DHX9 RNA-Seq in K562

General Information


RBP	DHX9
Cell_Line	K562
Method	CRISPR
Exp_Name	DHX9-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	DHX9-BGKcLV38-9
Rep2	DHX9-BGKcLV38-10
CN1	NT-BGKcLV38-1
CN2	NT-BGKcLV38-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	69.2
Rep2_WB	62.5
Antibody Cat#	A300-855A
Antibody Lot#	lot # 3
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1025

Experiment Information (Status: Submitting)

	BGKcLV38-9	BGKcLV38-9	BGKcLV38-10	BGKcLV38-10
idx	1426	1426	1427	1427
TRCN#_or_BGC#	BGC#0000920	BGC#0000920	BGC#0000920	BGC#0000920
shRNA_or_gRNA_sequence	GGTTATAATTACACTGGCAT	GGTTATAATTACACTGGCAT	GGTTATAATTACACTGGCAT	GGTTATAATTACACTGGCAT
PAM	ggg	ggg	ggg	ggg
Name	DHX9_81	DHX9_81	DHX9_81	DHX9_81
Sample_ID	BGKcLV38-9	BGKcLV38-9	BGKcLV38-10	BGKcLV38-10
transduction_Date	10/18/22	10/18/22	10/18/22	10/18/22
days	D6	D6	D6	D6
RBP_name	DHX9	DHX9	DHX9	DHX9
qPCR_result	0.0	0.0	0.0	0.0
Ave_qPCR	0.0	0.0
RT-qPCR_primer-F	ttggatgctgtgattgaagc	ttggatgctgtgattgaagc
RT-qPCR_primer-R	gattcgtcccaaaggagtca	gattcgtcccaaaggagtca
protein_conc	2935	2935	3258	3258
WB_result	69.2	no clear band on the position	62.5
Ave_WB	65.9
WB_DONE_date	10/26/22,12/12/22	7/3/23,7/19/23
MW	141KD	141KD
IP
antibody_Cat#	A300-855A	A300-854A	lot # 3	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	5588	5590	5589	5591

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DHX9	Product_ID: A300-855A Lot_ID: 3 Source: Bethyl Labs Target Name: DHX9-human

Experiment Status

	BGKcLV38-9	BGKcLV38-10
Sample_ID	BGKcLV38-9	BGKcLV38-10
Sample Name
Sample Name	DHX9-BGKcLV38-9	DHX9-BGKcLV38-10
RBP	DHX9	DHX9
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11022	11023

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV38-9	BGKcLV38-10
Sample #	57	58
Sample Name	DHX9-BGKcLV38-9	DHX9-BGKcLV38-10
Sample_Name_Alias
Index Well Position	G08	H08
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	322	298
Peak_Molarity	66.90	57.50
libSampleQC_DNA_Well	DNA_Library_set54-56/set2/G8.png	DNA_Library_set54-56/set2/H8.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set54-56/set1/A8.png	RNA_Library_set54-56/set1/B8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV38-9	BGKcLV38-10
RBP	DHX9	DHX9
Batch_ID	BGKcLV38	BGKcLV38
WB_result	69.200	62.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3428	3429

Sequencing Information

	BGKcLV38-9	BGKcLV38-10
Sample_ID	BGKcLV38-9	BGKcLV38-10
Sample Name	DHX9-BGKcLV38-9	DHX9-BGKcLV38-10
Pool ID	Pool-230127C	Pool-230127C
LocalServer_folder	set56	set56
total_reads	62,111,110	54,899,727
total_aligned_reads	58,314,756	51,651,296
unique_aligned_reads	54,095,619	47,704,819
percent_uniqueAligned	0.87095	0.86894
correlation_replicates	0.994564	0.994564
spikein_reads	19,868	18,604
percent_spikeins	0.00032	0.00034
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2301	2302

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
DHX9-BGKcLV38-9_S57_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2301	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	8307
DHX9-BGKcLV38-9_S57_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2301	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	8345
DHX9-BGKcLV38-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2301					GRCh38	V40	DHX9-BGKcLV38-9_S57_L002_R1_001.filtered.trimmed.paired.fastq.gz,DHX9-BGKcLV38-9_S57_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16959
DHX9-BGKcLV38-9_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	2301					GRCh38	V40	DHX9-BGKcLV38-9/Aligned.sortedByCoord.out.bam		ENCORE2	16997
DHX9-BGKcLV38-9_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	2301					GRCh38	V40	DHX9-BGKcLV38-9/Aligned.sortedByCoord.out.bam		ENCORE2	17035
DHX9-BGKcLV38-9_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	2301					GRCh38	V40	DHX9-BGKcLV38-9/Aligned.sortedByCoord.out.bam		ENCORE2	17073
DHX9-BGKcLV38-9_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	2301					GRCh38	V40	DHX9-BGKcLV38-9/Aligned.sortedByCoord.out.bam		ENCORE2	17111
DHX9-BGKcLV38-9_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2301					GRCh38	V40	DHX9-BGKcLV38-9_S57_L002_R1_001.filtered.trimmed.paired.fastq.gz,DHX9-BGKcLV38-9_S57_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17149
DHX9-BGKcLV38-10_S58_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2302	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	8306
DHX9-BGKcLV38-10_S58_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2302	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	8344
DHX9-BGKcLV38-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2302					GRCh38	V40	DHX9-BGKcLV38-10_S58_L002_R1_001.filtered.trimmed.paired.fastq.gz,DHX9-BGKcLV38-10_S58_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16958
DHX9-BGKcLV38-10_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	2302					GRCh38	V40	DHX9-BGKcLV38-10/Aligned.sortedByCoord.out.bam		ENCORE2	16996
DHX9-BGKcLV38-10_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	2302					GRCh38	V40	DHX9-BGKcLV38-10/Aligned.sortedByCoord.out.bam		ENCORE2	17034
DHX9-BGKcLV38-10_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	2302					GRCh38	V40	DHX9-BGKcLV38-10/Aligned.sortedByCoord.out.bam		ENCORE2	17072
DHX9-BGKcLV38-10_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	2302					GRCh38	V40	DHX9-BGKcLV38-10/Aligned.sortedByCoord.out.bam		ENCORE2	17110
DHX9-BGKcLV38-10_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2302					GRCh38	V40	DHX9-BGKcLV38-10_S58_L002_R1_001.filtered.trimmed.paired.fastq.gz,DHX9-BGKcLV38-10_S58_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17148