title: ΔBCHL Prha rep1

city: Ithaca

first: Martin

last: Wiedmann

state: NY

address: 341 Stocking Hall

department: Food Science

institute: Cornell University

description:
Total RNA was treated with Ribo-ZeroTM rRNA Removal Reagents (Bacteria)-Low Input for removal of 16S and 23S ribosomal RNA and enriched for mRNA
sigB_processed_data.xlsx
sliding_window_results_geo.txt

data_processing:
Raw data was generated by the Illumina pipeline software v1.8
the sequence reads were aligned to a 10403S genome using the BWA-MEM with default settings.The output was a SAM files for each sample. Used SAMTOOLS (Li, et al., PMID 1950593) to sort and index the SAM files obtained from BWA and convert them to BAM format. BAM files were converted to strand-specific base count files. Coverage at each base position along the chromosome was calculated by enumerating the number of reads that aligned to a given base for each DNA strand separately.
Differential expression of genes in different strains was statistically assessed using the BaySeq method implemented in the BaySeq 2.2.0 package available from Bioconductor. Genes were considered differentially expressed if they showed a false discovery rate (FDR) < 0.05 and a fold change (FC) ≥ 2.0 (meaning genes were upregulated on Prha-sigB) or FC ≤ 0.5 (meaning genes were downregulated on Prha-sigB).
Sliding window analysis: the 10403S genomes was divided into windows of 51 nt (window size) with 25 nt overlap (window sliding) and the RNA-Seq coverage was obtained for each of the 116,123 resulting windows. Bayseq version 2.2.0 was then used, as described above, to identify windows with significant differential expression between the ΔBCHL::Prha-sigB strain and the ΔBCHL::Prha strain. Fold change was also calculated as described above and windows presenting an FDR < 0.05 and FC > 2.0 were considered for further analysis. Windows matching the required thresholds were then sorted and overlapping windows were considered as being part of the same fragment. Fragments that were mapped to the same gene or operon were considered as being part of the same transcriptional unit (TU). The 5’ end of significant TUs were then manually scanned for promoter sequences, as described above.
Genome_build: ASM16869v2 (GenBank accession number: NC_017544)
Supplementary_files_format_and_content: An excel spreadsheet (.xlsx) file: Raw count data and normalized count data (from BaySeq output) for each coding gene in 10403S. BaySeq result (likelihood of being differentially expressed and False Discovery Rate). Fold Changes (ΔBCHL-RH/ΔBCHL-R) and whether the Fold Changes are above or below the thresholds (< 0.5 or > 2.0) are provided. And a text (.txt) file containing the output from BaySeq with normalized coverage for each 51 nt window and Fold Changes (ΔBCHL-RB/ΔBCHL-R)

organism: Listeria monocytogenes 10403S

source_name: BHI broth

growth_protocol: strains were streaked from frozen BHI stock, stored at -80°C in 15% glycerol, onto a BHI agar plate, followed by incubation at 37°C for 24 h. A single colony was subsequently inoculated into 5 ml of BHI broth in 16 mm tubes, followed by incubation at 37oC with shaking (230 rpm) for 18 h (Series 25 Incubator, New Brunswick Scientific, Edison, NJ). After 18 h, 50 μl BHI culture was inoculated into fresh 5 ml BHI broth and grown to OD600 0.4-0.5 at 37°C.

extract_protocol:
Total RNA was extracted by using RNA protect, proteinase K, and lysozyme, followed by Tri reagent with bead-beating. Total RNA was incubated with DNase in the presence of RNasin to remove remaining DNA.
Preparation of cDNA fragment libraries was performed using the ScriptSeqTM Complete Kit (Bacteria)-Low Input (Epicentre, Madison, WI), which is composed of Ribo-ZeroTM rRNA Removal Reagents (Bacteria)-Low Input, Magnetic Core Kit-Low Input, and ScriptSeqTM v2 RNA-Seq Library Preparation Kit.

treatment_protocol: 250 μl 1M rhamnose stock solution was added to 5 ml OD600 0.4-0.5 bacterial cultures (for a final concentration of 50 mM rhamnose), followed by incubation at 37°C for an additional 30 min.

value: 10403S::<delta>BCHL Prha

tag: growth stage

value: log phase

tag: induction

value: Rhamnose addition


title: ΔBCHL Prha-sigB rep3

status: Public on Oct 31 2017

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: strain

value: 10403S::<delta>BCHL Prha-sigB


title: ΔBCHL Prha-sigB rep2


title: ΔBCHL Prha rep2


title: SHAM 1

city: Leuven

first: Chandan

last: Kadur Nagaraju

state: Leuven

address: UZ Herestraat 49 box 704

department: Cardiovascular Science

country: Belgium

institute: KU Leuven

data_processing:
Default base calling software from Ilumina HiSeq 2500 was used to generate final FASTQ files
Genome_build: SusSCR10.2
Supplementary_files_format_and_content: wig

organism: Sus scrofa

source_name: SHAM adjacent Myocardium Fb

growth_protocol: Fb cells 3 regions (adjacent/remote myocardium and scar tissue) from porcine myocardial infarct heart isolated by enymatic digestion and culture for 4 days

extract_protocol:
Cells cultured on cover slip in 6 well plate were washed with PBS. Cells harvested by adding Qiazol and RNA was isolated using RNeasy mini kit
samples were sequenced on single-reads of 50bp on a HiSeq2500.

tag: tissue source

value: Fb cell isolated from adjacent myocardium tissue

tag: duration of culture


title: SHAM 2


title: Scar_2

data_processing:
Default base calling software from Illumina HiSeq 2500 was used to generate final FASTQ files
The FASTQ files were aligned to the reference genome Sscrofa 10.2 using STAR aligner followed by computation of estimated gene expression. This complete process was carried out by RNA-seq by expectation maximization software package.
The wiggle tracks were generated through the BAM files. For each base pair in the genome, the number of overlapping sequence reads was determined , averaged over a 10 bp window.
genome build: Sscrofa 10.2
Supplementary_files_format_and_content: wig

source_name: MI Scar tissue Fb

value: Fb cell isolated from Scar tissue


title: Scar_4


title: 5C_Thymocytes 2

city: Bradford

first: Natalia

middle: V.

last: Botchkareva

address: Richmond Road

country: United Kingdom

institute: University of Bradford

library_source: genomic

data_processing:
The 5C library sequencing data sets were de-multiplexed using Novobarcode (Novocraft)
The reads were aligned to the pseudo-genome consisting of all 5C probes (mm9) using Bowtie
The interactions were counted when both paired end reads could be uniquely mapped to the 5C probe pseudo-genome. Only interactions between forward-reverse probe pairs were considered as true counts.
Data were filtered using the following specifications.  First, we removed the probes that performed significantly differently in comparison to the overall probe sets.  A global average relationship between interaction frequency and genomic distance was calculated using Loess smoothing for each replicate dataset.  Contact profile for each probe across the interrogated region was compared to this average.  We removed the probes with the individual Loess of more or less than 0.85 of the scaled Z score distance from the global .  Next, we removed the signal interaction with very high contact frequency in comparison to their neighbors. We remove such interactions if they have a Z score of 25 or more . Finally, we normalized the profile of each probe so they could be quantitatively compared to each other as.  We calculated a global average relations between interaction frequency and genomic distance with Loess smoothing for each replicate separately
To detect the “true” statistically significant chromatin looping interactions between the individual restriction fragments, we applied a “5 C peak calling approach as described before [17, 43]. We called the significant 5C peaks for the 5C libraries separately. Peaks were defined as normalized ligation frequencies (signals) that are significantly higher than expected for the genomic distances separating the interacting fragments. Expected values were calculated as the average interaction frequency for each genomic distance by using Loess smoothing (alpha value 0.01). This provides a weighted average and a weighted standard deviation for each genomic distance. We assumed that the large majority of interactions were not significant looping contacts, and we interpreted these weighted averages as the expected interaction frequencies for given genomic distances. We then transformed observed 5C interaction frequencies into a Z score by calculating the (observed value-expected value)/standard deviation.  The calculated Z score distribution was fit to a Weibull distribution. p values were calculated for each Z score and transformed into q values for false discovery rate analysis. We used q-value threshold of 0.05 for the 5C peak calling. Only 5C peaks reproducible in both replicates in KCs or TCs were used for subsequent analysis
Genome_build: mm9
Supplementary_files_format_and_content: txt files with statistically significant chromatin looping interactions between the individual restriction fragments

molecule: genomic DNA

organism: Mus musculus

source_name: Primary thymocytes

extract_protocol:
Two 3C templates were constructed for freshly plated epidermal keratinocytes and primary thymocytes  . Briefly, epidermal keratinocytes isolated from mouse epidermis were seeded in the low calcium primary keratinocyte medium at high density on the collagen coated plate for 15 hours at 32oC, 8% CO2 and 90% humidity. The primary thymocytes were isolated as described above. Cells were washed twice with the growth medium and fixed with 1% formaldehyde (Electron Microscopy Systems) in the growth medium for 10 minutes at room temperature with gentle mixing every 2 minutes. The glycine was added to a final concentration of 125 mM. Quenching was initiated at room temperature and the cells were placed on ice for 5 min. The medium was removed and cells were washed ones with ice cold PBS and then fresh ice cold PBS was added. Cross-linked cells were collected, counted, pelleted by centrifugation in aliquots and quick-frozen. Cells were stored at -80oC. Per a 5C library, the frozen pallet of 6x107 cells 1.2 ml of lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM sodium chloride, 0.2% (vol/vol) Igepal C-630 (Sigma)) supplemented with 120 ul of protease inhibitor cocktail (Sigma) was added and cells were incubated on ice for 30 minutes. Cells were lysed using a 5 ml dounce homogenizer, washed twice with ice cold 1x NEBuffer2 buffer (10 mM Tris-HCl, 50 mM NaCl, 10 mM MgCl2, 1 mM DTT), and re-suspended in 630 ul of 1x NEBuffer2. Nuclear suspension was divided into 50 ul aliquots. To the nuclear suspension 312 ul of 1xNEBuffer2 was added. SDS was then added to a final concentration of 0.1% and lysates were incubated at 65oC for 10 min. Triton X-100 was then added to a final concentration of 1% to quench SDS. To each aliquot of solubilized chromatin 800 U of HindIII enzyme (New England Biolabs) was added and the digestion was performed overnight at 37oC with shaking. HindIII was inactivated by incubating lysates at 65oC for 30 min after addition of SDS to a final concentration of 1.56%. Ligation was performed under diluted conditions that promote intra-molecular ligation at 16oC for 4 hr in ligation buffer (1% Triton X-100, 0.1 mg/ml BSA, 1 mM ATP, 50 mM Tris-HCl (pH 7.5]) 10 mM MgCl2, 10 mM DTT) with 10 ul of T4 DNA ligase (Invitrogen). To reverse crosslinks, samples were then treated with 63.5 mg/ml Proteinase K (Invitrogen) at 65oC. Four hours later, Proteinase K was added again to 127 mg/ml and then incubated overnight at 65oC. DNA was purified by subjecting samples to a series of phenol and phenol-chloroform extractions before precipitation with ethanol. Pellets were re-suspended in 1–2 ml TE Buffer, pH8.0 and precipitation with ethanol. Pellets were re-suspended in 500 ul of TE buffer and treated with DNase-free RNase at final concentration of 100 ng/ul for 1 hour at 37oC. 3C templates were further purified using Amicon® Ultra Centrifugal 30K Filter for DNA Purification and Concentration (Millipore). Using the Millipore columns, samples were washed twice with 1X TE buffer. Following sample recovery from Millipore columns, initial sample volume was then restored with 1X TE buffer, pH 8.0. The concentration of the 3C template was assessed by gel electrophoresis with high molecular weight DNA ladder as a standard (Invitrogen) using TotalLab QuantTM gel densitometry software. Controls for DNA integrity (undigested chromatin control) and restriction digestion (no ligase control) were also checked and passed the quality control (data not shown). The quality of the 3C templates were further assessed by running the PCR with series of 2-fold dilutions of the templates with forward (ATGGAGACCTGCCGCCGGCTCATCACAC) and reverse (CGTGCTGTGACTTCGCACTTTTCTGATC) primers amplifying the product of head to head ligation of two HindIII sites located 1164bp apart ] using QuantTM gel densitometry software
5C library construction and sequencing. Two independent 5C libraries were constructed for each cell type. 5C probes were designed at HindIII restriction sites using the my5Csuite primer design tools  An alternating scheme was pursued in which reverse and forward probes were designed against every other fragment. Probes were excluded if unique mapping could not be achieved for fragments spanning highly repetitive sequences. Probe setting were as follows: U-BLAST, 3; S-BLAST, 50; MER, 800; MIN, FRAGSIZE, 100; MAX FRAGSIZE, 50000; OPT_TM, 65: and OPT_PSIZE, 40. The universal T7 sequence was tethered to all forward primers (TAATACGACTCACTATAGCC) and the reverse complement to the universal T3 sequence was tethered to all reverse probes (TATTAACCCTCACTAAAGGGA). In total, 381 forward probes and 382 reverse probes were designed, spanning 5.3 Mb EDC containing locus (Fig. 1b, S2 Table).To construct 5C libraries, first probes were annealed to the 3C templates at 48oC for 16 hours. Each multiplex annealing reaction contained 1xNEBuffer4 (New England Biolabs), 560 ng of 3C template and 0.4 fmole of each 5C probe. The annealed probes were nick ligated with 10 U of Taq ligase in 1x Taq ligase buffer (New England Biolabs) at 48oC for 1 hour. The resulting 5C library was amplified by PCR with 25 cycles using universal T7 (TAATACGACTCACTATAGCC) and T3 (TATTAACCCTCACTAAAGGGA) primers. 15 ligation reactions amplified in 6 PCR reactions each were performed to generate each 5C library. The PCR reactions for each 5C library were pooled before further processing. 5C library amplification reactions produced the products of expected size (101 bp), while the negative control PCR reactions (included no 5C template control, no ligation control or no 5C probe control) did not yield any PCR product (data not shown). 5C libraries were size fractioned (101 bp) and purified from the agarose gel using QIAquick gel purification kit (QIagene). 3’ A-tails were added using dATP and Taq polymerase, followed by subsequent ligation to bar-coded custom designed adaptor oligonucleotide [69] for Illumina pair-end sequencing. Adaptor-modified 5C libraries were purified after separation in the agarose gel using QIAquick gel purification kit (Qiagene). The purified libraries were amplified by 18 cycles of PCR with PE1.0 and PE2.0 primers (Illumina). The amplified libraries (233 bp) were purified from the agarose gel, quantified using Nanodrop 1000 spectrophotometer (Thermo Fisher) and send for the sequencing on the HiSeq 2000 system at the EMBL Genome Core Facility (Heidelberg, Germany).
5C

treatment_protocol:
Primary epidermal keratinocytes was isolated from the skin of the new-born C57Bl/6 mice. Briefly, the skin was removed from the neonatal mice and incubated with 0.25% trypsin in Hanks Balanced Salt solution overnight at 4 C, followed by separation of dermis from epidermis. Epidermis was placed into pre-chilled low calcium primary keratinocyte culture (EMEM, 4% chelated FBS, 0.05mM CaCl2, 0.4ug/ml hydrocortison, 5ug/ml insulin, 10mg/ml EGF, 10-10 M cholera toxin, 2x10-9 T3, 2mM L-glutamin, 100U/ml penicillin, 100ug/ml streptomycin) and triturated to obtain the single cell suspension. The cells were filtered through a 70 mm silicon strainer and were either seeded at high density at the low calcium primary keratinocyte medium onto collagen solution (0.97X Hanks Balanced Salt Solution (HBSS),
9.70μg/mL Bovine Serum Albumin (BSA),
19.40 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), 0.97 X Vitrogen-100® Collagen) coated culture dishes for 15 hours at 32oC in the atmosphere of 8% carbon dioxide and 90% humidity, or were used for FACS to isolated viable basal keratinocyte population. Primary thymocytes were isolated from C57Bl/6 mouse thymi. The thymi were transferred into pre-chilled T cell medium (Gibco® RPMI medium 1640 (ATCC modification), 10% foetal bovine serum, 0.1x 2-mercaptoethanol) and crushed to release total thymus T cell population. The cells were filtered through a 70 mm cell strainer, pelleted by centrifugation and re-suspended in Red Blood Cell lysis buffer (Sigma) for 3 min. Cell were then washed with the pre-chilled T-cell medium, re-suspended in the medium, filtered through a 70 mm cell strainer and counted using haemocytometer.

tag: cell type

value: Primary thymocytes from newborn mice

tag: passages

value: newborn


title: Scar_3


title: 5C_Keratinocytes 1

source_name: Primary epidermal keratinocytes

value: Primary epidermal keratynocytes from newborn mice


title: Scar_1


title: Fezf2 shRNA 4

city: Dunedin

first: Alison

middle: Jane

last: Clare

state: Otago

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

description:
Processed data file: DESeq analysis.txt
Processed data file: All samples_raw counts.txt

data_processing:
Real-time analysis was used for base-calling and bcl2fastq (v1.8.4) for file conversion and demultiplexing.
Reads were trimmed for adapter sequences and poor quality ends using fastq-mcf before mapping to mm10 whole genome using TopHat2 (v2.1.1).
Raw counts were generated using Ensembl reference genes downloaded from table browser (Sep 2016) and multiBamCov function in bedtools2 (v2.26.0).
Raw counts were loaded into R studio (R version 3.2.5) and converted to cpm before filtering out low expressed genes (cpm >8 in at least 4 samples). Differential expression analysis was performed using DESeq2 (version 1.10.1).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: All sample_raw counts.txt: Tab-delimited text file includes raw counts for all samples.
Supplementary_files_format_and_content: DESeq2 analysis.txt: Tab-delimited text file includes DESeq2 output for differential expression analysis.

source_name: M1, Fezf2 shRNA

extract_protocol:
Animals were perfused with 0.9% saline and the brain dissected out. Coronal sections (1 mm) were made using a TedPella matrix and the M1 region dissected out according to mCherry expression. Tissue was flash frozen in liquid nitrogen and RNA extracted using Trizol reagent. RNA was cleaned up using Zymo clean and concentrator 5 before library generation.
RNA libraries were prepared using Illumina TruSeq Standard Total RNA.

treatment_protocol: Male Swiss Webster mice (P21-P25) were injected into the primary motor cortex with lentivirus expressing either a Fezf2 shRNA or non-silencing shRNA (control) and mCherry reporter gene.

tag: strain/background

value: Swiss Webster

tag: age

tag: gender

value: Male

tag: tissue

value: Primary motor cortex (M1)

tag: shRNA


title: 5C_Thymocytes 1


title: 5C_Keratinocytes 2


title: LCX_4

source_name: MI remote myocardium Fb

value: Fb cell isolated from remote myocardium tissue


title: Fezf2 shRNA 3


title: LCX_1


title: LAD_4

source_name: MI adjacent myocardium Fb


title: ΔBCHL Prha rep3


title: LCX_3


title: Fezf2 shRNA 2


title: LCX_2


title: LAD_3


title: Non-silencing shRNA (control) 4

source_name: M1, non-silencing shRNA

value: Non-silencing control


title: LAD_1


title: ΔBCHL Prha-sigB rep1


title: SHAM 3


title: LAD_2


title: Fezf2 shRNA 1


title: Non-silencing shRNA (control) 3


title: Non-silencing shRNA (control) 1


title: Non-silencing shRNA (control) 2


title: T10-12A

city: Madrid

first: Jesus

last: del Mazo Martinez

address: C/ Ramiro de Maeztu 9

country: Spain

institute: Centro de Investigaciones Biologicas (CIB) - CSIC

description:
Total RNA < 100 bp length
This testis sample was taken after 12 days of culture of 10.5 dpp testes with medium supplemented with AlbuMAX I.

data_processing:
Illumina Casava1.7 software used for basecalling.
To assess the quality of the raw and trimming sequence libraries the FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) program was used. Then, adapters and low quality bases were removed according to BGI protocol
Assignment of reads to different small RNAs was performed by mapping them sequentially to the following databases: miRBase21, piRNA database and ncRNAdb from Ensembl. The pipeline is described  at J. Isoler-Alcaraz et al. 2017. Reads that mapped to multiple loci were divided by the total number of multi-mapped hits to avoid over-counting them.
To determine the expression of mature miRNAs, aligned reads to miRBase21 were re-aligned to the mouse genome (mm10) and processed with Htseq software (http://www-huber.embl.de/HTSeq) using a gff file of mature miRNAs from miRBase21.
Normalization and differential expression analyses were performed using the R Bioconductor package DESeq.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited files containing normalized expression of miRNAs by DESeq.

source_name: Testis

growth_protocol: Testis were obtained from mouse strain CD1 housed in pathogen-free (SPF), temperature (22°C ± 1°C) and humidity (50%–55%) conditions on a 12 h light/dark cycle with ad libitum access to food and water.

extract_protocol:
RNA was isolated using TRIsure reagent and Direct-zol RNA MiniPrep from cultured and non-cultured testis
RNA libraries were prepared for sequencing using standard Illumina protocols in BGI

treatment_protocol: Explants from prepuberal mice were cultured ex vivo in a gas-liquid interface over agarose at 34ºC in atmosphere of air plus 5% CO2

value: Testis

tag: age before culture

value: 10 days post-partum

tag: time of culture

value: 12 days

tag: culture medium supplement

value: Albumax I

tag: culture conditions

value: 12 days in a 5% CO2, 95% air atmosphere at 34ºC


title: T6-12K

description:
Total RNA < 100 bp length
This testis sample was taken after 12 days of culture of 6.5 dpp testes with medium supplemented with KSR.

value: 6 days post-partum

value: KSR


title: T10-12K

description:
Total RNA < 100 bp length
This testis sample was taken after 12 days of culture of 10.5 dpp testes with medium supplemented with KSR.


title: T10

description:
Total RNA < 100 bp length
This testis sample was obtained directly from a 10.5 dpp mouse, without culturing

value: 0 days


title: Rem2 KO_KCl (1)

city: Waltham

first: Suzanne

last: Paradis

state: MA

address: 415 South Street

department: Department of Biology

institute: Brandeis University

data_processing:
Fastq groomer was used to convert to sanger format  (Galaxy.org)
Reads were mapped to the mm10 genome using  tophat (Galaxy.org)
FPKM values for each gene in each condition was done using Cufflinks (Galaxy.org)
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with FPKM values.

source_name: Cultured neurons

growth_protocol: Cultured neurons were grown in Neurobasal medium with B27 supplement in 10cm dishes for 6 days

extract_protocol:
Cultured neurons were removed from plate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 500ng of total RNA for the construction of RNA-sequencing libraries.
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: All cultures were treated with 1uM Tetrodotoxin overnight from Day in vitro (DIV) 5-6 then on DIV 6, a subset of neurons were treated with 55mM KCl for 4hrs

tag: genotype

value: Rem2 flx/flx

value: brain

tag: brain region

value: cortex

value: Cultured neurons

value: Embryonic day 16.5


title: T6

description:
Total RNA < 100 bp length
This testis sample was obtained directly from a 6.5 dpp mouse, without culturing


title: Rem2 KO (2)


title: Rem2 KO (1)


title: T6-12A

description:
Total RNA < 100 bp length
This testis sample was taken after 12 days of culture of 6.5 dpp testes with medium supplemented with AlbuMAX I.


title: TAD

description:
Total RNA < 100 bp length
This testis sample was obtained directly from an adult mouse, without culturing

value: 2 months


title: Control (2)


title: Control_KCl (2)


title: V594 tumor

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

data_processing:
Sequenced on Miseq, base called with CASAVA 1.9
Alignment was done using bwa against mouse mm10 reference genome
Reads mapping to known B2 SINEs in repeatmasker track were counted and normalized FPKM values were computed using BamUtil
Genome_build: mm10

source_name: tumor_primary tissue

growth_protocol: not applicable

extract_protocol:
Total RNA was isolated with Trizol, phenol-chloroform extract, column-eluted
200 μg total RNA was primer extended using an oligonucleotide specific for B2 SINEs. Primer extension products were resolved on 8% polyacrylamide–7 M urea gels. For isolation of B2 products, the region of the gel corresponding to 130bp – 180 bp was isolated and placed in a 10 mL polypropylene tube containing 5 mL of G50 buffer (20 mM Tris-HCl, 300 mM NaCl, 2 mM EDTA, 0.2% SDS), flash frozen in liquid N2, and allowed to incubate overnight at RT. The following day the G50 buffer containing the isolated B2 products was phenol-chloroform extracted and ethanol precipitated. The B2 extension products were further 3’ poly dG-tailed using 20 U of terminal deoxynucleotidyl transferase (TDT, Fermentas) and 0.25 mM dGTP. After 3’ poly dG-tailing, the cDNAs were used as templates for 10 cycles of PCR amplification using an oligoC and B2 extension oligo that contained barcoded sequencing adapters.

treatment_protocol: no treatment

tag: strain background

value: mixed C57BL/6 and CD1

value: tumor

tag: tissue type

value: primary tissue


title: Control_KCl (1)


title: Control (1)


title: V325 tumor

tag: strain


title: V382 tumor


title: V382 TA muscle

source_name: TA muscle_primary tissue

value: tibialis anterior (TA) muscle


title: V594 TA muscle


title: DMSO2

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

country: China

institute: Life Sciences Institute, Zhejiang University

data_processing:
Sequencing reads were mapped to the mouse genome (mm9) with TopHat v2.0.14 coupled with Bowtie v2.1.0. The mapped reads were subjected to Cufflinks v2.2.1 with the reference annotation (UCSC gene models) to calculate the FPKM values of each gene.
Genome_build: mm9
Supplementary_files_format_and_content: the processed data files contain the FPKM values of each gene (gene id, FPKM value)

growth_protocol: Mouse AG- and PG-haESCs were cultured on feeder cells with ES medium or 2i culture medium54. ES medium consisted of DMEM with 15% fetal bovine serum (Thermo Fisher Scientific), 1% nucleosides (EMD Millipore), 1% glutamax (Thermo Fisher Scientific), 1% non-essential amino acid (Thermo Fisher Scientific), 1% β-mercaptoethanol (EMD Millipore), 1000 U/ml leukemia inhibitory factor (LIF; EMD Millipore), 100 U/ml penicillin and 100 μg/ml streptomycin. 2i culture medium contained the above ES medium supplemented with 3 μM CHIR99021 (Tocris) and 1 μM PD0325901 (Tocris). In general, haESCs were cultured in ES medium, unless noted otherwise.

extract_protocol: Total RNA was purified with an RNeasy Plus Mini kit (Qiagen). 150 ng of purified RNA was subjected to mRNA isolation and library preparation using a VAHTS Stranded mRNA-seq Library Prep Kit for Illumina (Vazyme) following manufacturer's instructions.

value: mouse haploid embryonic stem cells (ESCs)


title: DMSO1


title: V235 TA muscle


title: RDF1


title: Bulk RNA-Seq GFP+ rep1

city: Bethesda

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

data_processing:
Sequenced reads were mapped to Ensembl mouse gene set (GRCm38.p5) using STAR v2.5.1b
Transcript abundances in TPM were caculated by  RSEM/1.2.31
Single-cell RNA-seq data analysis were carried out using Seurat package
GRCm38.p5 (Ensembl)
Genome_build: tab-delimited text files include TPM values for each cell

molecule: polyA RNA

source_name: Kidney

extract_protocol:
Cells at 500-700 cells/ul were loaded to C1 IFC, single cell was captured in each champer. After cell lysis, reverse transcription, and PCR on the C1 system, cDNAs were harvested from each IFC outlet.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Male mice were grown and maintained in the Animal Facility of the NHLBI. 2 month-old mice were used in the experiments.

value: Kidney

tag: facs antibody

value: GFP fluoresence


title: Bulk RNA-Seq GFP+ rep2


title: Bulk RNA-Seq GFP- rep2


title: RDF2

tag: cell type


title: Rem2 KO_KCl (2)


title: HFD-post 4

city: Basel

first: Joaquín

last: Pérez-Schindler

address: Klingelbergstrasse 50 / 70

department: Biozentrum

country: Switzerland

institute: University of Basel

data_processing:
Reads were trimmed to remove adapter sequences and quality checked using fastqc software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were aligned using TopHat to mm9 version of the mouse genome (Trapnell et al., 2009).
The expression level of genes and comparison between different conditions to find significant changes in expression was done using cufflinks (Trapnell et al., 2012).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for all samples.

source_name: Skeletal muscle (quadriceps)

extract_protocol:
Muscles samples were collected from anesthetized (2.5 % isoflurane) mice under basal conditions or 3 h after maximal exercise. RNA extraction was performed using RNeasy Mini Kit (QIAGEN, #74104).
Libraries were prepared with TruSeq Stranded mRNA Library Prep Kit (Illumina). Sequencing was performed using the HiSeq2500 (Illumina).

value: Skeletal muscle

value: 16 weeks


title: Bulk RNA-Seq GFP- rep1


title: HFD-post 1


title: HFD-post 3


title: CON-post 4


title: HFD-pre 4


title: HFD-pre 2


title: CON-pre 3


title: CON-pre 4


title: CON-post 3


title: CON-post 2


title: CON-pre 2


title: CON-pre 1


title: HFD-pre 1


title: Mecp2-null rep 3

city: Blacksburg

first: Michelle

middle: L.

last: Olsen

state: VA

address: 970 Washington Street SW

department: School of Neuroscience

institute: Virginia Polytechnic and State University

data_processing:
Illumina HiSeq 2500 software was used for basecalling
Raw RNA-Seq reads were concatenated using the “Concatenate datasets tail-to-head” tool. The concatenated raw fastq reads were then trimmed using Trim Galore! (Galaxy version 0.4.2; Krueger F: Trim Galore!. http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adapter sequences and low quality base pairs with the following parameters: select “paired-end” library; trimming reads- automatic detection; trims 1 bp off every read from its 3’ end- yes; no removal of N bp from 3’ end of reads 1 and 2 (respectively); all other settings left at default. Trimmed fastq reads were then run through FastQC (Galaxy version 0.65; Andrews S.  http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) for additional quality control measures.
Reads were aligned to the mouse mm10 reference genome using TopHat (Galaxy version 2.1.0; Trapnell et al. 2012, Kim et al. 2013) using the following parameters: mean inner distance between mate pairs- 175; standard deviation for distance between mate pairs- 20; report discordant pair alignments- yes; all other settings left at default.
Aligned reads were assembled using Cufflinks (Galaxy version 0.0.7; Trapnell et al. 2010 and 2012) using the following parameters: max intron length- 300,000; min isoform fraction- 0.1; pre mRNA fraction- 0.15; perform quartile normalization- yes; use reference annotation- use reference annotation, with the iGenomes UCSC mm10 genome used as the reference annotation (https://support.illumina.com/sequencing/sequencing_software/igenome.html); perform bias correction- yes, reference sequence data- locally cached, using reference genome- mouse mm10; use multi-read correct- yes; job resource parameters- left at default values.
Following transcript assembly and estimated fragments per kilobase of transcript per million fragments mapped (FPKM) abundances, each sample’s assembled transcripts were merged using the Cuffmerge (Galaxy version 2.2.1.0; Trapnell et al. 2010 and 2012) tool with the following parameters: use reference annotation- yes, reference annotation- iGenomes UCSC mm10 genome; use sequence data- no; minimum isoform fraction- 0.05; job resources parameters- left at default.
Cuffdiff (Galaxy version 2.2.1.3; Trapnell et al. 2010 and 2012) was used to calculate statistical changes in gene expression using the following parameters: transcripts- output file from Cuffmerge step; omit tabular datasets- no; generate SQLite- yes; Input data type- SAM/BAM; condition 1- WT TopHat accepted hits files; condition 2- Mecp2Jae/y TopHat accepted hits files; library normalization method- quartile; dispersion estimation method- per-condition; false discovery rate- 0.05; minimum alignment count- 100; use multi-read correct- yes; perform bias correction- yes; reference sequence data- locally cached, reference genome mouse mm10; include read group datasets- yes; include count based output files- yes; apply length correction- cufflinks effective length correction; all other remaining parameters were left at default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Tabular file containing Cuffdiff output from gene differential expression testing. This includes FPKM values per genotype, p-value, q-value (or false discovery rate), chromosomal location, Log2 fold change expression (Mecp2Jae/WT), test stat per gene.

source_name: Whole cortex

extract_protocol:
Whole brains were dissected in ice-cold phosphate buffered saline, and then separated into the cerebellum, brain stem, midbrain, and hippocampus. One hemisphere of the whole cortex was dedicated for RNA and the other for protein isolation. RNA was isolated by placing the cortical hemisphere dedicated for RNA in 1 mL of RNAlater™ solution (Invitrogen/Thermo Fisher Scientific) and allowed to react at 4°C for at least 1 week. RNA was collected using the Invitrogen™ Ambion™ PureLink™ RNA Mini Kit (Fisher Scientific) according to manufacturer’s instructions, with the following modifications: 1) Tissue was homogenized in 1 mL lysis buffer with β-mercaptoethanol in a dounce homogenizer 5 times, rested on ice for 5 minutes, followed by another 5 rounds of homogenization; 2) Approximately 15 mg of the homogenate was removed and brought up to a final volume of 600 µL in lysis buffer with β-mercaptoethanol, then re-homogenized as described above. RNA was eluted in 30 µL of autoclaved and filtered Mill-Q® water. Samples were then DNase-treated and assessed for total RNA quality using the Agilent 2100 Bioanalyzer, followed by 2 rounds of poly A+ selection and conversion to cDNA.
TruSeq library generation kits were used according to the manufacturer’s instructions (Illumina). Library construction consisted of random fragmentation of the polyA mRNA, followed by cDNA production using random primers. The ends of the cDNA were repaired, A-tailed and adaptors ligated for indexing (up to 12 different barcodes per lane) during the sequencing runs. The cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for library quantitation (Kapa Biosystems) prior to cluster generation. Clusters were generated to yield approximately 725K-825K clusters/mm2. Cluster density and quality were determined during the run after the first base addition parameters were assessed.

value: Whole cortex

value: Mecp2-null (Mecp2Jae)

tag: Sex

value: Male


title: Mecp2-null rep 4


title: HFD-post 2


title: Mecp2-null rep 2


title: Mecp2-null rep 1


title: R7shHGFL Lin-CD29HiCD24+ BCSCs

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Following removal of primers and barcodes, raw reads were aligned to the mm9 genome using UCSC annotations.
Data were quantified, log2 transformed, and normalized using the DESeq algorithm.
Data were baselined to the median of all samples.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited with Gene ID, Gene Symbol, and RPKM

source_name: Breast cancer stem cells

growth_protocol: R7 murine breast cancer cell lines were derived from a mammary tumor from a transgenic MMTV_Ron mouse.

extract_protocol: Total RNA was extracted from BCSCs using the TRIZOL method

treatment_protocol: R7 cells were sorted based on the following: Lin-CD29HiCD24+.  Experimental conditions included bulk R7 parental BCSCs, sorted BCSCs, and sorted BCSCs treated with a short hairpin construct  targeting and knocking down Ron.

value: Lin-CD29HiCD24+ sorted

tag: treatment

value: shHGFL

tag: source

value: Breast cancer stem cells


title: WT rep 4

tag: age

value: WT


title: WT rep 3

tag: tissue


title: WT rep 1


title: TREX-KSHV_BAC36-48hr-input-R3

city: Xuzhou

first: Hui

last: Liu

state: Jiangsu

address: #1 Daxue Road

institute: China University of Mining and Technology

data_processing:
Library strategy: MeRIP-seq
Fastq file generated with CASAVA
m6A-seq reads were aligned to the corresponding genome (human / rat / KSHV_BAC16 / KSHV_BAC36) using Tophat 2.
m6A peaks called by exomePeak.
Differential m6A peaks was detected by the differential peak discovery algorithm bltest.
Motif analysis of m6A peaks was performed using the MEME package.
The expression of transcripts and isoforms were calculated using cufflinks based on the input samples.
The differential expression of transcripts and isoforms were calculated using cuffdiff, based on the input samples.
Genome_build: hg19, rn5
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Homo sapiens

source_name: TREX Cells

growth_protocol: Cells were grown at 37C, 5% CO2 in their respective growth media

extract_protocol:
Total RNA was extracted with Trizol and mRNA was purified using polydT beads. m6A-IP was then performed using an anti-m6A antibody from Synaptic Systems. The immunoprecipitated RNA (IP) and input for each sample was used to generate libraries.
10-25ng of mRNA was used for library preparation using the Illumina TruSeq stranded mRNA kit according to manufacturer’s protocol with two modifications. First, the elute-frag-prime stage was done at 80°C for 2 min to allow annealing without causing fragmentation. RNA was reverse transcribed into first strand cDNA using reverse transcriptase and random primers. Then, the second strand cDNA was synthesized using DNA Polymerase I and RNase H. The cDNA fragments then went through an end repair process with the addition of a single ‘A’ base followed by ligation of the adapters. The products were then purified and enriched by PCR amplification for 10 cycles to generate the final RNA-Seq library. The second modification was done to adjust the bead-DNA ratio to preserve smaller fragments during the adapter ligation double beads clean up step. A beads:DNA ratio of 1:3 instead of 1:1 was used. cDNA libraries were quantified and pooled for cBot amplification and subsequent sequencing on an Illumina HiSeq 2000.

treatment_protocol: See samples section

tag: infection status

value: Lytic 48hr

tag: cell line

value: TREX

tag: antibody

value: 1ug/ml doxycycline for 48 hours


title: CON-post 1


title: R7shRon Lin-CD29HiCD24+ BCSCs

extract_protocol:
Total RNA was extracted from BCSCs using the TRIZOL method
Illumina HiSeq2500

tag: genotype/variation

value: shRon knockdown


title: R7 parental

value: Bulk


title: TIME-KSHV_BAC36-latent-input-R3

source_name: TIME Cells

value: latent

value: TIME


title: R7 Lin-CD29HiCD24+ BCSCs


title: TREX-KSHV_BAC36-48hr-ip-R3

value: SYSY


title: TREX-KSHV_BAC36-latent-input-R3


title: HFD-pre 3

value: Skeletal muscle


title: WT rep 2


title: TREX-KSHV_BAC36-latent-ip-R3


title: TIME-uninf-ip-R3

value: Not infected


title: MSC-uninf-input-R3

source_name: MSC Cells

value: MSC


title: KMSC-KSHV_BAC36-latent-input-R3


title: KMSC-KSHV_BAC36-latent-ip-R3


title: iSLK-KSHV_BAC16-48hr-ip-R3

source_name: iSLK Cells

value: iSLK


title: iSLK-KSHV_BAC16-24hr-input-R3

value: Lytic 24hr

value: 1ug/ml doxycycline for 24 hours


title: iSLK-KSHV_BAC16-48hr-input-R3


title: MSC-uninf-ip-R3


title: TIME-KSHV_BAC36-latent-ip-R3


title: TIME-uninf-input-R3


title: iSLK-uninf-input-R3


title: iSLK-KSHV_BAC16-latent-ip-R3


title: iSLK-KSHV_BAC16-24hr-ip-R3


title: TIME-uninf-ip-R2


title: TREX-KSHV_BAC36-48hr-input-R2


title: TIME-uninf-input-R2


title: MSC-uninf-ip-R2


title: iSLK-KSHV_BAC16-latent-input-R3


title: TIME-KSHV_BAC36-latent-ip-R2


title: iSLK-KSHV_BAC16-48hr-ip-R2


title: iSLK-KSHV_BAC16-48hr-input-R2


title: TREX-KSHV_BAC36-latent-ip-R2


title: KMSC-KSHV_BAC36-latent-ip-R2


title: iSLK-uninf-ip-R3


title: TREX-KSHV_BAC36-48hr-ip-R2


title: TREX-KSHV_BAC36-latent-input-R2


title: TIME-KSHV_BAC36-latent-input-R2


title: KMSC-KSHV_BAC36-latent-input-R2


title: MSC-uninf-input-R2


title: iSLK-uninf-ip-R2


title: iSLK-uninf-input-R2


title: iSLK-KSHV_BAC16-24hr-ip-R2


title: iSLK-KSHV_BAC16-latent-ip-R2


title: iSLK-KSHV_BAC16-latent-input-R2


title: TREX-KSHV_BAC36-48hr-input

description:
PolyA RNA
Processed data file: TREX-KSHV_BAC36-48hr_input.genes.fpkm_tracking

data_processing:
Library strategy: MeRIP-Seq
Fastq files generated with CASAVA.
m6A-seq reads were aligned to the corresponding genome (human / rat / KSHV_BAC16 / KSHV_BAC36) using Tophat 2.
m6A peaks called by exomePeak.
Differential m6A peaks were detected by the differential peak discovery algorithm bltest.
Motif analysis of m6A peaks was performed using the MEME package.
The expression of transcripts and isoforms were calculated using cufflinks based on the input samples.
The differential expression of transcripts and isoforms were calculated using cuffdiff, based on the input samples.
Genome_build: hg19 (GRCh37), rn5 (Rnor_5.0)
Supplementary_files_format_and_content: *fpkm_tracking: Tab-delimited text files include RPKM values for each Sample.

source_name: TREX cells, lytic 48hr, doxycycline 48 hours, input

growth_protocol: Cells were grown at 37C, 5% CO2 in their respective growth media.

extract_protocol:
Total RNA was extracted with Trizol and mRNA was purified using polydT beads. m6A-IP was then performed using an anti-m6A antibody from Synaptic Systems. The immunoprecipitated RNA (IP) and input for each sample was used to generate libraries.
10-25ng of mRNA was used for library preparation using the Illumina TruSeq stranded mRNA kit according to manufacturer’s protocol with two modifications. First, the elute-frag-prime stage was done at 80°C for 2 min to allow annealing without causing fragmentation. RNA was reverse transcribed into first strand cDNA using reverse transcriptase and random primers. Then, the second strand cDNA was synthesized using DNA Polymerase I and RNase H. The cDNA fragments then went through an end repair process with the addition of a single 'A' base followed by ligation of the adapters. The products were then purified and enriched by PCR amplification for 10 cycles to generate the final RNA-Seq library. The second modification was done to adjust the bead-DNA ratio to preserve smaller fragments during the adapter ligation double beads clean up step. A beads:DNA ratio of 1:3 instead of 1:1 was used. cDNA libraries were quantified and pooled for cBot amplification and subsequent sequencing on an Illumina HiSeq 2000.

treatment_protocol: 1ug/ml doxycycline for 24 hours or 48 hours, or no treatment.


title: iSLK-KSHV_BAC16-24hr-input-R2


title: TIME-uninf-input

description:
PolyA RNA
Processed data file: TIME_input.genes.fpkm_tracking

source_name: TIME cells, not infected, no treatment, input


title: TIME-KSHV_BAC36-latent-input

description:
PolyA RNA
Processed data file: TIME-KSHV_BAC16-latent_input.genes.fpkm_tracking

source_name: TIME cells, latent, no treatment, input

value: Latent


title: TIME-KSHV_BAC36-latent-ip

source_name: TIME cells, latent, no treatment, m6A IP

value: anti-m6A (SYSY)


title: TREX-KSHV_BAC36-latent-ip

description:
PolyA RNA
Processed data file: TREX-KSHV_BAC36-latent_input.genes.fpkm_tracking

source_name: TREX cells, latent, no treatment, m6A IP


title: TIME-uninf-ip

source_name: TIME cells, not infected, no treatment, m6A IP


title: iSLK-uninf-input

description:
PolyA RNA
Processed data file: iSLK_input.genes.fpkm_tracking

source_name: iSLK cells, not infected, no treatment, input


title: MSC-uninf-input

description:
PolyA RNA
Processed data file: MSC_input.genes.fpkm_tracking

source_name: MSC cells, not infected, no treatment, input


title: KMSC-KSHV_BAC36-latent-input

description:
PolyA RNA
Processed data file: KMSC-KSHV_BAC16-latent_input.genes.fpkm_tracking

source_name: MSC cells, latent, no treatment, input


title: iSLK-KSHV_BAC16-latent-ip

description:
PolyA RNA
Processed data file: iSLK-KSHV_BAC16-latent_input.genes.fpkm_tracking

source_name: iSLK cells, latent, no treatment, m6A IP


title: iSLK-KSHV_BAC16-48hr-ip

description:
PolyA RNA
Processed data file: iSLK-KSHV_BAC16-48hr_input.genes.fpkm_tracking

source_name: iSLK cells, lytic 48hr, doxycycline 48 hours, m6A IP


title: MSC-uninf-ip

source_name: MSC cells, not infected, no treatment, m6A IP


title: KMSC-KSHV_BAC36-latent-ip

source_name: MSC cells, latent, no treatment, m6A IP


title: TREX-KSHV_BAC36-48hr-ip

source_name: TREX cells, lytic 48hr, doxycycline 48 hours, m6A IP


title: iSLK-KSHV_BAC16-24hr-input

description:
PolyA RNA
Processed data file: iSLK-KSHV_BAC16-24hr_input.genes.fpkm_tracking

source_name: iSLK cells, lytic 24hr, doxycycline 24 hours, input


title: iSLK-KSHV_BAC16-48hr-input

source_name: iSLK cells, lytic 48hr, doxycycline 48 hours, input


title: iSLK-uninf-ip

source_name: iSLK cells, not infected, no treatment, m6A IP


title: iSLK-KSHV_BAC16-latent-input

source_name: iSLK cells, latent, no treatment, input


title: iSLK-KSHV_BAC16-24hr-ip

source_name: iSLK cells, lytic 24hr, doxycycline 24 hours, m6A IP


title: mRCC 5133

city: Milwaukee

first: Liang

last: Wang

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

description: exosomal  miRNA

data_processing:
The RNA sequencing data (Fastq files) were mapped using software package (DNASTAR SeqMan NGen)
Mapped miRNA profiles were normalized to RPM (read per million mappable count)
332 common miRNAs with >8 RPMs were choosed, normalized to RPM and performed log2 calculation
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include RPM values after log2  for each Sample

source_name: Plasma

extract_protocol:
Exosomes were isolated from 250 μL of plasma using the ExoQuick exosome precipitation solution (System Biosciences, Mountain View, CA, USA). exosomal RNA was prepared using a miRNeasy Micro Kit (QIAGEN, Valencia, CA, USA)
RNA libraries were prepared following the instructions of the standard protocol (NEBNext Multiplex Small RNA Library Prep Set, NEB, Ipswich, MA, USA).

value: Male

tag: disease status

value: Metastatic renal cell carcinoma (mRCC)

value: plasma


title: mRCC 5128

description: exosomal  miRNA


title: mRCC 5129

description: exosomal  miRNA

value: Female


title: mRCC 5145

description: exosomal  miRNA


title: TREX-KSHV_BAC36-latent-input

source_name: TREX cells, latent, no treatment, input

value: TREX


title: mRCC 5122

description: exosomal  miRNA


title: mRCC 5130

description: exosomal  miRNA


title: mRCC 5123

description: exosomal  miRNA


title: mRCC 5121

description: exosomal  miRNA


title: mRCC 5114

description: exosomal  miRNA


title: mRCC 5112

description: exosomal  miRNA


title: mRCC 5111

description: exosomal  miRNA


title: mRCC 5104

description: exosomal  miRNA


title: mRCC 5101

description: exosomal  miRNA


title: mRCC 5095

description: exosomal  miRNA


title: mRCC 5094

description: exosomal  miRNA


title: mRCC 5080

description: exosomal  miRNA


title: mRCC 5079

description: exosomal  miRNA


title: mRCC 5078

description: exosomal  miRNA


title: mRCC 5075

description: exosomal  miRNA


title: mRCC 5059

description: exosomal  miRNA


title: mRCC 5092

description: exosomal  miRNA


title: mRCC 5056

description: exosomal  miRNA


title: mRCC 5087

description: exosomal  miRNA


title: mRCC 5058

description: exosomal  miRNA


title: mRCC 5069

description: exosomal  miRNA


title: mRCC 5038

description: exosomal  miRNA


title: mRCC 5041

description: exosomal  miRNA


title: mRCC 5040

description: exosomal  miRNA


title: mRCC 5033

description: exosomal  miRNA


title: mRCC 5116

description: exosomal  miRNA


title: mRCC 5050

description: exosomal  miRNA


title: mRCC 5068

description: exosomal  miRNA


title: mRCC 5027

description: exosomal  miRNA


title: mRCC 5053

description: exosomal  miRNA


title: mRCC 5035

description: exosomal  miRNA


title: mRCC 5026

description: exosomal  miRNA


title: mRCC 5021

description: exosomal  miRNA


title: mRCC 5012

description: exosomal  miRNA


title: mRCC 5076

description: exosomal  miRNA


title: shYEATS2_Rep2

city: Grand Rapids

first: Hong

last: Wen

state: Michigan

address: 333 Bostwick Ave. N.E.

department: Center for Epigenetics

institute: Van Andel Research Institute

description: antibody: None

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie2 v2.1.0; RNA-seq reads were aligned to hg19 genome using tophat v2.0.10
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS-1.3.6+B102; Scores represent the ChIP-seq tag numbers; RNA-seq htseq file include differential significance across treatment and control and the tag numbers in all samples
Supplementary_files_format_and_content: RNA-seq read counts were calculated using HTSeq 0.6.1p1

growth_protocol: Human H1299 cells (ATCC) were cultured in RPMI 1640 with 10% FBS (Cellgro) supplemented with 10% fetal bovine serum (Sigma), 5% CO2, 37 oC.

extract_protocol:
mRNA was prepared using the RNeasy Plus kit (Qiagen) and reverse-transcribed using the First Strand Synthesis kit (Invitrogen). Libraries were prepared using the Illumina TruSeq RNA Library Prep kit following the manufactory manual.
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.   mRNA was prepared using the RNeasy Plus kit (Qiagen) and reverse-transcribed using the iScript™ cDNA Synthesis Kit (Bio-Rad).
For ChIP-seq, sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using paired-end sequencing technology on Illumina HiSeq 2000 platform.  For RNA-seq, samples were prepared as instructed using the TruSeq mRNA Sample Preparation Kit v2 (Illumina, San Diego, CA) in accordance with the manufacturer's instructions. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles, DNA fragments were sequenced using single-end sequencing technology on Illumina paried-end on Illumina HiSeq2000 .

treatment_protocol: For shRNA knockdown, 293T cells were co-transfected with pMD2.G and pPAX2 (Addgene) together with pLKO-shRNA constructs or a non-targeting pLKO-shRNA (pLKO-shNT). Viral supernatants were harvested after 48 hrs. For infections, H1299 cells were incubated with viral supernatants in the presence of 8 µg/ml polybrene. After 48 hrs, puromycin (2 µg/ml) was added to the medium. Cells were grown with selection for 4-7 days to select for stable knockdown cells.

value: YEATS2 Knock Down


title: shYEATS2_Rep1

description: antibody: None


title: shCtrl_Rep2

description: antibody: None

value: shNT control vector


title: mRCC 5042

description: exosomal  miRNA


title: shCtrl_Rep1

description: antibody: None


title: ChIPSeq_H3K4me3 Rep2

description: antibody: Abcam, ab8580

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.   mRNA was prepared using the RNeasy Plus kit (Qiagen) and reverse-transcribed using the iScript™ cDNA Synthesis Kit (Bio-Rad).
For ChIP-seq, sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using paired-end sequencing technology on Illumina HiSeq 2000 platform.  For RNA-seq, samples were prepared as instructed using the TruSeq mRNA Sample Preparation Kit v2 (Illumina, San Diego, CA) in accordance with the manufacturer's instructions. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles, DNA fragments were sequenced using single-end sequencing technology on Illumina paried-end on Illumina HiSeq2000 .


title: ChIPSeq_H3K4me1 Rep2

description: antibody: Abcam, ab8895


title: 16019-10B

city: Los Angeles

first: Jeremie

last: Vitte

state: California

address: 675 Charles E Young Dr. S

institute: UCLA

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Aligned to mm10 using STAR spliced read aligner
Count read using HT-seq and using mm10 RefSeq as reference
Normalization (TMM), quantitation (RPKM) and differential expression analysis using edgeR and limma voom.
Genome_build: mm10
Supplementary_files_format_and_content: RPKM values

source_name: Tumor

growth_protocol: Tumors naturally occuring in mouse model

extract_protocol:
RiboPure Kit (Ambion/Life Technologies)
TruSeq Stranded RNA + RiboZero Gold

treatment_protocol: Tumors were dissected, frozen and preserved at -80ºC until RNA extraction

value: Tumor

tag: location

value: Meninges


title: 10321-9C

value: Vestibular N


title: mRCC 5029

description: exosomal  miRNA


title: ChIPSeq_H3K4me3 Rep1

description: antibody: Abcam, ab8580


title: 16017-9

value: Trigeminal N


title: 10074-9C

value: Cheek


title: 09189-29


title: 10074-11C


title: 09189-28


title: 16018-9

value: Retro-orbital


title: ChIPSeq_H3K9ac_shYEATS2 Rep2

description: antibody: Active Motif, 61251


title: 16016-9B


title: 16017-10


title: ChIPSeq_H3K4me1 Rep1

description: antibody: Abcam, ab8895


title: ChIPSeq_H3K9ac_Control Rep1

description: antibody: Active Motif, 61251


title: ChIPSeq_H3K9ac_shYEATS2 Rep1

description: antibody: Active Motif, 61251


title: 09204-9B


title: 09156-9A


title: ChIPSeq_H3K9ac_Control Rep2

description: antibody: Active Motif, 61251


title: ChIPSeq_ZZZ3

description: antibody: Rabbit 2616, Laszlo Tora lab


title: eHiC_10

city: Cleveland

first: Fulai

last: Jin

state: OH - OHIO

address: 10900 Euclid Avenue

institute: Case Western Reserve University

description: We added AAGCTT before the  6-41 bases, and the resulting 42 base were mapped to hg18 using bowtie. Barcode sequence are listed in the last field of the title line of each read in the fastq files. PCR duplicates are already removed in the processed reads file.

data_processing:
library strategy: easy Hi-C (eHi-C)
The paired-end Hi-C reads were mapped to human genome hg18 using BOWTIE.  The two reads were mapped independently and then merged into pairs using in-house script. After mapping, we further filter the reads requiring the positions of both ends to be exactly at the HindIII cutting sites.
The deep sequenced eHi-C library (eHiC_10) was prepared with UMI adapter, and the UMI barcode are includeded in the fastq files. PCR duplications were defined as identical PE reads also with the same UMI barcode. The eHi-C libraries sequenced on MiSeq (eHiC1~9) were not intended for deep sequencing and therefore were prepared without UMI barcode. We assume no PCR duplication in those libraries.
Genome_build: hg18
Supplementary_files_format_and_content: For each Hi-C replicate, the fragment-to-fragment frequency are provided in the txt file. The location of each fragment are provided in bed file (not included in the GEO records). More details in the 'README.txt'

source_name: fetal lung fibroblast

growth_protocol: IMR90 cells were grown as instructed by ATCC

extract_protocol:
After confluence, the cells were detached with trypsin and collected by spinning down at 900g for 5 minutes. Then the cells were fixed in 1% formaldehyde for 15 minutes at 37ºC, followed by 1/20 volume of 2.5M glycine at room temperature for 5 minutes to quench formaldehyde. The fixed cells were scrapped, washed in PBS and pelleted before stored in -80C.
In easy Hi-C, we begin with the in situ proximity ligation procedure and perform HindIII digestion and proximity ligation while keeping nuclei intact. Lligation was performed directly after HindIII digestion without end repair, leading to HindIII-digestible junction products. After nuclear lysis and reverse crosslink, the DNA are digested with more frequent 4-base cutter DpnII before self-ligation. The samples are next treated with exonuclease to remove DNA that failed to form self-circles, and contaminations from un-ligated ends and other linear DNA species. In order to enrich the ligation junction products, we then cut the self-circularized DNA again with HindIII, and only re-linearized junction DNA will be amplified during the library generation. Libraries were prepared according to Illumina's instruction or cited literatures.

value: fetal lung fibroblast

tag: experiment

value: easy Hi-C (eHi-C)

value: no

tag: restriction enzyme

value: HindIII


title: ChIPSeq_ZZZ3_shNT Control

description: antibody: Rabbit 2616, Laszlo Tora lab


title: ChIPSeq_ZZZ3_shYEATS2

description: antibody: Rabbit 2616, Laszlo Tora lab


title: ChIPSeq_H3K27ac

description: antibody: Abcam, ab4729


title: RNA_PANC1_gem_rep2

city: Boston

first: Oana

last: Ursu

address: 415 Main Street

institute: Broad Institute

data_processing:
RNAseq: We aligned reads to the human reference genome (hg19 assembly) using Tophat2 (version 2.0.8) (Trapnell, Pachter, & Salzberg, 2009). From the aligned reads, we quantified transcript abundance by FPKM, using Cuffdiff (version 2.0.2) (Trapnell et al., 2013) with the Gencode V15 gene annotations (protein-coding annotations only), taking into account only genes with at least 10 reads (c parameter) (Harrow et al., 2012).
DNaseI-hypersensitivity: We used the MACS algorithm (Hebenstreit et al., 2011), to identify peaks of hypersensitivity genome-wide, using the hg19 genome assembly and using a p-value cutoff of 1e-5.
Genome_build: hg19
Supplementary_files_format_and_content: For DNaseI-hypersensitivity samples, peaks are in bed format.
Supplementary_files_format_and_content: For RNAseq, the file is the output from running Cuffdiff (version 2.0.2) (Trapnell et al., 2013) with the Gencode V15 gene annotations (protein-coding annotations only). The columns are as specified in Cuffdiff: tracking_id, condition replicate, raw_frags, internal_scaled_frags, external_scaled_frags, FPKM, effective_length, status.

source_name: PANC1 cell line

growth_protocol:
We used PANC1 cells from American Type Culture Collection (ATCC), banked at Fox Chase Cancer Center (FCCC) until use. We cultured them in DMEM/10%FBS supplemented with 2 mM glutamine and 1% penicillin, streptomycin, and kanamycin (PSK) and maintained them at 37C in 5% CO2. Charcoal stripped (FCCC cell culture facility) and dialyzed FBS (Life Technologies; 26400–036) were used.
We used PANC1 cells from American Type Culture Collection (ATCC), banked at Fox Chase Cancer Center (FCCC) until use. We cultured them in DMEM/10%FBS supplemented with 2 mM glutamine and 1% penicillin, streptomycin, and kanamycin (PSK) and maintained them at 37C in 5% CO2. Charcoal stripped (FCCC cell culture facility) and dialyzed FBS (Life Technologies; 26400–036) were used.

extract_protocol:
RNA was extracted using the Quiagen Rneasy Plus Mini Kit
Samples were prepared using the Illumina mRNA sample-preparation guide (cat# RS-930-1001).
RNA was extracted using the Quiagen Rneasy Plus Mini Kit. For the DNaseI-hypersensitivity samples, we followed the protocol from (S.-S. C. Huang et al., 2013) "Intact nuclei were extracted from 50 million cells by incubating with NP-40 detergent and then digested with DNaseI. "
RNAseq samples were prepared using the Illumina mRNA sample-preparation guide (cat# RS-930-1001). For DNaseI-hypersensitivity samples, we followed the protocol from (S.-S. C. Huang et al., 2013) "Sequencing libraries were prepared with the Illumina sample preparation kit, specifically selecting the 100 to 300 bp fragments by gel electrophoresis."

treatment_protocol:
Cells were treated with gemcitabine (50nM)
Cells were treated either with vehicle (DMSO) or gemcitabine (50nM)

value: gemcitabine


title: RNA_PANC1_gem_rep1


title: DNaseI_PANC1_gem_rep1

extract_protocol:
Followed protocol from (S.-S. C. Huang et al., 2013) "Intact nuclei were extracted from 50 million cells by incubating with NP-40 detergent and then digested with DNaseI. "
Followed protocol from (S.-S. C. Huang et al., 2013) "Sequencing libraries were prepared with the Illumina sample preparation kit, specifically selecting the 100 to 300 bp fragments by gel electrophoresis."
RNA was extracted using the Quiagen Rneasy Plus Mini Kit. For the DNaseI-hypersensitivity samples, we followed the protocol from (S.-S. C. Huang et al., 2013) "Intact nuclei were extracted from 50 million cells by incubating with NP-40 detergent and then digested with DNaseI. "
RNAseq samples were prepared using the Illumina mRNA sample-preparation guide (cat# RS-930-1001). For DNaseI-hypersensitivity samples, we followed the protocol from (S.-S. C. Huang et al., 2013) "Sequencing libraries were prepared with the Illumina sample preparation kit, specifically selecting the 100 to 300 bp fragments by gel electrophoresis."


title: DNaseI_PANC1_veh_rep1

treatment_protocol:
Cells were treated with vehicle (DMSO)
Cells were treated either with vehicle (DMSO) or gemcitabine (50nM)

value: vehicle


title: Kc, CLAMP RNAi, 100U MNase, Replicate2 (Mnase-Seq)

first: Michael

last: Tolstorukov

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
Chromatin accessibility was evaluated as described previously (REF#13: Nat Commun. 2016;7: 11485).
Sequenced reads were aligned to the D. melanogaster reference genome (dm3) using Bowtie aligner.
Genomic positions with abnormally high numbers of mapped reads (Z-score=7) were identified, and the tags mapped to such positions were discarded. Frequencies of the mapped reads were computed in 100bp non-overlapping bins and normalized for the library size.
Slopes of linear regression lines fitted on the normalized read frequencies obtained for each titration point (1.5U, 6.25U, 25U, and 100U MNase concentrations) were calculated for each bin. Log-scale was used for the MNase concentrations in the fitting procedure.
The GC-content correction was applied to obtain the final accessibility scores (MACC values).
Genome_build: dm3
Supplementary_files_format_and_content: MACC scores are given in bedGraph files

organism: Drosophila melanogaster

source_name: Kc, CLAMP RNAi, 100U MNase

growth_protocol: Drosophila S2 and Kc cells were maintained at 25°C in Gibco Schnieder’s Drosophila media supplemented with 10% heat-inactivated Fetal Bovine Serum and 1.4X Antibiotic-Antimycotic. Cells were passaged every 2-3 days to maintain appropriate cell density.

extract_protocol:
After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions.
Preparation of sequencing libraries was performed as described previously in Bowman et al (2013).

treatment_protocol: RNAi for gfp, clamp, or msl2 was performed in T75 tissue culture flasks. A total of 1.2x10^7 S2 or Kc cells suspended in 6mLs of Gibco Schenieder’s Drosophila media without FBS were added to a T75 tissue culture flask containing 135μg dsRNA in 3mL ultra pure water. The cells were serum starved at room temperature for 45 minutes before the addition 6mLs of Gibco Schneider’s Drosophila media supplemented with 10% FBS to the flask containing the dsRNA and cells. Cells were incubated for 6 days and upon collection efficiency of the RNAi treatment was determined before performing MNase-seq.

tag: genotype

value: wild type

tag: mnase concentration

value: CLAMP RNAi

value: Kc


title: Kc, CLAMP RNAi, 25U MNase, Replicate2 (Mnase-Seq)

source_name: Kc, CLAMP RNAi, 25U MNase


title: RNA_PANC1_veh_rep1


title: Kc, CLAMP RNAi, 6.25U MNase, Replicate2 (Mnase-Seq)

source_name: Kc, CLAMP RNAi, 6.25U MNase


title: PC9 gefitinib resistant cells

city: Shanghai

first: Shimin

last: AN

address: 280, South Chongqing Road

department: Department of Pharmacology and Chemical Biology

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: The 'Expression Analysis' and 'Genome Annotation' spreadsheet in the 'supplementary table Annotation.xlsx'  includes RPKM values for each Sample and annotations, respectively.

source_name: non-small cell lung cancer

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

value: non-small cell lung cancer cells

tag: phenotype

value: gefitinib-resistant cells


title: RNA_PANC1_veh_rep2

tag: cell type


title: Kc, CLAMP RNAi, 1.5U MNase, Replicate2 (Mnase-Seq)

source_name: Kc, CLAMP RNAi, 1.5U MNase


title: Kc, CLAMP RNAi, 100U MNase, Replicate1 (Mnase-Seq)


title: ALDH positive PC9 cells

value: ALDH-positive cells


title: PC9 cells


title: Kc, CLAMP RNAi, 25U MNase, Replicate1 (Mnase-Seq)


title: Kc, CLAMP RNAi, 1.5U MNase, Replicate1 (Mnase-Seq)


title: Kc, CLAMP RNAi, 6.25U MNase, Replicate1 (Mnase-Seq)


title: PC9 cells treated with hypoxia (1% O2) for 1 week

tag: treated with

value: hypoxia (1% O2) for 1 week


title: Kc, GFP RNAi, 100U MNase, Replicate2 (Mnase-Seq)

source_name: Kc, GFP RNAi, 100U MNase

tag: treatment

value: GFP RNAi


title: shNR2E3 KO_1

city: Little Rock

first: Kyounghyun

last: Kim

state: AR

address: Rm 318 CI.3329 4104 Outpatient Circle

department: Pharmacology & Toxicology

institute: University of Arkansas Medical Sciences

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to hg19 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns; counts calculated by featureCounts.

source_name: Human HepG2 cell line_shNR2E3

growth_protocol: HepG2 cells are growing in 10 % Fetal bovine serum contaning Eagle's Minimum Essential Medium. For  subculturing, cells are treated with 0.25% (w/v) Trypsin- 0.53 mM.  EDTA solution

extract_protocol:
Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: shRNA trasnduced cells are selected out based on puromycin-resistantan gene in pLKO.1-puro Vector (MISSION shRNA, Sigma Aldrich).

value: HepG2 cells are adherent epithelial cells of hepatocellular carcinoma

tag: disease state

value: HepG2 was derived from a liver hepatocellular carcinoma of a 15 year old Caucasian male.

value: liver


title: Kc, GFP RNAi, 6.25U MNase, Replicate2 (Mnase-Seq)

source_name: Kc, GFP RNAi, 6.25U MNase


title: Control_I

source_name: Human HepG2 cell line_sh control


title: Kc, GFP RNAi, 100U MNase, Replicate1 (Mnase-Seq)


title: Kc, GFP RNAi, 25U MNase, Replicate1 (Mnase-Seq)

source_name: Kc, GFP RNAi, 25U MNase


title: PC9 cells treated with 0.1 uM gefitinib in hypoxia for 1 week

value: 0.1 uM gefitinib in hypoxia for 1 week


title: NIPP1_KO_testis_mouse2

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

data_processing:
Read trimming and filtering: Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.13 and Cutadapt 1.7.1. Using FastX 0.0.13 and ShortRead 1.16.3, we filtered subsequently small reads (length < 35 bp), polyA-reads (more than 90% of the bases equal A), ambiguous reads (containing N) and low quality reads (more than 50% of the bases < Q25). With Bowtie2 v2.2.4 we identified and removed reads that mapped to the spiked-in PhiX. Only fragments with both a read1 and read2 were kept. The number of processed fragments (i.e. paired reads) per sample then varied between 21,692,611 and 24,834,067.
Mapping: Processed reads were aligned with Tophat v2.0.13 to the reference genome of Mus musculus (GRCm38.73), as downloaded from the Genome Reference Consortium. Default Tophat parameter settings were used, except for ‘library-type=fr-firststrand’, ‘mate-inner-dist=50’, ‘mate-std-dev=20’, 'min-intron-length=50', 'max-intron-length=500,000', 'no-coverage-search', ‘no-mixed’ and 'read-realign-edit-dist=3'. Using Samtools 1.1, reads with a mapping quality smaller than 20 were removed from the alignments.
Counting: Transcript coordinates were extracted from the GRC reference annotation with Gffread from the Cufflinks v2.1.1 suite and merged to gene coordinates with mergeBed from the Bedtools v2.17.0 toolkit. The numbers of aligned reads per gene were summarized using HTSeq-count v0.6.1p1 with parameters 'm=union', 'stranded=reverse', 'a=0', 't=exon' and 'i=gene_id'.
Genome_build: GRCm38
Supplementary_files_format_and_content: One tab-delimited text file with raw read counts per gene and per sample. Gene IDs are Ensembl IDs.

source_name: NIPP1 KO_6 wks_tamoxifen treated_testis

growth_protocol: Mice housed in a SPF facility; 12h light/dark cycles; water and food at libitum

extract_protocol:
Adult testes were harvested 2 weeks after treatment with tamoxifen. RNA extracted from 40 mg of testis; GenEluteTM Mammalian Total RNA Miniprep kit (SIGMA). RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent).
Per sample, an amount of 5 µg of total RNA was used as input. Using the Illumina TruSeq® Stranded Total RNA Sample Prep Kit with Ribo-Zero Gold (protocol version Rev E. “October 2013”) rRNA is depleted from the total RNA samples using Ribo-Zero ribosomal RNA reduction chemistry. Subsequently, RNA was purified and fragmented and converted into first strand cDNA in a reverse transcription reaction using random primers. Next, double-stranded cDNA was generated in a second strand cDNA synthesis reaction using DNA Polymerase I and RNAse H. The cDNA fragments were extended with a  single ‘A’ base to the 3’ ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally an enrichmend PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Sequence-libraries of each sample were equimolarly pooled and sequenced on ½ run of a NextSeq500 flow-cell at 2x75 bp.

treatment_protocol: Treatment with tamoxifen (0.2 mg/g mouse; 4 intraperitoneal injections with the first injection at the age of 4 week) prior to testis removal and RNA extraction

tag: strain background

value: mixed

value: NIPP1 KO; UBC CRE-ERT2+/- Ppp1r8 fl/-

tag: age

value: 6 weeks

value: tamoxifen

value: total testis


title: PC9 cells treated with 0.1 uM gefitinib for 1 week

value: 0.1 uM gefitinib for 1 week


title: NIPP1_KO_testis_mouse4

tag: tissue


title: NIPP1_KO_testis_mouse3


title: NIPP1_CTR_testis_mouse4

source_name: NIPP1 control_6 wks_tamoxifen treated_testis

value: NIPP1 control; UBC CRE-ERT2+/- Ppp1r8 fl/+


title: S2, MSL2 RNAi, 100U MNase, Replicate2 (Mnase-Seq)

source_name: S2, MSL2 RNAi, 100U MNase

value: wild type

value: MSL2 RNAi


title: NIPP1_CTR_testis_mouse2


title: Kc, GFP RNAi, 25U MNase, Replicate2 (Mnase-Seq)

value: Kc


title: shNR2E3 KO_2

tag: cell line


title: S2, MSL2 RNAi, 6.25U MNase, Replicate2 (Mnase-Seq)

source_name: S2, MSL2 RNAi, 6.25U MNase


title: NIPP1_CTR_testis_mouse1


title: NIPP1_CTR_testis_mouse3


title: 003.84-Mob

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

data_processing:
Adaptors were trimmed
Alignment was performed using the STAR algorithm
Unaligned reads were then aligned using Bowtie 2 v 2.1.0
Aligned reads from both alignment steps were then combined
Transcripts were then quantified using a modified version of the expectation-maximization (E/M) algorithm in the Partek Flow software
Pseudocount of 1.0 was given to offset transcripts with 0 reads
miRNAs were filtered out
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file with RPKM values for each sample. Data from all 12 samples are in one file

source_name: Macrophages

extract_protocol:
RNA was isolated using the RNeasy kit from Qiagen according to the manufacturer's protocol. Concentrations of RNA samples were quantified using the NanoDrop 2000 spectrophotometer (Thermofisher) according to the manufacturer’s protocol. Quality was assessed by computing RNA integrity numbers (RINs) using the Agilent 2100 Bioanalyzer according to the manufacturer’s instructions.
Total RNA (800 ng) was ribosomal RNA (rRNA) depleted using the Low Input RiboMinus™ Eukaryote System v2 (Thermofisher) according to the manufacturer’s instructions. Samples were then vacuum concentrated and whole-transcriptome and barcoded libraries were prepared using the Ion Total RNA-Seq Kit v2 (Thermofisher) according to the manufacturer’s instructions. Size distribution of samples was assessed using the Agilent 2100 Bioanalyzer and 6000 RNA Pico kit. Library concentrations were quantified using the Agilent DNA 1000 assay and the 2100 Bioanalyzer according to the manufacturer’s instructions. Barcoded whole-transcriptome libraries were diluted to a 66 pM concentration and combined in equal volumes (13 µl each, 26 µl total) for sequencing with two samples per template preparation. All template reactions were performed on the Ion Chef Instrument using the Ion PI Hi-Q Chef kit (Thermofisher) according to the manufacturer’s instructions. Reactions were loaded onto Ion PI Chips v3 (Thermofisher) for sequencing on an Ion Proton sequencer according to the manufacturer’s protocol.

treatment_protocol: Monocytes from each of four healthy donors were differentiated by treatment with GM-CSF (GM-MDM), M-CSF (M-MDM) and M. obuense (Mob-MDM). The generated monocyte-derived macrophages (MDM) were then subjected to total RNA isolation.

tag: donor

value: Donor 4

tag: differentiation

value: M. obuense


title: 005.84-M1

value: GM-CSF


title: S2, MSL2 RNAi, 25U MNase, Replicate1 (Mnase-Seq)

source_name: S2, MSL2 RNAi, 25U MNase


title: 006.84-M2

value: M-CSF


title: S2, MSL2 RNAi, 6.25U MNase, Replicate1 (Mnase-Seq)


title: S2, MSL2 RNAi, 100U MNase, Replicate1 (Mnase-Seq)


title: Control_2

value: HepG2 cells are adherent epithelial cells of hepatocellular carcinoma

value: HepG2 was derived from a liver hepatocellular carcinoma of a 15 year old Caucasian male.


title: S2, MSL2 RNAi, 1.5U MNase, Replicate1 (Mnase-Seq)

source_name: S2, MSL2 RNAi, 1.5U MNase


title: 002.83-Mob

value: Donor 3


title: Kc, GFP RNAi, 1.5U MNase, Replicate2 (Mnase-Seq)

source_name: Kc, GFP RNAi, 1.5U MNase

value: GFP RNAi


title: Kc, GFP RNAi, 6.25U MNase, Replicate1 (Mnase-Seq)


title: Kc, GFP RNAi, 1.5U MNase, Replicate1 (Mnase-Seq)


title: S2, MSL2 RNAi, 25U MNase, Replicate2 (Mnase-Seq)


title: NIPP1_KO_testis_mouse1

value: mixed

tag: genotype/variation

value: NIPP1 KO; UBC CRE-ERT2+/- Ppp1r8 fl/-


title: S2, MSL2 RNAi, 1.5U MNase, Replicate2 (Mnase-Seq)


title: 003.83-M2


title: 001.82-Mob

value: Donor 2


title: bmh2_0 mM KCl_1

city: Leiden

first: Paul

last: van Heusden

address: Sylviusweg 72

department: Institute of Biology

country: Netherlands

institute: Leiden University

description: 0 mM KCl

data_processing:
CLC genomic workbench (Aarhus, Denmark) software was used for processing raw data.
Reads were trimmed to 17 bp.
Reads were aligned to a virtual tag library obtained by in silico digestion by NlaIII, cutting at 5’-CATG-3’, of S. cerevisiae sequences corresponding to open reading frames plus 200 bp downstream sequences.
Genome_build: FASTA sequence files of the 16 nuclear chromosomes and mitochondrial genome (S. cerevisiae S288c)(release: 03-Apr-2012)(www.yeastgenome.org).
Supplementary_files_format_and_content: Excel file with the number of reads (normalized to reads per million) aligning to each gene for all samples.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae BY4741 ∆bmh2

growth_protocol: Strains were grown overnight at 30 °C in Translucent YNB medium (Navarrete et al 2010, FEMS Yeast Research 10, 508) containing 50 mM KCl, supplemented with leucine, histidine, methionie and uracil. This culture was used to inoculate two times 50 ml of supplemented YNB medium containing 50 mM KCl yielding A600nm 0.1. These cultures were grown to A600nm 0.5 and cells were isolated by centrifugation. Cells from one culture were washed twice with supplemented YNB medium containing 50 mM KCl and resuspended in 50 ml supplemented YNB medium containing 50 mM KCl. Cells from the other culture were washed twice with supplemented YNB medium lacking KCl and resuspended in 50 ml supplemented YNB medium lacking KCl. Both cultures were incubated at 180 rpm at 30 °C. After 60 min the cultures were poured into plastic tubes and frozen in liquid nitrogen. Prior to RNA isolation, the frozen cultures were thawed on ice and cells were collected by centrifugation and transferred to Eppendorf tubes using ice-cold water.

extract_protocol:
RNA was isolated using the Ambion RiboPure yeast RNA Purification Kit (Life Technologies).
1 μg of total RNA was incubated with oligo-dT beads to capture the polyadenlyated RNA fraction. First- and second-strand cDNA synthesis was performed while the RNA was bound to the beads. While on the beads, samples were digested with NlaIII to retain a cDNA fragment from the most 3’ CATG to the poly(A)-tail. Subsequently, the GEX adapter 1 was ligated to the free 5’-end of the RNA, and a digestion with MmeI was performed, which cuts 17 bp downstream of the CATG site. At this point, the fragments detach from the beads. After dephosphorylation and phenol extraction, the GEX adapter 2 was ligated to the 3’-end of the tag. A PCR amplification with 15 cycles using Phusion polymerase was performed with primers complementary to the adapter sequences to enrich the samples for the desired fragments.

tag: strain

value: bmh2 mutant


title: 005.82-M2


title: bmh2_0 mM KCl_2

description: 0 mM KCl


title: 016.82-M1


title: bmh2_50 mM KCl_3

description: 50 mM KCl


title: S2, CLAMP RNAi, 25U MNase, Replicate2 (Mnase-Seq)

source_name: S2, CLAMP RNAi, 25U MNase

value: CLAMP RNAi


title: S2, CLAMP RNAi, 6.25U MNase, Replicate2 (Mnase-Seq)

source_name: S2, CLAMP RNAi, 6.25U MNase


title: bmh2_0 mM KCl_3

description: 0 mM KCl


title: S2, CLAMP RNAi, 100U MNase, Replicate1 (Mnase-Seq)

source_name: S2, CLAMP RNAi, 100U MNase


title: S2, CLAMP RNAi, 1.5U MNase, Replicate2 (Mnase-Seq)

source_name: S2, CLAMP RNAi, 1.5U MNase


title: bmh2_50 mM KCl_2

description: 50 mM KCl


title: S2, CLAMP RNAi, 100U MNase, Replicate2 (Mnase-Seq)


title: S2, CLAMP RNAi, 25U MNase, Replicate1 (Mnase-Seq)


title: 006.83-M1


title: FB3

city: Madrid

first: Carlos

last: Torroja

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Bioinformatics Unit

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

data_processing:
Illumina RTA software v 1.13.48.0
Fastq files extracted with CASAVA 1.8
Reads were pre-processed with Cutadapt 1.6.1, To remove TruSeq adaptor.
Resulting reads were mapped on the mouse transcriptome (Ensembl gene-build 65) and genome hg19, using RSEM v1.1.19.
Data were normalized using TMM with the Bioconductor package EdgeR
Differential expression were tested using GLM with the Bioconductor package EdgeR
Genome_build: Hs hg19, Mm Ensembl gene-build 65
Supplementary_files_format_and_content: [NormCounts.txt] TMM Normalized counts per million reads sequenced

source_name: Dermal Fibroblast Cells

growth_protocol: CPCS  purified from 3 human myocardial samples by c-kit immunoselection as described (Lauden et al, 2013; Boukouaci et al., 2014), 2. maintained in DMEM/F12 and Neurobasal medium (1:1) supplemented with 10% fetal bovine serum embryonic stem cell qualified (FBS ESCq), L-Glutamine (2 mM), Penicilline- Streptomycine (100 U/mL and 100 μg/mL), B27 supplement 0.5X, N2 supplement 0.5X, bFGF (10ng/mL) and ITS 0.5x, IGF-II (30ng/mL) and EGF (20ng/mL). Mesenchymal stem cells (MSC), (www.inbiobank.org) and Human foreskin fibroblasts (HDF American Type Culture Collection (ATCC, Manassas, VA, USA; catalog number CRL-2097); were maintained in Dulbecco’s Modified Eagle Medium-low glucose (DMEM-low glucose; Sigma) supplemented with 10% fetal bovine serum, 2 mM glutamine , penicillin 100 U/ml and streptomycin 1000 U/ml. All experiments were performed with cells that had undergone no more than 8 passages and maintained in 3% O2 5%CO2 atmosphere.

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) And then purified on Rneasy spin columns (Qiagen). RNA integrity (RNA Integrity Score ≥ 7.9)were determined and quantfied on Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard TrueSeq Illumina protocols

treatment_protocol: No treatment applied

value: HDF (FB3)

value: Fibroblasts


title: CPC3

source_name: Cardiac Progenitor Cells

value: CPC (H4a)

value: Stem Cells


title: CPC2

value: CPC (H3a)


title: FB1

value: HDF (FB1)


title: FB2

value: HDF (FB2)


title: CPC1

value: CPC (H1a)


title: 004.81-Mob

value: Donor 1

value: M. obuense


title: 014.81-M1

value: GM-CSF


title: bmh2_50 mM KCl_1

description: 50 mM KCl


title: MSC3

source_name: Mesenchymal Stem Cells

value: MSC (a45)


title: bmh1_0 mM KCl_3

description: 0 mM KCl

source_name: Saccharomyces cerevisiae BY4741 ∆bmh1

value: bmh1 mutant


title: bmh1_0 mM KCl_2

description: 0 mM KCl


title: 001.81-M2

value: M-CSF


title: S2, CLAMP RNAi, 6.25U MNase, Replicate1 (Mnase-Seq)

value: wild type


title: MSC2

value: MSC (a33)


title: S2, CLAMP RNAi, 1.5U MNase, Replicate1 (Mnase-Seq)

value: CLAMP RNAi


title: bmh1_0 mM KCl_1

description: 0 mM KCl


title: S2, GFP RNAi, 100U MNase, Replicate2 (Mnase-Seq)

source_name: S2, GFP RNAi, 100U MNase

value: GFP RNAi


title: MSC1

value: MSC (a19)


title: ZLW02_noadaptor

city: Hefei

first: chaoling

last: Wei

state: Anhui

address: 130 West Changjiang Road

institute: Anhui Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw reads were filtered using the Illumina pipeline filter (Solexa 0.3), and then further processed with an in-house program, ACGT101-v4.2-miR (LC Sciences, Houston, Texas, USA), to remove adapter dimers, junk, low complexity reads, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Unique sequences ranging from 18 to 26 nt in length were mapped with C. sinensis reference sequences
The mapped sequences were aligned against known plant miRNAs from a publicly available database (miRBase, Release 21; June 2014)16, and BLAST search was used to identify known miRNAs with no more than two mismatches.
The expression abundance of miRNAs (conserved and novel) in the three libraries was normalized to one million using the following normalization formula: normalized expression = original counts of miRNA/total count of clean reads × 1,000,000.
The miRNA microarray analysis was performed by LC Sciences, Houston, Texas, USA. Briefly, total RNA (5 µg) extracted from the GA, MW and CK plants was used as the starting material for microarray hybridization (three biological replicates were used). RNAs were size-fractionated using the YM-100 Microcon centrifugal filter (Millipore, Bedford, MA, USA). The fractionated sRNAs (<30 nt) were extended with a poly (A) tail at the 3′ end using poly (A) polymerase and ligated to an oligonucleotide tag for subsequent fluorescent dye staining.
Genome_build: Tea genome scaffolds and contigs from whole-genome shotgun sequencing and assembly, and the tea transcriptome sequences from the NCBI Sequence Read Archive (SRA, GenBank accession no. SRR1979118), and EST sequences, genomic survey sequences (GSS’s) and nucleotide sequences downloaded from the GenBank nucleotide databases at NCBI (http://www. ncbi.nlm.nih.gov).
Supplementary_files_format_and_content: The result data files are in Excel files with the identified miRNAs and microarray analysis

organism: Camellia sinensis

source_name: Leaves

growth_protocol: Clone cuttings from 3-year-old tea plants were cultured in pots (30-cm diameter, 35-cm height) and grown in a green house maintained at 23 ± 3°C with 65 ± 5% room humidity and a 16/8 h (day/light) photoperiod. The experimental plants were irrigated once a day, fertilized once a month, and covered with gauze to prevent interference from other insects. Healthy Shuchazao cuttings with uniform growth (25−30 cm in height) were used for our experiments.

extract_protocol:
Total RNA was extracted from the leaves of the CK, GA and MW tea plants using the total RNA purification kit (NorgenBiotek Corporation, Canada) according to the manufacturer’s instructions.
Three small RNA libraries were constructed according to the reported procedures. Briefly, small RNA fragments ranging from 18 to 30 nt in length were excised and purified from the gel, and subsequently ligated to Solexa adaptors at each end by T4 RNA ligase. Then, the adapter-ligated small RNAs were reverse transcribed to cDNA with Super Script II Reverse Transcriptase (Invitrogen), and the sRNA libraries were finally sequenced with the Solexa sequencing technology using an Illumina GAIIX system provided by LC Sciences (Houston, TX, USA).

treatment_protocol: The plant tissues were collected from tea leaves subjected to mechanical wounding (MW) and geometrid attack (GA) and from healthy control (CK) leaves

value: mechanical wounding (MW)


title: ZLW01_noadaptor

value: geometrid attack (GA)


title: S004450.l.rs.lib

city: Lund

last: Rovira

address: Medicon Village, Byggnad 404

department: Department of Clinical Sciences, Lund

country: Sweden

institute: Lund University

data_processing:
Base-calling using manufacturer's on-instrument software.
Demultiplexing was done with Picard.
Alignment was done against hg38 using Novoalign with settings -a TGGAATTCTCGGGTGCCAAGG -l 14 -h -1 -1 -t 90 -g 50 -x 15 -o SAM -o FullNW -r All 51 -e 51
MicroRNA expression was analyzed using custom Perl scripts and calculated as counts per million miRNA reads (cpm).
FusionCatcher version 0.99.4b16 was used to search RNA-seq data for chimeric transcripts with the --highly-sensitive option and all aligners (blat, star, bowtie2, and bwa)
Genome_build: Human genome reference GRCh38/hg38.

source_name: Primary breast tumour

extract_protocol:
TRIzol LS
Small RNA sequencing libraries were prepared from 500 ng total RNA using a protocol analogous with the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs), but with custom adapters to incorporate dual indexes. Pooled libraries were sequenced on a NextSeq 500 with High Output v2 75 cycle-kits (Illumina)

tag: scan-b external id

tag: sample fullname

tag: er-status

value: ER-


title: S004739.l.rs.lib


title: S2, GFP RNAi, 25U MNase, Replicate2 (Mnase-Seq)

source_name: S2, GFP RNAi, 25U MNase

tag: genotype

tag: mnase concentration


title: bmh1_50 mM KCl_2

description: 50 mM KCl


title: bmh1_50 mM KCl_1

description: 50 mM KCl


title: S2, GFP RNAi, 6.25U MNase, Replicate2 (Mnase-Seq)

source_name: S2, GFP RNAi, 6.25U MNase

tag: cell type


title: S2, GFP RNAi, 1.5U MNase, Replicate2 (Mnase-Seq)

source_name: S2, GFP RNAi, 1.5U MNase


title: S2, GFP RNAi, 25U MNase, Replicate1 (Mnase-Seq)


title: S004386.l.rs.lib


title: S004239.l.rs.lib


title: S004268.l.rs.lib

value: ER+


title: S002634.l.rs.lib


title: S2, GFP RNAi, 100U MNase, Replicate1 (Mnase-Seq)


title: LPL_Control_TSO_1

city: Zurich

first: Isabelle

last: Frey-Wagner

address: Raemistr. 100

department: Division of Gastroenterology

institute: University hospital Zurich

description:
6-10_LPL
LPL_TSO_1
result--LPL_TSO--over--LPL_Control.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,
Quality assessment based on the remaining reads using the FASTQC quality control tool version 0.10.
Genome_build: Ensembl OryCun2.0
Supplementary_files_format_and_content: tab-delimited text file include Identifier log2 Ratio pValue fdr for each group
Supplementary_files_format_and_content: normalized abundance measurement

organism: Oryctolagus cuniculus

source_name: Caecal lamina propria mononuclear cells

extract_protocol:
Caecal lamina propria mononuclear cells (LPMC) and epithelial cells (EC) were isolated for RNA extraction. Total RNA was isolated with the Qiacube system using the RNeasy Mini Kit with DNase digestion
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-polyA-unstranded. Read type: single-end-100bp

value: TSO

tag: colitis

value: Control

tag: time point


title: S002706.l.rs.lib


title: LPL_Control_TSO_2

description:
6-14_LPL
LPL_TSO_2
result--LPL_TSO--over--LPL_Control.txt

tag: treatment


title: LPL_DSS_TSO_3

description:
6-3_LPL
LPL_DSS_TSO_3
result--LPL_DSS_TSO--over--LPL_Control.txt

value: DSS


title: S2, GFP RNAi, 6.25U MNase, Replicate1 (Mnase-Seq)


title: LPL_DSS_TSO_2

description:
6-2_LPL
LPL_DSS_TSO_2
result--LPL_DSS_TSO--over--LPL_Control.txt


title: LPL_Control_TSO_3

description:
6-6_LPL
LPL_TSO_3
result--LPL_TSO--over--LPL_Control.txt


title: S002210.l.rs.lib


title: LPL_DSS_TSO_1

description:
6-11_LPL
LPL_DSS_TSO_1
result--LPL_DSS_TSO--over--LPL_Control.txt


title: bmh1_50 mM KCl_3

description: 50 mM KCl


title: S002480.l.rs.lib


title: S2, GFP RNAi, 1.5U MNase, Replicate1 (Mnase-Seq)


title: LPL_DSS_Vehicle_3

description:
6-7_LPL
LPL_DSS_3
result--LPL_DSS--over--LPL_Control.txt

value: Vehicle


title: S2, CLAMP RNAi, Replicate3 (START-Seq)

description: nuclear total RNA

data_processing:
Library strategy: Start RNA-seq
Analysis for Start-seq was performed as previously described (REF# 24: Science 2010;327: 335–8)
Alignment: Sequence reads were obtained, trimmed to 26nt starting at the 5'-most nucleotide and mapped to the Drosophila melanogaster DM3 genome using the MOM maximum oligonucleotide mapping tool.
All unique reads mapping with two or fewer mismatches were retained. Reads from biological replicates were merged and formatted to .bedgraph format for Forward and Reverse stands.
Genome_build: dm3
Supplementary_files_format_and_content: Reads from biological replicates were merged and formatted to .bedgraph format for Forward and Reverse stands.

molecule: nuclear RNA

source_name: S2, CLAMP RNAi

extract_protocol:
Total RNA was extracted from isolated nuclei using a standard TRIzol extraction following the manufacturer's directions.
Sequencing libraries were prepared generally according to the Ilumina TruSeq small RNA kit. A detailed protocol is available in Nechaev, S. et al. (2010).

treatment_protocol: RNAi for gfp or clamp was performed in T75 tissue culture flasks using a total of either 1.2x10^7 S2 or Kc cells. The cells were first suspended in 6mLs of Gibco Schenieder’s Drosophila media without FBS and added to a T75 tissue culture flask containing 135μg dsRNA in 3mL ultra pure water. The cells were serum starved at room temperature for 45 minutes before the addition 6mLs of Gibco Schneider’s Drosophila media supplemented with 10% FBS to the flask containing the dsRNA and cells. Cells were incubated for 6 days and upon collection efficiency of the RNAi treatment was determined before performing Start-sequencing.

value: clamp RNAi

tag: time

value: 6 days post RNAi incubation


title: S002131.l.rs.lib


title: S002130.l.rs.lib


title: S2, GFP RNAi, Replicate2 (START-Seq)

description: nuclear total RNA

source_name: S2, GFP RNAi

value: gfp RNAi


title: HDAC2 15-3

city: Davis

last: Knoepfler

state: CA

address: 1 Shields Ave

department: Cell Biology and Human Anatomy

institute: UC Davis School of Medicine

data_processing:
 illumina bclfastq 2.16.0 version for pipeline
TopHat v2.0.14, library-type fr-firststrand
Reads were counted and organized into a matrix using bioconductor package "summarizeOverlaps"
EdgeR (edgeR_3.14.0) was used to perform differential expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Text files with differentially expressed genes, log fold change, p-value, and FDR

source_name: 293FT HEK cells

growth_protocol: Cells were grown using standard cell culture techniquesin DMEM supplemented with 10% FBS and 1% L-glutamine

extract_protocol:
Total RNA was isolated from cells at 60-70% confluence utilizing the Nucleospin RNA kit (Macherey-Nagel, Ref #740955.5)
KAPA mRNA stranded kit (KK8401, Roche Catalog07962169001) for library preparation with poly-A enrichment

treatment_protocol: 293FT cells were transfected with guide RNA expressing plasmids targeting the first ATG of the HDAC2 gene, followed by puromycin selection to obtain clonal lines of HDAC2-null cells.


title: HDAC2 15-2


title: S001587.l.rs.lib


title: HDAC2 15-1


title: LPL_Control_Vehicle_3

description:
6-8_LPL
LPL_Control_3
result--LPL_DSS--over--LPL_Control.txt


title: S2, CLAMP RNAi, Replicate2 (START-Seq)

description: nuclear total RNA


title: S2, GFP RNAi, Replicate1 (START-Seq)

description: nuclear total RNA


title: HDAC2 14-3


title: LPL_Control_Vehicle_2

description:
6-4_LPL
LPL_Control_2
result--LPL_DSS--over--LPL_Control.txt


title: S2, CLAMP RNAi, Replicate1 (START-Seq)

description: nuclear total RNA


title: Kc, GFP RNAi, Replicate3 (START-Seq)

description: nuclear total RNA

source_name: Kc, GFP RNAi

value: Kc


title: HDAC2 14-1


title: HDAC2 14-2


title: S001455.l.rs.lib


title: S001532.l.rs.lib


title: S2, GFP RNAi, Replicate3 (START-Seq)

description: nuclear total RNA

value: wild type


title: S001473.l.rs.lib


title: S001135.l.rs.lib


title: LPL_Control_Vehicle_1

description:
6-15_LPL
LPL_Control_1
result--LPL_DSS--over--LPL_Control.txt


title: EC_Control_TSO_3

description:
6-6_EC
EC_TSO_3
result--EC_TSO--over--EC_Control.txt

source_name: Epithelial cells


title: Kc, CLAMP RNAi, Replicate3 (START-Seq)

description: nuclear total RNA

source_name: Kc, CLAMP RNAi


title: HDAC2 5-3


title: LPL_DSS_Vehicle_2

description:
6-12_LPL
LPL_DSS_2
result--LPL_DSS--over--LPL_Control.txt


title: S001040.l.rs.lib


title: EC_Control_TSO_2

description:
6-14_EC
EC_TSO_2
result--EC_TSO--over--EC_Control.txt


title: LPL_DSS_Vehicle_1

description:
6-1_LPL
LPL_DSS_1
result--LPL_DSS--over--LPL_Control.txt