DHX15 RNA-Seq in HepG2

General Information


RBP	DHX15
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DHX15-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	DHX15-BGHcLV39-13
Rep2	DHX15-BGHcLV39-14
CN1	NT-BGHcLV39-1
CN2	NT-BGHcLV39-2
Rep1_qPCR	26.9
Rep2_qPCR	9.5
Rep1_WB	76.7
Rep2_WB	75.4
Antibody Cat#	A300-390A
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1244

Experiment Information (Status: Submitting)

	BGHcLV39-13	BGHcLV39-14
idx	1213	1214
TRCN#_or_BGC#	BGC#0000912	BGC#0000912
shRNA_or_gRNA_sequence	GCGGCACCGGTTGGACCTAG	GCGGCACCGGTTGGACCTAG
PAM	ggg	ggg
Name	DHX15_96	DHX15_96
Sample_ID	BGHcLV39-13	BGHcLV39-14
transduction_Date	6/10/23	6/10/23
days	D6	D6
RBP_name	DHX15	DHX15
qPCR_result	26.9	9.5
Ave_qPCR	18.2
RT-qPCR_primer-F	tgggtgttctgaaggaagttg
RT-qPCR_primer-R	cgcccaggaatagttaggag
protein_conc	1455	1402
WB_result	76.7	75.4
Ave_WB	76.1
WB_DONE_date	7/3/23
MW	91kd
IP
antibody_Cat#	A300-390A	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	7404	7405

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DHX15	Product_ID: A300-390A Lot_ID: 1 Source: Bethyl Labs Target Name: DHX15-human

Experiment Status

	BGHcLV39-13	BGHcLV39-14
Sample_ID	BGHcLV39-13	BGHcLV39-14
Sample Name
Sample Name	DHX15-BGHcLV39-13	DHX15-BGHcLV39-14
RBP	DHX15	DHX15
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-12-30	2023-12-30
Project	ENCORE2	ENCORE2
Note
ID	11980	11981

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV39-13	BGHcLV39-14
Sample #	7	8
Sample Name	DHX15-BGHcLV39-13	DHX15-BGHcLV39-14
Sample_Name_Alias
Index Well Position	G01	H01
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	273	266
Peak_Molarity	40.30	34.70
libSampleQC_DNA_Well	DNA_Library_set63/set1/G9.png	DNA_Library_set63/set1/H9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set63/set1/G9.png	RNA_Library_set63/set1/H9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-08-30	2023-08-30
Sample_ID	BGHcLV39-13	BGHcLV39-14
RBP	DHX15	DHX15
Batch_ID	BGHcLV39	BGHcLV39
WB_result	76.700	75.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3750	3751

Sequencing Information

	BGHcLV39-13	BGHcLV39-14
Sample_ID	BGHcLV39-13	BGHcLV39-14
Sample Name	DHX15-BGHcLV39-13	DHX15-BGHcLV39-14
Pool ID	Pool-230830	Pool-230830
LocalServer_folder	set63	set63
total_reads	19,222,333	15,832,801
total_aligned_reads	14,657,378	10,967,509
unique_aligned_reads	13,819,946	10,354,580
percent_uniqueAligned	0.71895	0.65400
correlation_replicates	0.999027	0.999027
spikein_reads	13,086	6,488
percent_spikeins	0.00068	0.00041
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2649	2650

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
DHX15-BGHcLV39-13_S482_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2649	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	8634
DHX15-BGHcLV39-13_S482_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2649	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	8660
DHX15-BGHcLV39-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2649					GRCh38	V40	DHX15-BGHcLV39-13_S482_L004_R1_001.filtered.trimmed.paired.fastq.gz,DHX15-BGHcLV39-13_S482_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9931
DHX15-BGHcLV39-13_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	2649					GRCh38	V40	DHX15-BGHcLV39-13/Aligned.sortedByCoord.out.bam		ENCORE2	9957
DHX15-BGHcLV39-13_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	2649					GRCh38	V40	DHX15-BGHcLV39-13/Aligned.sortedByCoord.out.bam		ENCORE2	9983
DHX15-BGHcLV39-13_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	2649					GRCh38	V40	DHX15-BGHcLV39-13/Aligned.sortedByCoord.out.bam		ENCORE2	10009
DHX15-BGHcLV39-13_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	2649					GRCh38	V40	DHX15-BGHcLV39-13/Aligned.sortedByCoord.out.bam		ENCORE2	10035
DHX15-BGHcLV39-13_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2649					GRCh38	V40	DHX15-BGHcLV39-13_S482_L004_R1_001.filtered.trimmed.paired.fastq.gz,DHX15-BGHcLV39-13_S482_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10061
DHX15-BGHcLV39-14_S483_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2650	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	8635
DHX15-BGHcLV39-14_S483_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2650	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	8661
DHX15-BGHcLV39-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2650					GRCh38	V40	DHX15-BGHcLV39-14_S483_L004_R1_001.filtered.trimmed.paired.fastq.gz,DHX15-BGHcLV39-14_S483_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9932
DHX15-BGHcLV39-14_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	2650					GRCh38	V40	DHX15-BGHcLV39-14/Aligned.sortedByCoord.out.bam		ENCORE2	9958
DHX15-BGHcLV39-14_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	2650					GRCh38	V40	DHX15-BGHcLV39-14/Aligned.sortedByCoord.out.bam		ENCORE2	9984
DHX15-BGHcLV39-14_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	2650					GRCh38	V40	DHX15-BGHcLV39-14/Aligned.sortedByCoord.out.bam		ENCORE2	10010
DHX15-BGHcLV39-14_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	2650					GRCh38	V40	DHX15-BGHcLV39-14/Aligned.sortedByCoord.out.bam		ENCORE2	10036
DHX15-BGHcLV39-14_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2650					GRCh38	V40	DHX15-BGHcLV39-14_S483_L004_R1_001.filtered.trimmed.paired.fastq.gz,DHX15-BGHcLV39-14_S483_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10062