UTP18 RNA-Seq in HepG2

General Information


RBP	UTP18
Cell_Line	HepG2
Method	shRNA
Exp_Name	UTP18-BGHLV33-HepG2
ENCODE_series_ID	ENCSR692NPV
Batch_ID	BGHLV33
Pool ID	Pool-160912
Local_Set_Name	set33
ENCODE_KD_Exp_ID	ENCSR269ZAO
ENCODE_CN_Exp_ID	ENCSR691IVR
Rep1	UTP18_BGHLV33-35
Rep2	UTP18_BGHLV33-36
CN1	NT_BGHLV33-1
CN2	NT_BGHLV33-2
Rep1_qPCR	61.8
Rep2_qPCR	61.2
Rep1_WB	86.7
Rep2_WB	81.6
Antibody Cat#	A301-551A
Antibody Lot#	A301-551A
Antibody DCC ID	ENCAB362LIJ
Status	Released
Project	ENCODE3
ID	718

Experiment Information (Status: Released)

	BGHLV33-35	BGHLV33-36
idx	843	844
TRCN#_or_BGC#	TRCN0000143493	TRCN0000143493
shRNA_or_gRNA_sequence	GAGAAGTGGATACTTTGCCTT	GAGAAGTGGATACTTTGCCTT
PAM
Name	UTP18	UTP18
Sample_ID	BGHLV33-35	BGHLV33-36
transduction_Date	11/17/2015	11/17/2015
days
RBP_name	UTP18	UTP18
qPCR_result	61.8	61.2
Ave_qPCR	61.5
RT-qPCR_primer-F	ccacctcaaaagaagccagt
RT-qPCR_primer-R	tatccttccgaaaccgattg
protein_conc	5232	4818
WB_result	86.7	81.6
Ave_WB	84.1
WB_DONE_date	1/25/2016
MW	62kDa	WES
IP	1	1
antibody_Cat#	A301-551A	A301-551A
Antibody DCC ID	ENCAB362LIJ	ENCAB362LIJ
submitted_to_DCC_date	3/8/2016
Rep1_TPM	23.6	0
Rep2_TPM	22.7	0
Action
Library_start_date	3/9/2016	3/9/2016
repeat_library
Note
ID	2932	2933

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
UTP18	Product_ID: A301-551A Lot_ID: 1 Source: Bethyl Labs Target Name: UTP18-human

Experiment Status

	BGHLV33-35	BGHLV33-36
Sample_ID	BGHLV33-35	BGHLV33-36
Sample Name	UTP18_BGHLV33-35	UTP18_BGHLV33-36
Sample Name	UTP18_BGHLV33-35	UTP18_BGHLV33-36
RBP	UTP18	UTP18
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1223	1224

Library-Prep
Sequencing

Library-Prep Information

	BGHLV33-35	BGHLV33-36
Sample #
Sample Name	UTP18-BGHLV33-35	UTP18-BGHLV33-36
Sample_Name_Alias	UTP18_BGHLV33-35	UTP18_BGHLV33-36
Index Well Position	S15	S16
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/G1.png	DNA_Library_LV33-34-25B-32/set1/H1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/E3.png	RNA_Library_LV32-33-34/set1/F3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV33-35	BGHLV33-36
RBP	UTP18	UTP18
Batch_ID	BGHLV33	BGHLV33
WB_result	86.700	81.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2908	2909

Sequencing Information

	BGHLV33-35	BGHLV33-36
Sample_ID	BGHLV33-35	BGHLV33-36
Sample Name	UTP18_BGHLV33-35	UTP18_BGHLV33-36
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set33	set33
total_reads	72,478,302	69,305,456
total_aligned_reads	60,564,274	55,819,044
unique_aligned_reads	57,047,588	52,631,164
percent_uniqueAligned	0.78710	0.75941
correlation_replicates	0.998888	0.998888
spikein_reads	221,248	213,172
percent_spikeins	0.00305	0.00308
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1557	1558

Data Submission Information

	BGHLV33-35	BGHLV33-35
ENCODE_alias	brenton-graveley:UTP18_BGHLV33	brenton-graveley:UTP18-BGHLV33-HepG2
ENCODE_accession	ENCSR269ZAO	ENCSR692NPV
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV33-35	BGHLV33-35
Sample Name	UTP18_BGHLV33-35	UTP18_BGHLV33-35
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3151	7034

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
UTP18_BGHLV33-35_ATGTCA_L001_001.R1.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1557	HiSeq2500	100	paired-ended	1				NT_BGHLV33-1_GATCAG_L001_001.R1.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R1.fastq.gz	ENCODE3	21432
UTP18_BGHLV33-35_ATGTCA_L001_001.R2.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1557	HiSeq2500	100	paired-ended	2				NT_BGHLV33-1_GATCAG_L001_001.R2.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R2.fastq.gz	ENCODE3	21444
UTP18_BGHLV33-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1557					GRCh38	V40	UTP18_BGHLV33-35_ATGTCA_L001_001.R1.fastq.gz,UTP18_BGHLV33-35_ATGTCA_L001_001.R2.fastq.gz		ENCORE2	21456
UTP18_BGHLV33-35_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	1557					GRCh38	V40	UTP18_BGHLV33-35/Aligned.sortedByCoord.out.bam		ENCORE2	21468
UTP18_BGHLV33-35_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	1557					GRCh38	V40	UTP18_BGHLV33-35/Aligned.sortedByCoord.out.bam		ENCORE2	21480
UTP18_BGHLV33-35_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	1557					GRCh38	V40	UTP18_BGHLV33-35/Aligned.sortedByCoord.out.bam		ENCORE2	21492
UTP18_BGHLV33-35_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	1557					GRCh38	V40	UTP18_BGHLV33-35/Aligned.sortedByCoord.out.bam		ENCORE2	21504
UTP18_BGHLV33-35_quant.sf	ENCODE_DATA/set33/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1557					GRCh38	V40	UTP18_BGHLV33-35_ATGTCA_L001_001.R1.fastq.gz,UTP18_BGHLV33-35_ATGTCA_L001_001.R2.fastq.gz		ENCORE2	21516
UTP18_BGHLV33-36_CCGTCC_L001_001.R1.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1558	HiSeq2500	100	paired-ended	1				NT_BGHLV33-1_GATCAG_L001_001.R1.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R1.fastq.gz	ENCODE3	21433
UTP18_BGHLV33-36_CCGTCC_L001_001.R2.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1558	HiSeq2500	100	paired-ended	2				NT_BGHLV33-1_GATCAG_L001_001.R2.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R2.fastq.gz	ENCODE3	21445
UTP18_BGHLV33-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1558					GRCh38	V40	UTP18_BGHLV33-36_CCGTCC_L001_001.R1.fastq.gz,UTP18_BGHLV33-36_CCGTCC_L001_001.R2.fastq.gz		ENCORE2	21457
UTP18_BGHLV33-36_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	1558					GRCh38	V40	UTP18_BGHLV33-36/Aligned.sortedByCoord.out.bam		ENCORE2	21469
UTP18_BGHLV33-36_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	1558					GRCh38	V40	UTP18_BGHLV33-36/Aligned.sortedByCoord.out.bam		ENCORE2	21481
UTP18_BGHLV33-36_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	1558					GRCh38	V40	UTP18_BGHLV33-36/Aligned.sortedByCoord.out.bam		ENCORE2	21493
UTP18_BGHLV33-36_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	1558					GRCh38	V40	UTP18_BGHLV33-36/Aligned.sortedByCoord.out.bam		ENCORE2	21505
UTP18_BGHLV33-36_quant.sf	ENCODE_DATA/set33/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1558					GRCh38	V40	UTP18_BGHLV33-36_CCGTCC_L001_001.R1.fastq.gz,UTP18_BGHLV33-36_CCGTCC_L001_001.R2.fastq.gz		ENCORE2	21517