title: ER Ribosome profiling 4 h Tg 2


title: Cytosol Ribosome profiling 0.5 h Tg 1

status: Public on Oct 01 2015

type: SRA

city: Durham

first: David

last: Reid

state: NC

address: 436 Nanaline Duke Bldg., Box 3709 DUMC

department: Biochemistry

country: USA

institute: Duke University

library_source: transcriptomic

data_processing:
Map reads to transcriptome with Bowtie (no mismatches)
Quantify translation as RPKM
Genome_build: hg19 (longest transcript isoform)
Supplementary_files_format_and_content: Excel spreadsheet indicating RPKM values

molecule: total RNA

organism: Mus musculus

source_name: Mouse embryonic fibroblasts, GADD34-/-

growth_protocol: Cultured in DMEM + 10% FBS, 37C, 5% CO2

extract_protocol:
Pre-treatment with 180 uM cycloheximide for 30s. PBS wash. Release cytosol with digitonin. Extract remaining sample with dodecyl maltoside.
Ribosome profiling: Digest with Mnase (30 min 10 ug/ml, 37C), pellet ribosomes, extract RNA, PNK treat, gel isolation, library generation with NEB Directional Small RNA kit
mRNA-seq: RiboMinus, library prepataion using TruSeq RNA Sample Preparation Kit (Illumina)

treatment_protocol: Treatment with 1uM thapsigargin

tag: cell type

value: embryonic fibroblast

tag: treatment

value: 0.5 h Tg

tag: compartment

value: Cytosol

tag: analysis

value: Ribosome profiling

tag: replicate


title: ER Ribosome profiling 2 h Tg 2

value: 2 h Tg

value: ER


title: ER mRNA-seq 2 h Tg 2

value: mRNA-seq


title: ER Ribosome profiling 1 h Tg 2

value: 1 h Tg


title: Cytosol Ribosome profiling Untreated 1

value: Untreated


title: ER mRNA-seq 4 h Tg 2

value: 4 h Tg


title: ER Ribosome profiling 0.5 h Tg 2


title: ER Ribosome profiling Untreated 2


title: ER Ribosome profiling 4 h Tg 1


title: ER Ribosome profiling Untreated 1


title: E_2

city: Dallas

first: Min Soo

last: Kim

state: Texas

address: 5323 Harry Hines Blvd.

department: Department of Clinical Sciences

institute: University of Texas Southwestern

data_processing:
Illumina Casava1.7 software used for basecalling.
NGS-QC-Toolkit used to for filtering using default settings.
Bowtie2 (v 2.0.6) used for alignement.
HTSeq was used for read counting.
DESeq R package used for normalization and differential gene expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Individual sample read counts and combined normalized expression values using DESeq.

source_name: MEFs

growth_protocol: We performed RNA-Seq using either isolated adult mouse ventricular cardiomyocytes (CMs) or MEFs treated for three weeks with empty vector, GHMT (iCMs cell sorted using αMHC-GFP before RNA-Seq), or AGHMT (iCMs cell sorted using αMHC-GFP before RNA-Seq).

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using TruSeq Stranded RNA LT Kit from Illumina.

treatment_protocol: Mouse embryonic fibroblasts (MEF) were treated with empty vector, GHMT (Gata4, Hand2, Mef2c, and Tbx5) or AGMT(Akt,Gata4, Hand2, Mef2c, and Tbx5).

tag: strain

tag: cell population

value: mouse embryonic fibroblasts (MEFs)


title: CM_1

source_name: Cardiomyocyte

value: ventricular cardiomyocytes (CMs)


title: E_1


title: E_3


title: CM_3


title: ER Ribosome profiling 1 h Tg 1


title: AGHMT_3

source_name: iCM

value: iCMs cell sorted using αMHC-GFP


title: AGHMT_2


title: GHMT_3


title: GHMT_2


title: GHMT_1


title: CM_2


title: AGHMT_1


title: NIPBL_Mut3

city: Kansas City

first: Jennifer

last: Gerton

state: Missouri

address: 1000 E. 50th Street

institute: Stowers Institute for Medical Research

data_processing:
Images analysis and base calling was done using the solexa pipeline
Reads from three biological replicates for WT and NIPBL+/- were aligned to the mouse genome UCSC mm10 and to gene annotations from Ensembl 72 using TopHat 2.0.10 using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-Seq RPKM expression values were computed for each gene using edgeR.

source_name: Mouse embryonic fibroblasts

growth_protocol: MEFs were grown in DMEM supplemented with 10% fetal bovine serum (FBS). Cells of 3rd passage were used for RNA isolation for sequencing.

extract_protocol:
Total RNA from mouse ES cells was isolated with TRIzol Reagent (Life Technologies, 15596) following the manufacturer’s instructions. RNA was treated with DNase I (NEB, M0303S) to remove contaminated genomic DNA. After that, RNA was depleted of ribosomal RNA with the Ribo-Zero kit (Epicentre).
The ribo-depleted RNA samples were amplified with the TruSeq RNA Sample Prep Kit (Illumina) for Solexa sequencing.

tag: genotype

value: NIPBL-haploinsufficient

value: Mouse embryonic fibroblasts

tag: passages

tag: strains


title: WT3

value: wild type


title: 4F iTSC clone E

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: genomic

data_processing:
Genomic mapping of paired-end reads was performed with Bowtie2 (v2.2.3) using default parameters. Reads were mapped to the mouse genome build NCBIM37. Final data analysis was performed using SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: NCBIM37
Quantitated MeDIP-Seq files were generated using SeqMonk (v0.28.0). Probes were designed over CpG islands (as defined by illingsworth, 2008), then quantified, correcting for total read number and Log2 converted. The result file carries descriptive column headers and is tab-delimited; the relevant columns are: (1) ID; (2) Chromosome; (3) Start; (4) End; (13-20) log2 read count per CGI

molecule: genomic DNA

source_name: Reprogrammed MEF to TS clone

growth_protocol: all cells were grown in standard 70% conditioned TS medium supplemented with heparin and bfgf

extract_protocol:
DNA extracted according to standard protocols. DNA was used for MeDIP analysis as described previously (Senner et al., Stem Cells 2012).
Genomic DNA was fragmented by sonication (Diagenode Bioruptor), and adaptor ligated with paired-end adaptors 5’-PGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG-3’ and 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3’ (* Phosphorothioate group) and the NEBnext library preparation kit. Subsequently immunoprecipitaions with an anti-5-methylcytosine antibody were carried out in duplicate. IP duplicates –prepared for each sample – were pooled and MeDIP DNA libraries were column-purified (MinElute, Qiagen). MeDIP libraries were amplified by PCR for 12 cycles using distinct combinations of primers: PE 1.0 (Fw) AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, and various iPCR tag (Rv) primers (Quail et al, 2012) Amplified MeDIP libraries were  resolved by 2% agarose gel electrophoresis, and DNA fragments within the 300-500 nt range were cut out and DNA was purified using the Qiagen Gel extraction kit. 5mC immuno-precipitation efficiency was confirmed by analysing ES and TS  cell MeDIP pre- and post-amplification libraries by quantitative PCR for candidate loci (Elf5, Nanog). Library concentration was determined using KAPA Illumina SYBR Universal Lid Q Kit (ANACHEM) and by Bioanalyzer.

treatment_protocol: Doxycycline was added to induce expression of virally transduced transgenes in 4F MEFS to generate all 5 iTSC clones

tag: cell line

value: 4F iTSC clone E

tag: condition

value: Reprogrammed MEF to TS clone


title: WT1


title: ER Ribosome profiling 2 h Tg 1

value: embryonic fibroblast


title: 4F iTSC clone D

value: 4F iTSC clone D


title: 4F iTSC clone C

value: 4F iTSC clone C


title: ER Ribosome profiling 0.5 h Tg 1

value: 0.5 h Tg

value: Ribosome profiling


title: 4F iTSC clone A

value: 4F iTSC clone A


title: 4F iTSC clone B

value: 4F iTSC clone B


title: 4F MEFs

source_name: Mouse Embryonic Fibroblasts

value: 4F MEFs

value: Mouse Embryonic Fibroblasts - control


title: TS EGFP

source_name: Trophoblast Stem Cells

value: TS EGFP

value: Trophoblast Stem Cells - control


title: non-infected 6

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
base calling and de-multipexing using CASAVA version 1.8
Alignment withTopHat2 version v2.0.11 and Bowtie2 version 2.2.1 using the default parameters
Quantification with Partek Genomics Suite V6.6
reads mapped to each transcript against the RefSeq mm10 annotation download on April 2014
Normalization using DeSeq2
Genome_build: mm10

source_name: Mono-MDSC

growth_protocol: influenza infection

extract_protocol:
RNAeasy Plus mini kit (Qiagen)
ScriptSeq v2 Library preparation kit (Epicentre); polyT oligo attached magnetic beads

tag: Sex

value: female

tag: age

value: 10-14 weeks

tag: organ

value: spleen

tag: state

value: Resting

value: Monocytic myeloid-derived suppressor cells


title: non-infected 9


title: infected spleen 2

value: Activated


title: infected spleen 8


title: infected lung 7

value: lung


title: infected spleen 5


title: non-infected 3


title: NIPBL_Mut2

value: NIPBL-haploinsufficient

value: Mouse embryonic fibroblasts


title: infected lung 4


title: Exp2 C2 iMEFs Ezh2 -/-, replicate 2

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

data_processing:
Experiment 1 : Single-end reads were mapped on the Mouse reference genome (mm9) Using the Bowtie software (v0.12.8, Langmead B. Et al. 2012) Allowing one mismatch in the seed (28bp) And reporting one location in case of multiple mapping hits.
Experiment 1 : Peak calling for each sample was done with MACS2 2.0.10 with default parameters for histone analysis, By specifying a fragment size of 150bp and the Input DNA as Control.
Experiment 2 : Single-end 100bp reads were mapped on the Mouse reference genome (mm9) Using the Bowtie2 software (v2.1.0, Langmead B. Et al. 2012) Allowing one mismatch in the seed (22bp) And reporting one location in case of multiple mapping hits.
Experiment 2 : PCR duplicates were then removed using samtools
Experiment 2 : Peak calling for each sample was done with CCAT 3.0 with default parameters for histone analysis, By specifying a fragment size of 150bp and the Input DNA BAM file as Control.
Genome_build: mm9
Supplementary_files_format_and_content: bed files are the output of peak calling.
Supplementary_files_format_and_content: BigWig files are generated with HOMER (v3.17)

source_name: C2 iMEFs Ezh2 -/-

growth_protocol: Sample 1 to 16 iMEF cells grown in DMEM medium supplemented with 10% FCS, 100 mM non essential amino acids, 1 mM L-Glutamine.

extract_protocol: DNA was extracted by phenol-chloroform and precipitated. Experiment 1 : Sequencing was performed on SOLiD 5500 single reads 75bp. Experiment 2 : Sequencing was performed on Hi-Seq 2500 Illumina single reads 100bp.

treatment_protocol: 4-hydroxytamoxifen was used at a final concentration ranging from 1 nM to 1 μM

value: iMEFs

tag: antibody

value: H3K27me3 ChIP (clone 7b11)


title: WT2

value: wild type

tag: cell type


title: infected lung 1


title: Exp2 C2 iMEFs Ezh2 WT/WT, replicate 2

source_name: C2 iMEFs Ezh2 WT/WT


title: Exp2 C2 iMEFs Ezh2 pre-rescue condition, replicate 1

source_name: C2 iMEFs Ezh2 pre-rescue condition


title: Exp2 C2 iMEFs Ezh1 pre-rescue condition, replicate 1

source_name: C2 iMEFs Ezh1 pre-rescue condition


title: Exp2 C2 iMEFs Ezh2 WT/WT, replicate 1


title: Exp2 C2 iMEFs Ezh2 -/-, replicate 1


title: Exp2 C2 iMEFs Ezh2 WT/WT


title: RNA-seq DCR_KO-miR291

first: Gokhul

middle: Krishna

last: Kilaru

state: TEXAS

address: 6000 Harry Hines Boulevard

department: Department of Neuroscience

institute: University of Texas Southwestern Medical Center

data_processing:
Reads from ChIP-seq were mapped to the mouse genome (NCBI 37, mm9) using the short read, memory efficient aligner Bowtie (version-0.12.7) with option -p 8 --chunkmbs 256 -a --best --strata -m 20
Unique reads are considered by instructing Bowtie to refrain from reporting any alignments for reads that have more than 20 reportable alignments
Read densities and regions of statistically significant enrichment (“peaks”) were determined using MACS (Model-Based Analysis of ChIP-Seq, version 1.4.2) using default settings (Zhang et al., 2008). Peaks of ChIP-seq enrichment with p < 1e-9, relative to input, were considered significant and included in subsequent analyses. For the read density plots around TSSs ngs.plot software (Shen et al., 2014) was used with the options "-G mm9 -R tss -L 5000 -MW 3 -D refseq"
Reads from RNA-seq were mapped to the mouse genome (NCBI 37, mm9) using Tophat (v2.0.8) with option --mate-inner-dist 160 --coverage-search --microexon-search --max-multihits 20. Aligned reads and coverage tracks were then visualized on a local mirror of the UCSC Genome Browser.
Genome_build: mm9

source_name: mouse embryonic stem cells

growth_protocol: ES cells were cultured on irradiated mouse embryonic fibroblasts (MEFs). Before ChIP or RNA sample preparation MEFs were removed with MEF removal microbeads (Miltenyi) and cells plated on gelatinized plates overnight.

extract_protocol:
For ChIP 20 million ES cells were fixed, lysed and sonicated to 200 base pairs. Then, histone-DNA complexes were isolated with antibody.  For RNA-Seq RNA was isolated from ~10^6 cells using the RNAzolRT reagent
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~200-400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.                                    For RNAseq libraries were prepared either with the TruSeq RNA sample prep kit or the Directional RNA Sample prep kit (Illumina) and sequenced on a GAIIx.

value: mouse embryonic stem cells

value: DCR KO

tag: chip antibody


title: RNA-seq DCR_KO_Rep2


title: RNA-seq DCR_Flox-MOK

value: DCR Flox


title: RNA-seq DCR_KO_Rep1


title: RNA-seq DCR_Flox_Rep2


title: RNA-seq DCR_KO-MOK


title: Cytosol Ribosome profiling 4 h Tg 1

value: embryonic fibroblast

tag: treatment

value: 4 h Tg

tag: compartment

value: Cytosol

value: Ribosome profiling


title: RNA-seq DCR_Flox_Rep1


title: H3K27me3_ChIPSeq DCR_KO_H3K27ME3

value: H3K27me3 (Millipore, 07-449)


title: H3K27me3_ChIPSeq DCR_Flox_H3K27ME3


title: Input_DNA DCR_Flox_input-2


title: NIPBL_Mut1


title: Suz12_ChIPSeq DCR_KO_suz12

value: Suz12 (Cell Signaling, D39F6)


title: H1-15

city: New York

first: Christoph

last: Hafemeister

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

data_processing:
Reads aligned to the O. sativa Nipponbare - release 7 of the MSU Rice Genome Annotation Project reference genome - including 12 rice chromosomes, chloroplast, mitochondrion, Syngenta pseudomolecule, and the unanchored BAC pseudomolecule using Tophat version 2.0.6, discarding low-quality alignments (quality score below 1)
Counting number of reads that uniquely mapped to genes using HTSeq version 0.6.1
Normalization: compensation for variable sequencing depth between samples using the median-of-ratios method of DESeq2 version 1.6.3 and variance stabilizing transformation provided by the same package. The minimum expression value was subtracted so that zero read counts had an expression value of zero.
Genome_build: Release 7 of the MSU Rice Genome Annotation Project reference genome
Supplementary_files_format_and_content: tab-delimited text files with normalized read counts for each sample

organism: Oryza sativa

source_name: Rice leaf

growth_protocol: The rice plants were grown at IRRI in a 25 x 90 m field divided into equal size rainfed and irrigated sub-fields. The dry season and wet season experiments took place during the months of January-February 2013 and July-August 2013, respectively.

extract_protocol:
Frozen leaf tissue was ground manually with a mortar and pestle cooled in liquid nitrogen. Total RNA was extracted from about 200 to 400 µL of ground tissue using the RNeasy® Plant Mini Kit following manufacturer's instructions.
RNA treated with Baseline-ZERO Dnase, depleted of ribosomal RNA using Epicentre® Ribo-Zero Magnetic Kit for plant leaf tissue. Libraries constructed RNA libraries using the Epicentre® ScriptSeqTM v2 RNA-Seq Library Preparation Kit.
RNA-Seq, using HiSeq® 2000, 51 bp paired-end sequencing, with either 6 or 8 libraries per lane

tag: season

value: wet

tag: field

value: rainfed

tag: replicate

value: Palawan

tag: time point

tag: sampling date


title: Suz12_ChIPSeq DCR_Flox_suz12

tag: strain

tag: genotype


title: Jarid2_ChIPSeq DCR_KO_jarid2

value: Jarid2 (Abcam, ab48137)


title: Jarid2_ChIPSeq DCR_Flox_jarid2


title: H1-13


title: H1-14


title: Input_DNA DCR_Flox_input


title: H1-12


title: H1-10


title: H1-8


title: H1-9


title: H1-6


title: H1-5


title: H1-11


title: P1-15

value: irrigated


title: H1-3


title: H1-2


title: H1-4


title: P1-13


title: H1-1


title: P1-14


title: P1-12


title: P1-11


title: P1-10


title: P1-6


title: P1-5


title: P1-4


title: P1-7


title: P1-1


title: P1-8


title: P1-2


title: H2-14

value: Azucena


title: P1-3


title: RNA-seq DCR_Flox-miR291


title: H1-7


title: H2-11


title: H2-12


title: H2-15


title: H2-13


title: H2-8


title: H2-10


title: H2-9


title: H2-7


title: H2-5


title: H2-6


title: H2-3


title: H2-2


title: H2-1


title: P1-9


title: P2-14


title: P2-13


title: P2-10


title: P2-4


title: P2-8


title: P2-3


title: P2-6


title: P2-12


title: P2-9


title: P2-5


title: P2-11


title: P2-2


title: U1-15

value: dry

value: Pandan Wangi


title: U1-13


title: H2-4


title: U1-10


title: P2-1


title: U1-11


title: P2-7


title: U1-14


title: U1-8


title: U1-7


title: U1-5


title: U1-6


title: U1-2


title: U1-3


title: U1-4


title: U1-1


title: Z1-15


title: P2-15


title: Z1-14


title: Z1-9


title: Z1-13


title: Z1-12


title: U1-12


title: Z1-11


title: U1-9


title: Z1-5


title: Z1-7


title: Z1-3


title: Z1-4


title: U2-14


title: Z1-2


title: U2-12


title: Z1-6


title: U2-9


title: U2-11


title: U2-7


title: U2-15


title: U2-10


title: U2-6


title: U2-8


title: U2-4


title: U2-5


title: U2-3


title: Z1-8


title: U2-2


title: U2-1


title: Z1-10


title: Z2-15


title: Z2-14


title: Z1-1


title: Z2-12


title: Z2-11


title: U2-13


title: Z2-9


title: Z2-8


title: Z2-13


title: Z2-7


title: Z2-10


title: Z2-6


title: Z2-4


title: Z2-2


title: J1-14


title: J1-13


title: J1-11


title: Z2-1


title: J1-10


title: J1-15


title: J1-9


title: J1-12


title: J1-8


title: J1-7


title: J1-3


title: J1-5


title: J1-2


title: J1-6


title: J1-4


title: Z2-5


title: Z2-3


title: N1-14


title: N1-13


title: N1-11


title: N1-12


title: N1-10


title: N1-8


title: N1-6


title: N1-5


title: N1-9


title: N1-7


title: N1-2


title: N1-1


title: N1-3


title: J2-14


title: J2-11


title: J2-12


title: J2-13


title: J2-9


title: N1-15


title: J1-1


title: J2-8


title: J2-7


title: J2-5


title: J2-4


title: J2-3


title: J2-6


title: J2-2


title: J2-1


title: N1-4


title: N2-12


title: N2-11


title: N2-14


title: N2-9


title: N2-10


title: N2-8


title: N2-13


title: N2-7


title: N2-4


title: N2-3


title: N2-6


title: N2-2


title: T1-15


title: T1-14


title: T1-12


title: T1-13-bis


title: T1-11


title: T1-10


title: T1-9


title: N2-15


title: T1-8


title: T1-7


title: T1-2


title: T1-4


title: T1-3-bis


title: N2-1


title: N2-5


title: J2-15


title: T1-5


title: X1-5


title: X1-13


title: X1-3


title: T2-14


title: X1-11


title: X1-10


title: X1-15


title: X1-8


title: X1-1


title: T2-15


title: X1-14


title: T2-13


title: X1-9


title: X1-6-bis


title: X1-4


title: T2-12


title: T2-10


title: X1-2


title: T1-1


title: T2-8


title: T2-7


title: T2-9


title: X1-7-bis


title: T2-5


title: T2-6


title: T2-4


title: T2-11


title: T2-3


title: X2-5


title: X2-11


title: X2-10


title: X2-12


title: X2-8


title: X2-7


title: T2-1


title: X2-14


title: X2-6


title: LacO-roX2 rep2

city: Freiburg

first: Fidel

last: Ramirez

address: Stübeweg 51

department: Bioinformatics Unit

institute: Max Planck Institute for Immunobiology and Epigenetics

description: MOF ChIP-seq

data_processing:
Illumina Casava1.8 software was used for basecalling.
ChIP-seq reads were aligned to the Drosophila dm3 genome assembly using bowtie2 (v. 2.2.3) with standard options
deepTools 1.5.9.1 bamCompare was used compute log2 ratios of ChIP/input using 10bp bins. Scaling factors were computed using the total number of reads. The output is bigwig files.
Genome_build: dm3
Supplementary_files_format_and_content: bigwig files

organism: Drosophila melanogaster

growth_protocol: Flies (Drosophila melanogaster) were reared on a standard Drosophila medium at 25°C and 70% relative humidity on a 12h dark/12h light cycle. Transgenic flies carrying an autosomal roX2 allele downstream of lacO (lacO-roX2+p) were generated by integration of a 256-mer lac operon array followed by the roX2 coding sequence downstream of its putative endogenous promoter [the genomic region between roX2 (CR32665) and the last exon of the upstream CG11695 gene] into y1 M{vas-int.Dm}ZH-2A w*; M{3xP3-RFP.attP}ZH-86Fb embryos (Bloomington stock #24749) carrying an attP docking site at position 86F8 on chromosome arm 3R and codon-optimized ΦC31 integrase driven in the germline by the vasa promoter

extract_protocol:
For each replicate, 170 male larvae with roX2 inserted into the ectopic 86F8 site were grinded to powder in mortar with liquid nitrogen, and dounced with pestle B in NE buffer (15mM Hepes pH 7.6, 10mM KCl, 5mM MgCL2, 0.1mM EDTA, 0.5mM EGTA, 350mM sucrose, 0.1% Tween, 1mM DTT, protease inhibitors). The nuclei were fixed in 1.8% formaldehyde for 20 min at RT. After quenching for 5 min at RT with 125 mM glycine, nuclei was further dounced for 30 times. The nuclei was then washed 3x 5min in RIPA (25 mM HEPES pH 7.6, 150mM NaCl, 1 mM EDTA, 1% Triton-X 100, 0.1% SDS, 0.1% DOC, protease inhibitors). The nuclei was broken with a Branson 250 sonicator at duty cycle 40, intensity 3, and chromatin was sheared by a Covaris S200 sonicator at duty cycle 10, intensity 200 for 30 min.
For immunoprecipitation, MOF antibody was added and incubated over night at 4°C. Immunocomplexes were pulled down by protein A-Sepharose. The bead was washed by 4x RIPA buffer, 1x LiCl buffer (10 mM Tris at pH 8, 0.25 M LiCl, 0.5% NP-40, 0.5% DOC, 1 mM EDTA), and 3x TE buffer. The beads were resuspended in TE buffer. The input chromatin and the beads were shaked at 65°C O/N. After 30 min incubation at 37°C with RNaseA (0.2 mg/ml), followed by 2 hr Proteinase K digestion (0.05 mg/ml) at 50°C, DNA was purified using Minelute columns (Qiagen). Pair-end sequencing libraries were prepared using NEBNext® ChIP-Seq library prep reagent kit, according to manufacturer’s instruction. Samples were sequenced using Illumina HiSeq 2500.

tag: developmental stage

value: third instar

tag: tissue

value: whole larva

value: male

value: in house MOF antibody raised in rabbit


title: input lexO-roX2_rep1

description: ChIP-seq chromatin input

extract_protocol:
For each replicate, 170 male larvae with roX2 inserted into the ectopic VK33 site were grinded to powder in mortar with liquid nitrogen, and dounced with pestle B in NE buffer (15mM Hepes pH 7.6, 10mM KCl, 5mM MgCL2, 0.1mM EDTA, 0.5mM EGTA, 350mM sucrose, 0.1% Tween, 1mM DTT, protease inhibitors). The nuclei were fixed in 1.8% formaldehyde for 20 min at RT. After quenching for 5 min at RT with 125 mM glycine, nuclei was further dounced for 30 times. The nuclei was then washed 3x 5min in RIPA (25 mM HEPES pH 7.6, 150mM NaCl, 1 mM EDTA, 1% Triton-X 100, 0.1% SDS, 0.1% DOC, protease inhibitors). The nuclei was broken with a Branson 250 sonicator at duty cycle 40, intensity 3, and chromatin was sheared by a Covaris S200 sonicator at duty cycle 10, intensity 200 for 30 min.
For immunoprecipitation, MOF antibody was added and incubated over night at 4°C. Immunocomplexes were pulled down by protein A-Sepharose. The bead was washed by 4x RIPA buffer, 1x LiCl buffer (10 mM Tris at pH 8, 0.25 M LiCl, 0.5% NP-40, 0.5% DOC, 1 mM EDTA), and 3x TE buffer. The beads were resuspended in TE buffer. The input chromatin and the beads were shaked at 65°C O/N. After 30 min incubation at 37°C with RNaseA (0.2 mg/ml), followed by 2 hr Proteinase K digestion (0.05 mg/ml) at 50°C, DNA was purified using Minelute columns (Qiagen). Pair-end sequencing libraries were prepared using NEBNext® ChIP-Seq library prep reagent kit, according to manufacturer’s instruction. Samples were sequenced using Illumina HiSeq 2500.

tag: Sex

value: none (input)


title: X2-9


title: LacO-roX2 rep1

description: MOF ChIP-seq


title: X2-3


title: X2-4


title: input lexO-roX2_rep2

description: ChIP-seq chromatin input


title: X2-2


title: MNase MSL3 RNAi B

description: Mnase digestion

data_processing:
Basecalls performed using Illumina bcl2fastq 1.8.83
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3

source_name: cultured fruit fly cells

growth_protocol: S2 cells were cultured in Schneider's medium (Gibco) supplemented with 10% FCS and 0.05% Pluronic F-68 (Sigma-Aldrich) on shaking incubators at 27C at a density of 2-16 million/ml.

extract_protocol: Cells were permeabilized with NP-40. The chromatin was digested with microcccal nuclease (MNase) at 25¼C for 10 minutes. Digested chromatin was then analysed on an agarose gel to reveal the digestion pattern. The digestion pattern of each sample was exactly the same. The MNase digestion was stopped by addition of EDTA, NaCl and SDS to a final concentration of 20 mM, 150 mM and 1% respectively. The samples were placed on ice during handling to ensure that the MNase digestion was halted completely. The chromatin was then de-crosslinked overnight at 65¼C overnight in TE buffer. The sample was treated with RNaseA (0.2 mg/ml) for 30 minutes at 37¼C, and with Proteinase K (0.05 mg/ml) for 2 hours at 50¼C. Finally, DNA was purified using Minelute columns (Qiagen) and eluted in nuclease-free water. The eluted DNA was then analysed with the E-Gel Pre-cast Agarose Gels system (Invitrogen). Bands at positions corresponding to 150 bp, 300 bp, 450 bp, represented mono- di and tri-nucleosomes, respectively. The 150 bp fragment was purified from the E-gel according to manufacturers specifications and used to generate the library for the Illumina paired-end sequencing. To minimize the effect of PCR artefacts, only 3 cycles of PCR were performed in the library generation procedure.

tag: cell line

tag: restriction enzyme(s)

value: biological 2


title: MNase MSL2 RNAi B

description: Mnase digestion

data_processing:
Basecalls performed using Illumina bcl2fastq 1.8.82
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: MNase MSL3 RNAi A

description: Mnase digestion

data_processing:
Basecalls performed using Illumina bcl2fastq 1.8.81
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3

value: biological 1


title: X2-13


title: X2-1


title: MNase MSL2 RNAi A

description: Mnase digestion

data_processing:
Basecalls performed using Illumina bcl2fastq 1.8.80
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: T2-2


title: X2-15


title: X1-12


title: 4C-seq: ind9_S2_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.78
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3

extract_protocol: 4C-seq in S2 and Kc cells was carried out as described by Splinter et al.63 with minor modifications as following: 50-100 million S2 cells or Kc cells, fixed, were used for two biological replicates. DpnII (NEB) was used as the primary and Csp6I (ThermoScientific) as the secondary restriction enzyme. For each viewpoint, two 50ul PCR reactions (8 cycles with 5C annealing temperature, followed by 18 cycles with 63C) with 160ng of template each were prepared and the combined products cleaned up by a one-step purification using 1.6 volumes of AMPure XP magnetic beads (Beckmann Coulter) according to manufacturer's instructions. These viewpoint libraries were eluted in 20ul elution buffer (10mM Tris-HCl pH 8.5) and the molarities for each individual sample were estimated using the bioanalyzer DNA 7500 kit (Agilent Technologies). All different viewpoint libraries for one biological replicate were mixed equimolarly and sequenced on separate lanes on an Illumina HiSeq2500 DNA sequencer.

value: DpnII, Csp6I


title: 4C-seq: ind22_S2_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.72
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind4_S2_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.75
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind5_S2_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.76
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind25_S2_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.77
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind15_S2_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.69
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind6_S2_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.74
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind23_S2_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.73
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind16_S2_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.71
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind10_S2_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.60
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind19_S2_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.66
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind21_S2_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.68
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind14_S2_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.64
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind20_S2_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.67
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind13_S2_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.63
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind11_S2_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.61
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind9_S2_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.59
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: MNase GST

description: Mnase digestion

data_processing:
Basecalls performed using Illumina bcl2fastq 1.8.79
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind27_S2_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.55
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind25_S2_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.54
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind6_S2_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.58
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind4_S2_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.56
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind27_S2_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.70
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind23_S2_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.53
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind5_S2_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.57
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind12_S2_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.62
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind21_S2_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.51
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind22_S2_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.52
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind18_S2_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.65
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind11_S2_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.43
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: Emb_MO-Tbx5a_48hpf [miRNA-seq]

city: Pisa

first: Romina

last: D'Aurizio

state: PI

address: via Moruzzi 1

department: IIT

country: Italy

institute: CNR

description:
smallRNAseq after Mo-MOTbx5a injection
processed data; column '3' in 'seqRPM.txt'

data_processing:
Basecalls performed using GA-Pipeline v1.5
Sequenced reads were filtered for low quality and trimmed for 3' adaptor sequence.
Reads were algned to mirBase v16.0 using CLC-workbench
Expression values were normalized to reads per million (rpm)
Supplementary_files_format_and_content: tab-delimited text file includes normalized read count per sample

organism: Danio rerio

source_name: Embryos, MO-Tbx5a, 48hpf

growth_protocol: Zebrafish was raised and maintained under standard laboratory conditions (Westerfileld M zebrafish book) in Zebrafish Housing Systems (Tecniplast, Varese, Italy).

extract_protocol:
For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol (llumina Inc., San Diego, USA)
cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis (Invitrogen) and eluted into 300 µl elution buffer (Illumina) for at least 2 hours at room temperature, to enrich for molecules containing inserts in the range of 18–33 nt.

treatment_protocol: 1-cell stage zebrafish embryos were microinjected with 1,5 ng of morpholino against dre-Tbx5a (MO-Tbx5a) or with 1,5 ng of control morpholino

tag: strain background

value: AB

tag: infected with

value: embryo


title: 4C-seq: ind5_Kc_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.39
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3

value: Kc


title: 4C-seq: ind23_Kc_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.35
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind21_Kc_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.33
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: Rtf1_KD_rep2

city: Yokohama

first: Yuki

last: Yamaguchi

address: 4259 Nagatsuta

department: Life Science and Technology

country: Japan

institute: Institute of Science Tokyo

description: Rtf1 knockdown: replicate 2

data_processing:
Basecalling and trimming of adaptor sequence were performed using Torrent Suite Software.
Sequenced reads were mapped to the human genome GRch37.p9 and reads per kilobase of transcript per million reads mapped (RPKMs) were calculated using CLC Genomics Workbench 6.5.1 with default settings.
Genome_build: GRch37.p9
Supplementary_files_format_and_content: an Excel file including RPKM values for all the samples

organism: Homo sapiens

source_name: adenocarcinoma

extract_protocol:
Total RNAs were prepared at 4 or 7 days post-infection using the AGPC method.
Following the removal of rRNA using the RiboMinus Eukaryote Kit (Life Technologies), libraries were constructed using the Ion Total RNA-Seq Kit (Life Technologies).

treatment_protocol: HeLa cells were infected with recombinant lentivirus expressing no shRNA or expressing one of functionally validated shRNAs and selected in the presence of 5 µg/ml Blasticidin for pLenti6-based vectors or 1 µg/ml Puromycin for pRSI9-based vectors.

value: HeLa cells

value: Rtf1 knockdown


title: Ski8_KD_rep2

description: Ski8 knockdown: replicate 2

value: Ski8 knockdown


title: 4C-seq: ind20_Kc_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.32
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind19_Kc_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.31
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind13_S2_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.45
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind14_S2_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.46
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind19_S2_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.50
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind25_Kc_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.36
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind18_Kc_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.30
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind15_S2_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.47
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind10_S2_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.42
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: Ski8_KD_rep3

description: Ski8 knockdown: replicate 3


title: 4C-seq: ind9_Kc_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.41
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind4_Kc_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.38
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: Ski8_KD_rep1

description: Ski8 knockdown: replicate 1


title: Paf1_KD_rep3

description: Paf1 knockdown: replicate 3

value: Paf1 knockdown


title: Rtf1_KD_rep3

description: Rtf1 knockdown: replicate 3


title: Emb_MO-Ct_48hpf [miRNA-seq]

description:
smallRNAseq after Mo-Ct injection
processed data; column '4' in 'seqRPM.txt'

source_name: Embryos, MO-Ct, 48hpf

value: MO-C


title: 4C-seq: ind18_S2_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.49
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind16_S2_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.48
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind27_Kc_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.37
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: Rtf1_KD_rep1

description: Rtf1 knockdown: replicate 1


title: 4C-seq: ind12_S2_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.44
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind16_Kc_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.29
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind6_Kc_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.40
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: Paf1_KD_rep1

description: Paf1 knockdown: replicate 1

data_processing:
Basecalling and trimming of adaptor sequence were performed using Torrent Suite Software.
Sequenced reads were mapped to the human genome GRch37.p9 and reads per kilobase of transcript per million reads mapped (RPKMs) were calculated using CLC Genomics Workbench 6.5.1 with default settings.
Genome_build: GRch37.p9
Supplementary_files_format_and_content: an Excel file including RPKM values for all the samples


title: 4C-seq: ind15_Kc_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.28
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind14_Kc_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.27
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind12_Kc_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.26
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: WT_rep2

description: wild-type: replicate 2

value: wild-type


title: Paf1_KD_rep2

description: Paf1 knockdown: replicate 2


title: 4C-seq: ind10_Kc_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.24
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: WT_rep3

description: wild-type: replicate 3


title: 4C-seq: ind4_Kc_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.21
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind25_Kc_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.19
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind5_Kc_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.22
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind19_Kc_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.15
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: S. aureus in LB medium rep2

city: Aalborg East

first: Yijuan

last: Xu

address: Fredrik Bajers vej 7H

department: Department of biotechnology, chemistry and environmental engineering

country: Denmark

institute: Aalborg University

description: The isolated S. aureus from the infection was grown to OD600=0.5 at 37C with shaking (200 RPM)

data_processing:
Basecalls performed using CASAVA version 1.8.2, Hiseq control software: HCS 1.5.15.1/RTA 1.13/SAV 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Then using RNA-seq analysis function in CLC genomic workbench v. 6.5.1, the reads were mapped to SAU060112 genome allowing a minimum length fraction of 80% and minimum similarity fraction of 95%. The resulting output is a table summarizing the read mapping which includes Reads Per Kilobase of exon per Megabase of library size (RPKM), total mapped reads, uniquely mapped reads etc. for each gene.
The RNA-seq analysis output for each sample were used as input for differential gene expression using EdgeR.
Genome_build: SAU060112
Supplementary_files_format_and_content: tab-delimited text files include gene length, unique gene reads, total gene reads, RPKM values, chromosome region start and end for each Sample; The file "Supplementary_file_1.txt" is available on the series record and contains genes identified with differential expression and includes gene description, fold-change values and statistics.

organism: Staphylococcus aureus

source_name: Exponential growing S. aureus in LB medium

extract_protocol:
RNA was extracted with RiboPure Bacteria Kit (Ambion). Genomic DNA was removed with Dnase I treatment. MicroExpress (Ambion) was used to remove ribosomal RNA.
Illumina Truseq RNA sample preparation Kit v2 according to manufacturers instruction. Paired end sequenced using Truseq SBS kit v.3-HS Sequencing kit.

treatment_protocol: The samples were centrifuged at 13 000 g for 2 minutes. The pellets were snap-frozen in liquid nitrogen and stored at -80 C until RNA extraction

tag: genome


title: 4C-seq: ind21_Kc_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.16
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind22_Kc_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.17
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: WT_rep1

description: wild-type: replicate 1


title: S. aureus in LB medium rep1


title: J2-10

data_processing:
Reads aligned to the O. sativa Nipponbare - release 7 of the MSU Rice Genome Annotation Project reference genome - including 12 rice chromosomes, chloroplast, mitochondrion, Syngenta pseudomolecule, and the unanchored BAC pseudomolecule using Tophat version 2.0.6, discarding low-quality alignments (quality score below 1)
Counting number of reads that uniquely mapped to genes using HTSeq version 0.6.1
Normalization: compensation for variable sequencing depth between samples using the median-of-ratios method of DESeq2 version 1.6.3 and variance stabilizing transformation provided by the same package. The minimum expression value was subtracted so that zero read counts had an expression value of zero.
Genome_build: Release 7 of the MSU Rice Genome Annotation Project reference genome
Supplementary_files_format_and_content: tab-delimited text files with normalized read counts for each sample

value: wet

value: rainfed

value: Azucena


title: S. aureus in LB medium rep3


title: 4C-seq: ind9_Kc_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.23
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind14_Kc_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.11
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind16_Kc_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.13
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind18_Kc_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.14
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind12_Kc_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.10
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: S. aureus infected joint fluid

description: To remove human RNA, MICROBEnrich (Ambion) was used after RNA extraction with Ribopure Bacteria kit

source_name: S. aureus infected joint fluid from prosthetic knee

tag: age

value: 4 days after onset of acute infection


title: 4C-seq: ind6_Kc_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.8
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind10_Kc_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.9
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind20_S2_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.7
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind27_Kc_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.20
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind20_Kc_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.6
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind11_Kc_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.5
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind13_Kc_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.4
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind23_Kc_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.18
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: 4C-seq: ind15_Kc_1

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.12
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3