CDC40 RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV04-13	BG293LV04-14
idx	0	0
TRCN#_or_BGC#	TRCN0000001189	TRCN0000001189
shRNA_or_gRNA_sequence	CCGGGACCATGTTTGCTCCTGAGTTCTCGAGAACTCAGGAGCAAACATGGTCTTTTT	CCGGGACCATGTTTGCTCCTGAGTTCTCGAGAACTCAGGAGCAAACATGGTCTTTTT
PAM
Name	CDC40	CDC40
Sample_ID	BG293LV04-13	BG293LV04-14
transduction_Date	9/7/23	9/7/23
days	D4	D4
RBP_name	CDC40	CDC40
qPCR_result	75.6	74.4
Ave_qPCR	75.0
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	9900	9901

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV04-13	BG293LV04-14
Sample_ID	BG293LV04-13	BG293LV04-14
Sample Name
Sample Name	CDC40-BG293LV04-13	CDC40-BG293LV04-14
RBP	CDC40	CDC40
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2023-12-30	2023-12-30
Project	ENCORE2	ENCORE2
Note
ID	12518	12519

Library-Prep
Sequencing

Library-Prep Information

	BG293LV04-13	BG293LV04-14
Sample #	5	6
Sample Name	CDC40-BG293LV04-13	CDC40-BG293LV04-14
Sample_Name_Alias
Index Well Position	E01	F01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-10-10	2023-10-10
Lib_ID	Lib-231010	Lib-231010
Tecan_Location
Tecan
Tecan_date
Size_bp	269	267
Peak_Molarity	91.40	77.20
libSampleQC_DNA_Well	DNA_Library_set64/set1/E9.png	DNA_Library_set64/set1/F9.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set64/set1/E5.png	RNA_Library_set64/set1/F5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-12	2023-10-12
Sample_ID	BG293LV04-13	BG293LV04-14
RBP	CDC40	CDC40
Batch_ID	BG293LV04	BG293LV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4010	4011

Sequencing Information

	BG293LV04-13	BG293LV04-14
Sample_ID	BG293LV04-13	BG293LV04-14
Sample Name	CDC40-BG293LV04-13	CDC40-BG293LV04-14
Pool ID	Pool-231012	Pool-231012
LocalServer_folder	set64	set64
total_reads	25,675,309	17,091,974
total_aligned_reads	23,690,114	14,173,326
unique_aligned_reads	22,081,799	13,218,696
percent_uniqueAligned	0.86004	0.77339
correlation_replicates	0.983878	0.983878
spikein_reads	10,652	14,522
percent_spikeins	0.00041	0.00085
original_ReadLength	100	100
QC_Status	Submitting	Submitting
ID	2619	2620

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-BG293LV04-13_S5_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2619	NextSeq2000	100	paired-ended	1				NT-BG293LV04-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8682
CDC40-BG293LV04-13_S5_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2619	NextSeq2000	100	paired-ended	2				NT-BG293LV04-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8710
CDC40-BG293LV04-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2619					GRCh38	V40	CDC40-BG293LV04-13_S5_R1_001.filtered.trimmed.paired.fastq.gz,CDC40-BG293LV04-13_S5_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9759
CDC40-BG293LV04-13_Signal.Unique.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2619					GRCh38	V40	CDC40-BG293LV04-13/Aligned.sortedByCoord.out.bam		ENCORE2	9787
CDC40-BG293LV04-13_Signal.Unique.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2619					GRCh38	V40	CDC40-BG293LV04-13/Aligned.sortedByCoord.out.bam		ENCORE2	9815
CDC40-BG293LV04-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2619					GRCh38	V40	CDC40-BG293LV04-13/Aligned.sortedByCoord.out.bam		ENCORE2	9843
CDC40-BG293LV04-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2619					GRCh38	V40	CDC40-BG293LV04-13/Aligned.sortedByCoord.out.bam		ENCORE2	9871
CDC40-BG293LV04-13_quant.sf	ENCODE_DATA/set64/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2619					GRCh38	V40	CDC40-BG293LV04-13_S5_R1_001.filtered.trimmed.paired.fastq.gz,CDC40-BG293LV04-13_S5_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9899
CDC40-BG293LV04-14_S6_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2620	NextSeq2000	100	paired-ended	1				NT-BG293LV04-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8683
CDC40-BG293LV04-14_S6_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2620	NextSeq2000	100	paired-ended	2				NT-BG293LV04-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8711
CDC40-BG293LV04-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2620					GRCh38	V40	CDC40-BG293LV04-14_S6_R1_001.filtered.trimmed.paired.fastq.gz,CDC40-BG293LV04-14_S6_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9760
CDC40-BG293LV04-14_Signal.Unique.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2620					GRCh38	V40	CDC40-BG293LV04-14/Aligned.sortedByCoord.out.bam		ENCORE2	9788
CDC40-BG293LV04-14_Signal.Unique.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2620					GRCh38	V40	CDC40-BG293LV04-14/Aligned.sortedByCoord.out.bam		ENCORE2	9816
CDC40-BG293LV04-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2620					GRCh38	V40	CDC40-BG293LV04-14/Aligned.sortedByCoord.out.bam		ENCORE2	9844
CDC40-BG293LV04-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2620					GRCh38	V40	CDC40-BG293LV04-14/Aligned.sortedByCoord.out.bam		ENCORE2	9872
CDC40-BG293LV04-14_quant.sf	ENCODE_DATA/set64/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2620					GRCh38	V40	CDC40-BG293LV04-14_S6_R1_001.filtered.trimmed.paired.fastq.gz,CDC40-BG293LV04-14_S6_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9900