FUBP3 RNA-Seq in HepG2

General Information


RBP	FUBP3
Cell_Line	HepG2
Method	shRNA
Exp_Name	FUBP3-BGHLV12-HepG2
ENCODE_series_ID	ENCSR539XOU
Batch_ID	BGHLV12
Pool ID	Pool-150705
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR755KOM
ENCODE_CN_Exp_ID	ENCSR376RJN
Rep1	FUBP3-BGHLV12-27_17744
Rep2	FUBP3-BGHLV12-28_17745
CN1	NT-BGHLV12-a_17742
CN2	NT-BGHLV12-b_17743
Rep1_qPCR	88.4
Rep2_qPCR	89.2
Rep1_WB	81.2
Rep2_WB	86.7
Antibody Cat#	A303-012A
Antibody Lot#	A303-012A
Antibody DCC ID	ENCAB964AJF
Status	Released
Project	ENCODE3
ID	488

Experiment Information (Status: NotSatisfied)

	BGHLV12-27	BGHLV12-28
idx	27	28
TRCN#_or_BGC#	TRCN0000020576	TRCN0000020576
shRNA_or_gRNA_sequence	CCTCTTCGTATCACTGGAGAT	CCTCTTCGTATCACTGGAGAT
PAM
Name	FUBP3	FUBP3
Sample_ID	BGHLV12-27	BGHLV12-28
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	FUBP3	FUBP3
qPCR_result	88.4	89.2
Ave_qPCR	88.8
RT-qPCR_primer-F	GCAGCACCTACCAGGCGT
RT-qPCR_primer-R	AGGCCTTGCTGTAGTTGGG
protein_conc	4299	3010
WB_result	81.2	86.7
Ave_WB	84.0
WB_DONE_date	1/20/2015
MW	62kDa
IP	1	1
antibody_Cat#	A303-012A	A303-012A
Antibody DCC ID	ENCAB964AJF	ENCAB964AJF
submitted_to_DCC_date	5/6/2015
Rep1_TPM	18.7	0
Rep2_TPM	16.9	0
Action
Library_start_date	6/9/2014	6/9/2014
repeat_library
Note
ID	2074	2075

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
FUBP3	Product_ID: A303-012A Lot_ID: 1 Source: Bethyl Labs Target Name: FUBP3-human

Experiment Status

	BGHLV12-27	BGHLV12-27	BGHLV12-28	BGHLV12-28
Sample_ID	BGHLV12-27	BGHLV12-27	BGHLV12-28	BGHLV12-28
Sample Name	FUBP3-BGHLV12-27	FUBP3-BGHLV12-27_17744	FUBP3-BGHLV12-28	FUBP3-BGHLV12-28_17745
Sample Name	FUBP3-BGHLV12-27	FUBP3-BGHLV12-27_17744	FUBP3-BGHLV12-28	FUBP3-BGHLV12-28_17745
RBP	FUBP3	FUBP3	FUBP3	FUBP3
Cell_Line	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	NotSatisfied	Released	NotSatisfied	Released
Status_date	2019-06-26	2015-08-13	2019-06-26	2015-08-13
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
Note	Bad Correlation between replicates		Bad Correlation between replicates
ID	16	880	17	881

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-27	BGHLV12-27	BGHLV12-28	BGHLV12-28
Sample #
Sample Name	FUBP3-BGHLV12-27	FUBP3-BGHLV12-27C	FUBP3-BGHLV12-28	FUBP3-BGHLV12-28C
Sample_Name_Alias	FUBP3-BGHLV12-27	FUBP3-BGHLV12-27_17744	FUBP3-BGHLV12-28	FUBP3-BGHLV12-28_17745
Index Well Position	S20	S15	S21	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-09	2015-05-29	2014-06-09	2015-05-29
Lib_ID	Lib-140609	Lib-150529	Lib-140609	Lib-150529
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set2/E1.png	DNA_Library_LV20-22-23/set1/G5.png	DNA_Library_LV12/set2/F1.png	DNA_Library_LV20-22-23/set1/H5.png
RIN	9.3	9.3	9.4	9.4
libSample_RNA_Well	RNA_Library_LV12/set1/C3.png	RNA_Library_LV12/set1/C3.png	RNA_Library_LV12/set1/D3.png	RNA_Library_LV12/set1/D3.png
SampleQC_method		TapeStation		TapeStation
SampleQC_date
Sample_ID	BGHLV12-27	BGHLV12-27	BGHLV12-28	BGHLV12-28
RBP	FUBP3	FUBP3	FUBP3	FUBP3
Batch_ID	BGHLV12	BGHLV12	BGHLV12	BGHLV12
WB_result	81.200	81.200	86.700	86.700
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix		C		C
Lib_Status	SendToSequence	SendToSequence	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
ID	2010	2568	2011	2569

Sequencing Information

	BGHLV12-27	BGHLV12-27	BGHLV12-28	BGHLV12-28
Sample_ID	BGHLV12-27	BGHLV12-27	BGHLV12-28	BGHLV12-28
Sample Name	FUBP3-BGHLV12-27	FUBP3-BGHLV12-27_17744	FUBP3-BGHLV12-28	FUBP3-BGHLV12-28_17745
Pool ID	Pool-140701A	Pool-150705	Pool-140701A	Pool-150705
LocalServer_folder	set12	set12	set12	set12
total_reads	69,170,000	55,880,000	68,710,000	61,290,000
total_aligned_reads	64,512,804	51,064,432	53,981,496	55,258,572
unique_aligned_reads	60,980,710	48,160,122	51,190,634	52,074,162
percent_uniqueAligned	0.88161	0.86185	0.74502	0.84964
correlation_replicates	0.564754	0.985734	0.564754	0.985734
spikein_reads	492,754	323,404	392,554	311,126
percent_spikeins	0.00712	0.00579	0.00571	0.00508
original_ReadLength	100	100	100	100
QC_Status	BadCorrelation	Submitted	BadCorrelation	Submitted
ID	710	1160	711	1161

Data Submission Information

	BGHLV12-27	BGHLV12-27
ENCODE_alias	brenton-graveley:FUBP3-BGHLV12	brenton-graveley:FUBP3-BGHLV12-HepG2
ENCODE_accession	ENCSR755KOM	ENCSR539XOU
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-27	BGHLV12-27
Sample Name	FUBP3-BGHLV12-27_17744	FUBP3-BGHLV12-27_17744
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2956	6719

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-BGHLV12-27_17744_ATGTCA_L006_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1160	HiSeq2000	100	paired-ended	1				NT-BGHLV12-a_17742_AGTCAA_L006_R1_001.fastq.gz,NT-BGHLV12-b_17743_AGTTCC_L006_R1_001.fastq.gz	ENCODE3	12767
FUBP3-BGHLV12-27_17744_ATGTCA_L006_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1160	HiSeq2000	100	paired-ended	2				NT-BGHLV12-a_17742_AGTCAA_L006_R2_001.fastq.gz,NT-BGHLV12-b_17743_AGTTCC_L006_R2_001.fastq.gz	ENCODE3	12836
FUBP3-BGHLV12-27_17744_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1160					GRCh38	V40	FUBP3-BGHLV12-27_17744_ATGTCA_L006_R1_001.fastq.gz,FUBP3-BGHLV12-27_17744_ATGTCA_L006_R2_001.fastq.gz		ENCORE2	12906
FUBP3-BGHLV12-27_17744_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1160					GRCh38	V40	FUBP3-BGHLV12-27_17744/Aligned.sortedByCoord.out.bam		ENCORE2	12976
FUBP3-BGHLV12-27_17744_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1160					GRCh38	V40	FUBP3-BGHLV12-27_17744/Aligned.sortedByCoord.out.bam		ENCORE2	13046
FUBP3-BGHLV12-27_17744_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1160					GRCh38	V40	FUBP3-BGHLV12-27_17744/Aligned.sortedByCoord.out.bam		ENCORE2	13116
FUBP3-BGHLV12-27_17744_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1160					GRCh38	V40	FUBP3-BGHLV12-27_17744/Aligned.sortedByCoord.out.bam		ENCORE2	13186
FUBP3-BGHLV12-27_17744_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1160					GRCh38	V40	FUBP3-BGHLV12-27_17744_ATGTCA_L006_R1_001.fastq.gz,FUBP3-BGHLV12-27_17744_ATGTCA_L006_R2_001.fastq.gz		ENCORE2	13256
FUBP3-BGHLV12-28_17745_CCGTCC_L006_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1161	HiSeq2000	100	paired-ended	1				NT-BGHLV12-a_17742_AGTCAA_L006_R1_001.fastq.gz,NT-BGHLV12-b_17743_AGTTCC_L006_R1_001.fastq.gz	ENCODE3	12768
FUBP3-BGHLV12-28_17745_CCGTCC_L006_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1161	HiSeq2000	100	paired-ended	2				NT-BGHLV12-a_17742_AGTCAA_L006_R2_001.fastq.gz,NT-BGHLV12-b_17743_AGTTCC_L006_R2_001.fastq.gz	ENCODE3	12837
FUBP3-BGHLV12-28_17745_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1161					GRCh38	V40	FUBP3-BGHLV12-28_17745_CCGTCC_L006_R1_001.fastq.gz,FUBP3-BGHLV12-28_17745_CCGTCC_L006_R2_001.fastq.gz		ENCORE2	12907
FUBP3-BGHLV12-28_17745_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1161					GRCh38	V40	FUBP3-BGHLV12-28_17745/Aligned.sortedByCoord.out.bam		ENCORE2	12977
FUBP3-BGHLV12-28_17745_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1161					GRCh38	V40	FUBP3-BGHLV12-28_17745/Aligned.sortedByCoord.out.bam		ENCORE2	13047
FUBP3-BGHLV12-28_17745_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1161					GRCh38	V40	FUBP3-BGHLV12-28_17745/Aligned.sortedByCoord.out.bam		ENCORE2	13117
FUBP3-BGHLV12-28_17745_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1161					GRCh38	V40	FUBP3-BGHLV12-28_17745/Aligned.sortedByCoord.out.bam		ENCORE2	13187
FUBP3-BGHLV12-28_17745_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1161					GRCh38	V40	FUBP3-BGHLV12-28_17745_CCGTCC_L006_R1_001.fastq.gz,FUBP3-BGHLV12-28_17745_CCGTCC_L006_R2_001.fastq.gz		ENCORE2	13257