PPIG RNA-Seq in K562

General Information


RBP	PPIG
Cell_Line	K562
Method	shRNA
Exp_Name	PPIG-BGKLV29-K562
ENCODE_series_ID	ENCSR919QPP
Batch_ID	BGKLV29
Pool ID	Pool-151215B
Local_Set_Name	set29
ENCODE_KD_Exp_ID	ENCSR529MBZ
ENCODE_CN_Exp_ID	ENCSR032YMP
Rep1	PPIG_BGKLV29-47
Rep2	PPIG_BGKLV29-48
CN1	NT_BGKLV29-1
CN2	NT_BGKLV29-2
Rep1_qPCR	73.2
Rep2_qPCR	61.9
Rep1_WB	86.8
Rep2_WB	86.9
Antibody Cat#	A302-075A
Antibody Lot#	A302-075A
Antibody DCC ID	ENCAB460YIG
Status	Released
Project	ENCODE3
ID	672

Experiment Information (Status: Released)

	BGKLV29-47	BGKLV29-48
idx	582	583
TRCN#_or_BGC#	TRCN0000049326	TRCN0000049326
shRNA_or_gRNA_sequence	GCAGTCTGATTCTAAAGGAAA	GCAGTCTGATTCTAAAGGAAA
PAM
Name	PPIG	PPIG
Sample_ID	BGKLV29-47	BGKLV29-48
transduction_Date	8/11/2015	8/11/2015
days
RBP_name	PPIG	PPIG
qPCR_result	73.2	61.9
Ave_qPCR	67.5
RT-qPCR_primer-F	gtggagagctgattcccaaa
RT-qPCR_primer-R	tgaggaggaggaagatgatga
protein_conc	3575	3395
WB_result	86.8	86.9
Ave_WB	86.9
WB_DONE_date	9/18/2015
MW	89kDa
IP	1	1
antibody_Cat#	A302-075A	A302-075A
Antibody DCC ID	ENCAB460YIG	ENCAB460YIG
submitted_to_DCC_date	12/7/2015
Rep1_TPM	63.9258376	0
Rep2_TPM	40.4801334	0
Action
Library_start_date	11/2/2015	11/2/2015
repeat_library
Note	x	x
ID	663	664

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PPIG	Product_ID: A302-075A Lot_ID: 1 Source: Bethyl Labs Target Name: PPIG-human

Experiment Status

	BGKLV29-47	BGKLV29-48
Sample_ID	BGKLV29-47	BGKLV29-48
Sample Name	PPIG_BGKLV29-47	PPIG_BGKLV29-48
Sample Name	PPIG_BGKLV29-47	PPIG_BGKLV29-48
RBP	PPIG	PPIG
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	1032	1033

Library-Prep
Sequencing

Library-Prep Information

	BGKLV29-47	BGKLV29-48
Sample #
Sample Name	PPIG-BGKLV29-47	PPIG-BGKLV29-48
Sample_Name_Alias	PPIG_BGKLV29-47	PPIG_BGKLV29-48
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-02	2015-11-02
Lib_ID	Lib-151102	Lib-151102
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/C7.png	DNA_Library_LV28-29-30/set1/D7.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/G2.png	RNA_Library_LV29-30-31-32/set1/H2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV29-47	BGKLV29-48
RBP	PPIG	PPIG
Batch_ID	BGKLV29	BGKLV29
WB_result	86.800	86.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2718	2719

Sequencing Information

	BGKLV29-47	BGKLV29-48
Sample_ID	BGKLV29-47	BGKLV29-48
Sample Name	PPIG_BGKLV29-47	PPIG_BGKLV29-48
Pool ID	Pool-151215B	Pool-151215B
LocalServer_folder	set29	set29
total_reads	79,270,484	69,523,152
total_aligned_reads	72,393,722	62,522,732
unique_aligned_reads	65,545,920	56,815,852
percent_uniqueAligned	0.82686	0.81722
correlation_replicates	0.998223	0.998223
spikein_reads	426,890	331,986
percent_spikeins	0.00539	0.00478
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1387	1388

Data Submission Information

	BGKLV29-47	BGKLV29-47
ENCODE_alias	brenton-graveley:PPIG_BGKLV29	brenton-graveley:PPIG-BGKLV29-K562
ENCODE_accession	ENCSR529MBZ	ENCSR919QPP
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV29-47	BGKLV29-47
Sample Name	PPIG_BGKLV29-47	PPIG_BGKLV29-47
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3065	6863

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
PPIG_BGKLV29-47_TTAGGC_L002_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1387	HiSeq2500	100	paired-ended	1				NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20434
PPIG_BGKLV29-47_TTAGGC_L002_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1387	HiSeq2500	100	paired-ended	2				NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20464
PPIG_BGKLV29-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1387					GRCh38	V40	PPIG_BGKLV29-47_TTAGGC_L002_001.R1.fastq.gz,PPIG_BGKLV29-47_TTAGGC_L002_001.R2.fastq.gz		ENCORE2	20494
PPIG_BGKLV29-47_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1387					GRCh38	V40	PPIG_BGKLV29-47/Aligned.sortedByCoord.out.bam		ENCORE2	20524
PPIG_BGKLV29-47_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1387					GRCh38	V40	PPIG_BGKLV29-47/Aligned.sortedByCoord.out.bam		ENCORE2	20554
PPIG_BGKLV29-47_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1387					GRCh38	V40	PPIG_BGKLV29-47/Aligned.sortedByCoord.out.bam		ENCORE2	20584
PPIG_BGKLV29-47_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1387					GRCh38	V40	PPIG_BGKLV29-47/Aligned.sortedByCoord.out.bam		ENCORE2	20614
PPIG_BGKLV29-47_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1387					GRCh38	V40	PPIG_BGKLV29-47_TTAGGC_L002_001.R1.fastq.gz,PPIG_BGKLV29-47_TTAGGC_L002_001.R2.fastq.gz		ENCORE2	20644
PPIG_BGKLV29-48_TGACCA_L002_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1388	HiSeq2500	100	paired-ended	1				NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20435
PPIG_BGKLV29-48_TGACCA_L002_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1388	HiSeq2500	100	paired-ended	2				NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20465
PPIG_BGKLV29-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1388					GRCh38	V40	PPIG_BGKLV29-48_TGACCA_L002_001.R1.fastq.gz,PPIG_BGKLV29-48_TGACCA_L002_001.R2.fastq.gz		ENCORE2	20495
PPIG_BGKLV29-48_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1388					GRCh38	V40	PPIG_BGKLV29-48/Aligned.sortedByCoord.out.bam		ENCORE2	20525
PPIG_BGKLV29-48_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1388					GRCh38	V40	PPIG_BGKLV29-48/Aligned.sortedByCoord.out.bam		ENCORE2	20555
PPIG_BGKLV29-48_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1388					GRCh38	V40	PPIG_BGKLV29-48/Aligned.sortedByCoord.out.bam		ENCORE2	20585
PPIG_BGKLV29-48_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1388					GRCh38	V40	PPIG_BGKLV29-48/Aligned.sortedByCoord.out.bam		ENCORE2	20615
PPIG_BGKLV29-48_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1388					GRCh38	V40	PPIG_BGKLV29-48_TGACCA_L002_001.R1.fastq.gz,PPIG_BGKLV29-48_TGACCA_L002_001.R2.fastq.gz		ENCORE2	20645