title: BR.repo.min.Pc_DamIDSeq_rep2

description: DamID system used: DamFLP

data_processing:
Library strategy: DamID-Seq
Basecalling and filtering were performed using standard software of the Illumina HiSeq 2000.
The 51bp reads were first parsed (using custom scripts and cutadapt (Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17.1,10-2, 2011; http://dx.doi.org/10.14806/ej.17.1.200)) to extract the genomic DNA. The genomic DNA sequences were aligned to the reference genome (dm3) using bowtie2 with default parameters. Reads that did not align or aligned more than once were discarded. Also reads with a MAPQ score of less than 25 were discarded. Reads were then summed per GATC fragment, using HTSeq (Anders, S. et al. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics 31(2), 166-9, 2015). Next, the chromosomes “U”, “M” and “Uextra” were excluded from the subsequent analysis.
For the biological samples which were generated using multiple technical replicates ( uninduced Dam only controls from larval central brains), the read counts were summed over the technical replicates. Next,  the counts were normalized to the total number of reads per sample. For each biological replicate of the same tissue or cell type (larval central brain, larval fat bodies and repo+ glial cells of larval central brain), the normalized DamID scores were calculated as the log2 of the ratio of the Polycomb and Dam only control. Finally, the normalized DamID scores were averaged over the 2 biological replicates.
Genome_build: dm3
Supplementary_files_format_and_content: tabular text files, containing columns for GATC-fragment-ID, chromosome, start, end, DamID scores

extract_protocol:
Two μl of Proteinase K (20 mg/ml) [Roche, 03115887001] were added to dissected central brains and the sample was incubated at 65°C for 6 hours. Next, 1 μl of RNase A (100 mg/ml) [QIAGEN, 1007885] was added and the sample was incubate at 37°C for 30 minutes. The lysate was transferred to a pre-spun (1 minute at 14,000 rpm just prior to use) phase lock gel light 1.5ml tube [5prime, 2302800] and 100 μl of phenol:chloroform:isoamylalcohol (25:24:1) [Sigma-Aldrich, P2069] were added. The sample was mixed well by shaking and the tube was spun for 5 minutes at 14,000 rpm at room temperature. The upper phase (~90 μl) was transferred into a new tube. To precipitate DNA, 1 µl of glycogen (20 mg/ml) [Fermentas, R0561], 10 µl of 3M NaAc (pH 5.2) and 300 µl of ethanol were added, mixed well by inversion and the solution was kept overnight at -20°C. The tube was spun for 30 minutes at 14,000 rpm at 4°C. The supernatant was removed and the pellet was washed with 500 µl of ice cold 70% ethanol. The tube was spun for 5 minutes at 14,000 rpm at 4°C. The supernatant was carefully removed and the pellet was air dried for 15 minutes and dissolved in 12 µl of double distilled water. DNA concentration was measured using a NanoDrop spectrophotometer. Dam-methylated fragments were amplified as described previously (Vogel, M.J. et al. Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nat Protoc 2(6), 1467-78, 2007) using 500 ng of DNA as an input.
The amplified methylated DNA fragments were purified using QIAquick PCR Purification kit (QIAGEN, 28104) according to the manufacturer’s instructions. DNA was eluted in nuclease-free water (Ambion, AM9938). From 200 ng to 3 µg of the purified PCR products were diluted in 100 μl of nuclease-free water and transferred into a snap-cap microTUBE (6 × 16 mm) with AFA fiber (Covaris, 520045). DNA was sheared using the Covaris S2 instrument at the following settings: duty cycle = 10%, intensity = 5, cycles/burst = 200, time = 45 sec (as consequence, power = ~23W and bath temperature = ~4°C). The size of the DNA fragments before shearing was usually a smear in the range of 250–2000 bp with a peak at 600 bp, after shearing this was reduced to become a range of 100–500 bp with a peak around 300 bp. After shearing, the DNA was purified and concentrated using Agencourt magnetic beads (Beckman Coulter, A63881; 160 µl of beads were added to 100 µl of sheared DNA solution). DNA was eluted in 50 µl of nuclease-free water. DNA concentration was measured using an Agilent BioAnalyzer 2100 DNA 7500 chip (Agilent, 5067-1506). One μg of sheared material was used to prepare Illumina sequencing library with TruSeq DNA HT Sample Prep Kit (Illumina, FC-121-2003) according to the manufacturer’s instructions. Seven cycles of PCR were performed. This step included sample indexing. The library was quantified on an Agilent BioAnalyzer 2100 DNA 7500 chip that lists the product size distribution and quantifies the concentration in µg/µl and in nM.

treatment_protocol: Central brains were dissected from 20 larvae in 1×PBS [140 mM NaCl, 10 mM PO4 Buffer, 3 mM KCl; Invitrogen cat. no. 18912-014] using forceps and dissection needles and collected in 100 μl TENS solution [100 mM Tris-HCl (pH 8.0); 5 mM EDTA (pH 8.0); 200 mM NaCl; 0.2% SDS] at room temperature.

value: pooled male and female

value: brain without ventral nerve cord

tag: dam-fusion protein

value: Dam-Polycomb


title: BR.wt_RNASeq_rep1

status: Public on Mar 17 2016

type: SRA

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description:
For each replicate, central brains were dissected from 5 larvae of each indicated genotype.
processed data file: RNA-seq_Counts.txt, DESeq-processed_FB.control_vs_BR.txt
BR.1

library_source: transcriptomic

data_processing:
Basecalling and filtering were performed using standard software of the Illumina HiSeq 2000.
For each sample, reads were mapped against the Drosophila reference genome (dm3) using TopHat (Trapnell, C. et al. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 25(9), 1105-11, 2009), which was supplied with a known set of gene models. In order to get per sample absolute counts for every gene, HTSeq (Anders, S. et al. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics 31(2), 166-9, 2015) was used.
Differentially expressed genes were identified by using the R package DESeq (Anders, S. and Huber, W. Differential expression analysis for sequence count data. Genome Biol 11(10), R106, 2010; Anders, S. et al. Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat Protoc 8(9), 1765-86, 2013).
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text files

molecule: total RNA

organism: Drosophila melanogaster

source_name: larval central brain

growth_protocol: Flies were raised at 25°C on standard cornmeal/molasses/agar medium.

extract_protocol:
Tissue was homogenized in TRIzol reagent in a 15ml tube using a polytron DI 18 disperser (IKA). Total RNA extraction was performed according to the TRIzol reagent manufacturer’s instructions. Briefly, 0.2× volumes of chloroform (st. amylene) (Biosolve, 030810) was added to the homogenate and the tube was shaken vigorously. The tube was incubated for 3 minutes at room temperature and spun for 1 hour at 4120×g at 4°C. Approximately 70% of the upper aqueous phase was transferred into a new 15ml tube and 0.5× volume of isopropanol (Sigma-Aldrich, 33539) was added and mixed. The tube was incubated for 10 minutes at room temperature and spun for 30 minutes at 4120×g at 4°C. The supernatant was removed and the pellet was washed twice with 80% ethanol (Sigma-Aldrich, 32221). The total RNA pellet was air-dried for 8 minutes, dissolved in an appropriate volume of nuclease free water (Ambion, AM9938) and quantified using a NanoDrop spectrophotometer. The total RNA was further purified using the RNeasy MinElute Cleanup Kit (QIAGEN, 74204) according to the manufacturer’s instructions. Quality (RIN>8) and quantity of the total RNA was assessed by using an Agilent BioAnalyzer 2100 Nano chip (Agilent, 5067-1511).
Illumina TruSeq mRNA libraries were generated using the TruSeq RNA Library Preparation Kit v2 (Illumina, RS-122-2001/2) according to the manufacturer’s instructions. Briefly, polyadenylated RNA from intact total RNA was purified using oligo-dT beads. Following purification, the RNA was fragmented, random primed and reverse transcribed using SuperScript II Reverse Transcriptase (Invitrogen, 18064-014). Second strand synthesis was accomplished by using Polymerase I and RNase H. The generated cDNA fragments were 3′ end adenylated and ligated to Illumina paired-end sequencing adapters and subsequently amplified by 15 cycles of PCR. The libraries were analyzed using an Agilent BioAnalyzer 2100 DNA 7500 chip (Agilent, 5067-1506), diluted and pooled equimolar into a 10nM sequencing pool.

treatment_protocol: Central brains were dissected from 30 larvae in 1×PBS [140 mM NaCl, 10 mM PO4 Buffer, 3 mM KCl; Invitrogen cat. no. 18912-014] using forceps and dissection needles and collected in TRIzol reagent (Invitrogen, 15596-018) on ice.

tag: gender

value: male

tag: genotype

value: equal mix of the following 6 lines: [1] y,w; M{FL.hsp70P-Dam[4-HT-intein@L127C]}ZH51C  [2] y,w; M{FL.hsp70P-Dam[4-HT-intein@L127C]-PC}ZH51C  [3] y,w; M{FL.hsp70P-Dam[4-HT-intein@L127C]-H1}ZH51C  [4] y,w; M{FL.hsp70P-Dam[4-HT-intein@L127C]-HP1}ZH51C  [5] y,w; M{FL.hsp70P-Dam[4-HT-intein@L127C]-MRG15}ZH51C  [6] y,w; M{FL.hsp70P-Dam[4-HT-intein@L127C]-BRM}ZH51C

tag: developmental stage

value: wandering third instar larvae

tag: tissue


title: Sample_AH-26 Glioblastoma

city: Houston

first: Amy

middle: B

last: Heimberger

state: TX

address: 1400 Holcombe Blvd., FC7.2000

department: Neurosurgery

country: USA

institute: The University of Texas MD Anderson Cancer Center

description: Glioblastoma tissue sample corresponding to Sample_AH-26

data_processing:
Reads were aligned with BWA 0.5.7 to both refseq Ensembl64 transcriptome and hg19 genome.
Genome Analysis Toolkit (GATK) 2.8.1 was used to do base recalibration.
RNA-SeQC v1.1.7 was used to evaluate and report the sequencing quality and produce the fpkm gene expression values per sample.
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression profiles (fpkm) for 32 individual samples were assembled into one plain tex file separated by tab in which rows for genes and columns for samples.

organism: Homo sapiens

source_name: brain

extract_protocol:
Extract RNA using Qiagen Allprep DNA/RNA mini kit.
Tru-Seq RNA sample prep kit

treatment_protocol: PolyA selection

tag: tumor type

value: glioblastoma (Grade IV)


title: Gh2c rep1

city: Chongqing

first: quan

last: sun

address: Chongwen road 2#

department: College of Bioinformation

country: China

institute: Chongqing University of Posts and Telecommunications

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to cotton genome no more than 5 mismatches using the SOAP aligner/SOAP2 software after low-quality reads (reads with unknown sequences ‘N’), adaptor sequence fragments, and empty reads were removed
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
The GeneIDs in the processed data files represent (e.g. CotAD_22466, CotAD_64340, etc.), The cotton genome and cds sequences we download form http://cgp.genomics.org.cn (Free to register to use). The reference :(Li F, Fan G, Lu C, Xiao G, Zou C, Kohel RJ, Ma Z, Shang H, Ma X, Wu J et al: Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution.
Genome_build: ASM98774v1; NCBI WGS Project: LBLM01 (Gossypium hirsutum)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Gossypium hirsutum

source_name: stem tip

extract_protocol:
RNA was harvested using Plant RNA EASYspin Plus Kit(Aidlab, Peking, China).
RNA and miRNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Huazhong 94-3130

value: shoot apical

tag: age

value: the pre-budding stage, six pieces of leaf

value: normal branch


title: Dark-housed Emx-Cre 7.5hr light rep 2

city: Boston

first: Ivo

last: Spiegel

state: MA

address: 220 Longwood Ave

department: Department of Neurobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mm9 genome using TopHat (v2.0.13) and Bowtie (2.1.0.0)42. On average, ~70% of mapped IP reads were uniquely mapped to the mm9 genome allowing for 0 mismatches and were therefore assignable to genic features. Values from all IP libraries were normalized using Cufform (v2.2.1), and values from the Cuffnorm output file 'genes-Count_Table' (normalized reads) were taken as a proxy for gene expression. P-values were generated for each Cre-line for each Dark-Light conditions using Cuffdiff (v2.2.1) using the timeseries (-T) flag based on 3 biological replicates.
Genome_build: mm9
Supplementary_files_format_and_content: Standard bigWig-formatted files (.bw) represent bwa-aligned reads piled up with single-base-pair resolution and then averaged over tiles of width 20bp.
Supplementary_files_format_and_content: Values from all IP libraries were normalized using Cufform (v2.2.1), and values from the Cuffnorm output file 'genes-Count_Table' (normalized reads) were taken as a proxy for gene expression and are shown in the .xlsx file.  The first set of 25 columns represent the mean of 3 bioreplicates for each Cre line and each stimulation condition; each subsequent set of 25 reports one of 3 bioreplicates.

organism: Mus musculus

source_name: Mouse brain

extract_protocol:
RiboTag-purification accoriding to Spiegel et al (Cell, 2014) and Sanz et al (PNAS 2009)
All samples had RIN numbers above 8.0. 5-10 ng of RNA were SPIA-amplified with the Ovation RNA Amplification System V2, yielding 5-8 μg of cDNA per sample. SPIA-amplified samples from RiboTag-IP fractions were processed in triplicate. For preparing Seq-libraries, 2 mg of each amplified cDNA were fragmented to 200-400 bp using a Covaris S2 sonicator (Acoustic wave instruments) using the following parameters: duty cycle = 10%, intensity = 5, cycles per burst = 200, time: = 60 seconds, total time = 5 minutes. After validating the fragment length of the sonicated cDNA using a 2100 BioAnalyzer, 2 mg of the fragmented cDNA were used for Seq library preparation using the PrepX DNA kit on an Apollo 324 robot (IntegenX). Quality of completed Seq-libraries was assessed using a 2100 BioAnalyzer (Agilent, Palo Alto, CA) and the completed libraries were sequenced on an Illumina HiSeq 2000 instrument per the manufacturer's standard protocols for single-end 50-bp sequencing with single-index reads.
SPIA amplification of 5-10 ng ribosome bound RNA

value: 8 week

value: Visual cortex

tag: cre line

value: Emx

tag: housing

value: Dark

tag: light exposure

tag: replicate


title: Sample_AH-25 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-25


title: BR.repo.min.Pc_DamIDSeq_rep1

description: DamID system used: DamFLP

library_source: genomic

molecule: genomic DNA

source_name: repo+ glial cells of larval central brain


title: Dark-housed Emx-Cre 7.5hr light rep 1


title: Gh1e rep 3

value: seedling stage, have two pieces of leaf

value: nulliplex-branch


title: Standard-housed Emx-Cre rep 3

value: Standard


title: Dark-housed Emx-Cre 3hr light rep 3


title: BR.repo.min.Dam_DamIDSeq_rep2

description: DamID system used: DamFLP

value: pooled male and female

value: brain without ventral nerve cord

value: Dam only


title: BR.repo.min.Dam_DamIDSeq_rep1

description: DamID system used: DamFLP


title: Dark-housed Emx-Cre 3hr light rep 2


title: Sample_AH-24 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-24


title: Sample_AH-23 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-23


title: BR.wt_RNASeq_rep2

description:
For each replicate, central brains were dissected from 5 larvae of each indicated genotype.
processed data file: RNA-seq_Counts.txt, DESeq-processed_FB.control_vs_BR.txt
BR.2

value: male

value: equal mix of the following 6 lines: [1] y,w; M{FL.hsp70P-Dam[4-HT-intein@L127C]}ZH51C  [2] y,w; M{FL.hsp70P-Dam[4-HT-intein@L127C]-PC}ZH51C  [3] y,w; M{FL.hsp70P-Dam[4-HT-intein@L127C]-H1}ZH51C  [4] y,w; M{FL.hsp70P-Dam[4-HT-intein@L127C]-HP1}ZH51C  [5] y,w; M{FL.hsp70P-Dam[4-HT-intein@L127C]-MRG15}ZH51C  [6] y,w; M{FL.hsp70P-Dam[4-HT-intein@L127C]-BRM}ZH51C


title: FB.Pc_DamIDSeq_rep2

description: DamID system used: Dam4-HT-intein@L127C, induced by 25 µM 4-hydroxytamoxifen

source_name: larval fat bodies

growth_protocol: Flies were raised at 25°C on standard cornmeal/molasses/agar medium supplemented with 4-hydroxytamoxifen (Sigma-Aldrich, H7904) at a final concentration of 25 µM.

extract_protocol:
Four hundred μl of Lysis Buffer [5% sucrose; 100 mM Tris-HCl (pH 9.1); 50 mM EDTA (pH 8.0); 5% SDS] and 5 μl of Proteinase K (20 mg/ml) [Roche, 03115887001] were added to dissected fat bodies, the tissue was disrupted by passing through 21G needle 15-20 times and the sample was incubated at 55°C with 600 rpm shaking for 4 hours. Next, 2 μl of RNase A (100 mg/ml) [QIAGEN, 1007885] were added and the sample was incubate at 37°C for 30 minutes. The lysate was transferred to a pre-spun (1 minute at 14,000 rpm just prior to use) phase lock gel heavy 1.5ml tube [5prime, 2302810] and 500 μl of phenol:chloroform:isoamylalcohol (25:24:1) [Sigma-Aldrich, P2069] were added. The sample was mixed well by shaking and the tube was spun for 5 minutes at 14,000 rpm at room temperature. The upper phase was transferred to another pre-spun phase lock gel heavy 1.5ml tube. Five hundred μl of phenol:chloroform:isoamylalcohol (25:24:1) [Sigma-Aldrich, P2069] were added, mixed well by shaking and the tube was spun for 5 minutes at 14,000 rpm at room temperature. The upper phase (~400 μl) was transferred into a new tube. To precipitate DNA, 1 µl of glycogen (20 mg/ml) [Fermentas, R0561], 40 µl of 5M NaCl and 1 ml of ethanol were added, mixed well by inversion and the solution was kept overnight at -20°C. The tube was spun for 1 hour at 14,000 rpm at 4°C. The supernatant was removed and the pellet was washed with 500 µl of ice cold 70% ethanol. The tube was spun for 15 minutes at 14,000 rpm at 4°C. The supernatant was carefully removed and the pellet was air dried for 15 minutes and dissolved in 500 µl of double distilled water. The solution was applied to a microcon YM-30 centrifugal filter (Millipore, 42410) and spun for 12 minutes at 14,000×g at room temperature. This reduced the sample volume to ~10 µl. DNA was collected by inverting the microcon YM-30 centrifugal filter in a fresh tube and spinning for 3 minutes at 1,000×g at room temperature. The sample volume was adjusted to 12 µl with double distilled water. DNA concentration was measured using a NanoDrop spectrophotometer. Dam-methylated fragments were amplified as described previously (Vogel, M.J. et al. Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nat Protoc 2(6), 1467-78, 2007) using 500 ng of DNA as an input.
The amplified methylated DNA fragments were purified using QIAquick PCR Purification kit (QIAGEN, 28104) according to the manufacturer’s instructions. DNA was eluted in nuclease-free water (Ambion, AM9938). From 200 ng to 3 µg of the purified PCR products were diluted in 100 μl of nuclease-free water and transferred into a snap-cap microTUBE (6 × 16 mm) with AFA fiber (Covaris, 520045). DNA was sheared using the Covaris S2 instrument at the following settings: duty cycle = 10%, intensity = 5, cycles/burst = 200, time = 45 sec (as consequence, power = ~23W and bath temperature = ~4°C). The size of the DNA fragments before shearing was usually a smear in the range of 250–2000 bp with a peak at 600 bp, after shearing this was reduced to become a range of 100–500 bp with a peak around 300 bp. After shearing, the DNA was purified and concentrated using Agencourt magnetic beads (Beckman Coulter, A63881; 160 µl of beads were added to 100 µl of sheared DNA solution). DNA was eluted in 50 µl of nuclease-free water. DNA concentration was measured using an Agilent BioAnalyzer 2100 DNA 7500 chip (Agilent, 5067-1506). One μg of sheared material was used to prepare Illumina sequencing library with TruSeq DNA HT Sample Prep Kit (Illumina, FC-121-2003) according to the manufacturer’s instructions. Seven cycles of PCR were performed. This step included sample indexing. The library was quantified on an Agilent BioAnalyzer 2100 DNA 7500 chip that lists the product size distribution and quantifies the concentration in µg/µl and in nM.

treatment_protocol: Fat bodies were dissected from 10 larvae in 1×PBS [140 mM NaCl, 10 mM PO4 Buffer, 3 mM KCl; Invitrogen cat. no. 18912-014] using forceps and dissection needles and collected in 1×PBS solution on ice.

value: wandering third instar larvae

value: fat bodies

value: Dam-Polycomb


title: Gh1c rep3

value: Huazhong 94-3130

value: shoot apical


title: FB.Pc_DamIDSeq_rep1


title: Sample_AH-28 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-28

value: glioblastoma (Grade IV)


title: Sample_AH-21 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-21


title: Dark-housed Emx-Cre 3hr light rep 1

value: 8 week

value: Visual cortex


title: Gh1e rep 1


title: Dark-housed Emx-Cre 1hr light rep 3

value: Emx

value: Dark


title: Gh1c rep2

value: seedling stage, have two pieces of leaf

value: normal branch


title: FB.Dam_DamIDSeq_rep2


title: Gh1c rep1


title: Sample_AH-20 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-20


title: Dark-housed Emx-Cre 1hr light rep 2


title: FB.Dam_DamIDSeq_rep1


title: Sample_AH-1 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-1


title: BR.Pc.m_DamIDSeq_rep2

description: DamID system used: Dam4-HT-intein@L127C, uninduced


title: Dark-housed Emx-Cre 1hr light rep 1


title: Gh1e rep 2

value: nulliplex-branch


title: Sample_AH-19 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-19


title: Dark-housed Emx-Cre rep 3


title: BR.Pc.m_DamIDSeq_rep1

value: brain without ventral nerve cord


title: Dark-housed Emx-Cre rep 2


title: BR.Dam.m_DamIDSeq_rep2

value: Dam only


title: Sample_AH-18 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-18


title: Dark-housed Emx-Cre rep 1


title: Sample_AH-22 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-22


title: Sample_AH-17 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-17


title: nrpd1

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

description: small RNA

data_processing:
Briefly,clean reads with adapter trimmed were got from BGI. clean reads of size 18-85 nt were mapped to the Arabidopsis genome (TAIR10) using Bowtie (Langmead et al. 2009) with parameter -v 0 -k 10. Reads that can mapped to annotated structural RNAs were removed.
Genome_build: TAIR10
Supplementary_files_format_and_content: The bedGraph files were generated using genomeCoverageBed from bedtools with parameter  -bga -split

organism: Arabidopsis thaliana

source_name: seedling

extract_protocol: Small RNA samples were prepared from 2-week-old seedlings and were sequenced from BGI. To examine long small RNAs, small RNAs with length ~18-85nt were used.

value: nrpd1 mutant

value: seedling


title: P5 back skin_HF-ORS_2

city: New York

first: Michael

last: Rendl

state: NY

address: 1428 Madison Avenue

institute: Mount Sinai School of Medicine

data_processing:
All raw RNA sequencing reads were mapped to the mouse genome (mm10) with TopHat v2.0.3 coupled with the Bowtie2 aligner with default parameters.
Transcriptomes were assembled and fragments per kilo-base per million reads (FPKM) for each gene were computed with Cufflinks v2.1.1 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: P5 back skin_HF-ORS

extract_protocol:
Total RNA obtained from FACS-sorted cells was purified with the Absolutely RNA Nanoprep kit (Agilent), quantified with the NanoDrop spectrophotometer (Thermo Scientific) and measured for quality control by the Agilent Bioanalyzer. Samples with RIN (RNA integrity number) scores 8.8 and higher were further processed. 6ng starting material was reverse transcribed and amplified to 5-7µg cDNA with the RNA Ovation RNA-seq System V2 (NuGEN).
From 100ng amplified cDNA sequencing libraries were generated with 28 unique barcoded adapters (14 samples x 2 replicates) using the Ovation Ultralow DR Library System (NuGEN).

tag: strain background

value: mixture of FVB/N, C57BI/6J and CD1

value: postnatal day 5

value: back skin

tag: cell type

value: rest of the ORS

tag: cell fraction/population


title: BR.Dam.m_DamIDSeq_rep1

value: male

value: wandering third instar larvae


title: Sample_AH-15 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-15

value: glioblastoma (Grade IV)


title: P5 back skin_HF-SC_2

source_name: P5 back skin_HF-SC

value: Bulge stem cells precursors


title: P5 back skin_AA/ZZ-DP_2

source_name: P5 back skin_AA/ZZ-DP

tag: genotype/variation

value: Awl/Auchene and Zig-zag dermal papilla cells

value: Crabp1-GFP+/Lef1-RFP+/ITGA9Hi from dermal preparation of Crabp1-GFP


title: P5 back skin_G-DP_2

source_name: P5 back skin_G-DP

value: Guard dermal papilla cells

value: Crabp1-GFP-/Lef1-RFP+/ITGA9Hi from dermal preparation of Crabp1-GFP


title: Sample_AH-13 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-13


title: dcl234_nrpd1

description: small RNA

value: dcl2/3/4/nrpd1 mutant


title: Sample_AH-12 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-12


title: Sample_AH-14 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-14


title: P5 back skin_G/AA-DP_2

source_name: P5 back skin_G/AA-DP

value: Guard and Awl/Auchene dermal papilla cells

value: Sox2-GFP+/Lef1-RFP+/ITGA9Hi from dermal preparation of Sox2-GFP


title: smallRNA_Seq: dcl234

description: small RNA

data_processing:
Briefly,clean reads with adapter trimmed were got from BGI. clean reads of size 18-95 nt were mapped to the Arabidopsis genome (TAIR10) using Bowtie (Langmead et al. 2009) with parameter -v 0 -k 10. Reads that can mapped to annotated structural RNAs were removed.
Genome_build: TAIR10
Supplementary_files_format_and_content: The bedGraph files were generated using genomeCoverageBed from bedtools with parameter  -bga -split

extract_protocol: Small RNA samples were prepared from 2-week-old seedlings and were sequenced from BGI. To examine long small RNAs, small RNAs with length ~18-95 were used.

value: dcl234 mutant


title: smallRNA_Seq: dcl1234

description: small RNA

value: dcl1234 mutant

value: seedling


title: smallRNA_Seq: Col-0

description: small RNA

value: WT


title: Sample_AH-11 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-11


title: P5 back skin_ZZ-DP_2

source_name: P5 back skin_ZZ-DP

value: mixture of FVB/N, C57BI/6J and CD1

value: postnatal day 5

value: back skin

value: Zig-zag dermal papilla cells

value: Sox2-GFP-/Lef1-RFP+/ITGA9Hi from dermal preparation of Sox2-GFP


title: P5 back skin_Neg_2

source_name: P5 back skin_Neg

value: Mixture of negative cells

value: from dermal preparation of K14-H2BGFP


title: Sample_AH-10 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-10

value: glioblastoma (Grade IV)


title: BS_Seq: dcl1-201/2/3/4-2

description: treated with bisulfite

data_processing:
Raw data were first trimmed with adaptor and low-quality sequence (q<20) discarded
clean reads were mapped to the Arabidopsis genome (TAIR 10) using Bisulfite Sequence Mapping Program(BSMAP) allowing two mismatch
Genome_build: TAIR10
Supplementary_files_format_and_content: The wig files give methylation level for Cs (three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (converted_C / ( converted_C+ unconverted_C ) ).

source_name: 5-week seedling

extract_protocol: Genomic DNA was extracted from 2-week(or 5-week) seedlings and sent to BGI (Shenzhen, China) for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols.


title: Sample_AH-16 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-16


title: BS_Seq: dcl1-201/2/3/4-1

description: treated with bisulfite


title: miGb3e rep3

organism: Gossypium barbadense

value: shoot apical

value: the budding stage, about nine pieces of leaf

value: nulliplex-branch


title: P5 back skin_TAC_2

source_name: P5 back skin_TAC

value: Shh expressing matrix progenitors

value: K14-H2BGFPLo/Lef1-RFP+ from dermal preparation of K14-H2BGFP


title: BS_Seq: dcl2/3/4-A-1

description: treated with bisulfite


title: BS_Seq: dcl2/3/4-A-2

description: treated with bisulfite


title: miGb3e rep2


title: BS_Seq: Col-A-2

description: treated with bisulfite

value: Col-0 WT


title: miGb3c rep3

value: the budding stage, eleven pieces of leaf

value: normal branch


title: miGb3e rep1


title: BS_Seq: Col-A-1

description: treated with bisulfite

value: seedling


title: BS_Seq: ago4/6 replicate 2

description: treated with bisulfite

source_name: 2-week seedling


title: P5 back skin_Epi_2

source_name: P5 back skin_Epi

value: mixture of FVB/N, C57BI/6J and CD1

value: epidermal cells

value: K14-H2BGFP+ from epidermal preparation of K14-H2BGFP


title: P5 back skin_DF_2

source_name: P5 back skin_DF

value: postnatal day 5

value: back skin

value: Dermal fibroblasts

value: Lef1-RFP+/CD117-/ITGA9- from dermal preparation of K14-H2BGFP


title: miGb3c rep2

source_name: stem tip


title: P5 back skin_HF-ORS_1

value: rest of the ORS


title: BS_Seq: ago4/6 replaicate 1

description: treated with bisulfite


title: miGb2e rep3

value: shoot apical

value: pre-budding stage, about six pieces of leaf


title: BS_Seq: met1-1 replicate 2

description: treated with bisulfite


title: miGb3c rep1


title: miGb2e rep2

value: nulliplex-branch


title: P5 back skin_AA/ZZ-DP_1

value: Awl/Auchene and Zig-zag dermal papilla cells

value: Crabp1-GFP+/Lef1-RFP+/ITGA9Hi from dermal preparation of Crabp1-GFP


title: BS_Seq: ddc replicate 2

description: treated with bisulfite

value: ddc


title: miGb2e rep1


title: BS_Seq: met1-1 replicate 1

description: treated with bisulfite


title: P5 back skin_G-DP_1

value: Guard dermal papilla cells

value: Crabp1-GFP-/Lef1-RFP+/ITGA9Hi from dermal preparation of Crabp1-GFP


title: BS_Seq: ddc replicate 1

description: treated with bisulfite

value: seedling


title: P5 back skin_HF-SC_1

value: mixture of FVB/N, C57BI/6J and CD1

value: Bulge stem cells precursors


title: miGb2c rep3

value: pre-budding stage,about eight pieces of leaf

value: normal branch


title: P5 back skin_DP_2

source_name: P5 back skin_DP

value: postnatal day 5

value: back skin

value: Dermal papilla cells

value: Lef1-RFP+/ITGA9Hi from dermal preparation of K14-H2BGFP


title: BS_Seq: rdr1/2/6 replicate 2

description: treated with bisulfite


title: miGb2c rep2

value: shoot apical


title: P5 back skin_G/AA-DP_1

value: Guard and Awl/Auchene dermal papilla cells

value: Sox2-GFP+/Lef1-RFP+/ITGA9Hi from dermal preparation of Sox2-GFP


title: P5 back skin_ZZ-DP_1

value: Zig-zag dermal papilla cells

value: Sox2-GFP-/Lef1-RFP+/ITGA9Hi from dermal preparation of Sox2-GFP


title: BS_Seq: rdr1/2/6 replicate 1

description: treated with bisulfite


title: miGb2c rep1


title: P5 back skin_Neg_1

value: Mixture of negative cells

value: from dermal preparation of K14-H2BGFP


title: BS_Seq: dcl1-100

description: treated with bisulfite


title: BS_Seq: dcl2/3/4 replicate 2

description: treated with bisulfite


title: miGb1e rep 3

value: seedling stage, have two pieces of leaf

value: nulliplex-branch


title: miGb1e rep 2


title: P5 back skin_DP_1

value: mixture of FVB/N, C57BI/6J and CD1


title: BS_Seq: dcl2/3/4 replicate 1

description: treated with bisulfite

value: seedling


title: P5 back skin_DF_1

value: Dermal fibroblasts

value: Lef1-RFP+/CD117-/ITGA9- from dermal preparation of K14-H2BGFP


title: BS_Seq: nrpe1-11 replicate 2

description: treated with bisulfite


title: BS_Seq: nrpe1-11 replicate 1

description: treated with bisulfite


title: miGb1c rep3

value: normal branch


title: BS_Seq: nrpd1-3 replicate 2

description: treated with bisulfite


title: miGb1c rep1


title: Gb3e rep3

value: the budding stage, about nine pieces of leaf


title: BS_Seq: Col-0 repl1cate 2

description: treated with bisulfite

value: Col-0 WT


title: BS_Seq: nrpd1-3 replicate 1

description: treated with bisulfite


title: Gb3e rep2


title: BS_Seq: Col-0 replicate 1

description: treated with bisulfite


title: P5 back skin_Epi_1

value: postnatal day 5

value: back skin

value: epidermal cells

value: K14-H2BGFP+ from epidermal preparation of K14-H2BGFP


title: Healthy donor 7 pDCs

city: Parkville

first: CSL

last: Research

state: VIC

address: 30 Flemington Rd

country: Australia

institute: CSL Limited / bio21 Institute

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.58 and Real Time Analysis (RTA) v1.18.64, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 1.8.4 pipeline was used to generate the sequence data.
Reads were mapped to Homo sapiens GRCh37.p10 genome, using TopHat (TopHat v2.0.12, bowtie v2.2.5; Trapnell et al.,2009). TopHat parameters set to values other than default were --library-type fr-firststrand and --b2-very-sensitive.
Mapped reads were summaried on a gene level using Entrez ID gene annotation (NCBI 104, based on GRCh37.p10) and featureCounts (v1.4.6; Liao et al., 2014) software. The following featureCounts parameters were explicitly set: -t exon, -g gene_id, -s 2, and -Q 10.
Summarised read counts in this submission were NOT normalised nor filtered. We recommend using Bioconductor edgeR package functions: i) calcNormFactors (TMM method) to normalise between samples based on library sizes,  and ii) rpkm function to normalise between genes within a sample based on gene lengths (gene lengths are provided in all processed data files).
Genome_build: GRCh37.p10
Supplementary_files_format_and_content: All processed data files are in a tab delimited file format. They contain raw read counts summarised on a gene level according to NCBI 104 (Entez IDs) annotation.

molecule: polyA RNA

source_name: plasmacytoid dendritic cells

growth_protocol: Following culture, pDCs were isolated from PBMCs by FACS-sorting and immediately stored in RNAprotect cell reagent (Qiagen, Catalog number 76526) and frozen at -80 degrees celsius until RNA extraction.

extract_protocol:
RNA was extracted from pDCs using an Rneasy pus micro kit (Qiagen, catalog number 74034)
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Healthy donor PBMCs were cultured for 18 hours with 0.5μM CpG C, 0.5μg/ml imiquimod or media alone for 18 hours.

value: pDCs

value: blood

tag: donor

value: male

tag: stimulus

value: UT


title: Healthy donor 6 pDCs

tag: gender

value: female


title: Gb3e rep1

value: shoot apical

tag: genotype

value: nulliplex-branch


title: D15 fibrotic ear tissue Mus musculus

city: Lexington

first: Ashley

last: Seifert

state: Kentucky

address: 675 Rose St.

department: Biology

institute: University of Kentucky

description:
D15 fibrotic ear tissue
haib14AWS2783

data_processing:
Normalize raw data using Trinity
Build references for each species using RSEM
Calculate raw transcript expression for each time point in each species using RSEM
Calculate expression fold change and probability of differential expression using Ebseq
Genome_build: de novo-assembled transcriptome for Acomys, mm10 for Mus
Supplementary_files_format_and_content: .result files were generated for each species comparing all time points versus D0.  Probability of differential expression and fold change are reported.  Due to the method the data was processed in, fold changes reported in this list are D0/DX.  To get DX/D0, the inverse of the reported fold change is used.

source_name: Ear Tissue

extract_protocol:
tissue was frozen in liquid nitrogen, homgenized with ceramic beads in TriZol and extracted following TriZol protocol
HudsonAlpha directional RNAseq with ribosomal RNA reduction

tag: healing mechanism

value: ear tissue

value: D15 fibrotic ear tissue


title: Gb3c rep3

tag: tissue

value: the budding stage, eleven pieces of leaf


title: D10 fibrotic ear tissue Mus musculus

description:
D10 fibrotic ear tissue
haib14AWS2783

value: D10 fibrotic ear tissue


title: D20 fibrotic ear tissue Mus musculus

description:
D20 fibrotic ear tissue
haib14AWS2783

value: D20 fibrotic ear tissue


title: Gb3c rep2

value: normal branch


title: D5 fibrotic ear tissue Mus musculus

description:
D5 fibrotic ear tissue
haib14AWS2783

value: D5 fibrotic ear tissue


title: Gb3c rep1


title: D0 uninjured ear tissue Mus musculus

description:
D0 uninjured ear tissue
haib14AWS2783

value: D0 uninjured ear tissue


title: miGb1e rep 1

value: seedling stage, have two pieces of leaf


title: P5 back skin_TAC_1

value: mixture of FVB/N, C57BI/6J and CD1

value: postnatal day 5

value: back skin

value: Shh expressing matrix progenitors

value: K14-H2BGFPLo/Lef1-RFP+ from dermal preparation of K14-H2BGFP


title: Gb2e rep3

value: pre-budding stage, about six pieces of leaf


title: miGb1c rep2

value: shoot apical


title: Gb2e rep2

value: nulliplex-branch


title: Gb2e rep1


title: Gb2c rep2

value: pre-budding stage,about eight pieces of leaf


title: Gb2c rep1


title: Gb1e rep 2


title: Gb1e rep 3


title: Sam2LowGFP

city: New Haven

first: Jijun

last: Cheng

state: CT

address: 10 Amistad St.., Rm 214K

department: Genetics

institute: Yale University

data_processing:
Illumina sequencing data were analyzed using custom perl and matlab codes.
First, the fastq file was converted to fasta file. Second, sequence reads were separated into specific samples based on barcodes, and sgRNA backbone sequences were clipped. Third, sequences were mapped to the original source DNA sequences using bowtie, allowing either no mismatch (for all following analyses except noted otherwise), or one base mismatch (for estimation of sgRNA distance).
For estimation of library complexity, mapped unqiue sgRNAs were counted from the neg-GFP samples.
For enrichment analyses, sgRNA sequence read counts were first normalized based on total mapped read counts to derive read frequencies. Next, read frequency of every sgRNA within a given GFP-positive population were divided by those of the corresponding neg-GFP sample from the same biological replicate. To avoid division by 0, the minimal frequency in neg-GFP samples were set to 6.25x10-7, and minimal frequency in GFP-positive samples were set to 1x10-8. Log2 enrichment levels were then calculated and plotted. Positions for each sgRNA were represented by the positions of the last base in the targeting section of the sgRNA.
To estimate the distances between functional sgRNAs, only sgRNAs with NGG PAM sequences on either sense or antisense strands were calculated. The distances were defined by the distance between the last bases of the sgRNA target-recognition sections.
Genome_build: miRBase version 21
Supplementary_files_format_and_content: txt file including species of sgRNAs, input miRNA DNA that a sgRNA matched to and the start and end position, sense or antisense strands that it matched to,  and reads in different sorted samples.

source_name: BaF3 reporter line transduced with sgRNA library replicate 2 low-GFP

growth_protocol: The murine BaF3 hematopoietic cell line and reporter cells were cultured with RPMI 1640 medium containing 10% heat inactivated fetal bovine serum (Life Technologies), 1% of 100xPen/Strep/Glutamine (Life Technologies) and 3 ng/ml of recombinant murine IL-3 (Peprotech).

extract_protocol:
The murine BaF3 hematopoietic cell line was cultured with RPMI 1640 medium containing 10% heat inactivated fetal bovine serum (Life Technologies), 1% of 100xPen/Strep/Glutamine (Life Technologies) and 3 ng/ml of recombinant murine IL-3 (Peprotech). The BaF3 miR-142-3p reporter cell line was derived by infecting BaF3 cells with the lentiviral miR-142-3p reporter construct, resulting in low GFP levels representing reporting high endogenous miR-142 levels, whereas high GFP levels reporting low miR-142 levels. The screen was performed by infecting 10 million cells (BaF3 miR-142-3p screen cell line) with a retroviral sgRNA library, in three biological replicates (on two separate days).  Each infection replicate was performed by infecting five 6-well plate wells, with each well containing 2 million cells, and then combining cells from the five wells after overnight culture. The infection rate was ~30%.  Each infection replicate was diluted to a total of 50 ml culture medium, and cultured in a 150-mm dish for one day before puromycin selection (2 ug/ml). Cells were passaged every two days (or when necessary) by transferring 5 to 10 million cells to 50 ml fresh medium for each passage, with puromycin selection. Cells were FACS sorted 9 days after library infection, based on negative, low, medium and high GFP levels. The sorted GFP-positive populations were re-sorted after culturing for 3 days, to achieve higher purity. Genomic DNA were extracted from 2.5 million of neg-GFP populations, and 6x10^4 to 5x10^5 cells of low-, med- and high-GFP populations by proteinase K digestion, phenol/chloroform extraction, ethanol precipitation, and re-suspension in water.
To sequence the sgRNAs integrated into genomic DNA, genomic DNA samples were amplified by PCR using Phusion DNA polymerase (NEB), 200ng of genomic DNA and the following pair of primers. The sense primer aatgatacggcgaccaccgagatctacactggaaaggacgcgggatccG contains an Illumina adaptor sequence followed by the library vector sequence. The antisense primer caagcagaagacggcatacgagatcgtgatgctatttctagctctaaaac contains an Illumina adaptor sequence, followed by a 6-nucleotide library barcode sequence and sgRNA backbone sequence. For neg-GFP samples, ten PCR reactions (50 ul each) using a total of 1 ug genomic DNA template were pooled to avoid major loss of library complexity. All PCR products were purified from 3% agarose gel. PCR products were mixed (100ng of each neg-GFP-sample PCR products, and 5 ng of each GFP-positive-sample PCR products). The combined sample was sequenced using an Illumina Hi-Seq2000, using sequencing primer: tggaaaggacgcgggatccg. The sample was sequenced on one lane, containing 12 populations from 3 biological replicates, each consisting of 4 sgRNA library samples of neg-GFP, low_GFP, med-GFP and high-GFP.

treatment_protocol: Reporter cells transduced with sgRNA library were selected by 2ug/ml of puromycin and cultured for total of 9 days followed by FACS sorting neg-GFP, low-GFP, med-GFP and high-GFP cells.

tag: cell line

tag: cell transfection status

tag: gfp status

value: low-GFP


title: Healthy donor 4 pDCs

value: pDCs

value: blood

value: male

value: UT


title: Healthy donor 5 pDCs

value: female


title: Sam3MedGFP

source_name: BaF3 reporter line transduced with sgRNA library replicate 3 med-GFP

value: med-GFP


title: Sam3HighGFP

source_name: BaF3 reporter line transduced with sgRNA library replicate 3 high-GFP

value: high-GFP


title: Healthy donor 1 pDCs stimulated with IMQ

value: IMQ


title: Healthy donor 5 pDCs stimulated with IMQ


title: Sam3NegGFP

source_name: BaF3 reporter line transduced with sgRNA library replicate 3 neg-GFP

value: neg-GFP


title: Healthy donor 2 pDCs


title: Sam2MedGFP

source_name: BaF3 reporter line transduced with sgRNA library replicate 2 med-GFP


title: Healthy donor 6 pDCs stimulated with IMQ


title: Unsorted

source_name: BaF3 reporter line transduced with sgRNA library unsorted


title: Healthy donor 2 pDCs stimulated with IMQ


title: Healthy donor 1 pDCs


title: Sam2HighGFP

source_name: BaF3 reporter line transduced with sgRNA library replicate 2 high-GFP


title: Gb1e rep 1

tag: strain

tag: age

value: seedling stage, have two pieces of leaf


title: Healthy donor 6 pDCs stimulated with CpG

value: CPG


title: Healthy donor 7 pDCs stimulated with IMQ


title: Gb1c rep3

value: normal branch


title: Sam2NegGFP

source_name: BaF3 reporter line transduced with sgRNA library replicate 2 neg-GFP


title: Healthy donor 7 pDCs stimulated with CpG


title: Gb2c rep3


title: Sam3LowGFP

source_name: BaF3 reporter line transduced with sgRNA library replicate 3 low-GFP


title: 6CDay14

city: Guangzhou

first: Hao

last: Sun

address: Kaiyuan avenue 190

institute: GIBH

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie
Transcripts Per Million were  calculated using a protocol from RSEM
Genome_build: mm10
Supplementary_files_format_and_content: TPM

source_name: Mouse embryonic fibroblast

growth_protocol: MEFs was maintained in MEF medium (DMEM containing 10% FBS, 1mM Glutamax and 100X NEAA). For transdifferentiation, cells were seeded in 6-well plate at a desity of 5000 cell/well, and the grouth medium was changed to 6C.

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

treatment_protocol: Cells at day 0, 2, 5, 10, 15 were lysed by Trizol.

value: ICR

value: Mouse embryonic fibroblast

tag: day


title: Healthy donor 4 pDCs stimulated with IMQ


title: Sam1MedGFP

source_name: BaF3 reporter line transduced with sgRNA library replicate 1 med-GFP


title: 6CDay10


title: Healthy donor 5 pDCs stimulated with CpG


title: Gb1c rep2

value: shoot apical


title: 6CDay5


title: Healthy donor 4 pDCs stimulated with CpG


title: 6CDay2


title: Healthy donor 2 pDCs stimulated with CpG


title: Sam1NegGFP

source_name: BaF3 reporter line transduced with sgRNA library replicate 1 neg-GFP


title: Sam1LowGFP

source_name: BaF3 reporter line transduced with sgRNA library replicate 1 low-GFP


title: 6CDay0

description: MEF


title: P_0130

status: Public on Mar 16 2016

first: Adam

last: Labadorf

address: 72 East Concord Street E301

department: Neurology

institute: Boston University Medical School

data_processing:
Basecalls from CASAVA 1.7
QUALITY FILTERING: FASTX-toolkit version 0.0.13.2 fastq_quality filter with -Q 33  -q 20 -p 80; ADAPTER REMOVAL: cutadapt 1.2.1 with --minimum-length 15 option, READ COLLAPSING: FASTX-toolkit version 0.0.13.2 fastx_collapser
READ ALIGNMENT: bowtie-1.0.0 with no mismatches and 200 multimap limit using -v 0 -k 200; ANNOTATION: bedtools v2.2 intersectBed and miRBase v20
COUNTING: custom R-script counting miRNAs ±4 nucleotides from 5' annotated start location
DIFFERENTIAL EXPRESSION ANALYSIS: Using R: DESeq2 v1.40 for variance stabilizing transformation counts, ComBat (R package sva 3.10) for batch effect correction, LIMMA v3.20.8 with adjustment for death at death for statistical comparison between conditions
Genome_build: hg19
Supplementary_files_format_and_content: Processed files contain normalized counts for all samples, covariates file with additional sample information and differential expression results from LIMMA, in comma separated value format

source_name: prefrontal cortex (BA9)

extract_protocol:
QIAzol Lysis Reagent, miRNeasy purification
Illumina TruSeq Small RNA Preparation Kit

value: brain

tag: location

value: prefrontal cortex


title: Gb1c rep1

source_name: stem tip


title: P_0126


title: P_0132


title: Sam1HighGFP

source_name: BaF3 reporter line transduced with sgRNA library replicate 1 high-GFP


title: P_0134


title: P_0063


title: P_0135


title: P_0034


title: P_0136


title: P_0033


title: P_0133


title: P_0030


title: P_0029


title: P_0031


title: P_0026


title: P_0028


title: 88069_m_repA

city: Uppsala

first: Anna

last: Åsman

address: PO Box 7080

department: Molecular Sciences

country: Sweden

institute: Swedish University of Agricultural Sciences (SLU)

data_processing:
Trim adaptor and low quality reads using trimmomatic v0.32 (ILLUMINACLIP:$ADAPTOR:2:30:10 HEADCROP:13 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Map reads to P. Infestans genome using tophat 2.0.9 (-i 20 -I 5000 --min-segment-intron 20 --max-segment-intron 5000 --min-coverage-intron 20 --max-coverage-intron 5000 --read-realign-edit-dist 0 --microexon-search --library-type fr-firststrand)
Count reads mapping to genes using htseq-count v0.6.1 -s reverse
Genome_build: P. infestans strain T30-4, http://www.broadinstitute.org
Supplementary_files_format_and_content: s9[ab].counts, htseq-count file, read count in transcripts

organism: Phytophthora infestans

source_name: Mycelium

extract_protocol:
Mycelium was harvested and flash frozen in liquid nitrogen. Total RNA was extracted using the RNeasy Plant Mini kit (Qiagen).
Library preparation wad done from 1 microgram of total RNA using the Illumina TruSeq stranded mRNA HT library preparation kit including polyA selection, according to the manufacturer's protocol (#15031047 revE).

tag: isolate


title: 88069_m_repB


title: P_0023


title: Healthy donor 1 pDCs stimulated with CpG

source_name: plasmacytoid dendritic cells

tag: cell type

value: pDCs


title: P_0022


title: P_0021


title: P_0020


title: P_0016


title: P_0018


title: P_0013


title: P_0015


title: P_0019


title: P_0003


title: P_0014


title: P_0006


title: P_0012


title: P_0027


title: PCF RiboProf 427 replicate 3

city: SEATTLE

first: Gowthaman

last: Ramasamy

state: WASHINGTON

address: 307 WESTLAKE AVE N

department: GHBC

institute: SEATTLE BIOMEDICAL RESEARCH INSTITUTE

description:
Ribosome Profiling Seq
Pairs with PCFm3

data_processing:
RNAseq reads were aligned to the Tb927 genome TriTrypDB V5.0 using bowtie2 version 2.2.2 in local alignment mode with the following configurations -D 20 -R 3 -N 1 -L 20 -i S,1,0.50
Read counts for each of these regions of all genes were generated using HTSeq package. Any read overlapping the CDS or 5’ UTR region either partially or fully was assigned to that region. Both unique and multipmapping reads were considered for further analyses.
Raw read counts are normalized and analyzed using statistical package DESeq from bioconductor project.
Genome_build: Tb927 genome build  V5.1; TriTrypDB V9.0
Supplementary_files_format_and_content: Tab delimited files with raw read count data corresponding to the CDSregion (+46th base until stop codon).

organism: Trypanosoma brucei

source_name: Tb427 grown in vitro in HMI-9 medium

growth_protocol: In vitro bloodform Lister427 was grown in HMI-9 to a density of 8´105 to 1.5´106 cells/ml.

extract_protocol:
For in vivo blood form parasites, the blood from 2-3 infects rats was pooled and centrifuged and the buffy coat extracted and placed into 20 ml HMI-9 without serum pre-warmed to 37°C.  To arrest translation, cycloheximide was added to 100 μg/ml and incubated for 2 minutes at 37°.  To rapidly chill the cells, 300 ml of ice-cold phosphate buffered saline with glucose (PSG) was added and the cells were pelleted at 4°.  Only parasite populations with greater than 99% slender cells were used.  In vitro grown parasites were pelleted at 5000g and resuspended in 50 mls of media lacking serum.  Cycloheximide was added to 100 mg/ml at the cell incubated for 2min at room temperature (procyclic cells) or 37° (bloodform cells). Following cycloheximide treatment the cells were rapidly chilled with PSG and pelleted at 5000g.  Lysates from both type of parasite pellets were then prepared as following. Cell pellets were resuspended in Buffer A (10 mM Tris pH 7.4, 300 mM KCl, 10 mM MgCl2 plus protease inhibitors to approximately 1.3x109/ml.  Approximately one-third of the sample was placed into TRIzol (Life Technologies) for RNA extraction following manufacturer’s suggested protocol.  To the remainder, one-sixth volume of buffer A containing 0.2M sucrose and 1.2% Triton N-101 was added and the samples were dounced (30 strokes in a chilled homogenizer). After transfer to a prechilled microfuge tube, the samples were clarified by centrifugation in a microfuge at 15000 rpm for one minute.  The supernatant was withdrawn, pooled if needed, and then aliquots flash frozen in liquid nitrogen for storage at -70°C.
After thawing on ice, RNase I (Ambion) was added at 30 units/OD260 of lysate.  Samples were then incubated for 1 hour at room temperature.  RNase digestion was stopped by adding 400 units RNasin (Promega).  Samples were them layered over a 1 ml 1M sucrose cushion prepared in buffer A and ribosomes were pelleted by centrifuging for 4 hours at 70,000g in an SW55 rotor.  After removing the supernatant, the ribosomal pellet was resuspended in 500 μl buffer A with the MgCl2 replaced with 10 mM EDTA to dissociate the ribosomes and deplete larger rRNA fragments.  The protected fragments were then separated from contaminating ribosomal RNA by passage through an Amicon Ultra-4 or YM-100 column with 100,000 MW cutoff. After more than 400 μl had flowed through the membrane the RNA in the flow-through was extracted with phenol:CHCl3:iAA and the RNA precipitated.  Poly(A)+ RNA was isolated using Dynabeads mRNA Direct (Life Technologies).  RNA was fragmented as described Ingolia et all 2011.  Ribosomal protected fragments between 28 and 31 nucleotides and fragmented Poly(A)+ RNA between 30 and 70 nucleotides was isolated from 15% accrylimide gels and libraries prepared for sequencing.  For detailed protocol on generating sequencing libraries for both the ribosome protected and fragmented mRNA library see Ingolia et a 2011.  Briefly, following dephosphorylation the adapter Linker-1 (IDT) was ligated to the 3’ end of the fragment and the ligated product gel purified.  The adapter was used for priming reverse.  Following gel purification the cDNA was circularized with Circ Ligase (Epicenter Biotechnologies).  Circles containing ribosomal RNA were subtracted using biotinylated primers .  The final library was generated by PCR.To map the 5’ end of the transcripts, libraries enriched for the 5’ ends of mRNAs were constructed from three biological samples of strain 927 (2 PCF and 1 slBF selected from the biological samples above).  SL libraries were constructed as described Mittra B et al 2013.  In brief, RNA was prepared and cDNA synthesized using primer ending in a random 6 bases.  Second strand synthesis was primed using a primer that matches the T. brucei SL sequence.  The sequencing library was generated by PCR. Duplexed libraries were sequenced using Illumina GA II machines at the High Throughput Genomics Unit at the University of Washington to generate ~36 nt reads.

treatment_protocol: Cells were treated with 100 µg/ml cycloheximide for 2 min at either room temperature (procylic cells) or 37° (bloodform cells) to arrest elongating ribosomes.

tag: Stage

value: Procyclic Form


title: cBF mRNA 427 replicate 2

description: Pairs with cBFr2

value: cultrured bloodstream Form


title: PCF mRNA 427 replicate 1

description: Pairs with PCFr1


title: cBF mRNA 427 replicate 1

description: Pairs with cBFr1


title: PCF RiboProf 427 replicate 2

description:
Ribosome Profiling Seq
Pairs with PCFm2


title: cBF RiboProf 427 replicate 2

description:
Ribosome Profiling Seq
Pairs with cBFm2


title: PCF mRNA 427 replicate 2

description: Pairs with PCFr2


title: PCF RiboProf 427 replicate 1

description:
Ribosome Profiling Seq
Pairs with PCFm1


title: cerebellum_6MPN (sRNA-seq)

city: Los Angeles

first: Yibin

last: Wang

state: Ca

institute: University of California Los Angeles

description:
Sample 5
small RNA-Seq

data_processing:
Reads were trimmed with cutadapt to remove adapters and PCR primers. After trimming, only reads with minimum length 19 were kept.
Reads with low complexity were excluded where low complexity is defined as mono-, di-, tri-, or quad-nt of 5, 3, 2, 2, respectively.
Small RNAs were required to have length between 19 to 24 nt.
Genome_build: mm10 or hg19
Supplementary_files_format_and_content: tab-delimited text file containing small RNA counts

source_name: cerebellum

extract_protocol:
Tissue total RNA samples for cerebellum and testis were purchased from Zyagen. Total RNA of H1 cells was isolated using Trizol (Life Technologies). Additional column purification and DNaseI treatment were applied using Direct-zol RNA kit (Zymo Research).
Spike-in RNAs (Exiqon) were added into 1µg total RNA before library construction for the normalization control between tissue samples. Small RNA sequencing libraries were generated using NEBNext Small RNA library Prep kit and NEBNext multiplex oligos for Illumina according to the manufacturer’s instructions (NEB). The final libraries were purified from 6% PAGE gel, and their concentrations were measured using Qubit fluorometric assay (Life Technologies).

value: BALB/C

value: cerebellum

value: 6 months post-natal


title: testis_E14 (sRNA-seq)

description:
Sample 6
small RNA-Seq

source_name: testis

value: testis


title: testis_6MPN (sRNA-seq)

description:
Sample 9
small RNA-Seq


title: testis_E18 (sRNA-seq)

description:
Sample 7
small RNA-Seq


title: cerebellum_3WPN (sRNA-seq)

description:
Sample 4
small RNA-Seq

value: 3 weeks post-natal


title: cerebellum_E18 (sRNA-seq)

description:
Sample 3
small RNA-Seq


title: cerebellum_E14 (sRNA-seq)

description:
Sample 2
small RNA-Seq


title: wholebrain_E10 (sRNA-seq)

description:
Sample 1
small RNA-Seq

source_name: whole brain

value: whole brain


title: PCF mRNA 427 replicate 3

description: Pairs with PCFr3


title: cBF RiboProf 427 replicate 1

description:
Ribosome Profiling Seq
Pairs with cBFm1


title: testis_3WPN (rna-seq)

description:
rRNA depleted
Sample 3

data_processing:
Reads were aligned to mm10 using tophat2 with parameters -a 9 -g 1.
RPKM was calculated using in-house scripts for genes annotated in various databases (see Methods).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files contain RPKM

extract_protocol:
Tissue total RNA samples for testis were purchased from Zyagen. Total RNA of H1 cells was isolated using Trizol (Life Technologies). Additional column purification and DNaseI treatment were applied using Direct-zol RNA kit (Zymo Research). rRNA was depleted using RiboMinus Trnascriptome ioslatoin kit (Life Technologies) from 10µg total RNA. ERCC Spike-in (Life Technologies) was added to 500 ng of rRNA depleted RNA. mRNA was isolated using the NEBNext Poly(A) mRNA magnetic isolation module.
mRNA sequencing libraries were generated using the NEBNext Ultra directional RNA library Prep kit and NEBNext multiplex oligos for Illumina according to the manufacturer’s instruction (NEB). The final libraries’ concentrations were measured using the Qubit fluorometric assay (Life Technologies) and Bioanalyzer (Agilent) for the quality check.


title: testis_6MPN (rna-seq)

description:
rRNA depleted
Sample 4


title: testis_3WPN (sRNA-seq)

description:
Sample 8
small RNA-Seq


title: testis_E14 (rna-seq)

description:
rRNA depleted
Sample 1


title: testis_E18 (rna-seq)

description:
rRNA depleted
Sample 2


title: PCR-BS replicate 1

city: Cambridge

first: Dario

last: Beraldi

address: Robinson Way

country: United Kingdom

institute: Cambridge Research Institute

description:
Standard Bisulfite-Seq replicate
grm037_BS_plasb2_AD04

data_processing:
bcl files were converted to fastq using bcl2fastq v2.15.0.4 with defaut options.
Fastq reads where trimmed using trimugalore version 0.3.7 with cutadapt version 1.4.2. Option --stringency was set to 3.
Trimmed reads were aligned using bwameth.py (wrapper around bwa mem)
Mapping quality of reads with more then 10% mismatches was set to 0 using resetHighMismatchReads.py (https://code.google.com/p/bioinformatics-misc/source/browse/#svn%2Ftrunk)
Overlapping read pairs were clipped using clipOverlap in the BamUtil suite version 1.0.12.
The counts of converted and unconverted cytosine, i.e. the methylation status, in the P.berghei genome were obtained from the alignment files using bam2methylation.py (https://code.google.com/p/bioinformatics-misc/source/browse/#svn%2Ftrunk). Only reads with mapping quality 15 or above were considered and read bases with quality less than 13 were excluded from methylation calling. In addition, at each cytosine position the number of mismatches, i.e. the number of reads not A or C, was recorded.
Genome_build: The reference sequence for alignment was mouse genome version mm9 (UCSC) concatenated to Plasmodium berghei genome version 11 (http://plasmodb.org/common/downloads/release-11.0/PbergheiANKA/fasta/data/PlasmoDB-11.0_PbergheiANKAugenome.fasta)
Supplementary_files_format_and_content: 20140710.grm.met.txt.gz is a table of methylation calls in the Plasmodium berghei genome for each of the five libraries. The columns are:
chrom: Chromosome name
start: Cytosine position start (0 based)
end: Cytosine position end (always start+1)
strand: Strand of the cytosine
pct_met.<library id>: Percentage methylation (cnt_met / cnt_tot * 100) for sample <library id>
cnt_met.<library id>: Count of methylated (uncoverted) reads for sample <library id>
cnt_tot.<library id>: Total read depth for sample <library id> after filtering low quality reads and base calls.
p.fisher.<library id>: P-value from Fisher test for the null hypothesis that the observed methylation is not different from the error rate. Error rate is estimated from the number of calls different from C or T.
...
cnt_tot.all_rebuilt: Total read count for the ReBuilT libraries
cnt_met.all_rebuilt: Total methylation count for the ReBuilT libraries
p.all_rebuilt: Combined p value using Stouffer method from the individial ReBuilT libraries.
fdr.all_rebuilt: P-value in p.all_rebuilt adjusted using false discovery rate method.
cnt_tot.all_BS: Same as cnt_tot.all_rebuilt for the PCR-BS libraries
cnt_met.all_BS: Same as cnt_met.all_rebuilt for the PCR-BS libraries
p.all_BS: : Same as p.all_rebuilt for the PCR-BS libraries
fdr.all_BS: Same as fdr.all_rebuilt for the PCR-BS libraries
states: State inferred from the HMM model to identify runs of methylated cytosines. "u": Unmetylated run. "M": Methylated run
pct_met.all_rebuilt: Percentage methylation for the ReBuilT libraries (cnt_met.all_rebuilt / cnt_tot.all_rebuilt * 100)

organism: Plasmodium berghei ANKA

source_name: Mixed blood stages of malaria parasites

growth_protocol: 6-10 week old Thieler‟s original mice were injected intraperitoneally with 0.2 mL of 6 mg/mL phenylhydrazine, and three days later infected with 5x107 parasites (Plasmodium berghei ANKA strain, clone 233). From day 6 onwards tail smears were taken to assay parasitaemia. Mice were bled by cardiac puncture

extract_protocol: DNA extracted following standard protocols (Doolan, D. L. Methods in Molecular Medicine Volume 72: Malaria Methods and Protocols ed. Humana Press, Inc., Totowa, New Jersey, USA, pp. 25-40)

value: PCR-BS (standard Bisulfite-Seq)

value: Plasmodium berghei 2.34 ANKA strain


title: PCR-BS replicate 2

description:
Standard Bisulfite-Seq replicate
grm038_BS_plasb2_AD16


title: ReBuilT replicate 3

description:
PCR-free Bisulfite-Seq replicate (ReBuilT)
grm036_REBUiLT_AD12

value: ReBuilT (PCR-Free). 50 ng of P.berghei DNA was end repaired (NEBNext End Repair Module) and dA-tailed (NEBNext dA-tailing module), before ligation of custom adapter pair A (NEBNext Quick Ligation Module). Bisulfite conversion was achieved with the Zymo EZ DNA Methylation-Gold kit, following the manufacturers instructions. To recover damaged fragments we added 5 uL of 10 mM (5_-CAA GCA GAA GAC GGC ATA CGA GAT TGG TCA GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T-3_), 200 _M dNTPs, 10 uL VeraSeq Buffer II (Enzymatics) and 1U Veraseq Ultra (Enzymatics). Following incubation at 95 °C for 3 minutes and annealing at 54 °C for 45 seconds, extension at 72 °C was carried out for 30 minutes. The reaction mixture was incubated with 60 ug of streptavidin coated magnetic beads (Magnasphere Paramagnetic Particles, Promega) in 2x binding buffer (10 mM Tris-HCl pH 7.4, 1 mM EDTA, 2 M NaCl, 0.1 % Tween 20) for 20 minutes at room temperature. Beads were washed three times with 400 uL binding buffer before being end repaired. Beads were again washed three times with 400 uL binding buffer before dA-tailing, and a further three times with 400 uL binding buffer before ligation of adapter pair B. Finally, three washes with 400 uL binding buffer were followed by elution of the A,T,G,C strand with 50 mM NaOH at 60 °C for 15 minutes.


title: ReBuilT replicate 2

description:
PCR-free Bisulfite-Seq replicate (ReBuilT)
grm035_REBUiLT_AD06


title: ReBuilT replicate 1

description:
PCR-free Bisulfite-Seq replicate (ReBuilT)
grm034_REBUiLT_AD04


title: cerebellum_6MPN (deg-seq)

description: Sample 1

data_processing:
library strategy: degradome-seq
Reads were trimmed with cutadapt to remove adapters, PCR primers, and low quality regions. After trimming, only reads with minimum length 25 were kept.
Reads with low complexity were excluded where low complexity is defined as mono-, di-, tri-, or quad-nt of 5, 3, 2, 2, respectively.
After mapping reads to the reference genome, a binomial test with multiple hypothesis testing correction was applied to identify significant peaks (i.e. cleavage sites). These peaks are provided in bed format.
Genome_build: mm10 for cerebellum and testis; hg19 for H1
Supplementary_files_format_and_content: bed format containing significant peaks up to 4 nt in length

extract_protocol:
Tissue total RNA samples for cerebellum and testis were purchased from Zyagen. Total RNA of H1 cells was isolated using Trizol (Life Technologies). Additional column purification and DNaseI treatment were applied using Direct-zol RNA kit (Zymo Research).
To generate the degradome sequencing libraries, we used the global 5’ RACE library preparation method (Karvinov et al, 2010) with some modifications. Briefly, poly(A)+ mRNA was isolated from 400-500 µg of total RNA using Dynabead Oligo(dT) (Life Technologies) according to the manufacturer’s instructions. This procedure was repeated to increase the effectiveness of poly(A) selection. The NEBNext Small RNA library Prep kit was used for 5' adapter ligation, followed by reverse transcription using random hexamer primers containing the 3’ SR adapter sequence 5’-AGACGTGTGCTCTTCCGATCTNNNNNN.  PCR was conducted in 25 cycles at 94°C 15s, 60°C 30s, 70°C 1min. The final libraries were purified from 6% PAGE gel followed by AMPure XP Beads size selection (Beckman Coulter).


title: KO_MII

city: beijing

first: yujiao

last: dang

address: Yihe road

institute: BIOPIC

description: Bulk RNA seq

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
RNA-seq reads were aligned to the mouse refference genome (mm9) using Tophat software
gene expression level was calculated with Cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content: txt files reflect FPKM of each gene in Refseq.

source_name: mouse oocyte

growth_protocol: Mice were maintained under SPF conditions in a controlled environment of 20-22oC, with a 12/12 h light/dark cycle, 50-70% humidity, and food and water provided ad libitum. Animal care and experimental procedures were conducted in accordance with the Animal Research Committee guidelines of Zhejiang University.

extract_protocol:
60 oocytes/embryos were picked into the RLT lysis buffer, and RNA was prepared follow the protocol of QIAGEN's RNAeasy kit.
Cells were picked into the lysis buffer to extracted mRNAs; then the purifed mRNAs were used to construct the cDNA library with the NEB RNA library construct kit. The quality-ensured libraries were used for pair-end deep sequencing on Illumina HiSeq Sequencer.

treatment_protocol: Oocytes/embryos were collected from 21-23-day-old female WT and Btg4-/- mice after injection of PMSG/hCG and mated for embryos.

value: ICR

value: MII oocyte

value: Erk-/-


title: WT_MII

description: Bulk RNA seq

value: wildtype


title: Sample_J2_3 (glomerular, control)

first: Chengguo

last: Wei

address: 1428 Madison Ave1468 Madison Ave

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The RNA-seq data was analyzed by following the procedure described below. Briefly, after sequence quality filtering at a cutoff of a minimum quality score Q20 in at least 90% bases, the good quality reads were aligned to Reads were processed and aligned to the University of California Santa Cruz (UCSC) Mus musculus reference genome and transcriptome (build mm10) using the Burrows-Wheeler Aligner(bwa)
The reads that are uniquely aligned to the exon and splicing-junction sites for each transcript were combined to calculate as expression level for a corresponding transcript and further normalized based on reads per kilobase per million reads (RPKM) 16 in order to compare transcription levels among samples.
The transcrips with a low raw read count <100 in all the samples were excluded for downstream analysis. Gene expression value was transformed to the log 2 base scale. PCA was first performed to assess the sample correlations using the expression data of all the genes. The differentially expressed genes in STZ mice compared to control mice were identified by the R package DEGseq for sorted podocytes26 and we  selected the genes based on DEGseq  adjusted p <0.05 and 1.5 fold change in this 2:3 comparison on which a standard statistic test could not be applicable.
The limma test 20 was applied for analysis of data in isolated glomeruli. A specific gene was considered differentially expressed if the p-value given by these methods was ≤0.05. The Gene Ontology and pathway analysis for the differentially expressed genes were then performed with fold change cutoff of ≥1.5 using INGENUITY© IPA(http://www.ingenuity.com/products/ipa) and online tool Enrichr 3
The read coverage of gene functional elements was also visualized by IGV tool (Integrative Genome Viewer, http://www.broadinstitute.org/igv/) from the genome alignment file. Heatmap analysis was performed for the top fold changed 50 differential expression genes with DEGseq test after median center transformed using Multi-Experiment Viewer software
Genome_build: mm10
Supplementary_files_format_and_content: txt file reports processed normalized data

source_name: glomerular, control

growth_protocol: Animal studies were performed in accordance with the guidelines of and approved by the Institutional Animal Care and Use Committee at the Icahn School of Medicine at Mount Sinai (New York, NY). Mice were housed in a specific pathogen-free facility with free access to chow and water and a 12-hour day/night cycle. Breeding and genotyping was done according to standard procedures. NPHS2.rtTA22 and IRG mice (B6;C3-Tg(CAG-DsRed,-EGFP)5Gae/J)6 were purchased from The Jackson Laboratory (Bar Harbor, ME). IRG mouse line is engineered to express DsRed fluorescence protein in all cells in absence of Cre recombinase and EGFP in presence of Cre 6. LC1 transgenic mouse was a generous gift from MJ Moeller (University of Aachen, Germany) 23. To generate diabetic mice with inducible EGFP labeling in podocytes, we first crossed the IRG mice with eNOS-/- in C57BL/6 background (Jackson Laboratory), and then with NPHS2.rtTA and LC1 mice in order to generate the experimental NPHS2.rtTA;LC1;IRG; eNOS-/-  mice. For the induction of DsRed deletion, animals received doxycycline hydrochloride (Sigma-Aldrich) via drinking water (2 mg/ml with 5% sucrose) during pregnancy and nursing (embryonic deletion) up to 4 weeks of age. To increase the induction efficiency, the mice received doxycycline (2 mg/ml) orally from P6 to P18 three times per week 27. For induction of diabetes, male NPHS2.rtTA;LC1;IRG; eNOS-/- mice at 8 weeks of age were injected over 5 consecutive days with low-dose STZ (50 μg/g per day intraperitoneally; Sigma-Aldrich, St Louis, MO). Body weight and hindlimb blood glucose levels were monitored biweekly by glucometer readings. Diabetes was confirmed by fasting blood glucose level > 300mg/dl. The age- and sex-matched littermates injected with vehicle (CL-eNOS-/-) served as non-diabetic controls. Urine samples were collected biweekly. The mice were sacrificed at 10 weeks post-induction of diabetes.

extract_protocol:
Briefly, animals were perfused with 8ml bead solution and 2ml bead solution with enzymatic digestion buffer (Collagenase type II 300U/ml, Proetainse E 1mg/ml and Dnase I 50U/ml), which was pre-warmed at 37°C. At the end of perfusion, kidneys were removed, decapsulated, minced into 1 mm3 pieces, and digested in 3ml digestion buffer at 37 °C for 15min on a rotator (100 r.p.m). Digested tissue was then passed through a 100-μm cell strainer and collected by centrifugation. The pellet was resuspended in 2 ml of Hanks’ buffered salt solution and glomeruli were washed three times and collected using a magnet. The separated glomeruli were resuspended in 2 ml digestion buffer and incubated at 37 °C for another 40 min at 1400 r.p.m/min on a thermomixer. During the digestion period, the solution was vortexed every 10 min and sheared with a 27G needle every 15 min. Then, the solution was put on magnetic particle concentrator and supernatant was pooled. The suspension was then sieved through 40 um cell strainer and centrifuged at 1500 r.p.m for 5 min at 4°C.  After two-step approach for primary cell purification, single cells were resuspended in 0.5ml of HBSS supplemented with 2% fetal bovine serum, 25mM HEPES and 4'6-diamidino-2-phenylindole (1 mg/ml).
Total RNA was isolated from either isolated glomeruli or sorted podocytes by using RNeasy mini kit (Qiagen 74104) according to the manufacturer’s protocol. RNA concentrations were quantified using a Nano-drop Spectrophotometer at a wavelength of 260nm. RNA samples were then analyzed by Bioanalyzer at a concentration of 100-200 ng/ul to verify the concentration and the purity of samples. Only the samples with RNA integrity (RIN) values of >7.0 were used for mRNA sequencing at the Genomic Core Facility at Icahn School of Medicine at Mount Sinai School.

value: glomerulus

tag: agent

value: Control

tag: disease state


title: Sample_J2_4 (glomerular, control)

treatment_protocol: For induction of diabetes, male NPHS2.rtTA;LC1;IRG; eNOS-/- mice at 8 weeks of age were injected over 5 consecutive days with low-dose STZ (50 μg/g per day intraperitoneally; Sigma-Aldrich, St Louis, MO). Body weight and hindlimb blood glucose levels were monitored biweekly by glucometer readings. Diabetes was confirmed by fasting blood glucose level > 300mg/dl. The age- and sex-matched littermates injected with vehicle (CL-eNOS-/-) served as non-diabetic controls. Urine samples were collected bi


title: Sample_J2_1 (glomerular, control)


title: Sample_H1_5 (glomerular, STZ)

source_name: glomerular, STZ

value: STZ

value: diabetes


title: Sample_H1_3 (glomerular, STZ)


title: Sample_H1_2 (glomerular, STZ)


title: Sample_G1_2 (glomerular, STZ)


title: Sample_7SP (podocyte, STZ)

source_name: podocyte, STZ

value: podocyte


title: Sample_8CP (podocyte, control)

source_name: podocyte, control


title: Sample_J2_5 (glomerular, control)


title: WT_GV

description: Bulk RNA seq

value: GV oocyte


title: testis_6MPN (deg-seq)

description: Sample 2

value: BALB/C

value: 6 months post-natal


title: WT_2cell1

description: Bulk RNA seq


title: BTG4ko_2cell2

description: Bulk RNA seq


title: WT_ZYGOTE2

description: Bulk RNA seq

value: zygote


title: BTG4ko_2cell1

description: Bulk RNA seq


title: WT_ZYGOTE1

description: Bulk RNA seq


title: BTG4ko_ZYGOTE2

description: Bulk RNA seq


title: BTG4ko_ZYGOTE1

description: Bulk RNA seq


title: Sample_4_podo (podocyte, STZ)


title: KO_GV

description: Bulk RNA seq


title: BTG4ko_MII2

description: Bulk RNA seq

source_name: MII stage mouse oocyte


title: BTG4ko_MII1

description: Bulk RNA seq


title: WT_GV1

description: Bulk RNA seq

source_name: GV stage mouse oocyte


title: WT_MII1

description: Bulk RNA seq


title: WT_MII2

description: Bulk RNA seq


title: WT_GV2

description: Bulk RNA seq


title: BTG4ko_GV2

description: Bulk RNA seq


title: BTG4ko_GV1

description: Bulk RNA seq


title: WT_2cell2

description: Bulk RNA seq


title: HuES64

city: Jerusalem

first: Ido

last: Sagi

address: Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Reads were mapped to the human reference genome (NCBI/build37.2) using Tophat (version 2.0.4)
Fragments per kilobase of transcript per million mapped reads (FPKM) values were calculated using Cufflinks (version 2.0.2)
Genome_build: NCBI/build 37.2
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each sample

source_name: Diploid ES cell line

extract_protocol:
RNA was isolated using the Total RNA Purification Micro Kit (Norgen). For RNA sequencing analysis, poly(A) pull-down was used to enrich mRNAs from total RNA samples (200 ng–1 µg per sample, RIN > 8)
Libraries were prepared using the Illumina TruSeq RNA prep kit

tag: passage

tag: differentiation status

value: Undifferentiated


title: HuES53


title: P45R

city: Shanghai

first: Qing

last: Li

address: 600 YiShan Road

institute: Institute of Microsurgery on Extremities

description: small RNA

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to miRBase Release 19 using clc genomics workbench , max mismatches is 2
Transcripts per million (TPM) were calculated using a protocol from Wagner et al., theory in biosciences, 2012. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the number of the meta-transcript and by the number of the library.
Genome_build: rn4
Supplementary_files_format_and_content: tab-delimited table includes TPM values and read counts for each Sample

organism: Rattus norvegicus

source_name: control brain

extract_protocol:
After ischemia for 24hr, brain tissue were isolated, and the small RNAs were prepared using the mirVana™ miRNA Isolation kit (Ambion).Illumina TruSeq Small RNA Sample Prep Kit was used for the construction of sequencing libraries.
small RNA libraries were prepared with TruSeq Small RNA Kit

value: Sprague-Dawley

tag: model

value: middle cerebral artery occlusion


title: P71L

description: small RNA

source_name: ischemic brain


title: P72L

description: small RNA


title: P71R

description: small RNA


title: P61R

description: small RNA


title: P52L

description: small RNA


title: P45L

description: small RNA


title: H1 (deg-seq)

description: Sample 3

source_name: H1 (human embryonic stem cell line)

value: H1 ESC


title: smRNA12-2

city: Pohang

first: Hee Jung

last: Koo

address: Hyojadong San 31

country: South Korea

institute: Pohang University of Science and Technology

description: small RNA set2

data_processing:
Illumina Casava1.5 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and then mapped to TAIR10 whole genome using TopHat v1.4.0 (Trapnell et al., 2009)
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks (Trapnell et al., 2009)
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files including FPKM values for each sample

source_name: Arabidopsis leaf

extract_protocol:
RNA was isolated using WelPrepTM (WelGENE, Korea). Total RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer with an RNA Integrity Number (RIN) value greater than 8.5
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaf

tag: days after emergence


title: P61L

description: small RNA


title: smRNA8-2

description: small RNA set2

tag: tissue


title: smRNA16-2

description: small RNA set2


title: H1 (sRNA-seq)

description:
Sample 10
small RNA-Seq

tag: cell line


title: smRNA20-2

description: small RNA set2


title: smRNA28-2

description: small RNA set2


title: smRNA4-2

description: small RNA set2


title: P72R

description: small RNA


title: P52R

description: small RNA


title: smRNA24-1

description: small RNA set1


title: smRNA12-1

description: small RNA set1


title: smRNA20-1

description: small RNA set1


title: smRNA8-1

description: small RNA set1


title: smRNA16-1

description: small RNA set1


title: smRNA28-1

description: small RNA set1


title: totalRNA30-2

description: total RNA set2


title: totalRNA28-2

description: total RNA set2


title: totalRNA26-2

description: total RNA set2


title: totalRNA24-2

description: total RNA set2


title: smRNA24-2

description: small RNA set2


title: totalRNA20-2

description: total RNA set2


title: pES10 EB h-G1

description: Haploid EB cells in G1 (1c) derived from ES cells after the 5th sort + 13 days culture + 21 days differentiation

data_processing:
Reads were mapped to the human reference genome (GRCh37/hg19) using TopHat (version 2.0.8b)
Reads per kilobase of transcript per million mapped reads (RPKM) values were calculated using Cufflinks (version 2.1.1)
Genome_build: Ensembl/GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text file includes Abundance measurements (RPKM) for each sample

source_name: Haploid pES10-EB cells in G1 (1c)

extract_protocol:
RNA was isolated using the RNeasy Micro Kit or the RNeasy Mini Kit (Qiagen). For RNA sequencing analysis, poly(A) pull-down was used to enrich mRNAs from total RNA samples (200 ng–1 µg per sample)
Libraries were prepared using the Illumina TruSeq RNA prep kit v2

value: Haploid pES10-EB cells

tag: cell cycle phase

value: Differentiated


title: pES12 EB d-unsorted

description: Unsorted diploid EBs derived from ES cells after 21 days differentiation

source_name: Unsorted pES12-diploid EBs

value: Unsorted pES12-diploid EBs


title: pES10 EB d-unsorted

source_name: Unsorted pES10-diploid EBs

value: Unsorted pES10-diploid EBs


title: pES10 NPC h-G1

description: Haploid NCAM1+ NPCs in G1 (1c) derived from ES cells after 4th sort + 10 days culture + 10 days differentiation

source_name: Haploid NCAM1+ pES10-NPCs in G1 (1c)

value: Haploid NCAM1+ pES10-NPCs


title: pES10 EB d-G1

description: Diploid EB cells in G1 (2c) derived from ES cells after 21 days differentiation

source_name: Diploid pES10-EB cells in G1 (2c)

value: Diploid pES10-EB cells


title: totalRNA18-2

description: total RNA set2


title: pES12 d-G1 rep1

description: Diploid ES cells in G1 (2c), biological replicate 1

source_name: Diploid pES12 cells in G1 (2c) rep1

value: Diploid pES12 cells


title: totalRNA12-2

description: total RNA set2


title: totalRNA14-2

description: total RNA set2


title: pES12 h-G1 rep2

description: Haploid ES cells in G1 (1c), 5th sort, biological replicate 2

source_name: Haploid pES12 cells in G1 (1c) rep2

value: Haploid pES12 cells


title: pES12 d-G1 rep2

description: Diploid ES cells in G1 (2c), biological replicate 2

source_name: Diploid pES12 cells in G1 (2c) rep2


title: totalRNA16-2

description: total RNA set2


title: totalRNA10-2

description: total RNA set2


title: smRNA4-1

description: small RNA set1


title: d-pES10 d-G2/M

description: Diploid ES cells in G2/M from a diploid culture (4c)

source_name: Diploid pES10 cells in G2/M from a diploid culture (4c)

value: Diploid pES10 cells


title: totalRNA8-2

description: total RNA set2


title: h-pES10 d-G2/M

description: Diploid ES cells in G2/M from a mixed haploid-diploid culture (4c), 3rd sort

source_name: Diploid pES10 cells in G2/M from a mixed haploid-diploid culture (4c)


title: pES10 d-G1 rep1

source_name: Diploid pES10 cells in G1 (2c) rep1


title: totalRNA6-2

description: total RNA set2


title: totalRNA30-1

description: total RNA set1


title: totalRNA22-2

description: total RNA set2


title: pES10 h-G1 rep2

description: Haploid ES cells in G1 (1c), 4th sort, biological replicate 2

source_name: Haploid pES10 cells in G1 (1c) rep2

value: Haploid pES10 cells


title: pES10 d-G1 rep2

source_name: Diploid pES10 cells in G1 (2c) rep2


title: totalRNA28-1

description: total RNA set1


title: pES10 h-G1 rep1

description: Haploid ES cells in G1 (1c), 3rd sort, biological replicate 1

source_name: Haploid pES10 cells in G1 (1c) rep1


title: totalRNA4-2

description: total RNA set2


title: totalRNA22-1

description: total RNA set1


title: totalRNA24-1

description: total RNA set1


title: totalRNA20-1

description: total RNA set1


title: pES12 h-G1 rep1

description: Haploid ES cells in G1 (1c), 4th sort, biological replicate 1

source_name: Haploid pES12 cells in G1 (1c) rep1


title: totalRNA26-1

description: total RNA set1


title: totalRNA18-1

description: total RNA set1


title: AgXX.t90

city: Freiburg

first: Emanuel

last: Clauss-Lendzian

address: Hugstetter Straße 55

country: Germany

institute: University Medical Center

data_processing:
Raw sequencing reads were aligned to the reference genome of E. faecalis 12030 using Bowtie2 (version 2.2.3).
Post-processing of the SAM files into sorted BAM files was performed with SAMtools (version 1.2-207).
Length normalized confidence interval Fragments Per Kilobase of exon per Million fragments mapped (FPKM) values were obtained with Cufflinks using optimized settings for the Ion ProtonTM Sequencer.
Statistical analysis was carried out with the recently developed T-REx RNA sequencing expression analysis pipeline (de Jong et al., BMC Genomics, 2015) using the differential expression method of EdgeR.
A gene was considered significantly differentially expressed when the expression ratio was ≥|2.0| and the false discovery rate (FDR) adjusted p-value ≤ 0.05.
Genome_build: Enterococcus faecalis 12030
Supplementary_files_format_and_content: Tab-delimited txt files with GeneID, logFC, logCPM, LR, pvalue, adj_pvalue and Fold value for each contrast (= comparison of sample X versus sample Y).
Supplementary_files_format_and_content: Tab-delimited txt file with FPKM for all samples.

organism: Enterococcus faecalis

source_name: Cell

growth_protocol: Enterococcus faecalis 12030 was pre-cultured overnight at 37°C in Brain Heart Infusion (BHI, Oxoid Deutschland GmbH, Wesel, Germany) medium with constant agitation at 150 rpm and diluted in BHI medium to an OD600 of 0.05.

extract_protocol:
Cells from 30 ml culture were harvested by centrifugation for 1 min at 10 000 rpm and 4°C in a Sorvall RC6+ centrifuge (Thermo Scientific GmbH, Langenselbold, Germany). Cell pellets were immediately frozen in liquid nitrogen and stored at -80°C or directly used for RNA isolation. RNA was isolated using the ZR Fungal/Bacterial RNA MiniPrepTM Kit (Zymo Research, Freiburg, Germany) following the manufacturer's instructions. To recover total RNA including small RNAs, 1.5 volumes of absolute ethanol were added in step 5. Finally, total RNA was eluted with 50 µl DNase-/RNase-free water and stored at -80°C. RNA quantity and quality were assessed with Agilent RNA 6000 Nano and Pico Kits using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA). Residual contaminating DNA was digested with DNA-freeTM DNase (Ambion, Carlsbad, USA).
To remove rRNAs and tRNAs from the total RNA, MICROBExpressTM and MEGAclearTM Kits were applied. After purification, 500 ng of the enriched (m)RNA was fragmented with RNase III. Fragmented (m)RNA (50-100 ng) was used for the preparation of barcoded whole transcriptome cDNA libraries using the Ion Total RNA-Seq Kit v2 and Ion XpressTM RNA-Seq Barcode 1-16 Kits. Finally, strand-specific, multiplexed RNA sequencing was carried out on Ion PITM chips in an Ion ProtonTM Sequencer. All kits and devices for RNA sequencing were from Ambion, Carlsbad, USA and used according to the manufacturer's instructions.

treatment_protocol: E. faecalis 12030 cultures in mid-exponential growth phase (OD600 ≈ 0.6) were either subjected to metal stress by exposure to an AGXX®- or Ag-coated V2A steel mesh or exposed to an uncoated V2A steel mesh (12 cm2 each in 30 ml BHI medium to obtain a mesh-surface : medium-volume ratio of 0.4) followed by further incubation for 3, 6, 12, 24, 60 and 90 min at 37°C with constant agitation at 150 rpm. As control, no metal mesh was added.

tag: growth in the presence of steel mesh

value: AGXX

tag: exposure time [min]


title: YC-0909

city: Foshan

first: Ying

last: Yang

state: China/Guangdong

address: Xianhu road

institute: Foshan University

description: normal temperature treatment

data_processing:
Basecalls performed using CASAVA version 1.7
Raw reads were filtered using the following specifications:removing the reads with adapter and low quality reads (a read with unknown nucleotides larger than 5%, and more than 20% low quality value bases whose quality value is less than 10)
RNA-seq reads were aligned to the Grass Carp genome assembly and mRNA reference using HISAT with default parameter and calculater the FPKM for each gene.
Supplementary_files_format_and_content: FPKM files were generated using perl script.

organism: Ctenopharyngodon idella

source_name: normal temperature treatment

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: heat stress

value: spleen


title: AgXX.t60

tag: strain


title: totalRNA16-1

description: total RNA set1

source_name: Arabidopsis leaf


title: AgXX.t12


title: YG-0909

description: high temperature treatment

source_name: high temperature treatment


title: totalRNA14-1

description: total RNA set1


title: AgXX.t24


title: totalRNA10-1

description: total RNA set1


title: AgXX.t03


title: Ag.t90

value: Ag


title: totalRNA6-1

description: total RNA set1


title: totalRNA8-1

description: total RNA set1


title: Ag.t60


title: Ag.t24


title: Ag.t12


title: Ag.t06


title: Stau_rep3

city: Worcester

first: Isana

last: Veksler-Lublinsky

address: 373 Plantation Street

department: Molecular Medicine

institute: University of Massachusetts Medical School

description: small RNA profiling

data_processing:
Sequencing files in FastQ formats contain the following data format:  (3') adapter – sequence read –GNNNN (randomer sequence) – NNN (barcode) – adapter (5').
Sequencing files were processed using the Cutadapt method (version 1.2.1) (Martin 2011) to remove the adapter sequences with the following options -e 0.25 -g ATTGATGGTGCCTACAG -a GATCGTTCGGACTGTAGATC, and split into libraries according to barcode sequences.
Barcode and randomer sequences were removed.
Reads shorter than 16 nt were removed.
Reads were reverse complemented.
Reads with identical sequences were combined.
Reads were then aligned to the C. elegans genome (WormBase release WS215) using bowtie with arguments, -v 3 -f -B 1 -a–best –strata.
Alignments were then filtered based on the length of the reads and the number of mismatches as follows: for sequence lengths 16–17, 18–19, 20–24, or .24: zero, one, two, or three mismatches were allowed, respectively.
Genome_build: WS215
Supplementary_files_format_and_content: The tab delimeted text files contain unique sequence reads of smallRNA with counts for each sequence.

organism: Caenorhabditis elegans

growth_protocol: C. elegans were cultured on nematode growth media (NGM) (Brenner 1974) and fed with Escherichia coli HB101.  Synchronized populations of developmentally staged worms were obtained by standard methods (Stiernagle 2006).

extract_protocol:
Animal were collected and flash frozen in liquid nitrogen. Total RNA was extracted using Trizol reagent (Invitrogen). 20 mg of total RNA for each sample was used to isolate small RNA populations. RNA samples were run on a 15% PAGE/urea gel and small RNA populations were isolated from the gel with sizes ranging from 18–26 nucleotides (nt)
Sterling, C. H., I. Veksler-Lublinsky, and V. Ambros, 2015. An efficient and sensitive method for preparing cDNA libraries from scarce biological samples. Nucleic Acids Res. 43: e1.

tag: developmental stage

value: Young adults

tag: genotype


title: Stau_rep2

description: small RNA profiling


title: Stau_rep1

description: small RNA profiling


title: V2A.t90


title: WT_rep3

description: small RNA profiling

source_name: Wild Type (N2)

value: Wild Type (N2)


title: WT_rep2

description: small RNA profiling


title: V2A.t60


title: WT_rep1

description: small RNA profiling


title: AgXX.t06


title: totalRNA12-1

description: total RNA set1


title: V2A.t12


title: Control1.t0


title: V2A.t06


title: Control2.t0


title: V2A.t03