RAVER1 RNA-Seq in HepG2

General Information


RBP	RAVER1
Cell_Line	HepG2
Method	shRNA
Exp_Name	RAVER1-BGHLV14-HepG2
ENCODE_series_ID	ENCSR998CDN
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR576GOW
ENCODE_CN_Exp_ID	ENCSR491FOC
Rep1	RAVER1_BGHLV14-33
Rep2	RAVER1_BGHLV14-34
CN1	NT_BGHLV14-1
CN2	NT_BGHLV14-2
Rep1_qPCR	89.5
Rep2_qPCR	82.0
Rep1_WB	no clear band
Rep2_WB	no clear band
Antibody Cat#	A303-939A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB846NHA
Status	Released
Project	ENCODE3
ID	399

Experiment Information (Status: Released)

	BGHLV14-33	BGHLV14-34
idx	129	130
TRCN#_or_BGC#	TRCN0000074623	TRCN0000074623
shRNA_or_gRNA_sequence	GCCTCATTGCTCCTGTAATTT	GCCTCATTGCTCCTGTAATTT
PAM
Name	RAVER1	RAVER1
Sample_ID	BGHLV14-33	BGHLV14-34
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	RAVER1	RAVER1
qPCR_result	89.5	82.0
Ave_qPCR	85.8
RT-qPCR_primer-F	GTCCGGAGAAGGGCTCCTG
RT-qPCR_primer-R	GGCAAAGCTGCGTTTCTG
protein_conc	3788	3913
WB_result	no clear band	no clear band
Ave_WB
WB_DONE_date	3/19/2015	3/3/2016
MW	64kDa	wes
IP	1	1
antibody_Cat#	A303-939A	A303-939A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	5.9	0
Rep2_TPM	6.7	0
Action
Library_start_date	8/12/2014	8/12/2014
repeat_library
Note
ID	2188	2189

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV14-33	BGHLV14-34
Sample_ID	BGHLV14-33	BGHLV14-34
Sample Name	RAVER1_BGHLV14-33	RAVER1_BGHLV14-34
Sample Name	RAVER1_BGHLV14-33	RAVER1_BGHLV14-34
RBP	RAVER1	RAVER1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	524	525

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-33	BGHLV14-34
Sample #
Sample Name	RAVER1-BGHLV14-33	RAVER1-BGHLV14-34
Sample_Name_Alias	RAVER1_BGHLV14-33	RAVER1_BGHLV14-34
Index Well Position	S15	S16
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/set1/H11.png	DNA_Library_LV13-14/set1/A12.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/A8.png	RNA_Library_LV13-14-16/set1/B8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-33	BGHLV14-34
RBP	RAVER1	RAVER1
Batch_ID	BGHLV14	BGHLV14
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2206	2207

Sequencing Information

	BGHLV14-33	BGHLV14-34
Sample_ID	BGHLV14-33	BGHLV14-34
Sample Name	RAVER1_BGHLV14-33	RAVER1_BGHLV14-34
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	54,240,000	45,600,000
total_aligned_reads	49,091,270	40,931,266
unique_aligned_reads	46,144,892	38,505,148
percent_uniqueAligned	0.85075	0.84441
correlation_replicates	0.999114	0.999114
spikein_reads	260,402	181,346
percent_spikeins	0.00480	0.00398
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	848	849

Data Submission Information

	BGHLV14-33	BGHLV14-33
ENCODE_alias	brenton-graveley:RAVER1_BGHLV14	brenton-graveley:RAVER1-BGHLV14-HepG2
ENCODE_accession	ENCSR576GOW	ENCSR998CDN
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-33	BGHLV14-33
Sample Name	RAVER1_BGHLV14-33	RAVER1_BGHLV14-33
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2811	6887

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
RAVER1_BGHLV14-33_ATGTCA_L004_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	848	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13816
RAVER1_BGHLV14-33_ATGTCA_L004_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	848	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13878
RAVER1_BGHLV14-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	848					GRCh38	V40	RAVER1_BGHLV14-33_ATGTCA_L004_R1_001.fastq.gz,RAVER1_BGHLV14-33_ATGTCA_L004_R2_001.fastq.gz		ENCORE2	13940
RAVER1_BGHLV14-33_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	848					GRCh38	V40	RAVER1_BGHLV14-33/Aligned.sortedByCoord.out.bam		ENCORE2	14002
RAVER1_BGHLV14-33_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	848					GRCh38	V40	RAVER1_BGHLV14-33/Aligned.sortedByCoord.out.bam		ENCORE2	14064
RAVER1_BGHLV14-33_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	848					GRCh38	V40	RAVER1_BGHLV14-33/Aligned.sortedByCoord.out.bam		ENCORE2	14126
RAVER1_BGHLV14-33_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	848					GRCh38	V40	RAVER1_BGHLV14-33/Aligned.sortedByCoord.out.bam		ENCORE2	14188
RAVER1_BGHLV14-33_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	848					GRCh38	V40	RAVER1_BGHLV14-33_ATGTCA_L004_R1_001.fastq.gz,RAVER1_BGHLV14-33_ATGTCA_L004_R2_001.fastq.gz		ENCORE2	14250
RAVER1_BGHLV14-34_CCGTCC_L004_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	849	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13817
RAVER1_BGHLV14-34_CCGTCC_L004_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	849	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13879
RAVER1_BGHLV14-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	849					GRCh38	V40	RAVER1_BGHLV14-34_CCGTCC_L004_R1_001.fastq.gz,RAVER1_BGHLV14-34_CCGTCC_L004_R2_001.fastq.gz		ENCORE2	13941
RAVER1_BGHLV14-34_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	849					GRCh38	V40	RAVER1_BGHLV14-34/Aligned.sortedByCoord.out.bam		ENCORE2	14003
RAVER1_BGHLV14-34_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	849					GRCh38	V40	RAVER1_BGHLV14-34/Aligned.sortedByCoord.out.bam		ENCORE2	14065
RAVER1_BGHLV14-34_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	849					GRCh38	V40	RAVER1_BGHLV14-34/Aligned.sortedByCoord.out.bam		ENCORE2	14127
RAVER1_BGHLV14-34_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	849					GRCh38	V40	RAVER1_BGHLV14-34/Aligned.sortedByCoord.out.bam		ENCORE2	14189
RAVER1_BGHLV14-34_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	849					GRCh38	V40	RAVER1_BGHLV14-34_CCGTCC_L004_R1_001.fastq.gz,RAVER1_BGHLV14-34_CCGTCC_L004_R2_001.fastq.gz		ENCORE2	14251