FUS RNA-Seq in K562

General Information


RBP	FUS
Cell_Line	K562
Method	shRNA
Exp_Name	FUS-BGKLV13-K562
ENCODE_series_ID	ENCSR335TEE
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR325OOM
ENCODE_CN_Exp_ID	ENCSR084SCN
Rep1	FUS_BGKLV13_51
Rep2	FUS_BGKLV13_52
CN1	non-target_BGKLV13_73
CN2	non-target_BGKLV13_74
Rep1_qPCR	84.1
Rep2_qPCR	90.6
Rep1_WB	82.9
Rep2_WB	86.0
Antibody Cat#	A300-294A
Antibody Lot#	A300-294A
Antibody DCC ID	ENCAB598VSJ
Status	Released
Project	ENCODE3
ID	375

Experiment Information (Status: Released)

	BGKLV13-51	BGKLV13-52
idx	186	187
TRCN#_or_BGC#	TRCN0000039824	TRCN0000039824
shRNA_or_gRNA_sequence	GCTGATTACTTCAAGCAGATT	GCTGATTACTTCAAGCAGATT
PAM
Name	FUS	FUS
Sample_ID	BGKLV13-51	BGKLV13-52
transduction_Date	6/13/2014	6/13/2014
days
RBP_name	FUS	FUS
qPCR_result	84.1	90.6
Ave_qPCR	87.4
RT-qPCR_primer-F	GGCCAGAGCAGCTATTCTTC
RT-qPCR_primer-R	CAGTCGAGCCATATCCCTG
protein_conc	1891	2132
WB_result	82.9	86.0
Ave_WB	84.5
WB_DONE_date
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	196.067396	0
Rep2_TPM	138.889921	0
Action
Library_start_date	7/30/2014	7/30/2014
repeat_library
Note
ID	205	206

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

	BGKLV13-51	BGKLV13-52
Sample_ID	BGKLV13-51	BGKLV13-52
Sample Name	FUS_BGKLV13_51	FUS_BGKLV13_52
Sample Name	FUS_BGKLV13_51	FUS_BGKLV13_52
RBP	FUS	FUS
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	452	453

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-51	BGKLV13-52
Sample #
Sample Name	FUS-BGKLV13-51	FUS-BGKLV13-52
Sample_Name_Alias	FUS_BGKLV13_51	FUS_BGKLV13_52
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-30	2014-07-30
Lib_ID	Lib-140730	Lib-140730
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/D5.png	DNA_Library_LV13-14/set1/E5.png
RIN	9.6	9.5
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/G1.png	RNA_Library_LV13-14-16/set1/H1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-51	BGKLV13-52
RBP	FUS	FUS
Batch_ID	BGKLV13	BGKLV13
WB_result	82.900	86.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2154	2155

Sequencing Information

	BGKLV13-51	BGKLV13-52
Sample_ID	BGKLV13-51	BGKLV13-52
Sample Name	FUS_BGKLV13_51	FUS_BGKLV13_52
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	42,610,000	29,560,000
total_aligned_reads	40,458,582	28,003,340
unique_aligned_reads	37,188,910	25,801,030
percent_uniqueAligned	0.87277	0.87284
correlation_replicates	0.998566	0.998566
spikein_reads	126,482	76,836
percent_spikeins	0.00297	0.00260
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	796	797

Data Submission Information

	BGKLV13-51	BGKLV13-51
ENCODE_alias	brenton-graveley:FUS_BGKLV13	brenton-graveley:FUS-BGKLV13-K562
ENCODE_accession	ENCSR325OOM	ENCSR335TEE
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-51	BGKLV13-51
Sample Name	FUS_BGKLV13_51	FUS_BGKLV13_51
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2775	6722

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_BGKLV13_51_GGCTAC_L005_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	796	HiSeq2000	100	paired-ended	1				non-target_BGKLV13_73_GATCAG_L005_R1_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	13380
FUS_BGKLV13_51_GGCTAC_L005_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	796	HiSeq2000	100	paired-ended	2				non-target_BGKLV13_73_GATCAG_L005_R2_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	13432
FUS_BGKLV13_51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	796					GRCh38	V40	FUS_BGKLV13_51_GGCTAC_L005_R1_001.fastq.gz,FUS_BGKLV13_51_GGCTAC_L005_R2_001.fastq.gz		ENCORE2	13484
FUS_BGKLV13_51_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	796					GRCh38	V40	FUS_BGKLV13_51/Aligned.sortedByCoord.out.bam		ENCORE2	13536
FUS_BGKLV13_51_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	796					GRCh38	V40	FUS_BGKLV13_51/Aligned.sortedByCoord.out.bam		ENCORE2	13588
FUS_BGKLV13_51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	796					GRCh38	V40	FUS_BGKLV13_51/Aligned.sortedByCoord.out.bam		ENCORE2	13640
FUS_BGKLV13_51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	796					GRCh38	V40	FUS_BGKLV13_51/Aligned.sortedByCoord.out.bam		ENCORE2	13692
FUS_BGKLV13_51_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	796					GRCh38	V40	FUS_BGKLV13_51_GGCTAC_L005_R1_001.fastq.gz,FUS_BGKLV13_51_GGCTAC_L005_R2_001.fastq.gz		ENCORE2	13744
FUS_BGKLV13_52_CTTGTA_L005_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	797	HiSeq2000	100	paired-ended	1				non-target_BGKLV13_73_GATCAG_L005_R1_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	13381
FUS_BGKLV13_52_CTTGTA_L005_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	797	HiSeq2000	100	paired-ended	2				non-target_BGKLV13_73_GATCAG_L005_R2_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	13433
FUS_BGKLV13_52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	797					GRCh38	V40	FUS_BGKLV13_52_CTTGTA_L005_R1_001.fastq.gz,FUS_BGKLV13_52_CTTGTA_L005_R2_001.fastq.gz		ENCORE2	13485
FUS_BGKLV13_52_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	797					GRCh38	V40	FUS_BGKLV13_52/Aligned.sortedByCoord.out.bam		ENCORE2	13537
FUS_BGKLV13_52_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	797					GRCh38	V40	FUS_BGKLV13_52/Aligned.sortedByCoord.out.bam		ENCORE2	13589
FUS_BGKLV13_52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	797					GRCh38	V40	FUS_BGKLV13_52/Aligned.sortedByCoord.out.bam		ENCORE2	13641
FUS_BGKLV13_52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	797					GRCh38	V40	FUS_BGKLV13_52/Aligned.sortedByCoord.out.bam		ENCORE2	13693
FUS_BGKLV13_52_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	797					GRCh38	V40	FUS_BGKLV13_52_CTTGTA_L005_R1_001.fastq.gz,FUS_BGKLV13_52_CTTGTA_L005_R2_001.fastq.gz		ENCORE2	13745