STAU1 RNA-Seq in HepG2

General Information


RBP	STAU1
Cell_Line	HepG2
Method	shRNA
Exp_Name	STAU1-BGHLV30-HepG2
ENCODE_series_ID	ENCSR198NSW
Batch_ID	BGHLV30
Pool ID	Pool-151215B
Local_Set_Name	set30
ENCODE_KD_Exp_ID	ENCSR124KCF
ENCODE_CN_Exp_ID	ENCSR067GHD
Rep1	STAU1_BGHLV30-51
Rep2	STAU1_BGHLV30-52
CN1	NT_BGHLV30-1
CN2	NT_BGHLV30-2
Rep1_qPCR	86.8
Rep2_qPCR	88.6
Rep1_WB	90.5
Rep2_WB	92.0
Antibody Cat#	GTX106566
Antibody Lot#	GTX106566
Antibody DCC ID	ENCAB136ZLU
Status	Released
Project	ENCODE3
ID	687

Experiment Information (Status: Released)

	BGHLV30-51	BGHLV30-52
idx	739	740
TRCN#_or_BGC#	TRCN0000158514	TRCN0000158514
shRNA_or_gRNA_sequence	CAAGTGTTTGAGATTGCACTT	CAAGTGTTTGAGATTGCACTT
PAM
Name	STAU1	STAU1
Sample_ID	BGHLV30-51	BGHLV30-52
transduction_Date	8/25/2015	8/25/2015
days
RBP_name	STAU1	STAU1
qPCR_result	86.8	88.6
Ave_qPCR	87.7
RT-qPCR_primer-F	GCTGGAGGTGAATGGAAGAG
RT-qPCR_primer-R	GGCAAGTTCCGTTTAAGTGC
protein_conc	5095	4794
WB_result	90.5	92.0
Ave_WB	91.3
WB_DONE_date	9/9/2015
MW	63kDa
IP	1	1
antibody_Cat#	GTX106566	GTX106566
Antibody DCC ID	ENCAB136ZLU	ENCAB136ZLU
submitted_to_DCC_date	12/7/2015
Rep1_TPM	72.6	0
Rep2_TPM	78.8	0
Action
Library_start_date	11/5/2015	11/5/2015
repeat_library
Note	x	x
ID	2826	2827

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

Experiment Status

	BGHLV30-51	BGHLV30-52
Sample_ID	BGHLV30-51	BGHLV30-52
Sample Name	STAU1_BGHLV30-51	STAU1_BGHLV30-52
Sample Name	STAU1_BGHLV30-51	STAU1_BGHLV30-52
RBP	STAU1	STAU1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-04	2016-03-04
Project	ENCODE3	ENCODE3
Note
ID	1066	1067

Library-Prep
Sequencing

Library-Prep Information

	BGHLV30-51	BGHLV30-52
Sample #
Sample Name	STAU1-BGHLV30-51	STAU1-BGHLV30-52
Sample_Name_Alias	STAU1_BGHLV30-51	STAU1_BGHLV30-52
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-05	2015-11-05
Lib_ID	Lib-151105	Lib-151105
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/A12.png	DNA_Library_LV28-29-30/set1/B12.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/C7.png	RNA_Library_LV29-30-31-32/set1/D7.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV30-51	BGHLV30-52
RBP	STAU1	STAU1
Batch_ID	BGHLV30	BGHLV30
WB_result	90.500	92.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2758	2759

Sequencing Information

	BGHLV30-51	BGHLV30-52
Sample_ID	BGHLV30-51	BGHLV30-52
Sample Name	STAU1_BGHLV30-51	STAU1_BGHLV30-52
Pool ID	Pool-151215B	Pool-151215B
LocalServer_folder	set30	set30
total_reads	32,742,766	100,836,052
total_aligned_reads	28,905,976	89,248,518
unique_aligned_reads	27,283,390	84,155,464
percent_uniqueAligned	0.83326	0.83458
correlation_replicates	0.993743	0.993743
spikein_reads	104,198	242,978
percent_spikeins	0.00318	0.00241
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1407	1408

Data Submission Information

	BGHLV30-51	BGHLV30-51
ENCODE_alias	brenton-graveley:STAU1_BGHLV30	brenton-graveley:STAU1-BGHLV30-HepG2
ENCODE_accession	ENCSR124KCF	ENCSR198NSW
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV30-51	BGHLV30-51
Sample Name	STAU1_BGHLV30-51	STAU1_BGHLV30-51
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3082	6984

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_BGHLV30-51_GTCCGC_L004_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1407	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20726
STAU1_BGHLV30-51_GTCCGC_L004_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1407	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20760
STAU1_BGHLV30-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1407					GRCh38	V40	STAU1_BGHLV30-51_GTCCGC_L004_001.R1.fastq.gz,STAU1_BGHLV30-51_GTCCGC_L004_001.R2.fastq.gz		ENCORE2	20794
STAU1_BGHLV30-51_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1407					GRCh38	V40	STAU1_BGHLV30-51/Aligned.sortedByCoord.out.bam		ENCORE2	20828
STAU1_BGHLV30-51_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1407					GRCh38	V40	STAU1_BGHLV30-51/Aligned.sortedByCoord.out.bam		ENCORE2	20862
STAU1_BGHLV30-51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1407					GRCh38	V40	STAU1_BGHLV30-51/Aligned.sortedByCoord.out.bam		ENCORE2	20896
STAU1_BGHLV30-51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1407					GRCh38	V40	STAU1_BGHLV30-51/Aligned.sortedByCoord.out.bam		ENCORE2	20930
STAU1_BGHLV30-51_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1407					GRCh38	V40	STAU1_BGHLV30-51_GTCCGC_L004_001.R1.fastq.gz,STAU1_BGHLV30-51_GTCCGC_L004_001.R2.fastq.gz		ENCORE2	20964
STAU1_BGHLV30-52_GTGAAA_L004_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1408	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20727
STAU1_BGHLV30-52_GTGAAA_L004_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1408	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20761
STAU1_BGHLV30-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1408					GRCh38	V40	STAU1_BGHLV30-52_GTGAAA_L004_001.R1.fastq.gz,STAU1_BGHLV30-52_GTGAAA_L004_001.R2.fastq.gz		ENCORE2	20795
STAU1_BGHLV30-52_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1408					GRCh38	V40	STAU1_BGHLV30-52/Aligned.sortedByCoord.out.bam		ENCORE2	20829
STAU1_BGHLV30-52_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1408					GRCh38	V40	STAU1_BGHLV30-52/Aligned.sortedByCoord.out.bam		ENCORE2	20863
STAU1_BGHLV30-52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1408					GRCh38	V40	STAU1_BGHLV30-52/Aligned.sortedByCoord.out.bam		ENCORE2	20897
STAU1_BGHLV30-52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1408					GRCh38	V40	STAU1_BGHLV30-52/Aligned.sortedByCoord.out.bam		ENCORE2	20931
STAU1_BGHLV30-52_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1408					GRCh38	V40	STAU1_BGHLV30-52_GTGAAA_L004_001.R1.fastq.gz,STAU1_BGHLV30-52_GTGAAA_L004_001.R2.fastq.gz		ENCORE2	20965