DHX57 RNA-Seq in K562

General Information


RBP	DHX57
Cell_Line	K562
Method	CRISPR
Exp_Name	DHX57-BGKcLV17-K562
ENCODE_series_ID	ENCSR032QVH
Batch_ID	BGKcLV17
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR359ICP
ENCODE_CN_Exp_ID	ENCSR516TLX
Rep1	DHX57-BGKcLV17-11
Rep2	DHX57-BGKcLV17-12
CN1	NT-BGKcLV17-1
CN2	NT-BGKcLV17-2
Rep1_qPCR	59.4
Rep2_qPCR	62.3
Rep1_WB	82.1
Rep2_WB	81.9023796
Antibody Cat#	PA5-57548
Antibody Lot#	lot# UC2739261B
Antibody DCC ID	ENCAB163YWK
Status	Released
Project	ENCODE4
ID	144

Experiment Information (Status: Released)

	BGKcLV17-11	BGKcLV17-12
idx	618	619
TRCN#_or_BGC#	BGC#0000440	BGC#0000440
shRNA_or_gRNA_sequence	CAGACTGTTATACTGCACCA	CAGACTGTTATACTGCACCA
PAM	CGG	CGG
Name	DHX57_86	DHX57_86
Sample_ID	BGKcLV17-11	BGKcLV17-12
transduction_Date	7/2/19	7/2/19
days	Day 6	Day 6
RBP_name	DHX57	DHX57
qPCR_result	59.4	62.3
Ave_qPCR	60.9
RT-qPCR_primer-F	CTATTTTAATTCCTGCCCCGTT
RT-qPCR_primer-R	ACAGCAATTGCATCTTCCAAA
protein_conc	3899	4685
WB_result	82.1	81.9023796
Ave_WB	82.0
WB_DONE_date	2/4/21	WES
MW	156KD
IP	Rabbit / I
antibody_Cat#	PA5-57548	lot# UC2739261B
Antibody DCC ID	ENCAB163YWK
submitted_to_DCC_date
Rep1_TPM	3.6	0
Rep2_TPM	4.7	0
Action	Ready	Ready
Library_start_date	12/05/19	12/05/19
repeat_library
Note
ID	4734	4735

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DHX57	Product_ID: PA5-57548 Lot_ID: UC2739261B Source: Thermo Fisher Target Name: DHX57-human

Experiment Status

	BGKcLV17-11	BGKcLV17-12
Sample_ID	BGKcLV17-11	BGKcLV17-12
Sample Name
Sample Name	DHX57-BGKcLV17-11	DHX57-BGKcLV17-12
RBP	DHX57	DHX57
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5495	5496

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV17-11	BGKcLV17-12
Sample #	85	86
Sample Name	DHX57-BGKcLV17-11	DHX57-BGKcLV17-12
Sample_Name_Alias
Index Well Position	A11	B11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-31	2020-08-31
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	1-C2	1-D2
Tecan	29.68	30.32
Tecan_date	2019-12-10	2019-12-10
Size_bp	273	281
Peak_Molarity	23.60	25.90
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/C7.png	DNA_Library_set43-44/set1/D7.png
RIN	9.5	9.5
libSample_RNA_Well	RNA_Library_set43-44/set4/C2.png	RNA_Library_set43-44/set4/D2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV17-11	BGKcLV17-12
RBP	DHX57	DHX57
Batch_ID	BGKcLV17	BGKcLV17
WB_result	72.400	68.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	661	662

Sequencing Information

	BGKcLV17-11	BGKcLV17-12
Sample_ID	BGKcLV17-11	BGKcLV17-12
Sample Name	DHX57-BGKcLV17-11	DHX57-BGKcLV17-12
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	96,062,046	209,773,952
total_aligned_reads	88,754,320	187,758,132
unique_aligned_reads	80,903,314	170,745,254
percent_uniqueAligned	0.84220	0.81395
correlation_replicates	0.997419	0.997419
spikein_reads	25,216	71,940
percent_spikeins	0.00026	0.00034
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	163	164

Data Submission Information

	BGKcLV17-11	BGKcLV17-11	BGKcLV17-11	BGKcLV17-11	BGKcLV17-11	BGKcLV17-11	BGKcLV17-12	BGKcLV17-12	BGKcLV17-12	BGKcLV17-12
ENCODE_alias	brenton-graveley:DHX57-BGKcLV17	brenton-graveley:DHX57-BGKcLV17-11	brenton-graveley:L-DHX57-BGKcLV17-11	brenton-graveley:DHX57-BGKcLV17-11_S81_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DHX57-BGKcLV17-11_S81_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DHX57-BGKcLV17-K562	brenton-graveley:DHX57-BGKcLV17-12	brenton-graveley:L-DHX57-BGKcLV17-12	brenton-graveley:DHX57-BGKcLV17-12_S82_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DHX57-BGKcLV17-12_S82_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR359ICP	ENCBS802JLM	ENCLB001GKP	ENCFF545UCV	ENCFF418OWP	ENCSR032QVH	ENCBS317WWB	ENCLB770PJA	ENCFF638SLL	ENCFF164SOF
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	BGKcLV17-11	BGKcLV17-11	BGKcLV17-11	BGKcLV17-11	BGKcLV17-11	BGKcLV17-11	BGKcLV17-12	BGKcLV17-12	BGKcLV17-12	BGKcLV17-12
Sample Name	DHX57-BGKcLV17-11	DHX57-BGKcLV17-11	DHX57-BGKcLV17-11	DHX57-BGKcLV17-11	DHX57-BGKcLV17-11	DHX57-BGKcLV17-11	DHX57-BGKcLV17-12	DHX57-BGKcLV17-12	DHX57-BGKcLV17-12	DHX57-BGKcLV17-12
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43K_biosample_protocol	LV43K_library_protocol				LV43K_biosample_protocol	LV43K_library_protocol
protocol_URL		DHX57-BGKcLV17-11.pdf	L-DHX57-BGKcLV17-11.pdf				DHX57-BGKcLV17-12.pdf	L-DHX57-BGKcLV17-12.pdf
ID	41	164	328	526	578	7187	165	329	527	579

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
DHX57-BGKcLV17-11_S81_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	163	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	75
DHX57-BGKcLV17-11_S81_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	163	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	127
DHX57-BGKcLV17-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	163					GRCh38	V40	DHX57-BGKcLV17-11_S81_R1_001.filtered.trimmed.paired.fastq.gz,DHX57-BGKcLV17-11_S81_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24366
DHX57-BGKcLV17-11_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	163					GRCh38	V40	DHX57-BGKcLV17-11/Aligned.sortedByCoord.out.bam		ENCORE2	24418
DHX57-BGKcLV17-11_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	163					GRCh38	V40	DHX57-BGKcLV17-11/Aligned.sortedByCoord.out.bam		ENCORE2	24470
DHX57-BGKcLV17-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	163					GRCh38	V40	DHX57-BGKcLV17-11/Aligned.sortedByCoord.out.bam		ENCORE2	24522
DHX57-BGKcLV17-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	163					GRCh38	V40	DHX57-BGKcLV17-11/Aligned.sortedByCoord.out.bam		ENCORE2	24574
DHX57-BGKcLV17-11_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	163					GRCh38	V40	DHX57-BGKcLV17-11_S81_R1_001.filtered.trimmed.paired.fastq.gz,DHX57-BGKcLV17-11_S81_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24626
DHX57-BGKcLV17-12_S82_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	164	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	76
DHX57-BGKcLV17-12_S82_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	164	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	128
DHX57-BGKcLV17-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	164					GRCh38	V40	DHX57-BGKcLV17-12_S82_R1_001.filtered.trimmed.paired.fastq.gz,DHX57-BGKcLV17-12_S82_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24367
DHX57-BGKcLV17-12_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	164					GRCh38	V40	DHX57-BGKcLV17-12/Aligned.sortedByCoord.out.bam		ENCORE2	24419
DHX57-BGKcLV17-12_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	164					GRCh38	V40	DHX57-BGKcLV17-12/Aligned.sortedByCoord.out.bam		ENCORE2	24471
DHX57-BGKcLV17-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	164					GRCh38	V40	DHX57-BGKcLV17-12/Aligned.sortedByCoord.out.bam		ENCORE2	24523
DHX57-BGKcLV17-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	164					GRCh38	V40	DHX57-BGKcLV17-12/Aligned.sortedByCoord.out.bam		ENCORE2	24575
DHX57-BGKcLV17-12_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	164					GRCh38	V40	DHX57-BGKcLV17-12_S82_R1_001.filtered.trimmed.paired.fastq.gz,DHX57-BGKcLV17-12_S82_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24627