G3BP1 RNA-Seq in K562

General Information


RBP	G3BP1
Cell_Line	K562
Method	CRISPR
Exp_Name	G3BP1-BGKcLV11-K562
ENCODE_series_ID	ENCSR361QAM
Batch_ID	BGKcLV11
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR846OQD
ENCODE_CN_Exp_ID	ENCSR292PXV
Rep1	G3BP1-BGKcLV11-57
Rep2	G3BP1-BGKcLV11-58
CN1	NT-BGKcLV11-1
CN2	NT-BGKcLV11-2
Rep1_qPCR	6.2
Rep2_qPCR	0.0
Rep1_WB	63.6
Rep2_WB	51.9
Antibody Cat#	RN048PW
Antibody Lot#
Antibody DCC ID	ENCAB411RDE
Status	Released
Project	ENCODE4
ID	172

Experiment Information (Status: Released)

	BGKcLV11-57	BGKcLV11-58
idx	373	374
TRCN#_or_BGC#	BGC#0000191	BGC#0000191
shRNA_or_gRNA_sequence	AATTCCCGCCCGACCAGCAG	AATTCCCGCCCGACCAGCAG
PAM	GGG	GGG
Name	G3BP1_78F	G3BP1_78F
Sample_ID	BGKcLV11-57	BGKcLV11-58
transduction_Date	8/3/18	8/3/18
days	Day 6	Day 6
RBP_name	G3BP1	G3BP1
qPCR_result	6.2	0.0
Ave_qPCR	3.1
RT-qPCR_primer-F	TTGTGTTTGATGATTCTGAGCC
RT-qPCR_primer-R	ACATTCAGACGGACCTCACC
protein_conc	2684	2754
WB_result	63.6	51.9
Ave_WB	57.7
WB_DONE_date	2/4/19
MW	52kDa
IP	1
antibody_Cat#	RN048PW
Antibody DCC ID	ENCAB411RDE
submitted_to_DCC_date	3/5/19
Rep1_TPM	107.5	0
Rep2_TPM	120.6	0
Action	Ready	Ready
Library_start_date	03/13/19	03/13/19
repeat_library
Note
ID	4473	4474

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

	BGKcLV11-57	BGKcLV11-58
Sample_ID	BGKcLV11-57	BGKcLV11-58
Sample Name	G3BP1-BGKcLV11-57	G3BP1-BGKcLV11-58
Sample Name	G3BP1-BGKcLV11-57	G3BP1-BGKcLV11-58
RBP	G3BP1	G3BP1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2679	2680

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV11-57	BGKcLV11-58
Sample #	7	8
Sample Name	G3BP1-BGKcLV11-57	G3BP1-BGKcLV11-58
Sample_Name_Alias
Index Well Position	G01	H01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-13	2019-03-13
Lib_ID	Lib-190313	Lib-190313
Tecan_Location	1-G1	1-H1
Tecan	40.54	42.79
Tecan_date	2019-03-13	2019-03-13
Size_bp	285	313
Peak_Molarity	55.80	86.90
libSampleQC_DNA_Well	DNA_Library_set42/set1/G1.png	DNA_Library_set42/set1/H1.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set42/set1/G1.png	RNA_Library_set42/set1/H1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-13	2019-03-13
Sample_ID	BGKcLV11-57	BGKcLV11-58
RBP	G3BP1	G3BP1
Batch_ID	BGKcLV11	BGKcLV11
WB_result	63.600	51.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	7	8

Sequencing Information

	BGKcLV11-57	BGKcLV11-58
Sample_ID	BGKcLV11-57	BGKcLV11-58
Sample Name	G3BP1-BGKcLV11-57	G3BP1-BGKcLV11-58
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	44,668,936	52,492,640
total_aligned_reads	42,846,120	52,069,592
unique_aligned_reads	38,878,812	47,239,228
percent_uniqueAligned	0.87038	0.89992
correlation_replicates	0.995266	0.995266
spikein_reads	47,140	57,652
percent_spikeins	0.00106	0.00110
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	23	24

Data Submission Information

	BGKcLV11-57	BGKcLV11-57	BGKcLV11-57	BGKcLV11-57	BGKcLV11-57	BGKcLV11-57	BGKcLV11-58	BGKcLV11-58	BGKcLV11-58	BGKcLV11-58
ENCODE_alias	brenton-graveley:G3BP1-BGKcLV11	brenton-graveley:G3BP1-BGKcLV11-57	brenton-graveley:L-G3BP1-BGKcLV11-57	brenton-graveley:G3BP1-BGKcLV11-57_CAAGCTAG+ACATAGCG_HK3H2DSXX_S7_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:G3BP1-BGKcLV11-57_CAAGCTAG+ACATAGCG_HK3H2DSXX_S7_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:G3BP1-BGKcLV11-K562	brenton-graveley:G3BP1-BGKcLV11-58	brenton-graveley:L-G3BP1-BGKcLV11-58	brenton-graveley:G3BP1-BGKcLV11-58_TGGATCGA+GTGCGATA_HK3H2DSXX_S8_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:G3BP1-BGKcLV11-58_TGGATCGA+GTGCGATA_HK3H2DSXX_S8_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR846OQD	ENCBS906TKX	ENCLB760DGX	ENCFF713STX	ENCFF996MJO	ENCSR361QAM	ENCBS381YAF	ENCLB653MCY	ENCFF337IPL	ENCFF378KYQ
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV11-57	BGKcLV11-57	BGKcLV11-57	BGKcLV11-57	BGKcLV11-57	BGKcLV11-57	BGKcLV11-58	BGKcLV11-58	BGKcLV11-58	BGKcLV11-58
Sample Name	G3BP1-BGKcLV11-57	G3BP1-BGKcLV11-57	G3BP1-BGKcLV11-57	G3BP1-BGKcLV11-57	G3BP1-BGKcLV11-57	G3BP1-BGKcLV11-57	G3BP1-BGKcLV11-58	G3BP1-BGKcLV11-58	G3BP1-BGKcLV11-58	G3BP1-BGKcLV11-58
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		G3BP1-BGKcLV11-57.pdf	L-G3BP1-BGKcLV11-57.pdf				G3BP1-BGKcLV11-58.pdf	L-G3BP1-BGKcLV11-58.pdf
ID	763	821	903	973	1055	7227	822	904	974	1056

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-BGKcLV11-57_CAAGCTAG+ACATAGCG_HK3H2DSXX_S7_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	23	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	355
G3BP1-BGKcLV11-57_CAAGCTAG+ACATAGCG_HK3H2DSXX_S7_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	23	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	437
G3BP1-BGKcLV11-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	23					GRCh38	V40	G3BP1-BGKcLV11-57_CAAGCTAG+ACATAGCG_HK3H2DSXX_S7_L004_R1_001.filtered.trimmed.paired.fastq.gz,G3BP1-BGKcLV11-57_CAAGCTAG+ACATAGCG_HK3H2DSXX_S7_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23694
G3BP1-BGKcLV11-57_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	23					GRCh38	V40	G3BP1-BGKcLV11-57/Aligned.sortedByCoord.out.bam		ENCORE2	23776
G3BP1-BGKcLV11-57_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	23					GRCh38	V40	G3BP1-BGKcLV11-57/Aligned.sortedByCoord.out.bam		ENCORE2	23858
G3BP1-BGKcLV11-57_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	23					GRCh38	V40	G3BP1-BGKcLV11-57/Aligned.sortedByCoord.out.bam		ENCORE2	23940
G3BP1-BGKcLV11-57_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	23					GRCh38	V40	G3BP1-BGKcLV11-57/Aligned.sortedByCoord.out.bam		ENCORE2	24022
G3BP1-BGKcLV11-57_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	23					GRCh38	V40	G3BP1-BGKcLV11-57_CAAGCTAG+ACATAGCG_HK3H2DSXX_S7_L004_R1_001.filtered.trimmed.paired.fastq.gz,G3BP1-BGKcLV11-57_CAAGCTAG+ACATAGCG_HK3H2DSXX_S7_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24104
G3BP1-BGKcLV11-58_TGGATCGA+GTGCGATA_HK3H2DSXX_S8_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	24	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	356
G3BP1-BGKcLV11-58_TGGATCGA+GTGCGATA_HK3H2DSXX_S8_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	24	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	438
G3BP1-BGKcLV11-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	24					GRCh38	V40	G3BP1-BGKcLV11-58_TGGATCGA+GTGCGATA_HK3H2DSXX_S8_L004_R1_001.filtered.trimmed.paired.fastq.gz,G3BP1-BGKcLV11-58_TGGATCGA+GTGCGATA_HK3H2DSXX_S8_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23695
G3BP1-BGKcLV11-58_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	24					GRCh38	V40	G3BP1-BGKcLV11-58/Aligned.sortedByCoord.out.bam		ENCORE2	23777
G3BP1-BGKcLV11-58_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	24					GRCh38	V40	G3BP1-BGKcLV11-58/Aligned.sortedByCoord.out.bam		ENCORE2	23859
G3BP1-BGKcLV11-58_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	24					GRCh38	V40	G3BP1-BGKcLV11-58/Aligned.sortedByCoord.out.bam		ENCORE2	23941
G3BP1-BGKcLV11-58_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	24					GRCh38	V40	G3BP1-BGKcLV11-58/Aligned.sortedByCoord.out.bam		ENCORE2	24023
G3BP1-BGKcLV11-58_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	24					GRCh38	V40	G3BP1-BGKcLV11-58_TGGATCGA+GTGCGATA_HK3H2DSXX_S8_L004_R1_001.filtered.trimmed.paired.fastq.gz,G3BP1-BGKcLV11-58_TGGATCGA+GTGCGATA_HK3H2DSXX_S8_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24105