PRKRA RNA-Seq in K562

General Information


RBP	PRKRA
Cell_Line	K562
Method	CRISPR
Exp_Name	PRKRA-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	PRKRA-BGKcLV42-69
Rep2	PRKRA-BGKcLV42-70
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	57.1
Rep2_qPCR	61.8
Rep1_WB	87.1
Rep2_WB	91.5
Antibody Cat#	13490S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1554

Experiment Information (Status: Submitting)

	BGKcLV42-69	BGKcLV42-70
idx	0	0
TRCN#_or_BGC#	BGC#0001173	BGC#0001173
shRNA_or_gRNA_sequence	GATGTACTTGGCATTCCTTG	GATGTACTTGGCATTCCTTG
PAM	AGG	AGG
Name	PRKRA_74	PRKRA_74
Sample_ID	BGKcLV42-69	BGKcLV42-70
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	PRKRA	PRKRA
qPCR_result	57.1	61.8
Ave_qPCR	59.4
RT-qPCR_primer-F	ttccaagcaaccaaagaacc
RT-qPCR_primer-R	tccagccatgatgaatagcc
protein_conc	2083	2388
WB_result	87.1	91.5
Ave_WB	89.3
WB_DONE_date	5/14/24
MW	30kd
IP
antibody_Cat#	13490S	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	5833	5834

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PRKRA	Product_ID: 13490S Lot_ID: 1 Source: Cell Signaling Technology Target Name: PRKRA-human

Experiment Status

	BGKcLV42-69	BGKcLV42-70
Sample_ID	BGKcLV42-69	BGKcLV42-70
Sample Name
Sample Name	PRKRA-BGKcLV42-69	PRKRA-BGKcLV42-70
RBP	PRKRA	PRKRA
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13102	13103

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-69	BGKcLV42-70
Sample #	59	60
Sample Name	PRKRA-BGKcLV42-69	PRKRA-BGKcLV42-70
Sample_Name_Alias
Index Well Position	C08	D08
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	310	306
Peak_Molarity	99.20	109.00
libSampleQC_DNA_Well	DNA_Library_set73/set1/C8.png	DNA_Library_set73/set1/D8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/C8.png	RNA_Library_set73/set1/D8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-69	BGKcLV42-70
RBP	PRKRA	PRKRA
Batch_ID	BGKcLV42	BGKcLV42
WB_result	87.100	91.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4328	4329

Sequencing Information

	BGKcLV42-69	BGKcLV42-70
Sample_ID	BGKcLV42-69	BGKcLV42-70
Sample Name	PRKRA-BGKcLV42-69	PRKRA-BGKcLV42-70
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	39,843,641	39,105,831
total_aligned_reads	37,544,483	36,535,906
unique_aligned_reads	34,623,258	33,789,044
percent_uniqueAligned	0.86898	0.86404
correlation_replicates	0.997069	0.997069
spikein_reads	650	1,072
percent_spikeins	0.00002	0.00003
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3195	3196

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
PRKRA-BGKcLV42-69_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3195	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	30398
PRKRA-BGKcLV42-69_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3195	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	30488
PRKRA-BGKcLV42-69_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3195					GRCh38	V40	PRKRA-BGKcLV42-69_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRKRA-BGKcLV42-69_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31330
PRKRA-BGKcLV42-69_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	3195					GRCh38	V40	PRKRA-BGKcLV42-69_Aligned.sortedByCoord.out.bam		ENCORE2	31420
PRKRA-BGKcLV42-69_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	3195					GRCh38	V40	PRKRA-BGKcLV42-69_Aligned.sortedByCoord.out.bam		ENCORE2	31510
PRKRA-BGKcLV42-69_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	3195					GRCh38	V40	PRKRA-BGKcLV42-69_Aligned.sortedByCoord.out.bam		ENCORE2	31600
PRKRA-BGKcLV42-69_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	3195					GRCh38	V40	PRKRA-BGKcLV42-69_Aligned.sortedByCoord.out.bam		ENCORE2	31690
PRKRA-BGKcLV42-69_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3195					GRCh38	V40	PRKRA-BGKcLV42-69_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRKRA-BGKcLV42-69_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31780
PRKRA-BGKcLV42-70_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3196	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	30399
PRKRA-BGKcLV42-70_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3196	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	30489
PRKRA-BGKcLV42-70_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3196					GRCh38	V40	PRKRA-BGKcLV42-70_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRKRA-BGKcLV42-70_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31331
PRKRA-BGKcLV42-70_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	3196					GRCh38	V40	PRKRA-BGKcLV42-70_Aligned.sortedByCoord.out.bam		ENCORE2	31421
PRKRA-BGKcLV42-70_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	3196					GRCh38	V40	PRKRA-BGKcLV42-70_Aligned.sortedByCoord.out.bam		ENCORE2	31511
PRKRA-BGKcLV42-70_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	3196					GRCh38	V40	PRKRA-BGKcLV42-70_Aligned.sortedByCoord.out.bam		ENCORE2	31601
PRKRA-BGKcLV42-70_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	3196					GRCh38	V40	PRKRA-BGKcLV42-70_Aligned.sortedByCoord.out.bam		ENCORE2	31691
PRKRA-BGKcLV42-70_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3196					GRCh38	V40	PRKRA-BGKcLV42-70_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRKRA-BGKcLV42-70_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31781