UPF2 RNA-Seq in K562

General Information


RBP	UPF2
Cell_Line	K562
Method	shRNA
Exp_Name	UPF2-BGKLV21-K562
ENCODE_series_ID	ENCSR406VZO
Batch_ID	BGKLV21
Pool ID	Pool-160229
Local_Set_Name	set21
ENCODE_KD_Exp_ID	ENCSR810FHY
ENCODE_CN_Exp_ID	ENCSR438MDN
Rep1	UPF2_BGKLV21-65B
Rep2	UPF2_BGKLV21-66B
CN1	NT_BGKLV21-1B
CN2	NT_BGKLV21-2B
Rep1_qPCR	55.6
Rep2_qPCR	59.5
Rep1_WB	82.7
Rep2_WB	85.4
Antibody Cat#	A303-929A
Antibody Lot#	A303-929A
Antibody DCC ID	ENCAB821QZM
Status	Released
Project	ENCODE3
ID	598

Experiment Information (Status: Released)

	BGKLV21-65	BGKLV21-66
idx	336	337
TRCN#_or_BGC#	TRCN0000157152	TRCN0000157152
shRNA_or_gRNA_sequence	GCGAGATACGTCACAATGGTA	GCGAGATACGTCACAATGGTA
PAM
Name	UPF2	UPF2
Sample_ID	BGKLV21-65	BGKLV21-66
transduction_Date	10/9/2014	10/9/2014
days
RBP_name	UPF2	UPF2
qPCR_result	55.6	59.5
Ave_qPCR	57.6
RT-qPCR_primer-F	cgattaggaatggaggttaatca
RT-qPCR_primer-R	ttccaccattcggtaattgtaa
protein_conc	3198	2920
WB_result	82.7	85.4
Ave_WB	84.1
WB_DONE_date	8/19/2015
MW	148kDa
IP	1	1
antibody_Cat#	A303-929A	A303-929A
Antibody DCC ID	ENCAB821QZM	ENCAB821QZM
submitted_to_DCC_date	12/7/2015
Rep1_TPM	24.3962895	0
Rep2_TPM	17.3103154	0
Action
Library_start_date	2/4/2016	2/4/2016
repeat_library
Note	x	x
ID	377	378

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
UPF2	Product_ID: A303-929A Lot_ID: 1 Source: Bethyl Labs Target Name: UPF2-human

Experiment Status

	BGKLV21-65	BGKLV21-66
Sample_ID	BGKLV21-65	BGKLV21-66
Sample Name	UPF2_BGKLV21-65B	UPF2_BGKLV21-66B
Sample Name	UPF2_BGKLV21-65B	UPF2_BGKLV21-66B
RBP	UPF2	UPF2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-07	2016-03-07
Project	ENCODE3	ENCODE3
Note
ID	1139	1140

Library-Prep
Sequencing

Library-Prep Information

	BGKLV21-65	BGKLV21-66
Sample #
Sample Name	UPF2-BGKLV21-65B	UPF2-BGKLV21-66B
Sample_Name_Alias	UPF2_BGKLV21-65B	UPF2_BGKLV21-66B
Index Well Position	S15	S16
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/set2/A10.png	DNA_Library_LV31-21B/set1/H8.png
RIN	8.2	9.6
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/C12.png	RNA_Library_LV19-21-24/set1/D12.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV21-65	BGKLV21-66
RBP	UPF2	UPF2
Batch_ID	BGKLV21	BGKLV21
WB_result	82.700	85.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2836	2837

Sequencing Information

	BGKLV21-65	BGKLV21-66
Sample_ID	BGKLV21-65	BGKLV21-66
Sample Name	UPF2_BGKLV21-65B	UPF2_BGKLV21-66B
Pool ID	Pool-160229	Pool-160229
LocalServer_folder	set21	set21
total_reads	64,109,520	64,740,368
total_aligned_reads	59,348,014	59,216,776
unique_aligned_reads	54,450,832	54,309,506
percent_uniqueAligned	0.84934	0.83888
correlation_replicates	0.998588	0.998588
spikein_reads	309,690	309,310
percent_spikeins	0.00483	0.00478
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1485	1486

Data Submission Information

	BGKLV21-65	BGKLV21-65
ENCODE_alias	brenton-graveley:UPF2_BGKLV21-B	brenton-graveley:UPF2-BGKLV21-K562
ENCODE_accession	ENCSR810FHY	ENCSR406VZO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV21-65	BGKLV21-65
Sample Name	UPF2_BGKLV21-65B	UPF2_BGKLV21-65B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-07	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3102	7033

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
UPF2_BGKLV21-65B_ATGTCA_L008_001.R1.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1485	HiSeq2000	100	paired-ended	1				NT_BGKLV21-1B_CAGATC_L007_001.R1.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R1.fastq.gz	ENCODE3	15962
UPF2_BGKLV21-65B_ATGTCA_L008_001.R2.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1485	HiSeq2000	100	paired-ended	2				NT_BGKLV21-1B_CAGATC_L007_001.R2.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R2.fastq.gz	ENCODE3	16006
UPF2_BGKLV21-65B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1485					GRCh38	V40	UPF2_BGKLV21-65B_ATGTCA_L008_001.R1.fastq.gz,UPF2_BGKLV21-65B_ATGTCA_L008_001.R2.fastq.gz		ENCORE2	16050
UPF2_BGKLV21-65B_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	1485					GRCh38	V40	UPF2_BGKLV21-65B/Aligned.sortedByCoord.out.bam		ENCORE2	16094
UPF2_BGKLV21-65B_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	1485					GRCh38	V40	UPF2_BGKLV21-65B/Aligned.sortedByCoord.out.bam		ENCORE2	16138
UPF2_BGKLV21-65B_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	1485					GRCh38	V40	UPF2_BGKLV21-65B/Aligned.sortedByCoord.out.bam		ENCORE2	16182
UPF2_BGKLV21-65B_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	1485					GRCh38	V40	UPF2_BGKLV21-65B/Aligned.sortedByCoord.out.bam		ENCORE2	16226
UPF2_BGKLV21-65B_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1485					GRCh38	V40	UPF2_BGKLV21-65B_ATGTCA_L008_001.R1.fastq.gz,UPF2_BGKLV21-65B_ATGTCA_L008_001.R2.fastq.gz		ENCORE2	16270
UPF2_BGKLV21-66B_CCGTCC_L008_001.R1.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1486	HiSeq2000	100	paired-ended	1				NT_BGKLV21-1B_CAGATC_L007_001.R1.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R1.fastq.gz	ENCODE3	15963
UPF2_BGKLV21-66B_CCGTCC_L008_001.R2.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1486	HiSeq2000	100	paired-ended	2				NT_BGKLV21-1B_CAGATC_L007_001.R2.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R2.fastq.gz	ENCODE3	16007
UPF2_BGKLV21-66B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1486					GRCh38	V40	UPF2_BGKLV21-66B_CCGTCC_L008_001.R1.fastq.gz,UPF2_BGKLV21-66B_CCGTCC_L008_001.R2.fastq.gz		ENCORE2	16051
UPF2_BGKLV21-66B_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	1486					GRCh38	V40	UPF2_BGKLV21-66B/Aligned.sortedByCoord.out.bam		ENCORE2	16095
UPF2_BGKLV21-66B_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	1486					GRCh38	V40	UPF2_BGKLV21-66B/Aligned.sortedByCoord.out.bam		ENCORE2	16139
UPF2_BGKLV21-66B_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	1486					GRCh38	V40	UPF2_BGKLV21-66B/Aligned.sortedByCoord.out.bam		ENCORE2	16183
UPF2_BGKLV21-66B_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	1486					GRCh38	V40	UPF2_BGKLV21-66B/Aligned.sortedByCoord.out.bam		ENCORE2	16227
UPF2_BGKLV21-66B_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1486					GRCh38	V40	UPF2_BGKLV21-66B_CCGTCC_L008_001.R1.fastq.gz,UPF2_BGKLV21-66B_CCGTCC_L008_001.R2.fastq.gz		ENCORE2	16271