YTHDC2 RNA-Seq in HepG2

General Information


RBP	YTHDC2
Cell_Line	HepG2
Method	shRNA
Exp_Name	YTHDC2-BGHLV37-HepG2
ENCODE_series_ID	ENCSR542FEC
Batch_ID	BGHLV37
Pool ID	Pool-180109
Local_Set_Name	set40_H
ENCODE_KD_Exp_ID	ENCSR289HOV
ENCODE_CN_Exp_ID	ENCSR225PRV
Rep1	YTHDC2-BGHLV37-105C
Rep2	YTHDC2-BGHLV37-106C
CN1	non-target-BGHLV37-1C
CN2	non-target-BGHLV37-2C
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	79.6
Rep2_WB	83.7
Antibody Cat#	A303-025A
Antibody Lot#	A303-025A
Antibody DCC ID	ENCAB501IJS
Status	Released
Project	ENCODE4
ID	268

Experiment Information (Status: Released)

	BGHLV37-105	BGHLV37-105	BGHLV37-106	BGHLV37-106
idx	1017	1017	1018	1018
TRCN#_or_BGC#	TRCN0000153934	TRCN0000153934	TRCN0000153934	TRCN0000153934
shRNA_or_gRNA_sequence	CCTTCTACTTTCTCTGGGAAA	CCTTCTACTTTCTCTGGGAAA	CCTTCTACTTTCTCTGGGAAA	CCTTCTACTTTCTCTGGGAAA
PAM
Name	YTHDC2	YTHDC2	YTHDC2	YTHDC2
Sample_ID	BGHLV37-105	BGHLV37-105	BGHLV37-106	BGHLV37-106
transduction_Date	9/1/16	9/1/16	9/1/16	9/1/16
days
RBP_name	YTHDC2	YTHDC2	YTHDC2	YTHDC2
qPCR_result	0.0	0.0	0.0	0.0
Ave_qPCR	0.0	0.0
RT-qPCR_primer-F	TCCATGGAATGACAACAAGAA	TCCATGGAATGACAACAAGAA
RT-qPCR_primer-R	TGGAGCAACTGTTCACCAAC	TGGAGCAACTGTTCACCAAC
protein_conc	2277	2277	2444	2444
WB_result	79.6	76.1	83.7	70.2
Ave_WB	81.7	73.2
WB_DONE_date	9/13/16	4/18/24
MW	160kDa	160kDa
IP	1		1
antibody_Cat#	A303-025A	46324S	A303-025A	46324S
Antibody DCC ID	ENCAB501IJS		ENCAB501IJS
submitted_to_DCC_date	10/26/16
Rep1_TPM	5.5	0	0	0
Rep2_TPM	5.7	0	0	0
Action
Library_start_date	12/18/17		12/18/17
repeat_library
Note
ID	3110	3112	3111	3113

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
YTHDC2	Product_ID: A303-025A Lot_ID: 1 Source: Bethyl Labs Target Name: YTHDC2-human
YTHDC2	Product_ID: 46324S Lot_ID: 1 Source: Cell Signaling Technology Target Name: YTHDC2-human

Experiment Status

	BGHLV37-105	BGHLV37-106
Sample_ID	BGHLV37-105	BGHLV37-106
Sample Name
Sample Name	YTHDC2-BGHLV37-105C	YTHDC2-BGHLV37-106C
RBP	YTHDC2	YTHDC2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6447	6448

Library-Prep
Sequencing

Library-Prep Information

	BGHLV37-105	BGHLV37-106
Sample #	31	32
Sample Name	YTHDC2-BGHLV37-105C	YTHDC2-BGHLV37-106C
Sample_Name_Alias
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2018-01-02	2018-01-02
Lib_ID	Lib-180102	Lib-180102
Tecan_Location
Tecan
Tecan_date
Size_bp	284	316
Peak_Molarity	18.50	30.20
libSampleQC_DNA_Well	DNA_Library_set40/set1/A7.png	DNA_Library_set40/set1/B7.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set40/set1/G2.png	RNA_Library_set40/set1/H2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGHLV37-105	BGHLV37-106
RBP	YTHDC2	YTHDC2
Batch_ID	BGHLV37	BGHLV37
WB_result	79.600	83.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	954	955

Sequencing Information

	BGHLV37-105	BGHLV37-106
Sample_ID	BGHLV37-105	BGHLV37-106
Sample Name	YTHDC2-BGHLV37-105C	YTHDC2-BGHLV37-106C
Pool ID	Pool-180109	Pool-180109
LocalServer_folder	set40_H	set40_H
total_reads	38,998,170	25,063,990
total_aligned_reads	32,059,232	21,731,200
unique_aligned_reads	30,065,026	20,435,168
percent_uniqueAligned	0.77093	0.81532
correlation_replicates	0.998292	0.998292
spikein_reads	11,438	8,364
percent_spikeins	0.00029	0.00033
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	357	358

Data Submission Information

	BGHLV37-105	BGHLV37-105	BGHLV37-105	BGHLV37-105	BGHLV37-105	BGHLV37-105	BGHLV37-106	BGHLV37-106	BGHLV37-106	BGHLV37-106
ENCODE_alias	brenton-graveley:YTHDC2-BGHLV37-C	brenton-graveley:YTHDC2-BGHLV37-105C	brenton-graveley:L-YTHDC2-BGHLV37-105C	brenton-graveley:YTHDC2-BGHLV37-105C_GTCCGC_ACBYWVANXX_L003_001.R1.fastq.gz	brenton-graveley:YTHDC2-BGHLV37-105C_GTCCGC_ACBYWVANXX_L003_001.R2.fastq.gz	brenton-graveley:YTHDC2-BGHLV37-HepG2	brenton-graveley:YTHDC2-BGHLV37-106C	brenton-graveley:L-YTHDC2-BGHLV37-106C	brenton-graveley:YTHDC2-BGHLV37-106C_GTGAAA_ACBYWVANXX_L003_001.R1.fastq.gz	brenton-graveley:YTHDC2-BGHLV37-106C_GTGAAA_ACBYWVANXX_L003_001.R2.fastq.gz
ENCODE_accession	ENCSR289HOV	ENCBS021BDR	ENCLB034XYV	ENCFF186GHO	ENCFF374FNO	ENCSR542FEC	ENCBS783JOY	ENCLB048MFZ	ENCFF223VPY	ENCFF501OVX
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	BGHLV37-105	BGHLV37-105	BGHLV37-105	BGHLV37-105	BGHLV37-105	BGHLV37-105	BGHLV37-106	BGHLV37-106	BGHLV37-106	BGHLV37-106
Sample Name	YTHDC2-BGHLV37-105C	YTHDC2-BGHLV37-105C	YTHDC2-BGHLV37-105C	YTHDC2-BGHLV37-105C	YTHDC2-BGHLV37-105C	YTHDC2-BGHLV37-105C	YTHDC2-BGHLV37-106C	YTHDC2-BGHLV37-106C	YTHDC2-BGHLV37-106C	YTHDC2-BGHLV37-106C
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
		LV40_biosample_protocol	LV40_library_protocol				LV40_biosample_protocol	LV40_library_protocol
protocol_URL		YTHDC2-BGHLV37-105C.pdf	L-YTHDC2-BGHLV37-105C.pdf				YTHDC2-BGHLV37-106C.pdf	L-YTHDC2-BGHLV37-106C.pdf
ID	1456	1510	1566	1601	1638	7363	1511	1567	1602	1639

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
YTHDC2-BGHLV37-105C_GTCCGC_ACBYWVANXX_L003_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	357	HiSeq2500	100	paired-ended	1				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R1.fastq.gz,non-target-BGHLV37-2C_L001_001.R1.fastq.gz	ENCODE4	671
YTHDC2-BGHLV37-105C_GTCCGC_ACBYWVANXX_L003_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	357	HiSeq2500	100	paired-ended	2				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R2.fastq.gz,non-target-BGHLV37-2C_L001_001.R2.fastq.gz	ENCODE4	713
YTHDC2-BGHLV37-105C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	357					GRCh38	V40	YTHDC2-BGHLV37-105C_GTCCGC_ACBYWVANXX_L003_001.R1.fastq.gz,YTHDC2-BGHLV37-105C_GTCCGC_ACBYWVANXX_L003_001.R2.fastq.gz		ENCORE2	23274
YTHDC2-BGHLV37-105C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	357					GRCh38	V40	YTHDC2-BGHLV37-105C/Aligned.sortedByCoord.out.bam		ENCORE2	23308
YTHDC2-BGHLV37-105C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	357					GRCh38	V40	YTHDC2-BGHLV37-105C/Aligned.sortedByCoord.out.bam		ENCORE2	23342
YTHDC2-BGHLV37-105C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	357					GRCh38	V40	YTHDC2-BGHLV37-105C/Aligned.sortedByCoord.out.bam		ENCORE2	23376
YTHDC2-BGHLV37-105C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	357					GRCh38	V40	YTHDC2-BGHLV37-105C/Aligned.sortedByCoord.out.bam		ENCORE2	23410
YTHDC2-BGHLV37-105C_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	357					GRCh38	V40	YTHDC2-BGHLV37-105C_GTCCGC_ACBYWVANXX_L003_001.R1.fastq.gz,YTHDC2-BGHLV37-105C_GTCCGC_ACBYWVANXX_L003_001.R2.fastq.gz		ENCORE2	23444
YTHDC2-BGHLV37-106C_GTGAAA_ACBYWVANXX_L003_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	358	HiSeq2500	100	paired-ended	1				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R1.fastq.gz,non-target-BGHLV37-2C_L001_001.R1.fastq.gz	ENCODE4	672
YTHDC2-BGHLV37-106C_GTGAAA_ACBYWVANXX_L003_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	358	HiSeq2500	100	paired-ended	2				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R2.fastq.gz,non-target-BGHLV37-2C_L001_001.R2.fastq.gz	ENCODE4	714
YTHDC2-BGHLV37-106C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	358					GRCh38	V40	YTHDC2-BGHLV37-106C_GTGAAA_ACBYWVANXX_L003_001.R1.fastq.gz,YTHDC2-BGHLV37-106C_GTGAAA_ACBYWVANXX_L003_001.R2.fastq.gz		ENCORE2	23275
YTHDC2-BGHLV37-106C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	358					GRCh38	V40	YTHDC2-BGHLV37-106C/Aligned.sortedByCoord.out.bam		ENCORE2	23309
YTHDC2-BGHLV37-106C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	358					GRCh38	V40	YTHDC2-BGHLV37-106C/Aligned.sortedByCoord.out.bam		ENCORE2	23343
YTHDC2-BGHLV37-106C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	358					GRCh38	V40	YTHDC2-BGHLV37-106C/Aligned.sortedByCoord.out.bam		ENCORE2	23377
YTHDC2-BGHLV37-106C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	358					GRCh38	V40	YTHDC2-BGHLV37-106C/Aligned.sortedByCoord.out.bam		ENCORE2	23411
YTHDC2-BGHLV37-106C_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	358					GRCh38	V40	YTHDC2-BGHLV37-106C_GTGAAA_ACBYWVANXX_L003_001.R1.fastq.gz,YTHDC2-BGHLV37-106C_GTGAAA_ACBYWVANXX_L003_001.R2.fastq.gz		ENCORE2	23445