ATXN2L RNA-Seq in K562

General Information


RBP	ATXN2L
Cell_Line	K562
Method	CRISPR
Exp_Name	ATXN2L-BGKcLV26-K562
ENCODE_series_ID	ENCSR863PXE
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR585UBH
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	ATXN2L-BGKcLV26-39
Rep2	ATXN2L-BGKcLV26-40
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR	17.9
Rep2_qPCR	8.0
Rep1_WB	92.3
Rep2_WB	93.5
Antibody Cat#	A301-370A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB117ISE
Status	Released
Project	ENCODE4
ID	795

Experiment Information (Status: Released)

	BGKcLV26-39	BGKcLV26-40
idx	900	901
TRCN#_or_BGC#	BGC#0000645	BGC#0000645
shRNA_or_gRNA_sequence	GTGGCCCGTCGGCCCCCCGG	GTGGCCCGTCGGCCCCCCGG
PAM	GGG	GGG
Name	ATXN2L_89	ATXN2L_89
Sample_ID	BGKcLV26-39	BGKcLV26-40
transduction_Date	3/30/21	3/30/21
days	Day 6	Day 6
RBP_name	ATXN2L	ATXN2L
qPCR_result	17.9	8.0
Ave_qPCR	13.0
RT-qPCR_primer-F	gtatgccatccaccaccag
RT-qPCR_primer-R	ggctgctgtgattccagttt
protein_conc	5382	5495
WB_result	92.3	93.5
Ave_WB	92.9	?
WB_DONE_date	5/27/21	jess
MW	113kDa
IP	Rabbit / I
antibody_Cat#	A301-370A	LOT# 1
Antibody DCC ID	ENCAB117ISE	10/22/21
submitted_to_DCC_date
Rep1_TPM	140.1	0
Rep2_TPM	87.6	0
Action	Ready	Ready
Library_start_date	09/01/21	09/01/21
repeat_library
Note
ID	5032	5033

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ATXN2L	Product_ID: A301-370A Lot_ID: 1 Source: Bethyl Labs Target Name: ATXN2L-human

Experiment Status

	BGKcLV26-39	BGKcLV26-40
Sample_ID	BGKcLV26-39	BGKcLV26-40
Sample Name
Sample Name	ATXN2L-BGKcLV26-39	ATXN2L-BGKcLV26-40
RBP	ATXN2L	ATXN2L
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9771	9772

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-39	BGKcLV26-40
Sample #	29	30
Sample Name	ATXN2L-BGKcLV26-39	ATXN2L-BGKcLV26-40
Sample_Name_Alias
Index Well Position	E04	F04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-07-22	2021-07-22
Lib_ID	Lib-210722	Lib-210722
Tecan_Location
Tecan
Tecan_date
Size_bp	294	289
Peak_Molarity	123.00	116.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/E4.png	DNA_Library_set48-49/set1/F4.png
RIN	9.9	9.5
libSample_RNA_Well	RNA_Library_set48-49/set1/E4.png	RNA_Library_set48-49/set1/F4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-39	BGKcLV26-40
RBP	ATXN2L	ATXN2L
Batch_ID	BGKcLV26	BGKcLV26
WB_result	92.300	93.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1588	1589

Sequencing Information

	BGKcLV26-39	BGKcLV26-40
Sample_ID	BGKcLV26-39	BGKcLV26-40
Sample Name	ATXN2L-BGKcLV26-39	ATXN2L-BGKcLV26-40
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	55,720,810	71,578,738
total_aligned_reads	48,208,086	64,484,202
unique_aligned_reads	44,262,448	59,072,934
percent_uniqueAligned	0.79436	0.82529
correlation_replicates	0.998821	0.998821
spikein_reads	20,674	22,526
percent_spikeins	0.00037	0.00031
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1765	1766

Data Submission Information

	BGKcLV26-39	BGKcLV26-39	BGKcLV26-39	BGKcLV26-39	BGKcLV26-39	BGKcLV26-39	BGKcLV26-40	BGKcLV26-40	BGKcLV26-40	BGKcLV26-40
ENCODE_alias	brenton-graveley:ATXN2L-BGKcLV26	brenton-graveley:ATXN2L-BGKcLV26-39	brenton-graveley:L-ATXN2L-BGKcLV26-39	brenton-graveley:ATXN2L-BGKcLV26-39_S35_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ATXN2L-BGKcLV26-39_S35_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ATXN2L-BGKcLV26-K562	brenton-graveley:ATXN2L-BGKcLV26-40	brenton-graveley:L-ATXN2L-BGKcLV26-40	brenton-graveley:ATXN2L-BGKcLV26-40_S36_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ATXN2L-BGKcLV26-40_S36_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR585UBH	ENCBS252NUU	ENCLB569EAR	ENCFF005JZO	ENCFF195QAS	ENCSR863PXE	ENCBS471JPC	ENCLB613JKD	ENCFF977FCH	ENCFF963TMX
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV26-39	BGKcLV26-39	BGKcLV26-39	BGKcLV26-39	BGKcLV26-39	BGKcLV26-39	BGKcLV26-40	BGKcLV26-40	BGKcLV26-40	BGKcLV26-40
Sample Name	ATXN2L-BGKcLV26-39	ATXN2L-BGKcLV26-39	ATXN2L-BGKcLV26-39	ATXN2L-BGKcLV26-39	ATXN2L-BGKcLV26-39	ATXN2L-BGKcLV26-39	ATXN2L-BGKcLV26-40	ATXN2L-BGKcLV26-40	ATXN2L-BGKcLV26-40	ATXN2L-BGKcLV26-40
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2021-11-19	2021-11-19	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV48K_biosample_protocol	LV48K_library_protocol				LV48K_biosample_protocol	LV48K_library_protocol
protocol_URL		ATXN2L-BGKcLV26-39.pdf	L-ATXN2L-BGKcLV26-39.pdf				ATXN2L-BGKcLV26-40.pdf	L-ATXN2L-BGKcLV26-40.pdf
ID	3460	3554	3688	3822	3956	7096	3555	3689	3823	3957

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
ATXN2L-BGKcLV26-39_S35_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1765	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3858
ATXN2L-BGKcLV26-39_S35_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1765	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3908
ATXN2L-BGKcLV26-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1765					GRCh38	V40	ATXN2L-BGKcLV26-39_S35_L003_R1_001.filtered.trimmed.paired.fastq.gz,ATXN2L-BGKcLV26-39_S35_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25545
ATXN2L-BGKcLV26-39_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1765					GRCh38	V40	ATXN2L-BGKcLV26-39_S35_L003_R1_001.filtered.trimmed.paired.fastq.gz,ATXN2L-BGKcLV26-39_S35_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25595
ATXN2L-BGKcLV26-39_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1765					GRCh38	V40	ATXN2L-BGKcLV26-39/Aligned.sortedByCoord.out.bam		ENCORE2	26561
ATXN2L-BGKcLV26-39_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1765					GRCh38	V40	ATXN2L-BGKcLV26-39/Aligned.sortedByCoord.out.bam		ENCORE2	26611
ATXN2L-BGKcLV26-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1765					GRCh38	V40	ATXN2L-BGKcLV26-39/Aligned.sortedByCoord.out.bam		ENCORE2	26661
ATXN2L-BGKcLV26-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1765					GRCh38	V40	ATXN2L-BGKcLV26-39/Aligned.sortedByCoord.out.bam		ENCORE2	26711
ATXN2L-BGKcLV26-40_S36_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1766	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3859
ATXN2L-BGKcLV26-40_S36_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1766	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3909
ATXN2L-BGKcLV26-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1766					GRCh38	V40	ATXN2L-BGKcLV26-40_S36_L003_R1_001.filtered.trimmed.paired.fastq.gz,ATXN2L-BGKcLV26-40_S36_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25546
ATXN2L-BGKcLV26-40_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1766					GRCh38	V40	ATXN2L-BGKcLV26-40_S36_L003_R1_001.filtered.trimmed.paired.fastq.gz,ATXN2L-BGKcLV26-40_S36_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25596
ATXN2L-BGKcLV26-40_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1766					GRCh38	V40	ATXN2L-BGKcLV26-40/Aligned.sortedByCoord.out.bam		ENCORE2	26562
ATXN2L-BGKcLV26-40_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1766					GRCh38	V40	ATXN2L-BGKcLV26-40/Aligned.sortedByCoord.out.bam		ENCORE2	26612
ATXN2L-BGKcLV26-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1766					GRCh38	V40	ATXN2L-BGKcLV26-40/Aligned.sortedByCoord.out.bam		ENCORE2	26662
ATXN2L-BGKcLV26-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1766					GRCh38	V40	ATXN2L-BGKcLV26-40/Aligned.sortedByCoord.out.bam		ENCORE2	26712