UPF2 RNA-Seq in HepG2

General Information


RBP	UPF2
Cell_Line	HepG2
Method	shRNA
Exp_Name	UPF2-BGHLV17-HepG2
ENCODE_series_ID	ENCSR392IZZ
Batch_ID	BGHLV17
Pool ID	Pool-141001
Local_Set_Name	set17
ENCODE_KD_Exp_ID	ENCSR318OXM
ENCODE_CN_Exp_ID	ENCSR856ZRV
Rep1	UPF2_BGHLV17_39
Rep2	UPF2_BGHLV17_40
CN1	NT_BGHLV17_63
CN2	NT_BGHLV17_64
Rep1_qPCR	64.4
Rep2_qPCR	55.2
Rep1_WB	23.2
Rep2_WB	35.8
Antibody Cat#	A303-929A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB821QZM
Status	Released
Project	ENCODE3
ID	442

Experiment Information (Status: Released)

	BGHLV17-39	BGHLV17-40
idx	275	276
TRCN#_or_BGC#	TRCN0000157152	TRCN0000157152
shRNA_or_gRNA_sequence	GCGAGATACGTCACAATGGTA	GCGAGATACGTCACAATGGTA
PAM
Name	UPF2	UPF2
Sample_ID	BGHLV17-39	BGHLV17-40
transduction_Date	8/19/2014	8/19/2014
days
RBP_name	UPF2	UPF2
qPCR_result	64.4	55.2
Ave_qPCR	59.8
RT-qPCR_primer-F	cgattaggaatggaggttaatca
RT-qPCR_primer-R	ttccaccattcggtaattgtaa
protein_conc	3130	3287
WB_result	23.2	35.8
Ave_WB	29.5
WB_DONE_date	8/4/2015
MW	148kDa
IP	1	1
antibody_Cat#	A303-929A	A303-929A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	18.8	0
Rep2_TPM	14.8	0
Action
Library_start_date	9/26/2014	9/26/2014
repeat_library
Note
ID	2340	2341

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV17-39	BGHLV17-40
Sample_ID	BGHLV17-39	BGHLV17-40
Sample Name	UPF2_BGHLV17_39	UPF2_BGHLV17_40
Sample Name	UPF2_BGHLV17_39	UPF2_BGHLV17_40
RBP	UPF2	UPF2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	612	613

Library-Prep
Sequencing

Library-Prep Information

	BGHLV17-39	BGHLV17-40
Sample #
Sample Name	UPF2-BGHLV17-39	UPF2-BGHLV17-40
Sample_Name_Alias	UPF2_BGHLV17_39	UPF2_BGHLV17_40
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-26	2014-09-26
Lib_ID	Lib-140926	Lib-140926
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/A4.png	DNA_Library_LV16-17/set1/B4.png
RIN	7.2	7.6
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/A6.png	RNA_Library_LV16-17-18/set1/B6.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV17-39	BGHLV17-40
RBP	UPF2	UPF2
Batch_ID	BGHLV17	BGHLV17
WB_result	23.200	35.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2296	2297

Sequencing Information

	BGHLV17-39	BGHLV17-39	BGHLV17-40
Sample_ID	BGHLV17-39	BGHLV17-39	BGHLV17-40
Sample Name	UPF2_BGHLV17_39	UPF2_BGHLV17_39	UPF2_BGHLV17_40
Pool ID	Pool-141001	Pool-151215B	Pool-141001
LocalServer_folder	set17	set17	set17
total_reads	15,750,000	57,876,322	40,890,000
total_aligned_reads	14,429,468	53,616,070	37,668,290
unique_aligned_reads	13,642,338	50,608,066	35,596,786
percent_uniqueAligned	0.86618	0.87442	0.87055
correlation_replicates	0.982214		0.982214
spikein_reads	80,456	293,618	161,698
percent_spikeins	0.00511	0.00507	0.00395
original_ReadLength	100	100	100
QC_Status	Submitted	Submitted	Submitted
ID	938	1378	939

Data Submission Information

	BGHLV17-39	BGHLV17-39
ENCODE_alias	brenton-graveley:UPF2_BGHLV17	brenton-graveley:UPF2-BGHLV17-HepG2
ENCODE_accession	ENCSR318OXM	ENCSR392IZZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV17-39	BGHLV17-39
Sample Name	UPF2_BGHLV17_39	UPF2_BGHLV17_39
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2873	7032

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_BGHLV17_39_ATCACG_L005_001.R1.merged.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	938	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14520
UPF2_BGHLV17_39_ATCACG_L005_001.R2.merged.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	938	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14558
UPF2_BGHLV17_39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	938					GRCh38	V40	UPF2_BGHLV17_39_ATCACG_L005_001.R1.merged.fastq.gz,UPF2_BGHLV17_39_ATCACG_L005_001.R2.merged.fastq.gz		ENCORE2	14596
UPF2_BGHLV17_39_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	938					GRCh38	V40	UPF2_BGHLV17_39/Aligned.sortedByCoord.out.bam		ENCORE2	14634
UPF2_BGHLV17_39_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	938					GRCh38	V40	UPF2_BGHLV17_39/Aligned.sortedByCoord.out.bam		ENCORE2	14672
UPF2_BGHLV17_39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	938					GRCh38	V40	UPF2_BGHLV17_39/Aligned.sortedByCoord.out.bam		ENCORE2	14710
UPF2_BGHLV17_39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	938					GRCh38	V40	UPF2_BGHLV17_39/Aligned.sortedByCoord.out.bam		ENCORE2	14748
UPF2_BGHLV17_39_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	938					GRCh38	V40	UPF2_BGHLV17_39_ATCACG_L005_001.R1.merged.fastq.gz,UPF2_BGHLV17_39_ATCACG_L005_001.R2.merged.fastq.gz		ENCORE2	14786
UPF2_BGHLV17_40_CGATGT_L004_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	939	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14521
UPF2_BGHLV17_40_CGATGT_L004_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	939	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14559
UPF2_BGHLV17_40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	939					GRCh38	V40	UPF2_BGHLV17_40_CGATGT_L004_R1_001.fastq.gz,UPF2_BGHLV17_40_CGATGT_L004_R2_001.fastq.gz		ENCORE2	14597
UPF2_BGHLV17_40_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	939					GRCh38	V40	UPF2_BGHLV17_40/Aligned.sortedByCoord.out.bam		ENCORE2	14635
UPF2_BGHLV17_40_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	939					GRCh38	V40	UPF2_BGHLV17_40/Aligned.sortedByCoord.out.bam		ENCORE2	14673
UPF2_BGHLV17_40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	939					GRCh38	V40	UPF2_BGHLV17_40/Aligned.sortedByCoord.out.bam		ENCORE2	14711
UPF2_BGHLV17_40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	939					GRCh38	V40	UPF2_BGHLV17_40/Aligned.sortedByCoord.out.bam		ENCORE2	14749
UPF2_BGHLV17_40_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	939					GRCh38	V40	UPF2_BGHLV17_40_CGATGT_L004_R1_001.fastq.gz,UPF2_BGHLV17_40_CGATGT_L004_R2_001.fastq.gz		ENCORE2	14787