UBA2 RNA-Seq in HepG2

General Information


RBP	UBA2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	UBA2-BGHcLV43-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV43
Pool ID	Pool-240723
Local_Set_Name	set74
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	UBA2-BGHcLV43-57
Rep2	UBA2-BGHcLV43-58
CN1	NT-BGHcLV43-1
CN2	NT-BGHcLV43-2
Rep1_qPCR	78.4
Rep2_qPCR	76.9
Rep1_WB	95.6
Rep2_WB	87.2
Antibody Cat#	8688S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1591

Experiment Information (Status: Submitting)

	BGHcLV43-57	BGHcLV43-58
idx	1425	1426
TRCN#_or_BGC#	BGC#0001198	BGC#0001198
shRNA_or_gRNA_sequence	GTGTTACGAATTGTACAGCC	GTGTTACGAATTGTACAGCC
PAM	AGG	AGG
Name	UBA2_84	UBA2_84
Sample_ID	BGHcLV43-57	BGHcLV43-58
transduction_Date	6/6/24	6/6/24
days	D6	D6
RBP_name	UBA2	UBA2
qPCR_result	78.4	76.9
Ave_qPCR	77.6
RT-qPCR_primer-F	ggaatgggctaaatcaactgg
RT-qPCR_primer-R	acggaactggaggtttcctt
protein_conc	4091	4076
WB_result	95.6	87.2
Ave_WB	91.4
WB_DONE_date	6/28/24
MW	90kd
IP
antibody_Cat#	8688S	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	133	0
Rep2_TPM	141	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9680	9681

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV43-57	BGHcLV43-58
Sample_ID	BGHcLV43-57	BGHcLV43-58
Sample Name
Sample Name	UBA2-BGHcLV43-57	UBA2-BGHcLV43-58
RBP	UBA2	UBA2
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13272	13273

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV43-57	BGHcLV43-58
Sample #	45	46
Sample Name	UBA2-BGHcLV43-57	UBA2-BGHcLV43-58
Sample_Name_Alias
Index Well Position	E11	F11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-07-22	2024-07-22
Lib_ID	Lib-240722	Lib-240722
Tecan_Location
Tecan
Tecan_date
Size_bp	305	297
Peak_Molarity	83.70	93.60
libSampleQC_DNA_Well	DNA_Library_set74/set1/E6.png	DNA_Library_set74/set1/F6.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set74/set1/A12.png	RNA_Library_set74/set1/B12.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-23	2024-07-23
Sample_ID	BGHcLV43-57	BGHcLV43-58
RBP	UBA2	UBA2
Batch_ID	BGHcLV43	BGHcLV43
WB_result	95.600	87.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4404	4405

Sequencing Information

	BGHcLV43-57	BGHcLV43-58
Sample_ID	BGHcLV43-57	BGHcLV43-58
Sample Name	UBA2-BGHcLV43-57	UBA2-BGHcLV43-58
Pool ID	Pool-240723	Pool-240723
LocalServer_folder	set74	set74
total_reads	52,055,039	37,727,994
total_aligned_reads	49,705,435	35,249,112
unique_aligned_reads	46,770,830	33,058,429
percent_uniqueAligned	0.89849	0.87623
correlation_replicates	0.997173	0.997173
spikein_reads	22,748	18,426
percent_spikeins	0.00044	0.00049
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3271	3272

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
UBA2-BGHcLV43-57_S135_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3271	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30564
UBA2-BGHcLV43-57_S135_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3271	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30616
UBA2-BGHcLV43-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3271					GRCh38	V40	UBA2-BGHcLV43-57_S135_L003_R1_001.filtered.trimmed.paired.fastq.gz,UBA2-BGHcLV43-57_S135_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30668
UBA2-BGHcLV43-57_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3271					GRCh38	V40	UBA2-BGHcLV43-57_Aligned.sortedByCoord.out.bam		ENCORE2	30720
UBA2-BGHcLV43-57_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3271					GRCh38	V40	UBA2-BGHcLV43-57_Aligned.sortedByCoord.out.bam		ENCORE2	30772
UBA2-BGHcLV43-57_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3271					GRCh38	V40	UBA2-BGHcLV43-57_Aligned.sortedByCoord.out.bam		ENCORE2	30824
UBA2-BGHcLV43-57_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3271					GRCh38	V40	UBA2-BGHcLV43-57_Aligned.sortedByCoord.out.bam		ENCORE2	30876
UBA2-BGHcLV43-57_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3271					GRCh38	V40	UBA2-BGHcLV43-57_S135_L003_R1_001.filtered.trimmed.paired.fastq.gz,UBA2-BGHcLV43-57_S135_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30928
UBA2-BGHcLV43-58_S136_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3272	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30565
UBA2-BGHcLV43-58_S136_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3272	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30617
UBA2-BGHcLV43-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3272					GRCh38	V40	UBA2-BGHcLV43-58_S136_L003_R1_001.filtered.trimmed.paired.fastq.gz,UBA2-BGHcLV43-58_S136_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30669
UBA2-BGHcLV43-58_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3272					GRCh38	V40	UBA2-BGHcLV43-58_Aligned.sortedByCoord.out.bam		ENCORE2	30721
UBA2-BGHcLV43-58_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3272					GRCh38	V40	UBA2-BGHcLV43-58_Aligned.sortedByCoord.out.bam		ENCORE2	30773
UBA2-BGHcLV43-58_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3272					GRCh38	V40	UBA2-BGHcLV43-58_Aligned.sortedByCoord.out.bam		ENCORE2	30825
UBA2-BGHcLV43-58_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3272					GRCh38	V40	UBA2-BGHcLV43-58_Aligned.sortedByCoord.out.bam		ENCORE2	30877
UBA2-BGHcLV43-58_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3272					GRCh38	V40	UBA2-BGHcLV43-58_S136_L003_R1_001.filtered.trimmed.paired.fastq.gz,UBA2-BGHcLV43-58_S136_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30929