THOC1 RNA-Seq in K562

General Information


RBP	THOC1
Cell_Line	K562
Method	CRISPR
Exp_Name	THOC1-BGKcLV15-K562
ENCODE_series_ID	ENCSR155UKL
Batch_ID	BGKcLV15
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR921RQX
ENCODE_CN_Exp_ID	ENCSR404OHQ
Rep1	THOC1-BGKcLV15-59
Rep2	THOC1-BGKcLV15-60
CN1	NT-BGKcLV15-1
CN2	NT-BGKcLV15-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	93.4
Rep2_WB	90.4
Antibody Cat#	MA1-23261
Antibody Lot#	LOT# UA2692992
Antibody DCC ID	ENCAB917HFY
Status	Released
Project	ENCODE4
ID	137

Experiment Information (Status: Released)

	BGKcLV15-59	BGKcLV15-60
idx	601	602
TRCN#_or_BGC#	BGC#0000372	BGC#0000372
shRNA_or_gRNA_sequence	TCTTCAGTTTGCCCGAAGCG	TCTTCAGTTTGCCCGAAGCG
PAM	CGG	CGG
Name	THOC1-95	THOC1-95
Sample_ID	BGKcLV15-59	BGKcLV15-60
transduction_Date	4/2/19	4/2/19
days	Day 6	Day 6
RBP_name	THOC1	THOC1
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	TCTTTTTGGCCAGGCTTTTC
RT-qPCR_primer-R	AGGGTGCTTTCCTGCTCATT
protein_conc	5291	5174
WB_result	93.4	90.4
Ave_WB	91.9
WB_DONE_date	4/10/19	WES
MW	84KD
IP	Mouse / Ig
antibody_Cat#	MA1-23261	LOT# UA2692992
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	61	0
Rep2_TPM	71.8	0
Action	Ready	Ready
Library_start_date	05/30/19	05/30/19
repeat_library
Note
ID	4713	4714

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

	BGKcLV15-59	BGKcLV15-60
Sample_ID	BGKcLV15-59	BGKcLV15-60
Sample Name
Sample Name	THOC1-BGKcLV15-59	THOC1-BGKcLV15-60
RBP	THOC1	THOC1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5363	5364

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV15-59	BGKcLV15-60
Sample #	33	34
Sample Name	THOC1-BGKcLV15-59	THOC1-BGKcLV15-60
Sample_Name_Alias
Index Well Position	A05	B05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-30	2020-08-30
Lib_ID	Lib-200830	Lib-200830
Tecan_Location	3-A1	3-B1
Tecan	26.87	40.72
Tecan_date	2019-12-10	2019-12-10
Size_bp	263	279
Peak_Molarity	22.80	20.00
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/A5.png	DNA_Library_set43-44/set1/B5.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set43-44/set1/A5.png	RNA_Library_set43-44/set1/B5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV15-59	BGKcLV15-60
RBP	THOC1	THOC1
Batch_ID	BGKcLV15	BGKcLV15
WB_result	93.400	90.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	609	610

Sequencing Information

	BGKcLV15-59	BGKcLV15-60
Sample_ID	BGKcLV15-59	BGKcLV15-60
Sample Name	THOC1-BGKcLV15-59	THOC1-BGKcLV15-60
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	102,437,874	96,254,452
total_aligned_reads	100,752,162	86,199,662
unique_aligned_reads	91,896,864	78,760,772
percent_uniqueAligned	0.89710	0.81826
correlation_replicates	0.992254	0.992254
spikein_reads	74,166	49,396
percent_spikeins	0.00072	0.00051
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	115	116

Data Submission Information

	BGKcLV15-59	BGKcLV15-59	BGKcLV15-59	BGKcLV15-59	BGKcLV15-59	BGKcLV15-59	BGKcLV15-60	BGKcLV15-60	BGKcLV15-60	BGKcLV15-60
ENCODE_alias	brenton-graveley:THOC1-BGKcLV15	brenton-graveley:THOC1-BGKcLV15-59	brenton-graveley:L-THOC1-BGKcLV15-59	brenton-graveley:THOC1-BGKcLV15-59_S33_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:THOC1-BGKcLV15-59_S33_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:THOC1-BGKcLV15-K562	brenton-graveley:THOC1-BGKcLV15-60	brenton-graveley:L-THOC1-BGKcLV15-60	brenton-graveley:THOC1-BGKcLV15-60_S34_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:THOC1-BGKcLV15-60_S34_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR921RQX	ENCBS139TLH	ENCLB762LGN	ENCFF242STF	ENCFF599IHB	ENCSR155UKL	ENCBS629HFX	ENCLB436EBP	ENCFF076CXW	ENCFF541BOV
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	BGKcLV15-59	BGKcLV15-59	BGKcLV15-59	BGKcLV15-59	BGKcLV15-59	BGKcLV15-59	BGKcLV15-60	BGKcLV15-60	BGKcLV15-60	BGKcLV15-60
Sample Name	THOC1-BGKcLV15-59	THOC1-BGKcLV15-59	THOC1-BGKcLV15-59	THOC1-BGKcLV15-59	THOC1-BGKcLV15-59	THOC1-BGKcLV15-59	THOC1-BGKcLV15-60	THOC1-BGKcLV15-60	THOC1-BGKcLV15-60	THOC1-BGKcLV15-60
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43K_biosample_protocol	LV43K_library_protocol				LV43K_biosample_protocol	LV43K_library_protocol
protocol_URL		THOC1-BGKcLV15-59.pdf	L-THOC1-BGKcLV15-59.pdf				THOC1-BGKcLV15-60.pdf	L-THOC1-BGKcLV15-60.pdf
ID	33	148	312	510	562	7346	149	313	511	563

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-BGKcLV15-59_S33_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	115	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	111
THOC1-BGKcLV15-59_S33_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	115	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	163
THOC1-BGKcLV15-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	115					GRCh38	V40	THOC1-BGKcLV15-59_S33_R1_001.filtered.trimmed.paired.fastq.gz,THOC1-BGKcLV15-59_S33_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24402
THOC1-BGKcLV15-59_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	115					GRCh38	V40	THOC1-BGKcLV15-59/Aligned.sortedByCoord.out.bam		ENCORE2	24454
THOC1-BGKcLV15-59_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	115					GRCh38	V40	THOC1-BGKcLV15-59/Aligned.sortedByCoord.out.bam		ENCORE2	24506
THOC1-BGKcLV15-59_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	115					GRCh38	V40	THOC1-BGKcLV15-59/Aligned.sortedByCoord.out.bam		ENCORE2	24558
THOC1-BGKcLV15-59_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	115					GRCh38	V40	THOC1-BGKcLV15-59/Aligned.sortedByCoord.out.bam		ENCORE2	24610
THOC1-BGKcLV15-59_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	115					GRCh38	V40	THOC1-BGKcLV15-59_S33_R1_001.filtered.trimmed.paired.fastq.gz,THOC1-BGKcLV15-59_S33_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24662
THOC1-BGKcLV15-60_S34_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	116	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	112
THOC1-BGKcLV15-60_S34_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	116	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	164
THOC1-BGKcLV15-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	116					GRCh38	V40	THOC1-BGKcLV15-60_S34_R1_001.filtered.trimmed.paired.fastq.gz,THOC1-BGKcLV15-60_S34_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24403
THOC1-BGKcLV15-60_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	116					GRCh38	V40	THOC1-BGKcLV15-60/Aligned.sortedByCoord.out.bam		ENCORE2	24455
THOC1-BGKcLV15-60_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	116					GRCh38	V40	THOC1-BGKcLV15-60/Aligned.sortedByCoord.out.bam		ENCORE2	24507
THOC1-BGKcLV15-60_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	116					GRCh38	V40	THOC1-BGKcLV15-60/Aligned.sortedByCoord.out.bam		ENCORE2	24559
THOC1-BGKcLV15-60_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	116					GRCh38	V40	THOC1-BGKcLV15-60/Aligned.sortedByCoord.out.bam		ENCORE2	24611
THOC1-BGKcLV15-60_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	116					GRCh38	V40	THOC1-BGKcLV15-60_S34_R1_001.filtered.trimmed.paired.fastq.gz,THOC1-BGKcLV15-60_S34_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24663