ZC3H11A RNA-Seq in K562

General Information


RBP	ZC3H11A
Cell_Line	K562
Method	CRISPR
Exp_Name	ZC3H11A-BGKcLV11-K562
ENCODE_series_ID	ENCSR917XPN
Batch_ID	BGKcLV11
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR048AUX
ENCODE_CN_Exp_ID	ENCSR292PXV
Rep1	ZC3H11A-BGKcLV11-113
Rep2	ZC3H11A-BGKcLV11-114
CN1	NT-BGKcLV11-1
CN2	NT-BGKcLV11-2
Rep1_qPCR	11.0
Rep2_qPCR	0.0
Rep1_WB	72.3
Rep2_WB	70.9
Antibody Cat#	A301-524A
Antibody Lot#
Antibody DCC ID	ENCAB686PBA
Status	Released
Project	ENCODE4
ID	197

Experiment Information (Status: Released)

	BGKcLV11-113	BGKcLV11-114
idx	433	434
TRCN#_or_BGC#	BGC#0000162	BGC#0000162
shRNA_or_gRNA_sequence	TTACAACTGGTGGATGCGTG	TTACAACTGGTGGATGCGTG
PAM	GGG	GGG
Name	ZC3H11A_67F	ZC3H11A_67F
Sample_ID	BGKcLV11-113	BGKcLV11-114
transduction_Date	8/3/18	8/3/18
days	Day 6	Day 6
RBP_name	ZC3H11A	ZC3H11A
qPCR_result	11.0	0.0
Ave_qPCR	5.5
RT-qPCR_primer-F	tgcgaatcaccaaaagaaca
RT-qPCR_primer-R	tcacctgaagcctctttagctt
protein_conc	2279	2796
WB_result	72.3	70.9
Ave_WB	71.6
WB_DONE_date	9/13/18	wes
MW	89 kDa
IP	1
antibody_Cat#	A301-524A
Antibody DCC ID	ENCAB686PBA
submitted_to_DCC_date	2/22/19
Rep1_TPM	84.5	0
Rep2_TPM	93.2	0
Action	Ready	Ready
Library_start_date	03/13/19	03/13/19
repeat_library
Note
ID	4537	4538

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

	BGKcLV11-113	BGKcLV11-114
Sample_ID	BGKcLV11-113	BGKcLV11-114
Sample Name	ZC3H11A-BGKcLV11-113	ZC3H11A-BGKcLV11-114
Sample Name	ZC3H11A-BGKcLV11-113	ZC3H11A-BGKcLV11-114
RBP	ZC3H11A	ZC3H11A
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2701	2702

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV11-113	BGKcLV11-114
Sample #	29	30
Sample Name	ZC3H11A-BGKcLV11-113	ZC3H11A-BGKcLV11-114
Sample_Name_Alias
Index Well Position	E04	F04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-13	2019-03-13
Lib_ID	Lib-190313	Lib-190313
Tecan_Location	2-E2	2-F2
Tecan	51.70	65.45
Tecan_date	2019-03-13	2019-03-13
Size_bp	305	300
Peak_Molarity	63.80	102.00
libSampleQC_DNA_Well	DNA_Library_set42/set1/E4.png	DNA_Library_set42/set1/F4.png
RIN	10.0	9.6
libSample_RNA_Well	RNA_Library_set42/set1/E4.png	RNA_Library_set42/set1/F4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-13	2019-03-13
Sample_ID	BGKcLV11-113	BGKcLV11-114
RBP	ZC3H11A	ZC3H11A
Batch_ID	BGKcLV11	BGKcLV11
WB_result	72.300	70.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	29	30

Sequencing Information

	BGKcLV11-113	BGKcLV11-114
Sample_ID	BGKcLV11-113	BGKcLV11-114
Sample Name	ZC3H11A-BGKcLV11-113	ZC3H11A-BGKcLV11-114
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	41,878,362	48,304,436
total_aligned_reads	40,568,146	47,435,660
unique_aligned_reads	36,769,982	42,825,618
percent_uniqueAligned	0.87802	0.88658
correlation_replicates	0.995913	0.995913
spikein_reads	41,862	62,852
percent_spikeins	0.00100	0.00130
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	81	82

Data Submission Information

	BGKcLV11-113	BGKcLV11-113	BGKcLV11-113	BGKcLV11-113	BGKcLV11-113	BGKcLV11-113	BGKcLV11-114	BGKcLV11-114	BGKcLV11-114	BGKcLV11-114
ENCODE_alias	brenton-graveley:ZC3H11A-BGKcLV11	brenton-graveley:ZC3H11A-BGKcLV11-113	brenton-graveley:L-ZC3H11A-BGKcLV11-113	brenton-graveley:ZC3H11A-BGKcLV11-113_CCGTGAAG+CAGTGGAT_HK3H2DSXX_S29_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ZC3H11A-BGKcLV11-113_CCGTGAAG+CAGTGGAT_HK3H2DSXX_S29_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ZC3H11A-BGKcLV11-K562	brenton-graveley:ZC3H11A-BGKcLV11-114	brenton-graveley:L-ZC3H11A-BGKcLV11-114	brenton-graveley:ZC3H11A-BGKcLV11-114_TTACAGGA+TGACAAGC_HK3H2DSXX_S30_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ZC3H11A-BGKcLV11-114_TTACAGGA+TGACAAGC_HK3H2DSXX_S30_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR048AUX	ENCBS107VIY	ENCLB346ZVV	ENCFF247ZSP	ENCFF873YYX	ENCSR917XPN	ENCBS228QAA	ENCLB446XOR	ENCFF184YJW	ENCFF872CPC
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	BGKcLV11-113	BGKcLV11-113	BGKcLV11-113	BGKcLV11-113	BGKcLV11-113	BGKcLV11-113	BGKcLV11-114	BGKcLV11-114	BGKcLV11-114	BGKcLV11-114
Sample Name	ZC3H11A-BGKcLV11-113	ZC3H11A-BGKcLV11-113	ZC3H11A-BGKcLV11-113	ZC3H11A-BGKcLV11-113	ZC3H11A-BGKcLV11-113	ZC3H11A-BGKcLV11-113	ZC3H11A-BGKcLV11-114	ZC3H11A-BGKcLV11-114	ZC3H11A-BGKcLV11-114	ZC3H11A-BGKcLV11-114
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
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		ZC3H11A-BGKcLV11-113.pdf	L-ZC3H11A-BGKcLV11-113.pdf				ZC3H11A-BGKcLV11-114.pdf	L-ZC3H11A-BGKcLV11-114.pdf
ID	775	845	927	1031	1113	7367	846	928	1032	1114

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
ZC3H11A-BGKcLV11-113_CCGTGAAG+CAGTGGAT_HK3H2DSXX_S29_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	81	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	413
ZC3H11A-BGKcLV11-113_CCGTGAAG+CAGTGGAT_HK3H2DSXX_S29_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	81	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	495
ZC3H11A-BGKcLV11-113_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	81					GRCh38	V40	ZC3H11A-BGKcLV11-113_CCGTGAAG+CAGTGGAT_HK3H2DSXX_S29_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H11A-BGKcLV11-113_CCGTGAAG+CAGTGGAT_HK3H2DSXX_S29_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23752
ZC3H11A-BGKcLV11-113_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	81					GRCh38	V40	ZC3H11A-BGKcLV11-113/Aligned.sortedByCoord.out.bam		ENCORE2	23834
ZC3H11A-BGKcLV11-113_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	81					GRCh38	V40	ZC3H11A-BGKcLV11-113/Aligned.sortedByCoord.out.bam		ENCORE2	23916
ZC3H11A-BGKcLV11-113_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	81					GRCh38	V40	ZC3H11A-BGKcLV11-113/Aligned.sortedByCoord.out.bam		ENCORE2	23998
ZC3H11A-BGKcLV11-113_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	81					GRCh38	V40	ZC3H11A-BGKcLV11-113/Aligned.sortedByCoord.out.bam		ENCORE2	24080
ZC3H11A-BGKcLV11-113_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	81					GRCh38	V40	ZC3H11A-BGKcLV11-113_CCGTGAAG+CAGTGGAT_HK3H2DSXX_S29_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H11A-BGKcLV11-113_CCGTGAAG+CAGTGGAT_HK3H2DSXX_S29_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24162
ZC3H11A-BGKcLV11-114_TTACAGGA+TGACAAGC_HK3H2DSXX_S30_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	82	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	414
ZC3H11A-BGKcLV11-114_TTACAGGA+TGACAAGC_HK3H2DSXX_S30_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	82	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	496
ZC3H11A-BGKcLV11-114_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	82					GRCh38	V40	ZC3H11A-BGKcLV11-114_TTACAGGA+TGACAAGC_HK3H2DSXX_S30_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H11A-BGKcLV11-114_TTACAGGA+TGACAAGC_HK3H2DSXX_S30_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23753
ZC3H11A-BGKcLV11-114_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	82					GRCh38	V40	ZC3H11A-BGKcLV11-114/Aligned.sortedByCoord.out.bam		ENCORE2	23835
ZC3H11A-BGKcLV11-114_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	82					GRCh38	V40	ZC3H11A-BGKcLV11-114/Aligned.sortedByCoord.out.bam		ENCORE2	23917
ZC3H11A-BGKcLV11-114_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	82					GRCh38	V40	ZC3H11A-BGKcLV11-114/Aligned.sortedByCoord.out.bam		ENCORE2	23999
ZC3H11A-BGKcLV11-114_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	82					GRCh38	V40	ZC3H11A-BGKcLV11-114/Aligned.sortedByCoord.out.bam		ENCORE2	24081
ZC3H11A-BGKcLV11-114_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	82					GRCh38	V40	ZC3H11A-BGKcLV11-114_TTACAGGA+TGACAAGC_HK3H2DSXX_S30_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H11A-BGKcLV11-114_TTACAGGA+TGACAAGC_HK3H2DSXX_S30_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24163