title: Neuron Patient982 RTT Rep2

description: RNA-Seq

data_processing:
RNA sequencing was performed using Illumina HiSeq 2000. All sequencing was done by the Genomic and RNA Profiling Core at the UCLA. FastQC is used to quality control checks on raw sequence data.
Reads were aligned to the hg19  genome (GRCh37, gencode version 19 (Ensembl 74)) using STAR aligner v2.4.2a (Dobin et al., 2013) with default parameters. The mean average mappability for all 30 samples was around 80%.
The read counts per gene were obtained using the quantMode function in STAR.
These read counts are analogous to the expression level of the gene. Using the obtained raw counts, normalization and differential gene analysis were carried out using the DESeq2 (Love et al., 2014) package in the R environment. DESeq2 allows us to test for gene expression changes between samples in different conditions using more robust shrinkage estimation for dispersion and fold changes (Love et al., 2014). The default negative binomial generalized linear model with Wald test implemented in the package was used to identify significant differentially expression genes.
Genome_build: hg19 (GRCh37, gencode version 19 (Ensembl 74))
Supplementary_files_format_and_content: raw RNA-Seq counts

source_name: Neuron

growth_protocol: Two primary fibroblast lines GM17567 (1461A>G in the gene encoding methyl-CpG 521 binding protein 2 (MECP2)), and GM07982 (frameshift mutation, 705delG, in the gene encoding methyl-CpG binding protein 2 (MECP2)), from patients with Rett Syndrome were obtained from Coriell Cell Repositories. 1 x 105 fibroblasts were plated in a gelatin coated well of a 6 well plate in MEF media (DMEM/F12 + 10% FBS). After 8-12 hours, the cells were infected with reprogramming lentivirus that harbors polycystronic human Yamanaka factors (Oct4, Klf4, Sox2, cMyc) in DMEM medium containing 10ug/ml of polybrene and incubated overnight at 37 degree Celcius in 5% CO2 incubator. The following day, the viral media was aspirated, replaced with MEF media and cultured for 3 additional days. Cells were re-plated on the 5th day onto irradiated MEFs in MEF media. On day 6, the culturing media was changed to human ES media containing DMEM/F12 supplemented with L-glutamine, nonessential amino acids (NEAA), penicillin-streptomycin, knockout serum replacement (Invitrogen), and 10 ng/ml basic FGF. Cells were cultured in hiPSC media until iPSC-like colonies were formed. Reprogrammed colonies were further identified by live immunofluorescence staining with TRA-1-81 (Chemicon) then mechanically isolated. Individual colonies were isolated and maintained for at least 2 passages before genotyping analysis. For early passages, the iPSCs were propagated mechanically, whereas collagenase was used for subsequent passaging. hiPSCs were cultured as described previously in accordance with the UCLA ESCRO. For NPCs: Neural specification with neural rosette derivation, neuroprogenitor (NPC) purification, and further differentiation to neurons and glia were performed as described previously. Relative neuralization efficiency was analyzed by counting the number of neural rosette containing colonies over total number of iPSC colonies. 35 mm wells were analyzed over four separate experiments. The proliferation efficiency of NPCs was determined by at days 1, 3, and 5 by the total number of cells present in 35mm wells seeded at 200,000 cells on day 0. The cells were detached from the plates using accutase (Millipore) then total number of cells per well analyzed using Z1 Coulter particle counter (Beckman Coulter). For interneurons: For directed differentiation of interneurons, iPSCs were grown on plates coated with matrigel (Corning) until 80% confluency with mTeSR (Stem Cell Technologies).  Cells were then treated with DMEM/F12 (GIBCO) containing NEAA (GIBCO), GlutaMAX (GIBCO), bovine serum albumin (Sigma-Aldrich), ß-mercaptoethanol (Sigma-Aldrich), N2 (GIBCO), B27 (GIBCO), SB431542 (10uM; Cayman Chemical), LDN-193189 (100nM; Cayman Chemical) and XAV939 (2uM; Cayman Chemical) later transitioning to the media containing sonic hedgehog (20ng/mL; R&D) and purmorphamine (1uM; Cayman Chemical) as previously described (Maroof et al., 2013).  Cells were further differentiated into interneurons with neurobasal medium (GIBCO) containing N2 (GIBCO), B27 (GIBCO), ascorbic acid (Sigma-Aldrich), GlutaMAX (GIBCO), bovine serum albumin (Sigma-Aldrich), ß-mercaptoethanol (Sigma-Aldrich), neurotrophin-3 (10ng/mL; R&D), brain-derived neurotrophic factor (10ng/mL; R&D), and glial cell-derived neurotrophic factor (10ng/mL; R&D).

extract_protocol:
RNA purification was performed with Qiagen RNAeasy kit following the manufactures’s instruction.
Libraries were prepared according to the manufacturers guidelines using the TruSeq V2 kit (Illumina).

value: Neuron

tag: parental cell line

tag: phenotype

value: RTT


title: Neuron Patient982 RTT Rep1

status: Public on Jun 05 2018

type: SRA

city: Cambridge

first: Ayush

middle: T

last: Raman

state: MA

address: 75 Ames St

department: Epigenomics Program

country: USA

institute: Broad Institute of MIT and Harvard

description: RNA-Seq

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: Neuron Patient567 RTT Rep1

description: RNA-Seq


title: HeLa_mCherry_control_sorted_TSC-bs-seq_rep1

city: Nedlands

first: Christian

last: Pflueger

state: Western Australia

address: 6 Verdun Street

department: Harry Perkins Institute of Medical Research

country: Australia

institute: University of Western Australia

description: target solution capture bisulfite sequencing (TSC-bs-seq)

library_source: genomic

data_processing:
Whole Genome Bisulfite Sequencing by MethylC-seq. Reads were mapped to the human genome (hg19) with the Bowtie alignment algorithm (Langmead et al. 2009) with the following parameters: -e 1120 –O 20 –n 1 as previously reported (Lister et al. 2011).
ChIP-seq and ChIP-bisulfite seq. Reads were trimmed with Trimmomatic (Bolger et al. 2014) with the following parameters: ILLUMINACLIP:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:20, MINLEN:25. For ChIP-seq reads were mapped with the bowtie software package (Langmead et al. 2009) to the human genome (hg19) and non-uniquely mapped reads were discarded. For ChIP-bisulfite-seq reads were 10 bp hard trimmed on the 3' end (Accel-NGS Methyl-Seq DNA library kit requirement), mapped and methylation was called as using BS-Seeker2 (Guo et al. 2013) with default parameters (Bowtie 1), allowing for one mismatch.
bsPCR-seq. Reads were mapped and methylation was called as using BS-Seeker2 (Guo et al. 2013) with default parameters (Bowtie 1), allowing for one mismatch.
Genome_build: hg19
Supplementary_files_format_and_content: For the WGBS data the 'allC' file format is a tab-delimited text file with the following columns: 1) chromosome, 2) position, 3) strand, 4) context, 5) cytosine base calls, and 6) all base calls. For the ChIP-BS-seq data  the 'allC' file format is a tab-delimited text file with the following columns: 1) chromosome, 2) position, 3) position, 4) strand, 5) context, 6) cytosine base calls, and 7) all base calls. For the bsPCR-seq data the 'allC' file format is a tab-delimited text file with the following columns: 1) chromosome, 2) position, 3) position, 4) strand, 5) context, 6) cytosine base calls, and 7) all base calls.

molecule: genomic DNA

source_name: HeLa

growth_protocol: HeLa cells were cultured with DMEM (Dulbecco's Modified Eagle Medium, Life Tecnologies) supplemented with 10% (v/v) FBS (Life Technologies) and 1X (v/v) Glutamax (Life Technologies)

extract_protocol:
DNA extraction was performed with ISOLATE II Genomic DNA Kit (BIO-52067) according to manufacturer's instructions
Whole Genome Bisulfite Sequencing by MethylC-seq libraries were constructed as follows. Genomic DNA was extracted from cells using ISOLATE II genomic DNA extraction kit (Bioline, Cat no: BIO-52067) according to the manufacturer's instructions. 1 ug of genomic DNA was spiked with 0.5% (w/w) of unmethylated lambda phage DNA for the calculations of the non-conversion rate and sheared with a Covaris S2 sonicator to an average length of 200 bp. The sheared DNA was end-repaired, A-tailed and ligated to methylated Illumina TruSeq adapters and subjected to 4 cycles of PCR amplification using KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems). ChIP-seq libraries were constructed as follows. cells were harvested at 72 h by crosslinking in a final concentration of 1% formaldehyde. Crosslinking was stopped after 5 min by adding glycine to a final concentration of 125 mM. Crosslinked cells were washed in cold phosphate buffered saline, lysed using 1 ml low-salt IP buffer (150 mM NaCl, 50 mM Tris-HCl (pH7.5), 5 mM EDTA, NP-40 (0.5%), Triton X-100 (1%) containing protease inhibitors) and aliquoted at 0.5-1 × 10∧8 cells/ml. Cells are then sonicated to a fragment size range of 500–800 bp. Samples were then diluted in 1.7 ml low-salt buffer and incubated with 5 ug of anti-CTCF (Cell Signaling, 2899B) or anti-NRF1 antibody (Abcam, ab55744), respectively conjugated to a 50:50 mix of protein A/G Dynabeads (Invitrogen, M-280, 20 ul each). After wash steps, DNA was eluted, crosslinks were reversed, and immunoprecipitated DNA was purified by Agencourt AMPure XP beads (Beckman Coulter, Cat no: A63880). Libraries were prepared from the entire ChIP eluate volume containing either 1 ng or 0.1 ng input material per replicate for CTCF or NRF1, respectively, using the ThruPLEX DNA-seq 12S kit (Rubicon Genomics, R400429). After limited PCR amplification, libraries were purified using Agencourt AMPure XP beads (Beckman Coulter, Cat no: A63880). ChIP-bisulfite sequencing libraries were constructed as follows. Two 15 cm plates of cells were grown and doxycycline induced for three days. Cells were washed two times with 10 ml of PBS and crosslinked for 5 minutes in 50 mM HEPES-KOH, pH 7.5, 100 mM NaCl, 1mM EDTA, 1% formaldehyde. The crosslinking reaction was quenched by the addition of glycine to a final concentration of 125 mM and washed two times with phosphate buffered saline (PBS). All subsequent solutions were supplemented with a protease inhibitor cocktail from Sigma (Cat. # P8340). Cells were scraped off the plates with a rubber policeman in 10 ml of PBS and spun at 500 x g for 5 minutes in a swinging bucket rotor. The cell pellets were resuspended in 10 ml of 50 mM HEPES-KOH, pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, incubated on ice for 10 minutes and centrifuged at 3,000 rpm for 10 minutes in a swinging bucket rotor. Cell pellets were washed two times by adding gently adding 10 mM Tris-HCl, pH 8.1, 200 mM NaCl, 1 mM EDTA to the cell pellets trying not to disturb the pellets and centrifuged at 3,000 rpm for 5 min. Finally the cell pellets were resuspended in 0.1% SDS, 1 mM EDTA and transferred to a Covaris microTUBE. The chromatin was sheared with a Covaris S220 sonicator with the following settings: Time 5 min, duty cycle 5%, intensity 6, cycles per burst 200, temperature 4˚C, power mode frequency sweeping. Triton X-100 and NaCl were added to a final concentration of 1% and 150 mM respectively. The sheared chromatin was centrifuged at maximum speed in a microfuge for 15 minutes at 4˚C and the supernatant was transferred to a new tube. 2 ul of anti-H3K4me3 (Diagenode, Cat. # C15410003) or 4 ul of anti-phospho-Ser5 RNA polymerase antibody (Active Motif, Cat. # 39233) was added and incubated overnight at 4˚C. 30 ul of Protein G Dynabeads (Life Technologies) was added and incubated on a tube rotator for 90 minutes at 4˚C. The beads were washed two times with 20 mM HEPES-KOH, pH 7.9, 0.1% SDS, 150 mM NaCl, 1% Triton X-100 2 mM EDTA, two times with 20 mM HEPES-KOH, pH 7.9, 0.1% SDS, 500 mM NaCl, 1% Triton X-100 2 mM EDTA, one time with 100 mM Tris-HCl pH 7.5, 0.5 M LiCl, 1% NP-40, 1% Sodium Deoxycholate and one time with 10 mM Tris-HCl, pH 8.0, 1 mM EDTA. The DNA was eluted twice by incubating for 30 minutes in 25 ul of 20 mM HEPES-KOH, pH 7.9, 1 mM EDTA, 0.5% SDS, 0.5 mg/ml Proteinase K. To the 50 ul of eluted DNA, 3 ul of 3M Sodium Acetate, pH 5.3 and 0.5 ul 30 mg/ml RNase A was added and incubated overnight at 65˚C in a hybridization oven. 1.5 ul of 20 mg/ml proteinase K was added and incubated for 1 hour at 50˚C and the DNA was purified with a 2X volume of a homemade version of AMPure XP beads and eluted in 20 ul Tris-HCl, pH 8.0, 0.1 mM EDTA. Libraries were made with the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences) according to the manufacturer’s instructions.

treatment_protocol: Cells were seeded 24h prior to transfection. Cells were transfected transiently with plasmids containing the guide RNA, dC9Sun-D3A, dC9-D3A, mutant or mCherry controls. 48h post-transfection, cells were puromycin (2 ug/mL, Life technologies, Cat no: A1113803) for 48h. Cells were then harvested and subjected for DNA extraction for bsPCR-seq or cross-linked for ChIP-seq and ChIP-bs-seq experiments.

tag: cell type

value: human cervical cancer cell line

tag: plasmids


title: HeLa_dC9Sun-D3A_SHB_sgRNA_sorted_TSC-bs-seq_rep2

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3A (Addgene #100941) + pEf1a-SHB_1-gRNA-GFP


title: HeLa_mCherry_control_sorted_TSC-bs-seq_rep2


title: HeLa_dC9Sun-D3A_SHB_sgRNA_sorted_TSC-bs-seq_rep1


title: Ty1_aGCN4-D3A_Chip

description: chromatin immunoprecipitaiton sequencing (ChIP-seq)

tag: antibody


title: Neuron Patient982 Normal WT Rep1

description: RNA-Seq

value: WT


title: HeLa_dC9Sun-D3A_SHB_sgRNA_sorted_TSC-bs-seq_rep3


title: Neuron Patient982 Normal WT Rep2

description: RNA-Seq


title: Input_HA-dCas9_and_Ty1_aGCN4-D3A_10ng

description: input for dCas9 and aGCN4-D3A ChIP-seq


title: Neuron Patient567 Normal WT Rep1

description: RNA-Seq


title: NRF1_TMEM_ChIPbs_dC9Sun-mCherry_rep1

description: chromatin immunoprecipitaiton bisulfite sequencing (ChIP-bs-seq)

value: NRF1 (Abcam, ab55744)

value: pGK-dCas9-SunTag (Addgene #100943) + pEf1a-NLS-aGCN4-mCherry (Addgene #100945) + pEf1a-TMEM206_2-gRNA-GFP


title: NPC Patient982 RTT Rep2

description: RNA-Seq

source_name: NPC

value: NPC


title: HA_dCas9_Chip

value: HA (Biolegend, 901502)


title: Neuron Normal WT Rep1

description: RNA-Seq


title: HeLa_mCherry_control_sorted_TSC-bs-seq_rep3


title: NRF1_TMEM_ChIPbs_dC9Sun-D3A_rep3

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3A (Addgene #100941) + pEf1a-TMEM206_2-gRNA-GFP


title: NPC Patient982 RTT Rep1

description: RNA-Seq


title: NPC Patient567 RTT Rep1

description: RNA-Seq


title: NRF1_TMEM_ChIPbs_dC9Sun-D3A_rep2


title: NRF1_TMEM_ChIPbs_dC9Sun-D3A_rep1


title: NPC Patient567 RTT Rep2

description: RNA-Seq


title: NRF1_ChIP-seq_dC9Sun-D3A_input

description: input for NRF1 ChIP-seq


title: NRF1_ChIP-seq_dC9Sun-mCherry_TMEM206_rep2


title: NRF1_ChIP-seq_dC9Sun-mCherry_TMEM206_rep1


title: NRF1_ChIP-seq_dC9Sun-D3A_TMEM206_rep3


title: Neuron Patient567 RTT Rep2

description: RNA-Seq


title: NPC Patient982 Normal WT Rep2

description: RNA-Seq


title: NPC Patient982 Normal WT Rep1

description: RNA-Seq


title: NPC  Normal WT Rep1

description: RNA-Seq


title: NPC Patient567 Normal WT Rep1

description: RNA-Seq


title: NRF1_ChIP-seq_dC9Sun-D3A_TMEM206_rep1


title: NRF1_ChIP-seq_dC9Sun-D3A_TMEM206_rep2


title: NPC  Normal WT Rep2

description: RNA-Seq


title: iPSC Patient982 RTT Rep2

description: RNA-Seq

source_name: iPSC

value: iPSC


title: HeLa_CTCF_dC9Sun-D3A_CDCC85C_ChIP-bs-seq_rep2

value: CTCF (Cell Signaling, 2899B)

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3A (Addgene #100941) + pEf1a-CCDC85C_3-gRNA-GFP


title: iPSC Patient567 RTT Rep2

description: RNA-Seq


title: iPSC Patient982 Normal WT Rep1

description: RNA-Seq


title: HeLa_CTCF_dC9Sun-D3AMut_MIR152_ChIP-bs-seq_rep1

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3AMut (Addgene #100944) + pEf1a-MIR152_3-gRNA-GFP


title: iPSC Patient567 RTT Rep1

description: RNA-Seq


title: HeLa_CTCF_dC9Sun-D3A_MIR152_ChIP-bs-seq_rep2

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3A (Addgene #100941) + pEf1a-MIR152_3-gRNA-GFP


title: HeLa_CTCF_dC9Sun-D3A_CDCC85C_ChIP-bs-seq_rep1


title: iPSC Patient982 Normal WT Rep2

description: RNA-Seq


title: iPSC Patient982 RTT Rep1

description: RNA-Seq


title: HeLa_CTCF_dC9Sun-D3AMut_MIR152_ChIP-bs-seq_rep2


title: HeLa_CTCF_dC9Sun-D3A_SHB_ChIP-bs-seq_rep1


title: HeLa_CTCF_dC9Sun-D3AMut_MIR152_ChIP-seq_rep2

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3A (Addgene #100941) + pEf1a-MIR152-gRNA-GFP


title: iPSC Normal WT Rep2

description: RNA-Seq


title: HeLa_CTCF_dC9Sun-D3A_MIR152_ChIP-bs-seq_rep1


title: HeLa_CTCF_dC9Sun-D3A_CDCC85C_ChIP-seq_rep2


title: 2 days RTT Male

description:
Male Post Mortem
RNA-Seq

source_name: Frontal Lobe

value: Frontal Lobe

tag: age

value: 2 days

tag: Sex

value: Male


title: iPSC Normal WT Rep1

description: RNA-Seq


title: HeLa_CTCF_dC9Sun-D3A_MIR152_ChIP-seq_rep2

value: human cervical cancer cell line


title: HeLa_CTCF_dC9Sun-D3A_SHB_ChIP-seq_rep2

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3A (Addgene #100941) + pEf1a-SHB_1-gRNA-GFP


title: 1 year RTT Male

description:
Male Post Mortem
RNA-Seq

value: 1 year

value: RTT


title: HeLa_CTCF_dC9Sun-D3A_SHB_ChIP-bs-seq_rep2


title: HeLa_CTCF_dC9Sun-D3A_input_ChIP-seq

description: input for CTCF ChIP-seq


title: HeLa_CTCF_dC9Sun-D3AMut_MIR152_ChIP-seq_rep1


title: 19 year RTT Female

description:
Female Post Mortem
RNA-Seq

value: 19 years

value: Female

value: WT


title: HeLa_CTCF_dC9Sun-D3A_CDCC85C_ChIP-seq_rep1


title: iPSC Patient567 Normal WT Rep1

description: RNA-Seq


title: 18 year RTT Female

description:
Female Post Mortem
RNA-Seq

value: 18 years


title: HeLa_CTCF_dC9Sun-D3A_SHB_ChIP-seq_rep1


title: HeLa_CTCF_dC9Sun-D3A_MIR152_ChIP-seq_rep1


title: HeLa_untreated_WGBS

description: whole genome bisulfite sequencing (WGBS)


title: pLVP_dCas9_DNMT3A_highActivity_UNC5C_3_sgRNA_rep2

description: targeted PCR amplicons of bisulfite treated genomic DNA (bsPCR-seq)

value: pLVP-dCas9-DNMT3A-Puro_hActivity (Addgene #100938) + pEf1a-UNC5C_3-gRNA-GFP


title: pLVP_dCas9_DNMT3A_highActivity_rep3


title: pLVP_dCas9_DNMT3A_highActivity_UNC5C_3_sgRNA_rep1


title: pLVP_dCas9_DNMT3A_highActivity_UNC5C_3_sgRNA_rep3


title: pLVP_dCas9_DNMT3A_highActivity_Chr14_3_sgRNA_rep3

value: pLVP-dCas9-DNMT3A-Puro_hActivity (Addgene #100938) + pEf1a-CCDC85C_3-gRNA-GFP


title: pLVP_dCas9_DNMT3A_highActivity_rep2


title: pLVP_dCas9_DNMT3A_highActivity_Mir152_3_sgRNA_rep1

value: pLVP-dCas9-DNMT3A-Puro_hActivity (Addgene #100938) + pEf1a-MIR152_3-gRNA-GFP


title: pLVP_dCas9_DNMT3A_highActivity_Mir152_3_sgRNA_rep3


title: pLVP_dCas9_DNMT3A_highActivity_rep1


title: pLVP_dCas9_DNMT3A_highActivity_Mir152_3_sgRNA_rep2


title: pLVP_dCas9_DNMT3A_highActivity_Chr14_3_sgRNA_rep2


title: pGk_dcas9_SunTag_NLS_aGCN4_mCherry_UNC5C_3_sgRNA_rep2

value: pGK-dCas9-SunTag (Addgene #100943) + pEf1a-NLS-aGCN4-mCherry (Addgene #100945) + pEf1a-UNC5C_3-gRNA-GFP


title: dcas9_ST_aGCN4_mCherry_UNC5C_3_SHB_1_Mir152_3_Chr14_3_rep3

value: pGK-dCas9-SunTag (Addgene #100943) + pEf1a-NLS-aGCN4-mCherry (Addgene #100945) + pEf1a-UNC5C_3-gRNA-GFP + pEf1a-SHB_1-gRNA-GFP + pEf1a-MIR152_3-gRNA-GFP + pEf1a-CCDC85C_3-gRNA-GFP


title: dcas9_ST_aGCN4_mCherry_UNC5C_3_SHB_1_Mir152_3_Chr14_3_rep1


title: dcas9_ST_aGCN4_mCherry_UNC5C_3_SHB_1_Mir152_3_Chr14_3_rep2


title: pGk_dcas9_SunTag_NLS_aGCN4_mCherry_UNC5C_3_sgRNA_rep3


title: pGk_dcas9_SunTag_NLS_aGCN4_mCherry_SHB_1_sgRNA_rep3

value: pGK-dCas9-SunTag (Addgene #100943) + pEf1a-NLS-aGCN4-mCherry (Addgene #100945) + pEf1a-SHB_1-gRNA-GFP


title: pGk_dcas9_SunTag_NLS_aGCN4_mCherry_UNC5C_3_sgRNA_rep1


title: pGk_dcas9_SunTag_NLS_aGCN4_mCherry_SHB_1_sgRNA_rep2


title: pGk_dcas9_SunTag_NLS_aGCN4_mCherry_SHB_1_sgRNA_rep1


title: pGk_dcas9_SunTag_NLS_aGCN4_mCherry_Mir152_3_sgRNA_rep2

value: pGK-dCas9-SunTag (Addgene #100943) + pEf1a-NLS-aGCN4-mCherry (Addgene #100945) + pEf1a-MIR152_3-gRNA-GFP


title: pGk_dcas9_SunTag_NLS_aGCN4_mCherry_Mir152_3_sgRNA_rep3


title: pGk_dcas9_SunTag_NLS_aGCN4_mCherry_Chr14_3_sgRNA_rep3

value: pGK-dCas9-SunTag (Addgene #100943) + pEf1a-NLS-aGCN4-mCherry (Addgene #100945) + pEf1a-CCDC85C_3-gRNA-GFP


title: pGk_dcas9_SunTag_NLS_aGCN4_mCherry_Chr14_3_sgRNA_rep2


title: pGk_dcas9_SunTag_NLS_aGCN4_mCherry_Mir152_3_sgRNA_rep1


title: dcas9_ST_aGCN4_DNMT3A_UNC5C_3_SHB_1_Mir152_3_Chr14_3_rep3

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3A (Addgene #100941) + pEf1a-UNC5C_3-gRNA-GFP + pEf1a-SHB_1-gRNA-GFP + pEf1a-MIR152_3-gRNA-GFP + pEf1a-CCDC85C_3-gRNA-GFP


title: pGk_dcas9_SunTag_NLS_aGCN4_DNMT3A_BS_WT_SHB_1_sgRNA_rep3

value: human cervical cancer cell line


title: pGk_dcas9_SunTag_NLS_aGCN4_DNMT3A_WT_UNC5C_3_sgRNA_rep2

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3A (Addgene #100941) + pEf1a-UNC5C_3-gRNA-GFP


title: pGk_dcas9_SunTag_NLS_aGCN4_DNMT3A_WT_UNC5C_3_sgRNA_rep1


title: pGk_dcas9_SunTag_NLS_aGCN4_DNMT3A_BS_WT_SHB_1_sgRNA_rep2

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3A (Addgene #100941) + pEf1a-SHB_1-gRNA-GFP


title: pGk_dcas9_SunTag_NLS_aGCN4_DNMT3A_BS_WT_Mir152_3_sgRNA_rep3

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3A (Addgene #100941) + pEf1a-MIR152_3-gRNA-GFP


title: pGk_dcas9_SunTag_NLS_aGCN4_DNMT3A_BS_WT_Mir152_3_sgRNA_rep1


title: pGk_dcas9_SunTag_NLS_aGCN4_DNMT3A_WT_UNC5C_3_sgRNA_rep3


title: pGk_dcas9_SunTag_NLS_aGCN4_DNMT3A_BS_WT_SHB_1_sgRNA_rep1


title: pGk_dcas9_SunTag_NLS_aGCN4_DNMT3A_BS_WT_Chr14_3_sgRNA_rep2

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3A (Addgene #100941) + pEf1a-CCDC85C_3-gRNA-GFP


title: pGk_dCas9_mCherry_rep2


title: pGk_dcas9_SunTag_NLS_aGCN4_DNMT3A_BS_WT_Mir152_3_sgRNA_rep2


title: pGK_dCas9_DNMT3A_normActivity_UNC5C_3_sgRNA_rep3

value: pGK-dCas9-DNMT3A_nActivity (Addgene #100938) + pEf1a-UNC5C_3-gRNA-GFP


title: dcas9_ST_aGCN4_DNMT3A_UNC5C_3_SHB_1_Mir152_3_Chr14_3_rep1


title: pLVP_dCas9_DNMT3A_highActivity_Chr14_3_sgRNA_rep1


title: pGK_dCas9_DNMT3A_normActivity_UNC5C_3_sgRNA_rep2


title: pGk_dCas9_mCherry_rep3


title: pGk_dcas9_SunTag_NLS_aGCN4_DNMT3A_BS_WT_Chr14_3_sgRNA_rep1


title: pGk_dCas9_mCherry_rep1


title: pGK_dCas9_DNMT3A_normActivity_UNC5C_3_sgRNA_rep1


title: dcas9_ST_aGCN4_DNMT3A_UNC5C_3_SHB_1_Mir152_3_Chr14_3_rep2


title: pGK_dCas9_DNMT3A_normActivity_rep3


title: pGK_dCas9_DNMT3A_normActivity_Mir152_3_sgRNA_rep3

value: pGK-dCas9-DNMT3A_nActivity (Addgene #100938) + pEf1a-MIR152_3-gRNA-GFP


title: pGk_dcas9_SunTag_NLS_aGCN4_mCherry_Chr14_3_sgRNA_rep1


title: pGK_dCas9_DNMT3A_normActivity_rep1


title: pGK_dCas9_DNMT3A_normActivity_Chr14_3_sgRNA_rep3

value: pGK-dCas9-DNMT3A_nActivity (Addgene #100938) + pEf1a-CCDC85C_3-gRNA-GFP


title: pGK_dCas9_DNMT3A_normActivity_Mir152_3_sgRNA_rep2


title: pGK_dCas9_DNMT3A_normActivity_rep2


title: pGk_dcas9_SunTag_NLS_aGCN4_DNMT3A_BS_WT_Chr14_3_sgRNA_rep3


title: pEf1a_GFP_Puro_baseline_ctrl_rep1

description:
targeted PCR amplicons of bisulfite treated genomic DNA (bsPCR-seq)
pEf1a_GFP_Puro_r1.allC.txt.gz


title: pEf1a_GFP_Puro_baseline_ctrl_rep2

description:
targeted PCR amplicons of bisulfite treated genomic DNA (bsPCR-seq)
pEf1a_GFP_Puro_r2.allC.txt.gz


title: pGK_dCas9_DNMT3A_normActivity_Chr14_3_sgRNA_rep1


title: NLS_aGCN4_mCherry_rep1


title: NLS_aGCN4_mCherry_rep2


title: NLS_aGCN4_mCherry_rep3


title: NLS_aGCN4_DNMT3A_BS_WT_rep3


title: NLS_aGCN4_DNMT3A_BS_WT_rep1


title: NLS_aGCN4_DNMT3A_BS_WT_rep2


title: bsPCR-seq_titration_UNC5C4_sgRNA_aGCN4_DNMT3A_82ng_dCas9_SunTag_330ng

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3A (Addgene #100941) + pEf1a-UNC5C_4-gRNA-GFP


title: bsPCR-seq_titration_UNC5C4_sgRNA_aGCN4_DNMT3A_41ng_dCas9_SunTag_41ng


title: bsPCR-seq_titration_UNC5C4_sgRNA_aGCN4_DNMT3A_165ng_dCas9_SunTag_330ng


title: pGK_dCas9_DNMT3A_normActivity_Mir152_3_sgRNA_rep1


title: bsPCR-seq_titration_UNC5C4_sgRNA_aGCN4_DNMT3A_41ng_dCas9_SunTag_330ng


title: bsPCR-seq_titration_UNC5C4_sgRNA_aGCN4_DNMT3A_5ng_dCas9_SunTag_330ng


title: bsPCR-seq_titration_UNC5C4_sgRNA_aGCN4_DNMT3A_10ng_dCas9_SunTag_330ng


title: bsPCR-seq_titration_UNC5C4_sgRNA_aGCN4_DNMT3A_10ng_dCas9_SunTag_10ng


title: bsPCR-seq_titration_UNC5C4_sgRNA_aGCN4_DNMT3A_20ng_dCas9_SunTag_330ng


title: bsPCR-seq_titration_UNC5C4_sgRNA_aGCN4_DNMT3A_165ng_dCas9_SunTag_165ng


title: bsPCR-seq_titration_UNC5C4_sgRNA_aGCN4_DNMT3A_2ng_dCas9_SunTag_330ng


title: bsPCR-seq_titration_pBS_GFP_puro


title: bsPCR-seq_titration_UNC5C4_sgRNA_aGCN4_DNMT3A_330ng_dCas9_SunTag_330ng


title: HeLa_dC9Sun-D3A_SHB_sgRNA_sorted_bsPCR-seq_rep2


title: bsPCR-seq_titration_dCas9_SunTag

value: pGK-dCas9-SunTag (Addgene #100943)


title: HeLa_dC9Sun-D3A_SHB_sgRNA_sorted_bsPCR-seq_rep3


title: HeLa_mCherry_control_sorted_bsPCR-seq_rep3


title: HeLa_dC9Sun-D3A_SHB_sgRNA_sorted_bsPCR-seq_rep1


title: pGK_dCas9_DNMT3A_normActivity_Chr14_3_sgRNA_rep2


title: HeLa_mCherry_control_sorted_bsPCR-seq_rep2


title: HeLa_mCherry_control_sorted_bsPCR-seq_rep1


title: NRF1_bsPCR-seq_GCN4_RFP_TMEM206_gRNA_rep4

value: pGK-dCas9-SunTag (Addgene #100943) + pEf1a-NLS-aGCN4-mCherry (Addgene #100945) + pEf1a-TMEM206_2-gRNA-GFP


title: NRF1_bsPCR-seq_GCN4_RFP_TMEM206_gRNA_rep2


title: NRF1_bsPCR-seq_GCN4_RFP_TMEM206_gRNA_rep3


title: NRF1_bsPCR-seq_GCN4_DNMT3aWT_TMEM206_gRNA_rep9

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3A (Addgene #100941) + pEf1a-TMEM206_2-gRNA-GFP


title: NRF1_bsPCR-seq_GCN4_RFP_TMEM206_gRNA_rep1


title: NRF1_bsPCR-seq_GCN4_DNMT3aWT_TMEM206_gRNA_rep7


title: NRF1_bsPCR-seq_GCN4_DNMT3aWT_TMEM206_gRNA_rep8


title: NRF1_bsPCR-seq_GCN4_DNMT3aWT_TMEM206_gRNA_rep2


title: NRF1_bsPCR-seq_GCN4_DNMT3aWT_TMEM206_gRNA_rep4


title: NRF1_bsPCR-seq_GCN4_DNMT3aWT_TMEM206_gRNA_rep3


title: NRF1_bsPCR-seq_GCN4_DNMT3aWT_TMEM206_gRNA_rep1


title: NRF1_bsPCR-seq_GCN4_DNMT3aWT_TMEM206_gRNA_rep12


title: NRF1_bsPCR-seq_GCN4_DNMT3aWT_TMEM206_gRNA_rep6


title: NRF1_bsPCR-seq_GCN4_DNMT3aWT_TMEM206_gRNA_rep5


title: NRF1_bsPCR-seq_GCN4_DNMT3aWT_TMEM206_gRNA_rep11


title: HeLa_NRF1_TMEM206_sgRNA_selection_5

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3A (Addgene #100941) + pEf1a-TMEM206_5-gRNA-GFP


title: HeLa_NRF1_TMEM206_sgRNA_selection_6

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3A (Addgene #100941) + pEf1a-TMEM206_6-gRNA-GFP


title: HeLa_NRF1_TMEM206_sgRNA_selection_3

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3A (Addgene #100941) + pEf1a-TMEM206_3-gRNA-GFP


title: HeLa_NRF1_TMEM206_sgRNA_selection_4

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3A (Addgene #100941) + pEf1a-TMEM206_4-gRNA-GFP


title: pGK_dCas9_SunTag_NLS_aGCN4_DNMT3A_wt_SHB_1_sgRNA_rep2


title: HeLa_NRF1_TMEM206_sgRNA_selection_1

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3A (Addgene #100941) + pEf1a-TMEM206_1-gRNA-GFP


title: pEf1a_GFP_Puro_baseline_ctrl_rep3

value: human cervical cancer cell line


title: pGK_dCas9_SunTag_NLS_aGCN4_DNMT3A_wt_SHB_1_sgRNA_rep1


title: pGK_dCas9_SunTag_NLS_aGCN4_DNMT3A_wt_rep2

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3A (Addgene #100941)


title: pGK_dCas9_SunTag_NLS_aGCN4_DNMT3A_wt_rep1


title: pGK_dCas9_SunTag_NLS_aGCN4_DNMT3A_wt_chr14_3_sgRNA_rep1


title: pGK_dCas9_SunTag_NLS_aGCN4_DNMT3A_wt_chr14_3_sgRNA_rep2


title: pGK_dCas9_SunTag_NLS_aGCN4_DNMT3A_mut_SHB_1_sgRNA_rep1

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3AMut (Addgene #100944) + pEf1a-SHB_1-gRNA-GFP


title: pGK_dCas9_SunTag_NLS_aGCN4_DNMT3A_mut_MIR152_3_sgRNA_rep2

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3AMut (Addgene #100944) + pEf1a-MIR152_3-gRNA-GFP


title: NRF1_bsPCR-seq_GCN4_DNMT3aWT_TMEM206_gRNA_rep10


title: pGK_dCas9_SunTag_NLS_aGCN4_DNMT3A_mut_MIR152_3_sgRNA_rep1


title: pGK_dCas9_SunTag_NLS_aGCN4_DNMT3A_mut_chr14_3_sgRNA_rep2

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3AMut (Addgene #100944) + pEf1a-CCDC85C_3-gRNA-GFP


title: pGK_dCas9_SunTag_NLS_aGCN4_DNMT3A_wt_MIR152_3_sgRNA_rep2

value: pGK-dCas9-SunTag (Addgene #100943) + pEF1a-NLS-scFvGCN4-DNMT3A (Addgene #100941) + pEf1a-MIR152_3-gRNA-GFP


title: HeLa_NRF1_TMEM206_sgRNA_selection_2


title: pEf1a_GFP_Puro_pGK_dCas9_SunTag_rep2


title: pEf1a_GFP_Puro_rep1


title: NLS_aGCN4_DNMT3A_wt_rep1


title: pGK_dCas9_SunTag_NLS_aGCN4_DNMT3A_mut_chr14_3_sgRNA_rep1


title: pGK_dCas9_SunTag_NLS_aGCN4_DNMT3A_wt_MIR152_3_sgRNA_rep1


title: NLS_aGCN4_DNMT3A_wt_rep2


title: pEf1a_GFP_Puro_rep2


title: NLS_aGCN4_DNMT3A_mut_rep1


title: pEf1a_GFP_Puro_pGK_dCas9_SunTag_rep1


title: NLS_aGCN4_DNMT3A_mut_rep2


title: pGK_dCas9_SunTag_NLS_aGCN4_DNMT3A_mut_SHB_1_sgRNA_rep2


title: dpse_May_ATAC

status: Public on Jun 04 2018

city: Vienna

first: Jelle

last: Jacobs

address: Campus-Vienna-Biocenter 1

department: VBC

country: Austria

institute: Institute of molecular Pathology

data_processing:
Cleaning (fastq-mcf)
Mapping to their respective genomes using bowtie2
peaks were called for each sample using macs2 callpeak with parameter -g dm --nomodel
Genome_build: dana-all-chromosome-r1.3; dere-all-chromosome-r1.3; dmel-all-chromosome-r6.02; dmoj-all-chromosome-r1.3; dper-all-chromosome-r1.3; dpse-all-chromosome-r3.1; dsec-all-chromosome-r1.3; dsim-all-chromosome-r1.4; dvir-all-chromosome-r1.2; dwil-all-chromosome-r1.3; dyak-all-chromosome-r1.3
Supplementary_files_format_and_content: BigWigs for all ATAC-samples

organism: Drosophila pseudoobscura

source_name: D. Pseudoobscura_eye-antennal discs

growth_protocol: Normal flyfood, 25 degrees

extract_protocol:
Eye-antennal imaginal Disc were dissected from 3rd instar wandering larvae. The discs were immediately lysed and ATAC-seq was performed
Tn5 and nextera library prep

tag: genotype/species

value: Drosophila Pseudoobscura

value: 3rd instar-wandering

tag: treatment

value: Hand Dissections

value: eye-antennal discs


title: dana_Jun_ATAC

organism: Drosophila ananassae

source_name: D. Ananassae_eye-antennal discs

value: Drosophila Ananassae


title: dana_May_ATAC


title: dpse_June_ATAC


title: dmoj_Jun_ATAC

organism: Drosophila mojavensis

source_name: D. Mojavensis_eye-antennal discs

value: Drosophila Mojavensis


title: dmoj_May_ATAC


title: H23_H4K12ac_REP2

city: TSURUMI WARD YOKOHAMA

first: Aki

last: Minoda

state: KANAGAWA

address: 230-0045, 1 CHOME-7-22 SUEHIROCHO

department: IMS

country: Japan

institute: RIKEN YOKOHAMA

description:
H23_H4K12Ac_R2
ChIP-seq with  anti-H4K12ac antibody in H23 cells, replicate 2

data_processing:
the reads were aligned to hg19 using BWA
Genome_build: hg19
Supplementary_files_format_and_content: MACS2 narrow peaks, significance threshold: p-value = 0.01

source_name: H23_rabbit polyclonal

growth_protocol: H23 cell line (NCI-H23) was purchased from ATCC  (ATCC® CRL-5800™). Cells were cultured as recommended by ATCC in RPMI-1640 Medium containing 10% FBS and Penicillin/Streptomycin and sub-cultured every two days at the ratio of 1:3

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min at RT. The crosslink reaction was stopped by addition of Glycin at the final concentration of 0.2M. H23 Chromatin extract was prepared as follows: the cell pellets were dissolved and incubated in the ice-cold 0.1% SDS lysis buffer (50 mM Hepes KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate, 0.1% SDS, protease inhibitors) for 10 min on a rotation at 4°C. Following centrifugation, the cells were incubated in the ice-cold second lysis buffer (10 mM Tris-CL pH 8.0, 200 mM NaCl, 1 mM EDTA pH. 8.0, 0.5 mM EGTA pH 8.0, protease inhibitors) as described above. The cells were then dissolved in 0.5% SDS sonication buffer (3.106 cells per 135mg sonication buffer), directed to chromatin fragmentation by Covaris for 10 min
ChIP-seq library for sequencing was prepared as the manufacture's protocol: Mondrian™   SP+ Library Preparation (NuGen)

treatment_protocol: 48h prior to the treatment, H23 cells were cultured in a 15 cm plate at the density of 170,000 cells/mL (4 millions cells in one plate). On the day of treatment, the medium was replaced with the fresh medium containing 500nM JQ1 or an equivalent volume/percentage of DMSO, grown for 24h

tag: cell line

value: Non-small lung cancer cell

tag: antibody type

value: rabbit polyclonal

tag: antibody cat#, lot#


title: H23_H3K27ac_REP2

description:
H23_H3K27Ac_R2M
ChIP-seq with  anti-H3K27ac antibody in H23 cells, replicate 2

source_name: H23_mouse monoclonal

value: mouse monoclonal

value: Diagenode, Cat# MAb-184-050, Lot# 001-11


title: H23_H3K9me3_REP2

description:
H23_H3K9me3_R3
ChIP-seq with  anti-H3K9me3 antibody in H23 cells, replicate 2


title: H23_H3K27me3_REP2

description:
H23_H3K27me3_R2
ChIP-seq with  anti-H3K27me3 antibody in H23 cells, replicate 2


title: H23_H3K36me3_REP2

description:
H23_H3K36me3_BR2
ChIP-seq with  anti-H3K36me3 antibody in H23 cells, replicate 2

value: Abcam ab9050


title: H23_H4K5acK8ac_REP2

description:
H23_H4K5K8DiAc_R2
ChIP-seq with  anti-H4K5acK8ac antibody in H23 cells, replicate 2

value: self production/generation


title: H23_H4K5ac_REP2

description:
H23_H4K5Ac_R2
ChIP-seq with  anti-H4K5ac antibody in H23 cells, replicate 2


title: H23_H3K4me3_REP2

description:
H23_H3K4m3_R2M
ChIP-seq with  anti-H3K4me3 antibody in H23 cells, replicate 2


title: H23_H3K4me1_REP1

description:
H23_H3K4me1_R1
ChIP-seq with  anti-H3K4me1 antibody in H23 cells, replicate 1

value: Diagenode Cat# C15410194, Lot# A1862D


title: H23_H3K4me3_REP1

description:
H23_H3K4m3_R1M
ChIP-seq with  anti-H3K4me3 antibody in H23 cells, replicate 1


title: H23_BRD2_REP2

description:
H23_BRD2_R2
ChIP-seq with  anti-BRD2 antibody in H23 cells, replicate 2

value: Cell Signalling, Cat# D89B4, Lot# 002


title: INPUT

description:
INPUT
INPUT


title: H23_H3K27me3_REP1

description:
H23_H3K27me3_R1
ChIP-seq with  anti-H3K27me3 antibody in H23 cells, replicate 1


title: H23_H3K4me1_REP2

description:
H23_H3K4me1_R2M
ChIP-seq with  anti-H3K4me1 antibody in H23 cells, replicate 2


title: H23_H3K36me3_REP1

description:
H23_H3K36me3_BR1
ChIP-seq with  anti-H3K36me3 antibody in H23 cells, replicate 1


title: H23_H3K27ac_REP1

description:
H23_H3K27Ac_R1
ChIP-seq with  anti-H3K27ac antibody in H23 cells, replicate 1


title: H23_H3K9me3_REP1

description:
H23_H3K9me3_R1
ChIP-seq with  anti-H3K9me3 antibody in H23 cells, replicate 1


title: H23_H4K8ac_REP2

description:
H23_H4K8Ac_R2
ChIP-seq with  anti-H4K8ac antibody in H23 cells, replicate 2


title: H23_BRD2_REP1

description:
H23_BRD2_R1
ChIP-seq with  anti-BRD2 antibody in H23 cells, replicate 1


title: H23_H4K5ac_REP1

description:
H23_H4K5Ac_R1
ChIP-seq with  anti-H4K5ac antibody in H23 cells, replicate 1


title: H23_H4K12ac_REP1

description:
H23_H4K12Ac_R1
ChIP-seq with  anti-H4K12ac antibody in H23 cells, replicate 1


title: H23_H4K5acK8ac_REP1

description:
H23_H4K5K8DiAc_R1
ChIP-seq with  anti-H4K5acK8ac antibody in H23 cells, replicate 1


title: Human_Hs2_CB

city: Okazaki

first: Yasuhiro

last: Go

address: 38 Nishigonaka Myodaiji

department: Department of Brain Sciences, Center for Novel Science Initiatives

institute: National Institutes of Natural Sciences

data_processing:
Raw reads of four species were aligned to the reference genomes (human, hg19; chimpanzee, panTro4; gorilla, gorGor3; gibbon, nomLeu1) by “STAR” (parameters: outFilterMultimapNmax = 1, outFilterMatchNminOverLread = 0.95, outFilterMismatchNoverLmax = 0.05, outFilterIntronMotifs = RemoveNoncanonical).
PCR duplicates removal was then conducted using SAMtools and only uniquely mapped reads were considered as validity to avoid the estimation ambiguity.
We obtained chimpanzee, gorilla and gibbon orthologs of human genes (GENCODE v19) by reciprocal liftOver requiring the same exon orders and no less than 50% exons preserved.
Based on the annotations, numbers of reads were counted per gene per sample using htseq-count within HTSeq. Only genes with counts greater than 0 in all four species in at least one brain region were used in the following analysis
We took advantage of the median ratio method implemented in DESeq2 to normalize the gene abundance data for further comparisons across species and brain regions.
Genome_build: human, hg19; chimpanzee, panTro4; gorilla, gorGor3; gibbon, nomLeu1
Supplementary_files_format_and_content: tab-delimited text files include raw count, normalized count, and RPKM for each sample

molecule: polyA RNA

source_name: cerebellum

extract_protocol:
Brain dissection was performed from either fresh specimens or frozen tissue slabs by the same person to ensure sampling consistency between specimens. About 100 mg of dissected tissues were used and total RNA were extracted using RNeasy Plus Universal Kit (Qiagen). Quality and quantity measurements of extracted RNA were performed using NanoDrop (Thermo Fisher Scientific) and Qubit Fluorometer (Thermo Fisher Scientific), respectively, and the RNA Integrity Number (RIN) were determined using Bioanalyzer RNA 6000 Nano Kit (Agilent).
Sequencing libraries were prepared using the NEBNext mRNA Library Prep Kit for non-directional libraries and the NEBNext Ultra Directional RNA Library Prep Kit for directional libraries (New England BioLabs) according to the manufacturer’s instructions.

tag: individual id

tag: age (year)

value: male

tag: rin

tag: processing date


title: Human_Hs2_ACC

source_name: anterior cingulate cortex


title: Human_Hs2_V1C

source_name: primary visual cortex


title: Human_Hs2_PMC

source_name: premotor cortex


title: H23_H4K8ac_REP1

description:
H23_H4K8Ac_R1
ChIP-seq with  anti-H4K8ac antibody in H23 cells, replicate 1


title: Human_Hs5_DPFC

source_name: dorsolateral prefrontal cortex


title: LY2_shSRC1_BA_MeDIP

city: Dublin

first: Leonie

last: Young

address: York Street

department: Surgery

country: Ireland

institute: Royal College of Surgeons, Ireland

data_processing:
Reads were aligned to the hg19 genome from UCSC using Bowtie2 (default settings). Only uniquely alignable reads were kept.
BAM files were uploaded and processed by MEDIPS package in R. The methylation was assessed in window sizes of 100bp and differential coverage was established by applying the edgeR method as implemented in MEDIPS.
Wig files were generated using exportWIG function in the MEDIPS package using "rpkm" values
Genome_build: hg19
Supplementary_files_format_and_content: Wig files as generated by MEDIPS package

source_name: LY2 Breast Cancer Cell Line

growth_protocol: Endocrine resistant LY2 breast cancer cells were maintained in phenol red free Minimum Essential Medium Eagle (PRF-MEM, Sigma, Darmstadt, Germany) supplemented with 10 % charcoal dextran stripped fetal calf serum (CDS-FCS, Sigma), 1 % L-glutamine (LG, Sigma), 1 % penicillin-streptomycin (PS, Sigma) and 4-hydroxytamoxifen (4-OHT, Sigma) 10-8 mol/L. LY2 shSRC-1 and LY2 shNT cells were maintained in LY2 cell culture media containing puromycin (500 ng/mL, Sigma) to maintain stable knockdown expression.

extract_protocol:
DNA was extracted with average concentrations of 370 ng/µl determined by Qubit Fluorometer, micro plate reader, and nanodrop. The extracted DNA achieved a quantity of above the cut off of ≥ 5µg for all samples.
Genome DNA was fragmented to 100-500bp by sonication. DNA-end was repaired to overhang a 3'-dA, then adapters were ligated to the end of DNA fragments. Double-stranded DNA was denatured. Then DNA fragments were immunoprecipitated by 5mC antibody. Real-time PCR was used to validate the quality of immunoprecipitation. DNA fragments with proper size (usually 200-300bp, including adaptor sequence) were selected after PCR amplification. Then there was adequate library for sequencing.

value: Endocrine resistant breast cancer

value: Tamoxifen

tag: shRNA

value: shSRC1 (SRC1 targeted shRNA)

tag: replicate number

value: Replicate 2


title: Human_Hs5_VPFC

source_name: ventrolateral prefrontal cortex


title: Human_Hs5_STR

source_name: striatum


title: LY2_shSRC1_AA_MeDIP

value: Replicate 1


title: Human_Hs5_V1C


title: LY2_NT_BA_MeDIP

value: shNT (non-targeting shRNA)


title: LY2-SRC1-shRNA-n-4A

data_processing:
The RNA-seq alignment was carried out using Tophat2 (version 2.0.12) to Ensembl's GrCH37 version 75 transcriptome assembly
RNA-seq counts were calculated using HTSeq (version 0.6.1) and uploaded into R
The HTSeq counts were processed by DESeq2 and were assessed for differential expression
Genome_build: Ensembl GrCH37 version 75 transcriptome
Supplementary_files_format_and_content: DESeq normalised counts (counts(dds, normalized=T)

extract_protocol:
RNA was extracted using standard BGI extraction protocols. RNA was extracted with average concentrations of 500 ng/µl determined by QubitFluorometer, Agilent 2100 bioanalyser, and nanodrop. BGI analysed the RNA integrity using the Agilent 2100 bioanalyser achieving a >9.5 RNA integrity number for all samples. Total quantity of RNA was above the cut off of ≥ 5µg
LIbrary construction was carried out using Illumina®TruSeq  RNA Sample Prep Kit. After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. The suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library.

treatment_protocol: Prior to treatment, cells were steroid depleted for 72 hours, followed by 4-OHT [ 10^-7 M] treatment for 8 hours prior to RNA-sequencing.

value: endocrine-resistant breast cancer

value: Replicate 4


title: LY2-SRC1-shRNA-n-1A


title: LY2-SRC1-shRNA-n-2A


title: LY2-NT-shRNA-n-4A


title: LY2-SRC1-shRNA-n-3A

value: Replicate 3


title: LY2-NT-shRNA-n-3A


title: Human_Hs5_ACC


title: LY2-NT-shRNA-n-2A


title: LY2_NT_AA_MeDIP


title: Human_Hs2_VPFC


title: RPB_RNAseq

city: Taiyuan

first: lei

last: Bi

address: xinjian south road

country: China

institute: Shanxi medical university

data_processing:
Basecalls performed using Illumina Casava1.7 software
The clean reads were obtained by removing adapter sequences from raw reads which have been filtrated the low quality reads and removed reads of N ratio more than 5% with filter_fq software.Then transcriptome de novo assembly was carried out with short reads assembling program – Trinity, release-20130225 version with parameters:--seqType fq --min_contig_length 50   --group_pairs_distance 250 --path_reinforcement_distance 85   --min_kmer_cov 3
The uniquely mapped reads for some specific transcripts were counted by mapping reads to assembled sequences using SOAP(Release 2.21 version with parameters:-m 0 -x 500 -s 40 -l 35 -v 5 -r 1).Then calculation of unigenes expression was performed using FPKM (fragments per kilobase of transcript sequence per million mapped reads).
Genome_build: Rhodopseudomonas palustris AND srcdb_refseq [PROP]
Supplementary_files_format_and_content: All-Unigene.RPS.Coverage and All-Unigene.RPB.Coverage excel files include depth,coverage,length and are available on the sample records.  The file "annotation.txt" is available on the series record and contains raw read counts and FPKM values for each transcript.  FASTA files with assembled sequences are available on the series record.

organism: Rhodopseudomonas palustris

source_name: Rhodopseudomonas palustris treated with alpha-rhamnetin-3-rhamnose

growth_protocol: R. palustris strains  were cultured in conventional medium with the condition of 37 degrees Celsius and 2500lux of lighting- power for 72 hours.

extract_protocol:
Total RNA were respectively extracted from alpha-rhamnetin-3-rhamnose treatment (RPB) and control of Rhodopseudomonas palustris (RPS) cultured for just 72 hours with TRIzol reagent (life technology) according to the manufacturer’s protocol and treated with RNase-free DNase I (Taraka Biotechnology, China).
After validating on an Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System, the cDNA library was sequenced on a flow cell using Illumina HiSeq2000.

tag: culture time

value: 3 days

value: treated with alpha-rhamnetin-3-rhamnose


title: RRBS_NP3

city: Chicago

first: Benjamin

middle: D.

last: Singer

state: Illinois

address: 303 E. Superior St., Simpson Querrey 5th floor

institute: Northwestern University Feinberg School of Medicine

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl2fastq v2.17.1.14.
Reads were  trimmed of 10 base pairs from the 5’ end with TrimGalore! v0.4.3 to remove primer and adapter sequences.
Sequence alignment to the GRCm38/mm10 reference genome and methylation extraction ignoring 1 base at the 3’ end (after reviewing the M-bias plots) were performed with Bismark v0.16.3.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Bismark tab-delimited "coverage" files for cytosines in CpG context with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

organism: Mus musculus

source_name: Neonate_PBS_lung CD4+ T cells

growth_protocol: Male and female C57BL/6NJ mice received either 2.8 million CFUs of E. coli or PBS (control) via aspiration at day 5 (neonate) or day 15 (juvenile) of life.

extract_protocol:
48 hours post-aspiration, all groups were euthanized for isolation of lung CD4+ T cells by magnetic bead pre-enrichment and fluorescence-activated cell sorting. RNA and genomic DNA were obtained using the AllPrep DNA/RNA Micro Kit (Qiagen).
Genomic DNA was quantified with a Qubit 3.0 instrument. ~50-200 ng of genomic DNA was then digested with the restriction endonuclease MspI (New England BioLabs). Resulting fragments underwent size selection for fragments ~100-250-bp in length using SPRI beads (MagBio Genomics) and subsequent bisulfite conversion using the EZ DNA Methylation-Lightning Kit (Zymo Research) per the manufacturer’s protocol. Bisulfite conversion efficiency averaged 99.4% as estimated by the measured percent of unmethylated CpGs in λ-bacteriophage DNA (New England BioLabs N3013S) added at a 1:200 ratio to each sample. Libraries for Illumina-based sequencing were prepared with the Pico Methyl-Seq Library Prep Kit (Zymo Research) using Illumina TruSeq DNA methylation barcodes. Libraries were run on a High Sensitivity chip using an Agilent TapeStation 4200 to assess size distribution and overall quality of the amplified library. Fluorometric quantitation and TapeStation size distribution estimates permitted equimolar pooling, and six pooled libraries per run were sequenced on an Illumina NextSeq 500 instrument using the NextSeq 500/550 V2 High Output reagent kit (1 x 75 cycles).

tag: strain

value: Neonate

tag: exposure

value: PBS

tag: cell type

value: lung CD4+ T cells


title: RRBS_NP1

tag: age


title: RRBS_NP2


title: Human_Hs5_PMC

tag: Sex


title: RRBS_NE3

source_name: Neonate_E. coli_lung CD4+ T cells

value: E. coli


title: RRBS_NE2


title: 419_02

status: Public on Jun 08 2018

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Library strategy: eCLIP-seq
Takes output from raw files.  Run to trim off both 5’ and 3’ adapters on both reads. Command: quality-cutoff 6  -m 18  -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGT  AGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.metrics
Takes output from cutadapt round 1. Run to trim off the 3’ adapters on read 2, to control for double ligation events. Command: cutadapt -f fastq --match-read-wildcards  --times 1  -e 0.1  -O 5  --quality-cutoff 6  -m 18  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.metrics
Takes output from cutadapt round 2.  Maps to human specific version of RepBase used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir /path/to/RepBase_human_database_file --genomeLoad LoadAndRemove  --readFilesIn /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz --outSAMunmapped Within  --outFilterMultimapNmax 30  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam --outSAMattributes All  --readFilesCommand zcat  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam
Takes output from STAR rmRep.  Maps unique reads to the human genome.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir  /path/to/STAR_database_file --genomeLoad LoadAndRemove  --readFilesIn  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate1  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate2  --outSAMunmapped Within  --outFilterMultimapNmax 1  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --outSAMattributes All  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam
takes output from STAR genome mapping.  Custom random-mer-aware script for PCR duplicate removal. Command: barcode_collapse_pe.py  --bam /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --out_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  --metrics_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.metrics
Takes output from barcode collapse PE.  Sorts resulting bam file for use downstream.  Command: java  -Xmx2048m  -XX:+UseParallelOldGC  -XX:ParallelGCThreads=4  -XX:GCTimeLimit=50  -XX:GCHeapFreeLimit=10  -Djava.io.tmpdir=/full/path/to/files/.queue/tmp  -cp /path/to/gatk/dist/Queue.jar  net.sf.picard.sam.SortSam  INPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  TMP_DIR=/full/path/to/files/.queue/tmp  OUTPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  VALIDATION_STRINGENCY=SILENT  SO=coordinate  CREATE_INDEX=true
Takes output from sortSam, makes bam index for use downstream.  Command: samtools index  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam.bai
Takes inputs from multiple final bam files.  Merges the two technical replicates for further downstream analysis.  Command: samtools  merge  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam /full/path/to/files/file_R1.D08.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam
Takes output from sortSam, makes bam index for use downstream.  Command: samtools  index  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/CombinedID.merged.bam.bai
Takes output from sortSam.  Only outputs the second read in each pair for use with single stranded peak caller.  This is the final bam file to perform analysis on.  Command: samtools view -hb -f 128  /full/path/to/files/CombinedID.merged.bam  >  /full/path/to/files/CombinedID.merged.r2.bam
Takes results from samtools view.  Calls peaks on those files.  Command: clipper  -b /full/path/to/files/CombinedID.merged.r2.bam  -s hg19  -o /full/path/to/files/CombinedID.merged.r2.peaks.bed  --bonferroni  --superlocal  --threshold-method binomial  --save-pickle
Genome_build: hg19
Supplementary_files_format_and_content: bed format, contains clusters of predicted RBP binding

growth_protocol: HepG2 cells were grown under standard conditions (DMEM + 10% FBS + Pen/Strep (100U / mL)). K562 cells were grown in suspension in standard media (RPMI + 10% FBS + Pen/Strep (100U / mL)).

extract_protocol:
Cells were lysed in iCLIP lysis buffer, followed by limited digestion with RNase I (Ambion), immunoprecipitation of RBP-RNA complexes with a specific antibody of interest (Protein G sheep anti-rabbit Dynabeads), and stringent washes.
After dephosphorylation with FastAP (Thermo Fisher) and T4 PNK (NEB), a barcoded RNA adapter is ligated to the 3’ end (T4 RNA Ligase, NEB) (at this step, multiple replicates of the same RBP, or potentially RBPs of similar size and bound RNA amount, can be uniquely barcoded and pooled after ligation to simplify downstream steps - see Supplementary Fig. 2A). Ligations are performed on-bead (to allow washing away unincorporated adapter) in high concentration of PEG8000, which improves ligation efficiency to > 90%. Samples are then run on standard protein gels and transferred to nitrocellulose membranes, and a region 75 kDa (~150 nt of RNA) above the protein size is isolated and proteinase K (NEB) treated to isolate RNA. RNA is reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 5 (N5) or 10 (N10) random bases at the 5’ end) is then ligated to the cDNA fragment 3’ end (T4 RNA Ligase, NEB), performed with high concentration of PEG8000 (to improve ligation efficiency) and DMSO (to decrease inhibition of ligation due to secondary structure). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample is first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder is PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis.

treatment_protocol: While plated, HepG2 cells were crosslinked with UV (254 nm, 400 mJ/cm2). HepG2 cells were then isolated with cell scrapers, pelleted at 200g, and snap frozen. K562 suspension cells were pelleted at 200g and resuspended in 1X PBS to 20 million cells per mL. 60 million cells in 3 mL were UV crosslinked (254 nm, 400 mJ/cm2) per 10 cm dish, pelleted, and snap frozen.

tag: barcodes

tag: antibody

tag: antibody catalog#

tag: antibody lot#


title: RRBS_JP3

source_name: Juvenile_PBS_lung CD4+ T cells

value: Juvenile


title: RRBS_JP1


title: Human_Hs2_STR

value: male


title: RRBS_JE2

source_name: Juvenile_E. coli_lung CD4+ T cells


title: RRBS_JE1


title: HCD25.4

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

data_processing:
Quality checked using fastqc
Reads were aligned using HiSat
Reads counted using iGenomes annotation using Rsubread
Counts normalised and differentials found using DESeq
Genome_build: mm10
Supplementary_files_format_and_content: Two columns per file, the first giving the Gene ID, and the second giving raw read counts.

source_name: BM

extract_protocol:
Total RNA was isolated from using RNAeasy MicroKit (Qiagen)
Libraries were made using Nugen Ovation RNA-Seq System kits and Nugen Ovation Ultralow System V2 kits.

treatment_protocol: CLP populations were isolated from single cell suspension of BM cells by FACS

tag: genotype

value: WT

tag: sort strategy


title: LY2-NT-shRNA-n-1A

tag: cell line

tag: treatment

value: Tamoxifen


title: BLP3


title: Human_Hs2_DPFC

tag: individual id

tag: age (year)

tag: rin

tag: processing date


title: RRBS_JE3

tag: strain


title: HCD25.2


title: BLP2


title: ALP1


title: HCD25.1


title: RPS_RNAseq

source_name: Rhodopseudomonas palustris control

tag: culture time

value: untreated


title: BLP1


title: CLPLy6D+Gfra2- [T8-S6]

data_processing:
Quality checked using fastqc
Reads were aligned using HiSat or Tophat
Reads counted using iGenomes annotation using Rsubread. Or analysed using HOMER
Counts normalised and differentials found using DESeq
Genome_build: mm10
Supplementary_files_format_and_content: Two columns per file, the first giving the RefSeq ID, and the second giving raw read counts.


title: RRBS_NE1

tag: exposure

tag: cell type


title: CLPLy6D+Gfra2+ [T7-S6]


title: HCD25.5


title: CLPLy6D-Gfra2- [T6-S6]


title: CLPLy6D-Gfra2- [T1_S4]


title: CLPLy6D+Gfra2- [T5-S5]


title: CLPLy6D-Gfra2- [T3_S5]


title: RRBS_JP2

tag: age


title: CLPLy6D+Gfra2- [P8.2]


title: CLPLy6D+Gfra2- [P8.1]


title: HCD25.3


title: CLPLy6D+Gfra2+ [T4-S5]


title: ALP2


title: CLPLy6D-Gfra2- [P7.3]


title: esc_E(z)_small_RNA

city: Shanghai

first: Hui

last: Wang

email: wanghuisimm@sioc.ac.cn, mazj@sioc.ac.cn

address: Qiuyue Road 26

institute: Chinese Academy of Science

description:
20-29 nt size selected RNA
WT_vs_esc_E(z)_small_RNA_DESeq.csv

data_processing:
For ChIP-Seq, Sequencing reads were mapped to reference genome dm6 or mm10 respectively with Bowtie2 by default parameter. The peak regions were identified by homer function findPeaks with parameter –style histone -F 2 -size 3000 -minDist 5000. The overlapped peaks of replicate data-sets were found using homer function mergePeaks by default parameter. Bedtools were used to compare the peaks between different genotypes and aging stages. To get inter-peak regions, we used Bedtools to subtracted the peak regions from whole genome.
For quantitative comparison, the dm6 mapped reads were normalized to a scale factor using deeptools function bamCoverage with 10 bp bin size. The scale factor for each sample was calculated as reported (David A. Orlando et al., 2014) with a small modification. The percentage of mouse genome in input was set to the mm10 mapped reads in total mapping reads, rather than a constant. The ChIP intensity of each genes or regions were calculated using the Bwtool function bwtool summary.
For RNA-Seq comparison, Sequencing reads were mapped to dm6 with STAR by default parameter. The read counts for each genes were calculated by HTSeq-count. The count files were used as input to DESeq for differential expression analysis.
For small RNA-Seq, adapters were removed by fastx, microRNAs were identified by miRDeep2.
Genome_build: dm6 and mm10
Supplementary_files_format_and_content: bigwig files were generated by deeptools. DESeq was used for calling differential expression.

organism: Drosophila melanogaster

source_name: fly muscle

growth_protocol: Flies were cultured in standard media at 25ºC with 60% humidity unless otherwise specified. The control (WT) line used was 5905 (FlyBase ID FBst0005905, w1118). The given genotype male flies were collected at the day of eclosion and transferred to new vials every other day during aging process.

extract_protocol:
For ChIP-Seq, 5% mouse epigenome was used as internal control for H3K27me3 IP.
For RNA-Seq, RNA was isolated by TRIZol reagent, and polyA tail RNAs were selected.
For small RNA-seq, ~20-29 nt small RNA was recoveried by 15% TBE-UREA PAGE gels.
ChIP libraries were prepared according to instructions of NEB DNA library prep kit (NEB, E7370L). RNA libraries were prepared according to instructions of NEB Ultra RNA library prep kit (NEB, E7530L). Small RNA libraries were prepared by NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, E7300S).
ChIP-Seq or RNA-Seq or miRNA-seq

treatment_protocol: Fly muscles were harvested at the given age.

tag: tissue

value: muscle

value: 30 day


title: 30d_WT_small_RNA

description: 20-29 nt size selected RNA


title: Pcl_Su(z)12_small_RNA

description:
20-29 nt size selected RNA
WT_vs_Pcl_Su(z)12_smll_RNA_DESeq.csv


title: 30d_WT_ChIPSeq_input_rep4


title: 30d_esc_E(z)_ChIPSeq_input_rep2


title: 30d_esc_E(z)_ChIPSeq_rep2

tag: chip antibody

value: H3K27me3 (Millipore 07-449)


title: 3d_WT_ChIPSeq_input_rep4

value: 3 day


title: 3d_esc_E(z)_ChIPSeq_rep2


title: 3d_esc_E(z)_ChIPSeq_input_rep2


title: 3d_WT_ChIPSeq_rep4


title: 30d_WT_ChIPSeq_input_rep3


title: 3d_esc_E(z)_ChIPSeq_input_rep1


title: 3d_WT_ChIPSeq_input_rep3


title: 30d_Pcl_Su(z)12_ChIPSeq_input_rep2


title: 3d_esc_E(z)_ChIPSeq_rep1


title: 3d_WT_ChIPSeq_rep3


title: 30d_WT_ChIPSeq_rep3


title: CLPLy6D+Gfra2+ [T2_S4]


title: 3d_Pcl_Su(z)12_ChIPSeq_input_rep2


title: 3d_WT_ChIPSeq_input_rep2


title: 30d_WT_ChIPSeq_input_rep2


title: CLPLy6D-Gfra2- [P7.1]


title: 30d_Pcl_Su(z)12_ChIPSeq_rep2


title: 30d_WT_ChIPSeq_rep2


title: 3d_Pcl_Su(z)12_ChIPSeq_rep2


title: 3d_WT_ChIPSeq_rep2


title: 30d_WT_ChIPSeq_rep4


title: 30d_Pcl_Su(z)12_ChIPSeq_input_rep1


title: 30d_esc_E(z)_ChIPSeq_input_rep1


title: 3d_WT_ChIPSeq_input_rep1


title: 3d_Pcl_Su(z)12_ChIPSeq_input_rep1


title: 30d_WT_ChIPSeq_input_rep1


title: 30d_WT_ChIPSeq_rep1


title: 3d_Pcl_Su(z)12_ChIPSeq_rep1


title: dwil_June_ATAC

organism: Drosophila willistoni

source_name: D. Willistoni_eye-antennal discs

tag: genotype/species

value: Drosophila Willistoni

value: 3rd instar-wandering

value: Hand Dissections

value: eye-antennal discs


title: dwil_May_ATAC


title: 3d_WT_ChIPSeq_rep1


title: cell_lethal_ctrl_sample_a_10_eye-ant_discs

description: ATAC-seq

data_processing:
Cleaning (fastq-mcf)
Mapping to therespective genome (dm3) using bowtie2
peaks were called for each sample using macs2 callpeak with parameter -g dm  --nomodel
genome build: Drosophila melanogaster FlyBase version 5.13
Supplementary_files_format_and_content: BigWigs for all ATAC-samples

source_name: eye-antennal discs


title: cell_lethal-grh_mut_sample_b_10_eye-ant_discs

description: ATAC-seq

value: eyFLP; FRT42-cell_lethal/FRT42-Grh[IM]


title: cell_lethal_ctrl_sample_b_10_eye-ant_discs

description: ATAC-seq


title: Ga99_ctrl_sample_a_2_larval_brain

description: ATAC-seq

source_name: 3rd instar larval brains

growth_protocol: Normal flyfood, 18 degrees

extract_protocol:
The entire brain was dissected from 3rd instar wandering larvae. The brains were immediately lysed and ATAC-seq was performed
Tn5 and nextera library prep

treatment_protocol: early 3rd instar larvea were shifter to 29 degrees for 18 (a) and 24 (b) hours


title: cell_lethal-grh_mut_sample_a_10_eye-ant_discs

description: ATAC-seq


title: Chimpanzee_IYO_CB

organism: Pan troglodytes

source_name: cerebellum

value: IYO

tag: Sex

value: female


title: Chimpanzee_IYO_ACC

source_name: anterior cingulate cortex


title: Chimpanzee_IYO_HIP

source_name: hippocampus


title: Chimpanzee_IYO_STR


title: Chimpanzee_IYO_VPFC


title: UAS-grh_x_Ga99_sample_a_2_larval_brain

description: ATAC-seq

tag: genotype


title: UAS-grh_x_Ga99_sample_b_2_larval_brain

description: ATAC-seq


title: Chimpanzee_YOSHIO_PMC

source_name: premotor cortex

value: YOSHIO


title: Chimpanzee_IYO_V1C

source_name: primary visual cortex


title: Chimpanzee_IYO_DPFC

source_name: dorsolateral prefrontal cortex


title: Chimpanzee_YOSHIO_HIP


title: Chimpanzee_MAYUMI_CB

value: MAYUMI


title: Chimpanzee_MAYUMI_ACC


title: 30d_Pcl_Su(z)12_ChIPSeq_rep1


title: Chimpanzee_YOSHIO_VPFC

source_name: ventrolateral prefrontal cortex

value: male


title: Chimpanzee_YOSHIO_CB


title: Chimpanzee_YOSHIO_ACC


title: Chimpanzee_YOSHIO_STR

source_name: striatum


title: Chimpanzee_MAYUMI_HIP


title: Chimpanzee_MAYUMI_V1C


title: Chimpanzee_YOSHIO_DPFC


title: Chimpanzee_MAYUMI_VPFC


title: Chimpanzee_GENKI_STR

value: GENKI


title: Chimpanzee_GENKI_V1C


title: Chimpanzee_GENKI_PMC


title: Chimpanzee_MAYUMI_PMC


title: Chimpanzee_GENKI_VPFC


title: Optix_GFP_Pos_Cell_96

description:
scATAC-seq
Grh_regions_avgATAC_number_sc.tsv

data_processing:
Cleaning (fastq-mcf)
Mapping to the dm6 genome using bowtie2
Single cells were deduplicated using picard tools
The number of cells with reads present in each DGRP peak was counted using custom scripts
Genome_build: Drosophila melanogaster FlyBase version 6.03
Supplementary_files_format_and_content: Grh_regions_avgATAC_number_sc.tsv contains a matrix indicating how many single cells have reads present within each peak from the bulk DGRP data

source_name: eye progenitor cells (Optix-GFP positive) from 3rd instar wandering larvae eye antennal disc

extract_protocol:
Eye-antennal imaginal Disc were dissected from 3rd instar wandering larvae. The discs were dissociated with Trypsin 0.05% EDTA at 37'C for 45 minutes, filtered at 20µm and FACS soted based on GFP. Single cells were loaded into a Fluidigm C1 at a concentration of 1000 cells/µl. scATAC was performed as described previously (Buenrostro et al. 2015)
Tn5 and nextera library prep

value: FACS sorting

value: eye progenitor cells


title: Optix_GFP_Pos_Cell_91


title: Optix_GFP_Pos_Cell_94


title: Optix_GFP_Pos_Cell_95


title: Optix_GFP_Pos_Cell_90


title: CLPLy6D-Gfra2- [P7.2]

value: WT

tag: sort strategy


title: Optix_GFP_Pos_Cell_93


title: Chimpanzee_GENKI_DPFC


title: Optix_GFP_Pos_Cell_92


title: 30d_esc_E(z)_ChIPSeq_rep1

value: muscle

value: 30 day


title: Optix_GFP_Pos_Cell_88


title: Optix_GFP_Pos_Cell_87


title: Optix_GFP_Pos_Cell_89


title: Optix_GFP_Pos_Cell_86


title: Optix_GFP_Pos_Cell_85


title: Chimpanzee_MAYUMI_STR


title: Optix_GFP_Pos_Cell_84


title: Optix_GFP_Pos_Cell_81


title: Optix_GFP_Pos_Cell_83


title: Chimpanzee_MAYUMI_DPFC


title: Optix_GFP_Pos_Cell_80


title: Optix_GFP_Pos_Cell_82


title: Human_Hs7_HIP


title: Human_Hs9_HIP

value: CLO


title: Optix_GFP_Pos_Cell_79


title: Optix_GFP_Pos_Cell_77


title: Optix_GFP_Pos_Cell_78


title: Human_Hs4_HIP


title: Optix_GFP_Pos_Cell_76


title: Optix_GFP_Pos_Cell_75


title: Optix_GFP_Pos_Cell_74


title: Human_Hs1_STR


title: Human_Hs1_CB


title: Optix_GFP_Pos_Cell_73


title: Human_Hs1_ACC


title: Optix_GFP_Pos_Cell_71


title: Human_Hs1_V1C


title: Human_Hs1_DPFC


title: Optix_GFP_Pos_Cell_72


title: Optix_GFP_Pos_Cell_70


title: Human_Hs1_PMC


title: Optix_GFP_Pos_Cell_69


title: Optix_GFP_Pos_Cell_68


title: RNAseq_NP3

data_processing:
Basecalls performed using Illumina RTA2 software.
CASAVA v1.8.4 was used to convert bcl files to fastq files (default parameters).
Rsem v1.2.09 (STAR option) was used for running alignments to the GRCm38/mm10 mouse reference genome using the iGenomes annotation.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text file including raw counts values for each sample generated for uniquely mapped reads over exons was obtained using SeqMonk v1.38.2.

source_name: Neonate_PBS_lung CD4+ T cells

extract_protocol:
48 hours post-aspiration, all groups were euthanized for isolation of lung CD4+ T cells by magnetic bead pre-enrichment and fluorescence-activated cell sorting. RNA and genomic DNA were obtained using the AllPrep DNA/RNA Micro Kit (Qiagen).
cDNA was generated with the Nugen Ovation RNA-Seq System V2. Fragmentation was performed on a Covaris S2. Illumina-compatible adapter ligation and barcoding was followed by PCR amplification. A High Sensitivity chip on an Agilent Bioanalyzer 2100 was used to measure the size distribution and quality of amplified libraries. Library quantification was performed with the qPCR-based Kapa Library Quantification Kit or by Bioanalyzer. Equimolar concentrations of each library were pooled. Cluster generation and sequencing were performed on an Illumina HiSeq 2500 employing 100 x 100 paired end sequencing with the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit (200 cycles).

value: Neonate

value: PBS

value: lung CD4+ T cells


title: Human_Hs3_PMC


title: Human_Hs3_DPFC


title: RNAseq_NP2


title: Human_Hs3_CB


title: Human_Hs8_CB


title: RNAseq_NE3

source_name: Neonate_E. coli_lung CD4+ T cells

value: E. coli


title: RNAseq_NE2


title: Optix_GFP_Pos_Cell_67

value: 3rd instar-wandering

value: Hand Dissections


title: Optix_GFP_Pos_Cell_66


title: RNAseq_NP1


title: Human_Hs8_STR


title: RNAseq_NE1


title: RNAseq_JP3

source_name: Juvenile_PBS_lung CD4+ T cells

value: Juvenile


title: Human_Hs8_ACC


title: Optix_GFP_Pos_Cell_64


title: RNAseq_JP1


title: Optix_GFP_Pos_Cell_65


title: Human_Hs8_V1C


title: RNAseq_JP2


title: RNAseq_JE3

source_name: Juvenile_E. coli_lung CD4+ T cells


title: Human_Hs8_VPFC


title: Human_Hs8_PMC


title: RNAseq_JE1


title: Optix_GFP_Pos_Cell_61


title: RNAseq_JE2


title: Optix_GFP_Pos_Cell_63


title: Gorilla_Sakura_CB

organism: Gorilla gorilla

value: Sakura

value: female


title: Human_Hs8_DPFC

value: male


title: Gorilla_Sakura_STR


title: Gorilla_Sakura_ACC


title: Gorilla_Sakura_PMC


title: Gorilla_Sakura_V1C


title: Gorilla_Sakura_VPFC


title: Optix_GFP_Pos_Cell_60


title: Human_Hs6_CB


title: Human_Hs6_HIP


title: Gorilla_Sakura_DPFC


title: Chimpanzee_KENNY_CB

value: KENNY


title: Human_Hs6_STR


title: Optix_GFP_Pos_Cell_58

value: FACS sorting


title: Optix_GFP_Pos_Cell_57

value: eye progenitor cells


title: Chimpanzee_KENNY_STR


title: Human_Hs6_ACC


title: Chimpanzee_KENNY_ACC


title: Chimpanzee_KENNY_V1C


title: Gorilla_Sakura_HIP


title: Optix_GFP_Pos_Cell_62


title: Optix_GFP_Pos_Cell_56


title: Human_Hs6_V1C


title: Optix_GFP_Pos_Cell_55


title: Human_Hs6_PMC


title: Chimpanzee_KENNY_PMC


title: Chimpanzee_KENNY_VPFC


title: Optix_GFP_Pos_Cell_59


title: 30d_Suz12_RNASeq_rep2_head

description: processed data file: WT_vs_Suz12_head_DESeq.csv

data_processing:
For RNA-Seq comparison, Sequencing reads were mapped to dm6 with STAR by default parameter. The read counts for each genes were calculated by HTSeq-count. The count files were used as input to DESeq for differential expression analysis.
Genome_build: dm6
Supplementary_files_format_and_content: DESeq was used for calling differential expression. .CSV files contain the DESeq output.

source_name: fly head

extract_protocol:
For RNA-Seq, RNA was isolated by TRIZol reagent, and polyA tail RNAs were selected.
RNA libraries were prepared according to instructions of NEB Ultra RNA library prep kit (NEB, E7530L).

treatment_protocol: Fly heads were harvested at the given age.

value: head


title: 30d_Suz12_RNASeq_rep3_head


title: Human_Hs6_VPFC


title: Optix_GFP_Pos_Cell_54


title: 30d_Suz12_RNASeq_rep1_head


title: Chimpanzee_KENNY_DPFC


title: Human_Hs6_DPFC


title: 30d_Pcl_RNASeq_rep3_head

description: processed data file: WT_vs_Pcl_DESeq.csv


title: Optix_GFP_Pos_Cell_52


title: Chimpanzee_KENNY_HIP


title: Chimpanzee_REIKO_CB

value: REIKO


title: Optix_GFP_Pos_Cell_51


title: 30d_Pcl_RNASeq_rep2_head

value: 30 day


title: Chimpanzee_REIKO_HIP


title: dyak_June_ATAC

organism: Drosophila yakuba

source_name: D. Yakuba_eye-antennal discs

value: Drosophila Yakuba

value: eye-antennal discs


title: Chimpanzee_REIKO_STR


title: Optix_GFP_Pos_Cell_50


title: 30d_Pcl_RNASeq_rep1_head


title: 30d_Ez_RNASeq_rep3_head

description: processed data file: WT_vs_Ez_head_DESeq.csv


title: dyak_May_ATAC


title: 30d_Ez_RNASeq_rep2_head


title: Chimpanzee_REIKO_ACC


title: Optix_GFP_Pos_Cell_48


title: Chimpanzee_REIKO_V1C


title: 30d_Ez_RNASeq_rep1_head


title: Optix_GFP_Pos_Cell_47


title: Optix_GFP_Pos_Cell_49


title: Optix_GFP_Pos_Cell_53


title: 30d_esc_RNASeq_rep3_head

description: processed data file: WT_vs_esc_head_DESeq.csv


title: Chimpanzee_REIKO_PMC


title: Chimpanzee_REIKO_VPFC


title: Optix_GFP_Pos_Cell_44


title: 30d_esc_RNASeq_rep1_head


title: 30d_esc_RNASeq_rep2_head


title: 30d_WT_RNASeq_single_mutants_control_rep2_head

description: processed data file: WT_vs_esc_head_DESeq.csv, WT_vs_Ez_head_DESeq.csv, WT_vs_Pcl_DESeq.csv, and WT_vs_Suz12_head_DESeq.csv


title: Optix_GFP_Pos_Cell_42


title: 30d_WT_RNASeq_single_mutants_control_rep3_head


title: Chimpanzee_REIKO_DPFC


title: Optix_GFP_Pos_Cell_43


title: 30d_WT_RNASeq_single_mutants_control_rep1_head


title: Optix_GFP_Pos_Cell_40


title: 30d_esc_Ez_RNASeq_rep2_head

description: processed data file: WT_vs_esc_Ez_head_DESeq.csv


title: Optix_GFP_Pos_Cell_39


title: Optix_GFP_Pos_Cell_38


title: 30d_WT_RNASeq_esc_Ez_control_rep3_head


title: Optix_GFP_Pos_Cell_37


title: 30d_WT_RNASeq_esc_Ez_control_rep2_head


title: Optix_GFP_Pos_Cell_36


title: Optix_GFP_Pos_Cell_46


title: 30d_WT_RNASeq_esc_Ez_control_rep1_head


title: p55_RNASeq_rep3

source_name: fly muscle

value: muscle


title: Optix_GFP_Pos_Cell_34


title: Optix_GFP_Pos_Cell_33


title: p55_RNASeq_rep1


title: Optix_GFP_Pos_Cell_32


title: Optix_GFP_Pos_Cell_45


title: p55_RNASeq_rep2


title: Optix_GFP_Pos_Cell_31


title: Su(z)12_RNASeq_rep2


title: Optix_GFP_Pos_Cell_30


title: Su(z)12_RNASeq_rep3


title: 30d_esc_Ez_RNASeq_rep3_head


title: Optix_GFP_Pos_Cell_41


title: Pcl_RNASeq_rep3


title: Su(z)12_RNASeq_rep1


title: Optix_GFP_Pos_Cell_27


title: Pcl_RNASeq_rep2


title: Pcl_RNASeq_rep1


title: Optix_GFP_Pos_Cell_29


title: Optix_GFP_Pos_Cell_26


title: E(z)_RNASeq_rep2


title: Optix_GFP_Pos_Cell_25


title: Optix_GFP_Pos_Cell_24


title: Optix_GFP_Pos_Cell_35


title: 30d_esc_Ez_RNASeq_rep1_head


title: E(z)_RNASeq_rep3


title: E(z)_RNASeq_rep1


title: esc_RNASeq_rep3


title: Optix_GFP_Pos_Cell_23


title: Optix_GFP_Pos_Cell_22


title: Optix_GFP_Pos_Cell_21


title: Optix_GFP_Pos_Cell_19


title: esc_RNASeq_rep2


title: 30d_WT_RNASeq_single_mutants_control_rep1


title: 30d_WT_RNASeq_single_mutants_control_rep2


title: Optix_GFP_Pos_Cell_20


title: Optix_GFP_Pos_Cell_28


title: Optix_GFP_Pos_Cell_17


title: esc_RNASeq_rep1


title: esc_E(z)_RNASeq_rep2


title: Optix_GFP_Pos_Cell_18


title: esc_E(z)_RNASeq_rep3


title: esc_E(z)_RNASeq_rep1


title: 30d_WT_RNASeq_esc_E(z)_control_rep3


title: Optix_GFP_Pos_Cell_16


title: 30d_WT_RNASeq_single_mutants_control_rep3


title: Optix_GFP_Pos_Cell_13


title: 30d_WT_RNASeq_esc_E(z)_control_rep1


title: Optix_GFP_Pos_Cell_9


title: 30d_WT_RNASeq_esc_E(z)_control_rep2


title: exo2_1_NET_Seq_IP

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description:
NET_Seq_pombe.txt
library strategy: NET-seq
nascent RNA

data_processing:
After trimming of the 5’-adapter sequence, reads were uniquely mapped to the S. pombe reference genome (ASM294v2.30) using version 0.12.8 of Bowtie, with a tolerance of 2 mismatches, giving 3 to 10 million uniquely mapped reads.
Bioinformatics analyses used reads uniquely mapped on the reference genome.
Data were normalized on the total number of uniquely mapped reads.
Supplementary_files_format_and_content: A single tab-delimited text file including normalized tag densities (tag/nt) for each annotated feature (including XUTs) in each sample.

organism: Schizosaccharomyces pombe

source_name: Yeast cells

extract_protocol:
NET-Seq analysis was performed from two biological replicates of strains YAM2492 (Rpb3-flag) and YAM2507 (exo2-delta Rpb3-flag) of S. pombe.
Libraries were constructed according previously published protocol (Churchman and Weissman, 2012), with minor modifications, starting from 1L of exponentially growing cells. Ligation of DNA 3â€™-linker was performed as described (Marquardt et al., 2014), starting with 2-3 µg of purified nascent RNA. Ligated nascent RNA was then submitted to alkaline fragmentation for 20 minutes at 95°C. Single-end sequencing (50 nt) of the libraries was performed on a HiSeq 2500 sequencer, giving between 20 and 50 million reads.
NET-Seq is a sequencing of 3' end of nascent transcript produced by RNA Polymerase II. In this protocol, transcribing RNA Pol II is isolated, then nascent transcripts are purified and used to construct libraries, using a non-standard protocol described by Weismann's lab. These samples are called "IP" (as for ChIP). "Input" are control libraries constructed from the same biological samples, using the very same control but without purification of RNA Pol II. So they are similar to "total" RNA libraries, but constructed using the same protocol as IP, for comparison.

tag: genotype/variation

value: YAM2507 (Rpb3-flag exo2-delta) strain

tag: biological replicate

tag: sample type

value: IP


title: Optix_GFP_Pos_Cell_8

value: 3rd instar-wandering

tag: treatment


title: exo2_1_NET_Seq_IN

value: Input


title: Optix_GFP_Pos_Cell_11

value: Hand Dissections


title: Optix_GFP_Pos_Cell_10


title: exo2_2_NET_Seq_IP


title: Optix_GFP_Pos_Cell_7


title: Omni_ATAC_MCF-7_grh_KD

data_processing:
Cleaning (fastq-mcf)
Mapping to the respective genome (hg19) using bowtie2
peaks were called for each sample using macs2 callpeak with parameter  -g hg --nomodel
genome build: Genome Reference Consortium Human Build 37
Supplementary_files_format_and_content: BigWigs for all ATAC-samples

source_name: human cell line

growth_protocol: MCF7 cells were cultured at 37˚C and 5% CO2 in Dulbecco’s Modified Eagle’s Medium (ThermoFisher Scientific), supplemented with 10% fetal bovine serum (Lonza) and penicillin-streptomycin (ThermoFisher Scientific).

extract_protocol:
Cells were collected from their plates and Omni-ATAC was performed according to the standard protocol (Corces at al. Nature Methods 2017)
Tn5 and nextera library prep

treatment_protocol: Combined knockdown of GRHL1-3 was performed using a mix of the ON-TARGETplus GRHL1-3 siRNA SMARTpools (Dharmacon) at a final concentration of 50nM for each pool in opti-MEM medium (ThermoFisher Scientific). Omni-ATAC was performed after 48 hours.

value: MCF7 cell line

value: Collected from plate


title: Optix_GFP_Pos_Cell_15


title: Optix_GFP_Pos_Cell_6


title: Optix_GFP_Pos_Cell_14


title: Optix_GFP_Pos_Cell_4


title: Optix_GFP_Pos_Cell_12


title: NSC3 -undifferentiated

city: Cincinnati

first: Nurit

middle: Pereg

last: Azouz

state: Oh

address: 240 Albert Sabin Way

department: Allergy and Immunology

institute: Cincinnati Childrens Hospital Medical center

data_processing:
Data analysis was performed using the BioWardrobe (PMID: 26248465 )
Briefly, reads were mapped to the hg19 genome and RefSeq-based transcriptome using RNA-STAR (v. 2.4.2a and assigned to the RefSeq genes  using the BioWardrobe algorithm.
For ChIP-Seq, reads were mapped using BowTie and islands were identified using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: csv file includes RPKM values for each sample

source_name: NSC-undifferentiated

growth_protocol: Esophageal epithelial cell line (human telomerase reverse transcriptase–immortalized EPC2 cell line were grown at keratinocyte serum-free media containing epidermal growth factor (EGF; 1 ng/mL), bovine pituitary extract (50ug/mL), and 1X penicillin/streptomycin (Invitrogen, Carlsbad CA USA) Samples 1-9. RNA was collected from samples 7-9. Cells were seeded (day 0) and grown to confluence while fully submerged in low-calcium (CaCl2 0.09 mM) KSFM on 0.4-mm pore-size permeable supports (Corning Incorporated, Corning, NY). Confluent monolayers (day 2) were then switched to high-calcium (CaCl2 1.8 mM) KSFM for an additional 5 days. To induce epithelial stratification and differentiation, the culture medium was removed from the inner chamber of the permeable support to expose the cell monolayer to the air interface (day 7). Cells were harvested and RNA was collected at day 14 for samples 1-6.

extract_protocol:
Total RNA was isolated from cells with the RNeasy mini kit (Qiagen. Valencia, CA, USA) according to the manufacturer’s protocol. RNA was treated with On-Column DNase Digestion kit (Qiagen) according to the supplied protocol.
polyA stranded RNA-seq from total RNA

treatment_protocol: EPC2 cells were seeded (day 0) and grown to confluence while fully submerged in low-calcium (CaCl2 0.09 mM) KSFM on 0.4-mm pore-size permeable supports (Corning Incorporated, Corning, NY). Confluent monolayers (day 2) were then switched to high-calcium (CaCl2 1.8 mM) KSFM for an additional 5 days. To induce epithelial stratification and differentiation, the culture medium was removed from the inner chamber of the permeable support to expose the cell monolayer to the air interface (day 7). Differentiated esophageal epithelial equivalents were analyzed at day 14.

tag: cell line

value: Esophageal epithelial cells

tag: cell subtype

value: non-silencing control (NSC); undifferentiated EPC2 monolayer

tag: biowardrobe id


title: NSC1 -undifferentiated


title: CD34_neg_input_ChIPseq

city: Monterrey

first: Raquel

last: Cuevas Diaz Duran

address: Av Morones Prieto No. 3000, Colonia Los Doctores

department: Escuela de Medicina y Ciencias de la Salud

country: Mexico

institute: Tecnologico de Monterrey

data_processing:
Basecalling was performed with CASAVA v1.7 from Illumina
The 50-bp single-end ChIP-seq reads were aligned to the mouse reference genome mm10 using Bowtie2 with default parameters.
Peaks were called using MACS1.4 and filtered according to ENCODE's blacklist (https://sites.google.com/site/anshulkundaje/projects/blacklists), FDR <0.05, and fold-enrichment >10
Filtered peaks were annotated to the RefSeq mm10 annotation file using annotatePeaks.pl function in Homer
ATAC-seq paired-end reads were mapped to the mm10 reference genome using the Bowtie2 aligner with –X2000 for the alignment of fragments up to 2 kb in size, and with –k 4 to allow up to 4 multi-alignments.
Reads were filtered to remove unmapped reads, reads with unmapped mates, reads that are not primary alignments, low quality reads (MAPQ <30), mitochondrial mapping reads, and PCR duplicates using SAMtools and Picard Tools. Remaining reads were offset by +4 and -5 for positive and negative strands, respectively.
We used MACS2 for peak calling with parameters “-p 0.01 --nomodel –-shift 37 --extsize 73 --broad --keep-dup all". We generated larger enrichment regions known as “broadPeaks” and “gappedPeaks”. To obtain punctate peaks (“narrowPeaks”) we used MACS2 with parameters “-p 0.01 --nomodel –-shift 37 --extsize 73 –B --SMPR --keep-dup all --call-summits”.
The resulting narrow, gapped, and broad peaks were filtered using ENCODE’s blacklist and annotated to the mm10 reference genome.
Genome_build: mm10
Supplementary_files_format_and_content: AnnotatedPeaks

source_name: EML cell line

growth_protocol: EML cells were cultured in suspension in EML basic medium containing BHK cell culture medium at 37 °C, 5% CO2 in a cell culture incubator. The EML cells were maintained at low cell density (0.5–5 x 10^5 cells/ml) and the cultures were split every 2-3 days at the ratio of 1:5.

extract_protocol:
A total of 107 cells were used per ChIP experiment. Cells were cross-linked in 1% formaldehyde for 10 min at RT with rotation followed by addition of 0.125 M glycine to quench the cross-linking reaction. Cells were pelleted and washed twice with ice-cold PBS. Nuclei were isolated using nuclei lysis buffer and chromatin DNA was then sheared using a Bioruptor® sonicator (Diagenode). A sample of 1/100 volume of the sheared DNA was reserved for use as the input control sample. ChIP antibodies (SOX4, STAT3, and GABPα) or normal rabbit IgG were added to Dynabeads Protein A (Invitrogen) beads and incubated for 4 h at 4 °C with rotation. The Dynabeads-antibody complexes were then incubated with the sheared chromatin DNA overnight at 4 °C. After immunoprecipitation, RNase A and Proteinase K were added to the precipitated complex and the samples were incubated at 65 °C overnight with shaking to reverse the crosslinks. For ATAC-Seq, 50,000 cells separated by FACS were spun down and washed with cold PBS and then 50 μl of cold lysis buffer was added to the cell pellet. The Nextera DNA Library Prep Kit (Illumina) was used for the transposition reaction. The transposed DNA was purified using a Qiagen PCR Purification Kit (Qiagen). Purified DNA fragments were then amplified using NEBNext High-Fidelity PCR Master Mix (New England Biolabs). qPCR was performed to determine the appropriate number of additional PCR cycles, allowing us to stop amplification prior to saturation. A total of 10^5 cells were used for ATAC-Seq experiment. Cells were separated using MACS and FACS.
The ChIP-Seq libraries were prepared using the DNA SMART ChIP-Seq Kit (Clontech Laboratories) according to the manufacturer's instructions.  ATAC-Seq library was prepared following a published protocol (PMID:25559105). Libraries were quantified using the KAPA Library Quant Kit for Illumina Sequencing Platforms (KAPA BIosystems). All sequencing libraries were sequenced on an Illumina HiSeq 2000 Sequencer.

treatment_protocol: CD34+ and CD34- populations were separated using magnetic-activated cell sorting (MACS) and fluorescence-activated cell sorting (FACS)

tag: strain

value: IgG (Santa Cruz, sc-2027, lot k0507)


title: SPINK7_3

value: SPINK7 gene silencing (SPINK7); differentiated EPC2 cells


title: Optix_GFP_Pos_Cell_1

value: FACS sorting

value: eye progenitor cells


title: CD34_pos_ATACseq


title: CD34_neg_GABPa_ChIPseq

value: GABPa (Santa Cruz, sc-22810x, lot c2912)


title: CD34_pos_input_ChIPseq


title: SPINK7_2


title: exo2_2_NET_Seq_IN


title: SPINK7_1


title: grh-GFP_anti-GFP_EA2_ChIPmentation

data_processing:
Cleaning (fastq-mcf)
Mapping to the dm3 genome using bowtie2
peaks were called for each sample using macs2 callpeak with parameter -g dm (-nomodel for ATAC-seq) -keep-dup all -call-summits
Peaks were merged across the samples and the number of reads for each sample for every peak were obtained using featureCounts
The counts matrix was library size normailsed using R DESeq2
Genome_build: Drosophila melanogaster FlyBase version 5.13
Supplementary_files_format_and_content: raw_counts_matrix_30_ATAC_DGRP counts for all 30k accessible regions

source_name: eye-antennal discs

extract_protocol:
Head complexes were dissected from 3rd instar wandering larvae. After fixation the eye-antennal imaginal discs were disscested and the ChIPmentation protocol was applied.
Manga ChIP kit (upstate Milipore) Tn5 and nextera library prep

tag: antibody

value: anti-GFP Ab (ab290, Abcam)


title: NSC3

source_name: NSC

tag: cell type

value: non-silencing control (NSC); differentiated EPC2 cells


title: CD34_pos_STAT3_ChIPseq

value: STAT3 (Santa Cruz, sc-482x, lot B0615)


title: grh-GFP_anti-GFP_EA1_ChIPmentation

tag: age


title: dpse_Jul_2_ATAC

data_processing:
Cleaning (fastq-mcf)
Mapping to their respective genomes using bowtie2
peaks were called for each sample using macs2 callpeak with parameter -g dm --nomodel
Genome_build: dana-all-chromosome-r1.3; dere-all-chromosome-r1.3; dmel-all-chromosome-r6.02; dmoj-all-chromosome-r1.3; dper-all-chromosome-r1.3; dpse-all-chromosome-r3.1; dsec-all-chromosome-r1.3; dsim-all-chromosome-r1.4; dvir-all-chromosome-r1.2; dwil-all-chromosome-r1.3; dyak-all-chromosome-r1.3
Supplementary_files_format_and_content: BigWigs for all ATAC-samples

source_name: D. Pseudoobscura_eye-antennal discs

extract_protocol:
Eye-antennal imaginal Disc were dissected from 3rd instar wandering larvae. The discs were immediately lysed and ATAC-seq was performed
Tn5 and nextera library prep

value: Drosophila Pseudoobscura

tag: tissue

value: eye-antennal discs


title: dpse_Jul_1_ATAC

value: 3rd instar-wandering


title: Optix_GFP_Pos_Cell_5


title: NSC2 -undifferentiated


title: NSC2


title: NSC1


title: Optix_GFP_Pos_Cell_3


title: Optix_GFP_positive2_ATAC


title: Optix_GFP_positive1_ATAC


title: dere_Jul_2_ATAC

organism: Drosophila erecta

source_name: D. Erecta_eye-antennal discs

value: Drosophila Erecta


title: Optix_GFP_Pos_Cell_2

value: Hand Dissections


title: E21-2

city: Harbin

first: Zhi-Qiang

last: Du

address: 59 Mucai Street, XiangFang District

institute: Northeast Agricultural University

data_processing:
Short reads were generated on the Illumina platform.
Clean reads were generated by removing low quality and adaptor sequence containing reads.
Clean reads were aligned to the Galgal4 genome assembly using BWA with default configurations.
After performing the assessment of sequence saturation and read distribution on reference genes, the expression levels of each gene were calculated as FPKM using the number of reads uniquely mapped to the specific gene and the total number of uniquely mapped reads in the sample.
Genes and isoforms expression level are quantified
Genome_build: Galgal4
Supplementary_files_format_and_content: txt format, containing gene expression levels

organism: Gallus gallus

source_name: chicken liver at embryonic day 21 of the fat line

growth_protocol: chicken eggs were incubated for embryos

extract_protocol:
liver samples of chicken embryos were taken
libraries for digital gene expression were constructed

treatment_protocol: embryos from the fat and lean chicken lines were used

value: liver

tag: developmental stage

tag: chicken line

value: fat


title: Optix_GFP_negative2_ATAC


title: E21-1

source_name: chicken liver at embryonic day 21 of the lean line

value: lean


title: grh-GFP_anti-GFP_Wing_ChIPmentation

source_name: wing discs


title: Optix_GFP_negative1_ATAC


title: dere_Jul_1_ATAC

tag: genotype/species


title: E17-2

source_name: chicken liver at embryonic day 17 of the fat line


title: DGRP_29652.IR_ATAC

tag: genotype


title: E14-2

source_name: chicken liver at embryonic day 14 of the fat line


title: Omni_ATAC_MCF-7_NTC

value: MCF7 cell line

value: Collected from plate


title: E12-2

source_name: chicken liver at embryonic day 12 of the fat line


title: CD34_pos_SOX4_ChIPseq

tag: chip antibody

value: SOX4 (Santa Cruz, sc-17326x, lot D2012)


title: DGRP_28262.IR_ATAC


title: DGRP_28275.IR_ATAC


title: DGRP_28265.IR_ATAC


title: E7-1

source_name: chicken liver at embryonic day 7 of the lean line


title: DGRP_28202.IR_ATAC


title: dmel_CS_May_ATAC

source_name: D. Melanogaster_eye-antennal discs

value: Drosophila Melanogaster


title: E7-2

source_name: chicken liver at embryonic day 7 of the fat line


title: DGRP_28123.IR_ATAC


title: DGRP_28222.IR_ATAC


title: dmel_CS_June_ATAC


title: E17-1

source_name: chicken liver at embryonic day 17 of the lean line


title: DGRP_55031_ATAC


title: DGRP_25208.IR_ATAC


title: DGRP_28260.IR_ATAC


title: DGRP_25194.IR_ATAC


title: DGRP_25193.IR_ATAC


title: DGRP_29652_ATAC


title: DGRP_25186.IR_ATAC


title: E14-1

source_name: chicken liver at embryonic day 14 of the lean line


title: DGRP_29651_ATAC


title: DGRP_25185.IR_ATAC


title: E12-1

source_name: chicken liver at embryonic day 12 of the lean line


title: DGRP_28275_ATAC


title: DGRP_55026_ATAC


title: DGRP_55031.IR_ATAC


title: DGRP_28265_ATAC


title: pSA271_EA_ATAC

value: transgenic VK37(2L)22A3 insertion


title: DGRP_28262_ATAC


title: pSA271_wing_ATAC


title: DGRP_28243_ATAC


title: pSA270_wing_ATAC


title: pSA270_ATAC


title: DGRP_28206_ATAC


title: pSA269_EA_ATAC


title: DGRP_28224_ATAC


title: DGRP_28153_ATAC


title: pSA269_wing_ATAC


title: pSA268_wing_ATAC


title: DGRP_28123_ATAC


title: pSA268_EA_ATAC


title: DGRP_25174.IR_ATAC


title: DGRP_25199_ATAC


title: 30d_Pcl_Suz12_rep3_head

description: processed data file: WT_vs_Pcl_Suz12_head_DESeq.csv

source_name: fly head

value: head

value: 30 day


title: dvir_May_ATAC

organism: Drosophila virilis

source_name: D. Virilis_eye-antennal discs

value: Drosophila Virilis


title: DGRP_25208_ATAC

source_name: eye-antennal discs


title: 30d_WT_rep1_head


title: DGRP_25187_ATAC


title: 30d_Pcl_Suz12_rep1_head


title: 30d_WT_rep3_head


title: dvir_Jun_ATAC


title: DGRP_28260_ATAC


title: Gorilla_GON_CB

data_processing:
Raw reads of four species were aligned to the reference genomes (human, hg19; chimpanzee, panTro4; gorilla, gorGor3; gibbon, nomLeu1) by “STAR” (parameters: outFilterMultimapNmax = 1, outFilterMatchNminOverLread = 0.95, outFilterMismatchNoverLmax = 0.05, outFilterIntronMotifs = RemoveNoncanonical).
PCR duplicates removal was then conducted using SAMtools and only uniquely mapped reads were considered as validity to avoid the estimation ambiguity.
We obtained chimpanzee, gorilla and gibbon orthologs of human genes (GENCODE v19) by reciprocal liftOver requiring the same exon orders and no less than 50% exons preserved.
Based on the annotations, numbers of reads were counted per gene per sample using htseq-count within HTSeq. Only genes with counts greater than 0 in all four species in at least one brain region were used in the following analysis
We took advantage of the median ratio method implemented in DESeq2 to normalize the gene abundance data for further comparisons across species and brain regions.
Genome_build: human, hg19; chimpanzee, panTro4; gorilla, gorGor3; gibbon, nomLeu1
Supplementary_files_format_and_content: tab-delimited text files include raw count, normalized count, and RPKM for each sample

source_name: cerebellum

extract_protocol:
Brain dissection was performed from either fresh specimens or frozen tissue slabs by the same person to ensure sampling consistency between specimens. About 100 mg of dissected tissues were used and total RNA were extracted using RNeasy Plus Universal Kit (Qiagen). Quality and quantity measurements of extracted RNA were performed using NanoDrop (Thermo Fisher Scientific) and Qubit Fluorometer (Thermo Fisher Scientific), respectively, and the RNA Integrity Number (RIN) were determined using Bioanalyzer RNA 6000 Nano Kit (Agilent).
Sequencing libraries were prepared using the NEBNext mRNA Library Prep Kit for non-directional libraries and the NEBNext Ultra Directional RNA Library Prep Kit for directional libraries (New England BioLabs) according to the manufacturer’s instructions.

tag: individual id

value: GON

tag: age (year)

tag: Sex

value: male

tag: rin

tag: processing date


title: Pcl_Su(z)12_RNASeq_rep3

source_name: fly muscle

value: muscle


title: Gibbon_DAICHI_HIP

organism: Hylobates lar

source_name: hippocampus

value: DAICHI


title: dsim_May_ATAC

organism: Drosophila simulans

source_name: D. Simulans_eye-antennal discs

value: Drosophila Simulans

value: 3rd instar-wandering

tag: treatment

value: eye-antennal discs


title: Gorilla_GON_HIP


title: Gorilla_GON_STR

source_name: striatum


title: dsim_Jun_ATAC

value: Hand Dissections


title: Pcl_Su(z)12_RNASeq_rep1


title: 30d_WT_RNASeq_rep3


title: Pcl_Su(z)12_RNASeq_rep2


title: Gibbon_DAICHI_STR


title: 30d_WT_RNASeq_rep2


title: Gibbon_DAICHI_CB


title: 30d_Pcl_Suz12_rep2_head


title: Gorilla_GON_ACC

source_name: anterior cingulate cortex


title: Gibbon_DAICHI_ACC


title: Gorilla_GON_V1C

source_name: primary visual cortex


title: 30d_WT_rep2_head


title: 30d_WT_RNASeq_rep1


title: Gibbon_DAICHI_V1C


title: Gorilla_GON_PMC

source_name: premotor cortex


title: dsec_Jul_2_ATAC

organism: Drosophila sechellia

source_name: D. Sechellia_eye-antennal discs

value: Drosophila Sechellia


title: 3d_WT_RNASeq_rep2

value: 3 day


title: dsec_Jul_1_ATAC


title: dper_Jul_2_ATAC

organism: Drosophila persimilis

source_name: D. Persimilis_eye-antennal discs

value: Drosophila Persimilis


title: Gibbon_DAICHI_VPFC

source_name: ventrolateral prefrontal cortex


title: Gorilla_GON_DPFC

source_name: dorsolateral prefrontal cortex


title: Gibbon_DAICHI_PMC


title: 3d_WT_RNASeq_rep3


title: 3d_WT_RNASeq_rep1


title: Gibbon_DAICHI_DPFC


title: Rec1 GSI rep1 MYCP

status: Public on Jun 03 2018

city: Ann Arbor

first: Russell

middle: James Hubbard

last: Ryan

state: MI

address: 4306 Rogel Cancer Center, 1500 E Medical Center Dr.

department: Pathology

institute: University of Michigan Medical School

data_processing:
Library strategy: 4C-Seq
There is no single accepted processed  format for 4C-Seq, so we are providing the raw sequencing data only.
Genome_build: hg19

organism: Homo sapiens

source_name: Rec-1 cell line

extract_protocol:
Cells were crosslinked with 2% formaldehyde in PBS at room temperature for 10 minutes, followed by glycine quenching, washing in PBS, isolation of nuclei by hypotonic buffer lysis, and resuspension in primary restriction enzyme buffer. Primary digestion was accomplished by sequential addition of SDS, Triton-X100, and primary restriction enzyme while mixing at 37°C, followed by heat inactivation at 65°C. Ligation was performed after sample dilution in T4 ligase buffer by addition of T4 ligase at 16°C. Ligated DNA was isolated by proteinase K and RNAase A digestion, phenol-chloroform extraction, and ethanol precipitation. DNA was then digested with secondary restriction enzyme, heat inactivated, ligated with T4 ligase, and isolated by ethanol precipitation and QIAquick PCR purification columns.
To generate each 4C-Seq library, a total of 3.2 micrograms of 4C DNA was amplified across 16 separate 50-microliter PCR reactions containing Q5 high-fidelity polymerase mix (NEB) and oligonucleotides pairs consisting of universal illumina adaptor sequences, sample-specific barcodes, and viewpoint-specific primer sequences. Equal portions of each reaction were pooled and the PCR-amplified library was purified with 0.8 volumes of Ampure XP per volume of PCR product.

tag: cell line

value: Mantle cell lymphoma cell line

tag: drug treatment

value: GSI:Grown for 72 h in media containing Compound E (1μM)

tag: data type

tag: 4c-seq primary enzyme

value: NlaIII

tag: 4c-seq secondary enzyme

value: DpnII

tag: 4c-seq viewpoint primer 1 (reading)

value: AGCTGCTGGGAGGAGACATG

tag: 4c-seq viewpoint primer 2 (non-reading)

value: CCACGTCCTAACACCTCTAG


title: Rec1 GSI rep2 MYCP

tag: cell type


title: Rec1 GSI rep1 BNDME2

value: GAAGTAATAATGCCTGCATG

value: TATGTAAGGAACCACACAGAGA


title: Rec1 DMSO rep2 BNDME2

value: DMSO:Grown for 72 h in media containing vehicle (DMSO) only


title: Rec1 GSI rep1 BNDME1

value: AAAGAATGAGTGTGGCCATG

value: AGTTCAGGTATGCAAAGTGG


title: Rec1 GSI rep2 BNDME2