DDX21 RNA-Seq in HepG2

General Information


RBP	DDX21
Cell_Line	HepG2
Method	shRNA
Exp_Name	DDX21-BGHLV14-HepG2
ENCODE_series_ID	ENCSR899KUM
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR485ZTC
ENCODE_CN_Exp_ID	ENCSR003EKR
Rep1	DDX21_BGHLV14-9
Rep2	DDX21_BGHLV14-10
CN1	NT_BGHLV14-1_1
CN2	NT_BGHLV14-2_1
Rep1_qPCR	85.2
Rep2_qPCR	82.0
Rep1_WB	90.6
Rep2_WB	92.5
Antibody Cat#	RN090PW
Antibody Lot#	RN090PW
Antibody DCC ID	ENCAB315FWL
Status	Released
Project	ENCODE3
ID	387

Experiment Information (Status: Released)

	BGHLV14-9	BGHLV14-10
idx	103	104
TRCN#_or_BGC#	TRCN0000051198	TRCN0000051198
shRNA_or_gRNA_sequence	GCGGAGTTTCAGTAAAGCATT	GCGGAGTTTCAGTAAAGCATT
PAM
Name	DDX21	DDX21
Sample_ID	BGHLV14-9	BGHLV14-10
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	DDX21	DDX21
qPCR_result	85.2	82.0
Ave_qPCR	83.6
RT-qPCR_primer-F	TTGCTTTGATGTACCTACCGC
RT-qPCR_primer-R	AGTTCTGGTTGCTCTGTGGC
protein_conc	3745	3517
WB_result	90.6	92.5
Ave_WB	91.5
WB_DONE_date	6/24/2015
MW	87kDa
IP	1	1
antibody_Cat#	RN090PW	RN090PW
Antibody DCC ID	ENCAB315FWL	ENCAB315FWL
submitted_to_DCC_date	8/6/2015
Rep1_TPM	99.7	0
Rep2_TPM	125.5	0
Action
Library_start_date	7/30/2014	7/30/2014
repeat_library
Note
ID	2160	2161

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

	BGHLV14-9	BGHLV14-10
Sample_ID	BGHLV14-9	BGHLV14-10
Sample Name	DDX21_BGHLV14-9	DDX21_BGHLV14-10
Sample Name	DDX21_BGHLV14-9	DDX21_BGHLV14-10
RBP	DDX21	DDX21
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	497	496

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-9	BGHLV14-10
Sample #
Sample Name	DDX21-BGHLV14-9	DDX21-BGHLV14-10
Sample_Name_Alias	DDX21_BGHLV14-9	DDX21_BGHLV14-10
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-30	2014-07-30
Lib_ID	Lib-140730	Lib-140730
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/G8.png	DNA_Library_LV13-14/set1/F8.png
RIN	9.4	9.5
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/B5.png	RNA_Library_LV13-14-16/set1/A5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-9	BGHLV14-10
RBP	DDX21	DDX21
Batch_ID	BGHLV14	BGHLV14
WB_result	90.600	92.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2181	2180

Sequencing Information

	BGHLV14-9	BGHLV14-10
Sample_ID	BGHLV14-9	BGHLV14-10
Sample Name	DDX21_BGHLV14-9	DDX21_BGHLV14-10
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	47,670,000	50,020,000
total_aligned_reads	44,593,548	47,316,726
unique_aligned_reads	41,953,800	44,501,520
percent_uniqueAligned	0.88009	0.88967
correlation_replicates	0.997015	0.997015
spikein_reads	206,500	174,658
percent_spikeins	0.00433	0.00349
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	823	822

Data Submission Information

	BGHLV14-9	BGHLV14-9
ENCODE_alias	brenton-graveley:DDX21_BGHLV14	brenton-graveley:DDX21-BGHLV14-HepG2
ENCODE_accession	ENCSR485ZTC	ENCSR899KUM
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-9	BGHLV14-9
Sample Name	DDX21_BGHLV14-9	DDX21_BGHLV14-9
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2798	6642

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_BGHLV14-9_AGTCAA_L001_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	823	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_1_ACAGTG_L008_R1_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R1_001.fastq.gz	ENCODE3	13789
DDX21_BGHLV14-9_AGTCAA_L001_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	823	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_1_ACAGTG_L008_R2_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R2_001.fastq.gz	ENCODE3	13851
DDX21_BGHLV14-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	823					GRCh38	V40	DDX21_BGHLV14-9_AGTCAA_L001_R1_001.fastq.gz,DDX21_BGHLV14-9_AGTCAA_L001_R2_001.fastq.gz		ENCORE2	13913
DDX21_BGHLV14-9_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	823					GRCh38	V40	DDX21_BGHLV14-9/Aligned.sortedByCoord.out.bam		ENCORE2	13975
DDX21_BGHLV14-9_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	823					GRCh38	V40	DDX21_BGHLV14-9/Aligned.sortedByCoord.out.bam		ENCORE2	14037
DDX21_BGHLV14-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	823					GRCh38	V40	DDX21_BGHLV14-9/Aligned.sortedByCoord.out.bam		ENCORE2	14099
DDX21_BGHLV14-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	823					GRCh38	V40	DDX21_BGHLV14-9/Aligned.sortedByCoord.out.bam		ENCORE2	14161
DDX21_BGHLV14-9_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	823					GRCh38	V40	DDX21_BGHLV14-9_AGTCAA_L001_R1_001.fastq.gz,DDX21_BGHLV14-9_AGTCAA_L001_R2_001.fastq.gz		ENCORE2	14223
DDX21_BGHLV14-10_AGTTCC_L001_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	822	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_1_ACAGTG_L008_R1_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R1_001.fastq.gz	ENCODE3	13788
DDX21_BGHLV14-10_AGTTCC_L001_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	822	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_1_ACAGTG_L008_R2_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R2_001.fastq.gz	ENCODE3	13850
DDX21_BGHLV14-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	822					GRCh38	V40	DDX21_BGHLV14-10_AGTTCC_L001_R1_001.fastq.gz,DDX21_BGHLV14-10_AGTTCC_L001_R2_001.fastq.gz		ENCORE2	13912
DDX21_BGHLV14-10_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	822					GRCh38	V40	DDX21_BGHLV14-10/Aligned.sortedByCoord.out.bam		ENCORE2	13974
DDX21_BGHLV14-10_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	822					GRCh38	V40	DDX21_BGHLV14-10/Aligned.sortedByCoord.out.bam		ENCORE2	14036
DDX21_BGHLV14-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	822					GRCh38	V40	DDX21_BGHLV14-10/Aligned.sortedByCoord.out.bam		ENCORE2	14098
DDX21_BGHLV14-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	822					GRCh38	V40	DDX21_BGHLV14-10/Aligned.sortedByCoord.out.bam		ENCORE2	14160
DDX21_BGHLV14-10_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	822					GRCh38	V40	DDX21_BGHLV14-10_AGTTCC_L001_R1_001.fastq.gz,DDX21_BGHLV14-10_AGTTCC_L001_R2_001.fastq.gz		ENCORE2	14222