G3BP1 RNA-Seq in HepG2

General Information


RBP	G3BP1
Cell_Line	HepG2
Method	shRNA
Exp_Name	G3BP1-BGHLV12-HepG2
ENCODE_series_ID	ENCSR105ARZ
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR074UZM
ENCODE_CN_Exp_ID	ENCSR237YZT
Rep1	G3BP1-BGHLV12-33
Rep2	G3BP1-BGHLV12-34
CN1	NT-BGHLV12-01
CN2	NT-BGHLV12-02
Rep1_qPCR	53.8
Rep2_qPCR	63.0
Rep1_WB	80.0
Rep2_WB	84.6
Antibody Cat#	RN048PW
Antibody Lot#	RN048PW
Antibody DCC ID	ENCAB411RDE
Status	Released
Project	ENCODE3
ID	338

Experiment Information (Status: Released)

	BGHLV12-33	BGHLV12-34
idx	33	34
TRCN#_or_BGC#	TRCN0000008719	TRCN0000008719
shRNA_or_gRNA_sequence	GCCTGTAAGAAATACAGGATT	GCCTGTAAGAAATACAGGATT
PAM
Name	G3BP1	G3BP1
Sample_ID	BGHLV12-33	BGHLV12-34
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	G3BP1	G3BP1
qPCR_result	53.8	63.0
Ave_qPCR	58.4
RT-qPCR_primer-F	TTGTGTTTGATGATTCTGAGCC
RT-qPCR_primer-R	ACATTCAGACGGACCTCACC
protein_conc	1921	2859
WB_result	80.0	84.6
Ave_WB	82.3
WB_DONE_date	3/2/2016
MW	52kDa
IP	1	1
antibody_Cat#	RN048PW	RN048PW
Antibody DCC ID	ENCAB411RDE	ENCAB411RDE
submitted_to_DCC_date	3/8/2016
Rep1_TPM	8.5	0
Rep2_TPM	8.5	0
Action
Library_start_date	6/9/2014	6/9/2014
repeat_library
Note
ID	2080	2081

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
G3BP1	Product_ID: RN048PW Lot_ID: 1 Source: MBLI Target Name: G3BP1-human

Experiment Status

	BGHLV12-33	BGHLV12-34
Sample_ID	BGHLV12-33	BGHLV12-34
Sample Name	G3BP1-BGHLV12-33	G3BP1-BGHLV12-34
Sample Name	G3BP1-BGHLV12-33	G3BP1-BGHLV12-34
RBP	G3BP1	G3BP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	390	391

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-33	BGHLV12-34
Sample #
Sample Name	G3BP1-BGHLV12-33	G3BP1-BGHLV12-34
Sample_Name_Alias	G3BP1-BGHLV12-33	G3BP1-BGHLV12-34
Index Well Position	S25	S27
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/set2/H1.png	DNA_Library_LV12/set2/A2.png
RIN	9.5	9.4
libSample_RNA_Well	RNA_Library_LV12/set1/G3.png	RNA_Library_LV12/set1/H3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-33	BGHLV12-34
RBP	G3BP1	G3BP1
Batch_ID	BGHLV12	BGHLV12
WB_result	80.000	84.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2014	2015

Sequencing Information

	BGHLV12-33	BGHLV12-34
Sample_ID	BGHLV12-33	BGHLV12-34
Sample Name	G3BP1-BGHLV12-33	G3BP1-BGHLV12-34
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	57,160,000	56,530,000
total_aligned_reads	53,487,594	52,499,418
unique_aligned_reads	50,557,338	49,598,898
percent_uniqueAligned	0.88449	0.87739
correlation_replicates	0.994824	0.994824
spikein_reads	433,872	410,904
percent_spikeins	0.00759	0.00727
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	714	715

Data Submission Information

	BGHLV12-33	BGHLV12-33
ENCODE_alias	brenton-graveley:G3BP1-BGHLV12	brenton-graveley:G3BP1-BGHLV12-HepG2
ENCODE_accession	ENCSR074UZM	ENCSR105ARZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-33	BGHLV12-33
Sample Name	G3BP1-BGHLV12-33	G3BP1-BGHLV12-33
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2744	6727

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
G3BP1-BGHLV12-33_ACTGAT_L004_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	714	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12771
G3BP1-BGHLV12-33_ACTGAT_L004_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	714	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12840
G3BP1-BGHLV12-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	714					GRCh38	V40	G3BP1-BGHLV12-33_ACTGAT_L004_R1_001.fastq.gz,G3BP1-BGHLV12-33_ACTGAT_L004_R2_001.fastq.gz		ENCORE2	12910
G3BP1-BGHLV12-33_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	714					GRCh38	V40	G3BP1-BGHLV12-33/Aligned.sortedByCoord.out.bam		ENCORE2	12980
G3BP1-BGHLV12-33_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	714					GRCh38	V40	G3BP1-BGHLV12-33/Aligned.sortedByCoord.out.bam		ENCORE2	13050
G3BP1-BGHLV12-33_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	714					GRCh38	V40	G3BP1-BGHLV12-33/Aligned.sortedByCoord.out.bam		ENCORE2	13120
G3BP1-BGHLV12-33_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	714					GRCh38	V40	G3BP1-BGHLV12-33/Aligned.sortedByCoord.out.bam		ENCORE2	13190
G3BP1-BGHLV12-33_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	714					GRCh38	V40	G3BP1-BGHLV12-33_ACTGAT_L004_R1_001.fastq.gz,G3BP1-BGHLV12-33_ACTGAT_L004_R2_001.fastq.gz		ENCORE2	13260
G3BP1-BGHLV12-34_ATTCCT_L004_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	715	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12772
G3BP1-BGHLV12-34_ATTCCT_L004_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	715	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12841
G3BP1-BGHLV12-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	715					GRCh38	V40	G3BP1-BGHLV12-34_ATTCCT_L004_R1_001.fastq.gz,G3BP1-BGHLV12-34_ATTCCT_L004_R2_001.fastq.gz		ENCORE2	12911
G3BP1-BGHLV12-34_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	715					GRCh38	V40	G3BP1-BGHLV12-34/Aligned.sortedByCoord.out.bam		ENCORE2	12981
G3BP1-BGHLV12-34_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	715					GRCh38	V40	G3BP1-BGHLV12-34/Aligned.sortedByCoord.out.bam		ENCORE2	13051
G3BP1-BGHLV12-34_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	715					GRCh38	V40	G3BP1-BGHLV12-34/Aligned.sortedByCoord.out.bam		ENCORE2	13121
G3BP1-BGHLV12-34_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	715					GRCh38	V40	G3BP1-BGHLV12-34/Aligned.sortedByCoord.out.bam		ENCORE2	13191
G3BP1-BGHLV12-34_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	715					GRCh38	V40	G3BP1-BGHLV12-34_ATTCCT_L004_R1_001.fastq.gz,G3BP1-BGHLV12-34_ATTCCT_L004_R2_001.fastq.gz		ENCORE2	13261