CNOT3 RNA-Seq in HepG2

General Information


RBP	CNOT3
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CNOT3-BGHcLV43-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV43
Pool ID	Pool-240723
Local_Set_Name	set74
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	CNOT3-BGHcLV43-9
Rep2	CNOT3-BGHcLV43-10
CN1	NT-BGHcLV43-1
CN2	NT-BGHcLV43-2
Rep1_qPCR	41.7
Rep2_qPCR	28.9
Rep1_WB	76.3
Rep2_WB	75.1
Antibody Cat#	13300S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1571

Experiment Information (Status: Submitting)

	BGHcLV43-9	BGHcLV43-9	BGHcLV43-9	BGHcLV43-10	BGHcLV43-10	BGHcLV43-10
idx	1377	0	0	1378	0	0
TRCN#_or_BGC#	BGC#0001121	BGC#0001121	BGC#0001121	BGC#0001121	BGC#0001121	BGC#0001121
shRNA_or_gRNA_sequence	TGCCTCAAGAAGGTGTCCGA	TGCCTCAAGAAGGTGTCCGA	TGCCTCAAGAAGGTGTCCGA	TGCCTCAAGAAGGTGTCCGA	TGCCTCAAGAAGGTGTCCGA	TGCCTCAAGAAGGTGTCCGA
PAM	GGG	GGG	GGG	GGG	GGG	GGG
Name	CNOT3_90	CNOT3_90	CNOT3_90	CNOT3_90	CNOT3_90	CNOT3_90
Sample_ID	BGHcLV43-9	BGHcLV43-9	BGHcLV43-9	BGHcLV43-10	BGHcLV43-10	BGHcLV43-10
transduction_Date	6/6/24	6/6/24	6/6/24	6/6/24	6/6/24	6/6/24
days	D6	D6	D6	D6	D6	D6
RBP_name	CNOT3	CNOT3	CNOT3	CNOT3	CNOT3	CNOT3
qPCR_result	41.7	41.7	41.7	28.9	28.9	28.9
Ave_qPCR	35.3	35.3	35.3
RT-qPCR_primer-F	gagggagcagcagcagtagt	gagggagcagcagcagtagt	gagggagcagcagcagtagt
RT-qPCR_primer-R	ctgctcaaagccacctctg	ctgctcaaagccacctctg	ctgctcaaagccacctctg
protein_conc	2317	2317	2317	2970	2970	2970
WB_result	76.3	74.9	68.8	75.1	63.7	60.4
Ave_WB	75.7	69.3	64.6
WB_DONE_date	6/28/24	7/23/24	7/23/24
MW	105kd	105kd	105kd
IP
antibody_Cat#	13300S	40608S	A302-156A	lot # 1	lot # 1	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0	0	0
Rep2_TPM	0	0	0	0	0	0
Action	Ready			Ready
Library_start_date
repeat_library
Note
ID	9624	9626	9628	9625	9627	9629

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

	BGHcLV43-9	BGHcLV43-10
Sample_ID	BGHcLV43-9	BGHcLV43-10
Sample Name
Sample Name	CNOT3-BGHcLV43-9	CNOT3-BGHcLV43-10
RBP	CNOT3	CNOT3
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13232	13233

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV43-9	BGHcLV43-10
Sample #	5	6
Sample Name	CNOT3-BGHcLV43-9	CNOT3-BGHcLV43-10
Sample_Name_Alias
Index Well Position	E06	F06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-07-22	2024-07-22
Lib_ID	Lib-240722	Lib-240722
Tecan_Location
Tecan
Tecan_date
Size_bp	302	300
Peak_Molarity	94.00	78.30
libSampleQC_DNA_Well	DNA_Library_set74/set1/E1.png	DNA_Library_set74/set1/F1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set74/set1/A7.png	RNA_Library_set74/set1/B7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-23	2024-07-23
Sample_ID	BGHcLV43-9	BGHcLV43-10
RBP	CNOT3	CNOT3
Batch_ID	BGHcLV43	BGHcLV43
WB_result	76.300	75.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4364	4365

Sequencing Information

	BGHcLV43-9	BGHcLV43-10
Sample_ID	BGHcLV43-9	BGHcLV43-10
Sample Name	CNOT3-BGHcLV43-9	CNOT3-BGHcLV43-10
Pool ID	Pool-240723	Pool-240723
LocalServer_folder	set74	set74
total_reads	35,568,216	34,624,992
total_aligned_reads	32,875,915	32,244,232
unique_aligned_reads	31,002,506	30,369,965
percent_uniqueAligned	0.87164	0.87711
correlation_replicates	0.999599	0.999599
spikein_reads	7,682	21,898
percent_spikeins	0.00022	0.00063
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3231	3232

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-BGHcLV43-9_S95_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3231	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30523
CNOT3-BGHcLV43-9_S95_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3231	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30575
CNOT3-BGHcLV43-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3231					GRCh38	V40	CNOT3-BGHcLV43-9_S95_L003_R1_001.filtered.trimmed.paired.fastq.gz,CNOT3-BGHcLV43-9_S95_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30627
CNOT3-BGHcLV43-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3231					GRCh38	V40	CNOT3-BGHcLV43-9_Aligned.sortedByCoord.out.bam		ENCORE2	30679
CNOT3-BGHcLV43-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3231					GRCh38	V40	CNOT3-BGHcLV43-9_Aligned.sortedByCoord.out.bam		ENCORE2	30731
CNOT3-BGHcLV43-9_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3231					GRCh38	V40	CNOT3-BGHcLV43-9_Aligned.sortedByCoord.out.bam		ENCORE2	30783
CNOT3-BGHcLV43-9_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3231					GRCh38	V40	CNOT3-BGHcLV43-9_Aligned.sortedByCoord.out.bam		ENCORE2	30835
CNOT3-BGHcLV43-9_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3231					GRCh38	V40	CNOT3-BGHcLV43-9_S95_L003_R1_001.filtered.trimmed.paired.fastq.gz,CNOT3-BGHcLV43-9_S95_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30887
CNOT3-BGHcLV43-10_S96_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3232	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30522
CNOT3-BGHcLV43-10_S96_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3232	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30574
CNOT3-BGHcLV43-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3232					GRCh38	V40	CNOT3-BGHcLV43-10_S96_L003_R1_001.filtered.trimmed.paired.fastq.gz,CNOT3-BGHcLV43-10_S96_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30626
CNOT3-BGHcLV43-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3232					GRCh38	V40	CNOT3-BGHcLV43-10_Aligned.sortedByCoord.out.bam		ENCORE2	30678
CNOT3-BGHcLV43-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3232					GRCh38	V40	CNOT3-BGHcLV43-10_Aligned.sortedByCoord.out.bam		ENCORE2	30730
CNOT3-BGHcLV43-10_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3232					GRCh38	V40	CNOT3-BGHcLV43-10_Aligned.sortedByCoord.out.bam		ENCORE2	30782
CNOT3-BGHcLV43-10_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3232					GRCh38	V40	CNOT3-BGHcLV43-10_Aligned.sortedByCoord.out.bam		ENCORE2	30834
CNOT3-BGHcLV43-10_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3232					GRCh38	V40	CNOT3-BGHcLV43-10_S96_L003_R1_001.filtered.trimmed.paired.fastq.gz,CNOT3-BGHcLV43-10_S96_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30886