FUBP1 RNA-Seq in HepG2

General Information


RBP	FUBP1
Cell_Line	HepG2
Method	shRNA
Exp_Name	FUBP1-BGHLV37-HepG2
ENCODE_series_ID	ENCSR045SMK
Batch_ID	BGHLV37
Pool ID	Pool-180109
Local_Set_Name	set40_H
ENCODE_KD_Exp_ID	ENCSR736TAW
ENCODE_CN_Exp_ID	ENCSR225PRV
Rep1	FUBP1-BGHLV37-31C
Rep2	FUBP1-BGHLV37-32C
CN1	non-target-BGHLV37-1C
CN2	non-target-BGHLV37-2C
Rep1_qPCR	86.9
Rep2_qPCR	80.7
Rep1_WB	90.0
Rep2_WB	92.2
Antibody Cat#	GTX115154
Antibody Lot#	GTX115154
Antibody DCC ID	ENCAB000AUG
Status	Released
Project	ENCODE4
ID	263

Experiment Information (Status: Released)

	BGHLV37-31	BGHLV37-32
idx	943	944
TRCN#_or_BGC#	TRCN0000013293	TRCN0000013293
shRNA_or_gRNA_sequence	CGACTTGATGAAGATCTTAAT	CGACTTGATGAAGATCTTAAT
PAM
Name	FUBP1	FUBP1
Sample_ID	BGHLV37-31	BGHLV37-32
transduction_Date	9/1/16	9/1/16
days
RBP_name	FUBP1	FUBP1
qPCR_result	86.9	80.7
Ave_qPCR	83.8
RT-qPCR_primer-F	gaaaatgggtcaggcagttc
RT-qPCR_primer-R	gcccaggctgcactataatc
protein_conc	2893	3065
WB_result	90.0	92.2
Ave_WB	91.1
WB_DONE_date	9/16/16	WES
MW	68kDa
IP	1	1
antibody_Cat#	GTX115154	GTX115154
Antibody DCC ID	ENCAB000AUG	ENCAB000AUG
submitted_to_DCC_date	10/26/16
Rep1_TPM	43.5	0
Rep2_TPM	43.6	0
Action
Library_start_date	12/18/17	12/18/17
repeat_library
Note
ID	3036	3037

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

Experiment Status

	BGHLV37-31	BGHLV37-32
Sample_ID	BGHLV37-31	BGHLV37-32
Sample Name
Sample Name	FUBP1-BGHLV37-31C	FUBP1-BGHLV37-32C
RBP	FUBP1	FUBP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6437	6438

Library-Prep
Sequencing

Library-Prep Information

	BGHLV37-31	BGHLV37-32
Sample #	21	22
Sample Name	FUBP1-BGHLV37-31C	FUBP1-BGHLV37-32C
Sample_Name_Alias
Index Well Position	S07	S08
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	285	292
Peak_Molarity	8.04	9.08
libSampleQC_DNA_Well	DNA_Library_set40/set1/G5.png	DNA_Library_set40/set1/H5.png
RIN	9.4	9.4
libSample_RNA_Well	RNA_Library_set40/set1/E1.png	RNA_Library_set40/set1/F1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGHLV37-31	BGHLV37-32
RBP	FUBP1	FUBP1
Batch_ID	BGHLV37	BGHLV37
WB_result	90.000	92.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	944	945

Sequencing Information

	BGHLV37-31	BGHLV37-32
Sample_ID	BGHLV37-31	BGHLV37-32
Sample Name	FUBP1-BGHLV37-31C	FUBP1-BGHLV37-32C
Pool ID	Pool-180109	Pool-180109
LocalServer_folder	set40_H	set40_H
total_reads	63,454,888	64,550,866
total_aligned_reads	53,379,438	54,583,644
unique_aligned_reads	49,682,562	50,922,868
percent_uniqueAligned	0.78296	0.78888
correlation_replicates	0.997775	0.997775
spikein_reads	21,782	25,918
percent_spikeins	0.00034	0.00040
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	347	348

Data Submission Information

	BGHLV37-31	BGHLV37-31	BGHLV37-31	BGHLV37-31	BGHLV37-31	BGHLV37-31	BGHLV37-32	BGHLV37-32	BGHLV37-32	BGHLV37-32
ENCODE_alias	brenton-graveley:FUBP1-BGHLV37-C	brenton-graveley:FUBP1-BGHLV37-31C	brenton-graveley:L-FUBP1-BGHLV37-31C	brenton-graveley:FUBP1-BGHLV37-31C_CAGATC_ACBYWVANXX_L001_001.R1.fastq.gz	brenton-graveley:FUBP1-BGHLV37-31C_CAGATC_ACBYWVANXX_L001_001.R2.fastq.gz	brenton-graveley:FUBP1-BGHLV37-HepG2	brenton-graveley:FUBP1-BGHLV37-32C	brenton-graveley:L-FUBP1-BGHLV37-32C	brenton-graveley:FUBP1-BGHLV37-32C_ACTTGA_ACBYWVANXX_L001_001.R1.fastq.gz	brenton-graveley:FUBP1-BGHLV37-32C_ACTTGA_ACBYWVANXX_L001_001.R2.fastq.gz
ENCODE_accession	ENCSR736TAW	ENCBS212XWQ	ENCLB114XTP	ENCFF336SQD	ENCFF790WRB	ENCSR045SMK	ENCBS825KVU	ENCLB669VDG	ENCFF929SEM	ENCFF221UYQ
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	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
Sample_ID	BGHLV37-31	BGHLV37-31	BGHLV37-31	BGHLV37-31	BGHLV37-31	BGHLV37-31	BGHLV37-32	BGHLV37-32	BGHLV37-32	BGHLV37-32
Sample Name	FUBP1-BGHLV37-31C	FUBP1-BGHLV37-31C	FUBP1-BGHLV37-31C	FUBP1-BGHLV37-31C	FUBP1-BGHLV37-31C	FUBP1-BGHLV37-31C	FUBP1-BGHLV37-32C	FUBP1-BGHLV37-32C	FUBP1-BGHLV37-32C	FUBP1-BGHLV37-32C
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	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
Project	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-BGHLV37-31C.pdf	L-FUBP1-BGHLV37-31C.pdf				FUBP1-BGHLV37-32C.pdf	L-FUBP1-BGHLV37-32C.pdf
ID	1434	1466	1522	1578	1615	7222	1467	1523	1579	1616

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-BGHLV37-31C_CAGATC_ACBYWVANXX_L001_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	347	HiSeq2500	100	paired-ended	1				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R1.fastq.gz,non-target-BGHLV37-2C_L001_001.R1.fastq.gz	ENCODE4	645
FUBP1-BGHLV37-31C_CAGATC_ACBYWVANXX_L001_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	347	HiSeq2500	100	paired-ended	2				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R2.fastq.gz,non-target-BGHLV37-2C_L001_001.R2.fastq.gz	ENCODE4	687
FUBP1-BGHLV37-31C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	347					GRCh38	V40	FUBP1-BGHLV37-31C_CAGATC_ACBYWVANXX_L001_001.R1.fastq.gz,FUBP1-BGHLV37-31C_CAGATC_ACBYWVANXX_L001_001.R2.fastq.gz		ENCORE2	23252
FUBP1-BGHLV37-31C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	347					GRCh38	V40	FUBP1-BGHLV37-31C/Aligned.sortedByCoord.out.bam		ENCORE2	23286
FUBP1-BGHLV37-31C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	347					GRCh38	V40	FUBP1-BGHLV37-31C/Aligned.sortedByCoord.out.bam		ENCORE2	23320
FUBP1-BGHLV37-31C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	347					GRCh38	V40	FUBP1-BGHLV37-31C/Aligned.sortedByCoord.out.bam		ENCORE2	23354
FUBP1-BGHLV37-31C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	347					GRCh38	V40	FUBP1-BGHLV37-31C/Aligned.sortedByCoord.out.bam		ENCORE2	23388
FUBP1-BGHLV37-31C_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	347					GRCh38	V40	FUBP1-BGHLV37-31C_CAGATC_ACBYWVANXX_L001_001.R1.fastq.gz,FUBP1-BGHLV37-31C_CAGATC_ACBYWVANXX_L001_001.R2.fastq.gz		ENCORE2	23422
FUBP1-BGHLV37-32C_ACTTGA_ACBYWVANXX_L001_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	348	HiSeq2500	100	paired-ended	1				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R1.fastq.gz,non-target-BGHLV37-2C_L001_001.R1.fastq.gz	ENCODE4	646
FUBP1-BGHLV37-32C_ACTTGA_ACBYWVANXX_L001_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	348	HiSeq2500	100	paired-ended	2				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R2.fastq.gz,non-target-BGHLV37-2C_L001_001.R2.fastq.gz	ENCODE4	688
FUBP1-BGHLV37-32C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	348					GRCh38	V40	FUBP1-BGHLV37-32C_ACTTGA_ACBYWVANXX_L001_001.R1.fastq.gz,FUBP1-BGHLV37-32C_ACTTGA_ACBYWVANXX_L001_001.R2.fastq.gz		ENCORE2	23253
FUBP1-BGHLV37-32C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	348					GRCh38	V40	FUBP1-BGHLV37-32C/Aligned.sortedByCoord.out.bam		ENCORE2	23287
FUBP1-BGHLV37-32C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	348					GRCh38	V40	FUBP1-BGHLV37-32C/Aligned.sortedByCoord.out.bam		ENCORE2	23321
FUBP1-BGHLV37-32C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	348					GRCh38	V40	FUBP1-BGHLV37-32C/Aligned.sortedByCoord.out.bam		ENCORE2	23355
FUBP1-BGHLV37-32C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	348					GRCh38	V40	FUBP1-BGHLV37-32C/Aligned.sortedByCoord.out.bam		ENCORE2	23389
FUBP1-BGHLV37-32C_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	348					GRCh38	V40	FUBP1-BGHLV37-32C_ACTTGA_ACBYWVANXX_L001_001.R1.fastq.gz,FUBP1-BGHLV37-32C_ACTTGA_ACBYWVANXX_L001_001.R2.fastq.gz		ENCORE2	23423