RBM5 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-53	BGRSDLV02-54
idx	0	0
TRCN#_or_BGC#	TRCN0000312602	TRCN0000312602
shRNA_or_gRNA_sequence	CCGGACCATCACAGAGAGCGATATTCTCGAGAATATCGCTCTCTGTGATGGTTTTTTG	CCGGACCATCACAGAGAGCGATATTCTCGAGAATATCGCTCTCTGTGATGGTTTTTTG
PAM
Name	RBM5	RBM5
Sample_ID	BGRSDLV02-53	BGRSDLV02-54
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	RBM5	RBM5
qPCR_result	70.9	80.0
Ave_qPCR	75.5
RT-qPCR_primer-F	CCTTAGCTGAAAGGCAGCAG
RT-qPCR_primer-R	CACCAGCTCCTCCTCATTGT
protein_conc	0	0
WB_result
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9264	9265

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-53	BGRSDLV02-54
Sample_ID	BGRSDLV02-53	BGRSDLV02-54
Sample Name
Sample Name	RBM5-BGRSDLV02-53	RBM5-BGRSDLV02-54
RBP	RBM5	RBM5
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12368	12369

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-53	BGRSDLV02-54
Sample #	49	50
Sample Name	RBM5-BGRSDLV02-53	RBM5-BGRSDLV02-54
Sample_Name_Alias
Index Well Position	A07	B07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-09-26	2023-09-26
Lib_ID	Lib-230926	Lib-230926
Tecan_Location
Tecan
Tecan_date
Size_bp	295	291
Peak_Molarity	103.00	68.20
libSampleQC_DNA_Well	DNA_Library_set65/set1/A7.png	DNA_Library_set65/set1/B7.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set65/set1/A7.png	RNA_Library_set65/set1/B7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-53	BGRSDLV02-54
RBP	RBM5	RBM5
Batch_ID	BGRSDLV02	BGRSDLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3970	3971

Sequencing Information

	BGRSDLV02-53	BGRSDLV02-54
Sample_ID	BGRSDLV02-53	BGRSDLV02-54
Sample Name	RBM5-BGRSDLV02-53	RBM5-BGRSDLV02-54
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	42,730,827	35,148,623
total_aligned_reads	39,668,841	32,422,443
unique_aligned_reads	36,830,442	30,083,991
percent_uniqueAligned	0.86192	0.85591
correlation_replicates	0.996820	0.996820
spikein_reads	16,184	6,038
percent_spikeins	0.00038	0.00017
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2717	2718

Data Submission Information DCC submission information was not avaliable

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
RBM5-BGRSDLV02-53_S49_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2717	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8790
RBM5-BGRSDLV02-53_S49_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2717	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8866
RBM5-BGRSDLV02-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2717					GRCh38	V40	RBM5-BGRSDLV02-53_S49_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM5-BGRSDLV02-53_S49_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9355
RBM5-BGRSDLV02-53_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2717					GRCh38	V40	RBM5-BGRSDLV02-53/Aligned.sortedByCoord.out.bam		ENCORE2	9431
RBM5-BGRSDLV02-53_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2717					GRCh38	V40	RBM5-BGRSDLV02-53/Aligned.sortedByCoord.out.bam		ENCORE2	9507
RBM5-BGRSDLV02-53_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2717					GRCh38	V40	RBM5-BGRSDLV02-53/Aligned.sortedByCoord.out.bam		ENCORE2	9583
RBM5-BGRSDLV02-53_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2717					GRCh38	V40	RBM5-BGRSDLV02-53/Aligned.sortedByCoord.out.bam		ENCORE2	9659
RBM5-BGRSDLV02-53_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2717					GRCh38	V40	RBM5-BGRSDLV02-53_S49_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM5-BGRSDLV02-53_S49_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9735
RBM5-BGRSDLV02-54_S50_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2718	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8791
RBM5-BGRSDLV02-54_S50_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2718	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8867
RBM5-BGRSDLV02-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2718					GRCh38	V40	RBM5-BGRSDLV02-54_S50_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM5-BGRSDLV02-54_S50_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9356
RBM5-BGRSDLV02-54_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2718					GRCh38	V40	RBM5-BGRSDLV02-54/Aligned.sortedByCoord.out.bam		ENCORE2	9432
RBM5-BGRSDLV02-54_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2718					GRCh38	V40	RBM5-BGRSDLV02-54/Aligned.sortedByCoord.out.bam		ENCORE2	9508
RBM5-BGRSDLV02-54_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2718					GRCh38	V40	RBM5-BGRSDLV02-54/Aligned.sortedByCoord.out.bam		ENCORE2	9584
RBM5-BGRSDLV02-54_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2718					GRCh38	V40	RBM5-BGRSDLV02-54/Aligned.sortedByCoord.out.bam		ENCORE2	9660
RBM5-BGRSDLV02-54_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2718					GRCh38	V40	RBM5-BGRSDLV02-54_S50_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM5-BGRSDLV02-54_S50_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9736