SF3B1 RNA-Seq in HepG2

General Information


RBP	SF3B1
Cell_Line	HepG2
Method	shRNA
Exp_Name	SF3B1-BGHLV35-HepG2
ENCODE_series_ID	ENCSR144FRZ
Batch_ID	BGHLV35
Pool ID	Pool-160912
Local_Set_Name	set35
ENCODE_KD_Exp_ID	ENCSR896CFV
ENCODE_CN_Exp_ID	ENCSR264TUE
Rep1	SF3B1_BGHLV35-41
Rep2	SF3B1_BGHLV35-42
CN1	NT_BGHLV35-1
CN2	NT_BGHLV35-2
Rep1_qPCR	67.5
Rep2_qPCR	54.2
Rep1_WB	63.6
Rep2_WB	75.0
Antibody Cat#	ab66774
Antibody Lot#	ab66774
Antibody DCC ID	ENCAB022ALQ
Status	Released
Project	ENCODE3
ID	738

Experiment Information (Status: Released)

	BGHLV35-41	BGHLV35-42
idx	897	898
TRCN#_or_BGC#	TRCN0000000077	TRCN0000000077
shRNA_or_gRNA_sequence	CAACTCCTTATGGTATCGAAT	CAACTCCTTATGGTATCGAAT
PAM
Name	SF3B1	SF3B1
Sample_ID	BGHLV35-41	BGHLV35-42
transduction_Date	4/29/16	4/29/16
days
RBP_name	SF3B1	SF3B1
qPCR_result	67.5	54.2
Ave_qPCR	60.8
RT-qPCR_primer-F	ATCAAGTTGGGATCAGGCAG
RT-qPCR_primer-R	CAGGAGTCTCGCTTCCCTTT
protein_conc	3949	4558
WB_result	63.6	75.0
Ave_WB	69.3
WB_DONE_date	6/9/16	WES
MW	146kDa
IP
antibody_Cat#	ab66774	ab66774
Antibody DCC ID	ENCAB022ALQ
submitted_to_DCC_date	10/26/16
Rep1_TPM	0	0
Rep2_TPM	0	0
Action
Library_start_date	07/18/16	07/18/16
repeat_library
Note
ID	2986	2987

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SF3B1	Product_ID: ab66774 Lot_ID: GR216813-1 Source: Abcam Target Name: SF3B1-human

Experiment Status

	BGHLV35-41	BGHLV35-42
Sample_ID	BGHLV35-41	BGHLV35-42
Sample Name	SF3B1_BGHLV35-41	SF3B1_BGHLV35-42
Sample Name	SF3B1_BGHLV35-41	SF3B1_BGHLV35-42
RBP	SF3B1	SF3B1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1267	1268

Library-Prep
Sequencing

Library-Prep Information

	BGHLV35-41	BGHLV35-42
Sample #
Sample Name	SF3B1-BGHLV35-41	SF3B1-BGHLV35-42
Sample_Name_Alias	SF3B1_BGHLV35-41	SF3B1_BGHLV35-42
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-07-18	2016-07-18
Lib_ID	Lib-160718	Lib-160718
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV35/set1/C3.png	DNA_Library_LV35/set1/D3.png
RIN	9.8	10.0
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/C3.png	RNA_Library_LV35_LV36/set1/D3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV35-41	BGHLV35-42
RBP	SF3B1	SF3B1
Batch_ID	BGHLV35	BGHLV35
WB_result	63.600	75.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2952	2953

Sequencing Information

	BGHLV35-41	BGHLV35-42
Sample_ID	BGHLV35-41	BGHLV35-42
Sample Name	SF3B1_BGHLV35-41	SF3B1_BGHLV35-42
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set35	set35
total_reads	74,614,282	66,546,418
total_aligned_reads	59,195,942	51,878,748
unique_aligned_reads	55,827,944	48,929,168
percent_uniqueAligned	0.74822	0.73526
correlation_replicates	0.991679	0.991679
spikein_reads	110,394	84,302
percent_spikeins	0.00148	0.00127
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1601	1602

Data Submission Information

	BGHLV35-41	BGHLV35-41
ENCODE_alias	brenton-graveley:SF3B1_BGHLV35	brenton-graveley:SF3B1-BGHLV35-HepG2
ENCODE_accession	ENCSR896CFV	ENCSR144FRZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV35-41	BGHLV35-41
Sample Name	SF3B1_BGHLV35-41	SF3B1_BGHLV35-41
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3173	6942

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
SF3B1_BGHLV35-41_GTGGCC_L007_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1601	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21700
SF3B1_BGHLV35-41_GTGGCC_L007_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1601	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21726
SF3B1_BGHLV35-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1601					GRCh38	V40	SF3B1_BGHLV35-41_GTGGCC_L007_001.R1.fastq.gz,SF3B1_BGHLV35-41_GTGGCC_L007_001.R2.fastq.gz		ENCORE2	21752
SF3B1_BGHLV35-41_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1601					GRCh38	V40	SF3B1_BGHLV35-41/Aligned.sortedByCoord.out.bam		ENCORE2	21778
SF3B1_BGHLV35-41_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1601					GRCh38	V40	SF3B1_BGHLV35-41/Aligned.sortedByCoord.out.bam		ENCORE2	21804
SF3B1_BGHLV35-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1601					GRCh38	V40	SF3B1_BGHLV35-41/Aligned.sortedByCoord.out.bam		ENCORE2	21830
SF3B1_BGHLV35-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1601					GRCh38	V40	SF3B1_BGHLV35-41/Aligned.sortedByCoord.out.bam		ENCORE2	21856
SF3B1_BGHLV35-41_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1601					GRCh38	V40	SF3B1_BGHLV35-41_GTGGCC_L007_001.R1.fastq.gz,SF3B1_BGHLV35-41_GTGGCC_L007_001.R2.fastq.gz		ENCORE2	21882
SF3B1_BGHLV35-42_GTTTCG_L007_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1602	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21701
SF3B1_BGHLV35-42_GTTTCG_L007_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1602	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21727
SF3B1_BGHLV35-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1602					GRCh38	V40	SF3B1_BGHLV35-42_GTTTCG_L007_001.R1.fastq.gz,SF3B1_BGHLV35-42_GTTTCG_L007_001.R2.fastq.gz		ENCORE2	21753
SF3B1_BGHLV35-42_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1602					GRCh38	V40	SF3B1_BGHLV35-42/Aligned.sortedByCoord.out.bam		ENCORE2	21779
SF3B1_BGHLV35-42_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1602					GRCh38	V40	SF3B1_BGHLV35-42/Aligned.sortedByCoord.out.bam		ENCORE2	21805
SF3B1_BGHLV35-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1602					GRCh38	V40	SF3B1_BGHLV35-42/Aligned.sortedByCoord.out.bam		ENCORE2	21831
SF3B1_BGHLV35-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1602					GRCh38	V40	SF3B1_BGHLV35-42/Aligned.sortedByCoord.out.bam		ENCORE2	21857
SF3B1_BGHLV35-42_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1602					GRCh38	V40	SF3B1_BGHLV35-42_GTTTCG_L007_001.R1.fastq.gz,SF3B1_BGHLV35-42_GTTTCG_L007_001.R2.fastq.gz		ENCORE2	21883