CNOT7 RNA-Seq in K562

General Information


RBP	CNOT7
Cell_Line	K562
Method	shRNA
Exp_Name	CNOT7-BGKLV24-K562
ENCODE_series_ID	ENCSR219JLD
Batch_ID	BGKLV24
Pool ID	Pool-151101
Local_Set_Name	set24_2
ENCODE_KD_Exp_ID	ENCSR113PYX
ENCODE_CN_Exp_ID	ENCSR419JMU
Rep1	CNOT7_BGKLV24_7B
Rep2	CNOT7_BGKLV24_8B
CN1	non-target_BGKLV24_1B
CN2	non-target_BGKLV24_2B
Rep1_qPCR	92.4
Rep2_qPCR	89.8
Rep1_WB
Rep2_WB
Antibody Cat#	GTX118241
Antibody Lot#	LOT# 40667
Antibody DCC ID	ENCAB389TLX
Status	Released
Project	ENCODE3
ID	602

Experiment Information (Status: Released)

	BGKLV24-7	BGKLV24-8
idx	344	345
TRCN#_or_BGC#	TRCN0000017870	TRCN0000017870
shRNA_or_gRNA_sequence	GCTGACTATCAATACCAACTA	GCTGACTATCAATACCAACTA
PAM
Name	CNOT7	CNOT7
Sample_ID	BGKLV24-7	BGKLV24-8
transduction_Date	2/27/2015	2/27/2015
days
RBP_name	CNOT7	CNOT7
qPCR_result	92.4	89.8
Ave_qPCR	91.1
RT-qPCR_primer-F	GAGTGGTCCTCTGTGAAGGG
RT-qPCR_primer-R	TCTTCAGGCAAGTTAGAGTTGG
protein_conc	4123	4266
WB_result
Ave_WB	NO CLEAR BAND
WB_DONE_date	4/6/2015
MW	33kDa
IP	1	1
antibody_Cat#	GTX118241	GTX118241
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	17.0738428	0
Rep2_TPM	10.996456	0
Action
Library_start_date	9/2/2015	9/2/2015
repeat_library
Note	Balaji going to sent MBL AB
ID	391	392

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV24-7	BGKLV24-8
Sample_ID	BGKLV24-7	BGKLV24-8
Sample Name	CNOT7_BGKLV24_7B	CNOT7_BGKLV24_8B
Sample Name	CNOT7_BGKLV24_7B	CNOT7_BGKLV24_8B
RBP	CNOT7	CNOT7
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	884	885

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-7	BGKLV24-8
Sample #
Sample Name	CNOT7-BGKLV24-7B	CNOT7-BGKLV24-8B
Sample_Name_Alias	CNOT7_BGKLV24_7B	CNOT7_BGKLV24_8B
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-02	2015-09-02
Lib_ID	Lib-150902	Lib-150902
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/C5.png	DNA_Library_LV24-25-26/set1/D5.png
RIN	9.1	9.1
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/C1.png	RNA_Library_LV20-22-24/set1/D1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-7	BGKLV24-8
RBP	CNOT7	CNOT7
Batch_ID	BGKLV24	BGKLV24
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2572	2573

Sequencing Information

	BGKLV24-7	BGKLV24-8
Sample_ID	BGKLV24-7	BGKLV24-8
Sample Name	CNOT7_BGKLV24_7B	CNOT7_BGKLV24_8B
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set24_2	set24_2
total_reads	82,598,758	97,127,810
total_aligned_reads	78,828,794	94,140,270
unique_aligned_reads	71,601,346	85,388,492
percent_uniqueAligned	0.86686	0.87914
correlation_replicates	0.985805	0.985805
spikein_reads	270,074	361,244
percent_spikeins	0.00327	0.00372
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1214	1215

Data Submission Information

	BGKLV24-7	BGKLV24-7
ENCODE_alias	brenton-graveley:CNOT7_BGKLV24_B	brenton-graveley:CNOT7-BGKLV24-K562
ENCODE_accession	ENCSR113PYX	ENCSR219JLD
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-7	BGKLV24-7
Sample Name	CNOT7_BGKLV24_7B	CNOT7_BGKLV24_7B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2991	6624

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_BGKLV24_7B_TTAGGC_L001_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1214	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz	ENCODE3	17470
CNOT7_BGKLV24_7B_TTAGGC_L001_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1214	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCODE3	17494
CNOT7_BGKLV24_7B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1214					GRCh38	V40	CNOT7_BGKLV24_7B_TTAGGC_L001_001.R1.fastq.gz,CNOT7_BGKLV24_7B_TTAGGC_L001_001.R2.fastq.gz		ENCORE2	17518
CNOT7_BGKLV24_7B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1214					GRCh38	V40	CNOT7_BGKLV24_7B/Aligned.sortedByCoord.out.bam		ENCORE2	17542
CNOT7_BGKLV24_7B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1214					GRCh38	V40	CNOT7_BGKLV24_7B/Aligned.sortedByCoord.out.bam		ENCORE2	17566
CNOT7_BGKLV24_7B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1214					GRCh38	V40	CNOT7_BGKLV24_7B/Aligned.sortedByCoord.out.bam		ENCORE2	17590
CNOT7_BGKLV24_7B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1214					GRCh38	V40	CNOT7_BGKLV24_7B/Aligned.sortedByCoord.out.bam		ENCORE2	17614
CNOT7_BGKLV24_7B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1214					GRCh38	V40	CNOT7_BGKLV24_7B_TTAGGC_L001_001.R1.fastq.gz,CNOT7_BGKLV24_7B_TTAGGC_L001_001.R2.fastq.gz		ENCORE2	17638
CNOT7_BGKLV24_8B_TGACCA_L001_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1215	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz	ENCODE3	17471
CNOT7_BGKLV24_8B_TGACCA_L001_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1215	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCODE3	17495
CNOT7_BGKLV24_8B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1215					GRCh38	V40	CNOT7_BGKLV24_8B_TGACCA_L001_001.R1.fastq.gz,CNOT7_BGKLV24_8B_TGACCA_L001_001.R2.fastq.gz		ENCORE2	17519
CNOT7_BGKLV24_8B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1215					GRCh38	V40	CNOT7_BGKLV24_8B/Aligned.sortedByCoord.out.bam		ENCORE2	17543
CNOT7_BGKLV24_8B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1215					GRCh38	V40	CNOT7_BGKLV24_8B/Aligned.sortedByCoord.out.bam		ENCORE2	17567
CNOT7_BGKLV24_8B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1215					GRCh38	V40	CNOT7_BGKLV24_8B/Aligned.sortedByCoord.out.bam		ENCORE2	17591
CNOT7_BGKLV24_8B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1215					GRCh38	V40	CNOT7_BGKLV24_8B/Aligned.sortedByCoord.out.bam		ENCORE2	17615
CNOT7_BGKLV24_8B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1215					GRCh38	V40	CNOT7_BGKLV24_8B_TGACCA_L001_001.R1.fastq.gz,CNOT7_BGKLV24_8B_TGACCA_L001_001.R2.fastq.gz		ENCORE2	17639