CPSF4 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV03-9	BGRSDLV03-10
idx	0	0
TRCN#_or_BGC#	TRCN0000293550	TRCN0000293550
shRNA_or_gRNA_sequence	CCGGACGCCAACAGATGCACCAAAGCTCGAGCTTTGGTGCATCTGTTGGCGTTTTTTG	CCGGACGCCAACAGATGCACCAAAGCTCGAGCTTTGGTGCATCTGTTGGCGTTTTTTG
PAM
Name	CPSF4	CPSF4
Sample_ID	BGRSDLV03-9	BGRSDLV03-10
transduction_Date	9/29/23	9/29/23
days	4 days	4 days
RBP_name	CPSF4	CPSF4
qPCR_result	68.6	69.4
Ave_qPCR	69.0
RT-qPCR_primer-F	agacacagcctccagcaaag
RT-qPCR_primer-R	aactggatcaaggaggacga
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	9323	9324

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV03-9	BGRSDLV03-10
Sample_ID	BGRSDLV03-9	BGRSDLV03-10
Sample Name
Sample Name	CPSF4-BGRSDLV03-9	CPSF4-BGRSDLV03-10
RBP	CPSF4	CPSF4
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12606	12607

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV03-9	BGRSDLV03-10
Sample #	9	10
Sample Name	CPSF4-BGRSDLV03-9	CPSF4-BGRSDLV03-10
Sample_Name_Alias
Index Well Position	A06	B06
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	279	263
Peak_Molarity	64.90	61.50
libSampleQC_DNA_Well	DNA_Library_set66/set1/A7.png	DNA_Library_set66/set1/B7.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set66/set1/A2.png	RNA_Library_set66/set1/B2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-18	2023-10-18
Sample_ID	BGRSDLV03-9	BGRSDLV03-10
RBP	CPSF4	CPSF4
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	4042	4043

Sequencing Information

	BGRSDLV03-9	BGRSDLV03-10
Sample_ID	BGRSDLV03-9	BGRSDLV03-10
Sample Name	CPSF4-BGRSDLV03-9	CPSF4-BGRSDLV03-10
Pool ID	Pool-231018	Pool-231018
LocalServer_folder	set66	set66
total_reads	13,066,408	14,135,339
total_aligned_reads	11,346,357	12,348,723
unique_aligned_reads	10,548,066	11,474,791
percent_uniqueAligned	0.80727	0.81178
correlation_replicates	0.997848	0.997848
spikein_reads	3,070	292
percent_spikeins	0.00023	0.00002
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2761	2762

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
CPSF4-BGRSDLV03-9_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2761	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	8913
CPSF4-BGRSDLV03-9_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2761	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	8953
CPSF4-BGRSDLV03-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2761					GRCh38	V40	CPSF4-BGRSDLV03-9_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4-BGRSDLV03-9_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	8993
CPSF4-BGRSDLV03-9_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	2761					GRCh38	V40	CPSF4-BGRSDLV03-9/Aligned.sortedByCoord.out.bam		ENCORE2	9033
CPSF4-BGRSDLV03-9_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	2761					GRCh38	V40	CPSF4-BGRSDLV03-9/Aligned.sortedByCoord.out.bam		ENCORE2	9073
CPSF4-BGRSDLV03-9_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	2761					GRCh38	V40	CPSF4-BGRSDLV03-9/Aligned.sortedByCoord.out.bam		ENCORE2	9113
CPSF4-BGRSDLV03-9_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	2761					GRCh38	V40	CPSF4-BGRSDLV03-9/Aligned.sortedByCoord.out.bam		ENCORE2	9153
CPSF4-BGRSDLV03-9_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2761					GRCh38	V40	CPSF4-BGRSDLV03-9_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4-BGRSDLV03-9_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9193
CPSF4-BGRSDLV03-10_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2762	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	8910
CPSF4-BGRSDLV03-10_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2762	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	8950
CPSF4-BGRSDLV03-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2762					GRCh38	V40	CPSF4-BGRSDLV03-10_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4-BGRSDLV03-10_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	8990
CPSF4-BGRSDLV03-10_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	2762					GRCh38	V40	CPSF4-BGRSDLV03-10/Aligned.sortedByCoord.out.bam		ENCORE2	9030
CPSF4-BGRSDLV03-10_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	2762					GRCh38	V40	CPSF4-BGRSDLV03-10/Aligned.sortedByCoord.out.bam		ENCORE2	9070
CPSF4-BGRSDLV03-10_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	2762					GRCh38	V40	CPSF4-BGRSDLV03-10/Aligned.sortedByCoord.out.bam		ENCORE2	9110
CPSF4-BGRSDLV03-10_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	2762					GRCh38	V40	CPSF4-BGRSDLV03-10/Aligned.sortedByCoord.out.bam		ENCORE2	9150
CPSF4-BGRSDLV03-10_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2762					GRCh38	V40	CPSF4-BGRSDLV03-10_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4-BGRSDLV03-10_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9190