ADAT1 RNA-Seq in HepG2

General Information


RBP	ADAT1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ADAT1-BGHcLV25-HepG2
ENCODE_series_ID	ENCSR440OKZ
Batch_ID	BGHcLV25
Pool ID	Pool-210622
Local_Set_Name	set47
ENCODE_KD_Exp_ID	ENCSR051LWN
ENCODE_CN_Exp_ID	ENCSR953VMB
Rep1	ADAT1-BGHcLV25-11
Rep2	ADAT1-BGHcLV25-12
CN1	NT-BGHcLV25-1
CN2	NT-BGHcLV25-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	60.2
Rep2_WB	59.4
Antibody Cat#	PA5-98841
Antibody Lot#	UK2881574
Antibody DCC ID	ENCAB109YPJ
Status	Released
Project	ENCODE4
ID	14

Experiment Information (Status: Released)

	BGHcLV25-11	BGHcLV25-12
idx	718	719
TRCN#_or_BGC#	BGC#0000590	BGC#0000590
shRNA_or_gRNA_sequence	GGAACGTCCTCGGATGCCAA	GGAACGTCCTCGGATGCCAA
PAM	GGG	GGG
Name	ADAT1_91	ADAT1_91
Sample_ID	BGHcLV25-11	BGHcLV25-12
transduction_Date	2/18/21	2/18/21
days	D6	D6
RBP_name	ADAT1	ADAT1
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4154	4711
WB_result	60.2	59.4
Ave_WB	59.8
WB_DONE_date	2/26/21	JESS
MW	56kd
IP	Rabbit / I
antibody_Cat#	PA5-98841	UK2881574
Antibody DCC ID	ENCAB109YPJ
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/16/21	06/16/21
repeat_library
Note
ID	6873	6874

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

	BGHcLV25-11	BGHcLV25-12
Sample_ID	BGHcLV25-11	BGHcLV25-12
Sample Name
Sample Name	ADAT1-BGHcLV25-11	ADAT1-BGHcLV25-12
RBP	ADAT1	ADAT1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4
Note
ID	7833	7834

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV25-11	BGHcLV25-12
Sample #	31	32
Sample Name	ADAT1-BGHcLV25-11	ADAT1-BGHcLV25-12
Sample_Name_Alias
Index Well Position	G10	H10
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	301	296
Peak_Molarity	60.00	69.10
libSampleQC_DNA_Well	DNA_Library_set47/set1/G7.png	DNA_Library_set47/set1/H7.png
RIN	9.9	9.6
libSample_RNA_Well	RNA_Library_set47/set1/G4.png	RNA_Library_set47/set1/H4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-06-22	2021-06-22
Sample_ID	BGHcLV25-11	BGHcLV25-12
RBP	ADAT1	ADAT1
Batch_ID	BGHcLV25	BGHcLV25
WB_result	60.200	59.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1494	1495

Sequencing Information

	BGHcLV25-11	BGHcLV25-12
Sample_ID	BGHcLV25-11	BGHcLV25-12
Sample Name	ADAT1-BGHcLV25-11	ADAT1-BGHcLV25-12
Pool ID	Pool-210622	Pool-210622
LocalServer_folder	set47	set47
total_reads	143,137,756	129,995,430
total_aligned_reads	132,996,076	121,040,720
unique_aligned_reads	125,420,390	113,999,800
percent_uniqueAligned	0.87622	0.87695
correlation_replicates	0.997338	0.997338
spikein_reads	38,370	35,914
percent_spikeins	0.00027	0.00028
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	576	577

Data Submission Information

	BGHcLV25-11	BGHcLV25-11	BGHcLV25-11	BGHcLV25-11	BGHcLV25-11	BGHcLV25-11	BGHcLV25-12	BGHcLV25-12	BGHcLV25-12	BGHcLV25-12
ENCODE_alias	brenton-graveley:ADAT1-BGHcLV25	brenton-graveley:ADAT1-BGHcLV25-11	brenton-graveley:L-ADAT1-BGHcLV25-11	brenton-graveley:ADAT1-BGHcLV25-11_S91_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ADAT1-BGHcLV25-11_S91_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ADAT1-BGHcLV25-HepG2	brenton-graveley:ADAT1-BGHcLV25-12	brenton-graveley:L-ADAT1-BGHcLV25-12	brenton-graveley:ADAT1-BGHcLV25-12_S92_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ADAT1-BGHcLV25-12_S92_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR051LWN	ENCBS413SQG	ENCLB064OBF	ENCFF097BSM	ENCFF401ZPH	ENCSR440OKZ	ENCBS298SZT	ENCLB570QZE	ENCFF582GGC	ENCFF698YWW
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	BGHcLV25-11	BGHcLV25-11	BGHcLV25-11	BGHcLV25-11	BGHcLV25-11	BGHcLV25-11	BGHcLV25-12	BGHcLV25-12	BGHcLV25-12	BGHcLV25-12
Sample Name	ADAT1-BGHcLV25-11	ADAT1-BGHcLV25-11	ADAT1-BGHcLV25-11	ADAT1-BGHcLV25-11	ADAT1-BGHcLV25-11	ADAT1-BGHcLV25-11	ADAT1-BGHcLV25-12	ADAT1-BGHcLV25-12	ADAT1-BGHcLV25-12	ADAT1-BGHcLV25-12
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Submitted	Released	Released	Released	Released	Submitted	Released	Released	Released
Status_Date	2021-11-04	2022-02-04	2021-11-04	2021-11-04	2021-11-04	2022-03-02	2022-02-04	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		ADAT1-BGHcLV25-11.pdf	L-ADAT1-BGHcLV25-11.pdf				ADAT1-BGHcLV25-12.pdf	L-ADAT1-BGHcLV25-12.pdf
ID	3250	3287	3331	3375	3419	7065	3288	3332	3376	3420

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-BGHcLV25-11_S91_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	576	NovaSeq6000	100	paired-ended	1				NT-BGHcLV25-1_S85_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV25-2_S86_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3694
ADAT1-BGHcLV25-11_S91_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	576	NovaSeq6000	100	paired-ended	2				NT-BGHcLV25-1_S85_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV25-2_S86_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3740
ADAT1-BGHcLV25-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	576					GRCh38	V40	ADAT1-BGHcLV25-11_S91_L002_R1_001.filtered.trimmed.paired.fastq.gz,ADAT1-BGHcLV25-11_S91_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25383
ADAT1-BGHcLV25-11_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	576					GRCh38	V40	ADAT1-BGHcLV25-11_S91_L002_R1_001.filtered.trimmed.paired.fastq.gz,ADAT1-BGHcLV25-11_S91_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25427
ADAT1-BGHcLV25-11_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	576					GRCh38	V40	ADAT1-BGHcLV25-11/Aligned.sortedByCoord.out.bam		ENCORE2	26259
ADAT1-BGHcLV25-11_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	576					GRCh38	V40	ADAT1-BGHcLV25-11/Aligned.sortedByCoord.out.bam		ENCORE2	26303
ADAT1-BGHcLV25-11_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	576					GRCh38	V40	ADAT1-BGHcLV25-11/Aligned.sortedByCoord.out.bam		ENCORE2	26347
ADAT1-BGHcLV25-11_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	576					GRCh38	V40	ADAT1-BGHcLV25-11/Aligned.sortedByCoord.out.bam		ENCORE2	26391
ADAT1-BGHcLV25-12_S92_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	577	NovaSeq6000	100	paired-ended	1				NT-BGHcLV25-1_S85_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV25-2_S86_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3695
ADAT1-BGHcLV25-12_S92_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	577	NovaSeq6000	100	paired-ended	2				NT-BGHcLV25-1_S85_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV25-2_S86_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3741
ADAT1-BGHcLV25-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	577					GRCh38	V40	ADAT1-BGHcLV25-12_S92_L002_R1_001.filtered.trimmed.paired.fastq.gz,ADAT1-BGHcLV25-12_S92_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25384
ADAT1-BGHcLV25-12_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	577					GRCh38	V40	ADAT1-BGHcLV25-12_S92_L002_R1_001.filtered.trimmed.paired.fastq.gz,ADAT1-BGHcLV25-12_S92_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25428
ADAT1-BGHcLV25-12_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	577					GRCh38	V40	ADAT1-BGHcLV25-12/Aligned.sortedByCoord.out.bam		ENCORE2	26260
ADAT1-BGHcLV25-12_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	577					GRCh38	V40	ADAT1-BGHcLV25-12/Aligned.sortedByCoord.out.bam		ENCORE2	26304
ADAT1-BGHcLV25-12_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	577					GRCh38	V40	ADAT1-BGHcLV25-12/Aligned.sortedByCoord.out.bam		ENCORE2	26348
ADAT1-BGHcLV25-12_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	577					GRCh38	V40	ADAT1-BGHcLV25-12/Aligned.sortedByCoord.out.bam		ENCORE2	26392