SUPV3L1 RNA-Seq in HepG2

General Information


RBP	SUPV3L1
Cell_Line	HepG2
Method	shRNA
Exp_Name	SUPV3L1-BGHLV17-HepG2
ENCODE_series_ID	ENCSR283KPR
Batch_ID	BGHLV17
Pool ID	Pool-141001
Local_Set_Name	set17
ENCODE_KD_Exp_ID	ENCSR995RPB
ENCODE_CN_Exp_ID	ENCSR856ZRV
Rep1	SUPV3L1_BGHLV17_31
Rep2	SUPV3L1_BGHLV17_32
CN1	NT_BGHLV17_63
CN2	NT_BGHLV17_64
Rep1_qPCR	71.4
Rep2_qPCR	76.8
Rep1_WB	73.5
Rep2_WB	62.4
Antibody Cat#	A303-056A
Antibody Lot#	A303-056A
Antibody DCC ID	ENCAB067CNB
Status	Released
Project	ENCODE3
ID	439

Experiment Information (Status: Released)

	BGHLV17-31	BGHLV17-32
idx	267	268
TRCN#_or_BGC#	TRCN0000050349	TRCN0000050349
shRNA_or_gRNA_sequence	CCGATACATCAAATGGCCTTT	CCGATACATCAAATGGCCTTT
PAM
Name	SUPV3L1	SUPV3L1
Sample_ID	BGHLV17-31	BGHLV17-32
transduction_Date	8/19/2014	8/19/2014
days
RBP_name	SUPV3L1	SUPV3L1
qPCR_result	71.4	76.8
Ave_qPCR	74.1
RT-qPCR_primer-F	caaatgggaaacaggcttca
RT-qPCR_primer-R	catcctctggctggatctct
protein_conc	1926	1619
WB_result	73.5	62.4
Ave_WB	68.0
WB_DONE_date	1/20/2015
MW	88kDa
IP	1	1
antibody_Cat#	A303-056A	A303-056A
Antibody DCC ID	ENCAB067CNB	ENCAB067CNB
submitted_to_DCC_date	4/2/2015
Rep1_TPM	23	0
Rep2_TPM	18.7	0
Action
Library_start_date	9/26/2014	9/26/2014
repeat_library
Note
ID	2332	2333

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SUPV3L1	Product_ID: A303-056A Lot_ID: 1 Source: Bethyl Labs Target Name: SUPV3L1-human

Experiment Status

	BGHLV17-31	BGHLV17-32
Sample_ID	BGHLV17-31	BGHLV17-32
Sample Name	SUPV3L1_BGHLV17_31	SUPV3L1_BGHLV17_32
Sample Name	SUPV3L1_BGHLV17_31	SUPV3L1_BGHLV17_32
RBP	SUPV3L1	SUPV3L1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	606	607

Library-Prep
Sequencing

Library-Prep Information

	BGHLV17-31	BGHLV17-32
Sample #
Sample Name	SUPV3L1-BGHLV17-31	SUPV3L1-BGHLV17-32
Sample_Name_Alias	SUPV3L1_BGHLV17_31	SUPV3L1_BGHLV17_32
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-26	2014-09-26
Lib_ID	Lib-140926	Lib-140926
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/C3.png	DNA_Library_LV16-17/set1/D3.png
RIN	9.2	9.4
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/C5.png	RNA_Library_LV16-17-18/set1/D5.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV17-31	BGHLV17-32
RBP	SUPV3L1	SUPV3L1
Batch_ID	BGHLV17	BGHLV17
WB_result	73.500	62.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2290	2291

Sequencing Information

	BGHLV17-31	BGHLV17-32
Sample_ID	BGHLV17-31	BGHLV17-32
Sample Name	SUPV3L1_BGHLV17_31	SUPV3L1_BGHLV17_32
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set17	set17
total_reads	81,970,000	62,100,000
total_aligned_reads	73,192,670	55,049,612
unique_aligned_reads	69,169,932	52,047,836
percent_uniqueAligned	0.84384	0.83813
correlation_replicates	0.993132	0.993132
spikein_reads	274,562	182,736
percent_spikeins	0.00335	0.00294
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	932	933

Data Submission Information

	BGHLV17-31	BGHLV17-31
ENCODE_alias	brenton-graveley:SUPV3L1_BGHLV17	brenton-graveley:SUPV3L1-BGHLV17-HepG2
ENCODE_accession	ENCSR995RPB	ENCSR283KPR
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV17-31	BGHLV17-31
Sample Name	SUPV3L1_BGHLV17_31	SUPV3L1_BGHLV17_31
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2870	6996

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
SUPV3L1_BGHLV17_31_GTGGCC_L003_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	932	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14514
SUPV3L1_BGHLV17_31_GTGGCC_L003_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	932	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14552
SUPV3L1_BGHLV17_31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	932					GRCh38	V40	SUPV3L1_BGHLV17_31_GTGGCC_L003_R1_001.fastq.gz,SUPV3L1_BGHLV17_31_GTGGCC_L003_R2_001.fastq.gz		ENCORE2	14590
SUPV3L1_BGHLV17_31_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	932					GRCh38	V40	SUPV3L1_BGHLV17_31/Aligned.sortedByCoord.out.bam		ENCORE2	14628
SUPV3L1_BGHLV17_31_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	932					GRCh38	V40	SUPV3L1_BGHLV17_31/Aligned.sortedByCoord.out.bam		ENCORE2	14666
SUPV3L1_BGHLV17_31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	932					GRCh38	V40	SUPV3L1_BGHLV17_31/Aligned.sortedByCoord.out.bam		ENCORE2	14704
SUPV3L1_BGHLV17_31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	932					GRCh38	V40	SUPV3L1_BGHLV17_31/Aligned.sortedByCoord.out.bam		ENCORE2	14742
SUPV3L1_BGHLV17_31_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	932					GRCh38	V40	SUPV3L1_BGHLV17_31_GTGGCC_L003_R1_001.fastq.gz,SUPV3L1_BGHLV17_31_GTGGCC_L003_R2_001.fastq.gz		ENCORE2	14780
SUPV3L1_BGHLV17_32_GTTTCG_L003_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	933	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14515
SUPV3L1_BGHLV17_32_GTTTCG_L003_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	933	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14553
SUPV3L1_BGHLV17_32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	933					GRCh38	V40	SUPV3L1_BGHLV17_32_GTTTCG_L003_R1_001.fastq.gz,SUPV3L1_BGHLV17_32_GTTTCG_L003_R2_001.fastq.gz		ENCORE2	14591
SUPV3L1_BGHLV17_32_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	933					GRCh38	V40	SUPV3L1_BGHLV17_32/Aligned.sortedByCoord.out.bam		ENCORE2	14629
SUPV3L1_BGHLV17_32_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	933					GRCh38	V40	SUPV3L1_BGHLV17_32/Aligned.sortedByCoord.out.bam		ENCORE2	14667
SUPV3L1_BGHLV17_32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	933					GRCh38	V40	SUPV3L1_BGHLV17_32/Aligned.sortedByCoord.out.bam		ENCORE2	14705
SUPV3L1_BGHLV17_32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	933					GRCh38	V40	SUPV3L1_BGHLV17_32/Aligned.sortedByCoord.out.bam		ENCORE2	14743
SUPV3L1_BGHLV17_32_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	933					GRCh38	V40	SUPV3L1_BGHLV17_32_GTTTCG_L003_R1_001.fastq.gz,SUPV3L1_BGHLV17_32_GTTTCG_L003_R2_001.fastq.gz		ENCORE2	14781