CPSF6 RNA-Seq in 293T

Experiment Information (Status: Revoked)

	BG293LV02-7	BG293LV02-8
idx	0	0
TRCN#_or_BGC#	TRCN0000000154	TRCN0000000154
shRNA_or_gRNA_sequence	ACCATAGTAGATCACGAGAAA	ACCATAGTAGATCACGAGAAA
PAM
Name	CPSF6	CPSF6
Sample_ID	BG293LV02-7	BG293LV02-8
transduction_Date	3/20/23	3/20/23
days	D4	D4
RBP_name	CPSF6	CPSF6
qPCR_result	76.3	78.9
Ave_qPCR	77.6
RT-qPCR_primer-F	x
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	9802	9803

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV02-7	BG293LV02-8
Sample_ID	BG293LV02-7	BG293LV02-8
Sample Name
Sample Name	CPSF6-BG293LV02-7	CPSF6-BG293LV02-8
RBP	CPSF6	CPSF6
Cell_Line	293T	293T
Exp UID
Status	Revoked	Revoked
Status_date	2023-09-20	2023-09-20
Project	ENCORE2	ENCORE2
Note
ID	11564	11565

Library-Prep
Sequencing

Library-Prep Information

	BG293LV02-7	BG293LV02-8
Sample #	7	8
Sample Name	CPSF6-BG293LV02-7	CPSF6-BG293LV02-8
Sample_Name_Alias
Index Well Position	G01	H01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-04-12	2023-04-12
Lib_ID	Lib-230412	Lib-230412
Tecan_Location
Tecan
Tecan_date
Size_bp	288	291
Peak_Molarity	72.50	35.80
libSampleQC_DNA_Well	DNA_Library_set60-62/set2/G1.png	DNA_Library_set60-62/set2/H1.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set60-62/set1/G1.png	RNA_Library_set60-62/set1/H1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BG293LV02-7	BG293LV02-8
RBP	CPSF6	CPSF6
Batch_ID	BG293LV02	BG293LV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3594	3595

Sequencing Information

	BG293LV02-7	BG293LV02-8
Sample_ID	BG293LV02-7	BG293LV02-8
Sample Name	CPSF6-BG293LV02-7	CPSF6-BG293LV02-8
Pool ID	Pool-230417	Pool-230417
LocalServer_folder	set60	set60
total_reads	51,045,592	69,062,378
total_aligned_reads	43,123,254	56,999,524
unique_aligned_reads	39,947,479	53,175,803
percent_uniqueAligned	0.78258	0.76997
correlation_replicates	0.993616	0.993616
spikein_reads	102,630	128,784
percent_spikeins	0.00201	0.00186
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2465	2466

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-BG293LV02-7_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2465	NovaSeq6000	100	paired-ended	1				NT-BG293LV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7966
CPSF6-BG293LV02-7_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2465	NovaSeq6000	100	paired-ended	2				NT-BG293LV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8010
CPSF6-BG293LV02-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2465					GRCh38	V40	CPSF6-BG293LV02-7_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz,CPSF6-BG293LV02-7_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10759
CPSF6-BG293LV02-7_Signal.Unique.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2465					GRCh38	V40	CPSF6-BG293LV02-7/Aligned.sortedByCoord.out.bam		ENCORE2	10803
CPSF6-BG293LV02-7_Signal.Unique.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2465					GRCh38	V40	CPSF6-BG293LV02-7/Aligned.sortedByCoord.out.bam		ENCORE2	10847
CPSF6-BG293LV02-7_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2465					GRCh38	V40	CPSF6-BG293LV02-7/Aligned.sortedByCoord.out.bam		ENCORE2	10891
CPSF6-BG293LV02-7_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2465					GRCh38	V40	CPSF6-BG293LV02-7/Aligned.sortedByCoord.out.bam		ENCORE2	10935
CPSF6-BG293LV02-7_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2465					GRCh38	V40	CPSF6-BG293LV02-7_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz,CPSF6-BG293LV02-7_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10979
CPSF6-BG293LV02-8_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2466	NovaSeq6000	100	paired-ended	1				NT-BG293LV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7967
CPSF6-BG293LV02-8_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2466	NovaSeq6000	100	paired-ended	2				NT-BG293LV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8011
CPSF6-BG293LV02-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2466					GRCh38	V40	CPSF6-BG293LV02-8_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz,CPSF6-BG293LV02-8_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10760
CPSF6-BG293LV02-8_Signal.Unique.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2466					GRCh38	V40	CPSF6-BG293LV02-8/Aligned.sortedByCoord.out.bam		ENCORE2	10804
CPSF6-BG293LV02-8_Signal.Unique.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2466					GRCh38	V40	CPSF6-BG293LV02-8/Aligned.sortedByCoord.out.bam		ENCORE2	10848
CPSF6-BG293LV02-8_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2466					GRCh38	V40	CPSF6-BG293LV02-8/Aligned.sortedByCoord.out.bam		ENCORE2	10892
CPSF6-BG293LV02-8_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2466					GRCh38	V40	CPSF6-BG293LV02-8/Aligned.sortedByCoord.out.bam		ENCORE2	10936
CPSF6-BG293LV02-8_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2466					GRCh38	V40	CPSF6-BG293LV02-8_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz,CPSF6-BG293LV02-8_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10980