title: Fat body from juvenile hormone III-treated females rep D

city: Quebec City

first: Christopher

middle: Ian

last: Keeling

state: QC

address: 1055 rue du PEPS

department: Canadian Forest Service

country: Canada

institute: Natural Resources Canada

description: FJFB-D

data_processing:
Quality of the sequences was assessed with FastQC (version 0.10.1)
Sequences were filtered and trimmed with Trimmomatic (version 0.30), and bases with quality < 20 were trimmed from the 3' end of each read.  Sequences were dropped if the final trimmed length was less than 30 bp, or contained only Illumina TruSeq sequence.
SortMeRNA (version 1.9) was used to remove rRNA by comparison to eukaryotic rRNA databases (Burge et al. 2013, Quast et al. 2013) and MPB rRNA sequences (NCBI accessions AF308337 and AF308385).
Expression analysis was completed with Salmon (version 0.6.3) as part of Sailfish (Patro et al. 2014), using the transcriptome assembly described in BioProject PRJNA269763 as the reference. Only the filtered and trimmed RNAseq data that remained as intact pairs were used for counting.
Counts per million (cpm) data from Salmon were analysed in R (version 3.1.2) (R Core Team 2013) using edgeR_3.8.5 (Robinson et al. 2010) and limma_3.22.1 (Ritchie et al. 2015) packages.  Only those transcripts that had expression of greater than 10 cpm in at least four samples kept for further analysis.
Genome_build: The transcript assembly described in TSA accession number GDAR00000000
Supplementary_files_format_and_content: Combined-processed-cpm.txt A tab-delimited text file containing normalized cpms for all samples.
Supplementary_files_format_and_content: Combined-raw-cpm.txt A tab-delimited text file containing raw cpms originating from Salmon for all samples.

organism: Dendroctonus ponderosae

source_name: Fat body

growth_protocol: Adult beetles that emerged at room temperature from naturally infested lodgepole pine bolts were collected and stored in the dark at 4°C on moist KimWipes, and then used within one week.

extract_protocol:
Midguts and fat bodies were disected in insect saline and immediately frozen in liquid nitrogen.  The two tissue types were not collected from the same beetles.  RNA was extracted using Qiagen RNeasy Mini Plant Kit with on-column DNase treatment
RNA libraries were prepared using standard protocols at Canada's Michael Smith Genome Sciences Centre for mRNA purification and indexed paired-end Illumina sequencing.  Indexing was done as a 4-plex, with all sample types for one rep and one tissue combined (e.g. FAFB-A, FJFB-A, MAFB-A, and MJFB-A).

treatment_protocol: Beetles were treated topically on the abdominal venter with 10 micrograms of racemic juvenile hormone III (Sigma-Aldrich) in 0.5 microlitres of HPLC grade acetone, or 0.5 microlitres of HPLC grade acetone alone.  Beetles then kept in groups of 10-15 (separated by sex and treatment) in the dark at room temperature in 60 mL Dixie cups for 8 h.

value: Emerged adult

tag: Sex

value: Female

value: Fat body

tag: treatment

value: 8 h juvenile hormone III treatment


title: Midgut from juvenile hormone III-treated females rep D

status: Public on Feb 04 2016

type: SRA

description: FJMG-D

library_source: transcriptomic

molecule: total RNA

source_name: Anterior midgut

tag: age

tag: tissue

value: Anterior midgut


title: Midgut from acetone-treated females rep D

description: FAMG-D

value: 8 h acetone treatment


title: Fat body from acetone-treated males rep D

description: MAFB-D

value: Male


title: Midgut from juvenile hormone III-treated males rep D

description: MJMG-D


title: Midgut from juvenile hormone III-treated males rep C

description: MJMG-C


title: Fat body from acetone-treated females rep D

description: FAFB-D


title: Midgut from juvenile hormone III-treated males rep B

description: MJMG-B


title: Fat body from juvenile hormone III-treated males rep C

description: MJFB-C


title: Midgut from acetone-treated males rep D

description: MAMG-D


title: Midgut from acetone-treated males rep C

description: MAMG-C


title: Fat body from juvenile hormone III-treated males rep B

description: MJFB-B


title: Fat body from juvenile hormone III-treated males rep A

description: MJFB-A


title: Midgut from acetone-treated males rep B

description: MAMG-B


title: Midgut from juvenile hormone III-treated males rep A

description: MJMG-A


title: Midgut from acetone-treated males rep A

description: MAMG-A


title: maize leaf V12 rep 4

city: Newark

first: Shawn

middle: R

last: Thatcher

state: DE

address: 15 Innovation Way

country: USA

institute: University of Delaware

data_processing:
Illumina Casava software used for basecalling.
Tophat2 was used to map reads to genome and maize transcriptome (version 5a)
Cufflinks was used to discover novel transcripts
Cuffdiff was used to quantify known and novel transcripts
Genome_build: Maize genome version 5a
Supplementary_files_format_and_content: Tab-delimited FPKM expression

organism: Zea mays

source_name: maize leaf V12

growth_protocol: B73 maize plants were grown in a field in Woodland, CA in 2012. Plots were designed utilizing a randomized complete block design, with four biological replicates. Drought stress was applied by withholding water after stage V8.

extract_protocol:
Total RNA was isolated from frozen maize leaf tissues via Qiagen RNeasy kit for total RNA isolation (Qiagen, Valencia, California USA).
Standard Illumina

tag: genotype

tag: developmental stage

tag: growth condition

value: well-watered

value: leaf


title: Fat body from acetone-treated males rep C

description: MAFB-C


title: Fat body from acetone-treated males rep A

description: MAFB-A


title: maize ear V12 rep 1

source_name: maize ear V12

value: ear


title: Fat body from acetone-treated males rep B

description: MAFB-B


title: Midgut from juvenile hormone III-treated females rep B

description: FJMG-B


title: Fat body from juvenile hormone III-treated females rep C

description: FJFB-C


title: Midgut from juvenile hormone III-treated females rep A

description: FJMG-A


title: Midgut from juvenile hormone III-treated females rep C

description: FJMG-C


title: Fat body from juvenile hormone III-treated males rep D

description: MJFB-D


title: Midgut from acetone-treated females rep C

description: FAMG-C


title: Fat body from juvenile hormone III-treated females rep A

description: FJFB-A


title: Fat body from juvenile hormone III-treated females rep B

description: FJFB-B


title: Fat body from acetone-treated females rep B

description: FAFB-B


title: Midgut from acetone-treated females rep B

description: FAMG-B


title: Fat body from acetone-treated females rep C

description: FAFB-C


title: Midgut from acetone-treated females rep A

description: FAMG-A


title: Fat body from acetone-treated females rep A

description: FAFB-A


title: BLRP Control ChIP-Seq 2

city: Los Angeles

first: Thomas

middle: A

last: Vallim

state: CA

address: 650 Charles E. Young Drive South, A2-237 CHS

institute: UCLA

description: formaldehyde cross-linked

library_source: genomic

data_processing:
For ChIP-Seq samples, reads were aligned to the mm10 genome in Galaxy using Bowtie2 with default parameters. Aligned files were analyzed with HOMER (http://homer.salk.edu/homer/) to find peaks (MafG peaks were called relative to control using default findPeaks parameters excpet -P 0.00001, -size 200 and -F 10) and perform motif analysis (findMotifsGenome.pl). Motif analysis for the top 20 thousand peaks utilized descending peak scores for ranking.
Genome_build: mm10
Supplementary_files_format_and_content: Processed files are in the HOMER peak file format that is similar to BED file formatting. Each row represents a called peak relative to the input control. Genomic coordinates are relative to mm10 (NCBI 38) mouse assembly.

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse Liver

extract_protocol:
Mice were first euthanized with Isoflourane, livers liver was then macerated in PBS containing 1% formaldehyde and protease inhibitor cocktail 1 (PIC1, comprised of 1μg/ml leupeptin, 1.4μg/ml pepstatin, 0.2mg/ml PMSF (Sigma), 1mM EGTA, 1mM EDTA) for 10 minutes with gentle rotation at room temperature. Crosslinking was then stopped by the addition of glycine (0.125M) and samples were further incubated for 5 minutes at room temperature. Fixed livers were then placed on ice and then centrifuged (2,000 x g for 10 minutes) and the pellet resuspended in 8ml of PBS containing protease inhibitor cocktail. Resuspended pellets were gently homogenized and again centrifuged as above. The resulting pellet was resuspended in 5ml lysis buffer (5mM PIPES, pH 8.0, 85mM KCl, 0.5% NP-40 alternate) supplemented with protease inhibitor complex 2 (PIC2, 10μg/ml leupeptin, 5μg/ml pepstatin, 0.2mg/ml PMSF, 50μg/ml ALLN, Sigma). Nuclei were released after 30 strokes using a Dounce homogenizer and collected after centrifugation as above. Pellets were resuspended in 6ml homogenization buffer (10mM HEPES, pH 7.6, 25mM KCl, 1mM EDTA, 1mM EGTA, 1M Sucrose, 10% glycerol, 0.15mM spermine, supplemented with PIC1) and layered onto 3ml of the same buffer. Nuclei were then pelleted at 26,000rpm for 1 hour (Beckman SW41 rotor) and stored at -80ºC. Nuclear pellets were re-suspended in 0.3ml nuclear lysis buffer (50mM Tris pH 7.6, 10mM EDTA and 1% SDS), and diluted with 0.6ml immunoprecipitation (IP) dilution buffer (0.01% SDS, 1.1% Triton x100, 167mM NaCl, 16.7mM Tris pH 7.6, 1.2mM EDTA). For sonication, 0.3ml (1/3) of nuclear lysate was sonicated for 25-30 cycles 30 seconds on 30 seconds off at 4ºC with BioRuptor twin sonicator (Diagenode). Sonicated chromatin was then further diluted to 1ml with IP dilution buffer, which is sufficient for three ChIP reactions. The BLRP antibody (Genescript) was conjugated to Protein G Dynabeads (Life Technologies) in PBS containing 0.5% BSA overnight at 4ºC with gentle rotation. Sonicated DNA (0.33ml made up to 1ml in IP dilution buffer) was then incubated overnight with Protein G-BLRP beads at 4ºC with gentle rotation. For input samples, 10% was used. Samples were then washed twice with wash buffer I (20mM Tris, pH 7.4, 150mM NaCl, 0.1% SDS, 1% Triton X100, 2mM EDTA), three times with alternate wash buffer III (10mM Tris, pH 7.4, 250mM LiCl, 1% NP-40 alternate, 0.7% Deoxycholate, 1mM EDTA), two washes with 0.2% Triton X100 TE buffer and two final washes with 50mM NaCl containing TE buffer. Chromatin was recovered and DNA from IP and input was isolated after reverse crosslinking (incubating at 65ºC overnight in 0.3M NaCl and Proteinase K digestion) and DNA purified using gel/PCR extraction kit (Clontech).
ChIP-Seq: Sequencing libraries were prepared from collected DNA by blunting, A-tailing, adapter ligation using the Kapa Library Prep kit according to manufacturers instructions.

tag: strain

value: Ad BLRP Control

tag: chip (antibody)

value: Avi-tag (Vendor:Genescript,  cat# A01738)


title: BLRP Control ChIP-Seq 1

description: formaldehyde cross-linked


title: BLRP MafG ChIP-Seq 1

description: formaldehyde cross-linked

value: Ad BLRP MAFG


title: 3-way 4C multiplexed library  21 baits (ms_trip_mesc_II)

city: Rehovot

first: Pedro

last: Olivares-Chauvet

address: 234 Hertzl Street

department: Department of Computer Science and Applied Mathematics/Department of Biological Regulation

country: Israel

institute: Weizmann Institute of Science

description: processed data file:  mesc.tadj.gz

data_processing:
Cwalks were assembled using the cwalk pipeline with default parameters
3-way 4C maps were generated using UMI4C pipeline with a few modifications for filtering out fendchains of size three.
reads were mapped using bowtie2 with --reorder --local for cwalks and --reorder --end-to-end for 4C
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: [Cwalk] cadj.annot: annotated adjacency; tab separated text file with adjacency information, linked to cwalks, annotated by the epigenomic features of TADs who are visited by the cwalk; 38 fields  [chr1]: chromosome of side 1  [start1]: chrosomal coordinate of side 1  [chr2]: chromosome of side 2  [start2]: chromosomal coordinate of side 2  [comp]: component (cwalk) id  [amp_i]: phi29 amplification well id  [fid1]: restriction fragment id of side 1  [fid2]: restriction fragment id of side 2  [span1]: span of component 1  [span2]: span of component 2  [seq_batch]: sequencing batch  [n]: number of hops  [trans_n]: number of trans interfaces  [cmer_doms.dist.x]: distance to closest TAD for side 1  [cmer_doms.id.x]: id of domain hosting side 1  [cmer_doms.k4me3.x]: signal of k4me3 in domain side 1  [cmer_doms.size.x]: size of domain side 1  [cmer_doms.tor.x]: time of replication for domain side 1  [cmer_doms.mode.x]: classification of active or inactive for domain side 1  [cmer_doms.dist.y]: distance to closest TAD for side 2  [cmer_doms.id.y]: id of domain hosting side 2  [cmer_doms.k4me3.y]: signal of k4me3 in domain side 2  [cmer_doms.size.y]: size of domain side 2  [cmer_doms.tor.y]: time of replication for domain side 2  [cmer_doms.mode.y]: classification of active or inactive for domain side 2  [dom_n]: number of domains visited by cwalk  [tss_1]: distance to the closest tss from side 1  [k4me3_1]: distance to the closest peak of k4me3 from side 1   [k27me3_1]: distance to the closest peak of k27me3 from side 1  [actenh_1]: distance to the closest active enhancer from side 1  [ctcf_1]: distance to the closest ctcf from side 1  [border_1]: distance to the closest domain border for side 1  [tss_2]: distance to the closest tss from side 2  [k4me3_2]: distance to the closest peak of k4me3 from side 2   [k27me3_2]: distance to the closest peak of k27me3 from side 2  [actenh_2]: distance to the closest active enhancer from side 2  [ctcf_2]: distance to the closest ctcf from side 2  [border_2]: distance to the closest domain border for side 2
Supplementary_files_format_and_content: [3-way 4C]  tadj file: triplet adjacency file ; 6 fields   [chr1]: chromosome side 1  [chr2]: chromosome side 2  [start1]: coordinate side 1  [start2]: coordinate side 2  [mol]: number of different molecules supporting this triplet  [bait]: bait name

source_name: v6.5 mESC

extract_protocol:
Between 25 to 50 x 10e7 cells were used to perform in-nucleus ligation 3C; biotin fill-in was omitted. Briefly, adherent cells (mES) were incubated in the presence of trypsin (Biological Industries 03-053-1) for 8-10 minutes max at 37°C and passed through a cell strainer after harvesting to ensure a single-cell suspension. Cells (including K562 from now on) were washed 1x with phosphate-buffered saline (PBS) and resuspended PBS/FBS 10% and cross-linked in formaldehyde final concentration of 2% for 5 minutes at room temperature. After quenching with 0.125 M glycine and wash with PBS, cells were incubated in permeabilization buffer (10 mM Tris–HCl pH 8, 10 mM NaCl, 0.2 % NP-40 alternative (CALBIOCHEM 492016), Protease Inhibitor Cocktail (P8340 Sigma)) for 60 minutes at 4°C while slowly mixing. Cells were split into 5 M cell aliquots and washed 2x with cold PBS. After the second wash, cell pellets were then flash frozen on liquid nitrogen. Pellets were resuspended on 175.5 µl H2O and 24.5 µl DpnII RE buffer 10x. After addition of 3 µl of 20% SDS (final concentration of 0.3%), cells were incubated for 60 minutes at 37°C while agitating (750 RPM). Triton X-100 20% was added to a final concentration of 1.8% and incubated for 60 min at 37°C. Aliquots were then digested with 15 µl HC DpnII (NEB 50,000 U/ml) ON. Cells were centrifuged for 5 minutes at 600 g and washed 1x with PBS. Incubation of pellets for 20 minutes at 65°C was performed in order to heat-inactivate any DpnII residue. In-nucleus ligation was then performed incubating cells on ligation mix (415 µl H2O, 5 µl BSA (10mg/ml NEB) and 5 µl T4 ligation enzyme NEB (2x106 U/ml)) ON at 16°C.  Cross-link was reversed by incubating aliquots with 10 mg/ml proteinase K (Roche) at 65°C ON followed by the addition of 15 µl of RNase A (Roche) for 45 minutes at 37°C. DNA was purified with AmpureXP SPRI beads 1x (Beckman Coulter; A63881) with two elution rounds of 100 µl each with the aim of size selecting for the high molecular weight portion of the sample.
C-walks. Serial dilutions (1:10) of 3C template were performed to reach a final concentration of 10 pg/µl stock template. REPLI-g single cell kit (Qiagen 150343) protocol for purified genomic DNA was used under the recommendation of the manufacturers with a few modifications. To avoid contamination, all operations before the amplification step were performed under strict hygienic conditions (TC hood), thorough DNA decontamination with DNAZap (ThermoFisher) and UV irradiation of laboratory utensils. A single C-walk amplification reaction consisted of ~1 picogram of 3C material. Typically for 100 reactions, 10 µl of 10 pg/µl stock were mixed into 16.56 µl of sterile TE buffer and denatured at RT for 3 minutes by mixing with buffer D1 (5.83 µl DLB buffer + 20.83 scH2O; both from REPLI-g sc kit). Denaturation of DNA was stopped by addition of 50 µl buffer N1 (7.5 µl Stop solution + 42.5 µl scH2O; both REPLI-g sc kit) and stored on ice. A final Master Mix was prepared by mixing 400 µl of reaction buffer (290 µl Reaction Buffer + 90 µl scH2O + 20 µl Phi29 DNA polymerase; from REPLI-g sc kit). Alternatively, the enzyme can be substituted with NEB Phi29 (M0269S) using the same volume. An aliquot of 5 µl of the Master Mix was taken as negative control. Master Mix and DNA template were then mixed and kept on ice. Aliquots of 5 µl from the Master Mix were split into single wells on 96-well plates and incubated for 2 hours and 50 minutes at 30°C followed by a heat inactivation step of 3 minutes at 65°C. Additional 45 µl of H2O were added to each well after spinning down for a few seconds. The amplified material was cleaned with SPRI beads (2.5x) and resuspended in 100 µl. Phi29-amplified material (300-700 ng per library) was sonicated in Bioruptor (program: 11 cycles of 5s on, 90s off) in 0.1 ml Bioruptor Microtubes (C30010015) to reach a DNA fragment size between 900-1,500 bp, peaking at 1,200 bp. The sonicated DNA (42.5 µl) was then subjected to end-repair reaction (5µl 10x end-repair buffer + 2.5 µl end-repair mix (NEB E6050L)) at 20°C for 30 minutes. The DNA was cleaned with SPRI beads (2.2x) and eluted in 38µl EB. A-tailing reaction was performed with 5 µl NEB buffer 2, 4 µl Klenow (NEB M0212M) and 10 µl dATP 10nM for 30 minutes at 37°C, cleaned with AmpureXP beads (2.2x) and eluted in 30 µl EB. DNA template was ligated with 5 µl Illumina indexed adapters 0.75 µM, 5 µl T4 quick ligase (NEB M2200) and 40 µl 10x ligase buffer for 15 minutes at 25°C. Ligated template was then cleaned with SPRI beads (1.3x) and eluted in 41 µl. Each indexed template was PCR amplified on a final volume of 50 µl with the following reagents: 1 µl dNTPs (10 mM), 2 µl Illumina enrichment primer I and II mix 10mM, 1 µl Pfu ultra II Fusion HS DNA polymerase (Promega 600670), 5 µl Pfu ultra II Fusion buffer (Promega 600670) and 200 ng of Phi29-amplified material. PCR program: 2 minutes 95°C, 14 cycles of 30s 95°C, 30s 55°C, 60s 72°C, final extension of 10 minutes 72°C. Following the PCR reaction, products were cleaned with SPRI beads (1x) and quantified. Libraries were pooled in groups of 8 in equal quantities and ran on a 1% agarose gel, not loading more than 1000 ng per lane. Gel was excised selecting for an 800-1200 bp band. DNA was purified using minelute gel extraction kit (QIAGEN). Samples were then pooled all together and paired-end sequenced using the Illumina platform.
3way 4C.  5-10 µg of 3C template was taken to a volume of 200 µl Elution Buffer (EB, 10mM Tris-HCl, pH 8) and was sonicated at 4°C using Bioruptor; program: 5 cycles of 25s on, 60s off. The sonicated material was inspected by running 10 µl on agarose gel to assure size distribution of 700-900 bp. The sonicated DNA was subjected to end-repair reaction: 20µl 10x end-repair buffer and 10µl end-repair mix (NEB E6050L) were added to the mix and incubated at 20°C for 30 minutes. The DNA was cleaned by SPRI (2.2x) beads and eluted in 76 µl EB. A-tailing reaction was performed with 10 µl NEB buffer 2, 4 µl Klenow (NEB M0212M), and 10 µl dATP 10 nM. Following A-tailing, the 5’ ends of the DNA were dephosphorylated with 2 µl of Alkaline Phosphatase (NEB M0290S) at 50°C for 60 minutes, and the DNA was cleaned with SPRI beads (2x), then eluted in 67 µl EB. The DNA template was ligated in 1,000 ng aliquots with 5 µl Illumina indexed adapters 15 µM (final concentration 0.4 µM), 10 µl quick ligase mix and 80 µl 10x buffer (NEB M2200). To release the non-ligated strand of the adapter, the DNA was denatured at 95°C for 3 minutes, moved immediately to ice and cleaned with SPRI beads (1x) to select for the UMI-4C DNA template . Two nested PCR reactions were used for UMI-4C library construction. The PCR reactions were performed in 50 µl volume with the following reagents: 10 µl GoTaq Flexi buffer (Promega M792A), 3 µl MgCl 25mM (Promega A3511), 25 µM dNTPs, 2 µl bait primer pool 100 µM (final concentration of each bait varies depending on the pool size), 2 µl Illumina enrichment primer II 10 mM (0.4 mM final concentration), 1 µl GoTaq (Promega M3008) and 200 ng UMI-4C DNA template. PCR program: 2 minutes 95°C, 20 cycles of 30s 95°C, 30s 56°C, 60s 72°C, final extension of 5 minutes 72°C. Following the PCR reaction, products were cleaned with SPRI beads (1x). The second PCR reaction was identical to the first with the only difference on the primer pool. Second primer targets a nested sequence of the 4C bait and is attached with the Illumina I adapter. The program for the second PCR reaction was the same but performed for only 18 cycles.The amplified DNA was cleaned with SPRI beads (0.7x) and the size distribution was inspected using Tapestation D1000 (Agilent Technologies). Typically, libraries had a size distribution around 800-1000 bps. The libraries were then pooled to 10 nM and were multiplexed with other libraries for paired-end sequencin

tag: cell line

tag: cell type

value: Embryonic Stem Cells

tag: lineage

value: Embryonic

tag: library

value: 3way 4C


title: C57.1

first: Melinda

middle: K.

last: Duncan

address: 327 Wolf Hall

department: Biological Sciences

description: 30 C57Bl/6 E13.5 Biological replicate 1

data_processing:
Reads were trimmed using CLC Genomics Workbench 5.5.1with the following parameters: Max ambiguous bases:0; Minimum Q>0.01; minimum length 35bp
Reads were aligned to the Mus musculus genome using CLC Genomics Workbench 5.5.1
Unique gene counts were determined using CLC Genomics Workbench 5.5.1
Counts were normalized (CPM and RPKM) using R BioConductor EdgeR
Genome_build: Mus musculus GRCm38.77
Supplementary_files_format_and_content: tab-delimited: mgc gene symbol, ensembl gene ID, MGID, ensembl gene description, cpm, rpkm, raw count

source_name: C57Bl/6 mouse lens

extract_protocol:
RNA was extracted from pooled samples of 30 mouse lenses using the SV total RNA isolation System (Promega, Madison, WI) acording to the manufacturers recommended protocol.
cDNA libraries were constructed from total RNA by  were used to purifying mRNA from the total RNA samples using poly-T oligo attached magnetic beads and converted to a library of template molecules for cluster generation and DNA sequencing using the Illumina® TruSeq™ RNA Sample Preparation Kit v2.  Sequencing performed on a Illumina HiSeq 2500 using single-end 51bp sequencing.

value: wild type

value: Lens

tag: lenses per replicate


title: Prox1.3

description: 30 Prox1 cKO E13.5 Biological replicate 3

source_name: Prox1 cKO mouse lens

value: Prox1 cKO (Prox1 f/f MLR10Cre+)


title: Prox1.1

description: 30 Prox1 cKO E13.5 Biological replicate 1


title: C57.2

description: 30 C57Bl/6 E13.5 Biological replicate 2


title: Cwalk library from 1pg of 3C template amplified with Phi29 (ms_mesc_III)

description: processed data file:  mesc.cadj.annot.gz

value: C-walks


title: Prox1.2

description: 30 Prox1 cKO E13.5 Biological replicate 2


title: 3-way 4C multiplexed library  21 baits (ms_trip_mesc_I)

description: processed data file:  mesc.tadj.gz


title: 5iLAF SSEA4 positive replicate 1 RNA-seq

city: Montreal

first: William

middle: Abraham

last: Pastor

address: 3655 Promenade Sir William Osler

department: Biochemistry

institute: McGill University

data_processing:
Bisulfite Sequencing: Reads were aligned to the hg19 genome using BSMAP (Xi and Li, 2009) by allowing up to 2 mismatches and only retaining reads mapped to one location. Methylation ratio are calculated by #C/(#C+#T) at CG sites.
RNASeq: Reads were first aligned to hg19 gene annotation using Tophat (Trapnell et al., 2009) by allowing up to two mismatches and only keeping reads that mapped to one location. When reads did not mapped to the annotated genes, the reads were mapped to hg19 genome. Number of reads mapping to genes were calculated by HTseq (Anders et al., 2015) with default parameters. Expression levels were determined by RPKM (reads per kilobase of exons per million aligned reads).
Genome_build: hg19
Supplementary_files_format_and_content: Bisulfite seq: Methylation over mapped CGs. Column 1: chromosome; column 2: base; column 3: strand; column 4: C count; column 5: C+T count
Supplementary_files_format_and_content: RNAseq: Readcount by gene

molecule: polyA RNA

organism: Homo sapiens

source_name: 5iLAF SSEA4+ subpopulation UCLA1 hESCs

extract_protocol:
RNA for RNA-seq was extracted using the RNeasy Micro Kit (Qiagen) and quantified using a Nanodrop ND-1000 (Nanodrop)
RNA sequencing libraries were prepared using the Nugen RNA-seq System V2 with 5-100ng starting material.

tag: library type

value: Ovation RNASeq System V2

tag: passage number

value: 16 Passages as Primed cells, 13 passages during and after reversion, 3 passages after initial sorting


title: Cwalk library from 1pg of 3C template amplified with Phi29 (hs_k562_III)

description: processed data file:  k562.cadj.annot.gz

source_name: K-562 cells

value: Lymphoblastoid leukemia

value: Hematopoietic


title: Primed UCLA1 EpiLC day 16 RNA-seq replicate 1

source_name: Primed UCLA1 EpiLC day 16

value: Passage 27, 16 days of culture in EpiLC media


title: Primed UCLA1 EpiLC day 16 RNA-seq replicate 2

value: Passage 28, 16 days of culture in EpiLC media


title: Cwalk library from 1pg of 3C template amplified with Phi29 (hs_mesc_IV)


title: Cwalk library from 1pg of 3C template amplified with Phi29 (hs_k562_II)


title: Cwalk library from 1pg of 3C template amplified with Phi29 (hs_mesc_II)


title: Cwalk library from 1pg of 3C template amplified with Phi29 (hs_k562_I)


title: BLRP MafG ChIP-Seq 2

description: formaldehyde cross-linked


title: Cwalk library from 1pg of 3C template amplified with Phi29 (hs_mesc_I)


title: C57.3

description: 30 C57Bl/6 E13.5 Biological replicate 3


title: 3-way 4C multiplexed library  20 baits (ms_trip_k562_III)

description: processed data file:  k562.tadj.gz


title: Primed UCLA1 EpiLC day 8 bisulfite-seq replicate 1

source_name: Primed UCLA1 EpiLC day 8

value: Passage 27, 8 days of culture in EpiLC media


title: 3-way 4C multiplexed library  20 baits (ms_trip_k562_IV)

description: processed data file:  k562.tadj.gz


title: Primed UCLA1 EpiLC day 0 RNA-seq replicate 1

source_name: Primed UCLA1 EpiLC day 0

value: Passage 27


title: Primed UCLA1 EpiLC day 0 RNA-seq replicate 2

value: Passage 28


title: 3-way 4C multiplexed library  20 baits (ms_trip_k562_I)

description: processed data file:  k562.tadj.gz


title: 3-way 4C multiplexed library  20 baits (ms_trip_k562_II)

description: processed data file:  k562.tadj.gz


title: Cwalk library from 1pg of 3C template amplified with Phi29 (ms_k562_IV)


title: 5iLAF SSEA4 negative UCLA1 EpiLC day 16 RNA-seq replicate 1

source_name: 5iLAF SSEA4 negative UCLA1 EpiLC day 16

value: 16 Passages as Primed cells, 13 passages during and after reversion, 4 passages after initial sorting 16 days of culture in EpiLC media


title: Cwalk library from 1pg of 3C template amplified with Phi29 (ms_k562_I)


title: A2497 infected Hep2 cells 2

city: london

first: Tamsyn

middle: Ruth

last: Derrick

address: keppel street

country: United Kingdom

institute: london school of hygiene and tropical medicine

description: In vitro

data_processing:
"FastQ only" runs were performed on the MiSeq. MiSeq software performs basecalling. Quality of reads was eyeballed using FastQC.
FastQ files were uploaded to Galaxy (https://usegalaxy.org). Quality filtering and adaptor trimming protocol was performed using the workflow described in Majer, Caligiuri and Booth 2013 (A User-Friendly Computational Workflow for the Analysis of MicroRNA Deep Sequencing Data, Methods in Molecular Biology Volume 936, 2013, pp 35-45), with the following alterations: minimum quality score=30, 3' adaptor sequence to trim=TGGAATTCTCGGGTGCCAAGG, Maximum number of bases allowed outside of quality range=1. Trimmed and filtered  FastA files were  downloaded and saved.
FastA files downloaded from Galaxy were uploaded to MiRanalyzer (http://bioinfo5.ugr.es/miRanalyzer/miRanalyzer.php). ALIGNMENT OPTIONS: HOMO SAPIENS HG18; TICK “INPUT DATA IS ADAPTOR TRIMMED”; # MISMATCHES TO KNOWN LIBRARIES: KNOWN MIRNA’S = 0, OTHER KNOWN MIRNA (HOMOLOGOUS) = 0, TRANSCRIBED LIBRARIES (FORWARD) = 1, TRANSCRIBED LIBRARIES (REVERSE) = 1, GENOME = 2; MINIMUM LENGTH (SEED ALIGNMENT LENGTH FOR BOWTIE): KNOWN MIRNA’S = 17, OTHER KNOWN MIRNA (HOMOLOGOUS) = 17, TRANSCRIBED LIBRARIES (FORWARD) = 20, TRANSCRIBED LIBRARIES (REVERSE) = 20, GENOME = 19; MAKE SURE ‘REMOVE ADAPTOR’ BOX IS UNTICKED; OTHER PARAMETERS: MAX NUMBER OF MULTIPLE GENOME MAPPINGS = 5, THRESHOLD OF POSTERIOR PROBABILITY = 0.99; 19, MINIMUM # OF MODELS WHICH PREDICT MIRNA = 3, MINIMUM READ COUNT = 5; LEAVE ‘PREDICT JUST NEW MIR’ AND ‘DETECT JUST KNOWN MIR’ UNTICKED, TICK ‘FAST DETECTION OF NOVEL MIR’, UNTICK ‘INPUT IS IN SOLID COLOUR SPACE’
Aligned reads were downloaded from miRanalyzer. Read count files were loaded into R (http://www.r-project.org).
Differential analysis was performed on read count data using DESeq and EdgeR packages (Bioconductor, R). In both methods miRNA with an average read count across all samples of less than five were excluded from the analyses.
Genome_build: Hg18
Supplementary_files_format_and_content: Matrix of miRNA names against sample names, with a read count for each.

source_name: Cervical epithelial cell line

growth_protocol: Hep2 cells were cultured in MEM (Gibco) supplemented with 1% Gentamycin (Gibco), 10% FCS (Gibco), and 1% L-glutamine (Gibco). For experiments, cells were seeded in 12 well plates at 3x105 cells per well in MEM.

extract_protocol:
Extraction of total RNA and DNA from both clinical swab samples and in vitro derived samples was carried out using Norgen total RNA and DNA purification kit following the manufacturers instructions. For in vitro cultures 300ml lysis buffer (Norgen Biotek) was added to each well and cells were harvested by scraping. The cell lysate from each well was collected and total RNA and DNA purification was carried out immediately. Ocular swabs were thawed and added to a 1.5ml microcentrifuge tube containing 300ml lysis buffer (Norgen Biotek) and were vortexed for one minute. The swab was then discarded and total RNA and DNA purification was carried out immediately. Total RNA was quantified using Qubit® fluorometric quantitation (Life Technologies) and quality was assessed using an Agilent RNA 6000 pico kit on a 2100 Bioanalyzer instrument (Agilent technologies).
Small RNA libraries were prepared using TruSeq® Small RNA sample preparation kit (Illumina), carried out following the manufacturers instructions.

treatment_protocol: Hep2 and HCjE cells were infected with three different ocular derived serovar A Ct strains: A2497, its plasmid cured counterpart (A2497P-) and A/HAR-13. Cells were infected 24 hours after seeding at an MOI of 1 and in the absence of cycloheximide. These strains were provided by Kari and Caldwell (NIAID, NIH) and were used from stock cultures. Ct cultures and mock-infected cells were centrifuged at 1800rpm for one hour to facilitate infection and then incubated at 37°C in 5% CO2. Six replicates were carried out for each biological condition. At 48 hours post-infection, media was removed and cells were washed in 1X PBS prior to total RNA and DNA extraction.

value: Cervical epithelial cell line

tag: c. trachomatis strain


title: A2497 infected Hep2 cells 3

description: In vitro


title: A2497 infected Hep2 cells 1

description: In vitro


title: 5iLAF SSEA4 negative UCLA1 EpiLC day 0 RNA-seq replicate 2

source_name: 5iLAF SSEA4 negative UCLA1 EpiLC day 0

value: 16 Passages as Primed cells, 13 passages during and after reversion, 5 passages after initial sorting


title: 5iLAF SSEA4 negative UCLA1 EpiLC day 8 RNA-seq replicate 1

source_name: 5iLAF SSEA4 negative UCLA1 EpiLC day 8

value: 16 Passages as Primed cells, 13 passages during and after reversion, 4 passages after initial sorting 8 days of culture in EpiLC media


title: 5iLAF SSEA4 positive replicate 2 RNA-seq

value: 16 Passages as Primed cells, 13 passages during and after reversion, 4 passages after initial sorting


title: A2497P- infected Hep2 cells 2

description: In vitro


title: A2497P- infected Hep2 cells 3

description: In vitro


title: A2497P- infected Hep2 cells 1

description: In vitro


title: Primed UCLA1 comparison for UCLA20n

source_name: Primed SSEA4+ UCLA1 hESCs

value: Passage 31


title: 5iLAF UCLA20n RNA-seq technical replicate 1

source_name: 5iLAF SSEA4- subpopulation UCLA20n hESCs

value: Passage 20


title: 5iLAF SSEA4 negative replicate 2 RNA-seq

source_name: 5iLAF SSEA4- subpopulation UCLA1 hESCs

value: 16 Passages as Primed cells, 11 passages during and after reversion, 6 passages after initial sorting


title: 5iLAF SSEA4 negative replicate 4 RNA-seq

value: Ovation RNASeq System V2


title: 5iLAF SSEA4 negative replicate 1 RNA-seq

value: 16 Passages as Primed cells, 11 passages during and after reversion, 5 passages after sorting


title: Primed UCLA1 replicate 4 RNA-seq


title: Primed UCLA1 EpiLC day 8 bisulfite-seq replicate 2

value: Passage 28, 8 days of culture in EpiLC media


title: A2497 infected HCjE cells 3

description: In vitro

source_name: Conjunctival epithelial cell line

growth_protocol: HCjE cells were cultured in Keratinocyte serum free medium (K-sfm) (Gibco) supplemented with 25mg/ml BPE (Gibco), 0.2ng/ml EGF (Gibco), 0.4mM CaCl2 (Sigma) and 5% gentamycin and incubated at 37°C with 5% CO2. For experiments, HCjE cells were seeded in 12 well plates at 3x105 cells per well in K-sfm and switched to 1:1 K-sfm [with supplements]: DMEM/F12 [with 10% FCS, 1% gentamycin and 1% L-glutamine] (Gibco) upon infection 24 hours later.

value: Conjunctival epithelial cell line

value: HCjE


title: 5iLAF SSEA4 negative UCLA1 EpiLC day 8 RNA-seq replicate 2

value: 16 Passages as Primed cells, 13 passages during and after reversion, 5 passages after initial sorting 8 days of culture in EpiLC media


title: 5iLAF SSEA4 negative UCLA1 EpiLC day 0 RNA-seq replicate 1


title: Mock-infected Hep2 cells 3

description: In vitro

growth_protocol: Hep2 cells were cultured in MEM (Gibco) supplemented with 1% Gentamycin (Gibco), 10% FCS (Gibco), and 1% L-glutamine (Gibco). For experiments, cells were seeded in 12 well plates at 3x10(5) cells per well in MEM.


title: Primed UCLA1 replicate 2 RNA-seq

value: Passage 32


title: 5iLAF SSEA4 negative replicate 3 RNA-seq

value: 16 Passages as Primed cells, 13 passages during and after reversion, 3 passages after initial sorting


title: Mock-infected Hep2 cells 2

description: In vitro


title: 5iLAF SSEA4 negative UCLA1 EpiLC day 16 RNA-seq replicate 2

value: 16 Passages as Primed cells, 13 passages during and after reversion, 5 passages after initial sorting 16 days of culture in EpiLC media


title: A2497P- infected HCjE cells 2

description: In vitro


title: Primed UCLA1 EpiLC day 16 bisulfite-seq replicate 2

extract_protocol:
DNA for bisulfite sequencing was extracted using the Quick gDNA Mini-Prep Kit (Zymo) and quantified using the Qubit dsDNA High Sensitivity Kit (Life Technologies).
Bisulfite sequencing libraries were prepared using the Ovation Ultralow Methyl-Seq Library System (Nugen). Unmethylated Lambda phage DNA (NEB) was spiked in at 0.25% input DNA quantity to determine conversion efficiency, which was 99.3%-99.5% for all libraries.

value: Ovation Ultralow Methylseq

value: Passage 28, 16 days of culture in EpiLC media


title: Primed UCLA1 replicate 3 RNA-seq

value: Passage 26


title: A2497 infected HCjE cells 1

description: In vitro


title: Primed UCLA1 EpiLC day 0 bisulfite-seq replicate 2

value: Passage 28


title: Primed UCLA1 EpiLC day 0 bisulfite-seq replicate 1

value: Passage 27


title: Mock-infected Hep2 cells 1

description: In vitro

value: Cervical epithelial cell line


title: Mock-infected HCjE cells 1

description: In vitro


title: 5iLAF UCLA20n RNA-seq technical replicate 2

value: Passage 20


title: A2497P- infected HCjE cells 3

description: In vitro


title: A2497P- infected HCjE cells 1

description: In vitro


title: Primed UCLA1 EpiLC day 16 bisulfite-seq replicate 1

value: Passage 27, 16 days of culture in EpiLC media


title: Mock-infected HCjE cells 3

description: In vitro

growth_protocol: HCjE cells were cultured in Keratinocyte serum free medium (K-sfm) (Gibco) supplemented with 25mg/ml BPE (Gibco), 0.2ng/ml EGF (Gibco), 0.4mM CaCl2 (Sigma) and 5% gentamycin and incubated at 37°C with 5% CO2. For experiments, HCjE cells were seeded in 12 well plates at 3x10(5) cells per well in K-sfm and switched to 1:1 K-sfm [with supplements]: DMEM/F12 [with 10% FCS, 1% gentamycin and 1% L-glutamine] (Gibco) upon infection 24 hours later.


title: 5iLAF SSEA4 negative UCLA1 EpiLC day 0 bisulfite-seq replicate 2

value: 16 Passages as Primed cells, 13 passages during and after reversion, 5 passages after initial sorting


title: Healthy control 147

description: In vivo

source_name: Conjunctival epithelium swab sample

growth_protocol: Two conjunctival swabs (Puritan, USA) were taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) and were kept in the cold chain in the field and subsequently stored at -80°C. The swabs were pooled for RNA and DNA extraction.

value: Conjunctival epithelium


title: Mock-infected HCjE cells 2

description: In vitro


title: Healthy control 121

description: In vivo


title: A2497 infected HCjE cells 2

description: In vitro


title: Follicular trachoma case 156

description: In vivo


title: 5iLAF SSEA4 negative UCLA1 EpiLC day 16 bisulfite-seq replicate 2


title: H2O2_total_H3

city: Zurich

first: Michael

middle: O.

last: Hottiger

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

description: Chromatin of H2O2 treated sample pulled down with anti H3 antibody

data_processing:
library strategy: ChAP-Seq
Illumina
Raw reads were aligned to the human genome (hg38 assembly) using Bowtie in QuasR (R/Bioconductor) using folowing parameters: -m 1 --best --strata; PCR duplicates were removed using samtools -rmdup -s
Wiggle tracks were generated using QuasaR with following comand: qExportWig(), binsize=100
Genome_build: hg38
Supplementary_files_format_and_content: Wiggle tracks indicating reads per 100bp

source_name: A549 lung epithelial cells

growth_protocol: A549 cells were maintained in DMEM supplemented with 1% (v/v) penicillin/streptavidin and 10% (v/v) fetal calf serum

extract_protocol:
A549 cells were fixed in 4% formaldehyde, chromatin was isolated and sonicated after cell lysis with detergent buffer, and ADP-ribosylated fragments pulled-down with GST-RNF164 WWE
Ovation Ultralow Library Prep kit (NuGen)

treatment_protocol: A549 cells were treated with 1mM hydrogen peroxide in PBS + 1mM MgCl2 for 10 min

value: lung epithelial cells

tag: treated with

value: 1mM hydrogen peroxide

tag: chap bait

value: Anti H3 antibody (Abcam, ab1791, GR103451-I)


title: 5iLAF SSEA4 negative UCLA1 EpiLC day 16 bisulfite-seq replicate 1

value: 16 Passages as Primed cells, 13 passages during and after reversion, 4 passages after initial sorting 16 days of culture in EpiLC media


title: Healthy control 162

description: In vivo


title: Healthy control 149

description: In vivo


title: H2O2_input

description: Chromatin of H2O2 treated sample used as input

value: input material


title: 5iLAF UCLA20n bisulfite-seq replicate 2

value: Passage 21


title: 5iLAF SSEA4 negative UCLA1 replicate 2 bisulfite-seq

value: 16 Passages as Primed cells, 11 passages during and after reversion, 6 passages after initial sorting


title: 5iLAF UCLA20n bisulfite-seq replicate 1

value: Ovation Ultralow Methylseq


title: 5iLAF SSEA4 negative UCLA1 EpiLC day 0 bisulfite-seq replicate 1

value: 16 Passages as Primed cells, 13 passages during and after reversion, 4 passages after initial sorting


title: Primed UCLA1 replicate 1 RNA-seq

value: Ovation RNASeq System V2

value: Passage 31


title: 5iLAF SSEA4 negative UCLA1 replicate 1 bisulfite-seq

value: 16 Passages as Primed cells, 11 passages during and after reversion, 5 passages after sorting


title: 5iLAF SSEA4 positive UCLA1 replicate 2 bisulfite-seq


title: Primed UCLA1 replicate 3 bisulfite-seq

value: Passage 33


title: Untreated_total_H3

description: Chromatin of untreated sample pulled down with anti H3 antibody

value: none (untreated)


title: Follicular trachoma case 7

description: In vivo


title: 5iLAF SSEA4 negative UCLA1 replicate 3 bisulfite-seq


title: 5iLAF SSEA4 positive UCLA1 replicate 1 bisulfite-seq


title: Healthy control 112

description: In vivo


title: Untreated_WWE_wt_ChAPSeq

description: Chromatin of untreated sample pulled down with wild-type WWE domain

data_processing:
Library strategy: ChAP-Seq
Illumina
Raw reads were aligned to the human genome (hg38 assembly) using Bowtie in QuasR (R/Bioconductor) using folowing parameters: -m 1 --best --strata; PCR duplicates were removed using samtools -rmdup -s
Wiggle tracks were generated using QuasaR with following comand: qExportWig(), binsize=100
Genome_build: hg38
Supplementary_files_format_and_content: Wiggle tracks indicating reads per 100bp

tag: treatment

value: Untreated

value: RNF164 WWE domain, wt


title: H2O2_WWE_wt_ChAPSeq_2


title: Follicular trachoma case 137

description: In vivo

tag: tissue

value: Conjunctival epithelium


title: Primed UCLA1 replicate 1 bisulfite-seq


title: Follicular trachoma case 19

description: In vivo


title: H2O2_WWE_mut_ChAPSeq

description: Chromatin of H2O2 sample pulled down with mutant WWE domain

value: H2O2 treated

value: RNF164 WWE domain, R163A mut


title: H2O2_WWE_wt_ChAPSeq_1

description: Chromatin of H2O2 treated sample pulled down with wild-type WWE domain


title: Primed UCLA1 replicate 2 bisulfite-seq

value: Passage 32


title: BMI2

status: Public on Feb 03 2016

city: Cambridge

first: A

last: Bhutkar

state: MA

address: 77 Massachusetts Avenue

institute: MIT

description:
B2
A375 BMI1 overexpressing cells

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Sequence reads were trimmed to remove traces of the adapter sequence (AGATCGGAAGAGCGGTTCAGCAGGAATG) using the fastx toolkit (Hannon Lab, CSHL). Reads were mapped to the human transcriptome (UCSC annotation, genome build hg19) using rsem v1.2.12 and bowtie v1.0.1 with default options.
Genome_build: hg19
Supplementary_files_format_and_content: Microsoft Excel file includes estimated read counts (from rsem) per gene for each sample

source_name: A375 BMI1 overexpressing cells

growth_protocol: A375 cells were cultured in DMEM supplemented with 10% Fetal Bovine Serum (FBS).

extract_protocol:
Total RNA was isolated using using TRIzol® Reagent (Invitrogen Life Technologies) and purified with RNAeasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocol.

treatment_protocol: A375 cells were infected with lentiviruses that express GFP or murine BMI1


title: BMI1

description:
B1
A375 BMI1 overexpressing cells


title: GFP2

description:
G2
A375 Control cells, GFP overexpressin

source_name: A375 Control cells, GFP overexpressing cells


title: GFP1

description:
G1
A375 Control cells, GFP overexpressin


title: GFP3

description:
G3
A375 Control cells, GFP overexpressin


title: Follicular trachoma case 5

description: In vivo


title: Maf-DKO+MafB P300_ChIPSeq

city: Marseille

first: Julien

last: Maurizio

address: Centre d’Immunologie de Marseille-Luminy

country: France

institute: INSERM

data_processing:
Bowtie algorithm was executed for read alignments of WT BMM MafB_ChIPSeq sample (sample 33) and sequences from all the other ones were aligned by a probabilistic model from DNANexus. Quest algorithm was used for peak-calling.
A threshold based on the number of sequenced tags (Nseq) has been set up as Nseq/7,000,000. All regions with a number of repeated tags (with identical sequences/coordinates) above this threshold were filtered out to remove possible sequencing and/or alignment artefacts.
In order to accurately represent and further process the ChIP-seq and input control signals, the Watson and Crick strand tags need to be merged after elongation/size extension to the gel purified fragment size. The optimal elongation size of each ChIP-seq experiment was estimated in-silico by employing a step-wise 10bp chromosomal sequence tag shifting and score multiplication
Tag coordinates were subsequently elongated according to this estimated DNA fragment size, corresponding to the tag shift maximizing the score. Then, a nucleotide score representing the genome-wide overlap of elongated tags was computed across both strands
Wiggle files for genome-wide scores were generated following a binning step, calculating the average enrichment score every 50bp
Genome_build: mm9
Supplementary_files_format_and_content: bed files including enrichment values

source_name: Maf-DKO+MafB macrophages

growth_protocol: macrophages were grown sub-confluently in macrophage growth medium (Dulbecco’s modified medium (DMEM) with 20% L-cell sup, 1% sodium pyruvate and 1% L-Glutamate) as described (7). WT BMM macrophages were differentiated from total mouse bone marrow for 15 days in macrophage growth medium, selecting for adherent cells every 4 days.  For culture of AM, alveolar lavages were pooled from ten 1mL 37oC BAL washes (PBS without Mg++/Ca++, 2mM EDTA, 2% FBS (GE Healthcare) per mouse and stored on ice. RBC lysis was then performed at room temperature (RT) for 3 minutes (RBC Lysis Buffer, Invitrogen). Cells were plated at a density of 1.1 million cells per 10cm bacterial petri dish in complete medium (RPMI, 10 % FCS,1 % Pen/Strep, 1 % Pyruvate, 1 % Glutamate) supplemented with 1 % GM-CSF supernatant from J558L cells transfected with murine GM-CSF cDNA. For Maf-DKO+MafB: The pRetroX-Tet-On Advanced (Clontech, Cat.: 632104) and the pRetroX-Tight-Pur (632104) retroviral backbones were used for generating the flag-tagged MafB inducible macrophages. For this, Neor was replaced by Hygror and Puror by GFP in pRetroX-Tet-On Advanced and pRetroX-Tight-Pur Retroviruses, respectively. macrophages were first infected with the pRetroX-Tet-On-hygror retrovirus and selected for 2 weeks in medium containing 200μg/mL of Hygromycin B  (Lifetechnologies, Cat: 10687-010). Selected macrophages were next infected with the empty pRetroX-Tight-GFP or the pRetroX-Tight-GFP containing the flag-tagged MafB gene cloned downstream of the modified Tet-responsive promoter. GFP positive macrophages were then FACS sorted and cultured in absence of doxycycline.

extract_protocol: Cells cultured in plates were fixed by the addition of 1/10 volume of freshly made cross-linking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA, 0.5 mM EGTA, 50mM Hepes pH 7.8) directly to cell medium and incubation at room temperature (RT) for 10 minutes. Formaldehyde was then quenched for 5 minutes at RT by the addition of 2.5M Glycine solution to a final concentration of 125mM. Fixed cells were washed twice with cold PBS, scraped off the plate, counted, and transferred in 50ml Falcon tubes. Cells were then pelleted by centrifugation at 700g for 5 minutes at 4oC, snap-frozen in liquid nitrogen and stored at -80oC for storage or shipment on dry-ice. Each batch of 100 millions cells was lysed by adding 10 ml of ChIP Lysis Buffer (Santa Cruz Biotechnology, sc-45000) or RIPA buffer (1xPBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) containing Protease Inhibitor Cocktail (PIC). One complete PIC tablet (Roche, REF 11873580001) for 50 ml buffer or 1 mini PIC tablet (Roche, REF 11836153001) for 10ml buffer was used. After rotating the cell tube for 10-15 minutes at 4oC, nuclei were pelleted by centrifugation at 700g for 5 minutes at 4oC. Nuclei pellet was resuspended in 5ml of Santa Cruz Biotechnology ChIP Lysis Buffer High Salt (sc-45001) or RIPA buffer (1xPBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) containing PIC. Aliquots of 1ml containing 20 million nuclei were transferred into 1.5 ml low-bind microfuge tubes. The nuclei suspension was either sonicated immediately or snap-frozen in liquid nitrogen and stored at -80oC. The nuclei/chromatin suspension in each ml was sonicated (Sonics Vibra Cell, Model CV188, with Stepped Tip 1/8”-630-0422) on ice in 4oC cold room. Sonication was performed with 9 cycles of 30 seconds (s) ON at 60% intensity and 30 s OFF for chromosome modifications, H3k4me1 and H3K27ac, or with 8 cycles for transcription factors, P300 and PU.1. The sheared chromatin was centrifuged at 14krpm for 10-15 minutes, then transferred as in the supernatant into a new 1.5 tube and kept on ice for ChIP. For ChIP, 50 ul Invitrogen Dynabeads (7x108 beads/ml) were used for 20 millions cells, either anti-rabbit IgG (Cat. no. 112.03D) or anti-mouse IgG (Cat. no. 112.01D) depending on the source of the first antibody. The beads were first washed with PBS/BSA/PIC buffer (1x PBS, 5mg/ml BSA (Sigma, A3059-10G, Fraction V), Roche PIC (1 mini tablet for 10 ml or 1 complete tablet for 50 ml, added before use)) then washed beads were thoroughly resuspended in 1ml of PBS/BSA/PIC buffer in a 1.5 ml microfuge tube.  Tube was placed on a magnetic rack for 1 minute, then the supernatant was removed.  Wash was repeated twice by resuspending beads in 1 ml PBS/BSA/PIC buffer, rotating for 5 minutes and supernatant was removed as above. The beads were then coated with antibody by resuspending in 250 ul PBS/BSA/PIC buffer in each tube, adding 5 ug antibody, rotating overnight at 4 oC. The following antibodies were used: H3K4me1 (Abcam, ab8895), H3K4m3 (Abcam ab8580), H3K27ac (Abcam, ab4729), P300 (Santa Cruz Biotechnology, sc-585), PU.1 (Santa Cruz Biotechnology, sc-352), MafB (Bethyl IHC-101) and Flag M2 antibody (Sigma). After overnight incubation with antibody, the beads were pelleted by placing the tube on a magnetic rack for 1 minute followed by removing the supernatant. The beads were then washed 3 times with PBS/BSA/PIC buffer.  ChIP was carried out by adding the sheared chromatin suspension to the antibody-coated beads, rotating overnight at 4 oC, and followed by a series of washes. The beads were first washed once with 1ml of low salt wash Buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), then twice with high salt wash buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), three times with LiCl wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% GEPAL CA630, 1% Na-Deoxyholate), and twice with TE buffer.  ChIP DNA was eluted by adding 200 ul of ChIP Elution Buffer (Santa Cruz Biotechnology, sc-45003, or 1%SDS/0.1 M NaHCO3.) to each bead tube, vortexing to resuspend beads, and incubation at 65oC for 1 hour with vortexing every 15 minutes. After centrifugation for 3 minutes at RT and placing on a magnetic rack for 1 minute, ChIP DNA in the supernatant was transferred to a new tube. Reversing of crosslinks was done by incubation at 65oC overnight, and DNA was extracted with an equal volume of Phenol:Chloroform:IAA (24:24:1). After centrifugation at 14krpm for 3 minutes, ChIP DNA in the supernatant was transferred to a 2.0 ml low-bind tube. More DNA was extracted by adding 100 ul water to the Phenol:Chloroform phase and repeating the exaction. DNA extract was combined and mixed with 5 volumes of PBI (from Qiagen MinElute PCR Purification Kit, Cat# 28004). The pH of the mixture was adjusted with 3M NaAc pH5.2 to lower than 7.5 before apply to the column. The mixture turned back to yellow color, which is important for DNA to bind to Qiagen column. DNA was purified according to manufacturer's instructions, and eluted in 30 ul buffer EB. DNA concentration was measured with Qubit. 30ng  (P300, PU.1, MafB and Flag-MafB) to 100ng (H3K4me1 and H3K27ac) DNA were used to make each library. ChIP-seq libraries were made using adaptors from Illumina (FC102-1001) and other enzymes and reagents from NEB, following the Illumina ChIP-seq protocol with some minor modifications.  ChIP DNA was end repaired by T4 DNA polymerase (M0203S/L), Klenow DNA polymerase (M0210S/L), and T4 PNK (M0201S/L), and purified with Qiagen MinElute PCR Purification Kit. A-base was then added to the 3’ end by Klenow Fragment, 3’ to 5’ exo- (NEB, Cat# M0212S/L) and dATP. The Illumina adaptors (1ul of 1:10 dilution) were subsequently added to both ends by DNA Ligase (M2200S/L).  The adaptor-ligated DNA was sized selected for 200-400bp fragments by 2% low-melting agarose gel (Lonza, Cat# 50080), followed by purification by Qiagen MinElute Gel Extraction Kit (Cat# 28604). Library DNA was amplified in 100 ul reaction by Phusion PCR Master Mix (NEB, Cat# F-531S), primers SolexaPCR_F (5'- AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T -3') and SolexaPCR_R (5'- CAA GCA GAA GAC GGC ATA CGA GCT CTT CCG ATC T -3'). Libraries of H3K4me1 and H3K27ac were amplified by pre-denaturing at 98C for 30 sec followed by 10 cycles of (98C / 10s, 65C / 30s 72C / 30s), and extra 5 min at 72C at the end. For the P300 and PU.1 libraries, 12 cycles of PCR were used. After library DNA was purified, library concentration was measured by Qubit, and size distribution was determined by Bioanalyzer. Each ChIP-seq library was sequenced on 1 lane of Illumina GAIIx or Illumina HiSeq 2000 with 1x36 bases read length.

tag: genotype

value: Maf-DKO+MafB

tag: chip antibody

value: P300 (Santa Cruz Biotechnology, sc-585)

value: macrophages


title: WT BMM PU.1_ChIPSeq

source_name: bone marrow derived macrophages

value: wild type

value: PU.1 (Santa Cruz Biotechnology, sc-352)

value: bone marrow derived macrophages


title: Maf-DKO PU.1_ChIPSeq

source_name: Maf-DKO macrophages

value: Maf-DKO


title: BMI3

description:
B3
A375 BMI1 overexpressing cells


title: Maf-DKO input DNA


title: WT BMM P300_ChIPSeq


title: Maf-DKO P300_ChIPSeq


title: Maf-DKO+MafB H3K27ac_ChIPSeq

value: H3K27ac (Abcam, ab4729)


title: WT BMM H3K27ac_ChIPSeq


title: WT BMM H3K4me3_ChIPSeq

value: H3K4m3 (Abcam ab8580)


title: Maf-DKO H3K27ac_ChIPSeq


title: Maf-DKO H3K4me3_ChIPSeq


title: WT BMM H3K4me1_ChIPSeq

value: H3K4me1 (Abcam, ab8895)


title: Pbx1_MB

city: Bethesda

first: Hossein

last: Zare

address: 5o South Dr #1347

institute: NIH

description: ChIP-Seq

data_processing:
Illumina Casava1.8 software used for basecalling  and demultiplexing.
Sequenced reads were mapped to mm9 whole genome using Bowtie (Langmead et al, 2009), and TopHat(Trapnell C, et.al 2009) for RNA-Seq.
MacroH2A Peaks ,and ATAC-Seq enriched regions were called using MACS2  ( Zhang et al, 2008), with qvalue of 0.05, --gsize mm, with both narrow and broad peak calling options and the rest were defualt setting. Peak summit location, obtaiend through narrow peak calling, were moslty used for overlaping nad colocalization analysis.
FPKM(RPKM) and differential expression analysis was done using Cufflink/Cuffdiff (Trapnell C, et.al 2009) with multi-reads correction and geometric normalization
Genome_build: mm9
Supplementary_files_format_and_content: Peak files and the transcript file are in Excel format,  and other processed data files are in BigWig format generated from aligned reads after removign duplicates.

source_name: C2C12 cell line

growth_protocol: mouse skeletal muscle C2C12 cells  were  grown in high glucose- DMEM (Gibco), 20% fetal bovine serum (FBS, Gibco), Penicillin/streptomycin (1x, Gibco).

extract_protocol:
For ChIPSeq, lysates were cleared from sonicated nuclei and used for immunoprecipitation. For RNASeq, RNA was extracted according to TRIzol protocol (invitrogen). For ATACSeq, 5x104 C2C12 cells were pelleted, washed with 50ul of 1xPBS and lysed in 50ul of Lysis Buffer (10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% of IGEPAL CA-630).  To tag and fragment accessible chromatin, nuclei were centrifuged at 500x g for 10min and re-suspended in 40ul of transposition reaction mix with 2ul Tn5 transposase (Illumina Cat# FC-121-1030). The reaction was incubated at 37ºC with shaking at 300rpm for 30min.  DNA-fragments were then purified, and amplified by PCR (12-15 cycles based on the amplification curve).
For ChIPSeq, cells were cross-linked in 1% formaldehyde and lysate to extract nuclei. The chromatin was sonicated to 250 bp fragments. Histone-DNA complexes were isolated with anti-histone mH2A1.2 (Cell signaling, 4827S), anti-mH2A1 (Abcam, ab37264), anti-Pbx1 (Abnova, H00005087), anti-histone H3 (acetyl K27) (Abcam, ab4729), anti-trimethyl-histone H3 (Lys27) (Millipore, 07-449). 10ng of immuno-precipitated DNA fragments were used to prepare ChIP-seq libraries with the NEBNext RNA library prep kit (New England BioLabs) and Ovation SP Ultralow DR Multiplex system (Nugen) following the manufacturer’s protocol. For polyA RNA-Seq, Illumina protocol was followed.  ATACSeq samples were multiplexed using primers Ad2.1-4 paired with Ad1 for final library amplification as described previously (Buenrostro et al., 2013).

treatment_protocol: For differentiation, cells were placed in high-glucose DMEM media (Gibco) with 2% horse serum (Gibco) and Insulin, Frasferrin, Selenium (1x, Gibco).

tag: developmental stage

value: Myoblast


title: Input_MB

description: ChIP-Seq

tag: strain


title: AM input DNA

source_name: alveaolar macrophages

value: alveolar macrophages


title: WT BMM MafB_ChIPSeq

value: MafB (Bethyl IHC-101)


title: Pbx1_MT

description: ChIP-Seq

value: Myotubes


title: Maf-DKO+MafB Flag_ChIPSeq

value: Flag M2 antibody (Sigma)


title: AM PU.1_ChIPSeq


title: AM P300_ChIPSeq


title: WT BMM input DNA


title: Maf-DKO H3K4me1_ChIPSeq


title: PWDfXC3Hm antiDMC1 SSDS

first: Kevin

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to the mm10 genome assembly. The pipeline described in Khil et al. Genome Res. 2012 was used to align SSDS reads to the genome. For each sample, reads were aligned to the SNP modified genome(s) of the mouse strain(s) used. In the case of samples generated from F1 hybrid mice, reads were mapped to both parental genomes. The mapping of each read was compared between the alignments to the two parental genomes and a single mapping for each read was retained as follows: if the mapping was identical in both genomes, the read from the first parental genome was retained. If reads mapped to the same position (or ± 2 bp at either end) in both genomes but with fewer mismatches / indels in one, then that with the fewer mismatches / indels was retained. If a read mapped to one genome and not the other, that read was retained. If reads mapped to different positions in the parental genomes, both reads were discarded.
For SSDS DMC1 data, hotspots were called using MACS version 2.0.10. The following MACS arguments were used (--nomodel; --shiftsize: 400; --bw: 1000; -q: 0.1).
Genome_build: mm10
Supplementary_files_format_and_content: For each SSDS experiment, the associated BAM file contains all ssDNA fragments identified for that sample. Custom BAM tags describe properties of each read pair used for ssDNA detection:  it : ITR length  uh : microhomology length  os : microhomology offset  mm : # mismatches   DSB hotspots are provided in pseudo-bedgraph format (.tab) for each DMC1 SSDS sample. This is not a true bedgrpah format, as hotspot intervals may overlap as a result of the recentring procedure. Background corrected hotspot strength is listed in the fourth column. DSB hotspots in blacklisted regions were not used for analyses but are provided as separate files. For blacklisted hotspots, the strength is not corrected for background reads.
Supplementary_files_format_and_content: NOTE: The linked bams differ from 'raw' alignment bams, since they are critical for study interpretation. we use a bespoke and computationally intensive alignment pipeline that serves as an impediment to those wishing to examine our data.

source_name: Testis

extract_protocol:
For DMC1 SSDS, testicular samples were obtained frozen and were directly thawed in 1% paraformaldehyde and gently dissociated. Genomic DNA for whole genome sequencing was extracted from the testicular samples before fixation with the DNeasy Blood and Tissue kit (Qiagen).
DMC1 ChIP was performed as described previously (Smagulova et al., 2011; Khil et al., 2012; Brick et al., 2012) with minor modifications.  Sequencing libraries for anti-DMC1 were prepared following the method described in (Khil et al., 2012).
Single Stranded DNA Sequencing (SSDS)

tag: maternal strain

value: PWD/PhJ

tag: paternal strain

tag: antibody

value: Anti-DMC1 Santa Cruz (C-20, sc 8973)

tag: sequencing technique

value: SSDS


title: Prdm9-/- antiDMC1 SSDS


title: PWDfX13Rm antiDMC1 SSDS


title: PWDfXB6m antiDMC1 SSDS


title: PWDfXCASTm antiDMC1 SSDS

value: CAST/EiJ


title: PWDfXMOLm antiDMC1 SSDS

value: MOLF/EiJ


title: MOLfXB6m antiDMC1 SSDS


title: MOLfX13Rm antiDMC1 SSDS


title: 13RfX9R_Input SSDS


title: CASTfXB6m_Input SSDS


title: B6fXCASTm_Input SSDS


title: B6fX13Rm_Input SSDS


title: 13RfXB6m_Input SSDS


title: C3HfXCASTm antiDMC1 SSDS


title: CASTfXMOLm antiDMC1 SSDS


title: C3HfXMOLm antiDMC1 SSDS


title: CASTfXB6m antiDMC1 SSDS


title: C3H antiDMC1 SSDS


title: C3HfX13Rm antiDMC1 SSDS


title: B6 antiDMC1 SSDS


title: B6fXPWDm antiDMC1 SSDS


title: B6fXC3Hm antiDMC1 SSDS


title: B6fXCASTm antiDMC1 SSDS


title: B6fXMOLm antiDMC1 SSDS


title: CAST antiDMC1 SSDS


title: 0%DO-3

city: wuxi

first: Sun

last: Yang

address: lihu avenue

department: School of Biotechnology

country: China

institute: JIANGNAN UNIVERSITY

data_processing:
Illumina Casava software used for basecalling.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi, A., B. A. Williams, et al . Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 2008.5(7): 621-8
Genome_build: Corynebacterium glutamicum ATCC13032 GenBank: BA000036.3; http://www.ncbi.nlm.nih.gov/nuccore/42602314?report=fasta
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Corynebacterium glutamicum

source_name: bacteria

growth_protocol: The strain was firstly grown on seed medium (25 g glucose, 30 g corn syrup, 20 g (NH4)2SO4, 1g MgSO4, 1g KH2PO4 per liter of distilled H2O; pH 6.8) of a shaker for 12 h at 30 °C, 220 r/min. The seed was then transferred to second seed medium which is same with seed just in baffled-bottom flask, and then transferred to medium culture used for fermentation in a 5L fermentor (Applikon EZ-control) for 48 h. Three batches were conducted with three duplicate, one at high DO (50%), one at medium DO (30%) and one at low DO (0%). The medium composition of the three batches was: 30 g glucose, 15 g corn syrup, 20 g (NH4)2SO4, 1g MgSO4, 1g KH2PO4 per liter of distilled H2O; pH 6.8. The fermentation temperature was 30 °C. Samples were collected at 20 h (at the early of stable phase) from three independent batches for RNA sequencing and quantitative real-time RT-PCR analysis.

extract_protocol:
Samples were quenched in liquid nitrogen immediately after collection, and RNA was harvested using RNAiso plus (Takara, Dalian, China),Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: do level

tag: hours of fermentation


title: MOL antiDMC1 SSDS


title: 0%DO-2


title: 13R antiDMC1 SSDS


title: 50%DO-1


title: 0%DO-1


title: 30%DO-2


title: 50%DO-2


title: PWD antiDMC1 SSDS


title: B6 PRDM9bh DMC1 hotspots

status: Public on Feb 02 2016

city: Berkeley

first: Nicolas

last: Altemose

address: 327 Stanley Hall

department: Bioengineering

institute: University of California, Berkeley

data_processing:
single-stranded DNA sequencing was performed on HiSeq 2000 and HiSeq 2500 platforms (50 bp reads)
Alignment with a modified BWA mapper (Khil et al., 2012)
Peaks were called using an in-house algorithm R code available at https://github.com/anjali-hinch/hybrid-rescue
[Third-party reanalysis] To generate the dmc1hotspots_B6.PRDM9bb* files, we processed raw data from GSM869781 in the same manner as our in-house generated raw data
[Variant call file]  PWD mouse genome was sequenced at 50x coverage on Illumina HiSeq 2500 (Wafergen DNA library prep kit). Paired-end reads (151bp each) were aligned to the reference genome mm10 using the program Stampy, and variants were called using the variant caller Platypus.
Genome_build: mm10, except for three files (mm9); see names of processed data files
Supplementary_files_format_and_content: Tab-delimited .txt Peak files with column descriptions in commented header. Variant file.

source_name: whole adult testis

growth_protocol: All data was generated from in vivo tissue samples from ~10 week old male mice - no culturing was performed

extract_protocol:
Testes samples were stripped of the tunica and were snap frozen prior to processing. Single-stranged DNA sequencing and double-strand break detection occurred using a modified DMC1 ChIP seq protocol (Khil et al, 2012. Genome Research 22, 957-965) and H3K4Me3 ChIP seq occurred followly Hinch et al., 2014. PLoS Genetics 10, e1004503. Full experimental procedures are reported in Davies et al, 2016
Libraries were prepared according to Illumina's instructions

value: testis

tag: prdm9 genotype

value: anti-DMC1, Santa Cruz (C-20, sc-8973)


title: 30%DO-3


title: B6 PRDM9hh DMC1 hotspots

value: Humanized/Humanized


title: Naïve CD4+PMA DHS biorep2

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

data_processing:
Base-calling (CASAVA for Illumina or Bioscope for SOLiD)
Demultiplexing (Illumina only: bcl2fastq)
DNAse-seq reads were aligned to the mm9 genome assembly using Bowtie 1.00 to SAM to stdoutput using --all --best --strata --v 2 -m 1 -S
SAM to BAM conversion (samtools view -S stdinput -b -o stdoutput/bam file)
BAM file sorting (samtools sort - stdinput sorted_bam_file)
Optional BAM merging for SOLiD and Illumina datasets (samtools merge)
Optional indexing for footprinting (samtools index sorted_bam_file)
Tag shift (macs14)
Wig coverage track generation (macs14)
Peak detection (macs14)
Optional footprinting (wellingtion_footprints)
Genome_build: mm9
Supplementary_files_format_and_content: Variable step 10bp wig files depincting DNaseI hypersensitivity coverage

source_name: Naïve splenic CD4+ T-cells

growth_protocol: CD4 and CD8 single positive naive T cells were isolated from the spleens of C42 transgenic mice using MACS CD4 and CD8 T cell Isolation kits followed by enrichment for naive cells using MACS CD62L+ microbeads according to the manufacturer’s instructions (Miltenyi Biotec, Auburn, CA). CD4 and CD8 T-blast cells were generated from purified splenic cells cultured under activating conditions. CD4 or CD8 single positive T cells were isolated using MACS CD4 (L3T4) or CD8a (Ly2) microbeads. Cells were cultured at 5x105 cells/ml in IMDM and activated with 2ug/ml Concanavalin A for 40 hours. Cells were then maintained at 5x105 cells/ml in 50U/ml IL-2 (Peprotech) for an additional 2-3 days before harvesting. CD4 memory T cells were purified from splenocytes using the Easy Sep mouse memory CD4 T cell Isolation Kit according to the manufacturer’s instructions (Stem Cell Technologies).

extract_protocol:
NP-40 permeabilized cells were digested with DNase I for 3 minutes at 22oC as previously described (Bert et al). A range of DNase I concentrations was used to get the optimal digestion, the initial amounts varied depending on the cell type. Following DNA purification, samples were analyzed by qPCR comparing the amount of PCR product generated between regions expected to be DNase I hypersensitive (e.g. TBP promoter) and regions which should not be cleaved (e.g. a gene desert region of chromosome 1). Optimally digested samples gave a ratio of ~0.7. DNA fragments (80-300bp) were isolated from favorable samples by agarose gel extraction and further validated by qPCR analysis before library preparation.
Libraries were prepared from approximately 10ng DNA from DNaseI samples. Libraries for sequencing on the Solid platform were prepared according to the manufacturer’s instructions. Samples were sequenced using 50bp reads. All other libraries were prepared using the Tru-Seq library preparation kit according to the manufacturer’s instructions (Illumina). These samples were sequenced on the Illumina HiSeq platforms using 50bp single end reads

treatment_protocol: Cells were stimulated with 20ng/ml phorbol myristate acetate (PMA) and 2uM Calcium Ionophore (CaI) in IMDM supplemented with 50U/ml IL-2 at a concentration of 1x106 cells/ml for up to 4 hours.

tag: cell type

value: Naive splenic CD4+ T-cells

tag: pma treatment

value: 120 min

tag: dnasei origin

value: Worthington


title: H3K4me3.PWDB6F1.PRDM9ph.Rescue

description: note: Infertile and Rescue mice are littermates

data_processing:
reads mapped to mm10 with bwa followed by stampy (see bam headers)
duplicates removed by samtools rmdup
reads filtered using samtools view -F12 -q1
paired-end coordinates converted to bed (in-house perl script)
fragment depth computed using bedtools genomecov
force-calling of enrichment and haplotype calling performed using in-house R code (described in paper, hosted on website)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with column descriptions in commented header; each line corresponds to one DSB peak

extract_protocol:
The testis tunica was removed, the tubules disassociated with tweezers and fixed in 1% formaldehyde in PBS for 5 minutes followed by glycine quenching (125mM final conc.) for 5 minutes at room temperature. Following washing steps, pellets were resuspended in 900 μl cold RIPA lysis buffer, dounced 20 times and sonicated in 300 ul aliquots in a Bioruptor Twin sonication bath at 4°C for three 10-minute periods of 30s on, 30s off at high power, then cell debris was pelleted and removed and aliquots were pooled. For each sample, 50 μl of equilibrated magnetic beads  (Invitrogen M-280 Sheep Anti-Rabbit Dynabeads) were resuspended in 100 μl PBS/BSA and added to the chromatin samples for pre-clearing for 2h at 4°C with rotation. Beads were removed, and 100 μl of pre-cleared chromatin was set aside for the input control. 5 μl rabbit polyclonal anti-H3K4me3 antibody (Abcam ab8580) was added to the remaining pre-cleared chromatin and incubated overnight at 4°C with rotation. 50 μl beads were washed and resuspended as before, then incubated with the chromatin samples for 2h at 4°C with rotation. Beads were then washed and decrosslinked at 65°C, and for input controls, 50 μl of pre-cleared chromatin was used. After descrosslinking, samples were further incubated with 80μg RNAse A at 37°C for 60 minutes and then with 80μg Proteinase K at 55°C for 90 minutes. DNA was purified using a Qiagen MinElute reaction cleanup kit.     ChIP and total chromatin DNA samples were sequenced in multiplexed paired-end Illumina libraries, yielding 51bp reads. We prepared two biological replicates plus one genomic input control each for the Infertile (PWD×B6)F1_PRDM9-PWD/B6, Reciprocal (B6×PWD)F1_PRDM9-B6/PWD and Rescue (PWD×B6)F1_PRDM9-PWD/H mice, yielding roughly 40-50 million usable read pairs per replicate. For the B6_PRDM9-B6/B6 and B6_PRDM9-H/H mice, we prepared one biological replicate each (yielding 70-80 million usable read pairs per sample) and later split read pairs into pseudoreplicates. Sequencing reads were aligned to mm10 using BWA37 (options -q 10 -t 8) followed by Stampy38 (options -t 8 --bamkeepgoodreads), and reads not mapped in a proper pair with insert size smaller than 10kb were removed. Read pairs representing likely PCR duplicates were also removed by samtools rmdup. Pairs for which neither read had a mapping quality score greater than 0 were removed. Fragment coverage was computed using in-house code and the samtools and bedtools packages.
Libraries were prepared according to Illumina's instructions. The Infertile and Rescue samples were multiplexed together, as were the Reciprocal and B6 samples.

value: whole adult testis

value: PWD/Humanized

value: H3K4me3 (Abcam ab8580)


title: Input PWDB6F1.PRDM9ph.Rescue


title: C3HfXB6m antiDMC1 SSDS


title: 13RfXB6m antiDMC1 SSDS


title: B6fX13Rm antiDMC1 SSDS


title: Input PWDB6F1.PRDM9pb.Infertile


title: H3K4me3.PWDB6F1.PRDM9pb.Infertile


title: 50%DO-3


title: Input B6PWDF1.PRDM9pb.Reciprocal


title: H3K4me3.B6PWDF1.PRDM9pb.Reciprocal


title: Naïve CD4 DHS biorep2

growth_protocol: CD4 and CD8 single positive naive T cells were isolated from the spleens of C42 transgenic mice using MACS CD4 and CD8 T cell Isolation kits followed by enrichment for naive cells using MACS CD62L+ microbeads according to the manufacturer’s instructions (Miltenyi Biotec, Auburn, CA). CD4 and CD8 T-blast cells were generated from purified splenic cells cultured under activating conditions. CD4 or CD8 single positive T cells were isolated using MACS CD4 (L3T4) or CD8a (Ly2) microbeads. Cells were cultured at 5x105 cells/ml in IMDM and activated with 2g/ml Concanavalin A for 40 hours. Cells were then maintained at 5x105 cells/ml in 50U/ml IL-2 (Peprotech) for an additional 2-3 days before harvesting. CD4 memory T cells were purified from splenocytes using the Easy Sep mouse memory CD4 T cell Isolation Kit according to the manufacturer’s instructions (Stem Cell Technologies).

extract_protocol:
NP-40 permeabilised cells were digested with DNase I for 3 minutes at 22oC as previously described (Bert et al). A range of DNase I concentrations was used to get the optimal digestion, the initial amounts varied depending on the cell type. Following DNA purification, samples were analysed by qPCR comparing the amount of PCR product generated between regions expected to be DNase I hypersensitive (e.g. TBP promoter) and regions which should not be cleaved (e.g. a gene desert region of chromosome 1). Optimally digested samples gave a ratio of ~0.7. DNA fragments (80-300bp) were isolated from favourable samples by agarose gel extraction and further validated by qPCR analysis before library preparation.
Libraries were prepared from approximately 10ng DNA from DNaseI samples. Libraries for sequencing on the Solid platform were prepared according to the manufacturer’s instructions. Samples were sequenced using 50bp reads. All other libraries were prepared using the Tru-Seq library preparation kit according to the manufacturer’s instructions (Illumina). These samples were sequenced on the Illumina HiSeq platforms using 50bp single end reads

value: 0 min


title: hNPC input

city: Shanghai

first: Ying

last: Jin

address: 225 South Chongqing Road

institute: Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
CASAVA1.8.2 convert per-cycle *.bcl files into FASTQ files
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.7
peaks were called using MACS version 2.0.10 with the following setting: shift-size (73), q-value (0.01)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated by MACS2, the score represents number of bp fall into the single base pair region.

source_name: H9 derived NPCs

growth_protocol: H9 cells were maintained in mTeSR1 in BD hESC qualified matrigel coated dishes. Culture was daily changed, and hESCs were passaged using Accutase or 1mg/ml dispase.  hNPCs were differentiated from H9 cells using established protocol (Chambers SM, Nat Biotechnol, 2009; 27: 275–280). Briefly, we used Noggin (500ng/ml), SB431542 (10mM) and Compound C (10mM) to induce neural differentiaiton.Neural rosettes were picked up and replated onto matrigel coated dishes, and then dissociated into single NPCs and maintained in N2B27 medium supplemented with 10ng/ml bFGF. hNPCs were then passaged using 0.05% trypsin.

extract_protocol:
Lysates were clarified from sonicated nuclei and SOX2-DNA complexes and POI II-DNA complexes were immunoprecipitated with SOX2 antibody (R&D AF2018) or POI II antibody (Covance MMS-126R). Protein A and G Magenetic Dynabeads were used to capture antibody bound protein-DNA complexes.
ChIP-seq libraries preparation: The ChIP-enriched DNA samples were treated with end-repair of the DNA, adding ‘‘A” bases to the DNA, ligating sequencing adapters to DNA fragments, amplifying adapter-modified DNA by PCR and gel purification for ChIPseq using NEBNext Ultra DNA Library Prep Kit for Illumina. Purified libraries were sequenced on Illumina HiSeq2500 platforms.

value: hESC


title: T-Blast CD4 DHS biorep2

source_name: Blast-cultured splenic CD4+ T-cells

value: Blast-cultured splenic CD4+ T-cells


title: hNPC POI II ChIP-seq

value: POI II (Covance MMS-126R)


title: Input B6.PRDM9hh


title: H3K4me3.B6.PRDM9bb

description: Input B6.PRDM9hh was used with this sample for processed data analysis


title: hNPC SOX2 ChIP-seq


title: H3K4me3.B6.PRDM9hh


title: 30%DO-1


title: hESC Input


title: hESC SOX2 ChIP-Seq


title: hESC POI II ChIP-seq


title: hNPC SOX2 KD2

data_processing:
Basecalls performed using CASAVA.
RNA-Seq reads of each sample were firstly mapped to the hg19 genome assembly using TopHat 2.0.12 with default parameters.
Read counts were obtained from TopHat-generated BAM files using SAMtools 0.1.16.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RefSeq id and RPKM values for each Sample

source_name: H9 derived NPC

extract_protocol:
collecting the cells in Trizol Reagent ( Invitrogen, 15596026)
The cDNA libraries were constructed following the TruSeq™ RNA Sample Preparation Guide (Illumina). Briefly, total RNA was isolated with Trizol reagent, and the polyA RNA was isolated using the RNA Purification Beads (Illumina). The mRNAs were fragmented by incubation in Elute, Prime, Fragment Mix at 94℃ for 8min to obtain 120-200bp inserts.  Fist strand cDNA was synthesized with SuperScript II Reverse Transcriptase (Invitrogen) using random primer, and Ampure XP beads are used to isolated the double‐stranded (ds) cDNA synthesized by Second Strand Master Mix. The adapter was ligated to the A‐Tailing  fragment, and 12 cycles of PCR was performed to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library.  Purified libraries were quantified by Qubit® 2.0 Fluorometer and  validated by Agilent 2100 bioanalyzer to confirm the insert size and calculate the mole   concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina Genome Analyzer IIx for 75 cycles. The library construction and sequencing was performed at Shanghai Biotechnology Corporation.

treatment_protocol: we used one non-targeting (NT) siRNA, two sets of siRNAs targeting SOX2 and/or SOX3 to KD SOX2 and SOX3 (SOX2/3 KD-1 and SOX2/3-2) in hESCs and KD SOX2 (SOX2 KD-1 and SOX2 KD-2) in hNPCs repectively. hESC and hNPC cells were collected 48 hrs post transfection with siRNAs.

tag: transfection

value: second SOX2 siRNA (KD2)

tag: time point

value: 48 hours


title: hNPC SOX2 KD1

value: first SOX2 (KD1) siRNA


title: mouse ZT8_control_12

city: Philadelphia

first: Gregory

middle: Robert

last: Grant

state: PA

address: 3400 Civic Center Blvd.

department: Genetics

institute: University of Pennsylvania

data_processing:
CASAVA was used to demultiplex pooled samples and convert BCL to FASTQ. Multiple fastq files were combined into one file for the forward reads and one file for the reverse reads.
RNA-seq data were aligned to the mouse genome build mm9 by STAR (version 2.4.0f1) with the following parameters "--outFilterType BySJout --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMunmapped Within". Junction information from RefSeq gene models was provided using the "--sjdbGTFfile" argument.
Data were normalized using a resampling strategy, the code is available at https://github.com/itmat/Normalization . We performed gene-level normalization using default parameters for the mm9 genome.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: FINAL_master_list_of_genes_counts_MIN.Guangrui_WT_v_KO_timecourse.txt: Tab-delimited text file from gene-level normalization contains counts from Unique reads that only map to one gene.

source_name: Liver, WT, ZT8

growth_protocol: All mice were housed under 12h:12h LD conditions with free access to food and water unless specified. All procedures were approved by the University of Pennsylvania Institutional Animal Care and Use Committee. Bmal1f/f mice (PMID: 25512522) were obtained from C. Bradfield (University of Wisconsin, Madison, WI, USA). The floxed mice were crossed with a tamoxifen-inducible universal Cre (EsrCre) mice (Jackson Laboratories, Bar Harbor, ME) to yield Bmal1f/f-EsrCre mice. To generate inducible Bmal1 knockout (iKO) mice, Bmal1f/f-EsrCre mice were treated with tamoxifen as previously described (PMID: 22899986). Briefly, mice were administered with 50 µl (5 mg) of tamoxifen solution per day by oral gavage for 5 consecutive days. Cre- Bmal1f/f littermates treated with tamoxifen served as controls (Ctrl). Seven days after the last dose of tamoxifen, mice were kept under constant darkness for 36 h and then sacrificed. Four mice per genotype were sacrificed in darkness every 4h for 20h (6 time points).

extract_protocol:
Liver samples were quickly excised every four hour for 20 hours and snap-frozen in liquid nitrogen. Mouse liver (50 - 100 mg) was homogenized using magnetic beads and a TissueLyzer. Total RNA was isolated using Qiagen RNeasy Kit and the RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer.
Illumina TruSeq RNA Sample Prep v2 was used for library construction, according to manufacturer's instructions. Briefly, poly-A containing mRNA was isolated using poly-T oligo-attached magnetic beads and fragmented during elution. First strand cDNA was reverse transcribed from cleaved RNA fragments primed with random hexamers. Second strand cDNA was synthesized and isolated using Ampure XP beads. Blunt ends were created using 3' to 5' exonuclease activity and polymerase activity. A single "A" nucleotide was added to the 3' end and adapters were subsequently ligated onto the ends of the ds cDNA. Indices for multiplexing were attached during this ligation step. 13 cycles of PCR selectively amplified cDNA with adapter molecules on both ends. Using the molarity from Bioanalyzer (DNA 1000), libraries were diluted to 10nM. Libraries at 10nM were run on Bioanalyzer again (HighSensitivity DNA) and taking the lowest molarity, two samples with distinct barcodes were pooled. Clusters were generated using cBOT, and sequenced in one flow cell lane.

tag: strain/background

tag: genotype/variation

value: WT

tag: Sex

value: male

tag: age

value: 4-6 months

tag: weight

value: 30 gram

tag: housing type

value: group

tag: cage number

tag: tissue

value: liver

tag: sample collection time


title: mouse ZT8_KO_14

source_name: Liver, Bmal1 KO, ZT8

value: Bmal1 KO

value: 27 gram


title: mouse ZT4_KO_6

source_name: Liver, Bmal1 KO, ZT4


title: hNPC NT

value: non-targeting (NT) siRNA


title: mouse ZT8_KO_9

value: 31 gram


title: mouse ZT4_control_4

source_name: Liver, WT, ZT4

value: 29 gram


title: hESC SOX2/3 KD2

source_name: H9 ESC

value: second SOX2 and SOX3 siRNAs


title: mouse ZT20_KO_38

source_name: Liver, Bmal1 KO, ZT20

value: individual

value: not applicable


title: pdx3-4 rep 3

city: Geneva

first: Teresa

middle: B.

last: Fitzpatrick

state: Geneva

address: 30, Quai Ernest Ansermet

department: Department of Botany and Plant Biology

institute: University of Geneva

data_processing:
The quality control of the resulting reads was done with FastQC
The reads were mapped to the Arabidopsis TAIR10 Ensembl genome with the TopHat v.2 software
Genome_build: TAIR10 Ensembl genome
Supplementary_files_format_and_content: tab-delimited text files include raw counts of reads for each sample

organism: Arabidopsis thaliana

source_name: pdx3-4_rosette leaves

growth_protocol: 16 hours light / 8 hours dark cycles on soil

extract_protocol:
Entire rosettes were flash-frozen and ground on liquid nitrogen and total RNA was extracted with the PureLink® RNA Mini kit (Life Technologies). and polyA-selected using the TruSeq Stranded mRNA Sample Preparation LS kit (Illumina®).
The samples were polyA-selected using the TruSeq Stranded mRNA Sample Preparation LS kit (Illumina®).The nine samples were pooled and sequenced on an Illumina Hiseq2000 sequencing platform

tag: ecotype

value: 21 days

value: whole rosettes


title: hESC NT

value: 48 hours


title: hESC SOX2/3 KD1

value: first SOX2 and SOX3 siRNAs


title: mouse ZT20_KO_37

value: male


title: pdx3-4 rep 2


title: mouse ZT20_control_40

source_name: Liver, WT, ZT20

value: WT

value: 4-6 months


title: pdx3-3 rep 3

source_name: pdx3-3_rosette leaves


title: pdx3-3 rep 2


title: mouse ZT20_control_33


title: pdx3-3 rep 1


title: Col-0 rep 3

source_name: WT_rosette leaves

value: wild-type


title: pdx3-4 rep 1


title: mouse ZT16_KO_30

source_name: Liver, Bmal1 KO, ZT16

value: 28 gram

value: group

value: liver


title: mouse ZT16_control_32

source_name: Liver, WT, ZT16


title: mouse ZT16_KO_25

value: Bmal1 KO


title: mouse ZT12_KO_24

source_name: Liver, Bmal1 KO, ZT12

value: 27 gram


title: Col-0 rep 2


title: mouse ZT0_control_47

source_name: Liver, WT, ZT0


title: mouse ZT4_control_2


title: mouse ZT8_control_16


title: mouse ZT4_KO_5

value: 31 gram


title: mouse ZT0_control_42

value: 32 gram


title: mouse ZT20_control_35

value: 34 gram


title: mouse ZT20_KO_39

value: 23 gram


title: mouse ZT16_KO_31

value: individual

value: not applicable


title: mouse ZT16_control_27

value: 33 gram


title: mouse ZT16_control_28


title: mouse ZT16_KO_26


title: mouse ZT12_KO_20


title: mouse ZT12_KO_21


title: Col-0 rep 1

value: 21 days

value: whole rosettes


title: mouse ZT12_control_19

source_name: Liver, WT, ZT12

value: WT

value: male


title: mouse ZT0_KO_46

source_name: Liver, Bmal1 KO, ZT0

value: 4-6 months


title: mouse ZT12_KO_18

value: 25 gram


title: mouse ZT8_KO_10

value: 29 gram

value: group


title: 290714 0575-419neg ILC3

city: Durban

first: Alasdair

last: Leslie

address: 719 Umbilo Road

country: South Africa

institute: African Health Research Institute

data_processing:
Illumina bcl2fastq2.15.0.4 was used to generate .fastq files from .bcl files.
tophat2 was used to align the scRNA-seq data
rsem-1.2.3 generated an expression matrix in psuedocounts
Genome_build: hg19 ucsc genomestudio
edgeR modeled dispersion, normalized for library size, and conducted differential expression likelihood ratio tests
Supplementary_files_format_and_content: edgeR normalized counts per million with genes as rows and cell populations (samples) as columns

source_name: Peripheral Blood

extract_protocol:
Due to low cell counts, lysates were treated as single cells in an adapted SMART-Seq II protocol (Trombetta et al., Current Protocols in Molecular Biology, 2014, 107:II:4:22). Briefly, mRNA was extracted from lystates using SPRI beads and then reverse transcribed and amplified using a poly-adenylated RT primer and template switching SMART oligo.
Library construction followed from the protocol above (Trombetta et al.,).

treatment_protocol: Cells were sorted into RLT buffer by FACS, spun down, and snap frozen on dry ice.

tag: individual

value: Innate Lymphoid Cell 3

tag: hiv status

value: HIV-

tag: days post hiv-infection

value: uninfected


title: mouse ZT8_control_13

source_name: Liver, WT, ZT8

value: 31 gram

value: liver


title: mouse ZT4_KO_7

value: Bmal1 KO

value: 27 gram


title: mouse ZT8_control_11


title: mouse ZT12_control_22


title: 290714 0575-419neg ILC2

tag: cell type

value: Innate Lymphoid Cell 2


title: mouse ZT4_KO_1

value: 24 gram

value: individual

value: not applicable


title: 290714 0560-420neg ILC3


title: mouse ZT4_control_8

value: WT


title: mouse ZT8_KO_15

source_name: Liver, Bmal1 KO, ZT8

value: male

value: 26 gram


title: mouse ZT4_control_3

value: 4-6 months

value: 32 gram


title: 240614 0518-370neg ILC2


title: 240614 0518-370neg ILC3


title: 230514 0440-307neg ILC3


title: mouse ZT20_control_36

value: group


title: mouse ZT16_control_29

value: 28 gram


title: mouse ZT0_KO_44

value: 23 gram


title: mouse ZT12_control_23

value: 33 gram


title: 230514 0440-307neg ILC2

value: HIV-

value: uninfected


title: mouse ZT12_control_17

value: 34 gram

value: liver


title: mouse ZT0_KO_43

value: Bmal1 KO

value: 27 gram


title: 170714 0218-162neg ILC3

value: Innate Lymphoid Cell 3


title: 180314 0311-217HIVneg ILC2

value: Innate Lymphoid Cell 2


title: mouse ZT0_KO_41

value: 29 gram


title: mouse ZT0_control_48

value: WT

value: male


title: 170714 0218-162neg ILC2


title: mouse ZT0_control_45

value: 4-6 months

value: 31 gram

value: individual

value: not applicable


title: 090714 0394-274 ILC3


title: 090714 0394-274 ILC2


title: Memory+PMA CD4 DHS

source_name: Memory splenic CD4+ T-cells

value: Memory splenic CD4+ T-cells

tag: pma treatment

value: 120 min

tag: dnasei origin

value: Worthington


title: 080814 0292-xxxneg ILC3

value: HIV-

value: uninfected


title: Memory CD4 DHS

value: 0 min


title: T-Blast CD4+PMA JunB

data_processing:
Base-calling (CASAVA for Illumina or Bioscope for SOLiD)
Demultiplexing (Illumina only: bcl2fastq)
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie 1.00 to SAM to stdoutput using --all --best --strata --v 2 -m 1 -S
SAM to BAM conversion (samtools view -S stdinput -b -o stdoutput/bam file)
Optional BAM file sorting for merging (samtools sort - stdinput sorted_bam_file)
Optional BAM merging for SOLiD and Illumina datasets (samtools merge)
Tag shift (macs14)
Wig coverage track generation (macs14)
Peak detection (macs14)
Optional footprinting (wellingtion_footprints)
Genome_build: mm9
Supplementary_files_format_and_content: Variable step 10bp wig files depincting ChIP-Seq coverage

source_name: Blast-cultured splenic CD4+ T-cells

extract_protocol:
Chromatin was prepared and immunoprecipitation was carried out as previously described (Lichtinger et al) for the antibodies, H3K27ac (ab4729) and H3K4me2 (Millipore 07-030). For all other antibodies, JunB (sc-46), Runx1 (ab23980), Ets1 (sc-111), and BRD4 (Bethyl laboratories), chromatin was prepared as follows. Cells were resuspended in PBS at 3.3x106 cells/ml and cross-linked with 0.83mg/ml disuccinimidyl glutarate (DSG) for 45 minutes at room temperature with rotation. Cells were washed four times with PBS and further crosslinked in PBS at 2x106 cells/ml with 1% formaldehyde for 10 minutes at room temperature. Crosslinking was quenched with 0.125M glycine, cells were washed twice in PBS and incubated with Buffer A at 4oC for 10 minutes followed by buffer B at 4oC for 10 minutes. Double cross-linked chromatin was then used for immunoprecipitation as previously described (Lichtinger et al).
Libraries were prepared from approximately 10ng DNA from ChIP samples. Libraries for sequencing on the Solid platform were prepared according to the manufacturer’s instructions. Samples were sequenced using 50bp reads. All other libraries were prepared using the Tru-Seq library preparation kit according to the manufacturer’s instructions (Illumina). These samples were sequenced on the Illumina HiSeq platforms using 50bp single end reads

value: Blast-cultured splenic CD4+ T-cells

tag: antibody

value: JunB

tag: antibody vendor/catalog#


title: T-Blast+PMA CD4 DHS


title: mouse ZT20_KO_34

tag: strain/background

tag: genotype/variation

value: Bmal1 KO

value: group

value: liver


title: Naïve CD4+PMA DHS

source_name: Naïve splenic CD4+ T-cells

value: Naive splenic CD4+ T-cells


title: 290714 0560-420neg ILC2

value: Innate Lymphoid Cell 2


title: 010814 0500-355neg ILC2


title: 080814 0292-xxxneg ILC2


title: 220814 0444-312 ILC2

value: HIV+

tag: treatment

value: ART


title: 180314 0311-217HIVneg ILC3

value: Innate Lymphoid Cell 3


title: T-Blast CD4+PMA Runx1


title: T-Blast CD4 JunB


title: 220814 0444-312 ILC3


title: T-Blast CD4 Runx1


title: 150714 0444-312 3dR10 ILC3


title: 150714 0444-312 3dR10 ILC2


title: T-Blast CD4 Ets1


title: Naïve CD4 Runx1


title: 130115 0629-453 Acute ILC2


title: 130115 0629-453 Acute ILC3


title: 101214 0629-453 Acute ART+ ILC2


title: 010814 0500-355neg ILC3


title: T-Blast CD4+PMA H3K27ac


title: 041214 0629-453 Acute ART+ ILC2


title: T-Blast CD4 BRD4

value: Bethyl laboratories


title: T-Blast CD4+PMA BRD4


title: 041214 0629-453 Acute ART+ ILC3


title: T-Blast CD4 H3K27ac


title: 290714 0387-272 ILC3

value: Untreated


title: T-Blast CD8 DHS

source_name: Blast-cultured splenic CD8+ T-cells

value: Blast-cultured splenic CD8+ T-cells


title: 290714 0387-272 ILC2


title: T-Blast CD4+PMA H3K4me2

value: 120 min

value: Millipore 07-030


title: 170614 0387-272 ILC3


title: 170614 0387-272 ILC2


title: Naïve CD4 H3K4me2


title: T-Blast CD4 DHS

value: Worthington


title: Naïve CD4 DHS

value: 0 min


title: 110614 0387-272 ILC3


title: 110614 0387-272 ILC2


title: T-Blast CD4 H3K4me2

value: Blast-cultured splenic CD4+ T-cells


title: 170414 0450-318 ILC3


title: Naïve CD4 Ets1


title: 101214 0629-453 Acute ART+ ILC3


title: 170414 0450-318 ILC2


title: 180314 0450-318 ILC3


title: 180314 0450-318 ILC2


title: 110314 0450-318 ILC3


title: Rvb2 PIH1 deletion replicate 3

city: Kansas City

first: Gaye

middle: L

last: Hattem

state: Missouri

address: 1000 E. 50th Street

department: Proteomics

institute: Stowers Institute

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and mapped to SacCer3 whole genome using tophat version 2.0.3
Read counts for each gene were calculated with Rsubread 1.16.1, normalized counts were obtained using DESeq2 1.6.3
FPKM values were calculated with DESeq2 1.6.3
Genome_build: SacCer3

organism: Saccharomyces cerevisiae

source_name: yeast cells tagged with Rvb2

growth_protocol: 5 ml yeast cells were grown to an OD600 of 1.2 to 1.5 in YPD media by shaking at 30 °C, harvested and used for isolation of total RNA.

extract_protocol:
Standard protocols were followed to extract total RNA from yeast cells using the yeast RNA purification kit (Epicenter, Madison, WI) followed by enrichment of poly(A)+ RNA by oligo(dT) selection.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

tag: strain


title: 110314 0450-318 ILC2


title: Rvb2 PIH1 deletion replicate 2


title: Rvb2 PIH1 deletion replicate 1


title: Rvb2 TAH1 deletion replicate 2


title: Rvb2 TAH1 deletion replicate 3


title: PWD genomic DNA

description: library strategy: DNA-Seq

source_name: whole adult spleen

value: PWD/PhJ

value: spleen

tag: prdm9 genotype

value: PWD/PWD


title: Rvb2 WT replicate 3

value: wild type


title: (B6xPWD)F1 PRDM9hp DMC1 hotspots

source_name: whole adult testis

tag: tissue

value: testis

value: Humanized/PWD

tag: chip antibody

value: anti-DMC1, Santa Cruz (C-20, sc-8973)


title: Rvb2 WT replicate 2


title: (PWDxB6)F1 PRDM9ph DMC1 hotspots

value: PWD/Humanized


title: (B6xPWD)F1 PRDM9bp DMC1 hotspots


title: (B6xCAST)F1 PRDM9bc DMC1 hotspots


title: Naïve CD8 DHS

source_name: Naïve splenic CD8+ T-cells

value: Naive splenic CD8+ T-cells


title: Rvb1 TAH1 deletion replicate 2

source_name: yeast cells tagged with Rvb1


title: (PWDxB6)F1 PRDM9pb DMC1 hotspots


title: Rvb2 TAH1 deletion replicate 1


title: Rvb1 TAH1 deletion replicate 1


title: Rvb1 PIH1 deletion replicate 3


title: PWD PRDM9pp DMC1 hotspots


title: Rvb1 PIH1 deletion replicate 2


title: Rvb1 PIH1 deletion replicate 1