PARP1 RNA-Seq in K562

General Information


RBP	PARP1
Cell_Line	K562
Method	CRISPR
Exp_Name	PARP1-BGKcLV37-K562
ENCODE_series_ID
Batch_ID	BGKcLV37
Pool ID	Pool-230130
Local_Set_Name	set55
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	PARP1-BGKcLV37-27
Rep2	PARP1-BGKcLV37-28
CN1	NT-BGKcLV37-1
CN2	NT-BGKcLV37-2
Rep1_qPCR	75.4
Rep2_qPCR	78.6
Rep1_WB	77.8
Rep2_WB	73.2
Antibody Cat#	9532S
Antibody Lot#	lot # 10
Antibody DCC ID	NO ID
Status	Submitted
Project	ENCORE2
ID	1055

Experiment Information (Status: Submitting)

	BGKcLV37-27	BGKcLV37-27	BGKcLV37-28	BGKcLV37-28
idx	1379	1379	1380	1380
TRCN#_or_BGC#	BGC#0001043	BGC#0001043	BGC#0001043	BGC#0001043
shRNA_or_gRNA_sequence	CGAGTCGAGTACGCCAAGAG	CGAGTCGAGTACGCCAAGAG	CGAGTCGAGTACGCCAAGAG	CGAGTCGAGTACGCCAAGAG
PAM	CGG	CGG	CGG	CGG
Name	PARP1_96	PARP1_96	PARP1_96	PARP1_96
Sample_ID	BGKcLV37-27	BGKcLV37-27	BGKcLV37-28	BGKcLV37-28
transduction_Date	9/20/22	9/20/22	9/20/22	9/20/22
days	D6	D6	D6	D6
RBP_name	PARP1	PARP1	PARP1	PARP1
qPCR_result	75.4	75.4	78.6	78.6
Ave_qPCR	77.0	77.0
RT-qPCR_primer-F	aacaagcagcaagtgccttc	aacaagcagcaagtgccttc
RT-qPCR_primer-R	gacgtccccagtgcagtaat	gacgtccccagtgcagtaat
protein_conc	1590	1590	1556	1556
WB_result	77.8	54.0	73.2	59.1231
Ave_WB	75.5	56.6
WB_DONE_date	9/29/22	4/9/24,4/18/24	Licor
MW	113kd	Cleaved PARP
IP
antibody_Cat#	9532S	5625s	lot # 10	lot # 1
Antibody DCC ID	NO ID
submitted_to_DCC_date	8/29/23
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	5529	5531	5530	5532

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PARP1	Product_ID: 9532S Lot_ID: 10 Source: Cell Signaling Technology Target Name: PARP1-human
PARP1	Product_ID: 5625S Lot_ID: 1 Source: Cell Signaling Target Name: PARP1-human

Experiment Status

	BGKcLV37-27	BGKcLV37-28
Sample_ID	BGKcLV37-27	BGKcLV37-28
Sample Name
Sample Name	PARP1-BGKcLV37-27	PARP1-BGKcLV37-28
RBP	PARP1	PARP1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11094	11095

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV37-27	BGKcLV37-28
Sample #	33	34
Sample Name	PARP1-BGKcLV37-27	PARP1-BGKcLV37-28
Sample_Name_Alias
Index Well Position	A05	B05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-01-13	2023-01-13
Lib_ID	Lib-230113	Lib-230113
Tecan_Location
Tecan
Tecan_date
Size_bp	318	295
Peak_Molarity	46.60	48.60
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/A5.png	DNA_Library_set54-56/set1/B5.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set54-56/set1/A5.png	RNA_Library_set54-56/set1/B5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV37-27	BGKcLV37-28
RBP	PARP1	PARP1
Batch_ID	BGKcLV37	BGKcLV37
WB_result	77.800	73.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3404	3405

Sequencing Information

	BGKcLV37-27	BGKcLV37-28
Sample_ID	BGKcLV37-27	BGKcLV37-28
Sample Name	PARP1-BGKcLV37-27	PARP1-BGKcLV37-28
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	67,356,713	61,633,679
total_aligned_reads	61,789,702	58,119,088
unique_aligned_reads	57,474,842	53,965,013
percent_uniqueAligned	0.85329	0.87558
correlation_replicates	0.998446	0.998446
spikein_reads	13,288	7,282
percent_spikeins	0.00020	0.00012
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2277	2278

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
PARP1-BGKcLV37-27_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2277	NovaSeq6000	100	paired-ended	1				NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8394
PARP1-BGKcLV37-27_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2277	NovaSeq6000	100	paired-ended	2				NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8444
PARP1-BGKcLV37-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2277					GRCh38	V40	PARP1-BGKcLV37-27_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,PARP1-BGKcLV37-27_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25635
PARP1-BGKcLV37-27_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2277					GRCh38	V40	PARP1-BGKcLV37-27/Aligned.sortedByCoord.out.bam		ENCORE2	25685
PARP1-BGKcLV37-27_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2277					GRCh38	V40	PARP1-BGKcLV37-27/Aligned.sortedByCoord.out.bam		ENCORE2	25735
PARP1-BGKcLV37-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2277					GRCh38	V40	PARP1-BGKcLV37-27/Aligned.sortedByCoord.out.bam		ENCORE2	25785
PARP1-BGKcLV37-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2277					GRCh38	V40	PARP1-BGKcLV37-27/Aligned.sortedByCoord.out.bam		ENCORE2	25835
PARP1-BGKcLV37-27_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2277					GRCh38	V40	PARP1-BGKcLV37-27_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,PARP1-BGKcLV37-27_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25885
PARP1-BGKcLV37-28_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2278	NovaSeq6000	100	paired-ended	1				NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8395
PARP1-BGKcLV37-28_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2278	NovaSeq6000	100	paired-ended	2				NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8445
PARP1-BGKcLV37-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2278					GRCh38	V40	PARP1-BGKcLV37-28_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz,PARP1-BGKcLV37-28_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25636
PARP1-BGKcLV37-28_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2278					GRCh38	V40	PARP1-BGKcLV37-28/Aligned.sortedByCoord.out.bam		ENCORE2	25686
PARP1-BGKcLV37-28_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2278					GRCh38	V40	PARP1-BGKcLV37-28/Aligned.sortedByCoord.out.bam		ENCORE2	25736
PARP1-BGKcLV37-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2278					GRCh38	V40	PARP1-BGKcLV37-28/Aligned.sortedByCoord.out.bam		ENCORE2	25786
PARP1-BGKcLV37-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2278					GRCh38	V40	PARP1-BGKcLV37-28/Aligned.sortedByCoord.out.bam		ENCORE2	25836
PARP1-BGKcLV37-28_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2278					GRCh38	V40	PARP1-BGKcLV37-28_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz,PARP1-BGKcLV37-28_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25886