7 from human cerebral organoid experiment at 41d
whOrg4_D7_hOrg41d


title: whOrg4_D3_hOrg41d

description:
Single cell D3 from human cerebral organoid experiment at 41d
whOrg4_D3_hOrg41d


title: whOrg4_D11_hOrg41d

description:
Single cell D11 from human cerebral organoid experiment at 41d
whOrg4_D11_hOrg41d


title: whOrg4_D8_hOrg41d

description:
Single cell D8 from human cerebral organoid experiment at 41d
whOrg4_D8_hOrg41d


title: whOrg4_F9_hOrg41d

description:
Single cell F9 from human cerebral organoid experiment at 41d
whOrg4_F9_hOrg41d


title: whOrg4_C6_hOrg41d

description:
Single cell C6 from human cerebral organoid experiment at 41d
whOrg4_C6_hOrg41d


title: whOrg4_E2_hOrg41d

description:
Single cell E2 from human cerebral organoid experiment at 41d
whOrg4_E2_hOrg41d


title: whOrg4_C7_hOrg41d

description:
Single cell C7 from human cerebral organoid experiment at 41d
whOrg4_C7_hOrg41d


title: whOrg4_H4_hOrg41d

description:
Single cell H4 from human cerebral organoid experiment at 41d
whOrg4_H4_hOrg41d


title: whOrg4_D1_hOrg41d

description:
Single cell D1 from human cerebral organoid experiment at 41d
whOrg4_D1_hOrg41d


title: whOrg4_C5_hOrg41d

description:
Single cell C5 from human cerebral organoid experiment at 41d
whOrg4_C5_hOrg41d


title: whOrg4_C2_hOrg41d

description:
Single cell C2 from human cerebral organoid experiment at 41d
whOrg4_C2_hOrg41d


title: whOrg4_B9_hOrg41d

description:
Single cell B9 from human cerebral organoid experiment at 41d
whOrg4_B9_hOrg41d


title: whOrg4_C1_hOrg41d

description:
Single cell C1 from human cerebral organoid experiment at 41d
whOrg4_C1_hOrg41d


title: whOrg4_C12_hOrg41d

description:
Single cell C12 from human cerebral organoid experiment at 41d
whOrg4_C12_hOrg41d


title: whOrg4_B6_hOrg41d

description:
Single cell B6 from human cerebral organoid experiment at 41d
whOrg4_B6_hOrg41d


title: whOrg4_B5_hOrg41d

description:
Single cell B5 from human cerebral organoid experiment at 41d
whOrg4_B5_hOrg41d


title: whOrg4_B1_hOrg41d

description:
Single cell B1 from human cerebral organoid experiment at 41d
whOrg4_B1_hOrg41d


title: whOrg4_B4_hOrg41d

description:
Single cell B4 from human cerebral organoid experiment at 41d
whOrg4_B4_hOrg41d


title: whOrg4_B3_hOrg41d

description:
Single cell B3 from human cerebral organoid experiment at 41d
whOrg4_B3_hOrg41d


title: whOrg4_C8_hOrg41d

description:
Single cell C8 from human cerebral organoid experiment at 41d
whOrg4_C8_hOrg41d


title: whOrg4_B11_hOrg41d

description:
Single cell B11 from human cerebral organoid experiment at 41d
whOrg4_B11_hOrg41d


title: whOrg4_B10_hOrg41d

description:
Single cell B10 from human cerebral organoid experiment at 41d
whOrg4_B10_hOrg41d


title: whOrg4_A8_hOrg41d

description:
Single cell A8 from human cerebral organoid experiment at 41d
whOrg4_A8_hOrg41d


title: whOrg4_A6_hOrg41d

description:
Single cell A6 from human cerebral organoid experiment at 41d
whOrg4_A6_hOrg41d


title: whOrg4_C3_hOrg41d

description:
Single cell C3 from human cerebral organoid experiment at 41d
whOrg4_C3_hOrg41d


title: whOrg4_A7_hOrg41d

description:
Single cell A7 from human cerebral organoid experiment at 41d
whOrg4_A7_hOrg41d


title: whOrg4_A4_hOrg41d

description:
Single cell A4 from human cerebral organoid experiment at 41d
whOrg4_A4_hOrg41d


title: whOrg4_A10_hOrg41d

description:
Single cell A10 from human cerebral organoid experiment at 41d
whOrg4_A10_hOrg41d


title: whOrg4_A3_hOrg41d

description:
Single cell A3 from human cerebral organoid experiment at 41d
whOrg4_A3_hOrg41d


title: whOrg3_H4_hOrg37d

description:
Single cell H4 from human cerebral organoid experiment at 37d
whOrg3_H4_hOrg37d

value: 37 days


title: whOrg4_A2_hOrg41d

description:
Single cell A2 from human cerebral organoid experiment at 41d
whOrg4_A2_hOrg41d


title: whOrg3_H3_hOrg37d

description:
Single cell H3 from human cerebral organoid experiment at 37d
whOrg3_H3_hOrg37d


title: whOrg4_A5_hOrg41d

description:
Single cell A5 from human cerebral organoid experiment at 41d
whOrg4_A5_hOrg41d


title: whOrg3_H12_hOrg37d

description:
Single cell H12 from human cerebral organoid experiment at 37d
whOrg3_H12_hOrg37d


title: whOrg3_H11_hOrg37d

description:
Single cell H11 from human cerebral organoid experiment at 37d
whOrg3_H11_hOrg37d


title: whOrg3_H10_hOrg37d

description:
Single cell H10 from human cerebral organoid experiment at 37d
whOrg3_H10_hOrg37d


title: whOrg4_B8_hOrg41d

description:
Single cell B8 from human cerebral organoid experiment at 41d
whOrg4_B8_hOrg41d


title: whOrg3_G5_hOrg37d

description:
Single cell G5 from human cerebral organoid experiment at 37d
whOrg3_G5_hOrg37d


title: whOrg3_G9_hOrg37d

description:
Single cell G9 from human cerebral organoid experiment at 37d
whOrg3_G9_hOrg37d


title: whOrg3_G3_hOrg37d

description:
Single cell G3 from human cerebral organoid experiment at 37d
whOrg3_G3_hOrg37d


title: whOrg3_G2_hOrg37d

description:
Single cell G2 from human cerebral organoid experiment at 37d
whOrg3_G2_hOrg37d


title: whOrg3_F9_hOrg37d

description:
Single cell F9 from human cerebral organoid experiment at 37d
whOrg3_F9_hOrg37d


title: whOrg4_C10_hOrg41d

description:
Single cell C10 from human cerebral organoid experiment at 41d
whOrg4_C10_hOrg41d


title: whOrg3_H7_hOrg37d

description:
Single cell H7 from human cerebral organoid experiment at 37d
whOrg3_H7_hOrg37d


title: whOrg3_G11_hOrg37d

description:
Single cell G11 from human cerebral organoid experiment at 37d
whOrg3_G11_hOrg37d


title: whOrg3_F3_hOrg37d

description:
Single cell F3 from human cerebral organoid experiment at 37d
whOrg3_F3_hOrg37d


title: whOrg3_G12_hOrg37d

description:
Single cell G12 from human cerebral organoid experiment at 37d
whOrg3_G12_hOrg37d


title: whOrg4_A1_hOrg41d

description:
Single cell A1 from human cerebral organoid experiment at 41d
whOrg4_A1_hOrg41d


title: whOrg3_F4_hOrg37d

description:
Single cell F4 from human cerebral organoid experiment at 37d
whOrg3_F4_hOrg37d


title: whOrg3_F11_hOrg37d

description:
Single cell F11 from human cerebral organoid experiment at 37d
whOrg3_F11_hOrg37d


title: whOrg3_F7_hOrg37d

description:
Single cell F7 from human cerebral organoid experiment at 37d
whOrg3_F7_hOrg37d


title: whOrg3_F10_hOrg37d

description:
Single cell F10 from human cerebral organoid experiment at 37d
whOrg3_F10_hOrg37d


title: whOrg3_F12_hOrg37d

description:
Single cell F12 from human cerebral organoid experiment at 37d
whOrg3_F12_hOrg37d


title: whOrg3_E8_hOrg37d

description:
Single cell E8 from human cerebral organoid experiment at 37d
whOrg3_E8_hOrg37d


title: whOrg3_E7_hOrg37d

description:
Single cell E7 from human cerebral organoid experiment at 37d
whOrg3_E7_hOrg37d


title: whOrg3_F2_hOrg37d

description:
Single cell F2 from human cerebral organoid experiment at 37d
whOrg3_F2_hOrg37d


title: whOrg3_H8_hOrg37d

description:
Single cell H8 from human cerebral organoid experiment at 37d
whOrg3_H8_hOrg37d


title: whOrg3_E5_hOrg37d

description:
Single cell E5 from human cerebral organoid experiment at 37d
whOrg3_E5_hOrg37d


title: whOrg3_E3_hOrg37d

description:
Single cell E3 from human cerebral organoid experiment at 37d
whOrg3_E3_hOrg37d


title: whOrg3_E2_hOrg37d

description:
Single cell E2 from human cerebral organoid experiment at 37d
whOrg3_E2_hOrg37d


title: whOrg3_G10_hOrg37d

description:
Single cell G10 from human cerebral organoid experiment at 37d
whOrg3_G10_hOrg37d


title: whOrg3_E6_hOrg37d

description:
Single cell E6 from human cerebral organoid experiment at 37d
whOrg3_E6_hOrg37d


title: whOrg3_E12_hOrg37d

description:
Single cell E12 from human cerebral organoid experiment at 37d
whOrg3_E12_hOrg37d


title: whOrg3_E1_hOrg37d

description:
Single cell E1 from human cerebral organoid experiment at 37d
whOrg3_E1_hOrg37d


title: whOrg3_E11_hOrg37d

description:
Single cell E11 from human cerebral organoid experiment at 37d
whOrg3_E11_hOrg37d


title: whOrg3_E10_hOrg37d

description:
Single cell E10 from human cerebral organoid experiment at 37d
whOrg3_E10_hOrg37d


title: whOrg3_D8_hOrg37d

description:
Single cell D8 from human cerebral organoid experiment at 37d
whOrg3_D8_hOrg37d


title: 4C_Vax2_bait2_serum_to_2i_Day3

city: Nijmegen

first: Shuang-Yin

last: Wang

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: RIMLS

description: 4C PCR product. Barcode: GCCAGCATGGTTGAAGCTT

library_source: genomic

data_processing:
Illumina Casava software 1.8.2  used for basecalling of Hiseq2000 and NextSeq 500 data.
Library strategy: ChIP-seq. The reads were aligned to build version mm9 of the mouse genome using bwa (version 0.7.12) with default parameters. Only uniquely mapped reads were kept for downstream analysis. Reads from PCR duplicates were also removed. MACS (version 2.0.10.20130306), was used to identify regions of ChIP-seq enrichment over background using parameters --nomodel --broad.
Library strategy: RNA-seq. MMSEQ package was used to infer gene expression levels. Reads were mapped to mouse gene annotation (Ensemble release 67).
Library strategy: Capture Hi-C. The two ends of paired-end reads were mapped to the reference mouse genome (mm9) separately, using BWA MEM (version 0.7.12) with default parameters. Reads were filtered based on mapping quality score (both ends mapQ ≥ 10) and PCR duplicates were removed. Reads were removed if the two ends are from the same DpnII fragment. CHICAGO CHi-C analysis package (http://regulatorygenomicsgroup.org/chicago) was used to call significant contacts. To increase quality, the whole genome was windowed into 5 DpnII site tiles. Virtual baits were created by merging adjacent target regions. Interactions were filtered based on interaction score and number of reads (score ≥ 5 and at least 5 reads).
Library strategy: DNaseI-seq. The reads were aligned to build version mm9 of the mouse genome using bwa (version 0.7.12) with default parameters. Only uniquely mapped reads were kept for downstream analysis. Reads from PCR duplicates were also removed. MACS (version 2.0.10.20130306), was used to identify DNaseI hyper-sensitive sites using parameters --nomodel --broad.
Library strategy: 4C-seq. The initial step in the 4C-seq analysis is the alignment of the sequencing reads to a reduced genome of sequences that flank HindIII sites (fragment ends). Repetitive fragment ends were excluded from subsequent analysis. The reduced genome was based on mouse genome mm9.
Genome_build: mm9

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: All cell-culture was conducted in feeder-free condition.

extract_protocol: Libraries were prepared according to Illumina's instructions.

treatment_protocol: Serum-to-2i transition was carried out by washing the mESCs in serum medium twice with PBS and then switching to 2i Medium.

tag: developmental stage

tag: chip antibody


title: 4C_Vax2_bait2_Eed-_KO

treatment_protocol: Eed-/- mESC were grown feeder-free in DMEM containing 10% fetal calf serum in presence of LIF.


title: 4C_Vax2_bait2_2i

treatment_protocol: 2i mESCs were grown in serum free NDiff 227 supplemented with MEK inhibitor PD0325901 (1µM) and GSK3 inhibitor CHIR99021 (3µM) in presence of LIF.


title: whOrg3_F5_hOrg37d

description:
Single cell F5 from human cerebral organoid experiment at 37d
whOrg3_F5_hOrg37d


title: whOrg3_D7_hOrg37d

description:
Single cell D7 from human cerebral organoid experiment at 37d
whOrg3_D7_hOrg37d


title: 4C_Vax2_bait2_serum

treatment_protocol: Serum mESCs were grown in DMEM containing 10% fetal calf serum in presence of LIF, together called Serum medium.


title: 4C_Vax2_bait1_Eed-_KO

description: 4C PCR product. Barcode: CGAGTGGAGTAGGTAGAAGC


title: whOrg3_D9_hOrg37d

description:
Single cell D9 from human cerebral organoid experiment at 37d
whOrg3_D9_hOrg37d


title: whOrg3_D3_hOrg37d

description:
Single cell D3 from human cerebral organoid experiment at 37d
whOrg3_D3_hOrg37d


title: whOrg3_D5_hOrg37d

description:
Single cell D5 from human cerebral organoid experiment at 37d
whOrg3_D5_hOrg37d


title: whOrg3_D12_hOrg37d

description:
Single cell D12 from human cerebral organoid experiment at 37d
whOrg3_D12_hOrg37d


title: 4C_HoxD_bait2_serum

description: 4C PCR product. Barcode: ACAGTTCTGCAAGAAAGCTT


title: 4C_Vax2_bait2_serum_to_2i_Day1


title: whOrg3_E9_hOrg37d

description:
Single cell E9 from human cerebral organoid experiment at 37d
whOrg3_E9_hOrg37d


title: 4C_HoxD_bait2_2i


title: whOrg3_D11_hOrg37d

description:
Single cell D11 from human cerebral organoid experiment at 37d
whOrg3_D11_hOrg37d


title: whOrg3_D1_hOrg37d

description:
Single cell D1 from human cerebral organoid experiment at 37d
whOrg3_D1_hOrg37d


title: 4C_HoxD_bait2_Eed-_KO


title: 4C_HoxD_bait1_Eed-_KO

description: 4C PCR product. Barcode: AGATTAAGAAAACCCACAAGC


title: whOrg3_C7_hOrg37d

description:
Single cell C7 from human cerebral organoid experiment at 37d
whOrg3_C7_hOrg37d


title: 4C_HoxD_bait1_2i


title: whOrg3_C6_hOrg37d

description:
Single cell C6 from human cerebral organoid experiment at 37d
whOrg3_C6_hOrg37d


title: 4C_Vax2_bait1_serum


title: whOrg3_D4_hOrg37d

description:
Single cell D4 from human cerebral organoid experiment at 37d
whOrg3_D4_hOrg37d


title: whOrg3_C5_hOrg37d

description:
Single cell C5 from human cerebral organoid experiment at 37d
whOrg3_C5_hOrg37d


title: whOrg3_C4_hOrg37d

description:
Single cell C4 from human cerebral organoid experiment at 37d
whOrg3_C4_hOrg37d


title: whOrg3_C9_hOrg37d

description:
Single cell C9 from human cerebral organoid experiment at 37d
whOrg3_C9_hOrg37d


title: 4C_HoxD_bait1_serum


title: 4C_HoxA_bait2_Eed-_KO

description: 4C PCR product. Barcode: CCTGAGTAGGCCCTTACaag


title: whOrg3_C3_hOrg37d

description:
Single cell C3 from human cerebral organoid experiment at 37d
whOrg3_C3_hOrg37d


title: 4C_HoxD_bait1_serum_to_2i_Day1


title: 4C_HoxA_bait2_2i


title: whOrg3_C2_hOrg37d

description:
Single cell C2 from human cerebral organoid experiment at 37d
whOrg3_C2_hOrg37d


title: whOrg3_C1_hOrg37d

description:
Single cell C1 from human cerebral organoid experiment at 37d
whOrg3_C1_hOrg37d


title: 4C_HoxA_bait2_serum_to_2i_Day3


title: 4C_Vax2_bait1_2i

description: 4C PCR product. Barcode: CGAGTGGAGTAGGTAGAAGC


title: 4C_HoxA_bait2_serum_to_2i_Day1


title: 4C_HoxA_bait1_Eed-_KO

description: 4C PCR product. Barcode: CAGCATTTCACCCAAGCTT


title: whOrg3_B9_hOrg37d

description:
Single cell B9 from human cerebral organoid experiment at 37d
whOrg3_B9_hOrg37d


title: 4C_HoxA_bait1_2i


title: whOrg3_B5_hOrg37d

description:
Single cell B5 from human cerebral organoid experiment at 37d
whOrg3_B5_hOrg37d


title: whOrg3_B8_hOrg37d

description:
Single cell B8 from human cerebral organoid experiment at 37d
whOrg3_B8_hOrg37d


title: 4C_HoxA_bait1_serum


title: whOrg3_B2_hOrg37d

description:
Single cell B2 from human cerebral organoid experiment at 37d
whOrg3_B2_hOrg37d


title: whOrg3_B4_hOrg37d

description:
Single cell B4 from human cerebral organoid experiment at 37d
whOrg3_B4_hOrg37d


title: ChIPseq_H3K27ac_2i_BR1

value: H3K27ac (Anti-H3K27ac, C15410196-10, Diagenode)


title: ChIPseq_H3K27ac_2i_BR2


title: ChIPseq_H3K27ac_serum_to_2i_Day3_BR2


title: 4C_HoxD_bait1_serum_to_2i_Day3

description: 4C PCR product. Barcode: AGATTAAGAAAACCCACAAGC


title: whOrg3_B11_hOrg37d

description:
Single cell B11 from human cerebral organoid experiment at 37d
whOrg3_B11_hOrg37d


title: whOrg3_B10_hOrg37d

description:
Single cell B10 from human cerebral organoid experiment at 37d
whOrg3_B10_hOrg37d


title: ChIPseq_H3K27ac_serum_to_2i_Day1_BR2


title: whOrg3_A9_hOrg37d

description:
Single cell A9 from human cerebral organoid experiment at 37d
whOrg3_A9_hOrg37d


title: whOrg3_A7_hOrg37d

description:
Single cell A7 from human cerebral organoid experiment at 37d
whOrg3_A7_hOrg37d


title: ChIPseq_H3K27ac_serum_to_2i_Day3_BR1


title: ChIPseq_H3K27ac_serum_BR2


title: whOrg3_A8_hOrg37d

description:
Single cell A8 from human cerebral organoid experiment at 37d
whOrg3_A8_hOrg37d


title: whOrg3_C12_hOrg37d

description:
Single cell C12 from human cerebral organoid experiment at 37d
whOrg3_C12_hOrg37d


title: whOrg3_A6_hOrg37d

description:
Single cell A6 from human cerebral organoid experiment at 37d
whOrg3_A6_hOrg37d


title: whOrg3_A4_hOrg37d

description:
Single cell A4 from human cerebral organoid experiment at 37d
whOrg3_A4_hOrg37d


title: Chi-C_mESCs_serum_Eed_KO_BR2

description: Hi-C PCR product. Digestion: DpnII


title: ChIPseq_H3K27ac_serum_to_2i_Day1_BR1


title: whOrg3_A3_hOrg37d

description:
Single cell A3 from human cerebral organoid experiment at 37d
whOrg3_A3_hOrg37d


title: ChIPseq_H3K27ac_serum_BR1


title: whOrg3_A12_hOrg37d

description:
Single cell A12 from human cerebral organoid experiment at 37d
whOrg3_A12_hOrg37d


title: whOrg3_B3_hOrg37d

description:
Single cell B3 from human cerebral organoid experiment at 37d
whOrg3_B3_hOrg37d


title: Chi-C_mESCs_serum_to_2i_Day3_BR2

description: Hi-C PCR product. Digestion: DpnII


title: whOrg3_A2_hOrg37d

description:
Single cell A2 from human cerebral organoid experiment at 37d
whOrg3_A2_hOrg37d


title: Chi-C_mESCs_serum_to_2i_Day1_BR2

description: Hi-C PCR product. Digestion: DpnII


title: ChIPseq_Suz12_serum_to_2i_Day1_BR2

value: Suz12 (Anti-Suz12, ab1207, Abcam)


title: ChIPseq_Suz12_2i_BR2

data_processing:
Illumina Casava software 1.8.2  used for basecalling of Hiseq2000 and NextSeq 500 data.
Library strategy: ChIP-seq. The reads were aligned to build version mm9 of the mouse genome using bwa (version 0.7.12) with default parameters. Only uniquely mapped reads were kept for downstream analysis. Reads from PCR duplicates were also removed. MACS (version 2.0.10.20130306), was used to identify regions of ChIP-seq enrichment over background using parameters --nomodel --broad.
Genome_build: mm9


title: whOrg3_A11_hOrg37d

description:
Single cell A11 from human cerebral organoid experiment at 37d
whOrg3_A11_hOrg37d


title: ChIPseq_Suz12_serum_to_2i_Day1_BR1


title: ChIPseq_Suz12_serum_to_2i_Day3


title: whOrg3_A10_hOrg37d

description:
Single cell A10 from human cerebral organoid experiment at 37d
whOrg3_A10_hOrg37d


title: ChIPseq_Suz12_2i_BR1


title: ChIPseq_Suz12_serum_BR2


title: ChIPseq_Ring1B_2i_BR2

value: Ring1B (Anti-Ring1B, D22F2, Cell Signaling)


title: ChIPseq_Suz12_serum_BR1


title: ChIPseq_Ring1B_2i_BR1


title: whOrg2_F5_hOrg35d

description:
Single cell F5 from human cerebral organoid experiment at 35d
whOrg2_F5_hOrg35d

value: 35 days


title: whOrg2_F4_hOrg35d

description:
Single cell F4 from human cerebral organoid experiment at 35d
whOrg2_F4_hOrg35d


title: whOrg2_F7_hOrg35d

description:
Single cell F7 from human cerebral organoid experiment at 35d
whOrg2_F7_hOrg35d


title: whOrg3_A1_hOrg37d

description:
Single cell A1 from human cerebral organoid experiment at 37d
whOrg3_A1_hOrg37d


title: ChIPseq_Ring1B_serum_to_2i_Day1_BR1


title: whOrg2_F3_hOrg35d

description:
Single cell F3 from human cerebral organoid experiment at 35d
whOrg2_F3_hOrg35d


title: whOrg2_F12_hOrg35d

description:
Single cell F12 from human cerebral organoid experiment at 35d
whOrg2_F12_hOrg35d


title: 4C_HoxA_bait2_serum

description: 4C PCR product. Barcode: CCTGAGTAGGCCCTTACaag


title: ChIPseq_Ring1B_serum_to_2i_Day1_BR2


title: whOrg2_F11_hOrg35d

description:
Single cell F11 from human cerebral organoid experiment at 35d
whOrg2_F11_hOrg35d


title: whOrg2_F6_hOrg35d

description:
Single cell F6 from human cerebral organoid experiment at 35d
whOrg2_F6_hOrg35d


title: ChIPseq_H3K27me3_2i_BR2

value: H3K27me3 (Anti-H3K27me3, 07-449, Upstate)


title: whOrg2_F2_hOrg35d

description:
Single cell F2 from human cerebral organoid experiment at 35d
whOrg2_F2_hOrg35d


title: whOrg2_F9_hOrg35d

description:
Single cell F9 from human cerebral organoid experiment at 35d
whOrg2_F9_hOrg35d


title: whOrg2_F8_hOrg35d

description:
Single cell F8 from human cerebral organoid experiment at 35d
whOrg2_F8_hOrg35d


title: whOrg2_F10_hOrg35d

description:
Single cell F10 from human cerebral organoid experiment at 35d
whOrg2_F10_hOrg35d


title: ChIPseq_Ring1B_serum_BR2


title: ChIPseq_H3K27me3_2i_BR1


title: whOrg2_E8_hOrg35d

description:
Single cell E8 from human cerebral organoid experiment at 35d
whOrg2_E8_hOrg35d


title: ChIPseq_H3K27me3_serum_to_2i_Day3_BR1


title: whOrg2_E6_hOrg35d

description:
Single cell E6 from human cerebral organoid experiment at 35d
whOrg2_E6_hOrg35d


title: ChIPseq_H3K27me3_serum_to_2i_Day3_BR2


title: whOrg2_E9_hOrg35d

description:
Single cell E9 from human cerebral organoid experiment at 35d
whOrg2_E9_hOrg35d


title: whOrg2_E7_hOrg35d

description:
Single cell E7 from human cerebral organoid experiment at 35d
whOrg2_E7_hOrg35d


title: ChIPseq_Ring1B_serum_to_2i_Day3


title: ChIPseq_H3K27me3_serum_to_2i_Day1_BR2


title: whOrg2_E5_hOrg35d

description:
Single cell E5 from human cerebral organoid experiment at 35d
whOrg2_E5_hOrg35d


title: ChIPseq_H3K27me3_serum_BR2


title: ChIPseq_H3K27me3_serum_to_2i_Day1_BR1


title: ChIPseq_H3K27me3_serum_BR1


title: whOrg2_E3_hOrg35d

description:
Single cell E3 from human cerebral organoid experiment at 35d
whOrg2_E3_hOrg35d


title: whOrg2_E2_hOrg35d

description:
Single cell E2 from human cerebral organoid experiment at 35d
whOrg2_E2_hOrg35d


title: whOrg2_E4_hOrg35d

description:
Single cell E4 from human cerebral organoid experiment at 35d
whOrg2_E4_hOrg35d


title: ChIPseq_Ring1B_serum_BR1


title: CHi-C_mESCs_serum_to_2i_Day3_BR1

description: Hi-C PCR product. Digestion: DpnII


title: CHi-C_mESCs_serum_Eed_KO_BR1

description: Hi-C PCR product. Digestion: DpnII


title: whOrg2_E12_hOrg35d

description:
Single cell E12 from human cerebral organoid experiment at 35d
whOrg2_E12_hOrg35d


title: CHi-C_mESCs_2i_BR2

description: Hi-C PCR product. Digestion: DpnII


title: whOrg2_E11_hOrg35d

description:
Single cell E11 from human cerebral organoid experiment at 35d
whOrg2_E11_hOrg35d


title: CHi-C_mESCs_2i_BR1

description: Hi-C PCR product. Digestion: DpnII


title: whOrg2_E10_hOrg35d

description:
Single cell E10 from human cerebral organoid experiment at 35d
whOrg2_E10_hOrg35d


title: whOrg2_D9_hOrg35d

description:
Single cell D9 from human cerebral organoid experiment at 35d
whOrg2_D9_hOrg35d


title: CHi-C_mESCs_serum_to_2i_Day1_BR1

description: Hi-C PCR product. Digestion: DpnII


title: CHi-C_mESCs_serum_BR2

description: Hi-C PCR product. Digestion: DpnII


title: CHi-C_mESCs_serum_BR1

description: Hi-C PCR product. Digestion: DpnII


title: whOrg2_D7_hOrg35d

description:
Single cell D7 from human cerebral organoid experiment at 35d
whOrg2_D7_hOrg35d


title: whOrg2_D8_hOrg35d

description:
Single cell D8 from human cerebral organoid experiment at 35d
whOrg2_D8_hOrg35d


title: Input CT10 sonication

city: Houston

first: Bokai

last: Zhu

state: Texas

address: One Baylor Plaza, M813

department: MCB

country: USA

institute: Baylor College of Medicine

data_processing:
The sequences identified were mapped to the mouse genome (NCBI37/UCSC mm9) using BOWTIE function in Galaxy. Only the sequences uniquely mapped with no more than 2 mismatches were kept and used as valid reads. PCR duplicates were also removed. Mapped sequences from different replicates of REV-ERBα ChIP-Seq were pooled together for subsequent analysis
Peak calling was carried out by MACS (version 1.4.2 20120305) in Galaxy/Cistrome (options --mfold 10, 30 --pvalue 1e-5), on each ChIP-seq file against the matching input file.
To account for the different sequencing depths between samples, the signal files generated from MACS were normalized by Signal Extraction Scaling (SES) method (Meyer and Liu, 2014). The peak summits were used as the binding site centers, and the normalized signal files were used as the binding strength for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated by Galaxy/cistrome

source_name: liver

extract_protocol:
Lysates were clarified from sonicated (for BAF180 ChIP-Seq) or MNase-digested (for REV-ERBα ChIP-Seq) nuclei and Protein-DNA complexes were isolated with antibody.
Illumina sequencing libraries were prepared from the ChIP and input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina NextSeq 500 (75 nt reads, single-end for BAF180 ChIP-Seq). The resulting DNA libraries were quantified and sequenced on Illumina HiSeq 2500 Sequencing system (50nt reads, single end for REV-ERBα ChIP-Seq).

tag: strain

tag: Sex

value: Male

tag: age

value: 10-20 weeks

tag: genotype

value: Wild-type


title: BAF180 ChIP-seq CT22 AM antibody

value: BAF180 (Active Motif 61381)


title: whOrg2_D6_hOrg35d

description:
Single cell D6 from human cerebral organoid experiment at 35d
whOrg2_D6_hOrg35d


title: whOrg2_D5_hOrg35d

description:
Single cell D5 from human cerebral organoid experiment at 35d
whOrg2_D5_hOrg35d


title: BAF180 ChIP-seq CT10 Bethyl antibody


title: BAF180 ChIP-seq CT22 Bethyl antibody


title: whOrg2_D2_hOrg35d

description:
Single cell D2 from human cerebral organoid experiment at 35d
whOrg2_D2_hOrg35d


title: whOrg2_E1_hOrg35d

description:
Single cell E1 from human cerebral organoid experiment at 35d
whOrg2_E1_hOrg35d


title: Input CT10 MNase digestion

value: C57BL/6J/129 SV mixed background


title: whOrg2_D1_hOrg35d

description:
Single cell D1 from human cerebral organoid experiment at 35d
whOrg2_D1_hOrg35d


title: whOrg2_D12_hOrg35d

description:
Single cell D12 from human cerebral organoid experiment at 35d
whOrg2_D12_hOrg35d


title: SRC-2-/- REV-ERBα ChIP-Seq

value: REV-ERBα (Cell signaling 2124)


title: whOrg2_D11_hOrg35d

description:
Single cell D11 from human cerebral organoid experiment at 35d
whOrg2_D11_hOrg35d


title: whOrg2_C9_hOrg35d

description:
Single cell C9 from human cerebral organoid experiment at 35d
whOrg2_C9_hOrg35d


title: whOrg2_D4_hOrg35d

description:
Single cell D4 from human cerebral organoid experiment at 35d
whOrg2_D4_hOrg35d


title: whOrg2_C6_hOrg35d

description:
Single cell C6 from human cerebral organoid experiment at 35d
whOrg2_C6_hOrg35d


title: whOrg2_C5_hOrg35d

description:
Single cell C5 from human cerebral organoid experiment at 35d
whOrg2_C5_hOrg35d


title: Input_LNCaP cells, KD CHD1, DHT treated

city: Freiburg

first: Eric

last: Metzger

address: Breisacherstr. 66

institute: Uniklinik-Freiburg

data_processing:
ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the hg19 reference genome using bowtie 2
peak finding algorithm MACS
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are wiggle and bed files. The wig files include the read data mapped to the hg19 genome. The bed files contain the peaks that were obtained when normalizing the reads of the ChIP-Seq to the Input.

source_name: LNCaP cells

growth_protocol: Human LNCaP  cells were maintained in RPMI medium supplemented with 10 % FBS and glutamine. +/- DHT 10-7M 210min

extract_protocol:
Metzger, E., et al. Phosphorylation of histone H3 at threonine 11 establishes a novel chromatin mark for transcriptional regulation. Nat Cell Biol 10, 53-60 (2008).
Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the hg19 reference genome using bowtie 2
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).

tag: cell line

value: LNCaP prostate cancer cells

tag: protocol

value: CHD1 knockdown

tag: passages

tag: treatment

value: DHT


title: CHD1, ChIPseq, LNCaP cells, KD CHD1, DHT treated

value: anti-CHD1 (Bethyl, catalog# A301-218A, lot# A301-218A-1)


title: LSD1_K114me2_siG9apDHT

value: G9A knockdown

value: LSD1_K114me2 (Schüle Lab)


title: Input_LNCaP cells, KD LSD1, DHT treated

value: LSD1 knockdown


title: LSD1_K114me2, ChIPseq, LNCaP cells, KD LSD1, DHT treated


title: whOrg2_C3_hOrg35d

description:
Single cell C3 from human cerebral organoid experiment at 35d
whOrg2_C3_hOrg35d

value: Dissociated whole cerebral organoid


title: whOrg2_D3_hOrg35d

description:
Single cell D3 from human cerebral organoid experiment at 35d
whOrg2_D3_hOrg35d


title: whOrg2_C2_hOrg35d

description:
Single cell C2 from human cerebral organoid experiment at 35d
whOrg2_C2_hOrg35d


title: LNCaP cells DHT treated biological replicate 1

description: Sample name: 3a_LNCaP_plus_DHT_10-7M_6h

data_processing:
We aligned these reads to the hg19 build of the human genome using TopHat version 2
The aligned reads were counted with the homer software (analyzeRNA) and DEG’s were identified using DESeq
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file "CountsTable.txt" includes the overall read count for a specific transcript (indicated by the NM accession number).  "CountsTable.txt" values do not represent normalized data.

growth_protocol: Human LNCaP  cells were maintained in RPMI medium supplemented with 10 % dsFBS and glutamine.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files).

treatment_protocol: cells were treated with or without 10-7 M DHT for 6 hours

value: WT


title: LNCaP cells DHT treated biological replicate 3

description: Sample name: 3c_LNCaP_plus_DHT_10-7M_6h


title: LNCaP cells Control, biological replicate 3

description: Sample name: 1c_LNCaP

value: control


title: LNCaP cells DHT treated biological replicate 2

description: Sample name: 3b_LNCaP_plus_DHT_10-7M_6h


title: whOrg2_C12_hOrg35d

description:
Single cell C12 from human cerebral organoid experiment at 35d
whOrg2_C12_hOrg35d

value: 35 days


title: LNCaP cells Control, biological replicate 2

description: Sample name: 1b_LNCaP


title: Input_siG9apDHT


title: Input_LNCaP

description: Input

value: Control


title: whOrg2_C8_hOrg35d

description:
Single cell C8 from human cerebral organoid experiment at 35d
whOrg2_C8_hOrg35d


title: LNCaP cells Control, biological replicate 1

description: Sample name: 1a_LNCaP


title: whOrg2_B9_hOrg35d

description:
Single cell B9 from human cerebral organoid experiment at 35d
whOrg2_B9_hOrg35d


title: LSD1_K114me2, ChIPseq, LNCaP cells


title: whOrg2_B8_hOrg35d

description:
Single cell B8 from human cerebral organoid experiment at 35d
whOrg2_B8_hOrg35d


title: whOrg2_B7_hOrg35d

description:
Single cell B7 from human cerebral organoid experiment at 35d
whOrg2_B7_hOrg35d


title: LSD1_K114me2, ChIPseq, LNCaP cells, DHT treated


title: CHD1, ChIPseq, LNCaP cells, DHT treated


title: whOrg2_C10_hOrg35d

description:
Single cell C10 from human cerebral organoid experiment at 35d
whOrg2_C10_hOrg35d


title: CHD1, ChIPseq, LNCaP cells


title: whOrg2_B5_hOrg35d

description:
Single cell B5 from human cerebral organoid experiment at 35d
whOrg2_B5_hOrg35d


title: whOrg2_B3_hOrg35d

description:
Single cell B3 from human cerebral organoid experiment at 35d
whOrg2_B3_hOrg35d


title: whOrg2_B4_hOrg35d

description:
Single cell B4 from human cerebral organoid experiment at 35d
whOrg2_B4_hOrg35d


title: whOrg2_B2_hOrg35d

description:
Single cell B2 from human cerebral organoid experiment at 35d
whOrg2_B2_hOrg35d


title: whOrg2_C1_hOrg35d

description:
Single cell C1 from human cerebral organoid experiment at 35d
whOrg2_C1_hOrg35d


title: whOrg2_B11_hOrg35d

description:
Single cell B11 from human cerebral organoid experiment at 35d
whOrg2_B11_hOrg35d


title: WT REV-ERBα ChIP-Seq

value: Male

value: 10-20 weeks


title: whOrg2_B6_hOrg35d

description:
Single cell B6 from human cerebral organoid experiment at 35d
whOrg2_B6_hOrg35d


title: whOrg2_B12_hOrg35d

description:
Single cell B12 from human cerebral organoid experiment at 35d
whOrg2_B12_hOrg35d


title: whOrg2_A8_hOrg35d

description:
Single cell A8 from human cerebral organoid experiment at 35d
whOrg2_A8_hOrg35d


title: Lin28.KD.RNAseq

city: Atlanta

first: Bing

last: Yao

state: GA

address: 615 Michael St. Rm 323

department: Human Genetics

institute: Emory University

data_processing: RNA-seq reads were aligned using tophat v2.0.8 and differential RPKM expression values were extracted using cuffdiff v2.2.1

source_name: mouse ES cells E14

growth_protocol: The E14 mESC line was cultured on Mouse Embryonic Fibroblast (MEF) feeder cells as previously described (Ma et al., 2008). The medium contained DMEM supplemented with 15% FBS, GlutaMAX™-I (2 mM), sodium Pyruvate (1 mM), MEM nonessential amino acid (0.1 mM), Penicillin/Streptomycin (50 ug/ml each), β-mercaptoethanol (100 uM) and ESGRO-LIF (Millipore, ESG1106; 1000 U/ml).

extract_protocol:
Total RNA was extracted from mESCs by RNeasy (Qiagen), and 1 ug total RNA was primed with Oligo(dT)20 primers (Invitrogen) for cDNA synthesis.
For 5hmC capture and sequencing, five ug of genomic DNA was sonicated to 100-500 bp, and then mixed with 100 ul reaction buffer (50 mM HEPES at pH 8.0, 25 mM MgCl2, 250 uM UDP-6-N3-Glu and 2.25 uM wild-type beta-glucosyltransferase (beta-GT)). Reactions were incubated at 37°C for 1 hour, and DNA substrates were then purified by Qiagen DNA purification kit. 150 uM dibenzocyclooctyne modified biotin was mixed with beta-GT-modified DNA. The labelling reaction was performed at 37°C for 2 hours. The biotin-labeled DNA was enriched by Strepavidin-coupled Dynabeads (Dynabeads MyOneTM Streptavidin T1, Life Technologies) and purified by Qiagen DNA purification kit. 5mC experiments were performed according to the manufacturer's protocol (Active Motif). Briefly, five microgram of DNA was sonicated to 100-500bp, and then mixed with 10ul buffer C and water to form 95ul total pulldown reaction. 2ul 5mC antibody was incubated with sonicated DNA overnight. 25ul Protein G magnetic beads were added to capture 5mC antibody and its bound mC containing DNA. Wash 3x with buffer C and puriy the DNA with Qiagen PCR purification kit. The enriched methylated DNA was purified by Qiagen DNA purification kit. 5hmC- and 5mC-containing DNA was subjected to library preparation. 25ng of input genomic DNA or experimental enriched DNA were utilized for each library construction. 150-300 bp DNA fragments were selected by AMPure XP Beads (Beckman Coulter) after the adapter ligation. An Agilent 2100 BioAnalyzer was used to quantify the amplified DNA, qPCR was applied to accurately quantify the library concentration. 20 pM diluted libraries were used for sequencing. 50-cycle single-end sequencings were performed using Illumina HISeq 2000. Image processing and sequence extraction were done using the standard Illumina Pipeline. RNA-seq libraries were generated from duplicated samples per condition using the Illumina TruSeq RNA Sample Preparation Kit v2 following manufacturer's protocol. The RNA-seq libraries were sequenced as 50-cycle pair-end runs using Illumina HiSeq 2000.

treatment_protocol: Lentiviral pLKO.1 vectors encoding shRNAs targeting mouse Lin28A (Open Biosystems) were co-transfected with pMDL gag/pol RRE, pRSV-Rev and pCMV VSV-G into 293T cells using the calcium phosphate method. Transfected cells were incubated at 37°C in DMEM supplemented with 10% newborn calf serum for 24 hours. The medium was replaced with DMEM supplemented with 2% newborn calf serum and incubated for an additional 24 hours at 37°C. Viral supernatants were collected and filtered through a 0.45-μm syringe filter, supplemented with 10% FBS and 10 μg/mL polybrene. mESCs were infected with the viral supernatant and selected by 3 μg/ml puromycin for 3 days.

tag: antibodies/ip methods

tag: lentivirus vector


title: whOrg2_B1_hOrg35d

description:
Single cell B1 from human cerebral organoid experiment at 35d
whOrg2_B1_hOrg35d


title: whOrg2_B10_hOrg35d

description:
Single cell B10 from human cerebral organoid experiment at 35d
whOrg2_B10_hOrg35d


title: Lin28.scramble.RNAseq

value: scramble


title: whOrg2_C11_hOrg35d

description:
Single cell C11 from human cerebral organoid experiment at 35d
whOrg2_C11_hOrg35d


title: whOrg2_A4_hOrg35d

description:
Single cell A4 from human cerebral organoid experiment at 35d
whOrg2_A4_hOrg35d


title: whOrg2_A3_hOrg35d

description:
Single cell A3 from human cerebral organoid experiment at 35d
whOrg2_A3_hOrg35d


title: Lin28a_Triptolide_ChIPseq

value: FLAG antibody (Sigma F3165)


title: Lin28a_ctrl_ChIPseq


title: whOrg2_A2_hOrg35d

description:
Single cell A2 from human cerebral organoid experiment at 35d
whOrg2_A2_hOrg35d


title: E14_Lin28KD_5mC_seq.rep2

value: 5-Methylcytosine (5-mC) antibody (Active Motif 39649)


title: E14_Lin28KD_5mC_seq.rep1


title: whOrg2_C7_hOrg35d

description:
Single cell C7 from human cerebral organoid experiment at 35d
whOrg2_C7_hOrg35d


title: whOrg2_A9_hOrg35d

description:
Single cell A9 from human cerebral organoid experiment at 35d
whOrg2_A9_hOrg35d


title: whOrg2_A1_hOrg35d

description:
Single cell A1 from human cerebral organoid experiment at 35d
whOrg2_A1_hOrg35d


title: E14_Scramble_5mC_seq.rep1


title: E14_Scramble_5mC_seq.rep2


title: whOrg1_H9_hOrg33d_c1

description:
Single cell H9 from human cerebral organoid experiment at 33d chip 1
whOrg1_H9_hOrg33d_c1

value: 33 days


title: E14_Lin28KD_5hmC_seq

value: 5hmC biotin labelling and Strepavidin-coupled Dynabeads IP (Thermo Fisher 65601)


title: E14_Scramble_5hmC_seq


title: whOrg1_H6_hOrg33d_c2

description:
Single cell H6 from human cerebral organoid experiment at 33d chip 2
whOrg1_H6_hOrg33d_c2


title: whOrg1_H7_hOrg33d_c1

description:
Single cell H7 from human cerebral organoid experiment at 33d chip 1
whOrg1_H7_hOrg33d_c1


title: whOrg2_A11_hOrg35d

description:
Single cell A11 from human cerebral organoid experiment at 35d
whOrg2_A11_hOrg35d


title: LIN28.ChIPseq.rep2


title: whOrg1_H8_hOrg33d_c1

description:
Single cell H8 from human cerebral organoid experiment at 33d chip 1
whOrg1_H8_hOrg33d_c1


title: E14.Input


title: whOrg2_A6_hOrg35d

description:
Single cell A6 from human cerebral organoid experiment at 35d
whOrg2_A6_hOrg35d


title: DNaseI_2i


title: whOrg2_A5_hOrg35d

description:
Single cell A5 from human cerebral organoid experiment at 35d
whOrg2_A5_hOrg35d


title: LIN28.ChIPseq.rep1


title: whOrg1_H6_hOrg33d_c1

description:
Single cell H6 from human cerebral organoid experiment at 33d chip 1
whOrg1_H6_hOrg33d_c1


title: DNaseI_serum


title: whOrg2_A7_hOrg35d

description:
Single cell A7 from human cerebral organoid experiment at 35d
whOrg2_A7_hOrg35d


title: whOrg1_H4_hOrg33d_c1

description:
Single cell H4 from human cerebral organoid experiment at 33d chip 1
whOrg1_H4_hOrg33d_c1


title: whOrg1_H5_hOrg33d_c1

description:
Single cell H5 from human cerebral organoid experiment at 33d chip 1
whOrg1_H5_hOrg33d_c1


title: RNAseq_2i_BR1


title: whOrg1_H3_hOrg33d_c1

description:
Single cell H3 from human cerebral organoid experiment at 33d chip 1
whOrg1_H3_hOrg33d_c1


title: whOrg1_H2_hOrg33d_c2

description:
Single cell H2 from human cerebral organoid experiment at 33d chip 2
whOrg1_H2_hOrg33d_c2


title: RNAseq_serum_BR2


title: whOrg1_H2_hOrg33d_c1

description:
Single cell H2 from human cerebral organoid experiment at 33d chip 1
whOrg1_H2_hOrg33d_c1


title: RNAseq_serum_BR1

data_processing:
Illumina Casava software 1.8.2  used for basecalling of Hiseq2000 and NextSeq 500 data.
Library strategy: RNA-seq. MMSEQ package was used to infer gene expression levels. Reads were mapped to mouse gene annotation (Ensemble release 67).
Genome_build: mm9


title: whOrg2_A10_hOrg35d

description:
Single cell A10 from human cerebral organoid experiment at 35d
whOrg2_A10_hOrg35d


title: whOrg1_H1_hOrg33d_c2

description:
Single cell H1 from human cerebral organoid experiment at 33d chip 2
whOrg1_H1_hOrg33d_c2


title: ChIPseq_Input_serum


title: ChIPseq_H3K27ac_serum

value: H3K27ac (Anti-H3K27ac, C15410196-10, Diagenode)


title: ChIPseq_H3K27ac_2i


title: whOrg1_H10_hOrg33d_c1

description:
Single cell H10 from human cerebral organoid experiment at 33d chip 1
whOrg1_H10_hOrg33d_c1


title: whOrg1_H1_hOrg33d_c1

description:
Single cell H1 from human cerebral organoid experiment at 33d chip 1
whOrg1_H1_hOrg33d_c1


title: whOrg1_H12_hOrg33d_c1

description:
Single cell H12 from human cerebral organoid experiment at 33d chip 1
whOrg1_H12_hOrg33d_c1


title: whOrg1_H11_hOrg33d_c1

description:
Single cell H11 from human cerebral organoid experiment at 33d chip 1
whOrg1_H11_hOrg33d_c1


title: ChIPseq_H3K4me1_2i

value: H3K4me1 (Anti-H3K4me1, CS-037-100, Diagenode)


title: HthUbx_Kc167_Exp2_rep2

city: Cambridge

first: Robert

last: White

address: Downing Street

department: Physiology, Development and Neuroscience

country: United Kingdom

institute: University of Cambridge

description:
Both replicates have been used to call peaks and make the bedGraph file.
peaks and bedGraph files are available on the 'HthUbx' replicate 1 record: GSM1708990

data_processing:
Base call and quality scoring were performed using Real-Time Analysis (RTA) software version 2.0.
Sequencing reads in the raw fastq files were mapped to BDGP release 5 of the Drosophila melanogaster genome (UCSC dm3) using Bowtie1 (version 1.0.1) using default settings for paired-end mapping, a maximum insert size of 1000 bp for valid paired-end alignments (-X 1000) and reporting only uniquely mapped reads (-m 1).
Reads in the output SAM files were processed using Samtools (version 0.1.19) to generate BAM files. Reads from the individual like-replicates were then combined, and filtered using Bedtools (version 2.19.1) to remove the over-represented reads found at the exons of Ubx, Abd-A, Abd-B and Hth; artefacts of the expression vectors used in the transfections.
MACS2 (version 2.1.0.20140616) was used for peak calling using: default settings, the input sample specified as the control file (-c), the -f parameter set to process paired-end BAM files (-f BAMPE), a band width of 200 bp (--bw) and a q-value of 1e-2 or 1e-10 (-q). Binding profiles were generated as fragment pileup tracks in bedGraph format with pileup signal normalized per million reads (-B --SPMR).
Only peaks in euchromatin (chr2L, chr2R, chr3L, chr3R, chr4, chrX and chrM) were used for downstream analyses.
Genome_build: BDGP release 5 (UCSC dm3)
Supplementary_files_format_and_content: BED and bedGraph files were generated using MACS2 (version 2.1.0.20140616) as described above. The BED files contain the called peaks, and the associated peak scores represent −log10(qvalue). The bedGraph files are normalized per million reads and so the different Hox samples are visually comparable when visualized on a genome browser.  Both replicates were used in the peak calling process.

organism: Drosophila melanogaster

source_name: anti-GFP ChIP DNA from Kc167 cells expressing Ubx-GFP and Hth (Experiment 2)

extract_protocol:
Chromatin was prepared from FACS-sorted Hox-GFP expressing cells, and Hox-DNA complexes were immunopurified using anti-GFP antibody. Detailed protocol is described in associated publication.
Samples were processed and sequenced by Source BioScience. The Illumina TruSeq ChIP Sample Preparation Kit was used to generate indexed paired-end sequencing libraries in accordance with the manufacturer’s guide (Rev. A, August 2012) except that no size selection was performed. For the ChIP samples, the entire 10 µl volume of ChIP DNA was used for library preparation and 17 cycles of amplification were performed. For the input sample, 5-10 ng of input DNA were used for library preparation and 12 cycles of amplification were performed. Samples were either sequenced on the Illumina MiSeq (Experiment 1; Ubx, Abd-A, Abd-B and input) or HiSeq 2000 (Experiment 2; Ubx, mutant Ubx and Ubx+Hth) platforms to generate 36 bp or 100 bp reads respectively.

treatment_protocol: To investigate the binding of the different Hox proteins, Kc167 cells were transfected with an inducible expression vector and the GFP-tagged Hox protein transiently expressed before FACS-sorting the Hox-GFP expressing cells. To investigate the binding of Ubx in the presence of Hth, Hth was co-expressed with GFP-tagged Ubx from an inducible bicistronic vector in otherwise Hth non-expressing cells. Detailed protocol is described in associated publication.  In order to ensure that the binding profiles for the different samples are as comparable as possible:  1) Cells from the same mother-plate were used for all samples within each of the two experiments (so that the underlying chromatin state available for Hox binding is identical between samples).  2) Cells expressing the same level of GFP-tagged Hox were sorted for all samples across both experiments (so that the nuclear Hox protein concentration available for binding is the same between samples).

tag: cell line source

value: Female late embryo derived cell line

tag: antibody

value: anti-GFP


title: HthUbx_Kc167_Exp2_rep1

description: Both replicates have been used to call peaks and make the bedGraph file.


title: PE_2

city: San Antonio

first: Yidong

last: Chen

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: Mice received GCI+E2

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: mm9
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: C57BL/6-PELP1 FBKO

extract_protocol:
RNA was harvested using the RNeasy protocol (Qiagen) and the purity of prepared RNA was determined using Agilent 2100 BioAnalyzer.
Total RNA samples about 1 μg were used for sequencing library preparation according to Illumina TruSeq RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-read (SR) sequencing protocol.

treatment_protocol: Total RNA was isolated from ovariectomized FLOX and PELP1 FBKO mice (implanted with E2 mini pumps) that were subjected to GCI and sacrificed at 24 h reperfusion. Samples were subjected to RNAseq analysis

value: hippocampus

value: PELP1 FBKO


title: FE_2

description: Mice received GCI+E2

value: FLOXED


title: FE_1

description: Mice received GCI+E2


title: PE_1

description: Mice received GCI+E2


title: RNAseq_2i_BR2


title: MutantUbx_Kc167_Exp2_rep2

description:
Both replicates have been used to call peaks and make the bedGraph file.
peaks and bedGraph files are available on the 'MutantUbx' replicate 1 record: GSM1708988

source_name: anti-GFP ChIP DNA from Kc167 cells expressing mutant Ubx-GFP (Experiment 2)


title: MutantUbx_Kc167_Exp2_rep1


title: Ubx_Kc167_Exp2

source_name: anti-GFP ChIP DNA from Kc167 cells expressing Ubx-GFP (Experiment 2)


title: MNase-seq from WT yeast

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

description: MNase-seq from WT yeast

data_processing:
Base-calling and quality control were performed on an Illumina Hi-Seq (CASAVA et al) according to default parameters.
MNase-seq data were aligned to the yeast genome (sacCer2) using bowtie v1.0 (parameters -m 1 and --best).
Tracks (bigWigs) were created by taking aligned BED files, extending all tags 150 bp (to cover a nucleosome's length) and running the BEDTools script genomeCoverageBed to convert these to bedGraphs, then normalizing all results to the number of millions of reads sequenced. These files were then passed to the UCSC tool bedGraphToBigWig.
Genome_build: sacCer2
Supplementary_files_format_and_content: BigWig files are provided for browser views of the MNase-seq data in WT and mutant yeast

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: SK1 diploid yeast were first grown in YPD (2% dextrose, 2% bacto-peptone, 1% bacto yeast extract) from a starting OD600 of 0.2 to final OD600 of 0.8, and then transferred in YPA (2% KAc, 2% bacto- peptone, 1% bacto yeast extract) from an OD600 of 0.02 to 0.5–0.8 at 30°C.

extract_protocol:
After collection, the cells were cross-linked with formaldehyde, the cell wall was digested with Zymolyase, and the chromatin was digested with a titration of MNase. The resulting DNA was electrophoresed on an agarose gel, and an ideal digestion in which most of the genome (>80%) was digested into a mono-nucleosome was chosen (see Rando, 2010 in citation references).
The mononucleosomal DNA was then isolated, end-repaired for library preparation. MNase- seq libraries were constructed with NEBNext® UltraTM DNA Library Prep Kit for Illumina®. The DNA was size selected and amplified by PCR using the adaptor primers. The amplified DNA was then purified and used for cluster generation and sequencing on the Illumina® HiSeq system.

treatment_protocol: Cells were washed once with water and then inoculated into sporulation media (2% KAc supplemented for auxotrophic amino acids) at 2.0 OD600 and incubated at 30°C with vigorous agitation. WT and K44R cells were collected at 4hr after transferring to sporulation media.

tag: strain background

tag: genotype/variation

value: WT

tag: sporulation time


title: MNase-seq from H4K44R mutant yeast

description: MNase-seq from H4K44R mutant yeast

value: Mutant H4K44R


title: MEF_WT2_1

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

institute: German Center for Cancer Research

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
BS-mapping: bsmap 2.0
computation of methylation ratios: methratio.py (part of bsmap package)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig-format containing the genomic methylation ratios of the respective sample

source_name: Mouse embryonic fibroblasts

extract_protocol:
Genomic DNA was prepared following the published procedure by Mohn and colleagues (Mohn, Weber, Schübeler, & Roloff, Methods Mol Biol, 2009;507:55-64).
5 µg of high molecular weight DNA were used for fragmentation using the Covaris S2 AFA System in a total volume of 100 µl. Fragmentation-run parameters: Duty cycle 10%; Intensity: 5; Cycles/burst: 200; Time: 3 min; number of cycles: 3, resulting in a total fragmentation-time of 180 s. Fragmentation was confirmed with a 2100 Bioanalyzer (Agilent Technologies) using a DNA1000 chip. The fragmented DNAs were concentrated to a final volume of 75 µl using a DNA Speed Vac. End repair of fragmented DNA was carried out in a total volume of 100 µl using the Paired End DNA Sample Prep Kit (Illumina) as recommended by the manufacturer. For the ligation of the adaptors, the Illumina Early Access Methylation Adaptor Oligo Kit and the Paired End DNA Sample Prep Kit (Illumina) were used, as recommended by the manufacturer. For the size selection of the adaptor-ligated fragments, we used the E-Gel Electrophoresis System (Invitrogen) and a Size Select 2% precast agarose gel (Invitrogen). Each fragmented DNA was loaded on two lanes of the E-gel. Electrophoresis was carried out using the “Size Select” program for 16 min. According to the standard loaded (50 bp DNA Ladder, Invitrogen), 240 bp fragments were extracted from the gel, pooled, and directly transferred to bisulfite treatment without further purification. For the bisulfite treatment we used the EZ-DNA Methylation Kit (Zymo) as recommended by the manufacturer with the exception of a modified thermal profile for the bisulfite conversion reaction. The conversion was carried out in a thermal cycler using the following thermal profile: 95°C for 15 s, 50°C for 1 h, repeat from step 1, 15×, 4°C for at least 10 min. The libraries were subsequently amplified, using the Fast Start High Fidelity PCR System (Roche) with buffer 2, and Illuminas PE1.1 and PE2.1 amplification primers. PCR thermal profile: 95°C for 2 min, 95°C for 30 s, 65°C for 20 s, 72°C for 30 s, then repeat from step 2, 11×, 72°C for 7min, hold at 4°C. PCR reactions were purified on PCR purification columns (MinElute, Qiagen) and eluted in 20 µl elution buffer (Qiagen).

value: Wild type

tag: number of passages

value: Unknown


title: ChIPseq_Input_2i

tag: developmental stage

tag: chip antibody


title: H4 chIP-seq from WT yeast, replicate 2

data_processing:
Base-calling and quality control were performed on an Illumina Hi-Seq (CASAVA et al) according to default parameters.
ChIP-seq data were aligned to the yeast genome (sacCer2) using bowtie v1.0 (parameters -m 1 and --best).
Tracks (bigWigs) were created by taking aligned BED files and running the BEDTools script genomeCoverageBed to convert these to bedGraphs, then normalizing all results to the number of millions of reads sequenced. For each replicate, the H4 signal map was subtracted from the H4K44ac signal map. These files were then passed to the UCSC tool bedGraphToBigWig.
Genome_build: sacCer2
Supplementary_files_format_and_content: BigWig files are provided for browser views of the chIP-seq data

source_name: H4 chIP-seq from WT yeast

growth_protocol: SK1 diploid yeast were first grown in YPD (2% dextrose, 2% bacto-peptone, 1% bacto yeast extract) from a starting OD600 of 0.2 to final OD600 of 0.8, and then transferred in YPA (2% KAc, 2% bacto- peptone, 1% bacto yeast extract) from an OD600 of 0.02 to 0.5-0.8 at 30°C.

extract_protocol:
As described in Govin, J. et al. (2010). Genome- wide mapping of histone H4 serine-1 phosphorylation during sporulation in Saccharomyces cerevisiae. Nucleic acids research 38, 4599-4606.
ChIP-seq libraries were prepared using NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina® in accordance with the manufacturer’s instructions and subjected to single-end sequencing using an Illumina® HiSeq instrument.

treatment_protocol: Cells were washed once with water and then inoculated into sporulation media (2% KAc supplemented for auxotrophic amino acids) at 2.0 OD600 and incubated at 30°C with vigorous agitation.  WT and K44R cells were collected at 4hr after transferring to sporulation media ans subjected to ChIP experiment.

tag: strain

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat.#


title: H4 chIP-seq from WT yeast, replicate 1


title: H4K44ac chIP-seq from WT yeast, replicate 2

source_name: H4K44ac chIP-seq from WT yeast

value: Active Motif

value: custom-made


title: SRC-2-/- DNase-Seq high dose

data_processing:
The sequences identified were mapped to the mouse genome (NCBI37/UCSC mm9) using BOWTIE function in Galaxy. Only the sequences uniquely mapped with no more than 2 mismatches were kept and used as valid reads. PCR duplicates were also removed.
Peak calling was carried out by MACS (version 1.4.2 20120305) in Galaxy/Cistrome (options --mfold 10, 30 --pvalue 1e-5), on each DNase-seq file.
To account for the different sequencing depths between samples, the signal files generated from MACS were normalized by Signal Extraction Scaling (SES) method (Meyer and Liu, 2014). The peak summits were used as the binding site centers, and the normalized signal files were used as the binding strength for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated by Galaxy/cistrome

extract_protocol:
Mouse liver samples were submerged in PBS and cut into small pieces. After spinning down, nuclei were extracted by resuspending cells in sucrose homogenization buffer (300 mM sucrose, 10 mM Tris-HCl, pH 7.4, 15 mM NaCl, 5 mM MgCl2, 0.1 Mm EGTA, 60 mM KCl, 0.2% IGEPAL CA-630, 0.5 mM DTT and 1x Protease inhibitor) for 5 minutes on ice. The nuclei were spun down at 500g for 5min at 4 °C with brakes off and washed with reaction buffer (1x RDD (Qiagen) with 2% glycerol) using pipettes tips with cut-off ends. Gentle mixing was applied to minimize the breakage of the genomic DNA. The final nuclei were digested with different units of DNase I  in 1x reaction buffer on ice for 1h in a cold room
DNaseI assays and library construction were carried out using the standard protocols developed by John Stamatoyannopoulos laboratory (John et al., 2013).

value: C57BL/6J/129 SV mixed background

tag: Sex

value: Male

tag: age

value: 10-20 weeks

tag: genotype


title: SRC-2-/- DNase-Seq low dose


title: WT DNase-Seq high dose

value: Wild-type


title: ChIPseq_H3K4me1_serum

value: H3K4me1 (Anti-H3K4me1, CS-037-100, Diagenode)


title: MEF_DKO2_2

value: TET1/TET2 knocked out

tag: cell type

value: Mouse embryonic fibroblasts


title: MEF_DKO1_1


title: MEF_WT1_2


title: H4K44ac chIP-seq from WT yeast, replicate 1


title: MEF_DKO2_1


title: whOrg1_G8_hOrg33d_c2

description:
Single cell G8 from human cerebral organoid experiment at 33d chip 2
whOrg1_G8_hOrg33d_c2

tag: Stage

value: 33 days

tag: tissue

value: Dissociated whole cerebral organoid


title: MEF_WT1_1


title: whOrg1_G7_hOrg33d_c2

description:
Single cell G7 from human cerebral organoid experiment at 33d chip 2
whOrg1_G7_hOrg33d_c2


title: whOrg1_G8_hOrg33d_c1

description:
Single cell G8 from human cerebral organoid experiment at 33d chip 1
whOrg1_G8_hOrg33d_c1


title: whOrg1_G7_hOrg33d_c1

description:
Single cell G7 from human cerebral organoid experiment at 33d chip 1
whOrg1_G7_hOrg33d_c1


title: whOrg1_G6_hOrg33d_c2

description:
Single cell G6 from human cerebral organoid experiment at 33d chip 2
whOrg1_G6_hOrg33d_c2


title: whOrg1_G6_hOrg33d_c1

description:
Single cell G6 from human cerebral organoid experiment at 33d chip 1
whOrg1_G6_hOrg33d_c1


title: MEF_WT

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
Transcriptome-mapping: tophat 2.0
Evaluation of differential expression: DESeq
Genome_build: mm9
Supplementary_files_format_and_content: Matrix-format created by DESeq containing the expression levels and p-values for differential expression

extract_protocol:
RNA was extracted from frozen cell pellets using TRIzol (Invitrogen)
Sequencing libraries were prepared using 1µg of DNAse-treated total RNA in the first step of the TruSeq RNA Sample Preparation v2 protocol (Illumina, Part# 15026495 Rev. A) as recommended by the manufacturer.


title: whOrg1_G4_hOrg33d_c1

description:
Single cell G4 from human cerebral organoid experiment at 33d chip 1
whOrg1_G4_hOrg33d_c1


title: whOrg1_G3_hOrg33d_c1

description:
Single cell G3 from human cerebral organoid experiment at 33d chip 1
whOrg1_G3_hOrg33d_c1


title: whOrg1_G2_hOrg33d_c1

description:
Single cell G2 from human cerebral organoid experiment at 33d chip 1
whOrg1_G2_hOrg33d_c1


title: Input_Kc167_Exp1_rep2

source_name: Combined input DNA from Kc167 cells expressing Ubx-GFP, AbdA-GFP and AbdB-GFP (Experiment 1)

tag: cell line

tag: cell line source

value: Female late embryo derived cell line

value: none (input)


title: MEF_DKO


title: Input_Kc167_Exp1_rep1

tag: antibody


title: whOrg1_G1_hOrg33d_c1

description:
Single cell G1 from human cerebral organoid experiment at 33d chip 1
whOrg1_G1_hOrg33d_c1


title: AbdB_Kc167_Exp1_rep2

description:
Both replicates have been used to call peaks and make the bedGraph file.
peaks and bedGraph files are available on the AbdB replicate 1 record: GSM1708983

source_name: anti-GFP ChIP DNA from Kc167 cells expressing AbdB-GFP (Experiment 1)

value: anti-GFP


title: whOrg1_G11_hOrg33d_c1

description:
Single cell G11 from human cerebral organoid experiment at 33d chip 1
whOrg1_G11_hOrg33d_c1


title: whOrg1_G12_hOrg33d_c1

description:
Single cell G12 from human cerebral organoid experiment at 33d chip 1
whOrg1_G12_hOrg33d_c1


title: AbdA_Kc167_Exp1_rep2

description:
Both replicates have been used to call peaks and make the bedGraph file.
peaks and bedGraph files are available on the AbdA replicate 1 record: GSM1708981

source_name: anti-GFP ChIP DNA from Kc167 cells expressing AbdA-GFP (Experiment 1)


title: AbdB_Kc167_Exp1_rep1


title: whOrg1_G10_hOrg33d_c1

description:
Single cell G10 from human cerebral organoid experiment at 33d chip 1
whOrg1_G10_hOrg33d_c1


title: whOrg1_F6_hOrg33d_c2

description:
Single cell F6 from human cerebral organoid experiment at 33d chip 2
whOrg1_F6_hOrg33d_c2


title: whOrg1_C8_hOrg33d_c2

description:
Single cell C8 from human cerebral organoid experiment at 33d chip 2
whOrg1_C8_hOrg33d_c2


title: Ubx_Kc167_Exp1_rep2

description:
Both replicates have been used to call peaks and make the bedGraph file.
peaks and bedGraph files are available on the Ubx replicate 1 record: GSM1708979

source_name: anti-GFP ChIP DNA from Kc167 cells expressing Ubx-GFP (Experiment 1)


title: whOrg1_D2_hOrg33d_c2

description:
Single cell D2 from human cerebral organoid experiment at 33d chip 2
whOrg1_D2_hOrg33d_c2

source_name: iPSC 409B2


title: Ubx_Kc167_Exp1_rep1

description: Both replicates have been used to call peaks and make the bedGraph file.


title: whOrg1_G5_hOrg33d_c1

description:
Single cell G5 from human cerebral organoid experiment at 33d chip 1
whOrg1_G5_hOrg33d_c1


title: whOrg1_C11_hOrg33d_c2

description:
Single cell C11 from human cerebral organoid experiment at 33d chip 2
whOrg1_C11_hOrg33d_c2


title: mono-2

city: Wuhan P.R. China

first: Bin

address: No.1,Shizishan Street · Hongshan District · Wuhan · Hubei Province · 430070 · P.R.China

department: College of Plant Science and Technology

country: China

institute: Huazhong Agricultural University

description: similar to normal type

data_processing:
100bp paired-end reads were generated via Illumina HiSeqTM 2000
The clean reads were directly aligned to the reference genome of Brassica napus using Burrows-Wheeler Alignment (BWA version: 0.7.5a-r405), allowing up to 1 mismatched base.
The genes were assembled with Cufflinks according to a reference-guided method.
The differentially expressed genes between three different samples were computed on RNA-seq data by using CuffDiff2.
Genome_build: Brassica_napus.annotation_v5.gff3
Supplementary_files_format_and_content: Text files include the gene id, gene location, coverage of each reference gene and expression of gene (FPKM).

organism: Brassica napus

source_name: Leaf

growth_protocol: All of the samples were established in green house for transcriptomic analyses.

extract_protocol:
Using TRIzol reagent (Invitrogen, Life Technologies) according the manufacturer’s protocol, total RNA was extracted from two biological replicates (three plants per replicate) for each genotype.
NanoDrop ND 1000 (NanoDrop technologies) was used to initially calculate the quality and quantity of the extracted RNA, and then the RNA Integrity Number (RIN) value was assessed by Agilent Technologies 2100 Bioanalyzer (Agilent). Only when the value of RIN was higher than 8, the RNA was used to prepare the c-DNA library according to the TruSeq RNA Sample Prep v2 protocol

value: Leaf

tag: development

value: The newly expanded third leaves without petioles

tag: phenotype

value: Lost one C2 chromosome


title: whOrg1_C10_hOrg33d_c2

description:
Single cell C10 from human cerebral organoid experiment at 33d chip 2
whOrg1_C10_hOrg33d_c2


title: null-2

description: small light-green leaves, smaller plant size, shorter height, smaller flower, non-apical dominance

value: Lost one pair of  C2 chromosome


title: whOrg1_B7_hOrg33d_c2

description:
Single cell B7 from human cerebral organoid experiment at 33d chip 2
whOrg1_B7_hOrg33d_c2


title: null-1


title: mono-1

description: similar to normal type


title: whOrg1_B6_hOrg33d_c2

description:
Single cell B6 from human cerebral organoid experiment at 33d chip 2
whOrg1_B6_hOrg33d_c2


title: oro-1

description: normal type

value: normal


title: loin_low_8

status: Public on Dec 06 2015

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

data_processing:
Basecalls performed using CASAVA version 1.8.2
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters and poly-A sequences
Reads shorter than 36 bp and reads with a quality lower thanthe default of 20 were removed from the dataset.
Cleaned sequences were aligned to the Sus scrofa genome (assembly Sscrofa10.2) with reference annotation containing more than 21K genes listed in the Ensembl database.
Alignment and estimation of gene expression level were made using the RSEM package supported by Bowtie 2 aligner.
Differentially expressed genes, gene isoforms and their corresponding p-values were determined using the statistical methods edgeR, baySeq and DESeq2
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: raw.genes.csv [raw genes counts]
Supplementary_files_format_and_content: raw.isoforms.csv [raw isoforms counts]
Supplementary_files_format_and_content: results.genes.xlsx [edgeR, baySeq and DESeq2 results for differential expression analysis (high vs low) for ham and loin across genes ]
Supplementary_files_format_and_content: results.isoforms.xlsx [edgeR, baySeq and DESeq2 results for differential expression analysis (high vs low) for ham and loin across isoforms]

organism: Sus scrofa

growth_protocol: The pigs were maintained at the Pig Test Station of the National Research Institute of Animal Production in Chorzelów under the same housing and feeding conditions according to SKURTCh procedure.

extract_protocol:
RNA was isolated using TRI Reagent (Applied Biosystems) according to the manufacturer’s protocol. Samples of muscles were homogenised with beads using a Bullet Blender 24 homogenizer (Next Advance). RNA was purified by a bead method (Agencourt RNAClean XP kit) and its quality and quantity was assessed by a Qubit Fluorometer (Invitrogen) and TapeStation 2200 system (RNA tapes, Agilent). Ribosomal RNA was removed from 5000 ng of total RNA using a Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat) (Epicentre). The absence of rRNA was verified on the TapeStation 2200.
A TruSeq RNA Sample Preparation Kit v2 (Illumina) was used to prepare cDNA libraries from 100 ng aliquots of the RNA-depleted samples according to the manufacturer’s protocol. The cDNA samples were ligated with indexed adaptors in the order shown in Table 2. Finally, the libraries were amplified in 15 cycles of PCR and their quantity was estimated using the Qubit 2.0 Fluorometer and 2200 TapeStation D1000 tapes. The final concentration of the cDNA libraries was normalised to 10 nM, after which they were pooled .
The libraries were diluted according to a cluster generation protocol and loaded into a v3 Illumina flowcell (16 samples per line with four technical replicates)

tag: breed

value: Polish Landrace

value: 180 day-old

value: female

tag: shear force

value: low

value: longissimus dorsi muscle


title: whOrg1_B12_hOrg33d_c2

description:
Single cell B12 from human cerebral organoid experiment at 33d chip 2
whOrg1_B12_hOrg33d_c2

data_processing:
"freeIbis" was used as an efficient basecaller with calibrated quality scores for Illumina sequencers. (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.)
"leeHom" was used to trim adapters and merge Illumina sequencing reads. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.)
"deML" was used for robust demultiplexing of Illumina sequences using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.)
Reads were aligned against the human genome (build GRCh38.77 from ENSEMBLE) using TopHat v2.0.14. The genome was indexed using Bowtie v2.2.6
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks v2.2.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Master data frame including sample name, gene ID, and FPKM values for each single cell.


title: oro-2

description: normal type


title: loin_low_5

institute: National Research Institute of Animal Production


title: loin_low_6


title: loin_low_4


title: loin_low_1


title: loin_low_2


title: AbdA_Kc167_Exp1_rep1


title: whOrg1_F1_hOrg33d_c2

description:
Single cell F1 from human cerebral organoid experiment at 33d chip 2
whOrg1_F1_hOrg33d_c2


title: loin_high_8

value: Pulawska

value: high


title: loin_low_3


title: loin_high_7


title: loin_high_4


title: loin_high_5


title: loin_high_3


title: loin_high_2


title: loin_high_1


title: ham_low_8

value: semimembranosus muscle


title: loin_high_6


title: whOrg1_B1_hOrg33d_c2

description:
Single cell B1 from human cerebral organoid experiment at 33d chip 2
whOrg1_B1_hOrg33d_c2

value: 33 days

value: Dissociated whole cerebral organoid


title: ham_low_5


title: ham_low_7


title: ham_low_4


title: loin_low_7


title: ham_low_6


title: ham_high_7


title: ham_low_2


title: ham_high_6


title: ham_low_1


title: ham_high_5


title: ham_high_4


title: ham_high_8


title: ham_high_3


title: ham_high_2


title: fibre1_7

data_processing:
Basecalls performed using CASAVA version 1.8.2
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters and poly-A sequences.
The raw reads were aligned to the Sus scrofa genome (assembly Sscrofa10.2) as a reference, while the whole procedure was followed by alignment parameters from ENCODE3's STAR-RSEM pipeline
The quality control metrics across aligned reads per sample were obtained using RNA-SeQC software
Differentially expressed genes, gene isoforms and their corresponding p-values were determined using the statistical methods edgeR, baySeq and DESeq2
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: raw.genes.csv: raw genes counts
Supplementary_files_format_and_content: raw.isoforms.csv: raw isoforms counts
Supplementary_files_format_and_content: results.genes.xlsx: edgeR, baySeq and DESeq2 results for differential expression analysis (fibre1 vs fibre2B) across genes
Supplementary_files_format_and_content: results.isoforms.xlsx: edgeR, baySeq and DESeq2 results for differential expression analysis (fibre1 vs fibre2B) across isoforms

source_name: longissimus lumborum muscle

extract_protocol:
The samples of longissimus lumborum muscle (taken from the some part of muscle as samples for histological analysis) was collected immediately after slaughter and stored at -20°C in RNAlater solution (Ambion Inc., Austin, USA). Total RNA was isolated using TRI Reagent (Ambion, Life Technologies) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 300 ng of total RNA for the construction of sequencing libraries.

value: 23 week

tag: type i fiber [%]

tag: type iib fiber [%]

tag: gender


title: fibre1_6


title: fibre1_2


title: fibre1_17


title: fibre2B_14


title: fibre1_12


title: fibre2B_10


title: fibre1_1