CNOT10 RNA-Seq in HepG2

General Information


RBP	CNOT10
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CNOT10-BGHcLV22-HepG2
ENCODE_series_ID	ENCSR250LQB
Batch_ID	BGHcLV22
Pool ID	Pool-201204
Local_Set_Name	set46_H
ENCODE_KD_Exp_ID	ENCSR002NQQ
ENCODE_CN_Exp_ID	ENCSR704VPL
Rep1	CNOT10-BGHcLV22-9
Rep2	CNOT10-BGHcLV22-10
CN1	NT-BGHcLV22-1
CN2	NT-BGHcLV22-2
Rep1_qPCR	31.2
Rep2_qPCR	43.4
Rep1_WB	92.2
Rep2_WB	89.5
Antibody Cat#	A304-899A
Antibody Lot#	Lot# 1
Antibody DCC ID	ENCAB805LWE
Status	Released
Project	ENCODE4
ID	39

Experiment Information (Status: Released)

	BGHcLV22-9	BGHcLV22-10
idx	602	603
TRCN#_or_BGC#	BGC#0000500	BGC#0000500
shRNA_or_gRNA_sequence	ACTTGCTTGCAGTGCCTACG	ACTTGCTTGCAGTGCCTACG
PAM	TGG	TGG
Name	CNOT10 _91	CNOT10 _91
Sample_ID	BGHcLV22-9	BGHcLV22-10
transduction_Date	8/22/20	8/22/20
days	D6	D6
RBP_name	CNOT10	CNOT10
qPCR_result	31.2	43.4
Ave_qPCR	37.3
RT-qPCR_primer-F	ATCGAAAAGCCGTGAAGCTATT
RT-qPCR_primer-R	TCCAGAACATGCATCTCAAGC
protein_conc	3393	2867
WB_result	92.2	89.5
Ave_WB	90.8
WB_DONE_date	9/2/20	JESS
MW	82.3kDa
IP	Rabbit / I
antibody_Cat#	A304-899A	Lot# 1
Antibody DCC ID	ENCAB805LWE
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	6757	6758

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CNOT10	Product_ID: A304-899A Lot_ID: 1 Source: Bethyl Labs Target Name: CNOT10-human

Experiment Status

	BGHcLV22-9	BGHcLV22-10
Sample_ID	BGHcLV22-9	BGHcLV22-10
Sample Name
Sample Name	CNOT10-BGHcLV22-9	CNOT10-BGHcLV22-10
RBP	CNOT10	CNOT10
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7371	7372

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV22-9	BGHcLV22-10
Sample #	7	8
Sample Name	CNOT10-BGHcLV22-9	CNOT10-BGHcLV22-10
Sample_Name_Alias
Index Well Position	G01	H01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-11-24	2020-11-24
Lib_ID	Lib-201124	Lib-201124
Tecan_Location
Tecan
Tecan_date
Size_bp	284	280
Peak_Molarity	99.60	92.70
libSampleQC_DNA_Well	DNA_Library_set46/set1/G1.png	DNA_Library_set46/set1/H1.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set46/set1/G9.png	RNA_Library_set46/set1/H9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGHcLV22-9	BGHcLV22-10
RBP	CNOT10	CNOT10
Batch_ID	BGHcLV22	BGHcLV22
WB_result	92.200	89.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1382	1383

Sequencing Information

	BGHcLV22-9	BGHcLV22-10
Sample_ID	BGHcLV22-9	BGHcLV22-10
Sample Name	CNOT10-BGHcLV22-9	CNOT10-BGHcLV22-10
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_H	set46_H
total_reads	220,668,574	201,000,816
total_aligned_reads	180,339,428	160,026,854
unique_aligned_reads	168,836,152	149,814,056
percent_uniqueAligned	0.76511	0.74534
correlation_replicates	0.999209	0.999209
spikein_reads	100,150	66,562
percent_spikeins	0.00045	0.00033
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	488	489

Data Submission Information

	BGHcLV22-9	BGHcLV22-9	BGHcLV22-9	BGHcLV22-9	BGHcLV22-9	BGHcLV22-9	BGHcLV22-10	BGHcLV22-10	BGHcLV22-10	BGHcLV22-10
ENCODE_alias	brenton-graveley:CNOT10-BGHcLV22	brenton-graveley:CNOT10-BGHcLV22-9	brenton-graveley:L-CNOT10-BGHcLV22-9	brenton-graveley:CNOT10-BGHcLV22-9_CAAGCTAG+CGCTATGT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CNOT10-BGHcLV22-9_CAAGCTAG+CGCTATGT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CNOT10-BGHcLV22-HepG2	brenton-graveley:CNOT10-BGHcLV22-10	brenton-graveley:L-CNOT10-BGHcLV22-10	brenton-graveley:CNOT10-BGHcLV22-10_TGGATCGA+TATCGCAC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CNOT10-BGHcLV22-10_TGGATCGA+TATCGCAC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR002NQQ	ENCBS279OVC	ENCLB101YNN	ENCFF411VQE	ENCFF987GXR	ENCSR250LQB	ENCBS966NDP	ENCLB487YST	ENCFF259FQC	ENCFF935ELH
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV22-9	BGHcLV22-9	BGHcLV22-9	BGHcLV22-9	BGHcLV22-9	BGHcLV22-9	BGHcLV22-10	BGHcLV22-10	BGHcLV22-10	BGHcLV22-10
Sample Name	CNOT10-BGHcLV22-9	CNOT10-BGHcLV22-9	CNOT10-BGHcLV22-9	CNOT10-BGHcLV22-9	CNOT10-BGHcLV22-9	CNOT10-BGHcLV22-9	CNOT10-BGHcLV22-10	CNOT10-BGHcLV22-10	CNOT10-BGHcLV22-10	CNOT10-BGHcLV22-10
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46H_biosample_protocol	LV46H_library_protocol				LV46H_biosample_protocol	LV46H_library_protocol
protocol_URL		CNOT10-BGHcLV22-10.pdf	L-CNOT10-BGHcLV22-9.pdf				CNOT10-BGHcLV22-9.pdf	L-CNOT10-BGHcLV22-10.pdf
ID	2398	2433	2497	2561	2591	7147	2434	2498	2562	2592

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
CNOT10-BGHcLV22-9_CAAGCTAG+CGCTATGT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	488	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1353
CNOT10-BGHcLV22-9_CAAGCTAG+CGCTATGT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	488	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1417
CNOT10-BGHcLV22-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	488					GRCh38	V40	CNOT10-BGHcLV22-9_CAAGCTAG+CGCTATGT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT10-BGHcLV22-9_CAAGCTAG+CGCTATGT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25256
CNOT10-BGHcLV22-9_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	488					GRCh38	V40	CNOT10-BGHcLV22-9_CAAGCTAG+CGCTATGT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT10-BGHcLV22-9_CAAGCTAG+CGCTATGT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25354
CNOT10-BGHcLV22-9_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	488					GRCh38	V40	CNOT10-BGHcLV22-9/Aligned.sortedByCoord.out.bam		ENCORE2	26004
CNOT10-BGHcLV22-9_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	488					GRCh38	V40	CNOT10-BGHcLV22-9/Aligned.sortedByCoord.out.bam		ENCORE2	26034
CNOT10-BGHcLV22-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	488					GRCh38	V40	CNOT10-BGHcLV22-9/Aligned.sortedByCoord.out.bam		ENCORE2	26064
CNOT10-BGHcLV22-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	488					GRCh38	V40	CNOT10-BGHcLV22-9/Aligned.sortedByCoord.out.bam		ENCORE2	26094
CNOT10-BGHcLV22-10_TGGATCGA+TATCGCAC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	489	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1352
CNOT10-BGHcLV22-10_TGGATCGA+TATCGCAC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	489	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1416
CNOT10-BGHcLV22-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	489					GRCh38	V40	CNOT10-BGHcLV22-10_TGGATCGA+TATCGCAC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT10-BGHcLV22-10_TGGATCGA+TATCGCAC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25255
CNOT10-BGHcLV22-10_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	489					GRCh38	V40	CNOT10-BGHcLV22-10_TGGATCGA+TATCGCAC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT10-BGHcLV22-10_TGGATCGA+TATCGCAC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25353
CNOT10-BGHcLV22-10_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	489					GRCh38	V40	CNOT10-BGHcLV22-10/Aligned.sortedByCoord.out.bam		ENCORE2	26003
CNOT10-BGHcLV22-10_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	489					GRCh38	V40	CNOT10-BGHcLV22-10/Aligned.sortedByCoord.out.bam		ENCORE2	26033
CNOT10-BGHcLV22-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	489					GRCh38	V40	CNOT10-BGHcLV22-10/Aligned.sortedByCoord.out.bam		ENCORE2	26063
CNOT10-BGHcLV22-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	489					GRCh38	V40	CNOT10-BGHcLV22-10/Aligned.sortedByCoord.out.bam		ENCORE2	26093