Difference between revisions of "ChungKwon2013 RFX2"
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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 == | + | == 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)]. |
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− | == Genomic | + | * 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) | * 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.fa.gz (longest cDNA, 'Oktoberfest' version) | ||
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== Processed data == | == 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). | * 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_DirectDEdown_HGNC.xls : Functional modules enriched in genes down-regulated under Rfx2 knockdown + Rfx2 ChIP-seq peaks. (using DAVID 6.7) |
Latest revision as of 15:42, 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)
- 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