SF3B3 RNA-Seq in HepG2

General Information


RBP	SF3B3
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SF3B3-BGHcLV34-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV34
Pool ID	Pool-220720
Local_Set_Name	set54
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	SF3B3-BGHcLV34-49
Rep2	SF3B3-BGHcLV34-50
CN1	NT-BGHcLV34-1
CN2	NT-BGHcLV34-2
Rep1_qPCR	33.3
Rep2_qPCR	37.5
Rep1_WB	73.2
Rep2_WB	75.7
Antibody Cat#	A302-508A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB290RUF
Status	Submitted
Project	ENCORE2
ID	948

Experiment Information (Status: Submitting)

	BGHcLV34-49	BGHcLV34-50
idx	1119	1120
TRCN#_or_BGC#	BGC#0000866	BGC#0000866
shRNA_or_gRNA_sequence	ACGCACTGTCCAGACAGCGT	ACGCACTGTCCAGACAGCGT
PAM	TGG	TGG
Name	SF3B3_90	SF3B3_90
Sample_ID	BGHcLV34-49	BGHcLV34-50
transduction_Date	3/24/22	3/24/22
days	D6	D6
RBP_name	SF3B3	SF3B3
qPCR_result	33.3	37.5
Ave_qPCR	35.4
RT-qPCR_primer-F	cgttcctggccagttcttag
RT-qPCR_primer-R	ccaggggagatgaaatggta
protein_conc	3046	2707
WB_result	73.2	75.7
Ave_WB	74.5
WB_DONE_date	4/12/22
MW	136kd
IP
antibody_Cat#	A302-508A	LOT #1
Antibody DCC ID	ENCAB290RUF
submitted_to_DCC_date	8/16/22
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/17/22	06/17/22
repeat_library
Note
ID	7300	7301

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SF3B2	Product_ID: A301-605A Lot_ID: 1 Source: Bethyl Labs Target Name: SF3B2-human
SF3B3	Product_ID: A302-508A Lot_ID: 1 Source: Bethyl Labs Target Name: SF3B3-human

Experiment Status

	BGHcLV34-49	BGHcLV34-50
Sample_ID	BGHcLV34-49	BGHcLV34-50
Sample Name
Sample Name	SF3B3-BGHcLV34-49	SF3B3-BGHcLV34-50
RBP	SF3B3	SF3B3
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10817	10818

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV34-49	BGHcLV34-50
Sample #	21	22
Sample Name	SF3B3-BGHcLV34-49	SF3B3-BGHcLV34-50
Sample_Name_Alias
Index Well Position	E03	F03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-06-17	2022-06-17
Lib_ID	Lib-220617	Lib-220617
Tecan_Location
Tecan
Tecan_date
Size_bp	277	289
Peak_Molarity	52.50	18.30
libSampleQC_DNA_Well	DNA_Library_set54-56/set3/E7.png	DNA_Library_set54-56/set3/F7.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set54-56/set2/E3.png	RNA_Library_set54-56/set2/F3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-06-20	2022-06-20
Sample_ID	BGHcLV34-49	BGHcLV34-50
RBP	SF3B3	SF3B3
Batch_ID	BGHcLV34	BGHcLV34
WB_result	73.200	75.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3338	3339

Sequencing Information

	BGHcLV34-49	BGHcLV34-50
Sample_ID	BGHcLV34-49	BGHcLV34-50
Sample Name	SF3B3-BGHcLV34-49	SF3B3-BGHcLV34-50
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	60,279,678	41,649,244
total_aligned_reads	50,821,460	35,629,556
unique_aligned_reads	47,827,576	33,634,462
percent_uniqueAligned	0.79343	0.80756
correlation_replicates	0.995183	0.995183
spikein_reads	3,192	4,032
percent_spikeins	0.00005	0.00010
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2211	2212

Data Submission Information DCC submission information was not avaliable

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
SF3B3-BGHcLV34-49_S17_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2211	NovaSeq6000	100	paired-ended	1				NT-BGHcLV34-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8526
SF3B3-BGHcLV34-49_S17_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2211	NovaSeq6000	100	paired-ended	2				NT-BGHcLV34-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8576
SF3B3-BGHcLV34-49_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2211					GRCh38	V40	SF3B3-BGHcLV34-49/Aligned.sortedByCoord.out.bam		ENCORE2	17772
SF3B3-BGHcLV34-49_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2211					GRCh38	V40	SF3B3-BGHcLV34-49/Aligned.sortedByCoord.out.bam		ENCORE2	17822
SF3B3-BGHcLV34-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2211					GRCh38	V40	SF3B3-BGHcLV34-49/Aligned.sortedByCoord.out.bam		ENCORE2	17872
SF3B3-BGHcLV34-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2211					GRCh38	V40	SF3B3-BGHcLV34-49/Aligned.sortedByCoord.out.bam		ENCORE2	17922
SF3B3-BGHcLV34-49_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2211					GRCh38	V40	SF3B3-BGHcLV34-49_S17_R1_001.filtered.trimmed.paired.fastq.gz,SF3B3-BGHcLV34-49_S17_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17972
SF3B3-BGHcLV34-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2211					GRCh38	V40	SF3B3-BGHcLV34-49_S17_R1_001.filtered.trimmed.paired.fastq.gz,SF3B3-BGHcLV34-49_S17_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29313
SF3B3-BGHcLV34-50_S18_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2212	NovaSeq6000	100	paired-ended	1				NT-BGHcLV34-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8527
SF3B3-BGHcLV34-50_S18_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2212	NovaSeq6000	100	paired-ended	2				NT-BGHcLV34-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8577
SF3B3-BGHcLV34-50_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2212					GRCh38	V40	SF3B3-BGHcLV34-50/Aligned.sortedByCoord.out.bam		ENCORE2	17773
SF3B3-BGHcLV34-50_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2212					GRCh38	V40	SF3B3-BGHcLV34-50/Aligned.sortedByCoord.out.bam		ENCORE2	17823
SF3B3-BGHcLV34-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2212					GRCh38	V40	SF3B3-BGHcLV34-50/Aligned.sortedByCoord.out.bam		ENCORE2	17873
SF3B3-BGHcLV34-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2212					GRCh38	V40	SF3B3-BGHcLV34-50/Aligned.sortedByCoord.out.bam		ENCORE2	17923
SF3B3-BGHcLV34-50_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2212					GRCh38	V40	SF3B3-BGHcLV34-50_S18_R1_001.filtered.trimmed.paired.fastq.gz,SF3B3-BGHcLV34-50_S18_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17973
SF3B3-BGHcLV34-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2212					GRCh38	V40	SF3B3-BGHcLV34-50_S18_R1_001.filtered.trimmed.paired.fastq.gz,SF3B3-BGHcLV34-50_S18_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29314