CDC40 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-119	BG293LV06-120
idx	0	0
TRCN#_or_BGC#	TRCN0000001189	TRCN0000001189
shRNA_or_gRNA_sequence	CCGGGACCATGTTTGCTCCTGAGTTCTCGAGAACTCAGGAGCAAACATGGTCTTTTT	CCGGGACCATGTTTGCTCCTGAGTTCTCGAGAACTCAGGAGCAAACATGGTCTTTTT
PAM
Name	CDC40	CDC40
Sample_ID	BG293LV06-119	BG293LV06-120
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	CDC40	CDC40
qPCR_result	77.3	80.5
Ave_qPCR	78.9
RT-qPCR_primer-F
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	12254	12255

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-119	BG293LV06-120
Sample_ID	BG293LV06-119	BG293LV06-120
Sample Name
Sample Name	CDC40-BG293LV06-119B	CDC40-BG293LV06-120B
RBP	CDC40	CDC40
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13556	13557

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-119	BG293LV06-120
Sample #	119	120
Sample Name	CDC40-BG293LV06-119B	CDC40-BG293LV06-120B
Sample_Name_Alias
Index Well Position	G08	H08
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-02	2024-10-02
Lib_ID	Lib-241002	Lib-241002
Tecan_Location
Tecan
Tecan_date
Size_bp	276	282
Peak_Molarity	81.50	60.60
libSampleQC_DNA_Well	DNA_Library_set72/set1/G8.png	DNA_Library_set72/set1/H8.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set72/set1/G8.png	RNA_Library_set72/set1/H8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-04	2024-10-04
Sample_ID	BG293LV06-119	BG293LV06-120
RBP	CDC40	CDC40
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4544	4545

Sequencing Information

	BG293LV06-119	BG293LV06-120
Sample_ID	BG293LV06-119	BG293LV06-120
Sample Name	CDC40-BG293LV06-119B	CDC40-BG293LV06-120B
Pool ID	Pool-241004	Pool-241004
LocalServer_folder	set72	set72
total_reads	50,521,221	59,389,150
total_aligned_reads	47,951,393	56,225,543
unique_aligned_reads	45,197,819	53,026,939
percent_uniqueAligned	0.89463	0.89287
correlation_replicates	0.993567	0.993567
spikein_reads	133,656	224,140
percent_spikeins	0.00265	0.00377
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3113	3114

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
CDC40-BG293LV06-119B_S71_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3113	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29766
CDC40-BG293LV06-119B_S71_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3113	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29838
CDC40-BG293LV06-119B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3113					GRCh38	V40	CDC40-BG293LV06-119B_S71_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDC40-BG293LV06-119B_S71_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29910
CDC40-BG293LV06-119B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3113					GRCh38	V40	CDC40-BG293LV06-119B_Aligned.sortedByCoord.out.bam		ENCORE2	29982
CDC40-BG293LV06-119B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3113					GRCh38	V40	CDC40-BG293LV06-119B_Aligned.sortedByCoord.out.bam		ENCORE2	30054
CDC40-BG293LV06-119B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3113					GRCh38	V40	CDC40-BG293LV06-119B_Aligned.sortedByCoord.out.bam		ENCORE2	30126
CDC40-BG293LV06-119B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3113					GRCh38	V40	CDC40-BG293LV06-119B_Aligned.sortedByCoord.out.bam		ENCORE2	30198
CDC40-BG293LV06-119B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3113					GRCh38	V40	CDC40-BG293LV06-119B_S71_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDC40-BG293LV06-119B_S71_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30270
CDC40-BG293LV06-120B_S72_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3114	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29767
CDC40-BG293LV06-120B_S72_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3114	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29839
CDC40-BG293LV06-120B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3114					GRCh38	V40	CDC40-BG293LV06-120B_S72_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDC40-BG293LV06-120B_S72_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29911
CDC40-BG293LV06-120B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3114					GRCh38	V40	CDC40-BG293LV06-120B_Aligned.sortedByCoord.out.bam		ENCORE2	29983
CDC40-BG293LV06-120B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3114					GRCh38	V40	CDC40-BG293LV06-120B_Aligned.sortedByCoord.out.bam		ENCORE2	30055
CDC40-BG293LV06-120B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3114					GRCh38	V40	CDC40-BG293LV06-120B_Aligned.sortedByCoord.out.bam		ENCORE2	30127
CDC40-BG293LV06-120B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3114					GRCh38	V40	CDC40-BG293LV06-120B_Aligned.sortedByCoord.out.bam		ENCORE2	30199
CDC40-BG293LV06-120B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3114					GRCh38	V40	CDC40-BG293LV06-120B_S72_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDC40-BG293LV06-120B_S72_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30271