ADAT1 RNA-Seq in K562

General Information


RBP	ADAT1
Cell_Line	K562
Method	CRISPR
Exp_Name	ADAT1-BGKcLV26-K562
ENCODE_series_ID	ENCSR705CDT
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR122RJE
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	ADAT1-BGKcLV26-7
Rep2	ADAT1-BGKcLV26-8
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	70.3
Rep2_WB	74.4
Antibody Cat#	PA5-98841
Antibody Lot#	UK2881574
Antibody DCC ID	ENCAB109YPJ
Status	Released
Project	ENCODE4
ID	784

Experiment Information (Status: Released)

	BGKcLV26-7	BGKcLV26-8
idx	860	861
TRCN#_or_BGC#	BGC#0000590	BGC#0000590
shRNA_or_gRNA_sequence	GGAACGTCCTCGGATGCCAA	GGAACGTCCTCGGATGCCAA
PAM	GGG	GGG
Name	ADAT1_91	ADAT1_91
Sample_ID	BGKcLV26-7	BGKcLV26-8
transduction_Date	3/30/21	3/30/21
days	Day 6	Day 6
RBP_name	ADAT1	ADAT1
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3468	4862
WB_result	70.3	74.4
Ave_WB	72.4
WB_DONE_date	5/7/21	JESS
MW	56kd
IP	Rabbit / I
antibody_Cat#	PA5-98841	UK2881574
Antibody DCC ID	ENCAB109YPJ	10/22/21
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/01/21	09/01/21
repeat_library
Note
ID	4992	4993

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ADAT1	Product_ID: PA5-98841 Lot_ID: UK2881574 Source: Thermo Fisher Target Name: ADAT1-human

Experiment Status

	BGKcLV26-7	BGKcLV26-8
Sample_ID	BGKcLV26-7	BGKcLV26-8
Sample Name
Sample Name	ADAT1-BGKcLV26-7	ADAT1-BGKcLV26-8
RBP	ADAT1	ADAT1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9749	9750

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-7	BGKcLV26-8
Sample #	7	8
Sample Name	ADAT1-BGKcLV26-7	ADAT1-BGKcLV26-8
Sample_Name_Alias
Index Well Position	G01	H01
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	269	269
Peak_Molarity	33.80	24.50
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/G1.png	DNA_Library_set48-49/set1/H1.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set48-49/set1/G1.png	RNA_Library_set48-49/set1/H1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-7	BGKcLV26-8
RBP	ADAT1	ADAT1
Batch_ID	BGKcLV26	BGKcLV26
WB_result	70.300	74.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1566	1567

Sequencing Information

	BGKcLV26-7	BGKcLV26-8
Sample_ID	BGKcLV26-7	BGKcLV26-8
Sample Name	ADAT1-BGKcLV26-7	ADAT1-BGKcLV26-8
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	123,166,468	154,321,344
total_aligned_reads	99,667,304	125,720,426
unique_aligned_reads	90,921,920	114,545,212
percent_uniqueAligned	0.73820	0.74225
correlation_replicates	0.998227	0.998227
spikein_reads	70,410	34,604
percent_spikeins	0.00057	0.00022
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1743	1744

Data Submission Information

	BGKcLV26-7	BGKcLV26-7	BGKcLV26-7	BGKcLV26-7	BGKcLV26-7	BGKcLV26-7	BGKcLV26-8	BGKcLV26-8	BGKcLV26-8	BGKcLV26-8
ENCODE_alias	brenton-graveley:ADAT1-BGKcLV26	brenton-graveley:ADAT1-BGKcLV26-7	brenton-graveley:L-ADAT1-BGKcLV26-7	brenton-graveley:ADAT1-BGKcLV26-7_S13_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ADAT1-BGKcLV26-7_S13_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ADAT1-BGKcLV26-K562	brenton-graveley:ADAT1-BGKcLV26-8	brenton-graveley:L-ADAT1-BGKcLV26-8	brenton-graveley:ADAT1-BGKcLV26-8_S14_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ADAT1-BGKcLV26-8_S14_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR122RJE	ENCBS896MIR	ENCLB081FLD	ENCFF164DCK	ENCFF312YDQ	ENCSR705CDT	ENCBS223VKG	ENCLB324KJP	ENCFF610JIN	ENCFF580SLM
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	BGKcLV26-7	BGKcLV26-7	BGKcLV26-7	BGKcLV26-7	BGKcLV26-7	BGKcLV26-7	BGKcLV26-8	BGKcLV26-8	BGKcLV26-8	BGKcLV26-8
Sample Name	ADAT1-BGKcLV26-7	ADAT1-BGKcLV26-7	ADAT1-BGKcLV26-7	ADAT1-BGKcLV26-7	ADAT1-BGKcLV26-7	ADAT1-BGKcLV26-7	ADAT1-BGKcLV26-8	ADAT1-BGKcLV26-8	ADAT1-BGKcLV26-8	ADAT1-BGKcLV26-8
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		ADAT1-BGKcLV26-7.pdf	L-ADAT1-BGKcLV26-7.pdf				ADAT1-BGKcLV26-8.pdf	L-ADAT1-BGKcLV26-8.pdf
ID	3449	3532	3666	3800	3934	7066	3533	3667	3801	3935

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
ADAT1-BGKcLV26-7_S13_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1743	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	3836
ADAT1-BGKcLV26-7_S13_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1743	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	3886
ADAT1-BGKcLV26-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1743					GRCh38	V40	ADAT1-BGKcLV26-7_S13_L003_R1_001.filtered.trimmed.paired.fastq.gz,ADAT1-BGKcLV26-7_S13_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25523
ADAT1-BGKcLV26-7_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1743					GRCh38	V40	ADAT1-BGKcLV26-7_S13_L003_R1_001.filtered.trimmed.paired.fastq.gz,ADAT1-BGKcLV26-7_S13_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25573
ADAT1-BGKcLV26-7_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	1743					GRCh38	V40	ADAT1-BGKcLV26-7/Aligned.sortedByCoord.out.bam		ENCORE2	26539
ADAT1-BGKcLV26-7_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	1743					GRCh38	V40	ADAT1-BGKcLV26-7/Aligned.sortedByCoord.out.bam		ENCORE2	26589
ADAT1-BGKcLV26-7_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	1743					GRCh38	V40	ADAT1-BGKcLV26-7/Aligned.sortedByCoord.out.bam		ENCORE2	26639
ADAT1-BGKcLV26-7_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	1743					GRCh38	V40	ADAT1-BGKcLV26-7/Aligned.sortedByCoord.out.bam		ENCORE2	26689
ADAT1-BGKcLV26-8_S14_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1744	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	3837
ADAT1-BGKcLV26-8_S14_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1744	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	3887
ADAT1-BGKcLV26-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1744					GRCh38	V40	ADAT1-BGKcLV26-8_S14_L003_R1_001.filtered.trimmed.paired.fastq.gz,ADAT1-BGKcLV26-8_S14_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25524
ADAT1-BGKcLV26-8_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1744					GRCh38	V40	ADAT1-BGKcLV26-8_S14_L003_R1_001.filtered.trimmed.paired.fastq.gz,ADAT1-BGKcLV26-8_S14_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25574
ADAT1-BGKcLV26-8_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	1744					GRCh38	V40	ADAT1-BGKcLV26-8/Aligned.sortedByCoord.out.bam		ENCORE2	26540
ADAT1-BGKcLV26-8_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	1744					GRCh38	V40	ADAT1-BGKcLV26-8/Aligned.sortedByCoord.out.bam		ENCORE2	26590
ADAT1-BGKcLV26-8_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	1744					GRCh38	V40	ADAT1-BGKcLV26-8/Aligned.sortedByCoord.out.bam		ENCORE2	26640
ADAT1-BGKcLV26-8_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	1744					GRCh38	V40	ADAT1-BGKcLV26-8/Aligned.sortedByCoord.out.bam		ENCORE2	26690