title: Basal_BptfWT_ATACseq_Rep3b

description: Tn5 transposed purified DNA

source_name: BptfWT Mammary Cells


title: Basal_BptfKO_ATACseq_Rep2a

status: Public on Jun 13 2017

type: SRA

city: Cold Spring Harbor

first: Wesley

middle: D.

last: Frey

state: New York

address: One Bungtown Road

country: USA

institute: Cold Spring Harbor Laboratory

description: Tn5 transposed purified DNA

library_source: genomic

data_processing:
ATAC-seq reads were aligned to the mm9 genome assembly using Bowtie with no mismatches allowed and multi-mappers excluded
MACS was used for peak-calling from the mapped BAM file.  Parameters used for MACS included a tag size of 25bp and a strict p-value cutoff of 1.00e-5
Peaks were annotated using HOMER with the standard mm9 reference included with the software.  Location of peaks was then grouped into intergenic, promoter and genic (containing 5’UTR, Exons, Introns, Transcription Termination Sites, 3’UTR, ncRNA, miRNA, snoRNA, and rRNA) regions.  Pie Charts were made from the resulting HOMER output.
ROSE was preformed to identify putative enhancer regions using default conditions, which included a 2.5 Kb exclusion zone surrounding the TSS and a 12.5 Kb stitching distance.
The UCSC genome browser was used to analyze enhancers for overlap, using the table browser intersect function. Any overlap was enough to consider two regions “shared” and no overlap, between the enhancers defined the regions as ONLY being in one sample.
The comparison of differential enhancers was made into a venn diagram using Galaxy’s Cistrome server. Identification of genes closest to these differentially called enhancer regions, was preformed using Genomic Regions Enrichment of Annotations Tool (GREAT)
Homer was used to create histograms of MACS-called ATAC-seq peaks and MACS-called H3K27ac peaks using standard mm9 TSS annotations in Homer’s software package. Histograms of ATAC-seq peaks distribution around distal H3K27ac peaks were made by excluding H3K27ac peaks that associated with TSS/Promoter regions, as defined by HOMER.
Spearman correlation coefficients ranging from -1 to 1, where 1 indicates the strongest relationship between samples, were used to assess the integrity of the replicates.
DREME and TOMTOM were used to identify motifs in differential enhancer regions.  Parameters used for DREME include a default E-value threshold of 0.05 and a search of both the given strand and the reverse complement strand of the queried sequence.  TOMTOM was run with a default E-value of 0.05 a well.
Genome_build: mm9

molecule: genomic DNA

organism: Mus musculus

source_name: BptfKO Mammary Cells

growth_protocol: Eph4 Cells were grown in DMEM with 5% FBS

extract_protocol:
Nuclei obtained from Eph4 cells or FACS-sorted mammary epithelial cells were incubated with reagents from Illumina Nextera kit (Illumina), following DNA purification with purified with DNA Clean-up & Concentration kit (Zymo) according the manufacturer's instruction
Nextera treated, purified DNA was amplified and barcoded using previously described protocol (Buenrostro e at, 2013), then pooled for sequencing.

treatment_protocol: Tamoxifen was given to mice (total 15mg/kg body) prioir to cell isolation; Eph4 cells were treated for 24 hours with Bptf inhibitor AU-1 (5uM) or DMSO

tag: gender

value: Female

tag: tissue

value: Mammary Gland

tag: compartment

value: Basal

tag: cell type

value: Basal Mammary Epithelial Cells


title: WT-S2

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

library_source: transcriptomic

data_processing:
Illumina adaptor trimming with cutadapt-1.2.1 (--adapter=TGGAATTCTCGGGTGCCAAGG),
Discard reads of size under 15 bases,
Bowtie2 mapping versus mm10 (--local --very-sensitive-local -k 24),
Annotation versus gff mirbase v21, ensembl ncrna rel73, tRNAs and piRNA clusters from piRNAclusterDB.
Genome_build: mm10
Supplementary_files_format_and_content: 342_smallRNAseq.tableCount.txt: matrix count tables indicating for each features, the name , the feature type, a description, a genomic coordinate and the number of reads associated to this feature in each sample

molecule: total RNA

source_name: CD43- splenic B-cells from wt mice

extract_protocol:
CD43- splenic B-cells from wt, Em-deficient and 3'RR-deficient mice were cultured in conventional growth medium alone or with 5mg/ml of LPS for 2 days. Cells from two mice were pooled. Cellular RNA was then trisol-extracted.
1 µg of total RNA were ligated, reverse transcribed and amplified (17 cycles) with the reagents from the NextFlex small RNAseq kit V3 (Bioo scientific). Amplified libraries were quantified with the Bioanalyzer High Sensitivity DNA Kit (Agilent), pooled and size-selected from 140 nt to 160 nt with the LabChip XT DNA 300 Assay Kit (Caliper Lifesciences). Libraries were then sequenced on an Illumina Nextseq 500 Mid Flowcell with 75pb reads.

tag: cells

value: CD43- splenic B-cells

tag: stimulation

value: Stimulated with 5ug/ml LPS

tag: time of culture

value: Cultured for 2 days


title: Basal_BptfWT_ATACseq_Rep2b

description: Tn5 transposed purified DNA


title: Basal_BptfWT_ATACseq_Rep3a

description: Tn5 transposed purified DNA


title: WT-NS2

value: non stimulated


title: WT-S1


title: R0_p53_tetramer_delta_Cterm_EpiSELEX_seq

city: New York City

first: Harmen

middle: J

last: Bussemaker

address: 1212 Amsterdam Avenue, MC 2441

department: Biological Sciences

institute: Columbia University

data_processing:
Library strategy: EpiSELEX-seq
Fastq files were reverse-complemented and both forward and reverse-complement read merged into one (fastx_reverse_complement -Q33 -z ; FASTX toolkit 0.0.12;Hannon lab).
Next, fixed primer sites were trimmed using the following options: fastx_trimmer -Q33 -f 12 -l 41 –z (FASTX toolkit 0.0.12;Hannon lab).
Kmer counting and relative affinity estimates were computed using the R package bioconductor.org/packages/SELEX.
To filter for kmers that are aligned with the actual Protein:DNA interface, position-specific affinity matrices were calculated for each library and probes were scanned in a sliding-window approach in either orientation to find the optimal protein footprint. Only probes where a single offset contributed at least 95% to the overall probe affinity were retained.
Oligomer-based relative affinity tables for the unmethylated and methylated libraries were generated for the set of kmers that passed the filtering criterion.
Genome_build: randomized DNA
Supplementary_files_format_and_content: txt files contain two columns describing the relative affinity of individual kmers from the unmethylated and methylated libraries. Rownames contain the specific kmer sequences.

organism: Homo sapiens

source_name: in-vitro purification

extract_protocol: Libraries were amplified by using overhang primers targeting the GGTAGTGGAGG and GG-GAGGTGGAGTAGG parts of the library and adding the Illumina TruSEQ adapter and universal or Index primers respectively. During amplification the extracted, TF-bound DNA was split in two separate pools and Illumina primer landing sites were added from both orientations respectively (Universal-for & Index-rev or Index-for and Universal-rev). Next, Illumina-specific barcodes were added in a 5 cycles PCR to allow for multiplexing of multiple samples. In order to obtain unidirectional reads starting from the barcode end of the library, reads need to be reverse-complemented and merged with the forward reads.

tag: rounds of selection

tag: variable region length


title: Basal_BptfWT_ATACseq_Rep2a

description: Tn5 transposed purified DNA


title: R1_p53_tetramer_delta_Cterm_EpiSELEX_seq


title: WT-NS1


title: Basal_BptfWT_ATACseq_Rep1

description: Tn5 transposed purified DNA


title: EU-S1

source_name: CD43- splenic B-cells from Em-deficient mice


title: 3pRR-S2

source_name: CD43- splenic B-cells from 3'RR-deficient mice


title: EU-NS

description: EU-NS

data_processing:
Mapping with STAR_2.4.0a versus mm10,
Gene counting with featureCounts (subread-1.4.6-p1-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M " options.
Genome_build: mm10
Supplementary_files_format_and_content: 334_RNAseq.featurecounts.txt: Matrix gene count file with gene symbol in the first column and then all sample of the submission.

extract_protocol:
CD43- splenic B-cells from wt, Em-deficient and 3'RR-deficient mice were cultured in conventional growth medium alone or with 5mg/ml of LPS for 2 days. Cells from two different mice were pooled. Cellular RNA was then trisol-extracted.
Libraries were generated from 1µg of total RNA using Truseq Stranded Total RNA kit (Illumina). Libraries were then quantified with KAPA library quantification kit (Kapa biosystems) and pooled. 4nM of this pool were loaded on a Nextseq 500 high output flowcell and sequenced on a NextSeq 500 platform (Illumina) with 2 × 150bp paired-end chemistry.


title: WT-NS

description: WT-NS


title: 3pRR-S


title: EU-S

description: EU-S


title: 3pRR-NS


title: 3pRR-S1


title: WT-S

description: WT-S


title: 3pRR-NS1


title: EU-NS1


title: Huangguogan etiolated seedlings, sample 2

city: chengdu

first: bo

last: xiong

address: NO.211 Huimin

country: China

institute: Sichuan Agricultural University

data_processing: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality. The left files (read1 files) from all libraries/samples were pooled into one big left.fq file, and right files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity with min_kmer_cov set to 2 by default and all other parameters set default. Clean data were mapped back onto the assembled transcriptome. Readcount for each gene was obtained from the mapping results.

organism: Citrus reticulata x Citrus sinensis

source_name: leaves

growth_protocol: Seeds were presoaked for 4h, and incubated in 25°C for 3d, then sowed in pots filled with vermiculite and perlite (V : V = 1 : 1). Subsequently, these pots were transferred into a growth chamber set to 25°C, 12h light/12h dark period and 50-60% relative humidity of air, and watered every two days after seedling germination.

extract_protocol: A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2000 and paired-end reads were generated.

tag: cultivar

value: Huangguogan

value: leaves


title: Huangguogan multicoloured seedlings, sample 1


title: Huangguogan multicoloured seedlings, sample 2


title: Huangguogan multicoloured seedlings, sample 3


title: Shiranuhi etiolated seedlings, sample 1

organism: (Citrus unshiu x Citrus sinensis) x Citrus reticulata

value: Shiranuhi


title: Shiranuhi etiolated seedlings, sample 2


title: Huangguogan etiolated seedlings, sample 1


title: Shiranuhi multicoloured seedlings, sample 2


title: Shiranuhi etiolated seedlings, sample 3


title: Shiranuhi multicoloured seedlings, sample 1


title: Huangguogan green seedlings, sample 2


title: Shiranuhi multicoloured seedlings, sample 3


title: Shiranuhi green seedlings, sample 3


title: Huangguogan green seedlings, sample 3


title: R0_ATF4_PbxHoxA9b_EpiSELEX_seq


title: Huangguogan green seedlings, sample 1


title: 3pRR-NS2


title: Huangguogan etiolated seedlings, sample 3


title: Bptf_KO_Myoepithelial-Rep1

data_processing:
STAR  was used for mapping reads to the transcriptome, retaining only uniquely mapped reads.
Deseq was used to asses changes in expression levels simultaneously across multiple conditions and in multi-factor experimental designs, incorporating information from multiple replicates (2 biological replicates per cell type).
Gene Set Enrichment Analysis (GSEA) for global analysis of differentially expressed genes.
Additionally, the top 100 differentially expressed genes were loaded into the Enrichr for gene ontology enrichment analysis.
Genome_build: mm9

source_name: BptfKO Mice

extract_protocol:
FACS-sorted, mammary epithelial cells were collected and homogenized in TRIzol for RNA extraction.
Purified RNA was utilized for double strand cDNA synthesis utilizing the Ovation RNA-seq system (V2). RNA-seq  libraries were prepared and barcoded utilizing the Ovation ultralow DR multiplex system (Nugen), then pooled for sequencing.

treatment_protocol: Tamoxifen was given to mice (total 15mg/kg body) prioir to cell isolation

value: Myoepithelial Mammary Cells


title: Bptf_KO-Bsecs-Rep1

value: Mammary Epithelial Cells:Bsecs


title: Bptf_KO-Bsecs-Rep2


title: 24C

city: AURILLAC

first: Pierre

last: DELPECH

state: Auvergne Rhône Alpes

address: 20 côte de Reyne

department: MICA

institute: INRA

description: RNA after rRNA depletion

data_processing:
Basecalls performed using RTA v 1.9 (Illumina)
Concatenation of 4-5 fastq per samples
RNA seq were aligned on both genomes (S.aureus MW2+L.garvieae N201) using BWA (v0.7.5a-r405) aln with parameters -l 32 -k 2, BWA samse, samtools view -h -s -q 20 to suppress low quality alignment (to visualize alignements: … samtools view -bt to compress sam into bam files, samtools sort and index to obtain final alignment files)
Counting aligned reads: Htseq version 0.5.4p5 (i) with parameters –stranded=reverse –mode=union –type=CDS –idattr=ID for L. garvieae reads counting (ii) with parameters --stranded=reverse --mode=union --type=CDS –idattr=Dbxref for S. aureus reads counting
Differential expression analysis is carried out on count files for each conditions with R-packages DESeq, DESeq2, EdgeR, R v3.1.1
Genome_build: Lactococcus garvieae N201 (GOLD project ID: Gp0034836); Staphylococcus aureus MW2 (NCBI Reference Sequence: NC_003923)
Supplementary_files_format_and_content: Tab-delimited text files (file name = condition1_condition2_R-package used.txt) list only L. garvieae CDSs significatively differentially expressed (condition 1/condition 2) with log(fold-change) and p-values (raw and ajusted). Files are available in a tar archive located on the series record.

organism:
Staphylococcus aureus
Lactococcus garvieae

source_name: static co-culture replicate C

growth_protocol: Both strains were inoculated separately or in co-culture at 1E+06 cells.mL-1 for S. aureus or 1E+07 cells/mL for L. garvieae in BHI buffered at pH = 7 with phosphate buffer KH2PO4, 3H2O/K2HPO4 (KH2PO4, 3H2O, Riedel-de-Haen, Honeywell GmbH, Seelze, Germany; K2HPO4, Merck KGaA, Darmstadt, Germany) previously equilibrated at 30°C. Pure cultures and co-cultures of both strains were performed either under a high or under a low aeration level depending on the experiment. Low aeration level cultures were set in static fully filled and sealed 50-mL Nunc EZ Flip conical centrifuge tubes (Sigma-Aldrich, St. Louis, Missouri, USA). The high aeration level was obtained with a mechanical shaking at 150 rpm on 50-mL cultures in 250-mL erlenmeyers. All cultures were incubated at 30°C for 24h in an Infors HT Minitron (Infors AG, Bottmingen, Switzerland). After 9 h, 40 mL of each culture were centrifuged at 9,600 x g for 10 min at 4°C. The cell pellets were immediately frozen in an ethanol bath and then stored at -80°C.

extract_protocol:
Frozen cell pellets obtained from cultures at 9 h were suspended in 500 µL of cold Tris-EDTA buffer. Then, 25 µL of 20% SDS, 500 µL of phenol at pH 4, 3.5 µL of β-mercaptoethanol, and 600 mg of Zirconium beads were added. The solution was milled in a Retsch MM200 mixer mill (VERDER Group, Haan, Germany) at 30 hertz for two 2-minute runs with 2-minute cooling on ice in between. Next, 200 µL of chloroform were added. The solution was gently hand-mixed and centrifuged at 13,000 x g for 20 min at 4°C. Extraction of RNAs was then performed on the aqueous and translucent phase using NucleoSpin RNA-L or RNA-II kit (Macherey-Nagel, GmbH & Co. KG, Düren, Germany) following the suppliers instructions. Then we treated RNA extracts with rDNAse I using an Ambion DNA-free™ Kit (Ambion, Inc., Austin, Texas, USA) following the suppliers instructions. Absence of residual DNA was confirmed by qPCR with S. aureus gyrB gene primers. If needed, rDNAse I treatment was repeated until Cycle threshold (Ct) were > 30. The RNA extracts were quantified using a Nanodrop™ 2000C (Thermo Fisher Scientific Inc., Waltham, Massachusetts, USA). Ribosomal RNAs were depleted from the total RNA (2 x 5 µg of RNA by sample) using a Magnetic Kit RiboZero for Gram Positive Bacteria (Illumina Inc., San Diego, California, USA) according to the manufacturer’s instructions. The quality and concentration of RNA in each sample were assessed using a RNA 6000 pico kit (Agilent Technologies, Santa Clara, California, USA).
RNA libraries were prepared by the MGX Plateform (Montpellier GenomiX, CNRS, Montpellier, France) using Illumina kit (TruSeq Stranded mRNA Sample Preparation kit), devices and standard protocols (Illumina Inc.)

treatment_protocol: conservation at -80°C

tag: lactococcus garvieae strain

tag: staphylococcus aureus strain

tag: culture type

value: co-culture

tag: aeration level

value: low


title: Bptf_KO_Luminal-Rep1

source_name: BptfWT Mice

value: Luminal Mammary Epithelial Cells


title: 24A

description: RNA after rRNA depletion

source_name: static co-culture replicate A


title: 23C

description: RNA after rRNA depletion

source_name: aerated co-culture replicate C

value: high


title: Shiranuhi green seedlings, sample 2


title: Bptf_KO_Myoepithelial-Rep2

value: Female


title: Bptf_WT_Myoepithelial_RNAseq_Rep1

value: Mammary Gland


title: Bptf_WT_Myoepithelial_RNAseq_Rep2

value: Myoepithelial Mammary  Cells


title: 23A

description: RNA after rRNA depletion

source_name: aerated co-culture replicate A


title: Shiranuhi green seedlings, sample 1


title: Bptf_WT_Luminal_RNAseq_Rep2


title: 24B

description: RNA after rRNA depletion

source_name: static co-culture replicate B


title: 23B

description: RNA after rRNA depletion

source_name: aerated co-culture replicate B


title: Bptf_WT_Luminal_RNAseq_Rep1


title: S1

city: Paris

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Count on FAST DB gene annotations (GenoSplice) and normalization using Deseq
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes deseq normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2013_2 were also provide

source_name: Spermatids

growth_protocol: C57Bl/6 mice were maintained on a normal 12 hr light/dark cycle.

extract_protocol:
RNA was extracted and DNAse treated using the miRNeasy Mini Kit (Qiagen).
Library was prepared using the TruSeq Stranded mRNA kit protocol (Illumina technology) with an input total RNA of 1µg

treatment_protocol: Spermatocytes and spermatids were collected from 12-week-old male mice by gravimetric decantation (Sta-put).

value: Spermatids


title: S2


title: Bptf_KO_Luminal-Rep2


title: 7066_Chronic_control-2h rep2

city: Beijing

first: Mei

last: Zhao

address: 16 Lincui Road, Chaoyang District, Beijing 100101, China

description: 7066_CC-2h rep2

data_processing:
Base-calling was performed using Illumina CASAVA version 1.8.2
Adaptor sequence and low quality sequence were first trimmed by Trimmomatic-0.32 using the following configurations:ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50
RNA-Seq reads were mapped to mouse reference genome GRCm38(mm10) using tophat version 2.0.12 with the followling parameters: --mate-inner-dist 0 --mate-std-dev 100   --no-coverage-search --keep-fasta-order --fusion-search --transcriptome-index=Mus_musculus_GRCm38_76_gtf
Differentially expressed genes were detected by cufflinks version 2.2.1
Genome_build: GRCm38(mm10)
Supplementary_files_format_and_content: tab-delimited text files include average RPKM values and statistics in Cuffdiff output.

source_name: Prefrontal cortex

extract_protocol:
RNA was extracted from PFC tissues using Trizol (Invitrogen), then quantified using a NanoDrop 2000 (Thermo-Fisher Scientific, Waltham, MA, USA), and assessed with an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). The RNA integrity number (RIN) of each sample was >8.
Six cDNA libraries were prepared according to the manufacturer’s protocol (Illumina, San Diego, CA, USA). Paired-end 75-nt sequencing was performed using the Illumina HiSeq2000.

tag: strain

value: brain

tag: tissue compartment

value: Prefrontal cortex

tag: drug treatment

value: control

tag: time after final dose

value: 2 hours

tag: age

value: 10 weeks


title: 8074_Chronic_control-7d rep1

description: 8074_CC-7d rep1

tag: tissue

value: 7 days


title: 8058_Cocaine-7d rep1

description: 8058_C-7d rep1

value: cocaine


title: 8075_Chronic_control-7d rep2

description: 8075_CC-7d rep2


title: SB

source_name: Spermatocytes

tag: cell type

value: Spermatocytes


title: SD


title: S4


title: 7064_Cocaine-2h rep2

description: 7064_C-2h rep2


title: 7065_Chronic_control-2h rep1

description: 7065_CC-2h rep1


title: 7063_Cocaine-2h rep1

description: 7063_C-2h rep1


title: 2014_Cocaine-24h rep2

description: 2014_C-24h rep2

value: 24 hours


title: shPML

city: Stanford

first: Stephen

middle: B

last: Montgomery

state: CA

address: 300 Pasteur Dr

department: Pathology

institute: Stanford University

description: U2OS shPML

data_processing:
Sequencing reads were mapped using TopHat (version 2.0.0) to the known transcriptome (-G option; Gencode version 7 annotations) for the human reference genome (hg19) using default parameters (Trapnell et al. 2009).
Cufflinks (version 2.0.2) was used to quantify gene and isoform expression for known transcripts (-G option; Gencode version 7 annotations) using the default parameters (Trapnell et al. 2010).
Only uniquely aligned reads were used for expression quantification. Pairwise differential gene expression analysis was performed using Cuffdiff (Trapnell et al 2012) with the default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Cufflinks output for gene and transcript FPKM

source_name: U2OS Cell line

growth_protocol: Low passage U2OS osteosarcoma cells (source: ATCC, HTB-96) containing lentivirus-delivered shRNAs targeting luciferase (shControl, GTGCGTTGCTAGTACCAAC) or exon 4 of PML (shPML, AGATGCAGCTGTATCCAAG) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1µg/ml of puromycin at 37°C and 5% CO2. Cells were grown to 80% confluence in 10cm dishes prior to solubilization with Trizol.

extract_protocol:
Total RNA was extracted with Trizol and RNA quality was assessed with the Agilent Bioanalyzer 2100.
PolyA-purified mRNA was subsequently used for cDNA-library construction with the Illumina TruSeq RNA Preparation Kit. Strand specificity was performed with 2'-deoxyuridine 5'-triphosphate during second-strand synthesis. All samples were indexed with Illumina adapters and each cDNA library was sequenced on an Illumina HiSeq

value: U2OS osteosarcoma cell line

tag: genotype/variation

value: PML silencing


title: 3027_Cocaine-24h rep1

description: 3027_C-24h rep1 (Cocaine treatment)


title: 2013_Chronic_control-24h rep1

description: 2013_CC-24h rep1 (Chronic Control)


title: 8059_Cocaine-7d rep2

description: 8059_C-7d rep2


title: shControl

description: U2OS shControl


title: 2015_Chronic_control-24h rep2

description: 2015_CC-24h rep2


title: DGM-12719_M0_sm (RNA-seq)

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Expression analysis was performed using the human reference genome build GRCh37/hg19, STAR (2.3.1z13_r470) for aligning reads, RefSeq gene definitions (2014-06-02) and Cufflinks (v2.2, http://cufflinks.cbcb.umd.edu)
To correct for transcript length and depth of coverage raw paired-end sequenced reads were converted into fragments per kilobase of exon per million fragments sequenced (FPKM).
This process was carried out independently for each sample lane. Before running Cufflinks, Samtools (v0.1.18.0, http://samtools.sourceforge.net) was used to merge each sample's independent STAR results into one file. This file contains all the aligned reads for each read pair. Finally Cufflinks was run on the merged STAR output to produce a file with FPKM values for each sample
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM text files include the RefSeq unique ID with gene ID and location, gene ID  and the FPKM values for all samples

source_name: small airway epithelium brushing

extract_protocol:
Total RNA was extracted with TRIzol with subsequent RNA clean-up using the RNeasy  RNA purification kit to remove residual DNA
The TruSeq RNA v2 Sample Prep Kit (Illumina, San Diego, CA) was utilized as per protocol to generate cDNA
Samples were loaded onto an Illumina flowcell for paired-end 125 x 2 sequencing reactions using the Illumina HiSeq 2500.

tag: smoking status

value: waterpipe smoker

value: small airway epithelium brushing


title: WT_6

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Reads were trimmed of adapter sequences TCGTATGCCGTCTTCTGCTTG, ATCTCGTATGCCGTCTTCTGCTTG, CGACAGGTTCAGAGTTCTACAGTCCGACGATC GATCGGAAGAGCACACGTCTGAACTCCAGTCAC using cutadapt v1.9.1
Trimmed reads were aligned to RepBase v18.05 using STAR v2.4.01
Reads that didn't align to RepBase were aligned to ce11 using STAR v2.4.01
Featurecounts v1.5.0-p1 and DESeq2 were used to count and normalize genes for differential expression, respectively. Gene regions were described using WS254 (Wormbase) annotations.
Reads were removed of potential duplicates and combined respective to their WT or Adr condition for editing calls using samtools v1.3.1
Reads were filtered and removed using the following parameters: reads containing junction overhangs less than 10nt long, reads containing indels, reads containing mutations within 5nt of the 3' end, reads containing more than 1 non AG or TC antisense mutation
Reads were piled up using samtools 1.3.1 [-d 1000 -E -I -p -o -f -t DP,DV,DPR,INFO/DPR,DP4,SP]
Variants were called using bcftools 1.2.1 [-O -c -A -i -v]
Variants were filtered for and removed: known SNPs (wormbase WS254), positions covered by less than 5 reads, variants which were not A-G or T-C antisense
Variants were scored using a previously published bayesian method and filtered for those passing a 0.99 confidence parameter
Surviving variants from the Adr2- samples were filtered out.
Variants were annotated using bedtools 2.26 on WS254 annotations, prioritized using the following: 3'UTR, 5'UTR, CDS, Intron, mRNA, piRNA, ncRNA, tRNA, pre-ncRNA, miRNA, snoRNA, pre_miRNA, lincRNA, snRNA, antisense RNA, rRNA, pre-miRNA, downstream from gene, upstream from gene, downstream noncoding RNA, upstream noncoding RNA and scRNA
Genome_build: ce11
Supplementary_files_format_and_content: diffexp.tsv contains DESeq2-processed differential expression results for WS254 wormbase genes between WT and Adr2- knockout conditions. editing_calls.tsv contains all annotated editing calls removed of adr2- false positives. GSF973-Hundley-SarahD-1_S1_R1_001.polyATrim.adapterTrim.rmRep.sorted.rg.bam, GSF973-Hundley-SarahD-3_S3_R1_001.polyATrim.adapterTrim.rmRep.sorted.rg.bam, and GSF973-Hundley-SarahD-6_S6_R1_001.polyATrim.adapterTrim.rmRep.sorted.rg.bam contain ce11-aligned reads pertaining to WT neural C elegan RNA. GSF973-Hundley-SarahD-2_S2_R1_001.polyATrim.adapterTrim.rmRep.sorted.rg.bam, GSF973-Hundley-SarahD-5_S5_R1_001.polyATrim.adapterTrim.rmRep.sorted.rg.bam, and GSF973-Hundley-SarahD-7_S7_R1_001.polyATrim.adapterTrim.rmRep.sorted.rg.bam contain ce11-aligned reads pertaining to adr2 knockout neural C elegan RNA.

organism: Caenorhabditis elegans

source_name: WT

growth_protocol: Worm strains were cultured on NGM plates seeded with E. coli OP50.

extract_protocol:
Total RNA was isolated from neural cells or from whole worms at the L1 stage using Trizol (Invitrogen) followed by treatment with DNase (Fischer Scientific, Hampton, NH) and purification using the RNeasy Extraction Kit (Qiagen, Hilden, Germany).
RNA libraries were created from RNA isolated from three independent biological replicates of FACS sorted neural cells from the wild-type (BB76) and adr-2(-) (BB78) worm strains. PolyA+ beads (Invitrogen) were used to select for mRNA and libraries were generated using the KAPA Strand-Specific RNA Library Kit according to the manufacturer’s instructions.

treatment_protocol: Neural cells were isolated from first larval stage (L1) worms using a previously published method (Spencer et al., 2014). Eggs were released from gravid adult worms by incubating in 0.5 M NaOH in 1.2% NaClO for 6 min. Eggs were thoroughly washed with M9 buffer (3 g KH2PO4, 6 g Na2HPO4, 5 g NaCl, 1 ml 1 M MgSO4, H2O to 1 L) and cultured overnight at 20oC to synchronize worms in the first larval stage (L1). L1 worms were washed with dH2O and digested with freshly thawed SDS-DTT (200 mM DTT, 0.25% SDS, 20 mM HEPES, pH 8.0 3% sucrose, stored at -20oC) for 2 minutes on a nutator at room temperature. The digest was thoroughly washed with egg buffer (118 mM NaCl, 48 mM KCl, 2 mM CaCl2, 2 mM MgCl2 25 mM HEPES, pH 7.3 adjusted osmolarity to 340 mOsm with sucrose) and further digested in freshly made 15 mg/ml Pronase E (Sigma-Aldrich, St. Louis, MO) dissolved in egg buffer. During the 20 minute Pronase E digestion, the worms were mechanically disrupted using a 200 ml pipette tip. The released cells were washed and resuspended in egg buffer. Cells were stained with the Near IR Live/Dead Fixable dye (Invitrogen, Carlsbad, CA) for 30 minutes prior to FACS sorting to isolate GFP expressing neural cells. Cells were sorted on a BD FACSAria IIu sorter and analyzed using FACSDiva 6.1.1 software (Indiana University Bloomington-Flow Cytometry Core Facility). Events were thresholded on FSC-A and SSC-A parameters at a threshold of 600 and 700 respectively.  Cells were first gated on FSC-A vs. SSC-A, both analyzed on a log scale, and then doublet discrimination was done using SSC-H vs. SSC-W and FSC-H vs. FSC-W.  Single cells were subsequently gated for Near IR Live/Dead Fixable dye negative populations, with final gating set on a GFP-A vs. SSC-A plot with gates for GFP positive and GFP negative cells. 200,000 cells were sorted into 15ml conical tubes containing 1 ml Trizol. Both the sample and collected cells were kept at 4°C during and after the sort.

value: Neural cells


title: DGM-12697_M0_sm (RNA-seq)


title: batch 2 stim (IFN-beta)

city: San Francisco

first: Sasha

last: Targ

state: California

address: 513 Parnassus Ave S-965

institute: UCSF IHG

data_processing:
Data were processed according to the 10x Cell Ranger pipeline. Version 1.1 was used for processing samples A, B, and C, and version 1.2 was used for processing samples 2.1 and 2.2.
We followed the standard pipeline listed in the 10x software manual with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: .mat 10X gene barcode matrix;  Each row of this file is an entry for a non-zero count - the first column is the gene number, the second column is the cell, and the third column is the count.
Supplementary_files_format_and_content: genes.txt contains the ensembl gene ids in the same order as  *.mat files.
Supplementary_files_format_and_content: *_barcodes.tsv: Cell barcodes.
Supplementary_files_format_and_content: *.mtx: Gene barcode matrices.
Supplementary_files_format_and_content: *.total.tsne.df.tsv: Mapping files.
Supplementary_files_format_and_content: *.genes.tsv: Genes.

source_name: single cell RNA-seq_SLE patients (6 hours IFN-b stimulation)

extract_protocol:
Peripheral blood mononuclear cells were isolated from SLE and RA patient donors by the Core Immunologic Laboratory (CIL) at UCSF and frozen according to standard procedure.
RNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument.
droplet-based single cell RNA-Seq

tag: subject status

value: SLE patient

value: peripheral blood mononuclear cells (PBMCs)

tag: stimulated with

value: IFN-beta for 6hrs


title: batch 2 control

source_name: single cell RNA-seq_SLE patients (6 hours control)

value: none (control)


title: IFC rep2 (smallRNA-Seq)

city: zhengzhou

first: hongping

last: li

institute: Henan Agricultural University

data_processing: A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis (Li et al. 2010; Wei et al. 2011). A Public software package, CleaveLand3.0.1 was used for analyzing Degradome sequencing data.

organism: Zea mays

source_name: tissue: ovary

growth_protocol: Zea mays L. (maize) inbred Yu-A474 plants were grown at a research farm of Henan Agricultural University, Henan Province, China (34º53´N, 113 º35´E, 94 m altitude) under non-stress conditions during June-October 2014.

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

treatment_protocol: Under non-stress conditions.

tag: developmental state

value: before pollination

value: ovary

tag: phenotype

value: incompletely fused carpels (IFC)


title: WT rep2 (smallRNA-Seq)

value: wild-type (WT)


title: batch 1 sample B

source_name: single cell RNA-seq_SLE patients (well 2)


title: DGM-12750_M0_sm (RNA-seq)


title: IFC (degradome)

data_processing:
Library strategy: degradome-Seq
A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis (Li et al. 2010; Wei et al. 2011). A Public software package, CleaveLand3.0.1 was used for analyzing Degradome sequencing data.


title: IFC rep1 (smallRNA-Seq)


title: WT rep1 (smallRNA-Seq)


title: WT (degradome)


title: Adr2-_2


title: batch 1 sample A

source_name: single cell RNA-seq_SLE patients (well 1)


title: Adr2-_7


title: DGM-10159_M12_sm (RNA-seq)

value: nonsmoker


title: DGM-10475_M3_sm (RNA-seq)


title: Adr2-_5


title: WT_3


title: batch 1 sample C

source_name: single cell RNA-seq_SLE patients (well 3)


title: ZAT18 OE drought rep2

city: Wuhan

first: Zhulong

last: Chan

state: Hubei Province

address: No. 1, Shizishan St, Nanhu

department: College of Horticulture and Forestry Sciences

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for base calling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed
Supplementary_files_format_and_content: raw counts of sequencing reads

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
The rosette leaves of control and drought treated Col-0 and AtZAT18 transgenic plants were collected for RAN isolation following the standard Qiagen RNeasy mini kit protocol. RNA purity and integrity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaf

tag: ecotype

tag: treatment time

value: 10 days after drought

tag: genotype

value: ZAT18 overexpression lines


title: WT_1


title: ZAT18 OE drought rep1


title: WT drought rep2

value: WT


title: DGM-10565_M12_sm (RNA-seq)


title: WT drought rep1


title: Cultivated soybean df43

city: Nanchang

first: Dong

last: Wang

state: JiangXi

address: Hong Gu Tan New Road, No. 999

institute: Nanchang University

description: strand-specific RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptor and low quality sequences were trimmed with trim-galore (v0.3.3, --stringency 6); Clean reads were aligned to reference genomes (Gmax_275_Wm82.a2.v1) using tophat2  with following parameters: -N 6 --read-edit-dist 6.
Mapped reads were filtered with samtools with following parameters: -F 4 -q 1 -f 2; Raw counts of refrence genes were calculated with function "countOverlaps" in R package "GenomicAlignments"; "edgeR" was used to do differential expression (DE) analysis.
Genome_build: Gmax_275_Wm82.a2.v1
Supplementary_files_format_and_content: Text file including raw read count table for reference genes

organism: Glycine max

source_name: total RNAs, seeds

growth_protocol: For growing soybean plants, seeds were grown on fields.

extract_protocol:
Total RNAs were extracted using Trizol (Sigma), and then were treated with TURBO DNA-free kit (ambion) for removing DNA contamination.
Libraries were constructed through applying TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) in accordance with the manufacturer’s instruction.

tag: strain/ecotype

value: cultivar

value: seeds

tag: developmental stage

value: seeds after 13 days flowering


title: Cultivated soybean df3

description: strand-specific RNA-seq


title: Cultivated soybean df36

description: strand-specific RNA-seq


title: WT control rep2


title: Cultivated soybean df12

description: strand-specific RNA-seq


title: ZAT18 OE control rep1


title: Cultivated soybean df14

description: strand-specific RNA-seq


title: ZAT18 OE control rep2


title: MCF7.C.gro.rep1

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

description: nascent RNA

data_processing:
Library strategy: GRO-seq
Sequenced reads were aligned to a reference set of human curated protein-coding transcripts (plus the five human rRNA transcripts) using Bowtie. This reference set of transcripts was based on Ensembl's gene annotations. Only uniquely mapped reads were used in subsequent analyses. RNA expression and Ribosome-occupancy levels were estimated by calculating reads per kilobase of mRNA per million reads (RPKM) per transcript.
only genes covered by at least 20 reads were included in the analysis
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts values for each sample.

growth_protocol: MCF7 cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% heat-inactivated fetal calf serum in 5% CO2 at 37°C.

extract_protocol:
5 x 10^6 nuclei per condition were isolated and incubated 5 min at 30°C with equal volume of reaction buffer for the nuclear-run on (10 mM Tris-Cl pH 8.0, 5 mM MgCl2, 1mM DTT, 300 mM KCL, 20 units of SUPERase In, 1% sarkosyl, 500 µM ATP, GTP, and Br-UTP, 0.2 µM CTP+32P CTP). The reaction was stopped and RNA extracted with Trizol LS (Invitrogen) according to the manufacturer’s instructions. Base hydrolysis was performed using RNA fragmentation Reagents (Ambion) and the reaction was purified through p-30 RNAse-free spin column (BioRad). BrUTP labeled nascent transcripts were immunoprecipiated with anti-BrUTP agarose beads (Santa Cruz Biotech), washed once in binding buffer, once in low salt buffer (0.2X SSPE, 1 mM EDTA, 0.05% Tween-20), once in high salt buffer (0.25X SSPE, 1 mM EDTA, 0.05% Tween-20, 137.5 mM NaCl) and twice in TET buffer (TE with 0.05% Tween-20). Then, BrUTP-incorporated RNA was eluted with elution buffer (20 mM DTT, 300 mM NaCl, 5 mM Tris-Cl pH 7.5, 1 mM EDTA and 0.1% SDS) and RNA isolated with Trizol LS. End-repair of the enriched BrUTP-incorporated RNAs were achieved by the treatment with tobacco acid pyrophosphatase (TAP; Epicenter) to remove 5’-methyl guanosine caps, and followed by T4 polynucleotide kinase treatment (PNK; NEB) to remove 3’-phosphate group at low pH. Then, the BrU-incorporated RNAs were treated with T4 PNK at high pH in the presence of ATP to add 5’-phosphate group. The reaction was stopped and RNA was extracted with Trizol LS.
Sequencing libraries were generated from two biological replicates using TruSeq Small RNA kit from Illumina. Final libraries were two times cleaned-up and size-selected by Agencourt AMPure XP (Beckman Coulter)

treatment_protocol: No treatment

tag: cell line

tag: treatment


title: S3_2

city: SHANGHAI

first: SONG

last: GUO

address: RUIJIN 2TH ROAD

institute: Ruijin Hospital Affiliated to Shanghai Jiaotong University School of Medicine

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.1.8 mapping to reference genome
read counts were calculated and adjusted using HTseq Version 0.6.1
Genome_build: mm10_GRCm38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: ICR mice_endometrium_GnRH-agonist

growth_protocol: Five pregnant ICR strain mice were purchased from Shanghai Laboratory Animal Corporation (Shanghai, P. R. China), and each was housed in a single cage during the perinatal period. Female offspring were selected for use in this study. All mice were housed in the same temperature-controlled room, with alternating 12-h light/dark cycles, and allowed free access to chow and water. Groups of 16 female neonatal mice were dosed orally with 2.7  μmol/kg tamoxifen (Shanghai Fudan-Zhangjiang Bio-Pharmaceutical Co., Ltd., Shanghai, P. R. China) suspended in a peanut oil/lecithin/condensed milk mixture (2:0.2:3, by volume) on days 2–5 after birth (day of birth = Day 1). After 75 days, the 16 tamoxifen-treated mice were divided randomly into two groups on average. 8 mice received 1.5 μg/100 g bw/day of Decapetyl (Ferring GmbH, Kiel, Germany) intraperitoneal injection from day 3–9 of estrus. Another 8 mice were used as control group receiving the same amount of solvent without GnRH agonist. Four weeks later, all the female mice were mated with male mice from 19:00 to 07:00 overnight. In the following morning, females were checked for the presence of vaginal plug. The rate of seeing embolu was compared between the two groups. The day of vaginal plug formation was considered to be Day 1 of pregnancy. Mice were euthanized at 19:00–20:00 on Day 4 of pregnancy.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions. The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols. Samples were diluted and mixed, the mixture was processed on a OneTouch 2 instrument (Life Technologies) and enriched on a OneTouch 2 ES station (Life Technologies) for preparing the template-positive Ion PI™ Ion Sphere™ Particles (Life Technologies) according to Ion PI™ Template OT2 200 Kit v2.0 (Life Technologies). After enrichment, the mixed template-positive Ion PI™ Ion Sphere™ Particles of samples was loaded on to 1 P1v2 Proton Chip (Life Technologies) and sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies) by NovelBio Corp. Laboratory, Shanghai.

treatment_protocol: Uteri were removed and fixed in 10%formalin overnight, followed by dehydration in 70% ethanol. The tissues were paraffin wax-embedded, then sectioned and stained with hematoxylin and eosin (H&E) and smooth muscle actin. Three randomly selected sections were chosen for histopathology. These two testing methods were used to determine whether mice model of adenomyosis were successfully established. If the two tests were all positive, a diagnosis of adenomyosis was made. Only meeting these criteria, the endometrium can be used for the RNA seq.The endometrial tissues were scraped off using a curved needle, then snap-frozen in liquid nitrogen and stored at -80°C for the RNA seq.

tag: strain

value: ICR

value: Day 4 of pregnancy

value: endometrium

tag: group

value: GnRH agonist treatment group


title: S2_8

source_name: ICR mice_endometrium_no GnRH agonist

tag: tissue

value: Adenomyosis group


title: S2_7


title: MCF7.C.gro.rep2

description: nascent RNA


title: Pcgf1KO+ Pcgf1_flag RNAseq

city: Nanjing

first: Wukui

state: Jiangsu

address: 12 Xuefu Road

department: Model Animal Research Center

institute: Nanjing University

data_processing:
Mapping reads with the reference genome use TopHat 2.0.12
Assemble reads use Cufflinks 2.2.1
Gene expression level analysis HTSeq 0.6.0
Alternative splicing prediction use Cuffcompare 2.2.1
Differential expression gene analysis use DEGSeq 1.18.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: Pcgf1KO+ Pcgf1_flag, mESCs

growth_protocol: ES cells were cultured with mouse embryonic fibroblasts (MEFs) inactivated with mitomycin-C in DMEM supplemented with15% fetal calf serum , leukemia inhibitory factor , L-glutamine , non-essential amino acids , 0.1 mM betamercaptoethanol , and penicillin/streptomycin. All ES cell lines were maintained at 37°C in 5% CO2.

extract_protocol:
RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair、A-tailing and adapter added were implemented. The aimed products were retrieved by agarose gel electrophoresis and PCR was performed, then the library was completed.

treatment_protocol: Pcgf1 KO ES cells were generated by Cas9 technology. Pcgf1KO+Pcgf1_flag ES cells were established by lentiviral infection technology.

tag: cell type

value: mouse embryonic stem cells

value: Pcgf1KO+ Pcgf1_flag


title: S3_1


title: S2_6


title: S3_3


title: wildtype RNAseq

source_name: wildtype, mESCs

value: wild type


title: Pcgf1 KO RNAseq

source_name: Pcgf1 KO, mESCs


title: Vesuviano Sarno Rep2

city: Portici

first: Daniela

last: D'Esposito

address: Via Università 100

department: Department of Agriculture

country: Italy

institute: University of Naples Federico II

description: processed data file: Vesuviano_Sarno_FPKM_All_Replicates.txt

data_processing:
Basecalls performed using CASAVA, version 1.8.2
Quality control performed with RseQC, version 2.3.9
Read alignment with TopHat, version 2.0.6
Abundance estimation and differential expression analysis performed with Cufflinks, version  2.1.1, –multi-read-correct, –GTF-guide
Genome_build: S. lycopersicum version 2.40, San Marzano and Vesuviano genomes (Ercolano et al., 2014)
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample replicate

organism: Solanum lycopersicum

source_name: Fruit

growth_protocol: Tomato plants were cultivated in standard conditions in field in two locations of the Campania region, Sarno (SA) and Acerra (NA).

extract_protocol:
Total RNA was extracted from powdered fruit tomato samples following the protocol developed by Wang et al. (2009).
TruSeq RNA Sample Prep Kit v2

value: Red ripe

tag: cultivar

value: Vesuviano

tag: location

value: Sarno

value: fruit


title: Vesuviano Sarno Rep3


title: Wild soybean ys34

description: strand-specific RNA-seq

organism: Glycine soja

value: wild


title: Vesuviano Sarno Rep1


title: Wild soybean ys26

description: strand-specific RNA-seq


title: Vesuviano Acerra Rep3

description: processed data file: Vesuviano_Acerra_FPKM_All_Replicates.txt

value: Acerra


title: Vesuviano Acerra Rep2


title: Cultivated soybean df17

description: strand-specific RNA-seq

value: cultivar


title: Housefly_control rep3

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: UNIVERSITY OF FLORIDA

description: The flies came from the USDA Center for Medical Agricultural and Veterinary Entomology, Gainesville, FL, USA

data_processing:
Illumina Casava1.7 software used for basecalling.
Several quality measures were performed using the web interface/software program Galaxy’s FastQC command to check the data quality of the reads and detect any potential errors introduced during sequencing or library preparation. The Cutadapt software program was used to remove low quality reads from the final dataset. Reads with a Phred-like score of <40 and bases with a score <20 were excluded.  The genes or transcripts of M. domestica (38,323 sequences) from NCBI were used as reference sequences for RNA-Seq analysis  using the Bowtie2 mapper.
ICBR scripts along with SAMtools and the DESeq, EdgeR, and Bayseq (DEB) computational applications were applied to generate the gene expression data, including fold changes and p-values, to remove duplicates or artifacts from PCR, and choose uniquely mapped reads for gene expression analysis. Digital gene expression was assessed by counting the number of transcripts that mapped to a gene sequence
Genome_build: mus_refseq-38323.fasta
Supplementary_files_format_and_content: tab-delimited text files include the mapped read counts for each Sample

organism: Musca domestica

source_name: whole body

extract_protocol:
At 48 h post-challenge, PBS- and virus-injected females were placed individually in tubes containing aliquots of 1 ml of Tri-Reagent (Sigma-Aldrich). Each sample was homogenized by adding ~ 20 zirconium beads (BioSpec Products, Bartlesville, OK) followed by vigorous shaking (30s) in a bead-homogenizer (FastPrep® Instrument, Qbiogene, Carlsbad, CA). Total RNAs were extracted according to the TriReagent protocol. Ethanol-precipitated RNA pellets were suspended in 100 µl DEPC-treated water and treated with RNase-free DNase (Qiagen). The isopropanol-precipitated total RNAs were re-extracted using SV Total RNA Isolation Kit (Promega, Fitchburg, WI, USA). RNA quantity and quality were assessed using a NanoDrop 2000 spectrophotometer  and the Agilent 2100 Bioanalyzer.
Preparation and sequencing of RNA libraries were performed by ICBR/UF (Gainesville, FL USA) according to the manufacturer’s instructions (Illumina, Inc.) using the NextSeq500 platform. Briefly, the mRNA was enriched from 1 µg of total RNA per sample using oligo-dT attached magnetic beads and then subjected to thermal fragmentation using the elute, prime, and fragmentation mix from Illumina TruSeqTM v2 RNA sample preparation kit. RNA fragments were then converted to double-stranded (ds)-cDNA using reverse transcriptase and random primers provided in TruSeq RNA sample preparation kit. The ds- cDNA fragments were end-repaired by enzymatic polishing with T4 DNA polymerase and E. coli DNA polymerase I Klenow fragment. A single non-templated dA-tail was added to 3’-end of the repaired fragments and then ligated to NEB adaptors (NEBNext®Utra RNA library preparation kit). The required fragments were purified by AMPure beads (Agencourt; PN A63881) and enriched by PCR amplification. The amplified libraries were purified and quantified using the Agilent DNA high-sensitivity kit on an Agilent 2100 Bioanalyzer and qPCR.

treatment_protocol: Cohorts of synchronously infected houseflies were produced by injecting newly emerged females with filter-sterilized viremic SG homogenates, a treatment that guarantees symptomatic infection in 100% of the injected flies. Control flies were injected with sterile PBS.

value: whole body

value: MdSGHV

value: PBS-treated

tag: age

value: Adult female


title: WT control rep1

value: leaf

value: 10 days after drought

value: WT


title: Wild soybean ys1

description: strand-specific RNA-seq

value: seeds

value: seeds after 13 days flowering


title: Vesuviano Acerra Rep1


title: San Marzano Sarno Rep3

description: processed data file: San Marzano_Sarno_FPKM_All_Replicates.txt

value: San Marzano


title: Housefly_control rep2


title: Wild soybean ys17

description: strand-specific RNA-seq


title: San Marzano Sarno Rep2

value: Red ripe


title: Housefly_treatment rep3

value: virus-injected


title: Housefly_control rep1


title: Wild soybean ys16

description: strand-specific RNA-seq


title: Housefly_treatment rep2


title: Heinz Sarno Rep3

description: processed data file: Heinz_Sarno_FPKM_All_Replicates.txt

value: Heinz

value: Sarno


title: San Marzano Acerra Rep2

description: processed data file: San Marzano_Acerra_FPKM_All_Replicates.txt

value: fruit


title: Heinz Sarno Rep1


title: Heinz Sarno Rep2


title: Wild soybean ys29

description: strand-specific RNA-seq

value: wild


title: Heinz Acerra Rep2

description: processed data file: Heinz_Acerra_FPKM_All_Replicates.txt

value: Acerra


title: Heinz Acerra Rep1


title: San Marzano Acerra Rep3


title: San Marzano Acerra Rep1


title: Heinz Acerra Rep3


title: Housefly_treatment rep1

value: whole body


title: Wild soybean ys23

description: strand-specific RNA-seq


title: 20C

description: RNA after rRNA depletion

organism: Lactococcus garvieae

source_name: static pure culture replicate C

tag: lactococcus garvieae strain

tag: culture type

value: pure culture

tag: aeration level

value: low


title: 20A

description: RNA after rRNA depletion

source_name: static pure culture replicate A


title: San Marzano Sarno Rep1


title: 19C

description: RNA after rRNA depletion

source_name: aerated pure culture replicate C

value: high


title: 19B

description: RNA after rRNA depletion

source_name: aerated pure culture replicate B


title: 19A

description: RNA after rRNA depletion

source_name: aerated pure culture replicate A


title: stk_L1

first: Chunyan

last: Zhang

state: Hubei

address: Shizishan NO.1 Street

department: Huazhong agricultural university

institute: Chunyan Zhang

description: reference strain of serovar 2

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 streptococcus suis  05ZYH33 genome sequence with SOAPaligner/SOAP2. (GenBank Accession number. CP000407)
Samtools was used for data format conversion into SAM/BAM format.

organism: Streptococcus suis

source_name: Streptococcus suis 2 cell culture

growth_protocol: S. suis strains were grown in THB  at 37ºC under static conditions.

extract_protocol:
We used 100 ng enriched mRNA with Illumina mRNA-Seq sample preparation kit (Illumina,San Diego, CA) for library construction following manufacturer's protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Total RNA was extracted using RNA Midiprep kit (Promega, Madison, USA) according to the manufacturer’s protocol. Total RNA was treated with RNase-free DNase (Invitrogen, Carlsbad, CA) to remove traces of genomic DNA.  Bacterial 16S and 23S ribosomal RNAs were removed with a MICROBExpress ™ kit (Ambion, TX, USA). Small RNAs (i.e., tRNA and 5S rRNA) were not removed with this enrichment step.

tag: genotype/variation

value: [delta]stk

tag: growth protocol

value: cultured in TSB medium to middle exponential phase


title: SS2_L1

description: reference strain of serovar 2

value: wild type


title: 20B

description: RNA after rRNA depletion

data_processing:
Basecalls performed using RTA v 1.9 (Illumina)
Concatenation of 4-5 fastq per samples
RNA seq were aligned on both genomes (S.aureus MW2+L.garvieae N201) using BWA (v0.7.5a-r405) aln with parameters -l 32 -k 2, BWA samse, samtools view -h -s -q 20 to suppress low quality alignment (to visualize alignements: … samtools view -bt to compress sam into bam files, samtools sort and index to obtain final alignment files)
Counting aligned reads: Htseq version 0.5.4p5 (i) with parameters –stranded=reverse –mode=union –type=CDS –idattr=ID for L. garvieae reads counting (ii) with parameters --stranded=reverse --mode=union --type=CDS –idattr=Dbxref for S. aureus reads counting
Differential expression analysis is carried out on count files for each conditions with R-packages DESeq, DESeq2, EdgeR, R v3.1.1
Genome_build: Lactococcus garvieae N201 (GOLD project ID: Gp0034836); Staphylococcus aureus MW2 (NCBI Reference Sequence: NC_003923)
Supplementary_files_format_and_content: Tab-delimited text files (file name = condition1_condition2_R-package used.txt) list only L. garvieae CDSs significatively differentially expressed (condition 1/condition 2) with log(fold-change) and p-values (raw and ajusted). Files are available in a tar archive located on the series record.

source_name: static pure culture replicate B


title: ME49_3

status: Public on Jun 12 2017

first: Zhonglin

last: Tang

address: No. 2 Yuanmingyuan West Road, Beijing, 100193, P.R.China,

department: Institute of Animal Science

institute: Chinese Academy of Agricultural Sciences

data_processing:
Adaptors in the total RNA-seq reads were firstly trimmed by custom scripts.
Processed reads from each sample were aligned to the reference genome of Sus scrofa (version 10.2, downloaded from ENSEMBL) by using TopHat v2.1.0.
Assignment of reads to genes was performed using htseq-count
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: Sus scrofa 10.2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Sus scrofa

source_name: Meishan, ovary, 49 days post coitus, rep3

extract_protocol:
Total RNA was isolated using the TRIzol Reagent (Invitrogen, Carlsbad, CA, USA).  Genomic DNA was removed by DNase I (Qiagen, Beijing, China). The quantity and quality of the RNA were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, California, USA). Ribosomal RNA was depleted using Ribo-Zero Magnetic kit (Epicentre, Madison, WI ).
Strand-specific RNA libraries for the paired-end sequencing were prepared using SMART protocol.

tag: breed

value: Meishan

value: ovary

tag: time

value: 49 days post coitus


title: YE49_2

source_name: Large White, ovary, 49 days post coitus, rep2

value: Large White


title: YE49_1

source_name: Large White, ovary, 49 days post coitus, rep1


title: ME49_2

source_name: Meishan, ovary, 49 days post coitus, rep2


title: YE49_3

source_name: Large White, ovary, 49 days post coitus, rep3


title: Gaglioppo grafted on 17-37Mgt, Replicate C

city: Verona

first: Andrea

last: Minio

address: Via dell'Artigliere 8

department: Applied Biotechnologies

institute: Università di Verona

data_processing:
Basecalling with Casava (ver 1.8.2)
Alignment with TopHat v2.0.14 (running Bowtie2 ver.2.2.4) in very sensitive mode
Counts generation with Cufflinks ver.2.2.0
Differntial expressed genes with Deseq (ver 1.6.3)
Gene annotations can be found at http://genomes.cribi.unipd.it/grape/
Genome_build: Vitis vinifera PN40024 V1
Supplementary_files_format_and_content: tab-delimited text files include counts each sample

molecule: polyA RNA

organism: Vitis vinifera

source_name: non-senescing leaves

extract_protocol:
Total RNA was extracted using the Spectrum Plant Total RNA extraction kit
TruSeq RNA Sample Prep Kit v2

tag: rootstock

tag: replicate

value: C


title: Gaglioppo grafted on 17-37Mgt, Replicate A

value: A


title: Gaglioppo grafted on 41B, Replicate C


title: Gaglioppo grafted on 41B, Replicate A


title: Gaglioppo grafted on 41B, Replicate B

value: B


title: Gaglioppo grafted on 3309 Couderc, Replicate B

value: 3309 Couderc


title: Gaglioppo grafted on 3309 Couderc, Replicate A


title: Gaglioppo grafted on Kober 5BB, Replicate C

value: Kober 5BB


title: Gaglioppo grafted on 1103 Paulsen, Replicate C

value: 1103 Paulsen


title: Gaglioppo grafted on 17-37Mgt, Replicate B


title: Gaglioppo grafted on 1103 Paulsen, Replicate B


title: Gaglioppo grafted on Kober 5BB, Replicate A


title: 600cells_AD_mic_12

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science

description: Sorted cells enriched for from brain of AD mouse

data_processing:
bcl2fastq/2.15.0.4
alignment using bowtiebowtie2/2.1.0 using default parameters
PCR duplication were removed using picard-tools (v1.108). In case of paired  end samples if single end protocol was used a short read in R2 was used as a UMI
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: Whole brain

growth_protocol: Either whole brains, spinal cords, or specific parts of the brain (cortex or cerebellum), not excluding meninges and choroid plexus, were collected from mice following perfusion.

extract_protocol:
Reverse crosslinking and purify ChIPed DNA with AMPure beads
High troughput reChIP, developed from the iChIP protocol (Lara-Astiaso, Weiner et al. Science 2014

tag: enrichment

value: Brain

tag: chip antibody


title: Gaglioppo grafted on 1103 Paulsen, Replicate A


title: Gaglioppo grafted on Kober 5BB, Replicate B


title: 1200cells_AD_mic_3

tag: strain


title: 1200cells_wt_mic_8

description: Sorted cells enriched for from brain of WT mouse

tag: tissue


title: 1200cells_wt_mic_6


title: 470cells_AD_cd11c_P_9


title: 1200cells_AD_mic_2


title: 1200cells_AD_cd11c_P_1


title: ME49_1

source_name: Meishan, ovary, 49 days post coitus, rep1


title: AB2443

description:
polyA+ RNA
WT6m_cerebellum_mouse2_plate#1

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
read2 used to read cell and molecule barcodes only; Note: Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: Cerebellum

extract_protocol:
Single-cell suspensions of tissues for all mice, excluding the Trem2 experiment, were achieved using software‐controlled sealed homogenization system (Dispomix; http://www.biocellisolation.com) in PBS, followed by density gradient separation; Pellet was mixed with 40% percoll and centrifuged. Brains of Trem2 mice were processed as previously published (Wang et al., 2015).
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

tag: organ

tag: selection marker

tag: treatment

value: Alzheimer's disease

tag: mouse age

value: 6 months


title: AB2444

description:
polyA+ RNA
WT6m_cerebellum_mouse2_plate#2


title: AB2442

description:
polyA+ RNA
WT6m_cortex_mouse2_plate#2

source_name: Cortex


title: AB2440

description:
polyA+ RNA
WT6m_cerebellum_mouse1_plate#2


title: AB2441

description:
polyA+ RNA
WT6m_cortex_mouse2_plate#1


title: AB2439

description:
polyA+ RNA
WT6m_cerebellum_mouse1_plate#1


title: Gaglioppo grafted on 3309 Couderc, Replicate C


title: AB2438

description:
polyA+ RNA
WT6m_cortex_mouse1_plate#2


title: AB2435

description:
polyA+ RNA
AD6m_cerebellum_mouse2_plate#2


title: AB2436

description:
polyA+ RNA
AD6m_cerebellum_mouse2_plate#3


title: AB2432

description:
polyA+ RNA
AD6m_cortex_mouse2_plate#2


title: AB2433

description:
polyA+ RNA
AD6m_cortex_mouse2_plate#3


title: AB2434

description:
polyA+ RNA
AD6m_cerebellum_mouse2_plate#1


title: AB2428

description:
polyA+ RNA
AD6m_cerebellum_mouse1_plate#1


title: AB2429

description:
polyA+ RNA
AD6m_cerebellum_mouse1_plate#2


title: AB2427

description:
polyA+ RNA
AD6m_cortex_mouse1_plate#3


title: AB2345

description:
polyA+ RNA
WT6m_mouse3_plate#6


title: AB2430

description:
polyA+ RNA
AD6m_cerebellum_mouse1_plate#3


title: AB2343

description:
polyA+ RNA
WT6m_mouse3_plate#4


title: AB2340

description:
polyA+ RNA
WT6m_mouse3_plate#1


title: AB2342

description:
polyA+ RNA
WT6m_mouse3_plate#3


title: AB2339

description:
polyA+ RNA
WT6m_mouse2_plate#6


title: AB2341

description:
polyA+ RNA
WT6m_mouse3_plate#2


title: AB2425

description:
polyA+ RNA
AD6m_cortex_mouse1_plate#1


title: AB2336

description:
polyA+ RNA
WT6m_mouse2_plate#3


title: AB2437

description:
polyA+ RNA
WT6m_cortex_mouse1_plate#1


title: AB2331

description:
polyA+ RNA
AD6m_mouse3_plate#4


title: AB2334

description:
polyA+ RNA
WT6m_mouse2_plate#1


title: AB2333

description:
polyA+ RNA
AD6m_mouse3_plate#6


title: AB2338

description:
polyA+ RNA
WT6m_mouse2_plate#5


title: AB2335

description:
polyA+ RNA
WT6m_mouse2_plate#2


title: AB2330

description:
polyA+ RNA
AD6m_mouse3_plate#3


title: AB2431

description:
polyA+ RNA
AD6m_cortex_mouse2_plate#1


title: AB2337

description:
polyA+ RNA
WT6m_mouse2_plate#4


title: AB2329

description:
polyA+ RNA
AD6m_mouse3_plate#2


title: AB2328

description:
polyA+ RNA
AD6m_mouse3_plate#1


title: AB2332

description:
polyA+ RNA
AD6m_mouse3_plate#5


title: AB2344

description:
polyA+ RNA
WT6m_mouse3_plate#5


title: AB2426

description:
polyA+ RNA
AD6m_cortex_mouse1_plate#2


title: AB2327

description:
polyA+ RNA
AD6m_mouse2_plate#6


title: AB2326

description:
polyA+ RNA
AD6m_mouse2_plate#5


title: AB2325

description:
polyA+ RNA
AD6m_mouse2_plate#4


title: AB2324

description:
polyA+ RNA
AD6m_mouse2_plate#3


title: nHS29-K27

city: Brookings

first: Moul

last: Dey

state: South Dakota

address: SWG 440, Rotunda Lane

department: Health and Nutritional Sciences

institute: South Dakota State University

description: processed data file: nHS-K27.sorted.bw

data_processing:
The basic analysis of ChIP-Seq was based on the published protocol (Feng, Liu et al. 2012) utilizing Bowtie, version 1.0.0 (Langmead, Trapnell et al. 2009) and MACS, version 2.1.0 (Zhang, Liu et al. 2008)
Raw reads were quality checked using FastQC, version v0.10.1 (FastQC) and mapped onto the rat RN5 genome sequence using Bowtie, version 1.0.0 (Langmead, Trapnell et al. 2009).  The option of “-m 1” was activated so that only uniquely mapped reads were allowed to map.
The mapping results in SAM were converted to BAM and sorted according to coordinates using samtools, version 0.1.19 (Li, Handsaker et al. 2009). Mapping results of each ChIP sample and the input sample were subjected to ChIP enriched peak calling. The option of “--broad” was activated to optimize the calling algorithm for broad binding regions. The called peaks are annotated to the nearest TSS (Transcript Starting Site) using ChIPpeakAnno, version 3.2.0 (Zhu, Gazin et al. 2010).  ChIP quality control was performed using ChIPQC, version 1.2.2 (Carroll, Liang et al. 2014).
The previously mapped results (BAM) in replicates were merged using Samtools, version 0.1.19. The mapping statistics was extracted using Picard, version 1.90.
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: bigwig files were generated

organism: Rattus norvegicus

source_name: HF_STZ_neonatal heart

extract_protocol:
Five to six frozen heart tissues were pooled to make >250mg/sample and homogenized followed by chromatin isolation using P-2001 ChromaFlashTM Chromatin Extraction Kit (Epigentek, Farmingdale, NY). Chromatin was sheared using Episonic2000 Sonication System (Epigentek, Farmingdale, NY) in 300 μl of ChIP buffer. DNA fragment (100-300 bp) was quality-checked using Bioanalyzer analysis.
A ChIP-sequencing library was prepared using the EpiNext ChIP-Seq High Sensitivity Kit with amplification, DNA end polishing and adaptor ligation. 10 nM of sample libraries were provided for next generation sequencing on a HiSeq 2500.

treatment_protocol: Female Sprague-Dawley rats were randomized into four groups and fed high fat diet (HF) or control diet (CD) for 28 days prior to their breeding and throughout the pregnancy. On gestational day 14, each HF or CD group was treated with intraperitoneal injection of Streptozotocin (STZ, 65 mg/Kg) or citrate buffer (CB) as a control. Pups were normally delivered on gestational day 21 and sacrificed and their hearts were collected.

value: Sprague Dawley

tag: maternal diet/treatment

value: high fat diet (HF) + Streptozotocin (STZ, 65 mg/Kg)

tag: developmental stage

value: neonatal (pups delivered on gestational day 21)

value: heart

value: H3K27me3 (Epigentek, A-4039)


title: nHS29-K4

description: processed data file: nHS-K4.sorted.bw

value: H3K4me3 (Epigentek, A-4033)


title: nHS29-AC

description: processed data file: nHS-Ac.sorted.bw

value: H3Ac (Epigentek, A-4021)


title: nHS29-In

description: processed data file: nHS-In.sorted.bw


title: AB2323

description:
polyA+ RNA
AD6m_mouse2_plate#2

organism: Mus musculus


title: AB2322

description:
polyA+ RNA
AD6m_mouse2_plate#1


title: nHS11-In

description: processed data file: nHS-In.sorted.bw


title: nHS11-K27

description: processed data file: nHS-K27.sorted.bw


title: nHS11-K4

description: processed data file: nHS-K4.sorted.bw


title: AB1864

description:
polyA+ RNA
AD6m_mouse4_plate#1


title: nHS11-AC

description: processed data file: nHS-Ac.sorted.bw


title: AB1863

description:
polyA+ RNA
WT8m_mouse2_plate#1

value: 8 months


title: nHC30-K27

description: processed data file: nHC-K27.sorted.bw

source_name: HF_CB_neonatal heart

value: high fat diet (HF) + citrate buffer (CB)


title: nHC30-K4

description: processed data file: nHC-K4.sorted.bw


title: AB1746

description:
polyA+ RNA
ALS_control2_d80_plate#2

source_name: Spinal cord

value: Spinal cord

value: ALS

value: 80 days


title: AB1745

description:
polyA+ RNA
ALS_mouse3_d80_plate#2


title: AB1744

description:
polyA+ RNA
ALS_control1_d80_plate#2


title: nHC30-In

description: processed data file: nHC-In.sorted.bw


title: nHC30-AC

description: processed data file: nHC-Ac.sorted.bw


title: nHC24-K27

description: processed data file: nHC-K27.sorted.bw


title: AB1742

description:
polyA+ RNA
Trem2_KO_AD_cd11c_plate#2


title: AB1743

description:
polyA+ RNA
Trem2_KO_AD_cd11c_plate#3


title: nHC24-In

description: processed data file: nHC-In.sorted.bw


title: nHC24-K4

description: processed data file: nHC-K4.sorted.bw


title: AB1740

description:
polyA+ RNA
Trem2_KO_cd11c_plate#1


title: nHC24-AC

description: processed data file: nHC-Ac.sorted.bw


title: AB1739

description:
polyA+ RNA
Trem2_AD_cd11c_plate#2


title: AB1738

description:
polyA+ RNA
Trem2_AD_cd11c_plate#1


title: AB1736

description:
polyA+ RNA
Trem2_KO_AD_plate#3


title: nCS27-K4

description: processed data file: nCS-K4.sorted.bw

source_name: CD_STZ_neonatal heart

value: control diet (CD) + Streptozotocin (STZ, 65 mg/Kg)


title: nCS27-AC

description: processed data file: nCS-Ac.sorted.bw


title: nCS27-In

description: processed data file: nCS-In.sorted.bw


title: AB1735

description:
polyA+ RNA
Trem2_KO_AD_plate#2


title: AB1737

description:
polyA+ RNA
Trem2_WT_cd11c_plate#1


title: AB1734

description:
polyA+ RNA
Trem2_KO_AD_plate#1


title: AB1733

description:
polyA+ RNA
Trem2_KO_plate#3


title: nCS02-AC

description: processed data file: nCS-Ac.sorted.bw


title: AB1732

description:
polyA+ RNA
Trem2_KO_plate#2


title: nCS02-In

description: processed data file: nCS-In.sorted.bw


title: AB1731

description:
polyA+ RNA
Trem2_AD_plate#2


title: AB1730

description:
polyA+ RNA
Trem2_WT_plate#1


title: nCC26-In

description: processed data file: nCC-In.sorted.bw

source_name: CD_CB_neonatal heart

value: control diet (CD) + citrate buffer (CB)


title: AB1720

description:
polyA+ RNA
old_20m_mouse2_plate#2

value: Brain

value: Aging

value: 20 months


title: AB1741

description:
polyA+ RNA
Trem2_KO_AD_cd11c_plate#1

value: Alzheimer's disease

value: 6 months


title: AB1719

description:
polyA+ RNA
old_20m_mouse2_plate#2


title: AB1718

description:
polyA+ RNA
old_20m_mouse1_plate#1


title: nCS27-K27

description: processed data file: nCS-K27.sorted.bw

value: Sprague Dawley

value: neonatal (pups delivered on gestational day 21)


title: nCC21-K27

description: processed data file: nCC-K27.sorted.bw

value: heart

value: H3K27me3 (Epigentek, A-4039)


title: nCC26-AC

description: processed data file: nCC-Ac.sorted.bw

value: H3Ac (Epigentek, A-4021)


title: nCC21-K4

description: processed data file: nCC-K4.sorted.bw

value: H3K4me3 (Epigentek, A-4033)


title: nCC21-In

description: processed data file: nCC-In.sorted.bw


title: AB1716

description:
polyA+ RNA
young_7w_mouse2_plate#1

value: 7 weeks


title: AB1715

description:
polyA+ RNA
young_7w_mouse1_plate#1


title: nCC21-AC

description: processed data file: nCC-Ac.sorted.bw


title: nCS02-K4

description: processed data file: nCS-K4.sorted.bw


title: AB1714

description:
polyA+ RNA
AD1m_mouse1_plate#2

value: 1 month


title: AB1712

description:
polyA+ RNA
WT1m_mouse1_plate#1


title: nCS02-K27

description: processed data file: nCS-K27.sorted.bw


title: AB1711

description:
polyA+ RNA
AD9m_mouse1_plate#1

value: 9 months


title: AB1709

description:
polyA+ RNA
WT3m_mouse1_plate#1

value: 3 months


title: AB1710

description:
polyA+ RNA
AD3m_mouse1_plate#1


title: nCC26-K27

description: processed data file: nCC-K27.sorted.bw


title: AB1713

description:
polyA+ RNA
AD1m_mouse1_plate#1


title: AB1668

description:
polyA+ RNA
AD6m mouse2 plate#1 (first 4 lines), WT6m mouse2 plate#2 (rest of plate).


title: nCC26-K4

description: processed data file: nCC-K4.sorted.bw


title: AB1557

description:
polyA+ RNA
ALS_control1_d135_plate#1

value: Spinal cord

value: ALS

value: 135 days


title: AB1667

description:
polyA+ RNA
WT6m mouse2 plate#1

value: Brain


title: AB1558

description:
polyA+ RNA
ALS_mouse1_d135_plate#1


title: AB1554

description:
polyA+ RNA
ALS_mouse4_d80_plate#1

value: 80 days


title: AB1553

description:
polyA+ RNA
ALS_mouse3_d80_plate#1


title: AB1717

description:
polyA+ RNA
young_7w_mouse2_plate#2

value: Aging


title: AB1551

description:
polyA+ RNA
ALS_mouse2_d80_plate#1


title: AB1552

description:
polyA+ RNA
ALS_mouse2_d80_plate#2


title: AB1549

description:
polyA+ RNA
ALS_control3_d80 plate#1


title: AB1548

description:
polyA+ RNA
ALS_control2_d80 plate#1


title: AB1550

description:
polyA+ RNA
ALS_mouse1_d80_plate#1


title: AB1449

description:
polyA+ RNA
AD6m mouse1 plate#4

value: Alzheimer's disease

value: 6 months


title: AB1547

description:
polyA+ RNA
ALS_control1_d80 plate#1


title: AB1448

description:
polyA+ RNA
AD6m mouse1 plate#3


title: AB1446

description:
polyA+ RNA
WT6m mouse1 plate#3


title: AB1444

description:
polyA+ RNA
WT6m mouse1 plate#1


title: AB1442

description:
polyA+ RNA
AD6m mouse1 plate#1


title: AB1447

description:
polyA+ RNA
WT6m mouse1 plate#4


title: AB1445

description:
polyA+ RNA
AD6m mouse1 plate#2


title: A549_mRNA

city: Guangzhou

first: Gong

address: Huang-Pu Avenue West 601

department: Institute of Life and Health Engineering

institute: Jinan University

description: Ion torrent

data_processing:
Prefilter: the datasets created from ion torrent platform were filtered out the low-quality (Phred score<10) reads.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Mapping was performed using the hyper-accurate FANSe2 algorithm for quantitaion purpose.
Genome_build: hg19
Supplementary_files_format_and_content: .txt file includes log2 rpkm values

organism: Homo sapiens

source_name: Adenocarcinomic human alveolar basal epithelial cells (A549)

extract_protocol:
Total RNA of those cells were extracted using Trizol reagent.
10pg polyA+ mRNA was used as the input. mRNA was subjected to smart-seq2 method for illumina sequencing, and also in parallel subjected to low-input direct library construction of ion torrent sequencer.

tag: cell line

tag: input amount

value: 10pg polyA+ mRNA

tag: library construction

value: low-input direct library construction


title: AB1443

description:
polyA+ RNA
WT6m mouse1 plate#2


title: HBE_mRNA

description: Ion torrent

source_name: Human bronchial epithelial cells (HBE)

value: HBE


title: AB1556

description:
polyA+ RNA
ALS_mouse1_d135_plate#1


title: AB1555

description:
polyA+ RNA
ALS_control1_d135_plate#1


title: siBRMsiNS etoh replicate 3

city: Los Angeles

first: Brian

middle: Hae Kang

last: Lee

address: 1441 Eastlake Avenue, NOR 6316

department: Biochemistry and Molecular Medicine

institute: University of Southern California

data_processing:
NextSeq Control Software (NCS) v1.4 was used for base calling
After trimming the raw reads for quality and adapter sequence, the samples were mapped using TopHat 2.1.1 with default parameters against the GRCh38/hg38 human reference genome
Mapped reads were quantified to known UCSC genes using the GenomicAlignments R package
Gene expression levels were normalized with the upper quantile (UQ) method and lowly expressing genes were excluded such that genes with more than one count per million in at least 3 samples were analyzed
We implemented the remove unwanted variation (RUV) strategy to account for unknown nuisance technical effects between samples.
Differentially expressed genes were identified with edgeR using a 1.3-fold change in expression (log2 = 0.4) and false discovery rate adjusted p-value ≤ 0.05 as cutoffs
Genome_build: hg38
Supplementary_files_format_and_content: comma separated file (csv) containing CPM values with each gene represented in each row and the experimental conditions as columns

source_name: U2OS-GR⍺ cells

growth_protocol: Cells were grown in DMEM low glucose medium supplemented with 5% (vol/vol) FBS

extract_protocol:
Total RNA was extracted using TRIzol (Thermo Scientific) and 3 biological replicates for each condition were performed on different days.
RNA samples were reverse transcribed using iScript cDNA synthesis kit (Bio-Rad) and quality of the cDNA was assessed using Agilent Technologies 2100 Bioanalyzer and RT-qPCR analysis was performed for selected GR target genes as quality control. Standard illumina protocols were used to construct the library for sequencing.

treatment_protocol: siRNA transfection was performed using Lipofractamine RNAimax (invitrogen) according to the manufacturer's protocol. 48 h after siRNA transfection the cells were either treated for 8 hours with 100 nM dex (Sigma) or an equivalent amount of ethanol as control.

value: U2OS cell line stably transfected with GR{alpha}


title: siBRMsiNS dex replicate 3


title: siCHD9siHic5 dex replicate 3


title: siBRMsiHic5 dex replicate 3


title: siNSsiNS dex replicate 3


title: siCHD9siHic5 etoh replicate 3


title: siCHD9siNS etoh replicate 3


title: siHic5siNS dex replicate 3


title: siHic5siNS etoh replicate 3


title: siNSsiNS etoh replicate 3


title: siBRMsiHic5 dex replicate 2


title: siBRMsiHic5 etoh replicate 2


title: siBRMsiNS dex replicate 2


title: siCHD9siHic5 dex replicate 2


title: siCHD9siHic5 etoh replicate 2


title: siCHD9siNS dex replicate 2


title: siCHD9siNS etoh replicate 2


title: siBRMsiNS etoh replicate 2


title: 791: Macrophages_TPC1_None_4

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

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

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with TopHat2 (v2.0.3) against the hg19 reference genome
Gene and transcript information was extracted with Partek Genomics Suite (v6.6). Annotated data was normalized using statistical software R (v3.0.2) including DESeq2 package. Normalized read counts lower than 1 were set to the floor value 1.Genes were defined as expressed with normalized RNA-seq values ≥ 10.
Genome_build: hg19
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the hg19 reference genome

source_name: macrophage

growth_protocol: RPMI with gentamycin 5 mg/ml, pyruvate 100 mM, glutamax 200 mM and 10% Fetal Calf Serum

extract_protocol:
RNeasy kits (Qiagen)
1µg of total RNA was converted to RNA-seq libraries according to manufacturers' protocol with Illumina TruSeq RNA Sample Preparation Kit.

treatment_protocol: 24h co-incubation between TPC1 cell line and human primary macrophage

tag: sample id

value: TPC1 cell line

tag: donor

value: F


title: 774: Macrophages_TPC1_None_4

tag: time

value: E


title: siHic5siNS dex replicate 2


title: siBRMsiHic5 etoh replicate 3


title: 812: Macrophages_TPC1_None_24

value: G


title: siCHD9siNS dex replicate 3


title: 757: Macrophages_TPC1_None_4

value: C


title: 808: Macrophages_TPC1_None_4


title: 795: Macrophages_TPC1_None_24


title: siNSsiNS etoh replicate 2


title: 778: Macrophages_TPC1_None_24


title: siBRMsiHic5 dex replicate 1


title: 761: Macrophages_TPC1_None_24


title: siBRMsiNS dex replicate 1


title: 799: Macrophages_RPMI_None_4

value: RPMI


title: 816: Macrophages_RPMI_None_4


title: siBRMsiHic5 etoh replicate 1


title: siBRMsiNS etoh replicate 1


title: 782: Macrophages_RPMI_None_4


title: siCHD9siHic5 dex replicate 1


title: siCHD9siNS dex replicate 1


title: siCHD9siHic5 etoh replicate 1


title: 765: Macrophages_RPMI_None_4


title: 818: Macrophages_RPMI_None_24


title: siHic5siNS dex replicate 1


title: siHic5siNS etoh replicate 2


title: siCHD9siNS etoh replicate 1


title: 801: Macrophages_RPMI_None_24


title: 784: Macrophages_RPMI_None_24


title: siNSsiNS dex replicate 2


title: 767: Macrophages_RPMI_None_24


title: siHic5siNS etoh replicate 1


title: siNSsiNS etoh replicate 1


title: INTS12_ChIPseq_input

city: Cambridge

first: Alexander

last: Kheirallah

state: Cambridgeshire

address: Hills Road

department: Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
RNAseq alighnemnt performed using TopHat
RNAseq transcriptome assembly peroformed using Cufflinks
RNAseq differential gene expression performed using Cuffdiff (significant defined as q<0.05)
FPKM abundance per gene performed using Cuffnorm
ChIPseq alighnment performed with Bowtie2
ChIPseq peak calling perfmed with MACS2 (ChIP vs input control approach)
ChIPseq track signal performed by comparing ChIP vs input with fold enrichment option and total library size normalization. Generated bedGraphs were converted to wig files with 100bp resolution.
Genome_build: hg19
Supplementary_files_format_and_content: *metaMatrix.txt contains FPKM abundances per gene.
Supplementary_files_format_and_content: *.wig contains library size and background noise normalized signal tranck
Supplementary_files_format_and_content: *.narrowPeak contains inferred INTS12 binding sites at q<0.05

growth_protocol: Human bronchial epithelial cells HBECs were purchased from Clonetics-Biowhittaker (MD, USA). Cells were cultured in HBEC basal medium (BEGM) from Lonza (Berkshire, UK) prepared by addition of all the recommended supplements per manufacturer specifications excluding gentamicin. All laboratory experiments were performed using passage 3 cells. Prior to experiments cells were grown at 37oC with 5% CO2 until ~95% confluent with BEGM media change every ~48h

extract_protocol:
RNAseq: Total RNA was extracted using a mammalian total RNA prep kit with on-column DNaseI digestion
ChIP-seq: Unprecipitated genomic DNA (i.e. input control) was prepared from a pool of equal aliquots of the two donor samples. Genomic DNA regions of interest were isolated using 4 µg of antibody against INTS12 (Sigma cat. num. HPA03577) following manufacturer’s specifications (Active Motif).
RNA-seq: The sequencing libraries were prepared with Illumina TruSeq RNA Sample Prep Kit v2. mRNA was poly-A selected by capturing total RNA samples with oligo-dT coated magnetic beads. The mRNA was then fragmented and randomly primed. cDNA was synthesised using random primers. Finally a ready-for-sequencing library was prepared by end-repair, phosphorylation, A-tailing, adapter ligation and PCR amplification. Paired-end sequencing was performed on the HiSeq2000 platform (Illumina) using TruSeq v3 chemistry over 100 cycles yielding ~40 million reads per sample.
ChIP-seq: Libraries (Illumina) were prepared from the both ChIP and input DNAs and the resulting libraries were sequenced yielding ~40 million reads per two ChIP samples from each donor cells and one input control of both donors. DNA libraries obtained from single donor were sequenced on NextSeq 500 sequencing machine

treatment_protocol:
RNAseq: Effects of INTS12 depletion were assessed 120h and 48h after the initiation of interference.There were four experimental conditions: un-transfected cells, cells transfected with scrambled D-siRNA control, and cells transfected with D-siRNAs A and C. Each experimental condition was performed in three independent biological replicates.
ChIP-seq: Cells were formaldyhade fixed. Chromatin was isolated by the addition of lysis buffer. Genomic DNA for each replicate sample was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation.

tag: cell type

value: Human bronchial epithelial cells HBECs

tag: passage

tag: source

value: Lonza


title: INTS12_ChIPseq_D7F3158

tag: chip antibody

value: INTS12 (Sigma cat. num. HPA03577)


title: Stage 5 infected

city: New Delhi

first: Gopal

last: Joshi

state: Delhi

address: First Floor

department: Department of Botany

country: India

institute: Delhi University

description: small RNA profiling

data_processing:
Illumina Casava 1.7 software used for basecalling
Sequencing data was filtered through a pipeline of UEA small RNA workbench 3.0 with default parameters (Stocks et al. 2012). The sequences without 3’ adaptor and those trimmed sequences not lying between the specified sequence lengths were discarded and sequences with the length specified by the user (16-35 nt) were extracted. Further, low complexity sequences (sequences containing less than 3 distinct nucleotides), invalid tags with ‘N’ nucleotides, degradation products and other non-small RNAs were discarded. The fragments of rRNA, tRNA, snRNA or snoRNA were removed after being mapped on plant t/rRNAs sequences from “Rfam” (except miRNA), Arabidopsis tRNAs from “The Genomic tRNA Database”, and plant t/rRNA sequences from “EMBL” release 95.
For identification of miRNAs and their precursors, the clean putative small RNA reads obtained after filtration through elimination pipeline were aligned to tomato reference genome dataset (Solanaceae Genomics Project Assembly SL2.40 obtained from NCBI) (The Tomato Genome Consortium) with no mismatch by using miRCat pipeline of UEA sRNA tool kit with set parameters (Stocks et al. 2012).
Genome_build: Solanaceae Genomics Project Assembly SL2.40
Supplementary_files_format_and_content: The .txt files report abundance measurements of small RNA reads

source_name: ROOT

growth_protocol: Disease development study was conducted using root knot nematode, M. incognita. RKN was propagated on susceptible Indian tomato cv. Pusa Ruby in infection house at Department of Botany, University of Delhi, India. Infection studies were conducted under controlled growth conditions at 22oC with 16 hour light and 8 hour dark photoperiod. For miRNA studies, tomato susceptible cv., Pusa Ruby and tomato resistant transgenic line that contains Mi-1 resistance gene were used.

extract_protocol:
Root tissue of equal weight of each disease development stage was processed for RNA isolation using TRI reagent (Sigma-Aldrich, St. Louis, MO, U.S.A.) as per manufacturer’s instructions. The integrity of RNA was checked on 1.2% agarose gel and quantification was done through optical density measurement using nanovue (GE Healthcare Bio-sciences, Uppsala, Sweden).
In total 11 small RNA libraries were prepared including five infected disease development stages and their corresponding uninfected tissue of same age and a library of five-week old uninfected root tissue of susceptible tomato cv. Small RNA libraries from root tissue of each stage were prepared independently using Illumina small RNA sample preparation kit (Illumina, San Diego, CA, U.S.A.) according to manufacturer’s instructions. Briefly, an equal amount of total RNA of each stage was used for sequential ligation of 3’and 5’adapter using T4 RNA ligase. Adapter ligated small RNA was reverse transcribed using SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA, U.S.A.) and 3’ adapter specific RT-primer. cDNA prepared was amplified and product of approximately 147 bp was eluted through 6% polyacrylamide gel. The quality and quantity of cDNA libraries prepared were determined through Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, U.S.A.). High-throughput sequencing of libraries was performed using Illumina Hiseq 2000 system at Institute of Genomics and Integrative Biology, Delhi, India, according to manufacturer’s instructions.

treatment_protocol: The second juvenile stage (J2) is the only parasitic stage that was used for infecting plants, therefore, egg masses were detached manually from infected roots and kept in deionised water at room temperature for hatching of eggs into J2s. After 2-3 days, J2s were separated from unhatched eggs by passing the suspension of J2s through three to four layered kim wipes. The five-week old plantlets of both susceptible cv. and resistant line were grown in sterile soil and inoculated with 1500 J2s. The control plantlets were also raised that have not been exposed to nematode. For tissue collection, in susceptible cv. for 30 days and resistant line for 7 days, plantlets were uprooted, roots were quickly washed under cold tap water, excised from the plant and snap chilled in liquid nitrogen. Tissue was kept in -80o C for subsequent storage. The root tissue of uninfected plantlets of the same age was also harvested as control samples. The additional one plant was harvested on each day to study the lifecycle of nematode inside the root and progression of the disease through acid fuchsin staining (Bybd et al. 1983). After uprooting, roots were washed and suspended in 1.5% sodium hypochlorite bleach for 4 mins and then washed to remove excess bleach. For staining, roots were boiled for a minute in 0.2% acid fuchsin stain prepared in lactophenol followed by clearing of roots. The whole plant root system was observed under the inverted microscope (Carl Zeiss, Gottingen, Germany) and number of nematodes at their different development stage were counted. Five disease development stages of susceptible response and two disease development stages of resistance response were selected for further study on the basis of the rate of nematode invasion, a number of knots/galls formed on infected root, transition of varied developmental stages of nematode and progression of disease in the host.

tag: cultivar

value: Pusa ruby

tag: tissue

value: root

tag: age

value: 5 week old + (26dpi+27dpi+28dpi)

tag: uninfected or infected

value: infected


title: Stage 5 uninfected

description: small RNA profiling

value: uninfected


title: INTS12_ChIPseq_D195307


title: Stage 1 uninfected

description: small RNA profiling

value: 5 week old + (1dpi+2dpi+3dpi)


title: Stage 1 infected

description: small RNA profiling


title: Stage 3 uninfected

description: small RNA profiling

value: 5 week old + (13dpi+14dpi+15dpi)


title: Stage 2 uninfected

description: small RNA profiling

value: 5 week old + (5dpi+6dpi+7dpi)


title: Stage 2 infected

description: small RNA profiling


title: Stage 4 uninfected

description: small RNA profiling

value: 5 week old + (18dpi+19dpi+20dpi)


title: Stage 3 infected

description: small RNA profiling


title: 11-D3-Th1_S11_L001_R1_001

city: London

first: Reuben

last: McGregor

address: Great Maze Pond

institute: Kings College London

data_processing:
qiagen analysis pipeline for targeted RNAseq panels was used (http://www.qiagen.com/shop/genes-and-pathways/data-analysis-center-overview-page/?akamai-feo=off0
RNAseq was a targeted panel. Only targeted with primers at some 500 immunology genes.
adaptors trimmed, reads< 55bp droped, first 12bp dropped form every read (as they cointain molecular tags) and ampped using STAR RNA read mapper. Non mapped reads were dropped
bam files were then imported into PARTEk genomics suite for generation of RPKM values
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: tab-delimited text file (reubenmcg_RNASeq_results.gene.rpkm) includes RPKM values for each Sample

source_name: CD4+ T cell Peripheral Blood

extract_protocol:
FACS-sorted Th-like Tregs (2x105 per well) were activated with CD3/CD28 beads (ratio 1:4) for 72h. Cells were lysed in Trizol (Thermo Fisher Scientific) and RNA was isolated with Direct-Zol RNA MicroPrep w/Zymo-Spin columns (Cambridge Bioscience). RNA sequencing was performed using The Human Inflammation & Immunity Transcriptome RNA targeted panel (Qiagen). Samples were quantified with Agilent High Sensitivity DNA Kit (Agilent Technologies) and sequenced with Illumina MiSeq using MiSeq Reagent Kit v3 (150-cycle). 100ng of RNA was used to construct libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols provided but with kits procided by Qiagen

tag: t-helper like treg


title: 9-D3-Th2_S9_L001_R1_001


title: Stage 0 uninfected

description: small RNA profiling

value: 5 week old


title: 7-D2-Th1_S7_L001_R1_001