PKN2 RNA-Seq in K562

General Information


RBP	PKN2
Cell_Line	K562
Method	CRISPR
Exp_Name	PKN2-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	PKN2-BGKcLV42-67
Rep2	PKN2-BGKcLV42-68
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	45.6
Rep2_qPCR	48.4
Rep1_WB	83.9
Rep2_WB	88.5
Antibody Cat#	8697S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1553

Experiment Information (Status: Submitting)

	BGKcLV42-67	BGKcLV42-68
idx	0	0
TRCN#_or_BGC#	BGC#0001168	BGC#0001168
shRNA_or_gRNA_sequence	AAGTCCTCTTGAACTTCGGA	AAGTCCTCTTGAACTTCGGA
PAM	TGG	TGG
Name	PKN2_88	PKN2_88
Sample_ID	BGKcLV42-67	BGKcLV42-68
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	PKN2	PKN2
qPCR_result	45.6	48.4
Ave_qPCR	47.0
RT-qPCR_primer-F	atcagttgcactgcctggtt
RT-qPCR_primer-R	tcgagcttcaaaacagcaca
protein_conc	2630	2854
WB_result	83.9	88.5
Ave_WB	86.2
WB_DONE_date	5/14/24,5/23/24
MW	140kd
IP
antibody_Cat#	8697S	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	5831	5832

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PKN2	Product_ID: 8697S Lot_ID: 1 Source: Cell Signaling Technology Target Name: PKN2-human

Experiment Status

	BGKcLV42-67	BGKcLV42-68
Sample_ID	BGKcLV42-67	BGKcLV42-68
Sample Name
Sample Name	PKN2-BGKcLV42-67	PKN2-BGKcLV42-68
RBP	PKN2	PKN2
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13100	13101

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-67	BGKcLV42-68
Sample #	57	58
Sample Name	PKN2-BGKcLV42-67	PKN2-BGKcLV42-68
Sample_Name_Alias
Index Well Position	A08	B08
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	300	313
Peak_Molarity	101.00	92.80
libSampleQC_DNA_Well	DNA_Library_set73/set1/A8.png	DNA_Library_set73/set1/B8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/A8.png	RNA_Library_set73/set1/B8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-67	BGKcLV42-68
RBP	PKN2	PKN2
Batch_ID	BGKcLV42	BGKcLV42
WB_result	83.900	88.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4326	4327

Sequencing Information

	BGKcLV42-67	BGKcLV42-68
Sample_ID	BGKcLV42-67	BGKcLV42-68
Sample Name	PKN2-BGKcLV42-67	PKN2-BGKcLV42-68
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	53,729,782	50,702,217
total_aligned_reads	46,370,894	47,695,823
unique_aligned_reads	42,874,848	44,136,557
percent_uniqueAligned	0.79797	0.87051
correlation_replicates	0.980313	0.980313
spikein_reads	7,834	1,406
percent_spikeins	0.00015	0.00003
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3193	3194

Data Submission Information DCC submission information was not avaliable

File Information

Search:

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
PKN2-BGKcLV42-67_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3193					GRCh38	V40	PKN2-BGKcLV42-67_L001_R1_001.filtered.trimmed.paired.fastq.gz,PKN2-BGKcLV42-67_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31328
PKN2-BGKcLV42-67_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3193	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	30396
PKN2-BGKcLV42-67_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3193	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	30486
PKN2-BGKcLV42-67_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3193					GRCh38	V40	PKN2-BGKcLV42-67_L001_R1_001.filtered.trimmed.paired.fastq.gz,PKN2-BGKcLV42-67_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31778
PKN2-BGKcLV42-67_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	3193					GRCh38	V40	PKN2-BGKcLV42-67_Aligned.sortedByCoord.out.bam		ENCORE2	31688
PKN2-BGKcLV42-67_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	3193					GRCh38	V40	PKN2-BGKcLV42-67_Aligned.sortedByCoord.out.bam		ENCORE2	31598
PKN2-BGKcLV42-67_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	3193					GRCh38	V40	PKN2-BGKcLV42-67_Aligned.sortedByCoord.out.bam		ENCORE2	31508
PKN2-BGKcLV42-67_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	3193					GRCh38	V40	PKN2-BGKcLV42-67_Aligned.sortedByCoord.out.bam		ENCORE2	31418
PKN2-BGKcLV42-68_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3194					GRCh38	V40	PKN2-BGKcLV42-68_L001_R1_001.filtered.trimmed.paired.fastq.gz,PKN2-BGKcLV42-68_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31329
PKN2-BGKcLV42-68_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3194	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	30397
PKN2-BGKcLV42-68_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3194	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	30487
PKN2-BGKcLV42-68_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3194					GRCh38	V40	PKN2-BGKcLV42-68_L001_R1_001.filtered.trimmed.paired.fastq.gz,PKN2-BGKcLV42-68_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31779
PKN2-BGKcLV42-68_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	3194					GRCh38	V40	PKN2-BGKcLV42-68_Aligned.sortedByCoord.out.bam		ENCORE2	31689
PKN2-BGKcLV42-68_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	3194					GRCh38	V40	PKN2-BGKcLV42-68_Aligned.sortedByCoord.out.bam		ENCORE2	31599
PKN2-BGKcLV42-68_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	3194					GRCh38	V40	PKN2-BGKcLV42-68_Aligned.sortedByCoord.out.bam		ENCORE2	31509
PKN2-BGKcLV42-68_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	3194					GRCh38	V40	PKN2-BGKcLV42-68_Aligned.sortedByCoord.out.bam		ENCORE2	31419

Showing 1 to 16 of 16 entries