FUS RNA-Seq in HepG2

General Information


RBP	FUS
Cell_Line	HepG2
Method	shRNA
Exp_Name	FUS-BGHLV14-HepG2
ENCODE_series_ID	ENCSR728KDH
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR927JXU
ENCODE_CN_Exp_ID	ENCSR491FOC
Rep1	FUS_BGHLV14-21
Rep2	FUS_BGHLV14-22
CN1	NT_BGHLV14-1
CN2	NT_BGHLV14-2
Rep1_qPCR	84.8
Rep2_qPCR	84.2
Rep1_WB	92.2
Rep2_WB	93.6
Antibody Cat#	A300-294A
Antibody Lot#	A300-294A
Antibody DCC ID	ENCAB598VSJ
Status	Released
Project	ENCODE3
ID	393

Experiment Information (Status: Released)

	BGHLV14-21	BGHLV14-22
idx	117	118
TRCN#_or_BGC#	TRCN0000039824	TRCN0000039824
shRNA_or_gRNA_sequence	GCTGATTACTTCAAGCAGATT	GCTGATTACTTCAAGCAGATT
PAM
Name	FUS	FUS
Sample_ID	BGHLV14-21	BGHLV14-22
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	FUS	FUS
qPCR_result	84.8	84.2
Ave_qPCR	84.5
RT-qPCR_primer-F	GGCCAGAGCAGCTATTCTTC
RT-qPCR_primer-R	CAGTCGAGCCATATCCCTG
protein_conc	4638	4044
WB_result	92.2	93.6
Ave_WB	92.9
WB_DONE_date	1/14/2015
MW	53kDa
IP	1MW	1MW
antibody_Cat#	A300-294A	A300-294A
Antibody DCC ID	ENCAB598VSJ	ENCAB598VSJ
submitted_to_DCC_date	4/2/2015
Rep1_TPM	137.1	0
Rep2_TPM	152.1	0
Action
Library_start_date	8/12/2014	8/12/2014
repeat_library
Note
ID	2174	2175

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
FUS	Product_ID: A300-294A Lot_ID: 2 Source: Bethyl Labs Target Name: FUS-human

Experiment Status

	BGHLV14-21	BGHLV14-22
Sample_ID	BGHLV14-21	BGHLV14-22
Sample Name	FUS_BGHLV14-21	FUS_BGHLV14-22
Sample Name	FUS_BGHLV14-21	FUS_BGHLV14-22
RBP	FUS	FUS
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	508	509

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-21	BGHLV14-22
Sample #
Sample Name	FUS-BGHLV14-21	FUS-BGHLV14-22
Sample_Name_Alias	FUS_BGHLV14-21	FUS_BGHLV14-22
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-08-12	2014-08-12
Lib_ID	Lib-140812	Lib-140812
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/D10.png	DNA_Library_LV13-14/set1/E10.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/E6.png	RNA_Library_LV13-14-16/set1/F6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-21	BGHLV14-22
RBP	FUS	FUS
Batch_ID	BGHLV14	BGHLV14
WB_result	92.200	93.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2194	2195

Sequencing Information

	BGHLV14-21	BGHLV14-22
Sample_ID	BGHLV14-21	BGHLV14-22
Sample Name	FUS_BGHLV14-21	FUS_BGHLV14-22
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	54,980,000	55,910,000
total_aligned_reads	49,591,284	50,953,550
unique_aligned_reads	46,656,236	47,950,850
percent_uniqueAligned	0.84860	0.85764
correlation_replicates	0.999309	0.999309
spikein_reads	807,708	589,816
percent_spikeins	0.01469	0.01055
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	836	837

Data Submission Information

	BGHLV14-21	BGHLV14-21
ENCODE_alias	brenton-graveley:FUS_BGHLV14	brenton-graveley:FUS-BGHLV14-HepG2
ENCODE_accession	ENCSR927JXU	ENCSR728KDH
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-21	BGHLV14-21
Sample Name	FUS_BGHLV14-21	FUS_BGHLV14-21
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2804	6721

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
FUS_BGHLV14-21_TTAGGC_L003_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	836	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13800
FUS_BGHLV14-21_TTAGGC_L003_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	836	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13862
FUS_BGHLV14-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	836					GRCh38	V40	FUS_BGHLV14-21_TTAGGC_L003_R1_001.fastq.gz,FUS_BGHLV14-21_TTAGGC_L003_R2_001.fastq.gz		ENCORE2	13924
FUS_BGHLV14-21_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	836					GRCh38	V40	FUS_BGHLV14-21/Aligned.sortedByCoord.out.bam		ENCORE2	13986
FUS_BGHLV14-21_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	836					GRCh38	V40	FUS_BGHLV14-21/Aligned.sortedByCoord.out.bam		ENCORE2	14048
FUS_BGHLV14-21_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	836					GRCh38	V40	FUS_BGHLV14-21/Aligned.sortedByCoord.out.bam		ENCORE2	14110
FUS_BGHLV14-21_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	836					GRCh38	V40	FUS_BGHLV14-21/Aligned.sortedByCoord.out.bam		ENCORE2	14172
FUS_BGHLV14-21_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	836					GRCh38	V40	FUS_BGHLV14-21_TTAGGC_L003_R1_001.fastq.gz,FUS_BGHLV14-21_TTAGGC_L003_R2_001.fastq.gz		ENCORE2	14234
FUS_BGHLV14-22_TGACCA_L003_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	837	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13801
FUS_BGHLV14-22_TGACCA_L003_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	837	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13863
FUS_BGHLV14-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	837					GRCh38	V40	FUS_BGHLV14-22_TGACCA_L003_R1_001.fastq.gz,FUS_BGHLV14-22_TGACCA_L003_R2_001.fastq.gz		ENCORE2	13925
FUS_BGHLV14-22_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	837					GRCh38	V40	FUS_BGHLV14-22/Aligned.sortedByCoord.out.bam		ENCORE2	13987
FUS_BGHLV14-22_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	837					GRCh38	V40	FUS_BGHLV14-22/Aligned.sortedByCoord.out.bam		ENCORE2	14049
FUS_BGHLV14-22_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	837					GRCh38	V40	FUS_BGHLV14-22/Aligned.sortedByCoord.out.bam		ENCORE2	14111
FUS_BGHLV14-22_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	837					GRCh38	V40	FUS_BGHLV14-22/Aligned.sortedByCoord.out.bam		ENCORE2	14173
FUS_BGHLV14-22_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	837					GRCh38	V40	FUS_BGHLV14-22_TGACCA_L003_R1_001.fastq.gz,FUS_BGHLV14-22_TGACCA_L003_R2_001.fastq.gz		ENCORE2	14235