Difference between revisions of "ChungKwon2013 RFX2"

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(Processed data)
 
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Supplementary Website for Chung M-I, Kwon T, Tu F, Brooks ER, Gupta R, Meyer M, Baker JC, Marcotte EM, Wallingford JB, ''Coordinated genomic control of ciliogenesis and cell movement by RFX2'' (submitted).  
 
Supplementary Website for Chung M-I, Kwon T, Tu F, Brooks ER, Gupta R, Meyer M, Baker JC, Marcotte EM, Wallingford JB, ''Coordinated genomic control of ciliogenesis and cell movement by RFX2'' (submitted).  
  
== Raw data ==
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== Raw data (GSE50593)==
(Data is submitted to NCBI GEO. We will make post the link when our manuscript is accepted.)
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[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50593 GSE50593(NCBI GEO)] & [http://www.ncbi.nlm.nih.gov/sra?term=SRP029582 SRP029582(NCBI SRA)].
* RNA-seq, Control #1
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* RNA-seq, Control #2
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* RNA-seq, RFX2 Knock-down #1
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* RNA-seq, RFX2 Knock-down #2
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* ChIP-seq, RFX2-GFP
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* ChIP-seq, Control GFP
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== Genomic resource ==
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* RNA-seq, Control #1 (2x100 bp, paired-end)
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* RNA-seq, Control #2 (2x100 bp, paired-end)
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* RNA-seq, RFX2 Knock-down #1 (2x100 bp, paired-end)
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* RNA-seq, RFX2 Knock-down #2 (2x100 bp, paired-end)
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* ChIP-seq, RFX2-GFP (1x50 bp, single-end)
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* ChIP-seq, Control GFP (1x50 bp, single-end)
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You can download raw fastq files from http://data.marcottelab.org/ChungKwon2013_rfx2/fastq/
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== Genomic resources (database) ==
 
* ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla6.0/ (''X. laevis'' JGI 6.0 scaffolds)
 
* ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla6.0/ (''X. laevis'' JGI 6.0 scaffolds)
* http://daudin.icmb.utexas.edu/pub/XENLA_2012oct_cdna_longest.fa (longest cDNA, 'Oktoberfest' version)
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* http://daudin.icmb.utexas.edu/pub/annot/UTA/XENLA_2012oct_cdna_longest.fa.gz (longest cDNA, 'Oktoberfest' version)
* http://daudin.icmb.utexas.edu/pub/XB_XENLA_2012oct_longest.gene.gff3.gz ('Oktoberfest' GFF file for JGI 6.0 scaffods)
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* http://daudin.icmb.utexas.edu/pub/annot/UTA/XENLA_2012oct_cdna_longest.gene.gff3.gz ('Oktoberfest' GFF file for JGI 6.0 scaffods)
  
 
== Processed data ==
 
== Processed data ==
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* Alignments (sorted.bam files): http://data.marcottelab.org/ChungKwon2013_rfx2/bam/
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* SuppTable2.RFX2_rnaseq_chip.2012oct.xls : Direct target of RFX2 identified in this study (genes differentially expressed under Rfx2 knock-down + Rfx2 ChIP-seq peaks).  
 
* SuppTable2.RFX2_rnaseq_chip.2012oct.xls : Direct target of RFX2 identified in this study (genes differentially expressed under Rfx2 knock-down + Rfx2 ChIP-seq peaks).  
* HumanNetRFX2_HumanNet_new.cys : sub-network with genes differentially expressed under Rfx2 knockdown + Rfx2 ChIP-seq peaks. (need [http://www.cytoscape.org/ cytoscape] for browsing)
 
 
* DAVID6.7_RFX2_DirectDEdown_HGNC.xls : Functional modules enriched in genes down-regulated under Rfx2 knockdown + Rfx2 ChIP-seq peaks. (using DAVID 6.7)
 
* DAVID6.7_RFX2_DirectDEdown_HGNC.xls : Functional modules enriched in genes down-regulated under Rfx2 knockdown + Rfx2 ChIP-seq peaks. (using DAVID 6.7)
 
* DAVID6.7_RFX2_DirectDEup_HGNC.xls : Functional modules enriched in genes up-regulated under Rfx2 knockdown + Rfx2 ChIP-seq peaks. (using DAVID 6.7)
 
* DAVID6.7_RFX2_DirectDEup_HGNC.xls : Functional modules enriched in genes up-regulated under Rfx2 knockdown + Rfx2 ChIP-seq peaks. (using DAVID 6.7)

Latest revision as of 14:42, 8 May 2014

Supplementary Website for Chung M-I, Kwon T, Tu F, Brooks ER, Gupta R, Meyer M, Baker JC, Marcotte EM, Wallingford JB, Coordinated genomic control of ciliogenesis and cell movement by RFX2 (submitted).

Contents

Raw data (GSE50593)

GSE50593(NCBI GEO) & SRP029582(NCBI SRA).

  • RNA-seq, Control #1 (2x100 bp, paired-end)
  • RNA-seq, Control #2 (2x100 bp, paired-end)
  • RNA-seq, RFX2 Knock-down #1 (2x100 bp, paired-end)
  • RNA-seq, RFX2 Knock-down #2 (2x100 bp, paired-end)
  • ChIP-seq, RFX2-GFP (1x50 bp, single-end)
  • ChIP-seq, Control GFP (1x50 bp, single-end)

You can download raw fastq files from http://data.marcottelab.org/ChungKwon2013_rfx2/fastq/

Genomic resources (database)

Processed data

  • SuppTable2.RFX2_rnaseq_chip.2012oct.xls : Direct target of RFX2 identified in this study (genes differentially expressed under Rfx2 knock-down + Rfx2 ChIP-seq peaks).
  • DAVID6.7_RFX2_DirectDEdown_HGNC.xls : Functional modules enriched in genes down-regulated under Rfx2 knockdown + Rfx2 ChIP-seq peaks. (using DAVID 6.7)
  • DAVID6.7_RFX2_DirectDEup_HGNC.xls : Functional modules enriched in genes up-regulated under Rfx2 knockdown + Rfx2 ChIP-seq peaks. (using DAVID 6.7)

Videos

  • Video S1. Dynamics of GFP-IFT20 in a control multiciliated cell.
  • Video S2. Dynamics of GFP-IFT20 in a Ttc29-knockdown multiciliated cell.
  • Video S3. Cilia beating of a control multiciliated cell.
  • Video S4. Cilia beating of a Ribc2-knockdown multiciliated cell.
  • Video S5. The development of a control multiciliated cell.
  • Video S6. The insertion of a control multiciliated cell into the overlying
  • Video S7. The insertion of a Rfx2-knockdown multiciliated cell into the