CNOT2 RNA-Seq in K562

General Information


RBP	CNOT2
Cell_Line	K562
Method	CRISPR
Exp_Name	CNOT2-BGKcLV23-K562
ENCODE_series_ID	ENCSR693JZN
Batch_ID	BGKcLV23
Pool ID	Pool-201204
Local_Set_Name	set46_K
ENCODE_KD_Exp_ID	ENCSR663BBL
ENCODE_CN_Exp_ID	ENCSR877JEM
Rep1	CNOT2-BGKcLV23-29
Rep2	CNOT2-BGKcLV23-30
CN1	NT-BGKcLV23-1
CN2	NT-BGKcLV23-2
Rep1_qPCR	7.0
Rep2_qPCR	0.0
Rep1_WB	71.6
Rep2_WB	75.8
Antibody Cat#	A302-562A
Antibody Lot#	no lot#
Antibody DCC ID
Status	Released
Project	ENCODE4
ID	27

Experiment Information (Status: Released)

	BGKcLV23-29	BGKcLV23-30
idx	815	816
TRCN#_or_BGC#	BGC#0000501	BGC#0000501
shRNA_or_gRNA_sequence	GGGTTACTAACATTCCTCAA	GGGTTACTAACATTCCTCAA
PAM	GGG	GGG
Name	CNOT2_84	CNOT2_84
Sample_ID	BGKcLV23-29	BGKcLV23-30
transduction_Date	9/17/20	9/17/20
days	Day 6	Day 6
RBP_name	CNOT2	CNOT2
qPCR_result	7.0	0.0
Ave_qPCR	3.5
RT-qPCR_primer-F	TTATCAGGGCAGCAGAGACAG
RT-qPCR_primer-R	CGCAAATTTGGGGTAGAGATT
protein_conc	2934	2834
WB_result	71.6	75.8
Ave_WB	73.7
WB_DONE_date	10/13/20
MW	59.7KD
IP	Rabbit / I
antibody_Cat#	A302-562A	no lot#
Antibody DCC ID
submitted_to_DCC_date	NO ID
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	4935	4936

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKcLV23-29	BGKcLV23-30
Sample_ID	BGKcLV23-29	BGKcLV23-30
Sample Name
Sample Name	CNOT2-BGKcLV23-29	CNOT2-BGKcLV23-30
RBP	CNOT2	CNOT2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7443	7444

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV23-29	BGKcLV23-30
Sample #	45	46
Sample Name	CNOT2-BGKcLV23-29	CNOT2-BGKcLV23-30
Sample_Name_Alias
Index Well Position	E06	F06
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	296	289
Peak_Molarity	223.00	158.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/E6.png	DNA_Library_set46/set1/F6.png
RIN	9.3	8.7
libSample_RNA_Well	RNA_Library_set46/set2/E10.png	RNA_Library_set46/set2/F10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGKcLV23-29	BGKcLV23-30
RBP	CNOT2	CNOT2
Batch_ID	BGKcLV23	BGKcLV23
WB_result	71.600	75.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1420	1421

Sequencing Information

	BGKcLV23-29	BGKcLV23-30
Sample_ID	BGKcLV23-29	BGKcLV23-30
Sample Name	CNOT2-BGKcLV23-29	CNOT2-BGKcLV23-30
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_K	set46_K
total_reads	252,623,214	208,225,762
total_aligned_reads	235,547,948	194,393,274
unique_aligned_reads	213,731,110	177,845,320
percent_uniqueAligned	0.84605	0.85410
correlation_replicates	0.997682	0.997682
spikein_reads	94,368	78,874
percent_spikeins	0.00037	0.00038
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	526	527

Data Submission Information

	BGKcLV23-29	BGKcLV23-29	BGKcLV23-29	BGKcLV23-29	BGKcLV23-29	BGKcLV23-29	BGKcLV23-30	BGKcLV23-30	BGKcLV23-30	BGKcLV23-30
ENCODE_alias	brenton-graveley:CNOT2-BGKcLV23	brenton-graveley:CNOT2-BGKcLV23-29	brenton-graveley:L-CNOT2-BGKcLV23-29	brenton-graveley:CNOT2-BGKcLV23-29_ATGGCATG+GGTACCTT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CNOT2-BGKcLV23-29_ATGGCATG+GGTACCTT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CNOT2-BGKcLV23-K562	brenton-graveley:CNOT2-BGKcLV23-30	brenton-graveley:L-CNOT2-BGKcLV23-30	brenton-graveley:CNOT2-BGKcLV23-30_GCAATGCA+AACGTTCC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CNOT2-BGKcLV23-30_GCAATGCA+AACGTTCC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR663BBL	ENCBS721LOQ	ENCLB834XBA	ENCFF443NYA	ENCFF461TYE	ENCSR693JZN	ENCBS739YPH	ENCLB207LOE	ENCFF710DRC	ENCFF272CQB
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	BGKcLV23-29	BGKcLV23-29	BGKcLV23-29	BGKcLV23-29	BGKcLV23-29	BGKcLV23-29	BGKcLV23-30	BGKcLV23-30	BGKcLV23-30	BGKcLV23-30
Sample Name	CNOT2-BGKcLV23-29	CNOT2-BGKcLV23-29	CNOT2-BGKcLV23-29	CNOT2-BGKcLV23-29	CNOT2-BGKcLV23-29	CNOT2-BGKcLV23-29	CNOT2-BGKcLV23-30	CNOT2-BGKcLV23-30	CNOT2-BGKcLV23-30	CNOT2-BGKcLV23-30
Selected	Yes	No	Yes	Yes	Yes	Yes	No	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
			LV46K_library_protocol					LV46K_library_protocol
protocol_URL			L-CNOT2-BGKcLV23-29.pdf					L-CNOT2-BGKcLV23-30.pdf
ID	2417	2471	2535	2629	2663	7150	2472	2536	2630	2664

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
CNOT2-BGKcLV23-29_ATGGCATG+GGTACCTT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	526	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1390
CNOT2-BGKcLV23-29_ATGGCATG+GGTACCTT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	526	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1454
CNOT2-BGKcLV23-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	526					GRCh38	V40	CNOT2-BGKcLV23-29_ATGGCATG+GGTACCTT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT2-BGKcLV23-29_ATGGCATG+GGTACCTT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25293
CNOT2-BGKcLV23-29_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	526					GRCh38	V40	CNOT2-BGKcLV23-29_ATGGCATG+GGTACCTT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT2-BGKcLV23-29_ATGGCATG+GGTACCTT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25327
CNOT2-BGKcLV23-29_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	526					GRCh38	V40	CNOT2-BGKcLV23-29/Aligned.sortedByCoord.out.bam		ENCORE2	26131
CNOT2-BGKcLV23-29_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	526					GRCh38	V40	CNOT2-BGKcLV23-29/Aligned.sortedByCoord.out.bam		ENCORE2	26165
CNOT2-BGKcLV23-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	526					GRCh38	V40	CNOT2-BGKcLV23-29/Aligned.sortedByCoord.out.bam		ENCORE2	26199
CNOT2-BGKcLV23-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	526					GRCh38	V40	CNOT2-BGKcLV23-29/Aligned.sortedByCoord.out.bam		ENCORE2	26233
CNOT2-BGKcLV23-30_GCAATGCA+AACGTTCC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	527	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1391
CNOT2-BGKcLV23-30_GCAATGCA+AACGTTCC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	527	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1455
CNOT2-BGKcLV23-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	527					GRCh38	V40	CNOT2-BGKcLV23-30_GCAATGCA+AACGTTCC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT2-BGKcLV23-30_GCAATGCA+AACGTTCC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25294
CNOT2-BGKcLV23-30_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	527					GRCh38	V40	CNOT2-BGKcLV23-30_GCAATGCA+AACGTTCC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNOT2-BGKcLV23-30_GCAATGCA+AACGTTCC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25328
CNOT2-BGKcLV23-30_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	527					GRCh38	V40	CNOT2-BGKcLV23-30/Aligned.sortedByCoord.out.bam		ENCORE2	26132
CNOT2-BGKcLV23-30_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	527					GRCh38	V40	CNOT2-BGKcLV23-30/Aligned.sortedByCoord.out.bam		ENCORE2	26166
CNOT2-BGKcLV23-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	527					GRCh38	V40	CNOT2-BGKcLV23-30/Aligned.sortedByCoord.out.bam		ENCORE2	26200
CNOT2-BGKcLV23-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	527					GRCh38	V40	CNOT2-BGKcLV23-30/Aligned.sortedByCoord.out.bam		ENCORE2	26234