Difference between revisions of "TXGP Data Description"

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(TXGP_XENLA_RNA_SA11024)
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** ENGPU (''Engystomops pustulosus'' a.k.a. Túngara Frog or ''Physalaemus pustulosus'').
 
** ENGPU (''Engystomops pustulosus'' a.k.a. Túngara Frog or ''Physalaemus pustulosus'').
  
== TXGP_XENLA_BAC2k_SA09023 ==
+
== 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_XENLA_BAC5k_SA09023 ==
+
== TXGP data ==
 +
=== TXGP_XENLA_BAC2k_SA09023 (SOLiDv2)===
  
== TXGP_XENTR_WG5k_SA09023 ==
+
=== TXGP_XENLA_BAC5k_SA09023 (SOLiDv2) ===
  
== TXGP_XENLA_WG1500_SA10026 ==
+
=== TXGP_XENTR_WG5k_SA09023 (SOLiDv2) ===
  
== TXGP_XENLA_RNA_SA11017 ==
+
=== TXGP_XENLA_WG1500_SA10026 (SOLiDv3) ===
* SA11017_XENLA_Heart_JA11050v3BC10F3
+
* SA11017_XENLA_Heart_JA11050v3BC10F5
+
* SA11017_XENLA_Heart_JA11050v3BC10F3
+
* SA11017_XENLA_Heart_JA11050v3BC10F5
+
  
== TXGP_XENLA_RNA_SA11022 ==
+
=== TXGP_XENLA_RNA_SA11017 (SOLiDv3) ===
* SA11022_XENLA_Egg_JA11015v4BC001F3
+
* SA11017_XENLA_Heart_JA11050v3BC10F3 (24.0M)
* SA11022_XENLA_Egg_JA11015v4BC001F5
+
* SA11017_XENLA_Heart_JA11050v3BC10F5 (23.4M)
* SA11022_XENLA_Stage24_JA11015v2BC13F3
+
* SA11017_XENLA_Testis_JA11050v3BC04F3 (33.1M)
* SA11022_XENLA_Stage24_JA11015v2BC13F5
+
* SA11017_XENLA_Testis_JA11050v3BC04F5 (32.4M)
  
== TXGP_ENGPU_RNA_SA11022 ==
+
=== 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_XENLA_RNA_SA11024 ==
+
=== TXGP_ENGPU_RNA_SA11022 (SOLiDv3) ===
 +
 
 +
=== TXGP_XENLA_RNA_SA11024 (SOLiDv3) ===
 
* SA11024_XENLA_Liver_JA11055v2BC12F3 (21.0M)
 
* SA11024_XENLA_Liver_JA11055v2BC12F3 (21.0M)
 
* SA11024_XENLA_Liver_JA11055v2BC12F5 (22.0M)
 
* SA11024_XENLA_Liver_JA11055v2BC12F5 (22.0M)
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* SA11024_XENLA_Stomach_JA11055v4BC003F3 (27.8M)
 
* SA11024_XENLA_Stomach_JA11055v4BC003F3 (27.8M)
 
* SA11024_XENLA_Stomach_JA11055v4BC003F5 (29.1M)
 
* SA11024_XENLA_Stomach_JA11055v4BC003F5 (29.1M)
 +
 +
== Contributed Data ==
 +
We are looking for ''X. laevis'' RNA-seq data for building comprehensive gene models.
 +
 +
=== Amin2011_XENLA_RNA_UNC (Illumina HiSeq)===
 +
Data from [http://www.unc.edu/~fconlon/ Frank Conlon lab] at University of North Carolina at Chapel Hill.
 +
* Amin2011_XENLA_Stage38Heart_WT
 +
* AMin2011_XENLA_Stage45Heart_CtrlMO
  
 
----
 
----
 
[[Category:XenopusGenome]]
 
[[Category:XenopusGenome]]

Revision as of 13:09, 21 June 2011

Contents

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)

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.

Amin2011_XENLA_RNA_UNC (Illumina HiSeq)

Data from Frank Conlon lab at University of North Carolina at Chapel Hill.

  • Amin2011_XENLA_Stage38Heart_WT
  • AMin2011_XENLA_Stage45Heart_CtrlMO