SUPT6H RNA-Seq in HepG2

General Information


RBP	SUPT6H
Cell_Line	HepG2
Method	shRNA
Exp_Name	SUPT6H-BGHLV30-HepG2
ENCODE_series_ID	ENCSR198CNS
Batch_ID	BGHLV30
Pool ID	Pool-151215B
Local_Set_Name	set30
ENCODE_KD_Exp_ID	ENCSR281KCL
ENCODE_CN_Exp_ID	ENCSR067GHD
Rep1	SUPT6H_BGHLV30-53
Rep2	SUPT6H_BGHLV30-54
CN1	NT_BGHLV30-1
CN2	NT_BGHLV30-2
Rep1_qPCR	76.7
Rep2_qPCR	76.3
Rep1_WB	83.4
Rep2_WB	89.4
Antibody Cat#	A300-801A
Antibody Lot#	A300-801A
Antibody DCC ID	ENCAB683FFM
Status	Released
Project	ENCODE3
ID	688

Experiment Information (Status: Released)

	BGHLV30-53	BGHLV30-53	BGHLV30-54	BGHLV30-54
idx	741	741	742	742
TRCN#_or_BGC#	TRCN0000019733	TRCN0000019733	TRCN0000019733	TRCN0000019733
shRNA_or_gRNA_sequence	CCAACCGTGAATGGACTGTTT	CCAACCGTGAATGGACTGTTT	CCAACCGTGAATGGACTGTTT	CCAACCGTGAATGGACTGTTT
PAM
Name	SUPT6H	SUPT6H	SUPT6H	SUPT6H
Sample_ID	BGHLV30-53	BGHLV30-53	BGHLV30-54	BGHLV30-54
transduction_Date	8/25/2015	8/25/2015	8/25/2015	8/25/2015
days
RBP_name	SUPT6H	SUPT6H	SUPT6H	SUPT6H
qPCR_result	76.7	76.7	76.3	76.3
Ave_qPCR	76.5	76.5
RT-qPCR_primer-F	CGGCAAGTTCCTACTGGGAT	CGGCAAGTTCCTACTGGGAT
RT-qPCR_primer-R	TACCGGAATCCCTCTGGAGT	TACCGGAATCCCTCTGGAGT
protein_conc	4652	4652	3948	3948
WB_result	83.4	88.9	89.4	77.4
Ave_WB	86.4	83.1
WB_DONE_date	9/16/2015	6/28/2023
MW	199kDa	199kDa
IP
antibody_Cat#	A300-801A	15616S	A300-801A	lot # 1
Antibody DCC ID	ENCAB683FFM		ENCAB683FFM
submitted_to_DCC_date	12/7/2015	1/8/2024
Rep1_TPM	75.7	0	0	0
Rep2_TPM	57.9	0	0	0
Action
Library_start_date	11/5/2015		11/5/2015
repeat_library
Note	x		x
ID	2828	2830	2829	2831

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SUPT6H	Product_ID: A300-801A Lot_ID: 1 Source: Bethyl Labs Target Name: SUPT6H-human
SUPT6H	Product_ID: 15616S Lot_ID: 1 Source: Cell Signaling Technology Target Name: SUPT6H-human

Experiment Status

	BGHLV30-53	BGHLV30-54
Sample_ID	BGHLV30-53	BGHLV30-54
Sample Name	SUPT6H_BGHLV30-53	SUPT6H_BGHLV30-54
Sample Name	SUPT6H_BGHLV30-53	SUPT6H_BGHLV30-54
RBP	SUPT6H	SUPT6H
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-04	2016-03-04
Project	ENCODE3	ENCODE3
Note
ID	1068	1069

Library-Prep
Sequencing

Library-Prep Information

	BGHLV30-53	BGHLV30-54
Sample #
Sample Name	SUPT6H-BGHLV30-53	SUPT6H-BGHLV30-54
Sample_Name_Alias	SUPT6H_BGHLV30-53	SUPT6H_BGHLV30-54
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-05	2015-11-05
Lib_ID	Lib-151105	Lib-151105
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/C12.png	DNA_Library_LV28-29-30/set1/D12.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/E7.png	RNA_Library_LV29-30-31-32/set1/F7.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV30-53	BGHLV30-54
RBP	SUPT6H	SUPT6H
Batch_ID	BGHLV30	BGHLV30
WB_result	83.400	89.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2760	2761

Sequencing Information

	BGHLV30-53	BGHLV30-54
Sample_ID	BGHLV30-53	BGHLV30-54
Sample Name	SUPT6H_BGHLV30-53	SUPT6H_BGHLV30-54
Pool ID	Pool-151215B	Pool-151215B
LocalServer_folder	set30	set30
total_reads	48,325,292	75,799,870
total_aligned_reads	42,764,362	68,395,190
unique_aligned_reads	40,510,070	64,753,980
percent_uniqueAligned	0.83828	0.85428
correlation_replicates	0.999429	0.999429
spikein_reads	134,732	229,418
percent_spikeins	0.00279	0.00303
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1409	1410

Data Submission Information

	BGHLV30-53	BGHLV30-53
ENCODE_alias	brenton-graveley:SUPT6H_BGHLV30	brenton-graveley:SUPT6H-BGHLV30-HepG2
ENCODE_accession	ENCSR281KCL	ENCSR198CNS
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV30-53	BGHLV30-53
Sample Name	SUPT6H_BGHLV30-53	SUPT6H_BGHLV30-53
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3083	6994

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
SUPT6H_BGHLV30-53_GTGGCC_L004_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1409	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20728
SUPT6H_BGHLV30-53_GTGGCC_L004_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1409	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20762
SUPT6H_BGHLV30-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1409					GRCh38	V40	SUPT6H_BGHLV30-53_GTGGCC_L004_001.R1.fastq.gz,SUPT6H_BGHLV30-53_GTGGCC_L004_001.R2.fastq.gz		ENCORE2	20796
SUPT6H_BGHLV30-53_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1409					GRCh38	V40	SUPT6H_BGHLV30-53/Aligned.sortedByCoord.out.bam		ENCORE2	20830
SUPT6H_BGHLV30-53_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1409					GRCh38	V40	SUPT6H_BGHLV30-53/Aligned.sortedByCoord.out.bam		ENCORE2	20864
SUPT6H_BGHLV30-53_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1409					GRCh38	V40	SUPT6H_BGHLV30-53/Aligned.sortedByCoord.out.bam		ENCORE2	20898
SUPT6H_BGHLV30-53_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1409					GRCh38	V40	SUPT6H_BGHLV30-53/Aligned.sortedByCoord.out.bam		ENCORE2	20932
SUPT6H_BGHLV30-53_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1409					GRCh38	V40	SUPT6H_BGHLV30-53_GTGGCC_L004_001.R1.fastq.gz,SUPT6H_BGHLV30-53_GTGGCC_L004_001.R2.fastq.gz		ENCORE2	20966
SUPT6H_BGHLV30-54_GTTTCG_L004_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1410	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20729
SUPT6H_BGHLV30-54_GTTTCG_L004_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1410	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20763
SUPT6H_BGHLV30-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1410					GRCh38	V40	SUPT6H_BGHLV30-54_GTTTCG_L004_001.R1.fastq.gz,SUPT6H_BGHLV30-54_GTTTCG_L004_001.R2.fastq.gz		ENCORE2	20797
SUPT6H_BGHLV30-54_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1410					GRCh38	V40	SUPT6H_BGHLV30-54/Aligned.sortedByCoord.out.bam		ENCORE2	20831
SUPT6H_BGHLV30-54_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1410					GRCh38	V40	SUPT6H_BGHLV30-54/Aligned.sortedByCoord.out.bam		ENCORE2	20865
SUPT6H_BGHLV30-54_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1410					GRCh38	V40	SUPT6H_BGHLV30-54/Aligned.sortedByCoord.out.bam		ENCORE2	20899
SUPT6H_BGHLV30-54_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1410					GRCh38	V40	SUPT6H_BGHLV30-54/Aligned.sortedByCoord.out.bam		ENCORE2	20933
SUPT6H_BGHLV30-54_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1410					GRCh38	V40	SUPT6H_BGHLV30-54_GTTTCG_L004_001.R1.fastq.gz,SUPT6H_BGHLV30-54_GTTTCG_L004_001.R2.fastq.gz		ENCORE2	20967