DDX18 RNA-Seq in HepG2

General Information


RBP	DDX18
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DDX18-BGHcLV29-HepG2
ENCODE_series_ID	ENCSR076VZN
Batch_ID	BGHcLV29
Pool ID	Pool-211117
Local_Set_Name	set50_H
ENCODE_KD_Exp_ID	ENCSR992YRL
ENCODE_CN_Exp_ID	ENCSR462MFN
Rep1	DDX18-BGHcLV29-71
Rep2	DDX18-BGHcLV29-72
CN1	NT-BGHcLV29-1
CN2	NT-BGHcLV29-2
Rep1_qPCR	0
Rep2_qPCR	0
Rep1_WB	77.0
Rep2_WB	84.5
Antibody Cat#	A300-636A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB781GEV
Status	Submitted
Project	ENCODE4
ID	865

Experiment Information (Status: Released)

	BGHcLV29-71	BGHcLV29-72
idx	912	913
TRCN#_or_BGC#	BGC#0000748	BGC#0000748
shRNA_or_gRNA_sequence	GATGAACGCTTACCATTCCT	GATGAACGCTTACCATTCCT
PAM	GGG	GGG
Name	DDX18_86	DDX18_86
Sample_ID	BGHcLV29-71	BGHcLV29-72
transduction_Date	7/20	7/20
days	D6	D6
RBP_name	DDX18	DDX18
qPCR_result	0	0
Ave_qPCR	0
RT-qPCR_primer-F	aatgcagattcgggaacact
RT-qPCR_primer-R	ggctgttctacccacacgat
protein_conc	0	4490
WB_result	77.0	84.5
Ave_WB	80.7
WB_DONE_date	10/14/21
MW	75KD
IP	Rabbit / I
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	11/5/21	11/5/21
repeat_library
Note
ID	7091	7092

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

	BGHcLV29-71	BGHcLV29-72
Sample_ID	BGHcLV29-71	BGHcLV29-72
Sample Name
Sample Name	DDX18-BGHcLV29-71	DDX18-BGHcLV29-72
RBP	DDX18	DDX18
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10015	10016

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV29-71	BGHcLV29-72
Sample #	43	44
Sample Name	DDX18-BGHcLV29-71	DDX18-BGHcLV29-72
Sample_Name_Alias
Index Well Position	C06	D06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-11-01	2021-11-01
Lib_ID	Lib-211101	Lib-211101
Tecan_Location
Tecan
Tecan_date
Size_bp	295	292
Peak_Molarity	52.00	35.30
libSampleQC_DNA_Well	DNA_Library_set50/set1/C6.png	DNA_Library_set50/set1/D6.png
RIN	9.6	9.5
libSample_RNA_Well	RNA_Library_set50/set1/C12.png	RNA_Library_set50/set1/D12.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGHcLV29-71	BGHcLV29-72
RBP	DDX18	DDX18
Batch_ID	BGHcLV29	BGHcLV29
WB_result	77.000	84.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3130	3131

Sequencing Information

	BGHcLV29-71	BGHcLV29-72
Sample_ID	BGHcLV29-71	BGHcLV29-72
Sample Name	DDX18-BGHcLV29-71	DDX18-BGHcLV29-72
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_H	set50_H
total_reads	63,435,530	79,482,998
total_aligned_reads	58,988,322	74,841,530
unique_aligned_reads	55,662,442	70,609,772
percent_uniqueAligned	0.87746	0.88836
correlation_replicates	0.994884	0.994884
spikein_reads	6,228	5,760
percent_spikeins	0.00010	0.00007
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1911	1912

Data Submission Information

	BGHcLV29-71	BGHcLV29-71	BGHcLV29-71	BGHcLV29-71	BGHcLV29-71	BGHcLV29-71	BGHcLV29-72	BGHcLV29-72	BGHcLV29-72	BGHcLV29-72
ENCODE_alias	brenton-graveley:DDX18-BGHcLV29	brenton-graveley:DDX18-BGHcLV29-71	brenton-graveley:L-DDX18-BGHcLV29-71	brenton-graveley:DDX18-BGHcLV29-71_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX18-BGHcLV29-71_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX18-BGHcLV29-HepG2	brenton-graveley:DDX18-BGHcLV29-72	brenton-graveley:L-DDX18-BGHcLV29-72	brenton-graveley:DDX18-BGHcLV29-72_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX18-BGHcLV29-72_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR992YRL	ENCBS097LDJ	ENCLB281FMF	ENCFF650MIY	ENCFF263XOT	ENCSR076VZN	ENCBS697LCA	ENCLB398HSV	ENCFF372UHR	ENCFF411KRC
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	BGHcLV29-71	BGHcLV29-71	BGHcLV29-71	BGHcLV29-71	BGHcLV29-71	BGHcLV29-71	BGHcLV29-72	BGHcLV29-72	BGHcLV29-72	BGHcLV29-72
Sample Name	DDX18-BGHcLV29-71	DDX18-BGHcLV29-71	DDX18-BGHcLV29-71	DDX18-BGHcLV29-71	DDX18-BGHcLV29-71	DDX18-BGHcLV29-71	DDX18-BGHcLV29-72	DDX18-BGHcLV29-72	DDX18-BGHcLV29-72	DDX18-BGHcLV29-72
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV50H_biosample_protocol	LV50H_library_protocol				LV50H_biosample_protocol	LV50H_library_protocol
protocol_URL		DDX18-BGHcLV29-71.pdf	L-DDX18-BGHcLV29-71.pdf				DDX18-BGHcLV29-72.pdf	L-DDX18-BGHcLV29-72.pdf
ID	5863	5919	5991	6063	6135	6186	5920	5992	6064	6136

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-BGHcLV29-71_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1911	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5799
DDX18-BGHcLV29-71_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1911	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5841
DDX18-BGHcLV29-71_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1911					GRCh38	V40	DDX18-BGHcLV29-71_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX18-BGHcLV29-71_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18966
DDX18-BGHcLV29-71_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1911					GRCh38	V40	DDX18-BGHcLV29-71/Aligned.sortedByCoord.out.bam		ENCORE2	19024
DDX18-BGHcLV29-71_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1911					GRCh38	V40	DDX18-BGHcLV29-71/Aligned.sortedByCoord.out.bam		ENCORE2	19070
DDX18-BGHcLV29-71_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1911					GRCh38	V40	DDX18-BGHcLV29-71/Aligned.sortedByCoord.out.bam		ENCORE2	19116
DDX18-BGHcLV29-71_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1911					GRCh38	V40	DDX18-BGHcLV29-71/Aligned.sortedByCoord.out.bam		ENCORE2	19162
DDX18-BGHcLV29-71_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1911					GRCh38	V40	DDX18-BGHcLV29-71_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX18-BGHcLV29-71_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19208
DDX18-BGHcLV29-72_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1912	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5800
DDX18-BGHcLV29-72_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1912	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5842
DDX18-BGHcLV29-72_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1912					GRCh38	V40	DDX18-BGHcLV29-72_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX18-BGHcLV29-72_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18967
DDX18-BGHcLV29-72_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1912					GRCh38	V40	DDX18-BGHcLV29-72/Aligned.sortedByCoord.out.bam		ENCORE2	19025
DDX18-BGHcLV29-72_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1912					GRCh38	V40	DDX18-BGHcLV29-72/Aligned.sortedByCoord.out.bam		ENCORE2	19071
DDX18-BGHcLV29-72_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1912					GRCh38	V40	DDX18-BGHcLV29-72/Aligned.sortedByCoord.out.bam		ENCORE2	19117
DDX18-BGHcLV29-72_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1912					GRCh38	V40	DDX18-BGHcLV29-72/Aligned.sortedByCoord.out.bam		ENCORE2	19163
DDX18-BGHcLV29-72_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1912					GRCh38	V40	DDX18-BGHcLV29-72_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX18-BGHcLV29-72_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19209