title: v6.5-dC5 K27Ac_ChipSeq

city: Cambridge

description: Chromatin IP against dC5 K27Ac

data_processing:
Images analysis and base calling was done using the solexa pipeline.
Aligned using bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
Genome_build: mm9
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment and were generated with MACS 14 with parameters -w -S --nomodel --shiftsize=200. Counts are in reads-per-million.

source_name: Embryonic stem cells

growth_protocol: Grown and ChIPped in the Young Lab

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: chip antibody

value: Abcam AB4729

value: V6.5 PRDM14 dC5

tag: deleted region

value: v6.5-dC5 K27Ac_ChipSeq

tag: barcode (already removed)

value: TGACCA


title: FnrL_ChIP_Seq_Rep2

status: Public on Dec 15 2014

type: SRA

city: Madison

first: Timothy

middle: J

last: Donohue

state: WI

address: 1552 University Avenue

department: Bacteriology

country: USA

institute: University of Wisconsin - Madison

library_source: genomic

data_processing:
100 bp reads were trimmed to 70bp to remove unreliable base calls. 50bp reads were not trimmed
Mapping was done to the R. sphaeroides reference genome using SOAP version 2.21 allowing for 3 mismatches for 70bp reads and 2 mismatches for 50bp reads
Peaks were identified using MOSAiCS at a false discovery rate of 0.05 using a two-sample analysis with Input DNA or mock chip used as control.
Genome_build: Rhodobacter sphaeroides 2.4.1 GCA_000012905.2
Supplementary_files_format_and_content: Processed data files are provided as wig files with scores representing the normalized ratio of reads between a sample ChIP and INPUT DNA

molecule: genomic DNA

organism: Cereibacter sphaeroides

source_name: Bacteria culture (SIS - Photo)

growth_protocol: R. sphaeroides strains that were grown in 500 ml cultures in roux bottles either photosynthetically (bubbling with 95% N2, 5% CO2) on Sistrom's minimal media and harvested at exponential phase. Where necessary 1 to 5μL of IPTG was added at the start of the culture to induce protein expression.

extract_protocol:
At midexponential phase (~2×108 colony-forming units/ml), formaldehyde and sodium phosphate were added to a final concentration of 1% and 10 mM, respectively. This mixture was incubated at 30 °C for 4 min before glycine was added to 100 mM, and the solution was placed on ice for 30 min with gentle agitation to quench excess formaldehyde. Cells were centrifuged at 3000g, washed twice with chilled phosphate buffered saline, centrifuged, and flash-frozen at −80 °C. About 2×1010 cells were suspended in 0.5 ml of 100 mM Tris (pH 8.0), 300 mM NaCl, 2% Triton X-100, RNase A (0.5 μg) and 1 mM phenylmethylsulfonyl fluoride, and sonicated in a Misonix water bath for 8 mins with 10s pulses and intervals. Cell debris was removed by centrifugation for 10 min at 12,000g, and an aliquot was removed to analyze DNA fragmentation by agarose gel eletrophoresis (desired size of ~200–1000 bp with enrichment for ~500-bp molecules). The resulting supernatant was incubated with gentle mixing with 20 μl of Staphylococcus aureus protein A Sepharose beads (Sigma-Aldrich, St. Louis, MO) for 3 h at 4 °C as pretreatment to remove potential nonspecific binding to the beads. After the beads had been removed by centrifugation (5 min at 3000g), one-tenth of the sample was removed and used as non-antibody-treated control. Five microlitre of Myc epitope antibody (ab9132, Abcam plc) or FnrL polyclonal antibody was added and the mixture was incubated overnight at 4 °C with gentle mixing before being incubated with protein A Sepharose beads (30 μl) for 3 h at 4 °C. The beads were recovered by centrifugation; washed once (4 °C) with 250 mM LiCl, 100 mM Tris (pH 8.0), and 2% Triton X-100; washed twice with 600 mM NaCl, 100 mM Tris (pH 8.0), and 2% Triton X-100; washed twice with 300 mM NaCl, 100 mM Tris (pH 8.0), and 2% Triton X-100; and washed twice with TE buffer (10 mM Tris pH 8.0 and 1 mM EDTA). Protein–DNA complexes were eluted from the beads by incubating at 65 °C for 30 min in 50 mM Tris (pH 8.0), 10 nM EDTA, and 1% sodium dodecyl sulfate. The beads were removed by centrifugation, and protein–DNA cross-linking was reversed by incubating the samples for 12 h at 65 °C. DNA was purified using the QIAquick PCR Purification Kit. Samples were sent to UW-Madison Biotech center for further processing and sequencing.
Libraries were prepared according to Illumina's instructions by UW-Madison biotech center

tag: strain

tag: chip-antibody

value: FnrL polyclonal antibody


title: FnrL_Control_ChIP

source_name: Bacteria culture (Acetate - Photo)


title: E14.5 DRG (30ng, high volume)

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

library_source: transcriptomic

data_processing:
The raw image data is converted to basecalls with Casava 1.8+ and the indexed samples are demultiplexed into individual gzipped fastQ files with proprietary demultiplexer algorithm.  The fastQ files are then aligned to the transcriptome and the whole-genome with TopHat version 2.0.8 using Bowtie2 version 2.1.0.
The RPKM values were derived from the unique alignments to transcripts by RPKM_count.py in the RSeQC version 2.3 package of RNA-seq QC tools.
Genome build: GRCm38.p1
Supplementary_files_format_and_content: Excel spreadsheet including RPKM values for each Sample.

molecule: total RNA

organism: Mus musculus

source_name: E14.5 dorsal root ganglia (30ng high volume, total RNA, pooled sample)

extract_protocol:
1)  DRGs from eighteen E14.5 embryos were lysed in TRIzol-LS (Life Technologies, #10296-010).  2. The RNA was extracted according to M Southard-Smith's RNA isolation procedure from flow sorted cells found on the GUDMAP website (Southard-Smith Group protocols).  3. Following QC/QA on the Nanodrop and Bioanalyzer 'pico' chip the RNA concentration was adjusted to 100ng/ul and used as a master stock. This was used to make further dilutions as needed for the RNAseq experiments.
library_construction_protocol : 1) 3ng, 10ng or 30ng total RNA (in 9µl) was reverse transcribed and amplified using the SMARTer® Ultra™ Low Input RNA for Illumina® Sequencing - HV (Clontech, cat# 634828) according to the manufacturer’s instructions.  2) The cDNA was sheared for 3 minutes with the Covaris ultra-sonicator.   3) The libraries were prepared using VeraSeq™ ULtra DNA Polymerase (Enzymatics, cat# P7520L) for 12 cycles.  PCR conditions were 98°C for 30s; 12 cycles of 98°C for 10s, 64°C for 30s, 72°C for 30s; 72°C for 5 minutes and then hold at 4°C.  The forward primer used was: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT. The reverse primer with the indexes can be viewed on the GUDMAP website (Jain Group protocols).

treatment_protocol: DRGs were dissected from 18 E14.5 C57BL/6J embryos, pooled and lysed in TRIzol-LS (Life Technologies, #10296-010) per manufacturer’s protocol.

tag: genotype

value: wild type

tag: tissue

value: dorsal root ganglion

tag: theiler stage

tag: developmental stage

tag: Sex

value: unknown

tag: pooled sample

value: yes

tag: pool size

value: Dorsal root ganglia from 18 embryos


title: E14.5 DRG (3ng, low volume)

source_name: E14.5 dorsal root ganglia (3ng low volume, total RNA, pooled sample)

extract_protocol:
1)  DRGs from eighteen E14.5 embryos were lysed in TRIzol-LS (Life Technologies, #10296-010).  2. The RNA was extracted according to M Southard-Smith's RNA isolation procedure from flow sorted cells found on the GUDMAP website (Southard-Smith Group protocols).  3. Following QC/QA on the Nanodrop and Bioanalyzer 'pico' chip the RNA concentration was adjusted to 100ng/ul and used as a master stock. This was used to make further dilutions as needed for the RNAseq experiments.
library_construction_protocol : 1) 3ng, 10ng or 30ng total RNA (in 1µl) was reverse transcribed and amplified using the SMARTer® Ultra™ Low RNA Kit for Illumina® Sequencing (Clontech, cat# 634936) according to the manufacturer’s instructions.  2) The cDNA was sheared for 3 minutes with the Covaris ultra-sonicator.   3) The libraries were prepared using VeraSeq™ ULtra DNA Polymerase (Enzymatics, cat# P7520L) for 12 cycles.  PCR conditions were 98°C for 30s; 12 cycles of 98°C for 10s, 64°C for 30s, 72°C for 30s; 72°C for 5 minutes and then hold at 4°C.  The forward primer used was: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT. The reverse primer with the indexes can be viewed on the GUDMAP website (Jain Group protocols).


title: E14.5 DRG (10ng, low volume)

source_name: E14.5 dorsal root ganglia (10ng low volume, total RNA, pooled sample)


title: E14.5 DRG (10ng, high volume)

source_name: E14.5 dorsal root ganglia (10ng high volume, total RNA, pooled sample)


title: iPSC_WBS2-C2 (GDB-316_M) GTF2I ChIP-seq

city: Milano

first: Giuseppe

last: Testa

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology & University of Milano, Italy

description: Sonication was performed in a 1000uL vial, using Peak power 140, Duty Factor 5%, Cycle/Burst 200 for 15 minutes, to obtain a DNA bulk of 250bp.

data_processing:
Base calling and primary read filtering were performed according to Illumina protocols.
Reads were trimmed for adapter contamination using Scythe 0.981 with a minimum match of 3.
Alignment to the hg19 genome was performed with BowTie 1.0, allowing 2 mismatches and discarding multiply aligning reads.
Peaks were called using Macs 2.0.9 with default settings and ignoring duplicated reads. To generate BigWig tracks, aligned reads were extended by 180bp.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig tracks and BED files of peaks coordinates

organism: Homo sapiens

source_name: Fibroblast-derived iPSC

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen) according to manufacturer specifications.
About 10^8 iPSCs have been cross linked for 10 minutes in PBS containing 1% formaldehyde at room temperature. Crosslinking was quenched adding Glycine to a final concentration of 125mM for 5 minutes at room temperature. Cells nuclei were lysed using ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) and sonicated using the Covaris Sonicator (see sample description) to obtain a sheared chromatin DNA bulk of 250 bp. Sheared chromatin was incubated with GTF2I (15ug) or LSD1 (10ug) antibodies overnight rotating at 4 degree. The day after the antibody was recovered using Dynabeads Protein G (Life Technologies) and washed 4 times using washing buffers. Finally DNA was eluted using SDS containing elution buffer and decrossliked overnight at 65 degree. The third day decrosslinked DNA was digested using proteinase K for 60 minutes at 45 degree and purified using DNA-purification columns (Qiagen).

value: WBS

tag: donor

tag: gender

value: female

value: GTF2I (Bethyl A301-330A)

tag: flowcell id


title: ChIP-seq analysis of p65 in KB cells (p65 DMSO IL1)

status: Public on Dec 16 2014

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

description: ChIP-seq

data_processing:
Quality control of FASTQ files was done using FastQC.
Removal of low quality reads was done using fastx_toolkit-0.06
Reads were aligned to a pre-compiled index of the mouse hg19 genome using Bowtie (options: -k 1 -m 1) 0.12.5.
Duplicate reads were removed with Samtools' rmdup function.
Samtools was used to convert aligned reads to BAM format.
MACS 1.4 was used to call peaks at default settings
Genome_build: hg19
Supplementary_files_format_and_content: coverage Wiggle files were generated with Mscs1.4 at 10 bp resolution. Wig files were converted to bigwig using the wigToBigWig utility (UCSC)

source_name: KB cells

growth_protocol: cells were cultured in DMEM, 10% FCS, to subconfluency

extract_protocol:
ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris pH 8.1, 1mM PMSF, Roche protease inhibitor mix), followed by IP and purification of DNA
Sequencing libraries were prepared from 10 ng of immunoprecipitated DNA with the Illumina ChIPSeq DNA Sample Prep Kit according to Illuminas’ instructions

treatment_protocol: IL-1 alpha and inhibitors PHA-408 and 5Z-oxozeaenol were added directly to the cell culture medium

value: 10ng/ml IL-1alpha for 1 h

tag: antibody

value: anti-p65 (Santa Cruz, catalog# sc-372, Lot #K2210)


title: iPSC_WBS3-C2 (GDB-361_O) GTF2I ChIP-seq


title: iPSC_WBS1-C3 (GDB-339-C7) GTF2I ChIP-seq

value: male


title: v6.5 input_ChipSeq

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Chromatin IP against v6.5 input

growth_protocol:
Most common:  V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.
Grown and ChIPped in the Young Lab

value: Input

tag: cell type

value: V6.5 embryonic stem cells

value: v6.5 input_ChipSeq

value: CGTACG


title: FnrL_ChIP_Seq_Rep1


title: iPSC_AtWBS1-C2 (GDB-192_B) GTF2I ChIP-seq

value: AtWBS

tag: chip antibody


title: v6.5-dC2 K27Ac_ChipSeq

description: Chromatin IP against dC2 K27Ac

tag: antibody catalog number

value: Abcam AB4729

value: V6.5 PRDM14 dC2

tag: deleted region

value: v6.5-dC2 K27Ac_ChipSeq

value: ACAGTG


title: ChIP-seq analysis of H3K27Ac in KB cells (H3K27Ac)

description: ChIP-seq

value: Anti-H3K27Ac (Diagenode, catalog# 174-050, Lot #A7071-001P)


title: iPSC_CTL1R-C1 (GDB-339-1_B) ChIP-seq input

value: Control


title: v6.5-dC3 input_ChipSeq

description: Chromatin IP against dC3 input

growth_protocol: Grown and ChIPped in the Young lab

value: V6.5 PRDM14 dC3

value: v6.5-dC3 input_ChipSeq

tag: barcode (already removed)

value: ATCACG


title: iPSC_CTL1R-C3 (GDB-339-1_S) ChIP-seq input (for LSD1 experiment)

description: Sonication was performed in a 130uL vial, using Peak power 175, Duty Factor 10%, Cycle/Burst 200 for 8 minutes, to obtain a DNA bulk of 250bp.

value: female


title: v6.5-dC5 PolII_ChipSeq

description: Chromatin IP against dc5 PolII

value: RNA Pol II

value: Abcam AB817

value: V6.5 PRDM14 dC5

value: v6.5-dC5 PolII_ChipSeq

value: TGACCA


title: v6.5-dC5 input_ChipSeq

description: dC5 input jmjd6

value: Input

value: v6.5-dC5 input_ChipSeq

value: TTAGGC


title: v6.5-dC1 input_ChipSeq

description: Chromatin IP against dC1 input

value: V6.5 PRDM14 dC1

value: v6.5-dC1 input_ChipSeq

value: ACTGAT


title: v6.5-dC3 PolII_ChipSeq

description: Chromatin IP against dC3 PolII

value: v6.5-dC3 PolII_ChipSeq

value: CGATGT


title: v6.5-dC3 K27Ac_ChipSeq

description: Chromatin IP against dC3 K27Ac

value: Abcam AB4729

value: V6.5 PRDM14 dC3

value: v6.5-dC3 K27Ac_ChipSeq


title: iPSC_CTL2-C2 (Miff_3) ChIP-seq input

value: Control

value: Miff

value: male

value: GTF2I (Bethyl A301-330A)


title: iPSC_CTL1R-C1 (GDB-339-1_B) GTF2I ChIP-seq

value: female


title: iPSC_CTL1R-C3 (GDB-339-1_S) LSD1/KDM1A ChIP-seq

value: KDM1A (Abcam AB17721)


title: iPSC_CTL1R-C1 (GDB-339-1_B) igG ChIP-seq

value: igG (SantaCruz SC2027)


title: v6.5-dC1 PolII_ChipSeq

description: Chromatin IP against dC1 PolII

value: RNA Pol II

value: Abcam AB817

value: v6.5-dC1 PolII_ChipSeq

value: ATTCCT


title: iPSC_7dupASD2-C1 (GDB-242_K) GTF2I ChIP-seq


title: v6.5-dC2 input_ChipSeq

description: dC2 input

value: Input

value: V6.5 PRDM14 dC2

value: v6.5-dC2 input_ChipSeq

value: GCCAAT


title: v6.5 K27Ac_ChipSeq

description: Chromatin IP against v6.5 K27Ac

value: Abcam AB4729

value: V6.5 embryonic stem cells

value: v6.5 K27Ac_ChipSeq

value: ATCACG


title: iPSC_7dupASD1-C2 (GDB-Cf_G) ChIP-seq input

value: GDB-Cf

value: male


title: v6.5-dC1 K27Ac_ChipSeq

description: Chromatin IP against dC1 K27Ac

value: V6.5 PRDM14 dC1

value: v6.5-dC1 K27Ac_ChipSeq


title: iPSC_CTL1R-C3 (GDB-339-1_S) ChIP-seq input 2

value: Control

value: female

value: C26CLACXX, C1ULAACXX


title: iPSC_WBS4-C1 (GDB-306_O) ChIP-seq input

value: WBS

value: GTF2I (Bethyl A301-330A)


title: v6.5 PolII_ChipSeq

description: Chromatin IP against v6.5 PolII

value: RNA Pol II

value: Abcam AB817

value: v6.5 PolII_ChipSeq

value: GAGTGG


title: iPSC_CTL1R-C3 (GDB-339-1_S) GTF2I ChIP-seq, rep2


title: iPSC_CTL1R-C3 (GDB-339-1_S) GTF2I ChIP-seq, rep1

description: Failed QC. Sonication was performed in a 130uL vial, using Peak power 175, Duty Factor 10%, Cycle/Burst 200 for 8 minutes, to obtain a DNA bulk of 250bp.


title: iPSC_WBS1-C1 (GDB-339_C2) GTF2I ChIP-seq


title: iPSC_CTL1R-C3 (GDB-339-1_S) ChIP-seq input 1

description: Used to test antibodies. Sonication was performed in a 130uL vial, using Peak power 175, Duty Factor 10%, Cycle/Burst 200 for 8 minutes, to obtain a DNA bulk of 250bp.


title: iPSC_CTL1R-C3 (GDB-339-1_S) ChIP-seq input 3


title: iPSC_CTL1R-C3 (GDB-339-1_S) GTF2I ChIP-seq (Santa Cruz antibody)

value: GTF2I (Santa Cruz SC9943)


title: iPSC_7dupASD2-C3 (GDB-242_J) GTF2I ChIP-seq


title: v6.5-dC2 RNAPOLII_ChipSeq

description: Chromatin IP against dC2 RNAPOLII

value: V6.5 PRDM14 dC2

value: v6.5-dC2 RNAPOLII_ChipSeq

value: CAGATC


title: MSC WBS1-C1 (GDB-339_C2) ribo-zero RNAseq

description: Ribo-zero depleted RNA

data_processing:
Base calling and primary read filtering were performed according to Illumina protocols.
Reads were aligned to the hg19 transcriptome using TopHat 2.0.10. The alignment was first performed on the RefSeq transcriptome and all the reads that had an edit distance greater than 0 were realigned on the genome, allowing a maximum read edit distance of 3, and a maximum of 2 or 3 mismatches (respectively for 50bp and 100bp reads). 50bp stranded reads were analyzed using the “fr-firststrand” option.
Quantification of reads over the RefSeq transcriptome was performed with Cufflinks 2.2.1 using sequence-bias and multi-read corrections.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM matrix of all samples, normalized with Cuffnorm (geometric normalization).

source_name: Mesenchymal Stem Cells (MSC), iPSC-derived

growth_protocol: iPSC Colonies were grown in feeder-free condition on plates coated with human-qualified Matrigel (BD Biosciences) diluted 1:40 in DMEM-F12 and in mTeSR-1 (StemCell Technologies) medium. Single cell culture: Feeder-free iPSCs were also adapted to grow in single cell culture by dissociating them by a 3 minutes treatment with Accutase (Sigma) at 37°C and finally resuspended in a suitable volume of mTeSR-1 supplemented with 5 μM Y-27632 (Sigma), as described in Watanabe et al., Nat Biotechnol 25, 681-6 (2007). MSC differentiation and culture was performed as described in Menendez et al., Nat Protoc 8, 203-12 (2013).

extract_protocol:
RNA was extracted from iPSC lines using the RNeasy Micro Plus Kit (Qiagen) according to manufacturer specifications, substituting the genomic DNA elimination column by needle and Dnase treatment (Qiagen).
Library preparation performed using either Poly-A, RiboZero unstranded, or RiboZero stranded Illumina kits (see sample descriptions) according to manufacturer instructions.

tag: spike-in

value: ERCC ExFold mix 2

tag: library-type

value: stranded 51bp PE reads


title: MSC CTL1R-C3 (GDB-339-1_S) ribo-zero RNAseq

description: Ribo-zero depleted RNA

tag: genotype

value: ERCC ExFold mix 1


title: iPSC_CTL1R-C3 (GDB-339-1_S) GTF2I ChIP-seq (Cell Signaling antibody)

value: GTF2I (Cell Signalling 4562S)


title: MSC AtWBS1-C2 (GDB-192_B) ribo-zero RNAseq

description: Ribo-zero depleted RNA

value: AtWBS


title: MSC CTL2-C2 (Miff_3) ribo-zero RNAseq

description: Ribo-zero depleted RNA

value: Control

value: Miff

value: male


title: MSC CTL3-C1 (Bu1Cr3_1) ribo-zero RNAseq

description: Ribo-zero depleted RNA


title: MSC 7dupASD1-C2 (GDB-Cf_G) ribo-zero RNAseq

description: Ribo-zero depleted RNA

value: GDB-Cf


title: iPSC AtWBS1-C2 (GDB-192_B) Scramble, ribo-zero RNAseq

description:
Ribo-zero depleted RNA
Stable line derived from AtWBS1-C2, infected with scramble short hairpin.

source_name: Skin fibroblast-derived iPSC

value: female

tag: culture

value: Single-cell culture


title: MSC 7dupASD2-C1 (GDB-242_K) ribo-zero RNAseq

description: Ribo-zero depleted RNA


title: iPSC WBS4-C1 (GDB-306_O) GTF2I KD, ribo-zero RNAseq

description:
Ribo-zero depleted RNA
Stable line derived from WBS4-C1, infected with short hairpin sh2 against GTF2I.

value: WBS


title: iPSC CTL1R-C3 (GDB-339-1_S) Scramble, ribo-zero RNAseq

description:
Ribo-zero depleted RNA
Stable line derived from CTL1R-C3, infected with scramble short hairpin.


title: iPSC CTL1R-C3 (GDB-339-1_S) GTF2I KD, ribo-zero RNAseq

description:
Ribo-zero depleted RNA
Stable line derived from CTL1R-C3, infected with short hairpin sh2 against GTF2I.


title: iPSC 7dupASD2-C1 (GDB-242_K) Scramble, ribo-zero RNAseq

description:
Ribo-zero depleted RNA
Stable line derived from 7dupASD2-C1, infected with scramble short hairpin.


title: iPSC WBS2-C2 (GDB-316_M) GTF2I KD, ribo-zero RNAseq

description:
Ribo-zero depleted RNA
Stable line derived from WBS2-C2, infected with short hairpin sh2 against GTF2I.


title: iPSC WBS2-C2 (GDB-316_M) Scramble, ribo-zero RNAseq

description:
Ribo-zero depleted RNA
Stable line derived from WBS2-C2, infected with scramble short hairpin.


title: iPSC CTL1R-C1 (GDB-339-1_B) GTF2I KD, ribo-zero RNAseq

description:
Ribo-zero depleted RNA
Stable line derived from CTL1R-C1, infected with short hairpin sh2 against GTF2I.


title: iPSC CTL1R-C1 (GDB-339-1_B) Scramble, ribo-zero RNAseq

description:
Ribo-zero depleted RNA
Stable line derived from CTL1R-C1, infected with scramble short hairpin.


title: iPSC 7dupASD2-C1 (GDB-242_K) GTF2I KD, ribo-zero RNAseq

description:
Ribo-zero depleted RNA
Stable line derived from 7dupASD2-C1, infected with short hairpin sh2 against GTF2I.


title: iPSC WBS4-C1 (GDB-306_O) Scramble, ribo-zero RNAseq

description:
Ribo-zero depleted RNA
Stable line derived from WBS4-C1, infected with scramble short hairpin.


title: iPSC 7dupASD1-C2 (GDB-Cf_G) Scramble, ribo-zero RNAseq

description:
Ribo-zero depleted RNA
Stable line derived from 7dupASD1-C2, infected with scramble short hairpin.


title: iPSC 7dupASD1-C2 (GDB-Cf_G) GTF2I KD, ribo-zero RNAseq

description:
Ribo-zero depleted RNA
Stable line derived from 7dupASD1-C2, infected with short hairpin sh2 against GTF2I.


title: iPSC CTL2-C2 (Miff_3) polyA RNAseq

description: Poly-A RNA

value: Colonies in feeder-free condition

value: unstranded 100bp PE reads


title: iPSC CTL2-C1 (Miff_1) polyA RNAseq

description: Poly-A RNA


title: iPSC WBS1-C3 (GDB-339_C7) polyA RNAseq

description: Poly-A RNA


title: iPSC 7dupASD1-C1 (GDB-Cf_C) polyA RNAseq

description: Poly-A RNA


title: iPSC 7dupASD1-C3 (GDB-Cf_F) polyA RNAseq

description: Poly-A RNA


title: iPSC 7dupASD1-C2 (GDB-Cf_G) polyA RNAseq

description: Poly-A RNA


title: MSC WBS2-C1 (GDB-316_M) ribo-zero RNAseq

description: Ribo-zero depleted RNA


title: MSC WBS4-C1 (GDB-306_O) ribo-zero RNAseq

description: Ribo-zero depleted RNA


title: iPSC AtWBS1-C2 (GDB-192_B) GTF2I KD, ribo-zero RNAseq

description:
Ribo-zero depleted RNA
Stable line derived from AtWBS1-C2, infected with short hairpin sh2 against GTF2I.


title: iPSC WBS1-C1 (GDB-339_C2) polyA RNAseq

description: Poly-A RNA


title: iPSC WBS3-C1 (GDB-361_O) polyA RNAseq

description: Poly-A RNA


title: iPSC CTL3-C1 (Bu1Cr3_1) polyA RNAseq

description: Poly-A RNA


title: iPSC WBS3-C3 (GDB-361_E) polyA RNAseq

description: Poly-A RNA


title: iPSC WBS1-C2 (GDB-339_C3) polyA RNAseq

description: Poly-A RNA


title: iPSC WBS2-C2 (GDB-316_L) polyA RNAseq

description: Poly-A RNA


title: iPSC WBS2-C3 (GDB-316_B) polyA RNAseq

description: Poly-A RNA


title: iPSC WBS4-C2 (GDB-306_M) polyA RNAseq

description: Poly-A RNA


title: iPSC WBS4-C3 (GDB-306_E) polyA RNAseq

description: Poly-A RNA


title: iPSC WBS4-C1 (GDB-306_O) polyA RNAseq

description: Poly-A RNA


title: iPSC AtWBS1-C3 (GDB-192_D) polyA RNAseq

description: Poly-A RNA


title: iPSC AtWBS1-C1 (GDB-192_P) polyA RNAseq

description: Poly-A RNA


title: iPSC CTL1R-C3 (GDB-339-1_S) ribo-zero RNAseq

description: Ribo-zero depleted RNA


title: iPSC AtWBS1-C2 (GDB-192_B) polyA RNAseq

description: Poly-A RNA


title: iPSC CTL2-C2 (Miff_3) ribo-zero RNAseq

description: Ribo-zero depleted RNA


title: iPSC AtWBS1-C3 (GDB-192_D) ribo-zero RNAseq

description: Ribo-zero depleted RNA


title: iPSC WBS1-C1 (GDB-339_C2) ribo-zero RNAseq

description: Ribo-zero depleted RNA


title: iPSC CTL1R-C2 (GDB-339-1_R) ribo-zero RNAseq

description: Ribo-zero depleted RNA


title: iPSC WBS1-C3 (GDB-339_C7) ribo-zero RNAseq

description: Ribo-zero depleted RNA


title: iPSC 7dupASD2-C1 (GDB-242_K) ribo-zero RNAseq

description: Ribo-zero depleted RNA


title: Injury 2 input

first: John

last: Svaren

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

description: input

data_processing:
Illumina Pipeline
Casava 1.8.2
Reads were mapped to the Rattus norvegicus genome Rn5 using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) to produce SAM files for further analysis.
Peak finding performed using the R package MOSAiCS (MOdel-based one and two Sample Analysis and inference for ChIP-seq Data) controlled for a false discovery rate (FDR) at 0.05.
Statistically different peaks were determined using DBChIP
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: Bed files of called and differential peaks were generated by Mosaics and DBChIP. Bedgraph files were generated using Homer.

organism: Rattus norvegicus

source_name: sciatic nerve

growth_protocol: Male P25 Sprague Dawley rats (Harlan Laboratory) were housed with a normal light/dark cycles and ad libitum access to rat chow and water.

extract_protocol:
At 72 h post-operation, rats were sacrificed and freshly dissected rat sciatic nerve was minced in 1% formaldehyde for 10min and then quenched for 10min with glycine to a final concentration of 0.125M. Samples were sequentially lysed in buffers LB1, LB2, and LB3 + 0.03% SDS (Schmidt et. al., 2009).   DNA was fragmented to an average size of 0.5-2kb using 4x10min Bioruptor (Diagenode) cycles on the medium setting.  Each aliquot of sonicated chromatin (300ug) was incubated overnight at 4°C with 5ug of antibody.  A 10% aliquot was saved for input analysis.  An 80ul aliquot of Protein G Dynabead (Invitrogen) slurry was added to each ChIP sample for 4hrs at 4°C.  IPs were washed 5x in RIPA buffer than eluted at 65°C with reverse crosslinking buffer (50mM Tris, 10mM EDTA, 1% SDS).    ChIP DNA was purified by phenol chloroform extraction and resuspended in 10mM Tris pH 8.0. Antibody used in the study: H3K27ac (Active Motif 37133)
Libraries were prepared from sham/injured P25 sciatic nerve H3K27ac ChIP samples, and respective inputs, using the Illumina TruSeq ChIP Sample Preparation Kit.

treatment_protocol: In anesthetized rats, an incision (~5mm long) was made through the skin and sciatic nerve at the proximal lateral region of the femur. As a control, the contralateral leg also received a sham operation consisting of only a skin incision. The skin wound was sutured with rodent surgical staples. The nerve tissue distal to the transection or sham site was isolated for use in expression and ChIP experiments.

tag: strain

value: Sprague Dawley

tag: age

tag: stress

value: Injury

tag: tissue

value: sciatic nerve


title: iPSC 7dupASD1-C2 (GDB-Cf_G) ribo-zero RNAseq, biological replicate 2

description: Ribo-zero depleted RNA

tag: donor

value: ERCC ExFold mix 2


title: Injury 1 input

description: input

tag: gender


title: Sham 2 input

description: input

value: Sham


title: iPSC 7dupASD1-C2 (GDB-Cf_G) ribo-zero RNAseq, biological replicate 1

description: Ribo-zero depleted RNA


title: iPSC WBS3-C2 (GDB-361_F) polyA RNAseq

description: Poly-A RNA


title: iPSC WBS2-C1 (GDB-316_M) polyA RNAseq

description: Poly-A RNA


title: iPSC AtWBS1-C2 (GDB-192_B) ribo-zero RNAseq

description: Ribo-zero depleted RNA


title: Sham 1 input

description: input


title: iPSC WBS4-C1 (GDB-306_O) ribo-zero RNAseq

description: Ribo-zero depleted RNA


title: iPSC WBS3-C2 (GDB-361_O) ribo-zero RNAseq

description: Ribo-zero depleted RNA


title: Injury 1 H3K27ac ChIP-seq

description: ChIP DNA

extract_protocol:
At 72 h post-operation, rats were sacrificed and freshly dissected rat sciatic nerve was minced in 1% formaldehyde for 10min and then quenched for 10min with glycine to a final concentration of 0.125M. Samples were sequentially lysed in buffers LB1, LB2, and LB3 + 0.03% SDS (Schmidt et. al., 2009).   DNA was fragmented to an average size of 0.5-2kb using 4x10min Bioruptor (Diagenode) cycles on the medium setting.  Each aliquot of sonicated chromatin (300ug) was incubated overnight at 4°C with 5ug of antibody.  A 10% aliquot was saved for input analysis.  An 80ul aliquot of Protein G Dynabead (Invitrogen) slurry was added to each ChIP sample for 4hrs at 4°C.  IPs were washed 5x in RIPA buffer than eluted at 65°C with reverse crosslinking buffer (50mM Tris, 10mM EDTA, 1% SDS).    ChIP DNA was purified by phenol chloroform extraction and resuspended in 10mM Tris pH 8.0. Antibody used in the study: H3K27ac (Active Motif 39133)
Libraries were prepared from sham/injured P25 sciatic nerve H3K27ac ChIP samples, and respective inputs, using the Illumina TruSeq ChIP Sample Preparation Kit.

value: anti-H3K27ac (Active Motif, catalog# 39133, lot# 25812006)


title: pyloric-3

city: Santiago de Compostela

first: Diego

last: Robledo

address: Rúa Lope Gómez de Marzoa s/n CIBUS building

department: Genetics

country: Spain

institute: University of Santiago de Compostela

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Quality filtering and removal of residual adaptor sequences was conducted on read pairs using Trimmomatic
Filtered reads were mapped to turbot draft genome using Tophat2 (version 2.09) that leverages the short read aligner Bowtie2 (version 2.1.0). not published (Figueras et al. In preparation)
HTSeq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) was used to extract the raw reads from the mapping files.
Genome_build: Turbot draft genome is currenly unpublished (Figueras et al. In preparation)
Supplementary_files_format_and_content: tab-delimited text files include gene product names and raw read values for each Sample

organism: Scophthalmus maximus

source_name: Pyloric caeca

growth_protocol: Turbot were obtained from an E. scophthalmi-free farm in northwestern Spain and kept in the facilities of the Instituto de Acuicultura de Torre la Sal (IATS, Cabanes, Castellón, Spain) where they were acclimated for two weeks in two 500 L tanks per group with 5µm-filtered and UV-irradiated open flow sea water (37.5 ‰ salinity) at 19±1ºC.

extract_protocol:
Samples from the three organs (head kidney, spleen and pyloric caeca) were collected in cold RNAlater (Qiagen), kept at 4ºC overnight and then transferred to -20ºC. RNA extraction was performed using the RNeasy mini kit (Qiagen) with DNase treatment following manufacturer’s instructions. RNA quality and quantity were evaluated in a Bioanalyzer (Bonsai Technologies) and in a NanoDrop® ND-1000 spectrophotometer (NanoDrop® Technologies Inc), respectively.
The 12 samples were barcoded and prepared for sequencing by the Wellcome Trust Centre for Human Genetics, Oxford, using standard Illumina protocols.

treatment_protocol: Future inficted fish received 1 ml of intestinal scraping homogenates in Hank's Balanced Salt Solution (HBSS) from 20 donor fish, containing E. scophthalmi live parasites, whereas control fish were inoculated with the same amount of HBSS alone.

value: Pyloric caeca

tag: infection state

value: infected with Enteromyxum scophthalmi for 42 days


title: Sham 2 H3K27ac ChIP-seq

description: ChIP DNA


title: spleen-C

source_name: Spleen

value: Spleen

value: Control


title: pyloric-2


title: Input_OIS_SEN

city: Philadelphia

first: Shelley

middle: L

last: Berger

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Departments of Cell & Developmental Biology; Biology; Genetics

institute: University of Pennsylvania

description: ChIPseq of ER:RAS PD16 + 40HT of IMR90 cells

data_processing:
Basecalls performed using CASAVA 1.8.2 and filtered to only sequences passing the Illumina QC filter
Sequenced reads were mapped to hg18 using bowtie2 -t --phred33-quals -k1 -N 1 --n-ceil 0,0.15 -p 20 -x -U -S
Aligned reads normalized by library size (number of fragments), PCR duplicates were removed and subsequent reads piledup and converted to bigWig format
Genome_build: hg18
Supplementary_files_format_and_content: bigWig files represent pileups of the reads at each base.  bigWig files were normalized by library size and represent the number of reads at a given genomic location per million mapped reads and generated using UCSC wigToBigWig. bigWig files have PCR duplicates removed.

source_name: IMR90 human fiboblasts

growth_protocol: IMR90 cells (obtained from Coriell Institute for Medical Research, Camden, NJ) were grown in DMEM with 10% FBS and 1% penicillin/streptomycin at 3% oxygen. For senescence studies, cells were replicatively passaged until growth ceased. For the OIS studies, IMR90 cells were grown in standard media without phenol (phenol red free DMEM + 10% FBS). The cells were generated by retrovirally infecting normal IMR90 fibroblasts with pLNCX-ER:Ras and senescence was induced with 4-hydroxytamoxifen (4-OHT) (Sigma-Aldrich).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody according to the published protocol in Shah, P.P., et al. Genes Dev. 27(16):1787-1799 (2013).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell line

tag: growth protocol

tag: population doubling

value: none (input)


title: pyloric-1


title: PD79_RNAseq_IMR90

description: Ribodepleted-RNAseq

data_processing:
Basecalls performed using CASAVA 1.8.2 and filtered to only sequences passing the Illumina QC filter
Sequenced reads were mapped to hg18 whole genome using tophat 1.4.1 with parameters –solexa-quals, -p 12, --segment-length 18, -M, -G Homo_sapiens.NCBI36.54.gtf
Aligned reads normalized by library size (number of fragments), PCR duplicates were removed and subsequent reads piledup and converted to bigWig format
The FPKM file was generated with cufflinks version 2.1.1 and setting "-G <hg18 transcriptome file>."
Genome_build: hg18
Supplementary_files_format_and_content: Text file reporting FPKM values of the refseq genes in the two conditions.

growth_protocol: Cells were grown using standard conditions and RNA harvested when plates were 80% confluent

extract_protocol:
RNA was extracted using RNA easy mini kit.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols after ribo-depletion.


title: spleen-2


title: Sham 1 H3K27ac ChIP-seq

description: ChIP DNA

value: male

tag: chip antibody


title: AGS2

city: Dresden

first: Min Ae

last: Lee-Kirsch

address: Fetscherstraße 74

department: Universitätsklinikum Carl Gustav Carus

institute: TU Dresden

data_processing:
For data analyses a splice junction library with a length of 120 nucleotides (60+60) per splice junction was created based on known exon-exon junctions according to the Ensembl Genes annotation (v. 67, May 2012)
Alignment of the reads to the hg19 transcriptome was performed with pBWA
A counts-per-gene table was created based on the overlap of the uniquely mapped reads with the Ensembl Genes annotation for hg19, using BEDtools (v. 2.11)
RPKM (reads per kilobase per million reads) values were calculated based on the raw read counts and used as a measure of absolute expression levels.
Genome_build: hg19
Supplementary_files_format_and_content: excel file with RPKM counts table

source_name: fibroblast

growth_protocol: DMEM with 10% FCS

extract_protocol:
Total RNA from fibroblasts was extracted with the RNeasy Mini Kit (Qiagen) followed by DNase I digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols
Strand specific RNA-Seq (dUTP method)

treatment_protocol: untreated

tag: genotype/variation

value: AGS

tag: passages

value: passages 4-11

value: skin biopsies


title: AGS1


title: spleen-3


title: pyloric-C


title: spleen-1


title: PD38_RNAseq_IMR90

description: Ribodepleted-RNAseq


title: SLE2

value: SLE


title: kidney-C

source_name: Anterior kidney

value: Anterior kidney


title: LaminB1_OIS_SEN

value: Lamin B1 (Abcam, catalog #ab16048, lot#953293 )


title: SLE1


title: H3K9me3_OIS_SEN

growth_protocol: IMR90 cells (obtained from Coriell Institute for Medical Research, Camden, NJ) were grown in DMEM with 10% FBS and 1% penicillin/streptomycin at 3% oxygen. For senescence studies, cells were replicatively passaged until growth ceased. For the OIS studies, IMR90 cells were grown in standard media without phenol (phenol red free DMEM + 20% FBS + 500ug/ml G418). The cells were generated by retrovirally infecting normal IMR90 fibroblasts with pLNCX-ER:Ras and senescence was induced with 4-hydroxytamoxifen (4-OHT) (Sigma-Aldrich).


title: kidney-3


title: WT3

value: wildtype


title: Injury 2 H3K27ac ChIP-seq

description: ChIP DNA

value: Sprague Dawley

value: Injury

value: sciatic nerve


title: kidney-2


title: H3K9me3_OIS_PRO

description: ChIPseq of ER:RAS PD16 of IMR90 cells


title: H3K9me3_RS_SEN

description: ChIPseq of PD87 of IMR90 cells


title: iPSC 7dupASD2-C2 (GDB-242_J) ribo-zero RNAseq

description: Ribo-zero depleted RNA

value: female

value: Single-cell culture

tag: spike-in

value: ERCC ExFold mix 2

value: unstranded 100bp PE reads


title: kidney-1

value: infected with Enteromyxum scophthalmi for 42 days


title: WT2


title: CD8+ DC

status: Public on Dec 14 2014

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
polyA+ RNA
hematopoietic_cells_expression.xlsx

data_processing:
Illumina Casava1.8 software used for basecalling.
alignment: TopHat aligner with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: CD8+ Dendritic cells

growth_protocol: Samples 1-40:Bone marrows were extracted from femora and tibiae of C57BL/6J female mice (6 to 10 weeks old), growth in presence of GM-CSF (for moDC) or Flt3L (for pDC). Samples 41-50: cells were isolated from the indicated organ, filtered and stained with the indicated antibodies for FACS sorting

extract_protocol:
For RNA extraction, cells were harvested in Qiazol lysis solution (Qiagen), and total RNA was extracted using miRNeasy Mini Kit (Qiagen).
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science
3' RNA-seq for digital gene expression quantitation

treatment_protocol: (mentioned in the relevant samples)

value: Spleen

tag: selection marker


title: H3K9me3_RS_PRO

description: ChIPseq of PD24 of IMR90 cells


title: WT1


title: CD4+ DC

source_name: CD4+ Dendritic cells


title: pDC

source_name: pDC cells

value: mPDCA+


title: preDC

source_name: preDC cells

value: Bone Marrow


title: CDP

source_name: CDP cells

value: Flk2 high, c-kit intermediate-low


title: Ly6c+ monocyte

source_name: Ly6c+ monocyte cells


title: MDP

source_name: MDP cells

value: Lin-, Flk2 high, c-kit high.


title: MP

source_name: MP cells

value: Lin-, Flk2 low, C-kit high


title: pDC_OE-control

description:
polyA+ RNA
moDC_and_pDC_Genes_perturbation.xlsx

source_name: Flt3L derived cells

tag: treatment

value: Over expression control (GFP)


title: pDC_OE-Cebpb

value: Over expression Cebpb


title: pDC_sh-control

value: sh-control infected


title: pDC_sh-Irf8

value: sh-Irf8 infected


title: moDC_sh-Cebpb

source_name: GM-CSF derived cells

value: sh-Cebpb infected


title: pDC_4 hours CPG B

description:
polyA+ RNA
TLRs_stimulated_moDC_and_pDC.xlsx

value: 4 hours 5uM CpG B


title: pDC_6 hours CPG B

value: 6 hours 5uM CpG B


title: pDC_2 hours CPG B

value: 2 hours 5uM CpG B


title: pDC_6 hours PAM

value: 6 hour 100ng/ml PAM3CSK (PAM)


title: pDC_4 hours CPG A

value: 4 hours 5uM CpG A


title: pDC_1 hour CPG A

value: 1 hour 5uM CpG A


title: pDC_6 hours CPG A

value: 6 hours 5uM CpG A


title: pDC_1 hour CPG B

value: 1 hour 5uM CpG B


title: pDC_4 hours PAM

value: Bone Marrow

value: 4 hour 100ng/ml PAM3CSK (PAM)


title: pDC_2 hours PAM

value: 2 hour 100ng/ml PAM3CSK (PAM)


title: DN DC

source_name: DN Dendritic cells

value: Spleen


title: pDC_6 hour LPS

value: 6 hours 100ng/ml LPS


title: pDC_2 hour LPS

value: 2 hours 100ng/ml LPS


title: pDC_1 hour LPS

value: 1 hour 100ng/ml LPS


title: moDC_4 hours CPG B


title: pDC_NT

value: not treated (NT)


title: pDC_4 hour LPS

value: 4 hours 100ng/ml LPS


title: moDC_2 hours CPG B


title: moDC_1 hour CPG B


title: Ly6c- monocyte

source_name: Ly6c- monocyte cells


title: moDC_sh-control

value: sh-control infected


title: moDC_4 hours CPG A


title: moDC_6 hours CPG A


title: CD31+Kit+Ly6aGFP-_HC_03

first: Elaine

last: Dzierzak

address: 47 Little France Crescent

department: MRC Centre for Inflammation Research

institute: University of Edinburgh

data_processing:
Reads mapped to mm9 genome using tophat
BAM files converted to SAM by SAMTools and applied to Htseq to generate counts
Counts imported into R to generate count table
edgeR was used to analyse the generated count table for differential analysis
Genome_build: mm9
Supplementary_files_format_and_content: txt files contain raw counts for each sample

source_name: hematopoietic cells

extract_protocol:
Cells were lysed and RNA was isolated using mirVana miRNA Isolation Kit (AM1560, Ambion) according to manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: aorta-gonad-mesonephros

tag: genotype

tag: cell type

value: hematopoietic


title: moDC_6 hours PAM

tag: strain

value: 6 hour 100ng/ml PAM3CSK (PAM)


title: moDC_1 hour CPG A


title: CD31+Kit+Ly6aGFP-_HC_02


title: GS_RA

city: Illkirch-Graffenstaden

first: Maximiliano

middle: M.

last: Portal

state: Alsace

address: 1 rue Laurent Fries

department: Functional Genomics and Cancer

country: France

institute: IGBMC

description: Global small RNA retinoic acid treated

data_processing:
Datasets were pre-processed to remove reads displaying adaptor/adaptor ligation, adaptor contamination and size selected according to the experimental protocol used (reads shorter than 21 nt from  the small RNA datasets and shorter than 35 for the long RNA datasets were removed prior to mapping).
Final datasets were aligned using Tophat in conditions compatible with 36 bp reads to map potential exon/exon boundaries (--segment-mismatches 0 --segment-length 18 or --segment-mismatches 1 --segment-length 18) and Cufflinks v2.0.0 for transcript reconstruction as well as Bowtie Aligner 2 allowing up to 2 mismatches to map the reads to the human genome.
Basic capture performance was assessed using TEQC R package. For capture analysis, Bowtie Aligner was used to map the datasets to the RAM region allowing all possible alignments (-a option). Contiguous islands of coverage were further extracted using custom scripts.
Genome_build: hg19
Supplementary_files_format_and_content: Strand specific wig files were generated using a custom pipeline.

source_name: retinoic acid differentiated PLB985 cells

growth_protocol: PLB985 cells were grown in  RPMI medium supplemented with 25 mM HEPES, 10% FCS and glutamine.

extract_protocol:
Captured RNA was obtained using a custom protocol (details can be obtained from supplementary Materials and Methods for the original publication). Briefly, specific region captured probes were generated by random priming and used as a bait against fragmented total RNA or the small RNA fraction from PLB985 cells. After hybridization, captured RNAs were recovered in Trizol.
Strand specific RNA library construction was performed using a custom protocol as described in the original manuscript.

treatment_protocol: Retinoic acid induced differentiation of PLB985 cells was achieved by addition of 1 uM 9-cis retinoic acid during 6 days in culture. Control PLB985 cells were treated with ETOH (9-cis retinoic acid vehicle).

tag: sample type

value: global small

value: retinoic acid


title: GS_ETOH

description: Global small RNA ETOH treated

source_name: PLB985 cells

value: ETOH


title: CD31+Kit+Ly6aGFP-_HC_01

tag: tissue


title: GL_RA

description: Global long RNA retinoic acid treated

value: global long


title: CD31+Kit+Ly6aGFP+_HSC_03

source_name: hematopoietic stem cells

value: hematopoietic stem cell


title: GL_ETOH

description: Global long RNA ETOH treated


title: moDC_4 hours PAM

value: Bone Marrow

value: 4 hour 100ng/ml PAM3CSK (PAM)


title: pDC_1 hour PAM

value: 1 hours 100ng/ml PAM3CSK (PAM)


title: GS2

description: Global small RNA replicate 2


title: GS1

description: Global small RNA replicate 1


title: GL2

description: Global long RNA replicate 2


title: moDC_1 hour PAM


title: GL1

description: Global long RNA replicate 1


title: moDC_2 hours PAM

value: 2 hour 100ng/ml PAM3CSK (PAM)


title: moDC_6 hours CPG B

value: 6 hours 5uM CpG B


title: CD31+Kit+Ly6aGFP+_HSC_02


title: CD31+Kit+Ly6aGFP+_HSC_01


title: TS2

description: Captured small RNA replicate 2

value: capture small


title: TS1

description: Captured small RNA replicate 1


title: moDC_6 hour LPS

value: 6 hours 100ng/ml LPS


title: TL3

description: Captured long RNA replicate 3

value: capture long


title: CD31+Kit-Ly6aGFP+_HEC_03

source_name: hemogenic endothelial cells

value: hemogenic endothelial


title: TL2

description: Captured long RNA replicate 2


title: CD31+Kit-Ly6aGFP+_HEC_02

value: aorta-gonad-mesonephros


title: CD31+Kit-Ly6aGFP+_HEC_01


title: moDC_2 hour LPS

value: 2 hours 100ng/ml LPS


title: TL1

description: Captured long RNA replicate 1


title: moDC_1 hour LPS

value: 1 hour 100ng/ml LPS


title: CD31+Kit-Ly6aGFP-_EC_03

source_name: endothelial cells

value: endothelial


title: moDC_NT

value: not treated (NT)


title: CD31+Kit-Ly6aGFP-_EC_02


title: CD31+Kit-Ly6aGFP-_EC_01


title: moDC_ATAC

description: ATAC-seq

data_processing:
HISEQ split using cassava Y60,I10
alignment using bowtie 1.0.0. command (bowtie -a -m 1 --sam --best --strata -v 2 mm9)
tdf command( igvtools count -w 5 -e 200 )
Genome_build: mm9

growth_protocol: Bone marrows were extracted from femora and tibiae of C57BL/6J female mice (6 to 10 weeks old), growth in presence of GM-CSF (for moDC) or Flt3L (for pDC).

extract_protocol:
Cells were lysed and nuclei were treated with Tn5 transposase enzyme. Nuclei were clean up and treated with Proteinase K.
Tagmenteated DNA was isolated and undergoes two cycles of PCR amplification with indexing Nextra primers

value: moDC

value: Bone marrow


title: pDC_ATAC

description: ATAC-seq

value: pDC


title: H3K4me3_CHIP-seq

status: Public on Dec 13 2014

city: Illkirch

first: Patrick

last: Laurette

address: 1 Rue Laurent Fries

data_processing:
Image analysis and base calling were performed using the Illumina Eland pipeline V1.6 (Illumina)
Sequence reads were mapped to reference genome  Human, hg18 using Bowtie v0.12.7 with the following parameters -m 1 --strata --best.
Genome_build: hg18
Supplementary_files_format_and_content: bed tag density file with sequence reads mapped to the human genome hg18. All reads mapping with two or fewer mismatches were retained. Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/). Peak annotation was performed with GPAT(http://bips.u-strasbg.fr/GPAT/).

extract_protocol:
ChIP and ChIP-seq experiments were performed on chromatin from native 501Mel cells or the clone 8 cells according to standard protocols as previously described (Delacroix et al., 2010; Kobi et al., 2010).
The libraries were sequenced on Illumina GAIIx sequencer (Illumina, San Diego, CA, USA) as single-end 36 base reads following Illumina’s instructions

value: melanoma

value: H3K4me3 :Millipore (04-745)


title: Control_CHIP-seq

value: HA :IGBMC (12CA5)


title: RNAPII_CHIP-seq

value: Pol II :Santa-Cruz (Sc9001)


title: MITF_CHIP-seq


title: 6 hour post bisection, rep1

city: Irvine

first: Ali

last: Mortazavi

state: California

address: 2300 Biological Sciences III

department: Developmental & Cell Biology

institute: University of California Irvine

description:
Sample 7
processed data file: HM_RPKM.txt

data_processing:
RNA-seq reads were mapped to the Hydra magnipapillata reference transcriptome (GenBank) using Bowtie v.0.12.8 with the following options: -aS –offrate 1 –v 3.
Transcript expression levels and read counts were obtained using eXpress v.1.3.0 with the following options: --r-stranded.
Genome_build: Hydra_RP_1.0
Supplementary_files_format_and_content: tab-delimited text file with RPKM values for the indicated samples.

molecule: polyA RNA

organism: Hydra vulgaris

source_name: Regenerating head

growth_protocol: Animals of the 105 strain of Hydra magnipapillata were used for the isolation of RNA.  They were fed freshly hatched Artemia salina nauplii three times per week and cultured as described previously [Bode H, Berking S, David CN, Gierer A, Schaller H, Trenkner E (1973) Quantitative analysis of cell types during growth and morphogenesis in Hydra. Wilhelm Roux Arch EntwMech Org 171: 269-285.].  Animals were starved for 1 day before any tissue manipulation or isolation of RNA was carried out.

extract_protocol:
30 μl 3M sodium acetate and 400 ul Tris-EDTA saturated phenol were added to each sample and mixed. Then 80 μl of chloroform was added to each sample and placed on ice for 15 minutes. Subsequently, the samples were centrifuged for 20 minute at 14,000 RPM. Subsequent centrifugation steps were also carried out at this speed. The aqueous phase of each sample was transferred to a fresh tube and an equal volume of isopropanol added. The samples were stored at -20°C for 2 hours and then centrifuged at 4°C for 15 minutes. After removal of the fluid, the pellet was washed in 70% ethanol. Each pellet was dissolved in 30-100 μl DEPC-treated water and an equal volume of 5M LiCl added. The samples were stored on ice at 4°C overnight. Subsequently the samples were centrifuged for 30 minutes and the LiCl removed. The pellets were washed twice with 70% ethanol and air-dried. Finally, each pellet was dissolved in 10 μl DEPC treated water and subsequently used for poly(A) selection or stored at -80°C. The total RNA integrity was checked using Bioanalyzer. All samples had RIN numbers greater than 9.0.
The isolated total RNA was enriched for mRNA using two rounds of poly(A) selection with a Dynabeads mRNA DIRECT Kit (Invitrogen). Purified mRNA was fragmented with hydrolysis buffer containing magnesium ions, which was then used to prepare double stranded cDNA using Invitrogen’s SuperScript Double-stranded cDNA preparation kit. During second strand synthesis, dUNTP (Applied Biosystems) was used to label the second-strand. The Illumina sequencing library construction protocol of Myers Lab ChIP-seq protocol v.2011 was used for the preparation of multiplexed libraries. The samples were treated with Uracil N-glycosylase (Applied Biosystems) before the PCR amplification step to create the strand-specific RNA-seq libraries. 13-15 cycles of PCR were used depending on the initial amount of cDNA used for each sample. Libraries were sequenced as 50 bp multiplexed Illumina single-end reads on a HiSeq2500.

treatment_protocol: For each sample, 50 to 100 1-day starved asexual hydra with a young bud were selected to be pooled. Each animal of a sample was bisected at the region 1 (R1) / region 2 (R2) border (The Hydra were visually divided into four regions from the young bud to the head. The four regions are labelled as R1-R4 with R1 as the region closest to the head) and allowed to undergo head regeneration for a specific period of time (0, 2, 4, 6, 12 or 48 hours).  Then the R2-R3 region of each animal of a sample was isolated for RNA extraction. Each isolated R2-R3 region was dissolved in 0.4 ml of Solution D (guanidine isothiocyanate, 1M sodium citrate, 5% sarcosyl, 2-betamercaptoethanol) within 3 minutes of isolation. The dissolved tissue was either stored at -80°C or immediately used for total RNA isolation.

value: Regenerating head

tag: time

value: 6 hour post bisection


title: moDC_4 hour LPS

value: Bone Marrow

value: 4 hours 100ng/ml LPS


title: 12 hour post bisection, rep1

description:
Sample 9
processed data file: HM_RPKM.txt

value: 12 hour post bisection


title: 48 hour post bisection, rep2

description:
Sample 12
processed data file: HM_RPKM.txt

value: 48 hour post bisection


title: 12 hour post bisection, rep2

description:
Sample 10
processed data file: HM_RPKM.txt


title: 6 hour post bisection, rep2

description:
Sample 8
processed data file: HM_RPKM.txt


title: 0 hour post bisection, rep2

description:
Sample 2
processed data file: HM_RPKM.txt

value: 0 hour post bisection


title: 4 hour post bisection, rep1

description:
Sample 5
processed data file: HM_RPKM.txt

value: 4 hour post bisection


title: 2 hour post bisection, rep2

description:
Sample 4
processed data file: HM_RPKM.txt

value: 2 hour post bisection


title: 0 hour post bisection, rep1

description:
Sample 1
processed data file: HM_RPKM.txt


title: 4 hour post bisection, rep2

description:
Sample 6
processed data file: HM_RPKM.txt


title: 2 hour post bisection, rep1

description:
Sample 3
processed data file: HM_RPKM.txt


title: RRBS of naïve WIBR3 ESCs - Day 17

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

data_processing:
FASTQ files were generated using the Illumina CASAVA 1.8.2 software.
The plasmid introduces a CTAGANNNNNNATTGATT prefix at one read and an AATTCAATT prefix on the other read (were NNNNNN is the UMI). These prefixes were removed and the UMI recorded for each fragment. A small fraction of reads include longer prefixes that result from amplicons that did not undergo digestion by XbaI or EcoRI. These reads were identified and the longer prefixes were removed as well.
The reads were aligned to the hg19 reference genome using bismark version 0.7.7. Alignment was performed independently for each read of the read-pair. We expect each read to start at an MspI restriction site. Therefore we discarded reads that failed to align within 1bp of such sites. We also discarded read-pairs where each read aligned to remove MspI sites. On the other hand, in cases where one read uniquely mapped on a restriction site but its pair could not be mapped uniquely or could not be mapped at all, we attempted to re-align the entire read pair to the fragment.
To avoid PCR biases we grouped reads that map to the same MspI restriction site, have the same UMI and were ligated into the plasmid in the same orientation (positive or negative). Only the first such read was maintained and all other reads were dropped.
The methylation state of each CpG was extracted from the bismark output. For each CpG, the number of reads in which it was methylated or unmethylated was counted and recorded.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-separated text files containing CpG methylation values. The files' columns are: Column1: chromosome. Column 2: position of CpG. Column 3: seen count. Column 4: methylation count. Note that each CpG's coverage is given by column 3, and its methylation value by column4/column3. Files ending with _orig.cpgs.txt represent the data used in the associated publication. Files ending with _new.cpgs.txt represent the output of a newer, improved version of our computational pipeline.

source_name: Naïve WIBR3 ESCs

growth_protocol:
Primed Cells were expanded in DMEM/F12, 20%KSR and 8ng/ml FGF2 on irradiated Feeder cells.  Rock inhibitor was added 2-24 hours before splitting with trypsin. Naïve cells were expanded in WIS-NHSM conditions that include: KO-DMEM (Invitrogen 10829-018, 03-049) 500ml, Pen-strep 5ml (Biological Industries 03-033-1B), L-glutamine 5ml (Biological Industries 02-022-1B), NEAA – 5ml (Biological Industries 01-340-1B), 5gr Albumax I (Invitrogen - 11020021) (dissolve in media bottle for 30 minutes in RT)
- Insulin (Sigma I-1882) - add 6.25mg insulin per 1 bottle to give approximately additional 12.5microg/ml insulin)
- Apo-transferrin (Sigma T-1147), 100 μg/ml final concentration
- Progesterone (Sigma P8783), 0.02 μg/ml final concentration;
- Putrescine (SigmaP5780), 16 μg/ml final concentration
- Sodium selenite (Sigma S5261), add 5 μl of 3 mM stock solution per 500ml of medium.
- L-ascorbic acid 2-phosphate (Sigma  A8960) (50 μg/ml final concentration)
- 1) human LIF (in house produced or Peprotech # 300-05) – 10 μg total  (~20ng/ml final concentration) (2 vials)
- 2) FGF2 (Peprotech 100-18c or Rnd systems –4114-TC-01M) 8ng/ml final (1 vial)
- 3) TGFB1 – 1ng/ml final (Peprotech 100-21c-1000) (0.5 vial)
- 4) Chir99021 (Axon 1386)– 3μM final (1/3 vial)
- 5) PD0325901 (Axon 1408)– 1μM final (1 vial)
- 6) p38i SB203580– 5μM final(1 vial)
- 7) JNKi SP600125 (TOCRIS 1496)– 5μM final (1 vial).
- 8) ROCKi Y27632 (Axon 1683)-10μM final (2 vials or add fresh 1:1000 every media change)
- 9) PKCi (Go6983 – TOCRIS 2285)- 0.5μM (1 vial or add 1:2000 fresh every media change)

extract_protocol:
Genomic DNA was extracted from snap-frozen cell pellets (Quick-gDNA MiniPrep, Zymo Research). 300ng of DNA was then digested overnight with MspI (NEB R0106) followed by end-repair (NEB E6050) and addition of a 3’ overhang A using Klenow fragment (3'-5' Exo-, NEB M0212). The resulting DNA fragments were size-selected for ones shorter than 500bp using AMPure XP beads (Beckman Coulter A63881). 10ng of size-selected DNA was ligated, using quick T4 ligase (NEB M2200), into a cut and T-tailed plasmid containing a 6bp unique molecular identifier (UMI) sequence. The ligated plasmid was bisulfite converted and cleaned (EZ DNA methylation Gold kit, Zymo Research). The converted DNA was amplified using 25 cycles of PCR with GoTaq Hot Start polymerase (Promega M5005) and primers matching specific locations on the plasmid. The primer sites were cut from the amplicons using XbaI (NEB R0145) end EcoRI-HF (NEB R3101). Further details regarding the plasmid are available in Shipony Z et al. Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells. Nature 2014 Sep 4;513(7516):115-9.
RRBS fragments underwent addition of a 3’ overhang A using Klenow fragment (3'-5' Exo-, NEB M0212). The fragments were then ligated to Illumina compatible adapters using quick T4 ligase (NEB M2200) and amplified using 8 cycles of PCR with GoTaq Hot Start polymerase (Promega M5005) and primers matching the Illumina adapters. The final products underwent gel electrophoresis using NuSieve 3:1 agarose (Lonza 50094). Gel bands matching fragment sizes of 200-500bp were cut and the DNA was extracted (MinElute Gel Extraction Kit, Qiagen 28604). Libraries were then pooled and sequenced on HiSeq 2500 system according to the manufacturer’s procedures.

value: hESC

tag: pluripotent state

value: Naïve


title: Sample_9_Input

city: Shanghai

first: Ruitu

last: Lyu

address: 138 Yixueyuan Road Xuhui District

country: China

institute: Institutes of Biomedical Sciences Fudan University

data_processing:
base_calling: CASAVA package (Illumina v1.6)
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie-1.0.0
peaks were called using macs14 with the following setting:--pvalue=1e-5
Genome_build: hg19
Supplementary_files_format_and_content: bed and peak list,bg and Normalised density file

source_name: Normal placentas tissue

growth_protocol: Severely preeclamptic placentas and normal tissues were isolated from patients.

extract_protocol:
Genomic DNA of severely preeclamptic placentas and normal tissues was purified using the Qiagen Blood & Cell Culture DNA Mini Kit (Cat. No: 13323) and sonicated. Illumina barcode adapters were ligated before hMeDIP. Adaptor-ligated DNA (5 μg) was denatured and incubated with 3 μl of 5-hmC antibody (Active Motif) or 5 μg of 5-mC antibody (Eurogentec) at 4°C overnight. Antibody-DNA complexes were captured by protein A/G beads. The immunoprecipitated DNA was purified and sequenced following standard Illumina protocols.
Libraries were prepared for sequencing using standard Illumina protocols

value: normal placenta

tag: antibody


title: Sample_15_Input

source_name: Severely preeclamptic placentas tissue

value: severely preeclamptic placenta


title: Sample_10_Input


title: RRBS of primed WIBR3 ESCs

source_name: Primed WIBR3 ESCs

tag: cell line

value: Primed


title: RRBS of naïve WIBR3 ESCs - Day 12


title: Sample_28_Input


title: 48 hour post bisection, rep1

description:
Sample 11
processed data file: HM_RPKM.txt


title: Sample_28_MeDIP

tag: antibody catalog/vendor

value: BI-MECY-1000, Eurogentec


title: Sample_7_Input


title: Sample_9_MeDIP


title: Sample_10_MeDIP


title: Sample_40_MeDIP


title: Sample_14_Input


title: Sample_27_MeDIP


title: Sample_14_MeDIP


title: Sample_27_Input


title: Sample_7_MeDIP


title: Sample_27_hMeDIP

tag: antibody catalog/lot/vendor


title: Sample_10_hMeDIP


title: Sample_40_Input


title: Sample_28_hMeDIP


title: RRBS of Mbd3f/- MEF cells at day 8 after DOX induction

first: Asaf

last: Zviran

address: 234 Herzl Street

data_processing:
FASTQ files were generated using the Illumina CASAVA 1.8.2 software.
The plasmid introduces a CTAGANNNNNNATTGATT prefix at one read and an AATTCAATT prefix on the other read (were NNNNNN is the UMI). These prefixes were removed and the UMI recorded for each fragment. A small fraction of reads include longer prefixes that result from amplicons that did not undergo digestion by XbaI or EcoRI. These reads were identified and the longer prefixes were removed as well.
The reads were aligned to the mm9 reference genome using bismark version 0.5.3 with bowtie 0.12.7. Alignment was performed independently for each read of the read-pair. We expect each read to start at an MspI restriction site. Therefore we discarded reads that failed to align within 1bp of such sites. We also discarded read-pairs where each read aligned to remove MspI sites. On the other hand, in cases where one read uniquely mapped on a restriction site but its pair could not be mapped uniquely or could not be mapped at all, we attempted to re-align the entire read pair to the fragment.
To avoid PCR biases we grouped reads that map to the same MspI restriction site, have the same UMI and were ligated into the plasmid in the same orientation (positive or negative). Only the first such read was maintained and all other reads were dropped.
The methylation state of each CpG was extracted from the bismark output. For each CpG, the number of reads in which it was methylated or unmethylated was counted and recorded.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated text files containing CpG methylation values. The files' columns are: Column1: chromosome. Column 2: position of CpG. Column 3: seen count. Column 4: methylation count. Note that each CpG's coverage is given by column 3, and its methylation value by column4/column3. Files ending with _orig.cpgs.txt represent the data used in the paper. Files ending with _new.cpgs.txt represent the output of a newer, improved version of our computational pipeline.

source_name: Mbd3f/- MEF 8 days after DOX induction

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:
Genomic DNA was extracted from snap-frozen cell pellets (Quick-gDNA MiniPrep, Zymo Research). 300ng of DNA was then digested overnight with MspI (NEB R0106) followed by end-repair (NEB E6050) and addition of a 3’ overhang A using Klenow fragment (3'-5' Exo-, NEB M0212). The resulting DNA fragments were size-selected for ones shorter than 500bp using AMPure XP beads (Beckman Coulter A63881). 10ng of size-selected DNA was ligated, using quick T4 ligase (NEB M2200), into a cut and T-tailed plasmid containing a 6bp unique molecular identifier (UMI) sequence. The ligated plasmid was bisulfite converted and cleaned (EZ DNA methylation Gold kit, Zymo Research). The converted DNA was amplified using 25 cycles of PCR with GoTaq Hot Start polymerase (Promega M5005) and primers matching specific locations on the plasmid. The primer sites were cut from the amplicons using XbaI (NEB R0145) end EcoRI-HF (NEB R3101) followed by end-repair (NEB E6050). Further details regarding the protocol and the plasmid are available in Shipony Z et al. Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells. Nature 2014 Sep 4;513(7516):115-9.
RRBS fragments underwent addition of a 3’ overhang A using Klenow fragment (3'-5' Exo-, NEB M0212). The fragments were then ligated to Illumina compatible adapters using quick T4 ligase (NEB M2200) and amplified using 8 cycles of PCR with GoTaq Hot Start polymerase (Promega M5005) and primers matching the Illumina adapters. The final products underwent gel electrophoresis using NuSieve 3:1 agarose (Lonza 50094). Gel bands matching fragment sizes of 200-500bp were cut and the DNA was extracted (MinElute Gel Extraction Kit, Qiagen 28604). Libraries were then pooled and sequenced on HiSeq 2500 system according to the manufacturer’s procedures.

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

value: Mbd3f/- mouse embryonic fibroblast cells (MEFs) transgenic for DOX inducible OSKM reprogramming.

tag: stage in reprogramming

value: Day 8 after DOX induction


title: Sample_40_hMeDIP


title: RRBS of Mbd3f/- iPSCs

source_name: Mbd3f/- iPSC

tag: genotype/variation

value: Mbd3f/- mouse iPSCs transgenic for DOX inducible OSKM reprogramming.

value: IPSC


title: Sample_9_hMeDIP


title: Sample_14_hMeDIP


title: Sample_7_hMeDIP


title: RRBS of wild-type MEF cells at day 8 after DOX induction

source_name: WT MEF 8 days after DOX induction

value: Mbd3+/+ mouse embryonic fibroblast cells (MEFs) transgenic for DOX inducible OSKM reprogramming.


title: Sample_15_hMeDIP


title: RRBS of wild-type MEF cells at day 4 after DOX induction

source_name: WT MEF 4 days after DOX induction

value: Day 4 after DOX induction


title: RRBS of Mbd3f/- MEF cells before DOX induction

source_name: Mbd3f/- MEF

value: Before DOX induction


title: RRBS of wild-type MEF cells before DOX induction

source_name: WT MEF


title: RRBS of wild-type iPSCs

source_name: WT iPSC

value: Mbd3+/+ mouse iPSCs transgenic for DOX inducible OSKM reprogramming.


title: Sample_15_MeDIP


title: TS3

description: Captured small RNA replicate 3

value: capture small


title: RNA hMADS, KLF11 KD rep 1, Day 16

status: Public on Dec 12 2014

city: Odense M

first: Anne

last: Loft

address: Campusvej 55

department: Biochemistry & Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Alignment:
RNA reads were aligned to the human reference genome (version hg19) using Bowtie2 (Langmead and Salzberg 2012, Nat Met 9: 357-359) with standard parameters. Splice-junction reads were handled by creation of a pseudo-splice genome, similar to the strategy utilized in RSEQTools (Habegger et al. 2011, Bioinformatics 27: 281-283). Reads were filtered post-alignment for a MAPQ score greater than or equal to 30. The number of exon reads for all RefSeq genes were counted using Subread (Liao et al. 2013, Nucleic Acids Res 41: e108).
Differential expression:
Differential expression between two independent replicates of scramble and KLF11 knockdown samples (FDR<0.1) was determined using paired analysis with DESeq2 (Love et al. 2014, http://dx.doi.org/10.1101/002832).
Genome_build: hg19

source_name: human adipose-derived stem cells

growth_protocol: Human multipotent adipose-derived stem (hMADS-3) cells were cultured in DMEM (Lonza, low glucose) supplemented with 10% fetal bovine serum (Lonza), 10 mM Hepes, 2 mM L-glutamine (Lonza), penicillin (62.5 μg/ml), streptomycin (100 μg/ml), and 2.5 ng/ml hFGF2 (Peprotech).

extract_protocol:
Total RNA from hMADS cells was purified using TRIzol (Invitrogen) according to the manufacturer’s instructions. RNA was treated with Ribo-ZeroTM rRNA removal kit (Epicentre) and subjected to fragmentation and cDNA-synthesis using the TruSeq2 RNA kit (Illumina).
cDNA-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).

treatment_protocol: Two days post confluence (day 0) hMADS cells were induced to differentiate in DMEM/Ham`s F12 (Lonza) supplemented with 10 μg/ml transferrin, 1 μM dexamethasone, 500 μM 3-isobutyl-1-methylxanthine (MIX), 0.85 μM insulin, and 0.2 nM T3. At day 3 of differentiation, MIX and dexamethasone were omitted from the media and 0.5 μM rosiglitazone was added until day 9 of differentiation and again from day 13-16 for induction of brite adipocytes. Control white adipocytes were treated with DMSO from day 13-16. From day 16 and forth the differentiation medium of both white and brite adipocytes was depleted of rosiglitazone. White and brite hMADS adipocytes were harvested on day 19, unless stated otherwise.

value: human adipose-derived stem cells

tag: lentiviral transfection

value: Mature hMADS adipocytes (day 10) were incubated with lentivirus expressing shRNA against KLF11  for 24 hours.


title: RNA hMADS, Scramble rep2, Day 16

value: Mature hMADS adipocytes (day 10) were incubated with lentivirus expressing shRNA against Scramble  for 24 hours.


title: RNA hMADS brite rep 2, day 19

data_processing:
Alignment:
RNA reads were aligned to the human reference genome (version hg19) using Bowtie2 (Langmead and Salzberg 2012, Nat Met 9: 357-359) with standard parameters. Splice-junction reads were handled by creation of a pseudo-splice genome, similar to the strategy utilized in RSEQTools (Habegger et al. 2011, Bioinformatics 27: 281-283). Reads were filtered post-alignment for a MAPQ score greater than or equal to 30. The number of exon reads for all RefSeq genes were counted using Subread (Liao et al. 2013, Nucleic Acids Res 41: e108).
Differential expression:
Differential expression between three independent replicates of white and brite hMADS adipocytes (FDR<0.05) was determined using paired analysis with DESeq2 (Love et al. 2014, http://dx.doi.org/10.1101/002832).
Genome_build: hg19


title: RNA hMADS, Scramble rep1, Day 16


title: RNA hMADS, KLF11 KD rep 2, Day 16


title: H3K27ac hMADS, KLF11 KD, Day 16

data_processing:
Alignment:
Sequence reads were collapsed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Bowtie (Langmead B, et al., Genome Biol. 10:R25) was used to align each collapsed library to the human reference genome (version hg19) with the following parameters: “-m 3 –best –strata”, with all other parameters default.
Peak finding and visualization:
BedGraph files were created using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589)  for visualization of binding profiles
Genome_build: hg19

extract_protocol:
ChIP experiments were performed in mature hMADS adipocytes essentially as previously described (Siersbæk et al. 2012, MCB, 32: 3452-3463). For cross-linking of chromatin, 0.2 mM disuccinimidyl glutarate (DSG) was applied (Proteochem, Denver, CO) for 45 min followed by cross-linking using 1% formaldehyde for 10 min.
ChIP-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).

tag: chip antibody

value: H3K27ac (ab4729; Abcam)


title: RNA hMADS brite rep 3, day 19


title: H3K27ac hMADS Scramble, Day 16


title: RRBS of Mbd3f/- MEF cells at day 4 after DOX induction

source_name: Mbd3f/- MEF 4 days after DOX induction


title: RNA hMADS brite rep 1, day 19


title: RNA hMADS white rep 3, day 19


title: RNA hMADS white rep 2, day 19


title: RNA hMADS white rep 1, day 19


title: RNA hMADS rep1, day 0

data_processing:
Alignment:
RNA reads were aligned to the human reference genome (version hg19) using Bowtie2 (Langmead and Salzberg 2012, Nat Met 9: 357-359) with standard parameters. Splice-junction reads were handled by creation of a pseudo-splice genome, similar to the strategy utilized in RSEQTools (Habegger et al. 2011, Bioinformatics 27: 281-283). Reads were filtered post-alignment for a MAPQ score greater than or equal to 30. The number of exon reads for all RefSeq genes were counted using Subread (Liao et al. 2013, Nucleic Acids Res 41: e108).
Genome_build: hg19


title: KLF11 hMADS white rep1, day 19

data_processing:
Alignment:
Sequence reads were collapsed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Bowtie (Langmead B, et al., Genome Biol. 10:R25) was used to align each collapsed library to the human reference genome (version hg19) with the following parameters: “-m 3 –best –strata”, with all other parameters default.
Peak finding and visualization:
Regions enriched for KLF11 signal in white and brite hMADS adipocytes were identified using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576–589) with the “-factor” and “-size given” settings and a 0.1% FDR threshold. An additional stringency filter was applied, so only peaks >5 fold over the matching input control were kept for further analyses. Merged peak files were generated from the individual KLF11 peak files if the center of two or more peaks were within 250 bp. Peaks from these merged peak files were only included if having more than 15 tags per 10 M tags in a 400 bp window around the center of each merged peak. BedGraph files were created using HOMER for visualization of binding profiles.
Genome_build: hg19

value: anti-KLF11 (10D8; Novus Biologicals)


title: KLF11 hMADS brite rep1, day 19


title: KLF11 hMADS brite rep2, day 19


title: KLF11 hMADS white rep2, day 19


title: H3K27ac hMADS brite rep2, day 19

data_processing:
Alignment:
Sequence reads were collapsed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Bowtie (Langmead B, et al., Genome Biol. 10:R25) was used to align each collapsed library to the human reference genome (version hg19) with the following parameters: “-m 3 –best –strata”, with all other parameters default.
Peak finding and visualization:
BedGraph files were created using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589)  for visualization of binding profiles.
Genome_build: hg19


title: N. discreta 120h

city: New Haven

first: Jeffrey

middle: P

last: Townsend

state: CT

address: 135 College street

department: Biostatistics

institute: Yale School of Public Health

description:
dikaryotic
replicate1

data_processing:
The libraries were run on eight lanes of an Illumina HiSeq 2000, generating an average of 28 million single-end reads of 36 bases each.
the program Tophat v1.1.14 was used to perform spliced alignments of the tags against the N. discreta FGSC 8579 (v1) genome obtained from JGI Genome Portal (http://genome.jgi-psf.org/Neudi1/Neudi1.download.html)
We scored results only for tags that mapped to a single unique location in the genome (--max-multihits option was set to 1) with less than three mismatches (--splice-mismatches option was set to 2). We used the default settings for all other Tophat options. We tallied tags aligning to exons of genes with the program HTSeq v0.4.5p6
LOX v1.4 was applied to the tallies for each sample for each gene to estimate gene expression levels and credible intervals across developmental stages. LOX provides relative gene expression levels standardized by the lowest sample, with credible intervals
Genome_build: NA
Supplementary_files_format_and_content: LOX estimation for fold-changes

organism: Neurospora discreta

source_name: perithecia

growth_protocol: Crosses were performed by applying 2 ml of the suspension of mat a conidia in 1.5% Tween 60 (105 - 106 conidia/ml) to the surface of the mat A protoperithecia plates, at which point considerable disturbance to surface hyphae and other fungal tissues was unavoidable. Sexual development was monitored with a stereomicroscope until fully developed perithecia appeared

extract_protocol:
RNA was isolated from homogenized mycelia with TRI REAGENT (Invitrogen) and mRNA was purified using Dynabeads oligo(dT) magnetic separation (Invitrogen)
Standard Illumina HiSeq 2000 protocal

treatment_protocol: For transcriptomic analysis, all tissues and perithecia were immediately and rapidly frozen in liquid nitrogen as they were sampled, then stored at -80°C

value: FGSC8578 x FGSC8579

tag: timepoints

value: 120h after crossing


title: N. discreta 144h

description:
dikaryotic
replicate1

value: 144h after crossing


title: N. discreta 2h

description:
dikaryotic
replicate1

value: 2h after crossing


title: N. discreta 72h

description:
dikaryotic
replicate1

value: 72h after crossing


title: N. discreta 0h

description:
monokaryotic
replicate1

source_name: protoperithecia

value: oh before crossing


title: 3928A_s

city: Uppsala

first: Anna

last: Åsman

address: PO Box 7080

department: Molecular Sciences

country: Sweden

institute: Swedish University of Agricultural Sciences (SLU)

data_processing:
Sequenced reads were filtered for adaptor sequences using cutadapt v1.2.1, requiring at least 5 bases overlap. Only forward reads were used in the subsequent anaysis.
Consensus reference sequences for P. Infestans tRNA were constructued. Briefly, tRNA sequences for each codon were clustered using cd-hit, and a consensus sequence was obtained from the aligned sequences.
The data was mapped to the tRNA consensus sequences using SHRIMP2 (v2.2.2, -s). 001111110011111111,001111111100111111,001111111111001111,001111111111110011,001111111111111100 -n 1 -Q --strata -v 80% -o 10)
The number of reads mapping tRNA was asessed using samtools (v 0.1.19).
Genome_build: P. infestans strain T30-4, http://www.broadinstitute.org
Supplementary_files_format_and_content: Tab-delimited file showing the number of reads mapping to each tRNA.

organism: Phytophthora infestans

source_name: Isolate 3928A sporangium

extract_protocol:
Material from the four life cycle stages were harvested and flash frozen in liquid nitrogen. Total RNA was prepared with the mirVana™ miRNA Isolation Kit (Ambion), according to the manufacturer’s protocol.
RNA library preparation was done with the sRNA library protocol provided with the SOLiD Total RNASeq kit (Applied Biosystems). RNA sequencing wad done using the SOLiD (version 2) platform (Applied Biosystems).

tag: isolate

value: Sporangium


title: R0_s

source_name: Isolate R0 sporangium


title: R0_m

source_name: Isolate R0 mycelium

value: Mycelium


title: N. tetrasperma 144h

description:
dikaryotic
replicate1

data_processing:
The libraries were run on eight lanes of an Illumina HiSeq 2000, generating an average of 28 million single-end reads of 36 bases each.
the program Tophat v1.1.14 was used to perform spliced alignments of the tags against the N. tetrasperma FGSC 8579 (v1) genome obtained from JGI Genome Portal (http://genome.jgi-psf.org/Neute_matA2/Neute_matA2.download.html)
We scored results only for tags that mapped to a single unique location in the genome (--max-multihits option was set to 1) with less than three mismatches (--splice-mismatches option was set to 2). We used the default settings for all other Tophat options. We tallied tags aligning to exons of genes with the program HTSeq v0.4.5p6
LOX v1.4 was applied to the tallies for each sample for each gene to estimate gene expression levels and credible intervals across developmental stages. LOX provides relative gene expression levels standardized by the lowest sample, with credible intervals
Genome_build: NA
Supplementary_files_format_and_content: LOX estimation for fold-changes

organism: Neurospora tetrasperma

value: FGSC2508 x FGSC2509


title: 3928A_g

source_name: Isolate 3928A germinating sporangium

value: Germinating sporangium


title: R0_a

source_name: Isolate R0 germinating cyst

value: Germinating cyst, traces of germinating sporangium and zoospores


title: N. tetrasperma 120h

description:
dikaryotic
replicate1


title: 3928A_m

source_name: Isolate 3928A mycelium


title: RNA hMADS rep2, day 0


title: N. tetrasperma 96h

description:
dikaryotic
replicate1

value: 96h after crossing


title: N. tetrasperma 72h

description:
dikaryotic
replicate1


title: N. tetrasperma 24h

description:
dikaryotic
replicate1

value: 24h after crossing


title: N. tetrasperma 48h

description:
dikaryotic
replicate1

value: 48h after crossing


title: H3K27ac hMADS white rep2, day 19

value: human adipose-derived stem cells


title: N. discreta 48h

description:
dikaryotic
replicate1


title: N. discreta 96h

description:
dikaryotic
replicate1


title: N. discreta 24h

description:
dikaryotic
replicate1


title: N. tetrasperma 2h

description:
dikaryotic
replicate1


title: E16.5 Morc1 het ATAC-seq (Naked DNA)

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

description: library strategy: ATAC-seq

data_processing:
Data were collected using 50bp paired end sequencing on a HiSeq. Reads were aligned to mm9 using Bowtie with the parameters –X2000 and –m1. The –X2000 parameter allows the fragments less than 2kb to align and only unique aligning reads were collected (-m1). Duplicated reads were removed with samtools (rmdup function). Previous results show that for Tn5 transposase, the transposon binds as a dimer and insert two adaptors separated by 9bp. Thus, all reads aligned to the + strands were offset by +4bp, and all reads aligned to the – strands were offset by -5bp.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files. Coordinates, read density.

source_name: E16.5 sorted germ cells

extract_protocol:
FACS collected cells from individual mice were spun 500g x 5 minutes at 4°C. Cells were resuspended in 50μL lysis buffer (10mM Tris pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 1x Complete Protease Inhibitor(Roche)) and spun 10 minutes 500g 4°C to collect nuclei. The nuclei were resuspended in 50μL Transposase reaction (25μL 2xTagmentation buffer, 22.5μL water, 2.5μL Tn5 Transposase enzyme) and reacted for 30 minutes at 37°C on a PCR machine. The material was purified using a Qiagen MinElute protocol, eluting with 14μL EB.
The eluted material was amplified in 50μL volume using 1.25μM primer concentration and a 1x concentration NEBNext High-Fidelity Master-Mix (NEB) (Program: 72°C 5:00, 98°C 30s, 5x (98°C 10s, 63°C 30s, 72°C 1 minute), 4°C hold). After these 5 cycles of amplification, the tube was kept on ice.  A 5 μL aliquot was then removed and used to perform a 15 μL side reaction with identical concentrations of primer and enzyme, except that 0.6x SYBR Green (Invitrogen S-7563) is included to monitor amplification. This side reaction was amplified on a Stratagene Mx3005p qPCR (Agilent) system with the following amplification conditions (98°C 30s, 20x(98°C 10s, 63°C 30s, 72°C 1:100)). The number of additional cycles ‘N’ required to reach ¼ maximum fluorescence was observed. The purpose of this side reaction was to minimize the number of PCR cycles required used to generate the libraries, since length and GC bias increases with more amplification The remaining 45μL of the reaction was then further amplified (98°C 30s, N x (98°C 10s, 63°C 30s, 72°C 1:00), 4°C) and the libraries were puried by a Qiagen MinElute kit eluting with 20 μL volume

value: Morc1 het

tag: library type

value: Nextera Reagents (ATAC-seq)

value: sorted germ cells


title: N. tetrasperma 0h

description:
monokaryotic
replicate1


title: 3928A_a

source_name: Isolate 3928A germinating cyst


title: E16.5 Morc1 KO ATAC-seq Replicate 1

description: library strategy: ATAC-seq

value: Morc1 KO


title: H3K27ac hMADS brite rep1, day 19

data_processing:
Alignment:
Sequence reads were trimmed and collapsed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Bowtie (Langmead B, et al., Genome Biol. 10:R25) was used to align each collapsed library to the human reference genome (version hg19) with the following parameters: “-m 3 –best –strata”, with all other parameters default.
Peak finding and visualization:
BedGraph files were created using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589)  for visualization of binding profiles.
Genome_build: hg19

tag: cell type

value: H3K27ac (ab4729; Abcam)


title: L_D_sictr

city: Toronto

first: Housheng

middle: Hansen

last: He

state: Ontario

address: 101 College Street, PMCRT 11-305

department: Medical Biophysics

country: Canada

institute: UNIVERSITY HEALTH NETWORK

data_processing:
Illumina Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v2.0.0 or tophat v2.0.4
MACS2 was used to call peaks and generate bigwiggle file, cuffdiff v2.0.1 was used to identify differentially expressed genes
Genome_build: hg19
Supplementary_files_format_and_content: Peaks files for ChIP-seq samples.
Supplementary_files_format_and_content: Abundance counts for RNA-seq samples.

source_name: Prostate cancer cell line LNCaP

growth_protocol: The prostate cancer cell line LNCaP and VCaP were obtained from the American Type Culture Collection. LNCaP cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 2mM glutamine, 100 U/mL penicillin and 100 mg/mL streptomycin. VCaP cells were maintained in DMEM medium supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine, 100 U/mL penicillin, 100 mg/mL streptomycin.

extract_protocol:
LNCaP and VCaP cells were harvested by scraping from the plates.
Libraries were prepared according to Rubicon's instructions accompanying the ThruPLEX-FD kit (for ChIP-seq) or Illumina TruSeq RNA Sample Prep Kit v2 (for RNA-seq)

treatment_protocol: LNCaP and VCaP cells were starved in phenol-red-free medium supplemented with 10% charcoal stripped FBS for 3 days before hormone stimulation.

value: LNCaP

tag: transfection

value: control siRNA transfection

tag: passage


title: VCaP_D_LSD1

source_name: Prostate cancer cell line VCaP

value: VCaP

value: no treatment

value: LSD1 antibody (Abcam, ab17721, lot # GR79477-2)


title: R0_g

source_name: Isolate R0 germinating sporangium

tag: tissue


title: L_D_LSD1


title: H3K27ac hMADS white rep1, day 19


title: CBP hMADS white, day 19

value: anti-CBP (A-22, sc-369; Santa Cruz)


title: DHS hMADS brite, day 19

data_processing:
Alignment:
Sequence reads were trimmed and collapsed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Bowtie (Langmead B, et al., Genome Biol. 10:R25) was used to align each collapsed library to the human reference genome (version hg19) with the following parameters: “-m 3 –best –strata”, with all other parameters default.
Peak finding and visualization:
Regions enriched for DHS signal in white and brite hMADS adipocytes were identified using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589) with the “-factor” and “-size given” settings and a 0.1% FDR threshold. An additional stringency filter was applied, so only peaks >10 fold (DHS) over the matching input control were kept for further analyses. Merged peak files were generated from the individual DHS peak files if the center of two or more peaks were within 250 bp. Peaks from these merged peak files were only included if having more than 10 tags per 10 M tags in a 400 bp window around the center of each merged peak. BedGraph files were created using HOMER for visualization of binding profiles.
Genome_build: hg19

extract_protocol:
DNase I digestion was performed in mature hMADS adipocytes on ~10,000,000 million nuclei, essentially as previously described (Siersbæk et al., 2011, EMBO J, 30(8):1459-72), except that hMADS cells were harvested directly in Buffer A (15 mM Tris–HCl pH=8, 15 mM NaCl, 60 mM KCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine) and 120 U/ml DNase I (Roche, cat# 11 284 932 001) was used for digestion.
DHS-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).


title: CBP hMADS brite, day 19


title: P10.5 Morc1 KO ATAC-seq Replicate 1

description: library strategy: ATAC-seq

source_name: P10.5 sorted germ cells


title: DHS hMADS white, day 19


title: P10.5 Morc1 het ATAC-seq Replicate 1

description: library strategy: ATAC-seq


title: L_D_siLSD1

value: LSD1 siRNA transfection


title: P10.5 Morc1 KO bisuflite (3 replicates)

description: Bisulfite treated DNA

data_processing:
RNA-seq.  For all analyses, reads were trimmed to 50bp and those mapping to ribosomal RNA (GenBank identifiers: 18S NR_003278.3; 28S NR_003279.1; 5S D14832.1; 5.8S K01367.1) by up to three mismatches were discarded.  Reads were then mapped to known mm9 gene and repeat annotations by allowing up to two mismatches and only retaining reads that mapped to one location. When reads did not map to the annotated genes and repeats, the reads were mapped to the mm9 genome. Number of reads mapping to genes and repeats were determined by using HTSeq (doi: 10.1101/002824) using default parameters. Expression values were calculated as reads per kilobase of exons per million mapping reads (RPKM). Differential gene and repeat expression was determined by using DESeq47 using default parameters.
smRNA-seq. Adapter sequences were removed prior to all analyses. For analyzing piRNA reads over genes and repeats misexpressed in Morc1 KO: Reads were mapped to the mm9 genome using Bowtie by not allowing any mismatches, and retaining reads that only mapped to one location in the genome.
ChIP-seq. Previously published ChIP-seq data28 was obtained from GSE38165 in Gene Expression Omnibus. Reads were mapped to the mm9 genome using Bowtie by allowing up to two mismatches, and only retaining reads that mapped to one location in the genome. Reads mapping to the same location were collapsed into one read. For all analyses, the data were normalized to total number of mapping reads in the library
Bisulfite-seq. Reads were split into 50bp reads prior to mapping. Reads were mapped to the mm9 genome as well as the lambda genome using BS seeker248 using default parameters. Methylation levels were determined by #C/(#C+#T).
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq. Column1: Ensembl ID; Column2: chromosome; Column3: strand; Column4: start of gene; Column5: end of gene; Column6: name; Column7: number of reads; Column8: RPKM.
Supplementary_files_format_and_content: smRNA-seq. Reads with adapter sequences trimmed.
Supplementary_files_format_and_content: Bisulfite-seq. Bigwig files of fractional methylation levels (#C/(#C+#T)) in CG and CH (H=A,T or C) sequence contexts.
Supplementary_files_format_and_content: ChIP-seq. Wig files. Coordinates, read density.

extract_protocol:
DNA for bisulfite sequencing was extracted using the QiaAMP DNA Micro kit (Qiagen) and quantified using the Qubit dsDNA High Sensitivity Kit (Life Technologies).
Libraries were prepared using the Ovation Ultralow Methyl-Seq Library System (Nugen). 5ng – 25ng DNA was used as starting material. Matched mutant and control samples always contained identical quantities of DNA. Unmethylated Lambda phage DNA (NEB) was spiked in at 0.5% input DNA quantity to determine conversion efficiency, which was consistently >98%. Each library was prepared using DNA from one individual mouse.

value: Ovation Ultralow Methylseq


title: E16.5 Morc1 het H3K4me3 ChIP

description: ChIP DNA

extract_protocol: The ChIP-seq protocol was adapted from published sources. FACS sorted cells from an individual mouse were diluted to 292μL with room temperature 1xPBS. 8.11μL 37% Formaldehyde (Sigma) was added and the sample was incubated 10 minutes at room temperature with rocking. 48.8μL of 1M glycine was then added to yield a final concentration of 0.14M and the samples were quenched 30 minutes with rocking. Cells were then spun 425g for 10 minutes at RT. The cell pellet was flash frozen. After thawing, the cells were resuspended in 200μL Lysis buffer (50mM Tris-Cl pH 8.0, 20mM EDTA pH 8.0, 1% SDS, 1x Complete Protease Inhibitor(Roche)) and incubated on ice ten minutes. Samples were then subjected to a nine minutes disruption using a Bioruptor on “High” setting, with 30s/30s off disruption (so 4.5 minutes of disruption total). Samples were spun 14000g 10 minutes to remove insoluble material. The soluble sample was diluted to 500μL with dilution buffer (16.7mM Tris pH 8, 0.01% SDS, 1.1% TritonX-100, 1.2mM EDTA, 167mM NaCl) and 10% of material was saved as input. Sample was precleared with 30μL Protein A Dynabeads (Life Technologies) and preincubated 1hr. The cleared material was incubated with 1μL L anti-H3K4me3 antibody (Millipore 04-745) overnight. The samples were incubated with 30μL Protein A Dynabeads and the precipitated material was recovered with a magnet. The beads were washed 2x4 minutes with Buffer A (50mM HEPES pH 7.9, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 140mM NaCl), 2x4 minutes with Buffer B (50mM HEPES pH 7.9 0.1% SDS 1% Triton X-100 0.1% Deoxycholate, 1mM EDTA, 500mM NaCl) and 2x4 minutes with 10mM Tris/1mM EDTA. Bound material was eluted with 100μL Elution buffer (50mM Tris pH 8.0, 1mM EDTA, 1% SDS) at 65C for ten minutes and then eluted a second time with 150μL elution buffer. The input samples were thawed and diluted with 200μL buffer. Crosslinking of ChIP and input samples was reversed by incubating 16 hours at 65C. Samples were cooled and treated with 1.5μl of 10mg/mL RNaseA (PureLink RNAse A, Invitrogen #12091-021) for thirty minutes at 37C. 100μg of Proteinase K was then added and the samples treated for 2hr at 56C. The samples were then purified using a Qiagen Minelute kit. Samples were amplified by a SeqPlex DNA Amplification kit (Sigma) and then converted to libraries using an Ovation Rapid Library kit.

value: Sigma SeqPlex + Ovation Rapid Library System


title: E16.5 Morc1 het H3K4me3 input

description: Input for ChIP DNA


title: P2.5 Morc1 het bisulfite (3 replicates)

description: Bisulfite treated DNA

source_name: P2.5 sorted germ cells


title: E16.5 Morc1 het ATAC-seq Replicate 1

description: library strategy: ATAC-seq


title: E16.5 Morc1 KO bisulfite (4 replicates)

description: Bisulfite treated DNA


title: E16.5 Morc1 het bisulfite (5 replicates)

description: Bisulfite treated DNA


title: P10.5 Morc1 het smRNA-seq

description: smRNA

source_name: P10.5 whole testis

extract_protocol:
Total RNA was isolated from embryonic testes using Ribozol. Thirty μg total RNA was loaded on 12% urea-polyacrylamide (PAA) gel. The 19-30 nt fraction was excised and snap-frozen in liquid nitrogen in 400 μl 0.4M NaCl. RNA was eluted from the gel overnight at 16°C while shaken at 1,000 rpm  and then precipitated with 3 vol absolute ethanol. Pre-adenylated 3’ linker (/5`Phos/TGGAATTCTCGGGTGCCAAGGAACTC/3`ddC/; 5’DNA adenylation kit, NEB) was ligated to RNA over night at 4C using Truncated RNA Ligase 2 (NEB). Ligation reactions were loaded onto 10% urea-PAGE, the 45-56 nt fraction was excised and nucleic acids extracted as above. 5’ linker (rGrUrUrCrArGrArGrUrUrCrUrArCrArGrUrCrCrGrArCrGrArUrC) was ligated to the samples using RNA Ligase 1 (NEB) over night at 4C. Ligation reactions were loaded on 10% Urea-PAA gel, 72-83 nt fraction was excised and nucleic acids as above. Extracted samples were reverse-transcribed (primer sequence: GGAGTTCCTTGGCACCCGAGA) and library amplified by PCR using standard Illumina primers. Final libraries were excised from the agarose gel and sequenced.
 Since this is shaking, not centrifugation, we include rpm

value: In house smRNAseq method

value: whole testis


title: P10.5 Morc1 KO smRNA-seq

description: smRNA


title: E16.5 Morc1 KO smRNA-seq

description: smRNA

source_name: E16.5 whole testis


title: P2.5 Morc1 KO bisulfite (3 replicates)

description: Bisulfite treated DNA