G3BP2 RNA-Seq in K562

General Information


RBP	G3BP2
Cell_Line	K562
Method	shRNA
Exp_Name	G3BP2-BGKLV08-K562
ENCODE_series_ID	ENCSR272PIC
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR246SOU
ENCODE_CN_Exp_ID	ENCSR344XID
Rep1	G3BP2-LV08-33
Rep2	G3BP2-LV08-34
CN1	Nontarget-LV08-1_00003531
CN2	nontarget-LV08-2_00003531
Rep1_qPCR	71.9
Rep2_qPCR	73.8
Rep1_WB	86.8
Rep2_WB	89.1
Antibody Cat#	A302-040A
Antibody Lot#	A302-040A
Antibody DCC ID	ENCAB379SEC
Status	Released
Project	ENCODE3
ID	294

Experiment Information (Status: Released)

	BGKLV08-33	BGKLV08-34
idx	34	35
TRCN#_or_BGC#	TRCN0000047550	TRCN0000047550
shRNA_or_gRNA_sequence	CCACAAAGTATTATCTCTGAA	CCACAAAGTATTATCTCTGAA
PAM
Name	G3BP2	G3BP2
Sample_ID	BGKLV08-33	BGKLV08-34
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	G3BP2	G3BP2
qPCR_result	71.9	73.8
Ave_qPCR	72.8
RT-qPCR_primer-F	TGTTGGTAACTTGCCACATGAT
RT-qPCR_primer-R	ACACCCTTGGTATTGATGCG
protein_conc	3051	3226
WB_result	86.8	89.1
Ave_WB	87.9
WB_DONE_date	4/17/2015
MW	54kDa
IP	1	1
antibody_Cat#	A302-040A	A302-040A
Antibody DCC ID	ENCAB379SEC	ENCAB379SEC
submitted_to_DCC_date	8/6/2015
Rep1_TPM	46.5597335	0
Rep2_TPM	36.2438932	0
Action	Ready	Ready
Library_start_date	5/9/2014	5/9/2014
repeat_library
Note
ID	35	36

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
G3BP2	Product_ID: A302-040A Lot_ID: 1 Source: Bethyl Labs Target Name: G3BP2-human

Experiment Status

	BGKLV08-33	BGKLV08-34
Sample_ID	BGKLV08-33	BGKLV08-34
Sample Name	G3BP2-LV08-33	G3BP2-LV08-34
Sample Name	G3BP2-LV08-33	G3BP2-LV08-34
RBP	G3BP2	G3BP2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	294	295

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-33	BGKLV08-34
Sample #
Sample Name	G3BP2-BGKLV08-33	G3BP2-BGKLV08-34
Sample_Name_Alias	G3BP2-LV08-33	G3BP2-LV08-34
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-08	2014-05-08
Lib_ID	Lib-140508	Lib-140508
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV08/set5/C2.png	DNA_Library_LV35/set1/E4.png
RIN	9.2	9.3
libSample_RNA_Well	RNA_Library_LV08/set3/A1.png	RNA_Library_LV08/set3/B1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-33	BGKLV08-34
RBP	G3BP2	G3BP2
Batch_ID	BGKLV08	BGKLV08
WB_result	86.800	89.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1920	1921

Sequencing Information

	BGKLV08-33	BGKLV08-34
Sample_ID	BGKLV08-33	BGKLV08-34
Sample Name	G3BP2-LV08-33	G3BP2-LV08-34
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	43,790,000	47,900,000
total_aligned_reads	39,892,744	43,850,096
unique_aligned_reads	36,817,996	40,740,700
percent_uniqueAligned	0.84079	0.85054
correlation_replicates	0.994234	0.994234
spikein_reads	410,242	334,440
percent_spikeins	0.00937	0.00698
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	620	621

Data Submission Information

	BGKLV08-33	BGKLV08-33
ENCODE_alias	brenton-graveley:G3BP2-LV08	brenton-graveley:G3BP2-BGKLV08-K562
ENCODE_accession	ENCSR246SOU	ENCSR272PIC
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-33	BGKLV08-33
Sample Name	G3BP2-LV08-33	G3BP2-LV08-33
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2696	6730

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-LV08-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	620					GRCh38	V40	G3BP2-LV08-33_ACAGTG_L005_R1_001.fastq.gz,G3BP2-LV08-33_ACAGTG_L005_R2_001.fastq.gz		ENCORE2	12001
G3BP2-LV08-33_ACAGTG_L005_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	620	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003531_GATCAG_L005_R1_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	12057
G3BP2-LV08-33_ACAGTG_L005_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	620	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003531_GATCAG_L005_R2_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	12113
G3BP2-LV08-33_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	620					GRCh38	V40	G3BP2-LV08-33/Aligned.sortedByCoord.out.bam		ENCORE2	12169
G3BP2-LV08-33_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	620					GRCh38	V40	G3BP2-LV08-33/Aligned.sortedByCoord.out.bam		ENCORE2	12225
G3BP2-LV08-33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	620					GRCh38	V40	G3BP2-LV08-33/Aligned.sortedByCoord.out.bam		ENCORE2	12281
G3BP2-LV08-33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	620					GRCh38	V40	G3BP2-LV08-33/Aligned.sortedByCoord.out.bam		ENCORE2	12337
G3BP2-LV08-33_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	620					GRCh38	V40	G3BP2-LV08-33_ACAGTG_L005_R1_001.fastq.gz,G3BP2-LV08-33_ACAGTG_L005_R2_001.fastq.gz		ENCORE2	13336
G3BP2-LV08-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	621					GRCh38	V40	G3BP2-LV08-34_GCCAAT_L005_R1_001.fastq.gz,G3BP2-LV08-34_GCCAAT_L005_R2_001.fastq.gz		ENCORE2	12002
G3BP2-LV08-34_GCCAAT_L005_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	621	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003531_GATCAG_L005_R1_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	12058
G3BP2-LV08-34_GCCAAT_L005_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	621	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003531_GATCAG_L005_R2_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	12114
G3BP2-LV08-34_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	621					GRCh38	V40	G3BP2-LV08-34/Aligned.sortedByCoord.out.bam		ENCORE2	12170
G3BP2-LV08-34_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	621					GRCh38	V40	G3BP2-LV08-34/Aligned.sortedByCoord.out.bam		ENCORE2	12226
G3BP2-LV08-34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	621					GRCh38	V40	G3BP2-LV08-34/Aligned.sortedByCoord.out.bam		ENCORE2	12282
G3BP2-LV08-34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	621					GRCh38	V40	G3BP2-LV08-34/Aligned.sortedByCoord.out.bam		ENCORE2	12338
G3BP2-LV08-34_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	621					GRCh38	V40	G3BP2-LV08-34_GCCAAT_L005_R1_001.fastq.gz,G3BP2-LV08-34_GCCAAT_L005_R2_001.fastq.gz		ENCORE2	13337