ARHGEF2 RNA-Seq in HepG2

General Information


RBP	ARHGEF2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ARHGEF2-BGHcLV29-HepG2
ENCODE_series_ID	ENCSR013OUS
Batch_ID	BGHcLV29
Pool ID	Pool-211117
Local_Set_Name	set50_H
ENCODE_KD_Exp_ID	ENCSR191LWZ
ENCODE_CN_Exp_ID	ENCSR462MFN
Rep1	ARHGEF2-BGHcLV29-3
Rep2	ARHGEF2-BGHcLV29-4
CN1	NT-BGHcLV29-1
CN2	NT-BGHcLV29-2
Rep1_qPCR	0
Rep2_qPCR	0
Rep1_WB	98.4
Rep2_WB	98.4
Antibody Cat#	A301-928A
Antibody Lot#	LOT# 2
Antibody DCC ID
Status	Submitted
Project	ENCODE4
ID	846

Experiment Information (Status: Released)

	BGHcLV29-3	BGHcLV29-4
idx	834	835
TRCN#_or_BGC#	BGC#0000637	BGC#0000637
shRNA_or_gRNA_sequence	AGGATGCCCGCTATACCAAT	AGGATGCCCGCTATACCAAT
PAM	GGG	GGG
Name	ARHGEF2_96	ARHGEF2_96
Sample_ID	BGHcLV29-3	BGHcLV29-4
transduction_Date	7/20	7/20
days	D6	D6
RBP_name	ARHGEF2	ARHGEF2
qPCR_result	0	0
Ave_qPCR	0
RT-qPCR_primer-F	gcgatgccctgtacttgag
RT-qPCR_primer-R	tcggtcctcaaagtttcgat
protein_conc	3710	4327
WB_result	98.4	98.4
Ave_WB	98.4	position is different k562
WB_DONE_date	7/29/21	JESS
MW	112kDa
IP	Rabbit / I
antibody_Cat#	A301-928A	LOT# 2
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/5/21	11/5/21
repeat_library
Note
ID	7007	7008

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV29-3	BGHcLV29-4
Sample_ID	BGHcLV29-3	BGHcLV29-4
Sample Name
Sample Name	ARHGEF2-BGHcLV29-3	ARHGEF2-BGHcLV29-4
RBP	ARHGEF2	ARHGEF2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	9975	9976

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV29-3	BGHcLV29-4
Sample #	3	4
Sample Name	ARHGEF2-BGHcLV29-3	ARHGEF2-BGHcLV29-4
Sample_Name_Alias
Index Well Position	C01	D01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-11-01	2021-11-01
Lib_ID	Lib-211101	Lib-211101
Tecan_Location
Tecan
Tecan_date
Size_bp	292	285
Peak_Molarity	31.40	42.60
libSampleQC_DNA_Well	DNA_Library_set50/set1/C1.png	DNA_Library_set50/set1/D1.png
RIN	9.8	9.5
libSample_RNA_Well	RNA_Library_set50/set1/C7.png	RNA_Library_set50/set1/D7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGHcLV29-3	BGHcLV29-4
RBP	ARHGEF2	ARHGEF2
Batch_ID	BGHcLV29	BGHcLV29
WB_result	98.400	98.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3090	3091

Sequencing Information

	BGHcLV29-3	BGHcLV29-4
Sample_ID	BGHcLV29-3	BGHcLV29-4
Sample Name	ARHGEF2-BGHcLV29-3	ARHGEF2-BGHcLV29-4
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_H	set50_H
total_reads	57,776,480	60,450,484
total_aligned_reads	52,884,810	53,174,812
unique_aligned_reads	49,935,054	50,115,668
percent_uniqueAligned	0.86428	0.82904
correlation_replicates	0.997149	0.997149
spikein_reads	15,022	14,014
percent_spikeins	0.00026	0.00023
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1873	1874

Data Submission Information

	BGHcLV29-3	BGHcLV29-3	BGHcLV29-3	BGHcLV29-3	BGHcLV29-3	BGHcLV29-3	BGHcLV29-4	BGHcLV29-4	BGHcLV29-4	BGHcLV29-4
ENCODE_alias	brenton-graveley:ARHGEF2-BGHcLV29	brenton-graveley:ARHGEF2-BGHcLV29-3	brenton-graveley:L-ARHGEF2-BGHcLV29-3	brenton-graveley:ARHGEF2-BGHcLV29-3_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ARHGEF2-BGHcLV29-3_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ARHGEF2-BGHcLV29-HepG2	brenton-graveley:ARHGEF2-BGHcLV29-4	brenton-graveley:L-ARHGEF2-BGHcLV29-4	brenton-graveley:ARHGEF2-BGHcLV29-4_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ARHGEF2-BGHcLV29-4_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR191LWZ	ENCBS813CQS	ENCLB409RMC	ENCFF346MBE	ENCFF407JKE	ENCSR013OUS	ENCBS265LMY	ENCLB449WON	ENCFF931HCF	ENCFF680FVY
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	BGHcLV29-3	BGHcLV29-3	BGHcLV29-3	BGHcLV29-3	BGHcLV29-3	BGHcLV29-3	BGHcLV29-4	BGHcLV29-4	BGHcLV29-4	BGHcLV29-4
Sample Name	ARHGEF2-BGHcLV29-3	ARHGEF2-BGHcLV29-3	ARHGEF2-BGHcLV29-3	ARHGEF2-BGHcLV29-3	ARHGEF2-BGHcLV29-3	ARHGEF2-BGHcLV29-3	ARHGEF2-BGHcLV29-4	ARHGEF2-BGHcLV29-4	ARHGEF2-BGHcLV29-4	ARHGEF2-BGHcLV29-4
Selected	Yes	No	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
			LV50H_library_protocol					LV50H_library_protocol
protocol_URL			L-ARHGEF2-BGHcLV29-3.pdf					L-ARHGEF2-BGHcLV29-4.pdf
ID	5844	5881	5953	6025	6097	6167	5882	5954	6026	6098

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
ARHGEF2-BGHcLV29-3_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1873	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5761
ARHGEF2-BGHcLV29-3_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1873	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5803
ARHGEF2-BGHcLV29-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1873					GRCh38	V40	ARHGEF2-BGHcLV29-3_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,ARHGEF2-BGHcLV29-3_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18926
ARHGEF2-BGHcLV29-3_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1873					GRCh38	V40	ARHGEF2-BGHcLV29-3/Aligned.sortedByCoord.out.bam		ENCORE2	18984
ARHGEF2-BGHcLV29-3_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1873					GRCh38	V40	ARHGEF2-BGHcLV29-3/Aligned.sortedByCoord.out.bam		ENCORE2	19030
ARHGEF2-BGHcLV29-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1873					GRCh38	V40	ARHGEF2-BGHcLV29-3/Aligned.sortedByCoord.out.bam		ENCORE2	19076
ARHGEF2-BGHcLV29-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1873					GRCh38	V40	ARHGEF2-BGHcLV29-3/Aligned.sortedByCoord.out.bam		ENCORE2	19122
ARHGEF2-BGHcLV29-3_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1873					GRCh38	V40	ARHGEF2-BGHcLV29-3_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,ARHGEF2-BGHcLV29-3_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19168
ARHGEF2-BGHcLV29-4_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1874	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5762
ARHGEF2-BGHcLV29-4_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1874	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5804
ARHGEF2-BGHcLV29-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1874					GRCh38	V40	ARHGEF2-BGHcLV29-4_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,ARHGEF2-BGHcLV29-4_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18927
ARHGEF2-BGHcLV29-4_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1874					GRCh38	V40	ARHGEF2-BGHcLV29-4/Aligned.sortedByCoord.out.bam		ENCORE2	18985
ARHGEF2-BGHcLV29-4_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1874					GRCh38	V40	ARHGEF2-BGHcLV29-4/Aligned.sortedByCoord.out.bam		ENCORE2	19031
ARHGEF2-BGHcLV29-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1874					GRCh38	V40	ARHGEF2-BGHcLV29-4/Aligned.sortedByCoord.out.bam		ENCORE2	19077
ARHGEF2-BGHcLV29-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1874					GRCh38	V40	ARHGEF2-BGHcLV29-4/Aligned.sortedByCoord.out.bam		ENCORE2	19123
ARHGEF2-BGHcLV29-4_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1874					GRCh38	V40	ARHGEF2-BGHcLV29-4_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,ARHGEF2-BGHcLV29-4_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19169