ROR2 RNA-Seq in K562

General Information


RBP	ROR2
Cell_Line	K562
Method	CRISPR
Exp_Name	ROR2-BGKcLV35-K562
ENCODE_series_ID
Batch_ID	BGKcLV35
Pool ID	Pool-220720
Local_Set_Name	set54
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	ROR2-BGKcLV35-37
Rep2	ROR2-BGKcLV35-38
CN1	NT-BGKcLV35-1
CN2	NT-BGKcLV35-2
Rep1_qPCR	48.5
Rep2_qPCR	49.5
Rep1_WB	84.6
Rep2_WB	79.5
Antibody Cat#	A304-242A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB456BNU
Status	Submitted
Project	ENCORE2
ID	959

Experiment Information (Status: Submitting)

	BGKcLV35-37	BGKcLV35-38
idx	1314	1315
TRCN#_or_BGC#	BGC#0000792	BGC#0000792
shRNA_or_gRNA_sequence	CGGGAGCGCGCGTCGCACAG	CGGGAGCGCGCGTCGCACAG
PAM	AGG	AGG
Name	ROR2_94	ROR2_94
Sample_ID	BGKcLV35-37	BGKcLV35-38
transduction_Date	4/28/22	4/28/22
days	D6	D6
RBP_name	ROR2	ROR2
qPCR_result	48.5	49.5
Ave_qPCR	49.0
RT-qPCR_primer-F	cttcagctgcccaagtgtg
RT-qPCR_primer-R	ttgccgttcctctgtaatcc
protein_conc	4116	3497
WB_result	84.6	79.5
Ave_WB	82.1
WB_DONE_date	5/31/22
MW	105KD
IP
antibody_Cat#	A304-242A	LOT #1
Antibody DCC ID	ENCAB456BNU
submitted_to_DCC_date	8/16/22
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/17/22	06/17/22
repeat_library
Note
ID	5460	5461

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ROR2	Product_ID: A304-242A Lot_ID: 1 Source: Bethyl Labs Target Name: ROR2-human

Experiment Status

	BGKcLV35-37	BGKcLV35-38
Sample_ID	BGKcLV35-37	BGKcLV35-38
Sample Name
Sample Name	ROR2-BGKcLV35-37	ROR2-BGKcLV35-38
RBP	ROR2	ROR2
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10875	10876

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV35-37	BGKcLV35-38
Sample #	41	42
Sample Name	ROR2-BGKcLV35-37	ROR2-BGKcLV35-38
Sample_Name_Alias
Index Well Position	A06	B06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-06-17	2022-06-17
Lib_ID	Lib-220617	Lib-220617
Tecan_Location
Tecan
Tecan_date
Size_bp	290	284
Peak_Molarity	16.80	26.90
libSampleQC_DNA_Well	DNA_Library_set54-56/set3/A10.png	DNA_Library_set54-56/set3/B10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set54-56/set2/A6.png	RNA_Library_set54-56/set2/B6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-06-20	2022-06-20
Sample_ID	BGKcLV35-37	BGKcLV35-38
RBP	ROR2	ROR2
Batch_ID	BGKcLV35	BGKcLV35
WB_result	84.600	79.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3358	3359

Sequencing Information

	BGKcLV35-37	BGKcLV35-38
Sample_ID	BGKcLV35-37	BGKcLV35-38
Sample Name	ROR2-BGKcLV35-37	ROR2-BGKcLV35-38
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	66,644,566	70,903,448
total_aligned_reads	61,419,780	63,661,652
unique_aligned_reads	56,567,564	58,458,102
percent_uniqueAligned	0.84879	0.82447
correlation_replicates	0.995580	0.995580
spikein_reads	7,384	4,682
percent_spikeins	0.00011	0.00007
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2237	2238

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
ROR2-BGKcLV35-37_S43_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2237	NovaSeq6000	100	paired-ended	1				NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8512
ROR2-BGKcLV35-37_S43_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2237	NovaSeq6000	100	paired-ended	2				NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8562
ROR2-BGKcLV35-37_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2237					GRCh38	V40	ROR2-BGKcLV35-37/Aligned.sortedByCoord.out.bam		ENCORE2	17758
ROR2-BGKcLV35-37_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2237					GRCh38	V40	ROR2-BGKcLV35-37/Aligned.sortedByCoord.out.bam		ENCORE2	17808
ROR2-BGKcLV35-37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2237					GRCh38	V40	ROR2-BGKcLV35-37/Aligned.sortedByCoord.out.bam		ENCORE2	17858
ROR2-BGKcLV35-37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2237					GRCh38	V40	ROR2-BGKcLV35-37/Aligned.sortedByCoord.out.bam		ENCORE2	17908
ROR2-BGKcLV35-37_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2237					GRCh38	V40	ROR2-BGKcLV35-37_S43_R1_001.filtered.trimmed.paired.fastq.gz,ROR2-BGKcLV35-37_S43_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17958
ROR2-BGKcLV35-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2237					GRCh38	V40	ROR2-BGKcLV35-37_S43_R1_001.filtered.trimmed.paired.fastq.gz,ROR2-BGKcLV35-37_S43_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29299
ROR2-BGKcLV35-38_S44_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2238	NovaSeq6000	100	paired-ended	1				NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8513
ROR2-BGKcLV35-38_S44_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2238	NovaSeq6000	100	paired-ended	2				NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8563
ROR2-BGKcLV35-38_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2238					GRCh38	V40	ROR2-BGKcLV35-38/Aligned.sortedByCoord.out.bam		ENCORE2	17759
ROR2-BGKcLV35-38_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2238					GRCh38	V40	ROR2-BGKcLV35-38/Aligned.sortedByCoord.out.bam		ENCORE2	17809
ROR2-BGKcLV35-38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2238					GRCh38	V40	ROR2-BGKcLV35-38/Aligned.sortedByCoord.out.bam		ENCORE2	17859
ROR2-BGKcLV35-38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2238					GRCh38	V40	ROR2-BGKcLV35-38/Aligned.sortedByCoord.out.bam		ENCORE2	17909
ROR2-BGKcLV35-38_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2238					GRCh38	V40	ROR2-BGKcLV35-38_S44_R1_001.filtered.trimmed.paired.fastq.gz,ROR2-BGKcLV35-38_S44_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17959
ROR2-BGKcLV35-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2238					GRCh38	V40	ROR2-BGKcLV35-38_S44_R1_001.filtered.trimmed.paired.fastq.gz,ROR2-BGKcLV35-38_S44_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29300