G3BP2 RNA-Seq in HepG2

General Information


RBP	G3BP2
Cell_Line	HepG2
Method	shRNA
Exp_Name	G3BP2-BGHLV12-HepG2
ENCODE_series_ID	ENCSR605PVH
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR945UYL
ENCODE_CN_Exp_ID	ENCSR237YZT
Rep1	G3BP2-BGHLV12-35
Rep2	G3BP2-BGHLV12-36
CN1	NT-BGHLV12-01
CN2	NT-BGHLV12-02
Rep1_qPCR	85.7
Rep2_qPCR	91.9
Rep1_WB	no band
Rep2_WB
Antibody Cat#	A302-040A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB379SEC
Status	Released
Project	ENCODE3
ID	339

Experiment Information (Status: Released)

	BGHLV12-35	BGHLV12-36
idx	35	36
TRCN#_or_BGC#	TRCN0000047550	TRCN0000047550
shRNA_or_gRNA_sequence	CCACAAAGTATTATCTCTGAA	CCACAAAGTATTATCTCTGAA
PAM
Name	G3BP2	G3BP2
Sample_ID	BGHLV12-35	BGHLV12-36
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	G3BP2	G3BP2
qPCR_result	85.7	91.9
Ave_qPCR	88.8
RT-qPCR_primer-F	TGTTGGTAACTTGCCACATGAT
RT-qPCR_primer-R	ACACCCTTGGTATTGATGCG
protein_conc	2754	3065
WB_result	no band
Ave_WB
WB_DONE_date	2/26/2016
MW	54kDa	wes
IP	1	1
antibody_Cat#	A302-040A	A302-040A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	41.5	0
Rep2_TPM	40.2	0
Action
Library_start_date	6/9/2014	6/9/2014
repeat_library
Note
ID	2082	2083

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV12-35	BGHLV12-36
Sample_ID	BGHLV12-35	BGHLV12-36
Sample Name	G3BP2-BGHLV12-35	G3BP2-BGHLV12-36
Sample Name	G3BP2-BGHLV12-35	G3BP2-BGHLV12-36
RBP	G3BP2	G3BP2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	392	393

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-35	BGHLV12-36
Sample #
Sample Name	G3BP2-BGHLV12-35	G3BP2-BGHLV12-36
Sample_Name_Alias	G3BP2-BGHLV12-35	G3BP2-BGHLV12-36
Index Well Position	S01	S02
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/B2.png	DNA_Library_LV12/set2/C2.png
RIN	9.1	9.4
libSample_RNA_Well	RNA_Library_LV12/set1/A4.png	RNA_Library_LV12/set1/B4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-35	BGHLV12-36
RBP	G3BP2	G3BP2
Batch_ID	BGHLV12	BGHLV12
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2016	2017

Sequencing Information

	BGHLV12-35	BGHLV12-36
Sample_ID	BGHLV12-35	BGHLV12-36
Sample Name	G3BP2-BGHLV12-35	G3BP2-BGHLV12-36
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	72,930,000	79,690,000
total_aligned_reads	68,254,446	73,923,130
unique_aligned_reads	64,684,304	69,982,068
percent_uniqueAligned	0.88694	0.87818
correlation_replicates	0.998974	0.998974
spikein_reads	438,236	724,708
percent_spikeins	0.00601	0.00909
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	716	717

Data Submission Information

	BGHLV12-35	BGHLV12-35
ENCODE_alias	brenton-graveley:G3BP2-BGHLV12	brenton-graveley:G3BP2-BGHLV12-HepG2
ENCODE_accession	ENCSR945UYL	ENCSR605PVH
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-35	BGHLV12-35
Sample Name	G3BP2-BGHLV12-35	G3BP2-BGHLV12-35
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2745	6729

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
G3BP2-BGHLV12-35_ATCACG_L004_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	716	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12773
G3BP2-BGHLV12-35_ATCACG_L004_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	716	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12842
G3BP2-BGHLV12-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	716					GRCh38	V40	G3BP2-BGHLV12-35_ATCACG_L004_R1_001.fastq.gz,G3BP2-BGHLV12-35_ATCACG_L004_R2_001.fastq.gz		ENCORE2	12912
G3BP2-BGHLV12-35_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	716					GRCh38	V40	G3BP2-BGHLV12-35/Aligned.sortedByCoord.out.bam		ENCORE2	12982
G3BP2-BGHLV12-35_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	716					GRCh38	V40	G3BP2-BGHLV12-35/Aligned.sortedByCoord.out.bam		ENCORE2	13052
G3BP2-BGHLV12-35_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	716					GRCh38	V40	G3BP2-BGHLV12-35/Aligned.sortedByCoord.out.bam		ENCORE2	13122
G3BP2-BGHLV12-35_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	716					GRCh38	V40	G3BP2-BGHLV12-35/Aligned.sortedByCoord.out.bam		ENCORE2	13192
G3BP2-BGHLV12-35_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	716					GRCh38	V40	G3BP2-BGHLV12-35_ATCACG_L004_R1_001.fastq.gz,G3BP2-BGHLV12-35_ATCACG_L004_R2_001.fastq.gz		ENCORE2	13262
G3BP2-BGHLV12-36_CGATGT_L004_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	717	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12774
G3BP2-BGHLV12-36_CGATGT_L004_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	717	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12843
G3BP2-BGHLV12-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	717					GRCh38	V40	G3BP2-BGHLV12-36_CGATGT_L004_R1_001.fastq.gz,G3BP2-BGHLV12-36_CGATGT_L004_R2_001.fastq.gz		ENCORE2	12913
G3BP2-BGHLV12-36_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	717					GRCh38	V40	G3BP2-BGHLV12-36/Aligned.sortedByCoord.out.bam		ENCORE2	12983
G3BP2-BGHLV12-36_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	717					GRCh38	V40	G3BP2-BGHLV12-36/Aligned.sortedByCoord.out.bam		ENCORE2	13053
G3BP2-BGHLV12-36_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	717					GRCh38	V40	G3BP2-BGHLV12-36/Aligned.sortedByCoord.out.bam		ENCORE2	13123
G3BP2-BGHLV12-36_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	717					GRCh38	V40	G3BP2-BGHLV12-36/Aligned.sortedByCoord.out.bam		ENCORE2	13193
G3BP2-BGHLV12-36_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	717					GRCh38	V40	G3BP2-BGHLV12-36_CGATGT_L004_R1_001.fastq.gz,G3BP2-BGHLV12-36_CGATGT_L004_R2_001.fastq.gz		ENCORE2	13263