DDX20 RNA-Seq in HepG2

General Information


RBP	DDX20
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DDX20-BGHcLV10-HepG2
ENCODE_series_ID	ENCSR420IFR
Batch_ID	BGHcLV10
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR429OUR
ENCODE_CN_Exp_ID	ENCSR775ZWO
Rep1	DDX20-BGHcLV10-19
Rep2	DDX20-BGHcLV10-20
CN1	NT-BGHcLV10-1
CN2	NT-BGHcLV10-2
Rep1_qPCR	18.3
Rep2_qPCR	33.9
Rep1_WB	64.2
Rep2_WB	54.6
Antibody Cat#	A300-651A
Antibody Lot#	A300-651A
Antibody DCC ID	ENCAB711GME
Status	Released
Project	ENCODE4
ID	222

Experiment Information (Status: Released)

	BGHcLV10-19	BGHcLV10-20
idx	216	217
TRCN#_or_BGC#	BGC#0000111	BGC#0000111
shRNA_or_gRNA_sequence	TGAGATCCTGAGCGGTCCGC	TGAGATCCTGAGCGGTCCGC
PAM	AGG	AGG
Name	DDX20-92	DDX20-92
Sample_ID	BGHcLV10-19	BGHcLV10-20
transduction_Date	4/27/18	4/27/18
days	D6	D6
RBP_name	DDX20	DDX20
qPCR_result	18.3	33.9
Ave_qPCR	26.1
RT-qPCR_primer-F	ACCGAGTGCTCATCTTCTCG
RT-qPCR_primer-R	ACCATCGATGCGCTCATACT
protein_conc	2374	2150
WB_result	64.2	54.6
Ave_WB	59.4
WB_DONE_date	5/10/18	wes
MW	92
IP	1
antibody_Cat#	A300-651A	A300-651A
Antibody DCC ID	ENCAB711GME
submitted_to_DCC_date	9/6/18
Rep1_TPM	7	0
Rep2_TPM	12	0
Action	Ready	Ready
Library_start_date	8/7/18	8/7/18
repeat_library
Note
ID	6359	6360

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

	BGHcLV10-19	BGHcLV10-20
Sample_ID	BGHcLV10-19	BGHcLV10-20
Sample Name
Sample Name	DDX20-BGHcLV10-19	DDX20-BGHcLV10-20
RBP	DDX20	DDX20
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6295	6296

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV10-19	BGHcLV10-20
Sample #	55	56
Sample Name	DDX20-BGHcLV10-19	DDX20-BGHcLV10-20
Sample_Name_Alias
Index Well Position	C08	D08
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	268	274
Peak_Molarity	52.10	61.70
libSampleQC_DNA_Well	DNA_Library_set41/set5/C8.png	DNA_Library_set41/set5/D8.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_set41/set1/G7.png	RNA_Library_set41/set1/H7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-08-08	2018-08-08
Sample_ID	BGHcLV10-19	BGHcLV10-20
RBP	DDX20	DDX20
Batch_ID	BGHcLV10	BGHcLV10
WB_result	64.200	54.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	905	906

Sequencing Information

	BGHcLV10-19	BGHcLV10-20
Sample_ID	BGHcLV10-19	BGHcLV10-20
Sample Name	DDX20-BGHcLV10-19	DDX20-BGHcLV10-20
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	110,936,664	119,177,086
total_aligned_reads	107,010,264	114,525,530
unique_aligned_reads	99,124,106	106,310,230
percent_uniqueAligned	0.89352	0.89204
correlation_replicates	0.994387	0.994387
spikein_reads	194,994	253,070
percent_spikeins	0.00176	0.00212
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	311	312

Data Submission Information

	BGHcLV10-19	BGHcLV10-19	BGHcLV10-19	BGHcLV10-19	BGHcLV10-19	BGHcLV10-19	BGHcLV10-20	BGHcLV10-20	BGHcLV10-20	BGHcLV10-20
ENCODE_alias	brenton-graveley:DDX20-BGHcLV10	brenton-graveley:DDX20-BGHcLV10-19	brenton-graveley:L-DDX20-BGHcLV10-19	brenton-graveley:DDX20-BGHcLV10-19_GATCTATC+ATGAGGCT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX20-BGHcLV10-19_GATCTATC+ATGAGGCT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX20-BGHcLV10-HepG2	brenton-graveley:DDX20-BGHcLV10-20	brenton-graveley:L-DDX20-BGHcLV10-20	brenton-graveley:DDX20-BGHcLV10-20_AGCTCGCT+GCAGAATC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX20-BGHcLV10-20_AGCTCGCT+GCAGAATC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR429OUR	ENCBS292SMV	ENCLB697ZVK	ENCFF380IHJ	ENCFF298RFX	ENCSR420IFR	ENCBS223MPM	ENCLB763AYF	ENCFF619SXC	ENCFF187SFR
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	BGHcLV10-19	BGHcLV10-19	BGHcLV10-19	BGHcLV10-19	BGHcLV10-19	BGHcLV10-19	BGHcLV10-20	BGHcLV10-20	BGHcLV10-20	BGHcLV10-20
Sample Name	DDX20-BGHcLV10-19	DDX20-BGHcLV10-19	DDX20-BGHcLV10-19	DDX20-BGHcLV10-19	DDX20-BGHcLV10-19	DDX20-BGHcLV10-19	DDX20-BGHcLV10-20	DDX20-BGHcLV10-20	DDX20-BGHcLV10-20	DDX20-BGHcLV10-20
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-BGHcLV10-19.pdf	L-DDX20-BGHcLV10-19.pdf				DDX20-BGHcLV10-20.pdf	L-DDX20-BGHcLV10-20.pdf
ID	1120	1160	1230	1300	1370	7175	1161	1231	1301	1371

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-BGHcLV10-19_GATCTATC+ATGAGGCT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	311				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	507
DDX20-BGHcLV10-19_GATCTATC+ATGAGGCT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	311				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	577
DDX20-BGHcLV10-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	311	GRCh38	V40	DDX20-BGHcLV10-19_GATCTATC+ATGAGGCT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX20-BGHcLV10-19_GATCTATC+ATGAGGCT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26745
DDX20-BGHcLV10-19_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	311	GRCh38	V40	DDX20-BGHcLV10-19/Aligned.sortedByCoord.out.bam		ENCORE2	26815
DDX20-BGHcLV10-19_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	311	GRCh38	V40	DDX20-BGHcLV10-19/Aligned.sortedByCoord.out.bam		ENCORE2	26885
DDX20-BGHcLV10-19_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	311	GRCh38	V40	DDX20-BGHcLV10-19/Aligned.sortedByCoord.out.bam		ENCORE2	26955
DDX20-BGHcLV10-19_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	311	GRCh38	V40	DDX20-BGHcLV10-19/Aligned.sortedByCoord.out.bam		ENCORE2	27025
DDX20-BGHcLV10-19_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	311	GRCh38	V40	DDX20-BGHcLV10-19_GATCTATC+ATGAGGCT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX20-BGHcLV10-19_GATCTATC+ATGAGGCT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27095
DDX20-BGHcLV10-20_AGCTCGCT+GCAGAATC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	312				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	508
DDX20-BGHcLV10-20_AGCTCGCT+GCAGAATC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	312				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	578
DDX20-BGHcLV10-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	312	GRCh38	V40	DDX20-BGHcLV10-20_AGCTCGCT+GCAGAATC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX20-BGHcLV10-20_AGCTCGCT+GCAGAATC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26746
DDX20-BGHcLV10-20_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	312	GRCh38	V40	DDX20-BGHcLV10-20/Aligned.sortedByCoord.out.bam		ENCORE2	26816
DDX20-BGHcLV10-20_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	312	GRCh38	V40	DDX20-BGHcLV10-20/Aligned.sortedByCoord.out.bam		ENCORE2	26886
DDX20-BGHcLV10-20_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	312	GRCh38	V40	DDX20-BGHcLV10-20/Aligned.sortedByCoord.out.bam		ENCORE2	26956
DDX20-BGHcLV10-20_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	312	GRCh38	V40	DDX20-BGHcLV10-20/Aligned.sortedByCoord.out.bam		ENCORE2	27026
DDX20-BGHcLV10-20_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	312	GRCh38	V40	DDX20-BGHcLV10-20_AGCTCGCT+GCAGAATC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX20-BGHcLV10-20_AGCTCGCT+GCAGAATC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27096