DDX42 RNA-Seq in K562

General Information


RBP	DDX42
Cell_Line	K562
Method	CRISPR
Exp_Name	DDX42-BGKcLV08-K562
ENCODE_series_ID	ENCSR885FVH
Batch_ID	BGKcLV08
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR521WCW
ENCODE_CN_Exp_ID	ENCSR015KGT
Rep1	DDX42-BGKcLV08-21
Rep2	DDX42-BGKcLV08-22
CN1	NT-BGKcLV08-1
CN2	NT-BGKcLV08-2
Rep1_qPCR	15.9
Rep2_qPCR	18.5
Rep1_WB	72.3
Rep2_WB	72.3
Antibody Cat#	A303-353A
Antibody Lot#	A303-353A
Antibody DCC ID	ENCAB455YJZ
Status	Released
Project	ENCODE4
ID	201

Experiment Information (Status: Released)

	BGKcLV08-21	BGKcLV08-22
idx	246	247
TRCN#_or_BGC#	BGC#0000113	BGC#0000113
shRNA_or_gRNA_sequence	AGAAGAGCTGGTTGCCCCAA	AGAAGAGCTGGTTGCCCCAA
PAM	AGG	AGG
Name	DDX42-78F	DDX42-78F
Sample_ID	BGKcLV08-21	BGKcLV08-22
transduction_Date	3/8/18	3/8/18
days	Day 6	Day 6
RBP_name	DDX42	DDX42
qPCR_result	15.9	18.5
Ave_qPCR	17.2
RT-qPCR_primer-F	accctattcgagtggtgcag
RT-qPCR_primer-R	cgggtaagccagttccatt
protein_conc	3467	3443
WB_result	72.3	72.3
Ave_WB	72.3
WB_DONE_date	3/23/28
MW	103
IP	1
antibody_Cat#	A303-353A	A303-353A
Antibody DCC ID	ENCAB455YJZ
submitted_to_DCC_date	9/6/18
Rep1_TPM	69.8	0
Rep2_TPM	66.4	0
Action	Ready	Ready
Library_start_date	7/26/18	7/26/18
repeat_library
Note
ID	4346	4347

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX42	Product_ID: A303-353A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX42-human

Experiment Status

	BGKcLV08-21	BGKcLV08-22
Sample_ID	BGKcLV08-21	BGKcLV08-22
Sample Name
Sample Name	DDX42-BGKcLV08-21	DDX42-BGKcLV08-22
RBP	DDX42	DDX42
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6173	6174

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV08-21	BGKcLV08-22
Sample #	9	10
Sample Name	DDX42-BGKcLV08-21	DDX42-BGKcLV08-22
Sample_Name_Alias
Index Well Position	A02	B02
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	275	288
Peak_Molarity	53.40	51.30
libSampleQC_DNA_Well	DNA_Library_set41/set2/A2.png	DNA_Library_set41/set2/B2.png
RIN	9.7	9.5
libSample_RNA_Well	RNA_Library_set41/set1/A2.png	RNA_Library_set41/set1/B2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-07-27	2018-07-27
Sample_ID	BGKcLV08-21	BGKcLV08-22
RBP	DDX42	DDX42
Batch_ID	BGKcLV08	BGKcLV08
WB_result	72.300	72.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	859	860

Sequencing Information

	BGKcLV08-21	BGKcLV08-22
Sample_ID	BGKcLV08-21	BGKcLV08-22
Sample Name	DDX42-BGKcLV08-21	DDX42-BGKcLV08-22
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	177,413,278	111,718,794
total_aligned_reads	172,527,648	109,442,176
unique_aligned_reads	155,492,486	97,825,148
percent_uniqueAligned	0.87644	0.87564
correlation_replicates	0.996535	0.996535
spikein_reads	392,796	261,574
percent_spikeins	0.00221	0.00234
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	265	266

Data Submission Information

	BGKcLV08-21	BGKcLV08-21	BGKcLV08-21	BGKcLV08-21	BGKcLV08-21	BGKcLV08-21	BGKcLV08-22	BGKcLV08-22	BGKcLV08-22	BGKcLV08-22
ENCODE_alias	brenton-graveley:DDX42-BGKcLV08	brenton-graveley:DDX42-BGKcLV08-21	brenton-graveley:L-DDX42-BGKcLV08-21	brenton-graveley:DDX42-BGKcLV08-21_AGTTCAGG+CCAACAGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX42-BGKcLV08-21_AGTTCAGG+CCAACAGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX42-BGKcLV08-K562	brenton-graveley:DDX42-BGKcLV08-22	brenton-graveley:L-DDX42-BGKcLV08-22	brenton-graveley:DDX42-BGKcLV08-22_GACCTGAA+TTGGTGAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX42-BGKcLV08-22_GACCTGAA+TTGGTGAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR521WCW	ENCBS960ZMX	ENCLB931NBC	ENCFF115SUG	ENCFF796BDQ	ENCSR885FVH	ENCBS826MJI	ENCLB240FPK	ENCFF981ZFE	ENCFF417GGR
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	BGKcLV08-21	BGKcLV08-21	BGKcLV08-21	BGKcLV08-21	BGKcLV08-21	BGKcLV08-21	BGKcLV08-22	BGKcLV08-22	BGKcLV08-22	BGKcLV08-22
Sample Name	DDX42-BGKcLV08-21	DDX42-BGKcLV08-21	DDX42-BGKcLV08-21	DDX42-BGKcLV08-21	DDX42-BGKcLV08-21	DDX42-BGKcLV08-21	DDX42-BGKcLV08-22	DDX42-BGKcLV08-22	DDX42-BGKcLV08-22	DDX42-BGKcLV08-22
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		DDX42-BGKcLV08-21.pdf	L-DDX42-BGKcLV08-21.pdf				DDX42-BGKcLV08-22.pdf	L-DDX42-BGKcLV08-22.pdf
ID	1122	1164	1234	1304	1374	7181	1165	1235	1305	1375

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
DDX42-BGKcLV08-21_AGTTCAGG+CCAACAGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	265				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	511
DDX42-BGKcLV08-21_AGTTCAGG+CCAACAGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	265				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	581
DDX42-BGKcLV08-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	265	GRCh38	V40	DDX42-BGKcLV08-21_AGTTCAGG+CCAACAGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX42-BGKcLV08-21_AGTTCAGG+CCAACAGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26749
DDX42-BGKcLV08-21_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	265	GRCh38	V40	DDX42-BGKcLV08-21/Aligned.sortedByCoord.out.bam		ENCORE2	26819
DDX42-BGKcLV08-21_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	265	GRCh38	V40	DDX42-BGKcLV08-21/Aligned.sortedByCoord.out.bam		ENCORE2	26889
DDX42-BGKcLV08-21_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	265	GRCh38	V40	DDX42-BGKcLV08-21/Aligned.sortedByCoord.out.bam		ENCORE2	26959
DDX42-BGKcLV08-21_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	265	GRCh38	V40	DDX42-BGKcLV08-21/Aligned.sortedByCoord.out.bam		ENCORE2	27029
DDX42-BGKcLV08-21_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	265	GRCh38	V40	DDX42-BGKcLV08-21_AGTTCAGG+CCAACAGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX42-BGKcLV08-21_AGTTCAGG+CCAACAGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27099
DDX42-BGKcLV08-22_GACCTGAA+TTGGTGAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	266				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	512
DDX42-BGKcLV08-22_GACCTGAA+TTGGTGAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	266				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	582
DDX42-BGKcLV08-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	266	GRCh38	V40	DDX42-BGKcLV08-22_GACCTGAA+TTGGTGAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX42-BGKcLV08-22_GACCTGAA+TTGGTGAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26750
DDX42-BGKcLV08-22_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	266	GRCh38	V40	DDX42-BGKcLV08-22/Aligned.sortedByCoord.out.bam		ENCORE2	26820
DDX42-BGKcLV08-22_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	266	GRCh38	V40	DDX42-BGKcLV08-22/Aligned.sortedByCoord.out.bam		ENCORE2	26890
DDX42-BGKcLV08-22_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	266	GRCh38	V40	DDX42-BGKcLV08-22/Aligned.sortedByCoord.out.bam		ENCORE2	26960
DDX42-BGKcLV08-22_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	266	GRCh38	V40	DDX42-BGKcLV08-22/Aligned.sortedByCoord.out.bam		ENCORE2	27030
DDX42-BGKcLV08-22_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	266	GRCh38	V40	DDX42-BGKcLV08-22_GACCTGAA+TTGGTGAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX42-BGKcLV08-22_GACCTGAA+TTGGTGAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27100