FUBP3 RNA-Seq in K562

General Information


RBP	FUBP3
Cell_Line	K562
Method	CRISPR
Exp_Name	FUBP3-BGKcLV08-K562
ENCODE_series_ID	ENCSR765QHH
Batch_ID	BGKcLV08
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR619GGE
ENCODE_CN_Exp_ID	ENCSR015KGT
Rep1	FUBP3-BGKcLV08-35
Rep2	FUBP3-BGKcLV08-36
CN1	NT-BGKcLV08-1
CN2	NT-BGKcLV08-2
Rep1_qPCR	65.1
Rep2_qPCR	62.5
Rep1_WB	67.3
Rep2_WB	65.5
Antibody Cat#	A303-012A
Antibody Lot#	A303-012A
Antibody DCC ID	ENCAB964AJF
Status	Released
Project	ENCODE4
ID	205

Experiment Information (Status: Released)

	BGKcLV08-35	BGKcLV08-36
idx	260	261
TRCN#_or_BGC#	BGC#0000122	BGC#0000122
shRNA_or_gRNA_sequence	TGGGGTTCCGGTAAGTACAC	TGGGGTTCCGGTAAGTACAC
PAM	AGG	AGG
Name	FUBP3-92F	FUBP3-92F
Sample_ID	BGKcLV08-35	BGKcLV08-36
transduction_Date	3/8/18	3/8/18
days	Day 6	Day 6
RBP_name	FUBP3	FUBP3
qPCR_result	65.1	62.5
Ave_qPCR	63.8
RT-qPCR_primer-F	GCAGCACCTACCAGGCGT
RT-qPCR_primer-R	AGGCCTTGCTGTAGTTGGG
protein_conc	3835	4160
WB_result	67.3	65.5
Ave_WB	66.4
WB_DONE_date	3/15/18	WES
MW	61kDa
IP	1	1
antibody_Cat#	A303-012A	A303-012A
Antibody DCC ID	ENCAB964AJF
submitted_to_DCC_date	9/8/2018
Rep1_TPM	25.5	0
Rep2_TPM	23.4	0
Action	Ready	Ready
Library_start_date	7/26/18	7/26/18
repeat_library
Note
ID	4360	4361

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

	BGKcLV08-35	BGKcLV08-36
Sample_ID	BGKcLV08-35	BGKcLV08-36
Sample Name
Sample Name	FUBP3-BGKcLV08-35	FUBP3-BGKcLV08-36
RBP	FUBP3	FUBP3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6181	6182

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV08-35	BGKcLV08-36
Sample #	17	18
Sample Name	FUBP3-BGKcLV08-35	FUBP3-BGKcLV08-36
Sample_Name_Alias
Index Well Position	A03	B03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2018-10-01	2018-10-01
Lib_ID	Lib-181001	Lib-181001
Tecan_Location
Tecan
Tecan_date
Size_bp	277	292
Peak_Molarity	67.60	47.70
libSampleQC_DNA_Well	DNA_Library_set41/set2/A3.png	DNA_Library_set41/set2/B3.png
RIN	9.4	9.5
libSample_RNA_Well	RNA_Library_set41/set1/A3.png	RNA_Library_set41/set1/B3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-07-27	2018-07-27
Sample_ID	BGKcLV08-35	BGKcLV08-36
RBP	FUBP3	FUBP3
Batch_ID	BGKcLV08	BGKcLV08
WB_result	67.300	65.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	867	868

Sequencing Information

	BGKcLV08-35	BGKcLV08-36
Sample_ID	BGKcLV08-35	BGKcLV08-36
Sample Name	FUBP3-BGKcLV08-35	FUBP3-BGKcLV08-36
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	191,427,264	110,284,988
total_aligned_reads	182,636,184	102,746,258
unique_aligned_reads	164,821,896	92,639,666
percent_uniqueAligned	0.86102	0.84000
correlation_replicates	0.997138	0.997138
spikein_reads	357,330	202,394
percent_spikeins	0.00187	0.00184
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	273	274

Data Submission Information

	BGKcLV08-35	BGKcLV08-35	BGKcLV08-35	BGKcLV08-35	BGKcLV08-35	BGKcLV08-35	BGKcLV08-36	BGKcLV08-36	BGKcLV08-36	BGKcLV08-36
ENCODE_alias	brenton-graveley:FUBP3-BGKcLV08	brenton-graveley:FUBP3-BGKcLV08-35	brenton-graveley:L-FUBP3-BGKcLV08-35	brenton-graveley:FUBP3-BGKcLV08-35_TAATACAG+ATATTCAC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:FUBP3-BGKcLV08-35_TAATACAG+ATATTCAC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:FUBP3-BGKcLV08-K562	brenton-graveley:FUBP3-BGKcLV08-36	brenton-graveley:L-FUBP3-BGKcLV08-36	brenton-graveley:FUBP3-BGKcLV08-36_CGGCGTGA+GCGCCTGT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:FUBP3-BGKcLV08-36_CGGCGTGA+GCGCCTGT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR619GGE	ENCBS767AXM	ENCLB923MKA	ENCFF096IJG	ENCFF157BYT	ENCSR765QHH	ENCBS251CZU	ENCLB193GHJ	ENCFF210TDP	ENCFF097ZUS
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	BGKcLV08-35	BGKcLV08-35	BGKcLV08-35	BGKcLV08-35	BGKcLV08-35	BGKcLV08-35	BGKcLV08-36	BGKcLV08-36	BGKcLV08-36	BGKcLV08-36
Sample Name	FUBP3-BGKcLV08-35	FUBP3-BGKcLV08-35	FUBP3-BGKcLV08-35	FUBP3-BGKcLV08-35	FUBP3-BGKcLV08-35	FUBP3-BGKcLV08-35	FUBP3-BGKcLV08-36	FUBP3-BGKcLV08-36	FUBP3-BGKcLV08-36	FUBP3-BGKcLV08-36
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV41_biosample_protocol	LV41_library_protocol				LV41_biosample_protocol	LV41_library_protocol
protocol_URL		FUBP3-BGKcLV08-35.pdf	L-FUBP3-BGKcLV08-35.pdf				FUBP3-BGKcLV08-36.pdf	L-FUBP3-BGKcLV08-36.pdf
ID	1127	1174	1244	1314	1384	7224	1175	1245	1315	1385

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
FUBP3-BGKcLV08-35_TAATACAG+ATATTCAC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	273				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	521
FUBP3-BGKcLV08-35_TAATACAG+ATATTCAC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	273				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	591
FUBP3-BGKcLV08-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	273	GRCh38	V40	FUBP3-BGKcLV08-35_TAATACAG+ATATTCAC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,FUBP3-BGKcLV08-35_TAATACAG+ATATTCAC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26759
FUBP3-BGKcLV08-35_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	273	GRCh38	V40	FUBP3-BGKcLV08-35/Aligned.sortedByCoord.out.bam		ENCORE2	26829
FUBP3-BGKcLV08-35_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	273	GRCh38	V40	FUBP3-BGKcLV08-35/Aligned.sortedByCoord.out.bam		ENCORE2	26899
FUBP3-BGKcLV08-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	273	GRCh38	V40	FUBP3-BGKcLV08-35/Aligned.sortedByCoord.out.bam		ENCORE2	26969
FUBP3-BGKcLV08-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	273	GRCh38	V40	FUBP3-BGKcLV08-35/Aligned.sortedByCoord.out.bam		ENCORE2	27039
FUBP3-BGKcLV08-35_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	273	GRCh38	V40	FUBP3-BGKcLV08-35_TAATACAG+ATATTCAC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,FUBP3-BGKcLV08-35_TAATACAG+ATATTCAC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27109
FUBP3-BGKcLV08-36_CGGCGTGA+GCGCCTGT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	274				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	522
FUBP3-BGKcLV08-36_CGGCGTGA+GCGCCTGT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	274				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	592
FUBP3-BGKcLV08-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	274	GRCh38	V40	FUBP3-BGKcLV08-36_CGGCGTGA+GCGCCTGT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,FUBP3-BGKcLV08-36_CGGCGTGA+GCGCCTGT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26760
FUBP3-BGKcLV08-36_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	274	GRCh38	V40	FUBP3-BGKcLV08-36/Aligned.sortedByCoord.out.bam		ENCORE2	26830
FUBP3-BGKcLV08-36_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	274	GRCh38	V40	FUBP3-BGKcLV08-36/Aligned.sortedByCoord.out.bam		ENCORE2	26900
FUBP3-BGKcLV08-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	274	GRCh38	V40	FUBP3-BGKcLV08-36/Aligned.sortedByCoord.out.bam		ENCORE2	26970
FUBP3-BGKcLV08-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	274	GRCh38	V40	FUBP3-BGKcLV08-36/Aligned.sortedByCoord.out.bam		ENCORE2	27040
FUBP3-BGKcLV08-36_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	274	GRCh38	V40	FUBP3-BGKcLV08-36_CGGCGTGA+GCGCCTGT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,FUBP3-BGKcLV08-36_CGGCGTGA+GCGCCTGT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27110