CNOT2 RNA-Seq in 293T

Experiment Information (Status: Revoked)

	BG293LV02-3	BG293LV02-4
idx	0	0
TRCN#_or_BGC#	TRCN0000234898	TRCN0000234898
shRNA_or_gRNA_sequence	CCGGATGAATGGAGGAGACGTATTACTCGAGTAATACGTCTCCTCCATTCATTTTTTG	CCGGATGAATGGAGGAGACGTATTACTCGAGTAATACGTCTCCTCCATTCATTTTTTG
PAM
Name	CNOT2	CNOT2
Sample_ID	BG293LV02-3	BG293LV02-4
transduction_Date	3/20/23	3/20/23
days	D4	D4
RBP_name	CNOT2	CNOT2
qPCR_result	75.6	77.5
Ave_qPCR	76.5
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	9798	9799

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV02-3	BG293LV02-4
Sample_ID	BG293LV02-3	BG293LV02-4
Sample Name
Sample Name	CNOT2-BG293LV02-3	CNOT2-BG293LV02-4
RBP	CNOT2	CNOT2
Cell_Line	293T	293T
Exp UID
Status	Revoked	Revoked
Status_date	2023-09-20	2023-09-20
Project	ENCORE2	ENCORE2
Note
ID	11560	11561

Library-Prep
Sequencing

Library-Prep Information

	BG293LV02-3	BG293LV02-4
Sample #	3	4
Sample Name	CNOT2-BG293LV02-3	CNOT2-BG293LV02-4
Sample_Name_Alias
Index Well Position	C01	D01
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	293	305
Peak_Molarity	66.30	89.20
libSampleQC_DNA_Well	DNA_Library_set60-62/set2/C1.png	DNA_Library_set60-62/set2/D1.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set60-62/set1/C1.png	RNA_Library_set60-62/set1/D1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BG293LV02-3	BG293LV02-4
RBP	CNOT2	CNOT2
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	3590	3591

Sequencing Information

	BG293LV02-3	BG293LV02-4
Sample_ID	BG293LV02-3	BG293LV02-4
Sample Name	CNOT2-BG293LV02-3	CNOT2-BG293LV02-4
Pool ID	Pool-230417	Pool-230417
LocalServer_folder	set60	set60
total_reads	42,465,046	44,591,189
total_aligned_reads	35,576,662	38,500,411
unique_aligned_reads	33,160,928	35,847,094
percent_uniqueAligned	0.78090	0.80391
correlation_replicates	0.996226	0.996226
spikein_reads	155,966	126,176
percent_spikeins	0.00367	0.00283
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2461	2462

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
CNOT2-BG293LV02-3_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2461	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	7962
CNOT2-BG293LV02-3_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2461	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	8006
CNOT2-BG293LV02-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2461					GRCh38	V40	CNOT2-BG293LV02-3_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT2-BG293LV02-3_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10755
CNOT2-BG293LV02-3_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	2461					GRCh38	V40	CNOT2-BG293LV02-3/Aligned.sortedByCoord.out.bam		ENCORE2	10799
CNOT2-BG293LV02-3_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	2461					GRCh38	V40	CNOT2-BG293LV02-3/Aligned.sortedByCoord.out.bam		ENCORE2	10843
CNOT2-BG293LV02-3_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	2461					GRCh38	V40	CNOT2-BG293LV02-3/Aligned.sortedByCoord.out.bam		ENCORE2	10887
CNOT2-BG293LV02-3_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	2461					GRCh38	V40	CNOT2-BG293LV02-3/Aligned.sortedByCoord.out.bam		ENCORE2	10931
CNOT2-BG293LV02-3_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2461					GRCh38	V40	CNOT2-BG293LV02-3_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT2-BG293LV02-3_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10975
CNOT2-BG293LV02-4_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2462	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	7963
CNOT2-BG293LV02-4_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2462	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	8007
CNOT2-BG293LV02-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2462					GRCh38	V40	CNOT2-BG293LV02-4_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT2-BG293LV02-4_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10756
CNOT2-BG293LV02-4_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	2462					GRCh38	V40	CNOT2-BG293LV02-4/Aligned.sortedByCoord.out.bam		ENCORE2	10800
CNOT2-BG293LV02-4_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	2462					GRCh38	V40	CNOT2-BG293LV02-4/Aligned.sortedByCoord.out.bam		ENCORE2	10844
CNOT2-BG293LV02-4_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	2462					GRCh38	V40	CNOT2-BG293LV02-4/Aligned.sortedByCoord.out.bam		ENCORE2	10888
CNOT2-BG293LV02-4_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	2462					GRCh38	V40	CNOT2-BG293LV02-4/Aligned.sortedByCoord.out.bam		ENCORE2	10932
CNOT2-BG293LV02-4_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2462					GRCh38	V40	CNOT2-BG293LV02-4_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT2-BG293LV02-4_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10976