ADAT3 RNA-Seq in K562

General Information


RBP	ADAT3
Cell_Line	K562
Method	CRISPR
Exp_Name	ADAT3-BGKcLV23-K562
ENCODE_series_ID	ENCSR316JAN
Batch_ID	BGKcLV23
Pool ID	Pool-201204
Local_Set_Name	set46_K
ENCODE_KD_Exp_ID	ENCSR994EWL
ENCODE_CN_Exp_ID	ENCSR877JEM
Rep1	ADAT3-BGKcLV23-7
Rep2	ADAT3-BGKcLV23-8
CN1	NT-BGKcLV23-1
CN2	NT-BGKcLV23-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	73.0
Rep2_WB	73.6
Antibody Cat#	PA5-63626
Antibody Lot#	LOT# UK2881676B
Antibody DCC ID	ENCAB860NAK
Status	Released
Project	ENCODE4
ID	21

Experiment Information (Status: Released)

	BGKcLV23-7	BGKcLV23-8
idx	793	794
TRCN#_or_BGC#	BGC#0000561	BGC#0000561
shRNA_or_gRNA_sequence	CCGCTTCCAGGTGTTCCGCG	CCGCTTCCAGGTGTTCCGCG
PAM	GGG	GGG
Name	ADAT3_94	ADAT3_94
Sample_ID	BGKcLV23-7	BGKcLV23-8
transduction_Date	9/17/20	9/17/20
days	Day 6	Day 6
RBP_name	ADAT3	ADAT3
qPCR_result	xx	xx
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3021	3030
WB_result	73.0	73.6
Ave_WB	73.3
WB_DONE_date	10/2/20
MW	38KD
IP	Rabbit / I
antibody_Cat#	PA5-63626	LOT# UK2881676B
Antibody DCC ID	ENCAB860NAK
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	4913	4914

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ADAT3	Product_ID: PA5-63626 Lot_ID: UK2881676B Source: Thermo Fisher Target Name: ADAT3-human

Experiment Status

	BGKcLV23-7	BGKcLV23-8
Sample_ID	BGKcLV23-7	BGKcLV23-8
Sample Name
Sample Name	ADAT3-BGKcLV23-7	ADAT3-BGKcLV23-8
RBP	ADAT3	ADAT3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7431	7432

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV23-7	BGKcLV23-8
Sample #	33	34
Sample Name	ADAT3-BGKcLV23-7	ADAT3-BGKcLV23-8
Sample_Name_Alias
Index Well Position	A05	B05
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	295	296
Peak_Molarity	130.00	107.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/A5.png	DNA_Library_set46/set1/B5.png
RIN	8.6	8.9
libSample_RNA_Well	RNA_Library_set46/set2/A9.png	RNA_Library_set46/set2/B9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGKcLV23-7	BGKcLV23-8
RBP	ADAT3	ADAT3
Batch_ID	BGKcLV23	BGKcLV23
WB_result	73.000	73.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1408	1409

Sequencing Information

	BGKcLV23-7	BGKcLV23-8
Sample_ID	BGKcLV23-7	BGKcLV23-8
Sample Name	ADAT3-BGKcLV23-7	ADAT3-BGKcLV23-8
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_K	set46_K
total_reads	222,790,706	145,666,672
total_aligned_reads	196,230,976	135,076,354
unique_aligned_reads	178,142,902	122,756,958
percent_uniqueAligned	0.79960	0.84273
correlation_replicates	0.997287	0.997287
spikein_reads	185,246	87,662
percent_spikeins	0.00083	0.00060
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	514	515

Data Submission Information

	BGKcLV23-7	BGKcLV23-7	BGKcLV23-7	BGKcLV23-7	BGKcLV23-7	BGKcLV23-7	BGKcLV23-8	BGKcLV23-8	BGKcLV23-8	BGKcLV23-8
ENCODE_alias	brenton-graveley:ADAT3-BGKcLV23	brenton-graveley:ADAT3-BGKcLV23-7	brenton-graveley:L-ADAT3-BGKcLV23-7	brenton-graveley:ADAT3-BGKcLV23-7_TACCGAGG+AGTTCAGG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ADAT3-BGKcLV23-7_TACCGAGG+AGTTCAGG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ADAT3-BGKcLV23-K562	brenton-graveley:ADAT3-BGKcLV23-8	brenton-graveley:L-ADAT3-BGKcLV23-8	brenton-graveley:ADAT3-BGKcLV23-8_CGTTAGAA+GACCTGAA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ADAT3-BGKcLV23-8_CGTTAGAA+GACCTGAA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR994EWL	ENCBS796WSR	ENCLB185WYY	ENCFF527BFA	ENCFF133TKP	ENCSR316JAN	ENCBS546JGY	ENCLB299TPF	ENCFF992RHT	ENCFF955JHG
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	BGKcLV23-7	BGKcLV23-7	BGKcLV23-7	BGKcLV23-7	BGKcLV23-7	BGKcLV23-7	BGKcLV23-8	BGKcLV23-8	BGKcLV23-8	BGKcLV23-8
Sample Name	ADAT3-BGKcLV23-7	ADAT3-BGKcLV23-7	ADAT3-BGKcLV23-7	ADAT3-BGKcLV23-7	ADAT3-BGKcLV23-7	ADAT3-BGKcLV23-7	ADAT3-BGKcLV23-8	ADAT3-BGKcLV23-8	ADAT3-BGKcLV23-8	ADAT3-BGKcLV23-8
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Submitted	Released	Released	Released	Released	Submitted	Released	Released	Released
Status_Date	2021-06-02	2022-02-04	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2022-02-04	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		ADAT3-BGKcLV23-7.pdf	L-ADAT3-BGKcLV23-7.pdf				ADAT3-BGKcLV23-8.pdf	L-ADAT3-BGKcLV23-8.pdf
ID	2411	2459	2523	2617	2651	7068	2460	2524	2618	2652

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
ADAT3-BGKcLV23-7_TACCGAGG+AGTTCAGG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	514	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	1378
ADAT3-BGKcLV23-7_TACCGAGG+AGTTCAGG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	514	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	1442
ADAT3-BGKcLV23-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	514					GRCh38	V40	ADAT3-BGKcLV23-7_TACCGAGG+AGTTCAGG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,ADAT3-BGKcLV23-7_TACCGAGG+AGTTCAGG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25281
ADAT3-BGKcLV23-7_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	514					GRCh38	V40	ADAT3-BGKcLV23-7_TACCGAGG+AGTTCAGG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,ADAT3-BGKcLV23-7_TACCGAGG+AGTTCAGG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25315
ADAT3-BGKcLV23-7_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	514					GRCh38	V40	ADAT3-BGKcLV23-7/Aligned.sortedByCoord.out.bam		ENCORE2	26119
ADAT3-BGKcLV23-7_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	514					GRCh38	V40	ADAT3-BGKcLV23-7/Aligned.sortedByCoord.out.bam		ENCORE2	26153
ADAT3-BGKcLV23-7_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	514					GRCh38	V40	ADAT3-BGKcLV23-7/Aligned.sortedByCoord.out.bam		ENCORE2	26187
ADAT3-BGKcLV23-7_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	514					GRCh38	V40	ADAT3-BGKcLV23-7/Aligned.sortedByCoord.out.bam		ENCORE2	26221
ADAT3-BGKcLV23-8_CGTTAGAA+GACCTGAA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	515	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	1379
ADAT3-BGKcLV23-8_CGTTAGAA+GACCTGAA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	515	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	1443
ADAT3-BGKcLV23-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	515					GRCh38	V40	ADAT3-BGKcLV23-8_CGTTAGAA+GACCTGAA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,ADAT3-BGKcLV23-8_CGTTAGAA+GACCTGAA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25282
ADAT3-BGKcLV23-8_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	515					GRCh38	V40	ADAT3-BGKcLV23-8_CGTTAGAA+GACCTGAA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,ADAT3-BGKcLV23-8_CGTTAGAA+GACCTGAA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25316
ADAT3-BGKcLV23-8_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	515					GRCh38	V40	ADAT3-BGKcLV23-8/Aligned.sortedByCoord.out.bam		ENCORE2	26120
ADAT3-BGKcLV23-8_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	515					GRCh38	V40	ADAT3-BGKcLV23-8/Aligned.sortedByCoord.out.bam		ENCORE2	26154
ADAT3-BGKcLV23-8_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	515					GRCh38	V40	ADAT3-BGKcLV23-8/Aligned.sortedByCoord.out.bam		ENCORE2	26188
ADAT3-BGKcLV23-8_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	515					GRCh38	V40	ADAT3-BGKcLV23-8/Aligned.sortedByCoord.out.bam		ENCORE2	26222