DDX39B RNA-Seq in K562

General Information


RBP	DDX39B
Cell_Line	K562
Method	CRISPR
Exp_Name	DDX39B-BGKcLV17-K562
ENCODE_series_ID	ENCSR469JJP
Batch_ID	BGKcLV17
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR883MTV
ENCODE_CN_Exp_ID	ENCSR516TLX
Rep1	DDX39B-BGKcLV17-9
Rep2	DDX39B-BGKcLV17-10
CN1	NT-BGKcLV17-1
CN2	NT-BGKcLV17-2
Rep1_qPCR	24.0
Rep2_qPCR	26.5
Rep1_WB	61.8
Rep2_WB	56.9
Antibody Cat#	RN116PW
Antibody Lot#	lot #1
Antibody DCC ID	ENCAB574DNV
Status	Released
Project	ENCODE4
ID	143

Experiment Information (Status: Released)

	BGKcLV17-9	BGKcLV17-9	BGKcLV17-10	BGKcLV17-10
idx	616	616	617	617
TRCN#_or_BGC#	BGC#0000421	BGC#0000421	BGC#0000421	BGC#0000421
shRNA_or_gRNA_sequence	CCTGAGGGATGCACTCATGC	CCTGAGGGATGCACTCATGC	CCTGAGGGATGCACTCATGC	CCTGAGGGATGCACTCATGC
PAM	TGG	TGG	TGG	TGG
Name	DDX39B	DDX39B	DDX39B	DDX39B
Sample_ID	BGKcLV17-9	BGKcLV17-9	BGKcLV17-10	BGKcLV17-10
transduction_Date	7/2/19	7/2/19	7/2/19	7/2/19
days	Day 6	Day 6	Day 6	Day 6
RBP_name	DDX39B	DDX39B	DDX39B	DDX39B
qPCR_result	24.0	24.0	26.5	26.5
Ave_qPCR	25.3	25.3
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3922	3922	3826	3826
WB_result	61.8	63.7	56.9	69.64
Ave_WB	59.4	66.7
WB_DONE_date	9/6/19	6/28/23	WES
MW	49KD	49KD
IP	Rabbit / I
antibody_Cat#	RN116PW	47258S	lot #1	lot# 1
Antibody DCC ID
submitted_to_DCC_date		1/8/24
Rep1_TPM	406.6	0	0	0
Rep2_TPM	380.4	0	0	0
Action	Ready		Ready
Library_start_date	12/05/19		12/05/19
repeat_library
Note
ID	4730	4732	4731	4733

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX39B	Product_ID: RN116PW Lot_ID: 1 Source: MBLI Target Name: DDX39B-human
DDX39B	Product_ID: 47258S Lot_ID: 1 Source: Cell Signaling Technology Target Name: DDX39B-human

Experiment Status

	BGKcLV17-9	BGKcLV17-10
Sample_ID	BGKcLV17-9	BGKcLV17-10
Sample Name
Sample Name	DDX39B-BGKcLV17-9	DDX39B-BGKcLV17-10
RBP	DDX39B	DDX39B
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5493	5494

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV17-9	BGKcLV17-10
Sample #	83	84
Sample Name	DDX39B-BGKcLV17-9	DDX39B-BGKcLV17-10
Sample_Name_Alias
Index Well Position	G10	H10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-31	2020-08-31
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	1-A2	1-B2
Tecan	12.27	30.61
Tecan_date	2019-12-10	2019-12-10
Size_bp	276	271
Peak_Molarity	15.50	24.10
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/A7.png	DNA_Library_set43-44/set1/B7.png
RIN	9.2	9.2
libSample_RNA_Well	RNA_Library_set43-44/set4/A2.png	RNA_Library_set43-44/set4/B2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV17-9	BGKcLV17-10
RBP	DDX39B	DDX39B
Batch_ID	BGKcLV17	BGKcLV17
WB_result	61.800	56.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	659	660

Sequencing Information

	BGKcLV17-9	BGKcLV17-10
Sample_ID	BGKcLV17-9	BGKcLV17-10
Sample Name	DDX39B-BGKcLV17-9	DDX39B-BGKcLV17-10
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	212,896,970	202,061,060
total_aligned_reads	185,830,578	187,610,542
unique_aligned_reads	168,915,400	170,030,504
percent_uniqueAligned	0.79341	0.84148
correlation_replicates	0.987201	0.987201
spikein_reads	37,414	38,704
percent_spikeins	0.00018	0.00019
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	161	162

Data Submission Information

	BGKcLV17-9	BGKcLV17-9	BGKcLV17-9	BGKcLV17-9	BGKcLV17-9	BGKcLV17-9	BGKcLV17-10	BGKcLV17-10	BGKcLV17-10	BGKcLV17-10
ENCODE_alias	brenton-graveley:DDX39B-BGKcLV17	brenton-graveley:DDX39B-BGKcLV17-9	brenton-graveley:L-DDX39B-BGKcLV17-9	brenton-graveley:DDX39B-BGKcLV17-9_S79_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX39B-BGKcLV17-9_S79_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX39B-BGKcLV17-K562	brenton-graveley:DDX39B-BGKcLV17-10	brenton-graveley:L-DDX39B-BGKcLV17-10	brenton-graveley:DDX39B-BGKcLV17-10_S80_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX39B-BGKcLV17-10_S80_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR883MTV	ENCBS725UBT	ENCLB694SGM	ENCFF159GLQ	ENCFF609ZGF	ENCSR469JJP	ENCBS356QKB	ENCLB079ZXF	ENCFF820MIC	ENCFF159CHB
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV17-9	BGKcLV17-9	BGKcLV17-9	BGKcLV17-9	BGKcLV17-9	BGKcLV17-9	BGKcLV17-10	BGKcLV17-10	BGKcLV17-10	BGKcLV17-10
Sample Name	DDX39B-BGKcLV17-9	DDX39B-BGKcLV17-9	DDX39B-BGKcLV17-9	DDX39B-BGKcLV17-9	DDX39B-BGKcLV17-9	DDX39B-BGKcLV17-9	DDX39B-BGKcLV17-10	DDX39B-BGKcLV17-10	DDX39B-BGKcLV17-10	DDX39B-BGKcLV17-10
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43K_biosample_protocol	LV43K_library_protocol				LV43K_biosample_protocol	LV43K_library_protocol
protocol_URL		DDX39B-BGKcLV17-9.pdf	L-DDX39B-BGKcLV17-10.pdf				DDX39B-BGKcLV17-10.pdf	L-DDX39B-BGKcLV17-9.pdf
ID	40	162	326	524	576	7179	163	327	525	577

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
DDX39B-BGKcLV17-9_S79_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	161	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	74
DDX39B-BGKcLV17-9_S79_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	161	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	126
DDX39B-BGKcLV17-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	161					GRCh38	V40	DDX39B-BGKcLV17-9_S79_R1_001.filtered.trimmed.paired.fastq.gz,DDX39B-BGKcLV17-9_S79_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24365
DDX39B-BGKcLV17-9_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	161					GRCh38	V40	DDX39B-BGKcLV17-9/Aligned.sortedByCoord.out.bam		ENCORE2	24417
DDX39B-BGKcLV17-9_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	161					GRCh38	V40	DDX39B-BGKcLV17-9/Aligned.sortedByCoord.out.bam		ENCORE2	24469
DDX39B-BGKcLV17-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	161					GRCh38	V40	DDX39B-BGKcLV17-9/Aligned.sortedByCoord.out.bam		ENCORE2	24521
DDX39B-BGKcLV17-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	161					GRCh38	V40	DDX39B-BGKcLV17-9/Aligned.sortedByCoord.out.bam		ENCORE2	24573
DDX39B-BGKcLV17-9_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	161					GRCh38	V40	DDX39B-BGKcLV17-9_S79_R1_001.filtered.trimmed.paired.fastq.gz,DDX39B-BGKcLV17-9_S79_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24625
DDX39B-BGKcLV17-10_S80_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	162	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	73
DDX39B-BGKcLV17-10_S80_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	162	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	125
DDX39B-BGKcLV17-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	162					GRCh38	V40	DDX39B-BGKcLV17-10_S80_R1_001.filtered.trimmed.paired.fastq.gz,DDX39B-BGKcLV17-10_S80_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24364
DDX39B-BGKcLV17-10_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	162					GRCh38	V40	DDX39B-BGKcLV17-10/Aligned.sortedByCoord.out.bam		ENCORE2	24416
DDX39B-BGKcLV17-10_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	162					GRCh38	V40	DDX39B-BGKcLV17-10/Aligned.sortedByCoord.out.bam		ENCORE2	24468
DDX39B-BGKcLV17-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	162					GRCh38	V40	DDX39B-BGKcLV17-10/Aligned.sortedByCoord.out.bam		ENCORE2	24520
DDX39B-BGKcLV17-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	162					GRCh38	V40	DDX39B-BGKcLV17-10/Aligned.sortedByCoord.out.bam		ENCORE2	24572
DDX39B-BGKcLV17-10_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	162					GRCh38	V40	DDX39B-BGKcLV17-10_S80_R1_001.filtered.trimmed.paired.fastq.gz,DDX39B-BGKcLV17-10_S80_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24624