CPSF6 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-5	BG293LV06-6
idx	0	0
TRCN#_or_BGC#	TRCN0000000154	TRCN0000000154
shRNA_or_gRNA_sequence	ACCATAGTAGATCACGAGAAA	ACCATAGTAGATCACGAGAAA
PAM
Name	CPSF6	CPSF6
Sample_ID	BG293LV06-5	BG293LV06-6
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	CPSF6	CPSF6
qPCR_result	88.8	86.0
Ave_qPCR	87.4
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	12140	12141

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-5	BG293LV06-6
Sample_ID	BG293LV06-5	BG293LV06-6
Sample Name
Sample Name	CPSF6-BG293LV06-5	CPSF6-BG293LV06-6
RBP	CPSF6	CPSF6
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13442	13443

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-5	BG293LV06-6
Sample #	9	10
Sample Name	CPSF6-BG293LV06-5	CPSF6-BG293LV06-6
Sample_Name_Alias
Index Well Position	A02	B02
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-09-25	2024-09-25
Lib_ID	Lib-240925B	Lib-240925B
Tecan_Location
Tecan
Tecan_date
Size_bp	296	290
Peak_Molarity	58.00	83.50
libSampleQC_DNA_Well	DNA_Library_set71/set1/A2.png	DNA_Library_set71/set1/B2.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set71/set1/A2.png	RNA_Library_set71/set1/B2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-09-30	2024-09-30
Sample_ID	BG293LV06-5	BG293LV06-6
RBP	CPSF6	CPSF6
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4434	4435

Sequencing Information

	BG293LV06-5	BG293LV06-6
Sample_ID	BG293LV06-5	BG293LV06-6
Sample Name	CPSF6-BG293LV06-5	CPSF6-BG293LV06-6
Pool ID	Pool-240930	Pool-240930
LocalServer_folder	set71	set71
total_reads	37,866,996	34,401,638
total_aligned_reads	34,501,822	32,003,059
unique_aligned_reads	31,955,134	29,934,159
percent_uniqueAligned	0.84388	0.87014
correlation_replicates	0.971569	0.971569
spikein_reads	140,652	115,550
percent_spikeins	0.00371	0.00336
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3003	3004

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-BG293LV06-5_S9_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3003	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1merged_S1_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29317
CPSF6-BG293LV06-5_S9_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3003	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1merged_S1_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29381
CPSF6-BG293LV06-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3003					GRCh38	V40	CPSF6-BG293LV06-5_S9_L002_R1_001.filtered.trimmed.paired.fastq.gz,CPSF6-BG293LV06-5_S9_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29446
CPSF6-BG293LV06-5_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3003					GRCh38	V40	CPSF6-BG293LV06-5_Aligned.sortedByCoord.out.bam		ENCORE2	29510
CPSF6-BG293LV06-5_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3003					GRCh38	V40	CPSF6-BG293LV06-5_Aligned.sortedByCoord.out.bam		ENCORE2	29574
CPSF6-BG293LV06-5_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3003					GRCh38	V40	CPSF6-BG293LV06-5_Aligned.sortedByCoord.out.bam		ENCORE2	29638
CPSF6-BG293LV06-5_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3003					GRCh38	V40	CPSF6-BG293LV06-5_S9_L002_R1_001.filtered.trimmed.paired.fastq.gz,CPSF6-BG293LV06-5_S9_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29702
CPSF6-BG293LV06-6_S10_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3004	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1merged_S1_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29318
CPSF6-BG293LV06-6_S10_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3004	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1merged_S1_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29382
CPSF6-BG293LV06-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3004					GRCh38	V40	CPSF6-BG293LV06-6_S10_L002_R1_001.filtered.trimmed.paired.fastq.gz,CPSF6-BG293LV06-6_S10_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29447
CPSF6-BG293LV06-6_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3004					GRCh38	V40	CPSF6-BG293LV06-6_Aligned.sortedByCoord.out.bam		ENCORE2	29511
CPSF6-BG293LV06-6_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3004					GRCh38	V40	CPSF6-BG293LV06-6_Aligned.sortedByCoord.out.bam		ENCORE2	29575
CPSF6-BG293LV06-6_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3004					GRCh38	V40	CPSF6-BG293LV06-6_Aligned.sortedByCoord.out.bam		ENCORE2	29639
CPSF6-BG293LV06-6_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3004					GRCh38	V40	CPSF6-BG293LV06-6_S10_L002_R1_001.filtered.trimmed.paired.fastq.gz,CPSF6-BG293LV06-6_S10_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29703