DDX21 RNA-Seq in HepG2

General Information


RBP	DDX21
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DDX21-BGHcLV03-HepG2
ENCODE_series_ID	ENCSR703SNR
Batch_ID	BGHcLV03
Pool ID	Pool-160201
Local_Set_Name	BGHcLV03
ENCODE_KD_Exp_ID	ENCSR231RKU
ENCODE_CN_Exp_ID	ENCSR105NML
Rep1	DDX21_BGHcLV03-9
Rep2	DDX21_BGHcLV03-10
CN1	NT_BGHcLV03-1
CN2	NT_BGHcLV03-2
Rep1_qPCR	81.1
Rep2_qPCR	87.1
Rep1_WB	NO band, need add more protein
Rep2_WB
Antibody Cat#	RN090PW
Antibody Lot#	LOT# 001
Antibody DCC ID	ENCAB315FWL
Status	Archived
Project	ENCODE3
ID	570

Experiment Information (Status: Released)

	BGHcLV03-9	BGHcLV03-10
idx	9	10
TRCN#_or_BGC#	BGC#0000009	BGC#0000009
shRNA_or_gRNA_sequence	TTAATTGCACAGGCACGGAC	TTAATTGCACAGGCACGGAC
PAM
Name	DDX21-C1-A	DDX21-C1-A
Sample_ID	BGHcLV03-9	BGHcLV03-10
transduction_Date	12/16/2015	12/16/2015
days	D6	D6
RBP_name	DDX21	DDX21
qPCR_result	81.1	87.1
Ave_qPCR	84.1
RT-qPCR_primer-F	TTGCTTTGATGTACCTACCGC
RT-qPCR_primer-R	AGTTCTGGTTGCTCTGTGGC
protein_conc	2261	2391
WB_result	NO band, need add more protein
Ave_WB
WB_DONE_date	1/4/2016
MW	87kDa
IP	1
antibody_Cat#	RN090PW	RN090PW
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	100	0
Rep2_TPM	126	0
Action	Ready	Ready
Library_start_date	1/8/2016	1/8/2016
repeat_library
Note
ID	6150	6151

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV03-9	BGHcLV03-10
Sample_ID	BGHcLV03-9	BGHcLV03-10
Sample Name	DDX21_BGHcLV03-9	DDX21_BGHcLV03-10
Sample Name	DDX21_BGHcLV03-9	DDX21_BGHcLV03-10
RBP	DDX21	DDX21
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-09	2016-03-09
Project	ENCODE3	ENCODE3
Note
ID	1098	1097

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV03-9	BGHcLV03-10
Sample #
Sample Name	DDX21-BGHcLV03-9	DDX21-BGHcLV03-10
Sample_Name_Alias	DDX21_BGHcLV03-9	DDX21_BGHcLV03-10
Index Well Position	S01	S02
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/A2.png	DNA_Library_cLV02/set1/B2.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_cLV02/set1/C3.png	RNA_Library_cLV02/set1/D3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHcLV03-9	BGHcLV03-10
RBP	DDX21	DDX21
Batch_ID	BGHcLV03	BGHcLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2789	2788

Sequencing Information

	BGHcLV03-9	BGHcLV03-10
Sample_ID	BGHcLV03-9	BGHcLV03-10
Sample Name	DDX21_BGHcLV03-9	DDX21_BGHcLV03-10
Pool ID	Pool-160201	Pool-160201
LocalServer_folder	BGHcLV03	BGHcLV03
total_reads	55,276,584	58,762,064
total_aligned_reads	48,149,690	50,983,410
unique_aligned_reads	45,228,958	47,888,690
percent_uniqueAligned	0.81823	0.81496
correlation_replicates	0.996826	0.996826
spikein_reads	113,276	134,288
percent_spikeins	0.00205	0.00229
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1438	1437

Data Submission Information

	BGHcLV03-9	BGHcLV03-9
ENCODE_alias	brenton-graveley:DDX21_BGHcLV03	brenton-graveley:DDX21-BGHcLV03-HepG2
ENCODE_accession	ENCSR231RKU	ENCSR703SNR
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV03-9	BGHcLV03-9
Sample Name	DDX21_BGHcLV03-9	DDX21_BGHcLV03-9
Selected	Yes	No
Status	Released	Archived
Status_Date	2016-03-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3110	6641

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_BGHcLV03-9_ATCACG_L005_001.R1.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1438	HiSeq2500	100	paired-ended	1				NT_BGHcLV03-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22911
DDX21_BGHcLV03-9_ATCACG_L005_001.R2.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1438	HiSeq2500	100	paired-ended	2				NT_BGHcLV03-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22929
DDX21_BGHcLV03-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1438					GRCh38	V40	DDX21_BGHcLV03-9_ATCACG_L005_001.R1.fastq.gz,DDX21_BGHcLV03-9_ATCACG_L005_001.R2.fastq.gz		ENCORE2	22947
DDX21_BGHcLV03-9_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1438					GRCh38	V40	DDX21_BGHcLV03-9/Aligned.sortedByCoord.out.bam		ENCORE2	22965
DDX21_BGHcLV03-9_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1438					GRCh38	V40	DDX21_BGHcLV03-9/Aligned.sortedByCoord.out.bam		ENCORE2	22983
DDX21_BGHcLV03-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1438					GRCh38	V40	DDX21_BGHcLV03-9/Aligned.sortedByCoord.out.bam		ENCORE2	23001
DDX21_BGHcLV03-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1438					GRCh38	V40	DDX21_BGHcLV03-9/Aligned.sortedByCoord.out.bam		ENCORE2	23019
DDX21_BGHcLV03-9_quant.sf	ENCODE_DATA/BGHcLV03/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1438					GRCh38	V40	DDX21_BGHcLV03-9_ATCACG_L005_001.R1.fastq.gz,DDX21_BGHcLV03-9_ATCACG_L005_001.R2.fastq.gz		ENCORE2	23037
DDX21_BGHcLV03-10_CGATGT_L005_001.R1.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1437	HiSeq2500	100	paired-ended	1				NT_BGHcLV03-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22910
DDX21_BGHcLV03-10_CGATGT_L005_001.R2.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1437	HiSeq2500	100	paired-ended	2				NT_BGHcLV03-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22928
DDX21_BGHcLV03-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1437					GRCh38	V40	DDX21_BGHcLV03-10_CGATGT_L005_001.R1.fastq.gz,DDX21_BGHcLV03-10_CGATGT_L005_001.R2.fastq.gz		ENCORE2	22946
DDX21_BGHcLV03-10_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1437					GRCh38	V40	DDX21_BGHcLV03-10/Aligned.sortedByCoord.out.bam		ENCORE2	22964
DDX21_BGHcLV03-10_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1437					GRCh38	V40	DDX21_BGHcLV03-10/Aligned.sortedByCoord.out.bam		ENCORE2	22982
DDX21_BGHcLV03-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1437					GRCh38	V40	DDX21_BGHcLV03-10/Aligned.sortedByCoord.out.bam		ENCORE2	23000
DDX21_BGHcLV03-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1437					GRCh38	V40	DDX21_BGHcLV03-10/Aligned.sortedByCoord.out.bam		ENCORE2	23018
DDX21_BGHcLV03-10_quant.sf	ENCODE_DATA/BGHcLV03/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1437					GRCh38	V40	DDX21_BGHcLV03-10_CGATGT_L005_001.R1.fastq.gz,DDX21_BGHcLV03-10_CGATGT_L005_001.R2.fastq.gz		ENCORE2	23036