DDX20 RNA-Seq in K562

General Information


RBP	DDX20
Cell_Line	K562
Method	CRISPR
Exp_Name	DDX20-BGKcLV08-K562
ENCODE_series_ID	ENCSR084HUF
Batch_ID	BGKcLV08
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR867XAL
ENCODE_CN_Exp_ID	ENCSR015KGT
Rep1	DDX20-BGKcLV08-17
Rep2	DDX20-BGKcLV08-18
CN1	NT-BGKcLV08-1
CN2	NT-BGKcLV08-2
Rep1_qPCR	62.7
Rep2_qPCR	58.2
Rep1_WB	56.0
Rep2_WB	56.0
Antibody Cat#	A300-651A
Antibody Lot#	A300-651A
Antibody DCC ID	ENCAB711GME
Status	Released
Project	ENCODE4
ID	200

Experiment Information (Status: Released)

	BGKcLV08-17	BGKcLV08-18
idx	242	243
TRCN#_or_BGC#	BGC#0000111	BGC#0000111
shRNA_or_gRNA_sequence	TGAGATCCTGAGCGGTCCGC	TGAGATCCTGAGCGGTCCGC
PAM	AGG	AGG
Name	DDX20-92F	DDX20-92F
Sample_ID	BGKcLV08-17	BGKcLV08-18
transduction_Date	3/8/18	3/8/18
days	Day 6	Day 6
RBP_name	DDX20	DDX20
qPCR_result	62.7	58.2
Ave_qPCR	60.5
RT-qPCR_primer-F	GTGCAGCTCAAGGCCATC
RT-qPCR_primer-R	TGGTGGAGAACACACAGGTT
protein_conc	3633	3467
WB_result	56.0	56.0
Ave_WB	56.0
WB_DONE_date	3/9/18	wes
MW	92
IP	1
antibody_Cat#	A300-651A	A300-651A
Antibody DCC ID	ENCAB711GME
submitted_to_DCC_date	9/6/18
Rep1_TPM	8.2	0
Rep2_TPM	4.6	0
Action	Ready	Ready
Library_start_date	7/26/18	7/26/18
repeat_library
Note
ID	4342	4343

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX20	Product_ID: A300-651A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX20-human

Experiment Status

	BGKcLV08-17	BGKcLV08-18
Sample_ID	BGKcLV08-17	BGKcLV08-18
Sample Name
Sample Name	DDX20-BGKcLV08-17	DDX20-BGKcLV08-18
RBP	DDX20	DDX20
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6171	6172

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV08-17	BGKcLV08-18
Sample #	7	8
Sample Name	DDX20-BGKcLV08-17	DDX20-BGKcLV08-18
Sample_Name_Alias
Index Well Position	G01	H01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2018-10-01	2018-10-01
Lib_ID	Lib-181001	Lib-181001
Tecan_Location
Tecan
Tecan_date
Size_bp	276	288
Peak_Molarity	48.50	57.90
libSampleQC_DNA_Well	DNA_Library_set41/set2/G1.png	DNA_Library_set41/set2/H1.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set41/set1/G1.png	RNA_Library_set41/set1/H1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-07-27	2018-07-27
Sample_ID	BGKcLV08-17	BGKcLV08-18
RBP	DDX20	DDX20
Batch_ID	BGKcLV08	BGKcLV08
WB_result	56.000	56.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	857	858

Sequencing Information

	BGKcLV08-17	BGKcLV08-18
Sample_ID	BGKcLV08-17	BGKcLV08-18
Sample Name	DDX20-BGKcLV08-17	DDX20-BGKcLV08-18
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	90,565,334	80,879,204
total_aligned_reads	87,261,442	78,119,836
unique_aligned_reads	77,817,450	70,502,168
percent_uniqueAligned	0.85924	0.87170
correlation_replicates	0.994815	0.994815
spikein_reads	137,914	119,042
percent_spikeins	0.00152	0.00147
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	263	264

Data Submission Information

	BGKcLV08-17	BGKcLV08-17	BGKcLV08-17	BGKcLV08-17	BGKcLV08-17	BGKcLV08-17	BGKcLV08-18	BGKcLV08-18	BGKcLV08-18	BGKcLV08-18
ENCODE_alias	brenton-graveley:DDX20-BGKcLV08	brenton-graveley:DDX20-BGKcLV08-17	brenton-graveley:L-DDX20-BGKcLV08-17	brenton-graveley:DDX20-BGKcLV08-17_CAAGCTAG+ACATAGCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX20-BGKcLV08-17_CAAGCTAG+ACATAGCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX20-BGKcLV08-K562	brenton-graveley:DDX20-BGKcLV08-18	brenton-graveley:L-DDX20-BGKcLV08-18	brenton-graveley:DDX20-BGKcLV08-18_TGGATCGA+GTGCGATA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX20-BGKcLV08-18_TGGATCGA+GTGCGATA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR867XAL	ENCBS903RSI	ENCLB438WTF	ENCFF872CHN	ENCFF539YKJ	ENCSR084HUF	ENCBS314VQF	ENCLB483KAD	ENCFF641NTR	ENCFF432PEQ
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	BGKcLV08-17	BGKcLV08-17	BGKcLV08-17	BGKcLV08-17	BGKcLV08-17	BGKcLV08-17	BGKcLV08-18	BGKcLV08-18	BGKcLV08-18	BGKcLV08-18
Sample Name	DDX20-BGKcLV08-17	DDX20-BGKcLV08-17	DDX20-BGKcLV08-17	DDX20-BGKcLV08-17	DDX20-BGKcLV08-17	DDX20-BGKcLV08-17	DDX20-BGKcLV08-18	DDX20-BGKcLV08-18	DDX20-BGKcLV08-18	DDX20-BGKcLV08-18
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV41_biosample_protocol	LV41_library_protocol				LV41_biosample_protocol	LV41_library_protocol
protocol_URL		DDX20-BGKcLV08-17.pdf	L-DDX20-BGKcLV08-17.pdf				DDX20-BGKcLV08-18.pdf	L-DDX20-BGKcLV08-18.pdf
ID	1121	1162	1232	1302	1372	7176	1163	1233	1303	1373

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
DDX20-BGKcLV08-17_CAAGCTAG+ACATAGCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	263				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	509
DDX20-BGKcLV08-17_CAAGCTAG+ACATAGCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	263				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	579
DDX20-BGKcLV08-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	263	GRCh38	V40	DDX20-BGKcLV08-17_CAAGCTAG+ACATAGCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX20-BGKcLV08-17_CAAGCTAG+ACATAGCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26747
DDX20-BGKcLV08-17_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	263	GRCh38	V40	DDX20-BGKcLV08-17/Aligned.sortedByCoord.out.bam		ENCORE2	26817
DDX20-BGKcLV08-17_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	263	GRCh38	V40	DDX20-BGKcLV08-17/Aligned.sortedByCoord.out.bam		ENCORE2	26887
DDX20-BGKcLV08-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	263	GRCh38	V40	DDX20-BGKcLV08-17/Aligned.sortedByCoord.out.bam		ENCORE2	26957
DDX20-BGKcLV08-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	263	GRCh38	V40	DDX20-BGKcLV08-17/Aligned.sortedByCoord.out.bam		ENCORE2	27027
DDX20-BGKcLV08-17_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	263	GRCh38	V40	DDX20-BGKcLV08-17_CAAGCTAG+ACATAGCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX20-BGKcLV08-17_CAAGCTAG+ACATAGCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27097
DDX20-BGKcLV08-18_TGGATCGA+GTGCGATA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	264				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	510
DDX20-BGKcLV08-18_TGGATCGA+GTGCGATA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	264				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	580
DDX20-BGKcLV08-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	264	GRCh38	V40	DDX20-BGKcLV08-18_TGGATCGA+GTGCGATA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX20-BGKcLV08-18_TGGATCGA+GTGCGATA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26748
DDX20-BGKcLV08-18_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	264	GRCh38	V40	DDX20-BGKcLV08-18/Aligned.sortedByCoord.out.bam		ENCORE2	26818
DDX20-BGKcLV08-18_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	264	GRCh38	V40	DDX20-BGKcLV08-18/Aligned.sortedByCoord.out.bam		ENCORE2	26888
DDX20-BGKcLV08-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	264	GRCh38	V40	DDX20-BGKcLV08-18/Aligned.sortedByCoord.out.bam		ENCORE2	26958
DDX20-BGKcLV08-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	264	GRCh38	V40	DDX20-BGKcLV08-18/Aligned.sortedByCoord.out.bam		ENCORE2	27028
DDX20-BGKcLV08-18_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	264	GRCh38	V40	DDX20-BGKcLV08-18_TGGATCGA+GTGCGATA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX20-BGKcLV08-18_TGGATCGA+GTGCGATA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27098