DDX10 RNA-Seq in K562

General Information


RBP	DDX10
Cell_Line	K562
Method	CRISPR
Exp_Name	DDX10-BGKcLV28-K562
ENCODE_series_ID	ENCSR627QEI
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR002ODC
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	DDX10-BGKcLV28-67
Rep2	DDX10-BGKcLV28-68
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	51.7
Rep2_qPCR	51.7
Rep1_WB	61.1
Rep2_WB	62.6
Antibody Cat#	A300-617A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB959QKK
Status	Released
Project	ENCODE4
ID	842

Experiment Information (Status: Released)

	BGKcLV28-67	BGKcLV28-68
idx	1017	1018
TRCN#_or_BGC#	BGC#0000744	BGC#0000744
shRNA_or_gRNA_sequence	TGATAGGCCAGTTCTCTCGT	TGATAGGCCAGTTCTCTCGT
PAM	AGG	AGG
Name	DDX10_87	DDX10_87
Sample_ID	BGKcLV28-67	BGKcLV28-68
transduction_Date	7/12/21	7/12/21
days	Day 6	Day 6
RBP_name	DDX10	DDX10
qPCR_result	51.7	51.7
Ave_qPCR	51.7
RT-qPCR_primer-F	ggtcggcttcttcaacacat
RT-qPCR_primer-R	agcaaagcccatatccaaga
protein_conc	2671	2689
WB_result	61.1	62.6
Ave_WB	61.8
WB_DONE_date	6/30/21-2	JESS
MW	101KD
IP
antibody_Cat#	A300-617A	LOT #1
Antibody DCC ID	ENCAB959QKK
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/23/21	09/23/21
repeat_library
Note
ID	5151	5152

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX10	Product_ID: A300-617A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX10-human

Experiment Status

	BGKcLV28-67	BGKcLV28-68
Sample_ID	BGKcLV28-67	BGKcLV28-68
Sample Name
Sample Name	DDX10-BGKcLV28-67	DDX10-BGKcLV28-68
RBP	DDX10	DDX10
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9943	9944

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-67	BGKcLV28-68
Sample #	51	52
Sample Name	DDX10-BGKcLV28-67	DDX10-BGKcLV28-68
Sample_Name_Alias
Index Well Position	C11	D11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-21	2021-09-21
Lib_ID	Lib-210921	Lib-210921
Tecan_Location
Tecan
Tecan_date
Size_bp	305	309
Peak_Molarity	111.00	110.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/C7.png	DNA_Library_set48-49/set3/D7.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set48-49/set2/C7.png	RNA_Library_set48-49/set3/D8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-67	BGKcLV28-68
RBP	DDX10	DDX10
Batch_ID	BGKcLV28	BGKcLV28
WB_result	61.100	62.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2112	2113

Sequencing Information

	BGKcLV28-67	BGKcLV28-68
Sample_ID	BGKcLV28-67	BGKcLV28-68
Sample Name	DDX10-BGKcLV28-67	DDX10-BGKcLV28-68
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	80,335,190	173,169,484
total_aligned_reads	74,284,412	165,593,726
unique_aligned_reads	68,294,816	151,992,808
percent_uniqueAligned	0.85012	0.87771
correlation_replicates	0.995993	0.995993
spikein_reads	15,840	39,014
percent_spikeins	0.00020	0.00023
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1863	1864

Data Submission Information

	BGKcLV28-67	BGKcLV28-67	BGKcLV28-67	BGKcLV28-67	BGKcLV28-67	BGKcLV28-67	BGKcLV28-68	BGKcLV28-68	BGKcLV28-68	BGKcLV28-68
ENCODE_alias	brenton-graveley:DDX10-BGKcLV28	brenton-graveley:DDX10-BGKcLV28-67	brenton-graveley:L-DDX10-BGKcLV28-67	brenton-graveley:DDX10-BGKcLV28-67_S133_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX10-BGKcLV28-67_S133_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX10-BGKcLV28-K562	brenton-graveley:DDX10-BGKcLV28-68	brenton-graveley:L-DDX10-BGKcLV28-68	brenton-graveley:DDX10-BGKcLV28-68_S134_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX10-BGKcLV28-68_S134_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR002ODC	ENCBS065PAT	ENCLB933LVK	ENCFF757XQY	ENCFF188TZH	ENCSR627QEI	ENCBS047GNX	ENCLB047SAE	ENCFF723KEW	ENCFF749RWG
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV28-67	BGKcLV28-67	BGKcLV28-67	BGKcLV28-67	BGKcLV28-67	BGKcLV28-67	BGKcLV28-68	BGKcLV28-68	BGKcLV28-68	BGKcLV28-68
Sample Name	DDX10-BGKcLV28-67	DDX10-BGKcLV28-67	DDX10-BGKcLV28-67	DDX10-BGKcLV28-67	DDX10-BGKcLV28-67	DDX10-BGKcLV28-67	DDX10-BGKcLV28-68	DDX10-BGKcLV28-68	DDX10-BGKcLV28-68	DDX10-BGKcLV28-68
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-03-02	2022-01-29	2022-01-29	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV49_biosample_protocol	LV49_library_protocol				LV49_biosample_protocol	LV49_library_protocol
protocol_URL		DDX10-BGKcLV28-67.pdf	L-DDX10-BGKcLV28-67.pdf				DDX10-BGKcLV28-68.pdf	L-DDX10-BGKcLV28-68.pdf
ID	3496	3626	3760	3894	4028	7172	3627	3761	3895	4029

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
DDX10-BGKcLV28-67_S133_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1863	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3980
DDX10-BGKcLV28-67_S133_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1863	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	4038
DDX10-BGKcLV28-67_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1863					GRCh38	V40	DDX10-BGKcLV28-67_S133_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX10-BGKcLV28-67_S133_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19262
DDX10-BGKcLV28-67_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1863					GRCh38	V40	DDX10-BGKcLV28-67/Aligned.sortedByCoord.out.bam		ENCORE2	19320
DDX10-BGKcLV28-67_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1863					GRCh38	V40	DDX10-BGKcLV28-67/Aligned.sortedByCoord.out.bam		ENCORE2	19378
DDX10-BGKcLV28-67_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1863					GRCh38	V40	DDX10-BGKcLV28-67/Aligned.sortedByCoord.out.bam		ENCORE2	19436
DDX10-BGKcLV28-67_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1863					GRCh38	V40	DDX10-BGKcLV28-67/Aligned.sortedByCoord.out.bam		ENCORE2	19494
DDX10-BGKcLV28-67_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1863					GRCh38	V40	DDX10-BGKcLV28-67_S133_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX10-BGKcLV28-67_S133_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19552
DDX10-BGKcLV28-68_S134_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1864	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3981
DDX10-BGKcLV28-68_S134_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1864	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	4039
DDX10-BGKcLV28-68_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1864					GRCh38	V40	DDX10-BGKcLV28-68_S134_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX10-BGKcLV28-68_S134_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19263
DDX10-BGKcLV28-68_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1864					GRCh38	V40	DDX10-BGKcLV28-68/Aligned.sortedByCoord.out.bam		ENCORE2	19321
DDX10-BGKcLV28-68_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1864					GRCh38	V40	DDX10-BGKcLV28-68/Aligned.sortedByCoord.out.bam		ENCORE2	19379
DDX10-BGKcLV28-68_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1864					GRCh38	V40	DDX10-BGKcLV28-68/Aligned.sortedByCoord.out.bam		ENCORE2	19437
DDX10-BGKcLV28-68_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1864					GRCh38	V40	DDX10-BGKcLV28-68/Aligned.sortedByCoord.out.bam		ENCORE2	19495
DDX10-BGKcLV28-68_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1864					GRCh38	V40	DDX10-BGKcLV28-68_S134_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX10-BGKcLV28-68_S134_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19553