DDX6 RNA-Seq in K562

General Information


RBP	DDX6
Cell_Line	K562
Method	CRISPR
Exp_Name	DDX6-BGKcLV08-K562
ENCODE_series_ID	ENCSR787FAG
Batch_ID	BGKcLV08
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR298ASI
ENCODE_CN_Exp_ID	ENCSR015KGT
Rep1	DDX6-BGKcLV08-29
Rep2	DDX6-BGKcLV08-30
CN1	NT-BGKcLV08-1
CN2	NT-BGKcLV08-2
Rep1_qPCR	60.9
Rep2_qPCR	53.1
Rep1_WB	52.7
Rep2_WB	50.8
Antibody Cat#	A300-460A
Antibody Lot#
Antibody DCC ID	ENCAB348UON
Status	Released
Project	ENCODE4
ID	203

Experiment Information (Status: Released)

	BGKcLV08-29	BGKcLV08-30
idx	254	255
TRCN#_or_BGC#	BGC#0000117	BGC#0000117
shRNA_or_gRNA_sequence	AGGTCTAGCCGTTCAAGTAA	AGGTCTAGCCGTTCAAGTAA
PAM	GGG	GGG
Name	DDX6-87F	DDX6-87F
Sample_ID	BGKcLV08-29	BGKcLV08-30
transduction_Date	3/8/18	3/8/18
days	Day 6	Day 6
RBP_name	DDX6	DDX6
qPCR_result	60.9	53.1
Ave_qPCR	57.0
RT-qPCR_primer-F	TACCACAGCGAGCCTGTAGA
RT-qPCR_primer-R	TGTCACAGATCCAAACGAGC
protein_conc	3441	3554
WB_result	52.7	50.8
Ave_WB	51.8
WB_DONE_date	3/12/18	wes
MW	52kDa
IP	1	1
antibody_Cat#	A300-460A
Antibody DCC ID	ENCAB348UON
submitted_to_DCC_date	9/6/2018
Rep1_TPM	10.2	0
Rep2_TPM	7.3	0
Action	Ready	Ready
Library_start_date	7/26/18	7/26/18
repeat_library
Note
ID	4354	4355

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX6	Product_ID: A300-460A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX6-human

Experiment Status

	BGKcLV08-29	BGKcLV08-30
Sample_ID	BGKcLV08-29	BGKcLV08-30
Sample Name
Sample Name	DDX6-BGKcLV08-29	DDX6-BGKcLV08-30
RBP	DDX6	DDX6
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6177	6178

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV08-29	BGKcLV08-30
Sample #	13	14
Sample Name	DDX6-BGKcLV08-29	DDX6-BGKcLV08-30
Sample_Name_Alias
Index Well Position	E02	F02
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	276
Peak_Molarity	57.80	56.80
libSampleQC_DNA_Well	DNA_Library_set41/set2/E2.png	DNA_Library_set41/set2/F2.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set41/set1/E2.png	RNA_Library_set41/set1/F2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-07-27	2018-07-27
Sample_ID	BGKcLV08-29	BGKcLV08-30
RBP	DDX6	DDX6
Batch_ID	BGKcLV08	BGKcLV08
WB_result	52.700	50.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	863	864

Sequencing Information

	BGKcLV08-29	BGKcLV08-30
Sample_ID	BGKcLV08-29	BGKcLV08-30
Sample Name	DDX6-BGKcLV08-29	DDX6-BGKcLV08-30
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	202,447,112	75,955,170
total_aligned_reads	195,720,802	73,373,198
unique_aligned_reads	176,307,052	66,122,180
percent_uniqueAligned	0.87088	0.87054
correlation_replicates	0.998843	0.998843
spikein_reads	379,724	131,716
percent_spikeins	0.00188	0.00173
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	269	270

Data Submission Information

	BGKcLV08-29	BGKcLV08-29	BGKcLV08-29	BGKcLV08-29	BGKcLV08-29	BGKcLV08-29	BGKcLV08-30	BGKcLV08-30	BGKcLV08-30	BGKcLV08-30
ENCODE_alias	brenton-graveley:DDX6-BGKcLV08	brenton-graveley:DDX6-BGKcLV08-29	brenton-graveley:L-DDX6-BGKcLV08-29	brenton-graveley:DDX6-BGKcLV08-29_CCAAGTCT+AAGGATGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX6-BGKcLV08-29_CCAAGTCT+AAGGATGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX6-BGKcLV08-K562	brenton-graveley:DDX6-BGKcLV08-30	brenton-graveley:L-DDX6-BGKcLV08-30	brenton-graveley:DDX6-BGKcLV08-30_TTGGACTC+GGAAGCAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX6-BGKcLV08-30_TTGGACTC+GGAAGCAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR298ASI	ENCBS099EPI	ENCLB556NMK	ENCFF506HBX	ENCFF449JOE	ENCSR787FAG	ENCBS324CCL	ENCLB811YQC	ENCFF981YJO	ENCFF986GZZ
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	BGKcLV08-29	BGKcLV08-29	BGKcLV08-29	BGKcLV08-29	BGKcLV08-29	BGKcLV08-29	BGKcLV08-30	BGKcLV08-30	BGKcLV08-30	BGKcLV08-30
Sample Name	DDX6-BGKcLV08-29	DDX6-BGKcLV08-29	DDX6-BGKcLV08-29	DDX6-BGKcLV08-29	DDX6-BGKcLV08-29	DDX6-BGKcLV08-29	DDX6-BGKcLV08-30	DDX6-BGKcLV08-30	DDX6-BGKcLV08-30	DDX6-BGKcLV08-30
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
		LV41_biosample_protocol	LV41_library_protocol				LV41_biosample_protocol	LV41_library_protocol
protocol_URL		DDX6-BGKcLV08-29.pdf	L-DDX6-BGKcLV08-29.pdf				DDX6-BGKcLV08-30.pdf	L-DDX6-BGKcLV08-30.pdf
ID	1124	1168	1238	1308	1378	7185	1169	1239	1309	1379

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
DDX6-BGKcLV08-29_CCAAGTCT+AAGGATGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	269				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	515
DDX6-BGKcLV08-29_CCAAGTCT+AAGGATGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	269				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	585
DDX6-BGKcLV08-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	269	GRCh38	V40	DDX6-BGKcLV08-29_CCAAGTCT+AAGGATGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX6-BGKcLV08-29_CCAAGTCT+AAGGATGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26753
DDX6-BGKcLV08-29_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	269	GRCh38	V40	DDX6-BGKcLV08-29/Aligned.sortedByCoord.out.bam		ENCORE2	26823
DDX6-BGKcLV08-29_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	269	GRCh38	V40	DDX6-BGKcLV08-29/Aligned.sortedByCoord.out.bam		ENCORE2	26893
DDX6-BGKcLV08-29_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	269	GRCh38	V40	DDX6-BGKcLV08-29/Aligned.sortedByCoord.out.bam		ENCORE2	26963
DDX6-BGKcLV08-29_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	269	GRCh38	V40	DDX6-BGKcLV08-29/Aligned.sortedByCoord.out.bam		ENCORE2	27033
DDX6-BGKcLV08-29_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	269	GRCh38	V40	DDX6-BGKcLV08-29_CCAAGTCT+AAGGATGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX6-BGKcLV08-29_CCAAGTCT+AAGGATGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27103
DDX6-BGKcLV08-30_TTGGACTC+GGAAGCAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	270				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	516
DDX6-BGKcLV08-30_TTGGACTC+GGAAGCAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	270				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	586
DDX6-BGKcLV08-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	270	GRCh38	V40	DDX6-BGKcLV08-30_TTGGACTC+GGAAGCAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX6-BGKcLV08-30_TTGGACTC+GGAAGCAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26754
DDX6-BGKcLV08-30_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	270	GRCh38	V40	DDX6-BGKcLV08-30/Aligned.sortedByCoord.out.bam		ENCORE2	26824
DDX6-BGKcLV08-30_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	270	GRCh38	V40	DDX6-BGKcLV08-30/Aligned.sortedByCoord.out.bam		ENCORE2	26894
DDX6-BGKcLV08-30_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	270	GRCh38	V40	DDX6-BGKcLV08-30/Aligned.sortedByCoord.out.bam		ENCORE2	26964
DDX6-BGKcLV08-30_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	270	GRCh38	V40	DDX6-BGKcLV08-30/Aligned.sortedByCoord.out.bam		ENCORE2	27034
DDX6-BGKcLV08-30_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	270	GRCh38	V40	DDX6-BGKcLV08-30_TTGGACTC+GGAAGCAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX6-BGKcLV08-30_TTGGACTC+GGAAGCAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27104