PARP1 RNA-Seq in HepG2

General Information


RBP	PARP1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	PARP1-BGHcLV36-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV36
Pool ID	Pool-230130
Local_Set_Name	set55
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	PARP1-BGHcLV36-23
Rep2	PARP1-BGHcLV36-24
CN1	NT-BGHcLV36-1
CN2	NT-BGHcLV36-2
Rep1_qPCR	56.6
Rep2_qPCR	42.0
Rep1_WB
Rep2_WB
Antibody Cat#	9532S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1041

Experiment Information (Status: Submitting)

	BGHcLV36-23	BGHcLV36-24
idx	1154	1155
TRCN#_or_BGC#	BGC#0001043	BGC#0001043
shRNA_or_gRNA_sequence	CGAGTCGAGTACGCCAAGAG	CGAGTCGAGTACGCCAAGAG
PAM	CGG	CGG
Name	PARP1_96	PARP1_96
Sample_ID	BGHcLV36-23	BGHcLV36-24
transduction_Date	8/2/22	8/2/22
days	D6	D6
RBP_name	PARP1	PARP1
qPCR_result	56.6	42.0
Ave_qPCR	49.3
RT-qPCR_primer-F	aacaagcagcaagtgccttc
RT-qPCR_primer-R	gacgtccccagtgcagtaat
protein_conc	4430	4939
WB_result	position
Ave_WB
WB_DONE_date	9/7/22
MW	113kd
IP
antibody_Cat#	9532S	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	7335	7336

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV36-23	BGHcLV36-24
Sample_ID	BGHcLV36-23	BGHcLV36-24
Sample Name
Sample Name	PARP1-BGHcLV36-23	PARP1-BGHcLV36-24
RBP	PARP1	PARP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10944	10945

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV36-23	BGHcLV36-24
Sample #	3	4
Sample Name	PARP1-BGHcLV36-23	PARP1-BGHcLV36-24
Sample_Name_Alias
Index Well Position	C01	D01
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	312	300
Peak_Molarity	55.00	61.80
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/C1.png	DNA_Library_set54-56/set1/D1.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set54-56/set1/C1.png	RNA_Library_set54-56/set1/D1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGHcLV36-23	BGHcLV36-24
RBP	PARP1	PARP1
Batch_ID	BGHcLV36	BGHcLV36
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3374	3375

Sequencing Information

	BGHcLV36-23	BGHcLV36-24
Sample_ID	BGHcLV36-23	BGHcLV36-24
Sample Name	PARP1-BGHcLV36-23	PARP1-BGHcLV36-24
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	44,269,040	52,366,358
total_aligned_reads	40,563,695	47,904,890
unique_aligned_reads	38,450,902	45,332,385
percent_uniqueAligned	0.86857	0.86568
correlation_replicates	0.998582	0.998582
spikein_reads	11,830	7,550
percent_spikeins	0.00027	0.00014
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2247	2248

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-BGHcLV36-23_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2247	NovaSeq6000	100	paired-ended	1				NT-BGHcLV36-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8392
PARP1-BGHcLV36-23_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2247	NovaSeq6000	100	paired-ended	2				NT-BGHcLV36-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8442
PARP1-BGHcLV36-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2247					GRCh38	V40	PARP1-BGHcLV36-23_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,PARP1-BGHcLV36-23_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25633
PARP1-BGHcLV36-23_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	2247					GRCh38	V40	PARP1-BGHcLV36-23/Aligned.sortedByCoord.out.bam		ENCORE2	25683
PARP1-BGHcLV36-23_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	2247					GRCh38	V40	PARP1-BGHcLV36-23/Aligned.sortedByCoord.out.bam		ENCORE2	25733
PARP1-BGHcLV36-23_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	2247					GRCh38	V40	PARP1-BGHcLV36-23/Aligned.sortedByCoord.out.bam		ENCORE2	25783
PARP1-BGHcLV36-23_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	2247					GRCh38	V40	PARP1-BGHcLV36-23/Aligned.sortedByCoord.out.bam		ENCORE2	25833
PARP1-BGHcLV36-23_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2247					GRCh38	V40	PARP1-BGHcLV36-23_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,PARP1-BGHcLV36-23_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25883
PARP1-BGHcLV36-24_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2248	NovaSeq6000	100	paired-ended	1				NT-BGHcLV36-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8393
PARP1-BGHcLV36-24_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2248	NovaSeq6000	100	paired-ended	2				NT-BGHcLV36-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8443
PARP1-BGHcLV36-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2248					GRCh38	V40	PARP1-BGHcLV36-24_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,PARP1-BGHcLV36-24_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25634
PARP1-BGHcLV36-24_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	2248					GRCh38	V40	PARP1-BGHcLV36-24/Aligned.sortedByCoord.out.bam		ENCORE2	25684
PARP1-BGHcLV36-24_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	2248					GRCh38	V40	PARP1-BGHcLV36-24/Aligned.sortedByCoord.out.bam		ENCORE2	25734
PARP1-BGHcLV36-24_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	2248					GRCh38	V40	PARP1-BGHcLV36-24/Aligned.sortedByCoord.out.bam		ENCORE2	25784
PARP1-BGHcLV36-24_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	2248					GRCh38	V40	PARP1-BGHcLV36-24/Aligned.sortedByCoord.out.bam		ENCORE2	25834
PARP1-BGHcLV36-24_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2248					GRCh38	V40	PARP1-BGHcLV36-24_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,PARP1-BGHcLV36-24_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25884