COPB1 RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV47-9	BGHcLV47-10
idx	1613	1614
TRCN#_or_BGC#	BGC#0001228	BGC#0001228
shRNA_or_gRNA_sequence	ATAACCAGAAACCATGACGG	ATAACCAGAAACCATGACGG
PAM	CGG	CGG
Name	COPB1_89U	COPB1_89U
Sample_ID	BGHcLV47-9	BGHcLV47-10
transduction_Date	1/28/25	1/28/25
days	D6	D6
RBP_name	COPB1	COPB1
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	tgttgtgaaccaaaccagtga
RT-qPCR_primer-R	aaaggagacggcttttccac
protein_conc	1825	2027
WB_result	60.0	59.2
Ave_WB
WB_DONE_date	2/5/25
MW	107kd
IP	Rabbit / I
antibody_Cat#	A304-723A	LOT #1
Antibody DCC ID	ENCAB732UJL
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9802	9803

Western Blot

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

Experiment Status

	BGHcLV47-9	BGHcLV47-10
Sample_ID	BGHcLV47-9	BGHcLV47-10
Sample Name
Sample Name	COPB1-BGHcLV47-9	COPB1-BGHcLV47-10
RBP	COPB1	COPB1
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-05-14	2025-05-14
Project	ENCORE2	ENCORE2
Note
ID	14154	14155

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV47-9	BGHcLV47-10
Sample #	7	8
Sample Name	COPB1-BGHcLV47-9	COPB1-BGHcLV47-10
Sample_Name_Alias
Index Well Position	G08	H08
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-04-23	2025-04-23
Lib_ID	Lib-250423	Lib-250423
Tecan_Location
Tecan
Tecan_date
Size_bp	256	268
Peak_Molarity	33.40	45.90
libSampleQC_DNA_Well	DNA_Library_set78/set1/G6.png	DNA_Library_set78/set1/H6.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set78/set1/G1.png	RNA_Library_set78/set1/H1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-04-22	2025-04-22
Sample_ID	BGHcLV47-9	BGHcLV47-10
RBP	COPB1	COPB1
Batch_ID	BGHcLV47	BGHcLV47
WB_result	60.000	59.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4718	4719

Sequencing Information

	BGHcLV47-9	BGHcLV47-10	BGHcLV47-10
Sample_ID	BGHcLV47-9	BGHcLV47-10	BGHcLV47-10
Sample Name	COPB1-BGHcLV47-9	COPB1-BGHcLV47-10	COPB1-BGHcLV47-10
Pool ID	Pool-250422	Pool-250422	Pool-250822
LocalServer_folder	set78	set78	set78
total_reads	15,804,102	26,579,407	14,536,398
total_aligned_reads	13,375,313	22,148,034	12,163,228
unique_aligned_reads	12,561,977	20,798,197	11,426,286
percent_uniqueAligned	0.79486	0.78249	0.78605
correlation_replicates	0.995186	0.995186	0.995347
spikein_reads	28,916	66,004	36,328
percent_spikeins	0.00183	0.00248	0.00250
original_ReadLength	101	101	151
QC_Status	ReadyToSubmit	ReadyToSubmit	ReadyToSubmit
ID	3421	3422	3599

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-BGHcLV47-9_S48_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3421	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32553
COPB1-BGHcLV47-9_S48_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3421	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32587
COPB1-BGHcLV47-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3421					GRCh38	V40	COPB1-BGHcLV47-9_S48_L002_R1_001.filtered.trimmed.paired.fastq.gz,COPB1-BGHcLV47-9_S48_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32621
COPB1-BGHcLV47-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3421					GRCh38	V40	COPB1-BGHcLV47-9_Aligned.sortedByCoord.out.bam		ENCORE2	32655
COPB1-BGHcLV47-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3421					GRCh38	V40	COPB1-BGHcLV47-9_Aligned.sortedByCoord.out.bam		ENCORE2	32689
COPB1-BGHcLV47-9_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3421					GRCh38	V40	COPB1-BGHcLV47-9_Aligned.sortedByCoord.out.bam		ENCORE2	32723
COPB1-BGHcLV47-9_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3421					GRCh38	V40	COPB1-BGHcLV47-9_Aligned.sortedByCoord.out.bam		ENCORE2	32757
COPB1-BGHcLV47-9_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3421					GRCh38	V40	COPB1-BGHcLV47-9_S48_L002_R1_001.filtered.trimmed.paired.fastq.gz,COPB1-BGHcLV47-9_S48_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32791
COPB1-BGHcLV47-10_S49_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3422	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32552
COPB1-BGHcLV47-10_S49_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3422	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32586
COPB1-BGHcLV47-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3422					GRCh38	V40	COPB1-BGHcLV47-10_S49_L002_R1_001.filtered.trimmed.paired.fastq.gz,COPB1-BGHcLV47-10_S49_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32620
COPB1-BGHcLV47-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3422					GRCh38	V40	COPB1-BGHcLV47-10_Aligned.sortedByCoord.out.bam		ENCORE2	32654
COPB1-BGHcLV47-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3422					GRCh38	V40	COPB1-BGHcLV47-10_Aligned.sortedByCoord.out.bam		ENCORE2	32688
COPB1-BGHcLV47-10_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3422					GRCh38	V40	COPB1-BGHcLV47-10_Aligned.sortedByCoord.out.bam		ENCORE2	32722
COPB1-BGHcLV47-10_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3422					GRCh38	V40	COPB1-BGHcLV47-10_Aligned.sortedByCoord.out.bam		ENCORE2	32756
COPB1-BGHcLV47-10_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3422					GRCh38	V40	COPB1-BGHcLV47-10_S49_L002_R1_001.filtered.trimmed.paired.fastq.gz,COPB1-BGHcLV47-10_S49_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32790