CPSF6 RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV05-3	BG293LV05-4
idx	0	0
TRCN#_or_BGC#	TRCN0000000154	TRCN0000000154
shRNA_or_gRNA_sequence
PAM
Name	CPSF6	CPSF6
Sample_ID	BG293LV05-3	BG293LV05-4
transduction_Date	12/18/23	12/18/23
days	D4	D4
RBP_name	CPSF6	CPSF6
qPCR_result	77.6	84.9
Ave_qPCR	81.25
RT-qPCR_primer-F	TCTTTGCAAGATTGCCTTCA
RT-qPCR_primer-R	TCGTGATCTACTATGGTCCCTC
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	9975	9976

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV05-3	BG293LV05-4
Sample_ID	BG293LV05-3	BG293LV05-4
Sample Name
Sample Name	CPSF6-BG293LV05-3	CPSF6-BG293LV05-4
RBP	CPSF6	CPSF6
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2024-05-07	2024-05-07
Project	ENCORE2	ENCORE2
Note
ID	12836	12837

Library-Prep
Sequencing

Library-Prep Information

	BG293LV05-3	BG293LV05-4
Sample #	3	4
Sample Name	CPSF6-BG293LV05-3	CPSF6-BG293LV05-4
Sample_Name_Alias
Index Well Position	C07	D07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-01-16	2024-01-16
Lib_ID	Lib-240116	Lib-240116
Tecan_Location
Tecan
Tecan_date
Size_bp	281	281
Peak_Molarity	61.60	61.90
libSampleQC_DNA_Well	DNA_Library_set69/set1/C1.png	DNA_Library_set69/set1/D1.png
RIN	9.7	9.9
libSample_RNA_Well	RNA_Library_set69/set1/C6.png	RNA_Library_set69/set1/D6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-01-19	2024-01-19
Sample_ID	BG293LV05-3	BG293LV05-4
RBP	CPSF6	CPSF6
Batch_ID	BG293LV05	BG293LV05
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4184	4185

Sequencing Information

	BG293LV05-3	BG293LV05-4
Sample_ID	BG293LV05-3	BG293LV05-4
Sample Name	CPSF6-BG293LV05-3	CPSF6-BG293LV05-4
Pool ID	Pool-240119	Pool-240119
LocalServer_folder	set69	set69
total_reads	19,999,762	14,035,601
total_aligned_reads	16,643,094	11,623,445
unique_aligned_reads	15,379,397	10,732,226
percent_uniqueAligned	0.76898	0.76464
correlation_replicates	0.992686	0.992686
spikein_reads	4,594	1,964
percent_spikeins	0.00023	0.00014
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2903	2904

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
CPSF6-BG293LV05-3_S135_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2903	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28495
CPSF6-BG293LV05-3_S135_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2903	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28539
CPSF6-BG293LV05-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2903					GRCh38	V40	CPSF6-BG293LV05-3_S135_L002_R1_001.filtered.trimmed.paired.fastq.gz,CPSF6-BG293LV05-3_S135_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28583
CPSF6-BG293LV05-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2903					GRCh38	V40	CPSF6-BG293LV05-3/Aligned.sortedByCoord.out.bam		ENCORE2	28627
CPSF6-BG293LV05-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2903					GRCh38	V40	CPSF6-BG293LV05-3/Aligned.sortedByCoord.out.bam		ENCORE2	28671
CPSF6-BG293LV05-3_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2903					GRCh38	V40	CPSF6-BG293LV05-3/Aligned.sortedByCoord.out.bam		ENCORE2	28715
CPSF6-BG293LV05-3_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2903					GRCh38	V40	CPSF6-BG293LV05-3/Aligned.sortedByCoord.out.bam		ENCORE2	28759
CPSF6-BG293LV05-3_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2903					GRCh38	V40	CPSF6-BG293LV05-3_S135_L002_R1_001.filtered.trimmed.paired.fastq.gz,CPSF6-BG293LV05-3_S135_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28803
CPSF6-BG293LV05-4_S136_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2904	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28496
CPSF6-BG293LV05-4_S136_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2904	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28540
CPSF6-BG293LV05-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2904					GRCh38	V40	CPSF6-BG293LV05-4_S136_L002_R1_001.filtered.trimmed.paired.fastq.gz,CPSF6-BG293LV05-4_S136_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28584
CPSF6-BG293LV05-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2904					GRCh38	V40	CPSF6-BG293LV05-4/Aligned.sortedByCoord.out.bam		ENCORE2	28628
CPSF6-BG293LV05-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2904					GRCh38	V40	CPSF6-BG293LV05-4/Aligned.sortedByCoord.out.bam		ENCORE2	28672
CPSF6-BG293LV05-4_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2904					GRCh38	V40	CPSF6-BG293LV05-4/Aligned.sortedByCoord.out.bam		ENCORE2	28716
CPSF6-BG293LV05-4_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2904					GRCh38	V40	CPSF6-BG293LV05-4/Aligned.sortedByCoord.out.bam		ENCORE2	28760
CPSF6-BG293LV05-4_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2904					GRCh38	V40	CPSF6-BG293LV05-4_S136_L002_R1_001.filtered.trimmed.paired.fastq.gz,CPSF6-BG293LV05-4_S136_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28804