CNBP RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-19dox	BGRSDLV02-20dox
idx	0	0
TRCN#_or_BGC#	TRCN0000218324	TRCN0000218324
shRNA_or_gRNA_sequence	GTACCGGATTGAGGCTACAGCCTAATTACTCGAGTAATTAGGCTGTAGCCTCAATTTTTTTG	GTACCGGATTGAGGCTACAGCCTAATTACTCGAGTAATTAGGCTGTAGCCTCAATTTTTTTG
PAM
Name	CNBP	CNBP
Sample_ID	BGRSDLV02-19dox	BGRSDLV02-20dox
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	CNBP	CNBP
qPCR_result	94.3	93.4
Ave_qPCR	93.9
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	9230	9231

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-19dox	BGRSDLV02-20dox
Sample_ID	BGRSDLV02-19dox	BGRSDLV02-20dox
Sample Name
Sample Name	CNBP-BGRSDLV02-19dox	CNBP-BGRSDLV02-20dox
RBP	CNBP	CNBP
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12338	12339

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-19dox	BGRSDLV02-20dox
Sample #	19	20
Sample Name	CNBP-BGRSDLV02-19dox	CNBP-BGRSDLV02-20dox
Sample_Name_Alias
Index Well Position	C03	D03
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	287	292
Peak_Molarity	84.50	88.70
libSampleQC_DNA_Well	DNA_Library_set65/set1/C3.png	DNA_Library_set65/set1/D3.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set65/set1/C3.png	RNA_Library_set65/set1/D3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-19dox	BGRSDLV02-20dox
RBP	CNBP	CNBP
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	3940	3941

Sequencing Information

	BGRSDLV02-19dox	BGRSDLV02-20dox
Sample_ID	BGRSDLV02-19dox	BGRSDLV02-20dox
Sample Name	CNBP-BGRSDLV02-19dox	CNBP-BGRSDLV02-20dox
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	29,802,377	26,822,329
total_aligned_reads	26,666,686	23,943,090
unique_aligned_reads	24,891,667	22,373,374
percent_uniqueAligned	0.83522	0.83413
correlation_replicates	0.995524	0.995524
spikein_reads	1,528	784
percent_spikeins	0.00005	0.00003
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2687	2688

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
CNBP-BGRSDLV02-19dox_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2687	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	8756
CNBP-BGRSDLV02-19dox_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2687	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	8832
CNBP-BGRSDLV02-19dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2687					GRCh38	V40	CNBP-BGRSDLV02-19dox_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNBP-BGRSDLV02-19dox_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9321
CNBP-BGRSDLV02-19dox_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	2687					GRCh38	V40	CNBP-BGRSDLV02-19dox/Aligned.sortedByCoord.out.bam		ENCORE2	9397
CNBP-BGRSDLV02-19dox_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	2687					GRCh38	V40	CNBP-BGRSDLV02-19dox/Aligned.sortedByCoord.out.bam		ENCORE2	9473
CNBP-BGRSDLV02-19dox_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	2687					GRCh38	V40	CNBP-BGRSDLV02-19dox/Aligned.sortedByCoord.out.bam		ENCORE2	9549
CNBP-BGRSDLV02-19dox_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	2687					GRCh38	V40	CNBP-BGRSDLV02-19dox/Aligned.sortedByCoord.out.bam		ENCORE2	9625
CNBP-BGRSDLV02-19dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2687					GRCh38	V40	CNBP-BGRSDLV02-19dox_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNBP-BGRSDLV02-19dox_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9701
CNBP-BGRSDLV02-20dox_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2688	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	8757
CNBP-BGRSDLV02-20dox_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2688	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	8833
CNBP-BGRSDLV02-20dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2688					GRCh38	V40	CNBP-BGRSDLV02-20dox_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNBP-BGRSDLV02-20dox_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9322
CNBP-BGRSDLV02-20dox_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	2688					GRCh38	V40	CNBP-BGRSDLV02-20dox/Aligned.sortedByCoord.out.bam		ENCORE2	9398
CNBP-BGRSDLV02-20dox_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	2688					GRCh38	V40	CNBP-BGRSDLV02-20dox/Aligned.sortedByCoord.out.bam		ENCORE2	9474
CNBP-BGRSDLV02-20dox_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	2688					GRCh38	V40	CNBP-BGRSDLV02-20dox/Aligned.sortedByCoord.out.bam		ENCORE2	9550
CNBP-BGRSDLV02-20dox_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	2688					GRCh38	V40	CNBP-BGRSDLV02-20dox/Aligned.sortedByCoord.out.bam		ENCORE2	9626
CNBP-BGRSDLV02-20dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2688					GRCh38	V40	CNBP-BGRSDLV02-20dox_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNBP-BGRSDLV02-20dox_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9702