CHD3 RNA-Seq in HepG2

General Information


RBP	CHD3
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CHD3-BGHcLV10-HepG2
ENCODE_series_ID	ENCSR987PLV
Batch_ID	BGHcLV10
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR242DBX
ENCODE_CN_Exp_ID	ENCSR775ZWO
Rep1	CHD3-BGHcLV10-9
Rep2	CHD3-BGHcLV10-10
CN1	NT-BGHcLV10-1
CN2	NT-BGHcLV10-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	64.3
Rep2_WB	76.6
Antibody Cat#	#200314-7F6
Antibody Lot#
Antibody DCC ID	ENCAB509XJY
Status	Released
Project	ENCODE4
ID	220

Experiment Information (Status: Released)

	BGHcLV10-9	BGHcLV10-10
idx	206	207
TRCN#_or_BGC#	BGC#0000109	BGC#0000109
shRNA_or_gRNA_sequence	GACCGGGTCGGAAACGAAGA	GACCGGGTCGGAAACGAAGA
PAM	AGG	AGG
Name	CHD3-89	CHD3-89
Sample_ID	BGHcLV10-9	BGHcLV10-10
transduction_Date	4/27/18	4/27/18
days	D6	D6
RBP_name	CHD3	CHD3
qPCR_result	0.0	0.0
Ave_qPCR	0
RT-qPCR_primer-F	ACCGAGTGCTCATCTTCTCG
RT-qPCR_primer-R	ACCATCGATGCGCTCATACT
protein_conc	2442	2482
WB_result	64.3	76.6
Ave_WB	70.4
WB_DONE_date	5/29/18
MW	227kD
IP	FU'S
antibody_Cat#	#200314-7F6
Antibody DCC ID	ENCAB509XJY
submitted_to_DCC_date	9/6/18
Rep1_TPM	6	0
Rep2_TPM	5	0
Action	Ready	Ready
Library_start_date	8/7/18	8/7/18
repeat_library
Note
ID	8397	8398

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CHD3	Product_ID: 200314-7F6 Lot_ID: CD1016 Source: Zen Bioscience Target Name: CHD3-human

Experiment Status

	BGHcLV10-9	BGHcLV10-10
Sample_ID	BGHcLV10-9	BGHcLV10-10
Sample Name
Sample Name	CHD3-BGHcLV10-9	CHD3-BGHcLV10-10
RBP	CHD3	CHD3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6291	6292

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV10-9	BGHcLV10-10
Sample #	51	52
Sample Name	CHD3-BGHcLV10-9	CHD3-BGHcLV10-10
Sample_Name_Alias
Index Well Position	G07	H07
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	277	277
Peak_Molarity	58.30	56.30
libSampleQC_DNA_Well	DNA_Library_set41/set5/G7.png	DNA_Library_set41/set5/H7.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set41/set2/F11.png	RNA_Library_set41/set1/D7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-08-08	2018-08-08
Sample_ID	BGHcLV10-9	BGHcLV10-10
RBP	CHD3	CHD3
Batch_ID	BGHcLV10	BGHcLV10
WB_result	64.300	76.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	901	902

Sequencing Information

	BGHcLV10-9	BGHcLV10-10
Sample_ID	BGHcLV10-9	BGHcLV10-10
Sample Name	CHD3-BGHcLV10-9	CHD3-BGHcLV10-10
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	137,615,288	176,005,146
total_aligned_reads	130,812,200	170,816,824
unique_aligned_reads	122,096,948	158,418,098
percent_uniqueAligned	0.88723	0.90008
correlation_replicates	0.995535	0.995535
spikein_reads	205,166	321,628
percent_spikeins	0.00149	0.00183
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	307	308

Data Submission Information

	BGHcLV10-9	BGHcLV10-9	BGHcLV10-9	BGHcLV10-9	BGHcLV10-9	BGHcLV10-9	BGHcLV10-10	BGHcLV10-10	BGHcLV10-10	BGHcLV10-10
ENCODE_alias	brenton-graveley:CHD3-BGHcLV10	brenton-graveley:CHD3-BGHcLV10-9	brenton-graveley:L-CHD3-BGHcLV10-9	brenton-graveley:CHD3-BGHcLV10-9_AGGCAGAG+AGAATGCC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CHD3-BGHcLV10-9_AGGCAGAG+AGAATGCC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CHD3-BGHcLV10-HepG2	brenton-graveley:CHD3-BGHcLV10-10	brenton-graveley:L-CHD3-BGHcLV10-10	brenton-graveley:CHD3-BGHcLV10-10_GAATGAGA+GAGGCATT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CHD3-BGHcLV10-10_GAATGAGA+GAGGCATT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR242DBX	ENCBS194NHW	ENCLB370NMX	ENCFF264XKJ	ENCFF420PFZ	ENCSR987PLV	ENCBS406LFP	ENCLB212SBA	ENCFF301YJI	ENCFF166LXG
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	BGHcLV10-9	BGHcLV10-9	BGHcLV10-9	BGHcLV10-9	BGHcLV10-9	BGHcLV10-9	BGHcLV10-10	BGHcLV10-10	BGHcLV10-10	BGHcLV10-10
Sample Name	CHD3-BGHcLV10-9	CHD3-BGHcLV10-9	CHD3-BGHcLV10-9	CHD3-BGHcLV10-9	CHD3-BGHcLV10-9	CHD3-BGHcLV10-9	CHD3-BGHcLV10-10	CHD3-BGHcLV10-10	CHD3-BGHcLV10-10	CHD3-BGHcLV10-10
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		CHD3-BGHcLV10-9.pdf	L-CHD3-BGHcLV10-9.pdf				CHD3-BGHcLV10-10.pdf	L-CHD3-BGHcLV10-10.pdf
ID	1118	1157	1227	1297	1367	7135	1156	1226	1296	1366

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
CHD3-BGHcLV10-9_AGGCAGAG+AGAATGCC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	307				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	504
CHD3-BGHcLV10-9_AGGCAGAG+AGAATGCC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	307				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	574
CHD3-BGHcLV10-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	307	GRCh38	V40	CHD3-BGHcLV10-9_AGGCAGAG+AGAATGCC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,CHD3-BGHcLV10-9_AGGCAGAG+AGAATGCC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26742
CHD3-BGHcLV10-9_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	307	GRCh38	V40	CHD3-BGHcLV10-9/Aligned.sortedByCoord.out.bam		ENCORE2	26812
CHD3-BGHcLV10-9_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	307	GRCh38	V40	CHD3-BGHcLV10-9/Aligned.sortedByCoord.out.bam		ENCORE2	26882
CHD3-BGHcLV10-9_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	307	GRCh38	V40	CHD3-BGHcLV10-9/Aligned.sortedByCoord.out.bam		ENCORE2	26952
CHD3-BGHcLV10-9_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	307	GRCh38	V40	CHD3-BGHcLV10-9/Aligned.sortedByCoord.out.bam		ENCORE2	27022
CHD3-BGHcLV10-9_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	307	GRCh38	V40	CHD3-BGHcLV10-9_AGGCAGAG+AGAATGCC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,CHD3-BGHcLV10-9_AGGCAGAG+AGAATGCC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27092
CHD3-BGHcLV10-10_GAATGAGA+GAGGCATT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	308				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	503
CHD3-BGHcLV10-10_GAATGAGA+GAGGCATT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	308				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	573
CHD3-BGHcLV10-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	308	GRCh38	V40	CHD3-BGHcLV10-10_GAATGAGA+GAGGCATT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,CHD3-BGHcLV10-10_GAATGAGA+GAGGCATT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26741
CHD3-BGHcLV10-10_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	308	GRCh38	V40	CHD3-BGHcLV10-10/Aligned.sortedByCoord.out.bam		ENCORE2	26811
CHD3-BGHcLV10-10_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	308	GRCh38	V40	CHD3-BGHcLV10-10/Aligned.sortedByCoord.out.bam		ENCORE2	26881
CHD3-BGHcLV10-10_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	308	GRCh38	V40	CHD3-BGHcLV10-10/Aligned.sortedByCoord.out.bam		ENCORE2	26951
CHD3-BGHcLV10-10_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	308	GRCh38	V40	CHD3-BGHcLV10-10/Aligned.sortedByCoord.out.bam		ENCORE2	27021
CHD3-BGHcLV10-10_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	308	GRCh38	V40	CHD3-BGHcLV10-10_GAATGAGA+GAGGCATT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,CHD3-BGHcLV10-10_GAATGAGA+GAGGCATT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27091