PNPT1 RNA-Seq in K562

General Information


RBP	PNPT1
Cell_Line	K562
Method	shRNA
Exp_Name	PNPT1-BGKLV25-K562
ENCODE_series_ID	ENCSR791AGL
Batch_ID	BGKLV25
Pool ID	Pool-151101
Local_Set_Name	set25
ENCODE_KD_Exp_ID	ENCSR191VWK
ENCODE_CN_Exp_ID	ENCSR620PUP
Rep1	PNPT1-BGKLV25-39
Rep2	PNPT1-BGKLV25-40
CN1	NT_BGKLV25-1
CN2	NT_BGKLV25-2
Rep1_qPCR	43.5
Rep2_qPCR	43.0
Rep1_WB	88.8
Rep2_WB	82.9
Antibody Cat#	A303-917A
Antibody Lot#	A303-917A
Antibody DCC ID	ENCAB230SUL
Status	Released
Project	ENCODE3
ID	621

Experiment Information (Status: Released)

	BGKLV25-39	BGKLV25-40
idx	442	443
TRCN#_or_BGC#	TRCN0000035905	TRCN0000035905
shRNA_or_gRNA_sequence	CGCCAGAGATTGTGAAATATA	CGCCAGAGATTGTGAAATATA
PAM
Name	PNPT1	PNPT1
Sample_ID	BGKLV25-39	BGKLV25-40
transduction_Date	3/17/2015	3/17/2015
days
RBP_name	PNPT1	PNPT1
qPCR_result	43.5	43.0
Ave_qPCR	43.2
RT-qPCR_primer-F	TCCTACTGCCCTAGGATTAGAAGTT
RT-qPCR_primer-R	AAAGCCTCATTCTTCCATCG
protein_conc	3549	3003
WB_result	88.8	82.9
Ave_WB	85.8
WB_DONE_date	4/14/2015
MW	86kDa
IP	1	1
antibody_Cat#	A303-917A	A303-917A
Antibody DCC ID	ENCAB230SUL	ENCAB230SUL
submitted_to_DCC_date	5/4/2015
Rep1_TPM	14.5354861	0
Rep2_TPM	7.38029467	0
Action
Library_start_date	6/23/2015	6/23/2015
repeat_library
Note
ID	513	514

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PNPT1	Product_ID: A303-917A Lot_ID: 1 Source: Bethyl Labs Target Name: PNPT1-human

Experiment Status

	BGKLV25-39	BGKLV25-40
Sample_ID	BGKLV25-39	BGKLV25-40
Sample Name	PNPT1-BGKLV25-39	PNPT1-BGKLV25-40
Sample Name	PNPT1-BGKLV25-39	PNPT1-BGKLV25-40
RBP	PNPT1	PNPT1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	922	923

Library-Prep
Sequencing

Library-Prep Information

	BGKLV25-39	BGKLV25-40
Sample #
Sample Name	PNPT1-BGKLV25-39	PNPT1-BGKLV25-40
Sample_Name_Alias	PNPT1-BGKLV25-39	PNPT1-BGKLV25-40
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-23	2015-06-23
Lib_ID	Lib-150623	Lib-150623
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/C3.png	DNA_Library_LV24-25-26/set1/D3.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/E11.png	RNA_Library_LV22-23-25/set1/F11.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV25-39	BGKLV25-40
RBP	PNPT1	PNPT1
Batch_ID	BGKLV25	BGKLV25
WB_result	88.800	82.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2614	2615

Sequencing Information

	BGKLV25-39	BGKLV25-40
Sample_ID	BGKLV25-39	BGKLV25-40
Sample Name	PNPT1-BGKLV25-39	PNPT1-BGKLV25-40
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set25	set25
total_reads	128,796,714	64,141,918
total_aligned_reads	129,922,312	64,022,226
unique_aligned_reads	118,892,432	58,935,268
percent_uniqueAligned	0.92310	0.91883
correlation_replicates	0.997055	0.997055
spikein_reads	661,122	305,398
percent_spikeins	0.00513	0.00476
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1256	1257

Data Submission Information

	BGKLV25-39	BGKLV25-39
ENCODE_alias	brenton-graveley:PNPT1-BGKLV25	brenton-graveley:PNPT1-BGKLV25-K562
ENCODE_accession	ENCSR191VWK	ENCSR791AGL
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV25-39	BGKLV25-39
Sample Name	PNPT1-BGKLV25-39	PNPT1-BGKLV25-39
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3010	6860

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
PNPT1-BGKLV25-39_TTAGGC_L007_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1256	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19584
PNPT1-BGKLV25-39_TTAGGC_L007_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1256	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19620
PNPT1-BGKLV25-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1256					GRCh38	V40	PNPT1-BGKLV25-39_TTAGGC_L007_001.R1.fastq.gz,PNPT1-BGKLV25-39_TTAGGC_L007_001.R2.fastq.gz		ENCORE2	19656
PNPT1-BGKLV25-39_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1256					GRCh38	V40	PNPT1-BGKLV25-39/Aligned.sortedByCoord.out.bam		ENCORE2	19692
PNPT1-BGKLV25-39_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1256					GRCh38	V40	PNPT1-BGKLV25-39/Aligned.sortedByCoord.out.bam		ENCORE2	19728
PNPT1-BGKLV25-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1256					GRCh38	V40	PNPT1-BGKLV25-39/Aligned.sortedByCoord.out.bam		ENCORE2	19764
PNPT1-BGKLV25-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1256					GRCh38	V40	PNPT1-BGKLV25-39/Aligned.sortedByCoord.out.bam		ENCORE2	19800
PNPT1-BGKLV25-39_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1256					GRCh38	V40	PNPT1-BGKLV25-39_TTAGGC_L007_001.R1.fastq.gz,PNPT1-BGKLV25-39_TTAGGC_L007_001.R2.fastq.gz		ENCORE2	19990
PNPT1-BGKLV25-40_TGACCA_L007_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1257	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19585
PNPT1-BGKLV25-40_TGACCA_L007_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1257	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19621
PNPT1-BGKLV25-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1257					GRCh38	V40	PNPT1-BGKLV25-40_TGACCA_L007_001.R1.fastq.gz,PNPT1-BGKLV25-40_TGACCA_L007_001.R2.fastq.gz		ENCORE2	19657
PNPT1-BGKLV25-40_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1257					GRCh38	V40	PNPT1-BGKLV25-40/Aligned.sortedByCoord.out.bam		ENCORE2	19693
PNPT1-BGKLV25-40_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1257					GRCh38	V40	PNPT1-BGKLV25-40/Aligned.sortedByCoord.out.bam		ENCORE2	19729
PNPT1-BGKLV25-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1257					GRCh38	V40	PNPT1-BGKLV25-40/Aligned.sortedByCoord.out.bam		ENCORE2	19765
PNPT1-BGKLV25-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1257					GRCh38	V40	PNPT1-BGKLV25-40/Aligned.sortedByCoord.out.bam		ENCORE2	19801
PNPT1-BGKLV25-40_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1257					GRCh38	V40	PNPT1-BGKLV25-40_TGACCA_L007_001.R1.fastq.gz,PNPT1-BGKLV25-40_TGACCA_L007_001.R2.fastq.gz		ENCORE2	19991