title: Unassigned reads III

description: This Sample is a placeholder for runs containing unassigned reads. See the GSM1272338_README_unassigned_reads_info.txt.gz and GSE52596_barcode_info.txt.gz supplementary files.

data_processing:
Library strategy: Tag-Seq
Illumina Casava1.7 software used for basecalling.
Illumina sequence library is quality filtered using FASTX Toolkit 0.0.13 with parameters -q20 and -p50 and reads containing "N" are discarded.
EXPRSS libraries are separated using perfect match to the barcode (at 5' end). Each sub-library is quality filtered (-q20 and -p50) and artifact filtered using FASTX-toolkit.
Quality filtered library was aligned to the Arabidopsis thaliana Col-0 genome sequences (TAIR10) using Bowtie version 0.12.8 (-a -m 10 --best --strata) and selected reads with up to 10 reportable alignments. Unaligned reads from previous step are used to align to transcript sequences of Arabidopsis using Novoalign V2.08.03 (-s 1 -r A 100), since reads are from No-0 background. Tag to gene association is carried out using following considerations. Reads aligning in sense orientation with in each gene limits are assigned to that gene. A read aligning to all splice variant of a gene is counted once, and the reads uniquely aligning to various splice variants of a gene are pooled. Reads aligning to genes with overlapping gene limits are split equally between them. Reads aligning to more than 10 genes are discarded. Reads aligning to up to 10 genes are split equally between them. Reads aligning on the anti-sense strand of any gene are tested for if the read falls within 500bp from 3' end of another gene in sense direction. Otherwise reads are assigned as antisense tags for the specific gene. The tag assignment process was implemented in perl and scripts are available on request. Differential expression analysis was performed using the R statistical language version 2.15.3 with the Bioconductor package baySeq version 1.12.0 using 10000 iterations to estimate empirical distribution on the parameters of the Negative Binomial distribution.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files containing each genes tag counts for individual samples.

source_name: Leaf

growth_protocol: Arabidopsis thaliana (No-0 and slh1) plants were grown in short day conditions (10 h light / 14 h dark) for 4 weeks at 28°C after germination on MS plate.

extract_protocol:
Total RNA was extracted using the TRI reagent (Sigma) and 1-Bromo-3-chloropropane (Sigma), as per manufacturer's guidelines. RNA was precipitated with half volume of isopropanol and half volume of high salt precipitation buffer (0.8 M sodium citrate and 1.2 M sodium chloride). RNA samples were treated with DNaseI (Roche) according to the manufacturer's recommendation and phenol/chloroform extracted and ethanol precipitated.
Typically, 5 µg of total RNA was used to generate first strand cDNA using a oligo(dT) primer comprising P7 sequence of Ilumina flowcell. Double strand cDNA is synthesized as described previously [Okayama & Berg, Molecular and cellular biology 1982, 2:161-170]. Purified cDNA is subjected to Covaris shearing to a target size of 200bp (parameters: Intensity - 5, Duty cycle - 20%, Cycles/Burst - 200, Duration - 90seconds). End repairing and A-tailing of sheared cDNA is carried out as described by Illumina. Y-shaped adapters are ligated to A-tailed DNA and subjected to size selection on 1X TAE agarose gel. The gel-extracted library is PCR enriched and quantified using qPCR with previously sequenced similar size range Illumina library.

treatment_protocol: Arabidopsis No-0 and slh1 plants were grown for 4 weeks at 28°C after germination on MS plate. Plants were transferred to 21°C growth chamber at the beginning of the light cycle and samples were harvested at 0h, 6 h, 9 h and 24 h after transfer for total RNA extraction.

value: Nossen (No-0)

value: wild type, slh1

value: leaf

value: 4 weeks


title: slh1_24hr

status: Public on Jun 20 2014

type: SRA

city: Norwich

first: Ghanasyam

last: Rallapalli

address: Norwich Research Park

country: United Kingdom

institute: The Sainsbury Laboratory

library_source: transcriptomic

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Leaf, slh1, 24hr

tag: ecotype

tag: genotype/variation

tag: tissue

tag: age

tag: treatment

value: 21 °C

tag: timepoint

value: 24 h at 21°C


title: slh1_00hr

source_name: Leaf, slh1, 00hr

value: 28 °C

value: 00 h at 21°C


title: slh1_06hr

source_name: Leaf, slh1, 06hr

value: 06 h at 21°C


title: No-0_09hr

source_name: Leaf, wild type, 09hr

value: wild type

value: 09 h at 21°C


title: No-0_24hr

source_name: Leaf, wild type, 24hr


title: Input DNA Control

status: Public on Jun 19 2014

city: London

first: Fred

last: Dick

state: ON

address: Cancer Research Labs 790 Commissioners Road East

country: Canada

institute: Western University

library_source: genomic

data_processing:
Basecalls were performed using the Illumina pipeline 1.8.1.
In order to only align reads that were unique to the genome, ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie 1.0 using the parameters -S --best -m 1 --chunkmbs 500 -p 24 -t --un  --max. For all alignment steps, R1 and R2 reads were aligned seperately (i.e. as if they were single-end reads and not paired-end reads)
All remaining reads (those that were unaligned or aligned multiple places in the genome) were mapped to custom-made repeat indexes containing previously reported repeat instances (Day et al. 2010), as well as repeats from Repbase and Tandem Repeats Database. This was done using Bowtie 1.0 and the parameters -S --best -k 1  --chunkmbs 500 -p 24 -t --un
Reads that were still unaligned were re-mapped to the mm9 genome assembly using Bowtie 1.0 using the parameters -S --best -k 1  --chunkmbs 500 -p 24 -t --un
Peaks were called for the reads that aligned to the unique genome the first time using MACS version 1.4.2. The input DNA alignment file was used as the control ("-c" parameter), and other parameters used were -g mm -B -S --call-subpeaks. The "--call-subpeaks" option used PeakSplitter version 1.
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph files contain only "R2" reads that were aligned during the first alignment step to the mm9 genome. Bed files contain peaks that were found in each sample using the MACS data processing step, and only "R2" aligned reads. Scores represent -10log(pvalue).

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse embryonic fibroblasts

growth_protocol: Primary mouse embryonic fibroblasts were prepared and cultured using previously reported methods (Hurford et al. 1997).

extract_protocol:
ChIP was performed as previously described (Thillainadesan et al. 2008) using an antibody for CAP-D3.
Ths library was built using the NEB ChIP-Seq Library Prep kit for the Illumina platform. Through the use of Illumina v3 chemistry, sequencing of the library was then performed on a lane of an Illumina HiSeq 2500 instrument using the multiplex paired end protocol (2x100-bases).

tag: cell type

value: Mouse embryonic fibroblasts

tag: passage

value: Proliferating passage 4

tag: chip antibody


title: RbΔL/ΔL CAP-D3 ChIP-Seq


title: No-0_06hr

source_name: Leaf, wild type, 06hr


title: No-0_00hr

source_name: Leaf, wild type, 00hr


title: EXPRSS_Col-0_1hr_water_BioRep4

description:
Tag-seq
Barcode sequence: TTGGAT
Barcode position: 5' end of the read

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina sequence library is quality filtered using FASTX Toolkit 0.0.13 with parameters -q20 and -p50 and reads containing “N” are discarded. Read qualities are converted from Illumina fastq to sanger fastq format
EXPRSS:  EXPRSS libraries are separated using perfect match to the barcode (at 5' end). Each sub-library is quality filtered (-q20 and -p50) and artefact filtered using FASTX-toolkit.
NlaIII-DGE:  For NlaIII-DGE, FASTX Toolkit fastx_clipper is used to trim 3’ adapter sequence (parameters used -a TCGTATGCCGTCTTC -l 18 –c) and libraries are separated using barcodes (at 3' end) allowing up to 1 mismatch. Each sub-library is quality filtered (-q20 and -p50) and artefact filtered using FASTX-toolkit. For NlaIII-DGE libraires NlaIII recognition site (CATG) was added at 5’ end of each tag sequence and “FFFF” as fastq quality.
Quality filtered library was aligned to the Arabidopsis thaliana Col-0 genome sequences (TAIR10) using Bowtie version 0.12.8 (-a -m 10 --best --strata) and selected reads with up to 10 reportable alignments. Unaligned reads from previous step are used to align to transcript sequences of Arabidopsis using Bowtie version 0.12.8 (-a -m 100 --best --strata). Tag to gene association is carried out using following considerations. Reads aligning in sense orientation with in each gene limits are assigned to that gene. A read aligning to all splice variant of a gene is counted once, and the reads uniquely aligning to various splice variants of a gene are pooled. Reads aligning to genes with overlapping gene limits are split equally between them. Reads aligning to more than 10 genes are discarded. Reads aligning to up to 10 genes are split equally between them. Reads aligning on the anti-sense strand of any gene are tested for if the read falls within 500bp from 3’ end of another gene in sense direction. Otherwise reads are assigned as antisense tags for the specific gene. The tag assignment process was implemented in perl and scripts are available on request. Differential expression analysis was performed using the R statistical language version 2.15.3 with the Bioconductor package baySeq version 1.12.0 using 10000 iterations to estimate empirical distribution on the parameters of the Negative Binomial distribution
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files containing each genes tag counts for individual samples

source_name: Leaf discs

growth_protocol: Arabidopsis thaliana (Col-0) plants were grown under short-day conditions (8 hr light/16 hr dark cycles).

extract_protocol:
Typically 5 µg of total RNA was used to generate first strand cDNA using a oligo(dT) primer comprising P7 sequence of Ilumina flowcell. Double strand cDNA is synthesized as described previously [Okayama & Berg, Molecular and cellular biology 1982, 2:161-170]. Purified cDNA is subjected to Covaris shearing to a target size of 200bp (parameters: Intensity – 5, Duty cycle – 20%, Cycles/Burst – 200, Duration – 90seconds). End repairing and A-tailing of sheared cDNA is carried out as described by Illumina. Y-shaped adapters are ligated to A-tailed DNA and subjected to size selection on 1X TAE agarose gel. The gel-extracted library is PCR enriched and quantified using qPCR with previously sequenced similar size range Illumina library
Total RNA was extracted using the TRI reagent (Sigma) and 1-Bromo-3-chloropropane (Sigma), as per manufacturer’s guidelines. RNA was precipitated with half volume of isopropanol and half volume of high salt precipitation buffer (0.8 M sodium citrate and 1.2 M sodium chloride). RNA samples were treated with DNaseI (Roche) according to the manufacturer’s recommendation and phenol/chloroform extracted and ethanol precipitated.

treatment_protocol: Leaf discs from 5-week-old Col-0 plants were prepared 2 hours after start of light period and vacuum-infiltrated with water for 1 min. Leaf discs were placed in water in 50 mm petri dishes and left in the same growing conditions for ~20 h. A day after leaf disc generation the water in the petri dishes was replaced with water or 100 nm flg22 and samples were harvested 1 h after incubation.

value: Columbia (Col-0)

value: Leaf

value: 5 weeks old

value: water


title: Rb+/+ CAP-D3 ChIP-Seq


title: Rb+/+ ChIP-Seq

description: Sample 2

data_processing:
Basecalls were performed using the Illumina pipeline 1.8.1.
In order to only align reads that were unique to the genome, ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie 1.0 using the parameters -S --best -m 1 --chunkmbs 500 -p 24 -t --un  --max. For all alignment steps, R1 and R2 reads were aligned seperately (i.e. as if they were single-end reads and not paired-end reads)
All remaining reads (those that were unaligned or aligned multiple places in the genome) were mapped to custom-made repeat indexes containing previously reported repeat instances (Day et al. 2010), as well as repeats from Repbase and Tandem Repeats Database. This was done using Bowtie 1.0 and the parameters -S --best -k 1  --chunkmbs 500 -p 24 -t --un
Reads that were still unaligned were re-mapped to the mm9 genome assembly using Bowtie 1.0 using the parameters -S --best -k 1  --chunkmbs 500 -p 24 -t --un
Peaks were called for the reads that aligned to the unique genome the first time using MACS version 1.4.2. The input DNA alignment file was used as the control ("-c" parameter), and other parameters used were -g mm -B -S --call-subpeaks. The "--call-subpeaks" option used PeakSplitter version 1.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files contain the number of reads that aligned to various elements in the genome after completing all Bowtie alignments. These numbers are only for alignments of reads from "R2" files for each of the samples. The first text file of each sample (labelled with "all") shows the breakdown of all aligned reads, whereas the second text file (labelled "satellites") shows a more in-depth look of only the reads that aligned to satellite elements. Reads and alignments were sorted in accordance to Repbase data. Bed files contain peaks that were found in each sample using the MACS data processing step, and only "R2" aligned reads. Scores represent -10log(pvalue).

extract_protocol:
ChIP was performed as previously described (Thillainadesan et al. 2008) using an antibody for γH2AX.
Ths library was built using the NEB ChIP-Seq Library Prep kit for the Illumina platform. Through the use of Illumina v3 chemistry, sequencing of the library was then performed on a lane of an Illumina HiSeq 2500 instrument using the multiplex paired end protocol (2x100-bases).

value: embryonic fibroblasts

value: γH2AX (Millipore, Catalog# 05-636, Lot# 2116620)


title: RbΔL/+ ChIP-Seq

description: Sample 3

value: Rb ΔL/+


title: RbΔL/ΔL ChIP-Seq

description: Sample 4

value: Rb ΔL/ΔL


title: Rb-/- ChIP-Seq

description: Sample 5


title: KIT_AGSC

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
Basecalls performed using CASAVA
Sequenced reads were mapped to mm9 whole genome using tophat version 1.4.1 with parameters : -p 8 --splice-mismatches 1  --segment-mismatches 2 --solexa1.3-quals
FPKM and differential expression were calculated using the Cufflinks suite version 2.1.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Testis

extract_protocol:
Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit (Cat # 80004), ribosomal RNA was depleted using RiboZero kit.
Directional RNA library was prepared according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.

value: Spermatogonia

value: testis

tag: strain

value: postnatal week 8


title: THY1_AGSC


title: Input DNA

description: Sample 1


title: LPS_120min

city: Mannheim

first: Johanna

middle: Daniela

last: Schott

address: Franz-Volhard-Straße 6

department: Mannheim Institute for Innate Immunoscience

country: Germany

institute: Heidelberg University

description: RNA from RAW264.7 cells 120 min after LPS stimulation

data_processing:
Basecalling with CASAVA v1.8.2
Mapping to the mouse RefSeq transcriptome as downloaded from the UCSC Genome Browser mm10 refGene table on February 5, 2013.
Reads were summarized for genes with a in-house developed Perl script by counting each read only once per gene and ignoring reads that would map to isoforms of more than one gene (as defined by a common genesymbol).
Differential abundance was tested for with the Bioconductor package DESeq v1.10.1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Tab-delimited text file that contains, for each sample and gene, the read count that was obtained as described.

source_name: RAW264.7 cells, LPS_120min

growth_protocol: RAW264.7 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (PAA Laboratories), 2 mM L-glutamine, 100 U/ml penicillin and 0.1 mg/ml streptomycin (all PAN Biotech) at 37°C in 5% CO2.

extract_protocol:
RNA was purified with the EURx GeneMATRIX universal RNA purification kit, including a DNase on-column digestion.
RNA libraries were prepared for sequencing using the NEBNext Ultra Directional RNA Library Prep Kit after ribosomal RNA was removed with the Ribo-Zero™ Magnetic Kit (epicentre).

treatment_protocol: RAW264.7 cells were treated with LPS (100 ng/ml, Sigma, L2630, E. coli serotype O111:B4) for 0, 15, 30, 45, 60, 75, 90 and 120 min.

value: RAW264.7 macrophages

tag: agent

value: LPS

tag: time

tag: rna fraction

value: cytoplasmic


title: LPS_90min

description: RNA from RAW264.7 cells 90 min after LPS stimulation

source_name: RAW264.7 cells, LPS_90min


title: EXPRSS_Col-0_1hr_water_TechRep4

description:
Tag-seq
Barcode sequence: TCGT
Barcode position: 5' end of the read


title: LPS_30min

description: RNA from RAW264.7 cells 30 min after LPS stimulation

source_name: RAW264.7 cells, LPS_30min


title: slh1_09hr

source_name: Leaf, slh1, 09hr

value: Nossen (No-0)

value: leaf

value: 4 weeks

value: 21 °C

value: 09 h at 21°C


title: LPS_15min

description: RNA from RAW264.7 cells 15 min after LPS stimulation

source_name: RAW264.7 cells, LPS_15min


title: EXPRSS_Col-0_1hr_flg22_TechRep3

description:
Tag-seq
Barcode sequence: CGAT
Barcode position: 5' end of the read

value: Columbia (Col-0)

value: Leaf

value: 5 weeks old

value: 100nM flg22


title: LPS_0min

description: RNA purified from unstimulated RAW264.7 cells

source_name: RAW264.7 cells, LPS_0min

value: untreated


title: ATM-RP105-Rep2

status: Public on Jun 18 2014

city: Boston

first: Jiazhi

last: Hu

state: MA

address: 300 Longwood Ave

department: PCMM

country: USA

institute: Children's Hospital Boston

description:
25xI-SceI cassette integrated in one allele of c-myc intron one
HTGTS

data_processing:
Standard basecalling formats for 454 and Miseq reads
Miseq paired end reads required trimming and stitching using ea-utilsv1.1.2 (http://code.google.com/p/ea-utils) followed by CD-HITv4.5 (Li & Godzik, Bioinformatics 2006) to remove 100% duplicates
Both 454 and Miseq reads are aligned using Blat (Kent, Genome Research 2002) with a masked targeted locus.  Reads containing artifacts or duplicate junctions were filtered out.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); beginning (Qstart) and end (Qend) nucleotide position within the read of alignment; orientation of junction (strand); chromosome (Tname) and position (Tstart and Tend) of alignment to the genome build; the entire read sequence (raw) including stitched paired end reads; the experiment assocaited with the read (ExpID); and the RefGene feature the alignment is associated with (Genes; NA=no annotation)

source_name: Splenic IgM+ B cell

growth_protocol: Splenic B cells were isolated from mice at an age of 6-8 weeks and cultured in 15% FBS-containing RPMI medium supplemented with α-CD40 (1 μg/mL) plus IL4 (20 ng/mL) or RP105 (2 μg/mL).

extract_protocol:
Cells were collected and treated withlysis buffer (200mM NaCl, 0.2% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K)  at 55degC overnight before precipitation with isopropanol
Genomic DNA was digested with HaeIII enzyme, A-tailing on 3' end (Klenow exo-), and adapter ligation.  All libraries were blocked by EcoRV and XbaI to suppress amplification of germline or perfect repaired breaksites before PCR amplification with biotinylated primers, then streptavidin bead enrichment, emulsion PCR with nested primers, and a third PCR to include 454 or Miseq specific primers for sequencing.

treatment_protocol: Retroviral infection with I-SceI-GFP-expressing retrovirus was performed after 24 hrs following α-CD40/IL4 stimulation and cells harvested at day 4. For RP105 stimulation, infection was performed after 48hrs and cells harvested at day 5. For indicated experiments, ATM inhibitor KU55933 (10μM, Tocris) was added at time of infection and maintained for the whole duration of the stimulation.

value: Spleen

tag: target locus

value: c-myc intron one

tag: genotype

value: ATM-/-


title: ATM-RP105-Rep3


title: WT-RP105-Rep1

value: WT


title: WT-RP105-Rep3


title: ATMi-aCD40/IL4-Rep3


title: ATM-RP105-Rep1


title: WT-RP105-Rep2


title: ATMi-aCD40/IL4-Rep2


title: HeLaS3_emx1h_ChIP-seq

first: xie

last: zhan

country: China

data_processing:
Single reads uniquely mapped to human genome hg19 were obtained using Bowtie.
For each library, all other 4 libraries were used as control in pairwise peak calling by MACS14 with default settings.
Peaks with FDR<0.5% were subjected to subsequently analysis.
only peaks obtained over all 4 controls were saved.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

organism: Homo sapiens

source_name: HeLaS3_emx1 sgRNA

growth_protocol: HEK293T and HeLaS3 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 100 unit/ml penicillin, 100 μg/ml streptomycin, and 10% fetal bovine serum (FBS). The cells were transfected with indicated plasmids by either standard Calcium phosphate protocol or Lipofectamine 2000 (Invitrogen).

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 5 min at room temperature and formaldehyde was then inactivated by the addition of 125 mM glycine for 5 min at room temperature. Cells were rinsed twice with cold PBS, scraped, and collected in cold PBS, and centrifuged at 550gfor 5 min at 4 °C. The cell pellet (10^6 cells) was resuspended in 1ml ChIP cell lysis buffer (20 mMTrisHCl pH 8.0, 85 mMKCl, 0.5% NP40, 1 mM PMSF), incubated on ice for 20 minutes and then centrifuged at 550 g for 5 min at 4 °C. The pellet was resuspended in 0.2ml nuclei lysis buffer (50 mMTrisHCl pH 8.0, 10 mM EDTA, 0.1% SDS, 1 mM PMSF) and incubated on ice for 15 minutes. The lysate was sonicated (30 min total time, 30 s on, 30 s off, in 6 rounds of 5 min) in a Bioruptor (Diagenode). The lysate was centrifuged in a microfuge at 4 °C at 18,000 g for 30 min. Supernatant was collected, and 10 µl was saved as input. A single-chain anti-GFP nanobody was prepared as described before [Zhou ZX, Zhang MJ, Peng X, et al.Genome research 2013; 23: 705-715], and cross-linked to NHS-activated Sepharose beads(NERCB). 30 µl GBP beads were blocked with 500 µl 2XChIP dilution buffer (20 mMTrisHCl pH 8.0,200 mMNaCl,0.133% SDS, 1.33% Trition X-100), 450 µl H2O and 50 µl 10% BSA with rotation at 4 °C for 1 hour. 200 µl sonicated chromatin was pre-cleaned with 30 µl Sepharose beads (NERCB) with rotation at 4 °C for 1 hour in 600 µl total volume (200 µl sonicated chromatin, 300 µl 2×ChIP dilution buffer, 12 µl 100 mM PMSF and 88 µl H2O). GBP beads were resuspended in 600 µl pre-cleaned chromatin lysate to immunoprecipitate overnight at 4 °C. The next day, GBP beads were washed with 1 ml of low salt washing buffer(20 mMTrisHCl pH 8.0,150 mMNaCl,0.1% SDS, 1% Trition X-100, 2 mM EDTA), high salt washing buffer(20 mMTrisHCl pH 8.0, 500 mMNaCl, 0.1% SDS, 1% Trition X-100, 2 mM EDTA), LiCl wash buffer (20 mMTrisHCl pH 8.0, 0.25 mMLiCl, 1% NP40, 1% deoxycholate, 1mM EDTA), and TE+0.2% Trition X-100, respectively. Each wash was accomplished with rotation at 4 °C for 15 minutes. Chromatin was eluted at 65 °C for 2 hours in 200 µl ChIP elution buffer (10 mMTrisHCl pH 8.0,1 mMEDTA,0.2 mMNaCl, 0.4% SDS). Both input and immunoprecipitation samples were reversed cross-links at 65 °C overnight in 400 µl total volume with 300 mMNaCl. DNA was extracted with phenol/chloroform and precipitated with ethanol. Finally, the DNA was dissolved in 100 µl H2O.
Two biological repeat libraries for each -sgRNA control, sgRNA-emx1, and sgRNA-egfa-t1samples, were prepared and sequenced. 30-40 ng of immunoprecipitated DNA were used to prepare sequencing libraries for Illumina via NEBNext® DNA Library Prep Master Mix Set (NEB #E6040L) according to manufacturer’s protocol. DNA fragments around 200 bp were isolated by Agencourt AMPure XP(Beckman coulter) and PCR amplified with NEBNextmultiplexoligos for Illumina(#E7335,#E7500). The libraries were sequenced by Illumina Hi-seq 2000 at the Shenzhen Huada Genomics Institute (China) for single-end 50bp reads.

tag: cell line

tag: transfected with

value: emx1 sgRNA

value: GFP antibody


title: HeLaS3_Controlh_ChIP-seq

description: Controlh

source_name: HeLaS3_none (control)

value: none (control)


title: HeLaS3_egfa-t1h_ChIP-seq

source_name: HeLaS3_egfa-t1 sgRNA

value: egfa-t1 sgRNA


title: ATMi-aCD40/IL4-Rep1


title: LPS_60min

description: RNA from RAW264.7 cells 60 min after LPS stimulation

source_name: RAW264.7 cells, LPS_60min

value: RAW264.7 macrophages

value: LPS

value: cytoplasmic


title: HEK293T_egfa-t1-2_ChIP-seq

source_name: HEK293T_egfa-t1 sgRNA


title: HEK293T_emx1-1_ChIP-seq

source_name: HEK293T_emx1 sgRNA


title: RNA-seq untreated 3

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Illumina CASAVA pipeline version 1.8.2 used for basecalling
Reads were aligned to the mouse genome by Rsubread version 1.7.6
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation
Genome_build: mm9 (NCBI build 37.2)
Supplementary_files_format_and_content: tab-delimited text files were written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

source_name: Tri-transgenic leukemia A024

growth_protocol: Leukemia cells were FACS sorted directly from the bone marrow of leukemic Rag1 knockout mice

extract_protocol:
FACS sorted cell pellets were lysed and RNA prepared using QIAGEN RNEasy plus mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were either untreated or treated with Dox food for 3 days prior to harvesting

value: leukemia cells

tag: immunophenotype

value: GFPhigh

tag: cell source

value: bone marrow of leukemic mouse


title: RNA-seq d3 Dox 1

value: GFPmid

value: 3 days Dox (Pax5 restoration)


title: HEK293T_egfa-t1-1_ChIP-seq


title: HEK293T_emx1-2_ChIP-seq


title: RNA-seq untreated 2

value: untreated


title: LPS_45min

description: RNA from RAW264.7 cells 45 min after LPS stimulation

source_name: RAW264.7 cells, LPS_45min


title: HEK293T_Control-1_ChIP-seq

source_name: HEK293T_none (control)


title: RNA-seq ctrl

data_processing:
Run Time Analysis (RTA) V1.17.21.3 for Basecalling
Reads were aligned to the human genome by Rsubread version 1.12.6
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: tab-delimited text files were written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

source_name: Human B-ALL cell line REH-R

growth_protocol: REH cells were cultured in RPMI media supplemented with 20% FBS, 5mM L-glutamine and 100U/mL penicillin and 100 µg/m: streptomycin

extract_protocol:
RNA llibraries were prepared for sequencing using the QIAGEN RNEasy plus mini kit
NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: REH cells were treated with 1µg /mL doxycycline for 3 days prior to FACS sorting of GFP+ cells

value: tet-regulated IRES-GFP expression (control)

value: REH-R

value: B-ALL


title: RNA-seq d3 Dox 3


title: HEK293T_Control-2_ChIP-seq


title: RNA-seq untreated 1


title: RNA-seq normal pre-B 1

description:
Illumina CASAVA version 1.8.2
A069

data_processing:
Illumina CASAVA pipeline used for basecalling
RNA-seq reads were aligned to the mouse genome by Rsubread version 1.7.1
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation
Genome_build: mm9 (NCBI build 37.2)
Supplementary_files_format_and_content: tab-delimited text files were written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

source_name: pre-B cells

growth_protocol: Bone marrow cells were isolated from mice and pre-B cells were isolated using FACS

treatment_protocol: Mice were treated with Dox for 3 days, resulting in the expression of a GFP-linked control shRNA that is assumed to have minimal impact on global gene expression

value: pre-B cells

value: 3 days Dox (induction of control shRNA)

value: bone marrow of CAG-rtTA3;TRE-GFP-shLuc.1309 bitransgenic mouse


title: RNA-seq normal pre-B 2

description:
Illumina CASAVA version 1.8.2
B079


title: RNA-seq PAX5

value: tet-regulated PAX5-IRES-GFP expression


title: RNA-seq normal pre-B 3

description:
Illumina CASAVA version 1.8.0
B038


title: Mutant (EP61) T1 RP rep 2

city: Madison

first: Rembrandt

last: Haft

state: WI

address: 1550 Linden Dr. Room 5445

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin

description: This sample represents ribosome footprints from the indicated cells

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913).
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file).
Each dataset was normalized to reads per million per position prior to further analysis.
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the "all genes" dataset (see supplementary file for list of genes in "all genes", "low ribosome occupancy", and "high ribosome occupancy" gene sets)
Genome_build: NC_000913.2
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a "-" as the final character in the file name cover the minus strand of the genome; those with a "+" as the final character in the file name cover the plus strand of the genome.
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis.

organism: Escherichia coli

source_name: Aerobic culture

growth_protocol: Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks.

extract_protocol:
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels.
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR.

treatment_protocol: Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation.

tag: ethanol treatment

value: 40 g EtOH/L, 10 min

tag: ribosome-protected

value: Yes


title: Mutant (EP61) T2 RP rep 2

value: 40 g EtOH/L, 70 min


title: Mutant (EP61) T2 RP rep 1


title: Mutant (EP61) T1 RP rep 1


title: Mutant (EP61) T0 RP rep 1

value: no ethanol exposure


title: Mutant (EP61) T0 RP rep 2


title: Wild-type (MG1655) T2 RP rep 1


title: Wild-type (MG1655) T2 RP rep 2


title: Wild-type (MG1655) T1 RP rep 1


title: Wild-type (MG1655) T0 RP rep 2


title: Mutant (EP61) T2 RNA rep 1

description: This sample represents mRNA expressed in the indicated cells

value: No


title: Mutant (EP61) T0 RNA rep 1


title: Mutant (EP61) T1 RNA rep 1


title: Mutant (EP61) T0 RNA rep 2


title: Mutant (EP61) T2 RNA rep 2


title: Wild-type (MG1655) T0 RNA rep 1


title: Wild-type (MG1655) T1 RNA rep 1


title: Wild-type (MG1655) T1 RNA rep 2


title: Wild-type (MG1655) T0 RNA rep 2


title: Wild-type (MG1655) T2 RNA rep 1


title: Mutant (EP61) T1 RNA rep 2


title: Wild-type (MG1655) T2 RNA rep 2


title: Wild-type (MG1655) RNA-seq

description: wild-type strain

data_processing:
Basecalls performed using CASAVA version 1.7
RNA-seq reads were mapped to the E. coli K-12 MG1655 genome (GenBank ID U00096.2) using short oligonucleotide alignment program (SOAP)
Each dataset was normalized to reads per million per position prior to further analysis.
Genome_build: ASM584v1, U00096.2
Supplementary_files_format_and_content: Processed data files are WIG files normalized to reads per million per position.  Those designated "minus" cover the minus strand of the genome; those with designated "plus" cover the plus strand of the genome.

growth_protocol: Cells were grown in MOPS minimal medium with 0.2% glucose at 37 degrees C in gas-sparged Roux bottles to mid-log phase.

extract_protocol:
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels.
Library construction was performed as described in Parkhomchuk et al. 2009, Nucleic Acids Res 37: e123. Briefly, ribosome-depleted RNA was fragmented and used as template for cDNA synhtesis. dUTP was included in the second strand synthesis reaction in addition to dTTP to chemically mark the second strand. cDNAs were size-selected and ligated to sequencing adapters followed by dUTP cleavage to generate adapter-ligated single-stranded cDNAs.

treatment_protocol: Culture samples were transferred directly into an ice-cold ethanol/phenol stop solution, then collected by centrifugation and stored at -80°C until RNA extraction.


title: LPS_75min

description: RNA from RAW264.7 cells 75 min after LPS stimulation

source_name: RAW264.7 cells, LPS_75min

value: RAW264.7 macrophages

value: LPS

value: cytoplasmic


title: Wild-type (MG1655) T1 RP rep 2


title: RNA-seq d3 Dox 2

value: leukemia cells

value: GFPmid

tag: treatment

value: 3 days Dox (Pax5 restoration)

value: bone marrow of leukemic mouse


title: Normal Fibroblast (NF) [RNA-seq]

city: Houston

first: Valerie

last: LeBleu

state: TX

address: 1881 East Road

institute: MDACC

data_processing:
Applied Biosystems LifeScope software was used for basecalling.
Sequenced reads were mapped to mm10 genome using the default LifeScope RNA-Seq parameters.
DESeq (Anders & Huber, 2010) was used for assessment of transcript abundance measurements and doing differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include  transcript abundance measurements for each sample. The 'CAF90vsNF1493.xls' file contains expression fold change values.

source_name: Normal Fibroblast

extract_protocol:
RNA was extracted with Trizol reagent
RNA libraries were prepared for sequencing using standard SOLiD protocols

tag: strain background

value: mixed (C57BL/6 and BALB/c)

tag: genotype/variation

tag: tissue

value: normal pancreas

value: Normal Fibroblast


title: WT-aCD40/IL4-Rep4

value: Spleen

value: c-myc intron one

value: WT


title: Input

city: BETHESDA

first: Gary

last: Felsenfeld

state: MD

address: 9000 Rockville Pike

institute: NIDDK, NIH

description: Sample 3

data_processing:
Basecalls performed using RTA v1.17.21.3
Demultiplexing and alignment using CASAVA package v1.8.2, which uses the aligner ELANDv2
Peak calling performed using MACS1.4, which generated bed files
Genome_build: hg19
Supplementary_files_format_and_content: bed files report MACS peaks

growth_protocol: DMEM with 10% FBS

extract_protocol:
Sheared chromatin was pulled down by SRA probes or p68 antibody.
Library was prepared using MicroPlex Library Preparation kit (Diagenode, C05010010).

value: NTERA2 pluripotent stem cell line

tag: chip antibody

value: none (input)


title: Wild-type (MG1655) T0 RP rep 1

tag: strain

value: no ethanol exposure

value: Yes


title: Mutant (RL2325) RNA-seq

description: rho[L270M] derivative of wild-type strain


title: p68 ChIP-seq

description: Sample 2

value: p68 antibody (Bethyl Laboratories, catalog# A300-523A, lot# A300-523A-1)


title: WT-aCD40/IL4-Rep3


title: SRA ChIRP-seq

description: Sample 1

data_processing:
library strategy: ChIRP-Seq
Basecalls performed using RTA v1.17.21.3
Demultiplexing and alignment using CASAVA package v1.8.2, which uses the aligner ELANDv2
Peak calling performed using MACS1.4, which generated bed files
Genome_build: hg19
Supplementary_files_format_and_content: bed files report MACS peaks

tag: chirp oligonucletide

value: Customed oligo probes targeting lncRNA SRA


title: WT-aCD40/IL4-Rep1


title: WT-aCD40/IL4-Rep2


title: L4

status: Public on Jun 17 2014

city: Oslo

first: Adnan

last: Hashim

state: Oslo

address: NCMM - Forskningsparken, House 1, 3rd Floor - Gaustadalléen 21

department: NCMM (Centre for Molecular Medicine Norway)

country: Norway

institute: UiO (University of Oslo)

data_processing:
Basecalls was performed using CASAVA version 1.8
Adapter sequence was removed using  cutadapt tools that is part of iMir
To predict piRNAs, iMir uses piRNABank (tranlib), while miRAnalyzer version 0.3 was used for the identification of known miRNAs and other sncRNA.
putative piRNAs were predicted by using NCBI BLAST (v 2.2.28+) using a cut-off of evalue <0.01 against homologous species human and mouse.
Differential expression analisys of piRNAs and putative piRNAs was done using DESEQ 1.14.0 package from R Bioconductor setting a p-value ≤ 0.05 and a fold-change ≤-1.5 and ≥1.5
Genome_build: Baylor 3.4/rn4
Supplementary_files_format_and_content: Tab-delimited text files represent piRNAs. They were generated using iMir.

organism: Rattus norvegicus

source_name: liver, normal (sham-operated)

extract_protocol:
Total RNA was extracted from different rat liver samples using the standard RNA extraction method with TRIzol (Invitrogen, Carlsbad, CA, USA). RNA concentration in each sample was determined with a NanoDrop-1000 spectrophotometer (Thermo Fisher Scientific Italy, Cinisello Balsamo, Italia) and quality assessed with the Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano cartridges (Agilent Technologies, Santa Clara, CA, USA).
small RNA-Seq were performed by next generation sequencing (NGS) with sequencing-by-synthesis technology. 1 μg of total RNA was used in a library preparation according to the Illumina TruSeq small RNA sample preparation protocol (Illumina, USA). Sized smallRNA libraries were gel purified and sequenced on HiSeq 1500 (Illumina) at a concentration of 10pM for 50 plus 7 additional cycles for indexes sequencing

tag: protocol

value: control

tag: time

value: liver


title: Cancer Associated Fibroblast (CAF) [RNA-seq]

source_name: PDAC Fibroblast

value: pancreas cancer

tag: cell type

value: Cancer Associated Fibroblast (CAF)


title: L6


title: L3


title: 168h_PH2

source_name: liver, regeneration phase

value: partial hepatectomy


title: L1


title: L2


title: 168h_PH1


title: 48h_PH2


title: 48h_PH1


title: 24h_PH2


title: HDAC3 NSC 24h

city: Stockholm

first: Ola

last: Hermanson

address: Retzius Väg 8

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

data_processing:
Reads were mapped to the rat genome build rn4 by Bowtie
peaks were generated using Cis Genome with input control as background.
Genome_build: rn4
Supplementary_files_format_and_content: BED

source_name: rat NSC cells

growth_protocol: Neural Stem cells from disected cortex of E15,5 rat embryos were grown in the presense of FGF for 6h and 24h before fixation with formaldehyde

extract_protocol:
Sonicated nuclear extracts were incubated with antibodies
Libraries were prepared according to Illumina's instructions accompanying the ChIP-Seq DNA Sample Prep Kit (IP-102-1001).

treatment_protocol: ChIP seq was performed as described in methods. Full study is published as Castello-Branco et al (2014) Stem Cell reports

value: Cortex derived Neural stem cells

tag: pasage

value: Passage 2

value: FGF


title: 24h_PH1


title: HDAC2 NSC 24h

value: HDAC2 SC-7899


title: ATM-aCD40/IL4-Rep3

source_name: Splenic IgM+ B cell

value: Spleen

tag: target locus

value: c-myc intron one

tag: genotype

value: ATM-/-


title: IgG NSC 24h

value: IgG


title: ATM-aCD40/IL4-Rep2


title: ATM-aCD40/IL4-Rep1


title: Input NSC 24h

value: Input


title: IgG NSC 6h

value: 6 h


title: Input NSC 6h


title: B73 CSE 6DAP rep3

city: Tucson

first: Ramin

last: Yadegari

state: Arizona

address: 1140 E. South Campus Dr.

department: Plant Sciences

institute: University of Arizona

description: amplified poly-A RNA

data_processing:
Illumina Genome Analyzer IIx System
Sequenced reads were mapped to maize reference genome using Tophat1 with default parameters
Number of reads mapped to each gene were quantified by the intersectBed function implemented in the BEDTools package, and normalized by total count normalization method.
Genome_build: ZmB73_RefGen_v2.tar.gz
Supplementary_files_format_and_content: tab-delimited text files include count-based values for each gene

molecule: polyA RNA

organism: Zea mays

source_name: endosperm

growth_protocol: Plants of the reference maize genotype, B73, were grown under greenhouse conditions (16-h day) at the University of Arizona during January-June 2011, and self-pollinated to obtain 6-DAP kernels for laser-capture microdissection of the RNA.

extract_protocol:
RNA was extracted from laser-capture microdissected sections using an ARCTURUS PicoPure RNA Isolation Kit (Applied Biosystems), and treated with DNase (TURBO DNase, Ambion) before amplification.
Standard barcoded RNA-seq libraries were generated to facilitate sequencing of four samples using a single Illumina flowcell lane. Libraries were generated using protocols adapted from Illumina mRNA sample preparation protocol (cat. no 1004894 Rev.A).

value: central starchy endosperm

tag: age

value: 6 DAP


title: B73 CSE 6DAP rep4

description: amplified poly-A RNA


title: HDAC2 NSC 6h


title: L5

value: control


title: Embryo DNA_MeDIP

city: Ji'nan

first: Xingjun

last: Wang

state: Shandong

address: 202#, Gongye Bei Road

department: Biotechnology Research Center

institute: Shandong Academy of Agricultural Sciences

data_processing:
preprocessing using fastx(version:0.0.13)
mapping B73 Maize genome using Bowtie2(version: 2.0.5) with default parameters
peak detection using MACS(version:1.4) with default parameters
Genome_build: B73 Maize Genome
Supplementary_files_format_and_content: Bed files generated using MACS;bed files contained the genomic sites information of peaks

source_name: Maize tissue

growth_protocol: Maize endosperm and embryos were collected from B73 ears 14 days after self-pollination (DAP).

extract_protocol:
Genomic DNA of two tissues was extracted by CTAB method,DNA was sheared using the Bioruptor sonicator, and  Mehylated DNA  were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Embryo

value: 14 days after self-pollination

tag: antibody manufacturer

value: Diagenode


title: Endosperm DNA_MeDIP

value: Endosperm


title: B73 CSE 6DAP rep1

description: amplified poly-A RNA


title: B73 CSE 6DAP rep2

description: amplified poly-A RNA


title: HCC2157_Input

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Basecalls performed using CASAVA version 1.7 or 1.8.
ChIP-seq raw data was mapped by Bowtie using default parameters to hg19.
Each library after mapping was randomly sampled down without replacement to 15 million reads. Only one tag from each unique position was considered to avoid PCR biases from the sequencing.
The identification of ChIP-seq enriched regions including summits was performed using version 2.0 of MACS. Regions of enrichment comparing to input control exceeding a given threshold (q < 0.001) were called as peaks.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files of called peaks were generated using MACS2

source_name: breast cancer cells

extract_protocol:
To isolate chromatin, formaldehyde-cross-linked nuclei were sonicated using a Covaris focused-ultrasonicator. Following ChIP performed with specific antibodies and Dynabeads® Protein G (Invitrogen)
ChIP DNA was subjected to end repair, A-tailing, ligation of Illumia single end adaptor. Following PCR amplification for 18 cycles, the final library underwent gel purification.

treatment_protocol: Cells transfected with gene-specific or non-targeting siRNA pools were cultured for 5 days prior to the sample preparation.

tag: cell line

value: breast cancer cells

tag: transfection


title: HCC2157_H3K4me2ChIP_Control

treatment_protocol: Cells transfeted with gene-specific or non-targeting siRNA pools were cultured for 5 days prior to the sample preparation.

value: H3K4me2 (Millipore, 07-030)


title: HCC2157_H3K4me3ChIP_Control

value: H3K4me3 (Abcam, ab1012)


title: MDAMB231_Input


title: SUM159_Input


title: HCC2157_JARID1BChIP_Control

value: JARID1B (Novus Biologicals, 22260002)

value: siControl


title: SUM159_H3K4me3ChIP_Control


title: SUM159_CTCFChIP_Control

value: CTCF (Millipore, 07-729)


title: SUM159_H3K4me2ChIP_Control


title: MDAMB231_JARID1BChIP_Control


title: SUM159_JARID1BChIP_Control


title: SUM185_Input


title: SUM185_JARID1BChIP_Control


title: T47D_Input


title: MCF7_Input


title: SUM185_JARID1BChIP_siCTCF

value: siCTCF


title: T47D_JARID1BChIP_Control


title: MCF7_H3K4me3ChIP_siJARID1B


title: MCF7_H3K4me3ChIP_Control


title: MCF7_H3K4me2ChIP_siJARID1B


title: MCF7_H3K4me2ChIP_Control


title: MCF7_JARID1BChIP_Control


title: MCF7_JARID1BChIP_siCTCF


title: MDAMB231_RNAseq_siJARID1B

data_processing:
Basecalls performed using CASAVA version 1.7 or 1.8.
RNA-Seq raw data was mapped by Tophat to hg19.
Read counting and differential gene expression analysis were done using GFold  using significance cutoff = 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Text file (.cnt) of mapped read counts was generated using Gfold.

extract_protocol:
Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. Then polyA RNA were purified using the MACS mRNA isolation kit (Miltenyi Biotec).
PolyA RNA was fragmented by RNA fragmentation reagent (Ambion), and subjected to first strand synthesis by using SupeScript II (Invitrogen) and random hexamer oligos. The second strand was synthesized, and then subjected to end repair, A-tailing, ligation of Illumia paired end adaptor. Following PCR amplification for 18 cycles, the final library underwent gel purification.


title: HCC2157_RNAseq_Control

value: control siRNA


title: HCC2157_RNAseq_siJARID1B


title: MDAMB231_RNAseq_Control


title: SUM159_RNAseq_siJARID1B


title: SUM185_RNAseq_siCTCF


title: T47D_RNAseq_Control


title: T47D_RNAseq_siJARID1B


title: SUM185_RNAseq_Control


title: MCF7_RNAseq_siCTCF


title: SUM159_RNAseq_Control


title: MCF7_RNAseq_siJARID1B


title: MCF7_RNAseq_Control


title: LacZ_control

status: Public on Jun 16 2014

city: Stanford

first: Kun

last: Qu

state: CA

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

description: library strategy: ChIRP-Seq

data_processing:
Raw reads were uniquely mapped to Drosophila melanogaster reference genome (dm3 assembly) using bowtie (version 0.12.6) allowing maximum one mismatch
Even-Odd sequencing pairs were normalized for number of reads and merged, following Chu et al. 2011
Peaks for each sample were called using MACS algorithm (version 1.4.2) and summits were identified by ZINBA
Genome_build: dm3
Supplementary_files_format_and_content: processed ChIRP genomic tracks are in .bw format
Supplementary_files_format_and_content: called peaks are in .bed format

organism: Drosophila melanogaster

source_name: male third instar larval dorsal mesothoracic disc

growth_protocol: Cells were cultured according to cell line maintenance protocol from the Drosophila Genome Resource Center (dgrc.cgb.indiana.edu)

extract_protocol:
Purified DNA was extracted by gentle RNase elution and Qiagen column purification
For sequencing libraries we followed Illumina’s protocol.
Purification protocol: Following the ChIRP protocol in Chu et al., 2011, biotinylated DNA oligos antisense to the target RNA were added to crosslinked, sonicated chromatin for target hybridization. Biotinylated ChIRP oligos, RNA target, and associated chromatin/DNA were purified on streptavidin-functionalized magnetic beads. For ChIRP-seq, the recovered DNA was extracted from each sample.

treatment_protocol: Harvested cells were crosslinked with 1% glutaraldehyde or 1+3% formaldehyde following Chu et al. 2011 and Simon et al. 2011

value: dorsal mesothoracic disc

value: CME W1 cl.8+

value: third instar larva

tag: Sex

value: male

tag: chirp-seq target

value: LacZ control


title: roX1_D3_Odd

description: library strategy: ChIRP-Seq

tag: tissue

value: roX1 domain D3


title: roX1_D2_Even

description: library strategy: ChIRP-Seq

value: roX1 domain D2


title: roX1_U1_Odd

description: library strategy: ChIRP-Seq

value: roX1 domain U1


title: roX1_D2_Odd

description: library strategy: ChIRP-Seq


title: roX1_U1_Even

description: library strategy: ChIRP-Seq


title: Clone8_input

description: library strategy: ChIRP-Seq

value: input


title: MCF7_JARID1BChIP_siJARID1B

value: breast cancer cells

tag: chip antibody


title: Contextual fear conditioning rep3

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

data_processing:
Reads are mapped into hg19 assembly with Tophat
Gene reads count is calculated by Htseq-count with RefSeq gene annotation
Gene expression information (FPKM) is further obtained with R/Bioconductor
Genome_build: hg19
Supplementary_files_format_and_content: gene expression information (FPKM) in .txt file format

source_name: mPFC

growth_protocol: Standard animal husbandry

extract_protocol:
Total RNA was extracted using Qiagen's RNeasy Mini Kit  as per the manufacturer's instructions.
Libraries were prepared according to Illumina's instructions

treatment_protocol: For contextual fear conditioning, mice were exposed to the conditioning chamber (TSE Systems) for 3 min (habituation phase), after which they received 2 unsignaled foot shocks (2 sec duration, 0.8 mA, 30 sec intershock interval). Following the foot shocks, mice remained in the chamber for an additional 15 sec. Context controls were treated identically, but did not receive a foot shock. One hour following behavioral training, animals were sacrificed via cervical dislocation followed by decapitation and their mPFC dissected and snap-frozen on dry ice.

tag: strain

tag: treatment

value: Contextual fear conditioning

value: Brain (mPFC)

value: 3 months


title: Contextual fear conditioning rep4


title: Contextual fear conditioning rep1


title: Context control exposure rep4

value: Context control exposure


title: Contextual fear conditioning rep2


title: Context control exposure rep2


title: Context control exposure rep3


title: V

city: Dijon

first: ronan

last: quere

address: 7 bd Jeanne d'Arc

country: France

institute: Inserm U866

data_processing:
RNA was extracted (RNeasy Mini Kit, Qiagen) and concentrated (RNeasy MinElute Spin Columns, Qiagen).
RNA-seq was performed by the ProfileXpert platform (University of Lyon1, France).
RNA was quantified (Qubit, Life technologies) and quality was monitored using a Bioanalyzer (Agilent Technologies).
Libraries were generated with 200ng of total RNA using the TruSeq RNA Kit (TruSeq SR V3, Illumina)
and sequencing was performed on a HISeq 2000 using the TruSeq SBS Version3 kit (Illumina), which generate 51bp single reads.
Genome_build: For each library, more than 75 millions of reads were generated. Analysis of RNA-seq for differential gene and transcript expression was done following TopHat and Cufflinks informatics procedures (Trapnell et al., 2012).
Supplementary_files_format_and_content: Cuttdiff (.diff)

source_name: hematopoietic stem cells form old wild type mice

growth_protocol: no growth protocol

extract_protocol:
hematopoietic stem cells (HSC) were stained by antibodies (LSK: Lineage negative, Sca1+, c-Kit+) an sorted with a cell sorter (Aria BD bioscience)
We sorted and pooled 200,000 LSK from five Tif1γ-/- mice, five 20-month-old Wt mice and ten 4-month-old Wt mice. Wt mice used were littermate controls.

treatment_protocol: no treatment protocol

value: bone marrow

value: 20 months

value: wild type


title: SUM185_RNAseq_siJARID1B


title: Ko

source_name: hematopoietic stem cells from young Tif1g-/- mice

value: 4 months


title: HDAC3 NSC 6h

value: Cortex derived Neural stem cells

value: Passage 2

value: FGF

value: 6 h


title: Wt

source_name: hematopoietic stem cells from young wild type mice


title: Context control exposure rep1


title: roX1_Odd

description: library strategy: ChIRP-Seq

value: dorsal mesothoracic disc

value: CME W1 cl.8+

value: third instar larva

value: male


title: roX1_Even

description: library strategy: ChIRP-Seq


title: roX1_D3_Even

description: library strategy: ChIRP-Seq

value: roX1 domain D3


title: roX2_Odd

description: library strategy: ChIRP-Seq


title: IP flag PGC-1alpha rep.2

city: Basel

first: Christoph

last: Handschin

address: Spitalstrasse 41

country: Switzerland

institute: Biozentrum, University of Basel

data_processing:
The sequenced reads were filtered based on the quality score of each read and its alignments. Read were retained when Phred score >= 20, read length >= 25 bps and number of wrongly called nucleotides (Ns) <= 2.
Those reads that passed the filter were aligned to the mouse genome, UCSC mm9 assembly, using Bowtie version 0.12.7 (Langmead et al., 2009) using parameters --best --strata -a --m 100.
We used a peak calling algorithm as described in more detail in the manuscript. To identify regions that were significantly enriched in the ChIP, we passed a 200 bps long sliding window along the genome, sliding by 25 bps between consecutive windows, and estimated the fraction of all ChIP reads fIP that fall within the window, as well as the fraction fWCE of reads from the WCE that fall in the same window (which we estimate from a 2000 bps long window centered on the same genomic location). All regions with a Z-statistic larger than 4.5 as significantly enriched were defined as "peaks" and used for further analysis.
Genome_build: mm9

source_name: C2C12 myotubes, IP flag PGC-1alpha

growth_protocol: C2C12 cells were grown to 90% confluence in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 Units/ml penicillin and 100ug/ml streptomycin. The differentiation to myotubes was induced by changing the medium to DMEM supplemented with 2% horse serum for 72h. Follwing differentiation, the cells were cultivated in the presence of Flag-PGC-1alpha adenovirus.

extract_protocol:
Starting with approximately 1x10^8 C2C12 cells (crosslinked with formaldehyde), the chromatin immunoprecipitation was performed  according to the Agilent Mammalian ChIP-on-chip Protocol version 10.0 using magnetic beads (Dynabeads® Protein G, Invitrogen), which were previously coated with monoclonal anti-flag antibodies (Monoclonal ANTI-FLAG® M2 Antibody, Sigma).
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols

value: C2C12 myotubes


title: WCE rep.2

source_name: C2C12 myotubes, WCE


title: WCE rep.1


title: IP flag PGC-1alpha rep.1

value: Monoclonal ANTI-FLAG® M2 Antibody, Sigma


title: roX2_Even

description: library strategy: ChIRP-Seq


title: 110722_I684_FCB0AK9ABXX_L3_MELlanTARAAPEI-9 (AAgg)

status: Public on Jun 15 2014

city: Harbin

first: Peng

last: Gao

state: Heilongjiang Province

address: No. 59, Mucai Street

department: College of Horticulture

institute: Northeast Agricultural University

description:
Sample 2
Cucumis melo L.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, use trinity to get unigenes, then unigenes mapped to CM_protein_v3.5.fasta whole genome CDS (https://melonomics.net/files/Genome/) using blast
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Genome_build: Melon genome data (Garcia-Mas et al., 2012)
Supplementary_files_format_and_content: The .txt files report abundance measurements (RPKM)

organism: Cucumis melo

source_name: gynoecious

extract_protocol:
Tissues from each plant were collected at four different stages: true leave at 2-true-leaf stage (before transplanting), axillary buds and fresh leaves (one week after transplanting),  flower buds (< 2mm in length),  and flower buds before flowering. Each amount of tissues was collected from each RIL and the tissues from each RIL were kept separately in a freezer. Total RNA were also extracted separately, and bulks were made by mixing equal amount of total RNA .Total RNA was isolated using RNasey Plant kit (Qiagen, USA) according to the protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: AAgg

value: axillary buds, fresh leaves and flower buds mixed

tag: developmental stage

value: flower buds before flowering


title: 110722_I684_FCB0AK9ABXX_L4_MELlanTBRAAPEI-10 (AAGG)

description:
Sample 4
Cucumis melo L.

source_name: monoecious

value: AAGG


title: BY4741

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to sacCer3 whole genome using Tophat V2.0.4
gene expression levels were estimated as FPKM values and differential expressed genes were identified by the Cufflinks (v2.0.2) package
Genome_build: sacCer3
Supplementary_files_format_and_content: txt files include FPKM values for each Sample, diff file include the different expressed genes identified by Cufflinks.

organism: Saccharomyces cerevisiae

source_name: Yeast strain

growth_protocol: Yeast cells were cultured in 25mL YPD medium (1g/L yeast extract, 2g/L peptone, and 2g/L glucose) with an initial OD600 of 0.05.

extract_protocol:
The total RNA was extracted at early-stationary phase by the hot phenol method and then treated with RNase-free DNase I (TaKaRa) for 30 min according to the manufacturer’s protocols.
The poly (A) containing mRNA molecules were puriﬁed and the cDNA libraries were prepared according to the manufacturer’s instructions (Illumina).

tag: source

value: Laboratory


title: DY1

value: Chinese rice wine

value: wild type


title: IgG-2

city: Nice

first: Andreas

last: Schedl

address: Parc Valrose

department: iBV

institute: University of Nice

description: Sample 4

data_processing:
Libraries were sequenced on Illumina Genome Analyzer (GAII, MDC, Berlin).
Basecalls were generated using the Bustard module of the Illumina data pipeline
Genome_build: mm10
Supplementary_files_format_and_content: WT1_1.bed and WT1_2.bed.  Bed files for each replica containing the peak clusters generated using the GENOMATIX software suite.  Column headers: Chromosome | Start | End | Id | adj. p-value | Strand
Supplementary_files_format_and_content: IDR-overlapped-peaks_all.bed.  Bed file containing IDR scores for common peaks.  Column headers: Chromosome    | Start | End | Id | IDR score | Strand

source_name: Microdissected developing kidneys

growth_protocol: Wildtype mice (mixed genetic background) were kept under normal housing conditions with free access to food and water. Timed matings were set up and the day of vaginal plug counted as E0.

extract_protocol:
On day E18.5 pregnant females were sacrificed by cervical dislocation and kidneys from embryos dissected and diced in ice cold Hanks Buffered saline solution. After fixation tissue was disrupted and nuclei released by homogenization in a 15ml Potter S homogenizer with Teflon plunger (B.Braun) attached to a drill in 20mM HEPES pH7.4, 1mM EDTA, 150mM NaCl, 1%SDS, 0.125M glycine, 0.2mg/ml PMSF. Nuclei were collected by centrifugation (805g for 5min) and re-suspended for sonication in 20mM HEPES pH7.4, 1mM EDTA, 150mM NaCl, 0.4%SDS, 0.2mg/ml PMSF.
For library preparation, recovered DNA was digested with either AluI/MseI or HaeIII/MseI. Ends were filled and fragments A-tailed by treatment with GoTaq (Promega). Forked adapters (Illumina genomic DNA sample prep kit) were ligated to fragments and the resulting product was subject to 18 rounds of amplification using Illumina PCR primers and Pfx DNA polymerase (Invitrogen).

tag: genotype/variation

value: wildtype

value: mixed genetic background (C57Bl6 crossed with B6DBA/F1)

value: IgG [Santa Cruz, sc-2027]


title: IgG-1

description: Sample 3


title: 110724_I176_FCB09YJABXX_L7_MELlanTDRABPEI-1 (aaGG)

description:
Sample 3
Cucumis melo L.

source_name: hermaphrodite

value: aaGG


title: Wt1-2

description: Sample 2

value: WT1 (C-19) [Santa Cruz, sc-192]


title: 110722_I684_FCB0AK9ABXX_L1_MELlanTCRAAPEI-12 (aagg)

description:
Sample 1
Cucumis melo L.

source_name: andromonoecious

value: aagg


title: cMyc KO mESC

description:
single-end, directional RNA-seq library
embryonic stem cells, polyA RNA-selected

data_processing:
RNA-seq reads were aligned to the mouse genome (mm9) with tophat and uniquely mapped reads were assembled into transcripts with cufflink. Transcripts were annotated by comparing them to databases of known coding genes, lncRNAs, pseudogenes, rRNAs and repeats. lncRNAs were annotated by comparing them to existing annotations. Transcripts that did not match to anything known were termed unannotated. Since our sequencing and analysis protocols selected for poly-adenylated, and non-repetitive reads, we discarded reads that mapped to rRNAs and repeats. DESeq was used to normalize reads between samples, and log fold change of each transcript between WT and Dcr KO cells was calculated. FDR ≤ 0.05 was used to decide if a transcript was significantly up or down-regulated.
ChIP-seq reads were mapped to mouse genome (mm9) with bowtie allowing no mismatch.
Genome_build: mm9 from UCSC
Supplementary_files_format_and_content: The processed .exp.txt files contain tab-separated columns, the first column is the transcript ID, and the remaining columns represent normalized reads in respective mESCs. The processed .bedgraph files contain mapped reads of ChIP-seq libraries.

source_name: cMyc Knockout mouse embryonic stem cells

growth_protocol: Feeder-free WT, 3 lines of Dcr KO mESCs, cMycf/f and cMyc-/- were generated and maintained on gelatin as described previously (Calabrese et. al., PNAS, 2007).

extract_protocol: RNA-seq libraries are prepared using dUTP protocols (Parkhomchuk et. al., Nucleic Acids Res, 2009).

treatment_protocol: RNA is isolated from the cells using Trizol and poly(A)+ selected

tag: cell type

value: embryonic stem cells

tag: ChIP


title: Chromatin-IP of K36Me3 in Dcr KO

description:
ChIP library of K36Me3
embryonic stem cells

source_name: Dcr Knockout mouse embryonic stem cells

extract_protocol: ChIP-seq libraries are prepared using protocols outlined by O'Geen et. al. (O'Geen et. al., Methods Mol Biol, 2011).

value: antiH3K36me3 Abcam  (Cat #:ab9050,Lot #:GR66372-1)


title: Wt1-1

description: Sample 1


title: Chromatin-IP of K36Me3 in Dcr WT

source_name: Dcr Wild type mouse embryonic stem cells


title: Chromatin-IP of K4Me3 in Dcr KO

description:
ChIP library of K4Me3
embryonic stem cells

value: antiH3K4me3 Abcam (Cat #:ab8580, Lot #:GR87168-1)


title: control rep2

city: Edmonton

first: Marek

last: Michalak

state: Alberta

address: 87 Avenue

department: Biochemistry

institute: University of Alberta

description: NIH-3T3 untreated

data_processing:
Basecalling and demultiplexing was using CASAVA 1.8.1 with default setting
Adapters were trimmed using cutadapt with options specified to retain sequences in range of 18 – 27 bp
Read alignment, filtering and miRNA read counting was performed using miRanalyzer v. 2.0. MiRanalyzer uses bowtie short read aligner to match short sequences against the genome, known mature miRNA sequences, star miRNA sequences, miRNA generating hairpins, star sequences, which are not in miRBase and, finally, the library of other non-coding RNAs (RFAM). Corresponding sequences were uploaded from miRanalyzer website (http://bioinfo2.ugr.es/miRanalyzer/standalone.html). Finally, miRanalyzer performs prediction of novel miRNAs.
Read counts of uniquely mapped miRNAs were loaded into R; differentially expressed miRNAs were detected using DESeq v. 1.4.1 following the instructions provided in user manual.
Genome_build: mm9

source_name: NIH-3T3 cells

growth_protocol: NIH-3T3 cells seeded at same cell number and grown to confluency

extract_protocol:
TriZol (Promega) isolation of RNA
Small RNA libraries were prepared using TruSeq Small RNA Sample Preparation Kit following manufacturers instructions

treatment_protocol: 500 nM thapsigargin in media for 24 hours

value: fibroblast

value: control

tag: condition

value: tissue culture


title: Chromatin-IP of K4Me3 in Dcr WT


title: thapsigargin rep2

description: NIH-3T3 thap treated

value: thapsigargin


title: thapsigargin rep1

description: NIH-3T3 thap treated


title: control rep1

description: NIH-3T3 untreated


title: Dcr WT rep2

description:
paired-end, directional RNA-seq library
embryonic stem cells, polyA RNA-selected


title: Dcr WT rep1


title: siZNF217_rep1

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

data_processing:
fastq files were aligned to the hg19 genome using Tophat 2.0.9 with default parameters. The resulting aligned .bam files were used for cufflinks abundance measurements and cuffdiff differential gene expression anlaysis using the 2.1.1 Cufflinks software.
Genome_build: hg19
Supplementary_files_format_and_content: matrix describing the mean gene transcript abundances and the differential gene expression between siZNF217 and siScramble replicate experiments including statistical measurements of differential expression

source_name: MCF7, siZNF217

growth_protocol: The MCF7 breast cancer cell line was obtained from American Type Culture Collection and cultured in Dulbecco’s Modified Eagle’s Medium supplemented with 10% fetal bovine serum, 2mM Lglutamine and 1% penicillin/streptomycin.

extract_protocol:
RNA samples from triplicate biological replicates of MCF7 cells treated with scrambled siRNA or siZNF217 were extracted using the RNAeasy Kit (Qiagen).
2 ug of RNA samples were processed with the TruSeq RNA Sample Prep Kit (Illumina) to make RNA libraries following the Low-Throughput protocol. Libraries were pooled and sequenced using the HiSeq2500 platform at the UC Davis DNA Technologies Core Facility (http://dnatech.genomecenter.ucdavis.edu).

treatment_protocol: MCF7 cells were reverse-transfected at a density of 5 x 105 per well in 6-well culture plates. Transfection was performed using 100 nM siRNA targeting ZNF217 (OnTarget plus SMARTpool, Dharmacon, cat # L-004987-01) or non-targeting pool (OnTarget plus non-targeting pool, Dharmacon, cat # D-001810-10) using RNAiMax (Invitrogen) per the manufacturer’s instructions. RNA wascollected at 48h post-transfection.

value: breast cancer


title: siScram_rep3

source_name: MCF7, siScram


title: siZNF217_rep2


title: Dcr KO4


title: siZNF217_rep3


title: siScram_rep2


title: Dcr KO3


title: siScram_rep1


title: Dcr KO1


title: C57_M_sham_12wk_3

status: Public on Jun 14 2014

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

description: basecalling quality score: phred33

data_processing:
Illumina Casava1.6 and Casava1.8 software was used for basecalling; all 50 nt reads use phred33 quality scores, while all 42 nt reads use phred64 quality scores.
Sequence reads were mapped to the mRNA and lncRNA transcriptome, defined by a customized gtf, for the mm9 genome and associated bowtie index provided by Illumina iGenomes, using tophat v1.3.0 .
This gtf is supplied as a 'processed data file'.
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the gtf file.
We have not further normalized or manipulated the count data, preferring that each user perform sample (library) depth normalization using software such as DESeq or edgeR.
Genome_build: NCBIM37 / mm9
Supplementary_files_format_and_content: tab-delimited text files include htseq-count values for each mRNA and lncRNA (shown with its Noncode id).  Genomic locations of mRNAs and lncRNAs defined as the transcriptome are contained in the gtf file.

extract_protocol:
Hearts were removed and whole embryonic hearts, or ventricular apexes from adult hearts, were flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Polyadenylated RNA was isolated using oligo(dT) binding, followed by chemical fragmentation and preparation of non-strand-specific, single-end RNA-Seq libraries, as per the Supplement of Matkovich SJ, Hu Y, Eschenbacher WH, Dorn LE, Dorn GW, II. Direct and indirect involvement of microRNA-499 in clinical and experimental cardiomyopathy. Circ Res. 2012;111:521-31.
non-strand-specific, single-end RNA-Seq

tag: age (weeks)

tag: gender

value: male

value: heart


title: C57_M_sham_12wk_4

description: basecalling quality score: phred33


title: C57_M_TAC4wk_12wk_3

description: basecalling quality score: phred33


title: C57_M_TAC4wk_12wk_1

description: basecalling quality score: phred33


title: C57_F_TAC4wk_12wk_1

description: basecalling quality score: phred33

value: female


title: flox/flox cMyc mESC

source_name: cMyc Wild type mouse embryonic stem cells


title: C57_M_sham_12wk_1

description: basecalling quality score: phred33


title: C57_M_sham_12wk_2

description: basecalling quality score: phred33


title: C57_M_adult_16wk_4

description: basecalling quality score: phred64


title: C57_M_adult_16wk_3

description: basecalling quality score: phred64


title: C57_M_adult_16wk_6

description: basecalling quality score: phred64


title: C57_M_adult_6wk_4

description: basecalling quality score: phred64


title: C57_M_adult_16wk_2

description: basecalling quality score: phred64


title: C57_M_adult_6wk_5

description: basecalling quality score: phred64


title: C57_M_adult_6wk_3

description: basecalling quality score: phred64


title: C57_M_adult_16wk_1

description: basecalling quality score: phred64


title: C57_M_adult_6wk_6

description: basecalling quality score: phred64


title: C57_M_adult_6wk_1

description: basecalling quality score: phred64


title: C57_M_adult_6wk_2

description: basecalling quality score: phred64


title: C57_M_TAC4wk_12wk_2

description: basecalling quality score: phred33


title: C57_E13.5_7

description: basecalling quality score: phred33

value: unknown


title: C57_E13.5_6

description: basecalling quality score: phred33


title: C57_E13.5_4

description: basecalling quality score: phred33


title: C57_E13.5_5

description: basecalling quality score: phred33


title: C57_E13.5_2

description: basecalling quality score: phred33


title: FVB-fibro_smallRNA_3

data_processing:
miRNA-seq: IlluminaCasava1.8 software was used for basecalling; all reads use phred33 quality scores.
miRNA-seq: Indexes have been removed from the supplied raw data files. However, raw reads still contain Illumina sequencing adapters 3' to the termination of small RNAs. Thus, pre-processing of raw reads needs to involve sequence removal including, and 3' to, the Illumina adapter sequence.
miRNA-seq: The E-miR software package (Buermans et al 2010, see below) was used to map trimmed sequencing reads to the mouse genome and quantitate mapped reads.
miRNA-seq: Buermans HP, Ariyurek Y, van Ommen G, den Dunnen JT, t Hoen PA. New methods for next generation sequencing based microRNA expression profiling. BMC Genomics. 2010;11:716. PubMed PMID: 21171994; PubMed Central PMCID: PMC3022920.
miRNA-seq: We have not further normalized or manipulated the count data, preferring that each user perform sample (library) depth normalization using software such as DESeq or edgeR.
RNA-seq: IlluminaCasava1.8 software was used for basecalling; all reads use phred33 quality scores.
RNA-seq: Sequence reads were mapped to the mRNA and lncRNA transcriptome, defined by a customized gtf, for the mm9 genome and associated bowtie index provided by RNA-seq: Illumina iGenomes, using tophat v1.3.0 .
RNA-seq: This gtf is supplied as a 'processed data file'.
RNA-seq: htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the gtf file.
RNA-seq: We have not further normalized or manipulated the count data, preferring that each user perform sample (library) depth normalization using software such as DESeq or edgeR.
Genome_build: NCBIM37 / mm9
Supplementary_files_format_and_content: miRNA-seq: tab-delimited text files include microRNA names, Ensembl transcript information, chromosomal location, and counts.
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files include htseq-count values for each mRNA and lncRNA (shown with its Noncode id).  Genomic locations of mRNAs and lncRNAs defined as the transcriptome are contained in the gtf file.

extract_protocol:
Illumina TruSeq small RNA preparation kits (version C) were used for all library construction.  3' and 5' adapters capable of recognizing non-mRNA species were sequentially ligated to 1 microgram of total RNA, followed by reverse transcription, limited PCR amplification to add indexes, and size-selection.
Isolation medium or culture medium was removed from cells and RNA was directly harvested into Trizol reagent.

treatment_protocol: Cells from three adult, wild-type, FVB hearts were separated into cardiomyocyte and nonmyocyte fractions using Langendorff perfusion, collagenase digestion and gravity filtration; total RNA was prepared immediately from myocytes, while nonmyocytes were passaged twice to yield a culture of largely fibroblasts from which total RNA was prepared.

value: FVB/NJ

value: P1 culture of primary isolated fibroblasts


title: FVB-fibro_smallRNA_2


title: FVB-fibro_smallRNA_1


title: FVB-CM_smallRNA_3

value: Primary isolated cardiomyocytes


title: FVB-CM_smallRNA_2


title: FVB-fibro_polyA_2

extract_protocol:
Polyadenylated RNA was isolated using oligo(dT) binding, followed by chemical fragmentation and preparation of non-strand-specific, single-end RNA-Seq libraries, as per the Supplement of Matkovich SJ, Hu Y, Eschenbacher WH, Dorn LE, Dorn GW, II. Direct and indirect involvement of microRNA-499 in clinical and experimental cardiomyopathy. Circ Res. 2012;111:521-31.
Isolation medium or culture medium was removed from cells and RNA was directly harvested into Trizol reagent.


title: FVB-fibro_polyA_3


title: FVB-CM_smallRNA_1


title: FVB-CM_polyA_2


title: FVB-CM_polyA_1


title: FVB-fibro_polyA_1


title: C57_M_adult_16wk_5

description: basecalling quality score: phred64


title: MDA-MB-231_Ultra

city: Moncton

first: Nicolas

last: Crapoulet

state: NB

address: 35 Providence street

institute: Atlantic cancer research institute

description: exosomes are extracted from conditionned cell culture media

data_processing:
Torrent_Suite 3.4.2 used for basecalling
2 steps alignement for large RNA with tophat v2.0.6 and bowtie2 v2.0.2
alignement for small RNA with micro_razers v1.0
TMM normalization with edgeR for miRNA
RPKM normalisation
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values or normalised values for each Sample ...

source_name: breast

extract_protocol:
The conditioned cell culture media (from MCF-7 and MDA-MB-231 cells) were used to isolate EVs using the Vn96 peptide, ExoQuick and ultracentrifugation methods described above.  RNA from the isolated EVs was harvested with TRIZOL reagent (Life Technologies)
Barcoded cDNA libraries were prepared using RNA-Seq Version 2 kit from Life Technologies following their recommended protocol. Library preparations were assayed for both quality control and quantity using Experion DNA 1K chip (Life Technologies) and diluted to 16 pM concentration. Samples were sequenced using a Proton Sequencer from Life Technologies on a PI chip following the manufacturer recommended protocol. Each chip was loaded with ten samples.

tag: exosome purification

value: ultracentrifugation method


title: MDA-MB-231_VN96

tag: cell line

value: VN96 method


title: MCF7_Ultra


title: MCF7_Exo

value: Exoquick


title: StatDirPhiKZ_35min_B

city: Leuven

first: Bob

middle: Gordon

last: Blasdel

state: Vlaams-Brabant

address: Kasteelpark Arenberg 21, bus 2462

department: Afdeling Gentechnologie

country: Belgium

institute: KU Leuven

description: Non-Directional reads appropriate for statistical analysis of differential expression

data_processing:
Sequenced reads were trimmed for adaptor sequence, and then mapped to either the PhiKZ phage (AF399011.1) or P. aeruginosa whole genome using CLC Genomics Workbench 7.0.3 with strand specific alignment in some samples.
The comparisons of relative levels of expression for gene features between different time point after infection within both the phage and host genomes were made with the negative binomial distribution test using the DESeq Bioconductor package in R.
Genome_build: PhiKZ phage (AF399011.1) or P. aeruginosa whole genome
Supplementary_files_format_and_content: Tab-delimited text files include RPKM and TGR values for each gene feature of the phage or host for each sample. Additionally, two supplementary tab-delimited text files are included with relative expression values between timepoints calculated using the DESec Bioconductor package binomial distribution test in R for the gene features of either the phage or host.

organism: Phikzvirus phiKZ

source_name: Cells infected with PhiKZ phage

growth_protocol: Bacteriophage PhiKZ was amplified from confluent lysed agar plates, purified by 0.45µm filtration and concentrated after incubation in 10% PEG8000/1M NaCl according to standard procedures (Ceyssens et al., 2006). P. aeruginosa and its derivative strains were grown overnight in 5 ml LB medium to reach saturation. Cells were diluted 1:100 in 2-500 mL fresh medium, grown at 37°C and, in infection experiments, infected with MOI 5 at OD600 nm of 0.3. Cell growth (or phage infection) was halted at indicated time points by rapid cooling in ice water or by methods specific for RNA-seq samping (see below). Cells were harvested by centrifugation (6,000 x g), flash-frozen and stored at -80°C until use. The efficiency of infection was always checked by cell counts of the infected culture five minutes post infection, which should contain <5% surviving cells compared to the non-infected culture.

extract_protocol:
Cells intended for RNA sequencing were rapidly suspended in 1/10th volumes of ice cold stop solution (10% phenol in ethanol) and chilled to inhibit RNA transcription and degradation at indicated time points.  Cells were then collected by centrifugation (6,000 x g) and Total RNA was extracted from the resulting cell pellet by vigorously resuspending it in TRIzol (Ambion) and performing a classical phenol chloroform extraction followed by ethanol precipitation.  Remaining DNA was removed using TURBO DNAse (Ambion), the efficiency of which was checked by the absence of reporter PCR products of both bacterial and phage genes.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: infection

value: Infected

tag: host strain

value: PAO1 Krilov

tag: stage of infection

value: Late Infection

tag: directional reads

value: Non-Directional


title: StatDirPhiKZ_35min_A


title: PAO1_Neg_Cntrl_2

organism: Pseudomonas aeruginosa

source_name: Uninfected Cells

value: Uninfected


title: C57_E13.5_1

description: basecalling quality score: phred33

tag: tissue


title: PAO1_Neg_Cntrl_1


title: C57_E13.5_3

description: basecalling quality score: phred33

tag: strain


title: StatPhiKZ_10min_A

value: Middle Infection


title: DirPhiKZ_35min_2

description: Directional reads appropriate for the construction of operon maps

value: Directional


title: FVB-CM_polyA_3


title: StatDirPhiKZ_10min_B


title: DirPhiKZ_5min_2

value: Early Infection


title: DirPhiKZ_5min_1


title: Ribo-Seq Cre-carrying Msi1/Msi2 floxed line C4, TAM (E12.5)

status: Public on Jun 13 2014

first: Yarden

last: Katz

state: MA

address: 9 Cambridge Center

department: Dept. of Biology and Whitehead Institute

description:
monosome protected RNA
Ribo-Seq, single end
ribo_C4_TAM
ribo_ko1_ensGene.cds_only.rpkm.txt

data_processing:
Alignment to mouse genome (mm9) using Bowtie/Tophat followed by calculation of RPKM using constitutive exons of protein-coding (CDS-containing) genes.
Genome_build: mm9
Supplementary_files_format_and_content: RPKM values for samples. Contains the gene ID (Ensembl), the read counts in the set of constitutive exons, the length of the region being considered (sum of lengths of constitutive exons), and the RPKM value.

source_name: NSCs

extract_protocol: Ribosome profiling library

tag: time point

value: 48 hours

tag: treatment


title: RPB2_PolII_ZT02_R1

city: Lausanne

first: Kyle

middle: Bergin

last: Gustafson

state: Suisse

address: EPFL-UPNAE

department: IBI

institute: EPFL

data_processing:
do not remove duplicates
bowtie -t -S -n 3 --best --strata -a -m 5 -l 50 --chunkmbs 256 -p3
htsstation.epfl.ch > ChIP-seq
bedtools bamtobed
Genome_build: mm9
Supplementary_files_format_and_content: bed graph

source_name: liver

growth_protocol: C57/BL6 male, 12–14-wk-old (at time of sacrifice), mice were housed in a 12 h light/12 h dark (LD) regimen for 2 wk with water and food available ad libitum. They were then phase- entrained to a 12 h/12 h LD regimen with water ad libitum but food access between ZT12 and ZT24 for 7 d (ZT, Zeitgeber time; ZT0 is defined as the time when the lights are turned on and ZT12 as the time when lights are turned off).

extract_protocol:
A total of 1 ml of each chromatin suspension (containing about 60 mg of DNA) was incubated with 10 mg of anti-RPB2, 1.5 mg of anti-H3K36me3, or 1.5 mg of anti-H3K4me3 in buffer A (20 mM Tris/HCl (pH 7.5), 150 mM NaCl, 2 mM EDTA) overnight at 4uC on a rotating wheel. Ten ml of protein A bead suspension (25% slurry in buffer A), pre-blocked with 10 mg/ml of salmon sperm DNA and BSA at 4uC overnight, was then added and the incubation was continued for 1 h at room temperature on a rotating wheel. The beads were then washed with dialysis buffer and ChIP wash buffer. Protein–DNA complexes were eluted from the beads, de-cross-linked, and treated with RNase A and, subsequently, with proteinase K.
A total of 10–12 ng DNA were used for the preparation of the library. Libraries for ultra-high throughput sequencing were prepared with the ChIP-Seq DNA sample kit (Illumina) as recommended by the manufacturer.

treatment_protocol: The livers were perfused with 2 ml of PBS through the spleen and immediately collected. A small piece of liver tissue (approx. 100 mg) was snap-frozen in liquid nitrogen and kept at 280uC for RNA extraction. The remaining liver tissue was immediately homogenized in PBS containing 1% formalde- hyde for chromatin preparation. All animal care and handling was performed according to the State of Geneva’s law for animal protection.

value: liver

tag: age

tag: light/dark cycle

tag: water/food access

value: ad libitum/ZT12-24

tag: antibody

value: anti-RPB2, Santa Cruz Biotechnology, sc-673-18


title: DirPhiKZ_15min_2


title: Ribo-Seq Cre-carrying Msi1/Msi2 floxed line C4, No Tam (E12.5)

description:
monosome protected RNA
Ribo-Seq, single end
ribo_C4_NoTam
ribo_ko1_ensGene.cds_only.rpkm.txt

tag: developmental stage

value: No 4-OHT


title: Ribo-Seq MSI1, DOX (E12.5)

description:
monosome protected RNA
Ribo-Seq, single end
ribo_KH2MSI1_DOX
ribo_oe1_ensGene.cds_only.rpkm.txt

value: 72 hours

value: DOX 1ug/ml


title: Ribo-Seq Cre-less Msi1/Msi2 floxed control line C1, TAM (E12.5)

description:
monosome protected RNA
Ribo-Seq, single end
ribo_C1_TAM
ribo_ko1_ensGene.cds_only.rpkm.txt


title: Ribo-Seq MSI1, No Dox (E12.5)

description:
monosome protected RNA
Ribo-Seq, single end
ribo_KH2MSI1_NoDox
ribo_oe1_ensGene.cds_only.rpkm.txt

value: No Dox


title: Ribo-Seq Cre-less Msi1/Msi2 floxed control line C1, No Tam (E12.5)

description:
monosome protected RNA
Ribo-Seq, single end
ribo_C1_NoTam
ribo_ko1_ensGene.cds_only.rpkm.txt


title: Ribo-Seq KH2 control, DOX (E12.5)

description:
monosome protected RNA
Ribo-Seq, single end
ribo_KH2_DOX
ribo_oe1_ensGene.cds_only.rpkm.txt


title: MCF7_VN96

value: VN96 method


title: Cre-carrying Msi1/Msi2 floxed line C4, TAM (E12.5)

description:
RNA-Seq, paired end
E12.5_C4_TAM

extract_protocol: Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for paired end RNA sequencing using Illumina paired end sequencing primers.


title: Ribo-Seq KH2 control, No Dox (E12.5)

description:
monosome protected RNA
Ribo-Seq, single end
ribo_KH2_NoDox
ribo_oe1_ensGene.cds_only.rpkm.txt


title: Cre-carrying Msi1/Msi2 floxed line C4, No Tam (E12.5)

description:
RNA-Seq, paired end
E12.5_C4_NoTam


title: Cre-less Msi1/Msi2 floxed control line C1, No Tam (E12.5)

description:
RNA-Seq, paired end
E12.5_C1_NoTam


title: MSI2, No Dox (E12.5)

description:
RNA-Seq, paired end
E12.5_MSI2_NoDox


title: DirPhiKZ_35min_1

value: Infected


title: MSI1, No Dox (E12.5)

description:
RNA-Seq, paired end
E12.5_MSI1_NoDox


title: MSI1, DOX (E13.5)

description:
RNA-Seq, paired end
E13.5_MSI1_DOX_A


title: KH2 control, Dox (E12.5)

description:
RNA-Seq, paired end
E12.5_KH2_DOX


title: DirPhiKZ_15min_1

value: PAO1 Krilov


title: KH2 control, No Dox (E12.5)

description:
RNA-Seq, paired end
E12.5_KH2_NoDox


title: Ascl1_Input_Ctrl

city: Dallas

first: Jane

middle: E

last: Johnson

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: Ascl1 Input Ctrl

data_processing:
Basecalls performed using CASAVA
Sequence reads were mapped to the mm9 assembly of the mouse genome with Bowtie v0.12.9 (-q -m 1 -v 2 --best)
Duplicate reads were removed, and the remaining unique reads were normalized to a 10 million read count for peak calling analysis.
Peak calling was performed by HOMER using an FDR cutoff of 0.001. Putative peaks were required to have 4-fold enrichment over the control/input sample and a cumulative Poisson p-value of <0.0001
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files show sequence density across mm9 genome.

source_name: E12.5 Neural Tube

extract_protocol:
For Ptf1a and Rbpj E12.5 neural tube mouse embryos placed in Buffer A (15 mM HEPES pH 7.6, 60 mM KCl, 15 mM NaCl, 0.2 mM EDTA, 0.5 mM EGTA, 0.34 M sucrose) on ice. Nuclei were  liberated by Dounce homogenization and purified by centrifugation through a sucrose gradient (15 mM HEPES pH 7.6, 60 mM KCl, 15 mM NaCl, 0.1 mM EDTA, 0.25 mM EGTA, 1.25 M sucrose). Nuclei were then fixed in 1% formaldehyde for 10 minutes at 30°C, and fixation was terminated by adding glycine to a final concentration of 0.125 M. After centrifuging through another sucrose gradient, fixed nuclei were lysed in sonication buffer (1% Triton, 0.1% sodium deoxycholate, 150 mM NaCl, 50 mM Tris, 5 mM EDTA). Chromatin was sheared using a Diagenode Bioruptor for 30 minutes on high power with 30 second on:off cycles.
For Ascl1, ChIP E12.5 mouse neural tubes were dissected into PBS then fixed in 1% formaldehyde for 15 min and lysed in 1% SDS, 10 mM EDTA, and 50 mM Tris. Sonication was performed using a Bioruptor (Diagenode) at high power settings for 45 cycles (30 sec on/30 sec off).
All libraries were made according to Illumina’s ChIP-seq DNA sample prep protocol

value: ICR

value: none (input)


title: Ascl1_ChIP

description: Ascl1 ChIP

value: BD Pharmigen mouse anti-Ascl1 (catalog# 556604)


title: U937, D137N 3h

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor, low-quality, and artifact sequence, then mapped to hg19 with HIV genome using Tophat v.2.0.9 with parameters -p 4 --b2-very-sensitive
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using bam2rpkm v.0.06 from the University of Liverpool. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19 with HIV-1 NL4-3
Supplementary_files_format_and_content: tab-delimited text files include genes, transcripts, and RPKM values for each sample.

source_name: U937 monocytic cells infected with HIV-1-GFP

growth_protocol: U937 cells were grown in RPMI1640 supplemented with 10% fetal bovine serum, 100U/ml of penicillin, 100㎍/ml of streptomycin, and 2 mM GlutaMAX-I(Gibco). U937 cells (0.5 x 106 cells/ml) were seeded in 12-well plates and differentiated for 20 h in PMA (30 ng/ml). The cells were infected with 100 ng of viruses for 2 h and harvested at indicated time.

extract_protocol:
RNA was harvested using Trizol reagent. 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

tag: time points post-infection

tag: transduced gene

value: SAMHD1 D137N


title: miwi2KO_GermCellsTestis_MACS_H3K9me3_replicate2

city: Pasadena

first: Sergei

middle: A

last: Manakov

address: 1200 E California blvd, MC 147-75

department: Biology and Biological Engeneering

institute: California Institute of Technology

description:
MACS; Antibody: sc-53532, Santa Cruz, rat monoclonal, clone G8.8; Beads: anti-rat IgG Micro Beads (Miltenyi Biotec, 130-048-502)
DP97

data_processing:
To assess ChIP signal distribution genome-wide and on TE bodies we consider all reads that mapped to the genome (mm10) with bowtie 0.12.7(Langmead et al. 2009) of up to 10,000 positions allowing for zero mismatches. This cut-off was used to speed- up the computation without sacrificing relevant information: It eliminates, on average, only 0.25% of distinct sequences (0.3% to 0.6% reads) of which about a third are derived from simple repeats (Table S2). For each read, we assigned the multiplicity score (NH) equal to the total number of valid alignments of that read in the genome.
Next, we divided the genome into four genomic partitions: exons, introns, and transcription start sites (TSSs) of genes and the intergenic space. Exons were defined as the region of the genome covered by any of the exons annotated by RefSeq(Pruitt et al. 2009) (RefSeq Gene table was downloaded from the UCSC genome browser(Meyer et al. 2013)); introns were defined as the regions between exonic partitions within the boundaries of a region covered by RefSeq transcripts belonging to any gene. Regions that were between exonic partitions but outside of the gene boundaries were defined as the intergenic space. The TSSs of a given gene was defined as the 1-kB region around the 5' end of the most outstanding transcript annotated to that gene (±500 bp). After the genomic partitions were defined, we counted reads that were mapped within partitions. Each read count was weighed by the multiplicity score (NH) associated with the read, thus each read i incremented the sum of reads by 1/NHi. If a read overlapped with more than one partition, then the read was assigned to the partition that contained the readʼs 5'-nucleotide. With the weighted counts, we calculated how many reads were mapped to each individual partition. Then, for each of the four partition types, counts of reads in individual partitions were totaled. Finally, for each of the four partition types, the total counts of reads were converted into reads per kilobase of sequence per million mapped reads (RPKM) values in order to account for differences in library depths and differences in lengths of partitions.
ChIP signal in TE families and classes was defined in the manner analogous to the one described above for genomic partitions. We considered regions annotated by RepeatMasker (Smit, AFA, Hubley, R. RepeatModeler Open-1.0. 2008-2010 http://www.repeatmasker.org) in the UCSC genome browser for mm10 genome(Meyer et al. 2013) as belonging to a particular family of TEs to comprise one type of genomic partition. Similarly, partition types were defined for repeat classes such as LTRs, LINEs, and satellites. We then calculated how many weighted reads were mapped to each individual partition and subsequently totaled the counts for partitions of each type. Finally, for each partition type, the counts were converted into RPKM values. ChIP enrichment was defined as the ratio of RPKMs between ChIP and input libraries.
Genome_build: mm10
Supplementary_files_format_and_content: Description of fiellds in “gtf.tab” files: (1) Chromosome (2) start position (3) end position (4) type of genomic partition (5) RPKM (6) read count. Description of fields in “rmsk.tab” files: (1) Indexing field to speed chromosome range queries (2) Smith Waterman alignment score (3) Base mismatches in parts per thousand (4) Bases deleted in parts per thousand (5) Bases inserted in parts per thousand (6) Genomic sequence name (7) Start in genomic sequence (8) End in genomic sequence (9) -#bases after match in genomic sequence (10) Relative orientation + or - (11) Name of repeat (12) Class of repeat (13) Family of repeat (14) Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence (15) End in repeat sequence (16) -#bases after match (if strand is +) or start (if strand is -) in repeat sequence (17) First digit of id field in RepeatMasker .out file. Best ignored. (18) RPKM (19) read count

extract_protocol:
In case of testicular cells, fixed cells were sorted using either FACS or MACS. Cells were sonicated in lysis buffer, and histone-DNA complexes were isolated from the cleared lysate using a-H3K9me3 antibody.
ChIP-seq libraries were constructed using NEBNext ChIP-seq Library Prep Master Kit (NEB, E6240) and amplified using NEBNext Multiplex Oligos for Illumina (NEB, E7335). Final libraries were purified from 1.2% agarose gel - 200-450 bp fragments were excised. RNA-seq libraries were consucted using Illumina TruSeq RNA sample prep kit (v2, 48 rxns, RS-122-2001).

tag: strain background

value: post natal day 10

tag: genotype/variation

value: Miwi2 KO

tag: tissue/cell type

value: testicular germ cells, MACS-sorted

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: miwi2HET_GermCellsTestis_MACS_inputDNA_replicate3

description:
MACS; Antibody: sc-53532, Santa Cruz, rat monoclonal, clone G8.8; Beads: anti-rat IgG Micro Beads (Miltenyi Biotec, 130-048-502)
DP98

value: Miwi2 Het


title: miwi2HET_GermCellsTestis_MACS_H3K9me3_replicate3

description:
MACS; Antibody: sc-53532, Santa Cruz, rat monoclonal, clone G8.8; Beads: anti-rat IgG Micro Beads (Miltenyi Biotec, 130-048-502)
DP99


title: miwi2KO_GermCellsTestis_MACS_inputDNA_replicate2

description:
MACS; Antibody: sc-53532, Santa Cruz, rat monoclonal, clone G8.8; Beads: anti-rat IgG Micro Beads (Miltenyi Biotec, 130-048-502)
DP96


title: Cre-less Msi1/Msi2 floxed control line C1, TAM (E12.5)

description:
RNA-Seq, paired end
E12.5_C1_TAM

value: 48 hours


title: U937, D137N 1h


title: miwi2HET_GermCellsTestis_MACS_H3K9me3_replicate2

description:
MACS; Antibody: sc-53532, Santa Cruz, rat monoclonal, clone G8.8; Beads: anti-rat IgG Micro Beads (Miltenyi Biotec, 130-048-502)
DP95


title: U937, D137N 0h


title: miwi2HET_GermCellsTestis_MACS_inputDNA_replicate2

description:
MACS; Antibody: sc-53532, Santa Cruz, rat monoclonal, clone G8.8; Beads: anti-rat IgG Micro Beads (Miltenyi Biotec, 130-048-502)
DP94


title: MSI2, DOX (E12.5)

description:
RNA-Seq, paired end
E12.5_MSI2_DOX


title: U937, D207N 3h

value: SAMHD1 D207N


title: miwi2HET_SomaticCellsTestis_MACS_inputDNA_replicate2

description:
MACS; Antibody: sc-53532, Santa Cruz, rat monoclonal, clone G8.8; Beads: anti-rat IgG Micro Beads (Miltenyi Biotec, 130-048-502)
DP90

value: testicular somatic cells, MACS-sorted


title: miwi2HET_Liver_inputDNA_replicate4

value: liver


title: U937, D207N 1h


title: miwi2HET_Liver_H3K9me3_replicate4


title: MSI1, No Dox, technical replicate (E13.5)

description:
RNA-Seq, paired end
E13.5_MSI1_NoDox_B

value: 72 hours

value: No Dox


title: MSI1, No Dox (E13.5)

description:
RNA-Seq, paired end
E13.5_MSI1_NoDox_A


title: miwi2KO_GermCellsTestis_MACS_H3

description:
MACS; Antibody: sc-53532, Santa Cruz, rat monoclonal, clone G8.8; Beads: anti-rat IgG Micro Beads (Miltenyi Biotec, 130-048-502)
DP125

value: Histone H3, C-terminal antibody (pAb)

value: Active Motif


title: MSI1, DOX (E12.5)

description:
RNA-Seq, paired end
E12.5_MSI1_DOX

value: DOX 1ug/ml


title: miwi2HET_Liver_H3K9me3_replicate3