UBA2 RNA-Seq in K562

General Information


RBP	UBA2
Cell_Line	K562
Method	CRISPR
Exp_Name	UBA2-BGKcLV42-K562
ENCODE_series_ID
Batch_ID	BGKcLV42
Pool ID	Pool-240715
Local_Set_Name	set73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	UBA2-BGKcLV42-97
Rep2	UBA2-BGKcLV42-98
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	71.3
Rep2_qPCR	70.4
Rep1_WB	95.8
Rep2_WB	95.1
Antibody Cat#	8688S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1564

Experiment Information (Status: Submitting)

	BGKcLV42-97	BGKcLV42-98
idx	0	0
TRCN#_or_BGC#	BGC#0001196	BGC#0001196
shRNA_or_gRNA_sequence	GTGTTACGAATTGTACAGCC	GTGTTACGAATTGTACAGCC
PAM	AGG	AGG
Name	UBA2_84	UBA2_84
Sample_ID	BGKcLV42-97	BGKcLV42-98
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	UBA2	UBA2
qPCR_result	71.3	70.4
Ave_qPCR	70.9
RT-qPCR_primer-F	ggaatgggctaaatcaactgg
RT-qPCR_primer-R	acggaactggaggtttcctt
protein_conc	2583	2814
WB_result	95.8	95.1
Ave_WB	95.4
WB_DONE_date	5/10/24
MW	90kd
IP
antibody_Cat#	8688S	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5865	5866

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
UBA2	Product_ID: 8688S Lot_ID: 1 Source: Cell Signaling Technology Target Name: UBA2-human

Experiment Status

	BGKcLV42-97	BGKcLV42-98
Sample_ID	BGKcLV42-97	BGKcLV42-98
Sample Name
Sample Name	UBA2-BGKcLV42-97	UBA2-BGKcLV42-98
RBP	UBA2	UBA2
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13122	13123

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-97	BGKcLV42-98
Sample #	79	80
Sample Name	UBA2-BGKcLV42-97	UBA2-BGKcLV42-98
Sample_Name_Alias
Index Well Position	G10	H10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-06-21	2024-06-21
Lib_ID	Lib-240621	Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp	328	315
Peak_Molarity	130.00	81.60
libSampleQC_DNA_Well	DNA_Library_set73/set1/G10.png	DNA_Library_set73/set1/H10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/G10.png	RNA_Library_set73/set1/H10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-97	BGKcLV42-98
RBP	UBA2	UBA2
Batch_ID	BGKcLV42	BGKcLV42
WB_result	95.800	95.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4348	4349

Sequencing Information

	BGKcLV42-97	BGKcLV42-98
Sample_ID	BGKcLV42-97	BGKcLV42-98
Sample Name	UBA2-BGKcLV42-97	UBA2-BGKcLV42-98
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	69,856,383	44,060,860
total_aligned_reads	64,354,098	42,080,503
unique_aligned_reads	59,666,471	38,982,733
percent_uniqueAligned	0.85413	0.88475
correlation_replicates	0.992395	0.992395
spikein_reads	8,200	4,994
percent_spikeins	0.00012	0.00011
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3215	3216

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-BGKcLV42-97_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3215	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30418
UBA2-BGKcLV42-97_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3215	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30508
UBA2-BGKcLV42-97_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3215					GRCh38	V40	UBA2-BGKcLV42-97_L001_R1_001.filtered.trimmed.paired.fastq.gz,UBA2-BGKcLV42-97_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31350
UBA2-BGKcLV42-97_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3215					GRCh38	V40	UBA2-BGKcLV42-97_Aligned.sortedByCoord.out.bam		ENCORE2	31440
UBA2-BGKcLV42-97_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3215					GRCh38	V40	UBA2-BGKcLV42-97_Aligned.sortedByCoord.out.bam		ENCORE2	31530
UBA2-BGKcLV42-97_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3215					GRCh38	V40	UBA2-BGKcLV42-97_Aligned.sortedByCoord.out.bam		ENCORE2	31620
UBA2-BGKcLV42-97_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3215					GRCh38	V40	UBA2-BGKcLV42-97_Aligned.sortedByCoord.out.bam		ENCORE2	31710
UBA2-BGKcLV42-97_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3215					GRCh38	V40	UBA2-BGKcLV42-97_L001_R1_001.filtered.trimmed.paired.fastq.gz,UBA2-BGKcLV42-97_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31800
UBA2-BGKcLV42-98_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3216	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30419
UBA2-BGKcLV42-98_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3216	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30509
UBA2-BGKcLV42-98_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3216					GRCh38	V40	UBA2-BGKcLV42-98_L001_R1_001.filtered.trimmed.paired.fastq.gz,UBA2-BGKcLV42-98_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31351
UBA2-BGKcLV42-98_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3216					GRCh38	V40	UBA2-BGKcLV42-98_Aligned.sortedByCoord.out.bam		ENCORE2	31441
UBA2-BGKcLV42-98_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3216					GRCh38	V40	UBA2-BGKcLV42-98_Aligned.sortedByCoord.out.bam		ENCORE2	31531
UBA2-BGKcLV42-98_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3216					GRCh38	V40	UBA2-BGKcLV42-98_Aligned.sortedByCoord.out.bam		ENCORE2	31621
UBA2-BGKcLV42-98_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3216					GRCh38	V40	UBA2-BGKcLV42-98_Aligned.sortedByCoord.out.bam		ENCORE2	31711
UBA2-BGKcLV42-98_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3216					GRCh38	V40	UBA2-BGKcLV42-98_L001_R1_001.filtered.trimmed.paired.fastq.gz,UBA2-BGKcLV42-98_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31801