ARHGEF2 RNA-Seq in K562

General Information


RBP	ARHGEF2
Cell_Line	K562
Method	CRISPR
Exp_Name	ARHGEF2-BGKcLV26-K562
ENCODE_series_ID	ENCSR561KET
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR233MJI
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	ARHGEF2-BGKcLV26-31
Rep2	ARHGEF2-BGKcLV26-32
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR	22.2
Rep2_qPCR	16.0
Rep1_WB	49.8
Rep2_WB	57.6
Antibody Cat#	A301-928A
Antibody Lot#	LOT# 2
Antibody DCC ID	ENCAB200GVD
Status	Released
Project	ENCODE4
ID	793

Experiment Information (Status: Released)

	BGKcLV26-31	BGKcLV26-31	BGKcLV26-32	BGKcLV26-32
idx	888	890	889	891
TRCN#_or_BGC#	BGC#0000637	BGC#0000637	BGC#0000637	BGC#0000637
shRNA_or_gRNA_sequence	AGGATGCCCGCTATACCAAT	AGGATGCCCGCTATACCAAT	AGGATGCCCGCTATACCAAT	AGGATGCCCGCTATACCAAT
PAM	GGG	GGG	GGG	GGG
Name	ARHGEF2_96	ARHGEF2_96	ARHGEF2_96	ARHGEF2_96
Sample_ID	BGKcLV26-31	BGKcLV26-31	BGKcLV26-32	BGKcLV26-32
transduction_Date	3/30/21	3/30/21	3/30/21	3/30/21
days	Day 6	Day 6	Day 6	Day 6
RBP_name	ARHGEF2	ARHGEF2	ARHGEF2	ARHGEF2
qPCR_result	22.2	22.2	16.0	16.0
Ave_qPCR	19.1	19.1
RT-qPCR_primer-F	gcgatgccctgtacttgag	gcgatgccctgtacttgag
RT-qPCR_primer-R	tcggtcctcaaagtttcgat	tcggtcctcaaagtttcgat
protein_conc	5054	5054	4829	4829
WB_result	49.8	not as good as a301-928a	57.6
Ave_WB	53.7
WB_DONE_date	5/25/21	4/20/22	JESS
MW	115kDa	115kDa
IP	Rabbit / I	Rabbit / I
antibody_Cat#	A301-928A	A301-929A	LOT# 2	LOT# 1
Antibody DCC ID	ENCAB200GVD		10/22/21
submitted_to_DCC_date
Rep1_TPM	88.5	0	0	0
Rep2_TPM	91.8	0	0	0
Action	Ready		Ready
Library_start_date	09/01/21		09/01/21
repeat_library
Note
ID	5020	5022	5021	5023

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ARHGEF2	Product_ID: A301-928A Lot_ID: 2 Source: Bethyl Labs Target Name: ARHGEF2-human

Experiment Status

	BGKcLV26-31	BGKcLV26-32
Sample_ID	BGKcLV26-31	BGKcLV26-32
Sample Name
Sample Name	ARHGEF2-BGKcLV26-31	ARHGEF2-BGKcLV26-32
RBP	ARHGEF2	ARHGEF2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9767	9768

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-31	BGKcLV26-32
Sample #	25	26
Sample Name	ARHGEF2-BGKcLV26-31	ARHGEF2-BGKcLV26-32
Sample_Name_Alias
Index Well Position	A04	B04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-07-22	2021-07-22
Lib_ID	Lib-210722	Lib-210722
Tecan_Location
Tecan
Tecan_date
Size_bp	294	295
Peak_Molarity	110.00	119.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/A4.png	DNA_Library_set48-49/set1/B4.png
RIN	9.5	9.7
libSample_RNA_Well	RNA_Library_set48-49/set1/A4.png	RNA_Library_set48-49/set1/B4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-31	BGKcLV26-32
RBP	ARHGEF2	ARHGEF2
Batch_ID	BGKcLV26	BGKcLV26
WB_result	49.800	57.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1584	1585

Sequencing Information

	BGKcLV26-31	BGKcLV26-32
Sample_ID	BGKcLV26-31	BGKcLV26-32
Sample Name	ARHGEF2-BGKcLV26-31	ARHGEF2-BGKcLV26-32
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	89,983,608	60,280,680
total_aligned_reads	82,599,302	54,017,396
unique_aligned_reads	75,674,850	49,447,056
percent_uniqueAligned	0.84098	0.82028
correlation_replicates	0.999343	0.999343
spikein_reads	41,120	21,984
percent_spikeins	0.00046	0.00036
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1761	1762

Data Submission Information

	BGKcLV26-31	BGKcLV26-31	BGKcLV26-31	BGKcLV26-31	BGKcLV26-31	BGKcLV26-31	BGKcLV26-32	BGKcLV26-32	BGKcLV26-32	BGKcLV26-32
ENCODE_alias	brenton-graveley:ARHGEF2-BGKcLV26	brenton-graveley:ARHGEF2-BGKcLV26-31	brenton-graveley:L-ARHGEF2-BGKcLV26-31	brenton-graveley:ARHGEF2-BGKcLV26-31_S31_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ARHGEF2-BGKcLV26-31_S31_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ARHGEF2-BGKcLV26-K562	brenton-graveley:ARHGEF2-BGKcLV26-32	brenton-graveley:L-ARHGEF2-BGKcLV26-32	brenton-graveley:ARHGEF2-BGKcLV26-32_S32_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ARHGEF2-BGKcLV26-32_S32_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR233MJI	ENCBS158GLY	ENCLB377HZR	ENCFF432VBR	ENCFF244IQK	ENCSR561KET	ENCBS098LQT	ENCLB611BNQ	ENCFF955CLR	ENCFF881XBQ
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	BGKcLV26-31	BGKcLV26-31	BGKcLV26-31	BGKcLV26-31	BGKcLV26-31	BGKcLV26-31	BGKcLV26-32	BGKcLV26-32	BGKcLV26-32	BGKcLV26-32
Sample Name	ARHGEF2-BGKcLV26-31	ARHGEF2-BGKcLV26-31	ARHGEF2-BGKcLV26-31	ARHGEF2-BGKcLV26-31	ARHGEF2-BGKcLV26-31	ARHGEF2-BGKcLV26-31	ARHGEF2-BGKcLV26-32	ARHGEF2-BGKcLV26-32	ARHGEF2-BGKcLV26-32	ARHGEF2-BGKcLV26-32
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
		LV48K_biosample_protocol	LV48K_library_protocol				LV48K_biosample_protocol	LV48K_library_protocol
protocol_URL		ARHGEF2-BGKcLV26-31.pdf	L-ARHGEF2-BGKcLV26-31.pdf				ARHGEF2-BGKcLV26-32.pdf	L-ARHGEF2-BGKcLV26-32.pdf
ID	3458	3550	3684	3818	3952	7094	3551	3685	3819	3953

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-BGKcLV26-31_S31_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1761	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3854
ARHGEF2-BGKcLV26-31_S31_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1761	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3904
ARHGEF2-BGKcLV26-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1761					GRCh38	V40	ARHGEF2-BGKcLV26-31_S31_L003_R1_001.filtered.trimmed.paired.fastq.gz,ARHGEF2-BGKcLV26-31_S31_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25541
ARHGEF2-BGKcLV26-31_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1761					GRCh38	V40	ARHGEF2-BGKcLV26-31_S31_L003_R1_001.filtered.trimmed.paired.fastq.gz,ARHGEF2-BGKcLV26-31_S31_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25591
ARHGEF2-BGKcLV26-31_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1761					GRCh38	V40	ARHGEF2-BGKcLV26-31/Aligned.sortedByCoord.out.bam		ENCORE2	26557
ARHGEF2-BGKcLV26-31_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1761					GRCh38	V40	ARHGEF2-BGKcLV26-31/Aligned.sortedByCoord.out.bam		ENCORE2	26607
ARHGEF2-BGKcLV26-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1761					GRCh38	V40	ARHGEF2-BGKcLV26-31/Aligned.sortedByCoord.out.bam		ENCORE2	26657
ARHGEF2-BGKcLV26-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1761					GRCh38	V40	ARHGEF2-BGKcLV26-31/Aligned.sortedByCoord.out.bam		ENCORE2	26707
ARHGEF2-BGKcLV26-32_S32_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1762	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3855
ARHGEF2-BGKcLV26-32_S32_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1762	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3905
ARHGEF2-BGKcLV26-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1762					GRCh38	V40	ARHGEF2-BGKcLV26-32_S32_L003_R1_001.filtered.trimmed.paired.fastq.gz,ARHGEF2-BGKcLV26-32_S32_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25542
ARHGEF2-BGKcLV26-32_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1762					GRCh38	V40	ARHGEF2-BGKcLV26-32_S32_L003_R1_001.filtered.trimmed.paired.fastq.gz,ARHGEF2-BGKcLV26-32_S32_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25592
ARHGEF2-BGKcLV26-32_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1762					GRCh38	V40	ARHGEF2-BGKcLV26-32/Aligned.sortedByCoord.out.bam		ENCORE2	26558
ARHGEF2-BGKcLV26-32_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1762					GRCh38	V40	ARHGEF2-BGKcLV26-32/Aligned.sortedByCoord.out.bam		ENCORE2	26608
ARHGEF2-BGKcLV26-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1762					GRCh38	V40	ARHGEF2-BGKcLV26-32/Aligned.sortedByCoord.out.bam		ENCORE2	26658
ARHGEF2-BGKcLV26-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1762					GRCh38	V40	ARHGEF2-BGKcLV26-32/Aligned.sortedByCoord.out.bam		ENCORE2	26708