WBP4 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV03-41	BGRSDLV03-42
idx	0	0
TRCN#_or_BGC#	TRCN0000243159	TRCN0000243159
shRNA_or_gRNA_sequence	CCGGGCAACGAGGTGATGATCAATACTCGAGTATTGATCATCACCTCGTTGCTTTTTG	CCGGGCAACGAGGTGATGATCAATACTCGAGTATTGATCATCACCTCGTTGCTTTTTG
PAM
Name	WBP4	WBP4
Sample_ID	BGRSDLV03-41	BGRSDLV03-42
transduction_Date	9/29/23	9/29/23
days	4 days	4 days
RBP_name	WBP4	WBP4
qPCR_result	67.1	72.2
Ave_qPCR	69.7
RT-qPCR_primer-F	ttctgatggggaacaggaag
RT-qPCR_primer-R	ttctgggtcacttcctccat
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	9355	9356

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV03-41	BGRSDLV03-42
Sample_ID	BGRSDLV03-41	BGRSDLV03-42
Sample Name
Sample Name	WBP4-BGRSDLV03-41	WBP4-BGRSDLV03-42
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	12630	12631

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV03-41	BGRSDLV03-42
Sample #	33	34
Sample Name	WBP4-BGRSDLV03-41	WBP4-BGRSDLV03-42
Sample_Name_Alias
Index Well Position	A09	B09
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	271	266
Peak_Molarity	62.30	79.00
libSampleQC_DNA_Well	DNA_Library_set66/set1/A10.png	DNA_Library_set66/set1/B10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set66/set1/A5.png	RNA_Library_set66/set1/B5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-18	2023-10-18
Sample_ID	BGRSDLV03-41	BGRSDLV03-42
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	4066	4067

Sequencing Information

	BGRSDLV03-41	BGRSDLV03-42
Sample_ID	BGRSDLV03-41	BGRSDLV03-42
Sample Name	WBP4-BGRSDLV03-41	WBP4-BGRSDLV03-42
Pool ID	Pool-231018	Pool-231018
LocalServer_folder	set66	set66
total_reads	13,070,036	22,165,152
total_aligned_reads	11,428,099	19,787,044
unique_aligned_reads	10,635,280	18,345,141
percent_uniqueAligned	0.81371	0.82766
correlation_replicates	0.998608	0.998608
spikein_reads	5,204	2,538
percent_spikeins	0.00040	0.00011
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2785	2786

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-BGRSDLV03-41_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2785	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8938
WBP4-BGRSDLV03-41_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2785	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8978
WBP4-BGRSDLV03-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2785					GRCh38	V40	WBP4-BGRSDLV03-41_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,WBP4-BGRSDLV03-41_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9018
WBP4-BGRSDLV03-41_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	2785					GRCh38	V40	WBP4-BGRSDLV03-41/Aligned.sortedByCoord.out.bam		ENCORE2	9058
WBP4-BGRSDLV03-41_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	2785					GRCh38	V40	WBP4-BGRSDLV03-41/Aligned.sortedByCoord.out.bam		ENCORE2	9098
WBP4-BGRSDLV03-41_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	2785					GRCh38	V40	WBP4-BGRSDLV03-41/Aligned.sortedByCoord.out.bam		ENCORE2	9138
WBP4-BGRSDLV03-41_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	2785					GRCh38	V40	WBP4-BGRSDLV03-41/Aligned.sortedByCoord.out.bam		ENCORE2	9178
WBP4-BGRSDLV03-41_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2785					GRCh38	V40	WBP4-BGRSDLV03-41_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,WBP4-BGRSDLV03-41_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9218
WBP4-BGRSDLV03-42_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2786	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8939
WBP4-BGRSDLV03-42_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2786	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8979
WBP4-BGRSDLV03-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2786					GRCh38	V40	WBP4-BGRSDLV03-42_merged_R1_001.filtered.trimmed.paired.fastq.gz,WBP4-BGRSDLV03-42_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9019
WBP4-BGRSDLV03-42_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	2786					GRCh38	V40	WBP4-BGRSDLV03-42/Aligned.sortedByCoord.out.bam		ENCORE2	9059
WBP4-BGRSDLV03-42_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	2786					GRCh38	V40	WBP4-BGRSDLV03-42/Aligned.sortedByCoord.out.bam		ENCORE2	9099
WBP4-BGRSDLV03-42_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	2786					GRCh38	V40	WBP4-BGRSDLV03-42/Aligned.sortedByCoord.out.bam		ENCORE2	9139
WBP4-BGRSDLV03-42_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	2786					GRCh38	V40	WBP4-BGRSDLV03-42/Aligned.sortedByCoord.out.bam		ENCORE2	9179
WBP4-BGRSDLV03-42_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2786					GRCh38	V40	WBP4-BGRSDLV03-42_merged_R1_001.filtered.trimmed.paired.fastq.gz,WBP4-BGRSDLV03-42_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9219