PKM RNA-Seq in K562

General Information


RBP	PKM
Cell_Line	K562
Method	shRNA
Exp_Name	PKM-BGKLV21-K562
ENCODE_series_ID	ENCSR463EDG
Batch_ID	BGKLV21
Pool ID	Pool-160229
Local_Set_Name	set21
ENCODE_KD_Exp_ID	ENCSR978CSQ
ENCODE_CN_Exp_ID	ENCSR438MDN
Rep1	PKM2_BGKLV21-41B
Rep2	PKM2_BGKLV21-42B
CN1	NT_BGKLV21-1B
CN2	NT_BGKLV21-2B
Rep1_qPCR	35.4
Rep2_qPCR	24.7
Rep1_WB	55.1
Rep2_WB	45.7
Antibody Cat#	A303-660A
Antibody Lot#	A303-660A
Antibody DCC ID	ENCAB905ZIN
Status	Released
Project	ENCODE3
ID	597

Experiment Information (Status: Released)

	BGKLV21-41	BGKLV21-42
idx	312	313
TRCN#_or_BGC#	TRCN0000037611	TRCN0000037611
shRNA_or_gRNA_sequence	CGGGTGAACTTTGCCATGAAT	CGGGTGAACTTTGCCATGAAT
PAM
Name	PKM2	PKM2
Sample_ID	BGKLV21-41	BGKLV21-42
transduction_Date	10/9/2014	10/9/2014
days
RBP_name	PKM	PKM
qPCR_result	35.4	24.7
Ave_qPCR	30.0
RT-qPCR_primer-F	gggtgaactttgccatgaat
RT-qPCR_primer-R	ggtcagcacaatgaccacat
protein_conc	3128	3083
WB_result	55.1	45.7
Ave_WB	50.4
WB_DONE_date	3/27/2015
MW	58kDa
IP	1	1
antibody_Cat#	A303-660A	A303-660A
Antibody DCC ID	ENCAB905ZIN	ENCAB905ZIN
submitted_to_DCC_date	10/26/16
Rep1_TPM	295.20088	0
Rep2_TPM	225.355621	0
Action
Library_start_date	2/4/2016	2/4/2016
repeat_library
Note
ID	347	348

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PKM	Product_ID: A303-660A Lot_ID: 1 Source: Bethyl Labs Target Name: PKM-human

Experiment Status

	BGKLV21-41	BGKLV21-42
Sample_ID	BGKLV21-41	BGKLV21-42
Sample Name	PKM2_BGKLV21-41B	PKM2_BGKLV21-42B
Sample Name	PKM2_BGKLV21-41B	PKM2_BGKLV21-42B
RBP	PKM2	PKM2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-07	2016-03-07
Project	ENCODE3	ENCODE3
Note
ID	1137	1138

Library-Prep
Sequencing

Library-Prep Information

	BGKLV21-41	BGKLV21-42
Sample #
Sample Name	PKM-BGKLV21-41B	PKM-BGKLV21-42B
Sample_Name_Alias	PKM2_BGKLV21-41B	PKM2_BGKLV21-42B
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-02-04	2016-02-04
Lib_ID	Lib-160204	Lib-160204
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV31-21B/set1/E8.png	DNA_Library_LV31-21B/set1/F8.png
RIN	7.2	9.4
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/G10.png	RNA_Library_LV19-21-24/set1/H10.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV21-41	BGKLV21-42
RBP	PKM	PKM
Batch_ID	BGKLV21	BGKLV21
WB_result	55.100	45.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2834	2835

Sequencing Information

	BGKLV21-41	BGKLV21-42
Sample_ID	BGKLV21-41	BGKLV21-42
Sample Name	PKM2_BGKLV21-41B	PKM2_BGKLV21-42B
Pool ID	Pool-160229	Pool-160229
LocalServer_folder	set21	set21
total_reads	73,623,702	61,915,728
total_aligned_reads	67,066,392	56,724,102
unique_aligned_reads	61,407,158	51,859,926
percent_uniqueAligned	0.83407	0.83759
correlation_replicates	0.998494	0.998494
spikein_reads	444,544	349,842
percent_spikeins	0.00604	0.00565
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1483	1484

Data Submission Information

	BGKLV21-41	BGKLV21-41
ENCODE_alias	brenton-graveley:PKM2_BGKLV21-B	brenton-graveley:PKM-BGKLV21-K562
ENCODE_accession	ENCSR978CSQ	ENCSR463EDG
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV21-41	BGKLV21-41
Sample Name	PKM2_BGKLV21-41B	PKM2_BGKLV21-41B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-07	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3101	6858

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
PKM2_BGKLV21-41B_AGTCAA_L008_001.R1.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1483	HiSeq2000	100	paired-ended	1				NT_BGKLV21-1B_CAGATC_L007_001.R1.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R1.fastq.gz	ENCODE3	15950
PKM2_BGKLV21-41B_AGTCAA_L008_001.R2.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1483	HiSeq2000	100	paired-ended	2				NT_BGKLV21-1B_CAGATC_L007_001.R2.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R2.fastq.gz	ENCODE3	15994
PKM2_BGKLV21-41B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1483					GRCh38	V40	PKM2_BGKLV21-41B_AGTCAA_L008_001.R1.fastq.gz,PKM2_BGKLV21-41B_AGTCAA_L008_001.R2.fastq.gz		ENCORE2	16038
PKM2_BGKLV21-41B_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1483					GRCh38	V40	PKM2_BGKLV21-41B/Aligned.sortedByCoord.out.bam		ENCORE2	16082
PKM2_BGKLV21-41B_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1483					GRCh38	V40	PKM2_BGKLV21-41B/Aligned.sortedByCoord.out.bam		ENCORE2	16126
PKM2_BGKLV21-41B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1483					GRCh38	V40	PKM2_BGKLV21-41B/Aligned.sortedByCoord.out.bam		ENCORE2	16170
PKM2_BGKLV21-41B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1483					GRCh38	V40	PKM2_BGKLV21-41B/Aligned.sortedByCoord.out.bam		ENCORE2	16214
PKM2_BGKLV21-41B_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1483					GRCh38	V40	PKM2_BGKLV21-41B_AGTCAA_L008_001.R1.fastq.gz,PKM2_BGKLV21-41B_AGTCAA_L008_001.R2.fastq.gz		ENCORE2	16258
PKM2_BGKLV21-42B_AGTTCC_L008_001.R1.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1484	HiSeq2000	100	paired-ended	1				NT_BGKLV21-1B_CAGATC_L007_001.R1.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R1.fastq.gz	ENCODE3	15951
PKM2_BGKLV21-42B_AGTTCC_L008_001.R2.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1484	HiSeq2000	100	paired-ended	2				NT_BGKLV21-1B_CAGATC_L007_001.R2.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R2.fastq.gz	ENCODE3	15995
PKM2_BGKLV21-42B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1484					GRCh38	V40	PKM2_BGKLV21-42B_AGTTCC_L008_001.R1.fastq.gz,PKM2_BGKLV21-42B_AGTTCC_L008_001.R2.fastq.gz		ENCORE2	16039
PKM2_BGKLV21-42B_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1484					GRCh38	V40	PKM2_BGKLV21-42B/Aligned.sortedByCoord.out.bam		ENCORE2	16083
PKM2_BGKLV21-42B_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1484					GRCh38	V40	PKM2_BGKLV21-42B/Aligned.sortedByCoord.out.bam		ENCORE2	16127
PKM2_BGKLV21-42B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1484					GRCh38	V40	PKM2_BGKLV21-42B/Aligned.sortedByCoord.out.bam		ENCORE2	16171
PKM2_BGKLV21-42B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1484					GRCh38	V40	PKM2_BGKLV21-42B/Aligned.sortedByCoord.out.bam		ENCORE2	16215
PKM2_BGKLV21-42B_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1484					GRCh38	V40	PKM2_BGKLV21-42B_AGTTCC_L008_001.R1.fastq.gz,PKM2_BGKLV21-42B_AGTTCC_L008_001.R2.fastq.gz		ENCORE2	16259