DHX29 RNA-Seq in K562

General Information


RBP	DHX29
Cell_Line	K562
Method	CRISPR
Exp_Name	DHX29-BGKcLV42-K562
ENCODE_series_ID
Batch_ID	BGKcLV42
Pool ID	Pool-240715
Local_Set_Name	set73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	DHX29-BGKcLV42-23
Rep2	DHX29-BGKcLV42-24
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	58.0
Rep2_qPCR	57.8
Rep1_WB	55.7
Rep2_WB	53.4
Antibody Cat#	5926S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1535

Experiment Information (Status: Submitting)

	BGKcLV42-23	BGKcLV42-24
idx	0	0
TRCN#_or_BGC#	BGC#0001126	BGC#0001126
shRNA_or_gRNA_sequence	ATAGAATAGCATGCTGAGTG	ATAGAATAGCATGCTGAGTG
PAM	CGG	CGG
Name	DHX29_57	DHX29_57
Sample_ID	BGKcLV42-23	BGKcLV42-24
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	DHX29	DHX29
qPCR_result	58.0	57.8
Ave_qPCR	57.9
RT-qPCR_primer-F	caagctgcagcattcacact
RT-qPCR_primer-R	agtgatacccgtctctgcaa
protein_conc	3071	2558
WB_result	55.7	53.4
Ave_WB	54.6
WB_DONE_date	5/6/24
MW	155KD
IP
antibody_Cat#	5926S	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	5785	5786

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DHX29	Product_ID: 5926S Lot_ID: 1 Source: Cell Signaling Technology Target Name: DHX29-human

Experiment Status

	BGKcLV42-23	BGKcLV42-24
Sample_ID	BGKcLV42-23	BGKcLV42-24
Sample Name
Sample Name	DHX29-BGKcLV42-23	DHX29-BGKcLV42-24
RBP	DHX29	DHX29
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13064	13065

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-23	BGKcLV42-24
Sample #	21	22
Sample Name	DHX29-BGKcLV42-23	DHX29-BGKcLV42-24
Sample_Name_Alias
Index Well Position	E03	F03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-06-21	2024-06-21
Lib_ID	Lib-240621	Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp	289	291
Peak_Molarity	104.00	103.00
libSampleQC_DNA_Well	DNA_Library_set73/set1/E3.png	DNA_Library_set73/set1/F3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/E3.png	RNA_Library_set73/set1/F3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-23	BGKcLV42-24
RBP	DHX29	DHX29
Batch_ID	BGKcLV42	BGKcLV42
WB_result	55.700	53.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4290	4291

Sequencing Information

	BGKcLV42-23	BGKcLV42-24
Sample_ID	BGKcLV42-23	BGKcLV42-24
Sample Name	DHX29-BGKcLV42-23	DHX29-BGKcLV42-24
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	47,212,507	36,432,888
total_aligned_reads	39,782,376	32,804,164
unique_aligned_reads	36,582,348	30,317,276
percent_uniqueAligned	0.77484	0.83214
correlation_replicates	0.998727	0.998727
spikein_reads	1,926	3,626
percent_spikeins	0.00004	0.00010
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3157	3158

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
DHX29-BGKcLV42-23_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3157	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30358
DHX29-BGKcLV42-23_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3157	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30448
DHX29-BGKcLV42-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3157					GRCh38	V40	DHX29-BGKcLV42-23_L001_R1_001.filtered.trimmed.paired.fastq.gz,DHX29-BGKcLV42-23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31290
DHX29-BGKcLV42-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3157					GRCh38	V40	DHX29-BGKcLV42-23_Aligned.sortedByCoord.out.bam		ENCORE2	31380
DHX29-BGKcLV42-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3157					GRCh38	V40	DHX29-BGKcLV42-23_Aligned.sortedByCoord.out.bam		ENCORE2	31470
DHX29-BGKcLV42-23_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3157					GRCh38	V40	DHX29-BGKcLV42-23_Aligned.sortedByCoord.out.bam		ENCORE2	31560
DHX29-BGKcLV42-23_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3157					GRCh38	V40	DHX29-BGKcLV42-23_Aligned.sortedByCoord.out.bam		ENCORE2	31650
DHX29-BGKcLV42-23_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3157					GRCh38	V40	DHX29-BGKcLV42-23_L001_R1_001.filtered.trimmed.paired.fastq.gz,DHX29-BGKcLV42-23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31740
DHX29-BGKcLV42-24_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3158	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30359
DHX29-BGKcLV42-24_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3158	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30449
DHX29-BGKcLV42-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3158					GRCh38	V40	DHX29-BGKcLV42-24_L001_R1_001.filtered.trimmed.paired.fastq.gz,DHX29-BGKcLV42-24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31291
DHX29-BGKcLV42-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3158					GRCh38	V40	DHX29-BGKcLV42-24_Aligned.sortedByCoord.out.bam		ENCORE2	31381
DHX29-BGKcLV42-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3158					GRCh38	V40	DHX29-BGKcLV42-24_Aligned.sortedByCoord.out.bam		ENCORE2	31471
DHX29-BGKcLV42-24_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3158					GRCh38	V40	DHX29-BGKcLV42-24_Aligned.sortedByCoord.out.bam		ENCORE2	31561
DHX29-BGKcLV42-24_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3158					GRCh38	V40	DHX29-BGKcLV42-24_Aligned.sortedByCoord.out.bam		ENCORE2	31651
DHX29-BGKcLV42-24_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3158					GRCh38	V40	DHX29-BGKcLV42-24_L001_R1_001.filtered.trimmed.paired.fastq.gz,DHX29-BGKcLV42-24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31741