DIAPH1 RNA-Seq in HepG2

General Information


RBP	DIAPH1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DIAPH1-BGHcLV39-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV39
Pool ID	Pool-230830
Local_Set_Name	set63
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	DIAPH1-BGHcLV39-19
Rep2	DIAPH1-BGHcLV39-20
CN1	NT-BGHcLV39-1
CN2	NT-BGHcLV39-2
Rep1_qPCR	49.8
Rep2_qPCR	50.1
Rep1_WB	65.547
Rep2_WB	61.8
Antibody Cat#	A300-078A
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1245

Experiment Information (Status: Submitting)

	BGHcLV39-19	BGHcLV39-20
idx	1219	1220
TRCN#_or_BGC#	BGC#0000921	BGC#0000921
shRNA_or_gRNA_sequence	CGGGACATGGAGCCGCCCGG	CGGGACATGGAGCCGCCCGG
PAM	cgg	cgg
Name	DIAPH1_89	DIAPH1_89
Sample_ID	BGHcLV39-19	BGHcLV39-20
transduction_Date	6/10/23	6/10/23
days	D6	D6
RBP_name	DIAPH1	DIAPH1
qPCR_result	49.8	50.1
Ave_qPCR	50.0
RT-qPCR_primer-F	cagcaaattgccacagagaa
RT-qPCR_primer-R	tcttggcatcttccagttcc
protein_conc	1308	1492
WB_result	65.547	61.8
Ave_WB	63.7
WB_DONE_date	7/3/23,7/19/23
MW	142KD
IP
antibody_Cat#	A300-078A	lot# 1
Antibody DCC ID
submitted_to_DCC_date	9/6/23
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	7410	7411

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DIAPH1	Product_ID: A300-078A Lot_ID: 1 Source: Bethyl Labs Target Name: DIAPH1-human

Experiment Status

	BGHcLV39-19	BGHcLV39-20
Sample_ID	BGHcLV39-19	BGHcLV39-20
Sample Name
Sample Name	DIAPH1-BGHcLV39-19	DIAPH1-BGHcLV39-20
RBP	DIAPH1	DIAPH1
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-12-30	2023-12-30
Project	ENCORE2	ENCORE2
Note
ID	11982	11983

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV39-19	BGHcLV39-20
Sample #	9	10
Sample Name	DIAPH1-BGHcLV39-19	DIAPH1-BGHcLV39-20
Sample_Name_Alias
Index Well Position	A02	B02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-08-28	2023-08-28
Lib_ID	Lib-230828	Lib-230828
Tecan_Location
Tecan
Tecan_date
Size_bp	280	274
Peak_Molarity	53.70	51.00
libSampleQC_DNA_Well	DNA_Library_set63/set1/A10.png	DNA_Library_set63/set1/B10.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set63/set1/A10.png	RNA_Library_set63/set1/B10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-08-30	2023-08-30
Sample_ID	BGHcLV39-19	BGHcLV39-20
RBP	DIAPH1	DIAPH1
Batch_ID	BGHcLV39	BGHcLV39
WB_result	65.547	61.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3752	3753

Sequencing Information

	BGHcLV39-19	BGHcLV39-20
Sample_ID	BGHcLV39-19	BGHcLV39-20
Sample Name	DIAPH1-BGHcLV39-19	DIAPH1-BGHcLV39-20
Pool ID	Pool-230830	Pool-230830
LocalServer_folder	set63	set63
total_reads	13,787,401	17,584,855
total_aligned_reads	10,878,486	14,102,282
unique_aligned_reads	10,270,088	13,318,362
percent_uniqueAligned	0.74489	0.75738
correlation_replicates	0.999648	0.999648
spikein_reads	17,376	21,528
percent_spikeins	0.00126	0.00122
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2651	2652

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
DIAPH1-BGHcLV39-19_S484_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2651	NovaSeq6000	100	paired-ended	1				NT-BGHcLV39-1_S476_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8636
DIAPH1-BGHcLV39-19_S484_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2651	NovaSeq6000	100	paired-ended	2				NT-BGHcLV39-1_S476_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8662
DIAPH1-BGHcLV39-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2651					GRCh38	V40	DIAPH1-BGHcLV39-19_S484_L004_R1_001.filtered.trimmed.paired.fastq.gz,DIAPH1-BGHcLV39-19_S484_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9933
DIAPH1-BGHcLV39-19_Signal.Unique.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2651					GRCh38	V40	DIAPH1-BGHcLV39-19/Aligned.sortedByCoord.out.bam		ENCORE2	9959
DIAPH1-BGHcLV39-19_Signal.Unique.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2651					GRCh38	V40	DIAPH1-BGHcLV39-19/Aligned.sortedByCoord.out.bam		ENCORE2	9985
DIAPH1-BGHcLV39-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2651					GRCh38	V40	DIAPH1-BGHcLV39-19/Aligned.sortedByCoord.out.bam		ENCORE2	10011
DIAPH1-BGHcLV39-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2651					GRCh38	V40	DIAPH1-BGHcLV39-19/Aligned.sortedByCoord.out.bam		ENCORE2	10037
DIAPH1-BGHcLV39-19_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2651					GRCh38	V40	DIAPH1-BGHcLV39-19_S484_L004_R1_001.filtered.trimmed.paired.fastq.gz,DIAPH1-BGHcLV39-19_S484_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10063
DIAPH1-BGHcLV39-20_S485_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2652	NovaSeq6000	100	paired-ended	1				NT-BGHcLV39-1_S476_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8637
DIAPH1-BGHcLV39-20_S485_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2652	NovaSeq6000	100	paired-ended	2				NT-BGHcLV39-1_S476_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8663
DIAPH1-BGHcLV39-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2652					GRCh38	V40	DIAPH1-BGHcLV39-20_S485_L004_R1_001.filtered.trimmed.paired.fastq.gz,DIAPH1-BGHcLV39-20_S485_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9934
DIAPH1-BGHcLV39-20_Signal.Unique.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2652					GRCh38	V40	DIAPH1-BGHcLV39-20/Aligned.sortedByCoord.out.bam		ENCORE2	9960
DIAPH1-BGHcLV39-20_Signal.Unique.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2652					GRCh38	V40	DIAPH1-BGHcLV39-20/Aligned.sortedByCoord.out.bam		ENCORE2	9986
DIAPH1-BGHcLV39-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2652					GRCh38	V40	DIAPH1-BGHcLV39-20/Aligned.sortedByCoord.out.bam		ENCORE2	10012
DIAPH1-BGHcLV39-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2652					GRCh38	V40	DIAPH1-BGHcLV39-20/Aligned.sortedByCoord.out.bam		ENCORE2	10038
DIAPH1-BGHcLV39-20_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2652					GRCh38	V40	DIAPH1-BGHcLV39-20_S485_L004_R1_001.filtered.trimmed.paired.fastq.gz,DIAPH1-BGHcLV39-20_S485_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10064