title: ES cell indirect crosslinking

description:
Sample name: ES-indirect
crosslinked RNA

growth_protocol:
Undifferentiated mouse E14 ES cells were cultured under feeder-free conditions. ES cells were seeded on gelatin-coated dishes and were cultured in Dulbecco's modified Eagle medium (DMEM; GIBCO) supplemented with 15% fetal bovine serum (FBS; Gemini Gemcell), 0.055 mM 2-mercaptoethanol (Sigma), 2 mM Glutamax (GIBCO), 0.1 mM MEM nonessential amino acid (GIBCO), 5,000 U/ml penicillin/streptomycin (GIBCO) and 1,000 U/ml of LIF (Millipore). The cells were maintained in an incubator at 37 °C and 5 % CO2.
Mouse embryonic fibroblasts (MEFs) were cultivated in 15-cm dishes in DMEM (GIBCO) supplemented with 15% fetal bovine serum (FBS; Gemini Gemcell), 0.055 mM 2-mercaptoethanol (Sigma), 2 mM Glutamax (GIBCO), 0.1 mM MEM nonessential amino acid (GIBCO), 5,000 U/ml penicillin/streptomycin (GIBCO). MEFs were also maintained in an incubator at 37 °C and 5 % CO2.

extract_protocol:
Protein-RNA complex was eluted from streptavidin beads and RNA is recovered by digesting the bound protein. Eluted RNA was subjected to rigorous DNase treatment to eliminate DNA contamination. Purified RNAs were hybridized with a DNA probe that is complementary to the biotin-tagged RNA linker, and treated with T7 exonuclease to remove the non-ligated biotinylated RNA linkers. As a result, mainly the successfully ligated chimeric RNAs retained a biotin-tagged linker at the junction.
This chimeric RNA library was fragmented again to an average of 150 nucleotides, and the ligation junctions were pulled-down with streptavidin-coated magnetic beads. The end product was a library of ~150nt chimeric RNAs. This library was enriched with chimeras of in the form of 5'-R1-linker-R2, where R1 and R2 were fragments of interacting RNAs. This library was converted into cDNAs and sequenced with paired-end next-generation sequencing.

treatment_protocol:
Samples were crosslinked by a combination of formaldehyde and EGS. The first RNA fragmentation was performed by sonication and RNAs were trimmed into ~1000nt. rRNAs were remove by duplex-specific nuclease.
Cells were crosslinked, causing the interacting RNAs mediated by a RNA binding protein to be covalently linked to the bound protein. We then fragmented RNAs with RNAase I and and biotinylated the cysteine residues on proteins. The proteins including protein-RNA complexes were immobilized on streptavidin beads. The 5’ end of the RNA was then ligated with a biotin-tagged RNA linker on beads to facilitate subsequent selective purification of chimeric RNAs. Next, proximity-based ligation was carried out on beads under dilute conditions that favor ligations between crosslinked RNA fragments in the same complex.


title: Extracted RNA 5-day traced Lgr5+ cells replicate 3

status: Public on Jun 23 2016

type: SRA

city: Utrecht

first: Kay

last: Wiebrands

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

library_source: transcriptomic

data_processing:
Paired-end reads were aligned to the transcriptome using bwa. Paired-end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell-specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode, we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics, we converted the number of observed unique molecular identifiers into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: *.gene.coutt.csv: Tab-separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicate the cell number of the experiment, separated by an underscore. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.
Supplementary_files_format_and_content: expdata.txt: Tab-separated data file for final processed dataset without ERCC spike-ins, listing all genes (rows) and the number of sequenced transcripts. Column name indicate the experiment and cell number, separated by an underscore. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.
Supplementary_files_format_and_content: cel-seq_barcodes.txt: Tab-separated data file containing all cell-specific barcodes. First column contains barcode number and second column contains barcode sequence.

molecule: total RNA

organism: Mus musculus

extract_protocol:
Cells were sorted into Trizol (Life Technologies) and total RNA was isolated according to the manufacturer’s instructions, with the following alterations. RNA was precipitated overnight at -20 °C, with 2.5ug GlycoBlue (Life Technologies).
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina NextSeq500 using 75bp paired end sequencing.

tag: tissue

value: Small intestine

tag: strain

value: Lgr5-CreERT2 C57Bl6/J mice bred to a Rosa26LSL-YFP reporter mice


title: Extracted RNA 5-day traced Lgr5+ cells replicate 5


title: Extracted RNA 5-day traced Lgr5+ cells replicate 4


title: Malat1 RIA sample

city: La Jolla

first: Sheng

last: Zhong

state: California

address: 9500 Gilman Drive, Mail Code 0412

department: Bioengineering Department

country: USA

institute: University of California, San Diego

description: Malat1 antisense oligonucleotides used to pull down RNA from cell samples

data_processing:
The mapping method is the same as described in GSE61489 and is shown below.
Removing PCR duplicates. The forward read contains a 4nt sample barcode and a 6nt random barcode at the 5' end. A read pair was classified as a PCR duplicate of another read pair and is therefore discarded if the two read pairs had identical sequences and contained identical barcodes (10nt). The tool ‘remove_dup_PE.py’ provides this function, and generates a fastq/fasta file containing the non-duplicated reads, and reports the number of duplicates removed.
RNA were separately mapped to the mouse genome transcriptome and mm9/NCBI37 using Bowtie version 0.12.7 (24), and parameters -f -n 1 -l 15 -e 200 -p 9 –S. This step, implemented in ‘Stitch-seq_Aligner.py’ outputs the reads uniquely mapped to the genome. The aligned tab-delimited text files are results from this step.
The annotations were retrieved from Ensembl (release 67, mouse NCBIM37), including the genes of mRNAs, lincRNAs, rRNAs, snRNAs, snoRNAs, miRNAs, misc_RNAs, tRNAs, and transposons. The different genomic copies of the same transposon were considered as different genes in this analysis. The reads mapped to rRNAs were removed from further analysis. The number of uniquely aligned reads were counted on every gene. The reads mapped to transcriptome and genome is marked separately to indicate potential pre-mRNA alignment.
Genome_build: mm9

source_name: ES cells

growth_protocol: Undifferentiated mouse E14 ES cells were cultured under feeder-free conditions. ES cells were seeded on gelatin-coated dishes and were cultured in Dulbecco's modified Eagle medium (DMEM; GIBCO) supplemented with 15% fetal bovine serum (FBS; Gemini Gemcell), 0.055 mM 2-mercaptoethanol (Sigma), 2 mM Glutamax (GIBCO), 0.1 mM MEM nonessential amino acid (GIBCO), 5,000 U/ml penicillin/streptomycin (GIBCO) and 1,000 U/ml of LIF (Millipore). The cells were maintained in an incubator at 37 °C and 5 % CO2.

extract_protocol:
Cells were rinsed with PBS for 3 times and scraped off plates and centrifuged at 1500g for 5 minutes. Then pellets were lysed in lysis buffer (50mM Tris-HCl, pH7.0, 10mM EDTA, 1%SDS and freshly added DTT, phenylmethylsulphonyl fluoride (PMSF), Protease Inhibitor Cocktail Tablets). Lysate was incubated on ice for 20 minutes and sonicated by Covaris, and then diluted by two folds of hybridization buffer (500mM NaCl, 1%SDS, 100mM Tris-HCl, pH7.0, 10mMEDTA, 15%formamide, and freshly added DTT, PMSF, protease inhibitor, RNase-in). Antisense oligonucleotides for the target RNA were incubated with the lysate, rotating at 37 C overnight. Streptavidin beads were added to the hybridization buffer and incubated for 30 minutes at 37 C. Beads were accumulated by magnet rack and washed five times with wash buffer (2XSSC, 0.5%SDS, PMSF).RNA were eluted by 200ul RNA proteinase K buffer (100mMNaCl, 10mM TrisHCl, pH7.0, 1mM EDTA, 0.5%SDS, 1mg/ml proteinase K) and incubated at 50 C for 45 minutes, followed by 10 minutes boiling.
RNA was purified by Trizol. Eluted RNA was treated by DNase and converted into cDNA by Ovation V2 kit (NuGEN), and subsequently converted into sequencing library using KAPA Library Preparation Kit.

treatment_protocol: RNA pulldown based on antisense nucleotides is done following the method described in Kretz M. et al. (Nature. 2013 Jan 10;493(7431):231-5). Mouse ES cells were fixed by 1% glutaraldehyde for 10 minutes at room temperature, followed by 0.125 M glycine for 5 minutes to quench the reaction.

tag: treatment

value: Malat1 antisense


title: HEK293-1ng-1

city: Shanghai

first: Ligang

last: Wu

state: Shanghai

address: 320 Yueyang Road

department: Shanghai Institutes for biological Sciences

country: China

institute: Chinese Academy of Sciences

data_processing: The raw reads were quality filtered and collapsed with FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Read sequences longer than 17 nt after adapter trimming were aligned to the reference genome (mm10 for mouse, hg38 for human) with no mismatch allowed. The genome mapped reads were aligned to the libraries of miRNAs (miRBase v. 21), tRNAs, rRNAs, sn/snoRNAs (small nuclear/small nucleolar RNAs), endo-siRNA, piRNAs, and repetitive elements sequentially. Normalization was performed by dividing the read counts of the individual small RNA by the total number of reads mapped to the genome and presented as RPM.

organism: Homo sapiens

source_name: HEK293 cell lines

extract_protocol: cDNA libraries of small RNAs were constructed using HEK293 total  RNA, with threefold serial dilutions ranging from 100 to 1 ng. For  mouse oocyte and embryo samples, total RNA was extracted from  111 MII oocytes, 167 1C embryos, 137 2C embryos, 57 4C embryos,  102 8C embryos, 200 p1C embryos, or ~3 × 106 sperms using TRIzol  Reagent (Ambion) containing 45 mM MgCl2 (72), respectively. The  quantity of isolated RNA was measured with Qubit 2.0 Fluorometer  (Invitrogen). Each cDNA library of small RNAs was constructed using  10 ng of total RNA with two technical replicates.

tag: input dna

value: 1ng input of total RNA

tag: replicate

value: technical replicate 1

tag: cell line


title: HEK293-1ng-2

value: technical replicate 2


title: Mouse embryonic fibroblasts

description:
Sample name: MEF
crosslinked RNA

data_processing:
Library strategy: MARIO
MARIO-tools is a package of command-line tools for analyses of MARIO data. It is written in Python and R and is version controlled by GitHub. The full documentation is at http://mariotools.ucsd.edu/. The pipeline takes pair-end sequencing reads as input. The oligonucleotide sequences of the RNA linker and the sample barcodes used for multiplexed sequencing should also be provided to the pipeline. Script files mentioned below are all components from the pipeline.
Removing PCR duplicates. The forward read contains a 4nt sample barcode and a 6nt random barcode at the 5' end. A read pair was classified as a PCR duplicate of another read pair and is therefore discarded if the two read pairs had identical sequences and contained identical barcodes (10nt). The tool ‘remove_dup_PE.py’ provides this function, and generates a fastq/fasta file containing the non-duplicated reads, and reports the number of duplicates removed.
Assigning multiplexed sequencing reads into corresponding experimental samples. The tool ‘split_library_pairend.py’ assigns each pair-end read into a sample by matching the sample barcode in each read with those in the list of sample barcodes (a user input text file), generates a fastq/fasta file for the reads assigned to each sample, as well as a fastq/fasta file for the unassigned reads.
Recovering the cDNAs in the sequencing library. This step identifies the overlapping regions of the two ends of every read pair, if any. It also recovers the entire sequences of the cDNAs in the sequencing library, whenever possible. This function is achieved by ‘recoverFragment.py’, which uses local alignment to identify the overlapping regions. When the overlap was small (15bp or less) compared to read length (100bp on each end), local alignment could be insensitive. To overcome this insensitivity, ‘recoverFragment.py’ collects the read pairs without identifiable overlaps after the first alignment, truncates each read into one third of its length (retaining 33bp at the 3’ of each read), and repeats local alignment.
Parsing the chimeric cDNAs. This step categorizes the cDNAs based on their configurations. This takes the completely and partially recovered cDNA sequences, as well as the linker sequence as inputs. It identifies the location of the linker in the cDNA, and generates five categories of cDNAs based the locations of the linker sequence.
Mapping to the genome. Hereafter, all analyses were based on the RNA1-Linker-RNA2 type of read pairs. First, any cDNA containing less than 15bp on either the RNA1 or RNA2 side of linker was discarded, because it is unlikely to uniquely map a 15bp or less sequence to the genome in the mapping step. Then the two Mapping to the genome. RNA fragments on each side of the linker (RNA1 and RNA2) were separately mapped to the mouse genome mm9/NCBI37 using Tophat version 2.1.1. This step, implemented in ‘Stitch-seq_Aligner.py’ outputs the read pairs where both RNA1 and RNA2 were uniquely mapped to the genome. The aligned tab-delimited text files are results from this step.
The annotations were retrieved from Ensembl (release 67, mouse NCBIM37), including the genes of mRNAs, lincRNAs, rRNAs, snRNAs, snoRNAs, miRNAs, misc_RNAs, tRNAs, and transposons. The different genomic copies of the same transposon were considered as different genes in this analysis. The reads mapped to rRNAs were removed from further analysis. The number of uniquely aligned reads (from either RNA1 or RNA2 of the RNA1-Linker-RNA2 type) were counted on every gene. Any gene with a read count less than 5 was filtered out. Next, the association between any two genes was tested with Fisher’s exact test. The null hypothesis was that gene A and gene B independently contributed to the sequencing reads. The alternative hypothesis was that their contributions to read counts were associated. We denoted c_A, c_B as the read counts for gene A and gene B, respectively, and I_{A,B} as the read counts of co-appearance, where the two genes co-appeared on the same read pair. A Fisher’s exact test was carried out on each gene pair, with c_A, c_B, I_{A,B}, and the read counts on other genes besides gene A (gene B) as the test statistics. Both p-values and FDRs (Benjamini-Hochberg procedure) were calculated for every gene pair. This step outputs gene pairs with FDR < 0.05 and fold change (FC) >= 3. The FC was calculated as (I_{A,B} + 0.5) / (I'_{A,B} + 0.5), where I'_{A,B} was the co-appearing read counts in the control sample (ES-indirect). This step was implemented in ‘Select_strongInteraction_RNA.py’ which outputs strong interacting RNA pairs with information of their interaction regions, number of supporting pairs, p-value of significance, FDR and fold changes. The strong interaction clusters tab-delimited text files are from this step.
For further analysis steps to identify RNA interaction sites, calculating binding energies between the interaction sites, network analysis, intra-molecule cutting/ligation detection and RNA secondary structure prediction, please refer to corresponding manuscript.
Genome_build: mm9
Supplementary_files_format_and_content: The *fragment_paired_align.txt.gz file column headers: Chromosome_RNA_1, Start_RNA_1, End_RNA_1, Strand_RNA_1, Fragment_in_read_RNA_1, Reference_RNA_1, Type_RNA_1, Name_RNA_1, Sub_type_RNA_1, Strand_Properness_RNA_1, Read_ID, Chromosome_RNA_2, Start_RNA_2, END_RNA_2, Strand_RNA_2, Fragment_in_read_RNA_2, Reference_RNA_2, Type_RNA_2, Name_RNA_2, Sub_type_RNA_2, Strand_Properness_RNA_2.

source_name: Embryonic fibroblasts

treatment_protocol:
Samples were crosslinked by UV 254-nm wavelength. The first RNA fragmentation was performed by RNase I treatment and RNAs were trimmed into ~300nt. rRNAs were remove by Generead rRNA depletion kit (Qiagen).
Cells were crosslinked, causing the interacting RNAs mediated by a RNA binding protein to be covalently linked to the bound protein. We then fragmented RNAs with RNAase I and and biotinylated the cysteine residues on proteins. The proteins including protein-RNA complexes were immobilized on streptavidin beads. The 5’ end of the RNA was then ligated with a biotin-tagged RNA linker on beads to facilitate subsequent selective purification of chimeric RNAs. Next, proximity-based ligation was carried out on beads under dilute conditions that favor ligations between crosslinked RNA fragments in the same complex.


title: Actb RIA sample

description: Actb antisense oligonucleotides used to pull down RNA from cell samples

value: Actb antisense oligonucleotides


title: Extracted RNA 5-day traced Lgr5+ cells replicate 2


title: Extracted RNA 5-day traced Lgr5+ cells replicate 1


title: ES cell sample 2

description:
Sample name: ES-2
crosslinked RNA

treatment_protocol:
Samples were crosslinked by UV 254-nm wavelength. The first RNA fragmentation was performed by RNase I treatment and RNAs were trimmed into ~1000nt. rRNAs were remove by Generead rRNA depletion kit (Qiagen).
Cells were crosslinked, causing the interacting RNAs mediated by a RNA binding protein to be covalently linked to the bound protein. We then fragmented RNAs with RNAase I and and biotinylated the cysteine residues on proteins. The proteins including protein-RNA complexes were immobilized on streptavidin beads. The 5’ end of the RNA was then ligated with a biotin-tagged RNA linker on beads to facilitate subsequent selective purification of chimeric RNAs. Next, proximity-based ligation was carried out on beads under dilute conditions that favor ligations between crosslinked RNA fragments in the same complex.


title: HEK293-3.3ng-2

value: 3.3ng input of total RNA


title: HEK293-3.3ng-1


title: HEK293-10ng-1

value: 10ng input of total RNA


title: HEK293-33ng-2

value: 33ng input of total RNA


title: HEK293-33ng-1


title: HEK293-100ng-2

value: 100ng input of total RNA


title: HEK293-100ng-1


title: NR_D06

city: Santa Barbara

first: Kenneth

middle: S.

last: Kosik

address: UC Santa Barbara

department: NRI

institute: UCSB

description: single cell sequencing analysis

data_processing:
Reads were mapped to the hg19 human genome using Bowtie2 (Langmead and Salzberg, 2012), duplicate reads removed using SAMtools (Li et al., 2009) and the reads summarized on a gene annotation using RsubReads (Gentleman et al., 2004; Liao, Smyth, & Shi, 2013).
RNA-seq analysis was performed using Fluidigm SINGuLAR Analysis Toolset 2.0 R package.
For DE analysis, BioConductor package edgeR v.3.2.1 (Robinson et al., 2010) was used and genes with CPM less than 1 in less than four cells were discarded. FDR<=0.05 was used.
Genome_build: hg19
Supplementary_files_format_and_content: CPMs of each genes

molecule: polyA RNA

source_name: human embryonic stem cells

growth_protocol: Cerebral organoids were generated as in Lancaster et al. (Lancaster and Knoblich, 2014).

extract_protocol:
Cerebral organoids were dissociated into single cells and captured on C1 Single-Cell Auto Prep Integrated Fluidic Circuit (IFC) (Fluidigm). The RNA extraction and amplification was performed on the chip as described by the manufacturer.
cDNA was processed to prepare libraries using Nextera XT DNA Sample Preparation kit (Illumina) to sequence them on NextSeq500 platform (Illumina).

treatment_protocol: Briefly, human iPS cells were isolated in single-cell solution and plated in a 96-well ultra-low attachment plate in hESC media with ROCK-inhibitor and low bFGF for 5 to 6 days to form embryoid bodies (EBs). EBs were then transferred to 24-well ultra-low attachment plates in neural induction media containing N2 supplement for 4 to 5 days to form neuroepithelium, then embedded in matrigel droplets and cultured in 60 mm dishes in organoid differentiation media containing N2 and B27 supplements. Vitamin A was added after 4 days in organoid differentiation media, and organoids were incubated until indicated time points on an orbital shaker.

tag: cell type

value: cerebral organoid


title: NR_B06

description: single cell sequencing analysis


title: NR_C11

description: single cell sequencing analysis


title: NR_E08

description: single cell sequencing analysis


title: NR_B10

description: single cell sequencing analysis


title: NR_D10

description: single cell sequencing analysis


title: ES cell sample 1

description:
Sample name: ES-1
crosslinked RNA

data_processing:
Library strategy: MARIO
MARIO-tools is a package of command-line tools for analyses of MARIO data. It is written   in Python and R and is version controlled by GitHub. The full documentation is at http://mariotools.ucsd.edu/. The pipeline takes pair-end sequencing reads as input. The oligonucleotide sequences of the RNA linker and the sample barcodes used for multiplexed sequencing should also be provided to the pipeline. Script files mentioned below are all components from the pipeline.
Removing PCR duplicates. The forward read contains a 4nt sample barcode and a 6nt random barcode at the 5' end. A read pair was classified as a PCR duplicate of another read pair and is therefore discarded if the two read pairs had identical sequences and contained identical barcodes (10nt). The tool ‘remove_dup_PE.py’ provides this function, and generates a fastq/fasta file containing the non-duplicated reads, and reports the number of duplicates removed.
Assigning multiplexed sequencing reads into corresponding experimental samples. The tool ‘split_library_pairend.py’ assigns each pair-end read into a sample by matching the sample barcode in each read with those in the list of sample barcodes (a user input text file), generates a fastq/fasta file for the reads assigned to each sample, as well as a fastq/fasta file for the unassigned reads.
Recovering the cDNAs in the sequencing library. This step identifies the overlapping regions of the two ends of every read pair, if any. It also recovers the entire sequences of the cDNAs in the sequencing library, whenever possible. This function is achieved by ‘recoverFragment.py’, which uses local alignment to identify the overlapping regions. When the overlap was small (15bp or less) compared to read length (100bp on each end), local alignment could be insensitive. To overcome this insensitivity, ‘recoverFragment.py’ collects the read pairs without identifiable overlaps after the first alignment, truncates each read into one third of its length (retaining 33bp at the 3’ of each read), and repeats local alignment.
Parsing the chimeric cDNAs. This step categorizes the cDNAs based on their configurations. This takes the completely and partially recovered cDNA sequences, as well as the linker sequence as inputs. It identifies the location of the linker in the cDNA, and generates five categories of cDNAs based the locations of the linker sequence.
Mapping to the genome. Hereafter, all analyses were based on the RNA1-Linker-RNA2 type of read pairs. First, any cDNA containing less than 15bp on either the RNA1 or RNA2 side of linker was discarded, because it is unlikely to uniquely map a 15bp or less sequence to the genome in the mapping step. Then the two Mapping to the genome. RNA fragments on each side of the linker (RNA1 and RNA2) were separately mapped to the mouse genome mm9/NCBI37 using Tophat version 2.1.1. This step, implemented in ‘Stitch-seq_Aligner.py’ outputs the read pairs where both RNA1 and RNA2 were uniquely mapped to the genome. The aligned tab-delimited text files are results from this step.
The annotations were retrieved from Ensembl (release 67, mouse NCBIM37), including the genes of mRNAs, lincRNAs, rRNAs, snRNAs, snoRNAs, miRNAs, misc_RNAs, tRNAs, and transposons. The different genomic copies of the same transposon were considered as different genes in this analysis. The reads mapped to rRNAs were removed from further analysis. The number of uniquely aligned reads (from either RNA1 or RNA2 of the RNA1-Linker-RNA2 type) were counted on every gene. Any gene with a read count less than 5 was filtered out. Next, the association between any two genes was tested with Fisher’s exact test. The null hypothesis was that gene A and gene B independently contributed to the sequencing reads. The alternative hypothesis was that their contributions to read counts were associated. We denoted c_A, c_B as the read counts for gene A and gene B, respectively, and I_{A,B} as the read counts of co-appearance, where the two genes co-appeared on the same read pair. A Fisher’s exact test was carried out on each gene pair, with c_A, c_B, I_{A,B}, and the read counts on other genes besides gene A (gene B) as the test statistics. Both p-values and FDRs (Benjamini-Hochberg procedure) were calculated for every gene pair. This step outputs gene pairs with FDR < 0.05 and fold change (FC) >= 3. The FC was calculated as (I_{A,B} + 0.5) / (I'_{A,B} + 0.5), where I'_{A,B} was the co-appearing read counts in the control sample (ES-indirect). This step was implemented in ‘Select_strongInteraction_RNA.py’ which outputs strong interacting RNA pairs with information of their interaction regions, number of supporting pairs, p-value of significance, FDR and fold changes. The strong interaction clusters tab-delimited text files are from this step.
For further analysis steps to identify RNA interaction sites, calculating binding energies between the interaction sites, network analysis, intra-molecule cutting/ligation detection and RNA secondary structure prediction, please refer to corresponding manuscript.
Genome_build: mm9
Supplementary_files_format_and_content: The *fragment_paired_align.txt.gz file column headers: Chromosome_RNA_1, Start_RNA_1, End_RNA_1, Strand_RNA_1, Fragment_in_read_RNA_1, Reference_RNA_1,  Type_RNA_1, Name_RNA_1, Sub_type_RNA_1, Strand_Properness_RNA_1, Read_ID, Chromosome_RNA_2, Start_RNA_2, END_RNA_2, Strand_RNA_2, Fragment_in_read_RNA_2, Reference_RNA_2, Type_RNA_2, Name_RNA_2, Sub_type_RNA_2, Strand_Properness_RNA_2.

treatment_protocol:
Samples were crosslinked by UV 254-nm wavelength. The first RNA fragmentation was performed by RNase I treatment and RNAs were trimmed into ~1000nt. rRNAs were remove by duplex-specific nuclease.
Cells were crosslinked, causing the interacting RNAs mediated by a RNA binding protein to be covalently linked to the bound protein. We then fragmented RNAs with RNAase I and and biotinylated the cysteine residues on proteins. The proteins including protein-RNA complexes were immobilized on streptavidin beads. The 5’ end of the RNA was then ligated with a biotin-tagged RNA linker on beads to facilitate subsequent selective purification of chimeric RNAs. Next, proximity-based ligation was carried out on beads under dilute conditions that favor ligations between crosslinked RNA fragments in the same complex.


title: NR_C06

description: single cell sequencing analysis


title: NR_C03

description: single cell sequencing analysis


title: NR_D02

description: single cell sequencing analysis


title: NR_E04

description: single cell sequencing analysis


title: NR_E01

description: single cell sequencing analysis


title: NR_B05

description: single cell sequencing analysis


title: NR_C01

description: single cell sequencing analysis


title: NR_C12

description: single cell sequencing analysis


title: NR_D09

description: single cell sequencing analysis


title: NR_B07

description: single cell sequencing analysis


title: NR_A04

description: single cell sequencing analysis


title: HEK293-10ng-2


title: NR_D01

description: single cell sequencing analysis


title: NR_B08

description: single cell sequencing analysis


title: NR_F05

description: single cell sequencing analysis


title: NR_E05

description: single cell sequencing analysis


title: NR_D07

description: single cell sequencing analysis


title: NR_A01

description: single cell sequencing analysis


title: NR_B12

description: single cell sequencing analysis


title: NR_E09

description: single cell sequencing analysis


title: NR_A06

description: single cell sequencing analysis


title: NR_E07

description: single cell sequencing analysis


title: NR_C02

description: single cell sequencing analysis


title: NR_D08

description: single cell sequencing analysis


title: NR_E03

description: single cell sequencing analysis


title: NR_D05

description: single cell sequencing analysis


title: NR_F06

description: single cell sequencing analysis


title: NR_C09

description: single cell sequencing analysis


title: NR_C04

description: single cell sequencing analysis


title: NR_E02

description: single cell sequencing analysis


title: NR_D12

description: single cell sequencing analysis


title: NR_F04

description: single cell sequencing analysis


title: NR_C07

description: single cell sequencing analysis


title: NR_F07

description: single cell sequencing analysis


title: NR_B04

description: single cell sequencing analysis


title: NR_F08

description: single cell sequencing analysis


title: NR_D11

description: single cell sequencing analysis


title: NR_F01

description: single cell sequencing analysis


title: NR_D03

description: single cell sequencing analysis


title: NR_A05

description: single cell sequencing analysis


title: NR_B02

description: single cell sequencing analysis


title: NR_B11

description: single cell sequencing analysis


title: NR_C05

description: single cell sequencing analysis


title: NR_D04

description: single cell sequencing analysis


title: NR_F03

description: single cell sequencing analysis


title: NR_C08

description: single cell sequencing analysis


title: NR_B01

description: single cell sequencing analysis


title: NR_E06

description: single cell sequencing analysis


title: NR_E12

description: single cell sequencing analysis


title: NR_A03

description: single cell sequencing analysis


title: NR_C10

description: single cell sequencing analysis


title: NR_A10

description: single cell sequencing analysis


title: NR_B03

description: single cell sequencing analysis


title: Input_PH_WT_rep2_CHIPSeq

city: Montpellier

first: Bernd

last: Schuettengruber

address: 141, rue de la cardonille

country: France

institute: Institute de Génétique Humaine

library_source: genomic

data_processing:
Mapping - For each ChIP-seq experiment, we mapped short reads to the appropriate reference genome using Bowtie by specifying ‘-a –m 1 -best -strata’ options. Our reference genomes included the heterochromatic fraction of chromosomes and non-assembled contigs, and any read that could be mapped to more than one genomic locus was filtered from further processing.
Peak finding – For PH MACS 1,4 has been used with standard parameters, with genome size set to dm. For H3K27me3,  SICER has been used with 500bp windows, 2kb as gap and FDR at 10 %
Genome_build: dm³
Supplementary_files_format_and_content: bedgraph files were generated with custom scripts from raw aligned files, bed files were generated with MACS1.4 for PH and SICER for H3K27me3

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Embryo 16h-18h

extract_protocol:
Chromatin prepared from Drosophila embryos was immunoprecipitated with specific antibodies and precipitated DNA was isolated (see mat and methods for details)
Libraries were prepared according to Illumina's instructions

tag: genotype

value: WT

value: Embryo

tag: age

tag: antibody


title: PH_WT_rep2_ChIPSeq

value: PH


title: Input_PH_WT_rep1_CHIPSeq


title: K27me3_WT_rep2_ChIPSeq

value: K27me3 Millipore


title: PH_WT_rep1_ChIPSeq


title: NR_si-lnc-1

description: processed data file: lnc-filtered.merged.genes.fpkm.txt

data_processing:
The Illumina Next Seq500  Next Generation Sequencer software was used.
pair-end data were upload to Illumina Basespace(https://basespace.illumina.com/),TopHat Alignment(Version: 1.0.0) of Basespace app was used to map the reads to hg19.
Cufflinks Assembly & DE(Version: 1.1.0) from Basespace app was used to call the DE genes.
Genome_build: hg19
Supplementary_files_format_and_content: txt files with fpkm values for each gene

growth_protocol: SHSY5Y cells were grown in DMEM/F12 media supplemented with 10%FBS and antibiotic.

extract_protocol:
Cells were harvested after 72h and RNA was extracted using MirVana isolation kit
PolyA+ libraries were prepared using Illumina's  TrueSeq mRNA Stranded Kit according to the manufacturer’s instructions.

treatment_protocol: SHSY5Y cells were treated either with 50 nM of miR-143-3p mimic or 100 nM of siRNA specific for LncND. Scrambled siRNA or miRNA sequences were used as a negative control.

value: neural progenitors/neuroblastoma


title: NR_si-lnc-3


title: NR_si-lnc-2


title: NR_E10

description: single cell sequencing analysis


title: NR_si-ctrl-1


title: NR_E11

description: single cell sequencing analysis


title: NR_si-ctrl-2


title: NR_mir-ctrl-2

description: processed data file: mir-filtered.merged.genes.fpkm.txt


title: NR_mir-ctrl-1


title: Extracted RNA 8-week CD24+ control cells, non-traced replicate 1

value: Small intestine


title: NR_mir-143-1


title: Extracted RNA 8-week traced Lgr5+ cells, CD24+ fraction replicate 3

value: Lgr5-CreERT2 C57Bl6/J mice bred to a Rosa26LSL-YFP reporter mice


title: Extracted RNA 8-week traced Lgr5+ cells, CD24+ fraction replicate 2


title: Extracted RNA 8-week traced Lgr5+ cells, CD24+ fraction replicate 1


title: Extracted RNA 8-week traced Lgr5+ cells

source_name: Extracted RNA 8-week traced Lgr5+ cells


title: Extracted RNA 3-week CD24+ control cells, non-traced


title: Extracted RNA 3-week traced Lgr5+ cells, CD24+ fraction


title: APP-La-kd

status: Public on Jun 22 2016

city: Regensburg

first: Gerhard

last: Lehmann

address: Universitaetsstrasse 31

department: Biochemistry 1

country: Germany

institute: University of Regensburg

description: small RNA sequencing data

data_processing:
MiSeq analysis pipeline: MCS 2.4.1, RTA 1.18.54, MSR 2.4.60
3’ adapters were trimmed using cutadapt, all reads <18 nts and >35 nts, as well as untrimmed reads, were discarded.
Reads were collapsed, annotated using custom scripts to the indicated datatypes allowing one mismatch and no insertions/deletions.
All reads which mapped on sequences from two or more datatypes were counted as a separate group. Data were processed similarly for subgroups within the given datatype (e.g. miRNA families, tRNA isotype, etc.).
Within subgroups, annotations were counted to single records. The count of reads mapping on ambiguous annotations were split on affected annotations. Rpms were calculated on valid reads.
Genome_build: pre-tRNA: gtRNAdb, hg19, status 2015-11 (Chan and Lowe, 2009), sequences were extended by 100 nt genomic sequence at the 5’ end and at the 3’ end
Genome_build: mature tRNA: sequences from gtRNAdb were processed by removing introns at the indicated splice positions and CCA was added at the 3’end of the sequences
Genome_build: miRNAs: miRBase21, miRNA sequences
Genome_build: sequences for 5S rRNA, U6 snRNA, 7SL RNA, 7SK RNA, Y RNA and BC200 were obtained from the Repeat Masker USCS hg19.rmsk Table browser, status 2015-11
Genome_build: Sequences for snaR, vtRNA and RMRP were obtained from UCSC refGene (hg19)
Supplementary_files_format_and_content: Tab separated textfiles (number of reads, sequence, annotation). Annotations are comma separated. One Annotation include datatypes (e.g. miRNA), unique identifier/number, subgroup information (e.g. miRNA family), in brackets "{}" sequence length of annotation, in brackets "()" mismatch and position.

growth_protocol: HEK293 cells were cultivated in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 mg/mL streptomycin. Cells were grown under standard conditions at 37°C in 5% CO2 atmosphere.

extract_protocol:
For Ago-APPs, 100 µg of the GST-tagged TNRC6B 599-683 peptide were coupled to Glutathione Sepharose beads for 3 h at 4°C. Cells were washed with cold PBS and lysed in 1 ml of lysis buffer [25mM Tris (pH 7.5),150mM KCl, 0.5% (v/v) NP-40, 2mM EDTA, 1mM NaF, 1mM DTT and 0.5mM AEBSF]. The lysates were cleared by centrifugation at 17,000xg for 30 min, before  addition to the beads. After 3 h of rotation at 4°C, the beads were washed four times with wash buffer [50mM Tris–HCl (pH 7.5), 300mM KCl,1mM MgCl2 and 0.5% (v/v) NP-40] and once with PBS. For RNA extraction 200 µl proteinase K buffer [200mM Tris (pH 7.5), 300mM NaCl, 25mM EDTA, 2% SDS] containing 0.2 mg/ml proteinase K were added. The samples were incubated 30 min at 50°C, the RNA was then isolated with phenol/chloroform/isoamyl alcohol. Input samples were prepared by extracting total RNA directly from an aliquot of the lysates using TRIzol according to the manufacturer’s instructions.
In short, an adenylated adapter was ligated to the 3’ end of the total RNA and APP-enriched RNA by a truncated T4 RNA Ligase 2, followed by the ligation of a 5’ RNA-adapter by T4 RNA Ligase 1 (NEB). After reverse-transcription using a specific primer, the cDNA was amplified by PCR, gel-fractionated and bands or regions corresponding to miRNA-sized inserts were cut out. PCR products from these gel slices were eluted in elution buffer, precipitated and dissolved in water. The quality of the libraries was assessed by qPCR and Bioanalyzer measurements.

treatment_protocol: For knockdown experiments, cells were reverse transfected with RNAiMax according to the manufacturer’s instructions using 40 nM siRNA. Cells were expanded after 2 days and harvested at day 4 post-transfection.

tag: knockdown

value: La siRNA, S:r(AGAUUGGAUGCUUGCUGAA)dTdT, AS:r(UUCAGCAAGCAUCCAAUCU)dTdT

tag: affinity purification

value: GST-tagged TNRC6B 599-683 (Ago-APP)


title: APP-UB-kd

description: small RNA sequencing data

value: control siRNA, S:r(UUGUCUUGCAUUCGACUAAU)dT, AS:r(UUAGUCGAAUGCAAGACAAU)dT


title: K27me3_WT_rep1_ChIPSeq


title: Extracted RNA 8-week CD24+ control cells, non-traced replicate 2


title: Input-UB-kd

description: small RNA sequencing data


title: NR_mir-143-2


title: NR_si-ctrl-3


title: ChIP-seq from intestine (ENCLB411PRG)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR672UQX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on postnatal 0 day mouse intestine
experiment encode accession: ENCSR672UQX
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR898PML
encode release date: 2016-02-18
lab: Bing Ren, UCSD
library encode accession: ENCLB411PRG
size range: 300-500

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Mus musculus strain B6NTac;B6NCrl/Lap intestine tissue mixed sex postnatal (0 days)

value: intestine

value: tissue

tag: description

value: Intestine from 15 postnatal 0 day mice

tag: biosample encode accession

value: 0 day

tag: dev stage

value: postnatal

tag: Sex

value: pooled male and female

tag: health state

value: healthy

tag: lab

value: Len Pennacchio, LBNL

tag: link

value: ENCBS044AAA at ENCODE; https://www.encodeproject.org/ENCBS044AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: DNase-seq from retina (ENCLB141LSN)

description:
https://www.encodeproject.org/experiments/ENCSR488VEQ/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq on 14.5 day mixed embryonic mouse retina
experiment encode accession: ENCSR488VEQ
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB141LSN
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Mus musculus strain B6NCrl retina tissue mixed sex embryo (14.5 days)

value: retina

value: embryonic

value: John Stamatoyannopoulos, UW

value: ENCBS064LRV at ENCODE; https://www.encodeproject.org/ENCBS064LRV/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: DNase-seq from hindbrain (ENCLB771HRX)

description:
https://www.encodeproject.org/experiments/ENCSR469VGZ/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on postnatal mixed mouse hindbrain
experiment encode accession: ENCSR469VGZ
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB771HRX
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Mus musculus strain B6NCrl hindbrain tissue mixed sex postnatal (0 days)

value: hindbrain

value: ENCBS205AAE at ENCODE; https://www.encodeproject.org/ENCBS205AAE/


title: ChIP-seq from embryonic facial prominence (ENCLB210ANV)

description:
https://www.encodeproject.org/experiments/ENCSR990JMN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 15.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR990JMN
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR981PSX
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB210ANV
size range: 300-500

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (15.5 days)

value: embryonic facial prominence

value: Embryonic facial prominence from 78 embryonic 15.5 day mice

value: ENCBS543BPM at ENCODE; https://www.encodeproject.org/ENCBS543BPM/


title: DNase-seq from midbrain (ENCLB055DAX)

description:
https://www.encodeproject.org/experiments/ENCSR292QBA/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on 11.5 day embryonic mouse midbrain
experiment encode accession: ENCSR292QBA
assay title: DNase-seq
assembly: mm10
encode release date: 2015-10-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB055DAX
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Mus musculus strain B6NCrl midbrain tissue mixed sex embryo (11.5 days)

value: midbrain

value: tissue

value: ENCBS677BKM at ENCODE; https://www.encodeproject.org/ENCBS677BKM/


title: ChIP-seq from embryonic facial prominence (ENCLB064UPL)

description:
https://www.encodeproject.org/experiments/ENCSR990JMN/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 15.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR990JMN
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR981PSX
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB064UPL
size range: 300-500

value: Embryonic facial prominence from 62 embryonic 15.5 day mice

value: pooled male and female

value: healthy

value: ENCBS900XQR at ENCODE; https://www.encodeproject.org/ENCBS900XQR/


title: ChIP-seq from limb (ENCLB038ZBQ)

description:
https://www.encodeproject.org/experiments/ENCSR988BRP/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 15.5 day mouse limb
experiment encode accession: ENCSR988BRP
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR070OXL
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB038ZBQ
size range: 300-500

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (15.5 days)

value: limb

value: Limb from 62 embryonic 15.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS696JKV at ENCODE; https://www.encodeproject.org/ENCBS696JKV/


title: microRNA-seq from stomach (ENCLB943WQI)

description:
https://www.encodeproject.org/experiments/ENCSR986VCE/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on embryonic 15.5 day mouse stomach
experiment encode accession: ENCSR986VCE
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB943WQI
size range: <30

source_name: Mus musculus strain B6NCrl stomach tissue mixed sex embryo (15.5 days)

value: stomach

value: Stomach from 62 embryonic 15.5 day mice

value: embryonic

value: ENCBS355TAQ at ENCODE; https://www.encodeproject.org/ENCBS355TAQ/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: microRNA-seq from stomach (ENCLB304XXY)

description:
https://www.encodeproject.org/experiments/ENCSR986VCE/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on embryonic 15.5 day mouse stomach
experiment encode accession: ENCSR986VCE
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB304XXY
size range: <30

value: Stomach from 78 embryonic 15.5 day mice

value: ENCBS915SZN at ENCODE; https://www.encodeproject.org/ENCBS915SZN/


title: DNase-seq from neural tube (ENCLB123ELX)

description:
https://www.encodeproject.org/experiments/ENCSR312QVY/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on 11.5 day mixed embryonic mouse neural tube
experiment encode accession: ENCSR312QVY
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB123ELX
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Mus musculus strain B6NCrl neural tube tissue mixed sex embryo (11.5 days)

value: neural tube

value: tissue

value: John Stamatoyannopoulos, UW

value: ENCBS427RVU at ENCODE; https://www.encodeproject.org/ENCBS427RVU/


title: ChIP-seq from limb (ENCLB333JMU)

description:
https://www.encodeproject.org/experiments/ENCSR988BRP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 15.5 day mouse limb
experiment encode accession: ENCSR988BRP
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR070OXL
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB333JMU
size range: 300-500

value: Limb from 78 embryonic 15.5 day mice

value: pooled male and female

value: healthy

value: ENCBS735QNY at ENCODE; https://www.encodeproject.org/ENCBS735QNY/


title: ChIP-seq from liver (ENCLB747IGJ)

description:
https://www.encodeproject.org/experiments/ENCSR985UTP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 13.5 day mouse liver
experiment encode accession: ENCSR985UTP
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR220PXJ
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB747IGJ
size range: 300-500

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (13.5 days)

value: liver

value: Liver from embryonic 13.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS146FGW at ENCODE; https://www.encodeproject.org/ENCBS146FGW/


title: ChIP-seq from liver (ENCLB670JVI)

description:
https://www.encodeproject.org/experiments/ENCSR985UTP/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 13.5 day mouse liver
experiment encode accession: ENCSR985UTP
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR220PXJ
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB670JVI
size range: 300-500

value: embryonic

value: ENCBS373XWZ at ENCODE; https://www.encodeproject.org/ENCBS373XWZ/


title: Input-La-kd

description: small RNA sequencing data

value: La siRNA, S:r(AGAUUGGAUGCUUGCUGAA)dTdT, AS:r(UUCAGCAAGCAUCCAAUCU)dTdT


title: DNase-seq from embryo (ENCLB924SWL)

description:
https://www.encodeproject.org/experiments/ENCSR172RHR/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on 10.5 day mouse embryo.
experiment encode accession: ENCSR172RHR
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB924SWL
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Mus musculus strain B6NCrl embryo tissue mixed sex embryo (10.5 days)

value: embryo

value: ENCBS946QEY at ENCODE; https://www.encodeproject.org/ENCBS946QEY/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: microRNA-seq from stomach (ENCLB423VHK)

description:
https://www.encodeproject.org/experiments/ENCSR974QTI/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq  on embryonic 14.5 day mouse stomach
experiment encode accession: ENCSR974QTI
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-01-06
lab: Ali Mortazavi, UCI
library encode accession: ENCLB423VHK
size range: <30

source_name: Mus musculus strain B6NCrl stomach tissue mixed sex embryo (14.5 days)

value: stomach

value: tissue

value: single stomach from pup 1 pregnant 2 collected 7/17/2014

value: Barbara Wold, Caltech

value: ENCBS987ARB at ENCODE; https://www.encodeproject.org/ENCBS987ARB/


title: microRNA-seq from stomach (ENCLB057NCW)

description:
https://www.encodeproject.org/experiments/ENCSR974QTI/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq  on embryonic 14.5 day mouse stomach
experiment encode accession: ENCSR974QTI
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-01-06
lab: Ali Mortazavi, UCI
library encode accession: ENCLB057NCW
size range: <30

value: single stomach from pup 1 pregnant 2 collected 7/15/2014

value: pooled male and female

value: ENCBS715ONU at ENCODE; https://www.encodeproject.org/ENCBS715ONU/


title: ChIP-seq from neural tube (ENCLB325RAO)

description:
https://www.encodeproject.org/experiments/ENCSR973AYQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me2 ChIP-seq on embryonic 13.5 day mouse neural tube
experiment encode accession: ENCSR973AYQ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR295GGT
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB325RAO
size range: 300-500

source_name: Mus musculus strain B6NCrl neural tube tissue mixed sex embryo (13.5 days)

value: neural tube

value: Neural tube from embryonic 13.5 day mice

value: healthy

value: ENCBS956BQY at ENCODE; https://www.encodeproject.org/ENCBS956BQY/


title: ChIP-seq from embryonic facial prominence (ENCLB099MBG)

description:
https://www.encodeproject.org/experiments/ENCSR972WEN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 14.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR972WEN
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR329ZEN
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB099MBG
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap embryonic facial prominence tissue mixed sex embryo (14.5 days)

value: embryonic facial prominence

value: Craniofacial prominence from 24 embryonic 14.5 day mice

value: embryonic

value: Len Pennacchio, LBNL

value: ENCBS012AAA at ENCODE; https://www.encodeproject.org/ENCBS012AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: ChIP-seq from embryonic facial prominence (ENCLB434AFN)

description:
https://www.encodeproject.org/experiments/ENCSR972WEN/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 14.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR972WEN
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR329ZEN
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB434AFN
size range: 300-500

value: tissue

value: Craniofacial prominence from 34 embryonic 14.5 day mice

value: ENCBS024AAA at ENCODE; https://www.encodeproject.org/ENCBS024AAA/


title: ChIP-seq from hindbrain (ENCLB084XTC)

description:
https://www.encodeproject.org/experiments/ENCSR972MUO/
***************
biological replicate number: 2
technical replicate number: 2,1
description: H3K36me3 ChIP-seq on embryonic 13.5 day mouse hindbrain
experiment encode accession: ENCSR972MUO
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR545RUT
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB084XTC
size range: 300-500
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Mus musculus strain B6NCrl hindbrain tissue mixed sex embryo (13.5 days)

value: hindbrain

value: Hindbrain from embryonic 13.5 day mice

value: ENCBS296PIR at ENCODE; https://www.encodeproject.org/ENCBS296PIR/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from liver (ENCLB009SNM)

description:
https://www.encodeproject.org/experiments/ENCSR973UGS/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K27me3 ChIP-seq on postnatal 0 day mouse liver
experiment encode accession: ENCSR973UGS
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR617RDY
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB009SNM
size range: 300-500
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap liver tissue mixed sex postnatal (0 days)

value: liver

value: Liver from 15 postnatal 0 day mice

value: 0 day

value: postnatal

value: pooled male and female

value: ENCBS043AAA at ENCODE; https://www.encodeproject.org/ENCBS043AAA/


title: ChIP-seq from neural tube (ENCLB984BNZ)

description:
https://www.encodeproject.org/experiments/ENCSR973AYQ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me2 ChIP-seq on embryonic 13.5 day mouse neural tube
experiment encode accession: ENCSR973AYQ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR295GGT
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB984BNZ
size range: 300-500

value: neural tube

value: Neural tube from embryonic 13.5 day mice

value: embryonic

value: healthy

value: ENCBS549OYR at ENCODE; https://www.encodeproject.org/ENCBS549OYR/


title: ChIP-seq from stomach (ENCLB312NVO)

description:
https://www.encodeproject.org/experiments/ENCSR975QEX/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 15.5 day mouse stomach
experiment encode accession: ENCSR975QEX
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR240XQT
encode release date: 2016-03-16
lab: Bing Ren, UCSD
library encode accession: ENCLB312NVO
size range: 300-500

value: stomach

value: tissue

value: Stomach from 62 embryonic 15.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS355TAQ at ENCODE; https://www.encodeproject.org/ENCBS355TAQ/


title: ChIP-seq from stomach (ENCLB264ZIF)

description:
https://www.encodeproject.org/experiments/ENCSR969CPK/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on postnatal 0 day mouse stomach
experiment encode accession: ENCSR969CPK
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR050VUZ
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB264ZIF
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap stomach tissue mixed sex postnatal (0 days)

value: Stomach from 15 postnatal 0 day mice

value: ENCBS045AAA at ENCODE; https://www.encodeproject.org/ENCBS045AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: ChIP-seq from stomach (ENCLB534PWT)

description:
https://www.encodeproject.org/experiments/ENCSR969CPK/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 ChIP-seq on postnatal 0 day mouse stomach
experiment encode accession: ENCSR969CPK
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR050VUZ
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB534PWT
size range: 300-500

value: Stomach from pooled postnatal 0 day mice

value: 0 day

value: ENCBS561AAA at ENCODE; https://www.encodeproject.org/ENCBS561AAA/


title: ChIP-seq from lung (ENCLB571PQA)

description:
https://www.encodeproject.org/experiments/ENCSR969NXN/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 ChIP-seq on embryonic 16.5 day mouse lung
experiment encode accession: ENCSR969NXN
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR559FAB
encode release date: 2014-12-17
lab: Bing Ren, UCSD
library encode accession: ENCLB571PQA
size range: 300-500

source_name: Mus musculus strain B6NCrl lung tissue mixed sex embryo (16.5 days)

value: lung

value: Lung from 41 embyonic 16.5 day mice

value: pooled male and female

value: ENCBS833ZFI at ENCODE; https://www.encodeproject.org/ENCBS833ZFI/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from liver (ENCLB823UME)

description:
https://www.encodeproject.org/experiments/ENCSR973UGS/
***************
biological replicate number: 2
technical replicate number: 1,2
description: H3K27me3 ChIP-seq on postnatal 0 day mouse liver
experiment encode accession: ENCSR973UGS
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR617RDY
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB823UME
size range: 300-500
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: liver

value: Liver from pooled postnatal 0 day mice

value: postnatal

value: healthy

value: ENCBS559AAA at ENCODE; https://www.encodeproject.org/ENCBS559AAA/


title: ChIP-seq from liver (ENCLB198KUE)

description:
https://www.encodeproject.org/experiments/ENCSR966RAG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9ac ChIP-seq on postnatal 0 day mouse liver
experiment encode accession: ENCSR966RAG
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR617RDY
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB198KUE
size range: 300-500

value: tissue

value: Liver from 15 postnatal 0 day mice

value: Len Pennacchio, LBNL

value: ENCBS043AAA at ENCODE; https://www.encodeproject.org/ENCBS043AAA/


title: ChIP-seq from stomach (ENCLB716UZY)

description:
https://www.encodeproject.org/experiments/ENCSR975QEX/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K9me3 ChIP-seq on embryonic 15.5 day mouse stomach
experiment encode accession: ENCSR975QEX
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR240XQT
encode release date: 2016-03-16
lab: Bing Ren, UCSD
library encode accession: ENCLB716UZY
size range: 300-500

value: stomach

value: Stomach from 78 embryonic 15.5 day mice

value: embryonic

value: ENCBS915SZN at ENCODE; https://www.encodeproject.org/ENCBS915SZN/


title: ChIP-seq from embryonic facial prominence (ENCLB135TRE)

description:
https://www.encodeproject.org/experiments/ENCSR964RRJ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 14.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR964RRJ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR329ZEN
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB135TRE
size range: 300-500

value: embryonic facial prominence

value: Craniofacial prominence from 24 embryonic 14.5 day mice

value: ENCBS012AAA at ENCODE; https://www.encodeproject.org/ENCBS012AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: ChIP-seq from kidney (ENCLB054ZAL)

description:
https://www.encodeproject.org/experiments/ENCSR961PNM/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 15.5 day mouse kidney
experiment encode accession: ENCSR961PNM
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR780JSE
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB054ZAL
size range: 300-500

source_name: Mus musculus strain B6NCrl kidney tissue mixed sex embryo (15.5 days)

value: kidney

value: Kidney from 62 embryonic 15.5 day mice

value: pooled male and female

value: ENCBS924ZKF at ENCODE; https://www.encodeproject.org/ENCBS924ZKF/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from limb (ENCLB312QPH)

description:
https://www.encodeproject.org/experiments/ENCSR961MEP/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 11.5 day mouse limb
experiment encode accession: ENCSR961MEP
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR949ZLW
encode release date: 2016-03-17
lab: Bing Ren, UCSD
library encode accession: ENCLB312QPH
size range: 300-500

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (11.5 days)

value: limb

value: tissue

value: Limb from 88 embyronic 11.5 day mice

value: healthy

value: ENCBS681XPR at ENCODE; https://www.encodeproject.org/ENCBS681XPR/


title: ChIP-seq from limb (ENCLB002CNT)

description:
https://www.encodeproject.org/experiments/ENCSR961MEP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 11.5 day mouse limb
experiment encode accession: ENCSR961MEP
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR949ZLW
encode release date: 2016-03-17
lab: Bing Ren, UCSD
library encode accession: ENCLB002CNT
size range: 300-500

value: Limb from 109 embyronic 11.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS066IEL at ENCODE; https://www.encodeproject.org/ENCBS066IEL/


title: ChIP-seq from kidney (ENCLB265OSV)

description:
https://www.encodeproject.org/experiments/ENCSR961PNM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 15.5 day mouse kidney
experiment encode accession: ENCSR961PNM
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR780JSE
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB265OSV
size range: 300-500

value: Kidney from 78 embryonic 15.5 day mice

value: embryonic

value: ENCBS899UOK at ENCODE; https://www.encodeproject.org/ENCBS899UOK/


title: ChIP-seq from lung (ENCLB760ITU)

description:
https://www.encodeproject.org/experiments/ENCSR969NXN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-seq on embryonic 16.5 day mouse lung
experiment encode accession: ENCSR969NXN
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR559FAB
encode release date: 2014-12-17
lab: Bing Ren, UCSD
library encode accession: ENCLB760ITU
size range: 300-500

value: lung

value: Lung pooled from embyonic 16.5 day mice

value: ENCBS377RBN at ENCODE; https://www.encodeproject.org/ENCBS377RBN/


title: ChIP-seq from hindbrain (ENCLB411MXP)

description:
https://www.encodeproject.org/experiments/ENCSR953LFI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on embryonic 14.5 day mouse hindbrain
experiment encode accession: ENCSR953LFI
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR896PWV
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB411MXP
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap hindbrain tissue mixed sex embryo (14.5 days)

value: hindbrain

value: Hindbrain from 24 embryonic 14.5 day mice

value: pooled male and female

value: ENCBS004AAA at ENCODE; https://www.encodeproject.org/ENCBS004AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: ChIP-seq from heart (ENCLB027GUW)

description:
https://www.encodeproject.org/experiments/ENCSR956ZCG/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 15.5 day mouse heart
experiment encode accession: ENCSR956ZCG
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR424WHM
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB027GUW
size range: 300-500

source_name: Mus musculus strain B6NCrl heart tissue mixed sex embryo (15.5 days)

value: heart

value: tissue

value: Heart from 62 embryonic 15.5 day mice

value: ENCBS909LOF at ENCODE; https://www.encodeproject.org/ENCBS909LOF/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from intestine (ENCLB042FEH)

description:
https://www.encodeproject.org/experiments/ENCSR953KTY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-seq on embryonic 14.5 day mouse intestine
experiment encode accession: ENCSR953KTY
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR645QSY
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB042FEH
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap intestine tissue mixed sex embryo (14.5 days)

value: intestine

value: Intestine from 24 embryonic 14.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS008AAA at ENCODE; https://www.encodeproject.org/ENCBS008AAA/


title: ChIP-seq from hindbrain (ENCLB853LAE)

description:
https://www.encodeproject.org/experiments/ENCSR953LFI/
***************
biological replicate number: 2
technical replicate number: 1,2
description: H3K27me3 ChIP-seq on embryonic 14.5 day mouse hindbrain
experiment encode accession: ENCSR953LFI
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR896PWV
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB853LAE
size range: 300-500

value: Hindbrain from 34 embryonic 14.5 day mice

value: embryonic

value: ENCBS016AAA at ENCODE; https://www.encodeproject.org/ENCBS016AAA/


title: ChIP-seq from kidney (ENCLB075WID)

description:
https://www.encodeproject.org/experiments/ENCSR953HNY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 16.5 day mouse kidney
experiment encode accession: ENCSR953HNY
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR642DUV
encode release date: 2014-12-17
lab: Bing Ren, UCSD
library encode accession: ENCLB075WID
size range: 300-500

source_name: Mus musculus strain B6NCrl kidney tissue mixed sex embryo (16.5 days)

value: kidney

value: Kidney pooled from embyonic 16.5 day mice

value: ENCBS519MUD at ENCODE; https://www.encodeproject.org/ENCBS519MUD/


title: ChIP-seq from heart (ENCLB464GJW)

description:
https://www.encodeproject.org/experiments/ENCSR956ZCG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 15.5 day mouse heart
experiment encode accession: ENCSR956ZCG
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR424WHM
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB464GJW
size range: 300-500

value: Heart from 78 embryonic 15.5 day mice

value: pooled male and female

value: ENCBS595EMK at ENCODE; https://www.encodeproject.org/ENCBS595EMK/


title: ChIP-seq from midbrain (ENCLB491TAD)

description:
https://www.encodeproject.org/experiments/ENCSR951UWY/
***************
biological replicate number: 2
technical replicate number: 1,2
description: H3K36me3 ChIP-seq on postnatal 0 day mouse midbrain
experiment encode accession: ENCSR951UWY
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR889XXJ
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB491TAD
size range: 300-500
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap midbrain tissue mixed sex postnatal (0 days)

value: midbrain

value: tissue

value: Midbrain from pooled postnatal 0 day mice

value: 0 day

value: postnatal

value: ENCBS555AAA at ENCODE; https://www.encodeproject.org/ENCBS555AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: ChIP-seq from embryonic facial prominence (ENCLB239MTI)

description:
https://www.encodeproject.org/experiments/ENCSR964RRJ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 14.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR964RRJ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR329ZEN
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB239MTI
size range: 300-500

value: embryonic facial prominence

value: Craniofacial prominence from 34 embryonic 14.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS024AAA at ENCODE; https://www.encodeproject.org/ENCBS024AAA/


title: ChIP-seq from liver (ENCLB328MMB)

description:
https://www.encodeproject.org/experiments/ENCSR966RAG/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9ac ChIP-seq on postnatal 0 day mouse liver
experiment encode accession: ENCSR966RAG
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR617RDY
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB328MMB
size range: 300-500

value: liver

value: Liver from pooled postnatal 0 day mice

value: ENCBS559AAA at ENCODE; https://www.encodeproject.org/ENCBS559AAA/


title: ChIP-seq from kidney (ENCLB850SHR)

description:
https://www.encodeproject.org/experiments/ENCSR953HNY/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 16.5 day mouse kidney
experiment encode accession: ENCSR953HNY
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR642DUV
encode release date: 2014-12-17
lab: Bing Ren, UCSD
library encode accession: ENCLB850SHR
size range: 300-500

value: kidney

value: Kidney from 41 embyonic 16.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS529OHA at ENCODE; https://www.encodeproject.org/ENCBS529OHA/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from liver (ENCLB042OWL)

description:
https://www.encodeproject.org/experiments/ENCSR948RYN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 11.5 day mouse liver
experiment encode accession: ENCSR948RYN
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR573MJR
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB042OWL
size range: 300-500

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (11.5 days)

value: tissue

value: Liver from 109 embyronic 11.5 day mice

value: ENCBS746POP at ENCODE; https://www.encodeproject.org/ENCBS746POP/


title: microRNA-seq from adrenal gland (ENCLB513CUQ)

description:
https://www.encodeproject.org/experiments/ENCSR949VVK/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq  on postnatal 0 day mouse adrenals
experiment encode accession: ENCSR949VVK
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB513CUQ
size range: <30

source_name: Mus musculus strain B6NCrl adrenal gland tissue postnatal (0 days)

value: adrenal gland

value: 2 adrenals from pup1 pregnant 1

value: 0 day

value: postnatal

value: not collected

value: Barbara Wold, Caltech

value: ENCBS547NQN at ENCODE; https://www.encodeproject.org/ENCBS547NQN/


title: ChIP-seq from liver (ENCLB529MSA)

description:
https://www.encodeproject.org/experiments/ENCSR948RYN/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 11.5 day mouse liver
experiment encode accession: ENCSR948RYN
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR573MJR
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB529MSA
size range: 300-500

value: liver

value: Liver from pooled embryonic 11.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS522YOW at ENCODE; https://www.encodeproject.org/ENCBS522YOW/


title: microRNA-seq from adrenal gland (ENCLB881GRC)

description:
https://www.encodeproject.org/experiments/ENCSR949VVK/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq  on postnatal 0 day mouse adrenals
experiment encode accession: ENCSR949VVK
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB881GRC
size range: <30

value: 2 adrenals from pup2 pregnant 1

value: ENCBS386FVC at ENCODE; https://www.encodeproject.org/ENCBS386FVC/


title: ChIP-seq from hindbrain (ENCLB514GTP)

description:
https://www.encodeproject.org/experiments/ENCSR947QOH/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me2 ChIP-seq on embryonic 13.5 day mouse hindbrain
experiment encode accession: ENCSR947QOH
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR545RUT
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB514GTP
size range: 300-500

value: hindbrain

value: tissue

value: Hindbrain from embryonic 13.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS296PIR at ENCODE; https://www.encodeproject.org/ENCBS296PIR/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from intestine (ENCLB853PUO)

description:
https://www.encodeproject.org/experiments/ENCSR953KTY/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 ChIP-seq on embryonic 14.5 day mouse intestine
experiment encode accession: ENCSR953KTY
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR645QSY
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB853PUO
size range: 300-500

value: intestine

value: Intestine from 34 embryonic 14.5 day mice

value: ENCBS020AAA at ENCODE; https://www.encodeproject.org/ENCBS020AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: ChIP-seq from hindbrain (ENCLB215JHY)

description:
https://www.encodeproject.org/experiments/ENCSR947QOH/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me2 ChIP-seq on embryonic 13.5 day mouse hindbrain
experiment encode accession: ENCSR947QOH
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR545RUT
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB215JHY
size range: 300-500

value: ENCBS052EWC at ENCODE; https://www.encodeproject.org/ENCBS052EWC/


title: ChIP-seq from stomach (ENCLB803VGN)

description:
https://www.encodeproject.org/experiments/ENCSR940CMI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on postnatal 0 day mouse stomach
experiment encode accession: ENCSR940CMI
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR050VUZ
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB803VGN
size range: 300-500

value: stomach

value: Stomach from 15 postnatal 0 day mice

value: 0 day

value: postnatal

value: healthy

value: ENCBS045AAA at ENCODE; https://www.encodeproject.org/ENCBS045AAA/


title: microRNA-seq from skeletal muscle tissue (ENCLB843ACF)

description:
https://www.encodeproject.org/experiments/ENCSR940JVJ/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq  on postnatal 0 day mouse skeletal muscle
experiment encode accession: ENCSR940JVJ
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-01-06
lab: Ali Mortazavi, UCI
library encode accession: ENCLB843ACF
size range: <30

source_name: Mus musculus strain B6NCrl skeletal muscle tissue postnatal (0 days)

value: skeletal muscle tissue

value: tissue

value: single organ portion from 1 pup

value: not collected

value: Barbara Wold, Caltech

value: ENCBS015TUQ at ENCODE; https://www.encodeproject.org/ENCBS015TUQ/


title: microRNA-seq from skeletal muscle tissue (ENCLB022KUS)

description:
https://www.encodeproject.org/experiments/ENCSR940JVJ/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq  on postnatal 0 day mouse skeletal muscle
experiment encode accession: ENCSR940JVJ
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-01-06
lab: Ali Mortazavi, UCI
library encode accession: ENCLB022KUS
size range: <30

value: ENCBS482FSQ at ENCODE; https://www.encodeproject.org/ENCBS482FSQ/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from stomach (ENCLB599WRG)

description:
https://www.encodeproject.org/experiments/ENCSR929SEW/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 15.5 day mouse stomach
experiment encode accession: ENCSR929SEW
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR240XQT
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB599WRG
size range: 300-500

source_name: Mus musculus strain B6NCrl stomach tissue mixed sex embryo (15.5 days)

value: Stomach from 62 embryonic 15.5 day mice

value: embryonic

value: pooled male and female

value: Len Pennacchio, LBNL

value: ENCBS355TAQ at ENCODE; https://www.encodeproject.org/ENCBS355TAQ/


title: ChIP-seq from midbrain (ENCLB533NJJ)

description:
https://www.encodeproject.org/experiments/ENCSR929GXP/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K27me3 ChIP-seq on embryonic 14.5 day mouse midbrain
experiment encode accession: ENCSR929GXP
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR413VHH
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB533NJJ
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap midbrain tissue mixed sex embryo (14.5 days)

value: midbrain

value: Midbrain from 24 embryonic 14.5 day mice

value: ENCBS003AAA at ENCODE; https://www.encodeproject.org/ENCBS003AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: ChIP-seq from stomach (ENCLB492YZI)

description:
https://www.encodeproject.org/experiments/ENCSR940CMI/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on postnatal 0 day mouse stomach
experiment encode accession: ENCSR940CMI
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR050VUZ
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB492YZI
size range: 300-500

value: stomach

value: Stomach from pooled postnatal 0 day mice

value: 0 day

value: postnatal

value: healthy

value: ENCBS561AAA at ENCODE; https://www.encodeproject.org/ENCBS561AAA/


title: ChIP-seq from midbrain (ENCLB683UEQ)

description:
https://www.encodeproject.org/experiments/ENCSR929GXP/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 ChIP-seq on embryonic 14.5 day mouse midbrain
experiment encode accession: ENCSR929GXP
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR413VHH
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB683UEQ
size range: 300-500

value: tissue

value: Midbrain from 34 embryonic 14.5 day mice

value: ENCBS015AAA at ENCODE; https://www.encodeproject.org/ENCBS015AAA/


title: ChIP-seq from neural tube (ENCLB821CYC)

description:
https://www.encodeproject.org/experiments/ENCSR928IYZ/
***************
biological replicate number: 2
technical replicate number: 2,1
description: H3K27me3 ChIP-seq on embryonic 15.5 day mouse neural tube
experiment encode accession: ENCSR928IYZ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR351BDM
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB821CYC
size range: 300-500

source_name: Mus musculus strain B6NCrl neural tube tissue mixed sex embryo (15.5 days)

value: neural tube

value: Neural tube from 62 embryonic 15.5 day mice

value: embryonic

value: ENCBS206NRE at ENCODE; https://www.encodeproject.org/ENCBS206NRE/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from neural tube (ENCLB553QWL)

description:
https://www.encodeproject.org/experiments/ENCSR928IYZ/
***************
biological replicate number: 1
technical replicate number: 2,1
description: H3K27me3 ChIP-seq on embryonic 15.5 day mouse neural tube
experiment encode accession: ENCSR928IYZ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR351BDM
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB553QWL
size range: 300-500

value: Neural tube from 78 embryonic 15.5 day mice

value: pooled male and female

value: Len Pennacchio, LBNL

value: ENCBS944KEZ at ENCODE; https://www.encodeproject.org/ENCBS944KEZ/


title: ChIP-seq from neural tube (ENCLB689MDY)

description:
https://www.encodeproject.org/experiments/ENCSR918ZSJ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 13.5 day mouse neural tube
experiment encode accession: ENCSR918ZSJ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR295GGT
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB689MDY
size range: 300-500

source_name: Mus musculus strain B6NCrl neural tube tissue mixed sex embryo (13.5 days)

value: Neural tube from embryonic 13.5 day mice

value: ENCBS549OYR at ENCODE; https://www.encodeproject.org/ENCBS549OYR/


title: ChIP-seq from neural tube (ENCLB833HWI)

description:
https://www.encodeproject.org/experiments/ENCSR918ZSJ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 13.5 day mouse neural tube
experiment encode accession: ENCSR918ZSJ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR295GGT
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB833HWI
size range: 300-500

value: ENCBS956BQY at ENCODE; https://www.encodeproject.org/ENCBS956BQY/


title: ChIP-seq from lung (ENCLB529SEW)

description:
https://www.encodeproject.org/experiments/ENCSR924FJQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me2 ChIP-seq on embryonic 14.5 day mouse lung
experiment encode accession: ENCSR924FJQ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR280SYC
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB529SEW
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap lung tissue mixed sex embryo (14.5 days)

value: lung

value: Lung from 24 embryonic 14.5 day mice

value: healthy

value: ENCBS006AAA at ENCODE; https://www.encodeproject.org/ENCBS006AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: ChIP-seq from intestine (ENCLB061PSY)

description:
https://www.encodeproject.org/experiments/ENCSR919DDC/
***************
biological replicate number: 2
technical replicate number: 1,2
description: H3K36me3 ChIP-seq on embryonic 15.5 day mouse intestine
experiment encode accession: ENCSR919DDC
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR872UEE
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB061PSY
size range: 300-500
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Mus musculus strain B6NCrl intestine tissue mixed sex embryo (15.5 days)

value: intestine

value: tissue

value: Intestine from 62 embryonic 15.5 day mice

value: ENCBS836WEU at ENCODE; https://www.encodeproject.org/ENCBS836WEU/


title: ChIP-seq from hindbrain (ENCLB910EVO)

description:
https://www.encodeproject.org/experiments/ENCSR921ILW/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 15.5 day mouse hindbrain
experiment encode accession: ENCSR921ILW
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR685UUM
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB910EVO
size range: 300-500

source_name: Mus musculus strain B6NCrl hindbrain tissue mixed sex embryo (15.5 days)

value: hindbrain

value: Hindbrain from 62 embryonic 15.5 day mice

value: embryonic

value: ENCBS948UKU at ENCODE; https://www.encodeproject.org/ENCBS948UKU/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: microRNA-seq from neural tube (ENCLB275BAH)

description:
https://www.encodeproject.org/experiments/ENCSR917VKY/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on embryonic 13.5 day mouse neural tube
experiment encode accession: ENCSR917VKY
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-02-23
lab: Ali Mortazavi, UCI
library encode accession: ENCLB275BAH
size range: <30

value: neural tube

value: Neural tube from embryonic 13.5 day mice

value: pooled male and female

value: Len Pennacchio, LBNL


title: ChIP-seq from stomach (ENCLB741BSO)

description:
https://www.encodeproject.org/experiments/ENCSR916CBN/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on postnatal 0 day mouse stomach
experiment encode accession: ENCSR916CBN
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR050VUZ
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB741BSO
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap stomach tissue mixed sex postnatal (0 days)

value: stomach

value: Stomach from pooled postnatal 0 day mice

value: 0 day

value: postnatal

value: ENCBS561AAA at ENCODE; https://www.encodeproject.org/ENCBS561AAA/


title: ChIP-seq from hindbrain (ENCLB786NTG)

description:
https://www.encodeproject.org/experiments/ENCSR921ILW/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 15.5 day mouse hindbrain
experiment encode accession: ENCSR921ILW
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR685UUM
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB786NTG
size range: 300-500

value: tissue

value: Hindbrain from 78 embryonic 15.5 day mice

value: healthy

value: ENCBS958AHU at ENCODE; https://www.encodeproject.org/ENCBS958AHU/


title: ChIP-seq from stomach (ENCLB451XGD)

description:
https://www.encodeproject.org/experiments/ENCSR929SEW/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 15.5 day mouse stomach
experiment encode accession: ENCSR929SEW
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR240XQT
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB451XGD
size range: 300-500

value: Stomach from 78 embryonic 15.5 day mice

value: ENCBS915SZN at ENCODE; https://www.encodeproject.org/ENCBS915SZN/


title: ChIP-seq from stomach (ENCLB718ODS)

description:
https://www.encodeproject.org/experiments/ENCSR916CBN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on postnatal 0 day mouse stomach
experiment encode accession: ENCSR916CBN
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR050VUZ
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB718ODS
size range: 300-500

value: Stomach from 15 postnatal 0 day mice

value: ENCBS045AAA at ENCODE; https://www.encodeproject.org/ENCBS045AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: ChIP-seq from forebrain (ENCLB856CNI)

description:
https://www.encodeproject.org/experiments/ENCSR906UJW/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me2 ChIP-seq on postnatal 0 day mouse forebrain
experiment encode accession: ENCSR906UJW
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR398NCK
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB856CNI
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap forebrain tissue mixed sex postnatal (0 days)

value: forebrain

value: Forebrain from 15 postnatal 0 day mice

value: ENCBS038AAA at ENCODE; https://www.encodeproject.org/ENCBS038AAA/


title: microRNA-seq from neural tube (ENCLB667YOC)

description:
https://www.encodeproject.org/experiments/ENCSR917VKY/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on embryonic 13.5 day mouse neural tube
experiment encode accession: ENCSR917VKY
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-02-23
lab: Ali Mortazavi, UCI
library encode accession: ENCLB667YOC
size range: <30

value: neural tube

value: Neural tube from embryonic 13.5 day mice

value: embryonic

value: pooled male and female

value: Len Pennacchio, LBNL

value: ENCBS549OYR at ENCODE; https://www.encodeproject.org/ENCBS549OYR/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from forebrain (ENCLB522RNE)

description:
https://www.encodeproject.org/experiments/ENCSR906UJW/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me2 ChIP-seq on postnatal 0 day mouse forebrain
experiment encode accession: ENCSR906UJW
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR398NCK
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB522RNE
size range: 300-500

value: tissue

value: Forebrain of pooled postnatal 0 day mice

value: 0 day

value: postnatal

value: healthy

value: ENCBS554AAA at ENCODE; https://www.encodeproject.org/ENCBS554AAA/


title: ChIP-seq from liver (ENCLB634OGI)

description:
https://www.encodeproject.org/experiments/ENCSR898WIS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 14.5 day mouse liver
experiment encode accession: ENCSR898WIS
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR742WLX
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB634OGI
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap liver tissue mixed sex embryo (14.5 days)

value: liver

value: Liver from embryonic 14.5 day mice

value: ENCBS194VTP at ENCODE; https://www.encodeproject.org/ENCBS194VTP/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: ChIP-seq from liver (ENCLB119DHJ)

description:
https://www.encodeproject.org/experiments/ENCSR898WIS/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 14.5 day mouse liver
experiment encode accession: ENCSR898WIS
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR742WLX
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB119DHJ
size range: 300-500

value: ENCBS096GAJ at ENCODE; https://www.encodeproject.org/ENCBS096GAJ/


title: ChIP-seq from intestine (ENCLB976KLB)

description:
https://www.encodeproject.org/experiments/ENCSR898PML/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on postnatal 0 day mouse intestine
experiment encode accession: ENCSR898PML
assay title: ChIP-seq
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB976KLB
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap intestine tissue mixed sex postnatal (0 days)

value: Control

value: intestine

value: Intestine from 15 postnatal 0 day mice

value: ENCBS044AAA at ENCODE; https://www.encodeproject.org/ENCBS044AAA/


title: ChIP-seq from limb (ENCLB925TUQ)

description:
https://www.encodeproject.org/experiments/ENCSR905FFU/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 13.5 day mouse limb
experiment encode accession: ENCSR905FFU
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR465WTL
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB925TUQ
size range: 300-500

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (13.5 days)

value: limb

value: Limb from embryonic 13.5 day mice

value: embryonic

value: pooled male and female

value: Len Pennacchio, LBNL

value: ENCBS896ZED at ENCODE; https://www.encodeproject.org/ENCBS896ZED/


title: microRNA-seq from limb (ENCLB385XNA)

description:
https://www.encodeproject.org/experiments/ENCSR900DXS/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq  on embryonic 11.5 day mouse limb
experiment encode accession: ENCSR900DXS
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-01-06
lab: Ali Mortazavi, UCI
library encode accession: ENCLB385XNA
size range: <30

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (11.5 days)

value: tissue

value: Limb from 88 embyronic 11.5 day mice

value: healthy

value: ENCBS681XPR at ENCODE; https://www.encodeproject.org/ENCBS681XPR/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from hindbrain (ENCLB224KCA)

description:
https://www.encodeproject.org/experiments/ENCSR896PWV/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on embryonic 14.5 day mouse hindbrain
experiment encode accession: ENCSR896PWV
assay title: ChIP-seq
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB224KCA
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap hindbrain tissue mixed sex embryo (14.5 days)

value: hindbrain

value: Hindbrain from 24 embryonic 14.5 day mice

value: ENCBS004AAA at ENCODE; https://www.encodeproject.org/ENCBS004AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: ChIP-seq from hindbrain (ENCLB690ZIF)

description:
https://www.encodeproject.org/experiments/ENCSR896PWV/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control ChIP-seq on embryonic 14.5 day mouse hindbrain
experiment encode accession: ENCSR896PWV
assay title: ChIP-seq
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB690ZIF
size range: 300-500

value: Control

value: Hindbrain from 34 embryonic 14.5 day mice

value: ENCBS016AAA at ENCODE; https://www.encodeproject.org/ENCBS016AAA/


title: ChIP-seq from lung (ENCLB413TUK)

description:
https://www.encodeproject.org/experiments/ENCSR895BMP/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 15.5 day mouse lung
experiment encode accession: ENCSR895BMP
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR371AKO
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB413TUK
size range: 300-500

source_name: Mus musculus strain B6NCrl lung tissue mixed sex embryo (15.5 days)

value: lung

value: Lung from 62 embryonic 15.5 day mice

value: ENCBS217WPC at ENCODE; https://www.encodeproject.org/ENCBS217WPC/


title: ChIP-seq from forebrain (ENCLB257IOF)

description:
https://www.encodeproject.org/experiments/ENCSR894JAS/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K9me3 ChIP-seq on embryonic 11.5 day mouse forebrain
experiment encode accession: ENCSR894JAS
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR024JAN
encode release date: 2016-03-16
lab: Bing Ren, UCSD
library encode accession: ENCLB257IOF
size range: 300-500
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (11.5 days)

value: forebrain

value: Forebrain from 109 embyronic 11.5 day mice

value: embryonic

value: pooled male and female

value: Len Pennacchio, LBNL

value: ENCBS745VOM at ENCODE; https://www.encodeproject.org/ENCBS745VOM/


title: ChIP-seq from lung (ENCLB356FIY)

description:
https://www.encodeproject.org/experiments/ENCSR895BMP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 15.5 day mouse lung
experiment encode accession: ENCSR895BMP
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR371AKO
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB356FIY
size range: 300-500

value: tissue

value: Lung from 78 embryonic 15.5 day mice

value: healthy

value: ENCBS467HSM at ENCODE; https://www.encodeproject.org/ENCBS467HSM/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/