G3BP1 RNA-Seq in K562

General Information


RBP	G3BP1
Cell_Line	K562
Method	shRNA
Exp_Name	G3BP1-BGKLV11-K562
ENCODE_series_ID	ENCSR207TCU
Batch_ID	BGKLV11
Pool ID	Pool-140701
Local_Set_Name	set11
ENCODE_KD_Exp_ID	ENCSR792CBM
ENCODE_CN_Exp_ID	ENCSR129RWD
Rep1	G3BP1-LV11-13
Rep2	G3BP1-LV11-14
CN1	Nontarget-LV11-1
CN2	nontarget-LV11-2
Rep1_qPCR	58.6
Rep2_qPCR	55.3
Rep1_WB	19.9
Rep2_WB	9.5
Antibody Cat#	RN048PW
Antibody Lot#	LOT# 001
Antibody DCC ID	ENCAB411RDE
Status	Archived
Project	ENCODE3
ID	308

Experiment Information (Status: Released)

	BGKLV11-13	BGKLV11-14
idx	82	83
TRCN#_or_BGC#	TRCN0000008719	TRCN0000008719
shRNA_or_gRNA_sequence	GCCTGTAAGAAATACAGGATT	GCCTGTAAGAAATACAGGATT
PAM
Name	G3BP1	G3BP1
Sample_ID	BGKLV11-13	BGKLV11-14
transduction_Date	5/1/2014	5/1/2014
days
RBP_name	G3BP1	G3BP1
qPCR_result	58.6	55.3
Ave_qPCR	57.0
RT-qPCR_primer-F	TTGTGTTTGATGATTCTGAGCC
RT-qPCR_primer-R	ACATTCAGACGGACCTCACC
protein_conc	2457	2267
WB_result	19.9	9.5
Ave_WB	14.7
WB_DONE_date
MW
IP	1	1
antibody_Cat#	RN048PW	RN048PW
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	17.6025553	0
Rep2_TPM	9.66742612	0
Action	Ready	Ready
Library_start_date	5/19/2014	5/19/2014
repeat_library
Note
ID	87	88

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV11-13	BGKLV11-14
Sample_ID	BGKLV11-13	BGKLV11-14
Sample Name	G3BP1-LV11-13	G3BP1-LV11-14
Sample Name	G3BP1-LV11-13	G3BP1-LV11-14
RBP	G3BP1	G3BP1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-17	2014-09-17
Project	ENCODE3	ENCODE3
Note
ID	328	329

Library-Prep
Sequencing

Library-Prep Information

	BGKLV11-13	BGKLV11-14
Sample #
Sample Name	G3BP1-BGKLV11-13	G3BP1-BGKLV11-14
Sample_Name_Alias	G3BP1-LV11-13	G3BP1-LV11-14
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-19	2014-05-19
Lib_ID	Lib-140519	Lib-140519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV11/set1/H1.png	DNA_Library_LV11/set1/A2.png
RIN	9.3	9.1
libSample_RNA_Well	RNA_Library_LV11/set1/G1.png	RNA_Library_LV11/set1/H1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV11-13	BGKLV11-14
RBP	G3BP1	G3BP1
Batch_ID	BGKLV11	BGKLV11
WB_result	19.900	9.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1950	1951

Sequencing Information

	BGKLV11-13	BGKLV11-14
Sample_ID	BGKLV11-13	BGKLV11-14
Sample Name	G3BP1-LV11-13	G3BP1-LV11-14
Pool ID	Pool-140701	Pool-140701
LocalServer_folder	set11	set11
total_reads	59,260,000	65,360,000
total_aligned_reads	49,995,144	54,131,748
unique_aligned_reads	45,766,286	49,291,338
percent_uniqueAligned	0.77230	0.75415
correlation_replicates	0.991418	0.991418
spikein_reads	381,100	358,332
percent_spikeins	0.00643	0.00548
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	650	651

Data Submission Information

	BGKLV11-13	BGKLV11-13
ENCODE_alias	brenton-graveley:G3BP1-LV11	brenton-graveley:G3BP1-BGKLV11-K562
ENCODE_accession	ENCSR792CBM	ENCSR207TCU
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV11-13	BGKLV11-13
Sample Name	G3BP1-LV11-13	G3BP1-LV11-13
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-09-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2713	6728

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-LV11-13_CAGATC_L002_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	650	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12371
G3BP1-LV11-13_CAGATC_L002_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	650	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12419
G3BP1-LV11-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	650					GRCh38	V40	G3BP1-LV11-13_CAGATC_L002_R1_001.fastq.gz,G3BP1-LV11-13_CAGATC_L002_R2_001.fastq.gz		ENCORE2	12467
G3BP1-LV11-13_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	650					GRCh38	V40	G3BP1-LV11-13/Aligned.sortedByCoord.out.bam		ENCORE2	12515
G3BP1-LV11-13_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	650					GRCh38	V40	G3BP1-LV11-13/Aligned.sortedByCoord.out.bam		ENCORE2	12563
G3BP1-LV11-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	650					GRCh38	V40	G3BP1-LV11-13/Aligned.sortedByCoord.out.bam		ENCORE2	12611
G3BP1-LV11-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	650					GRCh38	V40	G3BP1-LV11-13/Aligned.sortedByCoord.out.bam		ENCORE2	12659
G3BP1-LV11-13_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	650					GRCh38	V40	G3BP1-LV11-13_CAGATC_L002_R1_001.fastq.gz,G3BP1-LV11-13_CAGATC_L002_R2_001.fastq.gz		ENCORE2	12707
G3BP1-LV11-14_ACTTGA_L002_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	651	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12372
G3BP1-LV11-14_ACTTGA_L002_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	651	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12420
G3BP1-LV11-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	651					GRCh38	V40	G3BP1-LV11-14_ACTTGA_L002_R1_001.fastq.gz,G3BP1-LV11-14_ACTTGA_L002_R2_001.fastq.gz		ENCORE2	12468
G3BP1-LV11-14_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	651					GRCh38	V40	G3BP1-LV11-14/Aligned.sortedByCoord.out.bam		ENCORE2	12516
G3BP1-LV11-14_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	651					GRCh38	V40	G3BP1-LV11-14/Aligned.sortedByCoord.out.bam		ENCORE2	12564
G3BP1-LV11-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	651					GRCh38	V40	G3BP1-LV11-14/Aligned.sortedByCoord.out.bam		ENCORE2	12612
G3BP1-LV11-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	651					GRCh38	V40	G3BP1-LV11-14/Aligned.sortedByCoord.out.bam		ENCORE2	12660
G3BP1-LV11-14_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	651					GRCh38	V40	G3BP1-LV11-14_ACTTGA_L002_R1_001.fastq.gz,G3BP1-LV11-14_ACTTGA_L002_R2_001.fastq.gz		ENCORE2	12708