SAP30BP RNA-Seq in K562

General Information


RBP	SAP30BP
Cell_Line	K562
Method	CRISPR
Exp_Name	SAP30BP-BGKcLV33-K562
ENCODE_series_ID	ENCSR057UBZ
Batch_ID	BGKcLV33
Pool ID	Pool-220418
Local_Set_Name	set53
ENCODE_KD_Exp_ID	ENCSR068YPI
ENCODE_CN_Exp_ID	ENCSR271ZAB
Rep1	SAP30BP-BGKcLV33-29
Rep2	SAP30BP-BGKcLV33-30
CN1	NT-BGKcLV33-1
CN2	NT-BGKcLV33-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	no band on the position
Rep2_WB
Antibody Cat#	A300-592A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCODE4
ID	899

Experiment Information (Status: Released)

	BGKcLV33-23	BGKcLV33-23	BGKcLV33-23	BGKcLV33-24	BGKcLV33-24	BGKcLV33-24
idx	1125	1202	1204	1126	1203	1205
TRCN#_or_BGC#	BGC#0000842	BGC#0000835	BGC#0000835	BGC#0000842	BGC#0000835	BGC#0000835
shRNA_or_gRNA_sequence	GTCGTCTCTCGCAGTTTACG	GTATGTCCCCTTGCCAAAAG	GTATGTCCCCTTGCCAAAAG	GTCGTCTCTCGCAGTTTACG	GTATGTCCCCTTGCCAAAAG	GTATGTCCCCTTGCCAAAAG
PAM	CGG	GGG	GGG	CGG	GGG	GGG
Name	SAP30BP_97	RUVBL1_83	RUVBL1_83	SAP30BP_97	RUVBL1_83	RUVBL1_83
Sample_ID	BGKcLV33-23	BGKcLV33-23	BGKcLV33-23	BGKcLV33-24	BGKcLV33-24	BGKcLV33-24
transduction_Date	12/7/21	2/22/22	2/22/22	12/7/21	2/22/22	2/22/22
days	D6	D6	D6	D6	D6	D6
RBP_name	SAP30BP	RUVBL1	RUVBL1	SAP30BP	RUVBL1	RUVBL1
qPCR_result		XX	XX		XX	XX
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	297	1923	1923	515	2307	2307
WB_result	23.9	53.6	52.8	25.7	50.7	51.0
Ave_WB	24.8	52.2	51.9
WB_DONE_date	1/19/22	3/7/22	3/23/22
MW	34kd	50kd	50kd
IP
antibody_Cat#	A302-832A	A304-716A	A304-717A	LOT #1	LOT #1	LOT #1
Antibody DCC ID		ENCAB336XYM	ENCAB639CYH		8/4/22	8/4/22
submitted_to_DCC_date		8/16/22
Rep1_TPM	0	0	0	0	0	0
Rep2_TPM	0	0	0	0	0	0
Action		Ready			Ready
Library_start_date		04/13/22			04/13/22
repeat_library
Note
ID	5265	5342	5344	5266	5343	5345

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RUVBL1	Product_ID: A304-716A Lot_ID: 1 Source: Bethyl Labs Target Name: RUVBL1-human
RUVBL1	Product_ID: A304-717A Lot_ID: 1 Source: Bethyl Labs Target Name: RUVBL1-human

Experiment Status

	BGKcLV33-23	BGKcLV33-23	BGKcLV33-24	BGKcLV33-24
Sample_ID	BGKcLV33-23	BGKcLV33-23	BGKcLV33-24	BGKcLV33-24
Sample Name
Sample Name	RUVBL1-BGKcLV33-23		RUVBL1-BGKcLV33-24
RBP	RUVBL1	SAP30BP	RUVBL1	SAP30BP
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Released	NotSatisfied	Released	NotSatisfied
Status_date	2022-10-28	2022-03-30	2022-10-28	2022-03-30
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4
Note
ID	10647	10709	10648	10710

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-23	BGKcLV33-24
Sample #	17	18
Sample Name	RUVBL1-BGKcLV33-23	RUVBL1-BGKcLV33-24
Sample_Name_Alias
Index Well Position	A03	B03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-04-06	2022-04-06
Lib_ID	Lib-220406	Lib-220406
Tecan_Location
Tecan
Tecan_date
Size_bp	294	286
Peak_Molarity	66.00	55.30
libSampleQC_DNA_Well	DNA_Library_set53/set1/A7.png	DNA_Library_set53/set1/B7.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set53/set1/A3.png	RNA_Library_set53/set1/B3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-23	BGKcLV33-24
RBP	RUVBL1	RUVBL1
Batch_ID	BGKcLV33	BGKcLV33
WB_result	53.600	50.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3278	3279

Sequencing Information

	BGKcLV33-23	BGKcLV33-24
Sample_ID	BGKcLV33-23	BGKcLV33-24
Sample Name	RUVBL1-BGKcLV33-23	RUVBL1-BGKcLV33-24
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	128,554,552	95,958,252
total_aligned_reads	117,231,700	87,856,220
unique_aligned_reads	107,374,358	80,658,262
percent_uniqueAligned	0.83524	0.84056
correlation_replicates	0.997903	0.997903
spikein_reads	32,116	25,560
percent_spikeins	0.00025	0.00027
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2045	2046

Data Submission Information

	BGKcLV33-23	BGKcLV33-23	BGKcLV33-23	BGKcLV33-23	BGKcLV33-23	BGKcLV33-23	BGKcLV33-24	BGKcLV33-24	BGKcLV33-24	BGKcLV33-24
ENCODE_alias	brenton-graveley:RUVBL1-BGKcLV33	brenton-graveley:RUVBL1-BGKcLV33-23	brenton-graveley:L-RUVBL1-BGKcLV33-23	brenton-graveley:RUVBL1-BGKcLV33-23_S71_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RUVBL1-BGKcLV33-23_S71_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RUVBL1-BGKcLV33-K562	brenton-graveley:RUVBL1-BGKcLV33-24	brenton-graveley:L-RUVBL1-BGKcLV33-24	brenton-graveley:RUVBL1-BGKcLV33-24_S72_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RUVBL1-BGKcLV33-24_S72_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR119PLU	ENCBS328MIH	ENCLB064DMG	ENCFF368UKQ	ENCFF103JRC	ENCSR031YNO	ENCBS126IJD	ENCLB708RGM	ENCFF243OKE	ENCFF400TRD
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV33-23	BGKcLV33-23	BGKcLV33-23	BGKcLV33-23	BGKcLV33-23	BGKcLV33-23	BGKcLV33-24	BGKcLV33-24	BGKcLV33-24	BGKcLV33-24
Sample Name	RUVBL1-BGKcLV33-23	RUVBL1-BGKcLV33-23	RUVBL1-BGKcLV33-23	RUVBL1-BGKcLV33-23	RUVBL1-BGKcLV33-23	RUVBL1-BGKcLV33-23	RUVBL1-BGKcLV33-24	RUVBL1-BGKcLV33-24	RUVBL1-BGKcLV33-24	RUVBL1-BGKcLV33-24
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV53_biosample_protocol	LV53_library_protocol				LV53_biosample_protocol	LV53_library_protocol
protocol_URL		RUVBL1-BGKcLV33-23.pdf	L-RUVBL1-BGKcLV33-23.pdf				RUVBL1-BGKcLV33-24.pdf	L-RUVBL1-BGKcLV33-24.pdf
ID	7479	7567	7677	7787	7897	7968	7568	7678	7788	7898

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
RUVBL1-BGKcLV33-23_S71_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2045	NovaSeq6000	100	paired-ended	1				NT-BGKcLV33-1_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6623
RUVBL1-BGKcLV33-23_S71_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2045	NovaSeq6000	100	paired-ended	2				NT-BGKcLV33-1_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6679
RUVBL1-BGKcLV33-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2045					GRCh38	V40	RUVBL1-BGKcLV33-23_S71_L002_R1_001.filtered.trimmed.paired.fastq.gz,RUVBL1-BGKcLV33-23_S71_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18100
RUVBL1-BGKcLV33-23_Signal.Unique.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2045					GRCh38	V40	RUVBL1-BGKcLV33-23/Aligned.sortedByCoord.out.bam		ENCORE2	18156
RUVBL1-BGKcLV33-23_Signal.Unique.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2045					GRCh38	V40	RUVBL1-BGKcLV33-23/Aligned.sortedByCoord.out.bam		ENCORE2	18212
RUVBL1-BGKcLV33-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2045					GRCh38	V40	RUVBL1-BGKcLV33-23/Aligned.sortedByCoord.out.bam		ENCORE2	18268
RUVBL1-BGKcLV33-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2045					GRCh38	V40	RUVBL1-BGKcLV33-23/Aligned.sortedByCoord.out.bam		ENCORE2	18324
RUVBL1-BGKcLV33-23_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2045					GRCh38	V40	RUVBL1-BGKcLV33-23_S71_L002_R1_001.filtered.trimmed.paired.fastq.gz,RUVBL1-BGKcLV33-23_S71_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18380
RUVBL1-BGKcLV33-24_S72_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2046	NovaSeq6000	100	paired-ended	1				NT-BGKcLV33-1_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6624
RUVBL1-BGKcLV33-24_S72_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2046	NovaSeq6000	100	paired-ended	2				NT-BGKcLV33-1_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6680
RUVBL1-BGKcLV33-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2046					GRCh38	V40	RUVBL1-BGKcLV33-24_S72_L002_R1_001.filtered.trimmed.paired.fastq.gz,RUVBL1-BGKcLV33-24_S72_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18101
RUVBL1-BGKcLV33-24_Signal.Unique.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2046					GRCh38	V40	RUVBL1-BGKcLV33-24/Aligned.sortedByCoord.out.bam		ENCORE2	18157
RUVBL1-BGKcLV33-24_Signal.Unique.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2046					GRCh38	V40	RUVBL1-BGKcLV33-24/Aligned.sortedByCoord.out.bam		ENCORE2	18213
RUVBL1-BGKcLV33-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2046					GRCh38	V40	RUVBL1-BGKcLV33-24/Aligned.sortedByCoord.out.bam		ENCORE2	18269
RUVBL1-BGKcLV33-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2046					GRCh38	V40	RUVBL1-BGKcLV33-24/Aligned.sortedByCoord.out.bam		ENCORE2	18325
RUVBL1-BGKcLV33-24_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2046					GRCh38	V40	RUVBL1-BGKcLV33-24_S72_L002_R1_001.filtered.trimmed.paired.fastq.gz,RUVBL1-BGKcLV33-24_S72_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18381