title: WT-clone_4-utr1-R2


title: WT-clone_4-utr2-R1

status: Public on Jan 13 2024

type: SRA

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite Universitätsmedizin Berlin

library_source: transcriptomic

data_processing:
poly-A sequences and adapters are trimmed with bbduk
Sequences are aligned using STAR aligner
Assembly: GRCh38
Supplementary files format and content: counts of reads per Gene

molecule: polyA RNA

organism: Homo sapiens

source_name: HEK-RAF-ER

extract_protocol:
RNA was extracted using Qiagen RNAeasy kit following manufacturers recommendation, without removal of DNA
Library was constructed using QuantSeq 3’ mRNA-Seq V2 Library Prep Kit V2

treatment_protocol: Cells were treated with tamoxifen (4OHT) to activate RAF activity

tag: cell line

value: HEK-RAF-ER

tag: genotype

value: WT

tag: clone

value: clone 4

tag: treatment

tag: time

tag: replicate


title: WT-clone_5-6_hrs-R1

value: clone 5

value: tamoxifen (4OHT)

value: 6 hrs


title: WT-clone_4-6_hrs-R2


title: WT-clone_5-18_hrs-R1

value: 18 hrs


title: WT-clone_4-6_hrs-R1


title: WT-clone_4-18_hrs-R1


title: WT-clone_4-18_hrs-R2


title: HEK_RAF_ER_12h_R1_GE

description: Gene expression library

library_source: transcriptomic single cell

data_processing:
Raw sequences reads were analysed using cellranger-6.1.1 with feature calling using the guide sequences as in feature_ref.csv.gz; standard 10x gene expression libraries were processed alone and together with the targeted sequencing results
Effects of individual KO (represented by the CRISPR guides) on gene expression were assessed using pseudo-bulk analysis in R using the package glmGamPoi.
Assembly: GRCh38
Supplementary files format and content: *.h5 files contain the single cell gene expression matrices. Untargeted contain only data from the standard runs.
Supplementary files format and content: *.protospacer_calls_per_cell.csv.gz contain the guide / feature assignement of cells

extract_protocol:
Approximately 20.000 cells were encapsulated in Gel Beads-in-emulsion (GEMs) and GEX and CRISPR libraries were generated using the 10x Chromium Single Cell 3' V3 with Feature Barcoding technology
Gene expression libraries were constructed as per manufacturers instruction. Targeted libraries were amplified with custom primers from the amplified cDNA library. Guide libraries were constructed using the direct capture method.
Direct Capture Perturb-seq: scRNA-seq, CRISPR-guides, targeted scRNA-seq

treatment_protocol: Cells were treated with tamoxifen to induce RAF/MAPK signalling for various times (6-18hrs)

tag: library type

value: mRNA

value: 4OHT (tamoxifen)


title: WT-clone_4-12_hrs-R2

value: 12 hrs


title: WT-clone_3-6_hrs-R2

value: clone 3


title: WT-clone_3-utr1-R1


title: WT-clone_3-6_hrs-R1


title: WT-clone_3-utr2-R2


title: WT-clone_3-18_hrs-R1


title: WT-clone_3-utr2-R1


title: WT-clone_3-12_hrs-R1


title: WT-clone_3-utr1-R2


title: WT-clone_2-12_hrs-R1

value: clone 2


title: WT-clone_2-utr2-R1


title: WT-clone_3-18_hrs-R2


title: WT-clone_2-utr1-R1


title: WT-clone_2-18_hrs-R1


title: WT-clone_4-12_hrs-R1


title: WT-clone_1-6_hrs-R2

value: clone 1


title: WT-clone_1-utr1-R2


title: WT-clone_1-utr2-R1


title: WT-clone_1-18_hrs-R2


title: WT-clone_1-6_hrs-R1


title: WT-clone_1-utr1-R1


title: WT-clone_2-6_hrs-R1


title: WT-clone_1-utr2-R2


title: WT-clone_1-12_hrs-R1


title: WT-clone_1-12_hrs-R2


title: FOS-mix-utr2-R1

value: FOS

value: mix


title: FOS-mix-12_hrs-R1


title: WT-clone_1-18_hrs-R1


title: FOS-mix-utr1-R1


title: FOS-mix-18_hrs-R1


title: FOS-mix-6_hrs-R1


title: WT-clone_3-12_hrs-R2


title: FOS-clone_1-utr1-R2


title: FOS-clone_1-6_hrs-R2


title: FOS-clone_1-utr1-R1


title: FOS-clone_1-6_hrs-R1


title: FOS-clone_1-utr2-R2


title: FOS-clone_1-12_hrs-R2


title: FOS-clone_1-12_hrs-R1


title: FOS-clone_1-18_hrs-R1


title: EGR1-clone_2-utr2-R1


title: EGR1-clone_2-utr1-R2


title: EGR1-clone_2-utr1-R1


title: EGR1-clone_2-12_hrs-R1


title: EGR1-clone_2-18_hrs-R2


title: EGR1-clone_2-18_hrs-R1


title: EGR1-clone_2-6_hrs-R2


title: EGR1-clone_1-utr2-R1


title: EGR1-clone_2-6_hrs-R1


title: EGR1-clone_1-6_hrs-R1


title: EGR1-clone_1-18_hrs-R1


title: EGR1-clone_1-utr2-R2


title: EGR1-clone_2-12_hrs-R2


title: EGR1-clone_1-utr1-R1


title: EGR1-clone_1-6_hrs-R2


title: EGR1-clone_1-12_hrs-R1


title: EGR1-clone_1-18_hrs-R2


title: EGR1-clone_1-utr1-R2


title: FOS-clone_1-utr2-R1


title: FOS_EGR1-clone_2-utr2-R2


title: FOS-clone_1-18_hrs-R2


title: FOS_EGR1-clone_2-utr2-R1


title: EGR1-clone_1-12_hrs-R2


title: FOS_EGR1-clone_2-utr1-R2


title: FOS_EGR1-clone_2-utr1-R1


title: FOS_EGR1-clone_2-6_hrs-R2


title: EGR1-clone_2-utr2-R2


title: FOS_EGR1-clone_2-6_hrs-R1


title: FOS_EGR1-clone_2-18_hrs-R1


title: FOS_EGR1-clone_2-12_hrs-R2


title: FOS_EGR1-clone_2-12_hrs-R1


title: FOS_EGR1-clone_1-utr1-R2


title: FOS_EGR1-clone_1-utr2-R1


title: FOS_EGR1-clone_1-utr2-R2


title: FOS_EGR1-clone_1-6_hrs-R2


title: FOS_EGR1-clone_1-utr1-R1


title: FOS_EGR1-clone_1-18_hrs-R1


title: EGR1_FOS-clone_3-utr1-R3


title: FOS_EGR1-clone_1-12_hrs-R2


title: EGR1_FOS-clone_3-utr2-R1


title: EGR1_FOS-clone_3-utr2-R2


title: EGR1_FOS-clone_3-utr2-R3


title: EGR1_FOS-clone_3-utr1-R1


title: EGR1_FOS-clone_3-6_hrs-R3


title: FOS_EGR1-clone_1-18_hrs-R2


title: EGR1_FOS-clone_3-6_hrs-R2


title: EGR1_FOS-clone_3-18_hrs-R3


title: EGR1_FOS-clone_3-utr1-R2


title: EGR1_FOS-clone_3-6_hrs-R1


title: EGR1_FOS-clone_3-12_hrs-R3


title: EGR1_FOS-clone_3-18_hrs-R2


title: FOS_EGR1-clone_2-18_hrs-R2


title: EGR1_FOS-clone_3-12_hrs-R2


title: EGR1_FOS-clone_3-12_hrs-R1


title: EGR1_FOS-clone_2-utr2-R3


title: EGR1_FOS-clone_2-utr2-R2


title: EGR1_FOS-clone_3-18_hrs-R1


title: EGR1_FOS-clone_2-utr2-R1


title: FOS_EGR1-clone_1-12_hrs-R1


title: FOS_EGR1-clone_1-6_hrs-R1


title: EGR1_FOS-clone_2-utr1-R1


title: EGR1_FOS-clone_2-utr1-R3


title: EGR1_FOS-clone_2-utr1-R2


title: EGR1_FOS-clone_2-6_hrs-R3


title: EGR1_FOS-clone_2-6_hrs-R2


title: EGR1_FOS-clone_2-6_hrs-R1


title: EGR1_FOS-clone_2-12_hrs-R3


title: EGR1_FOS-clone_2-18_hrs-R1


title: EGR1_FOS-clone_1-utr2-R3


title: EGR1_FOS-clone_2-18_hrs-R3


title: EGR1_FOS-clone_2-18_hrs-R2


title: EGR1_FOS-clone_1-utr1-R3


title: EGR1_FOS-clone_1-6_hrs-R3


title: EGR1_FOS-clone_1-utr2-R1


title: EGR1_FOS-clone_1-utr2-R2


title: EGR1_FOS-clone_2-12_hrs-R2


title: EGR1_FOS-clone_1-utr1-R2


title: EGR1_FOS-clone_1-18_hrs-R3


title: EGR1_FOS-clone_1-utr1-R1


title: EGR1_FOS-clone_1-18_hrs-R2


title: EGR1_FOS-clone_1-6_hrs-R1


title: EGR1_FOS-clone_1-6_hrs-R2


title: EGR1_FOS-clone_1-12_hrs-R3


title: EGR1_FOS-clone_1-18_hrs-R1


title: EGR1_FOS-clone_1-12_hrs-R1


title: Ascites, MDSC, 14day2

type: RNA

city: Purulia

first: Sankar

last: Bhattacharyya

state: West Bengal

address: Ranchi Road Sainik School

department: Zoology

country: India

institute: Sidho Kanho Birsha University

description: Gene expression of CD11b+ Gr1+ MDSC isolated from peritoneal cavity of 14day tumor bearing animal

hyb_protocol: Fragmentation of 600ng cRNA done by incubating at 60o for 30 minutes in 25x fragmentation buffer and 10x Gene Expression Blocking Agent in 25ul of total reaction volume. After completion of hybridisation reaction 25ul of 2xHi-RPM Hybridization Buffer is added to stop fragmentation reaction. 40ul of hybridization sample is dispense in the SureHyb gasket slide. Further the Gasket slides were assembled with gene expression microarray slide (G3 Mouse GE 8x60k microarray, Agilent whole genome microarray) . Hybridisation done at 65o C for 17 hours in Agilent hybridisation oven. Slides were afterwards using Gene expression wash buffers.

scan_protocol: Slides were scanned using SureScan Microarray scanner system with one color scan setting for 8X60K array slides immediately after washing followed by manufacturers guidelines.

data_processing: Image generated after scanning were analysed using Agilent feature extraction Software version 11.5.1. using default parameters (Protocol in use:GE1_1200_Jun14, Grid template no: 074809_D_F_20181026 at saturation value 778020 g). Further processing of data were done using GeneSpring 14.9 (Agilent Technologies).

molecule: total RNA

organism: Mus musculus

source_name: Peritoneal cavity

label_protocol: Using Low Input Quick Amp Labeling Kit, One color Cyanine-3 (Cy3) labelled complementary RNA were prepared from 10ng of RNA (Agilent technologies). Purification of amplified cRNA performed using RNeasy Mini Kit (QIAGEN, Valencia, CA). NanoDrop ND-1000 UV-VIS Spectrophotometer were used to quitify cRNA yield and dye incorporation.

growth_protocol: S-180 tumor cells were purchased from National Centre for Cell Science (NCCS), India and maitained in presence  of RPMI supplimented with 10% FBS in proper cell culture environment.

extract_protocol: After maintaining animals for 21 day, experimental samples as cells from bone marrow and peritoneal cavity collecting following euthanizations of all 4 tumor animal groups and control which is not treated with tumor cell. Total isolated cells from peritoneal cavity and bone marrow were washed twice using using sterile PBS and stained using CD11b-PE and Gr-1-BIOTIN. After 30 minutes of incubation streptavidin-pacific blue conjugation done. Again after 30 minutes incubation cells were resuspended in FACS buffer. MDSC which is CD11b-PE positive and Gr-1-Pacific blue positive were sorted using FACS Melody cell sorter (BD FACSMelodyTM cell sorter) instruments.  Total cellular RNA isolated from MDSC using RNA extraction kit (InvitrogenTM PureLinkTM RNA Mini Kit) followed by manufacturer’s protocol. RNA integrity measured using Agilent Bioanalyser and NanoDrop Lite (Thermo Scientific, Wilmington, DE).

treatment_protocol: Experimental animals were injected with 1x10^5 cells intraperitoneally in 100ul sterile PBS per mice, control tumor free animal also treated with 100ul PBS each. Animals were devided into four tumor groups which are 3day (3day post tumor innoculation), 7day (7day post tumor innoculation), 14day (14day post tumor innoculation) and 21day (21day post tumor innoculation) as tumor bearing groups. Each groups contains at least 12 animal each.

tag: tissue

value: Ascites

tag: age

value: 6-8 weeks

tag: gender

value: male

tag: cell type

value: Myeloid derived suppressor cells (MDSCs)


title: Ascites, MDSC, 7day2

description: Gene expression of CD11b+ Gr1+ MDSC isolated from peritoneal cavity of 7day tumor bearing animal


title: Ascites, MDSC, 14day1


title: EGR1_FOS-clone_2-12_hrs-R1

value: HEK-RAF-ER


title: Ascites, MDSC, 7day1


title: Ascites, MDSC, 21day1

description: Gene expression of CD11b+ Gr1+ MDSC isolated from peritoneal cavity of 21day tumor bearing animal


title: Ascites, MDSC, 3day2

description: Gene expression of CD11b+ Gr1+ MDSC isolated from peritoneal cavity of 3day tumor bearing animal


title: Ascites, MDSC, 3day1


title: CTR9_KD_H3K4me3_rep3

city: Boston

first: Jiawei

last: Zhao

state: Massachusetts

address: 1 Blackfan Circle

country: USA

institute: Boston Children's Hospital

library_source: genomic

data_processing:
fastq files aligned to hg38
aligned bam files converted to bigwig files using deepTools
bigwig files of three replicates were average to create mean bigwig files using UCSC tools
Assembly: hg38
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: HSPCs

growth_protocol: HSPCs grown in HSPC expansion medium (check the manuscript method section for the recipe of the growth medium)

extract_protocol:
Cells were fixed by 1%paraformaldehyde, then quenched by glycine. Cells were enzymatically sheared.
libraries were prepared by NEB DNA library prep kit following manufacturer's instruction

treatment_protocol: AAVS1 or partial CTR9 gRNA editing

value: HSPCs

value: partial CTR9 edited, H3K4me3 antibody


title: CTR9_KD_H3K79me2_rep2

value: partial CTR9 edited, H3K79me2 antibody


title: CTR9_KD_H3K79me2_rep3


title: CTR9_KD_H3K79me2_rep1


title: Ascites, MDSC, control2

description: Gene expression of CD11b+ Gr1+ MDSC isolated from  peritoneal cavity of control tumor free animal


title: Bone marrow, MDSC, 21day2

description: Gene expression of CD11b+ Gr1+ MDSC isolated from  bone marrow of 21day tumor bearing animal

source_name: Bone marrow

value: Bone marrow


title: CTR9_KD_H3K36me3_rep3

value: partial CTR9 edited, H3K36me3 antibody


title: Ascites, MDSC, control1


title: Ascites, MDSC, 21day2


title: Bone marrow, MDSC, 21day1


title: Bone marrow, MDSC, 14day2

description: Gene expression of CD11b+ Gr1+ MDSC isolated from  bone marrow of 14day tumor bearing animal


title: CTR9_KD_RNApolII_rep2

value: partial CTR9 edited, RPB1 antibody


title: CTR9_KD_H3K36me3_rep2


title: Bone marrow, MDSC, 14day1


title: CTR9_KD_RNApolII_rep3


title: CTR9_KD_H3K36me3_rep1


title: EGR1_FOS-clone_1-12_hrs-R2

value: tamoxifen (4OHT)

value: 12 hrs


title: CTR9_KD_RNApolII_rep1


title: Bone marrow, MDSC, 7day2

description: Gene expression of CD11b+ Gr1+ MDSC isolated from  bone marrow of 7day tumor bearing animal


title: Bone marrow, MDSC, control2

description: Gene expression of CD11b+ Gr1+ MDSC isolated from  bone marrow of control tumor free animal


title: Bone marrow, MDSC, 7day1


title: CTR9_KD_LEO1_rep3

value: partial CTR9 edited, LEO1 antibody


title: Bone marrow, MDSC, control1


title: Bone marrow, MDSC, 3day2

description: Gene expression of CD11b+ Gr1+ MDSC isolated from  bone marrow of 3day tumor bearing animal


title: CTR9_KD_LEO1_rep2


title: CTR9_KD_H3K4me3_rep2


title: CTR9_KD_H3K4me3_rep1


title: Bone marrow, MDSC, 3day1

description: Gene expression of CD11b+ Gr1+ MDSC isolated from bone marrow of 3day tumor bearing animal


title: CTR9_KD_CDC73_rep3

value: partial CTR9 edited, CDC73 antibody


title: CTR9_KD_PAF1_rep1

value: partial CTR9 edited, PAF1 antibody


title: CTR9_KD_PAF1_rep3


title: CTR9_KD_CDC73_rep2


title: CTR9_KD_PAF1_rep2


title: CTR9_KD_CDC73_rep1


title: CTR9_KD_MLLT3_rep3

value: partial CTR9 edited, MLLT3 antibody


title: AAVS1_H3K79me2_rep3

value: AAVS1 edited, H3K79me2 antibody


title: CTR9_KD_MLLT3_rep2


title: CTR9_KD_MLLT3_rep1


title: AAVS1_H3K79me2_rep2


title: run2a_8h_8h

data_processing:
Data was processed using snakemake-workflows rna-seq-star-deseq2 pipeline, v1.2.0
Assembly: GRCh38
Supplementary files format and content: counts resulting from the star aligner

extract_protocol:
Total RNA was extracted with Trizol.
Sequencing libraries were prepared using Illumina TruSeq mRNA Library Prep Kit v2 following manufacturers recommendation

treatment_protocol: Cells were treated with tamoxifen to induce RAF/MAPK signalling for various times (0.5-8h) and MAPK activity was blocked using AZD6422 inhibitor

tag: time of_measurement

tag: pulse length


title: run2a_8h_4h


title: CTR9_KD_LEO1_rep1


title: PBS3_lung_Clean_Data3

city: Raleigh

first: Zhenzhen

last: Wang

state: North Carolina

address: 1060 William Moore Dr

institute: North Carolina State University

data_processing:
Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC
We used HISAT2 to map reads to the genome of Oryza sativa (Version: RGAP 7). The mapped reads of each sample were assembled using StringTie.
Then, all transcriptomes from 8 Samples were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare.
After the ﬁnal transcriptome was generated, StringTie and Ballgown was used to estimate the expression levels of all transcripts.
StringTie was used to perform expression level for mRNAs by calculating FPKM.The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with parametric F-test comparing nested linear models (p value < 0.05) by R package Ballgown.
Assembly: BCM_Maur_2.0
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Mesocricetus auratus

source_name: Lung

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen).
Following purification, the poly(A) mRNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with a strand-specific library preparation by dUTP method.
The average insert size for the paired-end libraries was 300±50 bp. And then we performed the paired-end 2×150bp sequencing on an Illumina Hiseq 4000 at LC Sciences following the vendor's recommended protocol.

value: Lung

value: PBS


title: LSC-Exo1_lung_Clean_Data1

value: LSC-Exo


title: AAVS1_H3K79me2_rep1


title: AAVS1_H3K4me3_rep3

value: AAVS1 edited, H3K4me3 antibody


title: run2a_8h_2h

value: HEK-RAF-ER


title: AAVS1_H3K4me3_rep2

value: HSPCs


title: run2a_8h_1h


title: LSC-Exo2_lung_Clean_Data1


title: PBS1_lung_Clean_Data1


title: sham_lung_Clean_Data1


title: PBS2_lung_Clean_Data2


title: LSC-Exo4_lung_Clean_Data1


title: run2a_8h_0h


title: AAVS1_H3K4me3_rep1


title: LSC-Exo3_lung_Clean_Data1


title: run1b_8h_2h


title: run1a_8h_8h


title: run2a_8h_05h


title: AAVS1_H3K36me3_rep2

value: AAVS1 edited, H3K36me3 antibody


title: AAVS1_H3K36me3_rep1


title: AAVS1_H3K36me3_rep3


title: AAVS1_RNApolII_rep3

value: AAVS1 edited, RPB1 antibody


title: AAVS1_RNApolII_rep2


title: run1a_8h_4h


title: AAVS1_RNApolII_rep1


title: run1a_8h_1h


title: run1a_8h_2h


title: AAVS1_LEO1_rep3

value: AAVS1 edited, LEO1


title: run1a_8h_0h


title: run1a_8h_05h


title: AAVS1_LEO1_rep2


title: run1a_2h_8h


title: AAVS1_LEO1_rep1


title: AAVS1_CDC73_rep2

value: AAVS1 edited,CDC73 antibody


title: AAVS1_PAF1_rep3

value: AAVS1 edited, PAF1 antibody


title: AAVS1_PAF1_rep2


title: run1a_2h_4h

value: tamoxifen (4OHT)


title: AAVS1_PAF1_rep1


title: run1a_1h_8h


title: run1a_05h_8h


title: AAVS1_CDC73_rep3


title: AAVS1_MLLT3_rep3

value: AAVS1 edited, MLLT3 antibody


title: run1a_05h_2h


title: run1a_1h_2h


title: CTR9_KD_crosslinked_input_rep2

value: partial CTR9 edited


title: EV-siNC

city: Tainan

first: Shih-Chieh

last: Lin

address: No.1, University Road

department: Institute of Basic Medical Sciences

country: Taiwan

institute: College of Medicine, National Cheng Kung University

description:
LNCaP-EV-EnzaR-siNC
gene_expression_all_01132021.txt

data_processing:
QC: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Mapping: Clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Expression analysis: In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis: Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. The estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: gene_expression_all_01132021.txt: Tab-delimited text file includes raw counts and FPKM values for each Sample.

source_name: prostate cancer cells

growth_protocol: LNCaP and EnzaR cells were cultured in RPMI1640 medium with 10% FBS and 10 uM enzalutamide (only for EnzaR cells) in a humidified atmosphere of 5% CO2 and 95% air at 37℃.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: EnzaR cells were treated with siRNA against YAP1 or control siRNA (40 nM) for 48 hours. Moverover, LNCaP cells were treated with or without EnzaR-EVs isolated from control, YAP1- and CII-depleted EnzaR cells for 48 hours.

value: LNCaP

value: Prostate cancer cells

value: EnzaR-EV-siNC

tag: drug sensitivity

value: Enzalutamide-sensitive cells


title: AAVS1_crosslinked_input_rep3

value: AAVS1 edited


title: AAVS1_CDC73_rep1


title: EV-siCII

description:
LNCaP-EV-EnzaR-siCII
gene_expression_all_01132021.txt

value: EnzaR-EV-siCII


title: AAVS1_MLLT3_rep1


title: run1b_8h_0h


title: run1a_05h_1h


title: run1a_1h_4h


title: run1a_05h_4h


title: EV-siYAP1

description:
LNCaP-EV-EnzaR-siYAP1
gene_expression_all_01132021.txt


title: siYAP1_rep1

description:
EnzaR-siYAP1-1
gene_expression_all_01132021.txt

value: EnzaR

value: Enzalutamide-resistant cells


title: CTR9_KD_native_input_rep3

value: HSPCs


title: control

description:
LNCaP-con
gene_expression_all_01132021.txt

value: vehicle control


title: CTR9_KD_crosslinked_input_rep1


title: AAVS1_MLLT3_rep2


title: CTR9_KD_native_input_rep1


title: CTR9_KD_native_input_rep2


title: AAVS1_crosslinked_input_rep2


title: AAVS1_crosslinked_input_rep1


title: siNC_rep1

description:
EnzaR-siNC-1
gene_expression_all_01132021.txt

value: siNC


title: Batch 9 RNA

city: New York

first: Arnold

last: Han

state: New York

institute: Columbia University

description: Batch 9 RNA: 10x Genomics scRNA-seq of intestinal biopsies from "Batch 9" patients

data_processing:
Cell Ranger v5.0.0
Assembly: GRCh38
Supplementary files format and content: Raw processed files: Barcodes, features, and matrix for RNA and CITE. Metadata and processed RDS objects included.

source_name: Duodenum (Second part)

extract_protocol:
10X Genomics Chromium Platform
10X Genomics Chromium Single Cell 5’ V(D)J with Feature Barcoding Reagent Kits (CG000186) or Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 with Feature Barcode Technology for Cell Surface Protein (CG000208).

value: Duodenum (Second part)


title: AAVS1_native_input_rep3


title: CTR9_KD_crosslinked_input_rep3


title: Batch 8 RNA

description: Batch 8 RNA: 10x Genomics scRNA-seq of intestinal biopsies from "Batch 8" patients


title: AAVS1_native_input_rep2


title: Batch 7 RNA

description: Batch 7 RNA: 10x Genomics scRNA-seq of gluten challenge peripheral blood from "Batch 7" patients

source_name: PBMC

value: PBMC


title: siYAP1_rep2

description:
EnzaR-siYAP1-2
gene_expression_all_01132021.txt


title: siNC_rep2

description:
EnzaR-siNC-2
gene_expression_all_01132021.txt


title: Batch 5 RNA

description: Batch 5 RNA: 10x Genomics scRNA-seq of intestinal biopsies from "Batch 5" patients


title: scRNA-seq CTR9-g2

data_processing:
fastq files processed by cellranger count by default parameter
Genome_build: hg38
Supplementary_files_format_and_content: matrix file generated by cellranger pipeline

source_name: CD34+ cells

growth_protocol: CD34+ HSPCs grow in Stemspan serum free culture medium supplemented with cc100, TPO, UM171

extract_protocol:
CD34+CD45RA-CD90+ cells were flow sorted and packed into single cell droplets by 10XGenomics chromium controller
library constructed according to 10XGenomics single cell RNA seq library construction kit without modifications; 10XGenomics 3' single cell RNA seq

treatment_protocol: CD34+ HSPCs edited by AAVS1 control gRNA RNP and CTR9 gRNA RNP

value: CD34+ HSPCs

value: CTR9 gRNA


title: Batch 5 CITE-seq

description: Batch 5 CITE-seq: 10x Genomics CITE-seq of intestinal biopsies from "Batch 5" patients

data_processing:
Cell Ranger v5.0.0
Assembly: GRCh38
Supplementary files format and content: Raw processed files: Barcodes, features, and matrix for RNA and CITE. Metadata and processed RDS objects included.
Library strategy: CITE-Seq


title: run1a_4h_8h

value: HEK-RAF-ER

value: tamoxifen (4OHT)


title: AAVS1_native_input_rep1


title: Batch 4 CITE-seq

description: Batch 4 CITE-seq: 10x Genomics CITE-seq of intestinal biopsies/gluten challenge peripheral blood from "Batch 4" patients

source_name: Duodenum (Second part) / PBMC

value: Duodenum (Second part) / PBMC


title: scRNA-seq CTR9-g1


title: scRNA-seq AAVS1

value: AAVS1 control gRNA


title: Batch 3 RNA

description: Batch 3 RNA: 10x Genomics scRNA-seq of intestinal biopsies from "Batch 3" patients


title: Batch 2 CITE-seq

description: Batch 2 CITE-seq: 10x Genomics CITE-seq of intestinal biopsies from "Batch 2" patients


title: Batch 2 RNA

description: Batch 2 RNA: 10x Genomics scRNA-seq of intestinal biopsies from "Batch 2" patients


title: Pro-seq CTR9_KD -rep 2

data_processing:
Library strategy: Pro-seq
Read alignment by BWA
Genome_build: hg38; dm6
Supplementary_files_format_and_content: bigWig files generated by deepTools

extract_protocol:
2X nuclear run-on buffer consisted of (10 mM Tris (pH 8), 10 mM MgCl2, 1 mM DTT, 300mM KCl, 40uM/ea biotin-11-NTPs (Perkin Elmer), 0.8U/uL SuperaseIN (Thermo), 1% sarkosyl).  Run-on reactions were performed at 37¡C.
5' adapter ligation was per Reimer but with 15% PEG-8000 final. Eluted cDNA was amplified 5-cycles (NEBNext Ultra II Q5 master mix (NEB) with Illumina TruSeq PCR primers RP-1 and RPI-X) following the manufacturer's suggested cycling protocol for library construction. A portion of preCR was serially diluted and for test amplification to determine optimal amplification of final libraries.

tag: molecule subtype

value: nascent RNA


title: Batch 3 CITE-seq

description: Batch 3 CITE-seq: 10x Genomics CITE-seq of intestinal biopsies from "Batch 3" patients


title: Pro-seq CTR9_KD -rep 3


title: Batch 1 CITE-seq

description: Batch 1 CITE-seq: 10x Genomics CITE-seq of intestinal biopsies from "Batch 1" patients


title: Pro-seq control-rep 2

value: control


title: Batch 6 CITE-seq

description: Batch 6 CITE-seq: 10x Genomics CITE-seq of intestinal biopsies from "Batch 6" patients


title: Pro-seq control-rep 1


title: whole larvae, WT CFP, DMSO, 6 hours, rep 3

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
SLAMDUNK pipeline (https://t-neumann.github.io/slamdunk/)
Assembly: GRCz11
Supplementary files format and content: tcount output SLAMDUNK pipeline containing all results, conversion rates

organism: Danio rerio

source_name: whole larvae

extract_protocol: Zebrafish larvae were co-treated with DMSO or APAP and 4TU for 3 or 6 hours. Larvae were pooled (20 per sample) into TRIzol, and RNA was extracted using the Zymo Directzol kit. RNA was alkylated with iodoacetamide and cleaned up for sequencing.

value: whole larvae

value: WT CFP

value: DMSO

value: 6 hours


title: ZHQ-A-TCR

city: Guangzhou

first: Chao

last: Zhang

address: Zhongshan Er Road

department: Thoracic Oncology

country: China

institute: Guangdong Lung Cancer Institute

description: 10x Genomics TCR library

data_processing:
Basecalls performed using CASAVA version 1.8
For 3' and 5' GEX library, cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table. Seurat package (version: 2.3.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data. PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. CCA analysis in Seurat package was applied for combining 3’ scRNA-Seq data and 5’ scRNA-Seq data. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
For TCR library, cellranger (v3.1.0) was used to obtain the nucleotide sequences of α and β chain in each T cell. Then CDR3 sequence was annotated to calculate the frequency of each clonotype.
Genome_build: Ensembl/GRCh38
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: lung neoplasm-adjacent

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3’ V3 (46 samples) and 5' (16 samples) Reagent Kits (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ V3 and 5' Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

treatment_protocol: treatment naive

tag: histology

value: IAC

tag: Sex

value: M


title: ZHQ-T-TCR

description: 10x Genomics TCR library

source_name: lung neoplasm-tumor


title: XYJ-T-TCR

description: 10x Genomics TCR library

value: MIA

value: F


title: whole larvae, Nrf2KO UPRT, APAP, 6 hours, rep 3

value: Nrf2KO UPRT

value: APAP


title: XYJ-A-TCR

description: 10x Genomics TCR library


title: Batch 4 RNA

description: Batch 4 RNA: 10x Genomics scRNA-seq of intestinal biopsies/gluten challenge peripheral blood from "Batch 4" patients


title: whole larvae, WT CFP, DMSO, 6 hours, rep 2


title: whole larvae, WT CFP, DMSO, 6 hours, rep 1


title: whole larvae, Nrf2KO UPRT, APAP, 6 hours, rep 2


title: Pro-seq control-rep 3

value: CD34+ HSPCs


title: SDY-T-TCR

description: 10x Genomics TCR library


title: whole larvae, Nrf2KO UPRT, APAP, 6 hours, rep 1


title: SDY-A-TCR

description: 10x Genomics TCR library


title: LYH-T-TCR

description: 10x Genomics TCR library


title: whole larvae, Nrf2KO UPRT, DMSO, 6 hours, rep 2


title: LXZ-T-TCR

description: 10x Genomics TCR library


title: whole larvae, Nrf2KO UPRT, DMSO, 6 hours, rep 1


title: Pro-seq CTR9_KD -rep 1

value: CTR9 gRNA


title: whole larvae, WT UPRT, APAP, 6 hours, rep 2

value: WT UPRT


title: LHL-T-TCR

description: 10x Genomics TCR library


title: LXZ-A-TCR

description: 10x Genomics TCR library


title: LHL-A-TCR

description: 10x Genomics TCR library


title: whole larvae, WT UPRT, APAP, 6 hours, rep 1


title: whole larvae, WT UPRT, DMSO, 6 hours, rep 3


title: whole larvae, WT UPRT, DMSO, 6 hours, rep 2


title: whole larvae, WT UPRT, DMSO, 6 hours, rep 1


title: HP-T-TCR

description: 10x Genomics TCR library


title: HP-A-TCR

description: 10x Genomics TCR library


title: whole larvae, Nrf2KO UPRT, APAP, 3 hours, rep 3

value: 3 hours


title: whole larvae, Nrf2KO UPRT, APAP, 3 hours, rep 2


title: LYH-A-TCR

description: 10x Genomics TCR library


title: whole larvae, Nrf2KO UPRT, DMSO, 6 hours, rep 3


title: ZHQ-T

description: 10x Genomics 5' GEX library


title: whole larvae, Nrf2KO UPRT, DMSO, 3 hours, rep 2


title: whole larvae, Nrf2KO UPRT, DMSO, 3 hours, rep 3


title: whole larvae, Nrf2KO UPRT, DMSO, 3 hours, rep 1


title: whole larvae, WT UPRT, APAP, 6 hours, rep 3


title: SDY-T

description: 10x Genomics 5' GEX library


title: XYJ-A

description: 10x Genomics 5' GEX library


title: ZHQ-A

description: 10x Genomics 5' GEX library


title: LYH-A

description: 10x Genomics 5' GEX library


title: LXZ-T

description: 10x Genomics 5' GEX library


title: SDY-A

description: 10x Genomics 5' GEX library


title: XYJ-T

description: 10x Genomics 5' GEX library


title: whole larvae, WT UPRT, APAP, 3 hours, rep 3


title: LYH-T

description: 10x Genomics 5' GEX library


title: JGH-A-TCR

description: 10x Genomics TCR library

value: AIS


title: heartKLF15-WT +  pred  3

city: Cincinnati

first: Mattia

last: Quattrocelli

state: OH

address: 240 Sabin Way

institute: Cincinnati Children's Hospital Medical Center

data_processing:
A quality control check on the fastq files was performed using FastQC.
Upon passing basic quality metrics, the reads were trimmed to remove adapters and low-quality reads using default parameters in Trimmomatic 75 [Version 0.33].
The trimmed reads were then mapped to mm10 reference genome using default parameters with strandness (R for single-end and RF for paired-end) option in Hisat2 76 [Version 2.0.5].
In the next step, transcript/gene abundance was determined using kallisto 77 [Version 0.43.1].
We first created a transcriptome index in kallisto using Ensembl cDNA sequences for the reference genome. This index was then used to quantify transcript abundance in raw counts and counts per million (CPM).
Assembly: mm10
Supplementary files format and content: csv table containing isoform CPM

source_name: myocardium

extract_protocol:
RNA-seq was conducted on RNA extracted from myocardial tissue. Total RNA was extracted from cryo-pulverized, atria- and blood-deprived hearts with Trizol (#15596026; Thermo Fisher Scientific, Waltham, MA) and re-purified using the RNeasy Mini Kit (Cat #74104; Qiagen, Germantown, MD). RNA-seq was performed at the DNA Core (CCHMC) blinded to treatment groups.
150 to 300 ng of total RNA determined by Qubit (Cat#Q33238; Invitro-gen, Waltham, MA) high-sensitivity spectrofluorometric measurement was poly-A selected and reverse tran-scribed using Illumina’s TruSeq stranded mRNA library preparation kit (Cat# 20020595; Illumina, San Diego, CA).
Each sample was fitted with one of 96 adapters containing a different 8 base molecular barcode for high level multiplexing. After 15 cycles of PCR amplification, libraries were sequenced.

value: myocardium

value: 4 months-old

value: male

value: prednisone


title: whole larvae, WT UPRT, APAP, 3 hours, rep 2

value: whole larvae


title: JGH-T-TCR

description: 10x Genomics TCR library


title: whole larvae, WT UPRT, APAP, 3 hours, rep 1


title: whole larvae, WT UPRT, DMSO, 3 hours, rep 3

value: DMSO


title: LXZ-A

description: 10x Genomics 5' GEX library

value: IAC


title: whole larvae, Nrf2KO UPRT, APAP, 3 hours, rep 1


title: Adult liver, wildtype, 9hr

source_name: adult liver

extract_protocol: Adult zebrafish were treated with 4TU for various durations, and livers were dissected and placed in TRIzol. RNA was extracted using Zymo Directzol kit.

value: adult liver

value: WT CFP

value: 9 hours


title: Adult liver, UPRT, 9hr


title: Adult liver, UPRT, 3hr


title: LHL-A

description: 10x Genomics 5' GEX library

value: MIA

value: F


title: LHL-T

description: 10x Genomics 5' GEX library


title: Adult liver, UPRT, 1hr

value: 1 hour


title: Adult liver, UPRT, 6hr

value: 6 hours


title: whole larvae, WT UPRT, DMSO, 3 hours, rep 2

value: WT UPRT


title: whole larvae, WT UPRT, DMSO, 3 hours, rep 1

value: 3 hours


title: heartKLF15-WT + veh 3

value: vehicle


title: heartKLF15-WT +  pred  1

value: myocardium


title: heartKLF15-WT + veh 2

value: 4 months-old


title: liver, wt, dmso, 24hours, rep4

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were trimmed with trimgalore
Reads were aligned to the zebrafish reference genome using HiSAT2
Bam files were sorted and indexed
Reads were assigned to genes using htseq-count.
Assembly: GRCz11.98
Supplementary files format and content: Raw gene counts from htseq in matrix file, tab delimited format

source_name: liver

extract_protocol: Zebrafish livers were dissected, pooled (20 per sample) and placed into TRIzol for RNA extraction using the Zymo Directzol kit.

value: liver

value: wt

value: dmso


title: heartKLF15-KO +  pred  3

value: male

value: prednisone


title: heartKLF15-WT + veh 1


title: liver, wt, dmso, 24hours, rep3


title: liver, wt, dmso, 24hours, rep2


title: JGH-A

description: 10x Genomics 5' GEX library

value: AIS


title: heartKLF15-WT +  pred  2


title: JGH-T

description: 10x Genomics 5' GEX library


title: liver, wt, dmso, 12hours, rep3


title: HP-T

description: 10x Genomics 5' GEX library

value: IAC


title: HP-A

description: 10x Genomics 5' GEX library


title: liver, wt, dmso, 12hours, rep4


title: heartKLF15-KO +  pred  2


title: liver, wt, dmso, 12hours, rep2


title: heartKLF15-KO +  pred 1


title: liver, wt, dmso, 12hours, rep1


title: ZST-T

description: 10x Genomics 3' GEX library

value: M


title: heartKLF15-KO + veh 3


title: liver, wt, apap, 24hours, rep4

value: apap


title: WT-28°C, H4K5ac, ChIP

city: Shanghai

first: Wenhao

last: Xie

state: Shanghai

address: No. 2005, Songhu Road

department: School of Life Science

institute: Fudan University

data_processing:
Cutadapt (v3.5) was used to eliminate both adapters and low-quality sequencing reads from the raw reads.
The filtered reads were mapped to Arabidopsis thaliana genome (TAIR10) using Bowtie2 (v.2.4.5). We then used SAMtools (v.1.13) to remove the PCR duplicates and the low mapped quality reads.
MACS2 (v.2.2.7.1) was used to find peaks (p-value < 0.05). MAnorm (v.1.3.0) was used to identify the differentially peaks with the following thresholds: p-value < 0.05, fold change >1.2.
Then, the peaks were annotated by using ChIPpeakAnno (v.3.28.1) to find genes showing the improper H3K9ac and H4K5ac inductions in the pif4 mutant.
bamCoverage (v.3.5.1) was used to normalize the reads using RPKM, and computeMatrix (v.3.5.1) was used to calculate the enrichment signals.
Assembly: TAIR10
Supplementary files format and content: bigwig

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seedlings were grown on 1/2 MS medium under continuous white light at 22°C for 6 days.

extract_protocol:
Seedlings were harvested and fixed with the buffer containing 0.4 M sucrose, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 1% formaldehyde, and 1 mM PMSF.Chromatin was sonicated into DNA fragments around 200~500-bp in size using lysis buffer containing 50 mM HEPES (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1% SDS, 0.1% Na deoxycholate, 1% Triton X-100 and Protease Inhibitor cocktail.
The ChIP-seq libraries were constructed by following the manufacturer’s instructions of VAHTSTM Universal DNA Library Prep Kit (Vazyme).

treatment_protocol: Treated at 28°C (warm conditions) or 22°C (normal conditions) for 6 h.

value: seedlings

tag: antibody


title: WT-28°C, Input, ChIP

tag: genotype

value: Input


title: ZST-A

description: 10x Genomics 3' GEX library


title: liver, wt, apap, 24hours, rep3


title: heartKLF15-KO + veh 2


title: WT-28°C, H3K9ac, ChIP


title: WT-22°C, Input, ChIP


title: ZQM-T

description: 10x Genomics 3' GEX library


title: heartKLF15-KO + veh 1


title: liver, wt, apap, 24hours, rep2


title: ZQM-A

description: 10x Genomics 3' GEX library


title: ZJ-T2

description: 10x Genomics 3' GEX library

value: F


title: liver, wt, dmso, 24hours, rep1


title: ZJ-A2

description: 10x Genomics 3' GEX library


title: WT-22°C, H4K5ac, ChIP


title: liver, wt, apap, 24hours, rep1


title: liver, wt, apap, 12hours, rep3


title: pif4-28°C, Input, ChIP


title: GRKO_PRED3

value: cardiomyocyte-GR-KO


title: GRKO_PRED2


title: WT-22°C, H3K9ac, ChIP


title: pif4-28°C, H4K5ac, ChIP


title: WYQ-T

description: 10x Genomics 3' GEX library

value: MIA


title: liver, wt, apap, 12hours, rep4


title: WYQ-A

description: 10x Genomics 3' GEX library


title: liver, wt, apap, 12hours, rep2


title: liver, wt, apap, 12hours, rep1


title: pif4-22°C, Input, ChIP


title: WYH-T

description: 10x Genomics 3' GEX library


title: liver, nrf2KO, dmso, 24hours, rep4


title: GRKO_VEH2

value: vehicle


title: GRKO_VEH1

value: myocardium


title: pif4-28°C, H3K9ac, ChIP


title: pif4-22°C, H4K5ac, ChIP


title: WYH-A

description: 10x Genomics 3' GEX library


title: GRKO_PRED1

value: 4 months-old


title: WHM-T

description: 10x Genomics 3' GEX library


title: liver, nrf2KO, dmso, 24hours, rep3

value: liver


title: GRKO_VEH3


title: pif4-22°C, H3K9ac, ChIP


title: liver, nrf2KO, dmso, 24hours, rep2


title: WT_PRED1

value: cardiomyocyte-GR-WT


title: WT_VEH3


title: TRD-T

description: 10x Genomics 3' GEX library


title: unkIs9_K12wt_2

city: HK

first: Chaogu

last: Zheng

address: The University of Hong Kong, Pokfulam Road

department: School of Biological Science

country: Hong Kong

institute: University of Hong Kong

data_processing:
The trimmed sequencing reads were mapped to C. elegans reference genome (WB235) using STAR (2.7.10) with the option --quantMode geneCounts. The counts were then normalized and the differentially expressed genes were then identified using the standard pipeline of DESeq2 in R.
Assembly: WB235
Supplementary files format and content: tab-delimited text files contain the read count generated by STAR

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: The animals were bleached to obtain eggs, which were hatched in M9 overnight. The next day, L1s were seeded onto NGM plates with K12 WT bacteria and grown until L4 stage before being harvested.

extract_protocol:
The L4 animals were washed with water and the worm pellet was extracted using TRIzol reagent (Invitrogen). The library was constructed by BGI using the standard DNBSEQ Eukaryotic Strand-specific Transcriptome Resequencing service (P_Stranded Library & PE100 Seq).
The library was constructed by BGI using the standard DNBSEQ Eukaryotic Strand-specific Transcriptome Resequencing service (P_Stranded Library & PE100 Seq).

value: whole worm

value: Fed with K12 WT bacteria


title: TRD-A

description: 10x Genomics 3' GEX library


title: unkIs9_K12wt_1


title: WHM-A

description: 10x Genomics 3' GEX library


title: liver, nrf2KO, dmso, 12hours, rep4

value: dmso


title: WT_VEH2

value: male


title: unkIs7_K12wt_2


title: liver, nrf2KO, dmso, 12hours, rep3


title: SXZ-T

description: 10x Genomics 3' GEX library

value: IAC


title: WT_PRED3

value: prednisone


title: WT_VEH1


title: unkIs7_K12wt_1


title: liver, nrf2KO, dmso, 12hours, rep2


title: liver, nrf2KO, dmso, 12hours, rep1


title: CTR_K12wt_2

value: CGZ621 unkIs11[dat-1p::GFP]


title: PNP-T

description: 10x Genomics 3' GEX library

value: M


title: DSS-treated (D), ko, mice 05

city: Turku

first: Madhukar

last: Vedantham

address: Kiinamyllynkatu 10-D

country: Finland

institute: University of Turku

data_processing:
Raw data (raw reads) of fastq format were firstly processed through Novogene’s in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCm38.p6, gca_000001635_8
Supplementary files format and content: .XLSX file includes raw counts for each Sample
Supplementary files format and content: .XLSX file includes FPKM counts for each Sample

source_name: Distal colon

growth_protocol: We used the previously described body-wide Parp14 knockout mice (Cho et al, 2009) in a specific-pathogen-free area at Central Animal Laboratory of the University of Turku with free access to soy-free diet and water ad libitum. Parp14 knockout mice (Cho et al, 2009) were backcrossed for 10 generations to C57BL/6N background before starting experiments. Thereafter, heterozygous mice were inbred to generate homozygous littermates for experiments.

extract_protocol:
Total RNA was isolated from C57BL/6N mice distal colon tissues using TRIsure reagent (BIO-38033, Bioline Gmbh, Germany) and genomic DNA was digested using RNase-free DNase (rDNase) from Machery-Nagel as per the manufacturer’s instructions.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. To select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: Male mice of age 6-8 weeks were used for DSS treatment. They were allocated to two treatment groups, i.e., control and DSS, with similar body weight and littermate distribution. DSS (40,000 Da, TdB Consultancy AB, Uppsala, Sweden) solution was fresh, dissolved in autoclaved water to a 2.5% concentration, and administered to mice in drinking water during days 0-7 of the experiment. Control mice were matched to DSS-treated mice according to age, and starting weight, and were treated equally to DSS-treated mice, except that they did not receive DSS.

value: Distal colon

tag: strain

value: Male


title: SXZ-A

description: 10x Genomics 3' GEX library

value: F


title: WT_PRED2

tag: treatment


title: CTR_K12wt_1


title: DSS-treated (D), ko, mice 04


title: liver, nrf2KO, dmso, 24hours, rep1

tag: time


title: liver, nrf2KO, apap, 24hours, rep4

value: apap


title: PNP-A

description: 10x Genomics 3' GEX library


title: P17-3

city: xuzhou

first: Ruosi

last: Yao

state: China

institute: Xuzhou Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell line

value: multiple myeloma


title: liver, nrf2KO, apap, 24hours, rep3


title: DSS-treated (D), ko, mice 03


title: P17-2


title: OYX-T

description: 10x Genomics 3' GEX library

value: MIA


title: liver, nrf2KO, apap, 24hours, rep2


title: OYX-A

description: 10x Genomics 3' GEX library


title: DSS-treated (D), ko, mice 02


title: liver, nrf2KO, apap, 24hours, rep1


title: P17-1


title: MMH-T

description: 10x Genomics 3' GEX library

value: AIS


title: con-3

value: control


title: liver, nrf2KO, apap, 12hours, rep3

value: liver


title: DSS-treated (D), wt, mice 04

value: WT


title: DSS-treated (D), ko, mice 01


title: MMH-A

description: 10x Genomics 3' GEX library


title: con-2


title: LY-T

description: 10x Genomics 3' GEX library


title: liver, nrf2KO, apap, 12hours, rep4


title: con-1


title: liver, nrf2KO, apap, 12hours, rep2


title: DSS-treated (D), wt, mice 02


title: 102978-001-036

city: Leiden

first: Pim

last: van Gorp

state: Zuid-Holland

address: Albinusdreef 2

department: Experimental Cardiology

country: Netherlands

institute: Leiden University Medical Center

description:
D18, n=4
iAM-1 cells / 9d

data_processing:
Read counting was performed in the edgeR Bioconductor software package  (version 3.26.8) and in parallel normalized using depth normalization (counts per million, CPM) as well as length normalization (transcript per million, TPM).
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every individual as well as pooled sample

organism: Rattus norvegicus

source_name: iAM-1 cells

growth_protocol: iAM-1 cells were cultured in Advanced DMEM/F-12 (Thermo Fisher Scientific, cat# 12634010) supplemented with 2% FBS and 1⨯ GlutaMAX Supplement (Thermo Fisher Scientific). Prior to the initiation of cardiac differentiation the cells were proliferating by adding 100ng/ml doxycyclin to the culture medium

extract_protocol:
Total RNA was collected using Trizol and the Rneasy Mini Kit. The quality of the RNA samples designated for RNA-Seq was confirmed using the Advanced Analytical Fragment Analyzer.
cDNA was generated from total RNA samples with RNA integrity numbers above 7.5 using the NEBNext Ultra Directional RNA library preparation method including polyA enrichment (New England Biolabs, cat# E7420L). Sequencing was performed on a HiSeq 4000 system (Illumina, San Diego, CA). For each sample at least 20 million 150-bp paired-end reads were obtained.

treatment_protocol: During the differentiation phase no doxycyclin was added to the culture medium. During dedifferentiation 100ng/ml doxycyclin was added to the culture medium

value: wistar

value: iAM-1 cells

tag: day

tag: group

value: Dedifferentiation


title: liver, nrf2KO, apap, 12hours, rep1


title: DSS-treated (D), wt, mice 03

tag: tissue


title: LYJ-T

description: 10x Genomics 3' GEX library

value: IAC

tag: age


title: 102978-001-035

description:
D18, n=3
iAM-1 cells / 9c


title: DSS-treated (D), wt, mice 01


title: LYJ-A

description: 10x Genomics 3' GEX library


title: infected treated Replicate 5

city: Madison

first: Thibaut

last: Rosay

state: Wisconsin

department: MMI

institute: UW Madison

data_processing:
Demultiplexing, quality control, and adapter trimming were performed with bcl-convert (v4.1.5)
Assembly: GCF_000001635.27
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: Cecum

growth_protocol: tissue was collected 7 days after infection

extract_protocol:
Mammalian ribosomal RNA is depleted using the RiboCop kit from Lexogen
Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices

treatment_protocol: mice infected or not with Citrobacter rodentium and treated with or without GUSi

value: Cecum

tag: infection

value: C. rodentium infection

value: GUSi


title: LY-A

description: 10x Genomics 3' GEX library


title: 102978-001-034

description:
D18, n=2
iAM-1 cells / 9b


title: water (W), ko, mice 03

value: Distal colon

value: water


title: 102978-001-033

description:
D18, n=1
iAM-1 cells / 9a


title: DSS-treated (D), wt, mice 05

value: Male


title: LRH-T

description: 10x Genomics 3' GEX library

value: F


title: infected treated Replicate 4


title: water (W), ko, mice 02


title: 102978-001-032

description:
D12, n=4
iAM-1 cells / 8d


title: infected treated Replicate 2


title: 102978-001-031

description:
D12, n=3
iAM-1 cells / 8c


title: LRH-KA

description: 10x Genomics 3' GEX library


title: water (W), ko, mice 01


title: water (W), wt, mice 05


title: infected treated Replicate 1


title: water (W), wt, mice 04


title: LRH-A

description: 10x Genomics 3' GEX library


title: Infected replicate 5


title: LMY-T

description: 10x Genomics 3' GEX library


title: 102978-001-030

description:
D12, n=2
iAM-1 cells / 8b


title: water (W), wt, mice 03


title: 102978-001-028

description:
D11, n=4
iAM-1 cells / 7d


title: water (W), wt, mice 02


title: LMY-A

description: 10x Genomics 3' GEX library


title: Infected replicate 3


title: JWM-T

description: 10x Genomics 3' GEX library

value: M


title: 102978-001-029

description:
D12, n=1
iAM-1 cells / 8a


title: 102978-001-027

description:
D11, n=3
iAM-1 cells / 7c


title: Infected replicate 2


title: infected treated Replicate 3


title: LRH-KT

description: 10x Genomics 3' GEX library

value: MIA


title: Infected replicate 1


title: HYY-T2

description: 10x Genomics 3' GEX library


title: 102978-001-025

description:
D11, n=1
iAM-1 cells / 7a


title: pRPS3-mCherry-tPMA1-long_b2

city: Edinburgh

first: Edward

last: Wallace

address: Waddington 2.18, Max Born Crescent, King’s Buildings

department: School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

data_processing:
Read quality was checked with fastqc=0.11.9
Adapters were removed with cutadapt=1.18 (Options = --trim-n -O 1 -m 20)
Alignment was completed with hisat2=2.1.0 (Options = --no-spliced-alignment --no-unal --maxins 1500 -k 2)
Reads per gene were counted with featureCounts=2.00 (Options = -p -s 2 -R BAM)
Bed files were created with bedtools=2.30.0
Alignment quality was checked with multiQC=1.9
Bam files were create with samtools=1.11
Assembly: sacCer3 (R64-2)
Supplementary files format and content: Format: csv, Content: quantified reads ending in 3'-UTR region of reporter constructs, per construct
Supplementary files format and content: Format: csv, Content: raw read counts mapped to each gene across the genome, one file per sample.
Supplementary files format and content: Format: csv, Content: quantified reads ending in 3'-UTR region of control gene, per construct

organism: Saccharomyces cerevisiae

source_name: S.cerevisiae expressing plasmid with reporter gene pRPS3-mCherry-tPMA1-long_WT

growth_protocol: Yeast cultures were grown for 4h at 30degC, 200rpm, in liquid SC-Ura medium up to OD600=0.7

extract_protocol:
RNA extraction protocol: dx.doi.org/10.17504/protocols.io.beetjben
QuantSeq REV (Lexogen)
3'-end sequencing

tag: plasmid


title: JWM-A

description: 10x Genomics 3' GEX library


title: 102978-001-026

description:
D11, n=2
iAM-1 cells / 7b


title: pRPS3-mCherry-tPMA1-long_b1


title: 102978-001-024

description:
D10, n=4
iAM-1 cells / 6d


title: treated Replicate 5

value: Control


title: pRPS3-mCherry-tHSP26_b4

source_name: S.cerevisiae expressing plasmid with reporter gene pRPS3-mCherry-tHSP26_WT


title: treated Replicate 4


title: HYY-T1

description: 10x Genomics 3' GEX library


title: HYY-A2

description: 10x Genomics 3' GEX library


title: Infected replicate 4


title: treated Replicate 3


title: pRPS3-mCherry-tHSP26_b3


title: HYY-A1

description: 10x Genomics 3' GEX library


title: treated Replicate 2


title: HYS-T

description: 10x Genomics 3' GEX library


title: 102978-001-021

description:
D10, n=1
iAM-1 cells / 6a


title: 102978-001-022

description:
D10, n=2
iAM-1 cells / 6b


title: water (W), wt, mice 01


title: pHSP26-mCherry-tHSP26_b2

source_name: S.cerevisiae expressing plasmid with reporter gene pHSP26-mCherry-tHSP26_WT


title: treated Replicate 1


title: pRPS13-mCherry-tHSP26_b2

source_name: S.cerevisiae expressing plasmid with reporter gene pRPS13-mCherry-tHSP26_WT


title: pHSP26-mCherry-tHSP26_b1


title: HJY-T

description: 10x Genomics 3' GEX library


title: control replicate 4


title: 102978-001-020

description:
D9, n=4
iAM-1 cells / 5d

value: Differentiation


title: 102978-001-018

description:
D9, n=2
iAM-1 cells / 5b


title: control replicate 5


title: HYS-A

description: 10x Genomics 3' GEX library


title: HJY-A

description: 10x Genomics 3' GEX library


title: pRPS3-mCherry-tHSP26_b2


title: control replicate 3


title: 102978-001-023

description:
D10, n=3
iAM-1 cells / 6c


title: pRPS3-mCherry-tHSP26_b1


title: CZX-T

description: 10x Genomics 3' GEX library


title: pRPS13-mCherry-tHSP26_b1


title: 102978-001-019

description:
D9, n=3
iAM-1 cells / 5c


title: control replicate 2


title: pRPS3-mCherry-tTOS6_b2

source_name: S.cerevisiae expressing plasmid with reporter gene pRPS3-mCherry-tTOS6_WT


title: CXL-T

description: 10x Genomics 3' GEX library


title: pRPS3-mCherry-tTOS6_b1


title: 102978-001-017

description:
D9, n=1
iAM-1 cells / 5a


title: CZX-A

description: 10x Genomics 3' GEX library


title: control replicate 1


title: IECs_Amp_Tributyrin_rep3

city: Cleveland

first: Leah

last: Gates

state: Ohio

address: Case Western Reserve University

institute: Case Western Reserve University - Cleveland, OH

data_processing:
Transcript Quantification with Salmon (version 0.8.2)
Alignment of ChIPseq reads was done with Rsubread (version 1.30.6)
Normalization and rlog transformation of raw read counts in genes were performed using DESeq2 (version 1.20.0)
Assembly: Bsgenome.Mmusculus.UCSC.mm10 (version 1.4.0) and TxDb.Mmusculus.UCSC.mm10.knownGene (version 3.4.0)
Supplementary files format and content: fastq, bigwigs, counts

source_name: Intestinal epithelial cells

extract_protocol:
Intestinal epithelial cells were isolated using DTT/EDTA mechanical disruption followed by Dispase dignestion. RNA was harvested using RNAeasy isolation kits and genomic DNA was isolated following immunoprecipitation of sonicated chromatin.
Libraries were generated using NEBNext Ultra II kits.

treatment_protocol: Mice were treated with vehicle (10g/L Splenda) and with or without 1g/L Ampicillin for 7 days. On day 7, mice were gavaged with either mock gavage (25% glycerol) or tributyrin for 6 hours prior to tissue harvest.

value: Cecal intestinal epithelial cells

value: Ampicillin with tributyrin gavage


title: 102978-001-014

description:
D3, n=2
iAM-1 cells / 4b

value: wistar


title: 102978-001-015

description:
D3, n=3
iAM-1 cells / 4c

value: iAM-1 cells


title: 102978-001-016

description:
D3, n=4
iAM-1 cells / 4d


title: CXL-A

description: 10x Genomics 3' GEX library


title: IECs_Amp_Tributyrin_rep2


title: 102978-001-011

description:
D2, n=3
iAM-1 cells / 3c


title: DN_5

city: Yiwu

first: Qiang

last: Sun

state: Zhejiang

address: No. N1, Shangcheng Avenue

institute: Zhejiang University

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.20.1). In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.
Clean reads were aligned to the hg38 genome assembly using HISAT2 2.0.1 with default parameters.
Raw counts of genes in different samples were calculated using featureCounts (version 2.0.0) based on the annotation gtf file obtained from GENCODE version 23 (https://www.gencodegenes.org)
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: blood sample

extract_protocol:
Total RNA was extracted by Trizol reagent. RNA quality and concentration were measured by using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). Samples with sufficient amount of high-quality RNA (No contaminants, RNA integrity number > 5) were used for transcriptome library preparation.
mRNA was isolated using oligo (dT) beads (Thermo Fisher Scientific, USA) and fragmented using NEBNext Ultra RNA Library PrepKit for Illumina (New England Biolabs, USA) according to the manufacturer’s instructions.

tag: disease state

value: Diabetic Nephropathy

value: Blood


title: DN_2

description: Total RNA was extracted by Trizol reagent. RNA quality and concentration were measured by using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). Samples with sufficient amount of high-quality RNA (No contaminants, RNA integrity number > 5) were used for transcriptome library preparation.


title: 102978-001-013

description:
D3, n=1
iAM-1 cells / 4a


title: DN_3


title: IECs_Amp_Tributyrin_rep1


title: IECs_Amp_Mock_rep1

value: Ampicillin with mock gavage


title: DN_4


title: IECs_Amp_Mock_rep3


title: IECs_Vehicle_Mock_rep2

value: Vehcile with mock gavage


title: IECs_Amp_Mock_rep2


title: IECs_Input_DNA


title: DN_1


title: 102978-001-009

description:
D2, n=1
iAM-1 cells / 3a


title: 102978-001-007

description:
D1, n=3
iAM-1 cells / 2e


title: 102978-001-006

description:
D1, n=2
iAM-1 cells / 2b


title: 102978-001-005

description:
D1, n=1
iAM-1 cells / 2a


title: T2D_5

value: Type 2 Diabetes


title: IECs_Vehicle_Mock_rep1


title: 102978-001-008

description:
D1, n=4
iAM-1 cells / 2d


title: IECs_H3K4me3_ChIP

value: H3K4me3 (Active Motif 39159)


title: T2D_2


title: 102978-001-012

description:
D2, n=4
iAM-1 cells / 3d


title: T2D_1


title: IECs_Vehicle_Mock_rep3


title: 102978-001-010

description:
D2, n=2
iAM-1 cells / 3b


title: 102978-001-003

description:
D0, n=3
iAM-1 cells / 1c


title: 102978-001-002

description:
D0, n=2
iAM-1 cells / 1b


title: 102978-001-004

description:
D0, n=4
iAM-1 cells / 1d


title: T2D_4


title: IECs_H3K27ac_ChIP_rep2

value: H3K27ac (Active Motif 39133)


title: HV_4

value: Healthy volunteer


title: HV_5


title: IECs_H3K27bu_ChIP_rep2

value: H3K27bu (Millipore ABE2854)


title: HV_3


title: IECs_H3K27me3_ChIP

value: H3K27me3 (Cell Signaling 9733)


title: T2D_3


title: IECs_H3K27ac_ChIP_rep1


title: ZT21, HC [G610_71_RS72_S71]

status: Public on Jan 12 2024

city: State College

first: Aswathy

last: Sebastian

address: University Park

institute: PennState

data_processing:
Data quality was inspected using FastQC reports.
Data was mapped to the mouse reference genome and visualized in IGV.
Reads mapping to the genes were counted using featureCounts software.
Read count normalization and differential expression were performed using DESeq2 package in R.
Circadian genes were identified with JTK algorithm in the Metacycle program, specifying 24-hour window.
Over representation analysis was performed in R to identify the enriched KEGG and Reactome pathways.
Assembly: Mus musculus, GRCm38 build
Supplementary files format and content: Tab delimited file with gene-level raw read counts for each sample

source_name: dorsal hippocampus

extract_protocol:
RNA was harvested with the Rneasy mini kit (Qiagen). 250ng of total RNA was used to contstruct sequencing libraries
RNA libraries for RNA-seq were prepared using the Illumina Stranded mRNA Prep kit following manufacturer protocols

value: dorsal hippocampus

value: Sacrificed from homecage with ZT21 OLM group above


title: ZT21, HC [G610_23_RS70_S23]


title: ZT21, HC [G610_24_RS67_S24]


title: ZT9, HC [G610_69_RS66_S69]

value: Sacrificed from homecage with ZT9 OLM group above


title: ZT9, HC [G610_61_RS65_S61]


title: ZT21, HC [G610_64_RS68_S64]


title: ZT9, HC [G610_62_RS62_S62]


title: ZT21, OLM [G610_60_RS58_S60]

value: Trained in OLM at ZT21 (4a), sac'd 60m later


title: HV_1


title: ZT21, OLM [G610_20_RS57_S20]


title: HV_2


title: ZT9, OLM [G610_58_RS54_S58]

value: Trained in OLM at ZT9 (4p), sac'd 60m later


title: EC-PDC_siEfp_#A

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

country: Japan

institute: Saitama Medical University

description: Gene expression data from endometrial cancer patient-derived cells treated with siRNA targeting Efp (siEfp #A)

hyb_protocol: Approximately 5.5 micro g of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45 degrees centigrade for 16 hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix Transcriptome Analysis Console (TAC). RMA data.

label: biotin

source_name: Endometrial cancer patient-derived cells treated with siEfp #A

label_protocol: cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: Endometrial cancer patient-derived cells (EC-PDCs) were maintained in STEMPRO hESC SFM medium supplemented with 8 ng/mL bFGF, penicillin/streptomycin, 20 mmol/L Y27632, and 0.1 mmol/L 2-mercaptoethanol using ultra-low-attachment culture dish.

extract_protocol: Total RNA was extracted using ISOGEN reagent (Nippon Gene, Japan).

treatment_protocol: EC-PDCs were transfected with siRNA targeting Efp (siEfp #A) or control siRNA (siControl) for 60 hours.

tag: sirna

value: siEfp

tag: cell type


title: ZT9, HC [G610_22_RS64_S22]


title: ZT9, OLM [G610_57_RS53_S57]


title: EC-PDC_siControl

description: Gene expression data from endometrial cancer patient-derived cells treated with control siRNA

source_name: Endometrial cancer patient-derived cells treated with siControl

value: siControl


title: ZT9, OLM [G610_18_RS51_S18]


title: ZT21, OLM [G610_59_RS60_S59]


title: 102978-001-001

description:
D0, n=1
iAM-1 cells / 1a

value: wistar

value: iAM-1 cells

value: Differentiation


title: ZT9, HC [G610_21_RS61_S21]


title: ZT21, OLM [G610_19_RS59_S19]


title: ZT9, OLM [G610_66_RS50_S66]


title: ZT17, HC [G610_40_RS46_S40]

value: Sacrificed from homecage with ZT17 OLM group above


title: ZT21, OLM [G610_67_RS56_S67]


title: ZT21, OLM [G610_68_RS55_S68]


title: IECs_H3K27bu_ChIP_rep1

value: Cecal intestinal epithelial cells


title: ZT21, HC [G610_72_RS71_S72]


title: ZT9, OLM [G610_17_RS75_S17]


title: ZT5, HC [G610_14_RS39_S14]

value: Sacrificed from homecage with ZT5 OLM group above


title: ZT5, HC [G610_37_RS40_S37]


title: ZT17, HC [G610_55_RS48_S55]


title: ZT17, OLM [G610_52_RS36_S52]

value: Trained in OLM at ZT17 (12a), sac'd 60m later


title: ZT5, HC [G610_53_RS37_S53]


title: ZT17, HC [G610_56_RS47_S56]


title: ZT21, HC [G610_63_RS69_S63]


title: ZT17, OLM [G610_12_RS34_S12]


title: ZT17, HC [G610_15_RS44_S15]


title: ZT17, OLM [G610_36_RS32_S36]


title: ZT5, HC [G610_38_RS41_S38]


title: ZT17, OLM [G610_51_RS31_S51]


title: ZT5, OLM [G610_49_RS28_S49]

value: Trained in OLM at ZT5 (12p), sac'd 60m later


title: ZT5, HC [G610_13_RS42_S13]


title: ZT5, OLM [G610_10_RS27_S10]


title: ZT9, OLM [G610_65_RS52_S65]


title: ZT17, OLM [G610_11_RS35_S11]


title: ZT5, HC [G610_54_RS38_S54]


title: ZT17, HC [G610_16_RS43_S16]


title: ZT9, HC [G610_70_RS63_S70]


title: ZT13, HC [G610_32_RS24_S32]

value: Sacrificed from homecage with ZT13 OLM group above


title: ZT5, OLM [G610_33_RS30_S33]


title: ZT5, OLM [G610_50_RS29_S50]


title: ZT13, HC [G610_48_RS23_S48]


title: ZT17, HC [G610_39_RS45_S39]


title: ZT13, HC [G610_08_RS19_S8]


title: ZT1, HC [G610_46_RS17_S46]

value: Sacrificed from homecage with ZT1 OLM group above


title: ZT17, OLM [G610_35_RS33_S35]

value: dorsal hippocampus


title: ZT1, HC [G610_45_RS16_S45]


title: ZT1, HC [G610_29_RS15_S29]


title: ZT13, HC [G610_47_RS22_S47]


title: ZT13, HC [G610_07_RS20_S7]


title: ZT13, HC [G610_31_RS21_S31]


title: ZT1, HC [G610_06_RS14_S6]


title: ZT13, OLM [G610_27_RS12_S27]

value: Trained in OLM at ZT13 (8p), sac'd 60m later


title: ZT13, OLM [G610_03_RS7_S3]


title: ZT13, OLM [G610_28_RS10_S28]


title: ZT13, OLM [G610_44_RS74_S44]


title: ZT13, OLM [G610_43_RS8_S43]


title: ZT5, OLM [G610_09_RS26_S9]


title: ZT13, OLM [G610_04_RS9_S4]


title: ZT1, OLM [G610_26_RS6_S26]

value: Trained in OLM at ZT1 (8a), sac'd 60m later


title: ZT1, OLM [G610_42_RS5_S42]


title: ZT1, OLM [G610_02_RS73_S2]


title: ZT1, OLM [G610_41_RS4_S41]


title: ZT5, OLM [G610_34_RS25_S34]


title: ZT1, OLM [G610_01_RS1_S1]


title: ZT1, OLM [G610_25_RS3_S25]


title: ZT1, HC [G610_05_RS18_S5]


title: K562, TDD14_ZFfree_panelTDD14, biol. rep. 3

city: Richmond

first: Jessica

last: Davis

state: CA

address: 501 Canal Blvd

institute: Sangamo Therapeutics

description: IDT's rhAmpSeq Design Tool for CRISPR gene editing analysis was used to design multiplexed primer pools. Libraries were generated using each primer pool and IDT's rhAmpSeq CRISPR Library Kit along with rhAmpSeq Index Primers. Samples were run according to manufacturer’s instructions.  Forward and reverse reads were merged with SeqPrep. Reads were then demultiplexed followed by application of quality and amplicon filters. Amplicons within each sample were demultiplexed using an in-house script using the first 23 bp of reads. Processed data file contains the # of reads per amplicon and the frequency of bases per amplicon position across these reads. The percent of reads per amplicon that matched the expected hg38 amplicon sequence is indicated in the perc_non_indel column.

data_processing:
Basecalling: Illumina Real Time Analysis (RTA) v3
Demultiplexing: Illumina bcl2fastq v2.20.0.422, with parameters “--no-lane-splitting --barcode-mismatches 0”
Adaptor trim and read merging: SeqPrep v1.3.2, with parameters “-y I”
Sequence read quality filter: Custom script with minimum quality threshold of 14 over all bases
Indel detection and quantization: Custom script where reads are aligned to the intended hg38 amplicon using the Biopython v1.78 pairwise2.globalmd aligner with parameters match=8, mismatch=-5, gapopenA=-5, gapextendA=-0.1, gapopenB=-5, gapextendB=-0.1. Then indels are called based on alignment gaps. Bowtie v2 is run to remove sequences that map to an unintended locus. Then a position weight matrix is generated from the set of alignments using the “wildtype” sequences that had no indels.
Assembly: hg38
Supplementary files format and content: Excel sheet of all amplicons measured across all samples that lists reads measured per amplicon, percent matching the expected hg38 amplicon sequence, and frequency of bases per position.
Library strategy: Amplicon sequencing

source_name: bone marrow

growth_protocol: Cells were grown in RPMI-1640 growth medium supplemented with 10% FBS and 1x Penicillin-Streptomycin-Gentamycin (Gibco) and maintained at 37C with 5% CO2

extract_protocol:
Genomic DNA was isolated using QuickExtract to a final concentration of 1440 cells/µL
Potential base edited sites were amplified from genomic material isolated from transfected T cells using the rhAmpSeq™ CRISPR Library Kit (IDT). 6.4 µL of quick extract solution was used with 1 µL DMSO in the first rhAmpSeq™ PCR reaction, adjusting the total reaction volume to 25 µL. 10.2 µL of PCR 1 was used with 0.8 µL of DMSO in the second PCR reaction.

treatment_protocol: K562 cells were electroporated with pDNA using the SF cell line 96-well Nucleofector kit (Lonza, V4SC-2960) using manufacturer’s protocol. Nucleofector program 96-FF-120 was used to electroporate K562 cells with the pDNA mix on the Amaxa Nucleofector 96-well Shuttle System (Lonza).

value: bone marrow

value: lymphoblast

value: female

tag: biomaterial provider

value: ATCC


title: K562, TDD14_ZFfree_panelDddATDD14, biol. rep. 3

tag: Sex


title: K562, TDD14_ZFfree_panelDddATDD14, biol. rep. 4


title: K562, TDD14_ZFfree_panelDddA, biol. rep. 4


title: K562, TDD14_ZFfree_panelDddA, biol. rep. 3


title: K562, TDD14_ZFfree_panelDddATDD14, biol. rep. 2


title: K562, TDD14_ZFfree_panelTDD14, biol. rep. 2


title: K562, TDD14_ZFfree_panelDddA, biol. rep. 2


title: ZT1, HC [G610_30_RS13_S30]


title: K562, TDD14_ZFfree_panelDddATDD14, biol. rep. 1


title: K562, TDD14_ZFfree_panelTDD14, biol. rep. 4


title: K562, TDD14_ZFfree_panelTDD14, biol. rep. 1


title: K562, DddA-G1404_ZFfree_panelDddATDD14, biol. rep. 4


title: K562, DddA-G1404_ZFfree_panelTDD14, biol. rep. 4


title: K562, DddA-G1404_ZFfree_panelTDD14, biol. rep. 2


title: K562, TDD14_ZFfree_panelDddA, biol. rep. 1


title: K562, DddA-G1404_ZFfree_panelDddA, biol. rep. 3


title: K562, DddA-G1404_ZFfree_panelDddA, biol. rep. 4


title: K562, DddA-G1404_ZFfree_panelDddA, biol. rep. 1


title: K562, DddA-G1404_ZFfree_panelDddATDD14, biol. rep. 1


title: K562, DddA-G1404_ZFfree_panelTDD14, biol. rep. 3


title: K562, DddA-G1404_ZFfree_panelDddATDD14, biol. rep. 3


title: K562, DddA-G1404_ZFfree_panelDddATDD14, biol. rep. 2


title: K562, GFP_GFP_panelDddATDD14, biol. rep. 4


title: K562, DddA-G1404_ZFfree_panelDddA, biol. rep. 2


title: K562, GFP_GFP_panelTDD14, biol. rep. 3


title: K562, GFP_GFP_panelTDD14, biol. rep. 4


title: K562, GFP_GFP_panelTDD14, biol. rep. 2


title: K562, GFP_GFP_panelDddA, biol. rep. 3


title: K562, GFP_GFP_panelTDD14, biol. rep. 1


title: K562, GFP_GFP_panelDddA, biol. rep. 2


title: K562, GFP_GFP_panelDddATDD14, biol. rep. 2


title: K562, DddA-G1404_ZFfree_panelTDD14, biol. rep. 1


title: K562, GFP_GFP_panelDddA, biol. rep. 4


title: Tcell, TDD14_base-editing-nicking_panelTDD14, biol. rep. 3

source_name: Peripheral Blood Leukopak

growth_protocol: Cells were grown in X-Vivo 15 Serum-free Hematopoietic Cell Media (Lonza) with 20 mM HEPES (Gibco), 2 mM GlutaMax (Gibco), 1 mM Sodium Pyruvate (Corning), 1% MEM Vitamins Solution (Gibco), 5% Human AB Serum Heat-Inactivated (Valley Biomedical, #HP1022HI), and 100 IU/mL ProLeukin, IL-2

treatment_protocol: Cells were activated for 72 h using Dynabeads human T-activator CD3/CD28 (cells to beads ratio of 1:3; Life Technologies) and IL-2 (100 IU ml−1; Thermo Fisher) without antibiotics. BTX H-200 transfection system (voltage 250V, frequency 4ms, # pulse 1up to 12 depending on columns to be fed, set# of pulse at 1) was used to transfect mRNA for the ZF-base editors

value: Peripheral Blood Leukopak

value: Peripheral Blood CD4+/CD8+ T cells

value: male

value: Stemcells Technologies


title: Tcell, TDD14_base-editing-nicking_panelDddA, biol. rep. 4


title: Tcell, TDD14_base-editing-nicking_panelDddATDD14, biol. rep. 3


title: Tcell, TDD14_base-editing-nicking_panelDddA, biol. rep. 3


title: K562, GFP_GFP_panelDddATDD14, biol. rep. 1


title: Tcell, TDD14_base-editing-nicking_panelDddATDD14, biol. rep. 4


title: K562, GFP_GFP_panelDddATDD14, biol. rep. 3


title: Tcell, TDD14_base-editing-nicking_panelTDD14, biol. rep. 4


title: Tcell, TDD14_base-editing-nicking_panelDddATDD14, biol. rep. 2


title: Tcell, TDD14_base-editing-nicking_panelTDD14, biol. rep. 2


title: Liver from mouse YKV3361 [abp3361_S4_L004]

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

data_processing:
The bollito pipeline was used to perform read analysis, as follows: Sequencing quality was checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse reference genome (GRCm38, vM25 gene annotation from GENCODE) with STARsolo (STAR 2.7.3a). Seurat 3.2.2 was used to check the quality of sequenced cells, explore and quantify single-cell data, obtain cell clusters and specific gene markers.
Assembly: GRCm38
Supplementary files format and content: table with cluster markers (obtained with Seurat)

source_name: Liver

extract_protocol:
liver cells were isolated following a two-step protocol of Pronase/Collagenase digestion. Firstly, the liver was perfused with HBSS (Sigma #H6648) containing 0.2 mg/mL EDTA. Secondly, a perfusion with 0.4 mg/mL Pronase (Sigma #P5147) and 2 mg/mL Collagenase Type II (Worthington #LS004196) in HBSS was performed. Finally, the liver was perfused with HBSS containing 0.4mg/mL Pronase, 2 mg/mL Collagenase Type II and 0.1 mg/mL DNase I (Roche #R104159001). The liver was minced and further digested with HBSS containing 0.4 mg/mL Pronase, 2 mg/mL Collagenase Type II and 0.1 mg/mL Dnase I for 25 min with shaking at 37ºC. To stop digestion, DMEM (Thermo Fisher #31966047) was added. The resulting liver cell suspension was filtered and washed three times through centrifugation at 300g for 4 min in 2% FBS-PBS. The suspension was then subjected to density gradient centrifugation using 20% Percoll (GE Healthcare #17-0891-01) to remove dead cells. Resuspension of the cells in ACK lysis buffer (Thermo Fisher #A1049201) allowed the lysis of red blood cells. Cell suspension was then centrifuged and resuspended in 2% FBS-PBS to proceed with scRNA-seq analysis using 10X Genomics Chromium Single-Cell 3’ according to the manufacturer’s instructions.
Cell sample was loaded onto a 10x Chromium Single Cell GEM chip (10x Genomics) as described in the manufacturer's protocol (Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1, PN-1000121). Intended targeted cell recovery:  ~10,000 cells. Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, cDNA amplification and library construction were all performed as recommended by the manufacturer. scRNA-seq libraries were sequenced with an Illumina NextSeq 550 (using v2.5 reagent kits) in paired-end fashion (28bp + 56bp bases).

value: Liver

value: wild-type


title: Liver from mouse YKV3361 [abp3361_S4_L001]

description: Illumina NextSeq 550 (using v2.5 reagent kits)


title: Liver from mouse YKV3361 [abp3361_S4_L002]


title: Liver from mouse YKV3361 [abp3361_S4_L003]


title: Tcell, TDD14_base-editing-nicking_panelDddA, biol. rep. 1


title: K562, GFP_GFP_panelDddA, biol. rep. 1


title: Liver from mouse YKV3359 [abp3359_S2_L004]


title: Tcell, TDD14_base-editing-nicking_panelDddATDD14, biol. rep. 1


title: Tcell, TDD14_base-editing_panelDddA, biol. rep. 4


title: Tcell, TDD14_base-editing_panelDddATDD14, biol. rep. 4


title: Liver from mouse YKV3360 [abp3360_S3_L001]


title: Liver from mouse YKV3360 [abp3360_S3_L002]


title: Tcell, TDD14_base-editing-nicking_panelDddA, biol. rep. 2


title: Tcell, TDD14_base-editing-nicking_panelTDD14, biol. rep. 1


title: Tcell, TDD14_base-editing_panelTDD14, biol. rep. 4


title: Liver from mouse YKV3360 [abp3360_S3_L003]


title: Liver from mouse YKV3359 [abp3359_S2_L003]


title: Tcell, TDD14_base-editing_panelDddATDD14, biol. rep. 3


title: Liver from mouse YKV3359 [abp3359_S2_L002]


title: Tcell, TDD14_base-editing_panelDddATDD14, biol. rep. 2


title: Liver from mouse YKV3359 [abp3359_S2_L001]


title: Tcell, TDD14_base-editing_panelDddA, biol. rep. 3


title: Tcell, TDD14_base-editing_panelDddA, biol. rep. 2


title: Liver from mouse YKV3360 [abp3360_S3_L004]


title: Liver from mouse YKV3358 [abp3358_S1_L001]


title: Liver from mouse YKV3358 [abp3358_S1_L004]


title: Liver from mouse YKV3358 [abp3358_S1_L002]


title: Tcell, TDD14_base-editing_panelTDD14, biol. rep. 2


title: Liver from mouse YKV3358 [abp3358_S1_L003]


title: Tcell, TDD14_base-editing_panelTDD14, biol. rep. 1


title: ABP73

data_processing:
Eightyfive-base-pair single-end sequenced reads followed adapter and polyA tail removal as indicated by Lexogen. The resulting reads were analysed with the nextpresso pipeline as follows: sequencing quality was checked with FastQC v0.11.0 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse genome (GRCm38) with TopHat2 using Bowtie and Samtools, allowing 3 mismatches and 20 multihits. The GENCODE vM20.GRCm38.Ensembl95 gene annotation was used. Read counts were obtained with HTSeq. Differential expression and normalization was performed with DESeq2, keeping only those genes where the normalized count value was higher than 2 in at least 10% of the samples. Finally, those genes that had an adjusted p-value below 0.05 FDR were selected. GSEAPreranked was used to perform gene set enrichment analysis for the selected gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Supplementary files format and content: tab-delimited text files include normalized counts for each Sample

extract_protocol:
RNA was extracted using Rneasy Mini kit (QIAGEN)
Total RNA samples (250ng) were processed with the QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen, Cat.No. 015) by following manufacturer instructions. RNA quality scores were 7.2 on average (range 5.9-7.8) when assayed on a PerkinElmer LabChip analyzer. Library generation is initiated by reverse transcription with oligodT priming, and a second strand synthesis is performed from random primers. Primers from both steps contain Illumina-compatible sequences. Libraries are completed by PCR: this kit generates directional libraries stranded in the sense orientation, the read1 (the only read in single read format) has the sense orientation.  cDNA libraries are purified, applied to an Illumina flow cell for cluster generation and sequenced on an Illumina NextSeq 550 (with v2.5 reagent kits) by following manufacturer's protocols.

value: Li-TSC1KO RagAGTP

value: 24h fasting + rapamycin


title: ABP74


title: Tcell, TDD14_base-editing_panelTDD14, biol. rep. 3


title: ABP65

value: 24h fasting + 2h refed


title: ABP72


title: ABP59

value: wild type


title: ABP64


title: Tcell, GFP_GFP_panelDddATDD14, biol. rep. 3


title: Tcell, GFP_GFP_panelTDD14, biol. rep. 4


title: Tcell, GFP_GFP_panelDddA, biol. rep. 4


title: ABP58


title: Tcell, GFP_GFP_panelTDD14, biol. rep. 3


title: Tcell, GFP_GFP_panelDddA, biol. rep. 3


title: ABP63


title: Tcell, GFP_GFP_panelDddATDD14, biol. rep. 4


title: ABP56

value: 24h fasting


title: ABP54


title: ABP57


title: ABP55


title: Tcell, GFP_GFP_panelTDD14, biol. rep. 2


title: Tcell, GFP_GFP_panelDddA, biol. rep. 2


title: Tcell, GFP_GFP_panelDddATDD14, biol. rep. 2


title: ABP53


title: Tcell, TDD14_base-editing_panelDddATDD14, biol. rep. 1


title: Tcell, GFP_GFP_panelDddATDD14, biol. rep. 1


title: Tcell, GFP_GFP_panelDddA, biol. rep. 1


title: Tcell, TDD14_base-editing_panelDddA, biol. rep. 1


title: ABP50


title: Tcell, DddA-G1404_base-editing-nicking_panelTDD14, biol. rep. 4


title: ABP49


title: Tcell, DddA-G1404_base-editing-nicking_panelDddATDD14, biol. rep. 4


title: ABP52


title: Tcell, DddA-G1404_base-editing-nicking_panelTDD14, biol. rep. 3


title: ABP48


title: KO3CpG12h

city: Duesseldorf

first: Stefanie

last: Scheu

state: Nordrhein-Westfalen

address: Universitaetsstr. 1

department: Institute of Medical Microbiology and Hospital Hygiene

institute: University of Duesseldorf

data_processing:
Illumina bcl2fastq v2.17.1.4 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence (Illumina TrueSeq) and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides maximal 2), then mapped to mm10 whole genome using CLC Genomics Workbench v11.0.1 with standard parameters.
Counts per million (cpm) were calculated using EdgeR on usegalaxy.org with standard parameters. Multi-group comparisons were calculated using edgeR after grouping of samples (three biological replicates each) according to their respective experimental condition and filtering of low expressing genes based on a formula from Chen, Y., Lun, A.T., and Smyth, G.K. (2016). From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. F1000Res 5, 1438. . The resulting p values were corrected for multiple testing by FDR. A p value of ≤ 0.05 was considered significant. Cut-off for differential gene expression was set to 2 fold.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include cpm values for each sample.

growth_protocol: BM-derived Flt3-L cultured pDCs were generated as previously described (Scheu et al, PNAS 2008).

extract_protocol:
purification protocol: For RNA-Seq, BM-derived pDCs (CD3-CD19-CD11c+CD11blowB220+SiglecH+mPDCA1+) from wild-type and Batf-deficient mice were FACS purified using FACS Aria III (BD).
Libraries were prepared according to Illumina® ‘TruSeq Stranded mRNA Library Prep Kit’. Briefly, 200 ng total RNA were used for mRNA capturing, fragmentation, the synthesis of cDNA, adapter ligation and library amplification. Bead purified libraries were normalized and finally sequenced on the HiSeq 3000/4000 system (Illumina Inc. San Diego, CA, USA), following the manufacturer's protocols, with a read setup of 1 × 150 bp.

treatment_protocol: The WT and Batf-deficient pDCs were left untreated or stimulated with 1µM CpG 2216 (Tib Molbiol, Nr. 930507l) complexed to transfection reagent DOTAP (Roche) for 2, 6 or 12 hours. RNA was isolated by using NucleoSpin II RNA mini kit (Macherey- Nagel) and subjected to RNA-Seq.

value: pDC

tag: condition

value: CpG 12h

value: Batf-deficient


title: Tcell, DddA-G1404_base-editing-nicking_panelDddA, biol. rep. 4


title: KO1CpG12h

value: bone marrow

tag: genotype


title: KO2CpG12h

tag: strain


title: Tcell, DddA-G1404_base-editing-nicking_panelDddA, biol. rep. 3


title: Tcell, DddA-G1404_base-editing-nicking_panelDddATDD14, biol. rep. 3


title: Mel_Input

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: Input

data_processing:
The quality control of the fastq files was performed using FastQC.
The sequences were aligned on hg19 assembly using bowtie2. Duplicates were marked and filtered out using Picard tools MarkDuplicates and samtools.
The peak calling was performed using macs2 callpeak function. The parameter --broad was used for the Histone samples, not for the transcription factor samples.
Assembly: hg19
Supplementary files format and content: bigwig

source_name: normal choroidal melanocytes

growth_protocol: Normal uveal melanocytes from an healthy donors, obtained after enucleations were dissociated and maintained in culture from choroidal membranes from Pr Simon Saule’s lab and Dr Geraldine Liot. After enzymatic (with collagenase) and mechanical dissociation, primary cells were cultured in HAM/F12 supplemented with 10% FBS, Penicillin 100 U/mL, Streptomycin 100 U/mL, 2mM L-glutamine, 2.5µg/mL Amphotericin B. Extemporaneously completed media was supplemented with 0.1mM IBMX, 10ng/µL of Cholera toxin (10 ng/ml final), and 10mg/mL FGF and filter with a 0.22µm filter. Cell were maintained in a humidified atmosphere with 5% CO2 at 37°C , and culture medium was exchanged twice a week.

extract_protocol:
ChIP of H2AUb, H3K4me and H3K27me3 were performed from 6 millions of cells originating from Patient Derived Tumour grafts; magnetic Dynabeads coupled to Protein A were used for the IP (Invitrogen). Sonication was performed to obtain fragment size of 150-300 bp.
Chip of H3K27Ac and CTCF were performed according the Diagneode protocols. The chromatin was prepared using the iDeal ChIP-seq Kit for Transcription Factors (Diagenode Cat# C01010170). Chromatin was sheared using Bioruptor® Pico sonication device (Diagenode Cat# B01060001) combined with the Bioruptor® Water cooler for 10 cycles using a 30’’ [ON] 30’’ [OFF] settings to obtain fragment size of 150-300 bp. Per H3K27Ac and CTCF ChIP,  2 millions of cells were prepared in 100μl. The library preparation has been conducted by Diagenode ChIP-seq/ChIP-qPCR Profiling service (Diagenode Cat# G02010000). Libraries were prepared using IP-Star® Compact Automated System (Diagenode Cat# B03000002) from input and ChIP’d DNA using MicroPlex Library Preparation Kit v3 (96 indexes) (Diagenode Cat# C05010004). Optimal library amplification was assessed by qPCR using KAPA SYBR® FAST (Sigma-Aldrich) on LightCycler® 96 System (Roche) and by using High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Agilent). Libraries were then purified using Agencourt® AMPure® XP (Beckman Coulter) and quantified using Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854). Finally their fragment size was analised by High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Agilent).
Libraries were prepared accordingly to manufactures (TruSeq ChIP sample Prep Kit, Illumina). Sequencing was performed on a Illumina Hi-Seq 2500 (H2Aub, H3K4me3, H3k27me3) and on a Illumina NovaSeq (ChIPseq H3K27Ac, CTCF)

treatment_protocol: Cells obtained from subculture or cell sorting were counted and 6 million cells were resuspended in 1xPBS with 1%, v/v freshly opened formaldehyde at a concentration of  1x106 cells per 1ml PBS. Cells were icubated at room temperature for 15 minutes with gentle rocking. A glycine solution was added to a final concentration of 0.125M to quench the reaction. The mixture was incubated at room temperature for 5 minutes on rocker. Cells were centrifuged for 5 minutes at 300xG (1000rpm) at 4°C. The supernatant was discarded  into an appropriate collection container, and cells were resuspended in 1ml of cold 1X PBS and spin for 5 minutes at 00xG (1000rpm) at 4°C. The supernatant was discarded. This washing step was repeated one more time, the supernatant was removed and cell pellets were flash-freezon in a dry ice/ethanol bath and stored at -80°C before ChIPseq experiments

value: normal choroidal melanocytes

value: Primary Culture


title: Tcell, GFP_GFP_panelTDD14, biol. rep. 1

value: Peripheral Blood Leukopak


title: KO3CpG6h

value: CpG 6h


title: KO2CpG6h


title: Mel_H3K4me3


title: KO1CpG6h


title: KO3CpG2h

value: CpG 2h


title: Mel_H2Aub


title: ABP51

tag: treatment


title: KO2CpG2h


title: Tcell, DddA-G1404_base-editing-nicking_panelDddATDD14, biol. rep. 2

value: Peripheral Blood CD4+/CD8+ T cells

value: male

value: Stemcells Technologies


title: Tcell, DddA-G1404_base-editing-nicking_panelTDD14, biol. rep. 2


title: Tcell, DddA-G1404_base-editing-nicking_panelDddA, biol. rep. 2


title: KO3

value: naive


title: Mel_H3K27me3


title: Tcell, DddA-G1404_base-editing-nicking_panelTDD14, biol. rep. 1


title: KO2


title: KO1


title: liver, Untreated, scRNA-seq

city: New Haven

first: Carlos

last: Fernandez-Hernando

address: 10 Amistad St

institute: Yale University

description: 10x Genomics

data_processing:
Sample demultiplexing, aligning reads to the mouse mm10 reference genome (University of California, Santa Cruz) with Software Tools for Academics and Researchers (STAR) and unique molecular identifier (UMI) processing were processed using CellRanger software (version 7.1.0, https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

growth_protocol: Mice used in the experiemnt were kept in ventilated cages in pathogen gree facilities. Round-the-clock, 7-day/week veterinary care is provided by the veterinarians of Yale University.

extract_protocol:
Hepatic single-cell suspensions were prepared for submission for 10X single-cell RNA-sequencing and flow cytometry. Livers were perfused firstly with digestion cocktail containing 1.5mg/mL Collagenase I (Sigma; SCR103) and 0.5mg/mL DNase I (Roche; 4716728001) from the portal vein until tissue softens and then perfused with DMEM medium containing 10% FBS. Tissues were removed and placed in cold media before shaking to dissociate hepatic single-cell suspensions. Isolated suspensions were centrifuged at 60G for 2 minutes with 2 brakes to separate parenchymal fraction (Hepatocytes, Cholangiocytes) and non-parenchymal (NPC) fractions (Endothelial, Immune cells etc.). For parenchymal fractions, a 35% Percoll (Sigma; P1644) gradient was used to enrich for live cells after spinning at 500g for 5 mins. NPC fractions can be directly processed for flow cytometry or further enriched for single-cell RNA sequencing. To enrich for live NPCs, cells were stained with LIVE/DEAD Fixable Aqua Dead Cell Stain Kit (Invitrogen; L34957) before sorting on the FACSAria II Cell sorter. Purified parenchymal and NPC fractions were mixed at a 1:1 ratio before submission for single-cell sequencing.
Live cells enriched Parenchymal and NPC cells were encapsulated into droplets and processed following manufacturer’s specification using 10X Genomics GemCode technology. Equal numbers of cells per sample were loaded on a 10X Genomics Chromium controller instrument to generate single-cell Gel Beads in emulsion (GEM) at the Yale Center for Genome Analysis. Lysis and barcoded reverse transcription of polyadenylated mRNA from single cells were performed inside each GEM followed by complementary DNA (cDNA) generation using the Single-Cell 3’ Reagent Kits version 3.1 (10X Genomics). Libraries were sequenced on an Illumina Hiseq 4000 as 2 x 100 paired-end reads.

treatment_protocol: an-IP injection of CCl4 (Sigma-Aldrich no. 289116; NH2COCH2) was administered at a dose of 1 uL/g body weight to 10-week-old male Alb-CreERT2 Rosa26rbw mice. CCl4 was diluted in corn oil at a final volume of 50 μL. Untreated mice received a dose of 50 μL of corn oil. After 6 days, mice were euthanized and livers were collected for scRNA-seq analysis.

value: liver

value: parenchymal (hepatcoytes)

value: Alb-CreERT2 Rosa26rbw

value: untreated


title: Tcell, DddA-G1404_base-editing-nicking_panelDddATDD14, biol. rep. 1


title: Tcell, DddA-G1404_base-editing-nicking_panelDddA, biol. rep. 1


title: R9451

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

data_processing:
FASTQ files were mapped using STAR to GRCm38 genome build
Gene counts were obtained using featureCounts on GencodevM20 annotations
Assembly: GRCm38
Supplementary files format and content: gene_counts

source_name: PBMC

growth_protocol: 10% FBS in RPMI media supplemented with HEPES

extract_protocol:
Joint footpads were excised 6 days post-infection (dpi) and were digested in RPMI (Hyclone) with 10% heat-inactivated Fetal Bovine Serum (FBS; Biowest), supplemented with DNase I (50 mg/mL; Roche Applied Science), collagenase IV (20 mg/mL; Sigma-Aldrich), and dispase (2 U/mL; Invitrogen). The digestion was performed with slight agitation at 37°C for 3 hours before being filtered through a cell strainer (40 μm pore size). Red blood cells were subsequently lysed and cells were purified with Percoll solution (Sigma-Aldrich) diluted (35% vol/vol) in RPMI FBS. After the digestion and purification steps, joint-footpad cells were stained the LIVE/DEAD determination dye (Thermo Fisher Scientific) for 20 minutes. Thereafter, the cells were stained with the following antibodies: Rat anti-mouse CD45 (clone: 30-F11), Rat anti-mouse CD11b (Clone: M1/70), Rat anti-mouse Ly6C (clone: HK1.4), Rat anti-mouse Ly6G (clone: 1A8), Mouse anti-mouse CD64 (clone: X54-4/7.1) and Rat anti-mouse MHCII (clone: M5/114.15.2). All antibodies used for staining were purchased from BD Horizon, BioLegend or ThermoFisher Scientific. Stained cells were washed, resuspended in an appropriate buffer and the target cells of CD64+MHCII- and CD64+MHCII+ phenotype were sorted with FACS Aria III sorter (BD Biosciences).
Total RNA was extracted using the Arcturus PicoPure RNA Isolation kit (Thermo Fisher Scientific) according to the manufacturer's protocol. All mouse RNAs were analyzed on Agilent Bioanalyzer for quality assessment with RNA Integrity Number (RIN) ranging from 8.8 to 9.6 with a median of 9.5. cDNA libraries were prepared using 2 ng of total RNA and 1 µl of a 1:50,000 dilution of ERCC RNA Spike in Controls (Thermo Fisher Scientific) using the SMARTSeq v2 protocol 75 with the following modifications: 1. Addition of 20 µM template switching oligos (TSO); 2. Use of 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina). The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Labchip (Perkin Elmer). All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq 4000 system (~26 samples/lane).

treatment_protocol: Infected with DiD-labelled dengue virus

tag: mhcii


title: R9452


title: liver, CCl4, scRNA-seq

description: 10x Genomics

value: non-parenchymal cells