CPSF4L RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV04-107dox	BGRSDLV04-108dox
idx	0	0
TRCN#_or_BGC#	TRCN0000240294	TRCN0000240294
shRNA_or_gRNA_sequence	CCGGGGACGGTCCTCTGTGTAAATACTCGAGTATTTACACAGAGGACCGTCCTTTTTG	CCGGGGACGGTCCTCTGTGTAAATACTCGAGTATTTACACAGAGGACCGTCCTTTTTG
PAM
Name	CPSF4L	CPSF4L
Sample_ID	BGRSDLV04-107dox	BGRSDLV04-108dox
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	9471	9472

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV04-107dox	BGRSDLV04-108dox
Sample_ID	BGRSDLV04-107dox	BGRSDLV04-108dox
Sample Name
Sample Name	CPSF4L-BGRSDLV04-107dox	CPSF4L-BGRSDLV04-108dox
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	12708	12709

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV04-107dox	BGRSDLV04-108dox
Sample #	63	64
Sample Name	CPSF4L-BGRSDLV04-107dox	CPSF4L-BGRSDLV04-108dox
Sample_Name_Alias
Index Well Position	G08	H08
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	286	293
Peak_Molarity	66.40	49.50
libSampleQC_DNA_Well	DNA_Library_set68/set1/G8.png	DNA_Library_set68/set1/H8.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set68/set1/G8.png	RNA_Library_set68/set1/H8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-11-16	2023-11-16
Sample_ID	BGRSDLV04-107dox	BGRSDLV04-108dox
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	4136	4137

Sequencing Information

	BGRSDLV04-107dox	BGRSDLV04-108dox
Sample_ID	BGRSDLV04-107dox	BGRSDLV04-108dox
Sample Name	CPSF4L-BGRSDLV04-107dox	CPSF4L-BGRSDLV04-108dox
Pool ID	Pool-231116	Pool-231116
LocalServer_folder	set68	set68
total_reads	37,924,526	39,088,646
total_aligned_reads	35,060,130	36,146,877
unique_aligned_reads	33,114,481	34,115,429
percent_uniqueAligned	0.87317	0.87277
correlation_replicates	0.996420	0.996420
spikein_reads	1,972	7,956
percent_spikeins	0.00005	0.00020
original_ReadLength	151	151
QC_Status	Submitted	Submitted
ID	2899	2900

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-BGRSDLV04-107dox_S63_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2899	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27631
CPSF4L-BGRSDLV04-107dox_S63_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2899	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27695
CPSF4L-BGRSDLV04-107dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2899					GRCh38	V40	CPSF4L-BGRSDLV04-107dox_S63_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4L-BGRSDLV04-107dox_S63_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27759
CPSF4L-BGRSDLV04-107dox_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	2899					GRCh38	V40	CPSF4L-BGRSDLV04-107dox/Aligned.sortedByCoord.out.bam		ENCORE2	27823
CPSF4L-BGRSDLV04-107dox_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	2899					GRCh38	V40	CPSF4L-BGRSDLV04-107dox/Aligned.sortedByCoord.out.bam		ENCORE2	27887
CPSF4L-BGRSDLV04-107dox_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	2899					GRCh38	V40	CPSF4L-BGRSDLV04-107dox/Aligned.sortedByCoord.out.bam		ENCORE2	27951
CPSF4L-BGRSDLV04-107dox_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	2899					GRCh38	V40	CPSF4L-BGRSDLV04-107dox/Aligned.sortedByCoord.out.bam		ENCORE2	28015
CPSF4L-BGRSDLV04-107dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2899					GRCh38	V40	CPSF4L-BGRSDLV04-107dox_S63_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4L-BGRSDLV04-107dox_S63_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28079
CPSF4L-BGRSDLV04-108dox_S64_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2900	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27632
CPSF4L-BGRSDLV04-108dox_S64_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2900	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27696
CPSF4L-BGRSDLV04-108dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2900					GRCh38	V40	CPSF4L-BGRSDLV04-108dox_S64_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4L-BGRSDLV04-108dox_S64_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27760
CPSF4L-BGRSDLV04-108dox_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	2900					GRCh38	V40	CPSF4L-BGRSDLV04-108dox/Aligned.sortedByCoord.out.bam		ENCORE2	27824
CPSF4L-BGRSDLV04-108dox_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	2900					GRCh38	V40	CPSF4L-BGRSDLV04-108dox/Aligned.sortedByCoord.out.bam		ENCORE2	27888
CPSF4L-BGRSDLV04-108dox_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	2900					GRCh38	V40	CPSF4L-BGRSDLV04-108dox/Aligned.sortedByCoord.out.bam		ENCORE2	27952
CPSF4L-BGRSDLV04-108dox_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	2900					GRCh38	V40	CPSF4L-BGRSDLV04-108dox/Aligned.sortedByCoord.out.bam		ENCORE2	28016
CPSF4L-BGRSDLV04-108dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2900					GRCh38	V40	CPSF4L-BGRSDLV04-108dox_S64_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4L-BGRSDLV04-108dox_S64_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28080