title: MOLT4_dBET6_6h_1

description:
MOLT4 cells treated with dBET6 for 6h
MOLT4_dBET6_6h_0

data_processing:
Images analysis and base calling was done using the solexa pipeline.
alignment: HiSat using default settings
expression levels: Gene-level expression measurements for RefSeq genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file matix containing ERCC normalized FPKM values for each transcript

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions. External spike-in RNAs (ERCC ExFold RNA Spike-In kit, Ambion, 4456739) were added based on cell number. See manuscript for details.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: time point


title: MOLT4_dBET6_6h_2

status: Public on Sep 18 2017

type: SRA

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

description:
MOLT4 cells treated with dBET6 for 6h
MOLT4_dBET6_6h_1

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

growth_protocol: cells were cultured in RPMI-10%FCS

tag: cell line

tag: drug treatment


title: MOLT4_JQ1_6h_3

description:
MOLT4 cells treated with JQ1 for 6h
MOLT4_JQ1_6h_2


title: NET-seq DMSO Rep1

data_processing:
Reads are trimmed and aligned using STAR (v2.4.0) (Dobin et al., 2013)
For NET-seq data, only the position matching the 50 end of the sequencing read (after removal of the barcode), corresponding to the 30 end of the nascent RNA fragment, is recorded with a Python script using HTSeq package (Anders et al., 2015). Reverse transcription mispriming events are identified and removed when molecular barcode sequences match exactly to the genomic sequence adjacent to the aligned read. Reads that align to the same genomic position and contain identical barcodes are considered PCR duplication events and are removed. Splicing intermediates have 30 hydroxyls and will enter NET-seq libraries and contribute to the reads aligning to the exact single-nucleotide 30 ends of introns and 30 ends of exons.
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: BedGraph files (http://genome.ucsc.edu/goldenPath/help/bedgraph.html); Column1=chromosome; Column2=start (left most coordinate; 0 based; position included); Column3=end (right most coordinate; 0 based; position not included); Column4=Coverage (3'end nt for NET-seq and whole read for RNA-seq)

source_name: DMSO

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions. External spike-in RNAs (ERCC ExFold RNA Spike-In kit, Ambion, 4456739) were added based on cell number. See manuscript for details.
For NET-seq, the library preparation is performed as described by Churchman and Weissman (2011, 2012) with modifications. For 30 RNA ligation, a pre-adenylated DNA linker with a mixed random hexameric barcode sequence at its 50 end is used. cDNA containing the 30 end sequences of a subset of mature and heavily sequenced snRNAs, snoRNAs, rRNAs, and mitochondrial tRNAs are specifically depleted using biotinylated DNA oligos, as described by Ingolia et al.

tag: library type

value: 3'end RNA fragment sequencing

tag: treatment

value: DMSO

tag: molecule subtype

value: nascent RNA


title: MOLT4_dBET6_2h_2

description:
MOLT4 cells treated with dBET6 for 2h
MOLT4_dBET6_2h_1


title: MOLT4_dBET6_2h_3

description:
MOLT4 cells treated with dBET6 for 2h
MOLT4_dBET6_2h_2


title: MOLT4_JQ1_6h_1

description:
MOLT4 cells treated with JQ1 for 6h
MOLT4_JQ1_6h_0


title: MOLT4_JQ1_6h_2

description:
MOLT4 cells treated with JQ1 for 6h
MOLT4_JQ1_6h_1


title: MOLT4_JQ1_2h_3

description:
MOLT4 cells treated with JQ1 for 2h
MOLT4_JQ1_2h_2


title: MOLT4_dBET6_6h_3

description:
MOLT4 cells treated with dBET6 for 6h
MOLT4_dBET6_6h_2


title: MOLT4_JQ1_2h_1

description:
MOLT4 cells treated with JQ1 for 2h
MOLT4_JQ1_2h_0


title: MOLT4_JQ1_2h_2

description:
MOLT4 cells treated with JQ1 for 2h
MOLT4_JQ1_2h_1


title: MOLT4_DMSO_6h_2

description:
MOLT4 cells treated with DMSO for 6h
MOLT4_DMSO_6h_1


title: MOLT4_DMSO_2h_2

description:
MOLT4 cells treated with DMSO for 2h
MOLT4_DMSO_2h_1


title: MOLT4_DMSO_6h_3

description:
MOLT4 cells treated with DMSO for 6h
MOLT4_DMSO_6h_2


title: MOLT4_DMSO_6h_1

description:
MOLT4 cells treated with DMSO for 6h
MOLT4_DMSO_6h_0


title: MOLT4_DMSO_2h_1

description:
MOLT4 cells treated with DMSO for 2h
MOLT4_DMSO_2h_0


title: MOLT4_DMSO_2h_3

description:
MOLT4 cells treated with DMSO for 2h
MOLT4_DMSO_2h_2


title: Tumor6.RNAseq

city: La Jolla

first: Kees

last: Murre

state: CALIFORNIA

address: 9500 gilman drive, NSB 5114A

department: Biology

institute: UCSD

description: used for Fig. 7

data_processing:
RNAseq data were examined using Omics Pipe applying the RNA-seq count-based differential expression analysis pipeline. Quality control of the raw fastq files was performed using FastQC (Babraham Bioinformatics). Sequencing reads were aligned to the mouse genome (mm10) applying STAR aligner. Read quantification (exons) was performed using htseq-count with UCSC RefSeq annotation. The R BioConductor package DESeq2 was used to calculate size factors in order to normalize library sizes across replicates and calculate means and variances based on a negative binomial distribution model in order to detect differentially expressed genes based on adjusted p-values of < 0.05. Functional enrichment of the differentially expressed genes was done using ToppGene Suite, WebGestalt and Metascape.
genome build: mm9

organism: Mus musculus

growth_protocol: adult bone marrow single cell suspension were incubated with CD3e, B220, CD11b, GR1, TER119, CD117 and Flt3. Hematopoietic progenitor cells were collected through  depleting positive cells on Automacs. Selected cells were cultured on OP9-DL1 in 6 well plates with MEM containing 20% FCS, 2% PSG, FLT3L, recombinant IL-7 1-2 ng/ml.

extract_protocol: Primary tumor cells were harvested and immediately spun down, and washed with PBS. Cells were lysed with buffer RLT (Qiagen) and freezed at -80 degrees until used.

tag: strain

tag: genotype

value: ThymoDp(A)/p(A)

tag: chip antibody


title: MOLT4_dBET6_2h_1

description:
MOLT4 cells treated with dBET6 for 2h
MOLT4_dBET6_2h_0


title: Tumor5.RNAseq

description: used for Fig. 7


title: MOLT4_DMSO_pS2_POL2

library_source: genomic

data_processing:
For all samples, reads were aligned to their indicated build using bowtie2 with parameters -k 1.
MACS1.4 with p-value = 1e-9 and default parameters was used to call peaks and generate wiggles.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files: For all samples, aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

molecule: genomic DNA

source_name: T-ALL

extract_protocol:
Standard DNA extraction from MOLT4 cell lines using cell lysis.
Probe sonicator 3 minutes total sonication time (1 sec on, 4 sec off, 60% amplitude) on ice library prep with Rubicon TruePlex kit.

tag: antibody

value: RNA pol II CTD phospho Ser2

tag: antibody manufacturer

value: Active Motif

tag: antibody catalog number


title: Tumor4.RNAseq

description: used for supplemental figure


title: Hi-C DN3

description: used for supplemental figure

data_processing:
Reads were first trimmed from the 3’ end of sequences to GATC (MboI restriction enzyme site). Trimmed reads were aligned to mm10 with Bowtie software with parameters --chunkmbs 128 –mm -m1 --best --strata -p4 -S. The remainder of the analysis was performed using Homer. Only unique reads and paired end tags with more than 1.5x fragment length on the same chromosome separating them were retained. Sequence reads were checked for GC and nucleotide bias.
HiC matrix: A tab-delimited matrix M, the cell of the ith row and    jth column Mij indicates the interaction frequency between the ith locus    and jth locus. At 50K resolution, each locus has a size of 50K, so the ith    locus mean ((i-1)*50000+1)bp to (i*50000)bp region in corresponding    chromosome. The Matrix is KR normalized from the original read count    matrix. The KR normalization is identical to the KR normalization procedure    in the following paper: Rao, Suhas SP, et al. "A 3D map of the human genome    at kilobase resolution reveals principles of chromatin looping." *Cell* 159.7    (2014): 1665-1680.
genome build: mm9

source_name: in-vivo DN3 cells from RAG -/- mice

extract_protocol:
cells were harvested from RAG -/- mouse
We used in-situ Hi-C to generate a genome-wide contact map essentially as described (Rao, S. S. et al. Cell 159, 1665-1680 2014). Five million cells were extracted from RAG -/- mouse. Nuclei were resuspended in 0.5% SDS diluted in a final concentration of 1X NEB Buffer 2. Each sequencing library was incubated with USER enzyme for 15 minutes at 37oC after step 56. Final libraries were submitted to paired-end sequencing of 100 bp length on an Illumina HiSeq 4000.

value: RAG -/-


title: Ptulid_WT_WCE_135

city: new york

first: arturo

last: mendoza

state: ny

address: 1 east loop 15a

department: Division of Endocrinology, Diabetes and Metabolism

institute: weill cornell medicine

data_processing:
BCL files were demultiplexed using bcl2fastq 2.17.1.14 with standard parameters
Data was aligned to the mm10 reference genome using bowtie2 2.2.1 with insert size 50-150% of the average insert size
PCR duplicates were removed using the Picard MarkDuplicate tool in Picard version 2.8.1
Peakcalling was performed using MACS2 2.1.1 with the mm10 reference genome and using the appropriate WCE as control using the parameters --broad-cutoff 0.1 --broad --nomodel
Peaks across all samples were joined and the coverage under each peak in each sample was calculated using bedtools command multicov in bedtools version 2.26.0
Peaks that were <100 or >1000 nts wide were filtered out, as well as peaks where no sample had 4 times greater coverage than the largest WCE after library size normalization
Genome_build: mm10
Supplementary_files_format_and_content: peak_counts.csv is a comma seperated value file where each row contains information about 1 peak. The columns are an ID based on the genomic position, the chromosome the peak is on, the start position of the peak, the end position of the peak, the length of the peak, and the number of reads under the peak for each sample.

growth_protocol: Mice were maintained under a regular 12h light/12h dark cycle at constant temperature (23°C).

extract_protocol:
Nuclear lysates were sonicated and histone-DNA complexes were isolated with antibody.
After performing reverse cross linking on sheared chromatin the following steps were performed: end-repair, addition of A base to 3' end of DNA fragments, ligation of adapters to ends of DNA fragments, enrichment by PCR, and gel purification of PCR products.

treatment_protocol: At 6 weeks of age, separated cohorts of mice were either kept on standard chow diet or put on a diet with low iodine supplemented with 0.15% propylthiouracil (PTU/LID) (TD.95125; Envigo) for three weeks. All the mice were euthanized by asphyxiation with CO2 on day 21 of the experiment. Blood was collected by cardiac puncture. Tissues were quickly harvested and frozen in liquid nitrogen, then stored at -80°C.

tag: strain background

tag: genotype/variation

value: WT

tag: diet

value: PTU/LID

tag: tissue

value: liver


title: Ptulid_NCoRKO_WCE_211

value: NCoR1 KO


title: 1HT_N_RNAseq

description: used for Fig. 2

source_name: in-vitro DN2 cells

extract_protocol:
Harvested cells were stained with lineage marker, CD25, CD117, ghost dye red 780. Lineage negative DN2 cells were sorted by FACS AriaII and washed with PBS.
Total RNA was isolated using RNeasy Mini kit (Qiagen). RNA was treated with TURBO DNase (Life Technologies). mRNA was purified from total RNA using Dynabeads mRNA purification kit (Life Technologies). cDNA was generated with the First-strand synthesis kit (Life Technologies) using a random hexamers in presence of actinomycin D. Second-strand synthesis was performed with dUTP instead of dTTP. Sonicated cDNA was ligated to adaptors (NEBNext primer kit). The resulting DNA was treated with uracil-N-glycolsylase prior to PCR amplification with the indexing primers (NEBNext primer kit).

value: ThymoD+/p(A)


title: 2HT_N_RNAseq

description: used for Fig. 2


title: KO_1_GROseq.

description:
newly synthesized transcripts with bromouridine (BrU)
used for Fig. 2

data_processing:
Samples are mapped to reference genome mm9 by Bowtie (version 1.1.1), using following option: --best -m 1, and others as default. the bam file are then processed by Homer to create tag directory with the default setting of Homer makeTagDirectory, using option -tbp 1. Homer findPeak has been used to identify enriched regions.
genome build: mm9

extract_protocol:
Lived DN2 cells were selected on day10. Nuclei isolation was performed and freezed at -80 degree unitil used.
GRO-seq was performed as previously described (Lin et al. 2012). Duplicates of GRO-seq experiments were performed. Libraries were prepared with custom GRO-seq PCR primers and were selected by size by 2% agarose and sequenced for 50 cycles on Illumina HiSeq 2500.


title: Chow_WT_WCE_96

value: Chow


title: Chow_NCoRKO_WCE_122


title: ATAC-seq_tumor_6

description: used for Fig. 7

data_processing:
Samples are mapped to reference genome mm9 by Bowtie (version 1.1.1), using following option: --best -m 1, and others as default. the bam file are then processed by Homer to create tag directory with the default setting of Homer makeTagDirectory, using option -tbp 1. For ATAC open region, following options were used :-localSize 50000 -size 150-minDist 50 –fragLength 0, and we used the default setting for other peak/region calling.
genome build: mm9

extract_protocol:
Tumor cells were cultured on OP9-DL1, aMEM 20% FBS, IL7, FLT3-L. Cells were harvested and immediately spun down, and resuspended in PBS. Cells were fixed with 1% formaldehyde. Formaldehyde was quenched with 0.2 M glycine for 10 min. Fixed cells were stored at -80 degrees until use.
50000 cells were used for library preparation. Washed cells were resuspended in lysis buffer. After washing, cells were treated with transposition mix for 30 min at 37 degrees. Cycle of PCR amplification was determined by q-PCR. 100-800 bps of Libraries were selected from 2% agarose gel.


title: Tumor2.RNAseq

description: used for supplemental figure


title: KO_2_GROseq.


title: Ptulid_WT_27ac_135

value: H3K27ac (Active Motif, 39133)


title: Ptulid_WT_27ac_155


title: WT_1_GROseq.


title: WT_2_GROseq.


title: Ptulid_NCoRKO_27ac_211


title: Ptulid_NCoRKO_27ac_239


title: Chow_WT_27ac_106


title: Ptulid_NCoRKO_27ac_232


title: ATAC-seq_tumor_3

description: used for Fig. 7


title: Tumor3.RNAseq

description: used for Fig. 7


title: Tumor6_input

description: used for Fig. 7

extract_protocol:
Primary tumor cells were harvested and immediately spun down, and resuspended in PBS. Cells were fixed with 1% formaldehyde. Formaldehyde was quenched with 0.2 M glycine for 10 min. Fixed cells were stored at -80 degrees until use.
Libraries were prepared with NEBNext primer set. Fragment size was selected with AMPure beads (Beckman Coulter).


title: Chow_WT_27ac_99


title: Tumor5_input

description: used for Fig. 7

extract_protocol:
Tumor cells were cultured in aMEM 20% FBS, IL7, FLT3-L. Cells were harvested and immediately spun down, and resuspended in PBS. Cells were fixed with 1% formaldehyde. Formaldehyde was quenched with 0.2 M glycine for 10 min. Fixed cells were stored at -80 degrees until use.
Libraries were prepared with NEBNext primer set. Fragment size was selected with AMPure beads (Beckman Coulter).


title: Tumor5_SMC3 ChIP-seq

description: used for Fig. 7


title: Chow_WT_27ac_96


title: Tumor1 RNAseq

description: used for supplemental figure


title: Tumor3_SMC3 ChIP-seq

description: used for Fig. 7


title: Ptulid_WT_27ac_280


title: Chow_NCoRKO_27ac_190


title: Tumor3_input

description: used for Fig. 7


title: Chow_NCoRKO_27ac_122


title: SMC3 CHIP-seq 60min control

description: used for Fig. 6

data_processing:
Samples are mapped to reference genome mm9 by Bowtie (version 1.1.1), using following option: --best -m 1, and others as default. the bam file are then processed by Homer to create tag directory with the default setting of Homer makeTagDirectory, using option -tbp 1. Homer findPeak has been used to identify enriched regions.
genome build: mm9
processed data files format and content: bed file

growth_protocol: adult bone marrow single cell suspension were incubated with CD3e, B220, CD11b, GR1, TER119, CD117 and Flt3. Hematopoietic progenitor cells were collected through  depleting positive cells on Automacs. Selected cells were cultured on OP9-DL1 in 6 well plates with MEM containing 20% FCS, 2% PSG, FLT3L, recombinant IL-7 1-2 ng/ml.

extract_protocol:
Lived DN2 cells were selected on day10. Cells were cultured as control without OP9-DL1 n aMEM 20% FBS, IL7, FLT3-L, without actinomycin-d . Cells were harvested at 60 min, immediately spun down, and resuspended in PBS. Cells were fixed with 1% formaldehyde. Formaldehyde was quenched with 0.2 M glycine for 10 min. Fixed cells were stored at -80 degrees until use.
Libraries were prepared with NEBNext primer set. Fragment size was selected with AMPure beads (Beckman Coulter).


title: Chow_NCoRKO_27ac_146


title: H54-8

city: Gießen

first: Andreas

last: Gogol-Döring

address: Wiesenstraße 14

department: MNI

country: Germany

institute: Technische Hochschule MIttelhessen

description: PCR products

data_processing:
Library strategy: 4C-seq
The sequencing read pairs were processed as follows: First, we in-silico generated all possible self-ligation junction of the pEPI, i.e. all sequences that could be generated by completely digesting pEPI with either NlaIII or EcoRI and then ligating two of the fragments. If any one of the two reads belonging to a read pair mapped completely to one of these self-ligation junctions or to pEPI itself, then the read pair was discarded. In the remaining reads, we searched for pEPI marker sequences, i.e. sequences starting with the PCR primer and ending with the first downstream occurrence of the corresponding enzyme restriction site in pEPI. Read pairs containing the last 10bp of a pEPI marker sequence followed by a sequence of length ≥20bp not part of pEPI (i.e., possibly originating from the human genome), were selected for the subsequent analysis. All pEPI parts of the reads were stripped and the rest was mapped against the human reference genome (hg19) using the Bowtie 2 read mapping tool (29). A read pair was treated as a ‘hit’, if both reads in the pair could be uniquely and coherently mapped to genomic positions with distance of ≤ 1kb between each other. Redundant hits originating from identical read pairs were treated as a single hit. The hits were then assigned to the closest EcoRI site.
Genome_build: hg19
Supplementary_files_format_and_content: 6 column bed files. Each row corresponds to one contact site. The score column (column 5) contains the number of reads supporting the given contact site.

source_name: HeLa

extract_protocol:
4C using pEPI-EGFP as bait: Cells were crossliked with 1% formaldehyde, lysed and nuclei were digested with EcoRI; digested chromatin was extracted and ligated followed by a second digestion/ligation step with NlaIII resulting in circular DNA molecules. Genomic sequences were amlified using specific primer  within bait.
libraries were constructed by BGI Genomics Co., Ltd

tag: tissue origin

value: cervix carcinoma

tag: modified

value: pEPI-HS4opp transfected

value: HeLa


title: Tumor6_SMC3 ChIP-seq

description: used for Fig. 7


title: SMC3 CHIP-seq 30min AcD2

description: used for Fig. 6

extract_protocol:
Lived DN2 cells were selected on day10. Cells were cultured as control without OP9-DL1 n aMEM 20% FBS, IL7, FLT3-L, with 10 ug/ml of actinomycin-d . Cells were harvested at 30 min, immediately spun down, and resuspended in PBS. Cells were fixed with 1% formaldehyde. Formaldehyde was quenched with 0.2 M glycine for 10 min. Fixed cells were stored at -80 degrees until use.
Libraries were prepared with NEBNext primer set. Fragment size was selected with AMPure beads (Beckman Coulter).


title: SMC3 CHIP-seq 60min AcD2

description: used for Fig. 6

extract_protocol:
Lived DN2 cells were selected on day10. Cells were cultured as control without OP9-DL1 n aMEM 20% FBS, IL7, FLT3-L, with 10 ug/ml of actinomycin-d . Cells were harvested at 60 min, immediately spun down, and resuspended in PBS. Cells were fixed with 1% formaldehyde. Formaldehyde was quenched with 0.2 M glycine for 10 min. Fixed cells were stored at -80 degrees until use.
Libraries were prepared with NEBNext primer set. Fragment size was selected with AMPure beads (Beckman Coulter).


title: SMC3 CHIP-seq 30min control

description: used for Fig. 6

extract_protocol:
Lived DN2 cells were selected on day10. Cells were cultured as control without OP9-DL1 n aMEM 20% FBS, IL7, FLT3-L, without actinomycin-d . Cells were harvested at 30 min, immediately spun down, and resuspended in PBS. Cells were fixed with 1% formaldehyde. Formaldehyde was quenched with 0.2 M glycine for 10 min. Fixed cells were stored at -80 degrees until use.
Libraries were prepared with NEBNext primer set. Fragment size was selected with AMPure beads (Beckman Coulter).


title: SMC3 CHIP-seq 60min AcD1

description: used for Fig. 6


title: ATAC-seq_tumor_5

description: used for Fig. 7

extract_protocol:
Tumor cells were cultured in aMEM 20% FBS, IL7, FLT3-L. Cells were harvested and immediately spun down, and resuspended in PBS. Cells were fixed with 1% formaldehyde. Formaldehyde was quenched with 0.2 M glycine for 10 min. Fixed cells were stored at -80 degrees until use.
50000 cells were used for library preparation. Washed cells were resuspended in lysis buffer. After washing, cells were treated with transposition mix for 30 min at 37 degrees. Cycle of PCR amplification was determined by q-PCR. 100-800 bps of Libraries were selected from 2% agarose gel.


title: E55-13

description: PCR products

value: pEPI-EGFP transfected

tag: cell line


title: SMC3 CHIP-seq 30min AcD1

description: used for Fig. 6


title: In55-8

description: PCR products

value: pEPI-Intron transfected


title: T55In

description: PCR products


title: SMC3 CHIP-seq 15min control

description: used for Fig. 6

extract_protocol:
Lived DN2 cells were selected on day10. Cells were cultured as control without OP9-DL1 n aMEM 20% FBS, IL7, FLT3-L, without actinomycin-d . Cells were harvested at 15 min, immediately spun down, and resuspended in PBS. Cells were fixed with 1% formaldehyde. Formaldehyde was quenched with 0.2 M glycine for 10 min. Fixed cells were stored at -80 degrees until use.
Libraries were prepared with NEBNext primer set. Fragment size was selected with AMPure beads (Beckman Coulter).


title: SMC3 CHIP-seq 15min AcD2

description: used for Fig. 6

extract_protocol:
Lived DN2 cells were selected on day10. Cells were cultured as control without OP9-DL1 n aMEM 20% FBS, IL7, FLT3-L, with 10 ug/ml of actinomycin-d . Cells were harvested at 15 min, immediately spun down, and resuspended in PBS. Cells were fixed with 1% formaldehyde. Formaldehyde was quenched with 0.2 M glycine for 10 min. Fixed cells were stored at -80 degrees until use.
Libraries were prepared with NEBNext primer set. Fragment size was selected with AMPure beads (Beckman Coulter).


title: SMC3 CHIP-seq 15min AcD1

description: used for Fig. 6


title: T55E

description: PCR products


title: Pol II CHIP-seq 30min AcD2

description: used for Fig. 6


title: Pol II CHIP-seq 15min AcD2

description: used for Fig. 6


title: Pol II CHIP-seq 30min AcD1

description: used for Fig. 6


title: Pol II CHIP-seq 30min control

description: used for Fig. 6


title: Pol II CHIP-seq 15min AcD1

description: used for Fig. 6


title: F20_pvll

city: Seattle

first: Koichi

last: Hashikawa

state: WA

address: 1959 NE Pacific St. HSB J135

department: Neuroscience

institute: University of Washington

data_processing:
The RNA-seq libraries were then prepared using Clontech SMARTer Stranded Total RNA-Seq Kit (cat. no. 635006) and purified using AMPure beads (Beckman Coulter). The quantity of the library was examined using Qubit RNA HS assay Kit (Thermo Fisher Scientific) and qPCR. The quality of the library was determined using Bioanalyzer (Agilent). Once the libraries were deemed high quality (free of adaptor dimers and in concentration >2 nM), we pooled eight samples equimolarly and sequenced them by Illumina HiSeq 2500 using high output mode to achieve greater depth of coverage. Read alignment was carried out using HISAT2 (https://github.com/infphilo/hisat2) against the mouse mm10 reference genome obtained from Ensembl database (http://ensembl.org/)[
The alignment results were then exported to the open-source software Featurecounts to determine the number of reads for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: normalized counts per gene per sample

source_name: VMHpvll

extract_protocol:
coronal frozen sections of VgluT2-cre/Ai6 female mice. VMHpvlm and VMHpvll were microdissected using LCM. RNA extracted using picopure (ThermoFisher).
Clontech SMARTer Stranded Total RNA-Seq Kit

tag: background

tag: Sex

value: female


title: H3.3 ChIP-seq ThymoDp(A)/p(A)

description: used for Fig. 6

data_processing:
Samples are mapped to reference genome mm9 by Bowtie (version 1.1.1), using following option: --best -m 1, and others as default. the bam file are then processed by Homer to create tag directory with the default setting of Homer makeTagDirectory, using option -tbp 1. Homer findPeak has been used to identify enriched regions.
genome build: mm9
processed data files format and content: bed file with peak coordinates

extract_protocol:
Harvested cells were stained with lineage marker, CD25, CD117, ghost dye red 780. Cells were fixed with PBS containing 1% formaldehyde. Formaldehyde was quenched with 0.2 M glycine for 10 min. Lineage negative DN2 cells were sorted by FACS AriaII and washed with PBS. Fixed cells were stored at -80 degrees until use.
Libraries were prepared with NEBNext primer set. Fragment size was selected with AMPure beads (Beckman Coulter).

value: ThymoDp(A)/p(A)


title: H3.3 ChIP-seq ThymoD+/p(A)

description: used for Fig. 6


title: KH_161103_D


title: H3K4me3 ChIP-seq ThymoDp(A)/p(A)

description: used for Fig. 6


title: H3.3 ChIP-seq WT

description: used for Fig. 6


title: F19_pvll


title: KH_161103_C

source_name: VMHpvlm


title: Pol II CHIP-seq 15min control

description: used for Fig. 6


title: T34H

description: PCR products


title: H3K4me3 ChIP-seq ThymoD+/p(A)

description: used for Fig. 6


title: H3K4me1 ChIP-seq ThymoDp(A)/p(A)

description: used for Fig. 6


title: H3K4me3 ChIP-seq WT

description: used for Fig. 6


title: H3K4me1 ChIP-seq ThymoD+/p(A)

description: used for Fig. 6


title: F19_pvlm


title: F20_pvlm


title: H3K4me1 ChIP-seq WT

description: used for Fig. 6


title: CTCF ChIP-seq ThymoD+/p(A) 2

description: replicate 2

data_processing:
Samples are mapped to reference genome mm9 by Bowtie (version 1.1.1), using following option: --best -m 1, and others as default. the bam file are then processed by Homer to create tag directory with the default setting of Homer makeTagDirectory, using option -tbp 1. Homer findPeak has been used to identify enriched peaks.
genome build: mm9
processed data files format and content: bed file with peak coordinates


title: HT_2_GROseq.


title: HT_1_GROseq.


title: CTCF ChIP-seq ThymoD+/p(A) 1

description: used for Fig. 5,6


title: CTCF ChIP-seq WT

description: used for Fig. 5,6


title: PD_6_Perturbation-RRBS

first: Jiantao

last: Shi

address: 3 Blackfan Circle

institute: dana farber cancer institute

description: Msp1 digested bisulfite converted genomic DNA

data_processing:
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using bsmap with the following params: -v 0.05 -r 0 -s 16 -S 1 -p 8
Single CpG methylation levels were limited to those CpGs that had at least fivefold coverage.
The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files which contain CpG site methylation. Column headers are: chrom, chromStart, chromEnd, name (methylation level with coverage in brackets), score and strand.

source_name: ICM outgrowth cultured with PD

extract_protocol:
Genomic DNA and mRNA purifications from low input samples were performed as described by Maculay et al. 2015 with modifications. Briefly, the cells were mixed with 15 µl of RLT plus buffer (QIAGen) containing 1 U/µl of RNase inhibitor (SUPERase·In, ThermoFisher Scientific), 1% ß-mercaptoethanol (Sigma-Aldrich), and were then transferred to one well in a 96-well DNA LoBind plate (Eppendorf). After adding 10 µl of M-280 streptavidin bead-conjugated RT primer to each sample, the reaction was incubated at 72˚C for 3 min in a thermocycler followed by incubation at room temperature for 25 min with gentle rotation. The genomic DNA and mRNA were separated in a DynaMag™-96 Side Magnet (ThermoFisher Scientific).
Bead-tagged mRNA was subjected to reverse transcription as described previously in Maculay et. al 2015 and the genomic DNA in the supernatant was transferred to a fresh 96-well DNA LoBind plate. After reverse transcription, the cDNA was PCR amplified and RNA-seq library was generated according to the Smart-seq 2 protocol. Indexed RNA-seq libraries were pooled and sequenced in an Illumina Hiseq2500 sequencer.  Genomic DNA was isolated utilizing 1x Agencourt AMPure beads (Beckman Coulter) and was eluted to 15 µl of low TE buffer. RRBS library was generated as reported previously in Gu et. al 2013 with modifications. We utilized the CutSmart buffer (New England Biolabs) for all three enzymatic reactions including MspI digestion, end-repair/A-tailing and T4 DNA ligation. To minimize DNA loss, DNA purification step was eliminated after each enzymatic reaction. Briefly, the genomic DNA was digested by 16 units of MspI (New England Biolabs) for 80 min at 37˚C, and followed by heat inactivation at 65˚C for 15 min. The digested DNA fragments were end-repaired and A-tailed by adding 4 units of Klenow exo- (New England Biolabs), 0.03 mM dCTP, 0.03 mM dGTP and 0.3 mM dATP; ant the reaction was carried out at 30˚C for 25 min; 37˚C for 25 min followed by incubation at 70 ˚C for 10 min to inactive the enzyme. We then ligated the A-tailed DNA fragments with indexed adapters overnight at 16 ˚C by adding 2,000 units of T4 DNA ligase and 0.75 mM ATP and 7 nM of the adapters. The T4 ligase was heat-inactivated at 65 ˚C for 15 min before pooling libraries together. To remove adapter dimers, the library pool was cleaned up using 1.8X AMPure beads and the adapter-tagged DNA fragments were eluted to 30 µl of low TE buffer. The bisulfite conversion of the adapter-tagged DNA fragments ware conducted using a QIAGen EpiTect Fast Bisulfite Conversion Kit following the manufacturer’s instructions with a minor modification. We extended the bisulfite conversion time from 2 cycles of 10 min to 2 cycles of 20 min to achieve bisulfite conversion rates >99%. The bisulfite converted DNA fragments were PCR amplified according to the following thermocycler settings: 98 ˚C for 45 s, 6 cycles of 98 ˚C for 20 s, 58 ˚C for 30 s, 72 ˚C for 1 min and then 8-10 cycles of 98 ˚C for 20 s, 65 ˚C for 30 s, 72 ˚C for 1 min followed by a final extension cycle of 5 min at 72 ˚C. The PCR amplified library DNA was cleaned up using 1.3X AMPure beads and the RRBS libraries were paired-end sequenced for 2x100 cycles.  Only instances where the matched pool of Epiblast and ExE from a given replicate both had over 1 million CpGs covered at ≥5x were included for downstream analysis.  For each sample, 10 µl of M-280 streptavidin beads (ThermoFisher Scientific) were prepared per the manufacturer’s recommendations. Specifically, after washing with Solution A (0.1 N NaOH, 0.05 M NaCl) and B (0.1 M NaCl) sequentially, the beads were resuspended in 10 µl of 2x Washing and Binding buffer (10 mM Tris-HCl, 1 mM EDTA, 2 M NaCl) and then mixed with an equal volume of 2 µM of RT primer (Maculay et al. 2015). The mixture was incubated for 15 min at room temperature with gentle rotation. The bead-bound RT primer was collected in a magnate and was subsequently resuspended in 10 µl of binding buffer (10 mM Tris-HCl (PH 8.0), 167 mM NaCl, 0.05% Tween-20).

treatment_protocol: Outgrowth  experiments:  To generate controlled outgrowth data, ICM were immunosurgically isolated from BDF1x129S1/SvImJ strain blastocysts at 96hpf.  Briefly, oocytes were isolated by hormone priming from B6D2F1 females 12-14 hours after administration of hCG and fertilized by Intracytoplasmic Sperm Injection using piezo actuated injection of 129S1/SvIMJ strain sperm.  At 96 hrs post-fertilization, blastocysts were stripped of their zona pellucida by brief incubation in Acid Tyrode’s solution and incubated for 30 minutes in 1:10 diluted whole mouse antisera (Sigma) in CO2 equilibrated KSOM, followed by destruction of the trophectoderm by culture in 1:10 diluted Guinea Pig Complement Sera (Sigma).  After 15 minutes at 37ºC, the ICM separates from the complement-lysed TE and could be cleanly isolated by brief pulsing through a narrow glass capillary.  ICM were isolated in batches of ~12 per drop. Once isolated, ICM were then plated into basal N2/B27 media supplemented with 1000 U/mL LIF (made in house) and one of the following conditions; ‘2i’ supplemented with 1 mM PD0325901 and 3 mM CHIR99021 (Reagents Direct); ‘PD’ supplemented with  1 uM PD0325901 and 10 ng/mL BMP4 to promote outgrowth expansion (Peprotech), ‘FGF+CHIR’ supplemented with 25ng/mL mouse recombinant FGF4 (R and D) and 3 mM CHIR99021; and ‘FGF’ supplemented with 25ng/mL FGF4 only.  FGF4 was selected because it is the most highly expressed FGF family member in the preimplantation embryo and we sought to direct specific remethylation changes as is observed in vivo.  ICM were plated in gelatin treated tissue culture dishes plated with irradiated CF-1 strain embryonic fibroblasts to promote attachment.  The primary outgrowth from the ICM, characterized as a centrally expanding, three-dimensional mass, was isolated after 4 days of culture.  In all cases but the 2i condition, an outer layer of differentiated cells was apparent and removed using an identical strategy to removal of the extraembryonic endoderm from E6.5 samples described above.  However, under the FGF+CHIR condition, the ‘outer layer’ was often of the same size or larger than the internal outgrowth and only became defined during the latter portion of culture.  As such, we collected both interior and exterior portions as they could clearly be distinguished as mutually ICM-derived.  After incubation and either isolation or removal of external cells, outgrowths were serially washed through several KSOM drops under mineral oil before being snap frozen in minimal volume for RRBS and RNA-seq profiling.  Generation of KO embryos by CRISPR/Cas9 and zygotic injection:  Zygotic injection was performed essentially as described (Wang et. al, 2013 Cell) To improve the efficiency with which null alleles were generated, three separate guide RNA sequences were designed per target, prioritizing highly scored protospacer sequences with no high scoring off target sites using the CHOPCHOP web tool and at as 5’ most a coding exon as possible given these constraints.  Protospacer sequences were input into the following oligonucleotide primer pair and used to amplify off of the pX300 plasmid (Addgene): Forward primer, AGTCAGTTAATACGACTCACTATAGN19GTTTTAGAGCTAGAAATAGCAAG; Reverse primer, AAAAAAAGCACCGACTCGGTGCCAC.  Protospacer sequences that did not begin with a G to initiate T7 transcription were inserted and an additional 5’ G was added.  200 ng of gel purified, T7 promoter containing sgRNA templates were used to generate gRNAs by in vitro transcription using the MEGAshortscript™ T7 transcription kit (Thermo Fisher), followed by purification with phenol:chloroform and ethanol precipitation.  Translation competent spCas9 RNA was in vitro transcribed off of a similarly designed, T7 promoter driven template amplified off of the pX300 plasmid using the mMessage mMachine™ T7 Ultra kit (Thermo Fisher) and purified using the RNA Clean and Concentrator Kit (Zymo Research).  RNA was resuspended in an injection buffer comprised of 5 mM Tris-HCl, 0.1 mM EDTA, pH=7.4.  Zygotes were isolated from hormone primed B6D2F1females mated with B6D2F1 males as described above.  Shortly after the formation of visible pronuclei (Pronuclear Stage 3), zygotes were cytoplasmically injected with 100 ng/ul of all three targeted sgRNAs pooled 1:1:1 and 200 ng/ul Cas9 mRNA.  At E3.5, cavitated blastocyts were transferred in clutches of 10-15 into one uterine horn of pseudopregnant CD-1 strain mice (Charles River) that had been mated with vasectomized male Swiss-Weber strain mice (Taconic) two days prior.  To account for the ~1 day offset in developmental progression that results from uterine transfer, appropriately E6.5 stage conceptuses were isolated four days after uterine transfer and epiblast and extraembryonic ectoderm tissue were isolated.  Each replicate consisted of ≥4 embryos and all experimental series include replicates generated from at least two rounds of zygotic injection.  Care was taken to ensure epiblast and extraembryonic ectoderm tissue from matched embryos were included for each replicate set and RRBS data where both fractions did not cover >1 million CpGs at ≥5x coverage each were excluded from further analysis.

tag: developmental stage

value: ICM outgrowth

tag: treatment

value: PD


title: PD_5_Perturbation-RRBS


title: input ChIP-seq ThymoDp(A)/p(A) 2

description: replicate 2

data_processing:
Samples are mapped to reference genome mm9 by Bowtie (version 1.1.1), using following option: --best -m 1, and others as default. the bam file are then processed by Homer to create tag directory with the default setting of Homer makeTagDirectory, using option -tbp 1.
genome build: mm9
processed data files format and content: bed file with peak coordinates

tag: strain


title: Bisulfite seq DN2 p(A)/p(A)

description: used for Fig. 6

data_processing:
Analysis of bisulfite sequencing was performed using BSSeeker2 (Guo/Pellegrini, BMC    Genomics, 2013), HOMER (Heinz/Glass, Mol.Cell., 2010), and custom awk scripts. Specifically,    a bisulfite-sequencing amenable mm9 reference genome was built using the BSSeeker2 script    bs_seeker2-build.py with default options. Paired-end sequencing data was aligned to this    reference genome using the BSSeeker2 script bs_seeker2-align.py allowing 6 mismatches (-m    6) and a fragment length between 0 and 800 bases (-I 0 -X 800). PCR duplicates were removed    from paired end data using picard tools (https://broadinstitute.github.io/picard/). Unpaired reads    were saved, aligned individually with the same options, and merged with paired-end data.    Methylation levels were called using the BSSeeker2 script bs_seeker2-call_methylation.py with    default settings. BSSeeker2 methylation call data was reformatted to the allC format    (Lister/Ecker, Nature, 2009), and tag directories were created using HOMER’s    makeTagDirectory command with the -minCounts 5 option, thus including only those cytosines    covered by at least 5 reads. Downstream analysis comparing DNA methylation levels between    wild-type and ThymoD knockout cells included only those cytosines covered by 5 reads in both    data sets.
genome build: mm9

extract_protocol:
Harvested cells were stained with lineage marker, CD25, CD117, ghost dye red 780. Cells were fixed with PBS containing 1% formaldehyde. Formaldehyde was quenched with 0.2 M glycine for 10 min. Lineage negative DN2 cells were sorted by FACS AriaII and washed with PBS. Fixed cells were stored at -80 degrees until use.
1 ug of genomic DNA were fragmented with sonication, end-repaired with Epicentre End-It Kit, Added poly-A tail and ligated to TruSeq adapters. Fragments were purified with agarose gel and bisulfite converted by MethylCode kit.

tag: genotype


title: input ChIP-seq ThymoD+/p(A) 2

description: replicate 2

tag: chip antibody


title: PD_2_Perturbation-RRBS


title: PD_1_Perturbation-RRBS


title: input ChIP-seq WT 1

description: replicate 1


title: input ChIP-seq WT 2

description: replicate 2


title: input ChIP-seq ThymoD+/p(A) 1

description: replicate 1


title: FGF_WNT_outside_9_Perturbation-RRBS

source_name: ICM outgrowth cultured with FGF4 and CHIR, outside

value: FGF4 + CHIR


title: PD_3_Perturbation-RRBS


title: SMC3 ChIP-seq ThymoD+/p(A) 1

description: replicate 1


title: FGF_WNT_outside_7_Perturbation-RRBS


title: FGF_WNT_outside_6_Perturbation-RRBS


title: E1-1

description: PCR products


title: SMC3 ChIP-seq ThymoDp(A)/p(A) 1

description: replicate 1


title: PD_4_Perturbation-RRBS


title: FGF_WNT_outside_5_Perturbation-RRBS


title: input ChIP-seq ThymoDp(A)/p(A) 1

description: replicate 1


title: SMC3 ChIP-seq WT 2

description: used for Fig. 5,6

value: WT


title: Bisulfite seq DN2 WT

description: used for Fig. 6


title: FGF_WNT_outside_3_Perturbation-RRBS


title: FGF_WNT_outside_2_Perturbation-RRBS


title: CTCF ChIP-seq ThymoDp(A)/p(A)

description: used for Fig. 5,6


title: FGF_WNT_inside_9_Perturbation-RRBS

source_name: ICM outgrowth cultured with FGF4 and CHIR, inside


title: FGF_WNT_outside_8_Perturbation-RRBS


title: SMC3 ChIP-seq ThymoDp(A)/p(A) 2

description: used for Fig. 5,6


title: SMC3 ChIP-seq ThymoD+/p(A) 2

description: used for Fig. 5,6


title: ATAC DN2 ThymoDp(A)/p(A)1

description: used for Fig. 6

data_processing:
Samples are mapped to reference genome mm9 by Bowtie (version 1.1.1), using following option: --best -m 1, and others as default. the bam file are then processed by Homer to create tag directory with the default setting of Homer makeTagDirectory, using option -tbp 1. For ATAC open region, following options were used :-localSize 50000 -size 150-minDist 50 –fragLength 0, and we used the default setting for other peak/region calling.
genome build: mm9
processed data files format and content: bed file

extract_protocol:
Harvested cells were stained with lineage marker, CD25, CD117, ghost dye red 780. Lineage negative DN2 cells were sorted by FACS AriaII and washed with PBS.
50000 cells were used for library preparation. Washed cells were resuspended in lysis buffer. After washing, cells were treated with transposition mix for 30 min at 37 degrees. Cycle of PCR amplification was determined by q-PCR. 100-800 bps of Libraries were selected from 2% agarose gel.


title: FGF_WNT_inside_7_Perturbation-RRBS


title: FGF_WNT_inside_8_Perturbation-RRBS


title: ATAC DN2 ThymoDp(A)/p(A) 2

description: replicate 2


title: ATAC DN2 ThymoD+/p(A) 2

description: replicate 2


title: ATAC DN2 ThymoD+/p(A) 1

description: used for Fig. 6


title: SMC3 ChIP-seq WT 1

description: replicate 1


title: ATAC DN2 WT 2

description: replicate 2


title: FGF_WNT_inside_6_Perturbation-RRBS


title: 13308_5_B

city: London

first: M Joaquina

last: Delas

address: 1 Midland Road

department: Briscoe Lab

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Reads were mapped to the mm10 genome assembly yielding at least 106 aligned reads per sample
HTSeq-count was used to calculate gene counts and subsequently input them into DESeq2 for quality control analysis, size normalization and variance dispersion corrections.
Genome_build: mm10
Supplementary_files_format_and_content: variance estabilized transformation calculated using DESeq2 for all replicated of both hairpins tagetting a given lncRNA, and Renilla controls

molecule: polyA RNA

source_name: RN2 cells (MLL-AF9/NRASG12D)

growth_protocol: MLL-AF9;NRASG12D AML cells were cultured in RPMI-1640 with GlutaMaxTM (Gibco), supplemented with 10% heat-inactivated FBS (HyClone) and 1% Penicillin/Streptomycin (Gibco) under 7.5% CO2 culture conditions.

extract_protocol:
RNA extraction using TriZol
TruSeq Stranded Total RNA Library Prep Kit (Illumina)

treatment_protocol: Cells were transduced with a retroviral vector expressing an inducible shRNA. Infection percentage was kept to less than 30%. Single cell derived clonal cell lines were tested for homogeneous expression of the reported genes. Two cell lines per knockdown were used for further studies.

tag: knockdown

tag: shRNA

tag: clonal cell line

value: B


title: 13308_8_A

value: A


title: 9665_6_A


title: 13308_5_A


title: 12928_20_A


title: 9665_6_B


title: 13308_8_B


title: 12928_20_B


title: FGF_WNT_inside_5_Perturbation-RRBS


title: 9665_1_A


title: FGF_WNT_inside_3_Perturbation-RRBS


title: 9665_1_B


title: 7931_5_A


title: ATAC DN2 WT 1

description: used for Fig. 2,5,6


title: 12928_10_A


title: FGF_WNT_inside_2_Perturbation-RRBS


title: FGF_8_Perturbation-RRBS

source_name: ICM outgrowth cultured with FGF4


title: 11053_14_B


title: 12928_10_B


title: FGF_4_Perturbation-RRBS


title: 11053_14_A


title: FGF_7_Perturbation-RRBS


title: 11053_1_B


title: 11053_1_A


title: FGF_1_Perturbation-RRBS


title: 7358_5_B


title: 7358_8_B


title: 7358_8_A


title: 7931_4_A


title: 7661_5_A


title: 7931_5_B


title: 7358_5_A


title: 7931_4_B


title: Pvt1_9_B


title: Pvt1_9_A


title: ExE_WT_6_Perturbation-RRBS

source_name: Extraembryonic wild type

value: Extraembryonic ectoderm

tag: ko


title: ExE_WT_7_Perturbation-RRBS


title: ExE_Kdm2b_both_4_Perturbation-RRBS

source_name: Extraembryonic ectoderm with Kdm2b knockout (both isoforms)

value: Kdm2b long and short isoforms


title: ExE_WT_4_Perturbation-RRBS


title: ExE_WT_5_Perturbation-RRBS


title: Myc_1_C

value: Myc

value: C


title: ExE_Kdm2b_both_3_Perturbation-RRBS


title: 7661_1_A


title: FGF_5_Perturbation-RRBS


title: 7661_1_B


title: Myc_1_B


title: Renilla_713_C

value: Renilla


title: Myc_1_A


title: ExE_Kdm2b_both_1_Perturbation-RRBS


title: Renilla_713_B


title: Renilla_713_A


title: Pvt1_1_B


title: ExE_EED_8_Perturbation-RRBS

source_name: Extraembryonic ectoderm with Eed knockout

value: Eed


title: ExE_EED_3_Perturbation-RRBS


title: Pvt1_1_A


title: 3554_10_B


title: 7661_5_B


title: 3554_10_A


title: 3554_8_A


title: ExE_EED_2_Perturbation-RRBS


title: 1_270_c

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

country: Canada

institute: University of Toronto

description:
Sow 270
1_270_c

data_processing:
reads were trimed of adaptor sequences and poor quality bases
reads were aligned to mRNA sequences obtained from ENSEMBL SusScrofa10.2 build
aligned bam files were quantified using DESeq2
differential expression was calculated using limma after transformation of the data using voom
aligments were uising bowtie 2.0
Genome_build: SusScrofa10.2
Supplementary_files_format_and_content: a table of voom transformed read counts

organism: Sus scrofa

source_name: fetal brain

extract_protocol:
brains were homogenized in trizol reagent and extracted as per TRIZOL protocol. Samples were then cleaned up using Norgen Biotek total RNA kit (cat#37500)
As per Illumina RIBO gold

treatment_protocol: infection with zika virus, strain PRVABC59 (GenBank: KU501215)

tag: agent

tag: mode

value: mock


title: ExE_Dnmt3l_5_Perturbation-RRBS

source_name: Extraembryonic ectoderm with Dnmt3l knockout


title: ExE_Dnmt3l_4_Perturbation-RRBS


title: Epiblast_rep2_WGBS

data_processing:
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background.
Single CpG methylation levels were limited to those CpGs that had at least fivefold coverage.
The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files which contain CpG site methylation. Column headers are: chrom, chromStart, chromEnd, name (methylation level with coverage in brackets), score and strand.

source_name: proximal Epiblast

extract_protocol:
Genomic DNA for Whole Genome Bisulfite Sequencing was isolated according to Smith, Chan et. al, Nature, 2012 using a lysis buffer containing 300 ug/mL Proteinase K and 50 ng/mL DNAse-free RNAse, followed by phenol:chloroform extraction and ethanol precipitation.
Libraries were prepared using the Accel-NGS™ Bisulfite DNA library kit (Swift Biosciences) according to the manufacturers protocol.  Final libraries were generated from 10-12 PCR cycles.

treatment_protocol: Preparation of preimplantation and post-implantation samples was performed as described in Smith, Chan, et. al, Nature 2014. Briefly, B6D2F1 hybrid females between 5-8 wks old were serially primed with 5 IU Pregnant Mare Gonadotropin (Sigma) followed by 5 IU Human Chorionic Gonadotrophin (Millipore) after 46 hours, after which they were mated with B6D2F1 male mice ≤6 months old.  Zygotes from mated females were isolated from the oviduct the following morning (E0.5) and cultured in KSOM media (Millipore) droplets under mineral oil until E2.25.  The 8 cell sample was collected by careful monitoring of 4 cell embryos from ~E2 onwards and embryos were swapped into KSOM supplemented with 1 mg/ml aphidicolin (Sigma) to ensure synchronization and minimal entry into the fourth replication cycle.  8 cell embryos were collected within 4 hours of the first apparent embryo of this stage.  Prior to collection, embryos were serially transferred through Acid Tyrode’s solution (Sigma) to remove the Zona Pellucida and carefully pipetted with a drawn glass capillary through a 0.25% Trypsin-EDTA (Life Technologies) until the maternal polar bodies were removed.  E3.5 blastocysts were also treated with Acid Tyrode’s solution to remove the Zona and the ICM and TE of matched samples dissected using standard micromanipulation equipment (Eppendorf) and a Hamilton Thorne XYClone laser with 300 ms pulsing at 100% intensity.  Isolation of post-implantation tissues was performed as described in Chenowith and Tesar, Methods Mol Bio, 2010.  The decidua of mated female mice were isolated on the morning of E6.5 and the conceptus removed.  Then, under a stereomicroscope, the embryo was carefully bisected along the extraembryonic/embryonic axis, removing the ectoplacental cone from the extraembryonic ectoderm when apparent.  After separation, Epiblast and extraembryonic ectoderm incubated for 15 min at 4ºC in 0. 5% Trypsin, 2.5% Pancreatin dissolved in PBS and filtered through a 0.2 mm syringe filter and allowed to rest for 5-10 minutes in KSOM at room temperature.  Finally, visceral endoderm was removed by drawing the embryo through a narrow, flame drawn glass capillary and only embryo fragments with no apparent contamination were collected.  On average, matched ExE and Epiblast or ICM and TE samples from 5-10 embryos and from 20 or more 8 cell embryos were collected per assay.  Samples were snap frozen in minimal volume prior to extraction and next-generation library synthesis.

value: B6D2 F1

tag: tissue

value: proximal Epiblast


title: Epiblast_rep1_WGBS


title: ExE_rep1_WGBS

source_name: Extraembryonic Ectoderm

value: Extraembryonic Ectoderm


title: ExE_rep2_WGBS


title: TE_rep2_WGBS

source_name: Trophectoderm

value: Trophectoderm


title: TE_rep1_WGBS


title: 8_296_z

description:
Sow 296
8_296_z

value: Zika virus

value: female


title: 11_296_z

description:
Sow 296
11_296_z


title: ExE_Dnmt3l_1_Perturbation-RRBS


title: ICM_rep1_WGBS

source_name: Inner Cell Mass

value: Inner Cell Mass


title: 10_295_z

description:
Sow 295
10_295_z

value: male

value: intracerebrally


title: ICM_rep2_WGBS


title: 8cell_rep1_WGBS

source_name: precompacted 8 cell stage embryos

value: precompacted 8 cell stage embryos


title: 8cell_rep2_WGBS


title: ExE_rep2_RNA-seq

data_processing:
Alignment was performed using TopHat against mouse genome assembly mm10 with default settings.
Kallisto was used for quantification of transcript-level expression, which was reported as TPM.
Genome_build: mm10
Supplementary_files_format_and_content: *.tsv: text file contains transcript-level expression, represented as TPM.

extract_protocol:
RNA was isolated using the RNAeasy Micro Kit from Qiagen
RNA-seq libraries generated using the SMRT-seq v4 Ultralow Input Kit (Clontech) according to the manufacturer’s protocol using 10-11 LD PCR cycles. Libraries were generated from 150 pg of cDNA using the Nextera XT DNA library preparation kit (Illumina) using 12 PCR cycles.

treatment_protocol: Preparation of preimplantation and post-implantation samples was performed as described in Smith, Chan, et. al, Nature 2014. Briefly, B6D2F1 hybrid females between 5-8 wks old were serially primed with 5 IU Pregnant Mare Gonadotropin (Sigma) followed by 5 IU Human Chorionic Gonadotrophin (Millipore) after 46 hours, after which they were mated with B6D2F1 male mice ≤6 months old.  Zygotes from mated females were isolated from the oviduct the following morning (E0.5) and cultured in KSOM media (Millipore) droplets under mineral oil until E2.25.  The 8 cell sample was collected by careful monitoring of 4 cell embryos from ~E2 onwards and embryos were swapped into KSOM supplemented with 1 mg/ml aphidicolin (Sigma) to ensure synchronization and minimal entry into the fourth replication cycle.  8 cell embryos were collected within 4 hours of the first apparent embryo of this stage.  Prior to collection, embryos were serially transferred through Acid Tyrode’s solution (Sigma) to remove the Zona Pellucida and carefully pipetted with a drawn glass capillary through a 0.25% Trypsin-EDTA (Life Technologies) until the maternal polar bodies were removed.  E3.5 blastocysts were also treated with Acid Tyrode’s solution to remove the Zona and the ICM and TE of matched samples dissected using standard micromanipulation equipment (Eppendorf) and a Hamilton Thorne XYClone laser with 300 ms pulsing at 100% intensity.  Isolation of post-implantation tissues was performed as described in Chenowith and Tesar, Methods Mol Bio, 2010.  The decidua of mated female mice were isolated on the morning of E6.5 and the conceptus removed.  Then, under a stereomicroscope, the embryo was carefully bisected along the extraembryonic/embryonic axis, removing the ectoplacental cone from the extraembryonic ectoderm when apparent.  After separation, Epiblast and extraembryonic ectoderm incubated for 15 min at 4ºC in 0. 5% Trypsin, 2.5% Pancreatin dissolved in PBS and filtered through a 0.2 mm syringe filter and allowed to rest for 5-10 minutes in KSOM at room temperature.  Finally, visceral endoderm was removed by drawing the embryo through a narrow, flame drawn glass capillary and only embryo fragments with no apparent contamination were collected.  On average, matched ExE and Epiblast or ICM and TE samples from 5-10 embryos and from 20 or more 8 cell embryos were collected per assay. Samples were snap frozen in minimal volume prior to extraction and next-generation library synthesis.


title: ExE_Dnmt3b_6_Perturbation-RRBS

source_name: Extraembryonic ectoderm with Dnmt3b knockout

value: Extraembryonic ectoderm


title: ExE_Dnmt3l_2_Perturbation-RRBS


title: 3554_8_B

value: B


title: 2_295_z

description:
Sow 295
2_295_z


title: 7_295_z

description:
Sow 295
7_295_z


title: ExE_Dnmt3b_5_Perturbation-RRBS


title: ExE_EED_1_Perturbation-RRBS


title: ExE_Dnmt3b_4_Perturbation-RRBS


title: Epiblast_rep2_RNA-seq


title: Epiblast_rep1_RNA-seq


title: TE_rep2_RNA-seq


title: TE_rep1_RNA-seq


title: 5_270_c

description:
Sow 270
5_270_c


title: 3_296_z

description:
Sow 296
3_296_z


title: 6_270_c

description:
Sow 270
6_270_c


title: 4_270_c

description:
Sow 270
4_270_c


title: ExE_Dnmt3b_2_Perturbation-RRBS


title: ICM_rep2_RNA-seq


title: 8cell_rep2_RNA-seq


title: ICM_rep1_RNA-seq


title: ExE_Dnmt3b_3_Perturbation-RRBS


title: 8cell_rep1_RNA-seq


title: ExE_Dnmt3b_1_Perturbation-RRBS


title: 3_270_c

description:
Sow 270
3_270_c


title: ExE_Dnmt3a_6_Perturbation-RRBS

source_name: Extraembryonic ectoderm with Dnmt3a knockout


title: ExE_rep2_ATAC-seq

data_processing:
Library strategy: ATAC-seq
Reads were aligned to mouse genome mm10 using BWA with default parameters.
Duplicates were removed by function MarkDuplicates from Picard tool kit. Reads with low mapping quality (< 10) or in mitochondrial chromosome were removed.
NucleoATAC was used to generate Insert density.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files which contain insertion sites

extract_protocol:
Accessible chromatin was isolated according to Buenrostro et. al, Nature Methods, 2013 as the first step of the library construction protocol (see below).
Accessible chromatin was isolated according to Buenrostro et. al, Nature Methods, 2013 using a 10 μl reaction and incubation with the TN5 transposase mixture (Nextera DNA library preparation kit, Illumina) for 45 minutes.  Reaction was stopped according to the protocol described in Lara-Astiaso et. al, Science, 2014 and purified using Silane beads (Thermo Fisher) . Tagmented DNA was amplified for 12-14 cycles to generate the library.

treatment_protocol: Preparation of preimplantation and post-implantation samples was performed as described in Smith, Chan, et. al, Nature 2014. Briefly, B6D2F1 hybrid females between 5-8 wks old were serially primed with 5 IU Pregnant Mare Gonadotropin (Sigma) followed by 5 IU Human Chorionic Gonadotrophin (Millipore) after 46 hours, after which they were mated with B6D2F1 male mice ≤6 months old.  Zygotes from mated females were isolated from the oviduct the following morning (E0.5) and cultured in KSOM media (Millipore) droplets under mineral oil until E2.25.  The 8 cell sample was collected by careful monitoring of 4 cell embryos from ~E2 onwards and embryos were swapped into KSOM supplemented with 1 mg/ml aphidicolin (Sigma) to ensure synchronization and minimal entry into the fourth replication cycle.  8 cell embryos were collected within 4 hours of the first apparent embryo of this stage.  Prior to collection, embryos were serially transferred through Acid Tyrode’s solution (Sigma) to remove the Zona Pellucida and carefully pipetted with a drawn glass capillary through a 0.25% Trypsin-EDTA (Life Technologies) until the maternal polar bodies were removed.  E3.5 blastocysts were also treated with Acid Tyrode’s solution to remove the Zona and the ICM and TE of matched samples dissected using standard micromanipulation equipment (Eppendorf) and a Hamilton Thorne XYClone laser with 300 ms pulsing at 100% intensity.  Isolation of post-implantation tissues was performed as described in Chenowith and Tesar, Methods Mol Bio, 2010.  The decidua of mated female mice were isolated on the morning of E6.5 and the conceptus removed.  Then, under a stereomicroscope, the embryo was carefully bisected along the extraembryonic/embryonic axis, removing the ectoplacental cone from the extraembryonic ectoderm when apparent.  After separation, Epiblast and extraembryonic ectoderm incubated for 15 min at 4ºC in 0. 5% Trypsin, 2.5% Pancreatin dissolved in PBS and filtered through a 0.2 mm syringe filter and allowed to rest for 5-10 minutes in KSOM at room temperature.  Finally, visceral endoderm was removed by drawing the embryo through a narrow, flame drawn glass capillary and only embryo fragments with no apparent contamination were collected.  On average, matched ExE and Epiblast or ICM and TE samples from 5-10 embryos and from 20 or more 8 cell embryos were collected per assay .Samples were snap frozen in minimal volume prior to extraction and next-generation library synthesis.


title: 2_270_c

description:
Sow 270
2_270_c


title: ExE_rep1_RNA-seq


title: Epiblast_rep1_ATAC-seq


title: Epiblast_rep2_ATAC-seq


title: ExE_Dnmt3a_5_Perturbation-RRBS


title: Blastocyst_rep2_ATAC-seq

source_name: Blastocyst

value: Blastocyst


title: λN-FLAG with mKate2 reporter

city: Arlington

first: Alicia

middle: Kathryn

last: Rogers

state: Texas

address: 1225 W Mitchell Street

department: Department of Biology

institute: University of Texas at Arlington

description: Small RNA-Seq experiment

data_processing:
Sequenced reads were trimmed for adaptor sequence and mapped to dm3 whole genome and to the mKate2 reporter sequence or GFP reporter sequence accordingly using bowtie 0.12.7 with parameters -v 0 -m 10000 --best --strata
Sequenced reads were trimmed for adaptor sequence and mapped to RepBase using bowtie 0.12.7 with parameters -v 3 --best --strata
Genome_build: dm3
Genome_build: mKate2 reporter sequence (linked as supplementary file on the Series record)
Genome_build: GFP reporter sequence (https://doi.org/10.1126/science.aaa1039)
Genome_build: RepBase (http://www.girinst.org/repbase/)
Supplementary_files_format_and_content: bedGraph

organism: Drosophila melanogaster

source_name: λN-FLAG with mKate2 reporter

growth_protocol: Flies were kept at 24C and aged 3-5 days, atleast 2 of which were on yeast, before dissection.

extract_protocol:
Small RNAs (19-30nt) were isolated from total ovary RNA and then libraries were cloned using the NEBNext Small RNA Library Prep Kit for Illumina,
Total RNA was isolated from ovaries using Ribozol followed by precipitation.
Libraries were prepared using the NEBNext Small RNA Library Prep Set for Illumina according to the protocol using NEBNext Multiplex Oligos for Illumina.

value: <lambda>N-FLAG/mKate2-4xBoxB; MT-Gal4

value: ovaries


title: Male_cortex_6w_R106W_GROseq_rep2

city: Old Westbury

first: Ying-Tao

last: Zhao

state: NY

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

institute: New York Institute of Technology

description: nuclei

data_processing:
Basecalls performed using CASAVA version 1.8
For RNA-seq, the FASTQ files of each samples were mapped to the mouse mm10 genome by STAR (version 2.3.0) using the parameters of "--outFilterMultimapNmax 1 --outFilterMismatchNmax 3". The number of reads mapped to the whole gene body of each gene were counted using Perl scripts generated in-house. All comparisons were performed by the edgeR and DEseq2 R packages, and FDR < 0.05 was the criteria used to identify differentially expressed genes. For each comparison, the results from edgeR and DESeq2 were merged to avoid method-based biases. The mean fold changes and the mean FDRs generated from both methods were used for generating plots and heatmaps.
For GRO-seq, the FASTQ files of each samples were mapped to the mouse mm10 genome by STAR (version 2.3.0) using the parameters of "--outFilterMultimapNmax 1 --outFilterMismatchNmax 3". The number of reads mapped to the whole gene body of each gene were counted using Perl scripts generated in-house. All comparisons were performed by the edgeR package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count for each gene

source_name: Cortex

growth_protocol: Experiments were conducted in accordance with the ethical guidelines of the US National Institutes of Health and with the approval of the Institutional Animal Care and Use Committee of the University of Pennsylvania. All of the experiments described were performed using mice on a congenic sv129:C57BL/6 background with the knock-in/transgenic alleles backcrossed to C57BL/6 mice (Charles River) for at least five generations, unless otherwise stated. Mice were housed in a standard 12h light/12h dark cycle with access to ample amounts of food and water.

extract_protocol:
Total RNA was prepared from FACS-isolated cortical nuclei of male mice at 6 weeks (TAVI, T158M, R106W, 2-3 mice pooled per biological replicate, 4 replicates each), male mice at 12 weeks (TAVI, T158M, 2 mice pooled per biological replicate, 3 replicates each), and female mice at 18 weeks (TAVI, T158M, R106W, single mouse per biological replicate, 2 replicates each). Nuclei were isolated from fresh cortical tissue for FACS as previously described under ice-cold and nuclease-free conditions. Mouse cortices were rapidly resected on ice and subjected to dounce homogenization in homogenization buffer (0.32M sucrose, 5mM CaCl2, 3mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton, 0.1mM EDTA, Roche Complete Protease Inhibitor without EDTA). Homogenates were layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2 Roche Complete Protease Inhibitor without EDTA) and centrifuged at 25,000 rpm at 4°C for 2.5 hours using a Beckman SW25.1 swinging bucket rotor. Nuclei were resuspended & washed once in blocking buffer (1x PBS, 0.5% BSA (Sigma A4503), RNasin Plus RNase Inhibitor (Promega)) and pelleted using a tabletop centrifuge at 5000 RCF at 4°C for 10 minutes. Nuclei were resuspended in blocking buffer to a concentration of ~6x106 nuclei/ml, blocked for 20 minutes at 4°C with rotation, then incubated with Streptavidin Dylight 650 (1:1000, Fisher 84547) and Alexa 488-conjugated anti-NeuN antibody (1:1000, Millipore MAB377X) for 30 minutes at 4°C with rotation. After a 5-minute incubation with 1:1000 DAPI to enable singlet detection during FACS, labeled nuclei were washed for an additional 30 minutes at 4°C with blocking buffer, pelleted and resuspended in blocking buffer with 1% BSA. A BD Biosciences Influx cell sorter at the University of Pennsylvania Flow Cytometry and Cell Sorting Facility was used to identify cell type-specific populations of nuclei, and 1.2 – 2.5 x105 singlet nuclei from specified populations were directly sorted into Qiagen Buffer RLT Plus for immediate lysis and stabilization of RNA transcripts. Total nuclear RNA was processed using the Qiagen AllPrep DNA/RNA mini kit according to manufacturer instructions, with exception to the on-column DNaseI treatment. RNA was eluted from RNeasy mini spin columns and treated with DNaseI (Qiagen 79254) for 25 minutes at room temperature, then precipitated with glycogen/NaOAc and stored in ethonal at -80°C. Ethanol precipitation of nuclear RNA was carried out to completion prior to initiating RT-PCR or RNA-seq library construction.
For RNA-seq, the total amount of RNA isolated from a single aliquot of sorted nuclei wasused as input for library construction; hence differential gene expression comparisons betweenFACS-isolated Mecp2 control and mutant neurons is performed using RNA from equivalentnumbers of neuronal nuclei. Total RNA was depleted of ribosomal RNAs, subjected to 5minutes of heat fragmentation, and converted to strand-specific cDNA libraries using the TruSeqTotal RNA library prep kit with RiboZero depletion (Illumina). Multiplexed libraries weresequenced at the University of Pennsylvania Next Generation Sequencing Core facility using anIllumina HiSeq 2000/2500 that typically yielded 30-40M total reads per library.

tag: gender

tag: age

value: 6 week

tag: cell type

value: Cortical cells


title: ExE_Dnmt3a_4_Perturbation-RRBS


title: Male_cortex_6w_R106W_GROseq_rep1

description: nuclei


title: ExE_Dnmt3a_1_Perturbation-RRBS


title: Male_cortex_6w_WT_GROseq_rep2

description: nuclei

value: WT (TAVI)


title: λN-FLAG with GFP reporter

description: Small RNA-Seq experiment

source_name: λN-FLAG with GFP reporter

value: <lambda>N-FLAG/Tub-GFP-BoxB; MT-Gal4


title: ExE_Dnmt1_5_Perturbation-RRBS

source_name: Extraembryonic ectoderm with Dnmt1 knockout


title: Male_cortex_6w_WT_GROseq_rep1

description: nuclei


title: λN-FLAG-Piwi with GFP reporter

description: Small RNA-Seq experiment

source_name: λN-FLAG-Piwi with GFP reporter


title: Female_excitatory_18W_T158MKI_T158M_nuclear_RNAseq_rep1

description: nuclear total RNA

value: 18 week

value: Mecp2 tavi/T158M (T158M)

value: Cortical excitatory neurons


title: ExE_Dnmt1_4_Perturbation-RRBS


title: ExE_rep1_ATAC-seq

value: B6D2 F1

value: Extraembryonic Ectoderm


title: λN-GFP with GFP reporter

description: Small RNA-Seq experiment

source_name: λN-GFP with GFP reporter

value: <lambda>N-GFP/Tub-GFP-BoxB; MT-Gal4


title: ExE_Dnmt1_3_Perturbation-RRBS


title: λN-GFP-Piwi with GFP reporter

description: Small RNA-Seq experiment

source_name: λN-GFP-Piwi with GFP reporter


title: Female_excitatory_18W_R106WKI_R106W_nuclear_RNAseq_rep1

description: nuclear total RNA

value: female

value: Mecp2 tavi/R106W (R106W)


title: Female_excitatory_18W_R106WKI_R106W_nuclear_RNAseq_rep2

description: nuclear total RNA


title: Female_excitatory_18W_R106WKI_WT_nuclear_RNAseq_rep2

description: nuclear total RNA

value: Mecp2 tavi/R106W (TAVI)


title: Female_excitatory_18W_T158MKI_WT_nuclear_RNAseq_rep1

description: nuclear total RNA

value: Mecp2 tavi/T158M (TAVI)


title: λN-Armi (MT-gal4) NaIO4 treated replicate 2

description: NaIO4 treated Small RNA-Seq experiment

source_name: λN-Armi (MT-gal4) NaIO4 treated

extract_protocol:
Small RNAs (19-30nt) were isolated from total ovary RNA and then treated with 5xBorate Buffer and 200mM sodium periodate @ 25C for 30 minutes. The treated RNA was then ethanol precipitated and libraries were cloned using the NEBNext Small RNA Library Prep Kit for Illumina,
Total RNA was isolated from ovaries using Ribozol followed by precipitation.
Libraries were prepared using the NEBNext Small RNA Library Prep Set for Illumina according to the protocol using NEBNext Multiplex Oligos for Illumina.

value: <lambda>N-Armi/mKate2-4xBoxB; MT-Gal4


title: Female_excitatory_18W_WT_WT_nuclear_RNAseq_rep2

description: nuclear total RNA


title: Blastocyst_rep1_ATAC-seq

value: Blastocyst


title: λN-FLAG-Piwi with mKate2 reporter

description: Small RNA-Seq experiment

source_name: λN-FLAG-Piwi with mKate2 reporter

value: ovaries


title: ExE_Dnmt1_1_Perturbation-RRBS

value: Extraembryonic ectoderm


title: λN-Armi (MT-gal4) NaIO4 treated replicate 1

description: NaIO4 treated Small RNA-Seq experiment


title: Female_excitatory_18W_R106WKI_WT_nuclear_RNAseq_rep1

description: nuclear total RNA


title: Epi_WT_7_Perturbation-RRBS

source_name: Epiblast wild type

value: Epiblast

value: WT


title: Female_excitatory_18W_WT_WT_nuclear_RNAseq_rep1

description: nuclear total RNA

value: WT (TAVI)


title: Male_cortex_6w_R106W_nuclear_RNAseq_rep2

description: nuclear total RNA

value: male

value: 6 week

value: Cortical cells


title: Male_cortex_6w_R106W_nuclear_RNAseq_rep1

description: nuclear total RNA


title: Female_excitatory_18W_T158MKI_T158M_nuclear_RNAseq_rep2

description: nuclear total RNA

value: 18 week

value: Mecp2 tavi/T158M (T158M)

value: Cortical excitatory neurons


title: λN-Aub (MT-gal4) NaIO4 treated replicate 1

description: NaIO4 treated Small RNA-Seq experiment

source_name: λN-Aub (MT-gal4) NaIO4 treated

value: <lambda>N-Aub/mKate2-4xBoxB; MT-Gal4


title: Male_cortex_6w_R106W_wholeCell_RNAseq_rep2

description: whole cell total RNA


title: λN-Aub (MT-gal4) NaIO4 treated replicate 2

description: NaIO4 treated Small RNA-Seq experiment


title: Male_cortex_6w_WT_nuclear_RNAseq_rep1

description: nuclear total RNA


title: Female_excitatory_18W_T158MKI_WT_nuclear_RNAseq_rep2

description: nuclear total RNA

value: female


title: λN-Piwi (MT-gal4) NaIO4 treated replicate 2

description: NaIO4 treated Small RNA-Seq experiment

source_name: λN-Piwi (MT-gal4) NaIO4 treated

value: <lambda>N-Piwi/mKate2-4xBoxB; MT-Gal4


title: ExE_Dnmt1_2_Perturbation-RRBS


title: Male_cortex_6w_WT_wholeCell_RNAseq_rep2

description: whole cell total RNA


title: Epi_WT_5_Perturbation-RRBS


title: Male_cortex_6w_R106W_wholeCell_RNAseq_rep1

description: whole cell total RNA


title: Male_cortex_6w_WT_wholeCell_RNAseq_rep1

description: whole cell total RNA


title: λN-Zuc (MT-gal4) NaIO4 treated replicate 2

description: NaIO4 treated Small RNA-Seq experiment

source_name: λN-Zuc (MT-gal4) NaIO4 treated

value: <lambda>N-Zuc/mKate2-4xBoxB; MT-Gal4


title: Epi_Kdm2b_both_4_Perturbation-RRBS

source_name: Epiblast with Kdm2b knockout (both isoforms)

value: Kdm2b long and short isoforms


title: Epi_WT_4_Perturbation-RRBS


title: λN-Piwi (MT-gal4) NaIO4 treated replicate 1

description: NaIO4 treated Small RNA-Seq experiment


title: Epi_Kdm2b_both_3_Perturbation-RRBS


title: Male_inhibitory_6w_T158M_nuclear_RNAseq_rep3

description: nuclear total RNA

value: Cortical inhibitory neurons


title: Male_inhibitory_6w_T158M_nuclear_RNAseq_rep1

description: nuclear total RNA


title: λN-Zuc (MT-gal4) NaIO4 treated replicate 1

description: NaIO4 treated Small RNA-Seq experiment

value: ovaries


title: Male_inhibitory_6w_R106W_nuclear_RNAseq_rep4

description: nuclear total RNA


title: Male_inhibitory_6w_T158M_nuclear_RNAseq_rep4

description: nuclear total RNA


title: Male_inhibitory_6w_R106W_nuclear_RNAseq_rep3

description: nuclear total RNA


title: Epi_Kdm2b_both_1_Perturbation-RRBS


title: Male_inhibitory_6w_T158M_nuclear_RNAseq_rep2

description: nuclear total RNA


title: λN-GFP (MT-gal4) NaIO4 treated replicate 2

description: NaIO4 treated Small RNA-Seq experiment

source_name: λN-GFP (MT-gal4) NaIO4 treated

value: <lambda>N-GFP/mKate2-4xBoxB; MT-Gal4


title: Epi_WT_6_Perturbation-RRBS

value: Epiblast


title: Male_inhibitory_6w_R106W_nuclear_RNAseq_rep2

description: nuclear total RNA


title: Male_inhibitory_6w_R106W_nuclear_RNAseq_rep1

description: nuclear total RNA


title: λN-GFP (MT-gal4) NaIO4 treated replicate 1

description: NaIO4 treated Small RNA-Seq experiment


title: Male_inhibitory_6w_WT_nuclear_RNAseq_rep4

description: nuclear total RNA


title: λN-Piwi sh-AGO3 replicate 2

description: Small RNA-Seq experiment

source_name: λN-Piwi sh-AGO3


title: Male_inhibitory_6w_WT_nuclear_RNAseq_rep2

description: nuclear total RNA


title: Male_inhibitory_6w_WT_nuclear_RNAseq_rep3

description: nuclear total RNA


title: λN-Piwi sh-AGO3 replicate 1

description: Small RNA-Seq experiment


title: Male_inhibitory_6w_WT_nuclear_RNAseq_rep1

description: nuclear total RNA


title: Male_excitatory_6w_T158M_nuclear_RNAseq_rep4

description: nuclear total RNA


title: Male_excitatory_6w_T158M_nuclear_RNAseq_rep3

description: nuclear total RNA


title: Epi_EED_1_Perturbation-RRBS

source_name: Epiblast with Eed knockout

value: Eed


title: Epi_Dnmt3l_5_Perturbation-RRBS

source_name: Epiblast with Dnmt3l knockout


title: λN-Piwi sh-Aub replicate 2

description: Small RNA-Seq experiment

source_name: λN-Piwi sh-Aub


title: Epi_Dnmt3l_4_Perturbation-RRBS


title: Male_excitatory_6w_T158M_nuclear_RNAseq_rep2

description: nuclear total RNA

source_name: Cortex


title: Male_excitatory_6w_R106W_nuclear_RNAseq_rep3

description: nuclear total RNA


title: Male_excitatory_6w_R106W_nuclear_RNAseq_rep2

description: nuclear total RNA


title: λN-Piwi sh-Aub replicate 1

description: Small RNA-Seq experiment


title: Male_excitatory_6w_T158M_nuclear_RNAseq_rep1

description: nuclear total RNA


title: Epi_Dnmt3l_3_Perturbation-RRBS


title: Epi_EED_8_Perturbation-RRBS


title: λN-Piwi sh-Krimper replicate 1

description: Small RNA-Seq experiment

source_name: λN-Piwi sh-Krimper


title: Male_excitatory_6w_WT_nuclear_RNAseq_rep4

description: nuclear total RNA

value: WT (TAVI)


title: Epi_EED_3_Perturbation-RRBS


title: Epi_Dnmt3l_2_Perturbation-RRBS


title: Male_excitatory_6w_R106W_nuclear_RNAseq_rep1

description: nuclear total RNA

value: male


title: λN-Piwi sh-Krimper replicate 2

description: Small RNA-Seq experiment


title: Male_excitatory_6w_WT_nuclear_RNAseq_rep3

description: nuclear total RNA

value: 6 week


title: Epi_Dnmt3l_1_Perturbation-RRBS


title: λN-Piwi sh-Vasa replicate 2

description: Small RNA-Seq experiment

source_name: λN-Piwi sh-Vasa


title: Epi_EED_2_Perturbation-RRBS


title: λN-Piwi sh-Vasa replicate 1

description: Small RNA-Seq experiment


title: Epi_Dnmt3b_6_Perturbation-RRBS

source_name: Epiblast with Dnmt3b knockout


title: Male_excitatory_6w_WT_nuclear_RNAseq_rep2

description: nuclear total RNA


title: λN-Piwi sh-Armi replicate 2

description: Small RNA-Seq experiment

source_name: λN-Piwi sh-Armi


title: Male_excitatory_6w_R106W_nuclear_RNAseq_rep4

description: nuclear total RNA


title: λN-Piwi sh-Armi replicate 1

description: Small RNA-Seq experiment


title: Epi_Dnmt3b_5_Perturbation-RRBS


title: Epi_Dnmt3b_4_Perturbation-RRBS


title: λN-Piwi sh-Zuc replicate 1

description: Small RNA-Seq experiment

source_name: λN-Piwi sh-Zuc


title: λN-Piwi sh-THOC5 replicate 1

description: Small RNA-Seq experiment

source_name: λN-Piwi sh-THOC5


title: λN-Piwi sh-Cuff replicate 2

description: Small RNA-Seq experiment

source_name: λN-Piwi sh-Cuff


title: λN-Piwi sh-THOC5 replicate 2

description: Small RNA-Seq experiment


title: Epi_Dnmt3b_3_Perturbation-RRBS


title: λN-Piwi sh-Egg replicate 2

description: Small RNA-Seq experiment

source_name: λN-Piwi sh-Egg


title: Epi_Dnmt3b_2_Perturbation-RRBS


title: λN-Piwi sh-Cuff replicate 1

description: Small RNA-Seq experiment


title: λN-Piwi sh-Egg replicate 1

description: Small RNA-Seq experiment


title: λN-Piwi sh-Panx replicate 1

description: Small RNA-Seq experiment

source_name: λN-Piwi sh-Panx


title: λN-Piwi sh-White replicate 2

description: Small RNA-Seq experiment

source_name: λN-Piwi sh-White


title: Epi_Dnmt3a_4_Perturbation-RRBS

source_name: Epiblast with Dnmt3a knockout


title: Epi_Dnmt3a_2_Perturbation-RRBS


title: Epi_Dnmt1_5_Perturbation-RRBS

source_name: Epiblast with Dnmt1 knockout


title: λN-Piwi sh-White replicate 1

description: Small RNA-Seq experiment


title: Epi_Dnmt1_2_Perturbation-RRBS


title: Epi_Dnmt1_4_Perturbation-RRBS


title: Epi_Dnmt1_3_Perturbation-RRBS


title: Epi_Dnmt3a_1_Perturbation-RRBS


title: Epi_Dnmt3b_1_Perturbation-RRBS


title: λN-Zuc GFP-Piwi IP replicate 2

description: Small RNA-Seq experiment from Piwi Immunoprecipitation

source_name: λN-Zuc GFP-Piwi IP

extract_protocol:
Roughly 100 ovaries were dissected and lysed on ice in lysis buffer (0.5M Hepes-KOH pH7.4, 2M KOAc, 1M Mg(Oac)2, 1M DTT, 10% NP40, proteinase inhibitor cocktail, Rnasin Plus) and dounced and clarified by centrifugation @ 4C. The lysate was incubated with protein A|G beads pre-conjugated with rabbit polyclonal anti-GFP or anti-Piwi @ 4C for 2 hours. The immunoprecipitation and RNA isolation was carried out as described in Vagin et al 2006. A fifth of the RNA was CIP treated in NEB Buffer #3 for 30' @ 37C then ethanol precipitated after phenol:chloroform and chloroform extration. The CIP-treated RNA was then PNK treated with T4 Polynucleotide Kinase and γ-P32 ATP for 45' @ 37C. The PNK-treated RNA and remainder of the isolated RNA were added back together and then small RNAs (19-30nt) were isolated and then libraries were cloned using the NEBNext Small RNA Library Prep Kit for Illumina,
Total RNA was isolated from ovaries using Ribozol followed by precipitation.
Libraries were prepared using the NEBNext Small RNA Library Prep Set for Illumina according to the protocol using NEBNext Multiplex Oligos for Illumina.

tag: ip antibody

value: anti-GFP


title: Epi_Dnmt1_1_Perturbation-RRBS


title: λN-Zuc GFP-Piwi IP replicate 1


title: 2i_4_Perturbation-RRBS

source_name: ICM outgrowth under 2i condition

value: ICM outgrowth

value: PD + CHIR


title: λN-Aub Piwi IP replicate 2

source_name: λN-Aub Piwi IP

value: anti-Piwi


title: Epi_Dnmt3a_5_Perturbation-RRBS


title: λN-Piwi sh-Panx replicate 2

description: Small RNA-Seq experiment


title: λN-Aub Piwi IP replicate 1

value: <lambda>N-Aub/mKate2-4xBoxB; MT-Gal4


title: λN-Piwi GFP-Piwi IP replicate 2

source_name: λN-Piwi GFP-Piwi IP


title: λN-Piwi GFP-Piwi IP replicate 1


title: λN-Armi (MT-gal4) replicate 2

description: Small RNA-Seq experiment

source_name: λN-Armi (MT-gal4)

value: <lambda>N-Armi/mKate2-4xBoxB; MT-Gal4


title: λN-Armi (MT-gal4) replicate 1

description: Small RNA-Seq experiment


title: λN-Aub (MT-gal4) replicate 1

description: Small RNA-Seq experiment

source_name: λN-Aub (MT-gal4)


title: λN-Panx (MT-gal4) replicate 2

description: Small RNA-Seq experiment

source_name: λN-Panx (MT-gal4)

value: <lambda>N-Panx/mKate2-4xBoxB; MT-Gal4


title: λN-Aub (MT-gal4) replicate 2

description: Small RNA-Seq experiment


title: λN-Egg (MT-gal4) replicate 2

description: Small RNA-Seq experiment

source_name: λN-Egg (MT-gal4)

value: <lambda>N-Egg/mKate2-4xBoxB; MT-Gal4


title: λN-Egg (MT-gal4) replicate 1

description: Small RNA-Seq experiment


title: 2i_2_Perturbation-RRBS


title: FGF_WNT_outside_3_Perturbation-RNA-Seq

data_processing:
Alignment was performed using TopHat against mouse genome assembly mm10 with default settings.
Kallisto was used for quantification of transcript-level expression, which was reported as TPM.
Genome_build: mm10
Supplementary_files_format_and_content: text file contains transcript-level expression, represented as TPM.

source_name: ICM outgrowth cultured with FGF4 and CHIR, outside

value: FGF4 + CHIR


title: PD_4_Perturbation-RNA-Seq

source_name: ICM outgrowth cultured with PD

value: PD


title: PD_6_Perturbation-RNA-Seq


title: PD_5_Perturbation-RNA-Seq


title: FGF_WNT_outside_4_Perturbation-RNA-Seq


title: PD_2_Perturbation-RNA-Seq


title: λN-Arx (MT-gal4) replicate 2

description: Small RNA-Seq experiment

source_name: λN-Arx (MT-gal4)

value: <lambda>N-Arx/mKate2-4xBoxB; MT-Gal4

value: ovaries


title: PD_1_Perturbation-RNA-Seq


title: λN-Panx (MT-gal4) replicate 1

description: Small RNA-Seq experiment


title: FGF_WNT_outside_2_Perturbation-RNA-Seq


title: PD_3_Perturbation-RNA-Seq


title: Epi_Dnmt3a_6_Perturbation-RRBS

value: Epiblast


title: 2i_1_Perturbation-RRBS


title: λN-Arx (MT-gal4) replicate 1

description: Small RNA-Seq experiment


title: FGF_WNT_inside_4_Perturbation-RNA-Seq

source_name: ICM outgrowth cultured with FGF4 and CHIR, inside


title: λN-Piwi (MT-gal4) replicate 2

description: Small RNA-Seq experiment

source_name: λN-Piwi (MT-gal4)

value: <lambda>N-Piwi/mKate2-4xBoxB; MT-Gal4


title: Male_excitatory_6w_WT_nuclear_RNAseq_rep1

description: nuclear total RNA

source_name: Cortex

value: WT (TAVI)

value: Cortical excitatory neurons


title: FGF_WNT_inside_3_Perturbation-RNA-Seq


title: FGF_WNT_inside_2_Perturbation-RNA-Seq


title: FGF_8_Perturbation-RNA-Seq

source_name: ICM outgrowth cultured with FGF4


title: λN-Zuc (MT-gal4) replicate 2

description: Small RNA-Seq experiment

source_name: λN-Zuc (MT-gal4)

value: <lambda>N-Zuc/mKate2-4xBoxB; MT-Gal4


title: FGF_5_Perturbation-RNA-Seq


title: FGF_4_Perturbation-RNA-Seq


title: FGF_7_Perturbation-RNA-Seq


title: λN-Zuc (MT-gal4) replicate 1

description: Small RNA-Seq experiment


title: ExE_WT_6_Perturbation-RNA-Seq

source_name: Extraembryonic ectoderm wild type

value: Extraembryonic ectoderm

value: Eed


title: λN-Piwi (MT-gal4) replicate 1

description: Small RNA-Seq experiment


title: ExE_WT_7_Perturbation-RNA-Seq


title: λN-THOC5 (MT-gal4) replicate 2

description: Small RNA-Seq experiment

source_name: λN-THOC5 (MT-gal4)

value: <lambda>N-THOC5/mKate2-4xBoxB; MT-Gal4


title: FGF_1_Perturbation-RNA-Seq

value: ICM outgrowth


title: ExE_WT_5_Perturbation-RNA-Seq


title: ExE_WT_4_Perturbation-RNA-Seq


title: λN-GFP (MT-gal4) replicate 2

description: Small RNA-Seq experiment

source_name: λN-GFP (MT-gal4)

value: <lambda>N-GFP/mKate2-4xBoxB; MT-Gal4


title: λN-Cuff (MT-gal4) replicate 1

description: Small RNA-Seq experiment

source_name: λN-Cuff (MT-gal4)

value: <lambda>N-Cuff/mKate2-4xBoxB; MT-Gal4


title: ExE_Kdm2b_both_4_Perturbation-RNA-Seq

source_name: Extraembryonic ectoderm with Kdm2b knockout (long isoform)

value: Kdm2b long isoform


title: λN-Piwi sh-Zuc replicate 2

description: Small RNA-Seq experiment

source_name: λN-Piwi sh-Zuc


title: λN-Piwi (TJ-gal4) replicate 1

description: Small RNA-Seq experiment

source_name: λN-Piwi (TJ-gal4)

value: mKate2-4xBoxB/TJ-Gal4; <lambda>N-Piwi


title: λN-Cuff (MT-gal4) replicate 2

description: Small RNA-Seq experiment


title: λN-GFP (MT-gal4) replicate 1

description: Small RNA-Seq experiment


title: λN-Yb (TJ-gal4) replicate 2

description: Small RNA-Seq experiment

source_name: λN-Yb (TJ-gal4)

value: mKate2-4xBoxB/TJ-Gal4; <lambda>N-Yb


title: λN-GFP (TJ-gal4) replicate 1

description: Small RNA-Seq experiment

source_name: λN-GFP (TJ-gal4)

value: mKate2-4xBoxB/TJ-Gal4; <lambda>N-GFP


title: ExE_Kdm2b_both_3_Perturbation-RNA-Seq


title: λN-THOC5 (MT-gal4) replicate 1

description: Small RNA-Seq experiment


title: ExE_EED_2_Perturbation-RNA-Seq

source_name: Extraembryonic ectoderm with Eed knockout


title: λN-GFP (TJ-gal4) replicate 2

description: Small RNA-Seq experiment


title: ExE_EED_1_Perturbation-RNA-Seq


title: budding yeast wild-type cells, in vivo, 3% DMS

city: Fukuoka

first: Taichi

last: Umeyama

state: Fukuoka

address: Maidashi 3-1-1, Higashi-ku

department: School of Medicine

country: Japan

institute: Kyushu University

data_processing:
Library strategy: DMS-seq
Basecalls performed using CASAVA version 1.8.4
Sequenced reads were trimmed for adaptor sequence and masked for low-quality sequence, then mapped to S288C_reference_genome_R64-1-1_20110203 whole genome using bowtie v2.2.5 with parameters --no-mixed --no-discordant --very-sensitive
Genome_build: S288C_reference_genome_R64-1-1_20110203
Supplementary_files_format_and_content: bigWig

organism: Saccharomyces cerevisiae

source_name: budding yeast

growth_protocol: Saccharomyces cerevisiae cells were cultivated in YPD medium (1% (w/v) yeast extract, 2% (w/v) polypepton, 2% (w/v) dextrose) at 30°C overnight, diluted 10-fold in fresh YPD medium, and further grown at 30°C for 3 h.

extract_protocol:
The cells were treated with Zymolyase, then incubated with ProK/SDS. The solution was extracted with phenol/chloroform and combined with ethanol and precipitated by centrifugation. The pelette was treated with RNaseA and the solution was extracted once with phenol/chloroform and once with chloroform. The solution was combined with ethanol  and precipitated by centrifugation, then dissolved in water.
DNA was end-repaired using a combination of T4 DNA polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3’ to 5’ 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 4–8 cycles.

treatment_protocol: The cells were collected by centrifugation and resuspended in the conditioned medium at ~1×109 cells/ml, then 1-ml aliquot of the yeast cell suspension was combined with 30 μl of DMS and incubated at room temperature for 2 min.

tag: in vivo/in vitro

value: in vivo

value: wild type


title: λN-Piwi (TJ-gal4) replicate 2

description: Small RNA-Seq experiment

value: ovaries


title: Rat_old_skin_4

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

description:
old
RatJOB4_Haut

data_processing:
Extraction of read information in FastQ format was done using the tool bcl2astq v1.8.4 (provided by Illumina).
Reads were mapped using bwa aln (-n 2 -o 0 -e 0 -O 1000 -E 1000)
Only uniquely mapping reads were counted
Genome_build: RefSeq: mRNA sequences and NR_027324 of Rattus norvegicus from 16.06.2014
Supplementary_files_format_and_content: The Excel sheet includes raw counts for all genes and each sample.

organism: Rattus norvegicus

source_name: skin

extract_protocol:
Purification of RNA from collected tissue samples was done using Qiagen RNeasy Mini Kit following the manufacturer's description
Library preparation was done using Illumina's TruSeq RNA Library Prep Kit v2 kit following the manufacturer's description.

value: Wistar

value: skin

tag: Sex

value: male

value: 24 months


title: Rat_old_skin_3

description:
old
RatJOB3_Haut


title: dsbarc S2 cells - replicate 4

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

description: Sample S2 2.4 (internal ID 24364)

data_processing:
Basecalling RTA 1.18.64.0
The strand specific paired-end reads were screened for ribosomal RNA by aligning with BWA (v0.6.1) against known rRNA sequences (RefSeq). Non matching reads were considerd downstream.
The rRNA subtracted paired-end reads were aligned with TopHat (v1.4.1) against the Drosophila melanogaster genome (FlyBase r5.44) and a maxiumum of 6 missmatches.  Introns between 20-150000 bp are allowed which is based on FlyBase statistics. Maximum multihits was set to 1 and InDels as well as Microexon-search was enabled. Additionally, a gene model was provided as GTF (FlyBase r5.44).
Aligned reads in valid pairs are subjected to FPKM estimation with Cufflinks (v1.3.0). In this step bias detection and correction was performed. Furthermore, only those fragments compatible with FlyBase annotation (r5.44) were allowed and counted towards the number of mapped hits used in the FPKM denominator.  snRNA, rRNA, tRNA, snoRNA and pseudogenes are masked.
The aligned reads were counted with HTSeq. Counts for technical replicates are summed up. The polyA containing transcripts were subjected to differential expression analysis with DESeq. DESeq parameters were chosen to match the DESeq publication (Anders S, Huber W., 2010).
Genome_build: FlyBase dmel_r5.44
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (Standard output cufflinks); tab-delimited text file with differentially expressed genes for the whole analysis (standard output DESeq).

source_name: dsbarc S2 cells

growth_protocol: Flies expressing dicer2; asense-Gal4, UAS-CD8::GFP were crossed to flies with empty landing site VIE-260B (VDRC TID:60100) or barc RNAi (VDRC TID:107013) and the progeny was raised at 29C. Late 3rd instar larval brains were dissected and prepared for FACS-sorting. S2 cells were cultured in Schneider's medium + 10% heat-inactivated FBS and treated with dsRNA against mCherry or barc for 7days.

extract_protocol: Type I neuroblasts were FACS sorted from wild type (TID:60100) or barc RNAi, and RNA was isolated using Trizol LS reagent. S2 cells treated with dsRNA against mCherry or barc were washed and RNA was isolated using Trizol. For both experiments: Total RNA was enriched for polyA mRNA, fragmented and first strand and second strand (dUTP, instead dTTP was used) was generated. For the neuroblast sample, library preparation was done manually using the Illumina Kapa library prep kit, and for the S2 cell sample, library preparation was done with a robot using the Illumina NEB ultra Kit. For both samples, UGDase treatment was done to confer strand specificity.

value: S2 cells

tag: cell subtype

value: dsbarc S2 cells


title: ExE_Dnmt3l_5_Perturbation-RNA-Seq

source_name: Extraembryonic ectoderm with Dnmt3l knockout

tag: developmental stage

value: Extraembryonic ectoderm


title: Rat_old_skin_2

description:
old
RatJOB2_Haut

tag: strain


title: dsmCherry S2 cells - replicate 4

description: Sample S2 2.2 (internal ID 24366)

source_name: dsmCherry S2 cells

value: dsmCherry S2 cells


title: ExE_Kdm2b_both_1_Perturbation-RNA-Seq


title: dsmCherry S2 cells - replicate 3

description: Sample S2 2.1 (internal ID 24365)


title: ExE_EED_8_Perturbation-RNA-Seq

value: Eed


title: Rat_young_skin_4

description:
young
RatEJ4_Haut

value: 6 months


title: ExE_Dnmt3l_4_Perturbation-RNA-Seq


title: Rat_young_skin_3

description:
young
RatEJ3_Haut


title: Rat_old_skin_1

description:
old
RatJOB1_Haut


title: ExE_Dnmt3l_1_Perturbation-RNA-Seq


title: ExE_Dnmt3l_2_Perturbation-RNA-Seq


title: Rat_young_skin_5

description:
young
RatEJ5_Haut


title: dsbarc S2 cells - replicate 2

description: Sample S2 1.4 (internal ID 24360)


title: λN-Yb (TJ-gal4) replicate 1

description: Small RNA-Seq experiment


title: Rat_young_skin_2

description:
young
RatEJ2_Haut


title: ExE_EED_3_Perturbation-RNA-Seq


title: dsbarc S2 cells - replicate 1

description: Sample S2 1.3 (internal ID 24359)


title: dsmCherry S2 cells - replicate 2

description: Sample S2 1.2 (internal ID 24362)


title: ExE_Dnmt3b_6_Perturbation-RNA-Seq

source_name: Extraembryonic ectoderm with Dnmt3b knockout


title: Rat_young_skin_1

description:
young
RatEJ1_Haut


title: dsbarc S2 cells - replicate 3

description: Sample S2 2.3 (internal ID 24363)


title: Rat_old_liver_3

data_processing:
Extraction of read information in FastQ format was done using the tool bcl2astq v1.8.4 (provided by Illumina).
Reads were mapped using bwa aln (-n 2 -o 0 -e 0 -O 1000 -E 1000)
Only uniquely mapping reads were counted
Genome_build: RefSeq: mRNA sequences of Rattus norvegicus from 16.06.2014
Supplementary_files_format_and_content: The Excel sheet includes raw counts for all genes and each sample.

value: liver


title: ExE_Dnmt3b_5_Perturbation-RNA-Seq


title: Rat_old_liver_4


title: Rat_old_liver_1


title: ExE_Dnmt3b_4_Perturbation-RNA-Seq


title: dsmCherry S2 cells - replicate 1

description: Sample S2 1.1 (internal ID 24361)


title: Rat_young_liver_5


title: Rat_old_liver_2


title: Rat_young_liver_1


title: Rat_young_liver_3


title: Rat_young_liver_2


title: Rat_young_liver_4


title: ExE_Dnmt3b_2_Perturbation-RNA-Seq


title: ExE_Dnmt3b_1_Perturbation-RNA-Seq


title: ExE_Dnmt3b_3_Perturbation-RNA-Seq


title: poolJ_mouse3

data_processing:
Reads were extracted and mapped to the shRNAs of the corresponding pool using bowtie (allowing 0 mismatches). Fasta file for the shRNA also included
To analyze the depletion between the final timepoint and input, DESeq was used with Fit type “local”
Genome_build: NA
Supplementary_files_format_and_content: Screen_DESeq_allPools.xls contains the results of DESeq analysis, mjdelasv_GEO_AMLscreen-shRNAs.fasta contains the shRNAs names and sequence.

organism: synthetic construct

source_name: RN2 cells (MLL-AF9/NRASG12D)

growth_protocol: Pools of 50 shRNA vectors were used to produce virus and transduce AML cells at a low multiplicity of infection to minimize double infections. Cells were treated with 500 μg ml-1 G-418 (Roche Applied Science) from two days after infection until fully selected.

extract_protocol:
Library preparation was performed as previously described (Knott (2014) Mol Cell).
In brief, genomic DNA was extracted from the pre-injection pool and the bone marrow cell suspensions using the QIAamp Blood DNA Maxi Kit (Qiagen). For each sample, shRNA hairpins were extracted from genomic DNA in 96 separate 25-cycle PCR reactions where 2 mg of input DNA was included in each reaction.
Following this initial PCR, Illumina adapters were added via PCR, and samples were processed on the Illumina MiSeq platform.

treatment_protocol: 1 x 106 fully selected AML cells were injected in the tail vein of sublethally irradiated (4.5 Gy, 24h before injection) B6.SJL (CD45.1) female mice 6-8 weeks of age. For shRNA induction, animals were treated with doxycycline in the food (625 mg kg-1, Harlan Laboratories). Leukemic mice were euthanized 14 days after transplantation, at terminal disease stage, by CO2.

tag: shRNA pool

value: poolJ

tag: timepoint

value: bone marrow day 14


title: poolJ_mouse2


title: 2i_3_Perturbation-RRBS

data_processing:
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using bsmap with the following params: -v 0.05 -r 0 -s 16 -S 1 -p 8
Single CpG methylation levels were limited to those CpGs that had at least fivefold coverage.
The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files which contain CpG site methylation. Column headers are: chrom, chromStart, chromEnd, name (methylation level with coverage in brackets), score and strand.

source_name: ICM outgrowth under 2i condition

value: ICM outgrowth

tag: treatment

value: PD + CHIR


title: poolJ_mouse1


title: poolJ_input4

value: Injection pool


title: poolJ_input3


title: ExE_Dnmt3a_6_Perturbation-RNA-Seq

source_name: Extraembryonic ectoderm with Dnmt3a knockout


title: ExE_Dnmt3a_5_Perturbation-RNA-Seq


title: ExE_Dnmt3a_4_Perturbation-RNA-Seq


title: poolI_mouse3

value: poolI


title: poolJ_input1


title: poolJ_input2


title: ExE_Dnmt1_5_Perturbation-RNA-Seq

source_name: Extraembryonic ectoderm with Dnmt1 knockout


title: poolI_mouse2


title: poolI_mouse1


title: ExE_Dnmt3a_1_Perturbation-RNA-Seq


title: poolI_input4


title: ExE_Dnmt1_4_Perturbation-RNA-Seq


title: poolI_input3


title: ExE_Dnmt1_3_Perturbation-RNA-Seq


title: poolI_input1


title: poolI_input2


title: poolJ_mouse4


title: poolH_mouse5

value: poolH


title: poolH_mouse4


title: ExE_Dnmt1_2_Perturbation-RNA-Seq


title: ExE_Dnmt1_1_Perturbation-RNA-Seq


title: poolH_mouse1


title: poolH_mouse2


title: poolH_mouse3


title: poolH_input4


title: Epi_WT_6_Perturbation-RNA-Seq

source_name: Epiblast wild type

value: Epiblast


title: poolH_input2


title: poolH_input3


title: Epi_WT_5_Perturbation-RNA-Seq


title: poolG_mouse3

value: poolG


title: poolH_input1


title: Epi_WT_4_Perturbation-RNA-Seq


title: Epi_Kdm2b_both_3_Perturbation-RNA-Seq

source_name: Epiblast with Kdm2b knockout (both isoforms)

value: Kdm2b long and short isoforms


title: poolG_input4


title: poolG_input2


title: poolG_input3


title: poolG_mouse1


title: poolG_input1


title: Epi_Kdm2b_both_1_Perturbation-RNA-Seq


title: Epi_EED_8_Perturbation-RNA-Seq

source_name: Epiblast with Eed knockout


title: Epi_Kdm2b_both_4_Perturbation-RNA-Seq


title: poolF_mouse1

value: poolF


title: poolF_input3


title: Epi_EED_3_Perturbation-RNA-Seq


title: poolF_input2


title: poolF_input1


title: poolE_mouse5

value: poolE


title: Epi_WT_7_Perturbation-RNA-Seq


title: poolG_mouse4


title: Epi_Dnmt3l_5_Perturbation-RNA-Seq

source_name: Epiblast with Dnmt3l knockout


title: poolE_mouse4


title: Epi_EED_1_Perturbation-RNA-Seq


title: poolE_mouse3


title: poolE_mouse2


title: Epi_EED_2_Perturbation-RNA-Seq


title: poolG_mouse2


title: poolE_mouse1


title: Epi_Dnmt3l_4_Perturbation-RNA-Seq


title: poolE_input4


title: poolF_mouse3


title: poolF_mouse2


title: Epi_Dnmt3l_3_Perturbation-RNA-Seq


title: poolE_input3


title: poolE_input1


title: poolF_input4


title: poolE_input2


title: poolD_mouse4

value: poolD


title: Epi_Dnmt3l_2_Perturbation-RNA-Seq


title: poolD_mouse2


title: poolD_mouse3


title: Epi_Dnmt3l_1_Perturbation-RNA-Seq