title: RNAseq_HCT116.MS275_4

status: Public on Dec 16 2017

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

description:
RNA-Seq_HCT116
processed data file:
RNAseq_HCT116_raw_Readcounts_RNAseq_HCT116.txt

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform.
RNA-seq: Reads were trimmed using Trim Galore v0.4.2 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence. They were mapped to the mouse GRCm38 genome assembly using Tophat 2.0.12 (options -g2) guided by the gene models from the Ensembl v70 release. BAM files were imported to Seqmonk v36.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
ChIP-seq: Reads were trimmed using Trim Galore v0.4.2 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence. They were mapped to the mouse GRCm38 genome assembly using Bowtie 2 v2.2.5 (default parameters). BAM files were imported to Seqmonk v36.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCm38
Supplementary_files_format_and_content: RNA-Seq report: Quantitated RNA-Seq data file is tab delimited and contains the following columns: (1) gene name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) ID (Ensembl) (7) Description (Ensembl); (8-16) log2 RPM value.
Supplementary_files_format_and_content: ChIP-Seq report: Quantitated ChIP-Seq data file is tab delimited and contains the following columns: (1) Chromosome; (2) Start; (3) End; (4-12) log2 RPM value per 500 bp tile.

growth_protocol:
RNA-Seq_HCT116: HCT116 cells were grown in in DMEM media containing glucose and pyruvate, 10 % FBS, 2 mM L-glutamine, 100 units/ml penicillin and 100 µg/ml streptomycin
ChIP-Seq_HCT116: HCT116 cells were grown in in DMEM media containing glucose and pyruvate, 10 % FBS, 2 mM L-glutamine, 100 units/ml penicillin and 100 µg/ml streptomycin

extract_protocol:
RNA-Seq_colonepithelium: RNA was extracted using the RNeasy Plus Mini Kit (Qiagen), following the manufacturer’s instructions. Extracted RNA was quantified with Nanodrop and the quality assessed on a Bioanalyzer (Agilent).
RNA-Seq_colonepithelium: Library preparation was performed from 500 ng of RNA using the NEB Next® Ultra™ Directional RNA Library Prep Kit for Illumina® and the NEBNext® Poly(A) mRNA magnetic isolation module. Illumina Tru-Seq adaptors were used and library amplification was performed with the KAPA PCR Amplification kit (KAPA, Cat. KK2501) using 14 cycles.
RNA-Seq_HCT116: RNA was extracted using the RNeasy Plus Mini Kit (Qiagen), following the manufacturer’s instructions. Extracted RNA was quantified with Nanodrop and the quality assessed on a Bioanalyzer (Agilent).
RNA-Seq_HCT116: Library preparation was performed from 500 ng of RNA using the NEB Next® Ultra™ Directional RNA Library Prep Kit for Illumina® and the NEBNext® Poly(A) mRNA magnetic isolation module. Illumina Tru-Seq adaptors were used and library amplification was performed with the KAPA PCR Amplification kit (KAPA, Cat. KK2501) using 14 cycles.
ChIP-Seq_HCT116: Cells where trypsinized and fixed in 1 % formaldehyde for 10 minutes. After quenching with 0.125 M glycine cells were washed with PBS and processed for ChIP
ChIP-Seq_HCT116: Library preparation was performed from 0.8 ng of purified DNA using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® with the following modifications: Illumina Tru-Seq adaptors were used and library amplification was performed with the KAPA PCR Amplification kit (KAPA, Cat. KK2501) using 15 cycles.
ChIP-Seq_colonepithelium: Cells where trypsinized and fixed in 1 % formaldehyde for 10 minutes. After quenching with 0.125 M glycine cells were washed with PBS and processed for ChIP
ChIP-Seq_colonepithelium: Library preparation was performed from 5 ng of purified DNA using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® with the following modifications: Illumina Tru-Seq adaptors were used and library amplification was performed with the KAPA PCR Amplification kit (KAPA, Cat. KK2501) using 11 cycles.

treatment_protocol:
RNA-Seq_HCT116: HCT116 cells were treated with either 5µM MS275 or the same amount of DMSO for 18 hours.
ChIP-Seq_HCT116: HCT116 cells were treated with either 5µM MS275 or the same amount of DMSO for 18 hours.

tag: cell type

value: colon cancer, epithelial

tag: treated with

value: MS275 (entinostat) 5μM


title: RNAseq_HCT116.MS275_3

type: SRA

city: Cambridge

country: United Kingdom

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line


title: RNAseq_HCT116.MS275_1


title: RNAseq_HCT116.MS275_2


title: RNAseq_HCT116.DMSO_4

value: DMSO


title: RNAseq_HCT116.DMSO_3


title: P45-VH-2

status: Public on Dec 17 2017

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Paired-end sequencing (150 x 2) was performed using a Nextseq-500 (Illumina).
Reference genome sequence data from Homo sapiens were obtained from the University of California Santa Cruz Genome Browser Gateway (assembly ID: rn5). The reference genome index was built using SAMtools (v. 0.1.19) and the Bowtie2-build component of Bowtie2 (v. 2.1.0). Reads were mapped to the reference genome using Tophat2 (v. 2.0).
The number of fragments per kilobase per million mapped reads (fpkm) for each gene of 17,070 RefSeq (UCSC rn5) gene models was calculated using Cufflinks (v. 2.2.1).
Heat maps were constructed using Mev (v. 4.9.0). Statistical analyses and graph construction were performed using R (v. 3.3.0) and PYTHON (v. 2.7.6).
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Rattus norvegicus

source_name: Ventral hippocampus from P45

extract_protocol:
Total RNA was isolated from the infected cells using the RNeasy RNA extraction Mini-Kit (Qiagen) and the quality of the RNA was confirmed by agarose gel electrophoresis.
The sequencing library was prepared using the Illumina TruSeqStranded mRNA Sample Preparation Kits (Illumina).
The mRNA derived from total RNA using poly-T oligo-attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.

tag: tissue

value: Ventral hippocampal tissue

tag: age

value: Ventral hippocampus from P45 brain

tag: strain

value: Sprague-Dawley


title: H3K18crChIP_HCT116_ChIPMS275_2

description:
ChIP-Seq_HCT116
processed data file:
H3K18crChIP_colonepithelium_MACSpeaks_readcounts.txt

library_source: genomic

molecule: genomic DNA

tag: chip-antibody

value: H3K18cr antibody PTM Biolabs  (PTM-517)


title: H3K18crChIP_HCT116_ChIPMS275_3


title: RNAseq_HCT116.DMSO_1

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform.
RNA-seq: Reads were trimmed using Trim Galore v0.4.2 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence. They were mapped to the human GRCh38 genome assembly using Tophat 2.0.12 (options -g2) guided by the gene models from the Ensembl v70 release. BAM files were imported to Seqmonk v36.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
ChIP-seq: Reads were trimmed using Trim Galore v0.4.2 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence. They were mapped to the mouse GRCm38 genome assembly using Bowtie 2 v2.2.5 (default parameters). BAM files were imported to Seqmonk v36.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCh38
Supplementary_files_format_and_content: RNA-Seq report: Quantitated RNA-Seq data file is tab delimited and contains the following columns: (1) gene name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) ID (Ensembl) (7) Description (Ensembl); (8-16) log2 RPM value.
Supplementary_files_format_and_content: ChIP-Seq report: Quantitated ChIP-Seq data file is tab delimited and contains the following columns: (1) Chromosome; (2) Start; (3) End; (4-12) log2 RPM value per 500 bp tile.


title: H3K18crChIP_HCT116_ChIPMS275_1


title: H3K18crChIP_HCT116_ChIPDMSO_3


title: H3K18crChIP_HCT116_ChIPDMSO_2


title: H3K18crChIP_HCT116_ChIPDMSO_1


title: H3K18cr_ac_ChIP_HCT116_InputMS275

description:
ChIP-Seq_HCT116
processed data file:
H3K18cr_ac_ChIP_MACSpeaks.txt


title: H3K18acChIP_HCT116_ChIPMS275_1

value: H3K18ac antibody Abcam (ab1191)


title: H3K18acChIP_HCT116_ChIPDMSO_3


title: H3K18acChIP_HCT116_ChIPMS275_2


title: H3K18acChIP_HCT116_ChIPDMSO_1


title: H3K18acChIP_HCT116_ChIPDMSO_2


title: Shade Pulse, 10 hours since Dawn, Time 60 min return, replicate 1

first: Joseph

middle: Robert

last: Piechura

state: Massachusetts

address: 52 Oxford Street

department: FAS Center for Systems Biology

country: USA

institute: Harvard University

data_processing:
Read alignment: Bowtie, v 0129, -v 3 -m 1 -p 16 -t --best --un
Gene expression quantification: alignment output from Bowtie was read into Matlab using custom code To obtain gene expression values, we counted the number of coding-strand sequencing reads that had 5’ ends between the start and stop positions of the coding region of each gene
Gene expression normalization: To normalize gene expression values between samples, we utilized median normalization as described elsewhere (Anders and Huber, 2010) First, we calculated a pseudo-reference for each gene by determining the geometric mean of the expression counts for that gene across all samples, and calculated the ratio of the expression values with the appropriate pseudo-reference value We determined the median value of these ratios within each sample and took this as a size factor that estimates the sequencing depth of each sample To normalize, we divided all gene expression values within a sample by the appropriate size factor Gene expression values were further normalized by dividing the gene expression values by the length of the appropriate open reading frame To easily compare gene expression changes between each condition, we calculated the average expression of a gene over all time points in the Low Light condition Then, we divided the expression of that gene at each time point by the average Low Light expression, and took the Log2 of this ratio
Genome_build: Main chromosome: NC_007604.1; plasmid pANL (plasmid 1), NC_004073.2; plasmid pANS (plasmid 2), KT751091.1
Supplementary_files_format_and_content: Gene expression values for each gene are listed, calculated as described above. Data are reported for two separate biologcal replicates.

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: Clear Day-acclimated culture

growth_protocol: Wildtype Synechococcus elongatus PCC 7942 was grown in BG-11M media supplemented with 10 mM HEPES pH 80 constantly bubbled with 1% CO2 in air Cultures were maintained at OD750 03 with periodic dilution Cultures were grown in either a Low Light condition of 50 µmol photons m-2 s-1 or a Clear Day condition where light intensity varied parabolically, reaching a maximum of 600 µmol photons m-2 s-1 Cultures were grown in light for 12 hours, followed by 12 hours of darkness, for two cycles, and then sampled over the third light period On the fourth light period at 8 hours after light onset, we incresed the light intensity of the Low Light culture by 10 fold (High Light pulse) and decreased the light intensity of the Clear Day culture by 10 fold (Shade pulse) for 1 hour prior to returning the cultures to their original culture, and sampled them before, during, and after the perturbation The experiment was repeated twice for 2 biological replicates, and we report both datasets here

extract_protocol:
25 mL of OD750 03 culture was collected on a cellulose acetate filter and flash frozen Total RNA was isolated from cells using the Qiagen RNeasy mini kit
Ribosomal RNA was depleted from 125 µg of purified RNA using the Illumina Ribo-Zero rRNA removal kit, and strand specific RNA sequencing libraries were prepared using the Illumina Truseq Stranded mRNA sample prep kit

tag: hours since light onset (dawn)

tag: perturbation

value: 60 minutes since return to Clear Day

tag: light period

tag: replicate


title: Shade Pulse, 9.5 hours since Dawn, Time 30 min return, replicate 1

value: 30 minutes since return to Clear Day


title: Shade Pulse, 10 hours since Dawn, Time 60 min return, replicate 2


title: Shade Pulse, 9.25 hours since Dawn, Time 15 min return, replicate 2

value: 15 minutes since return to Clear Day


title: RNAseq_HCT116.DMSO_2


title: Shade Pulse, 9.25 hours since Dawn, Time 15 min return, replicate 1


title: Shade Pulse, 9 hours since Dawn, Time 60 min, replicate 2

value: 60 minutes in Shade pulse


title: Shade Pulse, 9 hours since Dawn, Time 60 min, replicate 1


title: Shade Pulse, 8.5 hours since Dawn, Time 30 min, replicate 2

value: 30 minutes in Shade pulse


title: H3K18acChIP_HCT116_ChIPMS275_3


title: Shade Pulse, 9.5 hours since Dawn, Time 30 min return, replicate 2


title: Shade Pulse, 8 hours since Dawn, Time 0, replicate 2

value: Shade pulse time 0 (prior to perturbation)


title: Shade Pulse, 8.25 hours since Dawn, Time 15 min, replicate 1

value: 15 minutes in Shade pulse


title: Shade Pulse, 8.25 hours since Dawn, Time 15 min, replicate 2


title: High Light Pulse, 10 hours since Dawn, Time 60 min return, replicate 2

source_name: Low Light-acclimated culture

value: 60 minutes since return to Low Light


title: High Light Pulse, 10 hours since Dawn, Time 60 min return, replicate 1


title: High Light Pulse, 9.5 hours since Dawn, Time 30 min return, replicate 1

value: 30 minutes since return to Low Light


title: High Light Pulse, 9.5 hours since Dawn, Time 30 min return, replicate 2


title: H3K18cr_ac_ChIP_HCT116_InputDMSO

value: colon cancer, epithelial


title: baf155.rep2

status: Public on Dec 18 2017

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

data_processing:
Sequencing Read Alignment: ChIP-seq libraries were sequenced on the Hi-Seq 2500 platforms. 36bp single end sequencing data was aligned to a reference mouse genome (mm9) downloaded from UCSC genome browser by using Bowtie. Unmapped and non-uniquely mapped reads were removed, and PCR duplicate reads were removed with Picard.
Peak Identification: H3K4me1 and H3K4me3 peaks were defined by using MACS2 with default parameters except following options “–m 5 50 –p 1e-5” for each biological replicate. After that we selected the best quality replicate for each modification based on number of identified peaks. From the best quality replicate, we only selected reproducible peaks at least two biological replicates. H3K4me1 and H3K4me3 peaks were merged together and classified into H3K4me1 peaks, H3K4me3 peaks, and common H3K4me1/me3 peaks. Chromatin regulator (CR) peaked regions were defined by comparing predefined H3K4me1/me3 peaked regions. Due to the limited quality of CR ChIP-seq results we first calculated input normalized CR ChIP-seq RPKMs on H3K4me1/me3 peaked regions for each biological replicate. If CR ChIP-seq RPKMs is enriched more than 1.5 fold compared to input RPKMs at least two biological replicates the h3k4me1/me3 peaked region was defined as occupied by the corresponding CR. H3K27ac ChIP-seq data was processed similarly as described in CR ChIP-seq data analysis except using 2-fold enrichment threshold when we define H3K27ac peaked regions. The density of histone modifications and CR binding was defined by taking average input normalized RPKMs of reproducible peaks across multiple biological replicates.
Clustering of CR-binding patterns: K-means clustering was performed for CR binding patterns according to poised enhancer and active enhancer regions. The peaks occupied by H3K4me1 but depleted by H3K4me3 were considered as enhancer regions after excluding upstream and downstream 2.5kb from RefSeq transcription start sites. Active enhancers were defined if the enhancer regions were overlapped with H3K27ac peaked regions (n=13,811). Otherwise the region was defined as poised enhancer regions (n=28,008). We performed K-mean clustering based on 13 CR binding patterns at active and poised enhancer regions separately, and generated 15 different clusters. Based on the enrichment of CR binding patterns in each cluster we manually assigned each cluster as ‘No CR bind’, ‘CR-specific bind’, and ‘Multiple CR bind’.
Identification of KMT2C/D dependent and independent H3K4me1 and H3K4me3 peaks: We defined KMT2C/D dependent and independent sites based on H3K4me1 levels between WT and KMT2C/D DKO cell lines. If the region is occupied by H3K4me1 more than 2-fold compared to input data and depleted more than 2-fold in KMT2C/D DKO cell lines the region was defined as a KMT2C/D dependent site, otherwise defined as a KMT2C/D independent site.
Analysis of CR-binding patterns in KMT2C/D DKO cell lines: To determine whether CR binding patterns are dependent on H3K4me1, we performed additional ChIP-seq for BRG1, SMC3, CHD1, PHF5A, MED23, PHRF1, and POUF51 for KMT2C/D DKO cell lines.  BRG1, SMC3, PHF5A, MED23, and PHRF1 were selected based on the strong association with H3K4me1 peaked regions in WT. POUF51 was selected as a negative control because POUF51 can be considered to bind as H3K4me1 independently.  Sequence read alignment was performed as described in WT CR ChIP-seq data. During downstream analysis of DKO cell lines we only considered CR ChIP-seq peaked regions defined in WT, resulting in 1939 peaks for BRG1, 20,412 peaks for CHD1, 12,225 peaks for POUF51, 2793 peaks for PHF5A, 7,425 peaks for PHRF1, 9,614 peaks for SMC3, and 6,712 peaks for MED23.
Genome_build: mm9

organism: Mus musculus

source_name: mESC

growth_protocol: mESCs were propagated on feeder cultures then passaged twice feeder free before crosslinking and harvesting.

extract_protocol:
Crosslinkedand sonicated chromatin was incubated with the ab indicated. Complex associated DNA was purified and sequenced.
Libraries were constructed as per manufacturers instructions for Illumina Tru-seq.

treatment_protocol: MLL3/4 DKO cells were obtained as referenceed in the manuscript.

tag: antibody

tag: antibody catalog#

tag: antibody vendor

value: santa cruz


title: High Light Pulse, 9.25 hours since Dawn, Time 15 min return, replicate 2

value: 15 minutes since return to Low Light


title: Shade Pulse, 8 hours since Dawn, Time 0, replicate 1


title: High Light Pulse, 9.25 hours since Dawn, Time 15 min return, replicate 1


title: High Light Pulse, 9 hours since Dawn, Time 60 min, replicate 2

value: 60 minutes in High Light pulse


title: High Light Pulse, 8.5 hours since Dawn, Time 30 min, replicate 1

value: 30 minutes in High Light pulse


title: High Light Pulse, 9 hours since Dawn, Time 60 min, replicate 1


title: High Light Pulse, 8.5 hours since Dawn, Time 30 min, replicate 2


title: High Light Pulse, 8.25 hours since Dawn, Time 15 min, replicate 2

value: 15 minutes in High Light pulse


title: High Light Pulse, 8 hours since Dawn, Time 0, replicate 1

value: High Light pulse time 0 (prior to perturbation)


title: High Light Pulse, 8.25 hours since Dawn, Time 15 min, replicate 1


title: Shade Pulse, 8.5 hours since Dawn, Time 30 min, replicate 1


title: High Light Pulse, 8 hours since Dawn, Time 0, replicate 2


title: Clear Day, 12 hours since dawn, replicate 2


title: Clear Day, 6 hours since dawn, replicate 2


title: Clear Day, 10 hours since dawn, replicate 1


title: Clear Day, 9 hours since dawn, replicate 1


title: Clear Day, 8 hours since dawn, replicate 2


title: Clear Day, 12 hours since dawn, replicate 1


title: Clear Day, 10 hours since dawn, replicate 2


title: Clear Day, 6 hours since dawn, replicate 1


title: Clear Day, 4 hours since dawn, replicate 2


title: Clear Day, 2 hours since dawn, replicate 2


title: Clear Day, 0.5 hours since dawn, replicate 1


title: Clear Day, 2 hours since dawn, replicate 1


title: Clear Day, 0.5 hours since dawn, replicate 2


title: Low Light, 10 hours since dawn, replicate 2


title: Low Light, 12 hours since dawn, replicate 2


title: Low Light, 10 hours since dawn, replicate 1


title: Low Light, 12 hours since dawn, replicate 1


title: Low Light, 9 hours since dawn, replicate 2


title: D8_Dnmt3a cKO_Acute

city: memphis

first: yiping

last: fan

state: tn

address: 262 Danny Thomas Place

institute: st jude children's hospital

data_processing:
Basecalling was performed using Illumina Casava 1.7
FASTQ sequences adapter trimmed (trimglore) and mapped to the mm10 genome by BSMAP
CpGs were extracted by the methratio.py in the BSMAP package
Genome_build: mm10
Supplementary_files_format_and_content: methylation ratio are in bed formats that contains methylation ratio for each CpG

source_name: Day 8_Acute GP33-specific Dnmt3a cKO CD8 T cells

extract_protocol:
DNA was extracted followed by bisulfite treatment for library prepration
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA Methylation Kit (Part# EGMK81312). Briefly, Bisulfite converted DNA was annealed with random hexamer with tagging sequence. DNA copy was synthesized using TruSeq DNA Methyl Polymerase. Then Exonuclease I was used to digest excess random primer.  The 3’ ends of the strands are then selectively tagged with a second specific sequence tag to generate di-tagged DNA using DNA polymerase. The di-tagged DNA with known sequence tags at both ends was cleaned up by the AMPureXP Beads. The dsDNA library was generated by PCR amplification with Illumina primers for 10 cycles and library fragments of ~350 bp (insert plus adaptor and PCR primer sequences). The library was purified by the AMPureXP Beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2500 following the manufacturer's protocols.

tag: genotype/variation

value: Dnmt3a cKO

value: Acute GP33-specific CD8 T cells

tag: time point

value: day 8


title: Clear Day, 8 hours since dawn, replicate 1


title: Clear Day, 9 hours since dawn, replicate 2


title: D4.5 MP_P14

source_name: Day 4.5_Acute WT Memory Precursor P14 cells

value: wild type

value: Acute Memory Precursor P14 cells

value: day 4.5


title: D8_WT_Acute

source_name: Day 8_Acute GP33-specific WT CD8 T cells


title: D4.5 TE_P14

source_name: Day 4.5_Acute WT Terminal Effector P14 cells

value: Acute Terminal Effector P14 cells


title: D8 TE_P14

source_name: Day 8_Acute WT Terminal Effector P14 cells


title: D8 MP_P14

source_name: Day 8_Acute WT Memory Precursor P14 cells


title: Low Light, 8 hours since dawn, replicate 1


title: Low Light, 8 hours since dawn, replicate 2


title: Low Light, 9 hours since dawn, replicate 1


title: Low Light, 6 hours since dawn, replicate 1


title: Naïve_P14

source_name: Naïve WT P14 CD8 T cells

value: P14 CD8 T cells


title: Low Light, 6 hours since dawn, replicate 2


title: H3K18crChIP_colonepithelium_Input_2

description:
ChIP-Seq_colonepithelium
processed data file:
H3K18crChIP_colonepithelium_MACSpeaks_readcounts.txt

value: colon epithelial


title: Clear Day, 4 hours since dawn, replicate 1


title: Low Light, 4 hours since dawn, replicate 2


title: Low Light, 4 hours since dawn, replicate 1


title: H3K18crChIP_colonepithelium_Input_1


title: Low Light, 2 hours since dawn, replicate 2


title: H3K18crChIP_colonepithelium_ChIP_2

value: H3K18cr antibody PTM Biolabs  (PTM-517)


title: Low Light, 2 hours since dawn, replicate 1


title: H3K18crChIP_colonepithelium_ChIP_1


title: Low Light, 0.5 hours since dawn, replicate 2


title: H3K4me3ChIP_colonepithelium_ChIP_3

description:
ChIP-Seq_colonepithelium
processed data file:
H3K4me3ChIP_colonepithelium_MACSpeaks_SEQMONK.txt


title: Mock ChIP experiment

data_processing:
Read alignment: Bowtie, v 0.12.9, -v 3 -m 1 -p 16 -t --best --un
Data normalization: alignment output from Bowtie was read into Matlab using custom code. Read counts of each sample were normalized to a Mock sample, which was identical to other experiments except a rabbit Igg antibody was used for isolation, using a custom-coded version of PeakSeq software (Rozowsky J et al 2009)
Peak calling: Peaks that were enriched in each sample significantly over the Mock experiment were identified using the PeakSeq algorithm (Rozowsky J et al 2009).
Enrichment calculation: Within each replicate, we determined the chromosomal position within each peak that had the highest measured normalized read counts. Then, we calculated an enrichment value at each timepoint by dividing the read counts in the sample at the determined peak maximum location by the read counts at the same position in the Mock dataset. To compare how enrichment changes after changes in light, we divided the enrichment of each peak at each timepoint by the enrichment of the peak at time 0 (8 hours after dawn in Low light for the High Light pulse, and 8 hours after dawn in Clear Day for the Shade pulse), and took the log2 of this ratio.
Peak filtering: Within each replicate, we only considered peaks that were enriched 3.5 fold or more above the Mock at at least one time point. Then, we only considered peaks that were detected by the above criteria in BOTH replicates.
Genome_build: Main chromosome: NC_007604.1; plasmid pANL (plasmid 1), NC_004073.2; plasmid pANS (plasmid 2), KT751091.1
Supplementary_files_format_and_content: Peak start and end position as determined by PeakSeq (Rozowksy J et al 2009).  Location of highest detected normalized read counts within the replicate (Peak max location). Minimum Q-value of the peak detected within each replicate as determined by PeakSeq (Rozowksy J et al 2009). Enrichment over mock, and Log2 change in enrichment from original condition, calculated as described above. We report processed data for both biological replicates.

source_name: Equal mass pool of all samples within a biological replicate

growth_protocol: Synechococcus elongatus PCC 7942 strain EOC 398, encoding a C-terminally FLAG tagged variant of the Beta prime subunit of RNA polymerase, was grown in BG-11M media supplemented with 10 mM HEPES pH 8.0 constantly bubbled with 1% CO2 in air. Cultures were maintained at OD750 0.3 with periodic dilution. Cultures were grown in either a Low Light condition of 50 µmol photons m-2 s-1 or a Clear Day condition where light intensity varied parabolically, reaching a maximum of 600 µmol photons m-2 s-1. Cultures were grown in light for 12 hours, followed by 12 hours of darkness, for three cycles. On the fourth light period at 8 hours after light onset, we incresed the light intensity of the Low Light culture by 10 fold (High Light pulse) and decreased the light intensity of the Clear Day culture by 10 fold (Shade pulse) for 1 hour, and sampled them before and after the perturbation. The time course was repeated twice for 2 biological replicates, and we report both datasets here.

extract_protocol:
120 mL of OD750 0.3 culture was crosslinked in 1% formaldehyde. Cells were lysed and fragmented genomic lysates were prepared using a Covaris acoustic sonication device. Protein-DNA complexes were isolated using antibody.
Sequencing libraries were prepared from purified ChIP DNA using the NEBNext Ultra II DNA Library Prep Kit.

value: Equal mass pool of samples from 9-10 hours since dawn

value: Pool of samples from both High Light pulse and Shade pulse

tag: chip antibody

value: Rabbit Igg (Sigma Aldrich, catalog number I5006)


title: RNAP ChIP, Shade Pulse, 9 hours since Dawn, Time 60 min, replicate 2

value: 60 minutes in Shade pulse

value: FLAG M2 mouse monoclonal antibody (Sigma-Aldrich, catalog number F1804, lot number SLBN5629V)


title: H3K4me3ChIP_colonepithelium_ChIP_2

tag: cell type


title: RNAseq_colonepithelium_3

description:
RNA-Seq_colonepithelium
processed data file:
RNAseq_colonepithelium_rawreadcountsmRNA.txt


title: RNAP ChIP, Shade Pulse, 8.25 hours since Dawn, Time 15 min, replicate 2

value: 15 minutes in Shade pulse


title: RNAseq_colonepithelium_2


title: RNAseq_colonepithelium_1


title: RNAP ChIP, Shade Pulse, 8.25 hours since Dawn, Time 15 min, replicate 1


title: RNAP ChIP, Shade Pulse, 8 hours since Dawn, Time 0, replicate 1

value: Shade pulse time 0 (prior to perturbation)


title: H3K4me3ChIP_colonepithelium_Input_1


title: Low Light, 0.5 hours since dawn, replicate 1


title: RNAP ChIP, High Light Pulse, 9 hours since Dawn, Time 60 min, replicate 1

value: 60 minutes in High Light pulse


title: RNAP ChIP, High Light Pulse, 8.25 hours since Dawn, Time 15 min, replicate 1

value: 15 minutes in High Light pulse


title: RpaB ChIP, Shade Pulse, 9 hours since Dawn, Time 60 min, replicate 2

value: anti-RpaB (made in-house)


title: RNAP ChIP, Shade Pulse, 8 hours since Dawn, Time 0, replicate 2


title: RNAP ChIP, High Light Pulse, 8 hours since Dawn, Time 0, replicate 2

value: High Light pulse time 0 (prior to perturbation)


title: RNAP ChIP, Shade Pulse, 9 hours since Dawn, Time 60 min, replicate 1


title: RNAP ChIP, High Light Pulse, 9 hours since Dawn, Time 60 min, replicate 2


title: RNAP ChIP, High Light Pulse, 8.25 hours since Dawn, Time 15 min, replicate 2


title: RpaB ChIP, Shade Pulse, 8.25 hours since Dawn, Time 15 min, replicate 1


title: RpaB ChIP, Shade Pulse, 8.25 hours since Dawn, Time 15 min, replicate 2


title: RpaB ChIP, High Light Pulse, 9 hours since Dawn, Time 60 min, replicate 2


title: RpaB ChIP, High Light Pulse, 9 hours since Dawn, Time 60 min, replicate 1


title: Q5_vent

data_processing:
Sequences were adaptor and quality trimmed using Trim Galore (v0.4.4)
Read were assembled with Pear v0.9.10, germline reads were removed using Bowtie2 v2.3.2 alignment to mm10, part of BabrahamLinkON v0.1 preclean step
Mispriming correction, UMI extraction was done with BabrahamLinkON v 0.1 preclean step
Deduplication and error correction was done with BabrahamLinkON v0.1 deduplicate step
Sequences were annotated with IgBlast v1.7.0 with IMGT reference and parsed with ChangO 0.3.7. Clonotype information was additionally added. All steps are part of BabrahamLinkON v0.1 assemble_clones step
Genome_build: mm10
Supplementary_files_format_and_content: tsv files containing annotated V(D)J sequences from IgBlast with IMGT reference

source_name: Splenic B cells

extract_protocol:
B cells from spleen isolated by depletin of unwated cells using 4 biotin antibodies and Miltenyi Biotec MACS LS columns. DNA was extracted with Qiagen DNeasy Blood & Tissue Kit (69504).
Libraried were constructed using the VDJ-seq protocol.

value: 12 weeks

value: Enriched B cells by MACS depletion


title: RpaB ChIP, Shade Pulse, 8 hours since Dawn, Time 0, replicate 1


title: RpaB ChIP, High Light Pulse, 8.25 hours since Dawn, Time 15 min, replicate 2


title: RpaB ChIP, Shade Pulse, 8 hours since Dawn, Time 0, replicate 2


title: 5ug


title: H3K4me3ChIP_colonepithelium_ChIP_1


title: RpaB ChIP, High Light Pulse, 8.25 hours since Dawn, Time 15 min, replicate 1


title: 500ng


title: RpaB ChIP, High Light Pulse, 8 hours since Dawn, Time 0, replicate 2


title: 2_5ug


title: 1ug


title: RpaA ChIP, Shade Pulse, 9 hours since Dawn, Time 60 min, replicate 2

value: anti-RpaA (made in-house)


title: RpaB ChIP, High Light Pulse, 8 hours since Dawn, Time 0, replicate 1


title: RpaA ChIP, Shade Pulse, 9 hours since Dawn, Time 60 min, replicate 1


title: RpaA ChIP, Shade Pulse, 8.25 hours since Dawn, Time 15 min, replicate 2


title: RpaB ChIP, Shade Pulse, 9 hours since Dawn, Time 60 min, replicate 1


title: RpaA ChIP, Shade Pulse, 8 hours since Dawn, Time 0, replicate 1


title: RpaA ChIP, High Light Pulse, 9 hours since Dawn, Time 60 min, replicate 2


title: RpaA ChIP, High Light Pulse, 9 hours since Dawn, Time 60 min, replicate 1


title: RpaA ChIP, High Light Pulse, 8.25 hours since Dawn, Time 15 min, replicate 2


title: RpaA ChIP, High Light Pulse, 8 hours since Dawn, Time 0, replicate 1


title: RpaA ChIP, High Light Pulse, 8 hours since Dawn, Time 0, replicate 2


title: RpaA ChIP, High Light Pulse, 8.25 hours since Dawn, Time 15 min, replicate 1


title: Linear plasmid

city: Milan

first: Fabrizio

last: d'Adda di Fagagna

state: Mi

address: Via Adamello 16

country: Italy

institute: IFOM - The FIRC Institute of Molecular Oncology

description: RNA products generated upon incubation of linear pLac-Tet plasmid in human cell extract

data_processing:
Reads were mapped to the pLac-Tet plasmid using Bowtie2 with a very sensitive local option (-D 20 -R 3 -N 0 -L 20 -i S,1,0.50).
Reads were splitted to two separate files according to their strand using Samtools view.
The coverage of each position was calculated using samtools mpileup.
Genome_build: Reference.fa (pLac-Tet plasmid prepared by cloning a fragment of 556 bp which contains an I-SceI site flanked by 3 Tet and 8 Lac repetitive elements into SfiI site of pMK-RQ vector made by GENEART)
Supplementary_files_format_and_content: bedgraph files showing the coverage of each position as calculated by samtools mpileup.

organism: Synthetic plasmid

source_name: pLac-Tet plasmid

extract_protocol:
Reaction RNA products were purified by phenol-chloroform extraction and precipitated overnight at -20°C in ethanol. Reaction RNA products were treated with DNase I and size-selected by gel.
Ion Total RNA-Seq Kit v2 for strand-specific RNA sequencing. No shearing step was performed in order to preserve the original length of the molecules.

treatment_protocol: Cell extracts were prepared from K562 cell line. The DNA substrate containing a DSB was prepared by digesting the pLac-Tet plasmid (GENEART) with I-SceI enzyme. For transcription reaction, 2 µg of cell-free extracts were incubated with 200 ng of linearized plasmid in a buffer containing 20 mM HEPES [pH 7.5], 3 mM MgCl2, 100 mM KCl, 0.2 mM EDTA, 0.5 mM DTT, 20% glycerol, 0.4 mM rATP, rCTP, rGTP each and 10 µCi  [α-32P]UTP for 1 h at 37°C in a total reaction volume of 25 µL. The reaction was stopped by the addition of 0.3 M Tris-HCl (pH 7.4 at 25°C), 0.3 M sodium acetate, 0.5% SDS, 2 mM EDTA and 3 µg/mL glycogen.

tag: plasmid

value: pLac-Tet


title: Sample_J7_25

status: Public on Dec 15 2017

city: Philadelphia

first: Junhyong

state: PA

address: 433 S University Avenue

department: Biology

institute: University of Pennsylvania

description:
PolyA RNA
Basecalling: bcl2fastq2 v2.17
Processed data file: mouse_RNA.txt

data_processing:
Basecalling was done with bcl2fastq versions 1.8.4 and 2.17. Included in the 'Description' field.
Low confidence nucleotides (with Phred score less than 20) were treated as unknown and replaced with Ns. Unknown nucleotides (Ns) at the ends of reads were trimmed. Poly-A and method-specific adapter sequences were trimmed from the 3’ end of reads using in-house software. Reads were aligned to the mouse reference genome, build mm10, and to spike-in transcript sequences using STAR (Spliced Transcripts Alignment to a Reference) aligner version 2.4.0h1. We provided STAR with mm10 annotations to generate a splice-junction loci database for use in alignment. We retained reads that aligned to at least 40% (paired-end) of trimmed length or 30bp, whichever was greater. In addition, we discarded reads with greater than 30% mismatched positions in trimmed length.
Uniquely aligned reads were assigned to mm10 gene annotations and to spike-in transcripts using Verse which functions identically to HTSeq's htseq-counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non-empty method.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: mouse_RNA.txt: Data file is tab-delimited text file containing gene abundance measurements.

source_name: astrocyte

growth_protocol:
Samples were extracted from mouse and cultured for 12 days.
Standard Primary Cell Culturing Conditions as described in Kaech and Banker, Nat. Protoc. 1, 2006.

extract_protocol:
Individual cells were collected by patch pipette.
Libraries made with Illumina TruSeq Stranded kit (RS-122-2101/2).

treatment_protocol: No treatment.

tag: strain/background

value: astrocyte

tag: source region

value: cortex

tag: source type

value: primary culture


title: Sample_J1_18


title: Sample_J362_8


title: Sample_J344_10


title: Sample_J343_5


title: Sample_J336_4


title: Sample_J348_13


title: Sample_J300_5


title: RpaA ChIP, Shade Pulse, 8 hours since Dawn, Time 0, replicate 2


title: RpaA ChIP, Shade Pulse, 8.25 hours since Dawn, Time 15 min, replicate 1


title: Sample_J333_8


title: Sample_J323_9


title: Sample_J317_16


title: Sample_J324_1


title: Sample_J334_10


title: Q5_Q5

tag: strain

tag: age


title: Sample_J299_11


title: Circular plasmid

description: RNA products generated upon incubation of circular pLac-Tet plasmid in human cell extract


title: Sample_J316_3


title: Sample_RS10

source_name: neuron

value: neuron

value: acute slice


title: Sample_J363_12


title: Sample_J342_2


title: Sample_J121_18


title: Sample_J123_2


title: Sample_J122_25


title: Sample_J120_13


title: Sample_J124_11


title: Sample_J119_12


title: Sample_J116_9


title: Sample_J117_10


title: Sample_J115_8


title: Sample_J112_4


title: Sample_J114_6


title: Sample_J113_5


title: Sample_J369_18


title: Sample_J328_12


title: Sample_J322_11


title: Sample_J329_18


title: Sample_J308_9


title: Sample_J215_13


title: Sample_J368_25


title: Sample_J287_6


title: Sample_J309_10


title: Sample_J351_19


title: Sample_J276_5


title: Sample_J290_4


title: Sample_J303_8


title: Sample_J341_5


title: Sample_J238_25


title: Sample_J234_16


title: Sample_J219_2


title: Sample_J289_5


title: Sample_J237_9


title: Sample_J293_1


title: Sample_J280_2


title: Sample_J264_19


title: Sample_J233_3


title: Sample_J271_18


title: Sample_J275_9


title: Sample_J288_8


title: Sample_J265_3


title: Sample_J263_25


title: Sample_F11b


title: Sample_J251_9

growth_protocol:
Samples were extracted from mouse and cultured for 15 days.
Standard Primary Cell Culturing Conditions as described in Kaech and Banker, Nat. Protoc. 1, 2006.


title: Sample_J301_18

growth_protocol:
Samples were extracted from mouse and cultured for 14 days.
Standard Primary Cell Culturing Conditions as described in Kaech and Banker, Nat. Protoc. 1, 2006.


title: Sample_J291_25


title: Sample_J255_10


title: Sample_J292_11


title: Sample_J225_16


title: Sample_J361_5


title: Sample_J228_3


title: Sample_J212_1


title: Sample_J213_8


title: Sample_J302_2


title: Sample_J281_8


title: Sample_J286_25


title: Sample_J269_13


title: Sample_J246_12


title: Sample_J270_11


title: Sample_J256_16


title: Sample_J221_8


title: Sample_CA1-4b

value: hippocampus CA1


title: Sample_J242_6


title: Sample_J214_2


title: Sample_P1b


title: Sample_J222_9


title: Sample_J241_10


title: Sample_J223_4


title: Sample_P24b


title: Sample_F11


title: Sample_J236_5


title: Sample_P21b


title: Sample_F1b


title: Sample_CA1_41b


title: Sample_CA1_34


title: Sample_CA1_41


title: Sample_CA1_29


title: Sample_CA1_35


title: Sample_P1S

value: hippocampus


title: Sample_2016R2N_5

growth_protocol:
Samples were extracted from mouse and cultured for 10 days.
Standard Primary Cell Culturing Conditions as described in Kaech and Banker, Nat. Protoc. 1, 2006.


title: Sample_P2S


title: Sample_2016R14N_13

growth_protocol:
Samples were extracted from mouse and cultured for 13 days.
Standard Primary Cell Culturing Conditions as described in Kaech and Banker, Nat. Protoc. 1, 2006.


title: Sample_P27


title: Sample_2016R5N_23


title: Sample_2016R3N_6


title: Sample_2016R11N_10


title: Sample_J50_8

growth_protocol:
Samples were extracted from mouse and cultured for 7 days.
Standard Primary Cell Culturing Conditions as described in Kaech and Banker, Nat. Protoc. 1, 2006.


title: Sample_2016R9N_19


title: Sample_2016R10N_23


title: Sample_J60_20


title: Sample_N5S


title: Sample_M9S


title: Sample_M1D


title: Sample_M1S


title: Sample_M9D


title: Sample_CA3_10

value: hippocampus CA3


title: Sample_CA1_20


title: Sample_CA1_25


title: Sample_CA1_24


title: Sample_P24


title: Sample_P19


title: Sample_P32


title: Sample_P33


title: Sample_J56_19


title: Sample_CA1-18


title: Sample_P17


title: Sample_P16


title: Sample_CA1-16


title: Sample_P15


title: Sample_M6S


title: Sample_P21


title: Sample_P20


title: Sample_CA3-8


title: Sample_F7


title: Sample_CA1-14


title: Lerx nrpd1a-4 (Col) exp2 rep 1

first: Mary

last: Gehring

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: mRNA-seq

data_processing:
Read filtering was performed using cutadapt (-0 6 -m 26 —discard-untrimmed) and trim_galore (-t 10; http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove low quality bases from the 5’ end of reads. Trimmed reads were assessed with fastqc.
Reads were aligned to TAIR10 using tophat (-N 2 -read-edit-dist 2; v2.0.13)
Following alignment, reads were classified by strain (Col or Ler) using SNPs (Pignatta et al., eLife, 2014). If classification at two SNP positions within the same read conflicted, that read was discarded.
Allele-specific read counts for each locus were generated by running ht-seq count on the reads classifed by strain (–m intersection-strict –-stranded=no).
In the case of libraries originating from crosses including a parent with the nrpd1 allele in the Ler background, reads originating from genes that retained the Col genotype even after multiple backcrosses into Ler were removed from downstream analysis. These loci are listed in colholdoutgeneIDsnrpd1.txt.
Genome_build: TAIR10, resequenced Ler-0 genome
Supplementary_files_format_and_content: allele_counts files contain RNA-seq data in tab-delimited format for each sample, with one row per gene.  Contains gene ID (locus_name), Col-assigned reads (Col), Ler-assigned reads (Ler), and total number of RNA-seq reads aligned to gene (total).
Supplementary_files_format_and_content: colholdoutgeneIDsnrpd1.txt file is the list of gene IDs not to be included in analysis for the nrpd1a-4 (Ler) female x nrpd1a-4 (Col) male samples (three reps) or their wild type counterparts, Ler female x Col male 6 days after pollination (2 reps). These loci remain as Col genotype in at least one of the the nrpd1a-4 (Ler) plants even after four backcrosses of nrpd1a-4 (Col) to Ler.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Endosperm

growth_protocol: Plants were grown in a greenhouse with 16-hour days at ~21 C. Flowers were emasculated 2 days before pollination. Seeds were dissected at six-seven DAP (approximately torpedo stage of embryogenesis).

extract_protocol:
Seeds from crosses between multiple individuals were hand-dissected and total endosperm isolated using the Ambion RNAqueous Micro Kit.
DNase I-treated RNA (Invitrogen, Life Technologies Corporation, Carlsbad, CA) was prepped by the Whitehead Genome Technology Core into mRNA-seq libraries using the SMARTerUltra-lowPOLYA-V4 prep kit. Amplification was for 12 cycles. Libraries were sequenced with a 40 bp single read standard cycle on a Hiseq2500.

treatment_protocol: no treatment

tag: genotype

value: Ler female x nrpd1a-4 (Col) male

tag: developmental stage

value: 6-7 days after pollination

tag: tissue

value: Endosperm


title: Lerx nrpd1a-4 (Col) exp2 rep 3

description: mRNA-seq


title: Lerx nrpd1a-4 (Col) exp2 rep 2

description: mRNA-seq


title: Sample_J332_25


title: Sample_P22


title: Ler x Col exp2 rep 3

description: mRNA-seq

value: Ler female x Col male


title: Ler x Col exp2 rep 1

description: mRNA-seq


title: Sample_CA3-9


title: Ler x Col exp2 rep 2

description: mRNA-seq


title: SCCO28 Control

city: Lausanne

first: Paolo

last: Angelino

address: Quartier Sorge, Bâtiment Génopode

department: BCF

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

data_processing:
Reads were trimmed by using Trimmomatic (v0.22) followed by mapping to the human hg19 reference genome using TopHat (v2.0.8b).
Gene expression levels were then evaluated using HTSeq package (release 0.5.4p1).
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq raw counts

extract_protocol:
Total RNA was extracted 5 days after shRNA infection for CSL knockdown cells using the directZol RNA miniprep kit (Zymo Research).
Library preparation using the Truseq kit (Illumina) was done with 4µg of total RNA. Single read was done on the Illumina HiSeq 2000 sequencer

tag: treatment

value: SCCO28 shRNA control


title: SCC13 shCSL n°1

value: SCC13 shCSL n 1


title: SCC13 Control

value: SCC13 shRNA control


title: SCC13 shCSL n°2

value: SCC13 shCSL n 2


title: HKC shCSL n°2 - rep2

source_name: HKC

value: HKC shCSL n 2 - replicate 2


title: HKC shCSL n°2 - rep1

value: HKC shCSL n 2 - replicate 1


title: HKC shCSL n°1 - rep2

value: HKC shCSL n 1 - replicate 2


title: CSL_ChIP-Seq

description: Immunoprecipitated CSL linked DNA

data_processing:
FASTQ file alignments were done using Burrows–Wheeler Aligner (http://bio-bwa.sourceforge.net), and with default parameters.
peak detection was done using MACS2 software (http://liulab.dfci.harvard.edu/MACS)
Genome_build: hg19
Supplementary_files_format_and_content: peak list from MACS2 in bed format

extract_protocol:
DNA was immunoprecipitated from 5 x 10e6 HKCs using 10 μl of CSL antibody per 10e6 cells, followed by quantification by fluorometry on a Qubit system (Invitrogen).
A total of 10 ng of DNA was used for library preparation using NEBNext ChIP-Seq Library Prep Kit (Illumina) according to manufacturer’s recommendation.

value: CSL antibody


title: IgG_ChIP-Seq

description: Immunoprecipitated IgG linked DNA

value: non-immune IgG control


title: KDM4(i) (repeat 2)

city: Freiburg

first: Eric

last: Metzger

address: Breisacherstr. 66

country: Germany

institute: Uniklinik-Freiburg

data_processing:
We aligned these reads to the hg19 build of the human genome using TopHat version 2
The aligned reads were counted with the homer software (analyzeRNA) and DEG’s were identified using DESeq
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file are text files that include the overall read count for a specific transcript (indicated by the NM accession number)

source_name: KDM4(i), BCSC1 cells

growth_protocol: BCSC1 cells were grown in MSC medium under low-oxygen conditions

extract_protocol:
RNA was harvested  from BCSC1 cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BCSC1 cells were treated with  10nm KDM4(i) for 18 hours

tag: cell line

value: breast triple negative tumor cell line BCSC1

value: 10 nM kDM4(i) for 18 hours


title: KDM4(i) (repeat 3)


title: control (repeat 3)

source_name: control, BCSC1 cells

value: vehicle


title: control (repeat 2)


title: SCCO28 shCSL n°2

value: SCCO28 shCSL n 2


title: ChIP_KDM4A

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

extract_protocol:
Metzger, E., et al. Phosphorylation of histone H3 at threonine 11 establishes a novel chromatin mark for transcriptional regulation. Nat Cell Biol 10, 53-60 (2008), Drosophila Spike in Chromatin was added in  H3K9me3 control and H3K9me3 (i) samples.
Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the hg19 reference genome using bowtie 2

treatment_protocol: BCSC1 cells were treated with  10nm KDM4(i) for 18 hours or infected with shRNA for 3 days

value: shRNA control

value: KDM4A (Schuele Lab; #5766, lot 21110)


title: Input_knockdown KDM4A_ChIP_KDM4A

source_name: Input_knockdown KDM4A_ChIP_KDM4A

value: shRNA KDM4A


title: SCCO28 shCSL n°1

value: SCCO28 shCSL n 1


title: ChIP H3K9me3_KDM4(i)

source_name: ChIP H3K9me3_KDM4(i)


title: Input_KDM4A


title: knockdown KDM4A_ChIP_KDM4A

source_name: knockdown KDM4A_ChIP_KDM4A


title: Input_H3K9me3_KDM4(i)


title: input_H3K9me3_control


title: ChIP_H3K9me3_control


title: HKC shCSL n°1 - rep1

value: HKC shCSL n 1 - replicate 1


title: HKC Control - rep2

value: HKC shRNA control - replicate 2


title: HKC Control - rep1

value: HKC shRNA control - replicate 1


title: KDM4(i) (repeat 1)


title: SKBR3.H4K8ac

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2.
ChIP-seq reads were aligned to the hg19 genome using Bowtie2 v2.1.0.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS-1.3.6; Scores represent the ChIP-seq tag numbers.

source_name: SKBR3 cells, H4K8ac ChIP

growth_protocol: Cells were plated and expanded on 150mm plates until a minimum of 3.5 x 10^5 cells per plate were reached. The media conditions and split ratio for each cell line is depicted in the Excel sheet entitled “Cell line conditions”. Media is replaced every other day, until the desired confluency is reached.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells are harvested from the 150mm plates under sterile conditions into a 50ml conical tube. Aliquots of 100-200ul of this stock are then counted using the Biorad Cell Counter. Counts are repeated three times and the number of cells per ml are then determined. For growth curves, the schema in the Powerpoint entitled “Growthcurveprotocol” is followed. Briefly, 500-5000 cells (for each cell line) were plated onto each well of a 96-well plate on day 0. For each cell line, a total of 7 replicate plates were seeded. The media was changed every other day (days 1, 3, 5, 7, 9, 11, and 13). One plate from each cell line was subjected to MTT proliferation assay every other day (days 1, 3, 5, 7, 9, 11, and 13).

value: Breast cancer cell line

value: Control


title: SKBR3.H3K23ac

source_name: SKBR3 cells, H3K23ac ChIP


title: RNAP ChIP, High Light Pulse, 8 hours since Dawn, Time 0, replicate 1

source_name: Low Light-acclimated culture

tag: hours since light onset (dawn)

tag: perturbation

value: High Light pulse time 0 (prior to perturbation)

value: FLAG M2 mouse monoclonal antibody (Sigma-Aldrich, catalog number F1804, lot number SLBN5629V)

tag: replicate


title: UACC812.H2BK120ub

source_name: UACC812 cells, H2BK120ub1 ChIP


title: UACC812.H3K23ac

source_name: UACC812 cells, H3K23ac ChIP


title: ZR751.H2BK120ub

source_name: ZR751 cells, H2BK120ub1 ChIP


title: ZR751.H4K8ac

source_name: ZR751 cells, H4K8ac ChIP


title: SKBR3.H2BK120ub

source_name: SKBR3 cells, H2BK120ub1 ChIP


title: UACC812.H4K8ac

source_name: UACC812 cells, H4K8ac ChIP


title: MCF7.H4K8ac

source_name: MCF7 cells, H4K8ac ChIP


title: MCF7.H3K23ac

source_name: MCF7 cells, H3K23ac ChIP


title: MCF10A.H3K23ac

source_name: MCF10A cells, H3K23ac ChIP


title: MCF10A.H4K8ac

source_name: MCF10A cells, H4K8ac ChIP


title: MCF10A.H2BK120ub

source_name: MCF10A cells, H2BK120ub1 ChIP


title: MB468.H4K8ac

source_name: MB468 cells, H4K8ac ChIP


title: MB468.H2BK120ub

source_name: MB468 cells, H2BK120ub1 ChIP


title: MB468.H3K23ac

source_name: MB468 cells, H3K23ac ChIP


title: MB436.H4K8ac

source_name: MB436 cells, H4K8ac ChIP


title: MB436.H2BK120ub

source_name: MB436 cells, H2BK120ub1 ChIP


title: MB436.H3K23ac

source_name: MB436 cells, H3K23ac ChIP


title: Sample_CA3_21

source_name: neuron

value: neuron

value: hippocampus CA3

value: acute slice


title: MB361.H4K8ac

source_name: MB361 cells, H4K8ac ChIP


title: MB361.H3K23ac

source_name: MB361 cells, H3K23ac ChIP


title: MB231.H4K8ac

source_name: MB231 cells, H4K8ac ChIP


title: MB361.H2BK120ub

source_name: MB361 cells, H2BK120ub1 ChIP


title: MB231.H3K23ac

source_name: MB231 cells, H3K23ac ChIP


title: MB231.H2BK120ub

source_name: MB231 cells, H2BK120ub1 ChIP


title: HCC1937.H4K8ac

source_name: HCC1937 cells, H4K8ac ChIP


title: HCC1954.H2BK120ub

source_name: HCC1954 cells, H2BK120ub1 ChIP


title: HCC1954.H4K8ac

source_name: HCC1954 cells, H4K8ac ChIP


title: MCF7.H2BK120ub

source_name: MCF7 cells, H2BK120ub1 ChIP


title: HCC1954.H3K23ac

source_name: HCC1954 cells, H3K23ac ChIP


title: 76NF2V.H2BK120ub

source_name: 76NF2V cells, H2BK120ub1 ChIP


title: HCC1937.H3K23ac

source_name: HCC1937 cells, H3K23ac ChIP


title: 76NF2V.H4K8ac

source_name: 76NF2V cells, H4K8ac ChIP


title: AU565.H4K8ac

source_name: AU565 cells, H4K8ac ChIP


title: HCC1937.Input.rep1

source_name: HCC1937 cells, input


title: AU565.H2BK120ub

source_name: AU565 cells, H2BK120ub1 ChIP


title: HCC1937.H3K79me2.rep2

source_name: HCC1937 cells, H3K79me2 ChIP


title: HCC1937.H3K9me3.rep1

source_name: HCC1937 cells, H3K9me3 ChIP

value: H3K9me3 (Abcam, ab8898)


title: HCC1937.H3K9me3.rep2


title: HCC1937.H3K9ac.rep2

source_name: HCC1937 cells, H3K9ac ChIP


title: HCC1937.H3K79me2.rep1

value: H3K79me2 (Abcam, ab3594)


title: HCC1937.H3K9ac.rep1


title: HCC1937.H3K4me3.rep2

source_name: HCC1937 cells, H3K4me3 ChIP


title: HCC1937.H3K4me1.rep1

source_name: HCC1937 cells, H3K4me1 ChIP

value: H3K4me1 (Abcam, ab8895)


title: HCC1937.H3K4me1.rep2


title: HCC1937.H3K36me3.rep2

source_name: HCC1937 cells, H3K36me3 ChIP


title: ZR751.H3K23ac

source_name: ZR751 cells, H3K23ac ChIP


title: HCC1937.H2BK120ub

source_name: HCC1937 cells, H2BK120ub1 ChIP


title: HCC1937.H3K36me3.rep1

value: H3K36me3 (Abcam, ab9050)


title: HCC1937.H3K27me3.rep1

source_name: HCC1937 cells, H3K27me3 ChIP

value: H3K27me3 (Millipore, 07-449)


title: HCC1937.H3K27me3.rep2


title: HCC1937.H3K27ac.rep1

source_name: HCC1937 cells, H3K27ac ChIP


title: HCC1937.Input.rep2


title: HCC1937.H3K27ac.rep2


title: 76NF2V.H3K23ac

source_name: 76NF2V cells, H3K23ac ChIP


title: MB468.Input.rep1

source_name: MB468 cells, input


title: MB468.H3K9me3.rep2

source_name: MB468 cells, H3K9me3 ChIP


title: MB468.H3K9me3.rep1


title: HCC1937.H3K4me3.rep1

value: H3K4me3 (Abcam, ab8580)


title: MB468.H3K9ac.rep2

source_name: MB468 cells, H3K9ac ChIP


title: MB468.H3K79me2.rep2

source_name: MB468 cells, H3K79me2 ChIP


title: MB468.H3K79me2.rep1


title: MB468.H3K27me3.rep1

source_name: MB468 cells, H3K27me3 ChIP


title: MB468.H3K36me3.rep1

source_name: MB468 cells, H3K36me3 ChIP


title: MB468.H3K27ac.rep2

source_name: MB468 cells, H3K27ac ChIP


title: MB468.H3K4me1.rep1

source_name: MB468 cells, H3K4me1 ChIP


title: MB468.H3K4me3.rep1

source_name: MB468 cells, H3K4me3 ChIP


title: MB468.Input.rep2


title: MB468.H3K4me1.rep2


title: MB468.H3K27me3.rep2


title: MB468.H3K4me3.rep2


title: MB468.H3K27ac.rep1


title: MB436.Input.rep2

source_name: MB436 cells, input


title: MB436.Input.rep1


title: MB436.H3K9me3.rep2

source_name: MB436 cells, H3K9me3 ChIP


title: MB436.H3K9ac.rep2

source_name: MB436 cells, H3K9ac ChIP


title: MB468.H3K36me3.rep2


title: MB436.H3K4me3.rep1

source_name: MB436 cells, H3K4me3 ChIP


title: MB436.H3K4me1.rep2

source_name: MB436 cells, H3K4me1 ChIP


title: MB436.H3K9me3.rep1


title: MB436.H3K9ac.rep1


title: MB436.H3K4me3.rep2


title: MB436.H3K79me2.rep2

source_name: MB436 cells, H3K79me2 ChIP


title: MB436.H3K36me3.rep2

source_name: MB436 cells, H3K36me3 ChIP


title: MB436.H3K79me2.rep1


title: MB436.H3K4me1.rep1


title: MB436.H3K27me3.rep1

source_name: MB436 cells, H3K27me3 ChIP


title: MB436.H3K27me3.rep2


title: MB436.H3K36me3.rep1


title: MB436.H3K27ac.rep1

source_name: MB436 cells, H3K27ac ChIP


title: MB436.H3K27ac.rep2


title: MB231.H3K9me3.rep2

source_name: MB231 cells, H3K9me3 ChIP


title: MB231.Input.rep1

source_name: MB231 cells, input


title: MB231.H3K9me3.rep1


title: MB231.H3K79me2.rep2

source_name: MB231 cells, H3K79me2 ChIP


title: MB231.H3K9ac.rep2

source_name: MB231 cells, H3K9ac ChIP


title: MB231.H3K4me3.rep1

source_name: MB231 cells, H3K4me3 ChIP


title: MB231.H3K4me1.rep1

source_name: MB231 cells, H3K4me1 ChIP


title: MB231.Input.rep2


title: MB231.H3K4me3.rep2


title: MB231.H3K79me2.rep1


title: MB231.H3K4me1.rep2


title: MB231.H3K36me3.rep2

source_name: MB231 cells, H3K36me3 ChIP


title: MB231.H3K9ac.rep1


title: MB231.H3K27me3.rep2

source_name: MB231 cells, H3K27me3 ChIP


title: MB231.H3K27me3.rep1


title: MB231.H3K27ac.rep1

source_name: MB231 cells, H3K27ac ChIP


title: HCC1954.Input.rep2

source_name: HCC1954 cells, input


title: HCC1954.Input.rep1


title: HCC1954.H3K9me3.rep2

source_name: HCC1954 cells, H3K9me3 ChIP


title: HCC1954.H3K9me3.rep1


title: MB468.H3K9ac.rep1

source_name: MB468 cells, H3K9ac ChIP


title: HCC1954.H3K9ac.rep1

source_name: HCC1954 cells, H3K9ac ChIP


title: HCC1954.H3K79me2.rep2

source_name: HCC1954 cells, H3K79me2 ChIP


title: HCC1954.H3K79me2.rep1


title: MB231.H3K27ac.rep2


title: HCC1954.H3K4me3.rep1

source_name: HCC1954 cells, H3K4me3 ChIP


title: HCC1954.H3K4me3.rep2


title: HCC1954.H3K4me1.rep2

source_name: HCC1954 cells, H3K4me1 ChIP


title: HCC1954.H3K4me1.rep1


title: HCC1954.H3K27me3.rep2

source_name: HCC1954 cells, H3K27me3 ChIP


title: HCC1954.H3K27ac.rep2

source_name: HCC1954 cells, H3K27ac ChIP


title: HCC1954.H3K27me3.rep1


title: AU565.Input.rep1

source_name: AU565 cells, input


title: AU565.Input.rep2


title: HCC1954.H3K27ac.rep1


title: MB231.H3K36me3.rep1


title: AU565.H3K9me3.rep2

source_name: AU565 cells, H3K9me3 ChIP


title: HCC1954.H3K9ac.rep2


title: AU565.H3K9me3.rep1


title: AU565.H3K4me3.rep1

source_name: AU565 cells, H3K4me3 ChIP


title: AU565.H3K23ac

source_name: AU565 cells, H3K23ac ChIP


title: AU565.H3K4me1.rep2

source_name: AU565 cells, H3K4me1 ChIP


title: AU565.H3K79me2.rep1

source_name: AU565 cells, H3K79me2 ChIP


title: AU565.H3K36me3.rep2

source_name: AU565 cells, H3K36me3 ChIP


title: AU565.H3K79me2.rep2


title: AU565.H3K36me3.rep1


title: AU565.H3K4me3.rep2


title: HCC1954.H3K36me3.rep1

source_name: HCC1954 cells, H3K36me3 ChIP


title: AU565.H3K27me3.rep1

source_name: AU565 cells, H3K27me3 ChIP


title: AU565.H3K27me3.rep2


title: AU565.H3K4me1.rep1


title: HCC1954.H3K36me3.rep2


title: SKBR3.Input.rep1

source_name: SKBR3 cells, input


title: SKBR3.Input.rep2


title: SKBR3.H3K9me3.rep2

source_name: SKBR3 cells, H3K9me3 ChIP


title: AU565.H3K27ac.rep1

source_name: AU565 cells, H3K27ac ChIP


title: AU565.H3K9ac.rep1

source_name: AU565 cells, H3K9ac ChIP


title: SKBR3.H3K9me3.rep1


title: SKBR3.H3K79me2.rep2

source_name: SKBR3 cells, H3K79me2 ChIP


title: SKBR3.H3K9ac.rep1

source_name: SKBR3 cells, H3K9ac ChIP


title: SKBR3.H3K79me2.rep1


title: SKBR3.H3K4me3.rep2

source_name: SKBR3 cells, H3K4me3 ChIP


title: SKBR3.H3K4me3.rep1


title: SKBR3.H3K36me3.rep1

source_name: SKBR3 cells, H3K36me3 ChIP


title: AU565.H3K27ac.rep2


title: SKBR3.H3K4me1.rep1

source_name: SKBR3 cells, H3K4me1 ChIP


title: SKBR3.H3K27ac.rep2

source_name: SKBR3 cells, H3K27ac ChIP


title: SKBR3.H3K27me3.rep2

source_name: SKBR3 cells, H3K27me3 ChIP


title: SKBR3.H3K27me3.rep1


title: UACC812.H3K9ac.rep2

source_name: UACC812 cells, H3K9ac ChIP


title: UACC812.H3K9me3.rep1

source_name: UACC812 cells, H3K9me3 ChIP


title: UACC812.H3K9ac.rep1


title: UACC812.H3K79me2.rep2

source_name: UACC812 cells, H3K79me2 ChIP


title: UACC812.H3K79me2.rep1


title: UACC812.H3K9me3.rep2


title: UACC812.H3K4me3.rep2

source_name: UACC812 cells, H3K4me3 ChIP


title: UACC812.H3K4me1.rep1

source_name: UACC812 cells, H3K4me1 ChIP


title: UACC812.H3K36me3.rep2

source_name: UACC812 cells, H3K36me3 ChIP


title: UACC812.Input.rep2

source_name: UACC812 cells, input


title: UACC812.H3K4me1.rep2


title: UACC812.H3K4me3.rep1


title: SKBR3.H3K9ac.rep2


title: UACC812.H3K36me3.rep1


title: UACC812.Input.rep1


title: SKBR3.H3K27ac.rep1


title: UACC812.H3K27me3.rep2

source_name: UACC812 cells, H3K27me3 ChIP


title: UACC812.H3K27me3.rep1


title: SKBR3.H3K36me3.rep2


title: UACC812.H3K27ac.rep2

source_name: UACC812 cells, H3K27ac ChIP


title: MB361.Input.rep2

source_name: MB361 cells, input


title: MB361.H3K9me3.rep1

source_name: MB361 cells, H3K9me3 ChIP


title: MB361.H3K9ac.rep2

source_name: MB361 cells, H3K9ac ChIP


title: MB361.H3K9me3.rep2


title: MB361.H3K9ac.rep1


title: MB361.H3K4me3.rep2

source_name: MB361 cells, H3K4me3 ChIP


title: MB361.H3K4me1.rep2

source_name: MB361 cells, H3K4me1 ChIP


title: MB361.H3K36me3.rep2

source_name: MB361 cells, H3K36me3 ChIP


title: MB361.H3K79me2.rep2

source_name: MB361 cells, H3K79me2 ChIP


title: MB361.H3K4me1.rep1


title: MB361.H3K27me3.rep2

source_name: MB361 cells, H3K27me3 ChIP


title: MB361.H3K4me3.rep1


title: MB361.H3K27ac.rep2

source_name: MB361 cells, H3K27ac ChIP


title: UACC812.H3K27ac.rep1


title: ZR751.H3K9me3.rep1

source_name: ZR751 cells, H3K9me3 ChIP


title: ZR751.H3K9me3.rep2


title: ZR751.Input.rep1

source_name: ZR751 cells, input


title: SKBR3.H3K4me1.rep2

source_name: SKBR3 cells, H3K4me1 ChIP


title: ZR751.Input.rep2


title: ZR751.H3K79me2.rep2

source_name: ZR751 cells, H3K79me2 ChIP


title: MB361.H3K79me2.rep1


title: ZR751.H3K9ac.rep1

source_name: ZR751 cells, H3K9ac ChIP


title: ZR751.H3K9ac.rep2


title: ZR751.H3K4me3.rep2

source_name: ZR751 cells, H3K4me3 ChIP


title: ZR751.H3K4me1.rep1

source_name: ZR751 cells, H3K4me1 ChIP


title: MB361.H3K27me3.rep1


title: ZR751.H3K4me1.rep2


title: ZR751.H3K36me3.rep2

source_name: ZR751 cells, H3K36me3 ChIP


title: ZR751.H3K79me2.rep1


title: ZR751.H3K36me3.rep1


title: MB361.Input.rep1

source_name: MB361 cells, input


title: MB361.H3K36me3.rep1


title: MCF7.H3K9ac.rep2

source_name: MCF7 cells, H3K9ac ChIP


title: ZR751.H3K27me3.rep2

source_name: ZR751 cells, H3K27me3 ChIP


title: MCF7.H3K9me3.rep2

source_name: MCF7 cells, H3K9me3 ChIP


title: MCF7.H3K9ac.rep1


title: ZR751.H3K27ac.rep1

source_name: ZR751 cells, H3K27ac ChIP


title: ZR751.H3K27ac.rep2


title: MCF7.H3K4me3.rep2

source_name: MCF7 cells, H3K4me3 ChIP


title: MCF7.H3K9me3.rep1


title: MCF7.H3K36me3.rep2

source_name: MCF7 cells, H3K36me3 ChIP


title: MB361.H3K27ac.rep1


title: MCF7.H3K27ac.rep1

source_name: MCF7 cells, H3K27ac ChIP


title: MCF7.H3K27me3.rep1

source_name: MCF7 cells, H3K27me3 ChIP


title: MCF10A.H3K9me3.rep1

source_name: MCF10A cells, H3K9me3 ChIP


title: MCF7.H3K79me2.rep1

source_name: MCF7 cells, H3K79me2 ChIP


title: MCF7.H3K79me2.rep2


title: MCF7.H3K4me1.rep1

source_name: MCF7 cells, H3K4me1 ChIP


title: MCF7.H3K4me1.rep2


title: MCF10A.H3K79me2.rep1

source_name: MCF10A cells, H3K79me2 ChIP


title: MCF10A.H3K79me2.rep2


title: ZR751.H3K4me3.rep1


title: MCF7.H3K36me3.rep1


title: MCF10A.H3K4me3.rep2

source_name: MCF10A cells, H3K4me3 ChIP


title: MCF7.H3K27me3.rep2


title: MCF10A.H3K4me3.rep1


title: MCF10A.H3K4me1.rep2

source_name: MCF10A cells, H3K4me1 ChIP


title: MCF10A.H3K4me1.rep1


title: MCF10A.H3K9me3.rep2


title: 76NF2V.Input.rep2

source_name: 76NF2V cells, input


title: 76NF2V.H3K9ac.rep2

source_name: 76NF2V cells, H3K9ac ChIP


title: MCF10A.H3K27ac.rep1

source_name: MCF10A cells, H3K27ac ChIP


title: MCF10A.H3K27me3.rep2

source_name: MCF10A cells, H3K27me3 ChIP


title: 76NF2V.Input.rep1


title: MCF10A.H3K27ac.rep2


title: 76NF2V.H3K9me3.rep2

source_name: 76NF2V cells, H3K9me3 ChIP


title: MCF10A.H3K36me3.rep1

source_name: MCF10A cells, H3K36me3 ChIP


title: 76NF2V.H3K9ac.rep1


title: 76NF2V.H3K4me3.rep1

source_name: 76NF2V cells, H3K4me3 ChIP


title: 76NF2V.H3K79me2.rep2

source_name: 76NF2V cells, H3K79me2 ChIP


title: 76NF2V.H3K4me3.rep2


title: 76NF2V.H3K4me1.rep2

source_name: 76NF2V cells, H3K4me1 ChIP


title: 76NF2V.H3K9me3.rep1


title: 76NF2V.H3K79me2.rep1


title: MCF7.H3K4me3.rep1

source_name: MCF7 cells, H3K4me3 ChIP


title: 76NF2V.H3K36me3.rep2

source_name: 76NF2V cells, H3K36me3 ChIP


title: 76NF2V.H3K4me1.rep1


title: ZR751.H3K27me3.rep1

source_name: ZR751 cells, H3K27me3 ChIP


title: 76NF2V.H3K36me3.rep1


title: MCF10A.H3K27me3.rep1


title: 76NF2V.H3K27me3.rep1

source_name: 76NF2V cells, H3K27me3 ChIP


title: MCF10A.H3K36me3.rep2


title: 76NF2V.H3K27ac.rep1

source_name: 76NF2V cells, H3K27ac ChIP


title: F DB3

city: Cincinnati

first: Shan

last: Lin

state: OH

address: 3333 Burnet Avenue, CCHMC

department: EHCB

institute: Cincinnati Children's Hospital Medical Center

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to hg19 using Tophat
number of reads was calculated for each Entrez gene
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: F DB, CD34+ HSPCs

growth_protocol: culture cells were maintaind in IMDM with 20% BIT and 10ng/mL of SCF, TPO, Flt3 ligand, IL-3 and IL-6

extract_protocol:
Cells were sorted for GFP+CD11b-. Total RNA was isolated from sorted cells using RNeasy Mini Kit (Qiagen).
PrepX mRNA Library kit (WaferGen)  was used with 1 ug of total RNA for the construction of sequencing libraries, the libraries were clustered by using IIIumina TruSeq PE Cluster kit

tag: donor

tag: genotype/variation

value: FOXO1 DNA binding deficient mutant

value: CD34+ HSPC

tag: cell etiology

value: UCB

tag: sorted for lineage


title: F WT1

source_name: F WT, CD34+ HSPCs

value: wildtype FOXO1

tag: cell type


title: MIT3

source_name: MIT, CD34+ HSPCs

value: Ctrl


title: MIT2


title: F DB1


title: MIT1


title: F WT3


title: C57BL/6J_Male_RestingBcell_184

first: Nicolas

last: Walker

address: Downing Street

department: Genetics

institute: University of Cambridge

data_processing:
The 125bp paired-end reads libraries were aligned using STAR v2.5.0a 1 (Dobin et al., 2013) against a custom reference genome containing the GRCm38 version of the mouse reference genome plus the sequence of the ERCC Spike-in RNAs and the ENSEMBL v76 annotation with the following parameters -- outFilterType BySJout -- alignSJoverhangMin 8 -- alignSJDBoverhangMin 1 -- outFilterMismatchNoverLmax 0.3 -- alignIntronMin 20 -- outFilterMismatchNmax 999 -- alignIntronMax 1000000 -- alignMatesGapMax 1000000 -- outFilterMultimapNmax 1 -- outSAMattrIHstart 0 -- outSAMmultNmax 1 -- outSAMstrandField intronMotif -- outSAMtype BAM SortedByCoordinate. Gene expression levels were estimated using HTSeq count (v0.5.4p3)2 (Anders et al., 2014) with parameters (-m intersection- nonempty -a 10 -i gene_id -s no) to count the number of unique read pairs that mapped to the genes in the ENSEMBL annotation v76 of the mouse Genome.
Genome_build: mm10

growth_protocol: C57BL/6 mice at 6-8 weeks of age were used for spleen collection purposes.

extract_protocol:
Naïve CD4+ T lymphocytes were purified from single-cell suspensions by MACS depletion of non-CD4+ T cells as well as regulatory T cells and TCRγ/δ+ T cells, using a cocktail of specific biotin conjugated antibodies against CD8a (Ly-2), CD45R (B220), CD49b (DX5), CD11b (Mac-1), Ter-119, CD25 and TCRγ/δ+ using the CD4+ CD62L+ T Cell Isolation Kit II (Miltenyi) to obtain an unlabeled pre-enriched CD4+ T cell fraction. Collected cells were suspended in PBS containing 2% FBS and Fc receptors were blocked with FcR blocking reagent for 10 minutes at 4°C (Miltenyi). Cells were further fluorescently stained with a combination of CD4-FITC (Miltenyi), CD44-APC clone IM7 (eBioscience), CD62L clone MEL-14 (BD Pharmingen), eFluor® 450 CD25 clone PC61.5 (eBioscience), for 10 minutes at 4°C, washed and then stained with DAPI (Life Technologies) to cell sort the live population of naïve CD4+, CD62Lhi, CD44lo, CD25- T lymphocytes using the MoFlo XDP system (Beckman Coulter). Samples were gated on single cells for doublet discrimination and non-viable cells were excluded using the viability dye 4’, 6 – diamidine – 2 – phenylindole (DAPI). AllPrep DNA/RNA Mini Kit (Qiagen) was used to perform simultaneous isolation of RNA and DNA from 10^6 sorted naïve CD4+ T cells and resting B cells.  All RNA samples were subjected to in-column RNase-Free DNase treatment (Qiagen) to remove traces of DNA contamination. RNA integrity was subsequently assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies) by using the RNA 6000 Pico Kit (Agilent Technologies). For each sample type 3 biological replicates were generated from male and female samples.
Purified male quiescent naïve CD4+ T and resting B cells were loaded onto a 5-10 μm C1 Single-Cell Auto Prep Integrated Fluidic Circuits (IFC) and captured following manufactures’ instructions. Capture efficiency for each cell type and IFC was determined using a microscope in order to remove in further analysis samples with no cell capture, debris or with two or more cells captured. Synthetic ERCC ExFold RNA Spike-In Mixes (Ambion®) were added at a 1:5000 (B cells) and 1:1000 (T cells) dilution to the cell lysis mix as controls to estimate the level of technical noise in further analysis. Cell lysis, reverse transcription and cDNA pre-amplification was performed in the Fluidigm C1™ Single-Cell Auto Prep System using the C1 Single-Cell Auto Prep Array (IFCs), the Auto Prep Reagent Kit for mRNA Seq (Fluidigm) and the SMARTer® Ultra™ Low RNA Kit (Clontech). Universal amplification was performed utilising the Advantage® 2 PCR Kit (Clontech). cDNA was harvested, quantified by Qubit® assays and diluted to 0.1–0.3 ng/ml. Single cell RNAseq libraries were prepared using the Nextera XT DNA Sample Preparation Kit (Illumina) and the Nextera Index Kit (Illumina) following the instructions in the Fluidigm manual ‘‘Using the C1TM Single-Cell Auto Prep System to Generate mRNA from Single Cells and Libraries for Sequencing.’’ Libraries were pooled, and 125bp paired-end sequencing was performed over two lanes of an Illumina HiSeq2000 instrument.

tag: Sex

value: Male

value: Resting B cell


title: C57BL/6J_Male_RestingBcell_187


title: C57BL/6J_Male_RestingBcell_185


title: C57BL/6J_Male_RestingBcell_186


title: C57BL/6J_Male_RestingBcell_183


title: C57BL/6J_Male_RestingBcell_182


title: MCF7.H3K27ac.rep2

source_name: MCF7 cells, H3K27ac ChIP

value: Breast cancer cell line

value: Control

tag: chip antibody


title: C57BL/6J_Male_RestingBcell_181

tag: strain


title: C57BL/6J_Male_RestingBcell_188


title: AU565.H3K9ac.rep2

source_name: AU565 cells, H3K9ac ChIP


title: AE2

source_name: AE, CD34+ HSPCs


title: AE1


title: C57BL/6J_Male_RestingBcell_179


title: C57BL/6J_Male_RestingBcell_178


title: C57BL/6J_Male_RestingBcell_180


title: C57BL/6J_Male_RestingBcell_177


title: 76NF2V.H3K27me3.rep2


title: F WT2


title: 76NF2V.H3K27ac.rep2


title: C57BL/6J_Male_RestingBcell_176


title: AE3


title: C57BL/6J_Male_RestingBcell_175


title: C57BL/6J_Male_RestingBcell_172


title: C57BL/6J_Male_RestingBcell_170


title: C57BL/6J_Male_RestingBcell_169


title: C57BL/6J_Male_RestingBcell_174


title: C57BL/6J_Male_RestingBcell_171


title: C57BL/6J_Male_RestingBcell_173


title: C57BL/6J_Male_RestingBcell_168


title: C57BL/6J_Male_RestingBcell_167


title: C57BL/6J_Male_RestingBcell_163


title: C57BL/6J_Male_RestingBcell_166


title: C57BL/6J_Male_RestingBcell_165


title: C57BL/6J_Male_RestingBcell_158


title: C57BL/6J_Male_RestingBcell_164


title: C57BL/6J_Male_RestingBcell_162


title: C57BL/6J_Male_RestingBcell_154


title: C57BL/6J_Male_RestingBcell_152


title: C57BL/6J_Male_RestingBcell_159


title: Ler x Ler_seed coat

description:
sRNA-seq
Barcode: TGACCA
singlebasecompilation.seedcoat.24.overallaverage.bed.gz

data_processing:
Analysis of sRNA libraries began with the trimming of low-quality read ends (fastq_quality_trimmer, -t 20 and -l 25; http://hannonlab.cshl.edu/fastx_toolkit/). Adapters were removed with cutadapt (-0 6 -m 26 —discard-untrimmed).
sRNA libraries prepared using the NEXTflex sRNA-Seq Kit v2 are appended with 4 base randomized barcodes immediately 3’ and 5’ of the sRNA read itself. These barcodes were used to remove PCR duplicates (any read of the same sRNA sequence with identical flanking barcodes on both ends) before being removed themselves.
Reads were aligned using Bowtie 1.1.1 with two mismatches allowed (-v 2 --best; Langmead et al., 2009), using a metagenomic approach to reduce mapping bias. In the case of crosses between A. thaliana Col and Ler ecotypes, a metagenome was constructed using the TAIR10 genome and the published Ler genome (Gan et al.,Nature, 2011). In the case of crosses between Col and Cvi ecotypes, a metagenome was constructed using a Cvi pseudogenome (1bp indels and SNP substitutions introduced into TAIR10 base genome) and the TAIR10 genome. Following alignment, reads aligning to either parent genome were converted back to TAIR10 coordinates. For A. lyrata, reads were aligned in the same manner to the published MN47 genome (Hu et al., Nat Genet, 2011).
Reads were classified by strain using SNPs (Pignatta et al., eLife, 2014, Klosinska et al., Nat Plants, 2016). If classification at two SNP positions within the same read conflicted, that read was discarded. All reads that overlapped annotated tRNAs, snRNAs, rRNAs, or snoRNAs were removed.
Spike-ins consisting of sRNAs isolated from Candida albicans were added to A. thaliana libraries during preparation.  Ultimately, spike-ins were not utilized in normalization, with library size-based normalization used instead.  Reads that mapped to the C. albicans genome (either uniquely or in addition to mapping to the Arabidopsis thaliana genome) were removed from further analysis.
A single base read depth value was created for 24nt sRNAs  —  each base of a read would contribute 1/24 of a read to an overlapping genomic position. Alignment files were run through bedtools genomecov (-d -scale: adjusted to account for individual library size; bedtools v. 2.23.0, bedtools.readthedocs.io/en/latest/index.html). Per-position values for all libraries pooled within a given analysis were averaged.
For *_emb_v_endo_24nt_300bp_stats.txt: 24nt sRNAs were binned into 300 base windows with 150 base overlaps, such that every position in the genome was covered by exactly 2 windows. Overlapping was performed using bedtools coverage (bedtools v. 2.23.0, bedtools.readthedocs.io/en/latest/index.html). sRNA window read values, classified as either embryo or endosperm, were used as input for DESeq2, with the sizeFactors command used to provide RPM normalization between libraries (Love et al., 2014). Output values were used to calculate average sRNA levels for all libraries at a given locus (mean log2 total counts) and the ratio of embryo expression to endosperm expression (log2 embryo/endosperm counts)
Genome_build: For A. thaliana libraries, TAIR10, resequenced Ler-0 genome (http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/fasta/UNMASKED/ler_0.v7.fas), Cvi pseudogenome (TAIR10+Cvi1.fa.gz  ). For A. lyrata libraries, published MN47 genome (Hu et al., Nat Genet, 2011).
Supplementary_files_format_and_content: singlebasecompilation and singlebase.bed files: bed files detailing every position of the genome, with the fourth column providing a normalized sRNA read coverage value for all embryo, endosperm, or seed coat libraries in the study. For A. thaliana, all libraries of the same tissue type were combined. For A. lyrata, KarxMN47 replicates of the same tissue type were combined and for MN47xMN47 replicates of the same tissue type were combined. Prefix designations for A. lyrata are K=Kar, M=MN47, E=embryo, N=endosperm, S=seedcoat. Female in cross listed first. For MN47xMN47 endosperm, only replicates MMN2 and MMN3 were combined. MMN1 was not used.
Supplementary_files_format_and_content: *_emb_v_endo_24nt_300bp_stats.txt: tab delimited text file including window position, mean sRNA coverage for all libraries, endosperm libraries, and embryo libraries, the log2 fold change between endosperm and embryo mean values, and associated statistical quantities. At = A. thaliana, KM = A. lyrata Kar female x MN47 male, MM = A. lyrata MN47 female x MN47 male.
Supplementary_files_format_and_content: *_allele_specific_24_300bp_values_*reps.txt: tab deliminted text file including chr/scaffold, start, end and allele-specific 24nt sRNA read counts in 300 bp windows across the genome. CLN = A. thaliana Col female x Ler male endosperm, LCN = A. thaliana Ler female x  Col male endosperm, CVN = A. thaliana Col female x Cvi male endosperm, VCN = A. thaliana Cvi female x Col male endosperm, KME = A. lyrata Kar female x MN47 male embryo, KMN = A. lyrata Kar female x MN47 male endosperm

source_name: Seed Coat

growth_protocol: A. thaliana plants were grown in a greenhouse with 16-hour days at ~21 C. Flowers were emasculated 2 days before pollination. Seeds were dissected at six DAP (approximately torpedo stage of embryogenesis). A. lyrata plants were grown in a growth chamber with 16-hour days at 20 C. Seeds were dissected at ~15 days after pollination, corresponding to the late torpedo/walking stick stage of embryogenesis.

extract_protocol:
Seeds from crosses between multiple individuals were hand-dissected and total embryo,endosperm, or seed coat RNA isolated using the Ambion RNAqueous Micro Kit.
The small RNA pool was separated from the larger RNA pool by sequential ethanol addition and filtering. The larger RNA pool was collected on filters after the addition of ethanol equivalent to 60% of the sample volume, and the small RNA pool was collected on filters after the addition of ethanol equivalent to 50% of the flowthrough volume from the larger RNA filter binding step.  Libraries for Illumina sequencing were constructed using the NEXTflex Small RNA-Seq Kit v2 as directed (Bioo Scientific Corporation, Austin, Texas). 40 base single-end sequencing of sRNA libraries was performed on an Illumina HiSeq 2000 machine.

value: Ler female x Ler male

value: 6 days after pollination

value: Seed Coat


title: C57BL/6J_Male_RestingBcell_157


title: Ler x Col_seed coat

description:
sRNA-seq
Barcode: TTAGGC
singlebasecompilation.seedcoat.24.overallaverage.bed.gz

value: Ler female x Col male


title: F DB2


title: C57BL/6J_Male_RestingBcell_155


title: Col x Ler_seed coat

description:
sRNA-seq
Barcode: CGATGT
singlebasecompilation.seedcoat.24.overallaverage.bed.gz

value: Col female x Ler male


title: C57BL/6J_Male_RestingBcell_150


title: C57BL/6J_Male_RestingBcell_161


title: D7_Kidney_ATAC-seq_rep2

first: John

middle: Justin

last: Milner

address: 9500 Gilman Dr. MC0377

institute: UCSD

data_processing:
Reads were aligned to mm10 by bowtie.
Only unique reads were kept.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

source_name: D7 Kidney P14

extract_protocol:
Single cell suspensions from the spleen, epithelium, or kidney of the small intestine were sorted by FACS.
The ATAC-Seq library was generated by Nextera sample prep kit (Illumina).

tag: age

value: 6-16 Weeks

value: Kidney

tag: cell population

value: CD8+ T cell


title: C57BL/6J_Male_RestingBcell_153


title: C57BL/6J_Male_RestingBcell_156


title: C57BL/6J_Male_RestingBcell_149


title: C57BL/6J_Male_RestingBcell_145


title: C57BL/6J_Male_RestingBcell_151


title: C57BL/6J_Male_RestingBcell_143


title: Cvi x Col rep 2_Embryo

description:
sRNA-seq
Barcode: GCCAAT
At_emb_v_endo_24nt_300bp_stats.txt

data_processing:
Analysis of sRNA libraries began with the trimming of low-quality read ends (fastq_quality_trimmer, -t 20 and -l 25; http://hannonlab.cshl.edu/fastx_toolkit/). Adapters were removed with cutadapt (-0 6 -m 26 ?discard-untrimmed).
sRNA libraries prepared using the NEXTflex sRNA-Seq Kit v2 are appended with 4 base randomized barcodes immediately 3' and 5' of the sRNA read itself. These barcodes were used to remove PCR duplicates (any read of the same sRNA sequence with identical flanking barcodes on both ends) before being removed themselves.
Reads were aligned using Bowtie 1.1.1 with two mismatches allowed (-v 2 --best; Langmead et al., 2009), using a metagenomic approach to reduce mapping bias. In the case of crosses between A. thaliana Col and Ler ecotypes, a metagenome was constructed using the TAIR10 genome and the published Ler genome (Gan et al.,Nature, 2011). In the case of crosses between Col and Cvi ecotypes, a metagenome was constructed using a Cvi pseudogenome (1bp indels and SNP substitutions introduced into TAIR10 base genome) and the TAIR10 genome. Following alignment, reads aligning to either parent genome were converted back to TAIR10 coordinates. For A. lyrata, reads were aligned in the same manner to the published MN47 genome (Hu et al., Nat Genet, 2011).
Reads were classified by strain using SNPs (Pignatta et al., eLife, 2014, Klosinska et al., Nat Plants, 2016). If classification at two SNP positions within the same read conflicted, that read was discarded. All reads that overlapped annotated tRNAs, snRNAs, rRNAs, or snoRNAs were removed.
Spike-ins consisting of sRNAs isolated from Candida albicans were added to A. thaliana libraries during preparation.  Ultimately, spike-ins were not utilized in normalization, with library size-based normalization used instead.  Reads that mapped to the C. albicans genome (either uniquely or in addition to mapping to the Arabidopsis thaliana genome) were removed from further analysis.
A single base read depth value was created for 24nt sRNAs  ?  each base of a read would contribute 1/24 of a read to an overlapping genomic position. Alignment files were run through bedtools genomecov (-d -scale: adjusted to account for individual library size; bedtools v. 2.23.0, bedtools.readthedocs.io/en/latest/index.html). Per-position values for all libraries pooled within a given analysis were averaged.
For *_emb_v_endo_24nt_300bp_stats.txt: 24nt sRNAs were binned into 300 base windows with 150 base overlaps, such that every position in the genome was covered by exactly 2 windows. Overlapping was performed using bedtools coverage (bedtools v. 2.23.0, bedtools.readthedocs.io/en/latest/index.html). sRNA window read values, classified as either embryo or endosperm, were used as input for DESeq2, with the sizeFactors command used to provide RPM normalization between libraries (Love et al., 2014). Output values were used to calculate average sRNA levels for all libraries at a given locus (mean log2 total counts) and the ratio of embryo expression to endosperm expression (log2 embryo/endosperm counts)
genome build: For A. thaliana libraries, TAIR10, resequenced Ler-0 genome (http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/fasta/UNMASKED/ler_0.v7.fas), Cvi pseudogenome (TAIR10+Cvi1.fa.gz). For A. lyrata libraries, published MN47 genome (Hu et al., Nat Genet, 2011).
processed data files format and content: singlebasecompilation and singlebase.bed files: bed files detailing every position of the genome, with the fourth column providing a normalized sRNA read coverage value for all embryo, endosperm, or seed coat libraries in the study. For A. thaliana, all libraries of the same tissue type were combined. For A. lyrata, KarxMN47 replicates of the same tissue type were combined and for MN47xMN47 replicates of the same tissue type were combined. Prefix designations for A. lyrata are K=Kar, M=MN47, E=embryo, N=endosperm, S=seedcoat. Female in cross listed first. For MN47xMN47 endosperm, only replicates MMN2 and MMN3 were combined. MMN1 was not used.
processed data files format and content: *_emb_v_endo_24nt_300bp_stats.txt: tab delimited text file including window position, mean sRNA coverage for all libraries, endosperm libraries, and embryo libraries, the log2 fold change between endosperm and embryo mean values, and associated statistical quantities. At = A. thaliana, KM = A. lyrata Kar female x MN47 male, MM = A. lyrata MN47 female x MN47 male.
processed data files format and content: *_allele_specific_24_300bp_values_*reps.txt: tab deliminted text file including chr/scaffold, start, end and allele-specific 24nt sRNA read counts in 300 bp windows across the genome. CLN = A. thaliana Col female x Ler male endosperm, LCN = A. thaliana Ler female x  Col male endosperm, CVN = A. thaliana Col female x Cvi male endosperm, VCN = A. thaliana Cvi female x Col male endosperm, KME = A. lyrata Kar female x MN47 male embryo, KMN = A. lyrata Kar female x MN47 male endosperm

source_name: Cvi x Col

growth_protocol: Plants were grown in a greenhouse with 16-hour days at ~21 C. Flowers were emasculated 2 days before pollination. Seeds were dissected at six DAP (approximately torpedo stage of embryogenesis). A. lyrata plants were grown in a growth chamber with 16-hour days at 20 C. Seeds were dissected at ~15 days after pollination, corresponding to the late torpedo/walking stick stage of embryogenesis.

extract_protocol:
Seeds from crosses between multiple individuals were hand-dissected and total embryo, endosperm, or seed coat RNA isolated using the Ambion RNAqueous Micro Kit.
The small RNA pool was separated from the larger RNA pool by sequential ethanol addition and filtering. The larger RNA pool was collected on filters after the addition of ethanol equivalent to 60% of the sample volume, and the small RNA pool was collected on filters after the addition of ethanol equivalent to 50% of the flowthrough volume from the larger RNA filter binding step.  Libraries for Illumina sequencing were constructed using the NEXTflex Small RNA-Seq Kit v2 as directed (Bioo Scientific Corporation, Austin, Texas). 40 base single-end sequencing of sRNA libraries was performed on an Illumina HiSeq 2000 machine.

tag: genotype

value: Cvi female x Col male

tag: developmental stage

value: Embryo


title: C57BL/6J_Male_RestingBcell_148


title: C57BL/6J_Male_RestingBcell_147


title: Cvi x Cvi rep 2_Embryo

description:
sRNA-seq
Barcode: CAGATC
At_emb_v_endo_24nt_300bp_stats.txt

source_name: Cvi x Cvi

value: Cvi female x Cvi male

tag: tissue


title: Col x Cvi rep 2_Embryo

description:
sRNA-seq
Barcode: ACAGTG
At_emb_v_endo_24nt_300bp_stats.txt

source_name: Col x Cvi

value: Col female x Cvi male


title: C57BL/6J_Male_RestingBcell_160


title: D7_spleen_ATAC-seq_rep1

source_name: D7 Spleen P14

value: Spleen


title: C57BL/6J_Male_RestingBcell_140

value: Male


title: C57BL/6J_Male_RestingBcell_146

value: Resting B cell


title: C57BL/6J_Male_RestingBcell_141


title: C57BL/6J_Male_RestingBcell_139


title: D7_IEL_ATAC-seq_rep2

source_name: D7 IEL P14

value: Small Intestine Epithelium


title: C57BL/6J_Male_RestingBcell_137


title: Sample_F6

description:
PolyA RNA
Basecalling: bcl2fastq v1.8.4
Processed data file: mouse_RNA.txt

source_name: neuron

tag: strain/background

value: neuron

tag: source region

value: cortex

tag: source type

value: acute slice


title: Sample_J353_6

source_name: astrocyte

value: astrocyte

value: primary culture


title: C57BL/6J_Male_RestingBcell_144


title: C57BL/6J_Male_RestingBcell_136


title: Ler x Ler rep 2_Embryo

source_name: Ler x Ler

value: Ler female x Ler male

value: 6 days after pollination


title: C57BL/6J_Male_RestingBcell_142


title: Col x Col_seed coat

description:
sRNA-seq
Barcode: ATCACG
singlebasecompilation.seedcoat.24.overallaverage.bed.gz

value: Col female x Col male

value: Seed Coat


title: D7_spleen_ATAC-seq_rep2

value: 6-16 Weeks

value: CD8+ T cell


title: C57BL/6J_Male_RestingBcell_134


title: D7_Kidney_ATAC-seq_rep1

value: Kidney


title: Sample_CA1-17

value: hippocampus CA1


title: Cvi x Col rep 1_Embryo

description:
sRNA-seq
Barcode: TTAGGC
At_emb_v_endo_24nt_300bp_stats.txt

value: Cvi female x Col male

value: Embryo


title: C57BL/6J_Male_RestingBcell_138

value: Male

value: Resting B cell


title: Sample_P14

value: neuron


title: Col x Cvi rep 1_Embryo

description:
sRNA-seq
Barcode: TGACCA
At_emb_v_endo_24nt_300bp_stats.txt

value: Col female x Cvi male


title: D7_IEL_ATAC-seq_rep1

value: Small Intestine Epithelium


title: Sample_J5_18_2

value: cortex


title: C57BL/6J_Male_RestingBcell_130


title: C57BL/6J_Male_RestingBcell_135


title: C57BL/6J_Male_RestingBcell_128


title: C57BL/6J_Male_RestingBcell_129


title: Ler x Col rep 1_Embryo

description:
sRNA-seq
Barcode: CGATGT
At_emb_v_endo_24nt_300bp_stats.txt

source_name: Ler x Col

value: Ler female x Col male


title: C57BL/6J_Male_RestingBcell_127


title: C57BL/6J_Male_RestingBcell_132


title: Sample_CA1-15

value: acute slice


title: Sample_J6_8min_20

value: primary culture


title: C57BL/6J_Male_RestingBcell_133


title: Sample_J8_23


title: Ler x Col rep 2_Embryo

value: 6 days after pollination


title: C57BL/6J_Male_RestingBcell_131


title: Col x Ler rep 2_Embryo

source_name: Col x Ler

value: Col female x Ler male


title: Col x Col rep 1_Embryo

description:
sRNA-seq
Barcode: ATCACG
At_emb_v_endo_24nt_300bp_stats.txt

source_name: Col x Col

value: Col female x Col male


title: C57BL/6J_Male_RestingBcell_123


title: C57BL/6J_Male_RestingBcell_126


title: C57BL/6J_Male_RestingBcell_121


title: Sample_J20_20

growth_protocol:
Samples were extracted from mouse and cultured for 6 days.
Standard Primary Cell Culturing Conditions as described in Kaech and Banker, Nat. Protoc. 1, 2006.


title: C57BL/6J_Male_RestingBcell_125


title: Sample_J5_18


title: Cvi x Cvi rep 2_Endosperm

value: Cvi female x Cvi male

value: Endosperm


title: Col x Ler rep 1_Embryo


title: Sample_J15_12


title: C57BL/6J_Male_RestingBcell_119


title: C57BL/6J_Male_RestingBcell_118


title: C57BL/6J_Male_RestingBcell_124


title: Col x Col rep 2_Embryo

description:
sRNA-seq
Barcode: ACTTGA
At_emb_v_endo_24nt_300bp_stats.txt


title: C57BL/6J_Male_RestingBcell_122


title: Ler x Ler rep 1_Embryo

value: Ler female x Ler male


title: Cvi x Col rep 2_Endosperm

description:
sRNA-seq
Barcode: TGACCA
VCN_allele_specific_24_300bp_values_2reps.txt
At_emb_v_endo_24nt_300bp_stats.txt

value: Cvi female x Col male


title: C57BL/6J_Male_RestingBcell_113


title: Sample_P5


title: Cvi x Col rep 1_Endosperm

description:
sRNA-seq
Barcode: ATCACG
VCN_allele_specific_24_300bp_values_2reps.txt
At_emb_v_endo_24nt_300bp_stats.txt


title: C57BL/6J_Male_RestingBcell_112


title: C57BL/6J_Male_RestingBcell_120


title: C57BL/6J_Male_RestingBcell_110


title: Sample_J6_4min_9


title: C57BL/6J_Male_RestingBcell_117


title: C57BL/6J_Male_RestingBcell_116


title: Sample_J10_11


title: C57BL/6J_Male_RestingBcell_107


title: C57BL/6J_Male_RestingBcell_106


title: C57BL/6J_Male_RestingBcell_114


title: C57BL/6J_Male_RestingBcell_104


title: Sample_CA1-4

value: hippocampus CA1


title: Cvi x Cvi rep 1_Endosperm


title: C57BL/6J_Male_RestingBcell_111

value: Male


title: C57BL/6J_Male_RestingBcell_103

value: Resting B cell


title: C57BL/6J_Male_RestingBcell_102


title: C57BL/6J_Male_RestingBcell_101


title: Col x Cvi rep 3_Endosperm

description:
sRNA-seq
Barcode: TTAGGC
CVN_allele_specific_24_300bp_values_3reps.txt
At_emb_v_endo_24nt_300bp_stats.txt


title: Sample_P4

value: neuron


title: C57BL/6J_Male_RestingBcell_99


title: C57BL/6J_Male_RestingBcell_109


title: Col x Cvi rep 2_Endosperm

description:
sRNA-seq
Barcode: ACAGTG
CVN_allele_specific_24_300bp_values_3reps.txt
At_emb_v_endo_24nt_300bp_stats.txt

value: Col female x Cvi male


title: C57BL/6J_Male_RestingBcell_108


title: Sample_P2


title: Ler x Col rep 2_Endosperm

description:
sRNA-seq
Barcode: GCCAAT
LCN_allele_specific_24_300bp_values_3reps.txt
At_emb_v_endo_24nt_300bp_stats.txt


title: Sample_CA1-3


title: C57BL/6J_Male_RestingBcell_97


title: Sample_CA1-5


title: Sample_F2


title: C57BL/6J_Male_RestingBcell_105


title: Ler x Ler rep 2_Endosperm


title: C57BL/6J_Male_NaiveCD4+Tcell_95

value: Naive CD4+ T cell


title: Col x Ler rep 2_Endosperm

description:
sRNA-seq
Barcode: CGATGT
CLN_allele_specific_24_300bp_values_2reps.txt
At_emb_v_endo_24nt_300bp_stats.txt


title: B16.PMIG.TIL#2

data_processing:
Tophat
HT-Seq Count
DESeq from BioConductor
Genome_build: UCSC mm10
Supplementary_files_format_and_content: gct

source_name: Tumor P14 control

extract_protocol:
Total RNA was extracted in TRIZoL reagent
PrepX RNA-seq libaray preparation kit (Integenex)

value: 6-16 Weeks

value: Tumor


title: Sample_F1

value: cortex

value: acute slice


title: C57BL/6J_Male_RestingBcell_115


title: Ler x Col rep 1_Endosperm

description:
sRNA-seq
Barcode: CGATGT
LCN_allele_specific_24_300bp_values_3reps.txt
At_emb_v_endo_24nt_300bp_stats.txt

value: Ler female x Col male

value: 6 days after pollination


title: Sample_CA3-2

value: hippocampus CA3


title: Ler x Ler rep 1_Endosperm


title: Ler x Col rep 3_Endosperm

description:
sRNA-seq
Barcode: ATCACG
LCN_allele_specific_24_300bp_values_3reps.txt
At_emb_v_endo_24nt_300bp_stats.txt


title: C57BL/6J_Male_NaiveCD4+Tcell_91


title: B16.PMIG.TIL#1


title: C57BL/6J_Male_RestingBcell_100


title: B16.OE.TIL#2

source_name: Tumor Runx3-overexpressing P14


title: Col x Cvi rep 1_Endosperm

description:
sRNA-seq
Barcode: TGACCA
CVN_allele_specific_24_300bp_values_3reps.txt
At_emb_v_endo_24nt_300bp_stats.txt


title: C57BL/6J_Male_RestingBcell_96


title: Col x Col rep 1_Endosperm

value: Col female x Col male


title: B16.OE.TIL#1


title: C57BL/6J_Male_RestingBcell_98


title: Sample_P1


title: nrpd1a-4 (Ler) x nrpd1a-4 (Col) rep 3

description:
mRNA-seq
colholdoutgeneIDsnrpd1.txt
Barcode: GTGAAA

data_processing:
Read filtering was performed using cutadapt (-0 6 -m 26 -discard-untrimmed) and trim_galore (-t 10; http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove low quality bases from the 5' end of reads. Trimmed reads were assessed with fastqc.
Reads were aligned to TAIR10 using tophat (-N 2 -read-edit-dist 2; v2.0.13)
Following alignment, reads were classified by strain (Col or Ler) using SNPs (Pignatta et al., eLife, 2014). If classification at two SNP positions within the same read conflicted, that read was discarded.
Allele-specific read counts for each locus were generated by running ht-seq count on the reads classifed by strain (-m intersection-strict -stranded=no).
In the case of libraries originating from crosses including a parent with the nrpd1 allele in the Ler background, reads originating from genes that retained the Col genotype even after multiple backcrosses into Ler were removed from downstream analysis. These loci are listed in colholdoutgeneIDsnrpd1.txt.
genome build: TAIR10, resequenced Ler-0 genome
processed data files format and content: allele_counts files contain RNA-seq data in tab-delimited format for each sample, with one row per gene.  Contains gene ID (locus_name), Col-assigned reads (Col), Ler-assigned reads (Ler), and total number of RNA-seq reads aligned to gene (total).
processed data files format and content: colholdoutgeneIDsnrpd1.txt file is the list of gene IDs not to be included in analysis for the nrpd1a-4 (Ler) female x nrpd1a-4 (Col) male samples (three reps) or their wild type counterparts, Ler female x Col male 6 days after pollination (2 reps). These loci remain as Col genotype in at least one of the the nrpd1a-4 (Ler) plants even after four backcrosses of nrpd1a-4 (Col) to Ler.

source_name: nrpd1a-4 (Ler) x nrpd1a-4 (Col)

growth_protocol: Plants were grown in a greenhouse with 16-hour days at ~21 C. Flowers were emasculated 2 days before pollination. Seeds were dissected at six DAP (approximately torpedo stage of embryogenesis).

extract_protocol:
Seeds from crosses between multiple individuals were hand-dissected and total endosperm RNA isolated using the Ambion RNAqueous Micro Kit.
DNase I-treated RNA (Invitrogen, Life Technologies Corporation, Carlsbad, CA) was used to prepare mRNA-seq libraries using the Truseq Stranded mRNA Library Prep Kit as directed (Illumina Inc., San Diego, CA). Amplification was for 15 cycles. Libraries were sequenced with 100x100 base paired end reads on an Illumina HiSeq 2000 machine.

value: Endosperm


title: B16.PMIG.Spleen#2

source_name: Spleen P14 control

value: Spleen


title: C57BL/6J_Male_NaiveCD4+Tcell_85


title: C57BL/6J_Male_NaiveCD4+Tcell_94


title: Col x Ler rep 1_Endosperm

description:
sRNA-seq
Barcode: TTAGGC
CLN_allele_specific_24_300bp_values_2reps.txt
At_emb_v_endo_24nt_300bp_stats.txt

value: Col female x Ler male


title: C57BL/6J_Male_NaiveCD4+Tcell_88


title: C57BL/6J_Male_NaiveCD4+Tcell_87


title: Col x Col rep 2_Endosperm


title: C57BL/6J_Male_NaiveCD4+Tcell_92


title: C57BL/6J_Male_NaiveCD4+Tcell_84


title: C57BL/6J_Male_NaiveCD4+Tcell_83


title: B16.PMIG.Spleen#1


title: nrpd1a-4 (Ler) x nrpd1a-4 (Col) rep 2

description:
mRNA-seq
colholdoutgeneIDsnrpd1.txt
Barcode: GTCCGC

value: nrpd1a-4 (Ler) female x nrpd1a-4 (Col) male


title: C57BL/6J_Male_NaiveCD4+Tcell_93

value: Male


title: nrpd1a-4 (Ler) x nrpd1a-4 (Col) rep 1

description:
mRNA-seq
colholdoutgeneIDsnrpd1.txt
Barcode: CCGTCC


title: C57BL/6J_Male_NaiveCD4+Tcell_80


title: C57BL/6J_Male_NaiveCD4+Tcell_82


title: T8.IEL.LCMV.D7.Gut#2

extract_protocol:
Total RNA was extracted in TRIZoL reagent
PrepX RNA-seq library preperation kit (Integenex)

value: Small Intestine Epithelium


title: T8.IEL.LCMV.D7.Gut#1


title: C57BL/6J_Male_NaiveCD4+Tcell_86


title: 20140304.A-20140114_NS_pyed

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

institute: University of Zürich

data_processing:
The sequences of the reads were quality trimmed using the program fastq_quality_trimmer
Sequencing reads were mapped to the Bc H111 genome using CLC Genomics Workbench v7.0 (CLCbio) allowing up to 2 mismatches per read
RNA-Seq count data were subsequently analyzed with the DESeq software (Anders & Huber 2010)
Genome_build: H111 genome sequence (accession no. HG938370, HG938371, and HG938372)
Supplementary_files_format_and_content: CLC exported tab-delimited text files include RPKM and mean values for each sample

organism: Burkholderia cenocepacia H111

source_name: H111 /pYedQ

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using hot phenol protocol (Pessi et al 2007) . Ds cDNA was produced and nugen librairies obtained.
RNA libraries were prepared using Ovation® Complete Prokaryotic RNA-Seq Library System

value: Bc H111 planktonic cells

tag: treatment

value: high c-di-GMP level, YedQ Cyclase

tag: growth

value: planktonic cells, OD600 equal 2.0

tag: medium

value: LB


title: C57BL/6J_Male_NaiveCD4+Tcell_81

value: Naive CD4+ T cell


title: C57BL/6J_Male_NaiveCD4+Tcell_74