DDX21 RNA-Seq in K562

General Information


RBP	DDX21
Cell_Line	K562
Method	CRISPR
Exp_Name	DDX21-BGKcLV02-K562
ENCODE_series_ID	ENCSR382UWL
Batch_ID	BGKcLV02
Pool ID	Pool-160201
Local_Set_Name	BGKcLV02
ENCODE_KD_Exp_ID	ENCSR384LKC
ENCODE_CN_Exp_ID	ENCSR163JUC
Rep1	DDX21_BGKcLV02-11
Rep2	DDX21_BGKcLV02-12
CN1	NT_BGKcLV02-1
CN2	NT_BGKcLV02-2
Rep1_qPCR	75.8
Rep2_qPCR	75.6
Rep1_WB	94.5
Rep2_WB	96.4
Antibody Cat#	RN090PW
Antibody Lot#	RN090PW
Antibody DCC ID	ENCAB315FWL
Status	Released
Project	ENCODE3
ID	582

Experiment Information (Status: Released)

	BGKcLV02-11	BGKcLV02-12
idx	13	14
TRCN#_or_BGC#	BGC#0000010	BGC#0000010
shRNA_or_gRNA_sequence	CGGGAAGGACTTAATTGCAC	CGGGAAGGACTTAATTGCAC
PAM
Name	DDX21-C2-A	DDX21-C2-A
Sample_ID	BGKcLV02-11	BGKcLV02-12
transduction_Date	12/15/2015	12/15/2015
days	day 6	day 6
RBP_name	DDX21	DDX21
qPCR_result	75.8	75.6
Ave_qPCR	75.7
RT-qPCR_primer-F	TTGCTTTGATGTACCTACCGC
RT-qPCR_primer-R	AGTTCTGGTTGCTCTGTGGC
protein_conc	3303	3388
WB_result	94.5	96.4
Ave_WB	95.4
WB_DONE_date	1/4/2016
MW	87kDa
IP	1
antibody_Cat#	RN090PW	RN090PW
Antibody DCC ID	ENCAB315FWL	ENCAB315FWL
submitted_to_DCC_date	9/28/16
Rep1_TPM	228.8	0
Rep2_TPM	130.7	0
Action	Ready	Ready
Library_start_date	1/8/2016	1/8/2016
repeat_library
Note
ID	4107	4108

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX21	Product_ID: RN090PW Lot_ID: 1 Source: MBLI Target Name: DDX21-human

Experiment Status

	BGKcLV02-11	BGKcLV02-12
Sample_ID	BGKcLV02-11	BGKcLV02-12
Sample Name	DDX21_BGKcLV02-11	DDX21_BGKcLV02-12
Sample Name	DDX21_BGKcLV02-11	DDX21_BGKcLV02-12
RBP	DDX21	DDX21
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-09	2016-03-09
Project	ENCODE3	ENCODE3
Note
ID	1085	1086

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV02-11	BGKcLV02-12
Sample #
Sample Name	DDX21-BGKcLV02-11	DDX21-BGKcLV02-12
Sample_Name_Alias	DDX21_BGKcLV02-11	DDX21_BGKcLV02-12
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-01-08	2016-01-08
Lib_ID	Lib-160108	Lib-160108
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_cLV02/set1/E4.png	DNA_Library_cLV02/set1/F4.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_cLV02/set1/G5.png	RNA_Library_cLV02/set1/H5.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV02-11	BGKcLV02-12
RBP	DDX21	DDX21
Batch_ID	BGKcLV02	BGKcLV02
WB_result	94.500	96.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2770	2771

Sequencing Information

	BGKcLV02-11	BGKcLV02-12
Sample_ID	BGKcLV02-11	BGKcLV02-12
Sample Name	DDX21_BGKcLV02-11	DDX21_BGKcLV02-12
Pool ID	Pool-160201	Pool-160201
LocalServer_folder	BGKcLV02	BGKcLV02
total_reads	62,966,568	79,727,460
total_aligned_reads	57,602,072	72,914,024
unique_aligned_reads	52,517,620	66,561,706
percent_uniqueAligned	0.83406	0.83487
correlation_replicates	0.998914	0.998914
spikein_reads	129,892	115,108
percent_spikeins	0.00206	0.00144
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1419	1420

Data Submission Information

	BGKcLV02-11	BGKcLV02-11
ENCODE_alias	brenton-graveley:DDX21_BGKcLV02	brenton-graveley:DDX21-BGKcLV02-K562
ENCODE_accession	ENCSR384LKC	ENCSR382UWL
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV02-11	BGKcLV02-11
Sample Name	DDX21_BGKcLV02-11	DDX21_BGKcLV02-11
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3104	6643

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
DDX21_BGKcLV02-11_CGTACG_L007_001.R1.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1419	HiSeq2500	100	paired-ended	1				NT_BGKcLV02-1_GGCTAC_L006_001.R1.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R1.fastq.gz	ENCODE3	22752
DDX21_BGKcLV02-11_CGTACG_L007_001.R2.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1419	HiSeq2500	100	paired-ended	2				NT_BGKcLV02-1_GGCTAC_L006_001.R2.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R2.fastq.gz	ENCODE3	22772
DDX21_BGKcLV02-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1419					GRCh38	V40	DDX21_BGKcLV02-11_CGTACG_L007_001.R1.fastq.gz,DDX21_BGKcLV02-11_CGTACG_L007_001.R2.fastq.gz		ENCORE2	22792
DDX21_BGKcLV02-11_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1419					GRCh38	V40	DDX21_BGKcLV02-11/Aligned.sortedByCoord.out.bam		ENCORE2	22812
DDX21_BGKcLV02-11_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1419					GRCh38	V40	DDX21_BGKcLV02-11/Aligned.sortedByCoord.out.bam		ENCORE2	22832
DDX21_BGKcLV02-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1419					GRCh38	V40	DDX21_BGKcLV02-11/Aligned.sortedByCoord.out.bam		ENCORE2	22852
DDX21_BGKcLV02-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1419					GRCh38	V40	DDX21_BGKcLV02-11/Aligned.sortedByCoord.out.bam		ENCORE2	22872
DDX21_BGKcLV02-11_quant.sf	ENCODE_DATA/BGKcLV02/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1419					GRCh38	V40	DDX21_BGKcLV02-11_CGTACG_L007_001.R1.fastq.gz,DDX21_BGKcLV02-11_CGTACG_L007_001.R2.fastq.gz		ENCORE2	22892
DDX21_BGKcLV02-12_GAGTGG_L008_001.R1.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1420	HiSeq2500	100	paired-ended	1				NT_BGKcLV02-1_GGCTAC_L006_001.R1.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R1.fastq.gz	ENCODE3	22753
DDX21_BGKcLV02-12_GAGTGG_L008_001.R2.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1420	HiSeq2500	100	paired-ended	2				NT_BGKcLV02-1_GGCTAC_L006_001.R2.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R2.fastq.gz	ENCODE3	22773
DDX21_BGKcLV02-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1420					GRCh38	V40	DDX21_BGKcLV02-12_GAGTGG_L008_001.R1.fastq.gz,DDX21_BGKcLV02-12_GAGTGG_L008_001.R2.fastq.gz		ENCORE2	22793
DDX21_BGKcLV02-12_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1420					GRCh38	V40	DDX21_BGKcLV02-12/Aligned.sortedByCoord.out.bam		ENCORE2	22813
DDX21_BGKcLV02-12_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1420					GRCh38	V40	DDX21_BGKcLV02-12/Aligned.sortedByCoord.out.bam		ENCORE2	22833
DDX21_BGKcLV02-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1420					GRCh38	V40	DDX21_BGKcLV02-12/Aligned.sortedByCoord.out.bam		ENCORE2	22853
DDX21_BGKcLV02-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1420					GRCh38	V40	DDX21_BGKcLV02-12/Aligned.sortedByCoord.out.bam		ENCORE2	22873
DDX21_BGKcLV02-12_quant.sf	ENCODE_DATA/BGKcLV02/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1420					GRCh38	V40	DDX21_BGKcLV02-12_GAGTGG_L008_001.R1.fastq.gz,DDX21_BGKcLV02-12_GAGTGG_L008_001.R2.fastq.gz		ENCORE2	22893