ADAT3 RNA-Seq in HepG2

General Information


RBP	ADAT3
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ADAT3-BGHcLV24-HepG2
ENCODE_series_ID	ENCSR713HFD
Batch_ID	BGHcLV24
Pool ID	Pool-210622
Local_Set_Name	set47
ENCODE_KD_Exp_ID	ENCSR840HSL
ENCODE_CN_Exp_ID	ENCSR671FDZ
Rep1	ADAT3-BGHcLV24-7
Rep2	ADAT3-BGHcLV24-8
CN1	NT-BGHcLV24-1
CN2	NT-BGHcLV24-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	72.7
Rep2_WB	80.0
Antibody Cat#	PA5-63626
Antibody Lot#	LOT# UK2881676B
Antibody DCC ID	ENCAB860NAK
Status	Released
Project	ENCODE4
ID	1

Experiment Information (Status: Released)

	BGHcLV24-7	BGHcLV24-8
idx	665	666
TRCN#_or_BGC#	BGC#0000561	BGC#0000561
shRNA_or_gRNA_sequence	CCGCTTCCAGGTGTTCCGCG	CCGCTTCCAGGTGTTCCGCG
PAM	GGG	GGG
Name	ADAT3_94	ADAT3_94
Sample_ID	BGHcLV24-7	BGHcLV24-8
transduction_Date	10/30/20	10/30/20
days	D6	D6
RBP_name	ADAT3	ADAT3
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	5934	6158
WB_result	72.7	80.0
Ave_WB	76.3
WB_DONE_date	11/18/20
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	06/16/21	06/16/21
repeat_library
Note
ID	6820	6821

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

	BGHcLV24-7	BGHcLV24-8
Sample_ID	BGHcLV24-7	BGHcLV24-8
Sample Name
Sample Name	ADAT3-BGHcLV24-7	ADAT3-BGHcLV24-8
RBP	ADAT3	ADAT3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4
Note
ID	7781	7782

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV24-7	BGHcLV24-8
Sample #	3	4
Sample Name	ADAT3-BGHcLV24-7	ADAT3-BGHcLV24-8
Sample_Name_Alias
Index Well Position	C07	D07
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	307
Peak_Molarity	98.70	91.50
libSampleQC_DNA_Well	DNA_Library_set47/set1/C4.png	DNA_Library_set47/set1/D4.png
RIN	9.6	9.8
libSample_RNA_Well	RNA_Library_set47/set1/C1.png	RNA_Library_set47/set1/D1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-06-22	2021-06-22
Sample_ID	BGHcLV24-7	BGHcLV24-8
RBP	ADAT3	ADAT3
Batch_ID	BGHcLV24	BGHcLV24
WB_result	72.700	80.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1466	1467

Sequencing Information

	BGHcLV24-7	BGHcLV24-8
Sample_ID	BGHcLV24-7	BGHcLV24-8
Sample Name	ADAT3-BGHcLV24-7	ADAT3-BGHcLV24-8
Pool ID	Pool-210622	Pool-210622
LocalServer_folder	set47	set47
total_reads	104,792,880	125,049,194
total_aligned_reads	93,894,360	113,716,328
unique_aligned_reads	88,481,266	107,206,470
percent_uniqueAligned	0.84434	0.85731
correlation_replicates	0.996507	0.996507
spikein_reads	65,568	44,170
percent_spikeins	0.00063	0.00035
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	548	549

Data Submission Information

	BGHcLV24-7	BGHcLV24-7	BGHcLV24-7	BGHcLV24-7	BGHcLV24-7	BGHcLV24-7	BGHcLV24-8	BGHcLV24-8	BGHcLV24-8	BGHcLV24-8
ENCODE_alias	brenton-graveley:ADAT3-BGHcLV24	brenton-graveley:ADAT3-BGHcLV24-7	brenton-graveley:L-ADAT3-BGHcLV24-7	brenton-graveley:ADAT3-BGHcLV24-7_S63_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ADAT3-BGHcLV24-7_S63_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ADAT3-BGHcLV24-HepG2	brenton-graveley:ADAT3-BGHcLV24-8	brenton-graveley:L-ADAT3-BGHcLV24-8	brenton-graveley:ADAT3-BGHcLV24-8_S64_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ADAT3-BGHcLV24-8_S64_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR840HSL	ENCBS373KON	ENCLB805PEV	ENCFF314LKZ	ENCFF739ULD	ENCSR713HFD	ENCBS504GSS	ENCLB758XGZ	ENCFF782WQY	ENCFF229RRD
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	BGHcLV24-7	BGHcLV24-7	BGHcLV24-7	BGHcLV24-7	BGHcLV24-7	BGHcLV24-7	BGHcLV24-8	BGHcLV24-8	BGHcLV24-8	BGHcLV24-8
Sample Name	ADAT3-BGHcLV24-7	ADAT3-BGHcLV24-7	ADAT3-BGHcLV24-7	ADAT3-BGHcLV24-7	ADAT3-BGHcLV24-7	ADAT3-BGHcLV24-7	ADAT3-BGHcLV24-8	ADAT3-BGHcLV24-8	ADAT3-BGHcLV24-8	ADAT3-BGHcLV24-8
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Submitted	Released	Released	Released	Released	Submitted	Released	Released	Released
Status_Date	2021-11-04	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		ADAT3-BGHcLV24-7.pdf	L-ADAT3-BGHcLV24-7.pdf				ADAT3-BGHcLV24-8.pdf	L-ADAT3-BGHcLV24-8.pdf
ID	3236	3259	3303	3347	3391	7067	3260	3304	3348	3392

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-BGHcLV24-7_S63_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	548	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	3696
ADAT3-BGHcLV24-7_S63_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	548	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	3742
ADAT3-BGHcLV24-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	548					GRCh38	V40	ADAT3-BGHcLV24-7_S63_L002_R1_001.filtered.trimmed.paired.fastq.gz,ADAT3-BGHcLV24-7_S63_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25385
ADAT3-BGHcLV24-7_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	548					GRCh38	V40	ADAT3-BGHcLV24-7_S63_L002_R1_001.filtered.trimmed.paired.fastq.gz,ADAT3-BGHcLV24-7_S63_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25429
ADAT3-BGHcLV24-7_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	548					GRCh38	V40	ADAT3-BGHcLV24-7/Aligned.sortedByCoord.out.bam		ENCORE2	26261
ADAT3-BGHcLV24-7_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	548					GRCh38	V40	ADAT3-BGHcLV24-7/Aligned.sortedByCoord.out.bam		ENCORE2	26305
ADAT3-BGHcLV24-7_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	548					GRCh38	V40	ADAT3-BGHcLV24-7/Aligned.sortedByCoord.out.bam		ENCORE2	26349
ADAT3-BGHcLV24-7_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	548					GRCh38	V40	ADAT3-BGHcLV24-7/Aligned.sortedByCoord.out.bam		ENCORE2	26393
ADAT3-BGHcLV24-8_S64_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	549	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	3697
ADAT3-BGHcLV24-8_S64_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	549	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	3743
ADAT3-BGHcLV24-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	549					GRCh38	V40	ADAT3-BGHcLV24-8_S64_L002_R1_001.filtered.trimmed.paired.fastq.gz,ADAT3-BGHcLV24-8_S64_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25386
ADAT3-BGHcLV24-8_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	549					GRCh38	V40	ADAT3-BGHcLV24-8_S64_L002_R1_001.filtered.trimmed.paired.fastq.gz,ADAT3-BGHcLV24-8_S64_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25430
ADAT3-BGHcLV24-8_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	549					GRCh38	V40	ADAT3-BGHcLV24-8/Aligned.sortedByCoord.out.bam		ENCORE2	26262
ADAT3-BGHcLV24-8_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	549					GRCh38	V40	ADAT3-BGHcLV24-8/Aligned.sortedByCoord.out.bam		ENCORE2	26306
ADAT3-BGHcLV24-8_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	549					GRCh38	V40	ADAT3-BGHcLV24-8/Aligned.sortedByCoord.out.bam		ENCORE2	26350
ADAT3-BGHcLV24-8_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	549					GRCh38	V40	ADAT3-BGHcLV24-8/Aligned.sortedByCoord.out.bam		ENCORE2	26394