PRKRA RNA-Seq in HepG2

General Information


RBP	PRKRA
Cell_Line	HepG2
Method	CRISPR
Exp_Name	PRKRA-BGHcLV43-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV43
Pool ID	Pool-240723
Local_Set_Name	set74
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	PRKRA-BGHcLV43-43
Rep2	PRKRA-BGHcLV43-44
CN1	NT-BGHcLV43-1
CN2	NT-BGHcLV43-2
Rep1_qPCR	46.1
Rep2_qPCR	36.7
Rep1_WB	88.6
Rep2_WB	86.9
Antibody Cat#	13490S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1585

Experiment Information (Status: Submitting)

	BGHcLV43-43	BGHcLV43-44
idx	1411	1412
TRCN#_or_BGC#	BGC#0001173	BGC#0001173
shRNA_or_gRNA_sequence	GATGTACTTGGCATTCCTTG	GATGTACTTGGCATTCCTTG
PAM	AGG	AGG
Name	PRKRA_74	PRKRA_74
Sample_ID	BGHcLV43-43	BGHcLV43-44
transduction_Date	6/6/24	6/6/24
days	D6	D6
RBP_name	PRKRA	PRKRA
qPCR_result	46.1	36.7
Ave_qPCR	41.4
RT-qPCR_primer-F	ttccaagcaaccaaagaacc
RT-qPCR_primer-R	tccagccatgatgaatagcc
protein_conc	2459	2480
WB_result	88.6	86.9
Ave_WB	87.8
WB_DONE_date	6/17/24
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	9664	9665

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

	BGHcLV43-43	BGHcLV43-44
Sample_ID	BGHcLV43-43	BGHcLV43-44
Sample Name
Sample Name	PRKRA-BGHcLV43-43	PRKRA-BGHcLV43-44
RBP	PRKRA	PRKRA
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13260	13261

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV43-43	BGHcLV43-44
Sample #	33	34
Sample Name	PRKRA-BGHcLV43-43	PRKRA-BGHcLV43-44
Sample_Name_Alias
Index Well Position	A10	B10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-07-22	2024-07-22
Lib_ID	Lib-240722	Lib-240722
Tecan_Location
Tecan
Tecan_date
Size_bp	296	299
Peak_Molarity	93.00	92.90
libSampleQC_DNA_Well	DNA_Library_set74/set1/A5.png	DNA_Library_set74/set1/B5.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set74/set1/E10.png	RNA_Library_set74/set1/F10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-23	2024-07-23
Sample_ID	BGHcLV43-43	BGHcLV43-44
RBP	PRKRA	PRKRA
Batch_ID	BGHcLV43	BGHcLV43
WB_result	88.600	86.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4392	4393

Sequencing Information

	BGHcLV43-43	BGHcLV43-44
Sample_ID	BGHcLV43-43	BGHcLV43-44
Sample Name	PRKRA-BGHcLV43-43	PRKRA-BGHcLV43-44
Pool ID	Pool-240723	Pool-240723
LocalServer_folder	set74	set74
total_reads	38,353,649	48,084,650
total_aligned_reads	34,253,369	44,655,117
unique_aligned_reads	32,159,357	42,006,226
percent_uniqueAligned	0.83850	0.87359
correlation_replicates	0.999036	0.999036
spikein_reads	23,700	17,946
percent_spikeins	0.00062	0.00037
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3259	3260

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-BGHcLV43-43_S123_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3259	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30552
PRKRA-BGHcLV43-43_S123_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3259	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30604
PRKRA-BGHcLV43-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3259					GRCh38	V40	PRKRA-BGHcLV43-43_S123_L003_R1_001.filtered.trimmed.paired.fastq.gz,PRKRA-BGHcLV43-43_S123_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30656
PRKRA-BGHcLV43-43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3259					GRCh38	V40	PRKRA-BGHcLV43-43_Aligned.sortedByCoord.out.bam		ENCORE2	30708
PRKRA-BGHcLV43-43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3259					GRCh38	V40	PRKRA-BGHcLV43-43_Aligned.sortedByCoord.out.bam		ENCORE2	30760
PRKRA-BGHcLV43-43_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3259					GRCh38	V40	PRKRA-BGHcLV43-43_Aligned.sortedByCoord.out.bam		ENCORE2	30812
PRKRA-BGHcLV43-43_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3259					GRCh38	V40	PRKRA-BGHcLV43-43_Aligned.sortedByCoord.out.bam		ENCORE2	30864
PRKRA-BGHcLV43-43_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3259					GRCh38	V40	PRKRA-BGHcLV43-43_S123_L003_R1_001.filtered.trimmed.paired.fastq.gz,PRKRA-BGHcLV43-43_S123_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30916
PRKRA-BGHcLV43-44_S124_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3260	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30553
PRKRA-BGHcLV43-44_S124_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3260	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30605
PRKRA-BGHcLV43-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3260					GRCh38	V40	PRKRA-BGHcLV43-44_S124_L003_R1_001.filtered.trimmed.paired.fastq.gz,PRKRA-BGHcLV43-44_S124_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30657
PRKRA-BGHcLV43-44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3260					GRCh38	V40	PRKRA-BGHcLV43-44_Aligned.sortedByCoord.out.bam		ENCORE2	30709
PRKRA-BGHcLV43-44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3260					GRCh38	V40	PRKRA-BGHcLV43-44_Aligned.sortedByCoord.out.bam		ENCORE2	30761
PRKRA-BGHcLV43-44_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3260					GRCh38	V40	PRKRA-BGHcLV43-44_Aligned.sortedByCoord.out.bam		ENCORE2	30813
PRKRA-BGHcLV43-44_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3260					GRCh38	V40	PRKRA-BGHcLV43-44_Aligned.sortedByCoord.out.bam		ENCORE2	30865
PRKRA-BGHcLV43-44_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3260					GRCh38	V40	PRKRA-BGHcLV43-44_S124_L003_R1_001.filtered.trimmed.paired.fastq.gz,PRKRA-BGHcLV43-44_S124_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30917