THOC1 RNA-Seq in HepG2

General Information


RBP	THOC1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	THOC1-BGHcLV16-HepG2
ENCODE_series_ID	ENCSR148XKD
Batch_ID	BGHcLV16
Pool ID	Pool-200102
Local_Set_Name	set43_H
ENCODE_KD_Exp_ID	ENCSR636PNL
ENCODE_CN_Exp_ID	ENCSR964HKT
Rep1	THOC1-BGHcLV16-57
Rep2	THOC1-BGHcLV16-58
CN1	NT-BGHcLV16-1
CN2	NT-BGHcLV16-2
Rep1_qPCR	21.6
Rep2_qPCR	49.0
Rep1_WB	76.2
Rep2_WB	80.6
Antibody Cat#	MA1-23261
Antibody Lot#	LOT# UA2692992
Antibody DCC ID	ENCAB917HFY
Status	Released
Project	ENCODE4
ID	158

Experiment Information (Status: Released)

	BGHcLV16-57	BGHcLV16-58
idx	487	488
TRCN#_or_BGC#	BGC#0000372	BGC#0000372
shRNA_or_gRNA_sequence	TCTTCAGTTTGCCCGAAGCG	TCTTCAGTTTGCCCGAAGCG
PAM	CGG	CGG
Name	THOC1-95	THOC1-95
Sample_ID	BGHcLV16-57	BGHcLV16-58
transduction_Date	4/16/19	4/16/19
days	D6	D6
RBP_name	THOC1	THOC1
qPCR_result	21.6	49.0
Ave_qPCR	35.3
RT-qPCR_primer-F	TCTTTTTGGCCAGGCTTTTC
RT-qPCR_primer-R	AGGGTGCTTTCCTGCTCATT
protein_conc	4947	4958
WB_result	76.2	80.6
Ave_WB	78.4
WB_DONE_date	4/25/19	WES
MW	84KD
IP	Mouse / Ig
antibody_Cat#	MA1-23261	LOT# UA2692992
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	26	0
Rep2_TPM	48	0
Action	Ready	Ready
Library_start_date	12/03/19	12/03/19
repeat_library
Note
ID	6638	6639

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
THOC1	Product_ID: MA1-23261 Lot_ID: UA2692992 Source: Thermo Fisher Target Name: THOC1-human

Experiment Status

	BGHcLV16-57	BGHcLV16-58
Sample_ID	BGHcLV16-57	BGHcLV16-58
Sample Name
Sample Name	THOC1-BGHcLV16-57	THOC1-BGHcLV16-58
RBP	THOC1	THOC1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5435	5436

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV16-57	BGHcLV16-58
Sample #	69	70
Sample Name	THOC1-BGHcLV16-57	THOC1-BGHcLV16-58
Sample_Name_Alias
Index Well Position	A09	B09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-31	2020-08-31
Lib_ID	Lib-200831	Lib-200831
Tecan_Location	2-C2	2-D2
Tecan	32.50	36.97
Tecan_date	2019-12-10	2019-12-10
Size_bp	291	289
Peak_Molarity	27.90	66.40
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/C4.png	DNA_Library_set43-44/set2/D4.png
RIN	9.4	9.6
libSample_RNA_Well	RNA_Library_set43-44/set1/C9.png	RNA_Library_set43-44/set1/D9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV16-57	BGHcLV16-58
RBP	THOC1	THOC1
Batch_ID	BGHcLV16	BGHcLV16
WB_result	76.200	80.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	645	646

Sequencing Information

	BGHcLV16-57	BGHcLV16-58
Sample_ID	BGHcLV16-57	BGHcLV16-58
Sample Name	THOC1-BGHcLV16-57	THOC1-BGHcLV16-58
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_H	set43_H
total_reads	133,281,150	298,382,948
total_aligned_reads	127,591,172	268,686,052
unique_aligned_reads	119,849,612	251,613,702
percent_uniqueAligned	0.89922	0.84326
correlation_replicates	0.964678	0.964678
spikein_reads	192,788	305,090
percent_spikeins	0.00145	0.00102
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	147	148

Data Submission Information

	BGHcLV16-57	BGHcLV16-57	BGHcLV16-57	BGHcLV16-57	BGHcLV16-57	BGHcLV16-57	BGHcLV16-58	BGHcLV16-58	BGHcLV16-58	BGHcLV16-58
ENCODE_alias	brenton-graveley:THOC1-BGHcLV16	brenton-graveley:THOC1-BGHcLV16-57	brenton-graveley:L-THOC1-BGHcLV16-57	brenton-graveley:THOC1-BGHcLV16-57_S65_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:THOC1-BGHcLV16-57_S65_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:THOC1-BGHcLV16-HepG2	brenton-graveley:THOC1-BGHcLV16-58	brenton-graveley:L-THOC1-BGHcLV16-58	brenton-graveley:THOC1-BGHcLV16-58_S66_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:THOC1-BGHcLV16-58_S66_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR636PNL	ENCBS666ZDP	ENCLB504VAA	ENCFF010XDI	ENCFF183XAT	ENCSR148XKD	ENCBS730TVL	ENCLB384ZKO	ENCFF615OEL	ENCFF696CXJ
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	BGHcLV16-57	BGHcLV16-57	BGHcLV16-57	BGHcLV16-57	BGHcLV16-57	BGHcLV16-57	BGHcLV16-58	BGHcLV16-58	BGHcLV16-58	BGHcLV16-58
Sample Name	THOC1-BGHcLV16-57	THOC1-BGHcLV16-57	THOC1-BGHcLV16-57	THOC1-BGHcLV16-57	THOC1-BGHcLV16-57	THOC1-BGHcLV16-57	THOC1-BGHcLV16-58	THOC1-BGHcLV16-58	THOC1-BGHcLV16-58	THOC1-BGHcLV16-58
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43H_biosample_protocol	LV43H_library_protocol				LV43H_biosample_protocol	LV43H_library_protocol
protocol_URL		THOC1-BGHcLV16-57.pdf	L-THOC1-BGHcLV16-57.pdf				THOC1-BGHcLV16-58.pdf	L-THOC1-BGHcLV16-58.pdf
ID	14	110	274	440	472	7345	111	275	441	473

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
THOC1-BGHcLV16-57_S65_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	147	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	27
THOC1-BGHcLV16-57_S65_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	147	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	59
THOC1-BGHcLV16-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	147					GRCh38	V40	THOC1-BGHcLV16-57_S65_R1_001.filtered.trimmed.paired.fastq.gz,THOC1-BGHcLV16-57_S65_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24190
THOC1-BGHcLV16-57_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	147					GRCh38	V40	THOC1-BGHcLV16-57/Aligned.sortedByCoord.out.bam		ENCORE2	24222
THOC1-BGHcLV16-57_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	147					GRCh38	V40	THOC1-BGHcLV16-57/Aligned.sortedByCoord.out.bam		ENCORE2	24254
THOC1-BGHcLV16-57_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	147					GRCh38	V40	THOC1-BGHcLV16-57/Aligned.sortedByCoord.out.bam		ENCORE2	24286
THOC1-BGHcLV16-57_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	147					GRCh38	V40	THOC1-BGHcLV16-57/Aligned.sortedByCoord.out.bam		ENCORE2	24318
THOC1-BGHcLV16-57_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	147					GRCh38	V40	THOC1-BGHcLV16-57_S65_R1_001.filtered.trimmed.paired.fastq.gz,THOC1-BGHcLV16-57_S65_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24350
THOC1-BGHcLV16-58_S66_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	148	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	28
THOC1-BGHcLV16-58_S66_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	148	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	60
THOC1-BGHcLV16-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	148					GRCh38	V40	THOC1-BGHcLV16-58_S66_R1_001.filtered.trimmed.paired.fastq.gz,THOC1-BGHcLV16-58_S66_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24191
THOC1-BGHcLV16-58_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	148					GRCh38	V40	THOC1-BGHcLV16-58/Aligned.sortedByCoord.out.bam		ENCORE2	24223
THOC1-BGHcLV16-58_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	148					GRCh38	V40	THOC1-BGHcLV16-58/Aligned.sortedByCoord.out.bam		ENCORE2	24255
THOC1-BGHcLV16-58_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	148					GRCh38	V40	THOC1-BGHcLV16-58/Aligned.sortedByCoord.out.bam		ENCORE2	24287
THOC1-BGHcLV16-58_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	148					GRCh38	V40	THOC1-BGHcLV16-58/Aligned.sortedByCoord.out.bam		ENCORE2	24319
THOC1-BGHcLV16-58_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	148					GRCh38	V40	THOC1-BGHcLV16-58_S66_R1_001.filtered.trimmed.paired.fastq.gz,THOC1-BGHcLV16-58_S66_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24351