title: at-seed-ler_wt_x_col_osd1_suvh7_1

source_name: AT F1-Seed  wt Landsberg x osd1 suvh7 Columbia

value: wt Landsberg x osd1 suvh7 Columbia


title: pure bone marrow RNA (BMO) CT

status: Public on Sep 28 2015

type: SRA

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

country: USA

institute: Washington University School of Medicine

library_source: transcriptomic

data_processing:
Illumina Casava1.8+ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ensembl release version 72 (R72) of human whole genome and transcriptome with TopHat version 2.0.8 using Bowtie2 version 2.1.0.
Both exon- and gene-level count data were generated by HTSeq (Anders et al. 2015) for differential expression analysis, and the raw count data at exon- and gene-levels were normalized by library size with a R package “edgeR” from Bioconductor (Robinson et al. 2010; Robinson and Oshlack 2010). As a result, the count per million (cpm) values were produced for calculation of fold-changes.
Genome_build: Ensembl release version R72 human reference genome
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample.

molecule: total RNA

organism: Homo sapiens

source_name: Original Bone Marrow RNA

extract_protocol:
Samples used in the study are commercially available RNAs derived from mixture of multiple cell lines and RNAs extracted from patient bone marrow specimens
The library preparation protocol was oligo-d(T)-priming based Clontech SMARTer Ultra Low RNA Kit for Illumina® Sequencing from Clontech (a Takara Bio Company, hereafter labeled as “ClonTech”).  A starting amount of 10 ng RNAs was processed in ClonTech assays, amplified cDNA was sheared using a Covaris E210 instrument. cDNA was then end repaired, A tailed, and standard Illumina adapters were ligated on. Libraries were then amplified with primers to incorporate a unique index to each sample.  In pooling of multiple libraries for running on a single lane, equal amount of library mass was determined by Qubit reading and Bioanalyzer for the 5 RNA libraries.  Lastly, pooled libraries were amplified with Illumina® TruSeq™ Cluster kits and sequenced with Illumina® sequencing primers on Illumina® HiSeq2500™ next-generation sequencing system as a high output single read 50 cycle run.

tag: cell type

value: human bone marrow sample


title: pre-pro-B cell methylC-Seq

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: pre-pro-B cell genome-wide methylC-Seq

library_source: genomic

data_processing:
Bismark (v0.7.12) was used to align reads to the mouse genome (mm9) and call CpG methylation status using default parameters. Bowtie2 v2.1.0 was used by Bismark for the alignment steps.
Only cytosines within a CpG context with more than 5 reads of coverage were used for all downstream analysis, including identification DMRs, browser graphs, and mCpG% historgrams, all of which were generated using HOMER (http://homer.salk.edu/)
Genome_build: mm9
Supplementary_files_format_and_content: Bismark CpG methylation report, tab-delimited text file (Columns, 1: chr, 2: position(mm9), 3: strand, 4: mC, 5: C, 6: context, 7: sequence context)

molecule: genomic DNA

organism: Mus musculus

source_name: multipotent progenitor

growth_protocol: Tcf(E2A)-deficient multipoint progenitors were derived from E2A-deficient fetal liver and grown in the presence of IL7, SCF and FLT3L on sub-confluent S17 stromal cells. B220 MACS enriched Rag1-deficient bone marrow cells were grown in Opti-MEM 10% FCS/ 2% PSG/ 50 μM β-mercaptoethanol in the presence of IL7 and SCF for 7 days.

extract_protocol: DNA was isolated from E2A-deficient pre-pro-B and pro-B cells, sonicated, end-repaired using the End-It procedure (Epicentre) and incubated in the presence of Klenow to add an A base to the 3'-end. TruSeq adapters were then ligated to fragmented DNA and purified using Agarose gel electrophoresis.  Bisulfite conversion was performed as described by the manufacturer (MethylCode).  Bisulfite treated DNA was amplified using a TruSeq PCR primer cocktail and Pfu Turbo Cx Polymerase, agarose purified and sequenced on an Illumina HiSeq 2000 sequencer.

value: Tcf3(E2A) deficient pre-pro-B

tag: genetic background

tag: genotype


title: at-seed-ler_wt_x_col_osd1_suvh7_2

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

data_processing:
TopHat v2.0.10; tophat2 -p 20 -g 1 -a 10 -i 40 -I 5000 -F 0 -r 130 -o
GFOLD
Genome_build: TAIR10
Supplementary_files_format_and_content: Gene counts, rpkm

organism: Arabidopsis thaliana

growth_protocol: Plants were grown in a growth cabinet under long day photoperiods (16 h light and 8 h dark) at 22°C. After 10 days, seedlings were transferred to soil and plants were grown in a growth chamber at 60% humidity and daily cycles of 16 h light at 22°C and 8 h darkness at 18°C.

extract_protocol:
For RNA sequencing, seeds from 20 siliques of Ler x Col, Ler x osd1, Ler x adm osd1, Ler x suvh7 osd1, and Ler x peg2 osd1 were harvested at 6 DAP into RNA later (Sigma-Aldrich) in duplicates and homogenized (Silamat S5; IvoclarVivadent) using glass beads (1.25-1.55 mm; Carl Roth). RNA was extracted following a modified protocol for the RNAqueous kit (Ambion, Life Technologies). RNA was purified by Qiagen RNeasy Plant Mini Kit (Qiagen) after residual DNA removed by 2 uL DNaseI (Thermo-Scientific).
The library was prepared using the Truseq RNA Sample Preparation Kit (Illumina)

treatment_protocol: For all crosses, designated female plants were emasculated and the pistils were hand-pollinated two days after emasculation.

tag: tissue

value: seed


title: m6A-CLIP/IP Brain

city: Bar Harbor

first: Shengdong

last: Ke

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
We required a minimum quality score of 20 at these index and barcode positions in addition to an average score of 20 for the remaining positions.
The remaining read sequences (actual RNA tags) were mapped to the reference genome (mm9 and hg18) by novoalign program (http://www.novocraft.com) with no more than 2 mismatches (substitutions, insertions or deletions) allowed per read. A minimum of 20nt matches was required and only those reads mapped uniquely to the genome (single hits) were kept. To remove PCR duplicates, we collapsed reads mapped to the same genomic locations (the same start and end) into a single read if they have the same barcode sequence; on the other side, reads mapped to the same location but with distinct barcodes were kept. This step removed PCR duplicates while retaining genuinely unique reads representing independent RNA fragments (the same analysis pipeline for m6A IP, CLIP and its input RNA fragments). To ensure reads unambiguously mapped in the genome, we further mapped the reads by two additional alignment programs (bowtie2 and tophat2). Different from bowtie2 and novoalign, tophat2 allowed mapping across exon-exon junctions. The mapping parameters for bowtie2: -k 4 and for tophat2: --library-type fr-firststrand -p 10, with other parameters in default setting. We kept reads uniquely mapped in the genome by all three programs and the reads which were not mappable by novoalign and bowtie2 but uniquely mapped to exon-exon junctions by tophat2 (requiring at least 4nt overlap on each exon).
Similar to previous m6A publications ((Meyer et al., 2012) (Batista et al., 2014)), we searched for the enriched m6A peak regions by scanning the genome using 20nt sliding windows, and evaluating the statistical significance of enrichment by Fisher Exact Test (m6A IP vs. input). Benjamini-Hochberg was implemented to adjust the p value to False Discovery Rate (FDR) for multiple testing. We identified a window as being sigificantly m6A enriched when its FDR was less than 0.05 and the fold of enrichment (m6A IP vs. input) was at least 4 fold in at least 2 out 3 biological replicates. Significantly m6A enriched 20nt windows were concatenated if they were adjacent to each other. Because we did size selection for 20nt~80nt RNA fragments, the resulted m6A peak regions would be mostly 40nt~200nt. We filtered out m6A peak regions less than 40nt. In some cases, m6A peak regions were longer than 200nt, suggesting multiple m6A sites within those peak regions. Thus we split them into multiple m6A peak regions with the minimum number of m6A peaks that could form such a concatenated window.
PolyA-Seq experiments for mouse brain, liver, human CD8 T cells and A549 cells (control vs knockdown) were performed according to Derti A et al (Derti et al., 2012). We followed a similar PolyA-Seq data analysis pipeline as previous publications ((Shepard et al., 2011) (Almada et al., 2013)). The sequenced library reads was first filtered by trimming T’s off the beginning of reads and removing reads that have a string of 12 or more T’s, and then aligned to the reference genomes (mm9 for mouse brain and liver, hg18 for human CD8 T cells and hg19 for A549 cells) by tophat2 with default settings. Only uniquely mapped reads were kept for downstream analysis. Reads that had more than five consecutive A’s or more than six A’s in the 10nt immediately downstream from the poly(A) junction were removed as they were likely due to internal priming. We then clustered reads that were within 50nt from each other by bedtools merge, and kept the polyA sites (i.e. read clusters) that had at least 4 reads total, with reads drawn from at least 2 biological replicates.
Genome_build: mm9, hg18
Supplementary_files_format_and_content: bed: m6A peak region and precise m6A site; wig: polyA site locations

source_name: Brain

growth_protocol: Human A549 cells were plated in 100mm dishes with regular DMEM (with 10% FBS+1x Penstrap) at 20% confluency. Using Lipofectamine® RNAiMAX Transfection Reagent (Cat. # 13778-150, Invitrogen Life Technologies), siRNAs were transfected. One additional siRNA boost was delivered at 48 hours following transfection. Cells were harvested at 96 hours after transfection. From Adult C57BL/6 mice, adult livers were collected and brains were harvested at postnatal day 2. All mice procedures were performed in accordance with the Section for Comparative Medicine at Oslo University Hospital and the Norwegian Animal Research Authority.

extract_protocol:
Total RNAs were isolated from cells and mouse tissues according to manufacturer’s instructions using TRIzol reagent (Cat.# 15596, Life Technologies), then was resuspended in RNA-free water, digested with RQ1 RNase-Free DNase (Cat. # M6101, Promega) for 20 min at 37°C and then subject to phenol/chloroform extraction and ethanol precipitation. The resulted total RNA pallet was resuspended in RNA-free water. PolyA+ RNAs were selected using Dynabeads® mRNA Purification Kit (Cat.# 61006, Invitrogen) according to the manufacturer’s protocol.
The PolyA+ RNA was fragmented to 20~80nt nucleotide fragments by alkaline hydrolysis (1mM EDTA, 6mM Na2CO3, 44mM NaHCO3, pH~9.3) at 95°C for 18 minutes, then the RNA fragments precipitated following standard ethanol precipitation. Dynabeads Protein A beads (250ul, Cat. # 10008D, Life Technologies) was pretreated with BSA (Cat. # B9000S, NEB) for 45 minutes at room temperature to reduce background. Anti-m6A rabbit polyclonal antibody (25ug, Cat. # 202003, Synaptic Systems) was then conjugated to Dynabeads Protein at room temperature for 1 hour. The fragmented polyA+ RNAs (3ug) were subject to PAGE selection for 20nt~80nt size and then incubated with the antibody in 1x PXL buffer (1x PBS, 0.1% SDS, 0.5% Sodium Deoxycholate and 0.5% NP-40) supplemented with 2% RNasin® Plus RNase Inhibitor (Cat. # N2615, Promega) for 2 hours at 4°C.  After incubation, the bead and antibody was washed 5 times by 4 different wash buffers: first twice by ice cold Nelson Low Salt Buffer (15mM Tris pH7.5 and 5mM EDTA), once by ice cold Nelson High Salt Buffer (15mM Tris pH7.5, 5mM EDTA, 2.5mM EGTA, 1% Triton X-100, 1% Sodium Deoxycholate, 0.1% SDS and 1M NaCl), once by ice cold Nelson Stringent Wash Buffer (15mM Tris pH7.5, 5mM EDTA, 2.5mM EGTA, 1% Triton X-100, 1% Sodium Deoxycholate, 0.1% SDS, 120mM NaCl and 25mM KCl) and last wash by ice cold NT-2 Buffer (50mM Tris pH7.4, 150mM NaCl, 1mM MgCl2 and 0.05% NP-40). After the stringent wash series, the bead and antibody was split into two halves: one half performed m6A-CLIP leg, and the other half had its bounded RNA eluted with 0.5mg/mL N6-methyladenosine sodium salt (Cat. # M2780, Sigma-Aldrich) at 4°C for 1 hour (m6A-IP leg).  The eluted RNA was ethanol precipitated and re-suspended in RNase-free water for downstream cDNA library preparation. The eluted RNA from m6A-IP step and the input RNA fragments were first treated with T4 PNK to remove its 3’phospho group and then ligated to 68 pmol pre-adenylated DNA linker (L32N from IDT) with T4 RNA ligase2, truncated KQ (Cat. # M0373L, NEB) overnight at 16°C. This ligation mixture was subject to 8% PAGE purification to harvest the ligated product. The purified RNAs from m6A-IP, m6A-CLIP and their input RNA fragments were all subject to the same BrdU-CLIP cDNA library preparation. The detailed BrdU-CLIP cDNA library protocol was described previously (Weyn-Vanhentenryck et al., 2014).
m6A-CLIP/IP

value: whole brain

tag: strain

tag: antibody

value: m6A antibody (Synaptic Systems, 202003)


title: 1:64 mixture of AGO and BMO CT

source_name: Mixed RNA of both (1:64)

growth_protocol: Samples used in the study are commercially available RNAs derived from mixture of multiple cell lines and RNAs extracted from patient bone marrow specimens

value: mixed sample of both (1:64)


title: pure bone marrow RNA (BMO)

extract_protocol:
Samples used in the study are commercially available RNAs derived from mixture of multiple cell lines and RNAs extracted from patient bone marrow specimens
The library preparation protocol was random priming based Ribo-Zero™ rRNA Removal Kits from Epicentre (an Illumina company, labeled as “RiboZero”). 1 ug were input with RiboZero protocol, RiboZero depleted RNA was chemically fragmented, then made into cDNA with Superscript III (Life Technologies) and random hexamers followed by a second strand reaction. cDNA was then end repaired, A tailed, and standard Illumina adapters were ligated on. Libraries were then amplified with primers to incorporate a unique index to each sample.  In pooling of multiple libraries for running on a single lane, equal amount of library mass was determined by Qubit reading and Bioanalyzer for the 5 RNA libraries.  Lastly, pooled libraries were amplified with Illumina® TruSeq™ Cluster kits and sequenced with Illumina® sequencing primers on Illumina® HiSeq2500™ next-generation sequencing system as a high output single read 50 cycle run.


title: 1:16 mixture of AGO and BMO CT

source_name: Mixed RNA of both (1:16)

value: mixed sample of both (1:16)


title: 1:4 mixture of AGO and BMO CT

source_name: Mixed RNA of both (1:4)

value: mixed sample of both (1:4)


title: 1:64 mixture of AGO and BMO


title: pure reference RNA (AGO)

source_name: Original Agilent Human Universal Reference RNA

value: mixture of multiple cell lines


title: 1:4 mixture of AGO and BMO


title: pro-B cell methylC-Seq

description: pro-B cell genome-wide methylC-Seq

source_name: progenitor B

value: Rag1 deficient pro-B


title: at-seed-ler_wt_x_col_wt_1

source_name: AT F1-Seed  wt Landsberg x wt Columbia

value: wt Landsberg x wt Columbia


title: at-seed-ler_wt_x_col_osd1_adm_1

source_name: AT F1-Seed  wt Landsberg x osd1 adm Columbia

value: wt Landsberg x osd1 adm Columbia


title: VN_seq_f8

status: Public on Sep 27 2015

city: Pathumthani

first: Philip

middle: James

last: Shaw

state: Pathumthani

address: 113 Phahonyothin Road

department: National Center for Genetic Engineering and Biotechnology

country: Thailand

institute: National Science and Technology Development Agency

description:
5' cap enriched mRNA
In vitro cultured malaria parasite

data_processing:
Basecalls performed using Illumina RTA 1.18.42
The raw reads from fastq files were first filtered to remove matches to rRNA by BLAST alignment using ncbi-blast-2.2.25+ with parameters:evalue 1e-4, perc_identity 90, outfmt 6, num_threads 8. Pre-processing was performed by trimming low-quality base-calls (N) from reads, followed by removal of exact duplicates and reads of low overall quality using the prinseq-lite-0.20.3 program with parameters: trim_ns_left 2, trim_ns_right 2, min_qual_mean 20, derep 1
The pre-processed reads were mapped mapped to the P. falciparum 3D7 2013-3-1 reference genome using Bowtie2 and TopHat2 programs with parameters: max-insertion-length 0, max-deletion-length 0, read-mismatches 10, read-gap-length 0, read-edit-dist 10, i 1, I 1360, g 1, p 8.
Potential duplicate and inaccurately mapped reads were removed using SAMtools with parameters: sort, rmdup -s, calmd. Gene expression counts were determined from counts of sense-strand reads (read 1 only) mapping within (complete and partial overlap) annotated genes using a custom Perl script.
Genome_build: P. falciparum 3D7 2013-3-1
Supplementary_files_format_and_content: tab-delimited text files of read counts to annotated sense strand of gene models

organism: Plasmodium falciparum K1

source_name: size-fraction no.8

growth_protocol: P. falciparum K1 strain was cultured in vitro according to standard procedures (Trager & Jensen (1976) Science 193:673-5 and Shaw et al. (2007) Mol Biochem Parasitol 155: 146-155).  The parasite culture was composed of human erythrocytes type O Rh+ in RPMI 1640 supplemented with 25 mM HEPES pH 7.4, 0.2% NaHCO3 0.2% glucose, 0.025 mg/ml hypoxanthine, 40 µg/ml gentamicin and 8% (v/v) pooled human serum. The culture was maintained in a 3% CO2 incubator at 37°C.

extract_protocol:
Parasites (mature stages, mostly trophozoite and schizonts) were harvested from culture and liberated from host cells by treatment with 0.15% (w/v) saponin for 5 min on ice. The liberated parasites were washed three times with 1xPBS (137 mM NaCl, 8 mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4, pH 7.4) to remove host cell debris and drug. Total RNA was extracted from parasites using Trizol reagent (Invitrogen) following the manufacturers’ recommendations. 5' capped mRNA was purified as described in Shaw et al. (2007) Mol Biochem Parasitol 155: 146-155. 1 mg of GST-PfeIF4E SP-sepharose purified protein was bound to 0.2 ml of glutathione-mag beads (Thermo Scientific). 100 micrograms of parasite total RNA was incubated for 15 min on ice with 0.1 ml suspension of the GST-PfeIF4E bound beads. The beads were washed four times with 1 ml 1xPBS and 5' capped mRNA eluted in 0.1% SDS  200 mM NaCl. Eluted mRNA was purified by acidic phenol:chloroform and ethanol precipitation. Genomic DNA was removed from mRNA using a Turbo DNA freeTM kit (Ambion, Applied Biosystems).
800 ng of 5' cap enriched mRNA was used to make unfractionated RNA library (f0). 7.2 μg of 5' cap enriched mRNA was denatured with RNA loading dye (Thermo scientific) and separated in 0.8 % agarose with 1x MOPS gel running buffer. 8 RNA fractions of different sized-RNA were obtained by gel-purification using a ZYMOClean RNA purification kit (ZYMO Research). Approx. 100-400 ng of RNA from each fraction was converted to strand-specific RNA-seq sequencing library using a TruSeq Stranded mRNA LT Sample Prep kit following the manufacturers’ recommendations (Illumina). A different TruSeq adapter was used for each RNA-seq library to allow pooling of samples for Illumina sequencing on the same flow cell. ). The RNA-seq libraries were quantified by QuantIT dsDNA High Sensitivity kit (Invitrogen) and by qPCR using a library quantification kit (Kapa Biosystems). Libraries were pooled in equimolar ratios and applied to a MiSeq flow cell at 12 pM with 1% phiX174 control library (Illumina). Paired-end sequencing was performed on two MiSeq v2 2x150 bp flow cells according to the manufacturers’ recommendations (Illumina). The raw data from the MiSeq instrument were de-multiplexed and fastq files generated for each RNA-seq library.


title: VN_seq_f7

source_name: size-fraction no.7


title: VN_seq_f4

source_name: size-fraction no.4


title: 1:16 mixture of AGO and BMO


title: VN_seq_f5

source_name: size-fraction no.5


title: VN_seq_f1

source_name: size-fraction no.1


title: VN_seq_f3

source_name: size-fraction no.3


title: VN_seq_f6

source_name: size-fraction no.6


title: VN_seq_f0

source_name: Unfractionated mRNA control


title: F - 380 ppm

city: Woods Hole

first: Amy

middle: Elizabeth

last: Maas

state: MA

address: 266 Woods Hole Road

department: Biology

institute: Woods Hole Oceanographic Institution

description: 380 ppm CO2

data_processing:
pre-processing by Hudson Alpha
Trimming of adapters and low quality sequences with Trimmomatic and combining of technical replicates
Transcriptome assembly with Trinity v. r2013-02-25 using default settings
Map reads to assembly using Bowtie
Calculate FPKM and differential expression using the edgeR statistical package
Genome_build: GAWL00000000
Supplementary_files_format_and_content: Tab-delimited table of GenBank identifiers with the FPKM normalized TMM counts for each individual.

organism: Clio pyramidata

source_name: whole body, without shell

growth_protocol: After capture, C. pyramidata were placed in filtered seawater and acclimated for at least 8 hours at 15°C in temperature-controlled waterbaths at densities < 15 individuals L-1. After acclimation,  individuals  were placed in separate 20 mL glass chambers with 0.2 micron filtered seawater for 9-11 hours. The water contained 25 mg L-1 each of streptomycin and ampicillin.

extract_protocol:
In the lab frozen individuals were weighed then removed from their shell to avoid both the possible pH interference due to the calcium carbonate of the structure and to avoid contamination by other taxa trapped in the shell. RNA was extracted using an RNA Purezol or the E.Z.N.A. Mollusc RNA Kit (Omega Biotek), and then eluted in 25-40 µL molecular biology grade water water.
Libraries were constructed using Tru-Seq RNA Sample Prep Kits by the commericail providers at the Genomic Sequences Laboratory of Hudson Alpha. These were then multiplexed and sequenced in replicate on two lanes of the Illumina platform (v. 1.9) as a 50bp paired-end sequencing HiSeq run.

treatment_protocol: The water that individuals were place in had been bubbled for 45-60 minutes with ambient air (~380 ppm CO2) or a certified gas mixture containing 800 ppm CO2. (verified with DIC measurements at the conclusion of experiments). At the conclusion of the experiments individuals were flash frozen for later analysis.

tag: developmental stage

value: adult

tag: stress

value: 380 ppm CO2


title: H - 380 ppm

description: 380 ppm CO2


title: B - 800 ppm

description: 800 ppm CO2

value: 800 ppm CO2


title: E - 380 ppm

description: 380 ppm CO2


title: VN_seq_f2

source_name: size-fraction no.2


title: G - 380 ppm

description: 380 ppm CO2


title: D - 800 ppm

description: 800 ppm CO2


title: A - 800 ppm

description: 800 ppm CO2


title: pure reference RNA (AGO) CT


title: Tgif2_ChIPSeq

status: Public on Sep 26 2015

city: Austin

first: Bum-Kyu

last: Lee

state: TX

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin

description: Chromatin IP against Tgif2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mouse mm9 genome using BWA version 0.5.9-r16.
Peaks were called using MACS peak caller with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include information regarding chromosome, peak start, peak end, peak score, and peak center for each peak

source_name: J1 ES cells containing BirA_Tgif2_ChIPSeq

growth_protocol: Mouse J1 ES cells were cultivated in 0.1% gelatin coated dishes using DMEM (Dulbecco’s modified Eagle’s medium) supplemented with 15% fetal bovine serum (FBS), 2 mM of L-glutamine, 0.1 mM of non-essential amino acid, 1% of nucleoside mix, 0.1 mM of ß-mercaptoethanol, 1000U/ml of recombinant leukemia inhibitory factor and 50 U/ml of Penicillin/Streptomycin.

extract_protocol:
ChIP was performed by cross-linking proteins to DNA using 1% formaldehyde solution in J1 mouse ES cells. Immunoprecipitated DNA was sequenced using Illumina sequencers.
Pull-downed DNA was applied for the generation of sequencing libraries using the NEB ChIP-seq library prep. kit (E6200L) following by manufacturer’s instructions.

tag: cell line

value: mouse embryonic stem cell

tag: genotype/variation

value: containing BirA

tag: chip antibody

value: streptavidin-conjugated beads (life technology, 64601).


title: BirA_control

description: Chromatin IP against Mock

source_name: embryonic stem cells

extract_protocol:
ChIP was performed by cross-linking proteins to DNA using 1% formaldehyde solution in J1 mouse ES cells. Immunoprecipitated DNA was sequenced using Illumina sequencers.
Pull-downed DNA was applied for the generation of sequencing libraries using the NEB ChIP-seq library prep. kit (E6200L ) following by manufacturer’s instructions.

value: J1 ES cells containing BirA


title: Smad3_ChIPseq

description: Chromatin IP against Smad3

value: Smad3 (Abcam, ab28379)


title: Tgif1_ChIPSeq

description: Chromatin IP against Tgif1

value: Tgif1 (Santa Cruz, SC9084X)


title: C - 800 ppm

description: 800 ppm CO2


title: HDAC1_ChIPSeq

description: Chromatin IP against HDAC1

value: HDAC1 (Abcam, ab7028)


title: Splenic adult

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

data_processing:
miRNAs were aligned using Mirdeep2's mapper.pl script to Mirbase's version 21 database of miRNAs using options -d -e -h -i -j -l 18 -m
Known miRNAs were quantified using Mirdeep2's quantifier.pl script using the option -d
Genome_build: mm9
Supplementary_files_format_and_content: Text file contains raw read counts and read counts that have been normalized by library depth (reads per million) for each miRNA for each sample

source_name: CD8+ T cells

extract_protocol:
Naive samples were isolated from spleens. Thymic samples were sorted if they were CD4-CD8+. Cells were isolated into Trizol, stored at -80, then RNA was extracted according to the standard Trizol protocol.
450 ng of total RNA was used with the Illumina TruSeq Small RNA Sample Preparation kit. kit. Libraries were sequenced on a Hi-Seq 2000, generating 50 bp reads.

tag: cell state

value: Naive splenic

tag: age

value: 2-3 months

value: CD8+ T cells


title: Thymic adult

value: Thymic


title: Thymic neonate

value: 6-7 days


title: Splenic neonate


title: Thymic newborn

value: 1 day


title: Splenic newborn


title: TARRBS-ko-rep2

city: Beijing

first: xiaomeng

last: liu

state: Beijing

address: Yiheyuan Road No.5

country: China

institute: Biodynamics Optical Imaging Center (BIOPIC), Peking University

description:
Total DNA extracted from cells
library strategy: TA-RRBS

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to refference genome (hg19) using TopHat and Cufflinks.
Differencial expression genes were analysed by Cuffdiff.
Unique mapping reads were used to call peaks by MACS(v1.4) software
Genome_build: hg19
Supplementary_files_format_and_content: txt files which include the FPKM information of each RNA-Seq sample
Supplementary_files_format_and_content: peak.bed files which include the peaks called by MACS(v1.4)
Supplementary_files_format_and_content: bedgraph files which depict the reads distribution among the genome
Supplementary_files_format_and_content: bed files which include the level of C and C+T of RRBS or TA-RRBS

source_name: Neural stem cell

growth_protocol: H9 hESCs (WiCell Research) and their PTEN knockout derivatives were maintained on Mitomycin C treated mouse embryonic fibroblasts (MEFs) in hESC medium or on Matrigel (BD Biosciences) coated plates in mTeSR medium (STEMCELL Technology). Human ESC-derived MSCs were maintained in Minimum Essential Medium (MEM) Alpha Medium supplemented with 10% FBS, and 0.1 mM NEAA with 1ng/ml bFGF. Human ESC-derived NSCs were maintained in  Medium containing 50% advance DMEM/F12 (Invitrogen),50%neurobasal,1% L-glutamine,10ng/ml hLIF,2mM SB431542,3mM CHIR99021,2% B27,and 1%N2.

extract_protocol:
Total DNA was extracted from the cells using the DNeasy Blood & Tissue Kit (Qiagen) following the manufacturer’s protocol.
For RRBS, 100-200ng of genomic DNA was digested with Msp I and purified by QIAquick PCR Purification kit (Qiagen)QIAquick kit. 50-600bp fragments were selected by 2% agarose gel. After addition of spike-in controls, samples were end-repaired, A-tailed and ligated to methylated adapters employing TruSeq DNA Sample Preparation Kit (Illumina). The ligated DNA was then treated with bisulfate using MethylCode Kit (Invitrogen) converting unmethylated cytosine (C) into uracil (U). Finally, sequencing libraries were prepared by PCR amplification with PfuTurbo C× Hotstart DNA polymerase (Agilent Technologies). For TA-RRBS, after 1-2ug of genomic DNA, per sample, was digested and fragment selected, the samples were treated with 40μM β-glucosyltransferase (β-GT) in 20μl volume for glucosylation of 5-hmC. Then the DNA was treated with 8.4 μg recombinant mouse Tet1(mTet1) in a 20μl reaction system and 5-methylcytosine (5-mC) was oxidized to 5-carboxylcytosine (5-caC). Next, the DNA was end-repaired, adenylated, and ligated with adaptors. Finally, the ligated DNA was treated by sodium-bisulfite and then amplified  with PfuTurbo C× Hotstart DNA polymerase (Agilent Technologies).

treatment_protocol: We sought to generate an isogenic human embryonic stem cell (hESC) line by knocking out the conserved 1th  exon of PTEN gene  by TALEN.

value: KO

value: Neural stem cell


title: TARRBS-wt-rep1

value: WT


title: RRBS-ko-rep2

description: Total DNA extracted from cells


title: RRBS-wt-rep2

description: Total DNA extracted from cells


title: igg_ChIP_Seq

description: Chromatin input

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody(anti-H3K4me3 (CST, 9751s), anti-H3K27me3 (CST, 9733) and normal rabbit IgG (Santa Cruz, SC-2027)).
Libraries were prepared by library construction NEBNext kit according to the manufacturer’s protocols.


title: TARRBS-ko-rep1


title: H3K27me3_wt_ChIP-Seq

description: Chromatin IP against H3K27me3


title: Nanog_ChIPseq

description: Chromatin IP against Nanog

value: streptavidin-conjugated beads


title: H3K4me3_ko_ChIP-Seq

description: Chromatin IP against H3K4me3


title: MSC_ko_rep2_RNA-Seq

description: Total RNA extracted from cells

source_name: Mesenchymal stem cell

extract_protocol:
Total RNA was extracted from the cells using the RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using library construction NEBNext kit following the standard protocols.

value: Mesenchymal stem cell


title: RRBS-wt-rep1

description: Total DNA extracted from cells


title: MSC_wt_rep2_RNA-Seq

description: Total RNA extracted from cells


title: H3K27me3_ko_ChIP-Seq

description: Chromatin IP against H3K27me3


title: H3K4me3_wt_ChIP-Seq

description: Chromatin IP against H3K4me3


title: MSC_wt_rep1_RNA-Seq

description: Total RNA extracted from cells


title: NSC_ko_rep1_RNA-Seq

description: Total RNA extracted from cells


title: NSC_wt_rep2_RNA-Seq

description: Total RNA extracted from cells


title: MSC_ko_rep1_RNA-Seq

description: Total RNA extracted from cells


title: MOLM-14_input_BRD4_iBET2_8

city: Cambridge

first: Matthew

middle: D.

last: Shair

address: 12 Oxford Street

department: Chemistry and Chemical Biology

institute: Harvard University

description:
input for MOLM-14_BRD4_iBET2_IN5121.fastq.gz
processed data file: MOLM14_BRD4_iBET_IDR.bed

data_processing:
Basecalls performed using CASAVA version 1.4
FastQC v.0.10.1 was used to check read quality metrics. If necessary, trim_galore v.0.3.3 was used with default settings to remove adapters, low-quality bases and trimmed reads < 20nt long after trimming.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie v.1.0.0 with flags -n 1 -m 1 --best --strata
Duplicate reads were removed with MarkDuplicates (picard tools v.1.79(1282))
In cases where peaks were used without subsequent ROSE enhancer analysis, SPP was used both for cross-correlation analysis and for peak finding using default parameters or FDR < 0.05. MACS2 was used either with default parameters or using --shiftsize to set the strand shift to match the SPP peak cross-correlation size. Peaks identified by both peak finders were retained. Regions on chrM or overlapping repeat elements (RepeatMasker bed file downloaded from UCSC 16 Nov. 2012) by > 70% were routinely excluded.
In cases where ROSE was used to identify enhancers and super-enhancers, MACS v.1.4 was run with the suggested parameters, namely -p 1e-9 --keep-dup=auto. MACS v1.4 peak bed files were converted to GFF format and used for ROSE with suggested parameters : -s 12500 -t 2000.
Genome_build: hg19

growth_protocol: MOLM-14 cells were grown in RPMI-1640 supplemented with 10% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries for Illumina sequencing were prepared using the Illumina TruSeq ChIP Sample Preparation kit with the following exceptions. After end-repair and A-tailing, ChIP DNA or whole cell extract DNA was ligated to Illumina RNA adaptors with unique indices. Alternatively, libraries were prepared using the KAPA Hyper Prep Kit for Illumina and ligated to unique Bioo Scientific NEXTflex barcode adaptors. Following ligation, libraries were amplified with 16-18 cycles of PCR and were then size-selected using a 2% gel cassette in the Pippin Prep System from Sage Science. For histone modifications and RNA pol II, DNA fragments of size 200-500bp were captured. For CDK8 and MED1, DNA fragments of size 200-450bp were captured. Libraries were quantified by qPCR utilizing the KAPA Biosystems Illumina Library Quantification kit.

value: MLL-AF9-rearranged AML

tag: treatment protocol

tag: chip epitope

value: input

tag: chromatin prep#

tag: ca sensitivity

value: sensitive


title: MOLM-14_BRD4_iBET2_8

description:
matched input: MOLM-14_input_BRD4_iBET2_IN5121.fastq.gz
processed data file: MOLM14_BRD4_iBET_IDR.bed

tag: cell type


title: TARRBS-wt-rep2


title: MOLM-14_BRD4_iBET1_7

description:
matched input: MOLM-14_input_BRD4_iBET1_IN5121.fastq.gz
processed data file: MOLM14_BRD4_iBET_IDR.bed


title: NSC_ko_rep2_RNA-Seq

description: Total RNA extracted from cells


title: MOLM-14_input_BRD4_iBET1_7

description:
input for MOLM-14_BRD4_iBET1_IN5121.fastq.gz
processed data file: MOLM14_BRD4_iBET_IDR.bed


title: MOLM-14_input_BRD4_DMSO1_5

description:
input for MOLM-14_BRD4_DMSO1_IN5121.fastq.gz
processed data file: MOLM14_BRD4_DMSO_IDR.bed

value: DMSO


title: RRBS-ko-rep1

description: Total DNA extracted from cells


title: MOLM-14_BRD4_DMSO2_6

description:
matched input: MOLM-14_input_BRD4_DMSO2_IN5121.fastq.gz
processed data file: MOLM14_BRD4_DMSO_IDR.bed


title: MOLM-14_BRD4_DMSO1_5

description:
matched input: MOLM-14_input_BRD4_DMSO1_IN5121.fastq.gz
processed data file: MOLM14_BRD4_DMSO_IDR.bed


title: MOLM-14_input_CDK8_iBET2_4

description:
input for MOLM-14_CDK8_iBET2_IN5121.fastq.gz
processed data file: MOLM14_CDK8_iBET_IDR.bed


title: MOLM-14_CDK8_iBET2_4

description:
matched input: MOLM-14_input_CDK8_iBET2_IN5121.fastq.gz
processed data file: MOLM14_CDK8_iBET_IDR.bed


title: MOLM-14_input_CDK8_iBET1_3

description:
input for MOLM-14_CDK8_iBET1_IN5121.fastq.gz
processed data file: MOLM14_CDK8_iBET_IDR.bed


title: MOLM-14_CDK8_iBET1_3

description:
matched input: MOLM-14_input_CDK8_iBET1_IN5121.fastq.gz
processed data file: MOLM14_CDK8_iBET_IDR.bed


title: MOLM-14_CDK8_DMSO2_2

description:
matched input: MOLM-14_input_CDK8_DMSO2_IN5121.fastq.gz
processed data file: MOLM14_CDK8_DMSO_IDR.bed


title: MOLM-14_input_CDK8_DMSO2_2

description:
input for MOLM-14_CDK8_DMSO2_IN5121.fastq.gz
processed data file: MOLM14_CDK8_DMSO_IDR.bed


title: NSC_wt_rep1_RNA-Seq

description: Total RNA extracted from cells


title: MOLM-14_CDK8_DMSO1_1

description:
matched input: MOLM-14_input_CDK8_DMSO1_IN5121.fastq.gz
processed data file: MOLM14_CDK8_DMSO_IDR.bed


title: sRNAs from Kem-I cell line, 2h after treatment with TGF-β1

status: Public on Sep 25 2015

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

country: France

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

data_processing:
Image analysis and base calling were performed using Pipeline Illumina v1.6 (for samples 1, 2, 3), and RTA v1.9 and Casava v1.8 (for samples 4, 5, 6, 7, 8, 9)
As the sRNA library deriving from the untreated (0h) Sav* cells presented with around two times less reads compared to the other libraries, it was sequenced twice and the corresponding reads were pooled prior any analysis.
Sequencing reads were preprocessed using the Dustmasker program and FASTX-Toolkit to filter out low complexity reads and remove instances of the 3' adapter.
Remaining reads of 15 to 32 nt in length were then mapped simultaneously to the human and the EBV genomes using Bowtie 0.12.7 by permitting up to 1 mismatch in the first 15 nucleotides of each read.
Only alignments from the lowest mismatch-stratum were recorded provided they didn't exceed a total number of 2 mismatches and reads that could map to more than 50 loci were discarded.
From there, all known Homo sapiens and EBV miRNAs (miRBase v.17) were annotated using BEDTools 2.16.2 by comparing their genomic coordinates to those of the aligned reads, and by keeping reads with at least 50% of their length inside the genomic feature.
During the quantification process, multiple mapped reads were weighted by the number of mapping sites in genomic features of interest.
To allow subsequent comparative expression analysis, miRNA measures were normalized per 10^5 miRNA reads (normRC - normalized readcount).
Genome_build: GRCh37/hg19 (UCSC repository) + NC_007605.1 (RefSeq)
Supplementary_files_format_and_content: Annotation files of the cellular and viral miRNAs are provided in tab-delimited format (*-cellular-and-viral-miRs-annot.txt: miR, normRC).

source_name: EBV+ BL cell line_TGF-β1_2h post treatment

growth_protocol: The EBV-positive BL cell lines Mutu-I, Kem-I and Sav* were maintained in RPMI 1640 medium (Invitrogen, France) supplemented with 2 mM of glutamine (Invitrogen, France), 100 μg/ml of primocin (CAYLA, Toulouse, France), and 10% heat-inactivated fetal calf serum (FCS) (Invitrogen, France).

extract_protocol:
Total RNAs were extracted from untreated (0h) and TGF-β1-treated Mutu-I, Kem-I and Sav* cells (2h and 24h post treatment) by using TRIzol reagent.
Smal RNA libraries were prepared from 25 μg of total RNA as previously described (Tuddenham et al. Small RNA deep sequencing identifies microRNAs and other small noncoding RNAs from human herpesvirus 6B. J. Virol. 86:1638-1649)

treatment_protocol: TGF-β1 stimulation was performed in this medium containing a reduced FCS concentration (0.5%). Purified recombinant TGF-β1 from Abcys (France) was added to a final concentration of 2 ng/ml

value: Kem

value: EBV-positive Burkitt's lymphoma (BL) cell line

tag: latency type

value: I

tag: tgf-β1 treatment

value: 2h post-treatment


title: sRNAs from Sav* cell line, 24h after treatment with TGF-β1

source_name: EBV+ BL cell line_TGF-β1_24h post treatment

value: Sav

value: 24h post-treatment


title: sRNAs from Sav* cell line, 2h after treatment with TGF-β1


title: sRNAs from Mutu-I cell line, 24h after treatment with TGF-β1

value: Mutu


title: sRNAs from Kem-I cell line, 24h after treatment with TGF-β1


title: sRNAs from untreated Sav* cell line

source_name: EBV+ BL cell line_untreated


title: sRNAs from untreated Kem-I cell line


title: SH-EZH2-FSS_n5

city: Cologne

first: Monika

last: Maleszewska

address: Joseph-Stelzmann-Strasse 9b

country: Germany

institute: Max Planck Institute for Biology of Ageing

data_processing:
FASTQ Groomer (v. 1.0.4) was used to groom the .fq files, and FastQC (v. 0.52) was used to assess the quality of the reads. Trim sequences tool (v. 1.0.0) was used to trim the reads.
Trimmed reads were checked again with FastQC and then were aligned to hg19 using TopHat2 (v. 0.6), and  iGenomes hg_19 (v. 1.1.3) was used for annotation.
Cufflinks (v.0.0.6) and CuffDiff (v. 0.0.7) were used to calculate FPKM values and to perform differential expression analyses. FDR correction was used, with q<0.05 as a cutoff for significant differences.
All steps were performed at usegalaxy.org and version numbers in brackets (v. ...) relate to the versions of software wrap-ups used, which were available as of July and August 2014.
Genome_build: hg19
Supplementary_files_format_and_content: tabular, CuffDiff output files of differential gene expression, as obtained from the usegalaxy.org platform, 3 files are delivered, presenting 3 different comparisons used in the related manuscript

source_name: HUVEC

growth_protocol: Human Umbilical Vein Endothelial Cells (HUVEC; Lonza, Basel, Switzerland) were used between passages 5 and 8, cultured in endothelial cell medium (ECM) as described before, 18  but with 5.5mM glucose and 10% heat-inactivated fetal calf serum (FCS; Lonza, Basel, Switzerland), in gelatin-coated dishes. For the FSS experiments, µ-Slides I 0.4 Luer (Ibidi, Planegg/Martinsried, Germany) were coated with gelatin, HUVEC were seeded at full confluency (approximately 60 000 cells/cm2) and incubated overnight under standard static cell culture conditions. Slides with confluent cell monolayers were attached to a fluidic unit (Ibidi, Planegg/Martinsried, Germany), connected to the pump (Ibidi, Planegg/Martinsried, Germany), and incubated under standard cell culture conditions. Inverted pressure was used to ensure the gas exchange in the culture medium. Fluid shear stress (FSS) of 20 dyne/cm2 was applied to the monolayers in the slides, for 72h. Static controls were cultured in the same incubator and the same medium, refreshed daily. (method quoted from the manuscript)

extract_protocol:
Cells were lysed with RLT-Plus lysis buffer containing beta-mercaptoethanol, and lysated were processed according to the protocol of the QIAGEN's RNEasy Plus Mini kit. RNA with RIN of 9 or higher was used for library preparation.
RNA library was created in accordance with the TruSeqTM RNA Sample Preparation v2 Guide (Illumina, San Diego, CA, USA), using the PerkinElmer Sciclone liquid handler, resulting in 330bp cDNA fragments.

value: HUVEC

tag: treatment

value: EZH2 knock-down

tag: culture condition

value: fluid shear stress 20 dyne/cm^2


title: sRNAs from Mutu-I cell line, 2h after treatment with TGF-β1


title: SH-EZH2-FSS_n4


title: MOLM-14_input_BRD4_DMSO2_6

description:
input for MOLM-14_BRD4_DMSO2_IN5121.fastq.gz
processed data file: MOLM14_BRD4_DMSO_IDR.bed


title: SCR-FSS_n5

value: scrambled control


title: SH-EZH2-FSS_n2


title: SCR-FSS_n2


title: sRNAs from untreated Mutu-I cell line


title: SCR-FSS_n4


title: SH-EZH2-static_n5

value: static


title: SH-EZH2-static_n4


title: SH-EZH2-static_n2


title: SCR-static_n5


title: SCR-static_n4


title: MOLM-14_input_CDK8_DMSO1_1

description:
input for MOLM-14_CDK8_DMSO1_IN5121.fastq.gz
processed data file: MOLM14_CDK8_DMSO_IDR.bed


title: K562_input_untreated_18

description: input for: K562_cdk8_8260

growth_protocol: K562 cells were grown in RPMI-1640 supplemented with 10% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.

value: CML

value: untreated

value: insensitive


title: SCR-static_n2


title: K562_CDK8_untreated_18

description: matched input: K562_input_8260


title: MV411_H3K27ac_untreated_17

description: matched input: MV411_input_pol2.k27ac_8270

growth_protocol: MV4;11 cells were grown in RPMI-1640 supplemented with 10% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.

value: MLL-AF4-rearranged AML

value: sensitive


title: MOLM14_H3K27ac_CA25_11

description: matched input: MOLM14_CA25_input_h3k27ac_IN5001

value: MLL-AF9-rearranged AML


title: MV411_CDK8_untreated_16

description: matched input: MV411_input_cdk8_8260


title: MV411_input_untreated_17

description: input for: MV411_pol2_8270, MV411_k27ac_8270

value: input


title: MOLM14_input_CA25_11

description: input for: MOLM14_CA25_1_h3k27ac_IN5001


title: MV411_input_untreated_16

description: input for: MV411_cdk8_8260


title: MOLM14_input_DMSO_9

description: input for: MOLM14_DMSO_1_h3k27ac_IN5001

value: DMSO


title: SET2_CDK8_untreated_14

description: matched input: SET2_input_2_IN5022

growth_protocol: SET2 cells were grown in RPMI-1640 supplemented with 20% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.

value: essential thrombocythemia


title: SET2_H3K27ac_untreated_15

description: matched input: SET2_input_IN4146


title: SET2_input_untreated_15

description: input for: SET2_h3k27ac_IN4146


title: MOLM14_input_CA25_8

description: input for: MOLM14_CA25_brd4_IN5001


title: SET2_input_untreated_14

description: input for: SET2_CDK8_2_IN5022


title: MOLM14_BRD4_DMSO_7

description: matched input: MOLM14_DMSO_input_brd4_IN5001


title: SET2_input_untreated_13

description: input for: SET2_CDK8_1_IN5022


title: rtt109t3_15116

city: Vienna

first: Michael

last: Tscherner

address: Dr. Bohr Gasse 9/2

department: Max F. Perutz Laboratories, Department for Medical Biochemistry

country: Austria

institute: Medical University of Vienna

data_processing:
Reads were trimmed using the FASTQ Quality Trimmer (FASTX-Toolkit) until total read quality >=30
Reads containing less than 90% bases with quality >=30 were filtered out using the FASTX-Toolkit
Reads were mapped onto the Assembly 21 of the C. albicans genome using NextGenMap (Sedlazeck, Bioinfromatics, 2013) with default parameters and reads mapped to rRNA loci were filtered out using bedtools intersect
Read counts were determined with HTSeq using the union mode (AndersS, Bioinformatics, 2014) and a reference annotation (C_albicans_SC5314_version_A21-s02-m07-r10; http://www.candidagenome.org). The annotation of the coding sequence assembly was used as transcript coordinates. For short non-coding RNAs (tRNAs, snRNAs, snoRNAs and ncRNAs) 20bp up- and downstream of their chromosomal coordinates were added before mapping.
Differential expression analysis was done with edgeR (RobinsonMD, Bioinformatics, 2010).
Genome_build: Assembly 21
Supplementary_files_format_and_content: tab delimited .txt files containing the output of the HTSeq analysis (read counts)

organism: Candida albicans

source_name: fungal cells

extract_protocol:
RNA was isolated using Trizol and glass bead lysis after which RNA was precipitated and DNase treated followed by a column purification step. 5μg total RNA was depleted of rRNAs using the RiboMinus Eukaryote System v2 (Invitrogen), rRNA-depleted RNA was fragmented using the NEBNext Magnesium RNA Fragmentation Module (NEB). First strand cDNA was synthesized with the SuperScript III Reverse Transcriptase (Invitrogen) and second strand synthesis was done using the NEBNext mRNA Second Strand Synthesis Module (NEB) according to the manufacturer’s instructions.
Library preparation was done using the KAPA DNA Library Preparation Kit (Kapa Biosystems) according to the manufacturer’s instructions.

tag: genotype

value: treated


title: rtt109t2_15120


title: SET2_CDK8_untreated_13

description: matched input: SET2_input_1_IN5022


title: MOLM14_input_CA25_12

description: input for: MOLM14_CA25_2_h3k27ac_IN5002


title: rtt109u3_15115


title: rtt109t1_15104


title: MOLM14_H3K27ac_CA25_12

description: matched input: MOLM14_CA25_input_h3k27ac_IN5002


title: MOLM14_input_DMSO_7

description: input for: MOLM14_DMSO_brd4_IN5001


title: rtt109u2_15119


title: MOLM14_H3K27ac_DMSO_10

description: matched input: MOLM14_DMSO_input_h3k27ac_IN5002


title: MOLM14_input_DMSO_10

description: input for: MOLM14_DMSO_2_h3k27ac_IN5002


title: rtt109u1_15103


title: cac2t3_15118


title: MOLM14_MED1_untreated_6

description: matched input: MOLM14_input_8270


title: MOLM14_input_untreated_6

description: input for: MOLM14_med1_8270


title: cac2t2_15122


title: MOLM14_H3K27ac_DMSO_9

description: matched input: MOLM14_DMSO_input_h3k27ac_IN5001


title: MOLM14_CDK8_b1_untreated_5

description: matched input: MOLM14_input_8257_J


title: cac2t1_15106


title: cac2u3_15117


title: MOLM14_BRD4_CA25_8

description: matched input: MOLM14_CA25_input_brd4_IN5001


title: cac2u1_15105


title: cac2u2_15121


title: hat1t5_12887


title: MOLM14_RNA PolII_CA25_3

description: matched input: MOLM14_CA25_input_8235

value: RNA PolII


title: MOLM14_input_untreated_4

description: input for: MOLM14_cdk8_b1_8257_R


title: hat1t4_12886


title: hat1t3_15114


title: MOLM14_RNA PolII_DMSO_2

description: matched input: MOLM14_dmso_input_8235


title: MOLM14_input_CA25_3

description: input for: MOLM14_CA25_pol2_8235


title: hat1t2_15110


title: HCT116_CA_3hrs_rep3

description: approx. 16 million cells were treated with DMSO for 3hrs

data_processing:
Illumina Casava1.7 software used for basecalling.
fastX version 0.0.13.2 software used for quality assement of raw fastq files. Commands used for tophat mapping all fastq files = -p 16 --b2-very-sensitive --no-novel-juncs --microexon-search --no-convert-bam --no-mixed --library-type fr-firststrand -G hg19.gtf
Aligned .sam files were then converted to bam files using samtools version 0.1.16 and reads aligned over annotated genes were quantified using htSeq version 0.6.1. Commands used for htSeq = count -f bam -s reverse -m intersection-nonempty -t exon -I gene_id .
DESeq counts are in the tab-delimited text file HCT116_3hrs_CA_DESeqFormattedIndividualValues.txt containing Transcript_ID in the first column and values for each sample in subsequent columns.
For use with GSEA, DESeq counts were normalized using the voom function of the R/Bioconductor package limma (as described in Genome Biol. 2014 Feb 3;15(2):R29). Normalized values are in the tab-delimited text file HCT116_3hrs_CA_vomo-normalized_DESeqValues.txt containing Transcript_ID in the first column and values for each sample in subsequent columns.
Genome_build: hg19

molecule: polyA RNA

source_name: HCT116 cells, CA, 3hrs

growth_protocol: HCT116 cells were grown in DMEM supplemented with 10% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.

extract_protocol:
RNA was harvested using Trizol reagent, then was further purified using the RNeasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were plated (15cm dish) in triplicate and grown to approximately 80% confluency, then incubated in the presence of DMSO or 100nM CA for 3hrs. Cells were then washed twice with cold PBS, and immediately harvested in Trizol.

value: 100nM CA for 3hrs


title: HCT116_CA_3hrs_rep2


title: MOLM14_H3K27ac_untreated_1

description: matched input: MOLM14_input_8209


title: HCT116_CA_3hrs_rep1


title: MOLM14_input_DMSO_2

description: input for :MOLM14_dmso_pol2_8235


title: hat1t1_15102


title: HCT116_DMSO_3hrs_rep3

source_name: HCT116 cells, DMSO, 3hrs


title: hat1u5_12883


title: HCT116_DMSO_3hrs_rep2


title: hat1u4_12882


title: MOLM14_H3K4me1_untreated_1

description: matched input: MOLM14_input_8209


title: MOLM14_input_untreated_1

description: input for: MOLM14_k4me1_8209, MOLM14_k27ac_8209


title: hat1u3_15113


title: T. tenax small RNA #1

city: Marburg

last: Daume

state: Hessen

address: Karl-von-Frisch-Strasse 10

department: Prokaryotic Small RNA Biology

institute: Max Planck Institute for Terrestrial Microbiology

description: small RNAs (<200 nt)

data_processing:
Software: All data processing steps were performed with CLC Genomic Workbench 8.0.1
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 by poly-T(60) adapter trimming (strand: minus; action: remove adapter; mismatch cost: 3; gap cost: 3; no internal end matches allowed; minimum end matches score: 3). The processed sequences were filtered by length (15 nt cutoff)
Read mapping: The trimmed sequences were mapped to the T. tenax reference genome (FN869859) using default settings (mismatch cost set to 4) and saved as a read track file.
Genome_build: T. tenax reference genome (GenBank accession FN869859)
Supplementary_files_format_and_content: The processed data file is in .wig (Wiggle) format. It contains the Mapping Graph track that was created from the coverage plot of the generated read track file.

organism: Thermoproteus tenax

source_name: liquid culture

growth_protocol: Cells were grown heterotrophically in Thermoproteus medium to logarithmic phase.

extract_protocol:
Cells were lysed by homogenization and small RNAs were isolated according to the mirVana miRNA Isolation Kit (Ambion). The extracted small RNAs were treated with T4-Polynucleotide Kinase (Ambion) to ensure proper adapter ligation of RNA termini.
cDNA libraries were prepared according to the TruSeq Small RNA Library Protocol (Illumina).

tag: strain

tag: developmental stage

value: logarithmic phase


title: MOLM14_CDK8_b1_untreated_4

description: matched input: MOLM14_input_8257_R

tag: cell line


title: hat1u1_15101


title: HCT116_DMSO_3hrs_rep1


title: hat1u2_15109


title: wtt5_12885

value: wild-type


title: wtt4_12884


title: wtt3_15112


title: wtt2_15108


title: wtu5_12881


title: MOLM14_input_untreated_5

description: input for: MOLM14_cdk8_b1_8257_J


title: SET2_CA_4hrs_rep3

description: 2,000,000 cells were treated with 25nM CA for 4hrs

data_processing:
Ion Torrent Suite Software software used for basecalling.
Convert BAM to FASTQ
Trim to BASEQ==10 using fastq_quality_trimmer MINREAD_LEN==50
Pass 1 mapping with rnaStar v2.3.0e
Pass 2 mapping of unmapped reads with BWA v0.7.5a
Merge mapped reads and ount using htseq-count -s yes -m intersection-strict (HTSeq v0.5.3p3)
Count normalization, sample clustering, and differential expression analysis using Bioconductor package DESeq. Genes with minimum absolute fold change log2(2), FDR 0.05 were deemed to be differentially expressed.
Genome_build: hg19

source_name: SET2 cells, CA, 4hrs

extract_protocol:
RNA was harvested using Qiagen RNeasy Mini Plus Kit
Libraries from 1 ug total RNA were prepared for sequencing using the mRNA direct Micro kit (Life Technologies) and standard Ion Proton protocols

treatment_protocol: Cells were plated (24-well) in triplicate at 1,000,000 cells/mL and incubated in the presence of DMSO or 25nM CA for 4hrs. Cells were then washed three times with cold PBS, and snap frozen.

value: 25nM CA 4hrs


title: wtu3_15111


title: SET2_CA_4hrs_rep2


title: SET2_DMSO_4hrs_rep2

description: 2,000,000 cells were treated with DMSO for 4hrs

source_name: SET2 cells, DMSO, 4hrs

value: DMSO 4hrs


title: SET2_CA_4hrs_rep1


title: SET2_DMSO_4hrs_rep1


title: wtu2_15107


title: wtu1_15099


title: SET2_DMSO_4hrs_rep3


title: Control-2_RNA-seq

status: Public on Sep 24 2015

city: Peiking

first: haibo

last: Han

address: 52 Fucheng Road, Haidian District

department: Department of Cell Biology

institute: Peking University School of Oncology

data_processing:
Basecalls performed using CASAVA version 1.4
aligned to the hg19 genome assembly using BWA .
Uniquely mapped reads with mapping quality >=20 were retrieved for downstream analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: text files include RPKM values for each Sample.

source_name: SMMC-7721 cells_control

extract_protocol:
Total RNA was harvested using Qiagen Kit.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The SMMC-7721 cells were transfected by PBX3 Lentivirus and blank lentivirus as control.

value: liver cancer

tag: passages


title: Control-1_RNA-seq


title: Healthy Control PMN from Donor 2 isolated by negative selection, TNF-alpha treated

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

country: United Kingdom

institute: University of Liverpool

description:
Healthy male donor aged 31 years (Donor 2)
TNF_gene_exp.diff; TNF_genes.fpkm_tracking

data_processing:
Sequenced reads were mapped to hg19 using Tophat v2.0.4 using --max-multihits 1 option
Mapped reads from each donor were input into Cuffdiff v2.0.2 as n=2 biological replicates for each experimental condition
Differential expression was calculated as FDR <= 0.05
Genome_build: hg19 (UCSC iGenomes)
Supplementary_files_format_and_content: genes.fpkm_tracking files contain RPKM values for each condition (using n=2 biological replicates), Poly versus Bead for each treatment condition; gene_exp.diff files contain RPKM values for each gene in each condition, the log2 fold difference between samples and the FDR value. An FDR value of 0.05 or less is significant "yes";

source_name: Peripheral blood neutrophils

growth_protocol: Neutrophils were isolated from heparinised peripheral blood and isolated either by Polymorphprep (Poly) density centrifugation, or StemCell untouched human neutrophil enrichment kit (Bead) as per manufacturers instructions. Erythrocytes were lysed using ammonium chloride hypotonic lysis buffer.

extract_protocol:
RNA was isolated from cell pellets using Trizol:chloroform and precipitated in isopropanol.  RNA was cleaned using Qiagen Rneasy kit including DNase digestion and resuspended in water.
Standard Illumina library protocol with poly-A enrichment of mRNA

treatment_protocol: Neutrophils were suspended in RPMI 1640 media plus Hepes plus L-glutamine, and incubated for 1h in the absence (UT) or presence of TNF-alpha (10ng/mL) or GM-CSF (5ng/mL)

value: Neutrophils

tag: isolation method

value: Negative selection (beads)

value: TNF-alpha (10ng/mL) 1h


title: Healthy Control PMN from Donor 2 isolated by Polymorphprep, GM-CSF treated

description:
Healthy male donor aged 31 years (Donor 2)
GM_gene_exp.diff; GM_genes.fpkm_tracking

value: Polymorphprep (poly)

value: GM-CSF (5ng/mL) 1h


title: Healthy Control PMN from Donor 2 isolated by Polymorphprep, TNF-alpha treated


title: S. pombe WT

city: Piscataway

first: Miguel

last: Zaratiegui

state: NJ

address: 604 allison rd

department: Molecular Biology and Biochemistry

institute: Rutgers, the State University of New Jersey

data_processing:
Basecalls performed using CASAVA version 1.4
Adapter trimming with custom scripts
Mapping to the pombe genome with Bowtie2
insertion count with bedtools genomecov -bga -strand [+|-] -5, with correction to reads per million
Displacement of insertion points in Crick strand by displacing insertion point 4 positions to the left so as to represent the first position after the cut in the Watson strand.
Genome_build: ASM294v2
Supplementary_files_format_and_content: Wig files generated by costom script from corrected bedgraph files

organism: Schizosaccharomyces pombe

source_name: transposition selected cells

growth_protocol: As previously described (Guo et al 2010 Genome Research 20:239-248). Twenty plates containing 16 independent patches were used for experiments in both wild-type and sap1-c backgrounds.

extract_protocol:
Pellets were resuspended in in 1mg/mL zymolyase 100T in CPS buffer (50mM citrate phosphate buffer, pH=5.6, 1.2M sorbitol), treated for 1 hr at 37°C (or until >90% have lost their refringence under brightfield microscopy), then spun down for 3’ at 3,000g and resuspended in 5xTE (50mM Tris-HCl, 5mM EDTA, pH=8). 1/10th volume of 10% SDS was added and cells were lysed by incubation at 65°C for 5 minutes. Next, KAc was added to 1.25M final and incubated 30’ on ice. Samples were then spun to remove cell debris and ethanol precipitated. DNA pellets were then brought up in TE + RNase A (100μg/mL) and treated for 1 hour at 42°C. Supernatant was extracted with phenol/chloroform/iso-amyl alcohol (pH=8) twice, then concentrated by ethanol precipitated a final time. Pellets were then washed with 70% ethanol once before being resuspended in a small volume of TE or EB (10mM Tris-HCl, pH=8).
After DNA purification, samples were digested with MseI to completion, purified and ligated to the oM536/oM537 linker. Libraries were prepared for high-throughput sequencing by PCR with oM538/544 (for WT), and oM538/543 (for sap1-c).

treatment_protocol: Independent transformants of S. pombe strains transformed with a nmt1 driven Tf1-neo expressing plasmid were patched onto EMM plates with 2g/L of appropriate drop-out mix lacking thiamine and grown for 4 days at 32°C.Cells were then replica plated onto 5-FOA twice to remove the expression plasmid and finally onto YES+G418 (500μg/mL) + FOA (1mg/mL.)


title: PBX3-1_RNA-seq

source_name: SMMC-7723 cells_overexpressing PBX3


title: Healthy Control PMN from Donor 2 isolated by negative selection, GM-CSF treated


title: PBX3-2_RNA-seq


title: Healthy Control PMN from Donor 1 isolated by negative selection, TNF-alpha treated

description:
Healthy female aged 26 years (Donor 1)
TNF_gene_exp.diff; TNF_genes.fpkm_tracking


title: Healthy Control PMN from Donor 1 isolated by Polymorphprep, TNF-alpha treated


title: Healthy Control PMN from Donor 1 isolated by Polymorphprep, GM-CSF treated

description:
Healthy female aged 26 years (Donor 1)
GM_gene_exp.diff; GM_genes.fpkm_tracking


title: Healthy Control PMN from Donor 2 isolated by negative selection, untreated

description:
Healthy male donor aged 31 years (Donor 2)
UT_gene_exp.diff; UT_genes.fpkm_tracking

value: Untreated 1h


title: wtu4_12880

value: untreated


title: Healthy Control PMN from Donor 1 isolated by Polymorphprep, untreated

description:
Healthy female aged 26 years (Donor 1)
UT_gene_exp.diff; UT_genes.fpkm_tracking


title: Healthy Control PMN from Donor 1 isolated by negative selection, untreated


title: S. pombe sap1-c


title: KBM7 cell line, haploid, biological replicate 2

city: Worcester

first: Bryan

middle: R

last: Lajoie

address: 368 Plantation St.

department: Program in Systems Biology

institute: UMMS

data_processing:
Library strategy: Hi-C
Iterative mapping and error correction of the chromatin interaction data were performed as previously described (Imakaev, M. et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat. Methods 9, 999-1003, doi:10.1038/nmeth.2148 (2012))
Genome_build: hg19

extract_protocol: Hi-C performed as previously described Nat. Methods 9, 999-1003, doi:10.1038/nmeth.2148 (2012)).


title: KBM7 cell line, clone 14, diploid, sample 051

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Basecalling and filtering were performed using standard software of the Illumina HiSeq 2000.
The 51bp reads are first parsed (using custom scripts and cutadapt {Martin, 2011, http://dx.doi.org/10.14806/ej.17.1.200}) to extract the different parts, i.e. the first 4 random bases (included to make cluster calling on the Illumina Hi-seq 2000 possible), 15bp of adapter sequence, and a stretch of gDNA starting with the GATC site. The gDNA sequences are aligned to the reference genome (hg19, chromosomes 1-22, X, Y, and M) using bowtie2 version 2.1.0, using the --very-sensitive mode and otherwise default parameters. Reads that did not align or aligned more than once were discarded. The remaining reads are assigned to GATC-fragments using a custom R-script. Only reads that precisely flanked a GATC site were associated with GATC-fragments, all other reads were discarded. Even though diploid cells have two copies of any GATC fragment, we are under-sequencing to such an extend that we assume that at most one of the two methylated GATC fragment is actually sequenced. However, if both chromosomes are methylated we will detect approximately twice as many GATC fragments in a methylated region as compared to when only a single chromosome in the region is methylated. Thus, also for diploid cells  the multiple reads aligning to the same position are counted as one. These reads were then aggregated in genomic segments of 100kb.
Next, the number of mappable unique reads per 100kb segment was divided by the maximum possible number of unique reads, which is determined by the total number of GATC motifs in the segment with uniquely mappable flanking sequences.  To determine these numbers we performed an in silico DnpI digest of the complete genomic reference sequence (chromosomes 1-22, X, Y, and M), defined the complete set of potential DamID-seq reads of 32bp length, and aligned these reads back to the reference genome using the same method and filter criteria as we used for the experimental reads (see above). We then summed the number of unique GATC-flanking reads for each 100kb segment.  Finally, the observed over expected read counts per 100 kb segment (OE) was calculated by taking the ratio of the two counts, and normalizing this ratio for the total number of observed (i.e. unique) reads.
Genome_build: hg19
Supplementary_files_format_and_content: OE values in 100kb windows

source_name: KBM7 cell line, clone 14, diploid

growth_protocol: KBM7 cells were cultured in IMDM 1X (Gibco), respectively, supplemented with 10% Fetal Bovine Serum (Thermo Scientific HyClone) and 1% penicillin and 1% streptomycin.

extract_protocol:
Based on the FCS and SSC profiles the 2% smallest cells that were double positive for the Fucci markers were single cell sorted in a PCR plate containing lysis buffer and proteinase K (Costar Thermowell). Each well contained 1μl of pick buffer (50mM Tris-HCl pH 8.3, 75mM KCl, 3mM MgCl2, 137mM NaCl) and 2μl of lysis buffer with proteinase K (10mM Tris acetate pH 7.5 (Sigma T1258), 10mM magnesium acetate (Sigma 63052), 50mM potassium acetate (Sigma 95843), 0.67% Tween-20 (Sigma P2287), 0.67% Igepal (Sigma I8896), 0.67mg/ml proteinase K (Roche 03115828001). Proteinase K digestion was performed at 42 °C for 4 hours in a thermoblock with heated lid, followed by heat inactivation for 10 minutes at 80 °C. In the following steps, reagents were added with an Eppendorf Mulipipette plus mounted with a 0.1 ml Combitip. Genomic DNA (gDNA) was digested for 4 hours by the addition of DpnI (1 unit) in 7μl 1* One-Phor-all-buffer plus (10mM Tris acetate, pH7.5, 10mM magnesium acetate, 50mM potassium acetate) at 37 °C, followed by heat inactivation at 80 °C for 20 minutes. Adaptor ligation was performed by the addition of 10μl ligation mix (2* Roche T4 ligation buffer, 0.5 units T4 ligase, 50μM double-stranded DamID adapter {Vogel, 2007, 17545983}) and incubated at 16 °C over night. Heat inactivation at 65 °C for 10 minutes the next day was followed by PCR amplification by the addition of 30 μl PCR mix (5 μl 10* Clontech Advantage cDNA reaction buffer, 4 μl dNTPs (2.5mM each), 1.25 μl primer (50 μM), 1 μl PCR advantage enzyme mix (50*) and 18.75 μl H2O).  The PCR reaction was performed with 21 extension steps as described in Vogel et al., 2008, Nature Protocols. The PCR primer consists of an additional 4 random nucleotides at the 5' end to meet the Illumina software requirements of generating reads with diverse starting sequences. Of the PCR material 8μL was submitted to standard 1% agarose gel electrophoresis for analytical purpose and the successfully amplified material was purified by column purification (Qiagen PCR purification kit). Next the samples were prepared for Illumina sequencing.
Of 1μg purified PCR product the 3’ or 5’ overhanging ends were blunted in a 50μl reaction following the manufacturers intructions (End-It DNA End-Repair Kit, Epicentre). Next, a 3’ adenine was added by incubation of the DNA at 37°C in a 50 μL reaction mix (1* New Engeland Biolabs restriction buffer 2, 200μM dATP, nuclease-free water) containing klenow 3′ → 5′ exo– (New Engeland Biolabs, 100 units final concentration). After incubating the samples for 45 minutes, the DNA was purified with 1.6X Agencourt AMPure XP beads (Beckman Coulter). To 250 μg of purified DNA Illumina Y-shaped adapters were ligated for two hours at room temperature in a 10μl reaction mix (1* Roche ligation buffer, 0.25 units T4 DNA (Roche 5units/μl, 50μM Y-adapter, nuclease-free water). Next, the T4 ligase reaction was heat inactivated at 65 °C for 10 minutes followed by DNA purification as described for the previous step. For the addition of the Illumina index primers a PCR reaction was performed with 100 ng DNA from the previous step in a 20 μl MyTaq red DNA polymerase (Bioline BIO21110) PCR reaction mixture (10μl 1* MyTaq reaction mixture, 0.25 μM Illumina P5 primer, 0.25 μM Illumina indexing primer, nuclease-free H2O). The DNA was amplified for 8 PCR amplification cycles (94 °C 1 minute, 94 °C 30 seconds, 58 °C 30 seconds and 72 °C for 30 seconds) after which 5 μl of each sample was analysed by agarose gel electrophoresis. For Illumina multiplex sequencing typically between 40 and 50 samples were mixed in equimolar ratios based on the agarose gel image.

treatment_protocol: Fifteen hours prior harvesting single cells Dam methylation was induced by treating the cells with 0.5 nM Shield1 (ClonTech) then collected in low serum medium (1%) and sorted on a BD FACSAria I (Becton Dickinson) based on cell size and expression of both Fucci markers.

tag: ploidy

tag: dam fusion


title: KBM7 cell line, clone 14, diploid, sample 050


title: KBM7 cell line, clone 14, diploid, sample 052


title: PBX3-chip-seq

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using BWA.
Uniquely mapped reads with mapping quality >=20 were retrieved for downstream analysis.
Peaks were called using MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: text file with called peaks and a tar archive with wiggle files

source_name: SMMC-7721 overexpressing PBX3

extract_protocol:
Cell lysates were clarified from sonicated nuclei and PBX3-DNA complexes were isolated with PBX3 antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: The SMMC-7721 cells were transfected by PBX3 Lentivirus.

tag: chip antibody

value: PBX3 (Abcam ab109173, lot/batch number GR-46727-7)


title: KBM7 cell line, clone 14, diploid, sample 048


title: KBM7 cell line, clone 14, diploid, sample 047


title: wtt1_15100


title: KBM7 cell line, clone 14, diploid, sample 045


title: KBM7 cell line, clone 14, diploid, sample 046


title: KBM7 cell line, clone 14, diploid, sample 044


title: Healthy Control PMN from Donor 1 isolated by negative selection, GM-CSF treated


title: KBM7 cell line, clone 14, diploid, sample 041


title: KBM7 cell line, clone 14, diploid, sample 043


title: KBM7 cell line, clone 14, diploid, sample 042


title: Healthy Control PMN from Donor 2 isolated by Polymorphprep, untreated


title: KBM7 cell line, clone 14, diploid, sample 037


title: KBM7 cell line, clone 14, diploid, sample 038


title: KBM7 cell line, clone 14, diploid, sample 039


title: KBM7 cell line, clone 14, diploid, sample 033


title: KBM7 cell line, clone 14, diploid, sample 034


title: KBM7 cell line, clone 14, diploid, sample 035


title: KBM7 cell line, clone 14, diploid, sample 032


title: KBM7 cell line, clone 14, diploid, sample 049


title: KBM7 cell line, clone 14, diploid, sample 031


title: KBM7 cell line, haploid, biological replicate 1


title: KBM7 cell line, clone 14, diploid, sample 024


title: KBM7 cell line, clone 14, diploid, sample 026


title: KBM7 cell line, clone 14, diploid, sample 040


title: KBM7 cell line, clone 14, diploid, sample 025


title: KBM7 cell line, clone 14, diploid, sample 030


title: KBM7 cell line, clone 14, diploid, sample 029


title: KBM7 cell line, clone 14, diploid, sample 028


title: KBM7 cell line, clone 14, diploid, sample 023


title: KBM7 cell line, clone 14, diploid, sample 036


title: KBM7 cell line, clone 14, diploid, sample 018


title: KBM7 cell line, clone 14, diploid, sample 019


title: KBM7 cell line, clone 14, diploid, sample 020


title: KBM7 cell line, clone 14, diploid, sample 015


title: KBM7 cell line, clone 14, diploid, sample 027


title: KBM7 cell line, clone 14, diploid, sample 017


title: KBM7 cell line, clone 14, diploid, sample 013


title: KBM7 cell line, clone 14, diploid, sample 014


title: KBM7 cell line, clone 14, diploid, sample 012


title: KBM7 cell line, clone 14, diploid, sample 021


title: P. croceum MMN 1

city: Lund

first: Anders

last: Tunlid

address: Sölvegatan 37

institute: Lund University

description: processed_data file = PIC_DE.tab

data_processing:
Genome sequences and annotations files in GFF-format were downloaded from the Joint Genome Insitute, JGI, at http://genome.jgi.doe.gov/. The format of these files are not accepted by the mapping software TopHat2 2.0.8b [1]. A custom made script was run to reformat the files (available on request).
TopHat2 was run with the settings: -T -x 1 -I 5000
The output file in BAM-format was sorted on positions with SAMtools 0.1.19-44428cd [2].
To count the number of reads mapping to genes the software htseq-count 0.5.4p3 [3] was run with the following parameters: -m intersection-nonempty -i gene_id -t CDS
The R package DESeq 1.10.1 [4] was used to normalize the raw read counts of each species and to identify differentially expressed genes, between FH and MMN, with a Benjamini-Hochberg adjusted p-value of < 0.01.
The Proteinortho 4.26 tool [5] was used with default settings to identify one-to-one orthologs in all nine species. The raw read counts of the orthologs were normalized using DESeq 1.14.0.
References:
[1] Kim D, et al. (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14(4):R36.
[2] Li H, et al.; 1000 Genome Project Data Processing Subgroup (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25(16):2078–2079.
[3] Anders S, Pyl PT, Huber W (2014) HTSeq – a Python framework to work with high-throughput sequencing data. Bioinformatics. doi:10.1093/bioinformatics/btu638
[4] Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11(10):R106.
[5] Lechner M, et al. (2011) Proteinortho: detection of (Co-)orthologs in large-scale analysis. BMC Bioinformatics 12(1):124.
Supplementary_files_format_and_content: The tar archive "all_species_DE.tab.tar.gz" contains the  tab-delimited files "*_DE.tab" with the following columns: Joint Genome Institute (JGI) gene model names, JGI protein IDs, normalized read counts for each of the replicates, fold change values between FH versus MMN, p values and p values adjusted for multiple testing with the Benjamini-Hochberg procedure; The tab-delimited file "Orthologs_Expression_Values.tab" contains ortholog IDs and the normalized expression values of the proteins in each ortholog group; The tab-delimited file "Orthologs_Protein_IDs.tab" contains ortholog IDs and the JGI protein IDs of the nine species in each ortholog group.

organism: Piloderma croceum

source_name: Mycelium_Piloderma croceum

growth_protocol: Nine fungal species were analyzed including five ECM and four BR fungi. The fungi were grown in Petri dishes on a layer of glass beads immersed in MMN medium. After 9 days of incubation (18 °C and in the dark), the MMN medium was removed with a sterile pipette. The glass beads and the mycelia were washed with 10 ml of sterile MilliQ (MQ) water, and 10 ml of MMN medium without N was added to induce an N-deprived mycelium. After 24 h the mycelium was again washed in MQ water, and finally the organic matter extracts (10 ml) were added. The organic matter extracts were supplemented with glucose to a final concentration similar to that in the MMN medium. The fungi were grown in either the MMN or the organic matter medium using three replicates, respectively. The cultures were incubated for seven days at 18 °C in the dark.

extract_protocol:
Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen) with the RLC buffer and the on-column DNase treatment according to the manufacturer. Total RNA was eluted in H2O and stored at -20°C until use. For quality assessments all samples were inspected using a RNA 6000 Nano kit on a 2100 Bioanalyzer (Agilent).
TruSeq mRNA-seq sample prep kit (Illumina)

treatment_protocol: The fungi were grown on either a minimum Melin-Norkrans medium (MMN) as a reference or a forest-hot litter extract (FH).

tag: tissue

value: Mycelium

tag: substrate

value: MMN

tag: barcode

value: GTGGCC

tag: genome build

value: Piloderma croceum F 1598 v1.0 (http://genome.jgi-psf.org/Pilcr1/Pilcr1.home.html)


title: P. croceum FH 1

description: processed_data file = PIC_DE.tab

value: FH

value: ACTTGA


title: P. croceum MMN 2

description: processed_data file = PIC_DE.tab

value: CGATGT


title: P. croceum FH 2

description: processed_data file = PIC_DE.tab

value: GATCAG


title: P. croceum FH 3

description: processed_data file = PIC_DE.tab

value: GTGAAA


title: KBM7 cell line, clone 14, diploid, sample 011


title: KBM7 cell line, clone 14, diploid, sample 009


title: KBM7 cell line, clone 14, diploid, sample 016


title: KBM7 cell line, clone 14, diploid, sample 022


title: RPF-siKrr1-3

city: Seoul

first: Joha

last: Park

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

description:
ribosome profiling
rRNA-depleted RNA

data_processing:
Sequence preprocess using FASTX_TOOLKIT. Firstly, fastq_quality_trimmer was applied with the minimum PHRED quality of 20. Next, 3' adapter sequence (TGGAATTCTCGGGTGCCAAGG) is clipped and low quality reads are discarded by fastq_quality_filter with the parameter of -q 20 -p 95. Lastly, reads are filtered by fastq_artifacts_filter.
Genome alignment. STAR aligner was used for mapping reads to mm10 mouse genome. Only uniquely mapped reads are used for the quantification
Counting reads. HTSeq-count is used to count reads mapped to the reference annotations. Illumina iGenome is given as reference annotations.
Genome_build: mm10
Supplementary_files_format_and_content: Raw read counts. tab-delimited text.

source_name: R1 mESC

growth_protocol: R1 mouse embryonic stem cells were maintained on 0.1% gelatin-coated dishes with ESC media (DMEM containing 15% FBS (Gibco), 1X nonessential amino acids (Gibco), 100 uM 2-mercaptoethanol (Sigma), and 1000 U/ml LIF (Millipore)).

extract_protocol: RNA-seq and Ribosome profiling libraries were prepared as described previously (Cho et al. 2012), according to the protocol of ARTseq Ribosome Profiling Kit (Epicentre) with minor modifications. Briefly, cell lysates were divided equally for RNA-seq library and ribosome profiling library. Lysates were digested by RNase I (Ambion) and gel purified in the range of 30 nt for ribosome profiling or 40-60 nt for RNA-seq library. The purified RNAs were subjected to reverse-transcription, after ligated with 3′ and 5′ adapter. The cDNA was used as a template for PCR amplification using Phusion polymerase (NEB). Reactions were separated by acrylamide gel and purified again. Quantify and characterize the purified cDNA libraries using bioanalyzer (Agilent) and Kapa library quantification kit, respectively. The libraries were sequenced on Illumina HiSeq 2000 (multiplexing 50 base single-end). All adapters and primers were synthesized by IDT.

treatment_protocol: R1 cells were transfected with 3 different control siRNAs and 3 different siRNAs targeting Krr1 for 48 hrs.

tag: cell type

value: embryonic stem cell


title: KBM7 cell line, clone 14, diploid, sample 007


title: KBM7 cell line, clone 14, diploid, sample 008


title: RPF-siKrr1-2

description:
ribosome profiling
rRNA-depleted RNA


title: RPF-siKrr1-1

description:
ribosome profiling
rRNA-depleted RNA


title: KBM7 cell line, clone 14, diploid, sample 006


title: RPF-Lipo

description:
ribosome profiling
rRNA-depleted RNA


title: KBM7 cell line, clone 14, diploid, sample 003


title: KBM7 cell line, clone 14, diploid, sample 005


title: P. croceum MMN 3

description: processed_data file = PIC_DE.tab

value: TTAGGC


title: RPF-siGFP

description:
ribosome profiling
rRNA-depleted RNA


title: KBM7 cell line, clone 14, diploid, sample 010


title: KBM7 cell line, clone 14, diploid, sample 002


title: RNAseq-siKrr1-3

description:
RNA-Seq
rRNA-depleted RNA


title: RNAseq-siKrr1-2

description:
RNA-Seq
rRNA-depleted RNA


title: KBM7 cell line, clone 14, diploid, sample 004


title: KBM7 cell line, clone 14, diploid, sample 001


title: KBM7 cell line, clone 14, haploid, sample 123

data_processing:
Basecalling and filtering were performed using standard software of the Illumina HiSeq 2000.
The 51bp reads are first parsed (using custom scripts and cutadapt {Martin, 2011, http://dx.doi.org/10.14806/ej.17.1.200}) to extract the different parts, i.e. the first 4 random bases (included to make cluster calling on the Illumina Hi-seq 2000 possible), 15bp of adapter sequence, and a stretch of gDNA starting with the GATC site. The gDNA sequences are aligned to the reference genome (hg19, chromosomes 1-22, X, Y, and M) using bowtie2 version 2.1.0, using the --very-sensitive mode and otherwise default parameters. Reads that did not align or aligned more than once were discarded. The remaining reads are assigned to GATC-fragments using a custom R-script. Only reads that precisely flanked a GATC site were associated with GATC-fragments, all other reads were discarded. Because single haploid cells have only one copy of any GATC fragment., multiple reads aligning to the same position must have originated from the same molecule and are therefore counted as one. These reads were then aggregated in genomic segments of 100kb.
Next, the number of mappable unique reads per 100kb segment was divided by the maximum possible number of unique reads, which is determined by the total number of GATC motifs in the segment with uniquely mappable flanking sequences.  To determine these numbers we performed an in silico DnpI digest of the complete genomic reference sequence (chromosomes 1-22, X, Y, and M), defined the complete set of potential DamID-seq reads of 32bp length, and aligned these reads back to the reference genome using the same method and filter criteria as we used for the experimental reads (see above). We then summed the number of unique GATC-flanking reads for each 100kb segment.  Finally, the observed over expected read counts per 100 kb segment (OE) was calculated by taking the ratio of the two counts, and normalizing this ratio for the total number of observed (i.e. unique) reads.
Genome_build: hg19
Supplementary_files_format_and_content: OE values in 100kb windows

source_name: KBM7 cell line, clone 14, haploid

extract_protocol:
Based on the FCS and SSC profiles the 2% smallest cells that were double positive for the Fucci markers were single cell sorted in a PCR plate containing lysis buffer and proteinase K (Costar Thermowell). Each well contained 1μl of pick buffer (50mM Tris-HCl pH 8.3, 75mM KCl, 3mM MgCl2, 137mM NaCl) and 2μl of lysis buffer with proteinase K (10mM Tris acetate pH 7.5 (Sigma T1258), 10mM magnesium acetate (Sigma 63052), 50mM potassium acetate (Sigma 95843), 0.67% Tween-20 (Sigma P2287), 0.67% Igepal (Sigma I8896), 0.67mg/ml proteinase K (Roche 03115828001). Proteinase K digestion was performed at 42 °C for 4 hours in a thermoblock with heated lid, followed by heat inactivation for 10 minutes at 80 °C. In the following steps, reagents were added with an Eppendorf Mulipipette plus mounted with a 0.1 ml Combitip. Genomic DNA (gDNA) was digested for 4 hours by the addition of DpnI (1 unit) in 7μl 1* One-Phor-all-buffer plus (10mM Tris acetate, pH7.5, 10mM magnesium acetate, 50mM potassium acetate) at 37 °C, followed by heat inactivation at 80 °C for 20 minutes. Adaptor ligation was performed by the addition of 10μl ligation mix (2* Roche T4 ligation buffer, 0.5 units T4 ligase, 50μM double-stranded DamID adapter {Vogel, 2007, 17545983}) and incubated at 16 °C over night. Heat inactivation at 65 °C for 10 minutes the next day was followed by PCR amplification by the addition of 30 μl PCR mix (5 μl 10* Clontech Advantage cDNA reaction buffer, 4 μl dNTPs (2.5mM each), 1.25 μl primer (50 μM), 1 μl PCR advantage enzyme mix (50*) and 18.75 μl H2O).  The PCR reaction was performed as described {Vogel, 2007, 17545983} with 21 extension steps The PCR primer consists of an additional 4 random nucleotides at the 5' end to meet the Illumina software requirements of generating reads with diverse starting sequences. Of the PCR material 8μL was submitted to standard 1% agarose gel electrophoresis for analytical purpose and the successfully amplified material was purified by column purification (Qiagen PCR purification kit). Next the samples were prepared for Illumina sequencing.
Of 1μg purified PCR product the 3’ or 5’ overhanging ends were blunted in a 50μl reaction following the manufacturers intructions (End-It DNA End-Repair Kit, Epicentre). Next, a 3’ adenine was added by incubation of the DNA at 37°C in a 50 μL reaction mix (1* New Engeland Biolabs restriction buffer 2, 200μM dATP, nuclease-free water) containing klenow 3′ → 5′ exo– (New Engeland Biolabs, 100 units final concentration). After incubating the samples for 45 minutes, the DNA was purified with 1.6X Agencourt AMPure XP beads (Beckman Coulter). To 250 μg of purified DNA Illumina Y-shaped adapters were ligated for two hours at room temperature in a 10μl reaction mix (1* Roche ligation buffer, 0.25 units T4 DNA (Roche 5units/μl, 50μM Y-adapter, nuclease-free water). Next, the T4 ligase reaction was heat inactivated at 65 °C for 10 minutes followed by DNA purification as described for the previous step. For the addition of the Illumina index primers a PCR reaction was performed with 100 ng DNA from the previous step in a 20 μl MyTaq red DNA polymerase (Bioline BIO21110) PCR reaction mixture (10μl 1* MyTaq reaction mixture, 0.25 μM Illumina P5 primer, 0.25 μM Illumina indexing primer (Table S2), nuclease-free H2O). The DNA was amplified for 8 PCR amplification cycles (94 °C 1 minute, 94 °C 30 seconds, 58 °C 30 seconds and 72 °C for 30 seconds) after which 5 μl of each sample was analysed by agarose gel electrophoresis. For Illumina multiplex sequencing typically between 40 and 50 samples were mixed in equimolar ratios based on the agarose gel image.

treatment_protocol: Fifteen hours prior harvesting single cells Dam methylation was induced by treating the cells with 0.5 nM Shield1 (ClonTech) then collected in low serum medium (1%) and sorted on a BD FACSAria I (Becton Dickinson) based on cell size and expression of both Fucci markers {Sakaue-Sawano, 2008, 18267078}.


title: RNAseq-siKrr1-1

description:
RNA-Seq
rRNA-depleted RNA


title: RNAseq-Lipo

description:
RNA-Seq
rRNA-depleted RNA


title: KBM7 cell line, clone 14, haploid, sample 120


title: KBM7 cell line, clone 14, haploid, sample 119


title: RNAseq-siGFP

description:
RNA-Seq
rRNA-depleted RNA


title: KBM7 cell line, clone 14, haploid, sample 122


title: KBM7 cell line, clone 14, haploid, sample 121


title: KBM7 cell line, clone 14, haploid, sample 117


title: 6-OHDA En2 SNpc

city: Paris

first: Hocine

last: Rekaik

address: 11, Place Marcelin Berthelot

department: CIRB

institute: College de France

data_processing:
Reads were filtered and mapped with Bowtie using the following parameters -n 2 -l 28 -e 70 -k 2 –best. Unmapped reads were removed and expression levels for Ensembl-annoted genes were estimated using htseq-count with the following parameters –m union –s yes –t exon. Differentially expressed genes  between wt and En1+/- samples were obtained using DESeq package version 1.8.3.
The annotated_expression_*.xlsx and Reads_count_*.xlsx files were generated by htseq-count.  The annotated_expression_*.xlsx files contain additional columns referring to genes annotation.
Supplementary_files_format_and_content: Reads_count_6OHDA_En.xlsx = Excel file containing genes expression level
Supplementary_files_format_and_content: annotated_diffana_6-OHDA-6-OHDA_En.xlsx = Excel file containing DESeq output for 6-OHDA and 6-OHDA/En differential expression
Genome_build: mm10

source_name: SNpc cells

extract_protocol:
Total RNA was extracted using Qiiagen RNeasy Lipid Tissue Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For Engrailed rescue experiments, a solution (2 µl) of bacterial recombinant En2 (300 ng; 4 µM) and colominic acid (3 µg) (Sonnier et al., 2007) or vehicle (NaCl 0.9%) was injected 30 min after 6-OHDA injection. SNpc tissue was obtained by performing 1 mm punches from 2 mm thick frozen coronal slices.

value: substantianigra pars compacta (SNpc)

tag: age

value: 8 weeks

value: wt

tag: protocol

value: 6-OHDA En2 injection


title: 6-OHDA SNpc

data_processing:
Reads were filtered and mapped with Bowtie using the following parameters -n 2 -l 28 -e 70 -k 2 –best. Unmapped reads were removed and expression levels for Ensembl-annoted genes were estimated using htseq-count with the following parameters –m union –s yes –t exon. Differentially expressed genes  between wt and En1+/- samples were obtained using DESeq package version 1.8.3.
The annotated_expression_*.xlsx and Reads_count_*.xlsx files were generated by htseq-count.  The annotated_expression_*.xlsx files contain additional columns referring to genes annotation.
Supplementary_files_format_and_content: Reads_count_6OHDA.xlsx = Excel file containing genes expression level
Genome_build: mm10

value: 6-OHDA injection


title: KBM7 cell line, clone 14, haploid, sample 118


title: RPF-siNC

description:
ribosome profiling
rRNA-depleted RNA


title: KBM7 cell line, clone 14, haploid, sample 116


title: KBM7 cell line, clone 14, haploid, sample 115


title: KBM7 cell line, clone 14, haploid, sample 113


title: KBM7 cell line, clone 14, haploid, sample 114


title: En2 infusion contra SNpc

description: annotated_diffana_gain-of-function_En1-ipsi-contra.xlsx

data_processing:
Reads were filtered and mapped with Bowtie using the following parameters -n 2 -l 28 -e 70 -k 2 –best. Unmapped reads were removed and expression levels for Ensembl-annoted genes were estimated using htseq-count with the following parameters –m union –s yes –t exon. Differentially expressed genes  between wt and En1+/- samples were obtained using DESeq package version 1.8.3.
The annotated_expression_*.xlsx and Reads_count_*.xlsx files were generated by htseq-count.  The annotated_expression_*.xlsx files contain additional columns referring to genes annotation.
Supplementary_files_format_and_content: annotated_expression_LMD-SNpc-+-En1-contra.xlsx = Excel file containing genes expression level
Genome_build: mm10

treatment_protocol: For Engrailed gain of function, the protein was infused unilaterally (Ipsi side) using osmotic pumps (7 days). mDA neurons in the SNpc labeled using the quick TH-staining protocol (Chung et al., 2005) were isolated by Laser Capture Microdissection (LMD7000, Leica).

value: En2 infusion contra


title: En1+/- SNpc

data_processing:
Reads were filtered and mapped with Bowtie using the following parameters -n 2 -l 28 -e 70 -k 2 –best. Unmapped reads were removed and expression levels for Ensembl-annoted genes were estimated using htseq-count with the following parameters –m union –s yes –t exon. Differentially expressed genes  between wt and En1+/- samples were obtained using DESeq package version 1.8.3.
The annotated_expression_*.xlsx and Reads_count_*.xlsx files were generated by htseq-count.  The annotated_expression_*.xlsx files contain additional columns referring to genes annotation.
Supplementary_files_format_and_content: annotated_expression_LMD-En1-+---SNpc.xlsx = Excel file containing genes expression level
Supplementary_files_format_and_content: annotated_diffana_loss-of-function_En1LacZ-WT.xlsx = Excel file containing DESeq output for wt vs En1+/- differential expression
Genome_build: mm10

treatment_protocol: mDA neurons in the SNpc labeled using the quick TH-staining protocol (Chung et al., 2005) were isolated by Laser Capture Microdissection (LMD7000, Leica).

value: 6 weeks


title: Wt SNpc

description: annotated_diffana_loss-of-function_En1LacZ-WT.xlsx

data_processing:
Reads were filtered and mapped with Bowtie using the following parameters -n 2 -l 28 -e 70 -k 2 –best. Unmapped reads were removed and expression levels for Ensembl-annoted genes were estimated using htseq-count with the following parameters –m union –s yes –t exon. Differentially expressed genes  between wt and En1+/- samples were obtained using DESeq package version 1.8.3.
The annotated_expression_*.xlsx and Reads_count_*.xlsx files were generated by htseq-count.  The annotated_expression_*.xlsx files contain additional columns referring to genes annotation.
Supplementary_files_format_and_content: annotated_expression_LMD-En1-WT-SNpc.xlsx = Excel file containing genes expression level
Genome_build: mm10


title: KBM7 cell line, clone 14, haploid, sample 112


title: RNAseq-siNC

description:
RNA-Seq
rRNA-depleted RNA


title: Newborn naïve [small RNA_Illumina]

description: processed data: Mirdeep_output_Illumina_updated.txt

data_processing:
miRNAs were aligned using Mirdeep2's mapper.pl script to Mirbase's version 21 database of miRNAs using options -d -e -h -i -j -l 18 -m
Known miRNAs were quantified using Mirdeep2's quantifier.pl script using the option -d
Genome_build: mm9
Supplementary_files_format_and_content: Text file contains read counts for each miRNA for each sample

source_name: CD8+ T cells

extract_protocol:
Cells were isolated into Trizol, stored at -80, then RNA was extracted according to the standard Trizol protocol.
450 ng of total RNA was used with the Illumina TruSeq Small RNA Sample Preparation kit. kit. Libraries were sequenced on a Hi-Seq 2000, generating 50 bp reads.

tag: cell state

value: Naïve

tag: animal age

value: 1 day

value: CD8+ T cells


title: Neonatal 15-dpi [RNA-seq]

description: Naïve CD8+ T cells from a neonatal donor were transferred into an adult recipient which was infected with Listeria, and the donor cells were isolated 15 days later

data_processing:
We trimmed off nucleotides from the ends if they had Phred quality scores <20
Reads that were at least 20 nt long after trimming were aligned to the genome using Tophat
Differential expression of genes between samples was determined using CuffDiff
Genome_build: mm9
Supplementary_files_format_and_content: Text file with the FPKM value and differential expression information for all coding genes that have an FPKM >1 in at least one sample

extract_protocol:
Cells were sorted into Trizol, stored at -80, then RNA was extracted according to the standard Trizol protocol.
25-100 ng of total RNA were used to generate libraries using the RNA Sample Preparation Kit v2 (Illumina)

treatment_protocol: For the effector CD8+ T cells, they were isolated from adult and neonatal mice, then transferred into a recipient adult mouse which was infected with Listeria. Five, seven, and fifteen days later, the cells were sorted.

value: Late effector (15dpi)

value: 6-7 days


title: KBM7 cell line, clone 14, haploid, sample 111


title: KBM7 cell line, clone 14, haploid, sample 109


title: KBM7 cell line, clone 14, haploid, sample 108


title: En2 infusion ipsi SNpc

data_processing:
Reads were filtered and mapped with Bowtie using the following parameters -n 2 -l 28 -e 70 -k 2 –best. Unmapped reads were removed and expression levels for Ensembl-annoted genes were estimated using htseq-count with the following parameters –m union –s yes –t exon. Differentially expressed genes  between wt and En1+/- samples were obtained using DESeq package version 1.8.3.
The annotated_expression_*.xlsx and Reads_count_*.xlsx files were generated by htseq-count.  The annotated_expression_*.xlsx files contain additional columns referring to genes annotation.
Supplementary_files_format_and_content: annotated_expression_LMD-SNpc-+-En1-ipsi.xlsx = Excel file containing genes expression level
Supplementary_files_format_and_content: annotated_diffana_gain-of-function_En1-ipsi-contra.xlsx = Excel file containing DESeq output for En2 infusion differential expression
Genome_build: mm10

tag: genotype

value: En2 infusion ipsi


title: Neonatal 7-dpi [RNA-seq]

description: Naïve CD8+ T cells from a neonatal donor were transferred into an adult recipient which was infected with Listeria, and the donor cells were isolated 7 days later

value: Peak effector (7dpi)


title: Neonatal 5-dpi [RNA-seq]

description: Naïve CD8+ T cells from a neonatal donor were transferred into an adult recipient which was infected with Listeria, and the donor cells were isolated 5 days later

value: Early effector (5dpi)


title: KBM7 cell line, clone 14, haploid, sample 106


title: Neonatal naïve [RNA-seq]


title: KBM7 cell line, clone 14, haploid, sample 105