UPF1 RNA-Seq in HepG2

General Information


RBP	UPF1
Cell_Line	HepG2
Method	shRNA
Exp_Name	UPF1-BGHLV33-HepG2
ENCODE_series_ID	ENCSR300WFS
Batch_ID	BGHLV33
Pool ID	Pool-160912
Local_Set_Name	set33
ENCODE_KD_Exp_ID	ENCSR689MIY
ENCODE_CN_Exp_ID	ENCSR691IVR
Rep1	UPF1_BGHLV33-33
Rep2	UPF1_BGHLV33-34
CN1	NT_BGHLV33-1
CN2	NT_BGHLV33-2
Rep1_qPCR	59.5
Rep2_qPCR	72.2
Rep1_WB	51.6
Rep2_WB	67.3
Antibody Cat#	RN108PW
Antibody Lot#	RN108PW
Antibody DCC ID	ENCAB730BOO
Status	Released
Project	ENCODE3
ID	717

Experiment Information (Status: Released)

	BGHLV33-33	BGHLV33-34
idx	841	842
TRCN#_or_BGC#	TRCN0000022257	TRCN0000022257
shRNA_or_gRNA_sequence	CCAACCCGATAAACCGATGTT	CCAACCCGATAAACCGATGTT
PAM
Name	UPF1	UPF1
Sample_ID	BGHLV33-33	BGHLV33-34
transduction_Date	11/17/2015	11/17/2015
days
RBP_name	UPF1	UPF1
qPCR_result	59.5	72.2
Ave_qPCR	65.8
RT-qPCR_primer-F	caacccgataaaccgatgtt
RT-qPCR_primer-R	ggtgatcttctccacgttcg
protein_conc	5231	4516
WB_result	51.6	67.3
Ave_WB	59.5
WB_DONE_date	2/8/2016
MW	124kDa	wes
IP
antibody_Cat#	RN108PW	RN108PW
Antibody DCC ID	ENCAB730BOO	ENCAB730BOO
submitted_to_DCC_date	3/8/2016
Rep1_TPM	13.7	0
Rep2_TPM	18.4	0
Action
Library_start_date	3/9/2016	3/9/2016
repeat_library
Note
ID	2930	2931

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

Experiment Status

	BGHLV33-33	BGHLV33-34
Sample_ID	BGHLV33-33	BGHLV33-34
Sample Name	UPF1_BGHLV33-33	UPF1_BGHLV33-34
Sample Name	UPF1_BGHLV33-33	UPF1_BGHLV33-34
RBP	UPF1	UPF1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1221	1222

Library-Prep
Sequencing

Library-Prep Information

	BGHLV33-33	BGHLV33-34
Sample #
Sample Name	UPF1-BGHLV33-33	UPF1-BGHLV33-34
Sample_Name_Alias	UPF1_BGHLV33-33	UPF1_BGHLV33-34
Index Well Position	S13	S14
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/E1.png	DNA_Library_LV33-34-25B-32/set1/F1.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/C3.png	RNA_Library_LV32-33-34/set1/D3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV33-33	BGHLV33-34
RBP	UPF1	UPF1
Batch_ID	BGHLV33	BGHLV33
WB_result	51.600	67.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2906	2907

Sequencing Information

	BGHLV33-33	BGHLV33-34
Sample_ID	BGHLV33-33	BGHLV33-34
Sample Name	UPF1_BGHLV33-33	UPF1_BGHLV33-34
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set33	set33
total_reads	77,164,730	67,482,642
total_aligned_reads	63,568,766	56,061,946
unique_aligned_reads	60,038,644	52,953,240
percent_uniqueAligned	0.77806	0.78469
correlation_replicates	0.998262	0.998262
spikein_reads	224,444	186,758
percent_spikeins	0.00291	0.00277
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1555	1556

Data Submission Information

	BGHLV33-33	BGHLV33-33
ENCODE_alias	brenton-graveley:UPF1_BGHLV33	brenton-graveley:UPF1-BGHLV33-HepG2
ENCODE_accession	ENCSR689MIY	ENCSR300WFS
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV33-33	BGHLV33-33
Sample Name	UPF1_BGHLV33-33	UPF1_BGHLV33-33
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3150	7030

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_BGHLV33-33_AGTCAA_L001_001.R1.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1555	HiSeq2500	100	paired-ended	1				NT_BGHLV33-1_GATCAG_L001_001.R1.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R1.fastq.gz	ENCODE3	21430
UPF1_BGHLV33-33_AGTCAA_L001_001.R2.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1555	HiSeq2500	100	paired-ended	2				NT_BGHLV33-1_GATCAG_L001_001.R2.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R2.fastq.gz	ENCODE3	21442
UPF1_BGHLV33-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1555					GRCh38	V40	UPF1_BGHLV33-33_AGTCAA_L001_001.R1.fastq.gz,UPF1_BGHLV33-33_AGTCAA_L001_001.R2.fastq.gz		ENCORE2	21454
UPF1_BGHLV33-33_Signal.Unique.strand+.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1555					GRCh38	V40	UPF1_BGHLV33-33/Aligned.sortedByCoord.out.bam		ENCORE2	21466
UPF1_BGHLV33-33_Signal.Unique.strand-.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1555					GRCh38	V40	UPF1_BGHLV33-33/Aligned.sortedByCoord.out.bam		ENCORE2	21478
UPF1_BGHLV33-33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1555					GRCh38	V40	UPF1_BGHLV33-33/Aligned.sortedByCoord.out.bam		ENCORE2	21490
UPF1_BGHLV33-33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1555					GRCh38	V40	UPF1_BGHLV33-33/Aligned.sortedByCoord.out.bam		ENCORE2	21502
UPF1_BGHLV33-33_quant.sf	ENCODE_DATA/set33/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1555					GRCh38	V40	UPF1_BGHLV33-33_AGTCAA_L001_001.R1.fastq.gz,UPF1_BGHLV33-33_AGTCAA_L001_001.R2.fastq.gz		ENCORE2	21514
UPF1_BGHLV33-34_AGTTCC_L001_001.R1.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1556	HiSeq2500	100	paired-ended	1				NT_BGHLV33-1_GATCAG_L001_001.R1.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R1.fastq.gz	ENCODE3	21431
UPF1_BGHLV33-34_AGTTCC_L001_001.R2.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1556	HiSeq2500	100	paired-ended	2				NT_BGHLV33-1_GATCAG_L001_001.R2.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R2.fastq.gz	ENCODE3	21443
UPF1_BGHLV33-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1556					GRCh38	V40	UPF1_BGHLV33-34_AGTTCC_L001_001.R1.fastq.gz,UPF1_BGHLV33-34_AGTTCC_L001_001.R2.fastq.gz		ENCORE2	21455
UPF1_BGHLV33-34_Signal.Unique.strand+.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1556					GRCh38	V40	UPF1_BGHLV33-34/Aligned.sortedByCoord.out.bam		ENCORE2	21467
UPF1_BGHLV33-34_Signal.Unique.strand-.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1556					GRCh38	V40	UPF1_BGHLV33-34/Aligned.sortedByCoord.out.bam		ENCORE2	21479
UPF1_BGHLV33-34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1556					GRCh38	V40	UPF1_BGHLV33-34/Aligned.sortedByCoord.out.bam		ENCORE2	21491
UPF1_BGHLV33-34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1556					GRCh38	V40	UPF1_BGHLV33-34/Aligned.sortedByCoord.out.bam		ENCORE2	21503
UPF1_BGHLV33-34_quant.sf	ENCODE_DATA/set33/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1556					GRCh38	V40	UPF1_BGHLV33-34_AGTTCC_L001_001.R1.fastq.gz,UPF1_BGHLV33-34_AGTTCC_L001_001.R2.fastq.gz		ENCORE2	21515