View source for ChungKwon2013 RFX2

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 (GSE50593)==
[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 (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) ==
* ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla6.0/ (''X. laevis'' JGI 6.0 scaffolds)
* http://daudin.icmb.utexas.edu/pub/annot/UTA/XENLA_2012oct_cdna_longest.fa.gz (longest cDNA, 'Oktoberfest' version)
* 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 ==
* Alignments (sorted.bam files): http://data.marcottelab.org/ChungKwon2013_rfx2/bam/

* 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