title: hibernation adipose small RNA

city: Guangzhou

first: Lihong

last: Yuan

state: Guangdong

address: 105 Xin-gang Xi road

institute: Guangdong Entomological Institute

description: Solexa small RNA sequencing

data_processing: Individual sequence reads with the base quality scores were produced by Illumina/Solexa. After removing the contaminant reads (the adapters, low quality and redundancy reads), the clean unique reads were mapped onto the Myotis lucifugus genome (http://www.ensembl.org/Myotis_lucifugus/Info/Index) using the program SOAP (Li et al. 2008), and the perfectly mapped reads were scan against the Metazoa mature microRNA of Sanger miRBase (Release 13) (Griffiths-Jones et al. 2008) to identify the homologs of known microRNAs using the program Patscan (Dsouza et al. 1997) with two mismatches allowed. Then, the non-conserved unique reads were screened against the non-coding RNA databases (Griffiths-Jones et al. 2008) to remove the contaminated sequences of tRNA, rRNA, snoRNA, and other ncRNA using SOAP, and those reads that matched genome more than 20 times were also removed to avoid self-contradiction of microRNA prediction (Friedlander et al. 2008). Finally, the remaining reads, including the conserved reads and non-conserved reads filtered the non-coding RNA reads and those mapped onto genome > 20, were denoted as the microRNA potential reads and used for microRNA identification.As microRNA and microRNA* may be both sequenced and from the same precursor, and to avoid repeated predictions and to reduce the required amount of calculation, the potential microRNA reads were searched against the genome, and the candidate reads whose distance in the reference genome are less than 150 nt were jointed and examined as one genomic block. For each block, 150 nt of upstream and downstream extension, were extracted for secondary structure prediction. Firstly, the inverted repeats (IR) with characters of stem-loop or hairpin structure were identified by Einverted of Emboss (Drew et al. 2001), with the parameters threshold = 30, match score = 3, mismatch score = 3, gap penalty = 6, and maximum repeat length = 240 as described by Jones-Rhoades and Bartel (Jones-Rhoades and Bartel 2004). Then the secondary structure of IR was predicted by RNAfold (I. L. Hofacker 1994) with 10 nt extended of upstream and downstream, and evaluated by MirCheck (Bonnet et al. 2004). For the precursors (hairpins) of microRNA located by the non-conserved reads which sequenced more than twice, were inspected manually in order to remove the false prediction. Predicted precursors that microRNAs and microRNA* were found in their both arms, or with two or more unique reads located at mature position were deemed as high probability. When several length variants of the same microRNA were sequenced, only variants with the highest representation were considered.Then, IDEG6 was implemented to identify the differential expressed genes, with P value of Chi-square test â¤ 0.01 as a threshold.

organism: Myotis pilosus

source_name: adipose tissue

extract_protocol: According to the manufacturerâs instruction, total RNA was isolated from bat brain and adipose tissues of hibernating and active states by the RNAiso kit (TakaRa). Small RNA cDNA libraries were constructed following the protocol of Morin et al. (2008). In brief, small RNA (18 ~ 30 nt) of each samples were purified and enriched from total RNA by polyacrylamide gel electrophoresis (PAGE), and ten microgram of small RNA of each were ligated with proprietary adapters used for cDNA synthesis and libraries construction; then Solexa sequencing-by-synthesis method were performed (Illumina).

treatment_protocol: Tissues of Myotis ricketti in hibernating and aroused states, which were collected and stored at -80 ÂºC, were used for RNA extraction and small RNA cDNA library preparation.

tag: state

value: hibernation

value: adult

value: adipose


title: aroused adipose small RNA

status: Public on Dec 31 2015

type: SRA

country: China

description: Solexa small RNA sequencing

library_source: transcriptomic

molecule: total RNA

value: aroused state

tag: developmental stage

tag: tissue


title: SULA RNA

city: Lincoln

first: Paul

last: Blum

state: NE

address: 1901 Vine St.

department: School of Biological Sciences

country: USA

institute: University of Nebraska-Lincoln

data_processing:
Alignment of reads to genome using TopHat
Gene counts generated using HTSeq
Gene expression analysis and normalization using DESeq2
Genome_build: ASM2474v1
Supplementary_files_format_and_content: the read counts per ORF calculated by RPKM.

organism: Saccharolobus solfataricus

source_name: SULA RNA

growth_protocol: Sulfolobus solfataricus 98/2 and its derivatives were grown in basal salts medium as modified by Brock. Complex medium contained tryptone 0.2% (w/v) and the medium was adjusted to the desired pH using sulfuric acid. All cultures were incubated at 80°C in glass screw-capped flasks with aeration in orbital baths. Planktonic growth was monitored by light absorption at a wavelength of 540 nanometers using a Cary 50 spectrophotometer.

extract_protocol:
Total RNA was isolated by phenol-chloroform extraction
Libraries were prepared according to Illumina's instructions

tag: strain background

tag: genotype/variation

value: wild-type parental strain


title: N22-Control

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

data_processing:
Illumina 1.8 pipeline used for basecalling
Low-quality reads and reads containg adaptor/primer contamination were filtered using NGS QC Toolkit v2.3. The filtered reads were pre-processed using modified perl script provided in the miRTools software.
After quality control, the identical reads were collapsed into a unique read and read count for each sequence was recorded. All the filtered unique reads from each sample were mapped on the rice genome.
Genome_build: Rice genome MSUv7.0 (ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/)
Supplementary_files_format_and_content: Processed data files are in fasta format containing collapsed unique reads after QC. Counts included.

organism: Oryza sativa

source_name: Seedlings

growth_protocol: Seedlings were grown in a culture room

extract_protocol:
Tissue samples were collected and frozen in liquid nitrogen. Total RNA was isolated using TRI reagent from Sigma
Libraries were prepared using Small RNA Sample Preparation Kit (Illumina) according to the manufacture’s protocol

tag: cultivar

value: Nagina 22

value: seedlings


title: aroused brain small RNA

description: Solexa small RNA sequencing

source_name: whole brain

value: brain


title: IR64-Desiccation stress [methylation]

library_source: genomic

data_processing:
Illumina 1.8 pipeline used for basecalling
Low-quality reads and reads containg adaptor/primer contamination were filtered using NGS QC Toolkit v2.3
Reads from each sample were aligned to the rice genome using Bismark and only the unique mapping were retained for further analysis. The Bismark ourput files were processed using Methylkit for identification of methylated cytosines.
Genome_build: Rice genome MSUv7.0 (ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/)
Supplementary_files_format_and_content: tab delimited text files include position and P-value of methylated cytosines for each sample

molecule: genomic DNA

extract_protocol:
Tissue samples were collected and frozen in liquid nitrogen. Genomic DNA was isolated using Qiagen DNeasy Minikit.
Genomic DNA samples were fragmented via sonication, end repired and adapters were ligated. The adapter-ligated DNA fragments were used for bisulphite conversion using EZ DNA Methylation-Gold kit. After size selection libraries were prepared using Illumina protocol.

treatment_protocol: Control, dessication and salinity treatments weregiven to seedlings of IR64, N22 and Pokkali rice cultivars. For dessication seedlings were kept on dry filter paper, for control RO water was used and 200 mM salt solution was used for salinity treatment.

tag: genotype/cultivar

tag: condition

value: Desiccation stress


title: IR64-Salinity stress [methylation]

value: Salinity stress


title: N22-Desiccation stress [methylation]

source_name: Nagina 22_Seedlings


title: IR64-Control


title: PK-Control

value: Pokkali


title: hibernation brain small RNA

description: Solexa small RNA sequencing


title: PK-Salinity stress [methylation]

description: PK-SS


title: N22-Control [methylation]

value: control


title: PK-Control [methylation]

description: PK-Control


title: L2

city: Zhengzhou

first: Xin Jian

last: Chen

state: Henan

address: Wenhua Road 95

department: College of Life Sciences

institute: Henan Agricultural University

description: Sample 2

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 about 377,200 and 361,659 non-redundant tags with high qualities in both samples were mapped to the reference sequences (94,544 non-redundant consensus sequences defined by the RNA-seq transcriptomic procedure,) from R. glutinosa leaf transcriptome (SRX269426)
The tags were mapped onto the RNA-Seq reference sequence allowing no more than 1nt mismatch. The number of unambiguous tags for each gene was calculated and then normalized as TPM (number of transcripts per million clean tags).
Genome_build: R. glutinosa leaf transcriptom (SRX269426)
Supplementary_files_format_and_content: processed tata text files include TPM values for each Sample

organism: Rehmannia glutinosa

source_name: The second year replanted R. glutinosa

growth_protocol: Our experimental plants of R. glutinosa, “Wen 85-5”, were grown in Wen Agricultural Institute, Jiaozuo City, Henan Province, China. The designed growing period was from the period from April 22, 2011 to November 30, 2011. A group of seedlings was grown in the field where R. glutinosa had not been planted for more than 10 years. The other group was grown in the field where the same cultivar had been grown in the previous year (planted on April 15, harvested on November 30, 2010). For convenience of description, we named the former group as the first year planted R. glutinosa and the latter group as the second year replanted ones.

extract_protocol:
Total RNA from each sample was isolated using a TriZOL reagent (TaKaRa Co., Tokyo, Japan) following the manufacturer’s instructions and treated with RNase free DNase I (Qiagen).
Sequence tag preparation was performed using the Solexa/Illumina Gene Expression Sample Prep Kit, according to the manufacturer’s instructions. Briefly, 6μg total RNA of each sample was treated with oligo-dT magnetic beads to purify the mRNA, and oligo-dT was then used to prime the reverse transcription reaction to synthesize ds cDNA. The Illumina adapter 1 was attached to the sticky 5' end of the ds cDNA produced by cleaving with NlaIII. cDNA fragments with 3' ends were purified through magnetic bead precipitation, and Illumina adapter 1 was added to the 5' ends. The junction between the Illumina adapter 1 sequence and the NlaIII site provides a 17bp downstream recognition site for MmeI. After removal of 3' fragments from magnetic bead precipitation, the resulting 21bp sequences attached to Illumina adaptor 1 were purified and ligated to Illumina adaptor 2 to form a cDNA tag library. These adapter-ligated cDNA tags were then enriched by 15 cycles of linear PCR, and the resulting 95bp fragments were purified by 6% TBE polyacrylamide gel electrophoresis. Fragments were then denatured and the resulting DNAs fixed to the Solexa flowcell. Sequencing by synthesis was performed using an Illumina HiSeq™ 2000 system according to the manufacturer’s protocols.

treatment_protocol: Two samples were separately collected from L1 (The first year planted R. glutinosa leaves ) and L2(the second year replanted R. glutinosa leaves ) root expansion stage  were seperately collected at root expansion stage.Each samples from leaves of five independent plants

tag: age

value: at root expansion stage (growing 3 months)

value: leaves


title: M434

city: Dummerstorf

first: Klaus

last: Wimmers

state: Mecklenburg-Vorpommern

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology

description: Sample name: 434

data_processing:
Illumina Casava1.7 software was used for basecalling.
Paired-end sequenced reads were trimmed for adaptor sequences and low-quality sequence. High-quality cleaned reads were then aligned to the Sscrofa10.2 assembly of the pig genome using tophat v2.0.3 and bowtie v0.12.7.0 with parameters -p 4 -r 150 --library-type fr-unstranded --read-mismatches 3 --mate-std-dev 75.
Read mapped for annotated genes counted by htseq-count using mode “intersection-nonempty”  and strand “no”, separately for the annotated genes and HSMM prediction, and then merged for each sample.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: Files include raw counts for each annotated and predicted gene for each Sample.  The *regcount files report abundance measurements representing tiling array region genes plus HSMM prediction.  The *allcount files report abundance measurements representing all genes plus HSMM prediction.

organism: Sus scrofa

source_name: muscle

extract_protocol:
Muscle was dissected, snap frozen in liquid nitrogen and stored at -80 °C until RNA extraction. Total RNA was extracted using Trizol reagent and treated with DNase I for 1 hour at 37 °C to remove DNA contamination. The RNA integrity was assessed using Bioanalyzer and a RIN cut off > 8.0.
TruSeq RNA libraries were constructed from 4 µg of total RNA using Illumina TruSeq RNA Sample Prep Kit v2(Cat#RS-122-2001). The DNA libraries were subjected to quality control on an Agilent Technologies 2100 Bioanalyzer using the Agilent DNA-1000 chip and to qPCR quantification using a KAPA Library quantification kit (KAPABIOSYSTEMS).

tag: drip

value: HI

value: muscle

value: post natal day 186

tag: gender

value: Male


title: M261

description: Sample name: 261

value: LO

value: post natal day 172


title: L1

description: Sample 1

source_name: The frist year planted R. glutinosa


title: M579

description: Sample name: 579

value: post natal day 179


title: M036

description: Sample name: 36

value: post natal day 167


title: M234

description: Sample name: 234

value: post natal day 189

value: Female


title: M559

description: Sample name: 559


title: M204

description: Sample name: 204

value: post natal day 181


title: M083

description: Sample name: 83

value: post natal day 173


title: M205

description: Sample name: 205


title: M424

description: Sample name: 424


title: M082

description: Sample name: 82


title: M199

description: Sample name: 199


title: 932T

first: LI

last: QingRong

address: No. 133 Yihenglu,Dongguanzhuang,Tianhe District

institute: The Sericulture and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences

description: Sample 2

data_processing:
OLB-1.9.4 software used for basecalling.
Data was flitered by masking for low-complexity or low-quality tags
Clean tags were mappet to the silkworm genome database
Genome_build: ASM15171v1
Supplementary_files_format_and_content: Tab-delimited .txt file reports abundance measurements.

organism: Bombyx mori

source_name: thermtolerant variety treated by high temperature

extract_protocol:
Midguts were removed, flash frozen by liquid nitrogen, and RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: variety

value: Midgut

value: day 2 of 5th instar

tag: stress

value: high temperature


title: 932

description: Sample 1

source_name: thermtolerant variety normal control

value: control


title: HYT

description: Sample 4

source_name: thermsensitive variety treated by high temperature

value: HY


title: HY

description: Sample 3

source_name: thermsensitive variety normal control


title: blastocyst-ND-tsRNA [RNA-seq]

city: Riverside

first: Junchao

last: Shi

state: CA

address: 900 University Ave

department: Division of Biomedical Sciences, School of Medicine

institute: University of California, Riverside

data_processing:
The raw data is processed by the following steps to get clean reads: 1) Remove reads with adapters; 2) Remove reads in which unknown bases are more than 5%; 3) Remove low quality reads (the percentage of low quality bases is over 15% in a read, we define the low quality base to be the base whose sequencing quality is no more than 19).
Map the clean reads to genome by TopHat v2.0.8b with default parameters except --b2-very-sensitive --no-convert-bam.
Fpkm are calculated based on bam files from tophat result using cufflinks with default parameters except --total-hits-norm -u --emit-count-table.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene id, gene locus, FPKM value and mapping status

organism: Mus musculus

source_name: mouse blastocyst embryo

growth_protocol: In brief, virgin female mice aged 6 week were selected as oocyte donors for superovulation, which were performed by intraperitoneal injection with 7.5IU PMSG, after 48h intraperitoneal injection with hCG. Oocytes were collected 12-18 hr after hCG administration, and zygotes were collected from the successfully mated female mouse.

extract_protocol:
5 embryos were pooled at each developmental stage and moved into the RNA lysis reagents to release all RNAs.
Transcriptome libraries were constructed according to Smart-Seq2 method.

treatment_protocol: Small RNAs isolated from HFD or ND mice sperm total RNAs with the nucleotide length ranging from 30-40 nt, with a concentration of 2ng/μl, or RNaseDfree water as control were microinjected into fertilized eggs of ICR background. The zygotes were then cultured in M16 (sigma) at 37°C in 5% CO2, and at the second day, transferred the 2Dcell embryos to potassium-supplemented simplex optimized medium (KSOM, EMD Millipore). The 8Dcell and late blastocyst stage embryos were collected at approximately 56h and 75 h after microinjection, respectively. To remove the zonapellucida, the selected embryos were transferred into an acidic solution drop (1 ml of PBS supplemented with 1 ml of 36% HCl) and all of the embryos without zonapellucida were washed carefully in dPBS for several times to remove all of the potential maternal contaminants.

tag: strain

value: ICR

tag: diet

value: Normal-diet (ND)

value: blastocyst embryo


title: blastocyst-HFD-tsRNA [RNA-seq]

value: High-fat-diet (HFD)


title: IR64-Control [methylation]

value: seedlings


title: NP-2d Input_ChIPSeq

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: Input Control

data_processing:
Bases were called using Illumina's CASAVA v1.8.2
Sequences were aligned to mm9 genome using Novoalign, only unique aligned reads were kept
Peaks were called using R package "chipseq" and customized R script
Genome_build: mm9
Supplementary_files_format_and_content: binary bedGraph files were generated using in house R scripts

source_name: Neural progenitor cells

growth_protocol: J1 mESCs were grown on gelatin-coated plates at 37°C in knockout DMEM (Invitrogen; Carlsbad, CA) supplemented with 10% ES-qualified fetal bovine serum, 1x non-essential amino acids, 100 μM β-mercaptoethanol, 2 mM L-glutamine, and 1,000 U/ml LIF (ESGRO, Millipore, USA). Mouse embryo brain tissue was obtained from cortex, ganglionic eminence and hippocampus at E15.5.

extract_protocol:
Cross-linked neuronal progenitor cells (2 days) and E15.5 mouse embryonic brain tissue were lysated, and neuclei were isolated. The nuclear pellet was re-suspended in 1 ml of cold shearing buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA, and 0.1% SDS) and chromatin was then sheared to 100-300 bp fragments using a Covaris S220 sonicator (Covaris; Woburn, MA) with the following settings; 12.5 min, 5% duty cycle, 140 Watts peak incident power, 200 cycles per burst. After adding 1% Triton X-100 and 150 mM NaCl (final concentrations) to the sheared chromatin and mixing, the solution was cleared by centrifugation at 14,000xg for 10 min at 4°C. Chromatin fragments were incubated with 2.5 μg of affinity purified anti-Tet3FL antibody (raised against a region of Tet3FL, amino acids 1-102) or IgG control (Santa Cruz; SC-2027) overnight at 4°C with rotation, and then immunoprecipitated using protein A magnetic beads (Millipore; Billerica, MA).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: Wild-type embryonic stem cells (J1) were cultured and differentiated as previously described (M. Bibel, J. Richter, E. Lacroix, Y. A. Barde, Nat Protoc 2, 1034 (2007)). NPCs at day 2 upon neural differntiation were used in our experiments.

tag: cell line

tag: cell type

value: ES-derived neural progenitor cells

tag: differentiation days

value: neural progeniter 2 days

tag: chip antibody


title: NP-2d IgG_ChIPSeq2

description: IgG Control

value: IgG (Santa Cruz, SC-2027)


title: 8-cell-ND-tsRNA [RNA-seq]

source_name: mouse 8-cell embryo

tag: tissue

value: 8-cell embryo


title: INPUT Chip-seq

city: Beijing

first: xiong

middle: will

last: wei

address: 7 Science Park Road ZGC Life Science Park

institute: NIBS,Beijing

description: using standard  protocol as cited in the paper

data_processing:
FASTX-Toolkit  for assessing sequencing quality
Alignment: Bowtie 2 version 2.2.1 for chip-seq  and TopHat v2.0.11 for RNA-seq
cufflinks v2.2.0 for RNA-seq assembling and differential analysis
peaks were called using MACS1.4
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: bedGraph files for RNA-seq and chip-seq

source_name: MEF cells

growth_protocol: DMEM plus 10% for both MEF and U2OS cells

extract_protocol:
NEBNext DNA Library Prep Master Mix Set for Illumina for RNA-seq and NEXTflex ChIP-seq Kit, Bioo Scientific for chip-seq
RNA-seq: For MEF cell line and U2OS cell line mRNA-seq, total RNA was extracted using a RNeasy MinElute Cleanup Kit (QIAGEN, Catalog no. 74204). Double-stranded cDNA was synthesized according to the mRNA Sequencing Sample Preparation Guide (part#1004898 Rev.D, Illumina, San Diego, CA) and single-end libraries were prepared using the NEBNext DNA Library Prep Master Mix Set for Illumina (New England BioLabs, Catalog no.74204 E6040L).   For RNA-seq of RNaseH treated MEF cells, the protocols were mainly adopted as previously described (Nat Methods 10: 623-629).  For qRNA-seq of MEF cells, the GeneRead rRNA Depletion Kit (Qiagen) was used to remove ribosome RNA.  Nascent RNA-seq of U2OS cells was performed as previously described (Science 322: 1845-1848), with the exception of not applying a strand specific method.
Chip-seq: ChIP-seq procedure as previously described (34, 35). For the Bmal1 ChIP-seq, the RIPA buffer was diluted 1 to 10 and the library was constructed using a commercially available kit (NEXTflex ChIP-seq Kit, Bioo Scientific). Samples were indexed using NEXTflex™ DNA Barcodes (Bioo Scientific). The library was qualified using an Agilent 2100 Bioanalyzer (Agilent) and quantified using KAPA Library Quantification Kits (Kappa Biosystems). Finally, the indexed libraries were sequenced using a HiSeq 2500 (Illumina).

value: embryonic-fibroblast

tag: genotype

value: wildtype

value: no


title: NP-2d Tet3FL_ChIPSeq rep1

description: Chromatin IP against mouse Tet3FL

value: mTet3FL (in house)


title: 8-cell-HFD-tsRNA [RNA-seq]


title: NP-2d Tet3FL_ChIPSeq rep2

description: Chromatin IP against mouse Tet3FL


title: WT_rnaseH+polyA+_RNA RNA-seq

description: RNaseH treated


title: WT_rnaseH+polyA+_RNA_s RNA-seq

description: RNaseH treated


title: WT_qk_RNA RNA-seq

description: qiagen GeneRead rRNA Depletion Kit


title: WT_polyA+_mRNA RNA-seq

description: oligoT matrix facilitated


title: WT_rnaseH+polyA-_RNA_s RNA-seq

description: RNaseH treated plus  oligoT matrix facilitated


title: WT_rnaseH+polyA-_RNA RNA-seq


title: WT-H3K4me3 Chip-seq

value: H3K4me3 (Abcam, AB8580)


title: WT-POL2 Chip-seq

value: POL2 (Santa Cruz, sc-899)


title: BM_rnaseH+polyA-_RNA RNA-seq


title: BM_rnaseH+polyA-_RNA_s RNA-seq


title: WT-H3K27ac Chip-seq

value: H3K27ac (Active Motif, 39133)


title: BM_polyA+_mRNA RNA-seq

description: oligoT matrix facilitated


title: BM_qk_RNA RNA-seq

description: qiagen GeneRead rRNA Depletion Kit


title: BM_rnaseH+polyA+_RNA_s RNA-seq

description: RNaseH treated


title: BM_rnaseH+polyA+_RNA RNA-seq

description: RNaseH treated


title: BM-POL2 Chip-seq


title: BM-H3K27ac Chip-seq


title: H3K27ac_ChipSeq_ipsc

city: Shanghai

first: Min

last: Li

address: 1239 Siping Road, Yangpu District

institute: Tongji University

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the following configurations:bowtie -v 2 -m1
Only these uniquely mapped reads were kept with the following command: samtools view -b -q 255 data.bam >uniquely_data.bam
peaks were called using macs2 version 2.1.0 with the default parameters plus --broad: macs2 -t treatment.bam -c input.bam --broad. H3K4me1, H3K27ac, H3K4me3, H3K27me3 and RNAPII peaks were called using macs version 1.4.1 with the following setting: macs14 -t treatment.bam -c input.bam --keep-dup auto -w -S --space 30 --fe-step=10.
Genome_build: mm9
Supplementary_files_format_and_content: broadPeak, bed

source_name: the corresponding 2nd iPS cell line

growth_protocol: The 2nd mouse embyronic fibroblast were derived from E13.5 tetraploid complementated all-iPS embryos and cultured with Feeder Medium. On passages 4, MEFs were plated on gelatin-coated dishes at appropriate density and the culture medium was changed to ES Medium supplemented with 1µg/ml Doxcycline and 50µg/ml Vitamin C to induce iPS cells. After 15days of induction, majority of cells were reprogrammed into Oct4-GFP+ ES-like colonies and we withrew Doxcycline and Vc from the medium. 3days later, the remaining dox-indenpent iPS cells were collected as day18 sample. The 2nd iPS cell line was established and maintained in ES medium supplemented with 2i(Gsk3i+Meki) with/without feeder. Feeder Medium contains DMEM supplemented with 10% (v/v) fetal bovine serum and 1 mM L-glutamine; ES Medium contains DMEM supplemented with 15% (v/v) fetal bovine serum , 1 mM L-glutamine, 0.1 mM mercaptoethanol, 1% nonessential amino acid stock,1% penicillin/streptomycin stock,1% nucleosides stock and 1000 U/ml LIF.

extract_protocol:
Reprogramming cells at different time point were trypsinized and washed twice with PBS. Cells were resuspended in PBS at a density of 107/ml and then chemically crosslinked by the addition of final 1% formaldehyde for 10 min at room temperature with gently rotation. Crosslinking was stopped by addition of glycine to a final concentration of 125 mM for 5 min at room temperature. Cells were washed twice with cold PBS and lysed in Lysis Buffer(10 mM Tris-HCl, pH 7.0, 10 mM NaCl, 3 mM MgCl2, 0.5% NP40; freshly added complete proteinase inhibitor cocktail (Roche)) at 4℃ for 15 min. Nuclei was collected by centrifugation and washed again with Lysis Buffer. Pellet was resuspended in ChIP Buffer I (300 mM NaCl, 3 mM EDTA, 1% NP40, 0.5% sodium deoxycholate, 0.1% SDS, 100 μg /ml BSA, 50 mM Tris, pH 8.0; freshly added proteinase inhibitor cocktail) and sheared by sonication to reduce the average DNA fragment size to 200-500 bp for analysis by q-PCR or 100-300 bp for analysis by sequencing. Antibodies were pre-coupled to protein G dynabeads. Generally, we used 10 μl protein G Dynabeads for 1 μg antibody. For transcription factor ChIP, we generally used 3 μg antibody for 30 μg chromatin per reaction; for histone ChIP, we used 1-2 μg antibody for 10-20 μg chromatin per reaction. After sonication, 1/10 of sheared chromatin was saved as input. The remaining chromatin was incubated with antibody-coupled dynabeads at 4℃ overnight. Beads were washed twice by ChIP Buffer I, four times by ChIP buffer II (100 mM Tris, pH 8.0, 500 mM LiCl, 1% NP40, 1% sodium deoxycholate) at 4℃ for 5 min with gently rotation. Beads were finally washed once by TE (10 mM Tris-HCl pH 8.0, 0.1 mM Na2EDTA) and transferred to a new tube for elution. Bound complexes were eluted twice in 100 μl Elution Buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 0.1% SDS; 0.25 mg/mL proteinase K added freshly) at 55℃ for 1 hr with shaking. The eluted chromatin was further reverse-crosslinked by overnight incubation at 65℃.Input chromatin was also treated to reverse crosslinking. Immunoprecipitated DNA and input DNA was extracted by phenol: chloroform: isoamyl alcohol (25:24:1, pH 8.0) and precipitated by ethonal with 100 μg /ml LPA as co-precipitant.
For the following sequencing analysis, 10-100 ng DNA mixed from two or three independent ChIP reactions was used to prepare ChIP-seq library following the NEB protocol with minor modifications. Briefly, DNA was end-repaired, dA-tailed and ligated with NEBNext adaptors. Following USER enzyme treatment, DNA was purified and size selected with 0.8X\0.4X AMpureXP beads (Beckman). Selected DNA was PCR amplified using Phusion (NEB) or Q5 (NEB) DNA polymerase for 12-14 cycles. PCR primers were from NEBNext Multiplex Oligos for Illumina kit (NEB). Different samples were tagged with different indexes and 3-4 ChIP-libraries were mixed as one lane sample in HiSeq 2000/HiSeq 2500.

value: established iPS cell line

value: H3K27ac-GFP/ Rosa26-M2rtTA transgenic background

tag: chip-antibody

value: anti-H3K27ac, Abcam(Ab4729)


title: Mbd2si-rep1

first: Yangming

last: Wang

address: 5 Yiheyuan Road

department: Institute of Molecular Medicine

institute: Peking University

description: average value of lane1 and lane2

data_processing:
Basecalls performed using CASAVA version 1.7
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v2.3.0
Fragments Per Kilobase of Transcript Per Million mapped reads (FPKM) were calculated by cufflinks from Trapnell C et al,Nat Biotechnol. 2010.
Genome_build: mm10
Supplementary_files_format_and_content: excel files include RPKM values for each Sample.

source_name: ESC

growth_protocol: 0.2 million Dgcr8-/- ESCs were plated in 6-well before transfection in normal culture.

extract_protocol:
Total RNA was prepared using Trizol (Invitrogen) and quantified on a BiodropsisBD2000 (OSTC)
RNA libraries were prepared for sequencing using standard Illumina pair-end protocols

treatment_protocol: 50 nM miRNA mimics (Dharmacon, Thermo Fisher)or siRNAs (GenePharma) were transfected into cells in each well of a six-well plate  with DharmaFECT1 (Dharmacon, Thermo Fisher) after 16h plating.

value: embryonic stem cells

tag: treatment/time

value: siMbd2 transfect/48h


title: miR294-rep2

description: average value of lane1 and lane2

value: miR-294 transfect/48h


title: BM-H3K4me3 Chip-seq


title: miR294-rep1

description: average value of lane1 and lane2


title: CTR-rep2

description: average value of lane1 and lane2

value: CTR transfect/48h


title: CTR-rep1

description: average value of lane1 and lane2


title: Brain IgG_ChIPSeq rep1

description: Chromatin IP against mouse Tet3FL

data_processing:
Bases were called using Illumina's CASAVA v1.8.2
Sequences were aligned to mm9 genome using Novoalign, only unique aligned reads were kept
Peaks were called using MACS 2.0 with default settings, and filtered to select the peaks with >= 10-fold enrichment
Genome_build: mm9
Supplementary_files_format_and_content: binary bedGraph files were generated using in house R scripts

source_name: Brain cells

value: Brain cells

value: differentiated


title: H3K27ac_ChipSeq_day5

source_name: reprogramming intermediate after 5days of induction

value: reprogramming intermediate


title: NP-2d Tet3FL_ChIPSeq

description: Chromatin IP against mouse Tet3FL

source_name: Neural progenitor cells_Tet3FL_ChIP

growth_protocol: J1 mESCs were grown on gelatin-coated plates at 37°C in knockout DMEM (Invitrogen; Carlsbad, CA) supplemented with 10% ES-qualified fetal bovine serum, 1x non-essential amino acids, 100 μM β-mercaptoethanol, 2 mM L-glutamine, and 1,000 U/ml LIF (ESGRO, Millipore, USA).

extract_protocol:
Cross-linked neuronal progenitor cells (2 days) were lysated, and neuclei were isolated. The nuclear pellet was re-suspended in 1 ml of cold shearing buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA, and 0.1% SDS) and chromatin was then sheared to 100-300 bp fragments using a Covaris S220 sonicator (Covaris; Woburn, MA) with the following settings; 12.5 min, 5% duty cycle, 140 Watts peak incident power, 200 cycles per burst. After adding 1% Triton X-100 and 150 mM NaCl (final concentrations) to the sheared chromatin and mixing, the solution was cleared by centrifugation at 14,000xg for 10 min at 4°C. Chromatin fragments were incubated with 1 μg of affinity purified anti-Tet3FL antibody (raised against a region of Tet3FL, amino acids 1-102) or IgG control (Santa Cruz; SC-2027) overnight at 4°C with rotation, and then immunoprecipitated using protein A magnetic beads (Millipore; Billerica, MA).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

value: ES-derived neural progenitor cells


title: Sample_IP_SCR2

city: Randwick

first: Tao

last: Liu

state: NSW

address: Lowy Cancer Research Centre

country: Australia

institute: Children's Cancer Institute Australia

data_processing:
Raw reads were aligned with BWA aln (version 0.7.12) against hg19 using default parameters.
For analyzing the effect of WDR5 on H3K4 trimethylation at N-Myc-binding and N-Myc nonbinding sites of gene promoters as well as enhancers, all canonical transcription start sites (TSS) were obtained, and read counts were generated in 50bp windows leading into and out of the TSS (at x=0), spanning +/- 1000bp of the TSS.
Genome_build: hg19
Supplementary_files_format_and_content: Read counts were determined using bedtools and normalised by the size of each input file.

organism: Homo sapiens

source_name: neuroblastoma BE(2)-C cells transfected with control siRNA

growth_protocol: BE(2)-C neuroblastoma cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA immunoprecipitated by the antibodies were purified and subjected to sequencing with Illumina HiSeq 2000 at Ramaciotti Centre for Genomics, University of New South Wales, Australia

treatment_protocol: BE(2)-C cells were treated with control siRNA and WDR5 siRNA-1 for 24 hours

value: peripheral nervous system tumour cell

value: H3K4me3 (Millipore, Millipore, 07-473, lot JBC1863338)


title: Brain Tet3FL_ChIPSeq rep2

description: Cromatin IP against mouse Tet3FL

value: mTet3FL (in house)


title: Sample_IgG_SCR

value: normal rabbit IgG (Santa Cruz, sc-2027, lot E1512)


title: Sample_IgG_WDR5

source_name: neuroblastoma BE(2)-C cells transfected with WDR5 siRNA-1


title: Brain Tet3FL_ChIPSeq rep1

description: Cromatin IP against mouse Tet3FL


title: Sample_Input_WDR5


title: Nalm6-TAmut 24h GRO-seq rep2

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1

country: Finland

institute: university of eastern finland

description:
nascent RNA
effect of TEL-AML1 expression on the nascent transcriptome in Nalm6 cells
Protocol: GRO-Seq

data_processing:
Libraries were sequenced for 51 cycles (single-end) on an Illumina HiSeq 2000, according to the manufacturer’s instructions.
GRO-Seq and RNA-Seq results were trimmed to remove A-stretches originating from the library preparation using the Homer software (homerTools trim) and from resulting sequences those shorter than 25 bp were discarded.  Sequence reads were further quality filtered with the FASTX software (-q 10 -p 97)
GRO-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.9 (-v 2 -k 3 -m 1 --best)
Bedgraphs were generated using the HOMER software. Data analysis was performed using HOMER and custom scripts http://biowhat.ucsd.edu/homer/
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph GRO-seq signal files

molecule: polyA RNA

source_name: Nalm6 pre-B-ALL cell line with inducible TEL-AML1-mut (dna-binding deficient) construct

growth_protocol: Nalm6 cells were cultured in RPMI (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) suppelemented with 2 mM L-glut, 100 U penicillin, 100 ug/ml streptomycin and 10% Tet System Approved FBS (Clontech, Mountain View, CA, USA).

extract_protocol:
GRO-Seq: Nuclei were extracted from 5-16 million cells and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol, DNase-treated, base-hydrolyzed and dephosphorylated with PNK. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads and precipitated overnight.
Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified. The recovered cDNA was circularized, linearized, amplified for 11-14 cycles. The final product was ran on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit. The final libraries were sequenced using an Illumina HiSeq 2000.

treatment_protocol: Expression of TEL-AML1, TEL-AML1-mut or control luciferase were induced with 500 ng/ml doxycycline (Clontech) at a concentration of 1 million cell/ml for 0h, 4h, 12h, or 24h.

tag: time

tag: construct

tag: replicate


title: Nalm6-TAmut 24h GRO-seq rep1


title: Nalm6-TA 24h GRO-seq rep1

source_name: Nalm6 pre-B-ALL cell line with inducible TEL-AML1 construct


title: Nalm6-TA 12h GRO-seq rep1


title: Nalm6-TA 12h GRO-seq rep2


title: Nalm6-TA 4h GRO-seq rep1

value: 4 h


title: Nalm6-TA 4h GRO-seq rep2


title: Nalm6-TA 24h GRO-seq rep2


title: Mbd2si-rep2

description: average value of lane1 and lane2


title: Nalm6-TA 0h GRO-seq rep1

value: 0 h


title: NP-2d IgG_ChIPSeq

description: Control

source_name: Neural progenitor cells_IgG_ChIP

value: IgG (Santa Cruz, SC-2027)


title: Sample_IP_WDR5


title: Nalm6-LUC 24h GRO-seq rep1

source_name: Nalm6 pre-B-ALL cell line with inducible LUC construct

value: LUC ctrl


title: H3K27ac LTEDT

city: London

first: Luca

last: Magnani

address: DuCane road

department: Surgery and Cancer

country: United Kingdom

institute: Imperial College London

description: H3K27ac LTEDT

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (Feburary, 2009) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 300 bp to create summary windows. Alignments were done using Bowtie 1.0.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) using default settings.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files

source_name: LTEDT

growth_protocol: Cells were cultured in DMEM containing 10%FCS or DCFCS (plus drugs, see Shaw et al 2006 for conditions).

extract_protocol:
Lysates were clarified from sonicated nuclei and H3K27ac--DNA complexes were isolated with antibody.
Libraries were prepared according to NEB DNA UltraKit's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 12 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated using Ampure SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the H-Seq2000 following the manufacturer's protocols.

value: LTED

value: H3K27ac (ab4729 abcam lot GR132150)

tag: protocol

value: DMEM without phenol + 10% DCS-FBS and1% Pen-Sprep-Glutamine + 100nM Tamoxifen


title: H3K27ac LTEDF

description: H3K27ac LTEDF

source_name: LTEDF

value: DMEM without phenol + 10% DCS-FBS and1% Pen-Sprep-Glutamine + 100nM Fulvestrant


title: HepG2 Control 2

city: D

first: Kate

last: Meyer

state: NC

address: 307 Research Drive Box 3711

department: Biochemistry

institute: Duke University School of Medicine

data_processing:
Barcodes used were NNNGGTTNN (HSreplicates1), NNNTTGTNN (HSrep2),  NNNCAATNN (CTLrep1), and NNNACCTNN (CTLrep2)
Alignment to hg19 was performed using novoalign
Genome_build: hg19
Supplementary_files_format_and_content: m6A sites were identified from single reads using CIMS (C2T transitions, p=0.1). Metagene profiles were performed using hg19 genomic annotations. For HEK control samples, miCLIP data from Linder et al (2015) were used.

source_name: HepG2 cells

growth_protocol: Cells were grown in standard growth media for each cell line

extract_protocol:
Total RNA was extracted using TRIzol reagent. RNA was then subjected to DNAseI treatment to remove any contaminating DNA. mRNA was then isolated using oligo(dT) Dynabeads (Invitrogen).
Library construction was performed using the miCLIP method to map m6A residues at single-nucleotide resolution: Linder et al, Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. Nature Methods, 2015 Aug;12(8):767-72.

treatment_protocol: For heat shock treatment, cells were transferred to a 42C incubator for 1h and then placed back at 37C for 6h.

value: human liver hepatocellular carcinoma cells

tag: antibody name

value: Rabbit anti-m6A (Abcam #ab151230)


title: Nalm6-LUC 24h GRO-seq rep2


title: H3K27ac LTED

description: H3K27ac LTED

source_name: LTED

value: DMEM without phenol + 10% DCS-FBS and1% Pen-Sprep-Glutamine


title: H3K27ac MCF7T

description: H3K27ac MCF7T

value: DMEM+10% FBS and 1% Pen-Sprep-Glutamine + 100nM Tamoxifen


title: HepG2 Control 1


title: H3K27ac MCF7F

description: H3K27ac MCF7F

value: DMEM+10% FBS and 1% Pen-Sprep-Glutamine + 100nM Fulvestrant


title: HepG2 Heat Shock 2


title: Brain IgG_ChIPSeq rep2

description: Control

value: Brain cells

value: differentiated


title: HPMEC 48h rep 1

city: Los Angeles

first: Kevin

last: Huang

address: Gonda BLDG Rm. 6554, P.O.Box 957088

department: Human Genetics

institute: UCLA

data_processing:
Raw reads from the Illumina HiSeq2000 were mapped to the hg19 genome and Refseq genes using default parameters in BWA
Uniquely mapped transcripts reads were transformed using the reads per kilobase per million (RPKM) metric
Genes with low expression in all stages (average RPKM<0.5) were filtered out for differential gene expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: metaRPKM.txt: matrix listing normalized (RPKM) expression values

source_name: HPMEC 48h hypoxia exposure

growth_protocol: Human pulmonary microvascular endothelial cells (HPMECs) were obtained from ScienCell Research Laboratories (Catalog #3000), and cultured according to company’s recommendations

extract_protocol:
Total RNA was extracted using Trizol.
Libraries were constructed following Illumina's Truseq sample preparation protocol.

treatment_protocol: HPMECs were first cultured in a 75cm2 flask until reaching 90% confluency, then passaged equally into 12 equivalent portions on 2 six-well plates. At 80% confluency, the cells were exposed to hypoxia (1% O2) for 0, 8, 24 and 48 hours.

value: human pulmonary microvascular endothelial cells

tag: hypoxia exposure

value: 48 hours


title: HPMEC 24h rep 3

source_name: HPMEC 24h hypoxia exposure

value: 24 hours


title: HEK Heat Shock 1

source_name: HEK293T cells

value: human embryonic kidney cells


title: HPMEC 48h rep 2


title: HPMEC 24h rep 1


title: HPMEC 24h rep 2


title: HepG2 Heat Shock 1


title: Sample_Input_SCR

value: peripheral nervous system tumour cell


title: HPMEC 8h rep 3

source_name: HPMEC 8h hypoxia exposure

value: 8 hours


title: HPMEC 8h rep 2


title: Xenografted leukemia [-T PDX M2]

city: Loma Linda

first: Kimberly

last: Payne

address: 11085 Campus Street, Mortensen Hall, First Floor

institute: Loma Linda University

description: -T PDX M2

data_processing:
Reads were mapped to the human genome (hg19) using RefSeq annotation
Transcript estimation was performed using RNA-Seq by Expectation Maximization method (Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC bioinformatics. 2011;12(323)
Differenential expression was performed using the EBSeq method (Leng N, Dawson JA, Thomson JA, et al. EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics. 2013;29(8):1035-1043.)
Genome_build: hg19
Supplementary_files_format_and_content: TPM

source_name: B cells

extract_protocol:
Qiagen Micro kit
RNA amplification with Nugen Ovation v2 kit and library preparation with Kapa mRNA-Seq kit

tag: primary

value: No

tag: xenograft

value: Yes

tag: agent


title: Xenografted leukemia [+T PDX M2]

description: +T PDX M2

value: TSLP


title: HPMEC 8h rep 1


title: Xenografted leukemia [+T PDX M1]

description: +T PDX M1


title: CRLF2 primary leukemia [Patient 2]

description: Patient 2


title: HPMEC 0h rep 2

source_name: HPMEC 0h hypoxia exposure

value: 0 hours


title: HPMEC 0h rep 1


title: SMN-GFP ChIP

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

data_processing:
Libraries were sequenced (single end reads) on the Illumina HiSeq 2500. Reads were extracted and demultiplexed from BCL files with blc2fastq version 1.8.3. For all samples except technical replicate 1 of POLR2A ChIP in Raji cells with SMN or GFP knockdown, adaptor sequences were removed.
Reads from technical replicate samples were combined and aligned to the human genome, build hg19, using Bowtie2 with settings -5 1 -3 2 -local (POLR2A ChIP in shGFP and shSMN Raji cells) or settings -local (other samples). Duplicate reads were removed to generate BAM files.
To generate 'meta-gene' alignment plots, reads were extended to 300 bp. Pileups – the number of fragments overlapping each genomic bp – were calculated, and were normalized by million mappable reads in the ChIP-seq library. Normalized pileups from different replicates (done with different antibodies) were then averaged to create FPM (fragments per million reads).
Genome_build: hg19
Supplementary_files_format_and_content: Figures showing the average (across represented genes) density of aligned ChIP fragments per million in the library, for each aligned base. Plots were generated directly from BAM files.

growth_protocol: HEK293 cells were grown in DMEM plus FBS , and stably transduced cell lines were maintained with 2μg/ml puromycin or with 2ul/ml hygromycin selection. Cells were harvested at 90% confluency.

extract_protocol:
10e7-10e8 cells were cross-linked for 10 min in 1% formaldehyde. Lysates were sonicated to a DNA fragment length range of 200-300 bp using a Bioruptor (Diagenode). RNAPII was immunoprecipitated with 2ug of antibodies and Dynabeads Protein G (Invitrogen). Subsequently, crosslinks were reversed at 65°C over night and bound DNA fragments were purified (EZ-10 Spin Column PCR Product Purification kit, Bio Basic).
Sequencing libraries were constructed using the TruSeq ChIP Sample Prep Kit (Illumina) according the manufacturer's instructions.

treatment_protocol: Expression of SMN-GFP was induced by overnight Dox induction (2ug/ml)

tag: genotype/variation

value: Expressing Dox inducible GFP-SMN fusion protein. Construct is hygromycin resistant.

tag: antibody

value: GFP (Abcam pAb Cat# 290)


title: H3K27ac MCF7

description: H3K27ac MCF7

source_name: MCF7 cells

tag: cell line

value: H3K27ac (ab4729 abcam lot GR132150)

value: DMEM+10% FBS and 1% Pen-Sprep-Glutamine


title: SMN ChIP

tag: cell type

value: SMN (Santa Cruz pAb Cat # H-195)


title: IgG ChIP

source_name: Raji (lymphocyte)

growth_protocol: Raji (suspension cells) were grown to confluency in RPMI plus 10% FBS and 1% Glutamate before harvest.

value: Raji (EBNA 1 positive)

value: Wild type

value: IgG (Invitrogen Cat # 10500C)


title: Nalm6-TA 0h GRO-seq rep2

value: 0 h


title: RNAPII ChIP, Wild-type RNAPII

growth_protocol: Raji (suspension cells) were grown to confluency in Tet-media before harvest.

treatment_protocol: Stably expressing amanitin resistant WT RNAPII (at 0.5mg/ml) with the endogenous RNAPII abolished by 3 day treatment of the drug at 2ug/ml. Grown in Tet- media.

value: Expressing amanitin-resistant wt POLR2A

value: RNAPII (N20) (Santa Cruz pAb Cat # sc-899)


title: RNAPII ChIP, R1810A mutant RNAPII

treatment_protocol: Expressing amanitin resistant R1810A mutant RNAPII (at 0.5mg/ml) with the endogenous RNAPII abolished by 3 day treatment of the drug at 2ug/ml. Grown in Tet- media.

value: Expressing amanitin-resistant R1810A mutant POLR2A


title: P6_Ttm

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

institute: St Vincent's Institute of Medical Research

data_processing:
Base calling
Barcode deconvolution and stripping
Alignment to mature miRNA database (miRBase)
Alignment of remaining reads to miRNA precursor database (miRBase)
Read abundance counting and normalization to library read size
Genome_build: miRBase 17
Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count

source_name: CD4+ T cells

growth_protocol: No cell culture involved

extract_protocol:
Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturer’s protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.
Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5’ end of each library.

treatment_protocol: Fresh heparinised venous blood or buffy coats were processed by Ficoll-Paque® centrifugation (Amersham Pharmacia Biotech AB) to recover peripheral blood mononuclear cells (PBMCs). PBMCs were stored in liquid nitrogen prior to T cell subset sorting. CD4+ T cells were enriched with anti-human CD4 microbeads (clone M-T466) (Miltenyi Biotec) then labeled with the following antibodies: CD4-Pacific Blue (clone RPA-T4), CD45RA-APC (clone HI100), CD45RO-PE (clone UCHL1), CD27-FITC (clone M-T271), CCR7-Percp*Cy5.5 (clone 150503) (BD Bioscience) and CD25-PE-Cy7 (clone BC96) (eBiosciences). The cells were FACS-sorted into 6 subsets: naïve (CD45RA+ CD45RO- CD25-), resting Treg (rTreg) (CD45RA+ CD45RO- CD25+), activated Treg (aTreg) (CD45RA- CD45RO+ CD25 ++), central memory (Tcm) (CD45RA- CD45RO+ CD25lo/- CD27+ CCR7+), transitional memory (Ttm) (CD45RA- CD45RO+ CD25lo/- CD27+ CCR7-) and effector memory (Tem) (CD45RA- CD45RO+ CD25lo/- CD27- CCR7-).

tag: status

tag: barcode

value: TCAACGGTAG


title: P4_Ttm

value: AGCCTAAGCT


title: RNAPII ChIP, shSMN 4h8

description:
RNAP2_geneAlignment_shGFP.pdf
2 technical replicates

growth_protocol: Raji cells were cultured in RPMI plus 10% FBS and 1% Glutamate, and stably transduced cells were maintained with 500μg/ml G418. Cells were grown to confluency before harvest.

treatment_protocol: Stable shRNA mediated knock down of SMN upon puromycin selection.

value: Expressing shRNA targeting SMN under CMV promoter.

value: RNAPII CTD, phospho-S5 (4h8) (Abcam mAb Cat # ab5408)


title: P7_Ttm


title: P5_Ttm


title: P3_Ttm


title: RNAPII ChIP, shGFP 4h8

treatment_protocol: Negative control with stable GFP knock down upon puromycin selection.

value: Expressing shRNA targeting GFP under CMV promoter.


title: RNAPII ChIP, shGFP 8wg16

value: RNAPII CTD (8wg16) (purified in the lab)


title: RNAPII ChIP, shSMN 8wg16


title: P6_Tem

value: GTGCATCCTA


title: P7_Tem


title: P1_Ttm


title: 5_CD4+ ILC1

city: Seattle

first: Scott

last: Presnell

state: WA

address: 1201 Ninth Avenue

institute: Benaroya Research Institute

description: Samples 5-6 are from the same subject

data_processing:
Base-calling was performed automatically in Illumina BaseSpace after sequencing; FASTQ reads were trimmed in Galaxy using FastqMcf (FastqMcf tool, v.1.0.0) to remove SMARTer adapter sequences
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0).
Reads representing potential PCR duplicates were removed in Galaxy using SAMTools rmdup (rmdup tool, v.1.0.1)
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Samples with low total raw counts (< 50,000; samples '13_CD4+ ILC1' and '14_CD4- ILC1') were removed prior to analysis.
Standard workflow in DESeq2 was followed to compare CD4+ vs. CD4- in ILC1 libraries using  raw counts. Default values for normalization, calculating dispersion, and fitting the model were used in the DESeq function. Similarly, default values for filtering, based on low counts and outliers using Cook's distance, were used in the results function.
Genome_build: GRCh37
Supplementary_files_format_and_content: ILC1rawCounts.csv: comma-separated matrix – first column contains Ensembl gene ID, remaining columns include raw read counts assigned for each library. Data represents all processing steps up to read counting, not including sample QC and analysis with DESeq2.

source_name: sorted CD4+ ILC1

extract_protocol:
Cell subsets were sorted, then lysed to release RNA, converted to cDNA, and amplified using the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech)
Sequencing libraries were constructed from the amplified cDNA using a modified protocol of the Nextera XT DNA sample preparation kit (Illumina), to generate Illumina-compatible libraries.

tag: cohort

value: Control; healthy control subject

tag: age (yrs)

tag: gender

value: Male

tag: tissue

value: Peripheral blood

value: sorted CD4+ ILC1


title: P4_Tem

value: CATTGTTAGC


title: 4_CD4- ILC1

description: Samples 3-4 are from the same subject

source_name: sorted CD4- ILC1

value: Female

value: sorted CD4- ILC1


title: P2_Tem


title: 3_CD4+ ILC1

description: Samples 3-4 are from the same subject


title: HPMEC 0h rep 3

value: human pulmonary microvascular endothelial cells

value: 0 hours


title: Xenografted leukemia [-T PDX M1]

description: -T PDX M1

value: No

value: Yes


title: P1_Tem


title: nascent_RNA-trough-rep2 RNA-seq

description: brdu-antibody aided

source_name: U2OS cells

value: U2OS (ATCC HTB-96)

value: bone osteosarcoma

tag: chip antibody

value: brdu antibody (sc-32323)


title: P4_Tcm


title: P7_Tcm


title: P2_Ttm

value: TCAACGGTAG


title: P3_Tem


title: P6_Tcm


title: 8_CD4- ILC1

description: Samples 7-8 are from the same subject


title: nascent_RNA-trough-rep1 RNA-seq

description: brdu-antibody aided


title: nascent_RNA-peak-rep2 RNA-seq

description: brdu-antibody aided


title: 7_CD4+ ILC1

description: Samples 7-8 are from the same subject


title: P5_Tcm


title: P3_Tcm


title: 6_CD4- ILC1

description: Samples 5-6 are from the same subject


title: nascent_RNA-peak-rep1 RNA-seq

description: brdu-antibody aided


title: P5_Tem


title: P1_Tcm


title: UCB HSC

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

description: Sample 4

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq: Sequence reads were aligned to hg19 using TopHat with default parameters
RNAseq: FPKM were obtained using CuffLinks with upper-quartile and GC normalization
Genome_build: hg19
Supplementary_files_format_and_content: RNAseq: tab-delimited FPKM values for each Refseq gene.

source_name: umbilical cord blood hematopoietic stem cells

extract_protocol:
RNA was harvested using Trizol treatment
Illumina TruSeq PE 51x2 (RNA-seq)


title: P7_aTreg


title: P5_aTreg

value: AGCCTAAGCT


title: 2_CD4- ILC1

description: Samples 1-2 are from the same subject


title: P4_aTreg


title: P2_aTreg


title: P3_aTreg


title: 1_CD4+ ILC1

description: Samples 1-2 are from the same subject


title: P7_rTreg


title: P6_rTreg

value: GTGCATCCTA


title: P2_Tcm


title: P2_rTreg


title: P4_rTreg


title: P1_rTreg


title: P2_Naive


title: P4_Naive


title: P1_Naive


title: P5_rTreg


title: P3_rTreg


title: P3_Naive


title: P6_Naive


title: P5_Naive


title: M10_Ttm

value: healthy


title: M9_Ttm


title: M8_Ttm


title: M12_Ttm


title: NKT-3_5

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

description: Surface Valpha14Jalpha18 TCR positive

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
RNA-seq reads were aligned to mm9 genome using tophat2 (version 2.0.6) with default parameters.
Aligned reads were assigned to genes and counted using cufflinks version  2.1.1) with default parameters and annotation file of mouse Entrez genes.
Genome_build: mm9 (NCBI version 37.2)
Supplementary_files_format_and_content: FPKM (cufflinks output, tab-separated values)

source_name: NKT stage-3

growth_protocol: DN1eP thymocytes were cultured for 10 days on OP9/Dll-1 stromal monolayer in the presence of mouse IL-2 (5 ng/ml) and mouse IL-7 (5 ng/ml), both from R&D, in a complete RPMI1640 culture medium supplemented with 10% FCS.

extract_protocol:
Thymocyted were highly purified using standard methods, including MACS sorting followed by FACS sorting, and RNA was prepared using RNeasy Micro Plus kit containing gDNA eliminator columns. RNA was analyzed for quantity and quality using Agilent Bioanalyzer 2100 equipment. and around 10-to-100 ng of total RNA was used with SMARTer Ultra Low Input RNA for Illumina Sequencing kit (Clontech) or Illumina TruSeq RNA Sample Prep Kit v2 for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: thymocyte

tag: strain

tag: age

value: 6-to-8 wk old


title: NKT-3_4

description: Surface Valpha14Jalpha18 TCR positive


title: NKT-3_6

description: Surface Valpha14Jalpha18 TCR positive


title: NKT-3_3

description: Surface Valpha14Jalpha18 TCR positive


title: NKT-3_2

description: Surface Valpha14Jalpha18 TCR positive


title: M12_Tem


title: P1_aTreg


title: M9_Tem


title: M10_Tem


title: M7_Ttm


title: NKT-3_1

description: Surface Valpha14Jalpha18 TCR positive


title: M12_Tcm


title: NKT-2_7

description: Surface Valpha14Jalpha18 TCR positive

source_name: NKT stage-2


title: NKT-2_5

description: Surface Valpha14Jalpha18 TCR positive


title: NKT-2_2

description: Surface Valpha14Jalpha18 TCR positive


title: NKT-2_3

description: Surface Valpha14Jalpha18 TCR positive


title: M30_aTreg


title: NKT-2_1

description: Surface Valpha14Jalpha18 TCR positive


title: M12_aTreg


title: M29_aTreg


title: NKT-2_4

description: Surface Valpha14Jalpha18 TCR positive


title: NKT-2_6

description: Surface Valpha14Jalpha18 TCR positive


title: P6_aTreg


title: M9_aTreg


title: M26_aTreg


title: NKT-1_4

description: Surface Valpha14Jalpha18 TCR positive

source_name: NKT stage-1


title: NKT-1_5

description: Surface Valpha14Jalpha18 TCR positive


title: M30_rTreg


title: NKT-1_3

description: Surface Valpha14Jalpha18 TCR positive


title: M27_rTreg


title: NKT-1_2

description: Surface Valpha14Jalpha18 TCR positive


title: NKT-1_1

description: Surface Valpha14Jalpha18 TCR positive


title: M26_rTreg


title: DN1eP-NKT_4

description: Surface Valpha14Jalpha18 TCR positive

source_name: DN1eP precursor derived NKT


title: DN1eP-NKT_3

description: Surface Valpha14Jalpha18 TCR positive


title: M7_aTreg


title: M9_Tcm


title: DN1eP-NKT_2

description: Surface Valpha14Jalpha18 TCR positive


title: M7_rTreg


title: M8_rTreg


title: M27_aTreg


title: DN1eP-NKT_1

description: Surface Valpha14Jalpha18 TCR positive


title: DN1eP_3

description: Surface Valpha14Jalpha18 TCR negative

source_name: DN1eP precursors


title: M12_naive


title: M7_naive


title: P7_Naive


title: N22-Desiccation stress

city: New Delhi

first: Mukesh

last: Jain

address: New Mehrauli Road

institute: Jawaharlal Nehru University

data_processing:
Illumina 1.3 pipeline used for basecalling
Low-quality reads and reads containing adapter/primer contamination were filtered using NGS QC Toolkit v2.2
FPKM for all the genes was calculated using the cuffdiff package provided in cufflinks
Genome_build: Rice genome MSUv7.0 (ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/)
Supplementary_files_format_and_content: tab delimited text files include FPKM values for each sample

source_name: Nagina 22_Seedlings

growth_protocol: Seedlings were grown in a culture room

extract_protocol:
Tissue samples were collected and frozen in liquid nitrogen. Total RNA was isolated using TRI reagent from Sigma
Libraries were prepared using mRNA-Seq Sample Prep kit (Illumina) according to the manufacturer’s protocol

treatment_protocol: Control, desiccation and salinity treatments were given to seedlings of IR64, N22 and Pokkali rice cultivars. For desiccation seedlings were kept on dry filter paper, for control RO water was used and 200 mM salt solution was used for salinity treatment.

tag: genotype/cultivar

value: Nagina 22

tag: condition

value: Desiccation stress

value: seedlings


title: IR64-Salinity stress

value: Salinity stress


title: PK-Control

value: Pokkali

value: control


title: DN1eP_2

description: Surface Valpha14Jalpha18 TCR negative


title: DN1eP_1

description: Surface Valpha14Jalpha18 TCR negative


title: M29_naive


title: IR64-Control


title: M12_rTreg

value: CATTGTTAGC


title: Caragana intermedia  _HIGSeq

first: Zhu

last: Jianfeng

address: Haidian District, Xiang Shan Road

department: Research Center of Saline and Alkali Land of State Forestry Administration

institute: Chinese Academy of Forestry

data_processing:
BGI small RNA analysis pipline software used for basecalling.
Remove low qulity reads strictly
Trim 3' adaptor sequence and remove 5' adaptor contaminants
Plot data distribution
Remove too small and polyA
Genome_build: no reference sequence used for read alignment
Supplementary_files_format_and_content: tab-delimited text files include the expression abundance for each unique sequence read

organism: Caragana korshinskii

source_name: seedlings

extract_protocol:
Roots, stems and leaves were collected from 3-week-old seedlings, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq Small RNA Sample Prep Kit (RS-200–0012) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: roots,stems and leaves of seedlings

value: three weeks after germination

tag: genotype

value: wild type


title: aft2 strain, time=3, replicate A

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

state: Barcelona

address: ED. IBB

department: Biochemistry & Mol. Biol.

country: Spain

institute: UNIVERSITAT AUTONOMA BARCELONA

description:
DELTAaft2-3-A
aft2_time-course_replicA.txt

data_processing:
Sequencing was performed in an Illumina MiSeq machine and the MiSeq Reagent Kit v3 (single end, 150 nt/read). Base calling done by MiSeq Reporter analysis software (generates *.bcl files)
Sequenced reads were trimmed for adaptor sequence and mapped against Saccharomyces_cerevisiae_NCBI_build3.1 genome using Bowtie2-2.1.0 (local alignment, sensitive mode)
Reads per Megabase of library size were calculated using the SeqMonk software with  CDS (+ 50 nt 5' and 3' extensions) probes. No correction for target size was made since no intragenome comparisons are made in the study.
Genome_build: EnsEMBL release 74 (EF4)
Supplementary_files_format_and_content: reads per million

organism: Saccharomyces cerevisiae

source_name: aft2 strain, time=3, replicate A

growth_protocol: Wild type W303-1A and its MML1086 derivative (Daft2) were grown in YPD medium until 1x107 cells/ml.

extract_protocol:
cells were collected and processed for total RNA isolation as in Bellí et al. (Yeast 14: 1127-1138, 1988)
Poly A (+) RNA was selected with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ref. E7490). Preparation of libraries was carried out with NEBNext® Ultra™ Directional RNA Library Prep Kit (Ref. E7420) and the Illumina oligo set 1 (Ref. E7335).

treatment_protocol: Sodium selenite was then added to reach a final concentration of 1 mM and growth continued. Cultures were rediluted in selenite-containing medium when required, to avoid reaching concentrations higher than 5x107 cells/ml.  Aliquots of the culture (6x108 cells) were taken after 1, 3 and 5 h of selenite treatment

value: strain MML1086 (W303-1A aft2::kanMX4)

value: delta aft2


title: aft2 strain, time=1, replicate A

description:
DELTAaft2-1-A
aft2_time-course_replicA.txt

source_name: aft2 strain, time=1, replicate A


title: aft2 strain, time=0, replicate A

description:
DELTAaft2-0-A
aft2_time-course_replicA.txt

source_name: aft2 strain, time=0, replicate A


title: aft2 strain, time=5, replicate A

description:
DELTAaft2-5-A
aft2_time-course_replicA.txt

source_name: aft2 strain, time=5, replicate A


title: aft2 strain, time=0, replicate B

description:
DELTAaft2-0-B
aft2_time-course_replicB.txt

source_name: aft2 strain, time=0, replicate B


title: Wild type strain, time=5, replicate B

description:
WT-5-B
WT_time-course_replicB.txt

source_name: Wild type strain, time=5, replicate B

value: strain W303-1A


title: Wild type strain, time=3, replicate B

description:
WT-3-B
WT_time-course_replicB.txt

source_name: Wild type strain, time=3, replicate B


title: Wild type strain, time=0, replicate B

description:
WT-0-B
WT_time-course_replicB.txt

source_name: Wild type strain, time=0, replicate B


title: aft2 strain, time=5, replicate B

description:
DELTAaft2-5-B
aft2_time-course_replicB.txt

source_name: aft2 strain, time=5, replicate B


title: aft2 strain, time=1, replicate B

description:
DELTAaft2-1-B
aft2_time-course_replicB.txt

source_name: aft2 strain, time=1, replicate B


title: PK-Salinity stress


title: Wild type strain, time=5, replicate A

description:
WT-5-A
WT_time-course_replicA.txt

source_name: Wild type strain, time=5, replicate A


title: Wild type strain, time=1, replicate B

description:
WT-1-B
WT_time-course_replicB.txt

source_name: Wild type strain, time=1, replicate B


title: aft2 strain, time=3, replicate B

description:
DELTAaft2-3-B
aft2_time-course_replicB.txt

source_name: aft2 strain, time=3, replicate B


title: Wild type strain, time=3, replicate A

description:
WT-3-A
WT_time-course_replicA.txt

source_name: Wild type strain, time=3, replicate A


title: IR64-Desiccation stress


title: DN1eP_4

description: Surface Valpha14Jalpha18 TCR negative

source_name: DN1eP precursors


title: Wild type strain, time=1, replicate A

description:
WT-1-A
WT_time-course_replicA.txt

source_name: Wild type strain, time=1, replicate A


title: cdc55(AWR5)_Ind_rep4

data_processing:
Base calling done by  MiSeq Reporter analysis software (generates *.bcl files)
Sequenced reads were trimmed for adaptor sequence and mapped against Saccharomyces_cerevisiae_NCBI_build3.1 genome using Bowtie2-2.1.0 (local alignment, sensitive mode)
Reads per Megabase of library size were calculated using the SeqMonk software using CDS + 100 nt 3' probes: no correction for target size was made since the library is essentially generated over the 3' of the gene.
Genome_build: EnsEMBL release 74 (EF4)

source_name: total yeast RNA

growth_protocol: yeast strains were grown overnight in rich YPD medium with doxycycline 15µg/ml (repressing conditions), then normalized to OD600=0.05.

extract_protocol:
total RNA was extracted from the samples using the RiboPureTM RNA Purification Kit yeast (Ambion, Carlsbad, CA, USA)
Libraries were prepared with the strand-specific QuantSeq 3’ mRNA kit (Lexogen, Greenland, NH,USA) using 0.5 μg of total RNA purified as above. The library provides reads that are generated towards the poly(A) tail, directly reflecting the mRNA sequence. The workflow is: 1) oligodT priming containing sequencing platform-compatible linker sequences. 2) Removal of RNA after first strand synthesis. 3) Second strand synthesis by random priming and a DNA polymerase. The random primer contains sequencing platform-compatible linker sequences. 4) Second strand synthesis is followed by a magnetic bead-based purification step. Library   amplification step introducing the sequences required for cluster generation on Illumina platforms.

treatment_protocol: Cultures (OD600=0.05. ) were resuspended in YPD medium with or without (inducing conditions) doxycycline 15µg/ml and grown for 6  prior sampling.

tag: genetic background

value: JA-100 cdc55 tetO:AWR5-GFP


title: cdc55(AWR5)_NoInd_rep3


title: Wild type strain, time=0, replicate A

description:
WT-0-A
WT_time-course_replicA.txt

source_name: Wild type strain, time=0, replicate A

tag: genotype/variation


title: cdc55(AWR5)_Ind_rep3


title: cdc55(AWR5)_NoInd_rep4


title: cdc55(AWR5)_Ind_rep1


title: WT(AWR5)_ind_rep3

value: JA-100 CDC55 tetO:AWR5-GFP


title: cdc55(AWR5)_Ind_rep2


title: N22-Control

source_name: Nagina 22_Seedlings


title: cdc55(AWR5)_NoInd_rep1


title: H3K4me3_ChIPSeq_PC2

city: Uppsala

first: Prasoon

last: Agarwal

state: Sweden

address: Dag Hammarshkojlds vag 20

department: IGP

country: Sweden

institute: Rudbeck Laboratory, Uppsala University

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Lifescope version 2.5 with default parameters.
Uniquely mapped using LifeScope version 2.5 and BioScope
peaks were called using MACS version 1.4.1 with the following setting: Default parameters.
Unique peaks (unique_PC1.bed, unique_PC2.bed) for each patient mark were obtained by using plasma cell H3K27me3 and H3K4me3 chipseq bam files as controls against each mark of all patients bam file. Thus obtaining 8 unique files with one plasma cell and in total 16 files with two plasma cell chipseq.
Genome_build: hg19

source_name: Normal Plasma cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to 5500 series SOLiD system instructions accompanying the Library Builder™ Fragment Core Kit for 5500 SOLiD™ (#Part no. 4463763).

treatment_protocol: Samples were not treated

value: Normal plasma cell derived from bone marrow

tag: antibody

value: H3K4me3(Milipore, 07-473)


title: input DNA_PC2

value: none (input)


title: WT(AWR5)_ind_rep1


title: input DNA_PC1


title: H3K4me3_ChIPSeq_PC1


title: H3K27me3_ChIPSeq_PC2

value: H3K27me3 (Millipore, 07-449)


title: WT(AWR5)_Noind_rep1


title: WT(AWR5)_Ind_rep4


title: H3K27me3_ChIPSeq_PC1


title: WT(AWR5)_NoInd_rep2


title: Patient_RNA-seq

description: Sample 1

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using Lifescope version 2.5 with default parameters.
Reads Per Kilobase of exon per model per Million mapped reads were calculated using  the formula RPKM = 10^9 x (ExonReadCount / (TotalReadCount x ExonLength))
Genome_build: hg19
Processed data files format and content: tab-delimited text file includes RPKM values for the patient RNA seq sample.

source_name: Malignant Plasma cells

growth_protocol: Freshly isolated CD138+ Plasma cell from MM patient bone marrow.

extract_protocol:
RNA was isolated using RNAeasy mini kit(Qiagen).
Libraries were prepared according to 5500 series SOLiD system instructions accompanying the Library Builder™ . First the RNA was concentrated using RiboMinus (RiboMinus™ Eukaryote System v2, Catalog Numbers A15020,). The rRNA depleted RNA is clean up on columns using the Concentrator module ((Cat. no. K1550-05) ). rRNA depleted RNA is quantified using  Qubit® RNA Assay Kit and Qubit® 2.0 Fluorometer. Then verification of rRNA depletion is done using Agilent RNA 6000 Pico Kit. Further, SOLiD™ Total RNA-Seq Kit (PN 4445374) to convert RNA transcripts expressed in a cell or tissue into a cDNA library for analysis on the Applied Biosystems SOLiD™ Sequencing System. Frist RNA is  fragmented into ~150bp fragments using enzyme RNaseIII afterwards the fragmented RNA is put in the library builder (Pat no. 4463421)were reverse transcription and size selection is done. Barcodes are put during the amplification step.

treatment_protocol: Samples were  not treated

value: CD 138+ Plasma cell derived from bone marrow

tag: patient mm stage

value: IgG lambda 2B


title: Patient 4 H3K27me3_ChIPSeq

description: Patient 4

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Lifescope version 2.5 with default parameters.
Uniquely mapped using LifeScope version 2.5 and BioScope
peaks were called using MACS version 1.4.1 with the following setting: Default parameters.
Unique peaks (unique_PC1.bed, unique_PC2.bed) for each patient mark were obtained by using plasma cell H3K27me3 and H3K4me3 chipseq bam files as controls against each mark of all patients bam file. Thus obtaining 8 unique files with one plasma cell and in total 16 files with two plasma cell chipseq.
Genome_build: hg19
Processed data files format and content: Bed files generated using MACS version 1.4.1
pat4_K27_peaks.bed = pat4_H3K27me3_peaks/Input
pat4_K27_unique_peaks.bed = pat4_H3K27me3_peaks/pat4_H3K4me3_peaks

tag: cell type

value: IgG lambda 2A

value: H3K27me3 (Millipore, Cat.no 07-449, Lot JBC1873477)


title: Patient 3 H3K27me3_ChIPSeq

description: Patient 3

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Lifescope version 2.5 with default parameters.
Uniquely mapped using LifeScope version 2.5 and BioScope
peaks were called using MACS version 1.4.1 with the following setting: Default parameters.
Unique peaks (unique_PC1.bed, unique_PC2.bed) for each patient mark were obtained by using plasma cell H3K27me3 and H3K4me3 chipseq bam files as controls against each mark of all patients bam file. Thus obtaining 8 unique files with one plasma cell and in total 16 files with two plasma cell chipseq.
Genome_build: hg19
Processed data files format and content: Bed files generated using MACS version 1.4.1
pat3_K27_peaks.bed = pat3_H3K27me3_peaks/Input
pat3_K27_unique_peaks.bed = pat3_H3K27me3_peaks/pat3_H3K4me3_peaks


title: Patient 2 H3K4me3_ChIPSeq

description: Patient 2

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Lifescope version 2.5 with default parameters.
Uniquely mapped using LifeScope version 2.5 and BioScope
peaks were called using MACS version 1.4.1 with the following setting: Default parameters.
Unique peaks (unique_PC1.bed, unique_PC2.bed) for each patient mark were obtained by using plasma cell H3K27me3 and H3K4me3 chipseq bam files as controls against each mark of all patients bam file. Thus obtaining 8 unique files with one plasma cell and in total 16 files with two plasma cell chipseq.
Genome_build: hg19
Processed data files format and content: Bed files generated using MACS version 1.4.1
pat2_K4_peaks.bed = pat2_H3K4me3_peaks/Input
pat2_K4_unique_peaks.bed = pat2_H3K4me3_peaks/pat2_H3K27me3_peaks

value: H3K4me3 (Milipore, Cat.no 07-473, Lot JBC1888194)


title: Patient 4 H3K4me3_ChIPSeq

description: Patient 4

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Lifescope version 2.5 with default parameters.
Uniquely mapped using LifeScope version 2.5 and BioScope
peaks were called using MACS version 1.4.1 with the following setting: Default parameters.
Unique peaks (unique_PC1.bed, unique_PC2.bed) for each patient mark were obtained by using plasma cell H3K27me3 and H3K4me3 chipseq bam files as controls against each mark of all patients bam file. Thus obtaining 8 unique files with one plasma cell and in total 16 files with two plasma cell chipseq.
Genome_build: hg19
Processed data files format and content: Bed files generated using MACS version 1.4.1
pat4_K4_peaks.bed = pat4_H3K4me3_peaks/Input
pat4_K4_unique_peaks.bed = pat4_H3K4me3_peaks/pat4_H3K27me3_peaks


title: input DNA

description: Input

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Lifescope version 2.5 with default parameters.
Uniquely mapped using LifeScope version 2.5 and BioScope
peaks were called using MACS version 1.4.1 with the following setting: Default parameters.
Unique peaks (unique_PC1.bed, unique_PC2.bed) for each patient mark were obtained by using plasma cell H3K27me3 and H3K4me3 chipseq bam files as controls against each mark of all patients bam file. Thus obtaining 8 unique files with one plasma cell and in total 16 files with two plasma cell chipseq.
Genome_build: hg19
Processed data files format and content: Bed files generated using MACS version 1.4.1

value: no antibody


title: Patient 2 H3K27me3_ChIPSeq

description: Patient 2

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Lifescope version 2.5 with default parameters.
Uniquely mapped using LifeScope version 2.5 and BioScope
peaks were called using MACS version 1.4.1 with the following setting: Default parameters.
Unique peaks (unique_PC1.bed, unique_PC2.bed) for each patient mark were obtained by using plasma cell H3K27me3 and H3K4me3 chipseq bam files as controls against each mark of all patients bam file. Thus obtaining 8 unique files with one plasma cell and in total 16 files with two plasma cell chipseq.
Genome_build: hg19
Processed data files format and content: Bed files generated using MACS version 1.4.1
pat2_K27_peaks.bed = pat2_H3K27me3_peaks/Input
pat2_K27_unique_peaks.bed = pat2_H3K27me3_peaks/pat3_H3K4me3_peaks


title: Patient 1 H3K27me3_ChIPSeq

description: Patient 1

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Lifescope version 2.5 with default parameters.
Uniquely mapped using LifeScope version 2.5 and BioScope
peaks were called using MACS version 1.4.1 with the following setting: Default parameters.
Unique peaks (unique_PC1.bed, unique_PC2.bed) for each patient mark were obtained by using plasma cell H3K27me3 and H3K4me3 chipseq bam files as controls against each mark of all patients bam file. Thus obtaining 8 unique files with one plasma cell and in total 16 files with two plasma cell chipseq.
Genome_build: hg19
Processed data files format and content: Bed files generated using MACS version 1.4.1
pat1_K27_peaks.bed = pat1_H3K27me3_peaks/Input
pat1_K27_unique_peaks.bed = pat1_H3K27me3_peaks/pat1_H3K4me3_peaks


title: Patient 3 H3K4me3_ChIPSeq

description: Patient 3

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Lifescope version 2.5 with default parameters.
Uniquely mapped using LifeScope version 2.5 and BioScope
peaks were called using MACS version 1.4.1 with the following setting: Default parameters.
Unique peaks (unique_PC1.bed, unique_PC2.bed) for each patient mark were obtained by using plasma cell H3K27me3 and H3K4me3 chipseq bam files as controls against each mark of all patients bam file. Thus obtaining 8 unique files with one plasma cell and in total 16 files with two plasma cell chipseq.
Genome_build: hg19
Processed data files format and content: Bed files generated using MACS version 1.4.1
pat3_K4_peaks.bed = pat3_H3K4me3_peaks/Input
pat3_K4_unique_peaks.bed = pat3_H3K4me3_peaks/pat3_H3K27me3_peaks


title: Patient 1 H3K4me3_ChIPSeq

description: Patient 1

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Lifescope version 2.5 with default parameters.
Uniquely mapped using LifeScope version 2.5 and BioScope
peaks were called using MACS version 1.4.1 with the following setting: Default parameters.
Unique peaks (unique_PC1.bed, unique_PC2.bed) for each patient mark were obtained by using plasma cell H3K27me3 and H3K4me3 chipseq bam files as controls against each mark of all patients bam file. Thus obtaining 8 unique files with one plasma cell and in total 16 files with two plasma cell chipseq.
Genome_build: hg19
Processed data files format and content: Bed files generated using MACS version 1.4.1
pat1_K4_peaks.bed = pat1_H3K4me3_peaks/Input
pat1_K4_unique_peaks.bed = pat1_H3K4me3_peaks/pat1_H3K27me3_peaks


title: Lon-HA-2

city: Hong Kong

first: Xin

last: Deng

address: To Yuen Building

department: Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description: processed_data file: lonmacs2_peaks.txt

data_processing:
ChIP-seq reads were mapped to the P. syringae pv. phaseolicola genomes, using TopHat (version 2.0.0) with two mismatches allowed.
Only the uniquely mapped reads were kept for the subsequent analyses.
The enriched peaks were identified using MACS software (version 2.0.0)
RhpR binding motif was identified by MEME.
Genome_build: P. syringae pv. Phaseolicola ASM1220v1
Supplementary_files_format_and_content: MACS output

organism: Pseudomonas syringae

source_name: liquid culture in minimal medium_Lon-HA

extract_protocol:
P. syringae was cultured in KB medium supplemented with spectinomycin until the mid-log phase (OD=0.6), before transfered to MM for 4h. Pellet was treated with 1% formaldehyde for 10 min at 37 °C. Cross-linking was stopped by addition of 125 mM glycine.
NEXTflex™ ChIP-Seq Kit (Bioo Scientific)

treatment_protocol: grow until mid-log phase in KB, then transfer to MM for 4h

value: pv. Phaseolicola ASM1220v1


title: Lon-HA-1

description: processed_data file: lonmacs2_peaks.txt


title: HrpL-Flag-1

description: processed_data file: hrpsmacs2_peaks.txt

source_name: liquid culture in minimal medium_HrpL-Flag


title: cdc55(AWR5)_NoInd_rep2


title: HrpR-Flag-2

description: processed_data file: hrpRmacs2_peaks.txt

source_name: liquid culture in minimal medium_HrpR-Flag


title: WT(AWR5)_ind_rep2


title: HrpR-Flag-1


title: WS_Rete_2C_9

city: Santa Cruz

first: Upasna

last: Sharma

state: California

address: 1156 High St

department: MCD Biology

institute: UCSC

data_processing:
Reads were aligned to mm10 RefSeq using Bowtie software in a sequencial manner first to rRNA, snRNA and miRNAs to eliminate any reads coming from them and then alinged to the genome
Genome_build: mm10
Supplementary_files_format_and_content: excel sheet with normalized gene counts

source_name: 2C embryo

growth_protocol: After fertilization by ICSI Zygotes developed in KSOM medium at 37 °C in 5% CO2 5% O2 for 28 hours

extract_protocol:
2C embryos were collected at 28 hours post-ICSI in 5ul of buffer TCL with 1% beta mercaptoethanol and frozen at -80C.
single-cell RNA-seq/Nextera kit

treatment_protocol: Zygotes were generated by ICSI from oocytes/females fed a Control diet and sperm/males fed either a Control or Low Protein diet. The sperm was isolated from either the Rete testis or the Cauda epididymis and injected either as a whole sperm or just the sperm head. Following fertilization by ICSI the zygotes developed for 28 hours (2C stage) and were harvested for single-embryo RNA-Seq.

value: FVB

tag: embryos collected at time after ivf

value: 28 hrs

tag: sperm injected

value: Rete whole sperm


title: WS_Rete_2C_6


title: WS_Rete_2C_8


title: WS_Rete_2C_12


title: WS_Rete_2C_7


title: WS_Rete_2C_11


title: WS_Rete_2C_5


title: WS_Cauda_2C_6

value: Cauda whole sperm


title: WS_Cauda_2C_5


title: Flag_CK1

source_name: liquid culture in minimal medium_Flag


title: WS_Rete_2C_4


title: WS_Cauda_2C_3


title: WS_Rete_2C_3


title: WS_Rete_2C_1


title: WS_Rete_2C_2


title: HrpS-Flag-2

description: processed_data file: hrpLtestmacs2_peaks.txt

source_name: liquid culture in minimal medium_HrpS-Flag


title: WS_Cauda_2C_8


title: WS_Cauda_2C_9


title: Flag_CK2


title: HrpL-Flag-2


title: HrpS-Flag-1


title: ReteLP_8

value: Rete sperm head (LP fed)


title: ReteLP_6


title: ReteLP_9


title: WS_Cauda_2C_10


title: ReteLP_7


title: WS_Cauda_2C_7


title: WS_Rete_2C_10


title: ReteLP_5


title: ReteLP_4


title: WS_Cauda_2C_4


title: ReteLP_3


title: ReteLP_24


title: ReteLP_20


title: ReteLP_21


title: ReteLP_22


title: ReteLP_23


title: ReteLP_2


title: ReteLP_15


title: ReteLP_16


title: ReteLP_12


title: ReteLP_17


title: ReteLP_19


title: WS_Cauda_2C_11


title: ReteLP_10


title: ReteLP_1


title: ReteLP_14


title: ReteControl_8

value: Rete sperm head (Control fed)


title: ReteControl_9


title: ReteControl_7


title: ReteControl_6


title: ReteLP_18


title: ReteControl_23


title: ReteControl_4


title: ReteControl_5


title: ReteControl_21


title: ReteControl_2


title: ReteControl_18


title: ReteLP_11


title: ReteControl_15


title: ReteControl_20


title: ReteControl_19


title: ReteControl_17


title: CaudaLP_7

value: Cauda sperm head (LP fed)


title: mature_RNA-trough-rep2 RNA-seq

city: Beijing

first: xiong

last: wei

address: 7 Science Park Road ZGC Life Science Park

institute: NIBS,Beijing

description: oligoT matrix facilitated

data_processing:
FASTX-Toolkit  for assessing sequencing quality
Alignment: Bowtie 2 version 2.2.1 for chip-seq  and TopHat v2.0.11 for RNA-seq
cufflinks v2.2.0 for RNA-seq assembling and differential analysis
peaks were called using MACS1.4
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: bedGraph files for RNA-seq and chip-seq

source_name: U2OS cells

growth_protocol: DMEM plus 10% for both MEF and U2OS cells

extract_protocol:
NEBNext DNA Library Prep Master Mix Set for Illumina for RNA-seq and NEXTflex ChIP-seq Kit, Bioo Scientific for chip-seq
RNA-seq: For MEF cell line and U2OS cell line mRNA-seq, total RNA was extracted using a RNeasy MinElute Cleanup Kit (QIAGEN, Catalog no. 74204). Double-stranded cDNA was synthesized according to the mRNA Sequencing Sample Preparation Guide (part#1004898 Rev.D, Illumina, San Diego, CA) and single-end libraries were prepared using the NEBNext DNA Library Prep Master Mix Set for Illumina (New England BioLabs, Catalog no.74204 E6040L).   For RNA-seq of RNaseH treated MEF cells, the protocols were mainly adopted as previously described (Nat Methods 10: 623-629).  For qRNA-seq of MEF cells, the GeneRead rRNA Depletion Kit (Qiagen) was used to remove ribosome RNA.  Nascent RNA-seq of U2OS cells was performed as previously described (Science 322: 1845-1848), with the exception of not applying a strand specific method.
Chip-seq: ChIP-seq procedure as previously described (34, 35). For the Bmal1 ChIP-seq, the RIPA buffer was diluted 1 to 10 and the library was constructed using a commercially available kit (NEXTflex ChIP-seq Kit, Bioo Scientific). Samples were indexed using NEXTflex™ DNA Barcodes (Bioo Scientific). The library was qualified using an Agilent 2100 Bioanalyzer (Agilent) and quantified using KAPA Library Quantification Kits (Kappa Biosystems). Finally, the indexed libraries were sequenced using a HiSeq 2500 (Illumina).

tag: cell line

value: U2OS (ATCC HTB-96)

value: bone osteosarcoma

value: no


title: ReteControl_14


title: ReteControl_1


title: ReteControl_10


title: ReteControl_16


title: CaudaLP_6


title: ReteControl_24


title: CaudaLP_3


title: CaudaLP_4


title: mature_RNA-peak-rep2 RNA-seq

description: oligoT matrix facilitated


title: mature_RNA-trough-rep1 RNA-seq

description: oligoT matrix facilitated


title: ReteControl_22


title: PC3_shCIC1

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to hg18 genome using Tophat 2.0.9(These options are changed in Tophat for alignment : --no-coverage-search, --segment-length 21, --bowtie1)
Cufflinks 2.2.1 was used to assemble mapped reads into transcripts and calculate their abundances.
Genome_build: hg18
Supplementary_files_format_and_content: diff

growth_protocol: PC3 cells were maintained in RPMI 1640 (HyClone, USA) with 10% fetal bovine serum and 1% penicillin/streptomycin(WELGENE, Korea).

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA).
For isolation of mRNA from total RNA, we used Oligotex mRNA mini kit (QIAGEN, USA). mRNA were fragmented by keeping it with 1x Superscript III reverse transcriptase buffer (Invitrogen, USA) for 4 minutes  at 95°C. The cDNA was synthesized by random hexamer and Superscript III reverse transcriptase.  Both ends of cDNA strands were filled using the Epicentre DNA END-Repair kit (Epicentre Biotechnologies, Madison, WI). Adenine was added at 3’ ends by  Taq DNA polymerase (New England Biolabs, Beverly, MA) under dATP conditions. Illumina’s adaptor oligomers was ligated at both ends using Quick Ligation kit (Qiagen, Germantown, MD). After purified twice, cDNA libraries are amplified using Solexa primers (Illumina, San Diego, CA) and Phusion PCR master mix (Thermo Scientific, Hudson, NH).

treatment_protocol: HEK293T cells were co-transfected with shCIC lentiviral vector and viral coat protein expressing plasmids using FuGENE(Promega, USA). The culture media of the transfected HEK293T cells, which contains virus, was collected, filtered, and used for infection. PC3 cells were treated with the viral soup and Polybrene(Sigma aldrich, USA), and selected by puromycin.

value: prostate cancer cell line

tag: transfection

value: shCIC


title: mature_RNA-peak-rep1 RNA-seq

description: oligoT matrix facilitated


title: CaudaLP_22


title: CaudaLP_24


title: CaudaLP_21


title: PC3_WT2

value: control


title: ReteControl_12


title: PC3_WT1


title: CaudaLP_19


title: M8_Tem

data_processing:
Base calling
Barcode deconvolution and stripping
Alignment to mature miRNA database (miRBase)
Alignment of remaining reads to miRNA precursor database (miRBase)
Read abundance counting and normalization to library read size
Genome_build: miRBase 17
Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count

source_name: CD4+ T cells

tag: status

value: healthy

tag: barcode

value: TCAACGGTAG


title: ReteControl_11


title: CaudaLP_17


title: M10_Tcm

value: CATTGTTAGC


title: CaudaLP_15


title: M7_Tem

value: AGCCTAAGCT


title: CaudaLP_18

value: FVB


title: CaudaLP_14

value: 28 hrs


title: M8_Tcm


title: M7_Tcm

value: GTGCATCCTA


title: M10_aTreg


title: PC3_shCIC2


title: M8_aTreg


title: CaudaLP_11


title: M9_rTreg


title: CaudaLP_12


title: CaudaLP_1


title: M10_rTreg


title: CaudaControl_7

value: Cauda sperm head (Control fed)


title: M10_naive


title: CaudaControl_9


title: M9_naive


title: M8_naive


title: CaudaControl_6


title: CaudaControl_5


title: CaudaControl_4


title: CaudaControl_3


title: CaudaControl_24


title: CaudaLP_13


title: CaudaControl_22


title: CaudaControl_19


title: CaudaControl_21


title: CaudaControl_2


title: CaudaControl_23


title: CaudaControl_17


title: CaudaControl_13


title: CaudaControl_10


title: CaudaControl_1


title: U6_4C_28_0126

source_name: 4C embryo

growth_protocol: Zygotes, generated by IVF using sperm from mice fed on control diet and oocytes from females on control diet, were microinjected 2 hours after IVF and then allowed to develop until late 2C stage in KSOM media. 32 hours post IVF the microinjected embryos were collected and frozen at -80C.

extract_protocol:
2C embryos positive for GFP signal were individually collected at 2C or 4C stage in 5ul of buffer TCL with 1% beta mercaptoethanol and frozen at -80C.
single-cell RNA-seq/Nextera kit

treatment_protocol: Zygotes were injected with either tRF-GlyGCC oligo with modified bases (tRF-GlyGCC), tRF-Gly-GCC antisense oligo (tRF-GlyGCC Antisense), H3.3-GFP mRNA(GFP), tRF-GluCTC (tRF-GluCTC) or sperm small RNA from control or low protein animals.

tag: rna injected

value: tRF-GlyGCC Antisense


title: U5_4C_7_0119

tag: strain


title: CaudaControl_18


title: U4_4C_84_0109_2


title: U5_4C_27_0126


title: U4_4C_72_0109


title: U4_4C_60_0318


title: U4_4C_6_0119


title: U4_4C_32_0311


title: U3_4C_95_0313


title: CaudaLP_2


title: U4_4C_96_0313


title: U4_4C_26_0126


title: U3_4C_83_0109_2


title: U3_4C_71_0109


title: CaudaControl_15


title: U3_4C_31_0311


title: U2_4C_4_0119


title: U2_4C_70_0109


title: U3_4C_59_0318


title: U3_4C_5_0119


title: CaudaControl_11


title: p08_14

source_name: embryo

growth_protocol: Zygote were generated by IVF using sperm from mice fed control diet or Low protein diet and oocytes from females on control diet.The embryos were then allowed to develop iin KSOM media until different developmental stages when they were collected and frozen at -80C.

extract_protocol:
Embryos were collected in 5ul of buffer TCL with 1% beta mercaptoethanol and frozen at -80C.
single-cell RNA-seq/Nextera kit

tag: development stage

tag: diet of males

value: Low Protein


title: U2_4C_24_0126


title: p07_38

value: M


title: U2_4C_30_0311


title: U1_4C_81_0109_2


title: p07_37


title: p07_36

value: Control


title: p07_35


title: U1_4C_57_0318


title: p07_27


title: M2_4C_3_0119


title: U1_4C_23_0126


title: p07_26


title: F5_LP3_0804

value: Low protein small RNA


title: p07_28


title: p07_25


title: U2_4C_58_0318


title: F5_LP1_0801


title: p07_06

value: Blast (Day late)


title: U2_4C_82_0109_2


title: F5_C3_0804

value: Control small RNA


title: p07_05


title: F5_C1_0804


title: F4_M9_0911

value: tRF-GlyGCC


title: p07_03


title: CaudaControl_14


title: p06_80


title: U1_4C_29_0311


title: F4_M8_0911


title: U5_4C_33_0311


title: F4_M7_0911


title: p06_78


title: F4_M6_0911


title: p06_77


title: F4_M3_0911


title: p06_64


title: p06_62


title: F4_M5_0911


title: F4_M3_0904


title: F5_LP2_0804


title: p06_61


title: p06_46


title: F4_M2_0911


title: p07_04


title: F5_G1_0904

value: GFP


title: F4_M1_0911


title: F4_M2_0904


title: p06_44


title: p07_02


title: p06_43


title: F4_M1_0904


title: F4_M11_0911


title: p06_35

value: B


title: p06_79


title: p06_36


title: F4_LP9_0804


title: F4_LP8_0804


title: F4_LP7_0804


title: p06_33


title: p06_34


title: F4_LP6_0804


title: p06_32


title: F4_LP5_0804


title: F4_LP4_0804


title: p06_11


title: p06_09


title: F4_LP3_0804


title: p06_08


title: p06_10


title: p06_07


title: F4_LP2_0804


title: p06_06


title: F4_LP1_0804


title: p06_04


title: p06_05


title: F4_LP3_0731


title: F4_LP2_0731


title: p06_03


title: F4_LP1_0731


title: p06_02


title: F4_LP1_0730


title: F4_LP11_0804


title: p06_01


title: F4_LP10_0804


title: F4_GluCTC6_0911

value: tRF-GluCTC


title: p05_96


title: p05_95


title: F4_G2_0911


title: F4_GluCTC5_0911


title: p05_94


title: p05_90


title: F4_G1_0911


title: F4_G2_0904


title: F4_C6_0804


title: p05_89


title: p05_87


title: F4_C5_0804


title: F4_GluCTC3_0911


title: p05_86


title: p05_83


title: F4_C4_0731


title: F4_C4_0804


title: F4_C3_0804


title: p05_85


title: F4_C2_0804


title: p05_82


title: p05_80


title: F4_C2_0731


title: p05_81


title: F4_C1_0804


title: F4_C1_0731


title: F3_M2_0904


title: p05_91


title: p05_77


title: p05_76


title: F3_M1_0904


title: p05_88


title: F3_LP2_0730


title: p05_74


title: p05_75


title: F3_LP3_0730


title: p05_73


title: F3_LP1_0804


title: p05_16


title: p05_15


title: F3_LP1_0731


title: F3_LP1_0801


title: p05_14


title: p05_13


title: F3_C2_0815


title: p05_12


title: F3_C2_0730


title: p05_79


title: p05_11


title: F3_C1_0815


title: p05_78


title: p05_10


title: p05_09


title: F3_C1_0731


title: F3_C1_0801


title: F2_M6_0911


title: p05_08


title: F3_LP2_0804


title: p05_07


title: p05_06


title: F2_M4_0911


title: F2_M5_0911


title: F2_M2_0911


title: p04_91


title: p04_90


title: F3_G1_0904


title: p04_89


title: F2_LP5_0723


title: p04_86


title: F2_LP3_0723


title: F2_LP4_0804


title: F2_LP2_0731


title: F2_LP3_0804


title: p04_85


title: p04_88


title: p04_83


title: p04_82


title: p04_81


title: F2_LP2_0804


title: p04_80


title: F2_LP1_0804


title: F2_LP2_0723


title: p04_38


title: p05_05


title: p04_37


title: F2_M1_0911


title: F2_LP1_0731


title: p04_36


title: F2_M1_0904


title: p04_32


title: F2_GluCTC2_0911


title: F2_GluCTC1_0911


title: p04_31


title: F2_G3_0911


title: F2_G1_0911


title: p04_30


title: p04_28


title: F2_G2_0911


title: p04_29


title: F2_LP1_0815


title: p04_27


title: F2_C4_0804


title: p04_25


title: F2_C3_0804


title: F2_G1_0904


title: F2_C2_0815


title: F2_C3_0731


title: p04_33


title: p04_34


title: p04_22


title: p04_24


title: F2_C2_0804


title: F2_GluCTC3_0911


title: F2_C2_0731


title: F2_LP1_0723


title: p04_21


title: F2_C2_0723


title: p04_23


title: p04_19


title: p04_20


title: F2_C1_0804


title: p04_18


title: F2_C1_0731


title: p04_26


title: p04_17


title: p04_16


title: F2_C1_0723


title: F2_C1_0730


title: F1_M4_0904


title: p04_15


title: F1_M3_0904


title: F1_M2_0911


title: p04_14


title: p04_12


title: p04_13


title: p04_11


title: F1_M2_0904


title: p04_07


title: p04_04


title: F1_LP6_0804


title: p04_10


title: p04_02


title: F1_LP5_0804


title: F1_LP4_0804


title: p04_01


title: F1_M1_0904


title: F1_M1_0911


title: F2_C1_0815


title: F1_LP3_0815


title: p03_93


title: F1_LP3_0804


title: p03_91


title: F1_LP3_0723


title: p03_92


title: p03_90


title: F1_LP1_0815


title: p03_88


title: F1_LP2_0723


title: p03_89


title: F1_LP2_0804


title: F1_LP1_0804


title: p03_87


title: F1_G2_0904


title: p03_86


title: p03_85


title: F1_G3_0904


title: p03_84


title: F1_C4_0804


title: p03_82


title: p03_83


title: p03_81


title: p03_80


title: F1_C5_0804


title: p03_79


title: F1_C4_0723


title: F1_C3_0815


title: F1_C3_0804


title: p03_78


title: F1_C3_0730


title: F1_LP1_0723


title: p03_77


title: p03_75


title: p03_76


title: F1_C2_0804


title: F1_C3_0723


title: p03_73


title: F1_C2_0723


title: F1_C2_0815


title: F1_C1_0815


title: F1_C6_0804


title: p03_71


title: p03_74


title: F1_C1_0730


title: C5_4C_53_0318


title: C5_4C_14_0126


title: F1_C1_0731


title: p03_63


title: p03_64


title: C4_4C_88_0313


title: p03_62