RPUSD2 RNA-Seq in K562

General Information


RBP	RPUSD2
Cell_Line	K562
Method	CRISPR
Exp_Name	RPUSD2-BGKcLV33-K562
ENCODE_series_ID	ENCSR705LEY
Batch_ID	BGKcLV33
Pool ID	Pool-220418
Local_Set_Name	set53
ENCODE_KD_Exp_ID	ENCSR563QCQ
ENCODE_CN_Exp_ID	ENCSR271ZAB
Rep1	RPUSD2-BGKcLV33-17
Rep2	RPUSD2-BGKcLV33-18
CN1	NT-BGKcLV33-1
CN2	NT-BGKcLV33-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	0.0
Rep2_WB	0.0
Antibody Cat#	A304-716A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCODE4
ID	896

Experiment Information (Status: Released)

	BGKcLV33-9	BGKcLV33-9	BGKcLV33-9	BGKcLV33-10	BGKcLV33-10	BGKcLV33-10
idx	1111	1184	1186	1112	1185	1187
TRCN#_or_BGC#	BGC#0000829	BGC#0000867	BGC#0000867	BGC#0000829	BGC#0000867	BGC#0000867
shRNA_or_gRNA_sequence	TGACGCTGGTGGCGACGCGA	CGAGGGCGACTCGACCACTG	CGAGGGCGACTCGACCACTG	TGACGCTGGTGGCGACGCGA	CGAGGGCGACTCGACCACTG	CGAGGGCGACTCGACCACTG
PAM	AGG	CGG	CGG	AGG	CGG	CGG
Name	RPUSD2_97	MTREX_95	MTREX_95	RPUSD2_97	MTREX_95	MTREX_95
Sample_ID	BGKcLV33-9	BGKcLV33-9	BGKcLV33-9	BGKcLV33-10	BGKcLV33-10	BGKcLV33-10
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	RPUSD2	MTREX	MTREX	RPUSD2	MTREX	MTREX
qPCR_result		45.5	45.5		39.5	39.5
Ave_qPCR		42.5	42.5
RT-qPCR_primer-F		aaatccttctaccagtttcagca	aaatccttctaccagtttcagca
RT-qPCR_primer-R		aatttggcaagctgctgtct	aatttggcaagctgctgtct
protein_conc	322	2075	2075	443	1768	1768
WB_result	88.7	86.6	81.1	85.3	80.7	76.9965822
Ave_WB	87.0	83.7	79.1
WB_DONE_date	2/4/22	3/14/22	3/16/22
MW	61kd	118kd	118kd
IP
antibody_Cat#	A305-209A	A300-614A	A300-615A	LOT #1	LOT #3	LOT #2
Antibody DCC ID		ENCAB831HEY	ENCAB965FKE		8/4/22	8/4/22
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		04/13/22			04/13/22
repeat_library
Note
ID	5251	5324	5326	5252	5325	5327

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
MTREX	Product_ID: A300-614A Lot_ID: 3 Source: Bethyl Labs Target Name: MTREX-human
MTREX	Product_ID: A300-615A Lot_ID: 2 Source: Bethyl Labs Target Name: MTREX-human

Experiment Status

	BGKcLV33-9	BGKcLV33-9	BGKcLV33-9	BGKcLV33-10	BGKcLV33-10	BGKcLV33-10
Sample_ID	BGKcLV33-9	BGKcLV33-9	BGKcLV33-9	BGKcLV33-10	BGKcLV33-10	BGKcLV33-10
Sample Name
Sample Name	SKIV2L2-BGKcLV33-9			SKIV2L2-BGKcLV33-10
RBP	SKIV2L2	RPUSD2	SKIV2L2	SKIV2L2	RPUSD2	SKIV2L2
Cell_Line	K562	K562	K562	K562	K562	K562
Exp UID
Status	Released	NotSatisfied	NotSatisfied	Released	NotSatisfied	NotSatisfied
Status_date	2022-10-28	2022-03-30	2022-03-30	2022-10-28	2022-03-30	2022-03-30
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
Note
ID	10639	10695	10759	10640	10696	10760

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-9	BGKcLV33-10
Sample #	9	10
Sample Name	SKIV2L2-BGKcLV33-9	SKIV2L2-BGKcLV33-10
Sample_Name_Alias
Index Well Position	A02	B02
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	308	302
Peak_Molarity	63.90	58.80
libSampleQC_DNA_Well	DNA_Library_set53/set1/A6.png	DNA_Library_set53/set1/B6.png
RIN	9.6	9.5
libSample_RNA_Well	RNA_Library_set53/set1/A2.png	RNA_Library_set53/set1/B2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-9	BGKcLV33-10
RBP	SKIV2L2	SKIV2L2
Batch_ID	BGKcLV33	BGKcLV33
WB_result	86.600	80.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3270	3271

Sequencing Information

	BGKcLV33-9	BGKcLV33-10
Sample_ID	BGKcLV33-9	BGKcLV33-10
Sample Name	SKIV2L2-BGKcLV33-9	SKIV2L2-BGKcLV33-10
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	122,765,928	139,116,018
total_aligned_reads	112,155,074	125,317,240
unique_aligned_reads	102,691,810	114,450,096
percent_uniqueAligned	0.83648	0.82270
correlation_replicates	0.997810	0.997810
spikein_reads	34,820	46,514
percent_spikeins	0.00028	0.00033
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2037	2038

Data Submission Information

	BGKcLV33-9	BGKcLV33-9	BGKcLV33-9	BGKcLV33-9	BGKcLV33-9	BGKcLV33-9	BGKcLV33-10	BGKcLV33-10	BGKcLV33-10	BGKcLV33-10
ENCODE_alias	brenton-graveley:SKIV2L2-BGKcLV33	brenton-graveley:SKIV2L2-BGKcLV33-9	brenton-graveley:L-SKIV2L2-BGKcLV33-9	brenton-graveley:SKIV2L2-BGKcLV33-9_S63_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SKIV2L2-BGKcLV33-9_S63_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SKIV2L2-BGKcLV33-K562	brenton-graveley:SKIV2L2-BGKcLV33-10	brenton-graveley:L-SKIV2L2-BGKcLV33-10	brenton-graveley:SKIV2L2-BGKcLV33-10_S64_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SKIV2L2-BGKcLV33-10_S64_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR300UBK	ENCBS383XHL	ENCLB230CRI	ENCFF973VVH	ENCFF811PCS	ENCSR423MBQ	ENCBS500BTR	ENCLB096WFW	ENCFF909ZGQ	ENCFF472LUW
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	BGKcLV33-9	BGKcLV33-9	BGKcLV33-9	BGKcLV33-9	BGKcLV33-9	BGKcLV33-9	BGKcLV33-10	BGKcLV33-10	BGKcLV33-10	BGKcLV33-10
Sample Name	SKIV2L2-BGKcLV33-9	SKIV2L2-BGKcLV33-9	SKIV2L2-BGKcLV33-9	SKIV2L2-BGKcLV33-9	SKIV2L2-BGKcLV33-9	SKIV2L2-BGKcLV33-9	SKIV2L2-BGKcLV33-10	SKIV2L2-BGKcLV33-10	SKIV2L2-BGKcLV33-10	SKIV2L2-BGKcLV33-10
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		SKIV2L2-BGKcLV33-9.pdf	L-SKIV2L2-BGKcLV33-9.pdf				SKIV2L2-BGKcLV33-10.pdf	L-SKIV2L2-BGKcLV33-10.pdf
ID	7475	7559	7669	7779	7889	7964	7560	7670	7780	7890

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
SKIV2L2-BGKcLV33-9_S63_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2037	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	6648
SKIV2L2-BGKcLV33-9_S63_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2037	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	6704
SKIV2L2-BGKcLV33-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2037					GRCh38	V40	SKIV2L2-BGKcLV33-9_S63_L002_R1_001.filtered.trimmed.paired.fastq.gz,SKIV2L2-BGKcLV33-9_S63_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18125
SKIV2L2-BGKcLV33-9_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	2037					GRCh38	V40	SKIV2L2-BGKcLV33-9/Aligned.sortedByCoord.out.bam		ENCORE2	18181
SKIV2L2-BGKcLV33-9_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	2037					GRCh38	V40	SKIV2L2-BGKcLV33-9/Aligned.sortedByCoord.out.bam		ENCORE2	18237
SKIV2L2-BGKcLV33-9_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	2037					GRCh38	V40	SKIV2L2-BGKcLV33-9/Aligned.sortedByCoord.out.bam		ENCORE2	18293
SKIV2L2-BGKcLV33-9_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	2037					GRCh38	V40	SKIV2L2-BGKcLV33-9/Aligned.sortedByCoord.out.bam		ENCORE2	18349
SKIV2L2-BGKcLV33-9_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2037					GRCh38	V40	SKIV2L2-BGKcLV33-9_S63_L002_R1_001.filtered.trimmed.paired.fastq.gz,SKIV2L2-BGKcLV33-9_S63_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18405
SKIV2L2-BGKcLV33-10_S64_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2038	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	6647
SKIV2L2-BGKcLV33-10_S64_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2038	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	6703
SKIV2L2-BGKcLV33-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2038					GRCh38	V40	SKIV2L2-BGKcLV33-10_S64_L002_R1_001.filtered.trimmed.paired.fastq.gz,SKIV2L2-BGKcLV33-10_S64_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18124
SKIV2L2-BGKcLV33-10_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	2038					GRCh38	V40	SKIV2L2-BGKcLV33-10/Aligned.sortedByCoord.out.bam		ENCORE2	18180
SKIV2L2-BGKcLV33-10_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	2038					GRCh38	V40	SKIV2L2-BGKcLV33-10/Aligned.sortedByCoord.out.bam		ENCORE2	18236
SKIV2L2-BGKcLV33-10_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	2038					GRCh38	V40	SKIV2L2-BGKcLV33-10/Aligned.sortedByCoord.out.bam		ENCORE2	18292
SKIV2L2-BGKcLV33-10_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	2038					GRCh38	V40	SKIV2L2-BGKcLV33-10/Aligned.sortedByCoord.out.bam		ENCORE2	18348
SKIV2L2-BGKcLV33-10_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2038					GRCh38	V40	SKIV2L2-BGKcLV33-10_S64_L002_R1_001.filtered.trimmed.paired.fastq.gz,SKIV2L2-BGKcLV33-10_S64_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18404