DDX18 RNA-Seq in K562

General Information


RBP	DDX18
Cell_Line	K562
Method	CRISPR
Exp_Name	DDX18-BGKcLV28-K562
ENCODE_series_ID	ENCSR986FVB
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR300LXO
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	DDX18-BGKcLV28-71
Rep2	DDX18-BGKcLV28-72
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	69.3
Rep2_qPCR	62.8
Rep1_WB	83.6
Rep2_WB	83.8
Antibody Cat#	A300-636A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB781GEV
Status	Released
Project	ENCODE4
ID	844

Experiment Information (Status: Released)

	BGKcLV28-71	BGKcLV28-72
idx	1021	1022
TRCN#_or_BGC#	BGC#0000748	BGC#0000748
shRNA_or_gRNA_sequence	GATGAACGCTTACCATTCCT	GATGAACGCTTACCATTCCT
PAM	GGG	GGG
Name	DDX18_86	DDX18_86
Sample_ID	BGKcLV28-71	BGKcLV28-72
transduction_Date	7/12/21	7/12/21
days	Day 6	Day 6
RBP_name	DDX18	DDX18
qPCR_result	69.3	62.8
Ave_qPCR	66.1
RT-qPCR_primer-F	aatgcagattcgggaacact
RT-qPCR_primer-R	ggctgttctacccacacgat
protein_conc	2930	2875
WB_result	83.6	83.8
Ave_WB	83.7
WB_DONE_date	6/30/21-2	JESS
MW	75KD
IP
antibody_Cat#	A300-636A	LOT #1
Antibody DCC ID	ENCAB781GEV
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/23/21	09/23/21
repeat_library
Note
ID	5155	5156

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX18	Product_ID: A300-636A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX18-human

Experiment Status

	BGKcLV28-71	BGKcLV28-72
Sample_ID	BGKcLV28-71	BGKcLV28-72
Sample Name
Sample Name	DDX18-BGKcLV28-71	DDX18-BGKcLV28-72
RBP	DDX18	DDX18
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9947	9948

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-71	BGKcLV28-72
Sample #	55	56
Sample Name	DDX18-BGKcLV28-71	DDX18-BGKcLV28-72
Sample_Name_Alias
Index Well Position	G11	H11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-21	2021-09-21
Lib_ID	Lib-210921	Lib-210921
Tecan_Location
Tecan
Tecan_date
Size_bp	314	304
Peak_Molarity	102.00	109.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/G7.png	DNA_Library_set48-49/set3/H7.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set48-49/set2/G7.png	RNA_Library_set48-49/set2/H7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-71	BGKcLV28-72
RBP	DDX18	DDX18
Batch_ID	BGKcLV28	BGKcLV28
WB_result	83.600	83.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2116	2117

Sequencing Information

	BGKcLV28-71	BGKcLV28-72
Sample_ID	BGKcLV28-71	BGKcLV28-72
Sample Name	DDX18-BGKcLV28-71	DDX18-BGKcLV28-72
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	166,555,330	103,665,814
total_aligned_reads	161,263,334	98,465,962
unique_aligned_reads	148,130,092	90,365,704
percent_uniqueAligned	0.88937	0.87170
correlation_replicates	0.998073	0.998073
spikein_reads	30,798	16,578
percent_spikeins	0.00018	0.00016
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1867	1868

Data Submission Information

	BGKcLV28-71	BGKcLV28-71	BGKcLV28-71	BGKcLV28-71	BGKcLV28-71	BGKcLV28-71	BGKcLV28-72	BGKcLV28-72	BGKcLV28-72	BGKcLV28-72
ENCODE_alias	brenton-graveley:DDX18-BGKcLV28	brenton-graveley:DDX18-BGKcLV28-71	brenton-graveley:L-DDX18-BGKcLV28-71	brenton-graveley:DDX18-BGKcLV28-71_S137_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX18-BGKcLV28-71_S137_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX18-BGKcLV28-K562	brenton-graveley:DDX18-BGKcLV28-72	brenton-graveley:L-DDX18-BGKcLV28-72	brenton-graveley:DDX18-BGKcLV28-72_S138_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX18-BGKcLV28-72_S138_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR300LXO	ENCBS282XIF	ENCLB782KHV	ENCFF561WBD	ENCFF469BFD	ENCSR986FVB	ENCBS515ZUG	ENCLB633OCK	ENCFF996AWJ	ENCFF287KAP
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	BGKcLV28-71	BGKcLV28-71	BGKcLV28-71	BGKcLV28-71	BGKcLV28-71	BGKcLV28-71	BGKcLV28-72	BGKcLV28-72	BGKcLV28-72	BGKcLV28-72
Sample Name	DDX18-BGKcLV28-71	DDX18-BGKcLV28-71	DDX18-BGKcLV28-71	DDX18-BGKcLV28-71	DDX18-BGKcLV28-71	DDX18-BGKcLV28-71	DDX18-BGKcLV28-72	DDX18-BGKcLV28-72	DDX18-BGKcLV28-72	DDX18-BGKcLV28-72
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-03-02	2022-01-29	2022-01-29	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV49_biosample_protocol	LV49_library_protocol				LV49_biosample_protocol	LV49_library_protocol
protocol_URL		DDX18-BGKcLV28-71.pdf	L-DDX18-BGKcLV28-71.pdf				DDX18-BGKcLV28-72.pdf	L-DDX18-BGKcLV28-72.pdf
ID	3498	3630	3764	3898	4032	7174	3631	3765	3899	4033

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
DDX18-BGKcLV28-71_S137_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1867	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3984
DDX18-BGKcLV28-71_S137_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1867	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	4042
DDX18-BGKcLV28-71_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1867					GRCh38	V40	DDX18-BGKcLV28-71_S137_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX18-BGKcLV28-71_S137_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19266
DDX18-BGKcLV28-71_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1867					GRCh38	V40	DDX18-BGKcLV28-71/Aligned.sortedByCoord.out.bam		ENCORE2	19324
DDX18-BGKcLV28-71_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1867					GRCh38	V40	DDX18-BGKcLV28-71/Aligned.sortedByCoord.out.bam		ENCORE2	19382
DDX18-BGKcLV28-71_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1867					GRCh38	V40	DDX18-BGKcLV28-71/Aligned.sortedByCoord.out.bam		ENCORE2	19440
DDX18-BGKcLV28-71_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1867					GRCh38	V40	DDX18-BGKcLV28-71/Aligned.sortedByCoord.out.bam		ENCORE2	19498
DDX18-BGKcLV28-71_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1867					GRCh38	V40	DDX18-BGKcLV28-71_S137_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX18-BGKcLV28-71_S137_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19556
DDX18-BGKcLV28-72_S138_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1868	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3985
DDX18-BGKcLV28-72_S138_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1868	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	4043
DDX18-BGKcLV28-72_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1868					GRCh38	V40	DDX18-BGKcLV28-72_S138_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX18-BGKcLV28-72_S138_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19267
DDX18-BGKcLV28-72_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1868					GRCh38	V40	DDX18-BGKcLV28-72/Aligned.sortedByCoord.out.bam		ENCORE2	19325
DDX18-BGKcLV28-72_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1868					GRCh38	V40	DDX18-BGKcLV28-72/Aligned.sortedByCoord.out.bam		ENCORE2	19383
DDX18-BGKcLV28-72_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1868					GRCh38	V40	DDX18-BGKcLV28-72/Aligned.sortedByCoord.out.bam		ENCORE2	19441
DDX18-BGKcLV28-72_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1868					GRCh38	V40	DDX18-BGKcLV28-72/Aligned.sortedByCoord.out.bam		ENCORE2	19499
DDX18-BGKcLV28-72_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1868					GRCh38	V40	DDX18-BGKcLV28-72_S138_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX18-BGKcLV28-72_S138_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19557