DROSHA RNA-Seq in HepG2

General Information


RBP	DROSHA
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DROSHA-BGHcLV05-HepG2
ENCODE_series_ID	ENCSR183FOX
Batch_ID	BGHcLV05
Pool ID	Pool-161129
Local_Set_Name	BGHcLV05
ENCODE_KD_Exp_ID	ENCSR991XFO
ENCODE_CN_Exp_ID	ENCSR481WJH
Rep1	DROSHA_BGHcLV05-13
Rep2	DROSHA_BGHcLV05-14
CN1	NT_BGHcLV05-1
CN2	NT_BGHcLV05-2
Rep1_qPCR	39.6
Rep2_qPCR	56.7
Rep1_WB	60.3
Rep2_WB	89.3
Antibody Cat#	#3364
Antibody Lot#	#3364
Antibody DCC ID	ENCAB953TNR
Status	Released
Project	ENCODE3
ID	579

Experiment Information (Status: Released)

	BGHcLV05-13	BGHcLV05-13	BGHcLV05-13	BGHcLV05-14	BGHcLV05-14	BGHcLV05-14
idx	49	49	86	50	50	87
TRCN#_or_BGC#	BGC#0000032	BGC#0000032	BGC#0000032	BGC#0000032	BGC#0000032	BGC#0000032
shRNA_or_gRNA_sequence	CTCGCCACCGCAGCTACGAA	CTCGCCACCGCAGCTACGAA	CTCGCCACCGCAGCTACGAA	CTCGCCACCGCAGCTACGAA	CTCGCCACCGCAGCTACGAA	CTCGCCACCGCAGCTACGAA
PAM
Name	DROSHA_7	DROSHA_7	DROSHA_7	DROSHA_7	DROSHA_7	DROSHA_7
Sample_ID	BGHcLV05-13	BGHcLV05-13	BGHcLV05-13	BGHcLV05-14	BGHcLV05-14	BGHcLV05-14
transduction_Date	7/12/16	7/12/16	7/12/16	7/12/16	7/12/16	7/12/16
days	DAY 6	DAY 6		DAY 6	DAY 6
RBP_name	DROSHA	DROSHA	DROSHA	DROSHA	DROSHA	DROSHA
qPCR_result	39.6	39.6		56.7	56.7
Ave_qPCR	48.1	48.1
RT-qPCR_primer-F	aggccagatgaatgatggac	aggccagatgaatgatggac
RT-qPCR_primer-R	cttgatggcctcttctccag	cttgatggcctcttctccag
protein_conc	4670	4670	0	3941	3941	0
WB_result	60.3	no clear band		89.3
Ave_WB	74.8
WB_DONE_date	7/20/16	7/20/16		wes	WES
MW	159 kDa	159 kDa		FU'S
IP		1IP
antibody_Cat#	#3364	A301-886A		#3364	A301-886A
Antibody DCC ID	ENCAB953TNR			ENCAB953TNR
submitted_to_DCC_date	10/26/16
Rep1_TPM	14	14	0	0	0	0
Rep2_TPM	15	15	0	0	0	0
Action	Ready			Ready
Library_start_date	08/15/16			08/15/16
repeat_library
Note
ID	6190	6192	6229	6191	6193	6230

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DROSHA	Product_ID: 3364 Lot_ID: 3 Source: Cell Signaling Technology Target Name: DROSHA-human

Experiment Status

	BGHcLV05-13	BGHcLV05-14
Sample_ID	BGHcLV05-13	BGHcLV05-14
Sample Name	DROSHA_BGHcLV05-13	DROSHA_BGHcLV05-14
Sample Name	DROSHA_BGHcLV05-13	DROSHA_BGHcLV05-14
RBP	DROSHA	DROSHA
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-12-12	2016-12-12
Project	ENCODE3	ENCODE3
Note
ID	1325	1326

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV05-13	BGHcLV05-14
Sample #
Sample Name	DROSHA-BGHcLV05-13	DROSHA-BGHcLV05-14
Sample_Name_Alias	DROSHA_BGHcLV05-13	DROSHA_BGHcLV05-14
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-08-15	2016-08-15
Lib_ID	Lib-160815	Lib-160815
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV37-38/set1/F1.png	DNA_Library_LV37-38/set1/G1.png
RIN	8.9	9.1
libSample_RNA_Well	RNA_Library_cLV04-05/set1/G7.png	RNA_Library_cLV04-05/set1/H7.png
SampleQC_method
SampleQC_date
Sample_ID	BGHcLV05-13	BGHcLV05-14
RBP	DROSHA	DROSHA
Batch_ID	BGHcLV05	BGHcLV05
WB_result	60.300	89.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	3016	3017

Sequencing Information

	BGHcLV05-13	BGHcLV05-14
Sample_ID	BGHcLV05-13	BGHcLV05-14
Sample Name	DROSHA_BGHcLV05-13	DROSHA_BGHcLV05-14
Pool ID	Pool-161129	Pool-161129
LocalServer_folder	BGHcLV05	BGHcLV05
total_reads	96,000,210	80,915,054
total_aligned_reads	55,606,410	56,617,230
unique_aligned_reads	52,218,800	53,016,626
percent_uniqueAligned	0.54394	0.65521
correlation_replicates	0.975659	0.975659
spikein_reads	61,008	93,696
percent_spikeins	0.00064	0.00116
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1669	1670

Data Submission Information

	BGHcLV05-13	BGHcLV05-13
ENCODE_alias	brenton-graveley:DROSHA_BGHcLV05	brenton-graveley:DROSHA-BGHcLV05-HepG2
ENCODE_accession	ENCSR991XFO	ENCSR183FOX
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV05-13	BGHcLV05-13
Sample Name	DROSHA_BGHcLV05-13	DROSHA_BGHcLV05-13
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-12-12	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3202	6672

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
DROSHA_BGHcLV05-13_GTCCGC_L003_001.R1.fastq.gz	ENCODE_DATA/BGHcLV05/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1669	HiSeq2500	100	paired-ended	1				NT_BGHcLV05-1_GATCAG_L002_001.R1.fastq.gz,NT_BGHcLV05-2_TAGCTT_L002_001.R1.fastq.gz	ENCODE3	23138
DROSHA_BGHcLV05-13_GTCCGC_L003_001.R2.fastq.gz	ENCODE_DATA/BGHcLV05/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1669	HiSeq2500	100	paired-ended	2				NT_BGHcLV05-1_GATCAG_L002_001.R2.fastq.gz,NT_BGHcLV05-2_TAGCTT_L002_001.R2.fastq.gz	ENCODE3	23150
DROSHA_BGHcLV05-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1669					GRCh38	V40	DROSHA_BGHcLV05-13_GTCCGC_L003_001.R1.fastq.gz,DROSHA_BGHcLV05-13_GTCCGC_L003_001.R2.fastq.gz		ENCORE2	23162
DROSHA_BGHcLV05-13_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1669					GRCh38	V40	DROSHA_BGHcLV05-13/Aligned.sortedByCoord.out.bam		ENCORE2	23174
DROSHA_BGHcLV05-13_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1669					GRCh38	V40	DROSHA_BGHcLV05-13/Aligned.sortedByCoord.out.bam		ENCORE2	23186
DROSHA_BGHcLV05-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1669					GRCh38	V40	DROSHA_BGHcLV05-13/Aligned.sortedByCoord.out.bam		ENCORE2	23198
DROSHA_BGHcLV05-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1669					GRCh38	V40	DROSHA_BGHcLV05-13/Aligned.sortedByCoord.out.bam		ENCORE2	23210
DROSHA_BGHcLV05-13_quant.sf	ENCODE_DATA/BGHcLV05/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1669					GRCh38	V40	DROSHA_BGHcLV05-13_GTCCGC_L003_001.R1.fastq.gz,DROSHA_BGHcLV05-13_GTCCGC_L003_001.R2.fastq.gz		ENCORE2	23222
DROSHA_BGHcLV05-14_GTGAAA_L003_001.R1.fastq.gz	ENCODE_DATA/BGHcLV05/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1670	HiSeq2500	100	paired-ended	1				NT_BGHcLV05-1_GATCAG_L002_001.R1.fastq.gz,NT_BGHcLV05-2_TAGCTT_L002_001.R1.fastq.gz	ENCODE3	23139
DROSHA_BGHcLV05-14_GTGAAA_L003_001.R2.fastq.gz	ENCODE_DATA/BGHcLV05/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1670	HiSeq2500	100	paired-ended	2				NT_BGHcLV05-1_GATCAG_L002_001.R2.fastq.gz,NT_BGHcLV05-2_TAGCTT_L002_001.R2.fastq.gz	ENCODE3	23151
DROSHA_BGHcLV05-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1670					GRCh38	V40	DROSHA_BGHcLV05-14_GTGAAA_L003_001.R1.fastq.gz,DROSHA_BGHcLV05-14_GTGAAA_L003_001.R2.fastq.gz		ENCORE2	23163
DROSHA_BGHcLV05-14_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1670					GRCh38	V40	DROSHA_BGHcLV05-14/Aligned.sortedByCoord.out.bam		ENCORE2	23175
DROSHA_BGHcLV05-14_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1670					GRCh38	V40	DROSHA_BGHcLV05-14/Aligned.sortedByCoord.out.bam		ENCORE2	23187
DROSHA_BGHcLV05-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1670					GRCh38	V40	DROSHA_BGHcLV05-14/Aligned.sortedByCoord.out.bam		ENCORE2	23199
DROSHA_BGHcLV05-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1670					GRCh38	V40	DROSHA_BGHcLV05-14/Aligned.sortedByCoord.out.bam		ENCORE2	23211
DROSHA_BGHcLV05-14_quant.sf	ENCODE_DATA/BGHcLV05/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1670					GRCh38	V40	DROSHA_BGHcLV05-14_GTGAAA_L003_001.R1.fastq.gz,DROSHA_BGHcLV05-14_GTGAAA_L003_001.R2.fastq.gz		ENCORE2	23223