ALKBH1 RNA-Seq in K562

General Information


RBP	ALKBH1
Cell_Line	K562
Method	CRISPR
Exp_Name	ALKBH1-BGKcLV23-K562
ENCODE_series_ID	ENCSR150QQM
Batch_ID	BGKcLV23
Pool ID	Pool-201204
Local_Set_Name	set46_K
ENCODE_KD_Exp_ID	ENCSR278CLE
ENCODE_CN_Exp_ID	ENCSR877JEM
Rep1	ALKBH1-BGKcLV23-13
Rep2	ALKBH1-BGKcLV23-14
CN1	NT-BGKcLV23-1
CN2	NT-BGKcLV23-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	87.2
Rep2_WB	88.045683
Antibody Cat#	PA5-92844
Antibody Lot#	LOT# UK2881304
Antibody DCC ID	ENCAB874JLV
Status	Released
Project	ENCODE4
ID	22

Experiment Information (Status: Released)

	BGKcLV23-13	BGKcLV23-14
idx	799	800
TRCN#_or_BGC#	BGC#0000562	BGC#0000562
shRNA_or_gRNA_sequence	AGGGGTCATCGACTTCTCGG	AGGGGTCATCGACTTCTCGG
PAM	CGG	CGG
Name	ALKBH1_95	ALKBH1_95
Sample_ID	BGKcLV23-13	BGKcLV23-14
transduction_Date	9/17/20	9/17/20
days	Day 6	Day 6
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	2702	3420
WB_result	87.2	88.045683
Ave_WB	87.6
WB_DONE_date	12/14/20
MW	44KD
IP	Rabbit / I
antibody_Cat#	PA5-92844	LOT# UK2881304
Antibody DCC ID	ENCAB874JLV
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	4919	4920

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

	BGKcLV23-13	BGKcLV23-14
Sample_ID	BGKcLV23-13	BGKcLV23-14
Sample Name
Sample Name	ALKBH1-BGKcLV23-13	ALKBH1-BGKcLV23-14
RBP	ALKBH1	ALKBH1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7433	7434

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV23-13	BGKcLV23-14
Sample #	35	36
Sample Name	ALKBH1-BGKcLV23-13	ALKBH1-BGKcLV23-14
Sample_Name_Alias
Index Well Position	C05	D05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-11-24	2020-11-24
Lib_ID	Lib-201124	Lib-201124
Tecan_Location
Tecan
Tecan_date
Size_bp	299	292
Peak_Molarity	93.70	106.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/C5.png	DNA_Library_set46/set1/D5.png
RIN	8.8	9.2
libSample_RNA_Well	RNA_Library_set46/set2/C9.png	RNA_Library_set46/set2/D9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGKcLV23-13	BGKcLV23-14
RBP	ALKBH1	ALKBH1
Batch_ID	BGKcLV23	BGKcLV23
WB_result	71.800	67.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1410	1411

Sequencing Information

	BGKcLV23-13	BGKcLV23-14
Sample_ID	BGKcLV23-13	BGKcLV23-14
Sample Name	ALKBH1-BGKcLV23-13	ALKBH1-BGKcLV23-14
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_K	set46_K
total_reads	146,284,284	150,665,900
total_aligned_reads	133,454,802	136,424,302
unique_aligned_reads	121,178,430	124,250,484
percent_uniqueAligned	0.82838	0.82468
correlation_replicates	0.986176	0.986176
spikein_reads	67,800	56,492
percent_spikeins	0.00046	0.00037
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	516	517

Data Submission Information

	BGKcLV23-13	BGKcLV23-13	BGKcLV23-13	BGKcLV23-13	BGKcLV23-13	BGKcLV23-13	BGKcLV23-14	BGKcLV23-14	BGKcLV23-14	BGKcLV23-14
ENCODE_alias	brenton-graveley:ALKBH1-BGKcLV23	brenton-graveley:ALKBH1-BGKcLV23-13	brenton-graveley:L-ALKBH1-BGKcLV23-13	brenton-graveley:ALKBH1-BGKcLV23-13_AGCCTCAT+TCTCTACT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ALKBH1-BGKcLV23-13_AGCCTCAT+TCTCTACT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ALKBH1-BGKcLV23-K562	brenton-graveley:ALKBH1-BGKcLV23-14	brenton-graveley:L-ALKBH1-BGKcLV23-14	brenton-graveley:ALKBH1-BGKcLV23-14_GATTCTGC+CTCTCGTC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ALKBH1-BGKcLV23-14_GATTCTGC+CTCTCGTC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR278CLE	ENCBS103TTP	ENCLB529ARE	ENCFF389CWK	ENCFF643QPE	ENCSR150QQM	ENCBS461EJN	ENCLB597TGG	ENCFF143VCK	ENCFF130QBE
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	BGKcLV23-13	BGKcLV23-13	BGKcLV23-13	BGKcLV23-13	BGKcLV23-13	BGKcLV23-13	BGKcLV23-14	BGKcLV23-14	BGKcLV23-14	BGKcLV23-14
Sample Name	ALKBH1-BGKcLV23-13	ALKBH1-BGKcLV23-13	ALKBH1-BGKcLV23-13	ALKBH1-BGKcLV23-13	ALKBH1-BGKcLV23-13	ALKBH1-BGKcLV23-13	ALKBH1-BGKcLV23-14	ALKBH1-BGKcLV23-14	ALKBH1-BGKcLV23-14	ALKBH1-BGKcLV23-14
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46K_biosample_protocol	LV46K_library_protocol				LV46K_biosample_protocol	LV46K_library_protocol
protocol_URL		ALKBH1-BGKcLV23-13.pdf	L-ALKBH1-BGKcLV23-13.pdf				ALKBH1-BGKcLV23-14.pdf	L-ALKBH1-BGKcLV23-14.pdf
ID	2412	2461	2525	2619	2653	7082	2462	2526	2620	2654

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-BGKcLV23-13_AGCCTCAT+TCTCTACT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	516	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1380
ALKBH1-BGKcLV23-13_AGCCTCAT+TCTCTACT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	516	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1444
ALKBH1-BGKcLV23-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	516					GRCh38	V40	ALKBH1-BGKcLV23-13_AGCCTCAT+TCTCTACT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,ALKBH1-BGKcLV23-13_AGCCTCAT+TCTCTACT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25283
ALKBH1-BGKcLV23-13_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	516					GRCh38	V40	ALKBH1-BGKcLV23-13_AGCCTCAT+TCTCTACT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,ALKBH1-BGKcLV23-13_AGCCTCAT+TCTCTACT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25317
ALKBH1-BGKcLV23-13_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	516					GRCh38	V40	ALKBH1-BGKcLV23-13/Aligned.sortedByCoord.out.bam		ENCORE2	26121
ALKBH1-BGKcLV23-13_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	516					GRCh38	V40	ALKBH1-BGKcLV23-13/Aligned.sortedByCoord.out.bam		ENCORE2	26155
ALKBH1-BGKcLV23-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	516					GRCh38	V40	ALKBH1-BGKcLV23-13/Aligned.sortedByCoord.out.bam		ENCORE2	26189
ALKBH1-BGKcLV23-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	516					GRCh38	V40	ALKBH1-BGKcLV23-13/Aligned.sortedByCoord.out.bam		ENCORE2	26223
ALKBH1-BGKcLV23-14_GATTCTGC+CTCTCGTC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	517	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1381
ALKBH1-BGKcLV23-14_GATTCTGC+CTCTCGTC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	517	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1445
ALKBH1-BGKcLV23-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	517					GRCh38	V40	ALKBH1-BGKcLV23-14_GATTCTGC+CTCTCGTC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,ALKBH1-BGKcLV23-14_GATTCTGC+CTCTCGTC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25284
ALKBH1-BGKcLV23-14_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	517					GRCh38	V40	ALKBH1-BGKcLV23-14_GATTCTGC+CTCTCGTC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,ALKBH1-BGKcLV23-14_GATTCTGC+CTCTCGTC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25318
ALKBH1-BGKcLV23-14_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	517					GRCh38	V40	ALKBH1-BGKcLV23-14/Aligned.sortedByCoord.out.bam		ENCORE2	26122
ALKBH1-BGKcLV23-14_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	517					GRCh38	V40	ALKBH1-BGKcLV23-14/Aligned.sortedByCoord.out.bam		ENCORE2	26156
ALKBH1-BGKcLV23-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	517					GRCh38	V40	ALKBH1-BGKcLV23-14/Aligned.sortedByCoord.out.bam		ENCORE2	26190
ALKBH1-BGKcLV23-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	517					GRCh38	V40	ALKBH1-BGKcLV23-14/Aligned.sortedByCoord.out.bam		ENCORE2	26224