PARP1 RNA-Seq in K562

General Information


RBP	PARP1
Cell_Line	K562
Method	CRISPR
Exp_Name	PARP1-BGKcLV13-K562
ENCODE_series_ID	ENCSR922GPD
Batch_ID	BGKcLV13
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR226HQD
ENCODE_CN_Exp_ID	ENCSR712CQC
Rep1	PARP1-BGKcLV13-49
Rep2	PARP1-BGKcLV13-50
CN1	NT-BGKcLV13-1
CN2	NT-BGKcLV13-2
Rep1_qPCR	73.6
Rep2_qPCR	74.6
Rep1_WB	97.2
Rep2_WB	98.9
Antibody Cat#	436300
Antibody Lot#	?
Antibody DCC ID
Status	Released
Project	ENCODE4
ID	182

Experiment Information (Status: Released)

	BGKcLV13-49	BGKcLV13-50
idx	494	495
TRCN#_or_BGC#	BGC#0000328	BGC#0000328
shRNA_or_gRNA_sequence	CGAGTCGAGTACGCCAAGAG	CGAGTCGAGTACGCCAAGAG
PAM	cgg	cgg
Name	PARP_96	PARP_96
Sample_ID	BGKcLV13-49	BGKcLV13-50
transduction_Date	11/28/18	11/28/18
days	Day 6	Day 6
RBP_name	PARP1	PARP1
qPCR_result	73.6	74.6
Ave_qPCR	74.1
RT-qPCR_primer-F	AAGAAATGCAGCGAGAGCAT
RT-qPCR_primer-R	ACCAGTGTGGGACTTTTCCA
protein_conc	4695	4349
WB_result	97.2	98.9
Ave_WB	98.1
WB_DONE_date	1/10/19	wes
MW	113, 66KD
IP	mouse
antibody_Cat#	436300	?
Antibody DCC ID	NO ID
submitted_to_DCC_date	3/11/19
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	03/18/19	03/18/19
repeat_library
Note
ID	4602	4603

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKcLV13-49	BGKcLV13-50
Sample_ID	BGKcLV13-49	BGKcLV13-50
Sample Name	PARP1-BGKcLV13-49	PARP1-BGKcLV13-50
Sample Name	PARP1-BGKcLV13-49	PARP1-BGKcLV13-50
RBP	PARP1	PARP1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2907	2908

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV13-49	BGKcLV13-50
Sample #	61	62
Sample Name	PARP1-BGKcLV13-49	PARP1-BGKcLV13-50
Sample_Name_Alias
Index Well Position	E08	F08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-18	2019-03-18
Lib_ID	Lib-190318	Lib-190318
Tecan_Location	1-E2	1-F2
Tecan	56.71	50.46
Tecan_date	2019-03-18	2019-03-18
Size_bp	285	289
Peak_Molarity	53.50	46.50
libSampleQC_DNA_Well	DNA_Library_set42/set1/E8.png	DNA_Library_set42/set1/F8.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set42/set1/E8.png	RNA_Library_set42/set1/F8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-18	2019-03-18
Sample_ID	BGKcLV13-49	BGKcLV13-50
RBP	PARP1	PARP1
Batch_ID	BGKcLV13	BGKcLV13
WB_result	97.200	98.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	61	62

Sequencing Information

	BGKcLV13-49	BGKcLV13-50
Sample_ID	BGKcLV13-49	BGKcLV13-50
Sample Name	PARP1-BGKcLV13-49	PARP1-BGKcLV13-50
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	55,117,978	58,272,088
total_aligned_reads	53,695,444	56,733,420
unique_aligned_reads	49,061,812	51,843,624
percent_uniqueAligned	0.89012	0.88968
correlation_replicates	0.998342	0.998342
spikein_reads	31,960	49,788
percent_spikeins	0.00058	0.00085
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	51	52

Data Submission Information

	BGKcLV13-49	BGKcLV13-49	BGKcLV13-49	BGKcLV13-49	BGKcLV13-49	BGKcLV13-49	BGKcLV13-50	BGKcLV13-50	BGKcLV13-50	BGKcLV13-50
ENCODE_alias	brenton-graveley:PARP1-BGKcLV13	brenton-graveley:PARP1-BGKcLV13-49	brenton-graveley:L-PARP1-BGKcLV13-49	brenton-graveley:PARP1-BGKcLV13-49_CGGAACTG+CACTACGA_HK3H2DSXX_S61_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PARP1-BGKcLV13-49_CGGAACTG+CACTACGA_HK3H2DSXX_S61_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PARP1-BGKcLV13-K562	brenton-graveley:PARP1-BGKcLV13-50	brenton-graveley:L-PARP1-BGKcLV13-50	brenton-graveley:PARP1-BGKcLV13-50_TAAGGTCA+TGTCGTAG_HK3H2DSXX_S62_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PARP1-BGKcLV13-50_TAAGGTCA+TGTCGTAG_HK3H2DSXX_S62_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR226HQD	ENCBS739NVD	ENCLB067IWK	ENCFF596FRE	ENCFF382SWU	ENCSR922GPD	ENCBS022VQF	ENCLB851FRO	ENCFF447JVU	ENCFF392VIA
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	BGKcLV13-49	BGKcLV13-49	BGKcLV13-49	BGKcLV13-49	BGKcLV13-49	BGKcLV13-49	BGKcLV13-50	BGKcLV13-50	BGKcLV13-50	BGKcLV13-50
Sample Name	PARP1-BGKcLV13-49	PARP1-BGKcLV13-49	PARP1-BGKcLV13-49	PARP1-BGKcLV13-49	PARP1-BGKcLV13-49	PARP1-BGKcLV13-49	PARP1-BGKcLV13-50	PARP1-BGKcLV13-50	PARP1-BGKcLV13-50	PARP1-BGKcLV13-50
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-BGKcLV13-49.pdf					L-PARP1-BGKcLV13-50.pdf
ID	782	859	941	1001	1083	7279	860	942	1002	1084

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-BGKcLV13-49_CGGAACTG+CACTACGA_HK3H2DSXX_S61_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	51	NovaSeq6000	100	paired-ended	1				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	383
PARP1-BGKcLV13-49_CGGAACTG+CACTACGA_HK3H2DSXX_S61_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	51	NovaSeq6000	100	paired-ended	2				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	465
PARP1-BGKcLV13-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	51					GRCh38	V40	PARP1-BGKcLV13-49_CGGAACTG+CACTACGA_HK3H2DSXX_S61_L004_R1_001.filtered.trimmed.paired.fastq.gz,PARP1-BGKcLV13-49_CGGAACTG+CACTACGA_HK3H2DSXX_S61_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23722
PARP1-BGKcLV13-49_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	51					GRCh38	V40	PARP1-BGKcLV13-49/Aligned.sortedByCoord.out.bam		ENCORE2	23804
PARP1-BGKcLV13-49_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	51					GRCh38	V40	PARP1-BGKcLV13-49/Aligned.sortedByCoord.out.bam		ENCORE2	23886
PARP1-BGKcLV13-49_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	51					GRCh38	V40	PARP1-BGKcLV13-49/Aligned.sortedByCoord.out.bam		ENCORE2	23968
PARP1-BGKcLV13-49_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	51					GRCh38	V40	PARP1-BGKcLV13-49/Aligned.sortedByCoord.out.bam		ENCORE2	24050
PARP1-BGKcLV13-49_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	51					GRCh38	V40	PARP1-BGKcLV13-49_CGGAACTG+CACTACGA_HK3H2DSXX_S61_L004_R1_001.filtered.trimmed.paired.fastq.gz,PARP1-BGKcLV13-49_CGGAACTG+CACTACGA_HK3H2DSXX_S61_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24132
PARP1-BGKcLV13-50_TAAGGTCA+TGTCGTAG_HK3H2DSXX_S62_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	52	NovaSeq6000	100	paired-ended	1				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	384
PARP1-BGKcLV13-50_TAAGGTCA+TGTCGTAG_HK3H2DSXX_S62_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	52	NovaSeq6000	100	paired-ended	2				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	466
PARP1-BGKcLV13-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	52					GRCh38	V40	PARP1-BGKcLV13-50_TAAGGTCA+TGTCGTAG_HK3H2DSXX_S62_L004_R1_001.filtered.trimmed.paired.fastq.gz,PARP1-BGKcLV13-50_TAAGGTCA+TGTCGTAG_HK3H2DSXX_S62_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23723
PARP1-BGKcLV13-50_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	52					GRCh38	V40	PARP1-BGKcLV13-50/Aligned.sortedByCoord.out.bam		ENCORE2	23805
PARP1-BGKcLV13-50_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	52					GRCh38	V40	PARP1-BGKcLV13-50/Aligned.sortedByCoord.out.bam		ENCORE2	23887
PARP1-BGKcLV13-50_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	52					GRCh38	V40	PARP1-BGKcLV13-50/Aligned.sortedByCoord.out.bam		ENCORE2	23969
PARP1-BGKcLV13-50_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	52					GRCh38	V40	PARP1-BGKcLV13-50/Aligned.sortedByCoord.out.bam		ENCORE2	24051
PARP1-BGKcLV13-50_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	52					GRCh38	V40	PARP1-BGKcLV13-50_TAAGGTCA+TGTCGTAG_HK3H2DSXX_S62_L004_R1_001.filtered.trimmed.paired.fastq.gz,PARP1-BGKcLV13-50_TAAGGTCA+TGTCGTAG_HK3H2DSXX_S62_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24133