DROSHA RNA-Seq in K562

General Information


RBP	DROSHA
Cell_Line	K562
Method	CRISPR
Exp_Name	DROSHA-BGKcLV42-K562
ENCODE_series_ID
Batch_ID	BGKcLV42
Pool ID	Pool-240715
Local_Set_Name	set73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	DROSHA-BGKcLV42-25
Rep2	DROSHA-BGKcLV42-26
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	79.0
Rep2_qPCR	78.2
Rep1_WB	72.2
Rep2_WB	65.0
Antibody Cat#	3364S
Antibody Lot#	lot # 5
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1536

Experiment Information (Status: Submitting)

	BGKcLV42-25	BGKcLV42-26
idx	0	0
TRCN#_or_BGC#	BGC#0001127	BGC#0001127
shRNA_or_gRNA_sequence	ACAGATCTGATTATGACCGA	ACAGATCTGATTATGACCGA
PAM	GGG	GGG
Name	DROSHA_93	DROSHA_93
Sample_ID	BGKcLV42-25	BGKcLV42-26
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	DROSHA	DROSHA
qPCR_result	79.0	78.2
Ave_qPCR	78.6
RT-qPCR_primer-F	aggccagatgaatgatggac
RT-qPCR_primer-R	cttgatggcctcttctccag
protein_conc	2364	2671
WB_result	72.2	65.0
Ave_WB	68.6
WB_DONE_date	5/6/24
MW	160kd
IP
antibody_Cat#	3364S	lot # 5
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5787	5788

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DROSHA	Product_ID: 3364s Lot_ID: 5 Source: Cell Signaling Technology Target Name: DROSHA-human

Experiment Status

	BGKcLV42-25	BGKcLV42-26
Sample_ID	BGKcLV42-25	BGKcLV42-26
Sample Name
Sample Name	DROSHA-BGKcLV42-25	DROSHA-BGKcLV42-26
RBP	DROSHA	DROSHA
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13066	13067

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-25	BGKcLV42-26
Sample #	23	24
Sample Name	DROSHA-BGKcLV42-25	DROSHA-BGKcLV42-26
Sample_Name_Alias
Index Well Position	G03	H03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-06-21	2024-06-21
Lib_ID	Lib-240621	Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp	279	282
Peak_Molarity	72.20	82.60
libSampleQC_DNA_Well	DNA_Library_set73/set1/G3.png	DNA_Library_set73/set1/H3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/G3.png	RNA_Library_set73/set1/H3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-25	BGKcLV42-26
RBP	DROSHA	DROSHA
Batch_ID	BGKcLV42	BGKcLV42
WB_result	72.200	65.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4292	4293

Sequencing Information

	BGKcLV42-25	BGKcLV42-26
Sample_ID	BGKcLV42-25	BGKcLV42-26
Sample Name	DROSHA-BGKcLV42-25	DROSHA-BGKcLV42-26
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	37,049,678	42,634,381
total_aligned_reads	27,945,360	35,850,940
unique_aligned_reads	25,700,525	32,995,770
percent_uniqueAligned	0.69368	0.77392
correlation_replicates	0.992260	0.992260
spikein_reads	4,536	5,890
percent_spikeins	0.00012	0.00014
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3159	3160

Data Submission Information DCC submission information was not avaliable

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-BGKcLV42-25_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3159	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30360
DROSHA-BGKcLV42-25_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3159	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30450
DROSHA-BGKcLV42-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3159					GRCh38	V40	DROSHA-BGKcLV42-25_L001_R1_001.filtered.trimmed.paired.fastq.gz,DROSHA-BGKcLV42-25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31292
DROSHA-BGKcLV42-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3159					GRCh38	V40	DROSHA-BGKcLV42-25_Aligned.sortedByCoord.out.bam		ENCORE2	31382
DROSHA-BGKcLV42-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3159					GRCh38	V40	DROSHA-BGKcLV42-25_Aligned.sortedByCoord.out.bam		ENCORE2	31472
DROSHA-BGKcLV42-25_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3159					GRCh38	V40	DROSHA-BGKcLV42-25_Aligned.sortedByCoord.out.bam		ENCORE2	31562
DROSHA-BGKcLV42-25_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3159					GRCh38	V40	DROSHA-BGKcLV42-25_Aligned.sortedByCoord.out.bam		ENCORE2	31652
DROSHA-BGKcLV42-25_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3159					GRCh38	V40	DROSHA-BGKcLV42-25_L001_R1_001.filtered.trimmed.paired.fastq.gz,DROSHA-BGKcLV42-25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31742
DROSHA-BGKcLV42-26_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3160	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30361
DROSHA-BGKcLV42-26_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3160	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30451
DROSHA-BGKcLV42-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3160					GRCh38	V40	DROSHA-BGKcLV42-26_L001_R1_001.filtered.trimmed.paired.fastq.gz,DROSHA-BGKcLV42-26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31293
DROSHA-BGKcLV42-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3160					GRCh38	V40	DROSHA-BGKcLV42-26_Aligned.sortedByCoord.out.bam		ENCORE2	31383
DROSHA-BGKcLV42-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3160					GRCh38	V40	DROSHA-BGKcLV42-26_Aligned.sortedByCoord.out.bam		ENCORE2	31473
DROSHA-BGKcLV42-26_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3160					GRCh38	V40	DROSHA-BGKcLV42-26_Aligned.sortedByCoord.out.bam		ENCORE2	31563
DROSHA-BGKcLV42-26_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3160					GRCh38	V40	DROSHA-BGKcLV42-26_Aligned.sortedByCoord.out.bam		ENCORE2	31653
DROSHA-BGKcLV42-26_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3160					GRCh38	V40	DROSHA-BGKcLV42-26_L001_R1_001.filtered.trimmed.paired.fastq.gz,DROSHA-BGKcLV42-26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31743