UTP18 RNA-Seq in K562

General Information


RBP	UTP18
Cell_Line	K562
Method	shRNA
Exp_Name	UTP18-BGKLV32-K562
ENCODE_series_ID	ENCSR398PSO
Batch_ID	BGKLV32
Pool ID	Pool-160425
Local_Set_Name	set32
ENCODE_KD_Exp_ID	ENCSR165VBD
ENCODE_CN_Exp_ID	ENCSR143COQ
Rep1	UTP18_BGKLV32-61
Rep2	UTP18_BGKLV32-62
CN1	NT_BGKLV32-1
CN2	NT_BGKLV32-2
Rep1_qPCR	83.5
Rep2_qPCR	90.8
Rep1_WB	93.6
Rep2_WB	95.0
Antibody Cat#	A301-551A
Antibody Lot#	A301-551A
Antibody DCC ID	ENCAB362LIJ
Status	Released
Project	ENCODE3
ID	715

Experiment Information (Status: Released)

	BGKLV32-61	BGKLV32-62
idx	660	661
TRCN#_or_BGC#	TRCN0000143493	TRCN0000143493
shRNA_or_gRNA_sequence	GAGAAGTGGATACTTTGCCTT	GAGAAGTGGATACTTTGCCTT
PAM
Name	UTP18	UTP18
Sample_ID	BGKLV32-61	BGKLV32-62
transduction_Date	10/1/2015	10/1/2015
days
RBP_name	UTP18	UTP18
qPCR_result	83.5	90.8
Ave_qPCR	87.1
RT-qPCR_primer-F	ccacctcaaaagaagccagt
RT-qPCR_primer-R	tatccttccgaaaccgattg
protein_conc	3267	3032
WB_result	93.6	95.0
Ave_WB	94.3
WB_DONE_date	12/3/2015
MW	62kDa
IP	1	1
antibody_Cat#	A301-551A	A301-551A
Antibody DCC ID	ENCAB362LIJ	ENCAB362LIJ
submitted_to_DCC_date	12/7/2015
Rep1_TPM	34.90398257	0
Rep2_TPM	27.00835701	0
Action
Library_start_date	3/7/2016	3/7/2016
repeat_library
Note
ID	745	746

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

	BGKLV32-61	BGKLV32-62
Sample_ID	BGKLV32-61	BGKLV32-62
Sample Name	UTP18_BGKLV32-61	UTP18_BGKLV32-62
Sample Name	UTP18_BGKLV32-61	UTP18_BGKLV32-62
RBP	UTP18	UTP18
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1181	1182

Library-Prep
Sequencing

Library-Prep Information

	BGKLV32-61	BGKLV32-62
Sample #
Sample Name	UTP18-BGKLV32-61	UTP18-BGKLV32-62
Sample_Name_Alias	UTP18_BGKLV32-61	UTP18_BGKLV32-62
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-07	2016-03-07
Lib_ID	Lib-160307	Lib-160307
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/E9.png	DNA_Library_LV33-34-25B-32/set1/F9.png
RIN	9.5	9.8
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/E2.png	RNA_Library_LV32-33-34/set1/F2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV32-61	BGKLV32-62
RBP	UTP18	UTP18
Batch_ID	BGKLV32	BGKLV32
WB_result	93.600	95.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2866	2867

Sequencing Information

	BGKLV32-61	BGKLV32-62
Sample_ID	BGKLV32-61	BGKLV32-62
Sample Name	UTP18_BGKLV32-61	UTP18_BGKLV32-62
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set32	set32
total_reads	84,608,884	81,631,188
total_aligned_reads	74,869,608	71,235,028
unique_aligned_reads	68,696,554	65,558,498
percent_uniqueAligned	0.81193	0.80311
correlation_replicates	0.988917	0.988917
spikein_reads	261,626	234,566
percent_spikeins	0.00309	0.00287
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1515	1516

Data Submission Information

	BGKLV32-61	BGKLV32-61
ENCODE_alias	brenton-graveley:UTP18_BGKLV32	brenton-graveley:UTP18-BGKLV32-K562
ENCODE_accession	ENCSR165VBD	ENCSR398PSO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV32-61	BGKLV32-61
Sample Name	UTP18_BGKLV32-61	UTP18_BGKLV32-61
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3130	7035

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_BGKLV32-61_ACAGTG_L004_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1515	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21214
UTP18_BGKLV32-61_ACAGTG_L004_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1515	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21244
UTP18_BGKLV32-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1515					GRCh38	V40	UTP18_BGKLV32-61_ACAGTG_L004_001.R1.fastq.gz,UTP18_BGKLV32-61_ACAGTG_L004_001.R2.fastq.gz		ENCORE2	21274
UTP18_BGKLV32-61_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1515					GRCh38	V40	UTP18_BGKLV32-61/Aligned.sortedByCoord.out.bam		ENCORE2	21304
UTP18_BGKLV32-61_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1515					GRCh38	V40	UTP18_BGKLV32-61/Aligned.sortedByCoord.out.bam		ENCORE2	21334
UTP18_BGKLV32-61_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1515					GRCh38	V40	UTP18_BGKLV32-61/Aligned.sortedByCoord.out.bam		ENCORE2	21364
UTP18_BGKLV32-61_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1515					GRCh38	V40	UTP18_BGKLV32-61/Aligned.sortedByCoord.out.bam		ENCORE2	21394
UTP18_BGKLV32-61_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1515					GRCh38	V40	UTP18_BGKLV32-61_ACAGTG_L004_001.R1.fastq.gz,UTP18_BGKLV32-61_ACAGTG_L004_001.R2.fastq.gz		ENCORE2	21424
UTP18_BGKLV32-62_GCCAAT_L004_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1516	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21215
UTP18_BGKLV32-62_GCCAAT_L004_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1516	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21245
UTP18_BGKLV32-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1516					GRCh38	V40	UTP18_BGKLV32-62_GCCAAT_L004_001.R1.fastq.gz,UTP18_BGKLV32-62_GCCAAT_L004_001.R2.fastq.gz		ENCORE2	21275
UTP18_BGKLV32-62_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1516					GRCh38	V40	UTP18_BGKLV32-62/Aligned.sortedByCoord.out.bam		ENCORE2	21305
UTP18_BGKLV32-62_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1516					GRCh38	V40	UTP18_BGKLV32-62/Aligned.sortedByCoord.out.bam		ENCORE2	21335
UTP18_BGKLV32-62_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1516					GRCh38	V40	UTP18_BGKLV32-62/Aligned.sortedByCoord.out.bam		ENCORE2	21365
UTP18_BGKLV32-62_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1516					GRCh38	V40	UTP18_BGKLV32-62/Aligned.sortedByCoord.out.bam		ENCORE2	21395
UTP18_BGKLV32-62_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1516					GRCh38	V40	UTP18_BGKLV32-62_GCCAAT_L004_001.R1.fastq.gz,UTP18_BGKLV32-62_GCCAAT_L004_001.R2.fastq.gz		ENCORE2	21425