CPSF4L RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV04-105	BGRSDLV04-106
idx	0	0
TRCN#_or_BGC#	TRCN0000240294	TRCN0000240294
shRNA_or_gRNA_sequence	CCGGGGACGGTCCTCTGTGTAAATACTCGAGTATTTACACAGAGGACCGTCCTTTTTG	CCGGGGACGGTCCTCTGTGTAAATACTCGAGTATTTACACAGAGGACCGTCCTTTTTG
PAM
Name	CPSF4L	CPSF4L
Sample_ID	BGRSDLV04-105	BGRSDLV04-106
transduction_Date	10/16/23	10/16/23
days	4 days	4 days
RBP_name	CPSF4L	CPSF4L
qPCR_result
Ave_qPCR
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	9469	9470

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV04-105	BGRSDLV04-106
Sample_ID	BGRSDLV04-105	BGRSDLV04-106
Sample Name
Sample Name	CPSF4L-BGRSDLV04-105	CPSF4L-BGRSDLV04-106
RBP	CPSF4L	CPSF4L
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12706	12707

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV04-105	BGRSDLV04-106
Sample #	61	62
Sample Name	CPSF4L-BGRSDLV04-105	CPSF4L-BGRSDLV04-106
Sample_Name_Alias
Index Well Position	E08	F08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-11-14	2023-11-14
Lib_ID	Lib-231114	Lib-231114
Tecan_Location
Tecan
Tecan_date
Size_bp	291	299
Peak_Molarity	40.90	57.50
libSampleQC_DNA_Well	DNA_Library_set68/set1/E8.png	DNA_Library_set68/set1/F8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set68/set1/E8.png	RNA_Library_set68/set1/F8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-11-16	2023-11-16
Sample_ID	BGRSDLV04-105	BGRSDLV04-106
RBP	CPSF4L	CPSF4L
Batch_ID	BGRSDLV04	BGRSDLV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4134	4135

Sequencing Information

	BGRSDLV04-105	BGRSDLV04-106
Sample_ID	BGRSDLV04-105	BGRSDLV04-106
Sample Name	CPSF4L-BGRSDLV04-105	CPSF4L-BGRSDLV04-106
Pool ID	Pool-231116	Pool-231116
LocalServer_folder	set68	set68
total_reads	47,564,466	42,623,935
total_aligned_reads	44,307,378	39,693,522
unique_aligned_reads	41,821,511	37,476,620
percent_uniqueAligned	0.87926	0.87924
correlation_replicates	0.997070	0.997070
spikein_reads	3,486	4,842
percent_spikeins	0.00007	0.00011
original_ReadLength	151	151
QC_Status	Submitted	Submitted
ID	2897	2898

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
CPSF4L-BGRSDLV04-105_S61_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2897	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27629
CPSF4L-BGRSDLV04-105_S61_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2897	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27693
CPSF4L-BGRSDLV04-105_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2897					GRCh38	V40	CPSF4L-BGRSDLV04-105_S61_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4L-BGRSDLV04-105_S61_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27757
CPSF4L-BGRSDLV04-105_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2897					GRCh38	V40	CPSF4L-BGRSDLV04-105/Aligned.sortedByCoord.out.bam		ENCORE2	27821
CPSF4L-BGRSDLV04-105_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2897					GRCh38	V40	CPSF4L-BGRSDLV04-105/Aligned.sortedByCoord.out.bam		ENCORE2	27885
CPSF4L-BGRSDLV04-105_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2897					GRCh38	V40	CPSF4L-BGRSDLV04-105/Aligned.sortedByCoord.out.bam		ENCORE2	27949
CPSF4L-BGRSDLV04-105_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2897					GRCh38	V40	CPSF4L-BGRSDLV04-105/Aligned.sortedByCoord.out.bam		ENCORE2	28013
CPSF4L-BGRSDLV04-105_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2897					GRCh38	V40	CPSF4L-BGRSDLV04-105_S61_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4L-BGRSDLV04-105_S61_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28077
CPSF4L-BGRSDLV04-106_S62_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2898	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27630
CPSF4L-BGRSDLV04-106_S62_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2898	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27694
CPSF4L-BGRSDLV04-106_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2898					GRCh38	V40	CPSF4L-BGRSDLV04-106_S62_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4L-BGRSDLV04-106_S62_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27758
CPSF4L-BGRSDLV04-106_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2898					GRCh38	V40	CPSF4L-BGRSDLV04-106/Aligned.sortedByCoord.out.bam		ENCORE2	27822
CPSF4L-BGRSDLV04-106_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2898					GRCh38	V40	CPSF4L-BGRSDLV04-106/Aligned.sortedByCoord.out.bam		ENCORE2	27886
CPSF4L-BGRSDLV04-106_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2898					GRCh38	V40	CPSF4L-BGRSDLV04-106/Aligned.sortedByCoord.out.bam		ENCORE2	27950
CPSF4L-BGRSDLV04-106_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2898					GRCh38	V40	CPSF4L-BGRSDLV04-106/Aligned.sortedByCoord.out.bam		ENCORE2	28014
CPSF4L-BGRSDLV04-106_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2898					GRCh38	V40	CPSF4L-BGRSDLV04-106_S62_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4L-BGRSDLV04-106_S62_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28078