DDX51 RNA-Seq in HepG2

General Information


RBP	DDX51
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DDX51-BGHcLV12-HepG2
ENCODE_series_ID	ENCSR529POX
Batch_ID	BGHcLV12
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR080NRY
ENCODE_CN_Exp_ID	ENCSR827PII
Rep1	DDX51-BGHcLV12-29
Rep2	DDX51-BGHcLV12-30
CN1	NT-BGHcLV12-1
CN2	NT-BGHcLV12-2
Rep1_qPCR	45.1
Rep2_qPCR	44.9
Rep1_WB	84.0
Rep2_WB	86.7
Antibody Cat#	A302-089A
Antibody Lot#
Antibody DCC ID	ENCAB820ZVZ
Status	Released
Project	ENCODE4
ID	167

Experiment Information (Status: Released)

	BGHcLV12-29	BGHcLV12-30
idx	289	290
TRCN#_or_BGC#	BGC#0000259	BGC#0000259
shRNA_or_gRNA_sequence	CGACCGAGCCGGCGACCAGG	CGACCGAGCCGGCGACCAGG
PAM	AGG	AGG
Name	DDX51_95	DDX51_95
Sample_ID	BGHcLV12-29	BGHcLV12-30
transduction_Date	8/17/18	8/17/18
days	D6	D6
RBP_name	DDX51	DDX51
qPCR_result	45.1	44.9
Ave_qPCR	45.0
RT-qPCR_primer-F	agcgacctctgtgtttctgc
RT-qPCR_primer-R	ggatgtggcagaccactctc
protein_conc	4465	4903
WB_result	84.0	86.7
Ave_WB	85.3
WB_DONE_date	2/4/19	wes
MW	72kda
IP
antibody_Cat#	A302-089A
Antibody DCC ID	ENCAB820ZVZ
submitted_to_DCC_date	2/22/19
Rep1_TPM	16	0
Rep2_TPM	6	0
Action	Ready	Ready
Library_start_date	03/13/19	03/13/19
repeat_library
Note
ID	6432	6433

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX51	Product_ID: A301-089A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX51-human

Experiment Status

	BGHcLV12-29	BGHcLV12-30
Sample_ID	BGHcLV12-29	BGHcLV12-30
Sample Name	DDX51-BGHcLV12-29	DDX51-BGHcLV12-30
Sample Name	DDX51-BGHcLV12-29	DDX51-BGHcLV12-30
RBP	DDX51	DDX51
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2807	2808

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV12-29	BGHcLV12-30
Sample #	37	38
Sample Name	DDX51-BGHcLV12-29	DDX51-BGHcLV12-30
Sample_Name_Alias
Index Well Position	E05	F05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-13	2019-03-13
Lib_ID	Lib-190313	Lib-190313
Tecan_Location	3-E1	3-F1
Tecan	52.42	51.49
Tecan_date	2019-03-13	2019-03-13
Size_bp	292	292
Peak_Molarity	77.90	135.00
libSampleQC_DNA_Well	DNA_Library_set42/set1/E5.png	DNA_Library_set42/set1/F5.png
RIN	9.9	9.7
libSample_RNA_Well	RNA_Library_set42/set1/E5.png	RNA_Library_set42/set1/F5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-13	2019-03-13
Sample_ID	BGHcLV12-29	BGHcLV12-30
RBP	DDX51	DDX51
Batch_ID	BGHcLV12	BGHcLV12
WB_result	84.000	86.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	37	38

Sequencing Information

	BGHcLV12-29	BGHcLV12-30
Sample_ID	BGHcLV12-29	BGHcLV12-30
Sample Name	DDX51-BGHcLV12-29	DDX51-BGHcLV12-30
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	46,997,214	36,212,868
total_aligned_reads	44,600,148	34,489,372
unique_aligned_reads	41,941,874	32,431,628
percent_uniqueAligned	0.89243	0.89558
correlation_replicates	0.997370	0.997370
spikein_reads	34,316	32,756
percent_spikeins	0.00073	0.00090
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	13	14

Data Submission Information

	BGHcLV12-29	BGHcLV12-29	BGHcLV12-29	BGHcLV12-29	BGHcLV12-29	BGHcLV12-29	BGHcLV12-30	BGHcLV12-30	BGHcLV12-30	BGHcLV12-30
ENCODE_alias	brenton-graveley:DDX51-BGHcLV12	brenton-graveley:DDX51-BGHcLV12-29	brenton-graveley:L-DDX51-BGHcLV12-29	brenton-graveley:DDX51-BGHcLV12-29_TCGTAGTG+AGACTTGG_HK3H2DSXX_S37_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX51-BGHcLV12-29_TCGTAGTG+AGACTTGG_HK3H2DSXX_S37_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX51-BGHcLV12-HepG2	brenton-graveley:DDX51-BGHcLV12-30	brenton-graveley:L-DDX51-BGHcLV12-30	brenton-graveley:DDX51-BGHcLV12-30_CTACGACA+GAGTCCAA_HK3H2DSXX_S38_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX51-BGHcLV12-30_CTACGACA+GAGTCCAA_HK3H2DSXX_S38_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR080NRY	ENCBS889KBU	ENCLB667WSG	ENCFF007KZA	ENCFF951XMC	ENCSR529POX	ENCBS568ITW	ENCLB195TZH	ENCFF004FMX	ENCFF569GOY
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	BGHcLV12-29	BGHcLV12-29	BGHcLV12-29	BGHcLV12-29	BGHcLV12-29	BGHcLV12-29	BGHcLV12-30	BGHcLV12-30	BGHcLV12-30	BGHcLV12-30
Sample Name	DDX51-BGHcLV12-29	DDX51-BGHcLV12-29	DDX51-BGHcLV12-29	DDX51-BGHcLV12-29	DDX51-BGHcLV12-29	DDX51-BGHcLV12-29	DDX51-BGHcLV12-30	DDX51-BGHcLV12-30	DDX51-BGHcLV12-30	DDX51-BGHcLV12-30
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
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		DDX51-BGHcLV12-29.pdf	L-DDX51-BGHcLV12-29.pdf				DDX51-BGHcLV12-30.pdf	L-DDX51-BGHcLV12-30.pdf
ID	748	791	873	963	1045	7183	792	874	964	1046

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
DDX51-BGHcLV12-29_TCGTAGTG+AGACTTGG_HK3H2DSXX_S37_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	13	NovaSeq6000	100	paired-ended	1				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	345
DDX51-BGHcLV12-29_TCGTAGTG+AGACTTGG_HK3H2DSXX_S37_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	13	NovaSeq6000	100	paired-ended	2				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	427
DDX51-BGHcLV12-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	13					GRCh38	V40	DDX51-BGHcLV12-29_TCGTAGTG+AGACTTGG_HK3H2DSXX_S37_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX51-BGHcLV12-29_TCGTAGTG+AGACTTGG_HK3H2DSXX_S37_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23684
DDX51-BGHcLV12-29_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	13					GRCh38	V40	DDX51-BGHcLV12-29/Aligned.sortedByCoord.out.bam		ENCORE2	23766
DDX51-BGHcLV12-29_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	13					GRCh38	V40	DDX51-BGHcLV12-29/Aligned.sortedByCoord.out.bam		ENCORE2	23848
DDX51-BGHcLV12-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	13					GRCh38	V40	DDX51-BGHcLV12-29/Aligned.sortedByCoord.out.bam		ENCORE2	23930
DDX51-BGHcLV12-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	13					GRCh38	V40	DDX51-BGHcLV12-29/Aligned.sortedByCoord.out.bam		ENCORE2	24012
DDX51-BGHcLV12-29_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	13					GRCh38	V40	DDX51-BGHcLV12-29_TCGTAGTG+AGACTTGG_HK3H2DSXX_S37_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX51-BGHcLV12-29_TCGTAGTG+AGACTTGG_HK3H2DSXX_S37_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24094
DDX51-BGHcLV12-30_CTACGACA+GAGTCCAA_HK3H2DSXX_S38_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	14	NovaSeq6000	100	paired-ended	1				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	346
DDX51-BGHcLV12-30_CTACGACA+GAGTCCAA_HK3H2DSXX_S38_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	14	NovaSeq6000	100	paired-ended	2				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	428
DDX51-BGHcLV12-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	14					GRCh38	V40	DDX51-BGHcLV12-30_CTACGACA+GAGTCCAA_HK3H2DSXX_S38_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX51-BGHcLV12-30_CTACGACA+GAGTCCAA_HK3H2DSXX_S38_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23685
DDX51-BGHcLV12-30_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	14					GRCh38	V40	DDX51-BGHcLV12-30/Aligned.sortedByCoord.out.bam		ENCORE2	23767
DDX51-BGHcLV12-30_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	14					GRCh38	V40	DDX51-BGHcLV12-30/Aligned.sortedByCoord.out.bam		ENCORE2	23849
DDX51-BGHcLV12-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	14					GRCh38	V40	DDX51-BGHcLV12-30/Aligned.sortedByCoord.out.bam		ENCORE2	23931
DDX51-BGHcLV12-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	14					GRCh38	V40	DDX51-BGHcLV12-30/Aligned.sortedByCoord.out.bam		ENCORE2	24013
DDX51-BGHcLV12-30_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	14					GRCh38	V40	DDX51-BGHcLV12-30_CTACGACA+GAGTCCAA_HK3H2DSXX_S38_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX51-BGHcLV12-30_CTACGACA+GAGTCCAA_HK3H2DSXX_S38_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24095