| Accession | GMS-64-83
URL copied to the clipboard |
| Title | Transcriptome and germ-cell development |
| Submit date | 2025-03-31 10:08:36 |
| Last update date | 2025-03-31 14:39:45 |
| Contact | Sung-Joon PARK park AT hgc.jp The University of Tokyo |
| Sharing | |
| Total file size | 44.48 GB |
| Keywords | Spermatogenesis Development Primordial germ cell |
| Experiment type | Bulk transcriptome analysis |
| Summary | Illumina SRA files were prepared from NCBI GEO; Primordial germ cells (PGC) at embryonic day E13.5 (GSM1064457), E14.5 (ERP015330), E16.5 (ERP015330), E18.5 (ERP015330), postnatal P0.5 (DRP002386), P2 (ERP015330), P7.5 (DRP002386), Data for PGCs is available at https://gmsuite.hgc.jp/gms_viewer.php?ACC=GMS-64-82 Spermatogonia; SG (GSM1069640), Spermatocytes; SC (GSM1069641), Spermatids; SD (GSM1069642), Spermatozoa; SZ (GSM1069643), Mouse embryonic fibroblast; MEF (GSM1643254), and Sertoli; SL (GSM1069639) |
| Citation(s) | https://pubmed.ncbi.nlm.nih.gov/23399596/ |
| Organism | Mouse |
| Cell (Tissue) | sperm |
| Protocol | |
| Data processing | Step1 (Quality control): Trimmomatic (ver. 0.36) assessed all the FASTQ files by using options "ILLUMINACLIP:adapter_file:2:30:10 LEADING:20 TRAILING:20 MINLEN:3" Step2 (Mapping): HISTA2 (ver.2.0.5) coupled with Bowtie2 (ver. 2.2.9) mapped the reads of each replicate to the mouse reference genome mm10 with options "-k 1 --dta --dta-cufflinks". |
| [739] | Mouse embryonic fibroblast (MEF) replicate 1 Browse Browse (All) Mouse (mm10); RNA-Seq |
 BAM MEF_1.bam (3.12 GB) |
| [740] | Mouse embryonic fibroblast (MEF) replicate 2 Browse Mouse (mm10); RNA-Seq |
BAM MEF_2.bam (3.35 GB) |
| [722] | Spermatocytes (SC) replicate 1 Browse Mouse (mm10); RNA-Seq |
BAM SC_1.bam (2.05 GB) |
| [723] | Spermatocytes (SC) replicate 2 Browse Mouse (mm10); RNA-Seq |
BAM SC_2.bam (2.43 GB) |
| [724] | Spermatocytes (SC) replicate 3 Browse Mouse (mm10); RNA-Seq |
BAM SC_3.bam (3.04 GB) |
| [725] | Spermatids (SD) replicate 1 Browse Mouse (mm10); RNA-Seq |
BAM SD_1.bam (1.45 GB) |
| [726] | Spermatids (SD) replicate 2 Browse Mouse (mm10); RNA-Seq |
BAM SD_2.bam (2.57 GB) |
| [727] | Spermatids (SD) replicate 3 Browse Mouse (mm10); RNA-Seq |
BAM SD_3.bam (2.73 GB) |
| [728] | Spermatogonia (SG) replicate 1 Browse Mouse (mm10); RNA-Seq |
BAM SG_1.bam (2.19 GB) |
| [730] | Spermatogonia (SG) replicate 2 Browse Mouse (mm10); RNA-Seq |
BAM SG_2.bam (2.39 GB) |
| [731] | Spermatogonia (SG) replicate 3 Browse Mouse (mm10); RNA-Seq |
BAM SG_3.bam (2.83 GB) |
| [736] | Sertoli (SL) replicate 1 Browse Mouse (mm10); RNA-Seq |
BAM SL_1.bam (2.73 GB) |
| [737] | Sertoli (SL) replicate 2 Browse Mouse (mm10); RNA-Seq |
BAM SL_2.bam (3.07 GB) |
| [738] | Sertoli (SL) replicate 3 Browse Mouse (mm10); RNA-Seq |
BAM SL_3.bam (3.08 GB) |
| [732] | Spermatozoa (SZ) replicate 1 Browse Mouse (mm10); RNA-Seq |
BAM SZ_1.bam (2.21 GB) |
| [733] | Spermatozoa (SZ) replicate 2 Browse Mouse (mm10); RNA-Seq |
BAM SZ_2.bam (2.38 GB) |
| [734] | Spermatozoa (SZ) replicate 3 Browse Mouse (mm10); RNA-Seq |
BAM SZ_3.bam (2.84 GB) |
| [742] | RNA-seq mappability in germ-cell development germcell_dev.png (177.55 KB) |
|
| [743] | Gene expression clustering transcriptome_changes.png (187.43 KB) |
|
| [762] | Gene expression profile (TPMs from E13.5 to SZ with SL and MEF) |
expression_profile.txt (2.31 MB) |
| [739] MEF_1.bam
Mouse embryonic fibroblast (MEF) replicate 1 application/octet-stream 3.12 GB MD5: 18e663817457dd1f2036ab266562eff5 |
| [740] MEF_2.bam
Mouse embryonic fibroblast (MEF) replicate 2 application/octet-stream 3.35 GB MD5: d89ad1e5b9d5b91fafb0244908ffd92e |
| [722] SC_1.bam
Spermatocytes (SC) replicate 1 application/octet-stream 2.05 GB MD5: c443facbbf5f5b3b63f8ed3546e795e0 |
| [723] SC_2.bam
Spermatocytes (SC) replicate 2 application/octet-stream 2.43 GB MD5: 6ddbe1e4d4b484036cb8568f60b781e1 |
| [724] SC_3.bam
Spermatocytes (SC) replicate 3 application/octet-stream 3.04 GB MD5: 922e1ccbf09adbed7ad31d150ba73089 |
| [725] SD_1.bam
Spermatids (SD) replicate 1 application/octet-stream 1.45 GB MD5: 4f6bb10a8190aa26c06b09016d61ab0c |
| [726] SD_2.bam
Spermatids (SD) replicate 2 application/octet-stream 2.57 GB MD5: 1a79bf9c83596162e153f9a2a20beebd |
| [727] SD_3.bam
Spermatids (SD) replicate 3 application/octet-stream 2.73 GB MD5: 282dd7c84aac68f04c6bf8b667c3c8b4 |
| [728] SG_1.bam
Spermatogonia (SG) replicate 1 application/octet-stream 2.19 GB MD5: f745f521dd1a2f23752f1474d7e20c62 |
| [730] SG_2.bam
Spermatogonia (SG) replicate 2 application/octet-stream 2.39 GB MD5: 6383f8f028d2e17cbede91b6d0f705e5 |
| [731] SG_3.bam
Spermatogonia (SG) replicate 3 application/octet-stream 2.83 GB MD5: 2f85703d8e07a92b040a18fe1544659f |
| [736] SL_1.bam
Sertoli (SL) replicate 1 application/octet-stream 2.73 GB MD5: c090f2fd6209567226a4864a1ffada48 |
| [737] SL_2.bam
Sertoli (SL) replicate 2 application/octet-stream 3.07 GB MD5: 2554131c72d4c275d2a52402ca7fbaa6 |
| [738] SL_3.bam
Sertoli (SL) replicate 3 application/octet-stream 3.08 GB MD5: 8bcd15cec7b4bf9ed68dd47208b617f9 |
| [732] SZ_1.bam
Spermatozoa (SZ) replicate 1 application/octet-stream 2.21 GB MD5: a8dff4be386e8a2e69ca17f710248a78 |
| [733] SZ_2.bam
Spermatozoa (SZ) replicate 2 application/octet-stream 2.38 GB MD5: 403dddc2d3d9861e922bed2164e228a0 |
| [734] SZ_3.bam
Spermatozoa (SZ) replicate 3 application/octet-stream 2.84 GB MD5: 5597f1ddc5c614eb14f43864e153dc04 |
| [742] germcell_dev.png
RNA-seq mappability in germ-cell development image/png 177.55 KB MD5: 3e720e1dd48b028300e4f23dfac85236 |
| [743] transcriptome_changes.png
Gene expression clustering image/png 187.43 KB MD5: 351cfe17b8e534680d9150794169b392 |
| [762] expression_profile.txt
Gene expression profile (TPMs from E13.5 to SZ with SL and MEF) text/plain 2.31 MB MD5: ff9fd822a15c48f435d60721ff214e93 |
