ATXN2 RNA-Seq in K562

Experiment Information (Status: Sequenced)

	BGKcLV51-17	BGKcLV51-18
idx	0	0
TRCN#_or_BGC#	BGC#0001453	BGC#0001453
shRNA_or_gRNA_sequence	GTCGCCGCGACCACCGAGG	GTCGCCGCGACCACCGAGG
PAM	AGG	AGG
Name	ATX2_88/ATXN2	ATX2_88/ATXN2
Sample_ID	BGKcLV51-17	BGKcLV51-18
transduction_Date	9/30/2025	9/30/2025
days	D6	D6
RBP_name	ATXN2	ATXN2
qPCR_result	48.6	32.1
Ave_qPCR	40.4
RT-qPCR_primer-F	ttcaacccacgttccttctc
RT-qPCR_primer-R	gctgttgatgacccaccata
protein_conc	2358	1959
WB_result	57.5	62.3
Ave_WB
WB_DONE_date	10/9/25
MW	140KD
IP
antibody_Cat#	A301-118A	old
Antibody DCC ID	ENCAB360GKL
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	6254	6255

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ATXN2	Product_ID: A301-118A Lot_ID: 2 Source: Bethyl Labs Target Name: ATXN2-human

Experiment Status

	BGKcLV51-17	BGKcLV51-18
Sample_ID	BGKcLV51-17	BGKcLV51-18
Sample Name
Sample Name	ATXN2-BGKcLV51-17	ATXN2-BGKcLV51-18
RBP	ATXN2	ATXN2
Cell_Line	K562	K562
Exp UID
Status	Sequenced	Sequenced
Status_date	2026-09-16	2026-09-16
Project	ENCORE2	ENCORE2
Note
ID	14568	14569

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV51-17	BGKcLV51-18
Sample #	3	4
Sample Name	ATXN2-BGKcLV51-17	ATXN2-BGKcLV51-18
Sample_Name_Alias
Index Well Position	C01	D01
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2026-05-18	2026-05-18
Lib_ID	Lib-260518	Lib-260518
Tecan_Location
Tecan
Tecan_date
Size_bp	289	299
Peak_Molarity	45.00	80.80
libSampleQC_DNA_Well	DNA_Library_set82/set1/C8.png	DNA_Library_set82/set1/D8.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set82/set1/C1.png	RNA_Library_set82/set1/D1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2026-05-21	2026-05-21
Sample_ID	BGKcLV51-17	BGKcLV51-18
RBP	ATXN2	ATXN2
Batch_ID	BGKcLV51	BGKcLV51
WB_result	57.500	62.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4842	4843

Sequencing Information

	BGKcLV51-17	BGKcLV51-18
Sample_ID	BGKcLV51-17	BGKcLV51-18
Sample Name	ATXN2-BGKcLV51-17	ATXN2-BGKcLV51-18
Pool ID	Pool-260528	Pool-260528
LocalServer_folder	set82	set82
total_reads	25,457,257	34,568,848
total_aligned_reads	20,665,981	32,602,076
unique_aligned_reads	19,294,510	30,411,687
percent_uniqueAligned	0.75792	0.87974
correlation_replicates	0.992703	0.992703
spikein_reads	59,210	107,408
percent_spikeins	0.00233	0.00311
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3543	3544

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
ATXN2-BGKcLV51-17_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3543	NovaSeq6000	100	paired-ended	1				NT-BGKcLV51-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33656
ATXN2-BGKcLV51-17_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3543	NovaSeq6000	100	paired-ended	2				NT-BGKcLV51-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33714
ATXN2-BGKcLV51-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3543					GRCh38	V40	ATXN2-BGKcLV51-17_R1.filtered.trimmed.paired.fastq.gz,ATXN2-BGKcLV51-17_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33772
ATXN2-BGKcLV51-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3543					GRCh38	V40	ATXN2-BGKcLV51-17_Aligned.sortedByCoord.out.bam		ENCORE2	33830
ATXN2-BGKcLV51-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3543					GRCh38	V40	ATXN2-BGKcLV51-17_Aligned.sortedByCoord.out.bam		ENCORE2	33888
ATXN2-BGKcLV51-17_Signal.Unique.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3543					GRCh38	V40	ATXN2-BGKcLV51-17_Aligned.sortedByCoord.out.bam		ENCORE2	33946
ATXN2-BGKcLV51-17_Signal.Unique.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3543					GRCh38	V40	ATXN2-BGKcLV51-17_Aligned.sortedByCoord.out.bam		ENCORE2	34004
ATXN2-BGKcLV51-17_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3543					GRCh38	V40	ATXN2-BGKcLV51-17_R1.filtered.trimmed.paired.fastq.gz,ATXN2-BGKcLV51-17_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34062
ATXN2-BGKcLV51-18_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3544	NovaSeq6000	100	paired-ended	1				NT-BGKcLV51-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33657
ATXN2-BGKcLV51-18_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3544	NovaSeq6000	100	paired-ended	2				NT-BGKcLV51-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33715
ATXN2-BGKcLV51-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3544					GRCh38	V40	ATXN2-BGKcLV51-18_R1.filtered.trimmed.paired.fastq.gz,ATXN2-BGKcLV51-18_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33773
ATXN2-BGKcLV51-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3544					GRCh38	V40	ATXN2-BGKcLV51-18_Aligned.sortedByCoord.out.bam		ENCORE2	33831
ATXN2-BGKcLV51-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3544					GRCh38	V40	ATXN2-BGKcLV51-18_Aligned.sortedByCoord.out.bam		ENCORE2	33889
ATXN2-BGKcLV51-18_Signal.Unique.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3544					GRCh38	V40	ATXN2-BGKcLV51-18_Aligned.sortedByCoord.out.bam		ENCORE2	33947
ATXN2-BGKcLV51-18_Signal.Unique.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3544					GRCh38	V40	ATXN2-BGKcLV51-18_Aligned.sortedByCoord.out.bam		ENCORE2	34005
ATXN2-BGKcLV51-18_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3544					GRCh38	V40	ATXN2-BGKcLV51-18_R1.filtered.trimmed.paired.fastq.gz,ATXN2-BGKcLV51-18_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34063