TXGP Data Description

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Contents

Naming convention

  • Directory name: '(project group)_(species code)_(sample type)_(run ID)'
  • File name: '(run ID)_(species code)_(description)_(sample prep ID,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 X. laevis BAC data

TXGP_XENLA_BAC2k_SA09023 (SOLiDv2)

  • One plate of CHORI-219 BAC library.
  • Mate-pair library with 2kb insertion.
  • SA09023_XENLA_96BAC2kb_F3.called.fastq.gz (1.8G)
  • SA09023_XENLA_96BAC2kb_R3.called.fastq.gz 1.8G

TXGP_XENLA_BAC5k_SA09023 (SOLiDv2)

One plate of CHORI-219 BAC library (sample as BAC2k_SA09023). Mate-pair library with 5kb insertion.

  • SA09023_XENLA_96BAC5kb_F3.called.fastq.gz 1.3G
  • SA09023_XENLA_96BAC5kb_R3.called.fastq.gz 1.4G

TXGP X. laevis whole genome data

  • J-strain from Mustafa Khokha (Yale University).
  • Mate-pair library with 1,500 bp insertion.

TXGP_XENLA_WG1500_SA10026 (SOLiDv3)

  • SA10026_XENLA_WG1500_HiAmp1ManF3 (80.1M)
  • SA10026_XENLA_WG1500_HiAmp1ManR3 (78.8M)
  • SA10026_XENLA_WG1500_HiAmp2ManF3 (77.0M)
  • SA10026_XENLA_WG1500_HiAmp2ManR3 (76.7M)
  • SA10026_XENLA_WG1500_HiAmpEZF3 (83.3M)
  • SA10026_XENLA_WG1500_HiAmpEZR3 (81.6M)
  • SA10026_XENLA_WG1500_LoAmpManF3 (65.0M)
  • SA10026_XENLA_WG1500_LoAmpManR3 (63.7M)

TXGP X. laevis RNA-seq data

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_Larnyx_JA11015v4BC002F3 (21.1M)
  • SA11022_ENGPU_Larnyx_JA11015v4BC002F5 (21.1M)

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)

TXGP X. tropicalis data

TXGP_XENTR_WG5k_SA09023 (SOLiDv2)

Contributed Data

We are looking for X. laevis RNA-seq data for building comprehensive gene models.

ConlonUNC_XENLA_RNA_Amin201106 (Illumina HiSeq)

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

  • ConlonLab2011_XENLA_Stage38Heart_WT (27.8M)
  • ConlonLab2011_XENLA_Stage45Heart_CtrlMO (33.2M)

ConlonUNC_XENTR_RNA_Amin201106 (Illumina HiSeq)

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

  • ConlonLab2011_XENTR_Heart_WT1
  • ConlonLab2011_XENTR_Heart_WT2

HarlandUBC_XENLA_RNA_Park201106: Single-end (50bp), Illumina HiSeq

Data from Richard Harland lab at University of California, Berkeley.

  • Park2011_XENLA_Arch1_WT.fastq.gz: read_count=101M, file_size=4.8GB
  • Park2011_XENLA_Arch2_WT.fastq.gz: read_count=102M, file_size=4.8GB
  • Park2011_XENLA_Arch3_WT.fastq.gz: read_count=96M, file_size=4.4GB
  • Park2011_XENLA_ArchD_WT.fastq.gz: read_count=115M, file_size=5.5GB
  • Park2011_XENLA_ArchV_WT.fastq.gz: read_count=103M, file_size=4.8G

LauBrandeis_XENLA_RNA_Lau201109