title: Day 24 replicate 1

description:
RNA harvested from cultured rat embryonic neurons 24 days after plating
D24-1-SLX-8483.L2DRBC14.bam-FPKM


title: BalillaORF5+_S1_rep1

status: Public on Jun 01 2017

type: SRA

city: shenzhen

first: yiming

last: yu

state: --- Select a state ---

address: 1088 Xueyuan Avenue

country: China

institute: Southern University of Science and Technology

library_source: transcriptomic

data_processing:
Raw reads was produced by Illumina HiSeq 2000
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
All the reads in sanger fastq format were mapped to the genome of Oryza sativa Japonica Group cultivar Nipponbare with Tophat. (IRGSP-1.0)
Cufflinks are used to assemble transcripts and estimate their abundances with default parameters.
Cuffdiff was used to find differential expressed genes with default parameters.

molecule: total RNA

organism: Oryza sativa

source_name: pistil

growth_protocol: All the rice plants were grown in the fields of experimental station of Huazhong Agricultural University, Wuhan, China.

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen) according to the manual. RNA yields and quality were measured using Nanodrop 2000 (Thermo Scientific), and further quantified using Qubit2.0 Fluorometer (Invitrogen). RNA integrity was evaluated using Experion RNA Analysis Kits (Bio-rad) and Experion Automated Electrophoresis Station (Bio-rad)
Each library was constructed using 3 μg total RNA using the TruSeq RNA Library Preparation Kit v2 (Illumina).

tag: Stage

tag: genotype/variation


title: BalillaORF5+_S2_rep1


title: BalillaORF5+_S1_rep2


title: Balilla_S3_rep2

value: Balilla


title: Day 24 replicate 0

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

description:
RNA harvested from cultured rat embryonic neurons 24 days after plating
D24-0-SLX-8483.L2DRBC13.bam-FPKM

data_processing:
Reads were aligned to the Rnor5.0/Ensembl V75 transcriptome using Tophat v2.0.8 with default parameters
Counts and differential gene expression were determined using CuffLinks v2.2.1 using default parameters
Genome_build: Rnor 5.0
Supplementary_files_format_and_content: Fastq files for raw data and FPKM values in tab-delimted txt format

organism: Rattus norvegicus

growth_protocol:
Cortical neurons were derived from E18 Sprague Dawley rat cortex, and were plated at the density of 100-150 cells/mm2. The medium used for plating was a combination of fresh B27 medium (neurobasal medium supplemented with 2% B27 and 1% Glutamax) and B27 medium conditioned by astrocytes.
Astrocytes were derived from P0-2 Sprague Dawley rat cortex, and were grown for 7-8 days before being frozen for future use. They were then thawed and further grown for another 5-6 days before being combined with neurons as co-culture, or used for B27 medium conditioning.

extract_protocol:
Total RNA was extracted from 1, 4, 8, 16, and 24 DIV cultures by using the Qiagen RNeasy Micro Kit (Qiagen, 74004)
RNA was subjected to whole-transcriptome amplification using NuGEN RNAseq v2 System followed by fragmentation to 200bp with a Diagenode Bioruptor Pico sonicator, The resulting fragments were then used to make bar-coded libraries using NuGEN Ovation Rapid DR Multiplex System

tag: strain

value: Sprague Dawley

tag: developemental stage

tag: tissue

value: Brain cortex

tag: cell type

value: Embryonic cortical neurons

tag: co-cultured with

value: primary rat astrocytes from P0-2 rats

tag: time point

value: 24 days after plating


title: Day 24 replicate 4

description:
RNA harvested from cultured rat embryonic neurons 24 days after plating
D24-4-SLX-9155.L2DRBC13.bam-FPKM


title: Balilla_S3_rep1


title: BalillaORF5+_S3_rep1


title: Day 16 replicate 4

description:
RNA harvested from cultured rat embryonic neurons 16 days after plating
D16-4-SLX-9155.L2DRBC11.bam-FPKM

value: 16 days after plating


title: Balilla_S2_rep1


title: Balilla_S2_rep2


title: Day 16 replicate 2

description:
RNA harvested from cultured rat embryonic neurons 16 days after plating
D16-2-SLX-8483.L2DRBC11.bam-FPKM


title: BalillaORF3+ORF5+_S1_rep2


title: Balilla_S1_rep2


title: AP2-I_Input, Rep 3

city: University Park

first: Manuel

last: Llinas

state: Pennsylvania

address: Millennium Science Complex

department: Biochemistry and Molecular Biology

country: USA

institute: Pennsylvania State University

description:
Dd2 AP2-I-GFP
Dd2 gene PfAP2-I with C-terminal GFP.
Processed data files: ap2i_r3_*.bedGraph

library_source: genomic

data_processing:
Raw reads were trimmed using trimmomatic version 0.33 and the following parameters: "ILLUMINACLIP:adapters.txt:2:2:2 SLIDINGWINDOW:36:30 MINLEN:36 TRAILING:30".
ChIP anti-GFP, anti-IgG, and input libraries were aligned to the Plasmodium falciparum Dd2 reference genome as found on GeneDB at: ftp://ftp.sanger.ac.uk/pub/pathogens/Plasmodium/falciparum/PF3K/PilotReferenceGenomes/DraftAnnotation/PfDd2/
Alignments were filtered using samtools and the following parameters: "-F 256 -F 2048 -F 1024 -q 30"
Peaks were called using MACS2 version 2.1.1.20160309 using the following flags: "-g g 2.15e7 --m 5 50 --extsize ${FRAGSIZE} --fix-bimodal --call-summits -B" where ${FRAGSIZE} was the average insert size estimated by Bioanalyzer.
Genome_build: PfDd2 draft assembly at GeneDB
Supplementary_files_format_and_content: BedGraph files were generated by MACS2. n
Supplementary_files_format_and_content: *gfp_treat_pileup.bedgraph: Normalized coverage track for the anti-GFP sequencing run when compared to the input sequencing run.
Supplementary_files_format_and_content: *igg_treat_pileup.bedgraph: Normalized coverage track for the anti-IgG sequencing run when compared to the input sequencing run.
Supplementary_files_format_and_content: *gfp_control_lambda.bedgraph: Normalized coverage track for the input as compared to the anti-GFP sequencing run.
Supplementary_files_format_and_content: *igg_control_lambda.bedgraph: Normalized coverage track for the input as compared to the anti-IgG sequencing run.

molecule: genomic DNA

organism: Plasmodium falciparum

source_name: PfAP2-I-GFP DNA, input

growth_protocol: P. falciparum parasites were cultured as previously described (Trager and Jensen, 1976) in RPMI 1640 media supplemented with hypoxanthine and 0.5% Albumax II (Invitrogen) in 2% or 5% haemotocrit. Parasite synchronization was done using an L-Alanine solution (Braun-Breton et al., 1988). Transfections were performed as previously described (Fidock and Wellems, 1997) and selected on either 2µg/ml blasticidin-S-HCl (BSD) or 2.5nM WR99210 (WR) or 1.5µM 5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)naphthalen-2-ylamine (DSM). All CRISPR/Cas9 parasite lines were generated by co-transfecting parasites with 30µg of pL7 plasmid and 30µg of the pUF1-Cas9 plasmid (Ghorbal et al., 2014). PfAP2-I-GFP::PfBDP1-HA-DD parasites were generated by growing parasites in the presence of 0.5µM Shld-1. When PfAP2-I-GFP parasites were used for transfection, the media was supplemented with BSD. When necessary, parasites were cycled ON/OFF drugs for at least 2 cycles and cloned by serial dilution in order to ensure that the population was clonal for plasmid integration.

extract_protocol:
The ChIP assay was performed as described in (Lopez-Rubio, 2012) with some modifications. Briefly, synchronized schizont stage parasite cultures were saponin-lysed until complete red blood cell lysis and formaldehyde-crosslinked. The isolated chromatin was sheared in SDS lysis buffer to obtain a fragment size of 100-150bp using an M220 focused-ultrasonicator (Covaris Inc.) and the following settings: 20% duty factor, 200 cycles per burst and total treatment time of 350s. After pre-clearing the chromatin with Magna ChIP protein A+G magnetic beads (Millipore), an input sample was collected and the rest of the chromatin was incubated overnight at 4C with 1μg of polyclonal anti-GFP antibody or, as control, the same amount of IgG. The immunoprecipitated chromatin was collected with Magna ChIP protein A+G magnetic beads (Millipore), extensively washed and eluted with elution buffer. The input and ChIP samples were reverse cross-linked overnight at 45C in the presence of 0.4M NaCl and purified. ChIP-qPCR was performed as described for ChIP-seq with few exceptions (details in supplemental experimental procedures of publication).
Barcoded libraries for Illumina TruSeq single-end sequencing were constructed using NEBNext DNA library preparation reagents (NEB) by following the standard Illumina library preparation protocol. The libraries were PCR-amplified using Kappa HiFi (Kappa Biosystems) and purified using Agencourt AMPure XP beads (Beckman Coulter). The quality and percentage of adaptor-ligated material of the final sequencing libraries were determined by running them on an Agilent 2100 Bioanalyzer (Agilent Technologies). The concentration of each library was determined using a Quant-iT dsDNA Broad-Range Assay kit (Invitrogen).

tag: strain/background

value: Schizont (40h post-invasion)

value: whole body

tag: chip antibody


title: Day 16 replicate 3

description:
RNA harvested from cultured rat embryonic neurons 16 days after plating
D16-3-SLX-8483.L2DRBC12.bam-FPKM


title: Day 16 replicate 1

description:
RNA harvested from cultured rat embryonic neurons 16 days after plating
D16-1-SLX-8483.L2DRBC10.bam-FPKM


title: Balilla_S1_rep1


title: AP2-I-antiGFP_ChIPSeq, Rep 3

source_name: PfAP2-I-GFP DNA, GFP ChIP

value: Anti-GFP (Abcam ab290)


title: AP2-I-antiIgG_ChIPSeq, Rep 3

source_name: PfAP2-I-GFP DNA, IgG ChIP

value: Anti-IgG (Abcam ab27472)


title: Day 16 replicate 0

description:
RNA harvested from cultured rat embryonic neurons 16 days after plating
D16-0-SLX-8483.L2DRBC09.bam-FPKM


title: AP2-I_Input, Rep 2

description:
Dd2 AP2-I-GFP
Dd2 gene PfAP2-I with C-terminal GFP.
Processed data files: ap2i_r2_*.bedGraph


title: Day 1 replicate 4

description:
RNA harvested from cultured rat embryonic neurons 1 day after plating
D1-4-SLX-9155.L2DRBC05.bam-FPKM

value: 1 day after plating


title: Day 1 replicate 3

description:
RNA harvested from cultured rat embryonic neurons 1 day after plating
D1-3-SLX-9155.L2DRBC04.bam-FPKM


title: Day 1 replicate 5

description:
RNA harvested from cultured rat embryonic neurons 1 day after plating
D1-5-SLX-9155.L2DRBC06.bam-FPKM


title: AP2-I-antiIgG_ChIPSeq, Rep 2


title: AP2-I-antiGFP_ChIPSeq, Rep 2


title: AP2-I_Input, Rep 1

description:
Dd2 AP2-I-GFP
Dd2 gene PfAP2-I with C-terminal GFP.
Processed data files: ap2i_r1_*.bedGraph


title: Day 1 replicate 2

description:
RNA harvested from cultured rat embryonic neurons 1 day after plating
D1-2-SLX-9155.L2DRBC03.bam-FPKM


title: Day 1 replicate 1

description:
RNA harvested from cultured rat embryonic neurons 1 day after plating
D1-1-SLX-9155.L2DRBC02.bam-FPKM


title: AP2-I-antiIgG_ChIPSeq, Rep 1


title: AP2-I-antiGFP_ChIPSeq, Rep 1


title: Day 1 replicate 0

description:
RNA harvested from cultured rat embryonic neurons 1 day after plating
D1-0-SLX-9155.L2DRBC01.bam-FPKM


title: Experimental 4

description:
Mouse Hypothalamus injected with AAV-CRE - Experimental 4
IGF0004619

data_processing:
Reads were aligned to GRCm38 using Tophat (v 0.11.2)
Counts were generated using HTSeq (v 0.6.0)
Differential expression analysis was performed using EdgeR.
EdgeR was used to generate (TMM) normalised abundance values in log2CPM
Genome_build: GRcm38
Supplementary_files_format_and_content: Normalised abundance values are represented in log2 counts per million (log2CPM) and stored in a tab-delimited matrix

organism: Mus musculus

source_name: Mouse Hypothalamus

extract_protocol:
RNA was extracted from microdissected mouse hypothalami 4 weeks after AAV injection
Illumina TruSeq mRNA sample prep kit was used to make sequencing libraries

treatment_protocol: Thrb-flox mice were injected with either GFP/Cre overexpressing adeno-associated viruses centrally to remove ThrB expression in the hypothalamus and animals were sacrificed 4 weeks after injection

tag: genotype

value: Thrb-flox

tag: treatment

value: AAV-CRE


title: Experimental 3

description:
Mouse Hypothalamus injected with AAV-CRE - Experimental 3
IGF0004618


title: Experimental 2

description:
Mouse Hypothalamus injected with AAV-CRE - Experimental 2
IGF0004617


title: CVxMC_F1_hybrid_ISOLATED_2

city: Stanford

first: Ryan

last: York

state: CA

address: 371 Serra Mall

institute: Stanford University

data_processing:
Illumina Casava1.7 software used for basecalling.
Adapters were removed and low-quality bases were trimmed using SeqPrep. Reads were then aligned with STAR V 2.4 (--outSAMattributes MD NH NM  --clip5pNbases 6)
Read quantification: Custom python scripts (available at github.com/TheFraserLab/ASEr)
Genome_build: M_zebra_UMD1
Supplementary_files_format_and_content: tab-delimited text files with allele-specific read counts for each sample and a tab-delimeted text file with the union of all samples

organism: Copadichromis virginalis x Mchenga conophoros

source_name: Whole brain

extract_protocol:
Trizol extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: male

tag: phenotype

value: isolated


title: Experimental 1

description:
Mouse Hypothalamus injected with AAV-CRE - Experimental 1
IGF0004616


title: Rat 24 ovary

city: Lexington

first: Gregg

middle: Brooks

last: Whitworth

state: VA

address: 204 West Washington St

department: Biology

institute: Washington and Lee Unversity

data_processing:
Raw sequencing reads in FASTQ format were filtered for quality and adapter sequences removed using Trimmomatic (v. 0.35) with the following parameters: a 4-base sliding window with average quality cutoff of 20, removal of leading and trailing low quality bases below the quality of 20 and a minimum read length of 119 bases.
Surviving reads were aligned to the Rattus norvegicus genome using the RGD gene model version 6.0, retrieved from ncbi.nlm.nih.gov on 03/23/2016, using STAR (v 2.5.1b) with the length of the annotated genome sequence specified as 124.
Gene expression estimation, expressed as fragments per kilobase per million reads (FPKM), was performed using RSEM (v. 1.2.29) with default options.
Genome_build: rn6
Supplementary_files_format_and_content: text files with TPM and FPKM

molecule: polyA RNA

source_name: ovary

growth_protocol: Female Sprague-Dawley rats (n = 60; P17) were obtained from Charles River and were housed with mothers until weaning at day 23. At weaning, rats were randomly assigned to either a HFHS (n = 32) or control diet (n = 28) group. The control group had ad libitum access to water and standard rat chow (Envigo – LM-485, 3.1 kcal/g, 17% calories from fat). The HFHS diet group had ad libitum access to water, a 32% sucrose solution, and high fat chow (Research Diets – D12492, 5.24 kcal/g, 60% of the calories derived from fat). Animals were housed in pairs in a climate-controlled environment with a 12:12 h light:dark cycle (lights on at 8 am). Animals were weighed and handled every other day. All animal procedures were approved for use by the Washington and Lee University Institutional Animal Care and Use Committee (Protocol # NT0717).

extract_protocol:
Immediately following removal, ovary tissue was flash frozen on liquid nitrogen and stored at -80 oC.  To purify total RNA, tissue was thawed in TRIzol and homogenized using mechanical disruption.  RNA was then purified using a commercial spin column kit, according to manufacturer’s instructions (Direct-zol RNA MiniPrep, Zymo Research R2053), and flash frozen on liquid nitrogen
Following poly(A) selection, cDNA libraries were prepared using the HiSeq SBS Kit (v. 4) with 4x-mutiplexing and the quality was verified by Bioanalyzer analysis. Sequencing was performed on the HiSeq 2500 platform, in paired-end 125 base-pair mode.  All four independent ovary samples were run in a single lane, which generated a total of 47,664 Mbp of sequence across 1.9 x 108 clusters with mean Q-scores all above 35.

treatment_protocol: After 11 weeks on diet, ovaries were removed from all of animals (OVX) and half were implanted with slow-release estradiol (E2) pellets (OVX+E) a week later. Surgeries were performed under isoflurane/oxygen gas mixture; isoflurane was set at 2.5% and the oxygen flow to 2.0L/min. Before creating the incisions, the animals were given an injection of marcaine on each side based on their diet (0.1 mL for control, 0.15 mL for HFHS, 0.2 mL for HFHS rats over 400 grams) in order to relieve any pain caused the surgery. The surgical area was sterilized and small incisions were made bilaterally to expose and remove the ovaries. The muscle layer was sutured and the skin layer was closed with clips. The surgical area was wiped with antibacterial cream. Ovaries were stored individually in 4% PFA at 4°C for 24 hours. Ovaries were subsequently stored in 30% sucrose at 4°C.

value: Sprague-Dawley

tag: diet

value: control

value: ovary


title: Control 3

description:
Mouse Hypothalamus injected with AAV-GFP - Control 3
IGF0004614

value: AAV-GFP


title: Rat 04 ovary

value: high-fat, high-sugar


title: Rat 07 ovary


title: CVxMC_F1_hybrid_ISOLATED_1


title: experiment-2, RNAseq data from ethanol-gavaged rats' nucleus accumbens, rep5

city: Gothenburg

first: Julia

last: Morud

address: Beroendemedicin, Box 410

country: Sweden

institute: University of Gothenburg

description: Transcriptome data from rat nucleus accumbens

data_processing:
Bcl to Fastq conversion was performed using bcl2Fastq v1.8 from the CASAVA software suite. The quality scale is Sanger / phred33 / Illumina 1.8+.
Sequenced reads were trimmed for low-quality sequences, then mapped to Rnor_6.0 whole genome using tophat2 v2.0.13 with parameters -p 8 -r 100
Number of reads mapping to each feacher (from SAM file) were calculated using htseq-count v0.5.3p3.
Differential expression analysis was done using DESeq2 package v1.6.2 form R/Bioconductor with the htseq-count result as an input.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The raw counts were generated from the aligned bam files (aligned with Tophat2) using htseq_count version 0.6.0.

source_name: Nucleus accumbens tissue from ethanol exposed rats_experiment2

extract_protocol:
Qiagen RNeasy Lipid tissue mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain

tag: tissue compartment

value: Nucleus accumbens

tag: breed

value: Wistar

tag: Sex

tag: developmental stage

value: adult


title: experiment-2, RNAseq data from ethanol-gavaged rats' nucleus accumbens, rep4


title: experiment-2, RNAseq data from ethanol-gavaged rats' nucleus accumbens, rep6


title: CVxMC_F1_hybrid_BUILDING_2

value: castle building


title: experiment-2, RNAseq data from ethanol-gavaged rats' nucleus accumbens, rep3


title: Control 1

description:
Mouse Hypothalamus injected with AAV-GFP - Control 1
IGF0004612

tag: strain


title: experiment-2, RNAseq data from ethanol-gavaged rats' nucleus accumbens, rep2


title: CVxMC_F1_hybrid_DIGGING_2

value: pit digging


title: experiment-2, RNAseq data from ethanol-gavaged rats' nucleus accumbens, rep1


title: EHCont_ATACseq

city: Kyoto

first: Kazuko

last: Miyazaki

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Institute for Life and Medical Sciences, Kyoto University

data_processing:
Illumina bcl2fastq-1.8.4 software used for basecalling.
Trimed reads were mapped to the mm9 reference genome using Bowtie (version 1.2.7) with the parameters –X2000 and –m1.
ATAC-seq read counts were calculated using HOMER.
Genome_build: mm9

source_name: sorted ETP

extract_protocol:
Cells in WT and dKO mice were sorted.
The open chromatin regions were examined by the ATAC-seq protocol developed and described in Buenrostro et al. (2013) and  Lara-Astiaso et al. (2014).

value: Wild type

value: fetal thymus


title: EHdKO_ATACseq


title: Rat 47 ovary


title: EHdKO_RNAseq_rep3

data_processing:
Illumina bcl2fastq-1.8.4 software used for basecalling.
Paired-end RNA-Seq reads were trimmed before mapping using fastx-trimmer tool.
TopHat (version 2.0.14) was used to map reads to the mouse reference genome (mm9)
Array Studio software (OmicSoft Corporation) was used to calculate raw read counts.
Abundance values (counts) were normalized and compared between control vs double KO mice using DESeq (version 2) .
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include the abundance values of control (3 samples) and dKO (3samples) with P-value generated by DESeq (version 2) .

extract_protocol:
Cells were sorted and total RNA was isolated from them using the RNeasy-Micro Kit (Qiagen). The total RNA was then processed for deep sequencing using SMARTer Ultra Low Input RNA kit  for Sequencing-v3 (Clontech) following the manufacturer’s protocol.
Liibraies were prepared fromt the sonicated DNA using Low Input Library Prep Kit (Clontech) following the manufacturer’s protocol. cDNA libraries were sequenced with a HiSeq 2500 sequencer (Illumina).


title: CVxMC_F1_hybrid_DIGGING_1


title: experiment-2, RNAseq data from water-gavaged rats' nucleus accumbens, rep5

source_name: Nucleus accumbens tissue from water exposed rats_experiment2


title: Azotobacter vinelandii wild-type (DJ) strain Day 2 grown in standard B Medium Supplemented with 20 mM NH4 [AV.RNA.43]

city: Saint Paul

first: Brett

middle: M

last: Barney

state: MN

address: 1500 Gortner Avenue

department: Bioproducts and Biosystems Engineering

institute: University of Minnesota

description:
AV.RNA.43
Processed data file: genes.fpkm_table.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence quality was accessed via FastQC, and Illumina TruSeq adapters were trimmed through Trimmomatic (version 0.33) using the following parameters: ILLUMINACLIP:all_illumina_adapters.fa:2:30:10:2:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:16 MINLEN:50
Raw paired-reads were mapped to modified genome of Azotobacter vinelandii (CP001157.1) using Hisat 2.0.2 with modified genome reference of A. vinelandii and following parameters:--dta-cufflinks --threads 8
Fragments per kilobase of exon per million fragments mapped (FPKM) were calculated using cuffquant and cuffnorm with default parameters.
Genome_build: Modified genome of Azotobacter vinelandii (GenBank: CP001157.1)
Supplementary_files_format_and_content: genes.fpkm_table.txt: Tab-delimited text file includes FPKM values for each Sample.

organism: Azotobacter vinelandii

source_name: whole cell lysate

growth_protocol: A. vinelandii strain DJ (a wild-type highly transformable strain with diminished alginate production) was obtained from Dennis Dean (Virginia Tech) and grown in standard Burk's (B) medium with or without supplemented ammonium at 30°C and 180 RPM. The Azotobacter vinelandii strain AZBB163 is deregulated for nitrogen fixation and releases substantial quantities of ammonium into the growth medium.

extract_protocol:
Samples for RNA isolation were flash frozen in liquid nitrogen and stored until needed. RNA was isolated by resuspending frozen cells in 1 mL of TRIzol reagent (Invitrogen, Grand Island, NY) and samples were vortexed intermittently for several minutes until fully dissolved. Following this, 200 mL of chloroform was added, vortexed, and then centrifuged at 12,000 g for 2 minutes. The upper phase was removed, and further purified using the Direct-zol RNA miniprep kit (Zymo Research, Irvine, CA). RNA was eluted and treated to remove background DNA following the manufacturer's directions using the RNase-free DNase I Set (Zymo Research, Irvine, CA) in a total volume of 100 mL for 10 min at room temp, and then suspended in 300 mL of TRIzol and again isolated using the Direct-zol miniprep kit. Isolated RNA quantity was measured using a NanoDrop 2000 spectrophotometer (Thermo Scientific, Waltham, MA). Ribosomal and transfer RNAs were removed from the total isolated RNA using the Ribo-Zero kit for Gram-Negative bacteria (Illumina Inc., San Diego, CA). Final mRNA fractions were concentrated using the RNA Clean & ConcentratorTM-5 (Zymo Research, Irvine, CA).
Samples were then sequenced by HiSeq 2500 Rapid Mode with 100-bp paired-end reads. Raw data from the RNA sequencing experiments was run through the rnaseq-pipeline (tophat/hisat) for the analysis of high-throughput sequence datasets through the University of Minnesota Supercomputing Institute. The pipeline utilized FastQC, Trimmomatic, and Bowtie 2. Cuffquant and Cuffnorm used to calculate fragments per kilobase of exon per million fragments mapped (FPKM) values for each gene. Further comparisons were made by exporting this data to Excel (Microsoft, Redmond, WA) for a further comparison of differences in transcriptional levels.

value: DJ

tag: genotype/variation

value: Wild-type

tag: medium supplement

value: 20 mM NH4

tag: growth stage

value: Day 2


title: EHdKO_RNAseq_rep2

tag: cell type

tag: tissue


title: Azotobacter vinelandii wild-type (DJ) strain Day 2 grown in standard B Medium Supplemented with 20 mM NH4 [AV.RNA8]

description:
AV.RNA8
Processed data file: genes.fpkm_table.txt

tag: strain/background


title: experiment-2, RNAseq data from water-gavaged rats' nucleus accumbens, rep4

value: male


title: Azotobacter vinelandii wild-type (DJ) strain Day 1 grown in standard B Medium Supplemented with 20 mM NH4 [AV.RNA7]

description:
AV.RNA7
Processed data file: genes.fpkm_table.txt

value: Day 1


title: Control 2

description:
Mouse Hypothalamus injected with AAV-GFP - Control 2
IGF0004613

value: Thrb-flox


title: EHCont_RNAseq_rep3


title: experiment-2, RNAseq data from water-gavaged rats' nucleus accumbens, rep2


title: CVxMC_F1_hybrid_BUILDING_1


title: EHdKO_RNAseq_rep1


title: experiment-2, RNAseq data from water-gavaged rats' nucleus accumbens, rep3


title: Azotobacter vinelandii wild-type (DJ) strain Day 2 grown in standard B Medium [AV.RNA6]

description:
AV.RNA6
Processed data file: genes.fpkm_table.txt


title: Azotobacter vinelandii wild-type (DJ) strain 15 hours grown in standard B Medium Supplemented with 20 mM NH4 [AV.RNA.42]

description:
AV.RNA.42
Processed data file: genes.fpkm_table.txt

value: 15 hours


title: EHCont_RNAseq_rep2


title: experiment-2, RNAseq data from water-gavaged rats' nucleus accumbens, rep1


title: Azotobacter vinelandii wild-type (DJ) strain Day 3 grown in standard B Medium [AV.RNA.48]

description:
AV.RNA.48
Processed data file: genes.fpkm_table.txt

value: Day 3


title: EHCont_RNAseq_rep1


title: experiment-2, RNAseq data from water-gavaged rats' nucleus accumbens, rep6

value: Brain


title: STAT1-/- HSCs treated with IFNγ-5

city: Kumamoto

first: Terumasa

last: Umemoto

address: 2-2-1, Honjo, Chuo-Ku

institute: Kumamoto University

description: processed data: STAT1_KO_control-vs-IFNg.txt

data_processing:
Life Technologies Torrent Suite v3.6 software were used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using CLC genomic workbench v7.0.4.
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: mm10
Supplementary_files_format_and_content: tab-delimited text files include read number and RPKM values for each Sample.

source_name: hematopoietic stem cells

extract_protocol:
After 5000 cultured HSCs were sorted, total RNA was extracted using ISOGEN reagent. First strand cDNA were synthesized using a SMARTer Pico cDNA amplification kit. Double-stranded cDNA was then amplified by 18 cycles of PCR.
RNA libraries were prepared for sequencing using standard Thermo Fisher Scientific protocols

value: (C57BL/6 X 129Sv) mixture

value: Bone marrow

tag: age

value: 8-10 weeks


title: STAT1-/- HSCs treated with IFNγ-4

tag: genotype


title: Azotobacter vinelandii wild-type (DJ) strain Day 1 grown in standard B Medium [AV.RNA.47]

description:
AV.RNA.47
Processed data file: genes.fpkm_table.txt


title: Not swim NSG - rep 2 (#7287)

city: Minneapolis

first: Alessandro

last: Magli

address: 2231 6th St SE

department: Medicine

description: not swim

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then processed using TopHat v2.0.9 (mapped to mm10)
The CuffDiff v2.2.1 package was used to identify differentially expressed genes between the Swum and Control groups for both 12 wild type and Fkrp-mutant animals. CuffDiff analysis was performed using a geometric normalization method, cutoff =10 for minimum alignment count and a False Discovery Rate (FDR) of 0.05. SQLite database generated by CuffDiff was used to display results as Volcano plot using CummeRbund. Statistically significant differentially expressed genes between Swum and Control animals were selected using cutoff=2 for Fold enrichment.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each treatment group (FKRP_swam; FKRP_ctrl; WT_swam: WT_ctrl)

source_name: Diaphragm

extract_protocol:
Diaphragm muscles were collected and snap frozen in liquid nitrogen. Total RNA was isolated using an RNA/Protein purification kit (Macherey-Nagel). Sequencing libraries were generated from total RNA at the University of Minnesota Genomic Center using the TruSeq RNA Sample Preparation kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When indicated, mice swam 1hour/day for 2 weeks

value: Diaphragm

value: 8-10 weeks old mice

value: NSG


title: STAT1-/- HSCs treated with IFNγ-3


title: Not swim NSG - rep 3 (#7286)

description: not swim


title: Azotobacter vinelandii wild-type (DJ) strain Day 2 grown in standard B Medium [mRNA2.AV]

description:
mRNA2.AV
Processed data file: genes.fpkm_table.txt


title: STAT1-/- HSCs treated with IFNγ-2


title: Azotobacter vinelandii wild-type (DJ) strain Day 1 grown in standard B Medium [AV.RNA5]

description:
AV.RNA5
Processed data file: genes.fpkm_table.txt


title: STAT1-/- HSCs treated with IFNγ-1


title: Swum NSG - rep 2 (#7289)

description: swam


title: Azotobacter vinelandii strain AZBB163 day 4 growth in standard B Medium [AV.RNA3]

description:
AV.RNA3
nifL gene was genetically modified by ~500 bp insertion.
Processed data file: genes.fpkm_table.txt

value: Mutated nifL

value: Day 4


title: STAT1-/- HSCs-4


title: STAT1-/- HSCs-3


title: Not swim FKRPP448L-NSG - rep 3 (#6873)

description: not swim


title: Azotobacter vinelandii strain AZBB163 day 3 growth in standard B Medium [mRNA3.AV]

description:
mRNA3.AV
nifL gene was genetically modified by ~500 bp insertion.
Processed data file: genes.fpkm_table.txt


title: Not swim FKRPP448L-NSG - rep 2 (#6871)

description: not swim


title: Azotobacter vinelandii strain AZBB163 day 2 growth in standard B Medium [AV.RNA2]

description:
AV.RNA2
nifL gene was genetically modified by ~500 bp insertion.
Processed data file: genes.fpkm_table.txt


title: Swum NSG - rep 1 (#7291)

description: swam


title: Azotobacter vinelandii strain AZBB163 day 2 growth in standard B Medium [AV.RNA1]

description:
AV.RNA1
nifL gene was genetically modified by ~500 bp insertion.
Processed data file: genes.fpkm_table.txt


title: STAT1-/- HSCs-1


title: Azotobacter vinelandii strain AZBB163 day 2 growth in standard B Medium [mRNA1.AV]

description:
mRNA1.AV
nifL gene was genetically modified by ~500 bp insertion.
Processed data file: genes.fpkm_table.txt


title: STAT1-/- HSCs-2


title: Not swim FKRPP448L-NSG - rep 1 (#6865)

description: not swim


title: Wt HSC treated with IFNγ+VN-4

description: processed data: WT_Control-vs-IFNg-vs-IFNg+VN.txt

value: wild type


title: Swum FKRPP448L-NSG - rep3 (#6758)

description: swam


title: Wt HSC treated with IFNγ+VN-2


title: Azotobacter vinelandii strain AZBB163 day 4 growth in standard B Medium [AV.RNA4]

description:
AV.RNA4
nifL gene was genetically modified by ~500 bp insertion.
Processed data file: genes.fpkm_table.txt


title: Wt HSC treated with IFNγ+VN-3


title: D6-6

city: Frederiksberg C

first: Irina

middle: Alexandra

last: Ionescu

address: Thorvaldsensvej 40

department: Department of Plant and Environmental Sciences

country: Denmark

institute: University of Copenhagen

data_processing:
Reads of all 21 samples were trimmed (using Trimmomatic v0.33) (Bolger, Lohse et al. 2014), removing reads shorter than 50 bp and with a quality score below 35.
These high quality reads were used as input to perform transcriptome assembly after normalization (Trinity v2.0.6) (Grabherr, Haas et al. 2011). Normalized reads were mapped against the human genome to remove possible contaminants. Only 0.15% of the reads mapped to the human genome and were discarded from further analyses. A Trinity de novo assembly was conducted, removing k-mers with only one count. Transcript redundancy was removed (with CD-HIT-EST v4.6) (Li and Godzik 2006), obtaining a raw assembly.
High quality reads from each sample were mapped to the transcriptome assembly with STAR (Dobin, Davis et al. 2013).
Expression levels, in terms of FPKM and posterior counts, were calculated (eXpress v1.5.1) (Roberts and Pachter 2013).
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample

organism: Prunus avium

source_name: sweet cherry flower buds

growth_protocol: Sweet cherry trees of the cultivar ‘Burlat’ grafted on the rootstock Saint Lucie GF 64 (SL 64) (P. mahaleb L.) were grown in the experimental orchard of La Maestra (Jumilla, Spain, 38.4764° N, 1.3222° W). ‘Burlat’ was chosen, because it is considered a reference cultivar for sweet cherry. The chill requirements of ‘Burlat’ in Jumilla are 934 chill units (CU).

extract_protocol:
Total RNA was extracted with the Spectrum Plant Power kit (Sigma-Aldrich) according to manufacturer’s instructions. Additions to the protocol were the following: PVPP (50 mg) was mixed with frozen ground plant material (50 mg) before the addition of lysis buffer and gDNA was degraded on column with RNAse-free DNAse (Qiagen). The resulting RNA was analyzed on a Bioanalyzer (2100, Agilent). All selected samples had an RNA Integrity Numbers above 9.
Total RNA was used in the Illumina TruSeq stranded mRNA library preparation kit according to manufacturer’s instructions.

treatment_protocol: When 720 CU were fulfilled in January 2015 (77 % of chill requirements), approximately one hundred 30 cm long branches were cut from the trees and transported to the laboratory in wet paper. Branches from three neighboring trees (tree 4, 5 and 6) were taken for each treatment group, representing three biological replicates. One treatment group was sprayed until drop-off with 2% Dormex (520g/L hydrogen cyanamide, AlzChem, Germany) in deionized water. The other treatment group was sprayed with deionized water as a control. The branches were placed in a growth chamber in controlled conditions (forcing conditions: 22-24°C, 70% relative humidity, constant light). The branches were immersed in tap water, which was changed every 5 days. Stems were cut 1 cm every week, to avoid xylem clogging. Hydrogen cyanamide- and control branches were sampled at 1, 3, 6, 8, 12, 15 and 18 days after treatment, always between 9 and 12 AM. At day 0, an untreated sample was collected (6 PM). For sampling of each biological replicate, the flower buds (stages A-D according to (Baggiolini 1952)) of one entire branch were combined. This was done to remove the bias of natural developmental heterogeneity. Samples were frozen immediately in liquid nitrogen and kept at -80°C until analysis.

tag: treatment

value: hydrogen cyanamide-treated

tag: replicate

value: biological replicate 3

tag: time point

value: day 6


title: D6-5

value: biological replicate 2


title: Swum NSG - rep 3 (#7290)

description: swam


title: Not swim NSG - rep 1 (#7288)

description: not swim


title: Swum FKRPP448L-NSG - rep2 (#6759)

description: swam


title: D6-4

value: biological replicate 1


title: Wt HSCs treated with IFNγ-4


title: D3-6

value: day 3


title: D3-5


title: NCAPH2_KD_Hist_chr3

city: Kansas City

first: Jennifer

last: Gerton

state: Missouri

address: 1000 E. 50th Street

institute: Stowers Institute for Medical Research

description:
forward primer: GGCTCCCTTCCTTTCCATCAAGATCT
reverse primer: GTTTCAGGTTGCTGTGGAATAAGACACCAT

data_processing:
Library strategy: 4C-seq
Images analysis and base calling was done using the solexa pipeline
The 4C libraries were barcoded and pooled together ran on a HiSeq 2500. The barcoded samples are demultiplexed, and separated by each bait primer types. The reads were processed by 4Cseqpipe pipeline.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files containing continuous-valued data in track format

source_name: Mouse embryonic stem cells

growth_protocol: V6.5 mouse embryonic stem cells (mESCs) were grown on irradiated MEFs in ESC-c mediua supplemented with 15% fetal bovine serum (FBS). MEFs were removed and the mESCs were pelleted down and cultured in two 150 mm dishes without MEFs until 80% confluent, when the cells were harvested for 4C.

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min and quenched with glycine. Crosslinked chromatin was digested with 200 U BglII for 4 hours at 37°C for 4 hours and an additional of 200U BglII overnight at 37°C, while shaking at 900 rpm.  After that, 10 % SDS was added to the sample and incubated for 25 min at 65°C while shaking at 900 rpm to inactivate the enzyme. Chromatin ends were ligated 100 U T4 DNA ligase under diluted conditions that favor junctions between cross-linked DNA fragments. 50 U NlaIII was added to the mixture and incubated overnight at 37°C. After that, chromatin ends were re-ligated. 4C DNA samples were barcoded and sequenced on Illumina HiSeq 2500.
The universal Illumina adaptors were added to the pimers of each chromatin sample for Solexa sequencing.

treatment_protocol: NCAPH2 was knocked down by shRNA (Sigma, TRCN0000175785). 2 μg/mL puromycin was added to the media for selection of the puromycin resistance cells. The media was changed daily and replaced with puromycin containing media for 5 days.

value: Mouse embryonic stem cells

tag: passages

tag: strains

value: NCAPH2 knock down


title: NCAPH2_KD_Hist_chr13

description:
forward primer: GTGAACTTACATTTTCTGCTGAAGAA
reverse primer: CTAAAGTTGATGGATTTTCAAGACAAG


title: Control_Hist_chr3

value: control


title: D3-4


title: Wt HSCs treated with IFNγ-1

value: Bone marrow


title: Wt HSCs treated with IFNγ-3

value: 8-10 weeks


title: Wt HSCs (Control for IFNγ and IFNγ+VN)-4


title: shNCAPH2_2

data_processing:
Images analysis and base calling was done using the solexa pipeline
Reads from Controls and NCAPH2 knockdown samples were aligned to the mouse genome UCSC mm9 and to gene annotations from Ensembl 72 using TopHat 2.0.10 using default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-Seq read counts were computed for each gene using edgeR.

growth_protocol: V6.5 mouse embryonic stem cells (mESCs) were grown on irradiated MEFs in ESC-c mediua supplemented with 15% fetal bovine serum (FBS). MEFs were removed and the mESCs were pelleted down and cultured in two 150 mm dishes without MEFs until 80% confluent, when the cells were harvested for RNA extraction.

extract_protocol:
Total RNA from mouse ES cells was isolated with TRIzol Reagent (ThermoFisher Scientific, 15596) following the manufacturer’s instructions. RNA was treated with DNase I (NEB, M0303S) to remove contaminated genomic DNA. After that, RNA was depleted of ribosomal RNA with the Ribo-Zero kit (Epicentre).
The ribo-depleted RNA samples were amplified with the TruSeq RNA Sample Prep Kit (Illumina) for Solexa sequencing.

treatment_protocol: 2 μg/mL puromycin was added to the media for selection of the puromycin resistance cells. The media was changed daily and replaced with puromycin containing media for 5 days.

tag: transfection


title: D1-5

value: day 1


title: D1-6


title: Wt HSC treated with IFNγ+VN-1


title: Control_Hist_chr13


title: shNCAPH2_1


title: Swum FKRPP448L-NSG - rep1 (#6752)

description: swam

value: Diaphragm

value: 8-10 weeks old mice


title: Wt HSCs (Control for IFNγ and IFNγ+VN)-2


title: shGFP_2

value: shGFP


title: W6-6

value: water-treated (control)


title: Wt HSCs (Control for IFNγ and IFNγ+VN)-3

value: wild type


title: W6-5


title: shGFP_1


title: Wt HSCs (Control for IFNγ and IFNγ+VN)-1


title: W6-4


title: shNCAPH2_TFIIIC_2

data_processing:
Images analysis and base calling was done using the solexa pipeline
Reads from control and knockdown samples were aligned to the mouse genome UCSC mm9.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files that contain continuous data to be displayed in the genome browser

growth_protocol: V6.5 mouse embryonic stem cells (mESCs) were grown on irradiated MEFs in ESC-c mediua supplemented with 15% fetal bovine serum (FBS). MEFs were removed and the mESCs were pelleted down and cultured in two 150 mm dishes without MEFs until 80% confluent, when the cells were harvested for ChIP.

extract_protocol:
Standard ChIP protocol was used. Briefly, nuclei were isolated using nuclearlysis buffer, followed by being lysed with SDS buffer to extract chromatin. The chromatin was sheared by Covaris sonicator to a size range of 300-700 base pairs. The chromatin samples were incubated with 6 μL antibodies overnight at 4°C with rotation, followed by incubation with Protein A/G dynabeads for 2 hours at 4°C with rotation. . The beads were washed twice with 0.1% SDS Lysis Buffer for 5 min each at 4°C, followed by washing twice with High Salt Wash Buffer for 5 min each at 4°C, followed by washing twice with Lithium Chloride Wash Buffer for 5 min each at 4°C. After that, the beads were washed with TE buffer with 0.2% Triton. Chromatin was eluted by adding elution buffer. Eluted chromatin was reverse cross-linked by adding 0.3M NaCl and incubating it overnight at 65°C, which is followed by treatment of 6 μL proteinase K. Chromatin was purified by Qiagen PCR purification kit (Qiagen, 28106), following the manufacturer’s protocol.
The Illumina adaptors were added to each chromatin sample for Solexa sequencing.

value: V6.5 Mouse embryonic stem cells

tag: chip antibody

tag: chip antibody provider

value: Bethyl

tag: chip antibody catalog number


title: W3-6

value: biological replicate 3


title: Wt HSCs treated with IFNγ-2

tag: strain


title: shNCAPH2_TFIIIC_1


title: Wt HSCs treated with VN-3

description: processed data: Wt_Control-vs-VN.txt


title: shTFIIIC_NCAPH2_2

value: shTFIIIC


title: Wt HSCs treated with VN-2

description: processed data: Wt_Control-vs-VN.txt


title: W3-4

value: biological replicate 1


title: D1-4

value: hydrogen cyanamide-treated


title: Wt HSCs treated with VN-1

description: processed data: Wt_Control-vs-VN.txt


title: Wt HSCs (Control for VN)-4

description: processed data: Wt_Control-vs-VN.txt


title: W1-6


title: Wt HSCs (Control for VN)-2

description: processed data: Wt_Control-vs-VN.txt


title: shGFP_NCAPH2_2


title: shGFP_TFIIIC_1


title: Wt HSCs (Control for VN)-3

description: processed data: Wt_Control-vs-VN.txt


title: Wt HSCs treated with VN-4

description: processed data: Wt_Control-vs-VN.txt


title: day0-6

value: before treatment

value: day 0


title: Wt HSCs (Control for VN)-1

description: processed data: Wt_Control-vs-VN.txt


title: shGFP_TFIIIC_2


title: day0-4


title: W1-4


title: day0-5

value: biological replicate 2


title: 2080128_TimePoint7_WholeBlood

city: Atlanta

first: Mary

last: Galinski

state: GA

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

institute: Emory University

description:
E04M99FGMmCyDaBM_Cynomolgi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E04M99FGMmCyDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx

data_processing:
Bases were called with Illumina RTA (Real-Time Analysis, v1.13.48) with default parameters.  FASTQC (v0.10.1) was used to assess data quality, but the data were not filtered at this stage.
To quantify gene expression,  RNA-Seq reads were mapped to the listed assembly and annotation using Tophat2 (Trapnell et al, 2013).  Default options were used with the exception that the command --library-type fr-secondstrand was used since reads were generated using a stranded library preparation method from Illumina.  This allowed differentiation between sense and antisense transcripts.  Only reads that map to a single location in the genome were included, to ensure high-confidence mapping.
Several quality control steps were used to verify the reliability of the data: linear correlation of estimated abundance of ERCC spike-in controls with known concentration; confirmation of 99.9% strand-specificity of the controls; less than 0.1% control fusion transcripts; and absence of 3’ bias in the controls was confirmed with RSeqC software (https://code.google.com/p/rseqc).  Transcript abundance levels were inferred using HTSeq v0.5.4 (http://www-huber.embl.de/users/anders/HTSeq/doc/).  HTSeq takes the short-read mapping file (bam) from tophat2 and the gene annotation file which contains the locations of all annotated genes.  Since some libraries were sequenced more deeply than others, the libraries were normalized before determining differential gene expression using the gene level expression files with the default parameters of DESeq v1.10.1 (http://www.bioconductor.org/packages/release/bioc/html/DESeq.html).
Genome_build: RNA-Seq reads were mapped to both a host and parasite genome.  Host: An early version of a new  assembly (as of 5/2014) of the rhesus macaque (MacaM assembly, v4.0, created by Aleksey Zimin at the University of Maryland, Rob Norgren at the University of Nebraska Medical Center and their colleagues.  The MacaM assembly has been deposited in GenBank under accession  PRJNA214746 ID: 214746. Parasite: PlasmoDB version 9.3 of the Plasmodium cynomolgi B strain genome assembly was used. The assembly has been deposited in GenBank under the accession PRJDA49901 ID: 49901.
Supplementary_files_format_and_content: Excel files contain normalized transcript abundances at the gene level, for each individual.  Abundances are further classified by experimental Time Point (1-7), and Specimen Type (Whole Blood).  One sample is from a transfusion donor, animal ID = CF97.
Supplementary_files_format_and_content: Gene Data Column headers are defined as follows:    'gene_name':  Identifiers of all Genes in the reference annotation.     'gene_symbol': Symbols of all Genes in the reference annotation.    'Sample ID / Raw File 1 / Raw File 2 /Normalized Read Counts':  Sample ID, Raw sequence file names for the sample, and Library size normalized and Log2 transformed read counts of all genes, from the Specimen Type, Individual ID, and Time Point listed directly below.     Notes:  There will be one read count column per specimen per NHP  (Non-Human-Primate) per Time Point. So, 1 * 5 * 7 = 35 columns with read counts.  Note that one NHP was euthanized during the experiment, so the total number of samples is 31.    0 as value for read counts of some genes Overlapping genes (sharing exons) were "collapsed" into a single gene for the purposes of RNA-Seq read assignments. So, the read count at such a locus is representative of the cumulative expression of all the genes at that locus. BUT, the entire read count is assigned to only one of the genes and the others in the locus are assigned 0.

organism:
Macaca mulatta
Plasmodium cynomolgi strain B

source_name: whole blood

growth_protocol: Animals approved for use were moved into experimental housing 10 days prior to the start of the experiment.

extract_protocol:
Whole blood (3 ml) was collected in Tempus tubes (Applied Biosystems) that also preserve mRNA; these samples include erythrocytes, platelets and granulocytes in addition to mononuclear lymphocytes.  RNA was extracted using Tempus-Spin RNA isolation kits. The quality of all RNA samples was confirmed using a Bioanalyzer, with an RNA Integrity Number (RIN) greater than 8 recorded for all samples.
Approximately 1 μg of total RNA per sample was converted to double-stranded cDNA using poly-A beads to enrich for mRNA, and Illumina TruSeq Stranded mRNA Sample Prep kits to generate strand-specific libraries.   As a quality control, 96 spike-in RNAs of known concentration and GC proportions (ERCC Spike-In Control, Life Technologies) were added to constitute approximately 1% of the total RNA for each library.  Adapters were ligated to facilitate 3-plex sequencing on an Illumina HiSeq2000 at the Yerkes Genomics Core, aiming for 80 million paired-end 100 base pair (bp) reads per library.

treatment_protocol: During the 100-day experiment, artemether was delivered on days 27 and 53 (corresponding to time points 3 and 4), for blood-stage treatment.  Chloroquine and primaquine were administered at the end of the study to treat liver- and blood-stages.

tag: gender

value: Male

tag: mahpic non human primate individual id

tag: infected with

value: Plasmodium cynomolgi strain B


title: 2080102_TimePointNA_WholeBlood


title: 2080122_TimePoint7_WholeBlood


title: W3-5

value: day 3


title: 2080123_TimePoint6_WholeBlood


title: 2080106_TimePoint7_WholeBlood


title: 2080115_TimePoint7_WholeBlood


title: Giant  panda_breast milk_30d.tar.gz

city: Wen’jiang,Chengu

first: long

middle: ke

last: ren

state: Sichuan

address: Huimin road, 211#

department: 1	Institute of Animal Genetics & Breeding

institute: sichuan agriculture university

data_processing:
Seven libraries were subjected to single-end sequencing in 36 nt reads using an Illumina Genome Analyzer II. The bioinformatics pipeline for miRNA discovery and profiling was carried out as previously described, with some improvements. All reads were counted and the identical reads were combined into a single kind. The raw reads were then subjected to a series of additional strict filters (such as the digital filters of base-call quality, reads length, and sequence comparison) with acceptance criteria derived from the statistics of mammalian and plant miRNAs in miRBase 21.0, respectively. The reads originated from known RNAs of the giant panda and bamboo (i.e., mRNA; rRNA, tRNA, snRNA, and snoRNA; and repetitive sequence elements) were also filtered. The raw reads that passed through a series of filters were mapped to all known pre-miRNAs of mammals and plants registered in miRBase 21.0, and the Giant Panda (Ailuropoda melanoleuca, AilMel1.0) and bamboo (http://www.ncgr.ac.cn/bamboo) genome using NCBI Local BLAST, respectively.
To conduct differential analysis, miRNA read in each library was normalized to obtain the expression of transcripts per million (RPM).
Genome_build: Ailuropoda melanoleuca, AilMel1.0; http://www.ncgr.ac.cn/bamboo; miRbase 21.0
Supplementary_files_format_and_content: identified miRNAs in each library with reads and normalized data

organism: Ailuropoda melanoleuca

source_name: breast milk

extract_protocol:
Three females were sampled in all, and each individual were sampled over multiple lactations, including 0, 3, 7, 15 and 30 days after delivery. Breast milk samples (5-10 ml) were collected from each stages. Total RNA isolated from individuals in five lactation stages (0, 7, 15 and 30 days after delivery) were pooled in equal quantities for each sta
small RNA libraries were prepared for sequencing using standard Illumina protocols

value: 30d after delivery

tag: sample type

value: breast milk


title: 2080129_TimePoint6_WholeBlood


title: 2080116_TimePoint6_WholeBlood


title: shTFIIIC_NCAPH2_1

tag: cell type


title: Giant  panda_breast milk_15d.tar.gz

tag: age

value: 15d after delivery


title: W1-5

value: water-treated (control)

value: day 1


title: 2080107_TimePoint6_WholeBlood


title: Giant  panda_breast milk_7d.tar.gz

value: 7d after delivery


title: shGFP_NCAPH2_1

value: V6.5 Mouse embryonic stem cells

value: shGFP

value: Bethyl


title: 2080120_TimePoint5_WholeBlood


title: Giant panda_breast milk_3d_replicate3.tar.gz

value: 3d after delivery


title: 2080104_TimePoint5_WholeBlood


title: 2080127_TimePoint4_WholeBlood


title: Giant panda_breast milk_3d_replicate1.tar.gz


title: Bamboo.tar.gz

organism: Bambusa vulgaris

source_name: bamboo

tag: tissue

value: leaf


title: Giant panda_breast milk_3d_replicate2.tar.gz


title: 2080121_TimePoint4_WholeBlood


title: 2080105_TimePoint4_WholeBlood


title: 2080126_TimePoint3_WholeBlood


title: 2080119_TimePoint3_WholeBlood


title: 2080110_TimePoint3_WholeBlood


title: 2080103_TimePoint3_WholeBlood


title: 2080112_TimePoint3_WholeBlood


title: Giant  panda_breast milk_0d.tar.gz

value: 0d after delivery


title: 2080124_TimePoint2_WholeBlood


title: 2080130_TimePoint2_WholeBlood


title: 2080117_TimePoint2_WholeBlood


title: 2080108_TimePoint2_WholeBlood


title: 2080125_TimePoint1_WholeBlood


title: 2080118_TimePoint1_WholeBlood


title: 2080111_TimePoint1_WholeBlood


title: 2080109_TimePoint1_WholeBlood


title: 2080131_TimePoint1_WholeBlood


title: 2080113_TimePoint5_WholeBlood


title: 2080114_TimePoint4_WholeBlood


title: 3OHC12 3

city: Canberra

first: Sylvain

last: Foret

state: ACT

address: Gould Building #116

department: Research School of Biology

country: Australia

institute: The Australian National University

description:
Curvibacter sp. AEP1.3 treated with OHC12-HSL
F3

data_processing:
base calling: bcl2fastq2-v2.16.0.10: bcl2fastq with default options
alignment: subread-1.4.6-p3: “subread-align -u -H -d 50 -D 600 -T 1 --BAMoutput -i AEP -r reads1 -R reads2 -o out”
read counting: subread-1.4.6-p3: “featureCounts -p -T 32 -F SAF -a $REF -o counts.txt *.bam”
Count files for individual samples were generated by splitting the featureCounts output
Genome_build: AEP1-3_1.0
Supplementary_files_format_and_content: [.txt] Tab separated with header. Fields are: "Geneid" "Chr" "Start" "End" "Strand" "Length" "counts"

organism: Curvibacter sp. AEP1.3

source_name: cell culture

growth_protocol: 500ml of R2A broth was innoculated with 1x10^5 CFU/ml Curvibacter sp. A1.3 of a fresh culture and incubated at 18C and 200 rpm until OD600 reached 0.145

extract_protocol:
RNA was extracted with RNA-easy (Quiagen)
TrueSeq Stranded mRNA LT - RiboZero Kit (Illumina)

treatment_protocol: 10 uM 3OC12-HSL, 10uM 3OHC12-HSL or 1:2000 ethyl acetate (with 0.01% acetic acid) were added to cultures for four hours.

tag: treatment


title: 3OHC12 4

description:
Curvibacter sp. AEP1.3 treated with OHC12-HSL
F4


title: 3OC12 5

description:
Curvibacter sp. AEP1.3 treated with OC12-HSL
E5


title: 3OC12 4

description:
Curvibacter sp. AEP1.3 treated with OC12-HSL
E4


title: 3OC12 1

description:
Curvibacter sp. AEP1.3 treated with OC12-HSL
E1


title: 3OHC12 5

description:
Curvibacter sp. AEP1.3 treated with OHC12-HSL
F5


title: 3OHC12 1

description:
Curvibacter sp. AEP1.3 treated with OHC12-HSL
F1


title: 3OC12 2

description:
Curvibacter sp. AEP1.3 treated with OC12-HSL
E2


title: solvent 2

description:
Curvibacter sp. AEP1.3 treated with solvent
D2

value: solvent


title: solvent 3

description:
Curvibacter sp. AEP1.3 treated with solvent
D3


title: MDA126

city: Houston

first: Andrea

last: Ochoa

state: TX

address: 1515 Holcombe

institute: UT MD Anderson Cancer Center

data_processing: The TorrentSuite Software was used to extract all fastq files, and total counts data.

organism: Homo sapiens

source_name: Bladder tumor

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit. Quality control was performed by NanoDrop ND-1000 and Agilent Bioanalyzer. 20 ng of small RNA was used for cDNA library preparation using the Ion Total RNA-Seq Kit v2. The Agilent Bioanalyzer was used to quantitate the cDNA library.
Ion Total RNA-Seq Kit v2

value: bladder tumor

tag: cstage

tag: age (at specimen collection)

tag: os censor

value: censored

tag: dss censor

tag: survival (mo)


title: NDH SDC

city: Columbus

first: Julie

middle: A

last: Reynolds

state: OH

address: 318 W 12th Ave, Aronoff Lab, rm 300

department: Evolution, Ecology, Organismal Biology

institute: Ohio State University

data_processing:
Raw reads obtained using Illumina's Sequencing Control Studio software version 2.8
Real-time sequencing image analysis and base calling by Illumina's Real-Time Analysis version 1.8.70
Extracted sequencing reads stored in file [Sample]_RawData.fq
Mappable sequences obtained from raw reads
Mapping mappable reads to reference database (i.e. Arthropod miRNAs reported in miRBase version 21
Multiple sample comparison
Genome_build: Jelly.SoapWFull65.broken.fasta (http://stash.osgconnect.net/+justinpeyton/Jelly.SoapWFull65.broken.fasta)
Supplementary_files_format_and_content: Processed files include text file showing sequencing mapping to miRBase and an excel file showing number of reads for each unique sequence in 6 samples.
Supplementary_files_format_and_content: Report_5931-comparisons_to_sbu.xlsx (reads and normalized reads for replicate samples)
Supplementary_files_format_and_content: comp_5931_uni_miRs.txt (raw sequences mapped to known Arthropod sequences in miRBase)
Supplementary_files_format_and_content: comp_5931_mir_aln.txt (quality scores for sequence mapping)

organism: Sarcophaga bullata

source_name: whole body

growth_protocol: Sarcophaga bullata larvae from mothers with no diapause history were reared at 18  degrees Celcius under either a a short-day (SD) photoperiod to induce diapause (dormancy) long-day (LD) photoperiod to avert diapause.  Flies were allowed to developed until they reached the phanerocephalic stage (i.e., the developmental stage when diapause is entered) at which time their RNA was extracted.

extract_protocol:
Total RNA was extracted from individual pupae with a mirVana kit (Ambion) according to the manufactuer's instructions.  Concentration was measured with a Nanodrop spectrophotometer. Equal amounts of total RNA from 3 pupae of the same type (SD or LD) was pooled prior to library construction
Illumina Truseq Small RNA Preparation kit according to the sample preparation guide.

tag: dipause state

value: Diapause

tag: developmental stage

value: pupae

tag: maternal diapause history

value: No diapause history

tag: photoperiod

value: Short day


title: NDH SDB


title: NDH SDA


title: NDH LD2P

value: Nondiapause

value: Long day


title: NDH LD3P


title: NDH LD1P


title: 3OC12 3

description:
Curvibacter sp. AEP1.3 treated with OC12-HSL
E3


title: Control RNAi batch 6

status: Public on May 31 2017

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

data_processing:
RNA-seq reads were aligned to the GRCh38 genome assembly using STAR version 2.4.1c
Gene-level expression quantitation was performed using rsem version 1.2.22
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file for each sample with gene id, transcript ids, length, effective length, expected count, TPM, FPKM

growth_protocol: HeLa Kyoto cells were grown in DMEM medium (PPA), supplemented with 10% FCS (Sigma-Aldrich) and 1% penicillin / streptomycin (PAA) at 37°C and 5% CO2

extract_protocol:
Total RNA from HeLaK cells subjected to PWWP2A siRNAs and control siRNAs was isolated utilizing the RNeasy mini kit (Qiagen) according to manufacturer’s instructions. The quality of the RNA (amount and integrity) was assessed using the BioAnalyzer and a RNA 6000 pico kit (Agilent). mRNA isolation, fragmentation, first and second strand cDNA synthesis and end repair were carried out using the NEBNext Ultra RNA library prep kit for Illumina (NEB) following the manufacturer’s instructions
cDNA sequencing libraries were established with the MicroPlex Library Preparation Kit (Diagenode) as described above

treatment_protocol: 2 x 10^5 HeLa Kyoto cells were seeded into 6-well plates 24 h prior to transfection to reach a confluence of 30 – 40%. Small interfering RNA (siRNA) stock solutions (100 µmol in 1xUniversal Buffer) were diluted 1:5 in sterile water. 4 µl Oligofectamine transfection reagent was diluted in 11 µl Opti-MEM and incubated at RT for 5 min. Meanwhile, 10 µl of siRNA dilution was mixed with 175 µl Opti-MEM. 15 µl transfection reagent dilution was added and incubated for 20 min at RT. Cells were washed twice with sterile PBS, growth medium replaced by 800 µl DMEM not containing FCS or antibiotics and the transfection mix added drop wise. After 4 h at 37°C in the incubator 500 µl DMEM supplemented with 30% FCS was added. Cells were harvested and analyzed 2 to 3 days after transfection.

tag: cell line

value: HeLa Kyoto cells

value: control siRNA

tag: experimental batch


title: Control RNAi batch 4


title: PWWP2A RNAi batch 2

value: PWWP2A siRNA


title: Control RNAi batch 5


title: PWWP2A RNAi batch 4


title: solvent 5

description:
Curvibacter sp. AEP1.3 treated with solvent
D5


title: PWWP2A RNAi batch 5


title: PWWP2A RNAi batch 3


title: 3OHC12 2

description:
Curvibacter sp. AEP1.3 treated with OHC12-HSL
F2


title: PWWP2A RNAi batch 6


title: Control RNAi batch 2


title: ChIP input batch 5

data_processing:
ChIP-seq reads were aligned to the GRCh38 genome assembly using bowtie version 1.1.1 parameter m=1
Aligned reads were extended to 200 bp
Coverage vectors were generated by counting overlapping fragments at each genomic position
Genome_build: GRCh38
Supplementary_files_format_and_content: bedgraph files with coverage

extract_protocol:
Immunoprecipitations were carried out with S1 mononucleosomes derived from HeLaK cells stably expressing GFP-tagged  H2A.Z.1, H2A.Z.2 or PWWP2A from 4 x 107 cells in 1.5 ml low-binding tubes. 25 µl slurry GFP-trap magnetic beads (ChromoTek) per IP were equilibrated in EX100 buffer (10 mM Hepes pH 7.6, 100 mM NaCl, 1.5 mM MgCl2, 0.5 mM EGTA, 10% glycerol (v/v), 10 mM β-glycerolphosphate, 1mM DTT, 1x protease inhibitors), added to mononucleosomes and incubated for 2.5 h at 4°C while rotating. Beads were quickly spun down, separated in a magnetic rack and the supernatant kept as non-bound fraction. For GFP-PWWP2A IPs, mononucleosomes prepared from stable HeLa Kyoto GFP-PWWP2A cell line were precleared with G-protein magnetic beads (Millipore) for 1 h at 4°C and subsequently incubated over night (ON) with 2 µl of GFP antibody (kind gift of Prof. Andreas Ladurner, LMU Munich) at 4°C while rotating. Next, 20 µl of magnetic G-protein beads equilibrated in EX100 buffer were incubated with the reaction for additional 4 h at 4°C while rotating. An IP with an unspecific rabbit IgG antibody served as negative control.  For native H3K4me3 IPs, mononucleosomes from wild type HeLaK cells were prepared. The MNase digestion protocol was optimized for the use of 4 x 106 cells per IP. The precleared mononucleosomes were incubated with 1 µl of a rabbit H3K4me3 antibody (Diagenode). Washed beads were resuspended in 100 µl TE, 3 µl 10% SDS and 5 µl of 20 mg/ml proteinase K were added and incubated for 1 h at 65 °C. Suspensions were vortexed briefly, magnetically separated and the supernatant transferred to a fresh tube. Beads were washed once with 100 µl TE containing 0.5 M NaCl, magnetically separated and the supernatant mixed with the first supernatant. Input fractions were processed in parallel. After Phenol/chlorophorm/isoamylalcohol extracting and ethanol precipitating the DNA, the IP DNA pellet was resuspended in 12 µl and the input DNA pellet in 32 µl 10 mM Tris-HCl (pH 7.5). DNA concentrations were determined with the Qubit dsDNA hs Kit (Invitrogen) and DNA size monitored on a 1000 DNA BioAnalyzer chip (Agilent).
Illumina Sequencing libraries were established with the MicroPlex Library Preparation Kit (Diagenode) following the manufacturer’s instructions with following variations. The number of step 5 amplification cycles was scaled according to the amount of input material. When purifying libraries after amplification, samples were incubated 15 min with AMpure beads instead of 5 min, ethanol washed beads were dried for 3 min at RT instead at 37°C and DNA was eluted in 22 µl 10 mM Tris-HCL pH 7.5 instead of TE

tag: chip antibody

value: none (input)


title: PWWP2A RNAi batch 1


title: Control RNAi batch 1


title: ChIP GFP-PWWP2A batch 4

value: ChromoTek GFP-trap


title: solvent 4

description:
Curvibacter sp. AEP1.3 treated with solvent
D4


title: ChIP H3K4me3 batch 5

value: anti-H3K4me3 (Diagenode C15410003)


title: solvent 1

description:
Curvibacter sp. AEP1.3 treated with solvent
D1


title: ChIP GFP-PWWP2A batch 3


title: ChIP input batch 4


title: ChIP input batch 2


title: ChIP input batch 3


title: ChIP input batch 1


title: ChIP GFP-H2A.Z.2 batch 2


title: ChIP GFP-H2A.Z.1 batch 2


title: ChIP GFP-H2A.Z.2 batch 1


title: ChIP GFP-H2A.Z.1 batch 1


title: Control RNAi batch 3


title: 6hpf_Dcp2DN

city: Kita-ku

first: Yuichiro

last: Mishima

state: Kyoto

address: Motoyama, Kamigamo,

department: Department of Frontier Life Sciences

institute: Kyoto Sangyo University

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were filtered with the quality cut-off 20 and minimum percentage 90.
Qualified reads were mapped to the zebrafish genome (Zv9/danRer7) using TopHat v1.4.0. with the gene model annotation Zv9.72.
Reads overlapping with UCSC RepeatMasker annotations (Zv9/danRer7) were discarded.
Differential expression levels between conditions were calculated using Cuffdiff v2.1.1. with the gene model annotation Zv9.72.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample, differential expression between condotions in log2 scale and statistical significance.

organism: Danio rerio

source_name: whole embryo

growth_protocol: fertilized eggs were obtained by natural breadings

extract_protocol:
Total RNA was extracted from 40–50 embryos using TRI Reagent (Molecular Research Center), treated with DNaseI (TAKARA) and purified with RNeasy Mini Kit (QIAGEN).
Libraries were prepared using TruSeq Stranded Total RNA with Ribo-Zero (Illumina).

tag: strain

value: AB

tag: experiments

tag: stages

value: 6 hpf


title: 6hpf_mock

value: control


title: SW620_input

city: Chuo-ku

first: Naoko

last: Iida

state: Tokyo

address: 5-1-1 Tsukiji

institute: National Cancer Center in Japan.

description: genomic DNA

data_processing:
ChIP-seq reads were aligned to the hg19 human genome using bowtie-1.1.2with the options -S -t -m 2 -n 2 --best –strata.
ChIP-seq reads aligning to the region were extended by 200 bp into using BEDTools (version 2.17.0).
Wiggle outputs were created by MACS 1.4.2 using parameters -p 1e-9 -w -S --space=50 to calculate read density in 50 bp bins.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment.

source_name: colon cancer cells

extract_protocol:
Cells were cross-linked in 1% formalin and were sonicated in SDS-lysis buffer. Chromatin was precipitated in ChIP dilution buffer using an anti-H3K27ac antibody. DNA was purified by phenol and chloroform extraction and ethanol precipitation.
Libraries were prepared according to Illumina's instructions. Libraries were sequenced using Illumina HiSeq4000.

tag: antibody


title: EV from 293T Cells Full Replicate 3

city: Gainesville

first: Thomas

last: Schmittgen

state: FL - FLORIDA

address: 2033 Mowry Road

department: Pharmacy

institute: Univ of Florida

description:
STS0018
Small RNA-Seq
Processed data file: NGS18 Processed_data_Matrix.xls

data_processing:
First, adapters were trimmed using fastx-clipper. Next, tRNA was removed by aligning to a tRNA "genome" using bowtie2.
The aligned reads were removed from further analysis. This step was repeated with another artificial genome consisting of only mtRNA and rRNA sequences. These trimmed and filtered reads were then aligned to miRBase using bowtie2.
The counts of aligned reads were used to tRNA, mtRNA, and rRNA as well as other calculations based on the trimmed fastq file and aligned BAM file (average read length, etc) in a custom script that outputs quality control parameters.
Finally, the aligned BAM files were used to generate counts tables for mature miRs using another custom script. These counts tables were passed into DESeq2 to perform differential expression analysis.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: NGS18_Processed_data_Matrix.xls: Excel file

source_name: EV from 293T cells

growth_protocol: HEK293T cells were cultured as adherent cells in T-flasks or 150 mm dishes using Dulbecco's Modified Eagle Medium (Life Technologies, Grand Island, NY) supplemented with 10% fetal bovine serum (FBS) (Sigma, St. Louis, MO). The collection of EVs from cells cultured used FBS that was first depleted of exogenous EVs by an 18 h centrifugation at 100,000 × rcf, 4° C. Cells were cultured in a 5% CO2/humidified air incubator. HEK293T cells were passaged using trypsin/EDTA and only passages less than 35 were used throughout the study. Cultures were scaled up to 12 or 24, 150 mm dishes prior to isolating the EVs.

extract_protocol:
EV collection protocol: EVs were isolated using a standard ultracentrifugation protocol. In brief, 0.4 L of cell culture supernatant was centrifuged at 300g for 10 min, transferred to clean tubes, and centrifuged at 2000g for 20 min to remove cell debris. The supernatant was transferred to clean tubes, and centrifuged at 10,000g for 30 min., followed by vacuum filtration using a 0.22-um filter (EMD Millipore, Billerica, MA). Filtered supernatant was transferred to ultracentrifuge tubes (#355622, Beckman Coulter, Brea, CA) and centrifuged at 110,000g for 4 hr in a Beckman Coulter Optima™ XE ultracentrifuge with a Type 45 Ti rotor. The EV pellet was washed once with chilled, sterile phosphate-buffered saline (PBS, pH 7.4), followed by resuspension in 0.3-0.6 ml PBS with 1% DMSO. EV protein yield was measured using Pierce™ BCA Protein Assay (Life Technologies).
RNA of the cells was isolated using the Trizol method, and RNA of EVs was isolated using Exiqon miRCURY RNA Isolation Kit (Cat#300110) according to the manufacturer's protocol.
Libraries were prepared according to Illumina's instructions accompanying the NEBNext® Multiplex Small RNA Library Prep Kit (E7300).

tag: cell type

value: extracellular vesicle (EV)

tag: passages


title: SW620_H3K27ac_ChIPSeq

description: genomic DNA


title: SW48_H3K27ac_ChIPSeq

description: genomic DNA


title: 293T Cells Full Replicate 2

description:
STS0014
Small RNA-Seq
Processed data file: NGS18 Processed_data_Matrix.xls

source_name: 293T cells

value: embryonic kidney cell line


title: SW48_input

description: genomic DNA


title: Caco2_H3K27ac_ChIPSeq

description: genomic DNA


title: RKO_H3K27ac_ChIPSeq

description: genomic DNA

value: RKO


title: RKO_input

description: genomic DNA


title: Caco2_input

description: genomic DNA


title: EV from 293T Cells Full Replicate 2

description:
STS0017
Small RNA-Seq
Processed data file: NGS18 Processed_data_Matrix.xls


title: 293T Cells Full Replicate 3

description:
STS0015
Small RNA-Seq
Processed data file: NGS18 Processed_data_Matrix.xls


title: EV from 293T Cells Empty Replicate 1

description:
STS0010
Small RNA-Seq
Processed data file: NGS18 Processed_data_Matrix.xls


title: 293T Cells Full Replicate 1

description:
STS0013
Small RNA-Seq
Processed data file: NGS18 Processed_data_Matrix.xls


title: 293T Cells Empty Replicate 3

description:
STS0009
Small RNA-Seq
Processed data file: NGS18 Processed_data_Matrix.xls


title: 293T Cells Empty Replicate 2

description:
STS0008
Small RNA-Seq
Processed data file: NGS18 Processed_data_Matrix.xls


title: EV from 293T Cells Empty Replicate 2

description:
STS0011
Small RNA-Seq
Processed data file: NGS18 Processed_data_Matrix.xls


title: 293T Cells Empty Replicate 1

description:
STS0007
Small RNA-Seq
Processed data file: NGS18 Processed_data_Matrix.xls


title: EV from 293T Cells Wild type Replicate 3

description:
STS0006
Small RNA-Seq
Processed data file: NGS18 Processed_data_Matrix.xls


title: RNAseq.Untransfected

city: Berkeley

first: Nicolas

last: Altemose

address: 327 Stanley Hall

department: Bioengineering

institute: University of California, Berkeley

description:
Uniquely Mapped Fragments: 82942607
Multiplex Group: 5

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

source_name: HEK293T cells

growth_protocol: Cells were grown in DMEM media (Sigma D6546) supplemented with 10% FBS (Sigma F7524), 1X L-Glutamine (Sigma G7513), and 1X penicillin/streptomycin (Sigma P0781) in flasks or plates at 37C with 5% CO2. Confluent cells were split 1:10 and passaged for no longer than one month before transfection.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen)
Libraries were prepared for sequencing using standard Illumina protocols by the Oxford Genomics Centre.

value: HEK293T (ATCC CRL-3216)

tag: transfected with


title: 293T Cells Wild type Replicate 1

description:
STS0001
Small RNA-Seq
Processed data file: NGS18 Processed_data_Matrix.xls


title: EV from 293T Cells Wild type Replicate 2

description:
STS0005
Small RNA-Seq
Processed data file: NGS18 Processed_data_Matrix.xls


title: 293T Cells Wild type Replicate 3

description:
STS0003
Small RNA-Seq
Processed data file: NGS18 Processed_data_Matrix.xls


title: EV from 293T Cells Wild type Replicate 1

description:
STS0004
Small RNA-Seq
Processed data file: NGS18 Processed_data_Matrix.xls


title: EV from 293T Cells Full Replicate 1

description:
STS0016
Small RNA-Seq
Processed data file: NGS18 Processed_data_Matrix.xls


title: RNAseq.ZFonly_HA

description:
Uniquely Mapped Fragments: 60581427
Multiplex Group: 5

treatment_protocol: 15 million cells were seeded in 30 ml growth medium in a T175 cell culture flask. The following morning, cells were transfected by mixing 30 ug total construct DNA into 800 ul OPTI-MEM (Life Technologies 31985062), then carefully adding 90 ul FuGENE-HD Transfection Reagent and flicking to mix, incubating at room temperature for 15 minutes, and then adding the mixture dropwise to each dish while swirling gently to mix.

value: HumanPRDM9 (B allele ZF array only)


title: EV from 293T Cells Empty Replicate 3

description:
STS0012
Small RNA-Seq
Processed data file: NGS18 Processed_data_Matrix.xls


title: RNAseq.ChimpPRDM9_HA

description:
Uniquely Mapped Fragments: 77251717
Multiplex Group: 5


title: ATACseq.noZF_HA.hs37d5

description:
Uniquely Mapped Fragments: 11789302
Multiplex Group: 4

extract_protocol:
ATAC libraries were prepared as described (Buenrostro et al., 2013). Briefly, 50,000 cells were lysed in 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630 and the nuclei were pelleted at 500xg for 10 minutes. The transposition reaction was carried out for 30 minutes at 37C using the Nextera DNA Sample Preparation Kit (Illumina) according to the manufacturer’s instructions. The libraries were purified using the MinElute PCR Purification Kit (Qiagen)
Libraries were prepared for sequencing using standard Illumina protocols by the Oxford Genomics Centre.

value: PRDM9 (no ZF array)


title: ATACseq.HumanPRDM9_HA.hs37d5

description:
Uniquely Mapped Fragments: 11814749
Multiplex Group: 4


title: ATACseq.Untransfected.hs37d5

description:
Uniquely Mapped Fragments: 11146480
Multiplex Group: 4


title: Sample 31 [CTRL 2 d35]

city: Martigny

first: Raphaelle

last: Luisier

state: Valais

address: Rue Marconi 19, PO Box 592

country: Switzerland

institute: Idiap Research Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and then mapped to h19 ribosomal RNA using bowtie v1.1.2 with parameters -q -p 8 -v 0. Unmapped reads were finally mapped to hg19 whole genome using tophat2 with parameters  -g 1 -p 8  --library-type fr-firststrand.
For differential gene and transcript expression analysis we ran Kallisto and Sleuth.  Kallisto was used to 1) build a transcript index from the Ensembl GRC38 release 85 Homo sapiens transcriptome (-k 31), 2) pseudo-align the RNA-seq reads to the transcriptome and 3) quantify transcript abundances (-b 100 --single -l 275 -s 50 --rf-stranded). We next identified differentially expressed transcripts and genes with Sleuth, a companion program that uses Kallisto results to differentiate between true biological expression differences and variation resulting from sources of experimental noise.
Genome_build: hg19
Supplementary_files_format_and_content: Relative transcript abundance and transcript per million as obtained from Kallisto software.

source_name: electrically mature motor neurons

growth_protocol: Dermal fibroblasts were cultured in OptiMEM +10% FCS medium. The following episomal plasmids were transfected for iPSC generation: pCXLE hOct4 shp53, pCXLE hSK and pCXLE hUL (Addgene), as previously reported [15]. Details of the lines used in this study are reported in Supplementary table 1. Two of the control lines used (control 2 and control 3) are commercially available and were purchased from Coriell (cat. number ND41866*C ) and ThermoFisher Scientific (cat. number A18945) respectively. Induced PSCs were maintained on Geltrex (Life Technologies) with Essential 8 Medium media (Life Technologies) and passaged using EDTA (Life Technologies, 0.5mM). All cell cultures were maintained at 37°Cand 5% carbon dioxide.

extract_protocol:
Total RNA was extracted from cells using the Maxwell RSC simplyRNA cells kit (Promega), that includes DNase treatment, according to manufacturer’s instructions.
1 ug of total RNA was subjected to Ribo-Zero treatment TruSeq Stranded mRNA preparation Kit (Illumina).

treatment_protocol: Motor neuron (MN)differentiation was carried out using an adapted version of a previously published protocol [Gupta et al. 2012]. Briefly, iPSCs were first differentiated to neuroepithelium by plating to 100% confluency in chemically defined medium consisting of DMEM/F12 Glutamax, Neurobasal, L-Glutamine, N2 supplement, non essential amino acids, B27 supplement, β-mercaptoethanol (all from Life Technologies) and insulin (Sigma). Treatment with small molecules from day 0-7 was as follows: 1μM Dorsomorphin (Millipore), 2μM SB431542 (TocrisBioscience), and 3μM CHIR99021 (MiltenyiBiotec) for 7 days. At day 8, the neuroepithelial layer was enzymatically dissociated using dispase(GIBCO, 1 mg/ml), plated onto laminin coated plates and next patterned for 7days with 0.5μM retinoic acid and 1μMPurmorphamine. At day 14 spinal cord MN precursors were treated with 0.1μM Purmorphamine for a further 4 days before being terminally differentiated in 0.1 mM Compound E (Enzo Life Sciences) to promote cell cycle exit.

value: electrically mature motor neurons

tag: diagnosis

value: none (control)

tag: patient id

value: Patient 3

tag: cell line id

value: CTRL 2

tag: genotype

value: Control

tag: days of differentiation


title: Sample 25 [CTRL 2 d21]

source_name: electrically immature motor neurons

value: electrically immature motor neurons


title: Sample 26 [CTRL 1 d21]

value: Patient 4

value: CTRL 1


title: Sample 18 [CTRL 2  iPSC]

source_name: iPSC cell

value: iPSC cell


title: Sample 30 [CTRL 1 d35]


title: Sample 27 [CTRL 1 d21]


title: 293T Cells Wild type Replicate 2

description:
STS0002
Small RNA-Seq
Processed data file: NGS18 Processed_data_Matrix.xls


title: ATACseq.ZFonly_HA.hs37d5

description:
Uniquely Mapped Fragments: 10859065
Multiplex Group: 4


title: Sample 14 [MUT 1 d35]

value: amyotrophic lateral dystrophy (ALS)

value: Patient 1

value: MUT 1


title: Sample 16 [CTRL 2 iPSC]


title: Sample 17 [CTRL 1  iPSC]


title: Sample 12 [MUT 3 d21]

value: Patient 2

value: MUT 3


title: Sample 11 [MUT 2 d21]

value: MUT 2


title: Sample 15 [MUT 3 d35]


title: Sample 1 [MUT 1 iPSC]


title: Sample 2 [MUT 2 iPSC]


title: Sample 3 [MUT 3 iPSC]


title: Sample 13 [MUT 1 d35]


title: RNAseq.HumanPRDM9_HA

description:
Uniquely Mapped Fragments: 83087497
Multiplex Group: 5

value: HEK293T (ATCC CRL-3216)


title: Sample 10 [MUT 2  d21]


title: siDAZAP1-03

city: Trieste

first: Maurizio

last: Romano

address: Via A. Valerio 28

department: Department of Life Sciences

country: Italy

institute: University of Trieste

description:
Replicate siDAZAP1-03
processed data file:
Control_vs_siDAZAP.DE.tsv
13_AGTTCC
9_rawCount and normCPM column in the GEN151110_R.profiling-table_NAR.xls

data_processing:
HiSeq Control Software v2.0.12.0, Basecalls performed with RTA v1.17.21.3
Reads were aligned to the human reference (GRCh38) using BWA-MEM (bwa-0.7.12) with standard parameters.
Only uniquely aligned reads were used for expression profiling
Gene expression was measured based on annotation GRCh38.ensembl_genes_77_all_exons using featureCounts (Subread package 1.4.6).
Raw read counts were converted to CPM values using TMM normalization (edgeR package)
Differential expression analysis was performed using the edgeR package. Features had to have a counts-per-million value of more than 1 in at least 3 samples or were removed.
Genome_build: GRCh38
Supplementary_files_format_and_content: File *.profiling-table.txt contains per line: Accession of featue, length of feature, length of exon-covered region, short description, raw read counts per sample, CPM values per sample
Supplementary_files_format_and_content: Files *.DE.tsv contain per line: Accession of featue, short description, log2 fold-change, log2 average CPM value, PValue, FDR

source_name: SH-SY5Y_siRNA anti-DAZAP1

growth_protocol: DMEM+FBS10%+Pen/Strep 1%

extract_protocol:
RNA was obtained using Eurogold Trifast (Euroclone, Milan, Italy), following the manufacturer’s instructions.
The RNA sequencing was performed by Eurofins (https://www.eurofinsgenomics.eu/) by using the TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Human neuroblastoma SH-SY-5Y cells were cultured in DMEM–Glutamax-I (Gibco-BRL, Life Technologies Inc., Frederick, MD, USA) supplemented with 10% fetal bovine serum (Gibco-BRL, Life Technologies Inc., Frederick, MD, USA) and Antibiotic-Antimycotic-stabilized suspension (SigmaAldrich, St. Louis, MO, USA) at 37°C incubator with humidified atmosphere of 5% CO2. The siRNA sense sequences used for silencing the different target proteins were the following: luciferase (control): uaaggcuaugaagagauac, TDP-43: gcaaagccaagaugagccu, DAZAP1: gagacucugcgcagcuacu. After twice gene silencing by Hyperfectamine (Qiagen Inc, Gaithersburg, Maryland), cells were collected and divided into two aliquots; one half for western blot and the other half for RT–PCR analysis.

value: neuroblastoma

tag: treated with

value: siRNA anti-DAZAP1


title: siTDP-43-03

description:
Replicate siTDP-43-03
processed data file:
Control_vs_siTDP-43.DE.tsv
12_AGTCAA
8_rawCount and normCPM column in the GEN151110_R.profiling-table_NAR.xls

source_name: SH-SY5Y_siRNA anti-TDP-43

value: siRNA anti-TDP-43


title: siLUC-03

description:
Replicate siLUC-03
processed data file:
11_CTTGTA
7_rawCount and normCPM column in the GEN151110_R.profiling-table_NAR.xls

source_name: SH-SY5Y_siRNA anti-Luciferase

value: siRNA anti-Luciferase


title: siDAZAP1-02

description:
Replicate siDAZAP1-02
processed data file:
Control_vs_siDAZAP.DE.tsv
8_ACTTGA
6_rawCount and normCPM column in the GEN151110_R.profiling-table_NAR.xls


title: Sample 29 [CTRL 2 d35]

value: electrically mature motor neurons

value: none (control)

value: Patient 3

value: CTRL 2


title: siLUC-02

description:
Replicate siLUC-02
processed data file:
6_GCCAAT
4_rawCount and normCPM column in the GEN151110_R.profiling-table_NAR.xls


title: siDAZAP1-01

description:
Replicate siDAZAP1-01
processed data file:
Control_vs_siDAZAP.DE.tsv
3_TTAGGC
3_rawCount and normCPM column in the GEN151110_R.profiling-table_NAR.xls


title: siTDP-43-02

description:
Replicate siTDP-43-02
processed data file:
Control_vs_siTDP-43.DE.tsv
7_CAGATC
5_rawCount and normCPM column in the GEN151110_R.profiling-table_NAR.xls


title: siTDP-43-01

description:
Replicate siTDP-43-01
processed data file:
Control_vs_siTDP-43.DE.tsv
2_CGATGT
2_rawCount and normCPM column in the GEN151110_R.profiling-table_NAR.xls


title: siLUC-01

description:
Replicate siLUC-01
processed data file:
1_ATCACG
1_rawCount and normCPM column in the GEN151110_R.profiling-table_NAR.xls


city: San Diego

first: Christopher

last: Adase

address: 2525 John Hopkins Ct

department: Dermatology

institute: UCSD

description:
siControl
Control shRNA + non-differentiation media

data_processing:
Trim bases using minimum Phred score of 30, removing reads below this value
Reads aligned via Bowtie 2 v2.2.5 to hg19, default parameter values used
Samples were quantified to RefSeq Transcripts - 2015-05-07
Normalized values via TMM method of normalization
Gene analysis used Partek Gene Specific Analysis (GSA) run on the gene level with default values except for the following parameter changes, Lowest average coverage = 1, Poisson: True, and TMM normalization. Gene filters used were FDR step up < 0.1
Values are reads per gene per condition
Genome_build: hg19
Supplementary_files_format_and_content: Text file. Specifically a space deliniated text file

source_name: Preadipocytes

growth_protocol: Preadipocytes grown in preadipocyte growth medium for up to 5 days until 80 – 90% confluence then medium was replaced with either preadipocyte medium or adipocyte differentiation medium.

extract_protocol:
RNA was isolated after 24 hours of treatment using a Ambion Purelink RNA Mini kit. Followed protocol to lyse cells. Cells were lysed with lysis buffer plus 1% Beta mercaptoethanol as in the protocol.
Libraries were prepared using a TruSeq HT library prep kit according to Illumina's instruction. Our samples are under index 2 (i5) adapters . Barcode: UNIQUE TO SAMPLE; common adapter: AATGATACGGCGACCACCGAGATCTACAC[i5]ACACTCTTTCCCTACACGACGCTCTTCCGATCT

treatment_protocol: Preadipocytes cells were seeded on 24-well plates (adipocyte group: 5.0 x 104/ well), incubated overnight, then transfected with control or PTH2R Silencer Select siRNA transfection via Lipofectamine RNAiMAX and grown in either preadipocyte medium or adipocyte differentiation medium.

value: Passage 3 preadipocytes

tag: transfection

value: Control shRNA


description:
siP2R
PTH2R knockdown (PTH2R shRNA) + non-differentiation media

value: PTH2R knockdown


title: Control shRNA + differentiation media

description:
Diff siControl
Control shRNA + differentiation media


title: patu8902_gegfp_a02_100nm_tram_r2

city: Boston

first: William

middle: C.

last: Hahn

state: MA

address: 450 Brookline Avenue; D1538

department: Medical Oncology

institute: Dana Farber Cancer Institute

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

source_name: Pancreas

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

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

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

tag: cell line

tag: grna

tag: treatment

value: 100 nM Trametinib

tag: treatment duration

value: 24 hours


title: patu8902_gcic_c10_dmso_r1

value: DMSO


title: patu8902_gcic_a01_100nm_tram_r2


title: patu8902_gcic_a01_dmso_r2


title: patu8902_gcic_a01_100nm_tram_r1


title: patu8902_gegfp_a02_dmso_r1


title: patu8902_gcic_a01_dmso_r1


title: patu8902_gcic_c10_100nm_tram_r2


title: hct116_gcic_c10_50nm_tram_r2

source_name: Colon

value: 50 nM Trametinib


title: patu8902_gcic_c10_100nm_tram_r1


title: patu8902_gegfp_a02_100nm_tram_r1


title: hct116_gcic_c10_50nm_tram_r1


title: hct116_gcic_c10_dmso_r2


title: hct116_gcic_a01_50nm_tram_r2


title: H4K20me1

city: Paris

first: Jean-Charles

last: Cadoret

address: 15 rue hélène Brion

country: France

institute: CNRS/ Université de Paris

data_processing:
ChIP-seq reads were mapped to the most recent human genome build (hg19) using Bowtie. Up to two mismatched base pairs were allowed. Sequence tags that mapped to more than one location in the genome were excluded. Peak discovery was performed using MACS2 using specific parameters (bandwidth setting=400, genome size= 2.7e+9, tag size=50, and mfold=32). Other parameters were left as default.
Genome_build: hg19
Supplementary_files_format_and_content: bed format that content coordinates and the name of peaks

growth_protocol: The human U2OS cell line was purchased from ATCC and were grown in Dulbecco’s modified Eagle’s medium (Invitrogen) with 10% fetal bovine serum (Sigma) at 37°C, 5% CO2 and 5% O2.

extract_protocol:
nuclei were extracted in swelling buffer, using Dounce homogenization, and diluted with sonication ChIP buffer to give a concentration of approximately 10 million cells per ChIP reaction in a volume of 1000 ul. Chromatin was sonicated to the average size of 200-400 bp. Reactions were performed in 1.5 ml sample tubes, using 40 ul of Protein G Dynabeads (Invitrogen) prebound with the appropriate antibody in each ChIP reaction. Washes were performed 3 times with Sonication buffer (50 mM Hepes pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1%SDS, 0.5 mM PMSF, Protease inhibitor cocktail (Roche)), 3 times with wash buffer A (Sonication buffer supplemented with 500mM NaCl), 3 times with wash buffer B (20 mM Tris, pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 0.5 mM PMSF, Roche protease inhibitor cocktail] and TE buffer pH 8.0 (10 mM Tris-Cl pH 8.0, 1 mM EDTA pH 8.0 supplemented with 50 mM NaCl).  200 μl of elution buffer (50 mM Tris pH 8.0, 1 mM EDTA, 1% SDS, 50mM NaHCO3) was added to the beads for 20 min at 65°C. Eluates were purified after reverse crosslink using QIAquick PCR Purification Kit (Qiagen).
Libraries were prepared with the Illumina ChIP-seq Sample Prep Kit as per the manufacturer’s instructions, and sequenced on an Illumina HiSeq 2500 platform with 50bp single end reads.

tag: chip antibody


title: hct116_gcic_c10_dmso_r1


title: H4K20me3


title: patu8902_gegfp_a02_dmso_r2


title: patu8902_gcic_c10_dmso_r2


title: hct116_gcic_a01_dmso_r1


title: hct116_gegfp_a02_50nm_tram_r2


title: hct116_gcic_a01_50nm_tram_r1


title: hct116_gcic_a01_dmso_r2


description:
Diff siP2R
PTH2R knockdown  (PTH2R shRNA) + differentiation media


title: hct116_gegfp_a02_dmso_r2


title: hct116_gegfp_a02_50nm_tram_r1


title: calu1_gcic_c10_50nm_tram_r2

source_name: Lung


title: calu1_gcic_c10_50nm_tram_r1


title: hct116_gegfp_a02_dmso_r1


title: Sample 28 [CTRL 2 d21]

value: electrically immature motor neurons

value: Control


title: calu1_gcic_a01_50nm_tram_r2


title: calu1_gcic_c10_dmso_r2


title: calu1_gcic_a01_dmso_r1


title: calu1_gcic_c10_dmso_r1


title: a375_gcic_c10_1nm_tram_r1

source_name: Skin

value: 1 nM Trametinib


title: calu1_gegfp_a02_dmso_r2


title: a375_gcic_c10_dmso_r2


title: calu1_gegfp_a02_dmso_r1


title: calu1_gcic_a01_50nm_tram_r1


title: a375_gcic_c10_1nm_tram_r2


title: a375_gcic_a01_1nm_tram_r2


title: calu1_gcic_a01_dmso_r2


title: calu1_gegfp_a02_50nm_tram_r1


title: a375_gcic_a01_dmso_r1


title: a375_gcic_c10_dmso_r1


title: a375_gcic_a01_1nm_tram_r1


title: a375_gegfp_a02_dmso_r2


title: a375_gcic_a01_dmso_r2


title: calu1_gegfp_a02_50nm_tram_r2


title: a375_gegfp_a02_dmso_r1


title: 3L

city: Balice

first: Ewelina

last: Semik-Gurgul

address: Krakowska 1

department: Department of Animal Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

data_processing:
Raw sequencing reads were first subjected to quality control using FastQC software (Babraham Bioinformatics, UK)
Low quality reads (phred-trimming set to 20, quality set to 20 and a minimum read length of 20 was required to pass the filter) and fragments containing adapter sequences were filtered with the use of FlexBar software (Dodt et al., 2012)
The aligned to the horse reference genome (EquCab2.0) using BSMAP (Yuanxin and Wei, 2009) with default options recommended for RRBS data, specifying the  enzyme cleavage site (MspI) and mapping only to two forward strands.
Genome_build: EquCab2.0
Supplementary_files_format_and_content: The percentage of methylation of individual CpG sites (for 3L and 3D samples) with coverage higher than 8 reads was determined using Methylation Caller software.
Supplementary_files_format_and_content: To identify differences in CpG methylation between sarcoid and control skin samples a methylKit software (Akalin et al., 2012) was applied.

organism: Equus caballus

source_name: sarcoid

extract_protocol:
DNA was isolated from tissue using a DNeasy Blood & Tissue kit (Qiagen, Hilden, Germany)
To quantify DNA methylation levels across genome RRBS methodology was used following Illumina protocol (RRBS_for_Methylation_Analysis_Guide_15021647_C protocol). Each DNA library was sequenced on one lane of a HiscanSQ platform (Illumina) using 75-bp single-end read. The sequencing was performed along with balanced control library obtained from the viral DNA (PhiX, Illumina).

treatment_protocol: The collected material was transferred into tubes and stored at -20°C.

tag: individual

value: horse 1

tag: tissue

value: tumour tissue


title: a375_gegfp_a02_1nm_tram_r2


title: 3D

source_name: control

value: tumour distant skin


title: ChIPseq.YFP_HumanPRDM9.antiH3K4me3.ProtocolN

description:
Uniquely Mapped Fragments: 77625060
Multiplex Group: 1

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

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

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

value: HEK293T (ATCC CRL-3216)

value: H3K4me3 (Abcam ab8580)


title: ChIPseq.YFP_HumanPRDM9.antiGFP.Rep2.ProtocolN

description:
Uniquely Mapped Fragments: 79526431
Multiplex Group: 1

value: GFP (Abcam ab290)