ARHGEF1 RNA-Seq in HepG2

General Information


RBP	ARHGEF1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ARHGEF1-BGHcLV27-HepG2
ENCODE_series_ID	ENCSR124EEV
Batch_ID	BGHcLV27
Pool ID	Pool-210908
Local_Set_Name	set48_H
ENCODE_KD_Exp_ID	ENCSR250QFO
ENCODE_CN_Exp_ID	ENCSR650TTU
Rep1	ARHGEF1-BGHcLV27-13
Rep2	ARHGEF1-BGHcLV27-14
CN1	NT-BGHcLV27-1
CN2	NT-BGHcLV27-2
Rep1_qPCR	37.6
Rep2_qPCR	42.8
Rep1_WB	50.9
Rep2_WB	57.6
Antibody Cat#	A302-701A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB133PSK
Status	Released
Project	ENCODE4
ID	810

Experiment Information (Status: Released)

	BGHcLV27-13	BGHcLV27-13	BGHcLV27-14	BGHcLV27-14
idx	779	779	780	780
TRCN#_or_BGC#	BGC#0000635	BGC#0000635	BGC#0000635	BGC#0000635
shRNA_or_gRNA_sequence	CCAGCGGCGGTTCGTGCAGG	CCAGCGGCGGTTCGTGCAGG	CCAGCGGCGGTTCGTGCAGG	CCAGCGGCGGTTCGTGCAGG
PAM	AGG	AGG	AGG	AGG
Name	ARHGEF1_91	ARHGEF1_91	ARHGEF1_91	ARHGEF1_91
Sample_ID	BGHcLV27-13	BGHcLV27-13	BGHcLV27-14	BGHcLV27-14
transduction_Date	5/18/21	5/18/21	5/18/21	5/18/21
days	D6	D6	D6	D6
RBP_name	ARHGEF1	ARHGEF1	ARHGEF1	ARHGEF1
qPCR_result	37.6	37.6	42.8	42.8
Ave_qPCR	40.2	40.2
RT-qPCR_primer-F	ctctgagaacggcaatggtg	ctctgagaacggcaatggtg
RT-qPCR_primer-R	gcaggaggtcactgaggatt	gcaggaggtcactgaggatt
protein_conc	2877	2877	3287	3287
WB_result	50.9	NO clear band	57.6
Ave_WB	54.2
WB_DONE_date	5/26/21	9/8/21	JESS	JESS
MW	102kDa	102kDa
IP	Rabbit / I	Rabbit / I
antibody_Cat#	A302-701A	A302-702A	LOT# 1
Antibody DCC ID	ENCAB133PSK		10/22/21
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	09/03/21		09/03/21
repeat_library
Note
ID	6940	6942	6941	6943

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ARHGEF1	Product_ID: A302-701A Lot_ID: 1 Source: Bethyl Labs Target Name: ARHGEF1-human

Experiment Status

	BGHcLV27-13	BGHcLV27-13	BGHcLV27-14	BGHcLV27-14
Sample_ID	BGHcLV27-13	BGHcLV27-13	BGHcLV27-14	BGHcLV27-14
Sample Name
Sample Name	ARHGEF1-BGHcLV27-13		ARHGEF1-BGHcLV27-14
RBP	ARHGEF1	ARHGEF1	ARHGEF1	ARHGEF1
Cell_Line	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	Released	NotSatisfied	Released	NotSatisfied
Status_date	2021-11-19	2021-09-15	2021-11-19	2021-09-15
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4
Note
ID	9683	9701	9684	9702

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV27-13	BGHcLV27-14
Sample #	87	88
Sample Name	ARHGEF1-BGHcLV27-13	ARHGEF1-BGHcLV27-14
Sample_Name_Alias
Index Well Position	C09	D09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-02	2021-09-02
Lib_ID	Lib-210902	Lib-210902
Tecan_Location
Tecan
Tecan_date
Size_bp	294	349
Peak_Molarity	126.00	118.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set2/C8.png	DNA_Library_set48-49/set2/D8.png
RIN	9.8	9.5
libSample_RNA_Well	RNA_Library_set48-49/set1/E8.png	RNA_Library_set48-49/set1/F8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-08	2021-09-08
Sample_ID	BGHcLV27-13	BGHcLV27-14
RBP	ARHGEF1	ARHGEF1
Batch_ID	BGHcLV27	BGHcLV27
WB_result	50.900	57.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1646	1647

Sequencing Information

	BGHcLV27-13	BGHcLV27-14
Sample_ID	BGHcLV27-13	BGHcLV27-14
Sample Name	ARHGEF1-BGHcLV27-13	ARHGEF1-BGHcLV27-14
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_H	set48_H
total_reads	99,072,022	58,112,682
total_aligned_reads	88,051,840	50,701,976
unique_aligned_reads	82,966,982	47,801,728
percent_uniqueAligned	0.83744	0.82257
correlation_replicates	0.993038	0.993038
spikein_reads	29,396	9,762
percent_spikeins	0.00030	0.00017
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1797	1798

Data Submission Information

	BGHcLV27-13	BGHcLV27-13	BGHcLV27-13	BGHcLV27-13	BGHcLV27-13	BGHcLV27-13	BGHcLV27-14	BGHcLV27-14	BGHcLV27-14	BGHcLV27-14
ENCODE_alias	brenton-graveley:ARHGEF1-BGHcLV27	brenton-graveley:ARHGEF1-BGHcLV27-13	brenton-graveley:L-ARHGEF1-BGHcLV27-13	brenton-graveley:ARHGEF1-BGHcLV27-13_S67_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ARHGEF1-BGHcLV27-13_S67_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ARHGEF1-BGHcLV27-HepG2	brenton-graveley:ARHGEF1-BGHcLV27-14	brenton-graveley:L-ARHGEF1-BGHcLV27-14	brenton-graveley:ARHGEF1-BGHcLV27-14_S68_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ARHGEF1-BGHcLV27-14_S68_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR250QFO	ENCBS841VVB	ENCLB908SOL	ENCFF312LKS	ENCFF158GWI	ENCSR124EEV	ENCBS368CDS	ENCLB104ZKE	ENCFF140PJK	ENCFF045WCR
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	BGHcLV27-13	BGHcLV27-13	BGHcLV27-13	BGHcLV27-13	BGHcLV27-13	BGHcLV27-13	BGHcLV27-14	BGHcLV27-14	BGHcLV27-14	BGHcLV27-14
Sample Name	ARHGEF1-BGHcLV27-13	ARHGEF1-BGHcLV27-13	ARHGEF1-BGHcLV27-13	ARHGEF1-BGHcLV27-13	ARHGEF1-BGHcLV27-13	ARHGEF1-BGHcLV27-13	ARHGEF1-BGHcLV27-14	ARHGEF1-BGHcLV27-14	ARHGEF1-BGHcLV27-14	ARHGEF1-BGHcLV27-14
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2021-11-19	2021-11-19	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV48H_biosample_protocol	LV48H_library_protocol				LV48H_biosample_protocol	LV48H_library_protocol
protocol_URL		ARHGEF1-BGHcLV27-13.pdf	L-ARHGEF1-BGHcLV27-13.pdf				ARHGEF1-BGHcLV27-14.pdf	L-ARHGEF1-BGHcLV27-14.pdf
ID	3438	3510	3644	3778	3912	7093	3511	3645	3779	3913

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
ARHGEF1-BGHcLV27-13_S67_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1797	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3788
ARHGEF1-BGHcLV27-13_S67_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1797	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3814
ARHGEF1-BGHcLV27-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1797					GRCh38	V40	ARHGEF1-BGHcLV27-13_S67_L003_R1_001.filtered.trimmed.paired.fastq.gz,ARHGEF1-BGHcLV27-13_S67_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25475
ARHGEF1-BGHcLV27-13_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1797					GRCh38	V40	ARHGEF1-BGHcLV27-13_S67_L003_R1_001.filtered.trimmed.paired.fastq.gz,ARHGEF1-BGHcLV27-13_S67_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25501
ARHGEF1-BGHcLV27-13_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1797					GRCh38	V40	ARHGEF1-BGHcLV27-13/Aligned.sortedByCoord.out.bam		ENCORE2	26439
ARHGEF1-BGHcLV27-13_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1797					GRCh38	V40	ARHGEF1-BGHcLV27-13/Aligned.sortedByCoord.out.bam		ENCORE2	26465
ARHGEF1-BGHcLV27-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1797					GRCh38	V40	ARHGEF1-BGHcLV27-13/Aligned.sortedByCoord.out.bam		ENCORE2	26491
ARHGEF1-BGHcLV27-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1797					GRCh38	V40	ARHGEF1-BGHcLV27-13/Aligned.sortedByCoord.out.bam		ENCORE2	26517
ARHGEF1-BGHcLV27-14_S68_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1798	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3789
ARHGEF1-BGHcLV27-14_S68_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1798	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3815
ARHGEF1-BGHcLV27-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1798					GRCh38	V40	ARHGEF1-BGHcLV27-14_S68_L003_R1_001.filtered.trimmed.paired.fastq.gz,ARHGEF1-BGHcLV27-14_S68_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25476
ARHGEF1-BGHcLV27-14_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1798					GRCh38	V40	ARHGEF1-BGHcLV27-14_S68_L003_R1_001.filtered.trimmed.paired.fastq.gz,ARHGEF1-BGHcLV27-14_S68_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25502
ARHGEF1-BGHcLV27-14_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1798					GRCh38	V40	ARHGEF1-BGHcLV27-14/Aligned.sortedByCoord.out.bam		ENCORE2	26440
ARHGEF1-BGHcLV27-14_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1798					GRCh38	V40	ARHGEF1-BGHcLV27-14/Aligned.sortedByCoord.out.bam		ENCORE2	26466
ARHGEF1-BGHcLV27-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1798					GRCh38	V40	ARHGEF1-BGHcLV27-14/Aligned.sortedByCoord.out.bam		ENCORE2	26492
ARHGEF1-BGHcLV27-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1798					GRCh38	V40	ARHGEF1-BGHcLV27-14/Aligned.sortedByCoord.out.bam		ENCORE2	26518