STAU1 RNA-Seq in K562

General Information


RBP	STAU1
Cell_Line	K562
Method	shRNA
Exp_Name	STAU1-BGKLV29-K562
ENCODE_series_ID	ENCSR177IMY
Batch_ID	BGKLV29
Pool ID	Pool-151215C
Local_Set_Name	set29
ENCODE_KD_Exp_ID	ENCSR777EDL
ENCODE_CN_Exp_ID	ENCSR032YMP
Rep1	STAU1_BGKLV29-57
Rep2	STAU1_BGKLV29-58
CN1	NT_BGKLV29-1
CN2	NT_BGKLV29-2
Rep1_qPCR	90.5
Rep2_qPCR	88.9
Rep1_WB	77.5
Rep2_WB	75.8
Antibody Cat#	GTX106566
Antibody Lot#	GTX106566
Antibody DCC ID	ENCAB136ZLU
Status	Released
Project	ENCODE3
ID	667

Experiment Information (Status: Released)

	BGKLV29-57	BGKLV29-57	BGKLV29-58	BGKLV29-58
idx	592	592	593	593
TRCN#_or_BGC#	TRCN0000158514	TRCN0000158514	TRCN0000158514	TRCN0000158514
shRNA_or_gRNA_sequence	CAAGTGTTTGAGATTGCACTT	CAAGTGTTTGAGATTGCACTT	CAAGTGTTTGAGATTGCACTT	CAAGTGTTTGAGATTGCACTT
PAM
Name	STAU1	STAU1	STAU1	STAU1
Sample_ID	BGKLV29-57	BGKLV29-57	BGKLV29-58	BGKLV29-58
transduction_Date	8/11/2015	8/11/2015	8/11/2015	8/11/2015
days
RBP_name	STAU1	STAU1	STAU1	STAU1
qPCR_result	90.5	90.5	88.9	88.9
Ave_qPCR	89.7	89.7
RT-qPCR_primer-F	GCTGGAGGTGAATGGAAGAG	GCTGGAGGTGAATGGAAGAG
RT-qPCR_primer-R	GGCAAGTTCCGTTTAAGTGC	GGCAAGTTCCGTTTAAGTGC
protein_conc	3652	3652	3746	3746
WB_result	77.5	81.8	75.8	68.5
Ave_WB	76.7	75.1
WB_DONE_date	9/9/2015	6/27/2023
MW	63kDa	63KD
IP	1		1
antibody_Cat#	GTX106566	A303-956A	GTX106566	LOT#1
Antibody DCC ID	ENCAB136ZLU		ENCAB136ZLU
submitted_to_DCC_date	12/7/2015	1/8/24
Rep1_TPM	32.1326624	0	0	0
Rep2_TPM	27.3504509	0	0	0
Action
Library_start_date	11/2/2015		11/2/2015
repeat_library
Note	x		x
ID	671	673	672	674

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
STAU1	Product_ID: GTX106566 Lot_ID: 40030 Source: GeneTex Target Name: STAU1-human
STAU1	Product_ID: A303-956A Lot_ID: 1 Source: Bethyl Labs Target Name: STAU1-human

Experiment Status

	BGKLV29-57	BGKLV29-58
Sample_ID	BGKLV29-57	BGKLV29-58
Sample Name	STAU1_BGKLV29-57	STAU1_BGKLV29-58
Sample Name	STAU1_BGKLV29-57	STAU1_BGKLV29-58
RBP	STAU1	STAU1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	1038	1039

Library-Prep
Sequencing

Library-Prep Information

	BGKLV29-57	BGKLV29-58
Sample #
Sample Name	STAU1-BGKLV29-57	STAU1-BGKLV29-58
Sample_Name_Alias	STAU1_BGKLV29-57	STAU1_BGKLV29-58
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-02	2015-11-02
Lib_ID	Lib-151102	Lib-151102
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/A8.png	DNA_Library_LV28-29-30/set1/B8.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/E3.png	RNA_Library_LV29-30-31-32/set1/F3.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV29-57	BGKLV29-58
RBP	STAU1	STAU1
Batch_ID	BGKLV29	BGKLV29
WB_result	77.500	75.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2722	2723

Sequencing Information

	BGKLV29-57	BGKLV29-58
Sample_ID	BGKLV29-57	BGKLV29-58
Sample Name	STAU1_BGKLV29-57	STAU1_BGKLV29-58
Pool ID	Pool-151215C	Pool-151215C
LocalServer_folder	set29	set29
total_reads	78,425,114	94,993,110
total_aligned_reads	67,403,050	82,928,016
unique_aligned_reads	61,702,102	75,574,438
percent_uniqueAligned	0.78676	0.79558
correlation_replicates	0.995417	0.995417
spikein_reads	295,584	333,306
percent_spikeins	0.00377	0.00351
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1356	1357

Data Submission Information

	BGKLV29-57	BGKLV29-57
ENCODE_alias	brenton-graveley:STAU1_BGKLV29	brenton-graveley:STAU1-BGKLV29-K562
ENCODE_accession	ENCSR777EDL	ENCSR177IMY
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV29-57	BGKLV29-57
Sample Name	STAU1_BGKLV29-57	STAU1_BGKLV29-57
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3068	6985

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
STAU1_BGKLV29-57_GATCAG_L007_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1356	HiSeq2500	100	paired-ended	1				NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20440
STAU1_BGKLV29-57_GATCAG_L007_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1356	HiSeq2500	100	paired-ended	2				NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20470
STAU1_BGKLV29-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1356					GRCh38	V40	STAU1_BGKLV29-57_GATCAG_L007_001.R1.fastq.gz,STAU1_BGKLV29-57_GATCAG_L007_001.R2.fastq.gz		ENCORE2	20500
STAU1_BGKLV29-57_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1356					GRCh38	V40	STAU1_BGKLV29-57/Aligned.sortedByCoord.out.bam		ENCORE2	20530
STAU1_BGKLV29-57_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1356					GRCh38	V40	STAU1_BGKLV29-57/Aligned.sortedByCoord.out.bam		ENCORE2	20560
STAU1_BGKLV29-57_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1356					GRCh38	V40	STAU1_BGKLV29-57/Aligned.sortedByCoord.out.bam		ENCORE2	20590
STAU1_BGKLV29-57_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1356					GRCh38	V40	STAU1_BGKLV29-57/Aligned.sortedByCoord.out.bam		ENCORE2	20620
STAU1_BGKLV29-57_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1356					GRCh38	V40	STAU1_BGKLV29-57_GATCAG_L007_001.R1.fastq.gz,STAU1_BGKLV29-57_GATCAG_L007_001.R2.fastq.gz		ENCORE2	20650
STAU1_BGKLV29-58_TAGCTT_L007_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1357	HiSeq2500	100	paired-ended	1				NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20441
STAU1_BGKLV29-58_TAGCTT_L007_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1357	HiSeq2500	100	paired-ended	2				NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20471
STAU1_BGKLV29-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1357					GRCh38	V40	STAU1_BGKLV29-58_TAGCTT_L007_001.R1.fastq.gz,STAU1_BGKLV29-58_TAGCTT_L007_001.R2.fastq.gz		ENCORE2	20501
STAU1_BGKLV29-58_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1357					GRCh38	V40	STAU1_BGKLV29-58/Aligned.sortedByCoord.out.bam		ENCORE2	20531
STAU1_BGKLV29-58_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1357					GRCh38	V40	STAU1_BGKLV29-58/Aligned.sortedByCoord.out.bam		ENCORE2	20561
STAU1_BGKLV29-58_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1357					GRCh38	V40	STAU1_BGKLV29-58/Aligned.sortedByCoord.out.bam		ENCORE2	20591
STAU1_BGKLV29-58_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1357					GRCh38	V40	STAU1_BGKLV29-58/Aligned.sortedByCoord.out.bam		ENCORE2	20621
STAU1_BGKLV29-58_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1357					GRCh38	V40	STAU1_BGKLV29-58_TAGCTT_L007_001.R1.fastq.gz,STAU1_BGKLV29-58_TAGCTT_L007_001.R2.fastq.gz		ENCORE2	20651