RANGAP1 RNA-Seq in K562

General Information


RBP	RANGAP1
Cell_Line	K562
Method	CRISPR
Exp_Name	RANGAP1-BGKcLV44-K562
ENCODE_series_ID
Batch_ID	BGKcLV44
Pool ID	Pool-241015
Local_Set_Name	set75
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	RANGAP1-BGKcLV44-51
Rep2	RANGAP1-BGKcLV44-52
CN1	NT-BGKcLV44-1
CN2	NT-BGKcLV44-2
Rep1_qPCR	57.0
Rep2_qPCR	52.4
Rep1_WB	62.7
Rep2_WB	62.4
Antibody Cat#	36067S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1606

Experiment Information (Status: Submitting)

	BGKcLV44-51	BGKcLV44-51	BGKcLV44-52	BGKcLV44-52
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0001048	BGC#0001048	BGC#0001048	BGC#0001048
shRNA_or_gRNA_sequence	GCCAAGACTCAGGTGGCCGG	GCCAAGACTCAGGTGGCCGG	GCCAAGACTCAGGTGGCCGG	GCCAAGACTCAGGTGGCCGG
PAM	ggg	ggg	ggg	ggg
Name	RANGAP1_82	RANGAP1_82	RANGAP1_82	RANGAP1_82
Sample_ID	BGKcLV44-51	BGKcLV44-51	BGKcLV44-52	BGKcLV44-52
transduction_Date	7/30/24	7/30/24	7/30/24	7/30/24
days	D6	D6	D6	D6
RBP_name	RANGAP1	RANGAP1	RANGAP1	RANGAP1
qPCR_result	57.0		52.4
Ave_qPCR	54.7
RT-qPCR_primer-F	GGTGGTCTCTGCCTTCCTAAAG
RT-qPCR_primer-R	CGAGGAGTTGAAAGCCTTCTGC
protein_conc	4257	4257	5331	5331
WB_result	62.7	84.5	62.4	85.5
Ave_WB	62.5	85.0
WB_DONE_date	8/12/24	8/12/24
MW	82KD	68KD
IP
antibody_Cat#	36067S	36067S	lot # 1	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	5930	5932	5931	5933

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RANGAP1	Product_ID: 36067S Lot_ID: 1 Source: Cell Signaling Technology Target Name: RANGAP1-human

Experiment Status

	BGKcLV44-51	BGKcLV44-51	BGKcLV44-52	BGKcLV44-52
Sample_ID	BGKcLV44-51	BGKcLV44-51	BGKcLV44-52	BGKcLV44-52
Sample Name
Sample Name	RANGAP1-BGKcLV44-51		RANGAP1-BGKcLV44-52
RBP	RANGAP1	RANGAP1	RANGAP1	RANGAP1
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2025-02-11	2024-10-08	2025-02-11	2024-10-08
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	13604	13648	13605	13649

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV44-51	BGKcLV44-52
Sample #	33	34
Sample Name	RANGAP1-BGKcLV44-51	RANGAP1-BGKcLV44-52
Sample_Name_Alias
Index Well Position	A10	B10
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-10	2024-10-10
Lib_ID	Lib-241010	Lib-241010
Tecan_Location
Tecan
Tecan_date
Size_bp	296	295
Peak_Molarity	82.80	85.10
libSampleQC_DNA_Well	DNA_Library_set75/set1/A10.png	DNA_Library_set75/set1/B10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set75/set1/A4.png	RNA_Library_set75/set1/B4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-15	2024-10-15
Sample_ID	BGKcLV44-51	BGKcLV44-52
RBP	RANGAP1	RANGAP1
Batch_ID	BGKcLV44	BGKcLV44
WB_result	62.700	62.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4592	4593

Sequencing Information

	BGKcLV44-51	BGKcLV44-52
Sample_ID	BGKcLV44-51	BGKcLV44-52
Sample Name	RANGAP1-BGKcLV44-51	RANGAP1-BGKcLV44-52
Pool ID	Pool-241015	Pool-241015
LocalServer_folder	set75	set75
total_reads	32,612,017	51,007,165
total_aligned_reads	30,921,548	48,516,774
unique_aligned_reads	28,471,848	44,876,771
percent_uniqueAligned	0.87305	0.87981
correlation_replicates	0.990268	0.990268
spikein_reads	84,550	99,378
percent_spikeins	0.00259	0.00195
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3303	3304

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
RANGAP1-BGKcLV44-51_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3303	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30960
RANGAP1-BGKcLV44-51_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3303	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31002
RANGAP1-BGKcLV44-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3303					GRCh38	V40	RANGAP1-BGKcLV44-51_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz,RANGAP1-BGKcLV44-51_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31044
RANGAP1-BGKcLV44-51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3303					GRCh38	V40	RANGAP1-BGKcLV44-51_Aligned.sortedByCoord.out.bam		ENCORE2	31086
RANGAP1-BGKcLV44-51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3303					GRCh38	V40	RANGAP1-BGKcLV44-51_Aligned.sortedByCoord.out.bam		ENCORE2	31128
RANGAP1-BGKcLV44-51_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3303					GRCh38	V40	RANGAP1-BGKcLV44-51_Aligned.sortedByCoord.out.bam		ENCORE2	31170
RANGAP1-BGKcLV44-51_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3303					GRCh38	V40	RANGAP1-BGKcLV44-51_Aligned.sortedByCoord.out.bam		ENCORE2	31212
RANGAP1-BGKcLV44-51_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3303					GRCh38	V40	RANGAP1-BGKcLV44-51_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz,RANGAP1-BGKcLV44-51_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31254
RANGAP1-BGKcLV44-52_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3304	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30961
RANGAP1-BGKcLV44-52_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3304	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31003
RANGAP1-BGKcLV44-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3304					GRCh38	V40	RANGAP1-BGKcLV44-52_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz,RANGAP1-BGKcLV44-52_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31045
RANGAP1-BGKcLV44-52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3304					GRCh38	V40	RANGAP1-BGKcLV44-52_Aligned.sortedByCoord.out.bam		ENCORE2	31087
RANGAP1-BGKcLV44-52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3304					GRCh38	V40	RANGAP1-BGKcLV44-52_Aligned.sortedByCoord.out.bam		ENCORE2	31129
RANGAP1-BGKcLV44-52_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3304					GRCh38	V40	RANGAP1-BGKcLV44-52_Aligned.sortedByCoord.out.bam		ENCORE2	31171
RANGAP1-BGKcLV44-52_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3304					GRCh38	V40	RANGAP1-BGKcLV44-52_Aligned.sortedByCoord.out.bam		ENCORE2	31213
RANGAP1-BGKcLV44-52_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3304					GRCh38	V40	RANGAP1-BGKcLV44-52_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz,RANGAP1-BGKcLV44-52_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31255