title: GMTGFPHand2_2: D14 GMTHand2_2_RNAseq

city: Dallas

first: Antonio

last: Fernandez-Perez

state: TX

address: 5323 Harry Hines Blvd

department: Internal Medicine-Cardiology

institute: UT Southwestern Medical Center

data_processing:
Raw FASTQ files were analyzed using FastQC v0.11.2(Andrews, 2010) and FastQ Screen v0.4.4
Reads were quality trimmed using fastq-mcf (ea-utils, v1.1.2-806).
trimmed reads were mapped to the hg19 assembly of the human genome (the University of California, Santa Cruz, version from igenomes) using Tophat(Kim et al., 2013)
Duplicated reads were marked using Picard tools (v1.127; https://broadinstitute.github.io/picard/), the RNA counts generated from FeatureCounts(Liao et al., 2013) were TMM normalized(Robinson and Oshlack, 2010)
differential expression analysis was performed using edgeR(Robinson et al., 2010)
For differential expression analysis, statistical cutoffs of FDR ≤ 0.05 and log2CPM ≥ 0 and were used to identify statistically significant and possibly biologically relevant differentially regulated genes
Genome_build: mm10
Supplementary_files_format_and_content: Gene counts matrices representing expression values (coma separated) were generated as described above. Each column represents an experimental condition, each row represents a single gene

source_name: E12.5 Mouse embryonic fibroblasts

growth_protocol: Induced MEFs were maintained in CM induction media until harvest time.

extract_protocol:
For RNA-seq libraries, around 40k GFP+ cells were sorted and collected for total RNA preparation after 14D post infection.
Follow TrueSeq Stranded mRNA with Ribo-Zeo assay as per manufacturers recommendations

value: FVB/NTac

value: E12.5 Mouse embryonic fibroblasts

tag: number of cells

tag: variation

value: Sorted for GFP fused to Hand2


title: GMTGFPHand2_1: D14 GMTHand2_1_RNAseq

status: Public on Jul 30 2019

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue


title: GFPHand2_1: D14 Hand2_1_RNAseq


title: GMTGFP_1: D14 GMT_1_RNAseq

value: Spiked with GFP for sorting


title: ADPKD patient 1

type: RNA

city: Seoul

first: Sumin

last: Oh

address: Cheongpa-ro 47-gil 100, Yongsan-gu

department: Department of Biological Science

country: South Korea

institute: Sookmyung Women's University

description:
patients with ADPKD undergoing nephrectomy
PKD_Patient_rep1

hyb_protocol: 100 ng of total RNA was used as an input into the labeling reaction, and labeled miRNA was hybridized to the array for 20 h at 55°C and 20 rpm, as described in the manufacturer’s protocol. After hybridization, the chips were washed and scanned using the Agilent DNA Microarray Scanner.

scan_protocol: Global miRNA gene expression analyses were performed on the Agilent Human miRNA Microarray Version 3 software (Agilent design IDs 021827) according to the manufacturer’s instructions (miRNA Microarray System with miRNA Complete Labeling and Hyb Kit protocol 2.1).

data_processing: The scanned images were analyzed with  GeneSpring GX11 TMEV4.1.

organism: Homo sapiens

source_name: ADPKD patient renal cyst tissue

label_protocol: Per RNAsample, 100 ng were used as input into the Agilent procedure as recommended by protocol  (miRNA Microarray System with miRNA Complete Labeling and Hyb Kit protocol 2.1).

extract_protocol: Total RNA was isolated from kidney tissue samples of non-ADPKD and ADPKD patients using a Trizol method according to the manufacturer’s instructions (Invitrogen Life Technologies).

tag: disease state

value: ADPKD

value: kidney


title: non-ADPKD 3

description:
non-ADPKD renal tissue samples were obtained from patients undergoing surgery for clear cell renal cell carcinoma, where malignant cell infiltration was excluded by histology.
PKD_Normal_rep3

source_name: non-ADPKD kidney tissue

value: non-ADPKD


title: GMTGFP_2: D14 GMT_2_RNAseq


title: non-ADPKD 2

description:
non-ADPKD renal tissue samples were obtained from patients undergoing surgery for clear cell renal cell carcinoma, where malignant cell infiltration was excluded by histology.
PKD_Normal_rep2


title: ADPKD patient 3

description:
patients with ADPKD undergoing nephrectomy
PKD_Patient_rep3


title: P0PM_1_S1: P0_12.5k_eHcn4_1_ATACseq

library_source: genomic

data_processing:
Paired-end 75 bp read length Fastq files were checked for quality using fastqc (v0.11.5) and fastq_screen (v0.11.4)
Reads were quality trimmed using fastq-mcf (ea-utils, v1.1.2-806).
Trimmed fastq files were mapped to mouse genome using bowtie2 (v2.3.3.1)
Duplicates were marked using picard-tools (v2.2.1) and blacklist regions were removed using bedtools (v2.7.1)
TN5 shifting of bam files was performed using the open-source Perl script "ATAC_BAM_shiftrt_gappedAlign.pl"
peaks were called using MACS version 2.1.0.20160309 with the following setting: Q-value < 0.05 and using the random background
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using HOMER. Scores represent normalized counts

molecule: genomic DNA

extract_protocol:
For the ATACseq libraries, induced MEFs were trypsinized, washed, and resuspended in FACS sorting buffer. 12.5k GFP+ cells were sorted per replicate and transpostion reaction.
In-house Tn5 transposase was used to insert sequencing adapters and fragmentate cDNA. Greenleaf primer sets (Buenrostro, J., 2015) were used to amplify the fragmented cDNA with 4-6 cycles (KAPA HiFi PCR Kits, catalog number KK2102). AMPure XP beads size selection was performed to recover fragments with length of 200 to 1000 bp.


title: Uninfected_2: D14 MEFs_2_RNAseq


title: non-ADPKD 1

description:
non-ADPKD renal tissue samples were obtained from patients undergoing surgery for clear cell renal cell carcinoma, where malignant cell infiltration was excluded by histology.
PKD_Normal_rep1


title: GMTGFPHand2aa32_1_S1: D14_12.5k_GHaa32MT_1_ATACseq


title: GMTGFPHand2aa32_1_S2: D14_12.5k_GHaa32MT_2_ATACseq


title: H3K27acWT1: ChIP-seq H3K27ac WT Alveolar macrophages #1

city: Solna

first: Taras

last: Kreslavsky

address: Nks Bioclinicum, J7:30, Visionsgatan 4

department: Department of Medicine, Solna (MedS)

country: Sweden

institute: Karolinska Institutet

data_processing:
ChIP-seq: For Bhlhe40 ChIP-seq, the reads were aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9), using the Bowtie program version 1.0.0; for H3K27ac ChIP-seq samples reads were aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9), using the Bowtie2 program (usegalaxy.eu; version 2.3.4.2). Resulting BAM files were processed with BAM to Wiggle  (usegalaxy.eu; version Version 2.6.4) and Wig/BedGraph-to-bigWig  (usegalaxy.eu; version Version 1.1.1) converters.
RNA-seq: Reads corresponding to mouse ribosomal RNAs (BK000964.1 and NR046144.1) were removed. The remaining reads were cut down to a read length of 44 nucleotides and aligned to the mouse transcriptome (genome assembly version of July 2007 NCBI37/mm9) using TopHat version 1.4.1 (Trapnell et al, 2009). The database generation of RefSeq-annotated genes was performed as previously described (Wöhner et al., 2016). To refine the annotation of immunoglobulin genes, the immunoglobulin l light-chain segments were replaced with their corresponding converted GRCm38.p3 annotations (Ensembl version 79) (Yates et al., 2016). The resulting number of genes was 24,732. For analysis of differential gene expression, the number of reads per gene was counted using HTseq version 0.5.3 (Anders et al, 2014) with the overlap resolution mode set to 'union'. The data sets were analyzed using the R package DESeq2 version 1.2.10 (Love et al, 2014). Sample normalizations and dispersion estimations were conducted using the default DESeq2 settings. Transcripts per million (TPM) were calculated from RNA-seq data, as described (Wagner et al, 2012).
Genome_build: MM9
Supplementary_files_format_and_content: RNA-seq: Excel table with 4 tabs: TPM values for all samples and output of DEseq2 for three pairwise comparisons, see ‘data processing step’ for details.  ChIP-seq: Bigwig files provided for all samples, see ‘data processing step’ for details.

source_name: Alveolar macrophages

extract_protocol:
No extraction
ChIP tagmentation protocol (Gustafsson et al, 2018)

value: Alveolar macrophages

tag: genotype

tag: strain background

tag: cell isolation

value: Ex vivo, FACS-sorted from digested lungs

tag: cell-sorting strategy

value: CD11c+ SiglecF+ CD11b low

tag: chip antibody

value: anti-H3K27ac Diagenode #C15410196


title: H3K27acDKO1: ChIP-seq H3K27ac DKO Alveolar macrophages #1


title: H3K27acDKO2: ChIP-seq H3K27ac DKO Alveolar macrophages #2


title: GMTGFPHand2_4_S8: D14_12.5k_GHMT_2_ATACseq


title: GMTGFPHand2_4_S4: D14_12.5k_GHMT_1_ATACseq


title: lymph node at baseline from patient 4

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-seq data was aligned using bowtie2 against hg38 version of the human genome and RSEM v1.2.31 software was used to estimate raw read counts and FPKM values using transcriptome information from Ensemble v84 set
DESeq2 was used to estimate significance of differential expression between groups
Genome_build: hg38
Supplementary_files_format_and_content: Prosessed file contains the raw counts for each gene as estimated by RSEM

source_name: lymph node

extract_protocol:
Cellular RNA was purified using the AllPrep DNA/RNA kit (Qiagen, Ventura CA) as specified by the manufacturer. RNA quality was validated using the Agilent TapeStation, and the High Sensitivity RNA Screentape (Agilent, Santa Clara, CA) and quantity was determined using the Qubit 2·0 Fluorometer (ThermoFisher Scientific, Waltham, MA)
cDNA was generated from 10 ng of total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio USA, Inc., Mountain View, CA) according to manufacturer’s directions. Then, 150 pg of the cDNA was used to prepare library for Illumina sequencing using the Nextera XT Library Prep Kit (Illumina, San Diego, CA) according to manufacturer’s directions.

tag: patientid

tag: treatment

value: baseline

value: lymph node


title: GFPHand2_3_S7: D14_12.5k_Hand2_2_ATACseq


title: GFPHand2_3_S3: D14_12.5k_Hand2_1_ATACseq


title: GFPHand2_2: D14 Hand2_2_RNAseq


title: H3K27acWT2: ChIP-seq H3K27ac WT Alveolar macrophages #2


title: ADPKD patient 2

description:
patients with ADPKD undergoing nephrectomy
PKD_Patient_rep2


title: Control_1_S1: D14_12.5k_MEFs_1_ATACseq


title: Control_1_S5: D14_12.5k_MEFs_2_ATACseq


title: Uninfected_1: D14 MEFs_1_RNAseq


title: Mouse_RNAseq_N5te_KD_V87_12

city: Copenhagen N

first: Janus

middle: Schou

last: Jakobsen

address: Ole Maaløes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

description:
See publication for FACS isolation regimen
Nt5e_KD_read_counts.xlsx

data_processing:
The Raw sequencing data was trimmed with Trimmomatic (v 0.32) with the paramters: ILLUMINACLIP:fastqc.fa:2:30:10 HEADCROP:X LEADING:22 SLIDINGWINDOW:4:22 MINLEN:25
The trimmed data was mapped to the genome (hg19, mm9) using TopHat2 (v2.0.9) using the parameters --b2-very-sensitive --library-type=fr-unstranded nd supplying the Enslemble GTF file to the --GTF argument (release 66 for both human and mouse).
The mapped reads were summarized into gene counts using the featureCounts() function, from the Rsubread R package (V1.16.1), using the same GTF file described above and with default parameters apart from isPairedEnd=TRUE.
Filtering and differential expression: Genes with at least 2 fragments uniquely mapping in at least 1 library we tested for differential expression. A gene was deemed differentially expressed if it was called as significant with a False Discovery Rate (FDR) corrected p-value < 0.01 by both edgeR and DESeq. Specifically the exactTest() function from EdgeR (v 3.12.0) (Robinson et al., 2010)[Ref: http://bioinformatics.oxfordjournals.org/content/26/1/139.short ] was used after TMM normalization and estimation of dispersion using both estimateCommonDisp() and estimateTagwiseDisp(). The DESeq() function from DESeq (v 1.18.0) (Anders and Huber, 2010) [Ref: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218662/ ] was used with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file with expression signal

source_name: Lp30 cells, tissue culture, exposed to shRNA KD

extract_protocol:
Qiagen, RNeasy Mini Kit
Illumina, TruSeq Library RNA Prep Kit v2

value: C57BL/6, Lp30 cells generated from floxed p30 using Mx-cre and Poly-IC injection. Tertiary, transplanted leukemia used for examinations

value: Tissue culture cells, expanded from FACS isolated Lp30 GMP-blasts,


title: Mouse_RNAseq_N5te_KD_V87_11

value: Tissue culture cells, expanded from Lp30 GMP-blasts, FACS isolated


title: Mouse_RNAseq_N5te_KD_V87_9


title: GMTGFP_2_S2: D14_12.5k_GMT_1_ATACseq


title: Mouse_RNAseq_N5te_KD_V86_6


title: Mouse_RNAseq_N5te_KD_SCR_4


title: Mouse_RNAseq_N5te_KD_SCR_3


title: Mouse_RNAseq_N5te_KD_V86_8


title: R3: resting epicardium (par3:eGFP) sample3

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

hyb_protocol: Labeled cDNA (3 mg) was resuspended in 1x GEx Hybridization buffer (Hi-RPM) and 1xBlocking reagent and hybridized to Zebrafish microarrays v3 (Agilent) during 17 hours at 65 oC.

scan_protocol: Arrays were scanned on an Agilent G2505C microarray scanner under default settings recommended by Agilent Technologies. Data was extracted using Agilent Feature Extraction software 10.7.3.1.

data_processing: Raw probe-level data was processed with limma Bioconductor package version 3.24.15, using “normexp” background correction method and “rma” to estimate correction parameters. To filter out low expressed probes, we used the 95% percentile of negative control probes on each array as cutoff. Only those probes being brighter than the cutoff on at least four arrays were kept. Normalized expression values were calculated using the “quantile” method.

organism: Danio rerio

source_name: resting epicardium (par3:eGFP)

label_protocol: 5 ng of total RNA was amplified to cDNA with the OVATION PicoSL WTA System V2 (Nugen) kit. Amplified cDNA (1.5 mg) was labeled with Cy3 using the Genomic DNA enzymatic labeling kit (Agilent).

extract_protocol: Starting from 5ng of initial material RNA was amplified to amounts ranging between 120 and 200 nl/µl per sample using a Ovation PICOSL WTA System V2 Amplification kit. was quantified using a NanoDrop-1000 spectrophotometer. Quality was controlled with a 2100 Bioanalyzer.

treatment_protocol: Samples R1 to R4 are from untreat adult zebrafish hearts. Samples A1 to A4 are from cryoinjured zebrafish hearts, extracted 3 days postinjury of the ventricular apexl

value: epicardium

tag: day post induction

value: uninjured


title: R4: resting epicardium (par3:eGFP) sample 4


title: A1: activated epicardium (wt1b:eGFP) sample 1

source_name: activated epicardium (wt1b:eGFP)

value: 3 days postcryoinjury


title: A4: activated epicardium (wt1b:eGFP) sample 4


title: A3: activated epicardium (wt1b:eGFP) sample 3


title: R2: resting epicardium (par3:eGFP) sample 2


title: A2: activated epicardium (wt1b:eGFP) sample 2


title: EAE_CNS_rep2

city: Hamburg

middle: A

last: Friese

address: Falkenried 94

department: Institut für Neuroimmunologie und Multiple Sklerose

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

data_processing:
calling of TCR clonotypes with mixcr 2.1.10
Genome_build: mm10
Supplementary_files_format_and_content: clonotype tables

source_name: Central nervous system

extract_protocol:
Qiagen AllPrep DNA/RNA Micro kit
TCR-seq from genomic DNA
Amplification of TCRβ gene rearrangements using a combination of specific primers for amplification of all IGMT-listed mouse V/J segments (HS Diagnomics Berlin)

value: C57BL/6 WT

tag: cell type

value: CD8-T cells

tag: immunization state

value: EAE

tag: gestational state

value: non-preg


title: EAE_periphery_rep1

source_name: Spleen and lymph nodes


title: EAE_CNS_rep3


title: EAE_periphery_rep2


title: GMTGFP_2_S6: D14_12.5k_GMT_2_ATACseq

value: FVB/NTac

value: E12.5 Mouse embryonic fibroblasts


title: EAE_CNS_rep1


title: Treg_Naive_non-preg_rep5

value: DEREG mouse

value: CD4+Foxp3+ Treg

value: Naive


title: EAE_periphery_rep3


title: Treg_Naive_non-preg_rep3


title: Treg_Naive_non-preg_rep2


title: Treg_Naive_non-preg_rep1


title: Treg_Naive_E18_rep5


title: Treg_Naive_E18_rep4


title: Mouse_RNAseq_N5te_KD_SCR_2


title: Treg_Naive_E18_rep3


title: Treg_Naive_E18_rep2


title: Treg_EAE_non-preg_rep4


title: Treg_EAE_non-preg_rep5


title: R1: resting epicardium (par3:eGFP) sample 1


title: Treg_Naive_E18_rep1


title: Treg_EAE_non-preg_rep3


title: Treg_EAE_E18_rep4


title: Treg_EAE_non-preg_rep1


title: Treg_EAE_non-preg_rep2


title: Treg_EAE_E18_rep2


title: Tcon_Naive_non-preg_rep5

value: CD4+Foxp3- Tcon


title: Tcon_Naive_non-preg_rep2


title: Tcon_Naive_non-preg_rep1


title: Treg_EAE_E18_rep1


title: Tcon_Naive_E18_rep5


title: Treg_EAE_E18_rep5


title: Tcon_Naive_E18_rep3


title: Tcon_Naive_E18_rep4


title: Tcon_Naive_E18_rep1


title: Tcon_Naive_E18_rep2


title: Tcon_EAE_non-preg_rep4


title: Tcon_EAE_non-preg_rep5


title: Tcon_EAE_non-preg_rep2


title: Tcon_EAE_non-preg_rep1


title: Tcon_EAE_E18_rep3


title: Tcon_EAE_E18_rep1


title: Tcon_EAE_E18_rep2


title: Tcon_Naive_non-preg_rep4


title: Tcon_EAE_E18_rep4


title: 82651: RNA-seq DKO Peritoneal macrophages #2

molecule: polyA RNA

source_name: Peritoneal macrophages

extract_protocol:
Rneasy Plus Mini Kit, Dynabeads mRNA purification kit
NEBNext Ultra II

value: Peritoneal macrophages

value: Ex vivo, FACS-sorted from peritoneal peritoneal lavage

value: CD11b+ F4/80+ MHCII intermediate Tim4+


title: 58638: RNA-seq DKO Alveolar macrophages  #1

value: Alveolar macrophages

value: Ex vivo, FACS-sorted from digested lungs

value: CD11c+ SiglecF+ CD11b low


title: 64305: RNA-seq WT Alveolar macrophages - mixed bone marrow chimeras #1

value: CD45.1+ CD45.2- CD11c+ SiglecF+ CD11b low


title: 82649: RNA-seq WT Peritoneal macrophages #2


title: Treg_EAE_E18_rep3


title: 58639: RNA-seq DKO Alveolar macrophages #2


title: 82650: RNA-seq DKO Peritoneal macrophages #1


title: 70136: Control track for Bhlhe40 ChIP-seq (mock’ precipitation sample without antibody)

value: Ex vivo, isolated from bronchoalveolar lavage fluid by adherence to plastic


title: 82648: RNA-seq WT Peritoneal macrophages #1


title: 64306: RNA-seq WT Alveolar macrophages - mixed bone marrow chimeras #2


title: 64308: RNA-seq DKO Alveolar macrophages - mixed bone marrow chimeras #2

value: CD45.1- CD45.2+ CD11c+ SiglecF+ CD11b low


title: 64307: RNA-seq DKO Alveolar macrophages - mixed bone marrow chimeras #1


title: 58636: RNA-seq WT Alveolar macrophages #1


title: Tcon_EAE_non-preg_rep3

value: EAE


title: Treg_Naive_non-preg_rep4

value: non-preg


title: Tcon_Naive_non-preg_rep3


title: 58637: RNA-seq WT Alveolar macrophages #2


title: ChIP-seq of 5M-GS cells using anti-H3K27me3 antibody replicate 2

city: Kyoto

first: mito

last: shinohara

state: Kyoto

address: Sakyo-ku, Yoshida Konoe

department: Medicine

country: Japan

institute: Kyoto University

description: histone-DNA complexes were isolated with anti-H3K27me3 antibody.

data_processing:
The sequencing run and the base call analysis were performed according to HiSeq 2500 System Guide [http://jp.support.illumina.com/downloads/hiseq_2500_user_guide_15035786.html] with TruSeq SBS kit v3-HS.
After the sequencing, sequence raw data was generated with processing by CASAVA-1.8.4 with version RTA 1.17.20.0/.
Sequenced reads were mapped to the reference genomes of mouse (mm10) using Bowtie version 1.1.2.
Peak calling and ChIP-seq data visualization were performed by DROMPA version 2.6.4.
The promoter sequence of a gene is defined by the region from -2,000 bp to +2,000 bp relative to the transcription start site (TSS).
Genome_build: mm10
Supplementary_files_format_and_content: Txt files include peak position, width and height.

source_name: Germline stem cells

growth_protocol: Germline stem cells were derived from Green mice (C57BL/6 Tg14(act-EGFP)OsbY01 mice) of DBA/2 background, and cultured for approximately 5 or 60 months, using culture medium based on Iscove’s modified MEM (Invitrogen, Carlsbad, CA), which was supplemented with 10 ng/ml human FGF2, 15 ng/ml recombinant rat GDNF (both from Peprotech, London, UK) and 1% fetal bovine serum (FBS).

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min. Soluble cell lysates were prepared by sonication or both MNase treatment and sonication.
Lysates were incubated with protein A or protein G Dynabeads conjugated with anti-H3K4me3 or anti-H3K27me3 antibodies, and bound fractions were eluted following manufacturer’s recommendation. After reversal of cross-linking for elutes and input samples, DNA from input and immunopreciptation fractions was sheared to an average size of approximately 150 bp by ultrasonication, and used for constructing ChIP-seq library.

treatment_protocol: Germline stem cells   from Green mice of DBA/2 background were cultured for 5 or 60 months.

value: testis

tag: genotype/variation

value: wild type

tag: antibody


title: ChIP-seq of 5M-GS cells using anti-H3K27me3 antibody replicate 1

value: Green mice (C57BL/6 Tg14(act-EGFP)OsbY01 mice) of DBA/2 background


title: ChIP-seq of 60M-GS cells using anti-H3K4me3 antibody replicate 1

description: histone-DNA complexes were isolated with anti-H3K4me3 antibody.


title: ChIP-seq of 5M-GS cells using anti-H3K4me3 antibody replicate 2


title: Tcon_EAE_E18_rep5

value: DEREG mouse


title: ChIP-seq of 5M-GS cells using anti-H3K4me3 antibody replicate 1


title: ChIP-seq of 60M-GS cells using anti-H3K27me3 antibody replicate 1


title: ChIP-seq of 60M-GS cells using anti-H3K27me3 antibody replicate 2


title: ChIP-seq of 60M-GS cells using anti-H3K4me3 antibody replicate 2


title: 70137: ChIP-seq Bhlhe40 WT Alveolar macrophages

value: anti-Bhlhe40 Novus Biologicals, NB100-1800, lot C2


title: WGBS from 60M-GS cells replicate 2

data_processing:
PBAT libraries were sequenced on the Illumina HiSeq 1500/2500 platform equipped with HCS v2.0.12 and RTA v1.17.21.3.
Raw sequence reads were trimmed to remove both poor quality calls and adapter sequences.
The resulting reads were aligned to the mouse reference genome (mm10) using Bismark v0.10.0 with the option “--pbat”.
CpG methylation calls were extracted from the mapping output of only uniquely aligned reads. Counts from the both strands of a given CpG were combined.
Genome_build: mm10
Supplementary_files_format_and_content: The genome-wide CpG methylation report is tab-delimited, and is in the following format: chromosome, position (mm10), count methylated, count non-methylated, and methylation level (%).

growth_protocol: Germline stem cells were derived from Green mice (C57BL/6 Tg14(act-EGFP)OsbY01 mice) of DBA/2 background, and cultured for approximately 5 or 60 months, using culture medium based on Iscove’s modified MEM (Invitrogen, Carlsbad, CA), which was supplemented with 10 ng/ml human FGF2, 15 ng/ml recombinant rat GDNF (both from Peprotech, London, UK) and 1% fetal bovine serum (FBS) (Kanatsu-Shinohara et al, 2014).

extract_protocol:
Genomic DNA was extracted from GS cells by the standard procedure.
WGBS libraries were prepared using the post-bisulfite adaptor tagging (PBAT) method.

treatment_protocol: Germline stem cells from Green mice of DBA/2 background were cultured for 5 or 60 months.


title: WGBS from 60M-GS cells replicate 1


title: WGBS from 5M-GS cells replicate 1


title: WGBS from 5M-GS cells replicate 2


title: BMDM_MK2/3-/-_360min_LPS_rep4

city: Duesseldorf

first: Christian

last: Ehlting

address: Moorenstrasse 5

department: Clinic for Gastroenterology, Hepatology and Infectiology

institute: University Hospital of the Heinrich-Heine-University Duesseldorf

description: Gene expression after 360min in LPS-treated murine BMDM

hyb_protocol: 0.825 µg of fragmented and Cy3-labeled cRNA was hybridized to the Microarray (G4852B) according to the manufacturer's protocol (One-Color Microarray-Based Gene Expression Analysis / Low Input Quick Amp Labeling; Agilent Technologies) at 65°C for 17 hours in the hybridization rotator.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner G2600D (protocol: AgilentG3_GX_1color; dye: green; scan region: Agilent HD; scan area: 61x21.6 mm; scan resolution 3µm; tiff file: 20 bit; green PMT gain: 100%). Signal intensities on 20 bit tiff images were calculated by Feature Extraction software (FE, Vers. 11.0.1.1; Agilent Technologies; Grid Template: 028005_D_F_20130207; Protocol: GE1_1100_Jul11_MultiDetrend_off; MetricSet: GE1_QCMT_Jul11).

data_processing: Signal intensities on 20 bit tiff images were calculated using Feature Extraction software (Vers. 11.0.1.1; Agilent Technologies). Probe signal intensities were quantile normalized across all samples to reduce inter-array variability. Input data pre-processing was concluded by baseline transformation to the median of all samples. Data analyses were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies).

source_name: Bone marrow derived macrophages (BMDM), MK2- and MK3-deficient, 360min LPS treatment, replicate 4

label_protocol: Synthesis of cDNA and subsequent fluorescent (Cy3) labelling of cRNA was performed from 100 ng total RNA according to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis / Low Input Quick Amp Labeling; Agilent Technologies), followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Bone marrow with prepared from the femur of male mice, than seeded on 15 cm culture dishes with  cell culture medium (incl. 1000 g/l glucose, 10% FCS and antibiotics) and incubated with 10 ng/ml M-CSF for 9 days until fully differentiated into macrophages.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Germany) following the manufacturer's recommendations. Thereafter, cDNA was generated using the Quantitect cDNA Synthesis Kit (Qiagen, Germany) including DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cells were treated with 100 ng/ml LPS, which was dissolved in cell culture medium, or with cell culture medium alone and incubated for 360 minutes  at 37 ºC in a humidified incubator with 5% CO2.

value: MK2- and MK3-deficient

tag: time point

tag: agent

value: LPS

value: Bone marrow derived macrophages (BMDM)

tag: gender

value: male

tag: age


title: BMDM_wt_360min_medium_rep4

source_name: Bone marrow derived macrophages (BMDM), wildtype, 360min medium treatment, replicate 4

value: wildtype

value: medium

tag: strain


title: BMDM_MK2/3-/-_360min_medium_rep1

source_name: Bone marrow derived macrophages (BMDM), MK2- and MK3-deficient, 360min medium treatment, replicate 1


title: BMDM_MK2/3-/-_360min_LPS_rep2

source_name: Bone marrow derived macrophages (BMDM), MK2- and MK3-deficient, 360min LPS treatment, replicate 2


title: BMDM_MK2/3-/-_360min_LPS_rep3

source_name: Bone marrow derived macrophages (BMDM), MK2- and MK3-deficient, 360min LPS treatment, replicate 3


title: BMDM_wt_360min_LPS_rep1

source_name: Bone marrow derived macrophages (BMDM), wildtype, 360min LPS treatment, replicate 1


title: BMDM_MK2/3-/-_120min_medium_rep2

description: Gene expression after 120min in LPS-treated murine BMDM

source_name: Bone marrow derived macrophages (BMDM), MK2- and MK3-deficient, 120min medium treatment, replicate 2

treatment_protocol: Cells were treated with 100 ng/ml LPS, which was dissolved in cell culture medium, or with cell culture medium alone and incubated for 120 minutes  at 37 ºC in a humidified incubator with 5% CO2.


title: BMDM_MK2-/-_360min_LPS_rep2

source_name: Bone marrow derived macrophages (BMDM), MK2-deficient, 360min LPS treatment, replicate 2


title: BMDM_wt_360min_LPS_rep3

source_name: Bone marrow derived macrophages (BMDM), wildtype, 360min LPS treatment, replicate 3


title: BMDM_MK2/3-/-_360min_LPS_rep1

source_name: Bone marrow derived macrophages (BMDM), MK2- and MK3-deficient, 360min LPS treatment, replicate 1


title: BMDM_MK2/3-/-_360min_medium_rep3

source_name: Bone marrow derived macrophages (BMDM), MK2- and MK3-deficient, 360min medium treatment, replicate 3


title: BMDM_MK2-/-_360min_LPS_rep4

source_name: Bone marrow derived macrophages (BMDM), MK2-deficient, 360min LPS treatment, replicate 4


title: BMDM_MK2/3-/-_120min_medium_rep1

source_name: Bone marrow derived macrophages (BMDM), MK2- and MK3-deficient, 120min medium treatment, replicate 1


title: BMDM_wt_360min_medium_rep3

source_name: Bone marrow derived macrophages (BMDM), wildtype, 360min medium treatment, replicate 3


title: BMDM_wt_360min_LPS_rep2

source_name: Bone marrow derived macrophages (BMDM), wildtype, 360min LPS treatment, replicate 2


title: BMDM_MK2-/-_360min_medium_rep3

source_name: Bone marrow derived macrophages (BMDM), MK2-deficient, 360min medium treatment, replicate 3


title: BMDM_MK2-/-_360min_medium_rep2

source_name: Bone marrow derived macrophages (BMDM), MK2-deficient, 360min medium treatment, replicate 2


title: BMDM_MK2-/-_360min_medium_rep4

source_name: Bone marrow derived macrophages (BMDM), MK2-deficient, 360min medium treatment, replicate 4


title: BMDM_MK2-/-_360min_medium_rep1

source_name: Bone marrow derived macrophages (BMDM), MK2-deficient, 360min medium treatment, replicate 1


title: BMDM_MK2/3-/-_120min_medium_rep3

source_name: Bone marrow derived macrophages (BMDM), MK2- and MK3-deficient, 120min medium treatment, replicate 3


title: BMDM_MK2-/-_360min_LPS_rep3

source_name: Bone marrow derived macrophages (BMDM), MK2-deficient, 360min LPS treatment, replicate 3


title: BMDM_wt_360min_medium_rep2

source_name: Bone marrow derived macrophages (BMDM), wildtype, 360min medium treatment, replicate 2


title: BMDM_wt_360min_medium_rep1

source_name: Bone marrow derived macrophages (BMDM), wildtype, 360min medium treatment, replicate 1


title: BMDM_MK2/3-/-_120min_LPS_rep3

source_name: Bone marrow derived macrophages (BMDM), MK2- and MK3-deficient, 120min LPS treatment, replicate 3


title: BMDM_MK2/3-/-_360min_medium_rep2

source_name: Bone marrow derived macrophages (BMDM), MK2- and MK3-deficient, 360min medium treatment, replicate 2


title: BMDM_MK2/3-/-_120min_medium_rep4

source_name: Bone marrow derived macrophages (BMDM), MK2- and MK3-deficient, 120min medium treatment, replicate 4


title: BMDM_MK2/3-/-_120min_LPS_rep4

source_name: Bone marrow derived macrophages (BMDM), MK2- and MK3-deficient, 120min LPS treatment, replicate 4


title: P0PM_2_S1: P0_12.5k_eHcn4_2_ATACseq

source_name: E12.5 Mouse embryonic fibroblasts

value: FVB/NTac

tag: tissue

value: E12.5 Mouse embryonic fibroblasts

tag: number of cells


title: BMDM_MK2-/-_360min_LPS_rep1

source_name: Bone marrow derived macrophages (BMDM), MK2-deficient, 360min LPS treatment, replicate 1


title: HL60-CD97-s-shRNA_1_biorepl2_techrepl2

city: New York

first: Christopher

middle: Y.

last: Park

state: New York

address: 550 First Avenue

department: Pathology

institute: New York University

data_processing:
For RNA-Seq data generated from HL60 cells and MA9 transformed mouse cells, raw fastq files were aligned to the hg19 and mm10 reference genomes, respectively. Read counts were extracted using R with Rsamtools package (v1.24.0) and differentially expressed genes analyzed using the DESeq2 package (v 1.12.3).
Genome_build: hg19 for HL60 RNA-seq
Genome_build: mm10 for MA9 RNA-seq
Supplementary_files_format_and_content: Read count files for i) HL60 RNA-seq data ii) MA9 RNA-seq data

source_name: Human AML cell line HL60

extract_protocol:
Samples were FACS-sorted into Trizol LS (Thermo Fisher, Rockford, Illinois).
Poly-A selected cDNA libraries were prepared using a SMARTer mRNA amplification kit (Clontech, Mountain View, California).

treatment_protocol: HL60 cell line was transduced with lentiviral vectors expressing scramble control sequences (scramble shRNA (s-shRNA)

value: Human AML cell line HL60


title: HL60-CD97-s-shRNA_1_biorepl2_techrepl1


title: HL60-CD97-s-shRNA_2_biorepl2_techrepl1


title: BMDM_MK2-/-_120min_LPS_rep2

source_name: Bone marrow derived macrophages (BMDM), MK2-deficient, 120min LPS treatment, replicate 2


title: HL60-CD97-s-shRNA_2_biorepl1_techrepl1


title: HL60-CD97-s-shRNA_1_biorepl1_techrepl2


title: HL60-CD97-s-shRNA_1_biorepl1_techrepl1


title: HL60-CD97-s-shRNA_2_biorepl2_techrepl2


title: HL60-CD97-shCD97.3_biorepl2_techrepl1

treatment_protocol: CD97 was knocked down(CD97-KD) in HL60 cell line using lentiviral vectors expressing two shRNAs targeting CD97 (shCD97.1 and shCD97.3).


title: BMDM_MK2-/-_120min_medium_rep3

source_name: Bone marrow derived macrophages (BMDM), MK2-deficient, 120min medium treatment, replicate 3


title: BMDM_MK2/3-/-_120min_LPS_rep2

source_name: Bone marrow derived macrophages (BMDM), MK2- and MK3-deficient, 120min LPS treatment, replicate 2


title: BMDM_wt_120min_medium_rep1

source_name: Bone marrow derived macrophages (BMDM), wildtype, 120min medium treatment, replicate 1


title: BMDM_wt_120min_medium_rep3

source_name: Bone marrow derived macrophages (BMDM), wildtype, 120min medium treatment, replicate 3


title: BMDM_wt_120min_LPS_rep3

source_name: Bone marrow derived macrophages (BMDM), wildtype, 120min LPS treatment, replicate 3


title: BMDM_wt_120min_LPS_rep2

source_name: Bone marrow derived macrophages (BMDM), wildtype, 120min LPS treatment, replicate 2


title: BMDM_MK2/3-/-_120min_LPS_rep1

source_name: Bone marrow derived macrophages (BMDM), MK2- and MK3-deficient, 120min LPS treatment, replicate 1


title: BMDM_MK2-/-_120min_LPS_rep3

source_name: Bone marrow derived macrophages (BMDM), MK2-deficient, 120min LPS treatment, replicate 3


title: BMDM_MK2-/-_120min_LPS_rep4

source_name: Bone marrow derived macrophages (BMDM), MK2-deficient, 120min LPS treatment, replicate 4


title: BMDM_MK2-/-_120min_medium_rep1

source_name: Bone marrow derived macrophages (BMDM), MK2-deficient, 120min medium treatment, replicate 1


title: BMDM_wt_120min_medium_rep2

source_name: Bone marrow derived macrophages (BMDM), wildtype, 120min medium treatment, replicate 2


title: BMDM_MK2-/-_120min_medium_rep2

source_name: Bone marrow derived macrophages (BMDM), MK2-deficient, 120min medium treatment, replicate 2


title: HL60-CD97-shCD97.3_biorepl1_techrepl2


title: BMDM_wt_120min_LPS_rep4

source_name: Bone marrow derived macrophages (BMDM), wildtype, 120min LPS treatment, replicate 4


title: BMDM_wt_120min_medium_rep4

source_name: Bone marrow derived macrophages (BMDM), wildtype, 120min medium treatment, replicate 4


title: HL60-CD97-s-shRNA_2_biorepl1_techrepl2


title: BMDM_wt_120min_LPS_rep1

source_name: Bone marrow derived macrophages (BMDM), wildtype, 120min LPS treatment, replicate 1


title: HL60-CD97-shCD97.3_biorepl1_techrepl1

source_name: Human AML cell line HL60


title: HL60-CD97-shCD97.3_biorepl2_techrepl2


title: HL60-CD97-shCD97.1_biorepl1_techrepl1


title: HL60-CD97-shCD97.1_biorepl1_techrepl2


title: HL60-CD97-shCD97.1_biorepl2_techrepl2


title: Human_ChIP_H3K27ac_CEBPAMONOALLELIC_200

description: See publication for FACS isolation regimen

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2 (default parameters).
Peaks were called using macs2. To increase the specificity of the enriched regions, we used a control sample prepared using a control anti-body (‘IgG’ control). Further, Irreproducible Discovery Rate (IDR) was used at a false discovery rate of 0.05 to filter out irreproducible regions between the two replicates.
Bigwig files for UCSC genome coverage visualization were generated using Samtools, Bedtools and UCSC wigtobigwig
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: FACS isolated GMP-phenotypic AML cells, from in vivo

extract_protocol:
Cells were lysed as described previously (Jakobsen JS, Waage J, Rapin N, Bisgaard HC, Larsen FS, Porse BT. Temporal mapping of CEBPA and CEBPB binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries. Genome Res. 2013;23(4):592-603.) in 300 μl lysis buffer,12 applying up/down pipetting 10 times using a 100 ul tip low retention tip. Samples were sonicated using a Bioruptor sonicator plus for 30 cycles, 15/30 seconds on/off, high setting, and debris pelleted by centrifuging cold at 14,000g for 10 minutes. Fragmentation of chromatin was evaluated on extracted DNA using either: 1) a c-Kit enriched 500,000 cell sample processed in parallel (one of six tubes sonicated simultaneously) and agarose gel electrophoresis or, 2) direct sample size inspection of a 20 ul aliquot using a Bioanalyzer. ChIP was performed essentially as described previously (Sandmann T, Jakobsen JS, Furlong EE. ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos. Nat Protoc. 2006;1(6):2839-2855) with ca. 125.000 cells for histone mark and ca. 250.000 cells for CEBPA ChIP. Quanta of used antibodies (CEBPA, Santa Cruz sc-61, lot#J0407, 0.2 ug; H3K27me3, Cell signaling #9733S, lot#2, 1 ul; H3K4me3, Cell signaling #9751S,  lot#2, 1 ul) and protein A beads (Sigma, cat#P9424 , 10 ul 50%/50% beads/RIPA-low salt (140 mM)) were optimized for low input amounts, using siliconized tubes (Biozym, cat#1267-2970).
NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (NEB #6200) or NEBNext Ultra I DNA Library Prep Kit for Illumina (NEB #7370), using bacterial carrier DNA as required, see: 'Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq', Jakobsen et al., BMC Genomics 2015

value: Whole bone marrow, FACs isolated


title: Human_RNAseq_AML_32

data_processing:
The Raw sequencing data was trimmed with Trimmomatic (v 0.32) with the paramters: ILLUMINACLIP:fastqc.fa:2:30:10 HEADCROP:X LEADING:22 SLIDINGWINDOW:4:22 MINLEN:25
The trimmed data was mapped to the genome (hg19, mm9) using TopHat2 (v2.0.9) using the parameters --b2-very-sensitive --library-type=fr-unstranded nd supplying the Enslemble GTF file to the --GTF argument (release 66 for both human and mouse).
The mapped reads were summarized into gene counts using the featureCounts() function, from the Rsubread R package (V1.16.1), using the same GTF file described above and with default parameters apart from isPairedEnd=TRUE.
Filtering and differential expression: Genes with at least 2 fragments uniquely mapping in at least 1 library we tested for differential expression. A gene was deemed differentially expressed if it was called as significant with a False Discovery Rate (FDR) corrected p-value < 0.01 by both edgeR and DESeq. Specifically the exactTest() function from EdgeR (v 3.12.0) (Robinson et al., 2010)[Ref: http://bioinformatics.oxfordjournals.org/content/26/1/139.short ] was used after TMM normalization and estimation of dispersion using both estimateCommonDisp() and estimateTagwiseDisp(). The DESeq() function from DESeq (v 1.18.0) (Anders and Huber, 2010) [Ref: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218662/ ] was used with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

extract_protocol:
Qiagen, RNeasy Mini Kit
Nugen Ovation RNA-Seq System V2


title: Human_ChIP_H3K27ac_CEBPABIALLELIC_199


title: Human_RNAseq_AML_33


title: Human_RNAseq_WT_111129

source_name: FACS isolated GMP-phenotypic healthy bone marrow cells, from in vivo


title: Human_RNAseq_WT_2019


title: Human_RNAseq_AML_38


title: HL60-CD97-shCD97.1_biorepl2_techrepl1


title: Human_ChIP_H3K27ac_H3K27AC_GMP_WT


title: Human_RNAseq_AML_31


title: 6h rep2 RNA

city: Duarte

first: Parijat

last: Senapati

address: 1500 E. Duarte Rd

institute: Beckman Research Institute, City of Hope

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 and dm3 composite genome assembly using bowtie (version 1.0.0) with the following parameters -m 1 -e 70 -k 1 -n 2 --best --chunkmbs 200. RNA-seq reads were aligned to the hg19 genome assembly using HISAT2 2.1.0 using default parameters. Stringtie 1.3.4 was used with default parameters to assemble transcripts and merged using --merge option in Stringtie.
peaks were called using MACS2 version 2.1.1.20160309 with broad peak calling option and q < 0.1 for broad regions and q < 0.05 for narrow regions
Genome_build: hg19 and dm3 for ChIP-seq; hg19 for RNA-seq
Supplementary_files_format_and_content: ChIP-seq: Peak files in BED format. RNA-seq: tab-delimited text files include raw counts for each transcript in each sample

source_name: MDA-MB-231_6h RNA

growth_protocol: MDA-MB-231 cells were grown in Dulbecco's modified Eagle's medium (DMEM) with high glucose (25mM) supplemented with 10% heat-inactivated Fetal Bovine Serum (v/v) and 1X antibiotics containing penicillin and streptomycinat 37°C, 5% CO2 in a humidified chamber.

extract_protocol:
Chromatin lysates were clarified from sonicated cells and histone-DNA complexes were isolated with respective antibodies.
Sequencing library preparation and reactions were conducted at City of Hope’s Integrative Genomics Core. ChIP-seq libraries were made using Illumina Tru-Seq library preparation kit and multiplexing barcodes compatible with Illumina HiSeq 2500 technology. RMA-seq libraries were prepared using Kapa Hyper Prep Kit (Kapa Biosystems)

treatment_protocol: Insulin treatment, MDA-MB-231 cells were serum depleted in DMEM high glucose medium containing 0.2% BSA for 24h and stimulated without (untreated) or with 100 nM Insulin for indicated time periods.

tag: cell line/tissue

value: Triple negative breast cancer cells

tag: passages

value: Insulin for 6 hours


title: 6h rep1 RNA


title: 3h rep2 RNA

source_name: MDA-MB-231_3h RNA

value: Insulin for 3 hours


title: 3h rep1 RNA


title: UT rep2 RNA

source_name: MDA-MB-231_UT RNA


title: UT rep1 RNA


title: 6h Input

source_name: MDA-MB-231_6h Input

tag: chip antibody

value: input


title: 6h rep2 H3K9ac

source_name: MDA-MB-231_6h H3K9ac

tag: treatment

value: H3K9ac, ab4441 (Abcam)


title: 3h Input

data_processing:
Basecalls performed using CASAVA version 1.4.
ChIP-seq reads were aligned to the hg19 and dm3 composite genome assembly using bowtie (version 1.0.0) with the following parameters -m 1 -e 70 -k 1 -n 2 --best --chunkmbs 200. RNA-seq reads were aligned to the hg19 genome assembly using HISAT2 2.1.0 using default parameters. Stringtie 1.3.4 was used with default parameters to assemble transcripts and merged using --merge option in Stringtie.
Peaks were called using MACS2 version 2.1.1.20160309 with broad peak calling option and q < 0.1 for broad regions and q < 0.05 for narrow regions
Genome_build: hg19 and dm3 for ChIP-seq; hg19 for RNA-seq
Supplementary_files_format_and_content: ChIP-seq: Peak files in BED format. RNA-seq: tab-delimited text files include raw counts for each transcript in each sample.

source_name: MDA-MB-231_3h Input

growth_protocol: MDA-MB-231 cells were grown in Dulbecco's modified Eagle's medium (DMEM) with high glucose (25mM) supplemented with 10% heat-inactivated Fetal Bovine Serum (v/v) and 1X antibiotics containing penicillin and streptomycin at 37°C, 5% CO2 in a humidified chamber.

extract_protocol:
Chromatin lysates were clarified from sonicated cells and histone-DNA complexes were isolated with respective antibodies.
Sequencing library preparation and reactions were conducted at City of Hope’s Integrative Genomics Core. ChIP-seq libraries were made using Illumina Tru-Seq library preparation kit and multiplexing barcodes compatible with Illumina HiSeq 2500 technology. RNA-seq libraries were prepared using Kapa Hyper Prep Kit (Kapa Biosystems).


title: 6h rep1 H3K9ac


title: 3h rep2 H3K9ac

data_processing:
Basecalls performed using CASAVA version 1.4.
ChIP-seq reads were aligned to the hg19 and dm3 composite genome assembly using bowtie (version 1.0.0) with the following parameters -m 1 -e 70 -k 1 -n 2 --best --chunkmbs 200. RNA-seq reads were aligned to the hg19 genome assembly using HISAT2 2.1.0 using default parameters. Stringtie 1.3.4 was used with default parameters to assemble transcripts and merged using --merge option in Stringtie.
Peaks were called using MACS2 version 2.1.1.20160309 with broad peak calling option and q < 0.1 for broad regions and q < 0.05 for narrow regions
Genome_build: hg19 and dm3 for ChIP-seq; hg19 for RNA-seq
Supplementary_files_format_and_content: ChIP-seq: Peak files in BED format. RNA-seq: tab-delimited text files include raw counts for each transcript in each sample

source_name: MDA-MB-231_3h H3K9ac

extract_protocol:
Chromatin lysates were clarified from sonicated cells and histone-DNA complexes were isolated with respective antibodies.
Sequencing library preparation and reactions were conducted at City of Hope’s Integrative Genomics Core. ChIP-seq libraries were made using Illumina Tru-Seq library preparation kit and multiplexing barcodes compatible with Illumina HiSeq 2500 technology. RNA-seq libraries were prepared using Kapa Hyper Prep Kit (Kapa Biosystems)


title: yFR927-isw1D_H3K4me3vsInput_20190416_rep2

type: genomic

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

description:
Biological replicate 2 of 2. H3K4me3 occupancy in  isw1D mutant cells. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR927-isw1D_H3K4me3vsInput_20190416_rep1-2__S.cerevisiaeApr11_197426
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in isw1D mutant cells.

hyb_protocol: Hybridization: Resuspend colored pellet in 110 uL of hybridization mix (100 uL DIG Easy Hyb buffer, 5 uL 10mg/mL Salmon Sperm DNA, 5 uL 8mg/mL yeast tRNA). Put at 95°C for 5 min. Put at 42°C for 10 min (keep samples at 42°C while waiting for hybridization). Follow standard Agilent chamber hybridization protocol. Incubate overnight (16-24h) at 42°C in Agilent hybridization oven at 20 rpm rotation speed.  Post-Hybridization Washes: Separate coverslip and slide in Wash buffer #1. Wash slides in Wash buffer #1 for 5 min at room temperature on an orbital shaker (cover the dish to avoid light on the slides). Wash in Wash buffer #2 pre-warmed at 31°C for 5 min on an orbital shaker. Take slides out of the buffer slowly to dry them. Wash Buffer #1: 6x SSPE, 0.005% N-lauroylsarcosine. Wash Buffer #2: 0.06x SSPE.  Stripping: Stripping is done in 1 L of 5 mM Potassium phosphate buffer pH 6.6 after scanning of the slides. Use a crystallization dish, and a metallic slide rack (use weighing spatulas to lift the rack from the bottom of the dish and avoid direct contact with the hot surface). Pour the stripping buffer, submerge the rack with slides (from 1 to 10) and heat it up slowly on heating plate until the liquid boils with big bubbles. It usually takes 20 to 25 min. Do not overboil it. Remove the rack and briefly rinse in a container with water. Slowly remove the rack from the liquid. 1M Potassium phosphate buffer pH 6.6: mix 3.81 mL of 1M K2HPO4 + 6.19 mL of 1M KH2PO4. Dilute 5 mL of this 1M solution in 1 L Milli-Q water to obtain 5 mM Potassium phosphate buffer pH 6.6.

scan_protocol: Standard_Innopsys_Yeast4x180K. Set the scan as follow: pixel size = 2µm; speed = 20; Scan Mode = Normal; Acquisition Mode = Simultaneous; Focus = Auto. Adjust manually the detection gain for 635 and 532 wavelengths in order to have less than 5% spot saturation.

data_processing:
The ChIP-chip data from individual replicates were normalized by setting the median of log2 ratios to zero. The duplicate were averaged and the data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100bp to generate data points in 10bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = median normalized

organism: Saccharomyces cerevisiae

label_protocol: Standard Yeast aa-dUTP Labeling. Blunting: Do everything on ice. Add 70 uL of the blunting solution (11 uL NEB Buffer #2, 0.5 uL BSA 10mg/mL, 0.5 uL 20mM dNTPs, 0.2 uL T4 DNA Polymerase 3U/uL, 57.8 uL ddH2O) to 40 uL of the resuspended DNA obtained at the end of the cleanup step. For Inputs, use 4uL + 36uL ddH2O. Incubate 20 min at 12°C. Precipitation: Add 11.5 uL 3M NaOAc pH 5.2 and 0.5 uL Glycogen 20mg/mL and vortex briefly. Extract with 120 uL Phenol/Chloroform/Isoamyl alcohol (25:24:1). Transfer 110 uL to a new tube and add 230 uL of cold 100% EtOH (-20°C). Spin 20 min at 4°C. Wash the pellet with 700 uL of cold 70% EtOH (-20°C) and spin 5 min at 4°C. Resuspend the pellet in 25 uL ddH2O and place on ice. Ligation: Thaw everything and do all manipulations on ice. Add 25 uL of ligase mix (10 uL 5x T4 Ligase Buffer, 6.7 uL 15uM unidirectional linkers, 0.5 uL T4 DNA Ligase (5U/uL), 8 uL ddH2O) to the resuspended pellet from the blunting step. Incubate overnight at 16°C. Precipitation: Add 6 uL 3M NaOAc pH 5.2 and vortex. Add 130 uL of cold 100% EtOH (-20°C) and incubate at least 30 min at -20°C. Centrifuge 20 min at 4°C at maximum speed. Wash the pellet (should be a smear on the side of the tube) with 500 uL cold 70% EtOH (-20°C). Spin 5 min at 4°C. Dry the pellet and resuspend in 25 uL ddH2O. Leave on ice for about 20 min, vortex, centrifuge briefly and put on ice. Labeling: Add 15 uL of PCR labeling mix (4 uL 10x ThermoPol Buffer, 2 uL 5mM aa-dUTP mix, 1.25 uL 40uM Oligo FR1, 7.75 uL ddH2O) to the pellet from the ligation step. Start the PCR program and during the first step (4 min at 55°C), add 10 uL of the polymerase mix (1 uL 10x ThermoPol buffer, 1 uL Taq Polymerase 5U/uL, 0.01 uL Pfu Polymerase Turbo 2.5U/uL, 8 uL ddH2O). PCR cycling conditions: 1) 4 min at 55°C; 2) 5 min at 72°C; 3) 2 min at 95°C; 4) 30 sec at 95°C; 5) 30 sec at 55°C; 6) 1 min at 72°C; 7) Repeat steps 4-6 31 more times; 8) 4 min at 72°C; 9) Forever at 4°C. Purify PCR reactions with QIAquick PCR purification kit (Qiagen), following manufacturer's protocol but use a Phosphate Wash buffer and a Phosphate Elution buffer instead of their buffers PE and EB, respectively. Also, wash the columns twice and elute with 50 uL elution buffer. Speed-vac the eluate to dryness. Resuspend the pellets with fresh 4.5 uL 0.1M Sodium Carbonate buffer pH 9.0. Add 4.5 uL of the appropriate NHS-ester Cy-dye. Fresh tubes of NHS-ester Cy-dyes should be resuspended in 73 uL DMSO. Mix well and incubate at room temperature in the dark for one hour. Add 35 uL 0.1M NaOAc pH 5.2. Purify using the QIAquick PCR purification kit (Qiagen), wash twice and elute in 50 uL. Mix both samples of a pair (Cy5 and Cy3) in the same tube. Speed-vac until 10-20uL are left. Phosphate Wash buffer (100 mL): 0.5 mL 1M KPO4 pH 8.5, 15.25 mL ddH2O, 84.25 mL 95% EtOH. Solution will be cloudy upon mixing. Phosphate Elution buffer (10 mL): 0.04 mL 1M KPO4 pH 8.5, 9.96 mL ddH2O. 1M KPO4 pH 8.5 (10 mL): 9.5 mL 1M K2HPO4, 0.5 mL 1M KH2PO4. 1M Sodium Carbonate buffer pH 9.0 (100 mL): 10.8g Na2CO3, 80 mL ddH2O and pH to 9.0 with concentrated HCl. Adjust volume to 100 mL with ddH2O. Dilute 1:10 when using. Solution will change composition over time. Use only if less than a month old.

growth_protocol: 50 mL of YPD (yeast extract-peptone-2% glucose) medium is inoculated at OD600 0.1 from an overnight preculture in the same medium and allowed to grow until it reachs OD600 around 0.8. Culture is poured in a 50 mL tube containing 1.4 mL 37% formaldehyde for crosslinking, and incubated on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5 mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4°C, 3000 rpm, resuspended in 40 mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid and transferred to 1.5 mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cell pellets snap-freezed in liquid nitrogen and stored at -80°C.

extract_protocol:
Cells are thawed on ice and resuspended in 700 uL Lysis buffer with protease inhibitors. 500 uL of acid-washed glass beads (Sigma) are added and the cells are lysed using a bead-beater (4 x 5 min cycles, with 5 min breaks on ice). The tubes are pierced with an 18-gauge syringe needle to allow transfer of lysate, but not beads. The pierced tubes are put in 2 mL collection tubes and spun briefly. The lysate is then homogenized by pipetting and sonicated 4x20sec at output 7 Watts, with a 1 min break between sonication cycles. The sonicated lysates are centrifuge for 5 min at 4°C max speed and the supernatant used immediately for ChIP (or saved and frozen at -80°C). Lysis buffer: 50mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 1mM PMSF, 1mM Benzamidine, 10ug/mL Aprotinin, 1ug/mL Leupeptin, 1ug/mL Pepstatin.
H3K4me3  ChIP. Antibody from Abcam (Ab8580). Protein G Dynabeads (12.5uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (0.625 μg/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate (150 uL of sonicated WCE + 450 uL of Lysis Buffer) are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.
Beads are spun down and supernatant is transferred to a new 1.5 mL tube. 350 uL of a mix of (345 uL TE, 3 uL RNAse A 10mg/mL, 2 uL Glycogen 20mg/mL) is added to the supernatant. Samples are vortexed and incubated at 37°C for 2 hr. 15 uL 10% SDS and 7.5 uL Proteinase K are then added, vortexed and incubated for another 2 hr at 37°C. The samples are then extracted twice with 400 uL phenol/chloroform/isoamyl alcohol (25:24:1). 14 uL of 5M NaCl is added to the final extract of about 350 uL. 1 mL of cold 100% EtOH (-20°C) is added and the samples are centrifuged at maximum speed for 20 min at 4°C. The supernatant is discarded and the pellet is washed with 700 uL of cold 70% EtOH (-20°C) and centrifuged 5 min at 4°C. The supernatant is discarded and the pellet resuspended in 50 uL TE and stored at -20°C.

tag: genotype


title: yFR930-chd1D_H3K4me3vsInput_20190416_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in chd1D mutant cells. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR930-chd1D_H3K4me3vsInput_20190416_rep1-2__S.cerevisiaeApr11_379531
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in chd1D mutant cells.


description:
Biological replicate 1 of 2. H3K4me3 occupancy in set2D mutant cells. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR348-set2D_H3K4me3vsInput_20190416_rep1-2__S.cerevisiaeApr11_848395
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in set2D mutant cells.


description:
Biological replicate 1 of 2. H3K4me3 occupancy in rco1D mutant cells. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR772-rco1D_H3K4me3vsInput_20190416_rep1-2__S.cerevisiaeApr11_637710
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in rco1D mutant cells.


title: 3h rep1 H3K9ac

tag: cell type


description:
Biological replicate 1 of 2. H3K4me3 occupancy in  isw1D mutant cells. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR927-isw1D_H3K4me3vsInput_20190416_rep1-2__S.cerevisiaeApr11_197426
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in isw1D mutant cells.


title: yFR116-WT_H3K4me3vsInput_20190416_rep1

description:
Biological replicate 1 of 2. H3K4me3 occupancy in WT cells. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR116-WT_H3K4me3vsInput_20190416_rep1-2__S.cerevisiaeApr11_933835
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in WT cells.


title: yFR772-rco1D_H3K4me3vsInput_20190416_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in  rco1D mutant cells. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR772-rco1D_H3K4me3vsInput_20190416_rep1-2__S.cerevisiaeApr11_637710
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in rco1D mutant cells.


title: UT rep2 H3K9ac

source_name: MDA-MB-231_UT H3K9ac


title: UT rep1 H3K9ac


title: yFR971_WT_80min37C_H3K4me3vsInput_20170927_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in WT cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_WT_80min37C_H3K4me3vsInput_20170927_FB_MN_rep1-2__S.cerevisiaeApr11_501555.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in WT cells treated 80 min at 37°C.

growth_protocol: 50 mL of YPD (yeast extract-peptone-2% glucose) medium is inoculated at OD600 0.1 from an overnight preculture in the same medium and allowed to grow until it reachs OD600 0.5. Cell cultures are then switched to 37°C and allowed to grow for additional 80 min. Culture is poured in a 50 mL tube containing 1.4 mL 37% formaldehyde for crosslinking, and incubated on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5 mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4°C, 3000 rpm, resuspended in 40 mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (1 mL) and transferred to 1.5 mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cell pellets snap-freezed in liquid nitrogen and stored at -80°C.

extract_protocol:
Cells are thawed on ice and resuspended in 700 uL Lysis buffer with protease inhibitors. 500 uL of acid-washed glass beads (Sigma) are added and the cells are lysed using a bead-beater (4 x 5 min cycles, with 5 min breaks on ice). The tubes are pierced with an 18-gauge syringe needle to allow transfer of lysate, but not beads. The pierced tubes are put in 2 mL collection tubes and spun briefly. The lysate is then homogenized by pipetting and sonicated 4x20sec at output 7 Watts, with a 1 min break between sonication cycles. The sonicated lysates are centrifuge for 5 min at 4°C max speed and the supernatant used immediately for ChIP (or saved and frozen at -80°C). Lysis buffer: 50mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 1mM PMSF, 1mM Benzamidine, 10ug/mL Aprotinin, 1ug/mL Leupeptin, 1ug/mL Pepstatin.
Beads are spun down and supernatant is transferred to a new 1.5 mL tube. 350 uL of a mix of (345 uL TE, 3 uL RNAse A 10mg/mL, 2 uL Glycogen 20mg/mL) is added to the supernatant. Samples are vortexed and incubated at 37°C for 2 hr. 15 uL 10% SDS and 7.5 uL Proteinase K are then added, vortexed and incubated for another 2 hr at 37°C. The samples are then extracted twice with 400 uL phenol/chloroform/isoamyl alcohol (25:24:1). 14 uL of 5M NaCl is added to the final extract of about 350 uL. 1 mL of cold 100% EtOH (-20°C) is added and the samples are centrifuged at maximum speed for 20 min at 4°C. The supernatant is discarded and the pellet is washed with 700 uL of cold 70% EtOH (-20°C) and centrifuged 5 min at 4°C. The supernatant is discarded and the pellet resuspended in 50 uL TE and stored at -20°C.

treatment_protocol:
switch to 37°C for 80 min
H3K4me3 ChIP. Antibody from Abcam (ab8580). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (2.5ug/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: MATα, leu2Δ1

value: H3K4me3 (Abcam ab8580)

treatment_protocol:
switch to 37°C for 80 min
none


description:
Biological replicate 1 of 2. H3K4me3 occupancy in chd1D mutant cells. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR930-chd1D_H3K4me3vsInput_20190416_rep1-2__S.cerevisiaeApr11_379531
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in chd1D mutant cells.


title: yFR116-WT_H3K4me3vsInput_20190416_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in WT cells. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR116-WT_H3K4me3vsInput_20190416_rep1-2__S.cerevisiaeApr11_933835
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in WT cells.


title: yFR973_spt16-197_80min37C_H3K4me3vsInput_20170927_rep1

description:
Biological replicate 1 of 2. H3K4me3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_H3K4me3vsInput_20170927_FB_MN_rep1-2__S.cerevisiaeApr11_48113.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

value: MATα, leu2Δ1, spt16-197


title: yFR348-set2D_H3K4me3vsInput_20190416_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in set2D mutant cells. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR348-set2D_H3K4me3vsInput_20190416_rep1-2__S.cerevisiaeApr11_848395
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in set2D mutant cells.


title: yFR1584_spt16-197_isw1D_80min37C_H3K4me3vsInput_20170927_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in isw1Δ/spt16-197 double mutant cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1584_spt16-197_isw1D_80min37C_H3K4me3vsInput_20170927_FB_MN_rep1-2__S.cerevisiaeApr11_643363.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in isw1Δ/spt16-197 double mutant cells treated 80 min at 37°C.

value: MATα, leu2Δ1, spt16-197, isw1Δ::KanMX4


title: yFR973_spt16-197_80min37C_H3K4me3vsInput_20170927_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_H3K4me3vsInput_20170927_FB_MN_rep1-2__S.cerevisiaeApr11_48113.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.


title: yFR971_WT_80min37C_H3K4me3vsInput_20170927_rep1

description:
Biological replicate 1 of 2. H3K4me3 occupancy in WT cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_WT_80min37C_H3K4me3vsInput_20170927_FB_MN_rep1-2__S.cerevisiaeApr11_501555.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in WT cells treated 80 min at 37°C.


title: yFR1588_isw2D_80min37C_H3K4me3vsInput_20170927_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in isw2Δ mutant cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1588_isw2D_80min37C_H3K4me3vsInput_20170927_FB_MN_rep1-2__S.cerevisiaeApr11_51978.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in isw2Δ mutant cells treated 80 min at 37°C.

value: MATα, leu2Δ1, isw2Δ::KanMX4


title: yFR1588_isw2D_80min37C_H3K4me3vsInput_20170927_rep1

description:
Biological replicate 1 of 2. H3K4me3 occupancy in isw2Δ mutant cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1588_isw2D_80min37C_H3K4me3vsInput_20170927_FB_MN_rep1-2__S.cerevisiaeApr11_51978.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in isw2Δ mutant cells treated 80 min at 37°C.


title: yFR1584_spt16-197_isw1D_80min37C_H3K4me3vsInput_20170927_rep1

description:
Biological replicate 1 of 2. H3K4me3 occupancy in isw1Δ/spt16-197 double mutant cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1584_spt16-197_isw1D_80min37C_H3K4me3vsInput_20170927_FB_MN_rep1-2__S.cerevisiaeApr11_643363.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in isw1Δ/spt16-197 double mutant cells treated 80 min at 37°C.


title: yFR1592_spt16-197_isw2D_80min37C_H3K4me3vsInput_20170927_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in isw2Δ/spt16-197 double mutant cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1592_spt16-197_isw2D_80min37C_H3K4me3vsInput_20170927_FB_MN_rep1-2__S.cerevisiaeApr11_87027.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in isw2Δ/spt16-197 double mutant cells treated 80 min at 37°C.

value: MATα, leu2Δ1, spt16-197, isw2Δ::KanMX4


title: yFR1562_spt16-197_chd1D_80min37C_H3K4me3vsInput_20170927_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in chd1Δ/spt16-197 double mutant cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1562_spt16-197_chd1D_80min37C_H3K4me3vsInput_20170927_FB_MN_rep1-2__S.cerevisiaeApr11_584807.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in chd1Δ/spt16-197 double mutant cells treated 80 min at 37°C.

value: MATα, leu2Δ1, spt16-197, chd1Δ::KanMX4


title: yFR1580_isw1D_80min37C_H3K4me3vsInput_20170927_rep1

description:
Biological replicate 1 of 2. H3K4me3 occupancy in isw1Δ mutant cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1580_isw1D_80min37C_H3K4me3vsInput_20170927_FB_MN_rep1-2__S.cerevisiaeApr11_820085.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in isw1Δ mutant cells treated 80 min at 37°C.

value: MATα, leu2Δ1, isw1Δ::KanMX4


title: yFR1562_spt16-197_chd1D_80min37C_H3K4me3vsInput_20170927_rep1

description:
Biological replicate 1 of 2. H3K4me3 occupancy in chd1Δ/spt16-197 double mutant cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1562_spt16-197_chd1D_80min37C_H3K4me3vsInput_20170927_FB_MN_rep1-2__S.cerevisiaeApr11_584807.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in chd1Δ/spt16-197 double mutant cells treated 80 min at 37°C.


title: yFR1580_isw1D_80min37C_H3K4me3vsInput_20170927_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in isw1Δ mutant cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1580_isw1D_80min37C_H3K4me3vsInput_20170927_FB_MN_rep1-2__S.cerevisiaeApr11_820085.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in isw1Δ mutant cells treated 80 min at 37°C.


title: UT Input

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 and dm3 composite genome assembly using bowtie (version 1.0.0) with the following parameters -m 1 -e 70 -k 1 -n 2 --best --chunkmbs 200. RNA-seq reads were aligned to the hg19 genome assembly using HISAT2 2.1.0 using default parameters. Stringtie 1.3.4 was used with default parameters to assemble transcripts and merged using --merge option in Stringtie.
Peaks were called using MACS2 version 2.1.1.20160309 with broad peak calling option and q < 0.1 for broad regions and q < 0.05 for narrow regions
Genome_build: hg19 and dm3 for ChIP-seq; hg19 for RNA-seq
Supplementary_files_format_and_content: ChIP-seq: Peak files in BED format. RNA-seq: tab-delimited text files include raw counts for each transcript in each sample.

source_name: MDA-MB-231_UT Input


title: yFR1558_chd1D_80min37C_H3K4me3vsInput_20170927_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in chd1Δ mutant cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1558_chd1D_80min37C_H3K4me3vsInput_20170927_FB_MN_rep1-2__S.cerevisiaeApr11_273310.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in chd1Δ mutant cells treated 80 min at 37°C.

value: MATα, leu2Δ1, chd1Δ::KanMX4


title: yFR1592_spt16-197_isw2D_80min37C_H3K4me3vsInput_20170927_rep1

description:
Biological replicate 1 of 2. H3K4me3 occupancy in isw2Δ/spt16-197 double mutant cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1592_spt16-197_isw2D_80min37C_H3K4me3vsInput_20170927_FB_MN_rep1-2__S.cerevisiaeApr11_87027.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in isw2Δ/spt16-197 double mutant cells treated 80 min at 37°C.


title: yFR1416_spt16-197-htz1D_H3K4me3vsH4_SPIKE-IN_Rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in  htz1Δ/spt16-197 double mutant cells treated 80 minutes at 37°C. Spike PhiX174 DNA was added to the extract prior to immunoprecipitation (Jeronimo et al. 2015). H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR1416_spt16-197-htz1D_H3K4me3vsH4_SPIKE-IN_Rep1-2_MN__S.cerevisiaeApr11_171031.bed
A genome browser-ready file for H3K4me3 occupancy (IP/H4) in htz1Δ/spt16-197 double mutant cells treated 80 min at 37°C.

value: MATα, leu2Δ1, spt16-197, htz1Δ::LEU2

treatment_protocol:
switch to 37°C for 80 min
H4 ChIP. Antibody from A. Verreault (ryH4). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (2 μL/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: ryH4 (A.Verreault)


title: yFR974_spt6-1004_H3K4me3vsH4_SPIKE-IN_Rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in  spt6-1004 mutant cells treated 80 minutes at 37°C. Spike PhiX174 DNA was added to the extract prior to immunoprecipitation (Jeronimo et al. 2015). H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR974_spt6-1004_H3K4me3vsH4_SPIKE-IN_Rep1-2_MN__S.cerevisiaeApr11_357403.bed
A genome browser-ready file for H3K4me3 occupancy (IP/H4) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


description:
Biological replicate 1 of 2. H3K4me3 occupancy in   htz1Δ/spt6-1004 double mutant cells treated 80 minutes at 37°C. Spike PhiX174 DNA was added to the extract prior to immunoprecipitation (Jeronimo et al. 2015). H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR1420_spt6-1004-htz1D_H3K4me3vsH4_SPIKE-IN_Rep1-2_MN__S.cerevisiaeApr11_695465.bed
A genome browser-ready file for H3K4me3 occupancy (IP/H4) in htz1Δ/spt6-1004 double mutant cells treated 80 min at 37°C.

value: MATα, his3Δ200, leu2Δ1, lys2-128δ, ura3-52, spt6-1004-FLAG, htz1Δ::LEU2


title: yFR1558_chd1D_80min37C_H3K4me3vsInput_20170927_rep1

description:
Biological replicate 1 of 2. H3K4me3 occupancy in chd1Δ mutant cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1558_chd1D_80min37C_H3K4me3vsInput_20170927_FB_MN_rep1-2__S.cerevisiaeApr11_273310.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in chd1Δ mutant cells treated 80 min at 37°C.


title: yFR1420_spt6-1004-htz1D_H3K4me3vsH4_SPIKE-IN_Rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in  htz1Δ/spt6-1004 double mutant cells treated 80 minutes at 37°C. Spike PhiX174 DNA was added to the extract prior to immunoprecipitation (Jeronimo et al. 2015). H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR1420_spt6-1004-htz1D_H3K4me3vsH4_SPIKE-IN_Rep1-2_MN__S.cerevisiaeApr11_695465.bed
A genome browser-ready file for H3K4me3 occupancy (IP/H4) in htz1Δ/spt6-1004 double mutant cells treated 80 min at 37°C.


description:
Biological replicate 1 of 2. H3K4me3 occupancy in  spt6-1004 mutant cells treated 80 minutes at 37°C. Spike PhiX174 DNA was added to the extract prior to immunoprecipitation (Jeronimo et al. 2015). H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR974_spt6-1004_H3K4me3vsH4_SPIKE-IN_Rep1-2_MN__S.cerevisiaeApr11_357403.bed
A genome browser-ready file for H3K4me3 occupancy (IP/H4) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


description:
Biological replicate 1 of 2. H3K4me3 occupancy in  htz1Δ/spt16-197 double mutant cells treated 80 minutes at 37°C. Spike PhiX174 DNA was added to the extract prior to immunoprecipitation (Jeronimo et al. 2015). H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR1416_spt16-197-htz1D_H3K4me3vsH4_SPIKE-IN_Rep1-2_MN__S.cerevisiaeApr11_171031.bed
A genome browser-ready file for H3K4me3 occupancy (IP/H4) in htz1Δ/spt16-197 double mutant cells treated 80 min at 37°C.


title: yFR973_spt16-197_80min37C_H2BubvsH2B_20161107_Rep2

description:
Biological replicate 2 of 2. H2Bub occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H2Bub ChIP sample (Cy5-labeled) was performed using a rabbit monoclonal antibody against H2Bub and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H2B.
SmthBED_yFR973_spt16-197_80min37C_H2BubvsH2B_20161107_Rep1-2_MN__S.cerevisiaeApr11_714622.bed
A genome browser-ready file for H2Bub occupancy (IP/H2B) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 min
H2Bub ChIP. Antibody from Cell Signaling Technology (#5546). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (3 μL/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: H2Bub (Cell Signaling Technology 5546)

treatment_protocol:
switch to 37°C for 80 min
H2B ChIP. Antibody from Abcam (ab1790). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (5 μg/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: H2B (Abcam ab1790)


title: yFR1480_Spt6-AA_90minRap_H3K4me3vsInput_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in Spt6-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 90 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1480_Spt6-AA_90minRap_H3K4me3vsInput_rep1-2_MN__S.cerevisiaeApr11_419766.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in Spt6-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 90 min.

growth_protocol: 50 mL of YPD (yeast extract-peptone-2% glucose) medium is inoculated at OD600 0.1 from an overnight preculture in the same medium. Cells are grown to an OD600 of ~0.5 and then treated with 1 μg/mL of rapamycin (Bio Basic Inc.) for 90 min. Culture is poured in a 50 mL tube containing 1.4 mL 37% formaldehyde for crosslinking, and incubated on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5 mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4°C, 3000 rpm, resuspended in 40 mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (~1 mL) and transferred to 1.5 mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cell pellets snap-freezed in liquid nitrogen and stored at -80°C.

treatment_protocol:
1 μg/mL of rapamycin for 90 min
H3K4me3 ChIP. Antibody from Abcam (ab8580). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (2.5ug/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: MATα, ade2-1, trp1-1, can1-100, leu2-3,112, his3-11,15, ura3, GAL, psi+, tor1-1, fpr1Δ::NAT, RPL13A-2xFKBP12::TRP1, SPT6-FRB::kanMX6

treatment_protocol:
1 μg/mL of rapamycin for 90 min
none


description:
Biological replicate 1 of 2. H3K4me3 occupancy in Spt6-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 90 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1480_Spt6-AA_90minRap_H3K4me3vsInput_rep1-2_MN__S.cerevisiaeApr11_419766.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in Spt6-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 90 min.


title: yFR1321_WT_90minRap_H3K4me3vsInput_rep1

description:
Biological replicate 1 of 2. H3K4me3 occupancy in WT cells treated with 1 μg/mL of rapamycin for 90 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1321_WT_90minRap_H3K4me3vsInput_rep1-2_MN__S.cerevisiaeApr11_965735.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in WT cells treated with 1 μg/mL of rapamycin for 90 min.


title: yFR1478_Spt16-AA_90minRap_H3K4me3vsInput_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in Spt16-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 90 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_90minRap_H3K4me3vsInput_rep1-2_MN__S.cerevisiaeApr11_852796.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 90 min.

value: MATα, ade2-1, trp1-1, can1-100, leu2-3,112, his3-11,15, ura3, GAL, psi+, tor1-1, fpr1Δ::NAT, RPL13A-2xFKBP12::TRP1, SPT16-FRB::kanMX6


description:
Biological replicate 1 of 2. H2Bub occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H2Bub ChIP sample (Cy5-labeled) was performed using a rabbit monoclonal antibody against H2Bub and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H2B.
SmthBED_yFR974_spt6-1004_80min37C_H2BubvsH2B_20161107_Rep1-2_MN__S.cerevisiaeApr11_954906.bed
A genome browser-ready file for H2Bub occupancy (IP/H2B) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


description:
Biological replicate 1 of 2. H3K4me3 occupancy in Spt16-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 90 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_90minRap_H3K4me3vsInput_rep1-2_MN__S.cerevisiaeApr11_852796.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 90 min.


description:
Biological replicate 1 of 2. H3K14ac occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K14ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K14ac and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR974_spt6-1004_80min37C_H3K14ac-H4_20161102_Rep1-2_MN__S.cerevisiaeApr11_162318.bed
A genome browser-ready file for H3K14ac occupancy (IP/H4) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 min
H3K14ac ChIP. Antibody from Millipore (07-353). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (3 μL/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: H3K14ac (Millipore 07-353)


title: yFR974_spt6-1004_80min37C_H2BubvsH2B_20161107_Rep2

description:
Biological replicate 2 of 2. H2Bub occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H2Bub ChIP sample (Cy5-labeled) was performed using a rabbit monoclonal antibody against H2Bub and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H2B.
SmthBED_yFR974_spt6-1004_80min37C_H2BubvsH2B_20161107_Rep1-2_MN__S.cerevisiaeApr11_954906.bed
A genome browser-ready file for H2Bub occupancy (IP/H2B) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


description:
Biological replicate 1 of 2. H2Bub occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H2Bub ChIP sample (Cy5-labeled) was performed using a rabbit monoclonal antibody against H2Bub and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H2B.
SmthBED_yFR973_spt16-197_80min37C_H2BubvsH2B_20161107_Rep1-2_MN__S.cerevisiaeApr11_714622.bed
A genome browser-ready file for H2Bub occupancy (IP/H2B) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.


title: yFR974_spt6-1004_80min37C_H3K14ac-H4_20161102_Rep2

description:
Biological replicate 2 of 2. H3K14ac occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K14ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K14ac and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR974_spt6-1004_80min37C_H3K14ac-H4_20161102_Rep1-2_MN__S.cerevisiaeApr11_162318.bed
A genome browser-ready file for H3K14ac occupancy (IP/H4) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


title: BMDM_MK2-/-_120min_LPS_rep1

description: Gene expression after 120min in LPS-treated murine BMDM

source_name: Bone marrow derived macrophages (BMDM), MK2-deficient, 120min LPS treatment, replicate 1

value: LPS

value: Bone marrow derived macrophages (BMDM)

value: male


title: yFR1222_htz1D_H3K4me3vsH4_SPIKE-IN_Rep1

description:
Biological replicate 1 of 2. H3K4me3 occupancy in  htz1Δ mutant cells treated 80 minutes at 37°C. Spike PhiX174 DNA was added to the extract prior to immunoprecipitation (Jeronimo et al. 2015). H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR1222_htz1D_H3K4me3vsH4_SPIKE-IN_Rep1-2_MN__S.cerevisiaeApr11_880938.bed
A genome browser-ready file for H3K4me3 occupancy (IP/H4) in htz1Δ mutant cells treated 80 min at 37°C.

value: MATα, leu2Δ1, htz1Δ::LEU2

value: H3K4me3 (Abcam ab8580)


description:
Biological replicate 1 of 2. H3K18ac occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K18ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K18ac and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR973_spt16-197_80min37C_H3K18ac-H4_20161102_Rep1-2_MN__S.cerevisiaeApr11_401897.bed
A genome browser-ready file for H3K18ac occupancy (IP/H4) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 min
H3K18ac ChIP. Antibody from Abcam (ab1191). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (3 μg/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: MATα, leu2Δ1, spt16-197

value: H3K18ac (Abcam ab1191)


title: yFR1222_htz1D_H3K4me3vsH4_SPIKE-IN_Rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in  htz1Δ mutant cells treated 80 minutes at 37°C. Spike PhiX174 DNA was added to the extract prior to immunoprecipitation (Jeronimo et al. 2015). H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR1222_htz1D_H3K4me3vsH4_SPIKE-IN_Rep1-2_MN__S.cerevisiaeApr11_880938.bed
A genome browser-ready file for H3K4me3 occupancy (IP/H4) in htz1Δ mutant cells treated 80 min at 37°C.


title: yFR974_spt6-1004_80min37C_H3K18ac-H4_20161102_Rep2

description:
Biological replicate 2 of 2. H3K18ac occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K18ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K18ac and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR974_spt6-1004_80min37C_H3K18ac-H4_20161102_Rep1-2_MN__S.cerevisiaeApr11_708393.bed
A genome browser-ready file for H3K18ac occupancy (IP/H4) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


description:
Biological replicate 1 of 2. H3K18ac occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K18ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K18ac and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR974_spt6-1004_80min37C_H3K18ac-H4_20161102_Rep1-2_MN__S.cerevisiaeApr11_708393.bed
A genome browser-ready file for H3K18ac occupancy (IP/H4) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


title: yFR971_SPT16-WT_80min37C_H2BubvsH2B_20161107_Rep2

description:
Biological replicate 2 of 2. H2Bub occupancy in WT cells treated 80 minutes at 37°C. H2Bub ChIP sample (Cy5-labeled) was performed using a rabbit monoclonal antibody against H2Bub and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H2B.
SmthBED_yFR971_SPT16-WT_80min37C_H2BubvsH2B_20161107_Rep1-2_MN__S.cerevisiaeApr11_57600.bed
A genome browser-ready file for H2Bub occupancy (IP/H2B) in WT cells treated 80 min at 37°C.

value: MATα, leu2Δ1


title: yFR973_spt16-197_80min37C_H3K14ac-H4_20161102_Rep2

description:
Biological replicate 2 of 2. H3K14ac occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K14ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K14ac and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR973_spt16-197_80min37C_H3K14ac-H4_20161102_Rep1-2_MN__S.cerevisiaeApr11_499915.bed
A genome browser-ready file for H3K14ac occupancy (IP/H4) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.