METAP2 RNA-Seq in K562

General Information


RBP	METAP2
Cell_Line	K562
Method	shRNA
Exp_Name	METAP2-BGKLV36-K562
ENCODE_series_ID	ENCSR772WSC
Batch_ID	BGKLV36
Pool ID	Pool-161129
Local_Set_Name	set36
ENCODE_KD_Exp_ID	ENCSR952QDQ
ENCODE_CN_Exp_ID	ENCSR424QCW
Rep1	METAP2_BGKLV36-35
Rep2	METAP2_BGKLV36-36
CN1	NT_BGKLV36-1
CN2	NT_BGKLV36-2
Rep1_qPCR	73.6
Rep2_qPCR	82.0
Rep1_WB	51.6
Rep2_WB	50.9
Antibody Cat#	A303-419A
Antibody Lot#	A303-419A
Antibody DCC ID	ENCAB441VBJ
Status	Released
Project	ENCODE3
ID	748

Experiment Information (Status: Released)

	BGKLV36-35	BGKLV36-36
idx	758	759
TRCN#_or_BGC#	TRCN0000050580	TRCN0000050580
shRNA_or_gRNA_sequence	CTTGGGAGAAAGTAAATACTT	CTTGGGAGAAAGTAAATACTT
PAM
Name	METAP2	METAP2
Sample_ID	BGKLV36-35	BGKLV36-36
transduction_Date	5/19/2016	5/19/2016
days
RBP_name	METAP2	METAP2
qPCR_result	73.6	82.0
Ave_qPCR	77.8
RT-qPCR_primer-F	gcagaagcacatcgacaagt
RT-qPCR_primer-R	tgcgtgaacagtcttccaac
protein_conc	4232	4963
WB_result	51.6	50.9
Ave_WB	51.2
WB_DONE_date	6/21/16
MW	53kdA
IP	1	1
antibody_Cat#	A303-419A	A303-419A
Antibody DCC ID	ENCAB441VBJ	ENCAB441VBJ
submitted_to_DCC_date	11/16/17
Rep1_TPM	71.5	0
Rep2_TPM	57.8	0
Action
Library_start_date	07/28/16	07/28/16
repeat_library
Note
ID	851	852

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
METAP2	Product_ID: A303-419A Lot_ID: 1 Source: Bethyl Labs Target Name: METAP2-human

Experiment Status

	BGKLV36-35	BGKLV36-36
Sample_ID	BGKLV36-35	BGKLV36-36
Sample Name	METAP2_BGKLV36-35	METAP2_BGKLV36-36
Sample Name	METAP2_BGKLV36-35	METAP2_BGKLV36-36
RBP	METAP2	METAP2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-12-12	2016-12-12
Project	ENCODE3	ENCODE3
Note
ID	1289	1290

Library-Prep
Sequencing

Library-Prep Information

	BGKLV36-35	BGKLV36-36
Sample #
Sample Name	METAP2-BGKLV36-35	METAP2-BGKLV36-36
Sample_Name_Alias	METAP2_BGKLV36-35	METAP2_BGKLV36-36
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-07-28	2016-07-28
Lib_ID	Lib-160728	Lib-160728
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV36/set1/C3.png	DNA_Library_LV36/set1/D3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/E6.png	RNA_Library_LV35_LV36/set1/F6.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV36-35	BGKLV36-36
RBP	METAP2	METAP2
Batch_ID	BGKLV36	BGKLV36
WB_result	51.600	50.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2974	2975

Sequencing Information

	BGKLV36-35	BGKLV36-36
Sample_ID	BGKLV36-35	BGKLV36-36
Sample Name	METAP2_BGKLV36-35	METAP2_BGKLV36-36
Pool ID	Pool-161129	Pool-161129
LocalServer_folder	set36	set36
total_reads	53,002,904	72,941,062
total_aligned_reads	47,978,708	65,558,252
unique_aligned_reads	43,884,314	59,481,136
percent_uniqueAligned	0.82796	0.81547
correlation_replicates	0.996452	0.996452
spikein_reads	111,848	143,466
percent_spikeins	0.00211	0.00197
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1623	1624

Data Submission Information

	BGKLV36-35	BGKLV36-35
ENCODE_alias	brenton-graveley:METAP2_BGKLV36	brenton-graveley:METAP2-BGKLV36-K562
ENCODE_accession	ENCSR952QDQ	ENCSR772WSC
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV36-35	BGKLV36-35
Sample Name	METAP2_BGKLV36-35	METAP2_BGKLV36-35
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3184	6811

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
METAP2_BGKLV36-35_TTAGGC_L002_001.R1.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1623	HiSeq2500	100	paired-ended	1				NT_BGKLV36-1_GATCAG_L008_001.R1.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R1.fastq.gz	ENCODE3	21902
METAP2_BGKLV36-35_TTAGGC_L002_001.R2.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1623	HiSeq2500	100	paired-ended	2				NT_BGKLV36-1_GATCAG_L008_001.R2.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R2.fastq.gz	ENCODE3	21920
METAP2_BGKLV36-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1623					GRCh38	V40	METAP2_BGKLV36-35_TTAGGC_L002_001.R1.fastq.gz,METAP2_BGKLV36-35_TTAGGC_L002_001.R2.fastq.gz		ENCORE2	21938
METAP2_BGKLV36-35_Signal.Unique.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1623					GRCh38	V40	METAP2_BGKLV36-35/Aligned.sortedByCoord.out.bam		ENCORE2	21956
METAP2_BGKLV36-35_Signal.Unique.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1623					GRCh38	V40	METAP2_BGKLV36-35/Aligned.sortedByCoord.out.bam		ENCORE2	21974
METAP2_BGKLV36-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1623					GRCh38	V40	METAP2_BGKLV36-35/Aligned.sortedByCoord.out.bam		ENCORE2	21992
METAP2_BGKLV36-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1623					GRCh38	V40	METAP2_BGKLV36-35/Aligned.sortedByCoord.out.bam		ENCORE2	22010
METAP2_BGKLV36-35_quant.sf	ENCODE_DATA/set36/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1623					GRCh38	V40	METAP2_BGKLV36-35_TTAGGC_L002_001.R1.fastq.gz,METAP2_BGKLV36-35_TTAGGC_L002_001.R2.fastq.gz		ENCORE2	22028
METAP2_BGKLV36-36_TGACCA_L002_001.R1.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1624	HiSeq2500	100	paired-ended	1				NT_BGKLV36-1_GATCAG_L008_001.R1.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R1.fastq.gz	ENCODE3	21903
METAP2_BGKLV36-36_TGACCA_L002_001.R2.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1624	HiSeq2500	100	paired-ended	2				NT_BGKLV36-1_GATCAG_L008_001.R2.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R2.fastq.gz	ENCODE3	21921
METAP2_BGKLV36-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1624					GRCh38	V40	METAP2_BGKLV36-36_TGACCA_L002_001.R1.fastq.gz,METAP2_BGKLV36-36_TGACCA_L002_001.R2.fastq.gz		ENCORE2	21939
METAP2_BGKLV36-36_Signal.Unique.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1624					GRCh38	V40	METAP2_BGKLV36-36/Aligned.sortedByCoord.out.bam		ENCORE2	21957
METAP2_BGKLV36-36_Signal.Unique.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1624					GRCh38	V40	METAP2_BGKLV36-36/Aligned.sortedByCoord.out.bam		ENCORE2	21975
METAP2_BGKLV36-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1624					GRCh38	V40	METAP2_BGKLV36-36/Aligned.sortedByCoord.out.bam		ENCORE2	21993
METAP2_BGKLV36-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1624					GRCh38	V40	METAP2_BGKLV36-36/Aligned.sortedByCoord.out.bam		ENCORE2	22011
METAP2_BGKLV36-36_quant.sf	ENCODE_DATA/set36/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1624					GRCh38	V40	METAP2_BGKLV36-36_TGACCA_L002_001.R1.fastq.gz,METAP2_BGKLV36-36_TGACCA_L002_001.R2.fastq.gz		ENCORE2	22029