UTP3 RNA-Seq in HepG2

General Information


RBP	UTP3
Cell_Line	HepG2
Method	shRNA
Exp_Name	UTP3-BGHLV33-HepG2
ENCODE_series_ID	ENCSR750ISF
Batch_ID	BGHLV33
Pool ID	Pool-160912
Local_Set_Name	set33
ENCODE_KD_Exp_ID	ENCSR910ECL
ENCODE_CN_Exp_ID	ENCSR691IVR
Rep1	UTP3_BGHLV33-37
Rep2	UTP3_BGHLV33-38
CN1	NT_BGHLV33-1
CN2	NT_BGHLV33-2
Rep1_qPCR	38.0
Rep2_qPCR	23.7
Rep1_WB	70.3
Rep2_WB	65.4
Antibody Cat#	A302-067A
Antibody Lot#	A302-067A
Antibody DCC ID	ENCAB872CCU
Status	Released
Project	ENCODE3
ID	719

Experiment Information (Status: Released)

	BGHLV33-37	BGHLV33-38
idx	845	846
TRCN#_or_BGC#	TRCN0000134895	TRCN0000134895
shRNA_or_gRNA_sequence	CCTAGGAGAAAGAAGATTGAT	CCTAGGAGAAAGAAGATTGAT
PAM
Name	UTP3	UTP3
Sample_ID	BGHLV33-37	BGHLV33-38
transduction_Date	11/17/2015	11/17/2015
days
RBP_name	UTP3	UTP3
qPCR_result	38.0	23.7
Ave_qPCR	30.9
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4496	4258
WB_result	70.3	65.4
Ave_WB	67.9
WB_DONE_date	2/12/2016
MW	55kDa	WES
IP	1	1
antibody_Cat#	A302-067A	A302-067A
Antibody DCC ID	ENCAB872CCU	ENCAB872CCU
submitted_to_DCC_date	3/8/2016
Rep1_TPM	16.6	0
Rep2_TPM	12.1	0
Action
Library_start_date	3/9/2016	3/9/2016
repeat_library
Note
ID	2934	2935

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
UTP3	Product_ID: A302-067A Lot_ID: 1 Source: Bethyl Labs Target Name: UTP3-human

Experiment Status

	BGHLV33-37	BGHLV33-38
Sample_ID	BGHLV33-37	BGHLV33-38
Sample Name	UTP3_BGHLV33-37	UTP3_BGHLV33-38
Sample Name	UTP3_BGHLV33-37	UTP3_BGHLV33-38
RBP	UTP3	UTP3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1225	1226

Library-Prep
Sequencing

Library-Prep Information

	BGHLV33-37	BGHLV33-38
Sample #
Sample Name	UTP3-BGHLV33-37	UTP3-BGHLV33-38
Sample_Name_Alias	UTP3_BGHLV33-37	UTP3_BGHLV33-38
Index Well Position	S18	S19
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/A2.png	DNA_Library_LV33-34-25B-32/set1/B2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/G3.png	RNA_Library_LV32-33-34/set1/H3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV33-37	BGHLV33-38
RBP	UTP3	UTP3
Batch_ID	BGHLV33	BGHLV33
WB_result	70.300	65.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2910	2911

Sequencing Information

	BGHLV33-37	BGHLV33-38
Sample_ID	BGHLV33-37	BGHLV33-38
Sample Name	UTP3_BGHLV33-37	UTP3_BGHLV33-38
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set33	set33
total_reads	55,831,272	72,875,160
total_aligned_reads	45,048,052	60,607,596
unique_aligned_reads	42,209,670	56,724,072
percent_uniqueAligned	0.75602	0.77837
correlation_replicates	0.998184	0.998184
spikein_reads	126,038	206,810
percent_spikeins	0.00226	0.00284
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1559	1560

Data Submission Information

	BGHLV33-37	BGHLV33-37
ENCODE_alias	brenton-graveley:UTP3_BGHLV33	brenton-graveley:UTP3-BGHLV33-HepG2
ENCODE_accession	ENCSR910ECL	ENCSR750ISF
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV33-37	BGHLV33-37
Sample Name	UTP3_BGHLV33-37	UTP3_BGHLV33-37
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3152	7036

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
UTP3_BGHLV33-37_GTCCGC_L002_001.R1.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1559	HiSeq2500	100	paired-ended	1				NT_BGHLV33-1_GATCAG_L001_001.R1.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R1.fastq.gz	ENCODE3	21434
UTP3_BGHLV33-37_GTCCGC_L002_001.R2.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1559	HiSeq2500	100	paired-ended	2				NT_BGHLV33-1_GATCAG_L001_001.R2.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R2.fastq.gz	ENCODE3	21446
UTP3_BGHLV33-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1559					GRCh38	V40	UTP3_BGHLV33-37_GTCCGC_L002_001.R1.fastq.gz,UTP3_BGHLV33-37_GTCCGC_L002_001.R2.fastq.gz		ENCORE2	21458
UTP3_BGHLV33-37_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	1559					GRCh38	V40	UTP3_BGHLV33-37/Aligned.sortedByCoord.out.bam		ENCORE2	21470
UTP3_BGHLV33-37_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	1559					GRCh38	V40	UTP3_BGHLV33-37/Aligned.sortedByCoord.out.bam		ENCORE2	21482
UTP3_BGHLV33-37_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	1559					GRCh38	V40	UTP3_BGHLV33-37/Aligned.sortedByCoord.out.bam		ENCORE2	21494
UTP3_BGHLV33-37_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	1559					GRCh38	V40	UTP3_BGHLV33-37/Aligned.sortedByCoord.out.bam		ENCORE2	21506
UTP3_BGHLV33-37_quant.sf	ENCODE_DATA/set33/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1559					GRCh38	V40	UTP3_BGHLV33-37_GTCCGC_L002_001.R1.fastq.gz,UTP3_BGHLV33-37_GTCCGC_L002_001.R2.fastq.gz		ENCORE2	21518
UTP3_BGHLV33-38_GTGAAA_L002_001.R1.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1560	HiSeq2500	100	paired-ended	1				NT_BGHLV33-1_GATCAG_L001_001.R1.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R1.fastq.gz	ENCODE3	21435
UTP3_BGHLV33-38_GTGAAA_L002_001.R2.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1560	HiSeq2500	100	paired-ended	2				NT_BGHLV33-1_GATCAG_L001_001.R2.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R2.fastq.gz	ENCODE3	21447
UTP3_BGHLV33-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1560					GRCh38	V40	UTP3_BGHLV33-38_GTGAAA_L002_001.R1.fastq.gz,UTP3_BGHLV33-38_GTGAAA_L002_001.R2.fastq.gz		ENCORE2	21459
UTP3_BGHLV33-38_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	1560					GRCh38	V40	UTP3_BGHLV33-38/Aligned.sortedByCoord.out.bam		ENCORE2	21471
UTP3_BGHLV33-38_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	1560					GRCh38	V40	UTP3_BGHLV33-38/Aligned.sortedByCoord.out.bam		ENCORE2	21483
UTP3_BGHLV33-38_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	1560					GRCh38	V40	UTP3_BGHLV33-38/Aligned.sortedByCoord.out.bam		ENCORE2	21495
UTP3_BGHLV33-38_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	1560					GRCh38	V40	UTP3_BGHLV33-38/Aligned.sortedByCoord.out.bam		ENCORE2	21507
UTP3_BGHLV33-38_quant.sf	ENCODE_DATA/set33/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1560					GRCh38	V40	UTP3_BGHLV33-38_GTGAAA_L002_001.R1.fastq.gz,UTP3_BGHLV33-38_GTGAAA_L002_001.R2.fastq.gz		ENCORE2	21519