WBP4 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV03-43dox	BGRSDLV03-44dox
idx	0	0
TRCN#_or_BGC#	TRCN0000243159	TRCN0000243159
shRNA_or_gRNA_sequence	CCGGGCAACGAGGTGATGATCAATACTCGAGTATTGATCATCACCTCGTTGCTTTTTG	CCGGGCAACGAGGTGATGATCAATACTCGAGTATTGATCATCACCTCGTTGCTTTTTG
PAM
Name	WBP4	WBP4
Sample_ID	BGRSDLV03-43dox	BGRSDLV03-44dox
transduction_Date	9/29/23	9/29/23
days	4 days	4 days
RBP_name	WBP4	WBP4
qPCR_result	62.8	61.3
Ave_qPCR	62.0
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	9357	9358

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV03-43dox	BGRSDLV03-44dox
Sample_ID	BGRSDLV03-43dox	BGRSDLV03-44dox
Sample Name
Sample Name	WBP4-BGRSDLV03-43dox	WBP4-BGRSDLV03-44dox
RBP	WBP4	WBP4
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12632	12633

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV03-43dox	BGRSDLV03-44dox
Sample #	35	36
Sample Name	WBP4-BGRSDLV03-43dox	WBP4-BGRSDLV03-44dox
Sample_Name_Alias
Index Well Position	C09	D09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-10-17	2023-10-17
Lib_ID	Lib-231017	Lib-231017
Tecan_Location
Tecan
Tecan_date
Size_bp	268	274
Peak_Molarity	83.70	76.20
libSampleQC_DNA_Well	DNA_Library_set66/set1/C10.png	DNA_Library_set66/set1/D10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set66/set1/C5.png	RNA_Library_set66/set1/D5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-18	2023-10-18
Sample_ID	BGRSDLV03-43dox	BGRSDLV03-44dox
RBP	WBP4	WBP4
Batch_ID	BGRSDLV03	BGRSDLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4068	4069

Sequencing Information

	BGRSDLV03-43dox	BGRSDLV03-44dox
Sample_ID	BGRSDLV03-43dox	BGRSDLV03-44dox
Sample Name	WBP4-BGRSDLV03-43dox	WBP4-BGRSDLV03-44dox
Pool ID	Pool-231018	Pool-231018
LocalServer_folder	set66	set66
total_reads	15,969,112	12,557,458
total_aligned_reads	14,501,542	11,224,740
unique_aligned_reads	13,415,160	10,415,506
percent_uniqueAligned	0.84007	0.82943
correlation_replicates	0.997669	0.997669
spikein_reads	2,162	730
percent_spikeins	0.00014	0.00006
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2787	2788

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
WBP4-BGRSDLV03-43dox_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2787	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8940
WBP4-BGRSDLV03-43dox_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2787	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8980
WBP4-BGRSDLV03-43dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2787					GRCh38	V40	WBP4-BGRSDLV03-43dox_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,WBP4-BGRSDLV03-43dox_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9020
WBP4-BGRSDLV03-43dox_Signal.Unique.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2787					GRCh38	V40	WBP4-BGRSDLV03-43dox/Aligned.sortedByCoord.out.bam		ENCORE2	9060
WBP4-BGRSDLV03-43dox_Signal.Unique.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2787					GRCh38	V40	WBP4-BGRSDLV03-43dox/Aligned.sortedByCoord.out.bam		ENCORE2	9100
WBP4-BGRSDLV03-43dox_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2787					GRCh38	V40	WBP4-BGRSDLV03-43dox/Aligned.sortedByCoord.out.bam		ENCORE2	9140
WBP4-BGRSDLV03-43dox_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2787					GRCh38	V40	WBP4-BGRSDLV03-43dox/Aligned.sortedByCoord.out.bam		ENCORE2	9180
WBP4-BGRSDLV03-43dox_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2787					GRCh38	V40	WBP4-BGRSDLV03-43dox_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,WBP4-BGRSDLV03-43dox_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9220
WBP4-BGRSDLV03-44dox_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2788	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8941
WBP4-BGRSDLV03-44dox_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2788	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8981
WBP4-BGRSDLV03-44dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2788					GRCh38	V40	WBP4-BGRSDLV03-44dox_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,WBP4-BGRSDLV03-44dox_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9021
WBP4-BGRSDLV03-44dox_Signal.Unique.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2788					GRCh38	V40	WBP4-BGRSDLV03-44dox/Aligned.sortedByCoord.out.bam		ENCORE2	9061
WBP4-BGRSDLV03-44dox_Signal.Unique.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2788					GRCh38	V40	WBP4-BGRSDLV03-44dox/Aligned.sortedByCoord.out.bam		ENCORE2	9101
WBP4-BGRSDLV03-44dox_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2788					GRCh38	V40	WBP4-BGRSDLV03-44dox/Aligned.sortedByCoord.out.bam		ENCORE2	9141
WBP4-BGRSDLV03-44dox_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2788					GRCh38	V40	WBP4-BGRSDLV03-44dox/Aligned.sortedByCoord.out.bam		ENCORE2	9181
WBP4-BGRSDLV03-44dox_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2788					GRCh38	V40	WBP4-BGRSDLV03-44dox_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,WBP4-BGRSDLV03-44dox_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9221