title: RNA-seq LE rep1

city: Daejeon

first: Byung-Kwan

last: Cho

address: 291 Daehak-ro

institute: KAIST

data_processing:
Basecalls performed using CASAVA version 1.4
Sequencing reads were mapped to the genome sequence from NCBI (AKFM00000000.1) using CLC genomics workbench (default parameter) after trimming of low quality regions [12]. RNA‐seq depth profiles are visualized using SignalMap (NimbleGen).
To obtain transcriptional units, we identified transfrags through pooling RNA‐seq libraries replicates for all three conditions. We merged nearby transfrags to reduce over-fragmentation if their distance is shorter than 40 bp but didn’t merge if their distance is longer than 100 bp to maximize median length ratio between sense transfrags and antisense transfrags. For the nearby transfrags of distance range from 40 bp to 100 bp, they are merged if p‐value of Wilcoxon rank test with two‐sided are less than 10‐20 which suggests that RNA‐seq profile of the two transfrags is statistically not different. Finally, we chose transfrags with high transcriptional expression level from DESeq analysis is over 25 percentile transcriptional level.  Predicted transfrags were classified into sense (sense to ORF), antisense (antisense to ORF), and intergenic (intergenic of ORFs). If a transfrag covers more than two gene annotations, it is divided into multiple transfrags corresponding to sense, antisense, and intergenic transfrags. This process was conducted by in‐house script and manual inspection was followed.   CPAT was used for the calculation of coding potential of transfrags and used for the selection of non-coding RNAs. Thus, we classified transfrags into five RNA classes by using transfrag size, coding potential, and location relative to gene annotation; mRNA (sense to protein coding genes and CPAT >= 0.364), lancRNA (antisense to protein coding genes, size >= 200 nt, and CPAT < 0.364), lincRNA (intergenic, size >= 200 nt, and CPAT < 0.364), sancRNA (antisense to protein coding genes, size < 200 nt, and CPAT < 0.364), and sincRNA (intergenic, size < 200 nt, and CPAT < 0.364).   Differentially expressed transfrags were conducted by using DESeq. In KEGG enriched pathway analysis, pathways that have p‐value lower than 0.01 by two‐tailed Fisher exact test are considered to be enriched with statistical significance.
The expression levels were based upon DESeq method.
Genome_build: AKFM00000000.1
Supplementary_files_format_and_content: gff and text file with expression levels from DESeq.

organism: Kluyveromyces marxianus

growth_protocol: K. marxianus var. marxianus ATCC 36907 (KM7) were obtained from Korean Collection for Type Culture (KCTC) and were grown in YBN-u media (0.67 % yeast nitrogen base without amino acids, uracil deprived amino acids and 2 % w/v dextrose) at 30 °C in a shaking incubator. They were sampled at three time points of early-exponential (EE; OD =~ 3), mid-exponential (ME; OD =~ 7), and late-exponential (LE; OD =~ 10) conditions with two biological replicates.

extract_protocol:
Cells were harvested by centrifugation and resuspended with lysis buffer, 20 mM Tris‐HCl (pH 7.5), 140 mM NaCl, 5 mM MgCl2, and 1% Triton‐X of 300 ul. Further, the resuspended cells were lysed with 1 mL TRIzol (Invitrogen) and incubated for 5 min at room temperature. After centrifuge for 15 min at 3000 rpm, the supernatant was transferred new tube and mixed with chloroform of 200 μl for 2‐3 min. After centrifugate for 15 min, the supernatant was mixed with 3 fold of 100% ethanol or equal fold of isopropanol, 2 μl glycogen, 3M sodium acetate. After centrifuge and resuspension, prepared RNA was washed with 70 % ethanol. After drying, RNA was resuspended to DEPC-treated water. To confirm the quality of extracted RNAs, total RNA was visualized using agarose gel electrophoresis.
To remove genomic DNA, the isolated RNA was incubated at 37 °C for 1 h with 4 U of rDNase I (Ambion) and 5 μl of 10× DNase I buffer (Ambion). The DNA-free RNA was purified by phenol-chloroform extraction and ethanol precipitation. Ribosomal RNA (rRNA) was removed by using Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat) (Epicentre) according to the manufacturer’s instructions. Ribosomal RNA-depleted RNAs were checked for quality control with Agilent 2200 TapeStation system (Agilent Technologies). 200 ng mRNA was then fragmented by incubation at 70 °C for 5 min with 10× Fragmentation buffer (Ambion). The reaction was terminated by adding 1 μl of Stop solution (Ambion) and the fragmented mRNA was purified by ethanol precipitation. For first strand cDNA synthesis, 3 μg of Random primers (Invitrogen) were added to the fragmented mRNA and denatured by incubation at 65 °C for 5 min. Then the following was added to the reaction: 2 μl of 10× RT buffer (Invitrogen), 1 μl of 10 mM dNTP mix, 4 μl of 25 mM MgCl2, 2 μl of 100 mM DTT, 1 μl of SuperScript III Reverse Transcriptase (200 U/μl, Invitrogen), and 1 μl of RNaseOUTTM (40 U/μl, Invitrogen). The mixture was incubated 10 min at 25 °C for annealing then 50 min at 50 °C for reverse transcription. The reaction was terminated by incubation at 85 °C for 5 min. Synthesized first strand cDNA was mixed with 3 fold of 100% ethanol, 2 μl glycogen, 3M sodium acetate and centrifuged and resuspended with RNase and DNase free water after drying. The following mixture was added to the purified cDNA for second strand synthesis: 1 μl of 10× RT buffer (Invitrogen), 0.5 μl of 25 mM MgCl2, 1 μl of 100 mM DTT, 2 μl of 10 mM mixture of each dNTP (dATP, dGTP, dCTP, and dUTP), 15 μl of 5× second-strand buffer (Invitrogen), 5 μl of Escherichia coli DNA polymerase (10 U/μl, Invitrogen), 1 μl of E. coli DNA ligase (10 U/μl, Invitrogen), and 1 μl of E. coli RNase H (2 U/μl, Invitrogen). The mixture was incubated at 16 °C for 2 h and synthesized cDNA was mixed with 3 fold of 100% ethanol, 2 μl glycogen, 3M sodium acetate and centrifuged and resuspended with RNase and DNase free water after drying. The libraries for Illumina sequencing were constructed using TruSeqTM DNA Sample Prep Kit (Illumina Inc.) according to the manufacturer’s instructions. Briefly, the synthesized cDNA was end-repaired and 3’-ends of the blunt fragments were adenylated for the adapter ligation. The adenylated DNA fragments were ligated with Illumina adapters. A fraction of the adapter-ligated DNA between 180 bp and 380 bp was size-selected from a 2% agarose gel after electrophoresis. Size-selected DNA was purified by using MinElute Gel Extraction Kit (Qiagen) according to manufacturer’s instructions and eluted in 1× TE buffer with low EDTA (10 mM Tris-HCl (pH 8.0), 0.1 mM EDTA) for the following enzyme reaction. For degradation of the second strand which contains dUTP instead of dTTP, 1 U of USER enzyme (NEB) was added to the purified DNA and incubated at 37 °C for 15 min. After 5 min incubation at 95 °C for enzyme inactivation, the library was enriched by PCR. The amplification was monitored on a CFX96TM Real-Time PCR Detection System (Bio-Rad) and stopped at the beginning of the saturation point. The amplified library was purified by using Agencourt AMPure XP beads and quantified using a Qubit 2.0 fluorometer (Invitrogen).

value: marxianus ATCC 36907 (KM7)

tag: growth phase

value: late exponential


title: RNA-seq LE rep2

status: Public on Aug 20 2016

type: SRA

country: South Korea

library_source: transcriptomic

molecule: total RNA

tag: strain


title: 20-27d HIT water-2

city: Madison

first: David

last: Wassarman

state: Wisconsin

address: 425 G. Henry Mall, Room 4250

department: Medical Genetics

country: USA

institute: University of Wisconsin

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were adapter and quality trimmed using the Skewer trimming program (v0.1.118)
Quality reads were aligned to Drosophila melanogaster using the STAR aligner (v2.4.2a)
Quantification of expression for each gene were calculated by RSEM (v1.2.22)
Expected read counts from RSEM were filtered for low/empty values and used for differential gene expression analysis using EdgeR (v3.10.5) or EBSeq (v1.8.0)
Genome_build: dm3
Supplementary_files_format_and_content: Gene read counts inferred by RSEM

organism: Drosophila melanogaster

source_name: whole male flies_20-27d HIT water

growth_protocol: Flies were maintained on molasses food at 25°C.

extract_protocol:
Whole fly RNA was harvested using Qiagen Rneasy plus mini kit (#74134) and Qiagen QIAshredder kit (#79654) according to manufacturer's instructions
Illumina TruSeq RNA Sample Prep Kit (Cat#RS 200-0012 ) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Aged flies were collected, and treated with our standard TBI protocol and placed on either food for 4 hours or 2 hours on water until RNA extraction.

tag: line

tag: gender

value: male

tag: age

tag: injury

value: injured; HIT (high impact trauma)

tag: diet

value: Water

tag: tissue

value: whole flies


title: 20-27d un-HIT water-3

source_name: whole male flies_20-27d un-HIT water

value: uninjured


title: Activated WT input replicate 2 DNA library

city: Baltimore

first: Christopher

middle: Jordan

last: Gamper

state: MD

address: 1650 Orleans St., CRB I, Rm. 209

department: Oncology

institute: Johns Hopkins University

description:
processed data file:
009_010_merged_WT_D8_enrich_vs_003_004_merged_WT_D8_total_mm9.50_peaks.bed

library_source: genomic

data_processing:
Bases were called using Bioscape Software using default parameters.  XSQ output was converted to csfasta and qual files using XSQ tools with default parameters.
SOLiD BioScope Software was used for sequence alignment to the mm9 reference genome using default parameters.  Output was processed to sorted SAM and BAM files.
Visualization of coverage was performed using the IGVTools package (count command) with default parameters to generate a tiled data file (TDF) file for faster display in IGV.
Replicate activated samples were merged for analysis.  Methylated regions were identified as peaks of aligned sequencing tags in the MBD enriched compared with total input fraction using MACS v1.4.1 with parameters -s 50 --nomodel --shiftsize=90 -g mm.  Output files were generated in BED format.
Genome_build: mm9
Supplementary_files_format_and_content: TDF files depict aligned read counts versus genome position.  BED files with header (chr, start, stop, peak, pVal) depict genomic intervals of MACS peaks sorted by chr position and numbered sequentially.  pVal = -10*log10(MACS p value).

molecule: genomic DNA

organism: Mus musculus

source_name: Day 8 DNMT3a WT OT1 CD8 T cells input DNA

growth_protocol: Splenocytes from DNMT3a WT and KO OT1 Thy1.1 mice were stained for CD8, CD62L, and CD44 and naive T cells were sorted as CD8+CD62L(high)CD44(low).

extract_protocol:
Genomic DNA was isolated from sorted T cells using the DNEasy kit (Qiagen) using the manufacturer's protocol for cultured cells and submitted for MBD-seq analysis by The Next Generation Sequencing Center at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins.
Two micrograms of DNA were sonicated to a modal size of ~150–250 bp, and end-repaired using the NEBNext SOLiD DNA library preparation kit end-repair module following the manufacturer’s protocol (New England Biolabs). After column-purification (using the Qiagen PCR purification kit), SOLiD P1 and P2 adapters lacking 5’ phosphate groups (Life Technologies) were ligated using the NEBNext adaptor ligation module and column-purified, and subjected to nick-translation by treating with Platinum Taq polymerase to remove the nick. Methylated regions were affinity enriched using 6xHis-MBD2-MBD protein immobilized on magnetic beads. (Guerrero-Preston, R. et al. (2014) Epigenetics, 9:7, 1031-1046, DOI: 10.4161/epi.29025). The methylation-enriched fraction was amplified using 10-12 cycles using the NEBNext amplification module and a non-enriched input fraction underwent 4-6 cycles of amplification.  Library fragments that were between 200–300 bp were size selected after agarose gel electrophoresis.

treatment_protocol: A portion of the cells were immediately processed for genomic DNA extraction as naive CD8 samples.  Aliquots of 500 cells were transferred by retroorbital vein injection into Thy1.2+ WT C57BL/6 recipients that were infected with 1e6 pfu Vaccinia-Ova to IV activate the T cells in vivo.  Activated cells were isolated 8 days after adoptive transfer by staining splenocytes and FACS sorting for CD8+Thy1.1+ cells.

tag: strain background

tag: genotype/variation

value: OT1 TCR transgenic; DNMT3a WT

tag: cell type

value: CD8 T cell

tag: activation

value: Day 8 post Vaccinia Ova


title: 20-27d un-HIT water-2


title: 0-7d HIT water-1

source_name: whole male flies_0-7d HIT water


title: 0-7d HIT water-2


title: Naive WT input DNA library

description:
processed data file:
007_WT_Naive_enrich_vs_001_WT_Naive_total_mm9.50_peaks.bed

source_name: Naive DNMT3a WT OT1 CD8 T cells input DNA

value: CD8 T cells

value: Naive


title: ma13_S37

city: Kunming

first: lei

last: shi

state: Yunnan

address: No.17 Longxin Road

country: China

institute: Kunming Institute of Zoology

description:
ce071572
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

data_processing:
Quality and adaptor trimming was performed using TrimGalore! with default parameters
Reads were mapped to the respective reference genomes (hg19, pantro4,rheMac3,macFas5 and nomLeu3) with bwa
Duplicate reads were removed using Picard
Identified SNPs using GATK v3.4 and standard hard filtering parameters ("QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0").
Genome_build: hg19, pantro4,rheMac3,macFas5 and nomLeu3
Supplementary_files_format_and_content: vcf (variant format files)

organism: Macaca fascicularis

source_name: Prefrontal Cortex

extract_protocol:
Genomic DNA was extracted according to the DNeasy Blood&Tissue Kit (QIAGEN) protocol.
DNA libraries were prepared for sequencing using Nextera XT DNA Sample Preparation protocol

value: Prefrontal Cortex

value: 7 years


title: 20-27d HIT water-3


title: 0-7d un-HIT water-2

source_name: whole male flies_0-7d un-HIT water


title: ma12_S36

description:
ce071426
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue


title: MOLM13_DMSO_24_1

city: Waltham

first: Huawei

last: Chen

state: MA

address: 35 Gatehouse Dr

institute: AstraZeneca

data_processing:
Reads were soft clipped and provided by the vendor
alignment and analysis were performed using bcbio-nextgen v0.7.7
STAR_2.3.1z_r395 was used for alignment
htseq v0.6.1 was used to calculate counts
FPKM was calculated using Cufflinks v2.1.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Cancer cell line

growth_protocol: Cell lines were grown under standard conditions

extract_protocol:
RNA isolation was carried out at Expression Analysis (http://www.q2labsolutions.com/)
Library construction was carried out at Expression Analysis (http://www.q2labsolutions.com/)

treatment_protocol: Cell lines were treated with either AZD5153 or DMSO for 24h

tag: cell line name

tag: treatment

value: DMSO

tag: treatment time

tag: tumor type

value: aml

tag: replicate


title: OCIAML2_DMSO_24_1


title: 20-27d HIT food-3

source_name: whole male flies_20-27d HIT food

value: Food


title: RNA-seq ME rep2

source_name: Kluyveromyces marxianus_mid exponential

value: marxianus ATCC 36907 (KM7)

tag: growth phase

value: mid exponential


title: LVP0_rep2 (lncRNA)

city: Los Angeles

first: Marlin

last: Touma

state: CA

address: 650 Charles E Young drive- MRL 3760

department: UCLA-Cardiovascular Research Laboratory

institute: UCLA

description: left ventricle, postnatal day 0

data_processing:
RNAseq reads were aligned to the mm10 genome assembly using STAR_2.4.0j with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Deep RNA-seq was performed using total RNA isolated from male C57B/6 mouse left ventricle (LV) and right ventricle (RV) at postnatal day 0 (P0, prior to the ductal closure), day 3 (P3, transition), and day 7 (P7, terminal differentiation of the vast majority of cardiomyocytes). Strand specific cDNA libraries were constructed from three LV and RV total RNAs samples (biological replicate) at each time point with the exception of only two RV samples for day 7.

extract_protocol:
Total RNA was isolated from LV and RV of male newborn mouse using the RNeasy Mini kit (Qiagen) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols
Strand specific libraries. Paired-end RNAseq

tag: strain

value: male

tag: ventricle

value: LV

tag: developmental stage

value: prior to the ductal closure


title: RNA-seq ME rep1


title: RNA-seq EE rep2

value: early exponential


title: RNA-seq EE rep1


title: 0-7d un-HIT water-1

tag: line

tag: gender

tag: age

value: uninjured

value: Water

value: whole flies


title: 20-27d un-HIT water-1

tag: injury

tag: diet

tag: tissue


title: 20-27d HIT food-1

value: injured; HIT (high impact trauma)


title: 20-27d HIT water-1


title: 0-7d HIT water-3


title: RPMI8226_DMSO_24_2

value: mm


title: KG1A_DMSO_24_2


title: KG1A_DMSO_24_1


title: 0-7d un-HIT water-3


title: RPMI8226_DMSO_24_1


title: OCIAML2_DMSO_24_2


title: MOLM13_DMSO_24_2


title: OPM2_DMSO_24_2


title: IM9_DMSO_24_2


title: MOLP8_DMSO_24_2


title: IM9_DMSO_24_1


title: OPM2_DMSO_24_1


title: 20-27d un-HIT food-1

source_name: whole male flies_20-27d un-HIT food


title: 0-7d HIT food-2

source_name: whole male flies_0-7d HIT food


title: 0-7d HIT food-3


title: 0-7d HIT food-1


title: 0-7d un-HIT food-3

source_name: whole male flies_0-7d un-HIT food


title: Input_rep2

city: Beijing

first: Guifeng

last: Wei

state: Beijing

address: 15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

description: Input

data_processing:
We mapped the paired-end sequencing reads to the human genome (hg19) sequence using bowtie2 with the “--no-mixed” parameter, and the duplicate reads were subsequently removed by Picard with default parameters. The enriched peaks were called by MACS2 (-f BAMPE --nomodel -m 10 50 --shiftsize 73), and filtered by significance (−log10 (q-score) ≥ 300). The adjacent “Odd” and “Even” peaks were merged if their distances were closer than 500 nt. Regions overlapping any enriched peaks called by the negative controls (LacZ oligoes) were discarded, and only the regions which share no sequence similarity with the LacZ oligo probes were kept for further analysis.
Genome_build: hg19

source_name: colorectal carcinoma

growth_protocol: HCT116 cells were cultured in McCoy 5A medium supplemented with 10% FBS (Life Technologies).

extract_protocol: High-throughput sequencing libraries were constructed from ChIRPed DNA with KAPA Hyper Prep Kit (Illumina) according to manufacturer’s instruction and sequenced on HiSeq 2500 System (Illumina) with paired-end 101 bp.

treatment_protocol: ChIRP was performed as described previously (Chu et al., 2012). Briefly, 20-mer non-overlap antisense DNA probes targeting SNHG1 full-length sequences were designed (http://www.singlemoleculefish.com). As non-specific controls, eight probes for targeting LacZ were selected from Chu et al. (Chu et al., 2011). All probes were biotinylated at the 5’-terminus with a C6 spacer. HCT116 cells were fixed with 1% formaldehyde for 10 min at room temperature, and crosslinking then quenched with 125mM glycine for 5min. The chromatin preparation, hybridization, wash and DNA elution steps were essentially performed as described. DNA was extracted by phenol: chloroform: isoamyl alcohol and precipitated with ethanol at -80°C overnight.

tag: cell line


title: Input_rep3

description: Input


title: Input_rep1

description: Input


title: MM1S_DMSO_24_2


title: 0-7d un-HIT food-2


title: MV411_DMSO_24_2


title: 0-7d un-HIT food-1


title: 20-27d un-HIT food-2


title: MM1S_DMSO_24_1


title: 20-27d HIT food-2


title: 20-27d un-HIT food-3


title: Even_rep2

description: Even probes targeting SNHG1 sequence


title: LacZ_rep3

description: control probes targeting LacZ


title: MV411_DMSO_24_1


title: MM1S_DMSO_24_3


title: WILL2_DMSO_24_2

value: dlbcl


title: Sample collected aftershift from 0.4 kPa ox to 0.8 kPa ox

city: Pisa

first: Pietro

last: Tonutti

address: Piazza Martiri delal Libertà

department: Life Sciences

country: Italy

institute: Scuola Superiore Sant'Anna

description:
D
genes.count_trackingDvsC

data_processing:
base-calling and overall quality value calculations were performed using the Illumina data processing pipeline version 1.8.2
Tophat2 (Kim et al., 2013) was used to align the reads onto the reference genome (Mdomestica_196_v1.0; www.phytozome.org) previously indexed with Bowtie2 (Lamgmead and Salzberg, 2012)
Cuffdiff (Trapnell et al., 2012) was used to: determine  the amount of reads mapping in different locations, normalize the counts as Reads Per Kilobase of exon per Million fragments mapped -RPKM- (Mortazavi et al., 2008), compare the expression between two different conditions, and  assess the significance of changes (expressed as Log2fold ratios)
Genome_build: Mdomestica_196_v1.0; www.phytozome.org)
Supplementary_files_format_and_content: gene count tables obtained by Cuffdiff/Cufflink

organism: Malus domestica

source_name: Slices (about 1 cm thick) of cortex tissue from the equatorial part of fruit

extract_protocol:
Total RNA was extracted as described by Botton et al. (2011). RNA quality and integrity were checked on a Bioanalyzer 2100 (Agilent, Santa Clara, CA)
Sequencing libraries were prepared using the TruSeq RNA Sample Prep kit (Illumina Inc.) according to the manufacturer’s instructions. Sequencing was carried out on an Illumina HiSeq2000 in two lane single-read 50bp

tag: cultivar

value: Granny Smith

value: cortex


title: LacZ_rep2

description: control probes targeting LacZ


title: MOLM13_AZD5153_24_1

tag: cell line name


title: Sample from Normoxic condition

description:
A
genes.count_trackingBvsA
genes.count_trackingCvsA


title: WILL2_DMSO_24_1

tag: treatment

value: DMSO


title: Even_rep3

description: Even probes targeting SNHG1 sequence


title: MOLP8_DMSO_24_1

tag: treatment time


title: Sample collected after 24 days at 0.8 kPa ox

description:
C
genes.count_trackingCvsB
genes.count_trackingCvsA


title: hu8_S7

description:
H2013352
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: Prefrontal Cortex

value: 52 years


title: OCILY19_DMSO_24_1

tag: tumor type


title: MOLM13_AZD5153_24_2

value: aml

tag: replicate


title: OCILY19_DMSO_24_2


title: Sample collected after 24 days at 0.4 kPa ox

description:
B
genes.count_trackingBvsA
genes.count_trackingCvsB


title: Even_rep1

description: Even probes targeting SNHG1 sequence


title: MV411_DMSO_24_3


title: OCIAML2_AZD5153_24_2


title: OCIAML2_AZD5153_24_1


title: Odd_rep1

description: Odd probes targeting SNHG1 sequence


title: Urine, Pt Z19

city: Richmond

first: Sarah

middle: J

last: Seashols-Williams

state: VA

address: 1015 Floyd Ave Box 843079

department: Forensic Science

institute: Virginia Commonwealth University

description: Urine (Z19)

data_processing:
basecalling and demultiplexed by Illumina software
Quality and adaptor trimming in Partek Flow using an miRNA pipeline, increased match times to 3.
Sequences with PHRED score >30 and of appropriate size were aligned to the human genome (GRCh38) using Bowtie 1.0, seed mismatch of 1, alignments per read of 3.
Data annotated to miRbase 20.
---
Genome_build: human genome GRCh38. miRbase v20.
Supplementary_files_format_and_content: CSV file of all samples sequenced, raw aligned and annotated sequence reads

source_name: Urine

extract_protocol:
Qiagen miRNeasy RNA extraction for blood, semen, perspiration, saliva, vaginal and menstrual secretions; Norgen Biotek for urine samples, MoBio Power Microbiome RNA extraction method for feces samples
NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Set 1)

treatment_protocol: venous blood collected using EDTA-Vacutainers; saliva, urine and semen untreated; feces, vaginal and menstrual secretions, perspiration collected on cotton swabs

tag: pt number

tag: source

value: Urine


title: hu6_S5_

description:
H2012386
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 45 years


title: Urine, Pt Z18

description: Urine (Z18)


title: hu7_S6

description:
H2013336
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 40 years


title: Odd_rep3

description: Odd probes targeting SNHG1 sequence


title: OPM2_AZD5153_24_2


title: KG1A_AZD5153_24_1


title: Odd_rep2

description: Odd probes targeting SNHG1 sequence


title: KG1A_AZD5153_24_2


title: hu9_S8

description:
H2013379
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 33 years


title: OPM2_AZD5153_24_1


title: Urine, Pt Z17

description: Urine (Z17)


title: hu21_S20

description:
H2012202
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 35 years


title: Perspiration, Pt 9625

description: Sweat (9625)

source_name: Perspiration

value: Perspiration


title: Urine, Pt Z16

description: Urine (Z16)


title: hu22_S21

description:
H200955
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 47 years


title: Vasectomized Semen, Pt 9624

description: Semen (Vas) (9624)

source_name: Vasectomized Semen

value: Vasectomized Semen


title: Menstrual secretion, Pt 7319

description: Menstrual Bld (7319)

source_name: Menstrual secretion

value: Menstrual secretion


title: IM9_AZD5153_24_1

value: mm


title: IM9_AZD5153_24_2


title: hu20_S19

description:
H2013381
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 38 years


title: hu2_S2

description:
H2012194
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 48 years


title: RPMI8226_AZD5153_24_2


title: Semen, Pt 9602

description: Semen (9602)

source_name: Semen

value: Semen


title: hu19_S18

description:
H200951
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 43 years


title: LacZ_rep1

description: control probes targeting LacZ


title: hu18_S17

description:
H2013314
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: Prefrontal Cortex

value: 39 years


title: MOLP8_AZD5153_24_2


title: hu5_S4

description:
H2012300
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue


title: hu4_S3

description:
H200965
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 34 years


title: RPMI8226_AZD5153_24_1


title: MV411_AZD5153_24_3

value: aml


title: Saliva, Pt 8425

description: Saliva (8425)

source_name: Saliva

value: Saliva


title: Perspiration, Pt 8419

description: Sweat (8419)


title: Feces, Pt 8407

description: Feces (8407)

source_name: Feces

value: Feces


title: MOLP8_AZD5153_24_1


title: Perspiration, Pt 8413

description: Sweat (8413)


title: MV411_AZD5153_24_1


title: hu17_S16

description:
H2012338
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

source_name: Prefrontal Cortex

value: 32 years


title: hu16_S15

description:
H2009149
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 50 years


title: Feces, Pt 8401

description: Feces (8401)


title: hu23_S22

description:
H200936
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 33 years


title: hu15_S14

description:
H002
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 40 years


title: MM1S_AZD5153_24_3


title: Semen, Pt 7520

description: Semen (7520)


title: MM1S_AZD5153_24_2


title: hu14_S13

description:
H2012274
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue


title: Semen, Pt 7322

description: Semen (7322)


title: WILL2_AZD5153_24_2

value: dlbcl


title: Menstrual secretion, Pt 7329

description: Menstrual Bld (7329)

value: Menstrual secretion


title: Saliva, Pt 7322

description: Saliva (7322)


title: WILL2_AZD5153_24_1


title: hu13_S12

description:
H004
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 28 years


title: hu12_S11

description:
H2013430
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 46 years


title: Vaginal secretion, Pt 7321

description: Vag Fluid (7321)

source_name: Vaginal secretion

value: Vaginal secretion


title: hu11_S10

description:
H2013422
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 52 years


title: MM1S_AZD5153_24_1

source_name: Cancer cell line

value: mm


title: OCILY19_AZD5153_24_2


title: Saliva, Pt 7321

description: Saliva (7321)


title: hu10_S9

description:
H2013390
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: Prefrontal Cortex


title: hu1_S1


title: Feces, Pt 7319

description: Feces (7319)


title: Saliva, Pt 7319

description: Saliva (7319)


title: 16HBE-CA16-12h

first: Jie

last: Song

address: Number 935 Jiaoling Load

institute: Institute of Medical Biology, Chinese Academy of Medicine Science and Peking Union Medical College

description: microRNA sequencing after 12h in 16HBE with CA16 infection

data_processing:
Adaptor sequences were ﬁrst trimmed from small RNA reads. After adaptor trimming, low-quality sequences, namely, those with undetermined nucleotides (Ns), those with quality scores (Q-scores) less than 10, and those with reads shorter than 18 nt, were discarded from all libraries.
Clipped high-quality sequences were clustered into unique reads, and sRNAs with a length of 18~35nt were identiﬁed.
non-coding RNAs, including ribosomal RNA (rRNA), transfer RNA (tRNA), and small nuclear RNA (snRNA), were eliminated based on reference sequences from Rfam (http://rfam.janelia.org/) and piRNA (http://pirnabank.ibab.ac.in/). Afterward, the clean reads were mapped to known miRNA precursors, and the mature miRNAs were deposited in miRBase 19.0 (available online: http://www.mirbase.org/).
Unmappable sequences were used to predict potentially novel candidate miRNAs with the Mfold RNA folding prediction web server (available online: http://mfold.rna.albany.edu/).
The samples were normalized by calculating tags per million of total RNA reads (TPM) and used to compare the relative abundances of specific miRNAs within each data set.
Supplementary_files_format_and_content: xlsx files are comprised of two sheets, one for knonw miRNAs, the other for novel miRNAs, and eacha sheet include gene_id,description and Tpm values for each Sample.

source_name: Human Bronchial Epithelial Cells

growth_protocol: 16HBEcells purchased from the Jennino Biological Technology were maintained in RPMI 1640 (Gibco, USA) supplemented with L-glutamine, penicillin, streptomycinand 10% foetal bovine serum (FBS, Gibco, USA)at 37°C in a 5% CO2-containing incubator.For in vitro virus infection, approximately 1×10516HBE cells per well were plated in 6-well platesand incubated overnight at 37°Cunder 5%CO2.

extract_protocol:
Samples from the above groups were sent to the National Engineering Center for Biochips in Shanghai.miRNA was extracted from each group of cells using amirVana™ miRNA Isolation Kit(Ambion, USA) according to the manufacturer’s instructions.RNA was further puriﬁed using a miRNeasyMini kit (Qiagen, Germany) following the manufacturer’s protocol. RNA concentration and RNA integrity wereassessed by capillary electrophoresis on an Agilent 2100 Bioanalyzer (Agilent Technologies, USA); only samples with an RNA integrity number (RIN) > 7 were used for miRNA profile analysis.
High-throughput sequencing is a useful tool for transcriptome studies, as it can capture almost all expressed transcripts, including known and novel transcripts. Additionally, it has lower background noise and higher sensitivity than microarrays[30]. Sequencing libraries of the above samples were generated using a standard TruSeq Small RNA sample preparation kit (Illumina, USA) according to manufacturer recommendations and then prepared for Illumina sequencing.

treatment_protocol: The 16HBE cellsgrown to 80% confluenceand infected with EV71 (sub-genotype C4, GenBank: EU812515.1) or CA16 strainG20 (sub-genotype B, GenBank: JN590244.1), which were isolated from an epidemic in Fuyang, China in 2008 and from an HFMD patient in Guangxi, China in 2010, respectively.

tag: infected with


title: OCILY19_AZD5153_24_1


title: 16HBE-CA16-6h

description: microRNA sequencing after 6h in 16HBE with CA16 infection


title: 16HBE-EV71-12h

description: microRNA sequencing after 12h in 16HBE with EV71 infection


title: 16HBE-CA16-0h

description: microRNA sequencing after 0h in 16HBE with CA16 infection


title: venous blood, Pt 7319

description: Blood (7319)

source_name: venous blood

value: venous blood


title: Vaginal secretion, Pt 7319

description: Vag Fluid (7319)


title: 16HBE-EV71-6h

description: microRNA sequencing after 6h in 16HBE with EV71 infection


title: Perspiration, Pt 7318

description: Sweat (7318)

value: Perspiration


title: 16HBE-EV71-0h

description: microRNA sequencing after 0h in 16HBE with EV71 infection


title: s.39791

city: Minneapolis

first: June

last: Baik

state: MN

address: 2231 6th St SE CCRB

institute: University of Minnesota

description: Flk-,Eng+ cells treated with IWR-1

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment. Parameters to rsem-calc-expression include: "--bowtie-m 200 --bowtie-n 2 --forward-prob 0.5 --seed-length 28 "
Genome_build: mm10
Supplementary_files_format_and_content: Excel .xls file containing Expected Counts and TPM expression estimates calculated by RSEM

source_name: Flk1-Eng+ +IWR-1_Set.3

growth_protocol: GFP-Bry ES cells were differentiated into embyoid bodies.

extract_protocol:
After 24 hours reaggregation, samples were collected and total RNAs were isolated using Trizol and RNA purification kit (Ambion).
cDNA libraries were prepared from 50 nanograms of total RNA and indexed with Illumina’s TruSeq RNA Sample Preparation Kit v2 (RS-122-2001 and RS-122-2002).  Final indexed cDNA libraries were pooled with 12 uniquely indexed TruSeq cDNA libraries for a total of 6 samples per lane.  Multiplexed samples were sequenced on an Illumina HiSeq 2500 with a single 51 bp read and a 7 bp index read. Base-calling and demultiplexing were performed using Casava (v1.8.2). Sequences were filtered and trimmed to remove low quality reads, adapters, and other sequencing artifacts. The remaining reads were aligned to 19084 Refseq genes extracted from the Illumina iGenomes reference, selecting only those with ‘NM_’ annotations.  Bowtie (v 0.12.9) was used for alignment, allowing two mismatches in a 28 bp seed [64]. Reads with more than 200 alignments were excluded from further analysis. RSEM (v1.2.3) was used to estimate isoform and relative gene expression levels (transcripts per million or “TPM”)

treatment_protocol: While reaggregating unsorted or sorted embryoid bodies, 10 uM IWR-1 or vehicle control DMSO were added into each sample.

value: reaggregated embryoid bodies

tag: cell type

value: GFP-Bry ES derived mesodermal cells

tag: sortedflag

value: Flk-,Eng+

value: 10 µM IWR-1


title: Vaginal secretion, Pt 7315

description: Vag Fluid (7315)


title: s.39785

description: Flk-,Eng+ cells treated with IWR-1

source_name: Flk1-Eng+ +IWR-1_Set.2


title: Feces, Pt 7318

description: Feces (7318)

value: Feces


title: Menstrual secretion, Pt 7318

description: Menstrual Bld (7318)


title: Vaginal secretion, Pt 7314

description: Vag Fluid (7314)


title: MV411_AZD5153_24_2

value: aml


title: Vasectomized Semen, Pt 7311

description: Semen (Vas) (7311)

value: Vasectomized Semen


title: venous blood, Pt 7311

description: Blood (7311)


title: s.39790

description: Flk-,Eng+ cells treated with DMSO

source_name: Flk1-Eng+ +DMSO_Set.3

value: DMSO


title: s.39779

description: Flk-,Eng+ cells treated with IWR-1

source_name: Flk1-Eng+ +IWR-1_Set.1


title: s.39784

description: Flk-,Eng+ cells treated with DMSO

source_name: Flk1-Eng+ +DMSO_Set.2


title: venous blood, Pt 7309

description: Blood (7309)


title: s.39778

description: Flk-,Eng+ cells treated with DMSO

source_name: Flk1-Eng+ +DMSO_Set.1


title: s.39783

description: Flk+,Eng+ cells treated with IWR-1

source_name: Flk1+Eng+ +IWR-1_Set.2

value: Flk+,Eng+


title: TNF-C-L2

city: La Jolla

first: Jonathan

middle: Ross

last: Hart

address: 10550 North Torrey Pines Road, BCC239

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

description: Sample name: TNF-C-FACS-Sorted_CTTGTA_L002_R1_001.fastq.gz

data_processing:
Basecalls performed using CASAVA version v1.8.2
Aligned with STAR 2.4.0k to HG38.p2 including LCHIT sequence with Gencode v22 junctions.  Coordinate sorted using STAR
Raw counts were generated using htseq_count 0.6.1 using the UCSC hg38 known gene transcripts from Illumina iGenomes
edgeR 3.2.4 in R 3.1.0 were used to normalize counts between samples and to make comparisons between groups.
Genome_build: hg38
Supplementary_files_format_and_content: Gene by sample normalized counts with comparisons between sample groups as additional columns(log2FC, p.value, and BH FDR corrected q.values)

source_name: LChIT 3.2 Bimodal cells

growth_protocol: Cells were grown in RPMI-1640 with 10% FBS throughout the experiment.

extract_protocol:
Total RNA was extracted using SimplyRNA LEV reagents on a Maxwell 16 instrument.  Genomic DNA was removed during this procedure using a captive DNAse
Libraries were prepared using NEBNext Ultra RNA library preparation kit reagents

treatment_protocol: TNF(10ng/uL) treatment was performed for 72hr

value: LChIT clone 3.2

tag: sgrna

value: Control

value: TNF


title: s.39777

description: Flk+,Eng+ cells treated with IWR-1

source_name: Flk1+Eng+ +IWR-1_Set.1


title: TNF-A-L2

description: Sample name: TNF-A-FACS-Sorted_TAGCTT_L002_R1_001.fastq.gz


title: TNF-B-L1

description: Sample name: TNF-B-FACS-Sorted_GGCTAC_L001_R1_001.fastq.gz


title: s.39788

description: Flk+,Eng+ cells treated with DMSO

source_name: Flk1+Eng+ +DMSO_Set.3


title: s.39782

description: Flk+,Eng+ cells treated with DMSO

source_name: Flk1+Eng+ +DMSO_Set.2


title: TNF-C-L1

description: Sample name: TNF-C-FACS-Sorted_CTTGTA_L001_R1_001.fastq.gz


title: TNF-A-L1

description: Sample name: TNF-A-FACS-Sorted_TAGCTT_L001_R1_001.fastq.gz


title: TNF-B-L2

description: Sample name: TNF-B-FACS-Sorted_GGCTAC_L002_R1_001.fastq.gz


title: s.39787

description: Unsorted cells treated with IWR-1

value: unsorted


title: s.39781

description: Unsorted cells treated with IWR-1


title: sgRNA-Control-C-L1

description: Sample name: sgRNA-Control-C-FACS-Sorted_GCCAAT_L001_R1_001.fastq.gz


title: s.39775

description: Unsorted cells treated with IWR-1


title: sgRNA-Control-B-L1

description: Sample name: sgRNA-Control-B-FACS-Sorted_ACAGTG_L001_R1_001.fastq.gz


title: s.39786

description: Unsorted cells treated with DMSO


title: Menstrual secretion, Pt 7315

description: Menstrual Bld (7315)

source_name: Menstrual secretion

value: Menstrual secretion


title: s.39780

description: Unsorted cells treated with DMSO


title: sgRNA-Control-A-L2

description: Sample name: sgRNA-Control-A-FACS-Sorted_TGACCA_L002_R1_001.fastq.gz


title: sgRNA-Control-A-L1

description: Sample name: sgRNA-Control-A-FACS-Sorted_TGACCA_L001_R1_001.fastq.gz


title: s.39789

description: Flk+,Eng+ cells treated with IWR-1

source_name: Flk1+Eng+ +IWR-1_Set.3


title: ma9_S33

description:
ma26183
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

organism: Macaca

source_name: Prefrontal Cortex

value: Prefrontal Cortex

tag: age

value: 12 years


title: ma8_S32

description:
ma02344
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue


title: ma7_S31

description:
ma072412
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 7 years


title: sgLTR-F2-B-L2

description: Sample name: sgLTR-F2-B-FACS-Sorted_ACTTGA_L002_R1_001.fastq.gz


title: s.39776

description: Flk+,Eng+ cells treated with DMSO

source_name: Flk1+Eng+ +DMSO_Set.1

value: reaggregated embryoid bodies


title: sgLTR-F2-C-L1

description: Sample name: sgLTR-F2-C-FACS-Sorted_GATCAG_L001_R1_001.fastq.gz


title: sgLTR-F2-A-L2

description: Sample name: sgLTR-F2-A-FACS-Sorted_CAGATC_L002_R1_001.fastq.gz


title: sgLTR-F2-B-L1

description: Sample name: sgLTR-F2-B-FACS-Sorted_ACTTGA_L001_R1_001.fastq.gz


title: sgRNA-Control-C-L2

description: Sample name: sgRNA-Control-C-FACS-Sorted_GCCAAT_L002_R1_001.fastq.gz


title: ma4_S28

description:
ma09072
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 5 years


title: sgLTR-F2-A-L1

description: Sample name: sgLTR-F2-A-FACS-Sorted_CAGATC_L001_R1_001.fastq.gz


title: ma5_S29

description:
ma030040
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 11 years


title: ma6_S30

description:
ma048
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 14 years


title: ma2_S26

description:
ma030064
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue


title: ma20_S44

description:
ma26300
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue


title: ma18_S42

description:
ma26304
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 13 years


title: sgRNA-Control-B-L2

description: Sample name: sgRNA-Control-B-FACS-Sorted_ACAGTG_L002_R1_001.fastq.gz


title: ma11_S35

description:
ma26871
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 8 years


title: ma17_S41

description:
ma26187
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue


title: ma1_S25

description:
ma080608
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: 6 years


title: s.39774

description: Unsorted cells treated with DMSO

value: GFP-Bry ES derived mesodermal cells

value: DMSO


title: ma10_S34

description:
ma26299
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue


title: ma19_S43

description:
ma26306
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue


title: sgLTR-F2-C-L2

description: Sample name: sgLTR-F2-C-FACS-Sorted_GATCAG_L002_R1_001.fastq.gz

value: LChIT clone 3.2


title: d1_Spleen_Mutant 2

status: Public on Aug 19 2016

city: Boston

first: Jeannie

last: Lee

address: 185 Cambridge Street

department: Molecular Biology

institute: HHMI, Massachusetts General Hospital, Harvard Medical School

data_processing:
Basecalling was performed using Illumina software version 1.9.
Sequenced reads were aligned using Tophat2.0.10 to GRCm38/mm10 with parameters --read-edit-dist 3 --read-mismatches 3 --read-gap-length 3 --mate-inner-dist 100 --mate-std-dev 100 --b2-very-sensitive --no-coverage-search --library-type fr-firststrand
Read counting was performed using htseq-count 0.6.1
Read count normalization and differential expression analysis performed using EdgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files showing normalized read counts (as calculated by EdgeR)

source_name: Post-natal day 1 Spleen (female)

extract_protocol:
For TTFs, total RNA was extracted using Trizol. For tissues, samples were homogenized using Tissue Lyzer II (Qiagen) before total RNA extraction using Trizol.
Ribosomal RNA was depleted from samples using RiboMinus Eukaryote System v2 (Thermo Fisher Scientific), DNAse treated, and size selected using Rneasy MinElute Cleanup kit (Qiagen). RNA was fragmented in buffer containing magnesium before first (Superscript III, Thermo Fisher Scientific) and second strand (NEBnext Ultra Directional RNA second strand synthesis module) cDNA synthesis. Subsequent library preparation was performed using NEBnext Chip-seq Library Prep Master Mix for Illumina (NEB), per manufacturer's instructions.

tag: Sex

value: female

value: Spleen

tag: genetic manupulation

value: Xist homozygous deletion


title: d1_Brain_Mutant 2

source_name: Post-natal day 1 Brain (female)

tag: tissue

value: Brain


title: d1_Liver_Mutant 2

source_name: Post-natal day 1 Liver (female)

value: Liver


title: d1_Brain_Control 2

value: Xist heterozygous deletion


title: d1_Liver_Control 2


title: d1_Spleen_Control 2


title: ma3_S27

description:
ma030030
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

value: Prefrontal Cortex


title: d1_Spleen_Mutant 1


title: d1_Brain_Control 1


title: d1_Liver_Control 1


title: d1_Brain_Mutant 1


title: CSR_Im_Ligase4_1_Rep3

city: Stanford

first: Richard

middle: L

last: Frock

state: California

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University

description: processed data file: CSR_Im_Ligase4_1.txt

data_processing:
Library strategy: LAM-HTGTS
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203)
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml)
A best-path searching algorithm was used to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site.
Discarded alignments were compared to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Duplicates were excluded by comparing the coordinates of the end of the bait alignment and the start of the prey alignment across all reads. A read was marked as a duplicate if it has a bait alignment offset within 2nt and a prey alignment offset within 2nt of another read’s bait and prey alignments.
Alpha switch region junctions mapping only within positions 114,500,088-114,502,837 on chromosome 12 were used for microhomology analysis to obviate any contributions of potential local joining events from the non-coding allele which contains a hybrid Sm-Sα (Nakamura et al., 1996)
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

growth_protocol: RPMI, 10% Fetal Calf Serum, 50mM 2-mercaptoethanol

extract_protocol:
DNA was extracted overnight at 55oC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, isopropanol preciptated/ethanol washed, and dissolved in 10mM Tris 1mM EDTA pH8.0 at 50oC for several hours
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203) using IgH Im primers described in Dong et al., 2015 Nature (PMC4592165) and Illumina Miseq sequencing

treatment_protocol: Genomic DNA as isolated after 72 hours of CSR stimulation

tag: cell line

tag: genotype

value: Ligase4-/- clone1

tag: csr stimulation

value: 20ng/mL IL-4, 1mg/mL αCD40, 1ng/mL TGFβ

tag: target locus

value: IgH Imu promoter

tag: extract_protocol (dna fragmentation/blocking methods)

value: Sonication/AflII blocking


title: CSR_Im_Ligase4_2_Rep2

description: processed data file: CSR_Im_Ligase4_2.txt

value: Ligase4-/- clone2


title: CSR_Im_Ligase4_2_Rep3


title: CSR_Im_Ligase4_1_Rep2


title: CSR_Im_Ligase4_2_Rep1


title: d1_Spleen_Control 1


title: Rep4_12hrs_post_E2

city: Chapel Hill

first: Jeanette

last: Baran-Gale

state: NC

address: 120 Mason Farm Rd.

institute: University of North Carolina at Chapel Hill

data_processing:
Reads were aligned to the hg19 genome using MapSplice
Sam-xlate (UBU) was used to translate genomic alignmets to transcriptomic alignments
RSEM was used to quantify gene expression
DESeq2 was used to assess differential expression
Genome_build: hg19
Supplementary_files_format_and_content: RSEM gene outputs

growth_protocol: MCF7 cells were cultured in DMEM/F12 media +10% FBS & 2nM GlutaMax for 24 hrs, then media was replced with phenol-red free DMEM/F12 +10% charcoal dextran stripped FBS + 2mM GlutaMax +0.1% EtOH. Cells were cultured for 72hrs in stripped media.

extract_protocol:
Total RNA was extracted using the Norgen Total RNA Purification Kit (#17200), and RNA Integrity was measured by Agilent Bioanalyzer 2100.
Libraries were generated using an Illumina TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: After 72hrs, the media was replaced with phenol-red free DMEM/F12 +10% charcoal dextran stripped FBS + 2mM GlutaMax +10nM Estradiol. Cells were cultured in estrogen supplemented media for the specified amount of time (0-24hrs).

tag: passage

tag: treated with

value: 10nM E2 for 12hr


title: Rep4_6hrs_post_E2

value: 10nM E2 for 6hr


title: CSR_Im_Ligase4_1_Rep1


title: Rep4_24hrs_post_E2

value: 10nM E2 for 24hr


title: CSR_Im_XLF_PAXX_2_Rep3

description: processed data file: CSR_Im_XLF_PAXX_2.txt

value: XLF-/-PAXX-/- clone 2


title: Rep4_5hrs_post_E2

value: 10nM E2 for 5hr


title: CSR_Im_XLF_PAXX_2_Rep2


title: CSR_Im_XLF_PAXX_2_Rep1


title: CSR_Im_XLF_PAXX_1_Rep2

description: processed data file: CSR_Im_XLF_PAXX_1.txt

value: XLF-/-PAXX-/- clone 1


title: Rep4_3hrs_post_E2

value: 10nM E2 for 3hr


title: CSR_Im_XLF_PAXX_1_Rep1


title: Rep4_2hrs_post_E2

value: 10nM E2 for 2hr


title: Rep4_4hrs_post_E2

value: 10nM E2 for 4hr


title: d1_Liver_Mutant 1

value: female

value: Liver

value: Xist homozygous deletion


title: Rep4_1hrs_post_E2

value: 10nM E2 for 1hr


title: CSR_Im_XLF_2_Rep3

description: processed data file: CSR_Im_XLF_2.txt

value: XLF-/- clone 2

value: 20ng/mL IL-4, 1mg/mL αCD40, 1ng/mL TGFβ


title: CSR_Im_XLF_2_Rep2

description: processed data file: CSR_Im_XLF_2.txt

value: IgH Imu promoter

value: Sonication/AflII blocking


title: Rep4_0hrs_post_E2

value: EtOH


title: Rep3_24hrs_post_E2


title: CSR_Im_XLF_2_Rep1

description: processed data file: CSR_Im_XLF_2.txt


title: CSR_Im_XLF_1_Rep3

description: processed data file: CSR_Im_XLF_1.txt

value: XLF-/- clone 1


title: Rep3_12hrs_post_E2

value: 10nM E2 for 12hr


title: Rep3_8hrs_post_E2

value: 10nM E2 for 8hr


title: CSR_Im_XLF_1_Rep1

description: processed data file: CSR_Im_XLF_1.txt


title: Rep3_5hrs_post_E2

value: 10nM E2 for 5hr


title: Rep4_8hrs_post_E2


title: CSR_Im_PAXX_2_Rep1

description: processed data file: CSR_Im_PAXX_2.txt

value: PAXX-/- clone 2


title: CSR_Im_PAXX_2_Rep2

description: processed data file: CSR_Im_PAXX_2.txt


title: CSR_Im_XLF_PAXX_1_Rep3

value: XLF-/-PAXX-/- clone 1


title: Rep3_6hrs_post_E2

value: 10nM E2 for 6hr


title: Rep3_3hrs_post_E2

value: 10nM E2 for 3hr


title: CSR_Im_XLF_1_Rep2

description: processed data file: CSR_Im_XLF_1.txt


title: Rep3_2hrs_post_E2

value: 10nM E2 for 2hr


title: CSR_Im_PAXX_1_Rep3

description: processed data file: CSR_Im_PAXX_1.txt

value: PAXX-/- clone 1


title: CSR_Im_PAXX_1_Rep1

description: processed data file: CSR_Im_PAXX_1.txt


title: CSR_Im_WT_Rep3

description: processed data file: CSR_Im_WT.txt

value: WT


title: CSR_Im_PAXX_1_Rep2

description: processed data file: CSR_Im_PAXX_1.txt


title: Rep3_1hrs_post_E2

value: 10nM E2 for 1hr


title: Rep2_24hrs_post_E2

value: 10nM E2 for 24hr


title: Rep2_12hrs_post_E2


title: CSR_Im_WT_Rep2

description: processed data file: CSR_Im_WT.txt

value: 20ng/mL IL-4, 1mg/mL αCD40, 1ng/mL TGFβ


title: Rep2_6hrs_post_E2


title: Rep3_0hrs_post_E2


title: Rep2_3hrs_post_E2


title: Rep2_5hrs_post_E2


title: Rep2_4hrs_post_E2

value: 10nM E2 for 4hr


title: Rep3_4hrs_post_E2


title: CSR_Im_PAXX_2_Rep3

description: processed data file: CSR_Im_PAXX_2.txt

value: IgH Imu promoter

value: Sonication/AflII blocking


title: Rep2_8hrs_post_E2


title: CSR_Im_WT_Rep1

description: processed data file: CSR_Im_WT.txt


title: Rep2_2hrs_post_E2


title: TTF_Mutant 2

source_name: Primary tail-tip fibroblast (female)

value: female

value: Primary tail-tip fibroblast

value: Xist homozygous deletion


title: Rep2_0hrs_post_E2

value: EtOH


title: Rep2_1hrs_post_E2


title: TTF_Control 3

value: Xist heterozygous deletion


title: TTF_Mutant 3


title: UAS-tsu RNAi rep1

first: Ruifeng

last: Li

address: Haidian

institute: Peking University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Aligned using the TopHat (v2.0.13) with the Ensembl Drosophila_melanogaster.BDGP5.78.gtf as a reference.
The transcription analysis was performed using Cufflinks (v2.2.1)
Genome_build: BDGP5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: UAS-tsu RNAi, third instar larval wing imaginal discs

extract_protocol:
Total RNA from pooled third instar larval wing imaginal discs (1000 pairs per sample preparation) expressing UAS-lacZ or UAS-tsu RNAi (VDRC#107385) driven by T80-Gal4 was extracted in duplicates using TRIzol. Poly(A)+ mRNAs were enriched using Dynabeads oligo (dT) beads (NEB). RT reactions and purification of cDNA templates were performed following the RNA-seq sample preparation protocol from Illumina. Each cDNA sample was sequenced on an IlluminaHiseq 2500 system.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: pre-EJC-defective

value: third instar larval wing imaginal discs


title: UAS-tsu RNAi rep2


title: TTF_Control 2


title: UAS-lacZ rep1

source_name: UAS-lacZ, third instar larval wing imaginal discs

value: wildtype


title: UAS-lacZ rep2


title: Staphylococcus aureus  biofilm cells_TTO 60 min_replicate 1

city: Changchun

last: Guo

address: Xi’an Road 5333#

institute: Jilin University

data_processing:
Illumina Casava1.7 software used for basecalling.
fastx(version:0.0.13) processed clean reads, and removed Q20<50% and length<20nt
Genome mapping performed with bowtie2(version:2-2.0.5)
BEDTool(version:2.16.1) counted RPKM for all genes expression
Differential gene analysis under fold-change>2 and Fisher-test<0.05
Genome_build: S. aureus strain ATCC 29213 reference genome (accession no. NC_002745.2 and NC_003140.1)
Supplementary_files_format_and_content: XLS file include RPKM values for each Sample

organism: Staphylococcus aureus

source_name: Staphylococcus aureus  biofilm cells_TTO

growth_protocol: Within biofilm, the overnight culture were inoculated to an initial OD600 and diluted in TSBg to obtain the final concentration of 1× 105cfu/ml, 30 ml bacterial suspension diluted in 0.25% glucose-supplemented TSB containing 1 × 105 cfu/ml into the culture dish, then incubated in air for 48 h at 37°C

extract_protocol:
Total RNA was extracted from mature biofilms and planktonic cells following the manufacturer’s protocol by the RNeasy Mini Kit (Cat#74106, Qiagen). Total RNA purified with RNase-free DNase I (Thermo Scientific). Quality analysis was performed on 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and then then transformed into the Tru-Seq libraries for sequencing on the Illumina HiSeq2500 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: TTO stock solution, prepared in dimethyl sulfoxide (DMSO), was added to the cultures, giving a final concentration of 1/2× MIBC (1 mg/ml), and the final concentration of DMSO was 0.1% (vol/vol) as control group. Then, the bacterial biofilm cells were further incubated for 60 min at 37°C

tag: strain

value: Standard strain ATCC29213

tag: developmental stage


title: TTF_Mutant 1


title: Staphylococcus aureus  biofilm cells_TTO 60 min_replicate 2


title: Ammonia25_2

first: Bao

last: Yi

address: No.2 Yuanmingyuan West Road

department: Institute of Animal Sciences

institute: Chinese Academy of Agricultural Sciences

data_processing:
Basecalls performed using CASAVA version 1.7
The adaptor sequences were removed and data were Q20, Q30 filtered
Fragments Per Kilobase of transcript per Million mapped fragments (FPKM) was calculated using bowtie2
Genome_build: Gallus_gallus-4.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Gallus gallus

source_name: Breast muscle

extract_protocol:
Total RNA of breast muscle was isolated with TRIzol reagent (Invitrogen) according to the manufacturer's instructions. mRNA was extracted from total RNA using oligo (dT) magnetic beads (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Arbor Acres

value: male

value: 42-day old

value: breast muscle

tag: ammonia exposure


title: Ammonia25_1


title: Staphylococcus aureus  biofilm cells_control 60min_replicate 2


title: Staphylococcus aureus  biofilm cells_control 60min_replicate 1


title: Ammonia3_2


title: Ammonia3_1


title: Jersey calf, day 8 relative to weaning [S6d_J_8]

city: Dunsany

first: Dayle

last: Johnston

state: Ireland

address: AGRIC

department: Animal and Bioscience Research Department

country: Ireland

institute: Teagasc

description:
Jersey calf, day 8 relative to weaning
S6d_J_8

data_processing:
Raw sequence reads were assessed for quality using FastQC (version 0.10.0).
Reads were aligned to the bovine genome UMD3.1 using the Spliced Transcripts Alignment to a Reference (STAR) aligner
Read counts were generated by using HTseq-count to convert aligned reads into counts per gene using the union model and the Ensembl UMD3.1 annotation of the bovine genome
Genome_build: UMD3.1
Supplementary_files_format_and_content: A tab-delimited matrix table text file containing raw counts of sequencing reads corresponding to genes identified with an ensemble IDs

organism: Bos taurus

source_name: whole blood

extract_protocol:
Total RNA was extracted from whole blood using the TempusTM Spin RNA Isolation Reagent Kit (Applied Biosystems; Foster City, California, USA), according to manufacturer's instructions. AbsoluteRNA Wash Solution (Applied Biosystems; Foster City, California, USA) was used for the DNase step.
Forty-eight individual libraries were prepared from a starting material of 1000 ng high quality total RNA using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina Inc; San Diego, CA, USA), according to manufacturer's instructions.

treatment_protocol: Holstein-Friesian and eight Jersey bull calves were group housed indoors and individually fed milk replacer and concentrate using an automatic feeder. Calves were gradually weaned by reducing milk-replacer from 6 litres to 0 litres over 14 days (d) (d -13 to d 0). Calves were blood sampled on d -14 (one day before gradual weaning), d 1 (one day after weaning from milk-replacer), and d 8 (eight days after weaning from milk-replacer). RNA-seq analysis was carried out on RNA extracted from whole blood.

tag: breed

value: Jersey

tag: day relative to weaning


title: Jersey calf, day 8 relative to weaning [S85d_J_8]

description:
Jersey calf, day 8 relative to weaning
S85d_J_8


title: Jersey calf, day 8 relative to weaning [S9d_J_8]

description:
Jersey calf, day 8 relative to weaning
S9d_J_8


title: Jersey calf, day 8 relative to weaning [S7d_J_8]

description:
Jersey calf, day 8 relative to weaning
S7d_J_8


title: Jersey calf, day 8 relative to weaning [S77d_J_8]

description:
Jersey calf, day 8 relative to weaning
S77d_J_8


title: Jersey calf, day 8 relative to weaning [S60d_J_8]

description:
Jersey calf, day 8 relative to weaning
S60d_J_8


title: Jersey calf, day 8 relative to weaning [S57d_J_8]

description:
Jersey calf, day 8 relative to weaning
S57d_J_8


title: SLE Sample 3 methyl-seq

city: Oklahoma City

first: Carol

middle: F.

last: Webb

state: OK

address: 800 Research Parkway, Suite 419

department: Medicine

institute: University of Oklahoma Health Sciences Center

data_processing:
Libraries were sequenced on an Illumina Hiseq 2000 instrument with paired-end 100bp reads.
Reads were aligned to the human reference genome hg19 using the aligner BWA-MEM followed by local realignment around problematic indel sequences using the Genome Analysis Tool Kit (GATK).
Genes with statistically significant methylation differences were defined using EpiCenter v. 1-6-1-8. Methylation differences were tested over promoters of the genes, defined as 2,000bp regions upstream of gene’ transcription start sites. The differentially methylated regions were visualized in the IGV integrative genomics viewer.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files were created from the final BAM files using a combination of BEDTools and UCSC conversion utilities.

source_name: peripheral blood mononuclear cells

growth_protocol: peripheral blood mononnuclear cells were isolated directly from SLE blood

extract_protocol:
Purified genomic DNA was isolated from frozen aliquots containing PBMCs using standard phenol/chloroform extraction protocols. Sample gDNA was fragmented on a Covaris S2 sonicator to an average size of ~350bp in length.  Fragmented DNA was subjected to MethylMiner Methylated DNA Enrichment Kit.
Illumina sequencing libraries were prepared using the Illumina Truseq DNA LT Sample Prep Kit.

tag: arid3a expression

value: high


title: Holstein-Friesian calf, day 8 relative to weaning [S49d_HF_8]

description:
Holstein-Friesian calf, day 8 relative to weaning
S49d_HF_8

value: Holstein-Friesian


title: SLE Sample 2 methyl-seq

value: low


title: SLE Sample 1 methyl-seq


title: SLE Sample 4 methyl-seq


title: Rep4_24hrs_post_E2 [miRNA-seq]

data_processing:
Reads were aligned to the hg19 geneome using Bowtie (only exact matches allowed).
Reads that fail to align perfectly were aligned (with error) to regions of the geneome where other reads previously aligned exactly.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized counts of miRNAs for all samples

extract_protocol:
Total RNA was extracted using the Norgen Total RNA Purification Kit (#17200), and RNA Integrity was measured by Agilent Bioanalyzer 2100.
Libraries were generated using an Bioo Scientific NextFLEX v2 kit

value: 10nM E2 for 24hr


title: Holstein-Friesian calf, day 8 relative to weaning [S20d_HF_8]

description:
Holstein-Friesian calf, day 8 relative to weaning
S20d_HF_8


title: Rep4_8hrs_post_E2 [miRNA-seq]

value: 10nM E2 for 8hr


title: Holstein-Friesian calf, day 8 relative to weaning [S56d_HF_8]

description:
Holstein-Friesian calf, day 8 relative to weaning
S56d_HF_8


title: Holstein-Friesian calf, day 8 relative to weaning [S32d_HF_8]

description:
Holstein-Friesian calf, day 8 relative to weaning
S32d_HF_8


title: Holstein-Friesian calf, day 8 relative to weaning [S25d_HF_8]

description:
Holstein-Friesian calf, day 8 relative to weaning
S25d_HF_8


title: Rep4_3hrs_post_E2 [miRNA-seq]

value: 10nM E2 for 3hr


title: Holstein-Friesian calf, day 8 relative to weaning [S33d_HF_8]

description:
Holstein-Friesian calf, day 8 relative to weaning
S33d_HF_8


title: Rep4_12hrs_post_E2 [miRNA-seq]

value: 10nM E2 for 12hr


title: TTF_Control 1

tag: Sex

value: female

value: Primary tail-tip fibroblast

value: Xist heterozygous deletion


title: Holstein-Friesian calf, day 8 relative to weaning [S27d_HF_8]

description:
Holstein-Friesian calf, day 8 relative to weaning
S27d_HF_8


title: Rep4_6hrs_post_E2 [miRNA-seq]

value: 10nM E2 for 6hr


title: Holstein-Friesian calf, day 8 relative to weaning [S48d_HF_8]

description:
Holstein-Friesian calf, day 8 relative to weaning
S48d_HF_8


title: Rep4_5hrs_post_E2 [miRNA-seq]

value: 10nM E2 for 5hr


title: Rep4_4hrs_post_E2 [miRNA-seq]

value: 10nM E2 for 4hr


title: Jersey calf, day 8 relative to weaning [S13d_J_8]

description:
Jersey calf, day 8 relative to weaning
S13d_J_8


title: Jersey calf, day 1 relative to weaning [S77c_J_1]

description:
Jersey calf, day 1 relative to weaning
S77c_J_1


title: Rep4_2hrs_post_E2 [miRNA-seq]

value: 10nM E2 for 2hr


title: Rep4_1hrs_post_E2 [miRNA-seq]

value: 10nM E2 for 1hr


title: Jersey calf, day 1 relative to weaning [S9c_J_1]

description:
Jersey calf, day 1 relative to weaning
S9c_J_1


title: Rep3_24hrs_post_E2 [miRNA-seq]


title: Rep3_12hrs_post_E2 [miRNA-seq]


title: Jersey calf, day 1 relative to weaning [S7c_J_1]

description:
Jersey calf, day 1 relative to weaning
S7c_J_1


title: Jersey calf, day 1 relative to weaning [S60c_J_1]

description:
Jersey calf, day 1 relative to weaning
S60c_J_1


title: Holstein-Friesian calf, day 1 relative to weaning [S32c_HF_1]

description:
Holstein-Friesian calf, day 1 relative to weaning
S32c_HF_1


title: Jersey calf, day 1 relative to weaning [S57c_J_1]

description:
Jersey calf, day 1 relative to weaning
S57c_J_1


title: Rep3_8hrs_post_E2 [miRNA-seq]


title: Rep3_6hrs_post_E2 [miRNA-seq]


title: Jersey calf, day 1 relative to weaning [S13c_J_1]

description:
Jersey calf, day 1 relative to weaning
S13c_J_1


title: Rep4_0hrs_post_E2 [miRNA-seq]

value: EtOH


title: Holstein-Friesian calf, day 1 relative to weaning [S56c_HF_1]

description:
Holstein-Friesian calf, day 1 relative to weaning
S56c_HF_1


title: Holstein-Friesian calf, day 1 relative to weaning [S49c_HF_1]

description:
Holstein-Friesian calf, day 1 relative to weaning
S49c_HF_1


title: Rep3_1hrs_post_E2 [miRNA-seq]


title: Rep3_5hrs_post_E2 [miRNA-seq]


title: Holstein-Friesian calf, day 1 relative to weaning [S25c_HF_1]

description:
Holstein-Friesian calf, day 1 relative to weaning
S25c_HF_1


title: Holstein-Friesian calf, day 1 relative to weaning [S20c_HF_1]

description:
Holstein-Friesian calf, day 1 relative to weaning
S20c_HF_1


title: Rep3_3hrs_post_E2 [miRNA-seq]


title: Holstein-Friesian calf, day 1 relative to weaning [S48c_HF_1]

description:
Holstein-Friesian calf, day 1 relative to weaning
S48c_HF_1


title: Rep3_2hrs_post_E2 [miRNA-seq]


title: Rep3_0hrs_post_E2 [miRNA-seq]


title: Jersey calf, day 1 relative to weaning [S6c_J_1]

description:
Jersey calf, day 1 relative to weaning
S6c_J_1

value: Jersey


title: Jersey calf, day -14 relative to weaning [S85a_J_14]

description:
Jersey calf, day -14 relative to weaning
S85a_J_14


title: Jersey calf, day -14 relative to weaning [S9a_J_14]

description:
Jersey calf, day -14 relative to weaning
S9a_J_14


title: Rep3_4hrs_post_E2 [miRNA-seq]


title: Jersey calf, day -14 relative to weaning [S7a_J_14]

description:
Jersey calf, day -14 relative to weaning
S7a_J_14


title: Rep2_5hrs_post_E2 [miRNA-seq]


title: Rep2_3hrs_post_E2 [miRNA-seq]


title: Rep2_24hrs_post_E2 [miRNA-seq]


title: Rep2_12hrs_post_E2 [miRNA-seq]


title: CA-24h-PBMC

description: microRNA sequencing after 24h in rhesus neonates PBMC with CA16 infection

data_processing:
Adaptor sequences were ﬁrst trimmed from small RNA reads. After adaptor trimming, low-quality sequences, namely, those with undetermined nucleotides (Ns), those with quality scores (Q-scores) less than 10, and those with reads shorter than 18 nt, were discarded from all libraries.
Clipped high-quality sequences were clustered into unique reads, and sRNAs with a length of 18~35nt were identiﬁed.
non-coding RNAs, including ribosomal RNA (rRNA), transfer RNA (tRNA), and small nuclear RNA (snRNA), were eliminated based on reference sequences from Rfam (http://rfam.janelia.org/) and piRNA (http://pirnabank.ibab.ac.in/). Afterward, the clean reads were mapped to known miRNA precursors, and the mature miRNAs were deposited in miRBase 19.0 (available online: http://www.mirbase.org/).
Unmappable sequences were used to predict potentially novel candidate miRNAs with the Mfold RNA folding prediction web server (available online: http://mfold.rna.albany.edu/).
The samples were normalized by calculating tags per million of total RNA reads (TPM) and used to compare the relative abundances of specific miRNAs within each data set.
Supplementary_files_format_and_content: xlsx files are comprised of two sheets, one for known miRNAs, the other for novel miRNAs, and eacha sheet include gene_id,description and Tpm values for each Sample.

organism: Macaca mulatta

source_name: PBMC - CA16 infection - 24h

growth_protocol: PBMCs were isolated from EDTA-anticoagulated whole blood samples from healthy neonatal rhesus monkeys with no known infections or any known diseases. The PBMCs were isolated by Ficoll-Hypaque gradient centrifugation according to the manufacturer’s instructions. Then, PBMCs plated onto 6-well plates at 2×105 cells per well were cultivated in 1640 medium (Gibco, USA) supplemented with 10% fetal bovine serum (FBS, Gibco, USA) plus penicillin and streptomycin and incubated overnight at 37°C in 5% CO2 in a humidified incubator.

extract_protocol:
miRNA extraction from each group of cells was performed as previously described using a standard mirVana™ miRNA Isolation Kit (Ambion, USA) protocol. RNA integrity was then evaluated using RNA 6000 Nano LabChips on an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). To further confirm RNA quality, total RNA degradation was estimated by reviewing electropherograms and the RNA integrity number (RIN) of each sample. Only samples with preserved 18S and 28S peaks and RIN values greater than 7 were selected for miRNA profile analysis. Qualified miRNA from three independent experiments of each group was mixed together respectively and used for subsequent library construction and deep sequencing.
High-throughput sequencing technology，as a powerful tool for transcriptome analysis, is not limited to detecting known transcripts, but also facilitates the discovery of novel transcripts. Additionally, it has lower background noise and higher sensitivity than microarrays[24]. Small RNA library construction and sequencing was carried out by the National Engineering Center for Biochip in Shanghai on an Illumina Hi-seq 2000 platform system. For all samples, small RNA libraries were constructed using a TruSeq Small RNA sample preparation kit (Illumina, USA) following the manufacturer’s instructions and were sequenced with an Illumina Genome Analyzer II system.

treatment_protocol: The EV71 virus strain (sub-genotype C4, GenBank: EU812515.1) that originated from an epidemic in Fuyang, China in 2008 and the CA16 virus G20 strain (sub-genotype B, GenBank: JN590244.1), which originated from an HFMD patient in Guangxi in 2010, were propagated in PBMCs at a multiplicity of infection (MOI) of 1 the following day. Cells were infected in triplicate and collected at 0, 24 and 48 hours post infection (hpi). Cells infected with EV71 and CA16 for 0 hpi were used as controls. We defined the different experimental groups as EV71-0h, EV71-24h, EV71-48h, CA16-0h, CA16-24h and CA16-48h.

value: PBMC


title: Jersey calf, day -14 relative to weaning [S13a_J_14]

description:
Jersey calf, day -14 relative to weaning
S13a_J_14


title: Holstein-Friesian calf, day 1 relative to weaning [S33c_HF_1]

description:
Holstein-Friesian calf, day 1 relative to weaning
S33c_HF_1

value: Holstein-Friesian


title: Rep2_0hrs_post_E2 [miRNA-seq]


title: Rep2_6hrs_post_E2 [miRNA-seq]


title: Rep2_4hrs_post_E2 [miRNA-seq]


title: Rep2_8hrs_post_E2 [miRNA-seq]


title: Holstein-Friesian calf, day -14 relative to weaning [S32a_HF_14]

description:
Holstein-Friesian calf, day -14 relative to weaning
S32a_HF_14


title: CA-48h-PBMC

description: microRNA sequencing after 48h in rhesus neonates PBMC with CA16 infection

source_name: PBMC - CA16 infection - 48h


title: Jersey calf, day -14 relative to weaning [S77a_J_14]

description:
Jersey calf, day -14 relative to weaning
S77a_J_14


title: UV60J naked DNA

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

description: Library strategy: CPD-seq

data_processing:
Base calling by Torrent_Suite 5.0.4
Fastq files were separated into individual libraries using A1-A3 barcodes, and the barcode sequences were trimmed, using a custom perl script
Fastq files were aligned to the yeast genome (SacCer3 or SacCer3+pUC19) using bowtie2-2.2.6 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
Only reads mapping to dipyrimidine (dipy) damage coordinate were retained in BED file using custom perl script
BED files were converted to WIG file using COUNT function of IGVTools
Background values at dipyrimidines were generated in WIG file using custom perl script
Genome_build: SacCer3
Supplementary_files_format_and_content: WIG files containing counts of CPD damage reads filtered for only dipyrimidine mapping sequences and including background value of 0.0 for dipyrimidines with no mapped sequencing reads

organism: Saccharomyces cerevisiae

source_name: Yeast naked DNA

growth_protocol: Yeast cultures (BY4741) were grown in YPD (yeast extract, peptone, dextrose) to OD600=0.8 in a yeast shaker.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with 250 μl of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA), 250 μl of PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and 150 μl of acid-washed glass beads, and vortexed vigorously twice, 2 min each time. After adding 200 μl of TE (10mM Tris-HCl, pH 7.5, 1 mM EDTA) buffer, cell lysates were centrifuged and the supernatant was mixed with 1 ml of ethanol to precipitate DNA at room temperature for 5 min. DNA pellet was dissolved in 200 μl of TE and incubated with 2 μl of RNase A/T1 (ThermoFisher Scientific) at 37˚C for 1 hr to remove RNA. DNA was subsequently purified with PCI extraction, ethanol precipitated, and disolved in sterile deionized H2O. The purified genomic DNA was quantified and 12 μg of DNA was used for each sequencing library preparation.
CPD-seq procedure is adopted from the recently published emRiboSeq method (Nature Protocols 2015 10, 1433Ð1444). Briefly, DNA fragments were first ligated to a double-stranded adaptor DNA trP1, and free 3'-OHs were blocked by  terminal transferase and dideoxy-ATP.  CPD lesions were  cleaved with T4 endonuclease V and apurinic/apyrimidinic (AP) endonuclease, APE 1, to generage new 3'-OHs. DNA was then ligated to adaptor  A. Three different barcoded A adaptors (A1: AAGAGGAT; A2: TTCGTGAT; and A3: CCTGAGAT) were used to generate libraries for different time points. DNA was purified with Streptavidin beads and amplified for 6 cycles in a PCR reaction with primers complimentary to A and trP1, and the resulting DNA libraries were used for DNA sequencing.

treatment_protocol: Cells were collected and resuspended in sterile deionized H2O and irradiated with 125 J/m2 of UVC. After UV irradiation, cells were spun down and resuspended in pre-warm YPD medium (yeast extract, peptone, dextrose) for repair. Aliquots (10 ml of yeast culture) were taken before UV irradiation (No UV), immediately after UV irradiation (0hr), and at different repair time points as indicated. Cells were spun down and kept at -80˚C until genomic DNA isolation. For UV irradiation of naked DNA, a total of 15 ug of yeast genomic DNA (isolated from un-irradiated yeast cells) was spotted on a clean microscope cover glass, 10 ul in each spot.  The cover glass with DNA spots was irradiated with 60 J/m2 or 90 J/m2 of UVC light.

value: Wild-type

tag: treatment

value: UV irradiated

tag: dose

tag: repair time


title: Jersey calf, day -14 relative to weaning [S6a_J_14]

description:
Jersey calf, day -14 relative to weaning
S6a_J_14


title: Holstein-Friesian calf, day 1 relative to weaning [S27c_HF_1]

description:
Holstein-Friesian calf, day 1 relative to weaning
S27c_HF_1


title: CA-0h-PBMC

description: microRNA sequencing after 0h in rhesus neonates PBMC with CA16 infection

source_name: PBMC - CA16 infection - 0h

tag: tissue


title: Rep2_2hrs_post_E2 [miRNA-seq]

tag: cell line


title: 2hr UV2

description: Library strategy: CPD-seq

source_name: Yeast cells

tag: genotype

value: 2 hr


title: Jersey calf, day -14 relative to weaning [S60a_J_14]

description:
Jersey calf, day -14 relative to weaning
S60a_J_14


title: Jersey calf, day -14 relative to weaning [S57a_J_14]

description:
Jersey calf, day -14 relative to weaning
S57a_J_14


title: EV-48h-PBMC

description: microRNA sequencing after 48h in rhesus neonates PBMC with EV71 infection

source_name: PBMC - EV71 infection - 48h


title: 0hr UV2

description:
Control for 20min and 2hr repair time points
Library strategy: CPD-seq

value: 0 hr


title: Rep2_1hrs_post_E2 [miRNA-seq]


title: EV-24h-PBMC

description: microRNA sequencing after 24h in rhesus neonates PBMC with EV71 infection

source_name: PBMC - EV71 infection - 24h


title: EV-0h-PBMC

description: microRNA sequencing after 0h in rhesus neonates PBMC with EV71 infection

source_name: PBMC - EV71 infection - 0h


title: 1hr UV

description: Library strategy: CPD-seq

value: 1 hr


title: No UV

description: Library strategy: CPD-seq


title: Holstein-Friesian calf, day -14 relative to weaning [S33a_HF_14]

description:
Holstein-Friesian calf, day -14 relative to weaning
S33a_HF_14


title: ChIP-seq analysis of N-Myc in human HSPCs, untreated, replicate 4

status: Public on Aug 18 2016

city: Cambridge

first: Charalampos

last: Lazaris

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

data_processing:
Basecalls performed using Illumina bcl2fastq.
ChIP-seq reads were aligned to the human genome (build hg19) using Bowtie2.
MACS2 was used for peak discovery. GenomicTools was used for ChIP-seq profile construction.
Genome_build: hg19
Supplementary_files_format_and_content: wig format containing genome-wide binding profile

source_name: bone marrow CD34+ cells, untreated

growth_protocol: Human bone marrow derived CD34+ cells were expanded for 3 days in cytokine supplemented medium (StemSpan CC110)

extract_protocol:
Thirty million human bone marrow CD34+ cells were fixed and used for ChIP and precipitated using 3 micrograms of antibody.
Libraries were generated as described before, including end-repair, A-tailing, adapter (Illumina Truseq system) ligation and PCR amplification.

treatment_protocol: no treatment

tag: cell type

value: human bone marrow hematopoietic stem and progenitor cells

tag: chip antibody

value: mouse monoclonal N-Myc antibody raised against N-terminal recombinant N-Myc of human origin, clone B8.4.B (Santa Cruz Biotechnology, Cat # sc-53993, Lot # K1315)


title: Jersey calf, day 1 relative to weaning [S85c_J_1]

description:
Jersey calf, day 1 relative to weaning
S85c_J_1


title: ChIP-seq analysis of N-Myc in human HSPCs, untreated, replicate 3


title: Holstein-Friesian calf, day -14 relative to weaning [S56a_HF_14]

description:
Holstein-Friesian calf, day -14 relative to weaning
S56a_HF_14


title: Holstein-Friesian calf, day -14 relative to weaning [S49a_HF_14]

description:
Holstein-Friesian calf, day -14 relative to weaning
S49a_HF_14


title: Holstein-Friesian calf, day -14 relative to weaning [S27a_HF_14]

description:
Holstein-Friesian calf, day -14 relative to weaning
S27a_HF_14


title: UV90J naked DNA

description: Library strategy: CPD-seq


title: Sequencing analysis of input in human HSPCs, untreated, replicate 3

value: none (input)


title: ChIP-seq analysis of N-Myc in human HSPCs, untreated, replicate 1


title: Healthy

city: Seoul

first: Jae-Hyung

address: 26 Kyungheedae-ro, Dongdaemun-gu

institute: Kyung Hee University

data_processing:
Illumina Casava software was used for basecalling.
All sequencing raw reads were aligned to the human genome reference hg19 using the GSNAP alignment tool (2013-11-27). Only uniquely and properly mapped read pairs were used for further analysis.
Expression levels of genes, the RPKM (reads per kilobase of exon per million mapped reads) measure was calculated (MORTAZAVI et al. 2008)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Gingival tissue samples from healthy individuals

extract_protocol:
Frozen tissues were disrupted in the lysis solution of mirVana RNA isolation kit (Thermo Fisher Scientific) using disposable pestle grinder system (Thermo Fisher Scientific).
After purification of mRNA molecules by poly-T oligo-attached magnetic beads followed by fragmentation, the RNA of approximately 300 bp size was isolated using gel electrophoresis. The cDNA synthesis and library construction was performed using the Illumina Truseq RNA sample preparation kit (Illumina, San Diego, CA) following the manufacturer’s protocol.

treatment_protocol: Gingival tissue samples were collected from chronic periodontitis patients or healthy individuals. On the basis of clinical and radiographic criteria, periodontitis-affected site had a probing depth of ≥ 4 mm, clinical attachment level of ≥ 4 mm, and bleeding on probing. A total of 10 gingival samples were collected from 9 periodontal healthy patients who visited Kyungpook National University hospital. Similarly, a total of 10 periodontitis tissue samples were obtained from 4 periodontitis patients with pocket depth of 4~6 mm, and 3 severe periodontitis patients with pocket depth of 7 mm or deeper. All patients were non-smoking and did not have untreated metabolic/systemic diseases nor associated with infection/autoimmune diseases at the time of tissue collection. The size of 3 mm2 gingival biopsies were obtained from the marginal gingiva during periodontal flap surgery and immediately stored in RNAlater solution (Thermo Fisher Scientific, Waltham, MA) at -70oC after removal of blood by brief washing in phosphate buffered saline. The study was approved by the institutional review board of the Kyungpook National University hospital with informed consent from all patients.

tag: disease

value: Healthy


title: 20min UV2

description: Library strategy: CPD-seq

value: 20 min


title: Periodontitis

source_name: Gingival tissue samples from chronic periodontitis patients

value: Chronic periodontitis


title: H3K9ac_DMSO_ChIPSeq

city: Geneva

first: Guillaume

last: Rey

address: Campus Biotech, Chemin des Mines 9

country: Switzerland

institute: University of Geneva

description:
NGS-9047_0559
NGS-9047_0565
CLOCK_BMAL1_DMSO_peaks.quantif.txt
CLOCK_BMAL1_6AN_peaks.quantif.txt

data_processing:
RNASeq: rRNA filtering with Bowtie
RNASeq: Tag mapping with TopHat
RNASeq: quantification with Cufflinks
ChIPSeq: Tag mapping with Bowtie2
CHIPSeqHOMER software suite for downstream analyses
Genome_build: RNASeq: hg38
Genome_build: ChIPSeq: hg38
Supplementary_files_format_and_content: RNASeq - cufflinks output files
Supplementary_files_format_and_content: ChIPSeq - HOMER output files

source_name: U2OS cells stably expressing Bmal1:Luc

growth_protocol: Bmal1:luc U2OS cells were grown in DMEM using standard cell culture methods.

extract_protocol:
RNA-Seq: Standard RNA extraction with Zymo Direct-zol™ RNA kits.  ChIP-Seq: Crosslinked nuclei from U2OS cells were sonicated and protein-DNA complexes were isolated with the following antibodies: anti-CLOCK (NB100-126; Novus Biologicals), anti-BMAL1 (ab3350; Abcam), anti-H3K9ac (ab4441; Abcam) and anti-H3K4me3 (#39159; Active Motif).
Illumina TrueSeq platform compatible dual-indexed multiplex library protocol was followed.

treatment_protocol: RNA-Seq: Cells were treated with 5mM 6AN or control (DMSO) and RNA was extracted at the indicated time points.  ChIP-Seq: Cells were treated with 5mM 6AN or control (DMSO) and RNA was extracted after 24h.

value: osteosarcoma cell line U2OS stably expressing Bmal1:Luc

tag: agent

value: DMSO

value: anti-H3K9ac (ab4441; Abcam)


title: H3K4me3_DMSO_ChIPSeq

description:
NGS-9043_0559
NGS-9043_0565
CLOCK_BMAL1_DMSO_peaks.quantif.txt
CLOCK_BMAL1_6AN_peaks.quantif.txt

value: anti-H3K4me3 (#39159; Active Motif)


title: Holstein-Friesian calf, day -14 relative to weaning [S20a_HF_14]

description:
Holstein-Friesian calf, day -14 relative to weaning
S20a_HF_14


title: Holstein-Friesian calf, day -14 relative to weaning [S48a_HF_14]

description:
Holstein-Friesian calf, day -14 relative to weaning
S48a_HF_14


title: H3K4me3_6AN_ChIPSeq

description:
NGS-9045_0559
NGS-9045_0565
CLOCK_BMAL1_DMSO_peaks.quantif.txt
CLOCK_BMAL1_6AN_peaks.quantif.txt


title: 0hr UV

description: Library strategy: CPD-seq

tag: strain


title: Input_DMSO_ChIPSeq

description:
NGS-9041_0559
ALL_peaks_merged.txt
CLOCK_BMAL1_DMSO_peaks.quantif.txt
CLOCK_BMAL1_6AN_peaks.quantif.txt


title: CLOCK_6AN_ChIPSeq

description:
NGS-9039_0559
ALL_peaks_merged.txt
CLOCK_BMAL1_DMSO_peaks.quantif.txt
CLOCK_BMAL1_6AN_peaks.quantif.txt

value: anti-CLOCK (NB100-126; Novus Biologicals)


title: ChIP-seq analysis of N-Myc in human HSPCs, untreated, replicate 2


title: ILC3B_K4me3_WT

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: ChIPed DNA

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

source_name: ILC3B K4me3 WT

growth_protocol: 8 to 9 weeks-old mice housed at the Weizmann Institute animal facility

extract_protocol:
Cells were extracted using the lamina propria dissociation kit (Miltenyi Biotech). Cells were crosslinked and FACS sorted into MACS buffer and Chromatin was analysed using iChIP (Lara-Aatiaso et al.) with our new modification iChIP-IVT
protocol developed by (Lara-Astiaso et al.) with our modification iChIP-IVT.

treatment_protocol: mice were given a combination of vancomycin (0.5 g/l), ampicillin (1 g/l), kanamycin (1 g/l), and metronidazole (1 g/l) in their drinking water.

value: Small intestine lamina propria

tag: chip antibody1


title: Sequencing analysis of input in human HSPCs, untreated, replicate 4


title: Sequencing analysis of input in human HSPCs, untreated, replicate 2


title: Sequencing analysis of input in human HSPCs, untreated, replicate 1


title: ILC3A_K27Ac_WT

description: ChIPed DNA

source_name: ILC3A K27Ac WT


title: Input_6AN_ChIPSeq

description:
NGS-9051_0559
ALL_peaks_merged.txt
CLOCK_BMAL1_DMSO_peaks.quantif.txt
CLOCK_BMAL1_6AN_peaks.quantif.txt


title: Holstein-Friesian calf, day -14 relative to weaning [S25a_HF_14]

description:
Holstein-Friesian calf, day -14 relative to weaning
S25a_HF_14

value: Holstein-Friesian


title: ILC2A_K27Ac_WT

description: ChIPed DNA

source_name: ILC2A K27Ac WT


title: ILC1B_K4me2_WT

description: ChIPed DNA

source_name: ILC1B K4me2 WT


title: BMAL1_6AN_ChIPSeq

description:
NGS-9035_0559
ALL_peaks_merged.txt
CLOCK_BMAL1_DMSO_peaks.quantif.txt
CLOCK_BMAL1_6AN_peaks.quantif.txt

value: anti-BMAL1 (ab3350; Abcam)


title: ILC3B_K27Ac_WT

description: ChIPed DNA

source_name: ILC3B K27Ac WT


title: CLOCK_DMSO_ChIPSeq

description:
NGS-9037_0559
ALL_peaks_merged.txt
CLOCK_BMAL1_DMSO_peaks.quantif.txt
CLOCK_BMAL1_6AN_peaks.quantif.txt


title: H3K9ac_6AN_ChIPSeq

description:
NGS-9048_0559
NGS-9048_0565
CLOCK_BMAL1_DMSO_peaks.quantif.txt
CLOCK_BMAL1_6AN_peaks.quantif.txt


title: ILC2A_K4me3_WT

description: ChIPed DNA

source_name: ILC2A K4me3 WT


title: ILC1A_K4me2_WT

description: ChIPed DNA

source_name: ILC1A K4me2 WT


title: ILC1B_K27Ac_WT

description: ChIPed DNA

source_name: ILC1B K27Ac WT


title: ILC3B_K4me2_WT

description: ChIPed DNA

source_name: ILC3B K4me2 WT


title: ILC2B_K4me3_WT

description: ChIPed DNA

source_name: ILC2B K4me3 WT


title: ILC3A_K4me2_WT

description: ChIPed DNA

source_name: ILC3A K4me2 WT


title: BMAL1_DMSO_ChIPSeq

description:
NGS-9033_0559
ALL_peaks_merged.txt
CLOCK_BMAL1_DMSO_peaks.quantif.txt
CLOCK_BMAL1_6AN_peaks.quantif.txt


title: ILC3A_K4me3_WT

description: ChIPed DNA

source_name: ILC3A K4me3 WT


title: ILC2A_K4me2_WT

description: ChIPed DNA

source_name: ILC2A K4me2 WT


title: ILC1A_K27Ac_WT

description: ChIPed DNA

source_name: ILC1A K27Ac WT


title: ILC1B_K4me3_WT

description: ChIPed DNA

source_name: ILC1B K4me3 WT


title: ILC1A_K4me3_WT

description: ChIPed DNA

source_name: ILC1A K4me3 WT


title: ILC2B_K27Ac_WT

description: ChIPed DNA

source_name: ILC2B K27Ac WT


title: WT_ILC3_B2T1.M (4.07)

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
alignment: hisat 0.1.5  with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8).
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl rna mm9 -d <List of tag dir> -count 3utr -condenseGenes -strand + -norm 1e7
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

extract_protocol:
Cells were extracted using the lamina propria dissociation kit (Miltenyi Biotech). Cells were FACS sorted into lysis buffer and RNA was processed from the lysates
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science
3' RNA-seq for digital gene expression quantitation

value: C57Bl/6 ROR<gamma>t-GFP

tag: organ

tag: selection marker


title: WT_ILC3_B1T3


title: ILC3_44_k4me2_Abx

description: ChIPed DNA

source_name: ILC3 44 k4me2 Abx


title: ILC2_45_k4me2_Abx

description: ChIPed DNA

source_name: ILC2 45 k4me2 Abx


title: ILC2_44_k4me2_Abx

description: ChIPed DNA

source_name: ILC2 44 k4me2 Abx


title: ILC1_45_k4me2_Abx

description: ChIPed DNA

source_name: ILC1 45 k4me2 Abx


title: Abx_ILC3_64

value: vancomycin (0.5 g/l), ampicillin (1 g/l),kanamycin (1 g/l), and metronidazole (1 g/l)


title: WT_ILC3_B2T3.M (4.65)


title: ILC2B_K4me2_WT

description: ChIPed DNA

source_name: ILC2B K4me2 WT


title: WT_ILC2_B2T3


title: WT_ILC2_B2T1


title: ILC1_44_k4me2_Abx

description: ChIPed DNA

source_name: ILC1 44 k4me2 Abx


title: WT_ILC2_B1T1


title: WT_ILC3_B2T2.M (4.84)


title: WT_ILC1_B2T2


title: WT_ILC1_B1T3


title: WT_ILC1_B1T2


title: Abx_ILC1_65


title: Abx_ILC3_65


title: WT_ILC3_B1T2


title: WT_ILC2_B2T2


title: WT_ILC3_B1T1


title: ILC3_77

description: Single read (read2 used to read sample barcodes and UMI only)

data_processing:
fastq using bcl2fastq
alignment using bowtie2  (--local,  mm9)
filter out reads that align to same place and sequence on R2 from nucleotides #1 to #15 are identical
makeTagDirectory -tbp
makeUCSCfile  -bigWig -fsize 1e20
Genome_build: mm9

source_name: ILC3 77

extract_protocol:
Cells were extracted using the lamina propria dissociation kit (Miltenyi Biotech). Cells were FACS sorted into MACS buffer and the open chromatin was profiled by the ATAC-seq protocol developed by (Buenrostro et al., 2013) with modifications described by (Lara-Astiaso et al., 2014).
protocol developed by (Buenrostro et al., 2013).


title: ILC1_76

source_name: ILC1 76


title: ILC2_77

source_name: ILC2 77


title: ILC3_45_k4me2_Abx

description: ChIPed DNA

source_name: ILC3 45 k4me2 Abx


title: Abx_ILC2_65


title: Abx_ILC2_64


title: WT_ILC2_B1T2


title: ILC3_WT89

source_name: ILC3 WT89


title: ILC2_WT92

source_name: ILC2 WT92


title: WT_ILC2_B1T3


title: WT_ILC1_B2T1


title: ILC3_WT92

source_name: ILC3 WT92


title: ILC1_WT89

source_name: ILC1 WT89


title: ILC3_76

source_name: ILC3 76


title: AB830

description: Note: Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header

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

extract_protocol:
Cells were extracted using the lamina propria dissociation kit (Miltenyi Biotech).
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantitation

value: Germ free

tag: developmental stage

value: adult


title: Abx_ILC1_64


title: ILC1_WT92

source_name: ILC1 WT92


title: ILC2_WT89

source_name: ILC2 WT89


title: AB831


title: ILC2_76

source_name: ILC2 76


title: WT_ILC1_B2T3


title: ILC1_77

source_name: ILC1 77


title: AB724


title: AB827


title: AB723


title: AB826


title: AB721


title: WT_ILC1_B1T1


title: AB824


title: AB719


title: AB825


title: AB726


title: AB714


title: AB718


title: AB828


title: AB727


title: AB716


title: AB712


title: AB720


title: AB710


title: AB711


title: AB713


title: AB715


title: AB829


title: AB725


title: AB709


title: AB682


title: AB642


title: AB681


title: AB643


title: AB684


title: AB641


title: AB717


title: AB589

source_name: antibiotics ILC


title: AB636


title: AB637


title: AB639


title: AB638


title: AB586


title: AB577


title: AB588


title: AB587


title: AB583


title: p28.2

first: Spyros

last: Darmanis

address: Clark Center, E300

department: Bioengineering

description:
Whole hippocampal tissue lysate
Tissue_sample_14

data_processing:
Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65).  We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore  (--stringency 1).
Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ).
Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample

source_name: hippocampus

extract_protocol:
Clontech SMARTer Kit version: v4
Qiagen AllPrep DNA/RNA Univeral Kit
Clontech's SMARTer RT and preamplification protocol
Nextera tagmentation protocol

tag: sample type

value: tissue

tag: age

value: post natal day 28

tag: cell/tissue type

value: hippocampus

tag: replicate

value: independent replicate 2


title: p7.1

description:
Whole hippocampal tissue lysate
Tissue_sample_4

value: post natal day 7

value: independent replicate 1


title: AB582

tag: treatment


title: p7.2

description:
Whole hippocampal tissue lysate
Tissue_sample_5


title: p28.3

description:
Whole hippocampal tissue lysate
Tissue_sample_15

value: independent replicate 3


title: AB454


title: p21.3

description:
Whole hippocampal tissue lysate
Tissue_sample_12

value: post natal day 21


title: p21.2

description:
Whole hippocampal tissue lysate
Tissue_sample_11


title: p28.1

description:
Whole hippocampal tissue lysate
Tissue_sample_13


title: p21.1

description:
Whole hippocampal tissue lysate
Tissue_sample_10


title: AB683


title: C99

description:
Single cell from mouse hippocampus
Single_cell_20

source_name: CA1 regular-spiking interneuron

extract_protocol:
Clontech SMARTer Kit version: v3
RNA extraction method: NA
Clontech's SMARTer RT and preamplification protocol
Nextera tagmentation protocol

value: single cell

value: post natal week 3-4

value: CA1 cholecystokinin cell


title: C97

description:
Single cell from mouse hippocampus
Single_cell_18

source_name: CA1 pyramidal cell

value: CA1 pyramidal cell


title: C95

description:
Single cell from mouse hippocampus
Single_cell_16


title: C94

description:
Single cell from mouse hippocampus
Single_cell_15