RBM5 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-55dox	BGRSDLV02-56dox
idx	0	0
TRCN#_or_BGC#	TRCN0000312602	TRCN0000312602
shRNA_or_gRNA_sequence	CCGGACCATCACAGAGAGCGATATTCTCGAGAATATCGCTCTCTGTGATGGTTTTTTG	CCGGACCATCACAGAGAGCGATATTCTCGAGAATATCGCTCTCTGTGATGGTTTTTTG
PAM
Name	RBM5	RBM5
Sample_ID	BGRSDLV02-55dox	BGRSDLV02-56dox
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	RBM5	RBM5
qPCR_result	83.9	83.2
Ave_qPCR	83.6
RT-qPCR_primer-F
RT-qPCR_primer-R
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	9266	9267

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-55dox	BGRSDLV02-56dox
Sample_ID	BGRSDLV02-55dox	BGRSDLV02-56dox
Sample Name
Sample Name	RBM5-BGRSDLV02-55dox	RBM5-BGRSDLV02-56dox
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	12370	12371

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-55dox	BGRSDLV02-56dox
Sample #	51	52
Sample Name	RBM5-BGRSDLV02-55dox	RBM5-BGRSDLV02-56dox
Sample_Name_Alias
Index Well Position	C07	D07
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	298	300
Peak_Molarity	79.00	65.40
libSampleQC_DNA_Well	DNA_Library_set65/set1/C7.png	DNA_Library_set65/set1/D7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set65/set1/C7.png	RNA_Library_set65/set1/D7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-55dox	BGRSDLV02-56dox
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	3972	3973

Sequencing Information

	BGRSDLV02-55dox	BGRSDLV02-56dox
Sample_ID	BGRSDLV02-55dox	BGRSDLV02-56dox
Sample Name	RBM5-BGRSDLV02-55dox	RBM5-BGRSDLV02-56dox
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	49,511,744	34,835,800
total_aligned_reads	45,492,781	32,468,543
unique_aligned_reads	42,123,233	30,097,625
percent_uniqueAligned	0.85077	0.86399
correlation_replicates	0.997679	0.997679
spikein_reads	8,566	5,322
percent_spikeins	0.00017	0.00015
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2719	2720

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-BGRSDLV02-55dox_S51_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2719	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8792
RBM5-BGRSDLV02-55dox_S51_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2719	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8868
RBM5-BGRSDLV02-55dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2719					GRCh38	V40	RBM5-BGRSDLV02-55dox_S51_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM5-BGRSDLV02-55dox_S51_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9357
RBM5-BGRSDLV02-55dox_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	2719					GRCh38	V40	RBM5-BGRSDLV02-55dox/Aligned.sortedByCoord.out.bam		ENCORE2	9433
RBM5-BGRSDLV02-55dox_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	2719					GRCh38	V40	RBM5-BGRSDLV02-55dox/Aligned.sortedByCoord.out.bam		ENCORE2	9509
RBM5-BGRSDLV02-55dox_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	2719					GRCh38	V40	RBM5-BGRSDLV02-55dox/Aligned.sortedByCoord.out.bam		ENCORE2	9585
RBM5-BGRSDLV02-55dox_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	2719					GRCh38	V40	RBM5-BGRSDLV02-55dox/Aligned.sortedByCoord.out.bam		ENCORE2	9661
RBM5-BGRSDLV02-55dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2719					GRCh38	V40	RBM5-BGRSDLV02-55dox_S51_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM5-BGRSDLV02-55dox_S51_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9737
RBM5-BGRSDLV02-56dox_S52_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2720	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8793
RBM5-BGRSDLV02-56dox_S52_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2720	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8869
RBM5-BGRSDLV02-56dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2720					GRCh38	V40	RBM5-BGRSDLV02-56dox_S52_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM5-BGRSDLV02-56dox_S52_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9358
RBM5-BGRSDLV02-56dox_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	2720					GRCh38	V40	RBM5-BGRSDLV02-56dox/Aligned.sortedByCoord.out.bam		ENCORE2	9434
RBM5-BGRSDLV02-56dox_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	2720					GRCh38	V40	RBM5-BGRSDLV02-56dox/Aligned.sortedByCoord.out.bam		ENCORE2	9510
RBM5-BGRSDLV02-56dox_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	2720					GRCh38	V40	RBM5-BGRSDLV02-56dox/Aligned.sortedByCoord.out.bam		ENCORE2	9586
RBM5-BGRSDLV02-56dox_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	2720					GRCh38	V40	RBM5-BGRSDLV02-56dox/Aligned.sortedByCoord.out.bam		ENCORE2	9662
RBM5-BGRSDLV02-56dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2720					GRCh38	V40	RBM5-BGRSDLV02-56dox_S52_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM5-BGRSDLV02-56dox_S52_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9738