FUBP1 RNA-Seq in K562

General Information


RBP	FUBP1
Cell_Line	K562
Method	shRNA
Exp_Name	FUBP1-BGKLV38-K562
ENCODE_series_ID	ENCSR452GOM
Batch_ID	BGKLV38
Pool ID	Pool-180109
Local_Set_Name	set40_K
ENCODE_KD_Exp_ID	ENCSR608IXR
ENCODE_CN_Exp_ID	ENCSR260BQC
Rep1	FUBP1-BGKLV38-37C
Rep2	FUBP1-BGKLV38-38C
CN1	NT-BGKLV38-1C
CN2	NT-BGKLV38-2C
Rep1_qPCR	94.2
Rep2_qPCR	89.6
Rep1_WB	80.3
Rep2_WB	73.0
Antibody Cat#	GTX115154
Antibody Lot#	GTX115154
Antibody DCC ID	ENCAB000AUG
Status	Released
Project	ENCODE4
ID	275

Experiment Information (Status: Released)

	BGKLV38-37	BGKLV38-37	BGKLV38-38	BGKLV38-38
idx	808	0	809	0
TRCN#_or_BGC#	TRCN0000013293	TRCN0000013293	TRCN0000013293	TRCN0000013293
shRNA_or_gRNA_sequence	CGACTTGATGAAGATCTTAAT	CGACTTGATGAAGATCTTAAT	CGACTTGATGAAGATCTTAAT	CGACTTGATGAAGATCTTAAT
PAM
Name	FUBP1	FUBP1	FUBP1	FUBP1
Sample_ID	BGKLV38-37	BGKLV38-37	BGKLV38-38	BGKLV38-38
transduction_Date	9/15/16	9/15/16	9/15/16	9/15/16
days
RBP_name	FUBP1	FUBP1	FUBP1	FUBP1
qPCR_result	94.2	94.2	89.6	89.6
Ave_qPCR	91.9	91.9
RT-qPCR_primer-F	gaaaatgggtcaggcagttc	gaaaatgggtcaggcagttc
RT-qPCR_primer-R	gcccaggctgcactataatc	gcccaggctgcactataatc
protein_conc	3265	3265	3141	3141
WB_result	80.3	95.3	73.0	89.6
Ave_WB	76.6	92.4
WB_DONE_date	9/29/16	3/14/19	WES	WES
MW	68kDa	68kDa
IP	1		1
antibody_Cat#	GTX115154	PA5-28061	GTX115154	PA5-28061
Antibody DCC ID	ENCAB000AUG	ENCAB745PWU	ENCAB000AUG
submitted_to_DCC_date	10/26/16	3/11/19
Rep1_TPM	62.5	62.5	0	0
Rep2_TPM	55.9	55.9	0	0
Action
Library_start_date	12/19/17	12/19/17	12/19/17	12/19/17
repeat_library
Note
ID	901	903	902	904

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
FUBP1	Product_ID: GTX115154 Lot_ID: 40401 Source: GeneTex Target Name: FUBP1-human
FUBP1	Product_ID: PA5-28061 Lot_ID: TL2692992A Source: Thermo Fisher Target Name: FUBP1-human

Experiment Status

	BGKLV38-37	BGKLV38-38
Sample_ID	BGKLV38-37	BGKLV38-38
Sample Name
Sample Name	FUBP1-BGKLV38-37C	FUBP1-BGKLV38-38C
RBP	FUBP1	FUBP1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6475	6476

Library-Prep
Sequencing

Library-Prep Information

	BGKLV38-37	BGKLV38-38
Sample #	59	60
Sample Name	FUBP1-BGKLV38-37C	FUBP1-BGKLV38-38C
Sample_Name_Alias
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2018-01-02	2018-01-02
Lib_ID	Lib-180102	Lib-180102
Tecan_Location
Tecan
Tecan_date
Size_bp	290	292
Peak_Molarity	11.90	19.40
libSampleQC_DNA_Well	DNA_Library_set40/set1/E9.png	DNA_Library_set40/set1/F9.png
RIN	9.4	9.0
libSample_RNA_Well	RNA_Library_set40/set1/E4.png	RNA_Library_set40/set1/F4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGKLV38-37	BGKLV38-38
RBP	FUBP1	FUBP1
Batch_ID	BGKLV38	BGKLV38
WB_result	80.300	73.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	982	983

Sequencing Information

	BGKLV38-37	BGKLV38-38	BGKLV38-38
Sample_ID	BGKLV38-37	BGKLV38-38	BGKLV38-38
Sample Name	FUBP1-BGKLV38-37C	FUBP1-BGKLV38-38C	FUBP1-BGKLV38-38C
Pool ID	Pool-180109	Pool-180109	Pool-180316
LocalServer_folder	set40_K	set40_K	set40_K
total_reads	33,256,302	22,573,618	52,272,780
total_aligned_reads	28,469,106	19,339,696	45,001,276
unique_aligned_reads	25,635,416	17,342,796	40,407,790
percent_uniqueAligned	0.77084	0.76828	0.77302
correlation_replicates	0.997335	0.997335
spikein_reads	6,660	7,098	16,554
percent_spikeins	0.00020	0.00031	0.00032
original_ReadLength	100	100	100
QC_Status	Submitted	Submitted	Submitted
ID	385	386	407

Data Submission Information

	BGKLV38-37	BGKLV38-37	BGKLV38-37	BGKLV38-37	BGKLV38-37	BGKLV38-37	BGKLV38-38	BGKLV38-38	BGKLV38-38	BGKLV38-38	BGKLV38-38	BGKLV38-38
ENCODE_alias	brenton-graveley:FUBP1-BGKLV38-C	brenton-graveley:FUBP1-BGKLV38-37C	brenton-graveley:L-FUBP1-BGKLV38-37C	brenton-graveley:FUBP1-BGKLV38-37C_AGTCAA_ACBYWVANXX_L005_001.R1.fastq.gz	brenton-graveley:FUBP1-BGKLV38-37C_AGTCAA_ACBYWVANXX_L005_001.R2.fastq.gz	brenton-graveley:FUBP1-BGKLV38-K562	brenton-graveley:FUBP1-BGKLV38-38C	brenton-graveley:L-FUBP1-BGKLV38-38C	brenton-graveley:FUBP1-BGKLV38-38C_AGTTCC_ACBYWVANXX_L005_001.R1.fastq.gz	brenton-graveley:FUBP1-BGKLV38-38C_AGTTCC_AHFKCFBCX2_L001_001.R1.fastq.gz	brenton-graveley:FUBP1-BGKLV38-38C_AGTTCC_ACBYWVANXX_L005_001.R2.fastq.gz	brenton-graveley:FUBP1-BGKLV38-38C_AGTTCC_AHFKCFBCX2_L001_001.R2.fastq.gz
ENCODE_accession	ENCSR608IXR	ENCBS386NLD	ENCLB059BQI	ENCFF439PTG	ENCFF002ZEP	ENCSR452GOM	ENCBS407FFA	ENCLB466UFH	ENCFF622GUD	ENCFF923NMY	ENCFF020BZP	ENCFF144DVD
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq1	file_fastq2	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV38-37	BGKLV38-37	BGKLV38-37	BGKLV38-37	BGKLV38-37	BGKLV38-37	BGKLV38-38	BGKLV38-38	BGKLV38-38	BGKLV38-38	BGKLV38-38	BGKLV38-38
Sample Name	FUBP1-BGKLV38-37C	FUBP1-BGKLV38-37C	FUBP1-BGKLV38-37C	FUBP1-BGKLV38-37C	FUBP1-BGKLV38-37C	FUBP1-BGKLV38-37C	FUBP1-BGKLV38-38C	FUBP1-BGKLV38-38C	FUBP1-BGKLV38-38C	FUBP1-BGKLV38-38C	FUBP1-BGKLV38-38C	FUBP1-BGKLV38-38C
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV40_biosample_protocol	LV40_library_protocol				LV40_biosample_protocol	LV40_library_protocol
protocol_URL		FUBP1-BGKLV38-37C.pdf	L-FUBP1-BGKLV38-37C.pdf				FUBP1-BGKLV38-38C.pdf	L-FUBP1-BGKLV38-38C.pdf
ID	1435	1468	1524	1646	1679	7223	1469	1525	1647	1648	1680	1681

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
FUBP1-BGKLV38-37C_AGTCAA_ACBYWVANXX_L005_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	385	HiSeq2500	100	paired-ended	1				NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R1.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R1.fastq.gz	ENCODE4	725
FUBP1-BGKLV38-37C_AGTCAA_ACBYWVANXX_L005_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	385	HiSeq2500	100	paired-ended	2				NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R2.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R2.fastq.gz	ENCODE4	768
FUBP1-BGKLV38-37C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	385					GRCh38	V40	FUBP1-BGKLV38-37C_AGTCAA_ACBYWVANXX_L005_001.R1.fastq.gz,FUBP1-BGKLV38-37C_AGTCAA_ACBYWVANXX_L005_001.R2.fastq.gz		ENCORE2	23472
FUBP1-BGKLV38-37C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	385					GRCh38	V40	FUBP1-BGKLV38-37C/Aligned.sortedByCoord.out.bam		ENCORE2	23506
FUBP1-BGKLV38-37C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	385					GRCh38	V40	FUBP1-BGKLV38-37C/Aligned.sortedByCoord.out.bam		ENCORE2	23540
FUBP1-BGKLV38-37C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	385					GRCh38	V40	FUBP1-BGKLV38-37C/Aligned.sortedByCoord.out.bam		ENCORE2	23574
FUBP1-BGKLV38-37C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	385					GRCh38	V40	FUBP1-BGKLV38-37C/Aligned.sortedByCoord.out.bam		ENCORE2	23608
FUBP1-BGKLV38-37C_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	385					GRCh38	V40	FUBP1-BGKLV38-37C_AGTCAA_ACBYWVANXX_L005_001.R1.fastq.gz,FUBP1-BGKLV38-37C_AGTCAA_ACBYWVANXX_L005_001.R2.fastq.gz		ENCORE2	23642
FUBP1-BGKLV38-38C_L001_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	386	HiSeq2500	100	paired-ended	1				NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R1.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R1.fastq.gz	ENCODE4	23450
FUBP1-BGKLV38-38C_L001_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	386	HiSeq2500	100	paired-ended	2				NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R2.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R2.fastq.gz	ENCODE4	23459
FUBP1-BGKLV38-38C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	386					GRCh38	V40	FUBP1-BGKLV38-38C_L001_001.R1.fastq.gz,FUBP1-BGKLV38-38C_L001_001.R2.fastq.gz		ENCORE2	23473
FUBP1-BGKLV38-38C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	386					GRCh38	V40	FUBP1-BGKLV38-38C/Aligned.sortedByCoord.out.bam		ENCORE2	23507
FUBP1-BGKLV38-38C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	386					GRCh38	V40	FUBP1-BGKLV38-38C/Aligned.sortedByCoord.out.bam		ENCORE2	23541
FUBP1-BGKLV38-38C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	386					GRCh38	V40	FUBP1-BGKLV38-38C/Aligned.sortedByCoord.out.bam		ENCORE2	23575
FUBP1-BGKLV38-38C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	386					GRCh38	V40	FUBP1-BGKLV38-38C/Aligned.sortedByCoord.out.bam		ENCORE2	23609
FUBP1-BGKLV38-38C_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	386					GRCh38	V40	FUBP1-BGKLV38-38C_L001_001.R1.fastq.gz,FUBP1-BGKLV38-38C_L001_001.R2.fastq.gz		ENCORE2	23643