DICER1 RNA-Seq in HepG2

General Information


RBP	DICER1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DICER1-BGHcLV16-HepG2
ENCODE_series_ID	ENCSR687ONJ
Batch_ID	BGHcLV16
Pool ID	Pool-200102
Local_Set_Name	set43_H
ENCODE_KD_Exp_ID	ENCSR428WVZ
ENCODE_CN_Exp_ID	ENCSR964HKT
Rep1	DICER1-BGHcLV16-13
Rep2	DICER1-BGHcLV16-14
CN1	NT-BGHcLV16-1
CN2	NT-BGHcLV16-2
Rep1_qPCR	48.9
Rep2_qPCR	61.9
Rep1_WB
Rep2_WB
Antibody Cat#	PA5-17021
Antibody Lot#	TL2693039
Antibody DCC ID	ENCAB330RCK
Status	Released
Project	ENCODE4
ID	147

Experiment Information (Status: Released)

	BGHcLV16-13	BGHcLV16-14
idx	441	442
TRCN#_or_BGC#	BGC#0000342	BGC#0000342
shRNA_or_gRNA_sequence	TGAATAGTGTCTGTCGTACC	TGAATAGTGTCTGTCGTACC
PAM	AGG	AGG
Name	DICER1-94	DICER1-94
Sample_ID	BGHcLV16-13	BGHcLV16-14
transduction_Date	4/16/19	4/16/19
days	D6	D6
RBP_name	DICER1	DICER1
qPCR_result	48.9	61.9
Ave_qPCR	55.4
RT-qPCR_primer-F	ACAAAAGCAACACAGATAAATGGG
RT-qPCR_primer-R	ACATCAGGCTCTCCTCCTCC
protein_conc	4211	4775
WB_result
Ave_WB
WB_DONE_date	4/25/19
MW	219KD
IP	Rabbit / I
antibody_Cat#	PA5-17021
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	14	0
Rep2_TPM	26	0
Action	Question	Question
Library_start_date	12/03/19	12/03/19
repeat_library
Note
ID	6586	6587

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV16-13	BGHcLV16-14
Sample_ID	BGHcLV16-13	BGHcLV16-14
Sample Name
Sample Name	DICER1-BGHcLV16-13	DICER1-BGHcLV16-14
RBP	DICER1	DICER1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5413	5414

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV16-13	BGHcLV16-14
Sample #	47	48
Sample Name	DICER1-BGHcLV16-13	DICER1-BGHcLV16-14
Sample_Name_Alias
Index Well Position	C06	D06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-31	2020-08-31
Lib_ID	Lib-200831	Lib-200831
Tecan_Location	1-E1	1-F1
Tecan	40.82	33.17
Tecan_date	2019-12-10	2019-12-10
Size_bp	278	277
Peak_Molarity	42.20	42.90
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/E1.png	DNA_Library_set43-44/set2/F1.png
RIN	9.8	9.4
libSample_RNA_Well	RNA_Library_set43-44/set1/E6.png	RNA_Library_set43-44/set1/F6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV16-13	BGHcLV16-14
RBP	DICER1	DICER1
Batch_ID	BGHcLV16	BGHcLV16
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	623	624

Sequencing Information

	BGHcLV16-13	BGHcLV16-14
Sample_ID	BGHcLV16-13	BGHcLV16-14
Sample Name	DICER1-BGHcLV16-13	DICER1-BGHcLV16-14
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_H	set43_H
total_reads	123,766,692	119,184,468
total_aligned_reads	113,258,346	112,084,748
unique_aligned_reads	106,151,696	105,152,022
percent_uniqueAligned	0.85768	0.88226
correlation_replicates	0.999111	0.999111
spikein_reads	172,182	193,884
percent_spikeins	0.00139	0.00163
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	125	126

Data Submission Information

	BGHcLV16-13	BGHcLV16-13	BGHcLV16-13	BGHcLV16-13	BGHcLV16-13	BGHcLV16-13	BGHcLV16-14	BGHcLV16-14	BGHcLV16-14	BGHcLV16-14
ENCODE_alias	brenton-graveley:DICER1-BGHcLV16	brenton-graveley:DICER1-BGHcLV16-13	brenton-graveley:L-DICER1-BGHcLV16-13	brenton-graveley:DICER1-BGHcLV16-13_S43_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DICER1-BGHcLV16-13_S43_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DICER1-BGHcLV16-HepG2	brenton-graveley:DICER1-BGHcLV16-14	brenton-graveley:L-DICER1-BGHcLV16-14	brenton-graveley:DICER1-BGHcLV16-14_S44_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DICER1-BGHcLV16-14_S44_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR428WVZ	ENCBS548VNU	ENCLB648PSZ	ENCFF632DVV	ENCFF136CKK	ENCSR687ONJ	ENCBS384YKN	ENCLB006SFL	ENCFF048JFN	ENCFF698UZM
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	BGHcLV16-13	BGHcLV16-13	BGHcLV16-13	BGHcLV16-13	BGHcLV16-13	BGHcLV16-13	BGHcLV16-14	BGHcLV16-14	BGHcLV16-14	BGHcLV16-14
Sample Name	DICER1-BGHcLV16-13	DICER1-BGHcLV16-13	DICER1-BGHcLV16-13	DICER1-BGHcLV16-13	DICER1-BGHcLV16-13	DICER1-BGHcLV16-13	DICER1-BGHcLV16-14	DICER1-BGHcLV16-14	DICER1-BGHcLV16-14	DICER1-BGHcLV16-14
Selected	Yes	No	Yes	Yes	Yes	Yes	No	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
			LV43H_library_protocol					LV43H_library_protocol
protocol_URL			L-DICER1-BGHcLV16-13.pdf					L-DICER1-BGHcLV16-14.pdf
ID	3	88	252	418	450	7188	89	253	419	451

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
DICER1-BGHcLV16-13_S43_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	125	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3
DICER1-BGHcLV16-13_S43_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	125	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	35
DICER1-BGHcLV16-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	125					GRCh38	V40	DICER1-BGHcLV16-13_S43_R1_001.filtered.trimmed.paired.fastq.gz,DICER1-BGHcLV16-13_S43_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24166
DICER1-BGHcLV16-13_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	125					GRCh38	V40	DICER1-BGHcLV16-13/Aligned.sortedByCoord.out.bam		ENCORE2	24198
DICER1-BGHcLV16-13_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	125					GRCh38	V40	DICER1-BGHcLV16-13/Aligned.sortedByCoord.out.bam		ENCORE2	24230
DICER1-BGHcLV16-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	125					GRCh38	V40	DICER1-BGHcLV16-13/Aligned.sortedByCoord.out.bam		ENCORE2	24262
DICER1-BGHcLV16-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	125					GRCh38	V40	DICER1-BGHcLV16-13/Aligned.sortedByCoord.out.bam		ENCORE2	24294
DICER1-BGHcLV16-13_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	125					GRCh38	V40	DICER1-BGHcLV16-13_S43_R1_001.filtered.trimmed.paired.fastq.gz,DICER1-BGHcLV16-13_S43_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24326
DICER1-BGHcLV16-14_S44_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	126	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	4
DICER1-BGHcLV16-14_S44_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	126	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	36
DICER1-BGHcLV16-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	126					GRCh38	V40	DICER1-BGHcLV16-14_S44_R1_001.filtered.trimmed.paired.fastq.gz,DICER1-BGHcLV16-14_S44_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24167
DICER1-BGHcLV16-14_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	126					GRCh38	V40	DICER1-BGHcLV16-14/Aligned.sortedByCoord.out.bam		ENCORE2	24199
DICER1-BGHcLV16-14_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	126					GRCh38	V40	DICER1-BGHcLV16-14/Aligned.sortedByCoord.out.bam		ENCORE2	24231
DICER1-BGHcLV16-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	126					GRCh38	V40	DICER1-BGHcLV16-14/Aligned.sortedByCoord.out.bam		ENCORE2	24263
DICER1-BGHcLV16-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	126					GRCh38	V40	DICER1-BGHcLV16-14/Aligned.sortedByCoord.out.bam		ENCORE2	24295
DICER1-BGHcLV16-14_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	126					GRCh38	V40	DICER1-BGHcLV16-14_S44_R1_001.filtered.trimmed.paired.fastq.gz,DICER1-BGHcLV16-14_S44_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24327