title: KSHV 6dpi Set 1

city: Cleveland

first: Kyle

last: Jung

email: jungk@ccf.org, kxj240@case.edu

state: OH

address: 9500 Euclid Ave. NE2-251

department: Cancer Biology

institute: Cleveland Clinic

data_processing:
Initial processing of the fastq files was done using 10X Genomics Cell Ranger v3.1. A custom reference was made that combined the human hg38 reference genome, KSHV JSC-1 reference genome (GQ994935.1), eGFP, and mRFP transcripts
Filtered gene matrices from Cell Ranger was used for further analysis with Seurat v3.

source_name: oral epithelial cells

growth_protocol: MatTek EpiOral tissues were received and reconsituted for 1 hour.

extract_protocol:
Mock and KSHV infected tissues were harvested at 3 days and 6 days post infection. Tissue inserts were removed from the 6-well plate and placed into a new 6-well plate with enough PBS to coat the bottom. The inside of the insert was then washed with PBS to collect the supernatant. The tissues where then carefully separated from the insert membrane and chopped into small pieces in DMEM. The cells are then incubated for 40 minutes in 2 mL of 1 mg/mL collagenase and dispase (Roche Cat. 10269638001) in a shaking incubator set to 37ºC and 250 rpm. The collagenase and dispase are then inactivated by adding 2 mL of DMEM and 10% FBS. The digested cells are then passed through a 0.45 um cell strainer and then washed with cold PBS with 0.04% BSA (ThermoFisher Cat. AM2618). The filtered cells are also passed through a flowmi cell strainer. Cells are counted with Invitrogen Countess II (ThermoFisher Cat. A27977).
Single Cell Libraries were prepared with the 10X Genomics Single Cell Gene Expression v2 kit (Set 1 and 2) or v3 kit (Set3). The Chromium Single Cell 3ʹ Reagent Kits v3 User Guide Rev A protocol was used for sample preparation and library generation.

treatment_protocol: Tissues were scored with a blunted 18g insulin syringe (BD Cat. 305196) and then infected on the apical side with 2 x 107 IU of KSHV.219 for 4 hr. Following the infection, the tissues were washed with DPBS twice, returned to an air-liquid interface, and kept in 26 ml of assay medium in 10-cm dish. Tissues are incubated at 37ºC for 3 or 6 days before harvesting while changing the media every 2 days.

tag: condition

value: KSHV infected 3D tissues harvested at 6dpi

value: oral epithelial cells

value: KSHV Infection (rKSHV.219)

tag: harvest timepoint

value: 6 days post infection

tag: set


title: KSHV 6dpi Set 3

status: Public on Jul 28 2022

type: SRA

country: USA

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: treatment


title: Mock 6dpi Set 2

value: Mock infected 3D tissues harvested at 6dpi

value: Mock Infection (PBS)


title: Mock 6dpi Set 3


title: Mock 3dpi Set 3

value: Mock infected 3D tissues harvested at 3dpi

value: 3 days post infection


title: KSHV 3dpi Set 3

value: KSHV infected 3D tissues harvested at 3dpi


title: KSHV 6dpi Set 2


title: Mock 3dpi Set 2


title: KSHV 3dpi Set 1


title: TCONV HA CAR - rep1

city: Memphis

first: Tian

last: Mi

state: TN

address: 262 Danny Thomas Pl MS351

department: Immunology

institute: St. Jude Children's Research Hospital

library_source: genomic

data_processing:
Basecalling was performed using Illumina Casava 1.7
Sequencing reads were aligned to the hg38 genome using the BSMAP v.2.90 software
CpG methylation levels were determined by methratio.py script from BSMAP
Assembly: hg38
Supplementary files format and content: txt files with columns of chr, loc, cov, meth

molecule: genomic DNA

source_name: HA-CAR T cells

growth_protocol: Naïve Tregs were flow-sorted as live CD4+CD127loCD25hi CD45RA+CD62Lhi cells and naïve CD4+ Tconvs cells were sorted as live CD4+ CD45RA+CD62Lhi. Cells were resuspended at 1x10^6 cells/ml in XH media (X-Vivo 15 (Lonza) with 5% human serum, 1% penicillin/streptavidin, 1% glutamine and phenol red) containing 300U IL2/ml (Proleukin) and were stimulated with a 3 bead : 1 cell ratio of Dynabead. On day 2 and 3, cells were transduced with a retrovirus containing a non-tonic signaling CAR (non-TS-CAR; CD19) or a TS one (HA CAR). At day 7, cells were collected and live CAR+ were flow sorted  and resuspended at 0.5x10^6 cells/ml in XH media containing 300U IL2/ml for an addition 3 days for conventional T cells and 4 days for Tregs. Then the beads were magnetically removed and cells were rested overnight. DNA was then extracted for DNA methylation.

extract_protocol:
DNA was extracted from the sorted cells by using a DNA-extraction kit (Qiagen) and then bisulfite treated using an EZ DNA methylation kit (Zymo Research).
Bisulfite-modified DNA sequencing libraries were generated using the EpiGenome kit (Epicentre) according to the manufacturer’s instructions. Bisulfite-modified DNA libraries were sequenced using Illumina HiSeq 4000 and NovaSeq 6000 systems

value: CD4+ TCONV cells

value: HA CAR


title: INPUT DAY3 DE WNT

status: Public on Jul 27 2022

city: Cincinnati

first: Shreyasi

last: Mukherjee

address: 3333 Burnet Ave

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
For RNA-Seq experiments, raw reads were quality-checked using  FASTQC and adapters were trimmed using cutadapt.
Reads were pseudo-aligned to the hg19 reference index using salmon.
The tximport package was then used for downstream analysis to convert transcript-level counts to gene-level estimates. Differential gene expression analysis was performed using DESeq2 using default parameters
For ChIP-Seq experiments, Reads were aligned to the hg19 genome using bowtie2
Duplicates were marked using Picard and removed using samtools
A consensus set of peaks were called for each TF at each stage using HOMER getDifferentialPeaksReplicates.pl using stage-matched input samples as background and -style factor.
Assembly: hg19
Supplementary files format and content: .bw' files are bigWig files for visualization of ChIP-Seq and ATAC-Seq data
Supplementary files format and content: .csv' files are TPM matrices from RNA-Seq experiment

source_name: Induced pluripotent stem cells

growth_protocol: iPS72.3 cells were routinely maintained in mTesr. HEK293T cells were maintained in high-glucose DMEM + 10% FBS

extract_protocol:
For RNA-Seq experiments, Total RNA was extracted using the Nucleospin RNA Extraction kit.For ChIP-Seq experiments, after differentiation to the desired stage, cells were dual crosslinked in plate with 1.5mM EGS and 1% formaldehyde. The fixation was then quenched with 125mM glycine. Cells were then washed twice and scraped in ice-cold PBS and resuspended in sonication buffer.
For RNA-Seq experiments, 300ng of total RNA was poly-A selected and reverse transcribed using Illumina’s TruSeq stranded mRNA library preparation kit (Illumina; 20020595). For ChIP-Seq experiments, DNA libraries were prepared using 1-5 ng of starting material using the SMARTer ThruPLEX DNA-Seq kit (Takara; R400674) according to manufacturer’s instructions.

treatment_protocol: DE differentiation was carried out in RPMI-1640 media supplemented with non-essential amino acids Cells were treated with 100ng/ml Activin A and 2um CHIR99021 for 24hrs. In the next two days, cells were treated with 100ng/ml Activin A and 2um CHIR99021 in RPMI-1640 with increasing concentrations (0.2% on Day 2, 2% on Day 3) of ES-grade FBS . HEK293T cells were treated with 10um CHIR for 24 hours wherever indicated.

tag: developmental stage

value: Day 3 definitive endoderm

value: 100ng/ml Activin + 50ng/ml WNT3A at Days 1-3


title: INPUT WT + SOX17 +WNT

source_name: HEK 293T Cells

value: 10 um CHIR for 24 hours


title: INPUT 4TCFKO +WNT


title: INPUT WT + WNT


title: INPUT DAY3 SOX17KO WNT


title: DAY3 DE SOX17KO WNT BCAT ChIP

tag: chip antibody

value: Invitrogen 71-2700


title: INPUT 4TCFKO + SOX17 + WNT


title: HEK293T 4TCFKO +SOX17 + WNT SOX17 ChIP

value: SOX17 R&D AF1924


title: KSHV 3dpi Set 2


title: INPUT WT - WNT

value: input


title: DAY3 WT DE WNT BCAT ChIP


title: HEK293T 4TCFKO -WNT SOX17 ChIP


title: HEK293T WT +WNT SOX17 ChIP


title: HEK293T WT -WNT SOX17 ChIP


title: Mock 3dpi Set 1


title: HEK293T 4TCFKO +WNT SOX17 ChIP


title: HEK293T WT +SOX17 + WNT SOX17 ChIP


title: HEK293T 4TCFKO +SOX17 + WNT BCAT ChIP


title: HEK293T WT +SOX17 + WNT BCAT ChIP


title: DAY0 SOX17R -DOX Rep1

library_source: transcriptomic

molecule: polyA RNA

value: pluripotent ES cells


title: HEK293T 4TCFKO +WNT BCAT ChIP


title: HEK293T WT -WNT BCAT ChIP


title: HEK293T WT +WNT BCAT ChIP


title: DE DAY3 SOX17R +DOX Rep3

value: 50ng/ml dox at Days 1-3


title: DAY0 SOX17R -DOX Rep2


title: INPUT 4TCFKO -WNT


title: HEK293T 4TCFKO -WNT BCAT ChIP


title: DE DAY3 SOX17R +DOX Rep1


title: DE DAY3 SOX17R +DOX Rep2


title: DE DAY3 SOX17R -DOX Rep3


title: SOX17 Rescue +DOX SOX17Rep1


title: DE DAY3 SOX17R -DOX Rep2


title: SOX17 Rescue -DOX BCAT Rep1


title: DE DAY3 SOX17R -DOX Rep1


title: INPUT SOX17 Rescue +DOX


title: DAY0 SOX17R -DOX Rep3


title: SOX17 Rescue -DOX SOX17 Rep1


title: 40min single-cell embryo replicate 4

status: Public on Jul 26 2022

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

description:
40min single-cell embryo replicate 4
20to60minute_samples_raw_count.tsv
40min-4

data_processing:
Raw sequence reads (fastq) were trimmed using the fastx_trimmer command from fastx-Toolkit (version 0.0.13; respectively 5 nt from 5' and 65 nt from 3' ends)
Sequencing adapter sequences were removed by Cutadapt (1.7.1)
Alignment and gene count were performed using STAR 2.5.0a to the mouse genome
Assembly: GRCm38
Supplementary files format and content: raw gene-level counts in tab-delikmited text format

organism: Mus musculus

source_name: Single-cell embryo

extract_protocol:
Single-cell embryo were directly lysed using Takara Clontech Smartseq lysis buffer with RNAse inhibitor
Whole transcriptome amplification and library preparation was performed using Takara Clontech Smarter Stranded Total RNA-Seq Kit Pico Input version 1

treatment_protocol: Epididymidal sperm isolated from 8- to 12-week-old Mus musculus musculus B6xDBA2F1 or Mus musculus castaneus (Cast) males was microinjected into MII Oocyte in-vitro. Injected Oocytes were then cultured for 2,4,6, 8 and 12 hours before harvesting for RNASeq

tag: tissue

value: Single-cell embryo

tag: strain

value: C57BL/6 X CAST

tag: age (min)

tag: replicate

tag: replicate id

tag: barcode


title: 60min single-cell embryo replicate 4

description:
60min single-cell embryo replicate 4
20to60minute_samples_raw_count.tsv
60min-4


title: 20min single-cell embryo replicate 3

description:
20min single-cell embryo replicate 3
20to60minute_samples_raw_count.tsv
20min-3


title: 60min single-cell embryo replicate 2

description:
60min single-cell embryo replicate 2
20to60minute_samples_raw_count.tsv
60min-2


title: 40min single-cell embryo replicate 2

description:
40min single-cell embryo replicate 2
20to60minute_samples_raw_count.tsv
40min-2


title: 20min single-cell embryo replicate 4

description:
20min single-cell embryo replicate 4
20to60minute_samples_raw_count.tsv
20min-4


title: 60min single-cell embryo replicate 3

description:
60min single-cell embryo replicate 3
20to60minute_samples_raw_count.tsv
60min-3


title: SOX17 Rescue +DOX BCATRep1


title: 40min single-cell embryo replicate 1

description:
40min single-cell embryo replicate 1
20to60minute_samples_raw_count.tsv
40min-1


title: 20min single-cell embryo replicate 1

description:
20min single-cell embryo replicate 1
20to60minute_samples_raw_count.tsv
20min-1


title: 60min single-cell embryo replicate 1

description:
60min single-cell embryo replicate 1
20to60minute_samples_raw_count.tsv
60min-1


title: 20min single-cell embryo replicate 2

description:
20min single-cell embryo replicate 2
20to60minute_samples_raw_count.tsv
20min-2


title: macrodiff_platesmerged.H3K4me1.3

city: Utrecht

first: Jake

last: Yeung

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
H3K4me1 Macrophage in vitro differentiation Day 2
scchix_macrophage_differentiation_count_mat.H3K4me1.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K4me1.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz

data_processing:
We generated count matrices by taking bam reads MAPQ > 40, defined by genomic bins (gastrulation H3K36me3+H3K9me3) or gene bodies (macrophage H3K36me3+H3K4me1).
We ran LDA on count matrices for single-incubation data. For projection: we fixed the LDA terms matrix and learned the topics matrix from deconvolved double-incubated reads.
Assembly: mm10

source_name: Macrophage

extract_protocol:
For in vitro differentiation of bone marrow-derived macrophages (BMDMs), bone marrow was aseptically collected by flushing tibia and femurs from euthanized wild-type male C57BL/6 mice with sterile RPMI and 10% FCS through a 70 micrometer cell strainer (Corning). To enrich for stem and progenitor cells, lineage marker-positive (Lin+) cells were depleted by magnetic-activated cell sorting (MACS) using mouse Lineage Cell Depletion kit (Miltenyi Biotec). Lin– cells were cultured on non-tissue culture treated plates (Corning) for 7 days in RPMI medium supplemented with 10% FCS, 100 IU / / mL  penicillin, 100 mg/mL streptomycin and 10 ng/mL recombinant murine M-CSF (Peprotech). Medium was refreshed after 3 days.     Every 24 hours, suspension cells were collected and adherend cells were harvested by incubating 10 minutes in 2 mM EDTA 0.5% BSA in PBS. Suspension and adherent cells were combined and stained with CellTrace fluorescent labels (ThermoFisher), according to manufacturer’s instructions. Briefly, cells were pelleted and resuspended in 37 degrees Celsius PBS containing fluorescent dyes (working concentrations CellTrace CSFE (CTC): 2.5 micro molar; CellTrace Yellow (CTY): 2.5 micromolar; CellTrace Far Red (CTFR): 0.5 micromolar) at a concentration of  1000000 cells/mL. Cells were incubated at 37 degrees Celsius protected from light for 20 minutes. Staining reactions were stopped by adding 2x volumes of 10% FCS and incubating for 5 minutes at room temperature, protected from light, after which cells were washed twice in PBS. The following combinations of labels were used: unstained (day 0), CTC (day 1), CTY (day 2), CTFR (day 3), CTC + CTY (day 4), CTC + CTFR (day 5), CTY + CTFR (day 6) and CTC + CTY + CTFR (day 7). After harvesting and staining, cells were fixed in 70% ethanol for 1 hour and stored for later by the sortChIC protocol.
Cells were processed in 0.5 mL protein low-binding tubes. Following steps are performed on ice. Cells were resuspended in 500 microliter Wash Buffer 47.5 mL H2O RNAse free,  1 mL 1 M HEPES pH 7.5 (Invitrogen),  1.5 mL 5M NaCl, 3.6 mL pure spermidine solution (Sigma Aldrich)).     Cells were pelleted at 600 gram for 3 minutes and resuspended in  400 microliter Wash Buffer 1 (wash buffer with 0.05 % saponin (Sigma Aldrich), protease inhibitor cocktail (Sigma Aldrich), 4 microliter 0.5M EDTA) containing the primary antibody (1:100 dilution for H3K4me1, H3K27me3 and H3K4me1+H3K27me3 Saponin has to be prepared fresh every time as a 10% solution in PBS). Cells were incubated overnight at 4 degrees Celsius on a roller, before they were washed once with 500 microliter Wash Buffer 2 (wash buffer with 0.05 percent saponin, protease inhibitor). Afterwards cells were resuspended in 500 microliter Wash Buffer 2 containing Protein A-Micrococcal Nuclease (pA-MNase) 3 nanogram per milliliter and incubated for 1 hour at 4 degrees Celsius on a roller.    Finally, cells were washed an additional 2 times with 500 microliter Wash Buffer 2 before passing it through a 70 micrometer cell strainer (Corning, 431751) and sorting G1 cells based on Hoechst staining on a BD Influx FACS machine into 384 well plates containing 50 nanoliter Wash buffer 3 (Wash buffer containing 0.05% saponin) and 5 microliter sterile filtered mineral oil (Sigma Aldrich) per well. Small volumes were distributed using a Nanodrop II system (Innovadyme).

tag: cell/sample type

value: :Macrophage

tag: age

value: 13 weeks

tag: antibody treatment


title: INPUT SOX17 Rescue -DOX


title: macrodiff_platesmerged.H3K4me1.4

description:
H3K4me1 Macrophage in vitro differentiation Day 3
scchix_macrophage_differentiation_count_mat.H3K4me1.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K4me1.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: macrodiff_platesmerged.H3K4me1.8

description:
H3K4me1 Macrophage in vitro differentiation Day 7
scchix_macrophage_differentiation_count_mat.H3K4me1.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K4me1.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: macrodiff_platesmerged.H3K4me1.7

description:
H3K4me1 Macrophage in vitro differentiation Day 6
scchix_macrophage_differentiation_count_mat.H3K4me1.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K4me1.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: macrodiff_platesmerged.H3K4me1.6

description:
H3K4me1 Macrophage in vitro differentiation Day 5
scchix_macrophage_differentiation_count_mat.H3K4me1.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K4me1.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: macrodiff_platesmerged.H3K4me1.5

description:
H3K4me1 Macrophage in vitro differentiation Day 4
scchix_macrophage_differentiation_count_mat.H3K4me1.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K4me1.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: macrodiff_platesmerged.H3K4me1.2

description:
H3K4me1 Macrophage in vitro differentiation Day 1
scchix_macrophage_differentiation_count_mat.H3K4me1.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K4me1.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: macrodiff_platesmerged.H3K4me1.1

description:
H3K4me1 Macrophage in vitro differentiation Day 0
scchix_macrophage_differentiation_count_mat.H3K4me1.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K4me1.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: macrodiff_platesmerged.H3K4me1-H3K36me3.7

description:
H3K4me1+H3K36me3 Macrophage in vitro differentiation Day 6
scchix_macrophage_differentiation_count_mat.H3K4me1-H3K36me3.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K36me3.RData
scchix_macrophage_differentiation_lda_projection.H3K4me1.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: macrodiff_platesmerged.H3K4me1-H3K36me3.5

description:
H3K4me1+H3K36me3 Macrophage in vitro differentiation Day 4
scchix_macrophage_differentiation_count_mat.H3K4me1-H3K36me3.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K36me3.RData
scchix_macrophage_differentiation_lda_projection.H3K4me1.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: macrodiff_platesmerged.H3K4me1-H3K36me3.3

description:
H3K4me1+H3K36me3 Macrophage in vitro differentiation Day 2
scchix_macrophage_differentiation_count_mat.H3K4me1-H3K36me3.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K36me3.RData
scchix_macrophage_differentiation_lda_projection.H3K4me1.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: macrodiff_platesmerged.H3K4me1-H3K36me3.4

description:
H3K4me1+H3K36me3 Macrophage in vitro differentiation Day 3
scchix_macrophage_differentiation_count_mat.H3K4me1-H3K36me3.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K36me3.RData
scchix_macrophage_differentiation_lda_projection.H3K4me1.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: macrodiff_platesmerged.H3K4me1-H3K36me3.2

description:
H3K4me1+H3K36me3 Macrophage in vitro differentiation Day 1
scchix_macrophage_differentiation_count_mat.H3K4me1-H3K36me3.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K36me3.RData
scchix_macrophage_differentiation_lda_projection.H3K4me1.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: macrodiff_platesmerged.H3K36me3.7

description:
H3K36me3 Macrophage in vitro differentiation Day 6
scchix_macrophage_differentiation_count_mat.H3K36me3.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K36me3.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: macrodiff_platesmerged.H3K36me3.2

description:
H3K36me3 Macrophage in vitro differentiation Day 1
scchix_macrophage_differentiation_count_mat.H3K36me3.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K36me3.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: macrodiff_platesmerged.H3K36me3.6

description:
H3K36me3 Macrophage in vitro differentiation Day 5
scchix_macrophage_differentiation_count_mat.H3K36me3.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K36me3.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: macrodiff_platesmerged.H3K36me3.1

description:
H3K36me3 Macrophage in vitro differentiation Day 0
scchix_macrophage_differentiation_count_mat.H3K36me3.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K36me3.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: macrodiff_platesmerged.H3K36me3.4

description:
H3K36me3 Macrophage in vitro differentiation Day 3
scchix_macrophage_differentiation_count_mat.H3K36me3.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K36me3.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: gastru_merged_K9m3

description:
Gasrulation H3K9me3 single incubation
scChIX_gastrulation_H3K36me3_and_H3K9me3_metadata_final.txt.gz
scChIX_gastrulation_K9m3_countmat.txt.gz
scChIX_gastrulation_K9m3_LDA_projection_output.RData

source_name: Gastrulation

extract_protocol:
Four to five embryos were pooled for each reported time (E9.5, E10.5, E11.5) point prior to single cell isolation. Pooled embryos were dissociated in TrypleE for 10min at room temperature. Undigested portions were physically removed and the remainder filtered through a 30 micrometer filter before the single cell suspension was split into 3 samples for each timepoint and each scChiX experiment. Per timepoint, two single cell samples were used each for a single antibody incubation (H3K36me3 or H3K9me3) and one sample for the double antibody incubation (H3K36me3 + H3K9me3). Antibody incubation was performed as described in the scChiX protocol prior to single cell capture using flow cytometry. DNA library was prepared for each sample using the scChiX protocol.
Cells were processed in 0.5 mL protein low-binding tubes. Following steps are performed on ice. Cells were resuspended in 500 microliter Wash Buffer 47.5 mL H2O RNAse free,  1 mL 1 M HEPES pH 7.5 (Invitrogen),  1.5 mL 5M NaCl, 3.6 mL pure spermidine solution (Sigma Aldrich)).     Cells were pelleted at 600 gram for 3 minutes and resuspended in  400 microliter Wash Buffer 1 (wash buffer with 0.05 % saponin (Sigma Aldrich), protease inhibitor cocktail (Sigma Aldrich), 4 microliter 0.5M EDTA) containing the primary antibody (1:100 dilution for H3K4me1, H3K27me3 and H3K4me1+H3K27me3 Saponin has to be prepared fresh every time as a 10% solution in PBS). Cells were incubated overnight at 4 degrees Celsius on a roller, before they were washed once with 500 microliter Wash Buffer 2 (wash buffer with 0.05 percent saponin, protease inhibitor). Afterwards cells were resuspended in 500 microliter Wash Buffer 2 containing Protein A-Micrococcal Nuclease (pA-MNase) 3 nanogram per milliliter and incubated for 1 hour at 4 degrees Celsius on a roller.    Finally, cells were washed an additional 2 times with 500 microliter Wash Buffer 2 before passing it through a 70 micrometer cell strainer (Corning, 431751) and sorting G1 cells based on Hoechst staining on a BD Influx FACS machine into 384 well plates containing 50 nanoliter Wash buffer 3 (Wash buffer containing 0.05% saponin) and 5 microliter sterile filtered mineral oil (Sigma Aldrich) per well. Small volumes were distributed using a Nanodrop II system (Innovadyme).

value: :embryo


title: macrodiff_platesmerged.H3K36me3.8

description:
H3K36me3 Macrophage in vitro differentiation Day 7
scchix_macrophage_differentiation_count_mat.H3K36me3.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K36me3.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: macrodiff_platesmerged.H3K4me1-H3K36me3.1

description:
H3K4me1+H3K36me3 Macrophage in vitro differentiation Day 0
scchix_macrophage_differentiation_count_mat.H3K4me1-H3K36me3.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K36me3.RData
scchix_macrophage_differentiation_lda_projection.H3K4me1.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: gastru_merged_K36-K9m3

description:
Gastrulation H3K36me3+H3K9me3 double-incubation
scChIX_gastrulation_H3K36me3_and_H3K9me3_metadata_final.txt.gz
scChIX_gastrulation_K36-K9m3_countmat.txt.gz
scChIX_gastrulation_double_cell_assignment.txt
scChIX_gastrulation_K36_LDA_projection_output.RData
scChIX_gastrulation_K9m3_LDA_projection_output.RData


title: BM_4H_rep2

city: Beijing

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

description: SCRB-seq

data_processing:
Processing sequencing data from SCRB-seq was performed as previously described. Sequencing adapters, template switch oligo (TSO) and ploly (A) tail sequences were trimmed from the raw sequencing data by using Cutadapt (v1.15) . Trimmed reads were then aligned to the mouse reference genome mm9 by using STAR (v2.6.0a). Deduplication was further performed on uniquely mapped reads according to UMI (unique molecular identifier). Gene expression levels were quantified for barcodes observed by using HTSeq (v0.11.2). Quality control was performed as described in our paper.
Assembly: mm9
Supplementary files format and content: comma-separated values files

source_name: bone marrow

extract_protocol:
Single cell suspensions of peripheral blood and bone marrow were prepared as previously described. Neutrophils were isolated by EasySepTM Mouse Neutrophil Enrichment Kit (Stem Cell). The isolated neutrophils were washed twice with PBS and maintained on ice for further experiments.
The SCRB-seq library was constructed as reported previously 33,34. Briefly, the individual cell was picked by the mouth pipette, lysed, and subjected to the first-strand cDNA synthesis. The second-strand cDNA was further synthesized, amplified, and fragmented. The RNA-seq library was then prepared by using the NEBNext Ultrall DNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer's instructions. The libraries were checked and pooled before the sequencing. Finally, the paired-end 150-bp sequencing was performed on the libraries on an Illumina HiSeq X-Ten platform (Novogene).

value: bone marrow

value: donor mice were intraperitoneally (i.p.) injected with a low dose of LPS (0.5 mg/kg, Sigma-Aldrich)


title: BM_4H_rep1

description: SCRB-seq


title: BM_0H_rep2

description: SCRB-seq

value: donor mice were intraperitoneally (i.p.) injected with PBS


title: gastru_merged_K36

description:
Gastrulation H3K36me3 single incubation
scChIX_gastrulation_H3K36me3_and_H3K9me3_metadata_final.txt.gz
scChIX_gastrulation_K36_countmat.txt.gz
scChIX_gastrulation_K36_LDA_projection_output.RData


title: BLOOD_0H_rep1

description: SCRB-seq

source_name: peripheral blood

value: peripheral blood


title: BM_0H_rep1

description: SCRB-seq


title: BLOOD_0H_rep2

description: SCRB-seq


title: macrodiff_platesmerged.H3K36me3.3

description:
H3K36me3 Macrophage in vitro differentiation Day 2
scchix_macrophage_differentiation_count_mat.H3K36me3.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K36me3.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: macrodiff_platesmerged.H3K4me1-H3K36me3.6

description:
H3K4me1+H3K36me3 Macrophage in vitro differentiation Day 5
scchix_macrophage_differentiation_count_mat.H3K4me1-H3K36me3.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K36me3.RData
scchix_macrophage_differentiation_lda_projection.H3K4me1.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: macrodiff_platesmerged.H3K4me1-H3K36me3.8

description:
H3K4me1+H3K36me3 Macrophage in vitro differentiation Day 7
scchix_macrophage_differentiation_count_mat.H3K4me1-H3K36me3.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K36me3.RData
scchix_macrophage_differentiation_lda_projection.H3K4me1.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: Spleen_Chronic_D5_CD8_TetPos_rep2_gex

status: Public on Jul 25 2022

city: Stanford

first: Ansuman

middle: T

last: Satpathy

state: CA

address: 300 Pasteur Drive

department: Pathology

institute: Stanford University

description: 5' gene expression library (10X Genomics)

data_processing:
Processed with cellranger pipeline, version 3.1.0
Assembly: mm10

source_name: CD8+ gp33+ T cells from spleen 5 dpi with LCMV-c13

extract_protocol: 10X Genomics Single Cell 5' Library & Gel Bead Kit (v1.1 Chemistry)

value: CD8+ gp33+ T cells


title: Spleen_Chronic_D5_CD8_TetNeg_rep2_gex

source_name: CD8+ gp33- T cells from spleen 5 dpi with LCMV-c13

value: CD8+ gp33- T cells


title: Spleen_Chronic_D5_CD8_TetPos_rep1_gex


title: Spleen_Chronic_D5_CD8_TetNeg_rep1_gex


title: P_4466_20799930978

status: Public on Jul 24 2022

city: Pozzuoli

first: Francesco

last: Panariello

state: Napoli

address: Via Campi Flegrei 34

country: Italy

institute: TIGEM

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1

source_name: Oronasopharingeal swab

extract_protocol:
RNA extraction was performed by using either the Maelstrom 9600 (TANBead) or GeneQuality X120 (AbAnalitica) automatic platforms according to manufacturer's specifications.
40-60uL unquantified swab RNA extract (1-5 ng/ul estimate) was treated with DNAse I (Life Technologies), purified and concentrated to a final volume of 5uL. Libraries were prepared using 3'DGE mRNA-seq clinical-grade sequencing service (Next Generation Diagnostic srl).

value: Heterogeneous cell types from the oronasopharingeal tract

tag: disease state

value: Control


title: macrodiff_platesmerged.H3K36me3.5

description:
H3K36me3 Macrophage in vitro differentiation Day 4
scchix_macrophage_differentiation_count_mat.H3K36me3.txt.gz
scchix_macrophage_differentiation_dat_meta_merged_H3K4me1_and_H3K36me3.txt.gz
scchix_macrophage_differentiation_lda_projection.H3K36me3.RData
scchix_macrophage_differentiation_pseudotime_inference.H3K4me1_and_H3K36me3.txt.gz


title: P_4466_207099931053


title: BLOOD_4H_rep2

description: SCRB-seq


title: P_4447_20799930699


title: P_4464_20702793161


title: P_4464_20702793156


title: P_4465_20799931235


title: P_4465_20799931035


title: P_4465_20799931196


title: P_4466_20799931056


title: P_4465_20799930898


title: P_4464_20702793153


title: P_4463_20702405409


title: P_4463_20702405406


title: P_4463_20702444352


title: BLOOD_4H_rep1

description: SCRB-seq


title: P_4454_00374051


title: P_4463_20702444347


title: P_4454_00374056


title: P_4454_00374037


title: P_4454_00374054


title: P_4455_20799930595


title: P_4455_20799930924


title: P_4463_20702444354


title: P_4455_20799930889


title: P_4456_20799930919


title: P_4456_20799930920


title: P_4456_20799930916


title: P_4456_20799930940


title: P_4463_20702405417


title: P_4448_20799930781


title: P_4447_20799930580


title: P_4448_20799930634


title: P_4448_20799930775


title: P_4448_20799930808


title: P_4448_20799930758


title: P_4448_20799930703


title: P_4454_20702444367

value: SARS-CoV-2 positive


title: P_4454_20702444308


title: P_4448_20799930548


title: P_4455_20799930836


title: P_4465_20799930903


title: P_4465_20799931234


title: P_4465_20799931169


title: P_4465_20799930991


title: P_4465_20799931215


title: P_4465_20799930968


title: P_4465_20799931225


title: P_4465_20799931170


title: P_4464_20799930984


title: P_4465_20799931149


title: P_4463_20702444406


title: P_4464_20799931165


title: P_4463_20702405412


title: P_4454_20799930601


title: P_4448_20799930734


title: P_4473_20799931357


title: P_4464_20702444418


title: P_4473_20799931355


title: P_4473_20799931352


title: 92860


title: P_4448_20799930570


title: P_4448_20799930562


title: P_4448_20799930568


title: P_4448_20799930543


title: P_4448_20799930566


title: P_4448_20799930515


title: P_4447_20799930831


title: P_4447_20799930830


title: P_4447_20702444305


title: P_4448_20799930590


title: P_4447_20799930587


title: P_4447_20702459674


title: P_4447_20702444300


title: P_4447_20702459672


title: P_4447_20702444301


title: P_4447_20702444298


title: P_4433_20799930_254


title: P_4422_00370849


title: P_4472_20799931349


title: P_4433_20702689_702


title: P_4448_20799930571


title: P_4447_20702459677


title: P_4422_003708900


title: P_4424_00369612


title: P_4424_00369651


title: P_4447_20702459675


title: P_4424_00369653


title: P_4433_20799930_253


title: P_4425_20799930_338


title: P_4425_20799930_336


title: P_4425_20799930_341


title: P_4424_00369625


title: P_4425_20799930_343


title: P_4425_20799930_345


title: P_4425_20702689_659


title: P_4425_20799930_355


title: P_4447_20702793121


title: P_4472_20799931353


title: P_4433_20799930_267


title: P_4425_20799930_399


title: P_4425_20799930_349


title: P_4425_20702689_651


title: 40min single-cell embryo replicate 3

description:
40min single-cell embryo replicate 3
20to60minute_samples_raw_count.tsv
40min-3


title: P_4425_20799930_344


title: P_4425_20799930_342


title: P_4425_20702689_974


title: P_4423_20702793_074


title: P_4433_20702689_700


title: P_4423_20702793_083


title: P_4425_20702689_673


title: P_4425_20702689_960


title: P_4423_20702793_084


title: P_4426_00335169


title: P_4426_00335163


title: P_4433_20799930_300


title: P_4427_20702459_587


title: P_4428_20702405_185


title: P_4426_00335175


title: P_4426_00335184


title: P_4431_00370958


title: P_4431_00370953


title: P_4427_20702689_933


title: P_4426_00335173


title: P_4427_20702459_635


title: P_4425_20799930_109


title: P_4427_20702689_922


title: P_4427_20702459_622


title: P_4428_20702405_184


title: P_4433_20799930_202


title: P_4431_00370935


title: P_4433_20799930_320


title: P_4431_00370957


title: P_4432_00363238


title: P_4432_00363231


title: P_4433_20799930_226


title: P_4433_20799930_360


title: P_4433_20799930_435


title: P_4433_20799930_195


title: P_4433_20799930_426


title: YL-R4-fNu-nRAD21-R2

city: Worcester

first: Yu

last: Liu

state: MA

address: 368 Plantation Street

department: Program in Systems Biology

institute: University of Massachusetts Medical School

description: HAP1 is a near-haploid human cell line that was derived from the male chronic myelogenous leukemia (CML) cell line KBM-7. HAP1 cells are adherent with fibroblast-like morphology.

data_processing:
Fastq files of Hi-C were mapped and parsed to generate cooler files using Distiller
Cooler files were directly processed for compartment and insulation pileup analysis using cooltools
Cooler files were transfer to cWord matrix files to generate contact heatmaps and analyze insulation and loop pileup
Fastq files of ChIPseq were mapped using Bowtie to generate sam files
HOMER (PMID 20513432) was used to generate tag and bigwig files and call peaks from sam files
DeepTools was used for ChIP signal stacking up
Assembly: hg19
Supplementary files format and content: cooler for Hi-C and BigWig files for ChIPseq

source_name: HAP1-RAD21-TEV cells

growth_protocol: HAP1-RAD21-TEV are grown in IMDM medium, with GlutaMAX, 10% FBS and 1% penicillin-streptomycin at 37C in 5% CO2

extract_protocol:
Nuclei were purified using hytonic buffer and after treatments, nuclei were fixed for Hi-C protocol
ChIPseq (PMID31522987)

treatment_protocol: TEV protease treatment: 15U/ml at 4C for overnight; NB contains 10mM PIPES pH 7.4, 2mM MgCl2 and 10mM KCl; NBS1 and NBS2 buffers are NB with 132mM and 200mM NaCl, respectively. NBS1 is physical conditional buffer.

tag: protocol

tag: enzyme

value: DpnII

tag: cell line

value: HAP1-RAD21-TEV cells


title: YL-NBS1-TEV-nRAD21-R8


title: YL-NBS1-IgG-R8


title: YL-WT-NB-CTCF-R2


title: YL-WT-NB-nRAD21-R2


title: YL-R4-fNu-IgG-R2


title: YL-NBS1-TEV-IgG-R8


title: YL-NBS1-nRAD21-R8


title: YL-NB-TEV-cRAD21-R7


title: YL-NBS1-TEV-cRAD21-R8


title: YL-NBS1-CTCF-R8


title: YL-NB-TEV-CTCF-R7


title: YL-WT-NB-IgG-R2


title: P_4432_00363220

tag: cell type


title: YL-NB-TEV-IgG-R7


title: YL-NBS1-cRAD21-R8


title: YL-NB-TEV-nRAD21-R7


title: YL-NBS1-TEV-CTCF-R8


title: YL-NB-IgG-R7


title: YL-NB-cRAD21-R7


title: YL-NB-nRAD21-R7


title: YL-WT-cell-R1-T1_S4_L002_R1_001

extract_protocol:
Nuclei were purified using hytonic buffer and after treatments, nuclei were fixed for Hi-C protocol
Hi-C 2.0 (PMID28435001)


title: YL-R4-NBnoON-R2-T1_S10_L003_R1_001


title: YL-WT-NBS2-ON-R15-T1

description:
HAP1 is a near-haploid human cell line that was derived from the male chronic myelogenous leukemia (CML) cell line KBM-7. HAP1 cells are adherent with fibroblast-like morphology.
YL-WT-NBS2-ON.20000.cool


title: YL-R4-fNu-CTCF-R2


title: YL-WT-NBS2-ON-R14-T1


title: YL-WT-NBS1-ON-R14-T1

description:
HAP1 is a near-haploid human cell line that was derived from the male chronic myelogenous leukemia (CML) cell line KBM-7. HAP1 cells are adherent with fibroblast-like morphology.
YL-WT-NBS1-ON.20000.cool


title: YL-WT-NB-ON-R15-T1

description:
HAP1 is a near-haploid human cell line that was derived from the male chronic myelogenous leukemia (CML) cell line KBM-7. HAP1 cells are adherent with fibroblast-like morphology.
YL-WT-NB-ON.20000.cool


title: YL-NB-CTCF-R7


title: YL-WT-NB-ON-R14-T1


title: RiboTag-KO_IP_Rep1

status: Public on Jul 23 2022

city: Hangzhou

first: Xiaoyu

last: Li

state: Zhejiang

address: 866 Yuhangtang Road

department: SCHOOL OF BASIC MEDICAL SCIENCES

institute: Zhejiang University

description: For tRNA-seq,  naïve CD4+ T cells were isolated from WT mice and activated with plate-bound anti-CD3 plus anti-CD28 in a 96-well plate for 0,6,18,48 hours. 200 ng small RNA fraction (<200 nt; mainly composed of mature tRNA) was purified from total RNA using MEGA clear Kit (Thermo Fisher Scientific). Purified small RNA was deacylated by incubating in 0.1 M Tris-HCl, pH 9 at 37°C for 45 minutes. For RiboTag-seq, 500 million naïve CD4+ T cells were isolated from WT (RiboTagflox/floxCd4Cre) and Trmt61a-KO (Trmt61aflox/floxRiboTagflox/floxCd4Cre) mice (activated with plate-bound anti-CD3 plus anti-CD28 in 96-well plate for 6 hours), and washed and treated with 100 μg/mL cycloheximide for 1 minute. Cells were washed in ice-cold PBS twice, and then RiboTag lysis buffer was added directly to the cells on ice as previously described. Cell lysates were passed through a 26-gauge needle 10 times and incubated for 30 min on ice to ensure complete lysis. Ribosome-RNA-containing supernatants were clarified by centrifugation at 12,000g for 10 min at 4 °C. Haemmaglutinin-conjugated magnetic beads (Pierce) were added to samples and incubated overnight under gentle inversion at 4 °C. Beads were washed three times for 10 min with gentle rotation in a high-salt buffer containing cycloheximide. RNA was eluted from HA-beads using Qiagen RLT buffer containing 2-Mercaptoethanol and anti-foaming DX reagent (Qiagen) by 30 s vortex pulsing. RNA was isolated using an RNAeasy micro kit. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA samples were transferred to the OE Biotech Co., Ltd. (Shanghai, China) for cDNA library preparation using NEBNext® Ultra II Directional RNA Library Prep Kit according to the manufacturer’s instructions.

data_processing:
Reads adapters were removed by Trim_galore ( v0.6.6)
For RNA-seq, Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the mm10 genome using Hisat2 (v2.0.5) ,and then featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. For Ribo-seq, the rRNA removed reads of each sample were mapped to the reference genome by Bowtie2(V 2.4.1) allowing no mismatches. For m1A-seq, clean reads were mapped to mm10 tRNA genome by bowtie2.
Assembly: mm10,mm10-tRNA
Supplementary files format and content: tRNA expression in txt file format
Supplementary files format and content: RiboTag-seq in bigwig file format
Library strategy: RiboTag-Seq

source_name: spleen

growth_protocol: Primary T cells were isolated from the spleens of age-matched WT and conditional knockout mice (8 weeks old). Naive CD4 T cells were purified by using EasySep Mouse Naïve CD4+ T Cell Isolation Kit (STEMCELL Technologies) according to the instructions, respectively. The purified T cells were cultured with X-VIVO mediums.

extract_protocol:
RNAseq: total RNA was extracted based on the manufacturer’s protocol by using TRIzol reagent (Invitrogen). Riboseq: we performed the ribosome profiling by strictly following the manual for the Illumina TruSeq Ribo Profile (Mammalian) Kit. m1Aseq: 200 ng small RNA fraction (<200 nt; mainly composed of mature tRNA) was purified from total RNA using MEGAclear Kit (Thermo Fisher Scientific).
RNAseq:RNA libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB) based on the manufacturer’s instructions. RiboTagseq: libraries were constructed using NEBNext® Multiple Small RNA Library Prep Set for Illumina® (no. E7300S, E7300L). m1Aseq: Purified small RNA was deacylated by incubating in 0.1 M Tris-HCl, pH 9 at 37°C for 45 min. Half of the deacylated small RNA fraction was subjected to demethylation treatment by using AlkB in vivo reaction. RNA samples were dephosphorylated with PNK (NEB) and ligated to 3’ RNA linker using T4 RNA ligase2, truncated KQ (NEB). Reverse transcription was carried using different reverse transcriptase for different samples. 5’ adaptor was ligated to cDNA and then amplified by PCR. PCR products were purified by 8% TBE gel.

treatment_protocol: The purified T cells were stimulated with plate-bound anti-CD3 (5 μg/ml) and anti-CD28 (2 μg/ml) in replicate wells of 96-well plates.

value: spleen

value: primary CD4 T cells

tag: genotype

tag: treatment


title: RiboTag-WT_input_Rep1

value: Trmt6-WT (RiboTagflox/floxCd4Cre)


title: RiboTag-KO_input_Rep2


title: RiboTag-KO_IP_Rep2


title: MAX-PCGF6KO_ChIP-seq

status: Public on Jul 22 2022

city: Wuhan

first: Chun

middle: Xian

last: Lan

address: Donghu Road 116, District Wuchang

department: Medical Research Institute

institute: Wuhan University

data_processing:
For ChIP-seq ,Illumina Casava1.7 software used for basecalling, the adapter was trimmed by Trim galore(v0.6.2). Then these reads were aligned to the human reference genome GRCh38 using Bowtie2 (v2.3.4.2) with the default parameters.The uniquely mapped reads were sorted by Samtools (v1.9) and then performed peak calling by MACS2(v2.1.2) with the callpeak module (the parameter --call-summits --nomodel --extsize 150 -p 0.005). The bam files were converted to the bigWig signal files by DeepTools(v3.3.0) with the bamCoverage module ,Homer was used to annotated nearby genes from the peaks obtained from MACS2 and to find motif that enrich in the binding sequence.
Assembly: GRCh38

growth_protocol: PGP1 cells were maintained in mTeSR1 (StemCell Technologies) on Matrigel-coated cell culture plate at 37℃ with 5% CO2.

extract_protocol:
For ChIP-seq, the PGP1 cells (~5x106 cells/repeat)  were crosslinked in 1% formaldehyde for 10 min at room temperature with rotation. Cross-linking was stopped by incubating with 0.125M glycine for 5 min at room temperature with rotation.Then cells were collected and treated in  cell lysis buffer (10mM Tris-HCl (pH 8.0), 140 mM NaCl, 0.2% NP-40) plus1x cOmplete Protease Inhibitor (Roche) and incubated on ice for 10 min to isolate nuclei. After washed once with cold DBPS, isolated nuclei were sonicated in Nuclear lysis buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA (pH 8.0), 1% SDS) with 1x cOmplete Protease Inhibitor (Roche) in Diagenode Bioruptor Pico to obtain 200-500bp chromatin fragments. The sonication condition was 10 cycles of 20s/on and 30s/off.  After centrifuging, the soluble sonicated fragments were incubated with 5ug antibody and Protein A/G Dynabeads with rotating overnight at 4 °C to enrich fragmented chormatin.Then the DNA fragments were eluted with the elution buffer (100mM NaHCO3 and 1%SDS) and reverse crosslinked at 67 °C over night. Finally, the immunoprecipitation DNA were purified with Phenol-chloroform Protocol for chip-seq. The DNA were sent to Geekgene (Beijing, China) for ChIP-seq library construction and sequencing.
libraries were prepared for sequencing using standard Illumina protocols.

value: iPSC


title: RiboTag-WT_input_Rep2


title: MAX-WT_ChIP-seq

source_name: iPSC

value: WT


title: tRNA-expression-AlkB_T0h_Rep1

data_processing:
Reads adapters were removed by Trim_galore ( v0.6.6)
For RNA-seq, Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the mm10 genome using Hisat2 (v2.0.5) ,and then featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. For Ribo-seq, the rRNA removed reads of each sample were mapped to the reference genome by Bowtie2(V 2.4.1) allowing no mismatches. For m1A-seq, clean reads were mapped to mm10 tRNA genome by bowtie2.
Assembly: mm10,mm10-tRNA
Supplementary files format and content: tRNA expression in txt file format
Supplementary files format and content: RiboTag-seq in bigwig file format

value: wild type


title: RiboTag-WT_IP_Rep1


title: tRNA-expression-AlkB_T6h_Rep2


title: tRNA-expression-AlkB_T18h_Rep2


title: tRNA-expression-AlkB_T6h_Rep1


title: tRNA-expression-AlkB_T18h_Rep1


title: RiboTag-WT_IP_Rep2


title: MYC-WT_ChIP-seq


title: tRNA-expression-AlkB_T0h_Rep2


title: E2F6-WT_ChIP-seq


title: MYC-PCGF6KO_ChIP-seq


title: tRNA-expression-AlkB_T48h_Rep2


title: SAMPLE_00000001_T02_AD

status: Public on Jul 21 2022

city: Kiel

first: Matthias

last: Hübenthal

state: SH

address: Rosalind-Franklin-Str. 9

department: Dermatology, Venereology and Allergy

country: Germany

institute: University Hospital Schleswig-Holstein

data_processing:
Illumina bcl2fastq v2.20.0.422 software used for basecalling
Illumina standard primers were trimmed using cutadapt (version 1.15)
Reads were mapped to the human reference genome (GRCh38, Ensembl release 99) using Tophat2 (version 2.1.1) and Bowtie 2 (version 2.3.2)
Mapped reads were cleaned and sorted using Samtools (version 1.5)
Number of reads for each gene was counted using HTSeq (version 0.10.0) and annotated according to Ensembl release 99
Assembly: GRCh38, Ensembl release 99
Supplementary files format and content: tab-delimited text file including raw counts of sequencing reads for each gene and sample, technical batches (cohort, shipping_time) removed using sva::ComBat_seq (verion 3.38.0)

source_name: Peripheral blood

extract_protocol:
Samples were stored in PAXgene blood RNA tubes (PreAnalytiX GmbH, Hombrechtikon Switzerland) at -80°C until automated isolation of total RNA with the PAXgene Blood miRNA Kit (PreAnalytiX GmbH) on the QIAcube (QIAGEN, Hilden, Germany)
RNA samples were prepared for sequencing using the Illumina Truseq® mRNA Protocol in combination with the RiboZero rRNA removal Kit and sequenced on the NovaSeq6000 with 2x100bp.

value: Peripheral blood

tag: cohort

value: TREATgermany

tag: shipping time

value: AD

tag: time point

value: 3 months after initiation of therapy

tag: agent

value: dupilumab


title: SAMPLE_00000114_T01_AD

tag: tissue

value: before initiation of therapy


title: SAMPLE_00000111_T01_AD


title: SAMPLE_00000052_T01_AD


title: tRNA-expression-AlkB_T48h_Rep1


title: E2F6-PCGF6KO_ChIP-seq


title: SAMPLE_00000033_T02_AD

value: ciclosporin


title: SAMPLE_00000052_T02_AD


title: SAMPLE_00000101_T01_AD


title: SAMPLE_00000048_T01_AD


title: SAMPLE_00000002_T02_AD


title: SAMPLE_00000040_T02_AD


title: SAMPLE_00000046_T01_AD


title: SAMPLE_00000096_T02_AD


title: SAMPLE_00000016_T01_AD


title: SAMPLE_00000122_T02_AD


title: SAMPLE_00000093_T02_AD


title: SAMPLE_00000086_T01_AD


title: SAMPLE_00000016_T02_AD


title: SAMPLE_00000019_T01_AD


title: SAMPLE_00000059_T01_AD


title: SAMPLE_00000114_T02_AD


title: SAMPLE_00000096_T01_AD


title: SAMPLE_00000082_T01_AD


title: SAMPLE_00000053_T02_AD


title: SAMPLE_00000015_T02_AD


title: SAMPLE_00000024_T01_AD


title: SAMPLE_00000121_T02_AD


title: SAMPLE_00000051_T01_AD


title: SAMPLE_00000036_T02_AD


title: SAMPLE_00000074_T02_AD


title: SAMPLE_00000066_T02_AD


title: SAMPLE_00000082_T02_AD


title: SAMPLE_00000112_T01_AD


title: SAMPLE_00000021_T01_AD


title: SAMPLE_00000012_T01_AD


title: SAMPLE_00000080_T02_AD


title: SAMPLE_00000036_T01_AD


title: SAMPLE_00000087_T02_AD


title: SAMPLE_00000029_T01_AD


title: SAMPLE_00000104_T01_AD


title: SAMPLE_00000046_T02_AD


title: SAMPLE_00000040_T01_AD


title: SAMPLE_00000055_T02_AD


title: SAMPLE_00000075_T02_AD


title: SAMPLE_00000071_T02_AD


title: SAMPLE_00000030_T02_AD


title: SAMPLE_00000060_T02_AD


title: SAMPLE_00000123_T02_AD


title: SAMPLE_00000024_T02_AD


title: SAMPLE_00000069_T01_AD


title: SAMPLE_00000029_T02_AD


title: SAMPLE_00000101_T02_AD


title: SAMPLE_00000087_T01_AD


title: SAMPLE_00000045_T02_AD


title: SAMPLE_00000086_T02_AD


title: SAMPLE_00000080_T01_AD


title: SAMPLE_00000018_T01_AD


title: SAMPLE_00000117_T02_AD


title: SAMPLE_00000037_T01_AD


title: SAMPLE_00000018_T02_AD


title: SAMPLE_00000071_T01_AD


title: SAMPLE_00000113_T02_AD


title: SAMPLE_00000074_T01_AD


title: SAMPLE_00000056_T01_AD


title: SAMPLE_00000124_T02_AD


title: SAMPLE_00000085_T01_AD


title: SAMPLE_00000033_T01_AD


title: SAMPLE_00000012_T02_AD


title: SAMPLE_00000015_T01_AD


title: SAMPLE_00000093_T01_AD


title: SAMPLE_00000004_T02_AD


title: SAMPLE_00000117_T01_AD


title: SAMPLE_00000121_T01_AD


title: SAMPLE_00000061_T01_AD


title: SAMPLE_00000060_T01_AD


title: SAMPLE_00000001_T01_AD


title: SAMPLE_00000039_T01_AD


title: SAMPLE_00000091_T01_AD


title: SAMPLE_00000037_T02_AD


title: SAMPLE_00000112_T02_AD


title: SAMPLE_00000107_T02_AD


title: SAMPLE_00000039_T02_AD


title: RiboTag-KO_input_Rep1


title: SAMPLE_00000043_T02_AD


title: SAMPLE_00000051_T02_AD


title: SAMPLE_00000045_T01_AD


title: SAMPLE_00000053_T01_AD


title: SAMPLE_00000007_T02_AD


title: YL-WT-NBS1-ON-R15-T1


title: SAMPLE_00000043_T01_AD


title: SAMPLE_00000061_T02_AD


title: SAMPLE_00000055_T01_AD


title: SAMPLE_00000097_T01_AD


title: SAMPLE_00000124_T01_AD


title: SAMPLE_00000113_T01_AD


title: SAMPLE_00000002_T01_AD


title: SAMPLE_00000069_T02_AD


title: SAMPLE_00000021_T02_AD


title: SAMPLE_00000056_T02_AD


title: SAMPLE_00000004_T01_AD


title: SAMPLE_00000111_T02_AD


title: SAMPLE_00000107_T01_AD


title: SAMPLE_00000066_T01_AD


title: SAMPLE_00000091_T02_AD


title: SAMPLE_00000123_T01_AD


title: SAMPLE_00000097_T02_AD


title: SAMPLE_00000030_T01_AD


title: SAMPLE_00000007_T01_AD


title: SAMPLE_00000057_TNN_HC

value: ADPSOKO

value: HC


title: SAMPLE_00000059_T02_AD


title: SAMPLE_00000109_TNN_AD


title: SAMPLE_00000062_TNN_AD


title: SAMPLE_00000058_TNN_HC


title: SAMPLE_00000064_TNN_HC


title: SAMPLE_00000075_T01_AD


title: SAMPLE_00000025_TNN_AD


title: SAMPLE_00000084_TNN_HC


title: SAMPLE_00000095_TNN_AD


title: SAMPLE_00000126_TNN_HC


title: SAMPLE_00000027_TNN_HC


title: SAMPLE_00000034_TNN_AD


title: SAMPLE_00000079_TNN_AD


title: SAMPLE_00000065_TNN_AD


title: SAMPLE_00000081_TNN_HC


title: SAMPLE_00000100_TNN_AD


title: SAMPLE_00000122_T01_AD


title: SAMPLE_00000125_TNN_HC


title: SAMPLE_00000005_TNN_HC


title: SAMPLE_00000038_TNN_HC


title: SAMPLE_00000031_TNN_AD


title: SAMPLE_00000078_TNN_AD


title: SAMPLE_00000088_TNN_HC


title: SAMPLE_00000042_TNN_AD


title: SAMPLE_00000022_TNN_AD


title: SAMPLE_00000006_TNN_AD


title: SAMPLE_00000054_TNN_HC


title: SAMPLE_00000099_TNN_HC


title: SAMPLE_00000041_TNN_AD


title: SAMPLE_00000044_TNN_HC


title: SAMPLE_00000090_TNN_AD


title: SAMPLE_00000083_TNN_AD


title: SAMPLE_00000003_TNN_HC


title: SAMPLE_00000073_TNN_HC


title: SAMPLE_00000009_TNN_AD


title: SAMPLE_00000115_TNN_HC


title: SAMPLE_00000013_TNN_HC


title: SAMPLE_00000011_TNN_HC


title: SAMPLE_00000108_TNN_HC


title: SAMPLE_00000098_TNN_HC


title: SAMPLE_00000077_TNN_HC


title: SAMPLE_00000032_TNN_AD


title: SAMPLE_00000076_TNN_AD


title: SAMPLE_00000068_TNN_HC


title: SAMPLE_00000028_TNN_HC


title: SAMPLE_00000070_TNN_HC


title: SAMPLE_00000094_TNN_HC


title: SAMPLE_00000049_TNN_HC


title: SAMPLE_00000102_TNN_HC


title: SAMPLE_00000008_TNN_HC


title: SAMPLE_00000035_TNN_AD


title: SAMPLE_00000010_TNN_AD


title: SAMPLE_00000103_TNN_AD


title: SAMPLE_00000110_TNN_AD


title: SAMPLE_00000072_TNN_HC


title: SAMPLE_00000106_TNN_AD


title: SAMPLE_00000047_TNN_AD


title: SAMPLE_00000116_TNN_HC


title: SAMPLE_00000127_TNN_AD


title: SAMPLE_00000050_TNN_HC


title: SAMPLE_00000120_TNN_AD


title: SAMPLE_00000067_TNN_AD


title: SAMPLE_00000089_TNN_HC


title: SAMPLE_00000023_TNN_HC


title: SAMPLE_00000119_TNN_HC


title: SAMPLE_00000118_TNN_HC


title: SAMPLE_00000092_TNN_AD


title: SAMPLE_00000105_TNN_HC


title: SAMPLE_00000063_TNN_HC


title: SAMPLE_00000014_TNN_HC


title: H3K9me3_Zmym2KO

status: Public on Jul 20 2022

first: Tuncay

last: Baubec

address: Padualaan 8

department: Department of Biology

institute: Utrecht University

description: ChIP

data_processing:
Reads were trimmed using trim_galore v0.6.6
Trimmed reads were aligned to the mm9 mouse genome BSgenome.Mmusculus.UCSC.mm9 using QuasR qAlign() in R with standard options
Wig files were created using QuasR qExportWig() function with scaling set to TRUE
Assembly: mm9
Supplementary files format and content: Wig track format: Read coverage per 100 bp bins

source_name: Mouse Embryonic Stem Cells

growth_protocol: ES cells were were cultivated on feeder cells or 0.2% gelatine coated dishes. ES cell growth medium consisted of DMEM (Invitrogen) supplemented with 15% foetal calf serum (Invitrogen), 1x non-essential amino acids (Invitrogen), 1mM L-glutamine, LIF and 0.001% beta-mercaptoethanol.

extract_protocol:
Approximately 15 x 10^6 cells were harvested per IP and fixed with 1 % methanol-free formaldehyde for 8 min. Cross-linking was quenched by adding glycine to a final concentration of 0.125 nM and incubated for 10 min at 4 ˚C on ice. Cells were pelleted at 600 x g for 5 min, washed with cold PBS and incubated for 10 min on ice in a buffer containing 10 mM EDTA, 10 mM Tris pH 8, 0.5 mM EGTA and 0.25 % Triton X-100. After centrifugation, cells were incubated in 1 mM EDTA, 10 mM Tris pH 8, 0.5 mM EGTA and 200 mM NaCl for 10 min on ice. Chromatin was extracted in a high salt buffer (HSB) containing 50 mM HEPES pH 7.5, 1 mM EDTA, 1 % Triton X-100, 0.1 % deoxycholate, 0.2 % SDS and 500 mM NaCl for 2 hours at 4 ˚C and chromatin was sheared using a Bioruptor Pico sonicator (Diagenode). 100 µg of chromatin was used per IP reaction with 30 µl of pre-blocked magnetic Protein A beads (Invitrogen). Beads were blocked with 1 mg of BSA and 100 ng of yeast tRNA (Sigma) in TE buffer containing proteinase inhibitor mix (Roche) before use. Prior to the IP, chromatin was pre-cleared with 20 µl of blocked beads for 1 hour at 4 ˚C. 5 % of input material was kept at -20 ˚C and de-crosslinked along the IP material. 5 µg of antibody was used per IP for overnight incubation at 4 ˚C. The next day, 30 µl of blocked beads were added to the chromatin and incubated for 4h at 4 ˚C. Beads were separated on a magnet and washed twice for 8 min with HSB, one time with 50 mM LiCl, 0.5 % NP-40, 0.5 % deoxycholate, 1 mM EDTA, and 10 mM Tris pH 8. After two additional washes with TE for 8 min, chromatin was eluted after 30 min incubation at 37 ˚C with 60 µg RNaseA (Roche) in 1 % SDS and 100 mM NaHCO3, followed by 3 h incubation adding 10 mM EDTA, 40 mM Tris pH 8 and 60 µg of Proteinase K (Roche). Final de-crosslinking was done overnight at 65 ˚C. Eluted material was cleaned up using phenol chloroform extraction and quantified using a Qubit 2.0 fluorometer (Thermo Scientific). The following antibodies were used for ChIP: H3K9me3 (Abcam ab8898 ).
ChIP-seq library using NEBNext ChIP-seq Library Prep Master Mix set for Illumina (NEB E6240)

value: embryonic stem cells

value: Zmym2 KO

tag: antibody


title: H3K9me3_wt

description: ChIP


title: H3K9me3_Atf7ipKO

description: ChIP

value: Atf7ip KO


title: PBMC15-Feature

status: Public on Jul 19 2022

first: Han

last: Zhu

address: G1105, 265 Campus Drive

department: Cardiovascular Medicine

description:
CITE-seq data
Surface Protein Feature Barcode Sequence
Processed data for this sample available on GSM6346312

library_source: other

data_processing:
Raw single-cell RNA-seq data were processed using 10x Genomics Cell Ranger (6.0.2) to demultiplex the FASTQ reads in order to align them to the human or mouse reference genomes and count the unique molecular identifier (UMI) (through the “cellranger count” function). Human reference used was GRCh38 and mouse reference was refdata-gex-mm10-2020-A, downloaded from the 10x website.
Raw T cell receptor (TCR) sequencing data were processed using 10x Genomics Cell Ranger (v4.0.3). In summary, the algorithm aligned FASTQ reads to human GRCh38 V(D)J reference genome (v4.0.0, from 10X Genomics) by using the “cellranger vdj” function, resulting in the assembly of V(D)J sequences and clonotypes (38).
Individual sample gene expression matrices were loaded into Seurat v4.0.0 R package (https://satijalab.org/seurat/) for further analysis.
To filter out poor quality data from cells with high mitochondrial gene expression likely to be dead/damaged cells (59), we removed cells with greater than >15% mitochondrial genes present (60). Additionally, we removed cells for which less than 500 genes were detected.
Assembly: h38, mouse (from 10x website - refdata-gex-mm10-2020-A.tar.gz) - https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest?
Supplementary files format and content: TCR-seq: *filtered_contig_annotations.csv
Supplementary files format and content: scRNA-seq, CITE-seq: *feature_bc_matrix.tar
Library strategy: CITE-seq

molecule: other

source_name: Mouse PBMCs

extract_protocol:
Frozen PBMCs were removed from liquid nitrogen and resuspended in warm RPMI media + 10% FBS (@ 37ºC) by adding 1 mL, 3 mL, 4 mL, 8 mL 16 mL media at 30-60 second intervals. Cells were washed and passed through a 40 um filter, centrifuged @ 300 rcf x 5 min and resuspended in PBS with 50 ul 1% BSA and Biolegend Fc Receptor Blocking Solution (Human TrueStain FcX (Cat. No. 422301) or Mouse TruStain PLUS (mouse) Fc block for 20 minutes. Afterwards, another 50 uL of antibody mastermix containing Biolegend TotalSeq-C antibodies for staining (see manuscript for full antibody list) for final manufacture-recommended concentration of 1.0 ug of antibody in 100 ul of staining buffer for every 1 million cells for a total of 10-15 minutes incubation. After incubation, cells were washed 2x by resuspending in 1.5 mL PBS + 1% RNase-free BSA (MACS BSA Stock Solution No. 130-091-376) and then 1 mL PBS + 0.04% BSA. 10 uL of cell suspension was then taken for counting and appropriate volume of PSA + 0.04% BSA was added (200-500 uL) to aim for final target concentration of 1-1.5 million cells/mL). Cells were then loaded into Chromium Next GEM Chip G (10x PN 2000177) to achieve 4000-6000 cells target cell recovery per non-multiplexed sample or 20,000-24,000 target cells per multiplexed sample if cell hashing was performed. If cell hashing was performed, the individual samples were pooled into one sample prior to running the Chromium Controller.
All steps from cDNA isolation to library preparation were completed according to 10x’s manufacturing protocols for the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1. Isolated cDNA was amplified (14 cycles), and then cDNA was allocated for TCR enrichment, feature barcode library generation, and 5’ cDNA library generation. cDNA and library quality was evaluated using the high sensitivity DNA kit on the Agilent 2100 Bioanalyzer.

value: PBMC

value: MRL/Pdcd1 -/- (Hash1-TotalSeqC), MRL/Pdcd1 -/- (Hash2-TotalSeqC)


title: SAMPLE_00000020_TNN_AD


title: PBMC12-Feature

description:
CITE-seq data
Surface Protein Feature Barcode Sequence
Processed data for this sample available on GSM6346309

value: Blood (Hash1-TotalSeqC), Heart(Hash2-TotalSeqC), Blood (Hash3-TotalSeqC), Heart (Hash4-TotalSeqC)

value: MRL(Hash1-TotalSeqC), MRL(Hash2-TotalSeqC), MRL/Pdcd1 -/- (Hash3-TotalSeqC), MRL/Pdcd1 -/- (Hash4-TotalSeqC)


title: PBMC13-Feature

description:
CITE-seq data
Surface Protein Feature Barcode Sequence
Processed data for this sample available on GSM6346310

value: Blood (Hash1-TotalSeqC), Heart(Hash2-TotalSeqC), Blood (Hash3-TotalSeqC), Heart (Hash4-TotalSeqC), Blood (Hash5-TotalSeqC), Heart (Hash6-TotalSeqC)

value: MRL(Hash1-TotalSeqC), MRL(Hash2-TotalSeqC), MRL/Pdcd1 -/- (Hash3-TotalSeqC), MRL/Pdcd1 -/- (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL (Hash6-TotalSeqC)


title: PBMC8-TCR

description:
single-cell TCR seq
Total TCR sequences

data_processing:
Raw single-cell RNA-seq data were processed using 10x Genomics Cell Ranger (6.0.2) to demultiplex the FASTQ reads in order to align them to the human or mouse reference genomes and count the unique molecular identifier (UMI) (through the “cellranger count” function). Human reference used was GRCh38 and mouse reference was refdata-gex-mm10-2020-A, downloaded from the 10x website.
Raw T cell receptor (TCR) sequencing data were processed using 10x Genomics Cell Ranger (v4.0.3). In summary, the algorithm aligned FASTQ reads to human GRCh38 V(D)J reference genome (v4.0.0, from 10X Genomics) by using the “cellranger vdj” function, resulting in the assembly of V(D)J sequences and clonotypes (38).
Individual sample gene expression matrices were loaded into Seurat v4.0.0 R package (https://satijalab.org/seurat/) for further analysis.
To filter out poor quality data from cells with high mitochondrial gene expression likely to be dead/damaged cells (59), we removed cells with greater than >15% mitochondrial genes present (60). Additionally, we removed cells for which less than 500 genes were detected.
Assembly: h38, mouse (from 10x website - refdata-gex-mm10-2020-A.tar.gz) - https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest?
Supplementary files format and content: TCR-seq: *filtered_contig_annotations.csv
Supplementary files format and content: scRNA-seq, CITE-seq: *feature_bc_matrix.tar
Library strategy: TCR-seq

value: Blood

value: MRL


title: PBMC15-TCR

description:
single-cell TCR seq
Total TCR sequences


title: PBMC7-TCR

description:
single-cell TCR seq
Total TCR sequences

value: Heart


title: PBMC14-TCR

description:
single-cell TCR seq
Total TCR sequences

value: Blood (Hash1-TotalSeqC), Heart(Hash2-TotalSeqC), Blood (Hash3-TotalSeqC), Heart (Hash4-TotalSeqC), Blood (Hash5-TotalSeqC), Heart (Hash6-TotalSeqC), Blood (Hash7-TotalSeqC), Heart (Hash8-TotalSeqC)

value: MRL(Hash1-TotalSeqC), MRL(Hash2-TotalSeqC), MRL/Pdcd1 -/- (Hash3-TotalSeqC), MRL/Pdcd1 -/- (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL (Hash6-TotalSeqC), MRL/Pdcd1 -/- (Hash7-TotalSeqC), MRL/Pdcd1 -/- (Hash8-TotalSeqC)


title: PBMC11-TCR

description:
single-cell TCR seq
Total TCR sequences

value: MRL/Pdcd1 -/-


title: PBMC7

description: scRNA-seq data

data_processing:
Raw single-cell RNA-seq data were processed using 10x Genomics Cell Ranger (6.0.2) to demultiplex the FASTQ reads in order to align them to the human or mouse reference genomes and count the unique molecular identifier (UMI) (through the “cellranger count” function). Human reference used was GRCh38 and mouse reference was refdata-gex-mm10-2020-A, downloaded from the 10x website.
Raw T cell receptor (TCR) sequencing data were processed using 10x Genomics Cell Ranger (v4.0.3). In summary, the algorithm aligned FASTQ reads to human GRCh38 V(D)J reference genome (v4.0.0, from 10X Genomics) by using the “cellranger vdj” function, resulting in the assembly of V(D)J sequences and clonotypes (38).
Individual sample gene expression matrices were loaded into Seurat v4.0.0 R package (https://satijalab.org/seurat/) for further analysis.
To filter out poor quality data from cells with high mitochondrial gene expression likely to be dead/damaged cells (59), we removed cells with greater than >15% mitochondrial genes present (60). Additionally, we removed cells for which less than 500 genes were detected.
Assembly: h38, mouse (from 10x website - refdata-gex-mm10-2020-A.tar.gz) - https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest?
Supplementary files format and content: TCR-seq: *filtered_contig_annotations.csv
Supplementary files format and content: scRNA-seq, CITE-seq: *feature_bc_matrix.tar


title: PBMC10-TCR

description:
single-cell TCR seq
Total TCR sequences


title: PBMC8

description: scRNA-seq data


title: PBMC15

description: scRNA-seq data


title: PBMC10

description: scRNA-seq data


title: PBMC12

description: scRNA-seq data


title: PBMC11

description: scRNA-seq data


title: PBMC13

description: scRNA-seq data


title: PBMC14

description: scRNA-seq data


title: RNA-seq_P39_Dnmt3a_cKO_rep2

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq and ChIP-seq datasets were performed as described in Li et al., Elife.2022 (PMID: 35604009)
Reads were trimmed to remove sequencing adapters and low-quality sequences (minimum Phred score 20) using Trim Galore (v0.5.0) in the paired-end mode.
Clean reads were mapped to the mouse mm10 (GRCm38) genome and the GENCODE annotated transcriptome (release M10) with STAR (Spliced Transcripts Alignment to a Reference, v2.5.1b).
Gene expression was estimated using RSEM (RNA-Seq by Expectation Maximization, v1.2.30).
Gene-level “expected count” from the RSEM results were rounded and fed into edgeR (v3.24.1) to call differentially expressed genes. Only genes that were expressed (with counts per million > 2) in at least two samples were kept. These counts were then normalized using the TMM method, and DE genes were then called in the quasi-likelihood F-test mode, requiring FDR < 0.05 and FC > 20%
Bigwig files for visualization were generated by running STAR in "inputAlignmentsFromBAM" with the previous generated BAM files as input to generate bedgraph files, and then converted to bigWig format using UCSC bedGraphToBigWig (v4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig tracks for visualization of RNA-seq and ChIP-seq datasets
Supplementary_files_format_and_content: tab delimited text files of gene expression levels estimated using RSEM v1.2.30. Gene IDs were from GENCODE annotation (M10).

molecule: nuclear RNA

source_name: Excitatory pyramidal neurons from frontal cortex of Dnmt3a cKO mice

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee.

extract_protocol:
The frontal cortex tissue was rapidly dissected from 1-2 adult mice on ice, and the INTACT method was used to affinity purify GFP+ nuclei. Isolated nuclei were resuspended in RL buffer for RNA purification using the Single-Cell RNA Purification Kit (Norgen 51800) with on-column DNase digestion following the standard kit protocol. The nuclear RNA concentration was determined using TapeStation (Agilent).
RNA was diluted to 1 ng/µl and a total of 5 ng processed for RNA-seq library preparation. RNA libraries were prepared using NuGen Ovation® RNA‑Seq System V2 for cDNA preparation following the product manual, cDNA purification using Zymo Research DNA Clean & Concentrator™-25 with modification from Ovation protocol. cDNA elution on 30-40 ul of TE. 1 ug of each sample was fragmented at 300bp using Covaris S2 (Sonolab S-series V2) and the rest of the library was prepared following protocol for KAPA LTP Library Preparation Kit, using Illumina indexed adapters.

tag: strain

value: C57BL6J/129 (name in Jackson Labs:B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ)

value: brain (frontal cortex)

value: excitatory pyramidal neurons

value: Postnatal day 39

tag: Sex

value: male


title: MethylC-seq_P39_Dnmt3a_cKO_rep1

data_processing:
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq and ChIP-seq datasets were performed as described in Li et al., Elife.2022 (PMID: 35604009)
MethylC-seq reads were processed as previously described using the methylpy pipeline (v1.3.2, https://github.com/yupenghe/methylpy and Lister et al., 2013) for alignment and mC calling. Briefly, computationally bisulfite-converted genome index was built using the a substituted genome file that masked SNPs called in the two mouse strains (see genomic DNA sequceing data processing and SNP calling),  appended with the lambda phage genomic sequence. MethylC-seq raw reads were first trimmed to remove sequencing adapters and low-quality sequences (minimum Phred score 10) using Cutadapt in paired-end mode. To acquire higher mappability, we treated the two ends of the clean reads as they were sequenced in single-end mode, and mapped them to the converted genome index with bowtie (v2.3.0) as aligner in the single-end pipeline of methylpy. Only reads uniquely mapped were kept, and clonal reads were removed. The bisulfite non-conversion rate was estimated using the spiked-in unmethylated lambda phage DNA. For each cytosine, a binomial test was performed to test whether the methylation levels are significantly greater than 0 with an FDR threshold of 0.01.
CG differentially methylated regions (DMRs) were identified using a previously reported method (Lister et al. 2013), which is implemented in the DMRfind function in methylpy. We required at least 3 differentially methylated sites within a particular DMR, and the maximum distance two significant sites can be to be included in the same DMR to be 500 nucleotides. DMRs were further filtered with an FDR cutoff of 0.01 and a post-filtering cutoff of methylation levels change greater than 30%.
To find DMVs, we first identified UMRs (undermethylated regions) and LMRs (low methylated regions) using MethylSeekR95 (v1.22.0) with m = 0.5, n = 7 and FDR < 0.05. DMVs were then defined as UMRs that with length ≥ 5 kb and mean methylation level ≤ 15%.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig tracks for visualization of RNA-seq and ChIP-seq datasets
Supplementary_files_format_and_content: tab delimited text files of methylcytosine calls (allC tables); columns in allc files are: column 1 - chromosome; column 2 - position (1-based); column 3 - strand; column 4 - class (context); column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value 0 or 1 indicating the result of statistical test for methylated cytosines)

extract_protocol:
The frontal cortex tissue was rapidly dissected from 1-2 adult mice on ice, and the INTACT method was used to affinity purify GFP+ nuclei. Isolated nuclei were resuspended in PBS for DNA purification using the DNeasy Blood and Tissue kit (Qiagen 69504) following the standard kit protocol.
MethylC-seq libraries were constructed as previously described [Urich M. et al. MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nature Protocols. 2015 Mar;10(3):475-83.]. All DNA obtained from the extraction was spiked with 0.5% unmethylated Lambda DNA. The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 200 bp, followed by end repair and addition of a 3’ A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA at 16˚C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). Adapter-ligated DNA (≤450 ng) was subjected to sodium bisulfite conversion using the MethylCode kit (Life Technologies, Carlsbad, CA) as per manufacturer’s instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 8 cycles of PCR with the following reaction composition: 25 µL of Kapa HiFi Hotstart Uracil+ Readymix (Kapa Biosystems, Woburn, MA) and 5 µl TruSeq PCR Primer Mix (Illumina) (50 µl final). The thermocycling parameters were: 95˚C 2 min, 98˚C 30 sec, then 8 cycles of 98˚C 15 sec, 60˚C 30 sec and 72˚C 4 min, ending with one 72˚C 10 min step. The reaction products were purified using AMPure XP beads. Up to two separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding up to two independent libraries from the same biological sample. MethylC-seq libraries were sequenced on Illumina HiSeq 4000.

tag: age


title: SAMPLE_00000026_TNN_AD

value: Peripheral blood

value: ADPSOKO

value: AD


title: SAMPLE_00000017_TNN_HC

value: HC


title: MethylC-seq_P39_Control_rep2

source_name: Excitatory pyramidal neurons from frontal cortex of control mice


title: RNA-seq_P39_Dnmt3a_cKO_rep1


title: RNA-seq_P39_Control_rep2


title: PBMC14-Feature

description:
CITE-seq data
Surface Protein Feature Barcode Sequence
Processed data for this sample available on GSM6346311

value: PBMC


title: PBMC13-TCR

description:
single-cell TCR seq
Total TCR sequences

value: Blood (Hash1-TotalSeqC), Heart(Hash2-TotalSeqC), Blood (Hash3-TotalSeqC), Heart (Hash4-TotalSeqC), Blood (Hash5-TotalSeqC), Heart (Hash6-TotalSeqC)

value: MRL(Hash1-TotalSeqC), MRL(Hash2-TotalSeqC), MRL/Pdcd1 -/- (Hash3-TotalSeqC), MRL/Pdcd1 -/- (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL (Hash6-TotalSeqC)


title: RNA-seq_P39_Control_rep1


title: exo AALE, KRASG12D, RNA, 2 [rnaEASY.aale.2.kras]

city: Santa Cruz

first: Daniel

last: Kim

state: California

address: McLaughlin Dr

department: Biomolecular Engineering

institute: UC Santa Cruz

description:
aale_exo_gencode_norm_counts.csv
aale_exo_gencode+rmsk_norm_counts.csv

data_processing:
Basecalled by relevant sequencing centers
Trimmed with Trimmomatic 0.39, quality assessed with FastQC and MultiQC
Reads quantified with Salmon 1.3.0 for RNA-seq, Reads aligned with nf-core ATAC pipeline for ATAC-seq
Assembly: hg38
Supplementary files format and content: bigWig format for UCSC genome browser integration
Supplementary files format and content: DESeqII normalized counts in CSV format with reference name included as gencode or gencode+rmsk

source_name: Lung Epithelial

extract_protocol:
exoRNeasy serum/plasma maxi kit (Qiagen) was used to isolate extracellular vesicles, which were quantified using Nanoparticle Tracking Analysis (Malvern, UK). 30 ml of AALE cell culture supernatant was filtered to remove particles larger than 0.8 um. The filtrate was precipitated with kit buffer and filtered through a column to collect extracellular vesicles. These vesicles were then lysed with QIAzol® lysis reagent
Smart Seq HT low input mRNA library prep kit (Takara). 2x150 PE reads.

value: Lung Epithelial

value: AALE

value: Human immortalized Lung Epithelial

value: KRAS G12D


title: exo AALE, pBABE control, RNA, 2 [rnaEASY.aale.2.ctrl]

value: KRAS WT


title: exo AALE, KRASG12D, RNA, 3 [rnaEASY.aale.3.kras]


title: exo AALE, KRASG12D, RNA, 1 [rnaEASY.aale.1.kras]


title: exo AALE, pBABE control, RNA, 1 [rnaEASY.aale.1.ctrl]


title: MethylC-seq_P39_Dnmt3a_cKO_rep2

value: C57BL6J/129 (name in Jackson Labs:B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ)


title: AALE, pBABE control, RNA, 3 [intra.aale.3.ctrl]

description:
aale_intra_gencode_norm_counts.csv
aale_intra_gencode+rmsk_norm_counts.csv

extract_protocol:
bulk RNA was isolated from cells using Quick-RNA MiniPrep kit (Zymogen)
1ug of total RNA was used as input for the TruSeq Stranded mRNA Sample Prep Kit (Illumina) according to manufacturer protocol. 2x100 PE reads


title: AALE, pBABE control, RNA, 2 [intra.aale.2.ctrl]


title: MethylC-seq_P39_Control_rep1

value: brain (frontal cortex)


title: AALE, pBABE control, ATAC

extract_protocol:
100,000 AALE cells were collected and centrifuged at 500xg for 5 minutes at 4C. Pellets were washed with ice-cold PBS and centrifuged. Pellets were resuspended in ice-cold lysis buffer. Tagmentation reaction and purification were conducted according to manufacturer’s protocol (Active Motif)
Active Motif ATAC-seq kit, 2x75bp PE reads


title: AALE, pBABE control, RNA, 1 [intra.aale.1.ctrl]


title: AALE, KRASG12D, RNA, 3 [intra.aale.3.kras]


title: AALE, KRASG12D, RNA, 2 [intra.aale.2.kras]


title: AALE, KRASG12D, ATAC


title: A10-B10-MCE12-MCE13-Feature

description:
CITE-seq data
Surface Protein Feature Barcode Sequence
Processed data for this sample available on GSM6346295

source_name: Human PBMCs

value: Blood

value: Immune Checkpoint Inhibitor

value: A10 (Group A, Hash3-TotalSeqC), B10 (Group B, Hash4-TotalSeqC), MCE12 (Group C, Hash1-TotalSeqC), MCE13 (Group C, Hash2-TotalSeqC)


title: AALE, KRASG12D, RNA, 1 [intra.aale.1.kras]


title: B12-MCE6-MCE7-Feature

description:
CITE-seq data
Surface Protein Feature Barcode Sequence
Processed data for this sample available on GSM6346294

value: B12 (Group B, Hash4-TotalSeqC), MCE6 (Group C, Hash 1-TotalSeqC), MCE7 (Group C, Hash2-TotalSeqC)


title: A8-B11-Feature

description:
CITE-seq data
Surface Protein Feature Barcode Sequence
Processed data for this sample available on GSM6346293

value: A8 (Group A, Hash4-TotalSeqC), B11 (Group B, Hash3-TotalSeqC)


title: A5-B14-Feature

description:
CITE-seq data
Surface Protein Feature Barcode Sequence
Processed data for this sample available on GSM6346296

value: A5 (Group A, Hash4-TotalSeqC), B14 (Group B, Hash3-TotalSeqC)


title: A6-A9-B13-B9-Feature

description:
CITE-seq data
Surface Protein Feature Barcode Sequence
Processed data for this sample available on GSM6346292

value: A6 (Group A, Hash1-TotalSeqC), A9 (Group A, Hash2-TotalSeqC), B9 (Group B, Hash3-TotalSeqC), B13 (Group B, Hash4-TotalSeqC)


title: A5-B14-TCR

description:
single-cell TCR seq
Total TCR sequences

value: PBMC


title: B12-MCE6-MCE7-TCR

description:
single-cell TCR seq
Total TCR sequences


title: A8-B11-TCR

description:
single-cell TCR seq
Total TCR sequences


title: A5-B14

description: scRNA-seq data


title: A6-A9-B13-B9-TCR

description:
single-cell TCR seq
Total TCR sequences


title: exo AALE, pBABE control, RNA, 3 [rnaEASY.aale.3.ctrl]


title: B12-MCE6-MCE7

description: scRNA-seq data


title: A8-B11

description: scRNA-seq data


title: HBEC, KRASG12V, RNA, 3 [intra.hbec.3.wt2_kras_v12]

description:
hbec_intra_gencode_norm_counts.csv
hbec_intra_gencode+rmsk_norm_counts.csv

source_name: Bronchus Epithelial

extract_protocol:
the bulk RNA was extracted using Direct-Zol RNA Miniprep Kit (Zymo Research)
UC Davis DNA Technologies and Expression Analysis Core Laboratory for poly-A strand specific library preparation. 2x150 PE reads

value: Bronchus Epithelial

value: HBEC

value: KRAS G12V


title: HBEC, LACZ, RNA, 3 [intra.hbec.3.wt2_lacz]


title: A6-A9-B13-B9

description: scRNA-seq data


title: A10-B10-MCE12-MCE13

description: scRNA-seq data


title: HBEC, KRASG12V, RNA, 1 [intra.hbec.1.wt2_kras_v12]


title: HBEC, LACZ, RNA, 1 [intra.hbec.1.wt2_lacz]


title: miR29_inhibition_2

city: Montreal

first: Gabrielle

last: Perron

state: Quebec

address: 845 Sherbrooke St W

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
RNA-seq reads were aligned to the GRCh38 genome assembly using HISAT2
RNA-seq reads to the human genome (GRCh38 assembly, Ensembl release 85) were counted using htseq-count, with a MAPQ score cutoff of >= 30
Differentially expressed genes were identified using DESeq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files contain raw counts for each sample

source_name: ACHN

growth_protocol: The established renal cell lines 786-O, A-498 and ACHN cells were purchased from the American Type Culture Collection (ATCC; Rockville, MD, USA) and cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using All Prep DNA/RNA/miRNA Universal kit (Qiagen) 48 hours after mimic/inhibitor transfection.
Library preparation was performed using NEB rRNA-depleted (HMR) stranded library preparation kit according to manufacturer's instructions.

treatment_protocol: Cells (100000 cells/well in 6-well plates) were reverse-transfected in antibiotic-free medium with 10 nM of a) miR-29 mimic or miRNA mimic control, or b) miR-29 inhibitor or miRNA inhibitor control, using Lipofectamine RNAiMAX Reagent (Invitrogen) according to the manufacturer’s recommendations.

value: Clear cell renal cell carcinoma cell line

value: ACHN

value: expressing miR-29 inhibitor


title: miR29_inhibition_3


title: miR29_inhibition_ctrl_3

value: expressing control inhibitor


title: miR29_inhibition_1


title: miR29_inhibition_ctrl_2


title: miR29_mimic_1

value: expressing miR-29 mimic


title: miR29_mimic_ctrl_3

value: expressing control mimic


title: miR29_mimic_2


title: miR29_mimic_ctrl_1

growth_protocol:
The established renal cell lines 786-O, A-498 and ACHN cells were purchased from the American Type Culture Collection (ATCC; Rockville, MD, USA) and cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C with 5% CO2.
The established renal cell lines 786-O, A-498 and ACHN cells were purchased from the American Type Culture Collection (ATCC; Rockville, MD, USA) and cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using All Prep DNA/RNA/miRNA Universal kit (Qiagen) 48 hours after mimic/inhibitor transfection.
Library preparation was performed using NEB rRNA-depleted (HMR) stranded library preparation kit according to manufacturer's instructions.
Total RNA was extracted using All Prep DNA/RNA/miRNA Universal kit (Qiagen) 48 hours after mimic/inhibitor transfection.
Library preparation was performed using NEB rRNA-depleted (HMR) stranded library preparation kit according to manufacturer's instructions.

treatment_protocol:
Cells (100000 cells/well in 6-well plates) were reverse-transfected in antibiotic-free medium with 10 nM of a) miR-29 mimic or miRNA mimic control, or b) miR-29 inhibitor or miRNA inhibitor control, using Lipofectamine RNAiMAX Reagent (Invitrogen) according to the manufacturer’s recommendations.
Cells (100000 cells/well in 6-well plates) were reverse-transfected in antibiotic-free medium with 10 nM of a) miR-29 mimic or miRNA mimic control, or b) miR-29 inhibitor or miRNA inhibitor control, using Lipofectamine RNAiMAX Reagent (Invitrogen) according to the manufacturer’s recommendations.


title: Ago2_WT_cytoplasm_2_CLIP

city: New Haven

first: Bluma

middle: J

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

description: whole testis cytoplasmic eCLIP IP rep 2

data_processing:
AGO2 IP and size-matched input control (SMInput) samples were demultiplexed as previously described using the script demux_paired_end.py (Van Nostrand et al., 2016). 3’ and 5’ adapters were trimmed using Cutadapt v1.18 (Martin, 2011) with default parameters. To eliminate artifacts from rRNA and other repetitive sequences, trimmed reads were then mapped to RepBase (mouse mm10 RepeatMasker, last modified time: 05-May-2017 06:32) using STAR software v.2.6.1d (Dobin et al., 2013). Unmapped reads recovered after the RepeatMasker step were then mapped to the mouse mm10 genome assembly with options --outFilterScoreMin 0 --outFilterScoreMinOverLread 0.33 --outFilterMatchNminOverLread 0.33 --alignEndsType Local. The script barcode_collapse_pe.py (Van Nostrand et al., 2016) was used to remove PCR duplicates based on unique molecular identifiers (UMIs). Peaks were called using the tag2peak.pl script from the CLIP Tool Kit (CTK) software (Shah et al., 2017) with an adjusted p-value threshold of 0.01 and normalized to the mm10 background model. Each AGO2 eCLIP replicate was also normalized to the corresponding SMInput data using the Peak_input_normalization_wrapper.pl script from (Van Nostrand et al., 2016). CTK was also used to track cross-link-induced mutation sites (CIMS) and cross-link-induced truncation sites (CITS) with a resolution of ±50nt at an empirical false discovery rate (FDR) of 0.01. Specific types of mutations, including deletions, substitutions and insertions, were detected by analysis of unique CLIP tags (trimmed mapped reads). Results were confirmed using an independent analysis pipeline.
Library strategy: eCLIP

organism: Mus

source_name: whole testis

extract_protocol:
Cytoplasmic fractions from adult mouse testes were crosslinked with 254nm UV light. Nuclei were lysed and sonicated in a Bioruptor sonicator (Diagenode) at 4C, 5 min, 30sec on/30sec off. The nuclear lysate was then digested with RNase I (AM2295, Thermo) and Turbo DNase (AM2239, Thermo), and immunoprecipitated using anti-AGO2 antibody (04-642, Millipore). Next, the protein-bound RNAs were ligated with 3’ end adapters. Protein-RNA complexes were subjected to gel electrophoresis and transferred to a membrane, and RNA was isolated by cutting the membrane at the expected size range.
Libraries were prepared as described in van Nostrand et al, 2016 and Biancon et al, 2022. cDNA was generated by reverse transcription, DNA adapter was ligated to the 3' end of the cDNA, and the library was amplified by PCR. Screening of subclones prior to high-throughput sequencing was performed for quality control.

tag: ip antibody

value: Millipore, 04-642

tag: condition

value: wild type

tag: genome build

value: .bed file with peaks


title: survivor_analysis___wildtype_3h_clone_6

status: Public on Jul 18 2022

city: Martinsried

first: Karl-Uwe

last: Reusswig

address: Am Klopferspitz 18

institute: Max Planck Institute of Biochemistry

data_processing:
Sequencing reads were mapped to the S. cerevisiae reference genome (sacCer3) using bwa mem (v 0.7.17-r1188) with default parameters and converted to BAM files using samtools (v 1.12)
Data were normalized for sequencing depth and multiple mapping reads were filtered out using bamCoverage from deepTools (v 3.5.1) with the settings "--binSize 50 --minMappingQuality 60 --normalizeUsing CPM" and saved as bigWig-files
Assembly: sacCer3
Supplementary files format and content: The bigWig-files represent sequencing-depth normalized coverage (CPM) of chromosomes.

organism: Saccharomyces cerevisiae

source_name: budding yeast cells

growth_protocol: Cells were grown in YP-media supplemented with 2% raffinose and 0.25 mM adenine at 30 °C to log-phase (OD600 0.5-0.7) and synchronized with α-factor (5-10 µg/ml) for 2:30 h. Cell cycle arrest was assessed by microscopy and by measurement of DNA content (flow cytometry).

extract_protocol:
Cells were mechanically lysed and chromatin was sheared by sonication to fragments of 200-500 bp. DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Libraries were prepared using NEBNext Ultra II DNA Library Prep kit following the manufacturer's instructions.

treatment_protocol: Replication was induced in G1-arrested cells by adding galactose to the medium (2% final concentration). To label newly synthesized DNA for EdU-ChIP, cells were also exposed to 100 µM EdU.

value: budding yeast cells

tag: chip-antibody

value: Streptavidin (Dynabeads M-280)

tag: timepoint

value: G1 arrest for 2 h, 3 h replication in G1, then plated on non-selective medium. Clone was grown to stationary phase in 5 ml medium before DNA isolation for sequencing


title: survivor_analysis___wildtype_3h_clone_9

tag: cell type


title: survivor_analysis___wildtype_3h_clone_2


title: survivor_analysis___wildtype_3h_clone_4


title: A10-B10-MCE12-MCE13-TCR

description:
single-cell TCR seq
Total TCR sequences

value: Blood

value: Immune Checkpoint Inhibitor

tag: disease state

value: A10 (Group A, Hash3-TotalSeqC), B10 (Group B, Hash4-TotalSeqC), MCE12 (Group C, Hash1-TotalSeqC), MCE13 (Group C, Hash2-TotalSeqC)


title: survivor_analysis___wildtype_3h_clone_3


title: survivor_analysis___wildtype_3h_clone_20


title: survivor_analysis___wildtype_3h_clone_8


title: survivor_analysis___wildtype_3h_clone_19


title: survivor_analysis___wildtype_3h_clone_7


title: miR29_inhibition_ctrl_1

tag: cell line

tag: genotype


title: survivor_analysis___wildtype_3h_clone_18


title: survivor_analysis___wildtype_3h_clone_16


title: Ago2_WT_cytoplasm_2_CLIPinput

description: whole testis cytoplasmic eCLIP input rep 2


title: survivor_analysis___wildtype_3h_clone_17


title: survivor_analysis___wildtype_3h_clone_15


title: survivor_analysis___wildtype_3h_clone_13


title: survivor_analysis___wildtype_3h_clone_14


title: survivor_analysis___wildtype_3h_clone_1


title: Ago2_WT_cytoplasm_1_CLIP

description: whole testis cytoplasmic eCLIP IP rep 1


title: survivor_analysis___wildtype_3h_clone_12


title: survivor_analysis___wildtype_3h_clone_10


title: survivor_analysis___wildtype_3h_clone_11


title: survivor_analysis___wildtype_0h_clone_5

value: G1 arrest for 2 h, 0 h replication in G1, then plated on non-selective medium. Clone was grown to stationary phase in 5 ml medium before DNA isolation for sequencing


title: survivor_analysis___wildtype_3h_clone_5


title: survivor_analysis___wildtype_0h_clone_3


title: survivor_analysis___wildtype_0h_clone_2


title: survivor_analysis___wildtype_0h_clone_1


title: survivor_analysis___bypassCDK_3h_clone_7


title: survivor_analysis___bypassCDK_3h_clone_9


title: survivor_analysis___bypassCDK_3h_clone_8


title: survivor_analysis___bypassCDK_3h_clone_6


title: survivor_analysis___bypassCDK_3h_clone_3


title: survivor_analysis___bypassCDK_3h_clone_19


title: survivor_analysis___bypassCDK_3h_clone_5


title: survivor_analysis___bypassCDK_3h_clone_2


title: survivor_analysis___bypassCDK_3h_clone_20


title: survivor_analysis___bypassCDK_3h_clone_18


title: survivor_analysis___bypassCDK_3h_clone_4


title: survivor_analysis___bypassCDK_3h_clone_16


title: survivor_analysis___bypassCDK_3h_clone_15


title: survivor_analysis___bypassCDK_3h_clone_13


title: survivor_analysis___bypassCDK_3h_clone_11


title: survivor_analysis___bypassCDK_3h_clone_14


title: survivor_analysis___bypassCDK_3h_clone_1


title: survivor_analysis___bypassCDK_0h_clone_5


title: survivor_analysis___bypassCDK_3h_clone_17


title: survivor_analysis___wildtype_0h_clone_4


title: survivor_analysis___bypassCDK_3h_clone_10


title: survivor_analysis___bypassCDK_0h_clone_3


title: survivor_analysis___bypassCDK_0h_clone_2


title: EdU-IP_in_S___control_rep2_totalDNA

value: 3 h replication in G1, then released to fresh medium containing 100 uM EdU and 200 mM HU for 90 min


title: survivor_analysis___bypassCDK_0h_clone_4


title: survivor_analysis___bypassCDK_3h_clone_12


title: EdU-IP_in_S___bypassCDKandDDK_rep2_totalDNA


title: EdU-IP_in_S___control_rep1_EdU-IP

data_processing:
Sequencing reads were mapped to the S. cerevisiae reference genome (sacCer3) using bwa mem (v 0.7.17-r1188) with default parameters and converted to BAM files using samtools (v 1.12)
Data were normalized for sequencing depth and multiple mapping reads were filtered out using bamCoverage from deepTools (v 3.5.1) with the settings "--binSize 50 --minMappingQuality 60 --normalizeUsing CPM" and saved as bigWig-files
Peaks were called using MACS2 (v2.2.7.1) with default parameters and the total DNA sample as the control
Assembly: sacCer3
Supplementary files format and content: The bigWig-files represent sequencing-depth normalized coverage (CPM) of chromosomes.
Supplementary files format and content: The summits of peaks called by MACS2 are provided as a bed-file


title: EdU-IP_in_S___bypassCDKandDDK_rep1_totalDNA


title: EdU-IP_in_S___bypassCDK_rep2_totalDNA


title: EdU-IP_in_S___bypassCDK_rep1_totalDNA


title: EdU-IP_in_S___control_rep2_EdU-IP


title: EdU-IP_in_S___bypassCDKandDDK_rep2_EdU-IP


title: 4_HSFA1V-RFP_ChIP, rep1

city: Sinagpore

first: Daisuke

last: Urano

address: 1 Research Link

country: Singapore

institute: Temasek Life Science Laboratory

data_processing:
Botwie 2 for genome mapping
Assembly: M. polymorpha: v5.1 from Marchantia.info
Supplementary files format and content: bigwig

organism: Marchantia polymorpha

source_name: gemmalings

growth_protocol: 14-day-old Tak1 and respecitive HSFA1V 0E lines gemma liquid grown in 1/2 B5, continuous

extract_protocol:
Nuclei was carried out by standard ChIP protocl, pull-down by tagRFP TRAP (Chromotek)
Libraries were prepared according to Illumina's instructions

treatment_protocol: M. polymorpha, gemmalings were grown in ½ x B5 liquid media for 7 days at continuous light and heat shocked at 37°C for 0

value: gemmalings

value: MpHSFA1V-tagRFP overexpression


title: 4_TAK-1_ChIP, rep2

value: Tak1, WT


title: 4_TAK-1_ChIP, rep1


title: P22

status: Public on Jul 17 2022

city: Philadelphia

first: Dwight

middle: Edward

last: Stambolian

state: PA

address: 422 Curie Blvd.

department: Opthalmalogy

institute: University of Pennsylvania

data_processing:
Gene count matrix was normalized and transformed into a natural log scale
Z-scores calculated across cells within each batch to further standardize log-transformed expression values.
Highly variable genes selected using 'filter_genes_dispersion' function from the Scanpy package.
Cell clustered into distinct cell types using DESC (a deep embedding clustering algorithm).
Assembly: HG38
Supplementary files format and content: txt file (gene x cell)

source_name: Retina

extract_protocol:
The human eyeball was immediately removed within 6 hours after death, and placed in cold phosphate buffered saline (PBS). The retina was carefully removed under a dissecting microscope, and the retina tissue was dissociated straightaway using the Papain dissociaton system (Worthington, Lakewood, NJ, USA) following the manufacturer's instructions.
To assess cell viability, cells were stained with 0.4% trypan blue (Mediatech, Inc., Manassas, VA, USA) and counted using a hemocytometer. Sc-RNA seq was carried out on the viable cells using Chromium 10x Genomics as per the manufacturer's recommendations.

tag: race

value: Caucasian

value: retina


title: P24


title: P23


title: P21


title: PBMC12-TCR

description:
single-cell TCR seq
Total TCR sequences

value: Blood (Hash1-TotalSeqC), Heart(Hash2-TotalSeqC), Blood (Hash3-TotalSeqC), Heart (Hash4-TotalSeqC)

value: PBMC

tag: treatment

value: MRL(Hash1-TotalSeqC), MRL(Hash2-TotalSeqC), MRL/Pdcd1 -/- (Hash3-TotalSeqC), MRL/Pdcd1 -/- (Hash4-TotalSeqC)


title: 4_HSFA1V-RFP_ChIP, rep2


title: EdU-IP_in_S___bypassCDK_rep2_EdU-IP


title: survivor_analysis___bypassCDK_0h_clone_1


title: EdU-IP_in_S___control_rep1_totalDNA


title: M23


title: M24


title: EdU-IP_in_S___bypassCDKandDDK_rep1_EdU-IP


title: M22


title: HBEC, LACZ, RNA, 2 [intra.hbec.2.wt2_lacz]

value: Bronchus Epithelial

value: HBEC

value: Human immortalized Lung Epithelial

value: KRAS WT


title: EdU-IP_in_S___bypassCDK_rep1_EdU-IP

value: budding yeast cells

value: Streptavidin (Dynabeads M-280)


title: M21