DHX57 RNA-Seq in HepG2

General Information


RBP	DHX57
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DHX57-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR293TRY
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR029VGU
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	DHX57-BGHcLV18-11
Rep2	DHX57-BGHcLV18-12
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	29.9
Rep2_qPCR	28.8
Rep1_WB	96.3
Rep2_WB	88.9
Antibody Cat#	PA5-57548
Antibody Lot#	lot# UC2739261B
Antibody DCC ID	ENCAB163YWK
Status	Released
Project	ENCODE4
ID	103

Experiment Information (Status: Released)

	BGHcLV18-11	BGHcLV18-12
idx	504	505
TRCN#_or_BGC#	BGC#0000440	BGC#0000440
shRNA_or_gRNA_sequence	CAGACTGTTATACTGCACCA	CAGACTGTTATACTGCACCA
PAM	CGG	CGG
Name	DHX57_86	DHX57_86
Sample_ID	BGHcLV18-11	BGHcLV18-12
transduction_Date	8/13/19	8/13/19
days	D6	D6
RBP_name	DHX57	DHX57
qPCR_result	29.9	28.8
Ave_qPCR	29.4
RT-qPCR_primer-F	CTATTTTAATTCCTGCCCCGTT
RT-qPCR_primer-R	ACAGCAATTGCATCTTCCAAA
protein_conc	3802	3498
WB_result	96.3	88.9
Ave_WB	92.6
WB_DONE_date	8/28/19	WES
MW	156KD
IP	Rabbit / I
antibody_Cat#	PA5-57548	lot# UC2739261B
Antibody DCC ID	ENCAB163YWK
submitted_to_DCC_date
Rep1_TPM	12	0
Rep2_TPM	19	0
Action	Ready	Ready
Library_start_date	12/11/19	12/11/19
repeat_library
Note
ID	6657	6658

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

	BGHcLV18-11	BGHcLV18-12
Sample_ID	BGHcLV18-11	BGHcLV18-12
Sample Name
Sample Name	DHX57-BGHcLV18-11	DHX57-BGHcLV18-12
RBP	DHX57	DHX57
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5623	5624

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-11	BGHcLV18-12
Sample #	129	130
Sample Name	DHX57-BGHcLV18-11	DHX57-BGHcLV18-12
Sample_Name_Alias
Index Well Position	C05	D05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	3-E2	3-F2
Tecan	41.22	40.69
Tecan_date	2019-12-16	2019-12-16
Size_bp	276	275
Peak_Molarity	31.00	29.60
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/C6.png	DNA_Library_set43-44/set2/D6.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set43-44/set4/G7.png	RNA_Library_set43-44/set4/H7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-11	BGHcLV18-12
RBP	DHX57	DHX57
Batch_ID	BGHcLV18	BGHcLV18
WB_result	96.300	88.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	705	706

Sequencing Information

	BGHcLV18-11	BGHcLV18-12
Sample_ID	BGHcLV18-11	BGHcLV18-12
Sample Name	DHX57-BGHcLV18-11	DHX57-BGHcLV18-12
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	182,442,366	160,706,670
total_aligned_reads	178,409,604	155,356,838
unique_aligned_reads	167,036,568	145,407,538
percent_uniqueAligned	0.91556	0.90480
correlation_replicates	0.992216	0.992216
spikein_reads	307,870	233,714
percent_spikeins	0.00169	0.00145
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	211	212

Data Submission Information

	BGHcLV18-11	BGHcLV18-11	BGHcLV18-11	BGHcLV18-11	BGHcLV18-11	BGHcLV18-11	BGHcLV18-12	BGHcLV18-12	BGHcLV18-12	BGHcLV18-12
ENCODE_alias	brenton-graveley:DHX57-BGHcLV18	brenton-graveley:DHX57-BGHcLV18-11	brenton-graveley:L-DHX57-BGHcLV18-11	brenton-graveley:DHX57-BGHcLV18-11_S45_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DHX57-BGHcLV18-11_S45_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DHX57-BGHcLV18-HepG2	brenton-graveley:DHX57-BGHcLV18-12	brenton-graveley:L-DHX57-BGHcLV18-12	brenton-graveley:DHX57-BGHcLV18-12_S46_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DHX57-BGHcLV18-12_S46_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR029VGU	ENCBS409OZE	ENCLB601VXU	ENCFF944SAL	ENCFF216MOP	ENCSR293TRY	ENCBS350MHP	ENCLB993LDK	ENCFF831RHN	ENCFF682NDX
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	BGHcLV18-11	BGHcLV18-11	BGHcLV18-11	BGHcLV18-11	BGHcLV18-11	BGHcLV18-11	BGHcLV18-12	BGHcLV18-12	BGHcLV18-12	BGHcLV18-12
Sample Name	DHX57-BGHcLV18-11	DHX57-BGHcLV18-11	DHX57-BGHcLV18-11	DHX57-BGHcLV18-11	DHX57-BGHcLV18-11	DHX57-BGHcLV18-11	DHX57-BGHcLV18-12	DHX57-BGHcLV18-12	DHX57-BGHcLV18-12	DHX57-BGHcLV18-12
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV44H_biosample_protocol	LV44H_library_protocol				LV44H_biosample_protocol	LV44H_library_protocol
protocol_URL		DHX57-BGHcLV18-11.pdf	L-DHX57-BGHcLV18-11.pdf				DHX57-BGHcLV18-12.pdf	L-DHX57-BGHcLV18-12.pdf
ID	50	180	346	596	648	7186	181	347	597	649

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-BGHcLV18-11_S45_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	211	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	177
DHX57-BGHcLV18-11_S45_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	211	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	229
DHX57-BGHcLV18-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	211					GRCh38	V40	DHX57-BGHcLV18-11_S45_R1_001.filtered.trimmed.paired.fastq.gz,DHX57-BGHcLV18-11_S45_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24897
DHX57-BGHcLV18-11_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	211					GRCh38	V40	DHX57-BGHcLV18-11/Aligned.sortedByCoord.out.bam		ENCORE2	24949
DHX57-BGHcLV18-11_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	211					GRCh38	V40	DHX57-BGHcLV18-11/Aligned.sortedByCoord.out.bam		ENCORE2	25001
DHX57-BGHcLV18-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	211					GRCh38	V40	DHX57-BGHcLV18-11/Aligned.sortedByCoord.out.bam		ENCORE2	25053
DHX57-BGHcLV18-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	211					GRCh38	V40	DHX57-BGHcLV18-11/Aligned.sortedByCoord.out.bam		ENCORE2	25105
DHX57-BGHcLV18-11_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	211					GRCh38	V40	DHX57-BGHcLV18-11_S45_R1_001.filtered.trimmed.paired.fastq.gz,DHX57-BGHcLV18-11_S45_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25157
DHX57-BGHcLV18-12_S46_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	212	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	178
DHX57-BGHcLV18-12_S46_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	212	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	230
DHX57-BGHcLV18-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	212					GRCh38	V40	DHX57-BGHcLV18-12_S46_R1_001.filtered.trimmed.paired.fastq.gz,DHX57-BGHcLV18-12_S46_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24898
DHX57-BGHcLV18-12_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	212					GRCh38	V40	DHX57-BGHcLV18-12/Aligned.sortedByCoord.out.bam		ENCORE2	24950
DHX57-BGHcLV18-12_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	212					GRCh38	V40	DHX57-BGHcLV18-12/Aligned.sortedByCoord.out.bam		ENCORE2	25002
DHX57-BGHcLV18-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	212					GRCh38	V40	DHX57-BGHcLV18-12/Aligned.sortedByCoord.out.bam		ENCORE2	25054
DHX57-BGHcLV18-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	212					GRCh38	V40	DHX57-BGHcLV18-12/Aligned.sortedByCoord.out.bam		ENCORE2	25106
DHX57-BGHcLV18-12_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	212					GRCh38	V40	DHX57-BGHcLV18-12_S46_R1_001.filtered.trimmed.paired.fastq.gz,DHX57-BGHcLV18-12_S46_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25158