FUBP3 RNA-Seq in K562

General Information


RBP	FUBP3
Cell_Line	K562
Method	shRNA
Exp_Name	FUBP3-BGKLV08-K562
ENCODE_series_ID	ENCSR914MAN
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR373KOF
ENCODE_CN_Exp_ID	ENCSR913CAE
Rep1	FUBP3-LV08-27
Rep2	FUBP3-LV08-28
CN1	Nontarget-LV08-1_00003527
CN2	nontarget-LV08-2_00003527
Rep1_qPCR	83.2
Rep2_qPCR	71.8
Rep1_WB	44.8
Rep2_WB	32.0
Antibody Cat#	A303-012A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB964AJF
Status	Archived
Project	ENCODE3
ID	290

Experiment Information (Status: Released)

	BGKLV08-27	BGKLV08-28
idx	28	29
TRCN#_or_BGC#	TRCN0000020576	TRCN0000020576
shRNA_or_gRNA_sequence	CCTCTTCGTATCACTGGAGAT	CCTCTTCGTATCACTGGAGAT
PAM
Name	FUBP3	FUBP3
Sample_ID	BGKLV08-27	BGKLV08-28
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	FUBP3	FUBP3
qPCR_result	83.2	71.8
Ave_qPCR	77.5
RT-qPCR_primer-F	GCAGCACCTACCAGGCGT
RT-qPCR_primer-R	AGGCCTTGCTGTAGTTGGG
protein_conc	2530	2695
WB_result	44.8	32.0
Ave_WB	38.4
WB_DONE_date
MW
IP	1	1
antibody_Cat#	A303-012A	A303-012A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	25.5097119	0
Rep2_TPM	23.4034597	0
Action	Ready	Ready
Library_start_date	5/5/2014	5/5/2014
repeat_library
Note
ID	27	28

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV08-27	BGKLV08-28
Sample_ID	BGKLV08-27	BGKLV08-28
Sample Name	FUBP3-LV08-27	FUBP3-LV08-28
Sample Name	FUBP3-LV08-27	FUBP3-LV08-28
RBP	FUBP3	FUBP3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	288	289

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-27	BGKLV08-28
Sample #
Sample Name	FUBP3-BGKLV08-27	FUBP3-BGKLV08-28
Sample_Name_Alias	FUBP3-LV08-27	FUBP3-LV08-28
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-05	2014-05-05
Lib_ID	Lib-140505	Lib-140505
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV08/set2/A2.png	DNA_Library_LV08/set2/B2.png
RIN	9.3	9.2
libSample_RNA_Well	RNA_Library_LV08/set2/C2.png	RNA_Library_LV08/set2/D2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-27	BGKLV08-28
RBP	FUBP3	FUBP3
Batch_ID	BGKLV08	BGKLV08
WB_result	44.800	32.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1910	1911

Sequencing Information

	BGKLV08-27	BGKLV08-28
Sample_ID	BGKLV08-27	BGKLV08-28
Sample Name	FUBP3-LV08-27	FUBP3-LV08-28
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	49,100,000	51,220,000
total_aligned_reads	43,594,652	44,466,356
unique_aligned_reads	39,900,326	40,732,422
percent_uniqueAligned	0.81263	0.79524
correlation_replicates	0.998898	0.998898
spikein_reads	344,454	452,838
percent_spikeins	0.00702	0.00884
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	610	611

Data Submission Information

	BGKLV08-27	BGKLV08-27
ENCODE_alias	brenton-graveley:FUBP3-LV08	brenton-graveley:FUBP3-BGKLV08-K562
ENCODE_accession	ENCSR373KOF	ENCSR914MAN
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-27	BGKLV08-27
Sample Name	FUBP3-LV08-27	FUBP3-LV08-27
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2693	6720

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
FUBP3-LV08-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	610					GRCh38	V40	FUBP3-LV08-27_ACTGAT_L004_R1_001.fastq.gz,FUBP3-LV08-27_ACTGAT_L004_R2_001.fastq.gz		ENCORE2	11995
FUBP3-LV08-27_ACTGAT_L004_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	610	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12051
FUBP3-LV08-27_ACTGAT_L004_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	610	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12107
FUBP3-LV08-27_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	610					GRCh38	V40	FUBP3-LV08-27/Aligned.sortedByCoord.out.bam		ENCORE2	12163
FUBP3-LV08-27_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	610					GRCh38	V40	FUBP3-LV08-27/Aligned.sortedByCoord.out.bam		ENCORE2	12219
FUBP3-LV08-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	610					GRCh38	V40	FUBP3-LV08-27/Aligned.sortedByCoord.out.bam		ENCORE2	12275
FUBP3-LV08-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	610					GRCh38	V40	FUBP3-LV08-27/Aligned.sortedByCoord.out.bam		ENCORE2	12331
FUBP3-LV08-27_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	610					GRCh38	V40	FUBP3-LV08-27_ACTGAT_L004_R1_001.fastq.gz,FUBP3-LV08-27_ACTGAT_L004_R2_001.fastq.gz		ENCORE2	13330
FUBP3-LV08-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	611					GRCh38	V40	FUBP3-LV08-28_ATTCCT_L004_R1_001.fastq.gz,FUBP3-LV08-28_ATTCCT_L004_R2_001.fastq.gz		ENCORE2	11996
FUBP3-LV08-28_ATTCCT_L004_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	611	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12052
FUBP3-LV08-28_ATTCCT_L004_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	611	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12108
FUBP3-LV08-28_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	611					GRCh38	V40	FUBP3-LV08-28/Aligned.sortedByCoord.out.bam		ENCORE2	12164
FUBP3-LV08-28_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	611					GRCh38	V40	FUBP3-LV08-28/Aligned.sortedByCoord.out.bam		ENCORE2	12220
FUBP3-LV08-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	611					GRCh38	V40	FUBP3-LV08-28/Aligned.sortedByCoord.out.bam		ENCORE2	12276
FUBP3-LV08-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	611					GRCh38	V40	FUBP3-LV08-28/Aligned.sortedByCoord.out.bam		ENCORE2	12332
FUBP3-LV08-28_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	611					GRCh38	V40	FUBP3-LV08-28_ATTCCT_L004_R1_001.fastq.gz,FUBP3-LV08-28_ATTCCT_L004_R2_001.fastq.gz		ENCORE2	13331