DDX17 RNA-Seq in K562

General Information


RBP	DDX17
Cell_Line	K562
Method	CRISPR
Exp_Name	DDX17-BGKcLV28-K562
ENCODE_series_ID	ENCSR646GHV
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR613ZVB
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	DDX17-BGKcLV28-69
Rep2	DDX17-BGKcLV28-70
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	47.8
Rep2_qPCR	45.7
Rep1_WB	61.8
Rep2_WB	52.7
Antibody Cat#	A300-509A
Antibody Lot#	LOT #2
Antibody DCC ID	ENCAB300RAY
Status	Released
Project	ENCODE4
ID	843

Experiment Information (Status: Released)

	BGKcLV28-69	BGKcLV28-70
idx	1019	1020
TRCN#_or_BGC#	BGC#0000745	BGC#0000745
shRNA_or_gRNA_sequence	GGTCTGGTGACGACCGATGG	GGTCTGGTGACGACCGATGG
PAM	CGG	CGG
Name	DDX17_95	DDX17_95
Sample_ID	BGKcLV28-69	BGKcLV28-70
transduction_Date	7/12/21	7/12/21
days	Day 6	Day 6
RBP_name	DDX17	DDX17
qPCR_result	47.8	45.7
Ave_qPCR	46.8
RT-qPCR_primer-F	tggacgaagctgacagaatg
RT-qPCR_primer-R	ggttgcactccacatcagtg
protein_conc	2547	2608
WB_result	61.8	52.7
Ave_WB	57.2
WB_DONE_date	7/7/21	JESS
MW	80KD
IP
antibody_Cat#	A300-509A	LOT #2
Antibody DCC ID	ENCAB300RAY
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	5153	5154

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX17	Product_ID: A300-509A Lot_ID: 2 Source: Bethyl Labs Target Name: DDX17-human

Experiment Status

	BGKcLV28-69	BGKcLV28-70
Sample_ID	BGKcLV28-69	BGKcLV28-70
Sample Name
Sample Name	DDX17-BGKcLV28-69	DDX17-BGKcLV28-70
RBP	DDX17	DDX17
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9945	9946

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-69	BGKcLV28-70
Sample #	53	54
Sample Name	DDX17-BGKcLV28-69	DDX17-BGKcLV28-70
Sample_Name_Alias
Index Well Position	E11	F11
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	320
Peak_Molarity	117.00	110.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/E7.png	DNA_Library_set48-49/set3/F7.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set48-49/set2/E7.png	RNA_Library_set48-49/set2/F7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-69	BGKcLV28-70
RBP	DDX17	DDX17
Batch_ID	BGKcLV28	BGKcLV28
WB_result	61.800	52.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2114	2115

Sequencing Information

	BGKcLV28-69	BGKcLV28-70
Sample_ID	BGKcLV28-69	BGKcLV28-70
Sample Name	DDX17-BGKcLV28-69	DDX17-BGKcLV28-70
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	153,620,470	108,998,454
total_aligned_reads	144,250,466	104,016,232
unique_aligned_reads	133,323,776	96,127,626
percent_uniqueAligned	0.86788	0.88192
correlation_replicates	0.997381	0.997381
spikein_reads	29,622	17,848
percent_spikeins	0.00019	0.00016
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1865	1866

Data Submission Information

	BGKcLV28-69	BGKcLV28-69	BGKcLV28-69	BGKcLV28-69	BGKcLV28-69	BGKcLV28-69	BGKcLV28-70	BGKcLV28-70	BGKcLV28-70	BGKcLV28-70
ENCODE_alias	brenton-graveley:DDX17-BGKcLV28	brenton-graveley:DDX17-BGKcLV28-69	brenton-graveley:L-DDX17-BGKcLV28-69	brenton-graveley:DDX17-BGKcLV28-69_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX17-BGKcLV28-69_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX17-BGKcLV28-K562	brenton-graveley:DDX17-BGKcLV28-70	brenton-graveley:L-DDX17-BGKcLV28-70	brenton-graveley:DDX17-BGKcLV28-70_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX17-BGKcLV28-70_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR613ZVB	ENCBS535FPO	ENCLB404UMJ	ENCFF972VWV	ENCFF279ATS	ENCSR646GHV	ENCBS555TAR	ENCLB793XVU	ENCFF694IFW	ENCFF309UNR
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	BGKcLV28-69	BGKcLV28-69	BGKcLV28-69	BGKcLV28-69	BGKcLV28-69	BGKcLV28-69	BGKcLV28-70	BGKcLV28-70	BGKcLV28-70	BGKcLV28-70
Sample Name	DDX17-BGKcLV28-69	DDX17-BGKcLV28-69	DDX17-BGKcLV28-69	DDX17-BGKcLV28-69	DDX17-BGKcLV28-69	DDX17-BGKcLV28-69	DDX17-BGKcLV28-70	DDX17-BGKcLV28-70	DDX17-BGKcLV28-70	DDX17-BGKcLV28-70
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		DDX17-BGKcLV28-69.pdf	L-DDX17-BGKcLV28-69.pdf				DDX17-BGKcLV28-70.pdf	L-DDX17-BGKcLV28-70.pdf
ID	3497	3628	3762	3896	4030	7173	3629	3763	3897	4031

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
DDX17-BGKcLV28-69_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1865	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	3982
DDX17-BGKcLV28-69_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1865	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	4040
DDX17-BGKcLV28-69_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1865					GRCh38	V40	DDX17-BGKcLV28-69_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX17-BGKcLV28-69_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19264
DDX17-BGKcLV28-69_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	1865					GRCh38	V40	DDX17-BGKcLV28-69/Aligned.sortedByCoord.out.bam		ENCORE2	19322
DDX17-BGKcLV28-69_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	1865					GRCh38	V40	DDX17-BGKcLV28-69/Aligned.sortedByCoord.out.bam		ENCORE2	19380
DDX17-BGKcLV28-69_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	1865					GRCh38	V40	DDX17-BGKcLV28-69/Aligned.sortedByCoord.out.bam		ENCORE2	19438
DDX17-BGKcLV28-69_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	1865					GRCh38	V40	DDX17-BGKcLV28-69/Aligned.sortedByCoord.out.bam		ENCORE2	19496
DDX17-BGKcLV28-69_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1865					GRCh38	V40	DDX17-BGKcLV28-69_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX17-BGKcLV28-69_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19554
DDX17-BGKcLV28-70_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1866	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	3983
DDX17-BGKcLV28-70_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1866	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	4041
DDX17-BGKcLV28-70_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1866					GRCh38	V40	DDX17-BGKcLV28-70_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX17-BGKcLV28-70_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19265
DDX17-BGKcLV28-70_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	1866					GRCh38	V40	DDX17-BGKcLV28-70/Aligned.sortedByCoord.out.bam		ENCORE2	19323
DDX17-BGKcLV28-70_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	1866					GRCh38	V40	DDX17-BGKcLV28-70/Aligned.sortedByCoord.out.bam		ENCORE2	19381
DDX17-BGKcLV28-70_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	1866					GRCh38	V40	DDX17-BGKcLV28-70/Aligned.sortedByCoord.out.bam		ENCORE2	19439
DDX17-BGKcLV28-70_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	1866					GRCh38	V40	DDX17-BGKcLV28-70/Aligned.sortedByCoord.out.bam		ENCORE2	19497
DDX17-BGKcLV28-70_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1866					GRCh38	V40	DDX17-BGKcLV28-70_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX17-BGKcLV28-70_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19555