|
| Status |
Public on Feb 03, 2023 |
| Title |
HEK-293 plus pCMV-TDP-43-APOBEC rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HEK-293
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK-293
treatment: pCMV-TDP-43-APOBEC
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
400 GFP-positive cells were isolated by FACS sorting and lysed in 100µl of Lysis buffer
Libaries were constructed using Smart-seq2 protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
CR_SEQ_2
|
| Data processing |
Trim reads:cutadapt -q 20 --trim-n --minimum-length=10 -o $file1 -p $file2 $infile1 $infile2
Align via STAR : STAR --runThreadN 8 --outFilterMismatchNoverLmax 0.06 --outFileNamePrefix $prefix"_" --outFilterMatchNmin 15 --outFilterMultimapNmax 1 --genomeDir $star_indices --outSJfilterReads Unique --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --alignMatesGapMax 25000 --readFilesIn $file1 $file2
remove PCR duplicates:java -Xmx4g -jar $PICARD_JAR MarkDuplicates --INPUT $input_for_picard --OUTPUT $dupremove_bam --METRICS_FILE dup.txt --VALIDATION_STRINGENCY LENIENT --REMOVE_DUPLICATES true --TMP_DIR tmp --ASSUME_SORTED true
generate raw read counts:python -m HTSeq.scripts.count -q -r pos -f bam $sort_out --stranded=no --minaqual=10 $gtf_file > $prefix"_unique_raw.txt"
generate transcript counts:stringtie -A $prefix"_gene_abundance.txt" -o $assembled_transcript -p 6 -e -G $gtf_file $sort_out
Assembly: GRChg38.p13
Supplementary files format and content: Bedgraph file listing all potential editing sites
|
| |
|
| Submission date |
Jan 23, 2023 |
| Last update date |
Feb 03, 2023 |
| Contact name |
Katharine Abruzzi |
| E-mail(s) |
katea@brandeis.edu
|
| Phone |
7817363161
|
| Organization name |
HHMI; Brandeis University
|
| Department |
Biology
|
| Lab |
Rosbash
|
| Street address |
415 South St.
|
| City |
Waltham |
| State/province |
MA |
| ZIP/Postal code |
02478 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE223556 |
Comparison of STAMP and TRIBE for identifying the targets of RNA-binding proteins in human and Drosophila cells [human] |
| GSE223557 |
Comparison of STAMP and TRIBE for identifying the targets of RNA-binding proteins in human and Drosophila cells |
|
| Relations |
| BioSample |
SAMN32881984 |
| SRA |
SRX19145050 |
