title: Eno1p PAR-CLIP-seq

city: Baltimore

first: Mallory

middle: Ann

last: Freeberg

state: MD

address: 3400 N Charles St

department: Department of Biology

institute: Johns Hopkins University

data_processing:
Base calling was performed according to Illumina's protocols.
Low-quality reads were removed if they met any of the following criteria: <18 nt, only homopolymer As, missing 3’ adapter, 5’-3’ adapter ligation products, 5’-5’ adapter ligation products, low quality (more than 4 bases with quality scores below 10 or more than 6 bases with a quality score below 13).
High-quality reads were aligned to the genome using Bowtie v0.12.7 with the parameters -f -v 3 -k 500 --best --strata.
Read counts in each library were normalized to the total number of mapped reads in millions (RPM).
Reads mapping uniquely to the genome with 0-2 T-to-C mismatches were used to generate read clusters defined as a continuous stretch of nucleotides covered by at least 1 read. Clusters were fitted with a Gaussian curve based on the aggregate RPM of each position in the cluster. Clusters containing no reads with at least 1 T-to-C mismatch were filtered off.
Genome_build: SGD/sacCer3 (April 2011) from S288C strain
Supplementary_files_format_and_content: Normalized read coverage for each binding site is presented.

organism: Saccharomyces cerevisiae

source_name: Whole cell

growth_protocol: Strain was grown at 30°C with rigorous shaking in synthetic defined (SD) media supplemented with 200 µM 4-thiouracil to OD600 = 0.7-0.8.

extract_protocol:
Cells were lysed in 1XPBS, 0.5% NP-40, 1X Complete Mini Protease Inhibitor, EDTA-free and cleared by sequential spins at 1,300Xg for 5 min and 20,000Xg for 10 min at 4°C. Clarified lysate was passed through a Costar Spin-X filter, mixed with RNase T1 to 1 U/µL, and incubated at 22°C for 15 min followed by 5 min incubation on ice. Lysate was then directly mixed with IgG magnetic beads (prepared by coupling rabbit IgG to Dynabeads M-270 Expoxy) to pull down Pfk2p::TAP.
RNase T1 digestion, CIP treatment, and 3’ DNA linker ligation were performed as follows: Beads were washed 3 times with 1XPBS, then incubated with 20 µL of 50 U/µL RNase T1 (1:20 dilution in 1XPBS) at 22°C for 15 min on Eppendorf Thermomixer (15 sec shaking at 1,000 rpm followed by 2 min rest interval), followed by 5 min incubation on ice. Beads were washed twice with wash buffer (1XPBS, 0.1% SDS, 0.5% deoxycholate, 0.5% NP-40), twice with high-salt wash buffer (5XPBS, 0.1% SDS, 0.5% deoxycholate, 0.5% NP-40), and twice with 1XPNK buffer (50 mM Tris pH 7.4,10 mM MgCl2, 0.5% NP-40). Beads were incubated with 20 µL of CIP mix (50 mM Tris pH 7.9, 100 mM NaCl, 10 mM MgCl2, 0.5 U/µL CIP) at 37°C for 15 min, with 15 sec shaking at 1,000 rpm followed by 2 min rest interval on Thermomixer. After CIP treatment, beads were washed twice with 1XPNK+EGTA buffer (50 mM Tris pH 7.4, 20 mM EGTA, 0.5% NP-40) and twice with 1XPNK buffer. Beads were incubated with 20 µL of ligation mix (50 mM Tris pH 7.4, 10 mM MgCl2, 0.5 mM DTT, 2 µM Pre-adenylated 3’ DNA linker, 25% PEG-8000, 10 U/µL T4 RNA ligase 2, truncated K227Q) at 16°C overnight (≥16 hr), with 15 sec shaking at 1,000 rpm followed by 2 min interval on Thermomixer. 5’ end phosphorylation was performed on-bead in 20 µL of PNK mix (70 mM Tris pH 7.6, 10 mM MgCl2, 5 mM DT, 1 µL P32 rATP (6000 Ci/mmol 10 mCi/mL), 1 U/µL T4 polynucleotide kinase) and incubated at 37°C for 15 min. 2 µL of 10 mM ATP was added to the mix, and the reaction was incubated for 10 min. Beads were removed, and the supernatant was loaded onto NuPAGE 4-12% Bis-Tris gel and run at 150 V for 35 min. Gel was transferred to Protran BA 85 nitrocellulose membrane (pore size 0.45 µm) using Novex wet transfer at 30 V for 1 hr. Crosslinked RNAs were visualized by autoradiography, and the corresponding Pfk2p band was excised and incubated with 500 µL of 4 mg/mL Proteinase K prepared in 1X PK buffer (100 mM Tris pH 7.5, 50 mM NaCl, 10 mM EDTA) for 20 min at 37°C on Thermomixer. 500 µL of 7M urea prepared in 1X PK buffer were added to the tube followed by another 20 min incubation at 37°C. Proteinase K digestion reaction was mixed with 1 mL of Phenol:Chloroform:Isoamyl Alcohol 25:24:1 by vortexing and spun for 5 min at 20,000Xg. Liquid phase was transferred to a new tube, mixed with 125 µL of 3 M NaOAc, 2.5 mL of 100% ethanol and 1 µL of 15 mg/mL glycoblue, and precipitated for 2 hr at -80°C. RNAs were collected by centrifugation for 20 min at 20,000Xg at room temperature followed by 2 washes with cold 75% ethanol. RNA pellets were resuspended in 10 µL of ligation mix (50 mM Tris pH 7.5, 10 mM MgCl2, 10 mM DTT, 1mM ATP, 0.1 mg/mL BSA, 2 µM 5’ RNA linker, 1 U/µL T4 RNA ligase, 1 U/µL SUPERase•In, 10% DMSO) and incubated at 15°C for 2 hr. Ligation reaction was terminated by adding 10 µL of 2X formamide gel loading buffer , heated for 2 min at 70°C, and then quickly chilled on ice. Samples were loaded onto 6% TBE UREA gel and run at 150 V for 45 min. After staining with 1X Sybr Gold Stain, gel piece corresponding to 70-90 nt RNA (80-100 nt ssDNA) was excised, crushed, and soaked in 400 µL of 0.3 M NaOAc overnight at room temperature. After removing gel pieces, the solution was combined with 1 mL of 100% EtOH and 1 µL of 15 mg/mL glycoblue and precipitated for 2 hr at -80°C. RNAs were collected by centrifugation for 20 min at 20,000Xg at room temperature, followed by two washes with cold 75% ethanol. After brief drying, RNAs were resuspended in 15 µL of H2O. 10 μL of ligated RNA was combined with 2 μL of 5 µM RT primer, heated at 65°C for 5 min, and then quickly chilled on ice, followed by addition of 1 µL of 10 mM dNTP, 1 μL of 0.1 M DTT, 4 μL of 5X First strand buffer, 1 μL of SUPERase•In (20 U/µL) and 1 µL of SuperScript III Reverse transcriptase, 200 U/µL. RT reaction was kept at 50°C for 45 min, 55°C for 15 min and 90°C for 5 min. A test PCR was performed with 2.5 µL of RT product in 50 µL PCR mix: 1X AccuPrime PCR buffer I, 0.5 µM P5 long primer, 0.5 µM P7 primer, 0.2 µL AccuPirme Taq High Fidelity, 5 U/µL. PCR was carried out with initial 3 min denaturation at 98°C, followed by 14-22 cycles of 80 sec denaturation at 98°C, 90 sec annealing and extension at 65°C, and termination with a final 5 min extension at 65°C. 15 µL PCR product was collected after 14, 18, and 22 cycles and analyzed on a 10% TBE gel at 150 V for 1 hr to determine optimal amplification cycles (the lowest cycle number required to generate 96-116 bp amplicons detected by Sybr Gold staining). 50 µL PCR reaction was carried out with the determined cycle number. Amplicons were purified using DNA clean and concentrator-5, run on 10% TBE gels at 150 V for 1 hr and stained with Sybr Gold. Gel piece corresponding to 96-116 bp DNA was excised, crushed, and soaked overnight in 400 µL 0.3 M NaOAc at room temperature. After removing gel pieces, solution was combined with 1 mL of 100% EtOH and 1 µL of 15 mg/mL glycoblue and precipitated for 2 hr at -80°C. DNAs were collected by centrifugation for 20 min at 20,000Xg at room temperature, followed by 2 washes with cold 75% ethanol. After brief drying, amplicons were resuspended in 20 µL of H2O. 5 µL of purified amplicons were used to seed a second round of PCR in 50 µL: 1X AccuPrime PCR buffer I, 0.5 µM Illumina Primer A, 0.5 µM Illumina Primer B, 0.2 µL AccuPirme Taq High Fidelity for 6-12 cycles. Second PCR amplicons were purified with DNA clean and concentrator-5 and sequenced on an Illumina HiSeq 2000 sequencer.

treatment_protocol: 50 mL of mid-log phase cultures (OD600 = 0.7-0.8) were pelleted for 5 min at 3,000Xg at room temperature, resuspended in 2 mL of 1XHBSS, transferred to 60 mm cell culture dish, placed on ice, and irradiated with 365nm UV at 150 mJ/cm2 4 times using a UVP CL-1000L UV crosslinker. Cells were pelleted for 2 min at 5,000Xg at 4°C. After removing 1X HBSS, the cells were frozen in liquid nitrogen.

tag: strain

value: (MATa his3<delta>1 leu2<delta>0 met15<delta>0 ura3<delta>0 ENO1-TAP::HIS5)

tag: 5'->3' barcode

value: ATCACG


title: Fba1p PAR-CLIP-seq

status: Public on May 31 2017

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

value: (MATa his3<delta>1 leu2<delta>0 met15<delta>0 ura3<delta>0 FBA1-TAP::HIS5)

value: GCCAAT


title: SD puf3∆ mRNA-seq Replicate 2

data_processing:
Base calling was performed according to Illumina's protocols.
Low-quality reads were removed if they met any of the following criteria: <18 nt, only homopolymer As, missing 3’ adapter, 5’-3’ adapter ligation products, 5’-5’ adapter ligation products, low quality (more than 4 bases with quality scores below 10 or more than 6 bases with a quality score below 13).
High-quality reads were aligned to S. cerevisiae genome version sacCer3 using Bowtie v0.12.7 with the parameters -k 275 -v 3 --best --strata.
Read counts in each library were normalized to the total number of mapped reads in millions (RPM).
Reads mapping uniquely to the genome with zero mismatches were were used to calculate RPM per kilobase of transcript (RPKM) for each gene.
Genome_build: SGD/sacCer3 (April 2011) from S288C strain
Supplementary_files_format_and_content: Normalized transcript abundance (RPKM) is presented for each transcript as the RPKM averaged across the replicate mRNA libraries.

molecule: polyA RNA

growth_protocol: For preparation of ribosome depleted mRNA-seq libraries, yeast strains were grown at 30°C with rigorous shaking in synthetic defined (SD) media supplemented with 200 µM 4-thiouracil (when indicated) to OD600 = 0.7-0.8.

extract_protocol:
Extract preparation and ribosome depletion using sucrose density gradients were carried out as described in the gPAR-CLIP procedure (without UV crosslinking, Freeberg et al. Gen Biol 2013).
PolyA+ mRNAs were enriched using oligo(dT)25 beads and converted into sequencing libraries as described in Levin et al. (Nature Methods 2010).

treatment_protocol: 50 mL of mid-log phase cultures were pelleted for 5 min at 3,000Xg at room temperature, resuspended in 2 mL of 1XHBSS, transferred to 60 mm cell culture dish, placed on ice, and irradiated with 365nm UV at 150 mJ/cm2 4 times using a UVP CL-1000L UV crosslinker. Cells were then pelleted for 2 min at 5,000Xg at 4°C. After removing 1X HBSS, the cells were frozen in liquid nitrogen.

value: BY4742 puf3<delta>::KAN

value: CGATGT


title: ChIPseq.YFP_HumanPRDM9.antiGFP.Rep1.ProtocolN

city: Berkeley

first: Nicolas

last: Altemose

state: CA

address: 327 Stanley Hall

department: Bioengineering

institute: University of California, Berkeley

description:
Uniquely Mapped Fragments: 80844035
Multiplex Group: 1

library_source: genomic

data_processing:
ChIP-seq: Reads were aligned to hg19 using BWA (v0.7.0-r313, option -q 10) followed by Stampy (v1.0.23_(r2059), option --bamkeepgoodreads). PCR duplicates, reads not mapped in a proper pair, reads with an insert size larger than 10 kb, and read pairs for which neither read had a mapping quality score greater than 0 were removed using samtools (v0.1.19-44428cd). For samples with only one replicate, fragments were split at random into two equally-sized pseudo-replicates. Fragment coverage from each replicate was then computed at each position in the genome using in-house code and the samtools (v0.1.19-44428cd) and bedtools (v2.23.0, genomecov -d) packages. Peaks were called using a custom peak calling algorithm (described in Gupta-Hinch et al. 2014). Enrichments and p-values are reported for the base with the maximum likelihood value within each peak region.
ATAC-seq: Reads were mapped to hs37d5 using BWA (v0.7.0-r313) followed by Stampy (v1.0.23_(r2059), with option --bamkeepgoodreads). PCR duplicates, mtDNA-mapped reads, reads not mapped in a proper pair, reads with mapping quality equal to 0, and pairs with an insert size larger than 2 kb were removed using samtools (v0.1.19-44428cd). Fragments were split by size into inter-nucleosome (51-100 bp) and mono-nucleosome fragments (180-247 bp), and the position of the central base in each fragment was reported.
RNA-seq: We created a custom reference sequence by merging the hs37d5 reference with the construct and vector sequences transfected into our cells. Data were analyzed using the Tuxedo software package. Reads were mapped and processed using TopHat (version 2.0.13, options --mate-inner-dist=250 --mate-std-dev 80 --transcriptome-index=Ensembl.GRCh37.genes.gtf); followed by Cufflinks, CuffQuant, and CuffDiff (version 2.2.1); then analyzed using CummeRbund.
Genome_build: hg19 (ChIP-seq), hs37d5 (ATAC-seq), hs37d5+ (RNA-seq)
Supplementary_files_format_and_content: bedgraph files contain fragment coverage data for each base across the 22 autosomes and X chromosome. For ChIP-seq samples, these values were used as inputs for de novo peak calling and force-calling. ChIP-seq peak call files are in tab-delimited text format, with one peak per rown and column headers indicating the contents of each column. For ATAC-seq samples, fragment coverage data were split into subsets representing internucleosome fragments (51-100 bp long) and mononucleosome fragments (180-247 bp long), and only the position of the central base of each fragment is reported. For RNA-seq samples, the final CuffDiff output file (tab-delimited diff format) is provided.

molecule: genomic DNA

organism: Homo sapiens

source_name: HEK293T cells

growth_protocol: Cells were grown in DMEM media (10% FCS, 1X NEAA, 2 mM L-Glut, Sigma D6546) in 200-ml roller bottles at 37C with 5% CO2

extract_protocol:
ChIP was performed as described in Gupta-Hinch et al. 2014
Libraries were prepared for sequencing using standard Illumina protocols by the Oxford Genomics Centre.

treatment_protocol: A transfection cocktail was prepared for each bottle by adding 0.5 mg of chloroform-purified construct DNA to 50 ml of serum-free DMEM (1X NEAA, 2 mM L-glut) and 1 mg polyethylenimine, followed by a 10-minute incubation, and then addition of 375 ug of kifunensine. After the cells reached 75% confluence, the growth medium was removed from each roller bottle and replaced with 200 ml low-serum DMEM (2% FCS, 1X NEAA, 2 mM L-Glut) and 50 ml transfection cocktail.

tag: cell line

value: HEK293T (ATCC CRL-3216)

tag: transfected with

tag: chip antibody

value: GFP (Abcam ab290)


title: ChIPseq.Untransfected.Input.ProtocolN

description:
Uniquely Mapped Fragments: 98664592
Multiplex Group: 2


title: ChIPseq.Untransfected.antiH3K4me3.Rep1.ProtocolN

description:
Uniquely Mapped Fragments: 59156993
Multiplex Group: 2

value: H3K4me3 (Abcam ab8580)


title: ChIPseq.Untransfected.antiH3K4me3.Rep2.ProtocolN

description:
Uniquely Mapped Fragments: 72839266
Multiplex Group: 2


title: PHF21A_def_female_rep1

city: Ann Arbor

first: Robert

middle: Scott

last: Porter

state: MI

address: 1241 E. Catherine St, Med Sci II, Rm. 5815

department: Human Genetics

institute: University of Michigan

data_processing:
Full length reads were mapped to hg19 using TopHat2 (v2.1.0) with Bowtie2 (v2.2.6). Only uniquely mapping reads were analyzed further.
BAM Files were converted to Bigwig files in a strand specific manner. Bigwigs were normalized to 10 million non-rRNA and non-mitochondrial reads.
DESEQ was used to call differential gene expression between sex-matched patient and control samples
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files represent genome coverage by the reads in a strand specific manner after normalizing to 10 million non-rRNA non-mtRNA reads. DESEQ files represent differential gene expression between pairs of samples (incorporating technical replicates).

source_name: patient-derived lymphoblasts

growth_protocol: Patient-derived lymphoblasts were maintained in RPMI Media 1640 with 10% FBS, 1x GlutaMAX, 1% Pen/Strep

extract_protocol:
RNA was isolated from two separate culture dishes using RNA purification kit from Life Technologies. PolyA mRNA was isolated using NEB Magentic mRNA isolation kit
Libraries were prepared using Direct Ligation of Adapters to First-strand cDNA as described in PMID: 25607527

tag: subject status

tag: subject gender

value: female

tag: cell type

value: lymphoblasts (EBV-transformed patient lymphocytes)


title: PHF21A_WT_female_rep2

value: unaffected, PHF21A-WT


title: a375_gegfp_a02_1nm_tram_r1

city: Boston

first: William

middle: C.

last: Hahn

state: MA

address: 450 Brookline Avenue; D1538

department: Medical Oncology

institute: Dana Farber Cancer Institute

data_processing:
Sequenced reads were trimmed for adaptor sequence and mapped to the reference human genome (hg19) using Tophat 2.0.11.
Transcript assembly, abundance estimation, and differential expression analysis were performed with Cufflinks 2.0.2.
Genome_build: hg19
Supplementary_files_format_and_content: For each parental cell line (A375, CALU1, HCT116, or PATU8902), there is a .diff file (tab delimited text file) containing gene-level expression differences obtained from the Cuffdiff module from Cufflinks 2.0.2. Average FKPM of technical replicates are shown, and genes that are significantly differentially regulated (q < 0.05) between different genetic perbations and/or treatments are labelled.

source_name: Skin

growth_protocol: Cells were seeded in uncoated 6 well plates (2E5 cells per well) and allowed to adhere overnight.

extract_protocol:
Total RNA was harvested using a  RNeasyMini kit (Qiagen 74104)
First strand cDNA was generated from 1.5 μg of total RNA using Oligo(dT)12-19 Primer (Invitrogen) and AfifinityScript Multiple Temperature Reverse Transcriptase (Aglient). Second strand cDNA was synthesized using an mRNA Second Strand Synthesis Module (#6111L). Libraries were prepared by tagmentation (Nextera XT DNA Sample Preparation Kit, Illumina) according to the manufacturer’s protocol, using index primers (Nextera XT Index kit, Illumina) to facilitate multiplexing. The concentration of each cDNA library was quantified with the KAPA Illumina ABI Quantification Kit (Kapa Biosystems). Libraries were normalized to 5 nM and pooled for sequencing

treatment_protocol: Cells were treated with DMSO or trametinib (Selleck) for 24 hours.

tag: grna

tag: treatment

value: 1 nM Trametinib

tag: treatment duration

value: 24 hours


title: Ins2+/- Diet A rep 4, muscle

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

data_processing:
kallisto version 0.42.3 was first used to build an index file for  the mouse reference transcriptome GRCm38 as downloaded from the Ensembl web site (www.ensembl.org). The sequence  reads for each sample were then quantified with the quant function of kallisto.
In-house Perl scripts were used to sum the  read counts at the transcript level for each gene and to create a matrix comprising the read counts for all the genes for all the  samples.
Differential expression analysis was then performed on the data from that matrix using the R package DESeq2.
Each sample was assessed with the quality control software RNA-SeQC (DeLuca et al., 2012) and the PtR script from the  trinity suite (Grabherr et al., 2011). Such quality control showed no outliers, and all the samples were therefore kept for  differential expression analyses.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab separated text file with ensembl gene id and counts from kallisto

organism: Mus musculus

source_name: triceps surae hindlimb muscle group

extract_protocol:
The livers and triceps surae hindlimb muscle groups were dissected from 25 week-old female mice euthanized after 4 h of fasting, flash frozen in liquid nitrogen, and stored at -80ºC for RNA sequencing. RNA isolation and purification from livers and triceps surae hindlimb muscle groups was performed using the Qiagen RNeasy Mini kit (Qiagen, Mississauga, ON, Canada).
Sequencing libraries were prepared with the TruSeq RNA Sample Preparation v2 kit (Illumina, San Diego, CA, USA), from 400 ng of total RNA. Sample quality was assessed using a BioAnalyzer, and samples were quantified using Oubit. Libraries were multiplexed and sequenced over two rapid-run lanes on HiSeq2500, and raw data were converted to fastq format with bcl2fastq-v1.8.4 (Illumina).

treatment_protocol:
Diet A: LabDiet 5LJ5 (PMI Nutrition International, St. Louis, MO, USA); a moderate-energy diet of 4.68 kcal/g, with 20% of calories from protein, 25% from fat, and 55% from carbohydrate.
Diet B: Research Diets D12330 (Research Diets, New Brunswick, NJ, USA); a high-energy diet of 5.56 kcal/g, with 16% of calories from protein, 58% from fat, and 26% from carbohydrate

tag: diet

value: A

value: stable; mixed C57BL/6 and 129

tag: tissue

value: triceps surae hindlimb muscle group

tag: age

value: 25 weeks old

tag: Sex

tag: genotype


title: PHF21A_def_female_rep2


title: H3_noPolyY

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Library strategy: MNase ChIP-seq
FastQ quality trimming using FastX (version 0.0.13)  and a cut-off value of 20
Adaptor trimming using cutadapt version 1.10
Readmapping using Bowtie 2 version 2.1.0
sorting and indexing of BAM files using samtools version 0.1.9-4428cd
Wiggle fill generation with COVERnant version 0.1
Genome_build: Tb927v24 or Tb427v24 (see processed file names)
Tb427v24:
http://tritrypdb.org/common/downloads/release-24/TbruceiLister427/fasta/data/TriTrypDB-24_TbruceiLister427_Genome.fasta
Tb927v24:
http://tritrypdb.org/common/downloads/release-9.0/TbruceiTREU927/fasta/data/TriTrypDB-9.0_TbruceiTREU927_Genome.fasta
Supplementary_files_format_and_content: wiggle

organism: Trypanosoma brucei brucei

source_name: T. brucei SM GT_210_nt noPolyY

growth_protocol: T. brucei Wt and genetically modified strains were cultured at 37°C in HMI-11 medium.

extract_protocol:
[MNase ChIP-seq] The cells were cross-linked with formaldehyde, permeabilized and treated with micrococcal nuclease (MNase). H2A.Z/H3-containing nucleosomes were immunoprecipitated using the respective antibody.
[RNA pol II ChIP-seq] The cells were cross-linked with formaldehyde, permeabilized and chromatin was fragmented via sonification. RNA pol II bound DNA was immunoprecipitated using BB2 antibody.
ChIP-seq libraries were constructed as described by in Wedel & Siegel, 2017.
[Small 3P-RNA-seq] Small total RNAs (<200 nt) were extracted and treated with Terminator exonuclease to enrich for primary transcripts (3P-RNA). One half of the sample was treated with Polyphosphatase and the other half was mock treated.
NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (New England BioLabs)

tag: strain background

value: LISTER

value: polyclonal H3 rabbit antiserum

tag: chip antibody details

value: From Gassen et al., 2012 (PMID 22941659)

tag: treated with

value: 2 µg/mL G418, 5 µg/mL hygromycin, 50 µg/mL blasticidin


title: Puf2p_targets

data_processing:
Library strategy: PAR-CLIP-seq
Base-calling: HiSeq Control Software (v1.5.15.1) and Real Time Analysis (v1.13.48.0)
De-multiplexing: CASAVA (v1.8.2)
Read alignment: Bowtie (v0.12.7) with parameters -v 3 -k 100 --best --strata --phred64-quals
Binding site generation: Overlapping reads with 0-2 T-to-C mismatches were clustered into peaks. Peaks were smoothed with a Gaussian smoothing technique described in Freeberg et al. (2013). Peaks with at least 1 T-to-C conversion event were kept as LARP1 binding sites. Read counts were summed per binding site, normalized to the number of million mapped reads per library, normalized to the gene RPKM value, and multiplied by 1,000 to account for the kilobase normalization of gene RPKM values.
Genome_build: SGD/sacCer3 (April 2011) from S288C strain
Supplementary_files_format_and_content: Tab-delimited file of Puf binding sites containing information on the genomic position of the binding site

growth_protocol: Strains were grown at 30°C with rigorous shaking in synthetic defined (SD) media supplemented with 200 µM 4-thiouracil (when indicated) to OD600 = 0.7-0.8.

extract_protocol:
Cells were lysed in 1XPBS, 0.5% NP-40, 1X Complete Mini Protease Inhibitor, EDTA-free and cleared by sequential spins at 1,300Xg for 5 min and 20,000Xg for 10 min at 4°C. Clarified lysate was passed through a Costar Spin-X filter (Corning CLS8160), mixed with RNase T1 (Fermentas EN0541) to 1 U/µL, and incubated at 22°C for 15 min followed by 5 min incubation on ice. Lysate was then directly mixed with IgG magnetic beads (prepared by coupling rabbit IgG (Sigma-Aldrich I5006) to Dynabeads M-270 Expoxy (Invitrogen 143-01)) to pull down Puf::TAP. RNase T1 digestion, CIP treatment, and 3’ DNA linker ligation were performed as described for Puf3p in Freeberg et al. (Gen Biol 2013). Afterwards, 5’ end phosphorylation was performed on-bead in 20 µL of PNK mix (70 mM Tris pH 7.6, 10 mM MgCl2, 5 mM DT, 1 µL P32 rATP (6000 Ci/mmol 10 mCi/mL Perkin Elmer BLU502Z500UC), 1 U/µL T4 polynucleotide kinase) and incubated at 37°C for 15 min. 2 µL of 10 mM ATP was added to the mix, and the reaction was incubated for 10 min. After SDS-PAGE and transfer, crosslinked RNAs were visualized by autoradiography, and the corresponding Puf band was excised.
Library construction was carried out as described for Puf3p in Freeberg et al. (Gen Biol 2013), omitting the 5’ end phosphorylation step.

treatment_protocol: 50 mL of mid-log phase cultures (OD600 of 0.7-0.8) were pelleted for 5 min at 3,000Xg at room temperature, resuspended in 2 mL of 1XHBSS (Invitrogen 14025), transferred to 60 mm cell culture dish (BD Biosciences 353002), placed on ice, and irradiated with 365nm UV at 150 mJ/cm2 4 times using a UVP CL-1000L UV crosslinker. Cells were then pelleted for 2 min at 5,000Xg at 4°C. After removing 1X HBSS, the cells were frozen in liquid nitrogen.

tag: strain

value: (MATa his3<delta>1 leu2<delta>0 met15<delta>0 ura3<delta>0 PUF2-TAP::HIS5)

value: CGATGT


title: Puf6p_targets

value: (MATa his3<delta>1 leu2<delta>0 met15<delta>0 ura3<delta>0 PUF6-TAP::HIS5)

value: GCCAAT


title: Puf1p_targets

value: (MATa his3<delta>1 leu2<delta>0 met15<delta>0 ura3<delta>0 PUF1-TAP::HIS5)

value: ATCACG


title: Pfk2p PAR-CLIP-seq

value: (MATa his3<delta>1 leu2<delta>0 met15<delta>0 ura3<delta>0 PFK2-TAP::HIS5)

tag: 5'->3' barcode


title: PHF21A_def_male_rep1

value: male

value: lymphoblasts (EBV-transformed patient lymphocytes)


title: PHF21A_WT_female_rep1

value: unaffected, PHF21A-WT

value: female


title: ChIPseq.YFP_HumanPRDM9.Input.ProtocolN

description:
Uniquely Mapped Fragments: 100861414
Multiplex Group: 1

tag: cell line

value: HEK293T (ATCC CRL-3216)

tag: transfected with

tag: chip antibody


title: H3_GT_210_nt

source_name: T. brucei SM GT_210_nt


title: H3_strongPolyY

source_name: T. brucei SM GT_210_nt strongPolyY


title: Ins2+/+ Diet B rep 5, muscle

value: B

value: stable; mixed C57BL/6 and 129

value: triceps surae hindlimb muscle group

value: 25 weeks old


title: Puf5p_targets

value: (MATa his3<delta>1 leu2<delta>0 met15<delta>0 ura3<delta>0 PUF5-TAP::HIS5)

value: ACAGTG


title: PHF21A_def_male_rep2

tag: subject status

tag: subject gender

tag: cell type


title: Ins2+/- Diet B rep 5, muscle


title: Ins2+/+ Diet B rep 4, muscle


title: SD puf3∆ mRNA-seq Replicate 1

value: BY4742 puf3<delta>::KAN


title: RPB9_ChIP

data_processing:
FastQ quality trimming using FastX (version 0.0.13)  and a cut-off value of 20
Adaptor trimming using cutadapt version 1.10
Readmapping using Bowtie 2 version 2.1.0
sorting and indexing of BAM files using samtools version 0.1.9-4428cd
Wiggle fill generation with COVERnant version 0.1
Genome_build: Tb927v24 or Tb427v24 (see processed file names)
Tb427v24:
http://tritrypdb.org/common/downloads/release-24/TbruceiLister427/fasta/data/TriTrypDB-24_TbruceiLister427_Genome.fasta
Tb927v24:
http://tritrypdb.org/common/downloads/release-9.0/TbruceiTREU927/fasta/data/TriTrypDB-9.0_TbruceiTREU927_Genome.fasta
Supplementary_files_format_and_content: wiggle

source_name: T. brucei  (BF) Wt

value: LISTER

value: affinity purified polyclonal BB2 antibody

value: From Bastin et al., 1996 (PMID 8813669)


title: PHF21A_WT_male_rep1


title: Puf4p_targets

value: (MATa his3<delta>1 leu2<delta>0 met15<delta>0 ura3<delta>0 PUF4-TAP::HIS5)

value: TGACCA


title: PHF21A_WT_male_rep2

value: male


title: Small_3P-RNA_seq_-PP


title: Ins2+/- Diet A rep 5, muscle

value: A


title: Ins2+/+ Diet A rep 5, muscle


title: Small_3P-RNA_seq_+PP

value: 20 units Polyphosphatase


title: Ins2+/+ Diet A rep 4, muscle

value: female


title: GT_210_nt_ChIP_8dpt

value: affinity purified polyclonal H2A.Z antibody

value: custom-made, published in this publication

value: 2 µg/mL G418, 5 µg/mL hygromycin, 50 µg/mL blasticidin


title: Ins2+/+ Diet A rep 3, muscle

value: stable; mixed C57BL/6 and 129

value: triceps surae hindlimb muscle group


title: GT_416_nt_input_8dpt

source_name: T. brucei SM GT_416_nt


title: GT_210_nt_input_8dpt


title: Ins2+/+ Diet B rep 3, muscle

value: B

value: 25 weeks old


title: Ins2+/+ Diet B rep 2, muscle


title: Ins2+/- Diet B rep 4, muscle


title: GT_416_nt_ChIP_8dpt


title: GT_416_nt_ChIP_97dpt

value: 2 µg/mL G418, 5 µg/mL hygromycin, 50 µg/mL blasticidin, 1 µg/mL doxycycline


title: Ins2+/- Diet B rep 3, muscle


title: GT_416_nt_input_97dpt

value: LISTER


title: GT_210_nt_input_21dpt


title: Ins2+/- Diet B rep 2, muscle


title: Ins2+/- Diet A rep 2, muscle


title: Ins2+/- Diet A rep 1, muscle


title: Ins2+/- Diet A rep 3, muscle


title: Ins2+/- Diet A rep 4, liver

source_name: liver

value: liver


title: Ins2+/- Diet B rep 1, muscle


title: Ins2+/- Diet B rep 5, liver


title: Ins2+/+ Diet B rep 5, liver


title: Ins2+/+ Diet B rep 4, liver


title: Ins2+/- Diet A rep 3, liver


title: Ins2+/+ Diet A rep 5, liver


title: Ins2+/+ Diet A rep 2, muscle


title: pool12

city: Münster

first: Shirin

last: Glander

state: Deutschland (DEU)

address: Domagkstraße 3

institute: University Münster

description: pool of late flowering RILs of Bur-0xCol-0 Recombinant Inbred Lines (RIL) provided by the Arabidopsis Stock Center at INRA Versailles (France)

data_processing:
Raw sequences were demultiplexed and read quality validated with FastQC.
Bad quality base calls were trimmed using the fastx-toolkit (Version 0.013, Li et al. 2009): quality score 33, quality threshold 20 and minimum length 30 base pair
Bowtie 2 (version 2-2.0.0-beta6, (Langmead & Salzberg 2012)
Tophat (version-2.0.5.Linux_x86_64) was used to discover splice sites and Cufflinks for assembling the transcriptome (Trapnell et al. 2010).
Read counts were calculated by counting the number of reads that mapped uniquely to the corresponding gene (isoforms were not considered). Lowly expressed genes with less than 20 reads over all samples were excluded from the analysis.
Genome_build: A. thaliana TAIR10
Supplementary_files_format_and_content: Matrix of raw read counts (1 sample per column), tab delimited

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Each line was grown individually in six replicates, each in 6cm diameter pots randomly allocated to 24 trays, each containing 35 pots. Seeds were stratified at 5°C for 3 days and grown in growth chambers (Elbanton BV, Holland, equipped with Sylvania Gro-Lux F36W /Gro (T8) fluorescent tubes and Osram 25 W 220 Lumen light bulbs) under long-day conditions (21°C, 16h light, 18°C, 8h dark). Trays were rotated within the chamber every other day. Flowering time was scored as the day to the first open flower.

extract_protocol:
RNA was isolated using the TRIzol extraction protocol (Life Technologies Copr. Carlsbad, USA). DNA traces were removed with the Ambion DNA-free kit (Life Technologies Copr. Carlsbad, USA) and purified RNA was stored in TE buffer at -80°C.
Single-read libraries were prepared with 1mg of total RNA per sample using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina Inc. San Diego, USA) based on poly-A RNA purification.

value: lateflowering

value: leaf

tag: time point

value: tp2 (28 days)


title: pool10


title: pool11


title: pool_9

description: pool of early flowering RILs of Bur-0xCol-0 Recombinant Inbred Lines (RIL) provided by the Arabidopsis Stock Center at INRA Versailles (France)

value: earlyflowering


title: Ins2+/+ Diet A rep 4, liver

tag: diet

value: A


title: Ins2+/+ Diet A rep 3, liver

tag: tissue


title: pool_7


title: Ins2+/- Diet B rep 4, liver

tag: age


title: GT_210_nt_ChIP_21dpt


title: Ins2+/+ Diet A rep 1, muscle

tag: Sex


title: Ins2+/+ Diet B rep 3, liver

tag: genotype


title: Ins2+/+ Diet B rep 1, muscle


title: pool_6

value: tp1 (14 days)


title: Ins2+/+ Diet A rep 2, liver

value: female


title: Ins2+/+ Diet B rep 2, liver


title: Ins2+/- Diet B rep 3, liver


title: Ins2+/- Diet B rep 2, liver


title: pool_5


title: pool_3


title: Ins2+/- Diet A rep 2, liver


title: pool_2


title: pool_1


title: Ins2+/- Diet A rep 1, liver


title: Col_2_3

description: parents of Bur-0xCol-0 Recombinant Inbred Lines (RIL) provided by the Arabidopsis Stock Center at INRA Versailles (France)

value: Col


title: Ins2+/+ Diet A rep 1, liver


title: Col_2_2


title: Cone_bipolars P13 rep2

city: Los Angeles

first: Yerbol

middle: Z.

last: Kurmangaliyev

address: 675 Charles E. Young Drive South

institute: University of California, Los Angeles

data_processing:
RNA sequencing reads were aligned to the reference mouse genome (GRCm38/mm10) using STAR (Dobin et al., 2013).
Raw gene expression counts were calculated for annotated genes (Ensembl 86) using STAR. We excluded genes with low levels of expression. In total, 13,812 genes with expression level of CPM (counts-per-million) > 4 in at least one sample were kept for further analysis.
Raw gene counts were then normalized using edgeR (TMM method, Robinson et al. 2010) and used for calculation of gene expression values as logCPM (log2-counts-per-million).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include logCPM values for all samples

source_name: Retina_Cone_bipolars P13

extract_protocol:
Cells were collected in Extraction buffer from the Arcturus PicoPure RNA Isolation kit after sorting and RNA was isolated using the same kit. mRNA was amplified in a linear fashion using the Arcuturus RiboAmp HS PLUS kit
cDNA libraries were generated using the TruSeq RNA Library Prep kit v2

value: Retina


title: Col_2_1


title: Cone_bipolars P13 rep1


title: Col_1_2


title: Rod_bipolars P13 rep2

source_name: Retina_Rod_bipolars P13


title: Rod_bipolars P13 rep1


title: Col_1_1


title: Bipolars P30 rep2

source_name: Retina_Bipolars P30

value: Bipolars


title: Bur_2_3

value: Bur


title: Ins2+/- Diet A rep 5, liver

value: stable; mixed C57BL/6 and 129


title: Bipolars P13 rep2

source_name: Retina_Bipolars P13


title: Bur_2_2


title: Bipolars P30 rep1


title: pool_4


title: Bipolars P13 rep1


title: Bur_1_3


title: Bur_2_1


title: Bipolars P7 rep2

source_name: Retina_Bipolars P7


title: Bur_1_2


title: Bur_1_1


title: Bipolars P7 rep1


title: Ins2+/- Diet B rep 1, liver

value: B


title: Cones P30 rep2

source_name: Retina_Cones P30

value: Cones


title: H2A.Z ChIP-seq

tag: strain background

value: affinity purified polyclonal H2A.Z antibody

value: custom-made, published in this publication


title: Cones P30 rep1


title: H3 ChIP-seq

value: LISTER

value: polyclonal H3 rabbit antiserum

tag: chip antibody details

value: From Gassen et al., 2012 (PMID 22941659)


title: Cones P13 rep1

source_name: Retina_Cones P13


title: Col_1_3

value: leaf


title: Cones P7 rep2

source_name: Retina_Cones P7


title: Cones P7 rep1


title: Rods P30 rep2

source_name: Retina_Rods P30

value: Rods


title: Rods P30 rep1


title: RNaseR-treated Small RNA S. acidocaldarius

city: Marburg

first: Alvaro

last: Orell

state: Hessen

address: Karl-von-Frisch-Str. 32

department: B

institute: Max Planck Institute for Terrestrial Microbiology

description: small RNAs (<200 nt)

data_processing:
(Software) CLC Genomics Workbench 9.5.3
(Raw Data Import) The raw data files were imported using the Illumina Import option (Illumina Pipeline 1.8 and removal of failed reads).
(Raw Data Processing) The raw data files were processed by quality score trimming (quality score trimming limit: 0.05; max. number of ambiguities: 2) and NEBNext 3' RNA adapter (AGACGTGTGCTCTTCCGATCT) trimming (strand: minus; action: remove adapter; mismatch cost: 3; gap cost: 5; cutoff internal end matches: 10 ; minimum end matches score: 5). The processed sequences were filtered by length (15 nt cutoff)
(Read Mapping) The trimmed sequences were mapped to the S. acidocaldarius reference genome (CP000077) using CLC default settings and saved as a read track file. The mapped reads (between 6 to 12 million reads per file) were extracted and sampled to 1.000.000 reads. These 1.000.000 reads were again mapped to the genome using CLC default settings.
Genome_build: S. acidocaldarius reference genome (CP000077)
Supplementary_files_format_and_content: The processed data files are in .wig (wiggle) format. They contain the mapping graphs of the three samples (each 1.000.000 mapped reads) which were created from the coverage plots of the generated read track files. Furthermore, the reference genome (Sulfolobus acidocaldarius DSM 639 (CP000077)) is included as .gkb (genbank) file, which is needed for the illustration of the mapping graph track.
Supplementary_files_format_and_content: instructions for .wig file importing: When working with CLC Genomics Workbench, import the .gkb file of S. acidocaldarius (genome file) via standard import. Rename the file to "CP000077". This step is critical for the illustration of the mapping graph. Convert the renamed file to a genome track (Toolbox -> Track tools -> Convert to Tracks -> Choose renamed file -> Create sequence track and save). Import the .wig file (via Import -> Tracks) and choose the converted genome track as reference track.

organism: Sulfolobus acidocaldarius

source_name: liquid culture

growth_protocol: Cells were grown in Brock medium to logarithmic phase.

extract_protocol:
Sample 1 & 2:Total RNA samples were isolated according to TriZol  protocol. Sample 3: Cells were lysed by homogenization and small RNAs were isolated according to the mirVana miRNA Isolation Kit (Ambion). 60 U of recombinant Ribonuclease R (RNase R) from E. coli (Epicentre, cat# RNR07250) were added to 10 μg small RNA of S. acidocaldarius MW001 and the reaction was carried out in 10 x reaction buffer at 37°C for 45 min. For all 3 samples, residual chromosomal DNA present in RNA samples was removed by RNase-free DNase I (Roche) treatment for 2 h at 37°C and preparation of the RNA-Seq libraries and Illumina HiSeq 2500 sequencing were performed at the Max-Planck Genome Centre, Cologne, according to their protocol.
cDNA libraries were prepared according to the NEBNext Small RNA Library Prep Set for Illumina.

tag: developmental stage

value: logarithmic phase


title: S. acidocaldarius Biofilm Growth

source_name: surface adhered culture

tag: strain


title: Rods P7 rep2

source_name: Retina_Rods P7


title: Rods P13 rep1

source_name: Retina_Rods P13


title: S. acidocaldarius Planktonic Growth


title: Rods P7 rep1


title: d4c7 PGCLC, Input

status: Public on May 30 2017

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: genomic DNA, Input

data_processing:
Read data were mapped on mouse mm10 genome by bowtie v1.1.2 with "-n 3 -m 1" option.
Mapped reads were sorted and format converted to bam using samtools v1.3 and picard-tools v2.1.0.
Genome_build: mm10
Supplementary_files_format_and_content: Tdf files are made using igvtools v2.3.52 with "-w 25 -e 250" options.

source_name: d4c7 PGCLC

growth_protocol: Embryonic stem cells (ESCs) were maintained in N2B27 supplemented with 2iLIF [N2B27 medium with 2i (PD0325901, 0.4 uM: Stemgent, San Diego, CA; CHIR99021, 3 uM: Stemgent) and LIF (1000 U/ml; Merck Millipore)] on a dish coated with poly-L-ornithine (0.01%; Sigma) and Laminin (10 ng/ml; BD Biosciences).  EpiLCs were induced by plating 1×10^5 ESCs on a well of a 12-well plate coated with human Plasma Fibronectin (16.7 mg/ml) in N2B27 medium containing Activin A (20 ng/ml), bFGF (12 ng/ml), and KSR (1%).  The PGCLCs were induced from d2 EpiLCs under a ﬂoating condition in a well of a low-cell-binding U-bottom 96-well plate (Thermo Fisher Scientific) in serum-free medium [GK15; GMEM (Thermo Fisher Scientific) with 15% KSR, 0.1 mM NEAA, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin, 0.1 mg/ml streptomycin, and 2 mM L-glutamine] in the presence of the cytokines BMP4 (500 ng/ml; R&D Systems), LIF (1000 U/ml; Merck Millipore), SCF (100 ng/ml; R&D Systems), and EGF (50 ng/ml; R&D Systems).    At the induction day 4, PGCLCs(d4PGCLCs) were sorted using Fluorescence-Activated Cell Sorting (FACS) with BV  fluorescence .     For expansion of d4 PGCLCs on plate, m220 feeder cells were prepared [The m220 cell line were cultured in a gelatin-coated plate in DMEM with 10% FCS.  Since m220 cells were highly vulnerable to mitomycin C (MMC) treatment, we established sublines of m220 resistant to MMC.  Briefly, single m220 cells were plated on wells of 96-well plates (6 plates) by FACS.  One week after the plating, cell growth was observed in approximately half of the wells.  After passaging the cells to one well of each of the two 96-well plates, one plate was frozen as a replica and the other plate was treated with MMC (4 ug/ml, 2 hrs).  At 10 days after MMC treatment, MMC resistance was evaluated by microscopic observation.  In total, 242 m220 sublines were established and 7 sublines showed high MMC resistance.  The m220-5 subline was primarily used for experiments].      The m220-5 cells were cultured for 3 passages with 10 uM of both Forskolin and Rolipram to permit adaptation to these compounds prior to MMC treatment (1-2 ug/ml, 2 hrs), since the MMC-treated m220-5 feeders were vulnerable to Forskolin (Sigma) and Rolipram (Abcam).  d4 PGCLCs or E9.5 PGCs (BDF1×Stella–EGFP) were sorted by FACS and plated on m220-5 cells in GMEM containing 10% KSR, 0.1 mM NEAA, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin, 0.1 mg/ml streptomycin, 1×GlutaMAX (Thermo Fisher Scientific), 2.5% FCS, 100 ng/ml SCF, 10 uM Forskolin, and 10 uM Rolipram.  In the case of E9.5 PGCs, effect of LIF (1000 U/ml) was also examined.  Half of the culture medium was changed every two days.

extract_protocol:
Cells were suspended in 1 mL of phosphate buffered saline (PBS) and fixed by adding 27 mL of 36.5% formalin (Sigma) for 10 min at room temperature.  Fixation was terminated by adding 110 mL of 1.5 mM glycine.  The fixed cells were washed twice in PBS containing 0.1% bovine serum albmin (BSA), and were lysed in 400 mL SDS-lysis buffer [50 mM Tris-HCl (pH 8.0) containing 1% SDS, 10 uM EDTA, and 1 mM PMSF] on ice for 10 min.  Chromatins were then solubilized using Bioruptor UCD250 with ice-chilled water, with 15 cycles of 30 sec sonication at the high power and 60 sec interval.  The sonication products were centrifuged at 16,000 g for 5 min.  The supernatants were diluted in 1 mL ChIP dilution buffer [16.7 mM Tris-HCl (pH 8.0), 0.01% SDS, 1.1% Triton X100, 1.2 mM EDTA, 167 mM NaCl, 1 mM SDS, 200 mg/mL tRNA (Roche)], and were divided into 0.1 mL as input DNA and 1.3 mL as ChIP samples.  The ChIP samples were mixed with the Dynabeads-antibody complexes and rotated at 4 ºC overnight.  The ChIP-ed Dynabeads were recovered using the DynaMag-2 magnet (Life Technologies), and washed with 200 mL of low salt buffer [20mM Tris-Cl (pH 8.0), containing 0.1% SDS, 1% Triton X100, 2 mM EDTA, and 150 mM NaCl], high salt buffer [20mM Tris-Cl (pH 8.0), containing 0.1% SDS, 1% Triton X100, 2 mM EDTA, and 500 mM NaCl], RIPA buffer [10mM Tris Cl (pH8.0), containing 1% Sodium deoxycholate, 1% NP40, 250 mM LiCl, and 1 mM EDTA], and TE buffer [10 mM Tris Cl (pH8.0), containing 1 mM EDTA].  The ChIP-ed Dynabeads were then incubated in new tubes containing 50 mL of Elution buffer (0.1 mM NaHCO3, 1% SDS, 10 mM DTT, and 0.06 mM tRNA) for 15 min at room temperature.  The supernatants were collected using DynaMag-2, and were reverse-crosslinked by adding 8 mL of 2.5 M NaCl and incubating at 65 ºC overnight.  Then, 2 mL of 0.5 M EDTA and 4 mL of 0.645 mg/mL proteinase K solution were added to reaction mixture, and further incubated at 45 ºC for 1 hr.  The ChIP-ed DNAs were then purified with Qiaquick PCR purification columns, using the buffer EB supplemented with 4 ng/mL tRNA (Qiagen).
The ChIP-ed and Input DNAs were sheared to an average size of about 150 bp by ultra-sonication (Covaris, Woburn, MA).  ChIP-ed DNAs obtained from 1×10^6 cells were then subjected to the procedures for SOLiD Fragment Library Preparation (Life Technologies) according to the manufacture’s instruction except for the ligation reaction that was performed overnight.  The libraries were amplified with 11-13 cycles of PCR for H3K4me3 and H3K27ac or 8 cycles for H3K9me2 and H3K27me3.

treatment_protocol: d4c7 PGCLCs were sorted sugin FACS with BV fluorescence.

tag: chip antibdy

value: Input

value: Blimp1-mVenus reporter; Stella-ECFP reporter (BVSC)

tag: cell sorting

value: FACS (BV+)


title: d4c7 PGCLC, H3K27me3_2

description:
genomic DNA, ChIP-ed
ChIP from 1x10^6 cells

value: anti-H3K27me3, MsIgG, CMA323


title: d4c7 PGCLC, H3K27me3_1


title: d4c7 PGCLC, H3K4me3_1

description:
genomic DNA, ChIP-ed
ChIP from 1x10^5 cells

value: anti-H3K4me3, MsIgG, CMA304


title: d4c7 PGCLC, H3K4me3_2


title: Cones P13 rep2

value: Retina


title: E12.5_F_Germ_2

description: 3'-RNAseq amplified from 1ng RNA

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-c -m 30 -a CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -g CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -a AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the mouse genome mm10 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels by cufflinks-2.2.0 using the “—compatible-hits-norm”, “—no-length-correction” “—max-mle-iterations 50000” and “—library-type fr-secondstrand” options and mm10 reference gene annotations with extended TTSs. We extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample.

source_name: E12.5 female germ cells (Stella-EGFP+)

growth_protocol:
Embryonic stem cells (ESCs) were maintained in N2B27 supplemented with 2iLIF [N2B27 medium with 2i (PD0325901, 0.4 uM: Stemgent, San Diego, CA; CHIR99021, 3 uM: Stemgent) and LIF (1000 U/ml; Merck Millipore)] on a dish coated with poly-L-ornithine (0.01%; Sigma) and Laminin (10 ng/ml; BD Biosciences).  EpiLCs were induced by plating 1×10^5 ESCs on a well of a 12-well plate coated with human Plasma Fibronectin (16.7 mg/ml) in N2B27 medium containing Activin A (20 ng/ml), bFGF (12 ng/ml), and KSR (1%).  The PGCLCs were induced from d2 EpiLCs under a ﬂoating condition in a well of a low-cell-binding U-bottom 96-well plate (Thermo Fisher Scientific) in serum-free medium [GK15; GMEM (Thermo Fisher Scientific) with 15% KSR, 0.1 mM NEAA, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin, 0.1 mg/ml streptomycin, and 2 mM L-glutamine] in the presence of the cytokines BMP4 (500 ng/ml; R&D Systems), LIF (1000 U/ml; Merck Millipore), SCF (100 ng/ml; R&D Systems), and EGF (50 ng/ml; R&D Systems).    At the induction day 4, PGCLCs(d4PGCLCs) were sorted using Fluorescence-Activated Cell Sorting (FACS) with BV  fluorescence .     For expansion of d4 PGCLCs on plate, m220 feeder cells were prepared [The m220 cell line were cultured in a gelatin-coated plate in DMEM with 10% FCS.  Since m220 cells were highly vulnerable to mitomycin C (MMC) treatment, we established sublines of m220 resistant to MMC.  Briefly, single m220 cells were plated on wells of 96-well plates (6 plates) by FACS.  One week after the plating, cell growth was observed in approximately half of the wells.  After passaging the cells to one well of each of the two 96-well plates, one plate was frozen as a replica and the other plate was treated with MMC (4 ug/ml, 2 hrs).  At 10 days after MMC treatment, MMC resistance was evaluated by microscopic observation.  In total, 242 m220 sublines were established and 7 sublines showed high MMC resistance.  The m220-5 subline was primarily used for experiments].      The m220-5 cells were cultured for 3 passages with 10 uM of both Forskolin and Rolipram to permit adaptation to these compounds prior to MMC treatment (1-2 ug/ml, 2 hrs), since the MMC-treated m220-5 feeders were vulnerable to Forskolin (Sigma) and Rolipram (Abcam).  d4 PGCLCs or E9.5 PGCs (BDF1×Stella–EGFP) were sorted by FACS and plated on m220-5 cells in GMEM containing 10% KSR, 0.1 mM NEAA, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin, 0.1 mg/ml streptomycin, 1×GlutaMAX (Thermo Fisher Scientific), 2.5% FCS, 100 ng/ml SCF, 10 uM Forskolin, and 10 uM Rolipram.  In the case of E9.5 PGCs, effect of LIF (1000 U/ml) was also examined.  Half of the culture medium was changed every two days.
The wild type female mice were mated with the SG mice to obtain wild type PGCs/germ cells.

extract_protocol:
Total RNAs from collected primordial germ cell were extracted with RNeasy Micro Kit (QIAGEN, 74004) according to the manufacture's instruction.
cDNAs were amplified according to Kurimoto et al., 2006, Nucleic Acids Research 34, e42, and then subjected to a librray preparation method on SOLiD5500xl according to Nakamura et al., 2015

treatment_protocol:
d4c3, d4c5, and d4c7 PGCLCs were sorted using FACS with BV fluorescence.
PGCs at E9.5 and male/female germ cells at E12.5 were sorted using FACS with SG fluorescence (see Kagiwada et al., 2013)

value: Stella-EGFP reporter (SG)

value: SG+


title: E12.5_F_Germ_1

description: 3'-RNAseq amplified from 1ng RNA


title: E12.5_M_Germ_1

description: 3'-RNAseq amplified from 1ng RNA

source_name: E12.5 male germ cells (Stella-EGFP+)


title: E12.5_M_Germ_2

description: 3'-RNAseq amplified from 1ng RNA


title: E9.5_PGC_2

description: 3'-RNAseq amplified from 1ng RNA

source_name: E9.5 PGC (Stella-EGFP+)


title: E9.5_PGC_1

description: 3'-RNAseq amplified from 1ng RNA


title: d4c7 PGCLC, H3K27ac_2

value: anti-H3K27ac, MsIgG, CMA309


title: pool_8

source_name: leaf

value: earlyflowering

value: tp2 (28 days)


title: d4c7 PGCLC_2

description: 3'-RNAseq amplified from 10ng RNA

source_name: d4c7 PGCLC (BVSC+)

value: BVSC+


title: d4c7 PGCLC_1

description: 3'-RNAseq amplified from 10ng RNA


title: Rods P13 rep2


title: d4c5 PGCLC_1

description: 3'-RNAseq amplified from 10ng RNA

source_name: d4c5 PGCLC (BVSC+)


title: d4c5 PGCLC_2

description: 3'-RNAseq amplified from 10ng RNA


title: d4c3 PGCLC_2

description: 3'-RNAseq amplified from 10ng RNA

source_name: d4c3 PGCLC (BVSC+)


title: Hippocampus_40_DR-AL

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

description: Hippocampus 40% DR switched to Ad-lib

data_processing:
Raw fastq files were imported into Strand software (v9.5, Agilent) for trimming, alignment and statistical analysis.  Sequence with a Q score of <30 were discarded, 1 base from the 3’ and 5’, and adaptors sequences were removed.
Reads were aligned to mm9 in an orientation-specific fashion and duplicate reads were removed. Raw counts and fpkm values were computed for each gene in each sample.
Data normalization and selection of differentially expressed genes was performed according to DESeq2 methodology.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes annotations,  FPKM values and raw counts for each gene, in each sample

source_name: Hippocampus_ad libitum after diet restricted

extract_protocol:
Allprep DNA/RNA Co-isolation kit from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DR is 40% Dietary restriction. Dietary restriction was started at 4 months of age of the animals.  DR-AL- is when animals after a period of DR (1 month) were switched to AL feeding. Mice were sacrificed at 5 months of age for the AL and DR group and 7 months for the DR-AL group.

value: Hippocampus

value: ad libitum after diet restricted

value: 7 months


title: d4c3 PGCLC_1

description: 3'-RNAseq amplified from 10ng RNA


title: d4c7 PGCLC, H3K27ac_1


title: Hippocampus_AL

description: Hippocampus AL

source_name: Hippocampus_ad libitum (AL)

value: ad libitum (AL)

value: 5 months


title: CD4+_Mock_day1_donor4

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building, 960 Republican St

institute: University of Washington

data_processing:
Sequences for each sample were obtained from NextSeq 500 NCS v1.3 software utilizing RTA v2 for basecalling.
Raw reads had their adapter sequences removed.  Reads from ribosomsal RNA was also removed after alignment to an index of human, mouse, and rat rRNA sequences.
Reads were then mapped against a human reference genome, hg19, using STAR (v2.4.0h1).  From the alignment, quantitative gene counts were produced using HTseq utilizing the human annotation associated with the genome.
Genes with counts in less than three samples were removed from the analysis leaving 14,932 genes across the 24 samples.  Remaining gene counts were then normalized with edgeR utilizing the weighted trimmed mean of M-values.
Differentially expressed genes were identified using edgeR between treatments and time points using paired donors and using the Benjamini-Hochberg multiple testing correction.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delineated text files with unnormalized counts for each sample (raw_count_matrix.txt), normalized counts for each sample (normalized_count_matrix.txt), or differential expression analysis results including log2 foldchanges, log2 CPMs, log ratios, p-values, and FDRs for every comparison between time and treatments (DE.txt)

source_name: CD4+ T-cells

extract_protocol:
Whole blood samples were collected from anonymous buffy coats from healthy adult donors according to a clinical protocol approved by the University of Texas Medical Branch at Galveston (UTMB) Institutional Review Board from the UTMB blood bank.  Peripheral blood mononuclear cells (PBMC) were isolated by Histopaque gradient as recommended by the manufacturer.  Then, CD4 + T cells were isolated from PBMCs using negative selection kit following manufacturer’s instructions.  Isolated CD4+ T cells from donors were cultured in RPMI1640 medium in the presence or absence of EBOV at MOI 3 or LPS at 500 ng/ml.  24 and 96 h post stimulation, cells were washed with PBS, lysed in 1 ml of TRIzol (ThermoFisher Scientific) and stored at -80 C.  RNA isolation was performed using Direct-zol RNA MiniPrep kit (Zymo Research).
Libraries were constructed using the Kapa Stranded mRNA-Seq Kit (Kapa Biosystems) according to the manufacturer’s instructions before being quality controlled and quantitated using the BioAnalzyer 2100 system and QuBit (Invitrogen).

tag: infection

value: Mock

tag: day

tag: donor


title: Hypothalamus_40_DR

description: Hypothalamus 40% DR

source_name: Hypothalamus_diet restricted

value: Hypothalamus

value: diet restricted


title: CD4+_Mock_day4_donor4


title: CD4+_LPS_day1_donor4

value: LPS


title: CD4+_EBOV_day4_donor4

value: EBOV


title: CD4+_EBOV_day1_donor4


title: Hypothalamus_AL

description: Hypothalamus AL

source_name: Hypothalamus_ad libitum (AL)


title: CD4+_LPS_day4_donor3


title: CD4+_EBOV_day4_donor3


title: Epi.Fat_40_DR

description: Epi 40% DR

source_name: Epididymal fat_diet restricted

value: Epididymal fat


title: CD4+_Mock_day1_donor2


title: CD4+_LPS_day4_donor2


title: Epi.Fat_40_DR-AL

description: Epi 40% DR switched to Ad-lib

source_name: Epididymal fat_ad libitum after diet restricted


title: CD4+_EBOV_day1_donor3


title: Colon_AL

description: Colon AL

source_name: Colon_ad libitum (AL)

value: Colon


title: Colon_40_DR

description: Colon 40% DR

source_name: Colon_diet restricted


title: CD4+_Mock_day4_donor3


title: CD4+_EBOV_day4_donor2


title: CD4+_LPS_day1_donor3


title: CD4+_Mock_day1_donor3


title: Epi.Fat_AL

description: Epi AL

source_name: Epididymal fat_ad libitum (AL)


title: Colon_40_DR-AL

description: Colon 40% DR switched to Ad-lib

source_name: Colon_ad libitum after diet restricted


title: CD4+_LPS_day1_donor2


title: amp1-32 mutant rep2

city: Busan

first: Ho Won

last: Jung

address: 37 Nakdong-Daero 550beon-gil, Saha-gu

department: Molecular Genetics

country: South Korea

institute: Dong-A University

description: amp1-32 nonsence mutation

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome to separate paired sequenced reads and unpaired sequenced reads to the reference using Trimmomatic-0.33 with parameters PE -phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Fragments Per Kilobase of exon per Million reads mapped (FPKM) were calculated using a protocol from Cole Trapnell et al.,
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Leaf

growth_protocol: A. thaliana ecotype Columbia-0 (Col-0) and amp1-32 plants (Col-0 background), were grown in potting mixture, in an environmentally controlled growth chamber (21±1 °C, 50~60 % relative humidity, 12 h day and 12 h night).

extract_protocol:
Leaves of plans were removed, and tota RNA was extracted using a combination of TriZol ® reagent, and a Qiagen RNeasy kit. Both the quantity and quality of total RNA were examined using a 2100 bioanalyzer
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Leaf

value: 3-week-old plants after sowing

value: amp1-32 knock-out mutant


title: Liver_40_DR

description: Liver 40% DR

source_name: Liver_diet restricted

value: Liver


title: Hypothalamus_40_DR-AL

description: Hypothalamus 40% DR switched to Ad-lib

source_name: Hypothalamus_ad libitum after diet restricted


title: CD4+_Mock_day1_donor1


title: CD4+_Mock_day4_donor1


title: Hippocampus_40_DR

description: Hippocampus 40% DR

source_name: Hippocampus_diet restricted


title: amp1-32 mutant rep1

description: amp1-32 nonsence mutation


title: WT rep2

description: wild-type Columbia-o

value: wild type


title: Liver_40_DR-AL

description: Liver 40% DR switched to Ad-lib

source_name: Liver_ad libitum after diet restricted


title: WT rep1

description: wild-type Columbia-o


title: CD4+_LPS_day4_donor4


title: Liver_AL

description: Liver AL

source_name: Liver_ad libitum (AL)


title: CD4+_Mock_day4_donor2


title: CD4+_LPS_day4_donor1


title: CD4+_EBOV_day1_donor2


title: CD4+_LPS_day1_donor1


title: 2H2O2>H2O2

city: davis

first: Ilias

last: Tagkopoulos

state: CALIFORNIA

address: 2063 kemper hall, 1 shields avenue

institute: university of california at davis

description: Bacteria grown for 24 h in M9+100 mM H2O2

data_processing:
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. Trimmed reads were aligned on most recent reference genome of Escherichia coli (U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). Finally, Cufflink is used to generate FPKM-normalized expression value for each gene.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: vcf, mutations called; fpkm_tracking, fpkm-normalized expression values

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Whole cell

extract_protocol:
Bacterial was harvested with 0.5 Vol of 5% Phenol in Ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using Rneasy.
Library constructed using KAPA Kit

tag: mutations

value: DlacZXY

tag: treatment

tag: time


title: 1But>But

description: Bacteria grown for 24 h in M9+0.6%n-butanol


title: 1pH>pH

description: Bacteria grown for 24 h in M9 pH 5.5

value: Bacteria grown for 24 h in M9 pH 5.5


title: 2pH>pH

description: Bacteria grown for 24 h in M9 pH 5.5


title: 1Osm>Osm

description: Bacteria grown for 24 h in M9+0.3M NaCl

value: Bacteria grown for 24 h in M9+0.3M NaCl


title: 2But>But

value: Bacteria grown for 24 h in M9+0.6%n-butanol


title: 2Osm>Osm

description: Bacteria grown for 24 h in M9+0.3M NaCl


title: 1H2O2>H2O2

value: Bacteria grown for 24 h in M9+100 mM H2O2


title: 1ButBis

description: Bacteria grown for 12 h in M9 + 0.6%n-butanol


title: 2M9Bis

description: Bacteria grown for 12 h in M9

value: Bacteria grown for 12 h in M9


title: 2M9>OsmBis

description: Bacteria grown for 12 h in M9 and other 12 hours in M9+0.3M NaCl


title: 1pH>H2O2

description: Bacteria grown for 12 h in M9 pH 5.5 and other 12 hours in M9+100 mM H2O2


title: 1H2O2>pH

description: Bacteria grown for 12 h in M9+100 mM H2O2 and other 12 hours in M9 pH 5.5


title: 2M9>pH

description: Bacteria grown for 12 h in M9 and other 12 hours in M9 pH5.5


title: T3

city: Portland

first: Tyler

last: Risom

state: Oregon

address: 2730 SW Moody Ave

department: Molecular Medical Genetics

institute: Oregon Health & Science University

description: PI3K/mTOR and BET inhibitor combination treated HCC1143.

data_processing:
Base calling - using Illumina RTA version 2.4.11
Demultiplexing was done with Bcl2fastq 2.17.1.14
Reads were trimmed to 44 bases (first 4 bases were discared, next 44 were kept, and remaining bases were also discarded).
Trimmed reads were aligned to hg19 with Bowtie version 1.0.0 (Up to 3 mismatches were allowed, but unique best matches were required.)
R scripts were used to count tags that aligned to the exons of UCSC RefSeq gene models and calculate RPKM values.
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary files  are tab delimited text files with tag counts and RPKM values for each RefSeq gene model.

source_name: HCC1143 cell line

growth_protocol: HCC1143 cells were cultured in RPMI 1640 + 10% fetal bovine serum and 10g/ml penn/strep, cells were maintained at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated using the QIAGEN Rneasy mini kit according to manufacturers protocol
Libraries were made with the Illumina Truseq Samples Prep v2 kit with 150ng RNA using manufacturer's protocol.
Poly A capture: total RNA was run on the Bioanalyzer (Agilent) to verify intactness. Following this test, RNA-seq libraries were constructed using the TruSeq RNA sample prep protocol (Illumina). Poly(A)+ RNA was isolated using oligo-dT bound to magnetic beads. Poly(A)+ RNA was then chemically fragmented. RNA fragments were converted to double stranded cDNA using random hexamer priming. Fragment ends were treated to remove overhanging nucleotides and then a single “A” was added to the 3’ end of each strand to facilitate ligation. Illumina adaptors with barcode sequences was ligated to the fragments. The resulting libraries were then amplified using polymerase chain reaction with a limited number of rounds. Unincorporated nucleotides and adaptor dimers were removed using AMPure XP beads (Agencourt). Libraries were combined for multiplexing and sequenced on the NextSeq 500

treatment_protocol: Two plates of each line were then treated with 1μM Trametinib, two plates with 1μM BEZ235, two plates with 1μM of both agents, and two plates with 0.05% DMSO as a control. Plates were incubated for 72hr, then total RNA was isolated using the QIAGEN RNeasy mini kit according to manufacturers instructions.

value: 1uM Trametinib

tag: cell line


title: TJ2

value: 1uM Trametinib + 1uM JQ1


title: TJ1

value: 1uM Trametnib + 1uM JQ1


title: CD4+_EBOV_day4_donor1

source_name: CD4+ T-cells

value: EBOV


title: TJ3


title: JQ1

value: 1uM JQ1


title: JQ2


title: CD4+_EBOV_day1_donor1


title: T2


title: D1

description: DMSO control

value: DMSO


title: T1


title: D2

description: DMSO control


title: 2M9>H2O2

description: Bacteria grown for 12 h in M9 and other 12 hours in M9+100 mM H2O2


title: 1But>OsmBis

description: Bacteria grown for 12 h in M9+0.6%n-butanol and other 12 hours in M9+0.3 M NaCl


title: 1pH

description: Bacteria grown for 12 h in M9 pH 5.5

value: Bacteria grown for 12 h in M9 pH 5.5


title: 2H2O2>pH

value: Bacteria grown for 12 h in M9+100 mM H2O2 and other 12 hours in M9 pH 5.5


title: 1H2O2

description: Bacteria grown for 12 h in M9 + 100 mM H2O2


title: 1M9>pH

value: Bacteria grown for 12 h in M9 and other 12 hours in M9 pH5.5


title: 2pH>H2O2

value: Bacteria grown for 12 h in M9 pH 5.5 and other 12 hours in M9+100 mM H2O2


title: 1M9>H2O2

value: Bacteria grown for 12 h in M9 and other 12 hours in M9+100 mM H2O2


title: B1

description: PI3K/mTOR inhibitor treated HCC1143.

value: 1uM BEZ235


title: BJ2

value: 1uM BEZ235 + 1uM JQ1


title: 2H2O2

value: DlacZXY

value: Bacteria grown for 12 h in M9 + 100 mM H2O2


title: B2

description: PI3K/mTOR inhibitor treated HCC1143.


title: D3

description: DMSO control


title: B3

description: PI3K/mTOR inhibitor treated HCC1143.


title: 2pH

description: Bacteria grown for 12 h in M9 pH 5.5


title: BJ3


title: 1But>Osm

value: Bacteria grown for 12 h in M9+0.6%n-butanol and other 12 hours in M9+0.3 M NaCl


title: 1Osm>But

description: Bacteria grown for 12 h in M9+0.3 M NaCl and other 12 hours in M9+0.6%n-butanol


title: 2M9>But

description: Bacteria grown for 12 h in M9 and other 12 hours in M9+0.6%n-butanol


title: 2M9>Osm

value: Bacteria grown for 12 h in M9 and other 12 hours in M9+0.3M NaCl


title: 1M9 rep2

description: Bacteria grown for 12 h in M9

value: Bacteria grown for 12 h in M9


title: 1But

value: Bacteria grown for 12 h in M9 + 0.6%n-butanol


title: 2Osm>But

value: Bacteria grown for 12 h in M9+0.3 M NaCl and other 12 hours in M9+0.6%n-butanol


title: 1Osm

description: Bacteria grown for 12 h in M9 + 0.3 M NaCl


title: 2M9 rep2

description: Bacteria grown for 12 h in M9


title: 2M9 rep1

description: Bacteria grown for 12 h in M9


title: BJ1


title: 35S:LSD1-GR rep2

city: Gent

first: Patrick

last: Willems

address: Technologiepark 927

department: PSB

country: Belgium

institute: Ghent University

description: DEX-treated 35S:LSD1-GR

data_processing:
Low quality base pairs (LEADING/TRAILING:10 and SLIDINGWINDOW:4:30) and short read sequences (min. length 36) were trimmed using Trimmomatic (v0.30).
Quality-filtered reads were aligned to the TAIR10 Arabidopsis reference genome using the spliced aligner GSNAP (version 2013-02-05)
The number of reads per gene was quantified using Htseq-count (v.0.6.1)
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: Table containing gene counts for all 12 samples as delivered by Htseq-count

source_name: DEX-treated 35S:LSD1-GR_rosette

growth_protocol: 2-week-old Ws-0, lsd1-1 mutant, 35Spro:LSD1-GFP and DEX-treated 35Spro:LSD1-GR plants grown on MS medium in 16 h photoperiod, PPFD: 100±25 µmol m ¯² s¯¹, temperature 22/18 °C day/night.

extract_protocol:
Total RNA isolation was performed using GeneMATRIX Universal RNA Purification Kit (EURX, Gdansk, Poland) with additional step of on-column DNAse I treatment in three biological repeats.
Library preparation and sequencing was performed at the VIB Nucleomics Core (www.nucleomics.be). Sequencing libraries were constructed with using the TruSeq Stranded mRNA Library Preparation Kit (Illumina).

treatment_protocol: Dexamethasone (DEX) induction was performed for 35Spro:LSD1-GR line. 2-week-old seedlings grown on 20 micron nylon mesh (ELKO Filtering Co., Miami, FL, US) on MS medium were transferred to MS medium supplemented with 30 μM DEX (Sigma-Aldrich, Saint Louis, MO, US). Other lines did not undergo any treatment prior to total RNA isolation.

tag: accession

value: Wassilewskija

tag: genotype/variation

value: DEX-treated 35S:LSD1-GR

tag: tissue

value: Rosette


title: 35S:LSD1-GFP rep3

tag: age


title: 35S:LSD1-GR rep1

description: DEX-treated 35S:LSD1-GR


title: 35S:LSD1-GR rep3

description: DEX-treated 35S:LSD1-GR


title: 2But>Osm


title: 1M9>But

value: Bacteria grown for 12 h in M9 and other 12 hours in M9+0.6%n-butanol


title: 35S:LSD1-GFP rep1


title: 1M9>Osm


title: 35S:LSD1-GFP rep2


title: lsd1-1 rep3


title: lsd1-1 rep2


title: Aorta smooth muscle cells AoSMC3

city: Madison

first: Oleg

last: Moskvin

state: WI

address: 1220 Capitol Court

institute: University of Wisconsin-Madison

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment. Parameters to rsem-calc-expression include: "--bowtie-m 200 --bowtie-n 2 --forward-prob 0.5 --seed-length 28 "
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files containing non-normalized "Expected Counts" and normalized "Transcripts Per Million" expression estimates calculated by RSEM.

growth_protocol: human embryonic stem cells (h1ESCs) directed towards mesendodermal differentiation in coculture with mouse bone marrow stromal cells OP9 for 2 days. APLNR+PDGFRa+ primitive posterior mesodermal cells were selected using magnetic sorting and grown in serum-free clonogenic cultures supplemented with FGF2.

extract_protocol:
Illustra RNA spin mini RNA isolation kit (GE healthcare).
Samples were then prepared for sequencing using the Illumina TruSeq RNA Sample Preparation Kit v2 (RS-122-2001), according to the manufacturer's protocol

treatment_protocol: 12 days mature colonies were differentiated into immature pericytes or immature smooth muscles cells under the influence of PDGF-BB or TGFb plus sphingosylphosphorylcholine (SPC), imPCs were further cultured on fibronectin and collagen coated plates in Pericytes Medium with added SB431542 (10μM) and PDGF-BB (50ng/ml) or SB431542 (10μM), PDGF-BB (10ng/ml), VEGF (10ng/ml), EGF2 (2ng/ml) for additional 6 days to generate Type 1 mature pericytes (PC1) and Type 2 mature pericytes (PC2) respectively.The SMCs were matured by culturing on human fibronectin and collagen-coated plates in complete EGM-2 medium (Lonza) with added PD0325901 MEK inhibitor (1μM) for an additional 6 days.

tag: cell type

value: Aorta smooth muscle cells


title: 2Osm

value: Bacteria grown for 12 h in M9 + 0.3 M NaCl


title: lsd1-1 rep1


title: 1M9 rep1

description: Bacteria grown for 12 h in M9


title: wild-type rep2

description: wild-type Ws-0

source_name: wild-type Ws-0_rosette

value: wild-type Ws-0


title: wild-type rep3

description: wild-type Ws-0


title: Aorta smooth muscle cells AoSMC2


title: wild-type rep1

description: wild-type Ws-0


title: NFC3 (Dil 1/1000)

city: Antwerpen

first: Bart

last: Cuypers

state: Antwerp

address: Middelheimlaan 1

department: Computer Science

institute: Adrem Data Lab

description:
Biological Replicate 3 of leishmania donovani promastigotes, 1/1000 diluted with human RNA, library prepared with SL-seq
processed data file: SL_Macrophages_Dilutions_counttable.txt

data_processing:
Read Trimming with Trimmomatic v0.35 and settings LEADING:20 TRAILING:20 ILLUMINACLIP:adapter.fa:2:40:15 SLIDINGWINDOW:4:20 MINLEN:36. For SL-seq, an extra preceding Trimmomatic step was performed on the R2 FASTQ files to hard-trim the first 21 bases, which correspond to the SL sequence (HEADCROP:21)
Step for amastigote samples only:  Mapping with tophat2 to the human reference genome (hg38) to filter out reads originating from the human reference genome (standard settings)
Step for amastigote samples only:  Conversion of unmapped reads to FASTQ files with the samtools sort -n and samtools fastq functions (samtools-1.3.1) for further analysis
Mapping of the reads to the LdBPKv2 reference genome with bwa mem (version 0.7.15, default settings) and conversion to sorted bam file with samtools-1.3.1
Generation of count tables with htseq-count version 0.6.1 and settings '-r name -f bam -t gene -i ID -s no'
Differential expression was determined with the DESEQ2 package in R
Genome_build: HG38 and LdBPKv2
Supplementary_files_format_and_content: tab delimited tekst files of count tables and of differentially expression analysis by DESEQ2

organism: Leishmania donovani

source_name: Cell Culture

extract_protocol:
Promastigotes were cultured at 26°C in HOMEM supplemented with 20% heat-inactivated fetal bovine serum (Biochrom) and were harvested on day 7 (STAT stage, stationary growth). The parasites were washed 3 times by centrifugation at 18000 g at 0 °C and resuspended in ice-cold PBS buffer. RNA was subsequently extracted with the AllPrep DNA/RNA Mini Kit (QIAGEN). This total RNA was diluted 1/1000 with Human Spleen Total RNA, ThermoFisher Scientific.
Spliced-Leader Seq

tag: life stage

value: Stationary Phase Promastigotes


title: NFC2 (Dil 1/100)

description:
Biological Replicate 3 of leishmania donovani promastigotes, 1/100 diluted with human RNA, library prepared with SL-seq
processed data file: SL_Macrophages_Dilutions_counttable.txt

extract_protocol:
Promastigotes were cultured at 26°C in HOMEM supplemented with 20% heat-inactivated fetal bovine serum (Biochrom) and were harvested on day 7 (STAT stage, stationary growth). The parasites were washed 3 times by centrifugation at 18000 g at 0 °C and resuspended in ice-cold PBS buffer. RNA was subsequently extracted with the AllPrep DNA/RNA Mini Kit (QIAGEN). This total RNA was diluted 1/100 with Human Spleen Total RNA, ThermoFisher Scientific.
Spliced-Leader Seq


title: Primary Placental Pericytes (PromoCell, GmbH, Germany) S.054045.0073118

source_name: Primary Cells


title: Mature Smooth Muscle Cells (mSMCs) S.054044.0073117

source_name: human embryonic stem cells (h1ESCs) derived Mesenchymal stem cells

value: Mature Smooth Muscle Cells (mSMCs)


title: Primary Brain Pericytes (ScienCell Research laboratories, USA) S.054046.0073119


title: Mature Smooth Muscle Cells (mSMCs) S.054043.0073116


title: Mature Smooth Muscle Cells (mSMCs) S.054042.0073115


title: NFB2 (Dil 1/100)

description:
Biological Replicate 2 of leishmania donovani promastigotes, 1/100 diluted with human RNA, library prepared with SL-seq
processed data file: SL_Macrophages_Dilutions_counttable.txt

extract_protocol:
Promastigotes were cultured at 26°C in HOMEM supplemented with 20% heat-inactivated fetal bovine serum (Biochrom) and were harvested on day 7 (STAT stage, stationary growth). The parasites were washed 3 times by centrifugation at 18000 g at 0 °C and resuspended in ice-cold PBS buffer. RNA was subsequently extracted with the AllPrep DNA/RNA Mini Kit (QIAGEN).
Spliced-Leader Seq


title: NFA3 (Dil 1/1000)

description:
Biological Replicate 1 of leishmania donovani promastigotes, 1/1000 diluted with human RNA, library prepared with SL-seq
processed data file: SL_Macrophages_Dilutions_counttable.txt


title: NFB1 (Control)

description:
Biological Replicate 2 of leishmania donovani promastigotes, undiluted, library prepared with SL-seq
processed data file: SL_Macrophages_Dilutions_counttable.txt


title: Immature smooth Muscle Cells (imSMCs) S.054041.0073114

value: Immature smooth Muscle Cells (imSMCs)


title: NFB3 (Dil 1/1000)

description:
Biological Replicate 2 of leishmania donovani promastigotes, 1/1000 diluted with human RNA, library prepared with SL-seq
processed data file: SL_Macrophages_Dilutions_counttable.txt


title: NFA2 (Dil 1/100)

description:
Biological Replicate 1 of leishmania donovani promastigotes, 1/100 diluted with human RNA, library prepared with SL-seq
processed data file: SL_Macrophages_Dilutions_counttable.txt


title: Immature smooth Muscle Cells (imSMCs) S.054040.0073113


title: Immature smooth Muscle Cells (imSMCs) S.054039.0073112


title: Pericyte Type 2 PC2) S.054038.0073111

value: Pericyte Type 2 PC2)


title: 2But

description: Bacteria grown for 12 h in M9 + 0.6%n-butanol

value: DlacZXY


title: Pericyte Type 2 PC2) S.054037.0073110


title: NFA1 (Control)

description:
Biological Replicate 1 of leishmania donovani promastigotes, undiluted, library prepared with SL-seq
processed data file: SL_Macrophages_Dilutions_counttable.txt


title: Pericyte Type 2 PC2) S.054036.0073109


title: Pericyte Type 1 (PC1) S.054035.0073108

value: Pericyte Type 1 (PC1)


title: SL-STAT3

description:
Biological Replicate 3 of leishmania donovani stationary stage promastigotes, library prepared with SL-seq
processed data file : SL_SEQ_LOGSTAT_counttable.txt, SL_SEQ_LOGSTAT_DESEQ2.txt, SL_SEQ_PROAMA_DESEQ2.txt


title: HCC1143_Combination

description: Combined Trametinib and BEZ235 treatment for cell line HCC1143.

data_processing:
Base calling - using Illumina RTA version 1.13.48.
Conversion to FASTQ using CASAVA v1.8.2
Reads were trimmed to 44 bases (first 4 bases were discared, next 44 were kept, and remaining bases were also discarded).
Trimmed reads were aligned to hg19 with Bowtie version 1.0.0 (Up to 3 mismatches were allowed, but unique best matches were required.)
R scripts were used to count tags that aligned to the exons of UCSC RefSeq gene models and calculate RPKM values.  Processed files contain the in exon tag counts and the RPKM nomalized values for each RefSeq gene model.
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary files  are tab delimited text files with tag counts and RPKM values for each RefSeq gene model.

growth_protocol: HCC1143 cells were cultured in RPMI 1640 + 10% fetal bovine serum and 10g/ml penn/strep, SUM149PT were cultured in HAMS F12 + 5% fetal bovine serum, 4g/ml insulin, 0.5g/ml hydrocortisone, 10mM HEPES and 10g/ml penn/strep. Cells were maintained at 37°C in a 5% CO2 atmosphere. Each line was typsinized and plated in 8 10cm plates and allowed to adhere for 18hr.

extract_protocol:
Total RNA was isolated with TriZol reagent.
Libraries were made with Agilent SureSelect Strand Specific RNA kits under manufacturer's protocol.

treatment_protocol: Two plates of each line were then treated with 1μM Trametinib, two plates with 1μM BEZ235, two plates with 1μM of both agents, and two plates with 0.05% DMSO as a control. Plates were incubated for 6 days, with media changed and drug replenished after 72hr. Following the incubation total RNA was isolated with TriZol reagent and lysates from the two biological replicate plates were combined. cDNA libraries were then created and samples were run through high throughput sequencing.

value: basal-like breast cancer

value: Trametinib and BEZ235


title: SL-STAT4

description:
Biological Replicate 4 of leishmania donovani stationary stage promastigotes, library prepared with SL-seq
processed data file : SL_SEQ_LOGSTAT_counttable.txt, SL_SEQ_LOGSTAT_DESEQ2.txt, SL_SEQ_PROAMA_DESEQ2.txt


title: Pericyte Type 1 (PC1) S.054034.0073107


title: SL-STAT2

description:
Biological Replicate 2 of leishmania donovani stationary stage promastigotes, library prepared with SL-seq
processed data file : SL_SEQ_LOGSTAT_counttable.txt, SL_SEQ_LOGSTAT_DESEQ2.txt, SL_SEQ_PROAMA_DESEQ2.txt


title: NFC1 (Control)

description:
Biological Replicate 3 of leishmania donovani promastigotes, undiluted, library prepared with SL-seq
processed data file: SL_Macrophages_Dilutions_counttable.txt


title: HCC1143_BEZ235

description: BEZ235 treatment for cell line HCC1143.


title: SL-STAT1

description:
Biological Replicate 1 of leishmania donovani stationary stage promastigotes, library prepared with SL-seq
processed data file : SL_SEQ_LOGSTAT_counttable.txt, SL_SEQ_LOGSTAT_DESEQ2.txt, SL_SEQ_PROAMA_DESEQ2.txt


title: Pericyte Type 1 (PC1) S.054033.0073106


title: SL-LOG4

description:
Biological Replicate 4 of leishmania donovani logarithmic stage promastigotes, library prepared with SL-seq
processed data file : SL_SEQ_LOGSTAT_counttable.txt, SL_SEQ_LOGSTAT_DESEQ2.txt

extract_protocol:
Promastigotes were cultured at 26°C in HOMEM supplemented with 20% heat-inactivated fetal bovine serum (Biochrom) and were harvested on day 4 (LOG stage, exponential growth). The parasites were washed 3 times by centrifugation at 18000 g at 0 °C and resuspended in ice-cold PBS buffer. RNA was subsequently extracted with the AllPrep DNA/RNA Mini Kit (QIAGEN).
Spliced-Leader Seq

value: Logaritmic Phase Promastigotes


title: HCC1143_DMSO

description: Control for cell line HCC1143.

value: DMSO


title: HCC1143_Trametinib

description: Trametinib treatment for cell line HCC1143.

value: Trametinib


title: Immature Pericytes (imPCs) S.054032.0073105

value: Immature Pericytes (imPCs)


title: SL-LOG3

description:
Biological Replicate 3 of leishmania donovani logarithmic stage promastigotes, library prepared with SL-seq
processed data file : SL_SEQ_LOGSTAT_counttable.txt, SL_SEQ_LOGSTAT_DESEQ2.txt


title: SL-LOG2

description:
Biological Replicate 2 of leishmania donovani logarithmic stage promastigotes, library prepared with SL-seq
processed data file : SL_SEQ_LOGSTAT_counttable.txt, SL_SEQ_LOGSTAT_DESEQ2.txt


title: SL-LOG1

description:
Biological Replicate 1 of leishmania donovani logarithmic stage promastigotes, library prepared with SL-seq
processed data file : SL_SEQ_LOGSTAT_counttable.txt, SL_SEQ_LOGSTAT_DESEQ2.txt


title: ILL-STAT4

description:
Biological Replicate 4 of leishmania donovani stationary stage promastigotes, library prepared with the Illumina stranded mRNA kit
processed data file : ILL_SEQ_LOGSTAT_counttable.txt, ILL_SEQ_LOGSTAT_DESEQ2.txt

extract_protocol:
Promastigotes were cultured at 26°C in HOMEM supplemented with 20% heat-inactivated fetal bovine serum (Biochrom) and were harvested on day 7 (STAT stage, stationary growth). The parasites were washed 3 times by centrifugation at 18000 g at 0 °C and resuspended in ice-cold PBS buffer. RNA was subsequently extracted with the AllPrep DNA/RNA Mini Kit (QIAGEN).
Illumina Stranded mRNA Seq


title: Immature Pericytes (imPCs) S.054030.0073103


title: FF4

city: Vienna

first: Artem

middle: V

last: Artemov

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

description: Freshwater stickleback in freshwater rep3

data_processing:
Basecalling with CASAVA 1.8.2 software
Reads were mapped  to gasAcu1 reference genome with Bismark software. For individual CpGs in each sample, we estimated total coverage and coverage with reads supporting DNA methylation
Genome_build: gasAcu1
Supplementary_files_format_and_content: DNA methylation values of individual CpGs are provided in 3 files: (1) a bed file (coord.bed.bz2) providing genomic coordinates of the profiled CpGs, (2) a table (space-delimited) with total read coverage (Cov.tab.bz2) of individual CpGs (rows) with bisulfite reads, columns represent  individual samples; (3) a table (space-delimited) showing read coverage (M.tab.bz2) with reads supporting cytosine methylation in a given positions, columns represent  individual samples. The lines and names of loci correspond between those three files.

organism: Gasterosteus aculeatus

source_name: Freshwater stickleback in freshwater

growth_protocol: Ten freshwater three-spined sticklebacks were collected in the Mashinnoye Lake, Republic of Karelia, Russia, in June-July 2014. The same number of marine three-spined sticklebacks were collected in the Kandalaksha Gulf Coast (15 km from the railway station Poyakonda, Republic of Karelia, Russia) during the same time frame. To equal physiological state of the fish, only males in breeding dress were collected.

extract_protocol:
DNA was isolated from gills (an organ, directly exposed to water environment) using standard method of DNA extraction from animal tissue (phenol-chloroform).
Two micrograms of genomic DNA from three-spined stickleback samples of G. aculeatus were digested using 60 U MspI (Fermentas, USA) in 50 μl at 37°С for 18–24 h, followed by QIAquick purification (Qiagen, Germany). The end of the digested DNA was repaired, and an adenine was added to the 3’ end of the DNA fragments according to the Illumina standard end repair and add_A protocol (Illumina, USA). Pre-annealed forked Illumina adaptors containing 5’- methylcytosine instead of cytosine was ligated to both ends of DNA fragments using standard Illumina adaptor ligation protocol (Illumina, USA). Ligated fragments were then separated by 2% agarose gel (Sigma-Aldrich, USA). Fragments between 170 bp and 350 bp, (includes adaptor length), were selected and cut from the gel. DNA from gel slices were purified using Qiagen Gel Extraction Kit (Qiagen, Germany). The sodium bisulfite treatment and subsequent clean-up of size selected DNA was performed with the EZ DNA MethylationTM Kit (ZymoResearch, USA) according to the manufacturer’s instructions. The bisulfite-treated DNA fragments were amplified using PCR and the following reaction: 5 μl of eluted DNA, 1 μl of NEB PE PCR two primers (1.0 and 2.0) and 45 μl Platinum PCR Supermix (Invitrogen, USA). The amplification conditions were as follows: 5 min at 95°C, 30 s at 98°C then 15 (10 s at 98°C, 30 s at 65°C, 30 s at 72°C), followed by 5 min at 72°C. The PCR reaction was purified by MinElute PCR Purification Kit (Qiagen), and final reduced representation bisulfite library was eluted in 15 μl EB buffer. The concentration of the final library was measured using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA).

treatment_protocol: To explore immediate epigenetic response of a stickleback to changes in osmotic conditions of the environment, five marine fish were kept for 4 days in fresh water (M@F) and, vice versa, five freshwater fish were kept for 4 days in marine water (F@M). Control samples were kept in their native habitats (marine samples in marine water (M@M), freshwater samples in fresh water (F@F)) to equal captivity stress influence.

tag: original population

value: Freshwater

value: gills


title: FF3

description: Freshwater stickleback in freshwater rep2


title: Mesenchymal Stem cells (MSCs) S.054029.0073102

value: Mesenchymal Stem cells (MSCs)


title: FF2

description: Freshwater stickleback in freshwater rep1


title: FM3

description: Freshwater stickleback in marine water rep3

source_name: Freshwater stickleback in marine water

value: fish kept for 4 days in marine water


title: ILL-STAT3

description:
Biological Replicate 3 of leishmania donovani stationary stage promastigotes, library prepared with the Illumina stranded mRNA kit
processed data file : ILL_SEQ_LOGSTAT_counttable.txt, ILL_SEQ_LOGSTAT_DESEQ2.txt

tag: strain


title: Mesenchymal Stem cells (MSCs) S.054028.0073101


title: Immature Pericytes (imPCs) S.054031.0073104


title: ILL-BPK282-2

description:
Biological Replicate 2 of murine macrophages infected with Leishmania donovani BPK282 amastigotes, library prepared with the Illumina stranded mRNA kit
processed data file: ILL_Macrophages_counttable.txt

organism:
Leishmania donovani
Homo sapiens

extract_protocol:
THP-1 cells (ATCC TIB202) were treated with 0.1 μM phorbol myristate acetate (PMA, Sigma) at 37°C for 48 h, after which they were washed and incubated with complete RPMI medium containing stationary phase L. donovani BPK282 promastigotes (macrophage:promastigote ratio of 1:10). After 4 h incubation at 37°C, the cells were washed 3 times with PBS and incubated for 24 h at 37°C. RNA was subsequently extracted with the RNAqueous micro kit (Ambion).
Illumina Stranded mRNA Seq

value: Intracellular Amastigote


title: Mesenchymal Stem cells (MSCs) S.054027.0073100


title: ILL-STAT1

description:
Biological Replicate 1 of leishmania donovani stationary stage promastigotes, library prepared with the Illumina stranded mRNA kit
processed data file : ILL_SEQ_LOGSTAT_counttable.txt, ILL_SEQ_LOGSTAT_DESEQ2.txt

value: Stationary Phase Promastigotes


title: FM2

description: Freshwater stickleback in marine water rep2


title: Mesenchymoangioblast (MAB) S.054026.0073099

value: Mesenchymoangioblast (MAB)


title: FM1

description: Freshwater stickleback in marine water rep1


title: Mesenchymoangioblast (MAB) S.054025.0073098


title: ILL-BPK275-2

description:
Biological Replicate 2 of murine macrophages infected with Leishmania donovani BPK275 amastigotes, library prepared with the Illumina stranded mRNA kit
processed data file: ILL_Macrophages_counttable.txt

extract_protocol:
THP-1 cells (ATCC TIB202) were treated with 0.1 μM phorbol myristate acetate (PMA, Sigma) at 37°C for 48 h, after which they were washed and incubated with complete RPMI medium containing stationary phase L. donovani BPK275 promastigotes (macrophage:promastigote ratio of 1:10). After 4 h incubation at 37°C, the cells were washed 3 times with PBS and incubated for 24 h at 37°C. RNA was subsequently extracted with the RNAqueous micro kit (Ambion).
Illumina Stranded mRNA Seq


title: ILL-BPK282-1

description:
Biological Replicate 1 of murine macrophages infected with Leishmania donovani BPK282 amastigotes, library prepared with the Illumina stranded mRNA kit
processed data file: ILL_Macrophages_counttable.txt


title: ILL-STAT2

description:
Biological Replicate 2 of leishmania donovani stationary stage promastigotes, library prepared with the Illumina stranded mRNA kit
processed data file : ILL_SEQ_LOGSTAT_counttable.txt, ILL_SEQ_LOGSTAT_DESEQ2.txt


title: ILL-LOG4

description:
Biological Replicate 4 of leishmania donovani logaritmic stage promastigotes, library prepared with the Illumina stranded mRNA kit
processed data file : ILL_SEQ_LOGSTAT_counttable.txt, ILL_SEQ_LOGSTAT_DESEQ2.txt

extract_protocol:
Promastigotes were cultured at 26°C in HOMEM supplemented with 20% heat-inactivated fetal bovine serum (Biochrom) and were harvested on day 4 (LOG stage, exponential growth). The parasites were washed 3 times by centrifugation at 18000 g at 0 °C and resuspended in ice-cold PBS buffer. RNA was subsequently extracted with the AllPrep DNA/RNA Mini Kit (QIAGEN).
Illumina Stranded mRNA Seq


title: MF5

description: Marine stickleback in freshwater rep3

source_name: Marine stickleback in freshwater

value: Marine

value: fish kept for 4 days in freshwater


title: ILL-BPK275-1

description:
Biological Replicate 1 of murine macrophages infected with Leishmania donovani BPK275 amastigotes, library prepared with the Illumina stranded mRNA kit
processed data file: ILL_Macrophages_counttable.txt


title: ILL-LOG3

description:
Biological Replicate 3 of leishmania donovani logaritmic stage promastigotes, library prepared with the Illumina stranded mRNA kit
processed data file : ILL_SEQ_LOGSTAT_counttable.txt, ILL_SEQ_LOGSTAT_DESEQ2.txt


title: SL-BPK282-2

description:
Biological Replicate 2 of murine macrophages infected with Leishmania donovani BPK282 amastigotes, library prepared with SL-seq
processed data file: SL_Macrophages_Dilutions_counttable.txt

extract_protocol:
THP-1 cells (ATCC TIB202) were treated with 0.1 μM phorbol myristate acetate (PMA, Sigma) at 37°C for 48 h, after which they were washed and incubated with complete RPMI medium containing stationary phase L. donovani BPK282 promastigotes (macrophage:promastigote ratio of 1:10). After 4 h incubation at 37°C, the cells were washed 3 times with PBS and incubated for 24 h at 37°C. RNA was subsequently extracted with the RNAqueous micro kit (Ambion).
Spliced-Leader Seq


title: MF4

description: Marine stickleback in freshwater rep2


title: MF3

description: Marine stickleback in freshwater rep1


title: ILL-NI-2-DIL

description:
Biological Replicate 2 of unifected murine macrophages,  library prepared with the Illumina stranded mRNA kit
processed data file: ILL_Macrophages_counttable.txt

extract_protocol:
THP-1 cells (ATCC TIB202) were treated with 0.1 μM phorbol myristate acetate (PMA, Sigma) at 37°C for 48 h, after which they were washed and incubated with complete RPMI medium. After 4 h incubation at 37°C, the cells were washed 3 times with PBS and incubated for 24 h at 37°C. RNA was subsequently extracted with the RNAqueous micro kit (Ambion).
Illumina Stranded mRNA Seq

value: Uninfected Control


title: ILL-LOG1

description:
Biological Replicate 1 of leishmania donovani logaritmic stage promastigotes, library prepared with the Illumina stranded mRNA kit
processed data file : ILL_SEQ_LOGSTAT_counttable.txt, ILL_SEQ_LOGSTAT_DESEQ2.txt


title: SL-BPK282-1

description:
Biological Replicate 1 of murine macrophages infected with Leishmania donovani BPK282 amastigotes, library prepared with SL-seq
processed data file: SL_Macrophages_Dilutions_counttable.txt


title: ILL-NI-1-DIL

description:
Biological Replicate 1 of unifected murine macrophages,  library prepared with the Illumina stranded mRNA kit
processed data file: ILL_Macrophages_counttable.txt


title: SL-BPK275-2

description:
Biological Replicate 2 of murine macrophages infected with Leishmania donovani BPK275 amastigotes, library prepared with SL-seq
processed data file: SL_Macrophages_Dilutions_counttable.txt, SL_SEQ_PROAMA_DESEQ2.txt

extract_protocol:
THP-1 cells (ATCC TIB202) were treated with 0.1 μM phorbol myristate acetate (PMA, Sigma) at 37°C for 48 h, after which they were washed and incubated with complete RPMI medium containing stationary phase L. donovani BPK275 promastigotes (macrophage:promastigote ratio of 1:10). After 4 h incubation at 37°C, the cells were washed 3 times with PBS and incubated for 24 h at 37°C. RNA was subsequently extracted with the RNAqueous micro kit (Ambion).
Spliced-Leader Seq


title: SL-NI-2-DIL

description:
Biological Replicate 2 of unifected murine macrophages, library prepared with SL-seq
processed data file: SL_Macrophages_Dilutions_counttable.txt

extract_protocol:
THP-1 cells (ATCC TIB202) were treated with 0.1 μM phorbol myristate acetate (PMA, Sigma) at 37°C for 48 h, after which they were washed and incubated with complete RPMI medium. After 4 h incubation at 37°C, the cells were washed 3 times with PBS and incubated for 24 h at 37°C. RNA was subsequently extracted with the RNAqueous micro kit (Ambion).
Spliced-Leader Seq


title: MM3

description: Marine stickleback in marine water rep2

source_name: Marine stickleback in marine water