SUB1 RNA-Seq in HepG2

General Information


RBP	SUB1
Cell_Line	HepG2
Method	shRNA
Exp_Name	SUB1-BGHLV14-HepG2
ENCODE_series_ID	ENCSR344MNS
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR997FOT
ENCODE_CN_Exp_ID	ENCSR491FOC
Rep1	SUB1_BGHLV14-57
Rep2	SUB1_BGHLV14-58
CN1	NT_BGHLV14-1
CN2	NT_BGHLV14-2
Rep1_qPCR	94.0
Rep2_qPCR	95.1
Rep1_WB	84.6
Rep2_WB	76.3
Antibody Cat#	A301-161A
Antibody Lot#	A301-161A
Antibody DCC ID	ENCAB835QRD
Status	Released
Project	ENCODE3
ID	408

Experiment Information (Status: Released)

	BGHLV14-57	BGHLV14-58
idx	153	154
TRCN#_or_BGC#	TRCN0000014970	TRCN0000014970
shRNA_or_gRNA_sequence	GTACGTTAGTGTTCGCGATTT	GTACGTTAGTGTTCGCGATTT
PAM
Name	SUB1	SUB1
Sample_ID	BGHLV14-57	BGHLV14-58
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	SUB1	SUB1
qPCR_result	94.0	95.1
Ave_qPCR	94.6
RT-qPCR_primer-F	tcgcgattttaaaggcaaag
RT-qPCR_primer-R	ctggctccattgttctggat
protein_conc	3584	3377
WB_result	84.6	76.3
Ave_WB	80.4
WB_DONE_date	6/10/2015
MW	14kDa
IP	1	1
antibody_Cat#	A301-161A	A301-161A
Antibody DCC ID	ENCAB835QRD	ENCAB835QRD
submitted_to_DCC_date	8/6/2015
Rep1_TPM	29.8	0
Rep2_TPM	24.6	0
Action
Library_start_date	8/12/2014	8/12/2014
repeat_library
Note
ID	2216	2217

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SUB1	Product_ID: A301-161A Lot_ID: 1 Source: Bethyl Labs Target Name: SUB1-human

Experiment Status

	BGHLV14-57	BGHLV14-58
Sample_ID	BGHLV14-57	BGHLV14-58
Sample Name	SUB1_BGHLV14-57	SUB1_BGHLV14-58
Sample Name	SUB1_BGHLV14-57	SUB1_BGHLV14-58
RBP	SUB1	SUB1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	540	541

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-57	BGHLV14-58
Sample #
Sample Name	SUB1-BGHLV14-57	SUB1-BGHLV14-58
Sample_Name_Alias	SUB1_BGHLV14-57	SUB1_BGHLV14-58
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-08-12	2014-08-12
Lib_ID	Lib-140812	Lib-140812
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set2/C2.png	DNA_Library_LV13-14/set2/D2.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/C10.png	RNA_Library_LV13-14-16/set1/D10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-57	BGHLV14-58
RBP	SUB1	SUB1
Batch_ID	BGHLV14	BGHLV14
WB_result	84.600	76.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2224	2225

Sequencing Information

	BGHLV14-57	BGHLV14-58
Sample_ID	BGHLV14-57	BGHLV14-58
Sample Name	SUB1_BGHLV14-57	SUB1_BGHLV14-58
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	52,580,000	43,740,000
total_aligned_reads	48,678,548	39,580,018
unique_aligned_reads	46,126,874	37,474,776
percent_uniqueAligned	0.87727	0.85676
correlation_replicates	0.997755	0.997755
spikein_reads	167,598	264,630
percent_spikeins	0.00319	0.00605
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	866	867

Data Submission Information

	BGHLV14-57	BGHLV14-57
ENCODE_alias	brenton-graveley:SUB1_BGHLV14	brenton-graveley:SUB1-BGHLV14-HepG2
ENCODE_accession	ENCSR997FOT	ENCSR344MNS
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-57	BGHLV14-57
Sample Name	SUB1_BGHLV14-57	SUB1_BGHLV14-57
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2819	6988

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
SUB1_BGHLV14-57_GATCAG_L007_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	866	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13832
SUB1_BGHLV14-57_GATCAG_L007_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	866	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13894
SUB1_BGHLV14-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	866					GRCh38	V40	SUB1_BGHLV14-57_GATCAG_L007_R1_001.fastq.gz,SUB1_BGHLV14-57_GATCAG_L007_R2_001.fastq.gz		ENCORE2	13956
SUB1_BGHLV14-57_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	866					GRCh38	V40	SUB1_BGHLV14-57/Aligned.sortedByCoord.out.bam		ENCORE2	14018
SUB1_BGHLV14-57_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	866					GRCh38	V40	SUB1_BGHLV14-57/Aligned.sortedByCoord.out.bam		ENCORE2	14080
SUB1_BGHLV14-57_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	866					GRCh38	V40	SUB1_BGHLV14-57/Aligned.sortedByCoord.out.bam		ENCORE2	14142
SUB1_BGHLV14-57_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	866					GRCh38	V40	SUB1_BGHLV14-57/Aligned.sortedByCoord.out.bam		ENCORE2	14204
SUB1_BGHLV14-57_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	866					GRCh38	V40	SUB1_BGHLV14-57_GATCAG_L007_R1_001.fastq.gz,SUB1_BGHLV14-57_GATCAG_L007_R2_001.fastq.gz		ENCORE2	14266
SUB1_BGHLV14-58_TAGCTT_L007_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	867	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13833
SUB1_BGHLV14-58_TAGCTT_L007_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	867	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13895
SUB1_BGHLV14-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	867					GRCh38	V40	SUB1_BGHLV14-58_TAGCTT_L007_R1_001.fastq.gz,SUB1_BGHLV14-58_TAGCTT_L007_R2_001.fastq.gz		ENCORE2	13957
SUB1_BGHLV14-58_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	867					GRCh38	V40	SUB1_BGHLV14-58/Aligned.sortedByCoord.out.bam		ENCORE2	14019
SUB1_BGHLV14-58_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	867					GRCh38	V40	SUB1_BGHLV14-58/Aligned.sortedByCoord.out.bam		ENCORE2	14081
SUB1_BGHLV14-58_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	867					GRCh38	V40	SUB1_BGHLV14-58/Aligned.sortedByCoord.out.bam		ENCORE2	14143
SUB1_BGHLV14-58_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	867					GRCh38	V40	SUB1_BGHLV14-58/Aligned.sortedByCoord.out.bam		ENCORE2	14205
SUB1_BGHLV14-58_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	867					GRCh38	V40	SUB1_BGHLV14-58_TAGCTT_L007_R1_001.fastq.gz,SUB1_BGHLV14-58_TAGCTT_L007_R2_001.fastq.gz		ENCORE2	14267