title: cMyc-25xI, rep4

description: processed data file: cmyc-25xI-WT.txt

source_name: spleen B cells+cMyc-25xI

value: spleen B cells

value: I-SceI retroviral infrection


title: ΔSα_1xI-5', clone #1, rep3

status: Public on Aug 26 2015

type: SRA

city: Boston

first: Junchao

last: Dong

state: MA

address: 1 Blackfan Circle

department: PCMM

country: USA

institute: Boston Children's Hospital, Harvard Medical School

description: processed data file: Sa_1xI-5BE clone #1_pooled_tlx.txt

library_source: genomic

data_processing:
library strategy: high-throughput genome-wide translocation sequencing (HTGTS)
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 or its derivative reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
We removed potential duplicates by comparing the coordinates of the end of the bait alignment and the start of the prey alignment across all reads. A read will be marked as a duplicate if it has a bait alignment offset within 2nt and a prey alignment offset within 2nt of another read’s bait and prey alignments.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Genome_build: mm9, mm9_129IgHC
Supplementary_files_format_and_content: tab delimited text files (translocation junctions) contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Tname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Tstart) and end (Tend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

molecule: genomic DNA

organism: Mus musculus

source_name: CH12F3 murine lymphoma cells_ΔSα_1xI-5', clone #1

extract_protocol:
DNA was extracted overnight at 55degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation
Translocation libraries were prepared using HTGTS.

treatment_protocol: Purified B cells were stimulated with either aCD40/IL4 or LPS/aIgD-dextran; I-SceI infection were performed at day 1 after stimulation with the presence of 4ug/ml polybrene; ATM inhibitor were added at day 1 at final concentration of 10mg/ml.

tag: cell type

value: CH12F3 murine lymphoma cells

tag: genetic variation

tag: activation method

tag: treatment protocol

value: I-SceI plasmid nucleofection

tag: target locus

tag: reference assembly

tag: growth protocol


title: cMyc-25xI, rep3

description: processed data file: cmyc-25xI-WT.txt


title: cMyc-25xI, rep2

description: processed data file: cmyc-25xI-WT.txt


title: ΔSγ1_2xI-H2AX, rep1

description: processed data file: ΔSγ1_2xI-H2AX-3'.txt

source_name: spleen B cells+ΔSγ1_2xI-H2AX

value: delta-S-gamma-1_2xI, H2AX-/-


title: cMyc-25xI, rep1

description: processed data file: cmyc-25xI-WT.txt


title: ΔSα_1xI-5', clone #2, rep2

description: processed data file: Sa_1xI-5BE clone #2_pooled_tlx.txt

source_name: CH12F3 murine lymphoma cells_ΔSα_1xI-5', clone #2


title: ΔSγ1_2xI-H2AX, rep3


title: ΔSγ1_2xI-ATM, rep2

description: processed data file: ΔSγ1_2xI-ATM-3'.txt

source_name: spleen B cells+ΔSγ1_2xI-ATM

value: delta-S-gamma-1_2xI, ATM-/-


title: ΔSγ1_2xI-ATM, rep1


title: ΔSγ1_2xI-H2AX, rep2


title: ΔSγ1_2xI-ATM, rep3


title: ΔSα_1xI-3', clone #2, rep3

description: processed data file: Sa_1xI-3BE clone #2_pooled_tlx.txt

source_name: CH12F3 murine lymphoma cells_ΔSα_1xI-3', clone #2


title: ΔSγ1_2xI-53BP1, rep2

description: processed data file: ΔSγ1_2xI-53BP1-3'.txt

source_name: spleen B cells+ΔSγ1_2xI-53BP1

value: delta-S-gamma-1_2xI, 53BP1-/-


title: ΔSγ1_2xI-53BP1, rep1


title: ΔSγ1_2xI-53BP1, rep4


title: ΔSγ1_2xI, rep4

description: processed data file: ΔSγ1_2xI-WT-3'.txt

source_name: spleen B cells+ΔSγ1_2xI


title: ΔSγ1_2xI, rep2

description: processed data file: ΔSγ1_2xI-WT-3'.txt


title: ΔSγ1_2xI-53BP1, rep3


title: ΔSγ1_2xI, rep1

description: processed data file: ΔSγ1_2xI-WT-3'.txt


title: ΔSγ1_2xI/ΔSµ_2xI-LPS, rep2

description: processed data file: ΔSγ1_2xI_ΔSµ_2xI_LPS-5'.txt

source_name: spleen B cells+ΔSγ1_2xI/ΔSµ_2xI-LPS


title: ΔSγ1_2xI/ΔSµ_2xI-LPS, rep1


title: ΔSγ1_2xI/ΔSµ_2xI-LPS, rep3


title: ΔSγ1_2xI/ΔSµ_2xI-5', rep4

description: processed data file: ΔSγ1_2xI_ΔSµ_2xI-5'.txt

source_name: spleen B cells+ΔSγ1_2xI/ΔSµ_2xI-5'


title: ΔSγ1_2xI/ΔSµ_2xI-5', rep3


title: ΔSγ1_2xI/ΔSµ_2xI-3', rep4

description: processed data file: ΔSγ1_2xI_ΔSµ_2xI-3'.txt; Sγ1_2xI_ΔSµ_2xI-3'_trans-Sm.txt

source_name: spleen B cells+ΔSγ1_2xI/ΔSµ_2xI-3'

value: mm9_2xIsceI_Su; mm9


title: ΔSγ1_2xI/ΔSµ_2xI-5', rep2


title: ΔSγ1_2xI/ΔSµ_2xI-5', rep1


title: ΔSγ1_2xI/ΔSµ_2xI-3', rep2


title: ΔSγ1_2xI/ΔSµ_2xI-3', rep3


title: ΔSγ1_2xI/ΔSµ_2xI-3', rep1


title: IgH_I-96k-53BP1-5', rep2

description: processed data file: IgH_I-96k-53BP1-5'.txt

source_name: spleen B cells+IgH_I-96k-53BP1-5'


title: IgH_I-96k-53BP1-5', rep1


title: IgH_I-96k-53BP1-3', rep2

description: processed data file: IgH_I-96k-53BP1-3'.txt

source_name: spleen B cells+IgH_I-96k-53BP1-3'


title: IgH_I-96k-53BP1-3', rep1


title: IgH_I-96k-5', rep3

description: processed data file: IgH_I-96k-5'.txt

source_name: spleen B cells+IgH_I-96k-5'


title: ΔSγ1_2xI, rep3

description: processed data file: ΔSγ1_2xI-WT-3'.txt


title: IgH_I-96k-5', rep2

description: processed data file: IgH_I-96k-5'.txt


title: IgH_I-96k-3', rep2

description: processed data file: IgH_I-96k-3'.txt

source_name: spleen B cells+IgH_I-96k-3'


title: IgH_I-96k-3', rep3

description: processed data file: IgH_I-96k-3'.txt


title: IgH_I-96k-3', rep4

description: processed data file: IgH_I-96k-3'.txt


title: HFF_PD74_woRotenone3

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

library_source: transcriptomic

data_processing:
FASTQ files were extracted using Illumina Casava software v1.8.2 (sample 1-24) or bcl2fastq v1.8.4 (sample 25-60)
FASTQ files were mapped using Tophat (v2.0.6) vs. the H.sapiens genome GRCh37.66 obtained from Ensembl
Uniquely mapped reads were counted for each gene_id using featureCounts v1.4.3-p1 (featureCounts -T 8 -a $GTF -s 0 -t exon -g gene_id -o featureCounts_gene.txt $SAMFILE)
RPKM values were computed using exon lengths provided by featureCounts and the sum of all mapped reads per sample
Genome_build: GRCh37.66
Supplementary_files_format_and_content: Excel file including raw counts and RPKM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: total RNA extracted from HFF fibroblasts

growth_protocol: The fibroblasts were maintained in the presence of rotenone throughout their span (from young PD till senescent) in culture in dim light, due to the light sensitive nature of rotenone [Dekker et al., 2011].

extract_protocol:
For library preparation an amount of around 1 μg of total RNA per sample was processed using Illumina’s TruSeqTM RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer’s instruction.
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol/chloroform extraction method. Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80 °C until use.

treatment_protocol: The media were changed and rotenone was supplemented every 3 days, due to the half-life of rotenone [Cabras et al., 2002].

tag: population doublings

tag: cell line

value: HFF

value: fibroblasts

tag: treatment


title: HFF_PD74_woRotenone2


title: HFF_PD74_woRotenone1


title: HFF_PD74_Rotenone1

value: 100 nM rotenone


title: HFF_PD74_Rotenone3


title: HFF_PD74_Rotenone2


title: ΔSγ1_2xI/ΔSµ_2xI-3', rep5


title: HFF_PD58_woRotenone3


title: HFF_PD58_woRotenone2


title: CGGBP1 shmiR - genomic DNA

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

description:
Whole genome
1064Sk normal human foreskin fibroblasts passage 12 transduced with lentivirus as indicated, genomic DNA extracted

data_processing:
ILLUMINA: Alignment
ILLUMINA: Removal of duplicate reads (mentioned in reports TXT files)
ILLUMINA: Normalization of bisulfite conversion efficiency by using 100% unmethylated Lambda Phage DNA spike in control
PACBIO: Alignment
PACBIO: consideration of only reads 100 bases or longer for methylation calculation
Genome_build: HG 19
Supplementary_files_format_and_content:
*report.txt: Bismarck Alignment Report
*PCR_alignment_to_consensus.txt: Supermatcher Alignment Output

growth_protocol: 10% FBS (Supplemented with Glutamine) in MEM (SIGMA)

extract_protocol:
DNA extracted using Qiagen Genomic DNA extraction kit.
NEXTflex Bisulfite (cat# 5119-01) Sequencing kit provided by Bioo Scientific for Illumina Seq. PacBio SMARTBLLl for PacBio sequencing
Mate Pairedfor Illumina and SmartBell for PacBio

treatment_protocol: Lentiviral transduction (MoI = 6)

value: Normal human foreskin fibroblasts

tag: passage

value: passage 12

tag: genotype/variation

value: Lentivirus (shmiR) transduced

tag: molecule subtype

value: Genomic DNA


title: Control shmiR - genomic DNA

source_name: 1064Sk normal human foreskin fibroblasts


title: HFF_PD58_Rotenone3


title: Control shmiR + bisulfite converted genomic DNA

description:
Whole genome (bisulfite converted)
1064Sk normal human foreskin fibroblasts passage 12 transduced with lentivirus as indicated, genomic DNA extracted and subjected to bisulfite conversion

value: Bisulfite converted genomic DNA


title: HFF_PD58_woRotenone1


title: HFF_PD58_Rotenone2


title: CGGBP1 shmiR + bisulfite converted genomic DNA


title: IgH_I-96k-5', rep1

description: processed data file: IgH_I-96k-5'.txt


title: HFF_PD34_Rotenone3


title: IgH_I-96k-3', rep1

description: processed data file: IgH_I-96k-3'.txt


title: HFF_PD34_Rotenone2


title: HFF_PD34_Rotenone1


title: HFF_PD30_woRotenone3


title: HFF_PD58_Rotenone1


title: HFF_PD34_woRotenone2


title: HFF_PD34_woRotenone1


title: HFF_PD30_woRotenone1


title: HFF_PD26_woRotenone3


title: HFF_PD30_woRotenone2


title: HFF_PD26_Rotenone2


title: HFF_PD26_Rotenone3


title: HFF_PD30_Rotenone3


title: HFF_PD30_Rotenone1


title: HFF_PD26_Rotenone1


title: HFF_PD30_Rotenone2


title: HFF_PD22_woRotenone3


title: HFF_PD26_woRotenone2


title: HFF_PD22_woRotenone1


title: HFF_PD34_woRotenone3


title: HFF_PD22_Rotenone3


title: HFF_PD22_Rotenone2


title: HFF_PD22_Rotenone1


title: 48  h

city: San Francisco

first: Matt

last: Thomson

state: CA

address: 600 16th Street

institute: UCSF

data_processing:
low quality reads removed <30
bowtie 2 alignment
reads per gene tabulate and FPKM computed
Genome_build: mm9
Supplementary_files_format_and_content: csv files, gene names and FPKM

source_name: mouse ES cells

growth_protocol: Cells grown in 2i media

extract_protocol:
Rneasy kit (Qiagen)
Lexogen SENSE kit
Random hetero-dimer

treatment_protocol: LED 300uW light induction for indicated time. Ibidi plate.

value: E14 ES cells

tag: vector

value: Brn2-RFP GAVPO induction cassette

tag: timepoints hours


title: 24  h


title: HFF_PD22_woRotenone2


title: 14  h


title: RUNX1ETO_floating_progenitors_ChIP-Seq

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

data_processing:
The sequence reads in fastq format were mapped to the mm10 mouse genome build using BWA. The resulting alignment files were used to generate density maps using bedtools and data was displayed using the UCSC Genome Browser
Regions of enrichment (peaks) of ChIP data were identified using MACS 1.4 and cisGenome  software. The resulting peaks common for the two peak calling methods were considered for further analysis. Peak overlaps, gene annotations were performed using in-house scripts.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Floating progenitors cells

extract_protocol:
For chromatin immunoprecipitation the cells were fixed with 1% formaldehyde (Thermo Scientific, 28906) for 10 minutes at room temperature. Then it was quenched with 1/10th volume of 2M glycine for 5 min followed by two washes with PBS. The PBS was completely removed and the pellet was stored at -80ºC till used. All the solutions used in ChIP (except the wash and elution buffers) contained 1x Halt protease inhibitor cocktail (Thermo Scientific 87786). Before ChIP, the cells were thawed on ice and resuspended in ice-cold Buffer A (10 mM Hepes, pH 8.0, EDTA  pH 8.0, 0.5 mM EGTA, pH 8.0, 0.25 % TritonX100). The cells were shaken for 10 minutes at room temperature and pelleted at 500g for 10 minutes. The supernatant was decanted, pellet was resuspended in ice-cold buffer B (10 mM Hepes, pH 8.0, 200 mM NaCl, 1 mM EDTA  pH 8.0, 0.5 mM EGTA, pH 8.0, 0.01 % TritonX100) and incubated at room temperature for 10 minutes. After pelleting, the cells were resuspended in ChIP buffer 1 (150 µl for 2 million cells, 25 mM Tris 1 M pH 8.0, 150 mM NaCl, 2 mM EDTA pH 8.0, 1% TritonX-100 and 0.25 % SDS), and sonicated at for 20-25 cycles (30 seconds on and 30 seconds off).  Two volumes of ice-cold  Chip dilution buffer II (25 mM Tris pH 8.0, 150mM NaCl, 2 mM EDTA pH 8.0, 1% TritonX-100, 7.5% Glycerol)  was added to the tube and centrifuged for 10 minutes. The supernatant was collected without disturbing the pellet. About 5% of the chromatin was stored in a separate tube for input.  Antibody coated Dynabeads (Invitrogen) were prepared as per manufacturer’s instructions by incubating the beads overnight with the antibody. Before mixing with the sonicated chromatin, the antibody was removed and the beads were washed twice with PBS.  The sonicated chromatin was added to the beads and rotated at 25 rpm at 4ºC for 2-3 hours. After incubation, the beads were separated from the chromatin suspension by keeping the tubes on a magnetic stand and the supernatant was removed.  The beads were washed once with ice-cold low salt buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA pH 8.0, 1% TritonX-100, 0.1% SDS), twice with high salt buffer (20 mM Tris pH 8.0, 500 mM NaCl, 2 mM EDTA pH 8.0, 1% TritonX-100, 0.1% SDS), twice with LiCl buffer (10 mM Tris pH 8.0, 250 mM lithium chloride, 1 mM EDTA pH 8.0, 0.5% NP40, 0.5% sodium-deoxycholate) and once with TE-NaCl buffer (TE pH 8.0 containing 50 mM sodium chloride). All the washings were done at rotating the tubes for 5-10 minutes at room temperature with cold wash solutions. The chromatin was eluted twice from the beads using elution buffer (100 mM NaHCO3, 1% SDS) and shaking at 1500 rpm for 15 minutes at room temperature. After adding 4 μl 5M sodium chloride and proteinase K, the pooled eluate was incubated at 65ºC overnight to reverse the crosslinks. The DNA was recovered by adding 1.8 volumes of Ampure beads (Beckman Coulter A63881). The beads were washed twice with 80% ethanol and the chromatin immunoprecipitated DNA was eluted from the Ampure beads in 0.1X TE.
The library preparation was done using the TruSeq ChIP sample prep kit (Illumina 15034288), with minor modifications. The size of the DNA fragments excised from gel after PCR, varied from 200-700 bp. Libraries were validated by doing qPCR for positive and negative control regions and libraries with no or very low signals from negative controls were chosen for sequencing. The DNA quality assessed by running 1 μl of the library on an Agilent Technologies 2100 Bioanalyser and the library concentration was determined by library quantification kit (Kapa Biosystems, Illumina KK4835). The libraries were pooled and subjected to massively parallel DNA sequencing on an Illumina Genome Analyzer.

tag: strain

value: ES-derived progenitors floating

tag: chip antibody


title: RUNX1_progenitors_expansion_uninduced_ChIP-Seq

source_name: myeloid progenitors_expansion cells

tag: cell type

value: ES-derived myeloid progenitors  expansion


title: RUNX1ETO_progenitors_expansion_ChIP-Seq

source_name: myeloid progenitors _expansion cells

value: ES-derived myeloid progenitors expansion


title: HFF_PD26_woRotenone1


title: RUNX1_progenitors_expansion_induced_ChIP-Seq


title: RUNX1ETO_HE_induced_ChIP_Seq

source_name: Hemogenic endothelium (HE) cells

value: ES-derived hemogenic endothelium


title: 6  h


title: 2  h


title: 0  h


title: RUNX1ETO_HE_uninduced_ChIP_Seq


title: P35_RNA-seq_rep3

status: Public on Aug 25 2015

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

description: Sox9-EGFP knockin mice were generated by introduction of an IRES-EGFP-pA cassette into the 3’ UTR of the endogenous Sox9 gen

data_processing:
Comprehensive database of known transcripts. A comprehensive transcript database were assembled from public databases [Ensembl and NCBI (build 37.2), AceView, and mRNAs from UCSC mm9] and merged into a combined set of non-redundant known transcript annotations using Cuffcompare (Trapnell et al., 2012; Trapnell et al., 2010).
Mapping reads. RNA-seq-derived reads were aligned independently for each SC-sample (three replicates per time condition) to the mouse genome (mm9) downloaded from the UCSC genome browser website (Kuhn et al., 2013) with TopHat (version 1.4.1) (Trapnell et al., 2009) using previously published approaches (Pauli et al., 2012; Trapnell et al., 2012). Briefly, to aid these alignments, the database of known non-redundant transcripts and EST alignments (from UCSC) were used to define an additional junction set (AJS) for each TopHat run. The junction outputs from individual TopHat runs were pooled and added to the AJS to allow TopHat to use junction information from all samples. TopHat was rerun on each sample using the resulting AJS. The output of this second run comprised the final alignment. Finally, individual sample alignments of each SC-isolated stage were pooled.
Transcriptome assembly. SC-individual stage transcriptomes were assembled with Cufflinks (version 1.2.0) by finding a parsimonious allocation of reads to the transcripts within a locus (Trapnell et al., 2012; Trapnell et al., 2010). Default settings were used.
Merging and classification of transcript fragments. The Cuffcompare program (Trapnell et al., 2012; Trapnell et al., 2010) was used to merge the individual transfrags into a combined set [non-redundant “union” of all transcript fragments that share all introns and exons], and to classify the resulting transcripts according to the known transcript annotation database into several classes.
Transcriptome quantification. The isoform-level abundances (expression level) were assessed using Cuffdiff (Trapnell et al., 2012; Trapnell et al., 2010) in Reads per kilobase of exon model per Million reads mapped (RPKM).  Expression data pre-processing. We next prepared a matrix of RPKM expression values based on the resulting transcriptome quantification with Cuffdiff. Then, expression data were log2-transformed after adding 0.05 to all RPKM values. Finally, the data were quantile normalized to reduce systematic effects and thus to allow direct comparison of the individual samples.
Genome_build: mm9
Supplementary_files_format_and_content: .bed files contain genome-wide read coverage statistics, in bedGraph format, obtained with the "genomeCoverageBed" utility in BEDTools (release 2.12.0); .gtf file contains the reconstructed transcripts obtained with cufflinks and subsequently classified with cuffcompare in the cufflinks suite of tools (release 1.2.0); .FPKM file contains the log2(FPKM) expression levels quantified with Cufflinks for each transfrag and each sample; the columns are tab-separated.

source_name: Sertoli cells

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit from Qiagen (Hombrechtikon, Switzerland) according to the manufacturer's protocol. Genomic DNA was removed by DNase treatment and confirmed by qPCR assay. RNA integrity was measured using an Agilent 2100 Bioanalyzer, and only samples with a RIN score >8.0 were advanced for library generation. Samples were then pooled to have at least 500 ng of RNA in triplicates for each stage.
500 ng total RNA was selected for poly A+ RNA isolation using Sera-Mag oligo(dT) beads (Thermo Scientific) and fragmented with the NEBNExt DNA library Prep Master Mix Set (New England BioLabs). Complementary DNA synthesis, end-repair, A-base addition, and ligation of the Illumina PCR adaptators were performed according to Illumina’s protocol. Libraries were then selected for 300-350 bp cDNA fragments on a 3.5% agarose gel and PCR-amplified using Phusion DNA polymerase (Finnzymes) for 15-18 cycles. PCR products were then purified on a 2% agarose gel and gel-extracted. Each library was quality controlled (product size and concentration) by an Agilent 2100 Bioanalyzer. Single-end libraries were sequenced as 60mers on a Genome Analyzer II flowcell according to Illumina’s protocol at depth of ~50-80 million single-end reads per library.

tag: genotype

value: Sox9-EGFP knockin mice were generated by introduction of an IRES-EGFP-pA cassette into the 3' UTR of the endogenous Sox9 gen

tag: Sex

value: Male

value: Sertoli cells

tag: tissue

value: testis

tag: age

value: 35 days


title: P35_RNA-seq_rep2


title: P18_RNA-seq_rep2

value: 18 days


title: P18_RNA-seq_rep3


title: P18_RNA-seq_rep1


title: P25_RNA-seq_rep2a

description:
Sox9-EGFP knockin mice were generated by introduction of an IRES-EGFP-pA cassette into the 3’ UTR of the endogenous Sox9 gen
Raw file Rep2a: P25_2_CGATGT_L004_R1_001.fastq.gz

value: 25 days


title: P35_RNA-seq_rep1


title: P25_RNA-seq_rep2b

description:
Sox9-EGFP knockin mice were generated by introduction of an IRES-EGFP-pA cassette into the 3’ UTR of the endogenous Sox9 gen
Raw file Rep2b = paired end file: P25_Pool_2_CGATGT_L008_R1_001.fastq.gz and P25_Pool_2_CGATGT_L008_R2_001.fastq.gz
Processed data for Sample P25_RNA-seq_rep2b have been combined with data from Sample P25_RNA-seq_rep2a and are available on the record GSM1443084.


title: P25_RNA-seq_rep3


title: P25_RNA-seq_rep1


title: P10_RNA-seq_rep2

value: 10 days


title: P10_RNA-seq_rep1


title: P5_RNA-seq_rep2

value: 5 days


title: 4  h


title: P10_RNA-seq_rep3


title: Irf8 cKO exp#1

city: Cincinnati

first: Harinder

state: OH

address: 333 Burnet Avenue

department: Immunobiology

institute: CCHMC

description:
cells were sorted by flow with B220+ FAShigh GL7high
IRF8cKO_GCBCell_RPKM_exp#1

data_processing:
Reads from LPS activated B cells were aligned to mm9 mouse genome assembly by using Tophat v2.0 (using options --no-discordant --no-novel-juncs --max-multihits 1 --no-mixed). Reads from GC B cells were aligned to mm10
Aligned reads were then used to build transcript model using cuffdiff from cufflinks v2.2 (with options --library-norm-method geometric) for LPS activated B cells. GC B cells transcript abundance  were quantified by DESeq.
All genes passing FDR criteria of 0.05 and exhibiting at least 2-fold change in expression were considered differentially expressed genes in LPS activated B cells
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values

source_name: GC B cells

growth_protocol: Naïve B cells were isolated from Irf8+/+ (wild type, WT) mice spleen and activated in vitro with 10μg/ml LPS. GC B cells were sorted from CD19cre/+ Irf8+/+ (Ctrl) or CD19cre/+ Irf8flox/flox (Irf8 cKO) mice on dpi 13 post NP-KLH immunization.

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using RNeasy Mini Kit.
For LPS activated B cells, llibraries were prepared for sequencing using TruSeq RNA Library Prep Kit v2 (Illumina) with standard protocols.For GC B cells, the small amount of total RNA were amplified with Ovation RNA-Seq System v2 (NuGEN). Then the double stranded cDNA were used to generate sequencing libraries with Nextera XT DNA Sample Preparation Kit (illumina).

value: GC B cells

value: CD19cre/+ Irf8flox/flox


title: Ctrl exp#2

description:
cells were sorted by flow with B220+ FAShigh GL7high
IRF8cKO_GCBCell_RPKM_exp#2

value: CD19cre/+ Irf8+/+


title: Irf8 cKO exp#2


title: IRF4hi* rep2

description:
cells were sorted by flow based on surface phenotype (CD138hi IgMhi, IRF4hi*)
IRF4hi.vs.IRF8hi.gene_exp

source_name: LPS actived B cells

value: LPS actived B cells


title: IRF8hi* rep1

description:
cells were sorted by flow based on surface phenotype (CD138lo IgMlo, IRF8hi*)
IRF4hi.vs.IRF8hi.gene_exp


title: IRF4hi* rep1


title: Ctrl exp#1


title: IRF8_CHIP_48hrs

data_processing:
Bowtie2 was used to align ChIPseq reads to mouse genome version mm9 for LPS activated B cells. GC B cells reads were aligned to mm9 using BWA algorithm with default settings.
Peaks were called using Homer2 with 500 bp sliding window and minimum gap of 1000 bp between peaks (options: –style factor –size 500 –minDist 1000) for LPS activated B cells. GC B cells peaks were called by MACS (p-value 1e-5).
Genome_build: mm9
Supplementary_files_format_and_content: Homer2 findPeaks output files and bed file.

growth_protocol: Naïve B cells were isolated from WT murine spleen B cells and activated in vitro with 10μg/ml LPS (Sigma).  GC B cells were sorted from WT mice on dpi 13 post NP-KLH immunization.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody
Libraries were prepared for sequencing usingTruSeq DNA LT Sample Prep Kit with standard protocols

tag: culture time

value: 48 hours

value: anti-IRF8 (Santa Cruz, C-19)


title: IRF8_CHIP_72hrs

value: 72 hours


title: IRF8_GCBcell

value: in vivo fresh cell


title: IRF4_CHIP_72hrs

value: anti-IRF4 (Santa Curz, M-17)


title: WT2

city: wuhan

first: Yanna

last: Gao

address: hongshan area, shizishan street

country: China

institute: Huazhong agricultural university

description:
FPKM.txt
Reads.txt

data_processing:
Illumina HiSeq™ 2000 used for RNA-Seq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Nicotiana tabacum K326 whole genome by Tophat.
Fragment Per Kilobase of exon model per Million mapped reads (FPKM) were calculated using a protocol from Trapnell, Cole, et al (2010).
Genome_build: Ntab-K326.  A fasta file of assembled sequences is linked as a supplementary file on the Series record.
Supplementary_files_format_and_content: tab-delimited text files include the number of FPKM and Reads values of each gene for each Sample.

organism: Nicotiana tabacum

source_name: leaf

extract_protocol:
The young primary leaf samples harvested  were frozen in liquid nitrogen and kept at -80°C until use. Total RNA was extracted using TRIzol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild-type

value: young primary leaf

tag: developmental stage

value: mature plant


title: WT1

description:
FPKM.txt
Reads.txt


title: P5_RNA-seq_rep1

value: Sox9-EGFP knockin mice were generated by introduction of an IRES-EGFP-pA cassette into the 3' UTR of the endogenous Sox9 gen

value: Male

value: Sertoli cells

value: testis


title: P5_RNA-seq_rep3

value: 5 days


title: T1

description:
FPKM.txt
Reads.txt

value: Wov transgenic


title: T2

description:
FPKM.txt
Reads.txt


title: K562_MidHU_B

city: Los Angeles

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

institute: UCLA

data_processing:
RRBS library reads from mouse and human cells were mapped to the mm9 and hg19 reference genomes, respectively, using BS-Seeker v2.0.32 (Guo et al., 2013), which called bowtie v0.12.9  (Langmead et al., 2009). Reads with adapter contamination were trimmed. The adapter sequence used for the contamination check was as follows: CGAGATCGGAAGAGCACACGTC, i.e. meCG end repair + A tail + 10.bp of Illumina adapter sequence.
Genome_build: mm9/hg19
Supplementary_files_format_and_content: CGmap files are produced by BS-Seeker2 and contain C and T counts per cytosine for both strands.
Supplementary_files_format_and_content: The format is fully described here: https://github.com/BSSeeker/BSseeker2#output-files
Supplementary_files_format_and_content: Briefly, each column of the represents the following:
Supplementary_files_format_and_content: (1) chromosome
Supplementary_files_format_and_content: (2) nucleotide on Watson (+) strand
Supplementary_files_format_and_content: (3) position
Supplementary_files_format_and_content: (4) context (CG/CHG/CHH)
Supplementary_files_format_and_content: (5) dinucleotide-context (CA/CC/CG/CT)
Supplementary_files_format_and_content: (6) methylation-level = #_of_C / (#_of_C + #_of_T)
Supplementary_files_format_and_content: (7) #_of_C (methylated C, the count of reads showing C here)
Supplementary_files_format_and_content: (8) = #_of_C + #_of_T (all Cytosines, the count of reads showing C or T here)

source_name: K562 human cells

growth_protocol: MEFs were derived at embryonic day 14.5 and cultured in MEF media (DMEM supplemented with 10% FBS, nonessential amino acids, L-glutamine, penicillin-streptomycin, β-mercaptoethanol) following standard procedures. K562 cells were purchased from ATCC and cultured in RPMI media (Gibco) with 10% FBS.  ATCC culture method suggestions were followed for expanding the cells.

extract_protocol:
Genomic DNA was isolated using the Blood and Cell Culture Mini Kit (Qiagen) with RNase A treatment (Life Technologies).
The RRBS libaries were generated at previously described by Orozco et al. with minor modifications. DNA purifications for each enzymatic reaction was carried out using AMPure XP beads (Beckman Coulter). Bisulfite conversion was performed using the Epitect kit (Qiagen) twice compared to manufacturer’s instruction to optimize the efficiency. Bisulfite-converted libraries were amplified using MyTaq Mix (Bioline) with the following program: (98° for 15 sec, 60° for 30 sec, 72° for 30 sec) 12 cycles, 72° for 5 min, 4°C storage.

treatment_protocol: MEFs at passage 1 or 2 post-derivation were seeded at a density of 6.0×104 cells per 12-well well and chemicals in MEF media and/or siRNAs in Opti-MEM media (Gibco) were added and incubated for 72 hours. K562 cells were cultured in RPMI media (Gibco) with 10% FBS then subjected to chemical treatment analogously to MEFs.

value: Hydroxyurea 0.4 mM (in 0.00004% DMSO final)


title: K562_MidHU_A


title: K562_MidAza-HU_A

value: 5-aza-2’-dC 0.1 uM AND Hydroxyurea 0.4 mM (in 0.00004% DMSO final)


title: K562_MidDMSO_A


title: K562_MidAza-HU_B


title: K562_MidAza_A

value: 5-aza-2’-dC 0.1 uM (in 0.00004% DMSO final)


title: K562_LowDMSO


title: K562_LowAza-HU

value: 5-aza-2’-dC 0.04 uM AND Hydroxyurea 0.16 mM (in 0.0001% DMSO final)


title: IRF4_CHIP_48hrs

value: LPS actived B cells

value: 48 hours


title: K562_HiDMSO


title: K562_HiAza

value: 5-aza-2’-dC 0.2 uM (in 0.0002% DMSO final)


title: K562_HiHU

value: Hydroxyurea 0.8 mM  (in 0.0002% DMSO final)


title: K562_HiAza-HU

value: 5-aza-2’-dC 0.2 uM AND  Hydroxyurea 0.8 mM  ( in 0.0002% DMSO final)


title: CTRL_EGF_NELFA_rep2

city: Miami

first: Alessandro

last: Gardini

state: FL

address: 1501 NW 10 Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

description:
molecule: genomic DNA
NELFA was profiled in a Hela cell clone upon EGF stimulation and depletion of INTS11

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
alignment (ChIPseq): bowtie 2.1.0 (end-to-end , sensitive))
alignment (RNAseq): tophat 2 (default parameters)
tag density files: RSeQC package was used to generate BigWiggle files
Genome_build: hg19
Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using RSeqQC package and the wigtobigWig script provided by UCSC.

source_name: HeLa cell line

growth_protocol: Wild-type Hela cells were cultivated in DMEM 10% FBS, starvation was performed for 48h in 0.5% FBS before EGF treatment

extract_protocol: ChIP-Seq: NEBNext ChIP-seq library kit (new England Biolabs)

treatment_protocol: Inducible cell clones were treated with doxycycline 1microgr/ml 72h before collection. EGF stimulation was performed for 20 minutes with 100ng/ml of recombinant EGF. RNA were extracted using QIAGEN Rneasy columns with on column DNAse treatment.

value: Hela cell line

value: control EGF

tag: antibody

value: IP with goat antibody sc-23599 (Santa Cruz)


title: DOX_EGF_NELFA_rep2

value: doxycyclin EGF


title: CTRL_EGF_chrom_rep2

description:
molecule: chromatin-RNA
cells were fractionated to extract the chromatin-associated fraction of RNA (Cell. 2012 Jul 20; 150(2): 279–290)

extract_protocol:
NEBNext Strand specific RNA-Seq  Sample Prep Kit (New England Biolabs, inc.)
RNA-Seq: Genomic DNA and ribosomal RNA was removed with Turbo DNA-free kit and RiboMinus Eukaryote Kit (Life Technologies).  The polyA and non-polyA fractions were isolated by running RNA samples three times through the Oligo(dT) Dynabeads (Life technologies) to ensure complete separation.  The resulting RNA fractions were subjected to strand-specific library preparation using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs
RNA-Seq: Subcellular fractionation was followed as described (Cell. 2012 Jul 20; 150(2): 279–290). The cell lysate was re-suspended in cold lysis buffer with 0.15% NP-40, and the sucrose buffer was used to isolate nuclei.  50% glycerol buffer and nuclei lysis buffer contains 1M Urea and 1% NP-40, were performed to isolate nucleoplasmic fraction and chromatin-bound RNA fraction.  Chromatin-bound RNA was isolated with Trizol protocol

value: HeLa Tet-inducible INTS11 shRNA cell clone


title: DOX_EGF_chrom_rep2


title: DOX_chrom_rep2

value: doxycyclin


title: K562_MidDMSO_B

tag: cell line


title: K562_MidAza_B

tag: treatment


title: CTRL_chrom_rep2

value: control


title: CTRL_chrom_rep1


title: CTRL_EGF_nonpolyA_rep2

description:
molecule: non polyA RNA
total RNA was ribosome-depleted and enriched for polyA or nonpolyA using Ambion (Life Tech) fractionation kit


title: DOX_EGF_chrom_rep1


title: DOX_chrom_rep1


title: CTRL_EGF_chrom_rep1


title: K562_LowHU

value: Hydroxyurea 0.16 mM (in 0.0001% DMSO final)


title: CTRL_nonpolyA_rep2


title: MEFs_LowAza-siRrm2

source_name: Mouse embryonic fibroblasts

value: Mouse embryonic fibroblasts

value: C57BL/6 x 129S4/SvJae

value: 5-aza-2’-dC 0.2 uM  AND siRNA Rrm2


title: IRF8hi* rep2


title: DOX_EGF_polyA_rep2

description:
molecule: polyA RNA
total RNA was ribosome-depleted and enriched for polyA or nonpolyA using Ambion (Life Tech) fractionation kit

molecule: polyA RNA


title: K562_LowAza

value: 5-aza-2’-dC 0.04 uM (in 0.0001% DMSO final)


title: MEFs_LowAza-Resv_B

value: 5-aza-2’-dC 0.2 uM AND  Resveratrol 20 uM


title: MEFs_LowAza-Resv_A


title: CTRL_EGF_polyA_rep2


title: MEFs_HighAza_B


title: CTRL_polyA_rep2


title: MEFs_HighAza_A


title: MEFs_siRrm2

value: siRNA Rrm2 (Ambion, 64497)


title: MEFs_Resv_B

value: Resveratrol 20 uM


title: CTRL_EGF_nonpolyA_rep1


title: CTRL_nonpolyA_rep1


title: MEFs_LowAza_B

value: 5-aza-2’-dC 0.2 uM


title: MEFs_LowAza_A


title: MEFs_Resv_A


title: DOX_EGF_polyA_rep1


title: CTRL_EGF_polyA_rep1


title: MEFs_Untreated_B

value: No treatment


title: CTRL_polyA_rep1


title: R9_WT_SN1_Sal_2_TAGCTT_L002_R1_001

city: New York

first: Venetia

last: Zachariou

state: New York

address: 1425 Madison Ave Icahn School of Medicine

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description: WT_naive_vs_WT_SNI_Sal.xlsx, WT_SNI_Sal_vs_KO_SNI_Sal.xlsx, WT_SNI Sal_vs_WT_SNI_DMI.xlsx

data_processing:
Bowtie2, version 2.1.0, parameters defaults
TopHat2, version 2.0.9, parameters --no-novel-juncs --b2-very-sensitive
Cuffdiff, version 2.1.1, parameters -b path_to/mm9.fa --multi-read-correct
Genome_build: NCBIM37
Supplementary_files_format_and_content: Spreadsheet of CuffDiff differential analysis result

source_name: Nucleus accumbens brain tissue

growth_protocol: Rgs9 wildtype and mutant mice were handled according to the animal care and use committees of the Icahn School of Medicine at Mount Sinai.

extract_protocol:
All samples were homogenized in Trizol and processed according to the manufacturer’s protocol. RNeasy Micro columns were used to further purify the RNA
Libraries were prepared according to the Illumina TruSeq RNA SamplePpreparation protocol and were sequenced on the Illumina HiSeq 2000

treatment_protocol: Chronic (15mg/kg, i.p., twice a day) administration of the tricyclic desipramine to Rgs9WT and Rgs9KO mice, that have been operated according to Spared Nerve Injury (SNI) protocol which results in the induction of neuropathic pain.

value: Saline (chronic, i.p., twice a day)

value: C57BL/6 background


title: R9_WT_naive_2_GGCTAC_L005_R1_001

description: WT_naive_vs_WT_SNI_Sal.xlsx, WT_naive_vs_KO_naive.xlsx

value: Control (naïve mice)


title: R9_WT_naive_3_CGTACG_L005_R1_001


title: DOX_EGF_K27_rep2

description:
molecule: genomic DNA
H3K27ac was profiled in a Hela cell clone upon EGF stimulation and depletion of INTS11

value: Hela cell line

value: doxycyclin EGF

value: IP with  rabbit anti-H3K27ac (Abcam ab4729, Lot:GR183919-2)


title: R9_WT_SN1_Sal_3_GTGGCC_L002_R1_001


title: DOX_K27_rep2

value: doxycyclin


title: CTRL_K27_rep2

value: control


title: R9_WT_SN1_DMI_2_TAGCTT_L001_R1_001

description: WT_SNI_DMI_vs_KO_SNI_DMI.xlsx, WT_SNI Sal_vs_WT_SNI_DMI.xlsx

value: Desipramine (chronic, i.p., twice a day)


title: R9_WT_naive_1_ACTTGA_L005_R1_001


title: R9_KO_naive_3_CGTACG_L006_R1_001

description: KO_naive_vs_KO_SNI_Sal.xlsx, WT_naive_vs_KO_naive.xlsx


title: CTRL_EGF_K27_rep2

value: control EGF


title: CTRL_EGF_NELFA_rep1

value: IP with goat antibody sc-23599 (Santa Cruz)


title: R9_WT_SN1_DMI_1_ATCACG_L001_R1_001


title: R9_WT_SN1_Sal_1_ATCACG_L002_R1_001


title: R9_KO_naive_1_ACTTGA_L006_R1_001


title: DOX_EGF_K27_rep1


title: R9_KO_naive_2_GGCTAC_L006_R1_001


title: MEFs_Untreated_A

value: Mouse embryonic fibroblasts

value: C57BL/6 x 129S4/SvJae


title: DOX_K27_rep1


title: R9_KO_SN1_Sal_3_ACTGAT_L004_R1_001

description: KO_naive_vs_KO_SNI_Sal.xlsx, KO_SNI Sal_vs_KO_SNI_DMI.xlsx, WT_SNI_Sal_vs_KO_SNI_Sal.xlsx


title: R9_KO_SN1_Sal_2_GATCAG_L004_R1_001


title: CTRL_EGF_K27_rep1


title: CTRL_K27_rep1


title: Input_IMR90_rep1

city: Illkirch

first: Anais

middle: Flore

last: Bardet

address: 1 rue Laurent Fries

institute: IGBMC

data_processing:
Basecalling was performed with the Illumina RTA 1.17.21.3 software with default parameters
Fastq files were generated with the Illumina bcl2fastq-1.8.4 software with options --use-bases-mask Y50n,I6n --fastq-cluster-count 100000000 --no-eamss
Read mapping was performed using Bowtie version 1.0.0 with parameters -v 3 -m 1 --best --strata
Bigwig files were generated by extending the reads to 150bp and calculating for each genomic position the read density normalized to one million reads in the library
Peak calling was performed using peakzilla with default parameters
Genome_build: hg19

growth_protocol: IMR90 cells (ATCC) were maintained in EMEM (Sigma M 4655) supplemented with 1% non-essential amino acids (NEAA) and 10% FBS.

extract_protocol:
Cells were cross-linked in the presence of 1% formaldehyde for 10 min at at room temperature. Crosslinking was stopped by addition of 125mM Glycine for 5 min. Cells were rinsed with 1x PBS and scraped off. Pellets were resuspended in buffer 1 (10 mM Tris (pH 8.0), 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100) and washed once buffer 2 (10 mM Tris (pH 8.0), 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl). Then cells were lysed in lysis buffer (50 mM HEPES/KOH (pH 7.5), 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% DOC, 0.1% SDS, protease inhibitors) and sonicated for 15min using a Covaris E210 (TR24-M (500035) and TR12x12 Tubes (520080), Settings: 5% duty cycle, intensity 4). 70ug of chromatin were incubated over night at 4°C with 7ul YAP antibody (Abcam, [EP1674Y] (ab52771) or 20ul TEAD1 antibody (BD Transduction LaboratoriesT (610922)), and for 2h with 25ul preblocked (tRNA, BSA) Dynabeads protein G. Beads were washed twice with  lysis buffer,  once with DOC buffer (10 mM Tris (pH 8.0), 0.25 M LiCl, 0.5% NP-40, 0.5% deoxycholate, 1 mM EDTA) and once with TE pH8.0, and bound chromatin was eluted in 1% SDS/0.1 M NaHCO3. After RNase A treatment, cross-linking was reversed by overnight incubation at 65 °C followed by proteinase K digestion. DNA was purified using the Minielute PCR purification kit (Qiagen). A sample of the input chromatin was treated in the same way to generate total input DNA. Input and ChIP-samples in duplicate were sequenced.
Libraries were prepared using the NEBNext ChIP-seq library reagent set for Illumina (New England BioLabs Inc.)  omitting the size selection step before PCR enrichment.

value: Mesothelioma cells


title: DOX_EGF_NELFA_rep1


title: R9_WT_SN1_DMI_3_GTGGCC_L001_R1_001


title: Yap1_IMR90_rep1

value: Anti-YAP1 antibody [EP1674Y]

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat.#


title: R9_KO_SN1_Sal_1_TTAGGC_L004_R1_001

tag: genotype/variation


title: Input_NCI-H2052_rep1

source_name: Mesothelioma cells

growth_protocol: NCI-H2052 malignant pleural mesothelioma were maintained in RPMI (72400, Gibco), supplemented with 10 % (v/v) fetal calf serum, 1 % (v/v) non-essential amino acids, 1 mM sodium pyruvate.

value: malignant pleural mesothelioma cells


title: R9_KO_SN1_DMI_3_ACTGAT_L003_R1_001

description: KO_SNI Sal_vs_KO_SNI_DMI.xlsx, WT_SNI_DMI_vs_KO_SNI_DMI.xlsx


title: Yap1_NCI-H2052_rep2

tag: chip antibody cat. #


title: R9_KO_SN1_DMI_2_GATCAG_L003_R1_001


title: ISC at P21 (RNA-seq)

city: Houston

first: Lanlan

last: Shen

address: 1100 Bates Ave.

institute: Baylor College of Medicine

data_processing:
Raw reads were mapped to mouse genome with bowtie (v0.12.7) and splice junction sites with Tophat (v2.0.0). The reference Mouse genome annotation file was downloaded from UCSC (http://genome.ucsc.edu/) as of August 30, 2011.
Mapping rates for all samples were between 55% and 65%.
Fragments per kilobase of exon model per million fragments mapped (FPKM) values were calculated using Cufflinks (version 2.1.1, http://cufflinks.cbcb.umd.edu).
Genome_build: mm9
Supplementary_files_format_and_content: Comma delimited FPKM values. Each row is an mRNA. The first column is the NCBI RefSeq accession name for the mRNA. The rest columns each represent a sample.

source_name: mouse colonic ISC

growth_protocol: in vivo

extract_protocol:
Qiagen ALLPREP DNA/RNA Mini kit for RNA extraction.
10ng of total RNA was used for cDNA synthesis.  First, a universal primer I with oligoT was used to get the first strand cDNA.  The free universal primer I was removed by exonulease I (Takara Bio Inc). PolyA tailing reaction was performed by Terminal Transferase (TdT) (Invitrogen). After that, a universal primer II was used to synthesize the second strand cDNA. PCR amplification was performed to enrich the dscDNA. The amplified cDNA was sized selected by running a 1% agarose gel and the fragment from 500bp-3kb was cut and purified. The gel purified fragment was sheared to 300-500bp.
The library preparation followed the standard DNA preparation protocol from Illumina. The Illumina library was quantified by picogreen assay (Invitrogen) and bioanalyzer (Agilent).  The quantified library was sequenced on Illumina Hiseq 2000 platform according to the manufacturer’s protocol.

value: colon

value: Postnatal day 21


title: R9_KO_SN1_DMI_1_TTAGGC_L003_R1_001

value: C57BL/6 background


title: differentiated epithelial cells at P21 (RNA-seq)

source_name: mouse colonic differentiated epithelium


title: differentiated epithelial cells at P0 (RNA-seq)

value: Postnatal day 0


title: Yap1_IMR90_rep2


title: differentiated epithelial cells at P21

data_processing:
Trim the adapter sequences at both ends. Top adapter: GATCGGAAGAGCACACGTCT. Bottom adapter: ACACTCTTTCCCTACACGACGCTCTTCCGATCT
Trim the low-quality tails.
Map the paired-end reads to mm9 by Bismark using bowtie 1. Paremeters: -n=2, -l=30, -e=70.
Map the unmapped reads under single-end mode by Bismark. Parameters: -n=1, -l=20.
Genome_build: mm9
Supplementary_files_format_and_content: tab-limited. 5 columns: chromosome, location, total count, methylated count, methylated/total
Supplementary_files_format_and_content: tab-separated methylation calls at each CpG site

extract_protocol:
Qiagen DNA Mini Kit was used to extract DNA
Following adapter ligation, bisulfite modification is by the EZ DNA Methylation-Direct kit (Zymo Research). The bisulfite modified DNA is amplified using adaptor-specific primers, and fragments of 200-500 bp are isolated by bead purification.
The quantity and size distribution of libraries are determined using the Pico Green fluorescence assay and the Agilent 2100 Bioanalyzer, respectively. The DNA is sequenced on the Illumina HiSeq 2000 as 100 bp paired-end reads, following the manufacturer's protocol. All libraries are individually ‘bar-coded’ for multiplexing.


title: Yap1_NCI-H2052_rep1


title: Input_SF268_rep1

source_name: SF268 glioblastoma cells

growth_protocol: SF268 cells were maintained in RPMI 1640 Medium, GlutaMAXT Supplement, 25mM HEPES (72400, Life Technologies) supplemented with 10% (v/v) fetal calf serum and 1 mM sodium pyruvate in a humidified incubator 37°C, 5% CO2 incubator.

value: Glioblastoma cells


title: H3K27ac_SF268_rep1

value: Histone H3K27ac antibody

value: Active Motif


title: Input_SF268_rep2


title: Tead1_SF268_rep1

value: BD Transduction Laboratories


title: H3K27ac_SF268_rep2


title: differentiated epithelial cells at P0


title: ISC at P0


title: Tead1_SF268_rep2


title: ISC at P21


title: Yap1_SF268_rep2


title: Yap1_SF268_rep1


title: X11pt3-3

city: Madison

first: Fahad

last: Alkhayyat

state: Wisconsin

address: 1550 linden dr.

department: Bacteriology

institute: UW Madison

data_processing:
The fastQC program was used to verify raw data quality.
The raw sequence reads were mapped to the genome using Subjunc aligner from Subread.
The alignment bam files were compared against the gene annotation GFF file, and raw counts for each gene were generated using the featureCounts tool from Subread.
The raw counts data were normalized using voom method from the R Limma package.
For transcripts assembly, Cufflinks program was used.
Genome_build: The A. nidulans FGSC4 genome and gene annotations (A_nidulans_FGSC_A4_version_s10-m03-r08_features.gff) were downloaded from AspGD.
Supplementary_files_format_and_content: A4.vs.A26_alldata.cvs: A4 DEG in reference to A26
Supplementary_files_format_and_content: x11pt3.vs.A26_alldata.cvs: x11pt3 DEG in reference to A26

organism: Aspergillus nidulans

source_name: Aspergillus nidulans ΔosaA veA1

extract_protocol:
Three biological replicates were analyzed for each strain. All strains were cultured in agitating liquid-submerged medium (vegetative growth) for 18 h, and then shifted to an air-exposed medium to induce development. All samples were collected at time point 12 h following developmental induction, total RNA was extracted usiing TRIzol kit, then submitted for library preparation and sequencing.
Strand specific library was prepared from total RNA using Illumina TruSeq Strand specific RNA sample preparation system. Briefly, mRNA was extracted from total RNA using polyA selection, followed by RNA fragmentation. Strand specific library was constructed by first-strand cDNA synthesis using random primers, followed by sample cleanup and the second-strand synthesis using DNA Polymerase I and RNase H. A single 'A' base was added to the cDNA fragments followed by ligation of the adapters. Final cDNA library was obtained by further purification and enrichment with PCR, and the quality was checked using Bioanalyzer 2100. The library was sequenced (PE100bp) using the Illumina HiSeq2500, with final of over 10 million high quality reads per sample.

value: mycelia

value: 12h post developmental induction


title: X11pt3-1


title: A26-3

source_name: Aspergillus nidulans FGSC26


title: A4-3

source_name: Aspergillus nidulans FGSC4


title: A26-1


title: A26-2


title: A4-2


title: ISC at P0 (RNA-seq)


title: A4-1


title: SlDZ3

status: Public on Aug 24 2015

city: Ann Arbor

first: John

last: Schiefelbein

state: Michigan

address: 830 North University Avenue

department: Molecular, Cellular, and Developmental Biology

institute: University of Michigan

data_processing:
Reads quality were checked by FastQC.
The first 15 bp of each read was trimmed to ensure high quality.
Reads were mapped to the mentioned reference annotation by Tophat2 with default setting.
Reads were quantified to RPKM by Cufflinks2 with default setting plus the correction for multi-read (-u)
Genome_build: see the reference that is listed in sample characteristics for each species.
Supplementary_files_format_and_content: A master tab-delimited text file (.csv)  includes RPKM values of different development zones for each gene .  There are two master sheets, one for gene expression of 3 development zones in 6 angiosperms, another for combined gene expression of elongation + differentiation zone in 7 vascular plants (6 angiosperms + selaginella).

organism: Solanum lycopersicum

source_name: Root differentiation zone

growth_protocol: Seeds were sterilized and germinated on agarose-solidified MS media under constant light at 21C.

extract_protocol:
The growing tips of the seedling primary roots were dissected along the longitudinal axis into 3 development zones.  RNA was extracted by Qiagen RNeasy Plant Mini Kit.
RNA libraries were constructed by Illumina TrueSeq kit according to manufacturer procedures.

tag: cultivar

value: Heinz 1706

tag: reference annotation used for mapping

value: Ensembl Release 19, SL2.4

value: 6 days after plating

value: root

tag: root zone

value: Root differentiation zone


title: SlDZ2


title: SlDZ1


title: SlEZ1

source_name: Root elongation zone

value: Root elongation zone


title: SlEZ2


title: SlM2

source_name: Root meristematic zone

value: Root meristematic zone


title: SlEZ3


title: SlM1


title: X11pt3-2


title: SlM3


title: ZmEZ1

organism: Zea mays

value: Ensembl Release 19, AGPv3

value: 4 days after plating


title: ZmMZ3


title: ZmMZ2


title: ZmMZ1


title: ZmDZ3


title: ZmEZ2


title: ZmDZ1


title: 10870ΔrocA

city: Reno

first: Eric

middle: W

last: Miller

state: Nevada

address: 1664 N Virginia St

department: Microbiology and Immunology

institute: University of Nevada Reno

data_processing:
CLC Genomics Workbench version 7.5.1 RNA-seq was used for basecalling and aligning the sequence reads to the MGAS315 genome (AE014174.1).  Parameters for alignment were set up:  Similar fraction=0.8, Length fraction=0.8, Mismatch cost=2, Insertion cost=3, and Deletion cost=3.  Normalization of the data was accomplished using the Kal's Z-test with FDR from the total read count.
Genome_build: AE014174.1
Supplementary_files_format_and_content: Excel files containing all coding regions from genome with raw and normalized expression values, RPKM, coding region nucleotide start and stop, Kal's Z-test calculations, and raw and normalized means.  The normalized means were used for calcuating transcript fold change between samples.

organism: Streptococcus pyogenes

source_name: Enriched mRNA

growth_protocol: All GAS strains were grown to an O.D.600 of 0.5

extract_protocol:
GAS cultures were incubated with RNAprotect™ (Qiagen) for >5 min at room temperature, pelleted and frozen at -80 °C overnight.  Cells were resuspended in RLT-BME and lysed using FastPrep Lysing Matrix B tubes (MP Biomedicals) in FastPrep-24 machine.  Samples were processed twice at speed 4 for 15 sec.  Total RNA was then isolated using miRNEasy Mini Kit (Qiagen) and eluted in nuclease-free water.  Off-column DNase treatments, using DNA-free DNase (Ambion), was performed at 37 °C.  The mRNA was then enriched using Ribo-Zero rRNA Removal Kit (Bacteria) to deplete rRNA contamination.
All cDNA libraries were constructed using ScriptSeq™ RNA-Seq Library Preparation Kit (Epicentre) and processed according to manufacturer's protocol.

tag: strains

value: Revertant strain

tag: genotype description

value: RocA deletion strain

value: RocA-


title: ZmEZ3


title: 10870::rocAM1

value: Complementation strain

value: M3 rocA gene replaced with M1 rocA gene in M3 background

tag: genotype

value: RocA+


title: opossum_FL_LS_rep2

city: La Jolla

first: Marcelo

last: Rivas

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

institute: University of California San Diego

data_processing:
Sequenced reads werepreprocessed to remove Illumina adaptors, and bases with qualities below 20 at the read's 3 prime end were trimmed. Reads from mouse, opossum, and pig were aligned using STAR (--outFilterMultimapNmax 10, --outFilterMismatchNmax 3, --outFilterScoreMin 0, --clip3pNbases 0, --clip5pNbases 0). Reads from bat were aligned using RSEM (--fragment-length-mean 425.0 --fragment-length-sd 150.0).
Gene expression (fragments per kilobase of transcript per million mapped reads, FPKM) were computed using cufflinks (for mouse, opossum, and pig) and RSEM (bat).
Genome_build: For mouse, opossum, and pig we used their corresponding Ensembl reference genomes and annotation assemblies: GRCm38 (mouse), BROADO5 (opossum), and Sscrofa10.2 (pig). For bat reads, we used as a reference a de novo assembly. In short, we merged all libraries (beginning, early, and late stages) and call a de novo transcriptome using Trinity, then from the resulting de novo transcriptome we filter out any sequence not matching the SwissProt database (blastx, e-value<1e-20).
Supplementary_files_format_and_content: Tab-delimited text files include either RSEM or CUFFLINKS gene expression FPKM values for each Sample

organism: Monodelphis domestica

extract_protocol:
Embryonic mice, opossums, bats and pigs with early (ES) or late (LS) stage forelimbs were obtained from a variety of sources. Forelimbs for the ES were harvested at Stage 14 for bat, E11 for mouse, Stage 28 for opossum and E22 for pig. For the LS, forelimbs were harvested at Stage 15 for bat, E12 for mouse, Stage 29 for opossum and E26 for pig. Limbs were removed from embryos and stored in RNALater in -20° C until further processing. RNA was extracted from tissues using E.Z.N.A. Total RNA Kit I (OMEGA bio-tek #R6834), and converted into RNASeq libraries with the Illumina TruSeq RNA Sample Preparation Kit (Illumina RS-122-2001)
Libraries were sequenced on an Illumina HiSeq 2500 housed in the Roy G. Carver Biotechnology Center at the University of Illinois.

tag: breed

value: Embryonic opossums obtained from timed matings in the breeding colonies housed in the Sears Lab at the Univ. of Illinois

tag: tissue

value: fore-limb

value: late-stage


title: MGAS10870

value: Parental/Wild-type strain

value: RocA null strain


title: opossum_FL_LS_rep3


title: opossum_FL_ES_rep5

value: early-stage


title: opossum_FL_ES_rep4


title: opossum_FL_ES_rep6


title: opossum_FL_LS_rep1


title: opossum_FL_ES_rep2


title: opossum_FL_ES_rep3


title: ZmDZ2

tag: age

value: root

value: Root differentiation zone


title: opossum_FL_ES_rep1

tag: developmental stage


title: input.DNaseI

city: Milan

first: Marco

middle: J.

last: Morelli

address: via Adamello 16

department: Center for Genomic Science of IIT@SEMM

country: Italy

institute: Istituto Italiano di Tecnologia

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v ; fastq_masker -Q33 -q 20 -r -N -v
Alignment to mm9 with bwa version 0.6.2; bwa aln -t 16 reffile fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
Significant peaks call using the Model-based Analysis of ChIP-Seq (MACS) 2.0.9, pvalue cutoff 1e-5;
Genome_build: mm9
Supplementary_files_format_and_content: bed files with enriched regions

source_name: Primary B cells

growth_protocol: Splenic B cells were isolated from 8 weeks old animal by incubation with B220 MicroBeads (Miltenyi Biotech) and enriched by magnetic cell sorting (MACS), according to the manufacturer’s instructions (Miltenyi Biotech).

extract_protocol: Libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers.

tag: strain

tag: cell type

value: B cells from spleen

value: mock


title: p53.wt.nonBcells.IR.4

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v ; fastq_masker -Q33 -q 20 -r -N -v
Read alignment with tophat 2.0.8: tophat -p 8 -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded R1.fastq R2.fastq
expression quantification with featureCounts 1.4.5 (options -T 2 -p -P) on mm9 standard gtf. Expression values, differently from regular RPKMs, were normalised to the total number of reads aligned on exons rather than library size.
Genome_build: mm9
Supplementary_files_format_and_content: text file with eRPKMs

source_name: Primary non-B cells

growth_protocol: Splenic non-B cells were isolated from 8 weeks old animal by depletion of B cells through incubation with B220 MicroBeads (Miltenyi Biotech), followed by magnetic cell sorting (MACS), according to the manufacturer’s instructions (Miltenyi Biotech).

extract_protocol:
Total RNA was purified using Trizol (Invitrogen), treated with Turbo DNase (Ambion) and purified with RNA Clean XP (Agencourt). 5 µg of purified RNA were then treated with Ribozero rRNA removal kit (Epicentre) and EtOH precipitated. RNA quality and removal of rRNA were checked with the Agilent 2100 Bioanalyzer (Agilent Technologies).
Libraries for RNA-Seq were then prepared with the TruSeq RNA Sample Prep Kits v2 (Illumina) following manufacturer instructions starting from the RNA fragmentation step.

value: non-B cells from spleen

tag: treatment

value: 4h 7Gy


title: p53.wt.Bcells.DNaseI


title: p53.wt.nonBcells.IR.3


title: p53.wt.Bcells.IR.3


title: p53.wt.nonBcells.IR.1


title: p53.wt.Bcells.IR.4


title: p53.wt.nonBcells.IR.2


title: p53.wt.Bcells.IR.1


title: pig_FL_LS

organism: Sus scrofa

value: Pig embryos obtained through timed ovulations following inseminations at the Univ. of Illinois pig farm


title: p53.wt.nonBcells.mock.4


title: pig_FL_ES


title: p53.wt.Bcells.IR.2


title: p53.wt.nonBcells.mock.2


title: Input_for_Nkx6.1_and_Olig2_chip_rep2

first: Yuichi

last: Nishi

address: 1425 San Pablo St.

department: Eli and Edythe Broad-CIRM Center for Regenerative Medicine

institute: University of Southern California

description:
Sample 13
Matching input DNA for sample 10 and 11
processed data file: Nkx61_CP33-ML2-ML17_heatmap.txt, Olig2_CP10-ML4-ML17_heatmap.txt

data_processing:
Basecalls performed using Illumina pipeline
The first 25bp of ChIP-seq reads were aligned to the unmasked mm9 genome using Eland allowing up to two mismatches (Samples 1-3, 507) or aligned against mm9 with Bowtie2 (version 2.2.4) to obtain SAM (Samples 4,8-13).
Unique reads were used to identify peaks using CisGenome peak caller in the 2-sample conditional binomial mode against matched input DNA data at FDR=0.01 cutoff
Heatmap comparison of rep1 and rep2 was performed by HOMER to generate _heatmap.txt output with the default settings.
Genome_build: mm9
Supplementary_files_format_and_content: bed files contain binding regions called in this analysis; heatmap.txt output file for heatmap comparision of rep1 and rep2

source_name: Neural progenitor cells

growth_protocol: Ventral neural progenitors were routinely generated from mouse ESCs by two days of suspension culture in DFNB (25% DMEM, 25% F12, 50% Neurobasal supplemented with 1xB27 [Life Technologies]) or DFNK (10% Knockout Serum Replacement [Life Technologies] in place of B27 in DFNB) followed by additional three days in DFNB with 500nM all-trans retinoic acid and 160-800nM Smoothened agonist (SAG, Calbiochem/EMD Millipore).

extract_protocol:
Cells were dissociated in trypsin then crosslinked in 1% formaldehyde at room-temperature for 30 minutes. Cells were lysed in lysis buffer (140mM NaCl, 0.5% NP40, 0.25% Triton-X 100, 10% glycerol, 1mM EDTA, 50mM HEPES-KOH, pH7.5) or (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) at 4˚C with agitation for 10 minutes then washed with Buffer 2 (200mM NaCl, 1mM EDTA, 0.5mM EGTA, 10mM Tris-Cl pH8.0) for 10 minutes at room-temperature. Chromatin was fragmented by sonication (Branson digital sonifier with microtip) in Buffer 3 (1mM EDTA, 0.5mM EGTA, 10mM Tris-Cl pH8.0). Lysate was cleared by centrifugation and supplemented with NaCl, NaDeoxycholate, and TritonX 100 to the final concentrations of 100mM, 0.1%, and 1%, respectively. Magnetic beads (Dynal/Invitrogen, sheep anti-mouse IgG, anti-rabbit IgG, and Protein G for mouse, rabbit, and goat antibodies, respectively) were blocked with a blocking buffer (5mg/ml BSA in PBS) then incubated with an antibody in the blocking buffer overnight. Unbound antibody was washed away by extensive wash with the blocking buffer. Beads/antibody complex was incubated with the lysate overnight at 4°C. Beads were washed 5 times with RIPA buffer (1% NP40, 0.7% NaDeoxycholate, 0.5M LiCl, 1mM EDTA, 50mM HEPES-KOH, pH7.5). DNA was eluted with elution buffer (1% SDS, 1mM EDTA, 50mM Tris-Cl, pH8.0) at 65˚C for 15 min, and the eluate was incubated further overnight at 65˚C to reverse crosslinking. DNA was purified by phenol/chloroform extraction and ethanol precipitation or by PCR purification kit (Qiagen). All buffers except RIPA buffer was supplemented with protease inhibitor cocktail mix (Roche).
Sequencing library was constructed using ChIP-Seq DNA Sample Prep Kit (Illumina IP-102-1001) according to the manufacturer's instruction. Briefly, DNA was blunted and phosphorylated with T4 and Klenow DNA polymerases and T4 PNK followed by adapter ligation with T4 DNA ligase. A range of 275-700bp was selected by gel purification and amplified with PCR primers 1.1 and 2.1 for 18 cycles (Sample 1-8).  Sequencing library was constructed using NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs, E7370) according to the manufacturer's instruction with 15 cycles of PCR amplification (Sample 9-13).

tag: strain background

value: Mixture of C57BL6/J, 129 Sv and Swiss Webster

tag: cell line

value: Rosa26-Gli1FLAG (YFP3.1 derivative)

value: ES-derived neural progenitors (ventral)

tag: chip antibody


title: Input_for_Nkx2.2chip_rep2

description:
Sample 12
Matching input DNA for sample 9
processed data file: Nkx22_CP11-ML6-ML36_heatmap.txt


title: p53.wt.Bcells.mock.3


title: Olig2_NPC_ChIP-seq_rep2

description:
Sample 11
processed data file: Olig2_CP10-ML4-ML17_heatmap.txt

value: Millipore (AB9610)


title: p53.wt.Bcells.mock.2


title: Nkx6.1_NPC_ChIP-seq_rep2

description:
Sample 10
processed data file: Nkx61_CP33-ML2-ML17_heatmap.txt

value: Cocktail of DSHB (F55A10, F55A12, F64A6B4, and F65A2), RD Systems  (AF5857) and custom (from T. Jessell)


title: p53.wt.nonBcells.mock.1


title: p53.null.nonBcells.IR.2


title: p53.wt.Bcells.mock.4


title: p53.null.nonBcells.IR.1


title: Nkx2.2_NPC_ChIP-seq_rep2

description:
Sample 9
processed data file: Nkx22_CP11-ML6-ML36_heatmap.txt

value: Cocktail of DSHB (74.5A5), Sigma (HPA003468), and custom (from T. Jessell)


title: mA2.lox.Cre_rep4

description:
mA2.lox.Cre parental cell line reference rep4
232-mA2-t60

data_processing:
Basecall was performed with the default pipeline for Illumina NextSeq
Sequence tags were aligned with the mm10 genome with STAR aligner
Differentially expressed genes were identified with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Expression values for all replicates and all analyzed genes (tab1) and fold repression values for genes repressed by at least one transgene by 2 fold

growth_protocol: mESCs were maintained in a serum free condition with CHIR99021, PD184352, and LIF on sparse feeder cells. Neural progenitors were derived by depleting feeder cells and culturing cells in suspension in neural differentiation basal medium (DFNB) for 2 days followed by 500nM all-trans retinoic acid treatment in DFNB.

extract_protocol:
NucleoSpin RNA column (Clontech)
Library was constructed with TruSeq kit (Illumina)

treatment_protocol: To activate transgene, neural progenitors were induced for 12hr with 1ug/ml doxycycline

value: ES-derived neural progenitor cells

tag: transgene


title: mA2.lox.Cre_rep5

description:
mA2.lox.Cre parental cell line reference rep5
234-mA2-t60


title: p53.wt.Bcells.mock.1


title: p53.null.Bcells.IR.2


title: p53.wt.nonBcells.mock.3


title: p53.null.nonBcells.mock.2


title: mA2.lox.Cre_rep1

description:
mA2.lox.Cre parental cell line reference rep1
210-mA2-t60


title: p53.null.Bcells.IR.1


title: iNkx6.1-P2A-Olig2_rep2

description:
Nkx6.1-P2A-Olig2 overexpression rep2
234-6pt1-O2-t60


title: iNkx6.1-P2A-Nkx2.2_rep2

description:
Nkx6.1-P2A-Nkx2.2 overexpression rep2
234-6pt1-2pt2-t60


title: iNkx6.1-P2A-Olig2_rep1

description:
Nkx6.1-P2A-Olig2 overexpression rep1
232-6pt1-O2-t60


title: p53.null.Bcells.mock.2


title: iNkx6.1-P2A-Nkx2.2_rep1

description:
Nkx6.1-P2A-Nkx2.2 overexpression rep1
232-6pt1-2pt2-t60


title: p53.null.Bcells.mock.1


title: Input

description: ChIP antibody: none

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 250 bp were incubated overnight at 65°C to reverse the crosslinks and purified.
Libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers.


title: iOlig2_rep1

description:
Olig2 overexpression rep1
214-O2-t60


title: iOlig2_rep2

description:
Olig2 overexpression rep2
215-O2-t60


title: p53.wt.nonBcells.mock

description: ChIP antibody: p53 NCL-p53-CM5p (Novocastra laboratories)

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 250 bp were immunoprecipitated using  p53 NCL-p53-CM5p (Novocastra laboratories) antibody.
Libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers.


title: p53.wt.Bcells.IR


title: iNkx2.2_rep2

description:
Nkx2.2 overexpression rep2
215-2pt2-t60


title: iNkx2.2_rep1

description:
Nkx2.2 overexpression rep1
212-2pt2-t60


title: p53.wt.Bcells.mock


title: p53.null.nonBcells.mock.1


title: YJG8: pS6-IP from 1% TMT stimulated olfactory epithelium

city: Durham

first: Hiroaki

last: Matsunami

state: NC

address: 264 CARL Building Box 3509 DUMC

department: Department of Molecular Genetics and Microbiology

institute: Duke University Medical Center

description:
pS6-IP from 1% TMT stimulated olfactory epithelium
1pTMT_litter4

data_processing:
we implemented a stepwise mapping scheme that allows reads aligned to multiple regions to be distributed proportionally to these regions based on the previous read counts from these regions (Mortazavi et al., 2008).
reads were aligned to mm10 by Bowtie with -m 20 -a, 100bp reads were trimmed to 50bp
the resulted mapping file was separated into 20 sub-files that includes reads only mapped to 1, 2, ... , 20 regions respectively. BEDTools was used to first count reads mapped to coding exons of genes using only uniquely mapped reads. Reads mapped to two regions were distributed based on read counts from uniquely mapped reads.
Genome_build: mm10
Supplementary_files_format_and_content: The first column contains gene names. The next 20 columns are read counts corresponding to the 20 iterations described above.

source_name: olfactory epithelium

extract_protocol:
homogenates of olfactory epithelium were incubated with pS6 antibody to immunoprecipitate mRNAs associated with pS6
mRNAs were reverse-transcribed into cDNA, which was then amplified and constructed into sequencing biraries using Illumina Nextera library prep kit.

treatment_protocol: mice were stiumlated withTMT or control for 1 hr.

value: post natal day 21

tag: ip antibody

value: pS6 antibody, Cell signaling, #2215


title: YJG7: pS6-IP from control olfactory epithelium

description:
pS6-IP from control olfactory epithelium
No_litter4


title: YJG6: pS6-IP from 100% TMT stimulated olfactory epithelium

description:
pS6-IP from 100% TMT stimulated olfactory epithelium
TMT_litter3


title: YJG9: pS6-IP from 100% TMT stimulated olfactory epithelium

description:
pS6-IP from 100% TMT stimulated olfactory epithelium
TMT_litter4


title: p53.null.spleen.IR

source_name: Primary splenic cells

growth_protocol: Splenic cells were isolated by by pressing the spleens through nylon cell strainers and subsequent hypotonic lysis of red blood cells.

value: spleen


title: mA2.lox.Cre_rep2

description:
mA2.lox.Cre parental cell line reference rep2
212-mA2-t60


title: Input DNA

city: Biella

first: Paola

last: Ostano

address: via Malta 3

institute: Fondazione Edo ed Elvo Tempia

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Burrows-Wheeler Aligner with default parameters
peaks were called using MACS software version 1.4 with default parameter
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated by MACS as output of the analysis

source_name: primary dermal fibroblasts

extract_protocol:
Chromatin from 10 milions fixed cells was fragmented to a size range of 100–300 bases with a Diagenode Bioruptor. Solubilized chromatin was immunoprecipitated with two different antibody against CSL. Antibody–chromatin complexes were pulled-down using protein A-sepharose, washed and then eluted. After cross-link reversal and proteinase K treatment, immunoprecipitated DNA was extracted with phenol-chloroform, ethanol precipitated, and treated with RNase.
ChIPed DNA was quantified by fluorometry on the Qubit system (Invitrogen). A total of 10 ng DNA were used for library preparation using NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina, as recommended by the manufacturer.

tag: body site

value: abdomen skin

tag: passage

tag: antibodies


title: YJG5: pS6-IP from 1% TMT stimulated olfactory epithelium

description:
pS6-IP from 1% TMT stimulated olfactory epithelium
1pTMT_litter3


title: CSL ChIPSeq_CellSignalling Ab

description: 10ul Ab / 1*10^6 cells

value: CSL (Cell Signaling RBPSUH Cat.No. 5313)


title: YJG3: pS6-IP from 100% TMT stimulated olfactory epithelium

description:
pS6-IP from 100% TMT stimulated olfactory epithelium
TMT_litter2


title: YJG2: pS6-IP from 1% TMT stimulated olfactory epithelium

description:
pS6-IP from 1% TMT stimulated olfactory epithelium
1pTMT_litter2


title: p53.wt.nonBcells.IR


title: M16_1_WT

city: Stony Brook

first: Ellen

last: Li

state: NY

address: Health Sciences Tower Level 17-080

institute: Stony Brook University

data_processing:
Fastq files were aligned to Mouse Gencode v2 using STAR 2.3.0
The read count for individual gene is processed by featureCounts
Genome_build: Gencode Release M2 (GRCm38.p2)
Supplementary_files_format_and_content: txt file contains read count

source_name: Proximal Colonic Mucosa RNA

extract_protocol:
Proximal colonic muscosal samples were quickly stored in RNAlater after euthinzation.  Total RNA and DNA were immediately extracted using TRI-Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Proximal Colonic Mucosa

value: 6 week-old

tag: genotype/variation

value: Wild-type mice


title: M18_2a_WT


title: iNkx6.1_rep1

description:
Nkx6.1 overexpression rep1
210-6pt1-t60


title: M17_1_WT


title: YJG1: pS6-IP from control olfactory epithelium

description:
pS6-IP from control olfactory epithelium
No_litter2


title: YJA10: pS6-IP from 100% TMT stimulated olfactory epithelium

description:
pS6-IP from 100% TMT stimulated olfactory epithelium
TMT_litter1


title: iNkx6.1_rep2

description:
Nkx6.1 overexpression rep2
211-6pt1-t60


title: M18_b_WT


title: M19_1_WT


title: mA2.lox.Cre_rep3

description:
mA2.lox.Cre parental cell line reference rep3
214-mA2-t60


title: M20_1_APC

value: APC Min/+


title: YJA7: pS6-IP from control olfactory epithelium

description:
pS6-IP from control olfactory epithelium
No_litter1


title: CSL ChIPSeq_HomeMade Ab

description: 5ug Ab / 1*10^6 cells

value: CSL (Eurogentech, Seraign, Belgium - Affinity purified rabbit polyclonal -Epitopes:aa 209-224, aa 426-440 )


title: M2_A_APC


title: YJG4: pS6-IP from control olfactory epithelium

description:
pS6-IP from control olfactory epithelium
No_litter3


title: M13_1_APC


title: N3_Jq1_BDNF

city: Philadelphia

first: Erica

last: Korb

state: PENNSYLVANIA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

data_processing:
RNA-seq reads were aligned to the mouse mm9 reference genome with a mouse transcriptome guide (NCBI37) using Tophat v2.0.11 Reads that mapped to the genome with two or fewer mismatches, and up to a maximum of 20 hits per read were kept.
Transcript abundances were quantified using Cufflinks v2.2.1
BDNF-induced transcripts were defined as those with FPKM >= 1 and significantly increased by BDNF treatment. Jq1-regulated transcripts were defined as those with FPKM >= 1 and significantly decreased or increased by Jq1 treatment.
Genome_build: mm9
Supplementary_files_format_and_content: cufflinks output file contains gene values for each sample seperately; gene_exp file contains cuffdiff output for all RNAseq datasets combined

source_name: Primary cortical neurons from E16.5 mice at 12 DIV

growth_protocol: Primary cortical neurons were isolated from E16.5 of C57BL/6 mice (Jackson Laboratories, Bar Harbor, ME). Briefly, cortex was dissection and cells were dissociated and plated at 1.2x10^6 cells/mL in Neurobasal media supplemented with Glutamax, penicillin/streptomycin, and B27. On day 3 additional media was added with AraC to prevent glial cell growth. Cells were grown for 12 days in vitro.

extract_protocol:
RNA was isolated from 10x10^6 neurons using the RNeasy Mini Kit (Qiagen, Gaithersburg, MD).
Samples were prepared as instructed using the TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA).
Illumina adapters #s were 1, 8, 10, 11, for N1, 2, 4, 7, 16  for N2, and 5, 6, 12, 19 for N3. Samples were grouped by biological replicate for 4/sequencing lane.

treatment_protocol: Neurons were treated with Jq1 at 250 nM or the negative enantiomer (-)Jq1 for 24 hours and then either left unstimulated or stimulated for 10 minutes with BDNF at 50ng/mL.

value: Primary cortical neurons

tag: small molecule inhibitor treatement

value: (+)Jq1 24 hours at 250nM

tag: stimulation

value: BDNF 10 minutes at 50ng/mL


title: N3_control_BDNF

value: (-)Jq1 24 hours at 250nM


title: YJA9: pS6-IP from 1% TMT stimulated olfactory epithelium

description:
pS6-IP from 1% TMT stimulated olfactory epithelium
1pTMT_litter1


title: N3_control

value: control


title: N3_Jq1


title: bat_FL_LS_rep1

organism: Carollia perspicillata

tag: breed

value: Bat embryos obtained from field collections in Trinidad

tag: tissue

value: fore-limb

value: late-stage


title: M17_2_WT

tag: age


title: M8_2_APC

tag: strain


title: M18_2b_APC


title: N2_Jq1

tag: developmental stage

tag: cell type


title: N1_Jq1


title: M10_2_APC


title: bat_FL_ES_rep1

value: early-stage


title: N1_control


title: N2_Jq1_BDNF


title: N1_control_BDNF


title: N2_control_BDNF


title: YJMi5: pS6-IP from 100% acetophenone stimulated olfactory epithelium

description:
Ac_litter1
pS6-IP from 100% acetophenone stimulated olfactory epithelium

data_processing:
we implemented a stepwise mapping scheme that allows reads aligned to multiple regions to be distributed proportionally to these regions based on the previous read counts from these regions (Mortazavi et al., 2008).
reads were aligned to mm10 by Bowtie with -m 20 -a, 100bp reads were trimmed to 50bp
the resulted mapping file was separated into 20 sub-files that includes reads only mapped to 1, 2, ... , 20 regions respectively. BEDTools was used to first count reads mapped to coding exons of genes using only uniquely mapped reads. Reads mapped to two regions were distributed based on read counts from uniquely mapped reads.
Genome_build: mm10
Supplementary_files_format_and_content: the first column contains gene names. the next 20 columns are read counts corresponding to the 20 iterations described above.

treatment_protocol: mice were stiumlated with acetophenone or control for 1 hr.

value: post natal day 21

value: pS6 antibody, Cell signaling, #2215


title: YJMi4: pS6-IP from control olfactory epithelium

description:
No_litter1
pS6-IP from control olfactory epithelium


title: OsDZ3

organism: Oryza sativa

tag: cultivar

value: Japonica

tag: reference annotation used for mapping

value: Ensembl Release 19, MSU6

value: 4 days after plating

value: root

tag: root zone

value: Root differentiation zone


title: WT3_R1

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description:
ATAC-seq
ATAC-seq in WT cells, biological replicate 1

data_processing:
raw data QC and genome alignment: All raw sequencing data was quality trimmed to a minimum phred score of 20 using trimmomatic 0.32. Alignment to reference genome mm9 was done with BWA 0.7.5; for ATAC-seq data (which was paired-end), read pairs where one pair passed quality trimming but the other did not were aligned separately and merged with the paired-end alignments.  PCR duplicates were removed using Picard MarkDuplicates and alignments with an edit distance greater than 2 to the reference, or that were mapped multiple times to the reference, were removed.
ChIP-seq peak calling: Peaks were called using Macs2 at a p-value threshold of 1e-5
ATAC-seq analysis: Read alignment positions were adjusted according to their strand: +4 bp for + strand alignments, and -5 bp for – strand alignments. Open chromatin regions were called using Zinba with a window size of 300 bp, an offset of 75 bp, and a posterior probability threshold of 0.8. For nucleosome positioning, properly paired alignments were filtered by their fragment size. Fragment sizes less than 100 bp were considered nucleosome free and replaced with a single BED region, and used as a background. Sizes between 180 and 247 bp were considered mononucleosomes and replaced with a single BED region; sizes between 315 and 473 bp were considered dinucleosomes and replaced with two BED regions, each spanning half the overall fragment length; and sizes between 558 and 615 bp were considered trinucleosomes and replaced with three BED regions, each spanning one third of the overall fragment length; the mono-, di-, and tri-nucleosome regions were concatenated and used as the nucleosome signal. The resulting BED regions were analyzed using danpos with the parameters –p 1 –a 1 –d 20 ––clonalcut 0 to identify regions enriched or depleted for nucleosomes. The ATAC-seq analysis was performed for each replicate individually, as well as on merged alignments from both replicates in each condition.
Genome_build: mm9
Supplementary_files_format_and_content: bed files: Fields are: chromosome, start, end, peak ID, -log10 p-value
Supplementary_files_format_and_content: bigWig files: treat_pileup.bw files are raw read counts. ATAC-seq bigWig files are normalized by read counts.

source_name: small pre-B cells

growth_protocol: Primary small pre-B cells (Lin-B220+CD43-IgM-FSClow) were isolated from WT and Brwd1-Mut mice bone marrow by flow sorting.

extract_protocol:
The DNA for ChIP-Seq libraries was purified by Qiagen PCR Purification Kit and the ATAC-Seq libraries were purified using a Qiagen PCR cleanup kit.
For ChIP-Seq DNA libraries were prepared from the sheared chromatin (200–600 bp) by University of Chicago sore facility at Institute for Genomics and Systems Biology, Department of Human Genetics. For ATAC-Seq, following purification of transposed DNA, we amplified library fragments using Nextera PCR Primers (Illumina Nextera Index kit) and NEBnext PCR master mix (New England lab, 0541) for a total of 10-12 cycles. The libraries were then purified using a Qiagen PCR cleanup kit.

treatment_protocol: Chromatin from flow sorted primary small pre-B cells (40-70×106) was used for each ChIP experiment with anti-H3K9Ac, anti-H3S10pK14Ac and anti-Brwd1 antibodies. Briefly, A ChIP assay kit was used according to the manufacturer’s instructions (Millipore 17-295) (Mandal et al., 2011). Samples were immunoprecipitated with anti-H3K9Ac (Millipore 06-942, Lot#2279810), anti-H3S10pK14Ac (Millipore 07-081, Lot#2200929) and anti-Brwd1 (E-15; sc-83517, Lot#J1508) antibodies. ATAC-Seq was performed as recently described (Buenrostro et al., 2013). Briefly, flow-sorted small pre-B cells (1x105) from WT and Brwd1mut mice were used for each ATAC-seq. To prepare nuclei, cells were centrifuged at 500g for 5 min, which was followed by a wash with ice cold  PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge. Supernatant was carefully pipetted away from the pellet after centrifugations. Immediately following the nuclei prep, the pellet was resuspended in the transposase reaction mix (25 μL 2X Tagment buffer, 2.5 μL Tagment DNA enzyme (Illumina, FC-121-1030) and 22.5 μL nuclease-free water). The transposition reaction was carried out at 37 °C for 30 min. Directly following transposition the sample was purified using a Qiagen MinElute kit.

tag: strain background

value: wild-type


title: Mut6_R1

description:
ATAC-seq
ATAC-seq in Pro-B -/- cells, biological replicate 2


title: Input_replicate2

description: Input DNA, biological replicate 2


title: WT4_R1

description:
ATAC-seq
ATAC-seq in WT cells, biological replicate 2


title: OsDZ1


title: Input_replicate1

description: Input DNA, biological replicate 1


title: N2_control

value: Primary cortical neurons


title: OsDZ2


title: OsEZ3

value: Root elongation zone


title: N1_Jq1_BDNF

value: (+)Jq1 24 hours at 250nM

value: BDNF 10 minutes at 50ng/mL


title: bat_FL_LS_rep2


title: H3K9Ac_replicate2

description: H3K9Ac ChIP-seq, biological replicate 2

tag: antibody vendor/catalog/lot


title: H3S10pK14Ac_replicate1

description: H3S10pK14Ac ChIP-seq, biological replicate 1


title: H3S10pK14Ac_replicate2

description: H3S10pK14Ac ChIP-seq, biological replicate 2


title: bat_FL_ES_rep2


title: OsEZ1


title: Gli3FLAG_NPC_ChIP-seq

description: Sample 4

growth_protocol: Ventral neural progenitors were routinely generated from mouse ESCs by two days of suspension culture in DFNB (25% DMEM, 25% F12, 50% Neurobasal supplemented with 1xB27 [Life Technologies]) or DFNK (10% Knockout Serum Replacement [Life Technologies] in place of B27 in DFNB) followed by additional three days in DFNB with 500nM all-trans retinoic acid and 160-800nM Smoothened agonist (SAG, Calbiochem/EMD Millipore).  To obtain dorsal characteristics in Gli3 profiling, SAG was omitted from the induction formula.

extract_protocol:
Cells were dissociated in trypsin then crosslinked in 1% formaldehyde at room-temperature for 30 minutes. Cells were lysed in lysis buffer (140mM NaCl, 0.5% NP40, 0.25% Triton-X 100, 10% glycerol, 1mM EDTA, 50mM HEPES-KOH, pH7.5) or (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) at 4˚C with agitation for 10 minutes then washed with Buffer 2 (200mM NaCl, 1mM EDTA, 0.5mM EGTA, 10mM Tris-Cl pH8.0) for 10 minutes at room-temperature. Chromatin was fragmented by sonication (Branson digital sonifier with microtip) in Buffer 3 (1mM EDTA, 0.5mM EGTA, 10mM Tris-Cl pH8.0). Lysate was cleared by centrifugation and supplemented with NaCl, NaDeoxycholate, and TritonX 100 to the final concentrations of 100mM, 0.1%, and 1%, respectively. Magnetic beads (Dynal/Invitrogen, sheep anti-mouse IgG, anti-rabbit IgG, and Protein G for mouse, rabbit, and goat antibodies, respectively) were blocked with a blocking buffer (5mg/ml BSA in PBS) then incubated with an antibody in the blocking buffer overnight. Unbound antibody was washed away by extensive wash with the blocking buffer. Beads/antibody complex was incubated with the lysate overnight at 4°C. Beads were washed 5 times with RIPA buffer (1% NP40, 0.7% NaDeoxycholate, 0.5M LiCl, 1mM EDTA, 50mM HEPES-KOH, pH7.5). DNA was eluted with elution buffer (1% SDS, 1mM EDTA, 50mM Tris-Cl, pH8.0) at 65˚C for 15 min, and the eluate was incubated further overnight at 65˚C to reverse crosslinking. DNA was purified by phenol/chloroform extraction and ethanol precipitation or by PCR purification kit (Qiagen). All buffers except RIPA buffer was supplemented with protease inhibitor cocktail mix (Roche).
Sequencing library was constructed using ChIP-Seq DNA Sample Prep Kit (Illumina IP-102-1001) according to the manufacturer's instruction. Briefly, DNA was blunted and phosphorylated with T4 and Klenow DNA polymerases and T4 PNK followed by adapter ligation with T4 DNA ligase. A range of 275-700bp was selected by gel purification and amplified with PCR primers 1.1 and 2.1 for 18 cycles.

value: 3xFLAG-Avi tag insertion at Gli3 initiation codon in V6.5

value: ES-derived neural progenitors (dorsal)

tag: chip antibody

value: anti-FLAG M2 clone

tag: chip antibody vendor

value: Sigma


title: GmDZ1

organism: Glycine max

value: Williams 82

value: Ensembl Release 19, v1


title: GmDZ2


title: OsEZ2


title: Brwd1_replicate1

description: Brwd1 ChIP-seq, biological replicate 1

tag: antibodies


title: YJA6: pS6-IP from 1% acetophenone stimulated olfactory epithelium

description:
1pAc_litter5
pS6-IP from 1% acetophenone stimulated olfactory epithelium

value: post natal day 21

tag: ip antibody

value: pS6 antibody, Cell signaling, #2215


title: H3K9Ac_replicate1

description: H3K9Ac ChIP-seq, biological replicate 1


title: GmEZ3


title: Mut5_R1

description:
ATAC-seq
ATAC-seq in Pro-B -/- cells, biological replicate 1

tag: genotype/variation


title: YJA4: pS6-IP from control olfactory epithelium

description:
No_litter5
pS6-IP from control olfactory epithelium


title: OsMZ3

value: Japonica

value: Ensembl Release 19, MSU6

value: Root meristematic zone


title: GmDZ3

value: 4 days after plating

value: root

value: Root differentiation zone


title: OsMZ2


title: YJA3: pS6-IP from 1% acetophenone stimulated olfactory epithelium

description:
1pAc_litter4
pS6-IP from 1% acetophenone stimulated olfactory epithelium


title: OsMZ1


title: YJ4: pS6-IP from 1% acetophenone stimulated olfactory epithelium

description:
1pAc_litter3
pS6-IP from 1% acetophenone stimulated olfactory epithelium


title: GmEZ2

value: Root elongation zone


title: GmEZ1


title: mouse_FL_LS_rep3

value: Embryonic mice obtained from timed matings in the breeding colonies housed in the Sears Lab at the Univ. of Illinois

value: fore-limb

value: late-stage


title: Brwd1_replicate2

description: Brwd1 ChIP-seq, biological replicate 2


title: YJA1: pS6-IP from control olfactory epithelium

description:
No_litter4
pS6-IP from control olfactory epithelium


title: YJ3: pS6-IP from control olfactory epithelium

description:
No_litter3
pS6-IP from control olfactory epithelium


title: YJ2: pS6-IP from 100% acetophenone stimulated olfactory epithelium

description:
Ac_litter2
pS6-IP from 100% acetophenone stimulated olfactory epithelium


title: input_for_Gli3chip

description: Matching input DNA for sample 4

value: 3xFLAG-Avi tag insertion at Gli3 initiation codon in V6.5

value: ES-derived neural progenitors (dorsal)


title: mouse_FL_LS_rep2


title: YJ1: pS6-IP from control olfactory epithelium

description:
No_litter2
pS6-IP from control olfactory epithelium


title: GmMZ1


title: GmMZ2


title: mouse_FL_LS_rep1


title: PTC16 - small RNAseq

city: Heidelberg

first: Javier

last: Perales-Paton

state: Baden-Württemberg

address: Im Neuenheimer Feld 267

department: Faculty of Medicine

institute: Heidelberg University

description: Second data set. Patient #16 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data

data_processing:
small RNAseq. STEP: Preprocessing. Illumina Small-RNA Adapter sequences were removed from raw reads using cutadapt software (v1.2.1), retrieving reads with lenghts from 17nt to 34 nt.
small RNAseq. STEP: Alignment. Remaining reads were aligned against human genome (hg19) using Bowtie algorithm (v.0.12.7; parameters: -n 0 -l 17 –best).
RNAseq. STEP: Alignment. Reads were aligned against human genome (hg19) using TopHat algorithm (v.2.0.4; parameters: --bowtie --segment-length 20 --genome-read-mismatches 2 –read-mismatches 2 --segment-mismatches 1 --max-multihits 5 --library-type fr-firststrand )
STEP: Counting tags. Counts of mapped reads in genomic locations (microRNA/exons respectively) were obtained using Htseq-count software (v0.5.4; intersection-nonempty mode; hg19 and miRBase v20)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each microRNA/gene for (Htseq-count output).

source_name: Thyroid tumor tissue

extract_protocol:
Surgically removed tissues were quickly frozen in liquid nitrogen until analysis. The samples were snap frozen on dry ice and stored at -80°C. Total RNA was extracted with TRIzol solution (Invitrogen), and the integrity of RNA was assessed using an Agilent BioAnalyzer 2100 (Agilent Technologies). All samples were collected with the informed consent of the patients and the experiments were approved by the Hospital Research Ethics Committee at Hospital Universitario La Paz.
Illumina® TruSeq® Small RNA & Illumina® TruSeq® Stranded mRNA

value: Thyroid tumor

tag: diagnosis

value: Papillary Thyroid Carcinoma

tag: sequenced molecule

value: small RNA


title: PTC15 - small RNAseq

description: Second data set. Patient #15 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data

tag: tissue


title: mouse_FL_ES_rep2

tag: breed

value: early-stage


title: PTC14 - small RNAseq

description: Second data set. Patient #14 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data


title: YJ6: pS6-IP from 100% acetophenone stimulated olfactory epithelium

description:
Ac_litter3
pS6-IP from 100% acetophenone stimulated olfactory epithelium

tag: strain

value: post natal day 21

value: pS6 antibody, Cell signaling, #2215


title: mouse_FL_ES_rep1

tag: developmental stage


title: PTC12 - small RNAseq

description: Second data set. Patient #12 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data


title: GmMZ3

value: Williams 82

value: Ensembl Release 19, v1

tag: age


title: HDF si-CSL_1

data_processing:
trimming: Trimmomatic v.0.22
alignment: TopHat v.2.0.8b
expression levels: HTSeq package, release 0.5.4p1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene expression values (expressed in count) for each Sample

source_name: HDF si-CSL

extract_protocol:
Total RNA was extracted using the directZol RNA miniprep kit (Zymo Research) with on-column DNase treatment. RNA quality was verified on the bioanalyzer (Agilent) with RIN > 8
Four ug of total RNA were used for library preparation using the Truseq kit (Illumina)

value: abdomen skin

tag: cell type

value: primary dermal fibroblasts

tag: passage

tag: transfected with

value: siRNA against CSL


title: PTC13 - small RNAseq

description: Second data set. Patient #13 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data


title: HDF si-CSL_2


title: PTC11 - small RNAseq

description: Second data set. Patient #11 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data


title: HDF si-CTRL

source_name: HDF si-CTRL

value: control siRNA


title: PTC10 - small RNAseq

description: Second data set. Patient #10 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data


title: PTC9 - small RNAseq

description: Second data set. Patient #9 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data


title: NTH8 - RNAseq

description: Patient #8 – Normal Thyroid tissue (NTH). RNAseq data

data_processing:
RNAseq. STEP: Alignment. Reads were aligned against human genome (hg19) using TopHat algorithm (v.2.0.4; parameters: --bowtie --segment-length 20 --genome-read-mismatches 2 –read-mismatches 2 --segment-mismatches 1 --max-multihits 5 --library-type fr-firststrand )
STEP: Counting tags. Counts of mapped reads in genomic locations (microRNA/exons respectively) were obtained using Htseq-count software (v0.5.4; intersection-nonempty mode; hg19 and miRBase v20)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each microRNA/gene for (Htseq-count output).

source_name: Normal Thyroid tissue

value: Normal Thyroid

value: mRNA


title: AtDZ3

organism: Arabidopsis thaliana

source_name: Root differentiation zone

extract_protocol:
The growing tips of the seedling primary roots were dissected along the longitudinal axis into 3 development zones.  RNA was extracted by Qiagen RNeasy Plant Mini Kit.
RNA libraries were constructed by Illumina TrueSeq kit according to manufacturer procedures.

tag: cultivar

value: Columbia

tag: reference annotation used for mapping

value: Ensembl Release 19, TAIR10

value: 4 days after plating

value: root

tag: root zone

value: Root differentiation zone


title: NTH7 - RNAseq

description: Patient #7 – Normal Thyroid tissue (NTH). RNAseq data

value: Papillary Thyroid Carcinoma


title: NTH5 - RNAseq

description: Patient #5 – Normal Thyroid tissue (NTH). RNAseq data


title: PTC17 - small RNAseq

description: Second data set. Patient #17 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data

value: Thyroid tumor

value: small RNA


title: AtDZ2


title: AtDZ1


title: NTH4 - RNAseq

description: Patient #4 – Normal Thyroid tissue (NTH). RNAseq data


title: NTH3 - RNAseq

description: Patient #3 – Normal Thyroid tissue (NTH). RNAseq data


title: NTH2 - RNAseq

description: Patient #2 – Normal Thyroid tissue (NTH). RNAseq data


title: AtEZ3

source_name: Root elongation zone

value: Root elongation zone


title: AtEZ2


title: NTH1 - RNAseq

description: Patient #1 – Normal Thyroid tissue (NTH). RNAseq data


title: PTC7 - RNAseq

description: Patient #7 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data


title: PTC8 - RNAseq

description: Patient #8 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data


title: PTC5 - RNAseq

description: Patient #5 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data


title: AtMZ3

source_name: Root meristematic zone

value: Root meristematic zone


title: PTC4 - RNAseq

description: Patient #4 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data


title: AtMZ1


title: AtMZ2


title: PTC1 - RNAseq

description: Patient #1 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data


title: PTC2 - RNAseq

description: Patient #2 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data


title: AtEZ1


title: CK

city: Nanning

first: Ying

last: Hu

address: Daxue

institute: Guangxi University

data_processing:
assembling: Trinity software(version: v2012-10-05)
annotation: NCBI blast 2.2.28+, Blast2GO v2.5
expression analysis: RSEM software
Genome_build: The unigene.fasta file containing all assembled sequences is linked as a supplementary file on the Series record.
Supplementary_files_format_and_content: Read counts

organism: Pinus massoniana

source_name: poor insect resistance

growth_protocol: Tender leaves, tender stems, old leaves and old stems

extract_protocol:
libraries were prepared according to a version of Illumina HiSeq2000's mRNA-Seq protocol adapted for small sample inputs
The sequence data were assembled using Trinity software (version: v2012-10-05; parameter settings: min_kmer_cov was set to 2; other parameters used the default values)

treatment_protocol: strain insect-resistant and poor insect resistance Pinus massoniana

tag: insect resistance

value: poorly resistant