title: RNA-seq siCont ActD 2h (biological replicate #2)

description: RNA-seq for HeLa total RNA 2h after actinomycin D treatment to control knockdown cells


title: mESC_Plate2_June2014_H7

status: Public on Dec 04 2014

type: SRA

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

country: USA

institute: Johns Hopkins University School of Medicine

description:
mESC_Plate2_June2014_H7
RnaSeq_single_cell_mESC_TPM.csv

library_source: transcriptomic

data_processing:
Alignment: A Bowtie index was created based on the UCSC knownGene transcriptome, and paired-end reads were directly aligned to this index.
Calculation of expression levels: RSEM was run on these alignments to generate expression level estimates, and these estimates (tau) were multiplied by 1,000,000 to yield estimates of transcripts per million (TPM) for each gene. These TPM estimates were then transformed into log space by taking ln(TPM+1), which we hereafter refer to in the Supplement as ln(TPM).
Genome_build: mm9
Supplementary_files_format_and_content: For single-cell RNA-Seq, tab-delimited text files providing RSEM ln-transformed transcript per million (TPM) values for each sample. For ChIP-Seq, total number of reads mapping to promoter regions +1500 bp to -500 bp from annotated transcription start sites.

molecule: total RNA

organism: Mus musculus

source_name: v6.5 mouse embryonic stem cells

growth_protocol: Described under 'culture conditions' in sample information.

extract_protocol:
mES or neural precursor cells were taken directly from culture, trypsinized, washed in PBS, spun down and resuspended at a concentration of 3 x 10^5 cell per mL of complete media, mixed 7:3 with C1 suspension reagent (Fluidigm), and loaded onto C1 Single-Cell Auto Prep chips (C1 chips; Fluidigm). After loading, each of the cell isolation chambers on the C1 chip was optically inspected for the presence of a cell.  Subsequently, these cells were lysed and SMART-Seq whole transcriptome amplified (WTA) products were prepared with the C1 System using the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech) and protocols provided by Fluidigm (full details available at www.fluidigm.com).
WTA products were harvested from the C1 chip, diluted to a concentration of 0.15 ng/μL, and cDNA libraries were prepared using Nextera XT DNA Sample preparation reagents (Illumina) as per the manufacturer’s recommendations, with minor modifications. Specifically, reactions were run at ¼ the recommended volume, the tagmentation step was extended to 10 minutes, and the extension time during the PCR step was increased from 30s to 60s. After the PCR step, all 96 samples were pooled without library normalization, cleaned twice with 0.9x AMPure XP SPRI beads (Beckman Coulter), and eluted in buffer TE. The pooled libraries were quantified using Quant-IT DNA High-Sensitivity Assay Kit (Invitrogen) and examined using a high-sensitivity DNA chip (Agilent). Finally, samples were sequenced deeply using either a HiSeq 2000 or a HiSeq 2500 sequencer (25 bp paired-end reads).

tag: cell type

value: v6.5 mouse embryonic stem cells

tag: culture conditions

value: serum+LIF


title: mESC_Plate2_June2014_H6

description:
mESC_Plate2_June2014_H6
RnaSeq_single_cell_mESC_TPM.csv


title: RNA-seq siCont ActD 1h (biological replicate #2)

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description: RNA-seq for HeLa total RNA 1h after actinomycin D treatment to control knockdown cells

data_processing:
The sequence reads were aligned to the spike-in RNA sequences (GenBank accessions M24537.1, X04603.1, L38424.1, and X17013.1) by Bowtie2 (Langmead and Salzberg, 2012) using  options “--end-to-end --sensitive -k 4”.
Scaling factor of a sample was calculated as geometric mean of ratios for valid spike-ins between geometric mean of read counts in all samples and read counts in the sample.
Spike-in RNAs with insufficient read counts (< 500) in any sample were excluded from the calculation. The reads not aligned to any spike-in RNAs were aligned to UCSC hg19 genome assembly using STAR (Dobin et al., 2013) with an option “--outFilterScoreMin 3” and splicing junction annotations generated from the NCBI RefSeq and the UCSC knownGene. The reduced RefSeq transcript set for non-overlapping representation was prepared as previously described (Chang et al., 2014b).
Reads mapped to each transcript were counted using BEDTools multicov (Quinlan and Hall, 2010) with default options. The read counts were scaled by the factors calculated from spike-in read counts. Transcripts not detected with enough reads (< 1,000 normalized reads in the siControl 0 hr sample) were removed to reduce noises.
Genome_build: hg19
Supplementary_files_format_and_content: A spreadsheet file contain normalized read counts by spike-in scaling; RS2-normalized-readcount.csv is for biological replicate #2 samples.

organism: Homo sapiens

growth_protocol: HeLa cells were maintained in DMEM (Welgene) supplemented with  10% fetal bovine serum (Welgene).

extract_protocol:
Total RNAs were extracted by TRIzol (Invitrogen), and the quality was checked by  Bioanalyzer 2100 (Agilent).
The same amount of control poly(A) spike-in (Affymetrix,  #900433) was mixed with each sample with the same amount of total RNA, and  subsequently rRNA was depleted by Ribo-Zero (Epicentre). RNA-seq libraries were  constructed using Illumina TruSeq RNA sample preparation kit v2.

treatment_protocol: HeLa cells were transfected twice with 40 nM of siRNAs using  Lipofectamine 2000 (Invitrogen). To block transcription, HeLa cells were treated with actinomycin D (Sigma, 4  μg/ml).

tag: cell line

value: HeLa

value: human cervical cancer cell line


title: input DNA

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

country: France

institute: IGBMC (CNRS/INSERM/UDS)

library_source: genomic

data_processing:
Base calling : Image analysis and base calling were performed using RTA 1.17.20 and CASAVA 1.8.2
Alignment : Reads were mapped to hg19 assembly of human genome using Bowtie aligner release<=1.0.0, with principle parameters: -m 1 --strata --best
Peak calling : Peaks were called using the Model-based Analysis of ChIP-Seq (MACS 1.4.2) algorithm, P value threshold(80)
Genome_build: hg19
Supplementary_files_format_and_content: MACS 1.4.2 peak calling file with the following collumns: chr, start,end,length,summit,tags,-10*LOG10(pvalue),fold_enrichment,FDR(%),peak name.

molecule: genomic DNA

source_name: HUVEC Cells

growth_protocol: HUVEC cells were grown in Dulbecco’s Modified Eagle Medium / Hams F-12- Kaighn's (DMEM/F12K (1:1) supplemented with 100 µg/ml Heparin, 50 µg/ml Endothelial Cell Growth Supplement, 2 mM Glutamine) 10% Fetal Calf Serum (FCS) and 40 µg/ml Gentamycin until 50-70% confluence

extract_protocol:
Lysates were clarified from sonicated nuclei and ELK3-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared using Truseq ChIP-Seq Sample Prep Kit (Illumina, IP-202-1012) following the manufacturer's protocol with some modifications. Briefly, 10 ng of ChIP enriched DNA or control DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 Poly Nucleotide Kinase . A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded adapters using T4 DNA ligase. The ligated products were enriched by PCR (30 sec at 98°C [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 14 cycles; 5 min at 72°C), then size selected and purified using Agencourt AMPure XP beads (#A63881, Beckman). Prior to analyses DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent). The libraries were loaded in the flowcell at 7pM concentration and clusters were generated using the Cbot (Illumina, SY-301-2002 ) and sequenced on the Illumina Genome Hiseq2500 as single-end 50 base reads following Illumina’s instructions

value: HUVEC cells (ATCC, CRL1730)

tag: antibody


title: mESC_Plate2_June2014_H3

description:
mESC_Plate2_June2014_H3
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_H5

description:
mESC_Plate2_June2014_H5
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_H4

description:
mESC_Plate2_June2014_H4
RnaSeq_single_cell_mESC_TPM.csv


title: RNA-seq siCont ActD 0h (biological replicate #2)

description: RNA-seq for HeLa total RNA 0h after actinomycin D treatment to control knockdown cells


title: TAIL-seq exp #8 Nucleus

description: TAIL-seq for HeLa nucleic RNAs, set #8

data_processing:
Library strategy: TAIL-Seq
The base calls and signal intensities were processed by Illumina RTA 1.17.21.3 for HiSeq 2500, or RTA 1.17.28 for MiSeq. The read 1 sequences were reanalyzed for more sensitive basecalling using AYB 2. The read 1 sequences were aligned to the common contaminants set, which is composed of rDNA repeat units (GenBank accession U13369.1), PhiX genome (GenBank accession J02482.1), Illumina TruSeq primer sequences, and all sequences for 5S and 5.8S rRNAs of respective species (retrieved from Rfam 11.0 of the Wellcome Trust Sanger Institute) using GSNAP 2013-03-31 with maximum 5% mismatches allowed. Clusters with any match to the contaminants were removed from the subsequent analyses. The sequences having completely identical nucleotides in the 21st to 35th cycle in read 1 (representative region of the insert) and the 1st to 15th cycle in read 2 (degenerate bases in 3′ adapter) are deduplicated by leaving only a cluster with the maximum PHRED quality sum of read 1. The degenerate and fixed delimiter sequence in 3′ adapter was clipped out from read 2 by searching perfect match of delimiter sequence (‘GTCAG’ as in the direction of read 2) between the 14th and 16th cycles in read 2. The clusters missing a delimiter sequence or having low diversity in degenerate region (at least two occurrences for all of A, C, G and T) were removed from further analyses.
The fluorescence signal intensities were processed into “Relative T signal” as described in our previous paper (Chang et al, 2014b). The signals from a spike-in sample were purified with an outlier filter based on robust Mahalanobis distance (mvoutlier package 1.9.9; quan=0.5, alpha=0.025). Random 500 clusters per each spike-in were chosen for parameter calculation of a Gaussian mixture hidden Markov model (GMHMM). We trained the model using Baum-Welch algorithm implemented in the GHMM library (http://ghmm.org) with topology and initial parameters shown in fig. S1A and table S7 and S8 (1,000 iterations). The procedure was iterated to maximize likelihood, not using any property (eg. designed length of poly(A) tail) of spike-ins. Relative T signals outside the range of [-5, 5] were clipped into the range for both training and later calculations.
The length of poly(A) tails were first measured with base call-based “Strategy II” described in fig. S1A. For clusters with the measured length is shorter than 8 nt, the length is called as the final poly(A) tail length. For the others, normalized T signals starting from the first position in T-stretch detected by Strategy II were analyzed with the GMHMM. The hidden states were decoded with the standard Viterbi algorithm implemented in the GHMM library. The number of cycles with state 1 and 2 was called as the length of poly(A) tail. For the estimation of performance, we applied the process to all spike-in samples except the clusters used for the parameter fitting of the model.
The remaining reads after contaminant filter and the first duplication filters were then aligned to the genome sequences (UCSC hg19, positions of splicing junctions were processed from the UCSC Genome Browser database for version of Jan 24, 2013) using GSNAP 2013-03-31. Three different versions of alignments to genome were used in this study. (1) R1 alignment: using only the full read 1 sequences which are 51 nt long. This was used for identification of a cluster. (2) R2 short alignment: using only 40 nt right next to the 3′ adapter of read 2. This was used in searching for the poly(A)-free 3′ hydroxyl ends. (3) paired alignment: using the full read 1 sequences and part of read 2 sequences trimmed of degenerate bases and delimiter. We filtered out poly(A) stretches encoded from genome using this alignment set. All the alignments were performed with maximum mismatches of 5%, minimum mapping quality of 3. All multi-mapped reads were removed. The remaining PCR artifacts with few mismatches were removed again using the R1 alignment with 15 degenerate bases inside the 3′ adapter region. To detect that kind of artifacts, we clustered the R1 alignments with maximum distance between mapped positions of 10 bp, they were then clustered again within the first cluster using degenerate bases from read 2 of respective reads with CD-HIT-EST 4.5.4 (word size=6, sequence identity=0.85). For a set of detected duplicates, we chose a read with maximum sum of PHRED quality in read 1 to leave.
For classification and transcript-level analyses, we compiled reference annotations for human and mouse using NCBI RefSeq, RepeatMasker, gtRNAdb, Rfam and miRBase databases (the first three were downloaded from the UCSC Genome Browser on Apr 25, 2013; Rfam version 11; miRBase version 19). The R1 alignments were annotated with intersection with the compiled annotations using BEDTools {Quinlan, 2010 #66}. When multiple annotations were overlapped to an alignment, we chose a class for the statistics requiring exclusive assignment of a genomic source type by the following priority: miRNA, rRNA, tRNA, Mt-tRNA, snoRNA, scRNA, srpRNA, snRNA, lncRNA, RNA, ncRNA, misc_RNA, Cis-reg, ribozyme, RC, IRES, frameshift_element, LINE, SINE, Simple_repeat, Low_complexity, Satellite, DNA, LTR, CDS, 3′ UTR, 5′ UTR, intron, Other, Unknown (higher priority first). The transcript-level analyses were performed using our custom non-redundant RefSeq (nrRefSeq) transcript set, which is a reduced set retaining only the longest isoform or transcript when regions overlap with each other. The positions of read 1 in nrRefSeq transcripts were positioned with BEDTools intersection between alignments to genome sequences and nrRefSeq annotation set, and then translated to the transcript-level coordination with in-house software.
As poly(A) tails were initially detected with a constraint that it must begin within the first 30 cycles, so the maximum detectable 3′ end modification of poly(A) tails was limited to the last 30 nucleotides of insert. To exclude A stretches obviously encoded from genomic sequence (with or without 3′ end modifications), we masked detected poly(A) tail ranges with read 2 alignments so that the 3′-most position of alignable (not clipped) is eliminated from poly(A) tail or its 3′ end modifications. All statistics regarding transcript-level modification rates were calculated for transcripts having more than 200 tags with poly(A) tails longer than 8 nt.
Genome_build: hg19
Supplementary_files_format_and_content: The spreadsheet files contain the poly(A) tail length distribution and 3' end modification frequencies next to poly(A) tails for all detected transcripts

growth_protocol: HeLa cells were maintained in DMEM (Welgene) supplemented with 10% fetal bovine serum (Welgene).

extract_protocol:
Total RNAs were extracted from HeLa cells by TRIzol reagent (Invitrogen, 15596-018) and purified by RNeasy MinElute column (Qiagen, 74204) according to manufacturer’s instruction.
TAIL-seq was carried out as described previously (Chang et al., 2014b). Briefly, 25-50 ug of total RNAs (>200 nt) were extracted by TRIzol (Invitrogen), purified by RNeasy MinElute column (Qiagen), and rRNA-depleted by using Ribo-zero kit (Epicentre). The RNAs were ligated to the biotinylated 3′ adaptor, and partially digested by RNase T1. The fragmented RNAs were pull-downed with streptavidin beads, phosphorylated at the 5′ end, and gel purified (500-1000 nt). The purified RNAs were ligated to the 5′ adaptor, reverse-transcribed, and amplified by PCR.

treatment_protocol: HeLa cells were transfected twice with 40 nM of siRNAs using Lipofectamine 2000 (Invitrogen). A mixture of 2-4 different siRNAs was used to knockdown each gene. In combinatorial knockdown, we mixed siRNA pools to have a final concentration of 40 nM.


title: NPCs_A5

description:
NPCs_A5
RnaSeq_single_cell_NPC_TPM.csv

value: Neural precursor cells derived from in vitro differentiation of v6.5 mouse embryonic stem cells

value: Selection in ITSFn, followed by expansion in N2+bFGF / laminin


title: TAIL-seq exp #8 Cytoplasm

description: TAIL-seq for HeLa cytoplasmic RNAs, set #8


title: TAIL-seq exp #3 siTUT47

description: TAIL-seq for TUT4/7 knockdown HeLa cells, set #3


title: mESC_Plate2_June2014_H11

description:
mESC_Plate2_June2014_H11
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_H10

description:
mESC_Plate2_June2014_H10
RnaSeq_single_cell_mESC_TPM.csv


title: RNA-seq siTUT47 ActD 4h

description: RNA-seq for HeLa total RNA 4h after actinomycin D treatment to TUT4/7 knockdown cells

data_processing:
The sequence reads were aligned to the spike-in RNA sequences (GenBank accessions M24537.1, X04603.1, L38424.1, and X17013.1) by Bowtie2 (Langmead and Salzberg, 2012) using options “--end-to-end --sensitive -k 4”.
Scaling factor of a sample was calculated as geometric mean of ratios for valid spike-ins between geometric mean of read counts in all samples and read counts in the sample.
Spike-in RNAs with insufficient read counts (< 500) in any sample were excluded from the calculation. The reads not aligned to any spike-in RNAs were aligned to UCSC hg19 genome assembly using STAR (Dobin et al., 2013) with an option “--outFilterScoreMin 3” and splicing junction annotations generated from the NCBI RefSeq and the UCSC knownGene. The reduced RefSeq transcript set for non-overlapping representation was prepared as previously described (Chang et al., 2014b).
Reads mapped to each transcript were counted using BEDTools multicov (Quinlan and Hall, 2010) with default options. The read counts were scaled by the factors calculated from spike-in read counts. Transcripts not detected with enough reads (< 1,000 normalized reads in the siControl 0 hr sample) were removed to reduce noises.
Genome_build: hg19
Supplementary_files_format_and_content: A spreadsheet file contain normalized read counts by spike-in scaling.

source_name: HeLa

extract_protocol:
Total RNAs were extracted by TRIzol (Invitrogen), and the quality was checked by Bioanalyzer 2100 (Agilent).
The same amount of control poly(A) spike-in (Affymetrix, #900433) was mixed with each sample with the same amount of total RNA, and subsequently rRNA was depleted by Ribo-Zero (Epicentre). RNA-seq libraries were constructed using Illumina TruSeq RNA sample preparation kit v2.

treatment_protocol: HeLa cells were transfected twice with 40 nM of siRNAs using Lipofectamine 2000 (Invitrogen). To block transcription, HeLa cells were treated with actinomycin D (Sigma, 4 μg/ml).


title: mESC_Plate2_June2014_H1

description:
mESC_Plate2_June2014_H1
RnaSeq_single_cell_mESC_TPM.csv


title: RNA-seq siTUT47 ActD 1h

description: RNA-seq for HeLa total RNA 1h after actinomycin D treatment to TUT4/7 knockdown cells


title: mESC_Plate2_June2014_H12

description:
mESC_Plate2_June2014_H12
RnaSeq_single_cell_mESC_TPM.csv


title: TAIL-seq exp #3 siCont

description: TAIL-seq for control knockdown HeLa cells, set #3


title: mESC_Plate2_June2014_G9

description:
mESC_Plate2_June2014_G9
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_G8

description:
mESC_Plate2_June2014_G8
RnaSeq_single_cell_mESC_TPM.csv


title: RNA-seq siTUT47 ActD 0h

description: RNA-seq for HeLa total RNA 0h after actinomycin D treatment to TUT4/7 knockdown cells


title: RNA-seq siCont ActD 4h

description: RNA-seq for HeLa total RNA 4h after actinomycin D treatment to control knockdown cells


title: mESC_Plate2_June2014_G7

description:
mESC_Plate2_June2014_G7
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_G6

description:
mESC_Plate2_June2014_G6
RnaSeq_single_cell_mESC_TPM.csv


title: RNA-seq siCont ActD 2h

description: RNA-seq for HeLa total RNA 2h after actinomycin D treatment to control knockdown cells


title: ELK3 Normoxia

value: hELK3 2005 (in house)


title: RNA-seq siCont ActD 1h

description: RNA-seq for HeLa total RNA 1h after actinomycin D treatment to control knockdown cells


title: mESC_Plate2_June2014_G5

description:
mESC_Plate2_June2014_G5
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_H2

description:
mESC_Plate2_June2014_H2
RnaSeq_single_cell_mESC_TPM.csv


title: RNA-seq siCont ActD 0h

description: RNA-seq for HeLa total RNA 0h after actinomycin D treatment to control knockdown cells


title: mESC_Plate2_June2014_G3

description:
mESC_Plate2_June2014_G3
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_G2

description:
mESC_Plate2_June2014_G2
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_G11

description:
mESC_Plate2_June2014_G11
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_G12

description:
mESC_Plate2_June2014_G12
RnaSeq_single_cell_mESC_TPM.csv


title: RNA-seq siTUT47 ActD 2h

description: RNA-seq for HeLa total RNA 2h after actinomycin D treatment to TUT4/7 knockdown cells


title: dnTCF1Emut Input

city: Irvine

first: Michael

last: Zeller

state: California

department: Computer Science

institute: University of California, Irvine

description:
Input sample (no immunoprecipitation) from uninduced dnTCF1Emut clonal cell line.  Sequenced at twice the coverage of the other samples.
dnTCF1Emut Input (a)

data_processing:
Demultiplexing and basecalls performed using CASAVA v1.8.2
Biological replicates FASTQ files pooled
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 v2.0.0 allowing up to 3 mismatches
Peaks were called using MACS v1.3 using only one unique read per genome position and a default peak score cutoff of 50
Genome_build: hg19
Supplementary_files_format_and_content: Peak files annotated using HOMER v3.16 and wiggle files generated using MACS v1.3

source_name: DLD1 colon cancer cells

growth_protocol: Grew cells in RPMI complete with doxycycline free FBS.  Cells were grown in RPMI complete with 10ug/mL blasticidin and 300ug/mL zeocin for 24 hours before induction

extract_protocol:
Used anti-FLAG conjugated magnetic beads from Sigma (A2220) to immunoprecipitate FLAG-tagged dnTCF1EWT and FLAG-tagged dnTCF1Emut
All libraries were prepared using the NEXTflex ChIP Seq kit from Biooscientific using 10ng as starting material

treatment_protocol: Used 1ug/mL Doxycycline for dnTCF1E induction

value: DLD1 colon cancer cells

tag: genotype/variation

tag: time (induction)

value: control

tag: chip antibody


title: dnTCF1Emut 0hrs

description:
0hrs (no doxycycline - no dnTCF1Emut overexpressed) ChIP-seq from dnTCF1Emut cell line.  First replicate
dnTCF1Emut 0hrs (a)
dnTCF1Emut 0hrs (b)

value: Anti-FLAG Beads Sigma (A2220)


title: dnTCF1Emut 2hrs

description:
ChIP-seq of 2hrs doxycycline induction of dnTCF1Emut. First replicate
dnTCF1Emut 2hrs (a)
dnTCF1Emut 2hrs (b)


title: mESC_Plate2_June2014_G1

description:
mESC_Plate2_June2014_G1
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_F9

description:
mESC_Plate2_June2014_F9
RnaSeq_single_cell_mESC_TPM.csv


title: dnTCF1EWT 2hrs

description:
ChIP-seq of 2hrs doxycycline induction of dnTCF1EWT. First replicate
dnTCF1EWT 2hrs (a)
dnTCF1EWT 2hrs (b)


title: dnTCF1EWT Input

description:
Input sample (no immunoprecipitation) from uninduced dnTCF1EWT clonal cell line.  First replicate
dnTCF1EWT Input (a)
dnTCF1EWT Input (b)


title: dnTCF1EWT 9hrs

description:
ChIP-seq of 9hrs doxycycline induction of dnTCF1EWT.  First replicate
dnTCF1EWT 9hrs (a)
dnTCF1EWT 9hrs (b)


title: mESC_Plate2_June2014_F7

description:
mESC_Plate2_June2014_F7
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_F4

description:
mESC_Plate2_June2014_F4
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_F8

description:
mESC_Plate2_June2014_F8
RnaSeq_single_cell_mESC_TPM.csv


title: Hfq-bound RNA from +Vir (virulence-induced) conditions

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

description:
Hfq-bound RNA
8_Hfq_Flag

data_processing:
Demultiplexing
Fastq quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 12 nt (via READemption)
Read mapping using segemehl (via READemption)
Coverage calculation and normalisation (via READemption)
Genome_build: NC_003062.2,NC_003063.2,NC_003064.2,NC_003065.3
Supplementary_files_format_and_content: wiggle

organism: Agrobacterium tumefaciens

source_name: bacteria

growth_protocol: Agrobacterium tumefaciens C58 strains were cultivated at 30 °C in YEB complex medium or AB minimal medium (pH 5.5, supplemented with 1% (w/v) glucose) (Schmidt-Eisenlohr et al., 1999). For virulence induction overnight cultures of A. tumefaciens were inoculated in AB medium to an OD600nm of 0.1 and grown for 6 h at 30 °C. Virulence gene expression was induced by addition of 0.1 mM acetosyringone (Sigma-Aldrich, Germany) and further cultivation at 23 °C for 16 h. Non virulence induced cultures were treated with equal volumes of DMSO.

extract_protocol:
Co-immunoprecipitation (coIP) experiments of Hfq3xFlag and bound RNAs were based on the procedure described in (Pfeiffer et al., 2007) with minor changes. 100 ml of A. tumefaciens wild-type and hfq3xFlag cultures grown to OD600nm 0.5 and 1.0 in YEB medium or under non-induced (+DMSO) and virulence-induced (+acetosyringone) conditions in AB medium were harvested and resuspended in 2 ml ice-cold lysis buffer (20 mM Tris (pH 7.5), 150 mM KCl, 1 mM MgCl2, 1 mM DTT). Cells were disrupted by French® Press (3 passes, 16,000 psi) and centrifuged at 10,000 x g, 4 °C, for 1 h. 10 ng monoclonal ANTI-3XFLAG® M2 antibody (Sigma-Aldrich, Germany) were coupled to 50 µl Dynabeads® Protein G (ThermoFisher Scientific, Life TechnologiesTM, USA) as described in the instruction manual, and incubated with the supernatant (3 h, 4 °C). Dynabeads® were separated on a magnet and washed 5x with PBS buffer. RNA was isolated using phenol/chloroform/isoamylalcohol and chloroform/isoamylalcohol followed by precipitation with ethanol and sodium acetate. After precipitation remaining DNA was digested by DNaseI (ThermoFisher Scientific, Life TechnologiesTM, USA) and RNA was precipitated as described before.
Preparation of cDNA libraries was performed at Vertis Biotechnology AG (Germany). Equal amounts of RNA samples were poly(A)-tailed and 5’-PPP were removed. The RNA adapter was ligated to the RNA 5’-monophosphate and reverse transcription was performed with oligo(dT)-adapter primers resulting in first-strand cDNA. Higher yields of DNA (20-30 ng µl-1) were gained by further PCR-based amplification using primers designed for TruSeq according to recommendations for Illumina (HiSeq). For multiplex sequencing a library specific barcode was part of the 3’- sequencing adapter. Purification was achieved using the Agencourt AMPure XP kit (Beckman Coulter Genomics, USA), followed by capillary electrophoresis.

tag: strain background

tag: vir induced with

value: 0.1 mM acetosyringone

tag: rip antibody

value: Monoclonal mouse ANTI-FLAG M2 antibody

tag: rip antibody vendor

value: Sigma

tag: rip antibody cat. #

tag: rip antibody batch #


title: mESC_Plate2_June2014_F5

description:
mESC_Plate2_June2014_F5
RnaSeq_single_cell_mESC_TPM.csv


title: Hfq-bound RNA from -Vir (non-induced) conditions

description:
Hfq-bound RNA
6_Hfq_Flag

value: DMSO (non-induced control)


title: control from +Vir (virulence-induced) conditions

description:
Hfq-bound RNA
7_WT_control

value: wild type (control)


title: mESC_Plate2_June2014_F2

description:
mESC_Plate2_June2014_F2
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_F3

description:
mESC_Plate2_June2014_F3
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_G4

description:
mESC_Plate2_June2014_G4
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_F12

description:
mESC_Plate2_June2014_F12
RnaSeq_single_cell_mESC_TPM.csv


title: control from -Vir (non-induced) conditions

description:
Hfq-bound RNA
5_WT_control


title: control from OD 1.0 (exponential) conditions

description:
Hfq-bound RNA
3_WT_control

tag: growth phase

value: OD 1.0 (exponential)


title: mESC_Plate2_June2014_F11

description:
mESC_Plate2_June2014_F11
RnaSeq_single_cell_mESC_TPM.csv

value: v6.5 mouse embryonic stem cells


title: mESC_Plate2_June2014_F10

description:
mESC_Plate2_June2014_F10
RnaSeq_single_cell_mESC_TPM.csv

value: serum+LIF


title: Hfq-bound RNA from OD 1.0 (exponential) conditions

description:
Hfq-bound RNA
4_Hfq_Flag


title: dnTCF1Emut 9hrs

description:
ChIP-seq of 9hrs doxycycline induction of dnTCF1Emut.  First replicate
dnTCF1Emut 9hrs (a)
dnTCF1Emut 9hrs (b)


title: control from OD 0.5 (exponential) conditions

description:
Hfq-bound RNA
1_WT_control

value: OD 0.5 (exponential)


title: mESC_Plate2_June2014_F1

description:
mESC_Plate2_June2014_F1
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_E9

description:
mESC_Plate2_June2014_E9
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_E6

description:
mESC_Plate2_June2014_E6
RnaSeq_single_cell_mESC_TPM.csv


title: Hfq-bound RNA from OD 0.5 (exponential) conditions

description:
Hfq-bound RNA
2_Hfq_Flag


title: mESC_Plate2_June2014_E8

description:
mESC_Plate2_June2014_E8
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_E5

description:
mESC_Plate2_June2014_E5
RnaSeq_single_cell_mESC_TPM.csv


title: dnTCF1EWT 0hrs

description:
0hrs (no doxycycline - no dnTCF1EWT overexpressed) ChIP-seq from dnTCF1EWT cell line.  First replicate
dnTCF1EWT 0hrs (a)
dnTCF1EWT 0hrs (b)


title: mESC_Plate2_June2014_E7

description:
mESC_Plate2_June2014_E7
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_E4

description:
mESC_Plate2_June2014_E4
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_E2

description:
mESC_Plate2_June2014_E2
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_E3

description:
mESC_Plate2_June2014_E3
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_E10

description:
mESC_Plate2_June2014_E10
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_D8

description:
mESC_Plate2_June2014_D8
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_E11

description:
mESC_Plate2_June2014_E11
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_D6

description:
mESC_Plate2_June2014_D6
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_D9

description:
mESC_Plate2_June2014_D9
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_D5

description:
mESC_Plate2_June2014_D5
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_D2

description:
mESC_Plate2_June2014_D2
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_E1

description:
mESC_Plate2_June2014_E1
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_D4

description:
mESC_Plate2_June2014_D4
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_D3

description:
mESC_Plate2_June2014_D3
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_D10

description:
mESC_Plate2_June2014_D10
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_D1

description:
mESC_Plate2_June2014_D1
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_C9

description:
mESC_Plate2_June2014_C9
RnaSeq_single_cell_mESC_TPM.csv


title: dsRBD_2_KO

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 12 nt
Read mapping using segemehl version 0.14
Coverage calculation and normalisation
Genome_build: DDB0169550, DDB0215018, DDB0215151, DDB0220052, DDB0232428, DDB0232429, DDB0232430, DDB0232431, DDB0232432, DDB0232433,DDB0237465, DIRS-1 element
Supplementary_files_format_and_content: wiggle

organism: Dictyostelium discoideum

source_name: vegetative cells

growth_protocol: Ax2 cells and derivates were grown axenically in HL5 liquid medium.

extract_protocol:
Small RNAs (< 200 nts) were extracted from 1 x 107 cells using the NucleoSpin® miRNA Kit (Macherey-Nagel)
RNA samples were poly-A-tailed and the 5’PPP was converted into 5’P before an RNA adaptor was ligated to the 5’-monphosphate of the RNA. A poly-T-oligo was then used as primer for cDNA synthesis and the resulting cDNAs were PCR amplified.

tag: strain

tag: genotype

value: knockout of DDB_G0269426 (gene of rbdB)

value: vegetative cells


title: mESC_Plate2_June2014_D11

description:
mESC_Plate2_June2014_D11
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_C7

description:
mESC_Plate2_June2014_C7
RnaSeq_single_cell_mESC_TPM.csv


title: AGNA_KO

value: knockout of DDB_G0276299 (gene of agnA)


title: AX_2_WT

value: wild type strain                             .


title: mESC_Plate2_June2014_C6

description:
mESC_Plate2_June2014_C6
RnaSeq_single_cell_mESC_TPM.csv


title: Sperm of high sugar fed male flies - Replicate 2

city: Badalona

first: Tanya

last: Vavouri

state: BARCELONA

address: Ctra de Can Ruti, Cami de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukemia Research Institute

description: Purified total RNA was treated with Ribo-ZeroTM rRNA removal kit from epicenter.

data_processing:
Reads were mapped using TopHat (Kim et al, 2013) v2.0.8 with -G option.
Gene expression values and significantly differentially expressed genes were calculated using Cuffdiff (Trapnell et al, 2012) v2.1.1 with upper quartile normalization and weighting multi-mapping reads (-N -u options).
Genome_build: BDGP5
Supplementary_files_format_and_content: Tab delimited text files. Gene expression values and statistical significance of differential expression calculated by CuffDiff.

organism: Drosophila melanogaster

source_name: Sperm

extract_protocol:
Purified total RNA, extracted with Trizol and treated with Ribo-ZeroTM rRNA removal kit from epicenter.
TruSeq® stranded sample preparation kit from Illumina.

tag: developmental stage

value: Adult male

tag: tissue

value: Spermatozoa

tag: treatment

value: 300g/L of sugar


title: mESC_Plate2_June2014_C5

description:
mESC_Plate2_June2014_C5
RnaSeq_single_cell_mESC_TPM.csv

tag: cell type

tag: culture conditions


title: RRPC_KO

value: knockout of DDB_G0280963 (gene of rrpC)


title: Sperm of high sugar fed male flies - Replicate 1


title: mESC_Plate2_June2014_D7

description:
mESC_Plate2_June2014_D7
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_C3

description:
mESC_Plate2_June2014_C3
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_C2

description:
mESC_Plate2_June2014_C2
RnaSeq_single_cell_mESC_TPM.csv


title: Sperm of medium sugar fed male flies - Replicate 2

value: 30g/L of sugar


title: mESC_Plate2_June2014_C12

description:
mESC_Plate2_June2014_C12
RnaSeq_single_cell_mESC_TPM.csv


title: F1 embryos of high sugar fed male flies - Replicate 2

source_name: Embryos

value: Stage 17 embryos

value: Whole animal


title: mESC_Plate2_June2014_C4

description:
mESC_Plate2_June2014_C4
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_C10

description:
mESC_Plate2_June2014_C10
RnaSeq_single_cell_mESC_TPM.csv


title: F1 embryos of high sugar fed male flies - Replicate 1


title: F1 embryos of medium sugar fed male flies - Replicate 2


title: TAIL-seq exp #13 siTUT247

description: TAIL-seq for TUT2, TUT4, TUT7 knockdown HeLa cells, set #13

extract_protocol:
Total RNAs were extracted from HeLa cells by TRIzol reagent (Invitrogen, 15596-018) and purified by RNeasy MinElute column (Qiagen, 74204) according to manufacturer’s instruction.
TAIL-seq was carried out as described previously (Chang et al., 2014b). Briefly, 25-50  ug of total RNAs (>200 nt) were extracted by TRIzol (Invitrogen), purified by RNeasy  MinElute column (Qiagen), and rRNA-depleted by using Ribo-zero kit (Epicentre). The  RNAs were ligated to the biotinylated 3′ adaptor, and partially digested by RNase T1.  The fragmented RNAs were pull-downed with streptavidin beads, phosphorylated at the  5′ end, and gel purified (500-1000 nt). The purified RNAs were ligated to the 5′ adaptor, reverse-transcribed, and amplified by PCR.

treatment_protocol: HeLa cells were transfected twice with 40 nM of siRNAs using  Lipofectamine 2000 (Invitrogen). A mixture of 2-4 different siRNAs was used  to knockdown each gene. In combinatorial knockdown, we mixed siRNA pools to have a  final concentration of 40 nM.

tag: cell line

value: HeLa

value: human cervical cancer cell line


title: mESC_Plate2_June2014_C8

description:
mESC_Plate2_June2014_C8
RnaSeq_single_cell_mESC_TPM.csv


title: F1 embryos of medium sugar fed male flies - Replicate 1


title: mESC_Plate2_June2014_D12

description:
mESC_Plate2_June2014_D12
RnaSeq_single_cell_mESC_TPM.csv


title: TAIL-seq exp #13 siTUT1356

description: TAIL-seq for TUT1, TUT3, TUT5, TUT6 knockdown HeLa cells, set #13


title: mESC_Plate2_June2014_B8

description:
mESC_Plate2_June2014_B8
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_B7

description:
mESC_Plate2_June2014_B7
RnaSeq_single_cell_mESC_TPM.csv


title: TAIL-seq exp #13 siLuc

description: TAIL-seq for control knockdown HeLa cells, set #13


title: mESC_Plate2_June2014_B6

description:
mESC_Plate2_June2014_B6
RnaSeq_single_cell_mESC_TPM.csv


title: TAIL-seq exp #12 TUT4 Knockout

description: TAIL-seq for TUT4 knockout HeLa cells, set #12


title: TAIL-seq exp #12 TUT7 Knockcout

description: TAIL-seq for TUT7 knockout HeLa cells, set #12


title: mESC_Plate2_June2014_B5

description:
mESC_Plate2_June2014_B5
RnaSeq_single_cell_mESC_TPM.csv


title: TAIL-seq exp #12 Mock

description: TAIL-seq for control for knockout HeLa cells, set #12


title: Sperm of medium sugar fed male flies - Replicate 1

description: Purified total RNA was treated with Ribo-ZeroTM rRNA removal kit from epicenter.


title: mESC_Plate2_June2014_C11

description:
mESC_Plate2_June2014_C11
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_B3

description:
mESC_Plate2_June2014_B3
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_B2

description:
mESC_Plate2_June2014_B2
RnaSeq_single_cell_mESC_TPM.csv


title: TAIL-seq exp #11 siTUT47 (siRNA set #1 and #2)

description: TAIL-seq for TUT4 and TUT7 knockdown HeLa cells, set #11


title: mESC_Plate2_June2014_B12

description:
mESC_Plate2_June2014_B12
RnaSeq_single_cell_mESC_TPM.csv


title: TAIL-seq exp #11 siTUT47 (siRNA set #1)


title: mESC_Plate2_June2014_B11

description:
mESC_Plate2_June2014_B11
RnaSeq_single_cell_mESC_TPM.csv


title: TAIL-seq exp #11 siTUT47 (siRNA set #2)


title: mESC_Plate2_June2014_B9

description:
mESC_Plate2_June2014_B9
RnaSeq_single_cell_mESC_TPM.csv


title: TAIL-seq exp #10 anti-PABP (biological replicate 2)

description: TAIL-seq for PABP immunoprecipitation from HeLa lysate, set #10


title: mESC_Plate2_June2014_B10

description:
mESC_Plate2_June2014_B10
RnaSeq_single_cell_mESC_TPM.csv


title: TAIL-seq exp #11 siCont

description: TAIL-seq for control knockdown HeLa cells, set #11


title: mESC_Plate2_June2014_A9

description:
mESC_Plate2_June2014_A9
RnaSeq_single_cell_mESC_TPM.csv


title: TAIL-seq exp #10 Input (biological replicate 1)

description: TAIL-seq for control for immunoprecipitation from HeLa lysate, set #10


title: mESC_Plate2_June2014_C1

description:
mESC_Plate2_June2014_C1
RnaSeq_single_cell_mESC_TPM.csv


title: TAIL-seq exp #10 anti-PABP (biological replicate 1)


title: TAIL-seq exp #7 siRRP41+siXRN1

description: TAIL-seq for RRP41/XRN1 knockdown HeLa cells, set #7


title: mESC_Plate2_June2014_B1

description:
mESC_Plate2_June2014_B1
RnaSeq_single_cell_mESC_TPM.csv


title: TAIL-seq exp #10 Input (biological replicate 2)


title: mESC_Plate2_June2014_A8

description:
mESC_Plate2_June2014_A8
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_B4

description:
mESC_Plate2_June2014_B4
RnaSeq_single_cell_mESC_TPM.csv


title: TAIL-seq exp #12 TUT2 Knockout

description: TAIL-seq for TUT2 knockout HeLa cells, set #12


title: TAIL-seq exp #7 siRRP41

description: TAIL-seq for RRP41 knockdown HeLa cells, set #7


title: mESC_Plate2_June2014_A5

description:
mESC_Plate2_June2014_A5
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_A4

description:
mESC_Plate2_June2014_A4
RnaSeq_single_cell_mESC_TPM.csv


title: TAIL-seq exp #7 siDIS3L2

description: TAIL-seq for DIS3L2 knockdown HeLa cells, set #7


title: TAIL-seq exp #7 siCont

description: TAIL-seq for control knockdown HeLa cells, #7


title: mESC_Plate2_June2014_A2

description:
mESC_Plate2_June2014_A2
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_A12

description:
mESC_Plate2_June2014_A12
RnaSeq_single_cell_mESC_TPM.csv


title: TAIL-seq exp #6 siCont

description: TAIL-seq for control knockdown HeLa cells, set #6


title: mESC_Plate2_June2014_A11

description:
mESC_Plate2_June2014_A11
RnaSeq_single_cell_mESC_TPM.csv


title: TAIL-seq exp #6 siLSM1

description: TAIL-seq for LCM1 knockdown HeLa cells, set #6


title: TAIL-seq exp #6 DCP mutant

description: TAIL-seq for HeLa cells overexpressed of DCP dominant negative mutant, set #6


title: TAIL-seq exp #5 siXRN1

description: TAIL-seq for XRN1 knockdown HeLa cells, set #5


title: mESC_Plate2_June2014_A3

description:
mESC_Plate2_June2014_A3
RnaSeq_single_cell_mESC_TPM.csv


title: mESC_Plate2_June2014_A7

description:
mESC_Plate2_June2014_A7
RnaSeq_single_cell_mESC_TPM.csv


title: TAIL-seq exp #4 PABP IP

description: TAIL-seq for HeLa cells (PABP immunoprecipitated), set #4


title: 6-TAMC_ST_2weeks

city: Madrid

first: Simón

last: Méndez-Ferrer

address: Calle Melchor Fernández Almagro, 3

institute: CNIC

description: 2 weeks treatment

data_processing:
libraries sequenced usign Illumina GAIIx single end 75nt
base-calling was produced by Illumina RTA Software v 1.13.48
demultiplexed fastq files were generated from the bcl files using picard tools
sequencing adaptor contaminations were removed using cutadapt
reads were mapped and gene expression quantified using rsem v1.17
counts were normalized using voom from Limma R package
Genome_build: NCBIM37 Genebuild Ensembl v65
Supplementary_files_format_and_content: tab separated file. Contains normalized counts. Samples in columns, Genes in rows

source_name: hematopoietic progenitors

growth_protocol: freshly isolated cells from the bone marrow of treated mice

extract_protocol:
Picopure RNA extraction kit
cDNA has been produced and amplified according to Ovation RNA-Seq System V2 Kit. Amplified cDNA was fragmented by sonication and sequencing adaptors ligated following Illumina protocol from TrueSeq DNA Library Preparation Kit

treatment_protocol: 1 or 2 weeks with tamoxifen or vehicle

tag: Stage

value: Adult

tag: gender

value: Male

value: tamoxifen

value: bone marrow


title: TAIL-seq exp #5 siCont

description: TAIL-seq for control knockdown HeLa cells, set #5


title: TAIL-seq exp #2 TUT7(ZCCHC6) KO

description: TAIL-seq for TUT7-null HeLa cells, set #2


title: 4-TAMA_ST_2weeks

description: 2 weeks treatment


title: 5-TAMB_ST_2weeks

description: 2 weeks treatment


title: TAIL-seq exp #4 Input

description: TAIL-seq for HeLa cells (total RNA), set #4


title: TAIL-seq exp #2 TUT4(ZCCHC11) KO

description: TAIL-seq for TUT4-null HeLa cells, set #2


title: 3-OILC_ST_2weeks

description: 2 weeks treatment

value: corn oil


title: 2-OILB_ST_2weeks

description: 2 weeks treatment


title: TAIL-seq exp #2 TUT2(GLD2) KO

description: TAIL-seq for TUT2-null HeLa cells, set #2


title: mESC_Plate2_June2014_A6

description:
mESC_Plate2_June2014_A6
RnaSeq_single_cell_mESC_TPM.csv

value: v6.5 mouse embryonic stem cells

value: serum+LIF


title: TAIL-seq exp #2 Mock

description: TAIL-seq for mock treatment HeLa cells, set #2


title: 1-OILA_ST_2weeks

description: 2 weeks treatment


title: TAIL-seq exp #1 siTUT247

description: TAIL-seq for TUT2,4,7 knockdown HeLa cells, set #1


title: 12-TAMC_LT_2weeks

description: 2 weeks treatment


title: TAIL-seq exp #1 siTUT1356

description: TAIL-seq for TUT1,3,5,6 knockdown HeLa cells, set #1


title: TAIL-seq exp #1 siLuc

description: TAIL-seq for control knockdown HeLa cells, set #1


title: 11-TAMB_LT_2weeks

description: 2 weeks treatment


title: mESC_Plate2_June2014_A10

description:
mESC_Plate2_June2014_A10
RnaSeq_single_cell_mESC_TPM.csv


title: Swr1_Input_(20130401_2_8)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Swr1 input, 10' MNase

data_processing: 1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. The Illumina sample was a mixture of yeast DNA and fly DNA so we also mapped the reads to release 5.30 of D.melanogaster (Sep 2010) obtained from FlyBase. If a read was mapped to multiple locations, one location was picked at random.  2. We extracted properly paired reads that were only mapped to yeast (Supplementary file .bed).

organism: Saccharomyces cerevisiae

source_name: Swr1 input

extract_protocol: Nuclear isolation, chromatin preparation, and immunoprecipitation were performed as described (PMID 23468649). Sequencing libraries were prepared as described (PMID 22025700), except that TruSeq adapters were used for multiplexing and the ratio of sample to Ampure beads was changed from 5:9 to 1:1 in the two cleanup steps to compensate for the longer length of the TruSeq adapters.

tag: cell

value: nuclei

value: MATa ade2-1 can1-100 his3-11, 15 leu2-3, 112 trp1-1 ura3-1 RAD5+ SWR1-3FLAG-kanMX4


title: mESC_Plate2_June2014_A1

description:
mESC_Plate2_June2014_A1
RnaSeq_single_cell_mESC_TPM.csv


title: 10-TAMA_LT_2weeks

description: 2 weeks treatment


title: 8-OILB_LT_2weeks

description: 2 weeks treatment


title: Sth1_Input_(20130118_1_4)

description: Sth1 input, 10' MNase

source_name: Sth1 input

value: MATa ade2-1 can1-100 his3-11, 15 leu2-3, 112 trp1-1 ura3-1 RAD5+ STH1-3FLAG-kanMX4


title: Sth1_IP_(20130118_1_3)

description: Sth1 IP, 10' MNase

source_name: Sth1 IP


title: 6-TAM3_MPP_1week

description: 1 week treatment


title: MnaseSeq_5_(20131010_2_12)

description: Ioc3 input, 10' MNase

data_processing: 1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. If a read was mapped to multiple locations, one location was picked at random.  2. We extracted properly paired reads that were only mapped to yeast (Supplementary file .bed).

source_name: Ioc3 input

value: MATa ade2-1 can1-100 his3-11, 15 leu2-3, 112 trp1-1 ura3-1 RAD5+ IOC3-3FLAG-kanMX4


title: MnaseSeq_4_(20131010_2_4)

description: Fun30 input, 10' MNase

source_name: Fun30 input

value: MATa ade2-1 can1-100 his3-11, 15 leu2-3, 112 trp1-1 ura3-1 RAD5+ FUN30-3FLAG-kanMX4


title: Ino80_Input_(20130401_2_6)

description: Ino80 input, 10' MNase

source_name: Ino80 input

value: MATa ade2-1 can1-100 his3-11, 15 leu2-3, 112 trp1-1 ura3-1 RAD5+ INO80-3FLAG-kanMX4


title: 5-TAM2_MPP_1week

description: 1 week treatment


title: 4-TAM1_MPP_1week

description: 1 week treatment


title: 3-OIL3_MPP_1week

description: 1 week treatment


title: Ino80_IP_(20130401_2_2)

description: Ino80 IP, 10' MNase

source_name: Ino80 IP


title: AKT-HUVEC (Hs)

city: New York

first: Der-I

last: Kao

state: NY

address: 1300 York Ave

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed  low-quality sequence, then mapped to hg19 for human and mm9 for mouse whole genome using Tophat v2.0.0.7 with default settings.
Fragments Per Kilobase of Transcript per Million mapped fragments  (RPKM) were calculated using a protocol from Trapnell et al., Nature Protocol, 2012. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: [FPKM_matrix_Hs.txt] This file includes FPKM values for BJ and AKT-HUVEC.
Supplementary_files_format_and_content: [FPKM_matrix_Mm.txt] This file includes FPKM values for MPEC and BJ (negative control).

extract_protocol:
RNA was extracted with Qiagen Rneasy mine followed by clean-up and DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Endothelial Cells (HUVEC)

tag: sources

value: AKT-activated human umbilical vein endothelial cells to be cultured in serum-free condition (a gift from Dr. Shahin Rafii)


title: 2-OIL2_MPP_1week

description: 1 week treatment


title: 1-OIL1_MPP_1week

description: 1 week treatment


title: Htz1_5min_Input_(20140320_1,2_10)

description: Htz1 input, 5' MNase

source_name: Htz1 input

value: MATalpha ade2-1 can1-100 his3-11, 15 leu2-3, 112 trp1-1 ura3-1 RAD5+ HTZ1-2L-3FLAG:KanMX


title: Htz1_5min_IP_1_(20140320_1,2_13)

description: Htz1 IP, 5' MNase

source_name: Htz1 IP


title: Htz1_20min_IP_1_(20140320_1,2_13)

description: Htz1 IP, 20' MNase


title: Htz1_20min_IP_2_(20140327_1,2_13)

description: Htz1 IP, 20' MNase


title: 9-OILC_LT_2weeks

description: 2 weeks treatment


title: Swr1_IP_(20130401_2_8)

description: Swr1 IP, 10' MNase

source_name: Swr1 IP


title: BJ (Hs)

source_name: BJ cells

value: fibroblasts

value: skin; foreskin

value: ATCC CRL-2522


data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for low-quality sequence, then mapped to hg19 whole genome using Tophat v2.0.0.7 with default settings.
Fragments Per Kilobase of Transcript per Million mapped fragments  (RPKM) were calculated using a protocol from Trapnell et al., Nature Protocol, 2012. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: [FPKM_matrix.txt] This file includes FPKM values for AKT, BJ, NONE, and MPEC

value: sorted Pdx1-EGFP+ pancreatic progenitors derived from Pdx1-EGFP HUES8

tag: hesc line

tag: co-culture conditions

value: none/before


title: BJ

source_name: sorted Pdx1-EGFP+ pancreatic progenitors

value: BJ


title: MPEC

value: MPEC


title: Methanol replicate 1

first: David

middle: A. C.

last: Beck

address: Benjamin Hall IRB, Rm 440, UW Box 355014

department: ChemE & eScience Institute

institute: University of Washington

data_processing:
The raw reads were aligned to the scaffold using BWA version 0.7.4-r385 with default parameters (Li and Durbin 2010).
The alignments were post-processed and sorted into BAM files with SAMTools version 0.1.19-44428cd (Li, Handsaker et al. 2009).
Reads were attributed to open reading frames (ORFs) using the htseq-count tool from the ‘HTSeq’ framework version 0.5.4p5 in the ‘intersection-nonempty’ mode (Anders 2014).
Genome_build: The M. universalis FAM5 genome to be used as the alignment scaffold was downloaded from MaGE (https://www.genoscope.cns.fr/agc/microscope/mage/ ) on March 31, 2014.
Supplementary_files_format_and_content: Locus tag and RPKM in text file

organism: Methyloversatilis universalis FAM5

source_name: Bacterial culture

growth_protocol: Cells pre-grown on methanol (10mM) were used for inoculation of methanol (25mM) or methylamine (35mM) cultures at 5:100 ratios (inoculum : fresh media). Cultures were grown to mid-exponential phase (OD600 0.4 ± 0.05).

extract_protocol:
An RNeasy Mini Kit (Qiagen©; Venlo, Netherlands) with two types of DNA digestions was used to isolate the mRNA. Initially, the DNA/RNA pellet was re-suspended in 80 mL of a DNase I (RNase-free) mixture (Ambion®; Austin, TX, USA) and incubated for 30 min at 37°C. Then, the samples were purified on RNeasy Mini Kit columns as described in the RNA cleanup section of the manual, including the optional on-column DNAse digestion. The MICROBExpress™ (Ambion®; Austin, TX, USA) kit was applied to each sample to reduce the rRNA concentration and increase the mRNA sequencing depth.
Illumina RNA-Seq library protocol was followed for single ended 36 bp reads

treatment_protocol: stop solution comprised of 5% water-equilibrated phenol, pH 6.6 (Sigma; St. Louis, MO, USA), and 95% ethanol (200 Proof; Deacon Labs, Inc., King of Prussia, PA, USA). The cells were collected by centrifugation at 4,300 × g at 4°C for 10 min. The resultant pellet was re-suspended in 0.75 mL of extraction buffer [2.5% CTAB (Sigma; St. Louis, MO, USA), 0.7 M NaCl, and 0.075 M pH 7.6 phosphate buffer] and transferred to a 2 mL sterilized screw-cap tube containing 0.75 mL of phenol:chloroform:isoamylic alcohol with a volume ratio of 25:24:1 (Ambion®; Austin, TX, USA), 0.5 g of 0.1 mm silica beads (Biospec products; Bartlesville, OK, USA), 0.2% SDS (Ambion®; Austin, TX, USA), and 0.2% lauryl sarkosine (Sigma; St. Louis, MO, USA). The mixtures were homogenized in a bead beater (Mini-Beadbeater; Biospec Products; Bartlesville, OK, USA) for 2 min (75% of the maximum power). The resulting slurry was centrifuged for 5 min at 4°C and 20,800 × g. The aqueous layer was transferred to a fresh tube containing 0.75 mL of chloroform:isoamylic alcohol with a volumetric ratio of 24:1 (Sigma; St. Louis, MO, USA) and centrifuged again for 5 min at 4°C and 20,800 × g to remove dissolved phenol. The aqueous phase was transferred to a new tube. MgCl2 (final concentration 3 mM), sodium acetate (10 mM, pH 5.5), and 0.8 mL icecold isopropanol were added. Nucleic acids were transferred to −80°C for overnight precipitation. Precipitated samples were centrifuged for 45 min at 4°C and 14,000 RPM (20,800 × g), washed with 0.5 mL of 75% ethanol (made from 200 proof; Deacon Labs, Inc., King of Prussia, PA, USA), and dried for 15 min at room temperature.

tag: growth conditions

value: methanol growth


title: H3K4me3_AIDmm_clone17

city: Bethesda

first: Marei

last: Dose

address: 9000 Rockville Pk

institute: National Institutes of Health

description:
Genetically engineered RAMOS cell line deficient for AID. Used to reveal AID dependent mutations by comparison with MSH2-/-; AIDtg; UGItg RAMOS cells.
processed data file: AIDmm.SNPs.bed.gz; Hotspots.AIDtgMSH2mmUgi.bed.gz

data_processing:
base-calling: Illumina CASAVA 1.8.0 to 1.8.2
ChIP-Seq_density: alignment: bowtie-0.12.8/bowtie -S -m 1 -p 20 -a --best --strata -n 2
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.18/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
ChIP-Seq_SE: alignment: bowtie-0.12.8/bowtie -S -m 1 -p 20 -a --best --strata -n 2
ChIP-Seq_SE: peak calling: MACS 1.4.2 with the flag ‘-p 1e9’
ChIP-Seq_SE: Super-enhancer calling:    ROSE (https://bitbucket.org/young_computation/rose.git) with ‘TSS_EXCLUSION_ZONE_SIZE=2000’
ChIP-Seq_mutations: align and fix read group: bwa  0.6.2-r126 ‘bwa aln –B 3 –n 2’ and ‘bwa samse –r <new_read_group_string>’
ChIP-Seq_mutations: flag and sort bam files: ‘samtools view –S –b –F4’ and 'samtools sort'
ChIP-Seq_mutations: deduplicate: picard 1.7.9 MarkDuplicates with ‘REMOVE_DUPLICATES=true
ChIP-Seq_mutations: GATK, version 2.5-2 RealignerTargetCreator (default settings)
ChIP-Seq_mutations: GATK, version 2.5-2 IndelRealigner with the flag ‘--consensusDeterminationModel KNOWNS_ONLY’
ChIP-Seq_mutations: GATK, version 2.5-2 BaseRecalibrator  (default settings)
ChIP-Seq_mutations: GATK, version 2.5-2 PrintReads  (default settings)
ChIP-Seq_mutations: GATK, version 2.5-2 UnifiedGenotyper with the flags ‘-stand_call_conf 4 -stand_emit_conf 4’
ChIP-Seq_mutations: hard filtering : custom software (python, bash) > 5bp from known indels; QUAL >= 20; GQ >= 20; DP >=3; callable in both WT replicates >=1 mutant sample
ChIP-Seq_mutations:  SNP counts:  custom software (R version 3.1.1 (2014-07-10)) remove AIDmm positions, count SNPs and callable bases per peak, obtain p-values using binomial distribution, BH correction
RNA-Seq: alignment: gsnap v. 2013-05-09
RNA-Seq: alignment:  normalized coverage: custom software
4C: bowtie-1.0; create bowtie index of all mm9 DpnII restriction fragment ends (40 bp from cut site)
4C: custom software; analyzed read pairs for presence of  correct bait sequence
4C: bowtie 1.0; if bait sequence present, align second read to DpnII fragment ends
4C: custom software, count number of hits to the left and right  end of each DpnII fragment
4C: For the analysis of local data, fragment densities were normalized  and displayed as described in [Van de Werken et al., PMID: 22961246]
ChIA-PET: Chia-PET tool: collapse redundant reads into non-redundant PET sequence
ChIA-PET: Chia-PET tool : analyze linker barcode composition to estimate error rate
ChIA-PET: Chia-PET tool: trim linkers
ChIA-PET: BatMis 3.0: align to mm9 reference, only perfectly and uniquely aligned reads are retained
ChIA-PET: Chia-PET tool: remove PCR duplicate (merge tags mapping within +/-2bp into one PET)
ChIA-PET: Chia-PET tool: categorize reads as either a self-ligation PET (two ends of the same DNA fragment) or and inter-ligation PET (two ends from two different DNA fragments in the same chromatin complex)
ChIA-PET: Chia-PET tool : classify inter-ligation PETs as intrachromosomal or interchromosomal PETs
ChIA-PET: Chia-PET tool : intrachromosomal PET connections supported by at least 2 independent PETs are provided in bed12 format with the thick ends representing the PET clusters on either end of the connection
ChIA-PET: Chia-PET processing pipeline is described in greater detail in Li et al., 2010 (PMCID: PMC2872882)
Genome_build: mm9 (if mouse) or hg19 (if human)

Supplementary_files_format_and_content: ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
ChIP-Seq: .SuperEnhancers.bed files contain super-enhancer intervals called based on H3K27Ac ChIP-Seq
ChIP-Seq: .SNPs.bed files contain the positions of mutations
ChIP-Seq:  the file k4me3.1kbmerge.pool.bed.gz contains the peak calls from pooled and downsampled RAMOS IP's used to identify hotspots
ChIP-Seq: the file me1.Nipbl.pos.bed.gz contains regulatory elements in RAMOS cells, called based on H3K4me1 and Nipbl ChIP-Seq
RNA-seq: .bigWig files contain extenden tag coverage in 100 nt windows divided by library size in millions to obtain normalized read coverage (rpm)
4C: *.tab files contain counts per fragment for DpnII fragments. Columns: chrom, start, end, counts_left_end, counts_right_end, norm_total_counts
ChIA-PET: .bed files show the significant connections that are supported by 2 or more independent PETs in a bed12 format

source_name: RAMOS

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 1 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. For native chip, chromatin was digested with Mnase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at  37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five micrograms of antibody were incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or Mnase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation.                RNA-Seq: Total RNA from 1e6  activated B cells was isolated by Trizol extraction.                                                                                4C-Seq: Ten million mouse B cells were crosslinked in 2% formaldehyde at room temperature for 10 min. The reaction was quenched by the addition of glycine (final concentration of 0.125 M). Cells were then washed with cold PBS and lysed (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% NP-40, 1× complete protease inhibitors (Roche)) at 4 °C for 1 h. Nuclei were incubated at 65 °C for 30 min, 37 °C for 30 min in 500 μl of restriction buffer (New England Biolabs DpnII buffer) containing 0.3% SDS. To sequester SDS, Triton X-100 was then added to a final concentration of 1.8%. DNA digestion was performed with 400 U of DpnII (New England Biolabs) at 37 °C overnight. After heat inactivation (65 °C for 30 min), the reaction was diluted to a final volume of 7 ml with ligation buffer containing 100 U T4 DNA Ligase (Roche) and incubated at 16 °C overnight. Samples were then treated with 500 μg Proteinase K (Ambion) and incubated overnight at 65 °C to reverse formaldehyde crosslinking. DNA was then purified by phenol extraction and ethanol precipitation. For circularization, the ligation junctions were digested with Csp6I (Fermentas) at 37 °C overnight. After enzyme inactivation and phenol extraction, the DNA was religated in a 7-ml volume (1,000 U T4 DNA Ligase, Roche). Three micrograms of 4C library DNA was amplified with Expand Long template PCR System (Roche). Thermal cycle conditions were DNA denaturing for 2 min at 94 °C, followed by 30 cycles of 15 s at 94 °C, 1 min at 58 °C, 3 min at 68 °C, and a final step of 7 min at 68 °C. Baits were amplified with inverse PCR primers as follows: Il4ra with DpnII_4C 5′-TCAGGTAGTTCCATGGGATC-3′, Il4ra_Csp6i 5′-ATCTCTGCACCAGACATCAG-3, IL21r_DpnII: CCAGACCTACTTAGCAGATC, and IL21r_Csp6i: ACTTAGACACTGCTCAGCTG.                                                                   ChIA-PET: RNA PolII ChIA-PET was performed as previously described (Fullwood et al., 2009, Goh et al., 2012 and Li et al., 2012). Briefly, RAMOS cells (up to 3e9 cells) were treated with 1% formaldehyde at room temperature for 10 min and then neutralized using 0.2 M glycine. The crosslinked chromatin was subjected to fragmentation with an average length of 300 bp by sonication. The anti-PolII monoclonal antibody 8WG16 (Covance, MMS-126R) was used to enrich PolII-bound chromatin fragments. A portion of ChIP DNA was eluted off from antibody-coated beads for concentration quantification using Picogreen fluorimetry and for enrichment analysis using quantitative PCR.
ChIP-Seq and 4C: DNA was blunt-ended with End-It DNA end repair kit (Epicenter) and A-tailed with Taq DNA polymerase (Invitrogen) in the presence of 200mM of dATP for 40 min at 70°C. Samples were purified by phenol-chloroform extraction after each reaction. Illumina compatible adaptors (Bioo Scientific) were then ligated with T4 DNA ligase (Enzymatics), and the reaction was purified once with AMpure XP magnetic beads (Beckman Coulter). Samples were PCR amplified for 12~15 cycles with KAPA HiFi DNA polymerase mix (KAPA Biosystems) and run on a 2% agarose gel and size-selected at 250–350 bp. 50 cycles of sequencing data were acquired on the HiSeq 2000 or 2500 (Illumina).                                                                                RNA-Seq: Standard RNA-Seq library preparation was performed following Illumina’s RNA-Seq protocol v2.                                                   ChIA-PET: For ChIA-PET library construction ChIP DNA fragments from two biological replicates were end-repaired using T4 DNA polymerase (NEB) and ligated to either linker A or linker B. Other than four nucleotides in the middle of the linkers that were used as nucleotide barcode, the two linkers share the same nucleotide sequences. After linker ligation, the two samples were combined for proximity ligation in diluted conditions. During the proximity ligation, DNA fragments within the same ChIP complex with the same linker were ligated, which generated the ligation products with homodimer linker composition. However, chimeric ligations between ChIP fragments that are bound in different chromatin complexes could also occur, thus producing ligation products with heterodimer linker composition. Following proximity ligation, the Paired-End-Tag (PET) constructs were extracted from the ligation products and the PET templates were subjected to paired-end sequencing using Illumina HiSeq.

tag: genotype/variation

value: AICDA-/-

value: Burkitt's lymphoma cell line

tag: chip antibody

value: Anti-trimethyl-Histone H3 (Lys4)

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #


title: Methylamine replicate 1

value: methylamine growth

tag: strain


title: Methylamine replicate 2


title: 7-OILA_LT_2weeks

description: 2 weeks treatment

value: Adult

value: Male

value: corn oil

tag: tissue

value: bone marrow


title: AKT

value: AKT-HUVEC


title: H3K4me3_AIDmm_clone12


title: H3K4me3_AIDmm_clone13


title: Htz1_20min_Input_(20140320_1,2_12)

description: Htz1 input, 20' MNase

value: nuclei

tag: genotype

value: MATalpha ade2-1 can1-100 his3-11, 15 leu2-3, 112 trp1-1 ura3-1 RAD5+ HTZ1-2L-3FLAG:KanMX


title: H3K4me3_AIDmm_clone9


title: Methanol replicate 2


title: H3K4me3_AIDmm_clone18


title: H3K4me3_AIDmm_clone8


title: H3K4me3_AIDmm_clone14


title: H3K4me3_AIDmm_clone15


title: H3K4me3_AIDmm_clone16


title: H3K4me3_AIDmm_clone11


title: H3K4me3_AIDmm_clone5


title: H3K4me3_AIDmm_clone4


title: H3K4me3_AIDmm_clone10


title: Htz1_5min_IP_2_(20140327_1,2_11)

description: Htz1 IP, 5' MNase


title: H3K4me3_AIDmm_clone7


title: tonsil_naiveB_i33

description: SE calls from all 4 samples were pooled with beops merge

source_name: tonsil B cell (naïve)

value: tonsil

value: Anti-Histone H3 (acetyl K27) antibody

value: Abcam


title: H3K4me3_AIDmm_clone3


title: tonsil_naiveB_i32


title: H3K4me3_AIDmm_clone1


title: H3K4me3_AIDmm_clone2


title: tonsil_GcB_i34

source_name: tonsil B cell (GC)


title: N.winogradskyi, single-culture, rep. 3

status: Public on Dec 03 2014

city: Corvallis

first: Luis

last: Sayavedra-Soto

state: OR

address: Cordley Hall 2082

department: Botany and Plant Pathology

institute: Oregon State University

data_processing:
Aligned reads using Bowtie version 2.1.0 to a Bowtie index containing the genomes of both organisms, with options "--no-mixed --threads 8 --reorder --no-unal --all --trim5 6 --trim3 10 -1 $sample/mate_1.fastq -2 $sample/mate_2.fastq -S $sample/alignments.sam"
Custom Python script matched alignments to gene annotations. Gene expression counts were aggregated from reads aligning unambiguously to each gene. A small list of homologs was used to resolve reads aligning ambiguously between the homologous genes to a single gene count.
NBPSeq version 0.1.8 was used to calculate differential gene expression by pairwise comparison.
Genome_build: N.europaea: gi|30407130|emb|AL954747.1| Nitrosomonas europaea ATCC 19718, complete  genome
Genome_build: N.winogradskyi: NC_007406.1, Contig6  [organism=Nitrobacter winogradskyi] [strain=Nb-255]
Supplementary_files_format_and_content: differential gene expression is tab-separated text output from NBPSeq

organism: Nitrobacter winogradskyi

source_name: cultures

growth_protocol: Chemostat cultures at D=0.008 h-1; N. europaea with 60 mM NH4+; N. winogradskyi with 60 mM NO2-; Co-culture with 60 mM NH4+;

extract_protocol:
Three biological replicates. Total RNA obtained using FastRNA kit (MP Biomedical). rRNA  removed with MICROBExpress (Ambion).
Standard illumina protocol; high-throughput; mRNASeq

treatment_protocol: Transcritome comparison of single cultures to co-culture

tag: phenotype

value: Nitritre oxidizer

tag: treatment

value: 60 mM NO2-


title: N.winogradskyi, single-culture, rep. 1

tag: cell line


title: ALE10

city: La Jolla

first: Bernhard

last: Palsson

state: CA

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

description: K-12 MG1655

data_processing:
Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v0.12.8 with parameters -X 1000 -n 2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v2.1.1 with the option --library-type fr-firststrand
Genome_build: ASM584v2
Supplementary_files_format_and_content: comma-delimited text files include RPKM values for each Sample.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Total RNA isolated from E. coli

growth_protocol: Cells were grown to mid-log phase aerobically at 37°C on M9 Supplemented with 4g/L D-Glucose

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cell culture was treated with the RNAprotect reagent (Qiagen).

value: Evolved


title: N.winogradskyi, single-culture, rep. 2


title: tonsil_GcB_i35


title: H3K4me3_AIDmm_clone6

value: AICDA-/-

value: Burkitt's lymphoma cell line


title: ALE8

description: K-12 MG1655


title: ALE9

description: K-12 MG1655


title: H3K27Ac_ramos

description:
for SE calling
processed data file: RAMOS_H3K27Ac_SuperEnhancers.bed.gz

value: WT


title: Input_ramos

description:
Input for SE calling
processed data file: RAMOS_H3K27Ac_SuperEnhancers.bed.gz


title: ALE3

description: K-12 MG1655


title: sRNAseq 72h 2nd replicate

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

description:
Sample 28
16-24-nt total RNA
72h sRNAseq after HCMV infection

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor, low-quality, and artifact sequence by using CutAdap-1.2.1, in-house python program, and FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
After preprocessing, the sequenced reads were mapped to human tRNA and rRNA sequences by Bowtie2-2.1.0 with -p 2 -k 2 --very-sensitive to remove reads mapped rRNA and tRNA.
After removing tRNA and rRNA mapped reads, the sequenced reads were mapped to hg19 with HCMV genome using Tophat v.2.0.9 with parameters -p 4 --b2-very-sensitive for mRNAseq and CLIPseq data and Bowtie2-2.1.0 with -p 2 -k 101 --score-min C,0,0 --mp 8,8 --np 8 for zero mismatch, --score-min C,-8,0 --mp 8,8 --np 8 for 1 mismatch for CLIPseq and sRNAseq data
Reads Per Kilobase of exon per Megabase of library size (RPKM) for mRNAseq and CLIPseq and Reads Per Million (RPM) for sRNAseq and CLIPseq were calculated in-house python program.
Genome_build: hg19 and HCMV Towne (FJ616285.1)
Supplementary_files_format_and_content: tab-delimited text files include genes, transcripts, and RPKM values for each sample.

source_name: Human foreskin fibroblasts

growth_protocol: Human foreskin fibroblasts were obtained from the American Type Culture Collection and cultured in complete Dulbecco’s modified Eagle’s medi-um (DMEM, Hyclone) supplemented with 10% FBS (Hyclone), 2 mM GlutaMAX-I, 100 U/mL penicillin, and 100 μg/mL streptomycin (Invitrogen) at 37 °C in the presence of 5% CO2.

extract_protocol:
CLIPseq was almost done by the instructions followed by Chi. et al, 2009, Nature. And RNA extraction with Trizol reagent (manufacturer's instruction) was used for mRNAseq and smallRNAseq.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Sample 1, 5, 9, 13, 17, 21 and 25 were uninfected. Others were infected with human cytomegalovirus (human perpesvirus 5).

tag: cell type

value: foreskin fibroblast

tag: infection

value: human perpesvirus 5

tag: time

tag: clip antibody


title: WT2

description: K-12 MG1655


title: ALE6

description: K-12 MG1655


title: ALE4

description: K-12 MG1655


title: ALE7

description: K-12 MG1655


title: ALE5

description: K-12 MG1655


title: ALE1

description: K-12 MG1655


title: sRNAseq 0h 2nd replicate

description:
Sample 25
16-24-nt total RNA
0h sRNAseq after HCMV infection

value: uninfected


title: sRNAseq 48h 2nd replicate

description:
Sample 27
16-24-nt total RNA
48h sRNAseq after HCMV infection


title: sRNAseq 72h 1st replicate

description:
Sample 24
16-24-nt total RNA
72h sRNAseq after HCMV infection


title: sRNAseq 24h 2nd replicate

description:
Sample 26
16-24-nt total RNA
24h sRNAseq after HCMV infection


title: WT1

description: K-12 MG1655


title: sRNAseq 48h 1st replicate

description:
Sample 23
16-24-nt total RNA
48h sRNAseq after HCMV infection


title: sRNAseq 24h 1st replicate

description:
Sample 22
16-24-nt total RNA
24h sRNAseq after HCMV infection


title: mRNAseq 0h 2nd replicate

description:
Sample 17
poly(A)-enriched total RNA
0h mRNAseq after HCMV infection

molecule: polyA RNA


title: Sample_MD_B9_mic_pre16

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Illumina Casava1.8 software used for basecalling.
alignment: tophat with deafult parameters
Expression table done using ESAT http://garberlab.umassmed.edu/software/esat/
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: Primary new-born derived microglia treated with TGFb1

growth_protocol: Extrected from new-born primary glial culture

extract_protocol:
miRNeasy (Qiagen)
see Jaitin et. al., Science 2014

treatment_protocol: TGFb1 (100ng/ml) was added to the cells

tag: organ

value: Primary microglia culture

tag: selection marker

value: Time following TGFb1 treatment

value: TGFb1 treatment

value: 16 hr


title: mRNAseq 72h 1st replicate

description:
Sample 16
poly(A)-enriched total RNA
72h mRNAseq after HCMV infection


title: mRNAseq 72h 2nd replicate

description:
Sample 20
poly(A)-enriched total RNA
72h mRNAseq after HCMV infection


title: mRNAseq 48h 2nd replicate

description:
Sample 19
poly(A)-enriched total RNA
48h mRNAseq after HCMV infection


title: mRNAseq 24h 2nd replicate

description:
Sample 18
poly(A)-enriched total RNA
24h mRNAseq after HCMV infection


title: mRNAseq 24h 1st replicate

description:
Sample 14
poly(A)-enriched total RNA
24h mRNAseq after HCMV infection


title: mRNAseq 48h 1st replicate

description:
Sample 15
poly(A)-enriched total RNA
48h mRNAseq after HCMV infection


title: Sample_MD_B8_mic_pre6

value: 6 hr


title: Sample_MD_B7_mic_pre6


title: CLIPseq 72h 3rd replicate_gene

description:
Sample 12
72h CLIPseq after HCMV infection

data_processing:
library strategy: AGO-CLIPseq
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor, low-quality, and artifact sequence by using CutAdap-1.2.1, in-house python program, and FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
After preprocessing, the sequenced reads were mapped to human tRNA and rRNA sequences by Bowtie2-2.1.0 with -p 2 -k 2 --very-sensitive to remove reads mapped rRNA and tRNA.
After removing tRNA and rRNA mapped reads, the sequenced reads were mapped to hg19 with HCMV genome using Tophat v.2.0.9 with parameters -p 4 --b2-very-sensitive for mRNAseq and CLIPseq data and Bowtie2-2.1.0 with -p 2 -k 101 --score-min C,0,0 --mp 8,8 --np 8 for zero mismatch, --score-min C,-8,0 --mp 8,8 --np 8 for 1 mismatch for CLIPseq and sRNAseq data
Reads Per Kilobase of exon per Megabase of library size (RPKM) for mRNAseq and CLIPseq and Reads Per Million (RPM) for sRNAseq and CLIPseq were calculated in-house python program.
Genome_build: hg19 and HCMV Towne (FJ616285.1)
Supplementary_files_format_and_content: tab-delimited text files include genes, transcripts, and RPKM values for each sample.

value: Anti-pan AGO 2A8 mAb (Diagenode, catalog# MAb-167-100, lot# 001)


title: Sample_MD_B6_mic_pre3

value: 3 hr


title: mRNAseq 0h 1st replicate

description:
Sample 13
poly(A)-enriched total RNA
0h mRNAseq after HCMV infection


title: CLIPseq 48h 3rd replicate_gene

description:
Sample 11
48h CLIPseq after HCMV infection


title: CLIPseq 24h 3rd replicate_gene

description:
Sample 10
24h CLIPseq after HCMV infection


title: Sample_MD_B5_mic_pre3


title: CLIPseq 72h 2nd replicate_gene

description:
Sample 8
72h CLIPseq after HCMV infection


title: CLIPseq 0h 3rd replicate_gene

description:
Sample 9
0h CLIPseq after HCMV infection


title: CLIPseq 48h 2nd replicate_gene

description:
Sample 7
48h CLIPseq after HCMV infection


title: CLIPseq 24h 2nd replicate_gene

description:
Sample 6
24h CLIPseq after HCMV infection


title: Sample_MD_B3_mic_pre1

value: 1 hr


title: CLIPseq 0h 2nd replicate_gene

description:
Sample 5
0h CLIPseq after HCMV infection


title: Sample_MD_B2_mic_pre0

value: time 0


title: CLIPseq 72h 1st replicate_gene

description:
Sample 4
72h CLIPseq after HCMV infection


title: sRNAseq 0h 1st replicate

description:
Sample 21
16-24-nt total RNA
0h sRNAseq after HCMV infection


title: CLIPseq 24h 1st replicate_gene

description:
Sample 2
24h CLIPseq after HCMV infection


title: CLIPseq 48h 1st replicate_gene

description:
Sample 3
48h CLIPseq after HCMV infection


title: CLIPseq 0h 1st replicate_gene

description:
Sample 1
0h CLIPseq after HCMV infection


title: CLIPseq 72h 3rd replicate_miR


title: Sample_MD_B12_mic_pre20

value: 20 hr


title: Sample_MD_B1_mic_pre0


title: CLIPseq 24h 3rd replicate_miR


title: CLIPseq 0h 3rd replicate_miR


title: CLIPseq 72h 2nd replicate_miR


title: Sample_MD_B11_mic_pre20


title: CLIPseq 48h 2nd replicate_miR


title: Sample_MD_B10_mic_pre16


title: Sample_MD_B4_mic_pre1


title: Sample_MD_A7_mon_pre6a

source_name: Bone marrow derived macrophages treated with TGFb1

growth_protocol: M-CSF suppplemented culture

value: bone marrow culture


title: Sample_MD_A9_mon_pre16a


title: CLIPseq 48h 1st replicate_miR


title: CLIPseq 24h 1st replicate_miR


title: Sample_MD_A6_mon_pre3b


title: RBM7/hRRP40 #2

city: Aarhus

first: Peter

last: Andersen

state: Denmark

address: Universitetsbyen 83

department: MBG

country: Denmark

institute: Aarhus University

data_processing:
Basecalls were done using CASAVA from Illumina
iCLIP sequencing reads were pre-processed using custom Perl scripts (from G. Kudla / D. Tollervey labs) and the FASTX toolkit (S. Andrews, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to remove barcode sequences, remove low-quality reads and collapse identical reads
Paired-end reads were mapped to hg19 using the tophat
Read coverage along the genome and in individual genomic regions was calculated using bedtools and custom awk and perl scripts
Genome_build: hg19
Supplementary_files_format_and_content: wig files

source_name: HeLa cells

growth_protocol: HeLa cells were grown in Dulbecco’s modified eagle medium (DMEM) containing 10% fetal bovine serum (FBS) and 1% Penicilin/Streptavidin, at 37°C, 5% CO2.

extract_protocol:
We utilized HeLa cells stably expressing a C-terminally Localization and Affinity Purification (LAP)-tagged RBM7 variant, including a GFP moiety, a TEV cleavage site and an S-tag protein. The cells were crosslinked cells with 300 mJ/cm2 at 254nm UV and treated cells as described in the original iCLIP protocol (Konig et al., 2010). Extracts derived from the RBM7-LAP cell line, or from non-tagged control cells, were subjected to IP using GFP-Trap nanobodies (Rothbauer et al., 2008). To improve specificity, we modified the iCLIP protocol by performing washes in stringent, semi-denaturing conditions (2M Urea, 0.5% Na-deoxycholate, 1000mM NaCl)(see supplemental Materials and Methods). Cells were collected from two 245x245mm plates and lysed by mild sonication 3x10sek at 20W (Branson 250) in 5 volumes of cold iCLIP lysis buffer (50 mM Tris/HCl, pH 8.0, 150 mM NaCl, 0.5% TritonX-100, 0.1% Na-deoxycholate, 2mM EDTA and protease inhibitors (Roche)). Extracts were treated with RNase I (5U/ml) for 3min and DNAse I (2U/ml) at 37°C. Cell lysates were centrifuged at 16000g for 15min at 4°C. Cleared extracts were mixed with pre-washed Dynabeads M-270 Epoxy (Life Technologies) coated with GFPtrap nanobodies and washed 3 times with lysis buffer after 60 min of incubation. For higher reproducibility, an additional step of on-bead RNase I treatment was introduced and followed by 3 washes in high salt buffer (50 mM Tris/HCl, pH 8.0, 1000 mM NaCl, 0.5% TritonX-100, 0.5% Na-deoxycholate, 2M Urea, 2mM EDTA) and 2 times with LiCl buffer (50 mM Tris/HCl, pH 8.0, 250 mM LiCl, 0.5% TritonX-100, 0.5% Na-deoxycholate, 2mM EDTA). After washes with no-salt buffer (50 mM Tris/HCl, pH 8.0, 0.2% (v/v) Tween, 10mM MgCl2), dephosphorylation of RNA was performed using FastAP (Fermentas) and followed by on-bead linker ligation. All the following steps were carried out as described in the original iCLIP protocol (Konig et al., 2010).
iCLIP protocol (Konig et al., 2010)

treatment_protocol: Cells were seeded at 50% confluence and grown for 24 hr before the first transfection. Transfections were performed using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions using siRNA against luciferase (RBM7 #1 and RBM7 #2) or hRRP40 (RBM7/hRRP40 #1 and RBM7/hRRP40 #2) at a final concentration of 15 nM of each siRNA (Supplementary Table S1). 24h after the first transfection in p15 plates cells were split and transfered onto 245x245mm plates. Next day the transfection was repeated. Cells were harvested 48 hr after the second transfection, preventing plates from being more than 90% confluent.

value: HeLa Kyoto

value: RBM7-LAP cell line

tag: protocol

value: Localization And Purification (LAP) tag

value: siRNA hRRP40


title: CLIPseq 72h 1st replicate_miR

value: foreskin fibroblast

value: human perpesvirus 5


title: Sample_MD_A4_mon_pre1b


title: RBM7 #1

value: siRNA luciferase


title: 4C-seq for 11 sub-threshold enhancers

city: Cambridge

first: Xinchen

last: Wang

state: MA

address: 32 Vassar St, D514

institute: MIT

data_processing:
Library strategy: 4C-seq
The initial step in the 4C-seq analysis is the alignment of the sequencing reads to a reduced genome of sequences that flank DpnII sites (fragment ends), using custom perl scripts. Due to their ambiguous nature in reporting contacts, repetitive fragment ends were excluded from subsequent analysis. The reduced genome was based on hg19.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files are in wiggle track format. Entries in the wiggle track represent genomic regions that overlap with DpnII fragment ends.

source_name: iPSC-derived cardiomyocytes

growth_protocol: Human iPSC-derived cardiomyocytes (iCMs) (Cellular Dynamics, Catalog #: CMc-100-010-001) were thawed according to manufacturer’s instructions and diluted to a final plating density of 0.2x106 cells per mL with plating medium (Cellular Dynamics, Catalog#: CMM-100-110-001).

extract_protocol:
The initial steps of the 4C procedure, as published before (Simonis et al., 2006, Nature Genetics (PMID 17033623)), remain unchanged. Cells are cross-linked using 2% formaldehyde for 10min at room temperature in PBS 10%FCS and nuclei are isolated, after which chromatin is digested with DpnII and subsequently ligated under diluted conditions.
After reversal of the cross-links, the DNA is purified and treated with Csp6I. After a second re-ligation step, the sample is purified and a 4C PCR is applied.

treatment_protocol: Cells were cross-linked using 2% formaldehyde for 10 minutes at room temperature in 10%FCS/PBS.

tag: cell-type

value: Human iPSC-derived cardiomyocytes (iCMs) (Cellular Dynamics, Catalog #:CMc-100-010-001)

tag: bait-barcode pairs


title: Sleckman-BLig4-ZF-11-Ind1-TGAGGTTATCTCG_S4_L001_R2_001

city: St. Louis

first: Jacqueline

last: Payton

state: MO

address: 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

description: Ligase IV -/- Line B PCR of Zinc Finger Nuclease Double Stranded DNA Break

data_processing:
Paired end reads from the MiSeq Desktop Sequencer were de-multiplexed by the sample indexes allowing for a maximum 1 base pair mismatch within the index.
For samples where the same Index was used, but different primer sequences were used, the appropiate sequences were first extracted by the appropaite primer sequence and then by the Index sequence.
Adaptor sequences were then clipped from reads 1 and 2 using FLEXBAR version 2.4 (parameters: -m 10 -u 5 -ae RIGHT -r -aa -at 0.5).  (Dodt, M., Roehr, J.T., Ahmed, R., and Dieterich, C. (2012). FLEXBAR-Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms. Biology (Basel) 1, 895-905.).
Paired reads were assembled using FLASH-1.2.7 software (parameters: -m 10 -M 100 -x 0.25). (Magoc, T., and Salzberg, S.L. (2011). FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957-2963.).
The assembly parameters were adjusted based on the read length distribution of a particular sample. When a sample was dominated by short reads that resulted in 100% sequence overlap between read 1 and 2,  ~50 bases from the end of the reads was removed using PrinSeq in order to the prevent mis-assembly. Schmieder, R., and Edwards, R. (2011). Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863-864.
The trimmed reads were assembled again by FLASH.
Individual assembled reads (contigs) were then aligned pairwise to the reference sequence using the MUSCLE aligner as a scheduled batch job using The Genome Institute clusters (parameters: default, reference sequences: for Igkappa GenBank NG_005612.1, for TCRbeta AC117678.16, for recombination substrate refer to Bredemeyer, A.L., Sharma, G.G., Huang, C.Y., Helmink, B.A., Walker, L.M., Khor, K.C., Nuskey, B., Sullivan, K.E., Pandita, T.K., Bassing, C.H., and Sleckman, B.P. (2006) ATM stabilizes DNA double-strand-break complexes during V(D)J recombination. Nature 442, 466-470).
Using customized Perl scripts, alignments with >5bp deletions on either strand (mis-assembled sequences due to poor sequence quality) were removed.
Using customized Perl scripts, alignments without >10 bps of continuous reference sequence (primer dimers) were removed.
Using customized Perl scripts, alignments where assembled sequences appeared to be longer than the full length coding end (usually mis-assembled reads, small deletions near coding end or insertions) were removed.
Using customized perl scripts, DNA end structures were then calculated and the structures from triplicate PCR reactions were pooled together into a single file. As a convention for calculation of DNA end structure, nucleotides at the ligation junction that could be assigned to either the 5’ or 3’ end were assigned to the 5’ end except for the analysis of Cas9 and Eb:ZFN DNA ends where the nucleotides were assigned to generate blunt and 4 nucleotide 5’ overhangs, respectively, when possible.
Using R, products smaller than 50 base pairs and products with only single reads were removed from further analysis.
Graphs were generated using customized R scripts.
Genome_build: For Igkappa GenBank NG_005612.1, for TCRbeta AC117678.16, for recombination substrate refer to Bredemeyer et al. Nature 442, 466-470)
Supplementary_files_format_and_content: .txt files reporting: ced (The distance of a particular 5' end from the double stranded DNA break), overhang (The length of the overhang associated with that particular 5' end. A negative value means a 5' overhang and a positive value means a 3' overhang. A zero value means a blunt end.), and u2..3. (The number of sequencing reads that had that particular  DNA end structure (position of 5' end and overhang).

source_name: Abelson transformed pre-B cells

growth_protocol: Abelson transformed pre-B cells were grown as previously described in the following paper: Bredemeyer, A.L., Sharma, G.G., Huang, C.Y., Helmink, B.A., Walker, L.M., Khor,  K.C., Nuskey, B., Sullivan, K.E., Pandita, T.K., Bassing, C.H., and Sleckman, B.P.  (2006). ATM stabilizes DNA double-strand-break complexes during V(D)J  recombination. Nature 442, 466-470.

extract_protocol:
DNA extraction was done as described in the following paper. Blondal, T., Thorisdottir, A., Unnsteinsdottir, U., Hjorleifsdottir, S., Aevarsson, A.,  Ernstsson, S., Fridjonsson, O.H., Skirnisdottir, S., Wheat, J.O., Hermannsdottir,  A.G., et al. (2005). Isolation and characterization of a thermostable RNA ligase 1  from a Thermus scotoductus bacteriophage TS2126 with good single-stranded  DNA ligation properties. Nucleic Acids Res 33, 135-142.
Sequencing adaptors for Illumina MiSeq Sequencing was done by PCR as described for the HCoDES procedure in the reference above. Amplified PCR products were then pooled in apporxomately equimolar concentrations for Illumiina MiSeq using 40% Phi-X.

treatment_protocol: Genomic DNA was isolated from Abelson kinase transformed pre-B cells harboring single double stranded DNA breaks. The genomic DNA was treated with single stranded DNA ligase followed by sodium bisulphite treatment and PCR as described for HCoDES in the following paper: Yair Dorsett1, Yanjiao Zhou2,3, Anthony T. Tubbs1, Bo-Ruei Chen1,  Caitlin Purman1, Baeck-Seung Lee1, Rosmy George1, Andrea L. Bredemeyer1,  Jiang-yang Zhao1, Erica Sodergen3*, George M. Weinstock3*,  , Nathon, D, Han4, Alejandro Reyes1,4,+, Eugene M. Oltz1, Dale Dorsett5, Ziva Misulovin5,  Jacqueline E. Payton1 and Barry P. Sleckman1 (2014), Molec Cell In Press

tag: sequencing run

value: set 8

value: Abelson transformed pre-B cells

tag: genotype/variation

value: Ligase IV -/- Line B PCR of Zinc Finger Nuclease DSB


title: Sample_MD_A3_mon_pre1a

tag: strain

value: Time following TGFb1 treatment

value: TGFb1 treatment


title: RBM7/hRRP40 #1


title: Sleckman-BLig4-ZF-11-Ind2-GCTTAGAATCTCG_S5_L001_R1_001


title: RBM7 #2


title: Sleckman-BLig4-ZF-11-Ind2-GCTTAGAATCTCG_S5_L001_R2_001


title: Sleckman-BLig4-ZF-11-Ind3-ATGACAGATCTCG_S6_L001_R2_001


title: Sleckman-BLig4-ZF-11-Ind3-ATGACAGATCTCG_S6_L001_R1_001


title: B-Lig4-CJ-7-48hr-Kappa-shNT-Ind-43-TGTGCCA_S15_L001_R2_001

description: Ligase IV -/- Line B CJ #7 Kappa PCR of RAG induced Double Stranded DNA Breaks at Jk1 of IgKappa locus

value: set 4

value: Ligase IV -/- Line B CJ #7 Kappa PCR of RAG-induced DSBs at Jk1 of IgKappa locus


title: Sample_MD_A1_mon_pre0a

value: time 0


title: CLIPseq 0h 1st replicate_miR

value: uninfected

value: Anti-pan AGO 2A8 mAb (Diagenode, catalog# MAb-167-100, lot# 001)


title: Sample_MD_A12_mon_pre20b

value: bone marrow culture

value: 20 hr


title: B-Lig4-CJ-7-48hr-Kappa-shNT-Ind-44-AACGGAG_S16_L001_R2_001


title: CLIPseq 0h 2nd replicate_miR


title: Sleckman-BLig4-ZF-11-Ind1-TGAGGTTATCTCG_S4_L001_R1_001


title: B-Lig4-CJ-7-48hr-Kappa-shNT-Ind-45-GATAGTT_S17_L001_R2_001


title: Sample 5 of control P21 exocrine pancreas

city: Houston

first: Ge

last: Li

state: TX

address: 1100 Bates St.

department: Pediatrics

institute: Baylor College of Medicine

data_processing:
Quality control was checked by FastQC (version 0.10.1).
Sequencing adptors and remaining MSA adaptors were trimmed by cutadapt program.
The trimmed reads were alignned to mouse genomes using bowtie aligner (version 0.12.9)
Sum of number of reads overlapping for each SmaI/XmaI interval wer counted.
The SmaI/XmaI intervals refer to genomic regions with SmaI/XmaI cut sites (cccggg) at both ends and within the distance of 60bp to 3kb, which are the regions that examined by MSA-seq.
Genome_build: NCBI37/mm9 mouse genome (Jul 2006 release)
Supplementary_files_format_and_content: The processed data are presented in .xlsx format, and present the read depth of each sample in each SmaI/XmaI interval.

source_name: exocrine pancreas

growth_protocol: SL mice were reared as 4 pups per litter from P1 to P21, and C mice were reared as 9 pups per little from P1 to P21.

extract_protocol:
Genomic DNA was isolated with phenol/chloroform extraction followed by ethanol precipitation
Libraries were constructed by MSA-seq. As a brief description of the MSA: 500ng of genomic DNA was serially digested with SmaI and XmaI followed by an adaptor ligation and adaptor mediated PCR amplification (Waterland et al, 2010 Plos Genetics). MSA products were sheared to 200-500bp, ligated to sequencing adaptors for paired-end read, and submitted for sequencing by Illumina HiSeq.

value: acinar cells

value: FVB

tag: litter size

tag: age


title: B-Lig4-CJ-7-48hr-Subst-shNT-Ind-67-AGGACCT_S21_L001_R2_001

description: Ligase IV -/- Line B CJ #7 PCR of RAG induced Double Stranded DNA Breaks at the Recombination Substrate

value: Ligase IV -/- Line B CJ #7 PCR of RAG-induced DSBs at the Recombination Substrate


title: Sample_MD_A5_mon_pre3a

value: 3 hr


title: B-Lig4-CJ-7-48hr-Subst-shNT-Ind-66-GACACAG_S20_L001_R2_001


title: Sample_MD_A11_mon_pre20a


title: Sample_MD_A10_mon_pre16b

value: 16 hr


title: Sample 4 of control P21 exocrine pancreas


title: Sample 2 of control P21 exocrine pancreas


title: Sleckman-LH8-110-inv-B5L-P548-K-Ind30-CTGGTGG_S23_L001_R2_001

description: Ligase IV -/- H2AX -/- Line #8 CJ #148 Substrate PCR for de novo DSBs. Sequences mixed with regular substrate PCR sequences. Pull out sequences of interest using primer specific primer sequence.

value: set 5


title: Sample_MD_A2_mon_pre0b


title: Sleckman-LH8-110-inv-B5L-P548-K-Ind29-GTTCTCA_S22_L001_R2_001

value: Abelson transformed pre-B cells

value: Ligase IV -/- H2AX -/- Line #8 CJ #148 Substrate PCR for de novo DSBs. Sequences mixed with regular substrate PCR sequences. Pull out sequences of interest using primer specific primer sequence.


title: mon_day7-2

description: INVIVO.xlsx

source_name: Monocyte cells sorted from spinal cord of injured mice

growth_protocol: In vivo-sorted cells

treatment_protocol: The spinal cords of deeply anesthetized mice were exposed by laminectomy at T12, and contusive (200 kdynes) centralized injury was  performed using the Infinite Horizon spinal cord impactor (Precision  Systems)

value: Spinal cord

value: Time following spinal cord injury

value: spinal cord injury

value: 7 days


title: Sample 1 of control P21 exocrine pancreas


title: Sleckman-LH8-110-inv-B5L-P548-K-Ind31-TGCCCAT_S24_L001_R2_001


title: mon_day7-1

description: INVIVO.xlsx


title: Sample 5 of small litter P180 endocrine pancreas

source_name: endocrine pancreas

value: pancreatic islets


title: CLIPseq 48h 3rd replicate_miR

value: foreskin fibroblast

value: human perpesvirus 5


title: MboII-Ind-7-KpnI-Ind7-AGACTGA_S65_L001_R2_001

description: KpnI control sample. Sequences mixed with other recombination substrte sequences. Pull out KpnI sequences using specific primer sequence for KpnI control.

value: set 4

value: KpnI control sample. Sequences mixed with other recombination substrate sequences. Pull out KpnI sequences using specific primer sequence for KpnI control.


title: Sleckman-ALig4-Cas9-Eb9314-Ind10-GGCAGCG_S1_L001_R1_001

description: LigaseIV -/- Line A CJ #1 PCR of Cas9 + Eb guide RNA induced break

value: set 8

value: LigaseIV -/- Line A CJ #1 PCR of Cas9 + Eb guide RNA-induced break


title: mon_day3-2

description: INVIVO.xlsx

value: 3 days


title: Sleckman-ALig4-Cas9-Eb9314-Ind10-GGCAGCG_S1_L001_R2_001


title: Sleckman-ALig4-Cas9-Eb9314-Ind11-CCATCAT_S2_L001_R1_001


title: CLIPseq 24h 2nd replicate_miR

value: Anti-pan AGO 2A8 mAb (Diagenode, catalog# MAb-167-100, lot# 001)


title: Sample 4 of small litter P180 endocrine pancreas

value: FVB


title: mon_day3-1

description: INVIVO.xlsx


title: Sleckman-ALig4-Cas9-Eb9314-Ind12-TAACAAG_S3_L001_R2_001


title: Sample 3 of small litter P180 endocrine pancreas


title: mon_day1-2

description: INVIVO.xlsx

value: 1 day


title: B-Lig4-CJ-7-48hr-Subst-shNT-Ind-68-TTTTCGG_S22_L001_R2_001

value: Abelson transformed pre-B cells

value: Ligase IV -/- Line B CJ #7 PCR of RAG-induced DSBs at the Recombination Substrate


title: Sleckman-ALig4-Cas9-Eb9314-Ind11-CCATCAT_S2_L001_R2_001


title: Sample 2 of small litter P180 endocrine pancreas


title: Sleckman-BLig4-Cas9-Eb9314-Ind7-AGACTGA_S4_L001_R2_001

description: LigaseIV -/- Line B CJ #7 PCR of Cas9 + Eb guide RNA induced break

value: LigaseIV -/- Line B CJ #7 PCR of Cas9 + Eb guide RNA-induced break


title: Sleckman-BLig4-Cas9-Eb9314-Ind7-AGACTGA_S4_L001_R1_001


title: Sleckman-BLig4-Cas9-Eb9314-Ind8-CTTGGAA_S5_L001_R1_001


title: mon_day1-1

description: INVIVO.xlsx

value: Spinal cord

value: Time following spinal cord injury


title: Sample 3 of control P21 exocrine pancreas

value: acinar cells


title: Sleckman-BLig4-Cas9-Eb9314-Ind8-CTTGGAA_S5_L001_R2_001


title: Sample 1 of small litter P180 endocrine pancreas

value: pancreatic islets


title: mon_16hr-2

description: INVIVO.xlsx

value: spinal cord injury

value: 16 hr


title: mon_16hr-1

description: INVIVO.xlsx


title: Sample 5 of control P180 endocrine pancreas


title: mic_time0-3

description: INVIVO.xlsx

source_name: Microglia sorted from spinal cord of injured mice

value: time 0


title: Sleckman-C5L-ZF-12-Ind4-CACCTCCATCTCG_S7_L001_R2_001

description: LigaseIV -/- 53BP1 -/- Line C ZF #12 PCR of Zinc Finger Nuclease induced Double Stranded DNA Break

value: set 7

value: LigaseIV -/- 53BP1 -/- Line C ZF #12 PCR of Zinc Finger Nuclease-induced DSB


title: Sleckman-BLig4-Cas9-Eb9314-Ind9-CCGATTA_S6_L001_R2_001

value: set 8


title: Sleckman-C5L-ZF-12-Ind5-ATCGAGCATCTCG_S8_L001_R1_001


title: Sample 3 of control P180 endocrine pancreas


title: Sleckman-C5L-ZF-12-Ind6-TACTCTAATCTCG_S9_L001_R1_001