TXGP Data Description
From Marcotte Lab
Naming convention
- Directory name: '(investigator)_(species code)_(sample type)_(SA#)'
- File name: '(SA#)_(species code)_(description)_(JA#,barcode,F3/F5/R3)'
- Species code
- XENLA (Xenopus laevis)
- XENTR (Xenopus tropicalis a.k.a. Silurana tropicalis)
- ENGPU (Engystomops pustulosus a.k.a. Túngara Frog or Physalaemus pustulosus).
Data pre-processing
- Remove reads with any no-call('N' in Illumina fastq file; '.' in SOLiD csfasta file).
- Remove low-complex reads, with less than 4 letters('0123' for color space, 'ATGC' for base space).
TXGP data
TXGP_XENLA_BAC2k_SA09023 (SOLiDv2)
TXGP_XENLA_BAC5k_SA09023 (SOLiDv2)
TXGP_XENTR_WG5k_SA09023 (SOLiDv2)
TXGP_XENLA_WG1500_SA10026 (SOLiDv3)
TXGP_XENLA_RNA_SA11017 (SOLiDv3)
- SA11017_XENLA_Heart_JA11050v3BC10F3 (24.0M)
- SA11017_XENLA_Heart_JA11050v3BC10F5 (23.4M)
- SA11017_XENLA_Testis_JA11050v3BC04F3 (33.1M)
- SA11017_XENLA_Testis_JA11050v3BC04F5 (32.4M)
TXGP_XENLA_RNA_SA11022 (SOLiDv3)
- SA11022_XENLA_Egg_JA11015v4BC001F3 (19.3M)
- SA11022_XENLA_Egg_JA11015v4BC001F5 (19.4M)
- SA11022_XENLA_Stage24_JA11015v2BC13F3 (16.5M)
- SA11022_XENLA_Stage24_JA11015v2BC13F5 (16.6M)
TXGP_ENGPU_RNA_SA11022 (SOLiDv3)
- SA11022_ENGPU_RNA_JA11015v4BC002F3
- SA11022_ENGPU_RNA_JA11015v4BC002F5
TXGP_XENLA_RNA_SA11024 (SOLiDv3)
- SA11024_XENLA_Liver_JA11055v2BC12F3 (21.0M)
- SA11024_XENLA_Liver_JA11055v2BC12F5 (22.0M)
- SA11024_XENLA_Lung_JA11055v2BC11F3 (35.1M)
- SA11024_XENLA_Lung_JA11055v2BC11F5 (36.7M)
- SA11024_XENLA_Stomach_JA11055v4BC003F3 (27.8M)
- SA11024_XENLA_Stomach_JA11055v4BC003F5 (29.1M)
Contributed Data
We are looking for X. laevis RNA-seq data for building comprehensive gene models.
Conlon2011_XENLA_RNA_UNC201106 (Illumina HiSeq)
Data from Frank Conlon lab at University of North Carolina at Chapel Hill.
- Conlon2011_XENLA_Stage38Heart_WT (27.8M)
- Conlon2011_XENLA_Stage45Heart_CtrlMO (33.2M)