ARHGEF1 RNA-Seq in K562

General Information


RBP	ARHGEF1
Cell_Line	K562
Method	CRISPR
Exp_Name	ARHGEF1-BGKcLV35-K562
ENCODE_series_ID
Batch_ID	BGKcLV35
Pool ID	Pool-220720
Local_Set_Name	set54
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	ARHGEF1-BGKcLV35-3
Rep2	ARHGEF1-BGKcLV35-4
CN1	NT-BGKcLV35-1
CN2	NT-BGKcLV35-2
Rep1_qPCR	xx
Rep2_qPCR	xx
Rep1_WB	69.7
Rep2_WB	68.6
Antibody Cat#	A302-701A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB133PSK
Status	Submitted
Project	ENCORE2
ID	951

Experiment Information (Status: Submitting)

	BGKcLV35-3	BGKcLV35-3	BGKcLV35-3	BGKcLV35-4	BGKcLV35-4	BGKcLV35-4
idx	1278	1280	1280	1279	1281	1281
TRCN#_or_BGC#	BGC#0000636	BGC#0000636	BGC#0000636	BGC#0000636	BGC#0000636	BGC#0000636
shRNA_or_gRNA_sequence	TCTCCGAGGATGTCCAGCGG	TCTCCGAGGATGTCCAGCGG	TCTCCGAGGATGTCCAGCGG	TCTCCGAGGATGTCCAGCGG	TCTCCGAGGATGTCCAGCGG	TCTCCGAGGATGTCCAGCGG
PAM	CGG	CGG	CGG	CGG	CGG	CGG
Name	ARHGEF1_92	ARHGEF1_92	ARHGEF1_92	ARHGEF1_92	ARHGEF1_92	ARHGEF1_92
Sample_ID	BGKcLV35-3	BGKcLV35-3	BGKcLV35-3	BGKcLV35-4	BGKcLV35-4	BGKcLV35-4
transduction_Date	4/28/22	4/28/22	4/28/22	4/28/22	4/28/22	4/28/22
days	D6	D6	D6	D6	D6	D6
RBP_name	ARHGEF1	ARHGEF1	ARHGEF1	ARHGEF1	ARHGEF1	ARHGEF1
qPCR_result	6.0	6.0	6.0	0.0	0.0	0.0
Ave_qPCR	3.0	3.0	3.0
RT-qPCR_primer-F	ctctgagaacggcaatggtg	ctctgagaacggcaatggtg	ctctgagaacggcaatggtg
RT-qPCR_primer-R	gcaggaggtcactgaggatt	gcaggaggtcactgaggatt	gcaggaggtcactgaggatt
protein_conc	3171	3171	3171	3172	3172	3172
WB_result	69.7	74.3	74.9	68.6	88.2244	81.526
Ave_WB	69.2	81.3	78.2
WB_DONE_date	5/31/22	4/18/24	4/18/24
MW	102kDa	102kDa	102kDa
IP	Rabbit / I	Rabbit / I
antibody_Cat#	A302-701A	A302-702A	3669S	LOT# 1	LOT# 1	lot# 3
Antibody DCC ID	ENCAB133PSK
submitted_to_DCC_date	8/16/22
Rep1_TPM	0	0	0	0	0	0
Rep2_TPM	0	0	0	0	0	0
Action	Ready			Ready
Library_start_date	06/17/22			06/17/22
repeat_library
Note
ID	5420	5422	5424	5421	5423	5425

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
ARHGEF1	Product_ID: 3669S Lot_ID: 3 Source: Cell Signaling Technology Target Name: ARHGEF1-human
ARHGEF1	Product_ID: A302-702A Lot_ID: 1 Source: Bethyl Labs Target Name: ARHGEF1-human

Experiment Status

	BGKcLV35-3	BGKcLV35-3	BGKcLV35-4	BGKcLV35-4
Sample_ID	BGKcLV35-3	BGKcLV35-3	BGKcLV35-4	BGKcLV35-4
Sample Name
Sample Name	ARHGEF1-BGKcLV35-3		ARHGEF1-BGKcLV35-4
RBP	ARHGEF1	ARHGEF1	ARHGEF1	ARHGEF1
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2023-04-14	2022-06-16	2023-04-14	2022-06-16
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	10859	10883	10860	10884

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV35-3	BGKcLV35-4
Sample #	25	26
Sample Name	ARHGEF1-BGKcLV35-3	ARHGEF1-BGKcLV35-4
Sample_Name_Alias
Index Well Position	A04	B04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-06-17	2022-06-17
Lib_ID	Lib-220617	Lib-220617
Tecan_Location
Tecan
Tecan_date
Size_bp	291	300
Peak_Molarity	27.80	9.83
libSampleQC_DNA_Well	DNA_Library_set54-56/set3/A8.png	DNA_Library_set54-56/set3/B8.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set54-56/set2/A4.png	RNA_Library_set54-56/set2/B4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-06-20	2022-06-20
Sample_ID	BGKcLV35-3	BGKcLV35-4
RBP	ARHGEF1	ARHGEF1
Batch_ID	BGKcLV35	BGKcLV35
WB_result	69.700	68.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3342	3343

Sequencing Information

	BGKcLV35-3	BGKcLV35-4
Sample_ID	BGKcLV35-3	BGKcLV35-4
Sample Name	ARHGEF1-BGKcLV35-3	ARHGEF1-BGKcLV35-4
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	50,416,166	50,638,176
total_aligned_reads	43,697,758	43,838,056
unique_aligned_reads	40,187,778	40,406,874
percent_uniqueAligned	0.79712	0.79795
correlation_replicates	0.979257	0.979257
spikein_reads	5,996	4,040
percent_spikeins	0.00012	0.00008
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2221	2222

Data Submission Information DCC submission information was not avaliable

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-BGKcLV35-3_S27_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2221	NovaSeq6000	100	paired-ended	1				NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8478
ARHGEF1-BGKcLV35-3_S27_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2221	NovaSeq6000	100	paired-ended	2				NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8528
ARHGEF1-BGKcLV35-3_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2221					GRCh38	V40	ARHGEF1-BGKcLV35-3/Aligned.sortedByCoord.out.bam		ENCORE2	17724
ARHGEF1-BGKcLV35-3_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2221					GRCh38	V40	ARHGEF1-BGKcLV35-3/Aligned.sortedByCoord.out.bam		ENCORE2	17774
ARHGEF1-BGKcLV35-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2221					GRCh38	V40	ARHGEF1-BGKcLV35-3/Aligned.sortedByCoord.out.bam		ENCORE2	17824
ARHGEF1-BGKcLV35-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2221					GRCh38	V40	ARHGEF1-BGKcLV35-3/Aligned.sortedByCoord.out.bam		ENCORE2	17874
ARHGEF1-BGKcLV35-3_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2221					GRCh38	V40	ARHGEF1-BGKcLV35-3_S27_R1_001.filtered.trimmed.paired.fastq.gz,ARHGEF1-BGKcLV35-3_S27_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17924
ARHGEF1-BGKcLV35-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2221					GRCh38	V40	ARHGEF1-BGKcLV35-3_S27_R1_001.filtered.trimmed.paired.fastq.gz,ARHGEF1-BGKcLV35-3_S27_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29265
ARHGEF1-BGKcLV35-4_S28_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2222	NovaSeq6000	100	paired-ended	1				NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8479
ARHGEF1-BGKcLV35-4_S28_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2222	NovaSeq6000	100	paired-ended	2				NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8529
ARHGEF1-BGKcLV35-4_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2222					GRCh38	V40	ARHGEF1-BGKcLV35-4/Aligned.sortedByCoord.out.bam		ENCORE2	17725
ARHGEF1-BGKcLV35-4_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2222					GRCh38	V40	ARHGEF1-BGKcLV35-4/Aligned.sortedByCoord.out.bam		ENCORE2	17775
ARHGEF1-BGKcLV35-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2222					GRCh38	V40	ARHGEF1-BGKcLV35-4/Aligned.sortedByCoord.out.bam		ENCORE2	17825
ARHGEF1-BGKcLV35-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2222					GRCh38	V40	ARHGEF1-BGKcLV35-4/Aligned.sortedByCoord.out.bam		ENCORE2	17875
ARHGEF1-BGKcLV35-4_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2222					GRCh38	V40	ARHGEF1-BGKcLV35-4_S28_R1_001.filtered.trimmed.paired.fastq.gz,ARHGEF1-BGKcLV35-4_S28_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17925
ARHGEF1-BGKcLV35-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2222					GRCh38	V40	ARHGEF1-BGKcLV35-4_S28_R1_001.filtered.trimmed.paired.fastq.gz,ARHGEF1-BGKcLV35-4_S28_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29266