title: drug_5uM-4

description:
uncntl_A3SS_vs_drug_5uM_A3SS.miso_bf
uncntl_A5SS_vs_drug_5uM_A5SS.miso_bf
uncntl_AFE_vs_drug_5uM_AFE.miso_bf
uncntl_ALE_vs_drug_5uM_ALE.miso_bf
uncntl_MXE_vs_drug_5uM_MXE.miso_bf
uncntl_RI_vs_drug_5uM_RI.miso_bf
uncntl_SE_vs_drug_5uM_SE.miso_bf
uncntl_TandemUTR_vs_drug_5uM_TandemUTR.miso_bf

value: 5 uM 1C8


title: MC_water2 [TGP02]

status: Public on Dec 19 2016

type: SRA

city: Osaka

first: Ko

last: Omura

address: 2-1-6 Kashima yodogawa-ku

country: Japan

institute: Astellas Pharma Inc.

library_source: genomic

data_processing:
The obtained tag sequences were mapped onto rat genome (NCBI Rn4) using BioScope 1.3.1 (Life Technologies).
For promoter analysis, arbitrary tag count values were calculated following formula and used as each gene DNA methylation state; normalized values = (number of sequence reads from 4500 bp upstream to 1125 bp downstream of transcription start site of each gene) * 50,000,000 / total coverage number.
Using summed mapped tags of 5 animals in whole genome as one sample, global identification of altered DNA methylation regions and obtaining DNA methylation status of RT1-CE5 were performed using Avadis NGS version 1.4.5 (Strand Life Sciences®, Bangalore, India).
Peak detection algorithm for ChIP analysis was applied to identify the peaks that significantly changed the tag number. Detecting condition: algorithm: enrichment peak detection, enrichment factor: 5, Window size (bp): 100, Minimum reads in window = 10, Window slide size (bp): 50, Minimum region size (bp): 150, Minimum reads in region = 15, Upstream padding distance for genes: 5000.
Genome_build: Rn4
Supplementary_files_format_and_content: Region_4500_1125 files were generated using microsoft Excel.; Scores represent DNA methylation state in promoter of each gene.; peak detection file was generated using Avadis NGS 1.4.5.; Enrichment factor represent hypo/hypermethylated region in livers treated with 30mg/kg of DEN compared with PB group.

molecule: genomic DNA

organism: Rattus norvegicus

source_name: liver

extract_protocol:
Liver DNA samples were obtained and soaked in RNAlater (Life Technologies) to stabilize DNA. Genomic DNA from 5 rat livers of each group was isolated using QIAamp® DNA Mini Kit (Qiagen, Hilden, Germany). Methylated genomic DNA were enriched by MethylMiner methylated DNA enrichment kit (Life Technologies).
For construction of standard fragment libraries, SOLiD Fragment Library Construction Kit (Life Technologies) was utilized. After ligation of adaptor to both end of each fragment, each DNA library was selected by its size (inserts were approximately 250 bp) using SOLiD Library Size Selection kit before nick translation, PCR amplification, bead attachment and emulsion PCR. Library was 50 base read sequenced using SOLiD 4 Analyzer.

treatment_protocol: The animals were treated for 1 or 2 weeks (30 mg/kg of DEN were treated for 1 week because of marked body weight loss) and withdrawn for 2 weeks, then, 500 ppm of phenobarbital was given in drinking water. One week after PB promotion, partial hepatectomy was carried out for all animals. After 6 weeks PB promotion, the animals were euthanized.

tag: initiation/promotion

value: 0.5% methylcellulose

tag: promotion

value: water

tag: timing of sampling

value: partialhepatectomy

tag: strain


title: uncntl-1

city: Heidelberg

first: Benjamin

middle: Andrew

last: Story

address: Meyerhofstrasse 1

department: Genomics

country: Germany

institute: European Molecular Biology Laboratory (EMBL)

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.4
Alignment to the human genome using TopHat v 2.0.13
Analysis of alternative splicing event differences using MISO v0.5.2
Genome_build: Ensembl hg19 v67
Supplementary_files_format_and_content: Pairwise comparisons of alternative splicing events, MISO output

molecule: total RNA

organism: Homo sapiens

source_name: HeLa cells

growth_protocol: HeLa-HIV cells (uninduced with doxycyclin) were grown in the presence of Iscove's Eagle medium + 10% fetal bovine serum grown at 37˚C in 5% CO2. 24 hour incubation of cells with 1C8 at the indicated concentrations.

extract_protocol:
Total RNA was purified using the RNAeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols
TrueSeq library from Illumina for RNA-Seq

tag: drug treatment


title: drug_5uM-2

treatment_protocol: 24 hour incubation of cells with 1C8 at the indicated concentrations


title: Ammon's Horn RNAseq [492544KOIE]

city: Newcastle upon Tyne

first: David

middle: J

last: Elliott

address: 1 Central parkway

department: Institute of Genetic Medcine

country: United Kingdom

institute: Newcastle University

data_processing:
Data filtering; seqtk 1.0; Trim-galore 0.3.5; Perl script to remove poly-N tails
Mapping; Tophat2 2.0.8b.Linux_x86_64
Counting reads mapped to genes; BEDTools 2.17.0
Testing for differentially expressed genes; DESeq2 1.0.19
Counting reads mapped to exons; dexseq_count.py
Testing for differentially used exons; DEXSeq 1.6.0
Genome_build: mm10
Supplementary_files_format_and_content: Tab-deleimited text files Gene count file and exon count files

molecule: polyA RNA

organism: Mus musculus

source_name: Knockout_Ammon's horm

growth_protocol: adult mice, kept under standard conditions, and dissected

extract_protocol:
Qiagen Rneasy plus kit
Illumina TruSeq mRNA library preparation

treatment_protocol: No special treatment

tag: strain background

value: Tstar null allele backcrossed onto the C57Bl6 background for 8 generations

tag: genotype/variation

value: Khdrbs3 Knockout

tag: age

value: adult

tag: tissue

value: Ammon's Horn


title: drug_5uM-1


title: Ezh2-LNA-short-RNA-longer_reads

city: Winnipeg

first: Athanasios

last: Zovoilis

state: MB

address: 745 Bannatyne Ave

department: Biochemistry and Medical Genetics

country: Canada

institute: University of Manitoba

description:
Short-RNA-seq
Processed data file: Ezh2-LNA-short-RNA-longer_reads-5ends.txt
The longer fragments of the MiSeq reads enabled single end 200nt reads that span the B2 RNA compared to the HiSeq2000 reads.

data_processing:
Base calling was performed based on the respective Illumina pipeline of either HiSeq or MiSeq system.
Trimming of adapter sequences was performed using cutadapt (DOI: http://dx.doi.org/10.14806/ej.17.1.200)  for the following adapter sequences: Short-RNA sequencing: AAGATCGGAAGAGCACACGTCT.  Paired end RNA sequencing: AAGATCGGAAGAGCACACGTCT  and  AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT for read 1 and read 2, respectively.
Mapping to the mm9 mouse genome: Raw short-RNA-seq, CHART-seq, ChIP-seq reads and the respective  sequenced input reads were mapped against mouse mm9 genome using default parameters of  bwa.0.5.5 (PMID: 20080505).  RNA sequencing reads were mapped against mouse mm9 transcriptome using tophat-2.1.0 (PMID:19289445) with the following parameters: bowtie1 -r -100 -N 20 --read-gap-length 10 --segment-mismatches 3  --read-edit-dist 20.
ChIP-seq/CHART-seq noise filtering: Using in home scripts and bedtools (PMID: 20110278) the resulting sam files were converted to bed files and enriched genomics regions against the input were filtered using SICER (PMID: 24743992) with a window and gap parameter of 300 and an FDR 0.05. Subsequently, CHART-seq reads of the B2 probe were filtered further against enriched regions of the negative CHART probe. The resulting filtered reads are presented as processed data files ending in *filtered.bed.
Short-RNA-seq 5'ends: 5' end genomic co-ordinates of the short-RNA-sequencing reads were extracted using in home text parsing scripts  from the bed files created as described in the previous step.  The resulting 5 end read files consisting of three columns (1st: Chr name, 2nd: position, 3rd: strand orientation of the reads' 5'end) were mapped and plotted against the B2 repeat start gemonic co-ordinates as defined by Repeat Masker for mm9 using Seqmonk. Subsequently read counts were normalized as described below. These are presented as processed data files ending in *5ends.txt in which the first column is the absolute distance in nt from repeat start and the second column is the relative read counts. We used the number of reads at position +1 as an internal normalization control. Alternatively, we normalized the number of cut sites to (i) total B2 RNA levels from the respective conventional RNA-seq performed in parallel, in order to exclude increased B2 expression as a confounding factor; and (ii) to tRNA levels which are POL-II-independent. Both normalization methods yielded similar conclusions. Because of single-end 50 nt sequencing, full length B2 RNA or fragments of >50 nt in short-RNA-seq would appear as 50-nt reads. In order to get a better insight into such cases we have also sequenced the short-RNA libraries with miseq in order to produce single end 200nt long reads that would span the full length of B2 RNA. These files include in their name the "short-RNA-longer_reads" term.
RNAseq:Using bedtools, sam files were converted to bedgraph files scaled for the total number of reads per sample and subsequently to bigwig (bw) files using the UCSC wigToBigWig utility.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files represent CHIP-seq or CHART-seq reads filtered against the input using SICER and in case of CHART also against the negative probe CHART sample. Txt files represent the relative counts (2nd column) of the mapped read 5'end of the sequenced short-RNAs (both rep1 and rep2) with regard to the start of the B2 loci (Repeat Masker). Big files represent read counts scaled to the total number of mapped reads.

source_name: NIH/3T3 cells

growth_protocol: NIH/3T3: DMEM plus Glutamax, 10%FBS, 1% Pen/Strep. ES cells:15% FBS, 1%Pen/Strep, high-glucose DMEM+GlutaMAX with supplemented with LIF and cultured on inactivated mouse embryonic fibroblasts feeder layers.

extract_protocol:
RNA: Trizol followed by depletion of ribosomal RNA using the ribominus V2 kit (Life technologies) and  size selection using the mirVana separation kit (Life technologies), DNA: Phenol-Chloroform
Libraries were prepared according to NEB instructions accompanying the following kits: ChIP/CHART-sequencing: NEBNext ChIP-seq library Prep Master MIX set, Short-RNA-sequencing:NEBnext  small RNA library construction kit (NEB), RNA-sequencing: NEBNext Ultra directional RNA library kit (NEB)

treatment_protocol: Heat Shock (45C) 15 minutes. Transfection with LNAs against B2 RNA (500nM) and Ezh2(25nM) for 24h.

tag: cell type

value: Fibroblast

tag: passages


title: B2LNA-short-RNA-longer_reads

description:
Short-RNA-seq
Processed data file: B2LNA-short-RNA-longer_reads-5ends.txt
The longer fragments of the MiSeq reads enabled single end 200nt reads that span the B2 RNA compared to the HiSeq2000 reads.


title: uncntl-3


title: MC_water1 [TGP01]


title: drug_20uM-1

description:
uncntl_A3SS_vs_drug_20uM_A3SS.miso_bf
uncntl_A5SS_vs_drug_20uM_A5SS.miso_bf
uncntl_AFE_vs_drug_20uM_AFE.miso_bf
uncntl_ALE_vs_drug_20uM_ALE.miso_bf
uncntl_MXE_vs_drug_20uM_MXE.miso_bf
uncntl_RI_vs_drug_20uM_RI.miso_bf
uncntl_SE_vs_drug_20uM_SE.miso_bf
uncntl_TandemUTR_vs_drug_20uM_TandemUTR.miso_bf


title: PreHS-short-RNA-longer_reads-2

description:
Short-RNA-seq
Processed data file: PreHS-short-RNA-longer_reads2-5ends.txt
The longer fragments of the MiSeq reads enabled single end 200nt reads that span the B2 RNA compared to the HiSeq2000 reads.


title: PostHS-short-RNA-longer_reads-1

description:
Short-RNA-seq
Processed data file: PostHS-short-RNA-longer_reads1-5ends.txt
The longer fragments of the MiSeq reads enabled single end 200nt reads that span the B2 RNA compared to the HiSeq2000 reads.


title: drug_1uM-4

description:
uncntl_A3SS_vs_drug_1uM_A3SS.miso_bf
uncntl_A5SS_vs_drug_1uM_A5SS.miso_bf
uncntl_AFE_vs_drug_1uM_AFE.miso_bf
uncntl_ALE_vs_drug_1uM_ALE.miso_bf
uncntl_MXE_vs_drug_1uM_MXE.miso_bf
uncntl_RI_vs_drug_1uM_RI.miso_bf
uncntl_SE_vs_drug_1uM_SE.miso_bf
uncntl_TandemUTR_vs_drug_1uM_TandemUTR.miso_bf

value: 1 uM 1C8


title: drug_5uM-3


title: drug_1uM-3


title: PostHS-short-RNA-longer_reads-2

description:
Short-RNA-seq
Processed data file: PostHS-short-RNA-longer_reads2-5ends.txt
The longer fragments of the MiSeq reads enabled single end 200nt reads that span the B2 RNA compared to the HiSeq2000 reads.


title: drug_20uM-3


title: PreHS-short-RNA-longer_reads-1

description:
Short-RNA-seq
Processed data file: PreHS-short-RNA-longer_reads1-5ends.txt
The longer fragments of the MiSeq reads enabled single end 200nt reads that span the B2 RNA compared to the HiSeq2000 reads.


title: drug_1uM-2


title: Ezh2-LNA rep 2 RNA-seq

source_name: Ezh2-LNA RNA-seq

value: NIH/3T3 Fibroblasts


title: Ezh2-LNA rep 1 RNA-seq


title: B2LNA rep 1 RNA-seq

source_name: B2LNA RNA-seq


title: drug_1uM-1


title: drug_10uM-2

description:
uncntl_A3SS_vs_drug_10uM_A3SS.miso_bf
uncntl_A5SS_vs_drug_10uM_A5SS.miso_bf
uncntl_AFE_vs_drug_10uM_AFE.miso_bf
uncntl_ALE_vs_drug_10uM_ALE.miso_bf
uncntl_MXE_vs_drug_10uM_MXE.miso_bf
uncntl_RI_vs_drug_10uM_RI.miso_bf
uncntl_SE_vs_drug_10uM_SE.miso_bf
uncntl_TandemUTR_vs_drug_10uM_TandemUTR.miso_bf


title: B2LNA rep 2 RNA-seq


title: drug_10uM-3


title: drug_10uM-4


title: drug_10uM-1


title: Post-H/S rep 1 RNA-seq

source_name: Post-H/S RNA-seq


title: drug_20uM-4


title: Pre-H/S rep 1 RNA-seq

source_name: Pre-H/S RNA-seq


title: Post-H/S rep 2 RNA-seq


title: Pre-H/S rep 2 RNA-seq


title: Ezh2-LNA rep 2 Short-RNA-seq

description:
Short-RNA-seq
Processed data file: Ezh2-LNA-short-RNA-5ends.txt

source_name: Ezh2-LNA Short-RNA-seq


title: drug_20uM-2


title: B2LNA rep 2 Short-RNA-seq

description:
Short-RNA-seq
Processed data file: B2LNA-short-RNA-5ends.txt

source_name: B2LNA Short-RNA-seq


title: Post-H/S rep 1 Input_ChIPSeq

source_name: Post-H/S Input_ChIPSeq

tag: chip antibody


title: Pre-H/S rep 1 Input_ChIPSeq

source_name: Pre-H/S Input_ChIPSeq


title: Post-H/S rep 1 Pol II S2P_ChIPSeq

source_name: Post-H/S Pol II S2P_ChIPSeq

value: Pol II S2P panel (Abcam, catalog# ab103968, lot# 139798-3)


title: B2LNA rep 1 Pol II S2P_ChIPSeq

source_name: B2LNA Pol II S2P_ChIPSeq


title: Post-H/S rep 1 Ezh2_ChIPSeq

source_name: Post-H/S Ezh2_ChIPSeq

value: Ezh2 (D2C9) (Cell Signaling Technology, catalog# 5246S, lot# 6)


title: WT_heart_saline solution

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

data_processing:
Approximately 25 million paired-end reads (2x100) /sample were collected on a Hiseq1500 sequencing system (Illumina)
Paired-end reads (cut at 1-85 bases)  were mapped against the mouse reference genome (GRCm38.p4/mm10) using STAR2.5  software to generate read alignments for each sample. Annotations Mus_musculus.GRCm38.82.gtf were obtained from ftp.Ensembl.org.
After transcripts assembling, gene level counts were obtained using HTSeq, followed by a library size normalization
Genome_build: GRCm38.p4/mm10
Supplementary_files_format_and_content: CSV file include CPM (count per million) values for each Sample.

source_name: heart ventricles_WT_saline

growth_protocol: WT and P2Y6 KO mice aged between 8 and 12 weeks were intraperitoneally injected with 50 mg/kg/day isoproterenol (Sigma Aldrich) or saline solution, daily during 7 days.

extract_protocol:
Mice were sacrificed and hearts were harvested and weighed. Ventricles were then stored in Trizol® reagent (Life Technologies) for RNA extraction
Indexed cDNA libraries were obtained using the TruSeq Stranded mRNA sample preparation kit (Illumina) following manufacturer recommendation.

value: heart ventricles

tag: developmental stage

value: 8-12 weeks old mice

tag: background strain

tag: genotype

value: WT

tag: treatment

value: saline solution


title: WT_heart_isoproterenol

source_name: heart ventricles_WT_isoproterenol

value: isoproterenol


title: P2Y6 KO_heart_isoproterenol

source_name: heart ventricles_P2Y6KO_isoproterenol

value: P2Y6-null (P2Y6 KO)


title: Post-H/S rep 1 H3K27me3_ChIPSeq

source_name: Post-H/S H3K27me3_ChIPSeq

value: H3K27me3 (Active Motif, catalog# 39155, lot# 23813016)


title: P2Y6 KO_heart_saline solution

source_name: heart ventricles_P2Y6KO_saline


title: Pre-H/S rep 1 Pol II S2P_ChIPSeq

source_name: Pre-H/S Pol II S2P_ChIPSeq


title: dosRS mutant treated with HC102A, rep 1

city: East Lansing

first: Robert

middle: B.

last: Abramovitch

state: MI

address: 567 Wilson Road

department: Microbiology and Molecular Genetics

country: USA

institute: Michigan State University

data_processing:
Illumina bcl2fastq (v1.8.4) was used to de-multiplex and convert reads to FASTQ format
Reads from each lane were combined into individual files using standard UNIX commands
Trimmomatic (v0.33)  was used to trim low quality bases and remove adapter sequences with a 4 bp sliding window, cutting when the read quality dropped below 15 or read length was less than 36 bp.
Bowtie (v1.1.2) was used to align trimmed reads to the M. tuberculosis CDC1551 genome (NCBI accession AE000516) with the -S option to produce SAM files as output.
HTSeq software suite (v0.6.0) was used to analyze aligned and determine counts per gene feature in the M. tuberculosis CDC1551 genome
edgeR (v3.2) was used to normalize data by estimating effective library sizes using trimmed mean M-values
R was used for statistical analysis and differential gene expression by fitting a negative binomial model to each set of conditions and testing for differences utilizing the GLM functionality edgeR package
Genome_build: M. tuberculosis CDC1551 genome (GCA_000669715) (NCBI accession AE000516)
Supplementary_files_format_and_content: Processed files are presented as .csv spreadsheets and represents the average of 2 biological replicates

organism: Mycobacterium tuberculosis

source_name: Bacterial cell

growth_protocol: Mtb strain CDC1551 was grown in standing T-25 flasks in 8 mL of medium seeded an initial OD of 0.1.  Cultures were incubated at 37C for 6 days.

extract_protocol:
RNA was extracted using the method Rohde, Abramovitch and Russell, Cell Host and Microbe, 2007. Briefly,  RNA was stabilized and isolated using a guanidine thiocyanate-based lysis buffer as previously described. Pelleted mycobacteria were lysed using 5 μg/ml lysozyme, hot Trizol, and physical disruption with silica beads in a BeadBeater. Total RNA was isolated by chloroform extraction followed by direct application to QIAGEN RNeasy column purification. Residual DNA contamination was removed using Turbo DNAfree DNase (Ambion).  RNA quality and integrity were examined using an Agilent Bioanalyzer prior to subjecting samples to rRNA depletion using the Epicentre Ribo-Zero depletion kit.
cDNA libraries were constructed using the Illumina TruSeq RNA library preparation kit (v2), omitting the polyA selection step. Multiplexing sequences are included in the title of the associated fastq.gz files.
After library quality control, sample libraries were pooled and sequenced in two lanes of an Illumina HiSeq 2500 Rapid Run flow cell (v1) in 50bp, single-end read format (SE50). After the sequencing run, reads were de-multiplexed and converted to FASTQ format using the Illumina bcl2fastq (v1.8.4) script.

treatment_protocol: Mtb cultures were treated with 40 mM of the compound of interest and following 6 days of incubation at 37C, RNA was isolated from the bacterial cultures and used for RNA-seq. For each condition, 2 biological replicates were performed.

value: CDC1551 (DdosRS mutant)

tag: chemical treatment


title: dosRS mutant treated with HC102A, rep 2


title: dosRS mutant treated with HC103A, rep 1


title: dosRS mutant treated with HC103A, rep 2


title: Pre-H/S rep 1 Ezh2_ChIPSeq

source_name: Pre-H/S Ezh2_ChIPSeq


title: dosRS mutant treated with HC101A, rep 2


title: dosRS mutant treated with HC101A, rep 1


title: dosRS mutant treated with DMSO, rep 2

value: DMSO


title: Pre-H/S rep 1 H3K27me3_ChIPSeq

source_name: Pre-H/S H3K27me3_ChIPSeq


title: dosRS mutant treated with DMSO, rep 1


title: WT treated with HC103A, rep 2


title: WT treated with HC103A, rep 1


title: Sample_1hShFL1

city: Shanghai

first: Lin

last: Li

address: 2005 Songhu Road

country: China

institute: Fudan University

data_processing:
Basecalls performed using bcl2fastq2 version 2.16.0.10
QC performed using trim_galore(0.3.7), FastQC(0.11.2) and RSeQC(2.6.2)
Alignment performed using tophat(2.0.14) and bowtie (2.2.3)
Assembly performed using cufflinks (2.2.1)
Annotation performed using blastx(2.2.28)
Normalization and DEG performed using cuffnorm (2.2.1),cuffdiff (2.2.1) and cuffcompare (2.2.1)
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample …

organism: Oryza sativa

source_name: the first leaf

growth_protocol: Dehusked seeds were surface-sterilized in 3% hydrogen peroxide solution, sown into sterile water under 37℃ for 24 hrs. The seeds under the similar development stage were selected to grow on 0.4% (w/v) agar or water (floating in 96 cell plate) at 28℃ under the continue white light condition.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols, done by Genergy Biotech Co. Ltd. (Genergy, Shanghai, China)

treatment_protocol: The seedlings were either left in white light or transferred to simulated shade (LED light, R: 16 μE•m -2 •s -1 and Blue: 1.3 μE•m -2 •s -1 ; FR light: 48 μE•m -2 •s -1, 28 ℃) for 1hr before the collections.

tag: cultivar

value: Nipponbare

value: the first leaf

value: 3 days old

value: plus 1hr shade

value: wild type


title: Sample_1hWLC2

source_name: coleoptile

value: coleoptile

value: 2 days old

value: plus 1hr white light


title: Sample_1hShFL2


title: Sample_1hWLC1


title: WT treated with HC102A, rep 2


title: Sample_1hWLFL1


title: Sample_1hShC2


title: Sample_1hShC1


title: WT treated with HC101A, rep 1


title: WT treated with HC102A, rep 1


title: WT treated with DMSO, rep 2


title: WT treated with HC101A, rep 2


title: Sample_1hWLFL2


title: RNAPII-CTDun_WT_37C_for_fft2Dfft3D_37C_rep2

city: Houston

first: Junwoo

last: Lee

state: Texas

address: 2120 El Paseo Street, Apt.603

department: Epigenetics and Molecular Carcinogenesis

institute: MD Anderson Cancer Center

data_processing:
The quality of fastq files were checked by fastqc and trimmed by trim_galore
The qualified fastq files were aligned to Spombe ASMv2 genome fa file using novoalign v3.03.02. Then, the aligned files were compressed and sorted by samtools v1.3.
The sorted BAM files of biological duplicates were compared by deeptools. If the duplicates were similar each other, they were merged and sorted by samtools v1.3.
The prepared merged BAM files were analyzed by deeptools to generate bigwig files and normalized values and profiles.
Genome_build: SpombeASMv2
Supplementary_files_format_and_content: bigwig files were generated by deeptools.

organism: Schizosaccharomyces pombe

source_name: S.pombe cells

growth_protocol: Cell culture were inoculated twice. Cell cultures were inoculated with shaking for aeration at proper temperatures.

extract_protocol:
Every ChIP-seq cells were grown up to mid-log phase and harvested after final 1% formaldehyde fixation and 125mM glycine quencing. Cells were harvested by centrifugation at 4 Celcius degrees and the cell pellets were washed by 15mL of pH7.5 TBS buffer per a conical tube. ChIP cells were disrupted by glass bead vortexing in ChIP  lysis buffer and sonicated by Sonic Dismembrator Model 500, Fisher Scientific. Debris of the sonicate was excluded by centrifugation by 14,800rpm at 4 Celcius degree. IP samples were aliqouted from the sonicate and immunoprecipiated by proper amount of antibody and protein A/G beads, washed by ChIP  lysis buffer for over-night at 4 Celcius degrees. IP samples were washed and eluted by proper buffers in  Sigmaprep spin column. Proteins in both IP and input samples were degraded by 2hr 30ug proteinase K rxn and de-crosslinked at 65 Celcius degrees for at least 8hrs. The IP and input DNA were eluted by Quiagen PCR purification kit.
General Manual of Truseq ChIP library preparation kit.

treatment_protocol: Final 1% formaldehyde fixation and 125mM glycine quencing were performed before cell harvest.

value: wildtype

tag: antibody

value: 920102; BioLegend

tag: phase

value: mid-log phase

tag: medium

value: YES (rich medium)


title: ura4+::priRNA1 ago1∆ + OE Flag-Ago1 D580A (spy3473 + pDM831) - sRNA sense

city: Durham

first: Nahid

last: Iglesias

state: NC

address: 101 Science Drive, CIEMAS Rm. 2323

department: Biomedical Engineering

institute: Duke University

data_processing:
Reads were aligned to the S. pombe genome using novoalign, normalized for reads per million, and visualized using IGV.
Genome_build: ASM294v2
Supplementary_files_format_and_content: Mapped reads were normalized to reads per million and visualized in Integrated Genome Viewer (IGV) in an IGV-viewable format.

growth_protocol: Cells were cultured overnight in EMM-LEU medium at 32°C and harvested at early log phase (OD600 = 1.2). ~0.5g of cells were used.

extract_protocol:
Total RNA was isolated using the mirVana kit (according to the manufacturer protocol)
Small RNA libraries were constructed as previously described (Halic and  Moazed, 2010). Briefly, 21-24nt RNA was size-selected on a 17.5% polyacrylamide/7M  urea gel and ligated to a 3’ adapter. The ligated species were size-selected on a 17.5%  polyacrylamide/7M urea gel and ligated to a 5’ adapter. RNA was then reverse  transcribed into cDNA and PCR-amplified in a two-step process. Amplified cDNA was  gel-purified and sequenced on an Illumina High-Seq platform.

tag: media

value: EMM -LEU

value: Flag antibody (Sigma, F1804)


title: ura4+::priRNA1-KAN leo1∆ + empty vector (spy6419 + pDM829)

description: CAGATC

data_processing:
Raw reads were separated by barcode. Barcode sequence were removed from the reads and attached to the identifier. Reads were mapped using bowtie with default configurations. Mapped reads were normalized to reads per million and visualized in Integrated Genome Viewer (IGV)
Genome_build: ASM294v2
Supplementary_files_format_and_content: Mapped reads were normalized to reads per million and visualized in Integrated Genome Viewer (IGV) in an IGV-viewable format.

growth_protocol: Cells were cultured overnight in EMM-LEU medium at 32°C and harvested at late log phase (OD600 = 1.5).

extract_protocol:
Cell pellets were resuspended in 600 μl lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate, 0.1% SDS, 1 mM PMSF, protease inhibitor tablet (Roche)), and disrupted by bead beating (MagNA Lyser, Roche) for 3x90 sec at 4500 rpm with 0.5 mm glass beads. Tubes were punctured and the flow-through was collected in a new tube by centrifugation. After sonication for 3x20 sec at 50% amplitude (Branson Digital Sonifier), the extract was centrifuged (Eppendorf 5415R) for 15 min at 13,000 rpm. The soluble chromatin was then transferred to a fresh tube. H3K9me2 (Abcam, Ab 1220) was preincubated with Dynabeads Protein A, and for each immunoprecipitation, 2 μg antibody bound to 30 μl beads was added to soluble chromatin. Samples were incubated for 2 hours at 4°C with rotation, after which the beads were collected on magnetic stands, and washed 3 times with 1 ml lysis buffer and once with 1 ml TE, and eluted with 50 μl preheated buffer (50 mM Tris.HCl pH 8.0, 10 mM EDTA, 1% SDS) at 65˚C for 15 min. The eluate was collected, and 75 μl 1XTE/0.67% SDS was added on the beads, the incubation was repeated and both elutions were combined. Immunoprecipitated samples were incubated overnight at 65˚C in the presence of 0 μg RNase A to reverse crosslink and RNase treated the samples, respectively. 5 μl proteinase K (Roche) was added and incubation was continued at 55°C for 1 h. Samples were purified using PCR purification kit (Qiagen).
Libraries for Illumina sequencing were constructed following the protocol detailed in Wong et al, 2013 (Wong, K. H., Jin, Y. and Moqtaderi, Z. 2013. Multiplex Illumina Sequencing Using DNA Barcoding. Current Protocols in Molecular Biology. 101:7.11:7.11.1–7.11.11.), starting with ~10 ng of immunoprecipitated DNA fragments. Each library was generated with custom-made adapters carrying unique 6 nt barcode sequences at the ligating end. Barcoded libraries were mixed and sequenced with Illumina HiSeq 2000.

treatment_protocol: Cells were fixed with 1% formaldehyde for 15 min at room temperature (RT), then quenched with 130 mM glycine for 5 min at RT, harvested by centrifugation, washed twice with TBS (50 mM Tris.HCl pH 7.6, 150 mM NaCl), and flash frozen.

value: H3K9me2 antibody (Abcam, Ab1220)


title: Untagged WT (spy137)

source_name: Untagged WT (spy137)

growth_protocol: Cells were cultured overnight in YES medium at 32°C and harvested at early log phase (OD600 = 0.8). ~5g of cells were used.

extract_protocol:
Nuclei were isolated and sRNA associated with Ago1 were immunoprecipitated with Flag antibody
Small RNA libraries were constructed as previously described (Halic and  Moazed, 2010). Briefly, 21-24nt RNA was size-selected on a 17.5% polyacrylamide/7M  urea gel and ligated to a 3’ adapter. The ligated species were size-selected on a 17.5%  polyacrylamide/7M urea gel and ligated to a 5’ adapter. RNA was then reverse  transcribed into cDNA and PCR-amplified in a two-step process. Amplified cDNA was  gel-purified and sequenced on an Illumina High-Seq platform.


title: RNAPII-CTDun_WT_37C_for_fft2Dfft3D_37C_rep1


title: ura4+::priRNA1 ago1∆ + OE Flag-Ago1 WT (spy3473 + pDM817) - sRNA sense


title: RNAPII-CTDS2P_WT_37C_for_fft2Dfft3D_37C_rep2

description: RNAPII_CTDS2P_fft2Dfft3D_mt-vs-wt_37C.bw

value: ab5095; abcam


title: 3xFlag-Ago1 WT (spy797)

source_name: 3xFlag-Ago1 WT (spy797)


title: WT treated with DMSO, rep 1

tag: strain

value: DMSO


title: RNAPII-CTDS2P_WT_37C_for_fft2Dfft3D_37C_rep1

tag: genotype/variation


title: ura4+::KAN leo1∆ + empty vector (spy6421 + pDM829)

description: GCCAAT


title: ura4+::priRNA1-KAN ago1∆ + OE Ago1 WT (spy3473 + pDM817)

description: TTAGGC


title: RNAPII-CTDun_fft2Dfft3D_37C


title: MNNG_treated_MIF_IP

city: Baltimore

first: Stephen

middle: Matthew

last: Eacker

state: MD

address: 733 N. Broadway Suite 731

department: Neurology

institute: Johns Hopkins University

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to genome using Bowtie2 v 2.0.5
BAM output coverted to SAM using SAMtools0.1.18
Peaks calls made using MACS 1.4.1 using default parameters, peaks found in MNNG-treated but not DMSO-treated samples were used for motif discovery.
MIF binding motif found using 3 different software packages: SeSiMCMC_4_3_6, b. Chipmunk v4.3+, c. MEMEchip v4.9.0.
.tdf files were generated from the associated .bam files using IGVtools (Broad Institute).  The .tdf files are IGV viewable files that describe the coverage of the given ChIP-seq or input library.
Genome_build: hg19
Supplementary_files_format_and_content: peak calls provided as BED files; IGV-viewable coverage provided in TDF files.

source_name: HeLa

growth_protocol: HeLa grown in DMEM+10%FBS in 10 cm dishes.

extract_protocol:
Lysates were clarified from sonicated nuclei and MIF-DNA complexes were isolated with antibody.
Libraries were prepared with Illumina Truseq DNA LT Sample Prep Kit with 15 cycles of PCR amplification.

treatment_protocol: Treated with DMSO (0.1%) or 50 µM MNNG for 15 minutes  and cells directly harvested

value: 50 µM MNNG for 15 min, returned to fresh media for 4h before harvest.

value: Goat polyclonal anti-MIF(Abcam ab38146)

tag: cell line

value: HeLa


title: RNAPII-CTDS2P_fft2Dfft3D_37C_rep2


title: MNNG_treated_MIF_Input


title: ura4+::priRNA1-KAN ago1∆ + empty vector (spy3473 + pDM829)

description: CGATGT


title: ura4+::priRNA1-KAN ago1∆ + OE Ago1 D580A (spy3473+ pDM831)

description: TGACCA


title: DMSO_treated_MIF_Input

value: DMSO(0.1%) for 15 min, returned to fresh media for 4h before harvest.


title: ura4+::KAN + OE Ago1 WT (spy3442 + pDM817)

description: ATCACG


title: input_WT_37C_rep1

status: Public on Dec 18 2016

value: WT

tag: antibody catalog/vendor


title: DMSO_treated_MIF_IP


title: input_WT_37C_rep2


title: input_WT_22C


title: input_WT_30C_rep1


title: H3_H3H4DD_22C_rep2

value: Home-made


title: H3_fft3DH3H4DD_22C_rep2


title: H3_H3H4DD_22C_rep1


title: RNAPII-CTDun_fft3DH3H4DD_22C_rep1

description: RNAPII-CTDun_fft3DH3H4DD_mt-vs-WT_22C.bw

value: Anti-RNA Polymerase II Antibody


title: H3_WT_22C_rep1


title: RNAPII-CTDun_H3H4DD_22C_rep2


title: RNAPII-CTDun_H3H4DD_22C_rep1


title: H3_WT_22C_rep2


title: H3_fft3D_22C_rep2


title: H3_fft3D_22C_rep1


title: RNAPII-CTDun_WT_22C_rep2


title: RNAPII-CTDS2P_fft3DH3H4DD_22C_rep2

description: RNAPII-CTDS2P_fft3DH3H4DD_mt-vs-WT_22C.bw

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody


title: RNAPII-CTDun_fft3D_22C_rep2


title: RNAPII-CTDun_fft3D_22C_rep1


title: RNAPII-CTDS2P_fft3DH3H4DD_22C_rep1


title: RNAPII-CTDS2P_H3H4DD_22C_rep2


title: RNAPII-CTDS2P_fft3D_22C_rep1


title: RNAPII-CTDS2P_fft2Dfft3D_37C_rep1


title: RNAPII-CTDS2P_WT_22C_rep2


title: H3_spt16-18_37C_rep2


title: RNAPII-CTDS2P_fft3D_22C_rep2


title: RNAPII-CTDS2P_H3H4DD_22C_rep1


title: input_WT_30C_rep2


title: RNAPII-CTDS2P_WT_22C_rep1


title: H3_spt16-18_37C_rep1


title: H3_fft3D_37C_rep2


title: RNAPII-CTDun_fft3DH3H4DD_22C_rep2


title: 1.0-2.0 cm panicles, NIL(MH), short-day growth conditions

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 18 and 34 nucleotides.
PARE: the adapter sequences were trimmed from raw sequence reads, and then the PARE sequences were trimmed to the lengths between 18 and 21 nucleotides.
For read alignment to the reference genome, we typically use Bowtie and only consider perfect matches. No matching data were included with these files.
The abundance measurements are raw counts; to normalize, we typically divide the raw count for a given read by the sum of abundances for all reads, and multiple this by an arbitrary round number (million, five million, ten million, etc)
Genome_build: RICE MSU 7 was used for downstream analyses.
Supplementary_files_format_and_content: [.txt] tag count (sequence plus abundance). This is the same format for both small RNA and PARE data.

organism: Oryza sativa Japonica Group

growth_protocol: Rice plants were grown in the field under long-day (daylength>14 h) and short-day (daylength<13.5 h) growth conditions during the rice-growing season in Wuhan, Hubei provice, China.

extract_protocol:
Total RNA was isolated following the instructions for an RNA extraction kit (TRIzol reagent, Invitrogen)
Small RNA libraries were prepared according to Illumina's instructions accompanying the TruSeq Small RNA Sample Prep Kit, and PARE library construction followed previously methods described in Zhai et al, Methods, 2014.

tag: tissue

value: panicles

tag: size

value: NIL(MH)

tag: grow condition

value: long-day

tag: library

value: Parallel Analysis of RNA Ends (PARE)


title: 1.0-2.0 cm panicles, 58S, short-day growth conditions

value: Nongken 58S


title: H3_fft3DH3H4DD_22C_rep1

value: YES (rich medium)


title: 1.0-2.0 cm panicles, 58S, long-day growth conditions


title: RNAPII-CTDun_WT_22C_rep1

value: 920102; BioLegend


title: H3_fft3D_37C_rep1


title: H3_WT_37C_rep1


title: RNAPII-CTDun_fft3Dspt16-1_37C_rep2

description: RNAPII-CTDun_fft3Dspt16-1_mt-vs-WT_37C.bw


title: H3_WT_37C_rep2


title: 1.0-2.0 cm panicles, pms1 RNAi positive, long-day growth conditions, biological replicate 2

value: PMS1T RNAi transgenic positive

value: small RNA


title: 1.0-2.0 cm panicles, pms1 RNAi negative, long-day growth conditions, biological replicate 2

value: PMS1T RNAi transgenic negative


title: RNAPII-CTDun_fft3Dspt16-1_37C_rep1


title: RNAPII-CTDun_spt16-1_37C_rep2


title: RNAPII-CTDun_spt16-1_37C_rep1


title: RNAPII-CTDun_fft3D_37C_rep2


title: 1.0-2.0 cm panicles, pms1 ox positive, long-day growth conditions, biological replicate 1

value: PMS1T OX transgenic positive


title: RNAPII-CTDun_fft3D_37C_rep1


title: 1.0-2.0 cm panicles, pms1 ox negative, long-day growth conditions, biological replicate 2

value: PMS1T OX transgenic negative


title: 3.0-4.0 mm florets, short-day growth conditions, NIL(MH), biological replicate 2

value: florets

value: short-day


title: RNAPII-CTDun_WT_37C_for_fft3Dxspt16-1_rep2

value: WT


title: RNAPII-CTDun_WT_37C_for_fft3Dxspt16-1_rep1

value: Anti-RNA Polymerase II Antibody


title: 3.0-4.0 mm florets, short-day growth conditions, NIL(MH), biological replicate 1


title: RNAPII-CTDS2P_fft3Dspt16-1_37C_rep2

description: RNAPII-CTDS2P_fft3Dspt16-1_mt-vs-WT_37C.bw

value: ab5095; abcam

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody


title: 1.0-2.0 cm panicles, short-day growth conditions, NIL(MH), biological replicate 2

value: panicles

value: NIL(MH)


title: 1.0-2.0 cm panicles, short-day growth conditions, NIL(MH), biological replicate 1


title: 0.5-1.0 cm panicles, short-day growth conditions, NIL(MH), biological replicate 2


title: 1.0-2.0 cm panicles, pms1 RNAi negative, long-day growth conditions, biological replicate 1

value: long-day


title: 1.0-2.0 cm panicles, NIL(MH), long-day growth conditions

value: Parallel Analysis of RNA Ends (PARE)


title: RNAPII-CTDS2P_fft3Dspt16-1_37C_rep1

value: YES (rich medium)


title: RNAPII-CTDS2P_spt16-1_37C_rep2


title: 0.5-1.0 cm panicles, short-day growth conditions, NIL(MH), biological replicate 1


title: RNAPII-CTDS2P_spt16-1_37C_rep1


title: 1.0-2.0 cm panicles, pms1 ox positive, long-day growth conditions, biological replicate 2


title: RNAPII-CTDS2P_fft3D_37C_rep1


title: 3.0-4.0 mm florets, long-day growth conditions, NIL(MH), biological replicate 2


title: 1.0-2.0 cm panicles, long-day growth conditions, NIL(MH), biological replicate 2


title: RNAPII-CTDS2P_WT_37C_for_fft3Dxspt16-1_rep1


title: RNAPII-CTDS2P_WT_37C_for_fft3Dxspt16-1_rep2


title: RNAPII-CTDS2P_fft3D_37C_rep2


title: 0.5-1.0 cm panicles, long-day growth conditions, NIL(MH), biological replicate 2


title: 1.0-2.0 cm panicles, pms1 ox negative, long-day growth conditions, biological replicate 1


title: GFP_Spt16-GFP_30C_rep2

value: sc-9996; Santa Cruz Biotech.

value: GFP


title: 0.5-1.0 cm panicles, long-day growth conditions, NIL(MH), biological replicate 1

value: small RNA


title: GFP_Spt16-GFP_30C_rep1


title: IgG_mouse_mock_30C

tag: genotype/variation:

value: 12-371; EMD Millipore

value: IgG


title: 1.0-2.0 cm panicles, pms1 RNAi positive, long-day growth conditions, biological replicate 1

tag: genotype

value: PMS1T RNAi transgenic positive


title: 3.0-4.0 mm florets, short-day growth conditions, 58S, biological replicate 2

value: florets

value: Nongken 58S


title: 3.0-4.0 mm florets, short-day growth conditions, 58S, biological replicate 1

value: short-day


title: FLAG_Snf21-5xFLAG_30C_rep1

value: F1804; SIGMA

value: Monoclonal ANTI-FLAG M2


title: FLAG_Snf21-5xFLAG_30C_rep2


title: 1.0-2.0 cm panicles, short-day growth conditions, 58S, biological replicate 2


title: FLAG_Ino80-5xFLAG_30C_rep2


title: FLAG_Fft3-5xFLAG_30C_rep2


title: 0.5-1.0 cm panicles, short-day growth conditions, 58S, biological replicate 2


title: 0.5-1.0 cm panicles, short-day growth conditions, 58S, biological replicate 1


title: FLAG_Fft2-5xFLAG_30C_rep2


title: 3.0-4.0 mm florets, long-day growth conditions, NIL(MH), biological replicate 1


title: FLAG_Fft3-5xFLAG_30C_rep1


title: FLAG_Ino80-5xFLAG_30C_rep1


title: 3.0-4.0 mm florets, long-day growth conditions, 58S, biological replicate 1


title: 1.0-2.0 cm panicles, long-day growth conditions, NIL(MH), biological replicate 1


title: 3.0-4.0 mm florets, long-day growth conditions, 58S, biological replicate 2


title: 1.0-2.0 cm panicles, long-day growth conditions, 58S, biological replicate 1


title: FLAG_mock_WT_30C_rep2


title: FLAG_Fft2-5xFLAG_30C_rep1


title: RNAPII-CTDun_Spt16-18_37C_rep2

value: 920102; BioLegend

value: Anti-RNA Polymerase II Antibody


title: 0.5-1.0 cm panicles, long-day growth conditions, 58S, biological replicate 2

value: panicles


title: 0.5-1.0 cm panicles, long-day growth conditions, 58S, biological replicate 1

value: long-day


title: RNAPII-CTDun_Spt16-18_37C_rep1


title: SDG711OX-BSseq

city: Wuhan

first: shaoli

last: zhou

state: Hubei

address: shizishan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

data_processing:
For ChIP-Seq, trimmomatic (version 0.32) was used to filter out low quality reads and crop all reads to a uniform length (45bp). Clean reads were mapped to the rice genome (RGAP version 7) by default allowing up to 2 mismatch using Bowtie2 (version 2.1.0). Peaks were called out by MACS software after removing potential duplicates of PCR by Samtools (version 0.1.17), with the default P value equal 1e-5. P value 1e-9 was used for calling out peaks of anti-SDG711, because of the largest percentage overlap of H3K27me3 marked genes and SDG711 bound genes. Gbrowse 2.0 was used to view the ChIP-Seq data. For Bisulfite-Seq, trimmomatic (version 0.32) was used to filter out low quality reads and BatMeth was used to align clean tags to the rice genome (RGAP version 7) by default parameters followed by removing PCR-amplified redundancy. Methylation levels were calculated by #C/(#C+#T).
Wig file generated by MACS software for Gbrowse view
CT.C3 files generated by BathMeth software containing all detected cytosine  methylation information
Genome_build: rice genome (RGAP version 7)

source_name: SDG711 over-expression seedling leaves

growth_protocol: Rice (Oryza sativa spp. japonica) plants used in this study for ChIP-Seq and BS-Seq analysis were from the ‘DongJin’ (DJ) background, including wild type (WT), callus culture- regenerated wild type (crWT), SDG711 over-expression (line 2, 4, 5 combined) (711OX) and RNAi lines (line3, 7, 9 combined) (711RNAi) as described previously in Liu et al., 2014. Seedling leaves from all genotypes were grown in one-half-strength Murashige and Skoog medium under a 16-h-light/8-h-dark cycle at 30°C for 12 DAG (day after germination)

extract_protocol:
Leaves were harvested and fixed in formaldehyde for chromatin cross-linking, About 2g of seedling leaves were crosslinked in 1% formaldehyde under vacuum. Chromatin was extracted and fragmented to 200-750 bp by sonication, and ChIP was performed using the following antibodies: H3K27me3 (a2363, ABclonal) and Anti-SDG711. Seedling leaves were harvested and frozen in liquid nitrogen for DNA extraction using the DNeasy plant mini kit (Qiagen).
DNA from ChIP was used to construct sequencing libraries following the protocol provided by Illumina TruSeq® ChIP Sample Prep Set A. Genomic DNA (5g) was used to generate BS-Seq libraries as described in Feng et al., 2011.

value: 12 day after germination seedling leaves

value: SDG711 over-expression


title: RNAPII-CTDun_snf22D_30C_rep2

value: YES (rich medium)


title: RNAPII-CTDun_swr1D_30C_rep1


title: crWT-BSseq

source_name: culture-regenerated WT seedling leaves

value: culture-regenerated Dongjin


title: RNAPII-CTDun_swr1D_30C_rep2


title: SDG711OX-H3K27me3


title: anti-SDG711

source_name: WT seedling leaves

value: Wild type Dongjin


title: RNAPII-CTDun_snf22D_30C_rep1


title: crWT-H3K27me3


title: RNAPII-CTDun_snf21-36_37C_rep1


title: RNAPII-CTDun_snf21-36_37C_rep2


title: 1.0-2.0 cm panicles, short-day growth conditions, 58S, biological replicate 1

value: small RNA


title: RNAPII-CTDun_WT_37C_rep2

value: WT


title: 1.0-2.0 cm panicles, long-day growth conditions, 58S, biological replicate 2


title: RNAPII-CTDun_WT_37C_rep1


title: RNAPII-CTDun_hrp3D_30C_rep2


title: RNAPII-CTDun_hrp1D_30C_rep1


title: RNAPII-CTDun_ies6D_30C_rep1


title: RNAPII-CTDun_hrp3D_30C_rep1


title: RNAPII-CTDun_hrp1D_30C_rep2


title: FLAG_mock_WT_30C_rep1


title: RNAPII-CTDS2P_Spt16-18_37C_rep1

value: ab5095; abcam

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody


title: RNAPII-CTDS2P_swr1D_30C_rep2


title: RNAPII-CTDS2P_Spt16-18_37C_rep2


title: RNAPII-CTDS2P_snf22D_30C_rep2


title: RNAPII-CTDS2P_swr1D_30C_rep1


title: RNAPII-CTDS2P_snf21-36_37C_rep2


title: RNAPII-CTDS2P_WT_37C_rep1


title: RNAPII-CTDS2P_WT_37C_rep2


title: RNAPII-CTDS2P_hrp3D_30C_rep2


title: RNAPII-CTDS2P_ies6D_30C_rep1


title: RNAPII-CTDS2P_ies6D_30C_rep2


title: RNAPII-CTDS2P_hrp3D_30C_rep1


title: RNAPII-CTDun_fft2Dfft3D_30C_rep2


title: RNAPII-CTDun_fft2Dfft3D_30C_rep1


title: RNAPII-CTDun_fft3D_30C_rep2


title: RNAPII-CTDun_ies6D_30C_rep2


title: RNAPII-CTDS2P_hrp1D_30C_rep2


title: RNAPII-CTDun_fft2D_30C_rep2


title: RNAPII-CTDun_fft1D_30C_rep1


title: RNAPII-CTDun_fft1D_30C_rep2


title: RNAPII-CTDun_fft2D_30C_rep1


title: RNAPII-CTDun_WT_30C_rep2


title: RNAPII-CTDS2P_snf21-36_37C_rep1


title: RNAPII-CTDS2P_snf22D_30C_rep1


title: RNAPII-CTDun_WT_30C_rep1


title: RNAPII-CTDun_fft3D_30C_rep1


title: RNAPII-CTDS2P_fft2Dfft3D_30C_rep1

description: RNAPII-CTDS2P_fft2Dfft3D_mt-vs-WT_30C.bw


title: RNAPII-CTDS2P_fft3D_30C_rep2


title: RNAPII-CTDS2P_fft2Dfft3D_30C_rep2


title: RNAPII-CTDS2P_fft2D_30C_rep1


title: RNAPII-CTDS2P_fft2D_30C_rep2


title: RNAPII-CTDS2P_fft3D_30C_rep1


title: RNAPII-CTDS2P_fft1D_30C_rep1


title: RNAPII-CTDS2P_fft1D_30C_rep2


title: RNAPII-CTDS2P_WT_30C_rep2


title: RNAPII-CTDS2P_WT_30C_rep1


title: RNAPII-CTDS2P_hrp1D_30C_rep1


title: Old (45do) posterior midguts

city: Los Angeles

first: Martin

last: RESNIK DOCAMPO

state: CA

address: 610 Charles E young Dr East

department: MCDB

institute: UCLA

description:
Total poly-A mRNA.
This Sample represents 3 biological replicates.
Processed data file: expressed_transcript_aging_RNAseq_posterior_midgut.txt
Processed data file: processed_aging_data.txt

data_processing:
Genomatix software was used for mapping spliced reads, making transcript assemblies, and for differential expression analysis.
Reads were first trimmed by removing adapter and Illumina-specific sequences. Next, trimmed reads were aligned against the Drosophila genome (ElDorado 08-2011) with default settings. Finally, a differential expression analysis was performed using the DESeq package method with a P‐value threshold of p<0.05.
Genome_build: ElDorado 08-2011
Supplementary_files_format_and_content: expressed_transcript_aging_RNAseq_posterior_midgut.txt: Tab-delimited text file includes number of reads and normalized expression values.
Supplementary_files_format_and_content: processed_aging_data.txt: Tab-delimited text file includes log2 fold change values for differential gene expression, p-values, p adjusted.

organism: Drosophila melanogaster

source_name: posterior midgut, 45 days old

growth_protocol: Flies raised at 25ºC.

extract_protocol:
Seventy-five female posterior midguts per condition after dissection were frozen at -80ºC in fresh Trizol buffer (TRizol Reagent, Life Technologies, 15596026; 5μg Linear Poly-Acrylamide Sigma 56575, 100ng of tRNA). Total RNA was extracted pooling midgut samples, followed by 5 rounds of freezing (liquid nitrogen)/thawing at 37ºC in a water bath. Samples then underwent 5 rounds of vortexing at RT for 30’’, letting stand at RT for 5 min to disrupt all RNA-protein complexes. Finally, RNA was isolated by phenol/chloroform extraction. Purified RNA was treated with DNase Q1 (Promega, M610A).
RNA-Seq libraries were prepared from three biological replicates for each experimental condition. The NEBNext poly(A)-mRNA magnetic isolation kit (NEB E7490S) was used to isolate poly(A)-mRNA from 4 μg of whole mRNA. cDNA libraries were generated using the NEBNext RNA Library Prep Kit for Illumina (NEB E6110S), and NEBNext Multiplex Oligos for Illumina (NEB E7335S) were used for multiplexing. All steps were performed according to manufacturer's directions.

tag: strain/background

value: Oregon R

value: wild type

tag: age

value: 45 days

value: posterior midgut

tag: Sex

value: female


title: Gli-RNAi

description:
Gli-RNAi is induced by RU486 (RU+).
Total poly-A mRNA.
This Sample represents 3 biological replicates.
Processed data file: expressed_transcripts_RNAseq_GLIrnai_posterior_midgut_EC.txt
Processed data file: GLIrnai_RNAseq posterior_midguts_differential expression.txt

data_processing:
Genomatix software was used for mapping spliced reads, making transcript assemblies, and for differential expression analysis.
Reads were first trimmed by removing adapter and Illumina-specific sequences. Next, trimmed reads were aligned against the Drosophila genome (ElDorado 08-2011) with default settings. Finally, a differential expression analysis was performed using the DESeq package method with a P‐value threshold of p<0.05.
Genome_build: ElDorado 08-2011
Supplementary_files_format_and_content: expressed_transcripts_RNAseq_GLIrnai_posterior_midgut_EC.txt: Tab-delimited text file includes number of reads and normalized expression values.
Supplementary_files_format_and_content: GLIrnai_RNAseq posterior_midguts_differential expression.txt: Tab-delimited text file includes log2 fold change values for differential gene expression, p-values, p adjusted.

source_name: posterior midgut, Gli-RNAi (RU+)

treatment_protocol: Gli-RNAi is induced by RU486 (RU+); addition of ethanol is used as a control (RU-; uninduced Gli-RNAi).

value: 5966GS-GAL4; UAS-Gli-RNAi

tag: condition

value: gliotactin knockdown in enterocytes

value: 9 days


title: Control

description:
Addition of ethanol is used as a control (RU-; uninduced Gli-RNAi).
Total poly-A mRNA.
This Sample represents 3 biological replicates.
Processed data file: expressed_transcripts_RNAseq_GLIrnai_posterior_midgut_EC.txt
Processed data file: GLIrnai_RNAseq posterior_midguts_differential expression.txt

source_name: posterior midgut, control (RU-)

value: control


title: osdrm2-H3K27me3

description: Chromatin IP against H3K27me3

data_processing:
Raw reads was generated by HiSeq 3000. Trimmomatic (version 0.32) was used to filter out low quality reads and crop all reads to a uniform length (45bp) (Bolger et al., 2014). Clean reads were mapped to the rice genome (RGAP version 7) by default allowing up to 2 mismatch using Bowtie2 (version 2.1.0) (Trapnell et al., 2012). Samtools (version 0.1.17) is used to remove potential PCR duplication. Peaks of H3K27me3 were called out by MACS software with the default P value (1e-5), and peaks of anti-SDG711 using P value=1e-9 because of the largest percentage overlap of H3K27me3 marked genes and SDG711 bound genes, and the output wig files were used for viewing the data by Gbrowse 2.0. For BS-seq anaylais, Trimmomatic (version 0.32) was used to filter out low quality reads and BatMeth (Lim et al., 2012) was used to align clean tags to the rice genome (RGAP version 7) by default parameters followed by removing PCR-amplified redundancy. Methylation levels were calculated by #C/(#C+#T).
Genome_build: RGAP version 7.0
Supplementary_files_format_and_content: tag numbers in each gene body

source_name: DongJin-seedling

growth_protocol: Rice (Oryza sativa spp. japonica) plants used in this study for ChIP-Seq and BS-Seq analysis were from the ‘DongJin’ (DJ) background callus culture-regenerated wild type (WT), SDG711 over-expression (line 2, 4, 5 combined) (711OX) and osdmr2 mutant plants as described previously (Liu et al., 2014). Seedling leaves of callus culture-regenerated wild type (WT), SDG711 over-expression lines or osdrm2 grown in one-half-strength Murashige and Skoog medium under a 16-h-light/8-h-dark cycle at 30°C for 12 DAG (day after germination) were harvested and frozen in liquid nitrogen for DNA, RNA or chromatin extraction.

extract_protocol:
About 2 g of seedling leaves were crosslinked in 1% formaldehyde under vacuum. Chromatin was extracted and fragmented to 200-750 bp by sonication, and ChIP was performed using the following antibodies: H3K27me3 (a2363, ABclonal) and anti-SDG711 (Liu et al., 2014). The precipitated samples were analyzed by high throughput sequencing. For genomic bisulfite sequencing, the total genomic DNA of callus culture- regenerated wild type (WT), SDG711 over-expression lines were prepared using the DNeasy plant mini kit (Qiagen). Genomic DNA (5 g) was used to generate BS-Seq libraries as previously described (Feng et al., 2011). Sequencing was performed at the Novogene Bioinformatics Technology Co. Ltd, China.
DNA from ChIP was used to construct sequencing libraries following the protocol provided by Illumina TruSeq® ChIP Sample Prep Set A described in http://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqchip/truseq-chip-sample-prep-guide-15023092-b.pdf.

value: 12 day seedling

value: DongJin

tag: antibody


title: WT-1

status: Public on Dec 17 2016

city: Hwasun, Jeollanam-do

first: Young-Kook

last: Kim

address: 264, Seoyang-ro

department: Department of Biochemistry

country: South Korea

institute: Chonnam National University Medical School

description: Sample name: 1-WT

data_processing:
The FASTQ sequences were aligned into the human reference genome (GRCh37/hg19) using STAR algorithm (Dobin et al. 2013), and assembled using Cufflinks (Trapnell et al. 2010).
We only selected transcripts with the average of FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values among different libraries larger than 1.
Also, we removed the transcripts with the FPKM values different more than two folds between duplicates of the same cell line.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM values for each transcript were calculated.

source_name: SNU-638 cells

extract_protocol:
Total RNA was extracted with TRIzol reagent (Life Technologies). 10 µg of RNA was used to enrich mRNAs with poly(A) tails using oligo(dT) Dynabeads (Life Technologies).
The sequencing libraries were made using TruSeq Stranded Total RNA Library Prep Kit (Illumina). The quality of the libraries was verified by Agilent 2100 Bioanalyzer (Agilent).


title: 221KO-1

description: Sample name: 2-221

value: knockout of miR-221


title: DKO-2

description: Sample name: 8-DKO

value: knockout of miR-221 and miR-222


title: 222KO-1

description: Sample name: 3-222

value: knockout of miR-222


title: 222KO-2

description: Sample name: 7-222


title: 221KO-2

description: Sample name: 6-221


title: WT-2

description: Sample name: 5-WT


title: DKO-1

description: Sample name: 4-DKO


title: GFP IP RNA experiment 2

city: Cambridge

first: Francisco

last: Navarro

address: Downing St

department: Department of Plant Sciences

institute: University of Cambridge

description:
rip_seq_norm_count.txt.gz
FN108

data_processing:
The RSEM package (version 1.1.19) in conjunction with the bowtie alignment algorithm (version 0.12.7)  was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to S. Pombe genes downloaded from PomBase (www.pombase.org) on 16th September 2013.
Differential expression analysis was performed with the edgeR package using Bioconductor (version 2.7) running with the R programming environment (version 2.12.1)
Genome_build: S.Pombe gtf downloaded from Pombase on 16th September 2013
Supplementary_files_format_and_content: Tab delimited text files containing gene-level counting of the sequenced reads with respect to S. Pombe genes downloaded from PomBase (www.pombase.org) on 16th September 2013.

source_name: exponentially growing cells

growth_protocol: cells were grown in minimal media (EMM) at 25°C. Samples were collected in early-mid exponential phase

extract_protocol:
RNA was extracted using hot phenol protocol (Lyne et al 2003)
RNA libraries were prepared for sequencing using standard Illumina protocols


title: GFP total RNA input experiment 3

description:
rip_seq_norm_count.txt.gz
FN111


title: Zfs1 IP RNA experiment 2

description:
rip_seq_norm_count.txt.gz
FN106


title: zfs1∆ delta experiment 2

description:
rna_seq_norm_count.txt.gz
FN116


title: zfs1∆ experiment 1

description:
rna_seq_norm_count.txt.gz
FN114


title: WT-2-H3K27me3

description: Chromatin IP against H3K27me3


title: WT experiment 2

description:
rna_seq_norm_count.txt.gz
FN115


title: GFP total RNA input experiment 1

description:
rip_seq_norm_count.txt.gz
FN4


title: WT experiment 1

description:
rna_seq_norm_count.txt.gz
FN113


title: Zfs1 total RNA input experiment 3

description:
rip_seq_norm_count.txt.gz
FN109


title: Young (5do) posterior midguts

source_name: posterior midgut, 5 days old

value: 5 days


title: normal condition T02

city: Chengdu

first: Zhenyu

last: Bai

address: 211 Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

description: CK-read T02

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Cufflinks are used for assemble transcripts and remap and quanlity gene-expression level, which is estimate by FPKM value.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Phormium tenax

source_name: leaves

extract_protocol:
total RNA was extracted with Trizol Reagent (Invitrogen), following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaf blade

value: One-year-old


title: GFP IP RNA experiment 3

description:
rip_seq_norm_count.txt.gz
FN112


title: Zfs1 IP RNA experiment 3

description:
rip_seq_norm_count.txt.gz
FN110


title: Zfs1 total RNA input experiment 2

description:
rip_seq_norm_count.txt.gz
FN105


title: GFP total RNA input experiment 2

description:
rip_seq_norm_count.txt.gz
FN107


title: Zfs1 IP RNA experiment 1

description:
rip_seq_norm_count.txt.gz
FN3


title: drought condition T01

description: treatment T01


title: Zfs1 total RNA input experiment 1

description:
rip_seq_norm_count.txt.gz
FN1


title: Jarid2 replicate 1

status: Public on Dec 16 2016

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description: chromatin IP against Jarid2

data_processing:
ChIPseq analysis: Alignment: Sequence reads were mapped to the Mouse genome (mm9, July 2007) using BOWTIE (PubMed ID 19261174) with the option -m 1.
Peak-calling: Peak detection was performed with MACS (PubMed ID: 18798982). ChIP profiles were produced by MACS in BedGraph. Peaks were reported in BED format.
Genome_build: mm9
Supplementary_files_format_and_content: Jarid2_sh_ct_14840.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: Jarid2_sh_4_14841.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: Jarid2_sh_ct_14840_peaks.bed (BED, signal enriched regions)
Supplementary_files_format_and_content: Jarid2_sh_4_14841_peaks.bed (BED, signal enriched regions)

source_name: Undifferentiated ES cells

growth_protocol: E14TG2a mouse ES cells were kept under feeder-free, 20% serum conditions with LIF on 0.1% gelatin coated dishes, as in (Morey et al., 2012)

extract_protocol:
ChIP experiments used about 20 million cells, using a protocol adapted from (Stock et al., 2007). For all ChIPs except those against EloB, cells were washed 2´ with PBS, and crosslinking was started by adding 1% formaldehyde in PBS to the plate, stopped by adding 0.125 M glycine, and cells were harvested by scraping and then pelleted. For ChIPs against EloB, cells were washed 2x with PBS, protein-protein crosslinking was performed with 40 ml ChIP Crosslink Gold (Diagenode, C01019027) or 2 mM DSP (ThermoFisher, cat 22586) in 10 ml PBS for 30 min, followed by two washes with PBS. Protein-DNA crosslinking (1% formaldehyde in PBS) was then performed on the plate for 10 min, stopped by 0.125 M glycine and cells were harvested by scraping and then pelleted. Cell pellets were resuspended and incubated for 10 min in 2 ml swelling buffer (25 mM HEPES [pH 7.9], 1.5 mM MgCl2, 10 mM KCl, 0.1% NP40, protein and phosphatase inhibitors) and the suspension was homogeneized (tight pestle, 50x). Nuclei were pelleted (3,000 g, 5 min) and resuspended in 1.3 ml sonication buffer (50 mM HEPES [pH 7.9], 140 mM Nacl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS, protease and phosphatase inhibitors). Sonication (Diagenode Bioruptor, 30 s ON/30 s OFF, high potency, 2x 8 cycles with fresh ice in between). Insoluble material was pelleted, and chromatin concentration and sonication efficiency was determined in the supernatant by DNA quantification or agarose gel after decrosslinking the extracts overnight. ChIPs were performed O.N. using 20-30 μg of DNA, 4 μg antibody (the amount of antibody for reaching full enrichment was titrated) and 25 μl of protein A dynabeads in 500 μl of sonication buffer. ChIPs were washed once with sonication buffer, once with buffer wash buffer A (50 mM HEPES [pH 7.9], 500 mM Nacl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS, protease and phosphatase inhibitors), once with  wash buffer B (20 mM Tris-Cl [pH 8.0], 250 mM LiCl, 1 mM EDTA, 0.5% Triton MP40, 0.5% Na-deoxycholate, protease and phosphatase inhibitors) twice with 1x TE pH 8.0 and eluted in 200 μl TE pH 8.0, 1% SDS followed by decrosslinking (O.N) and RNAse treatment. DNA was finally purified over PCR (Qiagen) and eluted in 55 μl water.
Libraries were prepared according to Illumina instructions.

treatment_protocol: To generate stable cell lines expressing shRNA targeted against C17orf96 , lentivirus was produced in 293T cells by calcium phosphate-mediated transfection of 5 mg plasmid. To generate stable C17orf96 –/– cell lines, 5 ug plasmids encoding sgRNAs were transfected using Lipofectamine 2000 (Invitrogen), according to the manufacturer´s instruction. Puromycin selection was performed for 1 day at 2 mg/ml, 1000 cells were split into a 10-cm dish, and clones were picked 10 days later. Clones were expanded into 6-well dishes, and C17orf96 expression was checked by Western blot. Supernatant was harvested after 48 hr, diluted 1:4, and used to infect E14 cells. Puromycin (2 mg/ml) was added for 2 days for selection. For siRNA experiments, 100,000 cells were seeded in 6-well plates and transfected 24 hr later with 20 μM siRNA using 7 μl Lipofectamine RNAimax (Invitrogen) and Optimem, according to manufacturer’s instructions. Transfections were repeated one day later, and cells were harvested after an additional 24 hr (i.e., 48 hr after the first transfection). Total RNA was isolated with RNeasy Plus Mini Kit (Qiagen) using protocol Appendix D. For siRNA experiments followed by ChIP, 1.2 million cells were seeded, and siRNA was transfected twice at 20 μM using using 70 μl Lipofectamine RNAimax (Invitrogen) and Optimem, according to manufacturer’s instructions. Transfections were repeated one day later, and cells were harvested after additional 24 hr (i.e. 48 hr after the first transfection).

tag: chip antibody

value: anti JARID2 rabbit Novus NB100-2214


title: Jarid2 upon C17orf96 knock-down

description: chromatin IP against Jarid2


title: Treat 3

city: London

first: Rodney

middle: Peter

last: DeKoter

state: Ontario

address: 1151 Richmond St

department: Microbiology and Immunology

institute: Western University

data_processing:
Data analysis was performed according to Trapnell, et al; 2012 using the tools available on Galaxy suite.
Standard Illumina sequencing adaptors (AGATCGGAAGAGC) and short reads were removed using Trim Galore! V0.2.8.1 in mate-paired mode, Trim low quality: 20, Maximum allowed error rate: 0.1, discard reads that became shorter than length: 20, RRBS specific settings: default.
Trimmed FASTQ files were aligned to the mouse genome (MM10) using the TopHat2 v2.0.9 in mate-paired mode, Mean inner distance between mate pairs: 140, std. dev for distance between mate pairs: 30.
Assembled transcript abundance and differential gene expression were determined using Cufflinks/CuffDiff v2.1.1. .Gff files for mouse transcripts were aquired from mouse UCSC mm10
Genome_build: mm10
Supplementary_files_format_and_content: .csv contains transcript abundance between control and treatment conditions

source_name: pro-B cells

growth_protocol: i660BM cells containing a PU.1-inducible system were grown as previously described (Christie, DA; 2014). Cells were grown in Iscove's Modified Dulbecco's Media (IMDM) (Wisent) supplemented with 5% of IL-7, 10% fetal bovine serum (Wisent) , 100 U/mL penicillin–streptomycin + 2 mM L-glutamine, and 5 × 10−5 mol/L 2-mercaptoethanol. Cells were maintained as a suspension at 1^6 cells/10 ml media and maintained at 37°C with 5% C02.

extract_protocol:
RNA was isolated from induced and non-induced cells using RNAeasy kit from Qiagen.
RNA libraries were prepared for sequencing using standard Illumina protocols
mRNASeq stranded

treatment_protocol: Cells were induced with 70 ng/ml doxycycline for 48 hours. Un-induced cells were used as a control.

tag: treatment

value: induced


title: Treat 1

tag: strain


title: Control 2

value: non-induced


title: Treat 2


title: Control 3


title: GFP IP RNA experiment 1

description:
rip_seq_norm_count.txt.gz
FN6


title: Input

data_processing:
Illumina HiSeq2000 .bam files provided by the sequencing core were processed using rmdup (version 1.0.0) to remove duplicate reads
Files were converted to FASTQ format using Bam-to-FASTA/Q (version 1.0.0) and reads groomed to remove Illumina adapter sequences with TrimGalore!(Krueger 2015) in Galaxy Suite (Giardine, Riemer et al. 2005; Blankenberg, Von Kuster et al. 2010; Goecks, Nekrutenko et al. 2010).
Single-end reads aligned to reference MGSCv37 (MM10) using Bowtie (Langmead, Trapnell et al. 2009).
Bowtie reported only the best alignment for each fragment (--best) with a maximum number of 2 mismatches with an average quality score of at least 70. Peaks called in MACS 1.4.1 with an mfold of (10,30) (Zhang, Liu et al. 2008).
Peak-calling was conducted for two biological replicates for each condition
Genome_build: MM10
Supplementary_files_format_and_content: .bed files representing regions of enrichment, and .wig files representing ChIP-signal were generated using MACS1.4.1.

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 minutes with rocking at room temperature, and cross-linking was terminated by addition of 125 mM glycine. Pellets were washed in cold PBS and snap frozen in liquid nitrogen. Cell pellets were lysed in buffer (50 mM Tris-HCl [pH 8.1], 10 mM EDTA, 1% SDS) containing Halt™ protease inhibitor mixture (Thermo Scientific). Chromatin fragmentation was conducted using 30 cycles of sonication on a Bioruptor (Diagenode). PU.1-chromatin complexes were immunoprecipitated overnight a 4°C with Rabbit polyclonal anti-mouse PU.1 (T-21) (Santa Cruz Biotechnology) or mouse control IgG (Abcam) conjugated to protein G dynabeads (Invitrogen, Burlington) on 300 ug of chromatin per sample. Bound beads were washed once in low salt wash buffer (0.1% SDS, 1% Triton-X-100, 2 mM EDTA, 20 mM Tris-HCl[pH 8.0], 150 mM NaCl), once with high salt wash buffer (0.1% SDS, 1% Triton-X-100, 2 mM EDTA, 20 mM Tris-HCL[pH 8.0], 500 mM NaCl), once with LiCl buffer (0.25 M LiCl, 1% NP-40, 1% Na-deoxycholate, 1mM EDTA, 10 mM Tris-HCl [pH 8.0]), and twice with Tris-EDTA buffer at pH 8.0. Immunocomplexes were eluted in elution buffer (1% SDS, 0.1 M NaHCO3) and the buffer adjusted to 200 mM NaCl. Cross-linking was reversed at 65°C overnight and DNA isolated using a Wizard SV Gel and PCR purification kit (Promega).
Libraries were generated robotically with 10 ng of fragmented DNA (100-300 bp) using the Kapa HTP Library Preparation Kit (Kapa Biosystems) as per the manufacturer’s recommendations except that adapters and PCR primers were diluted 100-fold, the size selection step was done after the PCR step and the number of PCR cycles increased by 6. Adapters and PCR primers were purchased from Integrated DNA Technologies whereas size selection has been performed on a Pippin Prep instrument (SAGE Biosciences Inc). Libraries were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (D-Mark). Average size fragment was determined using a LaChip GX (PerkinElmer) instrument. Libraries were sequenced on a single-end 100bp read length run on a HiSeq2000 (Illumina).

treatment_protocol: Chromatin pellets were prepared from uninduced cells and cells induced with 70 ng/ml doxycycline for 24 hours.

tag: chip-antibody


title: PU.1_3

value: Rabbit polyclonal anti-mouse PU.1 (T-21) (Santa Cruz Biotechnology)


title: PU.1_2


title: K562 cell cycle

first: Atray

last: Dixit

state: MA

address: 415 Main Street

institute: MIT

data_processing:
10x cellranger v1
Supplementary_files_format_and_content: .mtx file contains, gene id (in genenames.txt) (cell id) in cnames.txt and UMI counts. cbc_gbc_dict.txt contains assignments between cell id and perturbation id

source_name: Human erythroleukemia K562

extract_protocol: 3' polyA RNA seq; 10X Genomics Chromium Prep

tag: stimulation

value: unstimulated

tag: days post transduction

tag: cell line


title: WT_GV

city: beijing

first: yujiao

last: dang

address: Yihe road

institute: BIOPIC

description: Bulk RNA seq

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

source_name: mouse oocyte

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

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

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

value: ICR

tag: tissue

value: GV oocyte

value: wildtype


title: K562 TFs, High MOI


title: Dma_bisulfite_Ctr_rep2

city: Gent

first: Jana

last: Asselman

address: Coupure Links 653 (Building F, 2nd floor)

institute: Ghent University

data_processing:
Basecalling was performed using the Illumina Casava 1.5 software
Reads containing more than 5% N bases were omitted. The remaining reads were subsequently dynamically trimmed to the longest stretch of bases which had a Phred score higher or equal to 30 using Trim Galore! 0.3.2 software wit h standard settings
Trimmed reads were transformed into fully bisulfite-converted forward (C->T conversion) and reverse read (G->A conversion of the forward strand) versions, before being mapped to similarly converted versions of the genome (also C->T and G->A converted) using Bowtie2 v.2.1.0 (Langmead and Salzberg 2012) while setting the scoring function as --score_min L,0,-0.6. Non-uniquely mapping reads were discarded,
For each read covering a cytosine site the methylation state of that site was inferred using the Bismark_methylation_extractor tool from the Bismark 0.9.0 software (Krueger and Andrews 2011) by comparing the uniquely mapped read to the original, non-converted reference genome. Only cytosine sites with a minimum coverage of 5x were further considered
Genome_build: Dmagna v2.4, available through http://arthropods.eugenes.org/EvidentialGene/daphnia/daphnia_magna/Genome/
Supplementary_files_format_and_content: Tab-delimited count data files consisting of 4 columns: <chromosome>  <position> <count methylated> <count unmethylated>. Such files were generated for each cytosine context (CpG, CHG and CHH), each strand (original bottom 'OB'; original top 'OT') and each replicate (ctrl1; ctrl2; ctrl3) seperately.

organism: Daphnia magna

source_name: whole body tissue

growth_protocol: 0-24 old juniveles of Daphnia magna isolate Xinb3 (Routtu et al. ) were grown for 5 days in Adam medium (Routtu et al. ). All cultures were kept in controlled conditions at 20 ± 1°C, under white fluorescent lights at a 16h:8h light-dark cycle and at a light intensity of 14 µmoles·m-2·s-1. Daphnids were grown under a density of 20 animals per liter medium and were fed daily They were fed daily with an algal mixture consisting of Scenedesmus obliquus and Cryptomonas sp. (SAG 26.80 http://sagdb.uni-goettingen.de) at a final concentration of 108 cells per liter in a 95:5 ratio on cell basis (in the control treatment). The Microcystis treatment  consisted of a diet of 50% of M. aeruginosa, with the same carbon content as 0.5 * 108 cells of the control diet, and 50% of the control diet, a mixture of S. obliquus and Cryptomonas sp. as described above, in a  concentration of 0.5 * 108 cells per liter.Medium was renewed every other day.

extract_protocol:
Eighty daphnids per biological replicate were pooled, shock-frozen in liquid nitrogen and stored at -83°C until DNA extraction. Extraction of the total genomic material was performed using the MasterPure kit (Epicentre, Madison, WI, USA) according to the manufacturer’s protocol, including RNAse treatment.
Bisulfite library construction and sequencing were performed at BGI-Shenzhen (Shenzhen, Guangdong, China). Briefly, the extracted DNA was fragmented by sonication to a mean size of approximately 300 bp. After blunt ending and 3′-end addition of dA, Illumina methylated adapters (Illumina, San Diego, CA, USA) were added according to the manufacturer's instructions. The bisulfite conversion (C → U) was carried out using the EZ DNA methylation Gold kit (Zymo Research, Irvine, CA, USA) according to manufacturer’s instructions.

treatment_protocol: No treatment was applied

value: control diet

tag: clone


title: KO_MII

description: Bulk RNA seq

value: MII oocyte

value: Erk-/-


title: K562 TFs, 13 days


title: K562 TFs, 7 days


title: Dma_bisulfite_MC_rep2

value: diet with 50% Microcystis


title: Dma_bisulfite_MC_rep1


title: Dma_bisulfite_Ctr_rep3


title: Dma_bisulfite_Ctr_rep1


title: Dma_bisulfite_MC_rep3


title: 11a-wt1-WT

city: Ann Arbor

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

description:
mRNA/lncRNA  - rRNA-depleted
Sample 45628
FPKM_WT_2

data_processing:
QC: We checked the quality of the raw reads data for each sample using FastQC [1] (version 0.10.1) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content, etc.).
Aligment: We used the software package Tuxedo Suite for alignment, differential expression analysis, and post-analysis diagnostics [2, 3, 4]. Briefly, we aligned reads to the reference transcriptome including both mRNAs and lncRNSs (UCSC mm10) [5] using TopHat (version 2.0.9) and Bowtie (version 2.1.0.). We used default parameter settings for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments.
QC: We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
Normalization and Quantitation: We used Cufflinks/CuffDiff (version 2.1.1) for expression quantitation, normalization, and differential expression analysis, using UCSC mm10.fa as the reference genome sequence. For this analysis, we used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package.
Differential Expression: We used locally developed scripts to format and annotate the differential expression data output from CuffDiff. Briefly, we identified genes and transcripts as being differentially expressed based on three criteria: test status = “OK”, FDR < 0.05 and fold change ≥ ± 1.5.
Annotation: We annotated genes and isoforms with NCBI Entrez GeneIDs and text descriptions. We further annotated differentially expressed genes with Gene Ontology (GO) [6] terms using NCBI annotation.
Enrichment Testing: We used DAVID (version 6.7) [7] for enrichment analysis of the set of differentially expressed genes to identify significantly enriched functional categories.
Genome_build: MM10
Supplementary_files_format_and_content: .xls table of normalized expression values for each gene for each sample

source_name: adult cerebral cortex

growth_protocol: The Plat-/- Mice were grown in a specific pathogen free environment with ad libitum access water and standard chow. The wild-typ C57BL/6J were purchased from Jackson Labs

extract_protocol:
For RNA extraction brain tissue was lysed in Qiazol solution (Qiagen) using TissueLyser II (Qiagen) tissue homogenizer  follow by RNA isolation using the NucleoSpin RNA Midi kit (Macherey-Nagel).
The Agilent TapeStation was used to assess RNA quality. Samples with RINs (RNA Integrity Numbers) of eight or greater were prepped using the Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #RS-122-2001 and RS-122-2002). mRNA was isolated from 0.1-3 ug of total RNA by polyA+ purification, fragmented, and copied into first-strand cDNA using reverse transcriptase and random primers. 3' cDNA ends were then adenylated and adapters ligated. One of the adapters contained a 6-nucleotide barcode to enable multiplexing of samples. Products were purified and enriched by PCR to create the final cDNA library. Libraries were checked for quality and quantity by Agilent TapeStation and qPCR using a library quantification kit for Illumina sequencing platforms (catalog #KK4835, Kapa Biosystems, Wilmington, MA). Clonal clusters were generated using cBot (Illumina, Inc., San Diego, CA). Quadriplexed samples were sequenced using the HiSeq 2000 system (Illumina) with a 100-cycle paired-end run in high output mode using Version 3 reagents according to manufacturer's protocols.

treatment_protocol: The mice (four mice per genotype) were euthanized by CO2 inhalation. The brains were dissected out, the olfactory bulb and cerebellum removed, and the brains snap frozen in liquid nitrogen

value: cerebral cortex

value: 6 weeks

value: WT


title: 10a-tpa-wt3-WT

description:
mRNA/lncRNA  - rRNA-depleted
Sample 45627
FPKM_WT_1


title: 7a-tpa-h39-New

description:
mRNA/lncRNA  - rRNA-depleted
Sample 45624
FPKM_KO_6

value: Plat-/-


title: Control 1


title: 2a-tpa-h42-Old

description:
mRNA/lncRNA  - rRNA-depleted
Sample 45619
FPKM_KO_1


title: 5a-tpa-h58-New

description:
mRNA/lncRNA  - rRNA-depleted
Sample 45622
FPKM_KO_4


title: 1a-tpa-h63-Old

description:
mRNA/lncRNA  - rRNA-depleted
Sample 45618
FPKM_KO_0


title: 4a-tpa-h62-New

description:
mRNA/lncRNA  - rRNA-depleted
Sample 45621
FPKM_KO_3


title: 3a-tpa-h38-Old

description:
mRNA/lncRNA  - rRNA-depleted
Sample 45620
FPKM_KO_2


title: KO_GV

description: Bulk RNA seq


title: LE7

city: Cleveland

first: Tanu

last: Parmar

state: OH

address: 2085 adelbert road

department: Department of Ophthalmology and Visual Sciences

institute: Case Western Reserve University

description: whole eyes from 3 Abca4-/-Rdh8-/- mice, collected 7 days after light exposure

data_processing:
Base calls performed using bcl2fastq version 1.8.3
RNA-Seq reads were aligned to the mouse reference genome (mm9) using Tophat version 2 with default parameters
Differential expression was determined using Cuffdiff version 2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: FPKM values given in a data matrix in tab delimited format (gene by sample).

source_name: whole eye_light exposed

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was extracted using  Rneasy Mini Kit (Qiagen).  Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: 7 days after light exposure

value: whole eye


title: LE24

description: whole eyes from 3 Abca4-/-Rdh8-/- mice, collected 24 h after light exposure

value: 24 h after light exposure


title: 12a-wt2-WT

description:
mRNA/lncRNA  - rRNA-depleted
Sample 45629
FPKM_WT_3


title: WT_MII

description: Bulk RNA seq


title: LE3

description: whole eyes from 3 Abca4-/-Rdh8-/- mice, collected 3 h after light exposure

value: 3 h after light exposure


title: CON

description: whole eyes from 3 Abca4-/-Rdh8-/- mice, no treatmnet

source_name: whole eye_no light

value: no light (control)


title: AB1811

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: Well with cells infected with a pool of several gRNA and control gRNAs in BFP-reporter expressing lentiviruses

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

source_name: single cell-sorted mouse ex-vivo myeloid cells

growth_protocol: Bone marrows were flushed from hind leg bones from euthanized 6 to 8 weeks-old mice housed at the Weizmann Institute animal facility. Cell suspensions were obtained, red blood cells lysed, and cells grown on 6-well petri dishes on media supplemented with GM-CSF.

extract_protocol:
Cells were scrapped from the plate and stained with FACS markers antibodies as indicated above (selection marker).
3' end mRNA libraries were prepared for sequencing using CRISP-seq (Jaitin et al., Cell 2016), which includes a module of MARS-seq (Jaitin et al., Science 2014) and a module of UGI-seq.

treatment_protocol: Cells were infected on day 2 post plating with lentivirus vectors, each containing one gRNA and one fluorescent selection marker. On day 7, cells were challenged with LPS for 4 hours before harvest.

value: transgenic Cas9-GFP C57BL/6

tag: organ

value: bone marrow-derived

tag: selection marker

value: cells stimulated with lypopolysacharide (LPS) for 4 hours

tag: grna in the infecting vector

value: INF/AV gRNA pool (BFP)


title: AB1809


title: AB1810


title: 9a-tpa-wt4-WT

description:
mRNA/lncRNA  - rRNA-depleted
Sample 45626
FPKM_WT_0

tag: age

tag: genotype


title: AB1806


title: 8a-tpa-h32-New

description:
mRNA/lncRNA  - rRNA-depleted
Sample 45625
FPKM_KO_7


title: AB1804


title: AB1807


title: AB1801


title: AB1800


title: 6a-tpa-h36-Old

description:
mRNA/lncRNA  - rRNA-depleted
Sample 45623
FPKM_KO_5


title: AB1802


title: AB1803


title: AB1808


title: AB1798


title: AB1797


title: AB1796


title: AB1682

description: Donor LSK cells infected with a mix of Cebpb, Rela, Irf8, Stat1, Stat2, and two control (Oris and LacOp) gRNAs (BFP) lentiviruses

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

source_name: single cell-sorted  mouse donor (Cas9-GFP+) in vivo dendritic cells from the spleen

extract_protocol:
Cells were scrapped from the plate and stained with FACS markers antibodies as indicated above (selection marker).
3' end mRNA libraries were prepared for sequencing using CRISP-seq (Jaitin et al., Cell 2016), which includes a module of MARS-seq (Jaitin et al., Science 2014) and a module of UGI-seq.
single cell RNA-seq and UGI-seq for gene expression quantitation and gRNA identification, respectively.

value: wild-type and transgenic Cas9-GFP C57BL/6

value: spleen

value: mice injected with lypopolysacharide (LPS), 4 hours before experiment

value: in vivo mix (BFP)


title: AB1681

source_name: single cell-sorted  mouse donor (Cas9-GFP+) in vivo myeloid cells from the spleen


title: AB1680


title: AB1679


title: AB1677


title: AB1675


title: AB1676


title: AB1674


title: AB1805


title: AB1636

description: Well with cells infected with a mix of Cebpb, Irf4, Nfkb2, Stat1, Stat2, Irf9, Irf8 and control gRNAs and BFP lentiviruses

source_name: single cell-sorted  mouse ex-vivo myeloid cells

value: INF/AV mix2 (BFP)


title: AB1635


title: AB1634


title: AB1632


title: AB1633


title: AB1631


title: AB1799


title: AB1630


title: AB1595

description: Well with cells infected with a mix of Cebpb, Rela, Nfkb1, Nfkb2, Stat2, Irf9 and control gRNAs and BFP lentiviruses

value: INF/AV mix1 (BFP)


title: AB1599


title: AB1598


title: AB1584


title: AB1583


title: AB1601


title: AB1582


title: AB1597


title: AB1600


title: AB1596


title: AB1581


title: AB1594


title: AB1579


title: AB1578

value: INF/AV (inflammatory and antiviral transcription factor genes) mix1 (BFP)


title: AB1565

description: Well with cells infected with a mix of Cebpb, Spi1, Irf8 and control gRNA lentiviruses (all with the BFP selection marker)

value: developmental genes mix (BFP)


title: AB1564


title: AB1566


title: AB1563

description: Well with cells infected with a mix of Irf9-gRNA and Rela-gRNA lentiviruses, both with the BFP selection marker

value: Irf9 x Rela (BFP)


title: AB1562


title: AB1492

description: Well with cells infected with a mix of Itgam-gRNA BFP and Cebpb-gRNA mCherry lentiviruses

value: Itgam-BFP x Cebpb-mCherry


title: AB1525


title: AB1123

description: Well with cells infected with Cebpb-gRNA BFP or mCherry

value: unstimulated

value: Cebpb BFP


title: AB1499

description: Well with cells infected with a mix of Cebpb-gRNA BFP and Rela-gRNA mCherry lentiviruses

value: Cebpb BFP x Rela mCherry


title: AB1498

value: transgenic Cas9-GFP C57BL/6


title: AB1121

value: bone marrow-derived


title: AB1493


title: AB1348


title: AB1347

value: cells stimulated with lypopolysacharide (LPS) for 4 hours


title: AB1120


title: DC 3hr

source_name: Mouse BMDC, Cas9 mouse

tag: cell type

value: edited R1 embryonic stem cells and implanted in C57BL/6N

value: LPS


title: AB1118

description: control plate: well with cells infected with a mix of control (LacOp, LacZ, Oris) gRNA lentivirus with a BFP selection marker

value: control gRNA


title: NF-YB1_1

city: Shanghai

first: Jingjng

last: Xu

address: 300, Fenglin road

institute: SIPPE

data_processing:
Raw fastq data were trimmed using FASTX-Toolkit with Q30 (Phred score) and L25 (Length).
Cleaned data were then mapped to the rice reference genome (MSU7.0) using Bowtie2 with default parameters.
MACS2 was used for calling stronger but narrower peaks (q value < 0.05) and weaker but broader regions (q value<0.1) with default settings.
Genome_build: MSU7.0
Supplementary_files_format_and_content: enrichregion_peaks files include information about broader regions called by MACS2, MACS2_peaks files include information about narrower peaks called by MACS2, bed file includes the peak summits locations for every narrower peaks.

source_name: caryopsis coat

extract_protocol:
Caryopsis coats lysates were clarified from sonicated nuclei. OsNF-YB1-DNA complexes were isolated with GFP antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Prep Kit. ChIP DNA samples were subjected to end repair and A-base addition, followed by ligation with adapters. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: caryopsis coat

tag: developmental stage

value: 8-12 days after fertilization

value: anti-GFP antibody (ab290; Abcam)


title: NF-YB1_2

tag: chip antibody


title: AB1580

tag: treatment

value: INF/AV mix1 (BFP)


title: Input_2


title: DC 0hr


title: GEP_093

city: Redwood city

first: Anne

last: Chang

address: 450 Broadway street, Pavilion C

department: Dermatology

institute: Stanford University School of Medicine

data_processing:
Basecalls performed using  CASAVA v1.8.2
The raw reads from 3’-sequencing were aligned to human genome reference (hg19) using Bowtie 2 (version 2.1.0) (Langmead et al., 2009) with default parameters (-D 15 -R 2 -N 0 -L 22 -i S,1,1,15).
Reads, which aligned concordantly to the genome were counted according to the RefGene annotation from UCSC using DEGseq (v0.50.1).
The longest isoform were selected when there are multiple isoforms.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file with normalized reads count for each gene across all samples

source_name: sun-protected skin from healthy volunteer

extract_protocol:
Total RNA from full thickness skin biopsies of the sun protected upper inner arm skin was extracted using RNAeasy Fibrous Tissue Mini Kit (Qiagen, Germantown, MD).
The 3′ -end sequencing for expression quantification (3’-end seq) was performed as  described in Beck et al. (2010).

treatment_protocol: Skin biopsies by punch technique were performed after infiltration of the subcutaneous skin with 1% lidocaine with epinephrine diluted 1:1,000,000 for local anesthesia. The skin biopsies were 4 mm in diameter and included both dermis and epidermis. The samples were bisected, and half was preserved in formalin solution for staining with hematoxylin and eosin while the other half was preserved in RNAlater

tag: subject status

value: healthy volunteer

tag: ethnic background

value: European descent

tag: gender

value: female

value: skin biopsie from sun protected upper inner arm


title: GEP_092


title: GEP_099


title: Input_1


title: GEP_095


title: ZH11

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the rice genome (MSU7.0) using Tophat v2.0.13 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: MSU7.0
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: aleurone layer

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: aleurone layer

value: 8 day after fertilization


title: GEP_091


title: GEP_090


title: GEP_089


title: GEP_087


title: GEP_084


title: GEP_078


title: GEP_081


title: OsNF-YB1 RNAi


title: GEP_072


title: GEP_073


title: GEP_075


title: GEP_077


title: GEP_070


title: GEP_074


title: GEP_110


title: GEP_103


title: GEP_115


title: GEP_064


title: GEP_067


title: GEP_114


title: GEP_069


title: GEP_066


title: GEP_119


title: GEP_118


title: GEP_058


title: GEP_102


title: GEP_006


title: GEP_063


title: GEP_101


title: GEP_053


title: GEP_065


title: GEP_056


title: GEP_116


title: GEP_051


title: GEP_097


title: GEP_060


title: GEP_050


title: GEP_098


title: GEP_096


title: GEP_094


title: GEP_048


title: GEP_045


title: GEP_055


title: GEP_035


title: GEP_068


title: GEP_038


title: GEP_054


title: GEP_037


title: GEP_047


title: GEP_046


title: GEP_041


title: GEP_039


title: GEP_079


title: GEP_044


title: GEP_043


title: GEP_052


title: GEP_026


title: GEP_036


title: GEP_034


title: GEP_022


title: GEP_024


title: GEP_004


title: GEP_083


title: GEP_020


title: GEP_017


title: GEP_031


title: GEP_021


title: GEP_018


title: GEP_019


title: GEP_030


title: GEP_059


title: GEP_014


title: GEP_009


title: GEP_012


title: GEP_016


title: SP-Itgam_Cebpb.sca

description:
Well with cells infected with a mix of Itgam-gRNA BFP and Cebpb-gRNA mCherry lentiviruses
Sample 53

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: lists of gene counts; specific amplicons within genomic DNA;
Supplementary_files_format_and_content: CIGAR string as defined in SAM file sprcifications, showing count of uniq strings. This is used to estimate the editing percentage of the target loci.

source_name: ~4,000 bulk-sorted mouse ex-vivo myeloid cells

extract_protocol:
Cells were scrapped from the plate and stained with FACS markers antibodies as indicated above (selection marker).
3' end mRNA libraries were prepared for sequencing using CRISP-seq (Jaitin et al., Cell 2016), which includes a module of MARS-seq (Jaitin et al., Science 2014) and a module of UGI-seq.
single cell RNA-seq and UGI-seq for gene expression quantitation and gRNA identification, respectively (paired-end + i7 for sample index (7 bases))

tag: strain

value: transgenic Cas9-GFP C57BL/7

value: 6 to 8 weeks-old

value: hind leg bones

value: bone marrow

value: unstimulated

value: Itgam-BFP x Cebpb-mCherry


title: GEP_121


title: GEP_013


title: GEP_112


title: GEP_025


title: GEP_120


title: GEP_113


title: SP-Cebpb_Cebpb.sca

description:
Well with cells infected with a mix of Itgam-gRNA BFP and Cebpb-gRNA mCherry lentiviruses
Sample 51


title: SP-Itgam_Itgam.sca

description:
Well with cells infected with a mix of Itgam-gRNA BFP and Cebpb-gRNA mCherry lentiviruses
Sample 54


title: GEP_108


title: GEP_111


title: SP-Cebpb_Itgam.sca

description:
Well with cells infected with a mix of Itgam-gRNA BFP and Cebpb-gRNA mCherry lentiviruses
Sample 52


title: DP_Itgam.sca

description:
Well with cells infected with a mix of Itgam-gRNA BFP and Cebpb-gRNA mCherry lentiviruses
Sample 50


title: GEP_109


title: DP_Cebpb.sca

description:
Well with cells infected with a mix of Itgam-gRNA BFP and Cebpb-gRNA mCherry lentiviruses
Sample 49


title: GEP_105


title: DN_Itgam.sca

description:
Well with cells infected with a mix of Itgam-gRNA BFP and Cebpb-gRNA mCherry lentiviruses
Sample 48


title: GEP_100


title: GEP_104


title: DN_Cebpb.sca

description:
Well with cells infected with a mix of Itgam-gRNA BFP and Cebpb-gRNA mCherry lentiviruses
Sample 47


title: EC_Wnt5a_18

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

institute: Ludwig-Maximilians University Munich

data_processing:
For Smart-seq2 libraries: Sequencing reads were demultiplexed from the Nextera (i5 and i7) indices using deML (Renaud 2014, Bioinformatics)  Demultiplexed reads were aligned to the mouse genome mm10 and ERCC reference using NextGenMap (Sedlazeck et al., 2013)  Count data was generated from mapped reads using featureCounts (Liao et al., 2014) on ENSEMBL gene models (GRCm38.74)
For UMI-seq libraries: Reads were tagged with UMI and sample barcode using the Drop-seq pipeline (Macosko et al., 2015). Reads were aligned to the mouse genome mm10 using STAR (Dobin et al., 2013). Unique gene-wise counts were generated using the Drop-seq pipeline. Sample-barcode annotation can be found in additional file "UMIseq_niche_cells_barcode_annotation.txt". For data deposition, samples were demultiplexed using bamtools filter command.
Genome_build: mm10
Supplementary_files_format_and_content: sample- and gene-wise expression tables

source_name: EC niche cell

extract_protocol:
cDNA was synthesized, barcoded, pooled and pre-amplified according to Soumillon et al. 2014. 800 pg of the cDNA pool was used for library preparation using the Nextera XT Kit (Illumina)
Lineage-negative, Sca-1+, Kit+ (LSK) and niche cells were FACS sorted according to Istvanffy et al. 2011. Cells were sorted into lysis buffer composed of 0.2 % Triton-X100 and 0.5 U/µl RNAse Inhibitor

tag: niche genotype

tag: library protocol

value: UMI-seq


title: OBC_Wnt5a_12

source_name: OBC niche cell


title: EC_Wnt5a_17