DDX27 RNA-Seq in K562

General Information


RBP	DDX27
Cell_Line	K562
Method	shRNA
Exp_Name	DDX27-BGKLV19-K562
ENCODE_series_ID	ENCSR201NFZ
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR584LDM
ENCODE_CN_Exp_ID	ENCSR245BNJ
Rep1	DDX27_BGKLV19_11A
Rep2	DDX27_BGKLV19_12A
CN1	NT_BGKLV19_1A
CN2	NT_BGKLV19_2A
Rep1_qPCR	87.3
Rep2_qPCR	81.4
Rep1_WB	70.0
Rep2_WB	80.0
Antibody Cat#	A302-217A
Antibody Lot#	A302-217A
Antibody DCC ID	ENCAB626TGL
Status	Released
Project	ENCODE3
ID	465

Experiment Information (Status: Released)

	BGKLV19-11	BGKLV19-12
idx	218	219
TRCN#_or_BGC#	TRCN0000050003	TRCN0000050003
shRNA_or_gRNA_sequence	GCAGAGGAAAGGTCTCAGTTT	GCAGAGGAAAGGTCTCAGTTT
PAM
Name	DDX27	DDX27
Sample_ID	BGKLV19-11	BGKLV19-12
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	DDX27	DDX27
qPCR_result	87.3	81.4
Ave_qPCR	84.4
RT-qPCR_primer-F	agaaggggaaggaggcagt
RT-qPCR_primer-R	gcagagctttggcaattttc
protein_conc	2834	2543
WB_result	70.0	80.0
Ave_WB	75.0
WB_DONE_date	2/4/2015
MW
IP	1	1
antibody_Cat#	A302-217A	A302-217A
Antibody DCC ID	ENCAB626TGL	ENCAB626TGL
submitted_to_DCC_date	5/4/2015
Rep1_TPM	38.4198708	0
Rep2_TPM	30.0868986	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	237	238

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX27	Product_ID: A302-217A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX27-human

Experiment Status

	BGKLV19-11	BGKLV19-12
Sample_ID	BGKLV19-11	BGKLV19-12
Sample Name	DDX27_BGKLV19_11A	DDX27_BGKLV19_12A
Sample Name	DDX27_BGKLV19_11A	DDX27_BGKLV19_12A
RBP	DDX27	DDX27
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	660	661

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-11	BGKLV19-12
Sample #
Sample Name	DDX27-BGKLV19-11	DDX27-BGKLV19-12
Sample_Name_Alias	DDX27_BGKLV19_11A	DDX27_BGKLV19_12A
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-02	2014-10-02
Lib_ID	Lib-141002	Lib-141002
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/G6.png	DNA_Library_LV18-19/set1/H6.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/E1.png	RNA_Library_LV19-21-24/set1/F1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-11	BGKLV19-12
RBP	DDX27	DDX27
Batch_ID	BGKLV19	BGKLV19
WB_result	70.000	80.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2344	2345

Sequencing Information

	BGKLV19-11	BGKLV19-12
Sample_ID	BGKLV19-11	BGKLV19-12
Sample Name	DDX27_BGKLV19_11A	DDX27_BGKLV19_12A
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set19	set19
total_reads	38,220,000	38,150,000
total_aligned_reads	36,121,992	35,900,166
unique_aligned_reads	33,087,376	32,835,742
percent_uniqueAligned	0.86571	0.86070
correlation_replicates	0.997060	0.997060
spikein_reads	83,428	101,312
percent_spikeins	0.00218	0.00266
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	986	987

Data Submission Information

	BGKLV19-11	BGKLV19-11
ENCODE_alias	brenton-graveley:DDX27_BGKLV19	brenton-graveley:DDX27-BGKLV19-K562
ENCODE_accession	ENCSR584LDM	ENCSR201NFZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-11	BGKLV19-11
Sample Name	DDX27_BGKLV19_11A	DDX27_BGKLV19_11A
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2879	6648

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
DDX27_BGKLV19_11A_ACTGAT_L002_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	986	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1A_ATGTCA_L001_R1_001.fastq.gz,NT_BGKLV19_2A_CCGTCC_L001_R1_001.fastq.gz	ENCODE3	15520
DDX27_BGKLV19_11A_ACTGAT_L002_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	986	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1A_ATGTCA_L001_R2_001.fastq.gz,NT_BGKLV19_2A_CCGTCC_L001_R2_001.fastq.gz	ENCODE3	15530
DDX27_BGKLV19_11A_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	986					GRCh38	V40	DDX27_BGKLV19_11A_ACTGAT_L002_R1_001.fastq.gz,DDX27_BGKLV19_11A_ACTGAT_L002_R2_001.fastq.gz		ENCORE2	15540
DDX27_BGKLV19_11A_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	986					GRCh38	V40	DDX27_BGKLV19_11A/Aligned.sortedByCoord.out.bam		ENCORE2	15550
DDX27_BGKLV19_11A_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	986					GRCh38	V40	DDX27_BGKLV19_11A/Aligned.sortedByCoord.out.bam		ENCORE2	15560
DDX27_BGKLV19_11A_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	986					GRCh38	V40	DDX27_BGKLV19_11A/Aligned.sortedByCoord.out.bam		ENCORE2	15570
DDX27_BGKLV19_11A_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	986					GRCh38	V40	DDX27_BGKLV19_11A/Aligned.sortedByCoord.out.bam		ENCORE2	15580
DDX27_BGKLV19_11A_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	986					GRCh38	V40	DDX27_BGKLV19_11A_ACTGAT_L002_R1_001.fastq.gz,DDX27_BGKLV19_11A_ACTGAT_L002_R2_001.fastq.gz		ENCORE2	16358
DDX27_BGKLV19_12A_ATTCCT_L002_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	987	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1A_ATGTCA_L001_R1_001.fastq.gz,NT_BGKLV19_2A_CCGTCC_L001_R1_001.fastq.gz	ENCODE3	15521
DDX27_BGKLV19_12A_ATTCCT_L002_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	987	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1A_ATGTCA_L001_R2_001.fastq.gz,NT_BGKLV19_2A_CCGTCC_L001_R2_001.fastq.gz	ENCODE3	15531
DDX27_BGKLV19_12A_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	987					GRCh38	V40	DDX27_BGKLV19_12A_ATTCCT_L002_R1_001.fastq.gz,DDX27_BGKLV19_12A_ATTCCT_L002_R2_001.fastq.gz		ENCORE2	15541
DDX27_BGKLV19_12A_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	987					GRCh38	V40	DDX27_BGKLV19_12A/Aligned.sortedByCoord.out.bam		ENCORE2	15551
DDX27_BGKLV19_12A_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	987					GRCh38	V40	DDX27_BGKLV19_12A/Aligned.sortedByCoord.out.bam		ENCORE2	15561
DDX27_BGKLV19_12A_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	987					GRCh38	V40	DDX27_BGKLV19_12A/Aligned.sortedByCoord.out.bam		ENCORE2	15571
DDX27_BGKLV19_12A_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	987					GRCh38	V40	DDX27_BGKLV19_12A/Aligned.sortedByCoord.out.bam		ENCORE2	15581
DDX27_BGKLV19_12A_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	987					GRCh38	V40	DDX27_BGKLV19_12A_ATTCCT_L002_R1_001.fastq.gz,DDX27_BGKLV19_12A_ATTCCT_L002_R2_001.fastq.gz		ENCORE2	16359