PARP1 RNA-Seq in HepG2

General Information


RBP	PARP1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	PARP1-BGHcLV14-HepG2
ENCODE_series_ID	ENCSR439DQM
Batch_ID	BGHcLV14
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR202SRN
ENCODE_CN_Exp_ID	ENCSR750CPT
Rep1	PARP1-BGHcLV14-49
Rep2	PARP1-BGHcLV14-50
CN1	NT-BGHcLV14-1
CN2	NT-BGHcLV14-2
Rep1_qPCR	26.6
Rep2_qPCR	20.7
Rep1_WB	64.3
Rep2_WB	82.2
Antibody Cat#	436300
Antibody Lot#
Antibody DCC ID
Status	Released
Project	ENCODE4
ID	181

Experiment Information (Status: Released)

	BGHcLV14-49	BGHcLV14-49	BGHcLV14-50	BGHcLV14-50
idx	404	406	405	407
TRCN#_or_BGC#	BGC#0000328	BGC#0000328	BGC#0000328	BGC#0000328
shRNA_or_gRNA_sequence	CGAGTCGAGTACGCCAAGAG	CGAGTCGAGTACGCCAAGAG	CGAGTCGAGTACGCCAAGAG	CGAGTCGAGTACGCCAAGAG
PAM	cgg	cgg	cgg	cgg
Name	PARP_96	PARP_96	PARP_96	PARP_96
Sample_ID	BGHcLV14-49	BGHcLV14-49	BGHcLV14-50	BGHcLV14-50
transduction_Date	12/5/18	12/5/18	12/5/18	12/5/18
days	D6	D6	D6	D6
RBP_name	PARP1	PARP1	PARP1	PARP1
qPCR_result	26.6	26.6	20.7	20.7
Ave_qPCR	23.7	23.7
RT-qPCR_primer-F	AAGAAATGCAGCGAGAGCAT	AAGAAATGCAGCGAGAGCAT
RT-qPCR_primer-R	ACCAGTGTGGGACTTTTCCA	ACCAGTGTGGGACTTTTCCA
protein_conc	4436	4436	3959	3959
WB_result	64.3	76.8	82.2	88.9
Ave_WB	73.3	82.8
WB_DONE_date	1/10/19	1/10/19	wes	wes
MW	113KD, 66KD	66kd
IP	mouse	mouse
antibody_Cat#	436400	436400
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	107	107	0	0
Rep2_TPM	98	98	0	0
Action	Ready		Ready
Library_start_date	03/18/19		03/18/19
repeat_library
Note
ID	6549	6551	6550	6552

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV14-49	BGHcLV14-50
Sample_ID	BGHcLV14-49	BGHcLV14-50
Sample Name	PARP1-BGHcLV14-49	PARP1-BGHcLV14-50
Sample Name	PARP1-BGHcLV14-49	PARP1-BGHcLV14-50
RBP	PARP1	PARP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2987	2988

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV14-49	BGHcLV14-50
Sample #	81	82
Sample Name	PARP1-BGHcLV14-49	PARP1-BGHcLV14-50
Sample_Name_Alias
Index Well Position	A11	B11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-18	2019-03-18
Lib_ID	Lib-190318	Lib-190318
Tecan_Location	3-A1	3-B1
Tecan	72.89	93.60
Tecan_date	2019-03-18	2019-03-18
Size_bp	296	293
Peak_Molarity	43.90	56.30
libSampleQC_DNA_Well	DNA_Library_set42/set1/A11.png	DNA_Library_set42/set1/B11.png
RIN	9.3	9.5
libSample_RNA_Well	RNA_Library_set42/set1/A11.png	RNA_Library_set42/set1/B11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-18	2019-03-18
Sample_ID	BGHcLV14-49	BGHcLV14-50
RBP	PARP1	PARP1
Batch_ID	BGHcLV14	BGHcLV14
WB_result	64.300	82.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	81	82

Sequencing Information

	BGHcLV14-49	BGHcLV14-50
Sample_ID	BGHcLV14-49	BGHcLV14-50
Sample Name	PARP1-BGHcLV14-49	PARP1-BGHcLV14-50
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	60,838,472	52,191,836
total_aligned_reads	57,803,626	49,322,324
unique_aligned_reads	54,451,258	46,436,114
percent_uniqueAligned	0.89501	0.88972
correlation_replicates	0.996765	0.996765
spikein_reads	37,268	25,614
percent_spikeins	0.00061	0.00049
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	49	50

Data Submission Information

	BGHcLV14-49	BGHcLV14-49	BGHcLV14-49	BGHcLV14-49	BGHcLV14-49	BGHcLV14-49	BGHcLV14-50	BGHcLV14-50	BGHcLV14-50	BGHcLV14-50
ENCODE_alias	brenton-graveley:PARP1-BGHcLV14	brenton-graveley:PARP1-BGHcLV14-49	brenton-graveley:L-PARP1-BGHcLV14-49	brenton-graveley:PARP1-BGHcLV14-49_AACTGTAG+ACGCCGCA_HK3H2DSXX_S81_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PARP1-BGHcLV14-49_AACTGTAG+ACGCCGCA_HK3H2DSXX_S81_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PARP1-BGHcLV14-HepG2	brenton-graveley:PARP1-BGHcLV14-50	brenton-graveley:L-PARP1-BGHcLV14-50	brenton-graveley:PARP1-BGHcLV14-50_GGTCACGA+GTATTATG_HK3H2DSXX_S82_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PARP1-BGHcLV14-50_GGTCACGA+GTATTATG_HK3H2DSXX_S82_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR202SRN	ENCBS065JLX	ENCLB138IUC	ENCFF112QUW	ENCFF540KFR	ENCSR439DQM	ENCBS700LBH	ENCLB689GOM	ENCFF925HKI	ENCFF532MPJ
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV14-49	BGHcLV14-49	BGHcLV14-49	BGHcLV14-49	BGHcLV14-49	BGHcLV14-49	BGHcLV14-50	BGHcLV14-50	BGHcLV14-50	BGHcLV14-50
Sample Name	PARP1-BGHcLV14-49	PARP1-BGHcLV14-49	PARP1-BGHcLV14-49	PARP1-BGHcLV14-49	PARP1-BGHcLV14-49	PARP1-BGHcLV14-49	PARP1-BGHcLV14-50	PARP1-BGHcLV14-50	PARP1-BGHcLV14-50	PARP1-BGHcLV14-50
Selected	Yes	No	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
			LV42_library_protocol					LV42_library_protocol
protocol_URL			L-PARP1-BGHcLV14-49.pdf					L-PARP1-BGHcLV14-50.pdf
ID	760	815	897	999	1081	7278	816	898	1000	1082

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-BGHcLV14-49_AACTGTAG+ACGCCGCA_HK3H2DSXX_S81_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	49	NovaSeq6000	100	paired-ended	1				NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	381
PARP1-BGHcLV14-49_AACTGTAG+ACGCCGCA_HK3H2DSXX_S81_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	49	NovaSeq6000	100	paired-ended	2				NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	463
PARP1-BGHcLV14-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	49					GRCh38	V40	PARP1-BGHcLV14-49_AACTGTAG+ACGCCGCA_HK3H2DSXX_S81_L004_R1_001.filtered.trimmed.paired.fastq.gz,PARP1-BGHcLV14-49_AACTGTAG+ACGCCGCA_HK3H2DSXX_S81_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23720
PARP1-BGHcLV14-49_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	49					GRCh38	V40	PARP1-BGHcLV14-49/Aligned.sortedByCoord.out.bam		ENCORE2	23802
PARP1-BGHcLV14-49_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	49					GRCh38	V40	PARP1-BGHcLV14-49/Aligned.sortedByCoord.out.bam		ENCORE2	23884
PARP1-BGHcLV14-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	49					GRCh38	V40	PARP1-BGHcLV14-49/Aligned.sortedByCoord.out.bam		ENCORE2	23966
PARP1-BGHcLV14-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	49					GRCh38	V40	PARP1-BGHcLV14-49/Aligned.sortedByCoord.out.bam		ENCORE2	24048
PARP1-BGHcLV14-49_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	49					GRCh38	V40	PARP1-BGHcLV14-49_AACTGTAG+ACGCCGCA_HK3H2DSXX_S81_L004_R1_001.filtered.trimmed.paired.fastq.gz,PARP1-BGHcLV14-49_AACTGTAG+ACGCCGCA_HK3H2DSXX_S81_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24130
PARP1-BGHcLV14-50_GGTCACGA+GTATTATG_HK3H2DSXX_S82_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	50	NovaSeq6000	100	paired-ended	1				NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	382
PARP1-BGHcLV14-50_GGTCACGA+GTATTATG_HK3H2DSXX_S82_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	50	NovaSeq6000	100	paired-ended	2				NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	464
PARP1-BGHcLV14-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	50					GRCh38	V40	PARP1-BGHcLV14-50_GGTCACGA+GTATTATG_HK3H2DSXX_S82_L004_R1_001.filtered.trimmed.paired.fastq.gz,PARP1-BGHcLV14-50_GGTCACGA+GTATTATG_HK3H2DSXX_S82_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23721
PARP1-BGHcLV14-50_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	50					GRCh38	V40	PARP1-BGHcLV14-50/Aligned.sortedByCoord.out.bam		ENCORE2	23803
PARP1-BGHcLV14-50_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	50					GRCh38	V40	PARP1-BGHcLV14-50/Aligned.sortedByCoord.out.bam		ENCORE2	23885
PARP1-BGHcLV14-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	50					GRCh38	V40	PARP1-BGHcLV14-50/Aligned.sortedByCoord.out.bam		ENCORE2	23967
PARP1-BGHcLV14-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	50					GRCh38	V40	PARP1-BGHcLV14-50/Aligned.sortedByCoord.out.bam		ENCORE2	24049
PARP1-BGHcLV14-50_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	50					GRCh38	V40	PARP1-BGHcLV14-50_GGTCACGA+GTATTATG_HK3H2DSXX_S82_L004_R1_001.filtered.trimmed.paired.fastq.gz,PARP1-BGHcLV14-50_GGTCACGA+GTATTATG_HK3H2DSXX_S82_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24131