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| Status |
Public on May 10, 2023 |
| Title |
heads_FLAMseq_1 |
| Sample type |
SRA |
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| Source name |
heads
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: heads
developmental stage: adults
genotype: wild type (w1118)
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| Treatment protocol |
untreated
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| Growth protocol |
Flies were grown in 25C on standard apple juice based food
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| Extracted molecule |
total RNA |
| Extraction protocol |
For head transcriptomes, 3-day-old w1118 flies were collected and flash-frozen in liquid nitrogen and heads were used for RNA extraction.
FLAM-seq libraries were prepared as described in (Legnini, I, et al., 2019) (extended protocol available at 10.21203/rs.2.10045/v1) using 4µg total RNA from 3-day-old w1118 fly heads and 14-16h AEL embryos. After SMRTbell adapter addition, libraries were sequenced on 3 SMRTcells on a Sequel I PacBio sequencer. Three replicates were performed for each tissue. Reads were processed using the FLAMAnalysis pipeline described in (Legnini, I, et al., 2019, https://github.com/rajewsky-lab/FLAMAnalysis)
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Sequel |
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| Description |
polyA length estimates per gene, FLAIR assemblies
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| Data processing |
For FLAM-seq datasets, poly(A) tail length estimation was performed using https://github.com/rajewsky-lab/FLAMAnalysis (Legnini et al., 2019).
Processing of w1118_heads_flam-seq_pooled.isoforms.gtf: FLAIR (Tang et al., 2020) was used for transcriptome assembly. For each tissue and method, all sequencing replicates were merged into a FASTQ file before assembly. For each sample, during the FLAIR correct step, splice junction information from the respective RNA-seq datasets (short reads) was used to correct individual transcriptomes. For FLAIR collapse, the Eukaryotic Promoter Database EPD (Dreos et al., 2017) was provided to retain only reads with a supported TSS at their 5' end, using --max_ends 5 to allow for multiple 5?-3? end identification. A minimum of three full-length reads were required for an isoform to be collapsed in the assembly. The assembled transcriptomes were assessed for novel isoforms as well as structural categories using SQANTI3v.1.2 (Tardaguila et al., 2018).
Assembly: D. melanogaster Assembly: dm6_ensembl ; D. melanogaster Annotation: ensembl release 96
Supplementary files format and content: Files *_gene_polyA_length.csv: contains read name, gene to which read is assigned using FeatureCounts, unique molecular identifier sequence, tail length and tail sequence
Supplementary files format and content: Processed gtf (General Transfer Format) output of FLAIR assembly: each row represents an exon. Columns are: chromosome name, source, feature type, start, end, score, strand, in the 9th column: metadata assigned to each exon: gene_id, transcript_id, exon number
Library strategy: FLAM-seq
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| Submission date |
May 19, 2022 |
| Last update date |
May 10, 2023 |
| Contact name |
Valérie Hilgers |
| Organization name |
MPI of Immunobiology and Epigenetics
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| Street address |
Stübeweg 51
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| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
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| Platform ID |
GPL28354 |
| Series (2) |
| GSE203390 |
Sites of transcription initiation drive mRNA isoform selection [FLAMseq] |
| GSE203583 |
Sites of transcription initiation drive mRNA isoform selection |
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| Relations |
| BioSample |
SAMN28550002 |
| SRA |
SRX15377602 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6170878_w1118_heads_flam-seq_Rep1_gene_polyA_length.csv.gz |
4.1 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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