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Series GSE53412 Query DataSets for GSE53412
Status Public on Nov 17, 2014
Title The C. elegans SNAP complex component SNPC-4 coats piRNA domains and globally affects piRNA abundance
Organism Caenorhabditis elegans
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Third-party reanalysis
Summary Remarkably, tens of thousands of piwi-interacting RNAs (piRNAs) arise from a minimal number of discrete clustered regions in many organisms. However, it remains unclear if organization into these domains contributes to the highly coordinated, germline-specific expression of these small RNAs. Here, we show that SNPC-4, the DNA-binding subunit of the small nuclear RNA activating protein complex (SNAPc), binds piRNA clusters in a germline-specific manner and is required for global piRNA expression in C. elegans. Within piRNA domains, SNPC-4 not only binds at discrete sites through its established sequence motif, but also exhibits widely distributed binding across the region. Intriguingly, discrete peaks are not found at every piRNA, but instead occur frequently at Pol III-occupied tRNA genes, which have been previously implicated in chromatin organization. Given its unique binding pattern, we suggest that SNPC-4 promotes robust piRNA expression by establishing a permissive chromatin environment at clusters specifically in the germ line.
Overall design This data submission includes a total of 11 ChIP-seq samples and 2 RNA-seq samples.
The ChIP-seq samples include six timecourse samples (Emb-YA) and three tissue-specific samples (WA, GL, SO) for one factor called SNPC-4 (previously called GEI-11). The remaining two ChIP-seq samples are for pol II (AMA-1) and pol III (RPC-1) at one developmental stage. All of these samples were done in replicate, with inputs, yielding at least four sequencing files per sample. Some of the ChIP-seq samples already have fastq files submitted to GEO: (SNPC-4 EMB _GSE48744: GSM1183805, GSM1183806, GSM1183807, GSM1183808), (SNPC-4 L1_GSE48702: GSM1183629, GSM1183630, GSM1183631, GSM1183632), (SNPC-4 L2_GSE37809: GSM928364, GSM928365, GSM928366, GSM928367), (SNPC-4 L3_GSE35276: GSM864851, GSM864852, GSM864853, GSM864854), and (AMA-1_GSE15535: GSM389309, GSM389310, GSM389312, GSM389313). We are submitting fastq files for the remaining ChIP-seq datasets: SNPC-4 L4 - 4 files, SNPC-4 YA - 5 files, SNPC-4 WA - 4 files, SNPC-4 GL - 4 files, SNPC-4 SO - 4 files, and RPC-1 WA - 5 files. Thus we are submitting an additional 26 fastq files. Additionally, we are submitting processed files for all 11 datasets, consisting of one normalized file for the combined duplicate IP and one normalized file for the input sequence. In the case of the three tissue-specific samples for SNPC-4, we are submitting an additional processed (but not normalized) file that represents the IP data with input-subtracted. Thus, we are submitting a total of 25 processed files. NOTE: The processed files for the ChIP-seq samples that already have fastq files submitted to GEO (SNPC-4 EMB _GSE48744, etc.) are linked below as supplementary files at the foot of the Series record.
The RNA-seq samples represent one control (control_RNAseq) and one treatment (SNPC-4(RNAi)_RNA-seq)and were not duplicated. We are submitting one fastq file for each, as well as one processed data file for each, for a total of 2 fastq and 2 processed data files.
Contributor(s) Kasper D, Wang G, Gardner K, Johnstone T, Reinke V
Citation(s) 25373775
Submission date Dec 17, 2013
Last update date May 15, 2019
Contact name Valerie Reinke
Phone 203-785-5228
Organization name Yale University School of Medicine
Department Genetics
Lab Reinke lab
Street address 333 Cedar St
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
Platforms (1)
GPL9269 Illumina Genome Analyzer II (Caenorhabditis elegans)
Samples (14)
GSM1291066 SNPC-4 ChIP in staged L4s (5%)
GSM1291067 SNPC-4 input in staged L4s (5%)
GSM1291068 SNPC-4 ChIP in staged young adults (5%)
Reanalysis of GSM1183805
Reanalysis of GSM1183806
Reanalysis of GSM1183807
Reanalysis of GSM1183808
Reanalysis of GSM1183629
Reanalysis of GSM1183630
Reanalysis of GSM1183631
Reanalysis of GSM1183632
Reanalysis of GSM928364
Reanalysis of GSM928365
Reanalysis of GSM928366
Reanalysis of GSM928367
Reanalysis of GSM864851
Reanalysis of GSM864852
Reanalysis of GSM864853
Reanalysis of GSM864854
Reanalysis of GSM389309
Reanalysis of GSM389310
Reanalysis of GSM389312
Reanalysis of GSM389313
BioProject PRJNA232035
SRA SRP034589

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE53412_AMA-1_WA_L4_YA_IP_Rep0.density.scaled.bedgraph.gz 13.2 Mb (ftp)(http) BEDGRAPH
GSE53412_AMA-1_WA_L4_YA_input_Rep0.density.scaled.bedgraph.gz 13.1 Mb (ftp)(http) BEDGRAPH
GSE53412_RAW.tar 198.4 Mb (http)(custom) TAR (of BEDGRAPH, TXT)
GSE53412_SNPC4_EM_IP_Rep0.density.scaled.bedgraph.gz 13.1 Mb (ftp)(http) BEDGRAPH
GSE53412_SNPC4_EM_input_Rep0.density.scaled.bedgraph.gz 13.1 Mb (ftp)(http) BEDGRAPH
GSE53412_SNPC4_L1_IP_Rep0.density.scaled.bedgraph.gz 13.1 Mb (ftp)(http) BEDGRAPH
GSE53412_SNPC4_L1_input_Rep0.density.scaled.bedgraph.gz 13.0 Mb (ftp)(http) BEDGRAPH
GSE53412_SNPC4_L2_IP_Rep0.density.scaled.bedgraph.gz 13.1 Mb (ftp)(http) BEDGRAPH
GSE53412_SNPC4_L2_input_Rep0.density.scaled.bedgraph.gz 13.1 Mb (ftp)(http) BEDGRAPH
GSE53412_SNPC4_L3_IP_Rep0.density.scaled.bedgraph.gz 13.1 Mb (ftp)(http) BEDGRAPH
GSE53412_SNPC4_L3_input_Rep0.density.scaled.bedgraph.gz 13.1 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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