CNOT7 RNA-Seq in HepG2

General Information


RBP	CNOT7
Cell_Line	HepG2
Method	shRNA
Exp_Name	CNOT7-BGHLV22-HepG2
ENCODE_series_ID	ENCSR840NRJ
Batch_ID	BGHLV22
Pool ID	Pool-150705
Local_Set_Name	set22
ENCODE_KD_Exp_ID	ENCSR274KWA
ENCODE_CN_Exp_ID	ENCSR279HMU
Rep1	CNOT7-BGHLV22-5_17750
Rep2	CNOT7-BGHLV22-6_17751
CN1	non-target-BGHLV22-1_17746
CN2	non-target-BGHLV22-2_17747
Rep1_qPCR	78.2
Rep2_qPCR	72.5
Rep1_WB
Rep2_WB	NO CLEAR BAND
Antibody Cat#	GTX118241
Antibody Lot#	LOT# 40667
Antibody DCC ID	ENCAB389TLX
Status	Archived
Project	ENCODE3
ID	533

Experiment Information (Status: Released)

	BGHLV22-5	BGHLV22-6
idx	433	434
TRCN#_or_BGC#	TRCN0000017870	TRCN0000017870
shRNA_or_gRNA_sequence	GCTGACTATCAATACCAACTA	GCTGACTATCAATACCAACTA
PAM
Name	CNOT7	CNOT7
Sample_ID	BGHLV22-5	BGHLV22-6
transduction_Date	10/16/2014	10/16/2014
days
RBP_name	CNOT7	CNOT7
qPCR_result	78.2	72.5
Ave_qPCR	75.4
RT-qPCR_primer-F	GAGTGGTCCTCTGTGAAGGG
RT-qPCR_primer-R	TCTTCAGGCAAGTTAGAGTTGG
protein_conc	5343	4807
WB_result		NO CLEAR BAND
Ave_WB	NO CLEAR BAND
WB_DONE_date	4/6/2015
MW	28kd
IP	1	1
antibody_Cat#	GTX118241	GTX118241
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	20.1	0
Rep2_TPM	15.8	0
Action
Library_start_date	6/5/2015	6/5/2015
repeat_library
Note
ID	2500	2501

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV22-5	BGHLV22-6
Sample_ID	BGHLV22-5	BGHLV22-6
Sample Name	CNOT7-BGHLV22-5_17750	CNOT7-BGHLV22-6_17751
Sample Name	CNOT7-BGHLV22-5_17750	CNOT7-BGHLV22-6_17751
RBP	CNOT7	CNOT7
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	780	781

Library-Prep
Sequencing

Library-Prep Information

	BGHLV22-5	BGHLV22-6
Sample #
Sample Name	CNOT7-BGHLV22-5	CNOT7-BGHLV22-6
Sample_Name_Alias	CNOT7-BGHLV22-5_17750	CNOT7-BGHLV22-6_17751
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-05	2015-06-05
Lib_ID	Lib-150605	Lib-150605
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/E6.png	DNA_Library_LV20-22-23/set1/F6.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/B4.png	RNA_Library_LV19-21-24/set2/C4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV22-5	BGHLV22-6
RBP	CNOT7	CNOT7
Batch_ID	BGHLV22	BGHLV22
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2466	2467

Sequencing Information

	BGHLV22-5	BGHLV22-6
Sample_ID	BGHLV22-5	BGHLV22-6
Sample Name	CNOT7-BGHLV22-5_17750	CNOT7-BGHLV22-6_17751
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set22	set22
total_reads	49,620,000	53,330,000
total_aligned_reads	45,385,994	48,753,664
unique_aligned_reads	42,976,768	46,214,288
percent_uniqueAligned	0.86612	0.86657
correlation_replicates	0.998721	0.998721
spikein_reads	267,438	297,348
percent_spikeins	0.00539	0.00558
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1200	1201

Data Submission Information

	BGHLV22-5	BGHLV22-5
ENCODE_alias	brenton-graveley:CNOT7-BGHLV22	brenton-graveley:CNOT7-BGHLV22-HepG2
ENCODE_accession	ENCSR274KWA	ENCSR840NRJ
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV22-5	BGHLV22-5
Sample Name	CNOT7-BGHLV22-5_17750	CNOT7-BGHLV22-5_17750
Selected	Yes	No
Status	Released	Archived
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2922	6623

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
CNOT7-BGHLV22-5_17750_ACAGTG_L007_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1200	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16274
CNOT7-BGHLV22-5_17750_ACAGTG_L007_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1200	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16314
CNOT7-BGHLV22-5_17750_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1200					GRCh38	V40	CNOT7-BGHLV22-5_17750_ACAGTG_L007_R1_001.fastq.gz,CNOT7-BGHLV22-5_17750_ACAGTG_L007_R2_001.fastq.gz		ENCORE2	16412
CNOT7-BGHLV22-5_17750_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1200					GRCh38	V40	CNOT7-BGHLV22-5_17750/Aligned.sortedByCoord.out.bam		ENCORE2	16452
CNOT7-BGHLV22-5_17750_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1200					GRCh38	V40	CNOT7-BGHLV22-5_17750/Aligned.sortedByCoord.out.bam		ENCORE2	16492
CNOT7-BGHLV22-5_17750_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1200					GRCh38	V40	CNOT7-BGHLV22-5_17750/Aligned.sortedByCoord.out.bam		ENCORE2	16532
CNOT7-BGHLV22-5_17750_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1200					GRCh38	V40	CNOT7-BGHLV22-5_17750/Aligned.sortedByCoord.out.bam		ENCORE2	16572
CNOT7-BGHLV22-5_17750_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1200					GRCh38	V40	CNOT7-BGHLV22-5_17750_ACAGTG_L007_R1_001.fastq.gz,CNOT7-BGHLV22-5_17750_ACAGTG_L007_R2_001.fastq.gz		ENCORE2	16612
CNOT7-BGHLV22-6_17751_GCCAAT_L007_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1201	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16275
CNOT7-BGHLV22-6_17751_GCCAAT_L007_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1201	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16315
CNOT7-BGHLV22-6_17751_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1201					GRCh38	V40	CNOT7-BGHLV22-6_17751_GCCAAT_L007_R1_001.fastq.gz,CNOT7-BGHLV22-6_17751_GCCAAT_L007_R2_001.fastq.gz		ENCORE2	16413
CNOT7-BGHLV22-6_17751_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1201					GRCh38	V40	CNOT7-BGHLV22-6_17751/Aligned.sortedByCoord.out.bam		ENCORE2	16453
CNOT7-BGHLV22-6_17751_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1201					GRCh38	V40	CNOT7-BGHLV22-6_17751/Aligned.sortedByCoord.out.bam		ENCORE2	16493
CNOT7-BGHLV22-6_17751_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1201					GRCh38	V40	CNOT7-BGHLV22-6_17751/Aligned.sortedByCoord.out.bam		ENCORE2	16533
CNOT7-BGHLV22-6_17751_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1201					GRCh38	V40	CNOT7-BGHLV22-6_17751/Aligned.sortedByCoord.out.bam		ENCORE2	16573
CNOT7-BGHLV22-6_17751_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1201					GRCh38	V40	CNOT7-BGHLV22-6_17751_GCCAAT_L007_R1_001.fastq.gz,CNOT7-BGHLV22-6_17751_GCCAAT_L007_R2_001.fastq.gz		ENCORE2	16613