title: Larval stage 3 replicate C

status: Public on Jul 30 2017

city: Stanford

first: Aaron

middle: C

last: Daugherty

state: California

address: 300 Pasteur Dr

department: Genetics

institute: Stanford University

description: replicate C

data_processing:
Sequencing adaptors were trimmed using a custom script that aligns the 5’ ends of the forward read and reverse complement of the reverse read, and then removes any aligning sequence (minimum length 3).
All reads were aligned to the ce10 version of the C. elegans genome, including mitochondrial sequence, with bowtie2 (v2.1.0) with the following settings: --end-to-end, --no-mixed, and -X 2000.  Next, all samples were filtered for mapping quality (MAPQ >= 30) and PCR duplicates were marked using Picard tools (Broad Institute 2014), and subsequently removed
Every read was then adjusted for the binding footprint of Tn5 (9 bp) as previously described (Buenrostro et al. 2013); specifically reads were shifted 4 (positive strand) or 5 (negative strand) bp 5’ relative to the reference genome. Finally, to give optimal single-base resolution, reads were trimmed to the single 5’-most-base.
For every replicate, prior to calling peaks with MACS(Zhang et al. 2008) (v2.1), single-base reads were shifted 75bp 5’ to mimic read distributions of a 150 bp fragment of ChIP-seq, thereby allowing use of MACS. The following settings were used for MACS: -g 9e7, -q 5e-2, --nomodel, --extsize 150, -B, --keep-dup all, and --call-summits.  The resulting peaks included a portion that had multiple summits; in order to maximize our resolution these summits were subsequently separated into individual peaks by treating the midpoint between the two adjacent summits as the 5’ and 3’ end of each individual peak, respectively.
To identify only the most high-confidence set of peaks, peaks were called for each individual experimental replicate, as well as for pooled replicates from each stage (i.e. all single base pair reads for that stage, regardless of biological replicate), and for two pseudoreplicates which were generated by randomly splitting the pooled samples in half. Consensus peaks for each stage were then classified as any peaks called in the pooled-replicate sample that were at least 50% overlapping A) all biological replicates or B) both pseudoreplicates and at least 2 of the 3 biological replicates.
Genome_build: ce10

organism: Caenorhabditis elegans

source_name: whole organisms

growth_protocol: To synchronize the parents of each sample, well-fed mixed stage N2 worms from one 10cm or three 6cm plate(s) (approximately 500 worms) were treated with 10% bleach for 4 min to isolate early embryos (as described in Wormbook).  The resulting embryos (approximately 800) were grown to adulthood on 2-3 10cm plates.  As soon as the worms reached adulthood, they were placed on fresh 10cm plates at a density of approximately 100 worms per plate for synced egg-laying. After 45 min, the adults were removed, and the plates were returned to 20°C to allow the embryos to grow to the desired stages.  To collect the embryos, the egg-laying adults were collected, and approximately 50 ml of packed adults were washed once with M9 medium and bleached to yield early embryos as described in Wormbook.  Following the last wash after bleaching, the embryos were left in 100ml of M9 medium, and the tubes flash frozen in liquid nitrogen and kept at -80°C. The parents were also flash frozen and kept for providing genomic DNA controls. To collect larval stage 3 (L3) worms, plates were repeatedly checked after egg-laying to ensure no parents had remained.  36 hr after the start of the egg lay, L3 animals were collected from 2 of the 6 plates. Finally, 57 hr post egg lay one of the remaining plates was checked every 10 min to ensure that the majority of the plate was composed of young adult animals with no more than 1-2 eggs. At that point young adult animals were harvested. Immediately after collection, all worm samples were washed twice with M9 before being flash frozen and stored at -80°C.

extract_protocol:
Nuclei were purified from frozen samples as described (Haenni et al. 2012). Briefly, samples were thawed on ice, and then mixed with 150 ml of 2X nuclei purification buffer (20mM Hepes pH 7.6, 20mM KCl, 3mM MgCl2, 2mM EGTA, 0.5 M Sucrose, 0.05% Triton, 1mM DTT, 0.05M NaF, 40mM b-glycerophosphate, 2mM Na3VO4).  The samples were then transferred to a Wheaton stainless-steel homogenizer and were homogeneized with 3 plunger strokes.  The resulting samples were centrifuged at 200 g for 1 min to remove worm debris.  The supernatant was transferred to a fresh tube, and the remaining pellet was resuspended in 150 ml of 2X nuclei purification buffer and homogenized as described above.  The process was repeated until no visible pieces of worm remained (approximately 5 times).  The pooled supernatants were centrifuged at 200 g for 1 min to remove worm debris. Finally, the nuclei were pelleted at 1000 g for 10 min at 4°C. The purified nuclei were immediately used for the ATAC-seq protocol.
Briefly, the nuclei were resuspended in 47.5 ml of Nextera Tagmentation buffer (Nextera DNA Sample Preparation Kit) and incubated with 2.5 ml of the Tn5 transposase at 37°C for 30 min. Resulting DNA fragments were purified using a miniElute column (Qiagen) and amplified by NEBNext High-Fidelity PCR Master Mix in a total volume of 50 ml. The thermocycling protocol for this reaction was 72°C for 5 min, 98°C for 30 s and 5 cycles of 98°C for 10 s, 63°C for 30 s and 72°C for 1 min.  Every sample shared the Adapter1 primer, and had a unique barcoded Adapter2 primer (Supplemental Table 7).  To ensure over-amplification did not occur, after the initial 5 cycles, the number of remaining cycles required was estimated for each sample using qPCR (BioRad CFX96 Real-Time System).  To do so, a similar reaction to the above was set up (NEBNext, Adapter1 and a single Adapter2), with the addition of SybrGreen, and using 5 ml of the previous PCR as template.  The final volume was 15 ml, and the thermocyling was as above except that the initial incubation step was 98°C for 30 seconds, and 40 cycles were performed. The number of additional cycles was determined to be the number it took for the qPCR to reach one-third maximal fluorescence.  The original PCR was then resumed and each sample cycled as necessary. Following amplification, the samples were purified using QIAquick columns (Qiagen), and library quality was verified on an Agilent bioanalyzer. Sequencing was performed using 101 bp paired-end sequencing on an Illumina Hi-seq 2000.

tag: developmental stage

value: larval stage 3


title: input control

type: SRA

country: USA

description: To generate an input control for ATAC-seq, approximately 100 ml of packed adults was thawed and embryos were collected as described above to avoid any bacterial contamination. Next, genomic DNA was isolated by proteinase K treatment (0.2 mg/ml, 55°C for 3 hr before heat killing the protein at 95°C for 25 min), then RNase treatment (1.25 mg/ml, 37°C for 30 min).  gDNA was purified by double phenol/chloroform/isoamyl alcohol (25:24:1, pH 8.0) extraction, with an additional chloroform extraction, and precipitated with ethanol and NaOAc (3mM, pH 5.5), and resuspended in 50 ml TE (10mM Tris-HCl pH7.5, 1mM EDTA).  The gDNA was quantified using a Qubit, and 10ng used for a standard ATAC-seq protocol as described above.

library_source: genomic

molecule: genomic DNA

tag: strain


title: Young adult replicate C

description: replicate C

value: young adult


title: EGFP_rep1

status: Public on Jul 31 2017

city: Aarhus

first: Evdoxia

last: Karadoulama

address: C.F. Møllers Alle 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

library_source: transcriptomic

data_processing:
The RNA-Seq data was quality controled and trimmed using FastQC and Trimomomatics respectively.
The data was mapped using HISAT against hg19.
Uniquely mapped and properly paired reads were used for downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using Bedtools and bedGraphtoBigWig. The score represents strand specific per base genome coverage.

molecule: total RNA

organism: Homo sapiens

source_name: EGFP(control) total RNA replicate 1

growth_protocol: HeLa cells were cultured in standard DMEM medium supplemented with 10% FBS and penicillin-streptomycin mix.

extract_protocol:
RNA was extracted with Trizol and PureLink RNA Mini Kits (Thermo Scientific) and using on-column DNase I (PureLink DNase; Thermo Scientific) digestion according to the manufacturer’s manual.
Libraries were prepared, after rRNA-depletion using Ribo-Zero™ Magnetic Gold Kit (Human/Mouse/Rat; Illumina), using Illumina TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: siRNA transfections were performed targeting EGFP(control), ARS2, ZC3H18

tag: cell type

value: HeLa Kyoto

tag: transfection

value: EGFP(control)


title: Young adult replicate B

description: replicate B


title: Larval stage 3 replicate B

description: replicate B


title: D3 Egr1+/- E28 OS Close

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: Day3 Egr1+/- eyelid close

data_processing:
Basecalls performed using CASAVA 1.8. Raw reads were aligned to the mm8 genome assembly using Bowtie 0.12.9 or Tophat 2.0.11
Aligned reads are converted to bam format using samtools and RPKM model (reads per kilobase per million reads) was used to normalize gene expression values.
Genome_build: mm8

organism: Mus musculus

source_name: Eyes

growth_protocol: Egr1-/- C57BL/6 mice were from Taconic Farms and genotyping was performed by PCR with primer sequences from Taconic. The mice were backcrossed to BALB/c mice from the Jackson Laboratory for 5 generations in the initial backcross or 4 generations in the second backcross

extract_protocol:
Eyes were enucleated, put into eppendorf tubes filled with RNAlater (Thermo Fisher), and total RNA extracted using the RNeasy Mini Kit (Qiagen). Poly(A)+ RNA was selected twice from total RNA using Dynal oligo magnetic beads (Invitrogen). Double-stranded cDNA was synthesized using SuperScript (Invitrogen) and fragmented using Bioraptor (Diagenode). Adaptors (Illumina) were ligated to the dsDNA using T4 DNA ligase (New England Biolabs) after end-repair using End-It kit (Epicentre) and dA addition. Libraries were size-selected for 250-400 bp fragments, purified using 2% E-Gel (Invitrogen), and amplified for 18 cycles by PCR with PE 1.0 and PE 2.0 primers (Illumina) and Phusion High Fidelity PCR Master Mix.
PCR products were barcoded (indexed) and sequenced on Illumina HiSeq 2000 platform.

treatment_protocol: Eyes including the eyelids from neonatal and adult mice were enucleated and fixed in 4% glutaraldehyde for 30 min, in 10% formalin for >24 hr

value: BALB/c


title: D3 Egr1-/- E29 OD Close

description: Day3 Egr1-/- eyelid close


title: Early Embryo replicate B

description: replicate B

value: early embryo


title: Larval stage 3 replicate A

description: replicate A


title: D3 Egr1+/- E28 OD Close

description: Day3 Egr1+/- eyelid close


title: Young adult replicate A

description: replicate A


title: D3 Egr1-/- E24 OS Close

description: Day3 Egr1-/- eyelid close


title: Early Embryo replicate A

description: replicate A


title: D3 Egr1-/- E24 OD Open

description: Day3 Egr1-/- eyelid open


title: D3 Egr1-/- E29 OS Open

description: Day3 Egr1-/- eyelid open


title: D3 Egr1-/- E32 OS Open

description: Day3 Egr1-/- eyelid open


title: Newborn WT rep2

description: Newborn WT


title: Newborn Egr1KO rep2

description: Newborn Egr1-/-


title: 533536_2

city: Bar Harbor

first: Narayanan

last: Raghupathy

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description:
NOD_exp_75-REL1410_RCF1_NxP_vitaD_expected_counts_emase_m2.txt
PWK_exp_75-REL1410_RCF1_NxP_vitaD_expected_counts_emase_m2.txt

data_processing:
Basecalls were performed with CASAVA version 1.7.0
Fragmented fastq files from CASAVA were concatenated together, and then reads that did not pass quality filtering were removed with fastq_illumina_filter (http://cancan.cshl.edu/labmembers/gordon/fastq_illumina_filter/)
Read Alignment - Diploid transcriptomes (isoform sequences) derived from SNP and Indel adjusted parental genome fasta files (NOD and PWK) and corresponding gene annotation gtf files were used to construct Bowtie-compatible indexes with Bowtie 1.1.2.  The Bowtie aligner (version 1.1.2) was used to align reads to the diploid transcript sequences. Alignments with up to three mismatches (-v 3) were considered valid, but only the best “strata” of alignments were reported. For a given read, the best stratum is the alignment(s) with the least mismatches.
Allele,Isoform,gene,  Abundance Quantitation - Estimates of allele, isoform and gene-level abundance were obtained with EMASE. Bowtie alignment files in .bam format were input into the EMASE. For reads with multiple valid alignments, EMASE mplements an expectation-maximization (EM) algorithm that considers the gene/isoform/allele hierarchy and assigns all or a proportion of each multimapping read to one or more isoforms based on the number of uniquely-aligning reads to those transcripts.
Genome_build: Mouse GrCm38/mm10.
Supplementary_files_format_and_content: All processed data files are tab-deliminited txt files. Each file contains a data matrix with rows representing Ensembl gene id's and columns representing samples for one allele.

source_name: Liver

growth_protocol: We obtained male and female NOD/ShiLtJ (Stock No. 001976) and PWK/PhJ (Stock No. 003715) mice from The Jackson Laboratory (Bar Harbor, ME). Animals were received at 3 to 5 weeks of age, and given free access to food and water.  We fed mice one of two diets from Harlan Teklad Custom Research Diets with matched ingredients with the exception of cholecalciferol. The standard diet contained 0.009 g/Kg and the enriched diet contained 0.050 g/Kg of cholecalciferol. NOD and PWK mice were mated using a reciprocal cross design to obtain 24 male F1 progeny from each cross direction. We euthanized six mice from each cross-by-diet cohort at 15 weeks of age, and the remaining mice were euthanized at age 24 weeks. In total there are eight groups defined by the experimental factors (cross-direction, diet and age) and six biological replicates per group. The Animal Care and Use Committee at JAX approved the procedures in this protocol (AUS \#99057).

extract_protocol:
We collected liver tissue from the 48 F1 mice and stored it in RNAlater (Invitrogen) until processing. We isolated total RNA using the Trizol Plus RNA extraction kit (Life Technologies) with on-column DNase digestion, and purified mRNA from the total RNA using biotin tagged poly dT oligonucleotides and streptavidin beads.
We fragmented mRNA by enzyme digestion, and generated double-stranded cDNA by random hexamer priming. We generated indexed mRNA-Seq libraries from 1micro gram total RNA following the Illumina TruSeq unstranded protocol, and checked quality and quantity of the product using the Agilent Bioanalyzer and the Kapa Biosystems qPCR library quantitation method.

tag: sample

value: PWKxNOD F1

tag: age

tag: genotyped sex

value: Male

tag: diet

value: Vitamin D high

tag: block

tag: flowcell

tag: lane

tag: barcode

value: GCAAAGA


title: 532746_2

value: Vitamin D normal

value: AAGACCT


title: Newborn Egr1KO rep1

description: Newborn Egr1-/-


title: 532762_2

value: CAAGAGA


title: 533406_2

value: ACTTAGG


title: Newborn WT rep1

description: Newborn WT


title: Early Embryo replicate C

description: replicate C


title: 533950_2

value: NODxPWK F1

value: TAGCCTT


title: D3 Egr1-/- E32 OD Open

description: Day3 Egr1-/- eyelid open


title: 533376_2

value: TTCTGTC


title: Adult Egr1KO rep2

description: Adult Egr1-/-


title: Adult Egr1KO rep1

description: Adult Egr1-/-


title: 532720_2

value: CACTGCC


title: 532736_2

value: GTCGTTT


title: Adult WT

description: Adult WT


title: 532760_2


title: 533388_2


title: DM15Q cells, day3, repl 1

city: Pisa

first: Romina

last: D'Aurizio

state: PI

address: via Moruzzi 1

department: IIT

country: Italy

institute: CNR

description:
congenital DM1 myoblast
smallRNAseq
DM15Qd3.r1

data_processing:
Raw sequences were de-multiplexed using the Illumina MiSeq Base-calling software.
Cutadapt v.1.7.1 was used for trimming adapter sequences off the raw reads. Reads with N calls were discarded using FASTX_Toolkit v 0.0.14 and only reads with all base calls showing a Phred score higher than 30 were retained for further analysis.
miRExpress v2.1.4 was exploited to identify pre-miRNA sequences (miRBase v.21) allowing at least 90% of sequence identity and a length tolerance range of 4bp for mapping.
Expression values were normalized to reads per million (rpm).
Genome_build: miRBase v.21
Supplementary_files_format_and_content: Tab-delimited text file including normalized read count per sample.

source_name: DM15Q cells, day3

growth_protocol: 12,000 cells/cm2 were grown in HAM’S/F10 medium with 50 µg/ml Fetuin, 5 µg/ml Insulin, 0.5 mg/ml BSA and 20% FBS to subconflence.

extract_protocol:
RNA was extracted using miRNEasy MINI Kit (Qiagen)
RNA libraries were prepared for sequencing using TruSeq Small RNA Library Preparation Kits (Illumina)

treatment_protocol: Subconfluent cells were shifted to differentiation medium (MEM with 10 µg/ml, insulin, 10 ng/ml EGF and 0.5 mg/ml BSA) were samples at day 0 and day 3

value: fetal muscle myoblast

tag: genotype/variation

value: congenital DM1 (DM15Q)

tag: treatment

value: myoblast in differentiation medium

tag: time


title: DM15Q cells, day3, repl 2

description:
congenital DM1 myoblast
smallRNAseq
DM15Qd3.r2


title: 532744_2


title: 533404_2


title: MCBO  cells, day3, repl 2

description:
congenital DM1 myoblast
smallRNAseq
MCBOd3.r2

source_name: MCBO  cells, day3

value: congenital DM1 (MCBO)


title: MCBO cells, day3, repl 1

description:
congenital DM1 myoblast
smallRNAseq
MCBOd3.r1

source_name: MCBO cells, day3


title: 14SA cells, day3, repl 2

description:
wild type fetal myoblast
smallRNAseq
14SAd3.r2

source_name: 14SA cells, day3

value: wild type (14SA)


title: 533374_2

value: Male


title: 14SA cells, day3, repl 1

description:
wild type fetal myoblast
smallRNAseq
14SAd3.r1


title: 533392_2

value: PWKxNOD F1


title: 532752_2

value: Vitamin D high


title: Rictor_KO

city: Beijing

first: Dan

last: Liu

address: NO.1 Beichen West Road, Chaoyang District

country: China

institute: Beijing Institute of Genomics

data_processing:
RNAseq reads quality was controlled using FastQC version 0.10.1.
Reads were mapped to mm9 genome using TopHat,version 2.0.9.The Python package HTSeq was employed to statistical analyses of read counts.Test for differential expression based on a model using the negative binomial distribution model tools DEseq.
Genome_build: mm9
Supplementary_files_format_and_content: Processed_data_file is in txt format.With the following columns:Ensemble ID ,number of reads(KO),number of reads(WT)

source_name: Embryo tek+cell

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen).
libraries were constructed according to manufacturer's instructions.

value: AGM

tag: in vitro culture

value: 10 days

tag: doxcycline treatment

value: No

tag: genotype

value: Rictorf/f; Tie2-cre


title: DM15Q cells, day 0, repl 1

description:
congenital DM1 myoblast
smallRNAseq
DM15Qd0.r1

source_name: DM15Q cells, day 0

value: subconfluent myoblast

value: day 0


title: 533408_2

tag: strain

value: AAGACCT


title: MCBO  cells, day 0, repl 2

description:
congenital DM1 myoblast
smallRNAseq
MCBOd0.r2

source_name: MCBO  cells, day 0

tag: cell type


title: MCBO cells, day 0, repl 1

description:
congenital DM1 myoblast
smallRNAseq
MCBOd0.r1

source_name: MCBO cells, day 0


title: 533378_2

value: NODxPWK F1

value: CACTGCC


title: Rictor_WT

value: control tek+


title: 533420_2


title: 533362_2

value: Vitamin D normal

value: CAAGAGA


title: 532710_2

value: TTCTGTC


title: 532722_2

value: GCAAAGA


title: 532732_2

value: Male

value: TAGCCTT


title: EXON_gExon4_IL2RA+_72hrs_D2

city: San Francisco

first: Alexander

last: Marson

state: CA

address: 513 Parnassus Ave, HSW 1033

institute: UCSF

data_processing:
Fastq files for paired end sequencing of the IL2RA enhancer and exon edited sites were processed using Trimmomatic8 (leading: 15, trailing: 15, headcrop: 17, sliding window:4:15).
The trimmed fastq files were aligned to the human reference genome using the Burrows Wheeler Aligner (BWA-MEM) algorithm.
The samtools mpileup utility was used to quantify the total number of reads that mapped to each position surrounding the cut sites.
Genome_build: hg19

source_name: primary human naïve CD4+ T cells

extract_protocol:
Genomic DNA was extracted from sorted cells using QuickExtract (Epicentre). PCR amplicons from the edited regions were prepared for next-generation sequencing using a nested PCR strategy. The outer PCR (PCR1) generates a 600-700 bp amplicon using primers outside the region matching the HDR donor template. The inner PCR (PCR2) generates the ~250 bp amplicon to be sequenced.
For PCR1, genomic DNA from 5,000-10,000 sorted cells was amplified using PrimeStar GXL DNA Polymerase (Clontech, Cat. No. R050B) according to the following protocol: 98 °C, 2’; 30 cycles at 98 °C, 10”, 55 °C, 15”, 68 °C, 45”. PCR1 products were purified using SPRI beads and quantified using the Qubit dsDNA HS Assay Kit (Thermo). The purified products of PCR1 (20 ng/sample) were used as templates for PCR2 and amplified using PrimeStar GXL DNA Polymerase according to the following protocol: 98 °C, 2’; 10 cycles at 98 °C, 10”, 60 °C, 15”, 68 °C, 20”. PCR2 products were purified and quantified as done for PCR1. Indexed sequencing libraries were prepared with the TruSeq Nano DNA HT Library Prep Kit (Illumina, Cat. No. FC-121-4001) using 100 ng of purified PCR2 product. Libraries were pooled and 150 bp paired-end sequencing was performed with a MiSeq sequencer (Illumina).
Amplicon Sequencing

value: CD4+ T


title: EXON_gExon4_Bulk_72hrs_D2


title: 532716_2

value: PWKxNOD F1


title: 532754_2

value: Vitamin D high

value: GTCGTTT


title: EXON_gExon4_IL2RA+_72hrs_D1


title: 533380_2


title: 533364_2

value: ACTTAGG


title: EXON_gExon4_Bulk_72hrs_D1


title: EXON_gExon4_IL2RA-_72hrs_D1


title: 532724_2


title: DM15Q cells, day 0, repl 2

description:
congenital DM1 myoblast
smallRNAseq
DM15Qd0.r2

value: fetal muscle myoblast

value: congenital DM1 (DM15Q)

value: subconfluent myoblast


title: EXON_gExon4_IL2RA-_48hrs_D2


title: 533416_2


title: 532714_2


title: 532704_2

value: NODxPWK F1

value: AAGACCT


title: 14SA cells, day 0, repl 2

description:
wild type fetal myoblast
smallRNAseq
14SAd0.r2

source_name: 14SA cells, day 0

value: wild type (14SA)

value: day 0


title: 532702_2

value: Vitamin D normal


title: EXON_gExon4_Bulk_48hrs_D2


title: 533400_2


title: 532758_2

value: CACTGCC


title: 533410_2


title: EXON_gExon4_IL2RA+_48hrs_D1


title: EXON_gExon4_IL2RA-_48hrs_D1


title: EXON_gExon4_Bulk_48hrs_D1


title: 532742_2

value: CAAGAGA


title: EXON_gExon4_IL2RA-_72hrs_D2


title: EXON_gExon4_IL2RA+_24hrs_D2


title: EXON_gScramble_D2


title: 532730_2

value: Male


title: 532708_2


title: 533372_2

value: TAGCCTT


title: EXON_gExon4_IL2RA-_24hrs_D2

value: CD4+ T


title: EXON_gExon4_Bulk_24hrs_D2


title: 533398_2

value: PWKxNOD F1


title: 532756_2

value: Vitamin D high

value: TTCTGTC


title: TrpA_ME2

city: Curitiba

first: Christian

middle: Macagnan

last: Probst

state: PR

address: Rua Professor Algacyr Munhoz Mader, 3775

country: Brazil

institute: Instituto Carlos Chagas

description: Oligo-ME aRNA

data_processing:
Reads were aligned using the SHRIMP2 v2.2.2, with default parameter, except –strata -h 80% --max-alignments 1000
Sample read count normalization was performed by edgeR v. 3.12.0, Bioconductor suite, R v 3.2.3
Genome_build: MBSY00000000
Supplementary_files_format_and_content: Normalized read count for each Trypanosoma cruzi Dm28c gene cluster (SgdmA)

organism: Trypanosoma cruzi

source_name: Trypomastigote stage

growth_protocol: Parasite culture: T. cruzi Dm28c epimastigotes [32] were cultured at 28°C in LITB medium supplemented with 10% heat-inactivated fetal bovine serum (FBS) as previously described [33]. Tissue culture-derivedCell derived trypomastigote forms were obtained by infection of cultured Vero cell (ATCC® CCL-81™) at 37ºC in a humidified 5% CO2 atmosphere using a multiplicity of infection (MOI) of 10 parasites per host cell. Cell derived tTrypomastigotes were recovered after 4 days of infection, in the cell burst peak. HeLa culture: the human derived epithelial cell ATCC® CCL-2™ were grownth in 75 cm2 culture bottles at 37ºC in a humidified 5% CO2 atmosphere using DMEM medium supplemented with 10% FBS. When confluent, cells were detached from the culture flask by enzymatic treatment (0.01% trypsin, 0.1% EDTA in PBS), washed in PBS and passed to new bottles at cell density of 106 HeLa cells for each 75 cm2 culture bottle.

extract_protocol:
Total RNA was extracted from T. cruzi epimastigote and trypomastigote forms (5 × 108 cells) and from confluent HeLa cells with the RNeasy kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions, with an additional on-column DNase digestion step. Total RNA from HeLa cells were obtained from MessageAmpTM II aRNA Amplification Kit from Life Technologies® (#AMB1751-5). RNA integrity was assessed on an Agilent 2100 Bioanalyzer with RNA 6000 Nano LabChip kit, according to the manufacturer’s instructions. Polyadenylated RNA were purified from at least 50 µg of total RNA using PolyA+Track® mRNA Isolation System III from Promega® (#Z5300), according to the manufacturer's instructions. Polyadenylated RNA were purified from at least 50 µg of total RNA using PolyA+Track® mRNA Isolation System III from Promega® (#Z5300), according to the manufacturer's instructions. All mRNA amplification reactions were done using reagents from MessageAmpTM II aRNA Amplification Kit from Life Technologies® (#AMB1751-5). For classic Eberwine amplification method, first-strand cDNA was synthesized using a T7oligo(dT) primer that contains a T7 RNA polymerase promoter upstream to the poly-T tract; this promoter will further direct the in vitro mRNA synthesis (amplification). First, 100 ng of total RNA (in 11 µl) were mixed with first-strand cDNA reaction mix containing 1 µl of T7oligo(dT) primer, 2 µl first-strand buffer, 4 µl dNTPs, 1 µl RNase inhibitor and 1 µl ArrayScript Reverse Transcriptase and incubated for 2 hours at 42ºC. Second-strand cDNA was then synthesized for 2 hours at 16ºC using the total 20 µl first-strand product plus 80 µl of second strand mix containing 63 µl water, 10 µl second-strand buffer, 4 µl dNTPs, 2 µl DNA Polymerase and 1 µl of RNase H. Double-strand cDNA was then purified using PureLink® PCR Micro Kit from Life Technologies (#K310250) according manufacturer’s instructions. Eluted cDNA was adjusted to 16 µl and used as template for amplification reaction in a total volume of 40 µl containing 16 µl NTPs, 4 µl amplification buffer and 4 µl of T7 RNA polymerase; in vitro transcription took 14 hours at 37ºC. Amplified RNA (aRNA) was then purified using RNeasy MinElute CleanUp Kit (Qiagen, #74204), according to the manufacturer’s instructions. For specific amplification of spliced leader containing mRNA, we used a custom designed primer complementary to the last 21 bases of T. cruzi spliced leader (in bold) with an upstream T7 RNA polymerase promoter (in gray) (5'-GGCCAGTGAATTGTAATACG ACTCACTATAGGGAGGCGGTACAGTTTCTGTACTATATTG-3'), which we named T7SL. In this case, T7SL was used for second-strand cDNA synthesis, while first-strand cDNA was produced using random primers, accordingly to the second round amplification protocol of MessageAmpTM II aRNA Kit. Template total RNA was adjusted to 10 µl, mixed with 2 µl of "second round primers" (random primers) and incubated at 70ºC for 10 minutes followed by snap cool on ice to allow annealing of random primers to RNA. Then, 8 µl of reverse transcription master mix was added and first-strand cDNA synthesized at 42ºC for 2 hours. RNase H was added (1 µl) and sample incubated at 37ºC for 30 minutes to specifically degrade the remaining RNA. T7SL primer was added to a final concentration of 1 µM and the sample was incubated at 70ºC for 10 minutes and then placed on ice. Second-strand cDNA master mix without RNase H was added (74 µl) and the reaction incubated for 2 hours at 16ºC. Double-strand cDNA purification, in vitro transcription and aRNA purification was performed as described above.
Total RNA-Seq Kit (Life Technologies, #4445374) was used accordingly to manufacturer instructions. Briefly, RNA was fragmented using RNase III and cleaned up with Invitrogen RiboMinus™ Concentration Module. Strand-specific adaptors were hybridized and ligated to both extremities of RNA in an overnight reaction, followed by first-strand cDNA synthesis with reverse transcriptase. cDNA was purified using MinElute® PCR Purification Kit (Qiagen) and gel-based selected for size using a Novex TBE-Urea 6% gel (#EC6865bOX). On-gel cDNA was amplified by PCR using SOLiDTM RNA barcoding kit primers (Life Technologies, #4427046 and #4453189) and purified with Invitrogen PureLink® PCR Micro Kit. Amplified DNA was quantified with Qubit® dsDNA HS Assay Kit on a Qubit® 2.0 Fluorometer. Equal masses of each sample, containing specific barcodes, were pooled together and the mixture used as DNA template for emulsion PCR on Applied Biosystems SOLiD® EZ Bead™ E80 system  (#4453095). After 3' end modification with terminal transferase, template beads were deposited onto glass slides and libraries sequenced on a SOLiDTM 4 system using multiplex fragment sequencing protocol that generates about 700 millions 50 bases short reads per run.

treatment_protocol: No treatment

tag: Stage

value: trypomastigote

tag: mixture

value: no

tag: method

value: amplification and oligo-ME T7


title: EXON_gScramble_D1


title: 532738_2

tag: sample

tag: age

tag: genotyped sex

value: GCAAAGA


title: EXON_gExon4_IL2RA+_24hrs_D1


title: 532728_2

value: NODxPWK F1

tag: diet

tag: block

tag: flowcell

value: ACTTAGG


title: EXON_gExon4_IL2RA-_24hrs_D1


title: 532706_2

tag: lane

tag: barcode


title: 533366_2

value: AAGACCT


title: 533420_1


title: 533386_2


title: 533404_1


title: 532760_1


title: EXON_gExon4_Bulk_24hrs_D1


title: 532744_1


title: ENHANCER_gSNP_IL2RA+_72hrs_D2


title: ENHANCER_gSNP_IL2RA-_72hrs_D2


title: 533374_1

value: GTCGTTT


title: 533388_1


title: 532732_1


title: 533382_2


title: ENHANCER_gSNP_Bulk_72hrs_D2


title: evolved 9min rep6

city: Austin

first: Claus

last: Wilke

state: Texas

address: 2500 Speedway, A4800

department: Integrative Biology

institute: University of Texas at Austin

data_processing:
pseudoalignment and quantitation with kallisto v0.42.5 with parameters --single -l 450 -s 250
Genome_build: U00096.3 (E. coli K12) and NC_001604.1 (T7), excluding ribosomal genes, and with recoded gene 10 sequence (Bull, 2012, PMCID: PMC3457771) in place of wild-type sequence for analysis of recoded and evolved strains
Supplementary_files_format_and_content: tab-delimitted text files contain TPM (transcripts per million) values for each sample

organism: Escherichia coli

source_name: cell culture

extract_protocol:
RNA was isolated using Trizol reagent (Thermo Fisher Scientific)
Fragmentation and reverse transcription of RNA with random primers was carried out using the NEB First Strand Synthesis Module (New England Biolabs). Second strand synthesis was done with the NEBNext Ultra Directional RNA Second Strand Synthesis Module (New England Biolabs), then purified with 1.7x AMPURE Bead XP (Beckman Coulter). DNA end repair was carried out with the NEBNext end repair module, dA-tailing used the NEBNext dA-Tailing Module and adapter ligation used the NEBNext Quick Ligation module (New England Biolabs). PCR amplification was carried out for 10 rounds of synthesis using the NEBNext High-Fidelity PCR Master Mix with NEBNext USER Enzyme (New England Biolabs), samples were purified with 1.0x AMPURE Bead XP (Beckman Coulter). Library quality was verified on a Bio-Analyzer DNA chip (Agilent).

tag: infection

tag: t7 strain

value: evolved

tag: t7 genotype

value: evolved, codon-deoptimized gene 10

tag: time

value: 9 min post-infection


title: evolved 9min rep7


title: evolved 5min rep8

value: 5 min post-infection


title: 532710_1

tag: strain

value: Male

value: Vitamin D normal


title: 533400_1

value: PWKxNOD F1


title: ENHANCER_gSNP_IL2RA+_72hrs_D1

tag: cell type

value: CD4+ T


title: evolved 5min rep7


title: evolved 9min rep8


title: 533372_1

value: TAGCCTT


title: 533414_2

value: Vitamin D high


title: 533386_1


title: 532758_1

value: CACTGCC


title: 532742_1

value: CAAGAGA


title: ENHANCER_gSNP_IL2RA-_72hrs_D1


title: ENHANCER_gSNP_IL2RA+_48hrs_D2


title: 532708_1


title: evolved 5min rep6


title: 532730_1


title: ENHANCER_gSNP_Bulk_72hrs_D1


title: evolved 1min rep8

value: 1 min post-infection


title: evolved 1min rep7


title: 533414_1


title: ENHANCER_gSNP_IL2RA-_48hrs_D2


title: 533382_1

value: NODxPWK F1


title: 533416_1

value: TTCTGTC


title: evolved 1min rep6


title: 532756_1


title: EXON_gExon4_IL2RA+_48hrs_D2


title: 532738_1

value: GCAAAGA


title: ENHANCER_gSNP_Bulk_48hrs_D2


title: ENHANCER_gSNP_IL2RA+_48hrs_D1


title: ENHANCER_gSNP_IL2RA-_48hrs_D1


title: 532706_1


title: recoded 9min rep6

value: recoded

value: codon-deoptimized gene 10


title: recoded 5min rep8


title: 533536_1


title: 532762_1


title: ENHANCER_gSNP_Bulk_48hrs_D1


title: 532728_1

value: ACTTAGG


title: 532746_1

value: AAGACCT


title: recoded 9min rep8

value: 9 min post-infection


title: ENHANCER_Scrambled_24hrs_D2


title: 533376_1

value: Male


title: 533398_1

value: Vitamin D normal


title: recoded 9min rep7


title: 532736_1

value: GTCGTTT


title: ENHANCER_gCaRE4-Mix_IL2RA+_24hrs_D2

value: CD4+ T


title: 533406_1

value: PWKxNOD F1


title: recoded 5min rep7

value: 5 min post-infection


title: ENHANCER_gCaRE4-Mix_IL2RA-_24hrs_D2


title: 533366_1


title: recoded 1min rep8


title: 532720_1

value: CACTGCC


title: 533408_1

value: Vitamin D high


title: 533392_1


title: recoded 5min rep6


title: 532752_1

value: TAGCCTT


title: recoded 1min rep7

value: 1 min post-infection


title: ENHANCER_gSNP_IL2RA+_24hrs_D2


title: 533950_1

value: NODxPWK F1


title: recoded 1min rep6


title: 533362_1

value: CAAGAGA


title: 533378_1


title: ENHANCER_gSNP_IL2RA-_24hrs_D2


title: ENHANCER_gSNP_Bulk_24hrs_D2


title: 532702_1


title: WT 9min rep7

value: wild type

value: wild-type gene 10


title: 532722_1

value: GCAAAGA


title: WT 9min rep8


title: ENHANCER_Scrambled_24hrs_D1


title: ENHANCER_gCaRE4-Mix_IL2RA+_24hrs_D1


title: ENHANCER_gCaRE4-Mix_Bulk_24hrs_D2


title: 533410_1


title: WT 9min rep6


title: 532714_1

value: TTCTGTC


title: Rps3-TAP

city: Jupiter

first: Katrin

last: Karbstein

state: FL

address: 130 Scripps Way, Mail Code 2C2

institute: The Scripps Research Institute

description:
TAP-tagged ribosomes
Rps3TAP_comparison-DESeq.xlsx
R3T

data_processing:
Demultiplexed and quality filtered raw reads (fastq) generated from the NextSeq 500 (GPL19756) were trimmed to remove adaptor sequences using Flexbar 2.4
Sequences were aligned to the S. cerevisiae genome (S288C, SacCer3) from the Saccharomyces Genome Database using TopHat version 2.0.9
HT seq-count version 0.6.1 was used to generate gene counts
Non-messenger RNAs (tRNA, snoRNA, ncRNAs) and mitochondrial genes were removed
Counts were analyzed by DESeq2 using standard settings
Genome_build: sacCer3
Supplementary_files_format_and_content: Raw read count files were generated from HT seq-count after aligning to SacCer3
Supplementary_files_format_and_content: Normalized abundance and DESeq data were generated from raw read counts after removal of non-messenger RNAs and mitochondrial genes

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown to mid-log phase in YPD and harvested by centrifugation.

extract_protocol:
Cells were washed, collected in ice-cold lysis buffer, flash frozen in liquid nitrogen and then pulverized in a motor and pestle. Lysate was then incubated with IgG beads for 2h and then unbound flowthrough was collected and run over a 10%-50% sucrose gradients. Samples containing bound ribosomes, eluted by TEV cleavage, and unbound ribosomes, collected from the sucrose gradients, were extracted by phenol-chloroform. For Rps3-TAP cells, only the TEV elution was used for this analysis
Samples were DNase-treated, depleted of ribosomal RNA and prepared using the TruSeq Stranded Total RNA sample prep kit using standard Illumina protocols

treatment_protocol: All cultures were treated with 100µg/ml cycloheximide before harvesting.

value: BY4741 (S288C),  Rps3-TAP::HisMX6

tag: purification method

value: Affinity purification from cell lysate


title: 532754_1

value: Male


title: ENHANCER_gCaRE4-Mix_IL2RA-_24hrs_D1


title: 533396_1

value: Vitamin D normal


title: 532716_1


title: Plus_Rps26_3

description:
untagged ribosomes containing Rps26
FT3

source_name: Replicate 3

growth_protocol: Yeast cells were grown in YPGal, supplemented with 0.2 µg/ml doxycycline, to mid-log phase. Cells were then washed three times with prewarmed YPGal media and inoculated into YPD media at an OD600 of 0.15. After 4h, cells were harvested by centrifugation.

extract_protocol:
Cells were washed, collected in ice-cold lysis buffer, flash frozen in liquid nitrogen and then pulverized in a motor and pestle. Lysate was then incubated with IgG beads for 2h and then unbound flowthrough was collected and run over a 10%-50% sucrose gradients. Samples containing bound ribosomes, eluted by TEV cleavage, and unbound ribosomes, collected from the sucrose gradients, were extracted by phenol-chloroform.
Samples were DNase-treated, depleted of ribosomal RNA and prepared using the TruSeq Stranded Total RNA sample prep kit using standard Illumina protocols

treatment_protocol: All samples were treated with 0.2µg/ml doxycycline until switched to YPD and were treated with 100µg/ml cycloheximide before harvesting.

value: BY4741 (S288C),  HisMX6::pGAL1-Rps3 NatMX6::pGAL1-Rps26A Rps26B::KanMX6; pCM189--Rps3-TAP

value: Sucrose gradient fractionation from purification flowthrough


title: ENHANCER_gCaRE4-Mix_Bulk_24hrs_D1

value: CD4+ T


title: WT 5min rep7

value: 5 min post-infection


title: WT 5min rep6


title: Plus_Rps26_2

description:
untagged ribosomes containing Rps26
FT1

source_name: Replicate 2


title: Plus_Rps26_1

description:
untagged ribosomes containing Rps26
FT1

source_name: Replicate 1


title: 533364_1

value: ACTTAGG


title: WT 1min rep8


title: Minus_Rps26_3

description:
TAP-tagged ribosomes lacking Rps26
Elu3


title: 533396_2

value: PWKxNOD F1


title: ENHANCER_gSNP_IL2RA+_24hrs_D1


title: ENHANCER_gSNP_IL2RA-_24hrs_D1


title: WT 1min rep7

value: 1 min post-infection


title: 532704_1

value: NODxPWK F1

value: AAGACCT


title: Minus_Rps26_1

description:
TAP-tagged ribosomes lacking Rps26
Elu1


title: ENHANCER_gSNP_Bulk_24hrs_D1


title: WT 5min rep8

value: wild type


title: Minus_Rps26_2

description:
TAP-tagged ribosomes lacking Rps26
Elu2


title: clone_661_replicate_2_day_2

status: Public on Jul 29 2017

city: New York

first: Eric

last: Fritz

state: NY

address: 1230 York Ave., Box 39

institute: Rockefeller University

data_processing:
reads filtered with fastq_quality_filter with options "q 20 -Q33 -p 90"
filtered reads aligned to custom genome with Bowtie v. 1.0.0 and options "“--best --strata -v 2 -a -m 1"
gene abundance estimates generated with Cuffdiff v. 2.1.1
Genome_build: TREU927 v5, with VSG sequences added
Supplementary_files_format_and_content: tab-delimited file of gene abundance estimates generated by Cuffdiff

molecule: polyA RNA

organism: Trypanosoma brucei

source_name: T. brucei, strain 427, treated with tet for 2d (d2-ko)

extract_protocol:
Trizol extraction
poly-A+, dUTP RNA-Seq

tag: treatment

value: treated with tet for 2d (d2-ko)


title: clone_660_replicate_2_day_2


title: clone_660_replicate_1_day_2


title: clone_661_replicate_1_day_2


title: 532724_1

source_name: Liver

value: Vitamin D high

value: CAAGAGA


title: clone_661_replicate_1_day_1

source_name: T. brucei, strain 427, treated with tet for 1d (d1-ko)

value: treated with tet for 1d (d1-ko)


title: clone_661_replicate_2_day_1


title: WT 1min rep6

value: wild-type gene 10


title: clone_660_replicate_1_day_0

source_name: T. brucei, strain 427, untreated (wild-type)

value: untreated (wild-type)


title: 14SA cells, day 0, repl 1

description:
wild type fetal myoblast
smallRNAseq
14SAd0.r1

value: fetal muscle myoblast

tag: genotype/variation

value: wild type (14SA)

value: subconfluent myoblast

value: day 0


title: clone_660_replicate_2_day_1


title: clone_661_replicate_2_day_0


title: clone_661_replicate_1_day_0


title: 533380_1

tag: sample

value: Male

value: GCAAAGA


title: AF_Flox5_lung_2_m

city: Logroño

first: Jose

middle: Garcia

last: pichel

state: La Rioja

address: Piqueras 98

department: Oncology

country: Spain

institute: FUNDACIÓN RIOJA SALUD - CIBIR

data_processing:
Illumina base-calling was performed off-line with OLB v1.9.4
Sequenced reads were trimmed for adaptor sequence with Cutadapt and then mapped to mus musculus.GRCm38_71 whole genome using tophat v2.0.6.
Fragments Per Kilobase Of Exon Per Million Fragments Mapped (FPKM) were calculated using SeqSolve (Integromics). This analysis uses Cufflinks in order to quantify gene expression.
Genome_build: mus musculus.GRCm38_71 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text file including FPKM values for each Sample

source_name: Inferior lung lobes

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq totalRNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
totalRNA libraries were prepared for sequencing using standard Illumina protocols

value: C57BL/6 (enriched)

tag: tissue

value: lung

tag: genotype

value: UBC-CreERT2; Igf1rfl/fl (Igf1r-deficient mice)


title: AF_Cre3_lung_2_m

value: Igf1rfl/fl (normal/control)


title: AF_Cre2_lung_2_m


title: AF_Cre1_lung_2_m


title: SERPINA3 siRNA #3

city: Canton

first: Leqing

last: Zhu

state: Guangdong Province

address: East of Huangpu street 601

department: Biology

institute: Jinan University

data_processing:
Transcript levels were quantified in reads per kilobase of exon per million mapped reads (RPKM).
The RPKM reflects the molar concentration of a transcript in the starting sample by normalizing for gene length and for the total read number in the measurement. This allows comparison of transcript levels both within and between experiments.
The sequencing reads were analyzed using the computational pipeline of Bowtie, Tophat, and Cufflinks.
Genome_build: human
Supplementary_files_format_and_content: text file include RPKM values for each Sample

source_name: keratinocytes

growth_protocol: Primary human neonatal foreskin KC from 6 different donors were purchased from Thermo Fisher Scientific and maintained in EpiLife Medium containing 0.06 mM CaCl2 and S7 supplemental reagent under standard tissue culture conditions.

extract_protocol:
Total RNA were extracted from keratinocytes transfected with scrambled siRNA and SERPINA3 siRNA duplexes using Easypure RNA Kit (TRANSGEN Biotech, BeiJing).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: KCs were plated in 24 well plates at 1x105 per well the day before transfection. Cells were transfected with siRNA duplexes at final concentration of 10 nM using lipofectamine 2000 according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA). After 24 hours incubation, the cells were replaced with EpiLife supplemented either with 1.3 mM calcium for up to 120 hours. Then the cells were harvested for total RNA extraction.

value: foreskin

value: keratinocytes

tag: cell status

value: differentiated


title: AF_Flox3_lung_2_m


title: WT MEF Dox rep2

city: Istanbul

first: Batu

last: Erman

address: Orhanli, Tuzla

department: Biological Sciences and Bioengineering Program

country: Turkey

institute: Sabanci University

description: Doxorubicin treated 1microMolar 8 hours

data_processing:
Reads were mapped to the 2012 release of the Mus musculus genome (GRCm38.p2) using Genepattern software (version 3.8.1) and the Bowtie aligner (Bowtie2 version 2.1.0)
Reads Per Kilobase of transcript per Million mapped reads (RPKM) were calculated using the RNASeQC module (version 2) in GenePattern.
Read counts were analyzed using the R environment (R 3.0.2) and the DESeq package (version 1.18.0) according to the suggestions in DEseq’s vignette.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Mouse embryo fibroblasts

growth_protocol: MEF were cultured in DMEM, 10% heat inactivated Fetal Bovine Serum, 100U/ml Penicillin and 100ug/ml Streptomycin, cultured at 37oC with 5% CO2

extract_protocol:
Total RNA was extracted using Trizol (LifeTech 15596018)
RNA libraries were prepared for sequencing using standard protocols following the Illumina TruSeq_RNA_SamplePrep_Guide. After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000

treatment_protocol: Doxorubicin treated 1microMolar 8 hours

tag: background strain

value: 129Sv and C57Bl/6 mixed

tag: age

value: MEF

tag: passage

value: passage three

value: wildtype


title: PATZ1-/- MEF Dox rep1

description: Doxorubicin treated 1microMolar 8 hours


title: PATZ1-/- MEF Dox rep2

description: Doxorubicin treated 1microMolar 8 hours


title: WT MEF Dox rep1

description: Doxorubicin treated 1microMolar 8 hours


title: WT MEF Dox rep3

description: Doxorubicin treated 1microMolar 8 hours


title: SERPINA3 siRNA #1


title: SERPINA3 siRNA #2


title: Scramble siRNA 2


title: clone_660_replicate_2_day_0

value: untreated (wild-type)


title: Scramble siRNA 3


title: MEC1,Cell, 3

city: Heidelberg

first: Martina

last: Seiffert

address: Im Neuenheimer Feld 280

department: Department of Molecular Genetics

country: Germany

institute: German Cancer Research Center

data_processing:
Basecalls performed with Illumina RTA 1.18.64.
Trimming for adapters and small RNA primer (DPN II) using Cutadapt (v 1.1) with the parameters: --error-rate 0.1, --overlap 5 and --minimum-length 15.
A sequence library of non-coding RNAs was generated by extracting sequences from the GRCh37/hg19 reference genome based on the GENCODE 19 annotations.
Reads were aligned using STAR aligner (cite dobin2013star) (v 2.3.0e) in a two-step process similar to a multi-step procedure described previously (cite blume2015p53). First, reads were mapped to the sequence library of non-coding RNAs (based on GRCh37/hg19 + GENCODE 19). Subsequently, the reads non-uniquely aligned in the first step were further mapped to the complete human reference genome (GRCh37/hg19 + hs37d5 decoy sequences).
Additional parameters for STAR aligner: outFilterMismatchNmax 2, outFilterMismatchNoverLmax 0.05, alignIntronMax 1 outFilterMatchNminOverLread 0.95, outFilterScoreMinOverLread 0.95 and outFilterMatchNmin 16.
Read counts per non-coding RNA were counted using featurecounts with the parameter ‘isStrandSpecific’ set to 1 as ‘stranded’.
R package “DESeq2” (v 1.8.2) was used to obtain normalized read counts and to assess the differential expression of non-coding RNAs between exosomes and parental cells.
Genome_build: GRCh37/hg19 + hs37d5 decoy sequences
Supplementary_files_format_and_content: Tab-delimited text files provide read counts for non-coding RNAs (GENCODE 19).

source_name: MEC-1, cells

growth_protocol: MEC-1 cells were cultured in two-compartment INTEGRA CELLLine CL 1000 bioreactors (INTEGRA Biosciences) for exosome production. Seeding of cells was done according to manufacturer’s instructions in DMEM supplemented with 10% fetal calf serum and 1% penicillin/streptomycin. Except for the upper medium compartment, all medium for cell handling and culture was previously depleted of calf serum-derived exosomes by ultracentrifugation at 100,000 x g for 2h at 4 C. Exosomes were isolated from MEC-1 culture supernatant by serial centrifugation. In brief, cells and cell debris were removed by centrifugation at 300 x g and 10,000 x g, respectively, and exosomes were pelleted by repeated ultracentrifugation at 100,000 x g, 4 C for 2h.  The latter included a density-based separation of exosomes and protein aggregates via a 20% Optiprep cushion.

extract_protocol:
RNA of MEC-1 exosomes as well as parental cells was isolated via the miRNeasy Micro Kit (Qiagen) following manufacturer’s instructions for the isolation of small RNA (< 200nt).
Libraries were prepared via the NEBNext Multiplex Small RNA Prep Set for Illumina (Set1) with 30ng input RNA per sample and applying primers diluted 1:2 for RT and 1:1 for PCR, and adapters diluted 1:2. PCR amplification was set to 15 PCR cycles. Libraries were pooled equimolar (2 nM) and sequenced using HiSeq v4 platform (Illumina).

tag: cell line

tag: disease

value: chronic lymphocytic leukemia (CLL)


title: Scramble siRNA 1


title: PATZ1-/- MEF Dox rep3

description: Doxorubicin treated 1microMolar 8 hours


title: MEC1,Exo,5

source_name: MEC-1, exosomes from cell culture supernatant


title: MEC1,Exo,3


title: clone_660_replicate_1_day_1

value: treated with tet for 1d (d1-ko)


title: MEC1,Cell, 2


title: Mutant 2

city: Houston

first: Walid

middle: D

last: Fakhouri

state: TX

address: 1941 East Rd

department: Diagnostic and Biomedical Sciences

institute: University of Texas School of Dentistry at Houston

description: Sample 10

data_processing:
Illumina bcl2fastq v. 1.8.4 software was used for basecalling.
RNA-seq reads were aligned to the GRCm38/mm10 genome assembly using EasyAlign version 3.2
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Data in salivary.txt file are RSEM count data.

source_name: Mouse embryonic tissues

growth_protocol: Mouse embryonic tissues at E14.5

extract_protocol:
Extraction of total RNA using Qiagen kit
Libraries were prepared according to Genewiz Biotechnolgy using Illumina's 2500 instructions
rRNA depletion for RNA-seq library protocol and using Illumina 2500 sequence platform

value: Irf6 null


title: MEC1,Exo,2


title: Wild-type 2

description: Sample 9


title: AF_Flox2_lung_2_m


title: Mutant 1

description: Sample 8


title: MEC1,Cell, 1


title: E2166-Y-F-E4-T

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto Street

department: Enviromantal and Occupational health

institute: University of Pittsburgh

data_processing:
libraries were sequenced on an illumina HiSeq2500
fastq alignment using subread (v1.5.0)
read normilization and differental epression were generated using edgeR (v3.14.0)
Genome_build: mm10
Supplementary_files_format_and_content: edgeR output (significantly differnetialy expressed genes and raw counts)

source_name: APOE4+/+_TBI_brain tissue

extract_protocol:
Fourteen days post-injury, mice were anesthetized using Avertin (250 mg/kg of body weight, i.p.) and perfused transcardially with 20 ml of cold 0.1 M PBS
Brains were rapidly removed and a 1.5 mm coronal section of the brain, including the injury site, was taken by slicing the brain at − 2.5 mm and − 4.0 from bregma
Within the coronal slice, the hemispheres were separated, and the subcortical tissue was dissected out; hippocampal and cortical tissue were snap-frozen together for mRNA-seq
RNA was isolated from frozen cortices and hippocampi at the injury site and purified using RNeasy kit (Qiagen) according to the manufacturer recommendations
Libraries were generated by PCR enrichment including incorporation of barcodes to enable multiplexing

treatment_protocol:
A 4.5 mm diameter craniotomy was performed over the left parietal cortex using a dental drill
Once the bone flap was removed, mice in the CCI group received a single impact at 1.0 mm depth with a 3.0 mm diameter metal tip onto the cortex (3 m/s, 100 ms dwell time; Impact One, Leica)
Following the impact, the surgical site was sutured, triple antibiotic cream applied,
Sham mice received identical anesthesia and craniotomy, but did not receive impact and are considered negative controls

tag: strain background

tag: targeted replacement

tag: injury

value: TBI

value: Brain from cortices and hippocampi at the injury site


title: E2119-Y-F-E4-T


title: Wild-type 1

description: Sample 7

tag: strain


title: E2118-Y-F-E4-T


title: MEC1,Exo,4


title: E2117-Y-F-E4-S

source_name: APOE4+/+_Sham_brain tissue

value: Sham


title: E2106-Y-F-E4-S


title: E2073-Y-F-E4-S


title: F1372-Y-M-E3-S


title: E1794-Y-M-E4-S


title: D2438-Y-F-E3-S

source_name: APOE3+/+_Sham_brain tissue


title: D2439-Y-F-E3-T

source_name: APOE3+/+_TBI_brain tissue


title: E1751-Y-M-E4-T


title: E2075-Y-F-E4-S


title: D2392-Y-F-E3-T


title: D2389-Y-F-E3-S


title: D2383-Y-F-E3-T


title: D2353-Y-F-E3-S


title: E1727-Y-M-E4-T


title: E1818-Y-M-E4-S


title: E1829-Y-M-E4-T


title: MEC1,Exo,1


title: D2319-Y-F-E3-S


title: D1999-Y-M-E3-T


title: E2074-Y-F-E4-T


title: E1800-Y-M-E4-T


title: D2322-Y-F-E3-T


title: D1998-Y-M-E3-S


title: E1731-Y-M-E4-S


title: D1988-Y-M-E3-S


title: D1956-Y-M-E3-S


title: D1943-Y-M-E3-T


title: D1989-Y-M-E3-T


title: Neuroblastoma cell line NBL-S (seq)

status: Public on Jul 28 2017

city: Valencia

first: Jaime

last: Font de Mora

address: Avenida Fernando Abril Martorell, 106; Torre A,  5-07

institute: Instituto de Investigación Sanitaria La Fe

description: Human Comprehensive Cancer GeneRead DNAseq Targeted Panel (Qiagen)

data_processing:
Quality check by Fasq toolkit v0.11.4
Trimming and quality filtering by cutadapt v1.13
Alignment againts reference genome with BWA 0.7.15-r1140
TSV files were generated by uploading VCF files into Ion Reporter v5.0
Genome_build: hg19
Supplementary_files_format_and_content: In the TSV file, Locus and Genotype columns were initially used to identified potential rare variants that were further screened with Allele coverage and minor allele frequency (MAF) columns. In the Ref+/Ref-/Var+/Var-  column we considered only variants with balanced numbers of forward and reverse reads. Variant calls with MAF > 1% (1000 Genomes Project, http://www.internationalgenome.org) were excluded from further analyses.

source_name: Neuroblastoma cell line NBL-S

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol:
Genomic DNA was extracted from cell lines and tumors using standard proteinase K and phenol-chloroform extraction protocol. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
Amplicon library was prepared using GeneRead DNAseq Targeted HC Panel V2 (NGHS-501X-12, Qiagen) according to manufacturer instructions. DNA high-throughput sequencing was performed on Ion Proton instrument using Ion PI HiQ Sequencing Kit on the Ion PI sequencing chip (ThermoFisher Scientific)

value: Neuroblastoma cell line NBL-S


title: Neuroblastoma cell line SH-SY5Y (seq)

source_name: Neuroblastoma cell line SH-SY5Y

value: Neuroblastoma cell line SH-SY5Y


title: Neuroblastoma cell line SK-N-BE(2) (seq)

source_name: Neuroblastoma cell line SK-N-BE(2)

value: Neuroblastoma cell line SK-N-BE(2)


title: Neuroblastoma cell line NLF (seq)

source_name: Neuroblastoma cell line NLF

value: Neuroblastoma cell line NLF


title: Neuroblastoma cell line LA-N-1 (seq)

source_name: Neuroblastoma cell line LA-N-1

value: Neuroblastoma cell line LA-N-1


title: Neuroblastoma tumor A786 (seq)

source_name: Neuroblastoma tumor A786

tag: tumor

value: Primary neroblastoma


title: E1770-Y-M-E4-S


title: Neuroblastoma cell line SK-N-AS (seq)

source_name: Neuroblastoma cell line SK-N-AS

value: Neuroblastoma cell line SK-N-AS


title: Neuroblastoma tumor TI_809 (seq)

source_name: Neuroblastoma tumor TI_809


title: Neuroblastoma tumor TI_719 (seq)

source_name: Neuroblastoma tumor TI_719


title: Neuroblastoma tumor TI_773 (seq)

source_name: Neuroblastoma tumor TI_773


title: Neuroblastoma tumor TI_122 (seq)

source_name: Neuroblastoma tumor TI_122


title: Neuroblastoma tumor NBX_6 (seq)

description: Customized NB-panel. doi: 10.18632/oncotarget.16787

source_name: Neuroblastoma tumor NBX_6


title: Neuroblastoma cell line IMR-32 (seq)

source_name: Neuroblastoma cell line IMR-32

value: Neuroblastoma cell line IMR-32


title: Neuroblastoma tumor TI_423 (seq)

source_name: Neuroblastoma tumor TI_423


title: Neuroblastoma tumor TI_494 (seq)

source_name: Neuroblastoma tumor TI_494


title: Neuroblastoma tumor NBX_56 (seq)

description: Ion AmpliSeq™ Cancer Hotspot Panel v2 (ThermoFisher)

source_name: Neuroblastoma tumor NBX_56


title: D1973-Y-M-E3-T

source_name: APOE3+/+_TBI_brain tissue


title: Neuroblastoma tumor NBX_29 (seq)

source_name: Neuroblastoma tumor NBX_29


title: Neuroblastoma tumor NBX_34 (seq)

source_name: Neuroblastoma tumor NBX_34


title: Neuroblastoma tumor NBX_19 (seq)

source_name: Neuroblastoma tumor NBX_19


title: Neuroblastoma tumor NBX_18 (seq)

source_name: Neuroblastoma tumor NBX_18


title: Neuroblastoma tumor NBX_17 (seq)

source_name: Neuroblastoma tumor NBX_17


title: Neuroblastoma tumor NBX_49 (seq)

source_name: Neuroblastoma tumor NBX_49


title: at-endosperm-input_replicate2_col_wt_x_ler_osd

city: Uppsala

first: Juan

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description: Arabidopsis thaliana F1-endosperm of Columbia-0

data_processing:
ChIP-seq: Reads passing a quality control were mapped to the Arabidopsis (TAIR10) genome using Bowtie (Langmead, 2010) in single-end mode allowing for up to two mismatches. Mapped reads were deduplicated and extended to the estimated average length of the genomic fragments (270 bp). Coverage was estimated and normalized to 10 million of reads.
genome build: TAIR10
processed data files format and content: ChIP-seq: BedGraph files representing average values of Read per Ten Million Mapped reads for each 50 bp across the genome. Format:  <chromosme><bin_start><bin_end><read_per_ten_million>

organism: Arabidopsis thaliana

source_name: AT F1-Endosperm 2x Columbia x osd1 Landsberg

growth_protocol: All seeds were surface sterilized (5% sodium hypochlorite and 0.01% Triton X-100), stratified for 2 days at 4°C and germinated on half-strength Murashige and Skoog medium (1% sucrose) in long-day conditions (16 h light/8 h darkness; 21°C). Plants were transferred to soil after 10 to 12 days and grown under long day conditions.

extract_protocol:
INTACT-purified endosperm nuclei from 600-800 mg siliques were cross-linked 8 min with 1% formaldehyde and sonicated in 100 μl of NLB (Nuclei Lysis Buffer, 50 mM Tris-HCl pH8.0, 10 mM EDTA, 1% SDS, supplemented with Complete protease inhibitors) using a Bioruptor (Diagenode). 900 μl of ChIP dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, containing Complete protease inhibitors (Roche)) was added and chromatin was divided in different aliquots for an overnight incubation with antibodies. The following antibodies were used in this study: anti-Histone H3 (Sigma, #H9289,), H3K9me2 (Diagenode, #pAb‐060‐050). Antibodies IP were performed using Dynabeads (Invitrogen). DNA elution, de-crosslinking and purification steps were done using the IPure kit (Diagenode).
ChIP‐seq libraries were generated using the Microplex library preparation kit (Diagenode) following the manufacturer's protocol with 1 ng of starting material.

treatment_protocol: Material for 2x Col x osd1-2 cross was generated by pollinating dde2 INT plants with pollen of osd1-2 mutants.

value: endosperm

value: none (Input)

value: 4 days after pollination


title: at-endosperm-input_replicate1_col_wt_x_ler_osd


title: at-endosperm-h3_replicate2_col_wt_x_ler_osd


title: at-endosperm-h3_replicate1_col_wt_x_ler_osd


title: Neuroblastoma tumor TI_501 (seq)

source_name: Neuroblastoma tumor TI_501


title: at-endosperm-h3k9m2_replicate2_col_wt_x_ler_osd


title: at-endosperm-h3_replicate2_col_wt_x_col_2n-suvh2-9

source_name: AT F1-Endosperm 2x Columbia x 2x suvh2;9Columbia

treatment_protocol: Material for 2x Col x 2x suvh2;9 cross was generated by pollinating dde2 INT plants with pollen of 2x suvh2-2 suvh9-1 mutants.

value: 2x suvh2-2 suvh9-1


title: at-endosperm-input_replicate2_col_wt_x_col_2n-suvh2-9


title: at-endosperm-h3_replicate2_col_wt_x_col_4n-suvh2-9

source_name: AT F1-Endosperm 2x Columbia x 4x suvh2;9Columbia

treatment_protocol: Material for 2x Col x 4x suvh2;9 cross was generated by pollinating dde2 INT plants with pollen of 4x suvh2-2 suvh9-1 mutants.

value: 4x suvh2-2 suvh9-1


title: at-endosperm-h3k9m2_replicate2_col_wt_x_col_2n-suvh2-9


title: at-endosperm-h3k9m2_replicate2_col_wt_x_col_4n-suvh2-9


title: Neuroblastoma tumor TI_672 (seq)

source_name: Neuroblastoma tumor TI_672


title: at-endosperm-h3k9m2_replicate1_col_wt_x_ler_osd


title: at-endosperm-h3k9m2_replicate2_col_wt_x_col_4n-ahl10

source_name: AT F1-Endosperm 2x Columbia x 4x ahl10 Columbia

treatment_protocol: Material for 2x Col x 4x ahl10 cross was generated by pollinating dde2 INT plants with pollen of 4x ahl10 mutants.


title: at-endosperm-input_replicate2_col_wt_x_col_4n-ahl10


title: at-endosperm-input_replicate2_col_wt_x_col_2n-ahl10

source_name: AT F1-Endosperm 2x Columbia x 2x ahl10 Columbia

treatment_protocol: Material for 2x Col x 2x ahl10 cross was generated by pollinating dde2 INT plants with pollen of 2x ahl10 mutants.


title: at-endosperm-h3_replicate2_col_wt_x_col_2n-ahl10


title: at-endosperm-h3_replicate2_col_wt_x_col_wt

source_name: AT F1-Endosperm 2x Columbia x 2x Columbia

treatment_protocol: Material for 2x Col x 2x Col cross was generated by pollinating dde2 INT plants with pollen of 2x Col-0 plants.

value: 2x Col


title: at-endosperm-h3k9m2_replicate2_col_wt_x_col_2n-ahl10


title: at-endosperm-h3k9m2_replicate2_col_wt_x_col_wt


title: at-endosperm-h3_replicate2_col_wt_x_col_4n-ahl10


title: at-endosperm-input_replicate2_col_wt_x_col_wt


title: at-endosperm-h3k9m2_replicate1_col_wt_x_col_4n-ahl10


title: at-endosperm-h3_replicate1_col_wt_x_col_4n-ahl10


title: at-endosperm-input_replicate1_col_wt_x_col_2n-ahl10


title: at-endosperm-h3_replicate1_col_wt_x_col_2n-ahl10


title: at-endosperm-h3k9m2_replicate1_col_wt_x_col_2n-ahl10


title: at-endosperm-input_replicate1_col_wt_x_col_4n-ahl10


title: at-endosperm-h3k9m2_replicate1_col_wt_x_col_2n-suvh2-9


title: at-endosperm-h3_replicate1_col_wt_x_col_2n-suvh2-9


title: at-endosperm-input_replicate1_col_wt_x_col_2n-suvh2-9


title: at-endosperm-h3_replicate1_col_wt_x_col_4n-suvh2-9


title: at-endosperm-input_replicate1_col_wt_x_col_4n-suvh2-9


title: at-endosperm-h3_replicate2_col_wt_x_col_admosd

source_name: AT F1-Endosperm 2x Columbia x osd1 adm Columbia

treatment_protocol: Material for 2x Col x osd1-1 adm-2 cross was generated by pollinating dde2 INT plants with pollen of osd1-1 adm-2 mutants.

value: osd1-1 adm-2


title: at-endosperm-h3k9m2_replicate2_col_wt_x_col_admosd


title: at-endosperm-input_replicate2_col_wt_x_col_admosd


title: at-endosperm-h3_replicate2_col_wt_x_col_osd

source_name: AT F1-Endosperm 2x Columbia x osd1 Columbia

treatment_protocol: Material for 2x Col x osd1-1 cross was generated by pollinating dde2 INT plants with pollen of osd1-1 mutants.


title: at-endosperm-input_replicate2_col_wt_x_col_adm

source_name: AT F1-Endosperm 2x Columbia x adm Columbia

treatment_protocol: Material for 2x Col x adm-2 cross was generated by pollinating dde2 INT plants with pollen of adm-2 mutants.


title: at-endosperm-input_replicate1_col_wt_x_col_admosd


title: at-endosperm-h3k9m2_replicate1_col_wt_x_col_osd


title: at-endosperm-h3_replicate1_col_wt_x_col_admosd


title: at-endosperm-h3_replicate1_col_wt_x_col_adm


title: at-endosperm-h3_replicate1_col_wt_x_col_osd


title: at-endosperm-h3k9m2_replicate2_col_wt_x_col_osd


title: at-endosperm-h3k9m2_replicate1_col_wt_x_col_adm


title: at-endosperm-input_replicate1_col_wt_x_col_osd


title: at-endosperm-h3k9m2_replicate1_col_wt_x_col_wt


title: at-endosperm-BS_replicate1_col_wt_x_col_wt

data_processing:
Bisulfite-seq: For each mutant, the 125 bp reads from the Illumina BS sequence libraries from the two replicates were merged and trimmed to 100 bp by cutting 5 bp from the start and 20 bp from the end of each read. After this first trimming, each read was split in two 50 bp long reads in order to improve mapping efficiency.  Reads were mapped to the TAIR10 Arabidopsis genome using the Bismark read mapper (Krueger and Andrews, 2011) allowing up to one mismatch per read. Duplicated reads (aligning to the same genomic position) were eliminated before reporting methylation levels.
genome build: TAIR10
processed data files format and content: Bisulfite-seq: Three genome-wide cytosine methylation reports (for CG, CHG, CHH) per sample were created. These reports have the  following format:  <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>

extract_protocol:
Genomic DNA of INTACT-purified endosperm nuclei from 150-300 mg siliques was purified using the MagJET Plant Genomic DNA kit (Thermo Fisher Scientific), eluted in 80 μl of elution buffer, and sonicated for 30 cycles (30s on, 30s off at high power) using a Bioruptor (Diagenode). The bisulfite conversion was performed using the EpiTect Fast DNA Bisulfite Kit (Qiagen) during the library preparation.
Bisulfite libraries were generated with the Ovation Ultralow Methyl‐Seq Library Systems (NuGEN) following the manufacturer's protocol using 10 ng of starting DNA.


title: at-endosperm-h3_replicate1_col_wt_x_col_wt


title: at-endosperm-BS_replicate2_col_wt_x_col_wt


title: at-endosperm-BS_replicate2_col_wt_x_col_osd


title: at-endosperm-input_replicate1_col_wt_x_col_adm


title: at-endosperm-BS_replicate1_col_wt_x_col_osd


title: at-endosperm-input_replicate1_col_wt_x_col_wt


title: at-endosperm-h3_replicate2_col_wt_x_col_adm


title: at-endosperm-h3k9m2_replicate2_col_wt_x_col_adm


title: at-endosperm-BS_replicate1_col_wt_x_col_admosd


title: H2AfZKO_E16

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Brain

extract_protocol:
Cerebral cortex was dissected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: development stage

value: brain; telencephalic tissue


title: WT_E16


title: CD4_input_DNA

first: Hatice

middle: Ulku

last: Osmanbeyoglu

address: 5117 Centre Ave

data_processing:
Reads were first processed with Trimmomatic to remove the adaptor sequences and bases with quality scores below 20, and reads with less than 30 remaining bases were discarded
Trimmed reads were then aligned to mm10 mouse genome with the bowtie aligner
peaks were called using MACS2 using q value cut-off 0.01
Genome_build: mm10
Supplementary_files_format_and_content: bed filefor oeakswere generated using MACS2 using q value cut-off 0.01

source_name: CD4 T cells

growth_protocol: CD4+ T cells of wild-type mice were purified by MACS beads (Miltenyi)

extract_protocol:
Lysates were clarified from sonicated nuclei and GABPα-DNA complexes were isolated with anti-GABPα antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

value: CD4 T cells

tag: antibody


title: at-endosperm-input_replicate2_col_wt_x_col_osd


title: at-endosperm-h3k9m2_replicate1_col_wt_x_col_admosd


title: at-endosperm-input_replicate2_col_wt_x_col_4n-suvh2-9


title: at-endosperm-h3k9m2_replicate1_col_wt_x_col_4n-suvh2-9


title: cutC4

city: Madison

first: Federico

last: Rey

state: WI

address: 1550 Linden Dr.

institute: University of Wisconsin-Madison

description: stranded mRNA TruSeq Illumina Library

data_processing:
The first 10bp were trimmed to eliminate GC bias at the beginning of each read (FastX trimmer).
The 6bp Illumina adapter sequences were then clipped (FastX Clipper)
A quality filter was applied to eliminate any reads with a quality score < 30 (FastX Quality Filter).
Reads were then aligned to the mm9 reference genome constructed to include only annotated genes (NM_RegSeqs) by Bowtie 2 alignment (seed length = 28, 2 mismatches per seed allowed).
Expression level determined using RSEM v 1.2.23
Differential expression (fold change and PPDE) were calculated using Ebseq.
Genome_build: mm9
Supplementary_files_format_and_content: For each sample a txt file containing RSEM output continating the following columns transcript_id, gene_id, length, effective_length, expected_count, TPM, and FPKM IsoPctexpected counts, TPM, and FPKM (.gene.results.txt)

source_name: liver

growth_protocol: Animal care and study protocols were approved by the University of Wisconsin - Madison Animal Care and Use Committee. Mice were housed in the Microbial Sciences Building vivarium. Germ-free (GF) C57BL/6J mice, which were later colonized, were bred at the University of Wisconsin-Madison. GF mice were housed in plastic flexible vinyl gnotobiotic isolators. GF mice were inoculated via a single oral gavage with ~0.2 ml of the communities detailed below and kept in sealed filter-top gnotobiotic cages for 2 weeks. Mice were housed under standard conditions (12 h light:dark, temperature- and humidity-controlled conditions), and received ad libitum access to water and food. Diets were sterilized by irradiation and autoclaving. Sterility of germ-free animals was assessed by incubating freshly collected fecal samples under aerobic and anaerobic conditions using standard microbiology methods. Final dissection and data collection were performed at 9-weeks of age.

extract_protocol:
RNA was extracted first from frozen tissue using TRIzol and then using a Qiagen RNA-easy minikit with on column Dnase treatment.
Library was constructed using the Illumina TruSeq Stranded mRNA Library Preparation Kit

treatment_protocol: C57BL/6J mice were colonized with either the CC+ ( Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Escherichia_coli_MS_200-1 (WT)) or CC- ( Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Escherichia_coli_MS_200-1 (ΔcutC)) community. Mice were maintained for 2 weeks on a 1% choline diet after colonization. Mice were fasted for 4 hours prior to sacrifice. Mice were anesthetized using isoflurane administered in oxygen.

tag: community

value: CC-

tag: diet

value: 1% (wt/wt) choline


title: WT4

description: stranded mRNA TruSeq Illumina Library

value: CC+


title: cutC3

description: stranded mRNA TruSeq Illumina Library


title: cutC1

description: stranded mRNA TruSeq Illumina Library


title: cutC2

description: stranded mRNA TruSeq Illumina Library


title: WT2

description: stranded mRNA TruSeq Illumina Library


title: Repli-seq F121-9 hybrid mouse cells - Late S fraction - Rep 2

city: Tallahassee

first: David

middle: M

last: Gilbert

address: 319 Stadium Drive

institute: Florida State University

description:
processed data file:
F121-9_nesc_r2_R_T_.bedGraph
F121-9_nesc_r2_R_T_Loess.bedGraph
F121-9_nesc_r2_R_T_qnorm.bedGraph
F121-9_nesc_r2_T_clip_129_genparsed_mm10w50000gt100snp_unified_qnorm_loess0-01.bedGraph
F121-9_nesc_r2_T_clip_cas_genparsed_mm10w50000gt100snp_unified_qnorm_loess0-01.bedGraph

data_processing:
Reads are mapped on mm10 using bowtie2. F121-9 cells have also been parsed, between cas and 129 genome (“*cas*” and “*129*” files)
Coverage data are calculated from mapped reads using samtools and bedtools
Base 2 log of early to late coverage ratio is calculated on 50kb windows (“*_T_.bg” files)
Log Ratio data are quantile normalized using R package preprocessCore (“*_T_qnorm.bg” files)
Data are smoothed using R Loess function (“*_T_Loess.bg” files,  and “*unified_qnorm_loess0-01.bg” files for allele specific data)
Genome_build: mm10
Supplementary_files_format_and_content: processed data are coverage data on mm10 genome, they can be visualized using a genome viewer. To visualize them using UCSC genome viewer, add a bedgraph file header (see UCSC website for description of the header)

source_name: mESC

growth_protocol: 46C mESCs were cultured in mESC media supplemented with LIF. F121-9 ESC were cultured in N2B27+2i+LIF media.

extract_protocol:
Genome-wide replication timing profiles were constructed as previously described (Hiratani et al. 2008; Ryba et al. 2011). Briefly, cells were pulse labeled with BrdU and separated into early and late S-phase fractions by flow cytometry and processed either by NGS.
Sequencing libraries of BrdU-substituted DNA from early and late fractions were prepared by NEBNext Ultra DNA Library Prep Kit for Illumina (E7370).

value: F1 CASTx129 hybrid mouse (clone F121-9)

tag: cell line/type

value: ES cells

tag: s phase fraction

value: Late S fraction

tag: replicate


title: WT1

description: stranded mRNA TruSeq Illumina Library


title: Repli-seq F121-9 hybrid mouse cells - Late S fraction - Rep 1

description:
processed data file:
F121-9_nesc_r1_R_T_.bedGraph
F121-9_nesc_r1_R_T_Loess.bedGraph
F121-9_nesc_r1_R_T_qnorm.bedGraph
F121-9_nesc_r1_T_clip_129_genparsed_mm10w50000gt100snp_unified_qnorm_loess0-01.bedGraph
F121-9_nesc_r1_T_clip_cas_genparsed_mm10w50000gt100snp_unified_qnorm_loess0-01.bedGraph


title: Repli-seq F121-9 hybrid mouse cells - Early S fraction - Rep 2

value: Early S fraction


title: Repli-seq 46C mouse cells - Late S fraction

description:
processed data file:
46C_repli-seq_mm10_log_ratio_scaled.bedGraph

source_name: mouse ESC


title: at-endosperm-BS_replicate2_col_wt_x_col_admosd

tag: tissue

tag: genotype


title: E10 G1 Rep3

city: SAN FRANCISCO

first: Joan

last: Zape

address: 555 Mission Bay Blvd South

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat.
Fragments per kilobase per million  of library size (FPKM) was calculated using Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: E10.5 AGM

extract_protocol:
AGMs were isolated from E10.5 and E11.5 FucciRed and FucciGreen animals. G1 IAHC populations were sorted as SSEA-1-CD31+CD117+mKO2+ and S/G2/M IAHCs were sorted as SSEA-1-CD31+CD117+mAG+ .Total RNA was isolated and purified from sorted cells using the QIAGEN RNeasy Plus Micro Kit (#74034) following manufacturer’s instructions. RNA integrity was determined using a Bioanalyzer.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata

value: AGM

tag: age

value: Fucci Red


title: E10 SG2M Rep1

value: Fucci Green


title: Repli-seq 46C mouse cells - Early S fraction


title: Repli-seq F121-9 hybrid mouse cells - Early S fraction - Rep 1


title: E10 G1 Rep1


title: E10 G1 Rep2


title: E11 SG2M Rep3

source_name: E11.5 AGM


title: CD4_GABP_ChIPSeq

value: anti-GABPalpha (sc-22810X, Santa Cruz).


title: E10 SG2M Rep3


title: E11 SG2M Rep2


title: E10 SG2M Rep2


title: E11 SG2M Rep1


title: E11 G1 Rep2


title: E11 G1 Rep1


title: WT3

description: stranded mRNA TruSeq Illumina Library


title: SCANT_LMPP_D0_rep2

city: Bethesda

first: Damian

last: Kovalovsky

address: 9000 Rockville Ave

institute: National Cancer Institute

description:
Transcriptome analysis of lymphoid progenitors in Zbtb1-deficient mice
SCANT2_LMPP_D0

data_processing:
Basecalling with RTA v1.18.61
Demultiplexing with Bcl2fastq v1.8.4
Trimming with Trimmomatic v0.32
Mapping with STAR 2.4.0d
Read Count with htseq v0.6.1p1
Normalization and differential expression with DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text format; count data as content

source_name: ScanT (Zbtb1 mutant) LMPP before culture

growth_protocol: Cells were analyzed ex-vivo (D0) or grown on OP9-DL1 cocultures plus IL-7 and Flt3L for 24hs (D1)

extract_protocol:
RNA was extracted from sorted cells using qiagen Rneasy micro kit  and cDNA amplified using SMARTer Ultra Low RNA-Seq System
Nextera XT DNA Sample Prep Kit FC-131-1096

treatment_protocol: D1: IL7 (1ng/ml) Flt2L (5ng/ml), D0: no treatment

value: Zbtb1 mutant

tag: background strain

tag: cell type

value: lymphoid primed multipotent progenitors

tag: co-culture treatment


title: SCANT_LMPP_D0_rep1

description:
Transcriptome analysis of lymphoid progenitors in Zbtb1-deficient mice
SCANT3_LMPP_D0


title: SCANT_LMPP_D1_rep2

description:
Transcriptome analysis of lymphoid progenitors in Zbtb1-deficient mice
SCANT2_LMPP_D1

source_name: ScanT (Zbtb1 mutant) LMPP after culture


title: SCANT_CLP_D0_rep2

description:
Transcriptome analysis of lymphoid progenitors in Zbtb1-deficient mice
SCANT4_CLP_D0

source_name: ScanT (Zbtb1 mutant) CLP before culture

value: common lymphoid progenitors


title: SCANT_LMPP_D1_rep1

description:
Transcriptome analysis of lymphoid progenitors in Zbtb1-deficient mice
SCANT3_LMPP_D1


title: SCANT_LMPP_D0_rep3

description:
Transcriptome analysis of lymphoid progenitors in Zbtb1-deficient mice
SCANT1_LMPP_D0


title: SCANT_CLP_D1_rep2

description:
Transcriptome analysis of lymphoid progenitors in Zbtb1-deficient mice
SCANT4_CLP_D1

source_name: ScanT (Zbtb1 mutant) CLP after culture


title: SCANT_CLP_D0_rep1

description:
Transcriptome analysis of lymphoid progenitors in Zbtb1-deficient mice
SCANT5_CLP_D0


title: WT_LMPP_D0_rep2

description:
Transcriptome analysis of lymphoid progenitors in Zbtb1-deficient mice
WT2_LMPP_D0

source_name: Wild type LMPP before culture

value: wildtype


title: WT_LMPP_D1_rep3

description:
Transcriptome analysis of lymphoid progenitors in Zbtb1-deficient mice
WT1_LMPP_D1

source_name: Wild type LMPP after culture


title: WT_LMPP_D0_rep3

description:
Transcriptome analysis of lymphoid progenitors in Zbtb1-deficient mice
WT1_LMPP_D0


title: WT_CLP_D0_rep2

description:
Transcriptome analysis of lymphoid progenitors in Zbtb1-deficient mice
WT4_CLP_D0

source_name: Wild type CLP before culture


title: WT_LMPP_D1_rep2

description:
Transcriptome analysis of lymphoid progenitors in Zbtb1-deficient mice
WT2_LMPP_D1


title: WT_LMPP_D0_rep1

description:
Transcriptome analysis of lymphoid progenitors in Zbtb1-deficient mice
WT3_LMPP_D0


title: RS

city: Fuzhou

first: Chen

last: Lisong

address: Shangdian street NO.15

institute: Fujian Agriculture and Forestry University

data_processing:
Basecalls performed
Get rid of some contaminant reads from the fq file and get the final clean reads.
The clear reads were mapped to Citrus clementina genome (JGI version 1.1, http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Csinensis) using SOAP, only perfectly mapped sequences were retained and analyzed further. rRNAs, tRNAs, snRNAs and snoRNAs were removed from the sRNAs sequences through BLASTn search using NCBI Genebank database (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi/) and Rfam (12.0) database (http://www.sanger.ac.uk/resources/databases/rfam.html) (e = 0.01). The remaining sequences were aligned with known plant miRNAs from miRBase 21 (http://www.mirbase.org/).
Reads that were not annotated were used to predict novel miRNAs using a prediction software Mireap (http://sourceforge.net/projects/mireap/), which was developed by the BGI
Supplementary_files_format_and_content: microRNA sequences and counts

organism: Citrus sinensis

source_name: magnesium-sufficient roots

growth_protocol: 5-week-old seedlings of ‘Xuegan’ [Citrus sinensis (L.) Osbeck] were transplanted into 6 L pots containing fine river sand. Ten weeks after transplanting, each pot was supplied every other day with Mg-deficient (0 mM MgSO4) or Mg-sufficient (1 mM MgSO4, control) nutrient solution for 16 weeks. There were 10 replications per Mg treatment with 2 pots in a completely randomized design.

extract_protocol:
About 0.1 g mixed frozen Mg -sufficient and Mg -deficient roots from five replictations were used to extract RNA. Total RNA was extracted from frozen roots using TRIzol reagent (Invitrogen, Carlsbad, CA)
Small RNA samples were sequenced by Beijing Genomics Institute (BGI) (Shenzhen, Guangdong, China) using the high throughput pyrosequencing technology developed by Illumina. Two sRNA libraries were constructed, sRNAs were isolated from the total RNA by size fractionation with 15% Tris-borate-EDTA urea polyacrylamide gel (TBU). Then the sRNAs were ligated with 5' and 3' adaptor by T4 RNA ligase after being dephosphorylatd by alkaline phosphatase. The adaptor-ligated sRNAs were transcribed to single-stranded cDNA using Superscript II reverse transcriptase (Invitrogen). Thereafter, the single-stranded cDNA was used as templates for double-stranded synthesis by PCR amplification using the primer designed according to the adapter sequence. The obtained PCR products were sequenced on a Solexa sequencer (Illumina) at the Beijing Genomics Institute (BGI), Shenzhen, China.

treatment_protocol: RD(0 mM MgSO4，Mg-deficient，RD) , RS (Mg-sufficient,control, RS)

value: Fully expanded Citrus sinensis roots were excised from the seedlings


title: RD

source_name: magnesium-deficiect roots


title: WT_LMPP_D1_rep1

description:
Transcriptome analysis of lymphoid progenitors in Zbtb1-deficient mice
WT3_LMPP_D1


title: WT_CLP_D0_rep1

description:
Transcriptome analysis of lymphoid progenitors in Zbtb1-deficient mice
WT5_CLP_D0


title: WT_CLP_D1_rep2

description:
Transcriptome analysis of lymphoid progenitors in Zbtb1-deficient mice
WT4_CLP_D1

source_name: Wild type CLP after culture


title: E11 G1 Rep3

institute: UCSF


title: FXR-/-12

city: Clermont-Ferrand

middle: H

last: VOLLE

address: 28 place Henri Dunant

country: France

institute: INSERM

data_processing:
Image analysis and base calling were performed unsing RTA 1,18,61 and Casava1.8.2
Sequenced reads were trimmed for adaptor sequence, the number of reads corresponds to reads without adapter dimer. The average base quality of 95% of the positions of the reads must be over 30 to pass the platform criteria. A base quality of 30 means that there 1 chance out of 1000 that a given base has been miscalled during the Base Calling (i.e. probability of error = 0.001)
Regarding  quality control: For FastQC Version 0.10.1 was run using the following arguments --nogroup --casava. For  FastQScreen Version 0.3.1 was run using the following arguments: --subset 1000000 --bowtie '-p 2'. The --subset optionasks FastQScreen to use only a subset of reads to be mapped on enomes/DNA sequences.
Reads were mapped onto the mm10 assembly of the mouse genome using Tophat v2.0.10 (Kim et al., 2013) and the bowtie2 v2.1.0 aligner (Langmead et al., 2012).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file contains raw and normalized read counts.

source_name: Testis

extract_protocol:
Testis were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: testis

value: postnatal day 10

value: FXR-/-


title: FXR-/-11


title: FXR-/-8


title: WT9

value: wild-type


title: WT6


title: FXR-/-10


title: FXR-/-9


title: WT5


title: WT3


title: WT4


title: SCANT_CLP_D1_rep1

description:
Transcriptome analysis of lymphoid progenitors in Zbtb1-deficient mice
SCANT5_CLP_D1


title: Osr1 GCE/+ Rep 2

city: Paris

first: Mickael

last: Orgeur

address: 25-28 rue du Docteur Roux

institute: Institut Pasteur

data_processing:
Paired-end reads were mapped against the genome version mm9 of Mus musculus by using TopHat2 and the UCSC gene model annotation from iGenome as guide (default parameters, except for --mate-inner-dist 150 and --min-intron-length 50)
Aligned fragments (both reads from each pair correctly mapped) were counted at the gene level by using HTSeq-count (default parameters, except for --mode intersection-strict)
Differential expression analysis was carried out by using DESeq2 (alpha 0.05).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files containing the raw fragment counts for each gene feature for each replicate generated by HTSeq and used as input for DESeq2

source_name: Mesenchymal cells

extract_protocol:
Limbs of E13.5 Osr1 GCE/+ and Osr1 GCE/GCE embryos were extracted, minced and digested by using a collagenase solution. Cell suspensions were stained with propidium iodine. GFP-expressing live cells were sorted by using a FACS Aria II and collected directly into RLT buffer for RNA extraction (RNeasy mini kit, Qiagen).
RNA libraries were prepared by using the TruSeq RNA Library Preparation Kit v2 according to Illumina's intructions and subjected to high-throughput sequencing by using the Illumina HiSeq 2500 technology. 65-75 million of 50-bp paired-end reads were generated with a mean insert size of 150 bp.

value: limbs

tag: developmental stage

value: Heterozygous


title: Osr1 GCE/GCE Rep 2

value: Homozygous


title: Osr1 GCE/GCE Rep 1


title: Lhx6 ChIP Seq

first: Juhee

last: Jeong

state: New York

address: 345 E 24th St

department: Basic sciences and Craniofacial development

institute: New York University College of Dentistry

data_processing:
The sequence reads from each sample were aligned to the mouse genome (NCBI Build 37, mm9) using BWA algorithm (Li and Durbin, 2009)  The aligned sequence tags were extended in silico at the 3′-ends into 150-bp fragments, and the histograms of the fragment density along the genome were stored in BAR (Binary Analysis Results) files and visualized using Integrated Genome Browser (IGB) (Nicol et al., 2009)
LHX6 peaks were identified using MACS peak-finding algorithm (39) with the following parameters: band width = 150, model fold = 8,24, P-value cutoff = 1E-7.
Genome_build: mm9
Supplementary_files_format_and_content: peak

source_name: E11.5 Maxillary Arch

growth_protocol: Not applicable.

extract_protocol:
The maxillary arches were dissected from 47 of E11.5 CD-1 wild-type embryos in phosphate-buffered saline and snap-frozen on dry ice. The tissue was then sent to Active Motif, Inc. (Carlsbad, CA) for FactorPath™ service, which included chromatin preparation, ChIP-seq for LHX6, and bioinformatics analysis of the sequencing result to identify LHX6-enriched genomic regions (peaks). Twenty micrograms of the maxillary arch chromatin was used for ChIP with a rabbit polyclonal anti-LHX6 antibody   The tissue was then sent to Active Motif, Inc. (Carlsbad, CA) for HistonePathTM service, which included chromatin preparation, ChIP-seq for H3K27ac, and bioinformatics analysis of the sequencing result to identify H3K27ac-enriched genomic regions (peaks). 20 μg of the maxillary arch chromatin was used for ChIP with a rabbit polyclonal anti-H3K27Ac antibody (Active Motif, cat# AM 39133). Libraries for Illumina sequencing (Hi-Seq) were prepared from ChIP DNA and input chromatin as described (Labhart et al., 2005)
Libraries for Illumina sequencing (Hi-Seq) were prepared from ChIP DNA and input chromatin, and the sequence reads from each sample were aligned to the mouse genome (NCBI Build 37, mm 9) using BWA algorithm (73). The aligned sequence tags were extended in silico at the 3′-ends into 150-bp fragments, and the histograms of the fragment density along the genome were stored in BAR (Binary Analysis Results) files and visualized using Integrated Genome Browser (IGB).

treatment_protocol: Not applicable.

value: Wild-type (CD1)

tag: chip antibody

value: E11.5 Maxillary Arch


title: Input (Lhx6)


title: VB1

city: harbin

first: Ningning

last: Song

address: No.678. Haping Road

institute: Harbin Veterinary Research Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to BCG_str_Tokyo_172 whole genome using bowtie2(version: 2-2.0.5) with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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: Mycobacterium bovis BCG_str_Tokyo_172

organism: Mycobacterium tuberculosis variant bovis

source_name: BCG culture

growth_protocol: Mycobacterium bovis BCG str. Tokyo 172 strain was grown in Middlebrook 7H9 medium Becton Dickinson supplemented with 0.05% Tween 80(V/V), 10% ADC (Albumin-Dextrose-Catalase, BD) and 0.2% (V/V) glycerol, 37℃. The bacteria were incubated at 100 rpm with continuous shaking for 3 weeks until the culture reached an exponential phase.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Cat#74106, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: VB1 was added at a final concentration of 10 mM in 7H9 liquid medium

tag: treatment

value: vitamin B1

tag: strain


title: AA


title: Control 3

city: Würzburg

first: Corinna

last: Rosenbaum

address: Röntgenring 11

department: Department of Tissue Engineering and Regenerative Medicine

institute: University Hospital Wuerzburg

data_processing:
Basecalls and demultiplexing were performed using CASAVA for HiSeq2500 sequencing. Each sample was previously splitted into four samples indicated by name affix 'gp 1-4'
Mapping was performed with TopHat2 (v2.0.5, default settings) against the human reference genome assembly "hg19" with the annotation from Gencode "v17".
Gene quantification was calculated with a python script, “rpkmforgenes.py” from the Sandberg Laboratory (http://sandberg.cmb.ki.se/rnaseq/) at readcount and RPKM level (=reads per kilobase of exon model per million mapped reads) according to Mortazavi et al. using uniquely mapped reads.
Differential gene expression profiling was carried out exclusively based on readcount quantification via the DESeq2 package developed for RNA sequencing data.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample.

source_name: Rectal wall

extract_protocol:
RNA was isolated from frozen whole rectal wall samples with the RNAeasy Mini Plus Kit (Qiagen, Hilden, Germany) and checked for quality and quantity with Agilent’s 2100 Bioanalyzer using the RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, USA).
cDNA libraries were prepared using Illumina’s TruSeqTM RNA Sample Preparation v2 protocol. Sequencing was performed using an Illumina HiSeqTM 2500. Quality and quantity was checked with Agilent's 2100 Bioanalyzer using DNA 1000 Kit.

tag: disease state

value: Control

tag: gender

value: male

value: Rectal wall


title: ODS 1

value: ODS

value: female


title: Control 2


title: Invader 4 LTR Dnmt2 mutant, heat shock

city: Vienna

first: Schaefer

last: Matthias

state: AT

address: Schwarzspanierstrasse 17-I

department: Cell and Developmental Biology

country: Austria

institute: Medical University Vienna, Center for Anatomy & Cell Biology

description:
PCR product from Invader 4 LTR
alignment to LTR sequence

data_processing:
Linkers and barcode sequences were extracted from the 454 output. Barcoded reads representing each genotype and experimental condition were binned (raw data files: barcode-separated reads) and mapped to an Invader 4 LTR sequence (FBgn0063427) using pairwise sequence alignment (processed data files: alignment to Inv4_LTR). C at positions of Cs in Invader4 LTR scored as 0 in sequencing reads while Ts at positions of Cs scored as 1 (processed data files: matrix score of methylation_output).
Genome_build: aligned to DM3 Invader 4 LTR sequence (FBgn0063427); sequence available on series record.
Supplementary_files_format_and_content: text file with aligned reads and text file with methylation score for each sample.  Methylation scoring card (0:methylated; 1: not methylated). Methylation scores are provided only for the Cs in the sequence.

organism: Drosophila melanogaster

source_name: D2 mutant; hs, mixed adults, whole body

growth_protocol: Flies were cultured on standard fly food in a humidified incubator (60% humidity) at a 12/12 hour day-night light cycle

extract_protocol: Bisulfite conversion on 5 µg of genomic DNA was carried using the EpiTect Bisulfite Kit (Qiagen) according to the manufacturer’s instructions. 200 ng bisulfite-treated DNA was used as template in a first PCR reaction (35 cycles, annealing temperature= 50°C) to amplify regions in the canonical Invader4 LTR. Amplicons were gel-purified and 50 ng were used as template for a second PCR reaction (15 cycles, annealing temperature= 50°C) to re-amplify the amplicon and adding 454-sequencing adapters.

treatment_protocol: Adult flies were heat-shocked (37 C for one hour) in a water bath, followed by a recovery period of 5 hours at RT for heat shock samples, one and 3 days for recovery samples before extracting genomic DNA.

value: w1118; Dnmt2 mutant/Dnmt2 mutant

value: adults 3 days after hatching

value: mixed

value: whole body


title: Invader 4 LTR Dnmt2 mutant, standard

source_name: D2 mutant; control, mixed adults, whole body


title: Invader 4 LTR Dnmt2 mutant, Recovery 1 day

source_name: D2 mutant; R1, mixed adults, whole body


title: Control 1


title: ODS 3


title: NC, 1

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

data_processing:
Reads were mapped to the human genome (hg19) using TopHat v2.0.11 (http://tophat.cbcb.umd.edu) with the following default options with a TopHat transcript index built from Ensembl_GRCh37. Count files of the aligned sequencing reads were generated by the htseq-count script from the Python package HTSeq with union mode, using the GTF annotation file.
Genome_build: Ensembl_GRCh37(hg19)
Supplementary_files_format_and_content: count

source_name: HT-29 cells

growth_protocol: The human colorectal cancer cells HT-29 were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.

extract_protocol:
total RNA of HT-29 cells with different treatment was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cultured F.nucleatum was used to treat  the HT29 colorectal cancer cells, while the blank culture medium-teated HT29 CRC cells was used as negative controls.

value: human colorectal cancer cells

tag: agent


title: Invader 4 LTR ctrl Recovery 1 day

source_name: wild type; R1, mixed adults, whole body


title: Invader 4 LTR ctrl heat shock

source_name: wild type; hs, mixed adults, whole body


title: Invader 4 LTR Dnmt2 mutant. Recovery 3 days

source_name: D2 mutant; R3, mixed adults, whole body


title: Invader 4 LTR ctrl Recovery 3 days

source_name: wild type; R3, mixed adults, whole body


title: NC, 2


title: NC, 3


title: FN Treatment, 3

value: F. nucleatum