CPSF4 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV03-17	BGRSLV03-18
idx	0	0
TRCN#_or_BGC#	TRCN0000293550	TRCN0000293550
shRNA_or_gRNA_sequence	CCGGACGCCAACAGATGCACCAAAGCTCGAGCTTTGGTGCATCTGTTGGCGTTTTTTG	CCGGACGCCAACAGATGCACCAAAGCTCGAGCTTTGGTGCATCTGTTGGCGTTTTTTG
PAM
Name	CPSF4	CPSF4
Sample_ID	BGRSLV03-17	BGRSLV03-18
transduction_Date	1/30/23	1/30/23
days	D4	D4
RBP_name	CPSF4	CPSF4
qPCR_result	64.3	61.7
Ave_qPCR	63.0
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	8327	8328

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV03-17	BGRSLV03-18
Sample_ID	BGRSLV03-17	BGRSLV03-18
Sample Name
Sample Name	CPSF4-BGRSLV03-17	CPSF4-BGRSLV03-18
RBP	CPSF4	CPSF4
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	11382	11383

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV03-17	BGRSLV03-18
Sample #	13	14
Sample Name	CPSF4-BGRSLV03-17	CPSF4-BGRSLV03-18
Sample_Name_Alias
Index Well Position	E08	F08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-15	2023-02-15
Lib_ID	Lib-230215	Lib-230215
Tecan_Location
Tecan
Tecan_date
Size_bp	294	296
Peak_Molarity	81.80	143.00
libSampleQC_DNA_Well	DNA_Library_set58/set1/E8.png	DNA_Library_set58/set1/F8.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set58/set1/E2.png	RNA_Library_set58/set1/F2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-17	2023-02-17
Sample_ID	BGRSLV03-17	BGRSLV03-18
RBP	CPSF4	CPSF4
Batch_ID	BGRSLV03	BGRSLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3520	3521

Sequencing Information

	BGRSLV03-17	BGRSLV03-18
Sample_ID	BGRSLV03-17	BGRSLV03-18
Sample Name	CPSF4-BGRSLV03-17	CPSF4-BGRSLV03-18
Pool ID	Pool-230217	Pool-230217
LocalServer_folder	set58	set58
total_reads	44,325,743	44,315,033
total_aligned_reads	39,318,228	39,404,582
unique_aligned_reads	36,507,239	36,923,493
percent_uniqueAligned	0.82361	0.83320
correlation_replicates	0.996503	0.996503
spikein_reads	255,032	255,790
percent_spikeins	0.00575	0.00577
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2391	2392

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-BGRSLV03-17_S147_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2391	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8136
CPSF4-BGRSLV03-17_S147_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2391	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8178
CPSF4-BGRSLV03-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2391					GRCh38	V40	CPSF4-BGRSLV03-17_S147_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4-BGRSLV03-17_S147_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11257
CPSF4-BGRSLV03-17_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2391					GRCh38	V40	CPSF4-BGRSLV03-17/Aligned.sortedByCoord.out.bam		ENCORE2	11299
CPSF4-BGRSLV03-17_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2391					GRCh38	V40	CPSF4-BGRSLV03-17/Aligned.sortedByCoord.out.bam		ENCORE2	11341
CPSF4-BGRSLV03-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2391					GRCh38	V40	CPSF4-BGRSLV03-17/Aligned.sortedByCoord.out.bam		ENCORE2	11383
CPSF4-BGRSLV03-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2391					GRCh38	V40	CPSF4-BGRSLV03-17/Aligned.sortedByCoord.out.bam		ENCORE2	11425
CPSF4-BGRSLV03-17_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2391					GRCh38	V40	CPSF4-BGRSLV03-17_S147_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4-BGRSLV03-17_S147_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11467
CPSF4-BGRSLV03-18_S148_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2392	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8137
CPSF4-BGRSLV03-18_S148_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2392	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8179
CPSF4-BGRSLV03-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2392					GRCh38	V40	CPSF4-BGRSLV03-18_S148_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4-BGRSLV03-18_S148_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11258
CPSF4-BGRSLV03-18_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2392					GRCh38	V40	CPSF4-BGRSLV03-18/Aligned.sortedByCoord.out.bam		ENCORE2	11300
CPSF4-BGRSLV03-18_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2392					GRCh38	V40	CPSF4-BGRSLV03-18/Aligned.sortedByCoord.out.bam		ENCORE2	11342
CPSF4-BGRSLV03-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2392					GRCh38	V40	CPSF4-BGRSLV03-18/Aligned.sortedByCoord.out.bam		ENCORE2	11384
CPSF4-BGRSLV03-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2392					GRCh38	V40	CPSF4-BGRSLV03-18/Aligned.sortedByCoord.out.bam		ENCORE2	11426
CPSF4-BGRSLV03-18_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2392					GRCh38	V40	CPSF4-BGRSLV03-18_S148_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4-BGRSLV03-18_S148_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11468