ZC3H11A RNA-Seq in HepG2

General Information


RBP	ZC3H11A
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ZC3H11A-BGHcLV10-HepG2
ENCODE_series_ID	ENCSR748RVD
Batch_ID	BGHcLV10
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR544LEZ
ENCODE_CN_Exp_ID	ENCSR775ZWO
Rep1	ZC3H11A-BGHcLV10-53
Rep2	ZC3H11A-BGHcLV10-54
CN1	NT-BGHcLV10-1
CN2	NT-BGHcLV10-2
Rep1_qPCR	12.0
Rep2_qPCR	0.0
Rep1_WB	93.2
Rep2_WB	95.3
Antibody Cat#	A301-524A
Antibody Lot#
Antibody DCC ID	ENCAB686PBA
Status	Released
Project	ENCODE4
ID	228

Experiment Information (Status: Released)

	BGHcLV10-53	BGHcLV10-54
idx	250	251
TRCN#_or_BGC#	BGC#0000162	BGC#0000162
shRNA_or_gRNA_sequence	TTACAACTGGTGGATGCGTG	TTACAACTGGTGGATGCGTG
PAM	GGG	GGG
Name	ZC3H11A-67	ZC3H11A-67
Sample_ID	BGHcLV10-53	BGHcLV10-54
transduction_Date	4/27/18	4/27/18
days	D6	D6
RBP_name	ZC3H11A	ZC3H11A
qPCR_result	12.0	0.0
Ave_qPCR	6.0
RT-qPCR_primer-F	tgcgaatcaccaaaagaaca
RT-qPCR_primer-R	tcacctgaagcctctttagctt
protein_conc	3277	2638
WB_result	93.2	95.3
Ave_WB	94.3
WB_DONE_date	5/10/18	wes
MW	89 kDa
IP	1
antibody_Cat#	A301-524A
Antibody DCC ID	ENCAB686PBA
submitted_to_DCC_date	9/6/18
Rep1_TPM	32	0
Rep2_TPM	50	0
Action	Ready	Ready
Library_start_date	8/7/18	8/7/18
repeat_library
Note
ID	6393	6394

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ZC3H11A	Product_ID: A301-524A Lot_ID: 1 Source: Bethyl Labs Target Name: ZC3H11A-human

Experiment Status

	BGHcLV10-53	BGHcLV10-54
Sample_ID	BGHcLV10-53	BGHcLV10-54
Sample Name
Sample Name	ZC3H11A-BGHcLV10-53	ZC3H11A-BGHcLV10-54
RBP	ZC3H11A	ZC3H11A
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6307	6308

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV10-53	BGHcLV10-54
Sample #	67	68
Sample Name	ZC3H11A-BGHcLV10-53	ZC3H11A-BGHcLV10-54
Sample_Name_Alias
Index Well Position	G09	H09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2018-10-01	2018-10-01
Lib_ID	Lib-181001	Lib-181001
Tecan_Location
Tecan
Tecan_date
Size_bp	272	268
Peak_Molarity	44.90	42.20
libSampleQC_DNA_Well	DNA_Library_set41/set5/G9.png	DNA_Library_set41/set5/H9.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set41/set1/C9.png	RNA_Library_set41/set1/D9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-08-08	2018-08-08
Sample_ID	BGHcLV10-53	BGHcLV10-54
RBP	ZC3H11A	ZC3H11A
Batch_ID	BGHcLV10	BGHcLV10
WB_result	93.200	95.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	917	918

Sequencing Information

	BGHcLV10-53	BGHcLV10-54
Sample_ID	BGHcLV10-53	BGHcLV10-54
Sample Name	ZC3H11A-BGHcLV10-53	ZC3H11A-BGHcLV10-54
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	166,894,702	166,284,814
total_aligned_reads	160,693,864	162,134,422
unique_aligned_reads	149,421,468	150,173,142
percent_uniqueAligned	0.89530	0.90311
correlation_replicates	0.994380	0.994380
spikein_reads	299,978	284,160
percent_spikeins	0.00180	0.00171
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	323	324

Data Submission Information

	BGHcLV10-53	BGHcLV10-53	BGHcLV10-53	BGHcLV10-53	BGHcLV10-53	BGHcLV10-53	BGHcLV10-54	BGHcLV10-54	BGHcLV10-54	BGHcLV10-54
ENCODE_alias	brenton-graveley:ZC3H11A-BGHcLV10	brenton-graveley:ZC3H11A-BGHcLV10-53	brenton-graveley:L-ZC3H11A-BGHcLV10-53	brenton-graveley:ZC3H11A-BGHcLV10-53_ACTCGTGT+ATTGGAAC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ZC3H11A-BGHcLV10-53_ACTCGTGT+ATTGGAAC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ZC3H11A-BGHcLV10-HepG2	brenton-graveley:ZC3H11A-BGHcLV10-54	brenton-graveley:L-ZC3H11A-BGHcLV10-54	brenton-graveley:ZC3H11A-BGHcLV10-54_GTCTACAC+GCCAAGGT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ZC3H11A-BGHcLV10-54_GTCTACAC+GCCAAGGT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR544LEZ	ENCBS941VTX	ENCLB516VZB	ENCFF102EDV	ENCFF592EQR	ENCSR748RVD	ENCBS343EZL	ENCLB879NOS	ENCFF557EDO	ENCFF115WDV
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	BGHcLV10-53	BGHcLV10-53	BGHcLV10-53	BGHcLV10-53	BGHcLV10-53	BGHcLV10-53	BGHcLV10-54	BGHcLV10-54	BGHcLV10-54	BGHcLV10-54
Sample Name	ZC3H11A-BGHcLV10-53	ZC3H11A-BGHcLV10-53	ZC3H11A-BGHcLV10-53	ZC3H11A-BGHcLV10-53	ZC3H11A-BGHcLV10-53	ZC3H11A-BGHcLV10-53	ZC3H11A-BGHcLV10-54	ZC3H11A-BGHcLV10-54	ZC3H11A-BGHcLV10-54	ZC3H11A-BGHcLV10-54
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV41_biosample_protocol	LV41_library_protocol				LV41_biosample_protocol	LV41_library_protocol
protocol_URL		ZC3H11A-BGHcLV10-53.pdf	L-ZC3H11A-BGHcLV10-53.pdf				ZC3H11A-BGHcLV10-54.pdf	L-ZC3H11A-BGHcLV10-54.pdf
ID	1147	1214	1284	1354	1418	7366	1215	1285	1355	1419

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
ZC3H11A-BGHcLV10-53_ACTCGTGT+ATTGGAAC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	323				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	561
ZC3H11A-BGHcLV10-53_ACTCGTGT+ATTGGAAC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	323				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	631
ZC3H11A-BGHcLV10-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	323	GRCh38	V40	ZC3H11A-BGHcLV10-53_ACTCGTGT+ATTGGAAC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H11A-BGHcLV10-53_ACTCGTGT+ATTGGAAC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26799
ZC3H11A-BGHcLV10-53_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	323	GRCh38	V40	ZC3H11A-BGHcLV10-53/Aligned.sortedByCoord.out.bam		ENCORE2	26869
ZC3H11A-BGHcLV10-53_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	323	GRCh38	V40	ZC3H11A-BGHcLV10-53/Aligned.sortedByCoord.out.bam		ENCORE2	26939
ZC3H11A-BGHcLV10-53_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	323	GRCh38	V40	ZC3H11A-BGHcLV10-53/Aligned.sortedByCoord.out.bam		ENCORE2	27009
ZC3H11A-BGHcLV10-53_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	323	GRCh38	V40	ZC3H11A-BGHcLV10-53/Aligned.sortedByCoord.out.bam		ENCORE2	27079
ZC3H11A-BGHcLV10-53_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	323	GRCh38	V40	ZC3H11A-BGHcLV10-53_ACTCGTGT+ATTGGAAC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H11A-BGHcLV10-53_ACTCGTGT+ATTGGAAC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27149
ZC3H11A-BGHcLV10-54_GTCTACAC+GCCAAGGT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	324				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	562
ZC3H11A-BGHcLV10-54_GTCTACAC+GCCAAGGT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	324				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	632
ZC3H11A-BGHcLV10-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	324	GRCh38	V40	ZC3H11A-BGHcLV10-54_GTCTACAC+GCCAAGGT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H11A-BGHcLV10-54_GTCTACAC+GCCAAGGT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26800
ZC3H11A-BGHcLV10-54_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	324	GRCh38	V40	ZC3H11A-BGHcLV10-54/Aligned.sortedByCoord.out.bam		ENCORE2	26870
ZC3H11A-BGHcLV10-54_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	324	GRCh38	V40	ZC3H11A-BGHcLV10-54/Aligned.sortedByCoord.out.bam		ENCORE2	26940
ZC3H11A-BGHcLV10-54_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	324	GRCh38	V40	ZC3H11A-BGHcLV10-54/Aligned.sortedByCoord.out.bam		ENCORE2	27010
ZC3H11A-BGHcLV10-54_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	324	GRCh38	V40	ZC3H11A-BGHcLV10-54/Aligned.sortedByCoord.out.bam		ENCORE2	27080
ZC3H11A-BGHcLV10-54_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	324	GRCh38	V40	ZC3H11A-BGHcLV10-54_GTCTACAC+GCCAAGGT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H11A-BGHcLV10-54_GTCTACAC+GCCAAGGT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27150