title: 200078650237_R02C01


title: 200078650232_R03C02

status: Public on Feb 17 2020

type: genomic

city: Brisbane

first: Jacob

last: Gratten

address: 37 Kent Street

department: Mater Research Institute

country: Australia

institute: University of Queensland

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Genome Studio using standard recommended Illumina scanner setting

data_processing: Genome Studio software

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from SGPD samples using ??? according to standard instructions

tag: gender

value: Male

tag: disease-state

value: Parkinson's disease

tag: tissue

value: whole blood


title: 200078650232_R03C01


title: 200078650232_R04C01

value: Control


title: 200078650224_R05C02

value: Female


title: 200078650224_R06C02


title: 200078650232_R06C02


title: 200078650237_R03C01


title: 200078650237_R01C01


title: 200078650232_R01C01


title: F6281.CL1

status: Public on Feb 18 2020

type: SRA

city: São Paulo

first: Karina

middle: Griesi

last: Oliveira

state: SP

address: Rua Brentano, 292, Ap. 61

country: Brazil

institute: Hospital Albert Einstein

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 genome using TopHat2 v2.0.11.
Read counts per gene were summarized using HTSeq
Genes with FPKM<1 in more than a half of the samples were excluded from the next steps
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq files (.out) contains the count numbers sumarized per gene

molecule: polyA RNA

source_name: mixed neuronal cells

growth_protocol: iPSC-derived NPC were cultured in NB media (DMEM/F12, N2 and B27 supplement) with 20ng/ml of FGF and EGF and replated/expanded every 2-3 days; for neuron generation, NPCs were plated in a low density and then cultured for 4 weeks with NB media with 1uM of retinoic acid

extract_protocol:
RNA was harvested using NucleoSpin RNA extraction kit (Macherey-Nagel). Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: iPSC-derived

tag: disease status

value: ASD

value: mixed neuronal cells


title: 200078650224_R04C02


title: 200078650224_R03C02


title: 200078650224_R02C02


title: 200078650224_R06C01


title: 200078650232_R01C02


title: PolII ChIP-Seq P0.5 replicate 2

city: Vassilika Vouton, Herakleion

first: Iannis

last: Talianidis

state: Crete

address: 100 N. Plastira Str

department: Institute of Molecular Biology and Biotechnology

country: Greece

institute: Foundation for Research and Technology - Hellas

library_source: genomic

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer as well as standard Illumina base callers (bcl2fastq).
The RNA-Seq FASTQ files were mapped on the UCSC mm9 reference genome using tophat2 , with default settings and using additional transcript annotation data for the mm9 genome from Illumina iGenomes (http://cufflinks.cbcb.umd.edu/igenomes.html). The ChIP-Seq FASTQ files were also mapped to the mm9 genome using bwa  with standard parameters. The resulting BAM files were visualized in the UCSC Genome Browser using bedtools  and tools provided by the UCSC Genome Browser toolkit. Prior to any alignment or further analysis, the quality all the FASTQ files and the reads contained therein was inspected with the FastQC package.
The raw bam files were summarized to an exon read counts table and the exon read counts were filtered for artifacts as follows: if an annotated gene had up to 5 exons, read presence was required in at least 2 of the exons, else if an annotated gene had more than 5 exons, then read presence was required in at least 0.2x⌈E⌉ exons, where ⌈.⌉ is the ceiling mathematical function. After exon filtering, the final read counts for each gene model were calculated as the sums of their exon reads, creating a gene counts table where each row corresponded to an Ensembl gene model and each column corresponded to an RNA-Seq sample. The gene counts table was normalized using the Bioconductor package DESeq after removing genes that had zero counts over all samples. Genes presenting any of the following were excluded from further analysis: i) genes with length less than 500, ii) genes whose average reads per 100 bp was less than the 25th quantile of the total normalized distribution of average reads per 100bp, iii) genes with read counts below the median read counts of the total normalized count distribution. The resulting gene counts table was subjected to differential expression analysis using the Bioconductor package DESeq. Differentially expressed genes were identified with an FDR threshold of 0.05 and a fold change threshold of -1 and 1 (log2) scale for up and down regulated genes respectively. All the analyses and reporting  were performed within the Bioconductor package metaseqR.  For the transcription factor data (CEBPα, HNF4α), the two biological replicates for each developmental stage and their respective DNA input samples were subjected to peak calling using MACS 1.4  with the default settings for mouse genome. Prior to peak calling and in order to compensate for differences in library sizes between ChIP and Input DNA sequencing samples, the total number of reads of each sample was equalized by uniformly downsampling reads relatively to the sample with the lower number of reads. The putative binding sites returned by MACS were further filtered for artifacts by i) imposing an additional MACS FDR threshold of 0.1%, ii) excluding peaks demonstrating a fold enrichment less than 1 in log2 scale (where fold enrichment is the ratio of reads under a peak area in the ChIP sample to the respective number of reads in the Input DNA sample).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited files containing DESeq normalized counts for each Ensembl gene for RNA-Seq data. BED files with peak coordinates for ChIP-Seq data. BigWig signal files for ChIP-Seq data.

organism: Mus musculus

source_name: PolII ChIP-Seq P0.5

growth_protocol: Mice were maintained in grouped cages in a temperature-controlled, pathogen-free facility on a 12-hr light/dark cycle and fed by a standard chow diet (Altromin 1324; 19% protein, 5% fat) or High Fat Diet (34% crude Fat, 23% crude Protein, 5% crude fiber by Mucedola s.r.l.) and water ad libitum. All animal experiments were approved by the Prefecture of Attica and were performed in accordance with the respective national and European Union regulations. All the experiments were performed in randomly chosen age-matched male mice. No blinding was used in this study.

extract_protocol:
RNA preparation: Total RNA was prepared by homogenizing liver pieces in 10 volumes of Trizol reagent followed by the addition of 2 volumes of chlorophorm and centrifugation at 12000 g for 15 minutes. The aqueous phases were precipitated with isopropanol. Following resuspension in water RNAs were subjected to additional precipitation with ethanol. The RNA samples were digested with 10 units of DNase I for 10 min at 37 0C, followed by purification with phenol/chlorophorm extraction and ethanol precipitation. Chromatin immunoprecipitation: Liver tissue was minced to small pieces in PBS and after addition of formaldehyde to a 1% final concentration immediately was subjected to 10 strokes of dounce homogenization. Cross-linking was continued for 10 min and stopped by the addition of glycine at 0.125 M final concentration. Cross-linked cells were treated with a buffer containing 50 mM HEPES pH 7.5, 0.14 M NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40 and 0.25% Triton-X100, for 10 minutes and then with a buffer containing 0.2 M NaCl, 1 mM EDTA, 0.5 mM EGTA and 10 mM Tris-HCl pH 8.0 for 5 minutes. The nuclei were resuspended up to 4 ml with sonication buffer containing 10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate and 0.5% N-lauroylsarcosine and sonicated for 12 minutes in Covaris Sonicator instrument. After sonication, samples were supplemented with 400 μl of 10% Triton X-100 and centrifuged for 10 minutes at 20.000 rcf. After centrifugation, the extracted chromatin was incubated overnight with Dynabeads Protein G, that were prebound by 10 ug of the respective antibodies. The beads were washed six times with a buffer containing 50 mM Hepes pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, and 0.7% Na-deoxycholate, and then once with a buffer containing 20 mM Tris-HCl pH 7.6 and 150 mM NaCl. Immunoprecipitated chromatin was eluted from the beads and reverse crosslinked by overnight incubation with a buffer containing 50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1 % SDS, at 65 0C. Following incubation, samples were diluted by addition of one volume of TE. RNAs and proteins were removed by incubation with 20 ug/ml RNAse A for 30 minutes at 37 C, followed by incubation with 20 ug/ml Proteinase-K for 2 hours at 55 0C. DNA was extracted by phenol/chlorophorm and precipitated with ethanol. About 10 ng of the immunoprecipitated DNA and input DNA was used for library preparation.
Libraries were prepared using TruSeq or NEBNext Adaptors, depending on whether less or more than 6 indexes were included. In all cases, 25 μl of immunoprecipitated DNA was purified using the MinElute columns (Qiagen, 28604) and eluted with 10 ul elution buffer. The concentration of the eluted DNA was measured in Qubit using the dsDNA HS Assay Kit (Invitrogen Q32851). Subsequently, ten ng of ChIP or input DNA were subject to end repair, in a mix containing T4 DNA polymerase (NEB M0203L), Klenow fragment (NEB M0210L), T4 DNA PNK (NEB M0201L) and dNTPs in T4 DNA Ligase Buffer (NEB, B02025) at 20 °C for 30 min. Following end repair, samples were purified using the Agentcourt AMPURE XP system (Agentcourt A63881) and subject to A addition by incubation with dATP and Klenow 3’-->5’ exo- 37 °C for 30 min. Another AMPURE XP purification was performed and then Truseq or NEBNext adaptors were ligated using Quick Ligase in Quick Ligase Buffer. Following adaptor ligation, samples were incubated with 1.5 ul USER enzyme at 37 °C for 15 minutes, to cleave the adaptor hairpin loop. Purification and size selection was performed again by AMPURE XP and PCR amplification was performed using Truseq or NEBnext Primers in Kapa Hifi Hotstart mix. A final purification was performed and libraries were ready for Bioanalyzer assessment and sequencing.

treatment_protocol: The mice were not treated.

tag: strain

value: F1 mice (C57Bl6/CBA)

tag: age

value: 0.5 days postnatal

tag: genotype

value: Wild type

value: liver

tag: chip antibody

value: RNA-Pol-II

tag: chip antibody vendor

value: Euromedex

tag: chip antibody cat. #

tag: chip antibody lot #


title: 200078650232_R02C01


title: 200078650224_R04C01


title: 200078650224_R05C01


title: 200078650237_R04C01


title: 200078650224_R03C01


title: 200078650237_R05C01


title: 200078650187_R06C02


title: 200078650224_R01C01


title: 200078650187_R04C02


title: 200078650187_R04C01


title: 200078650187_R02C02


title: 200078650224_R01C02


title: 200078650159_R06C02


title: 200078650187_R03C02


title: 200078650187_R06C01


title: 200078650187_R01C02


title: 200078650187_R01C01


title: 200078650187_R02C01


title: 200078650187_R03C01


title: 200078650159_R01C02


title: 200078650159_R03C02


title: 200078650159_R04C02


title: 200078650159_R05C02


title: 200078650159_R06C01


title: 200078650159_R05C01


title: 200078650159_R04C01


title: 200078650159_R03C01


title: 200078650224_R02C01


title: 200078650159_R02C01


title: 200078650129_R05C02


title: 200078650129_R04C02


title: 200078650129_R06C02


title: 200078650129_R01C02


title: 200078650187_R05C01


title: 200078650129_R03C02


title: 200078650129_R01C01


title: 200078650129_R04C01


title: 200078650129_R06C01


title: 200078650123_R05C02


title: 200078650123_R06C02


title: 200078650129_R03C01


title: 200078650123_R05C01


title: 200078650123_R04C02


title: 200078650123_R01C02


title: 200078650123_R03C02


title: 200078650123_R02C01


title: 200078650123_R04C01


title: 200078650123_R03C01


title: 200078650129_R02C01


title: 200078650123_R06C01


title: 200078650123_R01C01


title: 200078650112_R06C02


title: 200078650159_R01C01


title: sh_417587_S14

city: Lausanne

first: Delphine

last: Grun

address: route Cantonale

country: Switzerland

institute: EPFL

description: organoids (KD)

data_processing:
hisat2 -k 5 --rna-strandness RF --seed 42 -p 7 -x
featureCounts -p -s 2 -T 4 -t exon -g gene_id -Q 10 -a
Genome_build: hg19
Supplementary_files_format_and_content: The .txt.gz.gz files contain read counts on genes

molecule: total RNA

source_name: brain organoids

growth_protocol: STEMdiff™ Cerebral Organoid Kit - STEMCELL Technologies #08570

extract_protocol:
TruSeq stranded mRNA sample preparation kit (Illumina)
High pure RNA isolation kit (Roche)
As recommended by illumina (TruSeq stranded mRNA sample preparation kit)

treatment_protocol: transduced cells were puromycin selected

tag: culture

tag: shRNA

value: KZFPs


title: 200078650112_R01C02


title: 200078650112_R04C02


title: 200078650112_R05C02


title: 200078650129_R05C01


title: 200078650112_R06C01


title: 200078650112_R02C02


title: 200078650112_R04C01


title: 200078650112_R03C01


title: 200078650112_R02C01


title: 200078650109_R03C02


title: 200078650109_R02C02


title: 200078650112_R05C01


title: 200078650109_R06C02


title: 200078650123_R02C02


title: 200078650109_R06C01


title: 200078650109_R01C02


title: 200078650109_R04C01


title: 200078650109_R05C01


title: 200078650089_R06C02


title: 200078650109_R02C01


title: 200078650089_R02C02


title: 200078650109_R01C01


title: 200078650089_R04C02


title: 200078650089_R05C02


title: 200078650089_R01C02


title: 200078650089_R06C01


title: 200078650089_R05C01


title: 200078650089_R04C01


title: 200078650064_R06C02


title: 200078650109_R05C02


title: 200078650064_R02C02


title: 200078650089_R03C01


title: 200078650064_R05C02


title: 200078650089_R01C01


title: 200078650064_R05C01


title: 200078650064_R06C01


title: 200078650064_R03C02


title: 200078650064_R03C01


title: 200078650051_R06C02


title: 200078650051_R05C02


title: 200078650064_R01C02


title: 200078650051_R04C02


title: 200078650109_R03C01


title: 200078650051_R04C01


title: 200078650051_R03C01


title: 200078650049_R06C02


title: 200078650051_R02C01


title: 200078650051_R02C02


title: 200078650049_R05C02


title: 200078650051_R01C01


title: 200078650051_R03C02


title: 200078650049_R05C01


title: 200078650049_R04C01


title: 200078650049_R01C02


title: 200078650049_R02C01


title: 200078650041_R06C02


title: 200078650064_R02C01


title: 200078650049_R03C01


title: 200078650041_R05C02


title: 200078650041_R02C02


title: 200078650064_R04C01


title: 200078650041_R01C02


title: 200078650041_R03C02


title: 200078650041_R04C02


title: 200078650041_R04C01


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title: 200078650051_R05C01


title: 200090280042_R01C02


title: 200090280042_R04C02


title: 200090280042_R02C02


title: 200078650049_R04C02


title: 200090280042_R05C02


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title: 200090280040_R05C02


title: 200090280040_R02C02


title: 200090280040_R06C01


title: 200090280040_R01C02


title: 200090280040_R05C01


title: 200090280040_R06C02


title: 200090280040_R03C01


title: 200090280040_R03C02


title: 200090280040_R02C01


title: 200090280040_R04C01


title: 200078650041_R01C01


title: 200090280040_R01C01


title: 200090280029_R05C02


title: 200090280029_R03C02


title: 200090280029_R04C01


title: 200090280029_R05C01


title: 200090280029_R06C01


title: 200090280029_R01C01


title: 200090280029_R03C01


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title: 200090270021_R04C01


title: 200090270021_R01C01


title: 200078650246_R03C02


title: 200078650246_R06C02


title: 200078650246_R04C02


title: 200090280029_R01C02


title: 200090280029_R06C02


title: 200090270021_R02C01


title: 200078650246_R05C02


title: 200078650246_R05C01


title: 200078650246_R06C01


title: 200078650246_R01C02


title: 200078650246_R02C02


title: 200090280029_R02C02


title: 200078650189_R03C02


title: 200078650189_R06C02


title: 200078650189_R05C02


title: 200078650246_R02C01


title: 200078650246_R01C01


title: 200078650246_R03C01


title: 200090270021_R03C02


title: 200078650189_R02C02


title: 200078650189_R05C01


title: 200078650189_R01C02


title: 200078650189_R06C01


title: 200090280029_R02C01


title: 200078650189_R03C01


title: 200078650189_R01C01


title: 200078650189_R02C01


title: 200078650118_R06C02


title: 200078650118_R01C02


title: 200078650118_R04C02


title: 200078650118_R05C02


title: 200078650118_R04C01


title: 200078650118_R06C01


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title: 200078650001_R05C02


title: 200078650118_R02C01


title: 200078650001_R03C01


title: 200078650001_R04C01


title: 200078650001_R01C02


title: 200078650001_R02C01


title: 200078650001_R06C01


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title: 200078650246_R04C01


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title: 200078650231_R04C02


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title: 200078650210_R03C01


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title: 200078650188_R02C01


title: 200078650194_R05C01


title: 200078650194_R03C01


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title: 200078650206_R01C02


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title: 200078650152_R06C01


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title: 3998888176_R03C02


title: 3998888176_R01C02


title: 3998888176_R05C01


title: 3998888176_R02C02


title: 3998888176_R03C01


title: 3998888176_R06C01


title: 3998888176_R04C01


title: 101070190002_R04C02


title: 3998888176_R02C01


title: 101070190002_R03C02


title: 3998888176_R01C01


title: 3998888069_R06C01


title: 101070190002_R02C02


title: 3998888087_R02C02


title: 3998888087_R04C02


title: 3998888087_R03C02


title: 3998888087_R06C02


title: 3998888087_R06C01


title: 3998888087_R01C02


title: 3998888087_R05C01


title: 3998888087_R03C01


title: 3998888087_R04C01


title: 3998888087_R02C01


title: 3998888087_R01C01


title: 3998888086_R03C02


title: 3998888086_R06C02


title: 3998888086_R06C01


title: 3998888086_R05C01


title: 3998888087_R05C02


title: 3998888086_R04C01


title: 3998888086_R02C01


title: 3998888086_R03C01


title: 3998888086_R01C01


title: 3998888083_R06C02


title: 3998888083_R04C02


title: 3998888083_R05C02


title: 3998888083_R02C02


title: 3998888083_R06C01


title: 3998888083_R01C02


title: 3998888083_R05C01


title: 3998888083_R04C01


title: 3998888023_R04C01


title: 3998888083_R02C01


title: 3998888083_R01C01


title: 3998888081_R06C02


title: 3998888081_R05C02


title: 3998888086_R05C02


title: 3998888081_R04C02


title: 3998888081_R03C02


title: 3998888086_R02C02


title: 3998888081_R01C02


title: 3998888086_R01C02


title: 3998888081_R05C01


title: 3998888081_R04C01


title: 3998888081_R06C01


title: 3998888081_R01C01


title: 3998888081_R02C01


title: 3998888080_R06C02


title: 3998888083_R03C02


title: 3998888065_R04C01


title: 3998888080_R05C02


title: 3998888080_R03C02


title: 3998888083_R03C01


title: 3998888080_R06C01


title: 3998888080_R05C01


title: 3998888080_R02C02


title: 3998888080_R01C02


title: 3998888080_R04C01


title: 3998888080_R01C01


title: 3998888071_R06C02


title: 3998888080_R02C01


title: 3998888081_R02C02


title: 3998888071_R05C02


title: 3998888080_R03C01


title: 3998888071_R04C02


title: 3998888071_R03C02


title: 3998888071_R05C01


title: 3998888071_R06C01


title: 3998888071_R04C01


title: 3998888081_R03C01


title: 3998888071_R03C01


title: 3998888071_R02C01


title: 3998888071_R01C01


title: 3998888068_R04C02


title: 3998888080_R04C02


title: 3998888068_R05C02


title: 3998888068_R06C02


title: 3998888068_R03C02


title: 3998888068_R01C02


title: 3998888068_R06C01


title: 3998888068_R05C01


title: 3998888068_R03C01


title: 3998888068_R02C01


title: 3998888061_R06C02


title: 3998888068_R01C01


title: 3998888061_R04C02


title: 3998888061_R05C02


title: 3998888071_R01C02


title: 3998888068_R04C01


title: 3998888061_R02C02


title: 3998888061_R01C02


title: 3998888061_R05C01


title: 3998888061_R06C01


title: 3998888061_R01C01


title: 3998888061_R02C01


title: 3998888061_R03C01


title: 3998888061_R04C01


title: 3998888059_R05C02


title: 3998888059_R04C02


title: 3998888059_R06C02


title: 3998888059_R02C02


title: 3998888068_R02C02


title: 3998888059_R01C02


title: 3998888059_R06C01


title: 3998888059_R05C01


title: 3998888059_R02C01


title: 3998888059_R01C01


title: 3998888059_R04C01


title: 3998888061_R03C02


title: 3998888045_R05C02


title: 3998888045_R03C02


title: 3998888045_R06C02


title: 3998888045_R02C02


title: 3998888045_R01C02


title: 3998888045_R06C01


title: 3998888045_R03C01


title: 3998888045_R01C01


title: 3998888042_R04C02


title: 3998888042_R05C02


title: 3998888045_R02C01


title: 3998888042_R03C02


title: 3998888042_R06C01


title: 3998888042_R05C01


title: 3998888042_R02C02


title: 3998888042_R04C01


title: 3998888042_R01C01


title: 3998888042_R02C01


title: 3998888041_R02C02


title: 3998888041_R04C02


title: 3998888042_R03C01


title: 3998888041_R01C02


title: 3998888041_R05C02


title: 3998888045_R05C01


title: 3998888041_R06C02


title: 3998888041_R05C01


title: 3998888041_R01C01


title: 3998888024_R05C02


title: 3998888042_R06C02


title: 3998888041_R03C01


title: 3998888041_R04C01


title: 3998888041_R02C01


title: 3998888045_R04C01


title: 3998888024_R06C02


title: 3998888024_R02C02


title: 3998888024_R01C02


title: 3998888042_R01C02


title: 3998888024_R04C01


title: 3998888024_R05C01


title: 3998888024_R02C01


title: 3998888022_R06C02


title: 3998888022_R05C02


title: 3998888024_R01C01


title: 3998888022_R04C02


title: 3998888022_R06C01


title: 3998888022_R01C02


title: 3998888024_R06C01


title: 3998888022_R03C02


title: 3998888024_R04C02


title: 3998888022_R05C01


title: 3998888022_R04C01


title: 3998888022_R03C01


title: 3998888022_R02C01


title: 3998888024_R03C02


title: 3998888022_R01C01


title: 3998888008_R04C02


title: 3998888008_R05C02


title: 3998888008_R06C02


title: 3998888008_R02C02


title: 3998888008_R01C02


title: 3998888008_R06C01


title: 3998888008_R03C02


title: 3998888024_R03C01


title: 3998888008_R05C01


title: 3998888008_R01C01


title: 3998888008_R04C01


title: 3998888008_R03C01


title: 3998888180_R06C02


title: 3998888180_R05C02


title: 3998888180_R03C02


title: 3998888180_R02C02


title: 3998888180_R06C01


title: 3998888180_R04C01


title: 3998888180_R05C01


title: 3998888180_R01C02


title: 3998888180_R03C01


title: 3998888180_R02C01


title: 3998888180_R01C01


title: 3998888177_R06C02


title: 3998888008_R02C01


title: 3998888177_R03C02


title: 3998888177_R05C02


title: 3998888177_R02C02


title: 3998888177_R04C02


title: 3998888177_R01C02


title: 3998888177_R06C01


title: 3998888180_R04C02


title: 3998888177_R05C01


title: KO2_LT_HSC_RNA-Seq

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

data_processing:
The base calling was performed by using BCL2Fastq pipeline (version: 0.3.1) and bcl2fastq (version 2.17.1.14).
RNA-Seq: alignment: tophat2 (2.0.14) in paired-end mode using -G --library-type fr-firststrand
RNA-Seq: FPKM generation: cuffnorm (2.2.1) using --library-type fr-firststrand
RNA-Seq: RPKM-normalized bedGraph generation: deeptools bamCoverage (2.4.2) using --normalizeUsing RPKM --effectiveGenomeSize 2652783500 --blackListFileName mm10.blacklist.bed
ATAC-Seq: alignment: bowtie2 (2.3.2) in paired-end mode using --very-sensitive-local
ATAC-Seq: peak calling and depth coverage generation (bedGraph): macs2 2.1.0 using -f BAMPE -g mm --keep-dup auto -B --SPMR
ATAC-Seq: bedGraph conversion to bigwig using bedGraphToBigWig (v4)
Genome_build: mm10
Supplementary_files_format_and_content: RNA-Seq: bigWig format, RPKM normalized depth coverages; text format, normalized FPKM values across all samples. ATAC-Seq: bigWig format, SPMR normalized depth coverages; narrowPeak format, ATAC-Seq peaks

growth_protocol: Ebf1+/- and Ebf1fl/fl mice were generated according to what has been previously described (Gyory et al., 2012). Prx1Cre, LepRCre and NG2Cre-ERTM mice were purchased from The Jackson Laboratory. C57BL/6 (CD45.2), B6.SJL (CD45.1), and 129/Sv animals were bred in-house. With the exception of Ebf1-/- mice, all strains were maintained on the C57BL/6 background. Due to perinatal mortality of Ebf1-/- mutants on C57Bl/6 background, Ebf1-/- animals were obtained by breeding Ebf1+/- mice (C57BL/6) to 129/Sv mice. Ebf1+/- F1 animals from those crosses were further intercrossed and the Ebf1-/-F2 generation was used for experiments. To induce NG2Cre-ERTM mediated recombination, 6-8 weeks old Ebf1fl/flNG2Cre-ERTM mice were treated with 5mg of Tamoxifen by oral gavage on days 1, 2, 4, 5 and 8. The animals were analyzed 6 weeks after Tamoxifen administration. Unless indicated otherwise, 8-14 week old male and female mice were used for experiments. All mice were bred in the animal facility of the MPI under specific pathogen free (SPF) conditions. All animal procedures were performed according to protocols approved by the German authorities and Regierungspräsidium Freiburg. Intact bones (femora and tibia) were chopped into small fragments and crushed in FACS buffer (PBS-2% FCS) using pestle and mortar. Bone marrow cells were collected and RBC lysis was performed. Next, the cells were washed with FACS buffer and stained for analysis. For sorting of HSPCs the cells were enriched by magnetic depletion. Briefly, the BM cells were labeled with a cocktail of biotinylated antibodies (CD3, CD19, B220, CD11b, Gr1 and Ter119) and then with streptavidin-conjugated magnetic nanobeads (BioLegend). The Lineage- cells obtained were stained with following antibodies: anti-lineage (CD3, CD19, B220, CD11b, Gr1 and Ter119), anti-Sca1, anti-c-kit, anti-CD135, anti-CD48, anti-150, and then further purified by FACS sorting. The immunophenotypes of assayed hematopoietic cells were as follow: LSKs (Lin-Sca1+c-kit+), HSCs (CD135-CD48-CD150+LSK), MPP3 (CD135-CD48+CD150-LSK), MPP4 (CD135+ CD150-LSK), CLPs (Lin-Sca1loc-kitloIL-7Rα+CD135+), pro-B cells (B220+CD43+), pre-B cells (B220loCD43-), rec-B cells (B220hiCD43-), B cells (B220+CD19+), T cells (CD3+), myeloid cells (Mac1+Gr1+) and erythroid cells (Ter119+). BD FACSAria Fusion was used for fluorescence-activated cell sorting and BD LSRFortessa was used for flow cytometry. Data were analyzed with FlowJo software (TreeStar).

extract_protocol:
Total RNA was prepared using RNeasy Micro Kit (Qiagen) according to manufacturer’s instructions. mRNA was enriched by using oligo dT magnetic beads for library preparation. Assays for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) were performed as described before (Buenrostro et al., 2015). To prepare nuclei, 10.000 cells were resuspended in 50 µL of cold lysis buffer (10 mM Tris•Cl at pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% [v/v] Igepal CA-630) and incubated for 15 min on ice. The supernatant was discarded after centrifugation, and the nuclei were used for transposition reaction immediately.
The RNA-seq libraries were prepared by using SMART-Seq v4 ultra-low input RNA library preparation protocol according to the manufacturer's instructions. The ATAC-seq libraries were prepared using the NEB Nextera DNA sample preparation kit according to the manufacturer's instructions.

treatment_protocol: Transplantations were performed using the CD45.1/CD45.2 congenic system. Recipient mice (8-10 week old) were lethally irradiated with 9.5 Gy (in split dose: 5Gy+4.5Gy, at least 3 hr apart) using a γ irradiator with a 137Cs source (Biobeam GM 8000). Purified donor cells together with competitive bone marrow cells were injected into the tail vein and hematopoietic reconstitution was monitored over time in peripheral blood. Adoptive transfer into primary Ebf1+/- (CD45.2+) recipients was performed with 1.5x104 FACS-sorted wild-type donor (CD45.1+) LSK cells. Adoptive transfer into Ebf1+/- secondary recipients was performed with 5x103 of CD45.1+ LSK cells FACS-sorted from the primary recipients, together with 0.5x106 of CD45.2+ competitive BM. In case of Prx1Cre animals, 150 FACS-purified HSCs from Ebf1fl/flPrx1Cre and Ebf1+/+Prx1Cre mice (CD45.2+) were transplanted together with 0.5x106 of CD45.1+ competitive BM into wild-type (CD45.1+) recipients.

tag: transplant status

value: LSK/CD150+ HSCs

tag: genotype/variation

value: Ebffl/fl PrxCre


title: 3998888177_R04C01


title: 3998888177_R03C01

value: Male


title: 3998888177_R02C01


title: 3998888177_R01C01

value: Parkinson's disease


title: KO1_LT_HSC_RNA-Seq


title: BH1 Replicate 1

type: RNA

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

description:
date: 3/28/2018
gene expression from dBigH1 induced S2 cells

hyb_protocol: 2.2 µg of cDNA was hybridized per microarray for 16 hours of hybridization at 45ºC, washing and staining of microarrays was performed using a Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA)

data_processing: Data was quantile normalized and RMA summarized using Bioconductor.

label: biotin

organism: Drosophila melanogaster

label_protocol: 25 ng total RNA per sample was processed using isothermal amplification SPIA Biotin System (NuGEN Technologies, Inc.)

growth_protocol: S2 cells were grown on Schneider’s insect Medium (Biowest) supplemented with 100 μg/ml streptomycin (Gibco), 100 units/ml penicilin (Gibco) and 10% FBS (Gibco). dBigH1::FLAG cells were maintained in Schneider's insect medium (Biowest) supplmented with 0.3 mg/ml Hygromycin B (Sigma) and for performing the experiments cells were grown on the same medium as S2 cells.

extract_protocol: Total RNA was extracted using  RNeasy Mini kit (Qiagen) according to manufacturer's recommendations.

treatment_protocol: Cells were treated with 1mM CuSo4  for 24h.

value: dBigH1 induced

tag: cell line

value: S2 cells


title: BH1 Replicate 3


title: S2 Replicate 1

description:
date: 3/28/2018
gene expression from wild type S2 cells

value: wild type


title: S2 Replicate 3


title: 3998888171_R06C02

tag: gender

value: Female

value: Control

value: whole blood


title: BH1 Replicate 2


title: S2 Replicate 2


title: 3998888171_R05C02

tag: disease-state


title: HSC_culture1_18h

city: München

first: sainitin

last: donakonda

state: Bavaria

address: Ismaningerstr. 22

department: Institute of Immunology

institute: TUM

description: replicate 1

hyb_protocol: Standard illumina hybridization protocol

scan_protocol: Standard illumina scannig protocol

data_processing: The data were normalised using robust spline normalization and differentially expressed genes were identified with lumi R package

source_name: CD14+ cells, Donor A

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: CD14+ cells were cocultured with LX2 in RMPI containing 10% FCS for 18h

tag: disease

value: healthy donor

value: wt- LX2


title: HSC_culture2_18h

description: replicate 1

source_name: CD14+ cells, Donor B


title: HSC culture3 CD44ko_18h

description: replicate 2

source_name: CD14+ cells, Donor C

value: CD44 ko LX2


title: 3998888171_R03C02

tag: tissue


title: WT2_LT_HSC_RNA-Seq

tag: cell type

value: Ebf+/+ PrxCre


title: HSC culture2 CD44ko_18h

description: replicate 1


title: HSC culture1 CD44ko_18h

description: replicate 1


title: HSC_culture3_18h

description: replicate 2


title: WT1_LT_HSC_RNA-Seq


title: lsm8-2 rrp4-2 rep 3

city: Copenhagen

first: Axel

last: Thieffry

state: Hovedstaden

address: Lersø Parkallé 42-44

department: R&D

country: Denmark

institute: BioPhero-FMC

description: double mutant

data_processing:
Basecalling with Illumina Cassava 1.8
Removal of adapters with cutadapt v2.3
Mapping on TAIR10 reference genome with STAR v2.7.0, only considering unique mappers and concordant pairs.
Mapping on TAIR10 reference genome with STAR v2.7.0, only considering unique mappers and concordant pairs.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files, one per strand, raw counts

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Following 12 days of growth in MS 1% under sterile conditions at room temperature and long-days luminosity, seedlings were transferred to liquid MS media 1% and allowed to acclimate 48 hours at 130 rpm prior to sample collection.

extract_protocol:
A pool of 10 intact whole seedlings was flash frozen and total RNA was extracted using TRI-Reagent. Polysaccharide precipitation was carried out using the double sodium acetate method.
Polysaccharide-free total RNA was sent to Novogene Co. (China) and underwent rRNA depletion (Ribo-zero) before construction of Paired-End 150 bp (250~300 bp insert size) libraries and Illumina sequencing. Lower fragment size selection was set to 200 bp.

tag: ecotype

value: lsm8-2 rrp4-2

value: 14 day-old


title: 3998888171_R01C02


title: 3998888171_R02C02


title: lsm8-2 rrp4-2 rep 2

description: double mutant

tag: age


title: 3998888171_R06C01


title: 3998888171_R05C01


title: lsm8-2 rrp4-2 rep 1

description: double mutant

tag: genotype


title: 3998888171_R03C01


title: 3998888171_R02C01


title: rrp4-2 rep 3

description: hypomorphic allele


title: sam5_rep3 control

city: Gent

first: Renate

last: De Smedt

address: Corneel Heymanslaan 10

department: Department of Biomolecular Medicine

country: Belgium

institute: Ghent University

data_processing:
Fastq files were aligned to hg38 with STARv2.42
Raw counts were generated by STARv2.42 on gencode v29
Genome_build: hg38
Supplementary_files_format_and_content: txt file with raw counts

source_name: Spleen

extract_protocol:
Total RNA was isolated using the miRNeasy Mini Kit (Qiagen).
QuantSeq 3′ mRNA-seq reverse Library Prep Kit (Lexogen)

treatment_protocol: T-ALL PDX splenocytes were ex vivo treated with 1µM PIM447 dihydrochloride or DMSO for 24 hours in RPMI supplemented with 10% FCS and 1% antibiotics.

value: CD45+ PDX spleen cells

tag: disease state

value: T-ALL

tag: host mouse strain

value: NSG


title: sam6_rep3 PIM447


title: sam4_rep2 PIM447


title: 3998888171_R01C01


title: rrp4-2 rep 2

description: hypomorphic allele


title: EA1026_01: Sorted rat myeloma cells

city: Sendai

first: Tsuyoshi

last: Shirai

state: Miyagi

address: 1-1 Seiryomachi

country: Japan

institute: Tohoku University

description: Gene expression data from sorted cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G.

data_processing: Array data was processed by Affymetrix GeneChip Command Console Software and Affymetrix Expression Console Software.

organism: Rattus norvegicus

source_name: Rat myeloma cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Conventional cell culture

extract_protocol: Total RNA was extracted using RNeasy mini kit (Qiagen) according to the manufacturer's instructions.

value: myeloma


title: 3998888170_R05C02

value: Male

value: Parkinson's disease


title: 3998888170_R03C02


title: rrp4-2 rep 1

description: hypomorphic allele


title: sam2_rep1 PIM447


title: 3998888170_R04C02


title: sam3_rep2 control


title: EA0728_01: Control rat myeloma cells

description: Gene expression data from control


title: sam1_rep1 control


title: lsm8-2 rep 3

description: T-DNA line


title: lsm8-2 rep 2

description: T-DNA line


title: 3998888170_R06C01


title: lsm8-2 rep 1

description: T-DNA line


title: 3998888170_R02C02


title: 3998888170_R05C01


title: CART19 cells, ATAC  Nalm6 BID KO Stim rep 3

city: St. Louis

first: Nathan

last: Singh

state: MO

country: USA

institute: Washington University School of Medicine

data_processing:
Adapters were trimmed using atactk (version 0.1.5)
Alignment using bowtie with the following flags:  --chunkmbs 2000 --sam --best --strata -m1 -X 2000
macs2 was used for peak calling using a FDR cutoff of 0.05
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files reflect the significant peaks yielded by macs2.

source_name: Primary human T cells engineered with CD19 CAR

growth_protocol: T cells were cultured and engineered as previously described (Singh, N. et al. Cancer Immunology Research, 2014)

extract_protocol:
cells were processed following the Omni ATAC-seq protocol. To isolate nuclei, cells were washed 2x with ice-cold PBS followed by resuspension in ATAC- resuspension buffer containing 0.1% NP40, 0.1% Tween-20 and 0.01% Digitonin. Cells were incubated on ice for 3 minutes and washed out with ATAC- resuspension buffer containing (0.1% Tween20). Nuclei were pelleted and transposed with Tn5 transposase.
nuclei were isolated from 50,000 sorted CART19 cells, followed by the transposition reaction using Tn5 transposase (Illumina) for 30 minutes at 37°C with 1000rp mixing.  Purification of transposed DNA was completed with DNA Clean and Concentrator (Zymo) and fragments were barcoded with ATAC-seq indices.  Final libraries were double size selected using AMPure beads prior to sequencing.

treatment_protocol: CART19 cells were co-cultured with Nalm6 cells at an effector:target ratio of 1:4.

tag: treatment condition

value: 15day exposure to BIDko Nalm6


title: CART19 cells, ATAC  Nalm6 BID KO Stim rep 2

value: Primary human T cells engineered with CD19 CAR


title: 3998888170_R03C01

value: Female


title: wt rep 3

description: wild type

value: wild type


title: 3998888170_R02C01

value: whole blood


title: CART19 cells, ATAC  Nalm6 BID KO Stim rep 1


title: 3998888170_R06C02


title: 3998888170_R01C01


title: 3998888109_R06C02


title: CART19 cells, ATAC  Nalm6 WT Stim rep 3

value: 15day exposure to WT Nalm6


title: 3998888170_R01C02

value: Control


title: CART19 cells, ATAC Nalm6 WT Stim rep 2


title: 3998888109_R04C02


title: wt rep 1

description: wild type


title: CART19 cells, ATAC  Nalm6 WT Stim rep 1


title: 3998888109_R05C02


title: 3998888171_R04C01


title: 3998888109_R06C01


title: 3998888109_R03C02


title: rrp4-2 replicate 2

description: hypomorphic allele

data_processing:
Basecalling with Illumina Cassava 1.8
FASTX Toolkit v0.0.13 was used to remove the linker sequences, to retain the first 25 nt from the 5’ end and to filter with a minimum threshold quality of Q30 in 50% of the remaining bases.
Cleaned reads were mapped on TAIR10 reference genome with Bowtie v1.1.2 with the parameters -t best -strata -v -k 10 -y -p 6 -phred33-quals -chunksmbs 512 -e 120 -q -un.
The 5’-end of the CAGE tags were counted at each genomic position to obtain a set CAGE transcription start sites (CTSSs).
CTSS coordinates were offset by 1 bp to account for the G-bias trimming.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files, one per strand, host the number of CAGE tags 5'-end per bp (raw count CTSSs)

extract_protocol:
A pool of 10 intact whole seedlings was flash frozen and total RNA was extracted using TRI-Reagent. Polysaccharide precipitation was carried out using the double sodium acetate method.
CAGE libraries were prepared as in (Takahashi et al., 2012) with a starting material of 5ug of total RNA. Phi-X spike-ins were added (30%) to each sequencing lane to account for low complexity of the 5' ends of the CAGE libraries


title: CART19 cells, ATAC  Resting rep 3

value: Resting cells


title: 3998888109_R05C01


title: rrp4-2 replicate 3

description: hypomorphic allele


title: rrp4-2 replicate 1

description: hypomorphic allele


title: 3998888170_R04C01


title: CART19 cells, ATAC Resting rep 2


title: 3998888109_R04C01


title: 3998888109_R02C01


title: 3998888109_R03C01


title: CART19 cells, ATAC Resting rep 1


title: hen2-4 replicate 3

description: T-DNA line


title: wt rep 2

description: wild type


title: hen2-4 replicate 2

description: T-DNA line


title: 3998888072_R06C02


title: 3998888109_R01C01


title: CART19 cells, Nalm6 BID KO Stim rep 3

description:
RNA_seq_raw_counts.csv
15_Day15_CAR19_RNA_BID

data_processing:
Reads were aligned using STAR (version 2.5.4b) using known gene model from GENCODE (release_27_hg19)
Quantification was achieved using the --quantMode GeneCounts flag.
Raw read counts were normalized using TMM normalization as implemented in edgeR followed by the voom transformation implented in the limma bioconducter package.
Differentially expressed genes were indentified using limma.
Genome_build: hg19
Supplementary_files_format_and_content: Raw read counts for each gene and sample

extract_protocol:
total RNA was extracted using Qiazol (Qiagen) from 300 CART19 cells and recovered by RNA Clean and Concentrator spin columns (Zymo) followed by incubation with Oligo-dT.  The transcription reaction was carried out on 100pg of cDNA for 1min at 55°C.
18 cycles of pre-amplification were performed followed by 14 cycles to add indexes/adaptors to prepare the libraries for sequencing.


title: 3998888109_R01C02


title: 3998888072_R05C02


title: hen2-4 replicate 1

description: T-DNA line


title: 3998888072_R04C02


title: 3998888072_R02C02


title: CART19 cells, Nalm6 BID KO Stim rep 1

description:
RNA_seq_raw_counts.csv
13_Day15_CAR19_RNA_BID


title: wt replicate 2

description: wild type

value: wt


title: CART19 cells, Nalm6 BID KO Stim rep 2

description:
RNA_seq_raw_counts.csv
14_Day15_CAR19_RNA_BID


title: 3998888072_R03C02


title: wt replicate 3

description: wild type


title: 3998888072_R06C01


title: 3998888072_R05C01


title: 3998888072_R01C02


title: wt replicate 1

description: wild type


title: 3998888072_R04C01


title: CART19 cells, Nalm6 WT Stim rep 3

description:
RNA_seq_raw_counts.csv
12_Day15_CAR19_RNA_WT


title: 3998888072_R02C01


title: CART19 cells, Nalm6 WT Stim rep 2

description:
RNA_seq_raw_counts.csv
11_Day15_CAR19_RNA_WT


title: 3998888072_R03C01


title: CART19 cells, Nalm6 WT Stim rep 1

description:
RNA_seq_raw_counts.csv
10_Day15_CAR19_RNA_WT


title: 3998888041_R06C01


title: SOX4_IP3

city: DALLAS

first: jianjing

last: Yang

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UT Southwestern Medical Center

data_processing:
Basecalls performed using bcl2fastq (v2.20)
ChIP-seq reads aligned to hg19 using bowtie2 (v2.3.3.1)
Alignments with mapping quality less than 10 were filtered out
Duplicate alignments were removed using picard-tools(v2.10)
Peaks were called using MACS (v2.1.1.20160309) with a q-value threshold of 0.05 and using the random background of ChIP samples as controls
Annotation of peaks and motif analysis was performed using HOMER(v4.9.1)
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using HOMER. Scores represent normalized counts per 10 million.

extract_protocol:
In brief, after HASOX4 overexpression, approximately total ~12×10e6 U251 cells (4 X 10cm plates) were crosslinked with methanol-free formaldehyde (Thermo Scientific, 28908). Then quench the crosslinking with glycine solution. After lysis and centrifugation, chromatin was sheared into 100-500 nucleotides length by Bioruptor Machine (Diagenode, B01010002). 10 µg chromatin solution was used for input. 150 µg of chromatin solution was applied for immunoprecipitation by 5 µg HA (Abcam; ab99110). Subsequently, 100 µl Magnetic Protein G Dynabeads (Life Technologies, 10003D) were resuspended in immunoprecipitation samples incubate for 2 hours at 4°C with gentle rotation to poll down primary antibody affinity chromatin fragments. After subsequently treated with RNase, Proteinase K and high concentration of NaCl solution (5M), Input and IP Chromatin was purified with a QIAquick PCR purification kit (Qiagen, 28104) according to kit manual. The chromatin concentration was determined by Qubit fluorometer and Qubit dsDNA HS assay kit (Life Technologies, Q32850) according to kit manual. For statistic, every groups were triplicated.
Libraries were synthesized from 10 ng purified input chromatin and 10 ng purified immunoprecipitated chromatin using a NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (New England Biolabs, E6240S) with NEBNext Multiplex Oligos for Illumina (New England Biolabs, E7335S). Replicate libraries were prepared from independent immunoprecipitations.
ChIP-seq: single end 50-base length sequencing reads were generated on an Illumina HiSeq 2500 System.

value: U251 glioblastoma cell

value: HA-SOX4 overexpression

tag: time

value: 3 days post virus infection

tag: antibody

value: anti-HA


title: 3998888067_R06C02


title: SOX4_IP2


title: CART19 cells, Resting rep 3

description:
RNA_seq_raw_counts.csv
3_Day0_CAR19_RNA


title: 3998888067_R05C02


title: 3998888067_R04C02


title: KO3_ADT2nd_LT_HSC_ATAC-Seq

value: secondary

value: LSK/CD150+ HSCs

value: Ebffl/fl PrxCre


title: SOX4_IP1


title: SOX4_Input

value: input


title: KO2_ADT2nd_LT_HSC_ATAC-Seq


title: CART19 cells, Resting rep 1

description:
RNA_seq_raw_counts.csv
1_Day0_CAR19_RNA


title: S2 R2 input

description:
genomic DNA
1887_28918_TTAGGC

data_processing:
FastQ files were aligned against the dm3 genome using Bowtie 0.12.5, allowing for 2 mismatches and reporting only unique hit alignments.
FastQC v011 was used to perform a quality control overview of FastQ files, aligned BAM files, and also for multiple hits and unaligned sequences.
Binary tracks for all reads in TDF format were generated with IGVTools 2.
Immunoprecipitation assessment (Gini coverage inequality) and PCA/MDS plots were genered using htSeqTools (Planet et al. 2012).
Peak Calling with the Drosophila default options was performed for IP vs their respective Input control sample usinc MACS 1.4.2 with options -g dm
Genome_build: dm3
Supplementary_files_format_and_content: BED files in MACS 1.4.2 format for ChIP vs Input peak calling

source_name: WT S2 cells

growth_protocol: S2 cells were grown on Schneider’s insect Medium (Biowest) supplemented with 100 μg/ml streptomycin (Gibco), 100 units/ml penicilin (Gibco) and 10% FBS (Gibco). dBigH1::FLAG and dBigH1ΔED::FLAG cells were maintained in Schneider's insect medium (Biowest) supplmented with 0.3 mg/ml Hygromycin B (Sigma) and for performing the experiments cells were grown on the same medium as S2 cells.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with polyclonal αdBigH1 and αH1 antibodies. Finally DNA was purified by standard phenol extraction.
3-5 ng DNA, quantified by Qubit dsDNA HS Assay Kit (Invitrogen) was used for library preparation. Endrepair, adenylation, ligation of adapters and PCR enrichment for 10 cycles was performed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s recommendations. Purified libraries were quantified by Qubit dsDNA HS Assay Kit (Invitrogen) and size distribution was evaluated using Bioanalyzer DNA 1000 assay (Agilent).

value: WT

value: S2 cells

tag: type

value: Input

tag: replicate

tag: chip antibody


title: KO1_ADT2nd_LT_HSC_ATAC-Seq

tag: transplant status

tag: genotype/variation


title: WT3_ADT2nd_LT_HSC_ATAC-Seq

value: Ebf+/+ PrxCre


title: S2 R2 Rpb3

description:
genomic DNA
1887_28918_TGACCA

tag: cell line

value: IP Rpb3

value: polyclonal αRpb3


title: 3998888067_R05C01

tag: gender

value: Female

tag: disease-state

value: Parkinson's disease

value: whole blood


title: delta mig R2 BigH1

description:
genomic DNA
1887_28918_GTTTCG

source_name: dBigH1ΔED induced S2 cells

value: dBigH1delta-ED induced

value: IP dBigH1

value: polyclonal αdBigH1


title: WT2_ADT2nd_LT_HSC_ATAC-Seq

tag: cell type


title: 3998888067_R01C02

value: Control

tag: tissue


title: 3998888067_R04C01


title: WT1_ADT2nd_LT_HSC_ATAC-Seq

value: secondary


title: KO2_ADT1st_LT_HSC_ATAC-Seq

value: primary

value: LSK/CD150+ HSCs


title: CART19 cells, Resting rep 2

description:
RNA_seq_raw_counts.csv
2_Day0_CAR19_RNA

value: Primary human T cells engineered with CD19 CAR

value: Resting cells


title: delta mig R1 BigH1

description:
genomic DNA
1887_28918_GGCTAC

value: S2 cells


title: 3998888072_R01C01

value: Male


title: BH1 R1 Rpb3

description:
genomic DNA
1887_28918_GCCAAT

source_name: dBigH1 induced S2 cells

value: dBigH1 induced


title: 3998888067_R03C01


title: 3998888067_R03C02


title: delta mig R1 input

description:
genomic DNA
1887_28918_GATCAG

value: Input


title: -/- adherent rep2

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Colletotrichum orbiculare Microarray 8x60K for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried by raise it slowly from buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 2um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) and GeneSpring GX12.1 using default parameters.

source_name: Neurospheres from one embryonic brain at E14.5

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low RNA Input Fluorescent Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Neurospheres were prepared from the ganglionic eminence in the telencephalon of E14.5 embryos. Neural stem cells (5×10^5) were cultured in sells of a 6-well plate for 7 days or the next passage to form neurospheres. Neurospheres were dispersed into single cells by Accutase (nacalai tesque).

extract_protocol: RNA was prepared using the Agilent RNA Isolation Mini kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Neurospheres were cultured on the ultra-low attachment plates for 7days in Neurobasal medium (Thermo Scientific) with B-27 supplememt, 20 ng/ml EGF, 20 ng/ml bFGF, Glutamax, Penicillin-Streptomycin and 5 micro g/ml hepari sodium salt. Equal volume of culture medium was added every 3 days.

value: HP1gamma KO

tag: treatment

value: adherent

value: brain

tag: developmental stage

value: neurospheres


title: 3998888067_R02C01

value: Female

value: whole blood


title: -/- floating rep3

tag: genotype

value: floating


title: 3998888067_R06C01

value: Control


title: KO1_ADT1st_LT_HSC_ATAC-Seq

value: Ebffl/fl PrxCre


title: delta mig R1 Rpb3

description:
genomic DNA
1887_28918_TAGCTT

value: dBigH1delta-ED induced

value: IP Rpb3

value: polyclonal αRpb3


title: WT2_ADT1st_LT_HSC_ATAC-Seq

value: primary

value: LSK/CD150+ HSCs

value: Ebf+/+ PrxCre


title: +/+ floating rep3

value: wild type


title: 3998888019_R06C02

value: Male

value: Parkinson's disease


title: KO2_LT_HSC_ATAC-Seq


title: WT1_ADT1st_LT_HSC_ATAC-Seq


title: 3998888019_R05C02


title: -/- floating rep2

value: HP1gamma KO


title: -/- adherent rep1

value: adherent

value: brain


title: delta mig R2 H1

description:
genomic DNA
1887_28918_CGTACG

value: S2 cells

value: IP H1

value: polyclonal αH1


title: S2 R1 Rpb3

description:
genomic DNA
1887_28918_CGATGT

value: WT


title: -/- floating rep1

value: floating

value: neurospheres


title: +/+ floating rep2


title: WT2_LT_HSC_ATAC-Seq


title: 3998888019_R03C02

value: Female

value: Control

value: whole blood


title: 3998888067_R01C01


title: BH1 R2 input

description:
genomic DNA
1887_28918_CAGATC

value: dBigH1 induced

value: Input


title: +/+ floating rep1

value: wild type


title: delta mig R2 Rpb3

description:
genomic DNA
1887_28918_ATGTCA

value: dBigH1delta-ED induced

value: IP Rpb3

value: polyclonal αRpb3


title: WT1_LT_HSC_ATAC-Seq

value: LSK/CD150+ HSCs

value: Ebf+/+ PrxCre


title: delta mig R1 H1

description:
genomic DNA
1887_28918_CTTGTA

value: S2 cells


title: delta mig R2 input

description:
genomic DNA
1887_28918_AGTTCC


title: S2 R1 input

description:
genomic DNA
1887_28918_ATCACG


title: KO3_ADT1st_LT_HSC_RNA-Seq

value: primary

value: Ebffl/fl PrxCre


title: 3998888019_R06C01

value: Male

value: Parkinson's disease


title: 3998888019_R01C02


title: BH1 R2 Rpb3

description:
genomic DNA
1887_28918_ACTTGA


title: 3998888019_R04C02


title: KO2_ADT1st_LT_HSC_RNA-Seq


title: Fibroblast, MDA-LM2 macrometastatic lung, biological rep3

city: Heidelberg

first: Maren

last: Pein

address: Im Neuenheimer Feld 280

department: Junior Research Group Metastatic Niches

institute: German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ)

description: Gene expression of sorted mouse lung fibroblasts from NSG mice 3 weeks after intravenous injection of highly metastatic MDA-MB-231-LM2 breast cancer cells

hyb_protocol: 5 ug of fragmented and labeled SPIA cDNA were hybridized for 17 h at 45 °C on Affymetrix GeneChip® Mouse Genome U430 2.0 Arrays.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays (P/N 702731).

data_processing: The raw data was normalised with R using function normalize.quantiles from Bioconductor package preprocessCore; normalization method is quantile normalization.

source_name: Fibroblasts sorted from lungs of NSG mice 3 weeks after i.v. injection of MDA-MB-231-LM2 cells (macrometastatic stage)

label_protocol: The Nugene Ovation® Pico WTA System V2 in combination with the Encore Biotin Module was used to generate labeled SPIA cDNA from input amounts of 2.5 ng total RNA. The label used was biotin.

extract_protocol: RNA extraction was performed using the Arcturus PicoPure Extraction Kit (ThermoFisher Scientific) according to the manufacturer’s protocol.

tag: metastatic stage

value: Macrometastasis


title: KO1_LT_HSC_ATAC-Seq


title: WT3_ADT1st_LT_HSC_RNA-Seq


title: BH1 R1 input

description:
genomic DNA
1887_28918_ACAGTG


title: Fibroblast, MDA-LM2 macrometastatic lung, biological rep2


title: 3998888019_R05C01

data_processing: Genome Studio software

extract_protocol: genomic DNA was extracted and purified from SGPD samples using ??? according to standard instructions

value: Female


title: Fibroblast, MDA macrometastatic lung, biological rep3

description: Gene expression of sorted mouse lung fibroblasts from NSG mice 3 weeks after intravenous injection of MDA-MB-231 breast cancer cells

source_name: Fibroblasts sorted from lungs of NSG mice 3 weeks after i.v. injection of MDA-MB-231 cells (macrometastatic stage)


title: Fibroblast, MDA macrometastatic lung, biological rep2


title: Fibroblast, MDA-LM2 macrometastatic lung, biological rep1


title: 3998888019_R04C01

source_name: whole blood

value: Control


title: 3998888019_R02C02

value: whole blood


title: 3998888019_R03C01


title: Fibroblast, MDA macrometastatic lung, biological rep1


title: R1 ctr IP H1

description:
genomic DNA
2001_22802_TTAGGC

source_name: wt S2 cells

growth_protocol: S2 cells were grown on Schneider’s insect Medium (Biowest) supplemented with 100 μg/ml streptomycin (Gibco), 100 units/ml penicilin (Gibco) and 10% FBS (Gibco). dBigH1::FLAG and dBigH1ΔDE::FLAG cells were maintained in Schneider's insect medium (Biowest) supplmented with 0.3 mg/ml Hygromycin B (Sigma) and for performing the experiments cells were grown on the same medium as S2 cells.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with polyclonal αdBigH1 and αH1 antibodies. Finally DNA was purified by standard phenol extraction.
10 ng DNA, quantified by Qubit dsDNA HS Assay Kit (Invitrogen) was used for library preparation. Endrepair, adenylation, ligation of adapters and PCR enrichment for 10 cycles was performed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s recommendations. Purified libraries were quantified by Qubit dsDNA HS Assay Kit (Invitrogen) and size distribution was evaluated using Bioanalyzer DNA 1000 assay (Agilent).

value: wt

value: IP H1

value: polyclonal αH1


title: WT2_ADT1st_LT_HSC_RNA-Seq


title: R1 1mM input

description:
genomic DNA
2001_22802_TGACCA

source_name: wt BigH1 1mM induced S2 cells

value: wt BigH1 1mM induced

value: Input


title: 3998888019_R02C01


title: Fibroblast, MDA-LM2 micrometastatic lung, biological rep3

description: Gene expression of sorted mouse lung fibroblasts from NSG mice 1 week after intravenous injection of highly metastatic MDA-MB-231-LM2 breast cancer cells

source_name: Fibroblasts sorted from lungs of NSG mice 1 week after i.v. injection of MDA-MB-231-LM2 cells (micrometastatic stage)

value: Micrometastasis


title: WT1_ADT1st_LT_HSC_RNA-Seq

value: LSK/CD150+ HSCs


title: Fibroblast, MDA-LM2 micrometastatic lung, biological rep2


title: 3998888019_R01C01


title: R2 1mM IP BigH1

description:
genomic DNA
2001_22802_GGCTAC

value: IP dBigH1

value: polyclonal αdBigH1


title: R1 1mM IP H1

description:
genomic DNA
2001_22802_GCCAAT

value: S2 cells


title: KO1_ADT1st_LT_HSC_RNA-Seq

value: primary

value: Ebffl/fl PrxCre


title: Fibroblast, MDA micrometastatic lung, biological rep3

description: Gene expression of sorted mouse lung fibroblasts from NSG mice 1 week after intravenous injection of MDA-MB-231 breast cancer cells

source_name: Fibroblasts sorted from lungs of NSG mice 1 week after i.v. injection of MDA-MB-231 cells (micrometastatic stage)


title: R2 1mM input

description:
genomic DNA
2001_22802_TAGCTT


title: R2 ctr IP H1

description:
genomic DNA
2001_22802_GATCAG


title: Fibroblast, MDA-LM2 micrometastatic lung, biological rep1


title: R2 1mM IP H1

description:
genomic DNA
2001_22802_CTTGTA


title: R1 ctr IP BigH1

description:
genomic DNA
2001_22802_CGATGT


title: R2 ctr input

description:
genomic DNA
2001_22802_CAGATC