COPB1 RNA-Seq in K562

General Information


RBP	COPB1
Cell_Line	K562
Method	CRISPR
Exp_Name	COPB1-BGKcLV46-K562
ENCODE_series_ID
Batch_ID	BGKcLV46
Pool ID	Pool-250312
Local_Set_Name	set77
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	COPB1-BGKcLV46-11
Rep2	COPB1-BGKcLV46-12
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR	11.6
Rep2_qPCR	21.0
Rep1_WB	80.4
Rep2_WB	76.9
Antibody Cat#	A304-724A
Antibody Lot#
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1636

Experiment Information (Status: Submitting)

	BGKcLV46-11	BGKcLV46-11	BGKcLV46-12	BGKcLV46-12
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0001228	BGC#0001228	BGC#0001228	BGC#0001228
shRNA_or_gRNA_sequence	ATAACCAGAAACCATGACGG	ATAACCAGAAACCATGACGG	ATAACCAGAAACCATGACGG	ATAACCAGAAACCATGACGG
PAM	CGG	CGG	CGG	CGG
Name	COPB1_89U	COPB1_89U	COPB1_89U	COPB1_89U
Sample_ID	BGKcLV46-11	BGKcLV46-11	BGKcLV46-12	BGKcLV46-12
transduction_Date	12/20/24	12/20/24	12/20/24	12/20/24
days	D6	D6	D6	D6
RBP_name	COPB1	COPB1	COPB1	COPB1
qPCR_result	11.6	11.6	21.0	21.0
Ave_qPCR	16.3	16.3
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4169	4169	3995	3995
WB_result	80.4	63.8	76.9	75.5363
Ave_WB
WB_DONE_date	12/31/24	1/31/25,1/13/25
MW
IP
antibody_Cat#	A304-724A	A304-723A		lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	5997	5999	5998	6000

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
COPB1	Product_ID: A304-724A Lot_ID: 1 Source: Bethyl Labs Target Name: COPB1-human
COPB1	Product_ID: A304-723A Lot_ID: 1 Source: Bethyl Labs Target Name: COPB1-human

Experiment Status

	BGKcLV46-11	BGKcLV46-11	BGKcLV46-12	BGKcLV46-12
Sample_ID	BGKcLV46-11	BGKcLV46-11	BGKcLV46-12	BGKcLV46-12
Sample Name
Sample Name	COPB1-BGKcLV46-11		COPB1-BGKcLV46-12
RBP	COPB1	COPB1	COPB1	COPB1
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2025-04-21	2025-02-10	2025-04-21	2025-02-10
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	14026	14076	14027	14077

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-11	BGKcLV46-12
Sample #	5	6
Sample Name	COPB1-BGKcLV46-11	COPB1-BGKcLV46-12
Sample_Name_Alias
Index Well Position	E01	F01
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-02-20	2025-02-20
Lib_ID	Lib-250220	Lib-250220
Tecan_Location
Tecan
Tecan_date
Size_bp	299	299
Peak_Molarity	96.40	90.00
libSampleQC_DNA_Well	DNA_Library_set77/set1/E7.png	DNA_Library_set77/set1/F7.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set77/set1/E1.png	RNA_Library_set77/set1/F1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-11	BGKcLV46-12
RBP	COPB1	COPB1
Batch_ID	BGKcLV46	BGKcLV46
WB_result	80.400	76.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4664	4665

Sequencing Information

	BGKcLV46-11	BGKcLV46-12
Sample_ID	BGKcLV46-11	BGKcLV46-12
Sample Name	COPB1-BGKcLV46-11	COPB1-BGKcLV46-12
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	40,646,825	49,433,218
total_aligned_reads	37,021,532	44,681,756
unique_aligned_reads	34,013,483	41,158,798
percent_uniqueAligned	0.83681	0.83261
correlation_replicates	0.990650	0.990650
spikein_reads	95,104	156,506
percent_spikeins	0.00234	0.00317
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3369	3370

Data Submission Information DCC submission information was not avaliable

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
COPB1-BGKcLV46-11_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3369	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32150
COPB1-BGKcLV46-11_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3369	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32200
COPB1-BGKcLV46-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3369					GRCh38	V40	COPB1-BGKcLV46-11_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,COPB1-BGKcLV46-11_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32250
COPB1-BGKcLV46-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3369					GRCh38	V40	COPB1-BGKcLV46-11_Aligned.sortedByCoord.out.bam		ENCORE2	32300
COPB1-BGKcLV46-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3369					GRCh38	V40	COPB1-BGKcLV46-11_Aligned.sortedByCoord.out.bam		ENCORE2	32350
COPB1-BGKcLV46-11_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3369					GRCh38	V40	COPB1-BGKcLV46-11_Aligned.sortedByCoord.out.bam		ENCORE2	32400
COPB1-BGKcLV46-11_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3369					GRCh38	V40	COPB1-BGKcLV46-11_Aligned.sortedByCoord.out.bam		ENCORE2	32450
COPB1-BGKcLV46-11_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3369					GRCh38	V40	COPB1-BGKcLV46-11_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,COPB1-BGKcLV46-11_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32500
COPB1-BGKcLV46-12_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3370	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32151
COPB1-BGKcLV46-12_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3370	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32201
COPB1-BGKcLV46-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3370					GRCh38	V40	COPB1-BGKcLV46-12_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,COPB1-BGKcLV46-12_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32251
COPB1-BGKcLV46-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3370					GRCh38	V40	COPB1-BGKcLV46-12_Aligned.sortedByCoord.out.bam		ENCORE2	32301
COPB1-BGKcLV46-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3370					GRCh38	V40	COPB1-BGKcLV46-12_Aligned.sortedByCoord.out.bam		ENCORE2	32351
COPB1-BGKcLV46-12_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3370					GRCh38	V40	COPB1-BGKcLV46-12_Aligned.sortedByCoord.out.bam		ENCORE2	32401
COPB1-BGKcLV46-12_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3370					GRCh38	V40	COPB1-BGKcLV46-12_Aligned.sortedByCoord.out.bam		ENCORE2	32451
COPB1-BGKcLV46-12_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3370					GRCh38	V40	COPB1-BGKcLV46-12_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,COPB1-BGKcLV46-12_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32501