title: C3H/HeJ hippocampus rep 2

description: Library size selection for miRNA


title: WT_LivTotRNA_ZT12

status: Public on Jan 18 2018

type: SRA

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

library_source: transcriptomic

data_processing:
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
Alignment to the mm10 genome was performed using the STAR aligner version 2.4.0k using the --outFilterIntronMotifs RemoveNoncanonical parameter
Nuclear RNA-Seq and total RNA-Seq normalized gene expression (fpkm) was quantified across all gene exons and introns separately, using the top-expressed isoform as a proxy for gene expression
Genome_build: mm10
Supplementary_files_format_and_content: fpkm normalized table exon reads (text table)
Supplementary_files_format_and_content: fpkm normalized table intron reads (text table)

molecule: total RNA

organism: Mus musculus

source_name: Liver

growth_protocol: Animals were maintained in a 12h:12h light:dark conditions. Mice were entrained to be fed only during the dark phase for one week prior to the tissue collection,

extract_protocol:
One portion of the liver was snap frozen to isolate total RNA, the rest of the tissue was homogenized to isolate liver nuclei and extract nuclear RNA. mRNA from either total liver tissue or liver nuclei was purified using Trizol reagent (Invitrogen)
Libraries were prepared using Illumina’s TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold according to manufacturer’s instructions

tag: time point

tag: strain

tag: tissue

value: total liver

tag: age

value: 14 weeks

tag: genotype

value: wild type


title: WT_LivTotRNA_ZT4


title: WT_LivTotRNA_ZT6


title: WT_LivTotRNA_ZT2


title: Input IgG

description: Input IgG

data_processing:
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
Alignment to the mm10 genome was performed using the STAR aligner version 2.4.0k using the --outFilterIntronMotifs RemoveNoncanonical parameter
The RIP-seq Reads uniquely mapping to the genome were used for peak calling with Homer. assuming the size of 500, extending the peaks to cover the full enriched region, assuming a fold enrichment of at least 2 over input reads, a poisson p-value threshold relative to input count of 1e-4
Genome_build: mm10
Supplementary_files_format_and_content: Peak files for each experiment with normalized tag count (txt file)

extract_protocol:
Liver was homogenized and ultracentrifuged on a sucrose cushion to isolate liver nuclei. Nuclear lysates were incubated with anti-NONO antibody-coated agarose beads and NONO-bound RNAs were extracted with Trizol reagent and sequenced.
Libraries were prepared using Illumina’s TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold according to manufacturer’s instructions

value: liver nuclei


title: WT_LivTotRNA_ZT0


title: RIP anti-NONO 10h re-fed (ZT22)

description: RIP anti-NONO 10h re-fed (ZT22)


title: Input anti-NONO 2h re-fed (ZT14)

description: Input anti-NONO 2h re-fed (ZT14)


title: RIP IgG

description: RIP IgG


title: C57BL/6J hippocampus rep 1

city: Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 3

department: Department of Psychology and Logopedics

country: Finland

institute: University of Helsinki

description: Library size selection for miRNA

data_processing:
Illumina Casava1.7 software for basecalling.
Adapter sequenced were trimmed from the reads, and they were mapped to mm10 mouse genome using bowtie v1.1.1 with parameters -q -v 3 -m 1 --best --strata, to allow SNPs between strains and miRNA editing.
Expressed miRNA-to-genome mismatch positions were called using FreeBayes FreeBayes v0.9.21 with parameters -F 0.01 -C 3 --pooled-continuous --min-base-quality 20 --min-coverage 10.
Alternatively, adapter sequences were removed and reads mapped directly to known miRNA (miRBase v21) and mouse genome mm10 using miRDeep2 v0.0.7, miraligner, and sRNAbench (sRNAtoolBox v1.0), to obtain miRNA and isomiR counts and to predict novel miRNAs.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: VCF file for miRNA-to-genome mismatch positions

growth_protocol: Mice were obtained from the Jackson Laboratory and singly housed for one week.

extract_protocol:
Samples were directly frozen in liquid nitrogen and stored in -80oC, and total RNA extracted with TriReagent.
miRNA libraries were prepared using Illumina TruSeq Small RNA Library Preparation kit and enriched for miRNA inserts by size selection using Covaris S-2. Library barcode is denoted as part of file name (6-letter index). Part of Hpc samples were resequenced (.2 extension in name).

treatment_protocol: Mice were killed by cervical dislobation. The brain was removed and dissections performed on a Petri dish filled with ice. Frontal cortex included 2 mm of the anterior part of the cortex. Hippocampus was dissected as a whole.

value: Wild type

value: 8 weeks

value: Hippocampus


title: C3H/HeJ hippocampus rep 1

description: Library size selection for miRNA


title: 129S1/SvImJ hippocampus rep 3

description: Library size selection for miRNA


title: RIP anti-NONO 2h re-fed (ZT14)

description: RIP anti-NONO 2h re-fed (ZT14)


title: Input anti-NONO fasted (ZT10)

description: Input anti-NONO fasted (ZT10)


title: RIP anti-NONO fasted (ZT10)

description: RIP anti-NONO fasted (ZT10)


title: 129S1/SvImJ hippocampus rep 2

description: Library size selection for miRNA


title: 129S1/SvImJ hippocampus rep 1

description: Library size selection for miRNA


title: A/J hippocampus rep 2

description: Library size selection for miRNA

value: A/J


title: A/J hippocampus rep 1

description: Library size selection for miRNA


title: FVB/NJ frontal cortex rep 3

description: Library size selection for miRNA

source_name: FVB/NJ_Frontal Cortex

value: FVB/NJ

value: Frontal Cortex


title: C57BL/6J hippocampus rep 3

description: Library size selection for miRNA


title: Input anti-NONO 10h re-fed (ZT22)

description: Input anti-NONO 10h re-fed (ZT22)


title: 20150814-45m-R2

city: Worcester

first: Job

last: Dekker

state: Massachusetts

address: 368 Plantation Street

department: Program in Systems Biology

country: USA

institute: UMass Medical School

library_source: genomic

data_processing:
cMapping Pipeline is publicly availalble at https://github.com/dekkerlab/cMapping This pipeline is describe in the publication by Lajoie et. Al., http://www.sciencedirect.com/science/article/pii/S1046202314003582?via%3Dihub
Cooler files were obtained from validpairs files. cooler is publicly available at https://github.com/mirnylab/cooler
Genome_build: galGal5
Genome_build: hg19
Supplementary_files_format_and_content: validpairs This format gives a list of the interacting pairs of loci in the genome, cooler: chromosome interractions in sparse form. For details, refer to  https://github.com/mirnylab/cooler

molecule: genomic DNA

organism: Gallus gallus

extract_protocol:
3 ml of 16% formaldehyde solution was added to the 50  ml tube to obtain a  final  concentration of 1%. The content was quickly mixed by inverting the tube twice and left at RT for 10 min for cross-linking.  2.5  ml  of  2.5  M  glycine  was  then  added  to  the  tube to  stop  cross-linking.  The content was quickly mixed by inverting the tube twice and left at RT for 5 min, and then on ice for at least 15 min.  Subsequently, cells were collected by centrifugation (2000 rpm, 10 min), and the cell pellet was frozen on dry ice and then stored at -80°C.
HiC was performed as in Belton et. al, 2012, http://www.sciencedirect.com/science/article/pii/S1046202312001168?via%3Dihub

treatment_protocol: 1-3   x107   CDK1as   wild   type   cells/sample   were   treated   with   1NM-PP1   (final concentration:  2  μ M)  for  10  h,  after  which  over  95%  were  in G2  (Fig.S14).  G2-arrested  cells were  collected  prior  to  1NM-PP1-washout.  To  release  cells  from  the  G2-arrest,  1NM-PP1  was washed  out  by  collecting  the  cells  by  centrifugation  (1300  rpm,  2-5  min,  depending  on  the volume of cultured cells, at RT) and suspending the cells in fresh media (10-20 ml). Cells were washed twice over a period of 10-20 min (depending on the number of cultures being processed simultaneously). These cells were suspended in fresh media and divided into flasks (one flask for each  time  point,  typically  1-3  x107  cells  per  flask)  and  returned  to  the  incubator  (counted  asTime=0  min).  At  each  time  point  (0,  2.5,  5,  7.5, 10,  30,  45,  60,  75  min),  a  flask  was  removed from  the  incubator  and  cells  with  media  were  transferred to  a  50  ml  falcon  tube,  which  was topped up with fresh media to 45 ml.

tag: phase

value: Prometaphase


title: 20150814-10m-R2

value: Prophase


title: 20150610-s45m-R1

tag: type

value: sorted


title: 20150812-G2-R1


title: 20150610-s75m-R1


title: 20150610-sG2-R1


title: 20150603-s30m-R1

value: WT


title: 20150610-s10m-R1


title: FVB/NJ frontal cortex rep 2

description: Library size selection for miRNA


title: 20150603-G2-R1


title: 20151009-10m-R1


title: 20150603-s60m-R1


title: FVB/NJ frontal cortex rep 1

description: Library size selection for miRNA


title: 20150814-75m-R2


title: DBA/2J frontal cortex rep 3

description: Library size selection for miRNA

source_name: DBA/2J_Frontal Cortex


title: 20150814-G2-R2


title: 20151009-0m-R1


title: 20151009-7m-R1


title: 20151009-2m-R1


title: 20151009-5m-R1


title: A/J hippocampus rep 3

description: Library size selection for miRNA


title: 20150609-60m-R1


title: DBA/2J frontal cortex rep 2

description: Library size selection for miRNA


title: 20150609-15m-R1


title: 20150603-s15m-R1


title: 20150609-30m-R1


title: 20150609-G2-R1


title: C3H/HeJ frontal cortex rep 3

description: Library size selection for miRNA

source_name: C3H/HeJ_Frontal Cortex


title: 20150609-5m-R1_


title: 92Pphase-10m-R1


title: 92PMphase-60m-R1


title: 87PMphase-30m-R1


title: 90G2-R2


title: NS-R1

value: NS


title: C3H/HeJ frontal cortex rep 1

description: Library size selection for miRNA


title: 129S1/SvImJ frontal cortex rep 3

description: Library size selection for miRNA

source_name: 129S1/SvImJ_Frontal Cortex


title: 129S1/SvImJ frontal cortex rep 2

description: Library size selection for miRNA


title: A/J frontal cortex rep 3

description: Library size selection for miRNA

source_name: A/J_Frontal Cortex


title: 90G2-R1


title: C57BL/6J frontal cortex rep 2

description: Library size selection for miRNA

source_name: C57BL/6J_Frontal Cortex


title: 90PMphase-30m-R2


title: 129S1/SvImJ frontal cortex rep 1

description: Library size selection for miRNA


title: C57BL/6J frontal cortex rep 1

description: Library size selection for miRNA


title: C57BL/6J frontal cortex rep 3

description: Library size selection for miRNA


title: A375-VR rep1

city: Madrid

first: Marta

last: Diaz Martinez

state: Madrid

address: Ramiro de Maeztu, 9

country: Spain

institute: Centro de Investigaciones Biológicas

description: Vemurafenib Resistant A375 melanoma cells

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using cutadapt version 1.7.1.
Trimmed reads were mapped to miRbase 21 using bowtie v1.0.0 with parameters -q --phred33-quals -v 0 --tryhard -k 1 --best --norc
Reads were assigned to microRNA ids and raw counts were produced
Normalized counts were generated with DESeq2 R package
Differential miRNA expression was determined with DESeq2 pipeline (Wald test fit type parametric)
Genome_build: miRbase 21
Supplementary_files_format_and_content: tab-delimited text files include counts for each sample and *norm_DESeq.csv files include normalized counts by size factors

organism: Homo sapiens

source_name: Melanoma cell line

growth_protocol: Melanoma cell lines were cultured in DMEM medium supplemented with 10% fetal bovine serum (Gibco, Paisley, UK)

extract_protocol:
mirVana miRNA Isolation kit (Thermo Fisher Scientific, Waltham, MA)
RNA libraries were prepared for sequencing using standard Illumina protocols for small RNAseq

treatment_protocol: Vemurafenib-resistant A375 cells were derived from parental A375 cells by treatment with sequential increases of vemurafenib (Selleckchem, Houston, TX) concentrations, from 10 nM to 1.3 μM, and were finally maintained as an uncloned resistant cell population in complete medium with 1.3 μM of VMF.

tag: cell type

value: BRAF V600E

tag: passages

tag: treatment

value: Vemurafenib


title: A/J frontal cortex rep 1

description: Library size selection for miRNA


title: DBA/2J frontal cortex rep 1

description: Library size selection for miRNA


title: A375-VR rep2


title: A/J frontal cortex rep 2

description: Library size selection for miRNA


title: A375 rep2

description: Non treated Parental A375 melanoma cells

value: non treated


title: C3H/HeJ frontal cortex rep 2

description: Library size selection for miRNA


title: 20160830-60m-R2


title: 20160830-30m-R2


title: 20160830-15m-R2


title: A375 rep1


title: 20160830-10m-R2


title: HelaS3-NS


title: om45BirA_srp72-AID_auxin30_2minCHX_2minBiotin_input

city: Cambridge

first: Jonathan

middle: S

last: Weissman

state: MA

address: 455 Main St

department: HHMI, Biology

institute: Whitehead Institute for Biomedical Research, MIT

description: Ribosome protected mRNA fragment. Sample barcode: CGAT

data_processing:
Base calls were called with Illumina CASAVA software
3' adaptor was trimmed using fastx_clipper with -l 24 (samples with barcode: -a AGATCGGAAGAGCACACGTCTGAACTC; samples without barcode: -a CTGTAGGCACCATCAAT
5' nucleotide was removed using fastx_trimmer -f 2
For samples with barcoded linker, barcodes were separated with fastx_barcode_splitter. The UMI (5 nt) and barcode (4 nt) were then removed from the 3' end of read using a custom script
Reads were aligned to rRNA, tRNA and cloning oligos using Bowtie v1.1.2. Unaligned (filtered) reads were aligned to a genomic index (sacCer3) using Tophat v2.1.1 with the following parameters: --bowtie1 --read-mismatches 0 --no-novel-juncs. Only uniquely-mapped reads were used for subsequent analysis.
Each alignment was assigned a specific P-site nucleotide using a 15 nt offset from the 3' end of the read. Gene level counts and rpkm were calculated using plastid cs count using a positions file that masks regions to which reads cannot uniquely align. For rpkm calculations, all reads mapping to any annotated exon (transcipt) were used for the denominator for total reads mapped.
Genome_build: sacCer3
Supplementary_files_format_and_content: Tab delimited file containing count and rpkm data

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown in SD media containing 0.125 ng/ml D-biotin to OD600 .4-.6.

extract_protocol:
Yeast cells were harvested by filtration, flash frozen, and cryogenically pulverized in a Retsch mixer-mill.
Footprinting was performed with RNase I, monosomes purified on 10-50% sucrose gradients and biotinylated ribosomes purified on streptavidin dynabeads. RNA was extracted with trizol and protected fragments gel purified. Ends were repaired with T4 PNK and ligated to a pre-adenylated linker with T4 RNA Ligase 2. In samples with sample barcode, pre-adenylated linker contained 5 nt UMI and 4 nt sample barcode. Unligated linkers were enzymatically removed and ligated fragments were gel purified, reverse transcribed and gel purified.  The cDNA was circularized then PCR amplified.
OTHER (ribosome profiling)

treatment_protocol: Cells were treated with 500 µM auxin for indicated times. For harvesting, where indicated, cells were treated with 100 µg/ml cycloheximide for 2 minutes prior to biotin induction with 10 nM biotin for the times shown.

value: srp72::srp72-AID-HA::LEU2 om45::OM45-mVenus-BirA::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI his3::OsTIR1-V5::URA3 leu2-delta-0 met15-delta-0 ura3-delta-0


title: 20160830-G2n-R2


title: om45BirA_srp72-AID_auxin0_2minCHX_2minBiotin_input

description: Ribosome protected mRNA fragment. Sample barcode: TAGC


title: tom20BirA_srp72-AID_auxin30_2minCHX_2minBiotin_input

description: Ribosome protected mRNA fragment. Sample barcode: GCTA

value: srp72::SRP72-AID-HA:OsTIR1::LEU2 tom20::TOM20-mVenus-BirA::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI leu2-3,112/leu2-3,112 trp1-1 /can1-100 ura3-1 ade2-1 his3-11,15


title: om45BirA_srp72-AID_auxin0_2minCHX_2minBiotin_pulldown


title: HelaS3-PM98


title: tom20BirA_srp72-AID_auxin30_2minCHX_2minBiotin_pulldown


title: om45BirA_srp72-AID_auxin30_2minCHX_2minBiotin_pulldown


title: 20160830-7m-R2


title: sec63BirA_srp72-AID_auxin60_noCHX_1minBiotin_pulldown

description: Ribosome protected mRNA fragment. Sample barcode: GACT

value: srp72::srp72-AID-HA::LEU2 sec63::SEC63-mVenus-BirA::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI his3::OsTIR1-V5::URA3 leu2-delta-0 met15-delta-0 ura3-delta-0


title: tom20BirA_srp72-AID_auxin0_2minCHX_2minBiotin_input


title: 20160830-G2p-R2


title: 20160919-30m-R2

value: CAPH-AID


title: KO thymic lymphoma Rep6

city: Edmonton

first: Qiumin

last: Tan

state: Alberta

address: 6-16 Medical Sciences Building

department: Cell Biology

country: Canada

institute: University of Alberta

description: BMTP set2 KO5

data_processing:
Illumina NextSeq 500
Raw reads were mapped to GENCODE GRCm38 (Primary assembly, release M15) using STAR aligner (STAR-2.5.3a)
Expression level for each gene was estimated using the --quantMode while performing the mapping with STAR. This read counts obtained are analogous to the expression level of the gene.
Using the obtained read counts, differential gene analyses were carried out using the DESeq2 package in the R environment.
Genome_build: GRCm38
Supplementary_files_format_and_content: Text files inclue read counts value for each gene; individual file for each sample.

source_name: Knockout lymphoma

growth_protocol: standard animal house conditions

extract_protocol:
AllPrep DNA/RNA kit
TruSeq Stranded mRNA Library Preparation Kit Set A (Illumina)

treatment_protocol: tamoxifen

value: Lymphoma

value: UBC-Cre/ERT2; Cic flox/flox as donor + TAM


title: sec63BirA_srp72-AID_auxin60_noCHX_1minBiotin_input


title: sec63BirA_srp72-AID_auxin30_noCHX_1minBiotin_pulldown


title: KO thymic lymphoma Rep4

description: UCK 192

value: UBC-Cre/ERT2; Cic flox/flox + TAM


title: 20160919-10m-R2


title: 20160919-60m-R2


title: KO thymic lymphoma Rep5

description: BMTP set1 KO6


title: 20160919-G2n-R2


title: C57BL/6J hippocampus rep 2

description: Library size selection for miRNA

value: Wild type

value: 8 weeks

value: Hippocampus


title: KO thymic lymphoma Rep3

description: UCK 147


title: sec63BirA_srp72-AID_auxin0_noCHX_1minBiotin_pulldown


title: 20160919-G2p-R2


title: tom20BirA_srp72-AID_auxin0_2minCHX_2minBiotin_pulldown


title: KO thymic lymphoma Rep2

description: CUCK 28


title: sec63BirA_srp72-AID_auxin0_noCHX_1minBiotin_input


title: KO thymic lymphoma Rep1

description: UCK 26


title: 20160714-60m-R1

value: Prometaphase


title: BirAubc6_srp72-AID_auxin60_2minCHX_2minBiotin_pulldown

description: Ribosome protected mRNA fragment

value: srp72::SRP72-AID-HA::LEU2 his3::pSEC63-BirA-mVenus-UBC6tailachor:OsTIR1-V5::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI leu2-delta-0 met15-delta-0 ura3-delta-0


title: 20160714-15m-R1


title: 20160919-7m-R2_

value: Prophase


title: 20160919-15m-R2


title: Control thymus Rep2

description: UCK 175

source_name: Control Thymus

value: Normal thymus

value: Cic flox/flox + TAM


title: Control thymus Rep3

description: UCK 207


title: Control thymus Rep1

description: UCK 174


title: BirAubc6_srp72-AID_auxin60_2minCHX_2minBiotin_input

description: Ribosome protected mRNA fragment


title: 20160714-10m-R1


title: 20160714-8m-R1


title: sec63BirA_srp72-AID_auxin30_noCHX_1minBiotin_input


title: BirAubc6_srp72-AID_auxin30_2minCHX_2minBiotin_pulldown

description: Ribosome protected mRNA fragment


title: BirAubc6_srp72-AID_auxin15_2minCHX_2minBiotin_pulldown

description: Ribosome protected mRNA fragment


title: BirAubc6_srp72-AID_auxin30_2minCHX_2minBiotin_input

description: Ribosome protected mRNA fragment


title: 20160714-G2n-R1


title: 20160714-30m-R1


title: BirAubc6_srp72-AID_auxin15_2minCHX_2minBiotin_input

description: Ribosome protected mRNA fragment


title: 20160714-G2p-R1


title: c57_drg_7day_2

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description: c57 drg 7day replicate 2

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Aligned to mm10 using STAR spliced read aligner
Count read using HT-seq and using mm10 RefSeq as reference
Normalization (TMM), quantitation (FPKM) and differential expression analysis using edgeR and limma voom.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values

source_name: c57 drg 7day 2

growth_protocol: Experiments were performed in adult (9-10 weeks old) male C57BL/6J mice (Jackson laboratory, Maine, USA).

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Nugen Ovation RNA Ultra Low Input (500 pg) +TruSeq Nano

treatment_protocol: Mice were anesthetized with isoflurane (2–4%) and SNI surgery performed; the tibial and common peroneal branches of the sciatic nerve were tightly ligated with a silk suture and transected distally while the sural nerve was left intact (10924808, 16542774).

value: dorsal root ganglion

tag: timepoint (days post sni)

tag: developmental stage

value: adult

tag: gender

value: male


title: Tert_neg_1

city: Stanford

first: Shengda

last: Lin

address: 269 Campus Dr. CCSR 1150

department: Medicine

institute: Stanford University

description: TERT(Low) cells from Mouse_1

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with TrimGalore 0.4.0, and then mapped to mm10 whole genome using tophat v2.0.13.
R packages "GenomicFeatures", "GenomicRanges", "GenomicAlignments", "Rsamtools" were used to generate the read count table.
Normalized read counts per gene were calculated using DEseq2.
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated values (CSV) files including count values for each sample, and a list of mapped genes and their respective statistical abundances.

source_name: hepatocytes

extract_protocol:
Hepatocytes were isolated by standard two-step collagenase perfusion. Cells were sorted into TRIzol-LS. Total RNA was extracted and purified using an RNeasy micro kit (Qiagen).
RNA-Seq libraries were constructed using a KAPA Stranded mRNA-Seq Kit (Kapa).

value: hepatocytes

value: 2 months

value: Tert(CreERT2/+); R26(LSL-Tomato/+)

tag: tert status

value: TERT(Low) cells


title: c57_drg_7day_1

description: c57 drg 7day replicate 1

source_name: c57 drg 7day 1


title: c57_drg_3_day_3

description: c57 drg 3 day replicate 3

source_name: c57 drg 3 day 3


title: Tert_pos_2

description: TERT(High) cells from Mouse_2

value: TERT(High) cells


title: Tert_pos_3

description: TERT(High) cells from Mouse_3


title: 20160726-30m-R1

value: CAPH-AID


title: 20160726-60m-R1


title: BirAubc6_srp72-AID_auxin0_2minCHX_2minBiotin_input

description: Ribosome protected mRNA fragment


title: Tert_neg_3

description: TERT(Low) cells from Mouse_3


title: 20160726-15m-R1


title: Tert_pos_1

description: TERT(High) cells from Mouse_1


title: BirAubc6_srp72-AID_auxin0_2minCHX_2minBiotin_pulldown

description: Ribosome protected mRNA fragment


title: c57_drg_3_day_1

description: c57 drg 3 day replicate 1

source_name: c57 drg 3 day 1


title: Tert_neg_2

description: TERT(Low) cells from Mouse_2


title: c57_drg_3_day_2

description: c57 drg 3 day replicate 2

source_name: c57 drg 3 day 2


title: pa0336 replicate  3

city: Warsaw

first: Maciej

last: Lirski

address: Pawińskiego 5a

department: Department of Protein Biosynthesis

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

description: Aligned bam files contain unaligned reads and flowspace information in header

data_processing:
Reads were filtered, and trimmed with Torrent Suite software using default settings.
Alignment was performed with Tmap aligner on PAO1-107 genome sequence (Pseudomonas Genome Database, www.pseudomonas.com) reporting all hits for multiple best read alignments.
Aligned reads were uploaded to Partek® Flow® software. Reads were quantified to PAO1-107 genome annotation (Pseudomonas Genome Database, www.pseudomonas.com) supplemented by novel transcripts and transcript boundaries generared by Rockhopper software (Ryan McClure et al. Nucleic Acids Research, 2013) using Partek® E/M (Estimation/Maximization) algorithm.
Normalization was performed in two steps using TMM and upper quartile methods.
Differential expression was analysed statistically with Partek® GSA (Gene Specific Analysis) using a multmodel approach assuming lognormal distribution with shrinkage of error values. Obtained p-values were FDR-corrected using Storey q-value (Storey JD. Ann. Statist., 2003). Genes with corrected p-values <= 0.05 were treated as significantly changed.
Genome_build: PAO1 107 (PGD)
Supplementary_files_format_and_content: Tab separated text file containing differential expression statistics for all identified transcripts

organism: Pseudomonas aeruginosa

source_name: cultured bacteria

extract_protocol:
RNA was isolated from the cell pellet with RNeasy Mini Kit (Qiagen). DNase I digestion using RapidOut DNA Removal Kit (Thermo Scientific) was applied to remove genomic DNA contamination. RNA quality and integrity was assessed with a Bioanalyzer (Agilent Technology) and concentration was estimated using a Nano Drop ND-1000 spectrophotometer.
Total RNA (800 ng) from three biological replicates of PAO1161RifR and 'rppH strains was spiked with ERCC RNA spike in mix 1 (Thermo Fisher, 4456740), rRNA depleted using Life Technologies RiboMinus™ Transcriptome Isolation Kit for bacteria (Thermo Fisher, K155004) and used for library preparation with Ion Total RNA-Seq Kit v2 (Thermo Fisher, 4475936) according to manufacturer’s manual. Libraries were subjected to clonal PCR using Ion PI™ Template OT2 200 Kit v3 (Thermo Fisher, 4488318) and Ion OneTouch™ 2 System (Thermo Fisher, 4474779). cDNA enriched beads were sequenced on Ion Proton™ Sequencer using Ion PI™ Sequencing 200 Kit v2 (Thermo Fisher, 4485149) and Ion PI™ Chip Kit v2 (Thermo Fisher,4482321).


title: 20160726-10m-R1


title: sec63BirA_srp72-AID_auxin30_2minCHX_2minBiotin_input

value: srp72::srp72-AID-HA::LEU2 sec63::SEC63-mVenus-BirA::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI his3::OsTIR1-V5::URA3 leu2-delta-0 met15-delta-0 ura3-delta-0


title: c57_drg_7day_3

description: c57 drg 7day replicate 3

source_name: c57 drg 7day 3


title: 20160726-8m-R1_


title: sec63BirA_srp72-AID_auxin60_2minCHX_2minBiotin_input


title: c57_drg_1_day_3

description: c57 drg 1 day replicate 3

source_name: c57 drg 1 day 3


title: 20160726-G2n-R1


title: pa0336 replicate  2


title: c57_drg_1_day_2

description: c57 drg 1 day replicate 2

source_name: c57 drg 1 day 2


title: pa0336 replicate  1


title: sec63BirA_srp72-AID_auxin15_2minCHX_2minBiotin_pulldown


title: c57_drg_1_day_1

description: c57 drg 1 day replicate 1

source_name: c57 drg 1 day 1


title: 20160726-G2p-R1


title: wild type replicate 2

value: PAO1161 RifR

value: wt


title: sec63BirA_srp72-AID_auxin15_2minCHX_2minBiotin_input


title: T02 treated with cadmium

city: Chengdu

first: Zhenyu

last: Bai

address: 211 Huimin Road, Wenjiang District

country: China

institute: Sichuan Agricultural University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step,clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Supplementary_files_format_and_content: FPKM

organism: Verbena bonariensis

source_name: leaves

extract_protocol:
total RNA was extracted with Trizol Reagent (Invitrogen), following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Finesse

value: A month old

value: 350 uMol/L Cadmium


title: c57_drg_naïve_3

description: c57 drg naïve replicate 3

source_name: c57 drg naïve 3

value: naïve


title: c57_drg_naïve_2

description: c57 drg naïve replicate 2

source_name: c57 drg naïve 2


title: wild type replicate 1


title: sec63BirA_srp72-AID_auxin0_2minCHX_2minBiotin_pulldown

description: Ribosome protected mRNA fragment. Sample barcode: AGTC


title: c57_drg_naïve_1

description: c57 drg naïve replicate 1

source_name: c57 drg naïve 1


title: sec63BirA_srp72-AID_auxin60_2minCHX_2minBiotin_pulldown

description: Ribosome protected mRNA fragment. Sample barcode: TCAG


title: T01 untreated

value: untreated


title: sec63BirA_srp72-AID_auxin0_2minCHX_2minBiotin_input

description: Ribosome protected mRNA fragment. Sample barcode: ATCG


title: mRNA_E11.5_forebrain_hs122_A5879-3_wtY_Male

status: Public on Jan 17 2018

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

description: Gene expression of whole forebrain

data_processing:
Basecalls performed using CASAVA
Reads were filtered cutadapt and aligned to the mm9 genome assembly using tophat
Genome_build: mm9
Supplementary_files_format_and_content: fpkm values of genes calculated by cufflinks

source_name: forebrain from wild-type male e11.5 mouse (hs122 line)

growth_protocol: Mice were maintained in an animal facilty under standard conditions.

extract_protocol:
Total RNA was extracted with Ambion RNAqueous Total RNA Isolation Kit
Ambion TURBO DNase treatment, Illumina TruSeq Stranded mRNA Sample Prep (according to manuf. protocol)
Total RNA was extracted with Ambion RNAqueous Total RNA Isolation Kit
Ambion TURBO DNase treatment, Illumina TruSeq Stranded mRNA Sample Prep (according to manuf. protocol)

treatment_protocol: None.  WT and KO mice were not subjected to any treatment.

value: FVB

value: forebrain

value: embryonic day 11.5

tag: genotype/variation

value: WT


title: mRNA_E11.5_forebrain_hs122_A7009-1_koY_Male

description: Gene expression of whole forebrain

source_name: forebrain from knockout male e11.5 mouse (hs122 line)

value: male

value: hs122 KO


title: mRNA_E11.5_forebrain_hs122_A7009-4_wtY_Male

description: Gene expression of whole forebrain


title: mRNA_E11.5_forebrain_hs122_A5879-8_koY_Male

description: Gene expression of whole forebrain


title: Six2_ChIP-Seq

first: Andrew

middle: P

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

data_processing:
Base call by bcl2fastq v. 2.17; adaptor and index sequences were trimmed
Fastq files were aligned using Novoalign
ChIP-Seq peaks were called using QuEST (Valouev et al., 2008)
peak files were generated by extracting the chromosome numbers coordinates and QuEST enrichment score from QuEST.out files
wig profiles were generated using QuEST; BigWig files were generated using Wig2BigWig published by UCSC genome browser
Genome_build: mm9
Supplementary_files_format_and_content: txt files containing peak coordinates; BigWig files containing UCSC genome browser visualization tracks

source_name: developing kidneys

extract_protocol:
Qiagen MinElute PCR Purification kit (#28004)
Rubicon ThruPlex genomic DNA library kit (#R400429)

value: CFW

tag: developing stage

tag: antibody

value: wild-type


title: sec63BirA_srp72-AID_auxin30_2minCHX_2minBiotin_pulldown

description: Ribosome protected mRNA fragment. Sample barcode: CTGA


title: wild type replicate 3

tag: strain


title: Hoxd11-BF_ChIP-Seq

value: FLAG (Sigma, #F1804)


title: Osr1-BF_ChIP-Seq


title: FLAG_ChIPSeq


title: Dog_MLHD_Bis_PCR_48

city: London

first: Robert

last: Lowe

address: 4 Newark Street

department: Blizard Institute

country: United Kingdom

institute: QMUL

description: Bis-PCR

data_processing:
Library strategy: Bis-PCR
Bismark (v0.13.1) was used to align  reads to the reference genome camFam using Bowtie2
Methylation counts were extracted using  https://bitbucket.org/lowelabqmul/methylation-extractor
Genome_build: canFam 3.1
Supplementary_files_format_and_content: chromosome,position,methylation count,total count

organism: Canis lupus familiaris

source_name: Buccal

extract_protocol:
Targeted bisulfite PCR-based analysis was performed using the 48.48 layout on the Fluidigm C1 system (Fluidigm, USA), coupled with Illumina MiSeq sequencing. Bisulfite PCR primers were designed using Primer3 (PMID:17485472),
DNA was bisfulite converted (EpiTect, Qiagen) prior to amplification. Amplicons from a single sample were pooled and individually indexed to create a multiplex library prior to sequencing on an Illumina MiSeq instrument using v3 chemistry.

tag: breed

value: MLHD

tag: tissue

value: buccal

tag: Sex

value: F


title: Dog_MLHD_Bis_PCR_47

description: Bis-PCR

tag: age


title: Wt1_ChIP-Seq

value: Wt1 (ProteinTech, 12609-1-AP)

tag: genotype


title: Dog_MLHD_Bis_PCR_46

description: Bis-PCR


title: hs123-mCherry

data_processing:
Raw data analysis and digital expression quantification was carried out using the Drop-seq published pipeline (PMID: 26000488) version 1.11. The alignment was performed using STAR (PMID: 23104886) version 2.4.1d.
For each one of the five libraries, the counts for each transcript were retrieved for the top 10,000 STAMPs. By means of the human cells spiked-in, the purity was determined using a 90% as cutoff (namely, if 90% or more of the transcripts assigned to a STAMP were from human or mouse, that STAMP was assigned to either a human or a mouse cell, otherwise it was considered as a doublet). After that, starting from the 50 STAMPs showing the highest number of detected transcripts, the doublet-rate was estimated as previously described (PMID: 26000488). The 51st STAMP was then added and the doublet-rate re-calculated, and so forth up to the 10,000th STAMP. A threshold on 90% doublet-rate was finally applied to the resulting curve, which in turn allowed the identification of a set of high-quality STAMPs. A further threshold on the minimum number of detected transcripts was applied, so that STAMPs showing less than 1,000 detected molecules were discarded. Results from the five libraries were then merged together.
Genome_build: mm10 (Genome Reference Consortium GRCm38) and hg19 (Genome Reference Consortium GRCh37)
Supplementary_files_format_and_content: dropseq_data.digital_expression.txt.gz: digital expression matrix, flat text files with tab delimiters; mm10_hg19.refFlat.gz: transcriptome combining mm10 genes, hg19 genes and transgenes, refFlat tabular format. Column headers (gene Name, name, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts, exonEnds)

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: embryonic forebrain and 293T/17 cells

extract_protocol:
Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads (ChemGene Beads, Lot 011416B). Cell concentration was set to 50 cells/µl. 2.5% 293T/17 human cells were added to each suspension.
As previously described (PMID: 26000488).

tag: strain (mouse)

tag: developmental stage (mouse)

value: gestational day e12.5

tag: tissue (mouse)

tag: enhancer


title: hs122-GFP (1)


title: hs122-GFP (2)


title: Dog_MLHD_Bis_PCR_42

description: Bis-PCR


title: Dog_MLHD_Bis_PCR_44

description: Bis-PCR

value: M


title: Dog_MLHD_Bis_PCR_43

description: Bis-PCR


title: Dog_MLHD_Bis_PCR_40

description: Bis-PCR


title: Dog_MLHD_Bis_PCR_45

description: Bis-PCR


title: Dog_MLHD_Bis_PCR_41

description: Bis-PCR


title: Dog_MLHD_Bis_PCR_36

description: Bis-PCR


title: Dog_MLHD_Bis_PCR_34

description: Bis-PCR


title: Dog_MLHD_Bis_PCR_33

description: Bis-PCR


title: Dog_MLHD_Bis_PCR_32

description: Bis-PCR


title: hs121-mCherry


title: Six2-BF_ChIP-Seq


title: Dog_MLHD_Bis_PCR_30

description: Bis-PCR


title: Dog_MLHD_Bis_PCR_38

description: Bis-PCR


title: Dog_MLHD_Bis_PCR_35

description: Bis-PCR


title: Dog_MLHD_Bis_PCR_28

description: Bis-PCR


title: Dog_MLHD_Bis_PCR_27

description: Bis-PCR


title: Dog_MLHD_Bis_PCR_26

description: Bis-PCR


title: Dog_FCR_Bis_PCR_23

description: Bis-PCR

value: FCR


title: Dog_MLHD_Bis_PCR_25

description: Bis-PCR


title: Dog_MLHD_Bis_PCR_39

description: Bis-PCR


title: Dog_FCR_Bis_PCR_21

description: Bis-PCR


title: Dog_FCR_Bis_PCR_22

description: Bis-PCR


title: Dog_FCR_Bis_PCR_19

description: Bis-PCR


title: Dog_FCR_Bis_PCR_16

description: Bis-PCR


title: Dog_FCR_Bis_PCR_17

description: Bis-PCR


title: Dog_FCR_Bis_PCR_18

description: Bis-PCR


title: Dog_FCR_Bis_PCR_13

description: Bis-PCR


title: Dog_FCR_Bis_PCR_15

description: Bis-PCR


title: Dog_FCR_Bis_PCR_24

description: Bis-PCR


title: Dog_MLHD_Bis_PCR_29

description: Bis-PCR


title: Dog_FCR_Bis_PCR_14

description: Bis-PCR


title: hs119-GFP


title: Dog_FCR_Bis_PCR_11

description: Bis-PCR


title: Dog_MLHD_Bis_PCR_37

description: Bis-PCR


title: Dog_FCR_Bis_PCR_9

description: Bis-PCR


title: Dog_FCR_Bis_PCR_7

description: Bis-PCR


title: Dog_FCR_Bis_PCR_5

description: Bis-PCR


title: Dog_FCR_Bis_PCR_6

description: Bis-PCR


title: Dog_FCR_Bis_PCR_4

description: Bis-PCR


title: Dog_FCR_Bis_PCR_8

description: Bis-PCR


title: Dog_FCR_Bis_PCR_12

description: Bis-PCR


title: Dog_FCR_Bis_PCR_20

description: Bis-PCR


title: Dog_FCR_Bis_PCR_2

description: Bis-PCR


title: Sample_3507, CD>WD_PBS

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

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

data_processing:
Illumina Casava1.81 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with Hisat2 (v2.0.6) against the mm10 reference genome
Gene and transcript information was extracted with Partek Genomics Suite (v6.6). Annotated data was normalized using statistical software R (v3.0.2) including DESeq2 package. Normalized read counts lower than 1 were set to the floor value 1.Genes were defined as expressed with normalized RNA-seq values ≥ 10.
Genome_build: mm10
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the mm10 reference transcriptome

source_name: granulocyte-monocyte progenitor (GMP) cells

extract_protocol:
For RNA-sequencing 10.000-50.000 sorted GMPs were collected immediately in Trizol containing b-mercaptoethanol. RNA was extracted using the RNeasy Micro RNA Isolation kit (Quiagen)
Library preparation for subsequent RNA-sequencing analysis was performed using the TruSeq. RNA Library Prep Kitv2 (Illumina) following manufacturer’s protocol instructions

treatment_protocol: Mice were intravenously injected with PBS (vehicle control) or E.coli derived ultrapure LPS (0111:B4; 10ug/ mouse) six hours prior to sacrifice

tag: cell type

value: Ldlr-/- NLRP3-/-

tag: stimulation

value: PBS

tag: diet

value: chow-diet>Western-diet

tag: batch


title: Sample_3508, CD>WD_LPS

value: granulocyte-monocyte progenitor (GMP) cells

value: LPS


title: Sample_3506, HFD_LPS

value: HFD


title: Sample_3505, HFD_LPS


title: Sample_3504, HFD_PBS


title: Sample_3502, CD_LPS

value: chow-diet


title: Dog_MLHD_Bis_PCR_31

description: Bis-PCR


title: Dog_FCR_Bis_PCR_10

description: Bis-PCR


title: Sample_3499, CD_PBS


title: Sample_2481, CD>WD_LPS


title: Sample_2478, CD>WD_LPS


title: Sample_2460, HFD_PBS


title: Sample_2475, CD>WD_PBS


title: Sample_3501, CD_LPS


title: Dog_FCR_Bis_PCR_3

description: Bis-PCR


title: Sample_1981

extract_protocol:
For RNA-sequencing 10.000-50.000 sorted HSPCs , CMPs and GMPs were collected immediately in Trizol containing b-mercaptoethanol. RNA was extracted using the RNeasy Micro RNA Isolation kit (Quiagen)
Library preparation for subsequent RNA-sequencing analysis was performed using the TruSeq. RNA Library Prep Kitv2 (Illumina) following manufacturer’s protocol instructions

value: GMP

value: Ldlr-/-

value: CD


title: Sample_2448, CD_PBS


title: Sample_2445, CD_PBS


title: Sample_1978


title: Sample_1980


title: Sample_2457, HFD_PBS


title: Sample_1976


title: Sample_1975


title: Dog_FCR_Bis_PCR_1

description: Bis-PCR


title: Sample_2454, CD_LPS


title: Sample_3500, CD_PBS


title: Input-2_S4

first: Helen

middle: M

last: Rowe

address: 90 Gower Street

department: Infection and Immunity

institute: University College London

description:
Input-2_S4_L001
Total input 2
processed data file:
Spreadsheet4 and Spreadsheet5

data_processing:
RNAseq reads were mapped to the mouse genome (GRCm38/mm10) using Bowtie2 v2.2.4 and Kallisto  (https://pachterlab.github.io/kallisto/) with default parameters (k-mers equal to 31).
Data were imported into R using the R package (tximport) and differentially expressed genes were identified with Deseq2 (https://f1000research.com/articles/4-1521/v1). P-values were adjusted for multiple testing with the Benjamini-Hochberg false-discovery-rate (FDR).
RNAseq reads were also mapped to rodent repbase (http://www.girinst.org/server/ RepBase/protected/RepBase20.06.fasta/rodrep.ref). The samtools v.1.19 idxstats utility was used to extract the number of mapped reads per repeat, that were inputed into the R package DESeq2 (https://bioconductor.org/packages/3.2/bioc/html/DESeq2.html) to identify differentially expressed repeats using empty as control. P-values were adjusted for multiple testing with the Benjamini-Hochberg false-discovery-rate (FDR) procedure.
For Chip-seq data, trim_galore v0.4.1 was used to remove adapters and for trimming reads. Reads were mapped against mm10 using bowtie2-2.2.4 with default parameters and duplicates were removed with picard-1.135.
TASOR peaks were called using MACS2 v2.1.1.20160309 with --nomodel parameter, extension size = 150 and total Inputs as controls. Consensus peaks between TASOR replicates were derived using Diffbind_2.4.8. Ooverlap of peaks with genes and repeats were obtained using bedtools-2.17.0 on mm10 data downloaded from the UCSC browser.
Chip-seq reads were also mapped to RepBase20.06.fasta/rodent.ref. The samtools v.1.19 idxstats and flgstat utilities were used to extract the number of mapped reads per repeat and calculate RPKMs in each sample.
Genome_build: mm10
Supplementary_files_format_and_content: 3 processed excel files for mRNA-seq, Spreadsheet1, Spreadsheet2 and Spreadsheet3. 2 processed excel files for ChIP-seq, Spreadsheet4 and Spreadsheet5.
Spreadsheet1: Corepressed genes
Spreadsheet2: Differentially expressed repeats
Spreadsheet3: TRIM28-TASOR corepressed genes
Spreadsheet4: TASOR ChIP mapping Repbase
Spreadsheet5: TASOR ChIP mapping the genome

source_name: Naïve ESCs_none (input)

growth_protocol: mouse ESCs were cultured on gelatin-coated plates (0.2%) in media containing 2 small-molecule inhibitors of MEK and GSK3 plus LIF (2i + LIF), as described (Ying et al., 2008, Ficz et al., 2013). Cells were split every other day using accutase (Gibco, A11105-01) and cultured for 7 days before transduction.

extract_protocol:
Total RNA was extracted using an RNeasy mini kit (Qiagen) and treated with DNase (Ambion AM1907). The RNA was quality checked on a 2200 Tapestation using the RNA ScreenTape assay (Agilent Technologies, Wokingham, UK) and the RNA concentration measured using a Qubit RNA High Sensitivity kit (LifeTechnologies, Paisley, UK). For ChIP-seq, After reverse-crosslinking, DNA was purified with a minElute PCR purification kit.
PolyA-tailed mRNA was separated and libraries were prepared using KAPA’s Stranded mRNASeq kit (Roche Diagnostics, Burgess Hill, UK) according to the manufacturer’s instructions using an input of 500 ng, a fragmentation incubation time of 6 minutes at 94°C, and 12 cycles of PCR for library amplification. Samples were sequenced on Illumina’s NextSeq500 (Illumina Cambridge, Chesterford, UK) using a high output 300 cycle paired-end run in order to map repetitive regions more accurately. Twenty-four libraries were multiplexed in the same run to achieve up to 16M reads/sample. Libraries were pooled in equimolar quantities, calculated from concentrations measured using the Qubit dsDNA High Sensitivity assay kit (Life Technologies, Paisley, UK) and fragment analysis using the D1000 High Sensitivity kit on the 2200 Tapestation (Agilent Technologies, Wokingham, UK).  For ChIP-seq, we used the NEBNext DNA Ultra II library prep kit from New England Biolabs. 1ng was used and 10 cycles of amplification were performed. Single 86bp read sequencing was performed with >100 million reads per sample.
Stranded mRNA-seq. For ChIPseq: single 86 bp read sequencing

treatment_protocol: Two days after transduction with the stated shRNAs,  the cells were selected with puromycin (1ug/ml) for at least 24 hours and until parallel puromycin-treated untransduced cells died. Total RNA was harvested 5 days post puromycin addition. ChIP-seq: sonication was performed on a bioruptor (Diagenode). Samples were sonicated at 10x106 cells per tube in 300ul lysis buffer for 15 to 20 cycles of 30sec ON/30sec OFF, high power, and fragment size was verified on 2% agarose gels. Chromatin was precleared with beads (protein G dynabeads, 10003D) before immunoprecipitations (IPs) with an antiboy to TASOR (Atlas, HPA017142) performed with 3x106 cells per IP. 10ug of antibody was used per IP.

value: Naive embryonic stem cells

tag: culture conditions

value: 2i+LIF culture

tag: chip antibody

value: none (input)


title: Tasor-1_S2

description:
Tasor-1_S2_L001
TASOR ChIP 1
processed data file:
Spreadsheet4 and Spreadsheet5

source_name: Naïve ESCs_TASOR

value: TASOR (Atlas, HPA017142)


title: Tasor-2_S3

description:
Tasor-2_S3_L001
TASOR ChIP 2
processed data file:
Spreadsheet4 and Spreadsheet5


title: Sample_2469, HFD_LPS


title: 3_2i_tasor

description:
3_2i_tasor_S14
Experiment 3: TASOR shRNA
processed data file:
Spreadsheet1, Spreadsheet2 & Spreadsheet 3

source_name: Naïve ESCs_TASOR shRNA

tag: transduced with

value: TASOR shRNA


title: Sample_3503, HFD_PBS


title: 3_2i_kap1

description:
3_2i_kap1_S12
Experiment 3: TRIM28 shRNA
processed data file:
Spreadsheet1, Spreadsheet2 & Spreadsheet 3

source_name: Naïve ESCs_TRIM28 shRNA

tag: strain

value: TRIM28 shRNA


title: 3_2i_eset

description:
3_2i_eset_S13
Experiment 3: SETDB1 shRNA
processed data file:
Spreadsheet1, Spreadsheet2 & Spreadsheet 3

source_name: Naïve ESCs_SETDB1 shRNA

value: SETDB1 shRNA


title: 3_2i_empty

description:
3_2i_empty_S11
Experiment 3: Control shRNA
processed data file:
Spreadsheet1, Spreadsheet2 & Spreadsheet 3

source_name: Naïve ESCs_Control shRNA

value: Control shRNA


title: Sample_1971

value: WD>CD


title: Sample_1979


title: Sample_1974

value: PBS


title: Sample_1972


title: Sample_1977


title: Sample_1970


title: Input-1_S1

description:
Input-1_S1_L001
Total input 1
processed data file:
Spreadsheet4 and Spreadsheet5


title: Sample_1969


title: 2_2i_atrx

description:
2_2i_atrx_S10
Experiment 2: ATRX shRNA
processed data file:
Spreadsheet1, Spreadsheet2 & Spreadsheet 3

source_name: Naïve ESCs_ATRX shRNA

value: ATRX shRNA


title: Sample_1968


title: 2_2i_kap1

description:
2_2i_kap1_S7
Experiment 2: TRIM28 shRNA
processed data file:
Spreadsheet1, Spreadsheet2 & Spreadsheet 3


title: 2_2i_empty

description:
2_2i_empty_S6
Experiment 2: Control shRNA
processed data file:
Spreadsheet1, Spreadsheet2 & Spreadsheet 3


title: 2_2i_tasor

description:
2_2i_tasor_S9
Experiment 2: TASOR shRNA
processed data file:
Spreadsheet1, Spreadsheet2 & Spreadsheet 3


title: 1_2i_atrx

description:
1_2i_atrx_S5
Experiment 1: ATRX shRNA
processed data file:
Spreadsheet1, Spreadsheet2 & Spreadsheet 3


title: 1_2i_tasor

description:
1_2i_tasor_S4
Experiment 1: TASOR shRNA
processed data file:
Spreadsheet1, Spreadsheet2 & Spreadsheet 3


title: 1_2i_eset

description:
1_2i_eset_S3
Experiment 1: SETDB1 shRNA
processed data file:
Spreadsheet1, Spreadsheet2 & Spreadsheet 3


title: Sample_1967


title: Sample_1973

value: LPS


title: 1_2i_kap1

description:
1_2i_kap1_S2
Experiment 1: TRIM28 shRNA
processed data file:
Spreadsheet1, Spreadsheet2 & Spreadsheet 3


title: input_NP_2

description: genotype: wild-type

data_processing:
Base call by bcl2fastq v. 2.17; adaptor and index sequences were trimmed
Fastq files were aligned using Novoalign
ChIP-Seq peaks were called using QuEST (Valouev et al., 2008)
peak files were generated by extracting the chromosome numbers coordinates and QuEST enrichment score from QuEST.out files
wig profiles were generated using QuEST; BigWig files were generated using Wig2BigWig published by UCSC genome browser
Genome_build: mm10
Supplementary_files_format_and_content: txt files containing peak coordinates; BigWig files containing UCSC genome browser visualization tracks

source_name: nephron progenitor cells

value: CFW

tag: developing stage

tag: antibody


title: input_NP_1

description: genotype: wild-type


title: Sample_1966

value: WD


title: 1_2i_empty

description:
1_2i_empty_S1
Experiment 1: Control shRNA
processed data file:
Spreadsheet1, Spreadsheet2 & Spreadsheet 3


title: Sample_1965

value: GMP


title: Ctcf_NP_ChIP-Seq_1

description: genotype: wild-type

value: CTCF (D31H2) XP® Rabbit mAb


title: Sample_1963

value: Ldlr-/-


title: Ctcf_NP_ChIP-Seq_2

description: genotype: wild-type


title: Wt1_NP_ChIP-Seq_2

description: genotype: wild-type

value: Wt1 (ProteinTech, 12609-1-AP)


title: 2_2i_eset

description:
2_2i_eset_S8
Experiment 2: SETDB1 shRNA
processed data file:
Spreadsheet1, Spreadsheet2 & Spreadsheet 3

value: Naive embryonic stem cells

value: 2i+LIF culture


title: Wt1_ChIP-Seq_1

description: genotype: wild-type


title: Sample_1962


title: Sample_1964


title: Osr1-BF_ChIP-Seq_2

description: genotype: Six2DE-Osr1BF

value: FLAG (Sigma, #F1804)


title: Wt_SNLD1_m6A_IP_3

city: Philadelphia

first: Guo-li

last: Ming

state: PA

address: Clinical Research Building  Suite 105, 415 Curie Boulevard

department: Neuroscience

institute: University of Pennsylvania

description:
MeRIP-seq
m6ALevel_rawcount.txt

data_processing:
For RNAseq and MeRIP-seq,ater adaptor trimming with Trimmomatic and quality control, sequence reads were mapped to the mouse genome (mm10) using the STAR aligner. Gene count tables were generated using STAR aligned to mm10 transcriptome and normalized using DESeq2
For m6A-CLIPseq, adapters, and the first three nucleotides of the sequencing read (derived from the TSO oligo) were removed by Trimmomatic. The remaining reads (> 20 nt) were then mapped to the mouse genome (mm10) using STAR aligner (--outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.08 --alignEndsType EndToEnd). After removal of PCR duplicates, uniquely mapped reads were used for CIMS analysis similar to previous studies (Linder et al., 2015; Moore et al., 2014; Zhang and Darnell, 2011).
Genome_build: mm10
Supplementary_files_format_and_content: raw count tables, bedgraph, bed

source_name: DRG

extract_protocol:
L4/5 DRGs were removed, flash frozen on dry ice, and total RNA was harvested using Trizol reagent. Poly(A) mRNA was then isolated using two rounds of selection with oligo(dT) magnetic beads.
Smart-seq2 protocol was used with 100ng of total RNA or 150ng mRNA for the construction of sequencing libraries.

treatment_protocol: A sham surgery or sciatic nerve crush

tag: tissue

value: L4/5 DRG

value: wild type

tag: rip antibody

value: m6A Ab, Synaptic Systems, Cat. 202003


title: Wt_Naive_m6A_CLIP

description: m6A-CLIPseq (miCLIP)

tag: genotype


title: Six2_ChIP-Seq_2

description: genotype: wild-type

value: Six2 (Proteintech,11562-1-AP)


title: Sample_1960


title: Sample_1109

value: CD


title: Sample_1961

value: PBS


title: Wt_SNL_m6A_CLIP

description: m6A-CLIPseq (miCLIP)


title: Sample_1106


title: Sample_2265

data_processing:
Illumina Casava1.81 software used for basecalling.
For Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) data analysis, short reads were aligned to the mouse genome version mm10 with Bowtie v1.1.1. Duplicate reads were flagged with Picard v1.134 prior to peak calling with MACS2 v2.1.0.20140616. Consensus peak regions across all samples were generated with the ‘reduce’ function of the Bioconductor GenomicRanges v1.26.3 package, followed by read counting per sample, which was done with bedtools multiBamCov v2.25.0. Blacklisted analysis regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm9-mouse/mm9-blacklist.bed.gz with coordinate adjustments by the LiftOver tool to mm10, https://genome.ucsc.edu/cgi-bin/hgLiftOver) as well as regions that were not consistently present across samples of the same analysis group were excluded from the analysis. Differentially accessible regions were determined with the DESeq2 v1.14.1 package and mapped to nearest genes with the ChIPseeker v1.10.3 package.
Genome_build: mm10
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the mm10 reference transcriptome

extract_protocol:
For ATAC-sequencing, 50.000 flow sorted HSPCs, CMPs and GMPs were collected in ice-cold HBSS containing 0.1%BSA and 2mM EDTA, and immediately processed following the protocol of Buenrosto, Greenleaf et al., Curr. Protoc. Mol. Biol., 2015
library preparation has been performed as described in the protocol of Buenrosto, Greenleaf et al., Curr. Protoc. Mol. Biol., 2015

value: WD>CD


title: Wt1_NP_ChIP-Seq_1

description: genotype: wild-type


title: Sample_2256


title: Wt_Naive_m6A_IP_2

description:
MeRIP-seq
m6ALevel_rawcount.txt


title: Mettl14cKO_SNLD1_3

description:
RNA-Seq
Mettl14_RNAseq_rawcounts.txt


title: Wt_SNLD1_m6A_Input_1

description:
MeRIP-seq
m6ALevel_rawcount.txt


title: Wt_SNLD1_m6A_Input_2

description:
MeRIP-seq
m6ALevel_rawcount.txt


title: Wt_SNLD1_m6A_IP_2

description:
MeRIP-seq
m6ALevel_rawcount.txt


title: Wt_Naive_m6A_IP_3

description:
MeRIP-seq
m6ALevel_rawcount.txt


title: Wt_Naive_m6A_IP_1

description:
MeRIP-seq
m6ALevel_rawcount.txt


title: Wt_Naive_m6A_Input_2

description:
MeRIP-seq
m6ALevel_rawcount.txt


title: Wt_SNLD1_m6A_IP_1

description:
MeRIP-seq
m6ALevel_rawcount.txt


title: Sample_2253


title: Mettl14cKO_SNLD1_2

description:
RNA-Seq
Mettl14_RNAseq_rawcounts.txt


title: Wt_Naive_m6A_Input_1

description:
MeRIP-seq
m6ALevel_rawcount.txt


title: Mettl14cKO_Naive_2

description:
RNA-Seq
Mettl14_RNAseq_rawcounts.txt


title: Mettl14cKO_Naive_3

description:
RNA-Seq
Mettl14_RNAseq_rawcounts.txt


title: Sample_2241


title: Mettl14cKO_SNLD1_1

description:
RNA-Seq
Mettl14_RNAseq_rawcounts.txt


title: Sample_2244


title: Mettl14cKO_Naive_1

description:
RNA-Seq
Mettl14_RNAseq_rawcounts.txt


title: WT_SNLD1_2

description:
RNA-Seq
Mettl14_RNAseq_rawcounts.txt


title: WT_SNLD1_3

description:
RNA-Seq
Mettl14_RNAseq_rawcounts.txt


title: WT_SNLD1_1

description:
RNA-Seq
Mettl14_RNAseq_rawcounts.txt


title: WT_Naive_3

description:
RNA-Seq
Mettl14_RNAseq_rawcounts.txt


title: WT_Naive_2

description:
RNA-Seq
Mettl14_RNAseq_rawcounts.txt


title: Six2_ChIPSeq_SJL_1

value: SJL/J

value: wild-type


title: Six2_ChIPSeq_SJL_2


title: input_ChIPSeq_B6


title: IgG_ChIPSeq

value: CFW

value: rabbit IgG


title: Six2_ChIPSeq_B6_2


title: input_ChIPSeq


title: E16.5_Six2-_mRNA_Seq_2

data_processing:
Base call by bcl2fastq v. 2.17; adaptor and index sequences were trimmed
Fastq files were aligned using TopHat2
Gene-level quantification was presented as TPM and calculated by Partek Genomic Suite
Genome_build: mm10
Supplementary_files_format_and_content: txt files containing TPM values by gene

extract_protocol:
Qiagen Rneasy micro kit (#74004)
Kapa stranded mRNA-Seq library (#KK8420)

tag: marker


title: E16.5_Six2+_mRNA_Seq_1


title: P2_Six2+_mRNA_Seq_2


title: E16.5_Cited1+_mRNA_Seq_3


title: E16.5_Cited1+_mRNA_Seq_2


title: P2_Six2+_mRNA_Seq_1


title: E16.5_Six2-_mRNA_Seq_1


title: E16.5_Six2+_mRNA_Seq_3


title: NMR_Bis_PCR_24

data_processing:
Library strategy: Bis-PCR
Bismark (v0.13.1) was used to align  reads to the reference genome camFam using Bowtie2
Methylation counts were extracted using  https://bitbucket.org/lowelabqmul/methylation-extractor
Genome_build: hetGla2
Supplementary_files_format_and_content: chromsome,position,methylation count,total count

organism: Heterocephalus glaber

source_name: Liver

extract_protocol:
Targeted bisulfite PCR-based analysis was performed using the 48.48 layout on the Fluidigm C1 system (Fluidigm, USA), coupled with Illumina NextSeq sequencing. Bisulfite PCR primers were designed using Primer3 (PMID:17485472),
DNA was bisfulite converted (EpiTect, Qiagen) prior to amplification. Amplicons from a single sample were pooled and individually indexed to create a multiplex library prior to sequencing on an Illumina NextSeq instrument.

value: Liver

tag: age (wks)


title: NMR_Bis_PCR_22


title: NMR_Bis_PCR_21


title: E16.5_Six2-_mRNA_Seq_3


title: NMR_Bis_PCR_23


title: NMR_Bis_PCR_20


title: WT_Naive_1

description:
RNA-Seq
Mettl14_RNAseq_rawcounts.txt


title: input_ChIPSeq_SJL


title: NMR_Bis_PCR_17


title: NMR_Bis_PCR_16


title: NMR_Bis_PCR_15


title: NMR_Bis_PCR_18


title: NMR_Bis_PCR_14


title: NMR_Bis_PCR_13


title: NMR_Bis_PCR_19


title: NMR_Bis_PCR_12


title: E16.5_Cited1+_mRNA_Seq_1


title: Six2_ChIPSeq_B6_1


title: E16.5_Six2+_mRNA_Seq_2


title: NMR_Bis_PCR_11


title: mRNA_hs122hs123_e115_FB_B3116-11_koY_M

description: Gene expression of whole forebrain

source_name: forebrain from knockout male e11.5 mouse (hs122/hs123 line)

value: FVB

value: forebrain

tag: gender

value: male

tag: age

value: embryonic day 11.5

tag: genotype/variation


title: NMR_Bis_PCR_10


title: NMR_Bis_PCR_8


title: mRNA_hs122hs123_e115_FB_B3116-5_wtY_M

description: Gene expression of whole forebrain

source_name: forebrain from wild-type male e11.5 mouse (hs122/hs123 line)

tag: cell type

value: WT


title: mRNA_hs119hs121_e115_FB_B2085-1_koY_M

description: Gene expression of whole forebrain

source_name: forebrain from knockout male e11.5 mouse (hs119/hs121 line)


title: mRNA_hs122hs123_e115_FB_B3003-2_wtY_M

description: Gene expression of whole forebrain


title: mRNA_hs122hs123_e115_FB_B3003-3_koY_M

description: Gene expression of whole forebrain


title: mRNA_hs119hs121_e115_FB_B2089-5_koY_M

description: Gene expression of whole forebrain


title: mRNA_hs119hs121_e115_FB_B2085-6_wtY_M

description: Gene expression of whole forebrain

source_name: forebrain from wild-type male e11.5 mouse (hs119/hs121 line)


title: NMR_Bis_PCR_5


title: mRNA_hs123_e115_2069-11_FB_wtY_male

description: Gene expression of whole forebrain

source_name: forebrain from wild-type male e11.5 mouse (hs123 line)


title: NMR_Bis_PCR_9


title: NMR_Bis_PCR_3


title: NMR_Bis_PCR_2


title: mRNA_hs119hs121_e115_FB_B2089-4_wtY_M

description: Gene expression of whole forebrain


title: mRNA_hs123_e115_2065-8_FB_wtY_male

description: Gene expression of whole forebrain


title: mRNA_hs123_e115_2069-10_FB_koY_male

description: Gene expression of whole forebrain

source_name: forebrain from knockout male e11.5 mouse (hs123 line)

value: hs123 KO


title: mRNA_hs123_e115_2065-9_FB_koY_male

description: Gene expression of whole forebrain


title: mRNA_hs121_e115_B1036-2_FB_koY_male

description: Gene expression of whole forebrain

source_name: forebrain from knockout male e11.5 mouse (hs121 line)

value: hs121 KO


title: mRNA_hs121_e115_B1036-1_FB_wtY_male

description: Gene expression of whole forebrain

source_name: forebrain from wild-type male e11.5 mouse (hs121 line)


title: NMR_Bis_PCR_1


title: mRNA_hs121_e115_A8229-3_FB_koY_male

description: Gene expression of whole forebrain


title: RNA-seq

city: Tel Aviv-Yafo

first: Tamir

last: Tuller

address: 30 Levanon st.

department: Biomedical Engineering Dept.

country: Israel

institute: Tel Aviv University

description: mRNA

data_processing:
Transcript sequences of Saccharomyces cerevisiae were obtained from Ensembl (R64 release 87), and UTR lengths were based on previously reported major transcript isoforms (mTIF, selecting the longest one available for each transcript, and using a default length of 500bp for missing UTRs) [PMID:23615609]. We trimmed adaptors (AGATCGGAAGAGCACACGTCT) from the reads using Cutadapt (version 1.12), and utilized Bowtie (version 1.2) to map them to the transcriptome. In the first phase, we discarded Ribo-seq reads that mapped to rRNA and tRNA sequences with Bowtie parameters ‘--n 2--seedlen 21 –k 1 --norc’. In the second phase, we mapped the remaining Ribo-seq reads, as well as RNA-seq reads, to the transcriptome with Bowtie parameters ‘-v 2 -a --strata --best --norc –m 200’. Unique alignments were first assigned to the ribosome occupancy profiles. For multiple alignments, the best alignments in terms of number of mismatches were kept. Then, multiple aligned reads were distributed between locations according to the distribution of unique ribosomal reads in the respective surrounding regions. The location of the A-site (for the upstream ribosome in the case of footprints containing pairs of ribosomes, i.e. dRPFs) was estimated for each read length by performing meta-gene analysis of the 5’-end of reads upstream to the start codon of ORFs (15nt and 17nt shifts for mRPF and dRPF profiles, respectively).
Genome_build: sacCer R64-1-1
Supplementary_files_format_and_content: The processed files contain RPKM values based on the number of reads that mapped to each CDS, in tab delimited format.

source_name: Saccharomyces cerevisiae

extract_protocol: Ribosome profiling was performed as previously described [PMID:19213877; PMID:22836135], with minor modifications. For depleting rRNA we utilized Ribo-Zero by EpiCentre. We utilized the small RNA sequencing kit from New England BioLabs. Sucrose gradient fractionation was employed for filtering reads with one or two ribosomes. Additional filtering of DNA with the relevant length before sequencing was performed with BluePippin.

tag: media

value: YPD

tag: sample type

value: total RNA


title: Ribo-seq, dRPF

description: ribosome protected RNA fragment (ribosome pair - dRPF)

value: ribosome protected RNA fragment


title: lesion for patient p23

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: RNA-seq for lesion from patient p23

data_processing:
The RNA-seq data was aligned against human (hg19 genome, Ensemble v75 transcriptome) or KSHV (NC_009333) genomes and transcriptomes using the bowtie2 algorithm, and RSEM v1.2.31 software was used to estimate read counts and FPKM values at the gene level
DESeq2 was used for differentail expression analysis
Genome_build: hg19, NC_009333
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene from human and KSHV transcriptome

source_name: control tissue from KS lesion

growth_protocol: A 4 mm cylindrical single-use punch was used to collect biopsy samples from a representative KS lesion and a second identical punch biopsy was collected from an uninvolved ipsilateral /contralateral site on the same individual. The collected tissues were treated overnight in RNALater (Ambion) to facilitate subsequent DNA/RNA extraction. RNALater was removed prior to freezing at -80˚C.

extract_protocol:
Genomic RNA was extracted from the homogenized sample with miRNeasy mini kit with on-column DNase I treament according to the manufacturer’s protocol (Qiagen, Hilden, Germany).
Library preparation was performed using the TruSeq™ RNA Library Prep Kit v2

treatment_protocol: Fresh frozen biopsies from KS lesions and ipsilateral/contralateral normal sites were homogenized by cryo-cracking (pulverizing) in liquid nitrogen

value: lesion

tag: patient


title: Ribo-seq, mRPF

description: ribosome protected RNA fragment (single ribosome - mRPF)


title: NMR_Bis_PCR_4


title: NMR_Bis_PCR_6


title: NMR_Bis_PCR_7


title: lesion for patient p22

description: RNA-seq for lesion from patient p22


title: lesion for patient p83

description: RNA-seq for lesion from patient p83


title: lesion for patient p32

description: RNA-seq for lesion from patient p32


title: control tissue for patient p23

description: RNA-seq for control tissue from patient p23

source_name: control tissue from KS patient

value: control


title: control tissue for patient p22

description: RNA-seq for control tissue from patient p22


title: control tissue for patient p32

description: RNA-seq for control tissue from patient p32


title: control tissue for patient p83

description: RNA-seq for control tissue from patient p83


title: mRNA_hs121_e115_A8229-5_FB_wtY_male

description: Gene expression of whole forebrain


title: input DNA, Day3, Suv39h1-KO

city: Paris

first: Luigia

last: Pace

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 version 2.1,0 with the following configurations : Method: Global alignment - 1 mismatch in seed alignment  Algorithm used: Choose uniquely the alignment with the best score
Islands were called using sicer version 1.1 with the following setting: windows size w = 500, gap size g = 1500, FDR = 0.05
Genome_build: mm10
Supplementary_files_format_and_content: bed files were generated using sicer version 1.1 and contain the delineation of significant islands

growth_protocol: CD8+ T cells were coltured in vitro for 3 days in medium supplemented with anti-CD3 and anti-CD28 Abs, and IL-2.

extract_protocol:
Formaldehyde-cross-linked chromatin was isolated from wild-type and Suv39h1-KO in vitro differentiated CD8+ T cells.
100-bp paired-end reads sequencing was performed on Illumina HiSeq2500

value: CD8+ T cells

tag: background strain

tag: chip antibody

value: none (input)


title: input DNA for native ChIP, Day0, wild-type

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 version 2.1,0 with the following configurations : Method: Global alignment - 1 mismatch in seed alignment  Algorithm used: Choose uniquely the alignment with the best score
Islands were called using sicer version 1.1 with the following setting: windows size w = 200, gap size g = 600, FDR = 0.05
Genome_build: mm10
Supplementary_files_format_and_content: bed files were generated using sicer version 1.1 and contain the delineation of significant islands

source_name: wild-type

growth_protocol: Naive and in vitro cultured CD8+ T cells on day 3 were analyzed for H3K9me3 enrichment by ChIP-seq

extract_protocol:
Native ChIP was performed for 4 millions of cells, resuspended in MNAse digestion buffer.
Sequencing was performed on Illumina HiSeq2500 sequencer at around 100 millions of paired-end reads per sample (150 bases as read length).

treatment_protocol: CD8+ T cells were cultured in vitro with anti-CD3 and anti-CD28 Abs in the presence of IL-2

value: CD8+ T Cells

tag: strain

tag: day


title: input DNA for native ChIP, Day3, wild-type


title: kb-OVA+ CD8+ T cells Suv39h1-KO, rep1, tech2

description:
Suv39h1 -/-, activated CD8 T cells, biological rep1, technical 2
Raw data are multiplexed. Raw data consist of paired-end reads. Read1 includes the Chromium barcode while Read2  is the biological read sequence.
Processed data available on GSM2833288.

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v1.3.1)
sample de-multiplexing, Cell Ranger Single Cell Software Suite (v1.3.1)
barcode processing, Cell Ranger Single Cell Software Suite (v1.3.1)
single-cell 3′ gene counting , Cell Ranger Single Cell Software Suite (v1.3.1)
alignment, Cell Ranger Single Cell Software Suite (v1.3.1)
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 Gene_Barcode Matrix files were generated using Cell Ranger Single Cell Software Suite (v1.3.1). For more information on the format and to read the matrix see : https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices. Technical replicates were aggregated using Cell Ranger Single Cell Software Suite (v1.3.1) command cellranger aggr.

growth_protocol: Naïve littermate and Suv39h1-KO CD8+ T cells, and day 7 post-infection Kb-OVA+ CD8+ T cells (from Listeria .m-OVA infected mice), were isolated by flowcytometry

extract_protocol:
Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3’ v2 Reagent Kit (10X Genomics) according to manufacturer’s protocol
Indexed sequencing libraries were constructed using the reagents from the Chromium Single Cell 3’ v2 Reagent Kit, following these steps: (1) fragmentation, end repair and A-tailing; (2) size selection with SPRI select; (3) adaptor ligation; (4) post ligation cleanup with SPRI select; (5) sample index PCR and cleanup with SPRI select beads.

tag: infection status

value: Listeria m.-OVA infected


title: input DNA, Day3, wild-type

value: wild-type


title: H3K9me3 native ChIPseq, Day3, wild-type

value: anti-H3K9me3 (Abcam #8898, batch 960144)


title: kb-OVA+ CD8+ T cells Suv39h1-KO, rep1, tech1

description:
Suv39h1 -/-, activated CD8 T cells, biological rep1, technical 1
Raw data are multiplexed. Raw data consist of paired-end reads. Read1 includes the Chromium barcode while Read2  is the biological read sequence.
Processed data file includes data for both GSM2833288 and GSM2833291.


title: H3K9me3 native ChIPseq, Day0, wild-type


title: kb-OVA+ CD8+ T cells  Suv39h1-KO, rep2

description:
Suv39h1 -/-, activated CD8 T cells, biological rep2
Raw data are multiplexed. Raw data consist of paired-end reads. Read1 includes the Chromium barcode while Read2  is the biological read sequence.


title: kb-OVA+ CD8+ T cells WT, rep1

description:
Wild-type, activated CD8 T cells, biological rep1
Raw data are multiplexed. Raw data consist of paired-end reads. Read1 includes the Chromium barcode while Read2  is the biological read sequence.


title: kb-OVA+ CD8+ T cells WT, rep2, tech2

description:
Wild-type, activated CD8 T cells, biological rep2, technical 2
Raw data are multiplexed. Raw data consist of paired-end reads. Read1 includes the Chromium barcode while Read2  is the biological read sequence.
Processed data available on GSM2833287.


title: Naive CD8+ T Suv39h1-KO, rep1

description:
Suv39h1 -/-, naive CD8 T cells, biological rep1
Raw data are multiplexed. Raw data consist of paired-end reads. Read1 includes the Chromium barcode while Read2  is the biological read sequence.

value: Naive


title: kb-OVA+ CD8+ T cells WT, rep2, tech1

description:
Wild-type, activated CD8 T cells, biological rep2, technical 1
Raw data are multiplexed. Raw data consist of paired-end reads. Read1 includes the Chromium barcode while Read2  is the biological read sequence.
Processed data file includes data for both GSM2833287 and GSM2833290.


title: d0061d2542d0384 C

status: Public on Jan 16 2018

city: Madison

first: Gina

last: Gordon

state: WI

address: 1415 Engineering Dr

department: Chemical and Biological Engineering

institute: University of Wisconsin Madison

data_processing:
Sequencing files were aligned to the chromsome (NC_010475), pAQ1 (NC_010476), pAQ3 (NC_010477), pAQ4 (NC_010478), pAQ5 (NC_010479), pAQ6 (NC_010480), and pAQ7 (NC_010474) using Bowtie2 (v 2.2.6) and samtools (v 1.2).
Counts for each feature in the general feature format (.gff) files were obtained with the htseq-count script using union mode and stranded set to reverse (HTseq v 0.6.1).
edgeR (v 3.16.5) was used to test for differential gene expression of each mutant compared to WT. Specifically, feature counts were loaded and filtered for all genes that had at least 1 read per million in 3 samples and tested for differential expression with exactTest using tagwise dispersion. P-values were adjusted with the Benjamini and Hochberg algorithm.
Genome_build: NC_010475, NC_010476, NC_010477, NC_010478, NC_010479, NC_010480, NC_010474
Supplementary_files_format_and_content: One .txt file contains counts for all gene features on the plasmid and chromosomes for each strain type (biological triplicate). The other .txt file contains gene expression data and the false discovery rate for each strain compared to WT.

organism: Picosynechococcus sp. PCC 7002

source_name: bacterial cells

growth_protocol: Strains were maintained on media A+ agar (1.5%) plates with the appropriate antibiotic or antibiotics (gentamicin 30 μg/ml, kanamycin 100 μg/ml, and streptomycin 100 μg/ml). Pre-cultures of 20 mL A+ media were bubbled with air overnight. The OD730nm was measured and 1 1L pyrex bottles filled with 900 mL media A+ was inoculated with pre-culture for an OD730nm = 0.01. Cultures were bubbled with air for 24 hours before harvesting 40 mL and adding 10 mL of cold stop solution (10% phenol in ethanol). Samples were spun down at 4°C in a Beckamn Coulter Avanti J-E Centrifuge at 10,000xg for 10 minutes. Supernatant was removed and cell pellets were frozen in liquid nitrogen and stored at -80°C.

extract_protocol:
RNA was extracted using the hot phenol method outlined in Khodursky A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. 2003. Escherichia coli spotted double-strand DNA microarrays: RNA extraction, labeling, hybridization, quality control, and data management. Methods Mol Biol 224:61–78.
RNA was submitted to the University of Wisconsin Biotechnology Gene Expression Center for RNA-sequencing. rRNA was removed with a Ribo-Zero Magnetic Kit and the library was created using a TruSeq Stranded Total RNA Library Kit. Samples were run on an Illumina HiSeq 2500.


title: d0061d2542d0384 B


title: d0061d2542d0384 A


title: d2542d0384 C


title: Naive CD8+ T cells WT, rep1

description:
Wild-type, naive CD8 T cells, biological rep1
Raw data are multiplexed. Raw data consist of paired-end reads. Read1 includes the Chromium barcode while Read2  is the biological read sequence.


title: d2542d0384 A


title: hs122-GFP Bulk Control

data_processing:
Raw data analysis and digital expression quantification was carried out using the Drop-seq published pipeline (PMID: 26000488) version 1.11. The alignment was performed using STAR (PMID: 23104886) version 2.4.1d.
Genome_build: mm10 (Genome Reference Consortium GRCm38)
Supplementary_files_format_and_content: dropseq_data.digital_expression.bulk.txt.gz: digital expression matrix, flat text files with tab delimiters; mm10_hg19.refFlat.gz: transcriptome combining mm10 genes, hg19 genes and transgenes, refFlat tabular format. Column headers (gene Name, name, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts, exonEnds)

source_name: embryonic forebrain

extract_protocol:
Total RNA was extracted using the RNAqueous Total RNA Isolation Kit (Thermo Fisher Scientific), then it was incubated with microbeads (ChemGene Beads, Lot 011416B).
As previously described (PMID: 26000488).

tag: strain (mouse)

value: FVB

tag: developmental stage (mouse)

value: gestational day e12.5

tag: tissue (mouse)

value: forebrain

tag: enhancer


title: d2542d0384 B


title: d0061d0384 C


title: d0061d0384 B


title: H3K9me3 ChIPseq, Day3, Suv39h1-KO

tag: genotype


title: H3K9me3 ChIPseq, Day3, wild-type


title: d0061d0384 A


title: d0384 C


title: d0384 A


title: d0061d2542 B


title: d0061d2542 A


title: d0384 B


title: d2542 C


title: d2542 A


title: d0061 A


title: WT B

value: WT


title: WT A


title: d0061 C


title: d2542 B


title: d0061 B


title: Pf-NF54-Schizont-Input

city: Nijmegen

first: Sabine

last: Fraschka

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen

description:
P. falciparum sample collection and chromatin preparation  P. falciparum parasites were cultured at 5% haematocrit based on the original protocol published by Trager and Jensen (Trager and Jensen, 1978). Growth synchronization was achieved by repeated sorbitol treatments (Lambros and Vanderberg, 1979). 3D7 parasites were cultivated with AB+ human RBCs in RPMI 1640/25 mM Hepes standard culture medium supplemented with 0.5% Albumax II. NF54 and NF135 parasites were cultivated with O+ human RBCs in RPMI 1640/25 mM Hepes standard culture medium supplemented with 10 % human serum. Pf2004/164tdTom parasites (Brancucci et al., 2015) were cultivated with AB+ human RBCs in RPMI 1640/25 mM Hepes standard culture medium supplemented with 10 % human serum. Pf2004/164tdTom gametocytes were generated by inducing sexual commitment as described (Brancucci et al., 2015). After re-invasion cultures were treated with 50mM N-acetylglucosamine (Fivelman et al., 2007) for three consecutive days to eliminate asexual parasites.  Chromatin from 3D7 ring stages, trophozoites or schizonts (approximately 0.75-1.5x109 parasites each) and from Pf2004/T164dTom schizonts, stage II/III gametocytes (day four after re-invasion) or stage IV/V gametocytes (day nine after re-invasion) (approximately 2x108 parasites each) was prepared by crosslinking cultures with 1% formaldehyde (Sigma F8775) for 15 min at 37ºC. Crosslinking reactions were quenched by 0.125 M glycine. Nuclei were isolated by releasing parasites from infected RBCs using 0.05% saponin followed by lysis in CLB (20 mM Hepes, 10 mM KCl, 1 mM EDTA, 1 mM EGTA, 0.65% NP-40, 1mM DTT, 1x protease inhibitor (Roche Diagnostics), pH 7.9). Nuclei were washed and snap-frozen in CLB supplemented with 50% glycerol. Chromatin from NF54 and NF135 parasites (approximately 2-4x109 parasites each) was prepared by passing the cultures through Plasmodipure filters (EuroProxima) to remove white blood cells prior to formaldehyde crosslinking for 10 min at 37ºC and quenching in 0.125 M glycine. Nuclei were isolated by releasing parasites from infected RBCs using 0.05% saponin followed by gentle homogenisation (pestle B, 15 strokes) in CLB2 (10 mM Tris-HCl, 3 mM MgCl2, 0.2% NP40, 1x protease inhibitor (Roche Diagnostics), pH 8.0) and centrifugation through a 0.25 M sucrose cushion (in CLB2) at 2000 rpm for 10 min at 4°C. Nuclei were snap-frozen in CLB2 supplemented with 20% glycerol. Frozen nuclei were thawed and resuspended in sonication buffer (50mM Tris-HCl, 1% SDS, 10mM EDTA, 1x protease inhibitor (Roche Diagnostics), pH 8.0) and sonicated for 20-24 cycles of 30 sec ON/30 sec OFF (setting high, BioruptorTM Next Gen, Diagenode). Chromatin fragment sizes ranged from 100-600 bp as determined by de-crosslinking a 50 l aliquot and running the purified DNA on a 1% agarose gel
Pf-NF54-Schizont-HP1_over_Pf-NF54-Schizont-Input.BedGraph.gz

data_processing:
RTA v2 software for base calling and bcl2fastq v2.16.0.10 conversion software for fastq conversion
Data were mapped with BWA samse (Version: 0.7.12-r1039) against the respective reference genome (P. berghei ANKA, P. chabaudi chabaudi, P. yoelii yoelii YM, P. falciparum 3D7 and P. knowlesi H from PlasmoDB version 26 and P. vivax P01 from PlasmoDB version 29. Pf2004 samples were additionally mapped against a draft Pf2004 genome assembly kindly provided by Thomas Otto (Welcome Trust Sanger Institute)
Sam files were converted to bam files and mapped reads were filtered to mapping quality ≥15 (SAM tools v1.2). Only uniquely mapped reads were used for further analysis.
BedGraph files were generated using bedtools genomecov with the option -bga and normalized using -scale and the scaling factor ‘1000000/amount of unique reads’.
Begraph log2 ratio were genereated using bedtools unionbedg
Genome_build: see second processing step
Supplementary_files_format_and_content: BedGraph log2 ratio files show the coverage as log2 ratio of ChIP over Input calculated using normalized BedGraph files

organism: Plasmodium falciparum

source_name: intraerythrocytic stage, schizont stage

extract_protocol:
Chromatin immunoprecipitations:  For each ChIP reaction, sonicated chromatin containing 500 ng of DNA was incubated in incubation buffer (0.75% SDS, 5% Triton-X-100, 750 mM NaCl, 5 mM EDTA, 2.5 mM EGTA, 100 mM Hepes, pH 7.4) with either 1 µg rabbit α-PfHP1 (for P. falciparum), 1 µg rabbit α-PvHP1 (for P. vivax and P. knowlesi) or 1 µg rabbit α-PbHP1 (for P. berghei, P. chaubaudi and P. yoelii) as well as 10 µl protA and 10 µl protG Dynabeads suspension (Life Technologies, #10008D and #10009D).    For each sample four ChIP reactions were prepared and incubated overnight at 4°C while rotating. Beads were washed twice with wash buffer 1 (0.1% SDS, 0.1% DOC, 1% Triton-X100, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM Hepes, pH 7.4), once with wash buffer 2 (0.1% SDS, 0.1% DOC, 1% Triton-X100, 500 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM Hepes, pH 7.4), once with wash buffer 3 (250 mM LiCl, 0.5% DOC, 0.5% NP-40, 1 mM EDTA, 0.5 mM EGTA, 20 mM Hepes, pH 7.4) and twice with wash buffer 4 (1 mM EDTA, 0.5 mM EGTA, 20 mM Hepes, pH 7.4). Each wash was performed for 5 min at 4°C while rotating. Subsequently, immunoprecipitated chromatin was eluted in elution buffer (1% SDS, 0.1M NaHCO3) at room temperature. The eluted chromatin samples and the corresponding input samples (sonicated input chromatin containing 500 ng DNA) were de-crosslinked in 1% SDS/0.1 M NaHCO3/1 M NaCl at 45°C overnight while shaking. For each parasite strain or species the separate ChIP samples were combined and the DNA was purified using QIAquick MinElute PCR columns (Qiagen).
For each sequencing library  2-10 ng of ChIP or input DNA were end-repaired, extended with 3′ A-overhangs and ligated to barcoded NextFlex adapters (Bio Scientific, #514122) as described previously (Hoeijmakers et al., 2011). Libraries were amplified (98°C for 2 min; four cycles 98°C for 20 sec, 62°C for 3 min; 62°C for 5 min) using KAPA HiFi HotStart ready mix (KAPA Biosystems, KM2602) and NextFlex primer mix (Bio Scientific, #514122) as described (Kensche et al., 2016). 225-325 bp fragments (including the 125 bp NextFlex adapter) were size-selected using a 2% E-Gel Size Select agarose gel (Invitrogen, #G6610-02) and amplified by PCR for eight or ten cycles under the same condition as described above. Library purification and removal of adapter dimers was performed with Agencourt AMPure XP beads in a 1:1 library:beads ratio (Beckman Coulter, #A63880).

tag: antibody

value: none/input


title: Pf-NF135-Schizont-Input

description:
P. falciparum sample collection and chromatin preparation  P. falciparum parasites were cultured at 5% haematocrit based on the original protocol published by Trager and Jensen (Trager and Jensen, 1978). Growth synchronization was achieved by repeated sorbitol treatments (Lambros and Vanderberg, 1979). 3D7 parasites were cultivated with AB+ human RBCs in RPMI 1640/25 mM Hepes standard culture medium supplemented with 0.5% Albumax II. NF54 and NF135 parasites were cultivated with O+ human RBCs in RPMI 1640/25 mM Hepes standard culture medium supplemented with 10 % human serum. Pf2004/164tdTom parasites (Brancucci et al., 2015) were cultivated with AB+ human RBCs in RPMI 1640/25 mM Hepes standard culture medium supplemented with 10 % human serum. Pf2004/164tdTom gametocytes were generated by inducing sexual commitment as described (Brancucci et al., 2015). After re-invasion cultures were treated with 50mM N-acetylglucosamine (Fivelman et al., 2007) for three consecutive days to eliminate asexual parasites.  Chromatin from 3D7 ring stages, trophozoites or schizonts (approximately 0.75-1.5x109 parasites each) and from Pf2004/T164dTom schizonts, stage II/III gametocytes (day four after re-invasion) or stage IV/V gametocytes (day nine after re-invasion) (approximately 2x108 parasites each) was prepared by crosslinking cultures with 1% formaldehyde (Sigma F8775) for 15 min at 37ºC. Crosslinking reactions were quenched by 0.125 M glycine. Nuclei were isolated by releasing parasites from infected RBCs using 0.05% saponin followed by lysis in CLB (20 mM Hepes, 10 mM KCl, 1 mM EDTA, 1 mM EGTA, 0.65% NP-40, 1mM DTT, 1x protease inhibitor (Roche Diagnostics), pH 7.9). Nuclei were washed and snap-frozen in CLB supplemented with 50% glycerol. Chromatin from NF54 and NF135 parasites (approximately 2-4x109 parasites each) was prepared by passing the cultures through Plasmodipure filters (EuroProxima) to remove white blood cells prior to formaldehyde crosslinking for 10 min at 37ºC and quenching in 0.125 M glycine. Nuclei were isolated by releasing parasites from infected RBCs using 0.05% saponin followed by gentle homogenisation (pestle B, 15 strokes) in CLB2 (10 mM Tris-HCl, 3 mM MgCl2, 0.2% NP40, 1x protease inhibitor (Roche Diagnostics), pH 8.0) and centrifugation through a 0.25 M sucrose cushion (in CLB2) at 2000 rpm for 10 min at 4°C. Nuclei were snap-frozen in CLB2 supplemented with 20% glycerol. Frozen nuclei were thawed and resuspended in sonication buffer (50mM Tris-HCl, 1% SDS, 10mM EDTA, 1x protease inhibitor (Roche Diagnostics), pH 8.0) and sonicated for 20-24 cycles of 30 sec ON/30 sec OFF (setting high, BioruptorTM Next Gen, Diagenode). Chromatin fragment sizes ranged from 100-600 bp as determined by de-crosslinking a 50 l aliquot and running the purified DNA on a 1% agarose gel
Pf-NF135-Schizont-HP1_over_Pf-NF135-Schizont-Input.BedGraph.gz


title: Pf-NF54-Schizont-HP1


title: Pf-NF135-Schizont-HP1


title: Pf-Pf2004-GamIV-V-Input

description:
P. falciparum sample collection and chromatin preparation  P. falciparum parasites were cultured at 5% haematocrit based on the original protocol published by Trager and Jensen (Trager and Jensen, 1978). Growth synchronization was achieved by repeated sorbitol treatments (Lambros and Vanderberg, 1979). 3D7 parasites were cultivated with AB+ human RBCs in RPMI 1640/25 mM Hepes standard culture medium supplemented with 0.5% Albumax II. NF54 and NF135 parasites were cultivated with O+ human RBCs in RPMI 1640/25 mM Hepes standard culture medium supplemented with 10 % human serum. Pf2004/164tdTom parasites (Brancucci et al., 2015) were cultivated with AB+ human RBCs in RPMI 1640/25 mM Hepes standard culture medium supplemented with 10 % human serum. Pf2004/164tdTom gametocytes were generated by inducing sexual commitment as described (Brancucci et al., 2015). After re-invasion cultures were treated with 50mM N-acetylglucosamine (Fivelman et al., 2007) for three consecutive days to eliminate asexual parasites.  Chromatin from 3D7 ring stages, trophozoites or schizonts (approximately 0.75-1.5x109 parasites each) and from Pf2004/T164dTom schizonts, stage II/III gametocytes (day four after re-invasion) or stage IV/V gametocytes (day nine after re-invasion) (approximately 2x108 parasites each) was prepared by crosslinking cultures with 1% formaldehyde (Sigma F8775) for 15 min at 37ºC. Crosslinking reactions were quenched by 0.125 M glycine. Nuclei were isolated by releasing parasites from infected RBCs using 0.05% saponin followed by lysis in CLB (20 mM Hepes, 10 mM KCl, 1 mM EDTA, 1 mM EGTA, 0.65% NP-40, 1mM DTT, 1x protease inhibitor (Roche Diagnostics), pH 7.9). Nuclei were washed and snap-frozen in CLB supplemented with 50% glycerol. Chromatin from NF54 and NF135 parasites (approximately 2-4x109 parasites each) was prepared by passing the cultures through Plasmodipure filters (EuroProxima) to remove white blood cells prior to formaldehyde crosslinking for 10 min at 37ºC and quenching in 0.125 M glycine. Nuclei were isolated by releasing parasites from infected RBCs using 0.05% saponin followed by gentle homogenisation (pestle B, 15 strokes) in CLB2 (10 mM Tris-HCl, 3 mM MgCl2, 0.2% NP40, 1x protease inhibitor (Roche Diagnostics), pH 8.0) and centrifugation through a 0.25 M sucrose cushion (in CLB2) at 2000 rpm for 10 min at 4°C. Nuclei were snap-frozen in CLB2 supplemented with 20% glycerol. Frozen nuclei were thawed and resuspended in sonication buffer (50mM Tris-HCl, 1% SDS, 10mM EDTA, 1x protease inhibitor (Roche Diagnostics), pH 8.0) and sonicated for 20-24 cycles of 30 sec ON/30 sec OFF (setting high, BioruptorTM Next Gen, Diagenode). Chromatin fragment sizes ranged from 100-600 bp as determined by de-crosslinking a 50 l aliquot and running the purified DNA on a 1% agarose gel
Pf-Pf2004-GamIV-V-HP1_over_Pf-Pf2004-GamIV-V-Input.BedGraph.gz
Pf-Pf2004-GamIV-V-HP1_over_Pf-Pf2004-GamIV-V-Input_Pf2004-assembly.BedGraph.gz

source_name: intraerythrocytic stage, gametocyte stage IV/V


title: Pf-Pf2004-GamIV-V-HP1


title: Pf-Pf2004-GamII-III-HP1

description:
P. falciparum sample collection and chromatin preparation  P. falciparum parasites were cultured at 5% haematocrit based on the original protocol published by Trager and Jensen (Trager and Jensen, 1978). Growth synchronization was achieved by repeated sorbitol treatments (Lambros and Vanderberg, 1979). 3D7 parasites were cultivated with AB+ human RBCs in RPMI 1640/25 mM Hepes standard culture medium supplemented with 0.5% Albumax II. NF54 and NF135 parasites were cultivated with O+ human RBCs in RPMI 1640/25 mM Hepes standard culture medium supplemented with 10 % human serum. Pf2004/164tdTom parasites (Brancucci et al., 2015) were cultivated with AB+ human RBCs in RPMI 1640/25 mM Hepes standard culture medium supplemented with 10 % human serum. Pf2004/164tdTom gametocytes were generated by inducing sexual commitment as described (Brancucci et al., 2015). After re-invasion cultures were treated with 50mM N-acetylglucosamine (Fivelman et al., 2007) for three consecutive days to eliminate asexual parasites.  Chromatin from 3D7 ring stages, trophozoites or schizonts (approximately 0.75-1.5x109 parasites each) and from Pf2004/T164dTom schizonts, stage II/III gametocytes (day four after re-invasion) or stage IV/V gametocytes (day nine after re-invasion) (approximately 2x108 parasites each) was prepared by crosslinking cultures with 1% formaldehyde (Sigma F8775) for 15 min at 37ºC. Crosslinking reactions were quenched by 0.125 M glycine. Nuclei were isolated by releasing parasites from infected RBCs using 0.05% saponin followed by lysis in CLB (20 mM Hepes, 10 mM KCl, 1 mM EDTA, 1 mM EGTA, 0.65% NP-40, 1mM DTT, 1x protease inhibitor (Roche Diagnostics), pH 7.9). Nuclei were washed and snap-frozen in CLB supplemented with 50% glycerol. Chromatin from NF54 and NF135 parasites (approximately 2-4x109 parasites each) was prepared by passing the cultures through Plasmodipure filters (EuroProxima) to remove white blood cells prior to formaldehyde crosslinking for 10 min at 37ºC and quenching in 0.125 M glycine. Nuclei were isolated by releasing parasites from infected RBCs using 0.05% saponin followed by gentle homogenisation (pestle B, 15 strokes) in CLB2 (10 mM Tris-HCl, 3 mM MgCl2, 0.2% NP40, 1x protease inhibitor (Roche Diagnostics), pH 8.0) and centrifugation through a 0.25 M sucrose cushion (in CLB2) at 2000 rpm for 10 min at 4°C. Nuclei were snap-frozen in CLB2 supplemented with 20% glycerol. Frozen nuclei were thawed and resuspended in sonication buffer (50mM Tris-HCl, 1% SDS, 10mM EDTA, 1x protease inhibitor (Roche Diagnostics), pH 8.0) and sonicated for 20-24 cycles of 30 sec ON/30 sec OFF (setting high, BioruptorTM Next Gen, Diagenode). Chromatin fragment sizes ranged from 100-600 bp as determined by de-crosslinking a 50 l aliquot and running the purified DNA on a 1% agarose gel
Pf-Pf2004-GamII-III-HP1_over_Pf-Pf2004-GamII-III-Input.BedGraph.gz
Pf-Pf2004-GamII-III-HP1_over_Pf-Pf2004-GamII-III-Input_Pf2004-assembly.BedGraph.gz

source_name: intraerythrocytic stage, gametocyte stage II/III


title: Pf-Pf2004-Schizont-Input

description:
P. falciparum sample collection and chromatin preparation  P. falciparum parasites were cultured at 5% haematocrit based on the original protocol published by Trager and Jensen (Trager and Jensen, 1978). Growth synchronization was achieved by repeated sorbitol treatments (Lambros and Vanderberg, 1979). 3D7 parasites were cultivated with AB+ human RBCs in RPMI 1640/25 mM Hepes standard culture medium supplemented with 0.5% Albumax II. NF54 and NF135 parasites were cultivated with O+ human RBCs in RPMI 1640/25 mM Hepes standard culture medium supplemented with 10 % human serum. Pf2004/164tdTom parasites (Brancucci et al., 2015) were cultivated with AB+ human RBCs in RPMI 1640/25 mM Hepes standard culture medium supplemented with 10 % human serum. Pf2004/164tdTom gametocytes were generated by inducing sexual commitment as described (Brancucci et al., 2015). After re-invasion cultures were treated with 50mM N-acetylglucosamine (Fivelman et al., 2007) for three consecutive days to eliminate asexual parasites.  Chromatin from 3D7 ring stages, trophozoites or schizonts (approximately 0.75-1.5x109 parasites each) and from Pf2004/T164dTom schizonts, stage II/III gametocytes (day four after re-invasion) or stage IV/V gametocytes (day nine after re-invasion) (approximately 2x108 parasites each) was prepared by crosslinking cultures with 1% formaldehyde (Sigma F8775) for 15 min at 37ºC. Crosslinking reactions were quenched by 0.125 M glycine. Nuclei were isolated by releasing parasites from infected RBCs using 0.05% saponin followed by lysis in CLB (20 mM Hepes, 10 mM KCl, 1 mM EDTA, 1 mM EGTA, 0.65% NP-40, 1mM DTT, 1x protease inhibitor (Roche Diagnostics), pH 7.9). Nuclei were washed and snap-frozen in CLB supplemented with 50% glycerol. Chromatin from NF54 and NF135 parasites (approximately 2-4x109 parasites each) was prepared by passing the cultures through Plasmodipure filters (EuroProxima) to remove white blood cells prior to formaldehyde crosslinking for 10 min at 37ºC and quenching in 0.125 M glycine. Nuclei were isolated by releasing parasites from infected RBCs using 0.05% saponin followed by gentle homogenisation (pestle B, 15 strokes) in CLB2 (10 mM Tris-HCl, 3 mM MgCl2, 0.2% NP40, 1x protease inhibitor (Roche Diagnostics), pH 8.0) and centrifugation through a 0.25 M sucrose cushion (in CLB2) at 2000 rpm for 10 min at 4°C. Nuclei were snap-frozen in CLB2 supplemented with 20% glycerol. Frozen nuclei were thawed and resuspended in sonication buffer (50mM Tris-HCl, 1% SDS, 10mM EDTA, 1x protease inhibitor (Roche Diagnostics), pH 8.0) and sonicated for 20-24 cycles of 30 sec ON/30 sec OFF (setting high, BioruptorTM Next Gen, Diagenode). Chromatin fragment sizes ranged from 100-600 bp as determined by de-crosslinking a 50 l aliquot and running the purified DNA on a 1% agarose gel
Pf-Pf2004-Schizont-HP1_over_Pf-Pf2004-Schizont-Input.BedGraph.gz
Pf-Pf2004-Schizont-HP1_over_Pf-Pf2004-Schizont-Input_Pf2004-assembly.BedGraph.gz


title: d0061d2542 C


title: Pf-Pf2004-GamII-III-Input


title: Pf-Pf2004-Schizont-HP1


title: Pf-3D7-Schizont-HP1

description:
P. falciparum sample collection and chromatin preparation  P. falciparum parasites were cultured at 5% haematocrit based on the original protocol published by Trager and Jensen (Trager and Jensen, 1978). Growth synchronization was achieved by repeated sorbitol treatments (Lambros and Vanderberg, 1979). 3D7 parasites were cultivated with AB+ human RBCs in RPMI 1640/25 mM Hepes standard culture medium supplemented with 0.5% Albumax II. NF54 and NF135 parasites were cultivated with O+ human RBCs in RPMI 1640/25 mM Hepes standard culture medium supplemented with 10 % human serum. Pf2004/164tdTom parasites (Brancucci et al., 2015) were cultivated with AB+ human RBCs in RPMI 1640/25 mM Hepes standard culture medium supplemented with 10 % human serum. Pf2004/164tdTom gametocytes were generated by inducing sexual commitment as described (Brancucci et al., 2015). After re-invasion cultures were treated with 50mM N-acetylglucosamine (Fivelman et al., 2007) for three consecutive days to eliminate asexual parasites.  Chromatin from 3D7 ring stages, trophozoites or schizonts (approximately 0.75-1.5x109 parasites each) and from Pf2004/T164dTom schizonts, stage II/III gametocytes (day four after re-invasion) or stage IV/V gametocytes (day nine after re-invasion) (approximately 2x108 parasites each) was prepared by crosslinking cultures with 1% formaldehyde (Sigma F8775) for 15 min at 37ºC. Crosslinking reactions were quenched by 0.125 M glycine. Nuclei were isolated by releasing parasites from infected RBCs using 0.05% saponin followed by lysis in CLB (20 mM Hepes, 10 mM KCl, 1 mM EDTA, 1 mM EGTA, 0.65% NP-40, 1mM DTT, 1x protease inhibitor (Roche Diagnostics), pH 7.9). Nuclei were washed and snap-frozen in CLB supplemented with 50% glycerol. Chromatin from NF54 and NF135 parasites (approximately 2-4x109 parasites each) was prepared by passing the cultures through Plasmodipure filters (EuroProxima) to remove white blood cells prior to formaldehyde crosslinking for 10 min at 37ºC and quenching in 0.125 M glycine. Nuclei were isolated by releasing parasites from infected RBCs using 0.05% saponin followed by gentle homogenisation (pestle B, 15 strokes) in CLB2 (10 mM Tris-HCl, 3 mM MgCl2, 0.2% NP40, 1x protease inhibitor (Roche Diagnostics), pH 8.0) and centrifugation through a 0.25 M sucrose cushion (in CLB2) at 2000 rpm for 10 min at 4°C. Nuclei were snap-frozen in CLB2 supplemented with 20% glycerol. Frozen nuclei were thawed and resuspended in sonication buffer (50mM Tris-HCl, 1% SDS, 10mM EDTA, 1x protease inhibitor (Roche Diagnostics), pH 8.0) and sonicated for 20-24 cycles of 30 sec ON/30 sec OFF (setting high, BioruptorTM Next Gen, Diagenode). Chromatin fragment sizes ranged from 100-600 bp as determined by de-crosslinking a 50 l aliquot and running the purified DNA on a 1% agarose gel
Pf-3D7-Schizont-HP1_over_Pf-3D7-Schizont-Input.BedGraph.gz