CNOT7 RNA-Seq in HepG2

General Information


RBP	CNOT7
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CNOT7-BGHcLV10-HepG2
ENCODE_series_ID	ENCSR548YWH
Batch_ID	BGHcLV10
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR836XZH
ENCODE_CN_Exp_ID	ENCSR775ZWO
Rep1	CNOT7-BGHcLV10-13
Rep2	CNOT7-BGHcLV10-14
CN1	NT-BGHcLV10-1
CN2	NT-BGHcLV10-2
Rep1_qPCR	85.7
Rep2_qPCR	84.5
Rep1_WB	71.3
Rep2_WB	75.8
Antibody Cat#	RN110PW
Antibody Lot#
Antibody DCC ID	ENCAB198KDI
Status	Released
Project	ENCODE4
ID	221

Experiment Information (Status: Released)

	BGHcLV10-13	BGHcLV10-14
idx	210	211
TRCN#_or_BGC#	BGC#0000218	BGC#0000218
shRNA_or_gRNA_sequence	TAGTAGCTCTATAGAGTCCT	TAGTAGCTCTATAGAGTCCT
PAM	GGG	GGG
Name	CNOT7-58	CNOT7-58
Sample_ID	BGHcLV10-13	BGHcLV10-14
transduction_Date	4/27/18	4/27/18
days	D6	D6
RBP_name	CNOT7	CNOT7
qPCR_result	85.7	84.5
Ave_qPCR	85.1
RT-qPCR_primer-F	GAGTGGTCCTCTGTGAAGGG
RT-qPCR_primer-R	TCTTCAGGCAAGTTAGAGTTGG
protein_conc	3227	3555
WB_result	71.3	75.8
Ave_WB	73.6
WB_DONE_date	5/29/18
MW	33kDa
IP
antibody_Cat#	RN110PW
Antibody DCC ID	ENCAB198KDI
submitted_to_DCC_date	9/6/18
Rep1_TPM	44	0
Rep2_TPM	86	0
Action	Ready	Ready
Library_start_date	8/7/18	8/7/18
repeat_library
Note
ID	6353	6354

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CNOT7	Product_ID: RN110PW Lot_ID: 1 Source: MBLI Target Name: CNOT7-human

Experiment Status

	BGHcLV10-13	BGHcLV10-14
Sample_ID	BGHcLV10-13	BGHcLV10-14
Sample Name
Sample Name	CNOT7-BGHcLV10-13	CNOT7-BGHcLV10-14
RBP	CNOT7	CNOT7
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6293	6294

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV10-13	BGHcLV10-14
Sample #	53	54
Sample Name	CNOT7-BGHcLV10-13	CNOT7-BGHcLV10-14
Sample_Name_Alias
Index Well Position	A08	B08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2018-10-01	2018-10-01
Lib_ID	Lib-181001	Lib-181001
Tecan_Location
Tecan
Tecan_date
Size_bp	276	275
Peak_Molarity	41.00	52.60
libSampleQC_DNA_Well	DNA_Library_set41/set5/A8.png	DNA_Library_set41/set5/B8.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set41/set1/E7.png	RNA_Library_set41/set1/F7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-08-08	2018-08-08
Sample_ID	BGHcLV10-13	BGHcLV10-14
RBP	CNOT7	CNOT7
Batch_ID	BGHcLV10	BGHcLV10
WB_result	71.300	75.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	903	904

Sequencing Information

	BGHcLV10-13	BGHcLV10-14
Sample_ID	BGHcLV10-13	BGHcLV10-14
Sample Name	CNOT7-BGHcLV10-13	CNOT7-BGHcLV10-14
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	240,142,288	123,571,304
total_aligned_reads	234,665,856	118,269,518
unique_aligned_reads	217,425,666	109,921,522
percent_uniqueAligned	0.90540	0.88954
correlation_replicates	0.995955	0.995955
spikein_reads	552,810	306,578
percent_spikeins	0.00230	0.00248
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	309	310

Data Submission Information

	BGHcLV10-13	BGHcLV10-13	BGHcLV10-13	BGHcLV10-13	BGHcLV10-13	BGHcLV10-13	BGHcLV10-14	BGHcLV10-14	BGHcLV10-14	BGHcLV10-14
ENCODE_alias	brenton-graveley:CNOT7-BGHcLV10	brenton-graveley:CNOT7-BGHcLV10-13	brenton-graveley:L-CNOT7-BGHcLV10-13	brenton-graveley:CNOT7-BGHcLV10-13_TGCGGCGT+CCTCGGTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CNOT7-BGHcLV10-13_TGCGGCGT+CCTCGGTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CNOT7-BGHcLV10-HepG2	brenton-graveley:CNOT7-BGHcLV10-14	brenton-graveley:L-CNOT7-BGHcLV10-14	brenton-graveley:CNOT7-BGHcLV10-14_CATAATAC+TTCTAACG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CNOT7-BGHcLV10-14_CATAATAC+TTCTAACG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR836XZH	ENCBS662RXQ	ENCLB243TQF	ENCFF077CID	ENCFF509QUZ	ENCSR548YWH	ENCBS856QCN	ENCLB349IKL	ENCFF185ASO	ENCFF165CCI
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	BGHcLV10-13	BGHcLV10-13	BGHcLV10-13	BGHcLV10-13	BGHcLV10-13	BGHcLV10-13	BGHcLV10-14	BGHcLV10-14	BGHcLV10-14	BGHcLV10-14
Sample Name	CNOT7-BGHcLV10-13	CNOT7-BGHcLV10-13	CNOT7-BGHcLV10-13	CNOT7-BGHcLV10-13	CNOT7-BGHcLV10-13	CNOT7-BGHcLV10-13	CNOT7-BGHcLV10-14	CNOT7-BGHcLV10-14	CNOT7-BGHcLV10-14	CNOT7-BGHcLV10-14
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV41_biosample_protocol	LV41_library_protocol				LV41_biosample_protocol	LV41_library_protocol
protocol_URL		CNOT7-BGHcLV10-13.pdf	L-CNOT7-BGHcLV10-13.pdf				CNOT7-BGHcLV10-14.pdf	L-CNOT7-BGHcLV10-14.pdf
ID	1119	1158	1228	1298	1368	7151	1159	1229	1299	1369

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
CNOT7-BGHcLV10-13_TGCGGCGT+CCTCGGTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	309				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	505
CNOT7-BGHcLV10-13_TGCGGCGT+CCTCGGTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	309				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	575
CNOT7-BGHcLV10-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	309	GRCh38	V40	CNOT7-BGHcLV10-13_TGCGGCGT+CCTCGGTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT7-BGHcLV10-13_TGCGGCGT+CCTCGGTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26743
CNOT7-BGHcLV10-13_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	309	GRCh38	V40	CNOT7-BGHcLV10-13/Aligned.sortedByCoord.out.bam		ENCORE2	26813
CNOT7-BGHcLV10-13_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	309	GRCh38	V40	CNOT7-BGHcLV10-13/Aligned.sortedByCoord.out.bam		ENCORE2	26883
CNOT7-BGHcLV10-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	309	GRCh38	V40	CNOT7-BGHcLV10-13/Aligned.sortedByCoord.out.bam		ENCORE2	26953
CNOT7-BGHcLV10-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	309	GRCh38	V40	CNOT7-BGHcLV10-13/Aligned.sortedByCoord.out.bam		ENCORE2	27023
CNOT7-BGHcLV10-13_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	309	GRCh38	V40	CNOT7-BGHcLV10-13_TGCGGCGT+CCTCGGTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT7-BGHcLV10-13_TGCGGCGT+CCTCGGTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27093
CNOT7-BGHcLV10-14_CATAATAC+TTCTAACG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	310				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	506
CNOT7-BGHcLV10-14_CATAATAC+TTCTAACG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	310				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	576
CNOT7-BGHcLV10-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	310	GRCh38	V40	CNOT7-BGHcLV10-14_CATAATAC+TTCTAACG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT7-BGHcLV10-14_CATAATAC+TTCTAACG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26744
CNOT7-BGHcLV10-14_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	310	GRCh38	V40	CNOT7-BGHcLV10-14/Aligned.sortedByCoord.out.bam		ENCORE2	26814
CNOT7-BGHcLV10-14_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	310	GRCh38	V40	CNOT7-BGHcLV10-14/Aligned.sortedByCoord.out.bam		ENCORE2	26884
CNOT7-BGHcLV10-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	310	GRCh38	V40	CNOT7-BGHcLV10-14/Aligned.sortedByCoord.out.bam		ENCORE2	26954
CNOT7-BGHcLV10-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	310	GRCh38	V40	CNOT7-BGHcLV10-14/Aligned.sortedByCoord.out.bam		ENCORE2	27024
CNOT7-BGHcLV10-14_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	310	GRCh38	V40	CNOT7-BGHcLV10-14_CATAATAC+TTCTAACG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT7-BGHcLV10-14_CATAATAC+TTCTAACG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27094