PKM RNA-Seq in HepG2

General Information


RBP	PKM
Cell_Line	HepG2
Method	shRNA
Exp_Name	PKM-BGHLV16-HepG2
ENCODE_series_ID	ENCSR216UHU
Batch_ID	BGHLV16
Pool ID	Pool-141001
Local_Set_Name	set16
ENCODE_KD_Exp_ID	ENCSR656DQV
ENCODE_CN_Exp_ID	ENCSR689PHN
Rep1	PKM2_BGHLV16_39
Rep2	PKM2_BGHLV16_40
CN1	NT_BGHLV16_1
CN2	NT_BGHLV16_2
Rep1_qPCR	67.4
Rep2_qPCR	67.7
Rep1_WB	43.0
Rep2_WB	50.4
Antibody Cat#	A303-660A
Antibody Lot#	A303-660A
Antibody DCC ID	ENCAB905ZIN
Status	Released
Project	ENCODE3
ID	422

Experiment Information (Status: Released)

	BGHLV16-39	BGHLV16-40
idx	207	208
TRCN#_or_BGC#	TRCN0000037611	TRCN0000037611
shRNA_or_gRNA_sequence	CGGGTGAACTTTGCCATGAAT	CGGGTGAACTTTGCCATGAAT
PAM
Name	PKM2	PKM2
Sample_ID	BGHLV16-39	BGHLV16-40
transduction_Date	7/31/2014	7/31/2014
days
RBP_name	PKM	PKM
qPCR_result	67.4	67.7
Ave_qPCR	67.6
RT-qPCR_primer-F	gggtgaactttgccatgaat
RT-qPCR_primer-R	ggtcagcacaatgaccacat
protein_conc	3847	3548
WB_result	43.0	50.4
Ave_WB	46.7
WB_DONE_date	3/31/2015
MW	58kDa
IP	1	1
antibody_Cat#	A303-660A	A303-660A
Antibody DCC ID	ENCAB905ZIN	ENCAB905ZIN
submitted_to_DCC_date	5/6/2015
Rep1_TPM	17.7	0
Rep2_TPM	16.6	0
Action
Library_start_date	9/23/2014	9/23/2014
repeat_library
Note
ID	2272	2273

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

	BGHLV16-39	BGHLV16-40
Sample_ID	BGHLV16-39	BGHLV16-40
Sample Name	PKM2_BGHLV16_39	PKM2_BGHLV16_40
Sample Name	PKM2_BGHLV16_39	PKM2_BGHLV16_40
RBP	PKM	PKM
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	570	571

Library-Prep
Sequencing

Library-Prep Information

	BGHLV16-39	BGHLV16-40
Sample #
Sample Name	PKM-BGHLV16-39	PKM-BGHLV16-40
Sample_Name_Alias	PKM2_BGHLV16_39	PKM2_BGHLV16_40
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-23	2014-09-23
Lib_ID	Lib-140923	Lib-140923
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/C8.png	DNA_Library_LV16-17/set1/D8.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/A2.png	RNA_Library_LV16-17-18/set1/B2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV16-39	BGHLV16-40
RBP	PKM	PKM
Batch_ID	BGHLV16	BGHLV16
WB_result	43.000	50.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2254	2255

Sequencing Information

	BGHLV16-39	BGHLV16-40
Sample_ID	BGHLV16-39	BGHLV16-40
Sample Name	PKM2_BGHLV16_39	PKM2_BGHLV16_40
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set16	set16
total_reads	37,610,000	35,340,000
total_aligned_reads	32,721,988	30,459,346
unique_aligned_reads	30,890,648	28,736,778
percent_uniqueAligned	0.82134	0.81315
correlation_replicates	0.999803	0.999803
spikein_reads	60,908	43,408
percent_spikeins	0.00162	0.00123
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	896	897

Data Submission Information

	BGHLV16-39	BGHLV16-39
ENCODE_alias	brenton-graveley:PKM2_BGHLV16	brenton-graveley:PKM-BGHLV16-HepG2
ENCODE_accession	ENCSR656DQV	ENCSR216UHU
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV16-39	BGHLV16-39
Sample Name	PKM2_BGHLV16_39	PKM2_BGHLV16_39
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2853	6857

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_BGHLV16_39_GTGGCC_L008_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	896	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14296
PKM2_BGHLV16_39_GTGGCC_L008_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	896	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14322
PKM2_BGHLV16_39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	896					GRCh38	V40	PKM2_BGHLV16_39_GTGGCC_L008_R1_001.fastq.gz,PKM2_BGHLV16_39_GTGGCC_L008_R2_001.fastq.gz		ENCORE2	14348
PKM2_BGHLV16_39_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	896					GRCh38	V40	PKM2_BGHLV16_39/Aligned.sortedByCoord.out.bam		ENCORE2	14374
PKM2_BGHLV16_39_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	896					GRCh38	V40	PKM2_BGHLV16_39/Aligned.sortedByCoord.out.bam		ENCORE2	14400
PKM2_BGHLV16_39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	896					GRCh38	V40	PKM2_BGHLV16_39/Aligned.sortedByCoord.out.bam		ENCORE2	14426
PKM2_BGHLV16_39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	896					GRCh38	V40	PKM2_BGHLV16_39/Aligned.sortedByCoord.out.bam		ENCORE2	14452
PKM2_BGHLV16_39_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	896					GRCh38	V40	PKM2_BGHLV16_39_GTGGCC_L008_R1_001.fastq.gz,PKM2_BGHLV16_39_GTGGCC_L008_R2_001.fastq.gz		ENCORE2	14478
PKM2_BGHLV16_40_GTTTCG_L008_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	897	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14297
PKM2_BGHLV16_40_GTTTCG_L008_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	897	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14323
PKM2_BGHLV16_40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	897					GRCh38	V40	PKM2_BGHLV16_40_GTTTCG_L008_R1_001.fastq.gz,PKM2_BGHLV16_40_GTTTCG_L008_R2_001.fastq.gz		ENCORE2	14349
PKM2_BGHLV16_40_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	897					GRCh38	V40	PKM2_BGHLV16_40/Aligned.sortedByCoord.out.bam		ENCORE2	14375
PKM2_BGHLV16_40_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	897					GRCh38	V40	PKM2_BGHLV16_40/Aligned.sortedByCoord.out.bam		ENCORE2	14401
PKM2_BGHLV16_40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	897					GRCh38	V40	PKM2_BGHLV16_40/Aligned.sortedByCoord.out.bam		ENCORE2	14427
PKM2_BGHLV16_40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	897					GRCh38	V40	PKM2_BGHLV16_40/Aligned.sortedByCoord.out.bam		ENCORE2	14453
PKM2_BGHLV16_40_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	897					GRCh38	V40	PKM2_BGHLV16_40_GTTTCG_L008_R1_001.fastq.gz,PKM2_BGHLV16_40_GTTTCG_L008_R2_001.fastq.gz		ENCORE2	14479