title: MBD3_-_-_ES_H3K4me3

city: Rehovot

first: Asaf

last: Zviran

address: 234 Herzl Street

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
ES_Mbd3_-_-_H3K4me3_peaks.bed: mm9

source_name: MBD3-/- ES

growth_protocol: ESCs, iPSCs, and 4-8 day DOX induced cells were expaned in N2B27 15% KSR  2i/LIF mouse ESC media;  MEF cells in DMEM + 15% FBS

extract_protocol:
Approximately 25*10^6 cells were cross-linked in formaldehyde (1% final concentration, 10 min at room temperature (RT)), and then quenched with glycine (5 min at RT). Fixed cells were lysed in 50mM HEPES KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40 alternative, 0.25% Triton supplemented with protease inhibitor at 4°C (Roche, 04693159001), centrifuged at 950 x g for 10 min and re-suspended in 0.2% SDS, 10mM EDTA, 140mM NaCl and 10mM Tris-HCL. Cells were then fragmented with a Branson Sonifier (model S-450D) at -4°C to a size range between 200 and 800 bp, and precipitated by centrifugation. 10 ug of antibody were pre-bound by incubating with Protein-G Dynabeads (Invitrogen100-07D) in blocking buffer (PBS supplemented with 0.5% TWEEN and 0.5% BSA) for 2 hours at room temperature. Washed beads were added to the chromatin lysate, and then incubated overnight. Samples were washed 5 times with RIPA buffer, twice with RIPA buffer supplemented with 500 mM NaCl, twice with LiCl buffer (10 mM TE, 250mM LiCl, 0.5% NP-40, 0.5% DOC), once with TE (10Mm Tris-HCl pH 8.0, 1mM EDTA), and then eluted in 0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris Hcl pH 8.0 at 65°C. Eluate was incubated in 65°C for 4 hours, and then treated sequentially with RNaseA (Roche, 11119915001) for 30 min and Proteinase K (NEB, P8102S) for two hours. DNA was purified with The Agencourt AMPure XP system (Beckman Coulter Genomics, A63881).
120ul SPRI AMPure XP beads (Agencourt) were added to the reverse-crosslinked samples, pipette-mixed 15 times and incubated for 2 minutes. Supernatant were separated from the beads using a magnet for 4 minutes. Beads were washed on the magnet with 70% ethanol and then air dried for 4 minutes. The DNA was eluted in 40 ul EB buffer (10 mM Tris-HCl pH 8.0) by pipette mixing 25 times. For the remainder of the library construction process (DNA end-repair, A-base addition, adaptor ligation and enrichment) a general SPRI cleanup involves addition of buffer containing 20% PEG and 2.5 M NaCl to the DNA reaction products (without moving them from their original well position). After thorough mixing and a 2-minute incubation at room temperature, plates are transferred to a magnet plate, incubated for 4 minutes and supernatant removed. Beads are then washed on the magnet with 150ul 70% ethanol and then air dried for 4 minutes. The DNA is eluted with 40ul of EB buffer by pipette mixing 25 times. Reagent kits are prepared in advance for all enzymatic steps (New England Biolabs). The DNA end-repair was performed by adding 27 µl of a master mix (17 µl master mix (5 ul T4 buffer, 5ul BSA-1mg/ml, 5ul ATP-10mM -2ul dNTPs 10 mM), 5 ul T4 PNK enzyme, 5 µl T4 polymerase (3 units) to each well. Samples were incubated in a thermal cycler at 12C for 15 min, 25C for 15 min, and finally cooled to 4C. The SPRI bead clean up method was used to purify the product (147 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). The A-base addition was performed by adding 20 µl master mix (17 µl A-base add mix, 3 µl Klenow (3’->5’ exonuclease) to each well and incubated at 37C for 30 min. in a thermal cycler. SPRI bead clean up method was used to purify the product (132 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 19 µl EB). Adaptor ligation was performed by adding 34 µl of a master mix (29 µl 2x DNA ligase buffer, 5 µl DNA ligase) to each well. Finally 5 µl PE Indexed oligo adaptors (0.75 uM ) was added to each well and samples were incubated 25C for 15 min in a thermal cycler. SPRI bead clean up with size selection was used to purify the ligated products (15.5 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). Finally, enrichment PCR was performed by adding 10 µl of a master mix (2 µl Forward/Reverse Index Primer, 0.5 µl dNTP mix, 5 µl 10x Pfu Ultra Buffer, 1 µl Pfu Ultra-II Fusion, 1.5 µl Nuclease free water) to each well. Plate was transferred to a thermal cycler and ran a Pfu amplification program at 95C for 2 min, 16 cycles of: 95C for 30 sec, 55C for 30 sec, 72C for 60 sec, and finally 72C for 10 min. The final SPRI clean up coupled to size selection was performed (35 µl SPRI beads was added to each sample and eluted in 40 µl). Approximately 5 picomoles of DNA library was then applied to each lane of the flow cell. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hiseq2000 Analyzer following the manufacturer's protocols.

treatment_protocol: DOX induction at day 0 at the relevant plate in final concentration of 2ug/ml

value: MBD3-/- mouse Embryonic Stem Cell (ESC)

tag: stage in reprogramming

value: ES

value: H3K4me3 (ab8580, Abcam)


title: MBD3_-_-_ES_H3K27me3

status: Public on Sep 12 2013

type: SRA

library_source: genomic

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
ES_Mbd3_-_-_H3K27me3_peaks.bed: mm9

molecule: genomic DNA

organism: Mus musculus

tag: genotype/variation

tag: chip antibody

value: H3K27me3 (07-449, Millipore)


title: MBD3_f_-_IPS_Mi2B

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
IPS_Mbd3_f_-_Mi2B_peaks.bed: mm9

source_name: MBD3flox/- iPSC

value: MBD3flox/- mouse Embryonic Fibroblast Cells (MEF) transgenic for DOX inducible OSKM reprogramming

value: iPSC

value: Mi2B (ab70469, Abcam)


title: MBD3_f_-_IPS_H3K27me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
IPS_Mbd3_f_-_H3K27me3_peaks.bed: mm9


title: ESC Pou5f1 replicate control_1 read counts

city: Los Angeles

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

country: USA

institute: UCLA

description: mouse embryonic stem cells

data_processing:
Two to seven 4C libraries were multiplexed and sequenced using the Illumina Genome Analyzer II to obtain 76 base pair (bp) reads or Illumina HIseq-2000 to obtain 100 bp reads.
The resultant reads were mapped to the mouse genome using Bowtie software (Langmead et al., 2009). Only reads that aligned to a unique position in the genome with no more than two sequence mismatches were retained for further analysis.
Reads that were successfully aligned to the genome were then remapped to the 736,199 unique HindIII sites along the genome (with respect to the 50bp upstream and downstream of the site) by matching their respective loci.
Genome_build: MM9
Supplementary_files_format_and_content: bedGraph-formatted files contain unqiue HindIII loci and associated 4C-seq read counts

source_name: cell culture

growth_protocol: standard cell culture

extract_protocol:
submitter has not supplied any information
submitter has not supplied any information

tag: cell type

value: ESCs

tag: strain

tag: cell line


title: MBD3_f_-_IPS_H3K4me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
IPS_Mbd3_f_-_H3K4me3_peaks.bed: mm9


title: MBD3_-_-_ES_Mi2B

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
ES_Mbd3_-_-_Mi2B_peaks.bed: mm9


title: MBD3_-_-_ES_WCE

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.


title: ESC Pou5f1 replicate 3a read counts

description: mouse embryonic stem cells


title: ESC Pou5f1 replicate 4b read counts

description: mouse embryonic stem cells


title: ESC Pou5f1 replicate 4a read counts

description: mouse embryonic stem cells


title: ESC Dppa2 replicate 1 read counts

description: mouse embryonic stem cells


title: EED-/- ESC Hoxa10 replicate 1 read counts

description: Eed mutant mouse embryonic stem cells

value: EED-/- ESCs

tag: genotype

value: EED-/-


title: MBD3_f_-_IPS_WCE


title: MBD3_f_-_4day_DOX_WCE

source_name: MBD3flox/- 4 days after dox induction

value: 4 days after DOX induction


title: MBD3_f_-_4day_DOX_H3K4me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
Mbd3_f_-_4_DAYS_H3K4me3_peaks.bed: mm9


title: MBD3_f_-_4day_DOX_H3K27me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
Mbd3_f_-_4_DAYS_K27me3_peaks.bed: mm9


title: ESC line C57BL6.10

city: Barcelona

first: Manuel

last: Serrano

state: Barcelona

address: Parc Científic de Barcelona, C/ Baldiri Reixac 10

department: Molecular Medicine

country: Spain

institute: IRB

description:
Isolation of poly A+ RNA from total RNA
CNIO in-house derived

library_source: transcriptomic

data_processing:
Read files were quality-checked with FastQC.
Reads were aligned with the mouse genome (GRCm38/mm10) with TopHat-2.0.4 (using Bowtie 0.12.7 and Samtools 0.1.16), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 1.3.0
Transcripts annotations used were Mus musculus GRCm38/mm10 from the UCSC Genome Browser
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tables were generated with Cufflinks 1.3.0 and contain transcripts abundance measured in FPKM values

molecule: total RNA

source_name: ESC line C57BL6.10

growth_protocol: All iPSCs and ESCs were grown in DMEM supplemented with KSR 15% and LIF on feeder mouse fibroblasts.

extract_protocol:
Total RNA was extracted combining the Trizol reagent (Life Technologies) with the RNeasy Mini kit (Qiagen).
1 µg of total RNA samples was used as provided by the user. RNA Integrity Numbers were in the range 9.8 to 10 when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fractions were purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by 9 cycles of PCR with Illumina PE primers. The resulting purified cDNA library of template molecules of known strand origin was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

value: ESC established cell line (passage 11)


title: MBD3_f_-_8day_DOX_Mi2B

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
Mbd3_f_-_8_DAYS_Mi2b_peaks.bed: mm9

source_name: MBD3flox/- 8 days after dox induction

value: 8 days after DOX induction


title: MBD3_f_-_8day_DOX_H3K4me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
Mbd3_f_-_8_DAYS_H3K4me3_peaks.bed: mm9


title: ESC Pou5f1 replicate 3b read counts

description: mouse embryonic stem cells


title: in vitro iPSC clone 9-10-5

description: Isolation of poly A+ RNA from total RNA

source_name: clone obtained from MEFs of embryo ID#9-10

value: in vitro generated iPSC (passage 7)

tag: protocol

value: doxycycline-inducible OSKM lentivirus

tag: transgenic line

value: reprogramming transgenic line B


title: ESC line JM8.F6

description:
Isolation of poly A+ RNA from total RNA
PubMed ID: 19525957

source_name: ESC line JM8.F6

value: ESC established cell line (passage 20)


title: in vivo iPSC clone 445-8

description: Isolation of poly A+ RNA from total RNA

source_name: clone obtained from the blood of mouse ID#445

value: in vivo generated iPSC (passage 7) from a whole-body reprogrammable mouse transplanted with wt bone marrow


title: MBD3_f_-_4day_DOX_Mi2B

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
Mbd3_f_-_4_DAYS_Mi2b_peaks.bed: mm9


title: MBD3_f_-_8day_DOX_WCE


title: in vitro iPSC clone 9545-1-9

description: Isolation of poly A+ RNA from total RNA

source_name: clone obtained from MEFs of embryo ID#9545-1

value: reprogramming transgenic line A


title: ESC line Bruce4

description:
Isolation of poly A+ RNA from total RNA
PubMed ID: 17828574

source_name: ESC line Bruce4

value: ESC established cell line (passage 16)


title: WT_IPS_H3K27me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
IPS_wt_H3K27me3_peaks.bed: mm9

source_name: WT iPSC

value: MBD3+/+ mouse Embryonic Fibroblast Cells (MEF) transgenic for DOX inducible OSKM reprogramming

value: H3K27me3 (07-449, Millipore)


title: in vitro iPSC clone 9545-2-4

description: Isolation of poly A+ RNA from total RNA

source_name: clone obtained from MEFs of embryo ID#9545-2


title: MBD3_f_-_MEF_WCE

source_name: MBD3flox/- MEF

value: MBD3flox/- mouse Embryonic Fibroblast Cells (MEF) transgenic for DOX inducible OSKM reprogramming

value: Before DOX induction


title: ESC Pou5f1 replicate 5b read counts

description: mouse embryonic stem cells

value: ESCs


title: MBD3_f_-_MEF_H3K27me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
MEF_Mbd3_f_-_H3K27me3_peaks.bed: mm9


title: WT_8day_DOX_WCE

source_name: WT 8 days after dox induction

value: 12 days after DOX induction


title: in vitro iPSC clone 9545-1-2

description: Isolation of poly A+ RNA from total RNA


title: WT_IPS_WCE

value: iPSC


title: in vivo iPSC clone 12708-6

description: Isolation of poly A+ RNA from total RNA

source_name: clone obtained from the blood of mouse ID#12708

value: in vivo generated iPSC (passage 7) from wt mouse transplanted with reprogrammable bone marrow


title: in vivo iPSC clone 12708-1

description: Isolation of poly A+ RNA from total RNA


title: MBD3_f_-_MEF_H3K4me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
MEF_Mbd3_f_-_H3K4me3_peaks.bed: mm9

value: H3K4me3 (ab8580, Abcam)


title: in vitro iPSC clone 9-10-1

description: Isolation of poly A+ RNA from total RNA


title: WT_IPS_Mi2B

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
IPS_wt_Mi2B_peaks.bed: mm9

value: Mi2B (ab70469, Abcam)


title: WT_4day_DOX_Mbd3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
WT_4_DAYS_Mbd3_peaks.bed: mm9

source_name: WT 4 days after dox induction

value: 6 days after DOX induction

value: Mbd3 (ab16057, Abcam & Bethyl laboratories A302-528\9A)


title: WT_4day_DOX_H3K4me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
WT_4_DAYS_H3K4me3_peaks.bed: mm9

value: 4 days after DOX induction


title: in vivo iPSC clone 445-1

description: Isolation of poly A+ RNA from total RNA

value: doxycycline-inducible OSKM lentivirus

value: reprogramming transgenic line B


title: WT_IPS_Mbd3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
IPS_wt_Mbd3_peaks.bed: mm9


title: pse_5

city: Lyon

first: Mathilde

last: PARIS

address: 32-34 avenue Tony Garnier

department: Institut de Genomique Fonctionnelle de Lyon

country: France

institute: CNRS

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were mapped to the genomes using tophat {Trapnell:2009dp}. Refined annotations of D. yakuba, D. pseudoobscura and D. virilis were based on the reference annotations (Flybase releases 1.3, 2.22 and 1.2 respectively) and mRNA-seq data obtained from pools of embryos. The reference annotations and mapped reads were given as inputs to cufflinks (version 1.0.3) {Roberts:2011hw} with the options –g and ‘--3-overhang-tolerance 300’. Statistics on the new annotations are given in Table S4.
mRNA measurements were obtained as follows: reads from single-embryo mRNA-seq were mapped to the genome sequence using tophat and mRNA levels were estimated using cufflinks {Trapnell:2010kd} and refined annotations (except D. melanogaster samples for which the reference annotation was used).
Genome_build: Apr. 2006 assembly (Flybase Release 5) of the D. melanogaster genome, the February 2006 assembly (Flybase release 2) of the D.pseudoobscura genome and the February 2006 assembly (Flybase release 1) of the D.virilis genome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Drosophila pseudoobscura

source_name: Blastoderm embryo

growth_protocol: Blastoderm embryos

extract_protocol:
total RNA was extracted using Trizol, according to manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Wild type

tag: tissue

value: whole embryo

tag: developmental stage

value: Blastoderm

value: wild type


title: WT_4day_DOX_Mi2B

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
WT_4_DAYS_Mi2b_peaks.bed: mm9

value: MBD3+/+ mouse Embryonic Fibroblast Cells (MEF) transgenic for DOX inducible OSKM reprogramming

value: 7 days after DOX induction


title: pse_4


title: pse_6


title: in vivo iPSC clone 435-2

description: Isolation of poly A+ RNA from total RNA

source_name: clone obtained from the blood of mouse ID#435

value: in vivo generated iPSC (passage 7) from whole-body reprogrammable mouse


title: WT_IPS_H3K4me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
IPS_wt_H3K4me3_peaks.bed: mm9


title: in vivo iPSC clone 12708-7

description: Isolation of poly A+ RNA from total RNA

value: reprogramming transgenic line A


title: WT_MEF_H3K27me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
MEF_wt_H3K27me3_peaks.bed: mm9

source_name: WT MEF

value: Before DOX induction

value: H3K27me3 (07-449, Millipore)


title: WT_8day_DOX_H3K4me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
WT_8_DAYS_H3K4me3_peaks.bed: mm9

value: 8 days after DOX induction

value: H3K4me3 (ab8580, Abcam)


title: WT_4day_DOX_WCE

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.


title: pse_3


title: WT_4day_DOX_H3K27me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
WT_4_DAYS_K27me3_peaks.bed: mm9

value: 5 days after DOX induction


title: WT_MEF_H3K4me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
MEF_wt_H3K4me3_peaks.bed: mm9


title: pse_2


title: WT_MEF_WCE


title: WT_8day_DOX_Mi2B

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
WT_8_DAYS_Mi2b_peaks.bed: mm9

value: 11 days after DOX induction

value: Mi2B (ab70469, Abcam)


title: input islet normal 1

city: Philadelphia

first: Jonathan

last: Schug

state: Pennsylvania

address: 12-156 Smilow Ctr Trans Research

department: School of Medicine

institute: University of Pennsylvania

data_processing:
Reads were aligned to the mosue genome (NCBI build; mm9) using Bowtie (with parameters -k 1 -m 1 --best --strata) to identify reads with unique best alignments.  Areas of enrichment were identified using HOMER. The resulting peaks analyzed in the manuscript were filtered to focus on peaks with at least 6-fold enrichment over background as well as requiring that they fall within 10KB of a TSS.
Genome_build: mm9
Supplementary_files_format_and_content: peaks

source_name: islet

extract_protocol: A single set of islets were extracted from a mouse and Nkx-6.1 and input ChIP-Seq libraries were prepared and sequenced.

value: pancreatic islet


title: pse_1


title: Nkx61 islet normal 1

tag: chip antibody manufacturer

value: Beta Cell Biology Consortium, Novo Nordisk

tag: chip antibody catalog #

tag: chip antibody lot #

tag: genetic background


title: C57Bl6/J Hop2-/- Anti-DMC1 Sample B

status: Public on Sep 11 2013

city: Bethesda

first: Kevin

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

description: library strategy: SSDS

data_processing:
For SSDS samples, reads were mapped to the mm9 genome using the modified bwa algorithm (bwa_ra), described in Khil et al., Genome Research 2012. Read pairs originating from type 1 single-stranded DNA were then selected. Fragments where both reads had a Qscore >= 30 were used.
Peak calling was performed on pooled SSDS samples for each genetic background as per Brick et al., Nature 2012.  Potential peak centres were identified using SISSRs. Adjacent (within 100 nt) putative centres were merged. True peak centres were identified as the midpoint between the median of the forward and reverse tag distributions in the 2 Kb region around each putative centre. Final peaks were defined as the 2 Kb region around the centre.
For ChIP-Seq samples, reads were mapped to the mm9 genome using the Illumina Genome Analyser CASAVA 1.8 Pipeline.  MACS v.1.4 was used to define peaks.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files: The fourth column in each bedGraph file represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Supplementary_files_format_and_content: ssDNA.bed files:  Processed ssDNA (type 1) for each sample - see Khil et al., Genome Research 2012. ssDNA coordinates are from the start to the end of the sequenced fragment. Column 4 contains quality scores for read 1 and read 2 separated by an underscore. Column 5 contains the ITR length and Microhomology length separated by an underscore.

source_name: Testis

growth_protocol: Cells were extracted from testis of euthanized mice and subjected to immunoprecipitation.

extract_protocol:
Lysates from mouse testis cells were crosslinked, sonicated and immunoprecipitated with anti-DMC1 or anti-H3K4me3 antibodies.
Size selection of library fragments of 150 - 250 bp was performed after PCR amplification. SSDS samples were denatured and quickly renatured before adapter ligation.

tag: antibody

value: Anti-DMC1 Santa Cruz (C-20, sc 8973)


title: Spo11 Gal/Gal Hop2 -/- Anti-DMC1 Sample A

description: library strategy: SSDS

value: Spo11 Gal/Gal Hop2-/-


title: C57Bl6/J Hop2-/- Anti-DMC1 Sample A

description: library strategy: SSDS


title: Spo11 Gal/Gal Hop2 -/- Anti-H3K4me3 Sample A

value: Anti-H3K4me3 Millipore (#07-473)


title: Spo11 Gal/Gal Anti-DMC1 Sample A

description: library strategy: SSDS

value: Spo11 Gal/Gal


title: Spo11 Gal/- Anti-DMC1 Sample A

description: library strategy: SSDS

value: Spo11 Gal/-


title: WT_MEF_Mbd3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.
Genome Build:
MEF_wt_Mbd3_peaks.bed: mm9

value: MBD3+/+ mouse Embryonic Fibroblast Cells (MEF) transgenic for DOX inducible OSKM reprogramming

value: Mbd3 (ab16057, Abcam & Bethyl laboratories A302-528\9A)


title: ventral pancreas, E10.5

city: London

first: Francesca

middle: M.

last: Spagnoli

address: Great Maze Pond

department: CGTRM

country: United Kingdom

institute: King's College London

data_processing:
reads were mapped to reference genome mm9 using TopHat (v 1.33) with paramaters: -a 8 -m 1 -i 40 -I 1000000 -F 0 --solexa1.3-quals -p 4 -r 150 --coverage-search --keep-tmp -z /bin/gzip --no-convert-bam
transcript assembly and differential expression were determined using Cufflinks (v 1.3.0) with UCSC reference annotation
a set of 14053 non-redundant Cufflinks genes was obtained by filtering for: 1) successful deconvolution of FPKM; 2) FPKM> 0 in a least 2 samples; 3) lower confidence level of FPKM > 0 in at least two samples; 4) in the case that multiple Cufflinks genes for one gene symbol existed, Cufflinks genes were further selected for the longest transcript length and the highest variability in the FPKM across all samples
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file contains FPKM values for non-redundant set of transcripts (14053 genes) in all 5 samples
Read statistics: number of raw paired-end reads: 109534481; number of mapped paired-end reads: 102391351; number of uniquely mapped paired-end reads: 95585063

source_name: ventral pancreas, E10.5

extract_protocol: RNA sequencing was performed using approximately 20 – 70 ng total RNA quantified by Agilent RNA 6000 Pico Kit (Agilent Technologies). Briefly, poly (A) RNA was isolated by two rounds of Oligo (dT)25 Dynabeads (Invitrogen) purification. Purified poly (A) RNA was fragmented at 94 oC for 3.5 minutes using 5 x fragmentation buffer (200 mM Tris-Acetate, pH 8.1, 500 mM KOAc, 150 mM MgOA), as previously described [Adamidi C, 2011; PMID: 21536722]. The fragmented RNA was purified by Agencourt RNAClean XP SPRI beads (Agencourt) and converted to first strand cDNA using random hexamer primers (Invitrogen) and SuperScript II Reverse Transcriptase (Invitrogen), followed by second strand cDNA synthesis with E.coli DNA pol I (Invitrogen) and RNAse H (Invitrogen) according to the manufacturer’s manuals. Then the paired-end sequencing library was prepared using NEBNext DNA Library Prep. Kit (NEB) following the Illumina mRNA-Seq library preparation protocol (Illumina). The prepared sequencing library was subsequently sequenced on Illumina HiSeq for 2 x 100 cycles following the standard protocol (Illumina).

value: ventral pancreas

tag: age


title: dorsal pancreas, E10.5

data_processing:
reads were mapped to reference genome mm9 using TopHat (v 1.33) with paramaters: -a 8 -m 1 -i 40 -I 1000000 -F 0 --solexa1.3-quals -p 4 -r 150 --coverage-search --keep-tmp -z /bin/gzip --no-convert-bam
transcript assembly and differential expression were determined using Cufflinks (v 1.3.0) with UCSC reference annotation
a set of 14053 non-redundant Cufflinks genes was obtained by filtering for: 1) successful deconvolution of FPKM; 2) FPKM> 0 in a least 2 samples; 3) lower confidence level of FPKM > 0 in at least two samples; 4) in the case that multiple Cufflinks genes for one gene symbol existed, Cufflinks genes were further selected for the longest transcript length and the highest variability in the FPKM across all samples
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file contains FPKM values for non-redundant set of transcripts (14053 genes) in all 5 samples
Read statistics: number of raw paired-end reads: 104526851; number of mapped paired-end reads: 99464506; number of uniquely mapped paired-end reads: 92694571

source_name: dorsal pancreas, E10.5

value: dorsal pancreas


title: medial foregut, E8.5

data_processing:
reads were mapped to reference genome mm9 using TopHat (v 1.33) with paramaters: -a 8 -m 1 -i 40 -I 1000000 -F 0 --solexa1.3-quals -p 4 -r 150 --coverage-search --keep-tmp -z /bin/gzip --no-convert-bam
transcript assembly and differential expression were determined using Cufflinks (v 1.3.0) with UCSC reference annotation
a set of 14053 non-redundant Cufflinks genes was obtained by filtering for: 1) successful deconvolution of FPKM; 2) FPKM> 0 in a least 2 samples; 3) lower confidence level of FPKM > 0 in at least two samples; 4) in the case that multiple Cufflinks genes for one gene symbol existed, Cufflinks genes were further selected for the longest transcript length and the highest variability in the FPKM across all samples
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file contains FPKM values for non-redundant set of transcripts (14053 genes) in all 5 samples
Read statistics: number of raw paired-end reads: 114786211; number of mapped paired-end reads: 108295227; number of uniquely mapped paired-end reads: 100177186

source_name: medial foregut, E8.5

value: medial foregut


title: foregut, E8.5

data_processing:
reads were mapped to reference genome mm9 using TopHat (v 1.33) with paramaters: -a 8 -m 1 -i 40 -I 1000000 -F 0 --solexa1.3-quals -p 4 -r 150 --coverage-search --keep-tmp -z /bin/gzip --no-convert-bam
transcript assembly and differential expression were determined using Cufflinks (v 1.3.0) with UCSC reference annotation
a set of 14053 non-redundant Cufflinks genes was obtained by filtering for: 1) successful deconvolution of FPKM; 2) FPKM> 0 in a least 2 samples; 3) lower confidence level of FPKM > 0 in at least two samples; 4) in the case that multiple Cufflinks genes for one gene symbol existed, Cufflinks genes were further selected for the longest transcript length and the highest variability in the FPKM across all samples
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file contains FPKM values for non-redundant set of transcripts (14053 genes) in all 5 samples
Read statistics: number of raw paired-end reads: 121497737; number of mapped paired-end reads: 115767182;  number of uniquely mapped paired-end reads: 107372262

source_name: foregut, E8.5

value: foregut


title: WT  LSK 4

status: Public on Sep 10 2013

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

description: Sample 4

data_processing:
Alignment using Tophat
Gene expression analysis using cuffdiff
Genome_build: HG19
Supplementary_files_format_and_content: The cuffdiff results of gene differential expression analysis are stored in gene_exp.diff.  The value_1 column reports abundance counts for Tgif1 KO and value_2 column reports abundance counts for WT.

source_name: WT, LSK  cells (Lineage-Sca-1+c-Kit+)

extract_protocol:
Approximately 200 ng RNA was harvested from LSK cells (Lin-Sca+c-Kit+) isolated from bone marrows of Tgif1-/- and Tgif1+/+ mice  by using RNeasy plus micro kit (Qiagen, Cat # 74034 )
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow

value: 8-12 weeks

value: WT

value: LSK  cells (Lineage-Sca-1+c-Kit+)


title: liver, E10.5

data_processing:
reads were mapped to reference genome mm9 using TopHat (v 1.33) with paramaters: -a 8 -m 1 -i 40 -I 1000000 -F 0 --solexa1.3-quals -p 4 -r 150 --coverage-search --keep-tmp -z /bin/gzip --no-convert-bam
transcript assembly and differential expression were determined using Cufflinks (v 1.3.0) with UCSC reference annotation
a set of 14053 non-redundant Cufflinks genes was obtained by filtering for: 1) successful deconvolution of FPKM; 2) FPKM> 0 in a least 2 samples; 3) lower confidence level of FPKM > 0 in at least two samples; 4) in the case that multiple Cufflinks genes for one gene symbol existed, Cufflinks genes were further selected for the longest transcript length and the highest variability in the FPKM across all samples
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file contains FPKM values for non-redundant set of transcripts (14053 genes) in all 5 samples
Read statistics: number of raw paired-end reads: 114436606; number of mapped paired-end reads: 109182827; number of uniquely mapped paired-end reads: 100309366

source_name: liver, E10.5

value: liver


title: WT  LSK 5

description: Sample 5


title: Tgif1 KO  LSK 3

description: Sample 3

source_name: Tgif1 KO, LSK  cells (Lineage-Sca-1+c-Kit+)


title: Tgif1 KO  LSK 1

description: Sample 1


title: WT LSK 6

description: Sample 6


title: C57Bl6/J Hop2-/- Anti-H3K4me3 Sample A


title: HighGlucose-small-RNAseq-rep1

city: Chapel Hill

first: Jeanette

last: Baran-Gale

state: NC

address: 120 Mason Farm Rd.

institute: University of North Carolina at Chapel Hill

data_processing:
Reads were first trimmed by cutAdapt (parameters -O 10 –e 0.1) to remove remnants of the 3’-adaptor sequence.
Trimmed reads of size 14-41  nt. were next aligned, without mismatches allowed, to the mm9 genome using Bowtie(parameter set: -q -a -m 20 -n 0 -e 70 ).
All aligned reads separated by less than 65 nt. or less were merged.  These merged windows were then extended by 5 nt. on either end. All reads that could not be aligned without mismatches, or those that aligned without mismatches only to regions of the genome lacking transcriptional activity, were aligned (with mismatches allowed) to the extended windows using SHRiMP2.
Aligned reads are grouped by 5’-start position (5’-isomiRs) and are annotated with respect to the 5’-start position of the annotated (miRBase r18) miRNA at the same locus.
Genome_build: mm9
Supplementary_files_format_and_content: Collapsed aligned reads in BED format. The "Name" field is the type of alignment (Exact= no mismatches; 4A18 = 4 matches, an A mismatch then 18 matches). The "Score" field is the number of reads at this position with exactly this type of alignment.

source_name: Cell line

growth_protocol: MIN6 cells were cultured in high glucose (25mM) DMEM supplemented with 10% heat-inactivated fetal bovine serum.

extract_protocol:
Cells were lysed and total RNA was extracted using Norgen total RNA purification kit. RNA quality was assessed by Agilent 2100 Bioanalyzer and samples with a RNA Integrity Number above 9.0 were selected.
Libraries were generated using the Illumina TruSeq small RNA preparation kit, and sequenced using the Illumina HiSeq.

tag: glucose


title: dcl234

city: Castanet

first: Matthias

last: Zytnicki

address: 24, Chemin de Borde-Rouge

department: Applied Mathematics and Informatics

institute: INRA

description:
sRNA-Seq
Sample 8

data_processing:
Adapters are trimmed from the reads. Reads ared onto the TAIR 9 genome using BowTie with up to 3 mismatches. Only unique matches are kept.
According to their genomic coordinates, reads are classified into young miRNA, old miRNA, ta-siRNA, endo-siRNA and inverted repeats.
MiRNA loci were retrieved from RFAM (release 19). To discriminate young miRNAs from old miRNAs, we downloaded DCL1-independent reads (GEO dataset GSM121456), mapped them, and stated that young miRNAs where the miRNAs such that no DCL1-independant read maps on their locus. Simply put, we expected that young miRNAs are DCL4-dependant.
Ta-siRNA loci are available from TAIR.
Other siRNA loci where retrieved from the prediction of (Lindow M, Jacobsen A, Nygaard S, Mang Y, Krogh A (2007) Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants. PLoS Comput Biol 3: e238). We only kept loci which did not overlap with miRNAs and tasiRNAs.
Endo-siRNA loci were extracted from PolIV-dependant loci given by (R. A. Mosher, F. Schwach, D. Studholme, D. C. Baulcombe (2008) PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis PNAS 2008 105 (8) 3145-3150).
Genome_build: TAIR9
Supplementary_files_format_and_content: Excel format (.xls), containing the normalized number of reads per feature: young miRNA, old miRNA, ta-siRNA, endo-siRNA, IR.

organism: Arabidopsis thaliana

source_name: floral tissue

growth_protocol: standard long-day conditions (16h of light and 8 h of dark at 20°C)

extract_protocol:
Frozen tissue was homogenized in a buffer containing 0.1 M NaCl, 2% sodium dodecyl sulphate (SDS), 50 mM Tris–HCl (pH 9.0), 10 mM ethylenediaminetetraacetic acid (pH 8.0) and 20 mM β-mercaptoethanol, and RNAs were extracted two times with phenol and recovered by ethanol precipitation.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ecotype

value: Col

tag: genotype/variation

value: mutant (dcl2dcl3dcl4)

tag: genotype description

value: lacking DCL2, DCL3, DCL3


title: Spo11 Gal/Gal Anti-H3K4me3 Sample A

value: Anti-H3K4me3 Millipore (#07-473)

tag: strain


title: Sample_Trisomy Female

city: Columbia

first: Lin

last: Sun

state: MO

address: 311 Tucker Hall

department: Biological Sciences

institute: University of Missouri

description: four biological repeats

data_processing:
We used TopHat to map the RNA-Seq reads of each replicate of each sample to the Drosophila melanogaster genome (dm3) (GenBank Assembly ID: GCA_000001215.2; RefSeq Assembly ID: GCF_000001215.2)in the UCSC genome browser  in conjunction with the RefSeq genome reference annotation
The threshold of mismatch was set to 2. Overall, ~80% of reads of each replicate were mapped to the genome
The reads that were mapped to a unique location on the genome were used to calculate the RNA counts of the genes. We used both our in-house tool (MULTICOM) and a public tool (HTseq)to calculate read counts of the genes in a replicate according to the genome mapping outputs and the RefSeq genome reference annotation.
The counts of the genes in a replicate calculated by MULTICOM or HTseq were normalized by dividing them by the total number of uniquely mapped reads in the replicate
Genome_build: dm3
Supplementary_files_format_and_content: Excel files with the averaged normalized reads for each genes of the biological repeats

organism: Drosophila melanogaster

source_name: Third instar larvae

growth_protocol: All the stocks are incubated at 25 degree

extract_protocol:
Total RNA was isolated using TRIZOL Reagent (Invitrogen) and  High-throughput sequencing services were performed at the University of Missouri DNA Core Facility
Libraries were constructed following the manufacturer’s protocol with reagents supplied in Illumina’s TruSeq RNA sample preparation kit (#RS-930-2001).

value: third instar larvae

tag: gender

value: female

tag: condition

value: trisomy 2L

tag: biological replicates

value: PF1, PF2, PF3, PF4


title: Sample_Male

description: four biological repeats

value: male

value: normal

value: CM1, CM2, CM3, CM4


title: HighGlucose-small-RNAseq-rep3

tag: cell line


title: HighGlucose-small-RNAseq-rep2


title: Spo11 Gal/Gal Anti-DMC1 Sample B

description: library strategy: SSDS

value: Anti-DMC1 Santa Cruz (C-20, sc 8973)

tag: genotype

value: Spo11 Gal/Gal


title: Sample_Trisomy Male

description: four biological repeats

tag: developmental stage

value: PM1, PM2, PM3, PM4


title: 35S::RTL1

description:
sRNA-Seq
Sample 7

value: over-expressing RTL1


title: OIS Ras-Induced H3K4me3

status: Public on Sep 09 2013

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

description: DNA immunoprecipitated by H3K4me3 (Abcam ab8580)

data_processing:
Galaxy was used to perform base-calls
Alignment was performed with bowtie v0.12.5 for replicative H3 and H3K4me3 (paired-end), for OIS H3 and H3K4me3 (single-end),  for lamin B1 (single-end alignment of paired-end data), and for H3K27me3 (single-end).
The processed data files aren't just tag-aligned BED files or wiggle files. They are locations of differential signal based on pairwise comparison of two samples. The replicative H3K4me3 mesas come from comparing GSM897556 and GSM897560 (normalized to the signal in GSM897555 and GSM897559). Likewise, the replicative H3K27me3 canyons and mesas come from comparing GSM897557 and GSM897561 (normalized the same way). The lamin B1 is scanned solely for regions of enrichment.
In-house scripts were used to detect canyons, mesas, and LADs among aligned sequence tags; these are available upon request
Wiggle/bigWig files were created by binning all aligned tags into non-overlapping 25 bp bins (250 bp for lamin B1), normalizing to the total number of aligned reads per sample, and then subtracting or dividing by a similarly normalized background measure (input for lamin B1 or H3 for histone lysine methylations) for each bin; H3K27me3 was divided and the other marks were subtracted.
Genome_build: hg18
Supplementary_files_format_and_content: BED files were generated using scripts that detect canyons, mesas, and LADs and define the boundaries of these loci
Supplementary_files_format_and_content: BIGWIG files as described above.

organism: Homo sapiens

source_name: OIS Ras-Induced H3K4me3

growth_protocol: IMR90 cells (obtained from Coriell Institute for Medical Research, Camden, NJ) were grown in standard tissue culture medium (DMEM with 10% FBS and 1% penicillin streptomycin) at 3% oxygen.  For senescence studies, cells were replicatively passaged until growth ceased. For OIS studies, cells were grown in phenol red-free DMEM + 20% FBS, L-glut and Pen/Strep (with 500 ug/ml G418).

extract_protocol: Cells in 10cm2 dishes were fixed in 1% formaldehyde for 10 minutes and fixation was quenched with addition of glycine to 125mM for an additional 5 minutes.  Cells were harvested by scraping from plates, and washed twice in 1xPBS before storage at -80C.  ChIP was performed as described in the Young lab protocol, except that extracts were sonicated twice for 9 minutes each round (30 seconds sonication with intermediate incubation of 30 seconds per round) using a Bioruptor (Diagenode). All ChIPs were performed using 500µg of extract 2µg of antibody per sample.  30µl of Protein G Dynabeads (Invitrogen 100.02D) were used per ChIP. For sequencing, 10ng ChIP DNA was used to make sequencing libraries using standard Illumina library single-end construction procedures.  Sequencing was performed on either Illumina GAIIx or Hi-Seq platforms (36bp, single-end and 50 or 100bp, single or paired-end reads, respectively).

treatment_protocol: Senescence cells were maintained in dishes for 2 weeks to ensure growth termination.  Senescence was determined by monitoring p16 upregulation, downregulation of cyclin genes, and by SA-beta galactosidase staining. Rad-inducible cells were created by retrovirally infecting normal IMR90 fibroblasts with pLNC-ER:Ras; ras was induced by delivering 4-hydroxytamoxifen (4-OHT) at a final concentration of 100 nM when changing media.

tag: cell type

value: primary human fibroblasts

value: Ras-induced cells

tag: population doubling

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: wt

description:
sRNA-Seq
Sample 1

value: Col

value: wild type


title: Senescent H3K27me3 ChIP R2

description: DNA immunoprecipitated by H3K27me3 (Abcam ab6002)

data_processing:
Galaxy was used to perform base-calls
Alignment was performed with bowtie v0.12.5 for replicative H3 and H3K4me3 (paired-end), for OIS H3 and H3K4me3 (single-end),  for lamin B1 (single-end alignment of paired-end data), and for H3K27me3 (single-end).
The processed data files aren't just tag-aligned BED files or wiggle files. They are locations of differential signal based on pairwise comparison of two samples. The replicative H3K4me3 mesas come from comparing GSM897556 and GSM897560 (normalized to the signal in GSM897555 and GSM897559). Likewise, the replicative H3K27me3 canyons and mesas come from comparing GSM897557 and GSM897561 (normalized the same way). The lamin B1 is scanned solely for regions of enrichment.
In-house scripts were used to detect canyons, mesas, and LADs among aligned sequence tags; these are available upon request
Genome_build: hg18
Supplementary_files_format_and_content: BED files were generated using scripts that detect canyons, mesas, and LADs and define the boundaries of these loci

source_name: Senescent H3K27me3 ChIP

value: senescent cells

tag: chip antibody lot #


title: Control H3K4me3

source_name: Control H3K4me3

value: control cells


title: Tgif1 KO  LSK 2

description: Sample 2

tag: tissue

value: bone marrow

tag: age

value: 8-12 weeks

value: LSK  cells (Lineage-Sca-1+c-Kit+)


title: Sample_Female

description: four biological repeats

value: third instar larvae

value: female

value: CF1,CF2, CF3, CF4


title: Proliferating Histone 3 ChIP R2

description: DNA immunoprecipitated by H3 (Abcam ab1791)

source_name: Proliferating Histone 3 ChIP

value: proliferating cells


title: Proliferating H3K27me3 ChIP R3

source_name: Proliferating H3K27me3 ChIP


title: Proliferating H3K27me3 ChIP R2


title: OIS Ras-Induced H3

source_name: OIS Ras-Induced H3


title: Control H3

source_name: Control H3


title: Senescent Histone 3 ChIP R2

source_name: Senescent Histone 3 ChIP


title: Senescent H3K4me3 ChIP

description: [delete]]

source_name: Senescent H3K4me3 ChIP

growth_protocol: IMR90 cells (obtained from Coriell Institute for Medical Research, Camden, NJ) were grown in standard tissue culture medium (DMEM with 10% FBS and 1% penicillin streptomycin) at 3% oxygen.  For senescence studies, cells were replicatively passaged until growth ceased.

extract_protocol: Cells in 10cm2 dishes were fixed in 1% formaldehyde for 10 minutes and fixation was quenched with addition of glycine to 125mM for an additional 5 minutes.  Cells were harvested by scraping from plates, and washed twice in 1xPBS before storage at -80C.  ChIP was performed as described in the Young lab protocol, except that extracts were sonicated twice for 9 minutes each round (30 seconds sonication with intermediate incubation of 30 seconds per round) using a Bioruptor (Diagenode). All ChIPs were performed using 500µg of extract 2µg of antibody per sample.  30µl of Protein G Dynabeads (Invitrogen 100.02D) were used per ChIP. For sequencing, 10ng ChIP DNA was used to make sequencing libraries using standard Illumina library single-end construction procedures.  Sequencing was performed on either Illumina GAIIx or Hi-Seq platforms (36bp, single-end or paired-end reads).

treatment_protocol: Senescence cells were maintained in dishes for 2 weeks to ensure growth termination.  Senescence was determined by monitoring p16 upregulation, downregulation of cyclin genes, and by SA-beta galactosidase staining.


title: Proliferating Histone 3 ChIP


title: Senescent H3K27me3 ChIP R1

description: [delete]]


title: BAM-5

city: Dunsany

first: Peter

last: Vegh

state: Meath

address: Grange, Batterjohn Crossroads

department: Animal & Bioscience Research Department

country: Ireland

institute: Teagasc

description: miRNA

data_processing:
Basecalls performed using CASAVA version 1.8.2
FastQC version 0.10.0 for QC checks
Adapter removal with Cutadapt version 1.0
Fastq quality filter version 0.0.13
Alignment to bovine genome with Novoalign version 2.07.11
Count of aligned reads with HTSeq-count (part of the HTSeq framework, version 0.5.3p3), using miRNA gene annotations from Ensembl version 66.
Discovery of novel miRNAs with miRDeep2 version 2.0.0.3, using Fastq quality filtered data (from step 4)
Genome_build: bosTau6
Supplementary_files_format_and_content: Tab-delimited text containing the tag per million counts for miRNA genes in all 8 samples

organism: Bos taurus

source_name: Lung lavage

growth_protocol: The frozen isolated alveolar macrophages were thawed and incubated in a 175cm2 flask in RPMI 1640 medium (supplemented with 10% FBS, 2.5 ug/mL amphotericin B, 2 mM L-glutamine, 100 ug/mL ampicillin, 25 ug/mL gentamycin), for 24 hours at 37°C, 5% CO2. After incubation, media was removed together with non adherent cells, and replaced with HBSS. After removing HBSS, adherent cells were dissociated with 15 mL non-enzymatic cell dissociation solution. Collected cells were pelleted at 400g for 5 min, then resuspended in 10 mL PBS, then counted with a haemocytometer. Cells were then pelleted again and were lysed for small RNA preparation.

extract_protocol:
Small RNA fractions were prepared by the Qiagen RNeasy Plus Mini kit, using the manufacturer's protocol's appendix E.
Libraries were prepared according to the manufacturer's protocol of the ScriptMiner Small RNA-Seq Library Preparation Kit (MultiPlex; Illumina-Compatible, Cat. No. SMMP101212), using 8uL small RNA as input material.

tag: animal number

value: Alveolar macrophage


title: BAM-8

description: miRNA


title: BAM-7

description: miRNA


title: BAM-2

description: miRNA


title: Senescent Histone 3 ChIP


title: BAM-3

description: miRNA


title: BAM-1

description: miRNA


title: BAM-6

description: miRNA


title: Proliferating H3K4me3 ChIP

source_name: Proliferating H3K4me3 ChIP


title: BAM-4

description: miRNA


title: Proliferating H3K27me3 ChIP R1


title: NP214 (mRNA-Seq)

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

data_processing:
Basecalling with Illumina pipeline software (SCS v2.8 / RTA v1.8).
36 bp reads were checked for quality using FastQC.
Reads were aligned to the rat genome (build rn4) using BWA (aln algorithm v0.6) with default settings.
Reads aligning to gene bodies according to Ensembl version 66 were counted using a custom python script.
Genome_build: RGSC_v3.4
Supplementary_files_format_and_content: Tab-delimited count matrix.

organism: Rattus norvegicus

source_name: dorsal hippocampus, ketogenic diet, pilocarpine treatment

growth_protocol: Male Wistar rats weighing 300-350 g (Charles-River) were kept in individual cages under controlled environmental conditions (12 h dark/light cycles, 20–23 °C and 50 % relative humidity) with drinking and feeding ad libitum.

extract_protocol:
For tissue preparation, ether anesthetized animals were decapitated, the sculls opened and cortex removed for preparation of dorsal hippocampus. Five mm thick hippocampus slices were prepared along the septo-temporal axis and collected in ice cold PBS, thereby, removing blood contamination. Hippocampi were snap frozen in liquid nitrogen and stored at -80oC until further use. Each probe was individually processed and not pooled with other samples. For downstream applications, hippocampus was homogenized in ice cold 1x PBS and divided into equal volumes for DNA and RNA extraction. 10 mg rat hippocampal tissue was used for total RNA extraction using the Trizol method, followed by DNase digestion. RNA quality was verified on the Shimadzu MultiNA capillary electrophoresis system (Shimadzu). Poly-A mRNA was isolated with Dynabead Oligo(dT) enrichment (Invitrogen).
Sequencing libraries were prepared using the NEBNext® mRNA Library Prep Reagent Set for Illumina® (New England Biolabs). Libraries were quantified on MultiNA system and sequenced at a concentration of 12 pM on the Genome Analyzer IIx (Illumina Inc, CA, USA) using the TruSeq version 5 cluster kit (cBot) and SBS kit (36 cycles).

treatment_protocol: Animals were either fed a standard or ketogenic diet. Representative animals were assigned to continuous video-electroencephalography monitoring. Electrodes were implanted before seizure induction and animals had time to recover for one week. To induce status epilepticus (SE), animals were injected with a single high dose of the muscarinic receptor agonist pilocarpine (PILO; 340 mg/kg, i.p.). Peripheral cholinergic effects were minimized by administration of methyl scopolamine (1 mg/kg, s.c.; 30 min before injection of pilocarpine). Animals that experienced no SE within 45 min after first pilocarpine administration were treated for a second time with half the application dose (175 mg/kg, i.p.). After 60 min SE duration, animals received administration of diazepam (8 mg/kg, i.m.). Age-matched control rats (CTRL) received methyl scopolamine and saline (0.9 % NaCl) injections only. SE was defined as minimum three Racine "class 5" behavioural seizures within ten minutes and was identified, where applicable, from EEG recordings by high-amplitude and -frequency discharges. All rats were continuously monitored (video or vEEG, 24h/7d) following pilocarpine injections. The observation period lasted 84 days.

tag: strain/background

value: Wistar

value: male

value: dorsal hippocampus

tag: diet

value: ketogenic

tag: treatment

value: pilocarpine


title: NP27 (mRNA-Seq)

source_name: dorsal hippocampus, standard diet, pilocarpine treatment

tag: gender

value: standard


title: Proliferating H3K27me3 ChIP R4

value: primary human fibroblasts

value: Abcam


title: NP73 (mRNA-Seq)

source_name: dorsal hippocampus, standard diet, control treatment

value: control


title: NP207 (mRNA-Seq)


title: NP72 (mRNA-Seq)


title: NP211 (mRNA-Seq)


title: NP82 (mRNA-Seq)


title: NP74 (mRNA-Seq)


title: 12W3 (mRNA-Seq)


title: 211 (MBD-Seq)

data_processing:
Basecalling with Illumina pipeline software (SCS v2.8 / RTA v1.8).
36 bp reads were checked for quality using FastQC.
Reads were aligned to the rat genome (build rn4) using BWA (aln algorithm v0.6) with default settings.
Variant peaks were called between each sample using MACS (version 1.4.0 rc2) with a fixed shift size of 75 bp and a significance cut-off of 10E-05.
Peaks were merged using bedtools, and reads across samples were counted for each peak using a custom python script.
Genome_build: RGSC_v3.4
Supplementary_files_format_and_content: Tab-delimited text file containing counts per peak region.

source_name: dorsal hippocampus, ketogenic diet, pilocarpine treated

extract_protocol:
For tissue preparation, ether anesthetized animals were decapitated, the sculls opened and cortex removed for preparation of dorsal hippocampus. Five mm thick hippocampus slices were prepared along the septo-temporal axis and collected in ice cold PBS, thereby, removing blood contamination. Hippocampi were snap frozen in liquid nitrogen and stored at -80oC until further use. Each probe was individually processed and not pooled with other samples. For downstream applications, hippocampus was homogenized in ice cold 1x PBS and divided into equal volumes for DNA and RNA extraction. 10 mg rat hippocampal tissue was used for DNA extraction using the DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. Briefly, 500 ng of rat hippocampal DNA from each animal was fragmented to a median size of 200-300 bp and subjected to methylated DNA capture according to the MethylMiner protocol (Invitrogen, Darmstadt, Germany). Enriched DNA was eluted at high salt concentrations (2 M NaCl).
Sequencing libraries were prepared using the NEBNext® DNA Library Prep Reagent Set for Illumina® (New England Biolabs). Libraries were quantified on MultiNA system and sequenced at a concentration of 12 pM on the Genome Analyzer IIx (Illumina Inc, CA, USA) using the TruSeq version 5 cluster kit (cBot) and SBS kit (36 cycles).


title: 203 (MBD-Seq)


title: 27 (MBD-Seq)

source_name: dorsal hippocampus, standard diet, pilocarpine treated


title: 72 (MBD-Seq)

source_name: dorsal hippocampus, standard diet, control treated


title: 2 (MBD-Seq)


title: 50 UM Ha 3

city: Giessen

first: Silke

last: Leutner

address: Rudolf-Buchheim-Straße 2

country: Germany

institute: Institute for Parasitology

data_processing:
Illumina Casava1.4 software used for basecalling.
TrueQuant elimination of PCR artefacts (GenXPro GmbH)
data was annotated to SmansoniAnnotatedCDS_SchistoDB-2.0, and tag-counts summed up in annotation counts
Genome_build: schistodb.net/schisto/ ;  SmansoniAnnotatedCDS_SchistoDB-2.0
Supplementary_files_format_and_content: data were normalized by tags per million
a filtering process was applied keeping only those transcripts that were detected in two out of three biological replicas in at least EM or UM
likelhood for gene expression was evaluated according to Audic & Claverie, 1997 using a perl-script from http://search.cpan.org/~scottzed/Bio-SAGE-Comparison-1.00/lib/Bio/SAGE/Comparison.pm
log2ratios were calculated

organism: Schistosoma mansoni

source_name: 50 UM Ha 3

growth_protocol: Worms were obtained by hepatoportal perfusion of hamsters 42 days (EM) or 67 days (UM) post infection with populations of mixed-sex cercaria or unisexual cercaria.

extract_protocol:
Total RNA was extracted using TriFast (PeqLab) following the manufacturer’s instructions.
GenXPro GmbH-Protocol, slightly changed from Matsumura et al. 2010

treatment_protocol: After perfusion EM were seperated from females. EM and UM were incubated in RNAlater (Ambion) over night, before storage at -80°C.

tag: Stage

value: unexperienced males

value: whole worms


title: 50 EM 5/6/7/9

value: experienced males


title: 50 EM 1/2/3/4


title: 71 (MBD-Seq)


title: Proliferating LaminB1 ChIP

source_name: Proliferating LaminB1 ChIP

tag: cell line

value: Lamin B1


title: 50 UM

source_name: 50 UM


title: 204 (MBD-Seq)


title: 82 (MBD-Seq)


title: 74 (MBD-Seq)


title: 73 (MBD-Seq)


title: RelA(S276A)_mutant_0hr_rep1

city: San Diego

first: Harry

middle: Aaron

last: Birnbaum

state: California

address: 4406 Dawes Street

institute: UCSD Chem and Biochem

description: unstimulated rela-/- immotalized MEF cells reconstituted with mouse RelA(S276A)

data_processing:
Illumina Hiseq 2000 with real time analysis version 1.13.48 was used for basecalling and Casava version 1.8.2 was used to extract reads
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 whole genome and searched for splice juntions, with TopHat v2.0.5 and Bowtie v2.0.0.7 with the following parameters to Tophat: --b2-very-sensitive --no-coverage-search -p 14
Used Cufflinks v2.0.2 with default parameters to align reads into transcripts and estimate abundances, used cuffmerge to merge the assemblies, and used cuffdiff to calculate differential gene and transcript expression levels
Imported the Fragments per Kilobase of exon per million fragments mapped (FPKM) values calculated by cufflinks to R using the cummeRbund v0.1.3 package
Genome_build: mm10
Supplementary_files_format_and_content: GTF files for each sample containing assembled isoforms, and one with the merged assemblies
Supplementary_files_format_and_content: tab-deliminited .fpkm_tracking files containing the gene and isoform level fpkm for each sample separately and one for the combined samples

extract_protocol:
RNA was extracted and purified as per the manufacturers protocol using the RNeasy kit (QIAGEN). 1 mg of the quantified RNA was reverse transcribed using superscript II RT system (Invitrogen) and poly-dT primers.
Libraries were prepared using Illumina's TruSeq kits for mRNA and smRNA libraries from totalRNA.

value: immortalized MEF


title: RelA(S276A)_mutant_1hr_rep1

description: rela-/- immotalized MEF cells reconstituted with mouse RelA(S276A) stimulated with 5 ng/ml TNF-alpha for 1 hr


title: RelA(S276A)_mutant_0hr_rep2


title: RelA(S276A)_mutant_2hr_rep1

description: rela-/- immotalized MEF cells reconstituted with mouse RelA(S276A) stimulated with 5 ng/ml TNF-alpha for 2 hr


title: RelA(S276A)_mutant_2hr_rep2


title: 207 (MBD-Seq)


title: NP070 (MBD-Seq)


title: RelA(TA2)_mutant_1hr_rep1

description: rela-/- immotalized MEF cells reconstituted with mouse RelA(L449A+F473A) stimulated with 5 ng/ml TNF-alpha for 1 hr


title: NP202K (MBD-Seq)


title: 50 UM Ha 10

source_name: 50 UM Ha 10


title: RelA(TA2)_mutant_0hr_rep1

description: unstimulated rela-/- immotalized MEF cells reconstituted with mouse RelA(L449A+F473A)


title: 55 EM

source_name: 55 EM


title: 12W3 (MBD-Seq)


title: RelA(TA2)_mutant_2hr_rep2

description: rela-/- immotalized MEF cells reconstituted with mouse RelA(L449A+F473A) stimulated with 5 ng/ml TNF-alpha for 2 hr


title: RelA(TA2)_mutant_1hr_rep2


title: RelA(TA2)_mutant_2hr_rep1


title: RelA(TA2)_mutant_0hr_rep2


title: WT_2hr_rep2

description: rela-/- immotalized MEF cells reconstituted with mouse RelA-wild type stimulated with 5 ng/ml TNF-alpha for 2 hr


title: WT_1hr_rep2

description: rela-/- immotalized MEF cells reconstituted with mouse RelA-wild type stimulated with 5 ng/ml TNF-alpha for 1 hr


title: RelA(S276A)_mutant_1hr_rep2


title: WT_2hr_rep1


title: WT_0hr_rep2

description: unstimulated rela-/- immotalized MEF cells reconstituted with mouse RelA-wild type


title: WT_0hr_rep1


title: WT_1hr_rep1


title: R1_dZn1_DP

status: Public on Sep 08 2013

first: Teresita

last: Arenzana

address: 675 Charles E. Young Dr. S., MRL 6-535

department: Microbiology, Immunology, and Molecular Genetics

data_processing:
Base calling was performed using HCS 1.3.8, RTA 1.10.36, Recipe Fragments 1.3.1/HiScanSQ 1.1.1 software bundle.
Reads were aligned to the mouse genome (mm9) using Tophat with the following parameters:-p 8 -a 8 -m 0 -i 70 -I 500000 -g 1 --library-type fr-stranded- --coverage-search --min-coverage-intron 50 --max-coverage-intron 20000 --no-closure-search --initial-read-mismatches 2 --segment-mismatches 2
Per base report of genome coverage (BedGraph) was obtained using the Bedtools suite.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph file values represent per base coverage of the genome, and was imported to UCSC Genome Browser to provide a visual representation of genome coverage

molecule: polyA RNA

source_name: DP thymocytes

extract_protocol:
Single cell suspensions were prepared from whole thymus of 4 week old mice. CD4+ CD8+ double positive cells were sorted on a FACSAriaII cell sorter. Total RNA was purified from Tri-Reagent LS using Qiagen RNEasy MinElute columns according to manufacturer protocol.
Illumina RNA TruSeq Sample Prep

tag: strain

tag: genotype

value: 4 week

tag: Sex

value: Female

value: Thymus


title: R2_dZn4_DP


title: R1_dZn4_DP


title: R2_dZn1_DP


title: Thymus wt input

city: San Francisco

first: Hilde

last: Schjerven

state: CA

address: 513 Parnassus Ave

department: Laboratory Medicine

institute: UCSF

data_processing:
Bowtie allignment through Galaxy (.bam)
Peaks: Peak detection was performed with Solesearch (http://havoc.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi) using the input DNA as a control.
Visualization BigWig file created with bedtools (.bigwig or .bedgraph).

source_name: Whole Thymus

growth_protocol: Single cell suspensions were prepared from whole thymus of 4 week old mice.

extract_protocol: Primary thymocytes were fixed in 1% formaldehyde for 10 minutes at room temperature, washed in PBS and snap frozen. Ikaros ChIP was performed with an Ab directed against the Ikaros N-terminal region (Hahm et al., 1994) and tested by PCR for enrichment at published and putative Ikaros binding sites (Primers are given in Table S2). Input DNA was prepared from wt primary thymocytes as negative control. Libraries were prepared for sequencing on the Illumina platform essentially as described (O'Geen et al., 2010). Raw sequences were mapped by Bowtie to the July 2007 annotation of mouse (Mus musculus) genome data (mm9), and significant peaks over background were called using the Sole-Search software (Langmead et al., 2009; Blahnik et al., 2010). Genome coverage visualization files were created with BEDtools and uploaded to the UCSC genome browser (http://genome.ucsc.edu) (Kent et al., 2002).

tag: genotype/variation

value: wt


title: Thymus Ikaros ZnF1-/- c3

tag: chip antibody

value: Ikaros-N terminal Ab (IkN)


title: R1_WT_DP

value: WT


title: Thymus wt_c3


title: sorted_Hardy_fraction_C+C'_Ikaros_ZnF1-/-

data_processing:
Raw data (fastq) was uploaded to the Galaxy website (http://galaxy.psu.edu/) and mapped with Tophat to the July 2007 annotation of mouse (Mus musculus) genome data (mm9), filtering for uniquely mapped reads (Giardine et al., 2005; Trapnell et al., 2009; Blankenberg et al., 2010a; Blankenberg et al., 2010b; Fujita et al., 2010; Goecks et al., 2010).
Genome coverage visualization files were created with BEDtools and uploaded to the UCSC genome browser (http://genome.ucsc.edu) (Kent et al., 2002).
Relative mRNA expression levels (RPKM) (Mortazavi et al., 2008) were calculated based on exonic reads obtained by using the software SeqMonk (Babraham Bioinformatics) and reference genome annotations from NCBI (mm9).
Filtering and calculation of Relative changes in expression levels between samples were analyzed in excel.
Genome_build: the July 2007 annotation of mouse (Mus musculus) genome data (mm9)
Supplementary_files_format_and_content: BEDGRAPH files display all mapped reads (generated from .bam file using Tophat in Galaxy).
Supplementary_files_format_and_content: Attached as supplemental file on the Series record is the unfiltered RPKM values for all annotated Refseq genes (as a Tab delimited .txt file)

source_name: sorted proB cells from primary Bone Marrow (BM)

growth_protocol: none - primary cells

extract_protocol: Illumina TruSeq

treatment_protocol: Single cell suspensions were prepared from sorted proB cells from mouse bone marrow (age of mice: 6-7 weeks).

value: bone marrow (BM)

tag: cell type

value: proB cells

tag: developmental stage

value: Hardy fraction C+C'


title: sorted_Hardy_fraction_C+C'_Ikaros_ZnF4-/-


title: sorted_Hardy_fraction_B_Ikaros_ZnF4-/-

value: Hardy fraction B


title: sorted_Hardy_fraction_B_wt

description: wt-B


title: sorted_Hardy_fraction_C+C'_wt

description: wt-C


title: BCR-ABL+_Ikaros_ZnF1-/-_d28

data_processing:
Raw data (fastq) was uploaded to the Galaxy website (http://galaxy.psu.edu/) and mapped with Tophat to the July 2007 annotation of mouse (Mus musculus) genome data (mm9), filtering for uniquely mapped reads (Giardine et al., 2005; Trapnell et al., 2009; Blankenberg et al., 2010a; Blankenberg et al., 2010b; Fujita et al., 2010; Goecks et al., 2010).
Genome coverage visualization files were created with BEDtools and uploaded to the UCSC genome browser (http://genome.ucsc.edu) (Kent et al., 2002).
Relative mRNA expression levels (RPKM) (Mortazavi et al., 2008) were calculated based on exonic reads obtained by using the software SeqMonk (Babraham Bioinformatics) and reference genome annotations from NCBI (mm9).
Filtering and calculation of Relative changes in expression levels between samples were analyzed in excel.
Genome_build: the July 2007 annotation of mouse (Mus musculus) genome data (mm9),
Supplementary_files_format_and_content: BIGWIG files display all mapped reads (generated from .bam file using Tophat in Galaxy).
Supplementary_files_format_and_content: Attached as supplemental file on the Series record is the unfiltered RPKM values for all annotated Refseq genes (as a Tab delimited .txt file)

source_name: BCR-Abl transformed in vitro cell culture

growth_protocol: Single cell suspensions were prepared from BCR-ABL transformed in vitro cell culture cells.

extract_protocol: polyA-enriched RNA was purified with the MicroPoly(A)Purist Kit (Ambion) according to the manufacturers protocol. cDNA library was prepared for the Illumina Sequencing platform using the fragmented double-stranded cDNA protocol (Nagalakshmi et al., 2010)

treatment_protocol: Retroviral transduction of primary whole BM suspensions with BCR-ABL-p185-IRES-YFP (at day 0)

value: BCR-ABL+ transformed proB-ALL

tag: time (days in in vitro culture)

value: 28 days


title: sorted_Hardy_fraction_B_Ikaros_ZnF1-/-

tag: tissue


title: wt Thymus rep1

data_processing: Raw data was uploaded to the Galaxy website (http://galaxy.psu.edu/) and mapped with Tophat to the July 2007 annotation of mouse (Mus musculus) genome data (mm9), filtering for uniquely mapped reads (Blankenberg et al., 2010; Goecks et al., 2010). Genome coverage visualization files were created in Galaxy (replicate 1) or with BEDtools (replicate 2) and uploaded to the UCSC genome browser (http://genome.ucsc.edu) (Kent et al., 2002). Tophat alignment through Galaxy resulted in .sam and .bedgraph files.

extract_protocol: Cell suspensions were prepared from 4 week old whole thymus and filtered through 70 m nylon cell strainer (BD Biosciences). RNA was prepared by the use of TRI Reagent (Molecular Research Center, Inc.) followed by purification using RNeasy kit (Qiagen) with on-column RNase-free DNase I treatment. For RNA-Seq analysis, cDNA library was prepared for the Illumina Sequencing platform using the fragmented double-stranded cDNA protocol (Nagalakshmi et al., 2010), and sequenced on an Illumina GAIIx machine with 76 bp single-end reads (replicate 1) or on an Illumina HiSeq machine with 50 bp single-end reads at the Broad Stem Cell Research Center High Throughput Sequencing Core at UCLA.

tag: age


title: BCR-ABL+_Ikaros_ZnF4-/-_d28


title: Thymus Ikaros ZnF4-/- c5


title: Thymus Ikaros ZnF1-/- c5


title: BCR-ABL+_Ikaros_ZnF4-/-_d21

value: 21 days


title: BCR-ABL+_wt_d28


title: BCR-ABL+_wt_d21


title: BCR-ABL+_Ikaros_ZnF1-/-_d21


title: Thymus_wt_c5

data_processing: Bowtie allignment through Galaxy (.bam)


title: Ikaros ZnF4-/- Thymus rep1


title: Ikaros ZnF1-/- Thymus rep2


title: wt Thymus rep2A


title: R2_WT_DP


title: wt Thymus rep2B


title: Ikaros ZnF4-/- Thymus rep2


title: SPSAWT_replicate3

status: Public on Sep 07 2013

city: Cincinnati

first: nupur

last: dasgupta

state: OH

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hopital Medical Center

description:
run0112_lane6_index11=T372_T417_T460SP~mouse_align
untreated Lung of 9V/null mice

data_processing:
mRNA-Seq reads were aligned to the mm9 version of the mouse genome reference using the TopHat/Cufflinks pipeline. First, sequences were aligned to the genome with TopHat , which efficiently aligned reads spanning known or novel splice junctions. Each sample was then independently processed with Cufflinks  in order to generate an initial transcriptome.   Finally, the Cuffmerge tool was used to merge the known and any novel isoforms into a single BAM file, and simultaneously extended partial transcripts.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
DESeq and edgeR were used to evaluate the DEGs from the mRNA-Seq data. DESeq via R script was performed on the filtered reads by Avadis NGS software using three functions (estimate size factors, estimate dispersions and negative binomial test).
For DESeq normalization, the sequencing depth is estimated by the read count of the gene with the median read count ratio across all genes.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include DESeq normalised values for each Sample

extract_protocol:
9V/null mice were sacrificed one wk after the last injection along with WT mice, lung, liver and spleen were collected for RNA analysis.
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: 9V/null mice were injected weeklyvia tail vein with 60U/kg/wk of imig or vela for 8 wks. Control 9V/null mice weere injected with same volume of saline.

value: 28 wks at the time of RNA isolation

tag: background strain

value: untreated

value: spleen


title: SPSAWT_replicate8

description:
run0112_lane6_index9=T460SP~mouse_align
untreated Lung of 9V/null mice


title: SPSAWT_replicate1

description:
run0110_lane7_index6=T373SP~mouse_align
untreated Lung of 9V/null mice


title: SPSAWT_replicate4

description:
run0112_lane6_index1=T376_T420_T461SP~mouse_align
untreated Lung of 9V/null mice


title: Ikaros ZnF1-/- Thymus rep1


title: SPSAKO_replicate7

description:
run0110_lane7_index5=T467_T481_T483SP~mouse_align
saline treated Spleen of 9V/null mice

value: saline


title: SPSAWT_replicate7

description:
run0112_lane7_index12=T373_T419_T421SP~mouse_align
untreated Lung of 9V/null mice


title: SPSAKO_replicate6

description:
run0110_lane7_index4=T465_T325_T326SP~mouse_align
saline treated Spleen of 9V/null mice


title: SPSAKO_replicate5

description:
run0110_lane7_index3=T462_T466_T482SP~mouse_align
saline treated Spleen of 9V/null mice


title: SPSAKO_replicate4

description:
run0110_lane7_index2=T483SP~mouse_align
saline treated Spleen of 9V/null mice


title: SPSAKO_replicate3

description:
run0110_lane7_index1=T482SP~mouse_align
saline treated Spleen of 9V/null mice


title: SPSAKO_replicate2

description:
run0110_lane6_index12=T481SP~mouse_align
saline treated Spleen of 9V/null mice


title: SPSAKO_replicate1

description:
run0110_lane6_index11=T467SP~mouse_align
saline treated Spleen of 9V/null mice


title: SPGCBKO_replicate4

description:
run0110_lane6_index7=T324SP~mouse_align
vela treated Spleen of 9V/null

value: GCB (velaglucerase)


title: SPGCBKO_replicate3

description:
run0110_lane6_index9=T471SP~mouse_align
vela treated Spleen of 9V/null


title: SPCZKO_replicate4

description:
run0110_lane5_index6=T480_T475_T476SP~mouse_align
imig treated Spleen of 9V/null mice

value: CZ (imiglucerase)


title: SPSAWT_replicate6

description:
run0112_lane6_index8=T420SP~mouse_align
untreated Lung of 9V/null mice


title: SPCZKO_replicate3

description:
run0110_lane5_index5=T480SP~mouse_align
imig treated Spleen of 9V/null mice


title: SPCZKO_replicate1

description:
run0110_lane5_index3=T375SP~mouse_align
imig treated Spleen of 9V/null mice


title: SPSAWT_replicate5

description:
run0112_lane6_index7=T376SP~mouse_align
untreated Lung of 9V/null mice


title: LVSAWT_replicate3

description:
run0110_lane5_index1=T374_T376_T461LV~mouse_align
saline treated Liver of WTmice

value: liver


title: LVSAWT_replicate4

description:
run0110_lane5_index2=T417_T419_T420LV~mouse_align
saline treated Liver of WTmice


title: LVSAKO_replicate3

description:
run0109_lane6_index8=T245_T462_T482LV~mouse_align
saline treated Liver of 9V/null mice


title: LVSAWT_replicate1

description:
run0109_lane6_index11=T372_T375_T460LV~mouse_align
saline treated Liver of WT mice


title: LVSAWT_replicate2

description:
run0109_lane6_index12=T373_T418_T421LV~mouse_align
saline treated Liver of WT mice


title: LVSAKO_replicate2

description:
run0109_lane6_index7=T244_T463_T481LV~mouse_align
saline treated Liver of 9V/null mice


title: LVSAKO_replicate4

description:
run0109_lane6_index9=T255_T464_T323LV~mouse_align
saline treated Liver of 9V/null mice


title: LVSAKO_replicate1

description:
run0109_lane6_index10=T257_T465_T467LV~mouse_align
saline treated Liver of 9V/null mice


title: SPSAWT_replicate2

description:
run0112_lane6_index10=T461SP~mouse_align
untreated Lung of 9V/null mice


title: LVGCBKO_replicate2

description:
run0109_lane5_index4=T249_T497_T498LV~mouse_align
vela treated Liver of 9V/null mice


title: LVGCBKO_replicate3

description:
run0109_lane5_index5=T250_T468_T471LV~mouse_align
vela treated Liver of 9V/null mice


title: LVGCBKO_replicate1

description:
run0109_lane5_index3=T246_T247_T470LV~mouse_align
vela treated Liver of 9V/null mice


title: LUSAWT_replicate4

description:
run0109_lane3_index6=T375_T419_T421LU~mouse_align
Saline treated Lung of WT mice

value: lung


title: LVCZKO_replicate3

description:
run0109_lane5_index1=T253_T502_T529LV~mouse_align
imig treated Liver of 9V/null mice


title: LVCZKO_replicate2

description:
run0109_lane3_index7=T476_T500_T528LV~mouse_align
imig treated Liver of 9V/null mice


title: LVCZKO_replicate4

description:
run0109_lane5_index2=T254_T478_T501LV~mouse_align
imig treated Liver of 9V/null mice


title: LUSAWT_replicate2

description:
run0109_lane3_index2=T372_T418_T461LU~mouse_align
Saline treated Lung of WT mice


title: SPGCBKO_replicate1

description:
run0110_lane6_index10=T324_T471_T468SP~mouse_align
vela treated Spleen of 9V/null


title: SPCZKO_replicate2

description:
run0110_lane5_index4=T476SP~mouse_align
imig treated Spleen of 9V/null mice


title: LVGCBKO_replicate4

description:
run0109_lane5_index6=T469_T472_T473LV~mouse_align
vela treated Liver of 9V/null mice


title: LUSAKO_replicate4

description:
run0109_lane2_index12=T323_T466_T483LU~mouse_align
saline treated Lung of 9V/null mice


title: LUSAKO_replicate3

description:
run0109_lane2_index9=T244_T467_T481LU~mouse_align
saline treated Lung of 9V/null mice


title: LUGCBKO_replicate4

description:
run0109_lane2_index8=T474_T497_T498LU~mouse_align
vela treated Lung of 9V/null mice


title: LUSAKO_replicate2

description:
run0109_lane2_index11=T463_T464_T482LU~mouse_align
saline treated Lung of 9V/null mice


title: LUGCBKO_replicate3

description:
run0109_lane2_index7=T246_T468_T469LU~mouse_align
vela treated Lung of 9V/null mice


title: LUGCBKO_replicate2

description:
run0109_lane1_index6=T249_T250_T470LU~mouse_align
vela treated Lung of 9V/null mice


title: SPGCBKO_replicate2

description:
run0110_lane6_index8=T468SP~mouse_align
vela treated Spleen of 9V/null


title: SPGCBKO_rep3

description:
vela treated Spleen of 9V/null
run0110_lane6_index9=T471SP~mouse_align

data_processing:
mRNA-Seq reads were aligned to the mm9 version of the mouse genome reference using the TopHat/Cufflinks pipeline. First, sequences were aligned to the genome with TopHat , which efficiently aligned reads spanning known or novel splice junctions. Each sample was then independently processed with Cufflinks  in order to generate an initial transcriptome.   Finally, the Cuffmerge tool was used to merge the known and any novel isoforms into a single BAM file, and simultaneously extended partial transcripts.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
DESeq and Mixed Model Anova were used to  evaluate the DEGs from the mRNA-Seq data and microrray data.
For DESeq normalization, the sequencing depth is estimated by the read count of the gene with the median read count ratio across all genes.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include DESeq normalised values for each Sample

extract_protocol:
9V/null mice were sacrificed one wk after the last injection along with WT mice,  lung, liver and spleen were collected for RNA analysis.
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.


title: LUCZKO_replicate4

description:
run0109_lane1_index3=T478_T499_T529LU~mouse_align
imig treated Lung of 9V/null mice


title: LUGCBKO_replicate1

description:
run0109_lane1_index5=T248_T471_T473LU~mouse_align
vela treated Lung of 9V/null mice


title: LUCZKO_replicate1

description:
run0109_lane1_index1=T475_T477_T480LU~mouse_align
imig treated Lung of 9V/null mice


title: LUCZKO_replicate2

description:
run0109_lane1_index2=T476_T500_T502LU~mouse_align
imig treated Lung of 9V/null mice


title: SPGCBKO_rep4

description:
vela treated Spleen of 9V/null
run0110_lane6_index7=T324SP~mouse_align


title: LVCZKO_replicate1

description:
run0109_lane3_index5=T321_T252_T477LV~mouse_align
imig treated Liver of 9V/null mice


title: SPCZKO_rep2

description:
imig treated Spleen of 9V/null mice
run0110_lane5_index4=T476SP~mouse_align


title: SPCZKO_rep3

description:
imig treated Spleen of 9V/null mice
run0110_lane5_index5=T480SP~mouse_align


title: LVGCBKO_rep4

description:
vela treated Liver of 9V/null mice
run0109_lane5_index6=T469_T472_T473LV~mouse_align


title: LUCZKO_replicate3

description:
run0109_lane1_index4=T479_T501_528LU~mouse_align
imig treated Lung of 9V/null mice


title: SPGCBKO_rep2

description:
vela treated Spleen of 9V/null
run0110_lane6_index8=T468SP~mouse_align


title: SPCZKO_rep4

description:
imig treated Spleen of 9V/null mice
run0110_lane5_index6=T480_T475_T476SP~mouse_align


title: SPGCBKO_rep1

description:
vela treated Spleen of 9V/null
run0110_lane6_index10=T324_T471_T468SP~mouse_align


title: LVGCBKO_rep1

description:
vela treated Liver of 9V/null mice
run0109_lane5_index3=T246_T247_T470LV~mouse_align


title: LVCZKO_rep 4

description:
imig treated Liver of 9V/null mice
run0109_lane5_index2=T254_T478_T501LV~mouse_align


title: LUSAWT_replicate3

description:
run0109_lane3_index4=T373_T374_T420LU~mouse_align
Saline treated Lung of WT mice


title: LVCZKO_rep 1

description:
imig treated Liver of 9V/null mice
run0109_lane3_index5=T321_T252_T477LV~mouse_align


title: LVCZKO_rep 2

description:
imig treated Liver of 9V/null mice
run0109_lane3_index7=T476_T500_T528LV~mouse_align


title: LUSAKO_replicate1

description:
run0109_lane2_index10=T245_T462_T484LU~mouse_align
saline treated Lung of 9V/null mice


title: LUGCBKO_rep4

description:
vela treated Lung of 9V/null mice
run0109_lane2_index8=T474_T497_T498LU~mouse_align


title: LUGCBKO_rep3

description:
vela treated Lung of 9V/null mice
run0109_lane2_index7=T246_T468_T469LU~mouse_align


title: LUGCBKO_rep2

description:
vela treated Lung of 9V/null mice
run0109_lane1_index6=T249_T250_T470LU~mouse_align


title: LUGCBKO_rep1

description:
vela treated Lung of 9V/null mice
run0109_lane1_index5=T248_T471_T473LU~mouse_align


title: LUCZKO_rep4

description:
imig treated Lung of 9V/null mice
run0109_lane1_index3=T478_T499_T529LU~mouse_align


title: LUCZKO_rep2

description:
imig treated Lung of 9V/null mice
run0109_lane1_index2=T476_T500_T502LU~mouse_align


title: LVGCBKO_rep3

description:
vela treated Liver of 9V/null mice
run0109_lane5_index5=T250_T468_T471LV~mouse_align


title: LUCZKO_rep1

description:
imig treated Lung of 9V/null mice
run0109_lane1_index1=T475_T477_T480LU~mouse_align


title: SPCZKO_rep1

description:
imig treated Spleen of 9V/null mice
run0110_lane5_index3=T375SP~mouse_align


title: LUSAWT_replicate1

description:
run0109_lane3_index12=T376_T417_T460LU~mouse_align
Saline treated Lung of WT mice