DDX28 RNA-Seq in K562

General Information


RBP	DDX28
Cell_Line	K562
Method	shRNA
Exp_Name	DDX28-BGKLV19-K562
ENCODE_series_ID	ENCSR683QAI
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR205VSQ
ENCODE_CN_Exp_ID	ENCSR661HEL
Rep1	DDX28_BGKLV19_13B
Rep2	DDX28_BGKLV19_14B
CN1	NT_BGKLV19_1B
CN2	NT_BGKLV19_2B
Rep1_qPCR	82.4
Rep2_qPCR	77.7
Rep1_WB
Rep2_WB	no band
Antibody Cat#	A300-761A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB993HVI
Status	Released
Project	ENCODE3
ID	466

Experiment Information (Status: Released)

	BGKLV19-13	BGKLV19-14
idx	220	221
TRCN#_or_BGC#	TRCN0000051762	TRCN0000051762
shRNA_or_gRNA_sequence	CCTGGTTCAGAAGATTGAGCT	CCTGGTTCAGAAGATTGAGCT
PAM
Name	DDX28	DDX28
Sample_ID	BGKLV19-13	BGKLV19-14
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	DDX28	DDX28
qPCR_result	82.4	77.7
Ave_qPCR	80.1
RT-qPCR_primer-F	gcaccgtcatcagttttgtg
RT-qPCR_primer-R	aaggctctttcaccgaggat
protein_conc	2594	2526
WB_result		no band
Ave_WB	no band
WB_DONE_date	1/8/2015
MW
IP	1	1
antibody_Cat#	A300-761A	A300-761A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	5.90782556	0
Rep2_TPM	4.02009067	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	241	242

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV19-13	BGKLV19-14
Sample_ID	BGKLV19-13	BGKLV19-14
Sample Name	DDX28_BGKLV19_13B	DDX28_BGKLV19_14B
Sample Name	DDX28_BGKLV19_13B	DDX28_BGKLV19_14B
RBP	DDX28	DDX28
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	662	663

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-13	BGKLV19-14
Sample #
Sample Name	DDX28-BGKLV19-13B	DDX28-BGKLV19-14B
Sample_Name_Alias	DDX28_BGKLV19_13B	DDX28_BGKLV19_14B
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-03	2014-10-03
Lib_ID	Lib-141003	Lib-141003
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/C7.png	DNA_Library_LV18-19/set1/D7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/G1.png	RNA_Library_LV19-21-24/set1/H1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-13	BGKLV19-14
RBP	DDX28	DDX28
Batch_ID	BGKLV19	BGKLV19
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2348	2349

Sequencing Information

	BGKLV19-13	BGKLV19-14
Sample_ID	BGKLV19-13	BGKLV19-14
Sample Name	DDX28_BGKLV19_13B	DDX28_BGKLV19_14B
Pool ID	Pool-141015	Pool-141015
LocalServer_folder	set19	set19
total_reads	58,660,000	56,150,000
total_aligned_reads	52,215,144	51,076,474
unique_aligned_reads	47,858,560	46,874,716
percent_uniqueAligned	0.81586	0.83481
correlation_replicates	0.999131	0.999131
spikein_reads	195,312	155,800
percent_spikeins	0.00333	0.00277
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	990	991

Data Submission Information

	BGKLV19-13	BGKLV19-13
ENCODE_alias	brenton-graveley:DDX28_BGKLV19	brenton-graveley:DDX28-BGKLV19-K562
ENCODE_accession	ENCSR205VSQ	ENCSR683QAI
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-13	BGKLV19-13
Sample Name	DDX28_BGKLV19_13B	DDX28_BGKLV19_13B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2880	6650

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
DDX28_BGKLV19_13B_TTAGGC_L002_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	990	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15102
DDX28_BGKLV19_13B_TTAGGC_L002_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	990	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15160
DDX28_BGKLV19_13B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	990					GRCh38	V40	DDX28_BGKLV19_13B_TTAGGC_L002_R1_001.fastq.gz,DDX28_BGKLV19_13B_TTAGGC_L002_R2_001.fastq.gz		ENCORE2	15218
DDX28_BGKLV19_13B_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	990					GRCh38	V40	DDX28_BGKLV19_13B/Aligned.sortedByCoord.out.bam		ENCORE2	15289
DDX28_BGKLV19_13B_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	990					GRCh38	V40	DDX28_BGKLV19_13B/Aligned.sortedByCoord.out.bam		ENCORE2	15347
DDX28_BGKLV19_13B_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	990					GRCh38	V40	DDX28_BGKLV19_13B/Aligned.sortedByCoord.out.bam		ENCORE2	15405
DDX28_BGKLV19_13B_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	990					GRCh38	V40	DDX28_BGKLV19_13B/Aligned.sortedByCoord.out.bam		ENCORE2	15463
DDX28_BGKLV19_13B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	990					GRCh38	V40	DDX28_BGKLV19_13B_TTAGGC_L002_R1_001.fastq.gz,DDX28_BGKLV19_13B_TTAGGC_L002_R2_001.fastq.gz		ENCORE2	16360
DDX28_BGKLV19_14B_TGACCA_L002_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	991	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15103
DDX28_BGKLV19_14B_TGACCA_L002_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	991	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15161
DDX28_BGKLV19_14B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	991					GRCh38	V40	DDX28_BGKLV19_14B_TGACCA_L002_R1_001.fastq.gz,DDX28_BGKLV19_14B_TGACCA_L002_R2_001.fastq.gz		ENCORE2	15219
DDX28_BGKLV19_14B_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	991					GRCh38	V40	DDX28_BGKLV19_14B/Aligned.sortedByCoord.out.bam		ENCORE2	15290
DDX28_BGKLV19_14B_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	991					GRCh38	V40	DDX28_BGKLV19_14B/Aligned.sortedByCoord.out.bam		ENCORE2	15348
DDX28_BGKLV19_14B_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	991					GRCh38	V40	DDX28_BGKLV19_14B/Aligned.sortedByCoord.out.bam		ENCORE2	15406
DDX28_BGKLV19_14B_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	991					GRCh38	V40	DDX28_BGKLV19_14B/Aligned.sortedByCoord.out.bam		ENCORE2	15464
DDX28_BGKLV19_14B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	991					GRCh38	V40	DDX28_BGKLV19_14B_TGACCA_L002_R1_001.fastq.gz,DDX28_BGKLV19_14B_TGACCA_L002_R2_001.fastq.gz		ENCORE2	16361