WDR77 RNA-Seq in K562

General Information


RBP	WDR77
Cell_Line	K562
Method	CRISPR
Exp_Name	WDR77-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	WDR77-BGKcLV42-105
Rep2	WDR77-BGKcLV42-106
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	30.8
Rep2_qPCR	33.6
Rep1_WB	49.8
Rep2_WB	59.1
Antibody Cat#	2018S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1568

Experiment Information (Status: Submitting)

	BGKcLV42-105	BGKcLV42-106
idx	0	0
TRCN#_or_BGC#	BGC#0001206	BGC#0001206
shRNA_or_gRNA_sequence	CAACGTGGTGGACGACCTGA	CAACGTGGTGGACGACCTGA
PAM	TGG	TGG
Name	WDR77_91	WDR77_91
Sample_ID	BGKcLV42-105	BGKcLV42-106
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	WDR77	WDR77
qPCR_result	30.8	33.6
Ave_qPCR	32.2
RT-qPCR_primer-F	ctgcctctcctcacaaggac
RT-qPCR_primer-R	cagcgggtatcccagagtaa
protein_conc	3206	2841
WB_result	49.8	59.1
Ave_WB	54.5
WB_DONE_date	5/10/24,5/23/24,6/21
MW	42kd
IP
antibody_Cat#	2018S	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	5873	5874

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
WDR77	Product_ID: 2018S Lot_ID: 1 Source: Cell Signaling Technology Target Name: WDR77-human

Experiment Status

	BGKcLV42-105	BGKcLV42-106
Sample_ID	BGKcLV42-105	BGKcLV42-106
Sample Name
Sample Name	WDR77-BGKcLV42-105	WDR77-BGKcLV42-106
RBP	WDR77	WDR77
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13130	13131

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-105	BGKcLV42-106
Sample #	87	88
Sample Name	WDR77-BGKcLV42-105	WDR77-BGKcLV42-106
Sample_Name_Alias
Index Well Position	G11	H11
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	291	302
Peak_Molarity	86.80	84.80
libSampleQC_DNA_Well	DNA_Library_set73/set1/G11.png	DNA_Library_set73/set1/H11.png
RIN	9.8	10.0
libSample_RNA_Well	RNA_Library_set73/set1/G11.png	RNA_Library_set73/set1/H11.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-105	BGKcLV42-106
RBP	WDR77	WDR77
Batch_ID	BGKcLV42	BGKcLV42
WB_result	49.800	59.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4356	4357

Sequencing Information

	BGKcLV42-105	BGKcLV42-106
Sample_ID	BGKcLV42-105	BGKcLV42-106
Sample Name	WDR77-BGKcLV42-105	WDR77-BGKcLV42-106
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	35,213,362	33,111,029
total_aligned_reads	30,193,847	29,004,424
unique_aligned_reads	27,749,240	26,664,835
percent_uniqueAligned	0.78803	0.80532
correlation_replicates	0.994610	0.994610
spikein_reads	6,182	4,692
percent_spikeins	0.00018	0.00014
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3223	3224

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
WDR77-BGKcLV42-105_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3223	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	30426
WDR77-BGKcLV42-105_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3223	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	30516
WDR77-BGKcLV42-105_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3223					GRCh38	V40	WDR77-BGKcLV42-105_L001_R1_001.filtered.trimmed.paired.fastq.gz,WDR77-BGKcLV42-105_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31358
WDR77-BGKcLV42-105_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	3223					GRCh38	V40	WDR77-BGKcLV42-105_Aligned.sortedByCoord.out.bam		ENCORE2	31448
WDR77-BGKcLV42-105_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	3223					GRCh38	V40	WDR77-BGKcLV42-105_Aligned.sortedByCoord.out.bam		ENCORE2	31538
WDR77-BGKcLV42-105_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	3223					GRCh38	V40	WDR77-BGKcLV42-105_Aligned.sortedByCoord.out.bam		ENCORE2	31628
WDR77-BGKcLV42-105_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	3223					GRCh38	V40	WDR77-BGKcLV42-105_Aligned.sortedByCoord.out.bam		ENCORE2	31718
WDR77-BGKcLV42-105_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3223					GRCh38	V40	WDR77-BGKcLV42-105_L001_R1_001.filtered.trimmed.paired.fastq.gz,WDR77-BGKcLV42-105_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31808
WDR77-BGKcLV42-106_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3224	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	30427
WDR77-BGKcLV42-106_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3224	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	30517
WDR77-BGKcLV42-106_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3224					GRCh38	V40	WDR77-BGKcLV42-106_L001_R1_001.filtered.trimmed.paired.fastq.gz,WDR77-BGKcLV42-106_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31359
WDR77-BGKcLV42-106_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	3224					GRCh38	V40	WDR77-BGKcLV42-106_Aligned.sortedByCoord.out.bam		ENCORE2	31449
WDR77-BGKcLV42-106_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	3224					GRCh38	V40	WDR77-BGKcLV42-106_Aligned.sortedByCoord.out.bam		ENCORE2	31539
WDR77-BGKcLV42-106_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	3224					GRCh38	V40	WDR77-BGKcLV42-106_Aligned.sortedByCoord.out.bam		ENCORE2	31629
WDR77-BGKcLV42-106_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	3224					GRCh38	V40	WDR77-BGKcLV42-106_Aligned.sortedByCoord.out.bam		ENCORE2	31719
WDR77-BGKcLV42-106_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3224					GRCh38	V40	WDR77-BGKcLV42-106_L001_R1_001.filtered.trimmed.paired.fastq.gz,WDR77-BGKcLV42-106_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31809