ASCC1 RNA-Seq in HepG2

General Information


RBP	ASCC1
Cell_Line	HepG2
Method	shRNA
Exp_Name	ASCC1-BGHLV12-HepG2
ENCODE_series_ID	ENCSR398ILX
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR193FFA
ENCODE_CN_Exp_ID	ENCSR237YZT
Rep1	ASCC1-BGHLV12-5
Rep2	ASCC--BGHLV12-6
CN1	NT-BGHLV12-01
CN2	NT-BGHLV12-02
Rep1_qPCR	95.7
Rep2_qPCR	95.4
Rep1_WB	52.6
Rep2_WB	78.4
Antibody Cat#	A303-871A
Antibody Lot#	A303-871A
Antibody DCC ID	ENCAB122UGS
Status	Released
Project	ENCODE3
ID	330

Experiment Information (Status: Released)

	BGHLV12-5	BGHLV12-6
idx	5	6
TRCN#_or_BGC#	TRCN0000136137	TRCN0000136137
shRNA_or_gRNA_sequence	GAATCATTTGATGGCCGAAAT	GAATCATTTGATGGCCGAAAT
PAM
Name	ASCC1	ASCC1
Sample_ID	BGHLV12-5	BGHLV12-6
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	ASCC1	ASCC1
qPCR_result	95.7	95.4
Ave_qPCR	95.6
RT-qPCR_primer-F	gaaagaccccaatgctgaag
RT-qPCR_primer-R	cggccatcaaatgattctct
protein_conc	2929	2868
WB_result	52.6	78.4
Ave_WB	65.5
WB_DONE_date	1/21/2015
MW	46kDa
IP	1	1
antibody_Cat#	A303-871A	A303-871A
Antibody DCC ID	ENCAB122UGS	ENCAB122UGS
submitted_to_DCC_date	5/4/2015
Rep1_TPM	6.5	0
Rep2_TPM	5.8	0
Action
Library_start_date	6/9/2014	6/9/2014
repeat_library
Note
ID	2052	2053

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ASCC1	Product_ID: A303-871A Lot_ID: 1 Source: Bethyl Labs Target Name: ASCC1-human

Experiment Status

	BGHLV12-5	BGHLV12-6
Sample_ID	BGHLV12-5	BGHLV12-6
Sample Name	ASCC1-BGHLV12-5	ASCC--BGHLV12-6
Sample Name	ASCC1-BGHLV12-5	ASCC--BGHLV12-6
RBP	ASCC1	ASCC1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	374	375

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-5	BGHLV12-6
Sample #
Sample Name	ASCC1-BGHLV12-5	ASCC1-BGHLV12-6
Sample_Name_Alias	ASCC1-BGHLV12-5	ASCC--BGHLV12-6
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-09	2014-06-09
Lib_ID	Lib-140609	Lib-140609
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set1/E1.png	DNA_Library_LV12/set1/F1.png
RIN	8.7	8.8
libSample_RNA_Well	RNA_Library_LV12/set1/E1.png	RNA_Library_LV12/set1/F1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-5	BGHLV12-6
RBP	ASCC1	ASCC1
Batch_ID	BGHLV12	BGHLV12
WB_result	52.600	78.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1996	1997

Sequencing Information

	BGHLV12-5	BGHLV12-6
Sample_ID	BGHLV12-5	BGHLV12-6
Sample Name	ASCC1-BGHLV12-5	ASCC--BGHLV12-6
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	64,200,000	65,070,000
total_aligned_reads	56,993,960	59,916,724
unique_aligned_reads	53,990,348	56,801,766
percent_uniqueAligned	0.84097	0.87293
correlation_replicates	0.997566	0.997566
spikein_reads	539,484	593,888
percent_spikeins	0.00840	0.00913
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	696	697

Data Submission Information

	BGHLV12-5	BGHLV12-5
ENCODE_alias	brenton-graveley:ASCC1-BGHLV12	brenton-graveley:ASCC1-BGHLV12-HepG2
ENCODE_accession	ENCSR193FFA	ENCSR398ILX
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-5	BGHLV12-5
Sample Name	ASCC1-BGHLV12-5	ASCC1-BGHLV12-5
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2736	6594

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
ASCC1-BGHLV12-5_ACAGTG_L001_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	696	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12753
ASCC1-BGHLV12-5_ACAGTG_L001_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	696	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12822
ASCC1-BGHLV12-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	696					GRCh38	V40	ASCC1-BGHLV12-5_ACAGTG_L001_R1_001.fastq.gz,ASCC1-BGHLV12-5_ACAGTG_L001_R2_001.fastq.gz		ENCORE2	12892
ASCC1-BGHLV12-5_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	696					GRCh38	V40	ASCC1-BGHLV12-5/Aligned.sortedByCoord.out.bam		ENCORE2	12962
ASCC1-BGHLV12-5_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	696					GRCh38	V40	ASCC1-BGHLV12-5/Aligned.sortedByCoord.out.bam		ENCORE2	13032
ASCC1-BGHLV12-5_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	696					GRCh38	V40	ASCC1-BGHLV12-5/Aligned.sortedByCoord.out.bam		ENCORE2	13102
ASCC1-BGHLV12-5_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	696					GRCh38	V40	ASCC1-BGHLV12-5/Aligned.sortedByCoord.out.bam		ENCORE2	13172
ASCC1-BGHLV12-5_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	696					GRCh38	V40	ASCC1-BGHLV12-5_ACAGTG_L001_R1_001.fastq.gz,ASCC1-BGHLV12-5_ACAGTG_L001_R2_001.fastq.gz		ENCORE2	13242
ASCC--BGHLV12-6_GCCAAT_L001_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	697	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12754
ASCC--BGHLV12-6_GCCAAT_L001_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	697	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12823
ASCC--BGHLV12-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	697					GRCh38	V40	ASCC--BGHLV12-6_GCCAAT_L001_R1_001.fastq.gz,ASCC--BGHLV12-6_GCCAAT_L001_R2_001.fastq.gz		ENCORE2	12893
ASCC--BGHLV12-6_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	697					GRCh38	V40	ASCC--BGHLV12-6/Aligned.sortedByCoord.out.bam		ENCORE2	12963
ASCC--BGHLV12-6_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	697					GRCh38	V40	ASCC--BGHLV12-6/Aligned.sortedByCoord.out.bam		ENCORE2	13033
ASCC--BGHLV12-6_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	697					GRCh38	V40	ASCC--BGHLV12-6/Aligned.sortedByCoord.out.bam		ENCORE2	13103
ASCC--BGHLV12-6_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	697					GRCh38	V40	ASCC--BGHLV12-6/Aligned.sortedByCoord.out.bam		ENCORE2	13173
ASCC--BGHLV12-6_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	697					GRCh38	V40	ASCC--BGHLV12-6_GCCAAT_L001_R1_001.fastq.gz,ASCC--BGHLV12-6_GCCAAT_L001_R2_001.fastq.gz		ENCORE2	13243