DHX15 RNA-Seq in K562

General Information


RBP	DHX15
Cell_Line	K562
Method	CRISPR
Exp_Name	DHX15-BGKcLV38-K562
ENCODE_series_ID
Batch_ID	BGKcLV38
Pool ID	Pool-230127C
Local_Set_Name	set56
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	DHX15-BGKcLV38-3
Rep2	DHX15-BGKcLV38-4
CN1	NT-BGKcLV38-1
CN2	NT-BGKcLV38-2
Rep1_qPCR	32.1
Rep2_qPCR	21.6
Rep1_WB	74.3
Rep2_WB	83.0
Antibody Cat#	A300-390A
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1023

Experiment Information (Status: Submitting)

	BGKcLV38-3	BGKcLV38-4
idx	1420	1421
TRCN#_or_BGC#	BGC#0000912	BGC#0000912
shRNA_or_gRNA_sequence	GCGGCACCGGTTGGACCTAG	GCGGCACCGGTTGGACCTAG
PAM	ggg	ggg
Name	DHX15_96	DHX15_96
Sample_ID	BGKcLV38-3	BGKcLV38-4
transduction_Date	10/18/22	10/18/22
days	D6	D6
RBP_name	DHX15	DHX15
qPCR_result	32.1	21.6
Ave_qPCR	26.8
RT-qPCR_primer-F	tgggtgttctgaaggaagttg
RT-qPCR_primer-R	cgcccaggaatagttaggag
protein_conc	2952	3471
WB_result	74.3	83.0
Ave_WB	78.7
WB_DONE_date	10/26/22
MW	91kd
IP
antibody_Cat#	A300-390A	lot# 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5582	5583

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

	BGKcLV38-3	BGKcLV38-4
Sample_ID	BGKcLV38-3	BGKcLV38-4
Sample Name
Sample Name	DHX15-BGKcLV38-3	DHX15-BGKcLV38-4
RBP	DHX15	DHX15
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11018	11019

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV38-3	BGKcLV38-4
Sample #	53	54
Sample Name	DHX15-BGKcLV38-3	DHX15-BGKcLV38-4
Sample_Name_Alias
Index Well Position	C08	D08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-01-19	2023-01-19
Lib_ID	Lib-230119	Lib-230119
Tecan_Location
Tecan
Tecan_date
Size_bp	309	310
Peak_Molarity	53.80	66.70
libSampleQC_DNA_Well	DNA_Library_set54-56/set2/C8.png	DNA_Library_set54-56/set2/D8.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set54-56/set1/E7.png	RNA_Library_set54-56/set1/F7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV38-3	BGKcLV38-4
RBP	DHX15	DHX15
Batch_ID	BGKcLV38	BGKcLV38
WB_result	74.300	83.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3424	3425

Sequencing Information

	BGKcLV38-3	BGKcLV38-4
Sample_ID	BGKcLV38-3	BGKcLV38-4
Sample Name	DHX15-BGKcLV38-3	DHX15-BGKcLV38-4
Pool ID	Pool-230127C	Pool-230127C
LocalServer_folder	set56	set56
total_reads	32,676,054	39,244,657
total_aligned_reads	29,618,962	35,984,481
unique_aligned_reads	27,481,686	33,521,372
percent_uniqueAligned	0.84103	0.85416
correlation_replicates	0.997109	0.997109
spikein_reads	11,698	10,718
percent_spikeins	0.00036	0.00027
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2297	2298

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-BGKcLV38-3_S53_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2297	NovaSeq6000	100	paired-ended	1				NT-BGKcLV38-1_S51_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8302
DHX15-BGKcLV38-3_S53_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2297	NovaSeq6000	100	paired-ended	2				NT-BGKcLV38-1_S51_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8340
DHX15-BGKcLV38-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2297					GRCh38	V40	DHX15-BGKcLV38-3_S53_L002_R1_001.filtered.trimmed.paired.fastq.gz,DHX15-BGKcLV38-3_S53_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16954
DHX15-BGKcLV38-3_Signal.Unique.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2297					GRCh38	V40	DHX15-BGKcLV38-3/Aligned.sortedByCoord.out.bam		ENCORE2	16992
DHX15-BGKcLV38-3_Signal.Unique.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2297					GRCh38	V40	DHX15-BGKcLV38-3/Aligned.sortedByCoord.out.bam		ENCORE2	17030
DHX15-BGKcLV38-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2297					GRCh38	V40	DHX15-BGKcLV38-3/Aligned.sortedByCoord.out.bam		ENCORE2	17068
DHX15-BGKcLV38-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2297					GRCh38	V40	DHX15-BGKcLV38-3/Aligned.sortedByCoord.out.bam		ENCORE2	17106
DHX15-BGKcLV38-3_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2297					GRCh38	V40	DHX15-BGKcLV38-3_S53_L002_R1_001.filtered.trimmed.paired.fastq.gz,DHX15-BGKcLV38-3_S53_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17144
DHX15-BGKcLV38-4_S54_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2298	NovaSeq6000	100	paired-ended	1				NT-BGKcLV38-1_S51_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8303
DHX15-BGKcLV38-4_S54_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2298	NovaSeq6000	100	paired-ended	2				NT-BGKcLV38-1_S51_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8341
DHX15-BGKcLV38-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2298					GRCh38	V40	DHX15-BGKcLV38-4_S54_L002_R1_001.filtered.trimmed.paired.fastq.gz,DHX15-BGKcLV38-4_S54_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16955
DHX15-BGKcLV38-4_Signal.Unique.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2298					GRCh38	V40	DHX15-BGKcLV38-4/Aligned.sortedByCoord.out.bam		ENCORE2	16993
DHX15-BGKcLV38-4_Signal.Unique.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2298					GRCh38	V40	DHX15-BGKcLV38-4/Aligned.sortedByCoord.out.bam		ENCORE2	17031
DHX15-BGKcLV38-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2298					GRCh38	V40	DHX15-BGKcLV38-4/Aligned.sortedByCoord.out.bam		ENCORE2	17069
DHX15-BGKcLV38-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2298					GRCh38	V40	DHX15-BGKcLV38-4/Aligned.sortedByCoord.out.bam		ENCORE2	17107
DHX15-BGKcLV38-4_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2298					GRCh38	V40	DHX15-BGKcLV38-4_S54_L002_R1_001.filtered.trimmed.paired.fastq.gz,DHX15-BGKcLV38-4_S54_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17145