CNOT10 RNA-Seq in K562

General Information


RBP	CNOT10
Cell_Line	K562
Method	CRISPR
Exp_Name	CNOT10-BGKcLV21-K562
ENCODE_series_ID	ENCSR224BFG
Batch_ID	BGKcLV21
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR644LYC
ENCODE_CN_Exp_ID	ENCSR854OFV
Rep1	CNOT10-BGKcLV21-7
Rep2	CNOT10-BGKcLV21-8
CN1	NT-BGKcLV21-1
CN2	NT-BGKcLV21-2
Rep1_qPCR	74.0
Rep2_qPCR	62.7
Rep1_WB	74.8
Rep2_WB	76.6
Antibody Cat#	A304-899A
Antibody Lot#	Lot# 1
Antibody DCC ID	ENCAB805LWE
Status	Released
Project	ENCODE4
ID	63

Experiment Information (Status: Released)

	BGKcLV21-7	BGKcLV21-8
idx	740	741
TRCN#_or_BGC#	BGC#0000500	BGC#0000500
shRNA_or_gRNA_sequence	ACTTGCTTGCAGTGCCTACG	ACTTGCTTGCAGTGCCTACG
PAM	TGG	TGG
Name	CNOT10 _91	CNOT10 _91
Sample_ID	BGKcLV21-7	BGKcLV21-8
transduction_Date	8/4/20	8/4/20
days	Day 6	Day 6
RBP_name	CNOT10	CNOT10
qPCR_result	74.0	62.7
Ave_qPCR	68.4
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4415	4830
WB_result	74.8	76.6
Ave_WB	75.7
WB_DONE_date	9/17/20	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	09/24/20	09/24/20
repeat_library
Note
ID	4860	4861

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

	BGKcLV21-7	BGKcLV21-8
Sample_ID	BGKcLV21-7	BGKcLV21-8
Sample Name
Sample Name	CNOT10-BGKcLV21-7	CNOT10-BGKcLV21-8
RBP	CNOT10	CNOT10
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6117	6118

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV21-7	BGKcLV21-8
Sample #	35	36
Sample Name	CNOT10-BGKcLV21-7	CNOT10-BGKcLV21-8
Sample_Name_Alias
Index Well Position	E04	F04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-09-24	2020-09-24
Lib_ID	Lib-200924	Lib-200924
Tecan_Location
Tecan
Tecan_date
Size_bp	309	308
Peak_Molarity	329.00	322.00
libSampleQC_DNA_Well	DNA_Library_set45/set1/E4.png	DNA_Library_set45/set1/F4.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set45/set1/E4.png	RNA_Library_set45/set1/F4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGKcLV21-7	BGKcLV21-8
RBP	CNOT10	CNOT10
Batch_ID	BGKcLV21	BGKcLV21
WB_result	74.800	76.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	809	810

Sequencing Information

	BGKcLV21-7	BGKcLV21-8
Sample_ID	BGKcLV21-7	BGKcLV21-8
Sample Name	CNOT10-BGKcLV21-7	CNOT10-BGKcLV21-8
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	197,433,120	121,922,578
total_aligned_reads	193,636,874	118,538,738
unique_aligned_reads	176,561,802	108,155,980
percent_uniqueAligned	0.89429	0.88709
correlation_replicates	0.993658	0.993658
spikein_reads	96,778	53,846
percent_spikeins	0.00049	0.00044
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	440	441

Data Submission Information

	BGKcLV21-7	BGKcLV21-7	BGKcLV21-7	BGKcLV21-7	BGKcLV21-7	BGKcLV21-7	BGKcLV21-8	BGKcLV21-8	BGKcLV21-8	BGKcLV21-8
ENCODE_alias	brenton-graveley:CNOT10-BGKcLV21	brenton-graveley:CNOT10-BGKcLV21-7	brenton-graveley:L-CNOT10-BGKcLV21-7	brenton-graveley:CNOT10-BGKcLV21-7_S29_R1_001.fastq.gz	brenton-graveley:CNOT10-BGKcLV21-7_S29_R2_001.fastq.gz	brenton-graveley:CNOT10-BGKcLV21-K562	brenton-graveley:CNOT10-BGKcLV21-8	brenton-graveley:L-CNOT10-BGKcLV21-8	brenton-graveley:CNOT10-BGKcLV21-8_S30_R1_001.fastq.gz	brenton-graveley:CNOT10-BGKcLV21-8_S30_R2_001.fastq.gz
ENCODE_accession	ENCSR644LYC	ENCBS252NYL	ENCLB610IIT	ENCFF728IRL	ENCFF320HML	ENCSR224BFG	ENCBS018RUQ	ENCLB746OKV	ENCFF203VRL	ENCFF979EZX
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	BGKcLV21-7	BGKcLV21-7	BGKcLV21-7	BGKcLV21-7	BGKcLV21-7	BGKcLV21-7	BGKcLV21-8	BGKcLV21-8	BGKcLV21-8	BGKcLV21-8
Sample Name	CNOT10-BGKcLV21-7	CNOT10-BGKcLV21-7	CNOT10-BGKcLV21-7	CNOT10-BGKcLV21-7	CNOT10-BGKcLV21-7	CNOT10-BGKcLV21-7	CNOT10-BGKcLV21-8	CNOT10-BGKcLV21-8	CNOT10-BGKcLV21-8	CNOT10-BGKcLV21-8
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV45K_biosample_protocol	LV45K_library_protocol				LV45K_biosample_protocol	LV45K_library_protocol
protocol_URL		CNOT10-BGKcLV21-7.pdf	L-CNOT10-BGKcLV21-7.pdf				CNOT10-BGKcLV21-8.pdf	L-CNOT10-BGKcLV21-8.pdf
ID	2104	2163	2233	2303	2373	7148	2164	2234	2304	2374

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-BGKcLV21-7_S29_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	440	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1212
CNOT10-BGKcLV21-7_S29_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	440	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1262
CNOT10-BGKcLV21-7_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	440					GRCh38	V40	CNOT10-BGKcLV21-7_S29_R1_001.filtered.trimmed.paired.fastq.gz,CNOT10-BGKcLV21-7_S29_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25205
CNOT10-BGKcLV21-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	440					GRCh38	V40	CNOT10-BGKcLV21-7_S29_R1_001.filtered.trimmed.paired.fastq.gz,CNOT10-BGKcLV21-7_S29_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27159
CNOT10-BGKcLV21-7_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	440					GRCh38	V40	CNOT10-BGKcLV21-7/Aligned.sortedByCoord.out.bam		ENCORE2	27209
CNOT10-BGKcLV21-7_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	440					GRCh38	V40	CNOT10-BGKcLV21-7/Aligned.sortedByCoord.out.bam		ENCORE2	27259
CNOT10-BGKcLV21-7_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	440					GRCh38	V40	CNOT10-BGKcLV21-7/Aligned.sortedByCoord.out.bam		ENCORE2	27309
CNOT10-BGKcLV21-7_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	440					GRCh38	V40	CNOT10-BGKcLV21-7/Aligned.sortedByCoord.out.bam		ENCORE2	27359
CNOT10-BGKcLV21-8_S30_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	441	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1213
CNOT10-BGKcLV21-8_S30_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	441	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1263
CNOT10-BGKcLV21-8_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	441					GRCh38	V40	CNOT10-BGKcLV21-8_S30_R1_001.filtered.trimmed.paired.fastq.gz,CNOT10-BGKcLV21-8_S30_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25206
CNOT10-BGKcLV21-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	441					GRCh38	V40	CNOT10-BGKcLV21-8_S30_R1_001.filtered.trimmed.paired.fastq.gz,CNOT10-BGKcLV21-8_S30_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27160
CNOT10-BGKcLV21-8_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	441					GRCh38	V40	CNOT10-BGKcLV21-8/Aligned.sortedByCoord.out.bam		ENCORE2	27210
CNOT10-BGKcLV21-8_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	441					GRCh38	V40	CNOT10-BGKcLV21-8/Aligned.sortedByCoord.out.bam		ENCORE2	27260
CNOT10-BGKcLV21-8_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	441					GRCh38	V40	CNOT10-BGKcLV21-8/Aligned.sortedByCoord.out.bam		ENCORE2	27310
CNOT10-BGKcLV21-8_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	441					GRCh38	V40	CNOT10-BGKcLV21-8/Aligned.sortedByCoord.out.bam		ENCORE2	27360