ALKBH1 RNA-Seq in HepG2

General Information


RBP	ALKBH1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ALKBH1-BGHcLV24-HepG2
ENCODE_series_ID	ENCSR318PEB
Batch_ID	BGHcLV24
Pool ID	Pool-210622
Local_Set_Name	set47
ENCODE_KD_Exp_ID	ENCSR076LFC
ENCODE_CN_Exp_ID	ENCSR671FDZ
Rep1	ALKBH1-BGHcLV24-9
Rep2	ALKBH1-BGHcLV24-10
CN1	NT-BGHcLV24-1
CN2	NT-BGHcLV24-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	85.0
Rep2_WB	86.0
Antibody Cat#	PA5-92844
Antibody Lot#	LOT# UK2881304
Antibody DCC ID	ENCAB874JLV
Status	Released
Project	ENCODE4
ID	2

Experiment Information (Status: Released)

	BGHcLV24-9	BGHcLV24-10
idx	667	668
TRCN#_or_BGC#	BGC#0000562	BGC#0000562
shRNA_or_gRNA_sequence	AGGGGTCATCGACTTCTCGG	AGGGGTCATCGACTTCTCGG
PAM	CGG	CGG
Name	ALKBH1_95	ALKBH1_95
Sample_ID	BGHcLV24-9	BGHcLV24-10
transduction_Date	10/30/20	10/30/20
days	D6	D6
RBP_name	ALKBH1	ALKBH1
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	GTGGCAAGGGTCCTGGTG
RT-qPCR_primer-R	ATAGGCTTGCCACTTGCTGA
protein_conc	4040	4085
WB_result	85.0	86.0
Ave_WB	85.5
WB_DONE_date	11/9/20
MW	44KD
IP	Rabbit / I
antibody_Cat#	PA5-92844	LOT# UK2881304
Antibody DCC ID	ENCAB874JLV
submitted_to_DCC_date	12/9/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/16/21	06/16/21
repeat_library
Note
ID	6822	6823

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ALKBH1	Product_ID: PA5-92844 Lot_ID: UK2881304 Source: Thermo Fisher Target Name: ALKBH1-human

Experiment Status

	BGHcLV24-9	BGHcLV24-10
Sample_ID	BGHcLV24-9	BGHcLV24-10
Sample Name
Sample Name	ALKBH1-BGHcLV24-9	ALKBH1-BGHcLV24-10
RBP	ALKBH1	ALKBH1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4
Note
ID	7783	7784

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV24-9	BGHcLV24-10
Sample #	5	6
Sample Name	ALKBH1-BGHcLV24-9	ALKBH1-BGHcLV24-10
Sample_Name_Alias
Index Well Position	E07	F07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-06-04	2021-06-04
Lib_ID	Lib-210604	Lib-210604
Tecan_Location
Tecan
Tecan_date
Size_bp	299	301
Peak_Molarity	74.40	74.30
libSampleQC_DNA_Well	DNA_Library_set47/set1/E4.png	DNA_Library_set47/set1/F4.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set47/set1/E1.png	RNA_Library_set47/set1/F1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-06-22	2021-06-22
Sample_ID	BGHcLV24-9	BGHcLV24-10
RBP	ALKBH1	ALKBH1
Batch_ID	BGHcLV24	BGHcLV24
WB_result	85.000	86.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1468	1469

Sequencing Information

	BGHcLV24-9	BGHcLV24-10
Sample_ID	BGHcLV24-9	BGHcLV24-10
Sample Name	ALKBH1-BGHcLV24-9	ALKBH1-BGHcLV24-10
Pool ID	Pool-210622	Pool-210622
LocalServer_folder	set47	set47
total_reads	107,444,896	100,411,038
total_aligned_reads	94,946,054	89,225,320
unique_aligned_reads	89,585,792	83,969,638
percent_uniqueAligned	0.83378	0.83626
correlation_replicates	0.978228	0.978228
spikein_reads	53,328	49,794
percent_spikeins	0.00050	0.00050
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	550	551

Data Submission Information

	BGHcLV24-9	BGHcLV24-9	BGHcLV24-9	BGHcLV24-9	BGHcLV24-9	BGHcLV24-9	BGHcLV24-10	BGHcLV24-10	BGHcLV24-10	BGHcLV24-10
ENCODE_alias	brenton-graveley:ALKBH1-BGHcLV24	brenton-graveley:ALKBH1-BGHcLV24-9	brenton-graveley:L-ALKBH1-BGHcLV24-9	brenton-graveley:ALKBH1-BGHcLV24-9_S65_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ALKBH1-BGHcLV24-9_S65_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ALKBH1-BGHcLV24-HepG2	brenton-graveley:ALKBH1-BGHcLV24-10	brenton-graveley:L-ALKBH1-BGHcLV24-10	brenton-graveley:ALKBH1-BGHcLV24-10_S66_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ALKBH1-BGHcLV24-10_S66_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR076LFC	ENCBS039NUK	ENCLB608DYU	ENCFF877KQI	ENCFF422WXX	ENCSR318PEB	ENCBS358QAI	ENCLB047FQP	ENCFF288NTH	ENCFF588OKX
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	BGHcLV24-9	BGHcLV24-9	BGHcLV24-9	BGHcLV24-9	BGHcLV24-9	BGHcLV24-9	BGHcLV24-10	BGHcLV24-10	BGHcLV24-10	BGHcLV24-10
Sample Name	ALKBH1-BGHcLV24-9	ALKBH1-BGHcLV24-9	ALKBH1-BGHcLV24-9	ALKBH1-BGHcLV24-9	ALKBH1-BGHcLV24-9	ALKBH1-BGHcLV24-9	ALKBH1-BGHcLV24-10	ALKBH1-BGHcLV24-10	ALKBH1-BGHcLV24-10	ALKBH1-BGHcLV24-10
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2022-03-02	2021-11-04	2021-11-04	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV47_biosample_protocol	LV47_library_protocol				LV47_biosample_protocol	LV47_library_protocol
protocol_URL		ALKBH1-BGHcLV24-9.pdf	L-ALKBH1-BGHcLV24-9.pdf				ALKBH1-BGHcLV24-10.pdf	L-ALKBH1-BGHcLV24-10.pdf
ID	3237	3261	3305	3349	3393	7081	3262	3306	3350	3394

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
ALKBH1-BGHcLV24-9_S65_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	550	NovaSeq6000	100	paired-ended	1				NT-BGHcLV24-1_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3707
ALKBH1-BGHcLV24-9_S65_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	550	NovaSeq6000	100	paired-ended	2				NT-BGHcLV24-1_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3753
ALKBH1-BGHcLV24-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	550					GRCh38	V40	ALKBH1-BGHcLV24-9_S65_L002_R1_001.filtered.trimmed.paired.fastq.gz,ALKBH1-BGHcLV24-9_S65_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25396
ALKBH1-BGHcLV24-9_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	550					GRCh38	V40	ALKBH1-BGHcLV24-9_S65_L002_R1_001.filtered.trimmed.paired.fastq.gz,ALKBH1-BGHcLV24-9_S65_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25440
ALKBH1-BGHcLV24-9_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	550					GRCh38	V40	ALKBH1-BGHcLV24-9/Aligned.sortedByCoord.out.bam		ENCORE2	26272
ALKBH1-BGHcLV24-9_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	550					GRCh38	V40	ALKBH1-BGHcLV24-9/Aligned.sortedByCoord.out.bam		ENCORE2	26316
ALKBH1-BGHcLV24-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	550					GRCh38	V40	ALKBH1-BGHcLV24-9/Aligned.sortedByCoord.out.bam		ENCORE2	26360
ALKBH1-BGHcLV24-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	550					GRCh38	V40	ALKBH1-BGHcLV24-9/Aligned.sortedByCoord.out.bam		ENCORE2	26404
ALKBH1-BGHcLV24-10_S66_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	551	NovaSeq6000	100	paired-ended	1				NT-BGHcLV24-1_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3706
ALKBH1-BGHcLV24-10_S66_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	551	NovaSeq6000	100	paired-ended	2				NT-BGHcLV24-1_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3752
ALKBH1-BGHcLV24-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	551					GRCh38	V40	ALKBH1-BGHcLV24-10_S66_L002_R1_001.filtered.trimmed.paired.fastq.gz,ALKBH1-BGHcLV24-10_S66_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25395
ALKBH1-BGHcLV24-10_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	551					GRCh38	V40	ALKBH1-BGHcLV24-10_S66_L002_R1_001.filtered.trimmed.paired.fastq.gz,ALKBH1-BGHcLV24-10_S66_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25439
ALKBH1-BGHcLV24-10_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	551					GRCh38	V40	ALKBH1-BGHcLV24-10/Aligned.sortedByCoord.out.bam		ENCORE2	26271
ALKBH1-BGHcLV24-10_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	551					GRCh38	V40	ALKBH1-BGHcLV24-10/Aligned.sortedByCoord.out.bam		ENCORE2	26315
ALKBH1-BGHcLV24-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	551					GRCh38	V40	ALKBH1-BGHcLV24-10/Aligned.sortedByCoord.out.bam		ENCORE2	26359
ALKBH1-BGHcLV24-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	551					GRCh38	V40	ALKBH1-BGHcLV24-10/Aligned.sortedByCoord.out.bam		ENCORE2	26403