WBP11 RNA-Seq in K562

General Information


RBP	WBP11
Cell_Line	K562
Method	CRISPR
Exp_Name	WBP11-BGKcLV23-K562
ENCODE_series_ID	ENCSR604BMU
Batch_ID	BGKcLV23
Pool ID	Pool-201204
Local_Set_Name	set46_K
ENCODE_KD_Exp_ID	ENCSR070AYA
ENCODE_CN_Exp_ID	ENCSR877JEM
Rep1	WBP11-BGKcLV23-65
Rep2	WBP11-BGKcLV23-66
CN1	NT-BGKcLV23-1
CN2	NT-BGKcLV23-2
Rep1_qPCR	23.0
Rep2_qPCR	21.0
Rep1_WB	57.1
Rep2_WB	53.1
Antibody Cat#	A304-855A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB949LDW
Status	Released
Project	ENCODE4
ID	36

Experiment Information (Status: Released)

	BGKcLV23-65	BGKcLV23-66
idx	851	852
TRCN#_or_BGC#	BGC#0000556	BGC#0000556
shRNA_or_gRNA_sequence	ACTTACGGGCTTGGTCTGTG	ACTTACGGGCTTGGTCTGTG
PAM	GGG	GGG
Name	WBP11_83	WBP11_83
Sample_ID	BGKcLV23-65	BGKcLV23-66
transduction_Date	9/17/20	9/17/20
days	Day 6	Day 6
RBP_name	WBP11	WBP11
qPCR_result	23.0	21.0
Ave_qPCR	22.0
RT-qPCR_primer-F	TGAACAGAAGAGGGCTCAACTT
RT-qPCR_primer-R	TGGCAAAGGAATACTCTCCACT
protein_conc	2233	2480
WB_result	57.1	53.1
Ave_WB	55.1
WB_DONE_date	10/7/20	JESS
MW	70KD
IP	Rabbit / I
antibody_Cat#	A304-855A	LOT# 1
Antibody DCC ID	ENCAB949LDW
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	4983	4984

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
WBP11	Product_ID: A304-855A Lot_ID: 1 Source: Bethyl Labs Target Name: WBP11-human

Experiment Status

	BGKcLV23-65	BGKcLV23-66
Sample_ID	BGKcLV23-65	BGKcLV23-66
Sample Name
Sample Name	WBP11-BGKcLV23-65	WBP11-BGKcLV23-66
RBP	WBP11	WBP11
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7461	7462

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV23-65	BGKcLV23-66
Sample #	63	64
Sample Name	WBP11-BGKcLV23-65	WBP11-BGKcLV23-66
Sample_Name_Alias
Index Well Position	G08	H08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-11-24	2020-11-24
Lib_ID	Lib-201124	Lib-201124
Tecan_Location
Tecan
Tecan_date
Size_bp	290	289
Peak_Molarity	140.00	132.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/G8.png	DNA_Library_set46/set1/H8.png
RIN	9.4	9.3
libSample_RNA_Well	RNA_Library_set46/set2/G12.png	RNA_Library_set46/set2/H12.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGKcLV23-65	BGKcLV23-66
RBP	WBP11	WBP11
Batch_ID	BGKcLV23	BGKcLV23
WB_result	57.100	53.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1438	1439

Sequencing Information

	BGKcLV23-65	BGKcLV23-66
Sample_ID	BGKcLV23-65	BGKcLV23-66
Sample Name	WBP11-BGKcLV23-65	WBP11-BGKcLV23-66
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_K	set46_K
total_reads	163,308,022	143,509,780
total_aligned_reads	154,332,484	136,853,296
unique_aligned_reads	140,913,652	124,367,826
percent_uniqueAligned	0.86287	0.86662
correlation_replicates	0.998105	0.998105
spikein_reads	64,582	63,384
percent_spikeins	0.00040	0.00044
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	544	545

Data Submission Information

	BGKcLV23-65	BGKcLV23-65	BGKcLV23-65	BGKcLV23-65	BGKcLV23-65	BGKcLV23-65	BGKcLV23-66	BGKcLV23-66	BGKcLV23-66	BGKcLV23-66
ENCODE_alias	brenton-graveley:WBP11-BGKcLV23	brenton-graveley:WBP11-BGKcLV23-65	brenton-graveley:L-WBP11-BGKcLV23-65	brenton-graveley:WBP11-BGKcLV23-65_TTGCCTAG+TAAGTGGT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:WBP11-BGKcLV23-65_TTGCCTAG+TAAGTGGT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:WBP11-BGKcLV23-K562	brenton-graveley:WBP11-BGKcLV23-66	brenton-graveley:L-WBP11-BGKcLV23-66	brenton-graveley:WBP11-BGKcLV23-66_CCATTCGA+CGGACAAC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:WBP11-BGKcLV23-66_CCATTCGA+CGGACAAC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR070AYA	ENCBS242DYL	ENCLB643SPT	ENCFF171ZQR	ENCFF006MAU	ENCSR604BMU	ENCBS935HUM	ENCLB281AWX	ENCFF307KAA	ENCFF681NFS
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	BGKcLV23-65	BGKcLV23-65	BGKcLV23-65	BGKcLV23-65	BGKcLV23-65	BGKcLV23-65	BGKcLV23-66	BGKcLV23-66	BGKcLV23-66	BGKcLV23-66
Sample Name	WBP11-BGKcLV23-65	WBP11-BGKcLV23-65	WBP11-BGKcLV23-65	WBP11-BGKcLV23-65	WBP11-BGKcLV23-65	WBP11-BGKcLV23-65	WBP11-BGKcLV23-66	WBP11-BGKcLV23-66	WBP11-BGKcLV23-66	WBP11-BGKcLV23-66
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46K_biosample_protocol	LV46K_library_protocol				LV46K_biosample_protocol	LV46K_library_protocol
protocol_URL		WBP11-BGKcLV23-65.pdf	L-WBP11-BGKcLV23-65.pdf				WBP11-BGKcLV23-66.pdf	L-WBP11-BGKcLV23-66.pdf
ID	2426	2489	2553	2647	2681	7350	2490	2554	2648	2682

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
WBP11-BGKcLV23-65_TTGCCTAG+TAAGTGGT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	544	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1410
WBP11-BGKcLV23-65_TTGCCTAG+TAAGTGGT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	544	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1474
WBP11-BGKcLV23-65_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	544					GRCh38	V40	WBP11-BGKcLV23-65_TTGCCTAG+TAAGTGGT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,WBP11-BGKcLV23-65_TTGCCTAG+TAAGTGGT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25313
WBP11-BGKcLV23-65_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	544					GRCh38	V40	WBP11-BGKcLV23-65_TTGCCTAG+TAAGTGGT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,WBP11-BGKcLV23-65_TTGCCTAG+TAAGTGGT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25347
WBP11-BGKcLV23-65_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	544					GRCh38	V40	WBP11-BGKcLV23-65/Aligned.sortedByCoord.out.bam		ENCORE2	26151
WBP11-BGKcLV23-65_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	544					GRCh38	V40	WBP11-BGKcLV23-65/Aligned.sortedByCoord.out.bam		ENCORE2	26185
WBP11-BGKcLV23-65_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	544					GRCh38	V40	WBP11-BGKcLV23-65/Aligned.sortedByCoord.out.bam		ENCORE2	26219
WBP11-BGKcLV23-65_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	544					GRCh38	V40	WBP11-BGKcLV23-65/Aligned.sortedByCoord.out.bam		ENCORE2	26253
WBP11-BGKcLV23-66_CCATTCGA+CGGACAAC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	545	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1411
WBP11-BGKcLV23-66_CCATTCGA+CGGACAAC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	545	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1475
WBP11-BGKcLV23-66_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	545					GRCh38	V40	WBP11-BGKcLV23-66_CCATTCGA+CGGACAAC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,WBP11-BGKcLV23-66_CCATTCGA+CGGACAAC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25314
WBP11-BGKcLV23-66_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	545					GRCh38	V40	WBP11-BGKcLV23-66_CCATTCGA+CGGACAAC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,WBP11-BGKcLV23-66_CCATTCGA+CGGACAAC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25348
WBP11-BGKcLV23-66_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	545					GRCh38	V40	WBP11-BGKcLV23-66/Aligned.sortedByCoord.out.bam		ENCORE2	26152
WBP11-BGKcLV23-66_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	545					GRCh38	V40	WBP11-BGKcLV23-66/Aligned.sortedByCoord.out.bam		ENCORE2	26186
WBP11-BGKcLV23-66_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	545					GRCh38	V40	WBP11-BGKcLV23-66/Aligned.sortedByCoord.out.bam		ENCORE2	26220
WBP11-BGKcLV23-66_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	545					GRCh38	V40	WBP11-BGKcLV23-66/Aligned.sortedByCoord.out.bam		ENCORE2	26254