WBP4 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV08-3	BGRSLV08-4
idx	0	0
TRCN#_or_BGC#	TRCN0000243159	TRCN0000243159
shRNA_or_gRNA_sequence	CCGGGCAACGAGGTGATGATCAATACTCGAGTATTGATCATCACCTCGTTGCTTTTTG	CCGGGCAACGAGGTGATGATCAATACTCGAGTATTGATCATCACCTCGTTGCTTTTTG
PAM
Name	WBP4	WBP4
Sample_ID	BGRSLV08-3	BGRSLV08-4
transduction_Date	4/22/23	4/22/23
days	D4	D4
RBP_name	WBP4	WBP4
qPCR_result	60.8	61.3
Ave_qPCR	61.0
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	8652	8653

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV08-3	BGRSLV08-4
Sample_ID	BGRSLV08-3	BGRSLV08-4
Sample Name
Sample Name	WBP4-BGRSLV08-3	WBP4-BGRSLV08-4
RBP	WBP4	WBP4
Cell_Line	Ribo-STAMP-293T	Ribo-STAMP-293T
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	11776	11777

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV08-3	BGRSLV08-4
Sample #	41	42
Sample Name	WBP4-BGRSLV08-3	WBP4-BGRSLV08-4
Sample_Name_Alias
Index Well Position	A06	B06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-05-02	2023-05-02
Lib_ID	Lib-230502	Lib-230502
Tecan_Location
Tecan
Tecan_date
Size_bp	287	291
Peak_Molarity	36.00	52.60
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/A6.png	DNA_Library_set60-62/set4/B6.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set60-62/set2/A6.png	RNA_Library_set60-62/set2/B6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BGRSLV08-3	BGRSLV08-4
RBP	WBP4	WBP4
Batch_ID	BGRSLV08	BGRSLV08
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3724	3725

Sequencing Information

	BGRSLV08-3	BGRSLV08-4
Sample_ID	BGRSLV08-3	BGRSLV08-4
Sample Name	WBP4-BGRSLV08-3	WBP4-BGRSLV08-4
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_R	set62_R
total_reads	22,052,109	21,338,194
total_aligned_reads	15,180,201	16,849,801
unique_aligned_reads	14,214,591	15,815,765
percent_uniqueAligned	0.64459	0.74120
correlation_replicates	0.992859	0.992859
spikein_reads	45,172	24,932
percent_spikeins	0.00205	0.00117
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2595	2596

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-BGRSLV08-3_S41_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2595	NovaSeq6000	100	paired-ended	1				NT-BGRSLV08-1_S39_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7892
WBP4-BGRSLV08-3_S41_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2595	NovaSeq6000	100	paired-ended	2				NT-BGRSLV08-1_S39_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7936
WBP4-BGRSLV08-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2595					GRCh38	V40	WBP4-BGRSLV08-3_S41_L003_R1_001.filtered.trimmed.paired.fastq.gz,WBP4-BGRSLV08-3_S41_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10197
WBP4-BGRSLV08-3_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2595					GRCh38	V40	WBP4-BGRSLV08-3/Aligned.sortedByCoord.out.bam		ENCORE2	10241
WBP4-BGRSLV08-3_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2595					GRCh38	V40	WBP4-BGRSLV08-3/Aligned.sortedByCoord.out.bam		ENCORE2	10285
WBP4-BGRSLV08-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2595					GRCh38	V40	WBP4-BGRSLV08-3/Aligned.sortedByCoord.out.bam		ENCORE2	10329
WBP4-BGRSLV08-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2595					GRCh38	V40	WBP4-BGRSLV08-3/Aligned.sortedByCoord.out.bam		ENCORE2	10373
WBP4-BGRSLV08-3_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2595					GRCh38	V40	WBP4-BGRSLV08-3_S41_L003_R1_001.filtered.trimmed.paired.fastq.gz,WBP4-BGRSLV08-3_S41_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10417
WBP4-BGRSLV08-4_S42_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2596	NovaSeq6000	100	paired-ended	1				NT-BGRSLV08-1_S39_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7893
WBP4-BGRSLV08-4_S42_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2596	NovaSeq6000	100	paired-ended	2				NT-BGRSLV08-1_S39_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7937
WBP4-BGRSLV08-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2596					GRCh38	V40	WBP4-BGRSLV08-4_S42_L003_R1_001.filtered.trimmed.paired.fastq.gz,WBP4-BGRSLV08-4_S42_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10198
WBP4-BGRSLV08-4_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2596					GRCh38	V40	WBP4-BGRSLV08-4/Aligned.sortedByCoord.out.bam		ENCORE2	10242
WBP4-BGRSLV08-4_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2596					GRCh38	V40	WBP4-BGRSLV08-4/Aligned.sortedByCoord.out.bam		ENCORE2	10286
WBP4-BGRSLV08-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2596					GRCh38	V40	WBP4-BGRSLV08-4/Aligned.sortedByCoord.out.bam		ENCORE2	10330
WBP4-BGRSLV08-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2596					GRCh38	V40	WBP4-BGRSLV08-4/Aligned.sortedByCoord.out.bam		ENCORE2	10374
WBP4-BGRSLV08-4_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2596					GRCh38	V40	WBP4-BGRSLV08-4_S42_L003_R1_001.filtered.trimmed.paired.fastq.gz,WBP4-BGRSLV08-4_S42_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10418