ATXN2L RNA-Seq in HepG2

General Information


RBP	ATXN2L
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ATXN2L-BGHcLV29-HepG2
ENCODE_series_ID	ENCSR383LJR
Batch_ID	BGHcLV29
Pool ID	Pool-211117
Local_Set_Name	set50_H
ENCODE_KD_Exp_ID	ENCSR234UAM
ENCODE_CN_Exp_ID	ENCSR248WTR
Rep1	ATXN2L-BGHcLV29-11B
Rep2	ATXN2L-BGHcLV29-12B
CN1	NT-BGHcLV29-1B
CN2	NT-BGHcLV29-2B
Rep1_qPCR	33.4
Rep2_qPCR	25.9
Rep1_WB	54.0
Rep2_WB	64.4
Antibody Cat#	A301-369A
Antibody Lot#	LOT# 1
Antibody DCC ID
Status	Submitted
Project	ENCODE4
ID	880

Experiment Information (Status: Released)

	BGHcLV29-11	BGHcLV29-12
idx	842	843
TRCN#_or_BGC#	BGC#0000645	BGC#0000645
shRNA_or_gRNA_sequence	GTGGCCCGTCGGCCCCCCGG	GTGGCCCGTCGGCCCCCCGG
PAM	GGG	GGG
Name	ATXN2L_89	ATXN2L_89
Sample_ID	BGHcLV29-11	BGHcLV29-12
transduction_Date	7/20	7/20
days	D6	D6
RBP_name	ATXN2L	ATXN2L
qPCR_result	33.4	25.9
Ave_qPCR	29.65
RT-qPCR_primer-F	gtatgccatccaccaccag
RT-qPCR_primer-R	ggctgctgtgattccagttt
protein_conc	0	4158
WB_result	54.0	64.4
Ave_WB	59.2	position is different k562
WB_DONE_date	7/29/21	JESS
MW	113kDa
IP	Rabbit / I
antibody_Cat#	A301-369A	LOT# 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/5/21	11/5/21
repeat_library
Note
ID	7017	7018

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV29-11	BGHcLV29-12
Sample_ID	BGHcLV29-11	BGHcLV29-12
Sample Name
Sample Name	ATXN2L-BGHcLV29-11B	ATXN2L-BGHcLV29-12B
RBP	ATXN2L	ATXN2L
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	9979	9980

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV29-11	BGHcLV29-11	BGHcLV29-12	BGHcLV29-12
Sample #	7	1	8	2
Sample Name	ATXN2L-BGHcLV29-11	ATXN2L-BGHcLV29-11B	ATXN2L-BGHcLV29-12	ATXN2L-BGHcLV29-12B
Sample_Name_Alias
Index Well Position	G01	C11	H01	D11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-11-01	2021-11-15	2021-11-01	2021-11-15
Lib_ID	Lib-211101	Lib-211115	Lib-211101	Lib-211115
Tecan_Location
Tecan
Tecan_date
Size_bp		263		257
Peak_Molarity		59.80		35.80
libSampleQC_DNA_Well		DNA_Library_set50/set1/G1.png		DNA_Library_set50/set1/H1.png
RIN		9.6		9.6
libSample_RNA_Well		RNA_Library_set50/set1/G7.png		RNA_Library_set50/set1/H7.png
SampleQC_method		TapeStation		TapeStation
SampleQC_date		2021-11-17		2021-11-17
Sample_ID	BGHcLV29-11	BGHcLV29-11	BGHcLV29-12	BGHcLV29-12
RBP	ATXN2L	ATXN2L	ATXN2L	ATXN2L
Batch_ID	BGHcLV29	BGHcLV29	BGHcLV29	BGHcLV29
WB_result	54.000	54.000	64.400	64.400
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix		B		B
Lib_Status	NotToSequence	SendToSequence	NotToSequence	SendToSequence
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4
ID	3094	3174	3095	3175

Sequencing Information

	BGHcLV29-11	BGHcLV29-12
Sample_ID	BGHcLV29-11	BGHcLV29-12
Sample Name	ATXN2L-BGHcLV29-11B	ATXN2L-BGHcLV29-12B
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_H	set50_H
total_reads	32,993,324	51,194,466
total_aligned_reads	27,290,256	41,365,304
unique_aligned_reads	25,644,926	38,755,204
percent_uniqueAligned	0.77728	0.75702
correlation_replicates	0.998757	0.998757
spikein_reads	2,088	1,942
percent_spikeins	0.00006	0.00004
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1913	1914

Data Submission Information

	BGHcLV29-11	BGHcLV29-11	BGHcLV29-11	BGHcLV29-11	BGHcLV29-11	BGHcLV29-11	BGHcLV29-12	BGHcLV29-12	BGHcLV29-12	BGHcLV29-12
ENCODE_alias	brenton-graveley:ATXN2L-BGHcLV29-B	brenton-graveley:ATXN2L-BGHcLV29-11B	brenton-graveley:L-ATXN2L-BGHcLV29-11B	brenton-graveley:ATXN2L-BGHcLV29-11B_S45_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ATXN2L-BGHcLV29-11B_S45_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ATXN2L-BGHcLV29-HepG2	brenton-graveley:ATXN2L-BGHcLV29-12B	brenton-graveley:L-ATXN2L-BGHcLV29-12B	brenton-graveley:ATXN2L-BGHcLV29-12B_S46_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ATXN2L-BGHcLV29-12B_S46_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR234UAM	ENCBS917JIO	ENCLB053HTH	ENCFF867XLY	ENCFF497MPT	ENCSR383LJR	ENCBS238XWI	ENCLB528CKU	ENCFF299OZQ	ENCFF907YAH
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	BGHcLV29-11	BGHcLV29-11	BGHcLV29-11	BGHcLV29-11	BGHcLV29-11	BGHcLV29-11	BGHcLV29-12	BGHcLV29-12	BGHcLV29-12	BGHcLV29-12
Sample Name	ATXN2L-BGHcLV29-11B	ATXN2L-BGHcLV29-11B	ATXN2L-BGHcLV29-11B	ATXN2L-BGHcLV29-11B	ATXN2L-BGHcLV29-11B	ATXN2L-BGHcLV29-11B	ATXN2L-BGHcLV29-12B	ATXN2L-BGHcLV29-12B	ATXN2L-BGHcLV29-12B	ATXN2L-BGHcLV29-12B
Selected	Yes	No	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
			LV50H_library_protocol					LV50H_library_protocol
protocol_URL			L-ATXN2L-BGHcLV29-11B.pdf					L-ATXN2L-BGHcLV29-12B.pdf
ID	6556	6557	6559	6567	6568	6571	6558	6560	6569	6570

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-BGHcLV29-11B_S45_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1913	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1B_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2B_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6259
ATXN2L-BGHcLV29-11B_S45_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1913	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1B_S43_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2B_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6263
ATXN2L-BGHcLV29-11B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1913					GRCh38	V40	ATXN2L-BGHcLV29-11B_S45_L001_R1_001.filtered.trimmed.paired.fastq.gz,ATXN2L-BGHcLV29-11B_S45_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18930
ATXN2L-BGHcLV29-11B_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1913					GRCh38	V40	ATXN2L-BGHcLV29-11B/Aligned.sortedByCoord.out.bam		ENCORE2	18988
ATXN2L-BGHcLV29-11B_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1913					GRCh38	V40	ATXN2L-BGHcLV29-11B/Aligned.sortedByCoord.out.bam		ENCORE2	19034
ATXN2L-BGHcLV29-11B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1913					GRCh38	V40	ATXN2L-BGHcLV29-11B/Aligned.sortedByCoord.out.bam		ENCORE2	19080
ATXN2L-BGHcLV29-11B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1913					GRCh38	V40	ATXN2L-BGHcLV29-11B/Aligned.sortedByCoord.out.bam		ENCORE2	19126
ATXN2L-BGHcLV29-11B_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1913					GRCh38	V40	ATXN2L-BGHcLV29-11B_S45_L001_R1_001.filtered.trimmed.paired.fastq.gz,ATXN2L-BGHcLV29-11B_S45_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19172
ATXN2L-BGHcLV29-12B_S46_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1914	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1B_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2B_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6260
ATXN2L-BGHcLV29-12B_S46_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1914	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1B_S43_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2B_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6264
ATXN2L-BGHcLV29-12B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1914					GRCh38	V40	ATXN2L-BGHcLV29-12B_S46_L001_R1_001.filtered.trimmed.paired.fastq.gz,ATXN2L-BGHcLV29-12B_S46_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18931
ATXN2L-BGHcLV29-12B_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1914					GRCh38	V40	ATXN2L-BGHcLV29-12B/Aligned.sortedByCoord.out.bam		ENCORE2	18989
ATXN2L-BGHcLV29-12B_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1914					GRCh38	V40	ATXN2L-BGHcLV29-12B/Aligned.sortedByCoord.out.bam		ENCORE2	19035
ATXN2L-BGHcLV29-12B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1914					GRCh38	V40	ATXN2L-BGHcLV29-12B/Aligned.sortedByCoord.out.bam		ENCORE2	19081
ATXN2L-BGHcLV29-12B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1914					GRCh38	V40	ATXN2L-BGHcLV29-12B/Aligned.sortedByCoord.out.bam		ENCORE2	19127
ATXN2L-BGHcLV29-12B_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1914					GRCh38	V40	ATXN2L-BGHcLV29-12B_S46_L001_R1_001.filtered.trimmed.paired.fastq.gz,ATXN2L-BGHcLV29-12B_S46_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19173