DHX33 RNA-Seq in K562

General Information


RBP	DHX33
Cell_Line	K562
Method	CRISPR
Exp_Name	DHX33-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	DHX33-BGKcLV38-5
Rep2	DHX33-BGKcLV38-6
CN1	NT-BGKcLV38-1
CN2	NT-BGKcLV38-2
Rep1_qPCR	10.9
Rep2_qPCR	28.1
Rep1_WB	57.0
Rep2_WB	67.0
Antibody Cat#	A300-800A
Antibody Lot#	lot# 2
Antibody DCC ID	ENCAB339AHV
Status	Submitted
Project	ENCORE2
ID	1024

Experiment Information (Status: Submitting)

	BGKcLV38-5	BGKcLV38-6
idx	1422	1423
TRCN#_or_BGC#	BGC#0000913	BGC#0000913
shRNA_or_gRNA_sequence	CTGGAAGACGGAGACAAGCG	CTGGAAGACGGAGACAAGCG
PAM	cgg	cgg
Name	DHX33_85	DHX33_85
Sample_ID	BGKcLV38-5	BGKcLV38-6
transduction_Date	10/18/22	10/18/22
days	D6	D6
RBP_name	DHX33	DHX33
qPCR_result	10.9	28.1
Ave_qPCR	19.5
RT-qPCR_primer-F	cctgactccaatgggaagaa
RT-qPCR_primer-R	cacagacagcagggagacaa
protein_conc	3157	3147
WB_result	57.0	67.0
Ave_WB	62.0
WB_DONE_date	10/26/22
MW	79kd
IP
antibody_Cat#	A300-800A	lot# 2
Antibody DCC ID	ENCAB339AHV
submitted_to_DCC_date	8/30/23
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5584	5585

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DHX33	Product_ID: A300-800A Lot_ID: 2 Source: Bethyl Labs Target Name: DHX33-human

Experiment Status

	BGKcLV38-5	BGKcLV38-6
Sample_ID	BGKcLV38-5	BGKcLV38-6
Sample Name
Sample Name	DHX33-BGKcLV38-5	DHX33-BGKcLV38-6
RBP	DHX33	DHX33
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11020	11021

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV38-5	BGKcLV38-6
Sample #	55	56
Sample Name	DHX33-BGKcLV38-5	DHX33-BGKcLV38-6
Sample_Name_Alias
Index Well Position	E08	F08
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	320	331
Peak_Molarity	76.60	82.70
libSampleQC_DNA_Well	DNA_Library_set54-56/set2/E8.png	DNA_Library_set54-56/set2/F8.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set54-56/set1/G7.png	RNA_Library_set54-56/set1/H7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV38-5	BGKcLV38-6
RBP	DHX33	DHX33
Batch_ID	BGKcLV38	BGKcLV38
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3426	3427

Sequencing Information

	BGKcLV38-5	BGKcLV38-6
Sample_ID	BGKcLV38-5	BGKcLV38-6
Sample Name	DHX33-BGKcLV38-5	DHX33-BGKcLV38-6
Pool ID	Pool-230127C	Pool-230127C
LocalServer_folder	set56	set56
total_reads	55,476,561	63,825,078
total_aligned_reads	50,025,234	59,605,774
unique_aligned_reads	46,371,724	55,107,448
percent_uniqueAligned	0.83588	0.86341
correlation_replicates	0.995350	0.995350
spikein_reads	12,942	17,888
percent_spikeins	0.00023	0.00028
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2299	2300

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
DHX33-BGKcLV38-5_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2299	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	8304
DHX33-BGKcLV38-5_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2299	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	8342
DHX33-BGKcLV38-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2299					GRCh38	V40	DHX33-BGKcLV38-5_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,DHX33-BGKcLV38-5_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16956
DHX33-BGKcLV38-5_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	2299					GRCh38	V40	DHX33-BGKcLV38-5/Aligned.sortedByCoord.out.bam		ENCORE2	16994
DHX33-BGKcLV38-5_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	2299					GRCh38	V40	DHX33-BGKcLV38-5/Aligned.sortedByCoord.out.bam		ENCORE2	17032
DHX33-BGKcLV38-5_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	2299					GRCh38	V40	DHX33-BGKcLV38-5/Aligned.sortedByCoord.out.bam		ENCORE2	17070
DHX33-BGKcLV38-5_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	2299					GRCh38	V40	DHX33-BGKcLV38-5/Aligned.sortedByCoord.out.bam		ENCORE2	17108
DHX33-BGKcLV38-5_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2299					GRCh38	V40	DHX33-BGKcLV38-5_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,DHX33-BGKcLV38-5_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17146
DHX33-BGKcLV38-6_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2300	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	8305
DHX33-BGKcLV38-6_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2300	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	8343
DHX33-BGKcLV38-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2300					GRCh38	V40	DHX33-BGKcLV38-6_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz,DHX33-BGKcLV38-6_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16957
DHX33-BGKcLV38-6_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	2300					GRCh38	V40	DHX33-BGKcLV38-6/Aligned.sortedByCoord.out.bam		ENCORE2	16995
DHX33-BGKcLV38-6_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	2300					GRCh38	V40	DHX33-BGKcLV38-6/Aligned.sortedByCoord.out.bam		ENCORE2	17033
DHX33-BGKcLV38-6_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	2300					GRCh38	V40	DHX33-BGKcLV38-6/Aligned.sortedByCoord.out.bam		ENCORE2	17071
DHX33-BGKcLV38-6_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	2300					GRCh38	V40	DHX33-BGKcLV38-6/Aligned.sortedByCoord.out.bam		ENCORE2	17109
DHX33-BGKcLV38-6_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2300					GRCh38	V40	DHX33-BGKcLV38-6_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz,DHX33-BGKcLV38-6_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17147