SF3B4 RNA-Seq in HepG2

General Information


RBP	SF3B4
Cell_Line	HepG2
Method	shRNA
Exp_Name	SF3B4-BGHLV12-HepG2
ENCODE_series_ID	ENCSR617SJU
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR148MQK
ENCODE_CN_Exp_ID	ENCSR603TCV
Rep1	SF3B4-BGHLV12-73
Rep2	SF3B4-BGHLV12-74
CN1	NT-BGHLV12-93
CN2	NT-BGHLV12-94
Rep1_qPCR	67.8
Rep2_qPCR	58.5
Rep1_WB	70.3
Rep2_WB	52.8
Antibody Cat#	A303-950A
Antibody Lot#	A303-950A
Antibody DCC ID	ENCAB647CFU
Status	Released
Project	ENCODE3
ID	353

Experiment Information (Status: Released)

	BGHLV12-73	BGHLV12-74
idx	73	74
TRCN#_or_BGC#	TRCN0000000039	TRCN0000000039
shRNA_or_gRNA_sequence	CCGTCCTATCACCGTATCTTA	CCGTCCTATCACCGTATCTTA
PAM
Name	SF3B4	SF3B4
Sample_ID	BGHLV12-73	BGHLV12-74
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	SF3B4	SF3B4
qPCR_result	67.8	58.5
Ave_qPCR	63.2
RT-qPCR_primer-F	acccacatgccaaaggatag
RT-qPCR_primer-R	tggcatagtcagcatcttcc
protein_conc	2869	2478
WB_result	70.3	52.8
Ave_WB	61.6
WB_DONE_date	3/2/2016
MW	44kDa
IP	1	1
antibody_Cat#	A303-950A	A303-950A
Antibody DCC ID	ENCAB647CFU	ENCAB647CFU
submitted_to_DCC_date	3/8/2015
Rep1_TPM	4.8	0
Rep2_TPM	4	0
Action
Library_start_date	6/12/2014	6/12/2014
repeat_library
Note
ID	2128	2129

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SF3B4	Product_ID: A303-950A Lot_ID: 1 Source: Bethyl Labs Target Name: SF3B4-human

Experiment Status

	BGHLV12-73	BGHLV12-74
Sample_ID	BGHLV12-73	BGHLV12-74
Sample Name	SF3B4-BGHLV12-73	SF3B4-BGHLV12-74
Sample Name	SF3B4-BGHLV12-73	SF3B4-BGHLV12-74
RBP	SF3B4	SF3B4
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	426	427

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-73	BGHLV12-74
Sample #
Sample Name	SF3B4-BGHLV12-73	SF3B4-BGHLV12-74
Sample_Name_Alias	SF3B4-BGHLV12-73	SF3B4-BGHLV12-74
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-12	2014-06-12
Lib_ID	Lib-140612	Lib-140612
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set3/G3.png	DNA_Library_LV12/set3/H3.png
RIN	9.6	9.4
libSample_RNA_Well	RNA_Library_LV12/set1/G7.png	RNA_Library_LV12/set1/H7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-73	BGHLV12-74
RBP	SF3B4	SF3B4
Batch_ID	BGHLV12	BGHLV12
WB_result	70.300	52.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2050	2051

Sequencing Information

	BGHLV12-73	BGHLV12-74
Sample_ID	BGHLV12-73	BGHLV12-74
Sample Name	SF3B4-BGHLV12-73	SF3B4-BGHLV12-74
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	71,770,000	65,240,000
total_aligned_reads	66,278,186	59,629,166
unique_aligned_reads	62,570,518	56,297,462
percent_uniqueAligned	0.87182	0.86293
correlation_replicates	0.999066	0.999066
spikein_reads	358,508	278,958
percent_spikeins	0.00500	0.00428
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	748	749

Data Submission Information

	BGHLV12-73	BGHLV12-73
ENCODE_alias	brenton-graveley:SF3B4-BGHLV12	brenton-graveley:SF3B4-BGHLV12-HepG2
ENCODE_accession	ENCSR148MQK	ENCSR617SJU
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-73	BGHLV12-73
Sample Name	SF3B4-BGHLV12-73	SF3B4-BGHLV12-73
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2762	6944

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
SF3B4-BGHLV12-73_CAGATC_L008_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	748	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12809
SF3B4-BGHLV12-73_CAGATC_L008_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	748	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12878
SF3B4-BGHLV12-73_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	748					GRCh38	V40	SF3B4-BGHLV12-73_CAGATC_L008_R1_001.fastq.gz,SF3B4-BGHLV12-73_CAGATC_L008_R2_001.fastq.gz		ENCORE2	12948
SF3B4-BGHLV12-73_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	748					GRCh38	V40	SF3B4-BGHLV12-73/Aligned.sortedByCoord.out.bam		ENCORE2	13018
SF3B4-BGHLV12-73_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	748					GRCh38	V40	SF3B4-BGHLV12-73/Aligned.sortedByCoord.out.bam		ENCORE2	13088
SF3B4-BGHLV12-73_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	748					GRCh38	V40	SF3B4-BGHLV12-73/Aligned.sortedByCoord.out.bam		ENCORE2	13158
SF3B4-BGHLV12-73_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	748					GRCh38	V40	SF3B4-BGHLV12-73/Aligned.sortedByCoord.out.bam		ENCORE2	13228
SF3B4-BGHLV12-73_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	748					GRCh38	V40	SF3B4-BGHLV12-73_CAGATC_L008_R1_001.fastq.gz,SF3B4-BGHLV12-73_CAGATC_L008_R2_001.fastq.gz		ENCORE2	13298
SF3B4-BGHLV12-74_ACTTGA_L008_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	749	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12810
SF3B4-BGHLV12-74_ACTTGA_L008_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	749	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12879
SF3B4-BGHLV12-74_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	749					GRCh38	V40	SF3B4-BGHLV12-74_ACTTGA_L008_R1_001.fastq.gz,SF3B4-BGHLV12-74_ACTTGA_L008_R2_001.fastq.gz		ENCORE2	12949
SF3B4-BGHLV12-74_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	749					GRCh38	V40	SF3B4-BGHLV12-74/Aligned.sortedByCoord.out.bam		ENCORE2	13019
SF3B4-BGHLV12-74_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	749					GRCh38	V40	SF3B4-BGHLV12-74/Aligned.sortedByCoord.out.bam		ENCORE2	13089
SF3B4-BGHLV12-74_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	749					GRCh38	V40	SF3B4-BGHLV12-74/Aligned.sortedByCoord.out.bam		ENCORE2	13159
SF3B4-BGHLV12-74_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	749					GRCh38	V40	SF3B4-BGHLV12-74/Aligned.sortedByCoord.out.bam		ENCORE2	13229
SF3B4-BGHLV12-74_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	749					GRCh38	V40	SF3B4-BGHLV12-74_ACTTGA_L008_R1_001.fastq.gz,SF3B4-BGHLV12-74_ACTTGA_L008_R2_001.fastq.gz		ENCORE2	13299