UPF1 RNA-Seq in K562

General Information


RBP	UPF1
Cell_Line	K562
Method	shRNA
Exp_Name	UPF1-BGKLV34-K562
ENCODE_series_ID	ENCSR531KGW
Batch_ID	BGKLV34
Pool ID	Pool-160912
Local_Set_Name	set34
ENCODE_KD_Exp_ID	ENCSR251ABP
ENCODE_CN_Exp_ID	ENCSR174OYC
Rep1	UPF1_BGKLV34-43
Rep2	UPF1_BGKLV34-44
CN1	NT_BGKLV34-1
CN2	NT_BGKLV34-2
Rep1_qPCR	59.7
Rep2_qPCR	51.8
Rep1_WB	66.6
Rep2_WB	53.2
Antibody Cat#	RN108PW
Antibody Lot#	RN108PW
Antibody DCC ID	ENCAB730BOO
Status	Released
Project	ENCODE3
ID	727

Experiment Information (Status: Released)

	BGKLV34-43	BGKLV34-43	BGKLV34-44	BGKLV34-44
idx	706	706	707	707
TRCN#_or_BGC#	TRCN0000022254	TRCN0000022254	TRCN0000022254	TRCN0000022254
shRNA_or_gRNA_sequence	GCATCTTATTCTGGGTAATAA	GCATCTTATTCTGGGTAATAA	CCAACCCGATAAACCGATGTT	CCAACCCGATAAACCGATGTT
PAM
Name	UPF1	UPF1	UPF1	UPF1
Sample_ID	BGKLV34-43	BGKLV34-43	BGKLV34-44	BGKLV34-44
transduction_Date	11/4/2015	11/4/2015	11/4/2015	11/4/2015
days
RBP_name	UPF1	UPF1	UPF1	UPF1
qPCR_result	59.7	59.7	51.8	51.8
Ave_qPCR	55.8	55.8
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3439	3439	3647	3647
WB_result	66.6	95.7	53.2	94.8
Ave_WB	59.9	95.3
WB_DONE_date	2/4/2016	7/19/23
MW	124kd	124kd	WES
IP
antibody_Cat#	RN108PW	12040S	RN108PW	lot # 3
Antibody DCC ID	ENCAB730BOO		ENCAB730BOO
submitted_to_DCC_date	3/8/2016	1/8/24
Rep1_TPM	27.21384307	0	0	0
Rep2_TPM	21.78873983	0	0	0
Action
Library_start_date	3/9/2016		3/9/2016
repeat_library
Note
ID	793	795	794	796

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
UPF1	Product_ID: RN108PW Lot_ID: 1 Source: MBLI Target Name: UPF1-human
UPF1	Product_ID: 12040S Lot_ID: 3 Source: Cell Signaling Technology Target Name: UPF1-human

Experiment Status

	BGKLV34-43	BGKLV34-44
Sample_ID	BGKLV34-43	BGKLV34-44
Sample Name	UPF1_BGKLV34-43	UPF1_BGKLV34-44
Sample Name	UPF1_BGKLV34-43	UPF1_BGKLV34-44
RBP	UPF1	UPF1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1243	1244

Library-Prep
Sequencing

Library-Prep Information

	BGKLV34-43	BGKLV34-44
Sample #
Sample Name	UPF1-BGKLV34-43	UPF1-BGKLV34-44
Sample_Name_Alias	UPF1_BGKLV34-43	UPF1_BGKLV34-44
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-09	2016-03-09
Lib_ID	Lib-160309	Lib-160309
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/C4.png	DNA_Library_LV33-34-25B-32/set1/D4.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/A6.png	RNA_Library_LV32-33-34/set1/B6.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV34-43	BGKLV34-44
RBP	UPF1	UPF1
Batch_ID	BGKLV34	BGKLV34
WB_result	66.600	53.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2928	2929

Sequencing Information

	BGKLV34-43	BGKLV34-44
Sample_ID	BGKLV34-43	BGKLV34-44
Sample Name	UPF1_BGKLV34-43	UPF1_BGKLV34-44
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set34	set34
total_reads	98,070,604	78,524,982
total_aligned_reads	83,680,860	66,058,770
unique_aligned_reads	76,728,248	60,573,558
percent_uniqueAligned	0.78238	0.77139
correlation_replicates	0.999219	0.999219
spikein_reads	317,258	239,000
percent_spikeins	0.00323	0.00304
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1577	1578

Data Submission Information

	BGKLV34-43	BGKLV34-43
ENCODE_alias	brenton-graveley:UPF1_BGKLV34	brenton-graveley:UPF1-BGKLV34-K562
ENCODE_accession	ENCSR251ABP	ENCSR531KGW
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV34-43	BGKLV34-43
Sample Name	UPF1_BGKLV34-43	UPF1_BGKLV34-43
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3161	7031

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
UPF1_BGKLV34-43_GGCTAC_L004_001.R1.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1577	HiSeq2500	100	paired-ended	1				NT_BGKLV34-1_CGTACG_L002_001.R1.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R1.fastq.gz	ENCODE3	21536
UPF1_BGKLV34-43_GGCTAC_L004_001.R2.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1577	HiSeq2500	100	paired-ended	2				NT_BGKLV34-1_CGTACG_L002_001.R2.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R2.fastq.gz	ENCODE3	21556
UPF1_BGKLV34-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1577					GRCh38	V40	UPF1_BGKLV34-43_GGCTAC_L004_001.R1.fastq.gz,UPF1_BGKLV34-43_GGCTAC_L004_001.R2.fastq.gz		ENCORE2	21576
UPF1_BGKLV34-43_Signal.Unique.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1577					GRCh38	V40	UPF1_BGKLV34-43/Aligned.sortedByCoord.out.bam		ENCORE2	21596
UPF1_BGKLV34-43_Signal.Unique.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1577					GRCh38	V40	UPF1_BGKLV34-43/Aligned.sortedByCoord.out.bam		ENCORE2	21616
UPF1_BGKLV34-43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1577					GRCh38	V40	UPF1_BGKLV34-43/Aligned.sortedByCoord.out.bam		ENCORE2	21636
UPF1_BGKLV34-43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1577					GRCh38	V40	UPF1_BGKLV34-43/Aligned.sortedByCoord.out.bam		ENCORE2	21656
UPF1_BGKLV34-43_quant.sf	ENCODE_DATA/set34/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1577					GRCh38	V40	UPF1_BGKLV34-43_GGCTAC_L004_001.R1.fastq.gz,UPF1_BGKLV34-43_GGCTAC_L004_001.R2.fastq.gz		ENCORE2	21676
UPF1_BGKLV34-44_CTTGTA_L004_001.R1.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1578	HiSeq2500	100	paired-ended	1				NT_BGKLV34-1_CGTACG_L002_001.R1.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R1.fastq.gz	ENCODE3	21537
UPF1_BGKLV34-44_CTTGTA_L004_001.R2.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1578	HiSeq2500	100	paired-ended	2				NT_BGKLV34-1_CGTACG_L002_001.R2.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R2.fastq.gz	ENCODE3	21557
UPF1_BGKLV34-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1578					GRCh38	V40	UPF1_BGKLV34-44_CTTGTA_L004_001.R1.fastq.gz,UPF1_BGKLV34-44_CTTGTA_L004_001.R2.fastq.gz		ENCORE2	21577
UPF1_BGKLV34-44_Signal.Unique.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1578					GRCh38	V40	UPF1_BGKLV34-44/Aligned.sortedByCoord.out.bam		ENCORE2	21597
UPF1_BGKLV34-44_Signal.Unique.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1578					GRCh38	V40	UPF1_BGKLV34-44/Aligned.sortedByCoord.out.bam		ENCORE2	21617
UPF1_BGKLV34-44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1578					GRCh38	V40	UPF1_BGKLV34-44/Aligned.sortedByCoord.out.bam		ENCORE2	21637
UPF1_BGKLV34-44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1578					GRCh38	V40	UPF1_BGKLV34-44/Aligned.sortedByCoord.out.bam		ENCORE2	21657
UPF1_BGKLV34-44_quant.sf	ENCODE_DATA/set34/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1578					GRCh38	V40	UPF1_BGKLV34-44_CTTGTA_L004_001.R1.fastq.gz,UPF1_BGKLV34-44_CTTGTA_L004_001.R2.fastq.gz		ENCORE2	21677