PARK7 RNA-Seq in K562

General Information


RBP	PARK7
Cell_Line	K562
Method	CRISPR
Exp_Name	PARK7-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	PARK7-BGKcLV42-63
Rep2	PARK7-BGKcLV42-64
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	76.7
Rep2_qPCR	68.4
Rep1_WB	82.8
Rep2_WB	83.0
Antibody Cat#	5560S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1551

Experiment Information (Status: Submitting)

	BGKcLV42-63	BGKcLV42-63	BGKcLV42-64	BGKcLV42-64
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0001165	BGC#0001165	BGC#0001165	BGC#0001165
shRNA_or_gRNA_sequence	CACGTCACCTGCACAGATGG	CACGTCACCTGCACAGATGG	CACGTCACCTGCACAGATGG	CACGTCACCTGCACAGATGG
PAM	CGG	CGG	CGG	CGG
Name	PARK7_71	PARK7_71	PARK7_71	PARK7_71
Sample_ID	BGKcLV42-63	BGKcLV42-63	BGKcLV42-64	BGKcLV42-64
transduction_Date	4/23/24	4/23/24	4/23/24	4/23/24
days	D6	D6	D6	D6
RBP_name	PARK7	PARK7	PARK7	PARK7
qPCR_result	76.7	76.7	68.4	68.4
Ave_qPCR	72.6	72.6
RT-qPCR_primer-F	tggtggttctaccaggaggt	tggtggttctaccaggaggt
RT-qPCR_primer-R	ggttttcctgctccttcagt	ggttttcctgctccttcagt
protein_conc	2747	2747	2603	2603
WB_result	82.8	68.2	83.0	68.0284
Ave_WB	82.9	68.1
WB_DONE_date	5/8/24, 5/23/24	6/245/24
MW	22kd	22kd
IP
antibody_Cat#	5560S	5933S	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	5825	5827	5826	5828

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PARK7	Product_ID: 5560S Lot_ID: 1 Source: Cell Signaling Technology Target Name: PARK7-human
PARK7	Product_ID: 5933S Lot_ID: 1 Source: Cell Signaling Target Name: PARK7-human

Experiment Status

	BGKcLV42-63	BGKcLV42-64
Sample_ID	BGKcLV42-63	BGKcLV42-64
Sample Name
Sample Name	PARK7-BGKcLV42-63	PARK7-BGKcLV42-64
RBP	PARK7	PARK7
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13096	13097

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-63	BGKcLV42-64
Sample #	53	54
Sample Name	PARK7-BGKcLV42-63	PARK7-BGKcLV42-64
Sample_Name_Alias
Index Well Position	E07	F07
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	297
Peak_Molarity	96.20	86.90
libSampleQC_DNA_Well	DNA_Library_set73/set1/E7.png	DNA_Library_set73/set1/F7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/E7.png	RNA_Library_set73/set1/F7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-63	BGKcLV42-64
RBP	PARK7	PARK7
Batch_ID	BGKcLV42	BGKcLV42
WB_result	82.800	83.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4322	4323

Sequencing Information

	BGKcLV42-63	BGKcLV42-64
Sample_ID	BGKcLV42-63	BGKcLV42-64
Sample Name	PARK7-BGKcLV42-63	PARK7-BGKcLV42-64
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	43,542,968	45,277,745
total_aligned_reads	38,134,294	40,288,475
unique_aligned_reads	35,171,962	37,200,895
percent_uniqueAligned	0.80775	0.82162
correlation_replicates	0.999232	0.999232
spikein_reads	1,900	478
percent_spikeins	0.00004	0.00001
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3189	3190

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
PARK7-BGKcLV42-63_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3189	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	30392
PARK7-BGKcLV42-63_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3189	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	30482
PARK7-BGKcLV42-63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3189					GRCh38	V40	PARK7-BGKcLV42-63_L001_R1_001.filtered.trimmed.paired.fastq.gz,PARK7-BGKcLV42-63_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31324
PARK7-BGKcLV42-63_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	3189					GRCh38	V40	PARK7-BGKcLV42-63_Aligned.sortedByCoord.out.bam		ENCORE2	31414
PARK7-BGKcLV42-63_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	3189					GRCh38	V40	PARK7-BGKcLV42-63_Aligned.sortedByCoord.out.bam		ENCORE2	31504
PARK7-BGKcLV42-63_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	3189					GRCh38	V40	PARK7-BGKcLV42-63_Aligned.sortedByCoord.out.bam		ENCORE2	31594
PARK7-BGKcLV42-63_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	3189					GRCh38	V40	PARK7-BGKcLV42-63_Aligned.sortedByCoord.out.bam		ENCORE2	31684
PARK7-BGKcLV42-63_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3189					GRCh38	V40	PARK7-BGKcLV42-63_L001_R1_001.filtered.trimmed.paired.fastq.gz,PARK7-BGKcLV42-63_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31774
PARK7-BGKcLV42-64_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3190	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	30393
PARK7-BGKcLV42-64_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3190	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	30483
PARK7-BGKcLV42-64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3190					GRCh38	V40	PARK7-BGKcLV42-64_L001_R1_001.filtered.trimmed.paired.fastq.gz,PARK7-BGKcLV42-64_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31325
PARK7-BGKcLV42-64_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	3190					GRCh38	V40	PARK7-BGKcLV42-64_Aligned.sortedByCoord.out.bam		ENCORE2	31415
PARK7-BGKcLV42-64_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	3190					GRCh38	V40	PARK7-BGKcLV42-64_Aligned.sortedByCoord.out.bam		ENCORE2	31505
PARK7-BGKcLV42-64_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	3190					GRCh38	V40	PARK7-BGKcLV42-64_Aligned.sortedByCoord.out.bam		ENCORE2	31595
PARK7-BGKcLV42-64_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	3190					GRCh38	V40	PARK7-BGKcLV42-64_Aligned.sortedByCoord.out.bam		ENCORE2	31685
PARK7-BGKcLV42-64_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3190					GRCh38	V40	PARK7-BGKcLV42-64_L001_R1_001.filtered.trimmed.paired.fastq.gz,PARK7-BGKcLV42-64_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31775