USP10 RNA-Seq in K562

General Information


RBP	USP10
Cell_Line	K562
Method	CRISPR
Exp_Name	USP10-BGKcLV37-K562
ENCODE_series_ID
Batch_ID	BGKcLV37
Pool ID	Pool-230130
Local_Set_Name	set55
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	USP10-BGKcLV37-55
Rep2	USP10-BGKcLV37-56
CN1	NT-BGKcLV37-1
CN2	NT-BGKcLV37-2
Rep1_qPCR	45.9
Rep2_qPCR	43.4
Rep1_WB	84.1
Rep2_WB	84.0
Antibody Cat#	A300-900A
Antibody Lot#	lot # 2
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1062

Experiment Information (Status: Submitting)

	BGKcLV37-55	BGKcLV37-55	BGKcLV37-55	BGKcLV37-56	BGKcLV37-56	BGKcLV37-56
idx	1407	1407	1407	1408	1408	1408
TRCN#_or_BGC#	BGC#0001071	BGC#0001071	BGC#0001071	BGC#0001071	BGC#0001071	BGC#0001071
shRNA_or_gRNA_sequence	CTTACCTCAACTGAAGATCG	CTTACCTCAACTGAAGATCG	CTTACCTCAACTGAAGATCG	CTTACCTCAACTGAAGATCG	CTTACCTCAACTGAAGATCG	CTTACCTCAACTGAAGATCG
PAM	AGG	AGG	AGG	AGG	AGG	AGG
Name	USP10_90	USP10_90	USP10_90	USP10_90	USP10_90	USP10_90
Sample_ID	BGKcLV37-55	BGKcLV37-55	BGKcLV37-55	BGKcLV37-56	BGKcLV37-56	BGKcLV37-56
transduction_Date	9/20/22	9/20/22	9/20/22	9/20/22	9/20/22	9/20/22
days	D6	D6	D6	D6	D6	D6
RBP_name	USP10	USP10	USP10	USP10	USP10	USP10
qPCR_result	45.9	45.9	45.9	43.4	43.4	43.4
Ave_qPCR	44.7	44.7	44.7
RT-qPCR_primer-F	ggaaaaactccctcctgtcc	ggaaaaactccctcctgtcc	ggaaaaactccctcctgtcc
RT-qPCR_primer-R	aacccctggagaaagcagtt	aacccctggagaaagcagtt	aacccctggagaaagcagtt
protein_conc	1819	1819	1819	1844	1844	1844
WB_result	84.1	93.2	81.8	84.0	88.6592	75.645
Ave_WB	84.0	90.9	78.7
WB_DONE_date	10/12/22	10/18/22	10/18/22
MW	87kd	87kd	87kd
IP
antibody_Cat#	A300-900A	A300-901A	8501	lot # 2	lot # 1	lot # 3
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0	0	0
Rep2_TPM	0	0	0	0	0	0
Action	Ready			Ready
Library_start_date
repeat_library
Note
ID	5565	5567	5569	5566	5568	5570

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
USP10	Product_ID: 8501 Lot_ID: 3 Source: Cell Signaling Technology Target Name: USP10-human
USP10	Product_ID: A300-900A Lot_ID: 2 Source: Bethyl Labs Target Name: USP10-human
USP10	Product_ID: A300-901A Lot_ID: Source: Bethyl Labs Target Name: USP10-human

Experiment Status

	BGKcLV37-55	BGKcLV37-55	BGKcLV37-55	BGKcLV37-56	BGKcLV37-56	BGKcLV37-56
Sample_ID	BGKcLV37-55	BGKcLV37-55	BGKcLV37-55	BGKcLV37-56	BGKcLV37-56	BGKcLV37-56
Sample Name
Sample Name	USP10-BGKcLV37-55			USP10-BGKcLV37-56
RBP	USP10	USP10	USP10	USP10	USP10	USP10
Cell_Line	K562	K562	K562	K562	K562	K562
Exp UID
Status	Submitting	NotSatisfied	NotSatisfied	Submitting	NotSatisfied	NotSatisfied
Status_date	2023-04-14	2023-01-03	2023-01-03	2023-04-14	2023-01-03	2023-01-03
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	11108	11144	11146	11109	11145	11147

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV37-55	BGKcLV37-56
Sample #	47	48
Sample Name	USP10-BGKcLV37-55	USP10-BGKcLV37-56
Sample_Name_Alias
Index Well Position	G06	H06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-01-13	2023-01-13
Lib_ID	Lib-230113	Lib-230113
Tecan_Location
Tecan
Tecan_date
Size_bp	301	296
Peak_Molarity	48.90	54.50
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/G6.png	DNA_Library_set54-56/set1/H6.png
RIN	9.9	9.7
libSample_RNA_Well	RNA_Library_set54-56/set1/G6.png	RNA_Library_set54-56/set1/H6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV37-55	BGKcLV37-56
RBP	USP10	USP10
Batch_ID	BGKcLV37	BGKcLV37
WB_result	84.100	84.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3418	3419

Sequencing Information

	BGKcLV37-55	BGKcLV37-56
Sample_ID	BGKcLV37-55	BGKcLV37-56
Sample Name	USP10-BGKcLV37-55	USP10-BGKcLV37-56
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	54,470,028	42,601,676
total_aligned_reads	51,680,065	39,699,239
unique_aligned_reads	47,895,704	36,951,265
percent_uniqueAligned	0.87930	0.86737
correlation_replicates	0.992781	0.992781
spikein_reads	4,286	5,990
percent_spikeins	0.00008	0.00014
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2291	2292

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
USP10-BGKcLV37-55_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2291	NovaSeq6000	100	paired-ended	1				NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8420
USP10-BGKcLV37-55_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2291	NovaSeq6000	100	paired-ended	2				NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8470
USP10-BGKcLV37-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2291					GRCh38	V40	USP10-BGKcLV37-55_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,USP10-BGKcLV37-55_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25661
USP10-BGKcLV37-55_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2291					GRCh38	V40	USP10-BGKcLV37-55/Aligned.sortedByCoord.out.bam		ENCORE2	25711
USP10-BGKcLV37-55_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2291					GRCh38	V40	USP10-BGKcLV37-55/Aligned.sortedByCoord.out.bam		ENCORE2	25761
USP10-BGKcLV37-55_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2291					GRCh38	V40	USP10-BGKcLV37-55/Aligned.sortedByCoord.out.bam		ENCORE2	25811
USP10-BGKcLV37-55_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2291					GRCh38	V40	USP10-BGKcLV37-55/Aligned.sortedByCoord.out.bam		ENCORE2	25861
USP10-BGKcLV37-55_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2291					GRCh38	V40	USP10-BGKcLV37-55_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,USP10-BGKcLV37-55_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25911
USP10-BGKcLV37-56_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2292	NovaSeq6000	100	paired-ended	1				NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8421
USP10-BGKcLV37-56_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2292	NovaSeq6000	100	paired-ended	2				NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8471
USP10-BGKcLV37-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2292					GRCh38	V40	USP10-BGKcLV37-56_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz,USP10-BGKcLV37-56_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25662
USP10-BGKcLV37-56_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2292					GRCh38	V40	USP10-BGKcLV37-56/Aligned.sortedByCoord.out.bam		ENCORE2	25712
USP10-BGKcLV37-56_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2292					GRCh38	V40	USP10-BGKcLV37-56/Aligned.sortedByCoord.out.bam		ENCORE2	25762
USP10-BGKcLV37-56_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2292					GRCh38	V40	USP10-BGKcLV37-56/Aligned.sortedByCoord.out.bam		ENCORE2	25812
USP10-BGKcLV37-56_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2292					GRCh38	V40	USP10-BGKcLV37-56/Aligned.sortedByCoord.out.bam		ENCORE2	25862
USP10-BGKcLV37-56_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2292					GRCh38	V40	USP10-BGKcLV37-56_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz,USP10-BGKcLV37-56_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25912