PARN RNA-Seq in K562

General Information


RBP	PARN
Cell_Line	K562
Method	shRNA
Exp_Name	PARN-BGKLV24-K562
ENCODE_series_ID	ENCSR052MDR
Batch_ID	BGKLV24
Pool ID	Pool-150615
Local_Set_Name	set24
ENCODE_KD_Exp_ID	ENCSR306IOF
ENCODE_CN_Exp_ID	ENCSR667PLJ
Rep1	PARN_BGKLV24_43_17622
Rep2	PARN_BGKLV24_44_17623
CN1	non-target_BGKLV24_1_17594
CN2	non-target_BGKLV24_2_17595
Rep1_qPCR	70.4
Rep2_qPCR	69.8
Rep1_WB	81.4
Rep2_WB	82.6
Antibody Cat#	GTX115020
Antibody Lot#	GTX115020
Antibody DCC ID	ENCAB392QEW
Status	Released
Project	ENCODE3
ID	567

Experiment Information (Status: Released)

	BGKLV24-43	BGKLV24-44
idx	380	381
TRCN#_or_BGC#	TRCN0000049744	TRCN0000049744
shRNA_or_gRNA_sequence	CCCAGACTCTTGGATACTAAA	CCCAGACTCTTGGATACTAAA
PAM
Name	PARN	PARN
Sample_ID	BGKLV24-43	BGKLV24-44
transduction_Date	2/27/2015	2/27/2015
days
RBP_name	PARN	PARN
qPCR_result	70.4	69.8
Ave_qPCR	70.1
RT-qPCR_primer-F	CCCTACACCCTGCAGAATCA
RT-qPCR_primer-R	GGCCAGCTTCCTCTTGACTA
protein_conc	4022	3953
WB_result	81.4	82.6
Ave_WB	82.0
WB_DONE_date	5/19/2015
MW	73kDa
IP	1	1
antibody_Cat#	GTX115020	GTX115020
Antibody DCC ID	ENCAB392QEW	ENCAB392QEW
submitted_to_DCC_date	8/6/2015
Rep1_TPM	32.6248066	0
Rep2_TPM	31.796614	0
Action
Library_start_date	5/22/2015	5/22/2015
repeat_library
Note
ID	439	440

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PARN	Product_ID: GTX115020 Lot_ID: 40884 Source: GeneTex Target Name: PARN-human

Experiment Status

	BGKLV24-43	BGKLV24-44
Sample_ID	BGKLV24-43	BGKLV24-44
Sample Name	PARN_BGKLV24_43_17622	PARN_BGKLV24_44_17623
Sample Name	PARN_BGKLV24_43_17622	PARN_BGKLV24_44_17623
RBP	PARN	PARN
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	874	875

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-43	BGKLV24-44
Sample #
Sample Name	PARN-BGKLV24-43	PARN-BGKLV24-44
Sample_Name_Alias	PARN_BGKLV24_43_17622	PARN_BGKLV24_44_17623
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-22	2015-05-22
Lib_ID	Lib-150522	Lib-150522
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/C4.png	DNA_Library_LV21-24/set1/D4.png
RIN	9.4	9.5
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/A5.png	RNA_Library_LV20-22-24/set1/B5.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-43	BGKLV24-44
RBP	PARN	PARN
Batch_ID	BGKLV24	BGKLV24
WB_result	81.400	82.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2562	2563

Sequencing Information

	BGKLV24-43	BGKLV24-44
Sample_ID	BGKLV24-43	BGKLV24-44
Sample Name	PARN_BGKLV24_43_17622	PARN_BGKLV24_44_17623
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set24	set24
total_reads	37,380,000	30,730,000
total_aligned_reads	35,277,220	29,095,062
unique_aligned_reads	32,276,784	26,695,734
percent_uniqueAligned	0.86348	0.86872
correlation_replicates	0.983736	0.983736
spikein_reads	154,026	142,212
percent_spikeins	0.00412	0.00463
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1096	1097

Data Submission Information

	BGKLV24-43	BGKLV24-43
ENCODE_alias	brenton-graveley:PARN_BGKLV24	brenton-graveley:PARN-BGKLV24-K562
ENCODE_accession	ENCSR306IOF	ENCSR052MDR
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-43	BGKLV24-43
Sample Name	PARN_BGKLV24_43_17622	PARN_BGKLV24_43_17622
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2988	6847

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
PARN_BGKLV24_43_17622_GTGGCC_L008_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1096	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17210
PARN_BGKLV24_43_17622_GTGGCC_L008_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1096	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17246
PARN_BGKLV24_43_17622_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1096					GRCh38	V40	PARN_BGKLV24_43_17622_GTGGCC_L008_R1_001.fastq.gz,PARN_BGKLV24_43_17622_GTGGCC_L008_R2_001.fastq.gz		ENCORE2	17282
PARN_BGKLV24_43_17622_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1096					GRCh38	V40	PARN_BGKLV24_43_17622/Aligned.sortedByCoord.out.bam		ENCORE2	17318
PARN_BGKLV24_43_17622_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1096					GRCh38	V40	PARN_BGKLV24_43_17622/Aligned.sortedByCoord.out.bam		ENCORE2	17354
PARN_BGKLV24_43_17622_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1096					GRCh38	V40	PARN_BGKLV24_43_17622/Aligned.sortedByCoord.out.bam		ENCORE2	17390
PARN_BGKLV24_43_17622_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1096					GRCh38	V40	PARN_BGKLV24_43_17622/Aligned.sortedByCoord.out.bam		ENCORE2	17426
PARN_BGKLV24_43_17622_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1096					GRCh38	V40	PARN_BGKLV24_43_17622_GTGGCC_L008_R1_001.fastq.gz,PARN_BGKLV24_43_17622_GTGGCC_L008_R2_001.fastq.gz		ENCORE2	17462
PARN_BGKLV24_44_17623_GTTTCG_L008_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1097	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17211
PARN_BGKLV24_44_17623_GTTTCG_L008_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1097	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17247
PARN_BGKLV24_44_17623_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1097					GRCh38	V40	PARN_BGKLV24_44_17623_GTTTCG_L008_R1_001.fastq.gz,PARN_BGKLV24_44_17623_GTTTCG_L008_R2_001.fastq.gz		ENCORE2	17283
PARN_BGKLV24_44_17623_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1097					GRCh38	V40	PARN_BGKLV24_44_17623/Aligned.sortedByCoord.out.bam		ENCORE2	17319
PARN_BGKLV24_44_17623_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1097					GRCh38	V40	PARN_BGKLV24_44_17623/Aligned.sortedByCoord.out.bam		ENCORE2	17355
PARN_BGKLV24_44_17623_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1097					GRCh38	V40	PARN_BGKLV24_44_17623/Aligned.sortedByCoord.out.bam		ENCORE2	17391
PARN_BGKLV24_44_17623_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1097					GRCh38	V40	PARN_BGKLV24_44_17623/Aligned.sortedByCoord.out.bam		ENCORE2	17427
PARN_BGKLV24_44_17623_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1097					GRCh38	V40	PARN_BGKLV24_44_17623_GTTTCG_L008_R1_001.fastq.gz,PARN_BGKLV24_44_17623_GTTTCG_L008_R2_001.fastq.gz		ENCORE2	17463