title: genomic DNA from post-mortem hippocampus 43

value: Other

value: post-mortem interval:46


title: genomic DNA from post-mortem hippocampus 38

status: Public on Dec 02 2019

type: genomic

city: Houston

first: Gabriel

middle: Rodrigo

last: Fries

state: TX

address: 1941 East Rd, Suite 5102A

department: Psychiatry

country: USA

institute: University of Texas Health Science Center

hyb_protocol: Standard Illumina Infinium hybridization protocol.

scan_protocol: Standard Illumina Infinium scan protocol. Scan performed on iScan microarray reader.

data_processing:
Raw data were uploaded to GenomeStudio (Illumina) and background-corrected.
Unmethylated and methylated signal intensities in Series supplementary file

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Infinium protocol.

extract_protocol: DNA was isolated from frozen hippocampal tissue using a modified protocol at the HBCC-NIMH. Briefly, pulverized hippocampal tissues were lysed in PureGene lysis solution (Qiagen, Hilden, Germany) containing proteinase K at 55º C overnight, followed by incubation with RNAse at room temperature for 15 minutes. After centrifugation at 14,000 rpm for 1 hour at 4º C and transfer of the supernatant to a new microtube, the DNA was precipitated by addition of cold isopropyl alcohol and further centrifugation at 14,000 rpm for 30 minutes. After a washing step with 90% ethanol and a final centrifugation at 14,000 rpm for 20 minutes, the pellet was air-dried and resuspended in TE buffer.

tag: Sex

value: Male

tag: group

value: Bipolar

tag: age at death

tag: race

value: Caucasian

tag: tissue

value: post-mortem interval:15

tag: tissue ph

value: post-mortem hippocampus


title: niPSC5_Rep2

type: SRA

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: genomic

data_processing:
Raw sequence reads were trimmed to remove poor quality reads, adapter contamination, and the first 6 base pairs, using Trim Galore (v0.6.1, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The remaining sequences were mapped using Bismark (v0.21.0) (Krueger and Andrews, 2011) to the human reference genome GRCh37 in paired-end mode. CpG methylation calls were extracted and analysed using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCh37
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

source_name: iPSC

extract_protocol:
DNA was purified from cell lysates and then used for library construction
Whole-genome bisulfite libraries were prepared using a post-bisulfite adaptor tagging (PBAT) strategy as previously described (Smallwood, et al. (2014). Nature Methods 11, 817–820), with some modifications. Bisulfite conversion was performed on cell lysates using the Imprint Zymo direct kit. After purification, 1st strand synthesis was performed using 6N-forward oligos for 37°C for 30min. Subsequently, samples were treated with Exonuclease I for 1hr at 37°C, and DNA was purified using AMPure XP beads (Agencourt). Samples were eluted in 2nd strand synthesis mix with 6N-reverse oligo and incubated at 37°C for 90min. DNA was purified and amplified with KAPA HiFi HotStart DNA Polymerase (KAPA Biosystems). The amplified libraries were purified and assessed for quality and quantity using High-Sensitivity DNA chips on the Agilent Bioanalyzer
post-bisulfite adaptor tagging (PBAT)

tag: background strain

value: Wild-type

tag: cell type

value: iPSC

tag: genotype

value: naive


title: WT_H3K27me3 ChIP-seq rep1

city: Lyon

first: Fabrice

last: Lavial

address: 28 rue Laennec

country: France

institute: CRCL

data_processing:
BWA was used for alignment of data to the mm9 genome with de-duplication performed using Picard tools, followed by peak calling using macs2 with narrow peak settings. To compare between control and netrin-1 conditions, homer annotatePeaks.pl was used with size = 2000, hist = 10 and –ghist used to generate read enrichments from both the control and netrin-1 sample using the control macs2 peaks. Data was then plotted in R using custom scripts
Genome_build: mm9
Supplementary_files_format_and_content: Coverage files used to plot the density composites for bivalent genes in figure 3k. Both for H3K27me3 and H3K4me3. Both text files output from Homer AnnotatePeaks after creating tag directories with the bam files.

organism: Mus musculus

growth_protocol: mESC are grown in serum/LIF conditions

extract_protocol: ChIP-seq is performed as previously described (Galonska et al., Cell Stem cell 2015)

treatment_protocol: mESC are stably transfected with ppy-cagg-ires-puro vector epty or encoding a netrin-1 transgene.

value: Embryonic stem cells

tag: genotype/variation

value: vector control

tag: chip antibody

tag: chip antibody info.


title: PC2_Rep1

value: conventional


title: Netrin_H3K27me3 ChIP-seq rep1

value: exogenously expressing netrin-1


title: dKO+EoVP16_cells_d5_dox (ChIP-seq)

city: Freiburg

first: Sebastian

middle: J.

last: Arnold

address: Albertstrasse 25

department: Pharmacology

country: Germany

institute: University of Freiburg

data_processing:
Reads were mapped to the mm10 genome using Galaxy platform Bowtie2 v2.3.4 with default settings. Results from biological duplicates were merged for subsequent analysis using Merge BAM files (picard v1.56.0). After removing duplicates with RmDup (samtools v1.3.1), peaks were detected using MACS2 (v2.1.1.20160309.4) with BAMPE format of the input file, default settings for building the shifting model and minimum q-value cut-off for detection of 0.05. Input served as control for MACS2 peak calling. Peaks were further filtered for the pile-up value (height of the peak at the summit, provided in the Peaks tabular file from MACS2) >60 for EoVP5 and >=36 for EoVP16 ChIP-seq. Peaks detected by MACS2 in the input control and dKO -dox control were subtracted from the genomic intervals detected in ChIP-seq treatment file using SubtractBed tool (bedtools v2.27.0) in Galaxy, where entire features were filtered out if the overlap of minimum 1 bp was found. Coverage files were created using the bamCoverage tool (deepTools v3.0.2) with bin size 10 bases and normalization to RPKM.
Mapping: For the RNA-seq results reads trimmed of the addapters were mapped to the mouse reference genome GRCm38/mm10 (iGenomes, Illumina), using Rsubread v1.28.1 package in R v3.4.3. For ATAC-seq and ChIP seq reads were mapped to mm10 genome using Bowtie2 v2.3.4 on the Galaxy platform.
Counting: Genomic features were counted for the RNA-seq analysis with the Rsubread::featureCounts function in Rsubread v1.28.1 package using genomic annotations as gtf files provided by the iGenomes reference genome bundles (archive-2015-07-17-32-40 and archive-2015-07-17-33-26 for GRCM38 and mm10, respectively).
Differential expression: Differential expression analysis was carried out using DESeq2 v1.18.1 in R, which applies Negative Binomial GLM fitting and Wald statistics on the count data. The results were filtered for adjusted p-value<0.05 and log2FC as indicated in the figure legends. Prior to fitting and statistical analysis, counts were normalized by library size (DESeq2::estimateSizeFactors) and gene-wise dispersion (DESeq2::estimateDispersions) to normalize the gene counts by gene-wise geometric mean over samples. Gene-wise scaling was performed on the normalized counts to cluster the counts for the expression tendency between the samples (stats::kmeans function). In addition, the counts were centered by setting the gene-wise mean to zero.
Coverage: For the generation of coverage files for RNA-seq, ATAC-seq and ChIP-seq analysis corresponding bam files from biological replicates were merged using Merge BAM files tool in Galaxy (picard v1.56.0) and the duplicates were removed by RmDup tool (samtools v1.3.1). Coverage files were created using bamCoverage tool (deepTools v3.0.2) with bin size 10 bases and reads per kilobase per million (RPKM) normalization.
Peak calling: Peaks were detected using MACS2 on the Galaxy platform (v2.1.1.20160309.4) with BAMPE format of the input file, default settings for building the shifting model and minimum q-value cut-off for detection of 0.05. For ChiP-seq of EoGFP and BraGFP peaks detected in the input control and dKO -dox control were subtracted from the genomic intervals detected in ChIP-seq treatment file using SubtractBed tool (bedtools v2.27.0) in Galaxy, where entire features were filtered out if the overlap of minimum 1 bp was found. For ChiP-seq of EoGFP and BraGFP peaks the resulting narrow peaks bed file was sorted and filtered for the pileup value (height of the peak at the summit, provided in the Peaks tabular file from MACS2) higher than 120 and 40, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: Processed RNA-seq results showing differential gene expression between WT and dKO contain normalized and scaled counts (RPKM) in Tab delimited txt format. Coverage files in BigWig format  for RNA-seq and ChIP-seq reads are normalized to RPKM. Bed files for EoGFP and BraGFP ChIP-seq contain coordinates of the peaks recognized after MACS2 peak calling and subsequent filtering for the pileup value.

source_name: 5 days dKO+EoVP16 embryoid bodies (ActA + dox)

growth_protocol:
Starting number of 2.5x10^5 dKO+EoV5 or dKO+EoVP16 cells were grown as EBs in suspension culture in 100 mm dishes for 2 days and treated with 30 ng/ml ActA and 5 µg/ml dox from day 2 to day 5 of differentiation. Uninduced cells were used as negative controls. On day 5 of differentiation, EBs were singularized by trypsinization and approximately 3x10^7 cells was used per ChIP.
A2lox.Cre Mouse ESCs were grown in the standard serum containing conditions with 1000 U/ml LIF, 3 mM CHIR99021 and 1 mM OD0325901 on the monolayer of mitotically inactivated STO feeder cells (SNL76/7). Prior to differentiation cells were depleted of feeders and 200 cells per 40 ml of serum-free Basal medium were grown as embryoid bodies (EBs) in ultra-low attachment plates for 2 days, or alternatively, 2.5x10^5 cells were grown as EBs in 10 mm non-adherent dishes in Basal medium. Cells were further treated and grown for 2-3 more days.

extract_protocol:
The protocol was modified from Schmidt et al., according to Singh et al. Briefly, ProteinG beads (50 μl per sample) were incubated with 5 μg of Anti-V5 Antibody (BioRad, MCA1360) overnight at 4°C. Cross-linking was performed with 2 mM disuccinimidyl glutarate (DSG, Thermo Fischer, 20593) in the SolutionA (50 mM Hepes, 100 mM NaCl, 1 mM EDTA and 0.5 mM EGTA) for 15 min followed by 1% formaldehyde (Sigma Aldrich, F8775) for additional 10 min. The reaction was stopped by adding 2.5 M Glycine for 5 min. Cells were lysed in Lysis buffer 1 (50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40 and 0.25% TritonX in H2O, pH7.5) with protease inhibitors (PI, Complete™ Protease Inhibitor Cocktail, Roche) for 10 min on a rotating wheel at 4°C. Next, pellets were incubated for 5 min at 4°C with Lysis buffer 2 with PI (10 mM Tris, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA in H2O, pH8), followed by resuspension in Lysis buffer 3 with PI (10 mM Tris, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% Lauroylsarcosine in H2O, pH8). The DNA was sonicated with the Bioruptor (Diagenode), at high amplitude for 10-12 cycles of 30 s ON/30 s OFF. TritonX was added to final concentration of 1%. 10% of the resulting lysate was kept as input control. Beads coupled to antibodies incubated with sonicated chromatin at 4°C overnight. Next, beads were washed on ice ten times with RIPA buffer (50 mM HEPES, 500 mM LiCl, 1 mM EDTA, 1% NP40 substitute, 0.7% Na-Deoxycholate in H2O, pH7.6) and once with TBS. DNA was removed from the beads with Elution buffer (50 mM Tris, 10mM EDTA, 1% SDS in H2O, pH8) for 6-18 h at 65°C. The supernatant was mixed with one volume of TE buffer (10 mM Tris, 1 mM EDTA in H2O, pH7.4), incubated with RNAse A at 37°C for 1 h, and ProteinaseK at 55°C for 2 h. Phenol-chloroform extraction of the DNA was performed and pellet  was resuspended in 50 μl of 10 mM Tris-HCl pH8.
Libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs), size selected on a 1.3% agarose gel by cutting out fragments between 200-650 bp of size and extracted from the gel using QIAquick gel extraction kit (Qiagen).

treatment_protocol: Cells were either treated with 30 ng/ml human recombinant ActivinA (ActA) from day 2 to day 5 of differentiation, or for the NECtrl samples with 100 ng/ml Noggin and 10 mM SB431542 for 1 day followed by 1 day treatment with 100 ng/ml Noggin and 10 ng/ml ActA. Dox-inducible cells were stimulated with 5 mg/ml dox from day 2 to day 5 of differentiation in the appropriate medium.

value: dKO

tag: day

tag: treatment

value: ActA + dox

value: anti-V5 (BioRad, MCA1360, Lot. 0915)


title: dKO+EoV5_cells_d5_dox (ChIP-seq)

source_name: 5 days dKO+EoV5 embryoid bodies (ActA + dox)


title: genomic DNA from post-mortem hippocampus 40

value: post-mortem interval:36


title: genomic DNA from post-mortem hippocampus 57

value: Female

value: post-mortem interval:22.5


title: genomic DNA from post-mortem hippocampus 35

value: Male

value: Bipolar

value: post-mortem interval:25.5


title: IR group vs. iPoC replicate 3

type: RNA

city: Taipei

first: Han Chen

last: Lin

state: 中正區

address: R642, 6F, No.1, Ren Ai Road Section 1

department: Institute of Anatomy and Cell Biology

country: Taiwan

institute: National Taiwan University

description: Liver tissue of ischemia-reperfusion group or ischemic postconditioning group were collected and total RNA was extracted from these liver tissues

hyb_protocol: Oligoarray control targets and hybridization buffer (Exiqon) were added, and samples were applied to microarray chips enclosed in MAUI Hybridization chamber for 16 hours at 56 ℃. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on GenePix 4000B microarray scanner. Images were quantified using Agilent GeneSpring (version 11.5)

data_processing: LOWESS normalized, background substracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

molecule: total RNA

organism: Rattus norvegicus

source_name: rat ischemia-reperfusion liver tissue

label_protocol: 1 μg total RNA were treated with CIP enzyme, and then labeled with Hy3(reference) or Hy5(test) according to the miRCURY LNATM microRNA Array Hi-Power Labeling kit instruction manual v1.0.

growth_protocol: Male Wistar rats weighing 200-250 g were used. All experiments and animal care were performed in accordance with the Guides for the Care and Use of Laboratory Animals (published by National Academy Press, Washington, DC,1996)

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions. RNA quality was measured by 2100 bioanalyzer (Agilent). The RNA integrity number (RIN) of each RNA sample should be greater than 7 for further miRNA microarray.

treatment_protocol: ischemia-reperfusion group: 45 mins ischmia followed by 240 mins reperfusion.    Ischemic postconditioning group: 45 mins ischemia followed by 1 minute's reperfusion and 1 minute's ischemia for 3 cycles, and then reperfusion for 240 minutes

value: liver

value: ischemia-reperfusion liver tissue

tag: strain

value: Wistar

source_name: rat ischemic postconditioning

value: ischemic postconditioning


title: IR group vs. iPoC replicate 2


title: genomic DNA from post-mortem hippocampus 34

value: Caucasian

value: post-mortem interval:18.5

value: post-mortem hippocampus


title: dKO+EoV5_cells_d5_nodox (ChIP-seq)


title: WT_H3K27me3 ChIP-seq rep3

value: Embryonic stem cells

value: vector control


title: WT_H3K27me3 ChIP-seq rep2


title: dKO+Six2_cells_d5_rep3 (RNA-seq)

description:
bamCoverage_RNAseq_Six2.bigwig
counts-DE-scaled-avg-sig-WT-dKO-Six2_p0.05_l2FC1.xlsx
counts-DE-scaled-avg-sig-Mesp1-Msgn1-Six2.xlsx
counts-DE-scaled-avg-sig-Mixl1-Foxa2-Six2.xlsx
nrm-counts-avg-Mesp1-Msgn1-Mixl1-Foxa2-Six2.xlsx

library_source: transcriptomic

data_processing:
For differential gene expression analysis sequenced reads were mapped to the mouse reference genome GRCm38/mm10 (iGenomes, Illumina) containing the chromosomes 1-19, X, Y and M using Rsubread v1.28.1 package in R v3.4.3. The genomic annotations used for the mapping, counting and downstream analyses were contained in gtf files provided by the iGenomes reference genome bundles (archive-2015-07-17-32-40 and archive-2015-07-17-33-26 for GRCM38 and mm10, respectively). Genomic features were counted using the Rsubread::featureCounts function. Differential expression analysis was carried out using DESeq2 v1.18.1 in R, which applies Negative Binomial GLM fitting and Wald statistics on the count data. The results were filtered for adjusted p-value<0.05 and log2FC. Prior to fitting and statistical analysis, counts were normalized by library size (DESeq2::estimateSizeFactors) and gene-wise dispersion (DESeq2::estimateDispersions) to normalize the gene counts by gene-wise geometric mean over samples.     Mapping for the creation of bigwig Coverage files was performed on Galaxy platform using Bowtie2 (v2.3.4) on mm10 reference genome with default settings. Obtained bam files from biological triplicates were merged using Merge BAM files tool in Galaxy (picard v1.56.0) and the duplicates were removed by RmDup tool (samtools v1.3.1). Coverage files were created using bamCoverage tool (deepTools v3.0.2) with bin size 10 bases and reads per kilobase per million (RPKM) normalization.
Mapping: For the RNA-seq results reads trimmed of the addapters were mapped to the mouse reference genome GRCm38/mm10 (iGenomes, Illumina), using Rsubread v1.28.1 package in R v3.4.3. For ATAC-seq and ChIP seq reads were mapped to mm10 genome using Bowtie2 v2.3.4 on the Galaxy platform.
Counting: Genomic features were counted for the RNA-seq analysis with the Rsubread::featureCounts function in Rsubread v1.28.1 package using genomic annotations as gtf files provided by the iGenomes reference genome bundles (archive-2015-07-17-32-40 and archive-2015-07-17-33-26 for GRCM38 and mm10, respectively).
Differential expression: Differential expression analysis was carried out using DESeq2 v1.18.1 in R, which applies Negative Binomial GLM fitting and Wald statistics on the count data. The results were filtered for adjusted p-value<0.05 and log2FC as indicated in the figure legends. Prior to fitting and statistical analysis, counts were normalized by library size (DESeq2::estimateSizeFactors) and gene-wise dispersion (DESeq2::estimateDispersions) to normalize the gene counts by gene-wise geometric mean over samples. Gene-wise scaling was performed on the normalized counts to cluster the counts for the expression tendency between the samples (stats::kmeans function). In addition, the counts were centered by setting the gene-wise mean to zero.
Coverage: For the generation of coverage files for RNA-seq, ATAC-seq and ChIP-seq analysis corresponding bam files from biological replicates were merged using Merge BAM files tool in Galaxy (picard v1.56.0) and the duplicates were removed by RmDup tool (samtools v1.3.1). Coverage files were created using bamCoverage tool (deepTools v3.0.2) with bin size 10 bases and reads per kilobase per million (RPKM) normalization.
Peak calling: Peaks were detected using MACS2 on the Galaxy platform (v2.1.1.20160309.4) with BAMPE format of the input file, default settings for building the shifting model and minimum q-value cut-off for detection of 0.05. For ChiP-seq of EoGFP and BraGFP peaks detected in the input control and dKO -dox control were subtracted from the genomic intervals detected in ChIP-seq treatment file using SubtractBed tool (bedtools v2.27.0) in Galaxy, where entire features were filtered out if the overlap of minimum 1 bp was found. For ChiP-seq of EoGFP and BraGFP peaks the resulting narrow peaks bed file was sorted and filtered for the pileup value (height of the peak at the summit, provided in the Peaks tabular file from MACS2) higher than 120 and 40, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: Processed RNA-seq results showing differential gene expression between WT and dKO contain normalized and scaled counts (RPKM) in Tab delimited txt format. Coverage files in BigWig format  for RNA-seq and ChIP-seq reads are normalized to RPKM. Bed files for EoGFP and BraGFP ChIP-seq contain coordinates of the peaks recognized after MACS2 peak calling and subsequent filtering for the pileup value.

source_name: 5 days dKO+Six2 embryoid bodies (ActA + dox)

growth_protocol:
Prior to differentiation, ESCs were depleted of feeders by splitting for 2-3 passages onto 0.1% gelatin-coated 60 mm dishes. For embryoid body (EB) formation, 200 cells in 40 μl ESGRO Complete Basal medium were grown in ultra-low attachment 96-well plates (Greiner BioOne) for 2 days until single EB had formed in every well. EBs were subsequently transferred into 60 mm non-adhesive dishes and allowed to further differentiate in ESGRO Complete Basal medium with 30 ng/ml human recombinant ActivinA (ActA, R&D systems). For doxycycline inducible expression of inserted constructs 5 µg/ml of dox was used from day 2 to day 5 of differentiation.
A2lox.Cre Mouse ESCs were grown in the standard serum containing conditions with 1000 U/ml LIF, 3 mM CHIR99021 and 1 mM OD0325901 on the monolayer of mitotically inactivated STO feeder cells (SNL76/7). Prior to differentiation cells were depleted of feeders and 200 cells per 40 ml of serum-free Basal medium were grown as embryoid bodies (EBs) in ultra-low attachment plates for 2 days, or alternatively, 2.5x10^5 cells were grown as EBs in 10 mm non-adherent dishes in Basal medium. Cells were further treated and grown for 2-3 more days.

extract_protocol:
RNA from differentiated embryoid bodies was extracted with RNeasy Mini Kit (Qiagen) with on-column DNAse digestion as recommended by the manufacturer.
Library preparation was carried out using 0.5 μg of RNA with NEBNext Ultra RNA library Prep Kit for Illumina (New England BioLabs). RNA from E7.5 epiblasts was isolated using RNeasy Micro kit (Qiagen). Libraries were prepared from 10 ng of RNA with the Ovation SoLo RNA-seq Systems kit (NuGEN).

value: dKO

value: ActA + dox


title: genomic DNA from post-mortem hippocampus 50

value: post-mortem interval:33.5


title: genomic DNA from post-mortem hippocampus 33

value: Female

value: post-mortem interval:30.5


title: dKO+Six2_cells_d5_rep2 (RNA-seq)


title: IR group vs. iPoCreplicate 1


title: genomic DNA from post-mortem hippocampus 30

value: Male

value: Control

value: Other

value: post-mortem interval:35.5


title: dKO+Six2_cells_d5_rep1 (RNA-seq)

description:
bamCoverage_RNaseq_Six2.bigwig
counts-DE-scaled-avg-sig-WT-dKO-Six2_p0.05_l2FC1.xlsx
counts-DE-scaled-avg-sig-Mesp1-Msgn1-Six2.xlsx
counts-DE-scaled-avg-sig-Mixl1-Foxa2-Six2.xlsx
nrm-counts-avg-Mesp1-Msgn1-Mixl1-Foxa2-Six2.xlsx


title: spy138 swi6delta [Swi6 (home made antibody)]

city: Durham

first: Nahid

last: Iglesias

state: NC

address: 101 Science Drive, CIEMAS Rm. 2323

department: Biomedical Engineering

institute: Duke University

description: barcode sequence: TAGCTAGTA

data_processing:
Raw reads were separated by barcode. Barcode sequence were removed from the reads and attached to the identifier. Reads were mapped using Bowtie's default parameters. Mapped reads were normalized to reads per million, tiled with igvtools, and visualized in Integrated Genome Viewer (IGV).
Genome_build: ASM294v2
Supplementary_files_format_and_content: Mapped reads were normalized to reads per million, tiled with igvtools for visualization in Integrated Genome Viewer (IGV).

organism: Schizosaccharomyces pombe

source_name: spy138 swi6delta

extract_protocol:
ChIP was performed essentially as described (Jih et al., 2017). Briefly, 50 ml of logarithmically growing cells were fixed with 1% formaldehyde for 15 min at room temperature, quenched with 130 mM glycine for 5 min, harvested and washed twice with 1x TBS (50 mM Tris-HCl, pH 7.5, 150 mM NaCl). Cells were resuspended in 500 µl lysis buffer (50 mM Hepes-KOH, pH 7.5, 500 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% SDS, and protease inhibitors) in 2 ml screw-cap tubes and lysed by bead beating with 1 ml acid-washed 0.5 mm glass beads with 6 cycles of 30 sec at 5000 rpm on a MagNA Lyser Instrument (Roche). Extracts were sonicated for 3x20 sec at 50% amplitude using a sonicator (Branson Digital Sonifier). For H3K9me2 ChIP, 2 µg of anti-H3K9me2 antibody (Abcam, ab1220) coupled to 30 µl Dynabeads Protein A (Invitrogen, 100-02D) was used for each immunoprecipitation. For H3K9me3 ChIP, 1 µg of anti-H3K9me3 antibody (Diagenode C15500003) was first incubated with 30 µl Dynabeads M-280 Streptavidin beads (Invitrogen, 11206D), followed by blocking with 5 µM biotin, according to the manufacturer's instructions, prior to be used for each immunoprecipitation. Half (250 µl for ChIP-seq) or one fifth (100 µl for ChIP-qPCR) of sheared chromatin lysate was added to the antibody-bead mixture and incubated for 2 hr at 4°C on a rotating device.
Immunoprecipitated DNA was cleaned up using the Qiagen PCR Purification Kit after reversing cross-links, RNaseA, and proteinase K treatment. Immunoprecipitated DNA was eluted from column with the provided elution buffer (50 ul x 2), subjected to additional shearing in a Qsonica water bath sonicator at 20% amplitude for 15 minutes of total shearing time (each cycle is 15” on + 15” off), followed by vacuum centrifugation to reduce the volume to 30 ul. DNA concentration was measured using Qubit dsDNA HS Kit.1 to 10 ng of immunoprecipitated DNA was used for standard Illumina library construction using barcoded adapters and protocol described previously (Wong et al., 2013). Libraries were pooled and sequenced on the Illumina HiSeq2000 or 2500.

tag: media

value: YEA

value: spy138 swi6delta

tag: antibody

value: Swi6 (home made antibody)


title: spy138 WT [Swi6 (home made antibody)]

description: barcode sequence: GTGGGATA

source_name: spy138 WT

value: spy138 WT


title: spy138 npp106delta [Swi6 (home made antibody)]

description: barcode sequence: ATCCTATTC

source_name: spy138 npp106delta

value: spy138 npp106delta


title: dKO+EoTBX_cells_d5_rep3(RNA-seq)

description:
bamCoverage_RNAseq_EoTBX.bigwig
counts-DE-scaled-avg-sig-EoFL-VP16-EnR-EoTBX_p0.05_l2FC1.xlsx

source_name: 5 days dKO+EoTBX embryoid bodies (ActA + dox)


title: genomic DNA from post-mortem hippocampus 28

tag: Sex

value: Bipolar

value: Caucasian

value: post-mortem interval:44

value: post-mortem hippocampus


title: genomic DNA from post-mortem hippocampus 32

tag: group

value: post-mortem interval:17


title: genomic DNA from post-mortem hippocampus 29

tag: age at death

value: post-mortem interval:27


title: spy138 npp106delta [H3K9me3 (Diagenode C15500003)]

description: barcode sequence: CGAACTGTG

value: H3K9me3 (Diagenode C15500003)


title: dKO+EoTBX_cells_d5_rep2 (RNA-seq)

value: dKO

value: ActA + dox


title: genomic DNA from post-mortem hippocampus 31

value: Female

tag: race

value: post-mortem interval:19


title: spy138 WT [H3K9me3 (Diagenode C15500003)]

description: barcode sequence: ACGTAGCTC


title: dKO+EoTBX_cells_d5_rep1 (RNA-seq)


title: spy137 Nur1-TAP clr4delta [Dynabeads Pan Mouse IgG (Invitrogen 11041)]

description: barcode sequence: TGCGGTTA

source_name: spy137 Nur1-TAP clr4delta

value: spy137 Nur1-TAP clr4delta


title: genomic DNA from post-mortem hippocampus 19

value: Control

value: Other

tag: tissue

value: post-mortem interval:28.5


title: spy137 Nur1-TAP [Dynabeads Pan Mouse IgG (Invitrogen 11041)]

description: barcode sequence: TATACCGT

source_name: spy137 Nur1-TAP

value: YEA

value: spy137 Nur1-TAP


title: genomic DNA from post-mortem hippocampus 18

value: Male

value: post-mortem interval:21.5

tag: tissue ph


title: genomic DNA from post-mortem hippocampus 21

value: Bipolar

value: post-mortem interval:30.5


title: genomic DNA from post-mortem hippocampus 22

value: post-mortem interval:18.5

value: post-mortem hippocampus


title: genomic DNA from post-mortem hippocampus 27

value: Caucasian

value: post-mortem interval:24


title: genomic DNA from post-mortem hippocampus 14

value: post-mortem interval:24.5


title: dKO+Foxa2_cells_d5_rep3 (RNA-seq)

description:
processed data files:
counts-DE-scaled-avg-sig-Mixl1-Foxa2_p0.05_l2FC1.xlsx
nrm-counts-avg-Mesp1-Msgn1-Mixl1-Foxa2.xlsx

source_name: 5 days dKO+Foxa2 embryoid bodies (ActA + dox)

value: dKO

value: ActA + dox


title: 100µM MEL rep2

city: Melbourne

first: Sajal

middle: Fatima

last: Zia

state: VIC

address: Agribio,  5 Ring Rd, Bundoora VIC 3083

department: Animal, Plant and Soil Sciences

country: Australia

institute: La Trobe University

data_processing:
bcl2fastq2 Conversion Software v2.20 was used to convert bcl to fastq files and remove adapter sequences
Read quality control was conducted by using the FastQC software (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The Kallisto program (Bray et al., 2016) was used to determine transcript abundance as transcripts per million (TPM) by pseudoalignment of reads to the Araport11 model transcriptome with a k-mer length of 31 (Cheng et al., 2017).
For differential gene expression analysis, the sleuth program was used which utilizes a Wald test to determine differential gene expression (Pimentel et al., 2017).
Genes with a false discovery rate (FDR) of < 0.05 and log2 fold change of at least 1.2 were classified as differentially expressed.
For functional analysis, gene ontology (GO) term enrichment of differentially expressed genes was conducted from a publicly available database (www.geneontology.org) and functional GO annotations for each gene was obtained from the bulk data retrieval tool in TAIR (www.arabidopsis.org).
Genome_build: pseudoalignment of reads to the Araport11 model transcriptome (www.arabport.org) with a k-mer length of 31 (Cheng et al., 2017).
Supplementary_files_format_and_content: The processed data files contains the TPM values for each gene across samples from the kallisto output

organism: Arabidopsis thaliana

source_name: rosette

growth_protocol: Seeds were germinated on Gamborg's B5 media (Phytotechnoloy Laboratory, USA) for 12 days after which they were transferred to control (0.1% EtOH), melatonin (5 or 100µM) or NAA(4.5µM) supplemented Gamborg's B5 media for 3 days. Growth conditions of the controlled environment room were 23°C, 56% relative humidity (RH), Light intensity 120 μmol m-2 s-1,   photoperiod: 16h/8h light/dark cycle

extract_protocol:
Rosettes were carefully separated from roots, immediately flash frozen in liquid nitrogen and stored at -80°C until further analysis. RNA was harvested using Spectrum™ Plant Total RNA kit (STRN250,Sigma, NSW, Australia) following manufacturer’s guidelines. Illumina TruSeq stranded mRNA library kit (Catalog # RS-122-9004) was used for construction of sequencing libraries.
Libraries were prepared using standard protocol by TruSeq stranded mRNA library kit (Illumina, Catalog # RS-122-9004)

tag: ecotype

value: rosette

value: wild type

tag: age

value: 15-day old


title: genomic DNA from post-mortem hippocampus 16

value: post-mortem interval:28.5


title: spy137 Lem2-TAP clr4delta [Dynabeads Pan Mouse IgG (Invitrogen 11041)]

description: barcode sequence: TCGCGTAC

source_name: spy137 Lem2-TAP clr4delta

value: YEA

value: spy137 Lem2-TAP clr4delta


title: genomic DNA from post-mortem hippocampus 15

value: Male

value: post-mortem interval:40.5


title: genomic DNA from post-mortem hippocampus 25

value: Female

value: Bipolar

value: post-mortem interval:36


title: 100µM MEL rep1

tag: genotype


title: genomic DNA from post-mortem hippocampus 24

value: Control

value: Other

value: post-mortem interval:31.5

value: post-mortem hippocampus


title: 5µM MEL rep3


title: genomic DNA from post-mortem hippocampus 10

value: Caucasian

value: post-mortem interval:29


title: 100µM MEL rep3

value: rosette


title: genomic DNA from post-mortem hippocampus 20

value: post-mortem interval:16


title: 5µM MEL rep2

value: wild type

value: 15-day old


title: spy1964 h- Nup211-GFP clr4delta [GFP (Abcam ab290)]

description: barcode sequence: GACACTCTA

source_name: spy1964 h- Nup211-GFP clr4delta

value: YEA

tag: genotype/variation

value: spy1964 h- Nup211-GFP clr4delta

value: GFP (Abcam ab290)


title: dKO+Mixl1_cells_d5_rep3 (RNA-seq)

source_name: 5 days dKO+Mixl1 embryoid bodies (ActA + dox)

value: dKO

value: ActA + dox


title: 4.5µM NAA rep3


title: genomic DNA from post-mortem hippocampus 13

value: Female

value: post-mortem interval:62.5


title: genomic DNA from post-mortem hippocampus 26

value: Male

value: Control

value: post-mortem interval:15.5


title: 4.5µM NAA rep2


title: genomic DNA from post-mortem hippocampus 11

value: Other

value: post-mortem interval:20.5

value: post-mortem hippocampus


title: 0.1% EtOH rep3

value: rosette


title: genomic DNA from post-mortem hippocampus 23

value: Bipolar

value: Caucasian

value: post-mortem interval:46.5


title: dKO+Mixl1_cells_d5_rep2 (RNA-seq)


title: spy1964 h- (no tag GFP control) [GFP (Abcam ab290)]

description: barcode sequence: AGTAGTGGC

source_name: spy1964 h- (no tag GFP control)

value: YEA

value: spy1964 h- (no tag GFP control)


title: dKO+Mixl1_cells_d5_rep1 (RNA-seq)


title: 4.5µM NAA rep1

value: wild type

value: 15-day old


title: 0.1% EtOH rep2


title: 0.1% EtOH rep1


title: spy137 Npp106-GFP clr4delta [GFP (Abcam ab290)]

description: barcode sequence: GCGTTTCGA

source_name: spy137 Npp106-GFP clr4delta

value: spy137 Npp106-GFP clr4delta

value: GFP (Abcam ab290)


title: tissue_mmu_liver_apap_ther_Proton

city: Bronx

first: Sanjeev

last: Gupta

state: NY

address: 1300 Morris Park Ave.

department: Medicine

institute: Albert Einstein College of Medicine

data_processing:
Basecalls performed using Ion Torrent Suite, default parameters
Raw RNA-seq reads were trimmed using fastq_quality_trimmer version 0.0.14 with default parameters
Trimmed RNA-seq reads were aligned to the mature miRNA assembly (release 21) using Shrimp2 version 2.2.3 with default parameters
Aligned RNA-seq reads were counted using custom Python script
Read counts from PGM and Proton were combined
Genome_build: mmu mature miRNA (release 21) from mirbase.org
Supplementary_files_format_and_content: Tab-delimited text files were generated using custom Python script; Scores represent number of aligned sequence fragments per gene

source_name: liver

extract_protocol:
Total RNA was isolated with Norgen total RNA purification kit (Norgen Biotek Corp., Canada), small RNAs were enriched using Ion Total RNA-Seq Kit v2 (Life Technologies)
small RNA libraries were prepared with Ion Total RNA-Seq Kit v2 according to the kit manual

tag: origin

value: liver

value: 500mg/kg acetaminophen+100µg/kg G-CSF


title: genomic DNA from post-mortem hippocampus 4

value: Male

value: Control

value: post-mortem interval:49


title: dKO+Msgn1_cells_d5_rep2 (RNA-seq)

description:
processed data files:
counts-DE-scaled-avg-sig-Mesp1-Msgn1_p0.05_l2FC1.xlsx
nrm-counts-avg-Mesp1-Msgn1-Mixl1-Foxa2.xlsx

source_name: 5 days dKO+Msgn1 embryoid bodies (ActA + dox)

value: dKO

value: ActA + dox


title: genomic DNA from post-mortem hippocampus 7

value: Female

value: Other

value: post-mortem interval:23.5

value: post-mortem hippocampus


title: dKO+Msgn1_cells_d5_rep3 (RNA-seq)


title: genomic DNA from post-mortem hippocampus 17

value: Bipolar

value: Caucasian

value: post-mortem interval:47.5


title: tissue_mmu_liver_apap_1_Proton

value: 500mg/kg acetaminophen


title: tissue_mmu_liver_Proton

value: untreated control


title: genomic DNA from post-mortem hippocampus 3

value: post-mortem interval:18


title: spy137 (no tag GFP control) [GFP (Abcam ab290)]

description: barcode sequence: ATCCTATTC

source_name: spy137 (no tag GFP control)

value: YEA

value: spy137 (no tag GFP control)

value: GFP (Abcam ab290)


title: dKO+Mesp1_cells_d5_rep3 (RNA-seq)

source_name: 5 days dKO+Mesp1 embryoid bodies (ActA + dox)


title: 5µM MEL rep1

value: rosette

value: wild type

value: 15-day old


title: genomic DNA from post-mortem hippocampus 6

value: Male

value: Control

value: post-mortem interval:13.5


title: exosome_mmu_hepa_apap_ther_Proton

source_name: primary hepatocytes exosome

value: primary hepatocytes culture medium

value: 20 mM acetaminophen+1 µg/ml G-CSF


title: dKO+Foxa2_cells_d5_rep2 (RNA-seq)

value: dKO

value: ActA + dox


title: dKO+Mesp1_cells_d5_rep2 (RNA-seq)


title: cells_mmu_hepa_apap_ther_Proton

source_name: primary hepatocytes

value: cultured primary hepatocytes


title: exosome_mmu_hepa_Proton


title: genomic DNA from post-mortem hippocampus 5

value: Caucasian

value: post-mortem interval:16

value: post-mortem hippocampus


title: genomic DNA from post-mortem hippocampus 1

value: post-mortem interval:26.5


title: dKO+Mesp1_cells_d5_rep1 (RNA-seq)

description:
processed data file:
counts-DE-scaled-avg-sig-Mesp1-Msgn1_p0.05_l2FC1.xlsx
nrm-counts-avg-Mesp1-Msgn1-Mixl1-Foxa2.xlsx


title: genomic DNA from post-mortem hippocampus 2

value: Female

value: Bipolar


title: exosome_mmu_serum_apap_Proton

source_name: serum exosome

value: blood

value: 500mg/kg acetaminophen+100µg/kg G-CSF


title: cells_mmu_hepa_Proton

value: untreated control


title: spy137 (no tag Flag control) [Flag (Sigma F1804)]

description: barcode sequence: TTAGGC

source_name: spy137 (no tag Flag control)

value: YEA

value: spy137 (no tag Flag control)

value: Flag (Sigma F1804)


title: genomic DNA from post-mortem hippocampus 9

value: Control

value: Other

value: post-mortem interval:32


title: spy138 Flag-swi6 WT dcr1delta [Flag (Sigma F1804)]

description: barcode sequence: TCGCGTAC

source_name: spy138 Flag-swi6 WT dcr1delta

value: spy138 Flag-swi6 WT dcr1delta


title: spy138 Flag-swi6 WT dcr1delta taz1delta [Flag (Sigma F1804)]

description: barcode sequence: TATACCGT

source_name: spy138 Flag-swi6 WT dcr1delta taz1delta

value: spy138 Flag-swi6 WT dcr1delta taz1delta


title: exosome_mmu_hepa_apap_Proton

value: primary hepatocytes culture medium

value: 20 mM acetaminophen


title: spy137 Npp106-GFP [GFP (Abcam ab290)]

description: barcode sequence: CGGACGTGG

source_name: spy137 Npp106-GFP

value: spy137 Npp106-GFP

value: GFP (Abcam ab290)


title: exosome_mmu_serum_Proton


title: spy138 Flag-swi6 WT dcr1delta taz1delta [H3K9me3 (Diagenode C15500003)]

description: barcode sequence: CTCTGTCT

value: H3K9me3 (Diagenode C15500003)


title: tissue_mmu_liver_apap_ther_PGM

value: liver


title: genomic DNA from post-mortem hippocampus 12

value: Male

value: post-mortem interval:33.5

value: post-mortem hippocampus


title: dKO+Foxa2_cells_d5_rep1 (RNA-seq)

source_name: 5 days dKO+Foxa2 embryoid bodies (ActA + dox)

value: dKO

value: ActA + dox


title: dKO_cells_d5_nodox_rep2 (RNA-seq)

description:
processed data file:
bamCoverage_RNAseq_dKO_nodox.bigwig

source_name: 5 days dKO+EoGFP embryoid bodies (ActA)

value: ActA


title: tissue_mmu_liver_apap_1_PGM

value: 500mg/kg acetaminophen


title: tissue_mmu_liver_PGM

value: untreated control


title: cells_mmu_hepa_apap_ther_PGM

value: cultured primary hepatocytes

value: 20 mM acetaminophen+1 µg/ml G-CSF


title: exosome_mmu_serum_apap_ther_Proton

value: blood


title: cells_mmu_hepa_apap_PGM


title: spy137 Mdn1-myc clr4delta [c-myc 9E10 (Covance MMS-150)]

description: barcode sequence: TGACGCAT

source_name: spy137 Mdn1-myc clr4delta

value: YEA

value: spy137 Mdn1-myc clr4delta

value: c-myc 9E10 (Covance MMS-150)


title: dKO_cells_d5_nodox_rep1 (RNA-seq)


title: dKO_cells_d5_nodox_rep3 (RNA-seq)


title: spy138 Flag-swi6 WT dcr1delta [H3K9me3 (Diagenode C15500003)]

description: barcode sequence: AGGTCAGT

value: spy138 Flag-swi6 WT dcr1delta


title: exosome_mmu_hepa_apap_ther_PGM

value: primary hepatocytes culture medium


title: spy137 Mdn1-myc swi6delta [c-myc 9E10 (Covance MMS-150)]

description: barcode sequence: GTTGTCCCA

source_name: spy137 Mdn1-myc swi6delta

value: spy137 Mdn1-myc swi6delta


title: dKO+BraEnR_cells_d5_rep2 (RNA-seq)

description:
processed data files:
bamCoverage_RNAseq_BraEnR.bigwig
DE-sig-BraEnRdox-vs-dKOnodox_p0.05_l2FC1.xlsx
counts-DE-scaled-avg-sig-BraFL-VP16-EnR_p0.05_l2FC1.xlsx

source_name: 5 days dKO+BraEnR embryoid bodies (ActA + dox)


title: dKO+BraEnR_cells_d5_rep3 (RNA-seq)


title: exosome_mmu_hepa_apap_PGM

value: 20 mM acetaminophen


title: dKO+BraEnR_cells_d5_rep1 (RNA-seq)


title: exosome_mmu_hepa_PGM


title: cells_mmu_hepa_apap_Proton


title: spy137 Mdn1-myc [c-myc 9E10 (Covance MMS-150)]

description: barcode sequence: CAGGAGGCG

source_name: spy137 Mdn1-myc

value: spy137 Mdn1-myc


title: cells_mmu_hepa_PGM


title: exosome_mmu_serum_apap_PGM

value: 500mg/kg acetaminophen+100µg/kg G-CSF


title: genomic DNA from post-mortem hippocampus 8

value: Female

value: Control

value: Caucasian

value: post-mortem interval:50

value: post-mortem hippocampus


title: spy138 Rix1-myc clr4delta [c-myc 9E10 (Covance MMS-150)]

description: barcode sequence: ACTAACTGC

source_name: spy138 Rix1-myc clr4delta

value: spy138 Rix1-myc clr4delta


title: dKO+BraVP16_cells_d5_rep3 (RNA-seq)

description:
processed data files:
bamCoverage_RNAseq_BraVP16.bigwig
DE-sig-BraVP16dox-vs-dKOnodox_p0.05_l2FC1.xlsx
counts-DE-scaled-avg-sig-BraFL-VP16-EnR_p0.05_l2FC1.xlsx

source_name: 5 days dKO+BraVP16 embryoid bodies (ActA + dox)

value: dKO

value: ActA + dox


title: spy137 Lem2-TAP [Dynabeads Pan Mouse IgG (Invitrogen 11041)]

description: barcode sequence: GCAGCCTC

source_name: spy137 Lem2-TAP

value: YEA

value: spy137 Lem2-TAP


title: exosome_mmu_serum_apap_ther_PGM

value: blood

value: 500mg/kg acetaminophen


title: exosome_mmu_serum_PGM

value: untreated control


title: spy138 Rix1-myc swi6delta [c-myc 9E10 (Covance MMS-150)]

description: barcode sequence: TTGAGTGT

source_name: spy138 Rix1-myc swi6delta

value: spy138 Rix1-myc swi6delta

value: c-myc 9E10 (Covance MMS-150)


title: dKO+BraVP16_cells_d5_rep1 (RNA-seq)


title: dKO+BraVP16_cells_d5_rep2 (RNA-seq)


title: spy138 Rix1-myc [c-myc 9E10 (Covance MMS-150)]

description: barcode sequence: GGTCCTTGA

source_name: spy138 Rix1-myc

value: spy138 Rix1-myc


title: spy137 Crb3-TAP clr4delta [Dynabeads Pan Mouse IgG (Invitrogen 11041)]

description: barcode sequence: GAGTTAAC

source_name: spy137 Crb3-TAP clr4delta

value: spy137 Crb3-TAP clr4delta


title: dKO+BraFL_cells_d5_rep3 (RNA-seq)

description:
processed data files:
bamCoverage_RNAseq_BraGFP.bigwig
DE-sig-BraGFPdox-vs-dKOnodox_p0.05_l2FC1.xlsx
counts-DE-scaled-avg-sig-BraFL-VP16-EnR_p0.05_l2FC1.xlsx
nrm-counts-avg-WT-BraKO-EoKO-dKO-BraGFP-EoGFP.xlsx

source_name: 5 days dKO+BraGFP embryoid bodies (ActA + dox)


title: spy137 Crb3-TAP swi6delta [Dynabeads Pan Mouse IgG (Invitrogen 11041)]

description: barcode sequence: GTCTACAT

source_name: spy137 Crb3-TAP swi6delta

value: spy137 Crb3-TAP swi6delta


title: dKO+BraFL_cells_d5_rep2 (RNA-seq)


title: PTC_1

city: Montreal

first: Gilbert

last: Bernier

state: Quebec

address: 5415 Boul. l’Assomption

country: Canada

institute: Hopital Maisonneuve-Rosemont

data_processing:
Hisat2 alignment on hg19
Counts using FeaturesCount software
DEseq on R for differential expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: counts

growth_protocol: GBM media: DMEM/F12 medium (Invitrogen) containing 0.25% glucose, N2 and B27 supplements, Heparin (2 μg/ml; Sigma), gentamicin (25 μg/ml; Invitrogen), human recombinant FGF2 (10 ng/ml; Peprotech), and human recombinant EGF (20 ng/ml; Sigma).

extract_protocol:
RNeasy columns
Ion Torrent protocol

tag: cell line

value: Glioblastoma Multiform (GBM) cell line


title: PTC_2


title: A1016_1


title: gCTL_1

value: Non targeting control


title: gCTL_2


title: gBMI1_2

value: BMI1 guide RNA


title: DMSO_1

value: DMSO


title: dKO+BraFL_cells_d5_rep1 (RNA-seq)

tag: day


title: gBMI1_1


title: A1016_2

tag: treatment


title: DMSO_2


title: spy137 (no tag IgG control) [Dynabeads Pan Mouse IgG (Invitrogen 11041)]

description: barcode sequence: CCATACAC

source_name: spy137 (no tag IgG control)

value: spy137 (no tag IgG control)


title: spy137 Crb3-TAP [Dynabeads Pan Mouse IgG (Invitrogen 11041)]

description: barcode sequence: CGCATTAA

source_name: spy137 Crb3-TAP

value: spy137 Crb3-TAP


title: dKO+EoEnR_cells_d5_rep3 (RNA-seq)

description:
processed data files:
bamCoverage_RNAseq_EoEnR.bigwig
DE-sig-EoEnRdox-vs-dKOnodox_p0.05_l2FC1.xlsx
counts-DE-scaled-avg-sig-EoFL-VP16-EnR_p0.05_l2FC1.xlsx

source_name: 5 days dKO+EoEnR embryoid bodies (ActA + dox)

value: dKO

value: ActA + dox


title: VD3 treatment rep2

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

data_processing:
All RNA-seq data were mapped to the mm10 genome for mouse using Tophat2 (v2.1.1), which was shown to be accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Then, duplicated reads for pair-end data were removed, but not single-end data by SAMtools (v1.5).
FPKM, read count matrix and differential gene expression were calculated by Cufflinks (v2.2.1) with parameters “-p 20 --FDR 0.05" and based on the  gene annotation assembed by cuffmerge.
Genome_build: mm10
Supplementary_files_format_and_content: expression Count and FPKM data

source_name: embryo

growth_protocol: mESCs were maintained in the presence of leukemia inhibitory factor (LIF, Millipore) in KO DMEM containing 15% ES qualified fetal calf serum or 20%KSR on mouse embryonic fibroblast (MEF) feeder cells.

extract_protocol:
RNA isolation and DNase treatment were according to instructions of RNeasy Mini Kit, QIAGEN
RNA libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol for RNA-seq libraries.

treatment_protocol: 1)  Treatment of MM401(100uM) and 1α,25-Dihydroxyvitamin D3 (Sigma Aldrich, D1530,  final concentration of 1uM) on mESCs for 5 day in LIF/Serum/KO DMEM medium; 2)Treatment of 1α,25-Dihydroxyvitamin D3 (Sigma Aldrich, D1530,  final concentration of 1uM) on mESCs for 5 day in LIF/Serum/KO DMEM medium. ESCs are cultured with feeder cells .

tag: cell type

value: embryonic stem cell, blastocyst derived

value: Mll1fl/fl; Cre-ER TM

tag: strain

tag: agent


title: VD3 treatment rep1


title: dKO+EoEnR_cells_d5_rep2 (RNA-seq)


title: VD3+MLL1 inhibition rep2

value: VD3 and MM-401 (Mll1i)


title: spy137 Flag-swi6 WT [Flag (Sigma F1804)]

description: barcode sequence: ACAGTG

source_name: spy137 Flag-swi6 WT

tag: media

value: YEA

value: spy137 Flag-swi6 WT

tag: antibody

value: Flag (Sigma F1804)


title: VD3+MLL1 inhibition rep1


title: spy138 Flag-swi6 WT clr4delta [H3K9me3 (Diagenode C15500003)]

description: barcode sequence: ATATAGGA

source_name: spy138 Flag-swi6 WT clr4delta

value: spy138 Flag-swi6 WT clr4delta

value: H3K9me3 (Diagenode C15500003)


title: ESCfl/fl rep2

value: untreated


title: ESCfl/fl rep1


title: dKO+EoEnR_cells_d5_rep1 (RNA-seq)


title: spy138 Flag-swi6 WT H3K9R [H3K9me3 (Diagenode C15500003)]

description: barcode sequence: AACCGTGT

source_name: spy138 Flag-swi6 WT H3K9R

value: spy138 Flag-swi6 WT H3K9R


title: pair_fed_1

city: Vienna

first: Andreas

last: Bergthaler

address: Lazarettgasse 14 AKH BT25.3

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder.
Transcriptome analysis is performed using the Tuxedo suite. Reads are mapped on the mouse reference genome (Mus musculus, Ensembl e87, December 2016) using TopHat2 (v2.0.10).
Cufflinks (v2.2.1) is further used to assemble transcripts from spliced read alignments, using the Ensembl e87 transcriptome as the reference as well as de novo assembly of transcript models.
Differential expression is assessed with Cuffdiff (v2.2.1). Transcriptome sets of all replicates for each sample group will be combined with Cuffmerge.
Genome_build: Ensembl version e87(December 2016) of the Mus musculus genome.
Supplementary_files_format_and_content: tab-delimited text file of normalised cufflinks FPKM

source_name: Liver

extract_protocol:
Total RNA was extracted after sample homogenisation using Qiazol lysis reagent according to manufacturer's instructions.
RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer).
Libraries will be pooled, diluted and sequenced on Illumina HiSeq 3000 using 50 bp single-read chemistry.

treatment_protocol: Mice were infected with 2x10^6 focal-forming units of  lymphocytic choriomeningitis virus (LCMV) clone 13 intravenously.

value: Liver


title: LCMV_2

value: LCMV Cl13


title: pair_fed_3


title: dKO+Msgn1_cells_d5_rep1 (RNA-seq)

source_name: 5 days dKO+Msgn1 embryoid bodies (ActA + dox)


title: LCMV_1


title: LCMV_3


title: uninfected_3

description: BSF_0362_HLV5TBBXX_1#uninfected_3_S29478


title: dKO+EoVP16_cells_d5_rep2 (RNA-seq)

description:
processed data files:
bamCoverage_RNAseq_EoVP16.bigwig
DE-sig-EoVP16dox-vs-dKOnodox_p0.05_l2FC1.xlsx
counts-DE-scaled-avg-sig-EoFL-VP16-EnR_p0.05_l2FC1.xlsx

source_name: 5 days dKO+EoVP16 embryoid bodies (ActA + dox)


title: dKO+EoVP16_cells_d5_rep3 (RNA-seq)


title: dKO+EoFL_cells_d5_rep3 (RNA-seq)

description:
processed data files:
bamCoverage_RNAseq_EoGFP.bigwig
DE-sig-EoGFPdox-vs-dKOnodox_p0.05_l2FC1.xlsx
counts-DE-scaled-avg-sig-EoFL-VP16-EnR_p0.05_l2FC1.xlsx
nrm-counts-avg-WT-BraKO-EoKO-dKO-BraGFP-EoGFP.xlsx

source_name: 5 days dKO+EoGFP embryoid bodies (ActA + dox)


title: spy138 Flag-swi6 WT H3K9R [Flag (Sigma F1804)]

description: barcode sequence: GCAGCCTC


title: dKO+EoVP16_cells_d5_rep1 (RNA-seq)


title: pair_fed_2


title: uninfected_1

description: BSF_0362_HLV5TBBXX_1#uninfected_1_S29476


title: spy1964 h- Nup211-GFP [GFP (Abcam ab290)]

description: barcode sequence: CTAGTCATG

source_name: spy1964 h- Nup211-GFP

value: spy1964 h- Nup211-GFP

value: GFP (Abcam ab290)


title: spy138 Flag-swi6 WT native ChIP purif2 [Flag (Sigma F1804)]

description: barcode sequence: TTCTGATG

source_name: spy138 Flag-swi6 WT native ChIP purif2

value: spy138 Flag-swi6 WT native


title: dKO+EoFL_cells_d5_rep2 (RNA-seq)

value: dKO


title: spy138 Flag-swi6 WT [Flag (Sigma F1804)]

description: barcode sequence: CCATACAC

source_name: spy138 Flag-swi6 WT

value: spy138 Flag-swi6 WT


title: X0d_old rep3

data_processing:
Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder.
Transcriptome analysis is performed using the Tuxedo suite. Reads are mapped on the mouse reference genome (Mus musculus, Ensembl e87, December 2016) using TopHat2 (v2.0.10).
Cufflinks (v2.2.1) is further used to assemble transcripts from spliced read alignments, using the Ensembl e87 transcriptome as the reference as well as de novo assembly of transcript models.
Differential expression is assessed with Cuffdiff (v2.2.1). Transcriptome sets of all replicates for each sample group will be combined with Cuffmerge.
Genome_build: Ensembl version e87 (December 2016) of the Mus musculus genome.
Supplementary_files_format_and_content: tab-delimited text file of normalized cufflinks FPKM

extract_protocol:
Total RNA was extracted after sample homogenisation using Qiazol lysis reagent according to manufacturer's instructions.
RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer).
Libraries will be pooled, diluted and sequenced on Illumina HiSeq 2000 using 50 bp single-read chemistry.

tag: gender

value: female

value: 123d old

tag: infection

value: control

tag: time


title: spy138 (no tag Flag control) [Flag (Sigma F1804)]

description: barcode sequence: GAGTTAAC

source_name: spy138 (no tag Flag control)

value: YEA

value: spy138 (no tag Flag control)


title: dKO+EoFL_cells_d5_rep1 (RNA-seq)

value: ActA + dox


title: X0d_old rep1

tag: tissue


title: X0d_old rep2


title: X123d rep3

value: 2-3 month old

value: 123 days post infection


title: dKO_cells_d5_rep2 (ATAC-seq)

description:
processed data file:
bamCoverage_ATAC_dKO.bigwig

data_processing:
Reads were mapped to the mm10 genome using Galaxy platform Bowtie2 v2.3.4 with default settings. Results from biological duplicates were merged for subsequent analysis using Merge BAM files (picard v1.56.0). After removing duplicates with RmDup (samtools v1.3.1), peaks were detected using MACS2 (v2.1.1.20160309.4) with BAMPE format of the input file, default settings for building the shifting model and minimum q-value cut-off for detection of 0.05. Coverage files were created using bamCoverage (deepTools v3.0.2)19 with bin size 10 bases and normalization to RPKM.
Mapping: For the RNA-seq results reads trimmed of the addapters were mapped to the mouse reference genome GRCm38/mm10 (iGenomes, Illumina), using Rsubread v1.28.1 package in R v3.4.3. For ATAC-seq and ChIP seq reads were mapped to mm10 genome using Bowtie2 v2.3.4 on the Galaxy platform.
Counting: Genomic features were counted for the RNA-seq analysis with the Rsubread::featureCounts function in Rsubread v1.28.1 package using genomic annotations as gtf files provided by the iGenomes reference genome bundles (archive-2015-07-17-32-40 and archive-2015-07-17-33-26 for GRCM38 and mm10, respectively).
Differential expression: Differential expression analysis was carried out using DESeq2 v1.18.1 in R, which applies Negative Binomial GLM fitting and Wald statistics on the count data. The results were filtered for adjusted p-value<0.05 and log2FC as indicated in the figure legends. Prior to fitting and statistical analysis, counts were normalized by library size (DESeq2::estimateSizeFactors) and gene-wise dispersion (DESeq2::estimateDispersions) to normalize the gene counts by gene-wise geometric mean over samples. Gene-wise scaling was performed on the normalized counts to cluster the counts for the expression tendency between the samples (stats::kmeans function). In addition, the counts were centered by setting the gene-wise mean to zero.
Coverage: For the generation of coverage files for RNA-seq, ATAC-seq and ChIP-seq analysis corresponding bam files from biological replicates were merged using Merge BAM files tool in Galaxy (picard v1.56.0) and the duplicates were removed by RmDup tool (samtools v1.3.1). Coverage files were created using bamCoverage tool (deepTools v3.0.2) with bin size 10 bases and reads per kilobase per million (RPKM) normalization.
Peak calling: Peaks were detected using MACS2 on the Galaxy platform (v2.1.1.20160309.4) with BAMPE format of the input file, default settings for building the shifting model and minimum q-value cut-off for detection of 0.05. For ChiP-seq of EoGFP and BraGFP peaks detected in the input control and dKO -dox control were subtracted from the genomic intervals detected in ChIP-seq treatment file using SubtractBed tool (bedtools v2.27.0) in Galaxy, where entire features were filtered out if the overlap of minimum 1 bp was found. For ChiP-seq of EoGFP and BraGFP peaks the resulting narrow peaks bed file was sorted and filtered for the pileup value (height of the peak at the summit, provided in the Peaks tabular file from MACS2) higher than 120 and 40, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: Processed RNA-seq results showing differential gene expression between WT and dKO contain normalized and scaled counts (RPKM) in Tab delimited txt format. Coverage files in BigWig format  for RNA-seq and ChIP-seq reads are normalized to RPKM. Bed files for EoGFP and BraGFP ChIP-seq contain coordinates of the peaks recognized after MACS2 peak calling and subsequent filtering for the pileup value.

source_name: 5 days dKO embryoid bodies (ActA)

growth_protocol:
Prior to differentiation, ESCs were depleted of feeders by splitting for 2-3 passages onto 0.1% gelatin-coated 60 mm dishes. For embryoid body (EB) formation, 200 cells in 40 μl ESGRO Complete Basal medium were grown in ultra-low attachment 96-well plates (Greiner BioOne) for 2 days until single EB had formed in every well. EBs were subsequently transferred into 60 mm non-adhesive dishes and allowed to further differentiate in ESGRO Complete Basal medium with 30 ng/ml human recombinant ActivinA (ActA, R&D systems).
A2lox.Cre Mouse ESCs were grown in the standard serum containing conditions with 1000 U/ml LIF, 3 mM CHIR99021 and 1 mM OD0325901 on the monolayer of mitotically inactivated STO feeder cells (SNL76/7). Prior to differentiation cells were depleted of feeders and 200 cells per 40 ml of serum-free Basal medium were grown as embryoid bodies (EBs) in ultra-low attachment plates for 2 days, or alternatively, 2.5x10^5 cells were grown as EBs in 10 mm non-adherent dishes in Basal medium. Cells were further treated and grown for 2-3 more days.

extract_protocol:
The protocol was modified from Buenrostro et al. EBs were trypsinized to single-cell suspension, washed with PBS, lysed and mixed with 50 µl of transposition reaction mix containing Tagment DNA Enzyme (Nextera DNA Library Preparation Kit, Illumina) and 0.2% Digitonin. The transposition reaction was carried out at 37°C for 30 min, purified using the Qiagen MinElute Kit and eluted in EB-buffer (Qiagen). DNA was amplified by PCR and purified with the Qiagen MinElute Kit (Qiagen, 28004).
Libraries were prepared using Nextera DNA Library Preparation Kit (New England BioLabs). The libraries were size-selected by polyacrylamide gel electrophoresis (PAGE) by loading the samples onto a 6% polyacrylamide gel and run in TBE buffer (89 mM Tris-HCl, 89 mM Boric acid, 2 mM Na2EDTA in H2O, pH 8.0). DNA was visualized with SYBRTMTM Gold Nucleic Acid Gel Stain (Invitrogen, 1:10,000 dilution in TBE-buffer). Gel containing fragments between 100-1,000 bp was cut and resuspended in Diffusion buffer (0.5 M CH3COONH4, 10 mM Mg(CH3COO)2, 1 mM Na2EDTA, 0.1% SDS in H2O) in a 1:1 ratio of buffer to gel (mg). After incubation at 37°C for 22 h samples were filtered using a 30 µm CellTrics strainer and purified using the QIAquick Gel Extraction Kit (Qiagen).

value: ActA


title: spy138 Flag-swi6 WT [H3K9me3 (Diagenode C15500003)]

description: barcode sequence: GATCAG

value: H3K9me3 (Diagenode C15500003)


title: spy138 Flag-swi6 WT native ChIP purif1 [Flag (Sigma F1804)]

description: barcode sequence: CTAGATTCG

source_name: spy138 Flag-swi6 WT native ChIP purif1

value: Flag (Sigma F1804)


title: uninfected_2

description: BSF_0362_HLV5TBBXX_1#uninfected_2_S29477

value: Liver


title: X123d rep1

value: LCMV Cl13


title: X60d rep3

value: 60 days post infection


title: spy138 (no tag Flag  control) native ChIP purif1 [Flag (Sigma F1804)]

description: barcode sequence: TCCAGCCTC

value: spy138 (no tag Flag  control) native


title: WT_cells_d5_rep2 (ATAC-seq)

description:
processed data file:
bamCoverage_ATAC_WT.bigwig

source_name: 5 days A2lox.Cre embryoid bodies (ActA)

value: WT


title: dKO_cells_d5_rep1 (ATAC-seq)

value: dKO


title: X60d rep2

value: female


title: Drosophila virilis_zt15_29C

city: Waltham

last: Kadener

state: MA

address: 415 South Street

institute: Brandeis University

data_processing:
quantification of tim isoforms looking manually the exon-exon juntion reads
Genome_build: dm3, droAnanas2, droSim1, droViri3, droYak2
Supplementary_files_format_and_content: table of tim isoform analysis; transcript quantification

molecule: polyA RNA

organism: Drosophila virilis

source_name: RNA from fly heads

growth_protocol: Flies were grown at different temperatures and heads were collected at different temperatures.

extract_protocol:
RNA extraction was done using TRI Reagent [SIGMA] following manufacturer´s protocol. The precipitated RNAwas taken for library preparation.
Libraries were constructed Stranded ligation-based, total-RNA libraries preparation was modified from (Engreitz et al., 2013) as described in Reddy et al 2018, Biorxiv.

tag: circadian timepoints

tag: temperature

value: fly heads


title: WT_cells_d5_rep1 (ATAC-seq)


title: Drosophila Melanogaster_zt18_29C_2

data_processing:
Read 1 was not used. Read 2 for each sample was processed as described (see bellow)
Ribosomal RNA was taken out using Bowtie2 aligner against the ribosomal RNA
Reads were aligned to dm3 genome using TopHat
The aligned reads were analyzed with cufflinks
Genome_build: dm3
Supplementary_files_format_and_content: table of reads; txt file with isoforms quantification

organism: Drosophila melanogaster

source_name: D. Melanogaster_zt18_29C_fly heads

growth_protocol: Flies were grown at different temperatures

extract_protocol:
The precipitated RNAwas taken for library preparation.
3’-seq libraries were prepared as previously described (Shishki et al., Afik et al., 2017)

treatment_protocol: RNA extraction was done using TRI Reagent [SIGMA] following manufacturer´s protocol.

value: Canton-S

tag: circadian timepoint

tag: replicate


title: Drosophila virilis_zt15_25C


title: Drosophila Melanogaster_zt11_29C_2

source_name: D. Melanogaster_zt11_29C_fly heads


title: Drosophila Melanogaster_zt15_29C_2

source_name: D. Melanogaster_zt15_29C_fly heads


title: Drosophila virilis_zt3_29C


title: Drosophila Melanogaster_zt23_29C_2

source_name: D. Melanogaster_zt23_29C_fly heads


title: H3K27ac_dKO_cells_d5 (ChIP-seq)

description:
processed data file:
bamCoverage_H3K27ac_dKO.bigwig

data_processing:
Mapping: For the RNA-seq results reads trimmed of the addapters were mapped to the mouse reference genome GRCm38/mm10 (iGenomes, Illumina), using Rsubread v1.28.1 package in R v3.4.3. For ATAC-seq and ChIP seq reads were mapped to mm10 genome using Bowtie2 v2.3.4 on the Galaxy platform.
Counting: Genomic features were counted for the RNA-seq analysis with the Rsubread::featureCounts function in Rsubread v1.28.1 package using genomic annotations as gtf files provided by the iGenomes reference genome bundles (archive-2015-07-17-32-40 and archive-2015-07-17-33-26 for GRCM38 and mm10, respectively).
Differential expression: Differential expression analysis was carried out using DESeq2 v1.18.1 in R, which applies Negative Binomial GLM fitting and Wald statistics on the count data. The results were filtered for adjusted p-value<0.05 and log2FC as indicated in the figure legends. Prior to fitting and statistical analysis, counts were normalized by library size (DESeq2::estimateSizeFactors) and gene-wise dispersion (DESeq2::estimateDispersions) to normalize the gene counts by gene-wise geometric mean over samples. Gene-wise scaling was performed on the normalized counts to cluster the counts for the expression tendency between the samples (stats::kmeans function). In addition, the counts were centered by setting the gene-wise mean to zero.
Coverage: For the generation of coverage files for RNA-seq, ATAC-seq and ChIP-seq analysis corresponding bam files from biological replicates were merged using Merge BAM files tool in Galaxy (picard v1.56.0) and the duplicates were removed by RmDup tool (samtools v1.3.1). Coverage files were created using bamCoverage tool (deepTools v3.0.2) with bin size 10 bases and reads per kilobase per million (RPKM) normalization.
Peak calling: Peaks were detected using MACS2 on the Galaxy platform (v2.1.1.20160309.4) with BAMPE format of the input file, default settings for building the shifting model and minimum q-value cut-off for detection of 0.05. For ChiP-seq of EoGFP and BraGFP peaks detected in the input control and dKO -dox control were subtracted from the genomic intervals detected in ChIP-seq treatment file using SubtractBed tool (bedtools v2.27.0) in Galaxy, where entire features were filtered out if the overlap of minimum 1 bp was found. For ChiP-seq of EoGFP and BraGFP peaks the resulting narrow peaks bed file was sorted and filtered for the pileup value (height of the peak at the summit, provided in the Peaks tabular file from MACS2) higher than 120 and 40, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: Processed RNA-seq results showing differential gene expression between WT and dKO contain normalized and scaled counts (RPKM) in Tab delimited txt format. Coverage files in BigWig format  for RNA-seq and ChIP-seq reads are normalized to RPKM. Bed files for EoGFP and BraGFP ChIP-seq contain coordinates of the peaks recognized after MACS2 peak calling and subsequent filtering for the pileup value.

extract_protocol:
The experiment was performed with ChIP-IT High Sensitivity kit (Active motif). 5 μg of Anti-H3K27ac antibody (Abcam, ab4729) was used.
Libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs) and size selection was performed on a 1.3% agarose gel by cutting out fragments between 200-650 bp of size and extracting from the gel using QIAquick gel extraction kit (Qiagen).

tag: genotype/variation

tag: chip antibody


title: H3K27ac_WT_cells_d5 (ChIP-seq)

description:
processed data file:
bamCoverage_H3K27ac_WT.bigwig

tag: day


title: X30d rep2

tag: age

value: 30 days post infection


title: Drosophila Melanogaster_zt3_29C_2

source_name: D. Melanogaster_zt3_29C_fly heads


title: spy138 (no tag Flag  control) native ChIP purif2 [Flag (Sigma F1804)]

description: barcode sequence: GGCAGACGA

value: YEA


title: X123d rep2

source_name: Liver


title: X60d rep1


title: X30d rep3


title: Drosophila virilis_zt15_18C


title: Drosophila Melanogaster_zt7_29C_2

source_name: D. Melanogaster_zt7_29C_fly heads


title: Drosophila virilis_zt3_25C


title: X30d rep1


title: Drosophila Melanogaster_zt23_29C_1


title: Input_cells_d5 (ChIP-seq)

description:
processed data file:
bamCoverage_ChIP_input.bigwig

data_processing:
Reads were mapped to the mm10 genome using Galaxy platform Bowtie2 v2.3.4 with default settings. Results from biological duplicates were merged for subsequent analysis using Merge BAM files (picard v1.56.0). After removing duplicates with RmDup (samtools v1.3.1), peaks were detected using MACS2 (v2.1.1.20160309.4) with BAMPE format of the input file, default settings for building the shifting model and minimum q-value cut-off for detection of 0.05.  Input served as control for MACS2 peak calling. Peaks were further filtered for the pile-up value (height of the peak at the summit, provided in the Peaks tabular file from MACS2) >120 for EoGFP and >40 for BraGFP ChIP-seq. Peaks detected by MACS2 in the input control and dKO -dox control were subtracted from the genomic intervals detected in ChIP-seq treatment file using SubtractBed tool (bedtools v2.27.0) in Galaxy, where entire features were filtered out if the overlap of minimum 1 bp was found. Coverage files were created using the bamCoverage tool (deepTools v3.0.2) with bin size 10 bases and normalization to RPKM. The peak detection by MACS2 is generated as bed file by adding the processed intervals from EoGFP and BraGFP experiments and combining overlapping intervals into a single interval using MergeBED (bedtools v2.27.0) function on Galaxy.
Mapping: For the RNA-seq results reads trimmed of the addapters were mapped to the mouse reference genome GRCm38/mm10 (iGenomes, Illumina), using Rsubread v1.28.1 package in R v3.4.3. For ATAC-seq and ChIP seq reads were mapped to mm10 genome using Bowtie2 v2.3.4 on the Galaxy platform.
Counting: Genomic features were counted for the RNA-seq analysis with the Rsubread::featureCounts function in Rsubread v1.28.1 package using genomic annotations as gtf files provided by the iGenomes reference genome bundles (archive-2015-07-17-32-40 and archive-2015-07-17-33-26 for GRCM38 and mm10, respectively).
Differential expression: Differential expression analysis was carried out using DESeq2 v1.18.1 in R, which applies Negative Binomial GLM fitting and Wald statistics on the count data. The results were filtered for adjusted p-value<0.05 and log2FC as indicated in the figure legends. Prior to fitting and statistical analysis, counts were normalized by library size (DESeq2::estimateSizeFactors) and gene-wise dispersion (DESeq2::estimateDispersions) to normalize the gene counts by gene-wise geometric mean over samples. Gene-wise scaling was performed on the normalized counts to cluster the counts for the expression tendency between the samples (stats::kmeans function). In addition, the counts were centered by setting the gene-wise mean to zero.
Coverage: For the generation of coverage files for RNA-seq, ATAC-seq and ChIP-seq analysis corresponding bam files from biological replicates were merged using Merge BAM files tool in Galaxy (picard v1.56.0) and the duplicates were removed by RmDup tool (samtools v1.3.1). Coverage files were created using bamCoverage tool (deepTools v3.0.2) with bin size 10 bases and reads per kilobase per million (RPKM) normalization.
Peak calling: Peaks were detected using MACS2 on the Galaxy platform (v2.1.1.20160309.4) with BAMPE format of the input file, default settings for building the shifting model and minimum q-value cut-off for detection of 0.05. For ChiP-seq of EoGFP and BraGFP peaks detected in the input control and dKO -dox control were subtracted from the genomic intervals detected in ChIP-seq treatment file using SubtractBed tool (bedtools v2.27.0) in Galaxy, where entire features were filtered out if the overlap of minimum 1 bp was found. For ChiP-seq of EoGFP and BraGFP peaks the resulting narrow peaks bed file was sorted and filtered for the pileup value (height of the peak at the summit, provided in the Peaks tabular file from MACS2) higher than 120 and 40, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: Processed RNA-seq results showing differential gene expression between WT and dKO contain normalized and scaled counts (RPKM) in Tab delimited txt format. Coverage files in BigWig format  for RNA-seq and ChIP-seq reads are normalized to RPKM. Bed files for EoGFP and BraGFP ChIP-seq contain coordinates of the peaks recognized after MACS2 peak calling and subsequent filtering for the pileup value.

source_name: 5 days dKO+EoGFP embryoid bodies (ActA)

growth_protocol:
Starting number of 2.5x10^5 dKO+EoGFP or dKO+BraGFP cells were grown as EBs in suspension culture in 100 mm dishes for 2 days and treated with 30 ng/ml ActA and 5 µg/ml dox from day 2 to day 5 of differentiation. Uninduced cells were used as negative controls. On day 5 of differentiation, EBs were singularized by trypsinization and approximately 3x10^7 cells was used per ChIP.
A2lox.Cre Mouse ESCs were grown in the standard serum containing conditions with 1000 U/ml LIF, 3 mM CHIR99021 and 1 mM OD0325901 on the monolayer of mitotically inactivated STO feeder cells (SNL76/7). Prior to differentiation cells were depleted of feeders and 200 cells per 40 ml of serum-free Basal medium were grown as embryoid bodies (EBs) in ultra-low attachment plates for 2 days, or alternatively, 2.5x10^5 cells were grown as EBs in 10 mm non-adherent dishes in Basal medium. Cells were further treated and grown for 2-3 more days.

extract_protocol:
The protocol was modified from Schmidt et al., according to Singh et al. Briefly, ProteinG beads (50 μl per sample) were incubated with 5 μg of Anti-GFP Antibody (Abcam, ab290) overnight at 4°C. Cross-linking was performed with 2 mM disuccinimidyl glutarate (DSG, Thermo Fischer, 20593) in the SolutionA (50 mM Hepes, 100 mM NaCl, 1 mM EDTA and 0.5 mM EGTA) for 15 min followed by 1% formaldehyde (Sigma Aldrich, F8775) for additional 10 min. The reaction was stopped by adding 2.5 M Glycine for 5 min. Cells were lysed in Lysis buffer 1 (50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40 and 0.25% TritonX in H2O, pH7.5) with protease inhibitors (PI, Complete™ Protease Inhibitor Cocktail, Roche) for 10 min on a rotating wheel at 4°C. Next, pellets were incubated for 5 min at 4°C with Lysis buffer 2 with PI (10 mM Tris, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA in H2O, pH8), followed by resuspension in Lysis buffer 3 with PI (10 mM Tris, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% Lauroylsarcosine in H2O, pH8). The DNA was sonicated with the Bioruptor (Diagenode), at high amplitude for 10-12 cycles of 30 s ON/30 s OFF. TritonX was added to final concentration of 1%. 10% of the resulting lysate was kept as input control. Beads coupled to antibodies incubated with sonicated chromatin at 4°C overnight. Next, beads were washed on ice ten times with RIPA buffer (50 mM HEPES, 500 mM LiCl, 1 mM EDTA, 1% NP40 substitute, 0.7% Na-Deoxycholate in H2O, pH7.6) and once with TBS. DNA was removed from the beads with Elution buffer (50 mM Tris, 10mM EDTA, 1% SDS in H2O, pH8) for 6-18 h at 65°C. The supernatant was mixed with one volume of TE buffer (10 mM Tris, 1 mM EDTA in H2O, pH7.4), incubated with RNAse A at 37°C for 1 h, and ProteinaseK at 55°C for 2 h. Phenol-chloroform extraction of the DNA was performed and pellet  was resuspended in 50 μl of 10 mM Tris-HCl pH8.
Libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs), size selected on a 1.3% agarose gel by cutting out fragments between 200-650 bp of size and extracted from the gel using QIAquick gel extraction kit (Qiagen).

tag: treatment


title: dKO+BraGFP_cells_d5_nodox (ChIP-seq)

description:
processed data file:
bamCoverage_ChIP_BraGFP_nodox.bigwig

source_name: 5 days dKO+BraGFP embryoid bodies (ActA)

value: anti-GFP (Abcam, ab290, Lot. GR3196305-1)


title: Drosophila virilis_zt3_18C


title: X8d rep3

tag: strain

value: 2-3 month old

value: 8 days post infection


title: Drosophila yakuba_zt15_29C

organism: Drosophila yakuba


title: Drosophila Melanogaster_zt18_29C_1


title: X8d rep2


title: Drosophila Melanogaster_zt15_29C_1


title: X8d rep1


title: Drosophila yakuba_zt15_25C


title: dKO+BraGFP_cells_d5_dox_rep2 (ChIP-seq)

description:
processed data files:
bamCoverage_ChIP_BraGFP_dox.bigwig
Peaks_ChIP_BraGFP_pileup40.bed
Peaks_merged_ChIP_BraGFPpileup40_EoGFPpileup120.bed

source_name: 5 days dKO+BraGFP embryoid bodies (ActA + dox)

value: ActA + dox


title: dKO+EoGFP_cells_d5_dox_rep2 (ChIP-seq)

description:
processed data files:
bamCoverage_ChIP_EoGFP_dox.bigwig
Peaks_ChIP_EoGFP_pileup120.bed
Peaks_merged_ChIP_BraGFPpileup40_EoGFPpileup120.bed

source_name: 5 days dKO+EoGFP embryoid bodies (ActA + dox)


title: Drosophila Melanogaster_zt7_29C_1


title: Drosophila Melanogaster_zt11_29C_1


title: dKO+EoGFP_cells_d5_nodox (ChIP-seq)

description:
processed data file:
bamCoverage_ChIP_EoGFP_nodox.bigwig

value: ActA


title: X2d rep2

value: 2 days post infection


title: X2d rep3

value: Liver


title: Drosophila yakuba_zt3_25C


title: X2d rep1

value: LCMV Cl13


title: Drosophila Melanogaster_zt3_29C_1


title: Drosophila yakuba_zt15_18C


title: dKO_embryo_E7.5_rep3 (RNA-seq)

description:
processed data files:
nrm-counts-avg-embryo-WT-BraKO-EoKO-dKO.xlsx
DE-sig-embryo-dKO-vs-WT_p0.05_l2FC1.xlsx

data_processing:
For differential gene expression analysis sequenced reads were mapped to the mouse reference genome GRCm38/mm10 (iGenomes, Illumina) containing the chromosomes 1-19, X, Y and M using Rsubread v1.28.1 package in R v3.4.3. The genomic annotations used for the mapping, counting and downstream analyses were contained in gtf files provided by the iGenomes reference genome bundles (archive-2015-07-17-32-40 and archive-2015-07-17-33-26 for GRCM38 and mm10, respectively). Genomic features were counted using the Rsubread::featureCounts function. Differential expression analysis was carried out using DESeq2 v1.18.1 in R, which applies Negative Binomial GLM fitting and Wald statistics on the count data. The results were filtered for adjusted p-value<0.05 and log2FC. Prior to fitting and statistical analysis, counts were normalized by library size (DESeq2::estimateSizeFactors) and gene-wise dispersion (DESeq2::estimateDispersions) to normalize the gene counts by gene-wise geometric mean over samples. Mapping for the creation of bigwig Coverage files was performed on Galaxy platform using Bowtie2 (v2.3.4) on mm10 reference genome with default settings. Obtained bam files from biological triplicates were merged using Merge BAM files tool in Galaxy (picard v1.56.0) and the duplicates were removed by RmDup tool (samtools v1.3.1). Coverage files were created using bamCoverage tool (deepTools v3.0.2) with bin size 10 bases and reads per kilobase per million (RPKM) normalization.
Mapping: For the RNA-seq results reads trimmed of the addapters were mapped to the mouse reference genome GRCm38/mm10 (iGenomes, Illumina), using Rsubread v1.28.1 package in R v3.4.3. For ATAC-seq and ChIP seq reads were mapped to mm10 genome using Bowtie2 v2.3.4 on the Galaxy platform.
Counting: Genomic features were counted for the RNA-seq analysis with the Rsubread::featureCounts function in Rsubread v1.28.1 package using genomic annotations as gtf files provided by the iGenomes reference genome bundles (archive-2015-07-17-32-40 and archive-2015-07-17-33-26 for GRCM38 and mm10, respectively).
Differential expression: Differential expression analysis was carried out using DESeq2 v1.18.1 in R, which applies Negative Binomial GLM fitting and Wald statistics on the count data. The results were filtered for adjusted p-value<0.05 and log2FC as indicated in the figure legends. Prior to fitting and statistical analysis, counts were normalized by library size (DESeq2::estimateSizeFactors) and gene-wise dispersion (DESeq2::estimateDispersions) to normalize the gene counts by gene-wise geometric mean over samples. Gene-wise scaling was performed on the normalized counts to cluster the counts for the expression tendency between the samples (stats::kmeans function). In addition, the counts were centered by setting the gene-wise mean to zero.
Coverage: For the generation of coverage files for RNA-seq, ATAC-seq and ChIP-seq analysis corresponding bam files from biological replicates were merged using Merge BAM files tool in Galaxy (picard v1.56.0) and the duplicates were removed by RmDup tool (samtools v1.3.1). Coverage files were created using bamCoverage tool (deepTools v3.0.2) with bin size 10 bases and reads per kilobase per million (RPKM) normalization.
Peak calling: Peaks were detected using MACS2 on the Galaxy platform (v2.1.1.20160309.4) with BAMPE format of the input file, default settings for building the shifting model and minimum q-value cut-off for detection of 0.05. For ChiP-seq of EoGFP and BraGFP peaks detected in the input control and dKO -dox control were subtracted from the genomic intervals detected in ChIP-seq treatment file using SubtractBed tool (bedtools v2.27.0) in Galaxy, where entire features were filtered out if the overlap of minimum 1 bp was found. For ChiP-seq of EoGFP and BraGFP peaks the resulting narrow peaks bed file was sorted and filtered for the pileup value (height of the peak at the summit, provided in the Peaks tabular file from MACS2) higher than 120 and 40, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: Processed RNA-seq results showing differential gene expression between WT and dKO contain normalized and scaled counts (RPKM) in Tab delimited txt format. Coverage files in BigWig format  for RNA-seq and ChIP-seq reads are normalized to RPKM. Bed files for EoGFP and BraGFP ChIP-seq contain coordinates of the peaks recognized after MACS2 peak calling and subsequent filtering for the pileup value.

source_name: E7.5 dKO mouse epiblast

growth_protocol: A2lox.Cre Mouse ESCs were grown in the standard serum containing conditions with 1000 U/ml LIF, 3 mM CHIR99021 and 1 mM OD0325901 on the monolayer of mitotically inactivated STO feeder cells (SNL76/7). Prior to differentiation cells were depleted of feeders and 200 cells per 40 ml of serum-free Basal medium were grown as embryoid bodies (EBs) in ultra-low attachment plates for 2 days, or alternatively, 2.5x10^5 cells were grown as EBs in 10 mm non-adherent dishes in Basal medium. Cells were further treated and grown for 2-3 more days.

extract_protocol:
RNA from E7.5 mouse epiblasts was extracted with Qiagen RNeasy Micro kit with on-column DNAse digestion as recommended by the manufacturer.
Libraries were prepared from 10 ng of RNA with the Ovation SoLo RNA-seq Systems kit (NuGEN).

tag: strain background

value: mixed 129S1/Sv and C57BL/6

value: T2J/2J;Eomes{delta}Epi (dKO)


title: Drosophila Melanogaster_zt23_25C_2

source_name: D. Melanogaster_zt23_25C_fly heads


title: X0d rep3

value: control


title: Drosophila yakuba_zt3_18C


title: Drosophila Melanogaster_zt18_25C_2

source_name: D. Melanogaster_zt18_25C_fly heads


title: X0d rep2


title: dKO_embryo_E7.5_rep1 (RNA-seq)


title: dKO+BraGFP_cells_d5_dox_rep1 (ChIP-seq)

value: dKO


title: Drosophila yakuba_zt3_29C


title: Drosophila Melanogaster_zt15_25C_2

source_name: D. Melanogaster_zt15_25C_fly heads


title: Drosophila Melanogaster_zt11_25C_2

source_name: D. Melanogaster_zt11_25C_fly heads


title: X0d rep1

value: female


title: EomesΔEpiembryo_E7.5_rep3 (RNA-seq)

description:
processed data file:
nrm-counts-avg-embryo-WT-BraKO-EoKO-dKO.xlsx

source_name: E7.5 EoKO mouse epiblast

value: Eomes{delta}Epi (EoKO)


title: dKO+EoGFP_cells_d5_dox_rep1 (ChIP-seq)


title: 2i-rep2

data_processing:
All RNA-seq data were mapped to the mm10 genome for mouse using Tophat2 (2.1.1), which was shown to be accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Then, duplicated reads for pair-end data were removed, but not single-end data by SAMtools (v1.5).
For RNA-seq, the bigwig files for visualization in Integrative Genomics Viewer (IGV) were generated from BAM files by using “bamCoverage” from deepTools with parameters “--ignoreDuplicates --normalizeUsingRPKM --skipNonCoveredRegions --binSize 50”.
Genome_build: mm10
Supplementary_files_format_and_content: expression Count and FPKM data

source_name: embryo

treatment_protocol: 1)  Treatment of MM401(100uM) or 4-Hydroxytamoxifen (4-OHT, 5µM ) on mESCs for 5 day in LIF/Serum/KO DMEM medium; 2) Treatment of 2i (PD03259010 at 1uM; CHIR99021at3uM) on ESCs for 5 day in LIF/KSR/KO-DMEM medium. mESCs are cultured with feeder cells .

tag: cell type

value: embryonic stem cell , blastocyst derived

tag: genotype

value: Mll1fl/fl; Cre-ER TM

tag: agent

value: 2i treated


title: Drosophila Melanogaster_zt7_25C_2

source_name: D. Melanogaster_zt7_25C_fly heads

value: Canton-S

value: fly heads


title: EomesΔEpiembryo_E7.5_rep1 (RNA-seq)


title: EVs high P4 - rep1

city: Pirassununga

first: Juliano

middle: Coelho

last: da Silveira

state: São Paulo

address: Duque de Caxias Norte 235

department: Veterinary Medicine

country: Brazil

institute: University of São Paulo

description:
VSD_FINAL_RAW_COUNTS.csv
sample name in processed data file:
16_S46_L004_R1_001

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed with TRIMMOMATIC (Bolger, AM, Lohse, M., & Usadel, B .; 2014), using the following parameters " threads 24 LEADING: 22 TRAILING: 22 SLIDINGWINDOW: 4: 26 MINLEN: 36 AVGQUAL: 24 "; considering  22 phred quality, minimum, at start /end of the read, medium of 22 phred quality and minimum read size of 36 bps
Samples that passed quality screening were then aligned with the Bos taurus genome (assembly ARS-UCD1.2), using STAR software (DOBIN et al .; 2013) using default parameters and a final report of  alignment quality was created using  FASTQC software (Andrews S., 2010) and MULTIQC software (EWELS et al., 2016).
Analysis of differential gene expression was performed using DESEQ2 (LOVE, MI, HUBER, W., ANDERS, S., 2014) R package considering Replicates as batch and Benjamini-Hochberg method ("BH") for adjusted p values <0.10, and a log2 fold change greater than 0.5 or less than -0.5.
Genome_build: assembly ARS-UCD1.2
Supplementary_files_format_and_content: ;-delimited text files from DESEQ2 variance stabilizing transformation (VST) function

organism: Bos taurus

source_name: cumulus cells

growth_protocol: COCs were mantained for 9 h in maturation media containing TCM 199 (GIBCO) buffered with sodium bicarbonate (25 mM), supplemented with sodium pyruvate (0.2mM), gentamycin sulfate  (50 μg/mL), follicle stimulating hormone (FSH; 0.5 μg/mL,  Folltropin-V, Bioniche Animal Health Belleville, Canada), human Chorionic Gonadotropin (hCG, 5 U/mL, Vetecor, Hertape Calier) and 10% EVs free FCS.

extract_protocol:
Total RNA content of cumulus cells was extracted using miRNeasy Mini Kit (QIAGEN), according to the manufacturer’s instruction.
The libraries were prepared with truseq stranded mRNA sample prep kit.

treatment_protocol: Small EVs isolated from 200 µL of low P4 and high P4 follicular fluid were resuspended in 200 µL of IVM medium.

value: Cumulus cells from bovine oocyte

tag: origin

value: 3 to 6 mm ovarian follicle

tag: developmental stage

value: 9 h of in vitro maturation

value: small EVs from high P4 follicle


title: EomesΔEpiembryo_E7.5_rep2 (RNA-seq)

description:
processed data files:
nrm-counts-avg-embryo-WT-BraKO-EoKO-dKO.xlsx


title: EVs low P4 - rep3

description:
VSD_FINAL_RAW_COUNTS.csv
sample name in processed data file:
23_S53_L004_R1_001

value: small EVs from low P4 follicle


title: dKO_embryo_E7.5_rep2 (RNA-seq)


title: Drosophila Melanogaster_zt3_25C_2

source_name: D. Melanogaster_zt3_25C_fly heads

tag: tissue


title: Mll1 deletion-rep2

description: Mlldel

value: 4-OHT treated


title: T2J/2Jembryo_E7.5_rep3 (RNA-seq)

source_name: E7.5 BraKO mouse epiblast

value: mixed 129S1/Sv and C57BL/6

value: T2J/2J (BraKO)


title: EVs low P4 - rep1

description:
VSD_FINAL_RAW_COUNTS.csv
sample name in processed data file:
15_S45_L004_R1_001


title: Drosophila Melanogaster_zt23_25C_1


title: Mll1 deletion-rep1

description: Mlldel


title: EVs high P4 - rep3

description:
VSD_FINAL_RAW_COUNTS.csv
sample name in processed data file:
24_S54_L004_R1_001


title: Drosophila Melanogaster_zt18_25C_1


title: T2J/2Jembryo_E7.5_rep2 (RNA-seq)


title: EVs free FCS - rep3

description:
VSD_FINAL_RAW_COUNTS.csv
sample name in processed data file:
22_S52_L004_R1_001


title: T2J/2Jembryo_E7.5_rep1 (RNA-seq)


title: EVs high P4 - rep2

description:
VSD_FINAL_RAW_COUNTS.csv
sample name in processed data file:
20_S50_L004_R1_001


title: MLL1 inhibition-rep2

value: MM401 treated


title: EVs free FCS - rep2

description:
VSD_FINAL_RAW_COUNTS.csv
sample name in processed data file:
18_S48_L004_R1_001


title: MLL1 inhibition-rep1


title: Drosophila Melanogaster_zt15_25C_1


title: Drosophila Melanogaster_zt11_25C_1


title: 2i-rep1


title: WT_embryo_E7.5_rep3 (RNA-seq)

source_name: E7.5 WT mouse epiblast

value: WT


title: Mll1fl/fl-rep2

description: WT

value: untreated


title: WT_embryo_E7.5_rep2 (RNA-seq)


title: EVs free FCS - rep1

description:
VSD_FINAL_RAW_COUNTS.csv
sample name in processed data file:
14_S44_L004_R1_001


title: EVs low P4 - rep2

description:
VSD_FINAL_RAW_COUNTS.csv
sample name in processed data file:
19_S49_L004_R1_001


title: Drosophila Melanogaster_zt7_25C_1


title: Mll1fl/fl-rep1

description: WT


title: wlung_PBS_7 [muc4657]

first: Lukas

last: Simon

address: 1 Baylor Plaza

department: THINC

institute: Baylor College of Medicine

description:
Drop-seq
MUC4657_S25_L005

data_processing:
For the single-cell RNA-seq data the Drop-Seq core computational pipeline was used for processing next generation sequencing reads of the scRNA-seq data, as previously described (Pubmed ID: 26000488). For the whole lung tissue and flow-sorted bulk RNA-seq data, STAR (Pubmed ID:  23104886) was used to align the reads to reference genome mm10 followed by featureCounts (Pubmed ID: 24227677) for gene summarization.
Genome_build: mm10
Supplementary_files_format_and_content: For the "High resolution" experiment: Raw count matrix (HighResolution_rawcounts.mtx) from Drop-seq experiments with 24051 genes and 34068 cells in market matrix format and corresponding column (HighResolution_barcodes.txt) and row (HighResolution_genes.txt) labels and cell-level metadata (WholeLung_cellinfo.csv). For the "Whole lung" experiment: Raw count matrix (WholeLung_rawcounts.mtx) from Drop-seq experiments with 23400 genes and 29297 cells in market matrix format and corresponding column (WholeLung_barcodes.txt) and row (WholeLung_genes.txt) labels and cell-level metadata (WholeLung_cellinfo.csv).

source_name: whole_lung_Whole lung_day0

extract_protocol:
Lung single cell suspensions were generated in the following manner. Briefly, after euthanasia, lung tissue was perfused with sterile saline through the heart and the right lung was tied off at the main bronchus. The left lung lobe was subsequently filled with 4% paraformaldehyde for later histologic analysis. Right lung lobes were removed, minced (tissue pieces at approx. 1 mm2), and transferred for mild enzymatic digestion for 20-30 min at 37°C in an enzymatic mix containing dispase (50 caseinolytic U/ml), collagenase (2 mg/ml), elastase (1 mg/ml), and DNase (30 µg/ml). Single cells were harvested by straining the digested tissue suspension through a 40 micron mesh. After centrifugation at 300 x g for 5 minutes, single cells were taken up in 1 ml of PBS (supplemented with 10% fetal calf serum), counted and critically assessed for single cell separation and overall cell viability. For Dropseq, cells were aliquoted in PBS supplemented with 0.04% of bovine serum albumin at a final concentration of 100 cells/µl.
Single cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads. Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing. For each sample, 1 ng of pre-amplified cDNA from an estimated 1000 cells was tagmented by Nextera XT (Illumina) with a custom P5 primer (Integrated DNA Technologies). Single cell libraries were sequenced in a 100 bp paired-end run on the Illumina HiSeq 4000 using 0.2 nM denatured sample and 5% PhiX spike-in. For priming of read 1, 0.5 µM Read1CustSeqB (primer sequence: GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC) was used.

value: Whole lung

tag: injury timecourse

tag: experiment

tag: number of cells


title: Drosophila Melanogaster_zt23_18C_2

source_name: D. Melanogaster_zt23_18C_fly heads

tag: circadian timepoint

tag: temperature

tag: replicate


title: wlung_d14_4 [muc4656]

description:
Drop-seq
MUC4656_S24_L005

source_name: whole_lung_Whole lung_day14


title: input (deletion)

data_processing:
All ChIP-seq data were mapped to the mm10 genome for mouse by using Bowtie2 (v2-2.2.4), which is ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. Then, we removed any duplicated reads for both pair-end and single-end data using SAMtools (v1.5)
For ChIP-seq data, the fold enrichment for visualization in IGV were normalized by MACS2 subcommands bdgopt and bdgcmp based on the ratio of tags after filtering between the treatment and input control.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig and peaks table

growth_protocol: mESCs were maintained in the presence of leukemia inhibitory factor (LIF, Millipore) in KO DMEM containing 5% ES qualified fetal calf serum and 15% KSR on Matrigel (feeder-free).

extract_protocol:
ChIP experiments were performed using ~4µg a-Mll1 antibody for 1E8 cells ; ~2ug a-H3K4me1/2/3 for 2E7 cells according to standard protocols. Crosslinking of the cells was performed with 1% PFA for 10 minutes, while ChIPed DNA was purified by Qiaquick PCR purification Kit (Qiagen).
Libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol.

treatment_protocol: Treatment of MM401(100uM) or 4-Hydroxytamoxifen (4-OHT, 5µM ) on mESCs for three passage (9 day) in LIF/5%Serum/15%KSR/KO DMEM medium.

value: embryonic stem cell , blastocyst derived


title: Drosophila Melanogaster_zt3_25C_1


title: NECtrl_d4_rep2 (RNA-seq)

description:
processed data file:
nrm-counts-avg-WT-dKO-NECtrl-epiSC.xlsx

source_name: 5 days A2lox.Cre embryoid bodies (Noggin + SB431542)

growth_protocol:
Prior to differentiation, ESCs were depleted of feeders by splitting for 2-3 passages onto 0.1% gelatin-coated 60 mm dishes. Embryoid bodies (EBs) were formed by using 200 cells in 40 μl of ESC medium without LIF and 2i in ultra-low attachment plates. After 2 days EBs were transferred in 60 mm dishes and treated with 100 ng/ml Noggin (R&D Systems) and 10 mM SB431542 (Tocris) for 1 more day with agitation. The next day medium was replaced for ESGRO Complete Basal medium containing 100 ng/ml Noggin and 10 ng/ml ActA and cells were grown for 1 more day.
A2lox.Cre Mouse ESCs were grown in the standard serum containing conditions with 1000 U/ml LIF, 3 mM CHIR99021 and 1 mM OD0325901 on the monolayer of mitotically inactivated STO feeder cells (SNL76/7). Prior to differentiation cells were depleted of feeders and 200 cells per 40 ml of serum-free Basal medium were grown as embryoid bodies (EBs) in ultra-low attachment plates for 2 days, or alternatively, 2.5x10^5 cells were grown as EBs in 10 mm non-adherent dishes in Basal medium. Cells were further treated and grown for 2-3 more days.

extract_protocol:
RNA from differentiated embryoid bodies was extracted with RNeasy Mini Kit (Qiagen) with on-column DNAse digestion as recommended by the manufacturer.
Library preparation was carried out using 0.5 μg of RNA with NEBNext Ultra RNA library Prep Kit for Illumina (New England BioLabs).

tag: genotype/variation

tag: day

value: Noggin + SB431543


title: NECtrl_d4_rep3 (RNA-seq)

tag: treatment

value: Noggin + SB431544


title: WT_embryo_E7.5_rep1 (RNA-seq)


title: wlung_d14_3 [muc4655]

description:
Drop-seq
MUC4655_S23_L005


title: MLL1deletion-H3K4me3-ChIP-Seq

value: Mll1fl/fl; Cre-ER TM

tag: strain


title: MLL1deletion-H3K4me2-ChIP-Seq


title: Drosophila Melanogaster_zt18_18C_2

source_name: D. Melanogaster_zt18_18C_fly heads

value: Canton-S

value: fly heads


title: wlung_d3_3 [muc4653]

description:
Drop-seq
MUC4653_S21_L005

source_name: whole_lung_Whole lung_day3


title: wlung_d21_4 [muc4649]

description:
Drop-seq
MUC4649_S19_L004

source_name: whole_lung_Whole lung_day21


title: MLL1deletion-H3K4me1-ChIP-Seq


title: Drosophila Melanogaster_zt11_18C_2

source_name: D. Melanogaster_zt11_18C_fly heads


title: dKO_cells_d5_rep3 (RNA-seq)

description:
processed data files:
bamCoverage_RNAseq_dKO.bigwig
nrm-counts-avg-WT-BraKO-EoKO-dKO.xlsx
DE-sig-dKO-vs-WT_p0.05_l2FC2.5.xlsx
nrm-counts-avg-dKO-vs-WT.xlsx

source_name: 5 days dKO embryoid bodies (ActA)

value: dKO

value: ActA


title: input (inhibtion)


title: wlung_d21_3 [muc4648]

description:
Drop-seq
MUC4648_S18_L004


title: Drosophila Melanogaster_zt7_18C_2

source_name: D. Melanogaster_zt7_18C_fly heads


title: dKO_cells_d5_rep2 (RNA-seq)

description:
processed data files:
bamCoverage_RNAseq_dKO.bigwig
nrm-counts-avg-WT-BraKO-EoKO-dKO.xlsx
nrm-counts-avg-WT-BraKO-EoKO-dKO.xlsx
DE-sig-dKO-vs-WT_p0.05_l2FC2.5.xlsx
nrm-counts-avg-dKO-vs-WT.xlsx


title: wlung_d14_2 [muc4647]

description:
Drop-seq
MUC4647_S17_L004


title: dKO_cells_d5_rep1 (RNA-seq)

description:
processed data files:
bamCoverage_RNAseq_dKO.bigwig
DE-sig-dKO-vs-WT_p0.05_l2FC2.5.xlsx
nrm-counts-avg-dKO-vs-WT.xlsx


title: Drosophila Melanogaster_zt3_18C_2

source_name: D. Melanogaster_zt3_18C_fly heads


title: EoKO_cells_d5_rep3 (RNA-seq)

description:
processed data file:
nrm-counts-avg-WT-BraKO-EoKO-dKO.xlsx

source_name: 5 days EoKO embryoid bodies (ActA)

value: EoKO


title: MLL1inhibition-H3K4me2-ChIP-Seq

source_name: embryo


title: Drosophila Melanogaster_zt23_18C_1


title: wlung_d7_5 [muc4645]

description:
Drop-seq
MUC4645_S15_L003

source_name: whole_lung_Whole lung_day7


title: Drosophila Melanogaster_zt18_18C_1


title: EoKO_cells_d5_rep2 (RNA-seq)


title: EoKO_cells_d5_rep1 (RNA-seq)


title: wlung_PBS_6 [muc4644]

description:
Drop-seq
MUC4644_S14_L003


title: Drosophila Melanogaster_zt15_18C_1

source_name: D. Melanogaster_zt15_18C_fly heads


title: NECtrl_d4_rep1 (RNA-seq)

value: Noggin + SB431542


title: Drosophila Melanogaster_zt15_18C_2


title: wlung_d3_2 [muc4643]

description:
Drop-seq
MUC4643_S13_L003


title: BraKO_cells_d5_rep3 (RNA-seq)

source_name: 5 days BraKO embryoid bodies (ActA)

value: BraKO


title: H3K4me2-ChIP-Seq


title: wlung_d28 [muc4642]

description:
Drop-seq
MUC4642_S12_L003

source_name: whole_lung_Whole lung_day28


title: Drosophila Melanogaster_zt7_18C_1


title: Drosophila Melanogaster_zt11_18C_1


title: BraKO_cells_d5_rep2 (RNA-seq)


title: H3K4me3-ChIP-Seq


title: BraKO_cells_d5_rep1 (RNA-seq)


title: H3K4me1-ChIP-Seq


title: Drosophila Melanogaster_zt3_18C_1


title: wlung_d28 [muc4641]

description:
Drop-seq
MUC4641_S11_L003


title: MLL1inhibition-H3K4me3-ChIP-Seq


title: input (MLL1)


title: wlung_d21_2 [muc4639]

description:
Drop-seq
MUC4639_S9_L002


title: wlung_PBS_5 [muc4640]

description:
Drop-seq
MUC4640_S10_L002

source_name: whole_lung_Whole lung_day0


title: WT_cells_d5_rep3 (RNA-seq)

description:
processed data files:
bamCoverage_RNAseq_WT.bigwig
nrm-counts-avg-WT-BraKO-EoKO-dKO.xlsx
DE-sig-dKO-vs-WT_p0.05_l2FC2.5.xlsx
nrm-counts-avg-dKO-vs-WT.xlsx

source_name: 5 days A2lox.Cre embryoid bodies (ActA)


title: wlung_d21_1 [muc4638]

description:
Drop-seq
MUC4638_S8_L002


title: MLL1inhibition-H3K4me1-ChIP-Seq


title: input (H3K4)