CNOT3 RNA-Seq in K562

General Information


RBP	CNOT3
Cell_Line	K562
Method	CRISPR
Exp_Name	CNOT3-BGKcLV42-K562
ENCODE_series_ID
Batch_ID	BGKcLV42
Pool ID	Pool-240715
Local_Set_Name	set73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	CNOT3-BGKcLV42-17
Rep2	CNOT3-BGKcLV42-18
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	8.6
Rep2_qPCR	13.4
Rep1_WB	84.1
Rep2_WB	86.8
Antibody Cat#	13300S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1532

Experiment Information (Status: Submitting)

	BGKcLV42-17	BGKcLV42-18
idx	0	0
TRCN#_or_BGC#	BGC#0001120	BGC#0001120
shRNA_or_gRNA_sequence	TGCCTCAAGAAGGTGTCCGA	TGCCTCAAGAAGGTGTCCGA
PAM	GGG	GGG
Name	CNOT3_90	CNOT3_90
Sample_ID	BGKcLV42-17	BGKcLV42-18
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	CNOT3	CNOT3
qPCR_result	8.6	13.4
Ave_qPCR	11.0
RT-qPCR_primer-F	gagggagcagcagcagtagt
RT-qPCR_primer-R	ctgctcaaagccacctctg
protein_conc	1325	1174
WB_result	84.1	86.8
Ave_WB	85.5
WB_DONE_date	5/8/24
MW	105kd
IP
antibody_Cat#	13300S	lot # 1
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	5777	5778

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CNOT3	Product_ID: 13300S Lot_ID: 1 Source: Cell Signaling Technology Target Name: CNOT3-human

Experiment Status

	BGKcLV42-17	BGKcLV42-18
Sample_ID	BGKcLV42-17	BGKcLV42-18
Sample Name
Sample Name	CNOT3-BGKcLV42-17	CNOT3-BGKcLV42-18
RBP	CNOT3	CNOT3
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13058	13059

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-17	BGKcLV42-18
Sample #	15	16
Sample Name	CNOT3-BGKcLV42-17	CNOT3-BGKcLV42-18
Sample_Name_Alias
Index Well Position	G02	H02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-06-21	2024-06-21
Lib_ID	Lib-240621	Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp	297	306
Peak_Molarity	50.60	52.70
libSampleQC_DNA_Well	DNA_Library_set73/set1/G2.png	DNA_Library_set73/set1/H2.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_set73/set1/G2.png	RNA_Library_set73/set1/H2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-17	BGKcLV42-18
RBP	CNOT3	CNOT3
Batch_ID	BGKcLV42	BGKcLV42
WB_result	84.100	86.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4284	4285

Sequencing Information

	BGKcLV42-17	BGKcLV42-18
Sample_ID	BGKcLV42-17	BGKcLV42-18
Sample Name	CNOT3-BGKcLV42-17	CNOT3-BGKcLV42-18
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	56,496,606	31,200,773
total_aligned_reads	47,904,526	24,879,022
unique_aligned_reads	44,309,401	22,932,480
percent_uniqueAligned	0.78428	0.73500
correlation_replicates	0.983982	0.983982
spikein_reads	9,120	6,176
percent_spikeins	0.00016	0.00020
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3151	3152

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
CNOT3-BGKcLV42-17_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3151	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30352
CNOT3-BGKcLV42-17_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3151	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30442
CNOT3-BGKcLV42-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3151					GRCh38	V40	CNOT3-BGKcLV42-17_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT3-BGKcLV42-17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31284
CNOT3-BGKcLV42-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3151					GRCh38	V40	CNOT3-BGKcLV42-17_Aligned.sortedByCoord.out.bam		ENCORE2	31374
CNOT3-BGKcLV42-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3151					GRCh38	V40	CNOT3-BGKcLV42-17_Aligned.sortedByCoord.out.bam		ENCORE2	31464
CNOT3-BGKcLV42-17_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3151					GRCh38	V40	CNOT3-BGKcLV42-17_Aligned.sortedByCoord.out.bam		ENCORE2	31554
CNOT3-BGKcLV42-17_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3151					GRCh38	V40	CNOT3-BGKcLV42-17_Aligned.sortedByCoord.out.bam		ENCORE2	31644
CNOT3-BGKcLV42-17_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3151					GRCh38	V40	CNOT3-BGKcLV42-17_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT3-BGKcLV42-17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31734
CNOT3-BGKcLV42-18_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3152	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30353
CNOT3-BGKcLV42-18_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3152	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30443
CNOT3-BGKcLV42-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3152					GRCh38	V40	CNOT3-BGKcLV42-18_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT3-BGKcLV42-18_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31285
CNOT3-BGKcLV42-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3152					GRCh38	V40	CNOT3-BGKcLV42-18_Aligned.sortedByCoord.out.bam		ENCORE2	31375
CNOT3-BGKcLV42-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3152					GRCh38	V40	CNOT3-BGKcLV42-18_Aligned.sortedByCoord.out.bam		ENCORE2	31465
CNOT3-BGKcLV42-18_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3152					GRCh38	V40	CNOT3-BGKcLV42-18_Aligned.sortedByCoord.out.bam		ENCORE2	31555
CNOT3-BGKcLV42-18_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3152					GRCh38	V40	CNOT3-BGKcLV42-18_Aligned.sortedByCoord.out.bam		ENCORE2	31645
CNOT3-BGKcLV42-18_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3152					GRCh38	V40	CNOT3-BGKcLV42-18_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT3-BGKcLV42-18_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31735